TRAP (Tandem Repeats Analysis Program)

TRF Version 4.00

Sequence: contig00000333

tutorial_data.fasta.s2.2.5.7.80.10.25.1000.txt.html

Found at i: i:3956 original size:11 final size:11

Alignment explanation

Indices: 3940--3967 Score: 49 Period size: 11 Copynumber: 2.5 Consensus size: 11 3930 TGTTCGGGGC 3940 TCTTTTTCTCT 1 TCTTTTTCTCT 3951 TCTTTTTCTCT 1 TCTTTTTCTCT * 3962 CCTTTT 1 TCTTTT 3968 GAATTCTTCT Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 11 16 1.00 ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71 Consensus pattern (11 bp): TCTTTTTCTCT Left flanking sequence: Indices 3440 -- 3939 AATGAATAAATTGAATAAAAGTGCAGATAAATGGAGAATTCGAGGAAGATATTCACAAAATCGAG ATCTTTTCCTCGGAGTTTCTTCGGATGAGGCGTTGCTGTTTCCAAAACGAACACAGCAACTCGCG GGCACTGCGGAGCCGATTCGGCGCCAAAATTAACGCTTTTTAGCGTCATCTGCGTCAAATTGAAC GGCGAAACCGAATTAATTACNAAAAACTAAATTAATTTGCGCCTTTAAGTGTTAAAAACGGGCCA AGAGGCGCAAAAAGANGGGGAGCAGCCGTCCCTGTGCTCCGACAGCCCCAGCTGTACAGACAGCA TGCGGCGCTGGCAGTGCGTGTGCCNGGTTTAAAATTAAATTAAATTATTTATTTTAATAAATTTG ANTAAATTTAATTTGTGGATTCTTTGTTTTCACCCGAGCNTTCGCGCGGAACCACCTCCAANCCC CGCNGGCCCCCGNCTGTCTTTGATCGGATCGGACTTGTTCGGGGC Right flanking sequence: Indices 3968 -- 4467 GAATTCTTCTTTTNCCAAAATTAATTTTATTTTACTTTAAGAACTTCAAACTCTCCGGGACGCCC CTTGTTGCTGCTTTTCTCNCCGAGGCNCACGGACCCCCCAGCGCCAAAANTGNCCTGCAGACTGC AAAGAAAATGCAGCAGCAGCAGACGCAGCAGCANGATCCGCAGCAGCAGCAGCAGCAACAGCANG CAGCAACAGCAGCNAGCAGCAGNCAGCAAANAAACCCAGNACNAGCTCNGCCCAATGCCGGAGGG GATGCCCTCAGCGGCAGCTTTGACTCGAGCCATGAGAGGTAAATAAATTAATTTTAAAAGAATTT CTTTTTTTCCCTTTAAAANTCTTCTAAAGCACTTTTCTCTCAACTCCAGTCTTCACTTTTCNTTC ACTTTGTTTCCCNTCGCCAGCCCNGCAGCAAATAGCCCAGCAGCAGCAGNCAGCAGCAGCAGCAA CAGCAGCAGCAGCAGCAACTAAAATCATTTGCTTCAGCGCCTCGA Found at i:4001 original size:5 final size:5 Alignment explanation

Indices: 3991--4006 Score: 25 Period size: 5 Copynumber: 3.2 Consensus size: 5 3981 NCCAAAATTA * 3991 ATTTT ATTTT ACTTT A 1 ATTTT ATTTT ATTTT A 4007 AGAACTTCAA Statistics Matches: 10, Mismatches: 1, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 5 10 1.00 ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69 Consensus pattern (5 bp): ATTTT Left flanking sequence: Indices 3491 -- 3990 TTCACAAAATCGAGATCTTTTCCTCGGAGTTTCTTCGGATGAGGCGTTGCTGTTTCCAAAACGAA CACAGCAACTCGCGGGCACTGCGGAGCCGATTCGGCGCCAAAATTAACGCTTTTTAGCGTCATCT GCGTCAAATTGAACGGCGAAACCGAATTAATTACNAAAAACTAAATTAATTTGCGCCTTTAAGTG TTAAAAACGGGCCAAGAGGCGCAAAAAGANGGGGAGCAGCCGTCCCTGTGCTCCGACAGCCCCAG CTGTACAGACAGCATGCGGCGCTGGCAGTGCGTGTGCCNGGTTTAAAATTAAATTAAATTATTTA TTTTAATAAATTTGANTAAATTTAATTTGTGGATTCTTTGTTTTCACCCGAGCNTTCGCGCGGAA CCACCTCCAANCCCCGCNGGCCCCCGNCTGTCTTTGATCGGATCGGACTTGTTCGGGGCTCTTTT TCTCTTCTTTTTCTCTCCTTTTGAATTCTTCTTTTNCCAAAATTA Right flanking sequence: Indices 4007 -- 4506 AGAACTTCAAACTCTCCGGGACGCCCCTTGTTGCTGCTTTTCTCNCCGAGGCNCACGGACCCCCC AGCGCCAAAANTGNCCTGCAGACTGCAAAGAAAATGCAGCAGCAGCAGACGCAGCAGCANGATCC GCAGCAGCAGCAGCAGCAACAGCANGCAGCAACAGCAGCNAGCAGCAGNCAGCAAANAAACCCAG NACNAGCTCNGCCCAATGCCGGAGGGGATGCCCTCAGCGGCAGCTTTGACTCGAGCCATGAGAGG TAAATAAATTAATTTTAAAAGAATTTCTTTTTTTCCCTTTAAAANTCTTCTAAAGCACTTTTCTC TCAACTCCAGTCTTCACTTTTCNTTCACTTTGTTTCCCNTCGCCAGCCCNGCAGCAAATAGCCCA GCAGCAGCAGNCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAACTAAAATCATTTGCTTCAGCG CCTCGAGGCGTTTTTGCTGCTACTCGATTTCTGTTTTTANTAATT Found at i:4115 original size:3 final size:3 Alignment explanation

Indices: 4107--4190 Score: 85 Period size: 3 Copynumber: 27.0 Consensus size: 3 4097 CAAAGAAAAT ** ** * * 4107 GCA GCA GCA GCA GAC GCA GCA GCA NGA TCC GCA GCA GCA GCA GCA GCA 1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA * * 4155 ACA GCA NGCA GCA ACA GCA GCNA GCA GCA GNCA GCA 1 GCA GCA -GCA GCA GCA GCA GC-A GCA GCA G-CA GCA 4191 AANAAACCCA Statistics Matches: 63, Mismatches: 15, Indels: 6 0.75 0.18 0.07 Matches are distributed among these distances: 3 54 0.86 4 9 0.14 ACGTcount: A:0.33, C:0.32, G:0.29, T:0.01 Consensus pattern (3 bp): GCA Left flanking sequence: Indices 3607 -- 4106 TTTTAGCGTCATCTGCGTCAAATTGAACGGCGAAACCGAATTAATTACNAAAAACTAAATTAATT TGCGCCTTTAAGTGTTAAAAACGGGCCAAGAGGCGCAAAAAGANGGGGAGCAGCCGTCCCTGTGC TCCGACAGCCCCAGCTGTACAGACAGCATGCGGCGCTGGCAGTGCGTGTGCCNGGTTTAAAATTA AATTAAATTATTTATTTTAATAAATTTGANTAAATTTAATTTGTGGATTCTTTGTTTTCACCCGA GCNTTCGCGCGGAACCACCTCCAANCCCCGCNGGCCCCCGNCTGTCTTTGATCGGATCGGACTTG TTCGGGGCTCTTTTTCTCTTCTTTTTCTCTCCTTTTGAATTCTTCTTTTNCCAAAATTAATTTTA TTTTACTTTAAGAACTTCAAACTCTCCGGGACGCCCCTTGTTGCTGCTTTTCTCNCCGAGGCNCA CGGACCCCCCAGCGCCAAAANTGNCCTGCAGACTGCAAAGAAAAT Right flanking sequence: Indices 4191 -- 4690 AANAAACCCAGNACNAGCTCNGCCCAATGCCGGAGGGGATGCCCTCAGCGGCAGCTTTGACTCGA GCCATGAGAGGTAAATAAATTAATTTTAAAAGAATTTCTTTTTTTCCCTTTAAAANTCTTCTAAA GCACTTTTCTCTCAACTCCAGTCTTCACTTTTCNTTCACTTTGTTTCCCNTCGCCAGCCCNGCAG CAAATAGCCCAGCAGCAGCAGNCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAACTAAAATCAT TTGCTTCAGCGCCTCGAGGCGTTTTTGCTGCTACTCGATTTCTGTTTTTANTAATTTCTTTAATT CTTTTTANTTTTTTAATTTGGAATTTAATTCCATTTGCTTTCCACTCTTTTGCTGCTGCTCATTT CCTTAATTCTTTTTGCTGCTGCTCCTGCTTCCCTTTTTGCTGCTGCTGCTTCGTTTTTTGCGGCA GTTGATTCCCCTCTTGCTGCTGCTGCTTTGCCTTTTGCTGCTGCT Found at i:4403 original size:3 final size:3 Alignment explanation

Indices: 4395--4439 Score: 74 Period size: 3 Copynumber: 14.7 Consensus size: 3 4385 GCAAATAGCC * 4395 CAG CAG CAG CAG NCAG CAG CAG CAG CAA CAG CAG CAG CAG CAG CA 1 CAG CAG CAG CAG -CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA 4440 ACTAAAATCA Statistics Matches: 39, Mismatches: 2, Indels: 2 0.91 0.05 0.05 Matches are distributed among these distances: 3 36 0.92 4 3 0.08 ACGTcount: A:0.36, C:0.33, G:0.29, T:0.00 Consensus pattern (3 bp): CAG Left flanking sequence: Indices 3895 -- 4394 CGCNGGCCCCCGNCTGTCTTTGATCGGATCGGACTTGTTCGGGGCTCTTTTTCTCTTCTTTTTCT CTCCTTTTGAATTCTTCTTTTNCCAAAATTAATTTTATTTTACTTTAAGAACTTCAAACTCTCCG GGACGCCCCTTGTTGCTGCTTTTCTCNCCGAGGCNCACGGACCCCCCAGCGCCAAAANTGNCCTG CAGACTGCAAAGAAAATGCAGCAGCAGCAGACGCAGCAGCANGATCCGCAGCAGCAGCAGCAGCA ACAGCANGCAGCAACAGCAGCNAGCAGCAGNCAGCAAANAAACCCAGNACNAGCTCNGCCCAATG CCGGAGGGGATGCCCTCAGCGGCAGCTTTGACTCGAGCCATGAGAGGTAAATAAATTAATTTTAA AAGAATTTCTTTTTTTCCCTTTAAAANTCTTCTAAAGCACTTTTCTCTCAACTCCAGTCTTCACT TTTCNTTCACTTTGTTTCCCNTCGCCAGCCCNGCAGCAAATAGCC Right flanking sequence: Indices 4440 -- 4939 ACTAAAATCATTTGCTTCAGCGCCTCGAGGCGTTTTTGCTGCTACTCGATTTCTGTTTTTANTAA TTTCTTTAATTCTTTTTANTTTTTTAATTTGGAATTTAATTCCATTTGCTTTCCACTCTTTTGCT GCTGCTCATTTCCTTAATTCTTTTTGCTGCTGCTCCTGCTTCCCTTTTTGCTGCTGCTGCTTCGT TTTTTGCGGCAGTTGATTCCCCTCTTGCTGCTGCTGCTTTGCCTTTTGCTGCTGCTGCTTCGCCT TTTGCTGCTGCTGATTCCCCTCTTGCTGCTGCTGTTTCTTTTGCTGCTGCTGATTCCCCTCTTGC TAATGCTGTTTCTTTTGCTGCTGCTGCTTCNTTCTCTTGCTGCCGCNTGCTGCTTTTGCGTTTGC TGCTGCTGNCTCCCCCNTNCTTGCTGCTGCTGCTTTTCCTTTTGTTGCTGNCTGCTTCTCCTCTT GCNTGCTGCTGCTGCTTTTCCTTTTGCTGCCGCTGCTCCCCCTCT Found at i:4405 original size:18 final size:17 Alignment explanation

Indices: 4382--4436 Score: 59 Period size: 15 Copynumber: 3.4 Consensus size: 17 4372 CGCCAGCCCN * 4382 GCAGCAAATAGCCCAGCA 1 GCAGCAAACAG-CCAGCA ** 4400 GCAGCAGNCAG-CAGCA 1 GCAGCAAACAGCCAGCA 4416 GCAGC-AACAG-CAGCA 1 GCAGCAAACAGCCAGCA 4431 GCAGCA 1 GCAGCA 4437 GCAACTAAAA Statistics Matches: 31, Mismatches: 5, Indels: 4 0.78 0.12 0.10 Matches are distributed among these distances: 15 13 0.42 16 10 0.32 18 8 0.26 ACGTcount: A:0.36, C:0.33, G:0.27, T:0.02 Consensus pattern (17 bp): GCAGCAAACAGCCAGCA Left flanking sequence: Indices 3882 -- 4381 CACCTCCAANCCCCGCNGGCCCCCGNCTGTCTTTGATCGGATCGGACTTGTTCGGGGCTCTTTTT CTCTTCTTTTTCTCTCCTTTTGAATTCTTCTTTTNCCAAAATTAATTTTATTTTACTTTAAGAAC TTCAAACTCTCCGGGACGCCCCTTGTTGCTGCTTTTCTCNCCGAGGCNCACGGACCCCCCAGCGC CAAAANTGNCCTGCAGACTGCAAAGAAAATGCAGCAGCAGCAGACGCAGCAGCANGATCCGCAGC AGCAGCAGCAGCAACAGCANGCAGCAACAGCAGCNAGCAGCAGNCAGCAAANAAACCCAGNACNA GCTCNGCCCAATGCCGGAGGGGATGCCCTCAGCGGCAGCTTTGACTCGAGCCATGAGAGGTAAAT AAATTAATTTTAAAAGAATTTCTTTTTTTCCCTTTAAAANTCTTCTAAAGCACTTTTCTCTCAAC TCCAGTCTTCACTTTTCNTTCACTTTGTTTCCCNTCGCCAGCCCN Right flanking sequence: Indices 4437 -- 4936 GCAACTAAAATCATTTGCTTCAGCGCCTCGAGGCGTTTTTGCTGCTACTCGATTTCTGTTTTTAN TAATTTCTTTAATTCTTTTTANTTTTTTAATTTGGAATTTAATTCCATTTGCTTTCCACTCTTTT GCTGCTGCTCATTTCCTTAATTCTTTTTGCTGCTGCTCCTGCTTCCCTTTTTGCTGCTGCTGCTT CGTTTTTTGCGGCAGTTGATTCCCCTCTTGCTGCTGCTGCTTTGCCTTTTGCTGCTGCTGCTTCG CCTTTTGCTGCTGCTGATTCCCCTCTTGCTGCTGCTGTTTCTTTTGCTGCTGCTGATTCCCCTCT TGCTAATGCTGTTTCTTTTGCTGCTGCTGCTTCNTTCTCTTGCTGCCGCNTGCTGCTTTTGCGTT TGCTGCTGCTGNCTCCCCCNTNCTTGCTGCTGCTGCTTTTCCTTTTGTTGCTGNCTGCTTCTCCT CTTGCNTGCTGCTGCTGCTTTTCCTTTTGCTGCCGCTGCTCCCCC Found at i:4528 original size:8 final size:8 Alignment explanation

Indices: 4502--4534 Score: 32 Period size: 8 Copynumber: 3.8 Consensus size: 8 4492 CTGTTTTTAN 4502 TAATTTCTT 1 TAATTT-TT 4511 TAATTCTTTT 1 TAA-T-TTTT * 4521 TANTTTTT 1 TAATTTTT 4529 TAATTT 1 TAATTT 4535 GGAATTTAAT Statistics Matches: 20, Mismatches: 2, Indels: 5 0.74 0.07 0.19 Matches are distributed among these distances: 8 9 0.45 9 4 0.20 10 5 0.25 11 2 0.10 ACGTcount: A:0.21, C:0.06, G:0.00, T:0.70 Consensus pattern (8 bp): TAATTTTT Left flanking sequence: Indices 4002 -- 4501 CTTTAAGAACTTCAAACTCTCCGGGACGCCCCTTGTTGCTGCTTTTCTCNCCGAGGCNCACGGAC CCCCCAGCGCCAAAANTGNCCTGCAGACTGCAAAGAAAATGCAGCAGCAGCAGACGCAGCAGCAN GATCCGCAGCAGCAGCAGCAGCAACAGCANGCAGCAACAGCAGCNAGCAGCAGNCAGCAAANAAA CCCAGNACNAGCTCNGCCCAATGCCGGAGGGGATGCCCTCAGCGGCAGCTTTGACTCGAGCCATG AGAGGTAAATAAATTAATTTTAAAAGAATTTCTTTTTTTCCCTTTAAAANTCTTCTAAAGCACTT TTCTCTCAACTCCAGTCTTCACTTTTCNTTCACTTTGTTTCCCNTCGCCAGCCCNGCAGCAAATA GCCCAGCAGCAGCAGNCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAACTAAAATCATTTGCTT CAGCGCCTCGAGGCGTTTTTGCTGCTACTCGATTTCTGTTTTTAN Right flanking sequence: Indices 4535 -- 5034 GGAATTTAATTCCATTTGCTTTCCACTCTTTTGCTGCTGCTCATTTCCTTAATTCTTTTTGCTGC TGCTCCTGCTTCCCTTTTTGCTGCTGCTGCTTCGTTTTTTGCGGCAGTTGATTCCCCTCTTGCTG CTGCTGCTTTGCCTTTTGCTGCTGCTGCTTCGCCTTTTGCTGCTGCTGATTCCCCTCTTGCTGCT GCTGTTTCTTTTGCTGCTGCTGATTCCCCTCTTGCTAATGCTGTTTCTTTTGCTGCTGCTGCTTC NTTCTCTTGCTGCCGCNTGCTGCTTTTGCGTTTGCTGCTGCTGNCTCCCCCNTNCTTGCTGCTGC TGCTTTTCCTTTTGTTGCTGNCTGCTTCTCCTCTTGCNTGCTGCTGCTGCTTTTCCTTTTGCTGC CGCTGCTCCCCCTCTTGCNTNGCNTGCTCCTTCCCTTCTTGCTGCTTCTGCTTCCCTTTTTGCTG TTGTTGCTTTCCGTCTTGCTGCNTGGTGTNTCCTTCTTTTGCTGC Found at i:4581 original size:24 final size:24 Alignment explanation

Indices: 4554--4627 Score: 66 Period size: 24 Copynumber: 2.9 Consensus size: 24 4544 TTCCATTTGC 4554 TTTCCACTCTTTTGCTGCTGCTCA 1 TTTCCACTCTTTTGCTGCTGCTCA * * 4578 TTTCCTTAATTCTTTTTGCTGCTGCTCC 1 TTTCC---ACTC-TTTTGCTGCTGCTCA 4606 TGCTTCC-CT-TTTTGCTGCTGCT 1 T--TTCCACTCTTTTGCTGCTGCT 4628 GCTTCGTTTT Statistics Matches: 41, Mismatches: 3, Indels: 12 0.73 0.05 0.21 Matches are distributed among these distances: 24 18 0.44 26 1 0.02 27 3 0.07 28 15 0.37 30 4 0.10 ACGTcount: A:0.05, C:0.31, G:0.14, T:0.50 Consensus pattern (24 bp): TTTCCACTCTTTTGCTGCTGCTCA Left flanking sequence: Indices 4054 -- 4553 GAGGCNCACGGACCCCCCAGCGCCAAAANTGNCCTGCAGACTGCAAAGAAAATGCAGCAGCAGCA GACGCAGCAGCANGATCCGCAGCAGCAGCAGCAGCAACAGCANGCAGCAACAGCAGCNAGCAGCA GNCAGCAAANAAACCCAGNACNAGCTCNGCCCAATGCCGGAGGGGATGCCCTCAGCGGCAGCTTT GACTCGAGCCATGAGAGGTAAATAAATTAATTTTAAAAGAATTTCTTTTTTTCCCTTTAAAANTC TTCTAAAGCACTTTTCTCTCAACTCCAGTCTTCACTTTTCNTTCACTTTGTTTCCCNTCGCCAGC CCNGCAGCAAATAGCCCAGCAGCAGCAGNCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAACTA AAATCATTTGCTTCAGCGCCTCGAGGCGTTTTTGCTGCTACTCGATTTCTGTTTTTANTAATTTC TTTAATTCTTTTTANTTTTTTAATTTGGAATTTAATTCCATTTGC Right flanking sequence: Indices 4628 -- 5127 GCTTCGTTTTTTGCGGCAGTTGATTCCCCTCTTGCTGCTGCTGCTTTGCCTTTTGCTGCTGCTGC TTCGCCTTTTGCTGCTGCTGATTCCCCTCTTGCTGCTGCTGTTTCTTTTGCTGCTGCTGATTCCC CTCTTGCTAATGCTGTTTCTTTTGCTGCTGCTGCTTCNTTCTCTTGCTGCCGCNTGCTGCTTTTG CGTTTGCTGCTGCTGNCTCCCCCNTNCTTGCTGCTGCTGCTTTTCCTTTTGTTGCTGNCTGCTTC TCCTCTTGCNTGCTGCTGCTGCTTTTCCTTTTGCTGCCGCTGCTCCCCCTCTTGCNTNGCNTGCT CCTTCCCTTCTTGCTGCTTCTGCTTCCCTTTTTGCTGTTGTTGCTTTCCGTCTTGCTGCNTGGTG TNTCCTTCTTTTGCTGCTGCTGCTTCCGCTCTTGCTGCTGCTGCTGTCCCTGCTGCTCCTTCCGC TCTTGCTGCTGCTGCTTCCTCTTTTGCTGCTGCTGCTCCCCGTTT Found at i:4602 original size:3 final size:3 Alignment explanation

Indices: 4594--4609 Score: 25 Period size: 3 Copynumber: 5.3 Consensus size: 3 4584 TAATTCTTTT * 4594 TGC TGC TGC TCC TGC T 1 TGC TGC TGC TGC TGC T 4610 TCCCTTTTTG Statistics Matches: 11, Mismatches: 2, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 3 11 1.00 ACGTcount: A:0.00, C:0.38, G:0.25, T:0.38 Consensus pattern (3 bp): TGC Left flanking sequence: Indices 4094 -- 4593 CTGCAAAGAAAATGCAGCAGCAGCAGACGCAGCAGCANGATCCGCAGCAGCAGCAGCAGCAACAG CANGCAGCAACAGCAGCNAGCAGCAGNCAGCAAANAAACCCAGNACNAGCTCNGCCCAATGCCGG AGGGGATGCCCTCAGCGGCAGCTTTGACTCGAGCCATGAGAGGTAAATAAATTAATTTTAAAAGA ATTTCTTTTTTTCCCTTTAAAANTCTTCTAAAGCACTTTTCTCTCAACTCCAGTCTTCACTTTTC NTTCACTTTGTTTCCCNTCGCCAGCCCNGCAGCAAATAGCCCAGCAGCAGCAGNCAGCAGCAGCA GCAACAGCAGCAGCAGCAGCAACTAAAATCATTTGCTTCAGCGCCTCGAGGCGTTTTTGCTGCTA CTCGATTTCTGTTTTTANTAATTTCTTTAATTCTTTTTANTTTTTTAATTTGGAATTTAATTCCA TTTGCTTTCCACTCTTTTGCTGCTGCTCATTTCCTTAATTCTTTT Right flanking sequence: Indices 4610 -- 5109 TCCCTTTTTGCTGCTGCTGCTTCGTTTTTTGCGGCAGTTGATTCCCCTCTTGCTGCTGCTGCTTT GCCTTTTGCTGCTGCTGCTTCGCCTTTTGCTGCTGCTGATTCCCCTCTTGCTGCTGCTGTTTCTT TTGCTGCTGCTGATTCCCCTCTTGCTAATGCTGTTTCTTTTGCTGCTGCTGCTTCNTTCTCTTGC TGCCGCNTGCTGCTTTTGCGTTTGCTGCTGCTGNCTCCCCCNTNCTTGCTGCTGCTGCTTTTCCT TTTGTTGCTGNCTGCTTCTCCTCTTGCNTGCTGCTGCTGCTTTTCCTTTTGCTGCCGCTGCTCCC CCTCTTGCNTNGCNTGCTCCTTCCCTTCTTGCTGCTTCTGCTTCCCTTTTTGCTGTTGTTGCTTT CCGTCTTGCTGCNTGGTGTNTCCTTCTTTTGCTGCTGCTGCTTCCGCTCTTGCTGCTGCTGCTGT CCCTGCTGCTCCTTCCGCTCTTGCTGCTGCTGCTTCCTCTTTTGC Found at i:4623 original size:21 final size:21 Alignment explanation

Indices: 4597--5223 Score: 483 Period size: 21 Copynumber: 29.6 Consensus size: 21 4587 TTCTTTTTGC * * 4597 TGCTGCTCCTGCTTCCCTTTT 1 TGCTGCTGCTGCTTCCCCTTT *** 4618 TGCTGCTGCTGCTTCGTTTTT 1 TGCTGCTGCTGCTTCCCCTTT * * * * * 4639 TGCGGCAGTTGATTCCCCTCT 1 TGCTGCTGCTGCTTCCCCTTT ** 4660 TGCTGCTGCTGCTTTGCCTTT 1 TGCTGCTGCTGCTTCCCCTTT * 4681 TGCTGCTGCTGCTTCGCCTTT 1 TGCTGCTGCTGCTTCCCCTTT * * 4702 TGCTGCTGCTGATTCCCCTCT 1 TGCTGCTGCTGCTTCCCCTTT * 4723 TGCTGCTGCTG-TT--TCTTT 1 TGCTGCTGCTGCTTCCCCTTT * * 4741 TGCTGCTGCTGATTCCCCTCT 1 TGCTGCTGCTGCTTCCCCTTT ** * 4762 TGCTAATGCTG-TT--TCTTT 1 TGCTGCTGCTGCTTCCCCTTT * * 4780 TGCTGCTGCTGCTTCNTTCTCTTGC 1 TGCTGCTGCTGCTTC---CCCTT-T * *** * 4805 TGCCGCNTGCTGCTTTTGCGTT 1 TGCTGC-TGCTGCTTCCCCTTT * * 4827 TGCTGCTGCTGNCTCCCCCNTNCT 1 TGCTGCTGCTG-CTTCCCC-T-TT ** 4851 TGCTGCTGCTGCTTTTCCTTT 1 TGCTGCTGCTGCTTCCCCTTT * * 4872 TGTTGCTGNCTGCTTCTCCTCTTGCN 1 TGCTGCTG-CTGCTTC-CC-CTT--T ** 4898 TGCTGCTGCTGCTTTTCCTTT 1 TGCTGCTGCTGCTTCCCCTTT * * * 4919 TGCTGCCGCTGCTCCCCCTCT 1 TGCTGCTGCTGCTTCCCCTTT * * * 4940 TGCNTNGCNTGCTCCTTCCCTTCT 1 TGC-T-GC-TGCTGCTTCCCCTTT * * 4964 TGCTGCTTCTGCTTCCCTTTT 1 TGCTGCTGCTGCTTCCCCTTT * * * * * 4985 TGCTGTTGTTGCTTTCCGTCT 1 TGCTGCTGCTGCTTCCCCTTT * ** * 5006 TGCTGCNTGGTGTNTCCTTCTTT 1 TGCTGC-TGCTGCTTCC-CCTTT * * 5029 TGCTGCTGCTGCTTCCGCTCT 1 TGCTGCTGCTGCTTCCCCTTT ** 5050 TGCTGCTGCTGCTGTCCC--- 1 TGCTGCTGCTGCTTCCCCTTT * * * 5068 TGCTGCT-C-C-TTCCGCTCT 1 TGCTGCTGCTGCTTCCCCTTT * 5086 TGCTGCTGCTGCTTCCTCTTT 1 TGCTGCTGCTGCTTCCCCTTT * * 5107 TGCTGCTGCTGCTCCCCGTTT 1 TGCTGCTGCTGCTTCCCCTTT * * * 5128 TCCTGCTGCTGCCTCACCTTT 1 TGCTGCTGCTGCTTCCCCTTT * *** 5149 TGCTGCTGCTGCTCCTTTTTT 1 TGCTGCTGCTGCTTCCCCTTT * * 5170 TGCTGCTGCTGCCTCGCCTTT 1 TGCTGCTGCTGCTTCCCCTTT * * 5191 TGCTGCTGCTGCGT-CCCGTT 1 TGCTGCTGCTGCTTCCCCTTT 5211 TGCTGCTGCTGCT 1 TGCTGCTGCTGCT 5224 GCTGCTGCAC Statistics Matches: 454, Mismatches: 122, Indels: 61 0.71 0.19 0.10 Matches are distributed among these distances: 15 3 0.01 17 1 0.00 18 40 0.09 19 5 0.01 20 20 0.04 21 273 0.60 22 31 0.07 23 21 0.05 24 34 0.07 25 11 0.02 26 15 0.03 ACGTcount: A:0.01, C:0.33, G:0.21, T:0.43 Consensus pattern (21 bp): TGCTGCTGCTGCTTCCCCTTT Left flanking sequence: Indices 4097 -- 4596 CAAAGAAAATGCAGCAGCAGCAGACGCAGCAGCANGATCCGCAGCAGCAGCAGCAGCAACAGCAN GCAGCAACAGCAGCNAGCAGCAGNCAGCAAANAAACCCAGNACNAGCTCNGCCCAATGCCGGAGG GGATGCCCTCAGCGGCAGCTTTGACTCGAGCCATGAGAGGTAAATAAATTAATTTTAAAAGAATT TCTTTTTTTCCCTTTAAAANTCTTCTAAAGCACTTTTCTCTCAACTCCAGTCTTCACTTTTCNTT CACTTTGTTTCCCNTCGCCAGCCCNGCAGCAAATAGCCCAGCAGCAGCAGNCAGCAGCAGCAGCA ACAGCAGCAGCAGCAGCAACTAAAATCATTTGCTTCAGCGCCTCGAGGCGTTTTTGCTGCTACTC GATTTCTGTTTTTANTAATTTCTTTAATTCTTTTTANTTTTTTAATTTGGAATTTAATTCCATTT GCTTTCCACTCTTTTGCTGCTGCTCATTTCCTTAATTCTTTTTGC Right flanking sequence: Indices 5224 -- 5723 GCTGCTGCACTTCGCGTTNTTTGCTGCAGCGCAGCCTCCACTCCCCTTCAAGTTGCAAAAAAATG ATTATCATTTATTATTAATTAATTAATTAATTTATTTATTTATTTANTNTTATTNNTAATTCAGG ATTGTCNTGTGGCCCCCCACCTGTTCTGGGACACACAGCCAGTGGTGAAGGCAGCGGAGCGGGCG GCGCTGGCCCCACAGGTGCAGCAAAGTGGAAATGAATTTNAAATTCTTTTTTCGATTTTGGAATT AAAAGAGAATAAATGAATAATTAATTTAAATCAAGCANATTTGGGAAATCCAGNCGGAGACGAAG ATGCANGCAAATCCNGGCAAAAAGATNCTTCNGGAATTCACNTTTACCNGCAGCAAAATAANCTC CCNAGNCAGCAAAACGNCTATTTGCTGCTGCAGCAAAACAAATTCCGTTTTCTGCTCCCCTTTGT CCCTTTATCCCGCCTTATCTTCCTAATGCAGCAGCAGCAGCAGCA Found at i:4626 original size:3 final size:3 Alignment explanation

Indices: 4618--4630 Score: 26 Period size: 3 Copynumber: 4.3 Consensus size: 3 4608 CTTCCCTTTT 4618 TGC TGC TGC TGC T 1 TGC TGC TGC TGC T 4631 TCGTTTTTTG Statistics Matches: 10, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 10 1.00 ACGTcount: A:0.00, C:0.31, G:0.31, T:0.38 Consensus pattern (3 bp): TGC Left flanking sequence: Indices 4118 -- 4617 AGACGCAGCAGCANGATCCGCAGCAGCAGCAGCAGCAACAGCANGCAGCAACAGCAGCNAGCAGC AGNCAGCAAANAAACCCAGNACNAGCTCNGCCCAATGCCGGAGGGGATGCCCTCAGCGGCAGCTT TGACTCGAGCCATGAGAGGTAAATAAATTAATTTTAAAAGAATTTCTTTTTTTCCCTTTAAAANT CTTCTAAAGCACTTTTCTCTCAACTCCAGTCTTCACTTTTCNTTCACTTTGTTTCCCNTCGCCAG CCCNGCAGCAAATAGCCCAGCAGCAGCAGNCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAACT AAAATCATTTGCTTCAGCGCCTCGAGGCGTTTTTGCTGCTACTCGATTTCTGTTTTTANTAATTT CTTTAATTCTTTTTANTTTTTTAATTTGGAATTTAATTCCATTTGCTTTCCACTCTTTTGCTGCT GCTCATTTCCTTAATTCTTTTTGCTGCTGCTCCTGCTTCCCTTTT Right flanking sequence: Indices 4631 -- 5130 TCGTTTTTTGCGGCAGTTGATTCCCCTCTTGCTGCTGCTGCTTTGCCTTTTGCTGCTGCTGCTTC GCCTTTTGCTGCTGCTGATTCCCCTCTTGCTGCTGCTGTTTCTTTTGCTGCTGCTGATTCCCCTC TTGCTAATGCTGTTTCTTTTGCTGCTGCTGCTTCNTTCTCTTGCTGCCGCNTGCTGCTTTTGCGT TTGCTGCTGCTGNCTCCCCCNTNCTTGCTGCTGCTGCTTTTCCTTTTGTTGCTGNCTGCTTCTCC TCTTGCNTGCTGCTGCTGCTTTTCCTTTTGCTGCCGCTGCTCCCCCTCTTGCNTNGCNTGCTCCT TCCCTTCTTGCTGCTTCTGCTTCCCTTTTTGCTGTTGTTGCTTTCCGTCTTGCTGCNTGGTGTNT CCTTCTTTTGCTGCTGCTGCTTCCGCTCTTGCTGCTGCTGCTGTCCCTGCTGCTCCTTCCGCTCT TGCTGCTGCTGCTTCCTCTTTTGCTGCTGCTGCTCCCCGTTTTCC Found at i:4921 original size:92 final size:85 Alignment explanation

Indices: 4723--4942 Score: 261 Period size: 92 Copynumber: 2.5 Consensus size: 85 4713 ATTCCCCTCT * * * * 4723 TGCTGCTGCTGTTTCTTTTGCTGCTGCTGATTCCCCTCTTGCTAATGCTGTTTCTTTTGCTGCTG 1 TGCTGCTGCTTTTCCTTTTGCTGCTGCTGCTCCCCCTCTTGCTAATGCTGTTTCTTTTGCTGCTG * * 4788 CTGCTTCNTTCTCTTGCTGC 66 CTGCTTCATCCTCTTGCTGC * * * ** 4808 CGCNTGCTGCTTTTGCGTTTGCTGCTGCTGNCTCCCCCNTNCTTGCTGCTGCTGCTTTTCCTTTT 1 TGC-TGCTGCTTTTCCTTTTGCTGCTGCTG-CTCCCCC-T-CTTGCTAATGCTG--TTT-CTTTT * 4873 GTTGCTGNCTGCTTC-TCCTCTTGCNTGC 59 GCTGCTG-CTGCTTCATCCTCTTGC-TGC * 4901 TGCTGCTGCTTTTCCTTTTGCTGCCGCTGCTCCCCCTCTTGC 1 TGCTGCTGCTTTTCCTTTTGCTGCTGCTGCTCCCCCTCTTGC 4943 NTNGCNTGCT Statistics Matches: 112, Mismatches: 14, Indels: 14 0.80 0.10 0.10 Matches are distributed among these distances: 85 2 0.02 86 23 0.21 87 5 0.04 88 1 0.01 89 16 0.14 90 1 0.01 91 10 0.09 92 42 0.38 93 12 0.11 ACGTcount: A:0.01, C:0.32, G:0.20, T:0.43 Consensus pattern (85 bp): TGCTGCTGCTTTTCCTTTTGCTGCTGCTGCTCCCCCTCTTGCTAATGCTGTTTCTTTTGCTGCTG CTGCTTCATCCTCTTGCTGC Left flanking sequence: Indices 4223 -- 4722 GAGGGGATGCCCTCAGCGGCAGCTTTGACTCGAGCCATGAGAGGTAAATAAATTAATTTTAAAAG AATTTCTTTTTTTCCCTTTAAAANTCTTCTAAAGCACTTTTCTCTCAACTCCAGTCTTCACTTTT CNTTCACTTTGTTTCCCNTCGCCAGCCCNGCAGCAAATAGCCCAGCAGCAGCAGNCAGCAGCAGC AGCAACAGCAGCAGCAGCAGCAACTAAAATCATTTGCTTCAGCGCCTCGAGGCGTTTTTGCTGCT ACTCGATTTCTGTTTTTANTAATTTCTTTAATTCTTTTTANTTTTTTAATTTGGAATTTAATTCC ATTTGCTTTCCACTCTTTTGCTGCTGCTCATTTCCTTAATTCTTTTTGCTGCTGCTCCTGCTTCC CTTTTTGCTGCTGCTGCTTCGTTTTTTGCGGCAGTTGATTCCCCTCTTGCTGCTGCTGCTTTGCC TTTTGCTGCTGCTGCTTCGCCTTTTGCTGCTGCTGATTCCCCTCT Right flanking sequence: Indices 4943 -- 5442 NTNGCNTGCTCCTTCCCTTCTTGCTGCTTCTGCTTCCCTTTTTGCTGTTGTTGCTTTCCGTCTTG CTGCNTGGTGTNTCCTTCTTTTGCTGCTGCTGCTTCCGCTCTTGCTGCTGCTGCTGTCCCTGCTG CTCCTTCCGCTCTTGCTGCTGCTGCTTCCTCTTTTGCTGCTGCTGCTCCCCGTTTTCCTGCTGCT GCCTCACCTTTTGCTGCTGCTGCTCCTTTTTTTGCTGCTGCTGCCTCGCCTTTTGCTGCTGCTGC GTCCCGTTTGCTGCTGCTGCTGCTGCTGCACTTCGCGTTNTTTGCTGCAGCGCAGCCTCCACTCC CCTTCAAGTTGCAAAAAAATGATTATCATTTATTATTAATTAATTAATTAATTTATTTATTTATT TANTNTTATTNNTAATTCAGGATTGTCNTGTGGCCCCCCACCTGTTCTGGGACACACAGCCAGTG GTGAAGGCAGCGGAGCGGGCGGCGCTGGCCCCACAGGTGCAGCAA Found at i:4977 original size:6 final size:6 Alignment explanation

Indices: 4966--4978 Score: 26 Period size: 6 Copynumber: 2.2 Consensus size: 6 4956 TCCCTTCTTG 4966 CTGCTT CTGCTT C 1 CTGCTT CTGCTT C 4979 CCTTTTTGCT Statistics Matches: 7, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 7 1.00 ACGTcount: A:0.00, C:0.38, G:0.15, T:0.46 Consensus pattern (6 bp): CTGCTT Left flanking sequence: Indices 4466 -- 4965 GAGGCGTTTTTGCTGCTACTCGATTTCTGTTTTTANTAATTTCTTTAATTCTTTTTANTTTTTTA ATTTGGAATTTAATTCCATTTGCTTTCCACTCTTTTGCTGCTGCTCATTTCCTTAATTCTTTTTG CTGCTGCTCCTGCTTCCCTTTTTGCTGCTGCTGCTTCGTTTTTTGCGGCAGTTGATTCCCCTCTT GCTGCTGCTGCTTTGCCTTTTGCTGCTGCTGCTTCGCCTTTTGCTGCTGCTGATTCCCCTCTTGC TGCTGCTGTTTCTTTTGCTGCTGCTGATTCCCCTCTTGCTAATGCTGTTTCTTTTGCTGCTGCTG CTTCNTTCTCTTGCTGCCGCNTGCTGCTTTTGCGTTTGCTGCTGCTGNCTCCCCCNTNCTTGCTG CTGCTGCTTTTCCTTTTGTTGCTGNCTGCTTCTCCTCTTGCNTGCTGCTGCTGCTTTTCCTTTTG CTGCCGCTGCTCCCCCTCTTGCNTNGCNTGCTCCTTCCCTTCTTG Right flanking sequence: Indices 4979 -- 5478 CCTTTTTGCTGTTGTTGCTTTCCGTCTTGCTGCNTGGTGTNTCCTTCTTTTGCTGCTGCTGCTTC CGCTCTTGCTGCTGCTGCTGTCCCTGCTGCTCCTTCCGCTCTTGCTGCTGCTGCTTCCTCTTTTG CTGCTGCTGCTCCCCGTTTTCCTGCTGCTGCCTCACCTTTTGCTGCTGCTGCTCCTTTTTTTGCT GCTGCTGCCTCGCCTTTTGCTGCTGCTGCGTCCCGTTTGCTGCTGCTGCTGCTGCTGCACTTCGC GTTNTTTGCTGCAGCGCAGCCTCCACTCCCCTTCAAGTTGCAAAAAAATGATTATCATTTATTAT TAATTAATTAATTAATTTATTTATTTATTTANTNTTATTNNTAATTCAGGATTGTCNTGTGGCCC CCCACCTGTTCTGGGACACACAGCCAGTGGTGAAGGCAGCGGAGCGGGCGGCGCTGGCCCCACAG GTGCAGCAAAGTGGAAATGAATTTNAAATTCTTTTTTCGATTTTG Found at i:5333 original size:4 final size:4 Alignment explanation

Indices: 5295--5334 Score: 45 Period size: 4 Copynumber: 10.2 Consensus size: 4 5285 AATGATTATC * * * * 5295 ATTT A-TT ATTA ATTA ATTA ATTA ATTT ATTT ATTT ATTT A 1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A 5335 NTNTTATTNN Statistics Matches: 33, Mismatches: 2, Indels: 2 0.89 0.05 0.05 Matches are distributed among these distances: 3 3 0.09 4 30 0.91 ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62 Consensus pattern (4 bp): ATTT Left flanking sequence: Indices 4795 -- 5294 NTTCTCTTGCTGCCGCNTGCTGCTTTTGCGTTTGCTGCTGCTGNCTCCCCCNTNCTTGCTGCTGC TGCTTTTCCTTTTGTTGCTGNCTGCTTCTCCTCTTGCNTGCTGCTGCTGCTTTTCCTTTTGCTGC CGCTGCTCCCCCTCTTGCNTNGCNTGCTCCTTCCCTTCTTGCTGCTTCTGCTTCCCTTTTTGCTG TTGTTGCTTTCCGTCTTGCTGCNTGGTGTNTCCTTCTTTTGCTGCTGCTGCTTCCGCTCTTGCTG CTGCTGCTGTCCCTGCTGCTCCTTCCGCTCTTGCTGCTGCTGCTTCCTCTTTTGCTGCTGCTGCT CCCCGTTTTCCTGCTGCTGCCTCACCTTTTGCTGCTGCTGCTCCTTTTTTTGCTGCTGCTGCCTC GCCTTTTGCTGCTGCTGCGTCCCGTTTGCTGCTGCTGCTGCTGCTGCACTTCGCGTTNTTTGCTG CAGCGCAGCCTCCACTCCCCTTCAAGTTGCAAAAAAATGATTATC Right flanking sequence: Indices 5335 -- 5725 NTNTTATTNNTAATTCAGGATTGTCNTGTGGCCCCCCACCTGTTCTGGGACACACAGCCAGTGGT GAAGGCAGCGGAGCGGGCGGCGCTGGCCCCACAGGTGCAGCAAAGTGGAAATGAATTTNAAATTC TTTTTTCGATTTTGGAATTAAAAGAGAATAAATGAATAATTAATTTAAATCAAGCANATTTGGGA AATCCAGNCGGAGACGAAGATGCANGCAAATCCNGGCAAAAAGATNCTTCNGGAATTCACNTTTA CCNGCAGCAAAATAANCTCCCNAGNCAGCAAAACGNCTATTTGCTGCTGCAGCAAAACAAATTCC GTTTTCTGCTCCCCTTTGTCCCTTTATCCCGCCTTATCTTCCTAATGCAGCAGCAGCAGCAGCAG A Found at i:5333 original size:12 final size:12 Alignment explanation

Indices: 5295--5334 Score: 52 Period size: 12 Copynumber: 3.4 Consensus size: 12 5285 AATGATTATC 5295 ATTTA-TTATTA 1 ATTTATTTATTA * * 5306 ATTAATTAATTA 1 ATTTATTTATTA * 5318 ATTTATTTATTT 1 ATTTATTTATTA 5330 ATTTA 1 ATTTA 5335 NTNTTATTNN Statistics Matches: 23, Mismatches: 5, Indels: 1 0.79 0.17 0.03 Matches are distributed among these distances: 11 4 0.17 12 19 0.83 ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62 Consensus pattern (12 bp): ATTTATTTATTA Left flanking sequence: Indices 4795 -- 5294 NTTCTCTTGCTGCCGCNTGCTGCTTTTGCGTTTGCTGCTGCTGNCTCCCCCNTNCTTGCTGCTGC TGCTTTTCCTTTTGTTGCTGNCTGCTTCTCCTCTTGCNTGCTGCTGCTGCTTTTCCTTTTGCTGC CGCTGCTCCCCCTCTTGCNTNGCNTGCTCCTTCCCTTCTTGCTGCTTCTGCTTCCCTTTTTGCTG TTGTTGCTTTCCGTCTTGCTGCNTGGTGTNTCCTTCTTTTGCTGCTGCTGCTTCCGCTCTTGCTG CTGCTGCTGTCCCTGCTGCTCCTTCCGCTCTTGCTGCTGCTGCTTCCTCTTTTGCTGCTGCTGCT CCCCGTTTTCCTGCTGCTGCCTCACCTTTTGCTGCTGCTGCTCCTTTTTTTGCTGCTGCTGCCTC GCCTTTTGCTGCTGCTGCGTCCCGTTTGCTGCTGCTGCTGCTGCTGCACTTCGCGTTNTTTGCTG CAGCGCAGCCTCCACTCCCCTTCAAGTTGCAAAAAAATGATTATC Right flanking sequence: Indices 5335 -- 5725 NTNTTATTNNTAATTCAGGATTGTCNTGTGGCCCCCCACCTGTTCTGGGACACACAGCCAGTGGT GAAGGCAGCGGAGCGGGCGGCGCTGGCCCCACAGGTGCAGCAAAGTGGAAATGAATTTNAAATTC TTTTTTCGATTTTGGAATTAAAAGAGAATAAATGAATAATTAATTTAAATCAAGCANATTTGGGA AATCCAGNCGGAGACGAAGATGCANGCAAATCCNGGCAAAAAGATNCTTCNGGAATTCACNTTTA CCNGCAGCAAAATAANCTCCCNAGNCAGCAAAACGNCTATTTGCTGCTGCAGCAAAACAAATTCC GTTTTCTGCTCCCCTTTGTCCCTTTATCCCGCCTTATCTTCCTAATGCAGCAGCAGCAGCAGCAG A Found at i:5684 original size:8 final size:8 Alignment explanation

Indices: 5671--5689 Score: 31 Period size: 8 Copynumber: 2.4 Consensus size: 8 5661 TTTTCTGCTC * 5671 CCCTTTGT 1 CCCTTTAT 5679 CCCTTTAT 1 CCCTTTAT 5687 CCC 1 CCC 5690 GCCTTATCTT Statistics Matches: 10, Mismatches: 1, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 8 10 1.00 ACGTcount: A:0.05, C:0.47, G:0.05, T:0.42 Consensus pattern (8 bp): CCCTTTAT Left flanking sequence: Indices 5171 -- 5670 GCTGCTGCTGCCTCGCCTTTTGCTGCTGCTGCGTCCCGTTTGCTGCTGCTGCTGCTGCTGCACTT CGCGTTNTTTGCTGCAGCGCAGCCTCCACTCCCCTTCAAGTTGCAAAAAAATGATTATCATTTAT TATTAATTAATTAATTAATTTATTTATTTATTTANTNTTATTNNTAATTCAGGATTGTCNTGTGG CCCCCCACCTGTTCTGGGACACACAGCCAGTGGTGAAGGCAGCGGAGCGGGCGGCGCTGGCCCCA CAGGTGCAGCAAAGTGGAAATGAATTTNAAATTCTTTTTTCGATTTTGGAATTAAAAGAGAATAA ATGAATAATTAATTTAAATCAAGCANATTTGGGAAATCCAGNCGGAGACGAAGATGCANGCAAAT CCNGGCAAAAAGATNCTTCNGGAATTCACNTTTACCNGCAGCAAAATAANCTCCCNAGNCAGCAA AACGNCTATTTGCTGCTGCAGCAAAACAAATTCCGTTTTCTGCTC Right flanking sequence: Indices 5690 -- 5725 GCCTTATCTTCCTAATGCAGCAGCAGCAGCAGCAGA Found at i:5714 original size:3 final size:3 Alignment explanation

Indices: 5706--5724 Score: 38 Period size: 3 Copynumber: 6.3 Consensus size: 3 5696 TCTTCCTAAT 5706 GCA GCA GCA GCA GCA GCA G 1 GCA GCA GCA GCA GCA GCA G 5725 A Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 16 1.00 ACGTcount: A:0.32, C:0.32, G:0.37, T:0.00 Consensus pattern (3 bp): GCA Left flanking sequence: Indices 5206 -- 5705 CCGTTTGCTGCTGCTGCTGCTGCTGCACTTCGCGTTNTTTGCTGCAGCGCAGCCTCCACTCCCCT TCAAGTTGCAAAAAAATGATTATCATTTATTATTAATTAATTAATTAATTTATTTATTTATTTAN TNTTATTNNTAATTCAGGATTGTCNTGTGGCCCCCCACCTGTTCTGGGACACACAGCCAGTGGTG AAGGCAGCGGAGCGGGCGGCGCTGGCCCCACAGGTGCAGCAAAGTGGAAATGAATTTNAAATTCT TTTTTCGATTTTGGAATTAAAAGAGAATAAATGAATAATTAATTTAAATCAAGCANATTTGGGAA ATCCAGNCGGAGACGAAGATGCANGCAAATCCNGGCAAAAAGATNCTTCNGGAATTCACNTTTAC CNGCAGCAAAATAANCTCCCNAGNCAGCAAAACGNCTATTTGCTGCTGCAGCAAAACAAATTCCG TTTTCTGCTCCCCTTTGTCCCTTTATCCCGCCTTATCTTCCTAAT Right flanking sequence: Indices 5725 -- 5725 A