TRAP (Tandem Repeats Analysis Program)

TRF Version 4.00

Sequence: contig00000040

tutorial_data.fasta.s4.2.5.7.80.10.25.1000.txt.html

Found at i: i:679 original size:3 final size:3

Alignment explanation

Indices: 671--696 Score: 52 Period size: 3 Copynumber: 8.7 Consensus size: 3 661 GGGAGGTCTC 671 CTG CTG CTG CTG CTG CTG CTG CTG CT 1 CTG CTG CTG CTG CTG CTG CTG CTG CT 697 TTAGTAGGAG Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 23 1.00 ACGTcount: A:0.00, C:0.35, G:0.31, T:0.35 Consensus pattern (3 bp): CTG Left flanking sequence: Indices 171 -- 670 GGAGCAAGAAGTTTGGTGCTGGCTCCTGTGCGCGCTTTGCAGCAGCAGAGCCTAAAGCCTCTGCT GCAATTCATTTTTTGCCGCCAATTTTGCACGCTGGGCTGCTAGTTCACCAGCCTTGCAGCAACAG TAGCAGCAGCAGCCAGCAGTGGCCGGCAGCAGCAGCAGCAGCAGCAGCGGCGGCAGCGACAGCAG CTGCTGCTGCATTGTCAGGAAGGACAGCGTTTACACCCAAGCTGCAGCGGATGGCGCTGCGCCTC TGATGCTCGAGTGACGCAGCTGCTGCACCTGCAGCCGACACAGCAGCAGCTGCAGCGCCACCAGC AACAGGAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCTCACAGCGACAGCGAACTTATCTCCA GAGACCCCAAATGTTTTGTCTCCGCTGCCTTGGAAAGGAGGCCCTCCCTTACTTTTGCTGCAGCA TTGGGGCCCCCCGAGCATTTTGCTGCAGCTGCCCAGGGAGGTCTC Right flanking sequence: Indices 697 -- 1044 TTAGTAGGAGGCGAAAGGTGTGGGCAGCAGCTGCTGGGGGGCCCCCAGNCTAAGGCCAGGGGGGC CCCCCAGGGCCAACTGGGGGGCCCCCTCAGCCCGGGACTTCAGCGGGGGAAAACAGAAAGGAGAA TCTGCAAAAGAGAAAAAGATGAAAAGAATGTTAAAGAAAATAAATGTTGTGAGAGAAGAAGAAGC AGCAGAAGCAGGGAGTTGGAGGGAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCACAGGCGAGGCG GCAAGGCCGCGGGGTGCTTCGATCTGCAGGCGGCCGAAGCTGCAGCAGAAGCAGCAGCAGCAGCA GGCAGCAGCAATGGGCGCGTTTT Found at i:888 original size:3 final size:3 Alignment explanation

Indices: 880--899 Score: 26 Period size: 3 Copynumber: 6.7 Consensus size: 3 870 ATGTTGTGAG * * 880 AGA AGA AGA AGC AGC AGA AG 1 AGA AGA AGA AGA AGA AGA AG 900 CAGGGAGTTG Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 3 15 1.00 ACGTcount: A:0.55, C:0.10, G:0.35, T:0.00 Consensus pattern (3 bp): AGA Left flanking sequence: Indices 380 -- 879 TCAGGAAGGACAGCGTTTACACCCAAGCTGCAGCGGATGGCGCTGCGCCTCTGATGCTCGAGTGA CGCAGCTGCTGCACCTGCAGCCGACACAGCAGCAGCTGCAGCGCCACCAGCAACAGGAGCAGCAG CAACAGCAGCAGCAGCAGCAGCAGCTCACAGCGACAGCGAACTTATCTCCAGAGACCCCAAATGT TTTGTCTCCGCTGCCTTGGAAAGGAGGCCCTCCCTTACTTTTGCTGCAGCATTGGGGCCCCCCGA GCATTTTGCTGCAGCTGCCCAGGGAGGTCTCCTGCTGCTGCTGCTGCTGCTGCTGCTTTAGTAGG AGGCGAAAGGTGTGGGCAGCAGCTGCTGGGGGGCCCCCAGNCTAAGGCCAGGGGGGCCCCCCAGG GCCAACTGGGGGGCCCCCTCAGCCCGGGACTTCAGCGGGGGAAAACAGAAAGGAGAATCTGCAAA AGAGAAAAAGATGAAAAGAATGTTAAAGAAAATAAATGTTGTGAG Right flanking sequence: Indices 900 -- 1044 CAGGGAGTTGGAGGGAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCACAGGCGAGGCGGCAAGGCC GCGGGGTGCTTCGATCTGCAGGCGGCCGAAGCTGCAGCAGAAGCAGCAGCAGCAGCAGGCAGCAG CAATGGGCGCGTTTT Found at