Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold729
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 33383
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:8543 original size:17 final size:17
Alignment explanation
Indices: 8521--8560 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
8511 ATTTCATTCA
8521 TGTTTAA-AATTTTAATG
1 TGTTTAATAA-TTTAATG
*
8538 TGTTTAATAATTTATTG
1 TGTTTAATAATTTAATG
8555 TGTTTA
1 TGTTTA
8561 TGTTTAAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (17 bp):
TGTTTAATAATTTAATG
Found at i:10693 original size:188 final size:190
Alignment explanation
Indices: 10374--10779 Score: 495
Period size: 188 Copynumber: 2.1 Consensus size: 190
10364 AGAAACGATG
* * * * *
10374 AAAACAGTCACTATTTCGATCTTTTCTTTCCACTTTCTCGAATCCAGTGGAGAGAAAATAAAATC
1 AAAACAGTCGCTATTTCGATATTTTCTTTCCACTTTCTCGAATCCAG-GCAGAGAAAAGAAAATA
* * *
10439 ATCAACTAAATACCGATCTAAAAAGTTCAAAACAGAGATAAAAACCCATAGCCACAACACAAAAT
65 ATCAACCAAATACCGATCTAAAAAGTTCAAAACAGAAATAAAAACCCATAGCCACAACAAAAAAT
* * * *
10504 T-C-AAAAACCTCGGTAAGAAGTGATACTATATCG-ATATATATACAT-GAAAGCAGGATTA
130 TACAAAAAAACTCAGTAACAAGTGATACTATATCGAATATATATACATAG-AAGAAGGATTA
10562 AAAACAGTCGCTATTTCGATATTTTCTTTCCACTTTCTCGAATCCA-GCA-AGTAAATAGAAAAT
1 AAAACAGTCGCTATTTCGATATTTTCTTTCCACTTTCTCGAATCCAGGCAGAG-AAA-AGAAAAT
* ** *
10625 AAAATCAACCAAATACCGATCTAAAGAGTTCAAAAC-GCAAAT-AAATTCCGTAGCCACAACAAA
64 --AATCAACCAAATACCGATCTAAAAAGTTCAAAACAG-AAATAAAAACCCATAGCCACAACAAA
10688 AAATTCAAAAGCAAAAAAACTCAGTAACAAGTGATACTATATCGATATATATATACATAGAAGAA
126 AAATT----A-CAAAAAAACTCAGTAACAAGTGATACTATATCGA-ATATATATACATAGAAGAA
10753 GGATTA
185 GGATTA
10759 AAAACAGTCGCTATTTCGATA
1 AAAACAGTCGCTATTTCGATA
10780 GAAAAAAAAT
Statistics
Matches: 187, Mismatches: 16, Indels: 21
0.83 0.07 0.09
Matches are distributed among these distances:
185 2 0.01
186 5 0.03
187 6 0.03
188 67 0.36
189 34 0.18
194 1 0.01
195 28 0.15
197 43 0.23
198 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.25
Consensus pattern (190 bp):
AAAACAGTCGCTATTTCGATATTTTCTTTCCACTTTCTCGAATCCAGGCAGAGAAAAGAAAATAA
TCAACCAAATACCGATCTAAAAAGTTCAAAACAGAAATAAAAACCCATAGCCACAACAAAAAATT
ACAAAAAAACTCAGTAACAAGTGATACTATATCGAATATATATACATAGAAGAAGGATTA
Found at i:14901 original size:24 final size:21
Alignment explanation
Indices: 14856--14901 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 21
14846 TAATAAAATT
*
14856 AACAATAAAACAATAGTTACA
1 AACAATAAAACAATAGTAACA
14877 AACAATAACAACAAAATAGTAACA
1 AACAATAA-AAC--AATAGTAACA
14901 A
1 A
14902 TATAATAGCG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 3 0.14
24 10 0.48
ACGTcount: A:0.65, C:0.15, G:0.04, T:0.15
Consensus pattern (21 bp):
AACAATAAAACAATAGTAACA
Found at i:18788 original size:25 final size:23
Alignment explanation
Indices: 18746--18798 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 23
18736 AACTTTATTT
*
18746 TTATTATTAATTCTATTATTGCTA
1 TTATTATTAATTCCATTATT-CTA
18770 CTTATTATT-ATTGCCATTATTCTA
1 -TTATTATTAATT-CCATTATTCTA
18794 TTATT
1 TTATT
18799 TCTTATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 5 0.19
24 6 0.23
25 15 0.58
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.58
Consensus pattern (23 bp):
TTATTATTAATTCCATTATTCTA
Found at i:24340 original size:31 final size:31
Alignment explanation
Indices: 24302--24370 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
24292 TTGTGGTACC
*
24302 AATGACTTAAATGAAAAATT-TCGAATAGTTT
1 AATGACTTAAAT-AAAAATTATCGAATAATTT
* *
24333 AATGACTTGAATCAAAATTATCGAATAATTT
1 AATGACTTAAATAAAAATTATCGAATAATTT
*
24364 GATGACT
1 AATGACT
24371 ATTTAGTAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 6 0.18
31 27 0.82
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (31 bp):
AATGACTTAAATAAAAATTATCGAATAATTT
Found at i:31665 original size:33 final size:35
Alignment explanation
Indices: 31628--31693 Score: 118
Period size: 33 Copynumber: 1.9 Consensus size: 35
31618 ATAAATGTGA
31628 ATATCTTCAAATTTCATC-TCTTA-AGCTAGAACT
1 ATATCTTCAAATTTCATCATCTTATAGCTAGAACT
31661 ATATCTTCAAATTTCATCATCTTATAGCTAGAA
1 ATATCTTCAAATTTCATCATCTTATAGCTAGAA
31694 ACTAGCTCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 18 0.58
34 5 0.16
35 8 0.26
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (35 bp):
ATATCTTCAAATTTCATCATCTTATAGCTAGAACT
Done.