Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold704
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: 44462
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Found at i:8340 original size:28 final size:29
Alignment explanation
Indices: 8309--8381 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 29
8299 GTTGTGAGAT
*
8309 TGGCACTAAGTGTGCG-GCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
8337 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
8366 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
8382 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
28 21 0.51
29 20 0.49
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:18614 original size:522 final size:522
Alignment explanation
Indices: 17630--19246 Score: 3045
Period size: 522 Copynumber: 3.1 Consensus size: 522
17620 ACCTTCAAAA
*
17630 ATGCATAATTTGTATAATCATTTCAAGTACTAAACTTACCTTAATTCCATGCCAAACACATCAAA
1 ATGCATAATTTGTATAATCATTTCAAGTACTAAACTTACCTTAATTTCATGCCAAACACATCAAA
17695 GAAAAACACACCTCCTAAATTAAGCTAATTTTATGGCCTAATATGCATCATGCATTGCATTACTC
66 GAAAAACACACCTCCTAAATTAAGCTAATTTTATGGCCTAATATGCATCATGCATTGCATTACTC
*
17760 ATTACCGAATCACCAAAACCAAACACATCAACCATATTAACCATGAACATATAAAACCAAACTTA
131 ATTACCGAATCACCAAAACCAAACACATCAAACATATTAACCATGAACATATAAAACCAAACTTA
17825 AGCATAATGATTAAGCCATTTTCACATGGCCTAATATATACAACTCAAAATCAAACATAATATAA
196 AGCATAATGATTAAGCCATTTTCACATGGCCTAATATATACAACTCAAAATCAAACATAATATAA
17890 CAAGCCTATACATGCCATATGTTCAAAGTTTCAAACTTATAAAATACCAAAATAATGATCGATAG
261 CAAGCCTATACATGCCATATGTTCAAAGTTTCAAACTTATAAAATACCAAAATAATGATCGATAG
17955 TGTGGCAAACTTCCTTGACGATCCCCGAGCTCGTAACTAGCTTTCCAAAATCAATAAAAAAATTA
326 TGTGGCAAACTTCCTTGACGATCCCCGAGCTCGTAACTAGCTTTCCAAAATCAATAAAAAAATTA
* * * * *
18020 AAATGCACACACAGTAAGCTTAAATAGCTTTGTAAGTCATAAGAAAATATATCAACAAAAGAATA
391 ACACGCACACATAGTAAGCTTAAATAGCTTAGTAAGTCATAAGAAAATATATCAACAAATGAATA
*
18085 TTAACATTATAATATCACTTGGCCGAATTTAAACAATTACATGTACATATAAATCACCTTTTATA
456 TTAACATTATAATATCACTTGGCCGAATTTAAACAATCACATGTACATATAAATCACCTTTTATA
18150 AC
521 AC
* *
18152 ATGCATAATTTGTATAATCATTTCAGGTACTAAACTTACCTTAATTTCATGCCAAACACAACAAA
1 ATGCATAATTTGTATAATCATTTCAAGTACTAAACTTACCTTAATTTCATGCCAAACACATCAAA
18217 GAAAAACACACCTCCTAAATTAAGCTAATTTTATGGCCTAATATGCATCATGCATTGCATTACTC
66 GAAAAACACACCTCCTAAATTAAGCTAATTTTATGGCCTAATATGCATCATGCATTGCATTACTC
18282 ATTACCGAATCACCAAAACCAAACACATCAAACATATTAACCATGAACATATAAAACCAAACTTA
131 ATTACCGAATCACCAAAACCAAACACATCAAACATATTAACCATGAACATATAAAACCAAACTTA
18347 AGCATAATGATTAAGCCATTTTCACATGGCCTAATATATACAACTCAAAATCAAACATAATATAA
196 AGCATAATGATTAAGCCATTTTCACATGGCCTAATATATACAACTCAAAATCAAACATAATATAA
18412 CAAGCCTATACATGCCATATGTTCAAAGTTTCAAACTTATAAAATACCAAAATAATGATCGATAG
261 CAAGCCTATACATGCCATATGTTCAAAGTTTCAAACTTATAAAATACCAAAATAATGATCGATAG
* *
18477 TGTGGCGAACTTCCTTGACGATCCCCGAGCCCGTAACTAGCTTTCCAAAATCAATAAAAAAATTA
326 TGTGGCAAACTTCCTTGACGATCCCCGAGCTCGTAACTAGCTTTCCAAAATCAATAAAAAAATTA
*
18542 ACACGCACACATGGTAAGCTTAAATAGCTTAGTAAGTCATAAGAAAATATATCAACAAATGAATA
391 ACACGCACACATAGTAAGCTTAAATAGCTTAGTAAGTCATAAGAAAATATATCAACAAATGAATA
18607 TTAACATTATAATATCACTTGGCCGAATTTAAACAATCACATGTACATATAAATCACCTTTTATA
456 TTAACATTATAATATCACTTGGCCGAATTTAAACAATCACATGTACATATAAATCACCTTTTATA
18672 AC
521 AC
*
18674 ATGCATAATTTGTATAATCATTTCAGGTACTAAACTTACCTTAATTTCATGCCAAACACATCAAA
1 ATGCATAATTTGTATAATCATTTCAAGTACTAAACTTACCTTAATTTCATGCCAAACACATCAAA
*
18739 GAAAAGCACACCTCCTAAATTAAGCTAATTTTATGGCCTAATATGCATCATGCATTGCATTACTC
66 GAAAAACACACCTCCTAAATTAAGCTAATTTTATGGCCTAATATGCATCATGCATTGCATTACTC
18804 ATTACCGAATCACCAAAACCAAACACATCAAACATATTAACCATGAACATATAAAACCAAACTTA
131 ATTACCGAATCACCAAAACCAAACACATCAAACATATTAACCATGAACATATAAAACCAAACTTA
18869 AGCATAATGATTAAGCCATTTTCACATGGCCTAATATATACAACTCAAAATCAAACATAATATAA
196 AGCATAATGATTAAGCCATTTTCACATGGCCTAATATATACAACTCAAAATCAAACATAATATAA
*
18934 CAAGCCTATACATGCCATATGTTCAAAGTTTCAAACTTATAAAATACCAAAATAATGATTGATAG
261 CAAGCCTATACATGCCATATGTTCAAAGTTTCAAACTTATAAAATACCAAAATAATGATCGATAG
* *
18999 TTTGGCAAACTTCCTTGACGATCCCCGAGCTTGTAACTAGCTTTCCAAAATCAATAAAAAAATTA
326 TGTGGCAAACTTCCTTGACGATCCCCGAGCTCGTAACTAGCTTTCCAAAATCAATAAAAAAATTA
19064 ACACGCACACATAGTAAGCTTAAATAGCTTAGTAAGTCATAAGAAAATATATCAACAAATGAATA
391 ACACGCACACATAGTAAGCTTAAATAGCTTAGTAAGTCATAAGAAAATATATCAACAAATGAATA
* *
19129 TTAACATTATAATATCACTTGGCCAAATTTAAACAATCACATGTACATATAAATCACCTTCTATA
456 TTAACATTATAATATCACTTGGCCGAATTTAAACAATCACATGTACATATAAATCACCTTTTATA
19194 AC
521 AC
*
19196 ATGCATAATTTGTATAATCATTTCAATTACTAAACTTACCTTAATTTCATG
1 ATGCATAATTTGTATAATCATTTCAAGTACTAAACTTACCTTAATTTCATG
19247 AACATAACTT
Statistics
Matches: 1070, Mismatches: 25, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
522 1070 1.00
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (522 bp):
ATGCATAATTTGTATAATCATTTCAAGTACTAAACTTACCTTAATTTCATGCCAAACACATCAAA
GAAAAACACACCTCCTAAATTAAGCTAATTTTATGGCCTAATATGCATCATGCATTGCATTACTC
ATTACCGAATCACCAAAACCAAACACATCAAACATATTAACCATGAACATATAAAACCAAACTTA
AGCATAATGATTAAGCCATTTTCACATGGCCTAATATATACAACTCAAAATCAAACATAATATAA
CAAGCCTATACATGCCATATGTTCAAAGTTTCAAACTTATAAAATACCAAAATAATGATCGATAG
TGTGGCAAACTTCCTTGACGATCCCCGAGCTCGTAACTAGCTTTCCAAAATCAATAAAAAAATTA
ACACGCACACATAGTAAGCTTAAATAGCTTAGTAAGTCATAAGAAAATATATCAACAAATGAATA
TTAACATTATAATATCACTTGGCCGAATTTAAACAATCACATGTACATATAAATCACCTTTTATA
AC
Found at i:19469 original size:42 final size:44
Alignment explanation
Indices: 19369--19471 Score: 124
Period size: 43 Copynumber: 2.4 Consensus size: 44
19359 AACTCGTACA
* * * *
19369 ATGCCTATGTCCCAGAC-GAGGTCTTACATGTAATCAACTATCG
1 ATGCCAATGTCCCAGACAGAGGGCTTACACGAAATCAACTATCG
*
19412 ATGCCACTGTCCCAGACAG-GGGCTTACACGAAATC-A-TATACG
1 ATGCCAATGTCCCAGACAGAGGGCTTACACGAAATCAACTAT-CG
19454 ATGCCAATGTCCCAGACA
1 ATGCCAATGTCCCAGACA
19472 TGATCCTCCA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
41 3 0.06
42 20 0.38
43 28 0.54
44 1 0.02
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (44 bp):
ATGCCAATGTCCCAGACAGAGGGCTTACACGAAATCAACTATCG
Found at i:24389 original size:16 final size:16
Alignment explanation
Indices: 24370--24400 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
24360 CTTCTTCACT
24370 TACTAACTTACTTAAA
1 TACTAACTTACTTAAA
*
24386 TACTTACTTACTTAA
1 TACTAACTTACTTAA
24401 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTAACTTACTTAAA
Found at i:24406 original size:20 final size:20
Alignment explanation
Indices: 24367--24406 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
24357 AAACTTCTTC
* *
24367 ACTTACTAACTTACTTAAAT
1 ACTTACTAACTTAATCAAAT
*
24387 ACTTACTTACTTAATCAAAT
1 ACTTACTAACTTAATCAAAT
24407 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTAACTTAATCAAAT
Found at i:32495 original size:55 final size:53
Alignment explanation
Indices: 32363--32559 Score: 175
Period size: 55 Copynumber: 3.6 Consensus size: 53
32353 ACTTACCATC
* *
32363 GCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAAT
1 GCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACCAAT
* * * * *
32416 GCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTTCCTTATAGTAACTTATCAAT
1 GCCATGTCTTGACATGGTCTTACATGGGATCC-TTGCCTTAT-G-AACTCACCAAT
* ** * *
32471 TCCATGTCTTGACATGGTCTTACATGATATCCTTGCC-TAAGAAACCTTACCAATT
1 GCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG-AA-CTCACCAA-T
* * *
32526 TCCAT-TCCTTGGCATGGTCTTACATGGTATCCTT
1 GCCATGT-CTTGACATGGTCTTACATGGGATCCTT
32560 AACCCCTAAT
Statistics
Matches: 119, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
52 2 0.02
53 36 0.30
54 11 0.09
55 68 0.57
56 2 0.02
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (53 bp):
GCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACCAAT
Found at i:35500 original size:39 final size:40
Alignment explanation
Indices: 35423--35569 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
35413 TAGCTCCTCG
* * *
35423 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
35463 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
35502 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
35542 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
35570 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:35580 original size:80 final size:80
Alignment explanation
Indices: 35469--35649 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
35459 CTCATTCAAT
* * *
35469 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
35532 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
35548 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
35612 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
35629 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
35650 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:35609 original size:40 final size:40
Alignment explanation
Indices: 35466--35649 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
35456 TAACTCATTC
* *
35466 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
35506 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
35546 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
35586 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
35627 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
35650 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:44050 original size:38 final size:38
Alignment explanation
Indices: 43925--44051 Score: 132
Period size: 39 Copynumber: 3.3 Consensus size: 38
43915 AAACTCATTC
*
43925 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACGA
1 AATGCCTTCGGGACTT-ACCCGGA-ATTAATAA-TCGCAC-A
* * *
43966 AATGCCTTC-GGACTTAACCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTACCCGGAATTAATA-ATCGCACA
* *
44004 AAGGCCTTCGGGACTTACCCGGAATTAATAATCACACA
1 AATGCCTTCGGGACTTACCCGGAATTAATAATCGCACA
*
44042 AATACCTTCG
1 AATGCCTTCG
44052 ATCTTAGTCC
Statistics
Matches: 72, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
38 26 0.36
39 31 0.43
40 6 0.08
41 9 0.12
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (38 bp):
AATGCCTTCGGGACTTACCCGGAATTAATAATCGCACA
Done.