Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2240
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: 43848
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Found at i:6496 original size:40 final size:40
Alignment explanation
Indices: 6359--6577 Score: 274
Period size: 40 Copynumber: 5.5 Consensus size: 40
6349 TTATTGGATG
* *
6359 ATATCCGGGCTAAGT--CGAAGG-ATTT-TGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
6395 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC---TAG-TGACT
6438 ATA-CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
**
6477 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
6517 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
6557 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
6578 ATACTTGGGT
Statistics
Matches: 162, Mismatches: 10, Indels: 19
0.85 0.05 0.10
Matches are distributed among these distances:
36 15 0.09
38 8 0.05
39 25 0.15
40 76 0.47
41 2 0.01
42 28 0.17
43 7 0.04
44 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:14527 original size:40 final size:40
Alignment explanation
Indices: 14472--14652 Score: 256
Period size: 40 Copynumber: 4.5 Consensus size: 40
14462 TATTCGAATG
*
14472 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACT
* * *
14512 ATATCTGGGCTAAGTCCTGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACT
**
14552 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACT
* * * *
14592 ATATCCGGGCTAAGACCCGAAGACATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACT
*
14632 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
14653 ATACTTGGGT
Statistics
Matches: 124, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 13 0.10
40 111 0.90
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACT
Found at i:21302 original size:27 final size:26
Alignment explanation
Indices: 21265--21332 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 26
21255 AGCATGGCTG
*
21265 CCAGAACAGATATTGTGATAGAGTCA
1 CCAGAACAGATATTGTGATAGAGCCA
*
21291 CCAGATACAGATATTGTGGTAGAGCCA
1 CCAGA-ACAGATATTGTGATAGAGCCA
*
21318 CTAGAAACAGATATT
1 CCAG-AACAGATATT
21333 TGTTGCATAG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.14
27 31 0.84
28 1 0.03
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (26 bp):
CCAGAACAGATATTGTGATAGAGCCA
Found at i:21512 original size:26 final size:26
Alignment explanation
Indices: 21456--21512 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
21446 AAATTAACCC
* *
21456 TAGGGTATAATGGTAATTTTGCACCT
1 TAGGGTATAATGATAATTTTGCAACT
*
21482 AAGGGTATAATGATAATTTT-CATACT
1 TAGGGTATAATGATAATTTTGCA-ACT
21508 TAGGG
1 TAGGG
21513 GTATTTTAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.37
Consensus pattern (26 bp):
TAGGGTATAATGATAATTTTGCAACT
Found at i:22629 original size:25 final size:22
Alignment explanation
Indices: 22575--22629 Score: 56
Period size: 25 Copynumber: 2.3 Consensus size: 22
22565 TTTTGGCCAG
22575 AGAAGAAAAGAAGGAGAAAAGA
1 AGAAGAAAAGAAGGAGAAAAGA
* *
22597 AAATAGAAGAAGAGAGGAGAAGAGA
1 AGA-AGAA-AAGA-AGGAGAAAAGA
22622 AGGAAGAA
1 A-GAAGAA
22630 TTCGGCACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 2 0.08
23 4 0.15
24 4 0.15
25 15 0.58
26 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.02
Consensus pattern (22 bp):
AGAAGAAAAGAAGGAGAAAAGA
Found at i:23363 original size:21 final size:22
Alignment explanation
Indices: 23338--23381 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
23328 TAAGAACTTT
23338 TTTTTA-TTATTATCTTT-TTTA
1 TTTTTACTT-TTATCTTTATTTA
23359 TTTTTACTTTTATCTTTATTTA
1 TTTTTACTTTTATCTTTATTTA
23381 T
1 T
23382 CTTCTGTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTACTTTTATCTTTATTTA
Found at i:27442 original size:22 final size:22
Alignment explanation
Indices: 27415--27536 Score: 72
Period size: 22 Copynumber: 5.3 Consensus size: 22
27405 CATGCATTTG
27415 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * **
27437 TGTGATGAATG-AGAACATGTACATA
1 TGTGAT-AAGGCCG-A-ATGGCCA-A
27462 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* *
27484 TGTGATGAATG-TGAACAT-G-CATA
1 TGTGAT-AAGGCCG-A-ATGGCCA-A
27507 TGTGTGATAAGGCCGAATGGCCAA
1 --TGTGATAAGGCCGAATGGCCAA
27531 TGTGAT
1 TGTGAT
27537 GAATATGAAC
Statistics
Matches: 74, Mismatches: 12, Indels: 28
0.65 0.11 0.25
Matches are distributed among these distances:
22 23 0.31
23 17 0.23
24 17 0.23
25 17 0.23
ACGTcount: A:0.33, C:0.13, G:0.30, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:27580 original size:21 final size:21
Alignment explanation
Indices: 27554--27627 Score: 60
Period size: 24 Copynumber: 3.3 Consensus size: 21
27544 AACATGCACT
27554 ATGTGATAAAGCGAATGGCCA
1 ATGTGATAAAGCGAATGGCCA
* * *
27575 ATGTGATAATGTGAACAT-GCATA
1 ATGTGATAAAGCG-A-ATGGC-CA
*
27598 TATGTGATAAGGCAGAATGGCCA
1 -ATGTGATAAAGC-GAATGGCCA
27621 ATGTGAT
1 ATGTGAT
27628 GAATGTGGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
21 11 0.27
22 10 0.24
23 6 0.15
24 13 0.32
25 1 0.02
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.26
Consensus pattern (21 bp):
ATGTGATAAAGCGAATGGCCA
Found at i:27664 original size:47 final size:47
Alignment explanation
Indices: 27342--27634 Score: 403
Period size: 47 Copynumber: 6.3 Consensus size: 47
27332 TTAGGATTTT
* ** * * * **
27342 ATGTGATGGATGTGAATGTGTATATATGAGCTAAGGCCGAATGGTAA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
27389 ATGTGATGAATGTGAACATGCATTTGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
27436 ATGTGATGAATGAGAACATGTACATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
27483 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
27530 ATGTGATGAATATGAACATGCA-CTATGTGATAAAG-CGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
27575 ATGTGAT-AATGTGAACATGCATATATGTGATAAGGCAGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
27621 ATGTGATGAATGTG
1 ATGTGATGAATGTG
27635 GAAGTGTATA
Statistics
Matches: 216, Mismatches: 27, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
44 13 0.06
45 28 0.13
46 26 0.12
47 149 0.69
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:27697 original size:46 final size:46
Alignment explanation
Indices: 27644--27734 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
27634 GGAAGTGTAT
* * *
27644 ATATGTGGGAAAGCCGAATGGTTAATGCGAAATGTGTATGAGATGG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
* * *
27690 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATG
27735 TGTATATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.34, C:0.07, G:0.32, T:0.27
Consensus pattern (46 bp):
ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
Found at i:27703 original size:138 final size:140
Alignment explanation
Indices: 27377--27673 Score: 375
Period size: 138 Copynumber: 2.1 Consensus size: 140
27367 ATGAGCTAAG
** * * * * *
27377 GCCGAATGGTAAATGTGATGAATGTGAACATGCATTTGTGTGATAAGGCCGAATGGCCAATGTGA
1 GCCGAATGGCCAATGCGATGAATATGAACATGCA-CTATGTGATAAAGCCGAATGGCCAATGTGA
* *
27442 TGAATGAGAACATGTACATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATA
65 TGAATGAGAACATGCACATATGTGATAAGGCAGAATGGCCAATGTGATGAATGTGAACATGCATA
* * *
27507 TGTGTGATAAG
130 TATGTGAGAAA
*
27518 GCCGAATGGCCAATGTGATGAATATGAACATGCACTATGTGATAAAG-CGAATGGCCAATGTGAT
1 GCCGAATGGCCAATGCGATGAATATGAACATGCACTATGTGATAAAGCCGAATGGCCAATGTGAT
* * * *
27582 -AATGTGAACATGCATATATGTGATAAGGCAGAATGGCCAATGTGATGAATGTGGAA-GTGTATA
66 GAATGAGAACATGCACATATGTGATAAGGCAGAATGGCCAATGTGATGAATGT-GAACATGCATA
*
27645 TATGTGGGAAA
130 TATGTGAGAAA
**
27656 GCCGAATGGTTAATGCGA
1 GCCGAATGGCCAATGCGA
27674 AATGTGTATG
Statistics
Matches: 136, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
138 75 0.55
139 20 0.15
140 10 0.07
141 31 0.23
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (140 bp):
GCCGAATGGCCAATGCGATGAATATGAACATGCACTATGTGATAAAGCCGAATGGCCAATGTGAT
GAATGAGAACATGCACATATGTGATAAGGCAGAATGGCCAATGTGATGAATGTGAACATGCATAT
ATGTGAGAAA
Found at i:30217 original size:46 final size:46
Alignment explanation
Indices: 30167--30335 Score: 200
Period size: 46 Copynumber: 3.7 Consensus size: 46
30157 TTGAGCATCC
*
30167 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCG
* * * *
30213 AACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CGTCCG
* * *
30260 AACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCG
*
30306 AGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTA
30336 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 57 0.55
47 29 0.28
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCG
Found at i:30326 original size:93 final size:92
Alignment explanation
Indices: 30161--30330 Score: 286
Period size: 93 Copynumber: 1.8 Consensus size: 92
30151 GGATGGTTGA
* *
30161 GCATCCAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGTT
1 GCATCCAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGTT
30226 GAGTCCGAGTTCGTGAGATGTAACTAG
66 GAGTCCGAGTTCGTGAGATGTAACTAG
* * *
30253 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCC-AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
30318 TGAGTCCGAGTTC
65 TGAGTCCGAGTTC
30331 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
92 6 0.08
93 66 0.92
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (92 bp):
GCATCCAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGTT
GAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:37541 original size:20 final size:19
Alignment explanation
Indices: 37503--37541 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
37493 ATGTAGCATA
* *
37503 AATGTTATTTTAAGTTATT
1 AATGTTATTATAAGATATT
37522 AATGTTAATTATAAGATATT
1 AATGTT-ATTATAAGATATT
37542 GATTTTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (19 bp):
AATGTTATTATAAGATATT
Done.