Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1978
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: 75026
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:1181 original size:19 final size:20
Alignment explanation
Indices: 1157--1194 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1147 TGGTACACCA
1157 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
1176 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
1195 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:1488 original size:46 final size:45
Alignment explanation
Indices: 1421--1588 Score: 171
Period size: 46 Copynumber: 3.6 Consensus size: 45
1411 CGCCCCTAAG
*
1421 TGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGGCGTT-GCATCCATAAA
* *
1467 TGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-T-CA
1 TGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTGCATCCATAAA
* * * * * *
1514 CGAACTCGGGCTCAACTCAACGAGTTCAGACATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGGC-GTTGCATCCATAAA
1560 TGAACTCGGACTCAACTCAACGAGTTCGG
1 TGAACTCGGACTCAACTCAACGAGTTCGG
1589 ATGCTCAACC
Statistics
Matches: 100, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 1 0.01
46 54 0.54
47 27 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (45 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGGCGTTGCATCCATAAA
Found at i:1534 original size:93 final size:93
Alignment explanation
Indices: 1422--1592 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
1412 GCCCCTAAGT
* * *
1422 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
1487 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * * *
1515 GAACTCGGGCTCAACTCAACGAGTTCAGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
1580 CGAGTTCGGATGC
66 CGAGTTCGGATGC
1593 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:7501 original size:22 final size:22
Alignment explanation
Indices: 7473--7595 Score: 74
Period size: 22 Copynumber: 5.3 Consensus size: 22
7463 ATGTGCATAT
7473 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* * *
7495 ATGTGATGAATG-TGAACAT-GCATA
1 ATGTGAT-AAGGCCG-A-ATGGC-CA
7519 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
* * *
7542 ATGTGATGAATG-TGAACAT-GCATA
1 ATGTGAT-AAGGCCG-A-ATGGC-CA
7566 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
7589 ATGTGAT
1 ATGTGAT
7596 GAATGTGAGC
Statistics
Matches: 75, Mismatches: 12, Indels: 28
0.65 0.10 0.24
Matches are distributed among these distances:
22 23 0.31
23 18 0.24
24 18 0.24
25 16 0.21
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:7688 original size:47 final size:47
Alignment explanation
Indices: 7466--7679 Score: 374
Period size: 47 Copynumber: 4.6 Consensus size: 47
7456 GATATGAATG
7466 TGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 TGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
7513 TGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 TGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
*
7560 TGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
1 TGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
* * *
7607 TGCATATGTGTGATAAGGCCAAATGGCCAATGTGATGAATATGAACA
1 TGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
* *
7654 TGCATATATGTGGTAAAGCCGAATGG
1 TGCATATATGTGATAAGGCCGAATGG
7680 ATAGTGTGAA
Statistics
Matches: 158, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 158 1.00
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.26
Consensus pattern (47 bp):
TGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
Found at i:7893 original size:37 final size:37
Alignment explanation
Indices: 7843--7955 Score: 172
Period size: 37 Copynumber: 3.1 Consensus size: 37
7833 GGAAATATAT
* * *
7843 TCCGGGTAAGACCCTATGACTACGTGTGAAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
7880 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* * *
7917 TCCGGGTAAGACTCGATAACTTCGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
7954 TC
1 TC
7956 TGAGCTAAAG
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:37579 original size:24 final size:23
Alignment explanation
Indices: 37527--37581 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
37517 CAACCGAATT
* *
37527 TGCACACATAGTGCTCGTCACAC
1 TGCACACATAGTGCTAGTCAAAC
37550 TCGCACACATAGTGCCATAGT-AAAC
1 T-GCACACATAGTG-C-TAGTCAAAC
37575 TGCACAC
1 TGCACAC
37582 TCAGTGCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 1 0.04
24 18 0.67
25 5 0.19
26 3 0.11
ACGTcount: A:0.31, C:0.33, G:0.16, T:0.20
Consensus pattern (23 bp):
TGCACACATAGTGCTAGTCAAAC
Found at i:41241 original size:22 final size:22
Alignment explanation
Indices: 41216--41338 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
41206 AGATATGTAT
41216 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* * ***
41238 ATGTGATGAATG-TGAAAGTGTATA
1 ATGTGAT-AAGGCCG-AA-TGGCCA
*
41262 TATGAGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
* * ***
41285 ATGTGATGAATG-TGAAAGTGTATA
1 ATGTGAT-AAGGCCG-AA-TGGCCA
41309 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
41332 ATGTGAT
1 ATGTGAT
41339 GAATGTGAAA
Statistics
Matches: 69, Mismatches: 22, Indels: 20
0.62 0.20 0.18
Matches are distributed among these distances:
22 22 0.32
23 16 0.23
24 16 0.23
25 15 0.22
ACGTcount: A:0.34, C:0.10, G:0.30, T:0.26
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:41271 original size:47 final size:47
Alignment explanation
Indices: 41213--41742 Score: 880
Period size: 47 Copynumber: 11.3 Consensus size: 47
41203 ACAAGATATG
41213 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
41260 TATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
41307 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
41354 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * *
41401 TATATGTGATAAGTCCTAATGGCCAATCTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * *
41448 TATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
41495 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * **
41542 TATATGTGACAAGGCCTAATGGCTGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
41589 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * * * * *
41636 TATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAAGGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
41683 TATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
41730 TAAATGTGATAAG
1 TATATGTGATAAG
41743 TCCCGAAGGG
Statistics
Matches: 451, Mismatches: 32, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 451 1.00
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.28
Consensus pattern (47 bp):
TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
Found at i:60860 original size:24 final size:24
Alignment explanation
Indices: 60828--60898 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
60818 CTGTCAGGAG
60828 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
60852 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
**
60876 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGTTGATAAGGGA
60899 GGAAATCTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.35, C:0.01, G:0.38, T:0.25
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:60910 original size:48 final size:48
Alignment explanation
Indices: 60828--60921 Score: 120
Period size: 48 Copynumber: 1.9 Consensus size: 48
60818 CTGTCAGGAG
** *
60828 AGGATTTAGGAGTTGATAAGGGATAGGATTTAGGAGTTGAT-AAGGGAT
1 AGGATTTAGGAGCAGATAAGGGA-AGGATCTAGGAGTTGATCAAGGGAT
60876 AGGATTTAGGAGCAGATAAGGG-AGGAAATCTAGGAGTTGATCAAGG
1 AGGATTTAGGAGCAGATAAGGGAAGG--ATCTAGGAGTTGATCAAGG
60922 AACAAGAGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
46 3 0.08
48 33 0.82
49 4 0.10
ACGTcount: A:0.35, C:0.03, G:0.37, T:0.24
Consensus pattern (48 bp):
AGGATTTAGGAGCAGATAAGGGAAGGATCTAGGAGTTGATCAAGGGAT
Found at i:62352 original size:27 final size:26
Alignment explanation
Indices: 62312--62422 Score: 141
Period size: 27 Copynumber: 4.2 Consensus size: 26
62302 AGGAAGCGTC
*
62312 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
* *
62339 CTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
62366 CTGGTGGCTCTGCCACATTATCTGTAT
1 CTGGTGGCTCTGCCACATTATCTG-AT
* * *
62393 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
62419 CTGG
1 CTGG
62423 CAGCCATGCT
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
26 12 0.16
27 62 0.84
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:62420 original size:53 final size:54
Alignment explanation
Indices: 62312--62422 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
62302 AGGAAGCGTC
* *
62312 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* *
62366 CTGGTGGCTCTGCCAC-ATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
62419 CTGG
1 CTGG
62423 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
53 19 0.37
54 33 0.63
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:68052 original size:40 final size:40
Alignment explanation
Indices: 67996--68213 Score: 314
Period size: 40 Copynumber: 5.5 Consensus size: 40
67986 TGGATGATAA
67996 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
* *
68036 TCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAATATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
*
68076 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCTATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
* **
68116 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
* * *
68156 CCGGGCTAAGTCCCGAAGGAATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATTT
**
68196 CC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
68214 TACTTGGTTG
Statistics
Matches: 162, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 16 0.10
40 146 0.90
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
Done.