Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold689
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: 48750
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Found at i:7258 original size:39 final size:40
Alignment explanation
Indices: 7213--7436 Score: 242
Period size: 40 Copynumber: 5.7 Consensus size: 40
7203 GCTCCTCGTT
* * * *
7213 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
7253 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
7292 CGAATGCCTTCGGGACTTAACCCGGATTTAGT-ACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
7331 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
7371 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
7412 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
7437 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 20, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
39 70 0.45
40 76 0.48
41 11 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:7316 original size:79 final size:77
Alignment explanation
Indices: 7213--7436 Score: 252
Period size: 79 Copynumber: 2.8 Consensus size: 77
7203 GCTCCTCGTT
* * *
7213 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCACACAAAGCCTTCGGGACTTAACCCGGA
7278 TTTAATAACTCGCA
65 TTT-ATAACTCGCA
* * * *
7292 CGAATGCCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCACACAAA-GCCTTCGGGACTTAACCCGG-
* *
7357 ATTTGTATCTCGCA
64 ATTTATAACTCGCA
* * * * *
7371 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-ACTCA-CACAAAGCCTTCGGGACTTAACCCG
7435 GA
63 GA
7437 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
78 12 0.10
79 79 0.65
80 25 0.20
81 6 0.05
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (77 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCACACAAAGCCTTCGGGACTTAACCCGGAT
TTATAACTCGCA
Found at i:7445 original size:41 final size:41
Alignment explanation
Indices: 7368--7445 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
7358 TTTGTATCTC
* * *
7368 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
7409 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
7446 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:15166 original size:39 final size:40
Alignment explanation
Indices: 15121--15344 Score: 242
Period size: 40 Copynumber: 5.7 Consensus size: 40
15111 GCTCCTCGTT
* * * *
15121 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
15161 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
15200 CGAATGCCTTCGGGACTTAACCCGGATTTAGT-ACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
15239 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
15279 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
15320 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
15345 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 20, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
39 70 0.45
40 76 0.48
41 11 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:15224 original size:79 final size:77
Alignment explanation
Indices: 15121--15344 Score: 252
Period size: 79 Copynumber: 2.8 Consensus size: 77
15111 GCTCCTCGTT
* * *
15121 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCACACAAAGCCTTCGGGACTTAACCCGGA
15186 TTTAATAACTCGCA
65 TTT-ATAACTCGCA
* * * *
15200 CGAATGCCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCACACAAA-GCCTTCGGGACTTAACCCGG-
* *
15265 ATTTGTATCTCGCA
64 ATTTATAACTCGCA
* * * * *
15279 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-ACTCA-CACAAAGCCTTCGGGACTTAACCCG
15343 GA
63 GA
15345 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
78 12 0.10
79 79 0.65
80 25 0.20
81 6 0.05
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (77 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCACACAAAGCCTTCGGGACTTAACCCGGAT
TTATAACTCGCA
Found at i:15353 original size:41 final size:41
Alignment explanation
Indices: 15276--15353 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
15266 TTTGTATCTC
* * *
15276 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
15317 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
15354 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:20284 original size:31 final size:31
Alignment explanation
Indices: 20249--20312 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
20239 CCTTTTCATA
*
20249 TTTCATATTTCATAACATTGGGCCAAAGCCT
1 TTTCATATTTCATAACACTGGGCCAAAGCCT
** *
20280 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCAAAGCCT
20311 TT
1 TT
20313 ACTATAAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCAAAGCCT
Found at i:20578 original size:25 final size:25
Alignment explanation
Indices: 20521--20604 Score: 91
Period size: 26 Copynumber: 3.4 Consensus size: 25
20511 CTGGAGGCCT
*
20521 AGCCTCTTTTAAT-AACTGGGGC-AA
1 AGCC-CTTTTGATAAACTGGGGCAAA
* *
20545 AGCCGTTTTGATAAACCGGGGCAAA
1 AGCCCTTTTGATAAACTGGGGCAAA
* *
20570 AGCCCTTTTCGGTAAACTGGGGAAAA
1 AGCCCTTTT-GATAAACTGGGGCAAA
20596 AGCCCTTTT
1 AGCCCTTTT
20605 TGCACTTCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
23 6 0.12
24 12 0.24
25 10 0.20
26 22 0.44
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (25 bp):
AGCCCTTTTGATAAACTGGGGCAAA
Found at i:20675 original size:20 final size:20
Alignment explanation
Indices: 20652--20698 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
20642 TTATGAATAC
20652 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
20672 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
20692 ATCATGT
1 ATCATGT
20699 ATATCAGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:23166 original size:72 final size:71
Alignment explanation
Indices: 23074--23228 Score: 177
Period size: 72 Copynumber: 2.2 Consensus size: 71
23064 TGTGATCAGG
* ** *
23074 CCCGTGAGTAACTCGCTGAGCGAGCATATCATGT-TAATGCTTTGGGGTCCGGGTGCTGACTTTG
1 CCCGTGAGTAGCTCAATGAGCGAGCAT-T-ACGTATAATGCTTTGGGGTCCGGGTGCTGACTTTG
*
23138 GGCATAAA
64 GGCACAAA
* * ** *
23146 CCGGTGAGTAGCTCAATGAGCGGGCATTACGTCATAATGCTTTGGGGTTTGGGTGCTGACTTTGT
1 CCCGTGAGTAGCTCAATGAGCGAGCATTACGT-ATAATGCTTTGGGGTCCGGGTGCTGACTTTGG
*
23211 GTACAAA
65 GCACAAA
23218 CCCGTGAGTAG
1 CCCGTGAGTAG
23229 TTTAAATGCG
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
70 3 0.04
71 1 0.01
72 65 0.94
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (71 bp):
CCCGTGAGTAGCTCAATGAGCGAGCATTACGTATAATGCTTTGGGGTCCGGGTGCTGACTTTGGG
CACAAA
Found at i:28367 original size:28 final size:29
Alignment explanation
Indices: 28336--28391 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
28326 CCGAAATACT
28336 GATAT-CATGGCCCAAAGCCAAATCAGTC
1 GATATGCATGGCCCAAAGCCAAATCAGTC
28364 GATATGCATGGCCCAAAGCCAAATCAGT
1 GATATGCATGGCCCAAAGCCAAATCAGT
28392 TTATCTCGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.18
Consensus pattern (29 bp):
GATATGCATGGCCCAAAGCCAAATCAGTC
Found at i:31378 original size:29 final size:29
Alignment explanation
Indices: 31321--31456 Score: 190
Period size: 29 Copynumber: 4.8 Consensus size: 29
31311 TACAGGTATC
*
31321 TGGCCCATTAAGCCC-AATCA--TATTCATA
1 TGGCCCATTAGGCCCAAATCACCTA-T-ATA
31349 TGGCCCATTAGGCCCAAATCACCTATATA
1 TGGCCCATTAGGCCCAAATCACCTATATA
*
31378 TGGCCCATTAGGCCCAAATCACCTGTATA
1 TGGCCCATTAGGCCCAAATCACCTATATA
* *
31407 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACCTATATA
31436 TGGCCCATTAGGCCC-AATCAC
1 TGGCCCATTAGGCCCAAATCAC
31457 GTTCATATTC
Statistics
Matches: 101, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
28 20 0.20
29 78 0.77
30 1 0.01
31 2 0.02
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.25
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACCTATATA
Found at i:35971 original size:29 final size:29
Alignment explanation
Indices: 35896--36021 Score: 143
Period size: 29 Copynumber: 4.4 Consensus size: 29
35886 TACTGGTATT
*
35896 TGGCCCATTAAGCCC-AATCA--TATTCATA
1 TGGCCCATTAGGCCCAAATCACCTA-T-ATA
*
35924 TGGCCTATT-GGCCCAAATCACCTATATA
1 TGGCCCATTAGGCCCAAATCACCTATATA
* *
35952 TGGCCCATTAGGCCCAAATCGCCTGTATA
1 TGGCCCATTAGGCCCAAATCACCTATATA
* *
35981 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACCTATATA
*
36010 TGGCCCGTTAGG
1 TGGCCCATTAGG
36022 ACCAGTCACG
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
27 4 0.05
28 24 0.28
29 55 0.65
30 2 0.02
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACCTATATA
Found at i:46628 original size:15 final size:15
Alignment explanation
Indices: 46581--46659 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
46571 CAAAGATAAC
*
46581 AAGAAAACC-GAAT-
1 AAGAAATCCAGAATA
46594 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
46609 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
46624 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
46639 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
46654 AAGAAA
1 AAGAAA
46660 CCAAGATACG
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
13 9 0.17
14 2 0.04
15 42 0.78
16 1 0.02
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:46628 original size:30 final size:30
Alignment explanation
Indices: 46581--46667 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
46571 CAAAGATAAC
46581 AAGAAAACC-GAAT-AAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
46609 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * *
46639 AAGAGATCCAGGATAAAGAAA-CCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
46668 CGATACTATG
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
28 7 0.14
29 11 0.22
30 31 0.63
ACGTcount: A:0.57, C:0.15, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Done.