Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2623
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: 31079
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Found at i:526 original size:39 final size:39
Alignment explanation
Indices: 464--602 Score: 158
Period size: 40 Copynumber: 3.5 Consensus size: 39
454 GCTACTCGTT
*
464 CAAATGCC-TCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGTTATAGTAACTCGCA
*
503 CAAATGCCTTCGGACTTAACCCGGATT-TAGTAACTCGCCA
1 CAAATGCCTTCGGACTTAGCCCGG-TTATAGTAACTCG-CA
* * *
543 CAAATGCCTTCGGGCTTTAGCCCGG-AATTAGTATCTCGCA
1 CAAATGCCTTCGGAC-TTAGCCCGGTTA-TAGTAACTCGCA
583 CAAATGCCTTCGGATCTTAG
1 CAAATGCCTTCGGA-CTTAG
603 TCCGATTGTG
Statistics
Matches: 86, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
39 29 0.34
40 39 0.45
41 18 0.21
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:585 original size:40 final size:39
Alignment explanation
Indices: 491--601 Score: 159
Period size: 40 Copynumber: 2.8 Consensus size: 39
481 AGCCCGGTTA
*
491 TAGTAACTCGCACAAATGCCTTCGGACTTAACCCGGATT
1 TAGTAACTCGCACAAATGCCTTCGGACTTAACCCGGAAT
* *
530 TAGTAACTCGCCACAAATGCCTTCGGGCTTTAGCCCGGAAT
1 TAGTAACTCG-CACAAATGCCTTCGGAC-TTAACCCGGAAT
*
571 TAGTATCTCGCACAAATGCCTTCGGATCTTA
1 TAGTAACTCGCACAAATGCCTTCGGA-CTTA
602 GTCCGATTGT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
39 10 0.16
40 34 0.53
41 20 0.31
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (39 bp):
TAGTAACTCGCACAAATGCCTTCGGACTTAACCCGGAAT
Found at i:8543 original size:79 final size:82
Alignment explanation
Indices: 8432--8616 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
8422 GCTACTCGTT
* *
8432 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
8495 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
8512 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
8575 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
8592 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
8617 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:8616 original size:40 final size:40
Alignment explanation
Indices: 8413--8616 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
8403 CGGAATTTAA
** *
8413 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
8453 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
8493 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
8532 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
8572 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
8612 CCGGA
1 CCGGA
8617 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:10540 original size:28 final size:28
Alignment explanation
Indices: 10500--10564 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
10490 ATGTACTAGA
*
10500 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
10528 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
10556 ATACCCCTA
1 ATACCCCTA
10565 GGGTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:10711 original size:28 final size:27
Alignment explanation
Indices: 10670--10759 Score: 101
Period size: 28 Copynumber: 3.2 Consensus size: 27
10660 AGGAAGCGTC
10670 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* **
10698 CTGGTGGCCCTGCCACGTATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
*
10725 CTGGTGGCACTACCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
10754 CTGGTG
1 CTGGTG
10760 ACTCTGTCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 22 0.42
28 23 0.44
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:10728 original size:27 final size:28
Alignment explanation
Indices: 10682--10759 Score: 95
Period size: 27 Copynumber: 2.8 Consensus size: 28
10672 GGTGGCTATG
* * *
10682 CCACAAATTATCTGTTCTGGTGGCCCTG
1 CCACAAAATATCTGTTCTGGTGGCACTA
**
10710 CCAC-GTATATCTGTTCTGGTGGCACTA
1 CCACAAAATATCTGTTCTGGTGGCACTA
10737 CCACAAAATATCTGTATCTGGTG
1 CCACAAAATATCTGT-TCTGGTG
10760 ACTCTGTCAC
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
27 22 0.54
28 12 0.29
29 7 0.17
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.32
Consensus pattern (28 bp):
CCACAAAATATCTGTTCTGGTGGCACTA
Found at i:11247 original size:19 final size:19
Alignment explanation
Indices: 11223--11261 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
11213 TTTTAATTAT
* *
11223 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
11242 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
11261 T
1 T
11262 ATGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:16020 original size:54 final size:55
Alignment explanation
Indices: 15916--16022 Score: 171
Period size: 55 Copynumber: 2.0 Consensus size: 55
15906 AAGGAAAAAC
** *
15916 AAAAAAAAAATGTTCATCTTTTATCATCCTTGGCCGAATGTTCTAAAGAAGAAAG
1 AAAAAAAAAATGTTCATCTTTTATCATCCTTGGCCGAAAATGCTAAAGAAGAAAG
*
15971 AAAAAAAAATTGTTCATCTTTTATCATCCTTGGCCGAAAATGCT-AAGAAGAA
1 AAAAAAAAAATGTTCATCTTTTATCATCCTTGGCCGAAAATGCTAAAGAAGAA
16023 GGGGGAAGGG
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
54 8 0.17
55 40 0.83
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (55 bp):
AAAAAAAAAATGTTCATCTTTTATCATCCTTGGCCGAAAATGCTAAAGAAGAAAG
Found at i:17085 original size:27 final size:27
Alignment explanation
Indices: 17054--17231 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
17044 TAAATTGTAC
*
17054 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
17081 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
17107 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
17135 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
17162 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * *
17190 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
17217 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
17232 GACTTAATAT
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 105 0.81
28 25 0.19
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:17115 original size:54 final size:55
Alignment explanation
Indices: 17054--17231 Score: 227
Period size: 54 Copynumber: 3.3 Consensus size: 55
17044 TAAATTGTAC
* **
17054 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
* * ** *
17109 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATG-T
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
* *
17162 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
*
17217 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
17232 GACTTAATAT
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
53 1 0.01
54 60 0.57
55 45 0.42
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
Found at i:25576 original size:46 final size:47
Alignment explanation
Indices: 25508--25596 Score: 153
Period size: 46 Copynumber: 1.9 Consensus size: 47
25498 ATAGGGAGAC
25508 CAAAATTCGAATCTGCTCCGCTCCTGCTCAGCGAAGATAAGATTCAT
1 CAAAATTCGAATCTGCTCCGCTCCTGCTCAGCGAAGATAAGATTCAT
* *
25555 CAAAATTCG-ATCTGCTTCGCTCCTGCTCAGTGAAGATAAGAT
1 CAAAATTCGAATCTGCTCCGCTCCTGCTCAGCGAAGATAAGAT
25597 CTAGTATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
46 31 0.77
47 9 0.22
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (47 bp):
CAAAATTCGAATCTGCTCCGCTCCTGCTCAGCGAAGATAAGATTCAT
Found at i:25759 original size:132 final size:132
Alignment explanation
Indices: 25542--25910 Score: 508
Period size: 132 Copynumber: 2.8 Consensus size: 132
25532 TGCTCAGCGA
* *
25542 AGATAAGATTCATCAAAATTCGATCTGCTTCGCTCCTGCTCAGTGAAGATAAGATCTAGTATTTA
1 AGATAAAATTCATCAAAATTCGATCTGCTTCACTCCTG-TCAGTGAAGATAAGATCTAGTATTTA
* *
25607 GCCTGCTCCACTCCTGCTCAGTGAAGA-AATGGCTGATGATTGGAATCTGCTCCATCGCCGGTAC
65 GCCTGCTCCACTCCTGCTCAGTGAAGATAA-GGCTGATGATTGAAATCTGCTCCATCGCCGATAC
*
25671 GTGG
129 ATGG
* * * *
25675 AGATAAAATTCATCAAAATTCGATCTGCTCCACTCTTGTCAGTGAAGATAAGATCTGGTGTTTAG
1 AGATAAAATTCATCAAAATTCGATCTGCTTCACTCCTGTCAGTGAAGATAAGATCTAGTATTTAG
* * ** **
25740 CCTGCTCCACTCCTACTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTTCCGATACAT
66 CCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGATTGAAATCTGCTCCATCGCCGATACAT
25805 GG
131 GG
* * * * * *
25807 AGATAAGACTT-GTCAAAATTTGATCTGCTTCACTCCTGTCAGTGAAGGTAAGATCTAGTCTATA
1 AGATAA-AATTCATCAAAATTCGATCTGCTTCACTCCTGTCAGTGAAGATAAGATCTAGTATTTA
25871 GCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGAT
65 GCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGAT
25911 ATCTGTAATC
Statistics
Matches: 206, Mismatches: 28, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
132 167 0.81
133 39 0.19
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (132 bp):
AGATAAAATTCATCAAAATTCGATCTGCTTCACTCCTGTCAGTGAAGATAAGATCTAGTATTTAG
CCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGATTGAAATCTGCTCCATCGCCGATACAT
GG
Done.