Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold950
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: 34876
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Found at i:1456 original size:29 final size:27
Alignment explanation
Indices: 1438--1507 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
1428 ATATTAAGTC
1438 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
1465 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
1493 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
1508 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:1501 original size:28 final size:28
Alignment explanation
Indices: 1438--1535 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
1428 ATATTAAGTC
*
1438 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
1465 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
1493 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
1522 CGCACACTTAGTGC
1 CGCACACTTAGTGC
1536 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:9538 original size:29 final size:27
Alignment explanation
Indices: 9520--9589 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
9510 ATATTAAGTC
9520 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
9547 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
9575 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
9590 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:9583 original size:28 final size:28
Alignment explanation
Indices: 9520--9617 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
9510 ATATTAAGTC
*
9520 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
9547 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
9575 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
9604 CGCACACTTAGTGC
1 CGCACACTTAGTGC
9618 AATCTCATGA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:13018 original size:162 final size:157
Alignment explanation
Indices: 12630--13100 Score: 619
Period size: 153 Copynumber: 3.0 Consensus size: 157
12620 GGCATTAGCT
* ** * * ** **
12630 GCGCTTCCTGAAAATACGGCAATATATAGAGAATTTGCGGCATTTTTTATAAAATGCCACAATAG
1 GCGCTTCCTGTAAACGCCGCAATATATCGAGAATTCACGGTGTTTTTTATAAAATGCCACAATAG
* * *
12695 GTGAAGCATTAGTGGCGGTTGTCTAAAACGCCACAAAAGTTTTGAGAAATACTACGTCGTGCATT
66 GTGAAGCATTAGCGGCGGTTGTCTAAAACGCCATAAAAGTTTTGAGAAATACGACGTCGTGCATT
12760 GGTGAGCTGTAGAGGCTTTA---G-CG
131 GGTGAGCTGTAGAGGCTTTAGCGGCCG
12783 GCGCTTCCTGTAAACGCCGCAATATATCGAGAATTCACGGTGTTTTTTATAAAATGCCACAATAG
1 GCGCTTCCTGTAAACGCCGCAATATATCGAGAATTCACGGTGTTTTTTATAAAATGCCACAATAG
12848 GTGAAGCATTAGCGGCGGTTGTCTAAAACGCCATAAAAGTTTTGAGAAATACGACGTCGTGCATT
66 GTGAAGCATTAGCGGCGGTTGTCTAAAACGCCATAAAAGTTTTGAGAAATACGACGTCGTGCATT
12913 GGTGAGCTGTAGAGGCTTTAGCGGCTTTAACG
131 GGTGAGCTGTAGAGGCTTTAGCGGC-----CG
* * *
12945 GCGCTTCCTGTAAACGCTGCAATATATCGAGAATTCACGGTGTTTTTTCTAAAACGCCACAATAG
1 GCGCTTCCTGTAAACGCCGCAATATATCGAGAATTCACGGTGTTTTTTATAAAATGCCACAATAG
* * * * * * *
13010 GTGAAGCATTAGCGACGGTTGTTTAAAAACACCGTAAAAGTTTTGATAAAAACGACGTCGT-CTT
66 GTGAAGCATTAGCGGCGGTTGTCT-AAAACGCCATAAAAGTTTTGAGAAATACGACGTCGTGC-A
* * *
13074 TTGGTGAGCTATAGGGGCATTAGCGGC
129 TTGGTGAGCTGTAGAGGCTTTAGCGGC
13101 GTTTTTTATT
Statistics
Matches: 282, Mismatches: 25, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
153 138 0.49
156 1 0.00
162 87 0.31
163 56 0.20
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (157 bp):
GCGCTTCCTGTAAACGCCGCAATATATCGAGAATTCACGGTGTTTTTTATAAAATGCCACAATAG
GTGAAGCATTAGCGGCGGTTGTCTAAAACGCCATAAAAGTTTTGAGAAATACGACGTCGTGCATT
GGTGAGCTGTAGAGGCTTTAGCGGCCG
Found at i:14914 original size:40 final size:40
Alignment explanation
Indices: 14884--15135 Score: 275
Period size: 40 Copynumber: 6.3 Consensus size: 40
14874 GCTACTCGTT
* *
14884 CAAATGCCTTTGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGTTATAGTAACTCGCA
*
14924 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-TTATAGTAACTCGCA
* *
14964 CAAATGCCTTCGGGACTTAACCCAGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCC-GGTTATAGTAACTCGCA
* *
15004 CAAATGCCTTCGGGACTTAACCCGAATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCG-GTTATAGTAACTCGCA
* *
15044 CAAATGCCTTCGGGACTTAACCCAGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCC-GGTTATAGTAACTCGCA
* * * * *
15084 TC-AATGCTTTCGGG-CTTAGCCCGG-AATTAGTATCTCGCA
1 -CAAATGCCTTCGGGACATAACCCGGTTA-TAGTAACTCGCA
15123 CAAATGCCTTCGG
1 CAAATGCCTTCGG
15136 ATCTTAGTCC
Statistics
Matches: 194, Mismatches: 10, Indels: 17
0.88 0.05 0.08
Matches are distributed among these distances:
38 2 0.01
39 29 0.15
40 158 0.81
41 5 0.03
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGTTATAGTAACTCGCA
Found at i:14996 original size:80 final size:80
Alignment explanation
Indices: 14884--15188 Score: 386
Period size: 80 Copynumber: 3.8 Consensus size: 80
14874 GCTACTCGTT
* * * *
14884 CAAATGCCTTTGGGACATAGCCC-GGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAACCCAGATT-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
14948 GATTTAGTAACTCGCA
65 GATTTAGTAACTCGCA
*
14964 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGA
1 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
15029 ATTTAGTAACTCGCA
66 ATTTAGTAACTCGCA
* *
15044 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCATC-AATGCTTTCGGG-CTTAGCCCG
1 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCA-CAAATGCCTTCGGGACTTAACCCG
* *
15107 GAATTAGTATCTCGCA
65 GATTTAGTAACTCGCA
** * * * * * *
15123 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAACCCAGATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCC
15186 GGA
64 GGA
15189 CATCATTCGA
Statistics
Matches: 201, Mismatches: 18, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
78 3 0.01
79 55 0.27
80 139 0.69
81 4 0.02
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATTTAGTAACTCGCA
Found at i:15090 original size:120 final size:119
Alignment explanation
Indices: 14884--15135 Score: 373
Period size: 120 Copynumber: 2.1 Consensus size: 119
14874 GCTACTCGTT
* * * *
14884 CAAATGCCTTTGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAACCCGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAG
*
14949 ATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCA
66 ATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAACCCAGAATTAGTAACTCGCA
*
15004 CAAATGCCTTCGGGACTTAACCCGAATT-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCA
1 CAAATGCCTTCGGGACATAACCCG-ATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCA
* * * *
15068 GATTTAGTAACTCGCATC-AATGCTTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
65 GATTTAGTAACTCGCA-CAAATGCCTTCGGGCTTAACCCAGAATTAGTAACTCGCA
15123 CAAATGCCTTCGG
1 CAAATGCCTTCGG
15136 ATCTTAGTCC
Statistics
Matches: 120, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
119 34 0.28
120 83 0.69
121 3 0.03
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (119 bp):
CAAATGCCTTCGGGACATAACCCGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAG
ATTTAGTAACTCGCACAAATGCCTTCGGGCTTAACCCAGAATTAGTAACTCGCA
Found at i:15165 original size:120 final size:120
Alignment explanation
Indices: 14884--15181 Score: 370
Period size: 120 Copynumber: 2.5 Consensus size: 120
14874 GCTACTCGTT
* * * ** * *
14884 CAAATGCCTTTGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAACCCGAATATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCAG
*
14949 ATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCA
66 ATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGAATTAGTAACTCGCA
* *
15004 CAAATGCCTTCGGGACTTAACCCGAATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAG
1 CAAATGCCTTCGGGACTTAACCCGAATATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCAG
* * * *
15069 ATTTAGTAACTCGCATC-AATGCTTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
66 ATTTAGTAACTCGCA-CAAATGCCTTCGGGACTTAACCCAGAATTAGTAACTCGCA
** * * *
15123 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTA
1 CAAATGCCTTCGGGA-CTTAACCCGAATATAGTAAC-TAGCACAAATGCCTTCGGGACTTA
15182 GCCCGGACAT
Statistics
Matches: 156, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
118 3 0.02
119 60 0.38
120 92 0.59
121 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (120 bp):
CAAATGCCTTCGGGACTTAACCCGAATATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCAG
ATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGAATTAGTAACTCGCA
Found at i:16367 original size:44 final size:44
Alignment explanation
Indices: 16317--16405 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
16307 TATTAGTTTA
16317 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTT
*
16361 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTT
16405 T
1 T
16406 CATGACATGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.22, C:0.24, G:0.07, T:0.47
Consensus pattern (44 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTT
Found at i:22192 original size:116 final size:118
Alignment explanation
Indices: 22013--22232 Score: 288
Period size: 116 Copynumber: 1.9 Consensus size: 118
22003 TACTCGTTCA
*
22013 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
22078 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTAGTAACTCGCAC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTAGTAACTCGCAC
* * **
22131 AATGCCTTCGGG-CTTAG-CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
22192 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
22233 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
115 4 0.04
116 61 0.69
117 12 0.13
118 12 0.13
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (118 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTAGTAACTCGCAC
Found at i:22232 original size:40 final size:40
Alignment explanation
Indices: 21992--22232 Score: 282
Period size: 40 Copynumber: 6.1 Consensus size: 40
21982 CGGAATTTAA
** *
21992 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
22032 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
22072 CCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
22112 CCGGAT-TAGTAACTCGCAC-AATGCCTTCGGG-CTTAG-
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
22148 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
22188 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
22228 CCGGA
1 CCGGA
22233 CATCATTCGA
Statistics
Matches: 177, Mismatches: 14, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
36 5 0.03
37 18 0.10
38 21 0.12
39 19 0.11
40 102 0.58
41 12 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:23408 original size:43 final size:46
Alignment explanation
Indices: 23359--23448 Score: 150
Period size: 45 Copynumber: 2.0 Consensus size: 46
23349 TATTAGTTTA
23359 TTGCCCATGC-TCTTATTTTA-TTCTTCCATTAACAC-AACATGTT
1 TTGCCCATGCTTCTTATTTTATTTCTTCCATTAACACAAACATGTT
*
23402 TTGCCCATGCTTCTTATTTTATTTTTTCCATTAACACAAACATGTT
1 TTGCCCATGCTTCTTATTTTATTTCTTCCATTAACACAAACATGTT
23448 T
1 T
23449 CATGACATGT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
43 10 0.23
44 10 0.23
45 14 0.33
46 9 0.21
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.47
Consensus pattern (46 bp):
TTGCCCATGCTTCTTATTTTATTTCTTCCATTAACACAAACATGTT
Found at i:27064 original size:1 final size:1
Alignment explanation
Indices: 27058--27111 Score: 63
Period size: 1 Copynumber: 54.0 Consensus size: 1
27048 TGATGTATAC
* * * * *
27058 TTTTTTTCTTTTTTTTTTTGTATTTTTCTTTTCTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
27112 CCAGTTTGGA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.02, C:0.06, G:0.02, T:0.91
Consensus pattern (1 bp):
T
Found at i:27079 original size:25 final size:25
Alignment explanation
Indices: 27051--27101 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
27041 AAATCTCTGA
27051 TGTATACTTT-TTTTCTTTTTTTTTT
1 TGTAT-CTTTCTTTTCTTTTTTTTTT
*
27076 TGTATTTTTCTTTTCTTTTTTTTTT
1 TGTATCTTTCTTTTCTTTTTTTTTT
27101 T
1 T
27102 TTTTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.06, C:0.08, G:0.04, T:0.82
Consensus pattern (25 bp):
TGTATCTTTCTTTTCTTTTTTTTTT
Found at i:27108 original size:25 final size:25
Alignment explanation
Indices: 27061--27112 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
27051 TGTATACTTT
27061 TTTTCTTTTTTTTTTTGTATTTTTC
1 TTTTCTTTTTTTTTTTGTATTTTTC
27086 TTTTCTTTTTTTTTTT-T-TTTTT-
1 TTTTCTTTTTTTTTTTGTATTTTTC
27108 TTTTC
1 TTTTC
27113 CAGTTTGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 5 0.19
23 5 0.19
24 1 0.04
25 16 0.59
ACGTcount: A:0.02, C:0.08, G:0.02, T:0.88
Consensus pattern (25 bp):
TTTTCTTTTTTTTTTTGTATTTTTC
Done.