Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_631
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: 54627
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Found at i:1793 original size:39 final size:41
Alignment explanation
Indices: 1692--1875 Score: 213
Period size: 40 Copynumber: 4.6 Consensus size: 41
1682 TTGAATGATG
* * *
1692 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAATA
* *
1732 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGTGTTACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAATA
*
1772 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
*
1811 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
* *
1851 ACCGGGCTATGTCCCGAA-GCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
1876 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 15
0.82 0.09 0.10
Matches are distributed among these distances:
39 42 0.34
40 72 0.58
41 10 0.08
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
Found at i:1828 original size:79 final size:81
Alignment explanation
Indices: 1692--1873 Score: 214
Period size: 79 Copynumber: 2.3 Consensus size: 81
1682 TTGAATGATG
* *
1692 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
*
1756 TGTGCGTGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
1771 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
1833 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
1851 ACCGGGCTATGTCCCGAA-GCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
1874 TGAACGAGTA
Statistics
Matches: 88, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
78 1 0.01
79 63 0.72
80 24 0.27
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:1882 original size:79 final size:78
Alignment explanation
Indices: 1745--1908 Score: 190
Period size: 79 Copynumber: 2.1 Consensus size: 78
1735 GGACTAAGAT
* * **
1745 CCGAAGGCATTTGTGCGTGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTA-CTA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAG-TAGCTA
*
1809 AATCCGGGTTAAGTC
65 AATCC-GGTTAAATC
* *
1824 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAA-GCATTTGAACGAGTAGCT
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTAGCT
* *
1887 ATATCCGGTTAAATT
64 AAATCCGGTTAAATC
1902 CCGAAGG
1 CCGAAGG
1909 TACGTGATTC
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
78 18 0.25
79 49 0.67
80 6 0.08
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTAGCTAA
ATCCGGTTAAATC
Found at i:5180 original size:23 final size:22
Alignment explanation
Indices: 5153--5197 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
5143 TTTGATCGTC
*
5153 AGAAATCATATGAAGATTTGAAA
1 AGAAAACATATGAA-ATTTGAAA
* *
5176 AGAAAAGATATTAAATTTGAAA
1 AGAAAACATATGAAATTTGAAA
5198 TCGGCGACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.56, C:0.02, G:0.16, T:0.27
Consensus pattern (22 bp):
AGAAAACATATGAAATTTGAAA
Found at i:16052 original size:26 final size:27
Alignment explanation
Indices: 16017--16067 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
16007 TTTAACCAAC
**
16017 CAGAACACACACAAATTTTAAAAATCA
1 CAGAACACACACAAAACTTAAAAATCA
*
16044 CAGAA-ACACAGAAAACTTAAAAAT
1 CAGAACACACACAAAACTTAAAAAT
16068 TGGGGCGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.59, C:0.20, G:0.06, T:0.16
Consensus pattern (27 bp):
CAGAACACACACAAAACTTAAAAATCA
Found at i:20264 original size:24 final size:24
Alignment explanation
Indices: 20237--20282 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
20227 AATGAGCCAA
*
20237 CATAA-ACCAACATTTTGACCAAGT
1 CATAAGACC-ACAATTTGACCAAGT
*
20261 CATAAGAGCACAATTTGACCAA
1 CATAAGACCACAATTTGACCAA
20283 CATTTTGAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.43, C:0.24, G:0.11, T:0.22
Consensus pattern (24 bp):
CATAAGACCACAATTTGACCAAGT
Found at i:22931 original size:40 final size:40
Alignment explanation
Indices: 22887--23070 Score: 147
Period size: 40 Copynumber: 4.3 Consensus size: 40
22877 GCTCCTCGTT
* *
22887 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATT-TAGTAACTCGCA
* *
22927 CAAATGCCTTCCGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* *
22967 CAAATGCCTTCGGGACTTAGTACTCGCCAATGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGAC-----A-T----AA--CCCGGATTTAGTAACTCGCA
* * * *
23019 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
23058 CAAATGCCTTCGG
1 CAAATGCCTTCGG
23071 ATCTTAGTCC
Statistics
Matches: 121, Mismatches: 10, Indels: 27
0.77 0.06 0.17
Matches are distributed among these distances:
39 33 0.27
40 48 0.40
41 3 0.02
45 1 0.01
46 1 0.01
50 2 0.02
51 1 0.01
52 32 0.26
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:23000 original size:26 final size:28
Alignment explanation
Indices: 22954--23037 Score: 99
Period size: 26 Copynumber: 3.1 Consensus size: 28
22944 TAACCCGGAT
22954 TTAGTAACTCGCACAAATGCCTTCGGGAC
1 TTAGT-ACTCGCACAAATGCCTTCGGGAC
*
22983 TTAGTACTCGC-C-AATGCC--C-GGAA
1 TTAGTACTCGCACAAATGCCTTCGGGAC
23006 TTAGTATCTCGCACAAATGCCTTCGGG-C
1 TTAGTA-CTCGCACAAATGCCTTCGGGAC
23034 TTAG
1 TTAG
23038 CCCGGAATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
23 9 0.19
24 6 0.13
25 1 0.02
26 12 0.26
27 1 0.02
28 11 0.23
29 7 0.15
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (28 bp):
TTAGTACTCGCACAAATGCCTTCGGGAC
Found at i:23052 original size:39 final size:39
Alignment explanation
Indices: 22998--23123 Score: 150
Period size: 39 Copynumber: 3.2 Consensus size: 39
22988 ACTCGCCAAT
22998 GCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTA
1 GCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTA
*
23037 GCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTA
1 GCCCGGAATTAGTATCTCGCACAAATGCCTTCGG-GCTTA
* * *
23077 GTCCGG-ATATGGTCA-CTTAGCACAAA-GCCTTCGGGACTTA
1 GCCCGGAAT-TAGT-ATC-TCGCACAAATGCCTTCGGG-CTTA
23117 GCCCGGA
1 GCCCGGA
23124 CATCATTCAA
Statistics
Matches: 75, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
39 36 0.48
40 30 0.40
41 9 0.12
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
GCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTA
Found at i:30977 original size:39 final size:40
Alignment explanation
Indices: 30820--31083 Score: 319
Period size: 40 Copynumber: 6.7 Consensus size: 40
30810 GCTCCTCGTT
* *
30820 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
30860 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * *
30900 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
30940 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
30979 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * *
31018 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGT-ATC-TCGCA
31059 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
31084 CATCATTCAA
Statistics
Matches: 205, Mismatches: 10, Indels: 17
0.88 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 75 0.37
40 114 0.56
41 14 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:32817 original size:43 final size:43
Alignment explanation
Indices: 32756--32841 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
32746 GTCACAGGCA
* * * *
32756 TCGCATCTATAATAAACTCGGACCACTTAACAAGCTCGGATGC
1 TCGCATCCATAATAAACTCAGACCACTCAACAAGCTCAGATGC
* *
32799 TCGCATCCATAATGAACTCAGACCACTCAACGAGCTCAGATGC
1 TCGCATCCATAATAAACTCAGACCACTCAACAAGCTCAGATGC
32842 CACATAACTC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.21
Consensus pattern (43 bp):
TCGCATCCATAATAAACTCAGACCACTCAACAAGCTCAGATGC
Found at i:41534 original size:285 final size:285
Alignment explanation
Indices: 41024--41599 Score: 1152
Period size: 285 Copynumber: 2.0 Consensus size: 285
41014 CATTCGGCCT
41024 TGTTTTAATTTTAGAAATTCTTTGTGCTTTTGATTGAAAAATCTTCGACTGATTATTTCTTTCGG
1 TGTTTTAATTTTAGAAATTCTTTGTGCTTTTGATTGAAAAATCTTCGACTGATTATTTCTTTCGG
41089 AATTCAGATTGAAAGAACTCCCAAGTAACCCGTTCTTCAGAACCACAGATATCAGCGTGTTTCAC
66 AATTCAGATTGAAAGAACTCCCAAGTAACCCGTTCTTCAGAACCACAGATATCAGCGTGTTTCAC
41154 TATTGGTACATATTGTCTCTCAGAAAAGATACATCACATTTAATAATTCACCAAGAGTACAAGAC
131 TATTGGTACATATTGTCTCTCAGAAAAGATACATCACATTTAATAATTCACCAAGAGTACAAGAC
41219 AATTCATTGAATACTCGAATCGTATTTTCGAGCTAGAACTCAAATCTCTCAAGATCATCATCAAC
196 AATTCATTGAATACTCGAATCGTATTTTCGAGCTAGAACTCAAATCTCTCAAGATCATCATCAAC
41284 ATTAGCTCTAAACTCTTCAGCGTCG
261 ATTAGCTCTAAACTCTTCAGCGTCG
41309 TGTTTTAATTTTAGAAATTCTTTGTGCTTTTGATTGAAAAATCTTCGACTGATTATTTCTTTCGG
1 TGTTTTAATTTTAGAAATTCTTTGTGCTTTTGATTGAAAAATCTTCGACTGATTATTTCTTTCGG
41374 AATTCAGATTGAAAGAACTCCCAAGTAACCCGTTCTTCAGAACCACAGATATCAGCGTGTTTCAC
66 AATTCAGATTGAAAGAACTCCCAAGTAACCCGTTCTTCAGAACCACAGATATCAGCGTGTTTCAC
41439 TATTGGTACATATTGTCTCTCAGAAAAGATACATCACATTTAATAATTCACCAAGAGTACAAGAC
131 TATTGGTACATATTGTCTCTCAGAAAAGATACATCACATTTAATAATTCACCAAGAGTACAAGAC
41504 AATTCATTGAATACTCGAATCGTATTTTCGAGCTAGAACTCAAATCTCTCAAGATCATCATCAAC
196 AATTCATTGAATACTCGAATCGTATTTTCGAGCTAGAACTCAAATCTCTCAAGATCATCATCAAC
41569 ATTAGCTCTAAACTCTTCAGCGTCG
261 ATTAGCTCTAAACTCTTCAGCGTCG
41594 TGTTTT
1 TGTTTT
41600 CAGATCTTGT
Statistics
Matches: 291, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
285 291 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (285 bp):
TGTTTTAATTTTAGAAATTCTTTGTGCTTTTGATTGAAAAATCTTCGACTGATTATTTCTTTCGG
AATTCAGATTGAAAGAACTCCCAAGTAACCCGTTCTTCAGAACCACAGATATCAGCGTGTTTCAC
TATTGGTACATATTGTCTCTCAGAAAAGATACATCACATTTAATAATTCACCAAGAGTACAAGAC
AATTCATTGAATACTCGAATCGTATTTTCGAGCTAGAACTCAAATCTCTCAAGATCATCATCAAC
ATTAGCTCTAAACTCTTCAGCGTCG
Found at i:44988 original size:28 final size:28
Alignment explanation
Indices: 44948--45101 Score: 274
Period size: 28 Copynumber: 5.5 Consensus size: 28
44938 TAAATTGTAC
44948 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
44976 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
45004 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
45032 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
45060 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
45087 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
45102 GACTTAATAT
Statistics
Matches: 124, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
27 24 0.19
28 100 0.81
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.34
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:45014 original size:56 final size:56
Alignment explanation
Indices: 44923--45101 Score: 279
Period size: 56 Copynumber: 3.2 Consensus size: 56
44913 GAGATTGGCG
* * * *
44923 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
44980 CTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
45036 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
45091 CTGAGTGTGCG
1 CTAAGTGTGCG
45102 GACTTAATAT
Statistics
Matches: 114, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
55 23 0.20
56 76 0.67
57 15 0.13
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
Found at i:53227 original size:28 final size:28
Alignment explanation
Indices: 53187--53340 Score: 256
Period size: 28 Copynumber: 5.5 Consensus size: 28
53177 TAAATTGTAC
53187 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
53215 AGCACTAAGTGTGTGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
53243 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
* *
53271 AGCACTAAGTGTGCGGGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
53299 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
53326 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
53341 GACTTAATAT
Statistics
Matches: 120, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
27 24 0.20
28 96 0.80
ACGTcount: A:0.25, C:0.11, G:0.29, T:0.34
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:53251 original size:56 final size:56
Alignment explanation
Indices: 53162--53340 Score: 261
Period size: 56 Copynumber: 3.2 Consensus size: 56
53152 GAGATTGGCG
* * * *
53162 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
* *
53219 CTAAGTGTGTGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
* *
53275 CTAAGTGTGCGGGTTTGATTATATAGCACTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
53330 CTGAGTGTGCG
1 CTAAGTGTGCG
53341 GACTTAATAT
Statistics
Matches: 111, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
55 23 0.21
56 74 0.67
57 14 0.13
ACGTcount: A:0.25, C:0.11, G:0.29, T:0.35
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
Done.