Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2275
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: 56279
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:4681 original size:41 final size:40
Alignment explanation
Indices: 4622--4732 Score: 138
Period size: 41 Copynumber: 2.8 Consensus size: 40
4612 CTCGAATGAT
* *
4622 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACTAC
1 ATCCGGACTAAGT-CCGAAGGCATTTGTGCTAAGCGACTAC
*
4663 ATCCGGACTAAGATCCGAAGGCATTTGTGCT-AGCGACTAT
1 ATCCGGACTAAG-TCCGAAGGCATTTGTGCTAAGCGACTAC
*
4703 ATCCGGGA-T-AGTCCGAAGGCATTTATGCTA
1 ATCC-GGACTAAGTCCGAAGGCATTTGTGCTA
4733 GTGACCATAT
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
38 17 0.27
39 2 0.03
40 13 0.21
41 30 0.48
42 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATCCGGACTAAGTCCGAAGGCATTTGTGCTAAGCGACTAC
Found at i:4732 original size:38 final size:39
Alignment explanation
Indices: 4620--4761 Score: 162
Period size: 38 Copynumber: 3.6 Consensus size: 39
4610 TACTCGAATG
* *
4620 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGATAAGT-CCGAAGGCATTTGTGCT-AGCGACT
*
4661 ACATCC-GGACTAAGATCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGA-TAAG-TCCGAAGGCATTTGTGCTAGCGACT
* * *
4701 ATATCCGGGAT-AGTCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGATAAGTCCGAAGGCATTTGTGCTAGCGACT
* *
4739 ATATCCGGGTTAAGACCGAAGGC
1 ATATCCGGGATAAGTCCGAAGGC
4762 CTTGTGCGAG
Statistics
Matches: 88, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
38 32 0.36
39 12 0.14
40 15 0.17
41 28 0.32
42 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (39 bp):
ATATCCGGGATAAGTCCGAAGGCATTTGTGCTAGCGACT
Found at i:12149 original size:20 final size:21
Alignment explanation
Indices: 12113--12160 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
12103 TATTGAAGCC
*
12113 CTGTAC-AGTTGAATAAT-AA
1 CTGTACTATTTGAATAATAAA
*
12132 CTGTACTATTTGACTAATAAA
1 CTGTACTATTTGAATAATAAA
12153 CTGTACTA
1 CTGTACTA
12161 ATTGGCCTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 6 0.24
20 9 0.36
21 10 0.40
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (21 bp):
CTGTACTATTTGAATAATAAA
Found at i:13955 original size:21 final size:22
Alignment explanation
Indices: 13909--13960 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
13899 TAGGGCCAAT
13909 TTAGTACAGTTTATTAGTCAAA
1 TTAGTACAGTTTATTAGTCAAA
13931 TTAGTACAGTTTATTAGTC-AA
1 TTAGTACAGTTTATTAGTCAAA
13952 TTAGTACAG
1 TTAGTACAG
13961 GGCTTCAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 11 0.37
22 19 0.63
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (22 bp):
TTAGTACAGTTTATTAGTCAAA
Found at i:21402 original size:39 final size:40
Alignment explanation
Indices: 21357--21524 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
21347 CGGGGTTTAG
* * *
21357 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
21396 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
21436 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
21476 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
21517 CCGGATAT
1 CCGGATAT
21525 CATTCGAGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.17
40 61 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:21507 original size:41 final size:40
Alignment explanation
Indices: 21380--21524 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
21370 CTCGCACAAG
* * * * *
21380 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
21420 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
21460 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
21501 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
21525 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:25200 original size:33 final size:33
Alignment explanation
Indices: 25119--25201 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 33
25109 ACATGACTGC
* *
25119 ACTGTATTGATACTGAATTA-GGCTAGGGCCCAC
1 ACTGTATTGATACTGAA-TAGGGCTAAGGCCCAA
*
25152 ACTG---T--TACTGTATAGGGCTAAGGCCCAA
1 ACTGTATTGATACTGAATAGGGCTAAGGCCCAA
25180 ACTGTATTGATACTGAATAGGG
1 ACTGTATTGATACTGAATAGGG
25202 TTCACGCCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
27 2 0.05
28 21 0.52
30 1 0.03
31 1 0.03
33 15 0.38
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (33 bp):
ACTGTATTGATACTGAATAGGGCTAAGGCCCAA
Found at i:26317 original size:27 final size:27
Alignment explanation
Indices: 26295--26401 Score: 124
Period size: 27 Copynumber: 4.0 Consensus size: 27
26285 AAAATTACTA
* *
26295 AAATACCCCTGTAAGGTAGAATTACCG
1 AAATACCCCTATAGGGTAGAATTACCG
* *
26322 AAATACCCTTATAGGGTAGAAATACCG
1 AAATACCCCTATAGGGTAGAATTACCG
*
26349 AAATACCCCTATAGGGTAGAATTACAG
1 AAATACCCCTATAGGGTAGAATTACCG
* * * * *
26376 AGATACCCTTGTGGGGTAAAATTACC
1 AAATACCCCTATAGGGTAGAATTACC
26402 ATTTTGCCCC
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (27 bp):
AAATACCCCTATAGGGTAGAATTACCG
Found at i:26393 original size:54 final size:53
Alignment explanation
Indices: 26295--26397 Score: 143
Period size: 54 Copynumber: 1.9 Consensus size: 53
26285 AAAATTACTA
* *
26295 AAATACCCCTGTAAGGTAGAATTACCGAAATACCCTTATAGGGTAGAAATACCG
1 AAATACCCCTATAAGGTAGAATTACAGAAATACCCTTATAGGGTA-AAATACCG
* * * *
26349 AAATACCCCTATAGGGTAGAATTACAGAGATACCCTTGTGGGGTAAAAT
1 AAATACCCCTATAAGGTAGAATTACAGAAATACCCTTATAGGGTAAAAT
26398 TACCATTTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
53 4 0.09
54 39 0.91
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (53 bp):
AAATACCCCTATAAGGTAGAATTACAGAAATACCCTTATAGGGTAAAATACCG
Found at i:26796 original size:16 final size:16
Alignment explanation
Indices: 26775--26814 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
26765 ATGGGCCAAA
26775 AACGGGCCAATGAGCC
1 AACGGGCCAATGAGCC
* *
26791 AACGGGCTAATGGGCC
1 AACGGGCCAATGAGCC
26807 AACGGGCC
1 AACGGGCC
26815 CACTTTGGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.28, C:0.30, G:0.35, T:0.07
Consensus pattern (16 bp):
AACGGGCCAATGAGCC
Found at i:27211 original size:27 final size:26
Alignment explanation
Indices: 27159--27217 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
27149 CCACATATAT
*
27159 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
27185 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
27212 ATATCT
1 ATATCT
27218 AGCAGCTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.36
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:34120 original size:47 final size:46
Alignment explanation
Indices: 34051--34178 Score: 157
Period size: 47 Copynumber: 2.7 Consensus size: 46
34041 TTATTGCTGA
* * * *
34051 TCCATGCATGTTTTTCTTTAATGCTTCAGCTGCTCATTTTAATGCCG
1 TCCATGCATGCTTTTCTTTAATGCTTCAGCAGCTC-CTTTAATGACG
* * *
34098 TCCATACATGCTTTTCTTTAATGCTTCAACAGCTCCTTTAATGATG
1 TCCATGCATGCTTTTCTTTAATGCTTCAGCAGCTCCTTTAATGACG
* *
34144 TCCCATGCTTGCTTTTCTTTAATGCTTCAGTAGCT
1 T-CCATGCATGCTTTTCTTTAATGCTTCAGCAGCT
34179 TTCAATGCCA
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
46 9 0.13
47 60 0.87
ACGTcount: A:0.19, C:0.24, G:0.13, T:0.44
Consensus pattern (46 bp):
TCCATGCATGCTTTTCTTTAATGCTTCAGCAGCTCCTTTAATGACG
Found at i:34656 original size:20 final size:21
Alignment explanation
Indices: 34631--34670 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
34621 ATGGAATGAG
*
34631 CAAACGAGCT-CATTGAGCTA
1 CAAACGAGCTGAATTGAGCTA
34651 CAAACGAGCTGAATTGAGCT
1 CAAACGAGCTGAATTGAGCT
34671 CAACAAGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.20
Consensus pattern (21 bp):
CAAACGAGCTGAATTGAGCTA
Found at i:40467 original size:11 final size:11
Alignment explanation
Indices: 40451--40475 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40441 TGTTTGCTCG
40451 TTTTGAATTTA
1 TTTTGAATTTA
40462 TTTTGAATTTA
1 TTTTGAATTTA
40473 TTT
1 TTT
40476 CGTTTTAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTGAATTTA
Found at i:40720 original size:7 final size:7
Alignment explanation
Indices: 40708--40732 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40698 TTATTAAATT
40708 AAGTTAA
1 AAGTTAA
40715 AAGTTAA
1 AAGTTAA
40722 AAGTTAA
1 AAGTTAA
40729 AAGT
1 AAGT
40733 GTTTATTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (7 bp):
AAGTTAA
Found at i:42364 original size:22 final size:24
Alignment explanation
Indices: 42320--42392 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
42310 TTAATGCGAC
*
42320 TATTACATTACTTAAAGAAGAGCAT
1 TATTACATCACTTAAAG-AGAGCAT
42345 TATT-CATCACTTAAAG-GAGC--
1 TATTACATCACTTAAAGAGAGCAT
* * *
42365 TGTTACATCATTTAAAGGAGAGTAT
1 TATTACATCACTTAAA-GAGAGCAT
42390 TAT
1 TAT
42393 ATATCCTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
20 3 0.08
21 10 0.26
22 5 0.13
23 3 0.08
24 11 0.29
25 6 0.16
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (24 bp):
TATTACATCACTTAAAGAGAGCAT
Found at i:46373 original size:34 final size:34
Alignment explanation
Indices: 46335--46403 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
46325 ATATACAAAG
*
46335 AGATAAACATATTTTTACATGCCTTTAGTTGACA
1 AGATAAACATATTTTTACATGCCTTTACTTGACA
46369 AGATAAACATATTTTTACATGCCTTTACTTGACA
1 AGATAAACATATTTTTACATGCCTTTACTTGACA
46403 A
1 A
46404 ATCAAATGAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (34 bp):
AGATAAACATATTTTTACATGCCTTTACTTGACA
Found at i:53200 original size:12 final size:12
Alignment explanation
Indices: 53183--53208 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53173 CATTCCGAAG
53183 TATATATATACA
1 TATATATATACA
53195 TATATATATACA
1 TATATATATACA
53207 TA
1 TA
53209 AGTATGCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATATATACA
Found at i:53721 original size:28 final size:28
Alignment explanation
Indices: 53658--53808 Score: 214
Period size: 28 Copynumber: 5.4 Consensus size: 28
53648 GAGATTGGCG
* * * *
53658 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
* *
53687 CTAAGTGTGCGAGCTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
53715 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
53743 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
53771 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
53798 CTGAGTGTGCG
1 CTAAGTGTGCG
53809 GACTTAATAT
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.21
28 75 0.66
29 14 0.12
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Done.