Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2722
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: 28900
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:4853 original size:27 final size:27
Alignment explanation
Indices: 4823--4929 Score: 144
Period size: 27 Copynumber: 4.0 Consensus size: 27
4813 AATCTCATAT
* *
4823 CTGTAGGCTAGTATTACTGAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
* *
4850 CTGTAGGGTAGAATTACTAAAATGCCC
1 CTGTAGGGTAGAATTACTGAAATACCC
* * *
4877 TTGTAGGATAGAATTACTGAAATGCCC
1 CTGTAGGGTAGAATTACTGAAATACCC
4904 CTGTAGGGTAGAATTACT-AAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
4930 TTGGTTTACA
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
26 7 0.10
27 63 0.90
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (27 bp):
CTGTAGGGTAGAATTACTGAAATACCC
Found at i:4893 original size:54 final size:53
Alignment explanation
Indices: 4824--4932 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 53
4814 ATCTCATATC
* * *
4824 TGTAGGCTAGTATTACTGAAATACCCCTGTAGGGTAGAATTACTAAAATGCCCT
1 TGTAGGATAGAATTACTGAAATACCCCTGTAGGGTAGAATTACT-AAATACCCT
*
4878 TGTAGGATAGAATTACTGAAATGCCCCTGTAGGGTAGAATTACTAAATACCCT
1 TGTAGGATAGAATTACTGAAATACCCCTGTAGGGTAGAATTACTAAATACCCT
4931 TG
1 TG
4933 GTTTACAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
53 10 0.20
54 41 0.80
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Consensus pattern (53 bp):
TGTAGGATAGAATTACTGAAATACCCCTGTAGGGTAGAATTACTAAATACCCT
Found at i:4954 original size:27 final size:27
Alignment explanation
Indices: 4939--5200 Score: 242
Period size: 27 Copynumber: 9.7 Consensus size: 27
4929 CTTGGTTTAC
** *
4939 AAAATTACCAAAATACCCTCGA-TTAG
1 AAAATTACCAAAATACCCTTAATTTGG
* *
4965 AAAATTACCAAAATACCCTTAGTTTGT
1 AAAATTACCAAAATACCCTTAATTTGG
* *
4992 AAAATTACCAAAATACCCCTAATTTGT
1 AAAATTACCAAAATACCCTTAATTTGG
** ** ** *
5019 AAAATTACTGAAATACCCTCGACCTGT
1 AAAATTACCAAAATACCCTTAATTTGG
* * * *
5046 AAAATTATCGAAATACCCTCAATTTGT
1 AAAATTACCAAAATACCCTTAATTTGG
* * *
5073 AAAATTACCAAAATACCTTTGACTTGG
1 AAAATTACCAAAATACCCTTAATTTGG
* *
5100 AAAATTACCGAAATACCCTTGATTTGG
1 AAAATTACCAAAATACCCTTAATTTGG
**
5127 AAAATTACTGAAATACCCTTAATTTGG
1 AAAATTACCAAAATACCCTTAATTTGG
**
5154 AAAATTA-CAGAAATACCCTTAATTTAC
1 AAAATTACCA-AAATACCCTTAATTTGG
5181 AAAATTA-CAGAAATACCCTT
1 AAAATTACCA-AAATACCCTT
5201 GACTTTTAAA
Statistics
Matches: 199, Mismatches: 35, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
26 19 0.10
27 180 0.90
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.29
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTTAATTTGG
Found at i:5079 original size:81 final size:81
Alignment explanation
Indices: 4922--5225 Score: 321
Period size: 81 Copynumber: 3.8 Consensus size: 81
4912 TAGAATTACT
** * *
4922 AAATACCCTTGGTTTACAAAATTACCAAAATACCCTCGA-TTAG-AAAATTACCA-AAATACCCT
1 AAATACCCTTAATTTGCAAAATTACCGAAATACCCTCGACTT-GTAAAATTA-CAGAAATACCCT
*
4984 TAGTTTGTAAAATTACCA
64 TAATTTGTAAAATTACCA
* * * * *
5002 AAATACCCCTAATTTGTAAAATTACTGAAATACCCTCGACCTGTAAAATTATC-GAAATACCCTC
1 AAATACCCTTAATTTGCAAAATTACCGAAATACCCTCGACTTGTAAAATTA-CAGAAATACCCTT
5066 AATTTGTAAAATTACCA
65 AATTTGTAAAATTACCA
* * * * * * * *
5083 AAATACCTTTGACTTGGAAAATTACCGAAATACCCTTGATTTGGAAAATTACTGAAATACCCTTA
1 AAATACCCTTAATTTGCAAAATTACCGAAATACCCTCGACTTGTAAAATTACAGAAATACCCTTA
*
5148 ATTTGGAAAATTA-CA
66 ATTTGTAAAATTACCA
* * * *
5163 GAAATACCCTTAATTTACAAAATTACAGAAATACCCTTGACTTTTAAAACTTACAGAAATACC
1 -AAATACCCTTAATTTGCAAAATTACCGAAATACCCTCGACTTGTAAAA-TTACAGAAATACC
5226 ATTGGTATCA
Statistics
Matches: 185, Mismatches: 33, Indels: 10
0.81 0.14 0.04
Matches are distributed among these distances:
80 36 0.19
81 137 0.74
82 12 0.06
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.30
Consensus pattern (81 bp):
AAATACCCTTAATTTGCAAAATTACCGAAATACCCTCGACTTGTAAAATTACAGAAATACCCTTA
ATTTGTAAAATTACCA
Found at i:5211 original size:27 final size:28
Alignment explanation
Indices: 4922--5225 Score: 237
Period size: 27 Copynumber: 11.2 Consensus size: 28
4912 TAGAATTACT
* **
4922 AAATACCCTTG-GTTTACAAAATTACCA-
1 AAATACCCTTGAATTTGTAAAATTA-CAG
* *
4949 AAATACCCTCG-ATTAG-AAAATTACCA-
1 AAATACCCTTGAATTTGTAAAATTA-CAG
*
4975 AAATACCCTT-AGTTTGTAAAATTACCA-
1 AAATACCCTTGAATTTGTAAAATTA-CAG
* *
5002 AAATACCCCT-AATTTGTAAAATTACTG
1 AAATACCCTTGAATTTGTAAAATTACAG
* **
5029 AAATACCCTCG-ACCTGTAAAATTATC-G
1 AAATACCCTTGAATTTGTAAAATTA-CAG
*
5056 AAATACCC-TCAATTTGTAAAATTACCA-
1 AAATACCCTTGAATTTGTAAAATTA-CAG
* * * *
5083 AAATACCTTTG-ACTTGGAAAATTACCG
1 AAATACCCTTGAATTTGTAAAATTACAG
* *
5110 AAATACCCTTG-ATTTGGAAAATTACTG
1 AAATACCCTTGAATTTGTAAAATTACAG
*
5137 AAATACCCTT-AATTTGGAAAATTACAG
1 AAATACCCTTGAATTTGTAAAATTACAG
**
5164 AAATACCCTT-AATTTACAAAATTACAG
1 AAATACCCTTGAATTTGTAAAATTACAG
*
5191 AAATACCCTTGACTTT-TAAAACTTACAG
1 AAATACCCTTGAATTTGTAAAA-TTACAG
5219 AAATACC
1 AAATACC
5226 ATTGGTATCA
Statistics
Matches: 233, Mismatches: 32, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
26 24 0.10
27 190 0.82
28 19 0.08
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.30
Consensus pattern (28 bp):
AAATACCCTTGAATTTGTAAAATTACAG
Found at i:5569 original size:41 final size:41
Alignment explanation
Indices: 5512--5591 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
5502 AGGAAGTATA
* *
5512 TGAGGATCGCATGGTTGCTTGACGATCGTGGATTCACCGAT
1 TGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCGAT
* *
5553 TGAGGATTGCATGGTTGCTTGATGACCGTGGATCCACCG
1 TGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
5592 GTGGCTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.19, C:0.20, G:0.33, T:0.29
Consensus pattern (41 bp):
TGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCGAT
Found at i:19289 original size:80 final size:78
Alignment explanation
Indices: 19205--19376 Score: 213
Period size: 79 Copynumber: 2.2 Consensus size: 78
19195 GGACTAAGAT
*
19205 CCGAAGGCATTTGTGCGAG-A-TACAAGTTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATAC
1 CCGAAGGCATTTGTGCGAGCATTA-AA--TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATAC
* *
19268 TAAATCCGGGTTAAGTC
62 TAAAACCGGGCTAAGTC
* * * *
19285 CCGAAGGCATTCGTGCGAGTCATTAAATCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAG-CATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
19350 AACCGGGCTATGTC
65 AACCGGGCTAAGTC
19364 CCGAAGGCATTTG
1 CCGAAGGCATTTG
19377 AACGAGGAGC
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
79 38 0.47
80 37 0.46
82 3 0.04
83 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGCATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
ACCGGGCTAAGTC
Found at i:19367 original size:39 final size:39
Alignment explanation
Indices: 19152--19374 Score: 207
Period size: 40 Copynumber: 5.6 Consensus size: 39
19142 TTGAATGCTG
* * * * * *
19152 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
19192 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
19232 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
* *
19272 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
19312 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
19351 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
19375 TGAACGAGGA
Statistics
Matches: 152, Mismatches: 24, Indels: 15
0.80 0.13 0.08
Matches are distributed among these distances:
39 37 0.24
40 105 0.69
41 10 0.07
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:19394 original size:79 final size:80
Alignment explanation
Indices: 19232--19409 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
19222 AGATACAAGT
* * * *
19232 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** *
19297 GTGCGAGTCATTAAA
66 GAACGAGTCACTAAA
* * * *
19312 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
* *
19376 GAACGAG-GAGCTATA
66 GAACGAGTCA-CTAAA
*
19391 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
19410 TACGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTCACTAAA
Found at i:26834 original size:41 final size:39
Alignment explanation
Indices: 26662--26885 Score: 209
Period size: 40 Copynumber: 5.6 Consensus size: 39
26652 TTGAATGCTG
* * * * * *
26662 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
26702 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
26742 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
*
26782 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTCATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTT-ACTAAA
*
26823 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
26862 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
26886 TGAACGAGGA
Statistics
Matches: 154, Mismatches: 22, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
39 30 0.19
40 85 0.55
41 39 0.25
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Done.