Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2736
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: 13464
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Found at i:519 original size:15 final size:14
Alignment explanation
Indices: 490--524 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
480 TTTTATTTAT
490 TTTCG-AAAAATCA
1 TTTCGTAAAAATCA
503 TTTCGTAAAATATCA
1 TTTCGTAAAA-ATCA
518 TTTCGTA
1 TTTCGTA
525 TCTTAATGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.25
14 4 0.20
15 11 0.55
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (14 bp):
TTTCGTAAAAATCA
Found at i:2326 original size:165 final size:166
Alignment explanation
Indices: 2012--2326 Score: 377
Period size: 165 Copynumber: 1.9 Consensus size: 166
2002 TCAAAAACAA
* * * * *
2012 TATTAGATACATTTTTAAAAATTTTACACCAAAGAAAATCCCCCCAAAAATATTATAGAATAGAA
1 TATTAGATACAATTATAAAAATTTTAAACCAAAGAAAATCCCCCCAAAAACATTATAGAATAAAA
* * *
2077 AACTCGTTTTTCGGGAAAAAGGAGATTTTAAAGAAAAAAAATCCAAACTCATGAAAAGGAATTAA
66 AACTCGTTTTTCGGGAAAAAGGAGAATTTAAAGAAAAAAAATCAAAACTCATGAAAAGGAATGAA
*
2142 TTGTTCAAAACTAATTTAATGGGAATTCTATGACAT
131 TTGTTAAAAACTAATTTAATGGGAATTCTATGACAT
* * * *
2178 TATTAGATA-AATTATAAAAATTTTAAACCAAAGAAAATCTCTCCAAAAACATTTATTGAGTAAA
1 TATTAGATACAATTATAAAAATTTTAAACCAAAGAAAATCCCCCCAAAAACA-TTATAGAATAAA
* * * ** *
2242 AAACTCGATTTTT-TGGAGAAAAGG-GAATTTCAAG-AAAAAATTCAAAACTCATGGGAATGAAT
65 AAACTCG-TTTTTCGGGA-AAAAGGAGAATTTAAAGAAAAAAAATCAAAACTCATGAAAAGGAAT
* * *
2304 GAATTTTTAAAAATTGATTTAAT
128 GAATTGTTAAAAACTAATTTAAT
2327 AATTAAATAA
Statistics
Matches: 124, Mismatches: 22, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
165 77 0.62
166 36 0.29
167 11 0.09
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (166 bp):
TATTAGATACAATTATAAAAATTTTAAACCAAAGAAAATCCCCCCAAAAACATTATAGAATAAAA
AACTCGTTTTTCGGGAAAAAGGAGAATTTAAAGAAAAAAAATCAAAACTCATGAAAAGGAATGAA
TTGTTAAAAACTAATTTAATGGGAATTCTATGACAT
Found at i:4142 original size:32 final size:32
Alignment explanation
Indices: 4088--4309 Score: 93
Period size: 32 Copynumber: 7.1 Consensus size: 32
4078 GGAATCACAT
*
4088 TTGTCTCTTTTCGAACAAGTCAAAATTGAAAC
1 TTGTCTCTTTTCGAACAAGTCAAAATTCAAAC
* * * *
4120 TTGTTTCTTTTTGAATAGGTCAAAATTCAAAC
1 TTGTCTCTTTTCGAACAAGTCAAAATTCAAAC
* * * * **
4152 TT-TATC-CTTCAAAAAAGATCAAAATTTTAAC
1 TTGTCTCTTTTCGAACAAG-TCAAAATTCAAAC
* * * *
4183 TAGTATCTTTTTGAA-AAGT-TAAATGTCAAAC
1 TTGTCTCTTTTCGAACAAGTCAAAAT-TCAAAC
* * * * **
4214 TTTTCTCTTTTTGAATAAATCAAAATTTGAAC
1 TTGTCTCTTTTCGAACAAGTCAAAATTCAAAC
* * * *
4246 CTGTGTC-TTTCTAA-ATAGGTCAAAAGT--AAC
1 TTGTCTCTTTTCGAACA-A-GTCAAAATTCAAAC
* *
4276 TTGTCTCTTTTCGAAGAAGTCCAAAACT-AAAC
1 TTGTCTCTTTTCGAACAAGT-CAAAATTCAAAC
4308 TT
1 TT
4310 ATATTTTTTT
Statistics
Matches: 140, Mismatches: 38, Indels: 24
0.69 0.19 0.12
Matches are distributed among these distances:
30 21 0.15
31 51 0.36
32 60 0.43
33 8 0.06
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (32 bp):
TTGTCTCTTTTCGAACAAGTCAAAATTCAAAC
Found at i:4389 original size:64 final size:62
Alignment explanation
Indices: 4233--4398 Score: 156
Period size: 64 Copynumber: 2.6 Consensus size: 62
4223 TTTGAATAAA
* *
4233 TCAAAATTTGAACCTGTGTCTTTCTAAATAGGTCAAAAGTAACTTGTCTCTTTTCGAAGAAG
1 TCAAAATTTGAACCTGTGTCTTTCTAAATAGGTTAAAAGTAACTTGTCTCTTTTCCAAGAAG
* * * * * * * * **
4295 TCCAAAA-CTAAACTTATATTTTTTTTAATAGGTTAGGAGTTAAACTTGTCTC-TTTCCAAGCAA
1 T-CAAAATTTGAACCTGTGTCTTTCTAAATAGGTTAAAAG-T-AACTTGTCTCTTTTCCAAG-AA
4358 G
62 G
* *
4359 TCAAAATTTGAGCCTGTGTCTTTCTAAATAGGTTGAAAGT
1 TCAAAATTTGAACCTGTGTCTTTCTAAATAGGTTAAAAGT
4399 CAAATTTATA
Statistics
Matches: 75, Mismatches: 24, Indels: 9
0.69 0.22 0.08
Matches are distributed among these distances:
62 22 0.29
63 19 0.25
64 34 0.45
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (62 bp):
TCAAAATTTGAACCTGTGTCTTTCTAAATAGGTTAAAAGTAACTTGTCTCTTTTCCAAGAAG
Found at i:5972 original size:32 final size:32
Alignment explanation
Indices: 5928--6021 Score: 89
Period size: 32 Copynumber: 2.9 Consensus size: 32
5918 ATCTCCATCA
* *
5928 TCAAAATTCAAACCTATATCTTTCTAAATATG
1 TCAAAAATCAAACCTATATCTTTCTAAATAAG
* * * * * * * *
5960 TTAAAAATCAAACTTTTCTTTTTTTGAACAAG
1 TCAAAAATCAAACCTATATCTTTCTAAATAAG
*
5992 TCAAAAGTCAAACCTATATCTTTCTAAATA
1 TCAAAAATCAAACCTATATCTTTCTAAATA
6022 GATTAGGAGT
Statistics
Matches: 43, Mismatches: 19, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.38
Consensus pattern (32 bp):
TCAAAAATCAAACCTATATCTTTCTAAATAAG
Found at i:6078 original size:64 final size:64
Alignment explanation
Indices: 5928--6070 Score: 189
Period size: 64 Copynumber: 2.2 Consensus size: 64
5918 ATCTCCATCA
* * * *
5928 TCAAAATTCAAACCTATATCTTTCTAAATATGTTAAAAATCAAACTTTTCTTTTTTTGAACAAG
1 TCAAAATTCAAACCTATATCTTTCTAAATATGTTAAAAATCAAACTTGTCTCTTTTCGAAAAAG
* ** *
5992 TCAAAAGTCAAACCTATATCTTTCTAAATA-GATTAGGAGTCAAACTTGTCTCTTTTCGAAAAAG
1 TCAAAATTCAAACCTATATCTTTCTAAATATG-TTAAAAATCAAACTTGTCTCTTTTCGAAAAAG
*
6056 TCAAAATTTAAACCT
1 TCAAAATTCAAACCT
6071 TTGTCTTTTT
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 1 0.01
64 67 0.99
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (64 bp):
TCAAAATTCAAACCTATATCTTTCTAAATATGTTAAAAATCAAACTTGTCTCTTTTCGAAAAAG
Found at i:6667 original size:21 final size:21
Alignment explanation
Indices: 6641--6707 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
6631 AGGAGTATAG
6641 TTGTATCGATACAATTGCATA
1 TTGTATCGATACAATTGCATA
* * *
6662 TTGTATTGATATAATTACATA
1 TTGTATCGATACAATTGCATA
*
6683 -TGTATCAATACAA-TGCATA
1 TTGTATCGATACAATTGCATA
6702 TTGTAT
1 TTGTAT
6708 GAATACATCT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
19 5 0.13
20 15 0.39
21 18 0.47
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (21 bp):
TTGTATCGATACAATTGCATA
Found at i:6706 original size:20 final size:21
Alignment explanation
Indices: 6641--6714 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 21
6631 AGGAGTATAG
*
6641 TTGTATCGATACAATTGCATA
1 TTGTATCAATACAATTGCATA
** * *
6662 TTGTATTGATATAATTACATA
1 TTGTATCAATACAATTGCATA
6683 -TGTATCAATACAA-TGCATA
1 TTGTATCAATACAATTGCATA
*
6702 TTGTATGAATACA
1 TTGTATCAATACA
6715 TCTTCGAATG
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
19 5 0.11
20 21 0.48
21 18 0.41
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (21 bp):
TTGTATCAATACAATTGCATA
Found at i:8403 original size:58 final size:58
Alignment explanation
Indices: 8068--8526 Score: 351
Period size: 58 Copynumber: 8.0 Consensus size: 58
8058 CTTTTATATC
* * * * * * *
8068 ATTTTCATGTCATCTAGGTCATTTTTCATGACTTAGAGATTTTGATGCAATTTCATGC
1 ATTTTGATGTCATTTAGGTCATTTTCCATGATTTAGGGACTTTGATGCAATTTCATGT
* * * * * * **
8126 ATTTTAATGTCATTTTGGTCATTTT-TAAGATCTAGGGACCTTGATGCAAATCCCATGT
1 ATTTTGATGTCATTTAGGTCATTTTCCATGATTTAGGGACTTTGATGC-AATTTCATGT
** * * * ** *
8184 -TTATTGGGGCCATTTAGGCCATTTTCCATGATCTAATGACTCTT-ATGCAATTT--TAT
1 ATT-TTGATGTCATTTAGGTCATTTTCCATGATTTAGGGACT-TTGATGCAATTTCATGT
* ** * * * * * * * *
8240 ATGTTGGGGTTATTTAGGTCATTTTCTAAGATCTAAGGACTTTCATACAAATTTTATGT
1 ATTTTGATGTCATTTAGGTCATTTTCCATGATTTAGGGACTTTGATGC-AATTTCATGT
* * * * * * *
8299 TTTTTGATGTCACTTAGTTCATTTT---TTACTTAAGGACTTTGATGCAATTTCATGC
1 ATTTTGATGTCATTTAGGTCATTTTCCATGATTTAGGGACTTTGATGCAATTTCATGT
* * *
8354 ATTTTGATATCAATTAGGTAATTTTCCATGATTTAGGGACTTTGATGCAATTTCATGT
1 ATTTTGATGTCATTTAGGTCATTTTCCATGATTTAGGGACTTTGATGCAATTTCATGT
* * *
8412 ATTTTGATGTCATTTAGGTCATTTTCTATGATCTAGAGACTTT-AGTGCAATTTCATGT
1 ATTTTGATGTCATTTAGGTCATTTTCCATGATTTAGGGACTTTGA-TGCAATTTCATGT
* * **
8470 ATTTTGATGTCATTTAGATCATTTTCCATAATTTAGGGACTTCAATGCAATTTCATG
1 ATTTTGATGTCATTTAGGTCATTTTCCATGATTTAGGGACTTTGATGCAATTTCATG
8527 AAGTTGAGAG
Statistics
Matches: 315, Mismatches: 72, Indels: 28
0.76 0.17 0.07
Matches are distributed among these distances:
55 30 0.10
56 51 0.16
57 24 0.08
58 173 0.55
59 35 0.11
60 2 0.01
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (58 bp):
ATTTTGATGTCATTTAGGTCATTTTCCATGATTTAGGGACTTTGATGCAATTTCATGT
Found at i:8543 original size:116 final size:116
Alignment explanation
Indices: 8333--8552 Score: 284
Period size: 116 Copynumber: 1.9 Consensus size: 116
8323 TTTACTTAAG
* * **
8333 GACTTTGATGCAATTTCATGCATTTTGATATCAATTAGGTAATTTTCCATGATTTAGGGACTTTG
1 GACTTTGATGCAATTTCATGCATTTTGATATCAATTAGATAATTTTCCATAATTTAGGGACTTCA
** * *
8398 ATGCAATTTCATGTATTTTGATGTCATTTAGGTCATTTTCTATGATCTAGA
66 ATGCAATTTCATGTAAGTTGAAGTCATTTAAGTCATTTTCTATGATCTAGA
* * * *
8449 GACTTT-AGTGCAATTTCATGTATTTTGATGTCATTTAGATCATTTTCCATAATTTAGGGACTTC
1 GACTTTGA-TGCAATTTCATGCATTTTGATATCAATTAGATAATTTTCCATAATTTAGGGACTTC
8513 AATGCAATTTCATG-AAGTTGAGAGAT-ATTTAAGTCATTTT
65 AATGCAATTTCATGTAAGTTGA-AG-TCATTTAAGTCATTTT
8553 TCATGACTTA
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
115 6 0.07
116 82 0.92
117 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (116 bp):
GACTTTGATGCAATTTCATGCATTTTGATATCAATTAGATAATTTTCCATAATTTAGGGACTTCA
ATGCAATTTCATGTAAGTTGAAGTCATTTAAGTCATTTTCTATGATCTAGA
Found at i:11162 original size:33 final size:32
Alignment explanation
Indices: 11120--11187 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
11110 CGTTACAAGC
*
11120 CAATGTATCGATACATTTTGTGATCTATCGATA
1 CAATGTATCGATACATATTGTG-TCTATCGATA
*
11153 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGTGTCTATCGATA
11185 CAA
1 CAA
11188 ATTTAGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 12 0.36
33 21 0.64
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (32 bp):
CAATGTATCGATACATATTGTGTCTATCGATA
Found at i:11245 original size:20 final size:20
Alignment explanation
Indices: 11220--11272 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
11210 CCAATGACTT
**
11220 GTATCGATACATTTTTTCAA
1 GTATCGATACATTTAGTCAA
*
11240 GTATCGATACATTTAGTCAT
1 GTATCGATACATTTAGTCAA
*
11260 GTATTGATACATT
1 GTATCGATACATT
11273 GTATCAATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (20 bp):
GTATCGATACATTTAGTCAA
Done.