Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2480
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: 10959
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Found at i:4560 original size:60 final size:59
Alignment explanation
Indices: 4410--4718 Score: 351
Period size: 59 Copynumber: 5.2 Consensus size: 59
4400 TATATAGTTG
* *
4410 TTGTTTAGGTTTCT-AGTTTTATCCAAGCCATTAGTTTAGCCTTAGTTTCACCTAAGTCA
1 TTGTTTAGGTTTCTGA-TTTTATCCAAGCCATTAGTTAAGTCTTAGTTTCACCTAAGTCA
* *
4469 TTGTTTAGGTTTCTGATTTTATCCAAACCATTTAGTTAAGTCTTAGTTTCACCCAAGTCA
1 TTGTTTAGGTTTCTGATTTTATCCAAGCCA-TTAGTTAAGTCTTAGTTTCACCTAAGTCA
* *
4529 -TGTTTAGGTTTCTGATTTTATCCAAACCCATTTAGTTAAGTTTTAG-TTCACCTAAGTCA
1 TTGTTTAGGTTTCTGATTTTATCC-AAGCCA-TTAGTTAAGTCTTAGTTTCACCTAAGTCA
** * * * * *
4588 TTGTTTAGGTTTCT-AGTTTCGTCCAGGCCATTAGTTGAGTATTGGTTTCACCCAAGTCA
1 TTGTTTAGGTTTCTGA-TTTTATCCAAGCCATTAGTTAAGTCTTAGTTTCACCTAAGTCA
* * * * * *
4647 TTGTTTAGATTTATGA-TTTATCCAATCCATTCGTTGAA-TCTTGGTTTCACCTAAATCA
1 TTGTTTAGGTTTCTGATTTTATCCAAGCCATTAGTT-AAGTCTTAGTTTCACCTAAGTCA
4705 TTGTTTAGGTTTCT
1 TTGTTTAGGTTTCT
4719 TGTTTCGTCT
Statistics
Matches: 214, Mismatches: 28, Indels: 17
0.83 0.11 0.07
Matches are distributed among these distances:
58 55 0.26
59 92 0.43
60 67 0.31
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.44
Consensus pattern (59 bp):
TTGTTTAGGTTTCTGATTTTATCCAAGCCATTAGTTAAGTCTTAGTTTCACCTAAGTCA
Found at i:4639 original size:118 final size:118
Alignment explanation
Indices: 4410--4753 Score: 405
Period size: 118 Copynumber: 2.9 Consensus size: 118
4400 TATATAGTTG
* * *
4410 TTGTTTAGGTTTCT-AGTTTTATCCAAGCCATTAGTTTAGCCTTAGTTTCACCTAAGTCATTGTT
1 TTGTTTAGGTTTCTGA-TTTTATCCAACCCATTAGTTAAGTCTTAGTTTCACCTAAGTCATTGTT
** ** * *
4474 TAGGTTTCTGATTTTATCCAAACCATTTAGTTAAGTCTTAGTTTCACCCAAGTCA
65 TAGGTTTCTG-TTTCGTCCAGGCCATTTAGTTGAGTCTTGGTTTCACCCAAGTCA
*
4529 -TGTTTAGGTTTCTGATTTTATCCAAACCCATTTAGTTAAGTTTTAG-TTCACCTAAGTCATTGT
1 TTGTTTAGGTTTCTGATTTTATCC-AACCCA-TTAGTTAAGTCTTAGTTTCACCTAAGTCATTGT
*
4592 TTAGGTTTCTAGTTTCGTCCAGGCCA-TTAGTTGAGTATTGGTTTCACCCAAGTCA
64 TTAGGTTTCT-GTTTCGTCCAGGCCATTTAGTTGAGTCTTGGTTTCACCCAAGTCA
* * * * * *
4647 TTGTTTAGATTTATGA-TTTATCCAATCCATTCGTTGAA-TCTTGGTTTCACCTAAATCATTGTT
1 TTGTTTAGGTTTCTGATTTTATCCAACCCATTAGTT-AAGTCTTAGTTTCACCTAAGTCATTGTT
*
4710 TAGGTTTCTTGTTTCGTCTAGGCCATTTCA-TTGAGTCTTGGTTT
65 TAGGTTTC-TGTTTCGTCCAGGCCATTT-AGTTGAGTCTTGGTTT
4754 TGCCTAAGTC
Statistics
Matches: 195, Mismatches: 20, Indels: 21
0.83 0.08 0.09
Matches are distributed among these distances:
116 9 0.05
117 46 0.24
118 70 0.36
119 57 0.29
120 13 0.07
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.45
Consensus pattern (118 bp):
TTGTTTAGGTTTCTGATTTTATCCAACCCATTAGTTAAGTCTTAGTTTCACCTAAGTCATTGTTT
AGGTTTCTGTTTCGTCCAGGCCATTTAGTTGAGTCTTGGTTTCACCCAAGTCA
Found at i:5548 original size:41 final size:41
Alignment explanation
Indices: 5503--6084 Score: 209
Period size: 41 Copynumber: 14.4 Consensus size: 41
5493 TTTCGACCTT
* * *
5503 TTGACTTGTTGTTTTTGTTTTGATCAACCTTTTCTTATTTG
1 TTGACTTGTTGGTTTTGTCTTGATCAACCCTTTCTTATTTG
** * * *
5544 TTGACTTGTTAGGTTTTGTC-CCAGCTAACCCTTTC--ATCTA
1 TTGACTTGTT-GGTTTTGTCTTGATC-AACCCTTTCTTATTTG
*
5584 TTGACTTGTTGGTTTTGTCTTGGTCAACCCTTTCTTATTTG
1 TTGACTTGTTGGTTTTGTCTTGATCAACCCTTTCTTATTTG
* * * ** *
5625 TTGACTTCTTGATTTTGTCTT-AGTCAA-CCTTTTTTAACCTA
1 TTGACTTGTTGGTTTTGTCTTGA-TCAACCCTTTCTT-ATTTG
** ** *
5666 TTGACTTGTACGTTCCGTCTT-AGTCAAACCTTT-TTATTTG
1 TTGACTTGTTGGTTTTGTCTTGA-TCAACCCTTTCTTATTTG
* * * * ** * *
5706 TTGACTT-ATCGATTTATC-ACAGTTAACCCTTTCATATTTG
1 TTGACTTGTTGGTTTTGTCTTGA-TCAACCCTTTCTTATTTG
* * * * *
5746 TTGACTTGTTGATTTTATC-TGGTCAA-ACATTCTTATTTG
1 TTGACTTGTTGGTTTTGTCTTGATCAACCCTTTCTTATTTG
* *** ** * * *
5785 TTGACTGGACAGTTTTGTCCCGATTAA-CTTCTTCTTATTAG
1 TTGACTTGTTGGTTTTGTCTTGATCAACCCT-TTCTTATTTG
* * * * * *
5826 TTG--TTATTAGTTTTATCTCGGTCAACCCTTTTTTTTATTTG
1 TTGACTTGTTGGTTTTGTCTTGATCAACCC--TTTCTTATTTG
*** ** * *
5867 TTGACTTG-TCAATTTGTCACGATCAACCC-TTCATGTTTG
1 TTGACTTGTTGGTTTTGTCTTGATCAACCCTTTCTTATTTG
* * * * **
5906 TTGACTTGTCAGTTTTTGTCTCGGTCAACTTTTTCTTATTTG
1 TTGACTTGT-TGGTTTTGTCTTGATCAACCCTTTCTTATTTG
* * ***
5948 TTGACTTATCGGTTTTGT-TTCGATCAATTTTTTCTTATTTG
1 TTGACTTGTTGGTTTTGTCTT-GATCAACCCTTTCTTATTTG
* * * *
5989 TTGACTTGTTAG-TTTGTCTTGTTCAACCCTTTCATATATG
1 TTGACTTGTTGGTTTTGTCTTGATCAACCCTTTCTTATTTG
** * *
6029 TTGAC---TCAGTTTTATCTTGGTCAA-CCTCTTCTTATTTG
1 TTGACTTGTTGGTTTTGTCTTGATCAACCCT-TTCTTATTTG
* **
6067 TTAACTTGTCAGTTTTGT
1 TTGACTTGTTGGTTTTGT
6085 TCTAACTAAC
Statistics
Matches: 396, Mismatches: 117, Indels: 56
0.70 0.21 0.10
Matches are distributed among these distances:
37 6 0.02
38 24 0.06
39 85 0.21
40 76 0.19
41 151 0.38
42 52 0.13
43 2 0.01
ACGTcount: A:0.17, C:0.18, G:0.15, T:0.51
Consensus pattern (41 bp):
TTGACTTGTTGGTTTTGTCTTGATCAACCCTTTCTTATTTG
Found at i:6108 original size:122 final size:120
Alignment explanation
Indices: 5860--6085 Score: 258
Period size: 119 Copynumber: 1.9 Consensus size: 120
5850 ACCCTTTTTT
* * *
5860 TTATTTGTTGACTTGTCAATTTGTCACGATCAACCCTTCATGTTTGTTGACTTGTCAGTTTTTGT
1 TTATTTGTTGACTTGTCAATTTGTCACGATCAACCCTTCATATATGTTGAC-T-TCAGTTTTTAT
* * * * * **
5925 CTCGGTCAACTTTTTCTTATTTGTTGACTTATCGGTTTTGTTTCGATCAATTTTTTC
64 CTCGGTCAACCTCTTCTTATTTGTTAACTTATCAGTTTTGTTTCGAACAATTTTTAA
* * ** *
5982 TTATTTGTTGACTTGTTAGTTTGTCTTGTTCAACCCTTTCATATATGTTGAC-TCAG-TTTTATC
1 TTATTTGTTGACTTGTCAATTTGTCACGATCAACCC-TTCATATATGTTGACTTCAGTTTTTATC
* *
6045 TTGGTCAACCTCTTCTTATTTGTTAACTTGTCAGTTTTGTT
65 TCGGTCAACCTCTTCTTATTTGTTAACTTATCAGTTTTGTT
6086 CTAACTAACC
Statistics
Matches: 89, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
119 41 0.46
120 4 0.04
122 31 0.35
123 13 0.15
ACGTcount: A:0.16, C:0.17, G:0.15, T:0.52
Consensus pattern (120 bp):
TTATTTGTTGACTTGTCAATTTGTCACGATCAACCCTTCATATATGTTGACTTCAGTTTTTATCT
CGGTCAACCTCTTCTTATTTGTTAACTTATCAGTTTTGTTTCGAACAATTTTTAA
Found at i:8263 original size:156 final size:156
Alignment explanation
Indices: 7891--8386 Score: 420
Period size: 156 Copynumber: 3.2 Consensus size: 156
7881 ACCTGATACT
* * * * * * * *
7891 CCTAAAGGACATAAAAAAAATTATATATGGGATGAACCTATCCTAAATACCCATCTTCAGCAT-A
1 CCTAAAGGAC-TTAAAAAGATTAGAAATGGGATGAACCTATCCTAAATGCCTACCTTCGGCATAA
* * * * * * * * *
7955 AAGTGGA-CTCAGTGACAACCT-AGAACTCGATTCTAAAAAATTACCAAACTGCCCCTA-GAGGA
65 AAGCGAACCT-AATAACAACCTAAG-ACTCGATTCCAAAAAATTACAAAAATGCCCCTATAAGTA
*** * *
8017 TACCTTCGACA-TAAAAGTA-CTAAATACC
128 TACCTTC-ACATTAAAAGTATCCCGACAAC
* * * * *
8045 CCAAAAAGACTTACAAAAAATTAGAAATGGGATGAACCTATCCTAAATGCCTATCTTGGGCATAA
1 CCTAAAGGACTTA-AAAAGATTAGAAATGGGATGAACCTATCCTAAATGCCTACCTTCGGCATAA
* * ** *
8110 AAGCGAACCTAATGACAACCTAAGAGTC-AGTTCCAAAAAATTATGAAAATGCCCCTATAAGTGT
65 AAGCGAACCTAATAACAACCTAAGACTCGA-TTCCAAAAAATTACAAAAATGCCCCTATAAGTAT
* *
8174 ATCTT-AGATGTAAAAGTATCCCGACAAC
129 ACCTTCACAT-TAAAAGTATCCCGACAAC
8202 CCTAAAGGACTTAAAAAGATTAGAAATGGGATGAACCTATCCTCAAAAT-CC-ACCTTCGGCATA
1 CCTAAAGGACTTAAAAAGATTAGAAATGGGATGAACCTATCCT--AAATGCCTACCTTCGGCATA
* * * ** * * **
8265 AAATCGAACCTAGTAACAACCTAGGACTCGATTTTAAGAAATTACAAAAATGCCTCTATGGGTAT
64 AAAGCGAACCTAATAACAACCTAAGACTCGATTCCAAAAAATTACAAAAATGCCCCTATAAGTAT
* *
8330 ACCTTCGACATTAAAAGTGTCCTGACAAC
129 ACCTTC-ACATTAAAAGTATCCCGACAAC
8359 CCTAAAGGACTT-AAAAGATTAGAAATGG
1 CCTAAAGGACTTAAAAAGATTAGAAATGG
8387 TGATTTTACT
Statistics
Matches: 278, Mismatches: 50, Indels: 26
0.79 0.14 0.07
Matches are distributed among these distances:
153 2 0.01
154 54 0.19
155 42 0.15
156 127 0.46
157 46 0.17
158 7 0.03
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (156 bp):
CCTAAAGGACTTAAAAAGATTAGAAATGGGATGAACCTATCCTAAATGCCTACCTTCGGCATAAA
AGCGAACCTAATAACAACCTAAGACTCGATTCCAAAAAATTACAAAAATGCCCCTATAAGTATAC
CTTCACATTAAAAGTATCCCGACAAC
Done.