Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2895
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: 26214
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:2948 original size:21 final size:20
Alignment explanation
Indices: 2913--2961 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
2903 ACCAGCTCAC
*
2913 TTGAGCTCGTTTTAGCTTGT
1 TTGAGCTCGTTTTAGCTCGT
*
2933 TTGAGCTTGATTTTAGCTCGT
1 TTGAGCTCG-TTTTAGCTCGT
*
2954 TTCAGCTC
1 TTGAGCTC
2962 ATTTGTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.47
Consensus pattern (20 bp):
TTGAGCTCGTTTTAGCTCGT
Found at i:5703 original size:133 final size:132
Alignment explanation
Indices: 5546--5837 Score: 413
Period size: 132 Copynumber: 2.2 Consensus size: 132
5536 ATTGATCTAT
* **
5546 TCCACTGCTATCTCAAGGAGATAAGATCTACAATCTTCAGTCTGCTTCCTTGATACCTCGGGAAG
1 TCCACTGCTATCTCAAGGAGATAAGATCTACAATCTTCAATCTGCTTCCTTGATACCTCAAGAAG
*
5611 ATAAGACTACAATCTTTGAACTGCTCCCTTACTACCTCAGGCAGATAAGGCTAGTGGCTAAAATT
66 ATAAGAC-ACAATCTTTGAACTGCTCCCTTACTACCTCAGGCAGATAAGGCTAGTGGCTAAAATC
5676 TGC
130 TGC
* * * *
5679 TCCACTGCTATCTCAGGGAGATAAGATCTACAATTTTTAATCTGCTTCCTTGCTACCTCAAGAAG
1 TCCACTGCTATCTCAAGGAGATAAGATCTACAATCTTCAATCTGCTTCCTTGATACCTCAAGAAG
* ** * * * *
5744 ATAGGACACAATCTTTGGCCTGCTCCCTTGCTACCTCAGGGAGATAAGGCTGGTGGCTAAAGTCT
66 ATAAGACACAATCTTTGAACTGCTCCCTTACTACCTCAGGCAGATAAGGCTAGTGGCTAAAATCT
5809 GC
131 GC
* * *
5811 TCCCCTACTACCTCAAGGAGATAAGAT
1 TCCACTGCTATCTCAAGGAGATAAGAT
5838 TCGCCATCTT
Statistics
Matches: 140, Mismatches: 19, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
132 76 0.54
133 64 0.46
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.28
Consensus pattern (132 bp):
TCCACTGCTATCTCAAGGAGATAAGATCTACAATCTTCAATCTGCTTCCTTGATACCTCAAGAAG
ATAAGACACAATCTTTGAACTGCTCCCTTACTACCTCAGGCAGATAAGGCTAGTGGCTAAAATCT
GC
Found at i:5789 original size:43 final size:45
Alignment explanation
Indices: 5551--5971 Score: 164
Period size: 44 Copynumber: 9.5 Consensus size: 45
5541 TCTATTCCAC
* * * ** *
5551 TGCTATCTCAAGGAGATAAGATCTACAATCTTCAGTCTGCTTCCT
1 TGCTACCTCAGGGAGATAAGATCTACAATCTTTAACCTGCTCCCT
*
5596 TGATACCTC-GGGAAGATAAGA-CTACAATCTTTGAA-CTGCTCCCT
1 TGCTACCTCAGGG-AGATAAGATCTACAATCTTT-AACCTGCTCCCT
* * * **** ** **
5640 TACTACCTCAGGCAGATAAG-GCTAGTGGCTAAAATTTGCTCCAC-
1 TGCTACCTCAGGGAGATAAGATCTACAATCTTTAACCTGCTCC-CT
* * * *
5684 TGCTATCTCAGGGAGATAAGATCTACAATTTTTAATCTGCTTCCT
1 TGCTACCTCAGGGAGATAAGATCTACAATCTTTAACCTGCTCCCT
* * * **
5729 TGCTACCTCAAGAAGATAGGA-C-ACAATCTTTGGCCTGCTCCCT
1 TGCTACCTCAGGGAGATAAGATCTACAATCTTTAACCTGCTCCCT
* ***** * * *
5772 TGCTACCTCAGGGAGATAAG-GCTGGTGGC-TAAAGTCTGCTCCCC
1 TGCTACCTCAGGGAGATAAGATCTACAATCTTTAA-CCTGCTCCCT
* * * * ** *
5816 TACTACCTCAAGGAGATAAGAT-TCGCCATCTTCGATCTGCTCCAC-
1 TGCTACCTCAGGGAGATAAGATCT-ACAATCTTTAACCTGCTCC-CT
* ** * * *
5861 TGCTATCTCAGGGAGATAAGATCTACAATCTTTAGTCTACTTCGT
1 TGCTACCTCAGGGAGATAAGATCTACAATCTTTAACCTGCTCCCT
* * * * *** * *
5906 TGCTACATCAGGAATATAA-AACTACAATCTTCGGCCTACTCCAT
1 TGCTACCTCAGGGAGATAAGATCTACAATCTTTAACCTGCTCCCT
* *
5950 TGCTACCTTAGGAAGATAAGAT
1 TGCTACCTCAGGGAGATAAGAT
5972 TCGCCATCTT
Statistics
Matches: 273, Mismatches: 85, Indels: 36
0.69 0.22 0.09
Matches are distributed among these distances:
43 37 0.14
44 127 0.47
45 105 0.38
46 4 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (45 bp):
TGCTACCTCAGGGAGATAAGATCTACAATCTTTAACCTGCTCCCT
Found at i:5865 original size:132 final size:133
Alignment explanation
Indices: 5546--5893 Score: 396
Period size: 132 Copynumber: 2.6 Consensus size: 133
5536 ATTGATCTAT
* * * * * **
5546 TCCACTGCTATCTCAAGGAGATAAGATCTACAATCTTCAGTCTGCTTCCTTGATACCTCGGGAAG
1 TCCACTACTACCTCAAGGAGATAAGATCTACAATCTTCAATCTGCTTCCCTGCTACCTCAAGAAG
*
5611 ATAAGACTACAATCTTTGAACTGCTCCCTTACTACCTCAGGCAGATAAGGCTAGTGGCTAAAATT
66 ATAAGACTACAATCTTTGAACTGCTCCCTTACTACCTCAGGCAGATAAGGCTAGTGGCTAAAATC
5676 TGC
131 TGC
* * * * * *
5679 TCCACTGCTATCTCAGGGAGATAAGATCTACAATTTTTAATCTGCTTCCTTGCTACCTCAAGAAG
1 TCCACTACTACCTCAAGGAGATAAGATCTACAATCTTCAATCTGCTTCCCTGCTACCTCAAGAAG
* ** * * * *
5744 ATAGGAC-ACAATCTTTGGCCTGCTCCCTTGCTACCTCAGGGAGATAAGGCTGGTGGCTAAAGTC
66 ATAAGACTACAATCTTTGAACTGCTCCCTTACTACCTCAGGCAGATAAGGCTAGTGGCTAAAATC
5808 TGC
131 TGC
* * * * * * *
5811 TCCCCTACTACCTCAAGGAGATAAGAT-TCGCCATCTTCGATCTGC-TCCACTGCTATCTCAGGG
1 TCCACTACTACCTCAAGGAGATAAGATCT-ACAATCTTCAATCTGCTTCC-CTGCTACCTCAAGA
5874 AGATAAGATCTACAATCTTT
64 AGATAAGA-CTACAATCTTT
5894 AGTCTACTTC
Statistics
Matches: 182, Mismatches: 29, Indels: 7
0.83 0.13 0.03
Matches are distributed among these distances:
131 4 0.02
132 104 0.57
133 65 0.36
134 9 0.05
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29
Consensus pattern (133 bp):
TCCACTACTACCTCAAGGAGATAAGATCTACAATCTTCAATCTGCTTCCCTGCTACCTCAAGAAG
ATAAGACTACAATCTTTGAACTGCTCCCTTACTACCTCAGGCAGATAAGGCTAGTGGCTAAAATC
TGC
Found at i:5876 original size:45 final size:45
Alignment explanation
Indices: 5806--6016 Score: 131
Period size: 45 Copynumber: 4.7 Consensus size: 45
5796 GTGGCTAAAG
* * * * *
5806 TCTGCTCCCCTACTACCTCAAGGAGATAAGATTCGCCATCTTCGA
1 TCTGCTCCACTGCTACCTCAGGGAGATAAGATTCACAATCTTCGA
* *
5851 TCTGCTCCACTGCTATCTCAGGGAGATAAGA-TCTACAATCTT-TA
1 TCTGCTCCACTGCTACCTCAGGGAGATAAGATTC-ACAATCTTCGA
* * ** * * * * * *
5895 GTCTACTTCGTTGCTACATCAGGAATATAAAACT-ACAATCTTCGG
1 -TCTGCTCCACTGCTACCTCAGGGAGATAAGATTCACAATCTTCGA
* * * * * * *
5940 CCTACTCCATTGCTACCTTAGGAAGATAAGATTCGCCATCTTCGA
1 TCTGCTCCACTGCTACCTCAGGGAGATAAGATTCACAATCTTCGA
* * **
5985 TTTGCCCCACTGCTATATCAGGGAGATAAGAT
1 TCTGCTCCACTGCTACCTCAGGGAGATAAGAT
6017 CTGTAAATTT
Statistics
Matches: 123, Mismatches: 38, Indels: 10
0.72 0.22 0.06
Matches are distributed among these distances:
44 36 0.29
45 86 0.70
46 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (45 bp):
TCTGCTCCACTGCTACCTCAGGGAGATAAGATTCACAATCTTCGA
Found at i:12474 original size:46 final size:46
Alignment explanation
Indices: 12424--12596 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
12414 TGGTTGAGCA
*
12424 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
12470 TCCGAACTCGTTGAGTTGAGTTCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
*
12517 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCAAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
12563 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
12597 GGGGCGGGTT
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 59 0.56
47 28 0.27
48 3 0.03
50 6 0.06
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:12580 original size:93 final size:93
Alignment explanation
Indices: 12421--12591 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
12411 GGATGGTTGA
* * *
12421 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCATTGAGT
*
12486 TGAGTTCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
12514 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCAAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCATTGAGT
12579 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
12592 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:14555 original size:25 final size:25
Alignment explanation
Indices: 14527--14583 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
14517 TTTGGCTTGA
**
14527 CATTTACTAAGCAATATCGGATATT
1 CATTTACTAAGCAATATCAAATATT
* *
14552 CATTTATTAGGCAATATCAAATATT
1 CATTTACTAAGCAATATCAAATATT
14577 CAATTTA
1 C-ATTTA
14584 TTCTTTAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (25 bp):
CATTTACTAAGCAATATCAAATATT
Found at i:20790 original size:9 final size:9
Alignment explanation
Indices: 20772--20844 Score: 61
Period size: 9 Copynumber: 8.6 Consensus size: 9
20762 TTTATTTAAG
20772 TTAA-GTGT
1 TTAATGTGT
20780 TTAATGTGT
1 TTAATGTGT
20789 TT--TGTGT
1 TTAATGTGT
20796 TTAATAAGTGT
1 TTAAT--GTGT
20807 TTAAATGTGT
1 TT-AATGTGT
*
20817 TTAATATG-
1 TTAATGTGT
20825 TT--TGT-T
1 TTAATGTGT
20831 TTAATGTGT
1 TTAATGTGT
20840 TTAAT
1 TTAAT
20845 TGTAGGTGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 19
0.72 0.03 0.26
Matches are distributed among these distances:
6 4 0.08
7 7 0.13
8 9 0.17
9 18 0.34
10 6 0.11
11 6 0.11
12 3 0.06
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (9 bp):
TTAATGTGT
Found at i:20817 original size:21 final size:22
Alignment explanation
Indices: 20791--20844 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
20781 TAATGTGTTT
20791 TGTGTTTAATAAG-TGTTTAAA
1 TGTGTTTAATAAGTTGTTTAAA
* *
20812 TGTGTTTAATATGTTTGTTTTAA
1 TGTGTTTAATAAG-TTGTTTAAA
20835 TGTGTTTAAT
1 TGTGTTTAAT
20845 TGTAGGTGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 12 0.41
23 17 0.59
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.56
Consensus pattern (22 bp):
TGTGTTTAATAAGTTGTTTAAA
Found at i:23675 original size:30 final size:30
Alignment explanation
Indices: 23641--23701 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
23631 TCCTTAACTC
23641 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
23671 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
23701 A
1 A
23702 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Done.