Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1696
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: 28432
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Found at i:3852 original size:28 final size:28
Alignment explanation
Indices: 3820--3901 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 28
3810 ACTATGAGTG
*
3820 TGATTAGGCTTGACGAGCCATATGAAAA
1 TGATTAGGCCTGACGAGCCATATGAAAA
* * * *
3848 TGATTGGGCCTGATGGGCCATATGAAAG
1 TGATTAGGCCTGACGAGCCATATGAAAA
* * * *
3876 TGATTGGGCCCGATGGGCCATATGAA
1 TGATTAGGCCTGACGAGCCATATGAA
3902 TGAGATGGGC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (28 bp):
TGATTAGGCCTGACGAGCCATATGAAAA
Found at i:6644 original size:39 final size:39
Alignment explanation
Indices: 6526--6787 Score: 284
Period size: 39 Copynumber: 6.6 Consensus size: 39
6516 GCTCCTCGTT
* * * *
6526 CAAATGCCTTCGGGACATAG-CCTGATTATAGTAAT-TCGTA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
6566 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
* *
6606 CAAATGCCTTCAGGCTTAGCTCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
*
6645 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCACA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
6684 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
* * *
6723 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGT-ATC-TCGCA
6764 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
6788 CATCATTCAA
Statistics
Matches: 196, Mismatches: 19, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
39 127 0.65
40 54 0.28
41 15 0.08
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:6771 original size:117 final size:119
Alignment explanation
Indices: 6526--6787 Score: 301
Period size: 118 Copynumber: 2.2 Consensus size: 119
6516 GCTCCTCGTT
* * * **
6526 CAAATGCCTTCGGGACATAG-CCTGATTATAGTAAT-TCGTACAAATGCCTTCGGGACTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCACACAAATGCCTTCGGGACTTAACCC
* *
6589 GGATTTAGTAACTCGCACAAATGCCTTCAGGCTTAGCTCGGAATTAGTATCTCGCA
64 GGAATTAGTAACTCGCACAAATGCCTTCAGGCTTAGCTCGGAATTAGTATCTAGCA
*
6645 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCACACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCACACAAATGCCTTCGGGACTTAACCCGG
*
6708 AATTAGTATCTCGCACAAATGCCTTC-GGATCTTAG-TCCGGATATT-GTCA-CTTAGCA
66 AATTAGTAACTCGCACAAATGCCTTCAGG--CTTAGCT-CGGA-ATTAGT-ATC-TAGCA
6764 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
6788 CATCATTCAA
Statistics
Matches: 125, Mismatches: 9, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
116 2 0.02
117 45 0.36
118 50 0.40
119 28 0.22
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (119 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCACACAAATGCCTTCGGGACTTAACCCGG
AATTAGTAACTCGCACAAATGCCTTCAGGCTTAGCTCGGAATTAGTATCTAGCA
Found at i:17137 original size:49 final size:50
Alignment explanation
Indices: 17059--17291 Score: 272
Period size: 49 Copynumber: 4.7 Consensus size: 50
17049 ATCTATTGTG
*
17059 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
* * * *
17109 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TT
* * * * * * * * **
17159 CGATCACGTATGTAGTACTAAATGTAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
* *
17209 AGGTCACGTGTGCAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
* *
17259 -GATCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTA
17292 TGCGTACCAG
Statistics
Matches: 150, Mismatches: 31, Indels: 5
0.81 0.17 0.03
Matches are distributed among these distances:
49 71 0.47
50 44 0.29
51 35 0.23
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
Found at i:17256 original size:101 final size:98
Alignment explanation
Indices: 17062--17291 Score: 298
Period size: 100 Copynumber: 2.3 Consensus size: 98
17052 TATTGTGAGG
* * * *
17062 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGATAATTGGTCGCATGTGTAGTACT
1 TCACATATGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAATTGGTCACATGTGCAGTACT
*
17127 AAGTGCAGGCTACTATGCGTACCCGATAACTTCGA
66 AAGTGCAGGCTACTACGCGTACCCGATAA-TT-GA
* * * ** *
17162 TCACGTATGTAGTACTAAATGTAGGCTACTACGTGTATCAGATGGTTAGGTCACGTGTGCAGTAC
1 TCACATATGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAATT-GGTCACATGTGCAGTAC
* *
17227 TAAGTGCAGGCTACTACGTGTACCGGATAATTGA
65 TAAGTGCAGGCTACTACGCGTACCCGATAATTGA
* *
17261 TCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 TCACATATGTAGTACTAAGTGCAGGCTACTA
17292 TGCGTACCAG
Statistics
Matches: 111, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
99 28 0.25
100 42 0.38
101 41 0.37
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.29
Consensus pattern (98 bp):
TCACATATGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAATTGGTCACATGTGCAGTACT
AAGTGCAGGCTACTACGCGTACCCGATAATTGA
Found at i:20989 original size:28 final size:28
Alignment explanation
Indices: 20947--21012 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
20937 CCAGTGCATG
* *
20947 CAGTAACAGTCTGGGCCTGAGCCCTATA
1 CAGTAACAGTCTGGGCCTAAGCCCAATA
* *
20975 CAGTAACAGTGTGGGCTTAAGCCCAATA
1 CAGTAACAGTCTGGGCCTAAGCCCAATA
*
21003 CAGTATCAGT
1 CAGTAACAGT
21013 ACAGTGCAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (28 bp):
CAGTAACAGTCTGGGCCTAAGCCCAATA
Found at i:22102 original size:37 final size:37
Alignment explanation
Indices: 22052--22123 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
22042 TCTTCAGTTC
22052 ACAAGCAAAGCACCAATCACCCTTGGCCACAACCTTT
1 ACAAGCAAAGCACCAATCACCCTTGGCCACAACCTTT
22089 ACAAGCAAAGCACCAATCACCCTTGGCCACAACCT
1 ACAAGCAAAGCACCAATCACCCTTGGCCACAACCT
22124 ACACAAGAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.36, C:0.39, G:0.11, T:0.14
Consensus pattern (37 bp):
ACAAGCAAAGCACCAATCACCCTTGGCCACAACCTTT
Found at i:26883 original size:30 final size:31
Alignment explanation
Indices: 26837--26894 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
26827 TTCCCGAGCC
26837 TAGGGGCAAAAGTGTAATTATGC-AAAAGTT
1 TAGGGGCAAAAGTGTAATTATGCTAAAAGTT
* * *
26867 TAGGGGTAAAATTGTAATTTTGCTAAAA
1 TAGGGGCAAAAGTGTAATTATGCTAAAA
26895 TTTGAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (31 bp):
TAGGGGCAAAAGTGTAATTATGCTAAAAGTT
Found at i:27365 original size:46 final size:46
Alignment explanation
Indices: 27315--27440 Score: 200
Period size: 46 Copynumber: 2.7 Consensus size: 46
27305 TGGTTGAGCA
*
27315 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
27361 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
27407 -CTCGAGCTCATTGAGTTGAGTCCAAGTTCACTTA
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
27441 GGGGTGGGTT
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
45 1 0.01
46 74 0.99
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Done.