Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3253
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: 35341
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Found at i:2143 original size:27 final size:26
Alignment explanation
Indices: 2108--2219 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
2098 AGCATGGCTG
* *
2108 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
2134 CCAGATACAGATAATCGTGGCAGAACCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
2162 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
2189 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
2216 CCAG
1 CCAG
2220 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.08
27 54 0.71
28 16 0.21
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:2172 original size:54 final size:54
Alignment explanation
Indices: 2108--2219 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
2098 AGCATGGCTG
*
2108 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAACCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAACCA
* * * *
2162 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAACCA
2216 CCAG
1 CCAG
2220 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAACCA
Found at i:3666 original size:24 final size:24
Alignment explanation
Indices: 3636--3704 Score: 120
Period size: 24 Copynumber: 2.9 Consensus size: 24
3626 TAGATTTCCT
**
3636 CCTTATCTGCTCCTAAATCCTATC
1 CCTTATCAACTCCTAAATCCTATC
3660 CCTTATCAACTCCTAAATCCTATC
1 CCTTATCAACTCCTAAATCCTATC
3684 CCTTATCAACTCCTAAATCCT
1 CCTTATCAACTCCTAAATCCT
3705 CTCCTGACAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.26, C:0.38, G:0.01, T:0.35
Consensus pattern (24 bp):
CCTTATCAACTCCTAAATCCTATC
Found at i:9970 original size:26 final size:26
Alignment explanation
Indices: 9940--10050 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
9930 AGCATGGCTG
* *
9940 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
9966 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
9994 CCAGAACAGA-ATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
10020 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
10047 CCAG
1 CCAG
10051 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 4, Indels: 9
0.85 0.04 0.10
Matches are distributed among these distances:
26 28 0.37
27 33 0.43
28 15 0.20
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:10010 original size:54 final size:53
Alignment explanation
Indices: 9940--10050 Score: 161
Period size: 54 Copynumber: 2.1 Consensus size: 53
9930 AGCATGGCTG
*
9940 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * *
9994 CCAGAACAGA-ATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
10047 CCAG
1 CCAG
10051 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
53 24 0.46
54 28 0.54
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.15
Consensus pattern (53 bp):
CCAGAACAGATAATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:11493 original size:24 final size:24
Alignment explanation
Indices: 11466--11536 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
11456 CTATATTTCC
**
11466 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
11490 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
11514 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
11537 CTCCTGACAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.25, C:0.38, G:0.01, T:0.35
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:15452 original size:40 final size:41
Alignment explanation
Indices: 15367--15551 Score: 127
Period size: 40 Copynumber: 4.6 Consensus size: 41
15357 ATTGAATGCT
* *
15367 GTCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-TATA
1 GTCCGGACTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTTA-A
* *
15408 -TCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTA-TTAA
1 GTCCGGACTAAG-TCCCGAAGGCATTTGTGCGAGATACTTAA
* ** *
15447 TTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTTAA
1 GTCCGGACTAAGTCCCGAAGGCATTTGTGCGAGATACTTAA
* * * *
15488 GTCCGG-GTTAGTCCCGAAGGCATTCGTGCGAG-T-TTTAAA
1 GTCCGGACTAAGTCCCGAAGGCATTTGTGCGAGATACTT-AA
* **
15527 ATCCGGGTTAAGTCCCGAAGGCATT
1 GTCCGGACTAAGTCCCGAAGGCATT
15552 GAATGAGTTA
Statistics
Matches: 117, Mismatches: 18, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
38 2 0.02
39 10 0.09
40 86 0.74
41 19 0.16
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (41 bp):
GTCCGGACTAAGTCCCGAAGGCATTTGTGCGAGATACTTAA
Found at i:15560 original size:39 final size:40
Alignment explanation
Indices: 15448--15598 Score: 137
Period size: 40 Copynumber: 3.8 Consensus size: 40
15438 AGTTATTAAT
* ** * * *
15448 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTTAAG
1 TCCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAAAA
** *
15489 TCCGGGTT-AGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACTAAAA
* *
15528 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAAA
* *
15568 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
15599 GAGCTATATC
Statistics
Matches: 93, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
39 39 0.42
40 46 0.49
41 8 0.09
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAAA
Found at i:15606 original size:40 final size:39
Alignment explanation
Indices: 15529--15611 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
15519 GTTTTAAAAT
* * *
15529 CCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATAA
* *
15568 CCGGGCTATGTCCCGAAGGCACTTGAACGAG-GAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCA-TTGAACGAGTGA-CTATAA
15608 CCGG
1 CCGG
15612 TTAAATTCCG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 20 0.54
40 17 0.46
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.22
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATAA
Found at i:23338 original size:40 final size:40
Alignment explanation
Indices: 23254--23437 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
23244 TTGAATGCTG
* * * *
23254 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
23293 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
23334 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
23374 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
23414 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
23438 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:23391 original size:80 final size:81
Alignment explanation
Indices: 23254--23434 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
23244 TTGAATGCTG
* * *
23254 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
23318 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
23334 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
23395 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
23414 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
23435 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:23458 original size:39 final size:38
Alignment explanation
Indices: 23335--23484 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
23325 GTTATTAATT
* ** * *
23335 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
23375 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
23414 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
23454 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
23485 GAGCTATATC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:23492 original size:40 final size:39
Alignment explanation
Indices: 23375--23497 Score: 97
Period size: 40 Copynumber: 3.1 Consensus size: 39
23365 GATACTAATT
* ** ** *
23375 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGT-TTTAAAA
1 CCGGGCTAAGTCCCGAAGGCATT-GAACGAGTGACTATAA
* * *
23414 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATAA
* *
23454 CCGGGCTATGTCCCGAAGGCACTTGAACGAG-GAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCA-TTGAACGAGTGA-CTATAA
23494 CCGG
1 CCGG
23498 TTAAATTCCG
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
39 25 0.36
40 44 0.64
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATAA
Found at i:25790 original size:40 final size:39
Alignment explanation
Indices: 25706--25929 Score: 265
Period size: 40 Copynumber: 5.6 Consensus size: 39
25696 TTGAATGATG
* * * *
25706 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
25746 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
25786 TCCGGGCTAAGCCCGAAGGCA-TTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
25824 TCCGGGTTAAGTCTCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTC-CGAAGGCATTTGTGCGAGTTACTAAA
*
25864 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
25905 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
25930 AACGAGGAGC
Statistics
Matches: 163, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
38 26 0.16
39 17 0.10
40 109 0.67
41 11 0.07
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:25927 original size:80 final size:80
Alignment explanation
Indices: 25706--25929 Score: 287
Period size: 78 Copynumber: 2.8 Consensus size: 80
25696 TTGAATGATG
* * * * *
25706 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCAT
*
25769 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAA
* *
25786 TCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTA-AATCCGGGTTAAGTCTCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCATT
*
25848 TGTGCGAGTTACTAAA
65 TGTGCGAGATACTAAA
* *
25864 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
25929 G
66 G
25930 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
77 2 0.02
78 48 0.38
79 25 0.20
80 48 0.38
81 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:33781 original size:40 final size:40
Alignment explanation
Indices: 33697--33920 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
33687 TTGAATGATG
* * * *
33697 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
33737 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
33777 TCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
33815 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
33855 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
33896 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
33921 AACGAGGAGC
Statistics
Matches: 165, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
38 25 0.15
39 19 0.12
40 111 0.67
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:33915 original size:80 final size:80
Alignment explanation
Indices: 33697--33920 Score: 296
Period size: 78 Copynumber: 2.8 Consensus size: 80
33687 TTGAATGATG
* * * * *
33697 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCAT
*
33760 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAA
*
33777 TCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTA-AATCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCATT
*
33839 TGTGCGAGTTACTAAA
65 TGTGCGAGATACTAAA
* *
33855 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
33920 G
66 G
33921 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
77 2 0.02
78 49 0.39
79 25 0.20
80 49 0.39
81 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Done.