Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1121
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: 40771
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:3768 original size:79 final size:81
Alignment explanation
Indices: 3632--3816 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
3622 TTGAATGATG
*
3632 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
3696 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
3711 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
3773 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
3791 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
3817 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:3830 original size:40 final size:40
Alignment explanation
Indices: 3633--3816 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
3623 TGAATGATGT
* * * *
3633 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
3673 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
3713 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
3751 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
3792 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
3817 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:3838 original size:79 final size:79
Alignment explanation
Indices: 3685--3849 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
3675 GGACTAAGAT
* **
3685 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
3750 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
3764 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
3827 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
3843 CCGAAGG
1 CCGAAGG
3850 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:11631 original size:39 final size:40
Alignment explanation
Indices: 11533--11713 Score: 176
Period size: 40 Copynumber: 4.5 Consensus size: 40
11523 ATGATGTCCG
* * * *
11533 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCC-
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCA
* *
11572 GGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCCA
1 GG-CTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCCA
* *
11613 GGCTAAG-CCCGAAAGCATTTGTGCGAGTTACTAAATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCA
* *
11652 GGTTAAGTCCCGAAGGCAATTT-TGCGAGTTACTATAA-CCG
1 GGCTAAGTCCCGAAGGC-ATTTGTGCGAGTTACTA-AATCCA
*
11692 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
11714 AACGAGTAGC
Statistics
Matches: 119, Mismatches: 14, Indels: 17
0.79 0.09 0.11
Matches are distributed among these distances:
39 39 0.33
40 64 0.54
41 16 0.13
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCA
Found at i:11696 original size:79 final size:81
Alignment explanation
Indices: 11530--11713 Score: 200
Period size: 79 Copynumber: 2.3 Consensus size: 81
11520 TGAATGATGT
*
11530 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
*
11594 GTGCGAGATACTAATT
66 GTGCGAGATACTAATA
* * * * * **
11610 CCAGGCTAAG-CCCGAAAGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGC-AT
*
11672 TT-TGCGAGTTACT-ATAA
64 TTGTGCGAGATACTAAT-A
*
11689 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
11714 AACGAGTAGC
Statistics
Matches: 86, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
78 3 0.03
79 50 0.58
80 33 0.38
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (81 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATA
Found at i:11735 original size:79 final size:79
Alignment explanation
Indices: 11582--11746 Score: 176
Period size: 79 Copynumber: 2.1 Consensus size: 79
11572 GGACTAAGAT
* **
11582 CCGAAGGCATTTGTGCGAGATACTAATTCCAGGCTAAGCCCGAAAGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCAGGCTAAGCCCGAAAGCATTTGAACGAGTTACTAA
*
11647 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * * *
11661 CCGAAGGCAATTT-TGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAG
1 CCGAAGGC-ATTTGTGCGAGATACTAAT-ACCAGGCTAAG-CCCGAAAGCATTTGAACGAGTTA-
* *
11723 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
11740 CCGAAGG
1 CCGAAGG
11747 TACGTGATTT
Statistics
Matches: 72, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
78 2 0.03
79 42 0.58
80 28 0.39
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCAGGCTAAGCCCGAAAGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:13605 original size:4 final size:4
Alignment explanation
Indices: 13598--13624 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
13588 TTTTTTTATT
13598 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
13625 TTCCTTAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:25768 original size:14 final size:14
Alignment explanation
Indices: 25751--25782 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
25741 AAAACTAAGT
25751 AAATAAAAAAATAA
1 AAATAAAAAAATAA
25765 AAATAAAAAAATAA
1 AAATAAAAAAATAA
25779 AAAT
1 AAAT
25783 CATTAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (14 bp):
AAATAAAAAAATAA
Found at i:28250 original size:21 final size:18
Alignment explanation
Indices: 28208--28252 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
28198 TTTTTCAAAC
28208 TCTTTTTCAAATCCTCTT
1 TCTTTTTCAAATCCTCTT
*
28226 TCTTTTATCACATCACTCATT
1 TCTTTT-TCAAATC-CTC-TT
28247 TCTTTT
1 TCTTTT
28253 GTACTCTCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 6 0.26
20 3 0.13
21 8 0.35
ACGTcount: A:0.18, C:0.27, G:0.00, T:0.56
Consensus pattern (18 bp):
TCTTTTTCAAATCCTCTT
Found at i:28364 original size:24 final size:24
Alignment explanation
Indices: 28293--28372 Score: 63
Period size: 24 Copynumber: 3.4 Consensus size: 24
28283 TCTTTTTCAG
* * *
28293 TTTTCTTTTCTTTTTCACACTCGT
1 TTTTCTTTTCTATCTCACACTCAT
* * * ***
28317 TTTTATTCTCAATCTCATTTTCAT
1 TTTTCTTTTCTATCTCACACTCAT
28341 TTTTCTTTTCTATCTCACACTCA-
1 TTTTCTTTTCTATCTCACACTCAT
*
28364 TCTTCTTTT
1 TTTTCTTTT
28373 TCTTTCATTT
Statistics
Matches: 40, Mismatches: 16, Indels: 1
0.70 0.28 0.02
Matches are distributed among these distances:
23 8 0.20
24 32 0.80
ACGTcount: A:0.14, C:0.25, G:0.01, T:0.60
Consensus pattern (24 bp):
TTTTCTTTTCTATCTCACACTCAT
Found at i:28386 original size:15 final size:16
Alignment explanation
Indices: 28361--28392 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
28351 TATCTCACAC
28361 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
28377 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
28392 T
1 T
28393 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:29281 original size:14 final size:14
Alignment explanation
Indices: 29264--29319 Score: 58
Period size: 14 Copynumber: 3.8 Consensus size: 14
29254 TCAATTTCGA
29264 TTTTTTTTCTTCTT
1 TTTTTTTTCTTCTT
**
29278 TTTTTTTAATTCTGAAT
1 TTTTTTTTCTTCT---T
*
29295 TTTTTCTTCTTCTT
1 TTTTTTTTCTTCTT
29309 TTTTTTTTCTT
1 TTTTTTTTCTT
29320 AAATACTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
14 22 0.67
17 11 0.33
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTTTTTTCTTCTT
Found at i:29284 original size:31 final size:32
Alignment explanation
Indices: 29244--29315 Score: 107
Period size: 30 Copynumber: 2.3 Consensus size: 32
29234 TTTCAATCAC
29244 TCTTTTTTTTTCAATT-TCG-ATTTTTT-TTCT
1 TCTTTTTTTTTCAATTCT-GAATTTTTTCTTCT
29274 TCTTTTTTTTT-AATTCTGAATTTTTTCTTCT
1 TCTTTTTTTTTCAATTCTGAATTTTTTCTTCT
29305 TCTTTTTTTTT
1 TCTTTTTTTTT
29316 TCTTAAATAC
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
29 5 0.13
30 19 0.49
31 15 0.38
ACGTcount: A:0.10, C:0.12, G:0.03, T:0.75
Consensus pattern (32 bp):
TCTTTTTTTTTCAATTCTGAATTTTTTCTTCT
Found at i:29297 original size:28 final size:30
Alignment explanation
Indices: 29244--29313 Score: 92
Period size: 28 Copynumber: 2.4 Consensus size: 30
29234 TTTCAATCAC
*
29244 TCTTTTTTTTTCAATTTCGATTTTTTTTCT
1 TCTTTTTTTTTCAATTTCGATATTTTTTCT
29274 TCTTTTTTTTT-AA-TTCTGA-ATTTTTTCT
1 TCTTTTTTTTTCAATTTC-GATATTTTTTCT
29302 TCTTCTTTTTTT
1 TCTT-TTTTTTT
29314 TTTCTTAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
28 15 0.41
29 11 0.30
30 11 0.30
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.74
Consensus pattern (30 bp):
TCTTTTTTTTTCAATTTCGATATTTTTTCT
Found at i:29378 original size:12 final size:12
Alignment explanation
Indices: 29361--29404 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
29351 GAATACAAAC
29361 TTTTTTTGAAATT
1 TTTTTTTGAAA-T
29374 TTTTTTTGAAAT
1 TTTTTTTGAAAT
* *
29386 TTTTTTTCAAGT
1 TTTTTTTGAAAT
29398 TTTTTTT
1 TTTTTTT
29405 TTATTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.18, C:0.02, G:0.07, T:0.73
Consensus pattern (12 bp):
TTTTTTTGAAAT
Found at i:29379 original size:13 final size:13
Alignment explanation
Indices: 29361--29405 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
29351 GAATACAAAC
29361 TTTTTTTGAAATT
1 TTTTTTTGAAATT
29374 TTTTTTTGAAA-T
1 TTTTTTTGAAATT
* *
29386 TTTTTTTCAAGTT
1 TTTTTTTGAAATT
29399 TTTTTTT
1 TTTTTTT
29406 TATTTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.18, C:0.02, G:0.07, T:0.73
Consensus pattern (13 bp):
TTTTTTTGAAATT
Found at i:37485 original size:22 final size:21
Alignment explanation
Indices: 37436--37485 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
37426 CCTCGTCTTT
*
37436 TTCTTTTGTTTCTTTTTCTAA
1 TTCTTTTCTTTCTTTTTCTAA
37457 -TCATTTTCTCTTCTTTTTC-AA
1 TTC-TTTTCT-TTCTTTTTCTAA
37478 CTTCTTTT
1 -TTCTTTT
37486 TCAATTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
20 2 0.08
21 7 0.29
22 13 0.54
23 2 0.08
ACGTcount: A:0.10, C:0.20, G:0.02, T:0.68
Consensus pattern (21 bp):
TTCTTTTCTTTCTTTTTCTAA
Found at i:37498 original size:11 final size:12
Alignment explanation
Indices: 37466--37497 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
37456 ATCATTTTCT
37466 CTTCTTTTTCAA
1 CTTCTTTTTCAA
37478 CTTCTTTTTCAA
1 CTTCTTTTTCAA
*
37490 TTTCTTTT
1 CTTCTTTT
37498 CTGTTTCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.12, C:0.22, G:0.00, T:0.66
Consensus pattern (12 bp):
CTTCTTTTTCAA
Done.