Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold708
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: 40114
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:868 original size:40 final size:40
Alignment explanation
Indices: 824--899 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
814 AGTGAATATA
*
824 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACAAGT
1 TCCGGACTAAGACCCGAAGGCATTTGTGCGAGATACAAGT
** * *
864 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATAC
1 TCCGGACTAAGACCCGAAGGCATTTGTGCGAGATAC
900 TAAAATCCGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
TCCGGACTAAGACCCGAAGGCATTTGTGCGAGATACAAGT
Found at i:921 original size:41 final size:40
Alignment explanation
Indices: 837--922 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
827 GGACTAAGAT
**
837 CCGAAGGCATTTGTGCGAGATACAAGTTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACAAAATCCGGGTTAAGCC
* *
877 CCGAAGGCCTTTGTGCGAGATACTAAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAAATCCGGGTTAAGCC
918 CCGAA
1 CCGAA
923 TGTGACAGCC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 22 0.54
41 19 0.46
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGATACAAAATCCGGGTTAAGCC
Found at i:8779 original size:39 final size:40
Alignment explanation
Indices: 8734--8958 Score: 224
Period size: 40 Copynumber: 5.7 Consensus size: 40
8724 GCTCCTCGTT
* * * *
8734 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
8774 C-AATGCCTTCGGGACTTAACCCGGATTTAATGACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
8813 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
8853 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
8893 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
8934 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
8959 CAGCATTCAA
Statistics
Matches: 155, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
39 37 0.24
40 104 0.67
41 14 0.09
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:8827 original size:40 final size:38
Alignment explanation
Indices: 8701--8958 Score: 200
Period size: 40 Copynumber: 6.5 Consensus size: 38
8691 AAATCACGTA
* * *
8701 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCA-AATG
1 CCTTCGGGACTTAACCCGGATTTAG-TACTCG--CACAATG
* * * *
8740 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATG
1 CCTTCGGGACTTAACCCGGATTTAGT-ACTCGCACAATG
*
8779 CCTTCGGGACTTAACCCGGATTTAATGACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGT-ACTCGCAC-AATG
*
8819 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGTA-CTCGCAC-AATG
* *
8859 CCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCACAAATG
1 CCTTCGGGACTTAACCCGG-ATTTAGTA-CTCGCAC-AATG
** * * * *
8899 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAG
1 CCTTCGGGA-CTTAACCCGGATTTAGT-AC-TCGCACAATG
*
8939 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
8959 CAGCATTCAA
Statistics
Matches: 180, Mismatches: 28, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
38 2 0.01
39 50 0.28
40 116 0.64
41 12 0.07
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (38 bp):
CCTTCGGGACTTAACCCGGATTTAGTACTCGCACAATG
Found at i:8967 original size:41 final size:41
Alignment explanation
Indices: 8890--8967 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
8880 CTTGTATCTC
* * *
8890 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
8931 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
8968 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:13478 original size:4 final size:4
Alignment explanation
Indices: 13469--13496 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
13459 AAGTTTTATT
13469 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
13497 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:14418 original size:21 final size:21
Alignment explanation
Indices: 14392--14454 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
14382 TTGGTATTTG
14392 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
14413 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
14434 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
14455 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:16549 original size:21 final size:20
Alignment explanation
Indices: 16521--16568 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
16511 GCAATCAGAC
16521 TTTT-TTTTCATATTTTCTT
1 TTTTCTTTTCATATTTTCTT
* *
16540 GTTTTCTTTTCTTGTTTTCTT
1 -TTTTCTTTTCATATTTTCTT
*
16561 TTTACTTT
1 TTTTCTTT
16569 CTTTTTTACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.06, C:0.12, G:0.04, T:0.77
Consensus pattern (20 bp):
TTTTCTTTTCATATTTTCTT
Found at i:16551 original size:13 final size:13
Alignment explanation
Indices: 16533--16562 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
16523 TTTTTTCATA
16533 TTTTCTTGTTTTC
1 TTTTCTTGTTTTC
16546 TTTTCTTGTTTTC
1 TTTTCTTGTTTTC
16559 TTTT
1 TTTT
16563 TACTTTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (13 bp):
TTTTCTTGTTTTC
Found at i:16563 original size:19 final size:19
Alignment explanation
Indices: 16541--16612 Score: 53
Period size: 19 Copynumber: 3.8 Consensus size: 19
16531 TATTTTCTTG
*
16541 TTTTCTTTTCTTGTTTT-CT
1 TTTTCTTTTCTT-TTTTACA
16560 TTTTAC-TTTCTTTTTTACA
1 TTTT-CTTTTCTTTTTTACA
* *
16579 TTTTCTCTTCTTTCTTTTTCA
1 TTTTCTTTTC-TT-TTTTACA
16600 --TTCTTTTCTTTTT
1 TTTTCTTTTCTTTTT
16613 CATTCAATTG
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
17 3 0.07
18 7 0.16
19 25 0.57
20 3 0.07
21 6 0.14
ACGTcount: A:0.06, C:0.18, G:0.01, T:0.75
Consensus pattern (19 bp):
TTTTCTTTTCTTTTTTACA
Found at i:16607 original size:15 final size:15
Alignment explanation
Indices: 16589--16617 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16579 TTTTCTCTTC
16589 TTTCTTTTTCATTCT
1 TTTCTTTTTCATTCT
16604 TTTCTTTTTCATTC
1 TTTCTTTTTCATTC
16618 AATTGAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTCTTTTTCATTCT
Found at i:17327 original size:21 final size:21
Alignment explanation
Indices: 17301--17363 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
17291 TTGGTATTTG
17301 GGAATTGGCT-CGAAATGGTAT
1 GGAATTGG-TACGAAATGGTAT
17322 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
17343 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
17364 ATGGTTCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 1 0.03
21 21 0.55
22 16 0.42
ACGTcount: A:0.29, C:0.06, G:0.33, T:0.32
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:20075 original size:45 final size:45
Alignment explanation
Indices: 20026--20213 Score: 313
Period size: 45 Copynumber: 4.2 Consensus size: 45
20016 TCGGCCATGG
* * * *
20026 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
20071 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
20116 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* *
20161 TGCTTCCTCAAATTCTCCCAGGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
20206 TGCTTCCT
1 TGCTTCCT
20214 TAATTTCATG
Statistics
Matches: 135, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 135 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:33921 original size:12 final size:13
Alignment explanation
Indices: 33906--33935 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
33896 AAAAAAACTC
33906 AAAAAAATTC-AA
1 AAAAAAATTCGAA
33918 AAAAAAATTCGAA
1 AAAAAAATTCGAA
33931 AAAAA
1 AAAAA
33936 CTAGTTTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.77, C:0.07, G:0.03, T:0.13
Consensus pattern (13 bp):
AAAAAAATTCGAA
Found at i:33990 original size:12 final size:12
Alignment explanation
Indices: 33973--34009 Score: 65
Period size: 12 Copynumber: 3.0 Consensus size: 12
33963 GGATATCAAG
33973 TTGTGAAAAAAA
1 TTGTGAAAAAAA
33985 TTGTGAAAAAAAA
1 TTGTG-AAAAAAA
33998 TTGTGAAAAAAA
1 TTGTGAAAAAAA
34010 AAGAGAGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.24
Consensus pattern (12 bp):
TTGTGAAAAAAA
Found at i:33996 original size:13 final size:13
Alignment explanation
Indices: 33973--34010 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
33963 GGATATCAAG
33973 TTGTG-AAAAAAA
1 TTGTGAAAAAAAA
33985 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
33998 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
34011 AGAGAGCTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 5 0.20
13 20 0.80
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.24
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:35434 original size:20 final size:20
Alignment explanation
Indices: 35411--35457 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
35401 GGGTTAAGAT
*
35411 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
35431 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
35451 TGAGCTG
1 TGAGCTG
35458 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:38493 original size:18 final size:18
Alignment explanation
Indices: 38472--38553 Score: 76
Period size: 18 Copynumber: 4.6 Consensus size: 18
38462 TTTTCACATC
*
38472 CTTTTTCAATCTCAATTT
1 CTTTTTCAATCTCAGTTT
* **
38490 CTTTTTCCATGACAGTTT
1 CTTTTTCAATCTCAGTTT
* *
38508 CTTTTACACTCTC-GTTT
1 CTTTTTCAATCTCAGTTT
* *
38525 CTTTCTTCAATCTCACTCT
1 CTTT-TTCAATCTCAGTTT
38544 CTTTTTCAAT
1 CTTTTTCAAT
38554 TTCTTGTTCC
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
17 8 0.16
18 35 0.71
19 6 0.12
ACGTcount: A:0.17, C:0.27, G:0.04, T:0.52
Consensus pattern (18 bp):
CTTTTTCAATCTCAGTTT
Done.