Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1160
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: 31401
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Found at i:4563 original size:31 final size:32
Alignment explanation
Indices: 4528--4667 Score: 169
Period size: 32 Copynumber: 4.4 Consensus size: 32
4518 AATCGCTACT
* *
4528 AGCCATAAGTA-CAGTAATATGATTGGCACAA
1 AGCCATCAGTAGCAGTAATATGATCGGCACAA
* *
4559 AGCCATCAGTAGTAGTAATATGATC-ACACAA
1 AGCCATCAGTAGCAGTAATATGATCGGCACAA
* * *
4590 AGCCATCAGTAGAAGTGATATGATCGGCACAC
1 AGCCATCAGTAGCAGTAATATGATCGGCACAA
* *
4622 AGCCTAT-AGTAACAGTAATATGACCGGCACAA
1 AGCC-ATCAGTAGCAGTAATATGATCGGCACAA
4654 AGCCATCAGTAGCA
1 AGCCATCAGTAGCA
4668 TCGCAAACAA
Statistics
Matches: 91, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
31 40 0.44
32 49 0.54
33 2 0.02
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (32 bp):
AGCCATCAGTAGCAGTAATATGATCGGCACAA
Found at i:4639 original size:63 final size:64
Alignment explanation
Indices: 4544--4665 Score: 167
Period size: 63 Copynumber: 1.9 Consensus size: 64
4534 AAGTACAGTA
* ** *
4544 ATATGATTGGCACAAAGCCATCAGTAGTAGTAATATGATC-ACACAAAGCCATCAGTAGAAGTG
1 ATATGATCGGCACAAAGCCATCAGTAACAGTAATATGACCGACACAAAGCCATCAGTAGAAGTG
* *
4607 ATATGATCGGCACACAGCCTAT-AGTAACAGTAATATGACCGGCACAAAGCCATCAGTAG
1 ATATGATCGGCACAAAGCC-ATCAGTAACAGTAATATGACCGACACAAAGCCATCAGTAG
4666 CATCGCAAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
63 32 0.63
64 19 0.37
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (64 bp):
ATATGATCGGCACAAAGCCATCAGTAACAGTAATATGACCGACACAAAGCCATCAGTAGAAGTG
Found at i:4752 original size:26 final size:27
Alignment explanation
Indices: 4709--4773 Score: 91
Period size: 26 Copynumber: 2.5 Consensus size: 27
4699 AGCAAAGCTG
4709 CCAGTAACAGTATATGTGCCA-AGCCA
1 CCAGTAACAGTATATGTGCCAGAGCCA
*
4735 CCAGTAACAGTGAT-TGTGTCAGAGCCA
1 CCAGTAACAGT-ATATGTGCCAGAGCCA
4762 CCAGT-ACAGTAT
1 CCAGTAACAGTAT
4774 TTCCTCCATA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
25 2 0.06
26 22 0.61
27 12 0.33
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.22
Consensus pattern (27 bp):
CCAGTAACAGTATATGTGCCAGAGCCA
Found at i:4940 original size:23 final size:24
Alignment explanation
Indices: 4835--4944 Score: 123
Period size: 24 Copynumber: 4.6 Consensus size: 24
4825 TCCATGCTCA
** *
4835 AAATCAGTCATACAATTCACAGAC
1 AAATCAGTCATTTAAATCACAGAC
***
4859 AAATCAGTCATACCAATCACAGAC
1 AAATCAGTCATTTAAATCACAGAC
4883 AAATCAGTCATTTAAATCACAGAC
1 AAATCAGTCATTTAAATCACAGAC
* * *
4907 AAATCAGTCATTTACATCTCGGAC
1 AAATCAGTCATTTAAATCACAGAC
*
4931 -AATCAATCATTTAA
1 AAATCAGTCATTTAA
4945 CCTCGAGGAC
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
23 12 0.16
24 64 0.84
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.25
Consensus pattern (24 bp):
AAATCAGTCATTTAAATCACAGAC
Found at i:7334 original size:9 final size:9
Alignment explanation
Indices: 7320--7353 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
7310 TGTGTAAATA
7320 TAATATAAT
1 TAATATAAT
7329 TAATATAAT
1 TAATATAAT
7338 TAATAT-A-
1 TAATATAAT
7345 TAATATAAT
1 TAATATAAT
7354 AGAGATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 6 0.26
8 2 0.09
9 15 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TAATATAAT
Found at i:9395 original size:21 final size:21
Alignment explanation
Indices: 9369--9411 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
9359 GTGATATTCT
*
9369 AACTTTTTATTGATTAAACTA
1 AACTTTTTATTCATTAAACTA
9390 AACTTTTTATTCATTAAACTA
1 AACTTTTTATTCATTAAACTA
9411 A
1 A
9412 GTGAGTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.47
Consensus pattern (21 bp):
AACTTTTTATTCATTAAACTA
Found at i:11554 original size:18 final size:16
Alignment explanation
Indices: 11527--11564 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
11517 ATGATGTGTA
*
11527 AATATAA-T-ATATTT
1 AATATAATTAATATAT
11541 AATATAATTAATATAT
1 AATATAATTAATATAT
11557 AATATAAT
1 AATATAAT
11565 AAGTGACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 1 0.05
16 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATATAATTAATATAT
Found at i:15316 original size:23 final size:23
Alignment explanation
Indices: 15284--15491 Score: 158
Period size: 22 Copynumber: 9.1 Consensus size: 23
15274 TATGTAAAGA
15284 GTAT-ATTGGTTGTGTTTGGAGG
1 GTATAATTGGTTGTGTTTGGAGG
*
15306 GTATAGTTGGTTGTGTTTGGAGG
1 GTATAATTGGTTGTGTTTGGAGG
* * * * *
15329 TTATATATATGGTGGTATTTTGCA-A
1 GTATA-AT-TGGTTGT-GTTTGGAGG
* * * * **
15354 GTACATTTGATTATGTTCAGAGG
1 GTATAATTGGTTGTGTTTGGAGG
*
15377 GTA-AATTGGTTGTGTTTGGAAG
1 GTATAATTGGTTGTGTTTGGAGG
* *
15399 GTATACTTGGTTGTGTTCGGAGG
1 GTATAATTGGTTGTGTTTGGAGG
*
15422 TTATATATATGGTTGTGTTTGGAGG
1 GTATA-AT-TGGTTGTGTTTGGAGG
* *
15447 GTA-AATTGGTTGTGTTTCGAGA
1 GTATAATTGGTTGTGTTTGGAGG
*
15469 GTA-AATTGGTTTTGTTTGG-GG
1 GTATAATTGGTTGTGTTTGGAGG
15490 GT
1 GT
15492 GATAGCTTTA
Statistics
Matches: 142, Mismatches: 36, Indels: 17
0.73 0.18 0.09
Matches are distributed among these distances:
21 3 0.02
22 54 0.38
23 50 0.35
24 4 0.03
25 26 0.18
26 5 0.04
ACGTcount: A:0.19, C:0.03, G:0.34, T:0.44
Consensus pattern (23 bp):
GTATAATTGGTTGTGTTTGGAGG
Found at i:19706 original size:23 final size:23
Alignment explanation
Indices: 19660--19824 Score: 147
Period size: 23 Copynumber: 7.2 Consensus size: 23
19650 GATATGTTGA
*
19660 AGGGTAT-ATTGATTGTGTTTGG
1 AGGGTATAATTGGTTGTGTTTGG
* *
19682 AGGGTATAGTTGGTTGTGTTCGG
1 AGGGTATAATTGGTTGTGTTTGG
* * *
19705 AGGTTATATATATGGTTTTGTTTTG
1 AGGGTATA-AT-TGGTTGTGTTTGG
* * *
19730 AGGGTACATTTGGTTGTGTTCGG
1 AGGGTATAATTGGTTGTGTTTGG
*
19753 AGGGTA-AATTAGTTGTGTTTGG
1 AGGGTATAATTGGTTGTGTTTGG
* ** *
19775 AGGCTATGTTTTGTTGTGTTTGG
1 AGGGTATAATTGGTTGTGTTTGG
*
19798 AGGGTA-AATTGGTTGTATTTGG
1 AGGGTATAATTGGTTGTGTTTGG
*
19820 TGGGT
1 AGGGT
19825 GATAGATTTA
Statistics
Matches: 112, Mismatches: 27, Indels: 8
0.76 0.18 0.05
Matches are distributed among these distances:
22 41 0.37
23 53 0.47
24 2 0.02
25 16 0.14
ACGTcount: A:0.16, C:0.02, G:0.36, T:0.45
Consensus pattern (23 bp):
AGGGTATAATTGGTTGTGTTTGG
Found at i:19793 original size:45 final size:45
Alignment explanation
Indices: 19660--19824 Score: 170
Period size: 45 Copynumber: 3.6 Consensus size: 45
19650 GATATGTTGA
* *
19660 AGGGTATATTGATTGTGTTTGGAGGGTATAG-TTGGTTGTGTTCGG
1 AGGGTAAATTGGTTGTGTTTGGAGGGTAT-GTTTGGTTGTGTTCGG
* * * **
19705 AGGTTATATATATGGTTTTGTTTTGAGGGTACATTTGGTTGTGTTCGG
1 AGGGTA-A-AT-TGGTTGTGTTTGGAGGGTATGTTTGGTTGTGTTCGG
* * * *
19753 AGGGTAAATTAGTTGTGTTTGGAGGCTATGTTTTGTTGTGTTTGG
1 AGGGTAAATTGGTTGTGTTTGGAGGGTATGTTTGGTTGTGTTCGG
* *
19798 AGGGTAAATTGGTTGTATTTGGTGGGT
1 AGGGTAAATTGGTTGTGTTTGGAGGGT
19825 GATAGATTTA
Statistics
Matches: 96, Mismatches: 20, Indels: 8
0.77 0.16 0.06
Matches are distributed among these distances:
45 56 0.58
46 2 0.02
47 3 0.03
48 35 0.36
ACGTcount: A:0.16, C:0.02, G:0.36, T:0.45
Consensus pattern (45 bp):
AGGGTAAATTGGTTGTGTTTGGAGGGTATGTTTGGTTGTGTTCGG
Found at i:22885 original size:27 final size:27
Alignment explanation
Indices: 22841--23120 Score: 355
Period size: 27 Copynumber: 10.4 Consensus size: 27
22831 TGCGATTTGT
* *
22841 GGGTAAAATGATCAAAATACCCTTGAA
1 GGGTAAAATGATCGAAATACCCTCGAA
* * *
22868 GGTTAAAATGACCGAAATACGCTCGAA
1 GGGTAAAATGATCGAAATACCCTCGAA
* *
22895 GGGTAAAATAACCGAAATACCCTCGAA
1 GGGTAAAATGATCGAAATACCCTCGAA
* *
22922 GGGTAAAATAACCGAAATACCCTCGAA
1 GGGTAAAATGATCGAAATACCCTCGAA
*
22949 GGGTAAAATGATCGAAATACCCTCCAA
1 GGGTAAAATGATCGAAATACCCTCGAA
* *
22976 GGGTAAAATGAAT-AAAACACCCTCGAA
1 GGGTAAAATG-ATCGAAATACCCTCGAA
*
23003 GGGTAAAATGACCGAAATACCCTCGAA
1 GGGTAAAATGATCGAAATACCCTCGAA
*
23030 GGGTAAAATGATTGAAATACCCTCGAA
1 GGGTAAAATGATCGAAATACCCTCGAA
* * * *
23057 GAGTAAAATGATAGAAATACCCCCGAT
1 GGGTAAAATGATCGAAATACCCTCGAA
* * *
23084 GTGTAAAATGATCGAAATACCCCCAAA
1 GGGTAAAATGATCGAAATACCCTCGAA
23111 GGGTAAAATG
1 GGGTAAAATG
23121 TCTGCTATAC
Statistics
Matches: 223, Mismatches: 28, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
26 1 0.00
27 220 0.99
28 2 0.01
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.18
Consensus pattern (27 bp):
GGGTAAAATGATCGAAATACCCTCGAA
Found at i:23340 original size:25 final size:25
Alignment explanation
Indices: 23309--23378 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
23299 TACTGTTACC
23309 GGCAGCTTTGCTGCGTTATTATTCT
1 GGCAGCTTTGCTGCGTTATTATTCT
23334 GGCAGCTTT-CTTGCGTTATTATTCT
1 GGCAGCTTTGC-TGCGTTATTATTCT
* *
23359 GGTAGCTTTGCTGCGATATT
1 GGCAGCTTTGCTGCGTTATT
23379 GGTGTGTTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
24 1 0.02
25 39 0.95
26 1 0.02
ACGTcount: A:0.13, C:0.19, G:0.24, T:0.44
Consensus pattern (25 bp):
GGCAGCTTTGCTGCGTTATTATTCT
Found at i:23744 original size:21 final size:21
Alignment explanation
Indices: 23718--23767 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
23708 ACAACTAAAC
*
23718 TAAACTAAACTTTGTATTGAT
1 TAAACTAAACTTTGTATTCAT
*
23739 TAAACTAAACTTTTTATTCAT
1 TAAACTAAACTTTGTATTCAT
23760 TAAACTAA
1 TAAACTAA
23768 GTGAGTTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (21 bp):
TAAACTAAACTTTGTATTCAT
Found at i:28088 original size:20 final size:21
Alignment explanation
Indices: 28065--28109 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
28055 AGGTGAGATT
* *
28065 CTAAA-TTTTTATTGATTAAA
1 CTAAACTTTGTATTCATTAAA
28085 CTAAACTTTGTATTCATTAAA
1 CTAAACTTTGTATTCATTAAA
28106 CTAA
1 CTAA
28110 GTGAGTTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.44
Consensus pattern (21 bp):
CTAAACTTTGTATTCATTAAA
Done.