Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3376
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: 35170
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:15878 original size:23 final size:22
Alignment explanation
Indices: 15827--15878 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
15817 CCTCGTCTTT
*
15827 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
15849 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
15872 TTCTTTT
1 TTCTTTT
15879 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:20248 original size:46 final size:46
Alignment explanation
Indices: 20195--20288 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
20185 AAAAGAAAAG
*
20195 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
20241 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
20287 AC
1 AC
20289 GCCACACTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
Found at i:21532 original size:21 final size:23
Alignment explanation
Indices: 21487--21533 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
21477 TCACCTGCAA
* *
21487 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
21510 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
21531 TAA
1 TAA
21534 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:26899 original size:16 final size:17
Alignment explanation
Indices: 26869--26909 Score: 66
Period size: 16 Copynumber: 2.4 Consensus size: 17
26859 CTTCTTCTTC
26869 TTTTTCACGAAAATTTTT
1 TTTTTCACG-AAATTTTT
26887 TTTTTCACG-AATTTTT
1 TTTTTCACGAAATTTTT
26903 TTTTTCA
1 TTTTTCA
26910 ACTTGATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 14 0.61
18 9 0.39
ACGTcount: A:0.22, C:0.12, G:0.05, T:0.61
Consensus pattern (17 bp):
TTTTTCACGAAATTTTT
Found at i:26968 original size:11 final size:11
Alignment explanation
Indices: 26952--26996 Score: 72
Period size: 11 Copynumber: 4.0 Consensus size: 11
26942 AACCAAATTT
26952 TTTTTTTTGAA
1 TTTTTTTTGAA
26963 TTTTTTTTTGAA
1 -TTTTTTTTGAA
*
26975 TTTTTTTTTAA
1 TTTTTTTTGAA
26986 TTTTTTTTGAA
1 TTTTTTTTGAA
26997 GAAACTACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 20 0.65
12 11 0.35
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:26968 original size:12 final size:12
Alignment explanation
Indices: 26951--26993 Score: 79
Period size: 12 Copynumber: 3.7 Consensus size: 12
26941 AAACCAAATT
26951 TTTTTTTTTGAA
1 TTTTTTTTTGAA
26963 TTTTTTTTTGAA
1 TTTTTTTTTGAA
26975 TTTTTTTTT-AA
1 TTTTTTTTTGAA
26986 TTTTTTTT
1 TTTTTTTT
26994 GAAGAAACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 10 0.32
12 21 0.68
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:26993 original size:14 final size:14
Alignment explanation
Indices: 26947--26983 Score: 60
Period size: 12 Copynumber: 2.8 Consensus size: 14
26937 ATGGAAACCA
26947 AATTTTTTTTTTTG
1 AATTTTTTTTTTTG
26961 AA--TTTTTTTTTG
1 AATTTTTTTTTTTG
26973 AATTTTTTTTT
1 AATTTTTTTTT
26984 AATTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 12 0.57
14 9 0.43
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.78
Consensus pattern (14 bp):
AATTTTTTTTTTTG
Found at i:28006 original size:21 final size:23
Alignment explanation
Indices: 27961--28007 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
27951 TCACCTGCAA
* *
27961 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
27984 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
28005 TAA
1 TAA
28008 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:32446 original size:79 final size:80
Alignment explanation
Indices: 32347--32567 Score: 202
Period size: 80 Copynumber: 2.8 Consensus size: 80
32337 CTCGTTCAAG
* * ** * *
32347 TGCCTTCGGGACATAGCCCGGTCA-TAGTAACTCATTC-AATGCCTTCGGGACTTAACCCGGATT
1 TGCCTTCGGGACATAACCCGG-AATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGA-A
*
32410 TTAA-AACTCGCACGAA
64 TTAATAACTCGCACAAA
* * *
32426 TGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAGGCCTTCGGGACTTAACCCGGAATT
1 TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
32491 AATAACTCGCACAAA
66 AATAACTCGCACAAA
* * ** * * *
32506 TACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGA-CATAACCCGGAAT-TAGTAACTCA-CACAAAGGCCTTCGGGACTTAACCCGGA
32568 CAGCATTCAA
Statistics
Matches: 118, Mismatches: 18, Indels: 11
0.80 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 37 0.31
80 74 0.63
81 6 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
AATAACTCGCACAAA
Found at i:32498 original size:80 final size:80
Alignment explanation
Indices: 32387--32567 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
32377 CTCATTCAAT
* * *
32387 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
32450 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
32466 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
32530 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
32547 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
32568 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:32527 original size:40 final size:40
Alignment explanation
Indices: 32384--32567 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
32374 TAACTCATTC
* *
32384 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
32424 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
32464 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
32504 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
32545 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
32568 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Done.