Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2322
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: 46596
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2653 original size:18 final size:20
Alignment explanation
Indices: 2625--2662 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
2615 GTTGTAAAGT
2625 TTTATTTTTTATTTA-TTTA
1 TTTATTTTTTATTTAGTTTA
2644 TTTA-TTTTTATTTAGTTTA
1 TTTATTTTTTATTTAGTTTA
2663 AATTTTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (20 bp):
TTTATTTTTTATTTAGTTTA
Found at i:4442 original size:22 final size:23
Alignment explanation
Indices: 4408--4451 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
4398 GATGAATTAT
4408 GTATGTCTTTGG-CGAAATTAAA
1 GTATGTCTTTGGCCGAAATTAAA
*
4430 GTATGT-TTCTGGCCGAATTTAA
1 GTATGTCTT-TGGCCGAAATTAA
4452 CTGTATGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 2 0.11
22 9 0.47
23 8 0.42
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (23 bp):
GTATGTCTTTGGCCGAAATTAAA
Found at i:6147 original size:13 final size:13
Alignment explanation
Indices: 6131--6175 Score: 83
Period size: 13 Copynumber: 3.5 Consensus size: 13
6121 AAAAAAAAGG
6131 AAAAAAATTCAAA
1 AAAAAAATTCAAA
6144 AAAAAAATTCAAA
1 AAAAAAATTCAAA
6157 AAAAAAA-TCAAA
1 AAAAAAATTCAAA
6169 AAAAAAA
1 AAAAAAA
6176 AAAAATAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 12 0.38
13 20 0.62
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.11
Consensus pattern (13 bp):
AAAAAAATTCAAA
Found at i:6175 original size:12 final size:12
Alignment explanation
Indices: 6131--6175 Score: 72
Period size: 12 Copynumber: 3.7 Consensus size: 12
6121 AAAAAAAAGG
*
6131 AAAAAAATTCAA
1 AAAAAAAATCAA
6143 AAAAAAAATTCAA
1 AAAAAAAA-TCAA
6156 AAAAAAAATCAA
1 AAAAAAAATCAA
6168 AAAAAAAA
1 AAAAAAAA
6176 AAAAATAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 19 0.61
13 12 0.39
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.11
Consensus pattern (12 bp):
AAAAAAAATCAA
Found at i:8905 original size:20 final size:19
Alignment explanation
Indices: 8879--8924 Score: 74
Period size: 20 Copynumber: 2.4 Consensus size: 19
8869 ACTCATTCCG
*
8879 AGCTCAAGTTAGCTCATTC
1 AGCTCAAGTCAGCTCATTC
8898 ATGCTCAAGTCAGCTCATTC
1 A-GCTCAAGTCAGCTCATTC
8918 AGCTCAA
1 AGCTCAA
8925 TTTAACTCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (19 bp):
AGCTCAAGTCAGCTCATTC
Found at i:9315 original size:20 final size:20
Alignment explanation
Indices: 9280--9317 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
9270 ATGTCTTTGG
*
9280 CCGAATTTAAGTATGTTTCT
1 CCGAATTTAAGCATGTTTCT
*
9300 CCGAATTTATGCATGTTT
1 CCGAATTTAAGCATGTTT
9318 TAAATGGTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.45
Consensus pattern (20 bp):
CCGAATTTAAGCATGTTTCT
Found at i:10925 original size:4 final size:4
Alignment explanation
Indices: 10916--10949 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
10906 TATTTTTATT
*
10916 TTTA TTTA TTTA TTTA TTTA TTTA CTTA GTTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA T
10950 ATTTTTATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 24 0.89
5 3 0.11
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:14712 original size:4 final size:4
Alignment explanation
Indices: 14703--14736 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
14693 TATTTTTATT
*
14703 TTTA TTTA TTTA TTTA TTTA TTTA CTTA GTTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA T
14737 ATTTTTATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 24 0.89
5 3 0.11
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:18083 original size:14 final size:14
Alignment explanation
Indices: 18064--18091 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18054 ATACATTGGA
18064 TAGATTCATGCATG
1 TAGATTCATGCATG
18078 TAGATTCATGCATG
1 TAGATTCATGCATG
18092 GGAAGATGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (14 bp):
TAGATTCATGCATG
Found at i:25343 original size:11 final size:12
Alignment explanation
Indices: 25313--25348 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
25303 GGAAACTAAT
25313 TTTTTTTTCAAA
1 TTTTTTTTCAAA
* *
25325 TTTTTTTTGAAT
1 TTTTTTTTCAAA
25337 TTTTTTTTCAAA
1 TTTTTTTTCAAA
25349 GAAACTACTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.22, C:0.06, G:0.03, T:0.69
Consensus pattern (12 bp):
TTTTTTTTCAAA
Found at i:26936 original size:19 final size:18
Alignment explanation
Indices: 26912--26954 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
26902 ACGAAATTTT
26912 AAAAAAATTGTATATATAA
1 AAAAAAATTGTATATA-AA
*
26931 AAAAAATTTGTATATAAA
1 AAAAAAATTGTATATAAA
26949 AAAAAA
1 AAAAAA
26955 GAGAAAGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (18 bp):
AAAAAAATTGTATATAAA
Found at i:32047 original size:14 final size:14
Alignment explanation
Indices: 32030--32060 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
32020 TTTCTGTTCA
*
32030 CTCTTTTTGTTTTT
1 CTCTTTTTCTTTTT
32044 CTCTTTTTCTTTTT
1 CTCTTTTTCTTTTT
32058 CTC
1 CTC
32061 GCTCAATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.74
Consensus pattern (14 bp):
CTCTTTTTCTTTTT
Found at i:37317 original size:26 final size:27
Alignment explanation
Indices: 37268--37319 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
37258 AAAGAGGGAT
* *
37268 AAAAAAGGAGAGGACGAAACAAAAGAA
1 AAAAAAGAAGAGGACAAAACAAAAGAA
*
37295 AAAAAAGAAGA-GACAAAAGAAAAGA
1 AAAAAAGAAGAGGACAAAACAAAAGA
37320 GTGAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.71, C:0.06, G:0.23, T:0.00
Consensus pattern (27 bp):
AAAAAAGAAGAGGACAAAACAAAAGAA
Found at i:46131 original size:21 final size:23
Alignment explanation
Indices: 46086--46132 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
46076 TCACCTGCAA
* *
46086 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
46109 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
46130 TAA
1 TAA
46133 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
Done.