Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2965
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: 47908
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:7990 original size:15 final size:15
Alignment explanation
Indices: 7970--8006 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
7960 ACTCTCCTCA
**
7970 TTCTTTTCTTTCTTT
1 TTCTTTTCACTCTTT
7985 TTCTTTTCACTCTTT
1 TTCTTTTCACTCTTT
8000 TTCTTTT
1 TTCTTTT
8007 TCTCGCTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.76
Consensus pattern (15 bp):
TTCTTTTCACTCTTT
Found at i:10110 original size:14 final size:14
Alignment explanation
Indices: 10086--10137 Score: 72
Period size: 13 Copynumber: 3.8 Consensus size: 14
10076 AAATTGAATA
10086 CAAACTTTTTTTTTT
1 CAAA-TTTTTTTTTT
*
10101 -GAATTTTTTTTTT
1 CAAATTTTTTTTTT
10114 CAAA-TTTTTTTTT
1 CAAATTTTTTTTTT
10127 CAAATTTTTTT
1 CAAATTTTTTT
10138 ACAATCTCGT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
13 23 0.70
14 10 0.30
ACGTcount: A:0.21, C:0.08, G:0.02, T:0.69
Consensus pattern (14 bp):
CAAATTTTTTTTTT
Found at i:29541 original size:18 final size:18
Alignment explanation
Indices: 29520--29554 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29510 TTTTTCTTTT
29520 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
29538 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
29555 TTTTTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:33011 original size:45 final size:45
Alignment explanation
Indices: 32947--33112 Score: 296
Period size: 45 Copynumber: 3.7 Consensus size: 45
32937 CATGAAATTA
* *
32947 AGGAAGCATTTGACCAACATCATGCATAATTCCTGGGAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
32992 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
33037 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTA
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
33082 AGGAAGCATTTGGCCAACATCATGCATAATT
1 AGGAAGCATTTGACCAACATCATGCATAATT
33113 TATTGATGCG
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 117 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (45 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
Found at i:33293 original size:22 final size:23
Alignment explanation
Indices: 33261--33304 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
33251 GATTCATTAA
*
33261 TTTTTAGTTATTT-TAGTTTGTG
1 TTTTTAATTATTTATAGTTTGTG
33283 TTTTTAATTATTTCATAGTTTG
1 TTTTTAATTATTT-ATAGTTTG
33305 CACATCATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
24 7 0.37
ACGTcount: A:0.18, C:0.02, G:0.14, T:0.66
Consensus pattern (23 bp):
TTTTTAATTATTTATAGTTTGTG
Found at i:35234 original size:21 final size:21
Alignment explanation
Indices: 35208--35250 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
35198 TGTACAGCAC
35208 TAAGTGTGCGATTTGACTATG
1 TAAGTGTGCGATTTGACTATG
35229 TAAGTGTGCGATTTGACTATG
1 TAAGTGTGCGATTTGACTATG
35250 T
1 T
35251 TGCACTAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.28, T:0.40
Consensus pattern (21 bp):
TAAGTGTGCGATTTGACTATG
Found at i:35276 original size:27 final size:27
Alignment explanation
Indices: 35203--35401 Score: 205
Period size: 27 Copynumber: 7.6 Consensus size: 27
35193 TAAATTGTAC
35203 AGCACTAAGTGTGCGATTTGACTA--T
1 AGCACTAAGTGTGCGATTTGACTATGT
35228 -G---TAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
35251 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
35277 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
35305 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
35333 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
35360 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
35387 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
35402 GACTCAATAT
Statistics
Matches: 147, Mismatches: 18, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
21 19 0.13
23 1 0.01
24 2 0.01
27 102 0.69
28 23 0.16
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:35332 original size:82 final size:81
Alignment explanation
Indices: 35229--35380 Score: 225
Period size: 82 Copynumber: 1.9 Consensus size: 81
35219 TTTGACTATG
* *
35229 TAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTGTGCG
1 TAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTGTGCG
35293 AATTGACCATGCGGCAC
65 AATTGACCATGCGGCAC
** *
35310 TAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCG
1 TAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGTGCG
*
35375 AGTTGA
65 AATTGA
35381 TTATATAGCA
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 11 0.17
82 51 0.81
83 1 0.02
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.30
Consensus pattern (81 bp):
TAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGTGCGA
ATTGACCATGCGGCAC
Found at i:35392 original size:82 final size:81
Alignment explanation
Indices: 35229--35401 Score: 213
Period size: 82 Copynumber: 2.1 Consensus size: 81
35219 TTTGACTATG
* *
35229 TAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGTGCGA
1 TAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGTGCGA
* *
35294 ATTGACCATGCGGCAC
66 ATTGACCATACAGCAC
** *
35310 TAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAGTGTGC
1 TAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAGTGTGC
* ** *
35374 GAGTTGATTATATAGCAC
64 GAATTGACCATACAGCAC
*
35392 TGAGTGTGCG
1 TAAGTGTGCG
35402 GACTCAATAT
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
81 12 0.15
82 66 0.85
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (81 bp):
TAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGTGCGA
ATTGACCATACAGCAC
Found at i:43448 original size:55 final size:54
Alignment explanation
Indices: 43332--43511 Score: 157
Period size: 55 Copynumber: 3.3 Consensus size: 54
43322 AAATTGTACA
** * * * *
43332 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGAGCGATTTGACTATGTT
1 GCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTGAGCGAATTGACCATGTG
*
43386 GCACTAAGTGTGCGAAATGAATATG-ATGCACTAAAGTGTGCGAATTGACCAT-TCG
1 GCACTAAGTGTGCGAAATGAATATGTA-GCACT-AAGTGAGCGAATTGACCATGT-G
** * * * ** * *
43441 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGGCGATTTGATTACGTA
1 GCACTAAGTGTGCGA-AATGAATATGTAGCACTAAGTG-AGCGAATTGACCATGTG
43497 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
43512 GTTGATTATA
Statistics
Matches: 103, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
53 1 0.01
54 28 0.27
55 36 0.35
56 36 0.35
57 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (54 bp):
GCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTGAGCGAATTGACCATGTG
Found at i:43461 original size:28 final size:27
Alignment explanation
Indices: 43331--43528 Score: 220
Period size: 27 Copynumber: 7.2 Consensus size: 27
43321 TAAATTGTAC
43331 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
43358 AGCACTAAGTGAGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
43385 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
43411 ATGCACTAAAGTGTGCGAATTGACCAT-T
1 A-GCACT-AAGTGTGCGATTTGACTATGT
*
43439 CGGCACTAAGTGTGCGAGTTTGACTATGT
1 -AGCACTAAGTGTGCGA-TTTGACTATGT
* *
43468 AGCACTAAGTGTGGCGATTTGATTACGT
1 AGCACTAAGTGT-GCGATTTGACTATGT
* * *
43496 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
43523 AGCACT
1 AGCACT
43529 GATGAGCGGA
Statistics
Matches: 145, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
27 80 0.55
28 60 0.41
29 5 0.03
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:46164 original size:13 final size:13
Alignment explanation
Indices: 46146--46193 Score: 69
Period size: 13 Copynumber: 3.6 Consensus size: 13
46136 TAGTTTCTCG
*
46146 AAAAAAAAAACTC
1 AAAAAAAAAATTC
*
46159 AAAAAAAAAATTT
1 AAAAAAAAAATTC
46172 AAAAAAAAAATTC
1 AAAAAAAAAATTC
46185 GAAAAAAAA
1 -AAAAAAAA
46194 CGAGTCCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
13 23 0.74
14 8 0.26
ACGTcount: A:0.79, C:0.06, G:0.02, T:0.12
Consensus pattern (13 bp):
AAAAAAAAAATTC
Found at i:47234 original size:20 final size:21
Alignment explanation
Indices: 47187--47238 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 21
47177 AAGAGAGACG
47187 AGAGAAAAAGAAACTTGAAAA
1 AGAGAAAAAGAAACTTGAAAA
47208 A-AGGAAACAA-AAA-TTGAAAA
1 AGA-GAAA-AAGAAACTTGAAAA
47228 AGAGAAAAAGA
1 AGAGAAAAAGA
47239 TTGGAGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
19 2 0.07
20 14 0.52
21 9 0.33
22 2 0.07
ACGTcount: A:0.69, C:0.04, G:0.19, T:0.08
Consensus pattern (21 bp):
AGAGAAAAAGAAACTTGAAAA
Done.