Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2919
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: 16958
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Found at i:4263 original size:46 final size:46
Alignment explanation
Indices: 4206--4381 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
4196 TATTTGGGCA
4206 TCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
** * *
4252 TCTGAACTCGTTGAGTTGAGTCCGAGTTCA-TGA--GATG-TAACTAGG
1 TCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * *
4297 CATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATACGAACG
1 --TCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
4345 CCCAAGCACTTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
4382 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 60 0.57
47 28 0.26
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (46 bp):
TCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:4361 original size:93 final size:93
Alignment explanation
Indices: 4202--4374 Score: 267
Period size: 93 Copynumber: 1.9 Consensus size: 93
4192 AGGATATTTG
* * * ** *
4202 GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCTGAACTCGTTGAG
1 GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATACGAACGTCCCAACACGTTGAG
4267 TTGAGTCCGAGTTCATGAGATGTAACTA
66 TTGAGTCCGAGTTCATGAGATGTAACTA
*
4295 GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATACGAACG-CCCAAGCACTTTGA
1 GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATACGAACGTCCCAA-CACGTTGA
4359 GTTGAGTCCGAGTTCA
65 GTTGAGTCCGAGTTCA
4375 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
92 3 0.04
93 69 0.96
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (93 bp):
GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATACGAACGTCCCAACACGTTGAG
TTGAGTCCGAGTTCATGAGATGTAACTA
Found at i:4719 original size:17 final size:17
Alignment explanation
Indices: 4699--4739 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
4689 TTGCATGTGA
4699 GCTTACTAAGCATTTAT
1 GCTTACTAAGCATTTAT
**
4716 GCTTACTCCGCATTTAT
1 GCTTACTAAGCATTTAT
4733 GCTTACT
1 GCTTACT
4740 CCCTCCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.41
Consensus pattern (17 bp):
GCTTACTAAGCATTTAT
Found at i:4740 original size:17 final size:17
Alignment explanation
Indices: 4708--4741 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4698 AGCTTACTAA
4708 GCATTTATGCTTACTCC
1 GCATTTATGCTTACTCC
4725 GCATTTATGCTTACTCC
1 GCATTTATGCTTACTCC
4742 CTCCTTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.12, T:0.41
Consensus pattern (17 bp):
GCATTTATGCTTACTCC
Found at i:7539 original size:27 final size:27
Alignment explanation
Indices: 7508--7684 Score: 203
Period size: 27 Copynumber: 6.6 Consensus size: 27
7498 TAAATTGTAC
*
7508 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
7535 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
7561 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
7589 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
7616 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
7643 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
7670 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
7685 GACTAATATA
Statistics
Matches: 128, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
27 128 1.00
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:7569 original size:54 final size:55
Alignment explanation
Indices: 7508--7684 Score: 225
Period size: 54 Copynumber: 3.3 Consensus size: 55
7498 TAAATTGTAC
* **
7508 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
* * ** *
7563 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATG-T
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
* * *
7616 AGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
*
7670 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
7685 GACTAATATA
Statistics
Matches: 105, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
53 1 0.01
54 104 0.99
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (55 bp):
AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
Found at i:7648 original size:81 final size:81
Alignment explanation
Indices: 7509--7663 Score: 231
Period size: 81 Copynumber: 1.9 Consensus size: 81
7499 AAATTGTACA
* * *
7509 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGT
7574 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
** *
7590 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAGTG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAGTG
*
7654 TGCGAGTTGA
65 TGCGAATTGA
7664 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
80 1 0.02
81 65 0.98
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:7675 original size:81 final size:81
Alignment explanation
Indices: 7505--7684 Score: 227
Period size: 81 Copynumber: 2.2 Consensus size: 81
7495 GATTAAATTG
* * *
7505 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
7570 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
7586 TGCGGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTA
1 TACAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTA
* **
7650 AGTGTGCGAGTTGATTA
65 AGTGTGCGAATTGACCA
* *
7667 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
7685 GACTAATATA
Statistics
Matches: 83, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
80 1 0.01
81 82 0.99
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:15453 original size:27 final size:27
Alignment explanation
Indices: 15422--15599 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
15412 TAAATTGTAC
*
15422 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
15449 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
15475 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
15503 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
15530 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * *
15558 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
15585 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
15600 GACTTAATAT
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 105 0.81
28 25 0.19
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:15483 original size:54 final size:55
Alignment explanation
Indices: 15422--15599 Score: 227
Period size: 54 Copynumber: 3.3 Consensus size: 55
15412 TAAATTGTAC
* **
15422 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
* * ** *
15477 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATG-T
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
* *
15530 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
*
15585 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
15600 GACTTAATAT
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
53 1 0.01
54 60 0.57
55 45 0.42
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
Done.