Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2416
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: 10619
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:508 original size:21 final size:20
Alignment explanation
Indices: 470--508 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
460 TTGAGCTCGT
*
470 TTTAGCTCGTTGAGCTCAAA
1 TTTAGCTCGTTCAGCTCAAA
490 TTTAGCTCGTTTCAGCTCA
1 TTTAGCTCG-TTCAGCTCA
509 TTCCTTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (20 bp):
TTTAGCTCGTTCAGCTCAAA
Found at i:751 original size:13 final size:13
Alignment explanation
Indices: 733--757 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
723 AATAGTTGTG
733 TGTTATTTAATTA
1 TGTTATTTAATTA
746 TGTTATTTAATT
1 TGTTATTTAATT
758 TTGTAGGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:3211 original size:10 final size:10
Alignment explanation
Indices: 3195--3252 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
3185 CAACTCCGAC
3195 CAGCTCAATT
1 CAGCTCAATT
* *
3205 GAGCTCATTT
1 CAGCTCAATT
3215 CAGCTCAA-T
1 CAGCTCAATT
3224 CGAGCTCAATT
1 C-AGCTCAATT
*
3235 TAGCTACAATT
1 CAGCT-CAATT
3246 CAGCTCA
1 CAGCTCA
3253 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:3218 original size:20 final size:20
Alignment explanation
Indices: 3195--3255 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
3185 CAACTCCGAC
3195 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
3215 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
3236 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
3256 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:5389 original size:30 final size:30
Alignment explanation
Indices: 5355--5451 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
5345 TAAACTAAAA
*
5355 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
5385 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
5415 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
5444 ATGAGCTA
1 -TGAGCTA
5452 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:7575 original size:22 final size:22
Alignment explanation
Indices: 7550--7592 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
7540 CACTCTCAAA
7550 TTTCTTTTCATTTCTTTTTCAT
1 TTTCTTTTCATTTCTTTTTCAT
**
7572 TTTCTTTTTTTTTCTTTTTCA
1 TTTCTTTTCATTTCTTTTTCA
7593 AAGGCTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTCTTTTCATTTCTTTTTCAT
Found at i:7591 original size:16 final size:16
Alignment explanation
Indices: 7550--7589 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
7540 CACTCTCAAA
7550 TTTCTTTTCATTTCTT
1 TTTCTTTTCATTTCTT
*
7566 TTTCATTTTC-TTTTTT
1 TTTC-TTTTCATTTCTT
7582 TTTCTTTT
1 TTTCTTTT
7590 TCAAAGGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 13 0.59
17 5 0.23
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTCTTTTCATTTCTT
Found at i:7675 original size:6 final size:5
Alignment explanation
Indices: 7653--7713 Score: 54
Period size: 5 Copynumber: 12.0 Consensus size: 5
7643 CTCTTGCCTC
* *
7653 TCTTT TCTTT T-TATT TCATTT TCTTT TCTTC TC-TT GCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT TC-TTT TCTTT
*
7699 TTTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT
7714 GTTTTCTCTT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
4 3 0.07
5 34 0.76
6 7 0.16
7 1 0.02
ACGTcount: A:0.03, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:7697 original size:36 final size:36
Alignment explanation
Indices: 7655--7723 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
7645 CTTGCCTCTC
7655 TTTTCTTTTTATTTCATTTTCTTT-TCTTCTCTTGCT
1 TTTTCTTTTTATTTC-TTTTCTTTGTCTTCTCTTGCT
* *
7691 TTTTCTTTTTTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTATTTCTTTTCTTTGTCTTCTCTT
7724 TACAAGAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 8 0.27
36 22 0.73
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (36 bp):
TTTTCTTTTTATTTCTTTTCTTTGTCTTCTCTTGCT
Found at i:8645 original size:10 final size:10
Alignment explanation
Indices: 8630--8668 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
8620 TTTTAACTCG
8630 ATTTTTTTTA
1 ATTTTTTTTA
*
8640 ATTTTTTTTCG
1 ATTTTTTTT-A
8651 A-TTTTTTTA
1 ATTTTTTTTA
8660 ATTTTTTTT
1 ATTTTTTTT
8669 TCGAATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 1 0.04
10 23 0.92
11 1 0.04
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (10 bp):
ATTTTTTTTA
Found at i:8672 original size:21 final size:21
Alignment explanation
Indices: 8627--8668 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
8617 TTTTTTTAAC
8627 TCGATTTTTTTTAATTTTTTT
1 TCGATTTTTTTTAATTTTTTT
8648 TCGA-TTTTTTTAATTTTTTT
1 TCGATTTTTTTTAATTTTTTT
8668 T
1 T
8669 TCGAATTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.76
Consensus pattern (21 bp):
TCGATTTTTTTTAATTTTTTT
Found at i:10396 original size:30 final size:30
Alignment explanation
Indices: 10362--10458 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
10352 TAAACTAAAA
10362 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
10392 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
10422 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
10451 ATGAGCTA
1 -TGAGCTA
10459 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Done.