Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2150
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: 31559
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Found at i:3984 original size:13 final size:13
Alignment explanation
Indices: 3966--3990 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3956 TAACCTACAA
3966 AATTAAATAACAT
1 AATTAAATAACAT
3979 AATTAAATAACA
1 AATTAAATAACA
3991 CACAACTATT
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAAATAACAT
Found at i:11515 original size:30 final size:30
Alignment explanation
Indices: 11481--11577 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
11471 TAAACTAAAA
11481 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
11511 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
11541 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
11570 ATGAGCTA
1 -TGAGCTA
11578 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
Found at i:13718 original size:15 final size:15
Alignment explanation
Indices: 13695--13737 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
13685 TCACTCTCAA
13695 ATTTCTTTTCATTTC
1 ATTTCTTTTCATTTC
*
13710 ATTTTTTTTCATTTTC
1 ATTTCTTTTCA-TTTC
*
13726 TTTTGCTTTTCA
1 ATTT-CTTTTCA
13738 AAGGCTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 10 0.43
16 7 0.30
17 6 0.26
ACGTcount: A:0.12, C:0.16, G:0.02, T:0.70
Consensus pattern (15 bp):
ATTTCTTTTCATTTC
Found at i:13747 original size:12 final size:12
Alignment explanation
Indices: 13732--13762 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
13722 TTTCTTTTGC
13732 TTTTCAAAGGCT
1 TTTTCAAAGGCT
13744 TTTTCAAAGGCT
1 TTTTCAAAGGCT
13756 TTTTCAA
1 TTTTCAA
13763 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:13832 original size:6 final size:5
Alignment explanation
Indices: 13810--13884 Score: 64
Period size: 5 Copynumber: 14.0 Consensus size: 5
13800 CTCTTGCCTC
*
13810 TCTTT TCTTT T-TATT TCATTT TCTTTT TCTTCT TCTTT GCTTTT TCTTTT
1 TCTTT TCTTT TCT-TT TC-TTT TC-TTT TCTT-T TCTTT TC-TTT TC-TTT
13860 TCTTT TCTTT TCTTT T-TTT CTCTTT
1 TCTTT TCTTT TCTTT TCTTT -TCTTT
13885 ACAAGAATGT
Statistics
Matches: 60, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
4 4 0.07
5 28 0.47
6 27 0.45
7 1 0.02
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:13858 original size:23 final size:22
Alignment explanation
Indices: 13828--13876 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 22
13818 TTTTATTTCA
13828 TTTTCTTTTTCTTCTTCTTTGCT
1 TTTTCTTTTTCTT-TTCTTTGCT
*
13851 TTTTCTTTTTCTTTTCTTTTCT
1 TTTTCTTTTTCTTTTCTTTGCT
13873 TTTT
1 TTTT
13877 TTCTCTTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (22 bp):
TTTTCTTTTTCTTTTCTTTGCT
Found at i:13877 original size:17 final size:17
Alignment explanation
Indices: 13810--13876 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 17
13800 CTCTTGCCTC
*
13810 TCTTTTC-TTTT-TATT
1 TCTTTTCTTTTTCTTTT
*
13825 TCATTTTCTTTTTCTTCT
1 TC-TTTTCTTTTTCTTTT
*
13843 TCTTTGCTTTTTCTTTT
1 TCTTTTCTTTTTCTTTT
13860 TCTTTTC-TTTTCTTTT
1 TCTTTTCTTTTTCTTTT
13876 T
1 T
13877 TTCTCTTTAC
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
15 2 0.05
16 15 0.34
17 23 0.52
18 4 0.09
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (17 bp):
TCTTTTCTTTTTCTTTT
Found at i:14753 original size:10 final size:10
Alignment explanation
Indices: 14738--14777 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
14728 ATATACTTCG
*
14738 ATTTTTTTTT
1 ATTTTTTTTA
*
14748 ATTTTTTTCA
1 ATTTTTTTTA
14758 ATTTTTTTTAA
1 ATTTTTTTT-A
14769 ATTTTTTTT
1 ATTTTTTTT
14778 CGAATTTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (10 bp):
ATTTTTTTTA
Found at i:14783 original size:12 final size:11
Alignment explanation
Indices: 14749--14784 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
14739 TTTTTTTTTA
14749 TTTTTTTCAAT
1 TTTTTTTCAAT
*
14760 TTTTTTTAAAT
1 TTTTTTTCAAT
14771 TTTTTTTCGAAT
1 TTTTTTTC-AAT
14783 TT
1 TT
14785 CCTCTTCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 17 0.77
12 5 0.23
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.72
Consensus pattern (11 bp):
TTTTTTTCAAT
Found at i:16511 original size:30 final size:30
Alignment explanation
Indices: 16477--16573 Score: 72
Period size: 30 Copynumber: 3.2 Consensus size: 30
16467 TAAACTAAAA
16477 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
16507 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* * * *
16537 TAAGTTGAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
16566 ATGAGCTA
1 -TGAGCTA
16574 GGAGTGAGCT
Statistics
Matches: 45, Mismatches: 19, Indels: 6
0.64 0.27 0.09
Matches are distributed among these distances:
29 2 0.04
30 40 0.89
31 3 0.07
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:23382 original size:12 final size:11
Alignment explanation
Indices: 23341--23381 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
23331 CGTATGCAAT
23341 TTTTTTTTCAA
1 TTTTTTTTCAA
23352 TTTTTTTTCAA
1 TTTTTTTTCAA
*
23363 TTTTTTTTCGA
1 TTTTTTTTCAA
23374 TTTTTTTT
1 TTTTTTTT
23382 TTTTTTTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:23388 original size:22 final size:22
Alignment explanation
Indices: 23339--23389 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
23329 ACCGTATGCA
23339 ATTTTTTTTTCAATTTTTTTTC
1 ATTTTTTTTTCAATTTTTTTTC
* *
23361 AATTTTTTTTCGATTTTTTTT-
1 ATTTTTTTTTCAATTTTTTTTC
23382 -TTTTTTTT
1 ATTTTTTTT
23390 GAATCTACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 7 0.27
22 19 0.73
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.80
Consensus pattern (22 bp):
ATTTTTTTTTCAATTTTTTTTC
Found at i:27413 original size:20 final size:20
Alignment explanation
Indices: 27390--27435 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
27380 CCAGCTCGAA
*
27390 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
27410 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
27430 TTAGCT
1 TTAGCT
27436 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:27417 original size:30 final size:30
Alignment explanation
Indices: 27382--27455 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
27372 AGTTTTCCCC
27382 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
27412 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
27442 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
27456 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:29818 original size:20 final size:20
Alignment explanation
Indices: 29795--29841 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
29785 AGGTTAAGAT
*
29795 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
29815 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
29835 TGAGCTG
1 TGAGCTG
29842 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Done.