Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_65 ID=scaffold_65-JGI_221_v2.0
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: 19760
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.32
Warning! 1902 characters in sequence are not A, C, G, or T
Found at i:4025 original size:14 final size:15
Alignment explanation
Indices: 4008--4068 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 15
3998 GATAAACTAA
4008 AAATATT-TTAAATT
1 AAATATTATTAAATT
4022 AAATATTATTAAA-T
1 AAATATTATTAAATT
* *
4036 -AATTTTATAAAATT
1 AAATATTATTAAATT
* *
4050 -ATTA-TATTATATT
1 AAATATTATTAAATT
4063 AAATAT
1 AAATAT
4069 AAATATAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
13 17 0.47
14 14 0.39
15 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATATTATTAAATT
Found at i:4559 original size:6 final size:6
Alignment explanation
Indices: 4513--4561 Score: 52
Period size: 5 Copynumber: 8.7 Consensus size: 6
4503 TAAATTTCTT
*
4513 ATTAAA A-TAAA AAT-AA ATATAAA ATTAAA ATT-AA ATT-AA ATTAAA
1 ATTAAA ATTAAA ATTAAA AT-TAAA ATTAAA ATTAAA ATTAAA ATTAAA
4558 ATTA
1 ATTA
4562 TTTTTTAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 18 0.47
6 16 0.42
7 4 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATTAAA
Found at i:4560 original size:11 final size:11
Alignment explanation
Indices: 4513--4561 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
4503 TAAATTTCTT
*
4513 ATTAAAATAAA
1 ATTAAATTAAA
*
4524 AATAAATATAAA
1 ATTAAAT-TAAA
4536 ATTAAAATT-AA
1 ATT-AAATTAAA
4547 ATTAAATTAAA
1 ATTAAATTAAA
4558 ATTA
1 ATTA
4562 TTTTTTAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
10 5 0.16
11 16 0.50
12 7 0.22
13 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATTAAATTAAA
Found at i:5270 original size:27 final size:28
Alignment explanation
Indices: 5239--5326 Score: 71
Period size: 28 Copynumber: 3.3 Consensus size: 28
5229 AGTGTAAAAC
5239 TATAAAAA-AATTAAAAATTAAAAATAT
1 TATAAAAAGAATTAAAAATTAAAAATAT
** *
5266 TATAAAAAGTTTTAAATATGT-AAAATAT
1 TATAAAAAGAATTAAAAAT-TAAAAATAT
* *
5294 TA-AAAAATAA--AAAATAATAAAAAT-T
1 TATAAAAAGAATTAAAA-ATTAAAAATAT
5319 TATAAAAA
1 TATAAAAA
5327 ATAATAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
25 7 0.15
26 11 0.23
27 13 0.27
28 16 0.33
29 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (28 bp):
TATAAAAAGAATTAAAAATTAAAAATAT
Found at i:5307 original size:17 final size:18
Alignment explanation
Indices: 5287--5336 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 18
5277 TTAAATATGT
*
5287 AAAATATTAAAAA-ATAA
1 AAAATAATAAAAATATAA
5304 AAAATAATAAAAATTTATAA
1 AAAATAATAAAAA--TATAA
5324 AAAATAATAAAAA
1 AAAATAATAAAAA
5337 CAACACATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 12 0.41
20 17 0.59
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAATAATAAAAATATAA
Found at i:5336 original size:10 final size:10
Alignment explanation
Indices: 5295--5336 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
5285 GTAAAATATT
5295 AAAA-AATAA
1 AAAATAATAA
5304 AAAATAATAA
1 AAAATAATAA
* *
5314 AAATTTATAA
1 AAAATAATAA
5324 AAAATAATAA
1 AAAATAATAA
5334 AAA
1 AAA
5337 CAACACATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
9 4 0.14
10 24 0.86
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAATAATAA
Found at i:5612 original size:17 final size:18
Alignment explanation
Indices: 5584--5617 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5574 ATATGAGTCT
5584 AAAATTATAAAAAAATTA
1 AAAATTATAAAAAAATTA
*
5602 AAAATTA-AAAATAATT
1 AAAATTATAAAAAAATT
5618 TTTTTTTCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATTATAAAAAAATTA
Found at i:16106 original size:18 final size:18
Alignment explanation
Indices: 16083--16120 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
16073 ATTAATTGAA
* *
16083 AATTAATTTAGTTAAATT
1 AATTAATTAAATTAAATT
16101 AATTAATTAAATTAAATT
1 AATTAATTAAATTAAATT
16119 AA
1 AA
16121 AAATATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
AATTAATTAAATTAAATT
Done.