Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1246
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: 33996
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:6016 original size:112 final size:114
Alignment explanation
Indices: 5852--6132 Score: 403
Period size: 113 Copynumber: 2.5 Consensus size: 114
5842 ATTTAATCAT
*
5852 ATTTAAACATAATTATTATTAAATAT-TTTAATTAAAATATAATTTAATAAAATTCTT-ATAATT
1 ATTTAAA-ATAATAATTATTAAATATATTTAA-TAAAATATAATTTAATAAAATTCTTAATAATT
* * *
5915 AATATTCTTATATG-ATTTACTCAAATCATATATATGATACTGTAAAATATAA
64 AATAGTCTTAT-TGAATTTACTCAAATCATATATATGATACTATAAAAGA-AA
*
5967 A-TTAAAATAATAATTATTAAATATAATTAA-AAAATATAATTTAATAAAATTCTTAATAATTAA
1 ATTTAAAATAATAATTATTAAATATATTTAATAAAATATAATTTAATAAAATTCTTAATAATTAA
6030 TAGTCTTATTGAATTTACTCAAATCATATATATGATACTATAAAAGAAA
66 TAGTCTTATTGAATTTACTCAAATCATATATATGATACTATAAAAGAAA
* *
6079 ATTTGAAATAATAA-TATTAAATATATTTAATTAAAATATTGATTTAATAAAATT
1 ATTTAAAATAATAATTATTAAATATATTTAA-TAAAATA-TAATTTAATAAAATT
6133 TAAAATAATT
Statistics
Matches: 151, Mismatches: 8, Indels: 14
0.87 0.05 0.08
Matches are distributed among these distances:
112 44 0.29
113 77 0.51
114 15 0.10
115 15 0.10
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (114 bp):
ATTTAAAATAATAATTATTAAATATATTTAATAAAATATAATTTAATAAAATTCTTAATAATTAA
TAGTCTTATTGAATTTACTCAAATCATATATATGATACTATAAAAGAAA
Found at i:7959 original size:23 final size:24
Alignment explanation
Indices: 7919--7965 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
7909 CTACGAATCT
*
7919 GCATAAACCAAATGAAAATTATAA
1 GCATAAACCAAATGAAAATAATAA
*
7943 GCATAAA-CAAATTAAAATAATAA
1 GCATAAACCAAATGAAAATAATAA
7966 TCTCCACCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.62, C:0.11, G:0.06, T:0.21
Consensus pattern (24 bp):
GCATAAACCAAATGAAAATAATAA
Found at i:14374 original size:29 final size:30
Alignment explanation
Indices: 14341--14398 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
14331 AAACCTTTTA
14341 TTTTCCCCCAAAA-TTTTACTCCCTCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTCCCAC
* * *
14370 TTTTCCCCTAAAACTTTTATTCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTCCCA
14399 TCCCACCTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.21, C:0.40, G:0.00, T:0.40
Consensus pattern (30 bp):
TTTTCCCCCAAAACTTTTACTCCCTCCCAC
Found at i:15053 original size:5 final size:5
Alignment explanation
Indices: 15043--15068 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
15033 GAACAAATAT
15043 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
15069 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:16475 original size:17 final size:18
Alignment explanation
Indices: 16453--16494 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
16443 GTTCAAGGTG
16453 TAATTAATTTAAA-TT-TT
1 TAATTAA-TTAAATTTATT
16470 TAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
16488 TAATTAA
1 TAATTAA
16495 AAACATATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.22
17 9 0.39
18 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:16490 original size:14 final size:14
Alignment explanation
Indices: 16453--16495 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
16443 GTTCAAGGTG
16453 TAATTAATTTAAATTTT
1 TAATTAA-TTAAA--TT
16470 TAATTAATTAAATT
1 TAATTAATTAAATT
*
16484 TATTTAATTAAA
1 TAATTAATTAAA
16496 AACATATTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 13 0.52
16 5 0.20
17 7 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATTAATTAAATT
Found at i:16691 original size:31 final size:29
Alignment explanation
Indices: 16627--16695 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
16617 ATAATAACGT
** *
16627 AAGTGACTAAAACGTAATATTTCAAACAT
1 AAGTGACTAAAACGTAATATGGCAAACAA
*
16656 AAGTGACTAAAATGTAATATGAGGCAAACAA
1 AAGTGACTAAAACGTAATAT--GGCAAACAA
16687 AAGTGACTA
1 AAGTGACTA
16696 TTTTTATAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.56
31 15 0.44
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.23
Consensus pattern (29 bp):
AAGTGACTAAAACGTAATATGGCAAACAA
Found at i:27826 original size:40 final size:40
Alignment explanation
Indices: 27771--27847 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
27761 ATAATATTTA
27771 TAGACTCGATTTATAAAAATGAGATCTCAGCTTTTTTGTT
1 TAGACTCGATTTATAAAAATGAGATCTCAGCTTTTTTGTT
* *
27811 TAGACTCGATTTATAAAAATGAGGTGTCAGCTTTTTT
1 TAGACTCGATTTATAAAAATGAGATCTCAGCTTTTTT
27848 TTTTTTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.42
Consensus pattern (40 bp):
TAGACTCGATTTATAAAAATGAGATCTCAGCTTTTTTGTT
Found at i:31350 original size:15 final size:15
Alignment explanation
Indices: 31325--31360 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
31315 TGTACAGACA
31325 ATGACATAGTTACAGC
1 ATGA-ATAGTTACAGC
31341 ATGAATAGTTACAGC
1 ATGAATAGTTACAGC
31356 ATGAA
1 ATGAA
31361 AGGGTAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (15 bp):
ATGAATAGTTACAGC
Done.