Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011204.1 Corchorus olitorius cultivar O-4 contig11237, whole genome shotgun sequence
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: 22135
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:106 original size:24 final size:25
Alignment explanation
Indices: 79--135 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
69 TTTTAGCTAC
* *
79 CTATTTATCTATTAT-TCTCTGTAT
1 CTATTTATCTATTATATCTCTATAG
*
103 CTATTTATCTATTTTATCTCTATAG
1 CTATTTATCTATTATATCTCTATAG
128 CTATTTAT
1 CTATTTAT
136 TTTTTTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 14 0.48
25 15 0.52
ACGTcount: A:0.23, C:0.16, G:0.04, T:0.58
Consensus pattern (25 bp):
CTATTTATCTATTATATCTCTATAG
Found at i:131 original size:25 final size:25
Alignment explanation
Indices: 79--143 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 25
69 TTTTAGCTAC
* * *
79 CTATTTATCTATTAT-TCTCTGTAT
1 CTATTTATCTATTTTATCTCTATAG
103 CTATTTATCTATTTTATCTCTATAG
1 CTATTTATCTATTTTATCTCTATAG
*
128 CTATTTAT-TTTTTTAT
1 CTATTTATCTATTTTAT
144 TATTTTACTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
24 21 0.58
25 15 0.42
ACGTcount: A:0.22, C:0.14, G:0.03, T:0.62
Consensus pattern (25 bp):
CTATTTATCTATTTTATCTCTATAG
Found at i:4366 original size:44 final size:44
Alignment explanation
Indices: 4273--4377 Score: 122
Period size: 44 Copynumber: 2.4 Consensus size: 44
4263 ACATAGTATT
4273 GTTATCAAAATTTCATAGGAAGACTATCAAAAGTTCATAAAGAG
1 GTTATCAAAATTTCATAGGAAGACTATCAAAAGTTCATAAAGAG
* * * ** * *
4317 CTTATCAAAATTTCATAGTG-TGATTATCGTAATTTCATATAGAG
1 GTTATCAAAATTTCATAG-GAAGACTATCAAAAGTTCATAAAGAG
*
4361 GTTATCACAATTTCATA
1 GTTATCAAAATTTCATA
4378 TTGTAGTTAT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 50 0.98
45 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.35
Consensus pattern (44 bp):
GTTATCAAAATTTCATAGGAAGACTATCAAAAGTTCATAAAGAG
Found at i:4378 original size:22 final size:22
Alignment explanation
Indices: 4274--4378 Score: 88
Period size: 22 Copynumber: 4.8 Consensus size: 22
4264 CATAGTATTG
*
4274 TTATCAAAATTTCATA-GGAAGA
1 TTATCAAAATTTCATATAG-AGA
* * * *
4296 CTATCAAAAGTTCATAAAGAGC
1 TTATCAAAATTTCATATAGAGA
*
4318 TTATCAAAATTTCATAGT-GTGA
1 TTATCAAAATTTCATA-TAGAGA
** *
4340 TTATCGTAATTTCATATAGAGG
1 TTATCAAAATTTCATATAGAGA
*
4362 TTATCACAATTTCATAT
1 TTATCAAAATTTCATAT
4379 TGTAGTTATA
Statistics
Matches: 65, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
21 1 0.02
22 63 0.97
23 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATATAGAGA
Found at i:7236 original size:18 final size:18
Alignment explanation
Indices: 7213--7308 Score: 84
Period size: 18 Copynumber: 5.3 Consensus size: 18
7203 TACAAAATAT
*
7213 TGTTCCACTACCGTAGGA
1 TGTTCCACTACCGCAGGA
* *
7231 TGTTCCACTACTGCAGAA
1 TGTTCCACTACCGCAGGA
* * *
7249 TGTTGCATTGCCGCAGGA
1 TGTTCCACTACCGCAGGA
* *
7267 TGTTCCACTACTGCAGAA
1 TGTTCCACTACCGCAGGA
* * **
7285 TGTTGCATTGTCGCAGGA
1 TGTTCCACTACCGCAGGA
7303 TGTTCC
1 TGTTCC
7309 GTTGCCGCAA
Statistics
Matches: 58, Mismatches: 20, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 58 1.00
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.30
Consensus pattern (18 bp):
TGTTCCACTACCGCAGGA
Found at i:7274 original size:36 final size:36
Alignment explanation
Indices: 7227--7308 Score: 155
Period size: 36 Copynumber: 2.3 Consensus size: 36
7217 CCACTACCGT
7227 AGGATGTTCCACTACTGCAGAATGTTGCATTGCCGC
1 AGGATGTTCCACTACTGCAGAATGTTGCATTGCCGC
*
7263 AGGATGTTCCACTACTGCAGAATGTTGCATTGTCGC
1 AGGATGTTCCACTACTGCAGAATGTTGCATTGCCGC
7299 AGGATGTTCC
1 AGGATGTTCC
7309 GTTGCCGCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (36 bp):
AGGATGTTCCACTACTGCAGAATGTTGCATTGCCGC
Found at i:19645 original size:56 final size:56
Alignment explanation
Indices: 19560--19674 Score: 203
Period size: 56 Copynumber: 2.1 Consensus size: 56
19550 TCCTGTTGGA
*
19560 AAAACTGATGTGAATAAGAAAACAAAGACAGCCTTGAGAGATTAAGAAACAATGAG
1 AAAACCGATGTGAATAAGAAAACAAAGACAGCCTTGAGAGATTAAGAAACAATGAG
* *
19616 AAAACCGATGTGAATAAGAAAACAGAGACAGCTTTGAGAGATTAAGAAACAATGAG
1 AAAACCGATGTGAATAAGAAAACAAAGACAGCCTTGAGAGATTAAGAAACAATGAG
19672 AAA
1 AAA
19675 CGGCTTTGAG
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.52, C:0.10, G:0.22, T:0.16
Consensus pattern (56 bp):
AAAACCGATGTGAATAAGAAAACAAAGACAGCCTTGAGAGATTAAGAAACAATGAG
Found at i:19661 original size:28 final size:27
Alignment explanation
Indices: 19574--19664 Score: 69
Period size: 28 Copynumber: 3.3 Consensus size: 27
19564 CTGATGTGAA
*
19574 TAAGAAAACAAAGACAGCCTTGAGAGAT
1 TAAGAAAACAGAGACAG-CTTGAGAGAT
* * * * *
19602 TAAG-AAACAATGAGAAAAC-CGATGTGAA
1 TAAGAAAAC-A-GAGACAGCTTGA-GAGAT
19630 TAAGAAAACAGAGACAGCTTTGAGAGAT
1 TAAGAAAACAGAGACAGC-TTGAGAGAT
19658 TAAGAAA
1 TAAGAAA
19665 CAATGAGAAA
Statistics
Matches: 46, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
27 12 0.26
28 24 0.52
29 10 0.22
ACGTcount: A:0.52, C:0.11, G:0.22, T:0.15
Consensus pattern (27 bp):
TAAGAAAACAGAGACAGCTTGAGAGAT
Found at i:20411 original size:17 final size:17
Alignment explanation
Indices: 20389--20421 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20379 TTTGTAAAGT
20389 TTGTTACACTAGATAGG
1 TTGTTACACTAGATAGG
*
20406 TTGTTATACTAGATAG
1 TTGTTACACTAGATAG
20422 CTCTATGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39
Consensus pattern (17 bp):
TTGTTACACTAGATAGG
Done.