Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017527.1 Corchorus olitorius cultivar O-4 contig17560, 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: 25974
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:5326 original size:11 final size:11
Alignment explanation
Indices: 5310--5349 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
5300 ATTTTAATTA
5310 ATATATTTAAG
1 ATATATTTAAG
*
5321 ATATATTTAATTA
1 ATATATTTAA--G
5334 ATATATTTAAG
1 ATATATTTAAG
5345 ATATA
1 ATATA
5350 CTAGTTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 15 0.60
13 10 0.40
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (11 bp):
ATATATTTAAG
Found at i:5334 original size:24 final size:24
Alignment explanation
Indices: 5302--5349 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
5292 TTATTTTAAT
5302 TTTAATTAATATATTTAAGATATA
1 TTTAATTAATATATTTAAGATATA
5326 TTTAATTAATATATTTAAGATATA
1 TTTAATTAATATATTTAAGATATA
5350 CTAGTTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (24 bp):
TTTAATTAATATATTTAAGATATA
Found at i:6271 original size:120 final size:120
Alignment explanation
Indices: 6124--6365 Score: 484
Period size: 120 Copynumber: 2.0 Consensus size: 120
6114 AAAATTAACT
6124 TAATTATTTTAAAAAATGATGAATAATTAATGATTAGGTAAATTATTTTAACTTTTAAACTTGAT
1 TAATTATTTTAAAAAATGATGAATAATTAATGATTAGGTAAATTATTTTAACTTTTAAACTTGAT
6189 AATAAGATTTTTGTTAGTTTATATTATAATTAAAATAATTGTAAAAGTTTATCTA
66 AATAAGATTTTTGTTAGTTTATATTATAATTAAAATAATTGTAAAAGTTTATCTA
6244 TAATTATTTTAAAAAATGATGAATAATTAATGATTAGGTAAATTATTTTAACTTTTAAACTTGAT
1 TAATTATTTTAAAAAATGATGAATAATTAATGATTAGGTAAATTATTTTAACTTTTAAACTTGAT
6309 AATAAGATTTTTGTTAGTTTATATTATAATTAAAATAATTGTAAAAGTTTATCTA
66 AATAAGATTTTTGTTAGTTTATATTATAATTAAAATAATTGTAAAAGTTTATCTA
6364 TA
1 TA
6366 CTATATTAAA
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 122 1.00
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (120 bp):
TAATTATTTTAAAAAATGATGAATAATTAATGATTAGGTAAATTATTTTAACTTTTAAACTTGAT
AATAAGATTTTTGTTAGTTTATATTATAATTAAAATAATTGTAAAAGTTTATCTA
Found at i:7594 original size:6 final size:6
Alignment explanation
Indices: 7583--7626 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
7573 ATATAGTAAG
* *
7583 TATAGA TATAGA TATAGA TATAAA TATAAA TATAGA TATAGA TA
1 TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TA
7627 ATTAAAAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (6 bp):
TATAGA
Found at i:9071 original size:12 final size:12
Alignment explanation
Indices: 9054--9080 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
9044 CAATGTGCCT
9054 TTGTCCTAACTC
1 TTGTCCTAACTC
9066 TTGTCCTAACTC
1 TTGTCCTAACTC
9078 TTG
1 TTG
9081 GTTCTATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.30, G:0.11, T:0.44
Consensus pattern (12 bp):
TTGTCCTAACTC
Found at i:10818 original size:32 final size:32
Alignment explanation
Indices: 10780--10841 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
10770 TCAGATTGGG
10780 TTAAATTTGGGTCAGATCGATTTGGGTTCGAA
1 TTAAATTTGGGTCAGATCGATTTGGGTTCGAA
* *
10812 TTAAATTTGGGTCAGGTTGATTTGGGTTCG
1 TTAAATTTGGGTCAGATCGATTTGGGTTCG
10842 GGTCAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.21, C:0.08, G:0.31, T:0.40
Consensus pattern (32 bp):
TTAAATTTGGGTCAGATCGATTTGGGTTCGAA
Found at i:11062 original size:31 final size:31
Alignment explanation
Indices: 11021--11082 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
11011 TTTTGTAAAA
* *
11021 CTTTTGAATCGACTATTATATCCTTAATTTT
1 CTTTTAAATCGACTATTATACCCTTAATTTT
*
11052 CTTTTAAATCGACTATTATACCCTTATTTTT
1 CTTTTAAATCGACTATTATACCCTTAATTTT
11083 AGAATATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.52
Consensus pattern (31 bp):
CTTTTAAATCGACTATTATACCCTTAATTTT
Found at i:11330 original size:83 final size:82
Alignment explanation
Indices: 11151--11309 Score: 219
Period size: 83 Copynumber: 1.9 Consensus size: 82
11141 TCTATTTTTA
* * * ** *
11151 TTTAATTAAATCTAATCTCTTTATAACTATTTTGTTTTTACCATTTTACTATTTTAATTTAAAAA
1 TTTAA-TAAATATAATCTCTTTATAACTATTCTATTTTTACCATTAAACTATTTTAATTCAAAAA
11216 ATAGATATATTAGAATTT
65 ATAGATATATTAGAATTT
11234 TTTAATTAAATATAATCTCTTTATAACTATTCTATTTTTACCATTAAACTATTTTAATTGCAAAA
1 TTTAA-TAAATATAATCTCTTTATAACTATTCTATTTTTACCATTAAACTATTTTAATT-CAAAA
**
11299 CTTAGATATAT
64 AATAGATATAT
11310 ATTATAATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
83 54 0.81
84 13 0.19
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.50
Consensus pattern (82 bp):
TTTAATAAATATAATCTCTTTATAACTATTCTATTTTTACCATTAAACTATTTTAATTCAAAAAA
TAGATATATTAGAATTT
Found at i:12327 original size:32 final size:32
Alignment explanation
Indices: 12291--12366 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
12281 TTTTTTCACG
**
12291 TTCGGGTTCGGGTTTTATT-GGGTTTTAGATAT
1 TTCGGGTTCGGGTTTT-TTCGGGTTGGAGATAT
* * *
12323 TTCGGGTTCTGGTTTTTTCGGGTTGGAGCTTT
1 TTCGGGTTCGGGTTTTTTCGGGTTGGAGATAT
12355 TTCGGGTTCGGG
1 TTCGGGTTCGGG
12367 CGAATTTGGG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
31 2 0.05
32 35 0.95
ACGTcount: A:0.07, C:0.11, G:0.36, T:0.47
Consensus pattern (32 bp):
TTCGGGTTCGGGTTTTTTCGGGTTGGAGATAT
Found at i:12341 original size:16 final size:16
Alignment explanation
Indices: 12291--12346 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
12281 TTTTTTCACG
*
12291 TTCGGGTTCGGGTTTT
1 TTCGGGTTCTGGTTTT
* * * *
12307 ATT-GGGTTTTAGATAT
1 -TTCGGGTTCTGGTTTT
12323 TTCGGGTTCTGGTTTT
1 TTCGGGTTCTGGTTTT
12339 TTCGGGTT
1 TTCGGGTT
12347 GGAGCTTTTT
Statistics
Matches: 29, Mismatches: 9, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
15 2 0.07
16 25 0.86
17 2 0.07
ACGTcount: A:0.07, C:0.09, G:0.32, T:0.52
Consensus pattern (16 bp):
TTCGGGTTCTGGTTTT
Found at i:16558 original size:23 final size:23
Alignment explanation
Indices: 16530--16575 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
16520 ATTCAGATTG
16530 TTTACTAAAATTATTAAATTCTA
1 TTTACTAAAATTATTAAATTCTA
16553 TTTACTAAAATTATTAAATTCTA
1 TTTACTAAAATTATTAAATTCTA
16576 ATAATGTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTACTAAAATTATTAAATTCTA
Found at i:17013 original size:90 final size:90
Alignment explanation
Indices: 16855--17031 Score: 318
Period size: 90 Copynumber: 2.0 Consensus size: 90
16845 TTTTGGGGGG
*
16855 TTTATGGTATTAATAGGTTAGTTGCTCATGATCGTCTTCTACTATGTATTTCAGATATATGACAG
1 TTTATGGTATTAATAGGTTAGTTGCTCATGATCGTCTTCTACTATGCATTTCAGATATATGACAG
16920 AGATGGACTTACTTTAGGTGAGCTT
66 AGATGGACTTACTTTAGGTGAGCTT
* * *
16945 TTTATGGTATTGATAGGTTAGTTGCTCATGATCGTCTTCTACTGTGCATTTCAGATATATGACCG
1 TTTATGGTATTAATAGGTTAGTTGCTCATGATCGTCTTCTACTATGCATTTCAGATATATGACAG
17010 AGATGGACTTACTTTAGGTGAG
66 AGATGGACTTACTTTAGGTGAG
17032 TTTGTGAAAG
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.24, C:0.13, G:0.23, T:0.40
Consensus pattern (90 bp):
TTTATGGTATTAATAGGTTAGTTGCTCATGATCGTCTTCTACTATGCATTTCAGATATATGACAG
AGATGGACTTACTTTAGGTGAGCTT
Found at i:18111 original size:3 final size:3
Alignment explanation
Indices: 18103--18131 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
18093 ATACACTAAT
18103 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
18132 TCTGTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:19925 original size:13 final size:13
Alignment explanation
Indices: 19907--19932 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19897 AACTTTATAA
19907 TAGTTTGTCCTGT
1 TAGTTTGTCCTGT
19920 TAGTTTGTCCTGT
1 TAGTTTGTCCTGT
19933 CGTTGTAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.15, G:0.23, T:0.54
Consensus pattern (13 bp):
TAGTTTGTCCTGT
Found at i:21976 original size:1 final size:1
Alignment explanation
Indices: 21972--22053 Score: 92
Period size: 1 Copynumber: 82.0 Consensus size: 1
21962 AAGAGGGGGG
* * * * *
21972 AAAAAAAAAGAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAACAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
22037 AACAAAACAAAACAAAA
1 AAAAAAAAAAAAAAAAA
22054 CAACACAGAT
Statistics
Matches: 65, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 65 1.00
ACGTcount: A:0.90, C:0.06, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:22012 original size:27 final size:27
Alignment explanation
Indices: 21972--22053 Score: 110
Period size: 27 Copynumber: 3.0 Consensus size: 27
21962 AAGAGGGGGG
*
21972 AAAAAAAAAGAAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAGAAAAAAAA
21999 AAAAAAAAAAAAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAGAAAAAAAA
* * * * *
22026 AAAACAAACAAAACAAAACAAAACAAA
1 AAAAAAAAAAAAAAAAAAGAAAAAAAA
22053 A
1 A
22054 CAACACAGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.90, C:0.06, G:0.04, T:0.00
Consensus pattern (27 bp):
AAAAAAAAAAAAAAAAAAGAAAAAAAA
Done.