Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022522.1 Corchorus olitorius cultivar O-4 contig22555, 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: 47777
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Found at i:860 original size:11 final size:11
Alignment explanation
Indices: 844--881 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
834 AGTGACAAAG
844 GAAAAAAGAAA
1 GAAAAAAGAAA
855 GAAAAAAGAAA
1 GAAAAAAGAAA
866 GAAAAAAG-AA
1 GAAAAAAGAAA
876 GAAAAA
1 GAAAAA
882 GAAGGTGTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 8 0.30
11 19 0.70
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:870 original size:10 final size:10
Alignment explanation
Indices: 846--884 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
836 TGACAAAGGA
846 AAAAAGAAAG
1 AAAAAGAAAG
856 AAAAAAGAAAG
1 -AAAAAGAAAG
867 AAAAA-AGAAG
1 AAAAAGA-AAG
877 AAAAAGAA
1 AAAAAGAA
885 GGTGTGGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 1 0.04
10 14 0.54
11 11 0.42
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:2267 original size:8 final size:9
Alignment explanation
Indices: 2249--2277 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
2239 TTTCGGCTGG
2249 AAAAAGAAA
1 AAAAAGAAA
2258 AAAAAGAAA
1 AAAAAGAAA
2267 AAAAAGAAA
1 AAAAAGAAA
2276 AA
1 AA
2278 CTCGACTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:10274 original size:95 final size:96
Alignment explanation
Indices: 10111--10302 Score: 368
Period size: 95 Copynumber: 2.0 Consensus size: 96
10101 TTGTCGAAAA
*
10111 AATGATTTCCTTAGTTTTGGTGTTATTCTTCAATGCAGTTTCTTAGCCTTTCTGTATGCAAATGC
1 AATGATTTCCTTAGTTTTGGTGTTATTCTTCAATGCAGTTTCTTAGCCTTTCTGTACGCAAATGC
10176 TGTTAGTTTCTTTTGCCATTTAT-ATCAGCT
66 TGTTAGTTTCTTTTGCCATTTATAATCAGCT
10206 AATGATTTCCTTAGTTTTGGTGTTATTCTTCAATGCAGTTTCTTAGCCTTTCTGTACGCAAATGC
1 AATGATTTCCTTAGTTTTGGTGTTATTCTTCAATGCAGTTTCTTAGCCTTTCTGTACGCAAATGC
10271 TGTTAGTTTCTTTTGCCATTTATAATCAGCT
66 TGTTAGTTTCTTTTGCCATTTATAATCAGCT
10302 A
1 A
10303 TTTGGACTGA
Statistics
Matches: 95, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
95 87 0.92
96 8 0.08
ACGTcount: A:0.20, C:0.17, G:0.16, T:0.47
Consensus pattern (96 bp):
AATGATTTCCTTAGTTTTGGTGTTATTCTTCAATGCAGTTTCTTAGCCTTTCTGTACGCAAATGC
TGTTAGTTTCTTTTGCCATTTATAATCAGCT
Found at i:18633 original size:5 final size:5
Alignment explanation
Indices: 18623--18652 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
18613 TAATCAAGAA
18623 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG
18653 GAAGAATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (5 bp):
TTTTG
Found at i:32465 original size:31 final size:32
Alignment explanation
Indices: 32422--32500 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 32
32412 GGTAATTTTC
*
32422 TCAGATCATTCGGGTTTCGGCTCAT-CTGGA-T
1 TCAGGTCATTCGGGTTTCGGCTC-TGCTGGATT
* *
32453 TCAGGTCATTCGGGTCTCGGGTCTGCTGGATT
1 TCAGGTCATTCGGGTTTCGGCTCTGCTGGATT
* *
32485 TAAGGTCATGCGGGTT
1 TCAGGTCATTCGGGTT
32501 CGGGTATTGG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 1 0.03
31 25 0.62
32 14 0.35
ACGTcount: A:0.14, C:0.20, G:0.32, T:0.34
Consensus pattern (32 bp):
TCAGGTCATTCGGGTTTCGGCTCTGCTGGATT
Found at i:32504 original size:31 final size:31
Alignment explanation
Indices: 32447--32505 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
32437 TTCGGCTCAT
* *
32447 CTGGATTCAGGTCATTCGGGTCTCGGGTCTG
1 CTGGATTAAGGTCATGCGGGTCTCGGGTCTG
32478 CTGGATTTAAGGTCATGCGGGT-TCGGGT
1 CTGGA-TTAAGGTCATGCGGGTCTCGGGT
32506 ATTGGCCTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 11 0.44
32 14 0.56
ACGTcount: A:0.12, C:0.19, G:0.37, T:0.32
Consensus pattern (31 bp):
CTGGATTAAGGTCATGCGGGTCTCGGGTCTG
Found at i:33101 original size:93 final size:93
Alignment explanation
Indices: 32979--33152 Score: 285
Period size: 93 Copynumber: 1.9 Consensus size: 93
32969 CATTGTTTAA
*
32979 ACTTCTATAATTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAACCTTATAAC
1 ACTTCTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAACCTTATAAC
33044 TATTTTATTTTTACCATTTTACTATTTT
66 TATTTTATTTTTACCATTTTACTATTTT
* * * * * *
33072 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTATTTATATCTAATATCCTTATACC
1 ACTTCTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAACCTTATAAC
33137 TATTTTATTTTTACCA
66 TATTTTATTTTTACCA
33153 CATTACTAAT
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.33, C:0.15, G:0.01, T:0.51
Consensus pattern (93 bp):
ACTTCTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAACCTTATAAC
TATTTTATTTTTACCATTTTACTATTTT
Found at i:33177 original size:93 final size:93
Alignment explanation
Indices: 32989--33177 Score: 270
Period size: 93 Copynumber: 2.0 Consensus size: 93
32979 ACTTCTATAA
*
32989 TTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAACCTTATAACTATTTTATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAACCTTATAACTATTTTATTT
** * * ** *
33054 TTACCATTTTACTATTTTACTTTTATAG
66 TTACCACATTACTAATTTAATTAAAAAG
* * * *
33082 TTTTACTCAACTAAAAACTCTATTTTTATTTATTTATATCTAATATCCTTATACCTATTTTATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAACCTTATAACTATTTTATTT
33147 TTACCACATTACTAATTTAATTAAAAAG
66 TTACCACATTACTAATTTAATTAAAAAG
33175 TTT
1 TTT
33178 AGATATAATA
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 84 1.00
ACGTcount: A:0.34, C:0.14, G:0.02, T:0.51
Consensus pattern (93 bp):
TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAACCTTATAACTATTTTATTT
TTACCACATTACTAATTTAATTAAAAAG
Found at i:33285 original size:28 final size:27
Alignment explanation
Indices: 33224--33276 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
33214 GACATTGTTT
**
33224 AAATTTTACAGTTTTTTGTTAGAAATA
1 AAATTTTACAGTTTTTTACTAGAAATA
33251 AAATTTTACAGTTATTTTACTAGAAA
1 AAATTTTACAGTT-TTTTACTAGAAA
33277 ATATATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (27 bp):
AAATTTTACAGTTTTTTACTAGAAATA
Found at i:36573 original size:26 final size:25
Alignment explanation
Indices: 36525--36575 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
36515 TTTCCATTAA
36525 TTTAATAATGGAATAATTAAAATATT
1 TTTAATAATGGAAT-ATTAAAATATT
36551 TTTAATAATGGCAAT-TTAGAAATAT
1 TTTAATAATGG-AATATTA-AAATAT
36576 ATTTGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 3 0.13
26 17 0.74
27 3 0.13
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (25 bp):
TTTAATAATGGAATATTAAAATATT
Found at i:39414 original size:2 final size:2
Alignment explanation
Indices: 39400--39436 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
39390 AAATCCCTTT
*
39400 TA TA TA T- TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39437 CATACGAGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:41623 original size:17 final size:17
Alignment explanation
Indices: 41601--41635 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
41591 ATTGACATGC
*
41601 TAAGCTTTTATACTTCT
1 TAAGCTTTAATACTTCT
41618 TAAGCTTTAATACTTCT
1 TAAGCTTTAATACTTCT
41635 T
1 T
41636 CATTGTTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (17 bp):
TAAGCTTTAATACTTCT
Done.