Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016296.1 Corchorus capsularis cultivar CVL-1 contig16317, 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: 34019
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:6905 original size:31 final size:31
Alignment explanation
Indices: 6834--6909 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
6824 CCTCTGTTAG
* * *
6834 GGGGTAAAATGTCGTGAATTTGGGAAGTTTA
1 GGGGTAAATTGTCGTGAATTTGGGAAATTCA
* * *
6865 GGGGCAAATTTTCTTGAATTT-GGAAATTCA
1 GGGGTAAATTGTCGTGAATTTGGGAAATTCA
6895 TGGGGTAAATTGTCG
1 -GGGGTAAATTGTCG
6910 CGATTTGAAG
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
30 7 0.20
31 28 0.80
ACGTcount: A:0.28, C:0.07, G:0.32, T:0.34
Consensus pattern (31 bp):
GGGGTAAATTGTCGTGAATTTGGGAAATTCA
Found at i:10286 original size:63 final size:62
Alignment explanation
Indices: 10184--10301 Score: 200
Period size: 63 Copynumber: 1.9 Consensus size: 62
10174 GTTAACTTTA
*
10184 TGGGGAGGGCACTTCATACTTTTAATTTTCTTTTCTGTTGGAAGAAAAATTTTAAAAGTTTC
1 TGGGGAGGGCACTTCATACTTTTAATTTTCTTTTATGTTGGAAGAAAAATTTTAAAAGTTTC
**
10246 TGGGGAGGGGCACTTCATACTTTTTCTTTTCTTTTATGTTGGAAGAAAAATTTTAA
1 TGGGGA-GGGCACTTCATACTTTTAATTTTCTTTTATGTTGGAAGAAAAATTTTAA
10302 TTCAACAATA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
62 6 0.12
63 46 0.88
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.42
Consensus pattern (62 bp):
TGGGGAGGGCACTTCATACTTTTAATTTTCTTTTATGTTGGAAGAAAAATTTTAAAAGTTTC
Found at i:10829 original size:16 final size:16
Alignment explanation
Indices: 10808--10850 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
10798 ACACACACAC
10808 ACATATATATATACAT
1 ACATATATATATACAT
*
10824 ACATATATATATATAT
1 ACATATATATATACAT
10840 ACACTATATAT
1 ACA-TATATAT
10851 TATTTTTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.40
Consensus pattern (16 bp):
ACATATATATATACAT
Found at i:12254 original size:11 final size:11
Alignment explanation
Indices: 12238--12264 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
12228 TATAGCCACA
12238 TTAATGTGATG
1 TTAATGTGATG
12249 TTAATGTGATG
1 TTAATGTGATG
12260 TTAAT
1 TTAAT
12265 AAGATTCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (11 bp):
TTAATGTGATG
Found at i:13119 original size:2 final size:2
Alignment explanation
Indices: 13114--13149 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
13104 TGTTACTACC
13114 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13150 AATCTATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23060 original size:22 final size:22
Alignment explanation
Indices: 23030--23072 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
23020 ATTTCGATTA
*
23030 ATCTAAAATGGAAAGAATAGGC
1 ATCTAAAATAGAAAGAATAGGC
*
23052 ATCTGAAATAGAAAGAATAGG
1 ATCTAAAATAGAAAGAATAGG
23073 TTCTGATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.07, G:0.23, T:0.19
Consensus pattern (22 bp):
ATCTAAAATAGAAAGAATAGGC
Found at i:23104 original size:1 final size:1
Alignment explanation
Indices: 23098--23138 Score: 55
Period size: 1 Copynumber: 41.0 Consensus size: 1
23088 ACTGAAAATG
* * *
23098 AAAAAAAAAAAAAGAAAGAAAAAAAAATAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
23139 TCAAATATTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.93, C:0.00, G:0.05, T:0.02
Consensus pattern (1 bp):
A
Found at i:23109 original size:14 final size:14
Alignment explanation
Indices: 23092--23139 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
23082 ATCCAAACTG
23092 AAAATGAAAAAAAA
1 AAAATGAAAAAAAA
*
23106 AAAAAGAAAGAAAAA
1 AAAATGAAA-AAAAA
*
23121 AAAATAAAAAAAAA
1 AAAATGAAAAAAAA
23135 AAAAT
1 AAAAT
23140 CAAATATTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.88, C:0.00, G:0.06, T:0.06
Consensus pattern (14 bp):
AAAATGAAAAAAAA
Found at i:29418 original size:20 final size:20
Alignment explanation
Indices: 29393--29432 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
29383 AGGCCATGTG
* *
29393 TTTTCTCTCTTTCTTTTTTT
1 TTTTCTATCTTTATTTTTTT
*
29413 TTTTCTATTTTTATTTTTTT
1 TTTTCTATCTTTATTTTTTT
29433 ATTAAGTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTCTATCTTTATTTTTTT
Found at i:29620 original size:107 final size:104
Alignment explanation
Indices: 29449--29709 Score: 382
Period size: 107 Copynumber: 2.5 Consensus size: 104
29439 TTTAGCCTTA
* * *
29449 AATTTCACTAAGTTTAGCCCCAAATTTAAATTTTATTTTTATTTCAAGGGTAAATTTCAAAATTA
1 AATTTCACTAAGTTTAGCCCCAAATTAAAATTTTA-TTTTATTTTAAGGGTAAATTCCAAAATTA
29514 ATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAACT
65 ATAA--TATTGTTATAGGGTTTTAGAAATAAAATACAAAACT
*
29556 AATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTCATTTTAAGGGTAAATTCCATAATTA
1 AATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTT-ATTTTAAGGGTAAATTCCAAAATTA
* * *
29621 ATAATATTGTTATAGGGTTTTAGAAATAAAATATATAATT
65 ATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAACT
**
29661 AA-TTCACTAAGTTTAG-CCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 AATTTCACTAAGTTTAGCCCCAAATTAAAATT-TTATTTTATTTTAAGGGT
29710 TAGAAAAATT
Statistics
Matches: 143, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
103 25 0.17
104 19 0.13
105 35 0.24
106 4 0.03
107 60 0.42
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (104 bp):
AATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTATTTTAAGGGTAAATTCCAAAATTAA
TAATATTGTTATAGGGTTTTAGAAATAAAATACAAAACT
Found at i:31462 original size:16 final size:17
Alignment explanation
Indices: 31441--31474 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
31431 AAAATGTATC
*
31441 ATTGATGGGAAA-AAAA
1 ATTGATGAGAAAGAAAA
31457 ATTGATGAGAAAGAAAA
1 ATTGATGAGAAAGAAAA
31474 A
1 A
31475 ATTTACTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.24, T:0.18
Consensus pattern (17 bp):
ATTGATGAGAAAGAAAA
Found at i:33985 original size:2 final size:2
Alignment explanation
Indices: 33978--34019 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
33968 TCATTTGTTT
33978 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.