Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012801.1 Corchorus capsularis cultivar CVL-1 contig12822, 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: 23632
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Found at i:16 original size:2 final size:2
Alignment explanation
Indices: 1--39 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
*
1 AT AT A- AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40 ACATACATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1091 original size:440 final size:439
Alignment explanation
Indices: 222--1137 Score: 1112
Period size: 440 Copynumber: 2.1 Consensus size: 439
212 TGGGTCCCAT
* * *
222 TCTCAATAAACAAATA-TTTTTTGTTGGATTATTTATCAAATGATCCCTATACTTTTACGCTTTT
1 TCTCCATAAACAAATATTTTTTTGTTGGATTATTTATCAAATGATCCCTATACTTTTACACTTTA
* * * * *
286 TGCTATTTAGTCCCTCACAAATTCTGGGTTGGACGATTGAACGTTTCGGCTTTAATTCTTATATT
66 TGCTATTTAATCCCTCACAAATTATAGATTGGACGATTGAACGGTTCGGCTTTAATTCTTATATT
* * * * * *
351 TTTTGTTTTACTTGTCTGATCAAGATTATTCAAGTGTCTATTAAAAGGTAATTCCATGATCTACA
131 TTCTATTCTACTTGTCCGATCAAGATGATTCAAGTGTCTATGAAAAGGTAATTCCATGATCTACA
* * * *
416 ACTTTCATGAAGGACTCAGAAGCCAATTTTGAGGTTTTAGTTCTAAAAAATGCTTCTGAAATTTT
196 ACTTTCATGAAGAACTCAAAAGCCAAGTTTAAGGTTTTAGTTCTAAAAAATGCTTCTGAAATTTT
* * *
481 GTGGTCTCGATTACCGGTCTATCTAATATTGTATAACTTTCAGTCCACTTGTCCGATTAAGGTTA
261 GTGGTCTCGATTACCGGTCTATCTAATATCGTACAACTTTCAGTCCACTTGTCCGATTAAGGGTA
546 TTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTTAGTCAAGGGCCTGAAAGCTGAAT
326 TTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTTAGTCAAGGGCCTGAAAGCTGAAT
* * * * * * *
611 TTGGTTAATGAGTTTCGTGGATGGTTCGAGAGGGAATTTTTATGTTTGG
391 TTGATTAATGAATTTCGAGGAGGGTTCAAGAGGGAATTTTTATATTTCG
* *
660 TCTCCATAAACAAATATTTTTTTTGCTGGATTATTTATCAAATGAT-CCTCATACTTTTTATACT
1 TCTCCATAAACAAATA-TTTTTTTGTTGGATTATTTATCAAATGATCCCT-ATAC-TTTTACACT
* * * * * * *
724 TTATGCTATTTAATCCTTTAC-AATTATAGATTGTACGATTTAACGCGTT-GGCTTTTATTTTTG
63 TTATGCTATTTAATCCCTCACAAATTATAGATTGGACGATTGAACG-GTTCGGCTTTAATTCTTA
* * * *
787 TATTTTCTATTCTATTTGTCCGATCAA-AGTGATTTAAGTGTCTATGAAAATGTAATTTCATGAT
127 TATTTTCTATTCTACTTGTCCGATCAAGA-TGATTCAAGTGTCTATGAAAAGGTAATTCCATGAT
* * * * *
851 CTACAA-TTTCCATGTAGAAGTCAAAAGCGAAGTTTAATGTTTTGGTTCTAAAAAATGCTTCTGA
191 CTACAACTTT-CATGAAGAACTCAAAAGCCAAGTTTAAGGTTTTAGTTCTAAAAAATGCTTCTGA
* * ** * * **
915 ATTTTTGTGGTTTCGATTGTCGGTCTATTTGATATCGTACAA-TTTTTGATCCACTTGTCCGATT
255 AATTTTGTGGTCTCGATTACCGGTCTATCTAATATCGTACAACTTTCAG-TCCACTTGTCCGATT
* * * *
979 GAGGGTGTTCAAGTGTCGGTTAAAAGTTTATTGTGTGATCTACGACTTTCA-TTAAGGGTCC-GA
319 AAGGGTATTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTT-AGTCAAGGG-CCTGA
* * * *
1042 AAGTTGAATTTGATTCATTAATTTCGAGGAGGGTTCAAGAGGTAATTTTTATATTTCG
382 AAGCTGAATTTGATTAATGAATTTCGAGGAGGGTTCAAGAGGGAATTTTTATATTTCG
* *
1100 TCTCCATAAACTAATATCTTTTTGTTGGATTATTTATC
1 TCTCCATAAACAAATATTTTTTTGTTGGATTATTTATC
1138 TAAAAACCCT
Statistics
Matches: 403, Mismatches: 65, Indels: 19
0.83 0.13 0.04
Matches are distributed among these distances:
438 15 0.04
439 31 0.08
440 328 0.81
441 29 0.07
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.42
Consensus pattern (439 bp):
TCTCCATAAACAAATATTTTTTTGTTGGATTATTTATCAAATGATCCCTATACTTTTACACTTTA
TGCTATTTAATCCCTCACAAATTATAGATTGGACGATTGAACGGTTCGGCTTTAATTCTTATATT
TTCTATTCTACTTGTCCGATCAAGATGATTCAAGTGTCTATGAAAAGGTAATTCCATGATCTACA
ACTTTCATGAAGAACTCAAAAGCCAAGTTTAAGGTTTTAGTTCTAAAAAATGCTTCTGAAATTTT
GTGGTCTCGATTACCGGTCTATCTAATATCGTACAACTTTCAGTCCACTTGTCCGATTAAGGGTA
TTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTTAGTCAAGGGCCTGAAAGCTGAAT
TTGATTAATGAATTTCGAGGAGGGTTCAAGAGGGAATTTTTATATTTCG
Found at i:8995 original size:35 final size:35
Alignment explanation
Indices: 8949--9017 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
8939 CAGATAAAAC
* *
8949 AATACTAGCTCTTCTAGAGCTTTCAATCAAATTTA
1 AATACTAGCTCTTCTAGAGCCTTCAATAAAATTTA
* *
8984 AATACTGGCTCTTCTGGAGCCTTCAATAAAATTT
1 AATACTAGCTCTTCTAGAGCCTTCAATAAAATTT
9018 GCACTATCCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (35 bp):
AATACTAGCTCTTCTAGAGCCTTCAATAAAATTTA
Found at i:9180 original size:12 final size:12
Alignment explanation
Indices: 9163--9196 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
9153 CTTTTATGCA
9163 ATATGATCAAGT
1 ATATGATCAAGT
9175 ATATGATCAAGT
1 ATATGATCAAGT
9187 ATATGA-CAAG
1 ATATGATCAAG
9197 GAAAAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 4 0.18
12 18 0.82
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (12 bp):
ATATGATCAAGT
Found at i:12856 original size:29 final size:29
Alignment explanation
Indices: 12814--12874 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
12804 TCATCCTTAA
12814 TATGACAACTTCGGGTGTCAAAATGATAC
1 TATGACAACTTCGGGTGTCAAAATGATAC
*
12843 TATGACAACTTCGGGTGTCAAAGTGATAC
1 TATGACAACTTCGGGTGTCAAAATGATAC
12872 TAT
1 TAT
12875 ATTTTTGATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (29 bp):
TATGACAACTTCGGGTGTCAAAATGATAC
Found at i:12921 original size:33 final size:32
Alignment explanation
Indices: 12879--12975 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 32
12869 TACTATATTT
*
12879 TTGATGTGACAACTCCAGTTGTCACTAATATGC
1 TTGATGTGACAACTCCAG-TGCCACTAATATGC
* *
12912 TTGATGTGACAACTTCAAGTGCCACTGATATGC
1 TTGATGTGACAAC-TCCAGTGCCACTAATATGC
*
12945 TTGATGTGACAACTTCAGGTGCCACTAATAT
1 TTGATGTGACAACTCCA-GTGCCACTAATAT
12976 TCAAGGGTAG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
32 2 0.04
33 50 0.89
34 4 0.07
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (32 bp):
TTGATGTGACAACTCCAGTGCCACTAATATGC
Found at i:13076 original size:32 final size:33
Alignment explanation
Indices: 13010--13083 Score: 105
Period size: 32 Copynumber: 2.2 Consensus size: 33
13000 ATAAATTTTA
* *
13010 ATGATAAAAGAAAGGTAGAATGAGGAGATTATGC
1 ATGAT-AAAGAAAGGTAGAATGAAGAGATCATGC
13044 ATGATAAAGAAAGGTAGAA-GAAGAGATCATGC
1 ATGATAAAGAAAGGTAGAATGAAGAGATCATGC
*
13076 ATGTTAAA
1 ATGATAAA
13084 TAAATTTTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 18 0.49
33 14 0.38
34 5 0.14
ACGTcount: A:0.49, C:0.04, G:0.27, T:0.20
Consensus pattern (33 bp):
ATGATAAAGAAAGGTAGAATGAAGAGATCATGC
Found at i:13196 original size:36 final size:36
Alignment explanation
Indices: 13144--13213 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
13134 TTTTAATCTT
*
13144 GATCATTTTGAGCTTCTTGATCGTCACTTAAACTCG
1 GATCATTTTGAACTTCTTGATCGTCACTTAAACTCG
* * *
13180 GATCTTTTTGAACTTCTTGATTGTTACTTAAACT
1 GATCATTTTGAACTTCTTGATCGTCACTTAAACT
13214 TGTACGATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (36 bp):
GATCATTTTGAACTTCTTGATCGTCACTTAAACTCG
Found at i:19105 original size:42 final size:42
Alignment explanation
Indices: 19050--19133 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
19040 AAAAAAAAAA
19050 AGACTAGTAAAACAGAGTTGGAATTGATAATAAGTGATAAAG
1 AGACTAGTAAAACAGAGTTGGAATTGATAATAAGTGATAAAG
19092 AGACTAGTAAAACAGAGTTGGAATTGATAATAAGTGATAAAG
1 AGACTAGTAAAACAGAGTTGGAATTGATAATAAGTGATAAAG
19134 TATTGAACAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.48, C:0.05, G:0.24, T:0.24
Consensus pattern (42 bp):
AGACTAGTAAAACAGAGTTGGAATTGATAATAAGTGATAAAG
Found at i:20916 original size:39 final size:39
Alignment explanation
Indices: 20872--20960 Score: 169
Period size: 39 Copynumber: 2.3 Consensus size: 39
20862 TTCAACTTGA
*
20872 TCTTCCTTTTCTCCTAGTTCTGGTTCGGGCTCCTTTTTT
1 TCTTCCTTTTCTCCTAGTTCTGGTTCGGGCTCCTTATTT
20911 TCTTCCTTTTCTCCTAGTTCTGGTTCGGGCTCCTTATTT
1 TCTTCCTTTTCTCCTAGTTCTGGTTCGGGCTCCTTATTT
20950 TCTTCCTTTTC
1 TCTTCCTTTTC
20961 CTTCTGCTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.03, C:0.29, G:0.13, T:0.54
Consensus pattern (39 bp):
TCTTCCTTTTCTCCTAGTTCTGGTTCGGGCTCCTTATTT
Found at i:22637 original size:15 final size:15
Alignment explanation
Indices: 22617--22648 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
22607 TGAAGCACTA
22617 TAATTTCTTTAAATT
1 TAATTTCTTTAAATT
22632 TAATTTCTTTAAATT
1 TAATTTCTTTAAATT
22647 TA
1 TA
22649 TTTAATACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (15 bp):
TAATTTCTTTAAATT
Found at i:23572 original size:30 final size:31
Alignment explanation
Indices: 23510--23584 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
23500 AAATTTGGTG
*
23510 AGGGACCCAATTGCTCAATTAACTCAACTTC
1 AGGGACCCAATTGCTCAACTAACTCAACTTC
* *
23541 AGGGACTCAATTGCTC-ACTAAGTTC-ACTTC
1 AGGGACCCAATTGCTCAACTAA-CTCAACTTC
*
23571 AGGGACCCATTTGC
1 AGGGACCCAATTGC
23585 ACATTTGCCC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 21 0.55
31 17 0.45
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (31 bp):
AGGGACCCAATTGCTCAACTAACTCAACTTC
Done.