Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015254.1 Corchorus capsularis cultivar CVL-1 contig15275, 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: 34265
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Found at i:9187 original size:19 final size:18
Alignment explanation
Indices: 9163--9199 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
9153 TTGAAGAGCT
9163 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
9182 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
9200 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Found at i:12711 original size:15 final size:15
Alignment explanation
Indices: 12691--12733 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
12681 CAAATCTTGC
12691 TGAAGTTGTCAAAGA
1 TGAAGTTGTCAAAGA
12706 TGAAGTTGTCAAAGA
1 TGAAGTTGTCAAAGA
*
12721 TGAAGTTCTCAAA
1 TGAAGTTGTCAAA
12734 TTACTTGGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (15 bp):
TGAAGTTGTCAAAGA
Found at i:21134 original size:19 final size:18
Alignment explanation
Indices: 21110--21146 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
21100 TTGAAGATTT
21110 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
21129 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
21147 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Found at i:22204 original size:36 final size:35
Alignment explanation
Indices: 22163--22281 Score: 156
Period size: 36 Copynumber: 3.4 Consensus size: 35
22153 TCTTTTCTAG
*
22163 ATTAAGCTCTTTATTAACTTCACTTAATTACCTTGA
1 ATTAAGCTCTTTATT-ACTTCACTTAATTACCCTGA
*
22199 ATTAAGTTCTTTATT-C-T-ACTTAATTACCCTGA
1 ATTAAGCTCTTTATTACTTCACTTAATTACCCTGA
22231 ATTAAGC-CTTTTATTGACTTCACTTAATTACCCTGA
1 ATTAAGCTC-TTTATT-ACTTCACTTAATTACCCTGA
*
22267 ATTAAGTTCTTTATT
1 ATTAAGCTCTTTATT
22282 TTACTTAATT
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
31 1 0.01
32 26 0.36
33 1 0.01
34 2 0.03
35 1 0.01
36 41 0.56
37 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.46
Consensus pattern (35 bp):
ATTAAGCTCTTTATTACTTCACTTAATTACCCTGA
Found at i:22225 original size:32 final size:32
Alignment explanation
Indices: 22184--22291 Score: 137
Period size: 32 Copynumber: 3.2 Consensus size: 32
22174 TATTAACTTC
*
22184 ACTTAATTACCTTGAATTAAGTTCTTTATTCT
1 ACTTAATTACCCTGAATTAAGTTCTTTATTCT
*
22216 ACTTAATTACCCTGAATTAAG-CCTTTTATTGACTT
1 ACTTAATTACCCTGAATTAAGTTC-TTTATT--C-T
*
22251 CACTTAATTACCCTGAATTAAGTTCTTTATTTT
1 -ACTTAATTACCCTGAATTAAGTTCTTTATTCT
22284 ACTTAATT
1 ACTTAATT
22292 TCCTTTCCTG
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
31 1 0.02
32 34 0.52
33 1 0.02
34 1 0.02
35 1 0.02
36 27 0.41
37 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (32 bp):
ACTTAATTACCCTGAATTAAGTTCTTTATTCT
Found at i:22244 original size:68 final size:68
Alignment explanation
Indices: 22163--22291 Score: 215
Period size: 68 Copynumber: 1.9 Consensus size: 68
22153 TCTTTTCTAG
*
22163 ATTAAGCTCTTTATTAACTTCACTTAATTACCTTGAATTAAGTTCTTTATTCTACTTAATTACCC
1 ATTAAGCTCTTTATTAACTTCACTTAATTACCCTGAATTAAGTTCTTTATTCTACTTAATTACCC
22228 TGA
66 TGA
* *
22231 ATTAAGC-CTTTTATTGACTTCACTTAATTACCCTGAATTAAGTTCTTTATTTTACTTAATT
1 ATTAAGCTC-TTTATTAACTTCACTTAATTACCCTGAATTAAGTTCTTTATTCTACTTAATT
22292 TCCTTTCCTG
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
67 1 0.02
68 56 0.98
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (68 bp):
ATTAAGCTCTTTATTAACTTCACTTAATTACCCTGAATTAAGTTCTTTATTCTACTTAATTACCC
TGA
Found at i:22367 original size:36 final size:36
Alignment explanation
Indices: 22320--22571 Score: 351
Period size: 36 Copynumber: 6.9 Consensus size: 36
22310 CTTGTGTCTT
* * * *
22320 TTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTCC
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTC
* *
22356 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTC
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTC
22392 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTC
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTC
* * *
22428 TTTACCTAGTTTTCTTGAGACTAAGCCAGTTCTTTTTTT
1 TTTACCTAGTTTCCTTGAAACTAAGCCAG-TC--TTTTC
* * * * *
22467 TTTACTTAATTTCCTTGAAATTAAGTCAGTCTATTC
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTC
22503 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTC
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTC
22539 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTT
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTT
22572 CTTTCAGTCT
Statistics
Matches: 193, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
36 162 0.84
37 2 0.01
38 2 0.01
39 27 0.14
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.44
Consensus pattern (36 bp):
TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTC
Found at i:22406 original size:111 final size:112
Alignment explanation
Indices: 22316--22568 Score: 331
Period size: 111 Copynumber: 2.3 Consensus size: 112
22306 TAAGCTTGTG
* *
22316 TCTT-TTTACTTAATTTCCTTGAAATTAAGCCAG-TC-TTTCCTTTACCTAATTTCCTTGAAATT
1 TCTTCTTTACCTAATTTCCTTGAAACTAAGCCAGTTCTTTTCCTTTACCTAATTTCCTTGAAATT
*
22378 AAGCCAGTCTTTTCTTTACCTAGTTTCC--TTGAAACTAAGCCAGTC
66 AAGCCAGTCTATTCTTTACCTAGTTTCCTTTTGAAACTAAGCCAGTC
* * * * ** *
22423 TTTTCTTTACCTAGTTTTCTTGAGACTAAGCCAGTTCTTTTTTTTTTACTTAATTTCCTTGAAAT
1 TCTTCTTTACCTAATTTCCTTGAAACTAAGCCAGTTC-TTTTCCTTTACCTAATTTCCTTGAAAT
*
22488 TAAGTCAGTCTATTCTTTACCTAGTTTCC--TTGAAACTAAGCCAGTC
65 TAAGCCAGTCTATTCTTTACCTAGTTTCCTTTTGAAACTAAGCCAGTC
* *
22534 TTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGT
1 TCTTCTTTACCTAATTTCCTTGAAACTAAGCCAGT
22569 CTTCTTTCAG
Statistics
Matches: 129, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
107 3 0.02
108 24 0.19
109 2 0.02
111 100 0.78
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.45
Consensus pattern (112 bp):
TCTTCTTTACCTAATTTCCTTGAAACTAAGCCAGTTCTTTTCCTTTACCTAATTTCCTTGAAATT
AAGCCAGTCTATTCTTTACCTAGTTTCCTTTTGAAACTAAGCCAGTC
Found at i:22581 original size:11 final size:11
Alignment explanation
Indices: 22565--22702 Score: 134
Period size: 11 Copynumber: 12.5 Consensus size: 11
22555 GAAACTAAGC
*
22565 CAGTCTTCTTT
1 CAGTCTTATTT
*
22576 CAGTCTTCTTT
1 CAGTCTTATTT
* *
22587 CAGTATTCTTT
1 CAGTCTTATTT
*
22598 CAGTCTGATTT
1 CAGTCTTATTT
*
22609 CAGT-TTAATAT
1 CAGTCTT-ATTT
*
22620 CAGTCTTATAT
1 CAGTCTTATTT
*
22631 CAGTCTAATTT
1 CAGTCTTATTT
*
22642 CAGTCTTTTTT
1 CAGTCTTATTT
*
22653 CAGTCTAATTT
1 CAGTCTTATTT
*
22664 CAGTCTTTTTT
1 CAGTCTTATTT
* *
22675 CAGTCTTCTAT
1 CAGTCTTATTT
*
22686 CAGTCTAATTT
1 CAGTCTTATTT
22697 CAGTCT
1 CAGTCT
22703 AACTTTGCCT
Statistics
Matches: 106, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
10 1 0.01
11 103 0.97
12 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.50
Consensus pattern (11 bp):
CAGTCTTATTT
Found at i:22907 original size:42 final size:41
Alignment explanation
Indices: 22846--22979 Score: 186
Period size: 42 Copynumber: 3.3 Consensus size: 41
22836 CTGAATTAGG
* *
22846 ACTATGTTTG-CTTTTCTTAATCACCATGGATAACAACTTCA
1 ACTATGTTTGACTTTTCTTAATCACCCTGGAT-ACAACTTTA
22887 ACTATGTTTGACTTTTCTTAATCACCCTGGATTACAACTTTA
1 ACTATGTTTGACTTTTCTTAATCACCCTGGA-TACAACTTTA
* *
22929 ACTATGTTTGAC-TTTCTT-ATCGCCCTGGAT-TAACTTTA
1 ACTATGTTTGACTTTTCTTAATCACCCTGGATACAACTTTA
22967 ACTATGTTTGACT
1 ACTATGTTTGACT
22980 ATCCAAATTA
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
38 19 0.22
39 1 0.01
40 10 0.12
41 16 0.19
42 39 0.45
43 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.43
Consensus pattern (41 bp):
ACTATGTTTGACTTTTCTTAATCACCCTGGATACAACTTTA
Found at i:23128 original size:15 final size:14
Alignment explanation
Indices: 23108--23137 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
23098 CCAACTTGGG
23108 ACCTTGACTTTGCTT
1 ACCTTGACTTT-CTT
23123 ACCTTGACTTTCTT
1 ACCTTGACTTTCTT
23137 A
1 A
23138 ATTATCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.17, C:0.27, G:0.10, T:0.47
Consensus pattern (14 bp):
ACCTTGACTTTCTT
Found at i:29049 original size:11 final size:12
Alignment explanation
Indices: 29025--29053 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
29015 TGGAGTAGCC
29025 GCACAAGACCGG
1 GCACAAGACCGG
29037 GCACAAG-CCGG
1 GCACAAGACCGG
29048 GCACAA
1 GCACAA
29054 CTGGCCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.34, C:0.34, G:0.31, T:0.00
Consensus pattern (12 bp):
GCACAAGACCGG
Found at i:31671 original size:32 final size:32
Alignment explanation
Indices: 31617--31679 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
31607 GGGTGTCATG
*** *
31617 TTCCCATTAGTTGTATTGGTCATAGT-CATATA
1 TTCCCATTAGTCACATTAGTCAT-GTACATATA
31649 TTCCCATTAGTCACATTAGTCATGTACATAT
1 TTCCCATTAGTCACATTAGTCATGTACATAT
31680 CCATTTTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 2 0.08
32 24 0.92
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (32 bp):
TTCCCATTAGTCACATTAGTCATGTACATATA
Done.