Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007511.1 Corchorus capsularis cultivar CVL-1 contig07532, 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: 26182
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:161 original size:1 final size:1
Alignment explanation
Indices: 155--183 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
145 TTTTCTGTTT
155 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
184 CTCCATTGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:996 original size:19 final size:18
Alignment explanation
Indices: 972--1007 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
962 TGAAGATTTC
972 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
991 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
1008 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:2307 original size:15 final size:16
Alignment explanation
Indices: 2287--2320 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2277 GATTGATTTC
*
2287 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
2302 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
2318 TTA
1 TTA
2321 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:2669 original size:30 final size:30
Alignment explanation
Indices: 2633--2701 Score: 138
Period size: 30 Copynumber: 2.3 Consensus size: 30
2623 CGATCCTCCT
2633 TCTTGGGGTTTTAAGTCGTTGAACGACTGC
1 TCTTGGGGTTTTAAGTCGTTGAACGACTGC
2663 TCTTGGGGTTTTAAGTCGTTGAACGACTGC
1 TCTTGGGGTTTTAAGTCGTTGAACGACTGC
2693 TCTTGGGGT
1 TCTTGGGGT
2702 CATAGTTTGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.14, C:0.16, G:0.32, T:0.38
Consensus pattern (30 bp):
TCTTGGGGTTTTAAGTCGTTGAACGACTGC
Found at i:4135 original size:18 final size:18
Alignment explanation
Indices: 4112--4146 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4102 GCGTGAATTG
4112 CCATTTCTGATGCCATTA
1 CCATTTCTGATGCCATTA
*
4130 CCATTTCTGTTGCCATT
1 CCATTTCTGATGCCATT
4147 TCTGACTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.29, G:0.11, T:0.43
Consensus pattern (18 bp):
CCATTTCTGATGCCATTA
Found at i:6899 original size:17 final size:17
Alignment explanation
Indices: 6879--6912 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6869 GCTAATAATA
6879 ATTATAAAATAATTATT
1 ATTATAAAATAATTATT
**
6896 ATTATTCAATAATTATT
1 ATTATAAAATAATTATT
6913 CCTAATTTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTATAAAATAATTATT
Found at i:19119 original size:2 final size:2
Alignment explanation
Indices: 19112--19139 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19102 ATCACATAAA
19112 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19140 TTCTAAACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19296 original size:17 final size:17
Alignment explanation
Indices: 19274--19306 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19264 GTGAGTATAA
*
19274 AATTTCATCTATATTAT
1 AATTTCATCCATATTAT
19291 AATTTCATCCATATTA
1 AATTTCATCCATATTA
19307 ATGTATAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTTCATCCATATTAT
Found at i:19482 original size:108 final size:104
Alignment explanation
Indices: 19355--19576 Score: 313
Period size: 108 Copynumber: 2.1 Consensus size: 104
19345 CAAAATTATA
* * *
19355 TTAATTAGA-TATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTTTAAGATTGG
1 TTAATTA-ATTATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTATAAGACTGA
*
19419 GATATTCGGAAAAAAGAAA-ACAAAAAATTGATTTAAGGATATTG
65 GATATTC-GAAAAAA-AAATA-AAAAAATTGA--TAAGCATATTG
* * *
19463 TTAATTAATTATATTAATTCTTGAACAAAATAATCCTACTTTACATTATAAATTATAAGGCTGAG
1 TTAATTAATTATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTATAAGACTGAG
19528 ATATTCGAAAAAAAAATAAAAAAATTGATAAGCATATTG
66 ATATTCGAAAAAAAAATAAAAAAATTGATAAGCATATTG
19567 TTAATTAATT
1 TTAATTAATT
19577 TTTACATTAT
Statistics
Matches: 105, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
104 20 0.19
106 13 0.12
107 9 0.09
108 63 0.60
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (104 bp):
TTAATTAATTATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTATAAGACTGAG
ATATTCGAAAAAAAAATAAAAAAATTGATAAGCATATTG
Found at i:20371 original size:31 final size:31
Alignment explanation
Indices: 20334--20392 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
20324 GTTAGATAAG
* *
20334 TAAGGATATAATAGGTATTTTAAAAGTTAAA
1 TAAGGATATAATAGGCATTTCAAAAGTTAAA
*
20365 TAAGGATATGATAGGCATTTCAAAAGTT
1 TAAGGATATAATAGGCATTTCAAAAGTT
20393 TCTCAAAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (31 bp):
TAAGGATATAATAGGCATTTCAAAAGTTAAA
Found at i:20432 original size:2 final size:2
Alignment explanation
Indices: 20420--20450 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
20410 TTATACATAG
*
20420 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20451 TTCTAAACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:22984 original size:41 final size:42
Alignment explanation
Indices: 22912--22995 Score: 152
Period size: 41 Copynumber: 2.0 Consensus size: 42
22902 ACAAAATTTC
*
22912 ATTTCTTAACTGAATTTTTCTTAAAATAATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
22954 ATTTCTTAACTGAA-TTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
22995 A
1 A
22996 CAGCCGCACG
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 27 0.66
42 14 0.34
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (42 bp):
ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
Found at i:24864 original size:134 final size:135
Alignment explanation
Indices: 24603--24964 Score: 426
Period size: 134 Copynumber: 2.6 Consensus size: 135
24593 CCAAAAGCTA
* * *
24603 ATGATTATTTAATTTTGCCACAAATAAATGAATCAATTAAT-ATTATGTTACAAAAAAATAAATT
1 ATGATTATTTATTTTTTCCATAAATAAATGAATCAATTAATAATTATGTTAC-AAAAAA-AAATT
* * *
24667 GATTGAACATCCAAAATAAGTAAATGAATCAAGTTAGTCCTTAGTTAACTTTACCAATCAAAGTT
64 GATTGAACAT----ACTAAATAAATGAATCAAGTTAGTCCTTAGTCAACTTTACCAATCAAAGTT
24732 ATAATTGATGG
125 ATAATTGATGG
* * * *
24743 ATGATTATTTATTTTTTCCATAAATAAATAAATCAATTACTAATTATATTAC-CAAAAAAATTGA
1 ATGATTATTTATTTTTTCCATAAATAAATGAATCAATTAATAATTATGTTACAAAAAAAAATTGA
* * ** *
24807 TTGAACATGCTAAATAAATGAATCAAGTTAGTCGTT-GATCAACTTTGTCAATTAAAGTTATAAT
66 TTGAACATACTAAATAAATGAATCAAGTTAGTCCTTAG-TCAACTTTACCAATCAAAGTTATAAT
*
24871 TGATTG
130 TGATGG
* *
24877 ATGATTATTTGATTTTGT-CATAAATAAATGAATCAATTAGTAATTATGTTAGCAAAAAAAATAG
1 ATGATTATTT-ATTTTTTCCATAAATAAATGAATCAATTAATAATTATGTTA-C-AAAAAAA-A-
24941 ATTGATTGAACATACTAAATAAAT
61 ATTGATTGAACATACTAAATAAAT
24965 TAGGGAATCA
Statistics
Matches: 192, Mismatches: 22, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
133 1 0.01
134 91 0.47
135 7 0.04
137 5 0.03
138 16 0.08
139 27 0.14
140 36 0.19
141 9 0.05
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.36
Consensus pattern (135 bp):
ATGATTATTTATTTTTTCCATAAATAAATGAATCAATTAATAATTATGTTACAAAAAAAAATTGA
TTGAACATACTAAATAAATGAATCAAGTTAGTCCTTAGTCAACTTTACCAATCAAAGTTATAATT
GATGG
Found at i:25141 original size:36 final size:36
Alignment explanation
Indices: 25098--25169 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
25088 TATGTTAGCA
25098 AAAAATAAATTGATTCAACATGCTAAATAAATAAAT
1 AAAAATAAATTGATTCAACATGCTAAATAAATAAAT
25134 AAAAATAAATTGATTCAACATGCTAAATAAATAAAT
1 AAAAATAAATTGATTCAACATGCTAAATAAATAAAT
25170 GAACCAAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.28
Consensus pattern (36 bp):
AAAAATAAATTGATTCAACATGCTAAATAAATAAAT
Found at i:25472 original size:138 final size:136
Alignment explanation
Indices: 25312--25637 Score: 507
Period size: 138 Copynumber: 2.4 Consensus size: 136
25302 CAAGTTAGTA
* *
25312 ATCGTTAGTTAATTTT-TCCAATCAAAGTTGTAATTGATTGATAATTATTTAATTTTACCAT-AA
1 ATCGTTAGTTAATTTTGT-CAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAA
* * *
25375 ATCGCTACAAAAA-ATTAACATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAGATAAA
65 ATCAC--CAAAAAGATTAACATAAATAAAAAAATCAATTAGTAATTATGTTACCAAAAAAATAAA
25439 TTATTGAAC
128 TTATTGAAC
25448 ATGTCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAA
1 A--TCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAA
*
25513 AATCACCAAAAAGATTACCATAAATAAAAAAATCAATTAGTAATTATGTTACCAAAAAAATAAAT
64 AATCACCAAAAAGATTAACATAAATAAAAAAATCAATTAGTAATTATGTTACCAAAAAAATAAAT
25578 TATTGAAC
129 TATTGAAC
* *
25586 AT-GTTAATTAATTTTGTCAATCAAAGTTGTAATTGATTGATGATTATCTAAT
1 ATCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATGATTATATAAT
25638 CAAAGTTGTA
Statistics
Matches: 177, Mismatches: 8, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
135 48 0.27
136 2 0.01
137 6 0.03
138 114 0.64
139 7 0.04
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (136 bp):
ATCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAA
TCACCAAAAAGATTAACATAAATAAAAAAATCAATTAGTAATTATGTTACCAAAAAAATAAATTA
TTGAAC
Found at i:25945 original size:2 final size:2
Alignment explanation
Indices: 25938--25969 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
25928 AAAGATAAAG
25938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25970 TAAAACTGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26029 original size:30 final size:30
Alignment explanation
Indices: 25995--26052 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
25985 TGGACAAAAG
25995 GAAATAAATTAATTACTTTATG-TTGATTGA
1 GAAATAAATTAATTACTTT-TGATTGATTGA
*
26025 GAAATATATTAATTACTTTTGATTGATT
1 GAAATAAATTAATTACTTTTGATTGATT
26053 AATTAGTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (30 bp):
GAAATAAATTAATTACTTTTGATTGATTGA
Done.