Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012406.1 Corchorus capsularis cultivar CVL-1 contig12427, 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: 41218
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:746 original size:2 final size:2
Alignment explanation
Indices: 739--766 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
729 TTACCTGCAG
739 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
767 CCTTGATGTG
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):
TA
Found at i:5303 original size:17 final size:17
Alignment explanation
Indices: 5283--5315 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5273 CTAAGGCGAA
5283 AACAAATTAACTTAATT
1 AACAAATTAACTTAATT
5300 AACAAATTAACTTAAT
1 AACAAATTAACTTAAT
5316 CCTATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (17 bp):
AACAAATTAACTTAATT
Found at i:19418 original size:32 final size:32
Alignment explanation
Indices: 19376--19437 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
19366 CATGGTAGAG
*
19376 TGTTAGACTCTTAGTTCTAGTATACATGGACC
1 TGTTAGACTCTTAGTTCTACTATACATGGACC
*
19408 TGTTGGACTCTTAGTTCTACTATACATGGA
1 TGTTAGACTCTTAGTTCTACTATACATGGA
19438 TCATGAGGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (32 bp):
TGTTAGACTCTTAGTTCTACTATACATGGACC
Found at i:19765 original size:158 final size:163
Alignment explanation
Indices: 19465--19787 Score: 494
Period size: 158 Copynumber: 2.0 Consensus size: 163
19455 CTACTATTAC
19465 GGAATATGAGTTTTCTTTGTAATTTATTTATTTGTATATTTAGTATGTTGGTAGTTATAAATGAA
1 GGAATATGAGTTTTCTTTGTAATTTATTTATTTGTATATTTAGTATGTT-GTAG-TATAAATGAA
* * *
19530 ATTAGATATTTGGCAATCCTTATTGATTTACGTACATTTCAATTTGTAAATAGGGACGCCAATGT
64 ATTAGAGATTTGACAATCCTAATTGATTTACGTACATTTCAATTTGTAAATAGGGACGCCAATGT
* *
19595 ATCAGCATATTCTCTAGCTAAGATTGAG-TAGATA
129 ATCAGCACATTCTCTAGCTAAGATTAAGCTAGATA
*
19629 GGAATGTGAGTTTTCTTTGTAATTTATTTATTTGTATATTTAGTATG-T-T-G-ATAAATGAAAT
1 GGAATATGAGTTTTCTTTGTAATTTATTTATTTGTATATTTAGTATGTTGTAGTATAAATGAAAT
* * *
19690 TAGAGATTTGACAATTCTAATTGATTTACGTACGTTTCAATTTGTAAATATGGACGCCAATGTAT
66 TAGAGATTTGACAATCCTAATTGATTTACGTACATTTCAATTTGTAAATAGGGACGCCAATGTAT
* *
19755 CAGTACATTCTCTAGTTAAGATTAAGCTAGATA
131 CAGCACATTCTCTAGCTAAGATTAAGCTAGATA
19788 ATCATGTGGT
Statistics
Matches: 147, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
158 92 0.63
159 6 0.04
160 1 0.01
161 1 0.01
163 1 0.01
164 46 0.31
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (163 bp):
GGAATATGAGTTTTCTTTGTAATTTATTTATTTGTATATTTAGTATGTTGTAGTATAAATGAAAT
TAGAGATTTGACAATCCTAATTGATTTACGTACATTTCAATTTGTAAATAGGGACGCCAATGTAT
CAGCACATTCTCTAGCTAAGATTAAGCTAGATA
Found at i:19863 original size:21 final size:20
Alignment explanation
Indices: 19830--19869 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
19820 TTATAATCTT
*
19830 TGATTATTCATTAATAAAAG
1 TGATTATTCATTAAAAAAAG
*
19850 TGATTATTTGATTAAAAAAA
1 TGATTA-TTCATTAAAAAAA
19870 TGTAACAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (20 bp):
TGATTATTCATTAAAAAAAG
Found at i:22472 original size:19 final size:19
Alignment explanation
Indices: 22448--22486 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
22438 AATTGGATAA
22448 GGATATG-GGAGATAAGTTT
1 GGATATGCGG-GATAAGTTT
22467 GGATATGTCGGGATAAGTTT
1 GGATATG-CGGGATAAGTTT
22487 TGCAATTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 9 0.50
21 2 0.11
ACGTcount: A:0.28, C:0.03, G:0.36, T:0.33
Consensus pattern (19 bp):
GGATATGCGGGATAAGTTT
Found at i:27107 original size:109 final size:109
Alignment explanation
Indices: 26954--27249 Score: 450
Period size: 109 Copynumber: 2.7 Consensus size: 109
26944 TAAATTAAAA
** *
26954 TGGTAAAAATAAAAAAAATTATATAAAATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGT
1 TGGTAAAAAT-AAAGTAATTATA-AAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGT
27018 AGAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
63 AGAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
27065 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
* *
27130 ATAAAATTTTATATTAGAAAAAATTTTAGTATATCCAAATTTTT
66 ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
* *
27174 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTA
27239 GTAGAATAAAA
61 GTAGAATAAAA
27250 CTATAATAGT
Statistics
Matches: 172, Mismatches: 7, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
109 120 0.70
110 13 0.08
111 11 0.06
114 28 0.16
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (109 bp):
TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
Found at i:27139 original size:17 final size:16
Alignment explanation
Indices: 27119--27160 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
27109 GAAAATAGAG
27119 TTTTTAGTAGAATAAAA
1 TTTTTAGTAGAA-AAAA
*
27136 TTTTATATTAGAAAAAA
1 TTTT-TAGTAGAAAAAA
27153 -TTTTAGTA
1 TTTTTAGTA
27161 TATCCAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 4 0.18
16 3 0.14
17 8 0.36
18 7 0.32
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (16 bp):
TTTTTAGTAGAAAAAA
Found at i:27919 original size:30 final size:29
Alignment explanation
Indices: 27823--27923 Score: 114
Period size: 29 Copynumber: 3.4 Consensus size: 29
27813 TAATCTACCA
* * *
27823 TTTTGCCCCCTAAACTTGTAGAGTTTAGACG
1 TTTTGCCCCCTAAACTT-CA-ATTTTGGACG
* *
27854 TTTTGCCCCAC-GAACTTCAATTTTGGACA
1 TTTTGCCCC-CTAAACTTCAATTTTGGACG
27883 TTTTGCCCCCTAAACTTCAATTTTGGGACG
1 TTTTGCCCCCTAAACTTCAATTTT-GGACG
27913 TTTTGCCCCCT
1 TTTTGCCCCCT
27924 CAACCTAACG
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.47
30 16 0.27
31 14 0.23
32 1 0.02
ACGTcount: A:0.20, C:0.28, G:0.16, T:0.37
Consensus pattern (29 bp):
TTTTGCCCCCTAAACTTCAATTTTGGACG
Found at i:28143 original size:29 final size:30
Alignment explanation
Indices: 28085--28161 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 30
28075 CGGAGCCGTT
*
28085 AAGTTGAGGGGGCAAAACGTCCCAAAATTG
1 AAGTTCAGGGGGCAAAACGTCCCAAAATTG
* * *
28115 AAGTTCAGGGGACAAAATGT-CCAAGATTG
1 AAGTTCAGGGGGCAAAACGTCCCAAAATTG
*
28144 AAGTTCGGGGGGCAAAAC
1 AAGTTCAGGGGGCAAAAC
28162 ATCTAAACGC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 23 0.57
30 17 0.43
ACGTcount: A:0.36, C:0.16, G:0.31, T:0.17
Consensus pattern (30 bp):
AAGTTCAGGGGGCAAAACGTCCCAAAATTG
Found at i:35529 original size:28 final size:30
Alignment explanation
Indices: 35457--35536 Score: 76
Period size: 31 Copynumber: 2.7 Consensus size: 30
35447 TTGAAGTGGT
*
35457 AAAAATA-CAAAAGTGGTCCCTCAAGTGGAGC
1 AAAAATAGC-AAATTGGTCCCTCAAGTGGA-C
*
35488 GAAAATAGCAAATTGGTCCCTCAAGT-GA-
1 AAAAATAGCAAATTGGTCCCTCAAGTGGAC
* *
35516 AAAAATATGCAATTTAGTCCC
1 AAAAATA-GCAAATTGGTCCC
35537 CTAAAATGGA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
28 6 0.14
29 11 0.26
30 2 0.05
31 22 0.52
32 1 0.02
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (30 bp):
AAAAATAGCAAATTGGTCCCTCAAGTGGAC
Found at i:37207 original size:26 final size:26
Alignment explanation
Indices: 37166--37257 Score: 139
Period size: 26 Copynumber: 3.5 Consensus size: 26
37156 AAATTCTCTT
* *
37166 CAATATCAAATCTCCTCAATCCACAA
1 CAATATCGAATTTCCTCAATCCACAA
*
37192 CAATATTGAATTTCCTCAATCCACAA
1 CAATATCGAATTTCCTCAATCCACAA
* *
37218 CAATATCAAATCTCCTCAATCCACAA
1 CAATATCGAATTTCCTCAATCCACAA
37244 CAATATCGAATTTC
1 CAATATCGAATTTC
37258 ATACCTTTCA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 58 1.00
ACGTcount: A:0.40, C:0.30, G:0.02, T:0.27
Consensus pattern (26 bp):
CAATATCGAATTTCCTCAATCCACAA
Found at i:38923 original size:47 final size:46
Alignment explanation
Indices: 38869--39012 Score: 211
Period size: 47 Copynumber: 3.1 Consensus size: 46
38859 ATTAGTATAG
*
38869 ATTATAATGAGAAAATAATAGTATTTAGAAATTATATATGTAATGAA
1 ATTATAATGAGAAAATAATA-TATTTAGAAATTATAAATGTAATGAA
* * *
38916 ATTATAATGAGGAAATAGTAATATTTATAAATTATAAATGTAATGAA
1 ATTATAATGAGAAAATAAT-ATATTTAGAAATTATAAATGTAATGAA
*
38963 ATTATAATTAGAAAAT-A-ATATTTAGAAATTATAAATGTAATGAA
1 ATTATAATGAGAAAATAATATATTTAGAAATTATAAATGTAATGAA
39007 ATTATA
1 ATTATA
39013 TTTAGAGATT
Statistics
Matches: 88, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
44 32 0.36
47 55 0.62
48 1 0.01
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (46 bp):
ATTATAATGAGAAAATAATATATTTAGAAATTATAAATGTAATGAA
Found at i:39024 original size:74 final size:74
Alignment explanation
Indices: 38936--39089 Score: 254
Period size: 74 Copynumber: 2.1 Consensus size: 74
38926 GGAAATAGTA
* *
38936 ATATTTATAAATTATAAATGTAATGAAATTATAATTAGAAAATAATATTTAGAAATTATAAATGT
1 ATATTTAGAAATTATAAATGTAATAAAATTATAATTAGAAAATAATATTTAGAAATTATAAATGT
39001 AATGAAATT
66 AATGAAATT
* * * *
39010 ATATTTAGAGATTATATATGTAATAAAATTATATTTAGAAAATAATATTTAGAAATTATATATGT
1 ATATTTAGAAATTATAAATGTAATAAAATTATAATTAGAAAATAATATTTAGAAATTATAAATGT
39075 AATGAAATT
66 AATGAAATT
39084 ATATTT
1 ATATTT
39090 TAAAAATAAT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (74 bp):
ATATTTAGAAATTATAAATGTAATAAAATTATAATTAGAAAATAATATTTAGAAATTATAAATGT
AATGAAATT
Found at i:39058 original size:44 final size:44
Alignment explanation
Indices: 39005--39270 Score: 315
Period size: 44 Copynumber: 6.1 Consensus size: 44
38995 AAATGTAATG
* * *
39005 AAATTATATTTAGAGATTATATATGTAATAAAATTATATTTAGA
1 AAATAATATTTAGAAATTATATATGTAATGAAATTATATTTAGA
39049 AAATAATATTTAGAAATTATATATGTAATGAAATTATATTTTA-A
1 AAATAATATTTAGAAATTATATATGTAATGAAATTATA-TTTAGA
* * * *
39093 AAATAATATTTAGAAATTATAAATGTGATGGAATCATATTTAGA
1 AAATAATATTTAGAAATTATATATGTAATGAAATTATATTTAGA
* * * * *
39137 AAATAATATTTAGAAATGA-ACAATGTAATGACATTATAATTACA
1 AAATAATATTTAGAAATTATA-TATGTAATGAAATTATATTTAGA
* * *
39181 AAATAATATTTAGAAATTATA-ATTGTAATGACACTATAATTAGA
1 AAATAATATTTAGAAATTATATA-TGTAATGAAATTATATTTAGA
* * *
39225 AAATAATATTAAGAAATTAAATATGTAATGAAATCATATTTA-A
1 AAATAATATTTAGAAATTATATATGTAATGAAATTATATTTAGA
39268 AAA
1 AAA
39271 CATTAAATTT
Statistics
Matches: 193, Mismatches: 23, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
43 10 0.05
44 177 0.92
45 6 0.03
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (44 bp):
AAATAATATTTAGAAATTATATATGTAATGAAATTATATTTAGA
Found at i:39102 original size:118 final size:121
Alignment explanation
Indices: 38890--39266 Score: 404
Period size: 118 Copynumber: 3.0 Consensus size: 121
38880 AAAATAATAG
* *
38890 TATTTAGAAATTATATATGTAATGAAATTATAATGAGGAAATAGTAATATTTATAAATTATAAAT
1 TATTTAGAAATTATATATGTAATAAAATTATAATGAGGAAATAGTAATATTTAGAAATTATAAAT
*
38955 GTAATGAAATTATAATTAGAAAATAATATTTAGAAATTATAAATGTAATGAAATTA
66 GTAATGAAATTATAATTAGAAAATAATATTTAGAAATTATAAATGTAATGAAATCA
* * * *
39011 TATTTAGAGATTATATATGTAATAAAATTATATTTA-GAAA-A-TAATATTTAGAAATTATATAT
1 TATTTAGAAATTATATATGTAATAAAATTATAATGAGGAAATAGTAATATTTAGAAATTATAAAT
* * *
39073 GTAATGAAATTATATTTTA-AAAATAATATTTAGAAATTATAAATGTGATGGAATCA
66 GTAATGAAATTATA-ATTAGAAAATAATATTTAGAAATTATAAATGTAATGAAATCA
* * * * ** * *
39129 TATTTAGAAAATAATATTTAGAAATGAACAATGTAATGACATTATAATTACAAAATAATATTTAG
1 TATTTAG-AAATTATATAT-GTAAT-AA-AAT-T-AT-A-ATGAGGA--A-ATAGTAATATTTAG
* * * *
39194 AAATTATAATTGTAATGACACTATAATTAGAAAATAATATTAAGAAATTA-AATATGTAATGAAA
55 AAATTATAAATGTAATGAAATTATAATTAGAAAATAATATTTAGAAATTATAA-ATGTAATGAAA
39258 TCA
119 TCA
39261 TATTTA
1 TATTTA
39267 AAAACATTAA
Statistics
Matches: 215, Mismatches: 24, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
118 74 0.34
119 12 0.06
120 8 0.04
121 34 0.16
122 3 0.01
123 1 0.00
124 2 0.01
125 1 0.00
126 3 0.01
127 1 0.00
129 1 0.00
130 1 0.00
131 6 0.03
132 68 0.32
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (121 bp):
TATTTAGAAATTATATATGTAATAAAATTATAATGAGGAAATAGTAATATTTAGAAATTATAAAT
GTAATGAAATTATAATTAGAAAATAATATTTAGAAATTATAAATGTAATGAAATCA
Found at i:41030 original size:23 final size:23
Alignment explanation
Indices: 41001--41049 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
40991 GACAATAGAC
41001 AAAGCTCTCACAAAGGAGTTCCA
1 AAAGCTCTCACAAAGGAGTTCCA
*
41024 AAAGCTCTCACATAGGAGTTCCA
1 AAAGCTCTCACAAAGGAGTTCCA
41047 AAA
1 AAA
41050 TAAACAAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.18
Consensus pattern (23 bp):
AAAGCTCTCACAAAGGAGTTCCA
Found at i:41127 original size:12 final size:12
Alignment explanation
Indices: 41110--41140 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
41100 GTTGGGTGAG
41110 AAGAAAAAAAGA
1 AAGAAAAAAAGA
41122 AAGAAAAAAAGA
1 AAGAAAAAAAGA
41134 AAGAAAA
1 AAGAAAA
41141 CTACATTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAGA
Done.