Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015716.1 Corchorus capsularis cultivar CVL-1 contig15737, 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: 28761
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:470 original size:166 final size:165
Alignment explanation
Indices: 155--472 Score: 417
Period size: 166 Copynumber: 1.9 Consensus size: 165
145 GTCGTTGATC
* * ** * *
155 AACTTTGTCAATCAAAGTTATAATCGATTGATGATTATTTGATTTTGTCATAAATGAATGAATCA
1 AACTTTGCCAATCAAAGTTATAATCAATTGATGATTATTACATTTTGCCATAAATAAATGAATCA
* * * * *
220 ATTAGTAATTATGTTAGCAAAAAAAATAGATTGATTGAACATACTAAATAAATTAGGGAATCAAA
66 ATTAGTAATTATGTTAGC-AAAAAAATAAATTGATTCAACATACTAAATAAATAAAGGAACCAAA
* *
285 TTAGTCGTTAATTAATTGCCAAAAAAATTAGTAATT
130 TTAGTCGCTAATAAATTGCCAAAAAAATTAGTAATT
*
321 AACTTTGCCAATCAAAGTTATAA-CTAATTGGTGATTATTACATTTTGCCATAAATAAATGAATC
1 AACTTTGCCAATCAAAGTTATAATC-AATTGATGATTATTACATTTTGCCATAAATAAATGAATC
* * *
385 AATTAGTAATTATGTTAGC-AAAAAATAAATTGATTCAACATGCTAAATAAATAAATGAACCAAG
65 AATTAGTAATTATGTTAGCAAAAAAATAAATTGATTCAACATACTAAATAAATAAAGGAACCAAA
449 TTAGTC-CTAAGTCAAAATTGCCAA
130 TTAGTCGCTAA-T--AAATTGCCAA
473 TCAAAGTTAC
Statistics
Matches: 131, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
163 3 0.02
164 44 0.34
165 1 0.01
166 83 0.63
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (165 bp):
AACTTTGCCAATCAAAGTTATAATCAATTGATGATTATTACATTTTGCCATAAATAAATGAATCA
ATTAGTAATTATGTTAGCAAAAAAATAAATTGATTCAACATACTAAATAAATAAAGGAACCAAAT
TAGTCGCTAATAAATTGCCAAAAAAATTAGTAATT
Found at i:746 original size:140 final size:139
Alignment explanation
Indices: 584--915 Score: 515
Period size: 140 Copynumber: 2.4 Consensus size: 139
574 AAGTTAGTGA
* * * *
584 TCGTTAGTTAATTTTTTCAATCAAAGTTGTAATTGATTGATAATTATTTAATTTTTCCAT-AAAT
1 TCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAAT
*
648 CGCTA-AAAAAAATTAACATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAAAATAAA
66 CGCCACAAAAAAATTAACATAAATAAATAAATCAATTAGTAATTATGTTACC---AAAAAATAAA
712 TTATTGAACATG
128 TTATTGAACATG
724 TCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAAT
1 TCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAAT
* *
789 CGCCACCAAAAAGATTACCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAATAAATT
66 CGCCA-CAAAAAAATTAACATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAATAAATT
854 ATTGAACATG
130 ATTGAACATG
* * * *
864 TTGTTAATTAATTTTGTCAATCAAAGTTGTAATTGATTAATGATTATCTAAT
1 TCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATGATTATATAAT
916 CAAAGTTGTA
Statistics
Matches: 178, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
140 126 0.71
141 8 0.04
143 44 0.25
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.38
Consensus pattern (139 bp):
TCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAAT
CGCCACAAAAAAATTAACATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAATAAATTA
TTGAACATG
Found at i:3365 original size:22 final size:23
Alignment explanation
Indices: 3319--3366 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
3309 TGTTGATCTG
* *
3319 TTTGAGTTATCAGTTTCCAGGTC
1 TTTGAGTTATCAGTCTCCAGATC
*
3342 TTTGAGTT-TGAGTCTCCAGATC
1 TTTGAGTTATCAGTCTCCAGATC
3364 TTT
1 TTT
3367 AGATCTTGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.17, C:0.17, G:0.21, T:0.46
Consensus pattern (23 bp):
TTTGAGTTATCAGTCTCCAGATC
Found at i:5135 original size:1 final size:1
Alignment explanation
Indices: 5129--5156 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
5119 TTCGTATTGC
5129 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
5157 CTGGGAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:14087 original size:18 final size:19
Alignment explanation
Indices: 14052--14087 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
14042 GGCTATTTTT
*
14052 TTTAAAAAAATAATTAATA
1 TTTAAAAAAATAAATAATA
14071 TTTAAAAAAA-AAATAAT
1 TTTAAAAAAATAAATAAT
14088 TTTGGTCTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TTTAAAAAAATAAATAATA
Found at i:14893 original size:178 final size:178
Alignment explanation
Indices: 14579--14906 Score: 444
Period size: 178 Copynumber: 1.8 Consensus size: 178
14569 GGAAGGATGA
* * *
14579 TCCACTTAATATTACATTACTTTTGCTCCGGATGTCTCATTGAGGTGATTCAAGTGTCTTTTAAA
1 TCCACTTAATAATACATAACTTTTGCTCCAGATGTCTCATTGAGGTGATTCAAGTGTCTTTTAAA
* ** * * *
14644 AGGTTGTTTTATGATCTACAACTTTCATGCATGACTCGAAAGCTAAATTTAATGTATCAAGTATA
66 AGGTTGTTTCATGATCTACAACTTTCATAAAGGACTCGAAAGCTAAATTTAATGTATCAAATACA
*
14709 AAAAATGTTTCTAAAAAATTAGTTCTTTCGTTTAGTGAGAGTAGACGG
131 AAAAATGCTTCTAAAAAATTAGTTCTTTCGTTTAGTGAGAGTAGACGG
* *
14757 TCCACTTTATAATACATAATTTTTGCTCCAGATGTC-CGATTGAGGTGATTCAAGTGT-TTGTTA
1 TCCACTTAATAATACATAACTTTTGCTCCAGATGTCTC-ATTGAGGTGATTCAAGTGTCTT-TTA
* * * * * *
14820 AAAGGTTGTTTCGTGATCTGCAACTTTCATAAAGGACTTGAAAGCTAAATTTGATTTTTCAAATA
64 AAAGGTTGTTTCATGATCTACAACTTTCATAAAGGACTCGAAAGCTAAATTTAATGTATCAAATA
* *
14885 CCAAAAATGCTTCTGAAAAATT
129 CAAAAAATGCTTCTAAAAAATT
14907 TATTTTTCGG
Statistics
Matches: 128, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
177 3 0.02
178 125 0.98
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.38
Consensus pattern (178 bp):
TCCACTTAATAATACATAACTTTTGCTCCAGATGTCTCATTGAGGTGATTCAAGTGTCTTTTAAA
AGGTTGTTTCATGATCTACAACTTTCATAAAGGACTCGAAAGCTAAATTTAATGTATCAAATACA
AAAAATGCTTCTAAAAAATTAGTTCTTTCGTTTAGTGAGAGTAGACGG
Found at i:15691 original size:21 final size:22
Alignment explanation
Indices: 15650--15705 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
15640 TTTTTTTTTA
* *
15650 TTTTAGAGATTAGAGTTTAGGG
1 TTTTAGGGATTAGAATTTAGGG
15672 TTTTAGGGATTA-AATTTAGGG
1 TTTTAGGGATTAGAATTTAGGG
* *
15693 GTTTAGGGTTTAG
1 TTTTAGGGATTAG
15706 GGGTTTACGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.25, C:0.00, G:0.32, T:0.43
Consensus pattern (22 bp):
TTTTAGGGATTAGAATTTAGGG
Found at i:15835 original size:21 final size:21
Alignment explanation
Indices: 15809--15852 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
15799 CCAATCTGGA
*
15809 TTGCTAAACACCGTCCCATTT
1 TTGCTAAACACCGCCCCATTT
**
15830 TTGCTATTCACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
15851 TT
1 TT
15853 TACGTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.34, G:0.09, T:0.39
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCATTT
Found at i:16134 original size:18 final size:20
Alignment explanation
Indices: 16096--16137 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
16086 GCTCGGCTAT
16096 TTTTTTTTTAAAATAATTAA
1 TTTTTTTTTAAAATAATTAA
16116 TTTTTTTTTAAAA-AA-TAA
1 TTTTTTTTTAAAATAATTAA
16134 TTTT
1 TTTT
16138 GGTCTAGCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 7 0.32
19 2 0.09
20 13 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTTTTTAAAATAATTAA
Found at i:16229 original size:32 final size:32
Alignment explanation
Indices: 16143--16276 Score: 218
Period size: 32 Copynumber: 4.2 Consensus size: 32
16133 ATTTTGGTCT
16143 AGCCGCCCCATGAGGGCGGCCTGCCGTGGC-A
1 AGCCGCCCCATGAGGGCGGCCTGCCGTGGCGA
* *
16174 AACCGCGCCAT-AGGGCGGCCTGCCGTGGCGA
1 AGCCGCCCCATGAGGGCGGCCTGCCGTGGCGA
* *
16205 AGCCGCCCCATGAGAGCGGCCTGCCGTGGAGA
1 AGCCGCCCCATGAGGGCGGCCTGCCGTGGCGA
16237 AGCCGCCCCATGAGGGCGGCCTGCCGTGGCGA
1 AGCCGCCCCATGAGGGCGGCCTGCCGTGGCGA
16269 AGCCGCCC
1 AGCCGCCC
16277 GTGGTGAAGC
Statistics
Matches: 93, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
30 18 0.19
31 19 0.20
32 56 0.60
ACGTcount: A:0.15, C:0.38, G:0.38, T:0.09
Consensus pattern (32 bp):
AGCCGCCCCATGAGGGCGGCCTGCCGTGGCGA
Found at i:16276 original size:64 final size:62
Alignment explanation
Indices: 16143--16276 Score: 216
Period size: 62 Copynumber: 2.1 Consensus size: 62
16133 ATTTTGGTCT
* *
16143 AGCCGCCCCATGAGGGCGGCCTGCCGTGGCAAACCGCGCCATAGGGCGGCCTGCCGTGGCGA
1 AGCCGCCCCATGAGAGCGGCCTGCCGTGGCAAACCGCCCCATAGGGCGGCCTGCCGTGGCGA
16205 AGCCGCCCCATGAGAGCGGCCTGCCGTGG-AGAAGCCGCCCCATGAGGGCGGCCTGCCGTGGCGA
1 AGCCGCCCCATGAGAGCGGCCTGCCGTGGCA-AA-CCGCCCCAT-AGGGCGGCCTGCCGTGGCGA
16269 AGCCGCCC
1 AGCCGCCC
16277 GTGGTGAAGC
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
61 1 0.01
62 30 0.45
63 8 0.12
64 28 0.42
ACGTcount: A:0.15, C:0.38, G:0.38, T:0.09
Consensus pattern (62 bp):
AGCCGCCCCATGAGAGCGGCCTGCCGTGGCAAACCGCCCCATAGGGCGGCCTGCCGTGGCGA
Found at i:16280 original size:15 final size:15
Alignment explanation
Indices: 16260--16291 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
16250 GGGCGGCCTG
16260 CCGTGGCGAAGCCGC
1 CCGTGGCGAAGCCGC
*
16275 CCGTGGTGAAGCCGC
1 CCGTGGCGAAGCCGC
16290 CC
1 CC
16292 TATAAGGGCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.41, G:0.38, T:0.09
Consensus pattern (15 bp):
CCGTGGCGAAGCCGC
Found at i:16300 original size:47 final size:47
Alignment explanation
Indices: 16228--16323 Score: 147
Period size: 47 Copynumber: 2.0 Consensus size: 47
16218 GAGCGGCCTG
* *
16228 CCGTGGAGAAGCCGCCCCATGAGGGCGGCCTGCCGTGGCGAAGCCGC
1 CCGTGGAGAAGCCGCCCCATAAGGGCGACCTGCCGTGGCGAAGCCGC
* * *
16275 CCGTGGTGAAGCCGCCCTATAAGGGCGACTTGCCGTGGCGAAGCCGC
1 CCGTGGAGAAGCCGCCCCATAAGGGCGACCTGCCGTGGCGAAGCCGC
16322 CC
1 CC
16324 CAGTGGGGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.16, C:0.35, G:0.38, T:0.11
Consensus pattern (47 bp):
CCGTGGAGAAGCCGCCCCATAAGGGCGACCTGCCGTGGCGAAGCCGC
Found at i:21436 original size:21 final size:21
Alignment explanation
Indices: 21412--21462 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
21402 AGCCTGCTGG
21412 TGTCCGGTGCTAGCTCGATGA
1 TGTCCGGTGCTAGCTCGATGA
*
21433 TGTCTGGTGCTAGCTCGATGA
1 TGTCCGGTGCTAGCTCGATGA
*
21454 TTTCCGGTG
1 TGTCCGGTG
21463 TTGTCCGGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.12, C:0.22, G:0.33, T:0.33
Consensus pattern (21 bp):
TGTCCGGTGCTAGCTCGATGA
Found at i:28298 original size:27 final size:27
Alignment explanation
Indices: 28268--28371 Score: 97
Period size: 27 Copynumber: 3.7 Consensus size: 27
28258 AGGGTCACCT
28268 AGGGGCATTTTGGTCATTTTCATATTC
1 AGGGGCATTTTGGTCATTTTCATATTC
* *
28295 AGGGGCATTTTAGTCATTTT-TTGCATTC
1 AGGGGCATTTTGGTCATTTTCAT--ATTC
* *
28323 AATGGTG-ATTTTGGTCATTTTTGCAT-TTA
1 -A-GGGGCATTTTGGTCA-TTTT-CATATTC
28352 AGGGGCATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
28372 TGCATTAAGG
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
26 1 0.02
27 26 0.42
28 15 0.24
29 12 0.19
30 7 0.11
32 1 0.02
ACGTcount: A:0.18, C:0.12, G:0.23, T:0.47
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTTCATATTC
Found at i:28343 original size:28 final size:28
Alignment explanation
Indices: 28268--28381 Score: 135
Period size: 28 Copynumber: 4.1 Consensus size: 28
28258 AGGGTCACCT
***
28268 AGGGGCATTTTGGTCATTTTCATATTC-
1 AGGGGCATTTTGGTCATTTTTGCATTCA
*
28295 AGGGGCATTTTAGTCATTTTTTGCATTCA
1 AGGGGCATTTTGGTCA-TTTTTGCATTCA
* *
28324 ATGGTG-ATTTTGGTCATTTTTGCATTTA
1 A-GGGGCATTTTGGTCATTTTTGCATTCA
28352 AGGGGCATTTTGGTCATTTTTGCATT-A
1 AGGGGCATTTTGGTCATTTTTGCATTCA
28379 AGG
1 AGG
28382 AATATTTAGG
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
27 22 0.29
28 40 0.53
29 10 0.13
30 3 0.04
ACGTcount: A:0.19, C:0.11, G:0.24, T:0.46
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTTGCATTCA
Done.