Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013289.1 Corchorus capsularis cultivar CVL-1 contig13310, 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: 29798
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:1053 original size:167 final size:165
Alignment explanation
Indices: 654--1081 Score: 501
Period size: 167 Copynumber: 2.6 Consensus size: 165
644 TGAGTCATTT
* *
654 GTCAATTGAGAAATGACTAAAAAGTTTAGTTATTTAATCCCCTTAAGAATC-----TTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * * * ** * *
714 TTAAGTAATCTACCAAGTAGGTAAAGACGAAAAAGATTAGTTCTCTAGCTCATCATCAATCCTTG
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCAAAAGCAAGCCTTG
* *
779 ATGAGGATCTTTTATTAATTCCACCACTCTATTCAA
130 ATGAGGATCTTTTAGTAATTCCACCACTCTATTAAA
* * * *
815 GTCCATTGAGAAATGACC-AAAGGATTACTTATTTAATCCCCTCAAGAATCAAAAGTCAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * *
879 TTAAGTAATTTGCCAAATAGGAAAAGACGAAAAAAATAAGTTTTCTAACTCCAAAAGCAAGCCTT
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACT-CAAAAGCAAGCCTT
* *
944 GGT-AGAGATCTTTTAGTAATTCCACTACTCTATTAAA
129 GATGAG-GATCTTTTAGTAATTCCACCACTCTATTAAA
* * * * *
981 GTCAATAGAAAAATGACCAAAAAGTCTAGTTATTTAATACCCTCAAGAATCAAAAGTTGGGATAT
1 GTCAATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* *
1046 TTAAGTAATCTGCCAAGTGGGAAAAAACGAAAAAAA
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAA
1082 AATTAGTTCT
Statistics
Matches: 222, Mismatches: 36, Indels: 12
0.82 0.13 0.04
Matches are distributed among these distances:
160 28 0.13
161 16 0.07
165 52 0.23
166 56 0.25
167 70 0.32
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (165 bp):
GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCAAAAGCAAGCCTTGA
TGAGGATCTTTTAGTAATTCCACCACTCTATTAAA
Found at i:1181 original size:15 final size:15
Alignment explanation
Indices: 1161--1191 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1151 AATACGTAGT
1161 ATATATAAATATATA
1 ATATATAAATATATA
*
1176 ATATATATATATATA
1 ATATATAAATATATA
1191 A
1 A
1192 ACTAATTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATATAAATATATA
Found at i:1662 original size:45 final size:45
Alignment explanation
Indices: 1612--1700 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
1602 GATTACTTCT
* * *
1612 CCAGCTCATCATTAA-TCCGGGGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCACCATTAAGT-CAGGGTAGGGATCTTATAGTAATTCCAC
1657 CCAGCTCACCATTAAGTCAGGGTAGGGATCTTATAGTAATTCCA
1 CCAGCTCACCATTAAGTCAGGGTAGGGATCTTATAGTAATTCCA
1701 GTACTCTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 39 0.98
46 1 0.03
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (45 bp):
CCAGCTCACCATTAAGTCAGGGTAGGGATCTTATAGTAATTCCAC
Found at i:8369 original size:33 final size:32
Alignment explanation
Indices: 8279--8375 Score: 124
Period size: 33 Copynumber: 3.0 Consensus size: 32
8269 CTCTTACAAC
* * *
8279 CAATGAAGTTGC-GGGCCTTCATCAAGCCGTTT
1 CAATGAAGTT-CACGGCCTTCATCACGCCTTTT
*
8311 CAATGAAGTTCACGGGCTTCCATCACGCCTTTT
1 CAATGAAGTTCACGGCCTT-CATCACGCCTTTT
8344 CAATGAAGTTCACTGGCCTTCATCACGCCTTT
1 CAATGAAGTTCAC-GGCCTTCATCACGCCTTT
8376 ACAAGTTGAG
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
31 1 0.02
32 15 0.26
33 36 0.63
34 5 0.09
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.30
Consensus pattern (32 bp):
CAATGAAGTTCACGGCCTTCATCACGCCTTTT
Found at i:12782 original size:29 final size:29
Alignment explanation
Indices: 12742--12813 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 29
12732 TGGCACGTAT
* **
12742 CTTTTTGTGTACGTGGCATGTCATGTGTCA
1 CTTTTTG-GTACGTGGCATGCCACATGTCA
*
12772 CTTTTTGGTACACGTGGCGTGCCACATGTCA
1 CTTTTTGGT--ACGTGGCATGCCACATGTCA
12803 CTTTTTGGTAC
1 CTTTTTGGTAC
12814 ACAGGCATGC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 4 0.11
30 7 0.19
31 25 0.69
ACGTcount: A:0.14, C:0.21, G:0.25, T:0.40
Consensus pattern (29 bp):
CTTTTTGGTACGTGGCATGCCACATGTCA
Found at i:14373 original size:11 final size:10
Alignment explanation
Indices: 14333--14386 Score: 58
Period size: 11 Copynumber: 5.3 Consensus size: 10
14323 TGCTCCTTGA
14333 AATAATTCTTC
1 AATAA-TCTTC
*
14344 AATGATCTTC
1 AATAATCTTC
14354 -AT-ATCTTC
1 AATAATCTTC
14362 AATAAGTCTTC
1 AATAA-TCTTC
14373 AATAAATCTTC
1 AAT-AATCTTC
14384 AAT
1 AAT
14387 CACGAACTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
8 6 0.16
9 4 0.11
10 6 0.16
11 20 0.53
12 2 0.05
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.41
Consensus pattern (10 bp):
AATAATCTTC
Found at i:17697 original size:14 final size:14
Alignment explanation
Indices: 17672--17711 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
17662 ATTAAGTTAG
17672 AAATTAAAAATTTAA
1 AAATT-AAAATTTAA
*
17687 AAATTAAAATTTGA
1 AAATTAAAATTTAA
17701 AAATTAAAATT
1 AAATTAAAATT
17712 GGGTTGCCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (14 bp):
AAATTAAAATTTAA
Found at i:26704 original size:16 final size:16
Alignment explanation
Indices: 26681--26778 Score: 124
Period size: 16 Copynumber: 6.1 Consensus size: 16
26671 GTTTTTTCAA
26681 GTCATTCGGGTTTCGG
1 GTCATTCGGGTTTCGG
* * *
26697 GTCGTTCGGGTCTCAG
1 GTCATTCGGGTTTCGG
26713 GTCATTCGGGTTTCGG
1 GTCATTCGGGTTTCGG
*
26729 GTCATTCGGGTCTCGG
1 GTCATTCGGGTTTCGG
* *
26745 GTCATTCGGGTTCCAG
1 GTCATTCGGGTTTCGG
* *
26761 ATCATTCGGGTCTCGG
1 GTCATTCGGGTTTCGG
26777 GT
1 GT
26779 TTACCGGGTC
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 67 1.00
ACGTcount: A:0.08, C:0.22, G:0.36, T:0.34
Consensus pattern (16 bp):
GTCATTCGGGTTTCGG
Found at i:26706 original size:9 final size:8
Alignment explanation
Indices: 26685--26755 Score: 69
Period size: 7 Copynumber: 8.9 Consensus size: 8
26675 TTTCAAGTCA
26685 TTCGGGT-
1 TTCGGGTC
26692 TTCGGGTC
1 TTCGGGTC
26700 GTTCGGGTC
1 -TTCGGGTC
*
26709 -TCAGGTC
1 TTCGGGTC
26716 ATTCGGGT-
1 -TTCGGGTC
26724 TTCGGGTC
1 TTCGGGTC
26732 ATTCGGGTC
1 -TTCGGGTC
26741 -TCGGGTC
1 TTCGGGTC
26748 ATTCGGGT
1 -TTCGGGT
26756 TCCAGATCAT
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
7 27 0.50
9 27 0.50
ACGTcount: A:0.06, C:0.21, G:0.38, T:0.35
Consensus pattern (8 bp):
TTCGGGTC
Found at i:26734 original size:48 final size:48
Alignment explanation
Indices: 26681--26778 Score: 144
Period size: 48 Copynumber: 2.0 Consensus size: 48
26671 GTTTTTTCAA
* * * *
26681 GTCATTCGGGTTTCGGGTCGTTCGGG-TCTCAGGTCATTCGGGTTTCGG
1 GTCATTCGGGTCTCGGGTCATTCGGGTTC-CAGATCATTCGGGTCTCGG
26729 GTCATTCGGGTCTCGGGTCATTCGGGTTCCAGATCATTCGGGTCTCGG
1 GTCATTCGGGTCTCGGGTCATTCGGGTTCCAGATCATTCGGGTCTCGG
26777 GT
1 GT
26779 TTACCGGGTC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 43 0.96
49 2 0.04
ACGTcount: A:0.08, C:0.22, G:0.36, T:0.34
Consensus pattern (48 bp):
GTCATTCGGGTCTCGGGTCATTCGGGTTCCAGATCATTCGGGTCTCGG
Found at i:26775 original size:32 final size:32
Alignment explanation
Indices: 26681--26778 Score: 151
Period size: 32 Copynumber: 3.1 Consensus size: 32
26671 GTTTTTTCAA
* *
26681 GTCATTCGGGTTTCGGGTCGTTCGGGTCTCAG
1 GTCATTCGGGTTTCGGGTCATTCGGGTCTCGG
26713 GTCATTCGGGTTTCGGGTCATTCGGGTCTCGG
1 GTCATTCGGGTTTCGGGTCATTCGGGTCTCGG
* * *
26745 GTCATTCGGGTTCCAGATCATTCGGGTCTCGG
1 GTCATTCGGGTTTCGGGTCATTCGGGTCTCGG
26777 GT
1 GT
26779 TTACCGGGTC
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.08, C:0.22, G:0.36, T:0.34
Consensus pattern (32 bp):
GTCATTCGGGTTTCGGGTCATTCGGGTCTCGG
Found at i:27296 original size:17 final size:17
Alignment explanation
Indices: 27274--27327 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
27264 AAATTGTATT
27274 GAATAAAAGATGATTTA
1 GAATAAAAGATGATTTA
*
27291 GAAT-AAA-TTG-TATT-
1 GAATAAAAGATGAT-TTA
27305 GAATAAAAGATGATTTA
1 GAATAAAAGATGATTTA
27322 GAATAA
1 GAATAA
27328 GTAAAAGGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 7 0.23
17 11 0.37
ACGTcount: A:0.52, C:0.00, G:0.17, T:0.31
Consensus pattern (17 bp):
GAATAAAAGATGATTTA
Found at i:27297 original size:31 final size:31
Alignment explanation
Indices: 27262--27327 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
27252 TACCAGTAAT
27262 ATAAATTGTATTGAATAAAAGATGATTTAGA
1 ATAAATTGTATTGAATAAAAGATGATTTAGA
27293 ATAAATTGTATTGAATAAAAGATGATTTAGA
1 ATAAATTGTATTGAATAAAAGATGATTTAGA
27324 ATAA
1 ATAA
27328 GTAAAAGGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (31 bp):
ATAAATTGTATTGAATAAAAGATGATTTAGA
Done.