Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010787.1 Corchorus capsularis cultivar CVL-1 contig10808, 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: 27679
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:46 original size:22 final size:22
Alignment explanation
Indices: 21--62 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
11 TAACAAAATT
*
21 TCATAATGAGGTTATCAAAAAA
1 TCATAAGGAGGTTATCAAAAAA
*
43 TCATAGGGAGGTTATCAAAA
1 TCATAAGGAGGTTATCAAAA
63 TTTGTAGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.26
Consensus pattern (22 bp):
TCATAAGGAGGTTATCAAAAAA
Found at i:96 original size:22 final size:22
Alignment explanation
Indices: 68--175 Score: 92
Period size: 22 Copynumber: 4.8 Consensus size: 22
58 CAAAATTTGT
*
68 AGTTATCAAGATTTCATAAGAA
1 AGTTATCAAAATTTCATAAGAA
* * *
90 AGTTATCAAAATTTTATAGGGA
1 AGTTATCAAAATTTCATAAGAA
* * *
112 GGTTTATCAAAATTTTATACGAA
1 AG-TTATCAAAATTTCATAAGAA
*
135 GATTTATCAAAATTTCATAACG-A
1 -AGTTATCAAAATTTCATAA-GAA
* *
158 GGTTATCAGAATTTCATA
1 AGTTATCAAAATTTCATA
176 GTGTGATTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
22 34 0.49
23 34 0.49
24 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (22 bp):
AGTTATCAAAATTTCATAAGAA
Found at i:120 original size:23 final size:23
Alignment explanation
Indices: 70--176 Score: 92
Period size: 23 Copynumber: 4.7 Consensus size: 23
60 AAATTTGTAG
* * * *
70 TTATCAAGATTTCATAAGAAAG-
1 TTATCAAAATTTCATAGGGAGGT
*
92 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGGAGGT
* * * *
115 TTATCAAAATTTTATACGAAGAT
1 TTATCAAAATTTCATAGGGAGGT
**
138 TTATCAAAATTTCATAACGAGG-
1 TTATCAAAATTTCATAGGGAGGT
*
160 TTATCAGAATTTCATAG
1 TTATCAAAATTTCATAG
177 TGTGATTATT
Statistics
Matches: 69, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
22 32 0.46
23 37 0.54
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.36
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGGAGGT
Found at i:164 original size:45 final size:44
Alignment explanation
Indices: 14--175 Score: 129
Period size: 45 Copynumber: 3.8 Consensus size: 44
4 GGGAGATTAA
* ** * * *
14 CAAAATTTCATAATGAGGTTATCAAAAAATCATAGGGAGGTTAT
1 CAAAATTTCATAACGAGGTTATCAAAATTTCATAAGAAAGTTAT
* *
58 CAAAATTT-GT----A-GTTATCAAGATTTCATAAGAAAGTTAT
1 CAAAATTTCATAACGAGGTTATCAAAATTTCATAAGAAAGTTAT
* ** * * *
96 CAAAATTTTATAGGGAGGTTTATCAAAATTTTATACGAAGATTTAT
1 CAAAATTTCATAACGAGG-TTATCAAAATTTCATAAGAA-AGTTAT
*
142 CAAAATTTCATAACGAGGTTATCAGAATTTCATA
1 CAAAATTTCATAACGAGGTTATCAAAATTTCATA
176 GTGTGATTAT
Statistics
Matches: 93, Mismatches: 17, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
38 29 0.31
39 2 0.02
43 2 0.02
44 9 0.10
45 31 0.33
46 20 0.22
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (44 bp):
CAAAATTTCATAACGAGGTTATCAAAATTTCATAAGAAAGTTAT
Found at i:185 original size:22 final size:22
Alignment explanation
Indices: 160--206 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
150 CATAACGAGG
* *
160 TTATCAGAATTTCATAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
*
182 TTATTAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
204 TTA
1 TTA
207 CTAACAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTGTGA
Found at i:217 original size:22 final size:22
Alignment explanation
Indices: 167--215 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
157 AGGTTATCAG
* *
167 AATTTCATAGTGTGATTATTAA
1 AATTTCAGAGTGTGATTACTAA
189 AATTTCAGAGTGTGATTACTAA
1 AATTTCAGAGTGTGATTACTAA
211 CAATT
1 -AATT
216 CATATGGAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (22 bp):
AATTTCAGAGTGTGATTACTAA
Found at i:273 original size:22 final size:22
Alignment explanation
Indices: 248--315 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
238 CATAACGTGA
*
248 TTATCAATATATCATATGGAGG
1 TTATCAAAATATCATATGGAGG
* * **
270 TTATCAACATCTCATAGTGTTGG
1 TTATCAAAATATCATA-TGGAGG
* *
293 TTATCAAAATTTCATATTGAGG
1 TTATCAAAATATCATATGGAGG
315 T
1 T
316 CTTCGAAATT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
22 18 0.50
23 18 0.50
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (22 bp):
TTATCAAAATATCATATGGAGG
Found at i:5168 original size:18 final size:17
Alignment explanation
Indices: 5136--5169 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5126 TTTGGTTCAG
5136 GTTAATAATATATTACC
1 GTTAATAATATATTACC
*
5153 GTTAGTAATGATATTAC
1 GTTAATAAT-ATATTAC
5170 TGCCAGTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (17 bp):
GTTAATAATATATTACC
Found at i:6021 original size:22 final size:22
Alignment explanation
Indices: 5996--6060 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 22
5986 TAACAAACCC
5996 CCCAAATTTATTTCATAAGAAA
1 CCCAAATTTATTTCATAAGAAA
* * *
6018 CCC-AA--CATTTCACAA-ATA
1 CCCAAATTTATTTCATAAGAAA
*
6036 CCCAAATTTATTTCATCAGAAA
1 CCCAAATTTATTTCATAAGAAA
6058 CCC
1 CCC
6061 TAGAATTCCA
Statistics
Matches: 32, Mismatches: 7, Indels: 8
0.68 0.15 0.17
Matches are distributed among these distances:
18 5 0.16
19 10 0.31
21 9 0.28
22 8 0.25
ACGTcount: A:0.42, C:0.28, G:0.03, T:0.28
Consensus pattern (22 bp):
CCCAAATTTATTTCATAAGAAA
Found at i:6139 original size:17 final size:17
Alignment explanation
Indices: 6114--6152 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
6104 ATTTACAACA
6114 GAAAACCTAATCTAATT
1 GAAAACCTAATCTAATT
* *
6131 GAAACCCTAATTTAATT
1 GAAAACCTAATCTAATT
6148 GAAAA
1 GAAAA
6153 AGAAAACCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.28
Consensus pattern (17 bp):
GAAAACCTAATCTAATT
Found at i:7356 original size:19 final size:20
Alignment explanation
Indices: 7310--7357 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
7300 TGTGGCACGC
*
7310 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
7332 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
7351 CACATGT
1 CACATGT
7358 CACGCCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:7362 original size:53 final size:53
Alignment explanation
Indices: 7277--7379 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
7267 GACGTGGCAC
* * ** *
7277 GCCACCTGTACCAAAATGTGACATGTGGCACGCCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATATACCAAAAAGTCGT
* *
7330 GCCACATGTACCAAAAAGTGACACATGTCACGCCACGTATACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATATACCAAAAAGT
7380 GACACGTGGC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.17
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATATACCAAAAAGTCGT
Found at i:7396 original size:31 final size:31
Alignment explanation
Indices: 7329--7427 Score: 108
Period size: 31 Copynumber: 3.2 Consensus size: 31
7319 CAAAAAGTCG
* *
7329 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
* * *
7360 CGCCACGTATACCAAAAAGTGACACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
** * * *
7391 TGCCACATGTTTCAAAAAATGGCACGTTGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
7422 TGCCAC
1 TGCCAC
7428 GTGCACAAAA
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.19
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACGTGGCA
Found at i:9922 original size:30 final size:30
Alignment explanation
Indices: 9886--9943 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
9876 TTCAGGGGCT
*
9886 AAATTGTCTATTAAACCATAGTATATGGCC
1 AAATTGTCTAATAAACCATAGTATATGGCC
*
9916 AAATTGTCTAATAAGCCATAGTATATGG
1 AAATTGTCTAATAAACCATAGTATATGG
9944 AGTACTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (30 bp):
AAATTGTCTAATAAACCATAGTATATGGCC
Found at i:10773 original size:11 final size:11
Alignment explanation
Indices: 10757--10781 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10747 TCCCCAATCT
10757 TTTAATCCTGA
1 TTTAATCCTGA
10768 TTTAATCCTGA
1 TTTAATCCTGA
10779 TTT
1 TTT
10782 GAATATTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (11 bp):
TTTAATCCTGA
Found at i:10894 original size:7 final size:7
Alignment explanation
Indices: 10884--10918 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
10874 ATAGGCTATA
*
10884 GCCAAAT
1 GCCAAAC
10891 GCCAAAC
1 GCCAAAC
10898 GCCAAAC
1 GCCAAAC
10905 GCCAAAC
1 GCCAAAC
10912 GCCAAAC
1 GCCAAAC
10919 AGGGCCGCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.43, C:0.40, G:0.14, T:0.03
Consensus pattern (7 bp):
GCCAAAC
Found at i:16378 original size:21 final size:21
Alignment explanation
Indices: 16339--16383 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
16329 ACATCTTGAG
*
16339 GTTAGTTCTTCCTCTTTTGGT
1 GTTAGTTCTTCCTCATTTGGT
* *
16360 GTTAGTTCTTCTTCATTTGTT
1 GTTAGTTCTTCCTCATTTGGT
16381 GTT
1 GTT
16384 CAATCTTGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.07, C:0.16, G:0.18, T:0.60
Consensus pattern (21 bp):
GTTAGTTCTTCCTCATTTGGT
Found at i:21816 original size:31 final size:31
Alignment explanation
Indices: 21730--21816 Score: 93
Period size: 32 Copynumber: 2.8 Consensus size: 31
21720 ACGGTGTCCG
* * *
21730 ACGTGGCACGCCACGTGTACCAAAAAATGAC
1 ACGTGGCATGCCACGTGTACAAAAAAAAGAC
* * * *
21761 ACATGGCATGCCACATGTTTCAAAAAAAAGGC
1 ACGTGGCATGCCACGTG-TACAAAAAAAAGAC
*
21793 ACGTGGCATGCCACGTGCACAAAA
1 ACGTGGCATGCCACGTGTACAAAA
21817 GGATACATAC
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
31 19 0.43
32 25 0.57
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (31 bp):
ACGTGGCATGCCACGTGTACAAAAAAAAGAC
Found at i:21864 original size:30 final size:30
Alignment explanation
Indices: 21828--21891 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
21818 GATACATACA
21828 ACGTGTCATTTTTTGTCCACGTGGCATGCC
1 ACGTGTCATTTTTTGTCCACGTGGCATGCC
21858 ACGTGTCATTTTTTGTCCACGTGGCATGCC
1 ACGTGTCATTTTTTGTCCACGTGGCATGCC
21888 ACGT
1 ACGT
21892 CGGACGTCGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.14, C:0.27, G:0.23, T:0.36
Consensus pattern (30 bp):
ACGTGTCATTTTTTGTCCACGTGGCATGCC
Found at i:21879 original size:18 final size:18
Alignment explanation
Indices: 21828--21880 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
21818 GATACATACA
21828 ACGTGTCATTTTTTGTCC
1 ACGTGTCATTTTTTGTCC
*
21846 ACGTGGCA-----TG-CC
1 ACGTGTCATTTTTTGTCC
21858 ACGTGTCATTTTTTGTCC
1 ACGTGTCATTTTTTGTCC
21876 ACGTG
1 ACGTG
21881 GCATGCCACG
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
12 9 0.33
13 2 0.07
17 2 0.07
18 14 0.52
ACGTcount: A:0.13, C:0.25, G:0.23, T:0.40
Consensus pattern (18 bp):
ACGTGTCATTTTTTGTCC
Done.