Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013467.1 Corchorus capsularis cultivar CVL-1 contig13488, 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: 79425
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1809 original size:21 final size:21
Alignment explanation
Indices: 1783--1827 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1773 GGATTAATAT
1783 TTATTGTAGAAATTGTAAGAA
1 TTATTGTAGAAATTGTAAGAA
1804 TTATTGTAGAAATTGTAAGAA
1 TTATTGTAGAAATTGTAAGAA
1825 TTA
1 TTA
1828 CAAGAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.40
Consensus pattern (21 bp):
TTATTGTAGAAATTGTAAGAA
Found at i:2662 original size:76 final size:76
Alignment explanation
Indices: 2579--2729 Score: 293
Period size: 76 Copynumber: 2.0 Consensus size: 76
2569 GGTTACATAT
2579 ATATATATATATATATATAGTGTTTTATTATATGAATTTATTATATGCTAAATTTACTTTTAAAC
1 ATATATATATATATATATAGTGTTTTATTATATGAATTTATTATATGCTAAATTTACTTTTAAAC
2644 AAAAAAAAAAA
66 AAAAAAAAAAA
2655 ATATATATATATATATATAGTGTTTTATTATATGAATTTATTATATGCTAAATTTACTTTTAAAC
1 ATATATATATATATATATAGTGTTTTATTATATGAATTTATTATATGCTAAATTTACTTTTAAAC
*
2720 CAAAAAAAAA
66 AAAAAAAAAA
2730 TTGTGAACCC
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (76 bp):
ATATATATATATATATATAGTGTTTTATTATATGAATTTATTATATGCTAAATTTACTTTTAAAC
AAAAAAAAAAA
Found at i:5610 original size:15 final size:16
Alignment explanation
Indices: 5590--5627 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5580 GTTTTTTATA
5590 TTAATTAA-TCATTGT
1 TTAATTAAGTCATTGT
*
5605 TTAATTAAGTGATTGT
1 TTAATTAAGTCATTGT
*
5621 TCAATTA
1 TTAATTA
5628 TTAGGAGACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (16 bp):
TTAATTAAGTCATTGT
Found at i:6509 original size:34 final size:36
Alignment explanation
Indices: 6440--6511 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 36
6430 TTTTGAAATT
6440 TGGTGGTCCTATTACTCAATGATGATATATAGATATA
1 TGGTGGTCCTATTACTCAA-GATGATATATAGATATA
*
6477 TGGTGGTCCTATTACTC-A-ATGATATATGGATATA
1 TGGTGGTCCTATTACTCAAGATGATATATAGATATA
6511 T
1 T
6512 ATAGTTACCA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 16 0.47
36 1 0.03
37 17 0.50
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (36 bp):
TGGTGGTCCTATTACTCAAGATGATATATAGATATA
Found at i:12476 original size:25 final size:25
Alignment explanation
Indices: 12431--12479 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
12421 TTTTAAATTC
*
12431 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
12456 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
12480 ACTCCCTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:12479 original size:21 final size:21
Alignment explanation
Indices: 12399--12480 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 21
12389 CATTTAGTAA
12399 TTAAATATATATTATTTATTTAT
1 TTAAA-ATATATTA-TTATTTAT
*
12422 TTTAAAT-TCATTATT-TATTAT
1 TTAAAATAT-ATTATTAT-TTAT
12443 TTAAAATATATTTATTATTTAT
1 TTAAAATATA-TTATTATTTAT
12465 TTAATAATATA-TATTA
1 TTAA-AATATATTATTA
12481 CTCCCTTTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
20 1 0.02
21 19 0.37
22 20 0.39
23 11 0.22
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (21 bp):
TTAAAATATATTATTATTTAT
Found at i:23049 original size:18 final size:18
Alignment explanation
Indices: 23026--23077 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
23016 GCCCAAAGTG
23026 TGGCATCATGTGCTCTTA
1 TGGCATCATGTGCTCTTA
23044 TGGCATCATGTGC-CTTTA
1 TGGCATCATGTGCTC-TTA
* *
23062 TGGCGTCTTGTGCTCT
1 TGGCATCATGTGCTCT
23078 CCATTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 1 0.03
18 28 0.93
19 1 0.03
ACGTcount: A:0.12, C:0.23, G:0.25, T:0.40
Consensus pattern (18 bp):
TGGCATCATGTGCTCTTA
Found at i:23566 original size:15 final size:14
Alignment explanation
Indices: 23542--23575 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
23532 TTAGTTGAAA
*
23542 GCAAGGCTAAGGCC
1 GCAAGCCTAAGGCC
23556 GACAAGCCTAAGGCC
1 G-CAAGCCTAAGGCC
23571 GCAAG
1 GCAAG
23576 ACGCTTACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.32, C:0.29, G:0.32, T:0.06
Consensus pattern (14 bp):
GCAAGCCTAAGGCC
Found at i:27785 original size:22 final size:22
Alignment explanation
Indices: 27760--27804 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
27750 TCTTTCACCC
*
27760 TTTTCAATGAGTCTGCTATTCA
1 TTTTCAATCAGTCTGCTATTCA
27782 TTTTCAATCAGTCTGCTATTCA
1 TTTTCAATCAGTCTGCTATTCA
27804 T
1 T
27805 CGAAGCTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.47
Consensus pattern (22 bp):
TTTTCAATCAGTCTGCTATTCA
Found at i:28293 original size:16 final size:16
Alignment explanation
Indices: 28241--28294 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
28231 AGCAAATTTA
28241 ATTTCTATATAATTAGC
1 ATTTCT-TATAATTAGC
*
28258 ATTTC-TATTATTATG-
1 ATTTCTTATAATTA-GC
*
28273 GTTTCTTATAATTAGC
1 ATTTCTTATAATTAGC
28289 ATTTCT
1 ATTTCT
28295 CGACGACAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
15 12 0.40
16 13 0.43
17 5 0.17
ACGTcount: A:0.28, C:0.11, G:0.07, T:0.54
Consensus pattern (16 bp):
ATTTCTTATAATTAGC
Found at i:28562 original size:45 final size:45
Alignment explanation
Indices: 28498--28596 Score: 180
Period size: 45 Copynumber: 2.2 Consensus size: 45
28488 GTAGATGCCG
*
28498 GTATCATAGCCTCCACACTTTTCATAATTAGCATAATCGTCATCA
1 GTATCATAGCCTCCACACTTTTCATAATTAACATAATCGTCATCA
28543 GTATCATAGCCTCCACACTTTTCATAATTAACATAATCGTCATCA
1 GTATCATAGCCTCCACACTTTTCATAATTAACATAATCGTCATCA
*
28588 GTATAATAG
1 GTATCATAG
28597 ATGTGATTAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.33
Consensus pattern (45 bp):
GTATCATAGCCTCCACACTTTTCATAATTAACATAATCGTCATCA
Found at i:31493 original size:5 final size:5
Alignment explanation
Indices: 31483--31514 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
31473 GGGATACTCA
*
31483 TTTCC TTTCC TTTCG TTTCC TTTCC TTTCC TT
1 TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC TT
31515 CCATTTACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.34, G:0.03, T:0.62
Consensus pattern (5 bp):
TTTCC
Found at i:39740 original size:15 final size:16
Alignment explanation
Indices: 39715--39744 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39705 TAAGACGTAG
39715 TCAATTAATTTCCTTA
1 TCAATTAATTTCCTTA
39731 TCAATT-ATTTCCTT
1 TCAATTAATTTCCTT
39745 CTTTTGTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.53
Consensus pattern (16 bp):
TCAATTAATTTCCTTA
Found at i:40389 original size:2 final size:2
Alignment explanation
Indices: 40382--40429 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
40372 TAGATATAGC
* *
40382 TA TA TA TA TA TA TA TA AA TA TA TA TA TG TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40424 TA TA TA
1 TA TA TA
40430 GTTATACTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:48283 original size:78 final size:78
Alignment explanation
Indices: 48132--48296 Score: 222
Period size: 78 Copynumber: 2.1 Consensus size: 78
48122 TAGAAGACAA
* * * * *
48132 GTCGATAATAGAAAACCAAGGGTGGAGATGGCTCGTAGTGGTCCTATTGAAAAACTTGTATCTGT
1 GTCGATAATAGAAAACCAAGGGTGGAGATGGCTCGTAGTGGCCCTATTGAAAAACCTGAACCTAT
*
48197 TTGCAGAAATCCT
66 TCGCAGAAATCCT
* * *
48210 GTCGATAATAGAAAATCAAGGGTGGAGATGGCTCGTGGTGGCCCTATTGAAAGACCTGAACCTAT
1 GTCGATAATAGAAAACCAAGGGTGGAGATGGCTCGTAGTGGCCCTATTGAAAAACCTGAACCTAT
* *
48275 TCGTAGAAATCTT
66 TCGCAGAAATCCT
*
48288 GTCTATAAT
1 GTCGATAAT
48297 GAAGGTTCTG
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (78 bp):
GTCGATAATAGAAAACCAAGGGTGGAGATGGCTCGTAGTGGCCCTATTGAAAAACCTGAACCTAT
TCGCAGAAATCCT
Found at i:50091 original size:4 final size:4
Alignment explanation
Indices: 50082--50109 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
50072 CCTTAATCTT
50082 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
50110 CGAGAGACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:56207 original size:21 final size:22
Alignment explanation
Indices: 56164--56208 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
56154 TAACTACTAG
*
56164 AAATCCAAATGTACCCAAAAAA
1 AAATCCAAATCTACCCAAAAAA
56186 AAATCCAAATCTACCCAAAAAA
1 AAATCCAAATCTACCCAAAAAA
56208 A
1 A
56209 TTTAACTACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.60, C:0.24, G:0.02, T:0.13
Consensus pattern (22 bp):
AAATCCAAATCTACCCAAAAAA
Found at i:63209 original size:2 final size:2
Alignment explanation
Indices: 63202--63228 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
63192 AACTCAAAAG
63202 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
63229 CAACCCTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65010 original size:10 final size:9
Alignment explanation
Indices: 64994--65018 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
64984 CTAGTAATTA
64994 ATTTTTTTT
1 ATTTTTTTT
65003 ATTTTTTTT
1 ATTTTTTTT
65012 ATTTTTT
1 ATTTTTT
65019 GACAAGAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:65719 original size:88 final size:86
Alignment explanation
Indices: 65620--65869 Score: 403
Period size: 81 Copynumber: 3.0 Consensus size: 86
65610 AGCGATACCA
65620 AACATAAATTACAATTTTCAACTGCAATTTTAAAAAGTACATCTCAAAAGTACTTCTTAGTTCTT
1 AACATAAATTACAATTTTCAACTGCAATTTTAAAAAGTACATCTCAAAAGTACTTCTT--TTCTT
65685 CCAAACCAAGTTTTTTCAAACCG
64 CCAAACCAAGTTTTTTCAAACCG
65708 AACATAAATTACAATTTTCAACTGCAATTTTAAAAAGTACATCTCAAAAGTA---C--TTCTTCC
1 AACATAAATTACAATTTTCAACTGCAATTTTAAAAAGTACATCTCAAAAGTACTTCTTTTCTTCC
65768 AAACCAAGTTTTTTCAAACCG
66 AAACCAAGTTTTTTCAAACCG
65789 AACATAAATTACAATTTTCAACTGCAATTTTAAAAAGTACATCTCAAAAGTA---C--TTCTTCC
1 AACATAAATTACAATTTTCAACTGCAATTTTAAAAAGTACATCTCAAAAGTACTTCTTTTCTTCC
*
65849 AAACCAAGGTTTTTCAAACCG
66 AAACCAAGTTTTTTCAAACCG
65870 CAACCAGAAT
Statistics
Matches: 161, Mismatches: 1, Indels: 7
0.95 0.01 0.04
Matches are distributed among these distances:
81 108 0.67
85 1 0.01
88 52 0.32
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.32
Consensus pattern (86 bp):
AACATAAATTACAATTTTCAACTGCAATTTTAAAAAGTACATCTCAAAAGTACTTCTTTTCTTCC
AAACCAAGTTTTTTCAAACCG
Found at i:75852 original size:54 final size:55
Alignment explanation
Indices: 75755--75862 Score: 166
Period size: 56 Copynumber: 2.0 Consensus size: 55
75745 GCTTCTAAAT
75755 AAAAAAAAAACATTATATAACACAATCAATTTTGTCATATATCCAAATGTCAAAAC
1 AAAAAAAAAACATTATATAACACAATCAATTTTGTCA-ATATCCAAATGTCAAAAC
* *
75811 AAAAAGAAAAACA-TATATAATACAATTAATTTTGTC-ATATCCAAATGTCAAA
1 AAAAA-AAAAACATTATATAACACAATCAATTTTGTCAATATCCAAATGTCAAA
75863 CATCAACACA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
54 16 0.33
56 26 0.53
57 7 0.14
ACGTcount: A:0.54, C:0.14, G:0.05, T:0.28
Consensus pattern (55 bp):
AAAAAAAAAACATTATATAACACAATCAATTTTGTCAATATCCAAATGTCAAAAC
Done.