Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006344.1 Corchorus capsularis cultivar CVL-1 contig06365, 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: 17852
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Found at i:1441 original size:31 final size:30
Alignment explanation
Indices: 1401--1479 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 30
1391 ATTTTTAGCC
*
1401 ACCAATTTGAGTCTAAACCTTTCAAAAGTTG
1 ACCAATTTGAG-CTAAACCTTTCAAAACTTG
1432 -CTCAATTTGAGCATAAACCTTTCAAAACTTG
1 AC-CAATTTGAGC-TAAACCTTTCAAAACTTG
1463 ACCAATTTGAGCCTAAA
1 ACCAATTTGAG-CTAAA
1480 AATAGGTGCC
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
30 2 0.05
31 39 0.91
32 2 0.05
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (30 bp):
ACCAATTTGAGCTAAACCTTTCAAAACTTG
Found at i:9239 original size:6 final size:6
Alignment explanation
Indices: 9221--9263 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
9211 GTTCAAGTGC
* * *
9221 TTGGAG TTAGAG TTGGAG TTGGAG TTGGAG TGGGAG TGGGAG T
1 TTGGAG TTGGAG TTGGAG TTGGAG TTGGAG TTGGAG TTGGAG T
9264 GGGGAGTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.19, C:0.00, G:0.51, T:0.30
Consensus pattern (6 bp):
TTGGAG
Found at i:11140 original size:36 final size:36
Alignment explanation
Indices: 11095--11266 Score: 204
Period size: 36 Copynumber: 4.7 Consensus size: 36
11085 GCAGTCAAAG
*
11095 GAACTTAATTCAGGGAAATTAAGTAAAAGTAGTTAA
1 GAACTTAATTCAGGGAAATTAAGTAAAAGCAGTTAA
* *
11131 GAACTTAATTCAGGGAAATTAGGTAAAAACAGTTAAA
1 GAACTTAATTCAGGGAAATTAAGTAAAAGCAGTT-AA
*
11168 GTACTTAATTCA-GGATAATTAAGTAAAAGCAGTT-A
1 GAACTTAATTCAGGGA-AATTAAGTAAAAGCAGTTAA
* * *
11203 GAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTCAA
1 G-A-ACTTAATTCAGGGAAATTAAGTAAAAGCAGTTAA
* **
11241 GGACTTAATTCAGGGTGATTAAGTAA
1 GAACTTAATTCAGGGAAATTAAGTAA
11267 GAAAAGCACA
Statistics
Matches: 118, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
35 2 0.02
36 57 0.48
37 55 0.47
38 4 0.03
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.28
Consensus pattern (36 bp):
GAACTTAATTCAGGGAAATTAAGTAAAAGCAGTTAA
Found at i:11188 original size:37 final size:35
Alignment explanation
Indices: 11073--11254 Score: 186
Period size: 37 Copynumber: 4.9 Consensus size: 35
11063 CATCGTATGC
* *
11073 ATTAAGTAAAGTGCAGTCAAAGGAACTTAATTCAGGGAA
1 ATTAAGTAAA-AGCAGTTAAA-G-ACTTAATTCA-GGAA
*
11112 ATTAAGTAAAAGTAGTT-AAGAACTTAATTCAGGGAA
1 ATTAAGTAAAAGCAGTTAAAG-ACTTAATTCA-GGAA
* *
11148 ATTAGGTAAAAACAGTTAAAGTACTTAATTCAGGATA
1 ATTAAGTAAAAGCAGTTAAAG-ACTTAATTCAGGA-A
*
11185 ATTAAGTAAAAGCAGTTAGAAGACTTAATTCAGGGTA
1 ATTAAGTAAAAGCAGTTA-AAGACTTAATTCA-GGAA
* * *
11222 ATTAAGTAAAATCAGTCAAGGACTTAATTCAGG
1 ATTAAGTAAAAGCAGTTAAAGACTTAATTCAGG
11255 GTGATTAAGT
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
35 2 0.02
36 46 0.37
37 59 0.47
38 9 0.07
39 10 0.08
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.27
Consensus pattern (35 bp):
ATTAAGTAAAAGCAGTTAAAGACTTAATTCAGGAA
Found at i:11247 original size:73 final size:72
Alignment explanation
Indices: 11073--11266 Score: 230
Period size: 73 Copynumber: 2.6 Consensus size: 72
11063 CATCGTATGC
* *
11073 ATTAAGTAAAGTGCAGTCAAAGGAACTTAATTCAGGGA-AATTAAGTAAAAGTAGTTAAGAACTT
1 ATTAAGTAAAAT-CAGTC-AAGG-ACTTAATTCA-GGATAATTAAGTAAAAGCAGTTAAGAACTT
11137 AATTCAGGGAA
62 AATTCAGGGAA
* * * *
11148 ATTAGGTAAAAACAGTTAAAGTACTTAATTCAGGATAATTAAGTAAAAGCAGTT-AGAAGACTTA
1 ATTAAGTAAAATCAG-TCAAGGACTTAATTCAGGATAATTAAGTAAAAGCAGTTAAG-A-ACTTA
*
11212 ATTCAGGGTA
63 ATTCAGGGAA
* *
11222 ATTAAGTAAAATCAGTCAAGGACTTAATTCAGGGTGATTAAGTAA
1 ATTAAGTAAAATCAGTCAAGGACTTAATTCAGGATAATTAAGTAA
11267 GAAAAGCACA
Statistics
Matches: 102, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
72 5 0.05
73 54 0.53
74 33 0.32
75 10 0.10
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.27
Consensus pattern (72 bp):
ATTAAGTAAAATCAGTCAAGGACTTAATTCAGGATAATTAAGTAAAAGCAGTTAAGAACTTAATT
CAGGGAA
Found at i:11327 original size:41 final size:41
Alignment explanation
Indices: 11265--11367 Score: 188
Period size: 41 Copynumber: 2.5 Consensus size: 41
11255 GTGATTAAGT
* *
11265 AAGAAAAGCACAGACTTAATTTCAAGGAACGAAATTAGGTA
1 AAGACAAGCACAGACTTAATTTCAAGGAAAGAAATTAGGTA
11306 AAGACAAGCACAGACTTAATTTCAAGGAAAGAAATTAGGTA
1 AAGACAAGCACAGACTTAATTTCAAGGAAAGAAATTAGGTA
11347 AAGACAAGCACAGACTTAATT
1 AAGACAAGCACAGACTTAATT
11368 CAGGGTAATT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.19
Consensus pattern (41 bp):
AAGACAAGCACAGACTTAATTTCAAGGAAAGAAATTAGGTA
Found at i:11577 original size:37 final size:37
Alignment explanation
Indices: 11464--11759 Score: 309
Period size: 37 Copynumber: 8.4 Consensus size: 37
11454 AGAACAGACA
* **
11464 AAGGACTTAATTCCAAGGAAAGGGAATTAAGTAGAGCA
1 AAGGACTTAATTCCAAGG-AAGGAAATTAAGTAGAGTT
* *
11502 AAGGACTTGATTCCAAGGAA-GAGAATCAAGTA-A--T
1 AAGGACTTAATTCCAAGGAAGGA-AATTAAGTAGAGTT
* *
11536 --GGACTTAATTTCAAGGGAGGAAATTAAGTAGAGTT
1 AAGGACTTAATTCCAAGGAAGGAAATTAAGTAGAGTT
*
11571 AAGGACTTAATTCCAAGGAAGGGAATTAAGTAGAGTT
1 AAGGACTTAATTCCAAGGAAGGAAATTAAGTAGAGTT
* *
11608 AAGGACTTAATTCCAAGGAAGGGAATTACGTAGAGTT
1 AAGGACTTAATTCCAAGGAAGGAAATTAAGTAGAGTT
*
11645 AAGGACTTAATTTCAAGGAAGGAAATTAAGT--AG--
1 AAGGACTTAATTCCAAGGAAGGAAATTAAGTAGAGTT
* *
11678 -AGGACTTGATTCTAA-G--GG-AATTAAGTAGAGTT
1 AAGGACTTAATTCCAAGGAAGGAAATTAAGTAGAGTT
* *
11710 AAGGACTTAATTTCAAGCAAGGAAATTAAGTCA-AGTT
1 AAGGACTTAATTCCAAGGAAGGAAATTAAGT-AGAGTT
*
11747 AGGGACTTAATTC
1 AAGGACTTAATTC
11760 AGGGTAATTA
Statistics
Matches: 217, Mismatches: 24, Indels: 35
0.79 0.09 0.13
Matches are distributed among these distances:
28 8 0.04
29 2 0.01
30 2 0.01
31 1 0.00
32 35 0.16
33 15 0.07
35 3 0.01
36 4 0.02
37 129 0.59
38 18 0.08
ACGTcount: A:0.41, C:0.09, G:0.25, T:0.25
Consensus pattern (37 bp):
AAGGACTTAATTCCAAGGAAGGAAATTAAGTAGAGTT
Found at i:11592 original size:18 final size:18
Alignment explanation
Indices: 11571--11629 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
11561 AAGTAGAGTT
11571 AAGGACTTAATTCCAAGG
1 AAGGACTTAATTCCAAGG
* * *
11589 AAGGGAATTAAGT--AGAGTT
1 AA-GGACTTAATTCCA-AG-G
11608 AAGGACTTAATTCCAAGG
1 AAGGACTTAATTCCAAGG
11626 AAGG
1 AAGG
11630 GAATTACGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
17 1 0.03
18 16 0.53
19 12 0.40
20 1 0.03
ACGTcount: A:0.41, C:0.10, G:0.27, T:0.22
Consensus pattern (18 bp):
AAGGACTTAATTCCAAGG
Found at i:11831 original size:74 final size:74
Alignment explanation
Indices: 11747--11967 Score: 245
Period size: 73 Copynumber: 3.0 Consensus size: 74
11737 AAGTCAAGTT
* *
11747 AGGGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAGGGCTTAATTCAGGGTAATTAAGTAG
1 AGGGACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAA-GACTTAATTCAGGGTAATTAAGTAG
*
11812 CGTCAATAAA
65 AGTCAATAAA
* * *
11822 AGGG-CTTAATTCAGGGTAATTAAGTAGAGTTAATAAAAGACTTAATTTAGGGTAATTAAGTGGA
1 AGGGACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAAGACTTAATTCAGGGTAATTAAGTAGA
11886 GTCAAT-AA
66 GTCAATAAA
* * ** ** *
11894 A-GAACTTAATCTAAAAAG-AGATTAAGTA-AAACAATAAAAGACTTAATTTAGGGTAATTAAGT
1 AGGGACTTAAT-T-CAGGGTA-ATTAAGTAGAGTCAATAAAAGACTTAATTCAGGGTAATTAAGT
*
11956 GGAGTCAATAAA
63 AGAGTCAATAAA
11968 GAACTTAATC
Statistics
Matches: 128, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
71 1 0.01
72 9 0.07
73 70 0.55
74 44 0.34
75 4 0.03
ACGTcount: A:0.43, C:0.08, G:0.21, T:0.28
Consensus pattern (74 bp):
AGGGACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAAGACTTAATTCAGGGTAATTAAGTAGA
GTCAATAAA
Found at i:11874 original size:36 final size:36
Alignment explanation
Indices: 11750--11976 Score: 237
Period size: 37 Copynumber: 6.2 Consensus size: 36
11740 TCAAGTTAGG
*
11750 GACTTAATTCAGGGTAATTAAGTAGCGTCAATAAAA
1 GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAA
* *
11786 GGGCTTAATTCAGGGTAATTAAGTAGCGTCAATAAAA
1 -GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAA
* *
11823 GGGCTTAATTCAGGGTAATTAAGTAGAGTTAATAAAA
1 -GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAA
* *
11860 GACTTAATTTAGGGTAATTAAGTGGAGTCAAT-AAA
1 GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAA
* ** **
11895 GAACTTAATCTAAAAAG-AGATTAAGTA-AAACAATAAAA
1 G-ACTTAAT-T-CAGGGTA-ATTAAGTAGAGTCAATAAAA
* *
11933 GACTTAATTTAGGGTAATTAAGTGGAGTCAAT-AAA
1 GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAA
11968 GAACTTAAT
1 G-ACTTAAT
11977 CTAAAAGAGA
Statistics
Matches: 163, Mismatches: 19, Indels: 17
0.82 0.10 0.09
Matches are distributed among these distances:
35 17 0.10
36 49 0.30
37 84 0.52
38 13 0.08
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.28
Consensus pattern (36 bp):
GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAA
Found at i:12001 original size:36 final size:36
Alignment explanation
Indices: 11888--12003 Score: 103
Period size: 36 Copynumber: 3.2 Consensus size: 36
11878 TAAGTGGAGT
11888 CAATAAAGAACTTAATCTAAAAAGAGATTAAGTAAAA
1 CAATAAAGAACTTAATCT-AAAAGAGATTAAGTAAAA
* ** * **
11925 CAATAAA-AGACTTAAT-TTAGGGTA-ATTAAGTGGAGT
1 CAATAAAGA-ACTTAATCTAAAAG-AGATTAAGT-AAAA
* *
11961 CAATAAAGAACTTAATCTAAAAGAGATTAAATCAAA
1 CAATAAAGAACTTAATCTAAAAGAGATTAAGTAAAA
11997 CAATAAA
1 CAATAAA
12004 AGGGCTTGAT
Statistics
Matches: 60, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
35 9 0.15
36 27 0.45
37 24 0.40
ACGTcount: A:0.54, C:0.09, G:0.13, T:0.24
Consensus pattern (36 bp):
CAATAAAGAACTTAATCTAAAAGAGATTAAGTAAAA
Found at i:12016 original size:73 final size:73
Alignment explanation
Indices: 11853--12005 Score: 281
Period size: 73 Copynumber: 2.1 Consensus size: 73
11843 AAGTAGAGTT
11853 AATAAAAGACTTAATTTAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCTAAAAAGAGATTA
1 AATAAAAGACTTAATTTAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCTAAAAAGAGATTA
*
11918 AGTAAAAC
66 AATAAAAC
11926 AATAAAAGACTTAATTTAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCT-AAAAGAGATTA
1 AATAAAAGACTTAATTTAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCTAAAAAGAGATTA
*
11990 AATCAAAC
66 AATAAAAC
11998 AATAAAAG
1 AATAAAAG
12006 GGCTTGATTT
Statistics
Matches: 78, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
72 25 0.32
73 53 0.68
ACGTcount: A:0.52, C:0.07, G:0.16, T:0.25
Consensus pattern (73 bp):
AATAAAAGACTTAATTTAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCTAAAAAGAGATTA
AATAAAAC
Found at i:13914 original size:130 final size:129
Alignment explanation
Indices: 13618--13874 Score: 325
Period size: 129 Copynumber: 2.0 Consensus size: 129
13608 AAGGATAGCT
** * * * * * *
13618 CATGTTATAACTTGTCATAACATTCATTCGCATCAATTGCATAAAGGCAAGAACCCTGATTATTC
1 CATGTTATAAAATCTCATAACATACATTGGAAACAATAGCATAAAGGCAAGAACCCTGATTATTC
* *
13683 ACAGAATTGTAAATGGTCACGGCTTTTGACTTGTGGAAGTTCCTACCAAATTGTGGAGGGACCC
66 ACAGAATTGTAAATGGTCACGACTTTTGACTTGTGCAAGTTCCTACCAAATTGTGGAGGGACCC
** * * * * *
13747 CATGTTATAACTTGTCATAACATTCATTTGCATCAATAGCATAAAGGCAAGAACCCTGATTATTC
1 CATGTTATAAAATCTCATAACATACATTGGAAACAATAGCATAAAGGCAAGAACCCTGATTATTC
* * *
13812 ACGGAATTTGTAAATGGTCACGACTTTTGGCTTGTGCAAGTTCTTACCAAATTGTGGAGGGAC
66 ACAGAA-TTGTAAATGGTCACGACTTTTGACTTGTGCAAGTTCCTACCAAATTGTGGAGGGAC
13875 TCCACACCTT
Statistics
Matches: 120, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
129 68 0.57
130 52 0.43
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (129 bp):
CATGTTATAAAATCTCATAACATACATTGGAAACAATAGCATAAAGGCAAGAACCCTGATTATTC
ACAGAATTGTAAATGGTCACGACTTTTGACTTGTGCAAGTTCCTACCAAATTGTGGAGGGACCC
Found at i:16536 original size:14 final size:14
Alignment explanation
Indices: 16517--16556 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
16507 CGAGTCGCAA
16517 AACAAAAAAAAAAC
1 AACAAAAAAAAAAC
16531 AAC-AAAAAAAAAC
1 AACAAAAAAAAAAC
16544 AA-AAAACAAAAAA
1 AACAAAA-AAAAAA
16557 AACCAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 15 0.62
14 9 0.38
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (14 bp):
AACAAAAAAAAAAC
Found at i:16542 original size:17 final size:17
Alignment explanation
Indices: 16514--16564 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
16504 AGCCGAGTCG
*
16514 CAAAACAAAAAAAAAACAA
1 CAAAA-AAAAACAAAA-AA
16533 CAAAAAAAAACAAAAAA
1 CAAAAAAAAACAAAAAA
*
16550 CAAAAAAAACCAAAA
1 CAAAAAAAAACAAAA
16565 TTTTGCAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 16 0.53
18 9 0.30
19 5 0.17
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (17 bp):
CAAAAAAAAACAAAAAA
Found at i:16547 original size:20 final size:19
Alignment explanation
Indices: 16514--16558 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
16504 AGCCGAGTCG
*
16514 CAAAACAAAAAAAAAACAA
1 CAAAAAAAAAAAAAAACAA
16533 CAAAAAAAAACAAAAAACAA
1 CAAAAAAAAA-AAAAAACAA
16553 -AAAAAA
1 CAAAAAA
16559 CCAAAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (19 bp):
CAAAAAAAAAAAAAAACAA
Found at i:16563 original size:10 final size:10
Alignment explanation
Indices: 16515--16564 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
16505 GCCGAGTCGC
16515 AAAACAAAAAA
1 AAAAC-AAAAA
16526 AAAACAACAAA
1 AAAACAA-AAA
*
16537 AAAA-AACAA
1 AAAACAAAAA
16546 AAAACAAAAA
1 AAAACAAAAA
*
16556 AAACCAAAA
1 AAAACAAAA
16565 TTTTGCAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
9 6 0.18
10 16 0.47
11 12 0.35
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAACAAAAA
Found at i:16564 original size:9 final size:9
Alignment explanation
Indices: 16514--16564 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
16504 AGCCGAGTCG
16514 CAAAACAAAA
1 CAAAA-AAAA
16524 -AAAAAACAA
1 CAAAAAA-AA
16533 CAAAAAAAA
1 CAAAAAAAA
*
16542 -ACAAAAAA
1 CAAAAAAAA
16550 CAAAAAAAA
1 CAAAAAAAA
16559 CCAAAA
1 -CAAAA
16565 TTTTGCAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
8 9 0.26
9 15 0.43
10 11 0.31
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (9 bp):
CAAAAAAAA
Done.