Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013625.1 Corchorus olitorius cultivar O-4 contig13658, 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: 78336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:623 original size:2 final size:2
Alignment explanation
Indices: 616--651 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
606 TCAAAAATAC
*
616 AT AT AT AT AT AT AG AT AT A- AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
652 ACGTAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:640 original size:17 final size:17
Alignment explanation
Indices: 618--652 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
608 AAAAATACAT
618 ATATATATATAGATATA
1 ATATATATATAGATATA
*
635 ATATATATATATATATA
1 ATATATATATAGATATA
652 A
1 A
653 CGTAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
ATATATATATAGATATA
Found at i:6126 original size:285 final size:289
Alignment explanation
Indices: 5591--6146 Score: 852
Period size: 285 Copynumber: 1.9 Consensus size: 289
5581 AACTTTAGAA
*
5591 TTAGGTCTCGAGATAAACATAAAAGTTGTAGATCTTGAAATCCTCTTTCCAACGGTACCTCATTT
1 TTAGGTCTCGAGATAAACATAAAAGTTATAGATCTTGAAATCCTCTTTCCAACGGTACCTC--TT
*
5656 GCATTTTTCTGAGCACTAGATCAAAATTTATGAATTTTCTTCCAAAACTGCTCTTGTGAAGTCAT
64 GCATTTTTCTGAGCACTAGATCAAAAGTTATGAATTTTCTTCCAAAACTGCTCTTGTGAAGTCAT
* * * *
5721 CTTTTGAATAGGATTTAACAATGTTGCATCAGATCTGAACCATTACTGCATCATAATTACTGATT
129 CCTTTGAATAGGATTTAACAATGCTACATCAGAGCTGAACCATTACTGCATCATAATTACTGATT
* * * * * **
5786 GGGCTTGGACTCCTTCTTTGTGCTTCCATATTAACGAATTGGGCCTAAGAATATCAGATTTAGGT
194 GGGCTTGGACTCCTTCTTTGGGCTTCCATATTAACAAATTAGACCTAAAAATATCAGATTTAGAC
5851 TTCAAGACATCTGGCCACCGGAACTGCAGAT
259 TTCAAGACATCTGGCCACCGGAACTGCAGAT
*
5882 TTAGGTCTCGAGTTAAACATAAAAGTTATAGATCTTG-AATCCTCTTTCCAACGGTA-C-C-T-C
1 TTAGGTCTCGAGATAAACATAAAAGTTATAGATCTTGAAATCCTCTTTCCAACGGTACCTCTTGC
** * *
5942 ATTTTTCTGAGCTTTGGAATCAAAAGTTATGAATTTTCTTCCAAAACTGCTCTTGTGAAGTCCTC
66 ATTTTTCTGAGCACTAG-ATCAAAAGTTATGAATTTTCTTCCAAAACTGCTCTTGTGAAGTCATC
* *
6007 CTTTGAATAGGATTTAACAATGCTACATCAGGGCTGAATCATTACTGCATCATAATTACTGATTG
130 CTTTGAATAGGATTTAACAATGCTACATCAGAGCTGAACCATTACTGCATCATAATTACTGATTG
* *
6072 GTCTTGGACTCCTTCTTTGGGCTTCCATATTAACAAATTAGATCTAAAAATATCAGATTTAGACT
195 GGCTTGGACTCCTTCTTTGGGCTTCCATATTAACAAATTAGACCTAAAAATATCAGATTTAGACT
6137 TCAAGACATC
260 TCAAGACATC
6147 CGGCTTGGCA
Statistics
Matches: 242, Mismatches: 22, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
284 15 0.06
285 171 0.71
288 1 0.00
289 1 0.00
290 19 0.08
291 35 0.14
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (289 bp):
TTAGGTCTCGAGATAAACATAAAAGTTATAGATCTTGAAATCCTCTTTCCAACGGTACCTCTTGC
ATTTTTCTGAGCACTAGATCAAAAGTTATGAATTTTCTTCCAAAACTGCTCTTGTGAAGTCATCC
TTTGAATAGGATTTAACAATGCTACATCAGAGCTGAACCATTACTGCATCATAATTACTGATTGG
GCTTGGACTCCTTCTTTGGGCTTCCATATTAACAAATTAGACCTAAAAATATCAGATTTAGACTT
CAAGACATCTGGCCACCGGAACTGCAGAT
Found at i:6358 original size:10 final size:10
Alignment explanation
Indices: 6339--6385 Score: 69
Period size: 10 Copynumber: 4.8 Consensus size: 10
6329 TTTAGAAATA
6339 TATCTATATC
1 TATCTATATC
*
6349 TATCTGTATC
1 TATCTATATC
6359 TATCTATATC
1 TATCTATATC
6369 TATCTATA-C
1 TATCTATATC
*
6378 TATATATA
1 TATCTATA
6386 AAAGTACGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
9 8 0.24
10 26 0.76
ACGTcount: A:0.32, C:0.17, G:0.02, T:0.49
Consensus pattern (10 bp):
TATCTATATC
Found at i:6364 original size:14 final size:14
Alignment explanation
Indices: 6337--6382 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
6327 AATTTAGAAA
6337 TATATCTA--TATC
1 TATATCTATCTATC
* *
6349 TATCTGTATCTATC
1 TATATCTATCTATC
6363 TATATCTATCTATAC
1 TATATCTATCTAT-C
6378 TATAT
1 TATAT
6383 ATAAAAGTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 6 0.22
14 15 0.56
15 6 0.22
ACGTcount: A:0.30, C:0.17, G:0.02, T:0.50
Consensus pattern (14 bp):
TATATCTATCTATC
Found at i:18180 original size:123 final size:127
Alignment explanation
Indices: 18029--18278 Score: 373
Period size: 131 Copynumber: 2.0 Consensus size: 127
18019 TTGTTTAAAT
* * *
18029 TTTTATAGTTTCACTAAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAT-CTT-TA-TA-
1 TTTTACAGTTTCACTAAACTAAAAACTCTATTTTTAGTTAATTAAAACTAATATCCTTATACTAT
*
18090 ATTTTTACCATTTTACTATCTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATAC
66 ATTTTTACCATTTTAATATCTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATAC
* *
18152 TTTTACAGTTTTACTCAACTAAAAACTCTATTTTTAGTTAATTAAAACTAATATCCTTATATCTA
1 TTTTACAGTTTCACTAAACTAAAAACTCTATTTTTAGTTAATTAAAACTAATATCCTTATA-CTA
*
18217 TTTTATTTTTACCATTTTAATATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAAT
65 ---TATTTTTACCATTTTAATATCTTAATTAAAAAACTTATATATATTAGAATTTTTTAAAT
18279 TTATTTCTTA
Statistics
Matches: 112, Mismatches: 7, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
123 49 0.44
124 3 0.03
125 2 0.02
127 2 0.02
131 56 0.50
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.49
Consensus pattern (127 bp):
TTTTACAGTTTCACTAAACTAAAAACTCTATTTTTAGTTAATTAAAACTAATATCCTTATACTAT
ATTTTTACCATTTTAATATCTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATAC
Found at i:22584 original size:2 final size:2
Alignment explanation
Indices: 22577--22607 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
22567 CGTTTTCCGA
22577 AT AT 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 AT AT A
22608 CCTCGGAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24517 original size:25 final size:25
Alignment explanation
Indices: 24489--24564 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 25
24479 TTATATGCAA
24489 TTAAAATTTTAAAAAATATATTTTG
1 TTAAAATTTTAAAAAATATATTTTG
*
24514 TTAAATTTTTTTAAAAAA-AT-TTTT-
1 TTAAA--ATTTTAAAAAATATATTTTG
**
24538 AAAAAATTTTAAAAAATTATATTTTG
1 TTAAAATTTTAAAAAA-TATATTTTG
24564 T
1 T
24565 AATAATTAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
22 10 0.25
24 5 0.12
25 13 0.32
26 2 0.05
27 10 0.25
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (25 bp):
TTAAAATTTTAAAAAATATATTTTG
Found at i:24536 original size:11 final size:11
Alignment explanation
Indices: 24522--24553 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
24512 TGTTAAATTT
24522 TTTTAAAAAAA
1 TTTTAAAAAAA
*
24533 TTTTTAAAAAA
1 TTTTAAAAAAA
24544 TTTTAAAAAA
1 TTTTAAAAAA
24554 TTATATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TTTTAAAAAAA
Found at i:24541 original size:10 final size:10
Alignment explanation
Indices: 24522--24555 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
24512 TGTTAAATTT
24522 TTTTAAAAAAA
1 TTTT-AAAAAA
24533 TTTTTAAAAAA
1 -TTTTAAAAAA
24544 TTTTAAAAAA
1 TTTTAAAAAA
24554 TT
1 TT
24556 ATATTTTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 6 0.27
12 4 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTTAAAAAA
Found at i:31906 original size:15 final size:15
Alignment explanation
Indices: 31886--31915 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
31876 TGGGAAAAGC
31886 AAAGTCATCTTCATT
1 AAAGTCATCTTCATT
31901 AAAGTCATCTTCATT
1 AAAGTCATCTTCATT
31916 TTGGTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (15 bp):
AAAGTCATCTTCATT
Found at i:32700 original size:25 final size:25
Alignment explanation
Indices: 32671--32721 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
32661 CTAATAAGTT
32671 ATTTGACCCTCCAACTTCTATTTGG
1 ATTTGACCCTCCAACTTCTATTTGG
32696 ATTTGACCCTCCAACTTCTATTTGG
1 ATTTGACCCTCCAACTTCTATTTGG
32721 A
1 A
32722 ACAATTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.22, C:0.27, G:0.12, T:0.39
Consensus pattern (25 bp):
ATTTGACCCTCCAACTTCTATTTGG
Found at i:40965 original size:3 final size:3
Alignment explanation
Indices: 40937--40982 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
40927 GACCAGATAT
*
40937 TAA TAA GTAA TCA TAA TTAA -AA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA -TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40983 AAAAGAAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.79
4 6 0.16
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:43156 original size:13 final size:13
Alignment explanation
Indices: 43130--43165 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
43120 AAAAGCTTGG
43130 TTTTGAAGAAGTGC
1 TTTTGAA-AAGTGC
43144 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
*
43157 TTTTTAAAA
1 TTTTGAAAA
43166 TTGGGTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:49246 original size:95 final size:95
Alignment explanation
Indices: 49080--49255 Score: 264
Period size: 95 Copynumber: 1.9 Consensus size: 95
49070 AGAGAATAGC
* *
49080 GGGTCGCGACCTGGCCATGCACCTGAGTCGCGACGCGGGTCGCGTGCAACCCGAGCCATGGCGGG
1 GGGTCGCGACCTGGCCATGCACCTGAGTCGCGACGCGGGTCGCGCGCAACCCGAGCCATAGCGGG
*
49145 TGGCGATCCGCACGCGGCCCACCATGGCGT
66 TCGCGATCCGCACGCGGCCCACCATGGCGT
* * * * *
49175 GGGTCGCGACCTGGCCATGGA-CTCGGGTCGTGATGCGGGTCGCGCGCGACCCGAGCCATAGCGG
1 GGGTCGCGACCTGGCCATGCACCT-GAGTCGCGACGCGGGTCGCGCGCAACCCGAGCCATAGCGG
49239 GTCGCGATCCGCACGCG
65 GTCGCGATCCGCACGCG
49256 ACCTTTTATC
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
94 2 0.03
95 70 0.97
ACGTcount: A:0.13, C:0.35, G:0.39, T:0.13
Consensus pattern (95 bp):
GGGTCGCGACCTGGCCATGCACCTGAGTCGCGACGCGGGTCGCGCGCAACCCGAGCCATAGCGGG
TCGCGATCCGCACGCGGCCCACCATGGCGT
Found at i:53762 original size:129 final size:130
Alignment explanation
Indices: 53527--53785 Score: 484
Period size: 129 Copynumber: 2.0 Consensus size: 130
53517 AGCATGGTCT
*
53527 CCCCTAATCTGTCTGAGAAACAAGATGATGTACCATTTTCCAAGTACGGCATGCATTCAATTTCC
1 CCCCTAATCTGTCTGAAAAACAAGATGATGTACCATTTTCCAAGTACGGCATGCATTCAATTTCC
53592 ATGATGTTCCTTGTCGGCATCCCATGAAGTTTCTTGGAAGGAATATCTGACTTAGAGCAAGCAAA
66 ATGATGTTCCTTGTCGGCATCCCATGAAGTTTCTTGGAAGGAATATCTGACTTAGAGCAAGCAAA
*
53657 CCCC-AATCTGTCTGAAAAACAAGATGATGTACCATTTTCCAAGTCCGGCATGCATTCAATTTCC
1 CCCCTAATCTGTCTGAAAAACAAGATGATGTACCATTTTCCAAGTACGGCATGCATTCAATTTCC
*
53721 ATGATGTTCCTTGTCGGCATCCCGTGAAGTTTCTTGGAAGGAATATCTGACTTAGAGCAAGCAAA
66 ATGATGTTCCTTGTCGGCATCCCATGAAGTTTCTTGGAAGGAATATCTGACTTAGAGCAAGCAAA
53786 TAACTCAGAT
Statistics
Matches: 126, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
129 122 0.97
130 4 0.03
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (130 bp):
CCCCTAATCTGTCTGAAAAACAAGATGATGTACCATTTTCCAAGTACGGCATGCATTCAATTTCC
ATGATGTTCCTTGTCGGCATCCCATGAAGTTTCTTGGAAGGAATATCTGACTTAGAGCAAGCAAA
Found at i:62765 original size:16 final size:15
Alignment explanation
Indices: 62727--62768 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
62717 ACAGAGGTTG
62727 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
62742 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
62757 ACTAGAAAACAA
1 AC-AGAAAACAA
62769 AACAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:71269 original size:17 final size:17
Alignment explanation
Indices: 71247--71280 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
71237 ACCTTTAAGC
71247 CTAAATCT-ATCACATAA
1 CTAAATCTCAT-ACATAA
71264 CTAAATCTCATACATAA
1 CTAAATCTCATACATAA
71281 ATCAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (17 bp):
CTAAATCTCATACATAA
Found at i:75599 original size:21 final size:21
Alignment explanation
Indices: 75575--75619 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
75565 TCAAAATTGA
*
75575 TTTACGACAAAATTTTAATTT
1 TTTACGACAAAATTTCAATTT
* * *
75596 TTTATGATAAAATTTCGATTT
1 TTTACGACAAAATTTCAATTT
75617 TTT
1 TTT
75620 TCAACTATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (21 bp):
TTTACGACAAAATTTCAATTT
Done.