Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016081.1 Corchorus olitorius cultivar O-4 contig16114, 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: 79232
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1999 original size:42 final size:43
Alignment explanation
Indices: 1948--2042 Score: 122
Period size: 45 Copynumber: 2.2 Consensus size: 43
1938 AGTGCATTAC
* * *
1948 CTAA-ATTCTA-CTCCATCTCTAGGTATTTCATCAAAATAAAT
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
1989 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
2034 CTAAATATT
1 CT-AATATT
2043 AATTGTTGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 30 0.65
46 6 0.13
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:4429 original size:19 final size:19
Alignment explanation
Indices: 4407--4457 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
4397 GGGCTGAAAT
4407 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
4426 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
4445 TAATT-ATTATTAA
1 TAATTAATTATTAA
4458 AAATCCCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:17659 original size:15 final size:15
Alignment explanation
Indices: 17641--17671 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17631 TAAGGGCTGA
*
17641 AATTAATTAATTATT
1 AATTAAATAATTATT
17656 AATTAAATAATTATT
1 AATTAAATAATTATT
17671 A
1 A
17672 TTTTATTGAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTAAATAATTATT
Found at i:23655 original size:25 final size:25
Alignment explanation
Indices: 23621--23669 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
23611 GATTGGTTTG
23621 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
23646 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
23670 GATTGTTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.33, T:0.12
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:24524 original size:21 final size:21
Alignment explanation
Indices: 24489--24530 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
24479 TATGGGTGTG
*
24489 TATGATTGTTTGGTTTGGTAGA
1 TATGATTGATTGGTTT-GTAGA
24511 TATGA-TGATTGGTTTGTAGA
1 TATGATTGATTGGTTTGTAGA
24531 GACTGAGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (21 bp):
TATGATTGATTGGTTTGTAGA
Found at i:24563 original size:25 final size:25
Alignment explanation
Indices: 24527--24575 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
24517 GATTGGTTTG
24527 TAGAGACTGAGCGAGAGTGCTCAAA
1 TAGAGACTGAGCGAGAGTGCTCAAA
24552 TAGAGA-TCGAGCGAGAGTGCTCAA
1 TAGAGACT-GAGCGAGAGTGCTCAA
24576 GATTGTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.35, C:0.16, G:0.33, T:0.16
Consensus pattern (25 bp):
TAGAGACTGAGCGAGAGTGCTCAAA
Found at i:25249 original size:42 final size:43
Alignment explanation
Indices: 25198--25291 Score: 120
Period size: 45 Copynumber: 2.2 Consensus size: 43
25188 AGTGCATTAC
* * * *
25198 CTAA-ATTCTA-CTCCATCTCTAGGTTATTTATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
25239 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA
25284 CTAATATT
1 CTAATATT
25292 AATTGTTGCT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 35 0.78
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.36
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:26101 original size:51 final size:51
Alignment explanation
Indices: 26025--26128 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
26015 TTAATCCTCA
26025 ATTTGGCCTTTAAATAATTTCCATAGCCACTAAAAATAATATATAGTATAT
1 ATTTGGCCTTTAAATAATTTCCATAGCCACTAAAAATAATATATAGTATAT
*
26076 ATTTGGCCTTTAAGTAATTTCCATAGCCACTAAAAATAATATATAGTATAT
1 ATTTGGCCTTTAAATAATTTCCATAGCCACTAAAAATAATATATAGTATAT
26127 AT
1 AT
26129 GTGATTCATA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (51 bp):
ATTTGGCCTTTAAATAATTTCCATAGCCACTAAAAATAATATATAGTATAT
Found at i:27131 original size:35 final size:35
Alignment explanation
Indices: 27086--27162 Score: 145
Period size: 35 Copynumber: 2.2 Consensus size: 35
27076 GAACAAATAC
27086 AAAACACTTTAGAACAAAATTATAAAAGAAAAGGAA
1 AAAAC-CTTTAGAACAAAATTATAAAAGAAAAGGAA
27122 AAAACCTTTAGAACAAAATTATAAAAGAAAAGGAA
1 AAAACCTTTAGAACAAAATTATAAAAGAAAAGGAA
27157 AAAACC
1 AAAACC
27163 AACCTTTAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 36 0.88
36 5 0.12
ACGTcount: A:0.64, C:0.10, G:0.10, T:0.16
Consensus pattern (35 bp):
AAAACCTTTAGAACAAAATTATAAAAGAAAAGGAA
Found at i:30877 original size:17 final size:17
Alignment explanation
Indices: 30855--30888 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
30845 TACTTCCAGA
30855 TAGCATCAATAGGGGTT
1 TAGCATCAATAGGGGTT
30872 TAGCATCAATAGGGGTT
1 TAGCATCAATAGGGGTT
30889 CATAGAGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (17 bp):
TAGCATCAATAGGGGTT
Found at i:31695 original size:32 final size:33
Alignment explanation
Indices: 31654--31716 Score: 110
Period size: 34 Copynumber: 1.9 Consensus size: 33
31644 GCTCTTACAA
31654 CCAATGAAGTT-ACGGGCCTTCATCACGCCGTT
1 CCAATGAAGTTAACGGGCCTTCATCACGCCGTT
31686 CCAATGAAGTTACACGGGCCTTCATCACGCC
1 CCAATGAAGTTA-ACGGGCCTTCATCACGCC
31717 TTTACAAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 11 0.38
34 18 0.62
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.22
Consensus pattern (33 bp):
CCAATGAAGTTAACGGGCCTTCATCACGCCGTT
Found at i:32863 original size:48 final size:48
Alignment explanation
Indices: 32802--32893 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 48
32792 ACTCAATTTT
* *
32802 AAAAAATTTGATGGGATATTTCCTTAAATTGAAAACTTTGAAAAAAAA
1 AAAAAATTGGATGGGATATTTCCCTAAATTGAAAACTTTGAAAAAAAA
* *
32850 AAAAAATTGGATGGGATCTTTCCCTAAATTGAAAATTTTGAAAA
1 AAAAAATTGGATGGGATATTTCCCTAAATTGAAAACTTTGAAAA
32894 CTTTGAAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.32
Consensus pattern (48 bp):
AAAAAATTGGATGGGATATTTCCCTAAATTGAAAACTTTGAAAAAAAA
Found at i:32973 original size:41 final size:42
Alignment explanation
Indices: 32883--32985 Score: 156
Period size: 42 Copynumber: 2.5 Consensus size: 42
32873 CTAAATTGAA
32883 AATTTTGAAAACTTTGAA-GAAAACTTGGTGGGATCTTTCCCT
1 AATTTTGAAAAC-TTGAATGAAAACTTGGTGGGATCTTTCCCT
* * *
32925 AATTTTGAAATCTTGAATGAAATCTTGGTGGGATTTTTCCCT
1 AATTTTGAAAACTTGAATGAAAACTTGGTGGGATCTTTCCCT
32967 AA-TTTGAAAACTTGAATGA
1 AATTTTGAAAACTTGAATGA
32986 CTTCTCTTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
41 21 0.38
42 35 0.62
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (42 bp):
AATTTTGAAAACTTGAATGAAAACTTGGTGGGATCTTTCCCT
Found at i:34405 original size:2 final size:2
Alignment explanation
Indices: 34400--34448 Score: 89
Period size: 2 Copynumber: 24.0 Consensus size: 2
34390 CCCAAAAAAA
34400 AT AT AT AT AT AT AT AT AT GAT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
34443 AT AT AT
1 AT AT AT
34449 CATAAAACAA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34706 original size:64 final size:65
Alignment explanation
Indices: 34605--34733 Score: 242
Period size: 64 Copynumber: 2.0 Consensus size: 65
34595 CCAACACAAG
*
34605 CTAAAGCCCAAGCAAACCAAAGCTAAAACCAAAAAGGCCCAACTAAGATTCT-ACCCTATTCCAA
1 CTAAAGCCCAACCAAACCAAAGCTAAAACCAAAAAGGCCCAACTAAGATTCTAACCCTATTCCAA
34669 CTAAAGCCCAACCAAACCAAAGCTAAAACCAAAAAGGCCCAACTAAGATTCTAACCCTATTCCAA
1 CTAAAGCCCAACCAAACCAAAGCTAAAACCAAAAAGGCCCAACTAAGATTCTAACCCTATTCCAA
34734 ATCTAAATTA
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
64 51 0.81
65 12 0.19
ACGTcount: A:0.46, C:0.32, G:0.09, T:0.14
Consensus pattern (65 bp):
CTAAAGCCCAACCAAACCAAAGCTAAAACCAAAAAGGCCCAACTAAGATTCTAACCCTATTCCAA
Found at i:40428 original size:29 final size:30
Alignment explanation
Indices: 40370--40436 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
40360 CATAGCAAAA
* *
40370 GGGCTTATCTGGCCAAAATTGGTAGTTCAG
1 GGGCTTATCTGGCCAAAATTGGAAATTCAG
* *
40400 GGGCTTTTTTGGCCAAAATT-GAAATTCAG
1 GGGCTTATCTGGCCAAAATTGGAAATTCAG
*
40429 AGGCTTAT
1 GGGCTTAT
40437 TCAACCGTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 13 0.42
30 18 0.58
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (30 bp):
GGGCTTATCTGGCCAAAATTGGAAATTCAG
Found at i:42359 original size:36 final size:33
Alignment explanation
Indices: 42286--42366 Score: 85
Period size: 33 Copynumber: 2.4 Consensus size: 33
42276 TCAGTTGCAA
* *
42286 AGGGAGAGAGAGGCTGAGGCTGCTCGGATTTAT
1 AGGGAGAGAGAGGCTGAGGCTGCTCAGATTTAG
*
42319 AGGGAGAGGGAGGCTGATGCTGCTGCTCAGAGTTT-G
1 AGGGAGAGAGAGGCTGA-G--GCTGCTCAGA-TTTAG
42355 AGGGAGA-AGAGG
1 AGGGAGAGAGAGG
42367 GAGTTAGAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
33 16 0.40
34 1 0.03
35 4 0.10
36 16 0.40
37 3 0.08
ACGTcount: A:0.25, C:0.11, G:0.46, T:0.19
Consensus pattern (33 bp):
AGGGAGAGAGAGGCTGAGGCTGCTCAGATTTAG
Found at i:46776 original size:19 final size:18
Alignment explanation
Indices: 46728--46799 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 18
46718 CACATGCGGA
46728 AATAATAAATGAATACATT
1 AATAATAAAT-AATACATT
46747 AATAA-ATAATAATAACATT
1 AATAATA-AATAAT-ACATT
* *
46766 AATAATAAATACTACGACT
1 AATAATAAATAATAC-ATT
*
46785 AATAATACATAATAC
1 AATAATAAATAATAC
46800 CACATGTTGT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 6 0.13
19 38 0.84
20 1 0.02
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (18 bp):
AATAATAAATAATACATT
Found at i:50345 original size:21 final size:21
Alignment explanation
Indices: 50307--50347 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
50297 AAACAGTAGG
**
50307 AAAGATTGAAAATGGAAGAAA
1 AAAGATTGAAAAAAGAAGAAA
*
50328 AAAGGTTGAAAAAAGAAGAA
1 AAAGATTGAAAAAAGAAGAA
50348 GAGAGAGAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAGATTGAAAAAAGAAGAAA
Found at i:52861 original size:15 final size:16
Alignment explanation
Indices: 52837--52876 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
52827 AGAGCTTGAA
*
52837 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
52852 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
52868 AGAAAACAA
1 AGAAAACAA
52877 AACAAAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:59290 original size:27 final size:26
Alignment explanation
Indices: 59260--59333 Score: 80
Period size: 26 Copynumber: 2.7 Consensus size: 26
59250 GAAAATATTA
*
59260 TTTTTTTTA-AA-ACGCAGGAACAAAAAT
1 TTTTTTTTATAAGACGCA--AA-AAAAAC
59287 TTTTTTTTATAAGACGCAAAAAAAAC
1 TTTTTTTTATAAGACGCAAAAAAAAC
59313 TTTTTTTTATCAAAGACGCAA
1 TTTTTTTTAT--AAGACGCAA
59334 GACAGAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
26 15 0.36
27 11 0.26
28 11 0.26
29 5 0.12
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (26 bp):
TTTTTTTTATAAGACGCAAAAAAAAC
Found at i:62650 original size:115 final size:115
Alignment explanation
Indices: 62448--62696 Score: 399
Period size: 115 Copynumber: 2.2 Consensus size: 115
62438 TGAAAGGAAT
* **
62448 TTTTAATCAATTAATGTTGAAAAATGAAACTTGAGTTTTCATCGATTAATACTACATCCATACAT
1 TTTTAATCGATTAATGTTGAAAAATGAAACTTGAAATTTCATCGATTAATACTACATCCATACAT
62513 GATGTCAACACTGCCACTTTTCTAAGTGAAGACTTAGTGAAAGCTCGAAG
66 GATGTCAACACTGCCACTTTTCTAAGTGAAGACTTAGTGAAAGCTCGAAG
* *
62563 TTTTAATCGATTAATGTTGAAACATGAAACTTGAAATTTCATCGATTAATACTGCATCCATACAT
1 TTTTAATCGATTAATGTTGAAAAATGAAACTTGAAATTTCATCGATTAATACTACATCCATACAT
* * * * *
62628 GCTGTCAACACTGCCACTTTTCTAAGTGAAGACTTGGTGAAGGCTTGGAG
66 GATGTCAACACTGCCACTTTTCTAAGTGAAGACTTAGTGAAAGCTCGAAG
*
62678 TTTTAGTCGATTAATGTTG
1 TTTTAATCGATTAATGTTG
62697 GAGTTAAAAC
Statistics
Matches: 123, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
115 123 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Consensus pattern (115 bp):
TTTTAATCGATTAATGTTGAAAAATGAAACTTGAAATTTCATCGATTAATACTACATCCATACAT
GATGTCAACACTGCCACTTTTCTAAGTGAAGACTTAGTGAAAGCTCGAAG
Found at i:66239 original size:18 final size:18
Alignment explanation
Indices: 66216--66250 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
66206 ACAAAAACTG
66216 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
66234 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
66251 TGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:66489 original size:35 final size:35
Alignment explanation
Indices: 66450--66524 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
66440 TTATATAAAC
*
66450 GAACACTTAAATGAACAATAAACGAGGCTGTTCGT
1 GAACACTTAAATGAACAATAAACAAGGCTGTTCGT
*
66485 GAACACTTAAATGAACAATAAACAAGTCTGTTCGT
1 GAACACTTAAATGAACAATAAACAAGGCTGTTCGT
66520 GAACA
1 GAACA
66525 TAAACGAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (35 bp):
GAACACTTAAATGAACAATAAACAAGGCTGTTCGT
Found at i:68976 original size:6 final size:6
Alignment explanation
Indices: 68961--68995 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
68951 TCAGATTCTT
68961 CAAA-A CAAACA CAAACA CAAACA CAAACA CAAACA
1 CAAACA CAAACA CAAACA CAAACA CAAACA CAAACA
68996 TCAACTTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAACA
Done.