Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023548.1 Corchorus olitorius cultivar O-4 contig23581, 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: 91832
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6306 original size:93 final size:93
Alignment explanation
Indices: 6201--6373 Score: 222
Period size: 93 Copynumber: 1.9 Consensus size: 93
6191 GCATGCCACA
* * *
6201 TGTCACTTTTTGAAACACATGGCATGCCACGTGTCAC-TTTTTGAAACACATGGCATGCCACGTG
1 TGTCACTTTTTGAAACACATGGCATGCCACATATCACTTTTTTG-AACACATGGCATGCCACATG
6265 TCACTTTTGGGTACACATGGCGTGATACG
65 TCACTTTTGGGTACACATGGCGTGATACG
* ** * * * *
6294 TGTCACTTTTTGATACATGTGGCATGCCACATATCGCTTTTTTGTACACGTGGCGTGCCACATGT
1 TGTCACTTTTTGAAACACATGGCATGCCACATATCACTTTTTTGAACACATGGCATGCCACATGT
* *
6359 CTCTTTTTGGTACAC
66 CACTTTTGGGTACAC
6374 GTGACATGTC
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
93 61 0.91
94 6 0.09
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (93 bp):
TGTCACTTTTTGAAACACATGGCATGCCACATATCACTTTTTTGAACACATGGCATGCCACATGT
CACTTTTGGGTACACATGGCGTGATACG
Found at i:6374 original size:31 final size:31
Alignment explanation
Indices: 6185--6381 Score: 198
Period size: 31 Copynumber: 6.4 Consensus size: 31
6175 TCCTTTTGTG
*
6185 CACGTGGCATGCCACATGTCACTTTTTGAAA
1 CACGTGGCATGCCACATGTCACTTTTTGATA
* * *
6216 CACATGGCATGCCACGTGTCACTTTTTGAAA
1 CACGTGGCATGCCACATGTCACTTTTTGATA
* * * *
6247 CACATGGCATGCCACGTGTCACTTTTGGGTA
1 CACGTGGCATGCCACATGTCACTTTTTGATA
* * ** *
6278 CACATGGCGTGATACGTGTCACTTTTTGATA
1 CACGTGGCATGCCACATGTCACTTTTTGATA
* * *
6309 CATGTGGCATGCCACATATCGCTTTTTTG-TA
1 CACGTGGCATGCCACATGTCAC-TTTTTGATA
* * *
6340 CACGTGGCGTGCCACATGTCTCTTTTTGGTA
1 CACGTGGCATGCCACATGTCACTTTTTGATA
*
6371 CACGTGACATG
1 CACGTGGCATG
6382 TCACGGCGGA
Statistics
Matches: 140, Mismatches: 24, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
30 6 0.04
31 128 0.91
32 6 0.04
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.32
Consensus pattern (31 bp):
CACGTGGCATGCCACATGTCACTTTTTGATA
Found at i:6857 original size:3 final size:3
Alignment explanation
Indices: 6849--6878 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
6839 TTTAATAAGC
6849 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6879 TTATTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:7082 original size:5 final size:5
Alignment explanation
Indices: 7072--7105 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
7062 TGAAACATTA
7072 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
7106 AAATATTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:8882 original size:31 final size:31
Alignment explanation
Indices: 8844--8902 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
8834 ATTATATATC
*
8844 AAAATCGTGACAATTTCCCCCGTTAAGTATT
1 AAAATCGTGACAATTTCCCACGTTAAGTATT
8875 AAAATCGTGACAATTTCCCACGTTAAGT
1 AAAATCGTGACAATTTCCCACGTTAAGT
8903 GGCCTAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.31
Consensus pattern (31 bp):
AAAATCGTGACAATTTCCCACGTTAAGTATT
Found at i:13715 original size:13 final size:13
Alignment explanation
Indices: 13697--13721 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13687 TCATGCAAAT
13697 TTCTTCATTTTTC
1 TTCTTCATTTTTC
13710 TTCTTCATTTTT
1 TTCTTCATTTTT
13722 TTACGGTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (13 bp):
TTCTTCATTTTTC
Found at i:20820 original size:15 final size:15
Alignment explanation
Indices: 20800--20841 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
20790 TTTTTAATTA
*
20800 AAAAAATATTTCAAT
1 AAAAAATATTTAAAT
*
20815 AAAAAATATTAAAAT
1 AAAAAATATTTAAAT
20830 -AAAAATATTTAA
1 AAAAAATATTTAA
20842 TTTTTTTGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAAAATATTTAAAT
Found at i:29187 original size:13 final size:13
Alignment explanation
Indices: 29169--29193 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29159 TTTTTACCAC
29169 CTTAAAATTATTG
1 CTTAAAATTATTG
29182 CTTAAAATTATT
1 CTTAAAATTATT
29194 TTTTGGCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
CTTAAAATTATTG
Found at i:36796 original size:22 final size:22
Alignment explanation
Indices: 36720--36890 Score: 138
Period size: 22 Copynumber: 7.9 Consensus size: 22
36710 TTTTACATGG
** *
36720 AGGTTAT-AAAAAATCATAGGA
1 AGGTTATCAAAATTTCATAGGT
* *
36741 AGATTA-CAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAGGT
* *
36762 AGGTTTATTAAAATTTCATAGTT
1 AGG-TTATCAAAATTTCATAGGT
36785 AGGTTATCAAAATTTCATATGG-
1 AGGTTATCAAAATTTCATA-GGT
* * * *
36807 CGTTTATCATAATTTCATAGAT
1 AGGTTATCAAAATTTCATAGGT
* *
36829 A-ATTATTAAAATTTCATAGGGT
1 AGGTTATCAAAATTTCATA-GGT
*
36851 -GGTTATCAAAATTTAATAGGGT
1 AGGTTATCAAAATTTCATA-GGT
36873 A-GTTATCAAAATTTCATA
1 AGGTTATCAAAATTTCATA
36891 AAAAATTCAA
Statistics
Matches: 120, Mismatches: 22, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
21 34 0.28
22 70 0.58
23 16 0.13
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGT
Found at i:36835 original size:65 final size:64
Alignment explanation
Indices: 36766--36890 Score: 173
Period size: 65 Copynumber: 1.9 Consensus size: 64
36756 ATAGGAAGGT
* * *
36766 TTATTAAAATTTCATA-GTTAGGTTATCAAAATTTCATATGGCGT-TTATCATAATTTCATAGAT
1 TTATTAAAATTTCATAGGGT-GGTTATCAAAATTTAATA-GG-GTATTATCAAAATTTCATAGAT
36829 AA
63 AA
36831 TTATTAAAATTTCATAGGGTGGTTATCAAAATTTAATAGGGTAGTTATCAAAATTTCATA
1 TTATTAAAATTTCATAGGGTGGTTATCAAAATTTAATAGGGTA-TTATCAAAATTTCATA
36891 AAAAATTCAA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
63 2 0.04
64 2 0.04
65 48 0.89
66 2 0.04
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.42
Consensus pattern (64 bp):
TTATTAAAATTTCATAGGGTGGTTATCAAAATTTAATAGGGTATTATCAAAATTTCATAGATAA
Found at i:37562 original size:20 final size:21
Alignment explanation
Indices: 37536--37575 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
37526 TTCGTTTTTG
* *
37536 TTTTTTTTTATTATTTCAACA
1 TTTTTTTTAATTACTTCAACA
37557 TTTTTTTTAATTACTTCAA
1 TTTTTTTTAATTACTTCAA
37576 AGTCAAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTTTTAATTACTTCAACA
Found at i:43398 original size:98 final size:98
Alignment explanation
Indices: 43278--43469 Score: 339
Period size: 98 Copynumber: 2.0 Consensus size: 98
43268 CTTGTTATTT
43278 CTCATCATTTGAGATTGATTTGGCAGATATTCAAAGAAGCAGTTTGGAAACTTATGATTCTGACG
1 CTCATCATTTGAGATTGATTTGGCAGATATTCAAAGAAGCAGTTTGGAAACTTATGATTCTGACG
* *
43343 GTTTGGAAACTTATAATTTTGTTTGGAAAATTC
66 GTTTGGAAACTTATAATTCTGATTGGAAAATTC
* * *
43376 CTCATCATTTGAGATTGATTTGGCAGATATTCAGAGAAGCGGTTTGGAAACTTATGATTCTGATG
1 CTCATCATTTGAGATTGATTTGGCAGATATTCAAAGAAGCAGTTTGGAAACTTATGATTCTGACG
43441 GTTTGGAAACTTATAATTCTGATTGGAAA
66 GTTTGGAAACTTATAATTCTGATTGGAAA
43470 TTTATAATTC
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (98 bp):
CTCATCATTTGAGATTGATTTGGCAGATATTCAAAGAAGCAGTTTGGAAACTTATGATTCTGACG
GTTTGGAAACTTATAATTCTGATTGGAAAATTC
Found at i:43443 original size:24 final size:24
Alignment explanation
Indices: 43416--43463 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
43406 TCAGAGAAGC
*
43416 GGTTTGGAAACTTATGATTCTGAT
1 GGTTTGGAAACTTATAATTCTGAT
43440 GGTTTGGAAACTTATAATTCTGAT
1 GGTTTGGAAACTTATAATTCTGAT
43464 TGGAAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.42
Consensus pattern (24 bp):
GGTTTGGAAACTTATAATTCTGAT
Found at i:43468 original size:20 final size:20
Alignment explanation
Indices: 43419--43503 Score: 89
Period size: 20 Copynumber: 4.0 Consensus size: 20
43409 GAGAAGCGGT
*
43419 TTGGAAACTTATGATTCTGA
1 TTGGAAACTTATAATTCTGA
43439 TGGTTTGGAAACTTATAATTCTGA
1 ----TTGGAAACTTATAATTCTGA
* *
43463 TTGGAAATTTATAATTCCGA
1 TTGGAAACTTATAATTCTGA
* *
43483 TTGAAAACTTATAATTTTGA
1 TTGGAAACTTATAATTCTGA
43503 T
1 T
43504 CTTAGTGGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
20 35 0.65
24 19 0.35
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.42
Consensus pattern (20 bp):
TTGGAAACTTATAATTCTGA
Found at i:46713 original size:24 final size:24
Alignment explanation
Indices: 46668--46713 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
46658 TGGACTTGAA
*
46668 GATGACTATGGAGATCATGGAAAG
1 GATGACTATGGAGATCAAGGAAAG
*
46692 GATGAGTATGGAG-TACAAGGAA
1 GATGACTATGGAGAT-CAAGGAA
46714 GCATGGCGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.39, C:0.07, G:0.35, T:0.20
Consensus pattern (24 bp):
GATGACTATGGAGATCAAGGAAAG
Found at i:47797 original size:18 final size:19
Alignment explanation
Indices: 47764--47802 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
47754 AAATATCTCC
47764 AATTAGGGCTAATTGCACA
1 AATTAGGGCTAATTGCACA
*
47783 AATTAGGTC-AATTGCACA
1 AATTAGGGCTAATTGCACA
47801 AA
1 AA
47803 AACAAGAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (19 bp):
AATTAGGGCTAATTGCACA
Found at i:53777 original size:8 final size:8
Alignment explanation
Indices: 53764--53788 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
53754 ATTCTTCAAT
53764 AGTCTTCA
1 AGTCTTCA
53772 AGTCTTCA
1 AGTCTTCA
53780 AGTCTTCA
1 AGTCTTCA
53788 A
1 A
53789 ATTATCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (8 bp):
AGTCTTCA
Found at i:55323 original size:7 final size:7
Alignment explanation
Indices: 55290--55345 Score: 51
Period size: 7 Copynumber: 8.1 Consensus size: 7
55280 TACTTGCAAA
*
55290 TTTAAAT
1 TTTAATT
*
55297 TTAAATT
1 TTTAATT
* *
55304 TTCAATG
1 TTTAATT
55311 TTTAATT
1 TTTAATT
55318 TTTAA-T
1 TTTAATT
*
55324 TTTAATC
1 TTTAATT
*
55331 TCTAATT
1 TTTAATT
55338 TTTAATT
1 TTTAATT
55345 T
1 T
55346 GATCTTATAT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
6 6 0.16
7 32 0.84
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (7 bp):
TTTAATT
Found at i:60798 original size:27 final size:26
Alignment explanation
Indices: 60748--60798 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
60738 ATTATTAAAG
*
60748 TATTTTATTTAGAAAATTTAAATTTT
1 TATTTTATTTAGAAAATTAAAATTTT
60774 TATTTTATTTAGAAAAATTAAAATT
1 TATTTTATTTAG-AAAATTAAAATT
60799 CTACATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (26 bp):
TATTTTATTTAGAAAATTAAAATTTT
Found at i:64747 original size:25 final size:25
Alignment explanation
Indices: 64713--64761 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
64703 CCAAACAATC
64713 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
64738 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
64762 CAAACCAATC
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:0.12, C:0.33, G:0.20, T:0.35
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:65641 original size:25 final size:25
Alignment explanation
Indices: 65607--65655 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
65597 ACAAACAATC
65607 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
65632 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
65656 CAAACTAATC
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:0.12, C:0.33, G:0.20, T:0.35
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:66230 original size:25 final size:25
Alignment explanation
Indices: 66195--66243 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
66185 CCAAACAATC
*
66195 TTGAGCGCTCTCGCTCGGTCTCTAA
1 TTGAGCACTCTCGCTCGGTCTCTAA
66220 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
66244 CAAACTAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.12, C:0.33, G:0.22, T:0.33
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAA
Found at i:79309 original size:6 final size:6
Alignment explanation
Indices: 79298--79338 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
79288 ATTACTTTCG
79298 CCATTA CCATTA CCATTA CCATTA CCATTA CCATTA CCATT
1 CCATTA CCATTA CCATTA CCATTA CCATTA CCATTA CCATT
79339 TCTCACATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (6 bp):
CCATTA
Found at i:84802 original size:23 final size:23
Alignment explanation
Indices: 84772--84817 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
84762 CTAATTAGGT
*
84772 ATATAATAATAGTATCCCTTGCC
1 ATATAATAATAGGATCCCTTGCC
84795 ATATAATAATAGGATCCCTTGCC
1 ATATAATAATAGGATCCCTTGCC
84818 CATTTCTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (23 bp):
ATATAATAATAGGATCCCTTGCC
Found at i:84859 original size:1 final size:1
Alignment explanation
Indices: 84855--84884 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
84845 CAAACAAATT
84855 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
84885 CGAGATCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:86176 original size:22 final size:23
Alignment explanation
Indices: 86148--86193 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
86138 ATTTGGAAAA
86148 TAAGGACAATCTCCCC-TTCACG
1 TAAGGACAATCTCCCCTTTCACG
86170 TAAGGACAATCTCCCCTTTCACG
1 TAAGGACAATCTCCCCTTTCACG
86193 T
1 T
86194 GATGGATTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.26, C:0.35, G:0.13, T:0.26
Consensus pattern (23 bp):
TAAGGACAATCTCCCCTTTCACG
Found at i:87653 original size:2 final size:2
Alignment explanation
Indices: 87648--87685 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
87638 TAATAACATA
*
87648 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
87686 TAAAGTTGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Done.