Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023315.1 Corchorus olitorius cultivar O-4 contig23348, 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: 47668
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:897 original size:29 final size:28
Alignment explanation
Indices: 859--913 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
849 TCCAAATTGC
859 AAGTTCAAGGGGCAAAACGTGCAAAATTA
1 AAGTTCAAGGGGCAAAACGT-CAAAATTA
*
888 AAGTTTAAGGGGCAAAACGTCAAAAT
1 AAGTTCAAGGGGCAAAACGTCAAAAT
914 CGTACAAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.45, C:0.13, G:0.24, T:0.18
Consensus pattern (28 bp):
AAGTTCAAGGGGCAAAACGTCAAAATTA
Found at i:5023 original size:29 final size:31
Alignment explanation
Indices: 4956--5035 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 31
4946 AACTTGTACG
*
4956 GTTTGGAC-GTTTTGCCCCCTGAATTTGTAT
1 GTTTGGACAGTTTTGCCCCCTGAATTTGAAT
*
4986 GTTTGGACAG-TTTGTCCCCTGAACTTT-AAT
1 GTTTGGACAGTTTTGCCCCCTGAA-TTTGAAT
* *
5016 -TTTGGACACTTTTGCTCCCT
1 GTTTGGACAGTTTTGCCCCCT
5036 AAGCAACAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
29 8 0.19
30 30 0.71
31 4 0.10
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (31 bp):
GTTTGGACAGTTTTGCCCCCTGAATTTGAAT
Found at i:5425 original size:22 final size:22
Alignment explanation
Indices: 5397--5441 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5387 AATTGGGCGA
5397 GCTCGGGCGGGTTCGGGTTCGG
1 GCTCGGGCGGGTTCGGGTTCGG
***
5419 GCTCGGGCTTTTTCGGGTTCGG
1 GCTCGGGCGGGTTCGGGTTCGG
5441 G
1 G
5442 TATTTTCGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.00, C:0.22, G:0.49, T:0.29
Consensus pattern (22 bp):
GCTCGGGCGGGTTCGGGTTCGG
Found at i:5433 original size:16 final size:16
Alignment explanation
Indices: 5414--5520 Score: 96
Period size: 16 Copynumber: 6.7 Consensus size: 16
5404 CGGGTTCGGG
5414 TTCGGGCTCGGGCT-TT
1 TTCGGGCTCGGG-TATT
*
5430 TTCGGGTTCGGGTATT
1 TTCGGGCTCGGGTATT
*
5446 TTCGGGCTCGGGT-TAA
1 TTCGGGCTCGGGTAT-T
* *
5462 GTCGGGTTCGGGTATT
1 TTCGGGCTCGGGTATT
5478 TTCGGGCTC-GG-ATT
1 TTCGGGCTCGGGTATT
*
5492 ATGTCGGGTTCGGGTATT
1 -T-TCGGGCTCGGGTATT
*
5510 TTCAGGCTCGG
1 TTCGGGCTCGG
5521 TCTCGGGTAG
Statistics
Matches: 73, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
14 3 0.04
15 5 0.07
16 58 0.79
17 4 0.05
18 3 0.04
ACGTcount: A:0.07, C:0.18, G:0.38, T:0.36
Consensus pattern (16 bp):
TTCGGGCTCGGGTATT
Found at i:5450 original size:32 final size:32
Alignment explanation
Indices: 5414--5520 Score: 162
Period size: 32 Copynumber: 3.3 Consensus size: 32
5404 CGGGTTCGGG
*
5414 TTCGGGCTCGGGCTT-TTTCGGGTTCGGGTATT
1 TTCGGGCTCGGG-TTATGTCGGGTTCGGGTATT
*
5446 TTCGGGCTCGGGTTAAGTCGGGTTCGGGTATT
1 TTCGGGCTCGGGTTATGTCGGGTTCGGGTATT
*
5478 TTCGGGCTCGGATTATGTCGGGTTCGGGTATT
1 TTCGGGCTCGGGTTATGTCGGGTTCGGGTATT
*
5510 TTCAGGCTCGG
1 TTCGGGCTCGG
5521 TCTCGGGTAG
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
31 2 0.03
32 67 0.97
ACGTcount: A:0.07, C:0.18, G:0.38, T:0.36
Consensus pattern (32 bp):
TTCGGGCTCGGGTTATGTCGGGTTCGGGTATT
Found at i:5548 original size:23 final size:23
Alignment explanation
Indices: 5517--5560 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5507 ATTTTCAGGC
* *
5517 TCGGTCTCGGGTAGGGTTCGGGT
1 TCGGGCTCGAGTAGGGTTCGGGT
*
5540 TCGGGCTCGAGTCGGGTTCGG
1 TCGGGCTCGAGTAGGGTTCGG
5561 ACTCGAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.05, C:0.20, G:0.48, T:0.27
Consensus pattern (23 bp):
TCGGGCTCGAGTAGGGTTCGGGT
Found at i:5554 original size:17 final size:17
Alignment explanation
Indices: 5534--5566 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5524 CGGGTAGGGT
*
5534 TCGGGTTCGGGCTCGAG
1 TCGGGTTCGGACTCGAG
5551 TCGGGTTCGGACTCGA
1 TCGGGTTCGGACTCGA
5567 ATTTGATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.24, G:0.42, T:0.24
Consensus pattern (17 bp):
TCGGGTTCGGACTCGAG
Found at i:5712 original size:13 final size:12
Alignment explanation
Indices: 5689--5740 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
5679 AAGTTTATTG
5689 ATAATATATAAT
1 ATAATATATAAT
5701 ATAATAATATAAT
1 ATAAT-ATATAAT
* *
5714 ATAAAAT-TATT
1 ATAATATATAAT
5725 ATCAATATAT-AT
1 AT-AATATATAAT
5737 ATAA
1 ATAA
5741 AGATTGAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
11 7 0.21
12 14 0.42
13 12 0.36
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:10923 original size:6 final size:6
Alignment explanation
Indices: 10912--10944 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
10902 ATAGACTAGA
10912 AAAAAG AAAAAG --AAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
10945 TTAAAAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.16
6 21 0.84
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:10933 original size:16 final size:16
Alignment explanation
Indices: 10912--10942 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
10902 ATAGACTAGA
10912 AAAAAGAAAAAGAAAG
1 AAAAAGAAAAAGAAAG
10928 AAAAAGAAAAAGAAA
1 AAAAAGAAAAAGAAA
10943 AATTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAGAAAG
Found at i:10950 original size:12 final size:12
Alignment explanation
Indices: 10912--10944 Score: 52
Period size: 10 Copynumber: 2.9 Consensus size: 12
10902 ATAGACTAGA
10912 AAAAAGAAAAAG
1 AAAAAGAAAAAG
10924 --AAAGAAAAAG
1 AAAAAGAAAAAG
10934 AAAAAGAAAAA
1 AAAAAGAAAAA
10945 TTAAAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.53
12 9 0.47
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:11655 original size:33 final size:33
Alignment explanation
Indices: 11605--11691 Score: 106
Period size: 33 Copynumber: 2.6 Consensus size: 33
11595 AAATGGTCGG
* *
11605 TGCCGCCCT-GCTAGGGCGGCGTGG-CTATGTCCA
1 TGCCGCCCTCGGT-GGGCGGCGTGGACT-TGGCCA
*
11638 TGCCGCCCTCGGTGGGCGGCATGGACTTGGCCA
1 TGCCGCCCTCGGTGGGCGGCGTGGACTTGGCCA
*
11671 TGGCGCCCTCGGTGGGCGGCG
1 TGCCGCCCTCGGTGGGCGGCG
11692 CCGACCAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
33 43 0.91
34 4 0.09
ACGTcount: A:0.07, C:0.33, G:0.41, T:0.18
Consensus pattern (33 bp):
TGCCGCCCTCGGTGGGCGGCGTGGACTTGGCCA
Found at i:11995 original size:29 final size:28
Alignment explanation
Indices: 11953--12008 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
11943 GTTATTCCAC
*
11953 GTTCTTTAGCGTTCTTGAAGATTAGAAAT
1 GTTCTTGAGCGTTCTTGAA-ATTAGAAAT
*
11982 GTTCTTGAGTGTTCTTGAAATTAGAAA
1 GTTCTTGAGCGTTCTTGAAATTAGAAA
12009 GTTTGAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (28 bp):
GTTCTTGAGCGTTCTTGAAATTAGAAAT
Found at i:13326 original size:33 final size:34
Alignment explanation
Indices: 13265--13330 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
13255 AAATGTAATT
13265 TTTTTATTAGTAAACCTCTTTTGTAGACTCTTTG
1 TTTTTATTAGTAAACCTCTTTTGTAGACTCTTTG
13299 TTTTTATTAGTAAACCTC-TTTGTAGACTCTTT
1 TTTTTATTAGTAAACCTCTTTTGTAGACTCTTT
13331 ATTTGTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 14 0.44
34 18 0.56
ACGTcount: A:0.21, C:0.15, G:0.11, T:0.53
Consensus pattern (34 bp):
TTTTTATTAGTAAACCTCTTTTGTAGACTCTTTG
Found at i:17246 original size:25 final size:25
Alignment explanation
Indices: 17218--17292 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 25
17208 TACTCCATAT
*
17218 AAATAATAATAGGAAAATAAAACAA
1 AAATAAAAATAGGAAAATAAAACAA
* * *
17243 AAAT-AGAA-A-G-AAA-GAAATAA
1 AAATAAAAATAGGAAAATAAAACAA
17263 AAATAAAAATAGGAAAATAAAACAA
1 AAATAAAAATAGGAAAATAAAACAA
17288 AAATA
1 AAATA
17293 GAAAGAAAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
20 9 0.23
21 6 0.15
22 2 0.05
23 2 0.05
24 6 0.15
25 14 0.36
ACGTcount: A:0.75, C:0.03, G:0.09, T:0.13
Consensus pattern (25 bp):
AAATAAAAATAGGAAAATAAAACAA
Found at i:17267 original size:45 final size:45
Alignment explanation
Indices: 17218--17303 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 45
17208 TACTCCATAT
*
17218 AAATAATAATAGGAAAATAAAACAAAAATAGAAAGAAAGAAATAA
1 AAATAAAAATAGGAAAATAAAACAAAAATAGAAAGAAAGAAATAA
17263 AAATAAAAATAGGAAAATAAAACAAAAATAGAAAGAAAGAA
1 AAATAAAAATAGGAAAATAAAACAAAAATAGAAAGAAAGAA
17304 GAGAAGAGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.74, C:0.02, G:0.12, T:0.12
Consensus pattern (45 bp):
AAATAAAAATAGGAAAATAAAACAAAAATAGAAAGAAAGAAATAA
Found at i:18106 original size:30 final size:30
Alignment explanation
Indices: 18044--18100 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
18034 TTTTGATTGA
18044 ATAAACATTTATGATTTTCATGATATAAAT
1 ATAAACATTTATGATTTTCATGATATAAAT
18074 ATAAACATTTAT-ATTTTCATGA-ATAAA
1 ATAAACATTTATGATTTTCATGATATAAA
18101 CATATATAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 5 0.19
29 10 0.37
30 12 0.44
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (30 bp):
ATAAACATTTATGATTTTCATGATATAAAT
Found at i:21139 original size:20 final size:19
Alignment explanation
Indices: 21105--21143 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
21095 TTGGAGTTGC
21105 CAGGAATCCATTTTGAGTGA
1 CAGGAATCCATTTTG-GTGA
21125 CAGGAATACCA-TTTGGTGA
1 CAGGAAT-CCATTTTGGTGA
21144 TGCTGGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 11 0.61
21 3 0.17
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (19 bp):
CAGGAATCCATTTTGGTGA
Found at i:26733 original size:6 final size:7
Alignment explanation
Indices: 26717--26741 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
26707 TTGATGAGTT
26717 AAAAGGA
1 AAAAGGA
26724 AAAAGGA
1 AAAAGGA
26731 AAAAGGA
1 AAAAGGA
26738 AAAA
1 AAAA
26742 TGCTGAGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
AAAAGGA
Found at i:37825 original size:93 final size:93
Alignment explanation
Indices: 37686--37870 Score: 316
Period size: 93 Copynumber: 2.0 Consensus size: 93
37676 TTATTTAAAT
* *
37686 TTTTATAGTTTTAGTCAACTAAAACCTCTATTTTTATTTAAATAAATCTAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAAATAAATCTAATATCCTTATAACTA
* *
37751 TTTTATTTTTACCATTTTACTATTTTAC
66 TTTTATTTTTACCATATTACTAATTTAC
* *
37779 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAAATAAATCTAATATCCTTATAACTA
37844 TTTTATTTTTACCATATTACTAATTTA
66 TTTTATTTTTACCATATTACTAATTTA
37871 ACTAAAAAGA
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 86 1.00
ACGTcount: A:0.33, C:0.14, G:0.02, T:0.51
Consensus pattern (93 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAAATAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATATTACTAATTTAC
Found at i:39645 original size:86 final size:86
Alignment explanation
Indices: 39455--39698 Score: 359
Period size: 85 Copynumber: 2.9 Consensus size: 86
39445 TTTTGTTTTT
39455 ATCTCTTTATAACTATTTTATTTTTACCATTTTACTATTTTAATTAAAAAAACTTAGA-G-ATAT
1 ATCTCTTTATAACTATTTTATTTTTACCATTTTACTATTTTAATTAAAAAAACTTAGATGTAT-T
*
39518 AGAAATTTTTTAATTAAATCTA
65 AGAATTTTTTTAATTAAATCTA
* **
39540 ATCTCTTTAGAACTATTTTATTTTTACCATTTTTTTATTTTAATTAAAAAAACTTAGATGTATTA
1 ATCTCTTTATAACTATTTTATTTTTACCATTTTACTATTTTAATTAAAAAAACTTAGATGTATTA
39605 GAATTTTTTTAATTAAATCTA
66 GAATTTTTTTAATTAAATCTA
* * ** * *
39626 ATCTCTTCATAACTATTTTATTTTTATCATTTTACTATTTTAATT-GCAAAACTTAAATATATTA
1 ATCTCTTTATAACTATTTTATTTTTACCATTTTACTATTTTAATTAAAAAAACTTAGATGTATTA
*
39690 TAATTTTTT
66 GAATTTTTT
39699 AAATAACATT
Statistics
Matches: 143, Mismatches: 14, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
85 78 0.55
86 63 0.44
87 2 0.01
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (86 bp):
ATCTCTTTATAACTATTTTATTTTTACCATTTTACTATTTTAATTAAAAAAACTTAGATGTATTA
GAATTTTTTTAATTAAATCTA
Found at i:44547 original size:17 final size:17
Alignment explanation
Indices: 44525--44575 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
44515 CAAAATATCT
44525 ATTTCAATTAAGTCTGG
1 ATTTCAATTAAGTCTGG
*
44542 ATTTCAACTTAATATCT-G
1 ATTTCAA-TTAA-GTCTGG
44560 -TTTCAATTAAGTCTGG
1 ATTTCAATTAAGTCTGG
44576 GTTTTGATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
15 3 0.10
16 5 0.17
17 13 0.45
18 5 0.17
19 3 0.10
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (17 bp):
ATTTCAATTAAGTCTGG
Found at i:44969 original size:25 final size:24
Alignment explanation
Indices: 44914--44969 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 24
44904 AATCGATACC
44914 TCGATATATCCATTGATATATCTG
1 TCGATATATCCATTGATATATCTG
* *
44938 TCAATATATTCATTCGATATATCTG
1 TCGATATATCCATT-GATATATCTG
*
44963 TGGATAT
1 TCGATAT
44970 CTGTATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.43
Consensus pattern (24 bp):
TCGATATATCCATTGATATATCTG
Done.