Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012499.1 Corchorus olitorius cultivar O-4 contig12532, 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: 7985
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Found at i:99 original size:13 final size:15
Alignment explanation
Indices: 81--116 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
71 AACCCAAAAG
81 AAAAGAAA-AA-GAA
1 AAAAGAAAGAAGGAA
94 AAAAGAAAGAAGGAA
1 AAAAGAAAGAAGGAA
109 AAAA-AAAG
1 AAAAGAAAG
117 GAGAAGACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.38
14 6 0.29
15 7 0.33
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAGGAA
Found at i:214 original size:46 final size:45
Alignment explanation
Indices: 154--269 Score: 144
Period size: 46 Copynumber: 2.5 Consensus size: 45
144 ACATTTTGAG
154 AAACTAATAAGGAAATGGGTCTTTAAAAAAGAAATGGACTTTGAAT
1 AAACTAATAAGGAAATGGG-CTTTAAAAAAGAAATGGACTTTGAAT
* * ** *
200 -TACTAAATAAGGAAATGGGCTCTAAAATGGTAATGGACTTTGAAT
1 AAACT-AATAAGGAAATGGGCTTTAAAAAAGAAATGGACTTTGAAT
*
245 GAAACTAATGAGGAAATGGGCTTTA
1 -AAACTAATAAGGAAATGGGCTTTA
270 TTAAAATGGA
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
45 25 0.42
46 31 0.53
47 3 0.05
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (45 bp):
AAACTAATAAGGAAATGGGCTTTAAAAAAGAAATGGACTTTGAAT
Found at i:378 original size:41 final size:41
Alignment explanation
Indices: 321--685 Score: 416
Period size: 41 Copynumber: 8.7 Consensus size: 41
311 GTCTACACCC
321 CTGTGTTATATATGTGTTTGGGGACTTTG-ATATAAATGCCT
1 CTGTGTTATATATGTGTTTGGGGACTTTGTA-ATAAATGCCT
* * *
362 CTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCC
1 CTGTGTTATATATGTGTTTGGGGACTTTGTAATA-A-ATGCCT
* *
405 CTGTGTTATATATGTGTTTGGGGACTTTG-ATATAGATGTCT
1 CTGTGTTATATATGTGTTTGGGGACTTTGTA-ATAAATGCCT
* *
446 CTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGGTGCC-
1 CTGTGTTATATATGTGTTTGGGGACTTTGTAATA-A-ATGCCT
* * *
488 CTTGTGTTATATATGTGTTTGGGGTCTTTGTAATAGATTCCT
1 C-TGTGTTATATATGTGTTTGGGGACTTTGTAATAAATGCCT
* *
530 CTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGGTGCCC
1 CTGTGTTATATATGTGTTTGGGGACTTTGTAATAAA--TGCCT
*
573 CTGTGTTATATATGTGTTTGGGGAC-TTG-AATATAGGTGCCT
1 CTGTGTTATATATGTGTTTGGGGACTTTGTAATA-A-ATGCCT
* * * *
614 CTGTGTTATATATGTGTTTGAGGACTTTTGGAATAGGGATGCCC
1 CTGTGTTATATATGTGTTTGGGGAC-TTTGTAATA--AATGCCT
658 CTGTGTTATATATGTGTTTGGGGACTTT
1 CTGTGTTATATATGTGTTTGGGGACTTT
686 TGGTTATTGG
Statistics
Matches: 276, Mismatches: 31, Indels: 32
0.81 0.09 0.09
Matches are distributed among these distances:
41 132 0.48
42 10 0.04
43 102 0.37
44 32 0.12
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (41 bp):
CTGTGTTATATATGTGTTTGGGGACTTTGTAATAAATGCCT
Found at i:418 original size:84 final size:84
Alignment explanation
Indices: 318--685 Score: 598
Period size: 84 Copynumber: 4.4 Consensus size: 84
308 TGTGTCTACA
*
318 CCCCTGTGTTATATATGTGTTTGGGGACTTTGATATAAATGCCTCTGTGTTATATATGTGTTTGA
1 CCCCTGTGTTATATATGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTTTGA
*
383 GGACTTTGTAATAGAGTTG
66 GGACTTTGTAATAGAGGTG
*
402 CCCCTGTGTTATATATGTGTTTGGGGACTTTGATATAGATGTCTCTGTGTTATATATGTGTTTGA
1 CCCCTGTGTTATATATGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTTTGA
467 GGACTTTGTAATAGAGGTG
66 GGACTTTGTAATAGAGGTG
* * *
486 CCCTTGTGTTATATATGTGTTTGGGGTCTTTG-TAATAGATTCCTCTGTGTTATATATGTGTTTG
1 CCCCTGTGTTATATATGTGTTTGGGGACTTTGAT-ATAGATGCCTCTGTGTTATATATGTGTTTG
*
550 AGGACTTTGTAATAAAGGTG
65 AGGACTTTGTAATAGAGGTG
*
570 CCCCTGTGTTATATATGTGTTTGGGGAC-TTGAATATAGGTGCCTCTGTGTTATATATGTGTTTG
1 CCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATATAGATGCCTCTGTGTTATATATGTGTTTG
*
634 AGGACTTTTGGAATAG-GGATG
65 AGGAC-TTTGTAATAGAGG-TG
655 CCCCTGTGTTATATATGTGTTTGGGGACTTT
1 CCCCTGTGTTATATATGTGTTTGGGGACTTT
686 TGGTTATTGG
Statistics
Matches: 264, Mismatches: 14, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
83 4 0.02
84 219 0.83
85 39 0.15
86 2 0.01
ACGTcount: A:0.20, C:0.11, G:0.27, T:0.43
Consensus pattern (84 bp):
CCCCTGTGTTATATATGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTTTGA
GGACTTTGTAATAGAGGTG
Found at i:1712 original size:78 final size:78
Alignment explanation
Indices: 1613--1778 Score: 244
Period size: 78 Copynumber: 2.1 Consensus size: 78
1603 AGTTATATAG
* * * * *
1613 TTTTACTCAATTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTTATTT
1 TTTTACTTAACTAAAAACTCTATTTTAATTTAATTAAATCTAATATCCTCATAACTATTTTATTT
1678 TACCAT-TTTACTA
66 TACCATATTT-CTA
*
1691 TTTTACTTAACTAAAAGCTCTATTTTAATTTAATTAAATCTAATATCCTCATAACTATTTTATTT
1 TTTTACTTAACTAAAAACTCTATTTTAATTTAATTAAATCTAATATCCTCATAACTATTTTATTT
*
1756 TACCATATTTTTA
66 TACCATATTTCTA
*
1769 TTTTAATTAA
1 TTTTACTTAA
1779 AAAAAATACA
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
78 76 0.96
79 3 0.04
ACGTcount: A:0.35, C:0.13, G:0.01, T:0.52
Consensus pattern (78 bp):
TTTTACTTAACTAAAAACTCTATTTTAATTTAATTAAATCTAATATCCTCATAACTATTTTATTT
TACCATATTTCTA
Found at i:3331 original size:42 final size:44
Alignment explanation
Indices: 3283--3372 Score: 139
Period size: 45 Copynumber: 2.1 Consensus size: 44
3273 CATTATCAAA
**
3283 ATTCTACT-C-CATCTCTAGGTAATTCATCAAAATAAAGCTAAT
1 ATTCTACTCCTCATCTCTAAATAATTCATCAAAATAAAGCTAAT
3325 ATTCTACTCCTTCATCTCTAAATAATTCATCAAAATAAAGCTAAT
1 ATTCTACTCC-TCATCTCTAAATAATTCATCAAAATAAAGCTAAT
3370 ATT
1 ATT
3373 AATTGTTGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
42 8 0.19
43 1 0.02
45 34 0.79
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (44 bp):
ATTCTACTCCTCATCTCTAAATAATTCATCAAAATAAAGCTAAT
Found at i:3982 original size:934 final size:930
Alignment explanation
Indices: 2147--4013 Score: 3137
Period size: 934 Copynumber: 2.0 Consensus size: 930
2137 ATTAATTACT
*
2147 ACAAGCAGGGCGGCCTGCGCTTGCGCTACAGTCATCTTCTTATTAGGACTATATTTTTTGTAGTT
1 ACAAGCAGGGCGGCCTGCGCTTGAGCTACAGTCATCTTCTTATTAGGACTATATTTTTTGTAGTT
*
2212 GTTTAAGTCGATTAGTAAGAAGATATTGCATTGGCTATAAGTTAATCAGTTAGGAGAAACTCATA
66 GTTTAAGTCGATTAGTAAGAAGATATTGCATTGGCTATAAGTTAATCACTTAGGAGAAACTCATA
*
2277 CATCGAAACAAATAATTCACATATATAAAGCAAAACACATGACCTCTCTCTAAAAGTGCATTATC
131 CATCGAAACAAATAATTCACATATATAAAGCAAAACACATGACCTCTCTCTAAAAATGCATTATC
*
2342 TAAATTCTACTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTCTACTCCTCCATCTCTA
196 AAAATTCTACTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTCTACTCCTCCATCTCTA
* * * *
2407 GATATTTCATCAAAATAAAGCTAATATTAATTGTTGCTAGAAATGTATGTTGATCATCTAAAAAT
261 AATAATTCATCAAAATAAAGCTAATATTAATTGTTGCT--AAATGCATGTTGATCATCTAAAAAA
* * *
2472 GCATAGTACGTTGCAGTCATTTTTTAATCTTGATTGCACTTGTTGAATTAATGAACTCGGGTAGG
324 GCATAGCACGCTGCAGTCATTTTTTAATCTTAATTGCACTTGTTGAATTAATGAACTCGGGTAGG
*
2537 TGAAAGAATTTGGCTTCTGCATAAGGAATGCCTAAGTTTTTGTAGTCAAGGAGCATGTATAGTTG
389 TGAAAGAATTTGACTTCTGCATAAGGAATGCCTAAGTTTTTGTAGTCAAGGAGCATGTATAGTTG
* *
2602 TCGTAGGAAAATTGAATTAGTTGAGAGCATTTGCAGAAACATATGTAATTTACACAATGCATTAC
454 TCGTAGGAAAATTGAACTAGTTGAGAGCATTTGCAGAAACATATGTAATTTACACAATGCATCAC
* * * * *
2667 AAAATCATTGTACTTAGCATTGGCTAATTGTAATATAAATCCAAATAAATCCAGATTTAGCTGAA
519 AAAATCATTGTACTTAGCATTGGCTAACTATAATATAAATCCAAATAAATCCAAATTTACCTCAA
*
2732 AATGTTGCGGTGAGAAGGGAAAGCTCTCCACTTTAGATTATGTCATCCTAAGGCGCTGCTTAATT
584 AATGTTGCGGTGAGAAGGGAAAGCTCTCCACTTTAGATTATGTCATCCTAAGGCGCTGCTAAATT
* * * *
2797 AAATGGAAGGATCTTATCAACGTTCATTTGGAAATTTTAGGAAACAGAACGGAGTTCATGTGAAA
649 AAATGGAAGGATCTTATCAACATCCATTTGGAAATTTTAGGAAACAGAACGAAGTCCATGTGAAA
* * *
2862 CCAATTCAGAGAAATGTTAGGGAAGAAGAAACCCACCCAAATAGAAATGAAGGCGAAAAGAAAAC
714 CCAATTCAGAGAAATGTTAAGGAAGAAGAAACCCACCCAAATAGAAATGAAGACGAAAAGAAAAA
* **
2927 AGAACTGGAATGTCAATAGTTTACCCATGAATCAACCATTATTGAAGATACATTTATAGCACCAG
779 AAAACTAAAATGTCAATAGTTTACCCATGAATCAACCATTATTGAAGATACATTTATAGCACCAG
*
2992 TCCTTTGGAATTCCGGCAGAGGAGTTGAACCGGTAAATCCTAATATCCAGACACAATTAATATGT
844 TCCTTTGGAATTCCGGCAGAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATTAATATGT
3057 AATTAAAACACACTTAATCATA
909 AATTAAAACACACTTAATCATA
* * * * * * *
3079 ACAAGTAGGTCGGTCTGTGCTTGAGCTGCAGTCATCTTTTTATTAGGGCTATATTTTTTGTAGTT
1 ACAAGCAGGGCGGCCTGCGCTTGAGCTACAGTCATCTTCTTATTAGGACTATATTTTTTGTAGTT
3144 GTTTAAGTCGATTAGTAAGAAGATATTGCATTGGCTATAAGTTAATCACTTAGGAGAAACTCATA
66 GTTTAAGTCGATTAGTAAGAAGATATTGCATTGGCTATAAGTTAATCACTTAGGAGAAACTCATA
* *
3209 CGTCGAAACAAATAATTCGCATATATAAAGCAAAACACATGACATCTCTTTCATTCTAAAAATGC
131 CATCGAAACAAATAATTCACATATATAAAGCAAAACACATGAC--CTC--TC--TCTAAAAATGC
*
3274 ATTATCAAAATTCTACTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTCTACTCCTTCA
190 ATTATCAAAATTCTACTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTCTACTCCTCCA
*
3339 TCTCTAAATAATTCATCAAAATAAAGCTAATATTAATTGTTGCT-TATGCATGTTGATCATCTAA
255 TCTCTAAATAATTCATCAAAATAAAGCTAATATTAATTGTTGCTAAATGCATGTTGATCATCTAA
* *
3403 AAAAGCATAGCACGCTGCGGTCA-TTTTTAATCTTAATTGCACTTGTTGAATTAATGAACTCGTG
320 AAAAGCATAGCACGCTGCAGTCATTTTTTAATCTTAATTGCACTTGTTGAATTAATGAACTCGGG
*
3467 TAGGTGAAAGAATTTGACTTCTGCATAAGGAATGCCTAATTTTTTGTAGTCAAGGAGCATGTATA
385 TAGGTGAAAGAATTTGACTTCTGCATAAGGAATGCCTAAGTTTTTGTAGTCAAGGAGCATGTATA
*
3532 GTTGTCGTAGGAAAATTGAACTAGTTGAGAGCCA-TTGCAGGAACATATGTAATTTACACAATGC
450 GTTGTCGTAGGAAAATTGAACTAGTTGAGAG-CATTTGCAGAAACATATGTAATTTACACAATGC
*
3596 ATCACAAAATCATTGTACTTAGCATTTGCTAACTATAATATAAATCCAAATAAATCCAAATTTAC
514 ATCACAAAATCATTGTACTTAGCATTGGCTAACTATAATATAAATCCAAATAAATCCAAATTTAC
* *
3661 CTCAAAATGTTGCGGTGAGAAGTGAAAGCTCTCCACTTTAGGTTATGTCATCCTAAGGCGCTGCT
579 CTCAAAATGTTGCGGTGAGAAGGGAAAGCTCTCCACTTTAGATTATGTCATCCTAAGGCGCTGCT
*
3726 AAATTAAATTGAAGGATCTTATCAACATCCATTTGGAAATTTTAGGAAACAGAACGAAGTCCATG
644 AAATTAAATGGAAGGATCTTATCAACATCCATTTGGAAATTTTAGGAAACAGAACGAAGTCCATG
*
3791 TGAAACCAATTCAGAGAAATGTTAAGGAAGAAGAAACCCACCCAAATAGAAATGAAGACGAAAGG
709 TGAAACCAATTCAGAGAAATGTTAAGGAAGAAGAAACCCACCCAAATAGAAATGAAGACGAAAAG
3856 AAAAAAAAACTAAAATGTCAATAGTTTACCCATGAATCAACCATTATTGAAGATACATTTATAGC
774 AAAAAAAAACTAAAATGTCAATAGTTTACCCATGAATCAACCATTATTGAAGATACATTTATAGC
* **
3921 ACTAGTCCTTTGGAATTCCGGCAGAGGAGTTTTACCGGTAAATCCTAATATCCACACACAATTAA
839 ACCAGTCCTTTGGAATTCCGGCAGAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATTAA
*
3986 TATGTAATTAAAACACATTTAATCATA
904 TATGTAATTAAAACACACTTAATCATA
4013 A
1 A
4014 ATATAAAAAT
Statistics
Matches: 873, Mismatches: 55, Indels: 12
0.93 0.06 0.01
Matches are distributed among these distances:
932 162 0.19
934 555 0.64
935 39 0.04
936 2 0.00
938 115 0.13
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (930 bp):
ACAAGCAGGGCGGCCTGCGCTTGAGCTACAGTCATCTTCTTATTAGGACTATATTTTTTGTAGTT
GTTTAAGTCGATTAGTAAGAAGATATTGCATTGGCTATAAGTTAATCACTTAGGAGAAACTCATA
CATCGAAACAAATAATTCACATATATAAAGCAAAACACATGACCTCTCTCTAAAAATGCATTATC
AAAATTCTACTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTCTACTCCTCCATCTCTA
AATAATTCATCAAAATAAAGCTAATATTAATTGTTGCTAAATGCATGTTGATCATCTAAAAAAGC
ATAGCACGCTGCAGTCATTTTTTAATCTTAATTGCACTTGTTGAATTAATGAACTCGGGTAGGTG
AAAGAATTTGACTTCTGCATAAGGAATGCCTAAGTTTTTGTAGTCAAGGAGCATGTATAGTTGTC
GTAGGAAAATTGAACTAGTTGAGAGCATTTGCAGAAACATATGTAATTTACACAATGCATCACAA
AATCATTGTACTTAGCATTGGCTAACTATAATATAAATCCAAATAAATCCAAATTTACCTCAAAA
TGTTGCGGTGAGAAGGGAAAGCTCTCCACTTTAGATTATGTCATCCTAAGGCGCTGCTAAATTAA
ATGGAAGGATCTTATCAACATCCATTTGGAAATTTTAGGAAACAGAACGAAGTCCATGTGAAACC
AATTCAGAGAAATGTTAAGGAAGAAGAAACCCACCCAAATAGAAATGAAGACGAAAAGAAAAAAA
AACTAAAATGTCAATAGTTTACCCATGAATCAACCATTATTGAAGATACATTTATAGCACCAGTC
CTTTGGAATTCCGGCAGAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATTAATATGTAA
TTAAAACACACTTAATCATA
Found at i:5157 original size:11 final size:11
Alignment explanation
Indices: 5129--5166 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
5119 ATGGTAAAAG
5129 TAAAATATT--
1 TAAAATATTAA
*
5138 TATAATATTAA
1 TAAAATATTAA
5149 TAAAATATTAA
1 TAAAATATTAA
5160 TAAAATA
1 TAAAATA
5167 AAAATAGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.32
11 17 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAAATATTAA
Found at i:5704 original size:13 final size:14
Alignment explanation
Indices: 5682--5711 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
5672 AATTTTAAAG
5682 AATATCATTTAAGA
1 AATATCATTTAAGA
5696 AATAT-ATTTAAGA
1 AATATCATTTAAGA
5709 AAT
1 AAT
5712 TATAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (14 bp):
AATATCATTTAAGA
Found at i:5769 original size:142 final size:145
Alignment explanation
Indices: 5449--5778 Score: 424
Period size: 142 Copynumber: 2.3 Consensus size: 145
5439 TTCCAATTTG
* * * * **
5449 TTAAAAT--TAAAATGGTAAAAGTAAGATATTTATAATA-TTAATAAAATAAAAATAGGGTATTT
1 TTAAAATAGTAAAATGGTAAAAATAAAATATTTATAA-AGAT-ATTAAATAAAAATAAAGTATTT
*
5511 AATAAAATAAAACTGTAAAATTTAAAAAATATATCATTGAAGAAATATATTTAAAAAAATTCTAA
64 AATAAAATAAAACTGTAAAATTTAAAAAATATATCATTGAAGAAATATATTTAAAAAAATTATAA
5576 TATATCAATTTTTTTAA
129 TATATCAATTTTTTTAA
* * * *
5593 TTAAAATAGTAAAATGGT-AAAATGAAATAGTTATAAAGATATTAAATAAAAATAAAGTTTTTAG
1 TTAAAATAGTAAAATGGTAAAAATAAAATATTTATAAAGATATTAAATAAAAATAAAGTATTTAA
* * * * * *
5657 TAGAATAAAACTG-CAAATTTTAAAGA-ATATCATTTAAGAAATATATTT-AAGAAATTATAATA
66 TAAAATAAAACTGTAAAATTTAAAAAATATATCATTGAAGAAATATATTTAAAAAAATTATAATA
5719 TATCTAA-TTTTTTAA
131 TATC-AATTTTTTTAA
5734 TTAAAATAGTAAAATGGTAAAAATAAAATATTTATAAAGATATTA
1 TTAAAATAGTAAAATGGTAAAAATAAAATATTTATAAAGATATTA
5779 TATTTAATTA
Statistics
Matches: 162, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
141 42 0.26
142 47 0.29
143 10 0.06
144 39 0.24
145 15 0.09
146 9 0.06
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.36
Consensus pattern (145 bp):
TTAAAATAGTAAAATGGTAAAAATAAAATATTTATAAAGATATTAAATAAAAATAAAGTATTTAA
TAAAATAAAACTGTAAAATTTAAAAAATATATCATTGAAGAAATATATTTAAAAAAATTATAATA
TATCAATTTTTTTAA
Done.