Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016388.1 Corchorus capsularis cultivar CVL-1 contig16409, 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: 18556
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:532 original size:27 final size:26
Alignment explanation
Indices: 493--562 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 26
483 GGTAAGGAAC
*
493 CAAATGACAAAAATGCTCCTGAATGCA
1 CAAATGACCAAAATGC-CCTGAATGCA
* * *
520 CAAATGACCAAAATACCCTTAGTGCA
1 CAAATGACCAAAATGCCCTGAATGCA
*
546 AAAATGACCAAAATGCC
1 CAAATGACCAAAATGCC
563 AATTAAGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
26 23 0.62
27 14 0.38
ACGTcount: A:0.46, C:0.24, G:0.13, T:0.17
Consensus pattern (26 bp):
CAAATGACCAAAATGCCCTGAATGCA
Found at i:1808 original size:24 final size:24
Alignment explanation
Indices: 1780--1826 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1770 AGCTAATTAG
* *
1780 TTTATGTTTTATCTTTAATTTTCC
1 TTTATCTTATATCTTTAATTTTCC
* *
1804 TTTATCTTATGTCTTTATTTTTC
1 TTTATCTTATATCTTTAATTTTC
1827 AAGTTTCATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.15, C:0.13, G:0.04, T:0.68
Consensus pattern (24 bp):
TTTATCTTATATCTTTAATTTTCC
Found at i:3369 original size:19 final size:18
Alignment explanation
Indices: 3345--3380 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3335 TGAAGATTTC
3345 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
3364 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
3381 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:5460 original size:62 final size:62
Alignment explanation
Indices: 5388--5523 Score: 218
Period size: 62 Copynumber: 2.2 Consensus size: 62
5378 GTTTAGGTTT
* * *
5388 TTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAATTA
1 TTATA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
* *
5451 TTTTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTATATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
5513 TTATATTTTAC
1 TTATATTTTAC
5524 CATTTTACTA
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
62 63 0.94
63 4 0.06
ACGTcount: A:0.38, C:0.12, G:0.01, T:0.49
Consensus pattern (62 bp):
TTATATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
Found at i:5583 original size:78 final size:78
Alignment explanation
Indices: 5454--5616 Score: 308
Period size: 78 Copynumber: 2.1 Consensus size: 78
5444 ATAATTATTT
*
5454 TATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATAT
1 TATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTATTATAT
*
5519 TTTACCATTTTAC
66 TTTACAATTTTAC
5532 TATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTATTATAT
1 TATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTATTATAT
5597 TTTACAATTTTAC
66 TTTACAATTTTAC
5610 TATTTTA
1 TATTTTA
5617 GTTAAAAAAA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
78 83 1.00
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (78 bp):
TATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTATTATAT
TTTACAATTTTAC
Found at i:8175 original size:39 final size:39
Alignment explanation
Indices: 8132--8276 Score: 202
Period size: 39 Copynumber: 3.7 Consensus size: 39
8122 TTACCCAATG
8132 ATCAAAGTCCTCAAACACATATAACACAGAGGCATCTAT
1 ATCAAAGTCCTCAAACACATATAACACAGAGGCATCTAT
* * * * *
8171 ATCAAAGTCCCCAAATACATATAACACAGGGGCAACTCT
1 ATCAAAGTCCTCAAACACATATAACACAGAGGCATCTAT
* *
8210 CTCAAAGTCCTCAAACACATATAACACAGAGCCATCTAT
1 ATCAAAGTCCTCAAACACATATAACACAGAGGCATCTAT
*
8249 ACCAAAGTCC-CTAAACACATATAACACA
1 ATCAAAGTCCTC-AAACACATATAACACA
8277 AGGGCAATTT
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
38 1 0.01
39 90 0.99
ACGTcount: A:0.43, C:0.29, G:0.09, T:0.19
Consensus pattern (39 bp):
ATCAAAGTCCTCAAACACATATAACACAGAGGCATCTAT
Found at i:8269 original size:78 final size:78
Alignment explanation
Indices: 8133--8283 Score: 257
Period size: 78 Copynumber: 1.9 Consensus size: 78
8123 TACCCAATGA
* * *
8133 TCAAAGTCCTCAAACACATATAACACAGAGGCATCTATATCAAAGTCCCCAAATACATATAACAC
1 TCAAAGTCCTCAAACACATATAACACAGAGCCATCTATACCAAAGTCCCCAAACACATATAACAC
*
8198 AGGGGCAACTCTC
66 AAGGGCAACTCTC
*
8211 TCAAAGTCCTCAAACACATATAACACAGAGCCATCTATACCAAAGTCCCTAAACACATATAACAC
1 TCAAAGTCCTCAAACACATATAACACAGAGCCATCTATACCAAAGTCCCCAAACACATATAACAC
8276 AAGGGCAA
66 AAGGGCAA
8284 TTTTCTTCTC
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 68 1.00
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.18
Consensus pattern (78 bp):
TCAAAGTCCTCAAACACATATAACACAGAGCCATCTATACCAAAGTCCCCAAACACATATAACAC
AAGGGCAACTCTC
Found at i:13302 original size:15 final size:15
Alignment explanation
Indices: 13282--13311 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
13272 AACTCTTAGT
13282 TCCAGCTTACCTAAA
1 TCCAGCTTACCTAAA
13297 TCCAGCTTACCTAAA
1 TCCAGCTTACCTAAA
13312 CCATGAGGTC
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:0.33, G:0.07, T:0.27
Consensus pattern (15 bp):
TCCAGCTTACCTAAA
Found at i:14166 original size:16 final size:16
Alignment explanation
Indices: 14145--14175 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
14135 TTGAAAAATA
14145 TTACTAAATATTTATT
1 TTACTAAATATTTATT
*
14161 TTACTAAATCTTTAT
1 TTACTAAATATTTAT
14176 AATATGTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TTACTAAATATTTATT
Found at i:15406 original size:204 final size:201
Alignment explanation
Indices: 14752--15497 Score: 1085
Period size: 201 Copynumber: 3.7 Consensus size: 201
14742 ATTTCATAAT
* * *
14752 TAATTAAATATTTAATATTAATACATATTCCATAAGGGGACACATGTCAATCCTTAAA--T----
1 TAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTTAAAGTTAAAC
** * * * * *
14811 CCTACATGTGCAGTTTGCTAAAATCCACTGACGG-GTATTTGTATAATTTTTCTTATAGAATTAT
66 CCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTA-TTGTATAAATTTTCTTATAGGATTAT
* * * **
14875 TATATAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGATTAAGAAGTTAATACATACCC
130 TATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTAACACATAATC
14940 CATTTCA
195 CATTTCA
* *
14947 TAATTAAATATTTAATATTAATATATATTCCCTAAGGGTACACATGTCAACCCTTAAACTTAAAC
1 TAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTTAAAGTTAAAC
* *
15012 CCCGCACGTGCAGTCTGCTAAACTCCACTGATGGTGTATTGTATAAATTTTCTTATAAGATTATT
66 CCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAAATTTTCTTATAGGATTATT
* * *
15077 ATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAACGGGTTAAGAAGTTGACGCAT-ATCC
131 ATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTAACACATAAT-C
15141 CATTTCA
195 CATTTCA
*
15148 TAATTAAATATTTAATATTAATATATATTCCCTAAGGGTACACATGTCAACCCTTAAAGTTAAAC
1 TAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTTAAAGTTAAAC
*
15213 CCCGCACGTGCAGTCTGCTAAACTCCATTGACGGTGTATTGTATAAATTTTCTTATACGGATTTA
66 CCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAAATTTTCTTATA-GGA-TTA
15278 CTTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTAACACATAA
129 -TTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTAACACATAA
15343 TCCATTTCA
193 TCCATTTCA
15352 TAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTTAAAGTTAAAC
1 TAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTTAAAGTTAAAC
* * * * ** * * *
15417 CTCGCACATGCAGTCTGTTAAACTCTACTGACAATGTATTATATAATTTTTCTTATAGGATAATT
66 CCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAAATTTTCTTATAGGATTATT
*
15482 ATACAATAAACTGTCA
131 ATACAATACACTGTCA
15498 AATTAAATTT
Statistics
Matches: 499, Mismatches: 40, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
195 54 0.11
197 1 0.00
201 250 0.50
202 7 0.01
203 6 0.01
204 179 0.36
205 2 0.00
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (201 bp):
TAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTTAAAGTTAAAC
CCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAAATTTTCTTATAGGATTATT
ATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTAACACATAATCC
ATTTCA
Found at i:15497 original size:405 final size:396
Alignment explanation
Indices: 14752--15497 Score: 1116
Period size: 405 Copynumber: 1.9 Consensus size: 396
14742 ATTTCATAAT
* *
14752 TAATTAAATATTTAATATTAATACATATTCCATAAGGGGACACATGTCAATCCTTAAATCCTACA
1 TAATTAAATATTTAATATTAATACATATTCCATAAGGGGACACATGTCAACCCTTAAATCCCACA
* * * *
14817 TGTGCAGTTTGCTAAAATCCACTGACGGGTATTTGTATAATTTTTCTTATAGAATTATTATATAA
66 CGTGCAGTCTGCTAAAATCCACTGACGGGTATTTGTATAAATTTTCTTATAGAATTATTATACAA
* *
14882 TACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGATTAAGAAGTTAATACATACCCCATTTCA
131 TACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGATTAAGAAGTTAACACATAACCCATTTCA
*
14947 TAATTAAATATTTAATATTAATATATATTCCCTAAGGGTACACATGTCAACCCTTAAACTTAAAC
196 TAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTTAAACTTAAAC
* *** * *
15012 CCCGCACGTGCAGTCTGCTAAACTCCACTGATGGTGTATTGTATAAATTTTCTTATAAGATTATT
261 CCCGCACATGCAGTCTGCTAAACTCCACTGACAATGTATTATATAAATTTTCTTATAAGATAATT
*
15077 ATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAACGGGTTAAGAAGTTGACGCATATCCC
326 ATACAATAAACTGTCAGTGTAAATTTTGGACTCCATAAACGGGTTAAGAAGTTGACGCATATCCC
15142 ATTTCA
391 ATTTCA
* * *
15148 TAATTAAATATTTAATATTAATATATATTCCCTAAGGGTACACATGTCAACCCTTAAAGTTAAAC
1 TAATTAAATATTTAATATTAATACATATTCCATAAGGGGACACATGTCAACCCTTAAA--T----
* * * *
15213 CCCGCACGTGCAGTCTGCTAAACTCCATTGACGGTGTA-TTGTATAAATTTTCTTATACGGATTT
60 CCCACACGTGCAGTCTGCTAAAATCCACTGACGG-GTATTTGTATAAATTTTCTTATA--GAATT
*
15277 ACTTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTAACACATA
122 A-TTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGATTAAGAAGTTAACACATA
*
15342 ATCCATTTCATAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTT
186 ACCCATTTCATAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTT
* * * * *
15407 AAAGTTAAACCTCGCACATGCAGTCTGTTAAACTCTACTGACAATGTATTATATAATTTTTCTTA
251 AAACTTAAACCCCGCACATGCAGTCTGCTAAACTCCACTGACAATGTATTATATAAATTTTCTTA
*
15472 TAGGATAATTATACAATAAACTGTCA
316 TAAGATAATTATACAATAAACTGTCA
15498 AATTAAATTT
Statistics
Matches: 309, Mismatches: 31, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
396 54 0.17
398 1 0.00
402 46 0.15
403 3 0.01
404 5 0.02
405 200 0.65
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (396 bp):
TAATTAAATATTTAATATTAATACATATTCCATAAGGGGACACATGTCAACCCTTAAATCCCACA
CGTGCAGTCTGCTAAAATCCACTGACGGGTATTTGTATAAATTTTCTTATAGAATTATTATACAA
TACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGATTAAGAAGTTAACACATAACCCATTTCA
TAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTTAAACTTAAAC
CCCGCACATGCAGTCTGCTAAACTCCACTGACAATGTATTATATAAATTTTCTTATAAGATAATT
ATACAATAAACTGTCAGTGTAAATTTTGGACTCCATAAACGGGTTAAGAAGTTGACGCATATCCC
ATTTCA
Found at i:15576 original size:21 final size:20
Alignment explanation
Indices: 15522--15592 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
15512 CTCCATATTG
*
15522 ACCTTATTAAA-TTCTAGTA
1 ACCTTATTAAATTTTTAGTA
* *
15541 ACCTTGTGAAGATTTTTAGTA
1 ACCTTATTAA-ATTTTTAGTA
*
15562 ACCTTATTAATATTTTTAATAA
1 ACCTTATTAA-ATTTTTAGT-A
15584 ACCTTATTA
1 ACCTTATTA
15593 TTTTTTTTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 8 0.19
20 1 0.02
21 23 0.55
22 10 0.24
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (20 bp):
ACCTTATTAAATTTTTAGTA
Found at i:16806 original size:23 final size:23
Alignment explanation
Indices: 16763--16806 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
16753 ATTTGGGGCG
*
16763 ATTAATTGATTTGTTTAGTTGGA
1 ATTAATTGAATTGTTTAGTTGGA
*
16786 ATTAATT-AATTGATTTGGTTG
1 ATTAATTGAATTG-TTTAGTTG
16807 AAAATATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.52
Consensus pattern (23 bp):
ATTAATTGAATTGTTTAGTTGGA
Found at i:17793 original size:29 final size:29
Alignment explanation
Indices: 17751--17816 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
17741 ACACTTATTC
17751 TACTCAATATTTTTTAGGAAAAAATTATG
1 TACTCAATATTTTTTAGGAAAAAATTATG
17780 TACTCAATATTTTTTAGGAAAAAATTATG
1 TACTCAATATTTTTTAGGAAAAAATTATG
17809 TACTCAAT
1 TACTCAAT
17817 TTGACATTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (29 bp):
TACTCAATATTTTTTAGGAAAAAATTATG
Found at i:18140 original size:184 final size:187
Alignment explanation
Indices: 17903--18264 Score: 599
Period size: 188 Copynumber: 1.9 Consensus size: 187
17893 ATATAGTAAC
*
17903 TAATGTTAAAACTAAGCAATTATATCAATCCATAATTTCGGTCAATTATATTTCCAATAAGATGC
1 TAATGTTAAAACTAAGCAATTATATCAATCCATAATTTCGGTCAATCATATTTCCAATAAGATGC
17968 ACAATTAGATGCAACACAAT-A-AT-TATGGAAGATTAACATTATTAGTCTTAATAAATTTTAGT
66 ACAATTAGATGCAACACAATAATATATATGGAAGATTAACATTATTAGTCTTAATAAATTTTAGT
*
18030 GATTTAATTTGAATAAAATCATATATATAAATAAATGACACATTCAAACTCCTATATAG
131 GATTTAATTTGAATAAAATCATATAT-T-AATAAAGGACACATTCAAACTCCTATATAG
*
18089 TAATGTTAAAACTAAGCGATTAT-T-AATCCATAATTTCGGTCAATCATATTTCCAATAAGATGC
1 TAATGTTAAAACTAAGCAATTATATCAATCCATAATTTCGGTCAATCATATTTCCAATAAGATGC
* *
18152 ACAATTAGATGTAACACAATAATTATATATGGAAGATTAACATTTTTAGTCTTAATAAATTTTAG
66 ACAATTAGATGCAACACAATAA-TATATATGGAAGATTAACATTATTAGTCTTAATAAATTTTAG
* *
18217 TGATTTAATTTGAATAAAATCGTATATTCATAAAGGACACATTCAAAC
130 TGATTTAATTTGAATAAAATCATATATTAATAAAGGACACATTCAAAC
18265 ATATGAATTG
Statistics
Matches: 165, Mismatches: 7, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
184 57 0.35
185 2 0.01
186 40 0.24
187 3 0.02
188 63 0.38
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (187 bp):
TAATGTTAAAACTAAGCAATTATATCAATCCATAATTTCGGTCAATCATATTTCCAATAAGATGC
ACAATTAGATGCAACACAATAATATATATGGAAGATTAACATTATTAGTCTTAATAAATTTTAGT
GATTTAATTTGAATAAAATCATATATTAATAAAGGACACATTCAAACTCCTATATAG
Done.