Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013534.1 Corchorus capsularis cultivar CVL-1 contig13555, 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: 29056
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1334 original size:20 final size:19
Alignment explanation
Indices: 1305--1348 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1295 TTGGGTTTAG
1305 TCAG-TTTTTTGAGTTCAGT
1 TCAGTTTTTTTGAG-TCAGT
1324 TCAGTTTTTTTGAGTCAGT
1 TCAGTTTTTTTGAGTCAGT
1343 T-AGTTT
1 TCAGTTT
1349 GAGTCTGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.21
19 10 0.42
20 9 0.38
ACGTcount: A:0.16, C:0.09, G:0.20, T:0.55
Consensus pattern (19 bp):
TCAGTTTTTTTGAGTCAGT
Found at i:8424 original size:21 final size:21
Alignment explanation
Indices: 8400--8443 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
8390 AAATAATGAC
8400 AAGTGTCCTTTTTTAATTTCT
1 AAGTGTCCTTTTTTAATTTCT
8421 AAGTGTCCTTTTTTAATTTCT
1 AAGTGTCCTTTTTTAATTTCT
8442 AA
1 AA
8444 TGTTATTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.55
Consensus pattern (21 bp):
AAGTGTCCTTTTTTAATTTCT
Found at i:23622 original size:70 final size:70
Alignment explanation
Indices: 23540--23772 Score: 288
Period size: 70 Copynumber: 3.2 Consensus size: 70
23530 TCATTTAGGT
*
23540 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCTTTATAATT
23604 ATTTTA
65 ATTTTA
*
23610 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATTTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATAT-CTT-T-A-TA
*
23675 TTATATTTTACCA
62 AT-TATTTT---A
* * * * *
23688 TTTTACTATTTTACCCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCTTTATAATTA
*
23753 TTATA
66 TTTTA
*
23758 TTTTACAATTTTACT
1 TTTTACTATTTTACT
23773 ATTTTAGTTA
Statistics
Matches: 142, Mismatches: 12, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
70 63 0.44
71 5 0.04
72 1 0.01
73 6 0.04
74 5 0.04
75 7 0.05
76 1 0.01
77 2 0.01
78 52 0.37
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.49
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCTTTATAATTA
TTTTA
Found at i:23622 original size:78 final size:77
Alignment explanation
Indices: 23540--23778 Score: 341
Period size: 78 Copynumber: 3.2 Consensus size: 77
23530 TCATTTAGGT
*
23540 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATAT-CTT-T-A-T
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACT
*
23600 AAT-TATTTT--A
65 ATTATATTTTACA
*
23610 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATTTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
23675 TTATATTTTACCA
66 TTATATTTTA-CA
* * *
23688 TTTTACTATTTTACCCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
23753 TTATATTTTACAA
66 TTATATTTTAC-A
23766 TTTTACTATTTTA
1 TTTTACTATTTTA
23779 GTTAAAAAAC
Statistics
Matches: 153, Mismatches: 6, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
70 49 0.32
71 5 0.03
72 1 0.01
73 1 0.01
74 3 0.02
75 6 0.04
77 1 0.01
78 87 0.57
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (77 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
TTATATTTTACA
Found at i:24485 original size:31 final size:31
Alignment explanation
Indices: 24450--24511 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
24440 TTATGTTTTT
24450 CAATTGTACCCTTATTTTTAAAACATATTTC
1 CAATTGTACCCTTATTTTTAAAACATATTTC
*
24481 CAATTGTACCCTTTTTTTTAAAACATATTTC
1 CAATTGTACCCTTATTTTTAAAACATATTTC
24512 TAAATTGCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.19, G:0.03, T:0.47
Consensus pattern (31 bp):
CAATTGTACCCTTATTTTTAAAACATATTTC
Found at i:25019 original size:22 final size:22
Alignment explanation
Indices: 24942--25084 Score: 114
Period size: 22 Copynumber: 6.5 Consensus size: 22
24932 TCACTTTGCA
* *
24942 GATTATCAAAGTTTCATAGTGT
1 GATTATCAAAATTTCATAATGT
*
24964 GACTATCAAAATTTCATAATGT
1 GATTATCAAAATTTCATAATGT
*
24986 GATTATCCAAATTTCATAATGT
1 GATTATCAAAATTTCATAATGT
*
25008 -AGTTA-CAAAAATTTCATAGAAG-
1 GA-TTATC-AAAATTTCATA-ATGT
* * **
25030 G-TAATCAAAATTTGATTTTGT
1 GATTATCAAAATTTCATAATGT
* * *
25051 GCTTATCAAAATTTCATAGTGA
1 GATTATCAAAATTTCATAATGT
*
25073 GATTAACAAAAT
1 GATTATCAAAAT
25085 ACTATAGGGA
Statistics
Matches: 95, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
20 1 0.01
21 14 0.15
22 78 0.82
23 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (22 bp):
GATTATCAAAATTTCATAATGT
Found at i:25144 original size:22 final size:22
Alignment explanation
Indices: 24944--25339 Score: 92
Period size: 22 Copynumber: 17.8 Consensus size: 22
24934 ACTTTGCAGA
* * *
24944 TTATCAAAGTTTCATAGTGTGA
1 TTATCAAAATTTCATAGTATGG
* * * *
24966 CTATCAAAATTTCATAATGTGA
1 TTATCAAAATTTCATAGTATGG
* * * *
24988 TTATCCAAATTTCATAATGTAG
1 TTATCAAAATTTCATAGTATGG
*
25010 TTA-CAAAAATTTCATAG-AAGG
1 TTATC-AAAATTTCATAGTATGG
* * ** * *
25031 TAATCAAAATTTGATTTTGTGC
1 TTATCAAAATTTCATAGTATGG
*
25053 TTATCAAAATTTCATAGTGA-GA
1 TTATCAAAATTTCATAGT-ATGG
* * * *
25075 TTAACAAAA-TACTATAGGGA-AG
1 TTATCAAAATTTC-ATA-GTATGG
* * *
25097 TTATCAACA-TTCCTAGGGA-GG
1 TTATCAAAATTTCATA-GTATGG
25118 TTATCAAAATTTCATAGTATGG
1 TTATCAAAATTTCATAGTATGG
* * **
25140 TTATCCAAATTTCATAGTGTAC
1 TTATCAAAATTTCATAGTATGG
** ** *
25162 CAATCAACCTTTCATAATTATTGTGG
1 TTATCAAAATTTCAT-AGTA---TGG
* * *
25188 TTATCAAAATTTTACAGTGA-AG
1 TTATCAAAATTTCATAGT-ATGG
* * *
25210 TCAGCAAAATTAATTTCAT-GTAGAGG
1 TTATC--AA--AATTTCATAGTA-TGG
** * *
25236 TTATCACTATTTTATAGTGTGG
1 TTATCAAAATTTCATAGTATGG
* * * *
25258 TTATCAAAGTTTCGTAATGTGG
1 TTATCAAAATTTCATAGTATGG
* * *
25280 TAATCAAAATTTAATAGGATGG
1 TTATCAAAATTTCATAGTATGG
* *
25302 TTATCGAAATTTTATAGTATGG
1 TTATCAAAATTTCATAGTATGG
*
25324 -TATCAAAGTTTCATAG
1 TTATCAAAATTTCATAG
25340 GGATTAGGGA
Statistics
Matches: 263, Mismatches: 91, Indels: 41
0.67 0.23 0.10
Matches are distributed among these distances:
21 45 0.17
22 184 0.70
23 5 0.02
24 4 0.02
25 4 0.02
26 21 0.08
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTATGG
Found at i:26614 original size:38 final size:35
Alignment explanation
Indices: 26550--26626 Score: 109
Period size: 38 Copynumber: 2.1 Consensus size: 35
26540 AATTTGGCAT
26550 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTTG-C-TTTGTC
**
26587 TTTGTTTCCAATCGTTGTATTTAATTTTGCTTTGTC
1 TTTGTTTCCAA-CGTCCTATTTAATTTTGCTTTGTC
26623 TTTG
1 TTTG
26627 GTCTTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 10 0.27
37 12 0.32
38 15 0.41
ACGTcount: A:0.13, C:0.17, G:0.13, T:0.57
Consensus pattern (35 bp):
TTTGTTTCCAACGTCCTATTTAATTTTGCTTTGTC
Found at i:26790 original size:19 final size:21
Alignment explanation
Indices: 26758--26800 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
26748 TTCTTTACTA
26758 TTACTTTTTAAATTT-AATATT
1 TTACTTTTTAAATTTCAAT-TT
26779 TTAC-TTTT-AATTTCAATTT
1 TTACTTTTTAAATTTCAATTT
26798 TTA
1 TTA
26801 AATGTCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (21 bp):
TTACTTTTTAAATTTCAATTT
Found at i:26997 original size:22 final size:22
Alignment explanation
Indices: 26969--27054 Score: 77
Period size: 22 Copynumber: 3.9 Consensus size: 22
26959 GGTCTCTATG
26969 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
26991 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
27014 -GGTTATCAAAATTCCAT-AGCG
1 TGGTTATCAAAATTTCATAAG-A
*
27035 TGGTTACCAAAAATTTCATA
1 TGGTTATC-AAAATTTCATA
27055 GGATCATGTT
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
20 1 0.02
22 36 0.73
23 12 0.24
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:27276 original size:22 final size:21
Alignment explanation
Indices: 27228--27535 Score: 101
Period size: 22 Copynumber: 13.8 Consensus size: 21
27218 TTTCATGGGG
* *
27228 AGGTTATCAAAATTTTATAGTG
1 AGGTTATCAAAATTTCATAG-A
*
27250 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GA
*
27272 AGGTTATAAAAGTCTCAATTTCATA-A
1 AGGTTAT-CAA-----AATTTCATAGA
* * *
27298 GAAG-TACCAAAATTTGATAGA
1 -AGGTTATCAAAATTTCATAGA
*
27319 AGGTTATC-AAATCTCATAG-
1 AGGTTATCAAAATTTCATAGA
* *
27338 AGTGACTATCAAAATTCCATAGAGA
1 AG-G-TTATCAAAATTTCAT--AGA
*
27363 TCAGATTATCGAAAATTT-ATAGA
1 --AGGTTATC-AAAATTTCATAGA
*
27386 AGATTATCAAAATTTCATAG-
1 AGGTTATCAAAATTTCATAGA
* *
27406 TGTTGTTATCAAAATTTCA-ATGCG
1 AG--GTTATCAAAATTTCATA-G-A
*
27430 AGGTTTATCAAAATTACATA-A
1 AGG-TTATCAAAATTTCATAGA
* *
27451 TGTGATTATCAGAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
* * * * *
27474 GGGGTCAACAAAATTTTATAAA
1 -AGGTTATCAAAATTTCATAGA
* *
27496 GAGGTTAGCAAAATTTCATAAA
1 -AGGTTATCAAAATTTCATAGA
*
27518 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
27536 AAATGTGATT
Statistics
Matches: 216, Mismatches: 40, Indels: 60
0.68 0.13 0.19
Matches are distributed among these distances:
19 2 0.01
20 28 0.13
21 22 0.10
22 108 0.50
23 21 0.10
24 5 0.02
25 8 0.04
26 9 0.04
27 4 0.02
28 9 0.04
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGA
Found at i:27391 original size:21 final size:21
Alignment explanation
Indices: 27288--27405 Score: 82
Period size: 20 Copynumber: 5.5 Consensus size: 21
27278 TAAAAGTCTC
*
27288 AATTTCATAAGAAG--TACCAA
1 AATTTCAT-AGAAGATTATCAA
* *
27308 AATTTGATAGAAGGTTATC-A
1 AATTTCATAGAAGATTATCAA
* * *
27328 AATCTCATAGAGTGACTATCAA
1 AATTTCATAGA-AGATTATCAA
*
27350 AATTCCATAGAGATCAGATTATCGAA
1 AATTTCAT--AGA--AGATTATC-AA
27376 AATTT-ATAGAAGATTATCAA
1 AATTTCATAGAAGATTATCAA
27396 AATTTCATAG
1 AATTTCATAG
27406 TGTTGTTATC
Statistics
Matches: 76, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
19 5 0.07
20 24 0.32
21 20 0.26
22 7 0.09
23 3 0.04
24 3 0.04
25 8 0.11
26 6 0.08
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31
Consensus pattern (21 bp):
AATTTCATAGAAGATTATCAA
Found at i:27669 original size:20 final size:20
Alignment explanation
Indices: 27641--27691 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
27631 TTATGGAGTA
27641 ATCAAAATTTCAAGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
* *
27661 ATTAAAA-TTCAGGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
27680 ATCAAAATTTCA
1 ATCAAAATTTCA
27692 TATTTTAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:27876 original size:23 final size:22
Alignment explanation
Indices: 27720--28218 Score: 228
Period size: 22 Copynumber: 22.8 Consensus size: 22
27710 TTTAAAAGAG
* *
27720 GGTTATCAAATTTTCATA-GTA
1 GGTTATCAAAATTTCATAGGGA
* *
27741 TGTAGATCAAAATTTCATAGGGA
1 GGT-TATCAAAATTTCATAGGGA
* * **
27764 GATTAACAAAATTTCATAATGA
1 GGTTATCAAAATTTCATAGGGA
* **
27786 GATTATCAAAAAATCATAGGGA
1 GGTTATCAAAATTTCATAGGGA
*
27808 GGTTATCAAAA-TT--T--GTA
1 GGTTATCAAAATTTCATAGGGA
* *
27825 -GTTATCAAGATTTCATAAGGA
1 GGTTATCAAAATTTCATAGGGA
* *
27846 AGTTATCAAAATTTTATAGGGA
1 GGTTATCAAAATTTCATAGGGA
* *
27868 GGTTTATCAAAATTTTATAGGAA
1 GG-TTATCAAAATTTCATAGGGA
* *
27891 GATTTATCAAAATTTCATAGCGA
1 G-GTTATCAAAATTTCATAGGGA
* * *
27914 GGTTATCACAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGGGA
* * * *
27936 GATTATCAAAATTTCAAAGTGT
1 GGTTATCAAAATTTCATAGGGA
* *
27958 GATTA-CTAACAA-TTCATATGGA
1 GGTTATC-AA-AATTTCATAGGGA
* * * ** *
27980 GGTTTTTAAATTTTCATAACGT
1 GGTTATCAAAATTTCATAGGGA
** * *
28002 GGTTATCAATGTATCATATGGA
1 GGTTATCAAAATTTCATAGGGA
* * **
28024 GGTTATCAACATCTCATAGTGTT
1 GGTTATCAAAATTTCATAG-GGA
* *
28047 GATTATCAAAATTTCATTGGGA
1 GGTTATCAAAATTTCATAGGGA
* **
28069 AGTTATCAAAATTTCATATTGA
1 GGTTATCAAAATTTCATAGGGA
* *
28091 GGTCT-TCAAAATTCCTTAGGGA
1 GGT-TATCAAAATTTCATAGGGA
* * * *
28113 GGTTAACTAAATTTCATAAGAA
1 GGTTATCAAAATTTCATAGGGA
** * ***
28135 GGTTAAAAAAATTTTATAAAAA
1 GGTTATCAAAATTTCATAGGGA
* * * *
28157 GGTTCTCGAAATCTCATA-GTA
1 GGTTATCAAAATTTCATAGGGA
* * * *
28178 TCGTTATTAAAATTTTATAGGAA
1 -GGTTATCAAAATTTCATAGGGA
*
28201 GGTTATCAAAAGTTCATA
1 GGTTATCAAAATTTCATA
28219 ATGGGATCAT
Statistics
Matches: 353, Mismatches: 106, Indels: 37
0.71 0.21 0.07
Matches are distributed among these distances:
16 9 0.03
17 4 0.01
19 2 0.01
21 9 0.03
22 267 0.76
23 62 0.18
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGGGA
Done.