Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012789.1 Corchorus capsularis cultivar CVL-1 contig12810, 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: 24904
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:10632 original size:156 final size:154
Alignment explanation
Indices: 10323--10688 Score: 370
Period size: 156 Copynumber: 2.3 Consensus size: 154
10313 CCGAGCTTCT
* * *
10323 CACCTCAAACTGTCCTTAAATGAAAAACTAGTATAAGTTTTTCATTCTAAGTCTGAATGAGCTGA
1 CACCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCA-TCTAAGTCTCAACGAGCTG-
* * *
10388 AACTTTGTCAAGGGACTTAGAATATCCATTTAAGACTATGGAAACAATTCTAAGTAAAACCGAGC
64 AACTTTGTCAAGAGACTTAGAATATCCATTGAAGACTATGGAAACAATTCTAAGTAAAACCGAAC
* * * *
10453 TCCTCTTGATGGCGAACTAGGTTTCT
129 TCCTCTAGATAGAGAACTAGGTTTCA
* * ** *
10479 CTCC-CTGAGTTGTCCTTAAATGAAAAACTAGCATAAGCTTTTCAGTCTAAGTC-CAACGAAGCT
1 CACCTC-AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCA-TCTAAGTCTCAACG-AGCT
* *
10542 G-A-TTTTTCACCAGTAGACTTAGATTATCCCCA-TGAAG-CTATGGGAAA-AATTCTAAGTAAA
63 GAACTTTGTCA--AG-AGACTTAGAATAT--CCATTGAAGACTAT-GGAAACAATTCTAAGTAAA
* * *
10602 ACCGAACT-CTCTAGCATAGAGAAGTTGGTTTGA
122 ACCGAACTCCTCTAG-ATAGAGAACTAGGTTTCA
*
10635 CACCTCAAACTGTCCTTAACTGAAAAACTAGCATAAGTTTTTCATACTAAGTCT
1 CACCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCAT-CTAAGTCT
10689 GTTTGAGATG
Statistics
Matches: 171, Mismatches: 27, Indels: 23
0.77 0.12 0.10
Matches are distributed among these distances:
153 6 0.04
154 1 0.01
155 12 0.07
156 139 0.81
157 10 0.06
158 3 0.02
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (154 bp):
CACCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATCTAAGTCTCAACGAGCTGAA
CTTTGTCAAGAGACTTAGAATATCCATTGAAGACTATGGAAACAATTCTAAGTAAAACCGAACTC
CTCTAGATAGAGAACTAGGTTTCA
Found at i:11245 original size:15 final size:16
Alignment explanation
Indices: 11220--11271 Score: 63
Period size: 15 Copynumber: 3.3 Consensus size: 16
11210 AGGGAGTAAT
11220 TTAATAATAATAATTA
1 TTAATAATAATAATTA
*
11236 TTAA-AATAATTATTA
1 TTAATAATAATAATTA
*
11251 TTAATTAAT-TTAATTA
1 TTAA-TAATAATAATTA
11267 TTAAT
1 TTAAT
11272 TTGGCCTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 15 0.48
16 13 0.42
17 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAATAATAATAATTA
Found at i:20936 original size:21 final size:19
Alignment explanation
Indices: 20888--20936 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
20878 TGAACTCATC
*
20888 ATTATTATTCAAAATATTT
1 ATTATTATTCAAAATATAT
*
20907 ATTATTTATTTAATAATATAT
1 ATTA-TTATTCAA-AATATAT
20928 ATATATTAT
1 AT-TATTAT
20937 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 4 0.16
20 7 0.28
21 12 0.48
22 2 0.08
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTATTATTCAAAATATAT
Found at i:22874 original size:19 final size:20
Alignment explanation
Indices: 22847--22884 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
22837 TACTATTATT
22847 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
22867 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
22885 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:23078 original size:22 final size:22
Alignment explanation
Indices: 23050--23152 Score: 91
Period size: 22 Copynumber: 4.6 Consensus size: 22
23040 TGTCTCTATG
23050 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
23072 TGGTTATTATAATTTCATGAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
23094 AGGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
23116 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
*
23138 TCAGGTTATTAAAAT
1 T--GGTTATCAAAAT
23153 CTCTTAGGTT
Statistics
Matches: 62, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
21 2 0.03
22 49 0.79
23 1 0.02
24 10 0.16
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:23348 original size:22 final size:21
Alignment explanation
Indices: 23300--23606 Score: 97
Period size: 22 Copynumber: 13.8 Consensus size: 21
23290 TTTCATGGGG
*
23300 AGGTTATCAAAATTTTATACTG-
1 AGGTTATCAAAATTTCATA--GA
*
23322 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GA
* *
23344 AGGTTAT-AAAAGTCTCAATTTCATA
1 AGGTTATCAAAA-TTTC-A--T-AGA
* * *
23369 AGGAGTACCAAAATTTGATAGA
1 AGG-TTATCAAAATTTCATAGA
* *
23391 ATGTTATC-AAATCTCATAGA
1 AGGTTATCAAAATTTCATAGA
* *
23411 CTGATTATCAAAATTTCATAAAGA
1 -AGGTTATCAAAATTTCAT--AGA
*
23435 TCGGATTATCAAAATTT-ATAGAA
1 -AGG-TTATCAAAATTTCATAG-A
*
23458 AGATTATCAAAATTTCATAG-
1 AGGTTATCAAAATTTCATAGA
* * *
23478 CGTTGTTATCAAAATTTCAAAGCG
1 AG--GTTATCAAAATTTCATAG-A
*
23502 AGGTTATCAAAATTACATA-A
1 AGGTTATCAAAATTTCATAGA
* * *
23522 TGTGATTATCAGAATTTTATAGA
1 AG-G-TTATCAAAATTTCATAGA
* * ** * *
23545 GGGGTCAAAAAAAATTTTATAAA
1 -AGGT-TATCAAAATTTCATAGA
* *
23568 GAGGTTGTCAAAATTTCATAAA
1 -AGGTTATCAAAATTTCATAGA
23590 GAGGTTATC-AAATTTCA
1 -AGGTTATCAAAATTTCA
23607 AAATGTGATT
Statistics
Matches: 213, Mismatches: 48, Indels: 49
0.69 0.15 0.16
Matches are distributed among these distances:
20 12 0.06
21 35 0.16
22 110 0.52
23 21 0.10
24 8 0.04
25 18 0.08
26 5 0.02
27 4 0.02
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGA
Found at i:23464 original size:21 final size:22
Alignment explanation
Indices: 23377--23477 Score: 93
Period size: 21 Copynumber: 4.6 Consensus size: 22
23367 TAAGGAGTAC
* *
23377 CAAAATTTGATAGAATG-TTAT
1 CAAAATTTCATAGAAAGATTAT
* **
23398 C-AAATCTCATAGACTGATTAT
1 CAAAATTTCATAGAAAGATTAT
23419 CAAAATTTCATA-AAGATCGGATTAT
1 CAAAATTTCATAGAA-A---GATTAT
23444 CAAAATTT-ATAGAAAGATTAT
1 CAAAATTTCATAGAAAGATTAT
23465 CAAAATTTCATAG
1 CAAAATTTCATAG
23478 CGTTGTTATC
Statistics
Matches: 66, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
20 12 0.18
21 21 0.32
22 13 0.20
24 4 0.06
25 16 0.24
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGAAAGATTAT
Found at i:23531 original size:44 final size:44
Alignment explanation
Indices: 23413--23538 Score: 121
Period size: 44 Copynumber: 2.8 Consensus size: 44
23403 CTCATAGACT
*
23413 GATTATCAAAATTTCATAAAGATCGGATTATCAAAATTTATAGAAA
1 GATTATCAAAATTTCATAAAGAT--GATTATCAAAATTTAAAGAAA
** * **
23459 GATTATCAAAATTTCATAGCGTTG-TTATCAAAATTTCAAAGCGA
1 GATTATCAAAATTTCATAAAGATGATTATCAAAATTT-AAAGAAA
* * * *
23503 GGTTATCAAAATTACATAATG-TGATTATCAGAATTT
1 GATTATCAAAATTTCATAAAGATGATTATCAAAATTT
23539 TATAGAGGGG
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
43 14 0.21
44 33 0.49
46 20 0.30
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (44 bp):
GATTATCAAAATTTCATAAAGATGATTATCAAAATTTAAAGAAA
Found at i:23738 original size:20 final size:20
Alignment explanation
Indices: 23713--23807 Score: 84
Period size: 22 Copynumber: 4.6 Consensus size: 20
23703 ATATGGAGTA
*
23713 ATCAAAATTTTAAGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
*
23733 ATCAAAA-TTCAGGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
* * *
23752 ATAAAAATTTCATATGAAGGTT
1 ATCAAAATTTCA-A-GGAGGAT
* *
23774 ATCAAAATTTCACAAGAGGGTT
1 ATCAAAATTTCA-AGGA-GGAT
23796 ATCAAAATTTCA
1 ATCAAAATTTCA
23808 TAGTATGTAG
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 16 0.26
20 11 0.18
21 1 0.02
22 33 0.54
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.29
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:23780 original size:22 final size:22
Alignment explanation
Indices: 23755--24003 Score: 149
Period size: 22 Copynumber: 11.5 Consensus size: 22
23745 GGAGGATATA
23755 AAAATTTCATATGAAGGTTATC
1 AAAATTTCATATGAAGGTTATC
* * *
23777 AAAATTTCACAAGAGGGTTATC
1 AAAATTTCATATGAAGGTTATC
* * *
23799 AAAATTTCATA-GTATGTAGATC
1 AAAATTTCATATGAAGGT-TATC
* * * * *
23821 AATATTTCATAGGGAGATTAAC
1 AAAATTTCATATGAAGGTTATC
23843 AAAATTTCATAATG-AGGTTATC
1 AAAATTTCAT-ATGAAGGTTATC
** * *
23865 AAAAAATCATAGGGAGGTTATC
1 AAAATTTCATATGAAGGTTATC
*
23887 AAAA--T--T-TGTA-GTTATC
1 AAAATTTCATATGAAGGTTATC
* * *
23903 AAGATTTCATAAGAAAGTTATC
1 AAAATTTCATATGAAGGTTATC
*
23925 AAAATTTTATAT-AGAGGTTTATC
1 AAAATTTCATATGA-AGG-TTATC
* * *
23948 AAAATTTTATAGGAAGATTTATC
1 AAAATTTCATATGAAG-GTTATC
*
23971 AAAATTTCATA-GCGAGGTTATC
1 AAAATTTCATATG-AAGGTTATC
*
23993 ACAATTTCATA
1 AAAATTTCATA
24004 GTGTGATTAT
Statistics
Matches: 176, Mismatches: 36, Indels: 30
0.73 0.15 0.12
Matches are distributed among these distances:
16 9 0.05
17 2 0.01
18 2 0.01
20 2 0.01
21 8 0.05
22 112 0.64
23 40 0.23
24 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (22 bp):
AAAATTTCATATGAAGGTTATC
Found at i:23948 original size:23 final size:22
Alignment explanation
Indices: 23898--23999 Score: 82
Period size: 23 Copynumber: 4.5 Consensus size: 22
23888 AAATTTGTAG
* * *
23898 TTATCAAGATTTCATAAGAAAG-
1 TTATCAAAATTTTATAAG-AGGT
23920 TTATCAAAATTTTATATAGAGGT
1 TTATCAAAATTTTATA-AGAGGT
* *
23943 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAAG-AGGT
* *
23966 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATA-AGAGGT
*
23988 TTATCACAATTT
1 TTATCAAAATTT
24000 CATAGTGTGA
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
22 28 0.42
23 38 0.57
24 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTTATAAGAGGT
Found at i:24013 original size:22 final size:22
Alignment explanation
Indices: 23966--24021 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
23956 ATAGGAAGAT
*
23966 TTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTCATAGCGAGA
* * *
23988 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGCGAGA
*
24010 TTATGAAAATTT
1 TTATCAAAATTT
24022 TAGAGTATGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCGAGA
Found at i:24097 original size:22 final size:22
Alignment explanation
Indices: 24072--24275 Score: 83
Period size: 22 Copynumber: 9.2 Consensus size: 22
24062 TATCGATATA
* *
24072 TCATATGGAGGTTATCAACATC
1 TCATATGGAGGTTATCAAAATT
**
24094 TCATAGTGTTGGTTATCAAAATT
1 TCATA-TGGAGGTTATCAAAATT
*
24117 TCAT-TGGGAAGTTATCAAAATT
1 TCATAT-GGAGGTTATCAAAATT
**
24139 TCATATTAAGGTCT-TCAAAATT
1 TCATATGGAGGT-TATCAAAATT
* * * * *
24161 CCTTAGGGAGGTTAACCAAATT
1 TCATATGGAGGTTATCAAAATT
* * ** *
24183 TCATAAGAAGGTTAAAAAAAAAT
1 TCATATGGAGGTT-ATCAAAATT
*** * *
24206 T-ATAAATAGGTTCTCGAAATT
1 TCATATGGAGGTTATCAAAATT
* * * *
24227 CCATA-GTATCGTTATTAAAATT
1 TCATATGGA-GGTTATCAAAATT
* *
24249 TCATAAGAAGGTTATCAAAATT
1 TCATATGGAGGTTATCAAAATT
24271 TCATA
1 TCATA
24276 ATGGGATCAT
Statistics
Matches: 132, Mismatches: 41, Indels: 18
0.69 0.21 0.09
Matches are distributed among these distances:
21 8 0.06
22 96 0.73
23 28 0.21
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATATGGAGGTTATCAAAATT
Found at i:24276 original size:22 final size:22
Alignment explanation
Indices: 24104--24276 Score: 95
Period size: 22 Copynumber: 7.9 Consensus size: 22
24094 TCATAGTGTT
**
24104 GGTTATCAAAATTTCATTGGGAA
1 GGTTATCAAAATTTCA-TAAGAA
**
24127 -GTTATCAAAATTTCATATTAA
1 GGTTATCAAAATTTCATAAGAA
* * * *
24148 GGTCT-TCAAAATTCCTTAGGGA
1 GGT-TATCAAAATTTCATAAGAA
* *
24170 GGTTAACCAAATTTCATAAGAA
1 GGTTATCAAAATTTCATAAGAA
** *
24192 GGTTAAAAAAAAATT-ATAA-ATA
1 GGTT-ATCAAAATTTCATAAGA-A
* * * *
24214 GGTTCTCGAAATTCCAT-AGTAT
1 GGTTATCAAAATTTCATAAG-AA
* *
24236 CGTTATTAAAATTTCATAAGAA
1 GGTTATCAAAATTTCATAAGAA
24258 GGTTATCAAAATTTCATAA
1 GGTTATCAAAATTTCATAA
24277 TGGGATCATA
Statistics
Matches: 109, Mismatches: 32, Indels: 19
0.68 0.20 0.12
Matches are distributed among these distances:
21 10 0.09
22 88 0.81
23 11 0.10
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAAGAA
Found at i:24403 original size:2 final size:2
Alignment explanation
Indices: 24396--24428 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
24386 CTAAAACTAG
24396 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24429 TGAGATCTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24645 original size:30 final size:31
Alignment explanation
Indices: 24596--24668 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 31
24586 TCTCAAAATC
*
24596 CAATTCAGGATACACCGTTACCA-TTTGTGT
1 CAATTCAGGATACAACGTTACCACTTTGTGT
* * * *
24626 CAATTTAGGATATAACGTTATCACTTTGTAT
1 CAATTCAGGATACAACGTTACCACTTTGTGT
* *
24657 TATTTCAGGATA
1 CAATTCAGGATA
24669 AAAATTAACG
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
30 19 0.56
31 15 0.44
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.38
Consensus pattern (31 bp):
CAATTCAGGATACAACGTTACCACTTTGTGT
Done.