Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011064.1 Corchorus capsularis cultivar CVL-1 contig11085, 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: 19766
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.36
Found at i:238 original size:2 final size:2
Alignment explanation
Indices: 231--261 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
221 ATGTTCAAAC
231 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 T
262 CTAATTTGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4687 original size:21 final size:21
Alignment explanation
Indices: 4663--4736 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 21
4653 GTTTCTGCCT
*
4663 TAATAATAAGATTAATTACTG
1 TAATAGTAAGATTAATTACTG
*
4684 TAATAGTAGGAGTT--TTAGTCT-
1 TAATAGTAAGA-TTAATTA--CTG
*
4705 TAATATTAAGATTAATTACTG
1 TAATAGTAAGATTAATTACTG
4726 TAATAGTAAGA
1 TAATAGTAAGA
4737 GTTTTAGTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
20 7 0.17
21 28 0.67
22 7 0.17
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.39
Consensus pattern (21 bp):
TAATAGTAAGATTAATTACTG
Found at i:4720 original size:42 final size:42
Alignment explanation
Indices: 4661--4744 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
4651 ATGTTTCTGC
*
4661 CTTAATAATAAGATTAATTACTGTAATAGTAGGAGTTTTAGT
1 CTTAATAATAAGATTAATTACTGTAATAGTAAGAGTTTTAGT
*
4703 CTTAATATTAAGATTAATTACTGTAATAGTAAGAGTTTTAGT
1 CTTAATAATAAGATTAATTACTGTAATAGTAAGAGTTTTAGT
4745 TGGATGTTGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (42 bp):
CTTAATAATAAGATTAATTACTGTAATAGTAAGAGTTTTAGT
Found at i:4926 original size:32 final size:32
Alignment explanation
Indices: 4890--4952 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
4880 GTACTGAAAC
*
4890 GCCACCAAAATAGCGGTGTTTCGGTACGGAAT
1 GCCACCAAAATAGCAGTGTTTCGGTACGGAAT
* **
4922 GCCACTAAAATAGCAGTGTTTTTGTACGGAA
1 GCCACCAAAATAGCAGTGTTTCGGTACGGAA
4953 ACGCCGTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (32 bp):
GCCACCAAAATAGCAGTGTTTCGGTACGGAAT
Found at i:5319 original size:30 final size:31
Alignment explanation
Indices: 5256--5329 Score: 105
Period size: 30 Copynumber: 2.4 Consensus size: 31
5246 AATCTGATTT
* * *
5256 TATCATGAATTGACACAATTCGATAACGTTA
1 TATCCTGAATTGACACAATTCGATAAAGGTA
*
5287 TATCCTGCATTGACACAATT-GATAAAGGTA
1 TATCCTGAATTGACACAATTCGATAAAGGTA
5317 TATCCTGAATTGA
1 TATCCTGAATTGA
5330 ATTTTAGGCA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
30 20 0.53
31 18 0.47
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32
Consensus pattern (31 bp):
TATCCTGAATTGACACAATTCGATAAAGGTA
Found at i:6111 original size:33 final size:33
Alignment explanation
Indices: 6064--6134 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
6054 AAAAATAGCC
* *
6064 GAGCCGCCCCAGTGGGGCGGCCTCGCCATGGTT
1 GAGCCGCCCAAGTGGGGCGGCCTCGCCACGGTT
* *
6097 GAGCCTCCCAAGTGGGGCGGCTTCGCCACGGTT
1 GAGCCGCCCAAGTGGGGCGGCCTCGCCACGGTT
6130 -AGCCG
1 GAGCCG
6135 TCCTCTTGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
32 4 0.12
33 29 0.88
ACGTcount: A:0.11, C:0.35, G:0.38, T:0.15
Consensus pattern (33 bp):
GAGCCGCCCAAGTGGGGCGGCCTCGCCACGGTT
Found at i:8370 original size:27 final size:27
Alignment explanation
Indices: 8332--8385 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
8322 TTCAAACCCA
8332 CACTTGTTCTGGATGAGATTGAGAGAT
1 CACTTGTTCTGGATGAGATTGAGAGAT
8359 CACTTGTTCTGGATGAGATTGAGAGAT
1 CACTTGTTCTGGATGAGATTGAGAGAT
8386 TTTGAAGGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.30, T:0.33
Consensus pattern (27 bp):
CACTTGTTCTGGATGAGATTGAGAGAT
Found at i:8908 original size:3 final size:3
Alignment explanation
Indices: 8900--8925 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
8890 TGAAATACTC
8900 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
8926 CTGAATTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:11856 original size:103 final size:105
Alignment explanation
Indices: 11676--11936 Score: 361
Period size: 103 Copynumber: 2.5 Consensus size: 105
11666 AATTTTTCTA
* * *
11676 ACCCTTAAAATAAAATTTTAATTTTAATTTG-GGCTAAACTTAGTG-AATTAATTATATATTTTA
1 ACCCTTAAAATAAAA-ATAAAATTTAATTTGAGGCTAAACTTAGTGAAATTAATTATATATTTTA
*
11739 TTTCTAAAACCCTATAACAAT-ATTATTAATTATGGAATTT
65 TTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
* * *
11779 ACCCTTAAAATGAAAAA-AAAA-TTAATTTGAGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAAT-AAAAATAAAATTTAATTTGAGGCTAAACTTAGTGAAATTAATTATATATTTTA
* *
11842 TTTCTAAAATCCTATAACAATAAATTATTAATTTTGAAATTT
65 TTTCTAAAACCCTATAACAAT-AATTATTAATTATGAAATTT
*
11884 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGCTAAACTTAGTAAAATTAA
1 ACCCTTAAAATAAAAATAAAA-TTTAATTTGAGGCTAAACTTAGTGAAATTAA
11937 GGCTAGACTA
Statistics
Matches: 139, Mismatches: 11, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
101 8 0.06
102 16 0.12
103 46 0.33
104 9 0.06
105 32 0.23
107 28 0.20
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTAATTTGAGGCTAAACTTAGTGAAATTAATTATATATTTTAT
TTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
Found at i:11958 original size:107 final size:103
Alignment explanation
Indices: 11744--11958 Score: 236
Period size: 107 Copynumber: 2.0 Consensus size: 103
11734 TTTTATTTCT
* *
11744 AAAACCCTATAACAATATTATTAATTATGGAATTTACCCTTAAAATGAAAAAAAAATTAATTTGA
1 AAAATCCTATAACAATATTATTAATTATGAAATTTACCCTTAAAATGAAAAAAAAATTAATTTGA
* ** * * ** ****
11809 GGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTCT
66 GGCTAAACTTAGTAAAATTAGGCTAGTACTAAATAAAA
*
11847 AAAATCCTATAACAATAAATTATTAATTTTGAAATTTACCCTTAAAAT-AAAAATAAAATTTTAA
1 AAAATCCTATAACAAT--ATTATTAATTATGAAATTTACCCTTAAAATGAAAAA-AAAA--TTAA
11911 TTTGAGGCTAAACTTAGTAAAATTAAGGCTAG-ACTAAATAAAA
61 TTTGAGGCTAAACTTAGTAAAATT-AGGCTAGTACTAAATAAAA
11954 AAAAT
1 AAAAT
11959 AAAAAAAAAA
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
103 15 0.16
104 5 0.05
105 32 0.35
107 36 0.39
108 4 0.04
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.35
Consensus pattern (103 bp):
AAAATCCTATAACAATATTATTAATTATGAAATTTACCCTTAAAATGAAAAAAAAATTAATTTGA
GGCTAAACTTAGTAAAATTAGGCTAGTACTAAATAAAA
Found at i:14643 original size:882 final size:881
Alignment explanation
Indices: 12892--14659 Score: 3518
Period size: 882 Copynumber: 2.0 Consensus size: 881
12882 ATGTGTGTGG
12892 CAATGCAGGATCAGTGGCCTACTTTTGGAGTTGCGCTGGTTTTTTGTCTACTGGTTTTGGGATCT
1 CAATGCAGGATCAGTGGCCTACTTTTGGAGTTGCGCTGGTTTTTTGTCTACTGGTTTTGGGATCT
12957 TGATTGCTGGATGGCTTCTGAGAGACCTTCCCATAATCTCGCACGTCTTTGGTTTAGGGCACTTT
66 TGATTGCTGGATGGCTTCTGAGAGACCTTCCCATAATCTCGCACGTCTTTGGTTTAGGGCACTTT
13022 TGTTCTACATTTATATTACTTATTACAGGGTTTGCTACTCAGTTCCTGTTATGCTATGCATATAT
131 TGTTCTACATTTATATTACTTATTACAGGGTTTGCTACTCAGTTCCTGTTATGCTATGCATATAT
13087 TACTGGTCGATATTCTAAACCAATTTCCATTGGGTGGCCAGTAAAAGCTTGCAATGGATTTGATG
196 TACTGGTCGATATTCTAAACCAATTTCCATTGGGTGGCCAGTAAAAGCTTGCAATGGATTTGATG
13152 GCCCTATTGCTTGCTCTATCTATTGCATTGCTGCATTCTTGGAATACTGACATGTTGCTTACTCT
261 GCCCTATTGCTTGCTCTATCTATTGCATTGCTGCATTCTTGGAATACTGACATGTTGCTTACTCT
13217 GTTTCTCTTGGTTATATGTACCATCTATGTCCATTCACTTGTGCAACTTCGATTTAGACCCCGTG
326 GTTTCTCTTGGTTATATGTACCATCTATGTCCATTCACTTGTGCAACTTCGATTTAGACCCCGTG
13282 ATATGGGCATTGTAGATCTGATGCTGCATGTGTCTATGGAGAGTTTGGTTTGCCTTATTCCCAGT
391 ATATGGGCATTGTAGATCTGATGCTGCATGTGTCTATGGAGAGTTTGGTTTGCCTTATTCCCAGT
13347 GGGTCTCGTGTTTGCATTGCATTAATTCTGCTGCTTTGTGCTGCTATTATTTTGTGTCGATGCCT
456 GGGTCTCGTGTTTGCATTGCATTAATTCTGCTGCTTTGTGCTGCTATTATTTTGTGTCGATGCCT
13412 CTTTTATTCTGCTACCAAGGGTGGCTGCCACTTCGAAAAAGACAAAGAGGATGATGAGAAATCTG
521 CTTTTATTCTGCTACCAAGGGTGGCTGCCACTTCGAAAAAGACAAAGAGGATGATGAGAAATCTG
13477 ATCAGGCCACTAACAGTGCCGACTCCACCCGAGTCAGTGATCATGAGAAATCAAGGCTAGACCTT
586 ATCAGGCCACTAACAGTGCCGACTCCACCCGAGTCAGTGATCATGAGAAATCAAGGCTAGACCTT
13542 TTACTTCTGTGCTAGATTTAATTTGATTATTATTATGTTATGCTTTGCACATATATGTCTTGGTG
651 TTACTTCTGTGCTAGATTTAATTTGATTATTATTATGTTATGCTTTGCACATATATGTCTTGGTG
13607 AATTTTGTAATTCATATCCCAGTGCAAGGACTAGAATTATATTATCGTACTGAATGTTGGTTGAA
716 AATTTTGTAATTCATATCCCAGTGCAAGGACTAGAATTATATTATCGTACTGAATGTTGGTTGAA
13672 ATACTTATTTGATCAAAAGGAGATATATAGAGGAAGTATAGTTATTCATCTTGATGCTCAAATTA
781 ATACTTATTTGATCAAAAGGAGATATATAGAGGAAGTATAGTTATTCATCTTGATGCTCAAATTA
13737 TCTTTTTAATTGGTATTAAAAAAAAGGCAAATTATA
846 TCTTTTTAATTGGTATTAAAAAAAAGGCAAATTATA
13773 CAATGCAGGATCAGTGGCCTACTTTTGGAGTTGCGCTGGTTTTTTGTCTACTGGTTTTGGGATCT
1 CAATGCAGGATCAGTGGCCTACTTTTGGAGTTGCGCTGGTTTTTTGTCTACTGGTTTTGGGATCT
13838 TGATTGCTGGATGGCTTCTGAGAGACCTTCCCATAATCTCGCACGTCTTTGGTTTAGGGCACTTT
66 TGATTGCTGGATGGCTTCTGAGAGACCTTCCCATAATCTCGCACGTCTTTGGTTTAGGGCACTTT
13903 TGTTCTACATTTATATTACTTATTACAGGGTTTTGCTACTCAGTTCCTGTTATGCTATGCATATA
131 TGTTCTACATTTATATTACTTATTACAGGG-TTTGCTACTCAGTTCCTGTTATGCTATGCATATA
13968 TTACTGGTCGATATTCTAAACCAATTTCCATTGGGTGGCCAGTAAAAGCTTGCAATGGATTTGAT
195 TTACTGGTCGATATTCTAAACCAATTTCCATTGGGTGGCCAGTAAAAGCTTGCAATGGATTTGAT
14033 GGCCCTATTGCTTGCTCTATCTATTGCATTGCTGCATTCTTGGAATACTGACATGTTGCTTACTC
260 GGCCCTATTGCTTGCTCTATCTATTGCATTGCTGCATTCTTGGAATACTGACATGTTGCTTACTC
14098 TGTTTCTCTTGGTTATATGTACCATCTATGTCCATTCACTTGTGCAACTTCGATTTAGACCCCGT
325 TGTTTCTCTTGGTTATATGTACCATCTATGTCCATTCACTTGTGCAACTTCGATTTAGACCCCGT
14163 GATATGGGCATTGTAGATCTGATGCTGCATGTGTCTATGGAGAGTTTGGTTTGCCTTATTCCCAG
390 GATATGGGCATTGTAGATCTGATGCTGCATGTGTCTATGGAGAGTTTGGTTTGCCTTATTCCCAG
14228 TGGGTCTCGTGTTTGCATTGCATTAATTCTGCTGCTTTGTGCTGCTATTATTTTGTGTCGATGCC
455 TGGGTCTCGTGTTTGCATTGCATTAATTCTGCTGCTTTGTGCTGCTATTATTTTGTGTCGATGCC
14293 TCTTTTATTCTGCTACCAAGGGTGGCTGCCACTTCGAAAAAGACAAAGAGGATGATGAGAAATCT
520 TCTTTTATTCTGCTACCAAGGGTGGCTGCCACTTCGAAAAAGACAAAGAGGATGATGAGAAATCT
14358 GATCAGGCCACTAACAGTGCCGACTCCACCCGAGTCAGTGATCATGAGAAATCAAGGCTAGACCT
585 GATCAGGCCACTAACAGTGCCGACTCCACCCGAGTCAGTGATCATGAGAAATCAAGGCTAGACCT
14423 TTTACTTCTGTGCTAGATTTAATTTGATTATTATTATGTTATGCTTTGCACATATATGTCTTGGT
650 TTTACTTCTGTGCTAGATTTAATTTGATTATTATTATGTTATGCTTTGCACATATATGTCTTGGT
14488 GAATTTTGTTAATTCATATCCCAGTGCAAGGACTAGAATTATATTATCGTACTGAATGTTGGTTG
715 GAATTTTG-TAATTCATATCCCAGTGCAAGGACTAGAATTATATTATCGTACTGAATGTTGGTTG
14553 AAATACTTATTTGATCAAAAGGAGATATATAGAGGAAGTATAGTTATTCATCTTGATGCTCAAAT
779 AAATACTTATTTGATCAAAAGGAGATATATAGAGGAAGTATAGTTATTCATCTTGATGCTCAAAT
14618 TATCTTTTTAATTGGTATTAAAAAAAAGGCAAATTATA
844 TATCTTTTTAATTGGTATTAAAAAAAAGGCAAATTATA
14656 CAAT
1 CAAT
14660 ACACCGTCAG
Statistics
Matches: 885, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
881 160 0.18
882 562 0.64
883 163 0.18
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.38
Consensus pattern (881 bp):
CAATGCAGGATCAGTGGCCTACTTTTGGAGTTGCGCTGGTTTTTTGTCTACTGGTTTTGGGATCT
TGATTGCTGGATGGCTTCTGAGAGACCTTCCCATAATCTCGCACGTCTTTGGTTTAGGGCACTTT
TGTTCTACATTTATATTACTTATTACAGGGTTTGCTACTCAGTTCCTGTTATGCTATGCATATAT
TACTGGTCGATATTCTAAACCAATTTCCATTGGGTGGCCAGTAAAAGCTTGCAATGGATTTGATG
GCCCTATTGCTTGCTCTATCTATTGCATTGCTGCATTCTTGGAATACTGACATGTTGCTTACTCT
GTTTCTCTTGGTTATATGTACCATCTATGTCCATTCACTTGTGCAACTTCGATTTAGACCCCGTG
ATATGGGCATTGTAGATCTGATGCTGCATGTGTCTATGGAGAGTTTGGTTTGCCTTATTCCCAGT
GGGTCTCGTGTTTGCATTGCATTAATTCTGCTGCTTTGTGCTGCTATTATTTTGTGTCGATGCCT
CTTTTATTCTGCTACCAAGGGTGGCTGCCACTTCGAAAAAGACAAAGAGGATGATGAGAAATCTG
ATCAGGCCACTAACAGTGCCGACTCCACCCGAGTCAGTGATCATGAGAAATCAAGGCTAGACCTT
TTACTTCTGTGCTAGATTTAATTTGATTATTATTATGTTATGCTTTGCACATATATGTCTTGGTG
AATTTTGTAATTCATATCCCAGTGCAAGGACTAGAATTATATTATCGTACTGAATGTTGGTTGAA
ATACTTATTTGATCAAAAGGAGATATATAGAGGAAGTATAGTTATTCATCTTGATGCTCAAATTA
TCTTTTTAATTGGTATTAAAAAAAAGGCAAATTATA
Found at i:14886 original size:19 final size:19
Alignment explanation
Indices: 14864--14901 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
14854 ATGTAATGTA
14864 ATGTAATAGTCTTTTTGTT
1 ATGTAATAGTCTTTTTGTT
14883 ATGTAATAGTCTTTTTGTT
1 ATGTAATAGTCTTTTTGTT
14902 GGGTTGATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.16, T:0.58
Consensus pattern (19 bp):
ATGTAATAGTCTTTTTGTT
Found at i:17954 original size:2 final size:2
Alignment explanation
Indices: 17949--17975 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17939 GGGGGACCAG
17949 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 T
17976 GATACATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.