Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013266.1 Corchorus capsularis cultivar CVL-1 contig13287, 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: 70115
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2374 original size:3 final size:3
Alignment explanation
Indices: 2354--2423 Score: 74
Period size: 3 Copynumber: 23.7 Consensus size: 3
2344 ATATATATAG
2354 TAT TAT T-T ATAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
2398 TAT ATAG TAG TAA TAT TAT TA- TAT TA
1 TAT -TAT TAT TAT TAT TAT TAT TAT TA
2424 GAATATACTC
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
2 5 0.08
3 51 0.86
4 3 0.05
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:6048 original size:31 final size:31
Alignment explanation
Indices: 6010--6109 Score: 109
Period size: 31 Copynumber: 3.3 Consensus size: 31
6000 TTAATTTGGC
6010 CAAATAAGGGCCTAACGTTATTGAAAATGCT
1 CAAATAAGGGCCTAACGTTATTGAAAATGCT
* * **
6041 CAAATAAGGGCTCGATC-TT-TT-AATTTGGC-
1 CAAATAAGGGC-CTAACGTTATTGAAAAT-GCT
*
6070 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATTGAAAATGCT
6101 CAAATAAGG
1 CAAATAAGG
6110 TCATGGCGTT
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
28 3 0.06
29 16 0.30
30 7 0.13
31 25 0.46
32 3 0.06
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATTGAAAATGCT
Found at i:6080 original size:29 final size:28
Alignment explanation
Indices: 5992--6081 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 28
5982 AAATAAGAAC
5992 CCGATCTTTTAATTTGGCCAAATAAGGG
1 CCGATCTTTTAATTTGGCCAAATAAGGG
* * **
6020 CCTAACGTTATTGAAAAT-GCTCAAATAAGGG
1 CCGATC-TT-TT-AATTTGGC-CAAATAAGGG
6051 CTCGATCTTTTAATTTGGCCAAATAAGGG
1 C-CGATCTTTTAATTTGGCCAAATAAGGG
6080 CC
1 CC
6082 TAACGTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
28 5 0.10
29 16 0.33
30 8 0.17
31 16 0.33
32 3 0.06
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (28 bp):
CCGATCTTTTAATTTGGCCAAATAAGGG
Found at i:6109 original size:60 final size:60
Alignment explanation
Indices: 5973--6109 Score: 229
Period size: 60 Copynumber: 2.3 Consensus size: 60
5963 AACGTTTGCC
* * *
5973 AAAATACTCAAATAAGAACCCGATCTTTTAATTTGGCCAAATAAGGGCCTAACGTTATTG
1 AAAATGCTCAAATAAGGACCCGATCTTTTAATTTGGCCAAATAAGGGCCTAACGTTATCG
* *
6033 AAAATGCTCAAATAAGGGCTCGATCTTTTAATTTGGCCAAATAAGGGCCTAACGTTATCG
1 AAAATGCTCAAATAAGGACCCGATCTTTTAATTTGGCCAAATAAGGGCCTAACGTTATCG
6093 AAAATGCTCAAATAAGG
1 AAAATGCTCAAATAAGG
6110 TCATGGCGTT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 72 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.27
Consensus pattern (60 bp):
AAAATGCTCAAATAAGGACCCGATCTTTTAATTTGGCCAAATAAGGGCCTAACGTTATCG
Found at i:6229 original size:60 final size:60
Alignment explanation
Indices: 6153--6270 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 60
6143 TTGGACTCCA
* *
6153 AGCCCTTATTTGAGCATTTTCGATAA-CGTTAGGCCCTTATTT-GACCAAATTAAAAGATTG
1 AGCCCTTATTTCAGCATTTT-GACAACCGTTAGGCCCTTATTTAG-CCAAATTAAAAGATTG
*
6213 AGCCCTTATTTCAGCATTTTGACAACCGTTAGGCCTTTATTTAGCCAAATTAAAAGAT
1 AGCCCTTATTTCAGCATTTTGACAACCGTTAGGCCCTTATTTAGCCAAATTAAAAGAT
6271 CAGACCCTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
59 4 0.08
60 48 0.91
61 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (60 bp):
AGCCCTTATTTCAGCATTTTGACAACCGTTAGGCCCTTATTTAGCCAAATTAAAAGATTG
Found at i:6279 original size:60 final size:60
Alignment explanation
Indices: 6153--6284 Score: 171
Period size: 60 Copynumber: 2.2 Consensus size: 60
6143 TTGGACTCCA
* * *
6153 AGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATTG
1 AGCCCTTATTTCAGCATTTTCGACAACGTTAGGCCCTTATTTGACCAAATTAAAAGATAG
*
6213 AGCCCTTATTTCAGCATTTT-GACAACCGTTAGGCCTTTATTT-AGCCAAATTAAAAGATCAG
1 AGCCCTTATTTCAGCATTTTCGACAA-CGTTAGGCCCTTATTTGA-CCAAATTAAAAGAT-AG
6274 A-CCCTTTATTT
1 AGCCC-TTATTT
6285 GGCAAACGTT
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
59 5 0.08
60 51 0.80
61 8 0.12
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (60 bp):
AGCCCTTATTTCAGCATTTTCGACAACGTTAGGCCCTTATTTGACCAAATTAAAAGATAG
Found at i:6334 original size:49 final size:51
Alignment explanation
Indices: 6230--6335 Score: 162
Period size: 52 Copynumber: 2.1 Consensus size: 51
6220 ATTTCAGCAT
* *
6230 TTTGACAACCGTTAGGCCTTTATTTAGCCAAATTAAAAGATCAGACCCTTTA
1 TTTGACAAACGTTAGGCCCTTATTTAGCCAAA-TAAAAGATCAGACCCTTTA
*
6282 TTTGGCAAACGTTAGGCCCTTATTTAGCC-AA-AAAAGATCAGACCCTTTA
1 TTTGACAAACGTTAGGCCCTTATTTAGCCAAATAAAAGATCAGACCCTTTA
6331 TTTGA
1 TTTGA
6336 ACATTTTAGC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
49 22 0.44
51 2 0.04
52 26 0.52
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (51 bp):
TTTGACAAACGTTAGGCCCTTATTTAGCCAAATAAAAGATCAGACCCTTTA
Found at i:7899 original size:31 final size:31
Alignment explanation
Indices: 7861--7924 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
7851 CAAAAAGTCG
*
7861 TGTCACATGTACCAAAAAGTGACACGTGGCA
1 TGTCACATGTACCAAAAAATGACACGTGGCA
** *
7892 TGTCACATGTTTCAAAAAATGGCACGTGGCA
1 TGTCACATGTACCAAAAAATGACACGTGGCA
7923 TG
1 TG
7925 CCACGTGCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.23
Consensus pattern (31 bp):
TGTCACATGTACCAAAAAATGACACGTGGCA
Found at i:9814 original size:29 final size:29
Alignment explanation
Indices: 9768--9839 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
9758 GTTGACGGGG
*
9768 CAAAACGTCCCAAAATTGAAATTC-AGAGGA
1 CAAAATGT-CCAAAATTGAAATTCAAG-GGA
* *
9798 CAAAATGTCCAAGATTGAAATTCAAGGGG
1 CAAAATGTCCAAAATTGAAATTCAAGGGA
*
9827 CAAAATATCCAAA
1 CAAAATGTCCAAA
9840 CACTACAAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 27 0.75
30 9 0.25
ACGTcount: A:0.47, C:0.18, G:0.17, T:0.18
Consensus pattern (29 bp):
CAAAATGTCCAAAATTGAAATTCAAGGGA
Found at i:10611 original size:8 final size:8
Alignment explanation
Indices: 10599--10636 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
10589 TTTGTTCGTT
*
10599 GGTTTGGT
1 GGTTTGGC
10607 GGTTTGGC
1 GGTTTGGC
*
10615 GGTTTAGC
1 GGTTTGGC
10623 GGTTTGGC
1 GGTTTGGC
10631 GGTTTG
1 GGTTTG
10637 AATCGCCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.03, C:0.08, G:0.47, T:0.42
Consensus pattern (8 bp):
GGTTTGGC
Found at i:10731 original size:2 final size:2
Alignment explanation
Indices: 10724--10800 Score: 57
Period size: 2 Copynumber: 43.5 Consensus size: 2
10714 CCGTTTAGTA
* *
10724 AT AT AT AT AT AT -T AT AT AT AT AT A- AT A- AT AC CT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
10762 AT AT A- AT -T AG AT AT -T AT -T AT AT AT AT A- AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10798 AT A
1 AT A
10801 ATTATTAAAC
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
1 10 0.17
2 49 0.83
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (2 bp):
AT
Found at i:10765 original size:34 final size:32
Alignment explanation
Indices: 10722--10805 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 32
10712 AACCGTTTAG
10722 TAATATATATATATTATATATATATAATA-ATA
1 TAATATATATATATTATATAT-TATAATATATA
* *
10754 CCTAATATATATA-ATTAGATATTATTATATATA
1 --TAATATATATATATTATATATTATAATATATA
10787 TAATAATATATATAATTAT
1 TAAT-ATATATAT-ATTAT
10806 TAAACGGTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
31 4 0.09
32 13 0.30
33 11 0.26
34 15 0.35
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.46
Consensus pattern (32 bp):
TAATATATATATATTATATATTATAATATATA
Found at i:20349 original size:30 final size:30
Alignment explanation
Indices: 20313--20376 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
20303 TTATGAAGGC
*
20313 ATGATCTCTCTATCGTAATTCCAAAGGCAA
1 ATGATCTCTCTATCGTAATTACAAAGGCAA
* * * *
20343 ATGATCTCTCTTTTGTTATTACAAAGTCAA
1 ATGATCTCTCTATCGTAATTACAAAGGCAA
20373 ATGA
1 ATGA
20377 GATGGATAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (30 bp):
ATGATCTCTCTATCGTAATTACAAAGGCAA
Found at i:27781 original size:36 final size:37
Alignment explanation
Indices: 27741--27820 Score: 99
Period size: 41 Copynumber: 2.1 Consensus size: 37
27731 CTTTCTTTGT
*
27741 GTGATTTAG-ATGATACTAAAGCATGGATGTTTATGC
1 GTGATTTAGAATAATACTAAAGCATGGATGTTTATGC
*
27777 GTGATTTAGACATCATAATACTAAAGCATGGATGTTTGTGC
1 GTGATTTAG--A--ATAATACTAAAGCATGGATGTTTATGC
27818 GTG
1 GTG
27821 TCATATTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
36 9 0.24
41 28 0.76
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (37 bp):
GTGATTTAGAATAATACTAAAGCATGGATGTTTATGC
Found at i:33398 original size:39 final size:39
Alignment explanation
Indices: 33344--33458 Score: 160
Period size: 39 Copynumber: 2.9 Consensus size: 39
33334 TAGGAGTGGG
* * *
33344 GGAGGGTCGAGCTACTCGAGTTCTTTGTCTTCGAGCG-GT
1 GGAGGGTCAAGCTACTCGAGTTCTTCGTCTTCGAG-GAGC
* *
33383 GGAGGGTCCAGCTACTCGAGTTCTTCGTCTTCAAGGAGC
1 GGAGGGTCAAGCTACTCGAGTTCTTCGTCTTCGAGGAGC
*
33422 GGAGGGTCAAGCTACTCGAGTTCTTCGTCTCCGAGGA
1 GGAGGGTCAAGCTACTCGAGTTCTTCGTCTTCGAGGA
33459 CTGCTGTTGT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 1 0.01
39 67 0.99
ACGTcount: A:0.17, C:0.23, G:0.33, T:0.27
Consensus pattern (39 bp):
GGAGGGTCAAGCTACTCGAGTTCTTCGTCTTCGAGGAGC
Found at i:33601 original size:102 final size:100
Alignment explanation
Indices: 33407--33599 Score: 243
Period size: 102 Copynumber: 1.9 Consensus size: 100
33397 CTCGAGTTCT
*
33407 TCGTCTTCAAGGAGCGGAGGGTCAAGCTACTCGAGTTCTTCGTCTCCGAGGACTGCTGTTGTTGG
1 TCGTCTTCAAGGAGCGGAGGGTCAAGCTACTCGAGTTCTTCGTCTCCGAGGACTGC--TTGCTGG
* * *
33472 GGTTGGAGTTGATGCCGGGTCAAAGTCGAAGTAAGAG
64 GGTTGGAGTTCATACCGAGTCAAAGTCGAAGTAAGAG
* * * *
33509 TCGTCTTCGAGGGGTGGAGGGTCCAA-CTACTCGAGTTCTTCGTCTTCGAGGACTGC-TGCTGGG
1 TCGTCTTCAAGGAGCGGAGGGT-CAAGCTACTCGAGTTCTTCGTCTCCGAGGACTGCTTGCTGGG
*
33572 TTTGGAGTTCATACC--GT-AAAGTCGAAGT
65 GTTGGAGTTCATACCGAGTCAAAGTCGAAGT
33600 CGGAGTCGAA
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
96 11 0.13
97 2 0.02
99 18 0.22
102 48 0.59
103 3 0.04
ACGTcount: A:0.19, C:0.20, G:0.34, T:0.28
Consensus pattern (100 bp):
TCGTCTTCAAGGAGCGGAGGGTCAAGCTACTCGAGTTCTTCGTCTCCGAGGACTGCTTGCTGGGG
TTGGAGTTCATACCGAGTCAAAGTCGAAGTAAGAG
Found at i:41562 original size:39 final size:42
Alignment explanation
Indices: 41495--41580 Score: 115
Period size: 39 Copynumber: 2.1 Consensus size: 42
41485 CTTCGAGGAG
* *
41495 TTCTTCGTCTTCTTCGAGTAGTGGAGGGTCGAGCTACTCGAC
1 TTCTTCGTCTTCGTCGAGTAGTGAAGGGTCGAGCTACTCGAC
* *
41537 TTCTTCGTCTTCGT-G-G-AGTGAAGGGTCGAGTTACTCGAG
1 TTCTTCGTCTTCGTCGAGTAGTGAAGGGTCGAGCTACTCGAC
41576 TTCTT
1 TTCTT
41581 TGTCGAAGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
39 25 0.62
40 1 0.03
41 1 0.03
42 13 0.32
ACGTcount: A:0.14, C:0.21, G:0.29, T:0.36
Consensus pattern (42 bp):
TTCTTCGTCTTCGTCGAGTAGTGAAGGGTCGAGCTACTCGAC
Found at i:44557 original size:18 final size:18
Alignment explanation
Indices: 44534--44570 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
44524 GGAGGTCTTT
* *
44534 TTCTTCTTCTTCGAGGAG
1 TTCTTCGTCTTCCAGGAG
44552 TTCTTCGTCTTCCAGGAG
1 TTCTTCGTCTTCCAGGAG
44570 T
1 T
44571 AGTGGAGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (18 bp):
TTCTTCGTCTTCCAGGAG
Found at i:52779 original size:42 final size:42
Alignment explanation
Indices: 52729--52828 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
52719 GAGGAGTTCT
52729 TCGTCTTCGAGTAGTGG-AGGGTCGAGCTACTCCAGTTCTTCA
1 TCGTCTTCGAGTAGTGGCA-GGTCGAGCTACTCCAGTTCTTCA
* * * * * *
52771 TCTTCTTCGTCG-AGTGGCAGTTTGAGCTACTCGAGTTCTTCT
1 TCGTCTTCG-AGTAGTGGCAGGTCGAGCTACTCCAGTTCTTCA
52813 TCGTCTTCGAGTAGTG
1 TCGTCTTCGAGTAGTG
52829 AAGGCCTTGC
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
41 1 0.02
42 44 0.94
43 2 0.04
ACGTcount: A:0.14, C:0.23, G:0.27, T:0.36
Consensus pattern (42 bp):
TCGTCTTCGAGTAGTGGCAGGTCGAGCTACTCCAGTTCTTCA
Found at i:55822 original size:2 final size:2
Alignment explanation
Indices: 55815--55839 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55805 CATCTTTTTC
55815 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 T
55840 TTACAAAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57180 original size:6 final size:6
Alignment explanation
Indices: 57164--57193 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
57154 TTACCAATCT
*
57164 TCTTCA CCTTCA TCTTCA TCTTCA TCTTCA
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA
57194 GAGACAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.37, G:0.00, T:0.47
Consensus pattern (6 bp):
TCTTCA
Found at i:67005 original size:15 final size:17
Alignment explanation
Indices: 66985--67018 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
66975 ATATACCATG
66985 ATTATT-ATTT-TTGTT
1 ATTATTAATTTATTGTT
67000 ATTATTAATTTATTGTT
1 ATTATTAATTTATTGTT
67017 AT
1 AT
67019 GTTAAAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 4 0.24
17 7 0.41
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (17 bp):
ATTATTAATTTATTGTT
Done.