Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010209.1 Corchorus capsularis cultivar CVL-1 contig10230, 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: 28637
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.31
Found at i:1850 original size:37 final size:38
Alignment explanation
Indices: 1809--1936 Score: 131
Period size: 37 Copynumber: 3.4 Consensus size: 38
1799 CACTCTTCAT
* *
1809 CGCAGAGCTCTCCTTATC-GCGGTAGCACCCTCTTTAC
1 CGCAGAGCTCTCCTTAGCTGCGGCAGCACCCTCTTTAC
* *
1846 CGCAGAGCTCTCC-TAGCTGCGGCGGCTCCCAT-TTTCAC
1 CGCAGAGCTCTCCTTAGCTGCGGCAGCACCC-TCTTT-AC
* * *
1884 CGTAGAGCTCTCCTT-GCTGCTGCAGGACCCTCTTTAC
1 CGCAGAGCTCTCCTTAGCTGCGGCAGCACCCTCTTTAC
1921 CGCAGCA-CTCTCCTTA
1 CGCAG-AGCTCTCCTTA
1937 CGAATCACAG
Statistics
Matches: 74, Mismatches: 10, Indels: 13
0.76 0.10 0.13
Matches are distributed among these distances:
36 3 0.04
37 40 0.54
38 30 0.41
39 1 0.01
ACGTcount: A:0.15, C:0.38, G:0.20, T:0.27
Consensus pattern (38 bp):
CGCAGAGCTCTCCTTAGCTGCGGCAGCACCCTCTTTAC
Found at i:2448 original size:2 final size:2
Alignment explanation
Indices: 2441--2471 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2431 TCAGCACATA
2441 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2472 AATAAGAGAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3121 original size:24 final size:23
Alignment explanation
Indices: 3069--3132 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
3059 GAAAAGACAG
* *
3069 TAAAAAGAAAAAAAAGCGTGAAAA
1 TAAAAAGAAATAAAAG-GGGAAAA
*
3093 GAAAAAGAAATAAAAGGGGAGAAA
1 TAAAAAGAAATAAAAGGGGA-AAA
*
3117 T-AAAAGAATTAAAAGG
1 TAAAAAGAAATAAAAGG
3133 AGATGAAGGG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 17 0.50
24 17 0.50
ACGTcount: A:0.67, C:0.02, G:0.22, T:0.09
Consensus pattern (23 bp):
TAAAAAGAAATAAAAGGGGAAAA
Found at i:3651 original size:19 final size:19
Alignment explanation
Indices: 3629--3665 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3619 ACAAAAACCC
3629 CGTAACTAGCCAAAATTGT
1 CGTAACTAGCCAAAATTGT
3648 CGTAACTAGCCAAAATTG
1 CGTAACTAGCCAAAATTG
3666 CAAGAATTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (19 bp):
CGTAACTAGCCAAAATTGT
Found at i:3678 original size:46 final size:46
Alignment explanation
Indices: 3602--3690 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
3592 CAAAATTTAC
* *
3602 CGTAACTAGCCAAAATTACAAAAACCCCGTAACTAGCCAAAATTGT
1 CGTAACTAGCCAAAATTACAAAAACCCCGTAACAAGACAAAATTGT
* * **
3648 CGTAACTAGCCAAAATTGCAAGAATTCCGTAACAAGACAAAAT
1 CGTAACTAGCCAAAATTACAAAAACCCCGTAACAAGACAAAAT
3691 CACCAAGGCA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.19
Consensus pattern (46 bp):
CGTAACTAGCCAAAATTACAAAAACCCCGTAACAAGACAAAATTGT
Found at i:7728 original size:31 final size:31
Alignment explanation
Indices: 7693--7791 Score: 105
Period size: 31 Copynumber: 3.3 Consensus size: 31
7683 AGAACCTAAA
*
7693 TAGTCCCTGTACTATTGAAAAAAGATCATTT
1 TAGTCCCTGTACTATTGAAAAAAGATCAATT
** * ***
7724 TAGTCCCTCCATTA-TGAAATCTG-TCAATT
1 TAGTCCCTGTACTATTGAAAAAAGATCAATT
7753 TAGTCCCTGTACTATT-AAAAAATGATCAATT
1 TAGTCCCTGTACTATTGAAAAAA-GATCAATT
7784 TAGTCCCT
1 TAGTCCCT
7792 CCGTGAAATG
Statistics
Matches: 52, Mismatches: 13, Indels: 6
0.73 0.18 0.08
Matches are distributed among these distances:
29 19 0.37
30 8 0.15
31 25 0.48
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.36
Consensus pattern (31 bp):
TAGTCCCTGTACTATTGAAAAAAGATCAATT
Found at i:16259 original size:13 final size:13
Alignment explanation
Indices: 16236--16272 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
16226 TGCCAAGAAA
16236 AAAATCTTATAAAT
1 AAAA-CTTATAAAT
16250 AAAACTTATAAAT
1 AAAACTTATAAAT
*
16263 AAAATTTATA
1 AAAACTTATA
16273 TCAAATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (13 bp):
AAAACTTATAAAT
Found at i:16484 original size:30 final size:31
Alignment explanation
Indices: 16446--16512 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
16436 GCCGCTAAAT
*
16446 TCAATTCAGGATACACCGTTA-CCATTTGTG
1 TCAATTCAGGATACAACGTTATCCATTTGTG
* * *
16476 TTAATTCAGGATATAACGTTATCGATTTGTG
1 TCAATTCAGGATACAACGTTATCCATTTGTG
16507 TCAATT
1 TCAATT
16513 TAGACAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 18 0.58
31 13 0.42
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (31 bp):
TCAATTCAGGATACAACGTTATCCATTTGTG
Found at i:17188 original size:32 final size:32
Alignment explanation
Indices: 17117--17188 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
17107 AATCACCATT
* * **
17117 AGAAAGGAAAAAGGGAAGAAAGGTAATCCATT
1 AGAAAGGAAAAAGGGAAGAAAGGAAATACAGA
17149 AGAAAGGAAAAA-GGAAGAAAGGAAATAACAGA
1 AGAAAGGAAAAAGGGAAGAAAGGAAAT-ACAGA
*
17181 AGCAAGGA
1 AGAAAGGA
17189 GACGATTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 13 0.38
32 21 0.62
ACGTcount: A:0.58, C:0.06, G:0.29, T:0.07
Consensus pattern (32 bp):
AGAAAGGAAAAAGGGAAGAAAGGAAATACAGA
Found at i:18652 original size:15 final size:15
Alignment explanation
Indices: 18632--18686 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
18622 TCTTAAGAAA
18632 AAACTTTCTAGTCTT
1 AAACTTTCTAGTCTT
***
18647 AAACTTTCTA-TAGAA
1 AAACTTTCTAGT-CTT
18662 AAACTTTCTAGTCTT
1 AAACTTTCTAGTCTT
18677 AAACTTTCTA
1 AAACTTTCTA
18687 TAGAAACTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
14 1 0.03
15 30 0.94
16 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.42
Consensus pattern (15 bp):
AAACTTTCTAGTCTT
Found at i:18666 original size:30 final size:30
Alignment explanation
Indices: 18630--18692 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
18620 TTTCTTAAGA
18630 AAAAACTTTCTAGTCTTAAACTTTCTATAG
1 AAAAACTTTCTAGTCTTAAACTTTCTATAG
18660 AAAAACTTTCTAGTCTTAAACTTTCTATAG
1 AAAAACTTTCTAGTCTTAAACTTTCTATAG
18690 AAA
1 AAA
18693 CTTCCAAACG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.38
Consensus pattern (30 bp):
AAAAACTTTCTAGTCTTAAACTTTCTATAG
Found at i:19084 original size:29 final size:29
Alignment explanation
Indices: 19045--19102 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
19035 AATCTGTAAA
19045 TTTTGACTACAGGACAATTATTCTCCAAT
1 TTTTGACTACAGGACAATTATTCTCCAAT
19074 TTTTGACTACAGGACAATTATTCTCCAAT
1 TTTTGACTACAGGACAATTATTCTCCAAT
19103 GCTACGTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (29 bp):
TTTTGACTACAGGACAATTATTCTCCAAT
Found at i:27743 original size:200 final size:194
Alignment explanation
Indices: 27244--28028 Score: 793
Period size: 190 Copynumber: 4.0 Consensus size: 194
27234 ATAAGTTCAC
* * *
27244 TATAAGAAATATTATATA-ATACATCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGG-TTTAA
1 TATAAGAAAAATTATACATATAC-T-ATCAGTGGAGTTTAGCAGACTGCACGTGCGGGGATTTAA
* * * *
27307 GGGTTGACATGTGTCCCCTTAGGGAATATGTATTAGTATTAAATATAAGATTAATTTTGAAATAT
64 GGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATAT---ATTAATTATGAAATAG
* *
27372 GGTATGTG----TC---ACCCGCTTATGGAGTCCAAAATTTACACTAACAGTGTATTGTATAATA
126 GGTATGTGTCAATCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTATATTGTATAATA
*
27430 ATCC
191 ATCT
* * * * **
27434 TATAAGAAAAATTATACAATACACCT-TCAGTGGAGTTTAGCAAATTGCAAGTGCTTGG-TTTAA
1 TATAAGAAAAATTATAC-ATATA-CTATCAGTGGAGTTTAGCAGACTGCACGTGCGGGGATTTAA
* * *
27497 GGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATAT-TTAACTGTGAAATGGGGT
64 GGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATATTAATTATGAAATAGGGT
* * * * *
27561 ATGTGTCAACTTCTTAACCCGTTTATGAAGTCCAAAATTCACACTGATAGTGTATTGTATAATAA
129 ATGTGTCAA--TCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTATATTGTATAATAA
27626 TCT
192 TCT
* *
27629 TATAAGAAAATTTATACATATACTATCAGTGGAGTTTAGCATACTGCACGTGCGGGGTTTAACTT
1 TATAAGAAAAATTATACATATACTATCAGTGGAGTTTAGCAGACTGCACGTGCGGGG----A-TT
* *
27694 TAAGGGTTGACATGTGTACCCTTAGAGAATATGTATTAATATCAAATAT-TTAATTATGAAAT-G
61 TAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATATTAATTATGAAATAG
* * * *
27757 GCGTATGTGTTAA-CTTAACCCGCTTATGGAGTCCAAAACTTACACTGACAATATATTATATAAT
126 G-GTATGTGTCAATCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTATATTGTATAAT
27821 AAT-T
190 AATCT
* * * **
27825 CTATAAGAAAAATTATAC-TATAC-ACGTCAATGGATTTTAGCAGGCTGCACGTG-TAGGATTTA
1 -TATAAGAAAAATTATACATATACTA--TCAGTGGAGTTTAGCAGACTGCACGTGCGGGGATTTA
* * *
27887 TGAGTTGACATGTGACGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAA
63 AGGGTTGACATGT---GTACCCTTAGGGAATATGTATTAATATTAAATA--T-ATTAATTATGAA
* * *
27952 ATAGAGTATGTGTCAATTTCTTAACCCGCTTATGGAGT-C-AAATTTACATTGACATTATATTGT
122 ATAGGGTATGTGTCAA--TCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTATATTGT
28015 ATAATAATCCT
185 ATAATAAT-CT
28026 TAT
1 TAT
28029 TATAAAGCTT
Statistics
Matches: 501, Mismatches: 58, Indels: 62
0.81 0.09 0.10
Matches are distributed among these distances:
186 19 0.04
190 91 0.18
191 16 0.03
192 6 0.01
193 3 0.01
194 61 0.12
195 63 0.13
196 9 0.02
197 85 0.17
198 23 0.05
199 31 0.06
200 74 0.15
201 20 0.04
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (194 bp):
TATAAGAAAAATTATACATATACTATCAGTGGAGTTTAGCAGACTGCACGTGCGGGGATTTAAGG
GTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATATTAATTATGAAATAGGGTAT
GTGTCAATCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTATATTGTATAATAATCT
Found at i:28385 original size:16 final size:16
Alignment explanation
Indices: 28360--28390 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28350 TCTACATATT
28360 ATAAAGATTTAGTAAA
1 ATAAAGATTTAGTAAA
*
28376 ATAAATATTTAGTAA
1 ATAAAGATTTAGTAA
28391 TATTTTTCAA
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:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
ATAAAGATTTAGTAAA
Done.