Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011099.1 Corchorus capsularis cultivar CVL-1 contig11120, 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: 46327
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3907 original size:1 final size:1
Alignment explanation
Indices: 3901--3929 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
3891 AACAATAGGG
3901 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3930 AACAGAGGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:7054 original size:12 final size:12
Alignment explanation
Indices: 7037--7068 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
7027 GATTGTCTTC
7037 TACAATTATTAG
1 TACAATTATTAG
*
7049 TACAATTATTAT
1 TACAATTATTAG
7061 TACAATTA
1 TACAATTA
7069 CAATGGGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (12 bp):
TACAATTATTAG
Found at i:12476 original size:24 final size:24
Alignment explanation
Indices: 12425--12479 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
12415 CGTCTTCATG
* *
12425 ATCATCATCTTCATCATCAGAAAT
1 ATCATCATCTTCATCACCAGAAAC
*
12449 ATCATCATCTTCAATCACCA-AAGC
1 ATCATCATCTTC-ATCACCAGAAAC
12473 ATCATCA
1 ATCATCA
12480 ATCTCCACAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 21 0.78
25 6 0.22
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.29
Consensus pattern (24 bp):
ATCATCATCTTCATCACCAGAAAC
Found at i:15515 original size:9 final size:9
Alignment explanation
Indices: 15501--15544 Score: 63
Period size: 9 Copynumber: 4.9 Consensus size: 9
15491 ACAAGATTTA
15501 AAAAAAAAC
1 AAAAAAAAC
15510 AAAAAAAAAC
1 -AAAAAAAAC
15520 AAAAAAAAC
1 AAAAAAAAC
*
15529 -AAAAACAC
1 AAAAAAAAC
15537 AAAAAAAA
1 AAAAAAAA
15545 AATCTACATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
8 7 0.23
9 15 0.48
10 9 0.29
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:15516 original size:11 final size:10
Alignment explanation
Indices: 15500--15545 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
15490 TACAAGATTT
15500 AAAAAAAAAC
1 AAAAAAAAAC
15510 AAAAAAAAAC
1 AAAAAAAAAC
15520 -AAAAAAAAC
1 AAAAAAAAAC
*
15529 --AAAAACAC
1 AAAAAAAAAC
15537 AAAAAAAAA
1 AAAAAAAAA
15546 ATCTACATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 7 0.22
9 9 0.28
10 16 0.50
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:15525 original size:19 final size:20
Alignment explanation
Indices: 15500--15546 Score: 71
Period size: 19 Copynumber: 2.4 Consensus size: 20
15490 TACAAGATTT
15500 AAAAAAAAACAAAAA-A-AA
1 AAAAAAAAACAAAAACACAA
15518 ACAAAAAAAACAAAAACACAA
1 A-AAAAAAAACAAAAACACAA
15539 AAAAAAAA
1 AAAAAAAA
15547 TCTACATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 1 0.04
19 14 0.54
20 8 0.31
21 3 0.12
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (20 bp):
AAAAAAAAACAAAAACACAA
Found at i:18449 original size:23 final size:23
Alignment explanation
Indices: 18419--18467 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
18409 GAGTAGATGA
*
18419 TTTAGCCTATGTGTAGGGTTTTT
1 TTTAGCCTATGTATAGGGTTTTT
18442 TTTAGCCTATGTATAGGGTTTTT
1 TTTAGCCTATGTATAGGGTTTTT
18465 TTT
1 TTT
18468 TTTTTTTTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.14, C:0.08, G:0.22, T:0.55
Consensus pattern (23 bp):
TTTAGCCTATGTATAGGGTTTTT
Found at i:21546 original size:3 final size:3
Alignment explanation
Indices: 21538--21577 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
21528 CAATATGAAA
21538 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
21578 ATATATGGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:26466 original size:109 final size:108
Alignment explanation
Indices: 26337--26546 Score: 357
Period size: 109 Copynumber: 1.9 Consensus size: 108
26327 TCCTAAATTT
*
26337 ATCAAATCATTTTTTCCATAGCGATATTGAGGCAATGTTCATATGTTCAGGTAGTCAGGTACTGC
1 ATCAAATCATTTTTTCCATAGCGATATTGAGGCAATGTTCATATGTTCAGGTAATCAGGTACTGC
* *
26402 TGTAAAAGCATTAGATCTCTCTTGATGAATGATTTAGGTATTG
66 TGCAAAAGCATTAGATCTCTCTTAATGAATGATTTAGGTATTG
* * *
26445 ATCAAATCATTTTTTTTCATAGTGATATTGAGGCAATGTTCATATGTTCGGGTAATCAGGTACTG
1 ATCAAATCA-TTTTTTCCATAGCGATATTGAGGCAATGTTCATATGTTCAGGTAATCAGGTACTG
26510 CTGCAAAAGCATTAGATCTCTCTTAATGAATGATTTA
65 CTGCAAAAGCATTAGATCTCTCTTAATGAATGATTTA
26547 AGTGATCAAA
Statistics
Matches: 95, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
108 9 0.09
109 86 0.91
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (108 bp):
ATCAAATCATTTTTTCCATAGCGATATTGAGGCAATGTTCATATGTTCAGGTAATCAGGTACTGC
TGCAAAAGCATTAGATCTCTCTTAATGAATGATTTAGGTATTG
Found at i:30249 original size:3 final size:3
Alignment explanation
Indices: 30241--30265 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
30231 GCTTAGCGTA
30241 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
30266 GTTTCTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:36915 original size:2 final size:2
Alignment explanation
Indices: 36908--36942 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
36898 ATTCCATGAT
36908 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
36943 GAAGGGGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:37255 original size:20 final size:22
Alignment explanation
Indices: 37230--37273 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
37220 TTTCTCTTCT
37230 CTTTTCTTTC-TC-CCTTTGCC
1 CTTTTCTTTCATCACCTTTGCC
*
37250 CTTTTCTTTCATCATCTTTGCC
1 CTTTTCTTTCATCACCTTTGCC
37272 CT
1 CT
37274 GAAAACCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
21 2 0.10
22 9 0.43
ACGTcount: A:0.05, C:0.36, G:0.05, T:0.55
Consensus pattern (22 bp):
CTTTTCTTTCATCACCTTTGCC
Found at i:39732 original size:2 final size:2
Alignment explanation
Indices: 39725--39752 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39715 TTCATTGGAT
39725 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39753 CTTTCTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41889 original size:60 final size:60
Alignment explanation
Indices: 41821--41974 Score: 200
Period size: 60 Copynumber: 2.6 Consensus size: 60
41811 ATATAAGGGT
* * *
41821 CTAACGTTTGTCAAAATACTTAAATAAGGGTCTGATCTTTTAATTTAATCAATTAAGGAC
1 CTAACGTTTGTCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTAATCAAATAAGGAC
* ** * ** *
41881 CTAACGTTTGTTAAAATGCTCAAATAAGAATCCGATCTTTTAATTTGGTCAAATAAGGGC
1 CTAACGTTTGTCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTAATCAAATAAGGAC
* *
41941 CTTACGTTTGCCAAAATGCTCAAATAAGGGTCTG
1 CTAACGTTTGTCAAAATGCTCAAATAAGGGTCTG
41975 GCATCGAAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 78 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (60 bp):
CTAACGTTTGTCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTAATCAAATAAGGAC
Found at i:42051 original size:31 final size:31
Alignment explanation
Indices: 42012--42146 Score: 132
Period size: 31 Copynumber: 4.4 Consensus size: 31
42002 AATTGACCCC
*
42012 AGGCCCTTATTTGAACATTTTCGGTAATGTT
1 AGGCCCTTATTTGAACATTTTCGATAATGTT
* **
42043 GGGCCCTTATTTGAGTATTTTCGATAATGTT
1 AGGCCCTTATTTGAACATTTTCGATAATGTT
** ** * *
42074 AGGCCCTTATTTGGCCAAATT--A-AAAGAT
1 AGGCCCTTATTTGAACATTTTCGATAATGTT
* *
42102 CGGACCCTTATTTGAGCATTTTCGATAATGTT
1 AGG-CCCTTATTTGAACATTTTCGATAATGTT
42134 AGGCCCTTATTTG
1 AGGCCCTTATTTG
42147 GCCAAATTAA
Statistics
Matches: 80, Mismatches: 20, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
28 6 0.08
29 15 0.19
31 53 0.66
32 6 0.08
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (31 bp):
AGGCCCTTATTTGAACATTTTCGATAATGTT
Found at i:42123 original size:60 final size:60
Alignment explanation
Indices: 42046--42206 Score: 261
Period size: 60 Copynumber: 2.7 Consensus size: 60
42036 TAATGTTGGG
* *
42046 CCCTTATTTGAGTATTTTCGATAATGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
1 CCCTTATTTGAGCATTTTCGATAATGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
42106 CCCTTATTTGAGCATTTTCGATAATGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
1 CCCTTATTTGAGCATTTTCGATAATGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
* **
42166 CCCTTATTTGAGCATTTT-GACAAATGTTAAACCCTTATTTG
1 CCCTTATTTGAGCATTTTCGA-TAATGTTAGGCCCTTATTTG
42207 AGTAATTAGC
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
59 2 0.02
60 93 0.98
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTCGATAATGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
Found at i:42175 original size:29 final size:29
Alignment explanation
Indices: 42077--42175 Score: 94
Period size: 29 Copynumber: 3.3 Consensus size: 29
42067 TAATGTTAGG
*
42077 CCCTTATTTGGCCAAATTAAAAGATCGGA
1 CCCTTATTTGGCCAAATTAAAAGATCAGA
** * * *
42106 CCCTTATTTGAG-CATTTTCGATAATG-TTAGG
1 CCCTTATTTG-GCCAAATT--A-AAAGATCAGA
42137 CCCTTATTTGGCCAAATTAAAAGATCAGA
1 CCCTTATTTGGCCAAATTAAAAGATCAGA
42166 CCCTTATTTG
1 CCCTTATTTG
42176 AGCATTTTGA
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
28 3 0.06
29 28 0.53
30 2 0.04
31 17 0.32
32 3 0.06
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.34
Consensus pattern (29 bp):
CCCTTATTTGGCCAAATTAAAAGATCAGA
Found at i:46230 original size:33 final size:33
Alignment explanation
Indices: 46134--46212 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
46124 CATTTACACT
* *
46134 GAGCCTCCCCACT-AGGATGGCTCAGCCACGGCG
1 GAGCCTCCCCACTAAGGA-GGCTCAACCATGGCG
46167 GAGCCTCCCCACTAAGGAGGCTCAACCATGGCG
1 GAGCCTCCCCACTAAGGAGGCTCAACCATGGCG
*
46200 GAGCCTCTCCACT
1 GAGCCTCCCCACT
46213 GGGGCGGCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
33 38 0.90
34 4 0.10
ACGTcount: A:0.20, C:0.39, G:0.27, T:0.14
Consensus pattern (33 bp):
GAGCCTCCCCACTAAGGAGGCTCAACCATGGCG
Done.