Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007676.1 Corchorus capsularis cultivar CVL-1 contig07697, 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: 48270
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--33 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1 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
34 TATGGACTAA
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:7430 original size:3 final size:3
Alignment explanation
Indices: 7422--7461 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
7412 ATATCGTTGG
7422 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
7462 TTGATTTGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:18564 original size:17 final size:18
Alignment explanation
Indices: 18538--18579 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
18528 CACCTTTGGC
* *
18538 ATTTTTACTT-ATTTCGT
1 ATTTTAACTTCATTTAGT
18555 ATTTTAACTTCATTTAGT
1 ATTTTAACTTCATTTAGT
*
18573 AATTTAA
1 ATTTTAA
18580 TTAGCACTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.57
Consensus pattern (18 bp):
ATTTTAACTTCATTTAGT
Found at i:22292 original size:12 final size:13
Alignment explanation
Indices: 22268--22300 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
22258 AAACGAAGAA
22268 GGAAAAGAAAAAAT
1 GGAAAA-AAAAAAT
22282 -GAAAAAAAAAAT
1 GGAAAAAAAAAAT
22294 GGAAAAA
1 GGAAAAA
22301 TCAGAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (13 bp):
GGAAAAAAAAAAT
Found at i:28079 original size:33 final size:33
Alignment explanation
Indices: 28031--28111 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
28021 CAAATAGTGT
* *
28031 TTTAGATGTTGTTTGCAATGATACTAAACCTAA
1 TTTAGGTGTTGTTTGCAATGACACTAAACCTAA
* *
28064 TTT-GAGTGTTGTTTGCAATGACACTAAATCTGA
1 TTTAG-GTGTTGTTTGCAATGACACTAAACCTAA
28097 TTTAGGTGTTGTTTG
1 TTTAGGTGTTGTTTG
28112 TGATGAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
32 1 0.02
33 40 0.95
34 1 0.02
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.43
Consensus pattern (33 bp):
TTTAGGTGTTGTTTGCAATGACACTAAACCTAA
Found at i:28155 original size:33 final size:33
Alignment explanation
Indices: 28115--28233 Score: 195
Period size: 33 Copynumber: 3.6 Consensus size: 33
28105 TTGTTTGTGA
28115 TGAAAATAGA-TCTGTTTTGGTTGATCATAGCAT
1 TGAAAATA-ATTCTGTTTTGGTTGATCATAGCAT
*
28148 TGCAAATAATTCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
*
28181 TGGAAATAATTCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
*
28214 TGAAAATAATTTTGTTTTGG
1 TGAAAATAATTCTGTTTTGG
28234 GTGAAAAGAA
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
32 1 0.01
33 80 0.99
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (33 bp):
TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
Found at i:35205 original size:12 final size:12
Alignment explanation
Indices: 35184--35232 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
35174 AAAGCAAAGC
*
35184 AAAT-TAAATCT
1 AAATCTAAATCA
35195 AAATCTAAATCA
1 AAATCTAAATCA
*
35207 AAATCTAAAACA
1 AAATCTAAATCA
* *
35219 GAATCTAAAGCA
1 AAATCTAAATCA
35231 AA
1 AA
35233 CAATAATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 4 0.12
12 28 0.88
ACGTcount: A:0.59, C:0.14, G:0.04, T:0.22
Consensus pattern (12 bp):
AAATCTAAATCA
Found at i:42174 original size:6 final size:6
Alignment explanation
Indices: 42159--42202 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
42149 AAAGCAAAGC
42159 AAAT-T AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA
42203 ACAGAATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.11
6 34 0.89
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATCT
Found at i:42214 original size:18 final size:18
Alignment explanation
Indices: 42159--42214 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
42149 AAAGCAAAGC
* *
42159 AAAT-TAAATCTAAATCT
1 AAATCTAAAACTAAATAT
* *
42176 AAATCTAAATCTAAATCT
1 AAATCTAAAACTAAATAT
42194 AAATCTAAAAC-AGAATAT
1 AAATCTAAAACTA-AATAT
42212 AAA
1 AAA
42215 GCAAACAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
17 5 0.14
18 30 0.86
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (18 bp):
AAATCTAAAACTAAATAT
Found at i:43715 original size:14 final size:14
Alignment explanation
Indices: 43696--43722 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43686 CTCCTACTAA
43696 ACTTAATTACCCTT
1 ACTTAATTACCCTT
43710 ACTTAATTACCCT
1 ACTTAATTACCCT
43723 GAATTTAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (14 bp):
ACTTAATTACCCTT
Found at i:43843 original size:99 final size:102
Alignment explanation
Indices: 43708--43973 Score: 360
Period size: 99 Copynumber: 2.6 Consensus size: 102
43698 TTAATTACCC
43708 TTACTTAATTACCCTGAATTTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTGATC
1 TTACTTAATTACCCTGAA-TTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTGATC
43773 AATGACTCACTTAA-T-T-AATTAAGTCGATTACTGAA
65 AATGACTCACTTAATTCTAAATTAAGTCGATTACTGAA
* * *
43808 TTACCTAATTACCCTGGATTAAGTTGACTACTGACTCACTTAATTACCCTGAATTAAGTTGATCA
1 TTACTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTGATCA
* * * * *
43873 CTGATTTACTTAATTACCCTAAATTAAGTTGATTACTGAC
66 ATGACTCACTTAATT---CTAAATTAAGTCGATTACTGAA
* *
43913 TTACTTAATTACCCTGAATTAAGTT-ATTAACTGACCTTACTCAATTACCCTGAATTAAGTT
1 TTACTTAATTACCCTGAATTAAGTTGATT-ACTGA-CTCACTTAATTACCCTGAATTAAGTT
43974 ACTGACTTAC
Statistics
Matches: 145, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
99 56 0.39
100 17 0.12
104 3 0.02
105 45 0.31
106 24 0.17
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.38
Consensus pattern (102 bp):
TTACTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTACCCTGAATTAAGTTGATCA
ATGACTCACTTAATTCTAAATTAAGTCGATTACTGAA
Found at i:44009 original size:76 final size:72
Alignment explanation
Indices: 43814--44079 Score: 351
Period size: 76 Copynumber: 3.6 Consensus size: 72
43804 TGAATTACCT
* * *
43814 AATTACCCTGGATTAAGTTGAC-TACTGACTCACTTAATTACCCTGAATTAAGTTGA-TCACTGA
1 AATTACCCTGAATTAAGTTGACTTACTGACTTACTTAATTACCCTGAATTAAGTT-ATTAACTGA
* *
43877 -TTTACTT
65 CCTTACTC
*
43884 AATTACCCTAAATTAAGTTGA-TTACTGACTTACTTAATTACCCTGAATTAAGTTATTAACTGAC
1 AATTACCCTGAATTAAGTTGACTTACTGACTTACTTAATTACCCTGAATTAAGTTATTAACTGAC
43948 CTTACTC
66 CTTACTC
*
43955 AATTACCCTGAATTAAGTTACTGACTTACTTTACTTACTTAATTACCCTGAATTAAGTTATTAAC
1 AATTACCCTGAATTAAG-T--TGACTTAC-TGACTTACTTAATTACCCTGAATTAAGTTATTAAC
44020 TGACCTTACTC
62 TGACCTTACTC
*
44031 AATTACCCTGAATTAAGTTACTGACTTACTTTACTTACTTAATTACCCT
1 AATTACCCTGAATTAAG-T--TGACTTAC-TGACTTACTTAATTACCCT
44080 TAATCAAATC
Statistics
Matches: 180, Mismatches: 8, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
69 1 0.01
70 56 0.31
71 21 0.12
72 1 0.01
74 3 0.02
75 4 0.02
76 94 0.52
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.39
Consensus pattern (72 bp):
AATTACCCTGAATTAAGTTGACTTACTGACTTACTTAATTACCCTGAATTAAGTTATTAACTGAC
CTTACTC
Found at i:44131 original size:35 final size:35
Alignment explanation
Indices: 43707--44125 Score: 431
Period size: 35 Copynumber: 11.8 Consensus size: 35
43697 CTTAATTACC
43707 CTTACTTAATTACCCTGAATTTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAA-TTAAGTTGATTACTGA
* * *
43743 CTCACTTAATTACCCTGAATTAAGTTGATCAATGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* *
43778 CTCACTTAA-T----T-AATTAAGTCGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* * * *
43807 ATTACCTAATTACCCTGGATTAAGTTGACTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* *
43842 CTCACTTAATTACCCTGAATTAAGTTGATCACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* *
43877 TTTACTTAATTACCCTAAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
43912 CTTACTTAATTACCCTGAATTAAGTT-ATTAACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATT-ACTGA
* *
43947 CCTTACTCAATTACCCTGAATTAAGTTACTGACTTACTTTA
1 -CTTACTTAATTACCCTGAATTAAG-T--TGA-TTAC-TGA
43988 CTTACTTAATTACCCTGAATTAAGTT-ATTAACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATT-ACTGA
* *
44023 CCTTACTCAATTACCCTGAATTAAGTTACTGACTTACTTTA
1 -CTTACTTAATTACCCTGAATTAAG-T--TGA-TTAC-TGA
* * * * *
44064 CTTACTTAATTACCCTTAATCAAATCGATTATTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
**
44099 CTTGTTTAATTACCCTGAATTAAGTTG
1 CTTACTTAATTACCCTGAATTAAGTTG
44126 CTTATTACTG
Statistics
Matches: 318, Mismatches: 43, Indels: 45
0.78 0.11 0.11
Matches are distributed among these distances:
29 21 0.07
30 2 0.01
34 5 0.02
35 154 0.48
36 70 0.22
37 5 0.02
39 4 0.01
40 49 0.15
41 8 0.03
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (35 bp):
CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
Found at i:47618 original size:36 final size:34
Alignment explanation
Indices: 47564--47651 Score: 90
Period size: 36 Copynumber: 2.4 Consensus size: 34
47554 CTAGAGAAAA
*
47564 ACCACCCTGGATCTTTCCGAACTG-AACTGAA-GAATG
1 ACCACCCT-GATCATTCCG-AC-GAAACTGAAGGAA-G
47600 ACCACCCTCGATCATTCCGACGCAAACTGAAGGAAG
1 ACCACCCT-GATCATTCCGACG-AAACTGAAGGAAG
47636 ACCACCCTGAGTCATT
1 ACCACCCTGA-TCATT
47652 GAAGTAAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
34 1 0.02
35 4 0.09
36 38 0.83
37 3 0.07
ACGTcount: A:0.31, C:0.32, G:0.18, T:0.19
Consensus pattern (34 bp):
ACCACCCTGATCATTCCGACGAAACTGAAGGAAG
Done.