Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020614.1 Corchorus olitorius cultivar O-4 contig20647, 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: 35516
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--67 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
43 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
68 AAGCTCTTCT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:8149 original size:29 final size:30
Alignment explanation
Indices: 8114--8171 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
8104 ACCTTTAGGG
*
8114 AAAAGGTCATATAAGGGCCT-AACGTTTCA
1 AAAAGGTCAAATAAGGGCCTCAACGTTTCA
* *
8143 AAAAGGTCAAATCAGGGCCTCAACTTTTC
1 AAAAGGTCAAATAAGGGCCTCAACGTTTC
8172 GATTCGGGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (30 bp):
AAAAGGTCAAATAAGGGCCTCAACGTTTCA
Found at i:9425 original size:29 final size:30
Alignment explanation
Indices: 9373--9430 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
9363 GACCCGAATC
*
9373 GAAAAGTTGAGGCCCTGATTTGACCTTTTT
1 GAAAAGTTGAGGCCCTGATATGACCTTTTT
* *
9403 GAAACGTT-AGGCCCTTATATGACCTTTT
1 GAAAAGTTGAGGCCCTGATATGACCTTTT
9431 CCCTAAAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (30 bp):
GAAAAGTTGAGGCCCTGATATGACCTTTTT
Found at i:15147 original size:60 final size:60
Alignment explanation
Indices: 15027--15290 Score: 294
Period size: 60 Copynumber: 4.5 Consensus size: 60
15017 AAAATTAAAA
* * * * *
15027 TTCCAAAAATGCCCCTCCGGTCGAAGGGTCCGCTTTTGCATTTCAAG--T--TTTTT--T
1 TTCCAAAAATACCCTTCCGGTCGAAGGGTTCACTTTTGAATTTCAAGTTTAATTTTTACT
* *
15081 TTCCAAAAATACCCTTCCGGTCGAAGGGTTCACTTCTGAATTTCAAGTTTAATTTTTAGT
1 TTCCAAAAATACCCTTCCGGTCGAAGGGTTCACTTTTGAATTTCAAGTTTAATTTTTACT
* * * *
15141 TACCAAAAATACCCTTCTGGTCGAAGGGTTCGCTTTTGCATTTCAAGTTTAA-TTTTACT
1 TTCCAAAAATACCCTTCCGGTCGAAGGGTTCACTTTTGAATTTCAAGTTTAATTTTTACT
* * *
15200 TTCCAATAATACCCTTCCAGTCGAAGGG-TCAGCTTTT-ACATTTCAAGTTCAATTTTTTCACT
1 TTCCAAAAATACCCTTCCGGTCGAAGGGTTCA-CTTTTGA-ATTTCAAGTTTAA-TTTTT-ACT
*
15262 TTCCAAAAATACCCTTCCGGACGAAGGGT
1 TTCCAAAAATACCCTTCCGGTCGAAGGGT
15291 CAGTTTTCCT
Statistics
Matches: 176, Mismatches: 22, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
54 41 0.23
56 1 0.01
58 7 0.04
59 47 0.27
60 48 0.27
61 4 0.02
62 28 0.16
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (60 bp):
TTCCAAAAATACCCTTCCGGTCGAAGGGTTCACTTTTGAATTTCAAGTTTAATTTTTACT
Found at i:15226 original size:59 final size:60
Alignment explanation
Indices: 15027--15290 Score: 319
Period size: 59 Copynumber: 4.5 Consensus size: 60
15017 AAAATTAAAA
* * *
15027 TTCCAAAAATGCCCCTCCGGTCGAAGGGTCCGCTTTTGCATTTCAAG--T--TTTTT--T
1 TTCCAAAAATACCCTTCCGGTCGAAGGGTTCGCTTTTGCATTTCAAGTTTAATTTTTACT
* * * *
15081 TTCCAAAAATACCCTTCCGGTCGAAGGGTTCACTTCTGAATTTCAAGTTTAATTTTTAGT
1 TTCCAAAAATACCCTTCCGGTCGAAGGGTTCGCTTTTGCATTTCAAGTTTAATTTTTACT
* *
15141 TACCAAAAATACCCTTCTGGTCGAAGGGTTCGCTTTTGCATTTCAAGTTTAA-TTTTACT
1 TTCCAAAAATACCCTTCCGGTCGAAGGGTTCGCTTTTGCATTTCAAGTTTAATTTTTACT
* * * *
15200 TTCCAATAATACCCTTCCAGTCGAAGGG-TCAGCTTTTACATTTCAAGTTCAATTTTTTCACT
1 TTCCAAAAATACCCTTCCGGTCGAAGGGTTC-GCTTTTGCATTTCAAGTTTAA-TTTTT-ACT
*
15262 TTCCAAAAATACCCTTCCGGACGAAGGGT
1 TTCCAAAAATACCCTTCCGGTCGAAGGGT
15291 CAGTTTTCCT
Statistics
Matches: 178, Mismatches: 21, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
54 41 0.23
56 1 0.01
58 7 0.04
59 49 0.28
60 48 0.27
61 4 0.02
62 28 0.16
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (60 bp):
TTCCAAAAATACCCTTCCGGTCGAAGGGTTCGCTTTTGCATTTCAAGTTTAATTTTTACT
Found at i:15254 original size:119 final size:116
Alignment explanation
Indices: 15029--15291 Score: 336
Period size: 119 Copynumber: 2.2 Consensus size: 116
15019 AATTAAAATT
* *
15029 CCAAAAATGCCCCTCCGGTCGAAGGGTCCGCTTTTGCATTTCAAGTTTTTTTTTCCAAAAATACC
1 CCAAAAATACCCTTCCGGTCGAAGGGTCCGCTTTTGCATTTCAAGTTTTTTTTTCCAAAAATACC
* * *
15094 CTTCCGGTCGAAGGGTTCACTTCTGAATTTCAAGTTTAA-TTTTT-AGTTA
66 CTTCCAGTCGAAGGGTTCACTTCTGAATTTCAAGTTCAATTTTTTCACTTA
* * *
15143 CCAAAAATACCCTTCTGGTCGAAGGGTTCGCTTTTGCATTTCAAGTTTAATTTTACTTTCCAATA
1 CCAAAAATACCCTTCCGGTCGAAGGGTCCGCTTTTGCATTTCAAG-TT--TTTT--TTTCCAAAA
* *
15208 ATACCCTTCCAGTCGAAGGG-TCAGCTT-TTACATTTCAAGTTCAATTTTTTCACTTT
61 ATACCCTTCCAGTCGAAGGGTTCA-CTTCTGA-ATTTCAAGTTCAATTTTTTCACTTA
*
15264 CCAAAAATACCCTTCCGGACGAAGGGTC
1 CCAAAAATACCCTTCCGGTCGAAGGGTC
15292 AGTTTTCCTG
Statistics
Matches: 127, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
114 41 0.32
115 2 0.02
117 4 0.03
118 5 0.04
119 42 0.33
120 5 0.04
121 28 0.22
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.36
Consensus pattern (116 bp):
CCAAAAATACCCTTCCGGTCGAAGGGTCCGCTTTTGCATTTCAAGTTTTTTTTTCCAAAAATACC
CTTCCAGTCGAAGGGTTCACTTCTGAATTTCAAGTTCAATTTTTTCACTTA
Found at i:19742 original size:5 final size:4
Alignment explanation
Indices: 19705--19749 Score: 63
Period size: 4 Copynumber: 10.8 Consensus size: 4
19695 AGCAATCAAA
*
19705 AAAG AAAG AAAG AACG AAAG AAAG AAAG AAAGG AAAGG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA-G AAA-G AAAG AAA
19750 TTTTAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 29 0.76
5 9 0.24
ACGTcount: A:0.71, C:0.02, G:0.27, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:21043 original size:69 final size:70
Alignment explanation
Indices: 20930--21084 Score: 224
Period size: 69 Copynumber: 2.2 Consensus size: 70
20920 AATGCTTTGA
* * *
20930 CTTTTCCATAAGTCAAACTCGCTTCCATACAAGTCAGTTTAAGTTTTGGTT-CTATCCAAGCA-G
1 CTTTTCCATAAGCCATACTCGCTTCCATACAAGTCAGTTCAAGTTTTGGTTGC-ATCCAAGCATG
20993 CAGGGG
65 CAGGGG
* * * *
20999 CTTTTCCACAAGCCATACTCGTTTCCATACGAGTCAGTTCAAGTTTTGGTTGCATCCAAGCATTC
1 CTTTTCCATAAGCCATACTCGCTTCCATACAAGTCAGTTCAAGTTTTGGTTGCATCCAAGCATGC
21064 AGGGG
66 AGGGG
21069 CTTTTCCATAAGCCAT
1 CTTTTCCATAAGCCAT
21085 TTTCAATGAA
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
69 54 0.71
70 22 0.29
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (70 bp):
CTTTTCCATAAGCCATACTCGCTTCCATACAAGTCAGTTCAAGTTTTGGTTGCATCCAAGCATGC
AGGGG
Found at i:21265 original size:47 final size:47
Alignment explanation
Indices: 21195--21318 Score: 203
Period size: 47 Copynumber: 2.6 Consensus size: 47
21185 AATCCAGGTA
*
21195 ATCTTTTCTCGCTTCCATGCGAGTCTACAATTTGGTGACCACAGTTG
1 ATCTTTTCTCGCTTCCATGCGAGTCTACAATTTAGTGACCACAGTTG
* *
21242 GTCTTTTCTCGCTTCCATGCGAGTCTACAGTTTAGTGACCACAGTTG
1 ATCTTTTCTCGCTTCCATGCGAGTCTACAATTTAGTGACCACAGTTG
* *
21289 ATCTTTTCTCGCTTCCACGCGAATCTACAA
1 ATCTTTTCTCGCTTCCATGCGAGTCTACAA
21319 AGGTGACCTA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 70 1.00
ACGTcount: A:0.19, C:0.27, G:0.18, T:0.35
Consensus pattern (47 bp):
ATCTTTTCTCGCTTCCATGCGAGTCTACAATTTAGTGACCACAGTTG
Found at i:21560 original size:62 final size:62
Alignment explanation
Indices: 21401--21683 Score: 338
Period size: 62 Copynumber: 4.5 Consensus size: 62
21391 AGTTTTGAAT
* * * *
21401 AAAGTCGACCTCAGATTGGTCTTCTTCAATTTCAGACCTCAGACAGGT-TTTTTTCAGTTTTA
1 AAAGTCGACCACGGACTGGTCTTCTTCAATTTCAGACCTCAGACAGGTCTTTCTT-AGTTTTA
* * *
21463 TTAAAGTCGA-CATCGGACCGGTCTTCTTCAGTTTCAGACCTCAGACAGGCCTTTCTTAGTTTTA
1 --AAAGTCGACCA-CGGACTGGTCTTCTTCAATTTCAGACCTCAGACAGGTCTTTCTTAGTTTTA
* * * * *
21527 AAAGTTGACCACGGACTGGTCTTCTTCAATTTCAGACGTTAAACAGATCTTTCTTAGTTCTT-
1 AAAGTCGACCACGGACTGGTCTTCTTCAATTTCAGACCTCAGACAGGTCTTTCTTAGTT-TTA
* * * *
21589 AAAGTCGACCACGGATTGGTCTTCTTCATTTTCAGACCTCAGATAGGTCTTTCTTAGTTTTT
1 AAAGTCGACCACGGACTGGTCTTCTTCAATTTCAGACCTCAGACAGGTCTTTCTTAGTTTTA
* *
21651 AAAGTCGACCATGGACTGGTCTTCTTCAGTTTC
1 AAAGTCGACCACGGACTGGTCTTCTTCAATTTC
21684 TTCTTCAGTT
Statistics
Matches: 188, Mismatches: 26, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
61 2 0.01
62 129 0.69
63 5 0.03
64 47 0.25
65 5 0.03
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (62 bp):
AAAGTCGACCACGGACTGGTCTTCTTCAATTTCAGACCTCAGACAGGTCTTTCTTAGTTTTA
Found at i:21687 original size:12 final size:12
Alignment explanation
Indices: 21670--21695 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21660 CATGGACTGG
21670 TCTTCTTCAGTT
1 TCTTCTTCAGTT
21682 TCTTCTTCAGTT
1 TCTTCTTCAGTT
21694 TC
1 TC
21696 AGACCTCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.27, G:0.08, T:0.58
Consensus pattern (12 bp):
TCTTCTTCAGTT
Found at i:23861 original size:150 final size:150
Alignment explanation
Indices: 23609--23882 Score: 417
Period size: 150 Copynumber: 1.8 Consensus size: 150
23599 GCATCAAAAG
*
23609 CCACTCTGCATTTGAATTTGAATGCTACTACTGAAGCCTACATACCTGTACTATTAGCTGAATTG
1 CCACTCTGCATTTGAATTTGAATGCTACCACTGAAGCCTACATACCTGTACTATTAGCTGAATTG
* * *
23674 CCGCCAAGAGTCCAAATATTCCGCCGTGAATAATAGCTAGCCATGGAGTGGCTTCAATACCAGTA
66 CCGCCAAGAGTCCAAATACTCCACCATGAATAATAGCTAGCCATGGAGTGGCTTCAATACCAGTA
23739 GAGCACAATGCCATCAGACA
131 GAGCACAATGCCATCAGACA
* * * *
23759 CCACTCTGCATTTGACTTTGAAT-CTACCACTGAAGCCTAGATACCTGTACT-GTATGCTGGATT
1 CCACTCTGCATTTGAATTTGAATGCTACCACTGAAGCCTACATACCTGTACTATTA-GCTGAATT
* * *
23822 TCCGCCAAGAGTCCAAATACTCTTACCATGAATGATAGCTAGCCATGGAGTGGCTTCAATA
65 GCCGCCAAGAGTCCAAATACTC-CACCATGAATAATAGCTAGCCATGGAGTGGCTTCAATA
23883 GCAGCGGAAA
Statistics
Matches: 111, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
148 2 0.02
149 53 0.48
150 56 0.50
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (150 bp):
CCACTCTGCATTTGAATTTGAATGCTACCACTGAAGCCTACATACCTGTACTATTAGCTGAATTG
CCGCCAAGAGTCCAAATACTCCACCATGAATAATAGCTAGCCATGGAGTGGCTTCAATACCAGTA
GAGCACAATGCCATCAGACA
Found at i:35253 original size:29 final size:30
Alignment explanation
Indices: 35193--35270 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 30
35183 GAGTTTTTAA
* *
35193 CCAACCCATTGTAGTTCTTAAAAATAATTC
1 CCAAACCATTGTACTTCTTAAAAATAATTC
* *
35223 CCAAACCATTGTACTT-TTAGAATTAATTC
1 CCAAACCATTGTACTTCTTAAAAATAATTC
* *
35252 CCAAACTATTGTATTTCTT
1 CCAAACCATTGTACTTCTT
35271 GCCACATCTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 25 0.61
30 16 0.39
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.38
Consensus pattern (30 bp):
CCAAACCATTGTACTTCTTAAAAATAATTC
Done.