Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018226.1 Corchorus olitorius cultivar O-4 contig18259, 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: 91528
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4136 original size:25 final size:24
Alignment explanation
Indices: 4099--4145 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
4089 CTAGAAAATT
4099 TGAAAAACTTTGATAGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
4125 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
4146 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.43, C:0.04, G:0.26, T:0.28
Consensus pattern (24 bp):
TGAAAAACTTTGATGATAGATGGA
Found at i:18360 original size:21 final size:21
Alignment explanation
Indices: 18336--18400 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
18326 CCGGGCATGA
*
18336 CCAGGCCATGTCGCGCAGCAG
1 CCAGGCCATGTCGCGCAACAG
*
18357 CCAGGCCA-G-CACGCAACGAGG
1 CCAGGCCATGTCGCGCAAC-A-G
*
18378 CCAGGCCATGTCGCGCACCAG
1 CCAGGCCATGTCGCGCAACAG
18399 CC
1 CC
18401 CGGGACTGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
19 6 0.17
20 2 0.06
21 20 0.56
22 2 0.06
23 6 0.17
ACGTcount: A:0.22, C:0.42, G:0.31, T:0.06
Consensus pattern (21 bp):
CCAGGCCATGTCGCGCAACAG
Found at i:19939 original size:30 final size:29
Alignment explanation
Indices: 19880--19939 Score: 68
Period size: 30 Copynumber: 2.0 Consensus size: 29
19870 AGTTATCTAG
* *
19880 TTTATGCTTTATCTTTAATTTTCCTTTAA
1 TTTATGCTTTATCTTTAAGTTTCCATTAA
*
19909 TTTATGTCTTTATTTTTCAAGTTT-CATTAA
1 TTTATG-CTTTATCTTT-AAGTTTCCATTAA
19939 T
1 T
19940 AAACTATCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 6 0.23
30 15 0.58
31 5 0.19
ACGTcount: A:0.22, C:0.12, G:0.05, T:0.62
Consensus pattern (29 bp):
TTTATGCTTTATCTTTAAGTTTCCATTAA
Found at i:20160 original size:17 final size:17
Alignment explanation
Indices: 20128--20161 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20118 TAAGTGTGGG
*
20128 GGGATGAATACTTGATA
1 GGGATGAATACATGATA
*
20145 GGGATGAATGCATGATA
1 GGGATGAATACATGATA
20162 TTATAATGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.32, T:0.26
Consensus pattern (17 bp):
GGGATGAATACATGATA
Found at i:33717 original size:21 final size:21
Alignment explanation
Indices: 33693--33742 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
33683 TTGTCGCTCG
*
33693 GCGCCCAGGCGA-AATGCCTCA
1 GCGCCCAGGCGACAAGGCC-CA
33714 GCGCCCAGGCGACAAGGCCCA
1 GCGCCCAGGCGACAAGGCCCA
33735 GCGCCCAG
1 GCGCCCAG
33743 CTCGATCCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.22, C:0.42, G:0.32, T:0.04
Consensus pattern (21 bp):
GCGCCCAGGCGACAAGGCCCA
Found at i:46539 original size:18 final size:18
Alignment explanation
Indices: 46518--46552 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
46508 GGGTAATTAC
*
46518 AAAAAAATTGTTTTCATA
1 AAAAAAAGTGTTTTCATA
*
46536 AAAAGAAGTGTTTTCAT
1 AAAAAAAGTGTTTTCAT
46553 GATAGAGGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (18 bp):
AAAAAAAGTGTTTTCATA
Found at i:52034 original size:20 final size:20
Alignment explanation
Indices: 51991--52040 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
51981 CTTCTATTAC
51991 CTTTATTCACAAATTCACTCA
1 CTTTA-TCACAAATTCACTCA
*
52012 CTTTATCATCAATTTCACT-A
1 CTTTATCA-CAAATTCACTCA
*
52032 CTTCATCAC
1 CTTTATCAC
52041 TTACAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 1 0.04
20 11 0.42
21 14 0.54
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (20 bp):
CTTTATCACAAATTCACTCA
Found at i:52144 original size:16 final size:17
Alignment explanation
Indices: 52116--52147 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
52106 TTTTCCATCA
52116 AAATTTATCAAGTTTTC
1 AAATTTATCAAGTTTTC
52133 AAATTT-TCAAGTTTT
1 AAATTTATCAAGTTTT
52148 GGAAAAGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.50
Consensus pattern (17 bp):
AAATTTATCAAGTTTTC
Found at i:54420 original size:16 final size:16
Alignment explanation
Indices: 54402--54476 Score: 71
Period size: 16 Copynumber: 4.7 Consensus size: 16
54392 AATTTTGGGT
* *
54402 ACCCAAACCCGAAATT
1 ACCCGAACCCGAAATG
* *
54418 ACCCGAATCC-AAACG
1 ACCCGAACCCGAAATG
*
54433 ACCCGAACCTGAAAATG
1 ACCCGAACCCG-AAATG
* *
54450 ACCCAAACCCAAAATG
1 ACCCGAACCCGAAATG
54466 ACCCGAACCCG
1 ACCCGAACCCG
54477 TTCAACCCGA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
15 11 0.24
16 22 0.49
17 12 0.27
ACGTcount: A:0.41, C:0.39, G:0.12, T:0.08
Consensus pattern (16 bp):
ACCCGAACCCGAAATG
Found at i:71546 original size:36 final size:30
Alignment explanation
Indices: 71478--71546 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
71468 TATTTAAATG
*
71478 ATCCGAATCCGAAAAGAACCGAACTCGGAA
1 ATCCAAATCCGAAAAGAACCGAACTCGGAA
71508 ATCCAAATCCGAAAAGAACCGAACTCGGAA
1 ATCCAAATCCGAAAAGAACCGAACTCGGAA
71538 ATCCAAATC
1 ATCCAAATC
71547 TCAAACCTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.45, C:0.28, G:0.16, T:0.12
Consensus pattern (30 bp):
ATCCAAATCCGAAAAGAACCGAACTCGGAA
Found at i:73593 original size:30 final size:28
Alignment explanation
Indices: 73558--73633 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 28
73548 TAACAGAAGG
73558 GGGGAAATTGGCCTAATTTTATTAATTAAA
1 GGGGAAATTGGCCTAA--TTATTAATTAAA
* * *
73588 GGGGAAATGTGGCAC-AATTATTAGTTCAG
1 GGGGAAAT-TGGC-CTAATTATTAATTAAA
73617 GGGGTAAATTGGCCTAA
1 GGGG-AAATTGGCCTAA
73634 AGTTGCAAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
28 1 0.03
29 19 0.49
30 12 0.31
31 6 0.15
32 1 0.03
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (28 bp):
GGGGAAATTGGCCTAATTATTAATTAAA
Found at i:74070 original size:153 final size:151
Alignment explanation
Indices: 73839--74297 Score: 757
Period size: 153 Copynumber: 3.0 Consensus size: 151
73829 GGTCAATCAC
* *
73839 AATAACCTTTTAAATTAAAATGGTAAGAATAAAATAATTATAAAAATATTGAATATAATTAAATG
1 AATAAACTTTTAAATTAAAATGGTAAGAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
*
73904 AAAATAGAGTTTTTAGTAGAATCAAACTATATATATAAAAAATTTTAATATATCCAAG-TTTTGA
66 AAAATAGAGTTTTTAGTAGAATCAAACTATATATATAAAAAATTTTAATATATCCAAGTTTTTAA
*
73968 TGAAAAATAGTAAAATGGTAAC
131 TGAAAAATAGTAAAAT-GTAAA
* * *
73990 AATAAACTTTTAAATTAAAATGGTAAAAATAAAAAAAAATTATAAAAATATTAAATTTAATTAAA
1 AATAAACTTTTAAATTAAAATGGTAAGAAT--AAAATAATTATAAAAATATTGAATTTAATTAAA
74055 TGAAAATAGAGTTTTTAGTAGAATCAAACTATATAT-TAAAAAATTTTAATATATCCAAGTTTTT
64 TGAAAATAGAGTTTTTAGTAGAATCAAACTATATATATAAAAAATTTTAATATATCCAAGTTTTT
74119 AATGAAAAATAGT--AATGTAAA
129 AATGAAAAATAGTAAAATGTAAA
*
74140 AATAAACTTTTAAATTAAAATTGTAAGAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
1 AATAAACTTTTAAATTAAAATGGTAAGAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
*
74205 AAGATAGAGTTTTTAGTAGAATCAAACTATATATCA-AAAAAATTTTAATATATCCAAGTTTTTA
66 AAAATAGAGTTTTTAGTAGAATCAAACTATATAT-ATAAAAAATTTTAATATATCCAAGTTTTTA
74269 ATGAAAAATAGTAAAATTGTAAA
130 ATGAAAAATAGTAAAA-TGTAAA
74292 AATAAA
1 AATAAA
74298 ATAATTATAA
Statistics
Matches: 288, Mismatches: 12, Indels: 15
0.91 0.04 0.05
Matches are distributed among these distances:
148 66 0.23
149 40 0.14
150 32 0.11
151 33 0.11
152 35 0.12
153 82 0.28
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.34
Consensus pattern (151 bp):
AATAAACTTTTAAATTAAAATGGTAAGAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
AAAATAGAGTTTTTAGTAGAATCAAACTATATATATAAAAAATTTTAATATATCCAAGTTTTTAA
TGAAAAATAGTAAAATGTAAA
Found at i:75289 original size:148 final size:150
Alignment explanation
Indices: 75030--75633 Score: 950
Period size: 148 Copynumber: 4.0 Consensus size: 150
75020 TTATAATTAC
* * **
75030 TTTATTTTTACTATTTTACTATTTTTCATTAAAAACTTGGATATATCAAAAAAATTTAATATATA
1 TTTATTTTTACCA-TTTACTATTTTTCATTAAAAACTTGGATATATTAAAAATTTTTAATATATA
75095 GTTTGATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTTATAATTATTTTATT
65 GTTTGATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTTATAATTATTTTATT
75160 TTTACCATTTTAATTTAAAAG
130 TTTACCATTTTAATTTAAAAG
* * * *
75181 TTTATTTTTACGA-TTACTATTTTTCATTAAAAACATAGATTTATTAAAAAATTTTT-ATATATA
1 TTTATTTTTACCATTTACTATTTTTCATTAAAAACTTGGATATATT-AAAAATTTTTAATATATA
*
75244 GTTTGATTC-ACAAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTTATAATTATTTT-TC
65 GTTTGATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTTATAATTATTTTAT-
*
75307 TTTTACCATTTTAATTAAAAAG
129 TTTTACCATTTTAATTTAAAAG
75329 TTTATTTTTACCA-TTACTATTTTTCATTAAAAACTTGGATATATTAAAAATTTTTAATATATAG
1 TTTATTTTTACCATTTACTATTTTTCATTAAAAACTTGGATATATTAAAAATTTTTAATATATAG
* * *
75393 TTTGATTCTACTAAGAACTCTATTTTCATTTAATTAAATTCAATATTTTTATATTTTTTTTATTT
66 TTTGATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTTATAATTATTTTATTT
*
75458 TTACCATTTTAATTTAAAAT
131 TTACCATTTTAATTTAAAAG
* * * *
75478 TTTATTGTTACCATTTTACTATTTTTCGTT-AAAACTTGGATATATTAAAATTTTTTAAAATATA
1 TTTATTTTTACCA-TTTACTATTTTTCATTAAAAACTTGGATATATTAAAAATTTTTAATATATA
*
75542 GTTTGATTTTACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTTATAATTATTTTATT
65 GTTTGATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTTATAATTATTTTATT
75607 TTTACCATTTTAATTTAAAAG
130 TTTACCATTTTAATTTAAAAG
*
75628 GTTATT
1 TTTATT
75634 ATTGTGATTG
Statistics
Matches: 417, Mismatches: 29, Indels: 15
0.90 0.06 0.03
Matches are distributed among these distances:
147 11 0.03
148 129 0.31
149 124 0.30
150 127 0.30
151 26 0.06
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (150 bp):
TTTATTTTTACCATTTACTATTTTTCATTAAAAACTTGGATATATTAAAAATTTTTAATATATAG
TTTGATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTTATAATTATTTTATTT
TTACCATTTTAATTTAAAAG
Found at i:76128 original size:43 final size:45
Alignment explanation
Indices: 76081--76170 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 45
76071 ATTATCTTAA
*
76081 TTCTACT-CT-ATCTCTAGGTAATTCATCAAAATAAAGTTAATAT
1 TTCTACTCCTAATCTCTAGATAATTCATCAAAATAAAGTTAATAT
76124 TTCTACTCCTCAATCTCTAGATAATTCATCAAAATAAAGTTAATAT
1 TTCTACTCCT-AATCTCTAGATAATTCATCAAAATAAAGTTAATAT
76170 T
1 T
76171 AATTGTTGCT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
43 7 0.16
44 2 0.05
46 34 0.79
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.39
Consensus pattern (45 bp):
TTCTACTCCTAATCTCTAGATAATTCATCAAAATAAAGTTAATAT
Found at i:81769 original size:35 final size:36
Alignment explanation
Indices: 81705--81775 Score: 135
Period size: 35 Copynumber: 2.0 Consensus size: 36
81695 AGAAGCTATC
81705 ATTATAAACTAGCAAAACGAATATGTCTACTTTCCT
1 ATTATAAACTAGCAAAACGAATATGTCTACTTTCCT
81741 ATTATAAACTAGCAAAA-GAATATGTCTACTTTCCT
1 ATTATAAACTAGCAAAACGAATATGTCTACTTTCCT
81776 TCTGAATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 18 0.51
36 17 0.49
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.34
Consensus pattern (36 bp):
ATTATAAACTAGCAAAACGAATATGTCTACTTTCCT
Found at i:85142 original size:12 final size:12
Alignment explanation
Indices: 85125--85197 Score: 92
Period size: 12 Copynumber: 5.9 Consensus size: 12
85115 CATCGATACC
85125 TCGATATATCCG
1 TCGATATATCCG
*
85137 TCGATATATCCA
1 TCGATATATCCG
**
85149 TCGATATATATG
1 TCGATATATCCG
*
85161 TTCGATATATCCA
1 -TCGATATATCCG
85174 TCGATATATCCG
1 TCGATATATCCG
85186 TTCGATATATCC
1 -TCGATATATCC
85198 ATTGATATCT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
12 31 0.61
13 20 0.39
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:85170 original size:25 final size:25
Alignment explanation
Indices: 85125--85205 Score: 119
Period size: 25 Copynumber: 3.3 Consensus size: 25
85115 CATCGATACC
*
85125 TCGATATATCCG-TCGATATATCCA
1 TCGATATATACGTTCGATATATCCA
*
85149 TCGATATATATGTTCGATATATCCA
1 TCGATATATACGTTCGATATATCCA
*
85174 TCGATATATCCGTTCGATATATCCA
1 TCGATATATACGTTCGATATATCCA
*
85199 TTGATAT
1 TCGATAT
85206 CTGTATTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
24 10 0.20
25 41 0.80
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (25 bp):
TCGATATATACGTTCGATATATCCA
Found at i:85205 original size:37 final size:37
Alignment explanation
Indices: 85125--85205 Score: 58
Period size: 37 Copynumber: 2.2 Consensus size: 37
85115 CATCGATACC
* * ***
85125 TCGATATATCCG-TCGATATATCCATCGATATATATGT
1 TCGATATATCCGATCGATATATACATTGATATAT-CCA
* *
85162 TCGATATATCC-ATCGATATATCCGTTCGATATATCCA
1 TCGATATATCCGATCGATATATACATT-GATATATCCA
*
85199 TTGATAT
1 TCGATAT
85206 CTGTATTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
37 29 0.81
38 7 0.19
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (37 bp):
TCGATATATCCGATCGATATATACATTGATATATCCA
Found at i:90024 original size:40 final size:40
Alignment explanation
Indices: 89980--90056 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
89970 CTTCTCAAAT
89980 ACCCATAACCAAACCGTAAACCTCAAAATCCCGGCGGCGG
1 ACCCATAACCAAACCGTAAACCTCAAAATCCCGGCGGCGG
90020 ACCCATAACCAAACCGTAAACCTCAAAATCCCGGCGG
1 ACCCATAACCAAACCGTAAACCTCAAAATCCCGGCGG
90057 TCTGATTGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.36, C:0.38, G:0.16, T:0.10
Consensus pattern (40 bp):
ACCCATAACCAAACCGTAAACCTCAAAATCCCGGCGGCGG
Done.