Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013461.1 Corchorus olitorius cultivar O-4 contig13494, 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: 40090
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1745 original size:18 final size:18
Alignment explanation
Indices: 1718--1767 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
1708 TTACTGGATG
1718 TTTATGTATGGAAAGGTA
1 TTTATGTATGGAAAGGTA
* *
1736 TTTTTGTATGGAAAGGTG
1 TTTATGTATGGAAAGGTA
1754 TTTATGTATGGAAA
1 TTTATGTATGGAAA
1768 TTGGAAAGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (18 bp):
TTTATGTATGGAAAGGTA
Found at i:1893 original size:24 final size:24
Alignment explanation
Indices: 1865--1939 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
1855 ATACAATTAA
1865 CAGAAACAGAGCATGCCTAAAACT
1 CAGAAACAGAGCATGCCTAAAACT
* * *
1889 CAGAAACAGAGCATTCCTAAACCC
1 CAGAAACAGAGCATGCCTAAAACT
*
1913 CAGAAACAGAGCAAGCCTAAAACT
1 CAGAAACAGAGCATGCCTAAAACT
1937 CAG
1 CAG
1940 GGCAATGCCT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.45, C:0.28, G:0.16, T:0.11
Consensus pattern (24 bp):
CAGAAACAGAGCATGCCTAAAACT
Found at i:11525 original size:36 final size:36
Alignment explanation
Indices: 11484--11559 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
11474 CTTCTACTCA
11484 GAAACAAATCAGTAATGAAGTAACAACTTTCAACTG
1 GAAACAAATCAGTAATGAAGTAACAACTTTCAACTG
11520 GAAACAAATCAGTAATGAAGTAACAACTTTCAACTG
1 GAAACAAATCAGTAATGAAGTAACAACTTTCAACTG
11556 GAAA
1 GAAA
11560 GTGTAAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.21
Consensus pattern (36 bp):
GAAACAAATCAGTAATGAAGTAACAACTTTCAACTG
Found at i:12737 original size:14 final size:13
Alignment explanation
Indices: 12718--12756 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
12708 AAATTGTAAA
12718 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
12731 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
12745 ATTTAAAAAATT
1 ATTTAAAAAATT
12757 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:12985 original size:122 final size:128
Alignment explanation
Indices: 12742--12995 Score: 403
Period size: 122 Copynumber: 2.0 Consensus size: 128
12732 ATTTAAGAAA
12742 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGT---AATAAAA
* *
12807 TAGATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
63 TACATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
12872 G
128 G
*
12873 TATATTT-AAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGT-A-AAAAT-C
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAATAAAATAC
*
12934 ATA-AA-GATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAAG
66 ATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
12995 T
1 T
12996 TTAAACAATG
Statistics
Matches: 119, Mismatches: 4, Indels: 9
0.90 0.03 0.07
Matches are distributed among these distances:
122 55 0.46
123 2 0.02
124 3 0.03
125 5 0.04
126 1 0.01
130 46 0.39
131 7 0.06
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (128 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAATAAAATAC
ATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:13825 original size:15 final size:15
Alignment explanation
Indices: 13805--13835 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
13795 ACAATACATT
13805 AACTATCAAATAGAA
1 AACTATCAAATAGAA
13820 AACTATCAAATAGAA
1 AACTATCAAATAGAA
13835 A
1 A
13836 CATGTTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (15 bp):
AACTATCAAATAGAA
Found at i:13882 original size:14 final size:14
Alignment explanation
Indices: 13863--13897 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
13853 CCTTTTAAAT
13863 TAAAATAGTAAAAA
1 TAAAATAGTAAAAA
*
13877 TAAAATGGTAAAAA
1 TAAAATAGTAAAAA
13891 TAAAATA
1 TAAAATA
13898 ATTATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (14 bp):
TAAAATAGTAAAAA
Found at i:20182 original size:11 final size:10
Alignment explanation
Indices: 20153--20180 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
20143 TGATGTAGGG
20153 TTTTTTTTGT
1 TTTTTTTTGT
20163 TTTTTTTTGT
1 TTTTTTTTGT
20173 TTTTTTTT
1 TTTTTTTT
20181 TGGCCACCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:22578 original size:7 final size:7
Alignment explanation
Indices: 22566--22596 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
22556 ATTTGACCTC
22566 TTTTTCT
1 TTTTTCT
22573 TTTTTCT
1 TTTTTCT
22580 TTTTTCT
1 TTTTTCT
22587 TTTTT-T
1 TTTTTCT
22593 TTTT
1 TTTT
22597 CATACGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTTTCT
Found at i:22939 original size:60 final size:60
Alignment explanation
Indices: 22846--22966 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
22836 TAGAAATGCG
22846 CTTGCAACAGTTAAAAGTTCTGAAGTTATTAGTGATGCAGGAACACCATCTGTGGAGCCA
1 CTTGCAACAGTTAAAAGTTCTGAAGTTATTAGTGATGCAGGAACACCATCTGTGGAGCCA
22906 CTTGCAACAGTTAAAAGTTCTGAAGTTATTAGTGATGCAGGAACACCATCTGTGGAGCCA
1 CTTGCAACAGTTAAAAGTTCTGAAGTTATTAGTGATGCAGGAACACCATCTGTGGAGCCA
22966 C
1 C
22967 CTTCGGAGCT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (60 bp):
CTTGCAACAGTTAAAAGTTCTGAAGTTATTAGTGATGCAGGAACACCATCTGTGGAGCCA
Found at i:24959 original size:88 final size:88
Alignment explanation
Indices: 24810--24984 Score: 314
Period size: 88 Copynumber: 2.0 Consensus size: 88
24800 TTCGTATCGG
24810 ATTTTTCAGTTTATGGTTAGAATAGAGTAATTTCAATTATAAGCAAAATTTTATATGTAATAAGT
1 ATTTTTCAGTTTATGGTTAGAATAGAGTAATTTCAATTATAAGCAAAATTTTATATGTAATAAGT
24875 AATTAAGTTAAATAAAAGAAAAC
66 AATTAAGTTAAATAAAAGAAAAC
* * * *
24898 ATTTTTCAGTTTATGGTTGGAATATAGTAATTTCAATTGTAAGTAAAATTTTATATGTAATAAGT
1 ATTTTTCAGTTTATGGTTAGAATAGAGTAATTTCAATTATAAGCAAAATTTTATATGTAATAAGT
24963 AATTAAGTTAAATAAAAGAAAA
66 AATTAAGTTAAATAAAAGAAAA
24985 TATTGTTAGA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 83 1.00
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.39
Consensus pattern (88 bp):
ATTTTTCAGTTTATGGTTAGAATAGAGTAATTTCAATTATAAGCAAAATTTTATATGTAATAAGT
AATTAAGTTAAATAAAAGAAAAC
Found at i:25857 original size:31 final size:31
Alignment explanation
Indices: 25821--25880 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
25811 ATTATGATTA
25821 AATGTAAACTATTATAAACTTGATATTTAGT
1 AATGTAAACTATTATAAACTTGATATTTAGT
25852 AATGTAAACTATTATAAACTTGATATTTA
1 AATGTAAACTATTATAAACTTGATATTTA
25881 CATCTTACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (31 bp):
AATGTAAACTATTATAAACTTGATATTTAGT
Found at i:28059 original size:27 final size:28
Alignment explanation
Indices: 28012--28071 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 28
28002 GGGCATTCAA
* *
28012 AAAAAGGTGTTACATGGGGTATCAAAAG
1 AAAAAGGTGTTACATGAGGTATAAAAAG
28040 AAAAAGGTGTTACAT-AGGTATAAAAAG
1 AAAAAGGTGTTACATGAGGTATAAAAAG
28067 AAAAA
1 AAAAA
28072 AAAAAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 15 0.50
28 15 0.50
ACGTcount: A:0.52, C:0.05, G:0.23, T:0.20
Consensus pattern (28 bp):
AAAAAGGTGTTACATGAGGTATAAAAAG
Found at i:28072 original size:28 final size:29
Alignment explanation
Indices: 28011--28072 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
28001 TGGGCATTCA
* *
28011 AAAAAAGGTGTTACATGGGGTATCAAAAG
1 AAAAAAGGTGTTACATGAGGTATAAAAAG
28040 -AAAAAGGTGTTACAT-AGGTATAAAAAG
1 AAAAAAGGTGTTACATGAGGTATAAAAAG
28067 AAAAAA
1 AAAAAA
28073 AAAAAAAGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 10 0.33
28 20 0.67
ACGTcount: A:0.53, C:0.05, G:0.23, T:0.19
Consensus pattern (29 bp):
AAAAAAGGTGTTACATGAGGTATAAAAAG
Found at i:33284 original size:40 final size:40
Alignment explanation
Indices: 33229--33321 Score: 186
Period size: 40 Copynumber: 2.3 Consensus size: 40
33219 TAATAACTTA
33229 ACATCCTACTGCAAAATATTTACTACTTAAAGATTTAAGC
1 ACATCCTACTGCAAAATATTTACTACTTAAAGATTTAAGC
33269 ACATCCTACTGCAAAATATTTACTACTTAAAGATTTAAGC
1 ACATCCTACTGCAAAATATTTACTACTTAAAGATTTAAGC
33309 ACATCCTACTGCA
1 ACATCCTACTGCA
33322 TTTGCAAAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.39, C:0.23, G:0.08, T:0.31
Consensus pattern (40 bp):
ACATCCTACTGCAAAATATTTACTACTTAAAGATTTAAGC
Found at i:33550 original size:29 final size:29
Alignment explanation
Indices: 33508--33564 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
33498 AGCTGTAGCC
*
33508 AAATCAGCAGGTACAAGATGCTTGAAGCT
1 AAATCAGCAAGTACAAGATGCTTGAAGCT
*
33537 AAATTAGCAAGTACAAGATGCTTGAAGC
1 AAATCAGCAAGTACAAGATGCTTGAAGC
33565 CATACTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (29 bp):
AAATCAGCAAGTACAAGATGCTTGAAGCT
Found at i:35120 original size:31 final size:30
Alignment explanation
Indices: 35038--35124 Score: 95
Period size: 29 Copynumber: 2.9 Consensus size: 30
35028 CTGTACTATG
35038 GAAAAAAGATCAATTTAGTCCCTCCATTAT
1 GAAAAAAGATCAATTTAGTCCCTCCATTAT
*** * *
35068 GAAATTTG-TTAATTTAGTCCCTCTATTATT
1 GAAAAAAGATCAATTTAGTCCCTCCATTA-T
* *
35098 GAAAAGAGATCAATTTAATCCCTCCAT
1 GAAAAAAGATCAATTTAGTCCCTCCAT
35125 GAAACGTGAC
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
29 18 0.41
30 11 0.25
31 15 0.34
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (30 bp):
GAAAAAAGATCAATTTAGTCCCTCCATTAT
Found at i:36470 original size:12 final size:12
Alignment explanation
Indices: 36453--36477 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36443 CTTACATGTC
36453 TAAGTGTTAGTT
1 TAAGTGTTAGTT
36465 TAAGTGTTAGTT
1 TAAGTGTTAGTT
36477 T
1 T
36478 TGGATGATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (12 bp):
TAAGTGTTAGTT
Found at i:38852 original size:12 final size:12
Alignment explanation
Indices: 38835--38859 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38825 TCATCATCCA
38835 AAACTAACACTT
1 AAACTAACACTT
38847 AAACTAACACTT
1 AAACTAACACTT
38859 A
1 A
38860 GACATGTAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (12 bp):
AAACTAACACTT
Done.