Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013438.1 Corchorus olitorius cultivar O-4 contig13471, 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: 27505
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1170 original size:15 final size:15
Alignment explanation
Indices: 1116--1172 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
1106 TCCGAACCGT
*
1116 ATGACCCGAAACCGAAA
1 ATGACCCG-AACC-CAA
*
1133 ACGACCC-AACCCAGA
1 ATGACCCGAACCCA-A
1148 ATTGACCCGAACCCAA
1 A-TGACCCGAACCCAA
1164 ATGACCCGA
1 ATGACCCGA
1173 CATTTGAGCG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
14 1 0.03
15 14 0.41
16 7 0.21
17 12 0.35
ACGTcount: A:0.40, C:0.37, G:0.16, T:0.07
Consensus pattern (15 bp):
ATGACCCGAACCCAA
Found at i:5895 original size:2 final size:2
Alignment explanation
Indices: 5888--5916 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5878 TTTGATTATG
5888 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 T
5917 GAAATTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7340 original size:32 final size:33
Alignment explanation
Indices: 7280--7342 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 33
7270 AACTTGTAAA
* *
7280 GGCGTGATGAATGCCTGTTTAACTTCATTGGAAT
1 GGCGTGATGAAGGCCCG-TTAACTTCATTGGAAT
7314 GGCGTGATGAAGGCCCG-TAACTTCATTGG
1 GGCGTGATGAAGGCCCGTTAACTTCATTGG
7343 TTGTAAGAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 12 0.44
34 15 0.56
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (33 bp):
GGCGTGATGAAGGCCCGTTAACTTCATTGGAAT
Found at i:8291 original size:24 final size:24
Alignment explanation
Indices: 8263--8310 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
8253 TATATAGGAA
8263 AATACTCAGCCCATATAAGCCCAT
1 AATACTCAGCCCATATAAGCCCAT
8287 AATACTCAGCCCATATAAGCCCAT
1 AATACTCAGCCCATATAAGCCCAT
8311 TGGATATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.33, G:0.08, T:0.21
Consensus pattern (24 bp):
AATACTCAGCCCATATAAGCCCAT
Found at i:8299 original size:14 final size:14
Alignment explanation
Indices: 8263--8301 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
8253 TATATAGGAA
8263 AATACTCAGCCCAT
1 AATACTCAGCCCAT
8277 -ATA---AGCCCAT
1 AATACTCAGCCCAT
8287 AATACTCAGCCCAT
1 AATACTCAGCCCAT
8301 A
1 A
8302 TAAGCCCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 8
0.72 0.00 0.28
Matches are distributed among these distances:
10 7 0.33
11 3 0.14
13 3 0.14
14 8 0.38
ACGTcount: A:0.38, C:0.33, G:0.08, T:0.21
Consensus pattern (14 bp):
AATACTCAGCCCAT
Found at i:9759 original size:31 final size:31
Alignment explanation
Indices: 9721--9788 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
9711 CGTTTTCTCT
*
9721 AAAAAAAAAAAAATTC-CTGCGTTTTTTATA
1 AAAAAAAAAAAAATTCTCTGCGTTTTTAATA
*
9751 AAAAAAAAAAAAATTCTTTGCGTTTTTAATA
1 AAAAAAAAAAAAATTCTCTGCGTTTTTAATA
9782 AAAAAAA
1 AAAAAAA
9789 TTTTGAGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 16 0.46
31 19 0.54
ACGTcount: A:0.56, C:0.07, G:0.06, T:0.31
Consensus pattern (31 bp):
AAAAAAAAAAAAATTCTCTGCGTTTTTAATA
Found at i:9875 original size:28 final size:28
Alignment explanation
Indices: 9833--9907 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 28
9823 TGCATTTTTG
9833 AAAAAAAAAAAGTTTTCG-GTTTTGCGAT
1 AAAAAAAAAAAGTTTT-GTGTTTTGCGAT
* *
9861 AAAAAAAATATGTTTTGTGTTTTGCG-T
1 AAAAAAAAAAAGTTTTGTGTTTTGCGAT
9888 CAAGAAAAAAAAA--TTTGTGT
1 -AA-AAAAAAAAAGTTTTGTGT
9908 CTGCGTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 9 0.22
28 24 0.60
29 7 0.17
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.35
Consensus pattern (28 bp):
AAAAAAAAAAAGTTTTGTGTTTTGCGAT
Found at i:13037 original size:21 final size:22
Alignment explanation
Indices: 12993--13044 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
12983 CCACTACCAA
* *
12993 GCCACAACCGGCCATTCACCGT
1 GCCACCACCGGCCATGCACCGT
13015 GCCACCACCGGCCATGC-CCGT
1 GCCACCACCGGCCATGCACCGT
*
13036 GCCATCACC
1 GCCACCACC
13045 ATTCCAAGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.19, C:0.50, G:0.19, T:0.12
Consensus pattern (22 bp):
GCCACCACCGGCCATGCACCGT
Found at i:14929 original size:11 final size:11
Alignment explanation
Indices: 14913--14942 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
14903 GAAGTTCGTG
*
14913 TTTGAAGACTA
1 TTTGAAGACAA
14924 TTTGAAGACAA
1 TTTGAAGACAA
14935 TTTGAAGA
1 TTTGAAGA
14943 TTTGAAGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (11 bp):
TTTGAAGACAA
Found at i:14947 original size:19 final size:17
Alignment explanation
Indices: 14923--14959 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
14913 TTTGAAGACT
14923 ATTTGAAGACAATTTGAAG
1 ATTTGAAGAC--TTTGAAG
14942 ATTTGAAGACTTTGAAG
1 ATTTGAAGACTTTGAAG
14959 A
1 A
14960 ATTATCTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
19 10 0.56
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (17 bp):
ATTTGAAGACTTTGAAG
Found at i:19558 original size:15 final size:16
Alignment explanation
Indices: 19529--19563 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
19519 GAAATTTTCT
*
19529 GAAAGAAGAATGAAAA
1 GAAAGAAGAAAGAAAA
19545 GAAAG-AGAAAGAAAA
1 GAAAGAAGAAAGAAAA
19560 GAAA
1 GAAA
19564 CAAATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (16 bp):
GAAAGAAGAAAGAAAA
Found at i:19639 original size:19 final size:19
Alignment explanation
Indices: 19610--19653 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
19600 TTTTGTAGAA
* *
19610 ATTTATTTCCCTCAAAATTT
1 ATTT-TTTCCCTAAAAAATT
19630 ATTTTTTCCCTAAAAAATT
1 ATTTTTTCCCTAAAAAATT
19649 ATTTT
1 ATTTT
19654 GGCCACGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTTTTCCCTAAAAAATT
Found at i:26269 original size:28 final size:28
Alignment explanation
Indices: 26232--26322 Score: 139
Period size: 28 Copynumber: 3.2 Consensus size: 28
26222 TTGAAGTGAC
*
26232 CCAAAATGCCCCTGGATGTGCAAAATGA
1 CCAAAATGCCCCTGGATATGCAAAATGA
*
26260 CCAAAATGCCCCTGGACATGCAAAATGA
1 CCAAAATGCCCCTGGATATGCAAAATGA
*
26288 CCAAAATGCCCTTGG-TCATGCAAAATGA
1 CCAAAATGCCCCTGGAT-ATGCAAAATGA
26316 CCAAAAT
1 CCAAAAT
26323 AAGAAGTAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (28 bp):
CCAAAATGCCCCTGGATATGCAAAATGA
Found at i:26760 original size:36 final size:36
Alignment explanation
Indices: 26720--27138 Score: 704
Period size: 36 Copynumber: 11.8 Consensus size: 36
26710 TCAACCTTTA
26720 AAGATGCTACACCGAGTCATCTAAATTCAACTTTGG
1 AAGATGCTACACCGAGTCATCTAAATTCAACTTTGG
26756 AAGATGCTACACCGAGTCATCTAAATTCAACTTTGG
1 AAGATGCTACACCGAGTCATCTAAATTCAACTTTGG
* *
26792 AAGATGCTACACCGAGTCATCTGAATTC-ACTTTAG
1 AAGATGCTACACCGAGTCATCTAAATTCAACTTTGG
*
26827 AAGATGCTACACTGAGTCATCTAAATTCAACTTTGG
1 AAGATGCTACACCGAGTCATCTAAATTCAACTTTGG
26863 AAGATGCTACACCGAGTCATCTAAATTCAACTTTGG
1 AAGATGCTACACCGAGTCATCTAAATTCAACTTTGG
* *
26899 AAGATGCTACACCGAGTCATCTGAATTC-ACTTTAG
1 AAGATGCTACACCGAGTCATCTAAATTCAACTTTGG
*
26934 AAGATGCTACACTGAGTCATCTAAATTCAACTTTGG
1 AAGATGCTACACCGAGTCATCTAAATTCAACTTTGG
* *
26970 AAGATGCTAAACCGAGTCATCTAAATTCATCTTTGG
1 AAGATGCTACACCGAGTCATCTAAATTCAACTTTGG
*
27006 -GGATGCTACACCGAGTCATCTAAATTCAACTTTGG
1 AAGATGCTACACCGAGTCATCTAAATTCAACTTTGG
*
27041 AAGATGCTACACCGAGTCATCTCAATTCAACTTTGG
1 AAGATGCTACACCGAGTCATCTAAATTCAACTTTGG
27077 -AGATGCTACACCGAGTCATCTAAATTCAACTTTGG
1 AAGATGCTACACCGAGTCATCTAAATTCAACTTTGG
*
27112 -AGATGCTACACCGAGTCATCTGAATTC
1 AAGATGCTACACCGAGTCATCTAAATTC
27139 CTGAAAATTT
Statistics
Matches: 359, Mismatches: 21, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
35 156 0.43
36 203 0.57
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (36 bp):
AAGATGCTACACCGAGTCATCTAAATTCAACTTTGG
Found at i:26854 original size:71 final size:72
Alignment explanation
Indices: 26720--27138 Score: 704
Period size: 71 Copynumber: 5.9 Consensus size: 72
26710 TCAACCTTTA
26720 AAGATGCTACACCGAGTCATCTAAATTCAACTTTGGAAGATGCTACACCGAGTCATCTAAATTCA
1 AAGATGCTACACCGAGTCATCTAAATTCAACTTTGGAAGATGCTACACCGAGTCATCTAAATTCA
26785 ACTTTGG
66 ACTTTGG
* * *
26792 AAGATGCTACACCGAGTCATCTGAATTC-ACTTTAGAAGATGCTACACTGAGTCATCTAAATTCA
1 AAGATGCTACACCGAGTCATCTAAATTCAACTTTGGAAGATGCTACACCGAGTCATCTAAATTCA
26856 ACTTTGG
66 ACTTTGG
*
26863 AAGATGCTACACCGAGTCATCTAAATTCAACTTTGGAAGATGCTACACCGAGTCATCTGAATTC-
1 AAGATGCTACACCGAGTCATCTAAATTCAACTTTGGAAGATGCTACACCGAGTCATCTAAATTCA
*
26927 ACTTTAG
66 ACTTTGG
* *
26934 AAGATGCTACACTGAGTCATCTAAATTCAACTTTGGAAGATGCTAAACCGAGTCATCTAAATTCA
1 AAGATGCTACACCGAGTCATCTAAATTCAACTTTGGAAGATGCTACACCGAGTCATCTAAATTCA
*
26999 TCTTTGG
66 ACTTTGG
* *
27006 -GGATGCTACACCGAGTCATCTAAATTCAACTTTGGAAGATGCTACACCGAGTCATCTCAATTCA
1 AAGATGCTACACCGAGTCATCTAAATTCAACTTTGGAAGATGCTACACCGAGTCATCTAAATTCA
27070 ACTTTGG
66 ACTTTGG
*
27077 -AGATGCTACACCGAGTCATCTAAATTCAACTTTGG-AGATGCTACACCGAGTCATCTGAATTC
1 AAGATGCTACACCGAGTCATCTAAATTCAACTTTGGAAGATGCTACACCGAGTCATCTAAATTC
27139 CTGAAAATTT
Statistics
Matches: 325, Mismatches: 20, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
70 26 0.08
71 235 0.72
72 64 0.20
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (72 bp):
AAGATGCTACACCGAGTCATCTAAATTCAACTTTGGAAGATGCTACACCGAGTCATCTAAATTCA
ACTTTGG
Found at i:26891 original size:107 final size:106
Alignment explanation
Indices: 26715--27138 Score: 735
Period size: 107 Copynumber: 4.0 Consensus size: 106
26705 CTGAATCAAC
26715 CTTTA-AAGATGCTACACCGAGTCATCTAAATTCAACTTTGGAAGATGCTACACCGAGTCATCTA
1 CTTTAGAAGATGCTACACCGAGTCATCTAAATTCAACTTTGGAAGATGCTACACCGAGTCATCTA
26779 AATTCAACTTTGGAAGATGCTACACCGAGTCATCTGAATTCA
66 AATTCAACTTTGG-AGATGCTACACCGAGTCATCTGAATTCA
*
26821 CTTTAGAAGATGCTACACTGAGTCATCTAAATTCAACTTTGGAAGATGCTACACCGAGTCATCTA
1 CTTTAGAAGATGCTACACCGAGTCATCTAAATTCAACTTTGGAAGATGCTACACCGAGTCATCTA
26886 AATTCAACTTTGGAAGATGCTACACCGAGTCATCTGAATTCA
66 AATTCAACTTTGG-AGATGCTACACCGAGTCATCTGAATTCA
* *
26928 CTTTAGAAGATGCTACACTGAGTCATCTAAATTCAACTTTGGAAGATGCTAAACCGAGTCATCTA
1 CTTTAGAAGATGCTACACCGAGTCATCTAAATTCAACTTTGGAAGATGCTACACCGAGTCATCTA
* * *
26993 AATTCATCTTTGGGGATGCTACACCGAGTCATCTAAATTCAA
66 AATTCAACTTTGGAGATGCTACACCGAGTCATCTGAATTC-A
* *
27035 CTTTGGAAGATGCTACACCGAGTCATCTCAATTCAACTTTGG-AGATGCTACACCGAGTCATCTA
1 CTTTAGAAGATGCTACACCGAGTCATCTAAATTCAACTTTGGAAGATGCTACACCGAGTCATCTA
27099 AATTCAACTTTGGAGATGCTACACCGAGTCATCTGAATTC
66 AATTCAACTTTGGAGATGCTACACCGAGTCATCTGAATTC
27139 CTGAAAATTT
Statistics
Matches: 304, Mismatches: 12, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
106 88 0.29
107 216 0.71
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (106 bp):
CTTTAGAAGATGCTACACCGAGTCATCTAAATTCAACTTTGGAAGATGCTACACCGAGTCATCTA
AATTCAACTTTGGAGATGCTACACCGAGTCATCTGAATTCA
Done.