Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015992.1 Corchorus olitorius cultivar O-4 contig16025, 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: 99397
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Found at i:55 original size:25 final size:26
Alignment explanation
Indices: 27--75 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
17 TAAACATAAT
27 AATAGATAAGTTAATTTA-TCCTAAC
1 AATAGATAAGTTAATTTATTCCTAAC
*
52 AATAGATTAGTTAATTTATTCCTA
1 AATAGATAAGTTAATTTATTCCTA
76 TTGTTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (26 bp):
AATAGATAAGTTAATTTATTCCTAAC
Found at i:4034 original size:11 final size:11
Alignment explanation
Indices: 4006--4037 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3996 ATTTTAATTT
4006 ATTTAATTAAA
1 ATTTAATTAAA
4017 A--TAATTAAA
1 ATTTAATTAAA
4026 ATTTAATTAAA
1 ATTTAATTAAA
4037 A
1 A
4038 AAAAGGGCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.47
11 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATTTAATTAAA
Found at i:4314 original size:13 final size:13
Alignment explanation
Indices: 4296--4326 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4286 CCCAAGTCGC
*
4296 TTAGATCCGAAGT
1 TTAGATCCAAAGT
4309 TTAGATCCAAAGT
1 TTAGATCCAAAGT
4322 TTAGA
1 TTAGA
4327 AGTTGAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (13 bp):
TTAGATCCAAAGT
Found at i:5948 original size:30 final size:29
Alignment explanation
Indices: 5914--5972 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
5904 CAGTTTTTAA
* *
5914 CCAAATCATAGTGATTTTTAAAAATAATTC
1 CCAAACCATAGT-ACTTTTAAAAATAATTC
* *
5944 CCAAACCATTGTACTTTTAAAATTAATTC
1 CCAAACCATAGTACTTTTAAAAATAATTC
5973 TCATTTCCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (29 bp):
CCAAACCATAGTACTTTTAAAAATAATTC
Found at i:13040 original size:25 final size:25
Alignment explanation
Indices: 13006--13083 Score: 156
Period size: 25 Copynumber: 3.1 Consensus size: 25
12996 TCTATCACGA
13006 GAACTACCGCATACGAATTCATTCC
1 GAACTACCGCATACGAATTCATTCC
13031 GAACTACCGCATACGAATTCATTCC
1 GAACTACCGCATACGAATTCATTCC
13056 GAACTACCGCATACGAATTCATTCC
1 GAACTACCGCATACGAATTCATTCC
13081 GAA
1 GAA
13084 AGGTTTTTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.33, C:0.31, G:0.13, T:0.23
Consensus pattern (25 bp):
GAACTACCGCATACGAATTCATTCC
Found at i:13695 original size:24 final size:24
Alignment explanation
Indices: 13667--13712 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
13657 TAGTAAAGAC
13667 TATCAATAATCAAGCTTTTCAATT
1 TATCAATAATCAAGCTTTTCAATT
*
13691 TATCAATCATCAAGCTTTTCAA
1 TATCAATAATCAAGCTTTTCAA
13713 GACGATCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.20, G:0.04, T:0.39
Consensus pattern (24 bp):
TATCAATAATCAAGCTTTTCAATT
Found at i:24901 original size:30 final size:30
Alignment explanation
Indices: 24865--24922 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
24855 AAAGCAGTAG
24865 CTGGGCATCCCCCAGAGACTGAACGACTCC
1 CTGGGCATCCCCCAGAGACTGAACGACTCC
24895 CTGGGCATCCCCCAGAGACTGAACGACT
1 CTGGGCATCCCCCAGAGACTGAACGACT
24923 TCCTCTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.24, C:0.38, G:0.24, T:0.14
Consensus pattern (30 bp):
CTGGGCATCCCCCAGAGACTGAACGACTCC
Found at i:28912 original size:24 final size:25
Alignment explanation
Indices: 28859--28908 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
28849 ACCAGGGGCA
*
28859 ACCCCCCAGGGGTACTGCTAGTCGCG
1 ACCCCCCAGGGGTACTACTAGTC-CG
*
28885 ACCCCCCCGGGAGTACTACTAGTC
1 ACCCCCCAGGG-GTACTACTAGTC
28909 ACCCCCGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.48
27 11 0.52
ACGTcount: A:0.18, C:0.40, G:0.26, T:0.16
Consensus pattern (25 bp):
ACCCCCCAGGGGTACTACTAGTCCG
Found at i:31628 original size:22 final size:22
Alignment explanation
Indices: 31603--31651 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
31593 GGAAACTACA
31603 CTTCGAATTTCGAGGCACGTCG
1 CTTCGAATTTCGAGGCACGTCG
*
31625 CTTCGAGTTTCGAGGCACGTCG
1 CTTCGAATTTCGAGGCACGTCG
31647 CTTCG
1 CTTCG
31652 GATTCTGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (22 bp):
CTTCGAATTTCGAGGCACGTCG
Found at i:40620 original size:3 final size:3
Alignment explanation
Indices: 40612--40640 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
40602 AGGTTTTTAT
40612 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
40641 TTTTTTGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:42545 original size:26 final size:26
Alignment explanation
Indices: 42495--42545 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
42485 GTATAAATTA
*
42495 GGCCAATTTTCTTGTTTTAATTTTTT
1 GGCCAATTTTCTTGTTTTAACTTTTT
*
42521 GGCCAATTTTCTTGTTTTGACTTTT
1 GGCCAATTTTCTTGTTTTAACTTTT
42546 GAATTAACGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (26 bp):
GGCCAATTTTCTTGTTTTAACTTTTT
Found at i:52619 original size:23 final size:22
Alignment explanation
Indices: 52588--52635 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
52578 GATCAAGCTG
52588 CTATATTGGTATATATTTATCAA
1 CTATATTGGTATATATTTAT-AA
*
52611 CTATTTTGGTATATATTTATAA
1 CTATATTGGTATATATTTATAA
52633 CTA
1 CTA
52636 GGGTAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.50
Consensus pattern (22 bp):
CTATATTGGTATATATTTATAA
Found at i:90565 original size:9 final size:9
Alignment explanation
Indices: 90551--90584 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
90541 CAAAAGCAGT
90551 TACAAATTG
1 TACAAATTG
90560 TACAAATT-
1 TACAAATTG
*
90568 TACAACTTG
1 TACAAATTG
90577 TACAAATT
1 TACAAATT
90585 CTTTCAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (9 bp):
TACAAATTG
Found at i:90594 original size:19 final size:17
Alignment explanation
Indices: 90550--90584 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
90540 TCAAAAGCAG
*
90550 TTACAAATTGTACAAAT
1 TTACAACTTGTACAAAT
90567 TTACAACTTGTACAAAT
1 TTACAACTTGTACAAAT
90584 T
1 T
90585 CTTTCAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (17 bp):
TTACAACTTGTACAAAT
Found at i:97943 original size:42 final size:44
Alignment explanation
Indices: 97896--97980 Score: 129
Period size: 45 Copynumber: 2.0 Consensus size: 44
97886 CATTACCTAA
*
97896 ATTCTACT-C-CATCTCTAGGTAATTCATCAAAATAAAGCTATT
1 ATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAGCTATT
*
97938 ATTCTACTCCTTCATCTCTAGATAATTCATTAAAATAAAGCTA
1 ATTCTACTCC-TCATCTCTAGATAATTCATCAAAATAAAGCTA
97981 ACTAGAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 8 0.21
43 1 0.03
45 29 0.76
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (44 bp):
ATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAGCTATT
Found at i:98419 original size:34 final size:38
Alignment explanation
Indices: 98349--98425 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
98339 GACATCCACA
*
98349 ACATACATGTATATTCATAACAAATTTATAATTAATTT
1 ACATACATGTATATGCATAACAAATTTATAATTAATTT
98387 ACATACATGTATATGCATAACAAATTTATAATTAATTT
1 ACATACATGTATATGCATAACAAATTTATAATTAATTT
98425 A
1 A
98426 TAATTATTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.40
Consensus pattern (38 bp):
ACATACATGTATATGCATAACAAATTTATAATTAATTT
Found at i:98423 original size:11 final size:11
Alignment explanation
Indices: 98409--98446 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
98399 ATGCATAACA
98409 AATTTATAATT
1 AATTTATAATT
98420 AATTTATAATT
1 AATTTATAATT
98431 -ATTTGATAATT
1 AATTT-ATAATT
*
98442 TATTT
1 AATTT
98447 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Done.