Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012674.1 Corchorus olitorius cultivar O-4 contig12707, 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: 40039
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Found at i:8067 original size:34 final size:34
Alignment explanation
Indices: 7984--8480 Score: 630
Period size: 34 Copynumber: 14.9 Consensus size: 34
7974 ATAGTATATA
*
7984 TTTTACTCTTTTTAGCTTAATTACCATTTACCA-
1 TTTTACTCTTTTTAACTTAATTACCATTTACCAT
* *
8017 TTTTACT-TTTTTAACTTAATTACTGA-ATACCAT
1 TTTTACTCTTTTTAACTTAATTAC-CATTTACCAT
8050 TTTTACTCTTTTTAACTTAATTACCATTTACCA-
1 TTTTACTCTTTTTAACTTAATTACCATTTACCAT
* * *
8083 TTTTAATCTTTTTAACTTAATTACTGA-ATACCAT
1 TTTTACTCTTTTTAACTTAATTAC-CATTTACCAT
8117 TTTTACTCTTTTTAACTTAATTACCATTTACCA-
1 TTTTACTCTTTTTAACTTAATTACCATTTACCAT
8150 TTTTACT-TTTTTAACTTAATTACCATTTACCAT
1 TTTTACTCTTTTTAACTTAATTACCATTTACCAT
* * *
8183 TTTTACTCTTTTTAACTTAATTACTGA-ATAGCAT
1 TTTTACTCTTTTTAACTTAATTAC-CATTTACCAT
*
8217 TTTTATTCTTTTTAACTTAATTACCATTTACCA-
1 TTTTACTCTTTTTAACTTAATTACCATTTACCAT
* *
8250 TTTTACTCTTTTTAACTTAATTACTGA-ATACCAT
1 TTTTACTCTTTTTAACTTAATTAC-CATTTACCAT
*
8284 TTTTACTCTTTTTAACTTAATTACCATTTATCA-
1 TTTTACTCTTTTTAACTTAATTACCATTTACCAT
* *
8317 TATTACTCCTTTTAACTTAATTACCATTTACCAT
1 TTTTACTCTTTTTAACTTAATTACCATTTACCAT
* *
8351 TTTTACTCTTTTTAACTTAATTACTGA-ATACCAT
1 TTTTACTCTTTTTAACTTAATTAC-CATTTACCAT
8385 TTTTACTCTTTTTAACTTAATTACCATTTACCA-
1 TTTTACTCTTTTTAACTTAATTACCATTTACCAT
*
8418 TTTTACTCTTTTTAACTTAATTACTTAATGTT---AT
1 TTTTACTCTTTTTAACTTAATTAC--CAT-TTACCAT
* *
8452 TTCTACTCTTTTTAACTTGATTACCATTT
1 TTTTACTCTTTTTAACTTAATTACCATTT
8481 TACTCTTTGA
Statistics
Matches: 406, Mismatches: 37, Indels: 44
0.83 0.08 0.09
Matches are distributed among these distances:
31 2 0.00
32 47 0.12
33 145 0.36
34 206 0.51
35 4 0.01
36 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.02, T:0.52
Consensus pattern (34 bp):
TTTTACTCTTTTTAACTTAATTACCATTTACCAT
Found at i:8127 original size:67 final size:67
Alignment explanation
Indices: 7984--8480 Score: 652
Period size: 67 Copynumber: 7.4 Consensus size: 67
7974 ATAGTATATA
* *
7984 TTTTACTCTTTTTAGCTTAATTACCATTTACCATTTTACT-TTTTTAACTTAATTACTGAATACC
1 TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACTCAATACC
8048 AT
66 AT
* *
8050 TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTAATCTTTTTAACTTAATTACTGAATACC
1 TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACTCAATACC
8115 AT
66 AT
*
8117 TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACT-TTTTTAACTTAATTAC-CATTTAC
1 TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACTCA-ATAC
8180 CAT
65 CAT
* * * * *
8183 TTTTACTCTTTTTAACTTAATTACTGA-ATAGCATTTTTATTCTTTTTAACTTAATTAC-CATTT
1 TTTTACTCTTTTTAACTTAATTAC-CATTTACCA-TTTTACTCTTTTTAACTTAATTACTCA-AT
8246 ACCA-
63 ACCAT
* * *
8250 TTTTACTCTTTTTAACTTAATTACTGA-ATACCATTTTTACTCTTTTTAACTTAATTAC-CATTT
1 TTTTACTCTTTTTAACTTAATTAC-CATTTACCA-TTTTACTCTTTTTAACTTAATTACTCA-AT
*
8313 ATCA-
63 ACCAT
* * *
8317 TATTACTCCTTTTAACTTAATTACCATTTACCATTTTTACTCTTTTTAACTTAATTACTGAATAC
1 TTTTACTCTTTTTAACTTAATTACCATTTACCA-TTTTACTCTTTTTAACTTAATTACTCAATAC
8382 CAT
65 CAT
* ***
8385 TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACTTAATGTT
1 TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACTCAATACC
8450 AT
66 AT
* *
8452 TTCTACTCTTTTTAACTTGATTACCATTT
1 TTTTACTCTTTTTAACTTAATTACCATTT
8481 TACTCTTTGA
Statistics
Matches: 396, Mismatches: 27, Indels: 15
0.90 0.06 0.03
Matches are distributed among these distances:
65 1 0.00
66 89 0.22
67 249 0.63
68 57 0.14
ACGTcount: A:0.28, C:0.18, G:0.02, T:0.52
Consensus pattern (67 bp):
TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACTCAATACC
AT
Found at i:8329 original size:101 final size:101
Alignment explanation
Indices: 7984--8441 Score: 630
Period size: 101 Copynumber: 4.6 Consensus size: 101
7974 ATAGTATATA
* * *
7984 TTTTACTCTTTTTAGCTTAATTACCATTTACCATTTTACT-TTTTTAACTTAATTACTGA-ATAC
1 TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTAC-CATTTAC
*
8047 CATTTTTACTCTTTTTAACTTAATTACCATTTACCA-
65 CATTTTTACTCTTTTTAACTTAATTACCATATACCAT
* * *
8083 TTTTAATCTTTTTAACTTAATTACTGA-ATACCATTTTTACTCTTTTTAACTTAATTACCATTTA
1 TTTTACTCTTTTTAACTTAATTAC-CATTTACCA-TTTTACTCTTTTTAACTTAATTACCATTTA
*
8147 CCA-TTTTACT-TTTTTAACTTAATTACCATTTACCAT
64 CCATTTTTACTCTTTTTAACTTAATTACCATATACCAT
* * * *
8183 TTTTACTCTTTTTAACTTAATTACTGA-ATAGCATTTTTATTCTTTTTAACTTAATTACCATTTA
1 TTTTACTCTTTTTAACTTAATTAC-CATTTACCA-TTTTACTCTTTTTAACTTAATTACCATTTA
*
8247 CCA-TTTTACTCTTTTTAACTTAATTACTGA-ATACCAT
64 CCATTTTTACTCTTTTTAACTTAATTAC-CATATACCAT
* * *
8284 TTTTACTCTTTTTAACTTAATTACCATTTATCATATTACTCCTTTTAACTTAATTACCATTTACC
1 TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACCATTTACC
*
8349 ATTTTTACTCTTTTTAACTTAATTACTGA-ATACCAT
66 ATTTTTACTCTTTTTAACTTAATTAC-CATATACCAT
8385 TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTAC
1 TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTAC
8442 TTAATGTTAT
Statistics
Matches: 330, Mismatches: 20, Indels: 16
0.90 0.05 0.04
Matches are distributed among these distances:
99 52 0.16
100 118 0.36
101 159 0.48
102 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.02, T:0.52
Consensus pattern (101 bp):
TTTTACTCTTTTTAACTTAATTACCATTTACCATTTTACTCTTTTTAACTTAATTACCATTTACC
ATTTTTACTCTTTTTAACTTAATTACCATATACCAT
Found at i:8576 original size:22 final size:22
Alignment explanation
Indices: 8529--8599 Score: 115
Period size: 22 Copynumber: 3.2 Consensus size: 22
8519 TTGAATTTAA
*
8529 TTACTGATTACCATTCTACCTTT
1 TTACTGATTACCATTTTA-CTTT
*
8552 TTACTGATTACTATTTTACTTT
1 TTACTGATTACCATTTTACTTT
8574 TTACTGATTACCATTTTACTTT
1 TTACTGATTACCATTTTACTTT
8596 TTAC
1 TTAC
8600 CAATGAATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
22 29 0.64
23 16 0.36
ACGTcount: A:0.23, C:0.20, G:0.04, T:0.54
Consensus pattern (22 bp):
TTACTGATTACCATTTTACTTT
Found at i:9062 original size:22 final size:22
Alignment explanation
Indices: 9015--9128 Score: 165
Period size: 22 Copynumber: 5.0 Consensus size: 22
9005 TTATTCATTG
9015 CTTTTTACTGATTACCATTTTTTA
1 CTTTTTACTGATTACCA--TTTTA
*
9039 CTTTTTATTGATTACCATTTTA
1 CTTTTTACTGATTACCATTTTA
**
9061 CTTTTTACTGATTGTCATTTTA
1 CTTTTTACTGATTACCATTTTA
*
9083 CTTTTTACTGATTGCCATTTTA
1 CTTTTTACTGATTACCATTTTA
9105 CTTTTTTACTGATTACCATTTTA
1 C-TTTTTACTGATTACCATTTTA
9128 C
1 C
9129 CATTTCAATT
Statistics
Matches: 83, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
22 46 0.55
23 21 0.25
24 16 0.19
ACGTcount: A:0.20, C:0.17, G:0.06, T:0.57
Consensus pattern (22 bp):
CTTTTTACTGATTACCATTTTA
Found at i:9896 original size:50 final size:51
Alignment explanation
Indices: 9727--10030 Score: 220
Period size: 51 Copynumber: 6.0 Consensus size: 51
9717 AGTCTTGATC
* * * *** * * *
9727 TTTACTATCTAAAAATCCAATTTTTGTTACCAAAACTACCAAAACCCAATC-
1 TTTACTACCTAAAGATCCAATTTTTATTGTTAAAATTACCAAGACTCAA-CA
* ** *
9778 TTTACTACCTAAAGACCCTTTTTTTATTGCTAAAATTACCAAGACTCAACA
1 TTTACTACCTAAAGATCCAATTTTTATTGTTAAAATTACCAAGACTCAACA
* * * *
9829 TTTGCTACCTAAAGATCCAATTTTT-TTGTTAAAATTACCAAAACTCGAGA
1 TTTACTACCTAAAGATCCAATTTTTATTGTTAAAATTACCAAGACTCAACA
* * * ** * *
9879 TTTACTACTTAAGGATCCAATTTTTGTTGTCCAAATTACCAAGACTCTACT
1 TTTACTACCTAAAGATCCAATTTTTATTGTTAAAATTACCAAGACTCAACA
* * ** * * *
9930 TTTATTACCCAAAGA-CTCAATTTTTATCATTAAAATTGCCAAGACTCTACC
1 TTTACTACCTAAAGATC-CAATTTTTATTGTTAAAATTACCAAGACTCAACA
* ** ** *
9981 TTTATTATCC-AAAGATTTAATTTTTATCATTAAAATTCCCAAGACTCAAC
1 TTTACTA-CCTAAAGATCCAATTTTTATTGTTAAAATTACCAAGACTCAAC
10031 CTTTTCAATC
Statistics
Matches: 205, Mismatches: 43, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
50 45 0.22
51 158 0.77
52 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (51 bp):
TTTACTACCTAAAGATCCAATTTTTATTGTTAAAATTACCAAGACTCAACA
Found at i:16234 original size:20 final size:20
Alignment explanation
Indices: 16209--16254 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
16199 GATCGACCGA
16209 AAGACCCCATGACAGGACGT
1 AAGACCCCATGACAGGACGT
16229 AAGACCCCATGACAGGACGT
1 AAGACCCCATGACAGGACGT
16249 AAGACC
1 AAGACC
16255 GACGAGCATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.30, G:0.24, T:0.09
Consensus pattern (20 bp):
AAGACCCCATGACAGGACGT
Found at i:16269 original size:70 final size:70
Alignment explanation
Indices: 16156--16304 Score: 212
Period size: 70 Copynumber: 2.1 Consensus size: 70
16146 CATTCTTGGT
* *
16156 CGTAAGACCCCATGACGAGCTGTTAGATCGACAAGCATCGACCGATCGACCGAAAGACCCCATGA
1 CGTAAGACCCCATGACGAGCTGTAAGACCGACAAGCATCGACCGATCGACCGAAAGACCCCATGA
16221 CAGGA
66 CAGGA
* *
16226 CGTAAGACCCCATGAC-AGGAC-GTAAGACCGACGAGCATCGACCGATCGACCGTAAGACCCCAT
1 CGTAAGACCCCATGACGA-G-CTGTAAGACCGACAAGCATCGACCGATCGACCGAAAGACCCCAT
* *
16289 GACGGGC
64 GACAGGA
16296 CGTAAGACC
1 CGTAAGACC
16305 GACGAGCATT
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
69 1 0.01
70 69 0.97
71 1 0.01
ACGTcount: A:0.32, C:0.32, G:0.26, T:0.11
Consensus pattern (70 bp):
CGTAAGACCCCATGACGAGCTGTAAGACCGACAAGCATCGACCGATCGACCGAAAGACCCCATGA
CAGGA
Found at i:16519 original size:50 final size:50
Alignment explanation
Indices: 16451--16588 Score: 179
Period size: 50 Copynumber: 2.8 Consensus size: 50
16441 CAATAAGGCC
* *
16451 GATCACACTCATTATCGGCAGTAACACCCCCTTGACGGGTAGTAAGATCA
1 GATCAGACTCATTATCGGCAGTAAAACCCCCTTGACGGGTAGTAAGATCA
* * * * *
16501 GATCAGACTGATTGTCGGCAGTAAAACCCCCCTGACGGGTGGTAAGATCG
1 GATCAGACTCATTATCGGCAGTAAAACCCCCTTGACGGGTAGTAAGATCA
* *
16551 GATCAAGA-TCATTATCGGAAGTAATACCCCCTTGACGG
1 GATC-AGACTCATTATCGGCAGTAAAACCCCCTTGACGG
16589 TTGGCAGGCG
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
50 72 0.96
51 3 0.04
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (50 bp):
GATCAGACTCATTATCGGCAGTAAAACCCCCTTGACGGGTAGTAAGATCA
Found at i:16800 original size:116 final size:116
Alignment explanation
Indices: 16590--16811 Score: 336
Period size: 116 Copynumber: 1.9 Consensus size: 116
16580 CCTTGACGGT
* *
16590 TGGCAGGCGGTGGAAAGCCGACCTTGACCAAGCACGGATAAAGAGCCCCCTTAAGGGTCTAGAGA
1 TGGCAGGCAGTGGAAAGCCGACCTTGACCAAGCACGAATAAAGAGCCCCCTTAAGGGTCTAGAGA
* *
16655 TACCAGCTGGCAGGCGGTGGAAAGTCGACCTCGACCAAGCATAGTCCCGGC
66 TACCAGCTGGCAGGCGCTGGAAAGCCGACCTCGACCAAGCATAGTCCCGGC
* * *
16706 TGGCAGGCAGTGGAGAGCCGACCTTGACCAAGCACGAATGAAGAGCCCTCTTAAGGGTCTAGAGA
1 TGGCAGGCAGTGGAAAGCCGACCTTGACCAAGCACGAATAAAGAGCCCCCTTAAGGGTCTAGAGA
** * * *
16771 TACTGGCTGGTAGGCGCTGGAGAGCCGACCTTGACCAAGCA
66 TACCAGCTGGCAGGCGCTGGAAAGCCGACCTCGACCAAGCA
16812 CGAATGAAGA
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
116 94 1.00
ACGTcount: A:0.27, C:0.26, G:0.32, T:0.15
Consensus pattern (116 bp):
TGGCAGGCAGTGGAAAGCCGACCTTGACCAAGCACGAATAAAGAGCCCCCTTAAGGGTCTAGAGA
TACCAGCTGGCAGGCGCTGGAAAGCCGACCTCGACCAAGCATAGTCCCGGC
Found at i:16820 original size:72 final size:71
Alignment explanation
Indices: 16701--16885 Score: 255
Period size: 72 Copynumber: 2.6 Consensus size: 71
16691 AAGCATAGTC
* *
16701 CCGGCTGGCAGGCAGTGGAGAGCCGACCTTGACCAAGCACGAATGAAGAGCCCTCTTAAGGGTCT
1 CCGGCTGGCAGGC-GTGGAGAGCCGACCTTGACCAAGCACGAATGAAGAACCCTCTTAAGGGTCC
*
16766 AG-AGATA
65 AGTA-AAA
* *
16773 CTGGCTGGTAGGCGCTGGAGAGCCGACCTTGACCAAGCACGAATGAAGAACCCTCTTAAGGGTCC
1 CCGGCTGGCAGGCG-TGGAGAGCCGACCTTGACCAAGCACGAATGAAGAACCCTCTTAAGGGTCC
16838 AGTAAAA
65 AGTAAAA
* * *
16845 CCGGCTGGCAGACGGTGGAAAGCCGACCTCGACCAAGCACG
1 CCGGCTGGCAGGC-GTGGAGAGCCGACCTTGACCAAGCACG
16886 GCACCGGCTA
Statistics
Matches: 100, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
71 1 0.01
72 97 0.97
73 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.31, T:0.14
Consensus pattern (71 bp):
CCGGCTGGCAGGCGTGGAGAGCCGACCTTGACCAAGCACGAATGAAGAACCCTCTTAAGGGTCCA
GTAAAA
Found at i:18018 original size:29 final size:29
Alignment explanation
Indices: 17947--18020 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
17937 TTTAACAATC
* *
17947 TAAGGGATTAATTTGTCCCAAAAAAAACA
1 TAAGAGATTATTTTGTCCCAAAAAAAACA
* *
17976 TAAGGGATTATTTTGTCCCAAAAGAAAGACG
1 TAAGAGATTATTTTGTCCCAAAA-AAA-ACA
*
18007 TAAGAGATTTTTTT
1 TAAGAGATTATTTT
18021 TGGTATTTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 22 0.56
30 3 0.08
31 14 0.36
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.31
Consensus pattern (29 bp):
TAAGAGATTATTTTGTCCCAAAAAAAACA
Done.