Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014668.1 Corchorus olitorius cultivar O-4 contig14701, 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: 46109
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3105 original size:22 final size:21
Alignment explanation
Indices: 3080--3133 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
3070 GAAGTTCGTG
3080 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
3102 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
3121 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
3134 TCAAGAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:8119 original size:127 final size:128
Alignment explanation
Indices: 7892--8144 Score: 420
Period size: 127 Copynumber: 2.0 Consensus size: 128
7882 AAGACATGCT
* * *
7892 TTGGAGAGATCTTGAAGACATGGACTCATGAATATTTTATATGGGATAATAACCAGCCCAGCTGG
1 TTGGAGAGATCTTGAAGACATGGACTCATGAATATATTATAAGGCATAATAACCAGCCCAGCTGG
* *
7957 GCCCATAATTGGAGTCAAAGCCCAATCTATGCGGCACAAACCCTGTGAAATATCCAATTCCTG
66 GCCCACAATTGGAGTCAAAGCCCAATCTATGCGGCACAAACCCCGTGAAATATCCAATTCCTG
*
8020 TTGGAGAGA-CGTTGAAGACATGGACTCATGAATA-ATTATAAGGCATAATAACCAGCCCAGTTG
1 TTGGAGAGATC-TTGAAGACATGGACTCATGAATATATTATAAGGCATAATAACCAGCCCAGCTG
*
8083 GGCCCACAATTGGAGTCAAAGCCCAATCTGTGCGGCACAAACCCCGTGAAATATCCAATTCC
65 GGCCCACAATTGGAGTCAAAGCCCAATCTATGCGGCACAAACCCCGTGAAATATCCAATTCC
8145 CGCAATACTA
Statistics
Matches: 117, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
127 85 0.73
128 32 0.27
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (128 bp):
TTGGAGAGATCTTGAAGACATGGACTCATGAATATATTATAAGGCATAATAACCAGCCCAGCTGG
GCCCACAATTGGAGTCAAAGCCCAATCTATGCGGCACAAACCCCGTGAAATATCCAATTCCTG
Found at i:11263 original size:25 final size:25
Alignment explanation
Indices: 11227--11274 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
11217 CCCTTCTCTC
* * *
11227 TCTTTTATCTAAAGATCAAAAAACT
1 TCTTTTAACTAAACATAAAAAAACT
11252 TCTTTTAACTAAACATAAAAAAA
1 TCTTTTAACTAAACATAAAAAAA
11275 ACTTGTTCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.02, T:0.33
Consensus pattern (25 bp):
TCTTTTAACTAAACATAAAAAAACT
Found at i:13402 original size:69 final size:69
Alignment explanation
Indices: 13289--13427 Score: 190
Period size: 69 Copynumber: 2.0 Consensus size: 69
13279 AAAACTAACA
* * * *
13289 ACTAAGGAAAAAATAGTGGGAACACTATTAATTACATCTCAATGCTAAAATTACATATAAATATA
1 ACTAAGGAAAAAATAGTAGGAACACCATTAATTACATCTCAATGCTAAAATTACATATAAAGACA
13354 ATGC
66 ATGC
* * * *
13358 ACTAAGGAAAAAATGGTAGGATCACCATTAATTTCGTC-CAAATGCTAAAATTACATATAAAGAC
1 ACTAAGGAAAAAATAGTAGGAACACCATTAATTACATCTC-AATGCTAAAATTACATATAAAGAC
13422 AATGC
65 AATGC
13427 A
1 A
13428 TTTCAAGCAA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
68 1 0.02
69 60 0.98
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.26
Consensus pattern (69 bp):
ACTAAGGAAAAAATAGTAGGAACACCATTAATTACATCTCAATGCTAAAATTACATATAAAGACA
ATGC
Found at i:38282 original size:177 final size:177
Alignment explanation
Indices: 37950--38282 Score: 470
Period size: 177 Copynumber: 1.9 Consensus size: 177
37940 TTTATTTAGC
* * *
37950 TAGCATGTTCAATCAATTTAGTTTTTTGCTAACGTAATTACAAATTAATTGATTTATTTATTTAT
1 TAGCATGTTCAATCAATTGAGTTTTTTGCTAACATAATTAC--A-TAATTGATTGATTTATTTAT
* * *
38015 GGAAAAATTAAATAATTATGAATAAATTATAACTTTGATTGGCAAAGTTAATTAACGACTAACTT
63 GGAAAAATTAAATAATCATCAATAAATTATAACTTTGATTGGCAAAGTTAACTAACGACTAACTT
** *
38080 GATTGCTTTATTTATTTAGCATGTTCTTTTTTTTTTGGCATCAATTTATT
128 GATTAATTTATCTATTTAGCATGTTCTTTTTTTTTTGGCATCAATTTATT
* *
38130 TAGCATGTTCAATCTATTGATTTTTTTTGCTAACATAATTAC-TAATTGATTGATTTATTTATGG
1 TAGCATGTTCAATCAATTGA-GTTTTTTGCTAACATAATTACATAATTGATTGATTTATTTATGG
* * * *
38194 TAAAATTATATAATCATCAATCAATTATAACTTTGATTGGCAAAGTTAACTAATGACTAACTTGA
65 AAAAATTAAATAATCATCAATAAATTATAACTTTGATTGGCAAAGTTAACTAACGACTAACTTGA
* *
38259 TTAATTTGTCTATTTATCATGTTC
130 TTAATTTATCTATTTAGCATGTTC
38283 AATAATTAAT
Statistics
Matches: 135, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
177 98 0.73
180 18 0.13
181 19 0.14
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (177 bp):
TAGCATGTTCAATCAATTGAGTTTTTTGCTAACATAATTACATAATTGATTGATTTATTTATGGA
AAAATTAAATAATCATCAATAAATTATAACTTTGATTGGCAAAGTTAACTAACGACTAACTTGAT
TAATTTATCTATTTAGCATGTTCTTTTTTTTTTGGCATCAATTTATT
Found at i:38564 original size:166 final size:163
Alignment explanation
Indices: 38186--38661 Score: 647
Period size: 166 Copynumber: 2.9 Consensus size: 163
38176 TGATTGATTT
* * * * *
38186 ATTTATGGTAAAATTATATAATCATCAATCAATTATAACTTTGATTGGCAAAGTTAACTAATGAC
1 ATTTATGGTAAAATTAAATAATCATCAATCAATTACAACTTTGATTGACAAAATTAACTAACGAC
* * * * *
38251 TAACTTGATTAATTTGTCTATTTATCATGTTCAATAATTAATTTTTTTGGTAACATAATCACTAA
66 TAACTTGATTCATTT-TTTATTTATCATGTTCAATAATTTATTTTTTTGGCAACATAATTACTAA
* *
38316 TTG---ATTTATTTATGGTTATTTTTTGGTAGCT
130 TTGATTATTTATTTATGGTAATTTTTTGGTAGCG
* * * *
38347 ATTTATGGTGAAATTAGATAATTATCAATCAATTAGAACTTTGATTGACAAAATTAACTAACGAC
1 ATTTATGGTAAAATTAAATAATCATCAATCAATTACAACTTTGATTGACAAAATTAACTAACGAC
38412 TAACTTGGATTCATTTATTTATTTATCATGTTCAATAATTTATTTTTTTGGCAACATAATTACTA
66 TAACTT-GATTCATTT-TTTATTTATCATGTTCAATAATTTATTTTTTTGGCAACATAATTACTA
*
38477 ATTGATTTATTTATTTATGGTAATTTTTTTGTAGCG
129 ATTGA-TTATTTATTTATGGTAATTTTTTGGTAGCG
38513 ATTTATGGTAAAATTAAATAATCATCAATCAATTACAACTTTGATTGACAAAATTAACTAAC-AG
1 ATTTATGGTAAAATTAAATAATCATCAATCAATTACAACTTTGATTGACAAAATTAACTAACGA-
* * *
38577 CTAACTTGATTCATTTTTTATTTAGCATGTTCAATCAATTTTATTTTTCT-GCTAACGTAATTAC
65 CTAACTTGATTCATTTTTTATTTATCATGTTCAAT-AA-TTTATTTTTTTGGC-AACATAATTAC
*
38641 TAATTGATTCGTTTATTTATG
127 TAATTGATT-ATTTATTTATG
38662 ACAAAATTAT
Statistics
Matches: 281, Mismatches: 24, Indels: 15
0.88 0.08 0.05
Matches are distributed among these distances:
161 64 0.23
162 56 0.20
164 18 0.06
165 16 0.06
166 127 0.45
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (163 bp):
ATTTATGGTAAAATTAAATAATCATCAATCAATTACAACTTTGATTGACAAAATTAACTAACGAC
TAACTTGATTCATTTTTTATTTATCATGTTCAATAATTTATTTTTTTGGCAACATAATTACTAAT
TGATTATTTATTTATGGTAATTTTTTGGTAGCG
Found at i:38757 original size:101 final size:99
Alignment explanation
Indices: 38578--38769 Score: 289
Period size: 101 Copynumber: 1.9 Consensus size: 99
38568 AACTAACAGC
* *
38578 TAACTTGATTCATTTTTTATTTAGCATGTTCAATCAATTTTATTTTTCTGCTAACGTAATTACTA
1 TAACTTGATTCATTTTTTATTTAGCATGTTCAATCAATTTTATTTTTCTACTAACATAATTACTA
38643 ATTGATTCGTTTATTTAT-GACAAAATTATAGGAG
66 ATTGATTCGTTTATTTATAG-CAAAATTATAGGAG
* *
38677 TAACTTTGAATTCATTTATTTATTTAGTATGTTCAATCAA-TTTATTTTTTTACTAACATAATTA
1 TAAC-TTG-ATTCATTT-TTTATTTAGCATGTTCAATCAATTTTATTTTTCTACTAACATAATTA
*
38741 CTAATTGATTCTTTTATTTATAGCAAAAT
63 CTAATTGATTCGTTTATTTATAGCAAAAT
38770 CAAATCACCA
Statistics
Matches: 84, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
99 4 0.05
100 3 0.04
101 55 0.65
102 22 0.26
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.49
Consensus pattern (99 bp):
TAACTTGATTCATTTTTTATTTAGCATGTTCAATCAATTTTATTTTTCTACTAACATAATTACTA
ATTGATTCGTTTATTTATAGCAAAATTATAGGAG
Found at i:38942 original size:142 final size:141
Alignment explanation
Indices: 38677--39063 Score: 557
Period size: 142 Copynumber: 2.7 Consensus size: 141
38667 ATTATAGGAG
38677 TAACTTTGAATTCATTTATTTATTTAGTATGTTCAATCAATTTATTTTTTTACTAACATAATTAC
1 TAAC-TTG-ATTCATTTATTTATTTAGTATGTTCAATCAATTTATTTTTTTAC-AACATAATTAC
* * * * *
38742 TAATTGATTCT-TTTATTTATAGCAAAATCAAATCACCATCAATCAATTATAACTTTGA-TAGAC
63 TAATTGATT-TATTTATTTATGGAAAAATTAAATAATCATCAATCAATTATAACTTTGATTAG-C
* * *
38805 ACAGTTGATTAACGAC
126 AAAGTTAACTAACGAC
*
38821 TAACTTGATTCATTTATTTATTTAGCATGTTCAATCAATTTATTTTTTTGACAACATAATTACTA
1 TAACTTGATTCATTTATTTATTTAGTATGTTCAATCAATTTATTTTTTT-ACAACATAATTACTA
*
38886 CATT-ATTTATTTATTTATGGAAAAATTAAATAATCATCCATCAATTATAACTTTGATTAGCAAA
65 -ATTGATTTATTTATTTATGGAAAAATTAAATAATCATCAATCAATTATAACTTTGATTAGCAAA
38950 GTTAACTAACGAC
129 GTTAACTAACGAC
*
38963 TAACTTGATTCATTTATTTATTTTGTATGTTCAATCAATTTATTTTTTT-CAACATAATTACTAA
1 TAACTTGATTCATTTATTTATTTAGTATGTTCAATCAATTTATTTTTTTACAACATAATTACTAA
* *
39027 TTGATTCATTTATTTATGGCAAAATTTAAATAATCAT
66 TTGATTTATTTATTTATGG-AAAAATTAAATAATCAT
39064 TAGCTTTTGG
Statistics
Matches: 223, Mismatches: 14, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
139 3 0.01
140 29 0.13
141 17 0.08
142 159 0.71
143 11 0.05
144 4 0.02
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (141 bp):
TAACTTGATTCATTTATTTATTTAGTATGTTCAATCAATTTATTTTTTTACAACATAATTACTAA
TTGATTTATTTATTTATGGAAAAATTAAATAATCATCAATCAATTATAACTTTGATTAGCAAAGT
TAACTAACGAC
Done.