Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018930.1 Corchorus olitorius cultivar O-4 contig18963, 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: 18094
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2191 original size:76 final size:75
Alignment explanation
Indices: 2042--2192 Score: 178
Period size: 76 Copynumber: 2.0 Consensus size: 75
2032 ACAAGGACCC
* * *
2042 CGACTCCACCTGGGCGCCCACATGGTTGCCTGATCACCCATGTGGTTTGCTTGAGAACCCAGGTG
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTGAACACCCATGTGGTTTGCCTGAGAACCCAGATG
2107 GGCAGTGTCA
66 GGCAGTGTCA
* * * * * **
2117 CGACTCCAGCTGGGTGCCCACATAGTTTGTCTGAAGACCCATGT-GTTTCGCCTGATCACCCAGA
1 CGACTCCACCTGGGCGCCCACAT-GGTTGCCTGAACACCCATGTGGTTT-GCCTGAGAACCCAGA
*
2181 TGGGCTGTGTCA
64 TGGGCAGTGTCA
2193 TAGCTCATCA
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
75 25 0.40
76 38 0.60
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.25
Consensus pattern (75 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTGAACACCCATGTGGTTTGCCTGAGAACCCAGATG
GGCAGTGTCA
Found at i:3372 original size:45 final size:45
Alignment explanation
Indices: 3321--3407 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
3311 TATCTAAATT
* *
3321 CTACTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTTTA
1 CTACTCCATCTCTAGATAATTCATCAAAATAAACCTAATATTTTA
*
3366 CTACTCCATCTCTATATAATTCATCAAAATAAACCTAATATT
1 CTACTCCATCTCTAGATAATTCATCAAAATAAACCTAATATT
3408 AATTGTTGCT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (45 bp):
CTACTCCATCTCTAGATAATTCATCAAAATAAACCTAATATTTTA
Found at i:4577 original size:278 final size:278
Alignment explanation
Indices: 4075--4579 Score: 931
Period size: 278 Copynumber: 1.8 Consensus size: 278
4065 ATCAACCATT
4075 ATTGCAGATACATTTATAGCACCAATCCTTTGGAATTCCGGCAGAGGAGTTGAACCGGTAAATCC
1 ATTGCAGATACATTTATAGCACCAATCCTTTGGAATTCCGGCAGAGGAGTTGAACCGGTAAATCC
4140 TAATATCCACACACAATTAATATGTGATTAAAACACACTTAATCATAAATATAAAATAATAAATT
66 TAATATCCACACACAATTAATATGTGATTAAAACACACTTAATCATAAATATAAAATAATAAATT
* *
4205 ACAAAAAGGGACATCAAGAAAAGTAAGGGAGGAAATTCATCGAGGGTCTTTTTAGTCACCCGAAA
131 ACAAAAAGGGACATCAAGAAAAGTAAAGGAGGAAATTCATCGAGGGCCTTTTTAGTCACCCGAAA
*
4270 AGTGAGAAAAGACCAAAAAAAGCCAAAAGGAGGCACCACATTAATCCTCAATTTGGCCTTTAAGT
196 AGTGAGAAAAGACAAAAAAAAGCCAAAAGGAGGCACCACATTAATCCTCAATTTGGCCTTTAAGT
4335 AATTTCCATAGTCACTAA
261 AATTTCCATAGTCACTAA
* *
4353 ATTGCAGATATATTTATAGCATCAATCCTTTGGAATTCCGGCAGAGGAGTTGAACCGGTAAATCC
1 ATTGCAGATACATTTATAGCACCAATCCTTTGGAATTCCGGCAGAGGAGTTGAACCGGTAAATCC
*
4418 TAATATCCACACACAATTAATATGTGATTTAAACACACTTAATCATAAATATAAAATAATAAATT
66 TAATATCCACACACAATTAATATGTGATTAAAACACACTTAATCATAAATATAAAATAATAAATT
4483 ACAAAAAAGGG-CATCAAGAAAAGTAAAGGAGGAAATTCATCGAGGGCCTTTTTAGTCACCCGAA
131 AC-AAAAAGGGACATCAAGAAAAGTAAAGGAGGAAATTCATCGAGGGCCTTTTTAGTCACCCGAA
*
4547 AAGTGAGAAAAGACAAAAAAAAGTCAAAAGGAG
195 AAGTGAGAAAAGACAAAAAAAAGCCAAAAGGAG
4580 ATCCTCAATT
Statistics
Matches: 219, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
278 211 0.96
279 8 0.04
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (278 bp):
ATTGCAGATACATTTATAGCACCAATCCTTTGGAATTCCGGCAGAGGAGTTGAACCGGTAAATCC
TAATATCCACACACAATTAATATGTGATTAAAACACACTTAATCATAAATATAAAATAATAAATT
ACAAAAAGGGACATCAAGAAAAGTAAAGGAGGAAATTCATCGAGGGCCTTTTTAGTCACCCGAAA
AGTGAGAAAAGACAAAAAAAAGCCAAAAGGAGGCACCACATTAATCCTCAATTTGGCCTTTAAGT
AATTTCCATAGTCACTAA
Found at i:6519 original size:27 final size:27
Alignment explanation
Indices: 6489--6561 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
6479 TATTTCTGAA
6489 ATTCCATTATTAAATAATATTCTAATT
1 ATTCCATTATTAAATAATATTCTAATT
*
6516 ATTCCATTATTAAATAATATTTTAATT
1 ATTCCATTATTAAATAATATTCTAATT
* *
6543 GTTCCATTACTAAAATAAT
1 ATTCCATTA-TTAAATAAT
6562 GGAAATTTAG
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 34 0.81
28 8 0.19
ACGTcount: A:0.41, C:0.11, G:0.01, T:0.47
Consensus pattern (27 bp):
ATTCCATTATTAAATAATATTCTAATT
Found at i:7801 original size:2 final size:2
Alignment explanation
Indices: 7794--7818 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7784 CTCAAACTAT
7794 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 T
7819 TTCTAACTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10870 original size:51 final size:51
Alignment explanation
Indices: 10769--10877 Score: 118
Period size: 51 Copynumber: 2.2 Consensus size: 51
10759 GTTCATCAAA
* **
10769 TTTTC-CTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
1 TTTTCTCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
*
10819 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGAC-ATACAAACACT-GTACACGTGT
1 TTTTCTCTTGTTT-AGATCTTGTCTCAGGACAAT-CAAACACTCGTACA-GTGT
*
10870 TTCTCTCT
1 TTTTCTCT
10878 CAGAAATAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
50 9 0.18
51 40 0.80
52 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.43
Consensus pattern (51 bp):
TTTTCTCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
Found at i:17643 original size:39 final size:39
Alignment explanation
Indices: 17612--18093 Score: 579
Period size: 39 Copynumber: 12.4 Consensus size: 39
17602 CAAGGTCTAT
* * *
17612 GTGCCAGAGCCCGAATACAAGCCCGAAGTCAAGTCCTAC
1 GTGCCCGAGCCCGAATACAAGCCCGAGGTCAAGCCCTAC
* * *
17651 GTGCCCGAGCCCAAATACAAGCCTGAGGTCAAGCACTAC
1 GTGCCCGAGCCCGAATACAAGCCCGAGGTCAAGCCCTAC
* *
17690 GTGTCCGAGCCCGAATACAAACCCGAGGTCAAGCCCTAC
1 GTGCCCGAGCCCGAATACAAGCCCGAGGTCAAGCCCTAC
* * * * *
17729 GTGCCCCAGACCGAATACAAGCCCGAGCTTAAGCCTTAC
1 GTGCCCGAGCCCGAATACAAGCCCGAGGTCAAGCCCTAC
* * * * ** *
17768 GAGCCCAAGTCTGTCTACAAGCACGAGGTCAAGCCCTAC
1 GTGCCCGAGCCCGAATACAAGCCCGAGGTCAAGCCCTAC
* *
17807 ATGCCCGAGCCCGAATATAAGCCCGAGGTCAAGCCCTAC
1 GTGCCCGAGCCCGAATACAAGCCCGAGGTCAAGCCCTAC
*
17846 GTGCCCGAGCCTGAATACAAGCCCGAGGTCAAGCCCTAC
1 GTGCCCGAGCCCGAATACAAGCCCGAGGTCAAGCCCTAC
* * *
17885 GTGCCCCAGCCCGAATACAAGCCCGAGGTTAAGCCTTAC
1 GTGCCCGAGCCCGAATACAAGCCCGAGGTCAAGCCCTAC
* * * * *
17924 GAGCCCAAGCCC-ATCTACAAGCACGAGGTCAAGCCCTAT
1 GTGCCCGAGCCCGA-ATACAAGCCCGAGGTCAAGCCCTAC
* *
17963 GTGCCCGAGCCCGAATATAAGCTCGAGGTCAAGCCCTAC
1 GTGCCCGAGCCCGAATACAAGCCCGAGGTCAAGCCCTAC
*
18002 GTGCCCGAGCCCGAATACATGCCCGAGGTCAAGCCCTAC
1 GTGCCCGAGCCCGAATACAAGCCCGAGGTCAAGCCCTAC
* ** ** * *
18041 GTGCCTGAGCCCGTCTACAAGCATGAGGTCAGGCCTTAC
1 GTGCCCGAGCCCGAATACAAGCCCGAGGTCAAGCCCTAC
18080 GTGCCCGAGCCCGA
1 GTGCCCGAGCCCGA
18094 G
Statistics
Matches: 371, Mismatches: 70, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
38 1 0.00
39 369 0.99
40 1 0.00
ACGTcount: A:0.27, C:0.35, G:0.24, T:0.14
Consensus pattern (39 bp):
GTGCCCGAGCCCGAATACAAGCCCGAGGTCAAGCCCTAC
Found at i:18052 original size:156 final size:155
Alignment explanation
Indices: 17627--18091 Score: 660
Period size: 156 Copynumber: 3.0 Consensus size: 155
17617 AGAGCCCGAA
* * * * * *
17627 TACAAGCCCGAAGTCAAGTCCTACGTGCCCGAGCCCAAATACAAGCCTGAGGTCAAGCACTACGT
1 TACAAGCACGAGGTCAAGCCCTACGTGCCCGAGCCCGAATATAAGCC-GAGGTCAAGCCCTACGT
* * * *
17692 GTCCGAGCCCGAATACAAACCCGAGGTCAAGCCCTACGTGCCCCAGACCGAATACAAGCCCGAGC
65 GCCCGAGCCCGAATACAAGCCCGAGGTCAAGCCCTACGTGCCCCAGCCCGAATACAAGCCCGAGG
* **
17757 TTAAGCCTTACGAGCCCAAGTCTGTC
130 TTAAGCCTTACGAGCCCAAGCCCATC
*
17783 TACAAGCACGAGGTCAAGCCCTACATGCCCGAGCCCGAATATAAGCCCGAGGTCAAGCCCTACGT
1 TACAAGCACGAGGTCAAGCCCTACGTGCCCGAGCCCGAATATAAG-CCGAGGTCAAGCCCTACGT
*
17848 GCCCGAGCCTGAATACAAGCCCGAGGTCAAGCCCTACGTGCCCCAGCCCGAATACAAGCCCGAGG
65 GCCCGAGCCCGAATACAAGCCCGAGGTCAAGCCCTACGTGCCCCAGCCCGAATACAAGCCCGAGG
17913 TTAAGCCTTACGAGCCCAAGCCCATC
130 TTAAGCCTTACGAGCCCAAGCCCATC
*
17939 TACAAGCACGAGGTCAAGCCCTATGTGCCCGAGCCCGAATATAAGCTCGAGGTCAAGCCCTACGT
1 TACAAGCACGAGGTCAAGCCCTACGTGCCCGAGCCCGAATATAAGC-CGAGGTCAAGCCCTACGT
* ** ** **
18004 GCCCGAGCCCGAATACATGCCCGAGGTCAAGCCCTACGTGCCTGAGCCCGTCTACAAGCATGAGG
65 GCCCGAGCCCGAATACAAGCCCGAGGTCAAGCCCTACGTGCCCCAGCCCGAATACAAGCCCGAGG
* * * *
18069 TCAGGCCTTACGTGCCCGAGCCC
130 TTAAGCCTTACGAGCCCAAGCCC
18092 GAG
Statistics
Matches: 278, Mismatches: 29, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
155 1 0.00
156 275 0.99
157 2 0.01
ACGTcount: A:0.27, C:0.35, G:0.24, T:0.14
Consensus pattern (155 bp):
TACAAGCACGAGGTCAAGCCCTACGTGCCCGAGCCCGAATATAAGCCGAGGTCAAGCCCTACGTG
CCCGAGCCCGAATACAAGCCCGAGGTCAAGCCCTACGTGCCCCAGCCCGAATACAAGCCCGAGGT
TAAGCCTTACGAGCCCAAGCCCATC
Done.