Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021527.1 Corchorus olitorius cultivar O-4 contig21560, 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: 21852
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Found at i:666 original size:252 final size:252
Alignment explanation
Indices: 146--666 Score: 848
Period size: 252 Copynumber: 2.1 Consensus size: 252
136 TTTTTTTTAA
* *
146 AAAAAAAATTTCAATAAAATAAAATATATTAAAAAAATATTTAATTTTTATTCCACGTGCCACCT
1 AAAATAAATGTCAATAAAATAAAATATATTAAAAAAATATTTAATTTTTATTCCACGTGCCACCT
* *
211 GCTACGTCAGCAAAAAAGACGGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGCAT
66 GCCACGTCAGCAAAAAAGACGGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGCAC
** * *
276 GTTAACGTGAGGGACCTCGGGTGATAGGTTCTGATAGTAGAGGGACGAATTTGTAGAAAAAAAAG
131 ACTAACGTGAGGGACCTCGGATGATAGGTTCTGATAGTAGAGGGACGAATTTATAGAAAAAAAAG
* * *
341 TACAGGGACCAAAATCAACATTTCGTATAGTACAGGGACTTCCCGGGCACTTTTACC
196 TACAGGAACCAAAATCAACATTTCGTATAGTACAGGGACCTCCCGGACACTTTTACC
* *
398 AAAATAAATTTCAATAAAATAAAATATATTAAAAAAATATTTAATTTTTATTCCACGTGTCACCT
1 AAAATAAATGTCAATAAAATAAAATATATTAAAAAAATATTTAATTTTTATTCCACGTGCCACCT
* *
463 GCCACGTCAGTAAAAAAGACGGTGTTAGTGCCACGTTAGCATATTTGACGGGTCTGTCACGGCAC
66 GCCACGTCAGCAAAAAAGACGGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGCAC
528 ACTAACGTGAGGGACCTCGGATGATAGGTTCTGATAGTAGAGGGACGAATTTATAGAAAAAAAAA
131 ACTAACGTGAGGGACCTCGGATGATAGGTTCTGATAGTAGAGGGACGAATTTATAG-AAAAAAAA
* *
593 GTACAGGAACCAAAATCAACATTTCGTATCGTACAGGGACCTCCCGGATACTTTTACC
195 GTACAGGAACCAAAATCAACATTTCGTATAGTACAGGGACCTCCCGGACACTTTTACC
*
651 GCAAA-AAA-GTCAATAA
1 -AAAATAAATGTCAATAA
667 CTTATGCAAA
Statistics
Matches: 250, Mismatches: 17, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
252 183 0.73
253 64 0.26
254 3 0.01
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (252 bp):
AAAATAAATGTCAATAAAATAAAATATATTAAAAAAATATTTAATTTTTATTCCACGTGCCACCT
GCCACGTCAGCAAAAAAGACGGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGCAC
ACTAACGTGAGGGACCTCGGATGATAGGTTCTGATAGTAGAGGGACGAATTTATAGAAAAAAAAG
TACAGGAACCAAAATCAACATTTCGTATAGTACAGGGACCTCCCGGACACTTTTACC
Found at i:1973 original size:16 final size:15
Alignment explanation
Indices: 1924--1973 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1914 TGTTTGGGAG
1924 GAAATGGGGAGGAAA
1 GAAATGGGGAGGAAA
*
1939 GAAGA-GGGGCGGAAA
1 GAA-ATGGGGAGGAAA
*
1954 GAAATGGGGAAGGAAG
1 GAAATGGGG-AGGAAA
1970 GAAA
1 GAAA
1974 CACTTCTTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 1 0.03
15 19 0.66
16 9 0.31
ACGTcount: A:0.46, C:0.02, G:0.48, T:0.04
Consensus pattern (15 bp):
GAAATGGGGAGGAAA
Found at i:3518 original size:16 final size:16
Alignment explanation
Indices: 3499--3539 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3489 TCCTCCTTAT
*
3499 TTTCTTTCCCTTGCTA
1 TTTCTTTCCCTTCCTA
3515 TTTCCTTT-CCTTCCTA
1 TTT-CTTTCCCTTCCTA
3531 TTTCTTTCC
1 TTTCTTTCC
3540 TCTCTACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.18
16 14 0.64
17 4 0.18
ACGTcount: A:0.05, C:0.34, G:0.02, T:0.59
Consensus pattern (16 bp):
TTTCTTTCCCTTCCTA
Found at i:5891 original size:38 final size:38
Alignment explanation
Indices: 5840--5917 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
5830 TAAATTTATT
5840 TTTATATTCTATCATTTAGCATTCAAGGATACTAAAAG
1 TTTATATTCTATCATTTAGCATTCAAGGATACTAAAAG
5878 TTTATATTCTATCATTTAGCATTCAAGGATACTAAAAG
1 TTTATATTCTATCATTTAGCATTCAAGGATACTAAAAG
5916 TT
1 TT
5918 GATGATAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (38 bp):
TTTATATTCTATCATTTAGCATTCAAGGATACTAAAAG
Found at i:13246 original size:16 final size:16
Alignment explanation
Indices: 13223--13270 Score: 87
Period size: 16 Copynumber: 3.0 Consensus size: 16
13213 AACTCCATTT
13223 ACCTTTTAACCAGCGC
1 ACCTTTTAACCAGCGC
*
13239 AGCTTTTAACCAGCGC
1 ACCTTTTAACCAGCGC
13255 ACCTTTTAACCAGCGC
1 ACCTTTTAACCAGCGC
13271 TACTATAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.25, C:0.35, G:0.15, T:0.25
Consensus pattern (16 bp):
ACCTTTTAACCAGCGC
Found at i:13692 original size:4 final size:4
Alignment explanation
Indices: 13683--13709 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
13673 CAATTGTCTA
13683 ATTT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT
13710 ACATATTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:15749 original size:6 final size:6
Alignment explanation
Indices: 15738--15769 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
15728 GACAAGTTTG
15738 CCCTAA CCCTAA CCCTAA CCCTAA CCCTAA CC
1 CCCTAA CCCTAA CCCTAA CCCTAA CCCTAA CC
15770 AACCCCCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.53, G:0.00, T:0.16
Consensus pattern (6 bp):
CCCTAA
Found at i:16341 original size:50 final size:50
Alignment explanation
Indices: 16282--16382 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
16272 GATTATTATT
16282 AGGATTTTGATATATTCTTTAGTTCTTTCTATGTAATTAACTATTAAGTC
1 AGGATTTTGATATATTCTTTAGTTCTTTCTATGTAATTAACTATTAAGTC
*
16332 AGGATTTTGATATATTCTTTAGTTCTTTCTATGTAATTAGCTATTAAGTC
1 AGGATTTTGATATATTCTTTAGTTCTTTCTATGTAATTAACTATTAAGTC
16382 A
1 A
16383 ATCTTGTTGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.50
Consensus pattern (50 bp):
AGGATTTTGATATATTCTTTAGTTCTTTCTATGTAATTAACTATTAAGTC
Found at i:16977 original size:11 final size:11
Alignment explanation
Indices: 16961--16991 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
16951 CTTGTTTTTT
16961 GTTTTTGTTTC
1 GTTTTTGTTTC
*
16972 GTTTTTGTTTT
1 GTTTTTGTTTC
16983 GTTTTTGTT
1 GTTTTTGTT
16992 ACGCTGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.03, G:0.19, T:0.77
Consensus pattern (11 bp):
GTTTTTGTTTC
Found at i:17201 original size:28 final size:29
Alignment explanation
Indices: 17142--17202 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
17132 ACATTTTCAT
* * *
17142 TATTTTTATTAAATTCTTTTTTTGCTACA
1 TATTTTTATCAAATTCTCTTTCTGCTACA
17171 TATTTTTATCAAATTCTACTTTCT-CT-CA
1 TATTTTTATCAAATTCT-CTTTCTGCTACA
17199 TATT
1 TATT
17203 AATGTGTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.21
29 18 0.64
30 4 0.14
ACGTcount: A:0.25, C:0.15, G:0.02, T:0.59
Consensus pattern (29 bp):
TATTTTTATCAAATTCTCTTTCTGCTACA
Found at i:17778 original size:53 final size:53
Alignment explanation
Indices: 17693--17798 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 53
17683 CACCCTTCAA
* *
17693 AATCTTTCATCTAAGCTCTAATGTCCGTTGCAATAGGATCAACTTCCCATCTT
1 AATCTTTCATCAAAGCTCTAATGTCCGCTGCAATAGGATCAACTTCCCATCTT
*
17746 AATCTTTCATCAAAGCTCTAATGTCTGCTGCAATAGGATCAACTTCCCATCTT
1 AATCTTTCATCAAAGCTCTAATGTCCGCTGCAATAGGATCAACTTCCCATCTT
17799 GGATCACCCT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.27, C:0.26, G:0.11, T:0.35
Consensus pattern (53 bp):
AATCTTTCATCAAAGCTCTAATGTCCGCTGCAATAGGATCAACTTCCCATCTT
Done.