Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019987.1 Corchorus olitorius cultivar O-4 contig20020, 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: 14499
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Found at i:3983 original size:2 final size:2
Alignment explanation
Indices: 3976--4010 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3966 CCATTATGTG
3976 TA TA TA TA TA 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 TA TA TA TA TA T
4011 CTACTGTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4300 original size:6 final size:6
Alignment explanation
Indices: 4284--4317 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
4274 GTTCCCATTT
*
4284 GAAAGAA GAAAAA GAAAAA GAAAAG GAAAAA GAA
1 GAAA-AA GAAAAA GAAAAA GAAAAA GAAAAA GAA
4318 TACTTGGCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 21 0.84
7 4 0.16
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:6023 original size:36 final size:36
Alignment explanation
Indices: 5977--6774 Score: 728
Period size: 36 Copynumber: 22.4 Consensus size: 36
5967 GATTCTTTAG
* * *
5977 TTTATTTCAGTTGATCCAGGGTGATCATTTCTTCAT
1 TTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAA
** * *
6013 TTTACCTCAGTTGATCTAGGGCGATCTTTTCTTCAG
1 TTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAA
* * * *
6049 TTTATTTCAGTTGACCCAGGGCGGTCCTCT-TTCAA
1 TTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAA
* * * *
6084 TTTATTTCAATCGACCCAGGGCGGTC-TTTCTTCAA
1 TTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAA
* ** *
6119 TTCATTTCAGTTTGATCCAGGATGATCTTTTCTTCAT
1 TTTATTTCAG-TTGATCCAGGGCGATCTTTTCTTCAA
** * *
6156 TTTACCTCAGTTGATCCAGGGCGATCCTTTCTTCAG
1 TTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAA
* * *
6192 TTTATTTTAGTTGATCCAGGGCGATCCTTTCTTCAG
1 TTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAA
* *
6228 TTTATTTCAGTTGA-CCTAGGGCGGTC-CTTCTTCAA
1 TTTATTTCAGTTGATCC-AGGGCGATCTTTTCTTCAA
* * *
6263 TTTATTTCAATTGACCCAGGGCGGTC-TTTCTTCAA
1 TTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAA
* * ** *
6298 TTCATTTCGGTTTGATCCAGGATGATCTTTTCTTCAT
1 TTTATTTCAG-TTGATCCAGGGCGATCTTTTCTTCAA
** * *
6335 TTTACCTCAGTTGATCCAGGGCGATCCTTTCTTCAG
1 TTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAA
* * ** *
6371 TTTATTTTAGTTGATCCAGGGCGACCCGTTCTTCAG
1 TTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAA
* * *
6407 TTTATTTCAAGTTGA-CCTAGGGTGGTCTTTTCATTCAG
1 TTTATTTC-AGTTGATCC-AGGGCGATCTTTTC-TTCAA
* *
6445 TTTATGTCAGTTGATCCAGGGCGATCTTTTATTCAA
1 TTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAA
* *
6481 TTTATTTCAGTCGATCCAGGGCGATCTTTCCTTCAA
1 TTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAA
* * * * * *
6517 TTTATTTTAGCTGACCCAGGGTGGTC-ATTCTTCAA
1 TTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAA
* *
6552 GTTATTTCAGTTGA-CCAAGGGCGGTC-TTTCTTCAA
1 TTTATTTCAGTTGATCC-AGGGCGATCTTTTCTTCAA
* * * *
6587 TTCATTTCAATTGATCCAGGACGATC-TTACTTCAA
1 TTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAA
* * *
6622 GTTATTTTAGTTGATCCAGGGCGATCTTTTCTTCAG
1 TTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAA
6658 TTTA---C--TTGA-CCGAGGGCGATCTTTTCTTCAA
1 TTTATTTCAGTTGATCC-AGGGCGATCTTTTCTTCAA
* * ** *
6689 TTTATTTCAATGGATCCAGGGTAATCTTTTCTTCAG
1 TTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAA
* * * *
6725 TTTATTTCAATTGATCCAGGGTGATCTTTTCTGCAG
1 TTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAA
6761 TTTATTTCAGTTGA
1 TTTATTTCAGTTGA
6775 CCGCAAATTG
Statistics
Matches: 627, Mismatches: 114, Indels: 42
0.80 0.15 0.05
Matches are distributed among these distances:
30 2 0.00
31 26 0.04
34 5 0.01
35 168 0.27
36 349 0.56
37 63 0.10
38 14 0.02
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.42
Consensus pattern (36 bp):
TTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAA
Found at i:6283 original size:179 final size:180
Alignment explanation
Indices: 5983--6776 Score: 830
Period size: 179 Copynumber: 4.5 Consensus size: 180
5973 TTAGTTTATT
* * ** * *
5983 TCAGTTGATCCAGGGTGATCATTTCTTCATTTTACCTCAGTTGATCTAGGGCGATCTTTTCTTCA
1 TCAGTTGATCCAGGGTGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCA
* * * *
6048 GTTTATTTCAGTTGACCCAGGGCGGTCC-TCTTTCAATTTATTTCAATCGACCCAGGGCGGTCTT
66 GTTTATTTCAGTTGACCTAGGGCGGTCCTTCATTCAATTTATTTCAATTGACCCAGGGCGATCTT
* *
6112 TCTTCAATTCATTTCAGTTTGATCCAGGATGATCTTTTCTTCATTTTACC
131 TCTTCAATTCATTTCAGTTTGATCCAGGACGATCTTTTCTTCAATTTACC
* *
6162 TCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTTAGTTGATCCAGGGCGATCCTTTCTTCA
1 TCAGTTGATCCAGGGTGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCA
*
6227 GTTTATTTCAGTTGACCTAGGGCGGTCCTTC-TTCAATTTATTTCAATTGACCCAGGGCGGTCTT
66 GTTTATTTCAGTTGACCTAGGGCGGTCCTTCATTCAATTTATTTCAATTGACCCAGGGCGATCTT
* * *
6291 TCTTCAATTCATTTCGGTTTGATCCAGGATGATCTTTTCTTCATTTTACC
131 TCTTCAATTCATTTCAGTTTGATCCAGGACGATCTTTTCTTCAATTTACC
* * * *
6341 TCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTTAGTTGATCCAGGGCGACCCGTTCTTCA
1 TCAGTTGATCCAGGGTGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCA
* * * * * *
6406 GTTTATTTCAAGTTGACCTAGGGTGGTCTTTTCATTCAGTTTATGTCAGTTGATCCAGGGCGATC
66 GTTTATTTC-AGTTGACCTAGGGCGGTC-CTTCATTCAATTTATTTCAATTGACCCAGGGCGATC
* * * * * **
6471 TTTTATTCAATTTATTTCAG-TCGATCCAGGGCGATCTTTCCTTCAATTTATT
129 -TTTCTTCAATTCATTTCAGTTTGATCCAGGACGATCTTTTCTTCAATTTACC
* * * * * *
6523 TTAGCTGACCCAGGGTGGT-CATTCTTCAAG-TTATTTCAGTTGA-CCAAGGGCGGT-CTTTCTT
1 TCAGTTGATCCAGGGTGATCCTTTCTTC-AGTTTATTTCAGTTGATCC-AGGGCGATCCTTTCTT
* * * * * * * * *
6584 CAATTCATTTCAATTGATCC-AGGACGAT-CTT-ACTTCAAGTTATTTTAGTTGATCCAGGGCGA
64 CAGTTTATTTCAGTTGA-CCTAGGGCGGTCCTTCA-TTCAATTTATTTCAATTGACCCAGGGCGA
* * **
6646 TC-TT-TTC--TTCAGTTT-A-CTTGA-CCGAGGGCGATCTTTTCTTCAATTTATT
127 TCTTTCTTCAATTCA-TTTCAGTTTGATCC-AGGACGATCTTTTCTTCAATTTACC
* * * * * * * *
6695 TCAATGGATCCAGGGTAATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGTGATCTTTTCTGCA
1 TCAGTTGATCCAGGGTGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCA
6760 GTTTATTTCAGTTGACC
66 GTTTATTTCAGTTGACC
6777 GCAAATTGGT
Statistics
Matches: 528, Mismatches: 71, Indels: 38
0.83 0.11 0.06
Matches are distributed among these distances:
171 2 0.00
172 45 0.09
173 29 0.05
174 24 0.05
175 2 0.00
176 1 0.00
177 29 0.05
179 247 0.47
180 38 0.07
181 28 0.05
182 67 0.13
183 16 0.03
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (180 bp):
TCAGTTGATCCAGGGTGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCA
GTTTATTTCAGTTGACCTAGGGCGGTCCTTCATTCAATTTATTTCAATTGACCCAGGGCGATCTT
TCTTCAATTCATTTCAGTTTGATCCAGGACGATCTTTTCTTCAATTTACC
Found at i:7032 original size:30 final size:30
Alignment explanation
Indices: 6985--7533 Score: 721
Period size: 30 Copynumber: 18.2 Consensus size: 30
6975 ACCATTCTAC
*
6985 ATCATTGCTTTATTTTAATCCTGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
*
7015 ATCGTTG-TTTCATTTTAATCCTGGTTGAGG
1 ATCATTGCTTT-ATTTTAATCCTGGTTGAGG
*
7045 AT-ATTTGCTTTACTTTAATCCTGGTTGAGG
1 ATCA-TTGCTTTATTTTAATCCTGGTTGAGG
* *
7075 ATAATTGCTTCATTTTAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
** *
7105 ATTGTTGCTTTACTTTAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
* *
7135 ATAATTGCTTCATTTTAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
* *
7165 ATCGTTACTTTATTTTAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
* *
7195 ATCGTTGCATTATTTTTAATCCTGGTTGAGG
1 ATCATTGCTTTA-TTTTAATCCTGGTTGAGG
* * *
7226 ATCAATGCTTTATTTCAATCCTGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
7256 ATCATTGCTTT-TTTTAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
* * *
7285 ATCATTGCTATATTTCAATCCTGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
7315 ATCATTGCTTTATTTTTAATCCTGGTTGAGG
1 ATCATTGCTTTA-TTTTAATCCTGGTTGAGG
*
7346 ATCATTGCTTTA-TTTAATCCTGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
7375 ATCATTGCTTTATTTTTAATCCTGGTTGAGG
1 ATCATTGCTTTA-TTTTAATCCTGGTTGAGG
* * *
7406 ATCATTGCTCTATTTTAACCCTGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
7436 ATCATTGCTTTATTTTTAATCCTGGTTGAGG
1 ATCATTGCTTTA-TTTTAATCCTGGTTGAGG
* ***
7467 ATCATTTCGCCATTTTAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
* * *
7497 ATC-TCTCCTTTATTTTAATCCTGTTTTAGG
1 ATCAT-TGCTTTATTTTAATCCTGGTTGAGG
7527 ATCATTG
1 ATCATTG
7534 TTTCATCAGT
Statistics
Matches: 454, Mismatches: 53, Indels: 24
0.85 0.10 0.05
Matches are distributed among these distances:
29 58 0.13
30 285 0.63
31 111 0.24
ACGTcount: A:0.20, C:0.15, G:0.19, T:0.46
Consensus pattern (30 bp):
ATCATTGCTTTATTTTAATCCTGGTTGAGG
Found at i:11209 original size:27 final size:26
Alignment explanation
Indices: 11178--11252 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 26
11168 AAGTGAGATT
*
11178 AAAATGGCTAAAATGCCCCTGAACATGC
1 AAAATGACTAAAATGCCCCTG-A-ATGC
* *
11206 -AAATGACCAAAATGCCCTTGAATGC
1 AAAATGACTAAAATGCCCCTGAATGC
11231 AAAAATGACCTAAAATGCCCCT
1 -AAAATGA-CTAAAATGCCCCT
11253 AGATGACCCT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
25 4 0.10
26 1 0.03
27 23 0.59
28 11 0.28
ACGTcount: A:0.41, C:0.25, G:0.15, T:0.19
Consensus pattern (26 bp):
AAAATGACTAAAATGCCCCTGAATGC
Done.