Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013535.1 Corchorus olitorius cultivar O-4 contig13568, 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: 21564
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:734 original size:56 final size:56
Alignment explanation
Indices: 620--735 Score: 146
Period size: 56 Copynumber: 2.1 Consensus size: 56
610 CTTTAACTAG
* * * * *
620 TATTATAATAAATCATATTCCCCTATCTCTACTTAATTATTCTTTCACACAATAAA
1 TATTATAATAAATCATATTCCCCAATCTCTACTTAATTATTCTATAAAAAAATAAA
*
676 TATTATAATAAATCCTA-TCTCCCAATCTCTACTTAATTATTCTATAAAATAAAT-AA
1 TATTATAATAAATCATATTC-CCCAATCTCTACTTAATTATTCTATAAAA-AAATAAA
732 TATT
1 TATT
736 TTCTTTTAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
55 2 0.04
56 47 0.90
57 3 0.06
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.41
Consensus pattern (56 bp):
TATTATAATAAATCATATTCCCCAATCTCTACTTAATTATTCTATAAAAAAATAAA
Found at i:1970 original size:93 final size:93
Alignment explanation
Indices: 1811--1998 Score: 349
Period size: 93 Copynumber: 2.0 Consensus size: 93
1801 CTTGGTGTTC
1811 TCTATTTATACTTATATGAACTAAGTAAGAACCCGTGCGCTACGCTGGCCAATATATTCTTATAG
1 TCTATTTATACTTATATGAACTAAGTAAGAACCCGTGCGCTACGCTGGCCAATATATTCTTATAG
1876 TTGATATGCTATAACCTTTAATTAATTT
66 TTGATATGCTATAACCTTTAATTAATTT
* * *
1904 TCTATTTATATTTATATGAACTAAGTAAGAATCCGTGCGCTACGCTGGCCAATATGTTCTTATAG
1 TCTATTTATACTTATATGAACTAAGTAAGAACCCGTGCGCTACGCTGGCCAATATATTCTTATAG
1969 TTGATATGCTATAACCTTTAATTAATTT
66 TTGATATGCTATAACCTTTAATTAATTT
1997 TC
1 TC
1999 AATAATGGGT
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.40
Consensus pattern (93 bp):
TCTATTTATACTTATATGAACTAAGTAAGAACCCGTGCGCTACGCTGGCCAATATATTCTTATAG
TTGATATGCTATAACCTTTAATTAATTT
Found at i:3226 original size:14 final size:15
Alignment explanation
Indices: 3193--3226 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3183 GTACTAAAAA
*
3193 TTCAGTACTTAATCT
1 TTCAGCACTTAATCT
3208 TTCAGCACTTAAT-T
1 TTCAGCACTTAATCT
3222 TTCAG
1 TTCAG
3227 TTTTATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (15 bp):
TTCAGCACTTAATCT
Found at i:7297 original size:253 final size:254
Alignment explanation
Indices: 6849--7355 Score: 980
Period size: 253 Copynumber: 2.0 Consensus size: 254
6839 AGAGACAAGC
6849 AGAGAAGTACTTAGCTCGCTTCAAGGAGTTAAGGAACAGGTGCCGCACACCTCTCCAGGAGGTAG
1 AGAGAAGTACTTAGCTCGCTTCAAGGAGTTAAGGAACAGGTGCCGCACACCTCTCCAGGAGGTAG
6914 AGTTCGTGCGCCTAGCTCAAAATGGACTTGAAATAGAGCTTCGAAAGAAGTTCGAAGGAGTTGAC
66 AGTTCGTGCGCCTAGCTCAAAATGGACTTGAAATAGAGCTTCGAAAGAAGTTCGAAGGAGTTGAC
6979 TTCAGAGACTTCTTCGAGATGTCAACCAAAGTGACAAGATATGAGACTCTCCTACGAGAGGAGAA
131 TTCAGAGACTTCTTCGAGATGTCAACCAAAGTGACAAGATATGAGACTCTCCTACGAGAGGAGAA
*
7044 TG-AAGTAGTTCATCTTATGGCACTTACTATCAAGAGCCAAATTTTGAACTTGGAATAG
196 TGAAAGAAGTTCATCTTATGGCACTTACTATCAAGAGCCAAATTTTGAACTTGGAATAG
7102 AGAGAAGTACTTAGCTCGCTTCAAGGAGTTAAGGAACAGGTGCCGCACACCTCTCCAGGAGGTAG
1 AGAGAAGTACTTAGCTCGCTTCAAGGAGTTAAGGAACAGGTGCCGCACACCTCTCCAGGAGGTAG
*
7167 AGTTCGTGCGCCTAGCTCAAAATGGACTTGACATAGAGCTTCGAAAGAAGTTCGAAGGAGTTGAC
66 AGTTCGTGCGCCTAGCTCAAAATGGACTTGAAATAGAGCTTCGAAAGAAGTTCGAAGGAGTTGAC
*
7232 TTCAGAGACTTCTTCGAGATGTCAACCAAGGTGACAAGATATGAGACTCTCCTACGAGAGGAGAA
131 TTCAGAGACTTCTTCGAGATGTCAACCAAAGTGACAAGATATGAGACTCTCCTACGAGAGGAGAA
7297 TGAAAGAAGTTCATCTTATGGCACTTACTATCAAGAGCCAAATTTTGAACTTGGAATAG
196 TGAAAGAAGTTCATCTTATGGCACTTACTATCAAGAGCCAAATTTTGAACTTGGAATAG
7356 CTGAGGTCAA
Statistics
Matches: 250, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
253 195 0.78
254 55 0.22
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.23
Consensus pattern (254 bp):
AGAGAAGTACTTAGCTCGCTTCAAGGAGTTAAGGAACAGGTGCCGCACACCTCTCCAGGAGGTAG
AGTTCGTGCGCCTAGCTCAAAATGGACTTGAAATAGAGCTTCGAAAGAAGTTCGAAGGAGTTGAC
TTCAGAGACTTCTTCGAGATGTCAACCAAAGTGACAAGATATGAGACTCTCCTACGAGAGGAGAA
TGAAAGAAGTTCATCTTATGGCACTTACTATCAAGAGCCAAATTTTGAACTTGGAATAG
Found at i:13571 original size:178 final size:176
Alignment explanation
Indices: 13249--13708 Score: 494
Period size: 178 Copynumber: 2.6 Consensus size: 176
13239 AATATAAACA
* ** * * * * * *
13249 TTTTAGAAGCATTTTTGGTATTTGAAAAATAAAATTTAACTTTCAAGTCCTACATGAAAGTTGAA
1 TTTTGGAAGCATTTTTTATACTTGAAACATTAAATTTAGCTTTCGAGTCCTACATGAAAGTTGTA
* * ** * *
13314 GATCATGAAACAGCCTTTTA-ACAGACACTTAAATCACCTCAATCGGACATCTGAAGCAAAAATT
66 GATCATGAAA-AACCTTTTATA-A-ACACTTGAATCACCTCAATAAGACATCTGAACCAAAAATA
* * * *
13378 ATGTATTATTAAGTGGACCGTTCATTCTCGCTAACCAAAAAAATTAATT
128 ATGTATTACTAAGTGGACCGTCCATTCCCGCTAACCAAAAAAACTAATT
**
13427 TTTTGGAAGCATTTTTTATACTTGAAACATTAAATTTAGCTTTCGAGTCCGGCATGAAAGTTGTA
1 TTTTGGAAGCATTTTTTATACTTGAAACATTAAATTTAGCTTTCGAGTCCTACATGAAAGTTGTA
* * * *
13492 GATCATAAAATAACCTTTTATGAAACACTTGAATCAGCTCAATAAGACATCTGGACCAAAAGTAA
66 GATCATGAAA-AACCTTTTAT-AAACACTTGAATCACCTCAATAAGACATCTGAACCAAAAATAA
* * * *
13557 TGT-TATACTAAGTGGATCGTCCATTCCCGTTAACCGAAATAACTAATT
129 TGTAT-TACTAAGTGGACCGTCCATTCCCGCTAACCAAAAAAACTAATT
* * * * * *
13605 ATTCGGAAGC-TTTTTTGATACTTAAAACATTAAATTTAGTTTTCGAGTCTTTCATGAAAGTTGT
1 TTTTGGAAGCATTTTTT-ATACTTGAAACATTAAATTTAGCTTTCGAGTCCTACATGAAAGTTGT
*
13669 AGATCATGGAAAAACCTTTTAATAAACGCTTGAATCACCT
65 AGATCAT-GAAAAACCTTTT-ATAAACACTTGAATCACCT
13709 TGATAGGATA
Statistics
Matches: 236, Mismatches: 40, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
177 7 0.03
178 222 0.94
179 6 0.03
180 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (176 bp):
TTTTGGAAGCATTTTTTATACTTGAAACATTAAATTTAGCTTTCGAGTCCTACATGAAAGTTGTA
GATCATGAAAAACCTTTTATAAACACTTGAATCACCTCAATAAGACATCTGAACCAAAAATAATG
TATTACTAAGTGGACCGTCCATTCCCGCTAACCAAAAAAACTAATT
Found at i:17736 original size:33 final size:32
Alignment explanation
Indices: 17658--17736 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
17648 GCCATTTAGT
* * *
17658 GTTCAAGGGTAATTTTATCCTTTTTTATTAAA
1 GTTCTAGGGTTATTCTATCCTTTTTTATTAAA
* *
17690 GTT-TAAGGATTATTCTATCTTTTTCTTATTAAA
1 GTTCT-AGGGTTATTCTATCCTTTT-TTATTAAA
17723 GTTCTAGGGTTATT
1 GTTCTAGGGTTATT
17737 TTTGTCTATC
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
32 18 0.47
33 19 0.50
34 1 0.03
ACGTcount: A:0.25, C:0.09, G:0.14, T:0.52
Consensus pattern (32 bp):
GTTCTAGGGTTATTCTATCCTTTTTTATTAAA
Found at i:18702 original size:31 final size:31
Alignment explanation
Indices: 18645--18703 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
18635 GTAAAACAAC
* **
18645 AAATTTTAAAAGTTTAAGGGGTAAAATGGTA
1 AAATATTAAAAGTTTAAGGGACAAAATGGTA
18676 AAATATTAAAAGTTTAAGGGACAAAATG
1 AAATATTAAAAGTTTAAGGGACAAAATG
18704 ACCAAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.49, C:0.02, G:0.20, T:0.29
Consensus pattern (31 bp):
AAATATTAAAAGTTTAAGGGACAAAATGGTA
Done.