Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017826.1 Corchorus olitorius cultivar O-4 contig17859, 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: 32003
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2388 original size:69 final size:69
Alignment explanation
Indices: 2243--2470 Score: 352
Period size: 67 Copynumber: 3.3 Consensus size: 69
2233 CAGATCTTGG
* * *
2243 CCAAGTCCTGTCCAGGACTTGGGCTGTTGAGGAATGCAAAAATACAGGACAAGACCTGGGCAGGA
1 CCAAGTCCTGTCCAGGACTTGTGCTGTTGAGGAGTGC-AAATTACAGGACAAGACCTGGGCAGGA
2308 GTTAC
65 GTTAC
* * *
2313 CCAAGTCCTGTCCCGGACTTGTGCTGTTGAAGAGTGCAAATTACAGGACAAGACCTGGGCGGGAG
1 CCAAGTCCTGTCCAGGACTTGTGCTGTTGAGGAGTGCAAATTACAGGACAAGACCTGGGCAGGAG
2378 TTAC
66 TTAC
* *
2382 CCAAGTCCTGTCCCGGACTTGTGC--TTGAGGAGCGCAAATTACAGGACAAGACCTGGGCAGGAG
1 CCAAGTCCTGTCCAGGACTTGTGCTGTTGAGGAGTGCAAATTACAGGACAAGACCTGGGCAGGAG
2445 TTAC
66 TTAC
*
2449 CCAAGTCCTGTCCAGGAGTTGT
1 CCAAGTCCTGTCCAGGACTTGT
2471 TGCGGGAAAT
Statistics
Matches: 147, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
67 60 0.41
69 54 0.37
70 33 0.22
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.21
Consensus pattern (69 bp):
CCAAGTCCTGTCCAGGACTTGTGCTGTTGAGGAGTGCAAATTACAGGACAAGACCTGGGCAGGAG
TTAC
Found at i:4399 original size:16 final size:16
Alignment explanation
Indices: 4374--4409 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4364 TGTGATTTGC
4374 TTTCCCTTCCTCCCTA
1 TTTCCCTTCCTCCCTA
* *
4390 TTTCCTTTCCTTCCTA
1 TTTCCCTTCCTCCCTA
4406 TTTC
1 TTTC
4410 TTTTATCCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.42, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTCCCTTCCTCCCTA
Found at i:9781 original size:37 final size:37
Alignment explanation
Indices: 9731--9801 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
9721 CTGCCCAGTA
9731 CAGGGCCTCATAAGAATTCAATCTCACCAAAATAGTT
1 CAGGGCCTCATAAGAATTCAATCTCACCAAAATAGTT
9768 CAGGGCCTCATAAGAATTCAATCTCACCAAAATA
1 CAGGGCCTCATAAGAATTCAATCTCACCAAAATA
9802 TGACTATGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.25, G:0.13, T:0.23
Consensus pattern (37 bp):
CAGGGCCTCATAAGAATTCAATCTCACCAAAATAGTT
Found at i:20459 original size:22 final size:22
Alignment explanation
Indices: 20344--20594 Score: 149
Period size: 22 Copynumber: 11.7 Consensus size: 22
20334 CTCTAACATA
* *
20344 GAAATATTGATAACCAAAC--T
1 GAAATTTTGATAACCACACTAT
* ** *
20364 GAAAATTTGATAACCTTATTAT
1 GAAATTTTGATAACCACACTAT
** * *
20386 GAAATTTCAATAACCTCCCTAT
1 GAAATTTTGATAACCACACTAT
*
20408 GAAAATTTGATAACCACACTAT
1 GAAATTTTGATAACCACACTAT
*
20430 GAAATTTTAATAACCACACTAT
1 GAAATTTTGATAACCACACTAT
* * *
20452 GAAATTTTGATAATCTCAGTAT
1 GAAATTTTGATAACCACACTAT
* *
20474 GAAGTTTTGATAATCCCCA-TAT
1 GAAATTTTGATAA-CCACACTAT
* * *
20496 GATATTTTGATAATCATACTAT
1 GAAATTTTGATAACCACACTAT
* * * *
20518 -AAA-ATTGGTAACAACACAAT
1 GAAATTTTGATAACCACACTAT
* *
20538 GAAAATTTTGATATCCTCA--A-
1 G-AAATTTTGATAACCACACTAT
* * * *
20558 AAAATTATGATAAACACACCAT
1 GAAATTTTGATAACCACACTAT
*
20580 GAAATTTCGATAACC
1 GAAATTTTGATAACC
20595 TTGTTATGAG
Statistics
Matches: 170, Mismatches: 51, Indels: 18
0.71 0.21 0.08
Matches are distributed among these distances:
19 13 0.08
20 25 0.15
21 6 0.04
22 115 0.68
23 11 0.06
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (22 bp):
GAAATTTTGATAACCACACTAT
Found at i:20646 original size:22 final size:22
Alignment explanation
Indices: 20615--20948 Score: 143
Period size: 22 Copynumber: 15.1 Consensus size: 22
20605 AATAAAACTG
* *
20615 TGATATCCTCTCTATGTAATTT
1 TGATAACCTCTCTATGAAATTT
* *
20637 TGATAACCTCTCCATAAAATTT
1 TGATAACCTCTCTATGAAATTT
*
20659 TCATAACCTC-CATATGAAATTT
1 TGATAACCTCTC-TATGAAATTT
* *
20681 TGTTAATTAACCTCCCTAAGAAATTT
1 TG---A-TAACCTCTCTATGAAATTT
* *
20707 TGATAA----GC-A-CAAATTT
1 TGATAACCTCTCTATGAAATTT
20723 TGATAACCTCCCTCCCTATGAAATTT
1 TGATAACCT--CT--CTATGAAATTT
* * *
20749 TGATAACCACACTATAAAATTT
1 TGATAACCTCTCTATGAAATTT
** * *
20771 CAATAACAT-TCGTATGAGATTT
1 TGATAACCTCTC-TATGAAATTT
* * **
20793 TGTTAACCTCCCTAAAAAATTT
1 TGATAACCTCTCTATGAAATTT
** * *
20815 TGATAAAGTTTTTATGAAATTT
1 TGATAACCTCTCTATGAAATTT
*
20837 TGATAACCTCTGTATGAAATTT
1 TGATAACCTCTCTATGAAATTT
* * * *
20859 TGATAA-CTACACAATGAAGTGT
1 TGATAACCT-CTCTATGAAATTT
*
20881 TGATAACCTC-CATATGAATTTT
1 TGATAACCTCTC-TATGAAATTT
* * *
20903 TGGT-AGCTATACTATGAAATTT
1 TGATAACCTCT-CTATGAAATTT
* *
20925 TAATAACCT-TCCTATGTAATTT
1 TGATAACCTCT-CTATGAAATTT
20947 TG
1 TG
20949 GTTTGATTGT
Statistics
Matches: 227, Mismatches: 61, Indels: 48
0.68 0.18 0.14
Matches are distributed among these distances:
16 12 0.05
17 1 0.00
18 1 0.00
21 8 0.04
22 160 0.70
23 8 0.04
24 2 0.01
25 2 0.01
26 32 0.14
27 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (22 bp):
TGATAACCTCTCTATGAAATTT
Found at i:20770 original size:112 final size:108
Alignment explanation
Indices: 20621--20820 Score: 258
Period size: 112 Copynumber: 1.8 Consensus size: 108
20611 ACTGTGATAT
* * * * *
20621 CCTCTCTATGTAATTTTGATAACCTCTCCATAAAATTTTC-ATAACCTCCATATGAAATTTTGTT
1 CCTCCCTATGAAATTTTGATAACCACACCATAAAA-TTTCAATAACATCCATATGAAATTTTG--
*
20685 AATTAACCTCCCTAAGAAATTTTGATAAGCACAAATTTTGATAACCTC
63 --TTAACCTCCCTAAAAAATTTTGATAAGCACAAATTTTGATAACCTC
* * * *
20733 CCTCCCTATGAAATTTTGATAACCACACTATAAAATTTCAATAACATTCGTATGAGATTTTGTTA
1 CCTCCCTATGAAATTTTGATAACCACACCATAAAATTTCAATAACATCCATATGAAATTTTGTTA
20798 ACCTCCCTAAAAAATTTTGATAA
66 ACCTCCCTAAAAAATTTTGATAA
20821 AGTTTTTATG
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
108 25 0.32
111 4 0.05
112 48 0.62
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.36
Consensus pattern (108 bp):
CCTCCCTATGAAATTTTGATAACCACACCATAAAATTTCAATAACATCCATATGAAATTTTGTTA
ACCTCCCTAAAAAATTTTGATAAGCACAAATTTTGATAACCTC
Found at i:23172 original size:16 final size:16
Alignment explanation
Indices: 23151--23186 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
23141 ATCAATAAAA
23151 AAAGTTGAATGACTAT
1 AAAGTTGAATGACTAT
23167 AAAGTTGAATGACTAT
1 AAAGTTGAATGACTAT
23183 AAAG
1 AAAG
23187 AATATACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (16 bp):
AAAGTTGAATGACTAT
Found at i:23289 original size:8 final size:8
Alignment explanation
Indices: 23276--23300 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
23266 TTTTATATAG
23276 TAGTAAGA
1 TAGTAAGA
23284 TAGTAAGA
1 TAGTAAGA
23292 TAGTAAGA
1 TAGTAAGA
23300 T
1 T
23301 GATACTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (8 bp):
TAGTAAGA
Found at i:24600 original size:12 final size:12
Alignment explanation
Indices: 24583--24610 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
24573 CTGGAGCACT
24583 GGTGATGGTGGA
1 GGTGATGGTGGA
24595 GGTGATGGTGGA
1 GGTGATGGTGGA
24607 GGTG
1 GGTG
24611 GTGGCGGCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.61, T:0.25
Consensus pattern (12 bp):
GGTGATGGTGGA
Done.