Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013831.1 Corchorus olitorius cultivar O-4 contig13864, 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: 13231
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Found at i:503 original size:153 final size:153
Alignment explanation
Indices: 1--538 Score: 776
Period size: 153 Copynumber: 3.5 Consensus size: 153
* * * *
1 TTGAGGTTTGCCAAATCGAAGACGATTTAAAACGTCACTGATGGGCCCCGATAGGCCCAAATAAC
1 TTGAGGTTTGCCAAATCGAAGACAATTCAAAACGTAACTAATGGGCCCCGATAGGCCCAAATAA-
66 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
65 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
*
131 CCATAAACAATGGAAAGAAAAGAAA
130 CCATAAACAATGGAAAGAAAAG-CA
* * * * *
156 ATGAGGATTGCCAAATACAAAGACGATTCAAAAACGTCAC-AGATGGGCCCCGATAGGCCCAAAA
1 TTGAGGTTTGCCAAAT-CGAAGACAATTC-AAAACGTAACTA-ATGGGCCCCGATAGGCCC-AAA
*
220 TAACAAGTGTTCCAAATGACCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
62 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* *
285 AGGCCGTACACAATGGAAAGAAAAGCA
127 AGGCCATAAACAATGGAAAGAAAAGCA
* * * * *
312 TTGAGGTTTGCCAAATCGAAGACAATTCAAAACAG-AACTACTAGGCCTCGATTGGCCCAATTAA
1 TTGAGGTTTGCCAAATCGAAGACAATTCAAAAC-GTAACTAATGGGCCCCGATAGGCCCAAATAA
* *
376 CAACTGTTCCAATTGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
65 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
441 CCATAAACAATGGAAAGAAAAGCA
130 CCATAAACAATGGAAAGAAAAGCA
* *
465 TTGAGGTTTGCCAAATCGAAGACAATTCAAAAC-TGAACTAATGGGCCTCGATAGGCACAAAATA
1 TTGAGGTTTGCCAAATCGAAGACAATTCAAAACGT-AACTAATGGGCCCCGATAGGC-CCAAATA
529 ACAAGTGTTC
64 ACAAGTGTTC
539 TGATACGAAT
Statistics
Matches: 344, Mismatches: 30, Indels: 19
0.88 0.08 0.05
Matches are distributed among these distances:
153 140 0.41
154 35 0.10
155 26 0.08
156 25 0.07
157 112 0.33
158 6 0.02
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (153 bp):
TTGAGGTTTGCCAAATCGAAGACAATTCAAAACGTAACTAATGGGCCCCGATAGGCCCAAATAAC
AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
CATAAACAATGGAAAGAAAAGCA
Found at i:1363 original size:21 final size:21
Alignment explanation
Indices: 1339--1472 Score: 200
Period size: 21 Copynumber: 6.4 Consensus size: 21
1329 CTTAGGCATT
*
1339 TCCAATGAGCTTGAAACCTT-C
1 TCCAATGAGCTTGGAA-CTTGC
*
1360 TCCAATGATCTTGGAACCTT-C
1 TCCAATGAGCTTGGAA-CTTGC
* *
1381 TCCAATGAACTTGGAACCTGC
1 TCCAATGAGCTTGGAACTTGC
1402 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
1423 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
1444 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
1465 TCCAATGA
1 TCCAATGA
1473 ACTTCTAGCA
Statistics
Matches: 106, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
20 2 0.02
21 104 0.98
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACTTGC
Found at i:5614 original size:31 final size:30
Alignment explanation
Indices: 5560--5617 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
5550 TGTACATTTC
* *
5560 ATTGGGTCCTTTTGAGTGGGTGTGAAGCAT
1 ATTGGGTACTTTTCAGTGGGTGTGAAGCAT
*
5590 ATTGGGCTACTTTTCAGTGTGTGTGAAG
1 ATTGGG-TACTTTTCAGTGGGTGTGAAG
5618 TATGTTGGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 6 0.25
31 18 0.75
ACGTcount: A:0.17, C:0.10, G:0.34, T:0.38
Consensus pattern (30 bp):
ATTGGGTACTTTTCAGTGGGTGTGAAGCAT
Found at i:11348 original size:18 final size:18
Alignment explanation
Indices: 11327--11362 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
11317 ATCACACTAT
11327 AGTAATTTAATACACATA
1 AGTAATTTAATACACATA
11345 AGTAATTTAATACACATA
1 AGTAATTTAATACACATA
11363 GAAATTAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (18 bp):
AGTAATTTAATACACATA
Done.