Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015618.1 Corchorus olitorius cultivar O-4 contig15651, 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: 34880
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:333 original size:17 final size:17
Alignment explanation
Indices: 292--335 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
282 TTTTGAGGAG
*
292 CTAATAAGGGAATGGGCT
1 CTAA-AAGGAAATGGGCT
*
310 TTAAAAGGAAATGGGCT
1 CTAAAAGGAAATGGGCT
*
327 CTGAAAGGA
1 CTAAAAGGA
336 TTAAACCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.39, C:0.09, G:0.32, T:0.20
Consensus pattern (17 bp):
CTAAAAGGAAATGGGCT
Found at i:5632 original size:17 final size:18
Alignment explanation
Indices: 5610--5645 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
5600 CAGTAATTTC
*
5610 TTTTTCTTTTTCCT-TCT
1 TTTTTCATTTTCCTATCT
5627 TTTTTCATTTTCCTATCT
1 TTTTTCATTTTCCTATCT
5645 T
1 T
5646 GTAATGACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTCATTTTCCTATCT
Found at i:5839 original size:20 final size:20
Alignment explanation
Indices: 5810--5855 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
5800 GATCCTGCAG
* *
5810 ATGC-AAATGTGAGATTAAT
1 ATGCAAAATGTGACATAAAT
5829 ATGCAAAATGTGACATAAAT
1 ATGCAAAATGTGACATAAAT
5849 ATGCAAA
1 ATGCAAA
5856 GGAACACAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.26
Consensus pattern (20 bp):
ATGCAAAATGTGACATAAAT
Found at i:6007 original size:27 final size:28
Alignment explanation
Indices: 5946--6027 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 28
5936 TGAGCAATGG
* *
5946 AGTAAAAATGACCACAATGCCTCCT-GA-
1 AGTACAAATGACCAAAATGCC-CCTAGAT
5973 AGTACAAATGACCAAAATGCCCCTAGAT
1 AGTACAAATGACCAAAATGCCCCTAGAT
* *
6001 A-TGCAAATGACTAAAATGCCCCTAGAT
1 AGTACAAATGACCAAAATGCCCCTAGAT
6028 GACCCTAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
26 3 0.06
27 45 0.92
28 1 0.02
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (28 bp):
AGTACAAATGACCAAAATGCCCCTAGAT
Found at i:9861 original size:28 final size:28
Alignment explanation
Indices: 9828--9892 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
9818 TGGTTTCCGA
9828 CTTGGGCTTTCAATGTTT-ATGTTATGCAT
1 CTTGGGCTTTCAAT-TTTCAT-TTATGCAT
* *
9857 -TTGGGCTTTTAATTTTCCTTTATGCAT
1 CTTGGGCTTTCAATTTTCATTTATGCAT
9884 CTTGGGCTT
1 CTTGGGCTT
9893 ATTTGGGCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 11 0.34
28 21 0.66
ACGTcount: A:0.14, C:0.15, G:0.20, T:0.51
Consensus pattern (28 bp):
CTTGGGCTTTCAATTTTCATTTATGCAT
Found at i:11938 original size:75 final size:75
Alignment explanation
Indices: 11870--12016 Score: 179
Period size: 74 Copynumber: 2.0 Consensus size: 75
11860 ATAGGAAACC
** * *
11870 TAATAAGGTTTATCAACTTCAAGATGTTGCATATCATCATTA-GAAACTTAGAATTTGAATTCAA
1 TAATAAGGTAAATCAACTTCAAGATGTTGCATAACATCATTAGGAAACTCAGAATTTGAATTCAA
11934 AATAGCAATA
66 AATAGCAATA
* * * * * **
11944 TGATCAGGTAAATCATCTTCAAGATGTTGCCTAACGTCATTAGGAAACTCATTATTTGAATTCAA
1 TAATAAGGTAAATCAACTTCAAGATGTTGCATAACATCATTAGGAAACTCAGAATTTGAATTCAA
*
12009 ATTAGCAA
66 AATAGCAA
12017 CCTTAGAAGG
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
74 34 0.57
75 26 0.43
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (75 bp):
TAATAAGGTAAATCAACTTCAAGATGTTGCATAACATCATTAGGAAACTCAGAATTTGAATTCAA
AATAGCAATA
Found at i:23178 original size:30 final size:30
Alignment explanation
Indices: 23142--23207 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
23132 AATAGTTAAT
23142 AAGTCATTAAAATTTGAGGGTATAAGAGAA
1 AAGTCATTAAAATTTGAGGGTATAAGAGAA
* *
23172 AAGTCATTAAAATTTGAGTGTATAAGAGGA
1 AAGTCATTAAAATTTGAGGGTATAAGAGAA
23202 AAGTCA
1 AAGTCA
23208 AGATAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.45, C:0.05, G:0.23, T:0.27
Consensus pattern (30 bp):
AAGTCATTAAAATTTGAGGGTATAAGAGAA
Found at i:23434 original size:13 final size:13
Alignment explanation
Indices: 23416--23443 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
23406 CCAAACGCAA
23416 ATTATATATATAT
1 ATTATATATATAT
23429 ATTATATATATAT
1 ATTATATATATAT
23442 AT
1 AT
23444 AAATTCAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTATATATATAT
Found at i:23500 original size:27 final size:28
Alignment explanation
Indices: 23470--23523 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
23460 TATATTTATT
* *
23470 AGTTAGTAGTATTTTTTT-TTCAAAAAA
1 AGTTAGTAGCATTTTTTTAATCAAAAAA
*
23497 AGTTATTAGCATTTTTTTAATCAAAAA
1 AGTTAGTAGCATTTTTTTAATCAAAAA
23524 GACAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (28 bp):
AGTTAGTAGCATTTTTTTAATCAAAAAA
Found at i:33367 original size:18 final size:18
Alignment explanation
Indices: 33336--33373 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
33326 TTATTCTTCT
*
33336 AATATTATTTTTTTAATTA
1 AATATTATTATTTT-ATTA
33355 AATA-TATTATTTTATTA
1 AATATTATTATTTTATTA
33372 AA
1 AA
33374 AAATTCTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 8 0.44
19 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
AATATTATTATTTTATTA
Done.