Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015298.1 Corchorus olitorius cultivar O-4 contig15331, 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: 12778
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:2406 original size:27 final size:26
Alignment explanation
Indices: 2369--2467 Score: 90
Period size: 27 Copynumber: 3.7 Consensus size: 26
2359 AGTGAGCTTA
*
2369 AAATGACCAAAATGCCCCTAAATATGT
1 AAATGA-CAAAATGCCCCTAAATATGC
* *
2396 AAATGATCAAAATGCCCCTGAATGTGC
1 AAATGA-CAAAATGCCCCTAAATATGC
* ** **
2423 AAATGACAAAAATGGCCCTGGACGTGC
1 AAATGAC-AAAATGCCCCTAAATATGC
2450 AAATGACAAAAATGCCCC
1 AAATGAC-AAAATGCCCC
2468 ATAGATGACC
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
26 1 0.02
27 62 0.98
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.18
Consensus pattern (26 bp):
AAATGACAAAATGCCCCTAAATATGC
Found at i:3027 original size:30 final size:30
Alignment explanation
Indices: 2987--3337 Score: 494
Period size: 30 Copynumber: 11.8 Consensus size: 30
2977 TTAACCGATG
2987 AAGCAATGATCCT-AAACCCA-GATTAAAATA
1 AAGCAATGATCCTCAAA--CAGGATTAAAATA
* * *
3017 AAGCGATGATCCTCAACCAAGATTAAAAT-
1 AAGCAATGATCCTCAAACAGGATTAAAATA
* *
3046 -AGCAATGATCCTCAACCAGGAGTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
* * *
3075 AAGCAATGATCCTCAACCATGATTAAAATG
1 AAGCAATGATCCTCAAACAGGATTAAAATA
3105 AAGCAATGATCCTCAAACAGGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
*
3135 AAGCAATGATCCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
*
3165 AAGCAATGATCCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
*
3195 AAGCAATGATCCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
*
3225 AAGCAATGATCCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
* * *
3255 AAGCAGTGCTCCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
* *
3285 AAGCAACGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAAAATA
*
3315 AAGCAATGATCCTCAACCAGGAT
1 AAGCAATGATCCTCAAACAGGAT
3338 CAAAGTGAAC
Statistics
Matches: 297, Mismatches: 20, Indels: 8
0.91 0.06 0.02
Matches are distributed among these distances:
28 25 0.08
29 2 0.01
30 268 0.90
31 2 0.01
ACGTcount: A:0.46, C:0.21, G:0.14, T:0.20
Consensus pattern (30 bp):
AAGCAATGATCCTCAAACAGGATTAAAATA
Found at i:3674 original size:35 final size:35
Alignment explanation
Indices: 3611--4054 Score: 442
Period size: 35 Copynumber: 12.6 Consensus size: 35
3601 CATTTTGTAG
* *
3611 TCAATTGAAATAAACTGCAGAGAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGA-AAGATCGCCCTGGA
* * * *
3647 TCTACCGAAGTAAATTGAAGAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * *
3682 TGAACTGAAATAAACTGAATAAAGATCGCCATGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * *
3717 TCAACTGAAATAAATTAAAGAAAGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* *
3752 TCAACTAAAATAAACTGAAGAAAGGATCGCCCTAGA
1 TCAACTGAAATAAACTGAAGAAA-GATCGCCCTGGA
* *
3788 TCAACTGAAATAAACTGAAGAAAGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* *
3823 TCAACTGAAATAAACTAAAGAAAGA-CTGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGATC-GCCCTGGA
*
3858 TCAACTGAAATAAACTGAAGAAAGGATCACCCTGGA
1 TCAACTGAAATAAACTGAAGAAA-GATCGCCCTGGA
* * * *
3894 TCAAACTGAAATAAACTGAA-ATAGGACCACCCTGGG
1 TC-AACTGAAATAAACTGAAGA-AAGATCGCCCTGGA
* * * * * *
3930 TCAATTGAAATGAATTGAATAAGGATCACCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * * *
3965 TCAACTGAAGTGAATTGAAGAAAGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * * *
4000 TCAGCTGAAATAAACTGGATAAAGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
*
4035 TCAACTGAAATGAACTGAAG
1 TCAACTGAAATAAACTGAAG
4055 CATCTGAATT
Statistics
Matches: 342, Mismatches: 59, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
34 1 0.00
35 252 0.74
36 70 0.20
37 19 0.06
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.18
Consensus pattern (35 bp):
TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
Found at i:3795 original size:106 final size:105
Alignment explanation
Indices: 3610--4045 Score: 496
Period size: 106 Copynumber: 4.1 Consensus size: 105
3600 CCATTTTGTA
* * ** * * * * * *
3610 GTCAATTGAAATAAACTGCAGAGAAGATCGCCCTGGATCTACCGAAGTAAATTGAAGAAAGATCG
1 GTCAACTGAAATAAATTAAAGA-AAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGATCG
* * *
3675 CCCTGGATGAACTGAAATAAACTGAATAAAGATCGCCATGG
65 CCCTGGATCAACTGAAATAAACTGAATAAAGACCGCCCTGG
*
3716 GTCAACTGAAATAAATTAAAGAAAGACCGCCCTGGGTCAACTAAAATAAACTGAAGAAAGGATCG
1 GTCAACTGAAATAAATTAAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAA-GATCG
* *
3781 CCCTAGATCAACTGAAATAAACTGAAGAAAGACCGCCCTGG
65 CCCTGGATCAACTGAAATAAACTGAATAAAGACCGCCCTGG
* * *
3822 GTCAACTGAAATAAACTAAAGAAAGACTGCCCTGGGTCAACTGAAATAAACTGAAGAAAGGATCA
1 GTCAACTGAAATAAATTAAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAA-GATCG
* *
3887 CCCTGGATCAAACTGAAATAAACTGAA-ATAGGACCACCCTGG
65 CCCTGGATC-AACTGAAATAAACTGAATA-AAGACCGCCCTGG
* * * * * * * * * * * *
3929 GTCAATTGAAATGAATTGAATAAGGATCACCCTGGATCAACTGAAGTGAATTGAAGAAAGACCGC
1 GTCAACTGAAATAAATTAAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGATCGC
* * *
3994 CCTGGGTCAGCTGAAATAAACTGGATAAAGACCGCCCTGG
66 CCTGGATCAACTGAAATAAACTGAATAAAGACCGCCCTGG
4034 GTCAACTGAAAT
1 GTCAACTGAAAT
4046 GAACTGAAGC
Statistics
Matches: 282, Mismatches: 44, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
105 67 0.24
106 141 0.50
107 74 0.26
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.18
Consensus pattern (105 bp):
GTCAACTGAAATAAATTAAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGATCGC
CCTGGATCAACTGAAATAAACTGAATAAAGACCGCCCTGG
Found at i:5615 original size:14 final size:13
Alignment explanation
Indices: 5581--5621 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
5571 AGCATCCTCG
* *
5581 TGAAAACAAATTT
1 TGAAAACCATTTT
5594 TGAAAACCATTTT
1 TGAAAACCATTTT
5607 TGAAAAACCATTTT
1 TG-AAAACCATTTT
5621 T
1 T
5622 TTTTGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (13 bp):
TGAAAACCATTTT
Done.