Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014667.1 Corchorus capsularis cultivar CVL-1 contig14688, 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: 28042
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:14254 original size:20 final size:21
Alignment explanation
Indices: 14229--14267 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
14219 TTTTTATAGT
*
14229 TATTTTTCTATAT-TTTTTGC
1 TATTTTTATATATGTTTTTGC
14249 TATTTTTATATATGTTTTT
1 TATTTTTATATATGTTTTT
14268 ACCCTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.72
Consensus pattern (21 bp):
TATTTTTATATATGTTTTTGC
Found at i:26443 original size:9 final size:9
Alignment explanation
Indices: 26429--26456 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
26419 TTAATTACGG
26429 TCTTAAACA
1 TCTTAAACA
26438 TCTTAAACA
1 TCTTAAACA
26447 TCTTAAACA
1 TCTTAAACA
26456 T
1 T
26457 ATAAACTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (9 bp):
TCTTAAACA
Found at i:26609 original size:22 final size:23
Alignment explanation
Indices: 26566--26610 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
26556 GTTTATAAGT
*
26566 AAAATAAAAAAAAATATTTTAAA
1 AAAATAAAAAAAAATATGTTAAA
26589 AAAATAAAAGAAAAA-A-GTTAAA
1 AAAATAAAA-AAAAATATGTTAAA
26611 GGATTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 10 0.50
24 5 0.25
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (23 bp):
AAAATAAAAAAAAATATGTTAAA
Found at i:26978 original size:221 final size:220
Alignment explanation
Indices: 26575--26979 Score: 461
Period size: 220 Copynumber: 1.8 Consensus size: 220
26565 TAAAATAAAA
* * * * **
26575 AAAAATATTTTAAAAAAATAAAAGAAAAAAGTTAAAGGATTAAATTGTATATAGTAAAATTAGGA
1 AAAAATATTTTAAAAAAATAAAAGAAAAAAATTAAAAGATTAAATTGTATAGAATAAAATTAAAA
* * * * *
26640 TGGACTAAATTGCATAGAATAAAAATGTTTGAGTGTATTCTATGAAAGGAATAAAGTTGAAGGGT
66 TAGACTAAATTGCATAGAAGAAAAATATATGAGTGTATTCTATGAAAAGAATAAAGTTGAAGGGT
* *
26705 TAAATCGTATAAAAAGAAATAATAGAGAGACCAAATAGAATAAAATAAATATTTTACGTTATATT
131 TAAATCGTATAAAAAGAAATAATAAAGAGACCAAATAGAATAAAAAAAATATTTTACGTTATATT
26770 TAAAGGGTATTAATAAGTAAAATTT
196 TAAAGGGTATTAATAAGTAAAATTT
*
26795 AAAAATATTTT-TAAAAATAAAAGAAATAAAATTAAAAGATTAAATTGTATAGAATAAAGTATTT
1 AAAAATATTTTAAAAAAATAAAAGAAA-AAAATTAAAAGATTAAATTGTATAGAATAAA--A-TT
* * * * *
26859 AAAATAG-C-AAATTGCATTGAAGAAAAATATATGAGGGTGT-TTCTGTGAAAATATTAAA-TTT
62 AAAATAGACTAAATTGCATAGAAGAAAAATATATGA--GTGTATTCTATGAAAAGAATAAAGTTG
*
26920 AAGGGTTAAAT-G-ATATAAAA-AAATAATATAAG-GACTAAATTA-AATAAAGTAAAAATATTT
125 AAGGGTTAAATCGTATA-AAAAGAAATAATA-AAGAGACCAAA-TAGAATAAA--AAAAATATTT
26980 GAGGACTATT
Statistics
Matches: 154, Mismatches: 20, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
219 37 0.24
220 47 0.31
221 44 0.29
222 16 0.10
223 10 0.06
ACGTcount: A:0.52, C:0.03, G:0.14, T:0.31
Consensus pattern (220 bp):
AAAAATATTTTAAAAAAATAAAAGAAAAAAATTAAAAGATTAAATTGTATAGAATAAAATTAAAA
TAGACTAAATTGCATAGAAGAAAAATATATGAGTGTATTCTATGAAAAGAATAAAGTTGAAGGGT
TAAATCGTATAAAAAGAAATAATAAAGAGACCAAATAGAATAAAAAAAATATTTTACGTTATATT
TAAAGGGTATTAATAAGTAAAATTT
Found at i:27906 original size:7 final size:7
Alignment explanation
Indices: 27896--27921 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
27886 CTTTTCTCAA
27896 GTAAATT
1 GTAAATT
27903 GTAAATT
1 GTAAATT
27910 GTAAATT
1 GTAAATT
27917 GTAAA
1 GTAAA
27922 AAGCTTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (7 bp):
GTAAATT
Done.