Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018137.1 Corchorus olitorius cultivar O-4 contig18170, 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: 39589
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:8574 original size:23 final size:21
Alignment explanation
Indices: 8542--8583 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
8532 ATATTGTTTA
*
8542 TAATTTATTTATTTTTGATTAGT
1 TAATTAATTT-TTTTT-ATTAGT
8565 TAATTAATTTTTTTTATTA
1 TAATTAATTTTTTTTATTA
8584 ATGCTTGCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 5 0.28
23 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (21 bp):
TAATTAATTTTTTTTATTAGT
Found at i:17257 original size:76 final size:76
Alignment explanation
Indices: 17100--17258 Score: 180
Period size: 76 Copynumber: 2.1 Consensus size: 76
17090 CTTACATTTT
* *
17100 TTTTTTTATAAATAATGGTCAAACATTAAACTTGTTAGACCAAGAGTGAATATCTAATTAGAGAC
1 TTTTTTTATAAATAATGGTCAAACATTAAACTTGTTAGACCAAAAGTGAACATCTAATTAGAGAC
17165 AGGGAGAGTAC
66 AGGGAGAGTAC
* * * * * * *
17176 CTTTTTTATAAATAATGGTCAAATATT-GAGTT-TATATGACTAAAAGTGGACATCTAATTAGGG
1 TTTTTTTATAAATAATGGTCAAACATTAAACTTGT-TA-GACCAAAAGTGAACATCTAATTAGAG
*
17239 ACAGAGG-GAGTGC
64 ACAG-GGAGAGTAC
17252 TTTTTTT
1 TTTTTTT
17259 TTCCATGAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
74 1 0.01
75 5 0.07
76 61 0.88
77 2 0.03
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.35
Consensus pattern (76 bp):
TTTTTTTATAAATAATGGTCAAACATTAAACTTGTTAGACCAAAAGTGAACATCTAATTAGAGAC
AGGGAGAGTAC
Found at i:27265 original size:47 final size:47
Alignment explanation
Indices: 27196--27289 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
27186 CTCTGGGTCT
*
27196 CGATTAATCCATAGTCGAGCCGTGTTGAACCCCCAAGTCAGGGAAAA
1 CGATTAATCCAGAGTCGAGCCGTGTTGAACCCCCAAGTCAGGGAAAA
27243 CGATTAATCCAGAGTCGAGCCGTGTTGAACCCCCAAGTCAGGGAAAA
1 CGATTAATCCAGAGTCGAGCCGTGTTGAACCCCCAAGTCAGGGAAAA
27290 TTCTCCTGGC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (47 bp):
CGATTAATCCAGAGTCGAGCCGTGTTGAACCCCCAAGTCAGGGAAAA
Found at i:31742 original size:22 final size:18
Alignment explanation
Indices: 31694--31732 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
31684 TTAGAGTACT
*
31694 CTACAGGCCCAGGTGATG
1 CTACAGGTCCAGGTGATG
31712 CTACAGGTCCAGGTGATG
1 CTACAGGTCCAGGTGATG
31730 CTA
1 CTA
31733 AGCCAAGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.26, G:0.31, T:0.21
Consensus pattern (18 bp):
CTACAGGTCCAGGTGATG
Found at i:34231 original size:23 final size:21
Alignment explanation
Indices: 34190--34231 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
34180 TTTCTAATAC
*
34190 ATATTTTTTTAAAATTAAATT
1 ATATTTTTTTAAAAATAAATT
34211 ATATATTTTTTAATAAATAAA
1 ATAT-TTTTTTAA-AAATAAA
34232 AGTAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 8 0.44
23 6 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATATTTTTTTAAAAATAAATT
Found at i:36126 original size:6 final size:6
Alignment explanation
Indices: 36091--36125 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
36081 GTTTTATTCT
*
36091 CAATGG CAATGG CAATGG CAATGG CAATGT CAATG
1 CAATGG CAATGG CAATGG CAATGG CAATGG CAATG
36126 TAGAGCAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (6 bp):
CAATGG
Found at i:38987 original size:24 final size:25
Alignment explanation
Indices: 38954--39010 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
38944 GTCAGCATTG
*
38954 AATTT-TTTAATGT-TTAATTCTTA
1 AATTTATTTAATGTCTTAATTATTA
*
38977 AATTTATTTAATGTCTTAATTATTC
1 AATTTATTTAATGTCTTAATTATTA
39002 AATTTATTT
1 AATTTATTT
39011 TACAATCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (25 bp):
AATTTATTTAATGTCTTAATTATTA
Done.