Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005760.1 Corchorus capsularis cultivar CVL-1 contig05778, 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: 10749
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.34
Found at i:3112 original size:15 final size:14
Alignment explanation
Indices: 3094--3164 Score: 64
Period size: 15 Copynumber: 5.3 Consensus size: 14
3084 TATCATTAAT
3094 TAATTAATCATAAAC
1 TAATTAAT-ATAAAC
3109 TAATTAA-AT--AC
1 TAATTAATATAAAC
3120 TAATTAATTATAAAC
1 TAATTAA-TATAAAC
3135 TAATT-ATAT--AC
1 TAATTAATATAAAC
*
3146 TAATTAAACATAAAC
1 TAATT-AATATAAAC
3161 TAAT
1 TAAT
3165 AAACTAAGTA
Statistics
Matches: 47, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
11 16 0.34
13 10 0.21
14 1 0.02
15 20 0.43
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.37
Consensus pattern (14 bp):
TAATTAATATAAAC
Found at i:3124 original size:26 final size:26
Alignment explanation
Indices: 3094--3164 Score: 115
Period size: 26 Copynumber: 2.7 Consensus size: 26
3084 TATCATTAAT
3094 TAATTAATCATAAACTAATTAAATAC
1 TAATTAATCATAAACTAATTAAATAC
* *
3120 TAATTAATTATAAACTAATTATATAC
1 TAATTAATCATAAACTAATTAAATAC
*
3146 TAATTAAACATAAACTAAT
1 TAATTAATCATAAACTAAT
3165 AAACTAAGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.37
Consensus pattern (26 bp):
TAATTAATCATAAACTAATTAAATAC
Found at i:3203 original size:52 final size:52
Alignment explanation
Indices: 3095--3204 Score: 125
Period size: 52 Copynumber: 2.1 Consensus size: 52
3085 ATCATTAATT
* * * * *
3095 AATTAATCATAAACTAATTAAATACTAATTAATTATAAACTAATTATATACT
1 AATTAAACATAAACTAATTAAATACTAACTAATTATAAACTAATCATAAACA
* *
3147 AATTAAACATAAACTAA-TAAACTAAGTAACTAATTA-AAATTAATCATAAACA
1 AATTAAACATAAACTAATTAAA-T-ACTAACTAATTATAAACTAATCATAAACA
3199 AATTAA
1 AATTAA
3205 TATTAAAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
51 4 0.08
52 35 0.71
53 10 0.20
ACGTcount: A:0.56, C:0.10, G:0.01, T:0.33
Consensus pattern (52 bp):
AATTAAACATAAACTAATTAAATACTAACTAATTATAAACTAATCATAAACA
Found at i:7747 original size:2 final size:2
Alignment explanation
Indices: 7740--7770 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7730 ATTTCAATTC
7740 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7771 CTAGTAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8237 original size:2 final size:2
Alignment explanation
Indices: 8230--8257 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8220 TTTAATTTTA
8230 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8258 TATGTACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8755 original size:19 final size:20
Alignment explanation
Indices: 8719--8756 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
8709 TAACCAGTTA
**
8719 TAAAAAAACTTTAGAGGTTT
1 TAAAAAAAAATTAGAGGTTT
8739 TAAAAAAAAATTA-AGGTT
1 TAAAAAAAAATTAGAGGTT
8757 ATAACTTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.32
Consensus pattern (20 bp):
TAAAAAAAAATTAGAGGTTT
Done.