Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005983.1 Corchorus capsularis cultivar CVL-1 contig06001, 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: 12561
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Found at i:2638 original size:25 final size:25
Alignment explanation
Indices: 2610--2662 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
2600 TCTTTCCAAC
2610 ACCAAAATCAAATCTGGGTTTCTGT
1 ACCAAAATCAAATCTGGGTTTCTGT
*
2635 ACCAAAATCAATTCTGGGTTTCTGT
1 ACCAAAATCAAATCTGGGTTTCTGT
2660 ACC
1 ACC
2663 TGACAGGTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (25 bp):
ACCAAAATCAAATCTGGGTTTCTGT
Found at i:4853 original size:17 final size:18
Alignment explanation
Indices: 4833--4866 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
4823 TTGGAGCATC
4833 GAAGAAGAA-GGAGAAAG
1 GAAGAAGAAGGGAGAAAG
4850 GAAGAAGAAGGGAGAAA
1 GAAGAAGAAGGGAGAAA
4867 ACAGTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (18 bp):
GAAGAAGAAGGGAGAAAG
Found at i:5059 original size:8 final size:8
Alignment explanation
Indices: 5046--5098 Score: 58
Period size: 8 Copynumber: 6.9 Consensus size: 8
5036 ATTGTTATAG
5046 TGATGATT
1 TGATGATT
5054 TGATGATT
1 TGATGATT
5062 TGATG--T
1 TGATGATT
* *
5068 TG-TTATAG
1 TGATGAT-T
5076 TGATGATT
1 TGATGATT
5084 TGATGATT
1 TGATGATT
5092 TGATGAT
1 TGATGAT
5099 GATTTTGGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 1 0.03
6 3 0.08
8 30 0.81
9 3 0.08
ACGTcount: A:0.25, C:0.00, G:0.26, T:0.49
Consensus pattern (8 bp):
TGATGATT
Found at i:5072 original size:30 final size:30
Alignment explanation
Indices: 5037--5096 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
5027 TGTGTTTGTA
5037 TTGTTATAGTGATGATTTGATGATTTGATG
1 TTGTTATAGTGATGATTTGATGATTTGATG
5067 TTGTTATAGTGATGATTTGATGATTTGATG
1 TTGTTATAGTGATGATTTGATGATTTGATG
5097 ATGATTTTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (30 bp):
TTGTTATAGTGATGATTTGATGATTTGATG
Found at i:6525 original size:29 final size:29
Alignment explanation
Indices: 6490--6547 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
6480 AGTTTTCAAA
6490 GCAAAATAAAAGACTTAAAACACAAAAAT
1 GCAAAATAAAAGACTTAAAACACAAAAAT
6519 GCAAAATAAAAGACTTAAAACACAAAAAT
1 GCAAAATAAAAGACTTAAAACACAAAAAT
6548 AAAAGTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.66, C:0.14, G:0.07, T:0.14
Consensus pattern (29 bp):
GCAAAATAAAAGACTTAAAACACAAAAAT
Found at i:10350 original size:3 final size:3
Alignment explanation
Indices: 10307--10337 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
10297 ATTATATATT
10307 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
10338 CTTGAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:11195 original size:2 final size:2
Alignment explanation
Indices: 11188--11230 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
11178 AAACTACTAA
* *
11188 AT AT AT AT AT AT AT AT AT TT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11230 A
1 A
11231 GTGACTAGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11820 original size:4 final size:4
Alignment explanation
Indices: 11811--11846 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
11801 ATATACATAG
*
11811 AAGA AAGA AAGA AAGA AGGA AAGA AAGA AA-A AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA A
11847 CTAAAAACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAGA
Done.