Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013997.1 Corchorus olitorius cultivar O-4 contig14030, 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: 8399
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Found at i:4944 original size:16 final size:17
Alignment explanation
Indices: 4870--4945 Score: 52
Period size: 16 Copynumber: 4.6 Consensus size: 17
4860 AAAAATTATT
*
4870 AAAATAAATATATAAAA
1 AAAATAAATAGATAAAA
* *
4887 AAAGT-AATAGATAAAT
1 AAAATAAATAGATAAAA
* * **
4903 AGAA-AAATAAGTTTTAA
1 AAAATAAAT-AGATAAAA
4920 AAAAT-AATA-ATAAAA
1 AAAATAAATAGATAAAA
4935 AAAATAAATAG
1 AAAATAAATAG
4946 GTATAGAGAT
Statistics
Matches: 41, Mismatches: 13, Indels: 10
0.64 0.20 0.16
Matches are distributed among these distances:
15 8 0.20
16 19 0.46
17 14 0.34
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.24
Consensus pattern (17 bp):
AAAATAAATAGATAAAA
Found at i:4966 original size:24 final size:24
Alignment explanation
Indices: 4938--4996 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
4928 AATAAAAAAA
* *
4938 ATAAATAGGTATAGAGA-TAAATAT
1 ATAAATAGGTACAGAGAGT-AATAG
*
4962 ATAAATAGATACAGAGAGTAATAG
1 ATAAATAGGTACAGAGAGTAATAG
4986 ATAAATAGGTA
1 ATAAATAGGTA
4997 AGTAAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 29 0.97
25 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.19, T:0.25
Consensus pattern (24 bp):
ATAAATAGGTACAGAGAGTAATAG
Found at i:5046 original size:27 final size:25
Alignment explanation
Indices: 5013--5143 Score: 88
Period size: 27 Copynumber: 5.5 Consensus size: 25
5003 AAAAGGATAA
5013 TAATAAATAAATAGTTAATAGCTAAAT
1 TAATAAATAAATAG-TAATAG-TAAAT
5040 TAATAAAT-AA-A--AATA-TAAA-
1 TAATAAATAAATAGTAATAGTAAAT
*
5059 TAGTAAATAAATAGATAATAGTTAAAT
1 TAATAAATAAATAG-TAATAG-TAAAT
*
5086 TAATAAAT-AA-A--AAGA-TAAA-
1 TAATAAATAAATAGTAATAGTAAAT
* *
5105 TATTAAATAAATAGATAATAGTTAAAC
1 TAATAAATAAATAG-TAATAG-TAAAT
5132 TAATAAATAAAT
1 TAATAAATAAAT
5144 CTTTTTGGTC
Statistics
Matches: 82, Mismatches: 6, Indels: 32
0.68 0.05 0.27
Matches are distributed among these distances:
19 14 0.17
20 12 0.15
21 2 0.02
22 7 0.09
24 7 0.09
25 2 0.02
26 12 0.15
27 26 0.32
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.31
Consensus pattern (25 bp):
TAATAAATAAATAGTAATAGTAAAT
Found at i:5069 original size:46 final size:46
Alignment explanation
Indices: 5002--5142 Score: 212
Period size: 46 Copynumber: 3.1 Consensus size: 46
4992 AGGTAAGTAA
* *
5002 AAAAAGGAT-AATAATAAATAAATAGTTAATAGCTAAATTAATAAAT
1 AAAAA-GATAAATAATAAATAAATAGATAATAGTTAAATTAATAAAT
* *
5048 AAAAATATAAATAGTAAATAAATAGATAATAGTTAAATTAATAAAT
1 AAAAAGATAAATAATAAATAAATAGATAATAGTTAAATTAATAAAT
* *
5094 AAAAAGATAAATATTAAATAAATAGATAATAGTTAAACTAATAAAT
1 AAAAAGATAAATAATAAATAAATAGATAATAGTTAAATTAATAAAT
5140 AAA
1 AAA
5143 TCTTTTTGGT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
45 2 0.02
46 85 0.98
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.28
Consensus pattern (46 bp):
AAAAAGATAAATAATAAATAAATAGATAATAGTTAAATTAATAAAT
Found at i:5111 original size:19 final size:20
Alignment explanation
Indices: 5089--5143 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
5079 GTTAAATTAA
5089 TAAATAAAAAGATAAATA-T
1 TAAATAAAAAGATAAATAGT
*
5108 TAAATAAATAGAT-AATAGT
1 TAAATAAAAAGATAAATAGT
*
5127 TAAACTAATAA-ATAAAT
1 TAAA-TAAAAAGATAAAT
5144 CTTTTTGGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 4 0.13
19 19 0.63
20 7 0.23
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAATAAAAAGATAAATAGT
Found at i:5808 original size:4 final size:4
Alignment explanation
Indices: 5801--5833 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
5791 TATATTAGAC
*
5801 TGAT TGAT TGAT TGAG TGAT TGAT TGAT TGAT T
1 TGAT TGAT TGAT TGAT TGAT TGAT TGAT TGAT T
5834 TGAATATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (4 bp):
TGAT
Done.