Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012296.1 Corchorus olitorius cultivar O-4 contig12329, 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: 12849
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.31
Found at i:1121 original size:2 final size:2
Alignment explanation
Indices: 1114--1173 Score: 79
Period size: 2 Copynumber: 31.0 Consensus size: 2
1104 ACAGACTTAA
* *
1114 AT AT AT AT AT A- AT AT TT AT AT AT AT AT AT AT TT A- 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
*
1154 AT AT AT AT AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1174 TAAATGATGA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5678 original size:2 final size:2
Alignment explanation
Indices: 5671--5695 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5661 TTATATTGTT
5671 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5696 TACTACAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9901 original size:4 final size:4
Alignment explanation
Indices: 9887--9968 Score: 71
Period size: 4 Copynumber: 20.2 Consensus size: 4
9877 AATTATATTA
* *
9887 AAAT AAAAT AAAT AAAT -AAT AGAT AAAT AAAT AAAT AGAT AGAA- AAAT
1 AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT
* *
9935 AAAT AAAA ATAAT AGAT AAAT AAA- AAGAT AAAT A
1 AAAT AAAT A-AAT AAAT AAAT AAAT AA-AT AAAT A
9969 GGTATATAGA
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
3 7 0.11
4 46 0.73
5 10 0.16
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:10011 original size:8 final size:8
Alignment explanation
Indices: 9894--10104 Score: 92
Period size: 8 Copynumber: 27.6 Consensus size: 8
9884 TTAAAATAAA
*
9894 ATAAATAA
1 ATAAATAG
9902 AT-AATAG
1 ATAAATAG
*
9909 ATAAATAA
1 ATAAATAG
9917 ATAAATAG
1 ATAAATAG
*
9925 ATAGAA-AA
1 ATA-AATAG
9933 ATAAATA-
1 ATAAATAG
9940 A-AAATA-
1 ATAAATAG
* *
9946 ATAGATAA
1 ATAAATAG
*
9954 ATAAAAAG
1 ATAAATAG
9962 ATAAATAG
1 ATAAATAG
* *
9970 GTATATAG
1 ATAAATAG
*
9978 ATAATTAG
1 ATAAATAG
*
9986 ATAAAGAG
1 ATAAATAG
* * *
9994 GTATAGAG
1 ATAAATAG
10002 ATAAATAG
1 ATAAATAG
10010 ATAAATAG
1 ATAAATAG
* **
10018 GTAGGTA-
1 ATAAATAG
* *
10025 AAAAAAAG
1 ATAAATAG
10033 AT-AATAG
1 ATAAATAG
10040 CTAATAAATAG
1 ---ATAAATAG
10051 AT-AATAG
1 ATAAATAG
*
10058 CTAAATTA-
1 ATAAA-TAG
10066 ATAAAT--
1 ATAAATAG
10072 A-AAA-AG
1 ATAAATAG
10078 ATAAATAG
1 ATAAATAG
*
10086 -TAAATAA
1 ATAAATAG
10093 AT-AATAG
1 ATAAATAG
10100 ATAAA
1 ATAAA
10105 ATAGCTATAA
Statistics
Matches: 150, Mismatches: 35, Indels: 36
0.68 0.16 0.16
Matches are distributed among these distances:
5 3 0.02
6 8 0.05
7 41 0.27
8 87 0.58
9 4 0.03
10 2 0.01
11 5 0.03
ACGTcount: A:0.63, C:0.01, G:0.12, T:0.24
Consensus pattern (8 bp):
ATAAATAG
Found at i:10073 original size:27 final size:26
Alignment explanation
Indices: 10041--10111 Score: 76
Period size: 27 Copynumber: 2.8 Consensus size: 26
10031 AGATAATAGC
*
10041 TAATAAATAGATAATAGCTAAATTAA
1 TAATAAATAGATAATAGCTAAATAAA
*
10067 TAAATAAAAAGATAAATAG-TAAATAAA
1 T-AATAAATAGAT-AATAGCTAAATAAA
*
10094 TAATAGATA-A-AATAGCTA
1 TAATAAATAGATAATAGCTA
10112 TAAAAAAATC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
23 5 0.13
24 2 0.05
25 1 0.03
26 7 0.18
27 18 0.47
28 5 0.13
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.27
Consensus pattern (26 bp):
TAATAAATAGATAATAGCTAAATAAA
Found at i:12375 original size:15 final size:16
Alignment explanation
Indices: 12349--12378 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12339 GCAGAGGGTT
12349 AAGAATAACAATTAAG
1 AAGAATAACAATTAAG
12365 AAGAA-AACAATTAA
1 AAGAATAACAATTAA
12379 ACTAGAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.07, G:0.10, T:0.17
Consensus pattern (16 bp):
AAGAATAACAATTAAG
Done.