Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016152.1 Corchorus olitorius cultivar O-4 contig16185, 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: 8663
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:2551 original size:42 final size:43
Alignment explanation
Indices: 2499--2592 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
2489 AGTGCATTAT
**
2499 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAAATAATTCATCAAAATAAAG
2540 CTAATATTCTACTCCTCCATCTCTAAATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAAATAATTCATCAAAATAAAG
2585 CTAATATT
1 CTAATATT
2593 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAAATAATTCATCAAAATAAAG
Found at i:3860 original size:2 final size:2
Alignment explanation
Indices: 3853--3897 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3843 TGGTTGTTTA
3853 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
3895 AT A
1 AT A
3898 CTAGTCTTAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3973 original size:19 final size:19
Alignment explanation
Indices: 3949--3985 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3939 TTTAAGTGAA
3949 AAAAAATATTAA-AATTAAT
1 AAAAAA-ATTAAGAATTAAT
3968 AAAAAAATTAAGAATTAA
1 AAAAAAATTAAGAATTAA
3986 ATTATTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (19 bp):
AAAAAAATTAAGAATTAAT
Found at i:4188 original size:2 final size:2
Alignment explanation
Indices: 4181--4213 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
4171 GTTGACTTAC
4181 AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
4214 TATTTTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6735 original size:26 final size:25
Alignment explanation
Indices: 6688--6738 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
6678 GGTACTGTAG
*
6688 AAATTTAATTTTTCTAAATAAAATA
1 AAATTTAATTTTTATAAATAAAATA
*
6713 AAATTTGAATTTTTATAAGTAAAATA
1 AAATTT-AATTTTTATAAATAAAATA
6739 TTTTAATGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (25 bp):
AAATTTAATTTTTATAAATAAAATA
Found at i:7566 original size:16 final size:16
Alignment explanation
Indices: 7547--7585 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
7537 GCTTTTTCAT
* *
7547 GTTCGGGTTTATTCGG
1 GTTCGGGTTCAGTCGG
*
7563 GTTCGGGTTCCGTCGG
1 GTTCGGGTTCAGTCGG
7579 GTTCGGG
1 GTTCGGG
7586 GTCGGGGTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.03, C:0.18, G:0.44, T:0.36
Consensus pattern (16 bp):
GTTCGGGTTCAGTCGG
Found at i:7591 original size:12 final size:12
Alignment explanation
Indices: 7574--7617 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
7564 TTCGGGTTCC
7574 GTCGGGTTCGGG
1 GTCGGGTTCGGG
*
7586 GTCGGGGTCGGG
1 GTCGGGTTCGGG
* *
7598 GTCGGTTTCAGG
1 GTCGGGTTCGGG
*
7610 CTCGGGTT
1 GTCGGGTT
7618 TGATTTCGAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.02, C:0.18, G:0.52, T:0.27
Consensus pattern (12 bp):
GTCGGGTTCGGG
Found at i:8067 original size:2 final size:2
Alignment explanation
Indices: 8060--8112 Score: 58
Period size: 2 Copynumber: 28.0 Consensus size: 2
8050 TAAAAATTAT
* * *
8060 TA TA TA TA TA TG TA TA AA GA T- TA TA T- TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8099 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
8113 AAGATTGAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
1 3 0.07
2 40 0.93
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Done.