Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017637.1 Corchorus olitorius cultivar O-4 contig17670, 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: 23194
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:532 original size:5 final size:5
Alignment explanation
Indices: 518--552 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
508 TCAAGTAATT
*
518 AAAGG AAAGG GAAGG AAAGG AAAGG AAAGG AAAGG
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG
553 GGAGGGAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:813 original size:20 final size:21
Alignment explanation
Indices: 780--826 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
770 AAAAAAGAAG
* *
780 AAAAAATTAGAAATTTTCAAC
1 AAAAAAATAGAAATCTTCAAC
801 AAAAAAATA-AAATCTTC-AC
1 AAAAAAATAGAAATCTTCAAC
*
820 AAGAAAA
1 AAAAAAA
827 GAGATGAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 8 0.35
20 7 0.30
21 8 0.35
ACGTcount: A:0.64, C:0.11, G:0.04, T:0.21
Consensus pattern (21 bp):
AAAAAAATAGAAATCTTCAAC
Found at i:2726 original size:32 final size:32
Alignment explanation
Indices: 2690--2813 Score: 205
Period size: 32 Copynumber: 3.9 Consensus size: 32
2680 CCATTTTGTA
*
2690 AACGGGCCTT-AAAATTTTGTCCAAGCCCATCC
1 AACGGG-CTTCAAATTTTTGTCCAAGCCCATCC
*
2722 AACGGGCTTCAAATTTTTGTCCAATCCCATCC
1 AACGGGCTTCAAATTTTTGTCCAAGCCCATCC
2754 AACGGGCTTCAAATTTTTGTCCAAGCCCATCC
1 AACGGGCTTCAAATTTTTGTCCAAGCCCATCC
*
2786 AACGGGTTTCAAATTTTTGTCCAAGCCC
1 AACGGGCTTCAAATTTTTGTCCAAGCCC
2814 TCCCAAATAT
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 3 0.03
32 84 0.97
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.29
Consensus pattern (32 bp):
AACGGGCTTCAAATTTTTGTCCAAGCCCATCC
Found at i:10581 original size:26 final size:26
Alignment explanation
Indices: 10551--10601 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
10541 CAAAATCTTT
*
10551 TTACCATTTTTGATT-TTTCCAAAAAC
1 TTACCAATTTT-ATTATTTCCAAAAAC
10577 TTACCAATTTTATTAATTTCCAAAA
1 TTACCAATTTTATT-ATTTCCAAAA
10602 TCTTCTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 3 0.14
26 10 0.45
27 9 0.41
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.45
Consensus pattern (26 bp):
TTACCAATTTTATTATTTCCAAAAAC
Found at i:12174 original size:16 final size:16
Alignment explanation
Indices: 12153--12209 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
12143 CGGGTTGATC
12153 GGGTTCGGGTCATTTT
1 GGGTTCGGGTCATTTT
* *
12169 GGGTTCAGGTC-GTTT
1 GGGTTCGGGTCATTTT
* * *
12184 GGATTCGGGTAATTTC
1 GGGTTCGGGTCATTTT
12200 GGGTTCGGGT
1 GGGTTCGGGT
12210 ACCCAAAATT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
15 11 0.34
16 21 0.66
ACGTcount: A:0.09, C:0.12, G:0.40, T:0.39
Consensus pattern (16 bp):
GGGTTCGGGTCATTTT
Found at i:12646 original size:20 final size:19
Alignment explanation
Indices: 12617--12654 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
12607 ACCCAACATC
12617 AAAACCCAAATAAATAAAT
1 AAAACCCAAATAAATAAAT
*
12636 AAAAGCCCAAATGAATAAA
1 AAAA-CCCAAATAAATAAA
12655 GCTGAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.66, C:0.16, G:0.05, T:0.13
Consensus pattern (19 bp):
AAAACCCAAATAAATAAAT
Found at i:15310 original size:23 final size:22
Alignment explanation
Indices: 15275--15320 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
15265 CTAAATTCGG
*
15275 GTCCAGTCGTCAAACCCGCGCGC
1 GTCCAGGCGTC-AACCCGCGCGC
*
15298 GTCCAGGCTTCAACCCGCGCGC
1 GTCCAGGCGTCAACCCGCGCGC
15320 G
1 G
15321 GCTAGTGCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.15, C:0.43, G:0.28, T:0.13
Consensus pattern (22 bp):
GTCCAGGCGTCAACCCGCGCGC
Found at i:19437 original size:62 final size:62
Alignment explanation
Indices: 19357--19474 Score: 148
Period size: 62 Copynumber: 1.9 Consensus size: 62
19347 CTCAGGTAGG
* * *
19357 GCCCGCGCGCGGCCAGTGCCAGG-AGGTGATGGATGTCGCTTGCCCGCGCGCGGCTTGTGTCA
1 GCCCGCGAGCGGCCAGTGCCAGGAAGGTGATGGACGT-GCTCGCCCGCGCGCGGCTTGTGTCA
* * * * *
19419 GCCCGCGAGTGGCTAGTGCCAGGAAGTTGGTGGACGTGCTCGCCCGTGCGCGGCTT
1 GCCCGCGAGCGGCCAGTGCCAGGAAGGTGATGGACGTGCTCGCCCGCGCGCGGCTT
19475 TCCTCAGGCT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
62 37 0.79
63 10 0.21
ACGTcount: A:0.10, C:0.31, G:0.41, T:0.19
Consensus pattern (62 bp):
GCCCGCGAGCGGCCAGTGCCAGGAAGGTGATGGACGTGCTCGCCCGCGCGCGGCTTGTGTCA
Done.