Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015926.1 Corchorus olitorius cultivar O-4 contig15959, 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: 37803
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:5664 original size:25 final size:25
Alignment explanation
Indices: 5630--5679 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
5620 TTGTCTGTTC
5630 ATGAATGGGTTTTAGAAGCTAATAT
1 ATGAATGGGTTTTAGAAGCTAATAT
5655 ATGAATGGGTTTTAGAAGCTAATAT
1 ATGAATGGGTTTTAGAAGCTAATAT
5680 GTGAGGAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (25 bp):
ATGAATGGGTTTTAGAAGCTAATAT
Found at i:12454 original size:2 final size:2
Alignment explanation
Indices: 12447--12474 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12437 TAACGTTTAA
12447 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
12475 CCCCATTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:13552 original size:18 final size:18
Alignment explanation
Indices: 13520--13567 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
13510 ACAAAAAATA
* *
13520 ATTTTTCTCTGTTCTTCTT
1 ATTTTTTTCTTTTCTT-TT
13539 -TTTTTTTCTTTTCTTTT
1 ATTTTTTTCTTTTCTTTT
13556 ATTTTTTT-TTTT
1 ATTTTTTTCTTTT
13568 GTGCTTGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.04, C:0.12, G:0.02, T:0.81
Consensus pattern (18 bp):
ATTTTTTTCTTTTCTTTT
Found at i:17718 original size:19 final size:19
Alignment explanation
Indices: 17694--17730 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
17684 AACTCCCTTC
17694 TTTTTTGGTATGAACTGTG
1 TTTTTTGGTATGAACTGTG
*
17713 TTTTTTGGTGTGAACTGT
1 TTTTTTGGTATGAACTGT
17731 TTTGATATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.05, G:0.27, T:0.54
Consensus pattern (19 bp):
TTTTTTGGTATGAACTGTG
Found at i:17741 original size:15 final size:17
Alignment explanation
Indices: 17723--17755 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
17713 TTTTTTGGTG
17723 TGAACTG-TTTT-GATA
1 TGAACTGCTTTTCGATA
17738 TGAACTGCTTTTCGATA
1 TGAACTGCTTTTCGATA
17755 T
1 T
17756 CTGTTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.45
Consensus pattern (17 bp):
TGAACTGCTTTTCGATA
Found at i:17813 original size:23 final size:23
Alignment explanation
Indices: 17787--17833 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
17777 TGTGTTTCTT
*
17787 GGTATCAATTGTGTTTT-TTTTTG
1 GGTATCAATTCT-TTTTCTTTTTG
*
17810 GGTATGAATTCTTTTTCTTTTTG
1 GGTATCAATTCTTTTTCTTTTTG
17833 G
1 G
17834 TCTCTCCTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.13, C:0.06, G:0.21, T:0.60
Consensus pattern (23 bp):
GGTATCAATTCTTTTTCTTTTTG
Found at i:33036 original size:30 final size:30
Alignment explanation
Indices: 33002--33066 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
32992 GTGGAAAGTC
33002 TAGAAATTTGAGAGGACAAGGAAGAGGTGG
1 TAGAAATTTGAGAGGACAAGGAAGAGGTGG
*
33032 TAGAAATTTGAGAGGACGAGGAAGAGGTGG
1 TAGAAATTTGAGAGGACAAGGAAGAGGTGG
33062 TAGAA
1 TAGAA
33067 GATAGTGAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.40, C:0.03, G:0.40, T:0.17
Consensus pattern (30 bp):
TAGAAATTTGAGAGGACAAGGAAGAGGTGG
Done.