Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019271.1 Corchorus olitorius cultivar O-4 contig19304, 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: 53677
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:28725 original size:11 final size:11
Alignment explanation
Indices: 28709--28733 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28699 TAATGTCTTC
28709 CTTTTCTTTTT
1 CTTTTCTTTTT
28720 CTTTTCTTTTT
1 CTTTTCTTTTT
28731 CTT
1 CTT
28734 CTTTTTGGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
CTTTTCTTTTT
Found at i:31928 original size:6 final size:6
Alignment explanation
Indices: 31917--31947 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
31907 AAAACGCTAA
*
31917 AGTTTC AGTTTC AGTTTC AGTTTC GGTTTC A
1 AGTTTC AGTTTC AGTTTC AGTTTC AGTTTC A
31948 TAAAATTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.48
Consensus pattern (6 bp):
AGTTTC
Found at i:36914 original size:5 final size:5
Alignment explanation
Indices: 36901--36930 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
36891 TCAAATTTGT
*
36901 GATTA GATTG GATTA GATTA GATTA GATTA
1 GATTA GATTA GATTA GATTA GATTA GATTA
36931 CTCAAACCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (5 bp):
GATTA
Found at i:42528 original size:21 final size:23
Alignment explanation
Indices: 42494--42537 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
42484 TTGATCGATC
*
42494 TAAAGAATCTAAA-CAAGAAAAA
1 TAAAGAATCTAAACCAACAAAAA
*
42516 TAAAGGAT-TAAACCAACAAAAA
1 TAAAGAATCTAAACCAACAAAAA
42538 CAGGAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.66, C:0.11, G:0.09, T:0.14
Consensus pattern (23 bp):
TAAAGAATCTAAACCAACAAAAA
Found at i:47102 original size:31 final size:31
Alignment explanation
Indices: 47067--47130 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
47057 AGAGTTTGTC
47067 TTTATTTTCTTA-TTTAGATTAGTATTAGGCT
1 TTTATTTTCTTATTTTAG-TTAGTATTAGGCT
*
47098 TTTATTTTCTTATTTTAGTTAGTATTGGGCT
1 TTTATTTTCTTATTTTAGTTAGTATTAGGCT
47129 TT
1 TT
47131 ATTGGCTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 26 0.84
32 5 0.16
ACGTcount: A:0.19, C:0.06, G:0.14, T:0.61
Consensus pattern (31 bp):
TTTATTTTCTTATTTTAGTTAGTATTAGGCT
Found at i:52459 original size:20 final size:21
Alignment explanation
Indices: 52434--52476 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
52424 TAATCGTGTC
*
52434 AAGACACGATTAACACG-TTT
1 AAGACACGAGTAACACGCTTT
*
52454 AAGACACGAGTGACACGCTTT
1 AAGACACGAGTAACACGCTTT
52475 AA
1 AA
52477 TTAACGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (21 bp):
AAGACACGAGTAACACGCTTT
Found at i:52947 original size:12 final size:12
Alignment explanation
Indices: 52930--52960 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
52920 TACCCTATGT
52930 AAACACGACACG
1 AAACACGACACG
52942 AAACACGACACG
1 AAACACGACACG
*
52954 GAACACG
1 AAACACG
52961 GATTGCCAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.32, G:0.19, T:0.00
Consensus pattern (12 bp):
AAACACGACACG
Done.