Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008069.1 Hibiscus syriacus cultivar Beakdansim tig00110567_pilon, 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: 64589
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1819 original size:19 final size:20
Alignment explanation
Indices: 1780--1822 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1770 GAAACCCCTT
**
1780 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAAATTTAA
1800 TGAAAACACAT-AAATTTAA
1 TGAAAACACATGAAATTTAA
1819 TGAA
1 TGAA
1823 GATAATGCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.30
Consensus pattern (20 bp):
TGAAAACACATGAAATTTAA
Found at i:4874 original size:13 final size:14
Alignment explanation
Indices: 4856--4885 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4846 TGTAGGAGTC
4856 TTTTCTTTTTCT-T
1 TTTTCTTTTTCTCT
4869 TTTTCTTTTTCTCT
1 TTTTCTTTTTCTCT
4883 TTT
1 TTT
4886 GTTGTAGCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTCTTTTTCTCT
Found at i:10730 original size:19 final size:20
Alignment explanation
Indices: 10689--10739 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
10679 GAAACCCCTT
*
10689 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
10709 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
10728 TGAAGATACATG
1 TGAAAATACATG
10740 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:14908 original size:19 final size:20
Alignment explanation
Indices: 14867--14917 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
14857 GAAACCCCTT
*
14867 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
14887 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
14906 TGAAGATACATG
1 TGAAAATACATG
14918 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:22240 original size:30 final size:33
Alignment explanation
Indices: 22204--22264 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
22194 AATGATTAAG
22204 ATGGAAAT-ATAA-ATAA-GAAATGGA-AGAAGA
1 ATGGAAATGATAAGA-AAGGAAATGGATAGAAGA
22234 ATGGAAATGATAAGAAAGGAAATGGATAGAA
1 ATGGAAATGATAAGAAAGGAAATGGATAGAA
22265 ATGTTATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 8 0.30
31 6 0.22
32 9 0.33
33 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.26, T:0.16
Consensus pattern (33 bp):
ATGGAAATGATAAGAAAGGAAATGGATAGAAGA
Found at i:22883 original size:19 final size:20
Alignment explanation
Indices: 22845--22887 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
22835 GAAACCCCTT
*
22845 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
22865 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
22884 TGAA
1 TGAA
22888 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:28738 original size:11 final size:11
Alignment explanation
Indices: 28724--28778 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
28714 AGGATGATTT
28724 AATGGTGATGA
1 AATGGTGATGA
*
28735 AATGGTAATGA
1 AATGGTGATGA
28746 AATGGTGATGA
1 AATGGTGATGA
* *
28757 TATAGGCG-TGA
1 AAT-GGTGATGA
28768 TAATGGTGATG
1 -AATGGTGATG
28779 GACAGATTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
11 28 0.80
12 7 0.20
ACGTcount: A:0.35, C:0.02, G:0.35, T:0.29
Consensus pattern (11 bp):
AATGGTGATGA
Found at i:49746 original size:15 final size:15
Alignment explanation
Indices: 49726--49765 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
49716 CCTTTGATAA
*
49726 CATTTCTTTCCATTT
1 CATTTCTTTCCAATT
49741 CATTTCTTAT-CAATT
1 CATTTCTT-TCCAATT
49756 CATTTCTTTC
1 CATTTCTTTC
49766 ATAATTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.57
Consensus pattern (15 bp):
CATTTCTTTCCAATT
Found at i:59319 original size:24 final size:23
Alignment explanation
Indices: 59292--59351 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
59282 CAACTTTTTT
59292 CTTTCTTTTTCTTCTTTTCGAGTG
1 CTTTCTTTTTCTTCTTTT-GAGTG
**
59316 CTTTCAATTTCTTCTTTTGAGTG
1 CTTTCTTTTTCTTCTTTTGAGTG
59339 CTTT-TATTTTCTT
1 CTTTCT-TTTTCTT
59352 TTCTGTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.08, C:0.18, G:0.10, T:0.63
Consensus pattern (23 bp):
CTTTCTTTTTCTTCTTTTGAGTG
Found at i:59341 original size:23 final size:24
Alignment explanation
Indices: 59299--59351 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
59289 TTTCTTTCTT
59299 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
59323 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
59346 TTTCTT
1 TTTCTT
59352 TTCTGTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:63533 original size:22 final size:22
Alignment explanation
Indices: 63507--63563 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
63497 AACTTTCTTT
63507 CTTTCTTTTCTTCTTTCGAGTG
1 CTTTCTTTTCTTCTTTCGAGTG
* *
63529 CTTTCAATTTC-TCTTTTGAGTG
1 CTTTC-TTTTCTTCTTTCGAGTG
*
63551 CTTTTATTTTCTT
1 C-TTTCTTTTCTT
63564 TGCTAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.09, C:0.19, G:0.11, T:0.61
Consensus pattern (22 bp):
CTTTCTTTTCTTCTTTCGAGTG
Done.