Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002053.1 Hibiscus syriacus cultivar Beakdansim tig00004179_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: 58312
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:3666 original size:21 final size:21
Alignment explanation
Indices: 3642--3684 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3632 AAACAGAAGA
3642 GAAAAAGAAGGGAGAATTGAG
1 GAAAAAGAAGGGAGAATTGAG
3663 GAAAAAGAAGGGAGAATTGAG
1 GAAAAAGAAGGGAGAATTGAG
3684 G
1 G
3685 TAGAGTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.40, T:0.09
Consensus pattern (21 bp):
GAAAAAGAAGGGAGAATTGAG
Found at i:6232 original size:11 final size:12
Alignment explanation
Indices: 6216--6244 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
6206 AGGGACAGTC
6216 TTTTTT-AATGA
1 TTTTTTAAATGA
6227 TTTTTTAAATGA
1 TTTTTTAAATGA
6239 TTTTTT
1 TTTTTT
6245 CCCCGTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (12 bp):
TTTTTTAAATGA
Found at i:19648 original size:7 final size:7
Alignment explanation
Indices: 19636--19663 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
19626 ATTGCTCCTT
19636 CTTCCAC
1 CTTCCAC
19643 CTTCCAC
1 CTTCCAC
19650 CTTCCAC
1 CTTCCAC
19657 CTTCCAC
1 CTTCCAC
19664 TCCTCCAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.57, G:0.00, T:0.29
Consensus pattern (7 bp):
CTTCCAC
Found at i:20225 original size:13 final size:13
Alignment explanation
Indices: 20201--20225 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20191 ATACTCTTAA
20201 AAAAATTTCTTTC
1 AAAAATTTCTTTC
20214 AAAAATTTCTTT
1 AAAAATTTCTTT
20226 ATTCTGTCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAAATTTCTTTC
Found at i:20440 original size:37 final size:36
Alignment explanation
Indices: 20370--20444 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 36
20360 TCATTAAACC
* *
20370 ATTTTATATTTTCAATTTTGTAAAAAAATTATATAA
1 ATTTTATAATTTAAATTTTGTAAAAAAATTATATAA
*
20406 ATTTTATGAATTTAAATTTTTTAAAGAAAA-TATATAA
1 ATTTTAT-AATTTAAATTTTGTAAA-AAAATTATATAA
20443 AT
1 AT
20445 ATTTTCCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 7 0.21
37 23 0.68
38 4 0.12
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (36 bp):
ATTTTATAATTTAAATTTTGTAAAAAAATTATATAA
Found at i:20959 original size:39 final size:39
Alignment explanation
Indices: 20890--20966 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
20880 TAAATCCAAG
*
20890 GTTTGCAAACACTTTAAGTTGCCTAAAGATGATGGAATT
1 GTTTGCAAACACTTCAAGTTGCCTAAAGATGATGGAATT
* * *
20929 GTTTGCAGACACTTCAAGGTT-CGTATAGATGATGGAAT
1 GTTTGCAAACACTTCAA-GTTGCCTAAAGATGATGGAAT
20967 CATTGATGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 30 0.91
40 3 0.09
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.32
Consensus pattern (39 bp):
GTTTGCAAACACTTCAAGTTGCCTAAAGATGATGGAATT
Found at i:23692 original size:59 final size:59
Alignment explanation
Indices: 23588--23734 Score: 145
Period size: 60 Copynumber: 2.4 Consensus size: 59
23578 GTATAATTGA
** * *
23588 GATGAAATTAGAATGTTTGAAAAGTTTGGGGAGAAATTTATAATGA-AGGTCATAGTTT-GG
1 GATGAAATTA-AATGTTT-AAAAGTTTAAGGACAAATTTAGAATGATA-GTCATAGTTTAGG
* *
23648 GATGAAATTGAAATGTTTAAAAGTTTAAGGACTAATTTAGAATGATAGTCATATTTTAGG
1 GATGAAATT-AAATGTTTAAAAGTTTAAGGACAAATTTAGAATGATAGTCATAGTTTAGG
* * **
23708 GATTAAAATAAAAAATTTAAAAGTTTA
1 GA-TGAAATTAAATGTTTAAAAGTTTA
23735 GGGATCAATT
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
59 31 0.42
60 36 0.49
61 6 0.08
ACGTcount: A:0.42, C:0.02, G:0.21, T:0.35
Consensus pattern (59 bp):
GATGAAATTAAATGTTTAAAAGTTTAAGGACAAATTTAGAATGATAGTCATAGTTTAGG
Found at i:37711 original size:15 final size:15
Alignment explanation
Indices: 37691--37726 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
37681 ATATTTAGCT
*
37691 GGGCGGGCCGATGTG
1 GGGCGGGCCGATGCG
*
37706 GGGCGGGCGGATGCG
1 GGGCGGGCCGATGCG
37721 GGGCGG
1 GGGCGG
37727 ATGCGGGGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.19, G:0.67, T:0.08
Consensus pattern (15 bp):
GGGCGGGCCGATGCG
Found at i:37724 original size:11 final size:11
Alignment explanation
Indices: 37710--37737 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
37700 GATGTGGGGC
37710 GGGCGGATGCG
1 GGGCGGATGCG
37721 GGGCGGATGCG
1 GGGCGGATGCG
37732 GGGCGG
1 GGGCGG
37738 GTAATGTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.18, G:0.68, T:0.07
Consensus pattern (11 bp):
GGGCGGATGCG
Found at i:38863 original size:2 final size:2
Alignment explanation
Indices: 38856--38910 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
38846 TGAAAATTTA
38856 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
38898 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
38911 CCTTATCATC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:44113 original size:23 final size:23
Alignment explanation
Indices: 44087--44182 Score: 183
Period size: 23 Copynumber: 4.2 Consensus size: 23
44077 TTAAAGAAAG
44087 AGAAACGAGTTTATGGAAGAAGA
1 AGAAACGAGTTTATGGAAGAAGA
44110 AGAAACGAGTTTATGGAAGAAGA
1 AGAAACGAGTTTATGGAAGAAGA
*
44133 AGAAACGGGTTTATGGAAGAAGA
1 AGAAACGAGTTTATGGAAGAAGA
44156 AGAAACGAGTTTATGGAAGAAGA
1 AGAAACGAGTTTATGGAAGAAGA
44179 AGAA
1 AGAA
44183 GAAAATGATT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 71 1.00
ACGTcount: A:0.48, C:0.04, G:0.31, T:0.17
Consensus pattern (23 bp):
AGAAACGAGTTTATGGAAGAAGA
Found at i:56450 original size:5 final size:5
Alignment explanation
Indices: 56440--56473 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
56430 TTAAATAAAA
56440 AATTC AATTC AATTC AATTC AATTC AATTC AATT
1 AATTC AATTC AATTC AATTC AATTC AATTC AATT
56474 AATAAGAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
AATTC
Done.