Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005060.1 Hibiscus syriacus cultivar Beakdansim tig00011360_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: 36647
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:1685 original size:12 final size:12
Alignment explanation
Indices: 1668--1697 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1658 CTCATAGTTT
1668 TTGTTGCAATTG
1 TTGTTGCAATTG
*
1680 TTGTTGGAATTG
1 TTGTTGCAATTG
1692 TTGTTG
1 TTGTTG
1698 TTATAATTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.03, G:0.30, T:0.53
Consensus pattern (12 bp):
TTGTTGCAATTG
Found at i:3025 original size:29 final size:29
Alignment explanation
Indices: 2982--3064 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
2972 CTCACCTAAC
2982 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
* *
3012 TAAATGATGTAAGCAATGATATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
*
3041 TAAATAATGTAAGCAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
3065 ATTTAGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:4512 original size:18 final size:18
Alignment explanation
Indices: 4469--4513 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
4459 CAAGTGCAGG
*
4469 AGGAGTTAGCCATGTCCA
1 AGGAGTTTGCCATGTCCA
*
4487 AGGAGTTTGCCATGTCTA
1 AGGAGTTTGCCATGTCCA
4505 AGGAGTTTG
1 AGGAGTTTG
4514 TCGAGCATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (18 bp):
AGGAGTTTGCCATGTCCA
Found at i:5045 original size:19 final size:19
Alignment explanation
Indices: 5021--5065 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
5011 TTTAGTTTCA
*
5021 AAATCATCCCAAAATCCCT
1 AAATCATCCCAAAATCCCC
5040 AAATCATCCCAAAATCCCC
1 AAATCATCCCAAAATCCCC
5059 AAATCAT
1 AAATCAT
5066 TCTAGCTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.44, C:0.36, G:0.00, T:0.20
Consensus pattern (19 bp):
AAATCATCCCAAAATCCCC
Found at i:6860 original size:23 final size:23
Alignment explanation
Indices: 6813--6862 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
6803 AATAATATAT
*
6813 TAGGTAGAGCTTATATAACGTAA
1 TAGGTAGAGCTTATATAACGAAA
*
6836 TAGGTAGTGCTTATATAA-GAAAA
1 TAGGTAGAGCTTATATAACG-AAA
6859 TAGG
1 TAGG
6863 AATTTAACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.40, C:0.06, G:0.24, T:0.30
Consensus pattern (23 bp):
TAGGTAGAGCTTATATAACGAAA
Found at i:6923 original size:87 final size:87
Alignment explanation
Indices: 6777--6938 Score: 261
Period size: 87 Copynumber: 1.9 Consensus size: 87
6767 ATGTTATATC
* * *
6777 ATTTAACCGGAAATATTATCATGTACAATAATATATTAGGTAGAGCTTATATAACGTAATAGGTA
1 ATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGAGCTTATATAACGTAATAGGTA
*
6842 GTGCTTATATAAGAAAATAGGA
66 GCGCTTATATAAGAAAATAGGA
** *
6864 ATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCTCTTATATAATGTAATAGGTA
1 ATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGAGCTTATATAACGTAATAGGTA
6929 GCGCTTATAT
66 GCGCTTATAT
6939 TGACCTATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 68 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (87 bp):
ATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGAGCTTATATAACGTAATAGGTA
GCGCTTATATAAGAAAATAGGA
Found at i:7450 original size:200 final size:201
Alignment explanation
Indices: 7097--7636 Score: 675
Period size: 200 Copynumber: 2.7 Consensus size: 201
7087 TTCTGGAAAA
* * * *
7097 AAGTGTCGATACATTAT-TTAGACCTATTTTCTCATAAAA-TCGGAATACTTT-TATCGGGTATA
1 AAGTGTCGATACATTATGTT-GACCTATTTTCTCATAAAACT-GGTATA-TTTATACCGGTTACA
* **
7159 TTGTAAATTTACCTATCACATCGTAATTATCGGTTTCGATA-TTTTTGGGATCGATACTTTTAAT
63 TTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA-AGTTTTTGGGATCGATACTTTTAAT
* * * *
7223 AAATGTATCGACACTTTGTGTGTGCACCCCGTT-TGACATTCATTATGGACAA-AATGTATCGAC
127 AAATGTATCGACACGTTATGCGTGCACCCCGTTGGGACATTCATTATGGACAATAA-GTATCGAC
7286 ACAAATT-TAAC
191 ACAAATTAT-AC
* * *
7297 AAGTGTCGATACTTTATGCTGACCTATTTTCTCATAAAACTGGTATATTTATACCTGTTACATTG
1 AAGTGTCGATACATTATGTTGACCTATTTTCTCATAAAACTGGTATATTTATACCGGTTACATTG
*
7362 TAAATTTACCTATTACATTATAATTATCGGTTTCGAAGTTATTGGGATCGATACTTTTAATAAAT
66 TAAATTTACCTATTACATTATAATTATCGGTTTCGAAGTTTTTGGGATCGATACTTTTAATAAAT
** * * *
7427 GTATCGACACGTTATGCGTGCACCTTGTTGGGGCATTCATTCTGGATAATAAGTATCGACACAAA
131 GTATCGACACGTTATGCGTGCACCCCGTTGGGACATTCATTATGGACAATAAGTATCGACACAAA
7492 TTATAC
196 TTATAC
* * * * * *
7498 AAGTGTCGGTACATTATGTTGACTTGTTTTCTAAT-TAACCGGTATATTTATACCGGTTACATTG
1 AAGTGTCGATACATTATGTTGACCTATTTTCTCATAAAACTGGTATATTTATACCGGTTACATTG
* * * * *
7562 TTAATTTACCTATTACATTATAATTATTGGTTTCGATGTTTTTGGGCTCGATAC-TTTAAGAAAA
66 TAAATTTACCTATTACATTATAATTATCGGTTTCGAAGTTTTTGGGATCGATACTTTTAA-TAAA
7626 TGTATCGACAC
130 TGTATCGACAC
7637 ATATTTAGGT
Statistics
Matches: 297, Mismatches: 35, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
199 9 0.03
200 222 0.75
201 63 0.21
202 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (201 bp):
AAGTGTCGATACATTATGTTGACCTATTTTCTCATAAAACTGGTATATTTATACCGGTTACATTG
TAAATTTACCTATTACATTATAATTATCGGTTTCGAAGTTTTTGGGATCGATACTTTTAATAAAT
GTATCGACACGTTATGCGTGCACCCCGTTGGGACATTCATTATGGACAATAAGTATCGACACAAA
TTATAC
Found at i:10138 original size:19 final size:19
Alignment explanation
Indices: 10116--10164 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
10106 TTACAATCAC
10116 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCTT
10135 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCTT
10154 ATACAAAATTA
1 ATACAAAATTA
10165 ACCCTACATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (19 bp):
ATACAAAATTATAAATCTT
Found at i:10139 original size:37 final size:38
Alignment explanation
Indices: 10093--10164 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 38
10083 AACTTTTCTC
* *
10093 ATCTCATACATAATTA-CAATCACATACAAAATTATAA
1 ATCTCATACAAAATTATAAATCACATACAAAATTATAA
* **
10130 ATCTTATACAAAATTATAAATCTTATACAAAATTA
1 ATCTCATACAAAATTATAAATCACATACAAAATTA
10165 ACCCTACATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 14 0.48
38 15 0.52
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.33
Consensus pattern (38 bp):
ATCTCATACAAAATTATAAATCACATACAAAATTATAA
Found at i:17116 original size:14 final size:14
Alignment explanation
Indices: 17097--17166 Score: 140
Period size: 14 Copynumber: 5.0 Consensus size: 14
17087 GGAAAAGTTG
17097 AGATGAATTCTAAA
1 AGATGAATTCTAAA
17111 AGATGAATTCTAAA
1 AGATGAATTCTAAA
17125 AGATGAATTCTAAA
1 AGATGAATTCTAAA
17139 AGATGAATTCTAAA
1 AGATGAATTCTAAA
17153 AGATGAATTCTAAA
1 AGATGAATTCTAAA
17167 CTTGTGGTTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 56 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (14 bp):
AGATGAATTCTAAA
Found at i:19283 original size:26 final size:26
Alignment explanation
Indices: 19251--19304 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
19241 ATTTAGTGTG
* *
19251 TATGGTGGGTACGACCTTATGTGTAT
1 TATGGTGGGCACGACCTTAGGTGTAT
19277 TATGGTGGGCACGACCTTAGGTGTAT
1 TATGGTGGGCACGACCTTAGGTGTAT
19303 TA
1 TA
19305 GCACTTCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.20, C:0.13, G:0.31, T:0.35
Consensus pattern (26 bp):
TATGGTGGGCACGACCTTAGGTGTAT
Found at i:24183 original size:14 final size:14
Alignment explanation
Indices: 24164--24220 Score: 114
Period size: 14 Copynumber: 4.1 Consensus size: 14
24154 ATGAATTCTA
24164 CTAAAAGATGAATT
1 CTAAAAGATGAATT
24178 CTAAAAGATGAATT
1 CTAAAAGATGAATT
24192 CTAAAAGATGAATT
1 CTAAAAGATGAATT
24206 CTAAAAGATGAATT
1 CTAAAAGATGAATT
24220 C
1 C
24221 ATAACTTGCG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 43 1.00
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (14 bp):
CTAAAAGATGAATT
Found at i:25638 original size:23 final size:24
Alignment explanation
Indices: 25604--25662 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 24
25594 TATAAAGGTC
*
25604 ACTTA-GTGTGTATGGTGGGCACGA
1 ACTTATGTGT-TATGGTGGGCACAA
*
25628 CCTTATGTGTATTATGGTGGGCACAA
1 ACTTATGTG--TTATGGTGGGCACAA
25654 ACTTATGTG
1 ACTTATGTG
25663 CATTAGCACT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 4 0.14
25 3 0.10
26 21 0.72
27 1 0.03
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.34
Consensus pattern (24 bp):
ACTTATGTGTTATGGTGGGCACAA
Found at i:25646 original size:26 final size:26
Alignment explanation
Indices: 25614--25667 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
25604 ACTTAGTGTG
* * *
25614 TATGGTGGGCACGACCTTATGTGTAT
1 TATGGTGGGCACAAACTTATGTGCAT
25640 TATGGTGGGCACAAACTTATGTGCAT
1 TATGGTGGGCACAAACTTATGTGCAT
25666 TA
1 TA
25668 GCACTTCGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (26 bp):
TATGGTGGGCACAAACTTATGTGCAT
Found at i:28090 original size:15 final size:15
Alignment explanation
Indices: 28070--28156 Score: 88
Period size: 15 Copynumber: 5.7 Consensus size: 15
28060 AATAAAATAT
28070 AAAATACAATATCAG
1 AAAATACAATATCAG
*
28085 AAAATACAATAACCTA-
1 AAAATACAAT-ATC-AG
28101 AAAATACAATA-CTAG
1 AAAATACAATATC-AG
* * *
28116 AAGATACAATAACAT
1 AAAATACAATATCAG
*
28131 AAAATACAATATTAG
1 AAAATACAATATCAG
28146 AAAATACAATA
1 AAAATACAATA
28157 ACATAATTAT
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
14 3 0.05
15 44 0.72
16 13 0.21
17 1 0.02
ACGTcount: A:0.62, C:0.13, G:0.05, T:0.21
Consensus pattern (15 bp):
AAAATACAATATCAG
Found at i:28108 original size:31 final size:30
Alignment explanation
Indices: 28068--28162 Score: 138
Period size: 30 Copynumber: 3.1 Consensus size: 30
28058 GTAATAAAAT
28068 ATAAAATACAATATCAGAAAATACAATAAC
1 ATAAAATACAATATCAGAAAATACAATAAC
* *
28098 CTAAAAATACAATA-CTAGAAGATACAATAAC
1 AT-AAAATACAATATC-AGAAAATACAATAAC
*
28129 ATAAAATACAATATTAGAAAATACAATAAC
1 ATAAAATACAATATCAGAAAATACAATAAC
28159 ATAA
1 ATAA
28163 TTATTAGAGG
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
30 31 0.54
31 26 0.46
ACGTcount: A:0.62, C:0.13, G:0.04, T:0.21
Consensus pattern (30 bp):
ATAAAATACAATATCAGAAAATACAATAAC
Found at i:29544 original size:42 final size:42
Alignment explanation
Indices: 29252--29555 Score: 170
Period size: 42 Copynumber: 7.2 Consensus size: 42
29242 TATTTATTAT
* * * * *
29252 CTTTAAAATTAAGG-CCTCTAATTTTTTAATCCTACTTTTTAT
1 CTTTATAATTGAGGTCC-CTAATTTTTCAATCTTACTTTTTAC
* * * * * **
29294 CATTATAATTGAGGTTCTTGATTTTTGAAATCCCACTTTTTTAC
1 CTTTATAATTGAGGTCCCTAATTTTT-CAATCTTAC-TTTTTAC
* * * *
29338 ATTTATAATTGATGACCCTAAGTTTTTCAAT-TTCACTTTGTAC
1 CTTTATAATTGAGGTCCCTAA-TTTTTCAATCTT-ACTTTTTAC
* * * * * * *
29381 TTTTATAATTGAGCT-CTTATGTTTTTCAATTTTAATTTCTAC
1 CTTTATAATTGAGGTCCCTA-ATTTTTCAATCTTACTTTTTAC
* * * * *
29423 CTTTATAATTGGGGCCCCTAA-TTTTCTATTCTCA-TTTTTAAG
1 CTTTATAATTGAGGTCCCTAATTTTTC-AATCTTACTTTTT-AC
* * * *
29465 CTTTAAAATTAAGGTTCCTAATTTTTTAAT-TTGACTTTTTAC
1 CTTTATAATTGAGGTCCCTAATTTTTCAATCTT-ACTTTTTAC
* *
29507 CTTTACAATTGAGGTCCCTAATTTTTCAATCATACTTTTTAC
1 CTTTATAATTGAGGTCCCTAATTTTTCAATCTTACTTTTTAC
*
29549 ATTTATA
1 CTTTATA
29556 GTTTAAACCC
Statistics
Matches: 193, Mismatches: 55, Indels: 28
0.70 0.20 0.10
Matches are distributed among these distances:
41 10 0.05
42 113 0.59
43 40 0.21
44 25 0.13
45 5 0.03
ACGTcount: A:0.26, C:0.16, G:0.08, T:0.50
Consensus pattern (42 bp):
CTTTATAATTGAGGTCCCTAATTTTTCAATCTTACTTTTTAC
Found at i:34715 original size:3 final size:3
Alignment explanation
Indices: 34709--34737 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
34699 ATTTATTATT
34709 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
34738 TATTATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:34754 original size:15 final size:15
Alignment explanation
Indices: 34731--34766 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
34721 ATAATAATAA
34731 TAATAATTATTATTAT
1 TAAT-ATTATTATTAT
34747 TAATATTATTATTAT
1 TAATATTATTATTAT
34762 TAATA
1 TAATA
34767 CTAATTACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TAATATTATTATTAT
Done.