Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006971.1 Hibiscus syriacus cultivar Beakdansim tig00017956_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: 59065
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:5228 original size:21 final size:21
Alignment explanation
Indices: 5204--5253 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
5194 CATTTTTACC
*
5204 CTAAATCTCAAAA-TCTCAAAT
1 CTAAATCTCAAAACCCT-AAAT
5225 CTAAAT-TCAAAACCCTAAAT
1 CTAAATCTCAAAACCCTAAAT
5245 CTTAAATCT
1 C-TAAATCT
5254 TAACCTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 11 0.44
21 13 0.52
22 1 0.04
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (21 bp):
CTAAATCTCAAAACCCTAAAT
Found at i:5304 original size:24 final size:24
Alignment explanation
Indices: 5274--5327 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
5264 AGGAAAAAAT
*
5274 ATTATTTTACTCTGAGTTAAAGAA
1 ATTATTTTACTCAGAGTTAAAGAA
* *
5298 ATTATTTTACTGAGAGTTAAATAA
1 ATTATTTTACTCAGAGTTAAAGAA
5322 A-TATTT
1 ATTATTT
5328 ATTTATGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (24 bp):
ATTATTTTACTCAGAGTTAAAGAA
Found at i:6520 original size:3 final size:3
Alignment explanation
Indices: 6456--6505 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
6446 TATATCAGTC
6456 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6504 AT
1 AT
6506 GTTTATGTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:9204 original size:53 final size:53
Alignment explanation
Indices: 9141--9250 Score: 211
Period size: 53 Copynumber: 2.1 Consensus size: 53
9131 GATATAAAGG
*
9141 TTCTTGAATACCTTCCTGATACACCTGAATCGTGAATGGTCATGAAACATCAA
1 TTCTTGAATACCTTCCTGATACACCTGAATCATGAATGGTCATGAAACATCAA
9194 TTCTTGAATACCTTCCTGATACACCTGAATCATGAATGGTCATGAAACATCAA
1 TTCTTGAATACCTTCCTGATACACCTGAATCATGAATGGTCATGAAACATCAA
9247 TTCT
1 TTCT
9251 AAATGCCTAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (53 bp):
TTCTTGAATACCTTCCTGATACACCTGAATCATGAATGGTCATGAAACATCAA
Found at i:11570 original size:64 final size:63
Alignment explanation
Indices: 11441--11609 Score: 218
Period size: 64 Copynumber: 2.7 Consensus size: 63
11431 TTGTTTAAGG
* * *
11441 TGCATCGATGCACATGCAGTGCATCGATGCAT--TAATTTAAAAAAAAACATCGAATAGGATTTA
1 TGCATCGATGCATA-GGAGTGCATCGATGCATCCTCA-TTAAAAAAAAACATCGAATAGGATTTA
* *
11504 TGCATCGATGCATAAGGAGTGCATCGATGCATCCTCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCAT-AGGAGTGCATCGATGCATCCTCATTAAAAAAAAACATCGAATAGGATTTA
*
11568 TGCATCGATGCAT-GGTGTGCATCGATGCATACCTCCATTAAA
1 TGCATCGATGCATAGGAGTGCATCGATGCAT-CCT-CATTAAA
11610 GATGAAAATG
Statistics
Matches: 95, Mismatches: 6, Indels: 9
0.86 0.05 0.08
Matches are distributed among these distances:
62 16 0.17
63 31 0.33
64 46 0.48
65 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAGGAGTGCATCGATGCATCCTCATTAAAAAAAAACATCGAATAGGATTTA
Found at i:12159 original size:21 final size:21
Alignment explanation
Indices: 12135--12187 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
12125 CTTGCATATG
12135 TATGTGATTCTTAAGGA-ATGA
1 TATGTGATTCTTAAGGACAT-A
* * *
12156 TATGTGGTCCTTCAGGACATA
1 TATGTGATTCTTAAGGACATA
12177 TATGT-ATTCTT
1 TATGTGATTCTT
12188 TGGAATATGT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 4 0.15
21 20 0.77
22 2 0.08
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (21 bp):
TATGTGATTCTTAAGGACATA
Found at i:12277 original size:103 final size:100
Alignment explanation
Indices: 12055--12278 Score: 367
Period size: 102 Copynumber: 2.2 Consensus size: 100
12045 GTAGAGGGTC
*
12055 TATGTGGTCCTTCGGGACATATATGTATCTTTGGAACATGTGTGAGGTCTGGTGAGACACATACT
1 TATGTGGTCCTT-AGGACATATATGTATCTTTGGAACATGTGTGAGGTCTGGTGAGACACATACT
* *
12120 TGATCCTTGCATATGTATGTGATTCTTAAGGAATGA
65 TGATCATTGCATATGTATATGATTCTTAAGGAATGA
*
12156 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAATATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTT-AGGACATATATGTA-TCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
12221 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
64 TTGATCATT-GCATATGTATATGATTCTTAAGGAATGA
12259 TATGTGGTCCTTATGGACAT
1 TATGTGGTCCTTA-GGACAT
12279 TATTATATGG
Statistics
Matches: 116, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
101 26 0.22
102 45 0.39
103 45 0.39
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (100 bp):
TATGTGGTCCTTAGGACATATATGTATCTTTGGAACATGTGTGAGGTCTGGTGAGACACATACTT
GATCATTGCATATGTATATGATTCTTAAGGAATGA
Found at i:12325 original size:23 final size:23
Alignment explanation
Indices: 12287--12349 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
12277 ATTATTATAT
12287 GGCAC-TACGGTGCAATTCTACGC
1 GGCACTTA-GGTGCAATTCTACGC
* *
12310 GGTACTTAGGTGCAATTCTACGT
1 GGCACTTAGGTGCAATTCTACGC
12333 GGCACTTAGGTGCAATT
1 GGCACTTAGGTGCAATT
12350 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 34 0.94
24 2 0.06
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (23 bp):
GGCACTTAGGTGCAATTCTACGC
Found at i:18963 original size:102 final size:103
Alignment explanation
Indices: 18739--18955 Score: 400
Period size: 102 Copynumber: 2.1 Consensus size: 103
18729 GTATAGGGTC
* * *
18739 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTGAAACATGTGTGAGGTCTGGTGAGACACATAC
18804 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
18842 TATGTGGTCCTTCGGGACATATATATATTC-TTGAAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTGAAACATGTGTGAGGTCTGGTGAGACACATAC
18906 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
18944 TATGTGGTCCTT
1 TATGTGGTCCTT
18956 ATGGACATTA
Statistics
Matches: 111, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
102 83 0.75
103 28 0.25
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATATATTCTTTGAAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:19006 original size:23 final size:23
Alignment explanation
Indices: 18980--19034 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
18970 ATGACACTAC
18980 GGTGCAATTCTACGCGGCACTCA
1 GGTGCAATTCTACGCGGCACTCA
* *
19003 GGTGCAATTCTACGTGGCACTTA
1 GGTGCAATTCTACGCGGCACTCA
19026 GGTGCAATT
1 GGTGCAATT
19035 ATATGAGCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (23 bp):
GGTGCAATTCTACGCGGCACTCA
Found at i:21923 original size:15 final size:16
Alignment explanation
Indices: 21905--21937 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
21895 AAGAATATTT
*
21905 TATTCCGAAA-TAAAA
1 TATTCCAAAACTAAAA
21920 TATTCCAAAACTAAAA
1 TATTCCAAAACTAAAA
21936 TA
1 TA
21938 CTAAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.55, C:0.15, G:0.03, T:0.27
Consensus pattern (16 bp):
TATTCCAAAACTAAAA
Found at i:27782 original size:32 final size:31
Alignment explanation
Indices: 27744--27821 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
27734 CGGGTCAATA
27744 TCGGGTCGGGTCAATACC-AGATCGATT-GATTT
1 TCGGGTC-GGTCAATACCGA-ATCGATTAGA-TT
* * *
27776 TTGGGTCGTTTAATACCGAATCGATTAGATT
1 TCGGGTCGGTCAATACCGAATCGATTAGATT
27807 TCGGGTCGGTCAATA
1 TCGGGTCGGTCAATA
27822 TTAGATTGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
31 29 0.76
32 9 0.24
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (31 bp):
TCGGGTCGGTCAATACCGAATCGATTAGATT
Found at i:28608 original size:16 final size:16
Alignment explanation
Indices: 28589--28628 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
28579 TTAATTTCGG
*
28589 TTTTGGTTCGGGTTAA
1 TTTTGGTTCGAGTTAA
* *
28605 TTTTGGTTCTAGTTGA
1 TTTTGGTTCGAGTTAA
28621 TTTTGGTT
1 TTTTGGTT
28629 TCGCTGAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.10, C:0.05, G:0.28, T:0.57
Consensus pattern (16 bp):
TTTTGGTTCGAGTTAA
Found at i:29353 original size:2 final size:2
Alignment explanation
Indices: 29346--29376 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29336 AATAATAAGA
29346 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29377 GGTGGTACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39015 original size:32 final size:31
Alignment explanation
Indices: 38972--39035 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 31
38962 CACTTATCTT
38972 AGTTTAAAATTAAAGTTCAATTCATAACATC
1 AGTTTAAAATTAAAGTTCAATTCATAACATC
39003 AGTTTAGAAATTAAAGTTCAATTCATAACATC
1 AGTTTA-AAATTAAAGTTCAATTCATAACATC
39035 A
1 A
39036 ACGAGACATC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 6 0.19
32 26 0.81
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.34
Consensus pattern (31 bp):
AGTTTAAAATTAAAGTTCAATTCATAACATC
Found at i:48224 original size:19 final size:19
Alignment explanation
Indices: 48170--48232 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 19
48160 AATTAAAATT
* *
48170 GATTTTTTTCGGTTCAGATC
1 GATTTTTTT-GGTTCGGTTC
**
48190 GATTTTTTT-AAT-GGTTC
1 GATTTTTTTGGTTCGGTTC
48207 GATTTTTTTGGTTCGGTTC
1 GATTTTTTTGGTTCGGTTC
48226 GATTTTT
1 GATTTTT
48233 CAATGAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
17 12 0.34
18 2 0.06
19 12 0.34
20 9 0.26
ACGTcount: A:0.13, C:0.10, G:0.21, T:0.57
Consensus pattern (19 bp):
GATTTTTTTGGTTCGGTTC
Done.