Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003059.1 Hibiscus syriacus cultivar Beakdansim tig00006376_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: 59659
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:4509 original size:13 final size:12
Alignment explanation
Indices: 4491--4553 Score: 55
Period size: 13 Copynumber: 5.5 Consensus size: 12
4481 GCTTGTTTTC
4491 TCTTTTTGAATTT
1 TCTTTTTG-ATTT
*
4504 TCTTTTT-CTTT
1 TCTTTTTGATTT
4515 TCTTTTCTGATTT
1 TCTTTT-TGATTT
4528 TCTTTTT--TTT
1 TCTTTTTGATTT
*
4538 T-TTTTT-CTTT
1 TCTTTTTGATTT
4548 TCTTTT
1 TCTTTT
4554 CTTTTTGCAC
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
9 5 0.11
10 8 0.18
11 13 0.30
12 2 0.05
13 16 0.36
ACGTcount: A:0.05, C:0.13, G:0.03, T:0.79
Consensus pattern (12 bp):
TCTTTTTGATTT
Found at i:4515 original size:5 final size:5
Alignment explanation
Indices: 4501--4558 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
4491 TCTTTTTGAA
* *
4501 TTTTC TTTTTC TTTTC TTTTC TGATTTTC TTTTT TTTTT TTTTC TTTTC
1 TTTTC -TTTTC TTTTC TTTTC ---TTTTC TTTTC TTTTC TTTTC TTTTC
4550 TTTTC TTTT
1 TTTTC TTTT
4559 TGCACTCCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
5 37 0.79
6 5 0.11
8 5 0.11
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:4520 original size:24 final size:23
Alignment explanation
Indices: 4491--4558 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 23
4481 GCTTGTTTTC
4491 TCTTTTTGAATTTTCTTTTTCTTT
1 TCTTTTTG-ATTTTCTTTTTCTTT
4515 TCTTTTCTGATTTTCTTTTT-TTT
1 TCTTTT-TGATTTTCTTTTTCTTT
*
4538 T-TTTTT-CTTTTC-TTTTCTTT
1 TCTTTTTGATTTTCTTTTTCTTT
4558 T
1 T
4559 TGCACTCCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
19 4 0.10
20 9 0.22
21 1 0.02
22 4 0.10
23 4 0.10
24 17 0.41
25 2 0.05
ACGTcount: A:0.04, C:0.13, G:0.03, T:0.79
Consensus pattern (23 bp):
TCTTTTTGATTTTCTTTTTCTTT
Found at i:10259 original size:30 final size:30
Alignment explanation
Indices: 10225--10283 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
10215 ATGTAAATAC
* * *
10225 ATTATATAATGTAATGATATTAAATGACAT
1 ATTATATAATGTAATAACATTAAAGGACAT
10255 ATTATATAATGTAATAACATTAAAGGACA
1 ATTATATAATGTAATAACATTAAAGGACA
10284 AAATTTGGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (30 bp):
ATTATATAATGTAATAACATTAAAGGACAT
Found at i:18253 original size:21 final size:20
Alignment explanation
Indices: 18225--18265 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
18215 TTGCCTTAAG
*
18225 AAGGTTTCTTTTGTATCTTC
1 AAGGTTTCTTTTCTATCTTC
18245 AAGGATTTCTTTTCTATCTTC
1 AAGG-TTTCTTTTCTATCTTC
18266 TTGTATTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.17, C:0.17, G:0.12, T:0.54
Consensus pattern (20 bp):
AAGGTTTCTTTTCTATCTTC
Found at i:21639 original size:24 final size:24
Alignment explanation
Indices: 21612--21699 Score: 115
Period size: 24 Copynumber: 3.7 Consensus size: 24
21602 ATCATAACAT
* *
21612 AATCCAGGTAAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCAGATCAG
21636 AATCCAGGTCAAGTATTCA-ATCAG
1 AATCCAGGTCAAGTA-TCAGATCAG
* *
21660 AATCCAAGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCAGATCAG
*
21684 AATCCAGGTCAGGTAT
1 AATCCAGGTCAAGTAT
21700 TATAATAGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
23 2 0.04
24 51 0.91
25 3 0.05
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCAGATCAG
Found at i:24184 original size:13 final size:13
Alignment explanation
Indices: 24166--24194 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
24156 GGTCAACGCC
24166 GGTCAACGGGTCG
1 GGTCAACGGGTCG
24179 GGTCAACGGGTCG
1 GGTCAACGGGTCG
24192 GGT
1 GGT
24195 AGGGTAGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.21, G:0.48, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:26344 original size:24 final size:23
Alignment explanation
Indices: 26327--26413 Score: 122
Period size: 24 Copynumber: 3.7 Consensus size: 23
26317 ATCATAACAT
26327 AATCCAGGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCAGATC-A
26351 AATCCAGGTCAAGTATTCA-ATCA
1 AATCCAGGTCAAGTA-TCAGATCA
*
26374 GAATCCAGGTCAAGTATCCGATCA
1 -AATCCAGGTCAAGTATCAGATCA
*
26398 AATCCAGGTCAGGTAT
1 AATCCAGGTCAAGTAT
26414 TATAATAGAA
Statistics
Matches: 58, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
23 18 0.31
24 37 0.64
25 3 0.05
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (23 bp):
AATCCAGGTCAAGTATCAGATCA
Found at i:26362 original size:12 final size:13
Alignment explanation
Indices: 26327--26408 Score: 52
Period size: 12 Copynumber: 6.8 Consensus size: 13
26317 ATCATAACAT
26327 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
26340 TAT-CAGATCAA-
1 AATCCAGGTCAAG
26351 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* * *
26364 TATTCA-ATC-AG
1 AATCCAGGTCAAG
26375 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
26388 TATCC-GATC-A-
1 AATCCAGGTCAAG
26398 AATCCAGGTCA
1 AATCCAGGTCA
26409 GGTATTATAA
Statistics
Matches: 49, Mismatches: 14, Indels: 13
0.64 0.18 0.17
Matches are distributed among these distances:
10 4 0.08
11 12 0.24
12 21 0.43
13 12 0.24
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (13 bp):
AATCCAGGTCAAG
Found at i:41418 original size:23 final size:24
Alignment explanation
Indices: 41392--41460 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 24
41382 TCTGAATATC
*
41392 TAAACGAACTTGTTCTTGAACAT-
1 TAAACGAACTTGTTCATGAACATA
* * *
41415 TAAATGAACATGTTCACGAACATA
1 TAAACGAACTTGTTCATGAACATA
*
41439 TAAACGAA-TATGTTCGTGAACA
1 TAAACGAACT-TGTTCATGAACA
41461 CCAAATGAAC
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
23 19 0.53
24 17 0.47
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (24 bp):
TAAACGAACTTGTTCATGAACATA
Found at i:41582 original size:35 final size:35
Alignment explanation
Indices: 41537--41618 Score: 121
Period size: 35 Copynumber: 2.3 Consensus size: 35
41527 CACGAATACG
*
41537 AAATTTTAAAAATAAACAAATGAACAATAACAT-A
1 AAATTTTAAAAATAAACAAACGAACAATAACATGA
* *
41571 AACATTTTAAAAATAAGCAAACGAACAATAATATGA
1 AA-ATTTTAAAAATAAACAAACGAACAATAACATGA
41607 AAATTTTAAAAA
1 AAATTTTAAAAA
41619 GACCAACAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
34 2 0.05
35 38 0.88
36 3 0.07
ACGTcount: A:0.62, C:0.09, G:0.05, T:0.24
Consensus pattern (35 bp):
AAATTTTAAAAATAAACAAACGAACAATAACATGA
Found at i:45710 original size:15 final size:15
Alignment explanation
Indices: 45690--45770 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
45680 TTCCAGAAAA
45690 TGAATTACTGGAATT
1 TGAATTACTGGAATT
45705 TGAATTACTGGAATT
1 TGAATTACTGGAATT
*
45720 TGAATTACTGGAA-A
1 TGAATTACTGGAATT
45734 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
45749 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
45763 TGAATTAC
1 TGAATTAC
45771 ATTTCTGTAA
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
14 25 0.42
15 35 0.58
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.36
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:45746 original size:29 final size:29
Alignment explanation
Indices: 45690--45770 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
45680 TTCCAGAAAA
*
45690 TGAATTACTGGAATTTGAATTACTGGAATT
1 TGAATTACTGGAA-ATGAATTACTGGAATT
45720 TGAATTACTGGAAATGAATTACTGGAATT
1 TGAATTACTGGAAATGAATTACTGGAATT
45749 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGG-AAATGAATTAC
45771 ATTTCTGTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
28 4 0.08
29 32 0.65
30 13 0.27
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.36
Consensus pattern (29 bp):
TGAATTACTGGAAATGAATTACTGGAATT
Found at i:45750 original size:44 final size:43
Alignment explanation
Indices: 45687--45770 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 43
45677 GTTTTCCAGA
**
45687 AAATGAATTACTGGAATTTGAATTACTGGAATTTGAATTACTGG
1 AAATGAATTACTGGAATTTGAATT-CTGGAAAATGAATTACTGG
45731 AAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 AAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
45771 ATTTCTGTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 14 0.37
44 24 0.63
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.35
Consensus pattern (43 bp):
AAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACTGG
Found at i:45776 original size:20 final size:20
Alignment explanation
Indices: 45753--45822 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
45743 GGAATTTGAA
45753 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
45773 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
45793 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
45813 TTCTGGAAAA
1 TTCTGGAAAA
45823 CATCTGGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:46040 original size:25 final size:25
Alignment explanation
Indices: 45989--46128 Score: 85
Period size: 25 Copynumber: 5.3 Consensus size: 25
45979 TTTACTAAAA
45989 TATTATTGAAATATATAAATAATATTAT
1 TATTATT-AAATATA-AAA-AATATTAT
46017 TCATTATTAAATATAAAAAA-ATTAT
1 T-ATTATTAAATATAAAAAATATTAT
*
46042 TATATATTAAA-ATAAAAATATAATAT
1 TAT-TATTAAATATAAAAA-ATATTAT
* * *
46068 CT-TATATT-ATTATAATATAAT-TGAT
1 -TAT-TATTAAATATAA-AAAATATTAT
46093 TATT-TTATAATATTAAAAATATATATAT
1 TATTATTA-AATA-TAAAAA-ATAT-TAT
46121 TATTATTA
1 TATTATTA
46129 TTATAAATAT
Statistics
Matches: 89, Mismatches: 8, Indels: 29
0.71 0.06 0.23
Matches are distributed among these distances:
23 2 0.02
24 11 0.12
25 23 0.26
26 23 0.26
27 7 0.08
28 14 0.16
29 9 0.10
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (25 bp):
TATTATTAAATATAAAAAATATTAT
Found at i:46082 original size:26 final size:25
Alignment explanation
Indices: 46033--46173 Score: 68
Period size: 26 Copynumber: 5.8 Consensus size: 25
46023 TTAAATATAA
**
46033 AAAAATT-AT-TA-TATATTAAAAT
1 AAAAATTAATATATTATATTATTAT
*
46055 AAAAATATAATATCTTATATTATTAT
1 AAAAAT-TAATATATTATATTATTAT
* * *
46081 AATATAATTGAT-TATTTTA-TAATATT
1 AA-A-AATTAATATATTATATTATTA-T
46107 AAAAA-TATATATATTATTATTATTAT
1 AAAAATTA-ATATATTA-TATTATTAT
* *
46133 AAATATTAATA-AATATATT-TTA-
1 AAAAATTAATATATTATATTATTAT
* *
46155 AATATTTAATA-ATTATATT
1 AAAAATTAATATATTATATT
46174 TTGATGAAAA
Statistics
Matches: 91, Mismatches: 16, Indels: 24
0.69 0.12 0.18
Matches are distributed among these distances:
22 21 0.23
23 5 0.05
24 10 0.11
25 13 0.14
26 29 0.32
27 10 0.11
28 3 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (25 bp):
AAAAATTAATATATTATATTATTAT
Found at i:46095 original size:23 final size:22
Alignment explanation
Indices: 46069--46140 Score: 54
Period size: 23 Copynumber: 3.1 Consensus size: 22
46059 ATATAATATC
* *
46069 TTATATTATTATAATATAATTGA
1 TTATATTATTATAATAAAAAT-A
* * *
46092 TTATTTTATAATATTAAAAATA
1 TTATATTATTATAATAAAAATA
* *
46114 TATATATTATTATTATTATAAATA
1 T-TATATTATTA-TAATAAAAATA
46138 TTA
1 TTA
46141 ATAAATATAT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
22 2 0.05
23 26 0.67
24 11 0.28
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (22 bp):
TTATATTATTATAATAAAAATA
Found at i:46133 original size:18 final size:18
Alignment explanation
Indices: 46072--46140 Score: 54
Period size: 18 Copynumber: 3.9 Consensus size: 18
46062 TAATATCTTA
*
46072 TATTATTATA-ATATAAT
1 TATTATTATATATATTAT
*
46089 TGATTATT-T-TATAATAT
1 T-ATTATTATATATATTAT
** *
46106 TAAAAATATATATATTAT
1 TATTATTATATATATTAT
*
46124 TATTATTATAAATATTA
1 TATTATTATATATATTA
46141 ATAAATATAT
Statistics
Matches: 38, Mismatches: 10, Indels: 7
0.69 0.18 0.13
Matches are distributed among these distances:
16 3 0.08
17 9 0.24
18 26 0.68
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (18 bp):
TATTATTATATATATTAT
Found at i:46156 original size:21 final size:22
Alignment explanation
Indices: 46127--46175 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
46117 ATATTATTAT
*
46127 TATTATAAATA-TTAATAAATA
1 TATTTTAAATATTTAATAAATA
*
46148 TATTTTAAATATTTAATAATTA
1 TATTTTAAATATTTAATAAATA
46170 TATTTT
1 TATTTT
46176 GATGAAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTTTAAATATTTAATAAATA
Found at i:46406 original size:42 final size:42
Alignment explanation
Indices: 46347--46466 Score: 195
Period size: 42 Copynumber: 2.9 Consensus size: 42
46337 ATGAATTACA
*
46347 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
46389 TTCCGGAAAACGAATTACGTGAAACAAACACAGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* * *
46431 TTTCGAAAAACGAATTACGTGAAACAAACATGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
46467 TTCGGGGAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.46, C:0.17, G:0.19, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:46825 original size:157 final size:154
Alignment explanation
Indices: 46518--46854 Score: 466
Period size: 157 Copynumber: 2.2 Consensus size: 154
46508 AACAGACCCT
* * * *
46518 AAATTTGAACCACATGCTCCTAAATCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTAG
1 AAATTTG-AGCACATGCTCCTAAACCATAATAGAAAACATGTGTACTTTCAATTCCTCTTTTTAG
* * *
46583 TAACAATTTTTTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCCTTATTTCTTTAATTCGTCA
65 TAACAATTTTTTTTTCAATTTAGTCCTTCAATTTTTCACAATCTCCTTATTTCTTCAATTCCTCA
* *
46648 TTTATTTTTAGTCTCTTTTTTTTTACC
130 TTTATTTTAAGTCAC--TTTTTTTACC
46675 AAATTTGAGTCACATGCTCCTAAACCATAATAGAAAACATGTGTACTTTCAATTCCTCTTTTT-G
1 AAATTTGAG-CACATGCTCCTAAACCATAATAGAAAACATGTGTACTTTCAATTCCTCTTTTTAG
* *
46739 ATAACAAAATCTTTTTTTT-TATTTAGTCCTTTAATTTTTCACAATCTCCTTATTTCTTCAATTC
65 -TAAC--AAT-TTTTTTTTCAATTTAGTCCTTCAATTTTTCACAATCTCCTTATTTCTTCAATTC
46803 CTCATTTATTTTAAGT-AC-TTTTTTACC
126 CTCATTTATTTTAAGTCACTTTTTTTACC
46830 AAATTTGAGCTACATGCTCCTAAAC
1 AAATTTGAGC-ACATGCTCCTAAAC
46855 TATAGTACCA
Statistics
Matches: 163, Mismatches: 11, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
154 1 0.01
155 32 0.20
156 2 0.01
157 61 0.37
158 1 0.01
159 58 0.36
160 8 0.05
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.47
Consensus pattern (154 bp):
AAATTTGAGCACATGCTCCTAAACCATAATAGAAAACATGTGTACTTTCAATTCCTCTTTTTAGT
AACAATTTTTTTTTCAATTTAGTCCTTCAATTTTTCACAATCTCCTTATTTCTTCAATTCCTCAT
TTATTTTAAGTCACTTTTTTTACC
Found at i:52214 original size:19 final size:20
Alignment explanation
Indices: 52173--52215 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
52163 GAGATGAGTC
* * *
52173 TTTTTAAAATAATTATTTGA
1 TTTTCAAAATAAATATATGA
52193 TTTTCAAAATAAATATAT-A
1 TTTTCAAAATAAATATATGA
52212 TTTT
1 TTTT
52216 ACCGAGATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
TTTTCAAAATAAATATATGA
Done.