Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001039.1 Hibiscus syriacus cultivar Beakdansim tig00002065_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: 55456
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:7647 original size:19 final size:19
Alignment explanation
Indices: 7625--7661 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
7615 TTGGCTTGAA
7625 AGAAAT-ATTTTGACACATG
1 AGAAATAATTTTGA-ACATG
7644 AGAAATAATTTTGAACAT
1 AGAAATAATTTTGAACAT
7662 CTACTAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (19 bp):
AGAAATAATTTTGAACATG
Found at i:13309 original size:55 final size:55
Alignment explanation
Indices: 13225--13710 Score: 534
Period size: 55 Copynumber: 8.8 Consensus size: 55
13215 ATACTTGAAA
* * * * * * *
13225 AATCTTCAA-ATAACGAGTCTGTTCCCTATTCTTTCAGGGAGTATAAAACTCAAAC
1 AATCTTCAACA-AACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
* * * * * * *
13280 AATCTTTAACAAACGTGTCTGATCCCTATTCATTCAGGGAGTATA-AGACTCAAAC
1 AATCTTCAACAAACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAAC
* ** * *
13335 AATCTTCAATAAACGGGTCCACTCCCTA-TCCGTTCAGGGAGTATAGAACTCGAAC
1 AATCTTCAACAAACGGGTCTGCTCTCTATTCC-TTCAGAGAGTATAGAACTCGAAC
* * * *
13390 GATCTTCATA-AAACGGTTCTGCTCTCTATTCATTCAGAGAGTATAGAACTCAAAC
1 AATCTTCA-ACAAACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
13445 AATCTTCAACAAACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AATCTTCAACAAACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
* *
13500 AATCTTCATA-AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAAAACTCGAAC
1 AATCTTCA-ACAAACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
* **
13555 AATCTTCAACAAATGGGTCCCCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AATCTTCAACAAACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
* * *
13610 AATCTTCATA-AAACGGGCCCGTTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AATCTTCA-ACAAACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
* * * ** *
13665 AATCTTCAACGAACTTGTTCACCTCCCTATTCCTTCAGAGAGTATA
1 AATCTTCAACAAAC-GGGTCTGCTCTCTATTCCTTCAGAGAGTATA
13711 TGACTCAATC
Statistics
Matches: 378, Mismatches: 41, Indels: 23
0.86 0.09 0.05
Matches are distributed among these distances:
54 6 0.02
55 341 0.90
56 31 0.08
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (55 bp):
AATCTTCAACAAACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
Found at i:15077 original size:7 final size:7
Alignment explanation
Indices: 15065--15258 Score: 57
Period size: 7 Copynumber: 29.6 Consensus size: 7
15055 TATTTTATTT
15065 ATTTTTC
1 ATTTTTC
15072 ATTTTTC
1 ATTTTTC
*
15079 TCTTTCTTC
1 -ATTT-TTC
*
15088 TTTTTTC
1 ATTTTTC
15095 -TTTTTC
1 ATTTTTC
15101 ATTTTT-
1 ATTTTTC
* *
15107 -TCTTCC
1 ATTTTTC
*
15113 ATTTTCCC
1 ATTTT-TC
15121 A-TTTTC
1 ATTTTTC
*
15127 -TATTTC
1 ATTTTTC
*
15133 -TTTTTT
1 ATTTTTC
*
15139 ACTTTTC
1 ATTTTTC
15146 ATTTTT-
1 ATTTTTC
**
15152 -TTCATC
1 ATTTTTC
15158 ATTTTTC
1 ATTTTTC
15165 A-TTTT-
1 ATTTTTC
*
15170 -TTTCTC
1 ATTTTTC
15176 ATTTTTC
1 ATTTTTC
*
15183 CTTTCTTC
1 ATTT-TTC
15191 -TTTTTC
1 ATTTTTC
*
15197 TTCTTTTC
1 AT-TTTTC
15205 ATTTTT-
1 ATTTTTC
*
15211 -TTATT-
1 ATTTTTC
15216 ATTTTTTC
1 A-TTTTTC
*
15224 A-TTAT-
1 ATTTTTC
15229 -TTTTTC
1 ATTTTTC
*
15235 ATTTTTT
1 ATTTTTC
15242 ATTTTTC
1 ATTTTTC
15249 ATTTTT-
1 ATTTTTC
15255 ATTT
1 ATTT
15259 CTTCTTCAAG
Statistics
Matches: 139, Mismatches: 26, Indels: 45
0.66 0.12 0.21
Matches are distributed among these distances:
5 16 0.12
6 29 0.21
7 72 0.52
8 19 0.14
9 3 0.02
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (7 bp):
ATTTTTC
Found at i:15096 original size:14 final size:14
Alignment explanation
Indices: 15066--15110 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 14
15056 ATTTTATTTA
15066 TTTTTCATTTTTCTC
1 TTTTTCATTTTT-TC
15081 TTTCTTC-TTTTTTC
1 TTT-TTCATTTTTTC
15095 TTTTTCATTTTTTC
1 TTTTTCATTTTTTC
15109 TT
1 TT
15111 CCATTTTCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.11
14 14 0.50
15 8 0.29
16 3 0.11
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTCATTTTTTC
Found at i:15155 original size:9 final size:9
Alignment explanation
Indices: 15141--15241 Score: 64
Period size: 9 Copynumber: 10.3 Consensus size: 9
15131 TCTTTTTTAC
15141 TTTTCATTT
1 TTTTCATTT
*
15150 TTTTCATCAT
1 TTTTCAT-TT
15160 TTTTCATTTT
1 TTTTCA-TTT
15170 TTTCTCATTTT
1 TTT-TCA-TTT
15181 TCCTTTC-TTCT
1 T--TTTCATT-T
*
15192 TTTTC-TTC
1 TTTTCATTT
15200 TTTTCATTT
1 TTTTCATTT
15209 TTTT-ATTATT
1 TTTTCA-T-TT
15219 TTTTCATTATT
1 TTTTCA-T-TT
15230 TTTTCATTT
1 TTTTCATTT
15239 TTT
1 TTT
15242 ATTTTTCATT
Statistics
Matches: 78, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
8 6 0.08
9 25 0.32
10 20 0.26
11 23 0.29
12 2 0.03
13 2 0.03
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTCATTT
Found at i:15162 original size:18 final size:18
Alignment explanation
Indices: 15141--15247 Score: 90
Period size: 19 Copynumber: 5.6 Consensus size: 18
15131 TCTTTTTTAC
15141 TTTTCATTTTTTTCATCAT
1 TTTTCATTTTTTTC-TCAT
15160 TTTTCATTTTTTTCTCAT
1 TTTTCATTTTTTTCTCAT
* * *
15178 TTTTCCTTTCTTCTTTTTCTT
1 TTTT-CATT-TT-TTTCTCAT
* *
15199 CTTTTCATTTTTTTATTATT
1 -TTTTCATTTTTTTCTCA-T
15219 TTTTCATTATTTTT-TCAT
1 TTTTCATT-TTTTTCTCAT
*
15237 TTTTTATTTTT
1 TTTTCATTTTT
15248 CATTTTTATT
Statistics
Matches: 73, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
17 3 0.04
18 16 0.22
19 31 0.42
20 10 0.14
21 9 0.12
22 4 0.05
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTCATTTTTTTCTCAT
Found at i:15163 original size:19 final size:17
Alignment explanation
Indices: 15122--15247 Score: 81
Period size: 19 Copynumber: 6.6 Consensus size: 17
15112 CATTTTCCCA
* *
15122 TTTTCTATTTCTTTTTTAC
1 TTTTC-ATTT-TTTTTCAT
15141 TTTTCATTTTTTTCATCAT
1 TTTTCATTTTTTT--TCAT
15160 TTTTCATTTTTTTCTCAT
1 TTTTCATTTTTTT-TCAT
* *
15178 TTTTCCTTTCTTCTTTTTCTT
1 TTTT-C-AT-TT-TTTTTCAT
*
15199 CTTTTCATTTTTTTATTATT
1 -TTTTCATTTTTTT-TCA-T
15219 TTTTCATTATTTTTTCAT
1 TTTTCATT-TTTTTTCAT
*
15237 TTTTTATTTTT
1 TTTTCATTTTT
15248 CATTTTTATT
Statistics
Matches: 87, Mismatches: 10, Indels: 22
0.73 0.08 0.18
Matches are distributed among these distances:
17 7 0.08
18 24 0.28
19 34 0.39
20 8 0.09
21 6 0.07
22 8 0.09
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTCATTTTTTTTCAT
Found at i:15177 original size:11 final size:10
Alignment explanation
Indices: 15141--15241 Score: 79
Period size: 11 Copynumber: 10.2 Consensus size: 10
15131 TCTTTTTTAC
15141 TTTTCA-TTT
1 TTTTCATTTT
**
15150 TTTTCATCAT
1 TTTTCATTTT
15160 TTTTCATTTT
1 TTTTCATTTT
15170 TTTCTCATTTT
1 TTT-TCATTTT
*
15181 TCCTTTC-TTCT
1 T--TTTCATTTT
*
15192 TTTTC--TTC
1 TTTTCATTTT
15200 TTTTCA-TTT
1 TTTTCATTTT
15209 TTTT-ATTATT
1 TTTTCATT-TT
15219 TTTTCATTATT
1 TTTTCATT-TT
15230 TTTTCATTTT
1 TTTTCATTTT
15240 TT
1 TT
15242 ATTTTTCATT
Statistics
Matches: 76, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
8 7 0.09
9 17 0.22
10 22 0.29
11 26 0.34
12 2 0.03
13 2 0.03
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTCATTTT
Found at i:15220 original size:103 final size:103
Alignment explanation
Indices: 15057--15254 Score: 248
Period size: 103 Copynumber: 1.9 Consensus size: 103
15047 TTTTATTTTA
15057 TTTTATTTATTTTTCATTTTTCTCTTTCTTCTTTTTTCTTTTTCATTTTTTCTTCCATTTTCCCA
1 TTTTATTTATTTTTCATTTTTCTCTTTCTTCTTTTTTCTTTTTCATTTTTTCTTCCATTTTCCCA
15122 TT-TTCTATTTC-TTTTTTACTTTTCATTTTTTTCATCAT
66 TTATT-T-TTTCATTTTTTACTTTTCATTTTTTTCATCAT
*
15160 TTTTCATTT-TTTTCTCATTTTTC-CTTTCTTC-TTTTTCTTCTTTTCATTTTTT-TAT-TATTT
1 TTTT-ATTTATTTT-TCATTTTTCTCTTTCTTCTTTTTTC-T-TTTTCATTTTTTCT-TCCATTT
** *
15220 TTTCATTATTTTTTCATTTTTTATTTTTCATTTTT
61 TCCCATTATTTTTTCATTTTTTACTTTTCATTTTT
15255 ATTTCTTCTT
Statistics
Matches: 84, Mismatches: 4, Indels: 14
0.82 0.04 0.14
Matches are distributed among these distances:
102 10 0.12
103 46 0.55
104 28 0.33
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (103 bp):
TTTTATTTATTTTTCATTTTTCTCTTTCTTCTTTTTTCTTTTTCATTTTTTCTTCCATTTTCCCA
TTATTTTTTCATTTTTTACTTTTCATTTTTTTCATCAT
Found at i:15237 original size:59 final size:58
Alignment explanation
Indices: 15130--15240 Score: 163
Period size: 59 Copynumber: 1.9 Consensus size: 58
15120 CATTTTCTAT
15130 TTCTTTTTTACTTTTCATTTTTTTCATCATTTTTCATTTTTTTCTCATTTTTCCTTTC
1 TTCTTTTTTACTTTTCATTTTTTTCATCATTTTTCATTTTTTTCTCATTTTTCCTTTC
* *
15188 TTCTTTTTCTTCTTTTCATTTTTTT-ATTATTTTTTCATTATTTTT-TCATTTTT
1 TTCTTTTT-TACTTTTCATTTTTTTCATCA-TTTTTCATT-TTTTTCTCATTTTT
15241 TATTTTTCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
58 11 0.23
59 32 0.67
60 5 0.10
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (58 bp):
TTCTTTTTTACTTTTCATTTTTTTCATCATTTTTCATTTTTTTCTCATTTTTCCTTTC
Found at i:24946 original size:45 final size:46
Alignment explanation
Indices: 24882--24978 Score: 144
Period size: 45 Copynumber: 2.1 Consensus size: 46
24872 TGTTATTCAC
*
24882 AAAAAAAATCCTAACCGCATGATATCTAATTCGCATGC-TTGTTCG
1 AAAAAAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
*
24927 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCATTTATTCG
1 AAAAA-AAATCCTAACCGCATGATATCTAATTCGCATGCA-TTATTCG
24974 AAAAA
1 AAAAA
24979 CGAAAATAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
45 33 0.70
46 3 0.06
47 11 0.23
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (46 bp):
AAAAAAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
Found at i:25385 original size:45 final size:47
Alignment explanation
Indices: 25317--25414 Score: 128
Period size: 45 Copynumber: 2.1 Consensus size: 47
25307 TGTTAATCAC
* * *
25317 AAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC-TTGTTCG
1 AAAAATAAATCCTAACCACATGATATCTAATTCACATGCATTATTCG
* *
25363 AAAAATAAA-CCTAACCATATGATATCTAGTTCACATGCATTTATTCG
1 AAAAATAAATCCTAACCACATGATATCTAATTCACATGCA-TTATTCG
25410 AAAAA
1 AAAAA
25415 CGAAAATAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
45 25 0.56
46 9 0.20
47 11 0.24
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (47 bp):
AAAAATAAATCCTAACCACATGATATCTAATTCACATGCATTATTCG
Found at i:25623 original size:436 final size:435
Alignment explanation
Indices: 24812--25682 Score: 1625
Period size: 436 Copynumber: 2.0 Consensus size: 435
24802 CTACCCACAT
24812 GCTGACTACCCAATCATGCTTTATCAGATCCTACCCAACATGATATCTACCCCCATGCTTTGTTA
1 GCTGACTACCCAATCATGCTTTATCAGATCCTACCCAACATGATATCTACCCCCATGCTTTGTTA
*
24877 TTCACAAAAAAAATCCTAACCGCATGATATCTAATTCGCATGCTTGTTCGAAAAATAAACCTAAC
66 ATCACAAAAAAAATCCTAACCGCATGATATCTAATTCGCATGCTTGTTCGAAAAATAAACCTAAC
* *
24942 CGCATGATATCTAGTTCGCATGCATTTATTCGAAAAACGAAAATAAATGACTCAAAAAAGCTTTT
131 CACATGATATCTAGTTCACATGCATTTATTCGAAAAACGAAAATAAATGACTCAAAAAAGCTTTT
25007 CCTTGTGTACCCTCCTCACAGGATTCTTAAGGTTCGAGTTTGGTTCAACCTAAGTTCAAGCTCTA
196 CCTTGTGTACCCTCCTCACAGGATTCTTAAGGTTCGAGTTTGGTTCAACCTAAGTTCAAGCTCTA
25072 TGTTCACTATATACTGGGTTCGGTTCTAAAGTAATAGGTTCTCGAATTGTCCTTGTCGGTGCCCC
261 TGTTCACTATATACTGGGTTCGGTTCTAAAGTAATAGGTTCTCGAATTGTCCTTGTCGGTGCCCC
* * * *
25137 CTTGGGTTGCCGAACCCTTAATCTTGGCCCATCACAGGCTTTAGGGGATCGAGTTCAATTTCGAG
326 CTTGGGCTACCGAACCCTCAATCTTGGCCCATCACAGGCTTTAAGGGATCGAGTTCAATTTCGAG
25202 GGAACACACCTCCTTATGTCCGTGCGAAGGTGAATACCATCACGA
391 GGAACACACCTCCTTATGTCCGTGCGAAGGTGAATACCATCACGA
25247 GCTGACTACCCAATCATGCTTTATCAGATCCTACCCAACATGATATCTACCCCCATGCTTTGTTA
1 GCTGACTACCCAATCATGCTTTATCAGATCCTACCCAACATGATATCTACCCCCATGCTTTGTTA
25312 ATCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTTGTTCGAAAAATAAACCTAA
66 ATCACAAAAA-AAATCCTAACCGCATGATATCTAATTCGCATGCTTGTTCGAAAAATAAACCTAA
*
25377 CCATATGATATCTAGTTCACATGCATTTATTCGAAAAACGAAAATAAATGACTCAAAAAAGCTTT
130 CCACATGATATCTAGTTCACATGCATTTATTCGAAAAACGAAAATAAATGACTCAAAAAAGCTTT
*
25442 TCCTTGTGTACCCTCCTCACAGGATTCTTAAGGTTCGGGTTTGGTTCAACCTAAGTTCAAGCTCT
195 TCCTTGTGTACCCTCCTCACAGGATTCTTAAGGTTCGAGTTTGGTTCAACCTAAGTTCAAGCTCT
*
25507 ATGTTCACTATATGCTGGGTTCGGTTCTAAAGTAATAGGTTCTCGAATTGTCCTTGTCGGTGCCC
260 ATGTTCACTATATACTGGGTTCGGTTCTAAAGTAATAGGTTCTCGAATTGTCCTTGTCGGTGCCC
*
25572 CCTTGGGCTACCGAACCCTCAATCTTGGCCCATCACAGGCTTTAAGGGATCGAGTTTAATTTCGA
325 CCTTGGGCTACCGAACCCTCAATCTTGGCCCATCACAGGCTTTAAGGGATCGAGTTCAATTTCGA
*
25637 GGGAACACACCTCCTTATGTCCGTGCGGAGGTGAATACCATCACGA
390 GGGAACACACCTCCTTATGTCCGTGCGAAGGTGAATACCATCACGA
25683 ACACCATAAG
Statistics
Matches: 423, Mismatches: 12, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
435 74 0.17
436 349 0.83
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (435 bp):
GCTGACTACCCAATCATGCTTTATCAGATCCTACCCAACATGATATCTACCCCCATGCTTTGTTA
ATCACAAAAAAAATCCTAACCGCATGATATCTAATTCGCATGCTTGTTCGAAAAATAAACCTAAC
CACATGATATCTAGTTCACATGCATTTATTCGAAAAACGAAAATAAATGACTCAAAAAAGCTTTT
CCTTGTGTACCCTCCTCACAGGATTCTTAAGGTTCGAGTTTGGTTCAACCTAAGTTCAAGCTCTA
TGTTCACTATATACTGGGTTCGGTTCTAAAGTAATAGGTTCTCGAATTGTCCTTGTCGGTGCCCC
CTTGGGCTACCGAACCCTCAATCTTGGCCCATCACAGGCTTTAAGGGATCGAGTTCAATTTCGAG
GGAACACACCTCCTTATGTCCGTGCGAAGGTGAATACCATCACGA
Found at i:30103 original size:23 final size:23
Alignment explanation
Indices: 30057--30121 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
30047 TAATTAAATT
*
30057 TAATATAAA-TTATAATTATAAAA
1 TAATATAAATTTA-AATTTTAAAA
* *
30080 TTATATAAATTTAAATTTTGAAA
1 TAATATAAATTTAAATTTTAAAA
* *
30103 TAATTTTAATTATAAATTT
1 TAATATAAATT-TAAATTT
30122 AAACTGATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
23 24 0.71
24 10 0.29
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TAATATAAATTTAAATTTTAAAA
Found at i:44098 original size:16 final size:16
Alignment explanation
Indices: 44068--44098 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44058 TAATATTGAA
*
44068 ACTTGAACTCGAAAAG
1 ACTTGAACTCAAAAAG
44084 ACTTGAACTCAAAAA
1 ACTTGAACTCAAAAA
44099 AAAAATTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.19
Consensus pattern (16 bp):
ACTTGAACTCAAAAAG
Done.