Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004875.1 Hibiscus syriacus cultivar Beakdansim tig00010988_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: 53569
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:521 original size:19 final size:18
Alignment explanation
Indices: 479--526 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
469 TGATGCAATT
* **
479 AGTATCGATACTGAGGTG
1 AGTATCGATACTAAGGAA
497 AGTATCGATACTAAGAGAA
1 AGTATCGATACTAAG-GAA
516 AGTATCGATAC
1 AGTATCGATAC
527 CATGGATTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (18 bp):
AGTATCGATACTAAGGAA
Found at i:1102 original size:60 final size:60
Alignment explanation
Indices: 1009--1293 Score: 430
Period size: 60 Copynumber: 4.8 Consensus size: 60
999 AACTGCTCTA
*
1009 AGATGAAAAGTTAAATGCCTAA-TGGTGCATTTTGGCAGAAAGGTGCCATTACTGCACGTT
1 AGATGAAAAGTTAAATGCCTAACT-GTGCATTTTGGCAGAAAGGTGCCATTAATGCACGTT
* * *
1069 AGATGAAAAGTTAAATGTCTAACTATGCATTTTGGCAGAAAGGTGCCATTAATGCAAGTT
1 AGATGAAAAGTTAAATGCCTAACTGTGCATTTTGGCAGAAAGGTGCCATTAATGCACGTT
* * * *
1129 AGATGAAGAGTTAAATGCCTAACGGTGCATTTTGGCAAAAATAG-GCCATTAATGCACGTT
1 AGATGAAAAGTTAAATGCCTAACTGTGCATTTTGGCAGAAA-GGTGCCATTAATGCACGTT
* * * *
1189 AGATGAAAAGTTAAATTCCTAACGGTGCATTTTGGCAGAAAGGAGCCATTACTGCACGTT
1 AGATGAAAAGTTAAATGCCTAACTGTGCATTTTGGCAGAAAGGTGCCATTAATGCACGTT
1249 AGATGAAAAGTTAAATGCCTAACTGTGCATTTTGGCAGAAAGGTG
1 AGATGAAAAGTTAAATGCCTAACTGTGCATTTTGGCAGAAAGGTG
1294 TAACATTCTC
Statistics
Matches: 203, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
59 1 0.00
60 200 0.99
61 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (60 bp):
AGATGAAAAGTTAAATGCCTAACTGTGCATTTTGGCAGAAAGGTGCCATTAATGCACGTT
Found at i:2098 original size:62 final size:63
Alignment explanation
Indices: 2028--2162 Score: 159
Period size: 63 Copynumber: 2.2 Consensus size: 63
2018 CATTCAACAG
* * *
2028 GTATCGATACCCTCTTGAAA-AAAAA-TCATCGAATATAA-TAAGTGTATCGATACACAGGTAGT
1 GTATCGATACCCCCTTGAAACAAAAACT-ATCAAATATAATTAA-TGTATCGATACACAGGCAGT
* * * * *
2090 GTATCGATACCCCCTTGAAACGAAAACTTTCAAATGTAATTTATGTATCGATACATAGGCAGT
1 GTATCGATACCCCCTTGAAACAAAAACTATCAAATATAATTAATGTATCGATACACAGGCAGT
2153 GTATCGATAC
1 GTATCGATAC
2163 ATCAGATAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
62 19 0.31
63 40 0.65
64 3 0.05
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (63 bp):
GTATCGATACCCCCTTGAAACAAAAACTATCAAATATAATTAATGTATCGATACACAGGCAGT
Found at i:3538 original size:60 final size:60
Alignment explanation
Indices: 3445--3659 Score: 304
Period size: 60 Copynumber: 3.6 Consensus size: 60
3435 GGGTGTTACA
* * *
3445 AAAGGTGTCAATAATGCAAGTTAGATGAAAAGTTAAATGTCTAACCGTGCATTTTGGCAG
1 AAAGGTGCCATTAATGCAAGTTAGATGAAAAGTTAAATGCCTAACCGTGCATTTTGGCAG
* * ** * *
3505 AAAGGTGCCATTACTGCACGTTAGATGAAAAGTTAAATGCCTAAATGTGTATTTTGGTAG
1 AAAGGTGCCATTAATGCAAGTTAGATGAAAAGTTAAATGCCTAACCGTGCATTTTGGCAG
* *
3565 AAATGTGCCATTAATGCAAGTTAGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCAG
1 AAAGGTGCCATTAATGCAAGTTAGATGAAAAGTTAAATGCCTAACCGTGCATTTTGGCAG
* * *
3625 AAATGTGCCATTACTGCACGTTAGATGAAAAGTTA
1 AAAGGTGCCATTAATGCAAGTTAGATGAAAAGTTA
3660 GAATAGTGCA
Statistics
Matches: 137, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 137 1.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (60 bp):
AAAGGTGCCATTAATGCAAGTTAGATGAAAAGTTAAATGCCTAACCGTGCATTTTGGCAG
Found at i:9646 original size:18 final size:18
Alignment explanation
Indices: 9623--9660 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
9613 AGGTCATGGT
9623 ATCGGTACTAGAAGAACA
1 ATCGGTACTAGAAGAACA
9641 ATCGGTACTAGAAGAACA
1 ATCGGTACTAGAAGAACA
9659 AT
1 AT
9661 ACCGATACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (18 bp):
ATCGGTACTAGAAGAACA
Found at i:10333 original size:60 final size:60
Alignment explanation
Indices: 10260--10516 Score: 300
Period size: 60 Copynumber: 4.3 Consensus size: 60
10250 AATTGCTCTA
* ** *
10260 AGATGAAAAGTTAAATGCTTAATTGTGCATTTTGGAAGAAATGTGTCATTAATGCAAGTT
1 AGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGAAGAAAGGTGTCATTAATGCAAGTT
** * * *
10320 AGATGAAAAGTTAAATGCCTAACGGTGCATTTT-GACAGAAAGGTACCATTAATACACGCT
1 AGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGA-AGAAAGGTGTCATTAATGCAAGTT
* * * * ** *
10380 AGATGAACAGTTAAATGTCTAACTGTGCATTTTGGCATTAAGATGTCATTAATGCAAGTT
1 AGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGAAGAAAGGTGTCATTAATGCAAGTT
* * * * * *
10440 AGATGAAAACTTAAATGCCTAATGGTTCATTTTGGCAGAAAGGTGTCATTATTGCACGTT
1 AGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGAAGAAAGGTGTCATTAATGCAAGTT
10500 AGATGAAAAGTTAAATG
1 AGATGAAAAGTTAAATG
10517 TAACACTCTC
Statistics
Matches: 162, Mismatches: 33, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
59 2 0.01
60 159 0.98
61 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (60 bp):
AGATGAAAAGTTAAATGCCTAACGGTGCATTTTGGAAGAAAGGTGTCATTAATGCAAGTT
Found at i:10473 original size:120 final size:121
Alignment explanation
Indices: 10260--10517 Score: 360
Period size: 120 Copynumber: 2.1 Consensus size: 121
10250 AATTGCTCTA
*
10260 AGATGAAAAGTTAAATG-CTTAATTGTGCATTTTGGAAGAAATGTGTCATTAATGCAAGTTAGAT
1 AGATGAAAAGTTAAATGTCTTAACTGTGCATTTTGGAAGAAATGTGTCATTAATGCAAGTTAGAT
*
10324 GAAAAGTTAAATGCCTAACGGTGCATTTTGACAGAAAGGTACCATTAATACACGCT
66 GAAAACTTAAATGCCTAACGGTGCATTTTGACAGAAAGGTACCATTAATACACGCT
* * **
10380 AGATGAACAGTTAAATGTC-TAACTGTGCATTTTGGCATTAA-GATGTCATTAATGCAAGTTAGA
1 AGATGAAAAGTTAAATGTCTTAACTGTGCATTTTGGAAGAAATG-TGTCATTAATGCAAGTTAGA
* * * ** * * *
10443 TGAAAACTTAAATGCCTAATGGTTCATTTTGGCAGAAAGGTGTCATTATTGCACGTT
65 TGAAAACTTAAATGCCTAACGGTGCATTTTGACAGAAAGGTACCATTAATACACGCT
10500 AGATGAAAAGTTAAATGT
1 AGATGAAAAGTTAAATGT
10518 AACACTCTCA
Statistics
Matches: 121, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
119 1 0.01
120 119 0.98
121 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (121 bp):
AGATGAAAAGTTAAATGTCTTAACTGTGCATTTTGGAAGAAATGTGTCATTAATGCAAGTTAGAT
GAAAACTTAAATGCCTAACGGTGCATTTTGACAGAAAGGTACCATTAATACACGCT
Found at i:11145 original size:27 final size:27
Alignment explanation
Indices: 11107--11177 Score: 124
Period size: 27 Copynumber: 2.6 Consensus size: 27
11097 GGGCTATGAA
* *
11107 ATTTATCCCAAAGGACCTATGTATTGT
1 ATTTGTCCCAAAAGACCTATGTATTGT
11134 ATTTGTCCCAAAAGACCTATGTATTGT
1 ATTTGTCCCAAAAGACCTATGTATTGT
11161 ATTTGTCCCAAAAGACC
1 ATTTGTCCCAAAAGACC
11178 ACTCCTTAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (27 bp):
ATTTGTCCCAAAAGACCTATGTATTGT
Found at i:12841 original size:60 final size:59
Alignment explanation
Indices: 12755--12984 Score: 291
Period size: 60 Copynumber: 3.8 Consensus size: 59
12745 TGCCTAGCTA
* *
12755 TGCATTTTGGCAGAAATGTGCCATTAATGCAAGTTAGATCAAAAGTTAAATGCATAACGG
1 TGCATTTTGGCAGAAAGGTGCCATTAATGCAAGTTAGATGAAAAGTTAAATGC-TAACGG
* ** *
12815 TGTATTTTGGCAGAAAGGTGTTATTAATACAAGTTAGATGAAAAGTTAAATGTCTAACGG
1 TGCATTTTGGCAGAAAGGTGCCATTAATGCAAGTTAGATGAAAAGTTAAATG-CTAACGG
* * * *
12875 TGCATTTTGAG-AGAAAGGGGTCATTACTGCACGTTAGATGAAAAGTTAAATGCCTAACGG
1 TGCATTTTG-GCAGAAAGGTGCCATTAATGCAAGTTAGATGAAAAGTTAAATG-CTAACGG
* * * *
12935 TGCATTTTGGCAAAAATGTGCCACTAATTCAAGTTAGATGAAAAGTTAAA
1 TGCATTTTGGCAGAAAGGTGCCATTAATGCAAGTTAGATGAAAAGTTAAA
12985 ACAATGTATT
Statistics
Matches: 146, Mismatches: 21, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
59 1 0.01
60 143 0.98
61 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.30
Consensus pattern (59 bp):
TGCATTTTGGCAGAAAGGTGCCATTAATGCAAGTTAGATGAAAAGTTAAATGCTAACGG
Found at i:15136 original size:27 final size:27
Alignment explanation
Indices: 15095--15183 Score: 90
Period size: 27 Copynumber: 3.3 Consensus size: 27
15085 GCGTCAACAA
* *
15095 ATATTCATCATATTAATTCAAATATTG
1 ATATTAATCACATTAATTCAAATATTG
* * *
15122 TTATTAATCGCATTAATTCAACTATTG
1 ATATTAATCACATTAATTCAAATATTG
* * *
15149 ATA-AAATTCACATTCATTCAAATATTA
1 ATATTAA-TCACATTAATTCAAATATTG
15176 ATATTAAT
1 ATATTAAT
15184 AATATTCATT
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
26 2 0.04
27 44 0.92
28 2 0.04
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.43
Consensus pattern (27 bp):
ATATTAATCACATTAATTCAAATATTG
Found at i:18029 original size:38 final size:38
Alignment explanation
Indices: 17987--18065 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 38
17977 AATTATAATT
17987 AATATTATTAAATTTATAATAAAAT-AAAAAATATTAAC
1 AATATTATTAAATTTATAAT-AAATGAAAAAATATTAAC
* * * * * *
18025 AATATTTTTTATTTTATTATAAATGTAAATATATTAAC
1 AATATTATTAAATTTATAATAAATGAAAAAATATTAAC
18063 AAT
1 AAT
18066 TTTTTTTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
37 4 0.12
38 30 0.88
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (38 bp):
AATATTATTAAATTTATAATAAATGAAAAAATATTAAC
Found at i:18252 original size:38 final size:38
Alignment explanation
Indices: 18201--18286 Score: 127
Period size: 38 Copynumber: 2.3 Consensus size: 38
18191 TTTCCCGTGC
*
18201 AACCACCAACCTACCTGAGATATTAATAGAAAATTAAT
1 AACCACCAACCTACCCGAGATATTAATAGAAAATTAAT
* * * *
18239 AACCACCAACCTACCCGAGTTATTAATGGATAATTATT
1 AACCACCAACCTACCCGAGATATTAATAGAAAATTAAT
18277 AACCACCAAC
1 AACCACCAAC
18287 TTATTGATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.43, C:0.26, G:0.08, T:0.23
Consensus pattern (38 bp):
AACCACCAACCTACCCGAGATATTAATAGAAAATTAAT
Found at i:18510 original size:38 final size:38
Alignment explanation
Indices: 18459--18534 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
18449 TTCAACCACC
* * *
18459 AACCACTAACCTA-CTCAGGTTATTAATGGATAATTAAT
1 AACCACCAACCTACCT-AGATTATTAATAGATAATTAAT
18497 AACCACCAACCTACCTAGATTATTAATAGATAATTAAT
1 AACCACCAACCTACCTAGATTATTAATAGATAATTAAT
18535 TACTGGTGCC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 32 0.94
39 2 0.06
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (38 bp):
AACCACCAACCTACCTAGATTATTAATAGATAATTAAT
Found at i:18573 original size:25 final size:25
Alignment explanation
Indices: 18545--18604 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
18535 TACTGGTGCC
** *
18545 ATTATTTTTTGTCATTATAATTAAT
1 ATTATTTTTCCTCATTATAATAAAT
18570 ATTATTTTTCCTCATTATAATAAAT
1 ATTATTTTTCCTCATTATAATAAAT
18595 ATTATTTTTC
1 ATTATTTTTC
18605 TACTACAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (25 bp):
ATTATTTTTCCTCATTATAATAAAT
Found at i:18989 original size:202 final size:205
Alignment explanation
Indices: 18740--19137 Score: 572
Period size: 202 Copynumber: 2.0 Consensus size: 205
18730 ACTTGAAAGT
* * *
18740 TTCTTCCGCAAGTTGATGTTATAAAAAACCTTTTCGAATTTCTTACTCATTTCTTTTTTATCTGC
1 TTCTTCCGCAAGTTGATGTTATAAAAAAACTTTTCGAATTTCTTACTCACTTCTTTTTTACCTGC
* *
18805 AACAACATATTAAAAATAATATTTTAATAACCTTTCCGAAATAGAGATATATTATTAAAATACGA
66 AACAACATATTAAAAATAATATTTTAAAAACCTTTCCGAAATAGACATATATTATTAAAATACGA
* *
18870 ATA-AATTTT-TTCCAATAATAC-T-TACA-TATTATAGATTGAAAGAAACTTTCGTTCAAAATT
131 ATATAATTTTATTCCAAGAATACTTATACATTATTATAGATTGAAAGAAAATTTCGTTCAAAATT
18930 TTCTCTACTA
196 TTCTCTACTA
*
18940 TTCTTCCGACAAGTTGATGTTATAAAAAAACTTTCTCGAATTTCTTACTCGCTTCTTTTTTACCT
1 TTCTTCCG-CAAGTTGATGTTATAAAAAAACTTT-TCGAATTTCTTACTCACTTCTTTTTTACCT
* * * * ****
19005 GCAACAATATATTAAAAATAATATTTTAAAAATCTTTTCGAAATAGACATATTTTATTTGTGTAC
64 GCAACAACATATTAAAAATAATATTTTAAAAACCTTTCCGAAATAGACATATATTATTAAAATAC
* * *
19070 GAATATAATTTTATTCGAAGAATACTTATATATTATTATAGATTGGAAGAAAATTTCGTTCAAAA
129 GAATATAATTTTATTCCAAGAATACTTATACATTATTATAGATTGAAAGAAAATTTCGTTCAAAA
19135 TTT
194 TTT
19138 ATGTGCTATT
Statistics
Matches: 172, Mismatches: 19, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
200 8 0.05
201 24 0.14
202 87 0.51
203 6 0.03
204 10 0.06
205 1 0.01
206 3 0.02
207 33 0.19
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (205 bp):
TTCTTCCGCAAGTTGATGTTATAAAAAAACTTTTCGAATTTCTTACTCACTTCTTTTTTACCTGC
AACAACATATTAAAAATAATATTTTAAAAACCTTTCCGAAATAGACATATATTATTAAAATACGA
ATATAATTTTATTCCAAGAATACTTATACATTATTATAGATTGAAAGAAAATTTCGTTCAAAATT
TTCTCTACTA
Found at i:20883 original size:2 final size:2
Alignment explanation
Indices: 20876--20906 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20866 GAATCGCTTC
20876 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
20907 AAGCTTGGGT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:39013 original size:36 final size:35
Alignment explanation
Indices: 38973--39040 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
38963 AGAGAACTGA
*
38973 TTCCTAGCAAACACAATTGACTGCCATGGATTATAG
1 TTCCTAGCAAACACAA-TGACTGCCATAGATTATAG
***
39009 TTCCTAGCATTGACAATGACTGCCATAGATTA
1 TTCCTAGCAAACACAATGACTGCCATAGATTA
39041 CATTGAACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 15 0.54
36 13 0.46
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29
Consensus pattern (35 bp):
TTCCTAGCAAACACAATGACTGCCATAGATTATAG
Found at i:52434 original size:96 final size:96
Alignment explanation
Indices: 52269--52558 Score: 474
Period size: 96 Copynumber: 3.0 Consensus size: 96
52259 GTTTCAGCAT
*
52269 GGTTCTGTCTAAAACTAGAGGGGTCTTTAATGGCAAACCTCTGGTAACTTCACCCCATCTATTAA
1 GGTTCTGTCTAAAACTGGAGGGGTC-TTAATGGCAAACCTCTGGTAACTTCACCCCATCTATTAA
* *
52334 CAAATTCCACGACAGTAATCCCATCTAATATA
65 CAAATTCCATGACAGTAATCCCATCTAACATA
*
52366 GGTTCTGTCTAAAACTGGAGGGGTCTTAATGGCAAGCCTCTGGTAACTTCACCCCATCTATTAAC
1 GGTTCTGTCTAAAACTGGAGGGGTCTTAATGGCAAACCTCTGGTAACTTCACCCCATCTATTAAC
* *
52431 AAATTTCATTG-CATTAATCCCATCTAACATA
66 AAATTCCA-TGACAGTAATCCCATCTAACATA
* * *
52462 GGTTCTGTCTAAAACTGGAGGGGTCTTAATGGCAAACCTCTGGTAACTTCATCCTAACTATTAAC
1 GGTTCTGTCTAAAACTGGAGGGGTCTTAATGGCAAACCTCTGGTAACTTCACCCCATCTATTAAC
52527 AAATTCCATGACAGTAATCCCATCTAACATA
66 AAATTCCATGACAGTAATCCCATCTAACATA
52558 G
1 G
52559 AGTGGTTCAT
Statistics
Matches: 179, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
95 2 0.01
96 152 0.85
97 25 0.14
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.30
Consensus pattern (96 bp):
GGTTCTGTCTAAAACTGGAGGGGTCTTAATGGCAAACCTCTGGTAACTTCACCCCATCTATTAAC
AAATTCCATGACAGTAATCCCATCTAACATA
Done.