Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006996.1 Hibiscus syriacus cultivar Beakdansim tig00018040_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: 95647
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Found at i:2429 original size:18 final size:18
Alignment explanation
Indices: 2402--2440 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2392 CCGAAAATTC
2402 ATTAAATATACATTTTTA
1 ATTAAATATACATTTTTA
* *
2420 ATTAATTATATATTTTTA
1 ATTAAATATACATTTTTA
2438 ATT
1 ATT
2441 TTATTGGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTAAATATACATTTTTA
Found at i:13593 original size:49 final size:48
Alignment explanation
Indices: 13487--13593 Score: 106
Period size: 49 Copynumber: 2.2 Consensus size: 48
13477 AAAAATTATC
* ** *
13487 GAAAATATTATTATTTTTATCAGTTTTGTTATTATTAGGCGTTTTACC
1 GAAAATGTTATTATTTTTATCAGTTTTGTTATTATTAGGCAATTTACA
**** * * *
13535 GGTTTTGTTATTTTTTTCTATCGGTTTTGTTATTGTTAGGCAATTTACA
1 GAAAATGTTATTATTTT-TATCAGTTTTGTTATTATTAGGCAATTTACA
13584 GAAAATGTTA
1 GAAAATGTTA
13594 AAAAAACATT
Statistics
Matches: 43, Mismatches: 15, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
48 11 0.26
49 32 0.74
ACGTcount: A:0.24, C:0.07, G:0.16, T:0.52
Consensus pattern (48 bp):
GAAAATGTTATTATTTTTATCAGTTTTGTTATTATTAGGCAATTTACA
Found at i:16300 original size:2 final size:2
Alignment explanation
Indices: 16289--16331 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
16279 ATTTTGAGTT
16289 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16330 TA
1 TA
16332 AATTTAAGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:18241 original size:35 final size:35
Alignment explanation
Indices: 18168--18244 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
18158 ATTACATTCT
* * * * *
18168 AAATTCCAAAATGCTTCAATTACATTCTAAACCTC
1 AAATTCAAAAATACTTCAATTACATGCCAAACCCC
*
18203 AAATTCAAAAATACTTCAATTACATGCCCAACCCC
1 AAATTCAAAAATACTTCAATTACATGCCAAACCCC
18238 AAATTCA
1 AAATTCA
18245 TAACCCATTC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.43, C:0.27, G:0.03, T:0.27
Consensus pattern (35 bp):
AAATTCAAAAATACTTCAATTACATGCCAAACCCC
Found at i:20214 original size:35 final size:34
Alignment explanation
Indices: 20168--20264 Score: 104
Period size: 35 Copynumber: 2.8 Consensus size: 34
20158 TAATGAATTA
* * *
20168 TGAATTTGAGGTTGGGCATGTAATTGAAGTATTTT
1 TGAATTTGAGGTTGAGAATGTAATTGAAGCA-TTT
* *
20203 TGAATTTGAGGTTTATAATGTAATTGAAGCATTT
1 TGAATTTGAGGTTGAGAATGTAATTGAAGCATTT
* * *
20237 TGAATTTTGGGGTTTAAAATGTAATTGA
1 TGAA-TTTGAGGTTGAGAATGTAATTGA
20265 TTATTGTGTT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
34 7 0.13
35 47 0.87
ACGTcount: A:0.30, C:0.02, G:0.25, T:0.43
Consensus pattern (34 bp):
TGAATTTGAGGTTGAGAATGTAATTGAAGCATTT
Found at i:20243 original size:34 final size:36
Alignment explanation
Indices: 20185--20264 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 36
20175 GAGGTTGGGC
* *
20185 ATGTAATTGAAGTATTTTTGAA-TTTGAGGTTTATA
1 ATGTAATTGAAGCATTTTTGAATTTTGAGGTTTAAA
*
20220 ATGTAATTGAAGCA-TTTTGAATTTTGGGGTTTAAA
1 ATGTAATTGAAGCATTTTTGAATTTTGAGGTTTAAA
20255 ATGTAATTGA
1 ATGTAATTGA
20265 TTATTGTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
34 7 0.17
35 34 0.83
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.45
Consensus pattern (36 bp):
ATGTAATTGAAGCATTTTTGAATTTTGAGGTTTAAA
Found at i:22335 original size:20 final size:20
Alignment explanation
Indices: 22289--22325 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
22279 TGTAAATATT
22289 AAATTTTAAAAATATATTCA
1 AAATTTTAAAAATATATTCA
22309 AAATTTTAAAAA-ATATT
1 AAATTTTAAAAATATATT
22326 TACTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATTTTAAAAATATATTCA
Found at i:22533 original size:13 final size:13
Alignment explanation
Indices: 22515--22614 Score: 65
Period size: 13 Copynumber: 7.7 Consensus size: 13
22505 TATAAACAAT
*
22515 TAATCAAACCAGC
1 TAATCAAATCAGC
* *
22528 TAATCAAATGAGT
1 TAATCAAATCAGC
* *
22541 TGATCAAACCAGC
1 TAATCAAATCAGC
* **
22554 TACTGGAATCAGC
1 TAATCAAATCAGC
* *
22567 TAATCAAATGAGT
1 TAATCAAATCAGC
* *
22580 TGATCAAACCAGC
1 TAATCAAATCAGC
* **
22593 TACTGGAATCAGC
1 TAATCAAATCAGC
22606 TAATCAAAT
1 TAATCAAAT
22615 GAGTTGATCA
Statistics
Matches: 58, Mismatches: 29, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
13 58 1.00
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (13 bp):
TAATCAAATCAGC
Found at i:22567 original size:39 final size:39
Alignment explanation
Indices: 22524--22685 Score: 270
Period size: 39 Copynumber: 4.2 Consensus size: 39
22514 TTAATCAAAC
22524 CAGCTAATCAAATGAGTTGATCAAACCAGCTACTGGAAT
1 CAGCTAATCAAATGAGTTGATCAAACCAGCTACTGGAAT
22563 CAGCTAATCAAATGAGTTGATCAAACCAGCTACTGGAAT
1 CAGCTAATCAAATGAGTTGATCAAACCAGCTACTGGAAT
* *
22602 CAGCTAATCAAATGAGTTGATCAAACCAGTTATTGGAAT
1 CAGCTAATCAAATGAGTTGATCAAACCAGCTACTGGAAT
* * *
22641 CGGCTAATCAAATGAGTCGATCAAACCAGTTACTGGAAT
1 CAGCTAATCAAATGAGTTGATCAAACCAGCTACTGGAAT
*
22680 CGGCTA
1 CAGCTA
22686 TCAGTTGTTT
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 118 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (39 bp):
CAGCTAATCAAATGAGTTGATCAAACCAGCTACTGGAAT
Found at i:22572 original size:26 final size:26
Alignment explanation
Indices: 22515--22630 Score: 70
Period size: 26 Copynumber: 4.5 Consensus size: 26
22505 TATAAACAAT
* *
22515 TAATCAAACCAGCTAATCAAATGAGT
1 TAATCAAACCAGCTAATCAAATCAGC
* * **
22541 TGATCAAACCAGCTACTGGAATCAGC
1 TAATCAAACCAGCTAATCAAATCAGC
** * * *
22567 TAATCAAATGAGTTGATCAAACCAGC
1 TAATCAAACCAGCTAATCAAATCAGC
* ** * * *
22593 TACTGGAATCAGCTAATCAAATGAGT
1 TAATCAAACCAGCTAATCAAATCAGC
*
22619 TGATCAAACCAG
1 TAATCAAACCAG
22631 TTATTGGAAT
Statistics
Matches: 61, Mismatches: 29, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
26 61 1.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (26 bp):
TAATCAAACCAGCTAATCAAATCAGC
Found at i:28718 original size:22 final size:22
Alignment explanation
Indices: 28693--28743 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
28683 CTGTTAGAGC
28693 CCGGCGATGGAAGCTGTGACTG
1 CCGGCGATGGAAGCTGTGACTG
*
28715 CCGGCGATGGAGGCTGTGACTG
1 CCGGCGATGGAAGCTGTGACTG
28737 CCGGCGA
1 CCGGCGA
28744 AAAAAGAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.16, C:0.25, G:0.43, T:0.16
Consensus pattern (22 bp):
CCGGCGATGGAAGCTGTGACTG
Found at i:46183 original size:13 final size:13
Alignment explanation
Indices: 46165--46208 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
46155 CACCCACCCC
46165 AAAAAAAAATTAA
1 AAAAAAAAATTAA
*
46178 AAAAAAAAACTAGA
1 AAAAAAAAATTA-A
46192 AGAAAAAATAATTAA
1 A-AAAAAA-AATTAA
46207 AA
1 AA
46209 TGGATGAGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 11 0.42
14 3 0.12
15 8 0.31
16 4 0.15
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.14
Consensus pattern (13 bp):
AAAAAAAAATTAA
Found at i:49616 original size:20 final size:21
Alignment explanation
Indices: 49577--49616 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
49567 AAGAGTTTAT
*
49577 ATAAATATATACATTTAAAAC
1 ATAAATATATACATTAAAAAC
*
49598 ATAATTATA-ACATTAAAAA
1 ATAAATATATACATTAAAAA
49617 TTATATCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAATATATACATTAAAAAC
Found at i:62588 original size:23 final size:23
Alignment explanation
Indices: 62560--62608 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
62550 ATGTCACGTC
62560 AATAAATTCAGAGATCAAAATAT
1 AATAAATTCAGAGATCAAAATAT
*
62583 AATAAATTCAGAGATCAAAATGT
1 AATAAATTCAGAGATCAAAATAT
62606 AAT
1 AAT
62609 GGTTTGATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.55, C:0.08, G:0.10, T:0.27
Consensus pattern (23 bp):
AATAAATTCAGAGATCAAAATAT
Found at i:74085 original size:19 final size:19
Alignment explanation
Indices: 74061--74125 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 19
74051 TTTTTTCATT
74061 AAAAAAATCGAACCGAACC
1 AAAAAAATCGAACCGAACC
* * **
74080 AAAAAATTCAAACC--ATT
1 AAAAAAATCGAACCGAACC
* *
74097 AAAAAAATCGATCTGAACC
1 AAAAAAATCGAACCGAACC
74116 GAAAAAAATC
1 -AAAAAAATC
74126 AATTTTGATT
Statistics
Matches: 33, Mismatches: 10, Indels: 5
0.69 0.21 0.10
Matches are distributed among these distances:
17 11 0.33
19 13 0.39
20 9 0.27
ACGTcount: A:0.58, C:0.20, G:0.08, T:0.14
Consensus pattern (19 bp):
AAAAAAATCGAACCGAACC
Found at i:74097 original size:36 final size:37
Alignment explanation
Indices: 74057--74127 Score: 108
Period size: 36 Copynumber: 1.9 Consensus size: 37
74047 GTGTTTTTTT
*
74057 CATTAAAAAAATCGAACCGAACC-AAAAAATTCAAAC
1 CATTAAAAAAATCGAACCGAACCGAAAAAAATCAAAC
* *
74093 CATTAAAAAAATCGATCTGAACCGAAAAAAATCAA
1 CATTAAAAAAATCGAACCGAACCGAAAAAAATCAA
74128 TTTTGATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
36 21 0.68
37 10 0.32
ACGTcount: A:0.58, C:0.20, G:0.07, T:0.15
Consensus pattern (37 bp):
CATTAAAAAAATCGAACCGAACCGAAAAAAATCAAAC
Found at i:83292 original size:32 final size:31
Alignment explanation
Indices: 83251--83314 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 31
83241 GATGTCCCGT
83251 TGATGTTATGAATTGAACTTTAATTTCTAAAC
1 TGATGTTATGAATTGAACTTTAATTT-TAAAC
83283 TGATGTTATGAATTGAACTTTAATTTTAAAC
1 TGATGTTATGAATTGAACTTTAATTTTAAAC
83314 T
1 T
83315 AAGATAAGTG
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:0.34, C:0.08, G:0.12, T:0.45
Consensus pattern (31 bp):
TGATGTTATGAATTGAACTTTAATTTTAAAC
Found at i:84113 original size:24 final size:22
Alignment explanation
Indices: 84093--84138 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
84083 TCATAATTAC
*
84093 TATT-TTAAAAATATATCTAAT
1 TATTATTAAAAAAATATCTAAT
84114 TATTATTAAAAAAATATCTAAT
1 TATTATTAAAAAAATATCTAAT
84136 TAT
1 TAT
84139 ATATGTGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (22 bp):
TATTATTAAAAAAATATCTAAT
Found at i:92794 original size:2 final size:2
Alignment explanation
Indices: 92787--92815 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
92777 ATGTACCACC
92787 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
92816 TCTTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:93541 original size:16 final size:16
Alignment explanation
Indices: 93520--93559 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
93510 ATTTCAGCGA
*
93520 AACCAAAATCAACTAG
1 AACCAAAATCAACCAG
* *
93536 AACCAAAATTAACCCG
1 AACCAAAATCAACCAG
93552 AACCAAAA
1 AACCAAAA
93560 CCGAAATTAA
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:0.57, C:0.28, G:0.05, T:0.10
Consensus pattern (16 bp):
AACCAAAATCAACCAG
Found at i:94388 original size:32 final size:31
Alignment explanation
Indices: 94314--94389 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 31
94304 ACCAATCTAA
*
94314 TATTGACCGACCCGAAATCTAATCGATTCGG
1 TATTGACCGACCCAAAATCTAATCGATTCGG
* *
94345 TATTAAACGACCCAAAAATC-AATCGA-TCTGG
1 TATTGACCGACCC-AAAATCTAATCGATTC-GG
94376 TATTGACCCGACCC
1 TATTGA-CCGACCC
94390 GATATTGACC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
30 2 0.05
31 24 0.65
32 11 0.30
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.24
Consensus pattern (31 bp):
TATTGACCGACCCAAAATCTAATCGATTCGG
Done.