Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004964.1 Hibiscus syriacus cultivar Beakdansim tig00011156_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: 42807
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2162 original size:13 final size:13
Alignment explanation
Indices: 2144--2178 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
2134 GTTATCCTAG
2144 AAGAAATATGGCA
1 AAGAAATATGGCA
2157 AAGAAATATGGCA
1 AAGAAATATGGCA
*
2170 AAAAAATAT
1 AAGAAATAT
2179 TATAAAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.60, C:0.06, G:0.17, T:0.17
Consensus pattern (13 bp):
AAGAAATATGGCA
Found at i:4439 original size:27 final size:27
Alignment explanation
Indices: 4382--4439 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
4372 ATTTTAAGCT
* *
4382 ATTTTACACTATAGGGGTATTTTGGTC
1 ATTTTACACTATAGGGGCATTTTGGTA
*
4409 ATTTTACACTTTAGGGGCATTATT-GTA
1 ATTTTACACTATAGGGGCATT-TTGGTA
4436 ATTT
1 ATTT
4440 ATCTATGGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 25 0.93
28 2 0.07
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.47
Consensus pattern (27 bp):
ATTTTACACTATAGGGGCATTTTGGTA
Found at i:7073 original size:20 final size:20
Alignment explanation
Indices: 7044--7082 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
7034 AAAATCTAAA
7044 GGCCGCAGAGCCTACCCAAG
1 GGCCGCAGAGCCTACCCAAG
* *
7064 GGCCGTAGAGCCTAGCCAA
1 GGCCGCAGAGCCTACCCAA
7083 TGGTCGCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.36, G:0.31, T:0.08
Consensus pattern (20 bp):
GGCCGCAGAGCCTACCCAAG
Found at i:7259 original size:24 final size:24
Alignment explanation
Indices: 7232--7294 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
7222 GAAATAAGAA
* *
7232 ATCAGAACAGAATTCAGATCAGAT
1 ATCAGAACAGAATCCAGACCAGAT
*
7256 ATCAGAACAGAATCCATACCAGAT
1 ATCAGAACAGAATCCAGACCAGAT
* *
7280 ATCATAATAGAATCC
1 ATCAGAACAGAATCC
7295 GGATAAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.21
Consensus pattern (24 bp):
ATCAGAACAGAATCCAGACCAGAT
Found at i:8812 original size:20 final size:22
Alignment explanation
Indices: 8780--8837 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 22
8770 TGACTTTTTG
8780 GTCAA-AGTCAACGGTCAA-AA
1 GTCAACAGTCAACGGTCAAGAA
8800 GTCAACAGT-AACGGTCAACGGAA
1 GTCAACAGTCAACGGTCAA--GAA
8823 GTCAACAGTCAACGG
1 GTCAACAGTCAACGG
8838 CTCGTTCCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 14 0.42
21 3 0.09
23 11 0.33
24 5 0.15
ACGTcount: A:0.40, C:0.22, G:0.24, T:0.14
Consensus pattern (22 bp):
GTCAACAGTCAACGGTCAAGAA
Found at i:10285 original size:30 final size:31
Alignment explanation
Indices: 10230--10313 Score: 127
Period size: 30 Copynumber: 2.7 Consensus size: 31
10220 TAGATTTATT
10230 CATGAATATTGATATAAATTTTAATAATTA-A
1 CATGAATATTGATATAAA-TTTAATAATTAGA
*
10261 CATGTATATTGATATAAATTTAATAATTAGA
1 CATGAATATTGATATAAATTTAATAATTAGA
*
10292 -ATGGATATTGATATAAATTTAA
1 CATGAATATTGATATAAATTTAA
10314 GTATTTTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
30 32 0.64
31 18 0.36
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (31 bp):
CATGAATATTGATATAAATTTAATAATTAGA
Found at i:10572 original size:20 final size:21
Alignment explanation
Indices: 10508--10582 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
10498 ATAAATAATA
*
10508 TTTATAAAAATTAATATATCT
1 TTTATAAAAATAAATATATCT
* *
10529 TTTATTAAAAATAAAAACA-C-
1 TTTA-TAAAAATAAATATATCT
*
10549 TTTAT-AAAATCAATATATCT
1 TTTATAAAAATAAATATATCT
10569 TTTATAAAAATAAA
1 TTTATAAAAATAAA
10583 ACGCTTTATA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
18 9 0.21
19 2 0.05
20 9 0.21
21 12 0.28
22 11 0.26
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTATAAAAATAAATATATCT
Found at i:10593 original size:38 final size:40
Alignment explanation
Indices: 10508--10594 Score: 133
Period size: 40 Copynumber: 2.2 Consensus size: 40
10498 ATAAATAATA
*
10508 TTTATAAAAATTAATATATCTTTTATTAAAAATAAAAACAC
1 TTTAT-AAAATCAATATATCTTTTATTAAAAATAAAAACAC
*
10549 TTTATAAAATCAATATATCTTTTA-TAAAAAT-AAAACGC
1 TTTATAAAATCAATATATCTTTTATTAAAAATAAAAACAC
10587 TTTATAAA
1 TTTATAAA
10595 TAACAATCTA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
38 14 0.32
39 7 0.16
40 18 0.41
41 5 0.11
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.39
Consensus pattern (40 bp):
TTTATAAAATCAATATATCTTTTATTAAAAATAAAAACAC
Found at i:15806 original size:2 final size:2
Alignment explanation
Indices: 15799--15832 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
15789 TCAAAATAGA
15799 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15833 CAAGTTAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15864 original size:15 final size:14
Alignment explanation
Indices: 15846--15875 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
15836 GTTAAACTAT
15846 AATACAAATATAAAA
1 AATACAAATA-AAAA
15861 AATACAAATAAAAA
1 AATACAAATAAAAA
15875 A
1 A
15876 TATAATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (14 bp):
AATACAAATAAAAA
Found at i:15890 original size:18 final size:19
Alignment explanation
Indices: 15867--15907 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
15857 AAAAAATACA
15867 AATAAAAAATATA-ATTAT
1 AATAAAAAATATATATTAT
*
15885 AAT-AAAAATATATTTTAT
1 AATAAAAAATATATATTAT
15903 AATAA
1 AATAA
15908 CTCACTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 9 0.45
18 10 0.50
19 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AATAAAAAATATATATTAT
Found at i:15893 original size:17 final size:18
Alignment explanation
Indices: 15871--15907 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
15861 AATACAAATA
15871 AAAAATATA-ATTATAAT
1 AAAAATATATATTATAAT
*
15888 AAAAATATATTTTATAAT
1 AAAAATATATATTATAAT
15906 AA
1 AA
15908 CTCACTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAATATATATTATAAT
Found at i:16322 original size:19 final size:18
Alignment explanation
Indices: 16298--16338 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
16288 AGGGGCTTTT
16298 ATAATAAAATGATTTATGA
1 ATAATAAAATGATTTAT-A
*
16317 ATAATAAACTGATTTATA
1 ATAATAAAATGATTTATA
16335 ATAA
1 ATAA
16339 AGATGAGAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (18 bp):
ATAATAAAATGATTTATA
Found at i:22466 original size:21 final size:21
Alignment explanation
Indices: 22442--22486 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
22432 GTGCAAATGG
22442 ACCCATACCGCCCAAAGGTAA
1 ACCCATACCGCCCAAAGGTAA
* *
22463 ACCCATACCGCCTAACGGTAA
1 ACCCATACCGCCCAAAGGTAA
22484 ACC
1 ACC
22487 ACCGGAATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.40, G:0.13, T:0.11
Consensus pattern (21 bp):
ACCCATACCGCCCAAAGGTAA
Found at i:28175 original size:23 final size:23
Alignment explanation
Indices: 28149--28194 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
28139 AATCTACGTT
28149 GTCCTTTGGAACAATACTATGTG
1 GTCCTTTGGAACAATACTATGTG
* * *
28172 GTCCTTTGGGACATTTCTATGTG
1 GTCCTTTGGAACAATACTATGTG
28195 ACACTTCGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (23 bp):
GTCCTTTGGAACAATACTATGTG
Found at i:28214 original size:24 final size:24
Alignment explanation
Indices: 28184--28235 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
28174 CCTTTGGGAC
* *
28184 ATTTCTATGTGACACTTCGGTGCA
1 ATTTCTAAGCGACACTTCGGTGCA
*
28208 ATTTCTAAGCGGCACTTCGGTGCA
1 ATTTCTAAGCGACACTTCGGTGCA
28232 ATTT
1 ATTT
28236 ATACGAGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (24 bp):
ATTTCTAAGCGACACTTCGGTGCA
Found at i:29285 original size:2 final size:2
Alignment explanation
Indices: 29280--29319 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
29270 AAATATTGTA
29280 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29320 TATTTAAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38982 original size:20 final size:21
Alignment explanation
Indices: 38943--38982 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
38933 TTTGGGTTTG
* *
38943 AGTATTGATATTGTGATGAAC
1 AGTATCGATACTGTGATGAAC
38964 AGTATCGATACTG-GATGAA
1 AGTATCGATACTGTGATGAA
38983 TTGGGGTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (21 bp):
AGTATCGATACTGTGATGAAC
Done.