Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006144.1 Hibiscus syriacus cultivar Beakdansim tig00014583_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: 73338
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:12095 original size:18 final size:18
Alignment explanation
Indices: 12072--12117 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
12062 GAGGAATGAA
12072 GCTTTTGTCAATTTTTAT
1 GCTTTTGTCAATTTTTAT
12090 GCTTTTGTCAATTTTTAT
1 GCTTTTGTCAATTTTTAT
* *
12108 ACATTTGTCA
1 GCTTTTGTCA
12118 GGGTATCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.20, C:0.13, G:0.11, T:0.57
Consensus pattern (18 bp):
GCTTTTGTCAATTTTTAT
Found at i:16571 original size:2 final size:2
Alignment explanation
Indices: 16564--16588 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16554 CGCGTGTATG
16564 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 T
16589 TATGAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20717 original size:35 final size:34
Alignment explanation
Indices: 20639--20718 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 34
20629 ATTTAAATTC
* *
20639 AACAAACTTACAATAAGAATTAAATGGTAAATGGT
1 AACAAAATTACAATAAGAATTAAATGGTAAAT-GA
*
20674 AACCAAATTACAATAACTGATATTAAATGGT-AAT-A
1 AACAAAATTACAATAA--GA-ATTAAATGGTAAATGA
20709 AACAAAATTA
1 AACAAAATTA
20719 ACTGAAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
35 23 0.61
37 5 0.13
38 10 0.26
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (34 bp):
AACAAAATTACAATAAGAATTAAATGGTAAATGA
Found at i:23451 original size:12 final size:12
Alignment explanation
Indices: 23426--23495 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
23416 ACGAAGATAT
* *
23426 CAGAAATCAAAA
1 CAGAATTCAGAA
23438 CAGAATTCAGAA
1 CAGAATTCAGAA
*
23450 CA-TATATCAGAA
1 CAGAAT-TCAGAA
* *
23462 CAGAATCCAGAT
1 CAGAATTCAGAA
*
23474 CAGAAATCAGAA
1 CAGAATTCAGAA
23486 CAGAATTCAG
1 CAGAATTCAG
23496 GTCATTTATC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:23458 original size:24 final size:24
Alignment explanation
Indices: 23431--23518 Score: 104
Period size: 24 Copynumber: 3.7 Consensus size: 24
23421 GATATCAGAA
* *
23431 ATCAAAACAGAATTCAGAACATAT
1 ATCAGAACAGAATTCAGATCATAT
* * *
23455 ATCAGAACAGAATCCAGATCAGAA
1 ATCAGAACAGAATTCAGATCATAT
* *
23479 ATCAGAACAGAATTCAGGTCATTT
1 ATCAGAACAGAATTCAGATCATAT
*
23503 ATCAGAACATAATTCA
1 ATCAGAACAGAATTCA
23519 AGTCGGAAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGATCATAT
Found at i:23528 original size:48 final size:48
Alignment explanation
Indices: 23424--23532 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 48
23414 AAACGAAGAT
* *
23424 ATCAGAAATCAAAACAGAATTCAGAACATATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGAACATATATCAGAACAGAATCAAG
** * *
23472 ATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACATAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAGAACATATATCAGAACAGAA-TCAAG
*
23521 -TCGGAAATCAGA
1 ATCAGAAATCAGA
23533 TAAAATATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
48 49 0.92
49 4 0.08
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGAACATATATCAGAACAGAATCAAG
Found at i:23530 original size:24 final size:24
Alignment explanation
Indices: 23425--23532 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
23415 AACGAAGATA
*
23425 TCAGAAATCAAAACAGAATTC-AG
1 TCAGAAATCAGAACAGAATTCAAG
* * * *
23448 AACATATATCAGAACAGAA-TCCAG
1 -TCAGAAATCAGAACAGAATTCAAG
*
23472 ATCAGAAATCAGAACAGAATTCAGG
1 -TCAGAAATCAGAACAGAATTCAAG
*** *
23497 TCATTTATCAGAACATAATTCAAG
1 TCAGAAATCAGAACAGAATTCAAG
*
23521 TCGGAAATCAGA
1 TCAGAAATCAGA
23533 TAAAATATTT
Statistics
Matches: 64, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 59 0.92
25 3 0.05
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.20
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAAG
Found at i:28609 original size:12 final size:11
Alignment explanation
Indices: 28567--28628 Score: 52
Period size: 12 Copynumber: 5.3 Consensus size: 11
28557 AGATATCAAA
*
28567 AATCAAAACAG
1 AATCAGAACAG
*
28578 AATTCAGAACAT
1 AA-TCAGAACAG
28590 ATATCAGAACAG
1 A-ATCAGAACAG
*
28602 AATCCAGATCAG
1 AAT-CAGAACAG
*
28614 AAATCGGAACAG
1 -AATCAGAACAG
28626 AAT
1 AAT
28629 TCAAGTAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
11 7 0.17
12 30 0.73
13 4 0.10
ACGTcount: A:0.52, C:0.18, G:0.15, T:0.16
Consensus pattern (11 bp):
AATCAGAACAG
Found at i:28623 original size:24 final size:24
Alignment explanation
Indices: 28566--28628 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
28556 AAGATATCAA
* * *
28566 AAATCAAAACAGAATTCAGAACAT
1 AAATCAGAACAGAATCCAGAACAG
* *
28590 ATATCAGAACAGAATCCAGATCAG
1 AAATCAGAACAGAATCCAGAACAG
*
28614 AAATCGGAACAGAAT
1 AAATCAGAACAGAAT
28629 TCAAGTAATT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.52, C:0.17, G:0.14, T:0.16
Consensus pattern (24 bp):
AAATCAGAACAGAATCCAGAACAG
Found at i:33740 original size:24 final size:24
Alignment explanation
Indices: 33711--33777 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
33701 AAGATATCAA
* *
33711 AAATCAAAACAGAATTCAGAACAT
1 AAATCAGAACAGAATTCAGAACAG
* * *
33735 ATATCAGAACAGAATCCAGATCAG
1 AAATCAGAACAGAATTCAGAACAG
*
33759 AAATCGGAACAGAATTCAG
1 AAATCAGAACAGAATTCAG
33778 GTAATTTATG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.51, C:0.18, G:0.15, T:0.16
Consensus pattern (24 bp):
AAATCAGAACAGAATTCAGAACAG
Found at i:33754 original size:12 final size:11
Alignment explanation
Indices: 33712--33773 Score: 52
Period size: 12 Copynumber: 5.3 Consensus size: 11
33702 AGATATCAAA
*
33712 AATCAAAACAG
1 AATCAGAACAG
*
33723 AATTCAGAACAT
1 AA-TCAGAACAG
33735 ATATCAGAACAG
1 A-ATCAGAACAG
*
33747 AATCCAGATCAG
1 AAT-CAGAACAG
*
33759 AAATCGGAACAG
1 -AATCAGAACAG
33771 AAT
1 AAT
33774 TCAGGTAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
11 7 0.17
12 30 0.73
13 4 0.10
ACGTcount: A:0.52, C:0.18, G:0.15, T:0.16
Consensus pattern (11 bp):
AATCAGAACAG
Found at i:37906 original size:17 final size:18
Alignment explanation
Indices: 37863--37903 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
37853 GAATTATATT
37863 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
37880 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
37898 ATTAAA
1 AGTAAA
37904 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:38318 original size:29 final size:29
Alignment explanation
Indices: 38282--38346 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
38272 TAGATCGGGG
* * * *
38282 AAATATAATCTAATCGGTGTTAGGTCAAA
1 AAATATAATCTAACCAGTATTAGATCAAA
*
38311 AAATATAATCTAACCAGTATTAGATCAAT
1 AAATATAATCTAACCAGTATTAGATCAAA
38340 AAATATA
1 AAATATA
38347 CCGATCACCG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.31
Consensus pattern (29 bp):
AAATATAATCTAACCAGTATTAGATCAAA
Found at i:43325 original size:60 final size:58
Alignment explanation
Indices: 43134--43326 Score: 174
Period size: 60 Copynumber: 3.2 Consensus size: 58
43124 TACATAATGT
* * ** * * * *
43134 ATCCTCAAAGTATGACCCTT-ATTTTAAATTAGTCTCTAAACTTTTAAATATTCTAATTTA
1 ATCC-CAAACTATGA-CCTTCATTCTAAATTAGTC-CCCAACTTTTGAACATTCCAATTTC
* * * *
43194 ATCCCTAAACTATGA-CTATCATTCCAAATTAGTACTCAAGCTTTTGAACATTTCAATTTC
1 ATCCC-AAACTATGACCT-TCATTCTAAATTAGTCCCCAA-CTTTTGAACATTCCAATTTC
43254 ATCCCCAAACTATGACCTTCATTCTAAATTAGTCCCCATACTTTTTGAACATTCCAATTTC
1 AT-CCCAAACTATGACCTTCATTCTAAATTAGTCCCCA-AC-TTTTGAACATTCCAATTTC
*
43315 ATCCCGAACTAT
1 ATCCCAAACTAT
43327 ACTTAAATAC
Statistics
Matches: 110, Mismatches: 15, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
58 2 0.02
59 6 0.05
60 76 0.69
61 26 0.24
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.38
Consensus pattern (58 bp):
ATCCCAAACTATGACCTTCATTCTAAATTAGTCCCCAACTTTTGAACATTCCAATTTC
Found at i:44125 original size:20 final size:19
Alignment explanation
Indices: 44080--44127 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
44070 ATAACCAACA
* *
44080 AATT-GCAACGCGATCTCG
1 AATTCGCAACGCGAACTCC
44098 AATTCGCAACGCGAACTCC
1 AATTCGCAACGCGAACTCC
44117 AATTTCGCAAC
1 AA-TTCGCAAC
44128 TCAGTTTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 4 0.15
19 14 0.54
20 8 0.31
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (19 bp):
AATTCGCAACGCGAACTCC
Found at i:44213 original size:20 final size:20
Alignment explanation
Indices: 44137--44213 Score: 84
Period size: 19 Copynumber: 3.9 Consensus size: 20
44127 CTCAGTTTCC
** *
44137 AAAATCGCAGTGTAAATAGT
1 AAAATCGCAACGTGAATAGT
44157 AAAAATCGCAACGTGAATAGT
1 -AAAATCGCAACGTGAATAGT
* *
44178 -AAACCACAACGTGAATAGT
1 AAAATCGCAACGTGAATAGT
*
44197 AAAATCGCAACGCGAAT
1 AAAATCGCAACGTGAAT
44214 TTAAAAAATC
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
19 17 0.36
20 13 0.28
21 17 0.36
ACGTcount: A:0.47, C:0.17, G:0.18, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGTGAATAGT
Found at i:44606 original size:20 final size:20
Alignment explanation
Indices: 44576--44662 Score: 93
Period size: 20 Copynumber: 4.3 Consensus size: 20
44566 CATATAGATT
*
44576 CGTTACGATTTTACTATTCA
1 CGTTACAATTTTACTATTCA
*
44596 TGTTACAATTTTACTATTCA
1 CGTTACAATTTTACTATTCA
* * *
44616 CATTACGATTTTTACTATTTA
1 CGTTAC-AATTTTACTATTCA
* * *
44637 CGTTGCGATTTTTCTATTCA
1 CGTTACAATTTTACTATTCA
44657 CGTTAC
1 CGTTAC
44663 GAAATTGGAG
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 37 0.70
21 16 0.30
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.48
Consensus pattern (20 bp):
CGTTACAATTTTACTATTCA
Found at i:44634 original size:41 final size:40
Alignment explanation
Indices: 44578--44664 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 40
44568 TATAGATTCG
*
44578 TTACGATTTTACTATTCATGTTACAATTTTACTATTCACA
1 TTACGATTTTACTATTCACGTTACAATTTTACTATTCACA
* * * * *
44618 TTACGATTTTTACTATTTACGTTGCGATTTTTCTATTCACG
1 TTACGA-TTTTACTATTCACGTTACAATTTTACTATTCACA
44659 TTACGA
1 TTACGA
44665 AATTGGAGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 6 0.15
41 34 0.85
ACGTcount: A:0.25, C:0.17, G:0.09, T:0.48
Consensus pattern (40 bp):
TTACGATTTTACTATTCACGTTACAATTTTACTATTCACA
Found at i:44701 original size:20 final size:20
Alignment explanation
Indices: 44678--44764 Score: 113
Period size: 20 Copynumber: 4.3 Consensus size: 20
44668 TGGAGTTTAT
44678 GTTGCGAATTTGA-TTTTAGC
1 GTTGCGAATTTGACTTTT-GC
* * *
44698 GTTGTGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGC
*
44718 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGC
*
44738 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGC
44758 GTTGCGA
1 GTTGCGA
44765 TTTACAGATT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 57 0.97
21 2 0.03
ACGTcount: A:0.17, C:0.11, G:0.26, T:0.45
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGC
Found at i:47800 original size:29 final size:29
Alignment explanation
Indices: 47758--47816 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
47748 GATATCTATC
*
47758 TAGAATATGCTTGAGAAGTCATTTGGTGA
1 TAGAATATGCTTGAGAAGTCATTTGCTGA
47787 TAGAATATGCTTGAGAAGTCATTTGCTGA
1 TAGAATATGCTTGAGAAGTCATTTGCTGA
47816 T
1 T
47817 TAGGTTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (29 bp):
TAGAATATGCTTGAGAAGTCATTTGCTGA
Found at i:67544 original size:252 final size:252
Alignment explanation
Indices: 67098--67834 Score: 1154
Period size: 252 Copynumber: 2.9 Consensus size: 252
67088 CTCCATCCGA
67098 GACCCGACCCGAATATATGAATTAGAAACCCGACCCGAACCGAAATAATAAAAAAATATTTTTAT
1 GACCCGACCCGAATATATGAATTAGAAACCCGA--C---CCGAAATAATAAAAAAATATTTTTAT
67163 TCAATAAAAATAGTGACTTAATTGAAAAAAT-TATATATAGA-GGGTATTATTGTAATTATTCCC
61 TCAATAAAAATAGTGACTTAATTGAAAAAATATATATATAGAGGGGTATTATTGTAATTATT-CC
*
67226 AAAATATAAGGTAAAATTATATATTTTTCGGGTCGGGTCGGGTATTTTTCACCCTAAACCCGAAC
125 TAAATATAAGGTAAAATTATATATTTTTCGGGTCGGGTCGGGTATTTTTCACCCTAAACCCGAAC
*
67291 CCGACCCGACCCGAATATCACACTTAAAAAA-CCGACTCGACCCGACCAAAATAAAGTTTCACCC
190 CCGACCCGACCC-AATATCACACTTAAAAAACCCGACCCGACCCGACC-AAATAAAGTTTCACCC
*
67355 GACCCGACCCGAATATATGAATTAGAAACCTGACCCGAAATAATAAAAAAATATTTTTATTCAAT
1 GACCCGACCCGAATATATGAATTAGAAACCCGACCCGAAATAATAAAAAAATATTTTTATTCAAT
* *
67420 AAAAACAGTGACTTAATTGAAAAAATATATATAGAGAGGGGTATTATTGTAATTATTCCTAAATA
66 AAAAATAGTGACTTAATTGAAAAAATATATATATAGAGGGGTATTATTGTAATTATTCCTAAATA
*
67485 TAAGGTAAAATTATATA-TTTTCGGGTCGGGTCAGGTATTTTTCACCCTAAACCCGAACCCGACC
131 TAAGGTAAAATTATATATTTTTCGGGTCGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACC
67549 CGACCCAAATATCACACTTAAAAAAACCCGACCCGACCCGACCAAATAAAGTTTCACCC
196 CGACCC-AATATCACACTT-AAAAAACCCGACCCGACCCGACCAAATAAAGTTTCACCC
* * *
67608 GACCCGACCTGAATATATGAATTAAAAACCCGACCTGAAATAAT-AAAAAA-A---TTATTCAAT
1 GACCCGACCCGAATATATGAATTAGAAACCCGACCCGAAATAATAAAAAAATATTTTTATTCAAT
67668 AAAAATAGTGACTTAATTGAAAAAA-ATTATATATAGAGGGGTATTATTGTAATTATTCCTAAAA
66 AAAAATAGTGACTTAATTGAAAAAATA-TATATATAGAGGGGTATTATTGTAATTATTCCT-AAA
67732 TATAAGGTAAAATTATATATTTTTTCGGGTCGGGTCGGGTA-TTTTCACCCTAAACCCGAACCCG
129 TATAAGGTAAAATTATATA-TTTTTCGGGTCGGGTCGGGTATTTTTCACCCTAAACCCGAACCCG
* * *
67796 ACTCGACCCAAGTATTACACTTAAAAAAACCTGACCCGA
193 ACCCGACCCAA-TATCACACTT-AAAAAACCCGACCCGA
67835 TCTGAACCCG
Statistics
Matches: 454, Mismatches: 17, Indels: 25
0.92 0.03 0.05
Matches are distributed among these distances:
247 1 0.00
248 65 0.14
249 24 0.05
250 56 0.12
251 20 0.04
252 126 0.28
253 95 0.21
254 34 0.07
255 1 0.00
257 32 0.07
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.27
Consensus pattern (252 bp):
GACCCGACCCGAATATATGAATTAGAAACCCGACCCGAAATAATAAAAAAATATTTTTATTCAAT
AAAAATAGTGACTTAATTGAAAAAATATATATATAGAGGGGTATTATTGTAATTATTCCTAAATA
TAAGGTAAAATTATATATTTTTCGGGTCGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACC
CGACCCAATATCACACTTAAAAAACCCGACCCGACCCGACCAAATAAAGTTTCACCC
Done.