Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007194.1 Hibiscus syriacus cultivar Beakdansim tig00018960_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: 74256
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Found at i:16733 original size:76 final size:76
Alignment explanation
Indices: 16572--16716 Score: 204
Period size: 76 Copynumber: 1.9 Consensus size: 76
16562 ATTTTAAATA
* * *
16572 TTATATTTTATCTTTGTTTTAGGTATTTTTGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTATTTTAGGTATTTTTGTTTAAATAGGTTTTAGTATTTTAATCAAGATTTA
* *
16637 GGATATTATTT
66 AGATATTATTC
*
16648 TTATATTTTATCTTTATTTTAGGTATTTTAT-TTTAAATA-GTTTTAAGTATTTTAATCAGGATT
1 TTATATTTTATCTTTATTTTAGGTATTTT-TGTTTAAATAGGTTTT-AGTATTTTAATCAAGATT
16711 TAAGAT
64 TAAGAT
16717 GTTTTAGCTT
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
75 5 0.08
76 56 0.90
77 1 0.02
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.59
Consensus pattern (76 bp):
TTATATTTTATCTTTATTTTAGGTATTTTTGTTTAAATAGGTTTTAGTATTTTAATCAAGATTTA
AGATATTATTC
Found at i:17356 original size:17 final size:18
Alignment explanation
Indices: 17333--17375 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
17323 TCTTTAAATT
17333 ATTTATTTAATTATT-TC
1 ATTTATTTAATTATTATC
* *
17350 TTTTATTTAATTCTTATC
1 ATTTATTTAATTATTATC
17368 ATTTATTT
1 ATTTATTT
17376 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTATTTAATTATTATC
Found at i:30166 original size:3 final size:3
Alignment explanation
Indices: 30158--30189 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
30148 TAAGTAAAAG
30158 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
30190 CCAATTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:33036 original size:17 final size:17
Alignment explanation
Indices: 32985--33055 Score: 54
Period size: 17 Copynumber: 4.1 Consensus size: 17
32975 AATTAAGAGT
*
32985 TAGTTTAATAAATGAAC
1 TAGTTTAATTAATGAAC
* * ** *
33002 TAGTCTGACGAATTAAC
1 TAGTTTAATTAATGAAC
33019 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
*
33036 TAACTTT-ATTCAATGAAC
1 T-AGTTTAATT-AATGAAC
33054 TA
1 TA
33056 TAACTTTATT
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
17 29 0.71
18 12 0.29
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:33050 original size:18 final size:18
Alignment explanation
Indices: 33029--33075 Score: 76
Period size: 20 Copynumber: 2.5 Consensus size: 18
33019 TAGTTTAATT
33029 AATGAACTAACTTTATTC
1 AATGAACTAACTTTATTC
33047 AATGAACTATAACTTTATTC
1 AATGAAC--TAACTTTATTC
33067 AATGAACTA
1 AATGAACTA
33076 GATGATTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.33
20 18 0.67
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (18 bp):
AATGAACTAACTTTATTC
Found at i:33061 original size:20 final size:20
Alignment explanation
Indices: 33036--33075 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
33026 ATTAATGAAC
33036 TAACTTTATTCAATGAACTA
1 TAACTTTATTCAATGAACTA
33056 TAACTTTATTCAATGAACTA
1 TAACTTTATTCAATGAACTA
33076 GATGATTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (20 bp):
TAACTTTATTCAATGAACTA
Found at i:37054 original size:17 final size:17
Alignment explanation
Indices: 37032--37074 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
37022 AATTAAGAGT
37032 TAGTTTAATAAATAAAC
1 TAGTTTAATAAATAAAC
* * *
37049 TAGTTTGATGAATTAAC
1 TAGTTTAATAAATAAAC
37066 TAGTTTAAT
1 TAGTTTAAT
37075 TAATGACCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.42
Consensus pattern (17 bp):
TAGTTTAATAAATAAAC
Found at i:37109 original size:20 final size:20
Alignment explanation
Indices: 37084--37124 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
37074 TTAATGACCT
37084 AACTTTATTCAATGAACTAG
1 AACTTTATTCAATGAACTAG
37104 AACTTTATTCAATGAACTAG
1 AACTTTATTCAATGAACTAG
37124 A
1 A
37125 TGCATGAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (20 bp):
AACTTTATTCAATGAACTAG
Found at i:43160 original size:18 final size:19
Alignment explanation
Indices: 43118--43160 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
43108 TTGGTTCACA
*
43118 GAATGTGAGATTACCAGTAG
1 GAATGTAAGATTACCAG-AG
*
43138 GAATGTAAGATTATCAG-G
1 GAATGTAAGATTACCAGAG
43156 GAATG
1 GAATG
43161 GGATTACTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.37, C:0.07, G:0.30, T:0.26
Consensus pattern (19 bp):
GAATGTAAGATTACCAGAG
Found at i:45233 original size:70 final size:68
Alignment explanation
Indices: 45108--45237 Score: 163
Period size: 70 Copynumber: 1.9 Consensus size: 68
45098 TTATTTGAAC
* * *
45108 ATAATATTAATAAAATAACATTTATTCAAACATAATACTTTTATATATATTTATTTGAATATAAC
1 ATAATATTAATAAAATAACATTTATTCAAACATAATACTTTTACACATATATATTT-AATATAAC
45173 TTAT
65 TTAT
* * * *
45177 ATAATCTTCAATAAAATAACATTTATTGAAACGTAATATTTTCTACACATA-ATATTTAATA
1 ATAATATT-AATAAAATAACATTTATTCAAACATAATACTTT-TACACATATATATTTAATA
45238 AATTACATAT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
69 11 0.21
70 35 0.67
71 6 0.12
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.42
Consensus pattern (68 bp):
ATAATATTAATAAAATAACATTTATTCAAACATAATACTTTTACACATATATATTTAATATAACT
TAT
Found at i:52227 original size:20 final size:20
Alignment explanation
Indices: 52198--52238 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
52188 TATGAAATTA
*
52198 TTTAAATATTT-TAGATTTT
1 TTTAAATATTTAAAGATTTT
52217 TTTAGAATATTTAAAGATTTT
1 TTTA-AATATTTAAAGATTTT
52238 T
1 T
52239 AAATAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
21 8 0.42
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (20 bp):
TTTAAATATTTAAAGATTTT
Found at i:52872 original size:2 final size:2
Alignment explanation
Indices: 52865--52919 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
52855 GATTTTCGTT
52865 TA TA TA 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
52907 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
52920 GAAATATTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53327 original size:19 final size:19
Alignment explanation
Indices: 53299--53335 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
53289 ACATTAGCAG
*
53299 TGCATGTTCTAGAATGCAC
1 TGCATATTCTAGAATGCAC
53318 TGCATATTCTAGAATGCA
1 TGCATATTCTAGAATGCA
53336 TATTCCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (19 bp):
TGCATATTCTAGAATGCAC
Found at i:53442 original size:36 final size:36
Alignment explanation
Indices: 53392--53473 Score: 128
Period size: 36 Copynumber: 2.3 Consensus size: 36
53382 GAAAACGGAC
* *
53392 ACTTGGATCGGAAGTGCCGATGCTTCCTTCCGTTCG
1 ACTTGAATCAGAAGTGCCGATGCTTCCTTCCGTTCG
*
53428 ACTTGAATCAGAAGTGTCGATGCTTCCTTCCGTTCG
1 ACTTGAATCAGAAGTGCCGATGCTTCCTTCCGTTCG
*
53464 ATTTGAATCA
1 ACTTGAATCA
53474 TCGGTGCACC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.33
Consensus pattern (36 bp):
ACTTGAATCAGAAGTGCCGATGCTTCCTTCCGTTCG
Found at i:58879 original size:18 final size:19
Alignment explanation
Indices: 58856--58894 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
58846 ATTTTGTATA
*
58856 ATTTTATT-AATATTTTTT
1 ATTTTATTGAATAATTTTT
58874 ATTTTATTGAATAATTTTT
1 ATTTTATTGAATAATTTTT
58893 AT
1 AT
58895 GGTAAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
ATTTTATTGAATAATTTTT
Found at i:64484 original size:19 final size:19
Alignment explanation
Indices: 64462--64526 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 19
64452 AATGGTATTG
64462 ATACCATAGTAGGGTATCA
1 ATACCATAGTAGGGTATCA
* *
64481 ATACCATAATATGGTAGTATCG
1 ATACCATAGTA-GG--GTATCA
*
64503 ATACCATGGTAGGGTTATCA
1 ATACCATAGTAGGG-TATCA
64523 ATAC
1 ATAC
64527 TAAGGAGCCA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 11 0.30
20 10 0.27
21 2 0.05
22 14 0.38
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.29
Consensus pattern (19 bp):
ATACCATAGTAGGGTATCA
Found at i:67849 original size:56 final size:56
Alignment explanation
Indices: 67776--68252 Score: 732
Period size: 56 Copynumber: 8.6 Consensus size: 56
67766 TAAGTATGCA
* *
67776 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGCGCACTATATATGT
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * * *
67832 AGAACTTAAGAAATTCATACTAAGTGGATGGATTTCCGTATGGTCACTATATGTTT
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
*
67888 AAAACTTAAGAAATTCATAC---GTGGATGAATTTCCATATGGGCACTATATGTGT
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* *
67941 ACAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGC
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
*
67997 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTTTATGTGT
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* *
68053 -AAATTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGC
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
*
68108 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTTTATGTGT
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * *
68164 -AAATTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTATATGTGC
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * * *
68219 AAAAC-TAGGAAATTTATACTAAGTGTATAAATTT
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTT
68253 TGTATTGGTA
Statistics
Matches: 384, Mismatches: 32, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
53 48 0.12
55 128 0.33
56 208 0.54
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (56 bp):
AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
Found at i:68092 original size:111 final size:112
Alignment explanation
Indices: 67776--68252 Score: 759
Period size: 111 Copynumber: 4.3 Consensus size: 112
67766 TAAGTATGCA
* * *
67776 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGCGCACTATATATGTAGAACTTAA
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTACAACTTAA
* * **
67841 GAAATTCATACTAAGTGGATGGATTTCCGTATGGTCACTATATGTTT
66 GAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGC
*
67888 AAAACTTAAGAAATTCATAC---GTGGATGAATTTCCATATGGGCACTATATGTGTACAACTTAA
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTACAACTTAA
67950 GAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGC
66 GAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGC
* *
67997 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTTTATGTGTA-AATTTAA
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTACAACTTAA
68061 GAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGC
66 GAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGC
* *
68108 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTTTATGTGTA-AATTTAA
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTACAACTTAA
*
68172 GAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTATATGTGC
66 GAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGC
* * * *
68219 AAAAC-TAGGAAATTTATACTAAGTGTATAAATTT
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTT
68253 TGTATTGGTA
Statistics
Matches: 346, Mismatches: 16, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
109 101 0.29
110 25 0.07
111 168 0.49
112 52 0.15
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (112 bp):
AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTACAACTTAA
GAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGC
Found at i:73325 original size:29 final size:30
Alignment explanation
Indices: 73258--73325 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 30
73248 AAAATTAAAG
* *
73258 TTCAT-ATATTTTAATTTTTAATTCTTTCT
1 TTCATAATATTTTAATATTTAATTATTTCT
* *
73287 TTCA-AA-ATTTTTATATTTACTTATTT-T
1 TTCATAATATTTTAATATTTAATTATTTCT
73314 TTCATAATATTT
1 TTCATAATATTT
73326 ATATGTTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
27 5 0.16
28 18 0.56
29 9 0.28
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (30 bp):
TTCATAATATTTTAATATTTAATTATTTCT
Done.