Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004837.1 Hibiscus syriacus cultivar Beakdansim tig00010905_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: 73813
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:14198 original size:18 final size:18
Alignment explanation
Indices: 14175--14211 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
14165 CATTTGTCAT
14175 ACATACATACATACATAC
1 ACATACATACATACATAC
* *
14193 ACATACATGCATGCATAC
1 ACATACATACATACATAC
14211 A
1 A
14212 ACAAAAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.27, G:0.05, T:0.22
Consensus pattern (18 bp):
ACATACATACATACATAC
Found at i:42407 original size:27 final size:29
Alignment explanation
Indices: 42377--42435 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 29
42367 GGTCCTCTCT
*
42377 CTGTTTATACAGTTGCAG-GTT-TGCATA
1 CTGTTCATACAGTTGCAGTGTTCTGCATA
* *
42404 CTGTTCGTATAGTTGCAGTGTTGCTGCATA
1 CTGTTCATACAGTTGCAGTGTT-CTGCATA
42434 CT
1 CT
42436 TTTTGAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 15 0.58
28 3 0.12
30 8 0.31
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.41
Consensus pattern (29 bp):
CTGTTCATACAGTTGCAGTGTTCTGCATA
Found at i:48685 original size:31 final size:31
Alignment explanation
Indices: 48650--48719 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
48640 GTTATTCAAC
* *
48650 TGATG-TAGTAGTTTGACTGTTACACTGATAA
1 TGATGATA-TAGTTCGACTGTTAAACTGATAA
48681 TGATGATATAGTTCGACTGTTAAACTGATAA
1 TGATGATATAGTTCGACTGTTAAACTGATAA
48712 TGATGATA
1 TGATGATA
48720 ATCTATGTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 34 0.94
32 2 0.06
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (31 bp):
TGATGATATAGTTCGACTGTTAAACTGATAA
Found at i:52795 original size:22 final size:22
Alignment explanation
Indices: 52770--52811 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
52760 ATTTTTTAAT
52770 ATTAAA-TAACAAAATAAATACC
1 ATTAAATTAACAAAA-AAATACC
*
52792 ATTAAATTAAGAAAAAAATA
1 ATTAAATTAACAAAAAAATA
52812 TAAATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (22 bp):
ATTAAATTAACAAAAAAATACC
Found at i:53957 original size:32 final size:31
Alignment explanation
Indices: 53908--53995 Score: 86
Period size: 32 Copynumber: 2.8 Consensus size: 31
53898 TTAATGTAAA
* * * *
53908 AGTTTGATAAATTTAATGATTATTTTGTGAT
1 AGTTAGATAAACTTAATGATTATTTTATAAT
* * *
53939 TGTTAGATAAAACTTAATGGTCATTTTATAAT
1 AGTTAGAT-AAACTTAATGATTATTTTATAAT
* *
53971 AGTTCGATAAATTTAATGATTATTT
1 AGTTAGATAAACTTAATGATTATTT
53996 GTAACTTTAG
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
31 20 0.45
32 24 0.55
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.48
Consensus pattern (31 bp):
AGTTAGATAAACTTAATGATTATTTTATAAT
Found at i:56053 original size:20 final size:20
Alignment explanation
Indices: 56030--56076 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
56020 GTTTCCAAAT
56030 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
* *
56050 TCGCGACGCGAATTTGTAAA
1 TCGCAACGCGAATCTGTAAA
*
56070 TCACAAC
1 TCGCAAC
56077 ACATAAGTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATCTGTAAA
Found at i:56127 original size:20 final size:21
Alignment explanation
Indices: 56073--56131 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 21
56063 TTGTAAATCA
*
56073 CAACACA-TAAGTCAAATTCG
1 CAACACAGAAAGTCAAATTCG
56093 CAACACAGAAA-TCAAATTCG
1 CAACACAGAAAGTCAAATTCG
**
56113 CAATGC-GAAAGTCAAATTC
1 CAACACAGAAAGTCAAATTC
56132 ATAACGCGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.12
20 28 0.82
21 2 0.06
ACGTcount: A:0.46, C:0.24, G:0.12, T:0.19
Consensus pattern (21 bp):
CAACACAGAAAGTCAAATTCG
Found at i:56140 original size:20 final size:20
Alignment explanation
Indices: 56081--56141 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
56071 CACAACACAT
*
56081 AAGTCAAATTCGCAACACAGA
1 AAGTCAAATTCGCAACGC-GA
*
56102 AA-TCAAATTCGCAATGCGA
1 AAGTCAAATTCGCAACGCGA
**
56121 AAGTCAAATTCATAACGCGA
1 AAGTCAAATTCGCAACGCGA
56141 A
1 A
56142 CTCCAATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 4 0.12
20 28 0.82
21 2 0.06
ACGTcount: A:0.46, C:0.21, G:0.15, T:0.18
Consensus pattern (20 bp):
AAGTCAAATTCGCAACGCGA
Found at i:56195 original size:20 final size:20
Alignment explanation
Indices: 56152--56218 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
56142 CTCCAATTTT
56152 GCAACGTGAATAGTAAAAATC
1 GCAACGTGAATAGT-AAAATC
*
56173 GCAACGTGAATAGTAAAAGC
1 GCAACGTGAATAGTAAAATC
** *
56193 GCAATATGAATAGTATAATC
1 GCAACGTGAATAGTAAAATC
56213 GCAACG
1 GCAACG
56219 AATCTATATG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 25 0.64
21 14 0.36
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (20 bp):
GCAACGTGAATAGTAAAATC
Found at i:56280 original size:23 final size:22
Alignment explanation
Indices: 56252--56297 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 22
56242 ATCATCCATC
56252 TATAATAATTTGTTGA-AAAAATA
1 TATAATAATTT-TT-ATAAAAATA
56275 TATAATAATTTTTATAAAAATA
1 TATAATAATTTTTATAAAAATA
56297 T
1 T
56298 TCGTACACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 1 0.05
22 10 0.45
23 11 0.50
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (22 bp):
TATAATAATTTTTATAAAAATA
Found at i:56629 original size:41 final size:42
Alignment explanation
Indices: 56579--56657 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 42
56569 GATTTTCTAA
* **
56579 ATTCGCGTTGCGATTTTT-CAATTCACGTTACGATTTTTACT
1 ATTCACGTTGCGATTTTTACAATTCACACTACGATTTTTACT
*
56620 ATTCACGTTGCGATTTTTACTATTCACACTACGATTTT
1 ATTCACGTTGCGATTTTTACAATTCACACTACGATTTT
56658 GGAAACTGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
41 17 0.52
42 16 0.48
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.46
Consensus pattern (42 bp):
ATTCACGTTGCGATTTTTACAATTCACACTACGATTTTTACT
Found at i:56639 original size:21 final size:21
Alignment explanation
Indices: 56565--56646 Score: 105
Period size: 21 Copynumber: 4.0 Consensus size: 21
56555 CAATAAGATT
*
56565 TTGCGATTTTCTA-AATTCGCG
1 TTGCGATTTT-TACAATTCACG
56586 TTGCGATTTTT-CAATTCACG
1 TTGCGATTTTTACAATTCACG
* *
56606 TTACGATTTTTACTATTCACG
1 TTGCGATTTTTACAATTCACG
*
56627 TTGCGATTTTTACTATTCAC
1 TTGCGATTTTTACAATTCAC
56647 ACTACGATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
20 18 0.33
21 37 0.67
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.46
Consensus pattern (21 bp):
TTGCGATTTTTACAATTCACG
Found at i:56654 original size:21 final size:21
Alignment explanation
Indices: 56579--56657 Score: 97
Period size: 21 Copynumber: 3.8 Consensus size: 21
56569 GATTTTCTAA
* * *
56579 ATTCGCGTTGCGATTTTT-CA
1 ATTCACGTTACGATTTTTACT
56599 ATTCACGTTACGATTTTTACT
1 ATTCACGTTACGATTTTTACT
*
56620 ATTCACGTTGCGATTTTTACT
1 ATTCACGTTACGATTTTTACT
**
56641 ATTCACACTACGATTTT
1 ATTCACGTTACGATTTT
56658 GGAAACTGAG
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
20 16 0.31
21 35 0.69
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.46
Consensus pattern (21 bp):
ATTCACGTTACGATTTTTACT
Found at i:67390 original size:27 final size:27
Alignment explanation
Indices: 67352--67404 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
67342 TCAGCAATAT
67352 ACCCCTTACAAGAACCAGAAAACCAAC
1 ACCCCTTACAAGAACCAGAAAACCAAC
67379 ACCCCTTACAAGAACCAGAAAACCAA
1 ACCCCTTACAAGAACCAGAAAACCAA
67405 AAAACAACCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.49, C:0.36, G:0.08, T:0.08
Consensus pattern (27 bp):
ACCCCTTACAAGAACCAGAAAACCAAC
Found at i:70644 original size:18 final size:18
Alignment explanation
Indices: 70621--70664 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
70611 TTAATTCCTT
70621 AATAGGTCTTTCAGTTTC
1 AATAGGTCTTTCAGTTTC
70639 AATAGGTCTTTCAGTTTC
1 AATAGGTCTTTCAGTTTC
70657 AATAGGTC
1 AATAGGTC
70665 GGTCTTGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (18 bp):
AATAGGTCTTTCAGTTTC
Done.