Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000314.1 Hibiscus syriacus cultivar Beakdansim tig00000593_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: 93022
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:21180 original size:16 final size:16
Alignment explanation
Indices: 21146--21186 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
21136 ATTTATTTCA
*
21146 GAATGATT-AAACGCT
1 GAATGATTCAAACACT
*
21161 GAATGATTCAAATACT
1 GAATGATTCAAACACT
21177 GAATGATTCA
1 GAATGATTCA
21187 TAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACACT
Found at i:23317 original size:2 final size:2
Alignment explanation
Indices: 23312--23355 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
23302 TATTGACAAT
23312 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
23354 TA
1 TA
23356 AAATTATGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55549 original size:16 final size:16
Alignment explanation
Indices: 55517--55557 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
55507 GTTTACTTCA
*
55517 GAATGATT-AAGTGCT
1 GAATGATTCAAATGCT
55532 GAATGATTCAAATGCT
1 GAATGATTCAAATGCT
55548 GAATGATTCA
1 GAATGATTCA
55558 GAGCCTCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.32
Consensus pattern (16 bp):
GAATGATTCAAATGCT
Found at i:57185 original size:2 final size:2
Alignment explanation
Indices: 57178--57207 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
57168 GGGTTAACTT
57178 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
57208 AAGAAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58490 original size:24 final size:24
Alignment explanation
Indices: 58463--58555 Score: 80
Period size: 24 Copynumber: 3.9 Consensus size: 24
58453 GATATCAAAA
*
58463 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * * *
58487 ATCATAATAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
58511 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* *
58535 GTCAAAACAGAATTCAAATCA
1 ATCAAAACAGAATTCAGATCA
58556 TAAATCAGAT
Statistics
Matches: 51, Mismatches: 16, Indels: 4
0.72 0.23 0.06
Matches are distributed among these distances:
23 2 0.04
24 47 0.92
25 2 0.04
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:61045 original size:15 final size:16
Alignment explanation
Indices: 61011--61059 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
61001 GGTCAACAGT
61011 GGTCAACGCCGGTCAAC
1 GGTCAACG-CGGTCAAC
*
61028 GGTCAACG-GGTTAAC
1 GGTCAACGCGGTCAAC
*
61043 GGTCAACG-AGTCAAC
1 GGTCAACGCGGTCAAC
61058 GG
1 GG
61060 GTAGGGTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 21 0.72
17 8 0.28
ACGTcount: A:0.27, C:0.27, G:0.33, T:0.14
Consensus pattern (16 bp):
GGTCAACGCGGTCAAC
Found at i:61055 original size:8 final size:7
Alignment explanation
Indices: 61020--61059 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
61010 TGGTCAACGC
61020 CGGTCAA
1 CGGTCAA
61027 CGGTCAA
1 CGGTCAA
*
61034 CGGGTTAA
1 C-GGTCAA
61042 CGGTCAA
1 CGGTCAA
61049 CGAGTCAA
1 CG-GTCAA
61057 CGG
1 CGG
61060 GTAGGGTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 16 0.55
8 13 0.45
ACGTcount: A:0.28, C:0.25, G:0.33, T:0.15
Consensus pattern (7 bp):
CGGTCAA
Found at i:61084 original size:18 final size:18
Alignment explanation
Indices: 61057--61104 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
61047 AACGAGTCAA
*
61057 CGGGTAGGGTTAACAGGT
1 CGGGTCGGGTTAACAGGT
* * *
61075 CGGGTCGGGTCAGCGGGT
1 CGGGTCGGGTTAACAGGT
61093 CGGGTCGGGTTA
1 CGGGTCGGGTTA
61105 TGACCGGTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.12, C:0.17, G:0.50, T:0.21
Consensus pattern (18 bp):
CGGGTCGGGTTAACAGGT
Found at i:63152 original size:24 final size:24
Alignment explanation
Indices: 63125--63231 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
63115 AAACGGAGAT
* *
63125 ATCAAAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* *
63149 ATCAGATATCATAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
63173 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
63197 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
63221 ATCAGAAATCA
1 ATCAGAAATCA
63232 GATAAAATAT
Statistics
Matches: 62, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.23
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:63231 original size:48 final size:48
Alignment explanation
Indices: 63125--63233 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
63115 AAACGGAGAT
* * * * *
63125 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATTCAA
* * * * * *
63173 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATTCAA
63221 ATCAGAAATCAGA
1 ATCAGAAATCAGA
63234 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATTCAA
Found at i:66684 original size:122 final size:123
Alignment explanation
Indices: 66505--66760 Score: 338
Period size: 128 Copynumber: 2.0 Consensus size: 123
66495 TTAGGGTGTT
* *
66505 ACATTTACGCTAGGTGTAAGTGGATCCTAATTC-ATATATATATATATC-AAGACCAATATGTAT
1 ACATTTACACTAAGTGTAAGTGGATCCTAA-TCAATATATATATATATCAAAGACCAATATGTAT
* *
66568 TTTAGAAAAAGATTAAAATTATATAAAATTTATTTTAAAATTTGAAAAAACAACCCATA
65 TTTAGAAAAAGAATAAAATTATATAAAATTTATTTTAAAATTTGAAAAAACAAACCATA
* * *
66627 ACATTTACACTAAGTGTAAGTGGATCCTAA-CATATATATATATATATATATATCAATATCAATA
1 ACATTTACACTAAGTGTAAGTGGATCCTAATC--A-ATATATATATATAT-CA--AAGACCAATA
* * *
66691 TGTATTTTAGAAAAAGAATAAAATTATATAAATTTTATTTTAAAATTTGAAAAAATAAATCATA
60 TGTATTTTAGAAAAAGAATAAAATTATATAAAATTTATTTTAAAATTTGAAAAAACAAACCATA
66755 ACATTT
1 ACATTT
66761 TAAATTATTT
Statistics
Matches: 116, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
120 1 0.01
122 28 0.24
124 14 0.12
128 73 0.63
ACGTcount: A:0.46, C:0.09, G:0.08, T:0.36
Consensus pattern (123 bp):
ACATTTACACTAAGTGTAAGTGGATCCTAATCAATATATATATATATCAAAGACCAATATGTATT
TTAGAAAAAGAATAAAATTATATAAAATTTATTTTAAAATTTGAAAAAACAAACCATA
Found at i:73186 original size:24 final size:23
Alignment explanation
Indices: 73159--73231 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
73149 ACATGTCCAT
73159 AAACATATTCATTTAAATGTTCAC
1 AAACATATTCATTT-AATGTTCAC
* * ***
73183 AAACATATTCGTTTAGTGTTTGT
1 AAACATATTCATTTAATGTTCAC
* *
73206 AAATATATTCATTTAATATTCAC
1 AAACATATTCATTTAATGTTCAC
73229 AAA
1 AAA
73232 TATGTTTATT
Statistics
Matches: 37, Mismatches: 12, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
23 24 0.65
24 13 0.35
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (23 bp):
AAACATATTCATTTAATGTTCAC
Found at i:73232 original size:23 final size:23
Alignment explanation
Indices: 73163--73243 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 23
73153 GTCCATAAAC
*
73163 ATATTCATTTAAATGTTCACAAAC
1 ATATTCATTT-AATGTTCACAAAT
* * ***
73187 ATATTCGTTTAGTGTTTGTAAAT
1 ATATTCATTTAATGTTCACAAAT
*
73210 ATATTCATTTAATATTCACAAAT
1 ATATTCATTTAATGTTCACAAAT
* *
73233 ATGTTTATTTA
1 ATATTCATTTA
73244 TAATAAAAAG
Statistics
Matches: 43, Mismatches: 14, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
23 34 0.79
24 9 0.21
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (23 bp):
ATATTCATTTAATGTTCACAAAT
Found at i:73902 original size:2 final size:2
Alignment explanation
Indices: 73895--73930 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
73885 ACTAGGTGTA
73895 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
73931 GATCCATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78754 original size:19 final size:19
Alignment explanation
Indices: 78730--78771 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
78720 TCTTTTTAAT
78730 ATTACAATT-TCATCTCAAA
1 ATTACAATTCTCAT-TCAAA
*
78749 ATTACAATTCTCATTCTAA
1 ATTACAATTCTCATTCAAA
78768 ATTA
1 ATTA
78772 TCATAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTACAATTCTCATTCAAA
Found at i:83655 original size:27 final size:27
Alignment explanation
Indices: 83624--83677 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
83614 TAGTAAATTT
83624 GTCACTTTCCACATCACTATAAATAAC
1 GTCACTTTCCACATCACTATAAATAAC
83651 GTCACTTTCCACATCACTATAAATAAC
1 GTCACTTTCCACATCACTATAAATAAC
83678 ATCTAATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.30, G:0.04, T:0.30
Consensus pattern (27 bp):
GTCACTTTCCACATCACTATAAATAAC
Found at i:85230 original size:3 final size:3
Alignment explanation
Indices: 85222--85250 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
85212 GGCATAACAT
85222 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
85251 GCATTTCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:88562 original size:19 final size:19
Alignment explanation
Indices: 88531--88568 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
88521 TAGATTAATA
88531 ACCAACAATTACATAAGATT
1 ACCAACAATTACA-AAGATT
88551 ACCAAC-ATTACAAAGATT
1 ACCAACAATTACAAAGATT
88569 GCCTAAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 6 0.33
20 6 0.33
ACGTcount: A:0.50, C:0.21, G:0.05, T:0.24
Consensus pattern (19 bp):
ACCAACAATTACAAAGATT
Done.