Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005234.1 Hibiscus syriacus cultivar Beakdansim tig00011848_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: 296100
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:244250 original size:29 final size:29
Alignment explanation
Indices: 244207--244289 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
244197 CTCACCTAAC
244207 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
244237 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
244266 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
244290 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:249015 original size:29 final size:29
Alignment explanation
Indices: 248972--249054 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
248962 CTCACCTAAC
248972 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
249002 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
249031 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
249055 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:258650 original size:155 final size:155
Alignment explanation
Indices: 258356--258665 Score: 604
Period size: 155 Copynumber: 2.0 Consensus size: 155
258346 GAAAAGAACT
258356 ACAATACCAACTAATATGTATTCTAAACCTCTATAGCATGATTGCGATGTAAATACCTTGTCGGC
1 ACAATACCAACTAATATGTATTCTAAACCTCTATAGCATGATTGCGATGTAAATACCTTGTCGGC
258421 TTCATTTTGTGACCTTTGAACTCTTTGGATTATTCCAGTTCATTTTTTCTCTACAGGGGTGAATT
66 TTCATTTTGTGACCTTTGAACTCTTTGGATTATTCCAGTTCATTTTTTCTCTACAGGGGTGAATT
258486 CAACTTGAACAATTTTGAAGATGGA
131 CAACTTGAACAATTTTGAAGATGGA
258511 ACAATACCAACTAATATGTATTCTAAACCTCTATACGCATGATTGCGATGTAAATACCTTGTCGG
1 ACAATACCAACTAATATGTATTCTAAACCTCTATA-GCATGATTGCGATGTAAATACCTTGTCGG
258576 CTTCATTTTGTGACCTTTGAACTCTTTGGATTATTCCAGTTCA-TTTTTCTCTACAGGGGTGAAT
65 CTTCATTTTGTGACCTTTGAACTCTTTGGATTATTCCAGTTCATTTTTTCTCTACAGGGGTGAAT
258640 TCAACTTGAACAATTTTGAAGATGGA
130 TCAACTTGAACAATTTTGAAGATGGA
258666 GTTCTATCAT
Statistics
Matches: 154, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
155 82 0.53
156 72 0.47
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.37
Consensus pattern (155 bp):
ACAATACCAACTAATATGTATTCTAAACCTCTATAGCATGATTGCGATGTAAATACCTTGTCGGC
TTCATTTTGTGACCTTTGAACTCTTTGGATTATTCCAGTTCATTTTTTCTCTACAGGGGTGAATT
CAACTTGAACAATTTTGAAGATGGA
Found at i:265552 original size:6 final size:6
Alignment explanation
Indices: 265533--265597 Score: 76
Period size: 6 Copynumber: 10.8 Consensus size: 6
265523 AAGTATATAT
* * * * *
265533 GTGTGT GTGCGC GTGTGC GTGTAC GTGTGC GTGTGC GTGTGT GTGTAC
1 GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC
*
265581 GTGTGC CTGTGC GTGTG
1 GTGTGC GTGTGC GTGTG
265598 TATTATGTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.03, C:0.15, G:0.46, T:0.35
Consensus pattern (6 bp):
GTGTGC
Found at i:265570 original size:24 final size:24
Alignment explanation
Indices: 265533--265597 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
265523 AAGTATATAT
* *
265533 GTGTGTGTGCGCGTGTGCGTGTAC
1 GTGTGCGTGTGCGTGTGCGTGTAC
*
265557 GTGTGCGTGTGCGTGTGTGTGTAC
1 GTGTGCGTGTGCGTGTGCGTGTAC
*
265581 GTGTGCCTGTGCGTGTG
1 GTGTGCGTGTGCGTGTG
265598 TATTATGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.03, C:0.15, G:0.46, T:0.35
Consensus pattern (24 bp):
GTGTGCGTGTGCGTGTGCGTGTAC
Found at i:267665 original size:31 final size:31
Alignment explanation
Indices: 267630--267754 Score: 205
Period size: 31 Copynumber: 4.0 Consensus size: 31
267620 AATTCGGTGA
* * *
267630 ATTCAATATATCCTTCTCACTAGGAACTCCC
1 ATTCAATATGTCATTCTCACTAGAAACTCCC
* *
267661 ATTCAATATGTCATTCTCACTAGGAACTCTC
1 ATTCAATATGTCATTCTCACTAGAAACTCCC
267692 ATTCAATATGTCATTCTCACTAGAAACTCCC
1 ATTCAATATGTCATTCTCACTAGAAACTCCC
267723 ATTCAATATGTCATTCTCACTAGAAACTCCC
1 ATTCAATATGTCATTCTCACTAGAAACTCCC
267754 A
1 A
267755 AACTCTTGGG
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 89 1.00
ACGTcount: A:0.31, C:0.29, G:0.07, T:0.33
Consensus pattern (31 bp):
ATTCAATATGTCATTCTCACTAGAAACTCCC
Found at i:269818 original size:19 final size:20
Alignment explanation
Indices: 269794--269839 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
269784 TTGTTATGAG
269794 TTTTAACCAT-AAAACTATA
1 TTTTAACCATAAAAACTATA
269813 TTTTAACCATAAAAACTATA
1 TTTTAACCATAAAAACTATA
269833 TTTTAAC
1 TTTTAAC
269840 AAACTCAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (20 bp):
TTTTAACCATAAAAACTATA
Found at i:270970 original size:19 final size:19
Alignment explanation
Indices: 270946--270984 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
270936 AGAGTTGACA
*
270946 TTTATTTTCAACTTACTAT
1 TTTATTTTCAACTTAATAT
270965 TTTATTTTCAACTTAATAT
1 TTTATTTTCAACTTAATAT
270984 T
1 T
270985 CAGAAACTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.13, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATTTTCAACTTAATAT
Found at i:272297 original size:21 final size:21
Alignment explanation
Indices: 272255--272305 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
272245 ATTTATCGTG
* *
272255 ATTGCGGCCGTCGCGGGCGCT
1 ATTGCGGCCGTCACGGACGCT
* *
272276 ATTGCGGCTGTCACGGATGCT
1 ATTGCGGCCGTCACGGACGCT
*
272297 ATTGAGGCC
1 ATTGCGGCC
272306 ATTGCGGGTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.12, C:0.27, G:0.37, T:0.24
Consensus pattern (21 bp):
ATTGCGGCCGTCACGGACGCT
Found at i:289172 original size:29 final size:29
Alignment explanation
Indices: 289123--289179 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
289113 CGAGAAGATT
*
289123 AGTCATGATTATTAACGATAGATACTCCG
1 AGTCATGATTATTAACAATAGATACTCCG
* *
289152 AGTCATGATTATTGACAATAGATGCTCC
1 AGTCATGATTATTAACAATAGATACTCC
289180 AAGAAGATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (29 bp):
AGTCATGATTATTAACAATAGATACTCCG
Found at i:289222 original size:37 final size:37
Alignment explanation
Indices: 289176--289270 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 37
289166 ACAATAGATG
* *
289176 CTCCAAGAAGATTAGTTAT-AGTTATCGACA-ACGGATA
1 CTCCAAGAAGATTAGTTATGA-TAATCGA-AGACGAATA
* *
289213 CTCCGAGAAGATTAGTTATGATAATCGAAGATGAATA
1 CTCCAAGAAGATTAGTTATGATAATCGAAGACGAATA
*
289250 CTCCTAGAAGATTAG-TATGAT
1 CTCCAAGAAGATTAGTTATGAT
289271 GAATACTGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
36 7 0.14
37 43 0.84
38 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (37 bp):
CTCCAAGAAGATTAGTTATGATAATCGAAGACGAATA
Found at i:291868 original size:3 final size:3
Alignment explanation
Indices: 291856--291911 Score: 87
Period size: 3 Copynumber: 18.7 Consensus size: 3
291846 TCTTCTTGTT
*
291856 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTGA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
291905 TT- TTA TT
1 TTA TTA TT
291912 GGCATCTACA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Done.