Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009136.1 Hibiscus syriacus cultivar Beakdansim tig00112636_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: 240531
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:160417 original size:36 final size:36
Alignment explanation
Indices: 160369--160450 Score: 146
Period size: 36 Copynumber: 2.2 Consensus size: 36
160359 TTTTTATAGG
160369 ATATTAATATCAATGAAACGAGCTTCGACTGAACCTT
1 ATATT-ATATCAATGAAACGAGCTTCGACTGAACCTT
160406 ATATTATATCAATGAAACGAGCTTCGACTGAACCTT
1 ATATTATATCAATGAAACGAGCTTCGACTGAACCTT
*
160442 ATATAATAT
1 ATATTATAT
160451 AATATAATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
36 39 0.89
37 5 0.11
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (36 bp):
ATATTATATCAATGAAACGAGCTTCGACTGAACCTT
Found at i:160452 original size:5 final size:5
Alignment explanation
Indices: 160442--160525 Score: 152
Period size: 5 Copynumber: 17.0 Consensus size: 5
160432 ACTGAACCTT
160442 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAT-
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
*
160491 ATATA ATATA ATATA ATATA ATGTA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA
160526 TAAATTAATT
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
4 4 0.05
5 72 0.95
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:169064 original size:20 final size:19
Alignment explanation
Indices: 169031--169069 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
169021 TTTTGCTATT
*
169031 AATTCATGTATAATGCATA
1 AATTCATGTATAATCCATA
*
169050 AATTACATGTTTAATCCATA
1 AATT-CATGTATAATCCATA
169070 TATTTCAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (19 bp):
AATTCATGTATAATCCATA
Found at i:190421 original size:18 final size:18
Alignment explanation
Indices: 190398--190439 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
190388 AATATAAGGG
190398 AGTAGGACCACGGCTTTT
1 AGTAGGACCACGGCTTTT
190416 AGTAGGACCACGGCTTTT
1 AGTAGGACCACGGCTTTT
*
190434 ACTAGG
1 AGTAGG
190440 GCGGCATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (18 bp):
AGTAGGACCACGGCTTTT
Found at i:190923 original size:37 final size:38
Alignment explanation
Indices: 190838--190923 Score: 106
Period size: 37 Copynumber: 2.3 Consensus size: 38
190828 ATTAAACCTT
*
190838 TTTTATATTTTTAATTTTGTAAAAAAAATTATATAAATA
1 TTTTATA-ATTTAATTTTGTAAAAAAAATTATATAAATA
* *
190877 --TTATGAATTTAATTTTTTAAAGAAAA-TATATAAATA
1 TTTTAT-AATTTAATTTTGTAAAAAAAATTATATAAATA
190913 TTTTATAATTT
1 TTTTATAATTT
190924 GTAATATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
36 10 0.24
37 26 0.63
38 5 0.12
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.51
Consensus pattern (38 bp):
TTTTATAATTTAATTTTGTAAAAAAAATTATATAAATA
Found at i:191086 original size:18 final size:19
Alignment explanation
Indices: 191062--191106 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
191052 CCCAGTAATC
191062 ATATTCC-CTGGTAATCTT
1 ATATTCCACTGGTAATCTT
*
191080 TTATTCCCACTGGTAATCTT
1 ATATT-CCACTGGTAATCTT
191100 ATATTCC
1 ATATTCC
191107 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.22, C:0.24, G:0.09, T:0.44
Consensus pattern (19 bp):
ATATTCCACTGGTAATCTT
Found at i:191094 original size:20 final size:20
Alignment explanation
Indices: 191069--191106 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
191059 ATCATATTCC
*
191069 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTATATTCCCA
191089 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
191107 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:194368 original size:6 final size:6
Alignment explanation
Indices: 194359--194392 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
194349 GGAGAAGCAA
194359 TGAGGG TGAGGG TGAGGG TGAGGG TGAGGG TGAG
1 TGAGGG TGAGGG TGAGGG TGAGGG TGAGGG TGAG
194393 ACGATCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.65, T:0.18
Consensus pattern (6 bp):
TGAGGG
Found at i:198072 original size:57 final size:56
Alignment explanation
Indices: 197963--198072 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 56
197953 TGATTATAGT
* ** *
197963 TTGGAGATAAATTTAAAATATTCAAAAGTTTAAGATCAATTTAAAATGAGAATAAA
1 TTGGAGATAAATTTAAAATATTAAAAAAATTAAGATCAATTTAAAATAAGAATAAA
* *
198019 TTGGAGATGAAA-TTAAAATATTTAAAAAAATTAATATTAATTTAAAATAAGAAT
1 TTGGAGAT-AAATTTAAAATA-TTAAAAAAATTAAGATCAATTTAAAATAAGAAT
198073 TATAATTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
56 16 0.35
57 30 0.65
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.34
Consensus pattern (56 bp):
TTGGAGATAAATTTAAAATATTAAAAAAATTAAGATCAATTTAAAATAAGAATAAA
Found at i:198466 original size:2 final size:2
Alignment explanation
Indices: 198459--198498 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
198449 AAAAATAAGA
* *
198459 AT AT AT AT GT TT 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 AT AT
198499 GTCATGAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:198991 original size:25 final size:25
Alignment explanation
Indices: 198961--199024 Score: 128
Period size: 25 Copynumber: 2.6 Consensus size: 25
198951 AAATTATGTC
198961 AAATTAAGTAAAAAGACTACATATG
1 AAATTAAGTAAAAAGACTACATATG
198986 AAATTAAGTAAAAAGACTACATATG
1 AAATTAAGTAAAAAGACTACATATG
199011 AAATTAAGTAAAAA
1 AAATTAAGTAAAAA
199025 TTTTTGATAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.59, C:0.06, G:0.11, T:0.23
Consensus pattern (25 bp):
AAATTAAGTAAAAAGACTACATATG
Found at i:202998 original size:3 final size:3
Alignment explanation
Indices: 202990--203014 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
202980 TAGTTGAAAT
202990 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
203015 CATTTGCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:209808 original size:2 final size:2
Alignment explanation
Indices: 209801--209828 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
209791 TATGCTAAAT
209801 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
209829 ACCAGATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:233399 original size:23 final size:23
Alignment explanation
Indices: 233348--233400 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
233338 TATGACAGTG
*
233348 TACAGCACCTTTGGCTCATGATA
1 TACAGTACCTTTGGCTCATGATA
233371 TACAGTACCTTTGGCTCATGATA
1 TACAGTACCTTTGGCTCATGATA
233394 TACAGTA
1 TACAGTA
233401 TGAAATGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (23 bp):
TACAGTACCTTTGGCTCATGATA
Found at i:237196 original size:11 final size:11
Alignment explanation
Indices: 237180--237212 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
237170 CATTGACCGA
237180 AGATGAGAGCC
1 AGATGAGAGCC
237191 AGATGAGAGCC
1 AGATGAGAGCC
237202 AGATGAGAGCC
1 AGATGAGAGCC
237213 GAGGAGATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.36, T:0.09
Consensus pattern (11 bp):
AGATGAGAGCC
Done.