Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008115.1 Hibiscus syriacus cultivar Beakdansim tig00110654_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: 308958
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:288352 original size:30 final size:30
Alignment explanation
Indices: 288318--288378 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
288308 ATCTGTAACT
*
288318 ATTTATACAGAAATTAAGT-TTGTTGAGTCA
1 ATTTATACAAAAATTAA-TCTTGTTGAGTCA
* *
288348 ATTTATATAAAAATTAATCTTGTTGGGTCA
1 ATTTATACAAAAATTAATCTTGTTGAGTCA
288378 A
1 A
288379 ATTCACTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.41
Consensus pattern (30 bp):
ATTTATACAAAAATTAATCTTGTTGAGTCA
Found at i:290084 original size:60 final size:60
Alignment explanation
Indices: 289962--290088 Score: 139
Period size: 60 Copynumber: 2.1 Consensus size: 60
289952 GAATATATGA
** * * ** * **
289962 ATAGTCAGGTGATCATTTTGCAATTTTTAATAGTCGAGGGACTTAATAAAGTATCATTCT
1 ATAGTCAAATGATCATTTTGCAACTTTTAATAGTCAAGAAACTTAATAAAGGATCACCCT
* *
290022 ATAGTCAAATGATCATTTTGTAACTTTTAATAGTCAATAAACTTAATAAAGCGAT-ACCCT
1 ATAGTCAAATGATCATTTTGCAACTTTTAATAGTCAAGAAACTTAATAAAG-GATCACCCT
290082 ATAGTCA
1 ATAGTCA
290089 GAGGACCATT
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 53 0.96
61 2 0.04
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (60 bp):
ATAGTCAAATGATCATTTTGCAACTTTTAATAGTCAAGAAACTTAATAAAGGATCACCCT
Found at i:290896 original size:2 final size:2
Alignment explanation
Indices: 290889--290913 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
290879 ACAATAAACG
290889 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
290914 GAAAGAAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:299867 original size:19 final size:18
Alignment explanation
Indices: 299843--299886 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
299833 GAGTATATGT
299843 TAATATAATATTAAAAATA
1 TAATAT-ATATTAAAAATA
*
299862 TAATAT-TATTAAAATTA
1 TAATATATATTAAAAATA
*
299879 TATTATAT
1 TAATATAT
299887 GTATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 15 0.68
18 1 0.05
19 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAATATATATTAAAAATA
Found at i:299910 original size:37 final size:37
Alignment explanation
Indices: 299850--299941 Score: 98
Period size: 37 Copynumber: 2.4 Consensus size: 37
299840 TGTTAATATA
*
299850 ATATTAAAAATATAATATTATTAA-AATTATATTATATG
1 ATATTAAAAAT-TAATA-TATTAATAATTATATTAAATG
* *
299888 TATATTAAATAATTAATA-ATTAATATTTTTATTAAATG
1 -ATATTAAA-AATTAATATATTAATAATTATATTAAATG
299926 ATATTAAAATATTAAT
1 ATATTAAAA-ATTAAT
299942 TTAATATTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
36 1 0.02
37 19 0.40
38 11 0.23
39 13 0.28
40 3 0.06
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (37 bp):
ATATTAAAAATTAATATATTAATAATTATATTAAATG
Found at i:299912 original size:46 final size:48
Alignment explanation
Indices: 299816--299914 Score: 116
Period size: 46 Copynumber: 2.1 Consensus size: 48
299806 GTAATATCAT
*
299816 ATATTATTATAATATATGAGTATATGTTAATATAATATTAAAAATATA
1 ATATTATTAAAATATATGAGTATATGTTAATATAATATTAAAAATATA
* * *
299864 ATATTATTAAAAT-TAT-ATTATATGTATATTA-AATAATTAATAAT-TA
1 ATATTATTAAAATATATGAGTATATGT-TAATATAAT-ATTAAAAATATA
299910 ATATT
1 ATATT
299915 TTTATTAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
46 18 0.40
47 15 0.33
48 12 0.27
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (48 bp):
ATATTATTAAAATATATGAGTATATGTTAATATAATATTAAAAATATA
Found at i:308364 original size:30 final size:29
Alignment explanation
Indices: 308330--308389 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
308320 TTTATGTTAG
* *
308330 GAGAGGCGACTTAAATTTTTAAAATTTCAA
1 GAGAGGCGACTTAAACTTATAAAA-TTCAA
*
308360 GAGAGGCGACTTGAACTTATAAAATTCAA
1 GAGAGGCGACTTAAACTTATAAAATTCAA
308389 G
1 G
308390 GGGGTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (29 bp):
GAGAGGCGACTTAAACTTATAAAATTCAA
Done.