Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003571.1 Hibiscus syriacus cultivar Beakdansim tig00007538_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: 77684
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 2
Found at i:75687 original size:15 final size:14
Alignment explanation
Indices: 75669--75710 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
75659 AAAATAAAAA
75669 AAATAAATAATAATG
1 AAATAAAT-ATAATG
75684 AAATAAATATAAT-
1 AAATAAATATAATG
*
75697 ATAATATATATAAT
1 A-AATAAATATAAT
75711 ATATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 1 0.04
14 16 0.64
15 8 0.32
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
AAATAAATATAATG
Found at i:75691 original size:19 final size:19
Alignment explanation
Indices: 75648--75702 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
75638 AATGAAGAAT
* *
75648 AAAAATAAGTAAAAATAAA
1 AAAAATAAATAATAATAAA
*
75667 AAAAATAAATAATAATGAA
1 AAAAATAAATAATAATAAA
*
75686 ATAAATATAAT-ATAATA
1 AAAAATA-AATAATAATA
75703 TATATAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 27 0.90
20 3 0.10
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (19 bp):
AAAAATAAATAATAATAAA
Found at i:75702 original size:14 final size:14
Alignment explanation
Indices: 75685--75811 Score: 89
Period size: 16 Copynumber: 8.6 Consensus size: 14
75675 ATAATAATGA
*
75685 AATAAATATAATAT
1 AATATATATAATAT
75699 AATATATATAATAT
1 AATATATATAATAT
75713 -ATATATATATATAT
1 AATATATATA-ATAT
75727 ATATATATATATATAT
1 A-ATATATATA-ATAT
*
75743 ATATATATATAGAGTAA
1 A-ATATATATA-A-TAT
* *
75760 AATAGA-AAAATAT
1 AATATATATAATAT
*
75773 AACATATAATAATAGT
1 AATATAT-ATAATA-T
*
75789 AATATGAAAATAA-AT
1 AATAT--ATATAATAT
75804 AATATATA
1 AATATATA
75812 AAAAAACCAA
Statistics
Matches: 92, Mismatches: 12, Indels: 19
0.75 0.10 0.15
Matches are distributed among these distances:
13 17 0.18
14 18 0.20
15 13 0.14
16 36 0.39
17 7 0.08
18 1 0.01
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (14 bp):
AATATATATAATAT
Found at i:75707 original size:2 final size:2
Alignment explanation
Indices: 75690--75753 Score: 107
Period size: 2 Copynumber: 33.5 Consensus size: 2
75680 AATGAAATAA
75690 AT AT A- AT AT A- AT AT AT AT A- 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 AT
75729 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
75754 GAGTAAAATA
Statistics
Matches: 59, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
1 3 0.05
2 56 0.95
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:76170 original size:20 final size:21
Alignment explanation
Indices: 76133--76185 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
76123 AACAATTCTC
76133 TTCATGAAAAGATTAAATCAT
1 TTCATGAAAAGATTAAATCAT
* *
76154 TTCATGAAATG-TTAAATCCT
1 TTCATGAAAAGATTAAATCAT
*
76174 TTCATCAAAAGA
1 TTCATGAAAAGA
76186 AAAGTCTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.34
Consensus pattern (21 bp):
TTCATGAAAAGATTAAATCAT
Found at i:76223 original size:20 final size:19
Alignment explanation
Indices: 76170--76225 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
76160 AAATGTTAAA
**
76170 TCCTTTCATCAAAAGAAAAG
1 TCCTTTCATC-AAAGGTAAG
* *
76190 TCTTTTAATCAAAGGTAAG
1 TCCTTTCATCAAAGGTAAG
76209 TCCTTTCATCGAAAGGT
1 TCCTTTCATC-AAAGGT
76226 CTTAACCTCT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (19 bp):
TCCTTTCATCAAAGGTAAG
Found at i:76312 original size:5 final size:5
Alignment explanation
Indices: 76302--76336 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
76292 AAGTTACAAG
76302 ACACA ACACA ACACA ACACA ACACA ACACA ACACA
1 ACACA ACACA ACACA ACACA ACACA ACACA ACACA
76337 CAAGTTACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (5 bp):
ACACA
Done.