Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003383.1 Hibiscus syriacus cultivar Beakdansim tig00007119_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: 45832
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3711 original size:13 final size:13
Alignment explanation
Indices: 3693--3723 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3683 AGATGACCGA
3693 TGGTTGGTAGTAT
1 TGGTTGGTAGTAT
3706 TGGTTGGTAGTAT
1 TGGTTGGTAGTAT
*
3719 GGGTT
1 TGGTT
3724 AAATGAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.00, G:0.42, T:0.45
Consensus pattern (13 bp):
TGGTTGGTAGTAT
Found at i:6196 original size:36 final size:37
Alignment explanation
Indices: 6121--6197 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 37
6111 ACAAGTTGAA
*
6121 AAAATTTACATATATTCTTTAAAAAAATTAAATTCAT
1 AAAATTTACATATATTCTTTAAAAAAATTAAAATCAT
* * * *
6158 AAAATTTATATA-ATTTTTTTACAAAATTGAAAAT-AT
1 AAAATTTACATATATTCTTTAAAAAAATT-AAAATCAT
6194 AAAA
1 AAAA
6198 AGGTTTAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
36 19 0.56
37 15 0.44
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.40
Consensus pattern (37 bp):
AAAATTTACATATATTCTTTAAAAAAATTAAAATCAT
Found at i:14854 original size:16 final size:17
Alignment explanation
Indices: 14816--14864 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
14806 TAACTTATCA
14816 ATAAAATTAAATTAATG
1 ATAAAATTAAATTAATG
* *
14833 ATAAAATTGATTTAAT-
1 ATAAAATTAAATTAATG
*
14849 ATAAAAATCAAATTAA
1 AT-AAAATTAAATTAA
14865 CCGAAATAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 2 0.08
17 24 0.92
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (17 bp):
ATAAAATTAAATTAATG
Found at i:26150 original size:57 final size:57
Alignment explanation
Indices: 26062--26176 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
26052 AGCCAATTTC
26062 TTTTATAATAGTTTCCCATCTTTATCCTTCTTTGTCTTCACAAATTTCCATTAACTT
1 TTTTATAATAGTTTCCCATCTTTATCCTTCTTTGTCTTCACAAATTTCCATTAACTT
26119 TTTTATAATAGTTTCCCATCTTTATCCTTCTTTGTCTTCACAAATTTCCATTAACTT
1 TTTTATAATAGTTTCCCATCTTTATCCTTCTTTGTCTTCACAAATTTCCATTAACTT
26176 T
1 T
26177 CTATTGCACC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.51
Consensus pattern (57 bp):
TTTTATAATAGTTTCCCATCTTTATCCTTCTTTGTCTTCACAAATTTCCATTAACTT
Found at i:36439 original size:2 final size:2
Alignment explanation
Indices: 36432--36462 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
36422 CCGGCAATTC
36432 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
36463 TTATTCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36575 original size:16 final size:16
Alignment explanation
Indices: 36535--36565 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36525 AATTGTTTTT
*
36535 TTATAATATAATATAG
1 TTATAAAATAATATAG
36551 TTATAAAATAATATA
1 TTATAAAATAATATA
36566 TGTTTGAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TTATAAAATAATATAG
Found at i:39899 original size:24 final size:24
Alignment explanation
Indices: 39865--39920 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
39855 TAAGCAAGGG
* *
39865 TGCAAATATTTATTTCCTGTACGA
1 TGCAAAGATTTATTTCCCGTACGA
39889 TGCAAAGATTTATTTCCCGTACGA
1 TGCAAAGATTTATTTCCCGTACGA
39913 TGCAAAGA
1 TGCAAAGA
39921 GACTTACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (24 bp):
TGCAAAGATTTATTTCCCGTACGA
Found at i:42755 original size:24 final size:24
Alignment explanation
Indices: 42710--42755 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
42700 GGTTTTGGAT
*
42710 TGGGTTTAGAGAGGAAGGAGAGAG
1 TGGGTTTAGAGAGGAAGAAGAGAG
*
42734 TGGGTTTTAGAG-GGGAGAAGAG
1 TGGG-TTTAGAGAGGAAGAAGAG
42756 GAGGCGCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.30, C:0.00, G:0.50, T:0.20
Consensus pattern (24 bp):
TGGGTTTAGAGAGGAAGAAGAGAG
Found at i:42901 original size:4 final size:4
Alignment explanation
Indices: 42892--42917 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
42882 CCTCTTCCAA
42892 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
42918 TATCTCTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Done.