Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006546.1 Hibiscus syriacus cultivar Beakdansim tig00015977_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: 65979
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:15988 original size:11 final size:11
Alignment explanation
Indices: 15980--16013 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
15970 GAAAAAGACA
15980 AAAAGAAGAAG
1 AAAAGAAGAAG
15991 AAAAGAA-AAG
1 AAAAGAAGAAG
*
16001 AAAAGAAAAAG
1 AAAAGAAGAAG
16012 AA
1 AA
16014 TTCAAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAAG
Found at i:15998 original size:5 final size:5
Alignment explanation
Indices: 15980--16009 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
15970 GAAAAAGACA
15980 AAAAG AAGAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AA-AAG AAAAG AAAAG AAAAG AAAA
16010 AGAATTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:22087 original size:17 final size:17
Alignment explanation
Indices: 22062--22101 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
22052 GTATGTTGTT
*
22062 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
22079 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
22096 CATTTA
1 CATTTA
22102 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:22184 original size:18 final size:18
Alignment explanation
Indices: 22161--22204 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
22151 ATGCATTTAG
22161 TTCATTAAATAAAGTTAT
1 TTCATTAAATAAAGTTAT
* *
22179 TTCATTGAATAATGTTAT
1 TTCATTAAATAAAGTTAT
22197 TTCATTAA
1 TTCATTAA
22205 TCAAACTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (18 bp):
TTCATTAAATAAAGTTAT
Found at i:26640 original size:2 final size:2
Alignment explanation
Indices: 26633--26680 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
26623 TGGAAACGGA
26633 AT AT AT AT AT AT AT 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 AT
26675 AT AT AT
1 AT AT AT
26681 GTTGGTGATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29082 original size:18 final size:19
Alignment explanation
Indices: 29044--29082 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
29034 AAGGAAAAAG
*
29044 AAGCACTCAAAAAGATTGA
1 AAGCACTCAAAAAGATAGA
29063 AAGCACTCAAAAAGA-AGA
1 AAGCACTCAAAAAGATAGA
29081 AA
1 AA
29083 AAGAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.10
Consensus pattern (19 bp):
AAGCACTCAAAAAGATAGA
Found at i:32840 original size:18 final size:19
Alignment explanation
Indices: 32802--32840 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
32792 AAGGAAAAAG
*
32802 AAGCACTCAAAAAGATTGA
1 AAGCACTCAAAAAGATAGA
32821 AAGCACTCAAAAAGA-AGA
1 AAGCACTCAAAAAGATAGA
32839 AA
1 AA
32841 AAGAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.10
Consensus pattern (19 bp):
AAGCACTCAAAAAGATAGA
Found at i:49972 original size:16 final size:14
Alignment explanation
Indices: 49951--50002 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 14
49941 TTTGAACTTC
49951 TCTTTTTCTTTCCTTT
1 TCTTTTT-TTT-CTTT
49967 TCTTTTTTTCTTCTTT
1 TC-TTTTTT-TTCTTT
*
49983 TCTTATTTTTC-TT
1 TCTTTTTTTTCTTT
49996 TCTTTTT
1 TCTTTTT
50003 GCACTCCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
13 8 0.25
14 3 0.09
15 5 0.16
16 9 0.28
17 7 0.22
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (14 bp):
TCTTTTTTTTCTTT
Found at i:49982 original size:21 final size:21
Alignment explanation
Indices: 49951--49999 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
49941 TTTGAACTTC
*
49951 TCTTT-TTCTTTCCTTTTCTTT
1 TCTTTCTTCTTTCCTTAT-TTT
*
49972 T-TTTCTTCTTTTCTTATTTT
1 TCTTTCTTCTTTCCTTATTTT
49992 TCTTTCTT
1 TCTTTCTT
50000 TTTGCACTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (21 bp):
TCTTTCTTCTTTCCTTATTTT
Found at i:49991 original size:17 final size:17
Alignment explanation
Indices: 49948--50001 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 17
49938 CTTTTTGAAC
*
49948 TTCTCTTTTTCTTTCCTT
1 TTCTTTTTTTCTTT-CTT
49966 TTCTTTTTTTC-TTCTT
1 TTCTTTTTTTCTTTCTT
49982 TTCTTATTTTTCTTTCTT
1 TTCTT-TTTTTCTTTCTT
50000 TT
1 TT
50002 TGCACTCCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
16 8 0.24
17 8 0.24
18 17 0.52
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (17 bp):
TTCTTTTTTTCTTTCTT
Found at i:53338 original size:24 final size:24
Alignment explanation
Indices: 53311--53359 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
53301 TTTGATCAAT
*
53311 TTGGACTTGTCTAGGTGTCAAGGG
1 TTGGACTTGTCTAGGCGTCAAGGG
53335 TTGGACTTGTCTAGGCGTCAAGGG
1 TTGGACTTGTCTAGGCGTCAAGGG
53359 T
1 T
53360 GTTAGGATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.16, C:0.14, G:0.37, T:0.33
Consensus pattern (24 bp):
TTGGACTTGTCTAGGCGTCAAGGG
Found at i:61219 original size:14 final size:13
Alignment explanation
Indices: 61201--61250 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
61191 TTGGAGTACA
61201 AAAAAAAGAAAAG
1 AAAAAAAGAAAAG
61214 ACAAAAAAG--AAG
1 A-AAAAAAGAAAAG
*
61226 AAAAGAAGAAAAG
1 AAAAAAAGAAAAG
61239 AAAAAGAAGAAA
1 AAAAA-AAGAAA
61251 TCCAAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 6 0.19
12 4 0.13
13 8 0.26
14 13 0.42
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:61220 original size:17 final size:18
Alignment explanation
Indices: 61200--61246 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
61190 ATTGGAGTAC
61200 AAAAAAAAGAAAAG-ACA
1 AAAAAAAAGAAAAGAACA
* *
61217 AAAAAGAAGAAAAGAAGA
1 AAAAAAAAGAAAAGAACA
61235 AAAGAAAAAGAA
1 AAA-AAAAAGAA
61247 GAAATCCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 13 0.52
18 5 0.20
19 7 0.28
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGAAAAGAACA
Found at i:61229 original size:8 final size:8
Alignment explanation
Indices: 61201--61250 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
61191 TTGGAGTACA
*
61201 AAAAAAAG
1 AAAAGAAG
*
61209 AAAAGACAA
1 AAAAGA-AG
61218 AAAAGAAG
1 AAAAGAAG
61226 AAAAGAAG
1 AAAAGAAG
61234 AAAAG-A-
1 AAAAGAAG
61240 AAAAGAAG
1 AAAAGAAG
61248 AAA
1 AAA
61251 TCCAAAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
6 5 0.14
7 2 0.06
8 22 0.61
9 7 0.19
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:61235 original size:25 final size:25
Alignment explanation
Indices: 61201--61249 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
61191 TTGGAGTACA
61201 AAAAAAAGAAAAGACAAAA-AAGAAG
1 AAAAAAAGAAAAGA-AAAAGAAGAAG
*
61226 AAAAGAAGAAAAGAAAAAGAAGAA
1 AAAAAAAGAAAAGAAAAAGAAGAA
61250 ATCCAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (25 bp):
AAAAAAAGAAAAGAAAAAGAAGAAG
Done.