Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009640.1 Hibiscus syriacus cultivar Beakdansim tig00117050_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: 8854
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Found at i:1845 original size:194 final size:196
Alignment explanation
Indices: 1368--1973 Score: 1010
Period size: 194 Copynumber: 3.1 Consensus size: 196
1358 TTTAAATTAG
*
1368 TATCGACACAAA-TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGAC-TATTCTCTCATAAAACCGGTATA
1432 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
65 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
1497 CGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAAA
130 CGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTTATTCATTCT-GGAAAA
1562 AAA
194 AAA
1565 TA-CGACACAAACTATATTAGTGTCGACACATTATTTAGAC-ATTCTCTCATAAAACCGGTATAA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTATTCTCTCATAAAACCGGTATAA
1628 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
1693 GACACTTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTTATTCATTCTGGAAAAAA
131 GACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTTATTCATTCTGGAAAAAA
1757 A
196 A
*
1758 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTTAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGAC-TATTCTCTCATAAAACCGGTATA
1822 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
65 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
1886 CGACACTTTTTATATATGGATCGACACTTT-T--G-AC-CCTTG--TTTT-TTCATTCTGGAAAA
130 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTTATTCATTCTGG-AAA
1943 AAAA
193 AAAA
*
1947 TATCGACAC-AACTATA-TAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
1974 TGACCCTTAA
Statistics
Matches: 397, Mismatches: 5, Indels: 24
0.93 0.01 0.06
Matches are distributed among these distances:
187 10 0.03
188 17 0.04
189 20 0.05
191 5 0.01
192 1 0.00
193 12 0.03
194 137 0.35
195 129 0.32
196 36 0.09
197 30 0.08
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (196 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTATTCTCTCATAAAACCGGTATAA
TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
GACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTTATTCATTCTGGAAAAAA
A
Found at i:2095 original size:19 final size:19
Alignment explanation
Indices: 2052--2095 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
2042 TATTCACATA
*
2052 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
2071 -AAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
2089 AAAATTA
1 AAAATTA
2096 ACTCGACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:3678 original size:15 final size:14
Alignment explanation
Indices: 3639--3686 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
3629 CATGACTCTC
*
3639 CTTCCTCCTCATTT
1 CTTCCTCCTCTTTT
3653 CTTCCAT-CTCTTCTT
1 CTTCC-TCCTCTT-TT
3668 CTTCCTCCTCTCTTT
1 CTTCCTCCTCT-TTT
3683 CTTC
1 CTTC
3687 TTCATATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 10 0.34
15 18 0.62
16 1 0.03
ACGTcount: A:0.04, C:0.44, G:0.00, T:0.52
Consensus pattern (14 bp):
CTTCCTCCTCTTTT
Found at i:4925 original size:22 final size:23
Alignment explanation
Indices: 4900--4946 Score: 87
Period size: 22 Copynumber: 2.1 Consensus size: 23
4890 TTGTGCCATC
4900 AAGGATCGACACAATT-CCTCCG
1 AAGGATCGACACAATTCCCTCCG
4922 AAGGATCGACACAATTCCCTCCG
1 AAGGATCGACACAATTCCCTCCG
4945 AA
1 AA
4947 TAGGTCGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (23 bp):
AAGGATCGACACAATTCCCTCCG
Found at i:6251 original size:20 final size:18
Alignment explanation
Indices: 6213--6261 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
6203 AATATATCCG
*
6213 TATCATTTTTACCGTTTT
1 TATCATTTTTACCGGTTT
6231 TATCATTTTGATACCGGTTT
1 TATCATTTT--TACCGGTTT
6251 TATCATATTTT
1 TATCAT-TTTT
6262 TACATGTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 9 0.33
19 1 0.04
20 14 0.52
21 3 0.11
ACGTcount: A:0.20, C:0.14, G:0.08, T:0.57
Consensus pattern (18 bp):
TATCATTTTTACCGGTTT
Found at i:6410 original size:20 final size:20
Alignment explanation
Indices: 6383--6429 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
6373 ACACTTTTAA
6383 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
6402 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
6423 TTTTACC
1 TTTTACC
6430 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:7390 original size:16 final size:18
Alignment explanation
Indices: 7369--7410 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
7359 AAGATATTTG
7369 ATTTATTAAT-A-TTTTT
1 ATTTATTAATAATTTTTT
7385 ATTTATTTAATAAATTTTTT
1 ATTTA-TTAAT-AATTTTTT
7405 ATTTAT
1 ATTTAT
7411 CTTATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 5 0.23
19 2 0.09
20 10 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTATTAATAATTTTTT
Found at i:7394 original size:17 final size:17
Alignment explanation
Indices: 7355--7422 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 17
7345 AATTATTTTA
* *
7355 ATTTAAGATATTTGATTT
1 ATTTAATAT-TTTTATTT
7373 A-TTAATATTTTTATTT
1 ATTTAATATTTTTATTT
7389 ATTTAATAAATTTTTTATTT
1 ATTTAAT--A-TTTTTATTT
7409 ATCTT-AT-TTTTTAT
1 AT-TTAATATTTTTAT
7423 CATTTTAGTG
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
16 15 0.35
17 11 0.26
18 1 0.02
19 1 0.02
20 13 0.30
21 2 0.05
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (17 bp):
ATTTAATATTTTTATTT
Done.