Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006046.1 Hibiscus syriacus cultivar Beakdansim tig00014298_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: 34575
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:73 original size:32 final size:31
Alignment explanation
Indices: 1--116 Score: 196
Period size: 31 Copynumber: 3.7 Consensus size: 31
*
1 AAAGGCAAATATGAACAGTTTACATATGTTT
1 AAAGGCACATATGAACAGTTTACATATGTTT
32 AAAGGCACATATGAACAGTTTACATATTGTTT
1 AAAGGCACATATGAACAGTTTACATA-TGTTT
*
64 AAAGACACATATGAACAGTTTACATATGTTT
1 AAAGGCACATATGAACAGTTTACATATGTTT
*
95 AAAGGCACCTATGAACAGTTTA
1 AAAGGCACATATGAACAGTTTA
117 TATTATGACC
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 50 0.62
32 30 0.38
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.31
Consensus pattern (31 bp):
AAAGGCACATATGAACAGTTTACATATGTTT
Found at i:12053 original size:18 final size:19
Alignment explanation
Indices: 12030--12072 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
12020 CAGTAATCAT
12030 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
* *
12048 ATTCCCACTTGTAATCTTAT
1 ATT-CCACTGGTAATCTTAC
12068 ATTCC
1 ATTCC
12073 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.19
20 14 0.67
ACGTcount: A:0.23, C:0.28, G:0.07, T:0.42
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:14399 original size:11 final size:11
Alignment explanation
Indices: 14367--14397 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
14357 CGGGGGTATT
14367 AAAATAAAATG
1 AAAATAAAATG
14378 AAAATAAAATG
1 AAAATAAAATG
14389 AAAAGTAAA
1 AAAA-TAAA
14398 TGTTAGGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (11 bp):
AAAATAAAATG
Found at i:17530 original size:34 final size:34
Alignment explanation
Indices: 17487--17552 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
17477 TTAGTTTCTC
17487 TATTCACTTTTTCTGATAACATTCTTTGGGTTTG
1 TATTCACTTTTTCTGATAACATTCTTTGGGTTTG
*
17521 TATTCACTTTTTCTGTTAACATTCTTTGGGTT
1 TATTCACTTTTTCTGATAACATTCTTTGGGTT
17553 ATTTCTCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.17, C:0.15, G:0.14, T:0.55
Consensus pattern (34 bp):
TATTCACTTTTTCTGATAACATTCTTTGGGTTTG
Found at i:22840 original size:31 final size:31
Alignment explanation
Indices: 22804--22862 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
22794 AACTTAAAAG
22804 AGTTTTACAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
22835 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
22863 CTATACAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:25781 original size:41 final size:41
Alignment explanation
Indices: 25724--25805 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
25714 ATCATTAAAT
*
25724 GATTAAAGACGATATTCGTGTATTCCTTTTTAATAAAATCC
1 GATTAAAGACAATATTCGTGTATTCCTTTTTAATAAAATCC
* *
25765 GATTAAAGATAATATTCGTGTATTCTTTTTTAATAAAATCC
1 GATTAAAGACAATATTCGTGTATTCCTTTTTAATAAAATCC
25806 ATATAATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.41
Consensus pattern (41 bp):
GATTAAAGACAATATTCGTGTATTCCTTTTTAATAAAATCC
Found at i:30598 original size:10 final size:10
Alignment explanation
Indices: 30583--30635 Score: 50
Period size: 10 Copynumber: 6.1 Consensus size: 10
30573 CATTTAATAA
30583 ATAAACGAAC
1 ATAAACGAAC
30593 ATAAACGAAC
1 ATAAACGAAC
30603 ----ACGAAC
1 ATAAACGAAC
30609 ATAAACGAAC
1 ATAAACGAAC
30619 ----ACGAAC
1 ATAAACGAAC
30625 ATAAACGAAC
1 ATAAACGAAC
30635 A
1 A
30636 ATTTTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 16
0.69 0.00 0.31
Matches are distributed among these distances:
6 12 0.34
10 23 0.66
ACGTcount: A:0.58, C:0.23, G:0.11, T:0.08
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:30608 original size:16 final size:16
Alignment explanation
Indices: 30587--30635 Score: 98
Period size: 16 Copynumber: 3.1 Consensus size: 16
30577 TAATAAATAA
30587 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
30603 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
30619 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
30635 A
1 A
30636 ATTTTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.57, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:31685 original size:14 final size:14
Alignment explanation
Indices: 31652--31685 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
31642 TGAATGGACA
31652 TAAACGAACATAAC
1 TAAACGAACATAAC
**
31666 CGAACGAACATAAC
1 TAAACGAACATAAC
31680 TAAACG
1 TAAACG
31686 TTCACGGACG
Statistics
Matches: 16, Mismatches: 4, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.24, G:0.12, T:0.12
Consensus pattern (14 bp):
TAAACGAACATAAC
Found at i:34352 original size:6 final size:6
Alignment explanation
Indices: 34335--34369 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
34325 TCAAAGTAAC
*
34335 CTTTCA CCTTCA CTTTCA C-TTCA CTTTCA CTTTCA
1 CTTTCA CTTTCA CTTTCA CTTTCA CTTTCA CTTTCA
34370 TCCATGACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.17, C:0.37, G:0.00, T:0.46
Consensus pattern (6 bp):
CTTTCA
Found at i:34358 original size:11 final size:11
Alignment explanation
Indices: 34335--34366 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
34325 TCAAAGTAAC
34335 CTTTCACCTTCA
1 CTTTCA-CTTCA
34347 CTTTCACTTCA
1 CTTTCACTTCA
34358 CTTTCACTT
1 CTTTCACTT
34367 TCATCCATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.16, C:0.38, G:0.00, T:0.47
Consensus pattern (11 bp):
CTTTCACTTCA
Found at i:34363 original size:17 final size:17
Alignment explanation
Indices: 34337--34369 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
34327 AAAGTAACCT
34337 TTCACCTTCACTTTCAC
1 TTCACCTTCACTTTCAC
*
34354 TTCACTTTCACTTTCA
1 TTCACCTTCACTTTCA
34370 TCCATGACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.36, G:0.00, T:0.45
Consensus pattern (17 bp):
TTCACCTTCACTTTCAC
Done.