Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006905.1 Hibiscus syriacus cultivar Beakdansim tig00017640_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: 67548
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:19177 original size:10 final size:10
Alignment explanation
Indices: 19162--19187 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
19152 ACTCAAAAAG
19162 AAGAAAAGGA
1 AAGAAAAGGA
19172 AAGAAAAGGA
1 AAGAAAAGGA
19182 AAGAAA
1 AAGAAA
19188 GAAAGTTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (10 bp):
AAGAAAAGGA
Found at i:24924 original size:28 final size:28
Alignment explanation
Indices: 24884--24937 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
24874 CTCACATTCA
24884 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
24912 CATAACAGCATGTTCATCATTTGTTT
1 CATAACAGCATGTTCATCATTTGTTT
24938 AGTTAATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.43
Consensus pattern (28 bp):
CATAACAGCATGTTCATCATTTGTTTTG
Found at i:26309 original size:26 final size:27
Alignment explanation
Indices: 26280--26332 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
26270 ATTCATCCTG
*
26280 AAAAA-AAATTTCGAAAATTAAAAAAA
1 AAAAACAAATTCCGAAAATTAAAAAAA
26306 AAAAACAAATTCCGAAAATTAAAAAAA
1 AAAAACAAATTCCGAAAATTAAAAAAA
26333 GAAATGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.72, C:0.08, G:0.04, T:0.17
Consensus pattern (27 bp):
AAAAACAAATTCCGAAAATTAAAAAAA
Found at i:28043 original size:24 final size:24
Alignment explanation
Indices: 28016--28070 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
28006 CCAACTTTTC
28016 TTTCTTTTTTCTTC-TTTTGAGTG
1 TTTCTTTTTTCTTCTTTTTGAGTG
**
28039 TTT-TCAATTTCTTCTTTTTGAGTG
1 TTTCT-TTTTTCTTCTTTTTGAGTG
*
28063 CTTCTTTT
1 TTTCTTTT
28071 CTAATTTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 5
0.71 0.15 0.15
Matches are distributed among these distances:
22 1 0.04
23 10 0.42
24 12 0.50
25 1 0.04
ACGTcount: A:0.07, C:0.15, G:0.11, T:0.67
Consensus pattern (24 bp):
TTTCTTTTTTCTTCTTTTTGAGTG
Found at i:44838 original size:19 final size:20
Alignment explanation
Indices: 44814--44867 Score: 83
Period size: 19 Copynumber: 2.7 Consensus size: 20
44804 TTCGGCCAAG
*
44814 ATCATGTATCTTCA-TTAAA
1 ATCATGTATTTTCATTTAAA
44833 ATCATGTATTTTCATTTAAA
1 ATCATGTATTTTCATTTAAA
44853 AGTCATGTATTTTCA
1 A-TCATGTATTTTCA
44868 AAGGGGTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.41
20 6 0.19
21 13 0.41
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.46
Consensus pattern (20 bp):
ATCATGTATTTTCATTTAAA
Found at i:47661 original size:28 final size:28
Alignment explanation
Indices: 47583--47664 Score: 155
Period size: 28 Copynumber: 2.9 Consensus size: 28
47573 CTCACATTCA
*
47583 CATAACAGCATGTTCATCATTTATTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
47611 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
47639 CATAACAGCATGTTCATCATTTGTTT
1 CATAACAGCATGTTCATCATTTGTTT
47665 AGTTAATTCA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (28 bp):
CATAACAGCATGTTCATCATTTGTTTTG
Found at i:54578 original size:19 final size:18
Alignment explanation
Indices: 54556--54591 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
54546 AAATTTTGGC
54556 TTTTTTGGCTCTTTTTTTG
1 TTTTTTGGC-CTTTTTTTG
*
54575 TTTTTTTGCCTTTTTTT
1 TTTTTTGGCCTTTTTTT
54592 TTTGCCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (18 bp):
TTTTTTGGCCTTTTTTTG
Found at i:54591 original size:13 final size:13
Alignment explanation
Indices: 54575--54603 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54565 TCTTTTTTTG
54575 TTTTTTTGCCTTT
1 TTTTTTTGCCTTT
54588 TTTTTTTGCCTTT
1 TTTTTTTGCCTTT
54601 TTT
1 TTT
54604 GGTTTTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTTTTTGCCTTT
Found at i:54593 original size:20 final size:20
Alignment explanation
Indices: 54556--54592 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54546 AAATTTTGGC
*
54556 TTTTTTGGCTCTTTTTTTGT
1 TTTTTTGCCTCTTTTTTTGT
54576 TTTTTTGCCT-TTTTTTT
1 TTTTTTGCCTCTTTTTTT
54593 TTGCCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (20 bp):
TTTTTTGCCTCTTTTTTTGT
Found at i:54609 original size:20 final size:19
Alignment explanation
Indices: 54549--54615 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 19
54539 TTTTTTGAAA
* *
54549 TTTTGGCTTTTTTGGCTCTT
1 TTTTTGCTTTTTTGG-TTTT
* *
54569 TTTTTGTTTTTTTGCCTTTTT
1 TTTTTGCTTTTTTG--GTTTT
54590 TTTTTGCCTTTTTTGGTTTT
1 TTTTTG-CTTTTTTGGTTTT
54610 TGTTTT
1 T-TTTT
54616 TTTTGTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
20 17 0.46
21 13 0.35
22 7 0.19
ACGTcount: A:0.00, C:0.10, G:0.15, T:0.75
Consensus pattern (19 bp):
TTTTTGCTTTTTTGGTTTT
Found at i:54987 original size:15 final size:15
Alignment explanation
Indices: 54967--55005 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
54957 CACGATAAGA
54967 ATAAATAAACAAAAG
1 ATAAATAAACAAAAG
**
54982 ATAAATAAATGAAAG
1 ATAAATAAACAAAAG
54997 ATGAAATAA
1 AT-AAATAA
55006 GATAATAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.69, C:0.03, G:0.10, T:0.18
Consensus pattern (15 bp):
ATAAATAAACAAAAG
Found at i:55439 original size:43 final size:47
Alignment explanation
Indices: 55385--55487 Score: 117
Period size: 50 Copynumber: 2.2 Consensus size: 47
55375 CTAAAGAATA
*
55385 AAAATATTAATAAACT-AAACA-TGTTTTAA-C-CC-TAATTCCTAAT
1 AAAATAATAAT-AACTAAAACATTGTTTTAACCACCTTAATTCCTAAT
*
55428 AAAATAATAATAACTAAAAATATTGTTTTAACCCAACCTTAATTCCTAAT
1 AAAATAATAATAACT-AAAACATTGTTTTAA-CC-ACCTTAATTCCTAAT
55478 AAAATAATAA
1 AAAATAATAA
55488 ATCTGATCCT
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
42 4 0.08
43 10 0.20
44 4 0.08
45 8 0.16
47 1 0.02
49 2 0.04
50 21 0.42
ACGTcount: A:0.50, C:0.15, G:0.02, T:0.33
Consensus pattern (47 bp):
AAAATAATAATAACTAAAACATTGTTTTAACCACCTTAATTCCTAAT
Done.