Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007222.1 Hibiscus syriacus cultivar Beakdansim tig00019109_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: 82561
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:149 original size:28 final size:26
Alignment explanation
Indices: 89--145 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
79 CTATTTACTG
*
89 CTTTATTTTTTTATGGCCTTATGGGA
1 CTTTATTTTTTTATGGCCTCATGGGA
*
115 CATTATTTTTCTCTATGG-CTCATGGGA
1 CTTTATTTTT-T-TATGGCCTCATGGGA
142 CTTT
1 CTTT
146 TATTACTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 9 0.35
27 12 0.46
28 5 0.19
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.51
Consensus pattern (26 bp):
CTTTATTTTTTTATGGCCTCATGGGA
Found at i:3686 original size:26 final size:26
Alignment explanation
Indices: 3635--3690 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
3625 TCAAATTTTT
* *
3635 ATTATTATTGTTTGTTTCGGACTATG
1 ATTATTATTGTTTGATTCGAACTATG
*
3661 ATTATTATT-TATTGATTCGAATTATG
1 ATTATTATTGT-TTGATTCGAACTATG
3687 -TTAT
1 ATTAT
3691 GCTTGTGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.25, C:0.05, G:0.14, T:0.55
Consensus pattern (26 bp):
ATTATTATTGTTTGATTCGAACTATG
Found at i:29744 original size:21 final size:22
Alignment explanation
Indices: 29694--29747 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
29684 ACTTTTAATA
*
29694 AAATAAATATATATAATTTTTTC
1 AAATAAATATATATAA-TTTATC
*
29717 -AA-CAATATATATAA-TTATC
1 AAATAAATATATATAATTTATC
29736 AAATAAATATAT
1 AAATAAATATAT
29748 TTTTAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
19 4 0.15
20 2 0.08
21 18 0.69
22 2 0.08
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (22 bp):
AAATAAATATATATAATTTATC
Found at i:31310 original size:13 final size:13
Alignment explanation
Indices: 31292--31316 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31282 ATATTTCCTG
31292 ATATATGTATAAA
1 ATATATGTATAAA
31305 ATATATGTATAA
1 ATATATGTATAA
31317 CCTTATGAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (13 bp):
ATATATGTATAAA
Found at i:37051 original size:2 final size:2
Alignment explanation
Indices: 37046--37072 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
37036 ACACACAAAC
37046 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
37073 AACGGTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:37699 original size:17 final size:18
Alignment explanation
Indices: 37662--37702 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
37652 ATATTATGTA
*
37662 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
37680 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
37697 TTTACT
1 TTTACT
37703 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:49618 original size:23 final size:23
Alignment explanation
Indices: 49592--49657 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
49582 CCCTCAATGA
*
49592 GGGAATCAGTTCCCATTCAAAGG
1 GGGAATCGGTTCCCATTCAAAGG
49615 GGGAATCGGTTCCCATTCAAAGG
1 GGGAATCGGTTCCCATTCAAAGG
*
49638 GGGAATCGGTTCCCCTTCAA
1 GGGAATCGGTTCCCATTCAA
49658 GGGTATCGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (23 bp):
GGGAATCGGTTCCCATTCAAAGG
Found at i:49628 original size:44 final size:45
Alignment explanation
Indices: 49569--49657 Score: 108
Period size: 46 Copynumber: 2.0 Consensus size: 45
49559 AGAACCCATT
* *
49569 GGGGGTATCGATTCCC-TCAATGAGGGAATCAGTTCCCATTCAAA
1 GGGGGAATCGATTCCCATCAAAGAGGGAATCAGTTCCCATTCAAA
* * * *
49613 GGGGGAATCGGTTCCCATTCAAAGGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATTCCCA-TCAAAGAGGGAATCAGTTCCCATTCAA
49658 GGGTATCGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
44 14 0.38
46 23 0.62
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (45 bp):
GGGGGAATCGATTCCCATCAAAGAGGGAATCAGTTCCCATTCAAA
Found at i:56323 original size:14 final size:14
Alignment explanation
Indices: 56306--56348 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
56296 AATTATAAAT
56306 CCTAAACCCTAATC
1 CCTAAACCCTAATC
* * *
56320 CCTAATCCCTACTT
1 CCTAAACCCTAATC
*
56334 CCTAAATCCTAATC
1 CCTAAACCCTAATC
56348 C
1 C
56349 TACAAAGAAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.30, C:0.42, G:0.00, T:0.28
Consensus pattern (14 bp):
CCTAAACCCTAATC
Found at i:62710 original size:5 final size:5
Alignment explanation
Indices: 62700--62724 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
62690 TAACATTCTG
62700 ATTCA ATTCA ATTCA ATTCA ATTCA
1 ATTCA ATTCA ATTCA ATTCA ATTCA
62725 TGGTTTACGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTCA
Found at i:62940 original size:31 final size:31
Alignment explanation
Indices: 62899--62971 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
62889 AAAACTAATG
62899 AATTGGTCACTAACATTATTGATGTATAAAA
1 AATTGGTCACTAACATTATTGATGTATAAAA
* * * * *
62930 AATTGATCACTAACATTTTTTATTTATAACA
1 AATTGGTCACTAACATTATTGATGTATAAAA
62961 AATTGGTCACT
1 AATTGGTCACT
62972 CAACGTTAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (31 bp):
AATTGGTCACTAACATTATTGATGTATAAAA
Found at i:67048 original size:12 final size:12
Alignment explanation
Indices: 67031--67057 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
67021 TTATAACTTA
67031 GGGTTTTAAGTT
1 GGGTTTTAAGTT
67043 GGGTTTTAAGTT
1 GGGTTTTAAGTT
67055 GGG
1 GGG
67058 GGTAGGGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.44
Consensus pattern (12 bp):
GGGTTTTAAGTT
Found at i:67283 original size:14 final size:14
Alignment explanation
Indices: 67266--67299 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
67256 AAAATTAAAG
67266 TTTATGATTTAAGA
1 TTTATGATTTAAGA
* *
67280 TTTAAGATTTAAGC
1 TTTATGATTTAAGA
67294 TTTATG
1 TTTATG
67300 CTTTGAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.15, T:0.50
Consensus pattern (14 bp):
TTTATGATTTAAGA
Found at i:68599 original size:31 final size:30
Alignment explanation
Indices: 68559--68663 Score: 104
Period size: 31 Copynumber: 3.4 Consensus size: 30
68549 ATAAATTTTC
* * *
68559 ATAATTTTAAGGACTATTTTATAATAATTTG
1 ATAAGTTTAATGACTATTTTGTAAT-ATTTG
* *
68590 ATAAGTTTAATTACTATGTTGTAACTATTTG
1 ATAAGTTTAATGACTATTTTGTAA-TATTTG
*
68621 ATAAAGTTTAATGACTTTTTTGTAATTATTTG
1 AT-AAGTTTAATGACTATTTTGTAA-TATTTG
68653 A-AGAGTTTAAT
1 ATA-AGTTTAAT
68664 AATCATTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
30 1 0.02
31 34 0.55
32 27 0.44
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (30 bp):
ATAAGTTTAATGACTATTTTGTAATATTTG
Found at i:68644 original size:32 final size:32
Alignment explanation
Indices: 68585--68663 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
68575 TTTTATAATA
*
68585 ATTTGAT-AAGTTTAATTACTATGTTGTAACT
1 ATTTGATAAAGTTTAATGACTATGTTGTAACT
* * *
68616 ATTTGATAAAGTTTAATGACTTTTTTGTAATT
1 ATTTGATAAAGTTTAATGACTATGTTGTAACT
*
68648 ATTTGA-AGAGTTTAAT
1 ATTTGATAAAGTTTAAT
68664 AATCATTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 16 0.38
32 26 0.62
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.49
Consensus pattern (32 bp):
ATTTGATAAAGTTTAATGACTATGTTGTAACT
Found at i:68958 original size:16 final size:17
Alignment explanation
Indices: 68920--68959 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
68910 GTTTCCTATC
68920 ATTTTTGTTCTTGTGAT
1 ATTTTTGTTCTTGTGAT
68937 ATTTTTGTTCTTGTGAT
1 ATTTTTGTTCTTGTGAT
68954 ATTTTT
1 ATTTTT
68960 ACATCAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.12, C:0.05, G:0.15, T:0.68
Consensus pattern (17 bp):
ATTTTTGTTCTTGTGAT
Found at i:78300 original size:47 final size:48
Alignment explanation
Indices: 78206--78301 Score: 158
Period size: 47 Copynumber: 2.0 Consensus size: 48
78196 TACAAGTTTT
78206 TAAGTCGAACTCTATTTTAAAATTTTCAAGTTGAGTCAAGAGAAACAATAG
1 TAAGTCGAACTCTATTTTAAAA---TCAAGTTGAGTCAAGAGAAACAATAG
78257 TAAGTCGAACTCTATTTTAAAA-CAAGTTGAGTCAAGAGAAACAAT
1 TAAGTCGAACTCTATTTTAAAATCAAGTTGAGTCAAGAGAAACAAT
78302 TAGAACTCGA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
47 23 0.51
51 22 0.49
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (48 bp):
TAAGTCGAACTCTATTTTAAAATCAAGTTGAGTCAAGAGAAACAATAG
Done.