Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005305.1 Hibiscus syriacus cultivar Beakdansim tig00012007_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: 68007
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:12654 original size:35 final size:39
Alignment explanation
Indices: 12560--12661 Score: 122
Period size: 39 Copynumber: 2.7 Consensus size: 39
12550 TTTTAAAAGT
* *
12560 AATTTAAAATATTAGGGTGAAATAATTTAAGAAAATATA
1 AATTTAGAATATTATGGTGAAATAATTTAAGAAAATATA
* * *
12599 AATTTAGAATTTTATAGTGAAATAATTTAAG-CAAT-T-
1 AATTTAGAATATTATGGTGAAATAATTTAAGAAAATATA
*
12635 GA-TTAGAATATTATGGTGAAATAATTT
1 AATTTAGAATATTATGGTGAAATAATTT
12662 TAAAAATTGG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
35 23 0.42
36 1 0.02
37 1 0.02
38 3 0.05
39 27 0.49
ACGTcount: A:0.47, C:0.01, G:0.14, T:0.38
Consensus pattern (39 bp):
AATTTAGAATATTATGGTGAAATAATTTAAGAAAATATA
Found at i:12670 original size:35 final size:36
Alignment explanation
Indices: 12543--12669 Score: 125
Period size: 35 Copynumber: 3.5 Consensus size: 36
12533 GAAATTAAAA
* * *
12543 GAAATAATTTT-AAAAGTAATTTAAAATATTAGGGT
1 GAAATAATTTTAAAAATTAATTTAGAATATTATGGT
* * *
12578 GAAATAATTTAAGAAAATATAAATTTAGAATTTTATAGT
1 GAAATAATTTTA-AAAAT-T-AATTTAGAATATTATGGT
* *
12617 GAAATAA-TTTAAGCAATTGA-TTAGAATATTATGGT
1 GAAATAATTTTAA-AAATTAATTTAGAATATTATGGT
12652 GAAATAATTTTAAAAATT
1 GAAATAATTTTAAAAATT
12670 GGTTGTGGAA
Statistics
Matches: 74, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
35 34 0.46
36 6 0.08
37 6 0.08
38 7 0.09
39 21 0.28
ACGTcount: A:0.49, C:0.01, G:0.13, T:0.38
Consensus pattern (36 bp):
GAAATAATTTTAAAAATTAATTTAGAATATTATGGT
Found at i:13350 original size:2 final size:2
Alignment explanation
Indices: 13343--13427 Score: 163
Period size: 2 Copynumber: 43.0 Consensus size: 2
13333 AATGATTTTC
13343 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13384 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
13426 AT
1 AT
13428 TAAGATATTT
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 81 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:14862 original size:2 final size:2
Alignment explanation
Indices: 14855--14890 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
14845 ATTGATTTTA
14855 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
14891 TTCTTCGTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16231 original size:60 final size:60
Alignment explanation
Indices: 16129--16270 Score: 171
Period size: 60 Copynumber: 2.4 Consensus size: 60
16119 AAACATATTA
* * * *
16129 ATAGTC-AAGTGACCATTTTATAACTTCTAATAGTCGAGAGACTCAACAAAATAACATCCT
1 ATAGTCAAAG-GACCATTTTATAACTTCTAATAATCGAGAGACTAAACAAAACAACACCCT
* * *
16189 ATAGTCAAAGGACCATTTTATAACTTTTAATAATCGATAGACTAAACAAAACAATACCCT
1 ATAGTCAAAGGACCATTTTATAACTTCTAATAATCGAGAGACTAAACAAAACAACACCCT
* *
16249 ATAGTTAGA-GACCATTTATATA
1 ATAGTCAAAGGACCATTT-TATA
16271 TTTTACACTT
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
59 8 0.11
60 60 0.85
61 3 0.04
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.30
Consensus pattern (60 bp):
ATAGTCAAAGGACCATTTTATAACTTCTAATAATCGAGAGACTAAACAAAACAACACCCT
Found at i:20209 original size:18 final size:17
Alignment explanation
Indices: 20186--20231 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
20176 TTCAGAGCTA
20186 AATCATTCAAAGTCTCTG
1 AATCATTCAAA-TCTCTG
*
20204 AATCATTCAGCATCTCTG
1 AATCATTCA-AATCTCTG
*
20222 AATTATTCAA
1 AATCATTCAA
20232 CGCTTAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 23 0.96
19 1 0.04
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.35
Consensus pattern (17 bp):
AATCATTCAAATCTCTG
Found at i:28018 original size:14 final size:15
Alignment explanation
Indices: 27987--28019 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
27977 ATGAAGAATG
27987 TGGAGAAGAGATAGAA
1 TGGAGAAGAGA-AGAA
28003 TGGAGAAGAG-AGAA
1 TGGAGAAGAGAAGAA
28017 TGG
1 TGG
28020 CCGTGAGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
16 10 0.59
ACGTcount: A:0.45, C:0.00, G:0.42, T:0.12
Consensus pattern (15 bp):
TGGAGAAGAGAAGAA
Found at i:30123 original size:45 final size:45
Alignment explanation
Indices: 30054--30204 Score: 239
Period size: 45 Copynumber: 3.3 Consensus size: 45
30044 TTTATTTTCG
*
30054 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGTTTA
1 TTTTTTGAAT-AA-GCATGCGAACTAGATATCATGCGGTTAGGTTTA
30101 TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGGTTTA
1 TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGGTTTA
* *
30146 TTTTTTGAATAAGCATGCGAATTAGATATCATGCGGTTATGATTTA
1 TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTA-GGTTTA
30192 TTTTTGTGAATAA
1 TTTTT-TGAATAA
30205 CAAAGCATGG
Statistics
Matches: 99, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
45 71 0.72
46 12 0.12
47 16 0.16
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.40
Consensus pattern (45 bp):
TTTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGGTTTA
Found at i:33548 original size:15 final size:15
Alignment explanation
Indices: 33528--33557 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
33518 ATTAGGCTCA
33528 ACAGGATGATGTTGC
1 ACAGGATGATGTTGC
33543 ACAGGATGATGTTGC
1 ACAGGATGATGTTGC
33558 GGGGAATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.33, T:0.27
Consensus pattern (15 bp):
ACAGGATGATGTTGC
Found at i:46935 original size:23 final size:22
Alignment explanation
Indices: 46909--46972 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
46899 CAGCTCATAT
46909 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* * *
46932 AATTGCACCGGAGTGTCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
*
46955 AATTACACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
46973 TATAATAATG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:47119 original size:103 final size:103
Alignment explanation
Indices: 46988--47205 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
46978 TAATGTCCAT
*
46988 AAGGACAACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCAACA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCAACA
* *
47053 GACCTCACACATGTTCTAAAGAATACATATATGTCCCG
66 GACCTCACACATATTCCAAAGAATACATATATGTCCCG
*
47091 AAGGACCACATATCATTCCTTAATAATCATATACATATGCCAAAGATCAAGTATGTGTCTCAACA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCAACA
*
47156 GACCTCACACCTATTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATATTCCAAAGAATACATATATGTCCCG
47194 AAGGACCACATA
1 AAGGACCACATA
47206 GACCCTCTAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCAACA
GACCTCACACATATTCCAAAGAATACATATATGTCCCG
Found at i:57565 original size:2 final size:2
Alignment explanation
Indices: 57558--57583 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57548 GAATATTTAA
57558 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
57584 TCTTATCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67549 original size:19 final size:22
Alignment explanation
Indices: 67525--67568 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
67515 AATGTTAAAC
*
67525 AAAA-ATGTTCATGAACAT-TA
1 AAAATATGTTCACGAACATATA
67545 AAAATATGTTCACGAACATATA
1 AAAATATGTTCACGAACATATA
67567 AA
1 AA
67569 CGAACATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 13 0.62
22 4 0.19
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.27
Consensus pattern (22 bp):
AAAATATGTTCACGAACATATA
Done.