Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003114.1 Hibiscus syriacus cultivar Beakdansim tig00006520_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: 89426
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:14448 original size:2 final size:2
Alignment explanation
Indices: 14441--14466 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14431 GGTTTCTAAT
14441 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
14467 ACCCACCAAA
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):
TA
Found at i:18921 original size:175 final size:175
Alignment explanation
Indices: 18630--18980 Score: 666
Period size: 175 Copynumber: 2.0 Consensus size: 175
18620 TTTCCCCCCC
18630 CCCCAAAATATCACCTATATCCTATAATATTCTCTATTAGACACTCTTCAGACTATTTTTCTATA
1 CCCCAAAATATCACCTATATCCTATAATATTCTCTATTAGACACTCTTCAGACTATTTTTCTATA
*
18695 TTTAAAACCCTTTGTAGTAAGGCGCCCTCCTATAACGAGCTTTACGTTGATATGGCGTCACGGGG
66 TTTAAAACCCTTTGTAGTAAGGCGCCCTCCTATAACGAGCTTTACGTTGATATGACGTCACGGGG
18760 GTACGCTTTACGCTGACATGGACACACGTGTTTAAAGCATGACCT
131 GTACGCTTTACGCTGACATGGACACACGTGTTTAAAGCATGACCT
* *
18805 CCCCAAAATATCACCTATATCTTATAATATTCTCTATTAGGCACTCTTCAGACTATTTTTCTATA
1 CCCCAAAATATCACCTATATCCTATAATATTCTCTATTAGACACTCTTCAGACTATTTTTCTATA
18870 TTTAAAACCCTTTGTAGTAAGGCGCCCTCCTATAACGAGCTTTACGTTGATATGACGTCACGGGG
66 TTTAAAACCCTTTGTAGTAAGGCGCCCTCCTATAACGAGCTTTACGTTGATATGACGTCACGGGG
*
18935 GTACGCTTTACGCTGACATGGACACACGTGTTTAAAGCGTGACCT
131 GTACGCTTTACGCTGACATGGACACACGTGTTTAAAGCATGACCT
18980 C
1 C
18981 TGAGGCGCGC
Statistics
Matches: 172, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
175 172 1.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (175 bp):
CCCCAAAATATCACCTATATCCTATAATATTCTCTATTAGACACTCTTCAGACTATTTTTCTATA
TTTAAAACCCTTTGTAGTAAGGCGCCCTCCTATAACGAGCTTTACGTTGATATGACGTCACGGGG
GTACGCTTTACGCTGACATGGACACACGTGTTTAAAGCATGACCT
Found at i:22626 original size:23 final size:22
Alignment explanation
Indices: 22600--22672 Score: 53
Period size: 23 Copynumber: 3.2 Consensus size: 22
22590 AAAATAAGCT
22600 TAAGAGCTTATGGAATTAAATGG
1 TAAGAGCTTATGG-ATTAAATGG
* *
22623 TAAGTA--TTTTGG-TAAAATAGG
1 TAAG-AGCTTATGGATTAAAT-GG
22644 CCTAAGAGCTTATGGGATTAAATGG
1 --TAAGAGCTTAT-GGATTAAATGG
22669 TAAG
1 TAAG
22673 TGTTTTGGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
20 5 0.13
21 2 0.05
22 6 0.16
23 12 0.32
24 4 0.11
25 4 0.11
26 5 0.13
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (22 bp):
TAAGAGCTTATGGATTAAATGG
Found at i:22650 original size:46 final size:45
Alignment explanation
Indices: 22547--22717 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 45
22537 GTAAGCATGC
* * ** *
22547 AAATTAGCTTACGAGCTTATGGAAT-AATGACAAGTATATTGGTA
1 AAATAAGCTTAAGAGCTTATGGAATAAATGGTAAGTATTTTGGTA
22591 AAATAAGCTTAAGAGCTTATGGAATTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTAAGAGCTTATGGAA-TAAATGGTAAGTATTTTGGTA
* * * *
22637 AAATAGGCCTAAGAGCTTATGGGATTAAATGGTAAGTGTTTTGGTA
1 AAATAAGCTTAAGAGCTTAT-GGAATAAATGGTAAGTATTTTGGTA
* * *
22683 AAATAAACTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTAAGAGCTTATGGAATAAATGGTAAG
22718 AGATTTTATC
Statistics
Matches: 109, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
44 22 0.20
45 14 0.13
46 70 0.64
47 3 0.03
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTAAGAGCTTATGGAATAAATGGTAAGTATTTTGGTA
Found at i:26084 original size:34 final size:33
Alignment explanation
Indices: 26042--26115 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
26032 AATGGTAATA
* *
26042 AACAAAATTAACCAAAATACATTAAGAAAAAATCC
1 AACAAATTTAA-CAAAATAAATTAA-AAAAAATCC
*
26077 AACAAATTTAACAAAATAAATTAAAATAAATCC
1 AACAAATTTAACAAAATAAATTAAAAAAAATCC
26110 AACAAA
1 AACAAA
26116 AATAATGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 14 0.39
34 12 0.33
35 10 0.28
ACGTcount: A:0.65, C:0.15, G:0.01, T:0.19
Consensus pattern (33 bp):
AACAAATTTAACAAAATAAATTAAAAAAAATCC
Found at i:26127 original size:33 final size:34
Alignment explanation
Indices: 26042--26134 Score: 98
Period size: 33 Copynumber: 2.7 Consensus size: 34
26032 AATGGTAATA
* *
26042 AACAAAATTAACCAAAATACATTAAGAAAAAATCC
1 AACAAAAATAA-CAAAATAAATTAAGAAAAAATCC
** *
26077 AACAAATTTAACAAAATAAATTAA-AATAAATCC
1 AACAAAAATAACAAAATAAATTAAGAAAAAATCC
** *
26110 AACAAAAATAATGAAATAAAGTAAG
1 AACAAAAATAACAAAATAAATTAAG
26135 TATTAAATGA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
33 27 0.55
34 12 0.24
35 10 0.20
ACGTcount: A:0.65, C:0.12, G:0.04, T:0.19
Consensus pattern (34 bp):
AACAAAAATAACAAAATAAATTAAGAAAAAATCC
Found at i:26656 original size:30 final size:30
Alignment explanation
Indices: 26600--26659 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
26590 CTCTAGGAGT
* *
26600 GGTCATAAAACTCTGTGATGGCGGCGGCGG
1 GGTCATAAAACTCGGTGACGGCGGCGGCGG
*
26630 GGTCATAAAAC-CAGGTGACGGTGGCGGCGG
1 GGTCATAAAACTC-GGTGACGGCGGCGGCGG
26660 CATCATCGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.22, C:0.20, G:0.42, T:0.17
Consensus pattern (30 bp):
GGTCATAAAACTCGGTGACGGCGGCGGCGG
Found at i:46528 original size:25 final size:24
Alignment explanation
Indices: 46495--46557 Score: 85
Period size: 23 Copynumber: 2.6 Consensus size: 24
46485 TACTATACTT
46495 GAAGAAAAAAATGAAAAAATAAAAA
1 GAAGAAAAAAATGAAAAAA-AAAAA
*
46520 GAAGAAAAAAAAG-AAAAAAAAAA
1 GAAGAAAAAAATGAAAAAAAAAAA
46543 GAA-AGAAAAAATGAA
1 GAAGA-AAAAAATGAA
46558 GAAGGAGGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 1 0.03
23 15 0.44
24 6 0.18
25 12 0.35
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (24 bp):
GAAGAAAAAAATGAAAAAAAAAAA
Found at i:46532 original size:12 final size:12
Alignment explanation
Indices: 46495--46553 Score: 75
Period size: 12 Copynumber: 4.8 Consensus size: 12
46485 TACTATACTT
*
46495 GAAGAAAAAAAT
1 GAAGAAAAAAAA
*
46507 GAAAAAATAAAAA
1 GAAGAAA-AAAAA
46520 GAAGAAAAAAAA
1 GAAGAAAAAAAA
46532 GAA-AAAAAAAA
1 GAAGAAAAAAAA
46543 GAAAGAAAAAA
1 G-AAGAAAAAA
46554 TGAAGAAGGA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
11 9 0.22
12 16 0.39
13 16 0.39
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (12 bp):
GAAGAAAAAAAA
Found at i:46551 original size:9 final size:8
Alignment explanation
Indices: 46496--46553 Score: 57
Period size: 8 Copynumber: 7.1 Consensus size: 8
46486 ACTATACTTG
46496 AAGAAAAA
1 AAGAAAAA
46504 AATGAAAAA
1 AA-GAAAAA
*
46513 ATA-AAAAG
1 A-AGAAAAA
46521 AAGAAAAAA
1 AAG-AAAAA
46530 AAGAAAAA
1 AAGAAAAA
*
46538 AA-AAAGA
1 AAGAAAAA
46545 AAGAAAAA
1 AAGAAAAA
46553 A
1 A
46554 TGAAGAAGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
7 7 0.17
8 19 0.46
9 14 0.34
10 1 0.02
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.03
Consensus pattern (8 bp):
AAGAAAAA
Found at i:46560 original size:15 final size:15
Alignment explanation
Indices: 46524--46553 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
46514 TAAAAAGAAG
46524 AAAAA-AAAGAAAAA
1 AAAAAGAAAGAAAAA
46538 AAAAAGAAAGAAAAA
1 AAAAAGAAAGAAAAA
46553 A
1 A
46554 TGAAGAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAGAAAAA
Found at i:47919 original size:135 final size:135
Alignment explanation
Indices: 47519--48009 Score: 734
Period size: 136 Copynumber: 3.6 Consensus size: 135
47509 CAAAAGAGGT
* *
47519 GGATCAGCATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTT
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACA-AGGGAGAAGAAGTT
*
47584 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTTGAATCAGTGACACCTCG
65 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
47649 CTTGAG
130 CTTGAG
* ** * * * *
47655 GAATTGACATTTCCAATGGAGAGTTTATAATGAGAAGAACTCATCAGAAAAAGGGAGAAGAAGTT
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATC-CAACAAGGGAGAAGAAGTT
47720 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
65 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
47785 CTTGAG
130 CTTGAG
* *
47791 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAATAAGTTC
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTC
* * * * *
47856 ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCA-CAGTATTTCGAGTCAGGGACGCCTCG
66 ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGA-CATTTCGAATCAGTGACACCTCG
47920 CTTGAG
130 CTTGAG
* * * *
47926 GGATCAACATTTTCAGTGAAGAGTTCATAATGAGAAAAACTCATCCAA-AAGAGAGAAGAAGTTC
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTC
* *
47990 ATAATGCGAAGAACTTGTTC
66 ATAATGAGAAGAGCTTGTTC
48010 AATCTAACAA
Statistics
Matches: 321, Mismatches: 32, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
134 32 0.10
135 124 0.39
136 163 0.51
137 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.25
Consensus pattern (135 bp):
GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTC
ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCGC
TTGAG
Found at i:47921 original size:271 final size:270
Alignment explanation
Indices: 47519--48009 Score: 752
Period size: 271 Copynumber: 1.8 Consensus size: 270
47509 CAAAAGAGGT
* *
47519 GGATCAGCATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTT
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTT
* * *
47584 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTTGAATCAGTGACACCTCG
66 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCAAGACATTTCGAATCAGGGACACCTCG
** * * * *
47649 CTTGAGGAATTGACATTTCCAATGGAGAGTTTATAATGAGAAGAACTCATCAGAAAAAGGGAGAA
131 CTTGAGGAATCAACATTTCCAATGAAGAGTTCATAATGAGAAAAACTCATC--AAAAAGAGAGAA
*
47714 GAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGAC
194 GAAGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGAC
47779 ACCTCGCTTGAG
259 ACCTCGCTTGAG
*
47791 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAC-GAGGGAGAATAAGTT
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTT
* * *
47855 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACAG-TATTTCGAGTCAGGGACGCCTC
66 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCA-AGACATTTCGAATCAGGGACACCTC
* * * *
47919 GCTTGAGGGATCAACATTTTCAGTGAAGAGTTCATAATGAGAAAAACTCATCCAAAAGAGAGAAG
130 GCTTGAGGAATCAACATTTCCAATGAAGAGTTCATAATGAGAAAAACTCATCAAAAAGAGAGAAG
*
47984 AAGTTCATAATGCGAAGAACTTGTTC
195 AAGTTCATAATGAGAAGAACTTGTTC
48010 AATCTAACAA
Statistics
Matches: 197, Mismatches: 21, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
269 35 0.18
271 114 0.58
272 48 0.24
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.25
Consensus pattern (270 bp):
GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTT
CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCAAGACATTTCGAATCAGGGACACCTCG
CTTGAGGAATCAACATTTCCAATGAAGAGTTCATAATGAGAAAAACTCATCAAAAAGAGAGAAGA
AGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACAC
CTCGCTTGAG
Found at i:79495 original size:2 final size:2
Alignment explanation
Indices: 79488--79527 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
79478 TTTAAAATTA
79488 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
79528 CTTAGCCTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:79905 original size:2 final size:2
Alignment explanation
Indices: 79898--79924 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
79888 GAAAATAAAT
79898 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
79925 CCTTAAAACT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:81322 original size:17 final size:18
Alignment explanation
Indices: 81280--81325 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
81270 ACTATTGAAT
*
81280 TTTAAGATTTTATATTCGA
1 TTTAA-ATTATATATTCGA
81299 TTTAAATTATATATTCGA
1 TTTAAATTATATATTCGA
81317 -TTAAATTAT
1 TTTAAATTAT
81326 TCGAATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 9 0.35
18 12 0.46
19 5 0.19
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (18 bp):
TTTAAATTATATATTCGA
Found at i:83082 original size:117 final size:117
Alignment explanation
Indices: 82934--83157 Score: 292
Period size: 117 Copynumber: 1.9 Consensus size: 117
82924 TAAAAATGAT
* * *
82934 CTTCTTTTGAAATCTAAAATAGAATTGGAAAATCAAAATGAAATGTTG-AGAAAGGAGTTAGAGC
1 CTTCTTTAGAAATCTAAAATAGAATTGGAAAATCAAAATGAAATATTGAAG-AAGGAGTTAGAAC
* *
82998 TTTCAAAAACGAAATCTGAAAACT-TTGAAAAATAAATTTTCGAATTAAACAAA
65 TTTCAAAAACGAAATCTG-AAACTATTGAAAAAGAAAATTTCGAATTAAACAAA
* * * *
83051 CTTCTTCTAGAAA-CTAAAATGGATTTTGAAAATCAAAATGAAATATTGAAGAAGGATTTAGAAC
1 CTTCTT-TAGAAATCTAAAATAGAATTGGAAAATCAAAATGAAATATTGAAGAAGGAGTTAGAAC
* * *
83115 TTTCAAAAATGAAATTTGAAAGTATTGAAAAAGAAAATTTCGA
65 TTTCAAAAACGAAATCTGAAACTATTGAAAAAGAAAATTTCGA
83158 TTTGAAAGTT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
116 4 0.04
117 81 0.88
118 7 0.08
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.29
Consensus pattern (117 bp):
CTTCTTTAGAAATCTAAAATAGAATTGGAAAATCAAAATGAAATATTGAAGAAGGAGTTAGAACT
TTCAAAAACGAAATCTGAAACTATTGAAAAAGAAAATTTCGAATTAAACAAA
Found at i:83572 original size:20 final size:21
Alignment explanation
Indices: 83540--83585 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
83530 ATGCATGAGT
83540 TTTTAATCTTAAATAATTATG
1 TTTTAATCTTAAATAATTATG
83561 TTTTAA-CTTAAATAATTATG
1 TTTTAATCTTAAATAATTATG
83581 TTTTA
1 TTTTA
83586 TCTCATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (21 bp):
TTTTAATCTTAAATAATTATG
Done.