Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008077.1 Hibiscus syriacus cultivar Beakdansim tig00110579_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: 593651
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:547796 original size:12 final size:12
Alignment explanation
Indices: 547779--547857 Score: 108
Period size: 12 Copynumber: 6.8 Consensus size: 12
547769 GCTCGACTGA
*
547779 AGCTCGATTTTG
1 AGCTCGATTGTG
*
547791 AGCTCGATTG-A
1 AGCTCGATTGTG
547802 AGCTCGATTGTG
1 AGCTCGATTGTG
**
547814 AGCTCGATT-CA
1 AGCTCGATTGTG
547825 AGCTCGATTGTG
1 AGCTCGATTGTG
547837 AGCTCGATTGTG
1 AGCTCGATTGTG
547849 AGCTCGATT
1 AGCTCGATT
547858 CAAGCTTGAC
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
11 19 0.33
12 39 0.67
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (12 bp):
AGCTCGATTGTG
Found at i:547797 original size:23 final size:23
Alignment explanation
Indices: 547767--547857 Score: 137
Period size: 23 Copynumber: 3.9 Consensus size: 23
547757 CTCGAGACTC
* *
547767 GAGCTCGACTGAAGCTCGATTTT
1 GAGCTCGATTGAAGCTCGATTGT
547790 GAGCTCGATTGAAGCTCGATTGT
1 GAGCTCGATTGAAGCTCGATTGT
*
547813 GAGCTCGATTCAAGCTCGATTGT
1 GAGCTCGATTGAAGCTCGATTGT
*
547836 GAGCTCGATTGTGAGCTCGATT
1 GAGCTCGATTG-AAGCTCGATT
547858 CAAGCTTGAC
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
23 53 0.85
24 9 0.15
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.31
Consensus pattern (23 bp):
GAGCTCGATTGAAGCTCGATTGT
Found at i:547821 original size:35 final size:36
Alignment explanation
Indices: 547780--547857 Score: 63
Period size: 35 Copynumber: 2.2 Consensus size: 36
547770 CTCGACTGAA
* * *
547780 GCTCGATTTTGAGCTCGA-TTGAAGCTCGATTGTGA
1 GCTCGATTGTGAGCTCGATTTCAAGCTCGATTGTAA
** * *
547815 GCTCGATT-CAAGCTCGATTGT-GAGCTCGATTGTGA
1 GCTCGATTGTGAGCTCGATT-TCAAGCTCGATTGTAA
547850 GCTCGATT
1 GCTCGATT
547858 CAAGCTTGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 7 0.18
35 30 0.79
36 1 0.03
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.33
Consensus pattern (36 bp):
GCTCGATTGTGAGCTCGATTTCAAGCTCGATTGTAA
Found at i:550451 original size:11 final size:11
Alignment explanation
Indices: 550435--550497 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
550425 ATATTATAGA
550435 ATTTTTAATAT
1 ATTTTTAATAT
550446 ATTTTTAA-A-
1 ATTTTTAATAT
550455 ATTTTATAAT-T
1 ATTTT-TAATAT
*** *
550466 ATCAATAATGT
1 ATTTTTAATAT
550477 ATTTTTAATAT
1 ATTTTTAATAT
550488 ATTTTTAATA
1 ATTTTTAATA
550498 ATGTAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:550579 original size:12 final size:12
Alignment explanation
Indices: 550562--550588 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
550552 GAGCTTTTCA
550562 AGTCGAATATCG
1 AGTCGAATATCG
550574 AGTCGAATATCG
1 AGTCGAATATCG
550586 AGT
1 AGT
550589 AGCTCATTTC
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:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (12 bp):
AGTCGAATATCG
Found at i:578127 original size:12 final size:13
Alignment explanation
Indices: 578107--578135 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
578097 TTCGTGCGAT
578107 TTTTCGTTATAAA
1 TTTTCGTTATAAA
578120 TTTT-GTTATAAA
1 TTTTCGTTATAAA
578132 TTTT
1 TTTT
578136 TTTTTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (13 bp):
TTTTCGTTATAAA
Found at i:581511 original size:35 final size:34
Alignment explanation
Indices: 581426--581512 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
581416 AATATAATTT
*
581426 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
581460 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
581498 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
581513 AATGAAATTC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:583858 original size:10 final size:10
Alignment explanation
Indices: 583839--583876 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
583829 CTTAAATAGA
*
583839 GAGAGTATTT
1 GAGAGAATTT
583849 GAGAGAATTT
1 GAGAGAATTT
583859 GAGAGAATTT
1 GAGAGAATTT
583869 GAGAGAAT
1 GAGAGAAT
583877 ATGGTGTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:585707 original size:24 final size:24
Alignment explanation
Indices: 585675--585723 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
585665 GTGTACTATG
585675 TATGTCTAAAAATTTATATAAGTC
1 TATGTCTAAAAATTTATATAAGTC
*
585699 TATGTCTAAAAATTTATGTAAGTC
1 TATGTCTAAAAATTTATATAAGTC
585723 T
1 T
585724 TACATTTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (24 bp):
TATGTCTAAAAATTTATATAAGTC
Found at i:589480 original size:24 final size:24
Alignment explanation
Indices: 589430--589498 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
589420 TTTATTATAA
* * * *
589430 GTATCAATTTCAAT-AAAAATTAT
1 GTATTAATTTAAATAAAAAAATAG
589453 GTATTAATTTAAATAAAAAAATAG
1 GTATTAATTTAAATAAAAAAATAG
**
589477 GTATTGGTTTAAATAAAGAAAA
1 GTATTAATTTAAATAAA-AAAA
589499 AACTCATACG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.32
24 22 0.58
25 4 0.11
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.35
Consensus pattern (24 bp):
GTATTAATTTAAATAAAAAAATAG
Found at i:589553 original size:2 final size:2
Alignment explanation
Indices: 589546--589573 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
589536 AAGTTACATC
589546 TA 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 TA
589574 GTTGTCACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:592890 original size:77 final size:78
Alignment explanation
Indices: 592762--592918 Score: 298
Period size: 77 Copynumber: 2.0 Consensus size: 78
592752 ACCGTCCAGC
592762 TCAGTTGGTAGAACGCAAGGTTCTTAACATTGAGGTTGTGGGATCGAGTTTTATAAAGGGCATTT
1 TCAGTTGGTAGAACGCAAGGTTCTTAACATTGAGGTTGTGGGATCGAGTTTTATAAAGGGCATTT
592827 TATAATTCGGATG
66 TATAATTCGGATG
*
592840 TCAGTTGGTAGAACGCAAGGTT-TTAACCTTGAGGTTGTGGGATCGAGTTTTATAAAGGGCATTT
1 TCAGTTGGTAGAACGCAAGGTTCTTAACATTGAGGTTGTGGGATCGAGTTTTATAAAGGGCATTT
592904 TATAATTCGGATG
66 TATAATTCGGATG
592917 TC
1 TC
592919 TTCCACGTAA
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
77 56 0.72
78 22 0.28
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.35
Consensus pattern (78 bp):
TCAGTTGGTAGAACGCAAGGTTCTTAACATTGAGGTTGTGGGATCGAGTTTTATAAAGGGCATTT
TATAATTCGGATG
Done.