Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002363.1 Hibiscus syriacus cultivar Beakdansim tig00004822_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: 77284
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:23803 original size:14 final size:14
Alignment explanation
Indices: 23786--23836 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
23776 AAAGTGATAG
23786 ATTTATAATTAAAT
1 ATTTATAATTAAAT
*
23800 ATTTATGATTAAA-
1 ATTTATAATTAAAT
*
23813 AATTATATATTAAAAAT
1 ATTTATA-ATT--AAAT
23830 ATTTATA
1 ATTTATA
23837 GAAAATATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
13 5 0.17
14 15 0.52
16 3 0.10
17 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (14 bp):
ATTTATAATTAAAT
Found at i:29543 original size:27 final size:27
Alignment explanation
Indices: 29512--29576 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
29502 TGTTCCGGGT
*
29512 TCGGGTCCTCTGGAGAGGGGGTTCATG
1 TCGGGTCCTCTCGAGAGGGGGTTCATG
**
29539 TCGGGTCCGATCGAGAGGGGGTTCATG
1 TCGGGTCCTCTCGAGAGGGGGTTCATG
29566 TCGGGTCCTCT
1 TCGGGTCCTCT
29577 TGATAATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.11, C:0.22, G:0.42, T:0.26
Consensus pattern (27 bp):
TCGGGTCCTCTCGAGAGGGGGTTCATG
Found at i:33651 original size:23 final size:23
Alignment explanation
Indices: 33625--33680 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
33615 ACTTACAAAC
*
33625 GTTAAATAAATATATTCGTAAAT
1 GTTAAATAAATATATTCATAAAT
* *
33648 GTTAAATAAATATGTTTATAAAT
1 GTTAAATAAATATATTCATAAAT
33671 GTTAAATAAA
1 GTTAAATAAA
33681 AAAAATATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (23 bp):
GTTAAATAAATATATTCATAAAT
Found at i:36693 original size:24 final size:24
Alignment explanation
Indices: 36623--36693 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 24
36613 AAGCATGGGT
36623 ACAACTTAATTACTTGTTATTGAA
1 ACAACTTAATTACTTGTTATTGAA
* * *
36647 ACTACATATATCTAC-AG-TA---AA
1 ACAACTTA-AT-TACTTGTTATTGAA
36668 ACAACTTAATTACTTGTTATTGAA
1 ACAACTTAATTACTTGTTATTGAA
36692 AC
1 AC
36694 TACATATATC
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 3 0.09
20 3 0.09
21 10 0.29
24 12 0.35
25 3 0.09
26 3 0.09
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (24 bp):
ACAACTTAATTACTTGTTATTGAA
Found at i:46705 original size:32 final size:33
Alignment explanation
Indices: 46664--46741 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
46654 TTTAAATAGT
* *
46664 TATTATTTTTTA-TATTAAT-ATATTTATGTAAA
1 TATTATTTTTTATTA-AAATAATATTTATATAAA
*
46696 TATTATTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATTAAAATAATATTTATATAAA
46729 TATTATTTATTTA
1 TATTATTT-TTTA
46742 GAATTATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
32 15 0.38
33 21 0.52
34 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
TATTATTTTTTATTAAAATAATATTTATATAAA
Found at i:46903 original size:17 final size:17
Alignment explanation
Indices: 46881--46934 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
46871 AATGTTAATA
46881 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
46898 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
46915 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
46932 TTT
1 TTT
46935 TTATAATATA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:48495 original size:21 final size:21
Alignment explanation
Indices: 48465--48512 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
48455 GCAGGGGTAC
* *
48465 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
48486 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
48507 ATGCCA
1 ATGCCA
48513 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:48542 original size:21 final size:21
Alignment explanation
Indices: 48516--48609 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
48506 TATGCCATCT
* *
48516 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
48537 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
48558 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
48579 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
48600 CCGCAGGGTT
1 CCGCAGGGTT
48610 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:49191 original size:33 final size:34
Alignment explanation
Indices: 49132--49228 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
49122 AAATGTTTTT
*
49132 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
49166 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
49199 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
49229 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:49235 original size:34 final size:33
Alignment explanation
Indices: 49130--49235 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
49120 ATAAATGTTT
*
49130 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
49164 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
49196 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
49231 TTAAA
1 TTAAA
49236 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:53775 original size:23 final size:22
Alignment explanation
Indices: 53749--53805 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
53739 TATAAAGTAC
*
53749 TAAAAGTATAATTGTAAATTAGT
1 TAAAA-TATAATTGTAAATTAAT
* * *
53772 TAAAAATCTAAATGTAATTTAAT
1 T-AAAATATAATTGTAAATTAAT
53795 TAAAATATAAT
1 TAAAATATAAT
53806 ATTTATAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
22 8 0.30
23 15 0.56
24 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.39
Consensus pattern (22 bp):
TAAAATATAATTGTAAATTAAT
Found at i:54718 original size:47 final size:47
Alignment explanation
Indices: 54664--54763 Score: 200
Period size: 47 Copynumber: 2.1 Consensus size: 47
54654 AAGTTAGGAT
54664 CAAATTAATAGAATGTGTAAGTAATGAGGACTAAATGTATAATTATA
1 CAAATTAATAGAATGTGTAAGTAATGAGGACTAAATGTATAATTATA
54711 CAAATTAATAGAATGTGTAAGTAATGAGGACTAAATGTATAATTATA
1 CAAATTAATAGAATGTGTAAGTAATGAGGACTAAATGTATAATTATA
54758 CAAATT
1 CAAATT
54764 TTATTAACTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.32
Consensus pattern (47 bp):
CAAATTAATAGAATGTGTAAGTAATGAGGACTAAATGTATAATTATA
Found at i:54748 original size:22 final size:22
Alignment explanation
Indices: 54675--54748 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
54665 AAATTAATAG
54675 AATGTGTAAGTAATGAGGACTA
1 AATGTGTAAGTAATGAGGACTA
* * ** ** *
54697 AATGTATAATTATACAAATTAATA
1 AATGTGTAAGTA-A-TGAGGACTA
54721 GAATGTGTAAGTAATGAGGACTA
1 -AATGTGTAAGTAATGAGGACTA
54744 AATGT
1 AATGT
54749 ATAATTATAC
Statistics
Matches: 35, Mismatches: 14, Indels: 6
0.64 0.25 0.11
Matches are distributed among these distances:
22 15 0.43
23 5 0.14
24 5 0.14
25 10 0.29
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.31
Consensus pattern (22 bp):
AATGTGTAAGTAATGAGGACTA
Found at i:54998 original size:23 final size:23
Alignment explanation
Indices: 54949--55011 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
54939 AATATTGTAT
* * * **
54949 TTTAATTAAATTATATTTATATT
1 TTTAACTAATTTATAATTATACG
54972 TTTAACTAATTTATAATTATACG
1 TTTAACTAATTTATAATTATACG
*
54995 TTT-AGTAATTTATAATT
1 TTTAACTAATTTATAATT
55012 TAATGTTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (23 bp):
TTTAACTAATTTATAATTATACG
Found at i:57937 original size:6 final size:6
Alignment explanation
Indices: 57926--57950 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
57916 TCTGGTTTTG
57926 GGGATT GGGATT GGGATT GGGATT G
1 GGGATT GGGATT GGGATT GGGATT G
57951 TGATCTTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (6 bp):
GGGATT
Found at i:62317 original size:2 final size:2
Alignment explanation
Indices: 62310--62340 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
62300 CCATCTTTCA
62310 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
62341 AAACTCTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:65865 original size:32 final size:31
Alignment explanation
Indices: 65795--65903 Score: 96
Period size: 32 Copynumber: 3.5 Consensus size: 31
65785 TAAGATTTTG
* * * *
65795 ATAAATTTTATGATCATTTTTTAGT-AGTTTA
1 ATAAATTTAATGATTATTTTATAATAAG-TTA
* *
65826 ATAAAATTTAATGATTGTTTTTATAATAA-TTCG
1 AT-AAATTTAATGATT-ATTTTATAATAAGTT-A
*
65859 ATAAATTTAATTATTATTTTATAATAAGTTA
1 ATAAATTTAATGATTATTTTATAATAAGTTA
*
65890 ATAAATTTAGTGAT
1 ATAAATTTAATGAT
65904 CAATTTATTA
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
31 25 0.40
32 27 0.44
33 9 0.15
34 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.50
Consensus pattern (31 bp):
ATAAATTTAATGATTATTTTATAATAAGTTA
Found at i:65882 original size:31 final size:32
Alignment explanation
Indices: 65823--65903 Score: 94
Period size: 31 Copynumber: 2.5 Consensus size: 32
65813 TTTTAGTAGT
*
65823 TTAATAAAATTTAATGATTGTTTTTATAATAA-
1 TTAAT-AAATTTAATGATTGATTTTATAATAAG
* *
65855 TTCGATAAATTTAATTATT-ATTTTATAATAAG
1 TT-AATAAATTTAATGATTGATTTTATAATAAG
*
65887 TTAATAAATTTAGTGAT
1 TTAATAAATTTAATGAT
65904 CAATTTATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
31 23 0.56
32 16 0.39
33 2 0.05
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.49
Consensus pattern (32 bp):
TTAATAAATTTAATGATTGATTTTATAATAAG
Found at i:65911 original size:31 final size:31
Alignment explanation
Indices: 65795--65911 Score: 74
Period size: 31 Copynumber: 3.7 Consensus size: 31
65785 TAAGATTTTG
* * * * * *
65795 ATAAATTTTATGATCATTTTTTAGTAGTTTA
1 ATAAATTTAATGATCAATTTATAATAATTCA
*** *
65826 ATAAAATTTAATGATTGTTTTTATAATAATTCG
1 AT-AAATTTAATGA-TCAATTTATAATAATTCA
* * *
65859 ATAAATTTAATTATTATTTTATAATAAGTT-A
1 ATAAATTTAATGATCAATTTATAATAA-TTCA
*
65890 ATAAATTTAGTGATCAATTTAT
1 ATAAATTTAATGATCAATTTAT
65912 TACTTTTGAA
Statistics
Matches: 67, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
31 32 0.48
32 22 0.33
33 13 0.19
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (31 bp):
ATAAATTTAATGATCAATTTATAATAATTCA
Found at i:66767 original size:42 final size:42
Alignment explanation
Indices: 66709--66791 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
66699 TATGCCCTGT
*
66709 TTTTCATATTAAGATTGAAATAATTATGGAGAAAAAAAGGGG
1 TTTTCATATTAAGATTGAAATAATTAAGGAGAAAAAAAGGGG
* *
66751 TTTTCATATTAAGATTGAAATAATTAAGGGGGAAAAAAGGG
1 TTTTCATATTAAGATTGAAATAATTAAGGAGAAAAAAAGGG
66792 TTTGAAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.45, C:0.02, G:0.23, T:0.30
Consensus pattern (42 bp):
TTTTCATATTAAGATTGAAATAATTAAGGAGAAAAAAAGGGG
Done.