Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005958.1 Hibiscus syriacus cultivar Beakdansim tig00013998_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: 104693
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:3920 original size:30 final size:31
Alignment explanation
Indices: 3861--3920 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
3851 TAAAATATTT
*
3861 TAAATAATTATTTTGAAAGAAACAAAATAAC
1 TAAATAATTATTGTGAAAGAAACAAAATAAC
* * *
3892 TAAATAATTA-TGTGCAAGATATAAAATAA
1 TAAATAATTATTGTGAAAGAAACAAAATAA
3921 TGTAAGTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.57, C:0.05, G:0.08, T:0.30
Consensus pattern (31 bp):
TAAATAATTATTGTGAAAGAAACAAAATAAC
Found at i:4534 original size:14 final size:15
Alignment explanation
Indices: 4510--4538 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4500 TAAACTATTC
4510 AAAAATATTGTTTAT
1 AAAAATATTGTTTAT
4525 AAAAAT-TTGTTTAT
1 AAAAATATTGTTTAT
4539 CGATTGAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (15 bp):
AAAAATATTGTTTAT
Found at i:4781 original size:13 final size:15
Alignment explanation
Indices: 4754--4785 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
4744 ATTAAAATTT
4754 ATTATCAAAAGAATA
1 ATTATCAAAAGAATA
4769 ATTA-CAAAA-AATA
1 ATTATCAAAAGAATA
4782 ATTA
1 ATTA
4786 ATACTTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 5 0.29
15 4 0.24
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.28
Consensus pattern (15 bp):
ATTATCAAAAGAATA
Found at i:12800 original size:18 final size:18
Alignment explanation
Indices: 12738--12804 Score: 64
Period size: 18 Copynumber: 3.6 Consensus size: 18
12728 TTTAAAAAGA
12738 GTCATTTAATAAAACTAC
1 GTCATTTAATAAAACTAC
* * *
12756 GCCGTTTAGAGAATAAAAATA-
1 GTCATTT----AATAAAACTAC
12777 GTCATTTAATAAAACTAC
1 GTCATTTAATAAAACTAC
12795 GTCATTTAAT
1 GTCATTTAAT
12805 GAAATTGTCC
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
17 9 0.24
18 15 0.39
21 5 0.13
22 9 0.24
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (18 bp):
GTCATTTAATAAAACTAC
Found at i:18676 original size:31 final size:31
Alignment explanation
Indices: 18603--18733 Score: 133
Period size: 31 Copynumber: 4.2 Consensus size: 31
18593 AGAGTCGAGT
* *
18603 GTATACCTATGTTCTATGGAACATTTGGACC
1 GTATACCTATGTTCTATGGAACATATGGACA
* * *
18634 GAATTACCTATG-TCTTTCGAGACATATGGACA
1 GTA-TACCTATGTTCTATGGA-ACATATGGACA
*
18666 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTATGGAACATATGGACA
* * *
18697 GTTTACCTAGGTTCT-TCGGAACCTATGGACA
1 GTATACCTATGTTCTAT-GGAACATATGGACA
18728 GT-TACC
1 GTATACC
18734 AAGGATCTTT
Statistics
Matches: 83, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
30 4 0.05
31 55 0.66
32 24 0.29
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (31 bp):
GTATACCTATGTTCTATGGAACATATGGACA
Found at i:18761 original size:30 final size:30
Alignment explanation
Indices: 18717--18788 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
18707 GTTCTTCGGA
* *
18717 ACCTATGGACAGTTACCAAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
*
18747 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
18777 ACCTCTGGATAG
1 ACCTCTGGATAG
18789 GTCCTTCGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCAAGGATCTTTATG
Found at i:22065 original size:64 final size:64
Alignment explanation
Indices: 21993--22149 Score: 153
Period size: 64 Copynumber: 2.5 Consensus size: 64
21983 TTGAAGGTGT
***
21993 ATCGATGCACAAGTAGTGCATCGATGCA-CTCTTTTAA-AATAGAAACATCGAATGCA-ATTAGT
1 ATCGATGCACAAGTAGTGCATCGATGCATC-CCAATAATAATA-AAACATCGAATGCATATTA-T
22055 GC
63 GC
* * * * *
22057 ATCGATGCATAAGGCA-TGCATCGATGCATCCCAATAATAATACAACATCGAATGTATTTTATGC
1 ATCGATGCACAA-GTAGTGCATCGATGCATCCCAATAATAATAAAACATCGAATGCATATTATGC
*
22121 ACCGATGCATCAA-TAGTGCATCGATGCAT
1 ATCGATGCA-CAAGTAGTGCATCGATGCAT
22150 ACCCTTATTG
Statistics
Matches: 76, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
63 1 0.01
64 63 0.83
65 12 0.16
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (64 bp):
ATCGATGCACAAGTAGTGCATCGATGCATCCCAATAATAATAAAACATCGAATGCATATTATGC
Found at i:23339 original size:31 final size:31
Alignment explanation
Indices: 23266--23392 Score: 89
Period size: 31 Copynumber: 4.1 Consensus size: 31
23256 AGAGTCGAGG
** * *
23266 GTATACCTATGTTCTATGGAACTTTTGGACCA
1 GTATACCTATGTTCTAACGAACATATGGA-CA
* **
23298 -AATTACCTATG-TCTTTCGAGACATATGGACA
1 GTA-TACCTATGTTCTAACGA-ACATATGGACA
*
23329 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTAACGAACATATGGACA
* * * *
23360 GTTTACCTAGGTTCT-TCGGAACCTATGGACA
1 GTATACCTATGTTCTAAC-GAACATATGGACA
23391 GT
1 GT
23393 TGCCAAGGAT
Statistics
Matches: 76, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
31 55 0.72
32 21 0.28
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (31 bp):
GTATACCTATGTTCTAACGAACATATGGACA
Found at i:23393 original size:31 final size:31
Alignment explanation
Indices: 23318--23393 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
23308 GTCTTTCGAG
* *
23318 ACATATGGACAGTATACCTATGTTCTAAGGA
1 ACATATGGACAGTTTACCTAGGTTCTAAGGA
**
23349 ACATATGGACAGTTTACCTAGGTTCTTCGGA
1 ACATATGGACAGTTTACCTAGGTTCTAAGGA
*
23380 ACCTATGGACAGTT
1 ACATATGGACAGTT
23394 GCCAAGGATC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (31 bp):
ACATATGGACAGTTTACCTAGGTTCTAAGGA
Found at i:23434 original size:30 final size:30
Alignment explanation
Indices: 23380--23451 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
23370 GTTCTTCGGA
* * *
23380 ACCTATGGACAGTTGCCAAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
*
23410 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
23440 ACCTCTGGATAG
1 ACCTCTGGATAG
23452 GTCATTCGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCAAGGATCTTTATG
Found at i:24258 original size:2 final size:2
Alignment explanation
Indices: 24219--24243 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24209 AGGTGAGATA
24219 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 A
24244 ATCTCGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27891 original size:17 final size:17
Alignment explanation
Indices: 27871--27930 Score: 102
Period size: 17 Copynumber: 3.4 Consensus size: 17
27861 AAACATCCTG
27871 AGAAACACAACACTCAA
1 AGAAACACAACACTCAA
27888 AGAAACACACAACACTCAA
1 AG-AA-ACACAACACTCAA
27907 AGAAACACAACACTCAA
1 AGAAACACAACACTCAA
27924 AGAAACA
1 AGAAACA
27931 TGTAAAGTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
17 22 0.54
18 4 0.10
19 15 0.37
ACGTcount: A:0.60, C:0.28, G:0.07, T:0.05
Consensus pattern (17 bp):
AGAAACACAACACTCAA
Found at i:27899 original size:19 final size:19
Alignment explanation
Indices: 27875--27930 Score: 98
Period size: 19 Copynumber: 3.1 Consensus size: 19
27865 ATCCTGAGAA
27875 ACACAACACTCAAAGAAAC
1 ACACAACACTCAAAGAAAC
27894 ACACAACACTCAAAG-AA-
1 ACACAACACTCAAAGAAAC
27911 ACACAACACTCAAAGAAAC
1 ACACAACACTCAAAGAAAC
27930 A
1 A
27931 TGTAAAGTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.43
18 4 0.11
19 16 0.46
ACGTcount: A:0.59, C:0.30, G:0.05, T:0.05
Consensus pattern (19 bp):
ACACAACACTCAAAGAAAC
Found at i:37444 original size:2 final size:2
Alignment explanation
Indices: 37437--37486 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
37427 AAACCCGTGA
37437 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
37479 AT AT AT AT
1 AT AT AT AT
37487 TGCTATAATC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38201 original size:2 final size:2
Alignment explanation
Indices: 38194--38225 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
38184 ATCATAACCC
38194 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
38226 GACCCAAGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58484 original size:20 final size:20
Alignment explanation
Indices: 58459--58496 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
58449 TATATAATAT
58459 ATTTGGTTTTGATT-GTTTGA
1 ATTTGG-TTTGATTAGTTTGA
58479 ATTTGGTTTGATTAGTTT
1 ATTTGGTTTGATTAGTTT
58497 ATATTGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.61
Consensus pattern (20 bp):
ATTTGGTTTGATTAGTTTGA
Found at i:66256 original size:16 final size:18
Alignment explanation
Indices: 66235--66281 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
66225 TAAGAGCCCC
66235 AGGGGTGGCACTT-T-TA
1 AGGGGTGGCACTTGTATA
*
66251 AGGGGT-G-ACTTGTATT
1 AGGGGTGGCACTTGTATA
66267 AGGGGTGGCACTTGT
1 AGGGGTGGCACTTGT
66282 GGAGGGGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 2 0.08
16 13 0.50
17 1 0.04
18 6 0.23
ACGTcount: A:0.17, C:0.11, G:0.40, T:0.32
Consensus pattern (18 bp):
AGGGGTGGCACTTGTATA
Found at i:67160 original size:24 final size:24
Alignment explanation
Indices: 67097--67153 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
67087 ATCAAAACAT
67097 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
67121 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
67145 AATCCAGGT
1 AATCCAGGT
67154 TAGGTATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCCGATCAG
Found at i:69653 original size:18 final size:18
Alignment explanation
Indices: 69630--69677 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
69620 GCCGGCCAAC
*
69630 GGTCAACGGGTCGGGTCG
1 GGTCAACAGGTCGGGTCG
*
69648 GGTCAACAGATCGGGTCG
1 GGTCAACAGGTCGGGTCG
69666 GGTCAACAGGTC
1 GGTCAACAGGTC
69678 AAACCGGTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.19, C:0.23, G:0.42, T:0.17
Consensus pattern (18 bp):
GGTCAACAGGTCGGGTCG
Found at i:71791 original size:24 final size:24
Alignment explanation
Indices: 71764--71815 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
71754 AACGGATATA
*
71764 TCAAAAATCAAAACATAATCCAGG
1 TCAAAAATCAAAACAAAATCCAGG
** * *
71788 TCAAGTATCAGATCAAAATCCAGG
1 TCAAAAATCAAAACAAAATCCAGG
71812 TCAA
1 TCAA
71816 GTATCCGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.21, G:0.12, T:0.19
Consensus pattern (24 bp):
TCAAAAATCAAAACAAAATCCAGG
Found at i:71815 original size:12 final size:13
Alignment explanation
Indices: 71780--71886 Score: 68
Period size: 12 Copynumber: 8.8 Consensus size: 13
71770 ATCAAAACAT
71780 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
71793 TAT-CAGATCAA-
1 AATCCAGGTCAAG
71804 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
71817 TATCC-GATC-AG
1 AATCCAGGTCAAG
*
71828 AATCCATGTCAAG
1 AATCCAGGTCAAG
* *
71841 TATCC-GATC-AG
1 AATCCAGGTCAAG
71852 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
71865 TATCC-GATC-AG
1 AATCCAGGTCAAG
*
71876 AATCCAAGTCA
1 AATCCAGGTCA
71887 GGTATTATAA
Statistics
Matches: 67, Mismatches: 19, Indels: 16
0.66 0.19 0.16
Matches are distributed among these distances:
11 20 0.30
12 29 0.43
13 18 0.27
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.21
Consensus pattern (13 bp):
AATCCAGGTCAAG
Found at i:71816 original size:24 final size:24
Alignment explanation
Indices: 71780--71891 Score: 179
Period size: 24 Copynumber: 4.7 Consensus size: 24
71770 ATCAAAACAT
* *
71780 AATCCAGGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCCGATCAG
71804 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
*
71828 AATCCATGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
71852 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
* *
71876 AATCCAAGTCAGGTAT
1 AATCCAGGTCAAGTAT
71892 TATAATAGAA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 82 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCCGATCAG
Found at i:74369 original size:18 final size:18
Alignment explanation
Indices: 74348--74386 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
74338 GGTCAACGCC
74348 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
74366 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
74384 GGT
1 GGT
74387 TGTGACCGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.21, G:0.51, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:87895 original size:95 final size:95
Alignment explanation
Indices: 87780--87978 Score: 389
Period size: 95 Copynumber: 2.1 Consensus size: 95
87770 ATGATACAAA
87780 ATTATAAGATAAGGGATATAGGGAAGATTTATAATTAAAGGAAACTATGGTATAAGAGTTATAAA
1 ATTATAAGATAAGGGATATAGGGAAGATTTATAATTAAAGGAAACTATGGTATAAGAGTTATAAA
87845 AATAAAAACTACAAAGCTTTATGAAAGAGT
66 AATAAAAACTACAAAGCTTTATGAAAGAGT
87875 ATTATAAGATAAGGGATATAGGGAAGATTTATAATTAAAGGAAACTATGGTATAAGAGTTATAAA
1 ATTATAAGATAAGGGATATAGGGAAGATTTATAATTAAAGGAAACTATGGTATAAGAGTTATAAA
*
87940 AATAAGAACTACAAAGCTTTATGAAAGAGT
66 AATAAAAACTACAAAGCTTTATGAAAGAGT
87970 ATTATAAGA
1 ATTATAAGA
87979 GTCATGTGAA
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 103 1.00
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.28
Consensus pattern (95 bp):
ATTATAAGATAAGGGATATAGGGAAGATTTATAATTAAAGGAAACTATGGTATAAGAGTTATAAA
AATAAAAACTACAAAGCTTTATGAAAGAGT
Found at i:88623 original size:20 final size:20
Alignment explanation
Indices: 88590--88644 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
88580 GAGGGTTCAT
* *
88590 AGGTCTTTCAGGACATACAG
1 AGGTCCTTCGGGACATACAG
*
88610 AGGTCCTTCGGGACATACAT
1 AGGTCCTTCGGGACATACAG
*
88630 AGGTCCTTTGGGACA
1 AGGTCCTTCGGGACA
88645 ATTTCACATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (20 bp):
AGGTCCTTCGGGACATACAG
Found at i:103266 original size:20 final size:19
Alignment explanation
Indices: 103216--103266 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
103206 ATACCTTTTT
*
103216 TTTTTTATATATTTTTTCA
1 TTTTTTATATATTTTTTAA
*
103235 -TTTTTAGATATTTTTATAA
1 TTTTTTATATATTTTT-TAA
*
103254 TTTTTTATCTATT
1 TTTTTTATATATT
103267 AAAGTTAGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 14 0.54
19 2 0.08
20 10 0.38
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTTTATATATTTTTTAA
Done.