Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000950.1 Hibiscus syriacus cultivar Beakdansim tig00001900_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: 65177
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:505 original size:60 final size:60
Alignment explanation
Indices: 367--544 Score: 190
Period size: 59 Copynumber: 3.1 Consensus size: 60
357 ATGAATTTTT
* ** * * * *
367 GGAT-AAATTGGAAGATTCAAAAGTTTGGGGACCAATTTAGAAA-G-GAATCATAATTTAA
1 GGATGAAATTGGAATATTCAAAAGTTTAAGGACTAATTTA-AAATGAGAGTCATAGTTTGA
* * *
425 GGATGATATTAGAATGTTCAAAAGTTTAAGGACTAATTTAAAATGAGAGTCATAGTTTGA
1 GGATGAAATTGGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGAGTCATAGTTTGA
* *
485 GGATGAAATTGGAATATTC-AAAG-TTAAGGA-TCATTTAAAAT-AGAGTTATAGTTTGA
1 GGATGAAATTGGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGAGTCATAGTTTGA
541 GGAT
1 GGAT
545 AGATAATGCA
Statistics
Matches: 102, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
56 18 0.18
57 10 0.10
58 14 0.14
59 33 0.32
60 27 0.26
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.31
Consensus pattern (60 bp):
GGATGAAATTGGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGAGTCATAGTTTGA
Found at i:3665 original size:12 final size:12
Alignment explanation
Indices: 3645--3680 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
3635 AGTTTATCCT
3645 AAAATTAAATTA
1 AAAATTAAATTA
*
3657 AAAACTAAATTA
1 AAAATTAAATTA
*
3669 AATATTAAATTA
1 AAAATTAAATTA
3681 GGTAAGTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAAATTA
Found at i:5167 original size:126 final size:126
Alignment explanation
Indices: 4937--5169 Score: 324
Period size: 126 Copynumber: 1.8 Consensus size: 126
4927 GTTAATTTAT
* * * * *
4937 CTCTCATCTTGATCAGGCAAAAAATGTCACACAAAATGGAGGTTATTCAACTCAACCGTTTCACT
1 CTCTCATCTTGATCAGACAAAAAAGGTCACACAAAATGCAGGTTACTCAACTCAACCATTTCACT
* * * *
5002 CGGAGCATGGGATTAGCTCAGTTCAAACAAATCAGGTCAATGATCTCACTAGACTGGTAAC
66 CAGAGCATGGGATTAACTCAGTCCAAACAAATCAAGTCAATGATCTCACTAGACTGGTAAC
* * * *
5063 CTCTCATCTTGATCAGACGAAAGAGGTCCCACAAAATGCAGGTTACTCGACTCAACCATTTCACT
1 CTCTCATCTTGATCAGACAAAAAAGGTCACACAAAATGCAGGTTACTCAACTCAACCATTTCACT
*
5128 CAGAGCATGTGG-TTAACTCAGTCCAAGCAAATCAAGTCAATG
66 CAGAGCATG-GGATTAACTCAGTCCAAACAAATCAAGTCAATG
5170 GTCGTATTGG
Statistics
Matches: 92, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
126 90 0.98
127 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (126 bp):
CTCTCATCTTGATCAGACAAAAAAGGTCACACAAAATGCAGGTTACTCAACTCAACCATTTCACT
CAGAGCATGGGATTAACTCAGTCCAAACAAATCAAGTCAATGATCTCACTAGACTGGTAAC
Found at i:5516 original size:184 final size:189
Alignment explanation
Indices: 5115--5524 Score: 632
Period size: 184 Copynumber: 2.2 Consensus size: 189
5105 TTACTCGACT
* *
5115 CAACCATTTCACTCAGAGCATGTGGTTAACTCAGTCCAAGCAAATCAAGTCAATGGTCGTATTGG
1 CAACCATTTCACTCAGAGCATGTGGTTAACTCAG--C-AGCAAATCAAGTCAATGATCATATTGG
* * *
5180 AATGGTAACCTCCCACTATATGCGAATCAATTATAATCTATTTACACTACATTATATAATCATTT
63 AATGGTAACCTCCCACTATATGCCAATCAATTATAACCTATTTACACTACATTATATAATCACTT
* *
5245 GTTAATTTATCTATAATCTTGATCAGACGGAACAACTCTCACACAATAGAGGTTATACAGCT
128 GTTAATTTATCTATAATCTTGATCAGACGGAACAACTCTCACACAATAGAAGTTATACAGCA
* **
5307 CAACCATTTCACTCAGAACATGTGGTT-GTTCAG-A-CAAATCAAGTCAATGATCATATTGGAAT
1 CAACCATTTCACTCAGAGCATGTGGTTAACTCAGCAGCAAATCAAGTCAATGATCATATTGGAAT
*
5369 GGTAACCTCCCACTATATGCCTATCAATTATAACCTATTTACACTACATTATAT-ATC-CTTGTT
66 GGTAACCTCCCACTATATGCCAATCAATTATAACCTATTTACACTACATTATATAATCACTTGTT
* **
5432 AATTTATCTATAATCTTGATCAGACGGAACAACTCTCAGACAATAGAAGTTATATGGCA
131 AATTTATCTATAATCTTGATCAGACGGAACAACTCTCACACAATAGAAGTTATACAGCA
5491 CAACCATTTCACTCAGAGCATGTGGTTAACTCAG
1 CAACCATTTCACTCAGAGCATGTGGTTAACTCAG
5525 TTAAGACAAG
Statistics
Matches: 200, Mismatches: 17, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
184 85 0.43
185 7 0.04
186 77 0.38
187 1 0.00
191 4 0.02
192 26 0.13
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.31
Consensus pattern (189 bp):
CAACCATTTCACTCAGAGCATGTGGTTAACTCAGCAGCAAATCAAGTCAATGATCATATTGGAAT
GGTAACCTCCCACTATATGCCAATCAATTATAACCTATTTACACTACATTATATAATCACTTGTT
AATTTATCTATAATCTTGATCAGACGGAACAACTCTCACACAATAGAAGTTATACAGCA
Found at i:9124 original size:2 final size:2
Alignment explanation
Indices: 9107--9144 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
9097 AAAACAAAAC
* *
9107 AT AT AA AT AT -T AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9145 ATAATAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9150 original size:3 final size:3
Alignment explanation
Indices: 9142--9188 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
9132 ATATATATTT
*
9142 ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
9189 TTAATATACT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:10451 original size:3 final size:3
Alignment explanation
Indices: 10445--10530 Score: 90
Period size: 3 Copynumber: 28.7 Consensus size: 3
10435 TGTATTATTT
*
10445 ATA ATA ATA ATA TTA ATA ATA ATA ATA TATA ATA A-A ATA TATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA -AT-A ATA
*
10492 A-A ATA AT- ATGA ATA ATA AT- ATA ATA ATA ATA ATA TTA AT
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
10531 GAAAACAAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
2 8 0.11
3 53 0.75
4 9 0.13
5 1 0.01
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:11167 original size:113 final size:112
Alignment explanation
Indices: 10831--11270 Score: 467
Period size: 113 Copynumber: 3.8 Consensus size: 112
10821 GAATTAAATT
* * *
10831 AAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTCCTTCTTCAAATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
* * *** * *
10896 GAAC--ACTTCTCGAAATGTTGATGCTGATCTATCTCCTTCTATGATATAATCAAAC-A
66 GAACTTAC-TCTGGAAA-----A-GCTGATCCATC-AAGT-AATGA-AT--TCAAGCAA
* * *
10952 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTATTATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
* * *
11017 GAACTTCCTCTGGAAAAGTTGATCCATCGAGTAATGAATTCAAGCAA
66 GAACTTACTCTGGAAAAGCTGATCCATCAAGTAATGAATTCAAGCAA
* *
11064 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTACTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTA
* * * *
11129 TGAACTCTAC-CTGGCAATGCTGATCCATCAAGTGATGAATTCGAGCAA
65 TGAACT-TACTCTGGAAAAGCTGATCCATCAAGTAATGAATTCAAGCAA
* *
11177 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTA
* *
11242 TGAACTT-CTTCTGGAACAGTTGATCCATC
65 TGAACTTAC-TCTGGAAAAGCTGATCCATC
11271 GAATGATGGA
Statistics
Matches: 276, Mismatches: 36, Indels: 22
0.83 0.11 0.07
Matches are distributed among these distances:
111 6 0.02
112 38 0.14
113 144 0.52
114 6 0.02
115 1 0.00
116 9 0.03
117 1 0.00
121 63 0.23
122 7 0.03
123 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (112 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
GAACTTACTCTGGAAAAGCTGATCCATCAAGTAATGAATTCAAGCAA
Found at i:11278 original size:113 final size:112
Alignment explanation
Indices: 10951--11285 Score: 469
Period size: 113 Copynumber: 3.0 Consensus size: 112
10941 ATAATCAAAC
* *
10951 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTATTATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * *
11015 ATGAACTTCCTCTGGAAAAGTTGATCCATCGAGTAATGAATTCAAGCA
66 ATGAACTTCTTCTGG-AAAGTTGATCCATCGAATGATGAATTCGAGCA
* * *
11063 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTACTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
11128 ATGAAC-TCTACCTGGCAATGCTGATCCATC-AAGTGATGAATTCGAGCA
66 ATGAACTTCT-TCTGG-AAAGTTGATCCATCGAA-TGATGAATTCGAGCA
* *
11176 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
11241 ATGAACTTCTTCTGGAACAGTTGATCCATCGAATGATGGATTCGA
66 ATGAACTTCTTCTGGAA-AGTTGATCCATCGAATGATGAATTCGA
11286 ATCTTTGAAA
Statistics
Matches: 195, Mismatches: 22, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
112 43 0.22
113 147 0.75
114 5 0.03
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (112 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTCTTCTGGAAAGTTGATCCATCGAATGATGAATTCGAGCA
Found at i:20963 original size:14 final size:16
Alignment explanation
Indices: 20946--20977 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20936 ATTATTTTTT
20946 TGAAT-TTTAT-TTAA
1 TGAATGTTTATCTTAA
20960 TGAATGTTTATCTTAA
1 TGAATGTTTATCTTAA
20976 TG
1 TG
20978 TAAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 5 0.31
16 6 0.38
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.53
Consensus pattern (16 bp):
TGAATGTTTATCTTAA
Found at i:21037 original size:15 final size:15
Alignment explanation
Indices: 21014--21045 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
21004 TGCAATGAAT
21014 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
21029 AATGCATGTATGCAA
1 AATGAATGTATGCAA
21044 AA
1 AA
21046 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:26569 original size:3 final size:3
Alignment explanation
Indices: 26563--26632 Score: 81
Period size: 3 Copynumber: 23.0 Consensus size: 3
26553 ATTATTTATT
*
26563 TAA TAA TAA TAA TATA TAA TAA TAA TAA TATA TAAA TAA -AA TAA TAC
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA-A T-AA TAA TAA TAA TAA
*
26610 GAA TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
26633 AAACAAATGG
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
2 4 0.07
3 46 0.79
4 7 0.12
5 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:26584 original size:16 final size:16
Alignment explanation
Indices: 26563--26632 Score: 85
Period size: 16 Copynumber: 4.6 Consensus size: 16
26553 ATTATTTATT
26563 TAATAATAATAATATA
1 TAATAATAATAATATA
26579 TAATAATAATAATATA
1 TAATAATAATAATATA
26595 T-A-AATAA-AATA-A
1 TAATAATAATAATATA
**
26607 TACGAATAATAATATAA
1 TAATAATAATAATAT-A
26624 TAATAATAA
1 TAATAATAA
26633 AAACAAATGG
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
12 2 0.04
13 4 0.09
14 10 0.22
15 5 0.11
16 17 0.37
17 8 0.17
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (16 bp):
TAATAATAATAATATA
Found at i:26600 original size:14 final size:15
Alignment explanation
Indices: 26565--26632 Score: 81
Period size: 14 Copynumber: 4.7 Consensus size: 15
26555 TATTTATTTA
26565 ATAATAATAATATAT
1 ATAATAATAATATAT
26580 AATAATAATAATATAT
1 -ATAATAATAATATAT
26596 A-AATAA-AATA-AT
1 ATAATAATAATATAT
*
26608 ACGAATAATAATATA-
1 A-TAATAATAATATAT
26623 ATAATAATAA
1 ATAATAATAA
26633 AAACAAATGG
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
12 3 0.06
13 4 0.09
14 18 0.38
15 6 0.13
16 16 0.34
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (15 bp):
ATAATAATAATATAT
Found at i:26695 original size:16 final size:16
Alignment explanation
Indices: 26674--26706 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
26664 CATAATTATT
26674 TTAAATGTTT-TAAAAA
1 TTAAAT-TTTATAAAAA
26690 TTAAATTTTATAAAAA
1 TTAAATTTTATAAAAA
26706 T
1 T
26707 ATTTTTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TTAAATTTTATAAAAA
Found at i:34895 original size:18 final size:18
Alignment explanation
Indices: 34852--34889 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
34842 GTGAAGTATG
*
34852 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
*
34870 AATGGTGTTGTTGTGGCA
1 AATGGTGTTGTCGTGGCA
34888 AA
1 AA
34890 GTGTGTAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.32
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:39600 original size:2 final size:2
Alignment explanation
Indices: 39593--39622 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39583 TGGTTTTCTG
39593 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
39623 GTTTATCGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42002 original size:13 final size:13
Alignment explanation
Indices: 41946--41994 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
41936 TGCGTCATAA
**
41946 ATTTATGACGTGC
1 ATTTATGACGCAC
* * *
41959 ATTTTTTACACAC
1 ATTTATGACGCAC
41972 ATTTATGACGCAC
1 ATTTATGACGCAC
41985 ATTTATGACG
1 ATTTATGACG
41995 TTCATTTAGC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (13 bp):
ATTTATGACGCAC
Found at i:55758 original size:19 final size:19
Alignment explanation
Indices: 55734--55790 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
55724 ATTTTGACCA
55734 TTTAGCCGCCCATGCATTG
1 TTTAGCCGCCCATGCATTG
*
55753 TTTAGCCGCCACACT-TATT-
1 TTTAGCCGCC-CA-TGCATTG
*
55772 TTCAGCCGCCCATGCATTG
1 TTTAGCCGCCCATGCATTG
55791 AATAACCTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
17 1 0.03
18 5 0.16
19 19 0.61
20 5 0.16
21 1 0.03
ACGTcount: A:0.18, C:0.33, G:0.18, T:0.32
Consensus pattern (19 bp):
TTTAGCCGCCCATGCATTG
Found at i:64169 original size:36 final size:36
Alignment explanation
Indices: 64119--64188 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 36
64109 TATAATTAAT
*
64119 TAATATTAGTAATTTACTTTA-GGATTATTATTATACA
1 TAATATTAGTAATTTAATTTATGG-TTA-TATTATACA
*
64156 TAATA-TATTAATTTAATTTATGGTTATATTATA
1 TAATATTAGTAATTTAATTTATGGTTATATTATA
64189 ATATAACATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 7 0.23
36 16 0.53
37 7 0.23
ACGTcount: A:0.39, C:0.03, G:0.07, T:0.51
Consensus pattern (36 bp):
TAATATTAGTAATTTAATTTATGGTTATATTATACA
Done.