Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007552.1 Hibiscus syriacus cultivar Beakdansim tig00021192_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: 80049
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2686 original size:20 final size:21
Alignment explanation
Indices: 2647--2693 Score: 78
Period size: 20 Copynumber: 2.3 Consensus size: 21
2637 TAATTATATC
*
2647 TTTATGACATGTTTCTTTTAT
1 TTTATGACATGTTTCATTTAT
2668 TTTATGACAT-TTTCATTTAT
1 TTTATGACATGTTTCATTTAT
2688 TTTATG
1 TTTATG
2694 GTACGTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTATGACATGTTTCATTTAT
Found at i:17266 original size:23 final size:23
Alignment explanation
Indices: 17238--17283 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
17228 ATTTTTTTTA
* *
17238 AATTAATGAATTATTAATTTATC
1 AATTAATGAATAATTAATATATC
*
17261 AATTAATTAATAATTAATATATC
1 AATTAATGAATAATTAATATATC
17284 CTTAAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (23 bp):
AATTAATGAATAATTAATATATC
Found at i:20277 original size:21 final size:21
Alignment explanation
Indices: 20248--20290 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20238 AATTTTAAAG
*
20248 GTACAATGATATGAACAAAAT
1 GTACAATGACATGAACAAAAT
* *
20269 GTACGATGACATGAACAGAAT
1 GTACAATGACATGAACAAAAT
20290 G
1 G
20291 ATACCATTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.12, G:0.21, T:0.21
Consensus pattern (21 bp):
GTACAATGACATGAACAAAAT
Found at i:21671 original size:3 final size:3
Alignment explanation
Indices: 21663--21704 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
21653 TACCTCATAT
21663 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21705 ATCTACATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:21817 original size:2 final size:2
Alignment explanation
Indices: 21766--21801 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
21756 AATGACAAAG
*
21766 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21802 TGTATTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25479 original size:6 final size:7
Alignment explanation
Indices: 25452--25477 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
25442 TTACAAAACG
25452 AAAAAAT
1 AAAAAAT
25459 AAAAAAT
1 AAAAAAT
25466 AAAAAAT
1 AAAAAAT
25473 AAAAA
1 AAAAA
25478 TACAGGCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:43984 original size:19 final size:19
Alignment explanation
Indices: 43960--43996 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
43950 ATGACCAACA
* *
43960 AAATCGTAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
43979 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
43997 CAGTTTCCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:44950 original size:24 final size:24
Alignment explanation
Indices: 44892--44938 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
44882 AGTCAGTATT
*
44892 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
*
44916 CGGACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
44939 TTGAATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:45133 original size:3 final size:3
Alignment explanation
Indices: 45125--45151 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
45115 ATATAACCCT
45125 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
45152 ATCCCCGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:45172 original size:14 final size:14
Alignment explanation
Indices: 45143--45179 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
45133 AGAAGAAGAA
45143 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
45158 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
45172 GAAGAAAA
1 GAAGAAAA
45180 TGCCACGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:47249 original size:18 final size:18
Alignment explanation
Indices: 47216--47250 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
47206 AGAAAAAGAC
**
47216 AATCAAAATCGTAATCAA
1 AATCAAAATCCCAATCAA
47234 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
47251 CAACCGGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:47560 original size:140 final size:140
Alignment explanation
Indices: 47308--47590 Score: 539
Period size: 140 Copynumber: 2.0 Consensus size: 140
47298 GAAAACGTTG
47308 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGA
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGA
47373 TTGAACATTGCTATGATCTGTTCAGTTCTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTCTTATCACTTATTACACATTCATTTGAATATCGCAACG
47438 CGAATTTGAC
131 CGAATTTGAC
*
47448 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGA
*
47513 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTCTTATCACTTATTACACATTCATTTGAATATCGCAACG
*
47578 CGAATTTGGC
131 CGAATTTGAC
47588 TAT
1 TAT
47591 CGTAACGTGA
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.43
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGA
TTGAACATTGCTATGATCTGTTCAGTTCTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:47591 original size:20 final size:20
Alignment explanation
Indices: 47561--47637 Score: 118
Period size: 20 Copynumber: 3.9 Consensus size: 20
47551 TTACACATTC
*
47561 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
47581 ATTTGGCTATCGTAACGTGA
1 ATTTGACTATCGCAACGCGA
47601 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
47621 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
47638 AGAAAATCGC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:47701 original size:20 final size:20
Alignment explanation
Indices: 47676--47719 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
47666 GCAACGCGAA
*
47676 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCATTGCGATT
47696 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
47716 TTGA
1 TTGA
47720 GTGGCAAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.45
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:49033 original size:20 final size:20
Alignment explanation
Indices: 48991--49034 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
48981 GAAACTTAAA
*
48991 ATCGCAACACGAAAATGATT
1 ATCGCAACACGAAAATGACT
* **
49011 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
49031 ATCG
1 ATCG
49035 TTGCGATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:50533 original size:18 final size:18
Alignment explanation
Indices: 50510--50544 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
50500 AGAAAAAGGC
*
50510 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
50528 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
50545 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:50854 original size:140 final size:140
Alignment explanation
Indices: 50602--50884 Score: 539
Period size: 140 Copynumber: 2.0 Consensus size: 140
50592 GAAAACGTTG
50602 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGA
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGA
50667 TTGAACATTGCTATGATCTGTTCAGTTCTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTCTTATCACTTATTACACATTCATTTGAATATCGCAACG
50732 CGAATTTGAC
131 CGAATTTGAC
*
50742 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGA
*
50807 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTCTTATCACTTATTACACATTCATTTGAATATCGCAACG
*
50872 CGAATTTGGC
131 CGAATTTGAC
50882 TAT
1 TAT
50885 CGTAACGTGA
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.43
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGA
TTGAACATTGCTATGATCTGTTCAGTTCTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:50885 original size:20 final size:20
Alignment explanation
Indices: 50862--50931 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
50852 TTCATTTGAA
50862 TATCGCAACGCGAATTTGGC
1 TATCGCAACGCGAATTTGGC
* * *
50882 TATCGTAACGTGAATTTGAC
1 TATCGCAACGCGAATTTGGC
50902 TATCGCAACGCGAATTTGGC
1 TATCGCAACGCGAATTTGGC
50922 TATCGCAACG
1 TATCGCAACG
50932 AGAAAATCGC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (20 bp):
TATCGCAACGCGAATTTGGC
Found at i:50910 original size:40 final size:40
Alignment explanation
Indices: 50855--50931 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
50845 TTACACATTC
*
50855 ATTTGAATATCGCAACGCGAATTTGGCTATCGTAACGTGA
1 ATTTGAATATCGCAACGCGAATTTGGCTATCGCAACGTGA
*
50895 ATTTGACTATCGCAACGCGAATTTGGCTATCGCAACG
1 ATTTGAATATCGCAACGCGAATTTGGCTATCGCAACG
50932 AGAAAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (40 bp):
ATTTGAATATCGCAACGCGAATTTGGCTATCGCAACGTGA
Found at i:50995 original size:20 final size:20
Alignment explanation
Indices: 50970--51013 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
50960 GCAACGCGAA
*
50970 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCATTGCGATT
50990 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
51010 TTGA
1 TTGA
51014 GTGGCAAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.45
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:52307 original size:20 final size:20
Alignment explanation
Indices: 52284--52327 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
52274 GAAACTTAAA
52284 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
52304 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
52324 ATCG
1 ATCG
52328 TTGCGATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:52734 original size:22 final size:22
Alignment explanation
Indices: 52706--52757 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
52696 GAGATAGACA
52706 GATTTCGCTGGAGATGGGGACG
1 GATTTCGCTGGAGATGGGGACG
*
52728 GATTTCGTTGGAGATGGGGACG
1 GATTTCGCTGGAGATGGGGACG
*
52750 GATGTCGC
1 GATTTCGC
52758 CGTAGAGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.17, C:0.13, G:0.44, T:0.25
Consensus pattern (22 bp):
GATTTCGCTGGAGATGGGGACG
Found at i:52949 original size:20 final size:20
Alignment explanation
Indices: 52926--52981 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
52916 TTATCGCAAC
52926 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
**
52946 GCGATTATGT-ATTATCGCGTT
1 GCGA-TA-GTCAGAATCGCGTT
*
52967 ACGATAGTCAGAATC
1 GCGATAGTCAGAATC
52982 ACATTTCTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
19 2 0.07
20 10 0.36
21 14 0.50
22 2 0.07
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCGTT
Found at i:52960 original size:41 final size:41
Alignment explanation
Indices: 52903--52981 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
52893 GAAAATCACA
* *
52903 TTGCGATTTTGTATTATCGCAACGCGATAGTCAGAATCGCG
1 TTGCGATTATGTATTATCGCAACACGATAGTCAGAATCGCG
***
52944 TTGCGATTATGTATTATCGCGTTACGATAGTCAGAATC
1 TTGCGATTATGTATTATCGCAACACGATAGTCAGAATC
52982 ACATTTCTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (41 bp):
TTGCGATTATGTATTATCGCAACACGATAGTCAGAATCGCG
Found at i:54511 original size:2 final size:2
Alignment explanation
Indices: 54495--54531 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
54485 ATTAATCAGT
*
54495 TA TA -A TA TT TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54532 TTTTATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:67087 original size:3 final size:3
Alignment explanation
Indices: 67079--67146 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
67069 GATTGCTCAA
67079 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
67127 AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AA
67147 AAACCATCTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:74627 original size:16 final size:16
Alignment explanation
Indices: 74606--74637 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
74596 ATAGGCCAAA
74606 ATGGCATCTCAGCAAT
1 ATGGCATCTCAGCAAT
74622 ATGGCATCTCAGCAAT
1 ATGGCATCTCAGCAAT
74638 TCTAAGTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (16 bp):
ATGGCATCTCAGCAAT
Done.