Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001527.1 Hibiscus syriacus cultivar Beakdansim tig00002993_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: 67207
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:3639 original size:14 final size:15
Alignment explanation
Indices: 3612--3643 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
3602 AAAATCTTTC
3612 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
3627 TTTCCCG-TCTGGAT
1 TTTCCCGTTCTGGAT
3641 TTT
1 TTT
3644 GATCTGCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:5203 original size:17 final size:17
Alignment explanation
Indices: 5181--5214 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5171 TTGTAAATGA
5181 ATTGATAATATATTTTT
1 ATTGATAATATATTTTT
*
5198 ATTGATAATTTATTTTT
1 ATTGATAATATATTTTT
5215 GTCTCTCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
ATTGATAATATATTTTT
Found at i:11364 original size:2 final size:2
Alignment explanation
Indices: 11357--11400 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
11347 GCATAAAAGC
11357 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
11399 AT
1 AT
11401 GAAATTTGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13111 original size:24 final size:24
Alignment explanation
Indices: 13073--13143 Score: 115
Period size: 24 Copynumber: 2.9 Consensus size: 24
13063 AACTCAAAAA
*
13073 AAAATTAGAAGCTCAATTGAAGCCT
1 AAAATTTG-AGCTCAATTGAAGCCT
13098 AAAATTTGAGCTCAATTGAAGCCT
1 AAAATTTGAGCTCAATTGAAGCCT
*
13122 AAAATTTGAGCTCAATTAAAGC
1 AAAATTTGAGCTCAATTGAAGC
13144 GAAATAATAG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
24 37 0.84
25 7 0.16
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (24 bp):
AAAATTTGAGCTCAATTGAAGCCT
Found at i:13749 original size:15 final size:16
Alignment explanation
Indices: 13714--13751 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 16
13704 TCCTTAACTC
13714 ATTTATACTCTCATCAAT
1 ATTT-TACTCTCA-CAAT
13732 ATTTTACTCTCA-AAT
1 ATTTTACTCTCACAAT
13747 ATTTT
1 ATTTT
13752 TTTAAACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
17 8 0.40
18 4 0.20
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTACTCTCACAAT
Found at i:13829 original size:24 final size:24
Alignment explanation
Indices: 13799--13848 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
13789 ATTGTATTTG
13799 ATATATTA-AATAATATTATAATAT
1 ATATATTATAATAATATT-TAATAT
**
13823 ATATATTATAATGTTATTTAATAT
1 ATATATTATAATAATATTTAATAT
13847 AT
1 AT
13849 CAAATACAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
ATATATTATAATAATATTTAATAT
Found at i:14756 original size:15 final size:15
Alignment explanation
Indices: 14712--14793 Score: 73
Period size: 14 Copynumber: 5.5 Consensus size: 15
14702 ATTTAATATC
14712 TTATTATAATTTTAA
1 TTATTATAATTTTAA
* *
14727 -TAATA-AATATTAA
1 TTATTATAATTTTAA
14740 TTATTA-AATATTTAA
1 TTATTATAAT-TTTAA
14755 TTATTATAATTTTAA
1 TTATTATAATTTTAA
**
14770 TAATATTATTTTTTTAA
1 T--TATTATAATTTTAA
14787 -TATTATA
1 TTATTATA
14794 TTAATATGTA
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
13 7 0.13
14 17 0.31
15 16 0.29
16 3 0.05
17 12 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATTATAATTTTAA
Found at i:14758 original size:40 final size:39
Alignment explanation
Indices: 14695--14774 Score: 94
Period size: 43 Copynumber: 2.0 Consensus size: 39
14685 TTATTTATTG
14695 AATATTAATTTAATATC-T-TATTATAATTTTAATAATA
1 AATATTAATTTAATATCTTATATTATAATTTTAATAATA
14732 AATATTAATTATTAAATAT-TTAATTATTATAATTTTAATAATA
1 AATATTAA-T-TT-AATATCTT-A-TATTATAATTTTAATAATA
14775 TTATTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
37 8 0.22
38 1 0.03
39 2 0.06
40 6 0.17
43 19 0.53
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (39 bp):
AATATTAATTTAATATCTTATATTATAATTTTAATAATA
Found at i:14948 original size:27 final size:27
Alignment explanation
Indices: 14909--14962 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
14899 AACTGAACCT
* *
14909 TTTTTCTTTAATAGTTAATCAAATCGAA
1 TTTTTCTTAAATA-TTAACCAAATCGAA
*
14937 TTTTTC-TAAATATTAACCGAATCGAA
1 TTTTTCTTAAATATTAACCAAATCGAA
14963 CTTTATTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 12 0.52
27 5 0.22
28 6 0.26
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (27 bp):
TTTTTCTTAAATATTAACCAAATCGAA
Found at i:18647 original size:8 final size:8
Alignment explanation
Indices: 18634--18664 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
18624 TTGGAGTGCA
18634 AAAAGAAG
1 AAAAGAAG
18642 AAAAGAAG
1 AAAAGAAG
18650 AAAAGAAG
1 AAAAGAAG
18658 AAAAGAA
1 AAAAGAA
18665 AAGAAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:18655 original size:13 final size:12
Alignment explanation
Indices: 18639--18678 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 12
18629 GTGCAAAAAG
18639 AAGAAAAGAAGAA
1 AAGAAAA-AAGAA
18652 AAGAAGAAAAGAA
1 AAGAA-AAAAGAA
18665 AAGAAAAAGAGAA
1 AAGAAAAA-AGAA
18678 A
1 A
18679 GCAAGCCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.12
13 20 0.80
14 2 0.08
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAGAA
Found at i:23909 original size:18 final size:19
Alignment explanation
Indices: 23868--23906 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
23858 TATCTTTTAT
23868 TTATTTCATTTCATTCTTA
1 TTATTTCATTTCATTCTTA
23887 TTATTTCA-TTCATTACTTA
1 TTATTTCATTTCATT-CTTA
23906 T
1 T
23907 ATTATTACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATTTCATTTCATTCTTA
Found at i:27331 original size:18 final size:21
Alignment explanation
Indices: 27308--27352 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
27298 GAACATGAAC
27308 AAAACAGA-A-ACACAG-GAG
1 AAAACAGAGAGACACAGAGAG
*
27326 AAAACAGAGAGACAGAGAGAG
1 AAAACAGAGAGACACAGAGAG
27347 AAAACA
1 AAAACA
27353 CACCTTCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 1 0.04
20 5 0.22
21 9 0.39
ACGTcount: A:0.62, C:0.13, G:0.24, T:0.00
Consensus pattern (21 bp):
AAAACAGAGAGACACAGAGAG
Found at i:28711 original size:11 final size:11
Alignment explanation
Indices: 28695--28719 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28685 TATTAGAGGT
28695 TTTTTATTTAA
1 TTTTTATTTAA
28706 TTTTTATTTAA
1 TTTTTATTTAA
28717 TTT
1 TTT
28720 AAATATTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTATTTAA
Found at i:29489 original size:2 final size:2
Alignment explanation
Indices: 29482--29511 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
29472 TGATCCCCTG
29482 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29512 AGTAACAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:36764 original size:17 final size:16
Alignment explanation
Indices: 36742--36783 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
36732 AAATTTGATC
36742 AAATAATTTAATATAAA
1 AAATAATTTAATA-AAA
*
36759 AAATAATATAATAAAA
1 AAATAATTTAATAAAA
*
36775 AATTAATTT
1 AAATAATTT
36784 TACATTCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATAATTTAATAAAA
Found at i:36845 original size:13 final size:13
Alignment explanation
Indices: 36827--36851 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36817 TTTATATAAT
36827 GAATTGATAGAAG
1 GAATTGATAGAAG
36840 GAATTGATAGAA
1 GAATTGATAGAA
36852 ATAATAATGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (13 bp):
GAATTGATAGAAG
Found at i:37868 original size:25 final size:25
Alignment explanation
Indices: 37813--37870 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
37803 AGATTAAAAC
37813 TATAATAATTGTTTATAATCATAAA
1 TATAATAATTGTTTATAATCATAAA
* * **
37838 TGTAATATATT-TTTATAATTATTGA
1 TATAATA-ATTGTTTATAATCATAAA
37863 TATAATAA
1 TATAATAA
37871 ATTGATCACT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
24 1 0.04
25 23 0.85
26 3 0.11
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (25 bp):
TATAATAATTGTTTATAATCATAAA
Found at i:38078 original size:2 final size:2
Alignment explanation
Indices: 38071--38112 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
38061 TCCAAGAGAA
38071 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
38113 GAAGTTTGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40238 original size:3 final size:3
Alignment explanation
Indices: 40230--40281 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
40220 ATTGCTCGAC
* * * *
40230 AAT AAT AAT AAT GAT -AT GAT -AT GAT ATT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40276 AAT AAT
1 AAT AAT
40282 TGTTTAGAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 4 0.09
3 39 0.91
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:43888 original size:20 final size:20
Alignment explanation
Indices: 43863--43912 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
43853 TGATCCATCC
* * *
43863 ATCTATTTATTTATTTATCT
1 ATCTATCTATTGATTTATCA
43883 ATCTATCTATTGATTTATCA
1 ATCTATCTATTGATTTATCA
43903 ATCTATCTAT
1 ATCTATCTAT
43913 ATATACGCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.28, C:0.14, G:0.02, T:0.56
Consensus pattern (20 bp):
ATCTATCTATTGATTTATCA
Found at i:55611 original size:35 final size:34
Alignment explanation
Indices: 55563--55632 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 34
55553 AAGAAATAAG
*
55563 TTTATAGGCATGCTTCTAATTTAGTTTATTAATA
1 TTTATAGGCATGCTTCTAATTTAGTATATTAATA
* *
55597 TTTATGGGCTATGCTTTTAATTTAGTATATTAATA
1 TTTATAGGC-ATGCTTCTAATTTAGTATATTAATA
55632 T
1 T
55633 AGTTTTTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 8 0.25
35 24 0.75
ACGTcount: A:0.29, C:0.07, G:0.13, T:0.51
Consensus pattern (34 bp):
TTTATAGGCATGCTTCTAATTTAGTATATTAATA
Found at i:57254 original size:16 final size:16
Alignment explanation
Indices: 57233--57265 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
57223 TTCAAGCAAA
57233 TCAATC-CTCACCTTTC
1 TCAATCTCTC-CCTTTC
57249 TCAATCTCTCCCTTTC
1 TCAATCTCTCCCTTTC
57265 T
1 T
57266 TATGTCTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.15, C:0.42, G:0.00, T:0.42
Consensus pattern (16 bp):
TCAATCTCTCCCTTTC
Found at i:59362 original size:24 final size:24
Alignment explanation
Indices: 59335--59396 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
59325 CGTTCGTGAA
59335 CGTTCGGTTATGTTCGTTTATATT
1 CGTTCGGTTATGTTCGTTTATATT
* *
59359 CGTTCGGTTATGTTCTTTTATGTT
1 CGTTCGGTTATGTTCGTTTATATT
**
59383 CGTTCATTTATGTT
1 CGTTCGGTTATGTT
59397 TAACCCAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.11, C:0.13, G:0.19, T:0.56
Consensus pattern (24 bp):
CGTTCGGTTATGTTCGTTTATATT
Found at i:60511 original size:16 final size:16
Alignment explanation
Indices: 60490--60556 Score: 84
Period size: 16 Copynumber: 4.3 Consensus size: 16
60480 GTCTCCAACG
*
60490 TTTATGTTCGTGTTTA
1 TTTATGTTCGTGTTCA
* *
60506 TTTATGTCCGTGTTCG
1 TTTATGTTCGTGTTCA
*
60522 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
60538 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
60552 TTTAT
1 TTTAT
60557 TAAATGAACG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
14 5 0.11
15 2 0.04
16 39 0.85
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Done.