Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006684.1 Hibiscus syriacus cultivar Beakdansim tig00016583_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: 67360
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:5599 original size:15 final size:15
Alignment explanation
Indices: 5579--5610 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
5569 TCAACAACTT
5579 ATTGAATGCATGACC
1 ATTGAATGCATGACC
5594 ATTGAATGCATGACC
1 ATTGAATGCATGACC
5609 AT
1 AT
5611 GTGACTGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (15 bp):
ATTGAATGCATGACC
Found at i:5697 original size:16 final size:16
Alignment explanation
Indices: 5674--5707 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
5664 TATCTTTAAC
5674 ACACACACGTATATATGT
1 ACACACAC--ATATATGT
5692 ACACACACATATATGT
1 ACACACACATATATGT
5708 CTTGTTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (16 bp):
ACACACACATATATGT
Found at i:13322 original size:24 final size:25
Alignment explanation
Indices: 13278--13325 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
13268 GAATGGAAAA
*
13278 TTTTCATACATATATATAATAATAG
1 TTTTCATAAATATATATAATAATAG
13303 TTTT-ATAAATATATCA-AATAATA
1 TTTTCATAAATATAT-ATAATAATA
13326 AATAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTTCATAAATATATATAATAATAG
Found at i:23760 original size:2 final size:2
Alignment explanation
Indices: 23753--23814 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
23743 TATATGCCAT
23753 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23795 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
23815 AAGTATTAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25163 original size:58 final size:58
Alignment explanation
Indices: 25067--25179 Score: 136
Period size: 58 Copynumber: 1.9 Consensus size: 58
25057 ATAGTCAAGT
* * ** ** * * * *
25067 GACCATTTTGTAACTTTTAATTGTTGGGGGACTCAATAAAGTAACATCTTATAGTTAG
1 GACCATTTTATAACTTTTAATAGTCAGAAGACTAAATAAAGCAACACCCTATAGTTAG
25125 GACCATTTTATAACTTTTAATAGTCAGAAGACTAAATAAAGCAACACCCTATAGT
1 GACCATTTTATAACTTTTAATAGTCAGAAGACTAAATAAAGCAACACCCTATAGT
25180 CAACGGACCA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
58 45 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (58 bp):
GACCATTTTATAACTTTTAATAGTCAGAAGACTAAATAAAGCAACACCCTATAGTTAG
Found at i:29042 original size:24 final size:24
Alignment explanation
Indices: 28924--29042 Score: 134
Period size: 24 Copynumber: 5.0 Consensus size: 24
28914 AAACATAAAT
*
28924 CATGTCAAGTATCATATCAGAAAT-
1 CATGTCAAGTATCAGATCAG-AATC
* * * *
28948 CAGGACAAGTAACAGATCATAATC
1 CATGTCAAGTATCAGATCAGAATC
*
28972 CAAGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCAGATCAGAATC
*
28996 CATGTC-AGATATCATATCAGAATC
1 CATGTCAAG-TATCAGATCAGAATC
*
29020 CATGTCAATTATCAGATCAGAAT
1 CATGTCAAGTATCAGATCAGAAT
29043 TCAAATCGAA
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
23 5 0.06
24 73 0.92
25 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.25
Consensus pattern (24 bp):
CATGTCAAGTATCAGATCAGAATC
Found at i:31582 original size:18 final size:18
Alignment explanation
Indices: 31561--31607 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
31551 CGGCGGTCAA
31561 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
31579 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
31597 CGGGTCTGGTC
1 CGGGTCGGGTC
31608 GAGTTATGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:31602 original size:13 final size:13
Alignment explanation
Indices: 31555--31584 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
31545 GGTCAACGGC
31555 GGTCAACGGGTCG
1 GGTCAACGGGTCG
31568 GGTCAACGGGTCG
1 GGTCAACGGGTCG
31581 GGTC
1 GGTC
31585 GGGTCAACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:33714 original size:24 final size:24
Alignment explanation
Indices: 33687--33762 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
33677 TATATCAAAA
* *
33687 ATCAAAACATAAATCGGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* *
33711 ATCATATCAGAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* * * *
33735 AACAGATCA-AAATCCAAGTCAAGT
1 ATCAAAACAGAAAT-CAGGTCAAGT
33759 ATCA
1 ATCA
33763 GATCAGAATC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 4 0.09
24 39 0.91
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAAAACAGAAATCAGGTCAAGT
Found at i:33816 original size:24 final size:24
Alignment explanation
Indices: 33704--33819 Score: 155
Period size: 24 Copynumber: 4.8 Consensus size: 24
33694 CATAAATCGG
* *
33704 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAT
* * *
33728 GTCAAGTAACAGATCAAAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
33752 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
33776 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
33800 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
33820 TCAAATCGAA
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
23 5 0.06
24 75 0.91
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:33835 original size:48 final size:48
Alignment explanation
Indices: 33737--33842 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 48
33727 GGTCAAGTAA
** *
33737 CAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCATGTCAGATAT
1 CAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAAAT
* * *
33785 CAGATCAGAATCCATGTCAAGTATCAGATCAGAATTCAAATC-GAAAAT
1 CAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAG-AAAT
33833 CAGAT-AAAAT
1 CAGATCAAAAT
33843 ATTCATATGA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
47 5 0.10
48 45 0.90
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (48 bp):
CAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAAAT
Found at i:37769 original size:19 final size:21
Alignment explanation
Indices: 37745--37784 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
37735 TTTTTTTATA
37745 CTATTA-TG-ACATATTTTCT
1 CTATTACTGAACATATTTTCT
37764 CTATTACTGTAACATATTTTC
1 CTATTACTG-AACATATTTTC
37785 AGTCGTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 2 0.11
22 10 0.56
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.50
Consensus pattern (21 bp):
CTATTACTGAACATATTTTCT
Found at i:49590 original size:18 final size:19
Alignment explanation
Indices: 49555--49591 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
49545 CACGGAATGT
49555 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
49575 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
49592 TGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:58699 original size:17 final size:17
Alignment explanation
Indices: 58666--58699 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
58656 GTGAAACAGA
* *
58666 CTTTTAAACATGTCAGG
1 CTTTTAAACAGGCCAGG
58683 CTTTTAAACAGGCCAGG
1 CTTTTAAACAGGCCAGG
58700 TCGAGCCTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (17 bp):
CTTTTAAACAGGCCAGG
Found at i:59339 original size:25 final size:25
Alignment explanation
Indices: 59302--59349 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
59292 TGATTTTGAA
59302 AAAAATGAAAGTTTAGGTACTAATC
1 AAAAATGAAAGTTTAGGTACTAATC
* * *
59327 AAAACTGATAGTTTATGTACTAA
1 AAAAATGAAAGTTTAGGTACTAA
59350 ATGTGTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (25 bp):
AAAAATGAAAGTTTAGGTACTAATC
Found at i:62164 original size:6 final size:6
Alignment explanation
Indices: 62135--62264 Score: 63
Period size: 6 Copynumber: 22.2 Consensus size: 6
62125 ATGCTACATA
* * * * * *
62135 TATATG TGTATG TATAT- TACATG TATATG TTTATA CATAT- TACATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
* * * * * *
62181 TATATG TGTATG TGTAT- T-TATG TTACATG TATATG TTTATA CATAT-
1 TATATG TATATG TATATG TATATG -TATATG TATATG TATATG TATATG
* * * *
62227 TATATG TATATC TGTATG TTAAATG TGTATG TATATG T
1 TATATG TATATG TATATG -TATATG TATATG TATATG T
62265 GTGTCTATGG
Statistics
Matches: 90, Mismatches: 27, Indels: 14
0.69 0.21 0.11
Matches are distributed among these distances:
4 3 0.03
5 12 0.13
6 68 0.76
7 7 0.08
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:62198 original size:23 final size:23
Alignment explanation
Indices: 62129--62245 Score: 99
Period size: 23 Copynumber: 4.8 Consensus size: 23
62119 GTATTTATGC
*
62129 TACATATATATGTGTATGTATAT
1 TACATGTATATGTGTATGTATAT
* **
62152 TACATGTATATGTTTATACATAT
1 TACATGTATATGTGTATGTATAT
62175 TACATGTATATGTGTATGTGTATTTATGT
1 TACATGTATATGTGTA--TGTA--TA--T
* **
62204 TACATGTATATGTTTATACATAT
1 TACATGTATATGTGTATGTATAT
* *
62227 TATATGTATATCTGTATGT
1 TACATGTATATGTGTATGT
62246 TAAATGTGTA
Statistics
Matches: 73, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
23 49 0.67
25 4 0.05
27 4 0.05
29 16 0.22
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.50
Consensus pattern (23 bp):
TACATGTATATGTGTATGTATAT
Found at i:62208 original size:52 final size:52
Alignment explanation
Indices: 62137--62245 Score: 182
Period size: 52 Copynumber: 2.1 Consensus size: 52
62127 GCTACATATA
*
62137 TATGTGTATGTATATTACATGTATATGTTTATACATATTACATGTATATGTG
1 TATGTGTATGTATATTACATGTATATGTTTATACATATTACATGTATATCTG
* * *
62189 TATGTGTATTTATGTTACATGTATATGTTTATACATATTATATGTATATCTG
1 TATGTGTATGTATATTACATGTATATGTTTATACATATTACATGTATATCTG
62241 TATGT
1 TATGT
62246 TAAATGTGTA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.29, C:0.06, G:0.15, T:0.50
Consensus pattern (52 bp):
TATGTGTATGTATATTACATGTATATGTTTATACATATTACATGTATATCTG
Found at i:62227 original size:29 final size:28
Alignment explanation
Indices: 62151--62233 Score: 77
Period size: 29 Copynumber: 3.0 Consensus size: 28
62141 TGTATGTATA
62151 TTACATGTATATGTTTATAC-A--TA--
1 TTACATGTATATGTTTATACTATTTATG
* **
62174 TTACATGTATATGTGTATGTGTATTTATG
1 TTACATGTATATGTTTAT-ACTATTTATG
62203 TTACATGTATATGTTTATACATATTATATG
1 TTACATGTATATGTTTATAC-TATT-TATG
62233 T
1 T
62234 ATATCTGTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
23 17 0.37
25 1 0.02
27 2 0.04
29 21 0.46
30 5 0.11
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.51
Consensus pattern (28 bp):
TTACATGTATATGTTTATACTATTTATG
Found at i:63861 original size:2 final size:2
Alignment explanation
Indices: 63856--63888 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
63846 TTCTTTTTTC
63856 AT AT AT AT 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 AT AT AT AT A
63889 CACACATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.