Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000787.1 Hibiscus syriacus cultivar Beakdansim tig00001525_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: 129779
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:106592 original size:7 final size:7
Alignment explanation
Indices: 106582--106627 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
106572 GAGTTTATGA
106582 TTTAGGG
1 TTTAGGG
*
106589 TTTAGAG
1 TTTAGGG
* *
106596 TTTATGT
1 TTTAGGG
106603 TTTAGGG
1 TTTAGGG
106610 TTTAGGG
1 TTTAGGG
106617 TTTAGGG
1 TTTAGGG
106624 TTTA
1 TTTA
106628 TTACAAATAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (7 bp):
TTTAGGG
Found at i:106598 original size:21 final size:21
Alignment explanation
Indices: 106572--106620 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
106562 ATCAGTTCGT
106572 GAGTTTATGATTTAGGGTTTA
1 GAGTTTATGATTTAGGGTTTA
*
106593 GAGTTTATGTTTTAGGGTTTA
1 GAGTTTATGATTTAGGGTTTA
*
106614 GGGTTTA
1 GAGTTTA
106621 GGGTTTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (21 bp):
GAGTTTATGATTTAGGGTTTA
Found at i:106627 original size:21 final size:21
Alignment explanation
Indices: 106572--106627 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
106562 ATCAGTTCGT
* *
106572 GAGTTTATGATTTAGGGTTTA
1 GAGTTTAGGGTTTAGGGTTTA
* *
106593 GAGTTTATGTTTTAGGGTTTA
1 GAGTTTAGGGTTTAGGGTTTA
*
106614 GGGTTTAGGGTTTA
1 GAGTTTAGGGTTTA
106628 TTACAAATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (21 bp):
GAGTTTAGGGTTTAGGGTTTA
Found at i:106817 original size:25 final size:26
Alignment explanation
Indices: 106772--106826 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
106762 AAAAATTAGT
106772 TATTAAAAATATTATCATTAGA-AATA
1 TATTAAAAATATTATCATTAGATAA-A
* *
106798 TATTAAATAT-TTGTCATTAGATAAA
1 TATTAAAAATATTATCATTAGATAAA
106823 TATT
1 TATT
106827 TTTTTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (26 bp):
TATTAAAAATATTATCATTAGATAAA
Found at i:107142 original size:11 final size:11
Alignment explanation
Indices: 107126--107188 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
107116 GTATTATAGA
107126 ATTTTTAATAT
1 ATTTTTAATAT
107137 ATTTTTAA-A-
1 ATTTTTAATAT
107146 ATTTTATAAT-T
1 ATTTT-TAATAT
*** * *
107157 ATCAATAGTGT
1 ATTTTTAATAT
107168 ATTTTTAATAT
1 ATTTTTAATAT
107179 ATTTTTAATA
1 ATTTTTAATA
107189 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:113463 original size:19 final size:22
Alignment explanation
Indices: 113429--113475 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 22
113419 ATTTAACGTG
113429 ATTTAATTTATAATTTTAT-AA
1 ATTTAATTTATAATTTTATAAA
113450 ATTTAA-TT-TAATTTTATAAA
1 ATTTAATTTATAATTTTATAAA
113470 ATTTAA
1 ATTTAA
113476 AGTGTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.36
20 10 0.40
21 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTAATTTATAATTTTATAAA
Found at i:113966 original size:2 final size:2
Alignment explanation
Indices: 113959--113985 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
113949 TTTGGCGTGC
113959 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 A
113986 AGAGTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:114838 original size:3 final size:3
Alignment explanation
Indices: 114830--114891 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
114820 TGTGCAGAGG
114830 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
114878 AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AG
114892 TGCCCAGCTG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:117149 original size:55 final size:55
Alignment explanation
Indices: 117058--117180 Score: 219
Period size: 55 Copynumber: 2.2 Consensus size: 55
117048 ACCCACCCGA
*
117058 ACCAGCGCAGCATCATGCCGACTTTGTCAACTTCCGGTCACCAGCATCATCTGTC
1 ACCAGCACAGCATCATGCCGACTTTGTCAACTTCCGGTCACCAGCATCATCTGTC
*
117113 ACCATCACAGCATCATGCCGACTTTGTCAACTTCCGGTCACCAGCATCATCTGTC
1 ACCAGCACAGCATCATGCCGACTTTGTCAACTTCCGGTCACCAGCATCATCTGTC
*
117168 ACCAGCGCAGCAT
1 ACCAGCACAGCAT
117181 TAGGTATGTC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 64 1.00
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.23
Consensus pattern (55 bp):
ACCAGCACAGCATCATGCCGACTTTGTCAACTTCCGGTCACCAGCATCATCTGTC
Found at i:122904 original size:13 final size:13
Alignment explanation
Indices: 122870--122904 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
122860 CATCCAAACA
122870 CTAGAAATATTTT
1 CTAGAAATATTTT
*
122883 CTTGAAAATATTTT
1 CTAG-AAATATTTT
122897 CTAGAAAT
1 CTAGAAAT
122905 GTAATTCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (13 bp):
CTAGAAATATTTT
Found at i:123606 original size:31 final size:31
Alignment explanation
Indices: 123568--123633 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
123558 ACACAACTAC
123568 GAACGTAGGATTTTAAGTTTGGAGAAAACTT
1 GAACGTAGGATTTTAAGTTTGGAGAAAACTT
123599 GAACGTAGGATTTTAAGTTTGGAGAAAACTT
1 GAACGTAGGATTTTAAGTTTGGAGAAAACTT
123630 GAAC
1 GAAC
123634 TTATAAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (31 bp):
GAACGTAGGATTTTAAGTTTGGAGAAAACTT
Found at i:124031 original size:16 final size:17
Alignment explanation
Indices: 124000--124032 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
123990 TATGTCGTTG
*
124000 AGCCAATGTTTTGAAAT
1 AGCCAATGTCTTGAAAT
124017 AGCCAATG-CTTGAAAT
1 AGCCAATGTCTTGAAAT
124033 CTTGTGTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (17 bp):
AGCCAATGTCTTGAAAT
Found at i:127938 original size:2 final size:2
Alignment explanation
Indices: 127926--127964 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
127916 CCACATGCAC
* *
127926 CT CT GT CT CT CT CT CT CT CT CT CT CT GT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
127965 ACCTTTCCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.46, G:0.05, T:0.49
Consensus pattern (2 bp):
CT
Found at i:127975 original size:22 final size:22
Alignment explanation
Indices: 127926--127978 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
127916 CCACATGCAC
*
127926 CTCTGTCTCTCTCTCTCTCTCT
1 CTCTGTCTCTCTCTCTCCCTCT
*
127948 CTCTGTCTCTCTCTCTCACCTTT
1 CTCTGTCTCTCTCTCTC-CCTCT
127971 C-CTGTCTC
1 CTCTGTCTC
127979 ATCCGTTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.02, C:0.45, G:0.06, T:0.47
Consensus pattern (22 bp):
CTCTGTCTCTCTCTCTCCCTCT
Found at i:129032 original size:15 final size:15
Alignment explanation
Indices: 129012--129041 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
129002 GAGACCATCC
129012 TCTTCACTTCTATAT
1 TCTTCACTTCTATAT
*
129027 TCTTCACTTTTATAT
1 TCTTCACTTCTATAT
129042 CCTCGTTATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.23, G:0.00, T:0.57
Consensus pattern (15 bp):
TCTTCACTTCTATAT
Done.