Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002073.1 Hibiscus syriacus cultivar Beakdansim tig00004236_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: 46736
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:1300 original size:47 final size:49
Alignment explanation
Indices: 1240--1335 Score: 169
Period size: 47 Copynumber: 2.0 Consensus size: 49
1230 AGTGTAACGA
1240 CGACAGAGCAACAACGAC-AGATGATTTCGGTA-GGTTTTGAGTGCACG
1 CGACAGAGCAACAACGACAAGATGATTTCGGTAGGGTTTTGAGTGCACG
*
1287 CGACGGAGCAACAACGACAAGATGATTTCGGTAGGGTTTTGAGTGCACG
1 CGACAGAGCAACAACGACAAGATGATTTCGGTAGGGTTTTGAGTGCACG
1336 GTGATGGTGA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 17 0.37
48 14 0.30
49 15 0.33
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.21
Consensus pattern (49 bp):
CGACAGAGCAACAACGACAAGATGATTTCGGTAGGGTTTTGAGTGCACG
Found at i:9248 original size:18 final size:18
Alignment explanation
Indices: 9214--9248 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9204 TTCCTCAGGT
*
9214 AATAATCCCCAATCCTTC
1 AATAATCCCCAACCCTTC
*
9232 AATAATCCCTAACCCTT
1 AATAATCCCCAACCCTT
9249 ATTCTGCATT
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:0.34, C:0.37, G:0.00, T:0.29
Consensus pattern (18 bp):
AATAATCCCCAACCCTTC
Found at i:14789 original size:31 final size:31
Alignment explanation
Indices: 14754--14854 Score: 127
Period size: 31 Copynumber: 3.3 Consensus size: 31
14744 AAATATTTTT
* *
14754 TTAATTTAACTCTTAAATTTTGGATAAAACA
1 TTAATTTAACTCTTAAACTTTGGATAAAATA
* *
14785 TTAATTCAA--CTTATAACTTTAGATAAAATA
1 TTAATTTAACTCTTA-AACTTTGGATAAAATA
14815 TTAATTTGAACT-TTAAACTTTGGATAAAATA
1 TTAATTT-AACTCTTAAACTTTGGATAAAATA
14846 TTAATTTAA
1 TTAATTTAA
14855 TTCATGAATT
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
29 4 0.07
30 21 0.35
31 32 0.53
32 3 0.05
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.43
Consensus pattern (31 bp):
TTAATTTAACTCTTAAACTTTGGATAAAATA
Found at i:15737 original size:20 final size:20
Alignment explanation
Indices: 15712--15760 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
15702 TACTGTTCAT
15712 TACTGTTCACACAGTATCGG
1 TACTGTTCACACAGTATCGG
15732 TACTGTTCACACAGTATCGG
1 TACTGTTCACACAGTATCGG
15752 TACTGTTCA
1 TACTGTTCA
15761 TCAAAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (20 bp):
TACTGTTCACACAGTATCGG
Found at i:22147 original size:42 final size:42
Alignment explanation
Indices: 22101--22187 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
22091 TTCCGATTAA
*
22101 TCTAGATTGATTTATTTCTTACACTTAACTTTGATAAACGAG
1 TCTAGATTGATTTATTTCGTACACTTAACTTTGATAAACGAG
*
22143 TCTAGATTGATTTATTTCGTACACTTAACTTTGATAAATGAG
1 TCTAGATTGATTTATTTCGTACACTTAACTTTGATAAACGAG
22185 TCT
1 TCT
22188 TTATATAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.44
Consensus pattern (42 bp):
TCTAGATTGATTTATTTCGTACACTTAACTTTGATAAACGAG
Found at i:23047 original size:28 final size:28
Alignment explanation
Indices: 23015--23080 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
23005 AAGCCCAATG
23015 AGCCCAACAAATTACCCGACCCAGTTCA
1 AGCCCAACAAATTACCCGACCCAGTTCA
* *
23043 AGCCCAATAGATTACCCGACCCAGTTCA
1 AGCCCAACAAATTACCCGACCCAGTTCA
23071 AGCCCAACAA
1 AGCCCAACAA
23081 CCGGAACTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.36, C:0.38, G:0.12, T:0.14
Consensus pattern (28 bp):
AGCCCAACAAATTACCCGACCCAGTTCA
Found at i:25993 original size:3 final size:3
Alignment explanation
Indices: 25985--26036 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
25975 TTTTTATATA
** * *
25985 TAT TAT TAT TAT CGT TAT T-T TAAT TAT TAT TAT TAG CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
26030 TAT TAT T
1 TAT TAT T
26037 TAACTTACAC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:27847 original size:24 final size:26
Alignment explanation
Indices: 27814--27862 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
27804 ATTTCTTATT
27814 TTTTTCATGT-A-TGTATATTCATATA
1 TTTTTCATGTAAGTGTATATT-ATATA
27839 TTTTT-ATGTAAGTGTATATTATAT
1 TTTTTCATGTAAGTGTATATTATAT
27863 TAGATTACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 4 0.18
25 10 0.45
26 8 0.36
ACGTcount: A:0.29, C:0.04, G:0.10, T:0.57
Consensus pattern (26 bp):
TTTTTCATGTAAGTGTATATTATATA
Found at i:34647 original size:10 final size:10
Alignment explanation
Indices: 34629--34659 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
34619 TTTAATACCT
34629 AAAATTTAAA
1 AAAATTTAAA
*
34639 AAAAATTAAA
1 AAAATTTAAA
34649 AAAATTTAAA
1 AAAATTTAAA
34659 A
1 A
34660 CATACCAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:34891 original size:3 final size:3
Alignment explanation
Indices: 34883--34908 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
34873 TGACATGACA
34883 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
34909 ATAATTACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Done.