Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005557.1 Hibiscus syriacus cultivar Beakdansim tig00012884_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: 55697
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:10387 original size:22 final size:23
Alignment explanation
Indices: 10362--10413 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
10352 TCCCTAAGGA
*
10362 CCACATA-GTTTACACCGAAGTG
1 CCACATAGGGTTACACCGAAGTG
*
10384 CCACATAGGGTTGCACCGAAGTG
1 CCACATAGGGTTACACCGAAGTG
*
10407 CAACATA
1 CCACATA
10414 TTTGTCCCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (23 bp):
CCACATAGGGTTACACCGAAGTG
Found at i:10425 original size:21 final size:21
Alignment explanation
Indices: 10399--10456 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
10389 TAGGGTTGCA
*
10399 CCGAAGTG-CAACATATTTGTC
1 CCGAAG-GACAACATAATTGTC
*
10420 CCGAAGGACCACATAATTGTC
1 CCGAAGGACAACATAATTGTC
* *
10441 CCGAAGAACCACATAA
1 CCGAAGGACAACATAA
10457 AACCCTCGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 1 0.03
21 32 0.97
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.19
Consensus pattern (21 bp):
CCGAAGGACAACATAATTGTC
Found at i:11031 original size:19 final size:20
Alignment explanation
Indices: 10984--11034 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
10974 ATCCCTCCAA
*
10984 TACCGATACTTCTCTTCAAGGG
1 TACCGATAC--CTCCTCAAGGG
*
11006 TATCGATACCTCCTCAA-GG
1 TACCGATACCTCCTCAAGGG
11025 TACCGATACC
1 TACCGATACC
11035 AATCTGGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 11 0.42
20 7 0.27
22 8 0.31
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.27
Consensus pattern (20 bp):
TACCGATACCTCCTCAAGGG
Found at i:14972 original size:15 final size:17
Alignment explanation
Indices: 14954--14991 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
14944 TTAAAAACCT
*
14954 AACAAAA-AAAACT-CG
1 AACAAAATAAAAATACG
14969 AACAAAATAAAAATACG
1 AACAAAATAAAAATACG
14986 AACAAA
1 AACAAA
14992 TCTTACTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 5 0.25
17 8 0.40
ACGTcount: A:0.71, C:0.16, G:0.05, T:0.08
Consensus pattern (17 bp):
AACAAAATAAAAATACG
Found at i:16698 original size:12 final size:12
Alignment explanation
Indices: 16681--16705 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16671 GTGGCATTAG
16681 TCTAATAATAGC
1 TCTAATAATAGC
16693 TCTAATAATAGC
1 TCTAATAATAGC
16705 T
1 T
16706 TTGGTCCCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TCTAATAATAGC
Found at i:17741 original size:14 final size:14
Alignment explanation
Indices: 17722--17750 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17712 TTATTTATAC
17722 ATCTTCAATATAAA
1 ATCTTCAATATAAA
17736 ATCTTCAATATAAA
1 ATCTTCAATATAAA
17750 A
1 A
17751 GTTTTCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (14 bp):
ATCTTCAATATAAA
Found at i:24700 original size:19 final size:19
Alignment explanation
Indices: 24676--24712 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
24666 GAATAATATA
24676 TTAAAAT-TATTTTATATTG
1 TTAAAATATA-TTTATATTG
24695 TTAAAATATATTTATATT
1 TTAAAATATATTTATATT
24713 AACAATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TTAAAATATATTTATATTG
Found at i:25049 original size:20 final size:20
Alignment explanation
Indices: 25024--25064 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
25014 TTGGTTCACG
*
25024 AAATGTAAGATTACCAGTGA
1 AAATGTAAGATTACCAATGA
25044 AAATGTAAGATTACCAATGA
1 AAATGTAAGATTACCAATGA
25064 A
1 A
25065 TAAGATTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.10, G:0.17, T:0.24
Consensus pattern (20 bp):
AAATGTAAGATTACCAATGA
Found at i:25296 original size:37 final size:37
Alignment explanation
Indices: 25223--25297 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
25213 GTTGGAAAAT
* *
25223 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
25260 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
25297 A
1 A
25298 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:32872 original size:33 final size:33
Alignment explanation
Indices: 32830--32896 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
32820 CCGTTTATCT
32830 CCTCACTCGCCACTTCTCCGCTGCGTCAGGTAA
1 CCTCACTCGCCACTTCTCCGCTGCGTCAGGTAA
32863 CCTCACTCGCCACTTCTCCGCTGCGTCAGGTAA
1 CCTCACTCGCCACTTCTCCGCTGCGTCAGGTAA
32896 C
1 C
32897 TCTGATTTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.15, C:0.43, G:0.18, T:0.24
Consensus pattern (33 bp):
CCTCACTCGCCACTTCTCCGCTGCGTCAGGTAA
Found at i:38934 original size:2 final size:2
Alignment explanation
Indices: 38927--38970 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
38917 GAAGGGATGA
*
38927 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38969 AT
1 AT
38971 GCATTTGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40763 original size:6 final size:6
Alignment explanation
Indices: 40752--41574 Score: 1530
Period size: 6 Copynumber: 139.2 Consensus size: 6
40742 AGTCATTCTC
40752 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
40800 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
40848 TATATG TATATG TATATG TATATG TATA-- TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
40894 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
40942 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
40990 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41038 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41086 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41134 TATATG TATATG TATATATG TATATG TATATG TATATG --TATG TATATG
1 TATATG TATATG --TATATG TATATG TATATG TATATG TATATG TATATG
41182 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41230 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41278 TATATG TATATG TATATG TATATG TATATG TATA-- TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41324 TATATG TATATG TATATG TATATG TATATG --TATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41370 --TATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41416 --TATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41462 TATATG TATATG TATATG TATATG TATATG TATATG --TATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41508 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41556 TATATG TATATG TATATG T
1 TATATG TATATG TATATG T
41575 TTTGAACTGG
Statistics
Matches: 801, Mismatches: 0, Indels: 32
0.96 0.00 0.04
Matches are distributed among these distances:
4 28 0.03
6 767 0.96
8 6 0.01
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TATATG
Done.