Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007590.1 Hibiscus syriacus cultivar Beakdansim tig00021851_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: 144369
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Found at i:14479 original size:21 final size:18
Alignment explanation
Indices: 14454--14497 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
14444 TATTTATATA
14454 TTATTAAATAAAACTATAGTT
1 TTATTAAAT--AA-TATAGTT
*
14475 TTATTTAATAATATAGTT
1 TTATTAAATAATATAGTT
14493 TTATT
1 TTATT
14498 TGATTCGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 12 0.55
19 2 0.09
21 8 0.36
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (18 bp):
TTATTAAATAATATAGTT
Found at i:19205 original size:14 final size:14
Alignment explanation
Indices: 19186--19216 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
19176 TAAACTAACT
19186 ATTGGATTAGCGGC
1 ATTGGATTAGCGGC
*
19200 ATTGGATTAGTGGC
1 ATTGGATTAGCGGC
19214 ATT
1 ATT
19217 ATAATTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.32, T:0.35
Consensus pattern (14 bp):
ATTGGATTAGCGGC
Found at i:39641 original size:30 final size:30
Alignment explanation
Indices: 39607--39663 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
39597 CAACCTCAAA
*
39607 AGGCGCACGCTTTCCCTCCTGATCCAGTCC
1 AGGCGAACGCTTTCCCTCCTGATCCAGTCC
39637 AGGCGAACGCTTTCCCTCCTGATCCAG
1 AGGCGAACGCTTTCCCTCCTGATCCAG
39664 GGATCGTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.16, C:0.40, G:0.21, T:0.23
Consensus pattern (30 bp):
AGGCGAACGCTTTCCCTCCTGATCCAGTCC
Found at i:40350 original size:30 final size:30
Alignment explanation
Indices: 40315--40391 Score: 145
Period size: 30 Copynumber: 2.6 Consensus size: 30
40305 GATAGCTGGC
*
40315 CTGATAGGGCAAGGAATTCTGTAGAAGTAG
1 CTGATAGGGCAAGGAATTCCGTAGAAGTAG
40345 CTGATAGGGCAAGGAATTCCGTAGAAGTAG
1 CTGATAGGGCAAGGAATTCCGTAGAAGTAG
40375 CTGATAGGGCAAGGAAT
1 CTGATAGGGCAAGGAAT
40392 GAAATAGCTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.21
Consensus pattern (30 bp):
CTGATAGGGCAAGGAATTCCGTAGAAGTAG
Found at i:47803 original size:27 final size:28
Alignment explanation
Indices: 47749--47809 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
47739 GCTTCGCTTT
*
47749 CCTGGCTTCGAAGAACCTCCTAACGGAC
1 CCTGGTTTCGAAGAACCTCCTAACGGAC
* **
47777 CCTGGTTTTGAAGAA-CTCCTTGCGGAC
1 CCTGGTTTCGAAGAACCTCCTAACGGAC
47804 CCTGGT
1 CCTGGT
47810 AGTTCACTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 16 0.55
28 13 0.45
ACGTcount: A:0.20, C:0.31, G:0.25, T:0.25
Consensus pattern (28 bp):
CCTGGTTTCGAAGAACCTCCTAACGGAC
Found at i:47962 original size:25 final size:25
Alignment explanation
Indices: 47934--47998 Score: 130
Period size: 25 Copynumber: 2.6 Consensus size: 25
47924 CCTTGAAGTC
47934 CCTCTCCTTACAGTCACTTTCAGTT
1 CCTCTCCTTACAGTCACTTTCAGTT
47959 CCTCTCCTTACAGTCACTTTCAGTT
1 CCTCTCCTTACAGTCACTTTCAGTT
47984 CCTCTCCTTACAGTC
1 CCTCTCCTTACAGTC
47999 GAGACTTTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.15, C:0.38, G:0.08, T:0.38
Consensus pattern (25 bp):
CCTCTCCTTACAGTCACTTTCAGTT
Found at i:65927 original size:240 final size:240
Alignment explanation
Indices: 65622--66101 Score: 960
Period size: 240 Copynumber: 2.0 Consensus size: 240
65612 CTGGAAGATG
65622 GAGATGAGTGCTTTGATCGACCTATTATTCTTATTCCTTAGGATAAGAAATATCCCACAATGAAA
1 GAGATGAGTGCTTTGATCGACCTATTATTCTTATTCCTTAGGATAAGAAATATCCCACAATGAAA
65687 GAGCTTGTAGTTTCTCATACCGAAAAAGAGGCGAATGAACTGCCAGATGAACCCCGACGACTAGA
66 GAGCTTGTAGTTTCTCATACCGAAAAAGAGGCGAATGAACTGCCAGATGAACCCCGACGACTAGA
65752 CTGGACGATAATTGATGCATTCATGAAGGATGGAACTTTTTATCACTCCCCTCTATCAGAAAAGG
131 CTGGACGATAATTGATGCATTCATGAAGGATGGAACTTTTTATCACTCCCCTCTATCAGAAAAGG
65817 AGGCTACAACAGGATCATCTTTGTCCGACTTTCCTCTCCACCAAA
196 AGGCTACAACAGGATCATCTTTGTCCGACTTTCCTCTCCACCAAA
65862 GAGATGAGTGCTTTGATCGACCTATTATTCTTATTCCTTAGGATAAGAAATATCCCACAATGAAA
1 GAGATGAGTGCTTTGATCGACCTATTATTCTTATTCCTTAGGATAAGAAATATCCCACAATGAAA
65927 GAGCTTGTAGTTTCTCATACCGAAAAAGAGGCGAATGAACTGCCAGATGAACCCCGACGACTAGA
66 GAGCTTGTAGTTTCTCATACCGAAAAAGAGGCGAATGAACTGCCAGATGAACCCCGACGACTAGA
65992 CTGGACGATAATTGATGCATTCATGAAGGATGGAACTTTTTATCACTCCCCTCTATCAGAAAAGG
131 CTGGACGATAATTGATGCATTCATGAAGGATGGAACTTTTTATCACTCCCCTCTATCAGAAAAGG
66057 AGGCTACAACAGGATCATCTTTGTCCGACTTTCCTCTCCACCAAA
196 AGGCTACAACAGGATCATCTTTGTCCGACTTTCCTCTCCACCAAA
66102 CATAGGGAGA
Statistics
Matches: 240, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
240 240 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (240 bp):
GAGATGAGTGCTTTGATCGACCTATTATTCTTATTCCTTAGGATAAGAAATATCCCACAATGAAA
GAGCTTGTAGTTTCTCATACCGAAAAAGAGGCGAATGAACTGCCAGATGAACCCCGACGACTAGA
CTGGACGATAATTGATGCATTCATGAAGGATGGAACTTTTTATCACTCCCCTCTATCAGAAAAGG
AGGCTACAACAGGATCATCTTTGTCCGACTTTCCTCTCCACCAAA
Found at i:79809 original size:2 final size:2
Alignment explanation
Indices: 79802--79835 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
79792 ATCCTTCTTT
* *
79802 TA TA TA TA TA TT TA TA TA AA 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
79836 ATAATAGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:80478 original size:25 final size:25
Alignment explanation
Indices: 80450--80499 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
80440 GACGTACCTA
* **
80450 CTTAGATACAGGCAAGGAAGTACAG
1 CTTAGAGACAGGCAACCAAGTACAG
80475 CTTAGAGACAGGCAACCAAGTACAG
1 CTTAGAGACAGGCAACCAAGTACAG
80500 AAGTAGGGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (25 bp):
CTTAGAGACAGGCAACCAAGTACAG
Found at i:108001 original size:21 final size:18
Alignment explanation
Indices: 107976--108019 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
107966 TATTTATATA
107976 TTATTAAATAAAACTATAGTT
1 TTATTAAAT--AA-TATAGTT
*
107997 TTATTTAATAATATAGTT
1 TTATTAAATAATATAGTT
108015 TTATT
1 TTATT
108020 TGATTCGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 12 0.55
19 2 0.09
21 8 0.36
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (18 bp):
TTATTAAATAATATAGTT
Found at i:112727 original size:14 final size:14
Alignment explanation
Indices: 112708--112738 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
112698 TAAACTAACT
112708 ATTGGATTAGCGGC
1 ATTGGATTAGCGGC
*
112722 ATTGGATTAGTGGC
1 ATTGGATTAGCGGC
112736 ATT
1 ATT
112739 ATAATTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.32, T:0.35
Consensus pattern (14 bp):
ATTGGATTAGCGGC
Found at i:133155 original size:30 final size:30
Alignment explanation
Indices: 133121--133177 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
133111 CAACCTCAAA
*
133121 AGGCGCACGCTTTCCCTCCTGATCCAGTCC
1 AGGCGAACGCTTTCCCTCCTGATCCAGTCC
133151 AGGCGAACGCTTTCCCTCCTGATCCAG
1 AGGCGAACGCTTTCCCTCCTGATCCAG
133178 GGATCGTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.16, C:0.40, G:0.21, T:0.23
Consensus pattern (30 bp):
AGGCGAACGCTTTCCCTCCTGATCCAGTCC
Found at i:133862 original size:30 final size:30
Alignment explanation
Indices: 133827--133903 Score: 145
Period size: 30 Copynumber: 2.6 Consensus size: 30
133817 GATAGCTGGC
*
133827 CTGATAGGGCAAGGAATTCTGTAGAAGTAG
1 CTGATAGGGCAAGGAATTCCGTAGAAGTAG
133857 CTGATAGGGCAAGGAATTCCGTAGAAGTAG
1 CTGATAGGGCAAGGAATTCCGTAGAAGTAG
133887 CTGATAGGGCAAGGAAT
1 CTGATAGGGCAAGGAAT
133904 GAAATAGCTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.21
Consensus pattern (30 bp):
CTGATAGGGCAAGGAATTCCGTAGAAGTAG
Found at i:141281 original size:27 final size:28
Alignment explanation
Indices: 141227--141287 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
141217 GCTTCGCTTT
*
141227 CCTGGCTTCGAAGAACCTCCTAACGGAC
1 CCTGGTTTCGAAGAACCTCCTAACGGAC
* **
141255 CCTGGTTTTGAAGAA-CTCCTTGCGGAC
1 CCTGGTTTCGAAGAACCTCCTAACGGAC
141282 CCTGGT
1 CCTGGT
141288 AGTTCACTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 16 0.55
28 13 0.45
ACGTcount: A:0.20, C:0.31, G:0.25, T:0.25
Consensus pattern (28 bp):
CCTGGTTTCGAAGAACCTCCTAACGGAC
Found at i:141440 original size:25 final size:25
Alignment explanation
Indices: 141412--141476 Score: 130
Period size: 25 Copynumber: 2.6 Consensus size: 25
141402 CCTTGAAGTC
141412 CCTCTCCTTACAGTCACTTTCAGTT
1 CCTCTCCTTACAGTCACTTTCAGTT
141437 CCTCTCCTTACAGTCACTTTCAGTT
1 CCTCTCCTTACAGTCACTTTCAGTT
141462 CCTCTCCTTACAGTC
1 CCTCTCCTTACAGTC
141477 GAGACTTTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.15, C:0.38, G:0.08, T:0.38
Consensus pattern (25 bp):
CCTCTCCTTACAGTCACTTTCAGTT
Done.