Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007241.1 Hibiscus syriacus cultivar Beakdansim tig00019189_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: 66152
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:3357 original size:25 final size:25
Alignment explanation
Indices: 3329--3386 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
3319 GCTAATAGAA
3329 TTAGTGAATAAGCTGAAAATATAAG
1 TTAGTGAATAAGCTGAAAATATAAG
3354 TTAGTGAATAAGCTGAAAATATAAG
1 TTAGTGAATAAGCTGAAAATATAAG
*
3379 CTAGTGAA
1 TTAGTGAA
3387 ATATGCCCAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.28
Consensus pattern (25 bp):
TTAGTGAATAAGCTGAAAATATAAG
Found at i:4474 original size:19 final size:19
Alignment explanation
Indices: 4425--4507 Score: 85
Period size: 19 Copynumber: 4.4 Consensus size: 19
4415 TGCATTGTGC
**
4425 TATGAATTTGAAAATAACA
1 TATGAATTTGAAAATAAGT
* * *
4444 TATAAATATGAAATTAAGT
1 TATGAATTTGAAAATAAGT
4463 TATGAATTTGAAAATAAGT
1 TATGAATTTGAAAATAAGT
* **
4482 TATGAGTCCGAAAATAAGT
1 TATGAATTTGAAAATAAGT
*
4501 TCTGAAT
1 TATGAAT
4508 CTGAGAATGA
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.34
Consensus pattern (19 bp):
TATGAATTTGAAAATAAGT
Found at i:4500 original size:38 final size:38
Alignment explanation
Indices: 4425--4507 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 38
4415 TGCATTGTGC
* *
4425 TATGAATTTGAAAATAACATATAAATATGAAATTAAGT
1 TATGAATTTGAAAATAACATATAAATACGAAAATAAGT
** * * *
4463 TATGAATTTGAAAATAAGTTATGAGTCCGAAAATAAGT
1 TATGAATTTGAAAATAACATATAAATACGAAAATAAGT
*
4501 TCTGAAT
1 TATGAAT
4508 CTGAGAATGA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.34
Consensus pattern (38 bp):
TATGAATTTGAAAATAACATATAAATACGAAAATAAGT
Found at i:4639 original size:39 final size:39
Alignment explanation
Indices: 4591--4673 Score: 132
Period size: 39 Copynumber: 2.1 Consensus size: 39
4581 AAAAATAATA
*
4591 TGATATGACTATTATGT-ATGATATTGTTTATCATGGCTT
1 TGATATGACTATTATGTAAT-ATATTATTTATCATGGCTT
*
4630 TGATATGACTATTATGTAATATATTATTTATCATGGTTT
1 TGATATGACTATTATGTAATATATTATTTATCATGGCTT
4669 TGATA
1 TGATA
4674 AAATCATGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
39 39 0.95
40 2 0.05
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.49
Consensus pattern (39 bp):
TGATATGACTATTATGTAATATATTATTTATCATGGCTT
Found at i:5989 original size:42 final size:42
Alignment explanation
Indices: 5937--6016 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
5927 TTACATTGAA
* * *
5937 AAAATCAATTACAACTATTAAATACTGGAAAATGTTTTACAT
1 AAAACCAATTACAACTATTAAACACTGGAAAATATTTTACAT
* *
5979 AAAACCAATTATAACTATTAAACAGTGGAAAATATTTT
1 AAAACCAATTACAACTATTAAACACTGGAAAATATTTT
6017 TCAACTATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (42 bp):
AAAACCAATTACAACTATTAAACACTGGAAAATATTTTACAT
Found at i:9041 original size:2 final size:2
Alignment explanation
Indices: 9034--9062 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9024 AATAATTAAT
9034 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9063 GTGTGACAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10034 original size:12 final size:12
Alignment explanation
Indices: 10019--10043 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10009 AATAAATAAG
10019 TGATTAAAATCC
1 TGATTAAAATCC
10031 TGATTAAAATCC
1 TGATTAAAATCC
10043 T
1 T
10044 AAGAAAACTA
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):
TGATTAAAATCC
Found at i:12005 original size:16 final size:17
Alignment explanation
Indices: 11967--12012 Score: 76
Period size: 18 Copynumber: 2.7 Consensus size: 17
11957 TGTTTATGAG
11967 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
11985 GGAATTGGAATCTGT-A
1 GGAATTGGAATCTGTAA
12001 GGAATTGGAATC
1 GGAATTGGAATC
12013 AAATTTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 13 0.46
18 15 0.54
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:12663 original size:37 final size:38
Alignment explanation
Indices: 12582--12669 Score: 115
Period size: 37 Copynumber: 2.3 Consensus size: 38
12572 TTTCACCCTA
* *
12582 AACCCGAACCCGACCCGAATATCACACATAAAAAAATCC
1 AACCCG-ACCCGACCCAAATATCACACATAAAAAAACCC
* * *
12621 GACCCGACTCGACCCAAATATCACAC-TTAAAAAACCC
1 AACCCGACCCGACCCAAATATCACACATAAAAAAACCC
12658 AACCCGACCCGA
1 AACCCGACCCGA
12670 ATAAAATAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
37 19 0.45
38 18 0.43
39 5 0.12
ACGTcount: A:0.42, C:0.39, G:0.09, T:0.10
Consensus pattern (38 bp):
AACCCGACCCGACCCAAATATCACACATAAAAAAACCC
Found at i:12677 original size:37 final size:38
Alignment explanation
Indices: 12599--12677 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 38
12589 ACCCGACCCG
* * * * *
12599 AATATCACACATAAAAAAATCCGACCCGACTCGACCCA
1 AATATCACACATAAAAAAACCCAACCCGACCCGAACAA
* *
12637 AATATCACAC-TTAAAAAACCCAACCCGACCCGAATAA
1 AATATCACACATAAAAAAACCCAACCCGACCCGAACAA
12674 AATA
1 AATA
12678 AAGTTTCATT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
37 24 0.71
38 10 0.29
ACGTcount: A:0.48, C:0.32, G:0.06, T:0.14
Consensus pattern (38 bp):
AATATCACACATAAAAAAACCCAACCCGACCCGAACAA
Found at i:12872 original size:32 final size:33
Alignment explanation
Indices: 12800--12876 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
12790 TTCACCCTAA
*
12800 ACCCGACCCGAATATCACACTTAAAAAAACCTG
1 ACCCGACCCGAATATCACACTTAAAAAAACCCG
*
12833 ACCCGACCTGAATATCACACTT-AAAAAACCCG
1 ACCCGACCCGAATATCACACTTAAAAAAACCCG
*
12865 ACTCGACCCGAA
1 ACCCGACCCGAA
12877 ATAATAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 19 0.47
33 21 0.52
ACGTcount: A:0.40, C:0.35, G:0.10, T:0.14
Consensus pattern (33 bp):
ACCCGACCCGAATATCACACTTAAAAAAACCCG
Found at i:12894 original size:174 final size:181
Alignment explanation
Indices: 12688--13055 Score: 556
Period size: 174 Copynumber: 2.0 Consensus size: 181
12678 AAGTTTCATT
*
12688 CGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAATAGTGACTTAA-TCTAACCC
1 CGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATTC-AACCC
12752 GACCCGAATTATATATATTTTCGGGTCGGTCCGT-TTTTTTCA-CC-CT-AAACCCGACCCGAAT
65 GACCCGAATTATATATATTTTCGGGTCGGTCC-TATTTTTTCACCCACTCAAACCCGACCCGAAT
* *
12813 ATCACACTTAAAAAAACCTGA-C-C-CGACCTGAATATCACACTTAAAAAACC
129 ATCACACTTAAAAAAACCTGACCACTCGACCCGAATACCACACTTAAAAAACC
* *
12863 CGACTCGACCCGAAATAATAAAAAA-TATTTTTATTTAATAAAAACAGTGACTTAATTCGACCCG
1 CGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATTCAACCCG
*
12927 ACCCGAATTATATATATTTTCGGGTCGGTCCTATTTTTTTACCCTAAACTCAAACCCGACCCGAA
66 ACCCGAATTATATATATTTTCGGGTCGGTCCTATTTTTTCACCC---ACTCAAACCCGACCCGAA
12992 TATCACACTTAAAAAAACCTGACCCGACTCGACCCGAATACCACACTTAAAAAACC
128 TATCACACTTAAAAAAACCTGA-CC-ACTCGACCCGAATACCACACTTAAAAAACC
13048 CGACCCGA
1 CGACCCGA
13056 ACAAAATAAA
Statistics
Matches: 173, Mismatches: 7, Indels: 16
0.88 0.04 0.08
Matches are distributed among these distances:
173 1 0.01
174 72 0.42
175 28 0.16
179 2 0.01
180 36 0.21
182 1 0.01
184 1 0.01
185 32 0.18
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (181 bp):
CGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATTCAACCCG
ACCCGAATTATATATATTTTCGGGTCGGTCCTATTTTTTCACCCACTCAAACCCGACCCGAATAT
CACACTTAAAAAAACCTGACCACTCGACCCGAATACCACACTTAAAAAACC
Found at i:13053 original size:37 final size:38
Alignment explanation
Indices: 12983--13055 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
12973 AACTCAAACC
* *
12983 CGACCCGAATATCACACTTAAAAAAACCTGACCCGACT
1 CGACCCGAATACCACACTTAAAAAAACCCGACCCGACT
13021 CGACCCGAATACCACACTT-AAAAAACCCGACCCGA
1 CGACCCGAATACCACACTTAAAAAAACCCGACCCGA
13056 ACAAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
37 15 0.45
38 18 0.55
ACGTcount: A:0.40, C:0.37, G:0.11, T:0.12
Consensus pattern (38 bp):
CGACCCGAATACCACACTTAAAAAAACCCGACCCGACT
Found at i:19711 original size:34 final size:34
Alignment explanation
Indices: 19668--19772 Score: 201
Period size: 34 Copynumber: 3.1 Consensus size: 34
19658 CCATAGAAGG
19668 TTGAGTCTATTGATCGGATAATCAATTGATATGT
1 TTGAGTCTATTGATCGGATAATCAATTGATATGT
19702 TTGAGTCTATTGATCGGATAATCAATTGATATGT
1 TTGAGTCTATTGATCGGATAATCAATTGATATGT
*
19736 TTGAGTTTATTGATCGGATAATCAATTGATATGT
1 TTGAGTCTATTGATCGGATAATCAATTGATATGT
19770 TTG
1 TTG
19773 GTACATGATT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 70 1.00
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.43
Consensus pattern (34 bp):
TTGAGTCTATTGATCGGATAATCAATTGATATGT
Found at i:20329 original size:50 final size:52
Alignment explanation
Indices: 20208--20334 Score: 195
Period size: 54 Copynumber: 2.4 Consensus size: 52
20198 CGATCGTTGG
20208 GTGTCGGTTGTTTCCAACTTTCGATCACTTTGCTTTTGCTTAGCTTCTTCTTTC
1 GTGTCGGTTGTTTCCAACTTTCGATCACTTTGCTTTTGCTTAG--TCTTCTTTC
*
20262 GTGTCGGTTATTTCCAACTTTCGATCACTTTGCTTTTGCTT-G-CTTCTTTC
1 GTGTCGGTTGTTTCCAACTTTCGATCACTTTGCTTTTGCTTAGTCTTCTTTC
* *
20312 GTGTCGGTTGTTCCCAACCTTCG
1 GTGTCGGTTGTTTCCAACTTTCG
20335 TTTTACCTTC
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
50 28 0.41
53 1 0.01
54 40 0.58
ACGTcount: A:0.09, C:0.25, G:0.18, T:0.47
Consensus pattern (52 bp):
GTGTCGGTTGTTTCCAACTTTCGATCACTTTGCTTTTGCTTAGTCTTCTTTC
Found at i:21083 original size:2 final size:2
Alignment explanation
Indices: 21076--21108 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
21066 TTTTACTCCT
21076 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21109 TCAAATCAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23437 original size:21 final size:21
Alignment explanation
Indices: 23413--23461 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
23403 TATGTATTCC
23413 ACCTCTAAATAATATTTCAAG
1 ACCTCTAAATAATATTTCAAG
23434 ACCTCTAAATAATATTTCAAG
1 ACCTCTAAATAATATTTCAAG
23455 ACCTCTA
1 ACCTCTA
23462 CAATCAAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.41, C:0.22, G:0.04, T:0.33
Consensus pattern (21 bp):
ACCTCTAAATAATATTTCAAG
Found at i:39270 original size:3 final size:3
Alignment explanation
Indices: 39262--39297 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
39252 CCAAATCACG
*
39262 TCT TCT TCT TCT TCT TTT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
39298 GCACACTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:41653 original size:31 final size:31
Alignment explanation
Indices: 41618--41684 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
41608 GAAAAAATTC
* *
41618 TTTAGACACTAAAAATCAATTTAAGGTATAG
1 TTTAGACACCAAAAATCAATTTAAGGTATAA
* * * *
41649 TTTAGATACCAAAAGTTAATTTAAGGTGTAA
1 TTTAGACACCAAAAATCAATTTAAGGTATAA
41680 TTTAG
1 TTTAG
41685 TAACCTAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (31 bp):
TTTAGACACCAAAAATCAATTTAAGGTATAA
Found at i:49704 original size:15 final size:16
Alignment explanation
Indices: 49675--49711 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
49665 TAAAATTATT
49675 TTTATAATATTAAATA
1 TTTATAATATTAAATA
49691 TTTATAAT-TTAAATA
1 TTTATAATATTAAATA
49706 TCTTAT
1 T-TTAT
49712 CTATAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTATAATATTAAATA
Found at i:56720 original size:42 final size:42
Alignment explanation
Indices: 56628--56772 Score: 213
Period size: 42 Copynumber: 3.5 Consensus size: 42
56618 TTACCTAGGC
* * * * *
56628 AGATGATACGAATACTTGTGTGAGAAT-ATTTGTAACGAGGC
1 AGATGATATGAATACTTGTGTGAGTATAATCTGTAACAAGGT
*
56669 AGATTATATGAATACTTGTGTGAGTATAATCTGTAACAAGGT
1 AGATGATATGAATACTTGTGTGAGTATAATCTGTAACAAGGT
56711 AGATGATATGAATACTTGTGTGAGTATAATCTGTAACAAGGT
1 AGATGATATGAATACTTGTGTGAGTATAATCTGTAACAAGGT
*
56753 AGAAGATATGAATAC-TGTGT
1 AGATGATATGAATACTTGTGT
56773 ATCTTCAAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
41 29 0.31
42 66 0.69
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (42 bp):
AGATGATATGAATACTTGTGTGAGTATAATCTGTAACAAGGT
Found at i:65955 original size:21 final size:21
Alignment explanation
Indices: 65931--65970 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
65921 TCTACTGAAA
* *
65931 CTCCACCTGTTTTGGAGTATG
1 CTCCACCTGCTGTGGAGTATG
65952 CTCCACCTGCTGTGGAGTA
1 CTCCACCTGCTGTGGAGTA
65971 CTACTTGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.33
Consensus pattern (21 bp):
CTCCACCTGCTGTGGAGTATG
Done.