Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003630.1 Hibiscus syriacus cultivar Beakdansim tig00007688_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: 59540
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:14258 original size:21 final size:21
Alignment explanation
Indices: 14224--14271 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
14214 AGTGTTATTT
* * *
14224 AAAATATTATTTTTTTTACCG
1 AAAATGTTAATTTTGTTACCG
*
14245 AAAATGTTAATTTTGTTACCT
1 AAAATGTTAATTTTGTTACCG
14266 AAAATG
1 AAAATG
14272 AATATTTTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (21 bp):
AAAATGTTAATTTTGTTACCG
Found at i:14921 original size:25 final size:24
Alignment explanation
Indices: 14885--14932 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
14875 TATCTTTCTT
14885 AATTTTAAATTTAAATATTTAATA
1 AATTTTAAATTTAAATATTTAATA
* *
14909 AATTATTATATTTTAATATTTAAT
1 AATT-TTAAATTTAAATATTTAAT
14933 CTTACTTCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
AATTTTAAATTTAAATATTTAATA
Found at i:18032 original size:18 final size:18
Alignment explanation
Indices: 18009--18044 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
17999 TTAAGAAAAT
18009 TCGCATACAATCAACTTC
1 TCGCATACAATCAACTTC
18027 TCGCATACAATCAACTTC
1 TCGCATACAATCAACTTC
18045 ACAGAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.06, T:0.28
Consensus pattern (18 bp):
TCGCATACAATCAACTTC
Found at i:18933 original size:20 final size:20
Alignment explanation
Indices: 18892--18933 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
18882 TAATTTTATT
* *
18892 TTTATTTTTCTCTTAAATTA
1 TTTATTTTTCTCTAAAAATA
18912 TTTA-TTTTCTTCTAAAAATA
1 TTTATTTTTC-TCTAAAAATA
18932 TT
1 TT
18934 ATATACTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATTTTTCTCTAAAAATA
Found at i:23268 original size:2 final size:2
Alignment explanation
Indices: 23214--23251 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
23204 TCTCTCCTTT
23214 TA TA TA TA TA TA TA TA TA TA TA TA 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 TA TA
23252 GTTTGTATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34887 original size:36 final size:36
Alignment explanation
Indices: 34826--35050 Score: 281
Period size: 36 Copynumber: 6.3 Consensus size: 36
34816 AAGTTTGCAT
* * *
34826 CGATTCAAGTCAAACGGAAGAAAGCATCGACACTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
* * *
34862 CGATTCAAGTCGAACAGAGGGAAGCATTGGCACTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
* * * **
34898 CAATTCAAATCGAACTGAAGGAAGCATCGGTTCTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
*
34934 CGATTCAAGTCGAACGGAAGGAAGTATCGGCACTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
* * *
34970 CGATTCAAGT-GAACGGAAGGAAACATCGACACTTT
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
* * *
35005 TGATTCAAATCGAACGGAAGGAAGCATAGGCACTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
35041 CGATTCAAGT
1 CGATTCAAGT
35051 GTTCATTTTT
Statistics
Matches: 157, Mismatches: 31, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
35 29 0.18
36 128 0.82
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (36 bp):
CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
Found at i:36212 original size:36 final size:36
Alignment explanation
Indices: 36151--36375 Score: 281
Period size: 36 Copynumber: 6.3 Consensus size: 36
36141 AAGTTTGCAT
* * *
36151 CGATTCAAGTCAAACGGAAGAAAGCATCGACACTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
* * *
36187 CGATTCAAGTCGAACAGAGGGAAGCATTGGCACTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
* * * **
36223 CAATTCAAATCGAACTGAAGGAAGCATCGGTTCTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
*
36259 CGATTCAAGTCGAACGGAAGGAAGTATCGGCACTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
* * *
36295 CGATTCAAGT-GAACGGAAGGAAACATCGACACTTT
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
* * *
36330 TGATTCAAATCGAACGGAAGGAAGCATAGGCACTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
36366 CGATTCAAGT
1 CGATTCAAGT
36376 GTTCATTTTT
Statistics
Matches: 157, Mismatches: 31, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
35 29 0.18
36 128 0.82
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (36 bp):
CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
Found at i:37539 original size:36 final size:36
Alignment explanation
Indices: 37478--37702 Score: 281
Period size: 36 Copynumber: 6.3 Consensus size: 36
37468 AAGTTTGCAT
* * *
37478 CGATTCAAGTCAAACGGAAGAAAGCATCGACACTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
* * *
37514 CGATTCAAGTCGAACAGAGGGAAGCATTGGCACTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
* * * **
37550 CAATTCAAATCGAACTGAAGGAAGCATCGGTTCTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
*
37586 CGATTCAAGTCGAACGGAAGGAAGTATCGGCACTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
* * *
37622 CGATTCAAGT-GAACGGAAGGAAACATCGACACTTT
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
* * *
37657 TGATTCAAATCGAACGGAAGGAAGCATAGGCACTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
37693 CGATTCAAGT
1 CGATTCAAGT
37703 GTTCATTTTT
Statistics
Matches: 157, Mismatches: 31, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
35 29 0.18
36 128 0.82
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (36 bp):
CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
Found at i:40420 original size:26 final size:26
Alignment explanation
Indices: 40384--40437 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
40374 AGTCAATTAC
40384 ATAGTTTATAAGAGGAAAATGTAGCA
1 ATAGTTTATAAGAGGAAAATGTAGCA
*
40410 ATAGTTTATAAGTGGAAAATGTAGCA
1 ATAGTTTATAAGAGGAAAATGTAGCA
40436 AT
1 AT
40438 GCTCTTTGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.30
Consensus pattern (26 bp):
ATAGTTTATAAGAGGAAAATGTAGCA
Found at i:43092 original size:30 final size:30
Alignment explanation
Indices: 43005--43093 Score: 108
Period size: 30 Copynumber: 3.0 Consensus size: 30
42995 AATAAAATGC
* *
43005 TCTCACCCCGTAAACATTCACACAACAATCC
1 TCTCAACCCGTAAACA-TCACACAACAATCA
*
43036 TCTCAA-CCGAAAACATCACACAACAATCA
1 TCTCAACCCGTAAACATCACACAACAATCA
* * *
43065 TCTCAACCCGTAAATATCACCCGACAATC
1 TCTCAACCCGTAAACATCACACAACAATC
43094 CTTTTATATT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 19 0.38
30 26 0.52
31 5 0.10
ACGTcount: A:0.39, C:0.38, G:0.04, T:0.18
Consensus pattern (30 bp):
TCTCAACCCGTAAACATCACACAACAATCA
Found at i:47079 original size:63 final size:63
Alignment explanation
Indices: 46997--47186 Score: 317
Period size: 63 Copynumber: 3.0 Consensus size: 63
46987 CAAGAGTCGA
* *
46997 AGAATTACCTATGTTTTTCGGGACATATTGACAGTATACATATGTTCTACGGAACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGACAGTATACATATGTTCTACGGAACATATGGAC
* * * *
47060 ATAATTACCTATGTCTTTCGGGACATATGGACAATATACCTATGTTCTACGAAACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGACAGTATACATATGTTCTACGGAACATATGGAC
*
47123 AGAATTACCTATGTCTTTCGGGACATATGGACAGTATACATATGTTCTAAGGAACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGACAGTATACATATGTTCTACGGAACATATGGAC
47186 A
1 A
47187 ATATACATAT
Statistics
Matches: 116, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 116 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (63 bp):
AGAATTACCTATGTCTTTCGGGACATATGGACAGTATACATATGTTCTACGGAACATATGGAC
Found at i:47156 original size:32 final size:31
Alignment explanation
Indices: 46997--47156 Score: 164
Period size: 32 Copynumber: 5.1 Consensus size: 31
46987 CAAGAGTCGA
*
46997 AGAATTACCTATGTTTTTCGGGACATATTGAC
1 AGAATTACCTATG-TTTTCGGGACATATGGAC
* * * *
47029 AGTA-TACATATGTTCTACGGAACATATGGAC
1 AGAATTACCTATGTT-TTCGGGACATATGGAC
*
47060 ATAATTACCTATGTCTTTCGGGACATATGGAC
1 AGAATTACCTATGT-TTTCGGGACATATGGAC
* **
47092 --AATATACCTATGTTCTACGAAACATATGGAC
1 AGAAT-TACCTATGTT-TTCGGGACATATGGAC
47123 AGAATTACCTATGTCTTTCGGGACATATGGAC
1 AGAATTACCTATGT-TTTCGGGACATATGGAC
47155 AG
1 AG
47157 TATACATATG
Statistics
Matches: 104, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
30 6 0.06
31 44 0.42
32 49 0.47
33 5 0.05
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (31 bp):
AGAATTACCTATGTTTTCGGGACATATGGAC
Found at i:47181 original size:16 final size:16
Alignment explanation
Indices: 47160--47213 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
47150 TGGACAGTAT
47160 ACATATGTTCTAAGGA
1 ACATATGTTCTAAGGA
** *
47176 ACATATGGAC-AA-TA
1 ACATATGTTCTAAGGA
47190 TACATATGTTCTAAGGA
1 -ACATATGTTCTAAGGA
47207 ACATATG
1 ACATATG
47214 GATAGTTTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
14 1 0.03
15 10 0.34
16 17 0.59
17 1 0.03
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.30
Consensus pattern (16 bp):
ACATATGTTCTAAGGA
Found at i:47252 original size:31 final size:31
Alignment explanation
Indices: 47002--47250 Score: 225
Period size: 31 Copynumber: 8.0 Consensus size: 31
46992 GTCGAAGAAT
* * * *
47002 TACCTATGTTTTTCGGGACATATTGACAGTA
1 TACCTATGTTCTACGGAACATATGGACAGTA
*
47033 TACATATGTTCTACGGAACATATGGACA-TAA
1 TACCTATGTTCTACGGAACATATGGACAGT-A
* * *
47064 TTACCTATG-TCTTTCGGGACATATGGACAATA
1 -TACCTATGTTC-TACGGAACATATGGACAGTA
* *
47096 TACCTATGTTCTACGAAACATATGGACAGAA
1 TACCTATGTTCTACGGAACATATGGACAGTA
* *
47127 TTACCTATG-TCTTTCGGGACATATGGACAGTA
1 -TACCTATGTTC-TACGGAACATATGGACAGTA
* * *
47159 TACATATGTTCTAAGGAACATATGGACAATA
1 TACCTATGTTCTACGGAACATATGGACAGTA
* * * *
47190 TACATATGTTCTAAGGAACATATGGATAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTA
* * * *
47221 TACCTAGGTTCTTCGAAACCTATGGACAGT
1 TACCTATGTTCTACGGAACATATGGACAGT
47251 TTTCGAGGTT
Statistics
Matches: 178, Mismatches: 32, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
30 1 0.01
31 125 0.70
32 51 0.29
33 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTA
Found at i:48005 original size:14 final size:14
Alignment explanation
Indices: 47986--48013 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
47976 TTCACTGTTC
47986 ACGGTATTGTTCAT
1 ACGGTATTGTTCAT
48000 ACGGTATTGTTCAT
1 ACGGTATTGTTCAT
48014 TGTTCATACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.43
Consensus pattern (14 bp):
ACGGTATTGTTCAT
Found at i:49809 original size:29 final size:31
Alignment explanation
Indices: 49775--49839 Score: 116
Period size: 29 Copynumber: 2.2 Consensus size: 31
49765 ACTGTAAAAA
49775 AAATAATTAAATAAAATACTAA-AAAAT-TT
1 AAATAATTAAATAAAATACTAACAAAATATT
49804 AAATAATTAAATAAAATACTAACAAAATATT
1 AAATAATTAAATAAAATACTAACAAAATATT
49835 AAATA
1 AAATA
49840 GAATAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 22 0.65
30 5 0.15
31 7 0.21
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (31 bp):
AAATAATTAAATAAAATACTAACAAAATATT
Found at i:50881 original size:23 final size:22
Alignment explanation
Indices: 50853--50896 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
50843 TTATGACTTT
50853 TAATATTTTAAAAATTAAAAAAA
1 TAATATTTT-AAAATTAAAAAAA
*
50876 TAATATTTTATAATTAAAAAA
1 TAATATTTTAAAATTAAAAAA
50897 TTATTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TAATATTTTAAAATTAAAAAAA
Found at i:50901 original size:19 final size:21
Alignment explanation
Indices: 50855--50909 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 21
50845 ATGACTTTTA
*
50855 ATATTTTAAAAATTAAAAAAAT
1 ATATTTT-ATAATTAAAAAAAT
50877 AATATTTTATAATT-AAAAAAT
1 -ATATTTTATAATTAAAAAAAT
50898 -TATTTTATAATT
1 ATATTTTATAATT
50910 TTAATAATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 12 0.39
21 7 0.23
22 5 0.16
23 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATTTTATAATTAAAAAAAT
Found at i:50946 original size:12 final size:12
Alignment explanation
Indices: 50929--50953 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50919 GAATAACTGC
50929 ATCTCTTAATCG
1 ATCTCTTAATCG
50941 ATCTCTTAATCG
1 ATCTCTTAATCG
50953 A
1 A
50954 GAGGCTGTAT
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:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (12 bp):
ATCTCTTAATCG
Found at i:58835 original size:13 final size:13
Alignment explanation
Indices: 58817--58843 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
58807 ACAAGGAAAC
58817 AATTTTTTTTTCT
1 AATTTTTTTTTCT
58830 AATTTTTTTTTCT
1 AATTTTTTTTTCT
58843 A
1 A
58844 TTGCGAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (13 bp):
AATTTTTTTTTCT
Done.