Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006264.1 Hibiscus syriacus cultivar Beakdansim tig00014940_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: 90478
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2036 original size:42 final size:37
Alignment explanation
Indices: 1958--2051 Score: 181
Period size: 37 Copynumber: 2.6 Consensus size: 37
1948 TATTACTGAG
1958 CTCGACTCGAACTCGAAAACTATAAATCTAAGCTCGA
1 CTCGACTCGAACTCGAAAACTATAAATCTAAGCTCGA
1995 CTCGACTCGAACTCGAAAACTATAAATCTAAGCTCGA
1 CTCGACTCGAACTCGAAAACTATAAATCTAAGCTCGA
2032 CTCGACTCG-ACTCGAAAACT
1 CTCGACTCGAACTCGAAAACT
2052 CGCGAGCCTA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 11 0.19
37 46 0.81
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (37 bp):
CTCGACTCGAACTCGAAAACTATAAATCTAAGCTCGA
Found at i:4201 original size:14 final size:14
Alignment explanation
Indices: 4178--4285 Score: 78
Period size: 14 Copynumber: 7.8 Consensus size: 14
4168 TCATGTATAT
4178 AACT-TAAACCATA
1 AACTCTAAACCATA
*
4191 AACTCTAAACCCT-
1 AACTCTAAACCATA
*
4204 AACATATAAACCATA
1 AAC-TCTAAACCATA
* *
4219 AACTATAAACCCTA
1 AACTCTAAACCATA
* * *
4233 AACACTGAACCTTA
1 AACTCTAAACCATA
* *
4247 AA-TCTCATCACATA
1 AACTCTAAAC-CATA
*
4261 AACTCTAAACCCTA
1 AACTCTAAACCATA
*
4275 AACCCTAAACC
1 AACTCTAAACC
4286 TTATAACATA
Statistics
Matches: 74, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
13 11 0.15
14 55 0.74
15 8 0.11
ACGTcount: A:0.47, C:0.31, G:0.01, T:0.21
Consensus pattern (14 bp):
AACTCTAAACCATA
Found at i:4295 original size:35 final size:34
Alignment explanation
Indices: 4187--4296 Score: 96
Period size: 35 Copynumber: 3.1 Consensus size: 34
4177 TAACTTAAAC
* *
4187 CATAAACTCTAAACCCTAACATATAAACCATA-AA
1 CATAAACTCTAAACCCTAAC-CATAAACCTTATAA
* * * * * *
4221 CTATAAACCCTAAACACTGAACCTTAAATCTCATCA
1 C-ATAAACTCTAAACCCT-AACCATAAACCTTATAA
*
4257 CATAAACTCTAAACCCTAAACCCTAAACCTTATAA
1 CATAAACTCTAAACCCT-AACCATAAACCTTATAA
4292 CATAA
1 CATAA
4297 TTAGAAGGAA
Statistics
Matches: 58, Mismatches: 15, Indels: 5
0.74 0.19 0.06
Matches are distributed among these distances:
34 1 0.02
35 52 0.90
36 5 0.09
ACGTcount: A:0.47, C:0.29, G:0.01, T:0.23
Consensus pattern (34 bp):
CATAAACTCTAAACCCTAACCATAAACCTTATAA
Found at i:5890 original size:21 final size:21
Alignment explanation
Indices: 5864--5908 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
5854 GATTTCTGAG
*
5864 CAAGGGGAATCGATACCCATT
1 CAAGGGGAACCGATACCCATT
*
5885 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
5906 CAA
1 CAA
5909 ACGAACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:6609 original size:21 final size:22
Alignment explanation
Indices: 6580--6623 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
6570 GTTGTATGAT
6580 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
6601 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
6623 A
1 A
6624 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:7513 original size:149 final size:148
Alignment explanation
Indices: 7333--7782 Score: 850
Period size: 149 Copynumber: 3.0 Consensus size: 148
7323 GAGTCGAGGG
7333 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
7398 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACA-TATTA
7463 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGCAAT
7482 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
7547 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGAC--ATTAT
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATATTAT
7610 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
7628 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
7693 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATATGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACAT-ATTA
*
7758 TATGGCACTATGGTGCAAT
130 TATGGCACTACGGTGCAAT
7777 TCTACG
1 TCTACG
7783 GGGCACTTCG
Statistics
Matches: 296, Mismatches: 2, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
146 145 0.49
149 151 0.51
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (148 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATATTAT
ATGGCACTACGGTGCAAT
Found at i:7805 original size:23 final size:23
Alignment explanation
Indices: 7761--7805 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
7751 ATCATTATAT
*
7761 GGCACTATGGTGCAATTCTACGG
1 GGCACTATGGTGCAATTATACGG
*
7784 GGCACT-TCGGTGCATTTATACG
1 GGCACTAT-GGTGCAATTATACG
7806 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (23 bp):
GGCACTATGGTGCAATTATACGG
Found at i:11087 original size:21 final size:21
Alignment explanation
Indices: 11061--11105 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
11051 GATTTCTGGG
* *
11061 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
11082 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
11103 CAA
1 CAA
11106 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:11808 original size:21 final size:22
Alignment explanation
Indices: 11779--11822 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
11769 GTTGTATGAT
11779 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
11800 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
11822 A
1 A
11823 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:13000 original size:149 final size:149
Alignment explanation
Indices: 12537--12989 Score: 879
Period size: 149 Copynumber: 3.0 Consensus size: 149
12527 GAGTCGAGGG
12537 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
* *
12602 ACTTGATCCCTAGAATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATAATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
12667 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
12686 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
12751 ACTTGATCCCTAGCATATGTATATAATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATAATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
12816 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
12835 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
12900 ACTTGATCCCTAGCATATGTATATAATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATAATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
12965 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
12984 TCTACG
1 TCTACG
12990 GGGCACTTCG
Statistics
Matches: 301, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 301 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATAATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:13012 original size:23 final size:23
Alignment explanation
Indices: 12968--13012 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
12958 ATCATTATAT
*
12968 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
12991 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
13013 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:14065 original size:185 final size:184
Alignment explanation
Indices: 13770--14140 Score: 609
Period size: 185 Copynumber: 2.0 Consensus size: 184
13760 ATTAAATTTT
* * * *
13770 AAATTTTAAATATATTATATATAACATATGGACTCAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATACAACATATGGACTAAGCCCAAACAATTTAAAACCCAATTAATAA
13835 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATAT-AAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATGAAA-TT
*
13899 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTAATTAAA
130 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
* * *
13955 AAATATTAAATATATTATATACAACATTTGGGCTAAGCCCAAACAATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATACAACATATGGACTAAGCCCAAACAATTTAAAACCCAATTAATAA
* * * *
14020 TTTAAGATCTAATAACTTTTAAATCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATGAAATTT
14085 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
14139 AA
1 AA
14141 CATTTAATTT
Statistics
Matches: 173, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
184 15 0.09
185 155 0.90
186 3 0.02
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (184 bp):
AAATATTAAATATATTATATACAACATATGGACTAAGCCCAAACAATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATGAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
Found at i:14635 original size:22 final size:22
Alignment explanation
Indices: 14610--14683 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
14600 AATTTAAAAC
14610 AAATATT-TTATTTTAAATAAAT
1 AAATATTATT-TTTTAAATAAAT
* *
14632 AAAT-TTACTTTTTATAATAATT
1 AAATATTATTTTTTA-AATAAAT
* *
14654 TAATATTATTTTTAAATATAAAT
1 AAATATTATTTTTTAA-ATAAAT
14677 AAATATT
1 AAATATT
14684 TAATATCTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
21 7 0.17
22 15 0.37
23 19 0.46
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATATTATTTTTTAAATAAAT
Found at i:14671 original size:21 final size:21
Alignment explanation
Indices: 14610--14683 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 21
14600 AATTTAAAAC
*
14610 AAATATTTTATTTTAAATAAAT
1 AAATATTAT-TTTTAAATAAAT
*
14632 AAAT-TTACTTTTTATAATAATT
1 AAATATTA-TTTTTA-AATAAAT
*
14654 TAATATTATTTTTAAATATAAAT
1 AAATATTATTTTT-AA-ATAAAT
14677 AAATATT
1 AAATATT
14684 TAATATCTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
21 7 0.17
22 20 0.48
23 15 0.36
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATATTATTTTTAAATAAAT
Found at i:15326 original size:21 final size:19
Alignment explanation
Indices: 15300--15338 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
15290 TTTATTTATT
15300 ATTATTATTATAATAATAATA
1 ATTATTATTA-AA-AATAATA
15321 ATTATTATTAAAAATAAT
1 ATTATTATTAAAAATAAT
15339 TATAGGCCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 2 0.11
21 10 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTATTATTAAAAATAATA
Found at i:15338 original size:16 final size:17
Alignment explanation
Indices: 15303--15341 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
15293 ATTTATTATT
*
15303 ATTATTATAATAATAATA
1 ATTATTAT-ATAAAAATA
15321 ATTATTAT-TAAAAATA
1 ATTATTATATAAAAATA
15337 ATTAT
1 ATTAT
15342 AGGCCCAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
18 8 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTATTATATAAAAATA
Found at i:16977 original size:119 final size:119
Alignment explanation
Indices: 16838--17072 Score: 287
Period size: 120 Copynumber: 2.0 Consensus size: 119
16828 ATTTTAATCC
* * * *
16838 TGTTTTAATAATTATTTATTTTTCAATAT-TAAG-AAAGGGCAGTCTAAAAACAACTGGATGTCC
1 TGTTTTAATAATTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTAAAAACAACTAGAAGT-C
* *
16901 ATTTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAATT-ATATATTAAT
65 ATTTTCTGATATTTCTAAATAAATAAATATACTA-TTTATAAATTAATATATTAAT
* * * ** *
16956 TGTTTTAATTAATTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTC
1 TGTTTTAA-TAATTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTAAAAACAACTAGAAGTC
* * *
17021 ATTTTCTGATATTTCTAAATAAGTAAATATATTATTTATATATTAATATATT
65 ATTTTCTGATATTTCTAAATAAATAAATATACTATTTATAAATTAATATATT
17073 TTTTTAAATT
Statistics
Matches: 98, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
118 8 0.08
119 29 0.30
120 41 0.42
121 20 0.20
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (119 bp):
TGTTTTAATAATTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTAAAAACAACTAGAAGTCA
TTTTCTGATATTTCTAAATAAATAAATATACTATTTATAAATTAATATATTAAT
Found at i:19945 original size:17 final size:16
Alignment explanation
Indices: 19916--19951 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
19906 TACATTCATA
*
19916 TTTTTATATTTGCATT
1 TTTTTATAGTTGCATT
19932 TTTTTCATAGTTGCATT
1 TTTTT-ATAGTTGCATT
19949 TTT
1 TTT
19952 ATGTTCGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.17, C:0.08, G:0.08, T:0.67
Consensus pattern (16 bp):
TTTTTATAGTTGCATT
Found at i:23568 original size:21 final size:21
Alignment explanation
Indices: 23542--23586 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
23532 GATTTCTGGG
* *
23542 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
23563 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
23584 CAA
1 CAA
23587 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:24771 original size:31 final size:31
Alignment explanation
Indices: 24733--24810 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
24723 AGAGTCGAGG
*
24733 GTTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTTACCTAGGTTC-TTCGAGACATATGGACA
* *
24764 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTTCGAGACATATGGACA
* *
24795 GTTTACCGAGGATCTT
1 GTTTACCTAGGTTCTT
24811 TATGACCTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
31 39 0.95
32 2 0.05
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGAGACATATGGACA
Found at i:24885 original size:29 final size:30
Alignment explanation
Indices: 24783--24882 Score: 148
Period size: 30 Copynumber: 3.3 Consensus size: 30
24773 GGTTCTTCGG
*
24783 GACCTATGGACAGTTTACCGAGGATCTTTAT
1 GACCTCTGGACAG-TTACCGAGGATCTTTAT
24814 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
24844 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
24873 GACCTCTGGA
1 GACCTCTGGA
24883 TAGGTCTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
29 18 0.28
30 35 0.54
31 12 0.18
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:27581 original size:21 final size:21
Alignment explanation
Indices: 27555--27599 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
27545 GATTTCTGGG
*
27555 CAAGGGGAATCGATACCCATT
1 CAAGGGGAACCGATACCCATT
*
27576 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
27597 CAA
1 CAA
27600 ACGACAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:28782 original size:31 final size:31
Alignment explanation
Indices: 28744--28810 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
28734 AGAGTCGAGG
*
28744 GTTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTTACCTAGGTTC-TTCGAGACATATGGACA
* *
28775 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTTCGAGACATATGGACA
28806 GTTTA
1 GTTTA
28811 TCGAGGATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGAGACATATGGACA
Found at i:28829 original size:31 final size:31
Alignment explanation
Indices: 28769--28923 Score: 192
Period size: 30 Copynumber: 5.1 Consensus size: 31
28759 TCGAGACATA
* * *** *
28769 TGGACAGTTTACCTAGGTTCTTCGGGACCTA
1 TGGACAGTTTACCGAGGATCTTTATGACCTC
*
28800 TGGACAGTTTATCGAGGATCTTTATGACCTC
1 TGGACAGTTTACCGAGGATCTTTATGACCTC
28831 TGGACAG-TTACCGAGGATCTTTATGACCTC
1 TGGACAGTTTACCGAGGATCTTTATGACCTC
28861 TGGACAG-TTACCGAGGATCTTTATGACCTC
1 TGGACAGTTTACCGAGGATCTTTATGACCTC
* * *
28891 TGGATAG-TTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTTACCGAGGATCTTTATGACCTC
28920 TGGA
1 TGGA
28924 TAGGTCCTTC
Statistics
Matches: 113, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
29 18 0.16
30 64 0.57
31 31 0.27
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (31 bp):
TGGACAGTTTACCGAGGATCTTTATGACCTC
Found at i:28926 original size:29 final size:30
Alignment explanation
Indices: 28794--28923 Score: 199
Period size: 30 Copynumber: 4.3 Consensus size: 30
28784 GGTTCTTCGG
* *
28794 GACCTATGGACAGTTTATCGAGGATCTTTAT
1 GACCTCTGGACAG-TTACCGAGGATCTTTAT
28825 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
28855 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
28885 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
28914 GACCTCTGGA
1 GACCTCTGGA
28924 TAGGTCCTTC
Statistics
Matches: 94, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
29 18 0.19
30 64 0.68
31 12 0.13
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.32
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:29699 original size:1 final size:1
Alignment explanation
Indices: 29693--29760 Score: 55
Period size: 1 Copynumber: 68.0 Consensus size: 1
29683 ATTATACTTG
* * * * ** * * *
29693 AAAAAAAAGAAAAAAAAGAAAAAAAAAGAAAAAAGAGGAAAAAGAAAAAAAAGAAAAAAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29758 AAA
1 AAA
29761 GGGGAGAAAT
Statistics
Matches: 51, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (1 bp):
A
Found at i:29708 original size:10 final size:9
Alignment explanation
Indices: 29692--29760 Score: 95
Period size: 9 Copynumber: 7.7 Consensus size: 9
29682 TATTATACTT
29692 GAAAAAAAA
1 GAAAAAAAA
29701 GAAAAAAAA
1 GAAAAAAAA
29710 GAAAAAAAA
1 GAAAAAAAA
*
29719 -AGAAAAAA
1 GAAAAAAAA
**
29727 GAGGAAAAA
1 GAAAAAAAA
29736 GAAAAAAAA
1 GAAAAAAAA
29745 GAAAAAAAAA
1 G-AAAAAAAA
29755 GAAAAA
1 GAAAAA
29761 GGGGAGAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
8 7 0.13
9 38 0.70
10 9 0.17
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:31433 original size:17 final size:17
Alignment explanation
Indices: 31411--31443 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
31401 TTAGAAGATG
31411 AACTGCATGATCGTCTA
1 AACTGCATGATCGTCTA
31428 AACTGCATGATCGTCT
1 AACTGCATGATCGTCT
31444 TCATTAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (17 bp):
AACTGCATGATCGTCTA
Found at i:33494 original size:54 final size:54
Alignment explanation
Indices: 33430--33585 Score: 258
Period size: 54 Copynumber: 2.9 Consensus size: 54
33420 AGAAATATTG
* * ***
33430 GCAGAAGCCACAAAAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
1 GCAGAAGCCACAAGAAAGGATGAATGCACTGTCAAATGTTTTACGAACATCTGA
33484 GCAGAAGCCACAAGAAAGGATGAATGCACTGTCAAATGTTTTACGAACATCTGA
1 GCAGAAGCCACAAGAAAGGATGAATGCACTGTCAAATGTTTTACGAACATCTGA
*
33538 GCAGAAGCCACAAGTAAGGATGAATGCACTGTCAAATGTTTTACGAAC
1 GCAGAAGCCACAAGAAAGGATGAATGCACTGTCAAATGTTTTACGAAC
33586 CAGTGATTAT
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 96 1.00
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.22
Consensus pattern (54 bp):
GCAGAAGCCACAAGAAAGGATGAATGCACTGTCAAATGTTTTACGAACATCTGA
Found at i:34018 original size:22 final size:21
Alignment explanation
Indices: 33950--34029 Score: 61
Period size: 22 Copynumber: 3.7 Consensus size: 21
33940 TACATCTACA
*
33950 CTTTTTAAAGATGATAGATTTT
1 CTTTTCAAAGATGATAGA-TTT
** * * *
33972 CACTTCAGAGATGACAAAATTT
1 CTTTTCAAAGATGA-TAGATTT
*
33994 CTTTTTAAAGATGATAGATTCT
1 CTTTTCAAAGATGATAGATT-T
*
34016 CTTTTCAAGGATGA
1 CTTTTCAAAGATGA
34030 AAACTTTATG
Statistics
Matches: 42, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
21 4 0.10
22 36 0.86
23 2 0.05
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (21 bp):
CTTTTCAAAGATGATAGATTT
Found at i:34825 original size:167 final size:164
Alignment explanation
Indices: 34544--34870 Score: 512
Period size: 167 Copynumber: 2.0 Consensus size: 164
34534 CACAAGAATG
* *
34544 AACCTTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAACATAATGAGAAA
1 AACCTTATCTGGAGATTGGGGCATGTTACCCAATCAACAAGTTATTT-AAAAACATAATGAGAAA
* **
34609 ACGATTTCCATAGTTTCTCATTTTATCTTTTCTAAAATAAAATTGTTGAAAAGTAAGAAAACGAT
65 ACGATTTCCAAAGTTTCTCATTCAATCTTTTCTAAAATAAAATTGTTGAAAAGTAAGAAAACGAT
*
34674 TTTCTTAGTTTTTTTTACTTATTAAACTATTTCCAAC
130 TTTCTTAG-TTTTTTTACTTAGTAAAC-ATTTCCAAC
* * *
34711 AACCTTATCTGGATATTGGGGCATGTTATCCAATCAACAAGTTATCTT-GAAACATAATGAGAAA
1 AACCTTATCTGGAGATTGGGGCATGTTACCCAATCAACAAGTTAT-TTAAAAACATAATGAGAAA
*
34775 ACGATTTCCAAAGTTTCTCATTCAATCTTTTCTGAAAATGAAATTGTTGAAAAGTAAGAAAACGA
65 ACGATTTCCAAAGTTTCTCATTCAATCTTTTCT-AAAATAAAATTGTTGAAAAGTAAGAAAACGA
34840 TTTTCTTAGTTTTTTTACTTAGTAAACATTT
129 TTTTCTTAGTTTTTTTACTTAGTAAACATTT
34871 TCCCTCGAAA
Statistics
Matches: 148, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
165 4 0.03
166 62 0.42
167 80 0.54
168 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (164 bp):
AACCTTATCTGGAGATTGGGGCATGTTACCCAATCAACAAGTTATTTAAAAACATAATGAGAAAA
CGATTTCCAAAGTTTCTCATTCAATCTTTTCTAAAATAAAATTGTTGAAAAGTAAGAAAACGATT
TTCTTAGTTTTTTTACTTAGTAAACATTTCCAAC
Found at i:34955 original size:36 final size:36
Alignment explanation
Indices: 34915--35108 Score: 163
Period size: 36 Copynumber: 5.3 Consensus size: 36
34905 GTTTTTCTTA
* *
34915 AAACAAACTTTGTCTCGCTCGAGACAGTTTCACTCG
1 AAACAAAATTTGTCTCACTCGAGACAGTTTCACTCG
* * * ** ** **
34951 AAACAGCAATTTATCTCACTTGAGATTGTTTTTCTTA
1 AAACA-AAATTTGTCTCACTCGAGACAGTTTCACTCG
* *
34988 AAACAAACTTTGTCTCACTCGAGACAGTTTCCCTCG
1 AAACAAAATTTGTCTCACTCGAGACAGTTTCACTCG
* * ** ** **
35024 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTA
1 AAACAA-AATTTGTCTCACTCGAGACAGTTTCACTCG
*
35061 AAACAAAATTTGTCTCGCTCGAGACAGTTTCACTCG
1 AAACAAAATTTGTCTCACTCGAGACAGTTTCACTCG
35097 AAACATAAATTT
1 AAACA-AAATTT
35109 CCATCACTCG
Statistics
Matches: 116, Mismatches: 39, Indels: 5
0.73 0.24 0.03
Matches are distributed among these distances:
36 58 0.50
37 58 0.50
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.34
Consensus pattern (36 bp):
AAACAAAATTTGTCTCACTCGAGACAGTTTCACTCG
Found at i:34964 original size:73 final size:73
Alignment explanation
Indices: 34869--35101 Score: 412
Period size: 73 Copynumber: 3.2 Consensus size: 73
34859 TAGTAAACAT
* *
34869 TTTCCCTCGAAACATCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTGTCTCGCT
1 TTTCACTCGAAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTGTCTCGCT
34934 CGAGACAG
66 CGAGACAG
* *
34942 TTTCACTCGAAACAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTGTCTCACT
1 TTTCACTCGAAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTGTCTCGCT
35007 CGAGACAG
66 CGAGACAG
* *
35015 TTTCCCTCGAAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCT
1 TTTCACTCGAAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTGTCTCGCT
35080 CGAGACAG
66 CGAGACAG
35088 TTTCACTCGAAACA
1 TTTCACTCGAAACA
35102 TAAATTTCCA
Statistics
Matches: 152, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 152 1.00
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.36
Consensus pattern (73 bp):
TTTCACTCGAAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTGTCTCGCT
CGAGACAG
Found at i:35453 original size:113 final size:113
Alignment explanation
Indices: 35108--35440 Score: 612
Period size: 113 Copynumber: 2.9 Consensus size: 113
35098 AACATAAATT
*
35108 TCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
1 TCCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
*
35173 GAAGAAGAAGTTCATAATGAGAAGAGTTTGTTCAACCTTTTACTCAAA
66 GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTACTCAAA
35221 TCCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
1 TCCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
*
35286 GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAA
66 GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTACTCAAA
35334 TCCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
1 TCCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
* *
35399 GAAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCCTTTT
66 GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAA-CCTTTT
35441 CCAAATTACA
Statistics
Matches: 214, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
113 208 0.97
114 6 0.03
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.26
Consensus pattern (113 bp):
TCCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTACTCAAA
Found at i:35519 original size:226 final size:223
Alignment explanation
Indices: 35108--35520 Score: 555
Period size: 226 Copynumber: 1.8 Consensus size: 223
35098 AACATAAATT
35108 TCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
1 TCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
* ** * * *
35173 GAAGAAGAAGTTCATAATGAGAAGAGTTTGTTCAACCTTTTACTCAAATCCATCACTCGATGGAT
66 GAAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTCAAATACATCACTAGAAGGAT
* * *
35238 CAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
131 CAGATTTTCCAGAGAAAGTTCATAATGAGAAGAACTAATCT--ACAA-GAAGAAGAAGTTCATAA
35303 TGAGAAGAGCTTGTTCAACCTTTTGCTCAAA
193 TGAGAAGAGCTTGTTCAACCTTTTGCTCAAA
*
35334 TCCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
1 TCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
35399 GAAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCCTTTT-C-CAAATTACATCA-TAGAAGG
66 GAAAAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CCTTTTACTCAAA-TACATCACTAGAAGG
* * * *
35461 AT-ATATTATCATCCCCAGCGGAAAAGTTCATAATTAGAAGAACTAATCTCCAAAGAAGAA
129 ATCAGATT-T--T--CCAG-AG-AAAGTTCATAATGAGAAGAACTAATCTAC-AAGAAGAA
35521 ATTATTCAAC
Statistics
Matches: 163, Mismatches: 14, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
224 3 0.02
225 12 0.07
226 103 0.63
227 7 0.04
229 10 0.06
230 3 0.02
231 25 0.15
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (223 bp):
TCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
GAAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTCAAATACATCACTAGAAGGAT
CAGATTTTCCAGAGAAAGTTCATAATGAGAAGAACTAATCTACAAGAAGAAGAAGTTCATAATGA
GAAGAGCTTGTTCAACCTTTTGCTCAAA
Found at i:35673 original size:3 final size:3
Alignment explanation
Indices: 35665--35703 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
35655 CATTTTTTAT
* *
35665 TTA TTA TTA TTA TTA TTA TAA TAA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
35704 AAAATAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:37380 original size:119 final size:119
Alignment explanation
Indices: 37233--37467 Score: 278
Period size: 120 Copynumber: 2.0 Consensus size: 119
37223 ATTTTAATCC
* * * * * *
37233 TGTTTTAATATTTCTTTATTTTTCAATAT-TAAG-AAAGGGCAGTCTTAAAACAACTGGATGTCC
1 TGTTTTAATAATTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGT-C
* *
37296 ATTTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAATT-ATATATTAAT
65 ATTTTCTGATATTTCTAAATAAATAAATATACTA-TTTATAAATTAATATATTAAT
* * ** *
37351 TGTTTTAATTAATTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTC
1 TGTTTTAA-TAATTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
* * *
37416 ATTTTCTGATATTTCTAAATAAGTAAATATATTATTTATATATTAATATATT
65 ATTTTCTGATATTTCTAAATAAATAAATATACTATTTATAAATTAATATATT
37468 TTTTTAAATT
Statistics
Matches: 97, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
118 8 0.08
119 27 0.28
120 41 0.42
121 21 0.22
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (119 bp):
TGTTTTAATAATTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCA
TTTTCTGATATTTCTAAATAAATAAATATACTATTTATAAATTAATATATTAAT
Found at i:39039 original size:2 final size:2
Alignment explanation
Indices: 39034--39101 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
39024 ACACACACAC
39034 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39076 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
39102 CTTTTGGAAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45608 original size:15 final size:16
Alignment explanation
Indices: 45588--45619 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
45578 TAAATTAAAG
45588 AATTTTTAA-ATTTTA
1 AATTTTTAATATTTTA
45603 AATTTTTAATATTTTA
1 AATTTTTAATATTTTA
45619 A
1 A
45620 TATTATCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AATTTTTAATATTTTA
Found at i:46009 original size:2 final size:2
Alignment explanation
Indices: 46002--46026 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45992 ATCTTAACTC
46002 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
46027 ATTATACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46663 original size:13 final size:13
Alignment explanation
Indices: 46629--46666 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
46619 TATTAATTAA
46629 AATTAAATAATTT
1 AATTAAATAATTT
**
46642 AATCCAATAATTT
1 AATTAAATAATTT
46655 AATTAAATAATT
1 AATTAAATAATT
46667 ATATTTTGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (13 bp):
AATTAAATAATTT
Found at i:51710 original size:2 final size:2
Alignment explanation
Indices: 51705--51743 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
51695 GTGTGTGTAC
51705 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51744 CACATGGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:51807 original size:38 final size:38
Alignment explanation
Indices: 51765--51876 Score: 215
Period size: 38 Copynumber: 2.9 Consensus size: 38
51755 AGGTCATTAA
*
51765 TGATCGGTATATTAAAAAGTTTAGACAACAATATGCGT
1 TGATCGGTATATTAAAAAGTTTAGACCACAATATGCGT
51803 TGATCGGTATATTAAAAAGTTTAGACCACAATATGCGT
1 TGATCGGTATATTAAAAAGTTTAGACCACAATATGCGT
51841 TGATCGGTATATTAAAAAGTTTAGACCACAATATGC
1 TGATCGGTATATTAAAAAGTTTAGACCACAATATGC
51877 ATTAACTCTT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
38 73 1.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.31
Consensus pattern (38 bp):
TGATCGGTATATTAAAAAGTTTAGACCACAATATGCGT
Found at i:53671 original size:15 final size:15
Alignment explanation
Indices: 53651--53680 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
53641 TTCAATTGGC
53651 TCATTGCAAATCCTT
1 TCATTGCAAATCCTT
53666 TCATTGCAAATCCTT
1 TCATTGCAAATCCTT
53681 CAAAGTTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.40
Consensus pattern (15 bp):
TCATTGCAAATCCTT
Found at i:55543 original size:5 final size:5
Alignment explanation
Indices: 55527--55621 Score: 69
Period size: 5 Copynumber: 19.8 Consensus size: 5
55517 TCGTTCGACC
* * *
55527 TTAT- TTATA TGATA TGATA TTATA TTATA TTATA TTATA TTAT- GTA-A
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* *
55574 CTTAT- TTATA TTATA TAATA -TAT- TTATA TTTCATA TTATG TTAT-
1 -TTATA TTATA TTATA TTATA TTATA TTATA -TT-ATA TTATA TTATA
55618 TTAT
1 TTAT
55622 GTGATTTATG
Statistics
Matches: 75, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
4 19 0.25
5 49 0.65
6 4 0.05
7 3 0.04
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:55610 original size:48 final size:48
Alignment explanation
Indices: 55526--55617 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 48
55516 TTCGTTCGAC
*
55526 CTTATTTATATGATATGATATTATATTATATTATATTATATTATGTAA
1 CTTATTTATATGATATAATATTATATTATATTATATTATATTATGTAA
* *
55574 CTTATTTATATTATATAATA-TAT-TTATATTTCATATTATGTTAT
1 CTTATTTATATGATATAATATTATATTATA-TT-ATATTATATTAT
55618 TTATGTGATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
46 5 0.13
47 5 0.13
48 29 0.74
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (48 bp):
CTTATTTATATGATATAATATTATATTATATTATATTATATTATGTAA
Found at i:59261 original size:31 final size:31
Alignment explanation
Indices: 59223--59281 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
59213 CAGGGATCAT
*
59223 ATTGCAAAC-AGACTAAATGTTGGGGGACCAC
1 ATTGCAAACGA-ACTAAATGTTAGGGGACCAC
*
59254 ATTGCAAACGAATTAAATGTTAGGGGAC
1 ATTGCAAACGAACTAAATGTTAGGGGAC
59282 TATATTACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.22
Consensus pattern (31 bp):
ATTGCAAACGAACTAAATGTTAGGGGACCAC
Found at i:61027 original size:7 final size:7
Alignment explanation
Indices: 61017--61057 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
61007 ATTATAATTT
61017 TTAAATA
1 TTAAATA
61024 TTAAATA
1 TTAAATA
61031 TTAAATA
1 TTAAATA
61038 TTAAATA
1 TTAAATA
61045 TTAAATA
1 TTAAATA
61052 TTAAAT
1 TTAAAT
61058 TTATTAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TTAAATA
Found at i:61915 original size:118 final size:118
Alignment explanation
Indices: 61710--62015 Score: 505
Period size: 118 Copynumber: 2.6 Consensus size: 118
61700 GAACATTTCT
* * *
61710 CAAGATGTGAATCGAGTAACACCAAGTTCGGTTACT---ACAACTACAGTCTCACATAGCCTCTA
1 CAAGATGTGAATCGAGCAACACCAAGTTCGGTTACTACAACAACTACAGTCTCACACAGCCTCGA
* *
61772 TATTTTATCGCCGGGGCCGCCCAACTTACACATGTCCGGAAGCAGCAAAAGCC
66 TAGTTTATCGCCGAGGCCGCCCAACTTACACATGTCCGGAAGCAGCAAAAGCC
61825 CAAGATGTGAATCGAGCAACACCAAGTTCGGTTACTACAACAACTACAGTCTCACACAGCCTCGA
1 CAAGATGTGAATCGAGCAACACCAAGTTCGGTTACTACAACAACTACAGTCTCACACAGCCTCGA
* *
61890 TAGTTTATCGCCGAGGCTGCCCAACTTACACATGTCCGGAAGCAGCAAATGCC
66 TAGTTTATCGCCGAGGCCGCCCAACTTACACATGTCCGGAAGCAGCAAAAGCC
*
61943 CAAGATGTGAATCGAGCAACACCAAGTTCGGTTACTACAACAACTACAG--TCACACAGCTTCGA
1 CAAGATGTGAATCGAGCAACACCAAGTTCGGTTACTACAACAACTACAGTCTCACACAGCCTCGA
62006 TAGTTTATCG
66 TAGTTTATCG
62016 TCAACAACTA
Statistics
Matches: 180, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
115 35 0.19
116 23 0.13
118 122 0.68
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (118 bp):
CAAGATGTGAATCGAGCAACACCAAGTTCGGTTACTACAACAACTACAGTCTCACACAGCCTCGA
TAGTTTATCGCCGAGGCCGCCCAACTTACACATGTCCGGAAGCAGCAAAAGCC
Found at i:62030 original size:37 final size:38
Alignment explanation
Indices: 61980--62056 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 38
61970 TCGGTTACTA
61980 CAACAACTACAG-TCACACAGCTTCGATAGTTTATCGT
1 CAACAACTACAGCTCACACAGCTTCGATAGTTTATCGT
62017 CAACAACTACAGTCTCACACAGCTTCGATAGTTTATCGT
1 CAACAACTACAG-CTCACACAGCTTCGATAGTTTATCGT
62056 C
1 C
62057 GGGGTTGCCC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 12 0.32
39 26 0.68
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (38 bp):
CAACAACTACAGCTCACACAGCTTCGATAGTTTATCGT
Found at i:62148 original size:155 final size:155
Alignment explanation
Indices: 61862--62148 Score: 502
Period size: 155 Copynumber: 1.9 Consensus size: 155
61852 TCGGTTACTA
61862 CAACAACTACAGTCTCACACAGCCTCGATAGTTTATCGCCGAGGCTGCCCAACTTACACATGTCC
1 CAACAACTACAGTCTCACACAGCCTCGATAGTTTATCGCCGAGGCTGCCCAACTTACACATGTCC
61927 GGAAGCAGCAAATGCCCAAGATGTGAATCGAGCAACACCAAGTTCGGTTACTACAACAACTACAG
66 GGAAGCAGCAAATGCCCAAGATGTGAATCGAGCAACACCAAGTTCGGTTACTACAACAACTACAG
61992 TCACACAGCTTCGATAGTTTATCGT
131 TCACACAGCTTCGATAGTTTATCGT
* * * *
62017 CAACAACTACAGTCTCACACAGCTTCGATAGTTTATCGTCGGGGTTGCCCAACTTACACATGTCC
1 CAACAACTACAGTCTCACACAGCCTCGATAGTTTATCGCCGAGGCTGCCCAACTTACACATGTCC
* * * *
62082 GGAAGCAGCAAATGCCCAAGATGTGAATCGAGTAACACCAAGTTTGGTTACTGCAACAACTGCAG
66 GGAAGCAGCAAATGCCCAAGATGTGAATCGAGCAACACCAAGTTCGGTTACTACAACAACTACAG
62147 TC
131 TC
62149 TCTCACAGCC
Statistics
Matches: 124, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
155 124 1.00
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (155 bp):
CAACAACTACAGTCTCACACAGCCTCGATAGTTTATCGCCGAGGCTGCCCAACTTACACATGTCC
GGAAGCAGCAAATGCCCAAGATGTGAATCGAGCAACACCAAGTTCGGTTACTACAACAACTACAG
TCACACAGCTTCGATAGTTTATCGT
Found at i:64580 original size:21 final size:21
Alignment explanation
Indices: 64555--64613 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
64545 TATTAATGTT
*
64555 TTAAAATTAATAATTTAA-TCA
1 TTAAAATTAACAATTTAACT-A
64576 TTAAAATTAACAATTTAACTA
1 TTAAAATTAACAATTTAACTA
*
64597 TTAAAATTACCAATTTA
1 TTAAAATTAACAATTTA
64614 TAATAAATCG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 34 0.97
22 1 0.03
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAAAATTAACAATTTAACTA
Found at i:65240 original size:69 final size:66
Alignment explanation
Indices: 65159--65293 Score: 207
Period size: 66 Copynumber: 2.0 Consensus size: 66
65149 TCAAAACCAT
* *
65159 CCCCATCGCCATTTTTTCAATAATTTATATGTTGTCATGCTGTATGCGAACGAGGAAGTTGGAAA
1 CCCCATCGCCATTTTTTCAACAATTTATATG-T-T-ATGCTGTATGCGAACGAGGAAGTCGGAAA
65224 AGAG
63 AGAG
* *
65228 CCCCATCGCCATTTTTTCAACAATTTATATGTTATGTTGTATGCGAACGAGGATGTCGGAAAAGA
1 CCCCATCGCCATTTTTTCAACAATTTATATGTTATGCTGTATGCGAACGAGGAAGTCGGAAAAGA
65293 G
66 G
65294 TCATTCTGTC
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
66 30 0.48
67 1 0.02
68 1 0.02
69 30 0.48
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (66 bp):
CCCCATCGCCATTTTTTCAACAATTTATATGTTATGCTGTATGCGAACGAGGAAGTCGGAAAAGA
G
Found at i:66188 original size:118 final size:112
Alignment explanation
Indices: 65962--66188 Score: 296
Period size: 118 Copynumber: 2.0 Consensus size: 112
65952 AAAAGGACAA
*
65962 GTTTGAAATCTATGAATAATGACCATTTTATAACTTTTAATAGTATAGAGACTTAAAAAATAATA
1 GTTTGAAATCTATGAATAATGACCATTTTATAACTTTTAATAGTAGAGAGACTTAAAAAATAATA
* *
66027 CCATATATCTAGAGGACCATTTCTTTACTTTACCCAATTTTTTCCTG
66 CCATATATCTAGAGGACCATTTCTGTACTTTACCCAATATTTTCCTG
*
66074 GTTTGAAATCTATGAATAGTTGGATGGCCATTTTATAACTTTTAATAGTAGAGAGACTTAATAAA
1 GTTTGAAATCTATGAATA-----ATGACCATTTTATAACTTTTAATAGTAGAGAGACTTAA-AAA
* * * *
66139 ATAATATCATATAGT-T-GAAGGACTATTTGTGTACTTTACCCCATATTTTC
60 ATAATACCATATA-TCTAG-AGGACCATTTCTGTACTTTACCCAATATTTTC
66189 TACTTTGTAT
Statistics
Matches: 99, Mismatches: 8, Indels: 10
0.85 0.07 0.09
Matches are distributed among these distances:
112 18 0.18
117 37 0.37
118 43 0.43
119 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (112 bp):
GTTTGAAATCTATGAATAATGACCATTTTATAACTTTTAATAGTAGAGAGACTTAAAAAATAATA
CCATATATCTAGAGGACCATTTCTGTACTTTACCCAATATTTTCCTG
Found at i:66771 original size:16 final size:16
Alignment explanation
Indices: 66747--66792 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
66737 TCTAAATTTT
* *
66747 TTTTTGAGTTCAATCC
1 TTTTCGAGTTCAAGCC
66763 TTTTCGAGTTCAAGCC
1 TTTTCGAGTTCAAGCC
66779 TTTTCGAGTTCAAG
1 TTTTCGAGTTCAAG
66793 TTTCAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.43
Consensus pattern (16 bp):
TTTTCGAGTTCAAGCC
Found at i:71501 original size:29 final size:29
Alignment explanation
Indices: 71456--71537 Score: 105
Period size: 28 Copynumber: 2.9 Consensus size: 29
71446 TAACGACAAT
**
71456 GAGCCGGTGAGAACGGCAAATTTGAGGGA
1 GAGCCGGTGAGAACGGCAAATTTGAGCAA
**
71485 GAGCCGGTGAGTGCGGCAAA-TTGAGCAA
1 GAGCCGGTGAGAACGGCAAATTTGAGCAA
*
71513 TAGCCGGTGAGAACGGC-AATTTGAG
1 GAGCCGGTGAGAACGGCAAATTTGAG
71538 ACAGGTAAGG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
27 2 0.04
28 25 0.56
29 18 0.40
ACGTcount: A:0.29, C:0.16, G:0.39, T:0.16
Consensus pattern (29 bp):
GAGCCGGTGAGAACGGCAAATTTGAGCAA
Found at i:87669 original size:3 final size:3
Alignment explanation
Indices: 87661--87711 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
87651 TGCAAAAAGC
87661 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
87709 ACA
1 ACA
87712 TAATAATAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:87717 original size:3 final size:3
Alignment explanation
Indices: 87711--87836 Score: 197
Period size: 3 Copynumber: 43.3 Consensus size: 3
87701 CAACAACAAC
87711 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
87758 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
87805 ATA AT- ATA A-A ACA ACA ACA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
87837 GGGTAAAGTA
Statistics
Matches: 118, Mismatches: 1, Indels: 8
0.93 0.01 0.06
Matches are distributed among these distances:
2 8 0.07
3 110 0.93
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:90055 original size:17 final size:17
Alignment explanation
Indices: 90033--90067 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
90023 TGTAATGGGT
90033 AAATAATACTTGTGTAG
1 AAATAATACTTGTGTAG
90050 AAATAATACTTGTGTAG
1 AAATAATACTTGTGTAG
90067 A
1 A
90068 TCGTGATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (17 bp):
AAATAATACTTGTGTAG
Done.