Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008029.1 Hibiscus syriacus cultivar Beakdansim tig00110505_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: 3983240
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 18
Found at i:4111 original size:9 final size:9
Alignment explanation
Indices: 4097--4125 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
4087 AGCCAAAGCA
4097 AAGAAAATG
1 AAGAAAATG
4106 AAGAAAATG
1 AAGAAAATG
4115 AAGAAAATG
1 AAGAAAATG
4124 AA
1 AA
4126 AAGAAGCTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.21, T:0.10
Consensus pattern (9 bp):
AAGAAAATG
Found at i:8753 original size:23 final size:23
Alignment explanation
Indices: 8726--8797 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
8716 GAATATCTTC
8726 TCATTTTCTACTATTAATCTCAG
1 TCATTTTCTACTATTAATCTCAG
* *
8749 TCATTTAT-T-TTAAT-ATCTTC--
1 TCATTT-TCTACTATTAATC-TCAG
8769 TCATTTTCTACTATTAATCTCAG
1 TCATTTTCTACTATTAATCTCAG
8792 TCATTT
1 TCATTT
8798 ATTTTTACTC
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
19 1 0.03
20 7 0.18
21 8 0.21
22 8 0.21
23 13 0.34
24 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (23 bp):
TCATTTTCTACTATTAATCTCAG
Found at i:8778 original size:43 final size:43
Alignment explanation
Indices: 8717--8802 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
8707 TTCCCAAGTG
8717 AATATCTTCTCATTTTCTACTATTAATCTCAGTCATTTATTTT
1 AATATCTTCTCATTTTCTACTATTAATCTCAGTCATTTATTTT
8760 AATATCTTCTCATTTTCTACTATTAATCTCAGTCATTTATTTT
1 AATATCTTCTCATTTTCTACTATTAATCTCAGTCATTTATTTT
8803 TACTCATTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.26, C:0.19, G:0.02, T:0.53
Consensus pattern (43 bp):
AATATCTTCTCATTTTCTACTATTAATCTCAGTCATTTATTTT
Found at i:8785 original size:24 final size:24
Alignment explanation
Indices: 8717--8786 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
8707 TTCCCAAGTG
8717 AATATCTTCTCATTTTCTACTATT
1 AATATCTTCTCATTTTCTACTATT
* ** *
8741 AATCTC-AGTCA--TT-TA-TTTT
1 AATATCTTCTCATTTTCTACTATT
8760 AATATCTTCTCATTTTCTACTATT
1 AATATCTTCTCATTTTCTACTATT
8784 AAT
1 AAT
8787 CTCAGTCATT
Statistics
Matches: 33, Mismatches: 8, Indels: 10
0.65 0.16 0.20
Matches are distributed among these distances:
19 8 0.24
20 5 0.15
21 2 0.06
22 2 0.06
23 5 0.15
24 11 0.33
ACGTcount: A:0.27, C:0.19, G:0.01, T:0.53
Consensus pattern (24 bp):
AATATCTTCTCATTTTCTACTATT
Found at i:12802 original size:13 final size:12
Alignment explanation
Indices: 12772--12805 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12762 TTTATGTTTT
*
12772 ATTTTTTAATTA
1 ATTTTTTAAATA
12784 ATTTTTTAAATA
1 ATTTTTTAAATA
*
12796 ATATTTTAAA
1 ATTTTTTAAA
12806 AATAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTTTTTAAATA
Found at i:14888 original size:42 final size:43
Alignment explanation
Indices: 14829--14922 Score: 154
Period size: 42 Copynumber: 2.2 Consensus size: 43
14819 ATGTAGCATT
14829 TGGCCTGGGAGTTTGATTCAGCAATCC-TTGTTGCACAGCCTG
1 TGGCCTGGGAGTTTGATTCAGCAATCCTTTGTTGCACAGCCTG
*
14871 TGGCCTGGGAGTTTGATTCAGTAATCCTTGTTGTTGCACAGCCTG
1 TGGCCTGGGAGTTTGATTCAGCAATCC-T-TTGTTGCACAGCCTG
14916 TGGCCTG
1 TGGCCTG
14923 TACGTACAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
42 26 0.54
45 22 0.46
ACGTcount: A:0.15, C:0.22, G:0.30, T:0.33
Consensus pattern (43 bp):
TGGCCTGGGAGTTTGATTCAGCAATCCTTTGTTGCACAGCCTG
Found at i:15036 original size:57 final size:57
Alignment explanation
Indices: 14948--15062 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 57
14938 ATTATAAATC
* *
14948 AAATACCAAGAGGAATATAATTTATTTAAGTATTTAATGCGTTTCCTTAATGGTTTG
1 AAATACCAAAAGGAATAGAATTTATTTAAGTATTTAATGCGTTTCCTTAATGGTTTG
*
15005 AAATACCAAAAGGAATAGAATTTATTTAAGTATTTAATGTGTTTCCTTAATGGTTTG
1 AAATACCAAAAGGAATAGAATTTATTTAAGTATTTAATGCGTTTCCTTAATGGTTTG
15062 A
1 A
15063 TGAGATAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.40
Consensus pattern (57 bp):
AAATACCAAAAGGAATAGAATTTATTTAAGTATTTAATGCGTTTCCTTAATGGTTTG
Found at i:16985 original size:14 final size:14
Alignment explanation
Indices: 16966--16993 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16956 CCGAGAACAT
16966 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
16980 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
16994 GGGCAACCGA
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:0.43, G:0.29, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:16995 original size:10 final size:10
Alignment explanation
Indices: 16943--16979 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
16933 ACACGTTGGG
16943 CATCCGAGGC
1 CATCCGAGGC
**
16953 CATCCGAGAA
1 CATCCGAGGC
16963 CATCCGAGGC
1 CATCCGAGGC
16973 CATCCGA
1 CATCCGA
16980 CCGAGGCCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.27, C:0.38, G:0.24, T:0.11
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:17003 original size:24 final size:24
Alignment explanation
Indices: 16963--17008 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
16953 CATCCGAGAA
*
16963 CATCCGAGGCCATCCGACCGAGGC
1 CATCCGAGGCCAACCGACCGAGGC
* *
16987 CATCCGAGGGCAACCGAGCGAG
1 CATCCGAGGCCAACCGACCGAG
17009 CTATGCGAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.37, G:0.33, T:0.07
Consensus pattern (24 bp):
CATCCGAGGCCAACCGACCGAGGC
Found at i:17078 original size:29 final size:29
Alignment explanation
Indices: 17045--17219 Score: 215
Period size: 29 Copynumber: 5.9 Consensus size: 29
17035 GAGCGAGGGT
17045 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
*
17074 AGGTCGCCCGGAGGGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
* * * **
17103 AAGTCGTCCGGAGGGCATGGCGACCTATGTGGGT
1 AGGTCGCCCGGAGTGCATGGCGACCTA-----CA
* *
17137 AGGTCGCCCTGAGTACATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
*
17166 AGATCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
*
17195 AGGTCGCCCGGAGTGCCTGGCGACC
1 AGGTCGCCCGGAGTGCATGGCGACC
17220 AACGGCCAAC
Statistics
Matches: 124, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
29 102 0.82
34 22 0.18
ACGTcount: A:0.20, C:0.30, G:0.35, T:0.15
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:17156 original size:92 final size:92
Alignment explanation
Indices: 17041--17219 Score: 286
Period size: 92 Copynumber: 1.9 Consensus size: 92
17031 AGCCGAGCGA
* *
17041 GGGTAGGTCGCCCGGAGTGCATGGCGACCTACAAGGTCGCCCGGAGGGCATGGCGACCTACAAAG
1 GGGTAGGTCGCCCGGAGTACATGGCGACCTACAAGATCGCCCGGAGGGCATGGCGACCTACAAAG
*
17106 TCGTCCGGAGGGCATGGCGACCTATGT
66 TCGCCCGGAGGGCATGGCGACCTATGT
* * *
17133 GGGTAGGTCGCCCTGAGTACATGGCGACCTACAAGATCGCCCGGAGTGCATGGCGACCTACAAGG
1 GGGTAGGTCGCCCGGAGTACATGGCGACCTACAAGATCGCCCGGAGGGCATGGCGACCTACAAAG
* *
17198 TCGCCCGGAGTGCCTGGCGACC
66 TCGCCCGGAGGGCATGGCGACC
17220 AACGGCCAAC
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
92 79 1.00
ACGTcount: A:0.20, C:0.29, G:0.36, T:0.15
Consensus pattern (92 bp):
GGGTAGGTCGCCCGGAGTACATGGCGACCTACAAGATCGCCCGGAGGGCATGGCGACCTACAAAG
TCGCCCGGAGGGCATGGCGACCTATGT
Found at i:17161 original size:63 final size:63
Alignment explanation
Indices: 17074--17192 Score: 177
Period size: 63 Copynumber: 1.9 Consensus size: 63
17064 GCGACCTACA
* *
17074 AGGTCGCCCGGAGGGCATGGCGACCTACAA-AGTCGTCCGGAGGGCATGGCGACCTATGTGGGT
1 AGGTCGCCCGGAGGACATGGCGACCTACAAGA-TCGCCCGGAGGGCATGGCGACCTATGTGGGT
* * *
17137 AGGTCGCCCTGAGTACATGGCGACCTACAAGATCGCCCGGAGTGCATGGCGACCTA
1 AGGTCGCCCGGAGGACATGGCGACCTACAAGATCGCCCGGAGGGCATGGCGACCTA
17193 CAAGGTCGCC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
63 49 0.98
64 1 0.02
ACGTcount: A:0.21, C:0.28, G:0.35, T:0.16
Consensus pattern (63 bp):
AGGTCGCCCGGAGGACATGGCGACCTACAAGATCGCCCGGAGGGCATGGCGACCTATGTGGGT
Found at i:21645 original size:2 final size:2
Alignment explanation
Indices: 21638--21667 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21628 TTACATTATG
21638 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
21668 ACAGTTAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 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:23051 original size:20 final size:20
Alignment explanation
Indices: 23022--23059 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
23012 TTTCAAAGTG
23022 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
23042 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
23060 TAATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:30650 original size:21 final size:21
Alignment explanation
Indices: 30608--30651 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
30598 ACCCCGAGAG
* *
30608 CTAGTTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
30629 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
30650 CT
1 CT
30652 CCTCCTCTGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:31609 original size:20 final size:20
Alignment explanation
Indices: 31580--31617 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31570 TTTCAAAGTG
31580 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
* *
31600 ATGCATCGATGTACCAAT
1 ATGCACCGATGCACCAAT
31618 TAATTTTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:31693 original size:91 final size:91
Alignment explanation
Indices: 31578--31751 Score: 219
Period size: 91 Copynumber: 1.9 Consensus size: 91
31568 TTTTTCAAAG
* * * *
31578 TGATGCACCGATGCACCAATCCATGCATCGATGTAC-CAATTAATTTTTC-AAACATCAAATTCA
1 TGATGCACCGATGCACCAAACCATGCATCGATGCACTC-A-GAATTTTTCAAAACATCAAATGCA
*
31641 TTTTATGCATCGATGCACTCAATGCATT
64 TTTCATGCATCGATGCACTCAATGCATT
* ** *
31669 TGATGCATCGATGCA-CAAGACCATGCATCGATGCACTCAGGCTTTTTCAAAACATCGAATGCAT
1 TGATGCACCGATGCACCAA-ACCATGCATCGATGCACTCAGAATTTTTCAAAACATCAAATGCAT
31733 TTCATGCATCGATGCACTC
65 TTCATGCATCGATGCACTC
31752 TTAGTGCACC
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
90 9 0.13
91 61 0.86
92 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.29
Consensus pattern (91 bp):
TGATGCACCGATGCACCAAACCATGCATCGATGCACTCAGAATTTTTCAAAACATCAAATGCATT
TCATGCATCGATGCACTCAATGCATT
Found at i:33198 original size:21 final size:22
Alignment explanation
Indices: 33160--33208 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
33150 GTCCTTCGGG
*
33160 ACATATATGTAATCCTTGGGA-
1 ACATATATGTAATCCTTGCGAC
*
33181 ACATATATG-AGATTCTTGCGAC
1 ACATATATGTA-ATCCTTGCGAC
33203 ACATAT
1 ACATAT
33209 TTGGTCCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.71
22 6 0.25
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (22 bp):
ACATATATGTAATCCTTGCGAC
Found at i:48681 original size:24 final size:25
Alignment explanation
Indices: 48641--48707 Score: 109
Period size: 25 Copynumber: 2.7 Consensus size: 25
48631 TCAAACCACT
48641 AAAAACATACTGTTTTTCTGCAGAA
1 AAAAACATACTGTTTTTCTGCAGAA
48666 AAAAACATACTGTTTTTCTGCAGAA
1 AAAAACATACTGTTTTTCTGCAGAA
*
48691 AAAATCAT-CTGGTTTTT
1 AAAAACATACT-GTTTTT
48708 TGGTAGTTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
24 2 0.05
25 38 0.95
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (25 bp):
AAAAACATACTGTTTTTCTGCAGAA
Found at i:50326 original size:22 final size:22
Alignment explanation
Indices: 50298--50341 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
50288 CATACTCATC
50298 AACTACTAACTTCATCATTCAA
1 AACTACTAACTTCATCATTCAA
50320 AACTACTAACTTCATCATTCAA
1 AACTACTAACTTCATCATTCAA
50342 CATTCTCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.27, G:0.00, T:0.32
Consensus pattern (22 bp):
AACTACTAACTTCATCATTCAA
Found at i:55207 original size:20 final size:20
Alignment explanation
Indices: 55182--55229 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
55172 GCAAGACTTG
55182 TTGTTTCAACAACAAGAAGT
1 TTGTTTCAACAACAAGAAGT
*
55202 TTGTTTCCACAACAAGAAGT
1 TTGTTTCAACAACAAGAAGT
55222 TTGTTTCA
1 TTGTTTCA
55230 TCGAGCACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (20 bp):
TTGTTTCAACAACAAGAAGT
Found at i:55905 original size:18 final size:18
Alignment explanation
Indices: 55873--55907 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55863 TTAGCAATCT
*
55873 TCAAAAACATGACTCTGG
1 TCAAAAACATAACTCTGG
*
55891 TCAAAAACCTAACTCTG
1 TCAAAAACATAACTCTG
55908 TTCGGTCCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.23
Consensus pattern (18 bp):
TCAAAAACATAACTCTGG
Found at i:56675 original size:17 final size:17
Alignment explanation
Indices: 56653--56691 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
56643 AAAGCATTTA
56653 GTCCAGTGGCTTGGGTG
1 GTCCAGTGGCTTGGGTG
56670 GTCCAGTGGCTTGGGTG
1 GTCCAGTGGCTTGGGTG
*
56687 CTCCA
1 GTCCA
56692 TTTCTATCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.08, C:0.23, G:0.41, T:0.28
Consensus pattern (17 bp):
GTCCAGTGGCTTGGGTG
Found at i:68825 original size:15 final size:15
Alignment explanation
Indices: 68805--68835 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
68795 CAACAGATAG
68805 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
68820 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
68835 A
1 A
68836 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:76417 original size:23 final size:23
Alignment explanation
Indices: 76378--76421 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
76368 ACTCTTTTTT
*
76378 TCTTTTTTCTTATATCACTGTTAA
1 TCTTTTTTCTTACATCA-TGTTAA
76402 TCTTTTTTCTT-CATCATGTT
1 TCTTTTTTCTTACATCATGTT
76422 TATAACAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 4 0.21
24 11 0.58
ACGTcount: A:0.16, C:0.18, G:0.05, T:0.61
Consensus pattern (23 bp):
TCTTTTTTCTTACATCATGTTAA
Found at i:77409 original size:22 final size:22
Alignment explanation
Indices: 77381--77493 Score: 103
Period size: 22 Copynumber: 5.4 Consensus size: 22
77371 TTGCATTTCG
77381 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
77403 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
* * **
77422 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
77441 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
77463 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
77485 CGTTGCGAT
1 CGTTGCGAT
77494 TTTCCAAATT
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 29 0.37
20 5 0.06
21 5 0.06
22 39 0.50
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:77426 original size:19 final size:19
Alignment explanation
Indices: 77402--77449 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
77392 TCTACAGTTG
77402 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
77421 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
77440 TCGTTGCGAT
1 TCGTTGCGAT
77450 AGTCTACAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:79834 original size:60 final size:58
Alignment explanation
Indices: 79770--79884 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 58
79760 TCAAATTGGA
* * *
79770 CCTTAAACTTTTAAATACTCTAATTTCATCCCCAAACTATTGTACTCATTTTAAATTATT
1 CCTTAAACTTTTAAACACTCCAATTTCATCCCCAAACTA-TG-ACTCATTCTAAATTATT
* * **
79830 CCTTAAACTTTTGAACATTCCAATTTCATCCTTAAACTATGACTCATTCTAAATT
1 CCTTAAACTTTTAAACACTCCAATTTCATCCCCAAACTATGACTCATTCTAAATT
79885 GGTCCCCAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
58 13 0.27
59 2 0.04
60 33 0.69
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.42
Consensus pattern (58 bp):
CCTTAAACTTTTAAACACTCCAATTTCATCCCCAAACTATGACTCATTCTAAATTATT
Found at i:80622 original size:26 final size:25
Alignment explanation
Indices: 80593--80679 Score: 59
Period size: 26 Copynumber: 3.2 Consensus size: 25
80583 TTTTAAGTTA
80593 TTTCTCGTCCTTGCTTTGCTAAGCTT
1 TTTCTC-TCCTTGCTTTGCTAAGCTT
*
80619 TTTCAT-TCTCTAATAGCTTTGCTAAGCTA
1 TTTC-TCTC-CT--T-GCTTTGCTAAGCTT
* * * *
80648 TTTCTCATTCTGGCTTTTCTAAGCCT
1 TTTCTC-TCCTTGCTTTGCTAAGCTT
80674 TTTCTC
1 TTTCTC
80680 ATATTCCTTC
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
25 2 0.04
26 23 0.48
27 1 0.02
28 2 0.04
29 19 0.40
30 1 0.02
ACGTcount: A:0.14, C:0.25, G:0.11, T:0.49
Consensus pattern (25 bp):
TTTCTCTCCTTGCTTTGCTAAGCTT
Found at i:81787 original size:29 final size:29
Alignment explanation
Indices: 81724--81779 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
81714 CTTTACCTTT
* *
81724 TCTCTCATAGCTTTTCTAAGCTTTTTCAC
1 TCTCTAATAGCTTTGCTAAGCTTTTTCAC
*
81753 TCTCTAATAGCTTTGCTAAGCTATTTC
1 TCTCTAATAGCTTTGCTAAGCTTTTTC
81780 TCATTCTAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.20, C:0.25, G:0.09, T:0.46
Consensus pattern (29 bp):
TCTCTAATAGCTTTGCTAAGCTTTTTCAC
Found at i:81797 original size:26 final size:26
Alignment explanation
Indices: 81760--81809 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
81750 CACTCTCTAA
81760 TAGCTTTGCTAAGCTATTTCTCATTC
1 TAGCTTTGCTAAGCTATTTCTCATTC
* * *
81786 TAGCTTTTCTAAGTTTTTTCTCAT
1 TAGCTTTGCTAAGCTATTTCTCAT
81810 ATTCCTTCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.18, C:0.20, G:0.10, T:0.52
Consensus pattern (26 bp):
TAGCTTTGCTAAGCTATTTCTCATTC
Found at i:83609 original size:15 final size:15
Alignment explanation
Indices: 83591--83622 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
83581 GGGAATGTTA
83591 TGGCAAACTTTCATC
1 TGGCAAACTTTCATC
83606 TGGCAAACTTTCATC
1 TGGCAAACTTTCATC
83621 TG
1 TG
83623 ACATTAGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (15 bp):
TGGCAAACTTTCATC
Found at i:90537 original size:24 final size:24
Alignment explanation
Indices: 90461--90537 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 24
90451 TATCCTAAGT
*
90461 TTAAAAATATATTTTTTATTCAATTTA
1 TTAAAAATATA--TTTTATTC-TTTTA
*
90488 TT--AAATATTTTTTATT-TTTTA
1 TTAAAAATATATTTTATTCTTTTA
90509 TTTAAAAATATATTTTATTCTTTTA
1 -TTAAAAATATATTTTATTCTTTTA
90534 TTAA
1 TTAA
90538 CTTAAAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
21 4 0.09
22 2 0.05
23 7 0.16
24 17 0.40
25 11 0.26
27 2 0.05
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (24 bp):
TTAAAAATATATTTTATTCTTTTA
Found at i:90548 original size:30 final size:30
Alignment explanation
Indices: 90512--90581 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
90502 TTTTTTATTT
* *
90512 AAAAATATATTTTATTCTTTTATTAACTTA
1 AAAAATATATTTTATTATTATATTAACTTA
* * *
90542 AAAAATATATTTTGTTATTATCTTAACTTT
1 AAAAATATATTTTATTATTATATTAACTTA
*
90572 AAATATATAT
1 AAAAATATAT
90582 ATATATATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.51
Consensus pattern (30 bp):
AAAAATATATTTTATTATTATATTAACTTA
Found at i:90581 original size:2 final size:2
Alignment explanation
Indices: 90574--90599 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
90564 TTAACTTTAA
90574 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
90600 TATTAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112356 original size:9 final size:9
Alignment explanation
Indices: 112344--112400 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 9
112334 TATTATTTTA
112344 TATTTAATT
1 TATTTAATT
*
112353 TATTTAA-G
1 TATTTAATT
112361 TATTTAATT
1 TATTTAATT
112370 TATTTAA--
1 TATTTAATT
* *
112377 TATTTTACT
1 TATTTAATT
112386 TATTTAATT
1 TATTTAATT
*
112395 TTTTTA
1 TATTTA
112401 CAGATATAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
7 6 0.15
8 7 0.18
9 26 0.67
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TATTTAATT
Found at i:112366 original size:17 final size:16
Alignment explanation
Indices: 112336--112393 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 16
112326 TATATTTTTA
*
112336 TTATTTTATATTTAAT
1 TTATTTAATATTTAAT
112352 TTATTTAAGTATTTAAT
1 TTATTTAA-TATTTAAT
* *
112369 TTATTTAATATTTTAC
1 TTATTTAATATTTAAT
112385 TTATTTAAT
1 TTATTTAAT
112394 TTTTTTACAG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 22 0.58
17 16 0.42
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (16 bp):
TTATTTAATATTTAAT
Found at i:112388 original size:16 final size:16
Alignment explanation
Indices: 112331--112397 Score: 75
Period size: 16 Copynumber: 4.2 Consensus size: 16
112321 TATTCTATAT
*
112331 TTTTA-TTATTTTATA
1 TTTTATTTATTTAATA
*
112346 TTTAATTTATTTAAGTA
1 TTTTATTTATTTAA-TA
*
112363 TTTAATTTATTTAATA
1 TTTTATTTATTTAATA
*
112379 TTTTACTTATTTAAT-
1 TTTTATTTATTTAATA
112394 TTTT
1 TTTT
112398 TTACAGATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
15 8 0.17
16 22 0.48
17 16 0.35
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (16 bp):
TTTTATTTATTTAATA
Found at i:118233 original size:19 final size:19
Alignment explanation
Indices: 118171--118246 Score: 107
Period size: 20 Copynumber: 3.9 Consensus size: 19
118161 TTACACATTC
*
118171 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACG-GA
*
118191 ATTTGACTATCGCAACATGA
1 ATTTGACTATCGCAAC-GGA
*
118211 ATTTGATTATCGCAACGGA
1 ATTTGACTATCGCAACGGA
118230 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
118247 AGAAAATCGC
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
19 18 0.36
20 32 0.64
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (19 bp):
ATTTGACTATCGCAACGGA
Found at i:118287 original size:20 final size:20
Alignment explanation
Indices: 118178--118287 Score: 90
Period size: 20 Copynumber: 5.8 Consensus size: 20
118168 TTCATTTGAA
*
118178 TATCGCAACGCGAATTTGAC
1 TATCGCAACGCGAATTAGAC
** * *
118198 TATCGCAACATGAATTTGAT
1 TATCGCAACGCGAATTAGAC
*
118218 TATCGCAACG-GAATTTGAC
1 TATCGCAACGCGAATTAGAC
*
118237 TATCGCAACGAG-A--A-A-
1 TATCGCAACGCGAATTAGAC
* *
118252 -ATCGCAAAGCGTATTAGAC
1 TATCGCAACGCGAATTAGAC
118271 TATCGCAACGCGAATTA
1 TATCGCAACGCGAATTA
118288 ACTTTCGCGT
Statistics
Matches: 73, Mismatches: 10, Indels: 14
0.75 0.10 0.14
Matches are distributed among these distances:
14 9 0.12
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 19 0.26
20 41 0.56
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (20 bp):
TATCGCAACGCGAATTAGAC
Found at i:118320 original size:20 final size:20
Alignment explanation
Indices: 118297--118348 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
118287 AACTTTCGCG
*
118297 TTGCGATTTTGGCTTTCACA
1 TTGCGATTTTGACTTTCACA
**
118317 TTGCGATTTTGACTTTCGTA
1 TTGCGATTTTGACTTTCACA
118337 TTGCGATTTTGA
1 TTGCGATTTTGA
118349 GTTTAGCGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.48
Consensus pattern (20 bp):
TTGCGATTTTGACTTTCACA
Found at i:119926 original size:21 final size:21
Alignment explanation
Indices: 119902--120004 Score: 109
Period size: 21 Copynumber: 4.9 Consensus size: 21
119892 GTGGGAGAGA
*
119902 CCTCTTCAACGATGACAGGGG
1 CCTCTTGAACGATGACAGGGG
**
119923 CCTCTTGAACGATGGGAGGGG
1 CCTCTTGAACGATGACAGGGG
* ** *
119944 ACTCTTGAGGGATGATAGGGG
1 CCTCTTGAACGATGACAGGGG
* *
119965 CCTCTTGAACGAT-AGGAGAGG
1 CCTCTTGAACGATGA-CAGGGG
119986 CCTCTTGAACGATGACAGG
1 CCTCTTGAACGATGACAGG
120005 TGAGTTGGTT
Statistics
Matches: 65, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
20 1 0.02
21 63 0.97
22 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.35, T:0.20
Consensus pattern (21 bp):
CCTCTTGAACGATGACAGGGG
Found at i:119949 original size:42 final size:42
Alignment explanation
Indices: 119895--120004 Score: 141
Period size: 42 Copynumber: 2.6 Consensus size: 42
119885 TTGAATGGTG
* *
119895 GGAGA-GACCTCTTCAACGATGACAGGGGCCTCTTGAACGATG
1 GGAGAGGA-CTCTTGAACGATGACAGGGGCCTCTTGAACGATA
* ** *
119937 GGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATA
1 GGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATA
*
119979 GGAGAGGCCTCTTGAACGATGACAGG
1 GGAGAGGACTCTTGAACGATGACAGG
120005 TGAGTTGGTT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 54 0.96
43 2 0.04
ACGTcount: A:0.25, C:0.19, G:0.36, T:0.19
Consensus pattern (42 bp):
GGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATA
Found at i:120511 original size:20 final size:20
Alignment explanation
Indices: 120486--120536 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
120476 TGAAACTTAA
*
120486 AATCGCAATGCAAAAATGAC
1 AATCGCAACGCAAAAATGAC
**
120506 AATCGCAACGCGGAAATGAC
1 AATCGCAACGCAAAAATGAC
*
120526 TATCGCAACGC
1 AATCGCAACGC
120537 GAATTTAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.41, C:0.25, G:0.20, T:0.14
Consensus pattern (20 bp):
AATCGCAACGCAAAAATGAC
Found at i:120537 original size:20 final size:20
Alignment explanation
Indices: 120499--120537 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
120489 CGCAATGCAA
120499 AAATGACAATCGCAACGCGG
1 AAATGACAATCGCAACGCGG
*
120519 AAATGACTATCGCAACGCG
1 AAATGACAATCGCAACGCG
120538 AATTTAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.26, G:0.23, T:0.13
Consensus pattern (20 bp):
AAATGACAATCGCAACGCGG
Found at i:120547 original size:20 final size:19
Alignment explanation
Indices: 120507--120579 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
120497 AAAAATGACA
*
120507 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATAACT
*
120527 ATCGCAACGCGAATTTAACT
1 ATCGCAACGCGAA-ATAACT
* * **
120547 ATCGTAATGCGAAATAAAA
1 ATCGCAACGCGAAATAACT
120566 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
120580 CTAAATTCGC
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
19 18 0.42
20 25 0.58
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (19 bp):
ATCGCAACGCGAAATAACT
Found at i:120614 original size:20 final size:20
Alignment explanation
Indices: 120585--120622 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
120575 CGAAACTAAA
*
120585 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCATT
120605 TTCGCATTGCGATTTTCA
1 TTCGCATTGCGATTTTCA
120623 CGTTGCGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.47
Consensus pattern (20 bp):
TTCGCATTGCGATTTTCATT
Found at i:120646 original size:33 final size:34
Alignment explanation
Indices: 120589--120664 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
120579 ACTAAATTCG
*
120589 CGTTGCGATTTTCATTTTCGCATTGCGATTTTCA
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
* *
120623 CGTTGCGATTTTTA-TTTCGCATTGCGATTATCC
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
120656 CGTTGCGAT
1 CGTTGCGAT
120665 AGTCAAATTC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 26 0.67
34 13 0.33
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
Found at i:120719 original size:20 final size:20
Alignment explanation
Indices: 120656--120723 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
120646 GCGATTATCC
**
120656 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
* *
120676 CCTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTTCG
120696 -GTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
120715 CGTTGCGAT
1 CGTTGCGAT
120724 TTTAAGTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.41
20 24 0.59
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:120905 original size:18 final size:18
Alignment explanation
Indices: 120882--120931 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
120872 TTTACTAAGC
120882 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
120900 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
120918 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
120932 TACGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:122664 original size:20 final size:20
Alignment explanation
Indices: 122641--122730 Score: 101
Period size: 20 Copynumber: 4.5 Consensus size: 20
122631 TCTGAAACTT
122641 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
122661 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
122681 ATTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** *
122701 ACGATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
122720 AAAATCGCAAC
1 AAAATCGCAAC
122731 GCAAAACTAA
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
19 12 0.20
20 47 0.80
ACGTcount: A:0.46, C:0.22, G:0.18, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:122728 original size:19 final size:19
Alignment explanation
Indices: 122641--122746 Score: 97
Period size: 20 Copynumber: 5.4 Consensus size: 19
122631 TCTGAAACTT
*
122641 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
*
122661 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
** *
122681 ATTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAA-ATG
**
122701 ACGATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
122720 AAAATCGCAACGCAAAACT-
1 AAAATCGCAACGCGAAA-TG
122739 AAAATCGC
1 AAAATCGC
122747 GTTGCGATTT
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
19 26 0.35
20 48 0.65
ACGTcount: A:0.46, C:0.23, G:0.17, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:122765 original size:14 final size:14
Alignment explanation
Indices: 122746--122782 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
122736 ACTAAAATCG
122746 CGTTGCGATTTTTT
1 CGTTGCGATTTTTT
122760 CGTTGCGATTTTTT
1 CGTTGCGATTTTTT
122774 CGTTGCGAT
1 CGTTGCGAT
122783 CATCGATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.08, C:0.16, G:0.24, T:0.51
Consensus pattern (14 bp):
CGTTGCGATTTTTT
Found at i:123154 original size:22 final size:22
Alignment explanation
Indices: 123120--123184 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
123110 TCTGAGAGAT
123120 GGAGAT-A-GACGGATTTCGCC
1 GGAGATGAGGACGGATTTCGCC
* *
123140 GGAGATGAGGACGGATTTTGTC
1 GGAGATGAGGACGGATTTCGCC
* * *
123162 AGAGATGGGGACGGATGTCGCC
1 GGAGATGAGGACGGATTTCGCC
123184 G
1 G
123185 TAGAGAGTGA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 6 0.17
21 1 0.03
22 28 0.80
ACGTcount: A:0.23, C:0.15, G:0.42, T:0.20
Consensus pattern (22 bp):
GGAGATGAGGACGGATTTCGCC
Found at i:123413 original size:20 final size:19
Alignment explanation
Indices: 123390--123435 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
123380 GGAAACTGAT
* *
123390 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
123410 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
123429 TTGCGAT
1 TTGCGAT
123436 TTTGTGGTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:123425 original size:19 final size:19
Alignment explanation
Indices: 123401--123437 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
123391 TGCGATACTG
*
123401 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
123420 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
123438 TGTGGTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:146624 original size:21 final size:21
Alignment explanation
Indices: 146598--146660 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
146588 GTCGAGGGTT
146598 TCATAGGTCCTTCGGGACAAC
1 TCATAGGTCCTTCGGGACAAC
*
146619 TCATAGGTCCTTCGGGACAAAT
1 TCATAGGTCCTTCGGGAC-AAC
*
146641 TCACAGGTCCTTCGGGACAA
1 TCATAGGTCCTTCGGGACAA
146661 ATTTCATATG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (21 bp):
TCATAGGTCCTTCGGGACAAC
Found at i:146651 original size:22 final size:22
Alignment explanation
Indices: 146597--146668 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
146587 AGTCGAGGGT
146597 TTCATAGGTCCTTCGGGAC-AA
1 TTCATAGGTCCTTCGGGACAAA
*
146618 CTCATAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
*
146640 TTCACAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
146662 TTTCATA
1 -TTCATA
146669 TGCCACTCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.40
22 22 0.49
23 5 0.11
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACAAA
Found at i:152498 original size:83 final size:83
Alignment explanation
Indices: 152397--152612 Score: 272
Period size: 84 Copynumber: 2.6 Consensus size: 83
152387 AAAATGGTAA
* * *
152397 ATTTAGCAGCATTTTTATACAAACGCCGCAATATGATTCATCTATAGTGAC-ATTTTTTGAACAA
1 ATTTAGCAGCATTTTTATACAAACGCCGCAATAGGGTTCATCTATAGTGACGATTTTTTCAACAA
*
152461 ACGCCGCAACAGAGTAGT
66 ACGACGCAACAGAGTAGT
* * ** * * *
152479 ACTTTAGCAGCGTTGTTATACAAAAACCGCAATAGGGTTCATATATAATGACGTTTTTTTCAACA
1 A-TTTAGCAGCATTTTTATACAAACGCCGCAATAGGGTTCATCTATAGTGACGATTTTTTCAACA
* *
152544 AACGACGTAATAGAGTAGT
65 AACGACGCAACAGAGTAGT
* *
152563 ATTTACGCGGCATTTTTATACAAACGTCGCAATAGGGTTCATCTATAGTG
1 ATTTA-GCAGCATTTTTATACAAACGCCGCAATAGGGTTCATCTATAGTG
152613 GCTTCACACC
Statistics
Matches: 110, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
82 1 0.01
83 46 0.42
84 63 0.57
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (83 bp):
ATTTAGCAGCATTTTTATACAAACGCCGCAATAGGGTTCATCTATAGTGACGATTTTTTCAACAA
ACGACGCAACAGAGTAGT
Found at i:152909 original size:41 final size:41
Alignment explanation
Indices: 152852--153010 Score: 158
Period size: 41 Copynumber: 3.9 Consensus size: 41
152842 TTTTTTTGAT
* * * * *
152852 CAAACGCCGCAAAAGACTCTTACTTTATTGGCGTTTGTGTA
1 CAAACACCGCTAAAGACTCATACTTTAGTGGCGTTTGTATA
* * *
152893 CAAACACCGCTAAAGACTCAGACTTTCGTGGGGTTTGTATA
1 CAAACACCGCTAAAGACTCATACTTTAGTGGCGTTTGTATA
* * * * *
152934 CAAACACCACTATATACTCATACTTTAGTGGCATTTTTATA
1 CAAACACCGCTAAAGACTCATACTTTAGTGGCGTTTGTATA
* **
152975 CAAACGCCGCTATAA-ACTTGTACTTTAGTGGCGTTT
1 CAAACACCGCTA-AAGACTCATACTTTAGTGGCGTTT
153011 TTGTAATAAA
Statistics
Matches: 95, Mismatches: 22, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
41 94 0.99
42 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (41 bp):
CAAACACCGCTAAAGACTCATACTTTAGTGGCGTTTGTATA
Found at i:153012 original size:41 final size:41
Alignment explanation
Indices: 152832--153047 Score: 134
Period size: 41 Copynumber: 5.2 Consensus size: 41
152822 AGTGGCATTT
* * *
152832 TTTAGTGGCCTTTTTTTGATCAAACGCCGC-AAAAGACTCT-TAC
1 TTTAGTGGCGTTTTTAT-A-CAAACGCCGCTATAA-ACT-TGTAC
* * * * *
152875 TTTATTGGCGTTTGTGTACAAACACCGCTA-AAGACTCAG-AC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTATAA-ACT-TGTAC
* * * * * * **
152916 TTTCGTGGGGTTTGTATACAAACACCACTATATACTCATAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTATAAACTTGTAC
*
152957 TTTAGTGGCATTTTTATACAAACGCCGCTATAAACTTGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTATAAACTTGTAC
* * * * * *
152998 TTTAGTGGCGTTTTTGTAATAAACGCCGCAATAATCATGTAA
1 TTTAGTGGCGTTTTTAT-ACAAACGCCGCTATAAACTTGTAC
153040 TTTAGTGG
1 TTTAGTGG
153048 TATTTTTTTT
Statistics
Matches: 138, Mismatches: 30, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
41 95 0.69
42 30 0.22
43 13 0.09
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTATACAAACGCCGCTATAAACTTGTAC
Found at i:153044 original size:42 final size:42
Alignment explanation
Indices: 152954--153107 Score: 166
Period size: 42 Copynumber: 3.6 Consensus size: 42
152944 TATATACTCA
* * * * *
152954 TACTTTAGTGGCATTTTTAT-ACAAACGCCGCTATAAACTTG
1 TACTTTAGTGGCGTTTTTATAATAAACGCCGCAATAATCATG
*
152995 TACTTTAGTGGCGTTTTTGTAATAAACGCCGCAATAATCATG
1 TACTTTAGTGGCGTTTTTATAATAAACGCCGCAATAATCATG
* ** * *
153037 TAATTTAGTGGTATTTTTTTTTAATAAACGCCGCAATAGTCATG
1 TACTTTAGTGG--CGTTTTTATAATAAACGCCGCAATAATCATG
* *
153081 TACCTTAGTGGCGTTTTTATTATAAAC
1 TACTTTAGTGGCGTTTTTATAATAAAC
153108 ACCACGATTG
Statistics
Matches: 93, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
41 18 0.19
42 39 0.42
44 36 0.39
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (42 bp):
TACTTTAGTGGCGTTTTTATAATAAACGCCGCAATAATCATG
Found at i:153098 original size:44 final size:44
Alignment explanation
Indices: 152976--153098 Score: 151
Period size: 44 Copynumber: 2.8 Consensus size: 44
152966 ATTTTTATAC
* * *
152976 AAACGCCGCTATAAACTTGTACTTTAGTGGCG--TTTTTGTAAT
1 AAACGCCGCAATAATCATGTACTTTAGTGGCGTTTTTTTGTAAT
* ** *
153018 AAACGCCGCAATAATCATGTAATTTAGTGGTATTTTTTTTTAAT
1 AAACGCCGCAATAATCATGTACTTTAGTGGCGTTTTTTTGTAAT
* *
153062 AAACGCCGCAATAGTCATGTACCTTAGTGGCGTTTTT
1 AAACGCCGCAATAATCATGTACTTTAGTGGCGTTTTT
153099 ATTATAAACA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 26 0.39
44 41 0.61
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (44 bp):
AAACGCCGCAATAATCATGTACTTTAGTGGCGTTTTTTTGTAAT
Found at i:155269 original size:8 final size:8
Alignment explanation
Indices: 155256--155300 Score: 90
Period size: 8 Copynumber: 5.6 Consensus size: 8
155246 ATTCATATGA
155256 CTCTCCCT
1 CTCTCCCT
155264 CTCTCCCT
1 CTCTCCCT
155272 CTCTCCCT
1 CTCTCCCT
155280 CTCTCCCT
1 CTCTCCCT
155288 CTCTCCCT
1 CTCTCCCT
155296 CTCTC
1 CTCTC
155301 ATTGCCTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 37 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (8 bp):
CTCTCCCT
Found at i:156522 original size:34 final size:34
Alignment explanation
Indices: 156476--156542 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
156466 CATTTACAAC
* *
156476 TCCCTAGTTTTTCACGGGCTAAACTAGAACCTTA
1 TCCCTAGCTTTTCAAGGGCTAAACTAGAACCTTA
* *
156510 TCCCTAGCTTTTCAAGGGCTCAGCTAGAACCTT
1 TCCCTAGCTTTTCAAGGGCTAAACTAGAACCTT
156543 TCCTTTTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.31
Consensus pattern (34 bp):
TCCCTAGCTTTTCAAGGGCTAAACTAGAACCTTA
Found at i:156910 original size:20 final size:20
Alignment explanation
Indices: 156885--156924 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
156875 GGCTTGATTT
156885 TACTGTAGCA-GTATCGATAC
1 TACTGTAG-AGGTATCGATAC
156905 TACTGTAGAGGTATCGATAC
1 TACTGTAGAGGTATCGATAC
156925 CCATTTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (20 bp):
TACTGTAGAGGTATCGATAC
Found at i:156994 original size:20 final size:20
Alignment explanation
Indices: 156952--157009 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
156942 ATTTTTGAGC
* * * *
156952 ATCGGTACTGTTAACACAGT
1 ATCGGTACTATTCATACAAT
156972 ATCGGTACTATTCATACAAT
1 ATCGGTACTATTCATACAAT
**
156992 ATCAATACTATTCATACA
1 ATCGGTACTATTCATACA
157010 GTATAATACT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (20 bp):
ATCGGTACTATTCATACAAT
Found at i:157019 original size:19 final size:20
Alignment explanation
Indices: 156977--157026 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
156967 ACAGTATCGG
156977 TACTATTCATACAATATCAA
1 TACTATTCATACAATATCAA
*
156997 TACTATTCATACAGTAT-AA
1 TACTATTCATACAATATCAA
157016 TACTATTCATA
1 TACTATTCATA
157027 AAAACATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.38
Consensus pattern (20 bp):
TACTATTCATACAATATCAA
Found at i:158391 original size:14 final size:13
Alignment explanation
Indices: 158356--158392 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
158346 TGAAATCTCT
158356 AAATCATTTTTCA
1 AAATCATTTTTCA
158369 AAATCATTTTTCA
1 AAATCATTTTTCA
158382 AAATCAATTTT
1 AAATC-ATTTT
158393 AGATTTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 18 0.78
14 5 0.22
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATCATTTTTCA
Found at i:159806 original size:20 final size:20
Alignment explanation
Indices: 159781--159845 Score: 98
Period size: 20 Copynumber: 3.3 Consensus size: 20
159771 TTCATTATTG
159781 TTCATACAGTATCGATACTA
1 TTCATACAGTATCGATACTA
159801 TTCATACA-TCATCGATACTA
1 TTCATACAGT-ATCGATACTA
*
159821 TTCATACAGTA-CAATACTA
1 TTCATACAGTATCGATACTA
159840 TTCATA
1 TTCATA
159846 AAAACATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
19 14 0.33
20 27 0.64
21 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (20 bp):
TTCATACAGTATCGATACTA
Found at i:165037 original size:21 final size:21
Alignment explanation
Indices: 165013--165073 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
165003 CTTTGATTTA
165013 TTATTATGGATTTCAA-TTTGG
1 TTATTATGGATTTCAAGTTT-G
165034 TTATTATGGATTTCAAGTTTG
1 TTATTATGGATTTCAAGTTTG
* *
165055 TT-TTATGGATATCATGTTT
1 TTATTATGGATTTCAAGTTT
165074 ATTGGATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 15 0.41
21 19 0.51
22 3 0.08
ACGTcount: A:0.23, C:0.05, G:0.18, T:0.54
Consensus pattern (21 bp):
TTATTATGGATTTCAAGTTTG
Found at i:168319 original size:18 final size:20
Alignment explanation
Indices: 168298--168353 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 20
168288 AGCACTTTTG
168298 TTATTTTTTTCATTTT-C-T
1 TTATTTTTTTCATTTTCCTT
168316 TTATTTTTTTC-TGTTTCCTT
1 TTATTTTTTTCAT-TTTCCTT
168336 TTCATTTTTTTCTATTTT
1 TT-ATTTTTTTC-ATTTT
168354 TCGAACTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 1 0.03
18 14 0.44
19 1 0.03
20 3 0.09
21 9 0.28
22 3 0.09
23 1 0.03
ACGTcount: A:0.09, C:0.12, G:0.02, T:0.77
Consensus pattern (20 bp):
TTATTTTTTTCATTTTCCTT
Found at i:175514 original size:21 final size:22
Alignment explanation
Indices: 175471--175538 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
175461 TGGAGAAAAT
* *
175471 AAGAGAAGAAGATAAAGAAATGA
1 AAGAGAAAAAGTTAAAG-AATGA
*
175494 GAGAGAAAAAGTTAAAG-ATGA
1 AAGAGAAAAAGTTAAAGAATGA
*
175515 AAGAGAAAAAAGTT-AATAATGA
1 AAGAG-AAAAAGTTAAAGAATGA
175537 AA
1 AA
175539 TATAAAAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
21 10 0.26
22 14 0.37
23 14 0.37
ACGTcount: A:0.63, C:0.00, G:0.24, T:0.13
Consensus pattern (22 bp):
AAGAGAAAAAGTTAAAGAATGA
Found at i:175527 original size:22 final size:23
Alignment explanation
Indices: 175493--175538 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
175483 TAAAGAAATG
175493 AGAGAGAAAAAGTTAA-AGATGAA
1 AGAGAGAAAAAGTTAATA-ATGAA
175516 AGAGA-AAAAAGTTAATAATGAA
1 AGAGAGAAAAAGTTAATAATGAA
175538 A
1 A
175539 TATAAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (23 bp):
AGAGAGAAAAAGTTAATAATGAA
Found at i:184244 original size:36 final size:36
Alignment explanation
Indices: 184204--184336 Score: 239
Period size: 36 Copynumber: 3.7 Consensus size: 36
184194 ACGGTGCTAG
* *
184204 ACATTGATACACGAATGTACCAAAGGTGATATGATA
1 ACATTGATACACGAATGTATCAAAGATGATATGATA
*
184240 ACATTGATACACGAATGTATCAAAGCTGATATGATA
1 ACATTGATACACGAATGTATCAAAGATGATATGATA
184276 ACATTGATACACGAATGTATCAAAGATGATATGATA
1 ACATTGATACACGAATGTATCAAAGATGATATGATA
184312 ACATTGATACACGAATGTATCAAAG
1 ACATTGATACACGAATGTATCAAAG
184337 CTGACAATGG
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 94 1.00
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (36 bp):
ACATTGATACACGAATGTATCAAAGATGATATGATA
Found at i:188919 original size:23 final size:23
Alignment explanation
Indices: 188893--188945 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
188883 CACCACAGCT
*
188893 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
188916 CGTAGAATTGCACCGAAGTTCCA
1 CGTAGAAATGCACCGAAGTGCCA
188939 CGTAGAA
1 CGTAGAA
188946 TTGTACCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:188946 original size:23 final size:23
Alignment explanation
Indices: 188901--188961 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
188891 CTCGTATAAA
188901 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
188924 TGCACCGAAGTTCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
188947 TGTACC-ATAGTGCCA
1 TGCACCGA-AGTGCCA
188962 TATAGATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 1 0.03
23 33 0.97
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:189224 original size:31 final size:30
Alignment explanation
Indices: 189180--189239 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
189170 TATTGTATAG
189180 ACATATAATTTCCAT-ACCTTCATCACATAA
1 ACATATAATTTCCATCA-CTTCATCACATAA
* *
189210 ACATATCATGTTCCATCACTTTATCACATA
1 ACATATAAT-TTCCATCACTTCATCACATA
189240 GCTTATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 17 0.65
32 1 0.04
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.35
Consensus pattern (30 bp):
ACATATAATTTCCATCACTTCATCACATAA
Found at i:196095 original size:31 final size:30
Alignment explanation
Indices: 196050--196109 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
196040 TATATTATAG
196050 ACATATAATTTCCAT-ACCTTCATCACATAA
1 ACATATAATTTCCATCA-CTTCATCACATAA
* *
196080 ACATATCATGTTCCATCACTTTATCACATA
1 ACATATAAT-TTCCATCACTTCATCACATA
196110 GCTTATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 17 0.65
32 1 0.04
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.35
Consensus pattern (30 bp):
ACATATAATTTCCATCACTTCATCACATAA
Found at i:196180 original size:25 final size:22
Alignment explanation
Indices: 196152--196209 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 22
196142 CTTAATGCAT
196152 ATAATATGAATTCATGTCATGTATC
1 ATAATATGAA-T-ATGTC-TGTATC
196177 ATAATATGAA-ATGTCTGTATC
1 ATAATATGAATATGTCTGTATC
*
196198 AAAATATTGAAT
1 ATAATA-TGAAT
196210 CTATACTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 11 0.37
22 9 0.30
25 10 0.33
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (22 bp):
ATAATATGAATATGTCTGTATC
Found at i:201249 original size:12 final size:12
Alignment explanation
Indices: 201232--201270 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
201222 ATTGGATTCG
201232 TCTGAACTTGAT
1 TCTGAACTTGAT
* *
201244 TCTGAATTTGGT
1 TCTGAACTTGAT
*
201256 TATGAACTTGAT
1 TCTGAACTTGAT
201268 TCT
1 TCT
201271 AGATCTAATT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (12 bp):
TCTGAACTTGAT
Found at i:203191 original size:28 final size:28
Alignment explanation
Indices: 203148--203232 Score: 134
Period size: 28 Copynumber: 3.0 Consensus size: 28
203138 TCAACCAGAA
* * *
203148 CTGAGTCAACTAATCCAAGTTAACTCGT
1 CTGATTCAACTCATCCGAGTTAACTCGT
203176 CTGATTCAACTCATCCGAGTTAACTCGT
1 CTGATTCAACTCATCCGAGTTAACTCGT
*
203204 CTGATTCAACTCATCCGAGTCAACTCGT
1 CTGATTCAACTCATCCGAGTTAACTCGT
203232 C
1 C
203233 CGAGTTAACC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.29
Consensus pattern (28 bp):
CTGATTCAACTCATCCGAGTTAACTCGT
Found at i:203236 original size:14 final size:14
Alignment explanation
Indices: 203150--203237 Score: 77
Period size: 14 Copynumber: 6.3 Consensus size: 14
203140 AACCAGAACT
*
203150 GAGTCAACTAATCC
1 GAGTCAACTCATCC
* * * *
203164 AAGTTAACTCGTCT
1 GAGTCAACTCATCC
*
203178 GATTCAACTCATCC
1 GAGTCAACTCATCC
* * *
203192 GAGTTAACTCGTCT
1 GAGTCAACTCATCC
*
203206 GATTCAACTCATCC
1 GAGTCAACTCATCC
*
203220 GAGTCAACTCGTCC
1 GAGTCAACTCATCC
203234 GAGT
1 GAGT
203238 TAACCCGTTG
Statistics
Matches: 54, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
14 54 1.00
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.28
Consensus pattern (14 bp):
GAGTCAACTCATCC
Found at i:206350 original size:26 final size:26
Alignment explanation
Indices: 206311--206360 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
206301 CCAGAAGGCA
*
206311 CTGACTAGATCTTCTAGAAACTGTTG
1 CTGACTAGACCTTCTAGAAACTGTTG
*
206337 CTGACTGGACCTTCTAGAAACTGT
1 CTGACTAGACCTTCTAGAAACTGT
206361 CACATCAGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (26 bp):
CTGACTAGACCTTCTAGAAACTGTTG
Found at i:214698 original size:28 final size:29
Alignment explanation
Indices: 214659--214716 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
214649 AATTGACCGT
214659 TATATAATTGATGATACTAA-AAAACAAA
1 TATATAATTGATGATACTAATAAAACAAA
* *
214687 TATATAATTGATGATATTAATTAAACAAA
1 TATATAATTGATGATACTAATAAAACAAA
214716 T
1 T
214717 GGTATCAGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.34
Consensus pattern (29 bp):
TATATAATTGATGATACTAATAAAACAAA
Found at i:226440 original size:9 final size:9
Alignment explanation
Indices: 226409--226459 Score: 54
Period size: 9 Copynumber: 6.0 Consensus size: 9
226399 CTGCAAAAAG
*
226409 AATTAATTA
1 AATTAAATA
226418 AA-TAAA-A
1 AATTAAATA
*
226425 TATTAAATA
1 AATTAAATA
226434 AATTAAAT-
1 AATTAAATA
*
226442 ACTTAAATA
1 AATTAAATA
226451 AATTAAATA
1 AATTAAATA
226460 CAAAATATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 2 0.06
8 14 0.41
9 18 0.53
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
AATTAAATA
Found at i:226440 original size:17 final size:17
Alignment explanation
Indices: 226410--226457 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
226400 TGCAAAAAGA
*
226410 ATTAATTAAA-TAAAAT
1 ATTAAATAAATTAAAAT
226426 ATTAAATAAATT-AAAT
1 ATTAAATAAATTAAAAT
226442 ACTTAAATAAATTAAA
1 A-TTAAATAAATTAAA
226458 TACAAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 14 0.50
17 12 0.43
18 2 0.07
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTAAATAAATTAAAAT
Found at i:226458 original size:17 final size:17
Alignment explanation
Indices: 226411--226460 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
226401 GCAAAAAGAA
* *
226411 TTAATTAAATAAAATA-
1 TTAAATAAATTAAATAC
226427 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
226444 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
226461 AAAATATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAATAAATTAAATAC
Found at i:240867 original size:30 final size:30
Alignment explanation
Indices: 240827--240947 Score: 97
Period size: 30 Copynumber: 4.1 Consensus size: 30
240817 GCTAAACCAA
*
240827 AAAAATAGAAAATTAGAGGACTAAAATAGT
1 AAAAACAGAAAATTAGAGGACTAAAATAGT
** * * * *
240857 AATTACAGAAACTTAGGGGGCTAAAATAGC
1 AAAAACAGAAAATTAGAGGACTAAAATAGT
240887 ACAAAACA-AAAATCTA-AGGACTAAAATAAG-
1 A-AAAACAGAAAAT-TAGAGGACTAAAAT-AGT
* * *
240917 AAAAACATAAATTTAAAGGACT-AAATAGT
1 AAAAACAGAAAATTAGAGGACTAAAATAGT
240946 AA
1 AA
240948 TTACGAAACA
Statistics
Matches: 72, Mismatches: 13, Indels: 13
0.73 0.13 0.13
Matches are distributed among these distances:
28 2 0.03
29 14 0.19
30 48 0.67
31 8 0.11
ACGTcount: A:0.57, C:0.09, G:0.15, T:0.19
Consensus pattern (30 bp):
AAAAACAGAAAATTAGAGGACTAAAATAGT
Found at i:241735 original size:18 final size:18
Alignment explanation
Indices: 241714--241748 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
241704 CACTTAAAAA
* *
241714 CTTTGAAACCCTTAACCC
1 CTTTCAAACCCTAAACCC
241732 CTTTCAAACCCTAAACC
1 CTTTCAAACCCTAAACC
241749 AAAGATGATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.40, G:0.03, T:0.26
Consensus pattern (18 bp):
CTTTCAAACCCTAAACCC
Found at i:242346 original size:3 final size:3
Alignment explanation
Indices: 242332--242374 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
242322 TGTAAAAATG
* *
242332 TAA TAT TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
242375 TAAATTAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:247650 original size:3 final size:3
Alignment explanation
Indices: 247642--247711 Score: 99
Period size: 3 Copynumber: 24.0 Consensus size: 3
247632 CCTCAATTTT
* *
247642 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATT GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
247689 AT- ATA ATA ATA ATT ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
247712 TATAGTCTCG
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
2 4 0.07
3 55 0.93
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:247885 original size:20 final size:20
Alignment explanation
Indices: 247860--247908 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
247850 TCCTACCTAG
* *
247860 AGGTTTTACAGATGACCCGA
1 AGGTTTTACAAATCACCCGA
*
247880 AGGTTTTACAAATCACCCGG
1 AGGTTTTACAAATCACCCGA
247900 AGGATTTTA
1 AGG-TTTTA
247909 ATTTTCTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (20 bp):
AGGTTTTACAAATCACCCGA
Found at i:248021 original size:20 final size:20
Alignment explanation
Indices: 247973--248027 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
247963 AAAAACATCC
* *
247973 TACCCTGAGGTTTTACAGAT
1 TACCCGGAGGTTTTACAAAT
* * *
247993 GAACGGGAGGTTTTACAAAT
1 TACCCGGAGGTTTTACAAAT
*
248013 TACCCGGAGGATTTA
1 TACCCGGAGGTTTTA
248028 ATTTGTAGAA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (20 bp):
TACCCGGAGGTTTTACAAAT
Found at i:248096 original size:118 final size:120
Alignment explanation
Indices: 247843--248130 Score: 440
Period size: 118 Copynumber: 2.4 Consensus size: 120
247833 AATCAAAAAT
*
247843 AAAAACATCCTA-CCTAGAGGTTTTACAGATGACCCGAAGGTTTTACAAATCACCCGGAGGATTT
1 AAAAACATCCTACCCT-GAGGTTTTACAGATGACCCGGAGGTTTTACAAATCACCCGGAGGATTT
*
247907 TAATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTTTATCATTTTCATGA
65 TAATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCACTTTATCATTTTCATGA
* * *
247963 AAAAACATCCTACCCTGAGGTTTTACAGATGAACGGGAGGTTTTACAAATTACCCGGAGGA-TTT
1 AAAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGTTTTACAAATCACCCGGAGGATTTT
* * * *
248027 AA-TTTGTAGAACATTAAATGAGAAACTTTGAAAATTACTTTCTCATTTTCATGC
66 AATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCACTTTATCATTTTCATGA
* *
248081 GAAAACATCCTACCCTGAGGTTTTATAGATGACCCGGA-GTTTTACAAATC
1 AAAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGTTTTACAAATC
248131 TGTGGACATT
Statistics
Matches: 153, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
117 11 0.07
118 81 0.53
119 5 0.03
120 53 0.35
121 3 0.02
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (120 bp):
AAAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGTTTTACAAATCACCCGGAGGATTTT
AATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCACTTTATCATTTTCATGA
Found at i:248152 original size:99 final size:100
Alignment explanation
Indices: 247999--248230 Score: 355
Period size: 99 Copynumber: 2.4 Consensus size: 100
247989 AGATGAACGG
* * * * *
247999 GAGGTTTTACAAATTACCCGGAGGATTT---AATTTGTAGAACATTAAATGAGAAACTTTGAAAA
1 GAGGTTTTACAGATGACCCGGAGGTTTTACAAATCTGT-GGACATTAAATGAGAAACTTTGAAAA
*
248061 TTACTTTCTCATTTTCATGCGAAAACATCCTACCCT
65 TCACTTTCTCATTTTCATGCGAAAACATCCTACCCT
*
248097 GAGGTTTTATAGATGACCCGGA-GTTTTACAAATCTGTGGACATTAAATGAGAAACTTTGAAAAT
1 GAGGTTTTACAGATGACCCGGAGGTTTTACAAATCTGTGGACATTAAATGAGAAACTTTGAAAAT
*
248161 CGCTTTCTCATTTTCATGCGAAAACATCCTACCCT
66 CACTTTCTCATTTTCATGCGAAAACATCCTACCCT
248196 GAGGTTTTACAGATGACCCGGAGGTTTTACAAATC
1 GAGGTTTTACAGATGACCCGGAGGTTTTACAAATC
248231 AAGAAACCCT
Statistics
Matches: 121, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
97 4 0.03
98 19 0.16
99 80 0.66
100 18 0.15
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Consensus pattern (100 bp):
GAGGTTTTACAGATGACCCGGAGGTTTTACAAATCTGTGGACATTAAATGAGAAACTTTGAAAAT
CACTTTCTCATTTTCATGCGAAAACATCCTACCCT
Found at i:250984 original size:9 final size:9
Alignment explanation
Indices: 250966--250999 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 9
250956 AACTTCTTCT
250966 TTTTTCTTTA
1 TTTTT-TTTA
250976 TTTTTTTTA
1 TTTTTTTTA
250985 TTTTTTTTTA
1 -TTTTTTTTA
250995 TTTTT
1 TTTTT
251000 GCTATTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:251005 original size:19 final size:20
Alignment explanation
Indices: 250965--251006 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
250955 CAACTTCTTC
**
250965 TTTTTTCTTTATTTTTTTTA
1 TTTTTTCTTTATTTTTGCTA
250985 TTTTTT-TTTATTTTTGCTA
1 TTTTTTCTTTATTTTTGCTA
251004 TTT
1 TTT
251007 GAAACTTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.10, C:0.05, G:0.02, T:0.83
Consensus pattern (20 bp):
TTTTTTCTTTATTTTTGCTA
Found at i:263017 original size:3 final size:3
Alignment explanation
Indices: 263009--263065 Score: 82
Period size: 3 Copynumber: 19.7 Consensus size: 3
262999 CTCAGTTTTG
**
263009 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TTG TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
263055 TAA TAA TAA TA
1 TAA TAA TAA TA
263066 TATAGTTTCG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 4 0.08
3 44 0.92
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:272638 original size:22 final size:21
Alignment explanation
Indices: 272586--272644 Score: 93
Period size: 20 Copynumber: 2.8 Consensus size: 21
272576 GATTTCTGGG
272586 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
272607 CAA-GGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
*
272627 CAATGGGGAATCGATACC
1 CAA-GGGGAATCGGTACC
272645 TCTCAAGCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 20 0.57
21 3 0.09
22 12 0.34
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.19
Consensus pattern (21 bp):
CAAGGGGAATCGGTACCCATT
Found at i:272723 original size:23 final size:22
Alignment explanation
Indices: 272679--272723 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
272669 AATCTCATAG
*
272679 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
*
272701 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
272724 AAAATGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:274279 original size:23 final size:23
Alignment explanation
Indices: 274245--274336 Score: 148
Period size: 23 Copynumber: 4.0 Consensus size: 23
274235 CATTATTATA
*
274245 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
274268 CGGCACTCCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
274291 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
274314 TGGCACTTCGGTGCAATTATACG
1 TGGCACTTCGGTGCAATTCTACG
274337 AGCTGTGGTG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.27
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:277378 original size:35 final size:34
Alignment explanation
Indices: 277293--277379 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
277283 ATTTGATATT
* *
277293 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATAAAATGG
* *
277327 TAAATGATAACCAAATTACAATAACTGATATAAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATAAAATGG
277365 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
277380 ACTAAAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 5 0.11
38 9 0.20
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.25
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATAAAATGG
Found at i:277998 original size:18 final size:18
Alignment explanation
Indices: 277975--278010 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
277965 GCGATGACGA
277975 CATCATATATGGCTGCGG
1 CATCATATATGGCTGCGG
277993 CATCATATATGGCTGCGG
1 CATCATATATGGCTGCGG
278011 TGGCTGCTGG
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:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (18 bp):
CATCATATATGGCTGCGG
Found at i:279709 original size:110 final size:111
Alignment explanation
Indices: 279515--279735 Score: 383
Period size: 110 Copynumber: 2.0 Consensus size: 111
279505 ATTACAAAAA
* *
279515 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
279580 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
279626 TTAATTCTTAATCTAATAATCATGCA-TATAATAAATC-ACTAAATATTACTAATAATTTAAATT
1 TTAATTCTTAATCTAATAATCATGCATTA-AATAAATCAACTAAATATTACTAATAATTTAAATT
*
279689 AAATTAAAACGTTAAAATGTTACCGTATTAGCAAAGTGTAGAGATAT
65 AAATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
279736 ATGATTTCTA
Statistics
Matches: 105, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
110 72 0.69
111 33 0.31
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:282680 original size:38 final size:37
Alignment explanation
Indices: 282606--282682 Score: 93
Period size: 38 Copynumber: 2.1 Consensus size: 37
282596 GTTCGAAAAT
* *
282606 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
* *
282643 ATTTATATAATTTTTTTGTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTT-TAAAAAATTAAAAATCATAAA
282681 AT
1 AT
282683 GTTTAATGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 8 0.24
38 14 0.41
39 12 0.35
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
Found at i:286085 original size:31 final size:31
Alignment explanation
Indices: 286049--286108 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
286039 AACTTAAAAG
*
286049 AGTTTTACAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
286080 AGTTTTACACTACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
286109 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:286618 original size:20 final size:20
Alignment explanation
Indices: 286570--286631 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
286560 AACTTAAATC
*
286570 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
286590 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
286608 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
286627 AAAAT
1 AAAAT
286632 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:286715 original size:62 final size:63
Alignment explanation
Indices: 286626--286784 Score: 247
Period size: 62 Copynumber: 2.6 Consensus size: 63
286616 TTATATGATA
286626 TAAAATTAAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTT-AAAAATTAATAT
1 TAAAATT-AATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
*
286689 TAAAATTAATATCTATAATATAATATTACAAAATTAATATTTAATTTATTTAAAAAATTGATAT
1 TAAAATTAATATCTATAATATAATATTA-AAAATTAATATTTAATTTATTTAAAAAATTAATAT
*
286753 TAAAATTAAAATC-A-AATATAATA-T-AAAATTAA
1 TAAAATTAATATCTATAATATAATATTAAAAATTAA
286785 ATATAAAACC
Statistics
Matches: 92, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
59 8 0.09
61 1 0.01
62 30 0.33
63 30 0.33
64 23 0.25
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (63 bp):
TAAAATTAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:286728 original size:40 final size:36
Alignment explanation
Indices: 286647--286729 Score: 105
Period size: 40 Copynumber: 2.2 Consensus size: 36
286637 ATCTATAATA
*
286647 TAATATTAAAAATTAATATTTAATTTATTTAAAAAT
1 TAATATTAAAAATTAATATTTAATTAATTTAAAAAT
286683 TAATATT-AAAATTAATATCTATAATATAATATTACAAAAT
1 TAATATTAAAAATTAATAT-T-TAAT-TAAT-TTA-AAAAT
286723 TAATATT
1 TAATATT
286730 TAATTTATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
35 11 0.27
36 8 0.20
37 4 0.10
38 3 0.07
39 3 0.07
40 12 0.29
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (36 bp):
TAATATTAAAAATTAATATTTAATTAATTTAAAAAT
Found at i:294215 original size:21 final size:21
Alignment explanation
Indices: 294190--294233 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
294180 ATTTTGATAT
294190 TATTTT-TATAAAA-ATCAAAAA
1 TATTTTGT-TAAAATAT-AAAAA
294211 TATTTTGTTAAAATATAAAAA
1 TATTTTGTTAAAATATAAAAA
294232 TA
1 TA
294234 AAATAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
TATTTTGTTAAAATATAAAAA
Found at i:296945 original size:15 final size:15
Alignment explanation
Indices: 296930--296982 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
296920 CCGGTTTCGG
*
296930 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACC-G-A
*
296947 TTTTTAAAAAACCGA
1 TTTTAAAAAAACCGA
*
296962 TTATAAAAAAACCGA
1 TTTTAAAAAAACCGA
296977 TTTTAA
1 TTTTAA
296983 TATTCCAGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
15 18 0.58
16 1 0.03
17 12 0.39
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (15 bp):
TTTTAAAAAAACCGA
Found at i:297401 original size:13 final size:13
Alignment explanation
Indices: 297380--297434 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
297370 AAGTTCGATA
*
297380 AATTCAAATACTT
1 AATTGAAATACTT
297393 AATTGAAATACTT
1 AATTGAAATACTT
* *
297406 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
297420 AATTGAAATACTT
1 AATTGAAATACTT
297433 AA
1 AA
297435 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:297516 original size:32 final size:33
Alignment explanation
Indices: 297420--297518 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
297410 AACTCAACAT
* * *
297420 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
297453 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
297486 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
297518 A
1 A
297519 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:297537 original size:21 final size:21
Alignment explanation
Indices: 297513--297552 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
297503 ACTTCAAGTT
297513 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
297534 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
297553 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:299872 original size:12 final size:12
Alignment explanation
Indices: 299855--299900 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
299845 TTCGGATAAA
299855 AACCGGTTTTTT
1 AACCGGTTTTTT
299867 AACCGGTTTTTTT
1 AACCGG-TTTTTT
299880 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
299894 ATCCGGT
1 AACCGGT
299901 AAAAAACCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:299885 original size:15 final size:14
Alignment explanation
Indices: 299854--299893 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
299844 TTTCGGATAA
299854 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
299867 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
299880 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
299894 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:300015 original size:27 final size:28
Alignment explanation
Indices: 299983--300040 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
299973 AAAAAACCGG
*
299983 TTTTTCCCAAAACCGG-T-TTCGGATATT
1 TTTTTCACAAAACCGGATATTCGGAT-TT
*
300010 TTTTTCACAAAATCGGATATTCGGATTT
1 TTTTTCACAAAACCGGATATTCGGATTT
300038 TTT
1 TTT
300041 GTGCACCCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 14 0.52
28 6 0.22
29 7 0.26
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (28 bp):
TTTTTCACAAAACCGGATATTCGGATTT
Found at i:300163 original size:32 final size:32
Alignment explanation
Indices: 300127--300191 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
300117 TATTGTGGTC
300127 CCATTTGCATCTCTCATTGCACATGAATGCCT
1 CCATTTGCATCTCTCATTGCACATGAATGCCT
300159 CCATTTGCATCTCTCATTGCACATGAATGCCT
1 CCATTTGCATCTCTCATTGCACATGAATGCCT
300191 C
1 C
300192 AGGAGACATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.22, C:0.32, G:0.12, T:0.34
Consensus pattern (32 bp):
CCATTTGCATCTCTCATTGCACATGAATGCCT
Done.