Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008620.1 Hibiscus syriacus cultivar Beakdansim tig00111582_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: 13158977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 62 of 64
Found at i:12511416 original size:85 final size:84
Alignment explanation
Indices: 12511180--12511549 Score: 377
Period size: 85 Copynumber: 4.3 Consensus size: 84
12511170 TCGCTAAAGT
* * * * * * *
12511180 TAGCGGCGTTTGTGGGAAAAAAATGCCGCAATCGGTCTAAATCTATAGCGGCGTTTTCTAAAAAA
1 TAGCGGCGTTT-TTGG-AACAAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTCT-AGAAA
* * *
12511245 ACGCCGCAACAGGTCGGCTCTA
63 ACGCCGCAAAAGGTCAGATCTA
* * * * *
12511267 TAGCGGCGCTTTTCGGAACAAACGCCGCAATAAGTCGAGCTCTATAGCGTCGTTTTCGGAGAAAA
1 TAGCGGCG-TTTTTGGAACAAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTC-TAGAAAA
*
12511332 CGCCGCAAAAGGTCAAATCTA
64 CGCCGCAAAAGGTCAGATCTA
* *
12511353 TAGCGGCGTTTTTGGAACAAACGCCGCAATAGGTCGAGATCAATAACGGCGTTTTCTATGAAAAC
1 TAGCGGCGTTTTTGGAACAAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTCTA-GAAAAC
*
12511418 GCCGCAAAATGTCAGATCTA
65 GCCGCAAAAGGTCAGATCTA
** * * *
12511438 TAGCGGCGTTTTTGGAGA-AAACGTTGCAAAAGGTC-AGATTTATAGCGGCGTTTT-TGGAATAA
1 TAGCGGCGTTTTTGGA-ACAAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTCTAG-A-AA
* **
12511500 ACGCCGTAAAATTTCAGATCTA
63 ACGCCGCAAAAGGTCAGATCTA
*
12511522 TAGCGGCGTTTTTGGATGCAAACGCCGC
1 TAGCGGCGTTTTTGGA-ACAAACGCCGC
12511550 TAATTATCGT
Statistics
Matches: 239, Mismatches: 37, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
82 1 0.00
83 2 0.01
84 55 0.23
85 103 0.43
86 64 0.27
87 11 0.05
88 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (84 bp):
TAGCGGCGTTTTTGGAACAAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTCTAGAAAACG
CCGCAAAAGGTCAGATCTA
Found at i:12511534 original size:42 final size:41
Alignment explanation
Indices: 12511220--12511537 Score: 325
Period size: 42 Copynumber: 7.5 Consensus size: 41
12511210 ATCGGTCTAA
** * *
12511220 ATCTATAGCGGCGTTTTCTAAAAAAACGCCGCAACAGGTCGG
1 ATCTATAGCGGCGTTTT-TGGAAAAACGCCGCAAAAGGTCAG
* *
12511262 CTCTATAGCGGCGCTTTTCGGAACAAACGCCGCAATAA-GTCGAG
1 ATCTATAGCGGCG-TTTTTGGAA-AAACGCCGCAA-AAGGTC-AG
* * * *
12511306 CTCTATAGCGTCGTTTTCGGAGAAAACGCCGCAAAAGGTCAA
1 ATCTATAGCGGCGTTTTTGGA-AAAACGCCGCAAAAGGTCAG
*
12511348 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAATAGGTCGAG
1 ATCTATAGCGGCGTTTTTGGAA-AAACGCCGCAAAAGGTC-AG
* * * *
12511391 ATCAATAACGGCGTTTTCTATG-AAAACGCCGCAAAATGTCAG
1 ATCTATAGCGGCGTTTT-T-GGAAAAACGCCGCAAAAGGTCAG
**
12511433 ATCTATAGCGGCGTTTTTGGAGAAAACGTTGCAAAAGGTCAG
1 ATCTATAGCGGCGTTTTTGGA-AAAACGCCGCAAAAGGTCAG
* * **
12511475 ATTTATAGCGGCGTTTTTGGAATAAACGCCGTAAAATTTCAG
1 ATCTATAGCGGCGTTTTTGGAA-AAACGCCGCAAAAGGTCAG
12511517 ATCTATAGCGGCGTTTTTGGA
1 ATCTATAGCGGCGTTTTTGGA
12511538 TGCAAACGCC
Statistics
Matches: 232, Mismatches: 31, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
40 1 0.00
41 3 0.01
42 139 0.60
43 71 0.31
44 17 0.07
45 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (41 bp):
ATCTATAGCGGCGTTTTTGGAAAAACGCCGCAAAAGGTCAG
Found at i:12511545 original size:127 final size:129
Alignment explanation
Indices: 12511180--12511549 Score: 387
Period size: 127 Copynumber: 2.9 Consensus size: 129
12511170 TCGCTAAAGT
* * * ** * *
12511180 TAGCGGCGTTTGTGGGAAAAAAATGCCGCAATCGGTCTAAATCTATAGCGGCGTTTTCT-AAAAA
1 TAGCGGCGTTT-TCGG-AGAAAACGCCGCAAAAGGTC-AAATCTATAGCGGCGTTTT-TGGAACA
* * * * *
12511244 AACGCCGCAACAGGTCG-GCTCTATAGCGGCGCTTTTCGGA-ACAAACGCCGCAATAAGTCGAGC
62 AACGCCGCAAAAGGTCGAGATCTATAGCGGCG-TTTTTGGATGCAAACGCCGCAATAAGTCGAGA
12511307 TCTA
126 TCTA
*
12511311 TAGCGTCGTTTTCGGAGAAAACGCCGCAAAAGGTCAAATCTATAGCGGCGTTTTTGGAACAAACG
1 TAGCGGCGTTTTCGGAGAAAACGCCGCAAAAGGTCAAATCTATAGCGGCGTTTTTGGAACAAACG
* * * *
12511376 CCGCAATAGGTCGAGATCAATAACGGCGTTTTCT--ATGAAAACGCCGCAA-AATGTC-AGATCT
66 CCGCAAAAGGTCGAGATCTATAGCGGCGTTTT-TGGATGCAAACGCCGCAATAA-GTCGAGATCT
12511437 A
129 A
* ** * * *
12511438 TAGCGGCGTTTTTGGAGAAAACGTTGCAAAAGGTCAGATTTATAGCGGCGTTTTTGGAATAAACG
1 TAGCGGCGTTTTCGGAGAAAACGCCGCAAAAGGTCAAATCTATAGCGGCGTTTTTGGAACAAACG
* **
12511503 CCGTAAAATTTC-AGATCTATAGCGGCGTTTTTGGATGCAAACGCCGC
66 CCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGATGCAAACGCCGC
12511550 TAATTATCGT
Statistics
Matches: 202, Mismatches: 30, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
125 1 0.00
126 17 0.08
127 88 0.44
128 56 0.28
129 27 0.13
130 3 0.01
131 10 0.05
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (129 bp):
TAGCGGCGTTTTCGGAGAAAACGCCGCAAAAGGTCAAATCTATAGCGGCGTTTTTGGAACAAACG
CCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGATGCAAACGCCGCAATAAGTCGAGATCTA
Found at i:12516273 original size:41 final size:41
Alignment explanation
Indices: 12516219--12516603 Score: 314
Period size: 41 Copynumber: 9.4 Consensus size: 41
12516209 TTGTAAACAC
* * *
12516219 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCGCTAAAGTACGACTCTATTGCGGCGTTTGTATAA
* * * * *
12516260 AAATGCCGCTAAAGAACGTA-TTTATAGCGGCGTTTGAATAA
1 AAACGCCGCTAAAGTACG-ACTCTATTGCGGCGTTTGTATAA
* * ** * *
12516301 AAACGCCACTAAAGTATGTGTCTATAGCGGCTTTTGTATAA
1 AAACGCCGCTAAAGTACGACTCTATTGCGGCGTTTGTATAA
* * *
12516342 AAACGCCGCTAAAGTACTACTCTTTTGCGGTGTTTGTATAAA
1 AAACGCCGCTAAAGTACGACTCTATTGCGGCGTTTGTAT-AA
* * * *
12516384 AAACGCCGCTAAAGTACTACTCTGTTGCGGCGTTTAT-TGA
1 AAACGCCGCTAAAGTACGACTCTATTGCGGCGTTTGTATAA
* * * * *
12516424 AAACGCC-ATAATA-TATGAACCCTATTGCGGCGTTTTTATTA
1 AAACGCCGCTAA-AGTACG-ACTCTATTGCGGCGTTTGTATAA
* * * ** *
12516465 AAACGCCGCTAAAGTACTACTATGTCACGGCGTTTGTTTAAA
1 AAACGCCGCTAAAGTACGACTCTATTGCGGCGTTTGTAT-AA
* * * *
12516507 AAACGCCACT-ATGGATGAAC-CTATTGCGGCGTTTGTATAA
1 AAACGCCGCTAAAGTACG-ACTCTATTGCGGCGTTTGTATAA
* * *
12516547 AAACGCCACTAAAGTACTACTCTGTTGCGGCGTTTTGTATAA
1 AAACGCCGCTAAAGTACGACTCTATTGCGGCG-TTTGTATAA
12516589 AAACGCCGCTAAAGT
1 AAACGCCGCTAAAGT
12516604 TACTATTTTG
Statistics
Matches: 271, Mismatches: 60, Indels: 25
0.76 0.17 0.07
Matches are distributed among these distances:
39 5 0.02
40 39 0.14
41 150 0.55
42 77 0.28
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (41 bp):
AAACGCCGCTAAAGTACGACTCTATTGCGGCGTTTGTATAA
Found at i:12517834 original size:17 final size:16
Alignment explanation
Indices: 12517808--12517940 Score: 62
Period size: 17 Copynumber: 8.2 Consensus size: 16
12517798 TATAAAATAT
12517808 AAAATATAAAAATAATCA
1 AAAAT-TAAAAAT-ATCA
* *
12517826 AAAATTAAATATATTA
1 AAAATTAAAAATATCA
* *
12517842 AAAATTAAAATTATTA
1 AAAATTAAAAATATCA
*
12517858 AAATTTTAAAAATAT--
1 AAA-ATTAAAAATATCA
*
12517873 -ATATTAAAAATAT-A
1 AAAATTAAAAATATCA
*
12517887 AAAA-T-AAAATTTCTA
1 AAAATTAAAAATATC-A
* *
12517902 AAATTTTAAAATATATTA
1 AAA-ATTAAAA-ATATCA
* *
12517920 CAAATTATAAAATATTA
1 AAAATTA-AAAATATCA
12517937 AAAA
1 AAAA
12517941 ACAACAAAAT
Statistics
Matches: 89, Mismatches: 16, Indels: 21
0.71 0.13 0.17
Matches are distributed among these distances:
13 16 0.18
14 2 0.02
15 6 0.07
16 20 0.22
17 28 0.31
18 14 0.16
19 3 0.03
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATTAAAAATATCA
Found at i:12517835 original size:23 final size:22
Alignment explanation
Indices: 12517792--12517892 Score: 82
Period size: 24 Copynumber: 4.4 Consensus size: 22
12517782 AAGAATATTT
12517792 TAAAAATATAAAATATAAAATA
1 TAAAAATATAAAATATAAAATA
12517814 TAAAAATAATCAAAA-ATTAAATATA
1 TAAAAAT-AT-AAAATA-TAAA-ATA
*
12517839 TTAAAAAT-TAAAATTATTAAAATTT
1 -TAAAAATATAAAA-TA-TAAAA-TA
* *
12517864 TAAAAATATATATTA-AAAATA
1 TAAAAATATAAAATATAAAATA
12517885 TAAAAATA
1 TAAAAATA
12517893 AAATTTCTAA
Statistics
Matches: 66, Mismatches: 4, Indels: 19
0.74 0.04 0.21
Matches are distributed among these distances:
21 9 0.14
22 11 0.17
23 7 0.11
24 19 0.29
25 13 0.20
26 7 0.11
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAAATATAAAATATAAAATA
Found at i:12517841 original size:9 final size:8
Alignment explanation
Indices: 12517794--12517939 Score: 80
Period size: 9 Copynumber: 18.5 Consensus size: 8
12517784 GAATATTTTA
12517794 AAAATA-T
1 AAAATATT
12517801 AAAATA-T
1 AAAATATT
*
12517808 AAAATATA
1 AAAATATT
*
12517816 AAAATAATC
1 AAAAT-ATT
12517825 AAAA-ATT
1 AAAATATT
12517832 AAATATATT
1 AAA-ATATT
12517841 AAAA-ATT
1 AAAATATT
12517848 AAAATTATT
1 AAAA-TATT
*
12517857 AAAATTTT
1 AAAATATT
12517865 AAAA-A-T
1 AAAATATT
*
12517871 -ATATATT
1 AAAATATT
12517878 AAAA-ATAT
1 AAAATAT-T
12517886 AAAA-A-T
1 AAAATATT
*
12517892 AAAATTTCT
1 AAAATAT-T
*
12517901 AAAATTTT
1 AAAATATT
12517909 AAAATATATT
1 -AAA-ATATT
12517919 ACAAAT-TAT
1 A-AAATAT-T
12517928 AAAATATT
1 AAAATATT
12517936 AAAA
1 AAAA
12517940 AACAACAAAA
Statistics
Matches: 112, Mismatches: 9, Indels: 35
0.72 0.06 0.22
Matches are distributed among these distances:
5 2 0.02
6 7 0.06
7 28 0.25
8 33 0.29
9 36 0.32
10 6 0.05
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (8 bp):
AAAATATT
Found at i:12517895 original size:6 final size:7
Alignment explanation
Indices: 12517794--12517896 Score: 52
Period size: 7 Copynumber: 13.7 Consensus size: 7
12517784 GAATATTTTA
12517794 AAAATAT
1 AAAATAT
12517801 AAAATAT
1 AAAATAT
12517808 AAAATAT
1 AAAATAT
12517815 AAAAATAAT
1 -AAAAT-AT
12517824 CAAAA-ATT
1 -AAAATA-T
12517832 AAATATATT
1 AAA-ATA-T
12517841 AAAA-ATT
1 AAAATA-T
12517848 AAAATTATT
1 AAAA-TA-T
*
12517857 AAAATTTT
1 AAAA-TAT
12517865 AAAAATAT
1 -AAAATAT
* *
12517873 ATATTA-
1 AAAATAT
12517879 AAAATAT
1 AAAATAT
12517886 AAAA-AT
1 AAAATAT
12517892 AAAAT
1 AAAAT
12517897 TTCTAAAATT
Statistics
Matches: 79, Mismatches: 7, Indels: 20
0.75 0.07 0.19
Matches are distributed among these distances:
6 10 0.13
7 33 0.42
8 11 0.14
9 25 0.32
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (7 bp):
AAAATAT
Found at i:12517905 original size:35 final size:36
Alignment explanation
Indices: 12517834--12517904 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 36
12517824 CAAAAATTAA
12517834 ATATATTAAAAATTAAAATTATTAAAATTTTAAAAAT
1 ATATATTAAAAATTAAAA-TATTAAAATTTTAAAAAT
12517871 ATATATTAAAAATATAAAA-A-TAAAATTTCTAAAA
1 ATATATTAAAAAT-TAAAATATTAAAATTT-TAAAA
12517905 TTTTAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
35 8 0.25
36 6 0.19
37 13 0.41
38 5 0.16
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (36 bp):
ATATATTAAAAATTAAAATATTAAAATTTTAAAAAT
Found at i:12517939 original size:44 final size:44
Alignment explanation
Indices: 12517829--12517939 Score: 131
Period size: 44 Copynumber: 2.5 Consensus size: 44
12517819 ATAATCAAAA
*
12517829 ATTAAATATATTAAAAATTAAAATTATTAAAATTTTAAAAATATAT
1 ATTAAAAATA-TAAAAATTAAAATTATTAAAATTTT-AAAATATAT
12517875 ATTAAAAATATAAAAA-TAAAATT-TCTAAAATTTT-AAA-ATAT
1 ATTAAAAATATAAAAATTAAAATTAT-TAAAATTTTAAAATATAT
*
12517916 ATTACAAATTATAAAATATTAAAA
1 ATTA-AAAATATAAAA-ATTAAAA
12517940 AACAACAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
41 8 0.14
42 13 0.22
43 2 0.03
44 21 0.36
45 6 0.10
46 9 0.15
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (44 bp):
ATTAAAAATATAAAAATTAAAATTATTAAAATTTTAAAATATAT
Found at i:12523202 original size:37 final size:37
Alignment explanation
Indices: 12523129--12523203 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
12523119 GTTGGAAAAT
* *
12523129 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
12523166 ATTTATATATATATT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATATAT-T-TTCTTTAAAAAATTGAAAATCATAAA
12523203 A
1 A
12523204 AGATTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 16 0.48
38 15 0.45
39 2 0.06
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:12524735 original size:2 final size:2
Alignment explanation
Indices: 12524728--12524752 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12524718 TTATTATTAT
12524728 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12524753 TTATTTAATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12524786 original size:8 final size:8
Alignment explanation
Indices: 12524721--12524800 Score: 69
Period size: 8 Copynumber: 10.2 Consensus size: 8
12524711 ACTAGTATTA
12524721 TTAT-TAT
1 TTATATAT
12524728 TATATATAT
1 T-TATATAT
*
12524737 ATATATAT
1 TTATATAT
*
12524745 ATATATAT
1 TTATATAT
*
12524753 TTATTTAAT
1 TTATAT-AT
*
12524762 TTA-ACA-
1 TTATATAT
*
12524768 TTA-AAAT
1 TTATATAT
12524775 TTATATAT
1 TTATATAT
12524783 TTATATAT
1 TTATATAT
12524791 TTATATAT
1 TTATATAT
12524799 TT
1 TT
12524801 TTTCCTTTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
6 5 0.08
7 5 0.08
8 43 0.70
9 8 0.13
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (8 bp):
TTATATAT
Found at i:12524892 original size:17 final size:18
Alignment explanation
Indices: 12524870--12524903 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12524860 AAATATATTG
12524870 TTTTTGTAT-TGTTTTTA
1 TTTTTGTATCTGTTTTTA
*
12524887 TTTTTGTTTCTGTTTTT
1 TTTTTGTATCTGTTTTT
12524904 TAATTCCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.06, C:0.03, G:0.12, T:0.79
Consensus pattern (18 bp):
TTTTTGTATCTGTTTTTA
Found at i:12524948 original size:15 final size:15
Alignment explanation
Indices: 12524930--12524979 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
12524920 TTTCCTTTTT
12524930 TTGTTTTATTTAATC
1 TTGTTTTATTTAATC
*
12524945 TTGTTTTATTTATTCATT
1 TTGTTTTATTTA---ATC
*
12524963 TTGTTTTATTTCATC
1 TTGTTTTATTTAATC
12524978 TT
1 TT
12524980 TATTCATCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 16 0.55
18 13 0.45
ACGTcount: A:0.16, C:0.08, G:0.06, T:0.70
Consensus pattern (15 bp):
TTGTTTTATTTAATC
Found at i:12524968 original size:18 final size:15
Alignment explanation
Indices: 12524928--12524973 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
12524918 TTTTTCCTTT
12524928 TTTTGTTTTATTTAA
1 TTTTGTTTTATTTAA
*
12524943 TCTTGTTTTATTTATTCA
1 TTTTGTTTTATTTA---A
12524961 TTTTGTTTTATTT
1 TTTTGTTTTATTT
12524974 CATCTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 13 0.50
18 13 0.50
ACGTcount: A:0.15, C:0.04, G:0.07, T:0.74
Consensus pattern (15 bp):
TTTTGTTTTATTTAA
Found at i:12524997 original size:33 final size:33
Alignment explanation
Indices: 12524928--12525002 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
12524918 TTTTTCCTTT
*
12524928 TTTTGTTTTATTTAATCTTGTTTTATTTATTCA
1 TTTTGTTTTATTTAATCTTGTTTCATTTATTCA
*
12524961 TTTTGTTTTATTTCATCTT-TATTCATCTTATT-A
1 TTTTGTTTTATTTAATCTTGT-TTCAT-TTATTCA
*
12524994 TTTTATTTT
1 TTTTGTTTT
12525003 GTCTTATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 1 0.03
33 31 0.84
34 5 0.14
ACGTcount: A:0.17, C:0.08, G:0.04, T:0.71
Consensus pattern (33 bp):
TTTTGTTTTATTTAATCTTGTTTCATTTATTCA
Found at i:12525009 original size:18 final size:16
Alignment explanation
Indices: 12524994--12525035 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
12524984 CATCTTATTA
12524994 TTTTATTTTGTCTTAT
1 TTTTATTTTGTCTTAT
*
12525010 TTTTATTTTTATCTTTAT
1 TTTTA-TTTTGTC-TTAT
12525028 TTTTATTT
1 TTTTATTT
12525036 ATTTTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 5 0.22
17 9 0.39
18 9 0.39
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTTATTTTGTCTTAT
Found at i:12525026 original size:12 final size:11
Alignment explanation
Indices: 12525010--12525042 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
12525000 TTTGTCTTAT
12525010 TTTTATTTTTA
1 TTTTATTTTTA
12525021 TCTTTATTTTTA
1 T-TTTATTTTTA
12525033 -TTTATTTTTA
1 TTTTATTTTTA
12525043 AATATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.48
11 1 0.05
12 10 0.48
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:12525042 original size:6 final size:6
Alignment explanation
Indices: 12525006--12525035 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
12524996 TTATTTTGTC
*
12525006 TTATTT TTATTT TTATCT TTATTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT
12525036 ATTTTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (6 bp):
TTATTT
Found at i:12525089 original size:19 final size:20
Alignment explanation
Indices: 12525047--12525089 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
12525037 TTTTTAAATA
*
12525047 TTTTTCCTTTTTATCTTTAT
1 TTTTTCCTTTTTATCTTTAC
12525067 TTTTTCC-TTTTAT-TTCTAC
1 TTTTTCCTTTTTATCTT-TAC
12525086 TTTT
1 TTTT
12525090 AGGGTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 12 0.57
20 7 0.33
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTCCTTTTTATCTTTAC
Found at i:12527998 original size:31 final size:31
Alignment explanation
Indices: 12527960--12528115 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
12527950 CCCGAAGGAC
* * *
12527960 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
12527991 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
12528022 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
12528053 CAGTCTATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
12528084 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
12528115 C
1 C
12528116 CCTCAACCCT
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:12532545 original size:31 final size:31
Alignment explanation
Indices: 12532507--12532724 Score: 357
Period size: 31 Copynumber: 7.0 Consensus size: 31
12532497 CCCGAAGGAC
* * *
12532507 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
12532538 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
12532569 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
12532600 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
12532631 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
** *
12532662 CAGTATATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
12532693 CAGTCCATATGTCCCGAAGAACATAGATAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
12532724 C
1 C
12532725 CCTCGACCCT
Statistics
Matches: 176, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
31 175 0.99
32 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:12535130 original size:22 final size:22
Alignment explanation
Indices: 12535098--12535139 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
12535088 GAAGGACCAC
*
12535098 TATGTCTCGAAGGACCACTGTA
1 TATGTCCCGAAGGACCACTGTA
12535120 TATGTCCCGAAGGACCACTG
1 TATGTCCCGAAGGACCACTG
12535140 ATAATCCCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (22 bp):
TATGTCCCGAAGGACCACTGTA
Found at i:12541977 original size:18 final size:18
Alignment explanation
Indices: 12541956--12542023 Score: 84
Period size: 18 Copynumber: 3.8 Consensus size: 18
12541946 ATATTTGTCT
*
12541956 CGAATGACCACT-ATGTCC
1 CGAAGGACCACTGA-GTCC
*
12541974 CGAAAGACCACTGAGTCC
1 CGAAGGACCACTGAGTCC
* *
12541992 CGTAGGACCACTGAGTCT
1 CGAAGGACCACTGAGTCC
12542010 CGAAGGACCACTGA
1 CGAAGGACCACTGA
12542024 TAATCCCTCG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
18 43 0.98
19 1 0.02
ACGTcount: A:0.29, C:0.31, G:0.24, T:0.16
Consensus pattern (18 bp):
CGAAGGACCACTGAGTCC
Found at i:12542290 original size:2 final size:2
Alignment explanation
Indices: 12542285--12542315 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12542275 ACACACACAC
12542285 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 A
12542316 AAAGTATGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12548737 original size:188 final size:182
Alignment explanation
Indices: 12548379--12548748 Score: 686
Period size: 188 Copynumber: 2.0 Consensus size: 182
12548369 ATTCGAGCTA
12548379 CAATGGGCAAAATATAAAGACCTTGTGAGTATATGGAGATCATTATTAGTAATCTATCAGCTCCA
1 CAATGGGCAAAATATAAAGACCTTGTGAGTATATGGAGATCATTATTAGTAATCTATCAGCTCCA
12548444 TGGAGAATGGGAACCAAGGAGTAAAGCTGGTGGAGTACCGGAAGCTAAATTGGATTTGCTCGAAG
66 TGGAGAATGGGAACCAAGGAGTAAAGCTGGTGGAGTACCGGAAGCTAAATTGGATTTGCTCGAAG
12548509 AATCAATAAAGTTACCTTCCACTATGTGCCTAGGGAAGAAAATAAAATGATT
131 AATCAATAAAGTTACCTTCCACTATGTGCCTAGGGAAGAAAATAAAATGATT
12548561 CAATGGGGCAAAATATAAAGACCTTGTGAGTATATGGAGATTCATTATTAGTAATCTATCAGCTC
1 CAAT-GGGCAAAATATAAAGACCTTGTGAGTATATGGAGA-TCATTATTAGTAATCTATCAGCTC
12548626 CATGGAGAATGGGAAACCAAGGATGTAAAGCTGGTGGAGTACCGGAAGCTAATATTGGATTTGCT
64 CATGGAGAATGGG-AACCAAGGA-GTAAAGCTGGTGGAGTACCGGAAGCTAA-ATTGGATTTGCT
12548691 CGAAGAATTCAATAAAGTTACCTTCCACTATGTGCCTAGGGAAGAAAATAAAATGATT
126 CGAAGAA-TCAATAAAGTTACCTTCCACTATGTGCCTAGGGAAGAAAATAAAATGATT
12548749 GATGCTTTAG
Statistics
Matches: 182, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
182 4 0.02
183 35 0.19
184 37 0.20
185 9 0.05
186 28 0.15
187 19 0.10
188 50 0.27
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (182 bp):
CAATGGGCAAAATATAAAGACCTTGTGAGTATATGGAGATCATTATTAGTAATCTATCAGCTCCA
TGGAGAATGGGAACCAAGGAGTAAAGCTGGTGGAGTACCGGAAGCTAAATTGGATTTGCTCGAAG
AATCAATAAAGTTACCTTCCACTATGTGCCTAGGGAAGAAAATAAAATGATT
Found at i:12550176 original size:6 final size:6
Alignment explanation
Indices: 12550165--12550192 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
12550155 CTAAATTAAA
12550165 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
12550193 GGAATAAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:12551514 original size:24 final size:24
Alignment explanation
Indices: 12551470--12551516 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
12551460 ATAAAGAACC
*
12551470 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
12551494 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
12551517 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:12561199 original size:10 final size:10
Alignment explanation
Indices: 12561184--12561217 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
12561174 AAGATAGTAA
12561184 AATAAAAAAT
1 AATAAAAAAT
12561194 AATAAAAAAT
1 AATAAAAAAT
*
12561204 AAGAAGAAAAT
1 AATAA-AAAAT
12561215 AAT
1 AAT
12561218 CCTCACGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 14 0.67
11 7 0.33
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (10 bp):
AATAAAAAAT
Found at i:12561735 original size:24 final size:24
Alignment explanation
Indices: 12561691--12561737 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
12561681 ATAAAGAACC
*
12561691 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
12561715 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
12561738 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:12565823 original size:24 final size:24
Alignment explanation
Indices: 12565796--12565847 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
12565786 AACGAATATA
*
12565796 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
12565820 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
12565844 TCAA
1 TCAA
12565848 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:12565848 original size:24 final size:24
Alignment explanation
Indices: 12565816--12565934 Score: 161
Period size: 24 Copynumber: 5.0 Consensus size: 24
12565806 AAACATAAAT
*
12565816 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
*
12565840 CAGGTCAAGTAACAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
12565864 CAAGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
12565888 CATGTCATA-TATCAGATCAGAATC
1 CAGGTCA-AGTATCAGATCAGAATC
*
12565912 CATGTCAAGTATCAGATCAGAAT
1 CAGGTCAAGTATCAGATCAGAAT
12565935 TCAAATCGAA
Statistics
Matches: 87, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
23 4 0.05
24 82 0.94
25 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:12565950 original size:48 final size:48
Alignment explanation
Indices: 12565852--12565952 Score: 141
Period size: 48 Copynumber: 2.1 Consensus size: 48
12565842 GGTCAAGTAA
** *
12565852 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCATGTCATATAT
1 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCATAAAT
* *
12565900 CAGATCAGAATCCATGTCAAGTATCAGATCAGAATTCAAATCGA-AAAT
1 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATC-ATAAAT
12565948 CAGAT
1 CAGAT
12565953 AAAATATTCA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 46 0.98
49 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.24
Consensus pattern (48 bp):
CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCATAAAT
Found at i:12568424 original size:31 final size:31
Alignment explanation
Indices: 12568387--12568451 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
12568377 GTCGGTCAAC
* *
12568387 GGTCAACGAGTCGGGTCAACAGGTCGGGTCG
1 GGTCAACGAGTCAGGTAAACAGGTCGGGTCG
* *
12568418 GGTCAACGGGTCAGGTAAACGGGTCGGGTCG
1 GGTCAACGAGTCAGGTAAACAGGTCGGGTCG
12568449 GGT
1 GGT
12568452 TATAACCGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.18, C:0.20, G:0.45, T:0.17
Consensus pattern (31 bp):
GGTCAACGAGTCAGGTAAACAGGTCGGGTCG
Found at i:12568427 original size:13 final size:13
Alignment explanation
Indices: 12568411--12568447 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
12568401 GTCAACAGGT
12568411 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
* *
12568424 CGGGTCAGGTAAA
1 CGGGTCGGGTCAA
12568437 CGGGTCGGGTC
1 CGGGTCGGGTC
12568448 GGGTTATAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.16, C:0.22, G:0.46, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:12569690 original size:18 final size:18
Alignment explanation
Indices: 12569669--12569714 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 18
12569659 TTTTCTTTTC
12569669 TTTTGTTTTATTTAATCA
1 TTTTGTTTTATTTAATCA
12569687 --TT-TTTTATTTAATCA
1 TTTTGTTTTATTTAATCA
12569702 TTTTGTTTTATTT
1 TTTTGTTTTATTT
12569715 CATCTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 13 0.52
16 2 0.08
17 2 0.08
18 8 0.32
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (18 bp):
TTTTGTTTTATTTAATCA
Found at i:12570775 original size:2 final size:2
Alignment explanation
Indices: 12570770--12570806 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
12570760 ATATACTTTA
*
12570770 AT AT AT AT AT AT AT CT 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 A
12570807 GTGGAGTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12571693 original size:70 final size:70
Alignment explanation
Indices: 12571611--12571749 Score: 235
Period size: 70 Copynumber: 2.0 Consensus size: 70
12571601 TTTATTATGG
12571611 TACCAAATCCCATCATAGTAGGACCAATATAACTTGTATAGAGTT-TCTAGACTATAGACTTAAT
1 TACCAAATCCCATCATAGTAGGACCAATATAACTTGTATAGAGTTATCTAGA-TATAGACTTAAT
*
12571675 TAGGGA
65 CAGGGA
* *
12571681 TACCAAATCCCATCATTGTAGGACCAATATAACTTGTATAGAGTTATCTAGATATAGATTTAATC
1 TACCAAATCCCATCATAGTAGGACCAATATAACTTGTATAGAGTTATCTAGATATAGACTTAATC
12571746 AGGG
66 AGGG
12571750 TAAGTGAATG
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
70 59 0.91
71 6 0.09
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (70 bp):
TACCAAATCCCATCATAGTAGGACCAATATAACTTGTATAGAGTTATCTAGATATAGACTTAATC
AGGGA
Found at i:12573773 original size:19 final size:21
Alignment explanation
Indices: 12573749--12573793 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
12573739 TTTTATTGAA
12573749 TTTTATT-CACTTTTAATT-T
1 TTTTATTGCACTTTTAATTAT
* *
12573768 TTTTATTGCATTTTTATTTAT
1 TTTTATTGCACTTTTAATTAT
12573789 TTTTA
1 TTTTA
12573794 AAAAAATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.32
20 9 0.41
21 6 0.27
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTATTGCACTTTTAATTAT
Found at i:12577140 original size:11 final size:12
Alignment explanation
Indices: 12577124--12577182 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 12
12577114 TTATTGTATC
12577124 TCTTTCA-AATA
1 TCTTTCATAATA
12577135 TCTTTCATAACTA
1 TCTTTCATAA-TA
* * *
12577148 TATTTTTATTATCA
1 T-CTTTCATAAT-A
12577162 TCTTTCA-AATA
1 TCTTTCATAATA
12577173 TCTTTCATAA
1 TCTTTCATAA
12577183 CTATATTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
11 15 0.41
12 6 0.16
13 8 0.22
14 8 0.22
ACGTcount: A:0.32, C:0.17, G:0.00, T:0.51
Consensus pattern (12 bp):
TCTTTCATAATA
Found at i:12577150 original size:38 final size:38
Alignment explanation
Indices: 12577110--12577193 Score: 136
Period size: 38 Copynumber: 2.3 Consensus size: 38
12577100 TGTGTATATA
*
12577110 TATATTATT-GTATC-TCTTTCAAATATCTTTCATAAC
1 TATATTTTTAGTATCATCTTTCAAATATCTTTCATAAC
*
12577146 TATATTTTTATTATCATCTTTCAAATATCTTTCATAAC
1 TATATTTTTAGTATCATCTTTCAAATATCTTTCATAAC
12577184 TATATTTTTA
1 TATATTTTTA
12577194 TTATTATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
36 8 0.18
37 4 0.09
38 32 0.73
ACGTcount: A:0.31, C:0.14, G:0.01, T:0.54
Consensus pattern (38 bp):
TATATTTTTAGTATCATCTTTCAAATATCTTTCATAAC
Found at i:12577194 original size:38 final size:37
Alignment explanation
Indices: 12577120--12577197 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 37
12577110 TATATTATTG
12577120 TATCTCTTTCAAATATCTTTCATAACTATATTTTTAT
1 TATCTCTTTCAAATATCTTTCATAACTATATTTTTAT
12577157 TATCATCTTTCAAATATCTTTCATAACTATATTTTTAT
1 TATC-TCTTTCAAATATCTTTCATAACTATATTTTTAT
12577195 TAT
1 TAT
12577198 TATTTTTCCG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 4 0.10
38 36 0.90
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (37 bp):
TATCTCTTTCAAATATCTTTCATAACTATATTTTTAT
Found at i:12577577 original size:144 final size:150
Alignment explanation
Indices: 12577389--12577683 Score: 539
Period size: 144 Copynumber: 2.0 Consensus size: 150
12577379 TCATATCATT
12577389 TAATCGGCTACAATCTTTTAACATGATTAAACTCATTTTAAAAATTTACCGCAATCCCACTTTTA
1 TAATCGGCTACAATCTTTTAACATGATTAAACTCATTTTAAAAATTTACCGCAATCCCACTTTTA
12577454 TATATAAATATATATTATAATATATATATCATC-TTATT-TCA-T-TCCACTTA-TGAACTCTTA
66 TATATAAATATATATTATAATATATATATCATCTTTATTGTCATTATCCACTTATTGAACTCTTA
12577514 AGTTTACAAAG-TTCTCAAA
131 AGTTTACAAAGTTTCTCAAA
12577533 TAATCGGCTACAATCTTTTAACATGATTAAACTCATTTTAAAAATTTACCGCAATCCCACTTTTA
1 TAATCGGCTACAATCTTTTAACATGATTAAACTCATTTTAAAAATTTACCGCAATCCCACTTTTA
12577598 TATATAAATATATATTATAATATATATATCATCTTTATTGTCATTCATCCACTTATTGAACTCTT
66 TATATAAATATATATTATAATATATATATCATCTTTATTGTCATT-ATCCACTTATTGAACTCTT
12577663 AAGTTTACAAAGTTTCTCAAA
130 AAGTTTACAAAGTTTCTCAAA
12577684 ACTTACAAAG
Statistics
Matches: 144, Mismatches: 0, Indels: 7
0.95 0.00 0.05
Matches are distributed among these distances:
144 98 0.68
145 5 0.03
146 3 0.02
147 1 0.01
149 8 0.06
150 21 0.15
151 8 0.06
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (150 bp):
TAATCGGCTACAATCTTTTAACATGATTAAACTCATTTTAAAAATTTACCGCAATCCCACTTTTA
TATATAAATATATATTATAATATATATATCATCTTTATTGTCATTATCCACTTATTGAACTCTTA
AGTTTACAAAGTTTCTCAAA
Found at i:12577691 original size:19 final size:19
Alignment explanation
Indices: 12577667--12577716 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
12577657 ACTCTTAAGT
12577667 TTACAAAGTTTCTCAAAAC
1 TTACAAAGTTTCTCAAAAC
12577686 TTACAAAGTTTCTCAAAAC
1 TTACAAAGTTTCTCAAAAC
12577705 TTACAAAGTTTC
1 TTACAAAGTTTC
12577717 ACATCCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (19 bp):
TTACAAAGTTTCTCAAAAC
Found at i:12577790 original size:2 final size:2
Alignment explanation
Indices: 12577785--12577810 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12577775 CCATTTTTTC
12577785 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
12577811 TATCTCTACT
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:12584873 original size:29 final size:29
Alignment explanation
Indices: 12584831--12584920 Score: 153
Period size: 29 Copynumber: 3.1 Consensus size: 29
12584821 CCCGACCCGA
12584831 GTGCTATTTTCGTAAATATTTTTAAAAGG
1 GTGCTATTTTCGTAAATATTTTTAAAAGG
**
12584860 GTGCTATTTTCGTAAATATTTTTAAAAAT
1 GTGCTATTTTCGTAAATATTTTTAAAAGG
*
12584889 GTGTTATTTTCGTAAATATTTTTAAAAGG
1 GTGCTATTTTCGTAAATATTTTTAAAAGG
12584918 GTG
1 GTG
12584921 TTAGTTTCAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.47
Consensus pattern (29 bp):
GTGCTATTTTCGTAAATATTTTTAAAAGG
Found at i:12585553 original size:2 final size:2
Alignment explanation
Indices: 12585546--12585613 Score: 100
Period size: 2 Copynumber: 34.0 Consensus size: 2
12585536 GATTTGATAA
* * *
12585546 AT AT AT AT GT TT AC 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
*
12585588 AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
12585614 TTCACTGAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12586554 original size:22 final size:20
Alignment explanation
Indices: 12586529--12586571 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
12586519 TCATGATGAG
12586529 ATATGGAAGATAAAGATGGTTT
1 ATATGG-AGAT-AAGATGGTTT
*
12586551 ATATGGATATAAGATGGTTT
1 ATATGGAGATAAGATGGTTT
12586571 A
1 A
12586572 AGTAATGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 3 0.15
22 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.26, T:0.35
Consensus pattern (20 bp):
ATATGGAGATAAGATGGTTT
Found at i:12586871 original size:64 final size:63
Alignment explanation
Indices: 12586737--12586895 Score: 212
Period size: 64 Copynumber: 2.5 Consensus size: 63
12586727 TTGTTCAGTG
* * * *
12586737 TGTATCGATGCACAGGAAGTGCATCGATGCACCCCTTAAAATGGAAACATCGAATGCAATTGG
1 TGTATCGATGCATAGGAAGTGCATCGATGCACCCCTTAAAATGAAAACATCGAAGGCAATTGA
* * *
12586800 TGCATCGATGCATAAGG-AGTGCATCGATGCATCCCCTTAAAATGAAAACATCGAAGGTAATTTA
1 TGTATCGATGCAT-AGGAAGTGCATCGATGCA-CCCCTTAAAATGAAAACATCGAAGGCAATTGA
* *
12586864 TGTATCGATGCATGGGTAGTGCATCGATGCAC
1 TGTATCGATGCATAGGAAGTGCATCGATGCAC
12586896 ATGTTAAAGA
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 28 0.33
64 56 0.67
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (63 bp):
TGTATCGATGCATAGGAAGTGCATCGATGCACCCCTTAAAATGAAAACATCGAAGGCAATTGA
Found at i:12586928 original size:20 final size:20
Alignment explanation
Indices: 12586883--12586940 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
12586873 GCATGGGTAG
12586883 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
12586907 TGCGTCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
12586927 TGCATCGATGCACT
1 TGCATCGATGCACT
12586941 TCAAGGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 2 0.06
24 12 0.38
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:12589183 original size:31 final size:31
Alignment explanation
Indices: 12589098--12589204 Score: 101
Period size: 31 Copynumber: 3.5 Consensus size: 31
12589088 GGGTCGAGGG
* *
12589098 TTTATCTATGTTCTACGGAACATATGGACAA
1 TTTACCTATGTTCTAAGGAACATATGGACAA
*** *
12589129 TTTTACCT-TG-TCTTTCGAGACATATAGACAA
1 -TTTACCTATGTTCTAAGGA-ACATATGGACAA
* *
12589160 TATACCTATGTTCTAAGGAACATATGGACAG
1 TTTACCTATGTTCTAAGGAACATATGGACAA
*
12589191 TTTACCTAGGTTCT
1 TTTACCTATGTTCT
12589205 TCGGGACCTA
Statistics
Matches: 59, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
30 11 0.19
31 37 0.63
32 11 0.19
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTACCTATGTTCTAAGGAACATATGGACAA
Found at i:12589540 original size:2 final size:2
Alignment explanation
Indices: 12589527--12589570 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
12589517 GAATACAATG
12589527 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12589570 T
1 T
12589571 GTTTTGTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12589591 original size:33 final size:33
Alignment explanation
Indices: 12589556--12589619 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
12589546 TATATATATA
*
12589556 TATAT-ATAT-ATATATGT-TTTGTTATATGAAT
1 TATATGATATGATATATGTGTGTGTTA-ATGAAT
12589587 TATATGATATGATATATGTGTGTGTTAATGAAT
1 TATATGATATGATATATGTGTGTGTTAATGAAT
12589620 ATTGTATATG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 5 0.17
32 4 0.14
33 14 0.48
34 6 0.21
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (33 bp):
TATATGATATGATATATGTGTGTGTTAATGAAT
Found at i:12589602 original size:12 final size:11
Alignment explanation
Indices: 12589527--12589604 Score: 69
Period size: 10 Copynumber: 7.5 Consensus size: 11
12589517 GAATACAATG
12589527 TATATGATATA
1 TATATGATATA
12589538 TATAT-ATATA
1 TATATGATATA
12589548 TATAT-ATATA
1 TATATGATATA
12589558 TATAT-ATATA
1 TATATGATATA
* ** *
12589568 TATGTTTTGT-
1 TATATGATATA
12589578 TATATGA-AT-
1 TATATGATATA
12589587 TATATGATATGA
1 TATATGATAT-A
12589599 TATATG
1 TATATG
12589605 TGTGTGTTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
9 8 0.14
10 35 0.62
11 7 0.12
12 6 0.11
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (11 bp):
TATATGATATA
Found at i:12595891 original size:41 final size:41
Alignment explanation
Indices: 12595869--12595969 Score: 193
Period size: 41 Copynumber: 2.5 Consensus size: 41
12595859 ACAACTGTAG
*
12595869 ACTATCGCAACGCGAACTGAAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
12595910 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
12595951 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
12595970 CAACGCGAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
Found at i:12595897 original size:20 final size:20
Alignment explanation
Indices: 12595872--12595944 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
12595862 ACTGTAGACT
*
12595872 ATCGCAACGCGAACTGAAAA
1 ATCGCAACGCGAAATGAAAA
** * **
12595892 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
12595913 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
12595933 ATCGCAACGCGA
1 ATCGCAACGCGA
12595945 TTTTCAACTA
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.40, C:0.26, G:0.19, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:12595973 original size:21 final size:21
Alignment explanation
Indices: 12595869--12595973 Score: 97
Period size: 21 Copynumber: 5.1 Consensus size: 21
12595859 ACAACTGTAG
*
12595869 ACTATCGCAACGCGAACTG-A
1 ACTATCGCAACGCGAAATGCA
** ** *
12595889 AAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
12595910 ACTATCGCAACGCGAAATG-A
1 ACTATCGCAACGCGAAATGCA
** ** *
12595930 AAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
12595951 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
12595972 AC
1 AC
12595974 GCGAATTTGC
Statistics
Matches: 63, Mismatches: 20, Indels: 3
0.73 0.23 0.03
Matches are distributed among these distances:
20 29 0.46
21 34 0.54
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.18
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:12597134 original size:29 final size:29
Alignment explanation
Indices: 12597097--12597195 Score: 108
Period size: 29 Copynumber: 3.3 Consensus size: 29
12597087 TTTCATTCAA
* * * *
12597097 GTATATAAAGTATTTTTTGATCAAAGTTG
1 GTATCTAAAGTATTTTTTGGTCAAAATAG
*
12597126 GTATCTAAACTTATCTTTTTGGTCAAAATAG
1 GTATCTAAA-GTAT-TTTTTGGTCAAAATAG
* *
12597157 GTACCTAAAGTATTTTATGGTCAAAATAG
1 GTATCTAAAGTATTTTTTGGTCAAAATAG
*
12597186 GTAGCTAAAG
1 GTATCTAAAG
12597196 CAGGGTTTCA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 32 0.54
30 6 0.10
31 21 0.36
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.38
Consensus pattern (29 bp):
GTATCTAAAGTATTTTTTGGTCAAAATAG
Found at i:12599551 original size:2 final size:2
Alignment explanation
Indices: 12599544--12599589 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
12599534 TTGGTAAGAT
12599544 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12599586 TA TA
1 TA TA
12599590 ATGTTTAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12619227 original size:45 final size:45
Alignment explanation
Indices: 12619163--12619266 Score: 208
Period size: 45 Copynumber: 2.3 Consensus size: 45
12619153 GAATGTAAAA
12619163 GAGCAGAGCTAATTTAAAATATATTATGAGTTTTACTTGGCTCAG
1 GAGCAGAGCTAATTTAAAATATATTATGAGTTTTACTTGGCTCAG
12619208 GAGCAGAGCTAATTTAAAATATATTATGAGTTTTACTTGGCTCAG
1 GAGCAGAGCTAATTTAAAATATATTATGAGTTTTACTTGGCTCAG
12619253 GAGCAGAGCTAATT
1 GAGCAGAGCTAATT
12619267 GATAGGTAGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.34
Consensus pattern (45 bp):
GAGCAGAGCTAATTTAAAATATATTATGAGTTTTACTTGGCTCAG
Found at i:12620938 original size:105 final size:106
Alignment explanation
Indices: 12620792--12621000 Score: 323
Period size: 105 Copynumber: 2.0 Consensus size: 106
12620782 ACAAATACAA
*
12620792 TAGTTCTCTTATAAAAAAATTATTCTTTCACAATTTTTTCAATAAATTTGAATCTTAAAATATGA
1 TAGTTCTCTTATAAAAAAATTATTCTTTCACAATTTTTTCAATAAATTTAAATCTTAAAATATGA
* *
12620857 TTTAATAAATTTAAACCTTGAAAAAAAATCTATTAATTTAG
66 TCTAATAAATTTAAACCTTCAAAAAAAATCTATTAATTTAG
*
12620898 TAGTTCT-TTA-ATAAAAAATTATTCTTTCGCAATTTTTTCAATAAATTTAAATCTTAAAATATG
1 TAGTTCTCTTATA-AAAAAATTATTCTTTCACAATTTTTTCAATAAATTTAAATCTTAAAATATG
* * * *
12620961 ATCTAATACATTTAAATCTTCAAATAAGATCTATTAATTT
65 ATCTAATAAATTTAAACCTTCAAAAAAAATCTATTAATTT
12621001 GACTAAAATT
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
104 1 0.01
105 86 0.91
106 7 0.07
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (106 bp):
TAGTTCTCTTATAAAAAAATTATTCTTTCACAATTTTTTCAATAAATTTAAATCTTAAAATATGA
TCTAATAAATTTAAACCTTCAAAAAAAATCTATTAATTTAG
Found at i:12620973 original size:28 final size:28
Alignment explanation
Indices: 12620937--12620993 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
12620927 CAATTTTTTC
*
12620937 AATAAATTTAAATCTTAAAATATGATCT
1 AATAAATTTAAATCTTAAAATAAGATCT
* *
12620965 AATACATTTAAATCTTCAAATAAGATCT
1 AATAAATTTAAATCTTAAAATAAGATCT
12620993 A
1 A
12620994 TTAATTTGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.37
Consensus pattern (28 bp):
AATAAATTTAAATCTTAAAATAAGATCT
Found at i:12625481 original size:81 final size:79
Alignment explanation
Indices: 12625297--12625561 Score: 406
Period size: 81 Copynumber: 3.3 Consensus size: 79
12625287 CCTTACGGAC
* * *
12625297 CTAAGGATAT-CTTGGGTAGGCCCAAGGCATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCATAA
1 CTAAGGATATCCTTGGGTAGGCCCAAGGTATATCCTTAGGTTGGTTCCTTTTGCTGTGTGCTTAA
*
12625361 GGTAACCCTAAGAT
66 GGTAACCCTACGAT
** *
12625375 CTAAGGATGCCCTTGGGTAGGCCCAAGGTATATCCTTAGGTTGGTTCCTTTTTGTTGTGTGCTTA
1 CTAAGGATATCCTTGGGTAGGCCCAAGGTATATCCTTAGGTTGGTTCC-TTTTGCTGTGTGCTTA
12625440 AGGTAACCCTACGAAT
65 AGGTAACCCTACG-AT
* *
12625456 CTAAGGATGTCCTTGGGTAGACCCAAGGTATATCCTTAGGTTGGTTCCCTTTTGCTGTGTGCTTA
1 CTAAGGATATCCTTGGGTAGGCCCAAGGTATATCCTTAGGTTGGTT-CCTTTTGCTGTGTGCTTA
12625521 AGGTAACCCTACGGAT
65 AGGTAACCCTAC-GAT
12625537 CTAAGGATATCCTTGGGTAGGCCCA
1 CTAAGGATATCCTTGGGTAGGCCCA
12625562 TAGACCTAAG
Statistics
Matches: 170, Mismatches: 12, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
78 8 0.05
79 36 0.21
80 25 0.15
81 98 0.58
82 3 0.02
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (79 bp):
CTAAGGATATCCTTGGGTAGGCCCAAGGTATATCCTTAGGTTGGTTCCTTTTGCTGTGTGCTTAA
GGTAACCCTACGAT
Found at i:12628663 original size:17 final size:17
Alignment explanation
Indices: 12628641--12628677 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
12628631 CACTTCTCCC
12628641 CTTTAAAACATTTAACA
1 CTTTAAAACATTTAACA
12628658 CTTTAAAACATTTAACA
1 CTTTAAAACATTTAACA
12628675 CTT
1 CTT
12628678 CTCCCTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (17 bp):
CTTTAAAACATTTAACA
Found at i:12630957 original size:21 final size:20
Alignment explanation
Indices: 12630908--12630971 Score: 96
Period size: 20 Copynumber: 3.2 Consensus size: 20
12630898 AAAACCAGAA
*
12630908 CCCC-AGGGGGGTATC-GATT
1 CCCCTAGGGGGGAATCAG-TT
12630927 CCCCTAGGGGGGAATCAGTT
1 CCCCTAGGGGGGAATCAGTT
12630947 CCCCTAGGGGGGAATCAGTT
1 CCCCTAGGGGGGAATCAGTT
12630967 CCCCT
1 CCCCT
12630972 TCAAAGGGGG
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
19 4 0.10
20 37 0.88
21 1 0.02
ACGTcount: A:0.17, C:0.30, G:0.33, T:0.20
Consensus pattern (20 bp):
CCCCTAGGGGGGAATCAGTT
Found at i:12631012 original size:43 final size:40
Alignment explanation
Indices: 12630908--12631012 Score: 90
Period size: 43 Copynumber: 2.6 Consensus size: 40
12630898 AAAACCAGAA
* *
12630908 CCCC-AGGGGGGTATCGATTCCCCTAGGGGGGAATCAGTT
1 CCCCTAGGAGGGTATCGATTCCCCTAAGGGGGAATCAGTT
* * *
12630947 CCCCTAGGGGGGAATC-AGTTCCCCTTCAAAGGGGGAATCGGTT
1 CCCCTAGGAGGGTATCGA-TTCCCC-T--AAGGGGGAATCAGTT
*
12630990 -CCCTCATGAGGGTATCGATTCCC
1 CCCCT-AGGAGGGTATCGATTCCC
12631013 TCTGCACTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
39 5 0.09
40 16 0.30
41 1 0.02
42 4 0.08
43 26 0.49
44 1 0.02
ACGTcount: A:0.19, C:0.28, G:0.31, T:0.22
Consensus pattern (40 bp):
CCCCTAGGAGGGTATCGATTCCCCTAAGGGGGAATCAGTT
Found at i:12634841 original size:22 final size:21
Alignment explanation
Indices: 12634800--12634839 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12634790 GAGTTTATTT
*
12634800 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
12634821 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
12634840 ACTATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:12636510 original size:193 final size:197
Alignment explanation
Indices: 12636166--12636555 Score: 736
Period size: 193 Copynumber: 2.0 Consensus size: 197
12636156 TTTCTCAACC
12636166 AAAGTCTTCGTCCACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCT
1 AAAGTCTTCGTCCACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCT
12636231 TTCTTTTGAGGACAAAGAGTAACCTTACAAACCCTCAAGAATTATACCCCAAATTCTTGAGAACA
66 TTCTTTTGAGGACAAAGAGTAACCTTACAAACCCTCAAGAATTATACCCCAAATTCTTGAGAACA
12636296 CTATCTCCCAAAGAGACAATAC-AATTTGCAAACTTACATGGAAATCCTCACAAGGTA-ATTGTT
131 CTATCTCCCAAAGAGACAATACAAATTTGCAAACTTACATGGAAATCCTCACAAGGTAGATTGTT
12636359 TG
196 TG
12636361 AAAGTCTTCGTCCACTACCTTAGCTAT-CAC-CTAAGGATTTTCCACAAATTCACTAATTTGTCT
1 AAAGTCTTCGTCCACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCT
12636424 TTCTTTTGAGGACAAAGAGTAACCTTACAAA-CCTCAAGAATTATACCCCAAATTCTTGAGAACA
66 TTCTTTTGAGGACAAAGAGTAACCTTACAAACCCTCAAGAATTATACCCCAAATTCTTGAGAACA
12636488 CTATCTCCCAAAGAGAACAATACAAATTTGCAAACTTACATGGAAATCCTCACAAGGTAGATTGT
131 CTATCTCCCAAAGAG-ACAATACAAATTTGCAAACTTACATGGAAATCCTCACAAGGTAGATTGT
12636553 TTG
195 TTG
12636556 CACAATTCTA
Statistics
Matches: 192, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
192 48 0.25
193 71 0.37
194 38 0.20
195 35 0.18
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (197 bp):
AAAGTCTTCGTCCACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCT
TTCTTTTGAGGACAAAGAGTAACCTTACAAACCCTCAAGAATTATACCCCAAATTCTTGAGAACA
CTATCTCCCAAAGAGACAATACAAATTTGCAAACTTACATGGAAATCCTCACAAGGTAGATTGTT
TG
Found at i:12637749 original size:35 final size:35
Alignment explanation
Indices: 12637642--12637749 Score: 105
Period size: 35 Copynumber: 3.2 Consensus size: 35
12637632 AATGAATATC
*
12637642 TATCTAAACGACTTTAGTGGTGAATAAAATGTAAA
1 TATCTAAACGACTTTAGTGGTGAATGAAATGTAAA
* ** ** * **
12637677 TATCTAAATGACCGTAGTGGCAAATG-CA--TATC
1 TATCTAAACGACTTTAGTGGTGAATGAAATGTAAA
*
12637709 TATCTAAACAACTTTAGTGGTGAATGAAATGTAAA
1 TATCTAAACGACTTTAGTGGTGAATGAAATGTAAA
12637744 TATCTA
1 TATCTA
12637750 TGACCCTAGT
Statistics
Matches: 52, Mismatches: 18, Indels: 6
0.68 0.24 0.08
Matches are distributed among these distances:
32 22 0.42
33 1 0.02
34 1 0.02
35 28 0.54
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (35 bp):
TATCTAAACGACTTTAGTGGTGAATGAAATGTAAA
Found at i:12637791 original size:65 final size:66
Alignment explanation
Indices: 12637632--12637801 Score: 191
Period size: 67 Copynumber: 2.6 Consensus size: 66
12637622 CCTAGCGACG
* * * * * * *
12637632 AATGAATATCTATCTAAACGACTTTAGTGGTGAATAAAATGTAAATATCTAAATGACCGTAGTGG
1 AATGCATATATATCTAAACAACCTTAGTGGTGAATGAAATGTAAATATCT-AATGACCCTAGTGC
12637697 CA
65 CA
* *
12637699 AATGCATATCTATCTAAACAACTTTAGTGGTGAATGAAATGTAAATATCT-ATGACCCTAGTGCC
1 AATGCATATATATCTAAACAACCTTAGTGGTGAATGAAATGTAAATATCTAATGACCCTAGTGCC
*
12637763 G
66 A
**
12637764 AATG-AGTATATATCTAAGTAACCTTAGTGGTGAGATGA
1 AATGCA-TATATATCTAAACAACCTTAGTGGTGA-ATGA
12637802 TGAATACATA
Statistics
Matches: 91, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 1 0.01
65 39 0.43
66 4 0.04
67 47 0.52
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.31
Consensus pattern (66 bp):
AATGCATATATATCTAAACAACCTTAGTGGTGAATGAAATGTAAATATCTAATGACCCTAGTGCC
A
Found at i:12639665 original size:21 final size:21
Alignment explanation
Indices: 12639641--12639691 Score: 50
Period size: 23 Copynumber: 2.4 Consensus size: 21
12639631 GAAAAGATCG
12639641 AAAACATGCCA-AAAAACAGA
1 AAAACATGCCATAAAAACAGA
* *
12639661 TAAAATCGTGTCATAAAAACAGA
1 -AAAA-CATGCCATAAAAACAGA
*
12639684 AAATCATG
1 AAAACATG
12639692 TCATGAAGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
21 7 0.29
22 8 0.33
23 9 0.38
ACGTcount: A:0.57, C:0.16, G:0.12, T:0.16
Consensus pattern (21 bp):
AAAACATGCCATAAAAACAGA
Found at i:12639693 original size:21 final size:21
Alignment explanation
Indices: 12639640--12639695 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
12639630 AGAAAAGATC
*
12639640 GAAAA-CATGCCA-AAAAACA
1 GAAAATCATGTCATAAAAACA
*
12639659 GATAAAATCGTGTCATAAAAACA
1 G--AAAATCATGTCATAAAAACA
12639682 GAAAATCATGTCAT
1 GAAAATCATGTCAT
12639696 GAAGGCATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 1 0.03
21 16 0.53
22 5 0.17
23 8 0.27
ACGTcount: A:0.54, C:0.16, G:0.12, T:0.18
Consensus pattern (21 bp):
GAAAATCATGTCATAAAAACA
Found at i:12640939 original size:3 final size:3
Alignment explanation
Indices: 12640931--12640980 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
12640921 AATCTATTTA
12640931 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12640979 AT
1 AT
12640981 CTGTTTTCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:12652995 original size:20 final size:20
Alignment explanation
Indices: 12652972--12653014 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
12652962 TGTAATTGAG
* *
12652972 TAATGTTTTGTATAATTAAA
1 TAATATTTTATATAATTAAA
* *
12652992 TAATATTTTATGTAATTAGA
1 TAATATTTTATATAATTAAA
12653012 TAA
1 TAA
12653015 CTATATAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (20 bp):
TAATATTTTATATAATTAAA
Found at i:12658885 original size:21 final size:21
Alignment explanation
Indices: 12658844--12658887 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
12658834 AAAAAAAAAT
*
12658844 TCGGATATACGAACTTTCGGA
1 TCGGATATACGAACTTCCGGA
*
12658865 TCGGATATATGAA-TATCCGGA
1 TCGGATATACGAACT-TCCGGA
12658886 TC
1 TC
12658888 TAAATGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (21 bp):
TCGGATATACGAACTTCCGGA
Found at i:12660380 original size:21 final size:22
Alignment explanation
Indices: 12660356--12660399 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
12660346 GATCGCTTTG
12660356 ATAAAATTTTA-AAAAATCCAT
1 ATAAAATTTTATAAAAATCCAT
* *
12660377 ATAATATTTTATAAGAATCCAT
1 ATAAAATTTTATAAAAATCCAT
12660399 A
1 A
12660400 CCTCATGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.36
Consensus pattern (22 bp):
ATAAAATTTTATAAAAATCCAT
Found at i:12661682 original size:23 final size:23
Alignment explanation
Indices: 12661656--12661711 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
12661646 TTATCTTCAA
**
12661656 ATTAATGAGAATTTTTTTAAAAT
1 ATTAATGAGAATAATTTTAAAAT
* *
12661679 ATTATATGAAAATAATTTTAAATT
1 ATTA-ATGAGAATAATTTTAAAAT
*
12661703 TTTAATGAG
1 ATTAATGAG
12661712 TTGAATTGAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 8 0.31
24 18 0.69
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.46
Consensus pattern (23 bp):
ATTAATGAGAATAATTTTAAAAT
Found at i:12662023 original size:20 final size:20
Alignment explanation
Indices: 12661998--12662037 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
12661988 TTATTCGTTG
12661998 AATTTTTAAAATTATAAAAT
1 AATTTTTAAAATTATAAAAT
*
12662018 AATTTTTAAAATTATCAAAT
1 AATTTTTAAAATTATAAAAT
12662038 TATTATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTTTTAAAATTATAAAAT
Found at i:12662259 original size:23 final size:23
Alignment explanation
Indices: 12662229--12662276 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
12662219 CAAAACAATT
* *
12662229 ATTTTAATATAGTTTAATGAGTC
1 ATTTTAATATAATTTAATGACTC
12662252 ATTTTAATATAATTTAATGACTC
1 ATTTTAATATAATTTAATGACTC
12662275 AT
1 AT
12662277 AATGTACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (23 bp):
ATTTTAATATAATTTAATGACTC
Found at i:12663120 original size:15 final size:14
Alignment explanation
Indices: 12663079--12663121 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
12663069 AAGAATGAAT
12663079 TAAA-AAAAAGAAA
1 TAAAGAAAAAGAAA
12663092 TAAAGAAAATAGAAA
1 TAAAGAAAA-AGAAA
*
12663107 TAAATGTAAAAGAAA
1 TAAA-GAAAAAGAAA
12663122 ATAATAGTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 4 0.15
14 4 0.15
15 14 0.54
16 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (14 bp):
TAAAGAAAAAGAAA
Found at i:12665077 original size:105 final size:105
Alignment explanation
Indices: 12664890--12665466 Score: 1028
Period size: 105 Copynumber: 5.5 Consensus size: 105
12664880 CCACTGCCAG
* *
12664890 TTGCATTGTCTAGAGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATG
1 TTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATG
*
12664955 TTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAAC
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
* *
12664995 TTGCGTTGTCTGGAGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATG
1 TTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATG
*
12665060 TTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAAC
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
* *
12665100 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAATTTGAGAAATG
1 TTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATG
*
12665165 TTTGTTGACAACCAGCAGTCCCTTCGTCGTGAAGTTGAAC
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
* *
12665205 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTCGAGAAATG
1 TTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATG
12665270 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
12665310 TTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATG
1 TTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATG
*
12665375 TTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
* *
12665415 TTGTGTTGTCTAGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTG
1 TTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
12665467 GGTAAAACCT
Statistics
Matches: 456, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 456 1.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (105 bp):
TTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATG
TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
Found at i:12676913 original size:15 final size:14
Alignment explanation
Indices: 12676876--12676914 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
12676866 AATGAATTAA
12676876 AAAAAGAAATAAAG
1 AAAAAGAAATAAAG
12676890 AAAATAGAAATAAATG
1 AAAA-AGAAATAAA-G
*
12676906 TAAAAGAAA
1 AAAAAGAAA
12676915 ATAATAGTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 4 0.18
15 14 0.64
16 4 0.18
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (14 bp):
AAAAAGAAATAAAG
Found at i:12684922 original size:24 final size:24
Alignment explanation
Indices: 12684852--12684911 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
12684842 TAATTAATTC
12684852 AAAAATTATTATTATATCAATTTT
1 AAAAATTATTATTATATCAATTTT
12684876 AAAAATTATTATTATATCAATTTT
1 AAAAATTATTATTATATCAATTTT
12684900 AAAAATTATTAT
1 AAAAATTATTAT
12684912 ATCATCTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAAATTATTATTATATCAATTTT
Found at i:12686017 original size:17 final size:17
Alignment explanation
Indices: 12685995--12686039 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
12685985 ACTGTACTTA
*
12685995 TATATGCCAATATAATC
1 TATATGTCAATATAATC
*
12686012 TATATGTAATATATAATC
1 TATATGTCA-ATATAATC
12686030 T-TATGTCAAT
1 TATATGTCAAT
12686040 TCAACGTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 2 0.08
17 13 0.54
18 9 0.38
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (17 bp):
TATATGTCAATATAATC
Found at i:12686409 original size:56 final size:56
Alignment explanation
Indices: 12686317--12686441 Score: 196
Period size: 56 Copynumber: 2.2 Consensus size: 56
12686307 TATACGTATT
* * * *
12686317 TGTTTGTTTATTTTTAAAGGTATTTATACTCGTATATTTATTTCTGAATACGTTCG
1 TGTTTGTTCATTTTTAAAGATATTCATACTCATATATTTATTTCTGAATACGTTCG
*
12686373 TGTTTGTTCATTTTTAAAGATATTCATATTCATATATTTATTTCTGAATACGTTCG
1 TGTTTGTTCATTTTTAAAGATATTCATACTCATATATTTATTTCTGAATACGTTCG
*
12686429 TGTCTGTTCATTT
1 TGTTTGTTCATTT
12686442 AATGTTAGCG
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.54
Consensus pattern (56 bp):
TGTTTGTTCATTTTTAAAGATATTCATACTCATATATTTATTTCTGAATACGTTCG
Found at i:12686459 original size:23 final size:23
Alignment explanation
Indices: 12686433--12686483 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
12686423 CGTTCGTGTC
*
12686433 TGTTCATTTAATGTTAGCGAATA
1 TGTTCATTTAACGTTAGCGAATA
** * *
12686456 TGTTTGTTTAACGTTTGTGAATA
1 TGTTCATTTAACGTTAGCGAATA
12686479 TGTTC
1 TGTTC
12686484 GTTCGTATAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.49
Consensus pattern (23 bp):
TGTTCATTTAACGTTAGCGAATA
Found at i:12690524 original size:18 final size:18
Alignment explanation
Indices: 12690486--12690524 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
12690476 TGAATACAAC
* *
12690486 AAAGAAAATTAAGAATCA
1 AAAGAAAAATAAGAATAA
*
12690504 AAAGAAAAATAAGACTAA
1 AAAGAAAAATAAGAATAA
12690522 AAA
1 AAA
12690525 TAATAAACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.72, C:0.05, G:0.10, T:0.13
Consensus pattern (18 bp):
AAAGAAAAATAAGAATAA
Found at i:12696052 original size:20 final size:20
Alignment explanation
Indices: 12696029--12696080 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
12696019 CGTTAAGGAA
*
12696029 TGCATCGATACACTGTATAG
1 TGCATCGATACACTGTAGAG
**
12696049 TGCATCGATATTCTGTAGAG
1 TGCATCGATACACTGTAGAG
12696069 TGCATCGATACA
1 TGCATCGATACA
12696081 TACCTTCATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (20 bp):
TGCATCGATACACTGTAGAG
Found at i:12700064 original size:31 final size:31
Alignment explanation
Indices: 12700028--12700168 Score: 210
Period size: 31 Copynumber: 4.5 Consensus size: 31
12700018 CATAGATTCT
* * *
12700028 GAAGAACCTAGGTAATCAGTCCATCTGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
* * *
12700059 AAAGAATATAGGTAAACAATCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
* *
12700090 GAAGAACATAGGTAAACATTCCATATGTCTC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
12700121 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
12700152 GAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
12700169 CCTCGACCCT
Statistics
Matches: 98, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 98 1.00
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:12701067 original size:22 final size:21
Alignment explanation
Indices: 12701042--12701101 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
12701032 TTCGCTTGAG
*
12701042 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
12701064 GGGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
12701084 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
12701102 CCCAGAAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 17 0.47
21 9 0.25
22 10 0.28
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:12705122 original size:31 final size:30
Alignment explanation
Indices: 12705084--12705239 Score: 204
Period size: 31 Copynumber: 5.0 Consensus size: 30
12705074 CCCGAAGTAC
* * *
12705084 CAGTCCATAGATTCCGAAGAACCTAGGTAAT
1 CAGTCCATAG-TCCCGAAGAACATAGGTAAA
* *
12705115 CAGTCCATCTGTCCCGAAGAATATAGGTAAA
1 CAGTCCAT-AGTCCCGAAGAACATAGGTAAA
*
12705146 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATA-GTCCCGAAGAACATAGGTAAA
*
12705177 CAGTCCATATGTCTCGAAGAACATAGGTAAA
1 CAGTCCATA-GTCCCGAAGAACATAGGTAAA
12705208 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATA-GTCCCGAAGAACATAGGTAAA
12705239 C
1 C
12705240 CCTCGACCCT
Statistics
Matches: 112, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
31 111 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (30 bp):
CAGTCCATAGTCCCGAAGAACATAGGTAAA
Found at i:12705184 original size:62 final size:62
Alignment explanation
Indices: 12705097--12705239 Score: 232
Period size: 62 Copynumber: 2.3 Consensus size: 62
12705087 TCCATAGATT
* * * *
12705097 CCGAAGAACCTAGGTAATCAGTCCATCTGTCCCGAAGAATATAGGTAAACAATCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAATCCATATGTC
* *
12705159 CCGAAGAACATAGGTAAACAGTCCATATGTCTCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAATCCATATGTC
12705221 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
12705240 CCTCGACCCT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 75 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.20
Consensus pattern (62 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAATCCATATGTC
Found at i:12706156 original size:22 final size:21
Alignment explanation
Indices: 12706125--12706184 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
12706115 TTCGCTTGAG
*
12706125 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
*
12706147 GTGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
12706167 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
12706185 CCCAAAAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 16 0.47
21 9 0.26
22 9 0.26
ACGTcount: A:0.18, C:0.27, G:0.23, T:0.32
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:12707118 original size:16 final size:16
Alignment explanation
Indices: 12707079--12707121 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
12707069 AGCATCAGTT
*
12707079 CTTATCACTCAAAATC
1 CTTATCAATCAAAATC
* *
12707095 ATTAATCAATCAAATTC
1 CTT-ATCAATCAAAATC
12707112 CTTATCAATC
1 CTTATCAATC
12707122 TTTAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
CTTATCAATCAAAATC
Found at i:12709071 original size:2 final size:2
Alignment explanation
Indices: 12709053--12709101 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
12709043 ATCATCTATC
* *
12709053 AT AT -T AT AT AA AC 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
12709094 AT AT AT AT
1 AT AT AT AT
12709102 CATAACTCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12709966 original size:31 final size:31
Alignment explanation
Indices: 12709930--12710054 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
12709920 CCCGAAGGAC
* * *
12709930 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
12709961 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
12709992 CAGTCTATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
12710023 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
12710054 C
1 C
12710055 CCTCGACCCT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:12710973 original size:22 final size:21
Alignment explanation
Indices: 12710942--12711001 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
12710932 TTTGCTTGAG
*
12710942 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
*
12710964 GTGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
12710984 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
12711002 CCCAGAAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 16 0.47
21 9 0.26
22 9 0.26
ACGTcount: A:0.18, C:0.27, G:0.23, T:0.32
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:12713315 original size:20 final size:20
Alignment explanation
Indices: 12713292--12713343 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
12713282 CGTTAAGGAA
*
12713292 TGCATCGATACACTGTATAG
1 TGCATCGATACACTGTAGAG
**
12713312 TGCATCGATATTCTGTAGAG
1 TGCATCGATACACTGTAGAG
12713332 TGCATCGATACA
1 TGCATCGATACA
12713344 TACCTTCATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (20 bp):
TGCATCGATACACTGTAGAG
Found at i:12714342 original size:31 final size:31
Alignment explanation
Indices: 12714221--12714345 Score: 135
Period size: 31 Copynumber: 4.0 Consensus size: 31
12714211 AGAGTCGAGG
12714221 GTTTACCTATGTTCTACGGGACATATGGACA
1 GTTTACCTATGTTCTACGGGACATATGGACA
* * *
12714252 GTTTTACCTATG-TCTTTCGAGACATATAGACA
1 G-TTTACCTATGTTC-TACGGGACATATGGACA
* * *
12714284 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGGACATATGGACA
* * * *
12714315 GTTTAACTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGGACATATGGACA
12714346 ATTACCGAGG
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
31 48 0.64
32 27 0.36
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGGACATATGGACA
Found at i:12718908 original size:155 final size:157
Alignment explanation
Indices: 12718619--12718930 Score: 610
Period size: 155 Copynumber: 2.0 Consensus size: 157
12718609 GTAATTATGA
12718619 AAACTCTGAACCCCATAAGGATTTGATTCGTTAGGTGTCTCATCAAAGTCATCACCCTCACCTTG
1 AAACTCTGAACCCCATAAGGATTTGATTCGTTAGGTGTCTCATCAAAGTCATCACCCTCACCTTG
12718684 CAACCCAGGACTTACATTGCTAAATGATAATTGATTCCCTTCTCCAGAAGAATTCTGACCTTGCA
66 CAACCCAGGACTTACATTGCTAAATGATAATTGATTCCCTTCTCCAGAAGAATTCTGACCTTGCA
12718749 ACGACTGATC-TTGATAACTCCATTAT
131 ACGACTGATCTTTGATAACTCCATTAT
12718775 AAACTC-GAACCCCATAAGGATTTGATTCGTTAGGTGTCTCATCAAAGTCATCACCCTCACCTTG
1 AAACTCTGAACCCCATAAGGATTTGATTCGTTAGGTGTCTCATCAAAGTCATCACCCTCACCTTG
12718839 CAACCCAGGACTTACATTGCTAAATGATAATTGATTCCCTTCTCCAGAAGAATTCTGACCTTGCA
66 CAACCCAGGACTTACATTGCTAAATGATAATTGATTCCCTTCTCCAGAAGAATTCTGACCTTGCA
12718904 ACGACTGATCTTTGATAACTCCATTAT
131 ACGACTGATCTTTGATAACTCCATTAT
12718931 TATATGTCAG
Statistics
Matches: 155, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
155 133 0.86
156 22 0.14
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.30
Consensus pattern (157 bp):
AAACTCTGAACCCCATAAGGATTTGATTCGTTAGGTGTCTCATCAAAGTCATCACCCTCACCTTG
CAACCCAGGACTTACATTGCTAAATGATAATTGATTCCCTTCTCCAGAAGAATTCTGACCTTGCA
ACGACTGATCTTTGATAACTCCATTAT
Found at i:12729488 original size:35 final size:35
Alignment explanation
Indices: 12729400--12729489 Score: 110
Period size: 35 Copynumber: 2.6 Consensus size: 35
12729390 TATGTCATCT
** *
12729400 GTGTTCAGGACTCGGATTTGGTAATCATGTTATCC
1 GTGTTCAGGTTTCGGATTTGGTAATCACGTTATCC
* *
12729435 GTGTTCATGATTT-GGATTTTGTAATCACGTTATCC
1 GTGTTCA-GGTTTCGGATTTGGTAATCACGTTATCC
*
12729470 GTGTTCAGGTTTCAGATTTG
1 GTGTTCAGGTTTCGGATTTG
12729490 TTGAAGTTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
34 4 0.09
35 39 0.87
36 2 0.04
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.42
Consensus pattern (35 bp):
GTGTTCAGGTTTCGGATTTGGTAATCACGTTATCC
Found at i:12733964 original size:28 final size:28
Alignment explanation
Indices: 12733924--12733977 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
12733914 ATAGTTTAAA
12733924 CTACCAATTTTAAAAGATAAAATAAACT
1 CTACCAATTTTAAAAGATAAAATAAACT
* *
12733952 CTACC-ATATTTAAAATATAAATTAAA
1 CTACCAAT-TTTAAAAGATAAAATAAA
12733978 TTTACGTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.31
Consensus pattern (28 bp):
CTACCAATTTTAAAAGATAAAATAAACT
Found at i:12743823 original size:5 final size:5
Alignment explanation
Indices: 12743809--12743847 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
12743799 GTCTTGCTCT
*
12743809 TCTTC GCTTC TCTTC TCTTC TCTTC TCGCTTC TCTTC TC
1 TCTTC TCTTC TCTTC TCTTC TCTTC T--CTTC TCTTC TC
12743848 GCTCCTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 25 0.83
7 5 0.17
ACGTcount: A:0.00, C:0.41, G:0.05, T:0.54
Consensus pattern (5 bp):
TCTTC
Found at i:12743840 original size:22 final size:24
Alignment explanation
Indices: 12743800--12743847 Score: 82
Period size: 22 Copynumber: 2.1 Consensus size: 24
12743790 TAATGGCATG
12743800 TCTTGCTCTTCTTCGCTTCTCTTC
1 TCTTGCTCTTCTTCGCTTCTCTTC
12743824 TCTT-CTCTTC-TCGCTTCTCTTC
1 TCTTGCTCTTCTTCGCTTCTCTTC
12743846 TC
1 TC
12743848 GCTCCTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 14 0.58
23 6 0.25
24 4 0.17
ACGTcount: A:0.00, C:0.40, G:0.06, T:0.54
Consensus pattern (24 bp):
TCTTGCTCTTCTTCGCTTCTCTTC
Found at i:12743842 original size:12 final size:12
Alignment explanation
Indices: 12743805--12743850 Score: 69
Period size: 12 Copynumber: 3.9 Consensus size: 12
12743795 GCATGTCTTG
12743805 CTCTTCTTCGCTT
1 CTCTTC-TCGCTT
12743818 CTCTTCT--CTT
1 CTCTTCTCGCTT
12743828 CTCTTCTCGCTT
1 CTCTTCTCGCTT
12743840 CTCTTCTCGCT
1 CTCTTCTCGCT
12743851 CCTTTAACCT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.32
12 15 0.48
13 6 0.19
ACGTcount: A:0.00, C:0.41, G:0.07, T:0.52
Consensus pattern (12 bp):
CTCTTCTCGCTT
Found at i:12744299 original size:23 final size:23
Alignment explanation
Indices: 12744273--12744339 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
12744263 CACCACAGCT
*
12744273 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
*
12744296 CGTAGAATTGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
12744319 CGTAGAATTACATCGAAGTGC
1 CGTAGAAATGCACCGAAGTGC
12744340 TATATAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:12745933 original size:20 final size:22
Alignment explanation
Indices: 12745897--12745954 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 22
12745887 TCCCCTTTGA
**
12745897 AGTGCATCGATATATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
12745917 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
12745940 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
12745955 CTACCCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.47
22 1 0.03
23 3 0.09
24 13 0.41
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:12748281 original size:19 final size:19
Alignment explanation
Indices: 12748257--12748300 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
12748247 ATGTCTCAGC
*
12748257 CACAAGTATTTTCTTTAAT
1 CACAAGTATTATCTTTAAT
12748276 CACAAGTATTATCTTTAAT
1 CACAAGTATTATCTTTAAT
12748295 CA-AAGT
1 CACAAGT
12748301 GATGCTATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (19 bp):
CACAAGTATTATCTTTAAT
Found at i:12755416 original size:6 final size:6
Alignment explanation
Indices: 12755407--12755452 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
12755397 CCTATTTAAG
*
12755407 AAAATA AAAAT- -AAATA AAAATA ATAAATA ATAATA TAAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA A-AAATA AAAATA -AAAATA AAAA
12755453 CTATATAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.12
6 19 0.56
7 11 0.32
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (6 bp):
AAAATA
Found at i:12755423 original size:10 final size:10
Alignment explanation
Indices: 12755408--12755450 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
12755398 CTATTTAAGA
12755408 AAATAAAAAT
1 AAATAAAAAT
12755418 AAATAAAAAT
1 AAATAAAAAT
12755428 -AATAAATAAT
1 AAATAAA-AAT
12755438 -AATATAAAAT
1 AAATA-AAAAT
12755448 AAA
1 AAA
12755451 AACTATATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 6 0.20
10 20 0.67
11 4 0.13
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:12755433 original size:13 final size:13
Alignment explanation
Indices: 12755415--12755452 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
12755405 AGAAAATAAA
12755415 AATAAATAAAAAT
1 AATAAATAAAAAT
*
12755428 AATAAATAATAAT
1 AATAAATAAAAAT
12755441 -ATAAAATAAAAA
1 AAT-AAATAAAAA
12755453 CTATATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 2 0.09
13 20 0.91
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAAATAAAAAT
Found at i:12755460 original size:21 final size:20
Alignment explanation
Indices: 12755409--12755463 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
12755399 TATTTAAGAA
12755409 AATAAA-AATAA-ATAAAAAT
1 AATAAATAATAATAT-AAAAT
12755428 AATAAATAATAATATAAAAT
1 AATAAATAATAATATAAAAT
12755448 AA-AAACTATATAATAT
1 AATAAA-TA-ATAATAT
12755464 TATATTTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
19 9 0.28
20 14 0.44
21 9 0.28
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (20 bp):
AATAAATAATAATATAAAAT
Found at i:12755488 original size:17 final size:17
Alignment explanation
Indices: 12755468--12755500 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12755458 TAATATTATA
12755468 TTTTCAAAAATAATATG
1 TTTTCAAAAATAATATG
*
12755485 TTTTCAAAAATTATAT
1 TTTTCAAAAATAATAT
12755501 ATTATATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (17 bp):
TTTTCAAAAATAATATG
Found at i:12755542 original size:42 final size:44
Alignment explanation
Indices: 12755448--12755544 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 44
12755438 AATATAAAAT
* *
12755448 AAAAACTATATA-A-TATTATATTTTCAAAAATAATATGTTTTC
1 AAAAACTATATATATTATTATATTTTCAAAAATAATATGTTCTA
*
12755490 AAAAA-T-TATATATTA-TATATGTTTCCAAAA-AAT-TGTTCTA
1 AAAAACTATATATATTATTATAT-TTTCAAAAATAATATGTTCTA
12755530 AAAAACTATATATAT
1 AAAAACTATATATAT
12755545 GTTTTCAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
40 14 0.30
41 11 0.23
42 22 0.47
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (44 bp):
AAAAACTATATATATTATTATATTTTCAAAAATAATATGTTCTA
Found at i:12755574 original size:14 final size:13
Alignment explanation
Indices: 12755541--12755574 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
12755531 AAAACTATAT
*
12755541 ATATGTTTTCAAA
1 ATATATTTTCAAA
12755554 ATATATTTTCAAA
1 ATATATTTTCAAA
12755567 ACTATATT
1 A-TATATT
12755575 ATATACGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (13 bp):
ATATATTTTCAAA
Found at i:12755617 original size:111 final size:107
Alignment explanation
Indices: 12755485--12755794 Score: 319
Period size: 111 Copynumber: 2.8 Consensus size: 107
12755475 AAATAATATG
*
12755485 TTTTCAAAAATTATATATTATATATGTTTCCAAAAAATTGTTCTAAAAA-ACTATATATATGTTT
1 TTTT-AAAAACTATATATTATATATGTTTCCAAAAAATTGTTCTAAAAACA-TATATATATGTTT
*
12755549 TCAAAATATATTTTCAAAACTATATTATATACGTTTTCAAAAATCG-
64 TCAAAA-ATATTTTCAAAACTACATTATATA--TTTTCAAAAATCGA
** * *
12755595 TTTTTGAAACTATATA-TATTATATGTTTTC-AAAAATGTGTT-TCCAAAACTATATAATATATG
1 TTTTAAAAACTATATATTA-TATATGTTTCCAAAAAAT-TGTTCT-AAAAAC-ATAT-ATATATG
*
12755657 TTTTCAAAAACGTATTTTCAAAACCACATTATATATTTTCAAAAATCGA
61 TTTTCAAAAA--TATTTTCAAAACTACATTATATATTTTCAAAAATCGA
* * *
12755706 TTTTAAAAACTATATATTATATGT-TTTCAAAAAAACACT-TTCTAAAAACTATATATTATATGT
1 TTTTAAAAACTATATATTATATATGTTTC-CAAAAA-ATTGTTCTAAAAAC-ATATA-TATATGT
*
12755769 TTTCAAAAAATATTTTAAAAACTACA
62 TTTC-AAAAATATTTTCAAAACTACA
12755795 AATGCCCCTG
Statistics
Matches: 168, Mismatches: 16, Indels: 32
0.78 0.07 0.15
Matches are distributed among these distances:
108 9 0.05
109 27 0.16
110 39 0.23
111 58 0.35
112 34 0.20
113 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.42
Consensus pattern (107 bp):
TTTTAAAAACTATATATTATATATGTTTCCAAAAAATTGTTCTAAAAACATATATATATGTTTTC
AAAAATATTTTCAAAACTACATTATATATTTTCAAAAATCGA
Found at i:12755656 original size:37 final size:36
Alignment explanation
Indices: 12755448--12755792 Score: 224
Period size: 35 Copynumber: 9.2 Consensus size: 36
12755438 AATATAAAAT
*
12755448 AAAAACTATATAATATTATATTTTCAAAAATAATATGTTTTC
1 AAAAACTATATAATA-TATGTTTTC---AA-AA-ATGTTTTC
* * * *
12755490 AAAAATTATATATTATATATGTTTCCAAAAAATTGTTCTA
1 AAAAACTATATA--ATATATGTTTTC-AAAAA-TGTTTTC
*
12755530 AAAAAC--TAT-ATATATGTTTTCAAAATATATTTTC
1 AAAAACTATATAATATATGTTTTCAAAA-ATGTTTTC
* *
12755564 -AAAACTATATTATATACGTTTTCAAAAATCGTTTT-
1 AAAAACTATATAATATATGTTTTCAAAAAT-GTTTTC
**
12755599 TGAAACTATATATATTATATGTTTTCAAAAATGTGTTTC
1 AAAAACTATATA-A-TATATGTTTTCAAAAATGT-TTTC
* *
12755638 CAAAACTATATAATATATGTTTTCAAAAACGTATTTTC
1 AAAAACTATATAATATATGTTTTCAAAAA--TGTTTTC
* * *
12755676 -AAAACCACAT--TATATATTTTCAAAAATCGATTTT-
1 AAAAACTATATAATATATGTTTTCAAAAAT-G-TTTTC
* ***
12755710 AAAAACTATATATTATATGTTTTCAAAAAAACACTTTC
1 AAAAACTATATAATATATGTTTTC--AAAAATGTTTTC
* *
12755748 TAAAAACTATATATTATATGTTTTCAAAAAATATTTT-
1 -AAAAACTATATAATATATGTTTTC-AAAAATGTTTTC
12755785 AAAAACTA
1 AAAAACTA
12755793 CAAATGCCCC
Statistics
Matches: 249, Mismatches: 30, Indels: 54
0.75 0.09 0.16
Matches are distributed among these distances:
33 6 0.02
34 8 0.03
35 44 0.18
36 36 0.14
37 40 0.16
38 37 0.15
39 42 0.17
40 12 0.05
41 3 0.01
42 11 0.04
43 7 0.03
44 3 0.01
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.41
Consensus pattern (36 bp):
AAAAACTATATAATATATGTTTTCAAAAATGTTTTC
Found at i:12755697 original size:35 final size:35
Alignment explanation
Indices: 12755531--12755792 Score: 203
Period size: 37 Copynumber: 7.2 Consensus size: 35
12755521 ATTGTTCTAA
12755531 AAAACTATA-TATATGTTTTCAAAATA--TATTTTC
1 AAAACTATATTATATGTTTTCAAAA-ACGTATTTTC
*
12755564 AAAACTATATTATATACGTTTTCAAAAATCGT-TTTTG
1 AAAACTATATTATAT--GTTTTCAAAAA-CGTATTTTC
* * * *
12755601 AAACTATATATATTATATGTTTTCAAAAATGTGTTTCC
1 AAA--A-CTATATTATATGTTTTCAAAAACGTATTTTC
12755639 AAAACTATATAATATATGTTTTCAAAAACGTATTTTC
1 AAAACTATAT--TATATGTTTTCAAAAACGTATTTTC
* * * *
12755676 AAAACCACATTATATATTTTCAAAAATCG-ATTTTA
1 AAAACTATATTATATGTTTTCAAAAA-CGTATTTTC
*** *
12755711 AAAACTATATATTATATGTTTTCAAAAAAACACTTTCTA
1 AAAAC--TATATTATATGTTTTCAAAAACGTA-TTT-TC
* *
12755750 AAAACTATATATTATATGTTTTCAAAAA-ATATTTTA
1 AAAAC--TATATTATATGTTTTCAAAAACGTATTTTC
12755786 AAAACTA
1 AAAACTA
12755793 CAAATGCCCC
Statistics
Matches: 192, Mismatches: 19, Indels: 35
0.78 0.08 0.14
Matches are distributed among these distances:
33 9 0.05
34 7 0.04
35 31 0.16
36 20 0.10
37 61 0.32
38 23 0.12
39 31 0.16
40 10 0.05
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.41
Consensus pattern (35 bp):
AAAACTATATTATATGTTTTCAAAAACGTATTTTC
Found at i:12755719 original size:72 final size:71
Alignment explanation
Indices: 12755498--12755738 Score: 224
Period size: 72 Copynumber: 3.3 Consensus size: 71
12755488 TCAAAAATTA
* * * * * *
12755498 TATATTATATATGTTTCCAAAAAATTG-TTCTAAAA-AACTATATATATGTTTTCAAAATAT-AT
1 TATATAATATATGTTTTC-AAAAATCGTTTTTAAAACCAC-ATATATATATTTTCAAAA-ATGAT
12755560 TTTCAAAAC
63 TTTCAAAAC
* * * * *
12755569 TATATTATATACGTTTTCAAAAATCGTTTTTGAAACTATATATATTATATGTTTTCAAAAATG-T
1 TATATAATATATGTTTTCAAAAATCGTTTTTAAAACCACATATA-TATA--TTTTCAAAAATGAT
12755633 GTTTCCAAAAC
63 -TTT-CAAAAC
12755644 TATATAATATATGTTTTCAAAAA-CGTATTTTCAAAACCACAT-TATATATTTTCAAAAATCGAT
1 TATATAATATATGTTTTCAAAAATCGT-TTTT-AAAACCACATATATATATTTTCAAAAAT-GAT
*
12755707 TTTAAAAAC
63 TTTCAAAAC
*
12755716 TATATATTATATGTTTTCAAAAA
1 TATATAATATATGTTTTCAAAAA
12755739 AACACTTTCT
Statistics
Matches: 143, Mismatches: 15, Indels: 23
0.79 0.08 0.13
Matches are distributed among these distances:
70 7 0.05
71 27 0.19
72 42 0.29
73 7 0.05
74 20 0.14
75 33 0.23
76 7 0.05
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (71 bp):
TATATAATATATGTTTTCAAAAATCGTTTTTAAAACCACATATATATATTTTCAAAAATGATTTT
CAAAAC
Done.