Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, 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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 56 of 109
Found at i:11067919 original size:2 final size:2
Alignment explanation
Indices: 11067907--11067945 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
11067897 ATGAGATTCT
* *
11067907 TA TA TA AA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11067946 CCATCACTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:11073858 original size:11 final size:10
Alignment explanation
Indices: 11073844--11073901 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 10
11073834 AATTTTATTT
11073844 AAAAAAAATCAA
1 AAAAAAAAT--A
11073856 AAAATAAAATA
1 AAAA-AAAATA
11073867 AAAATAAAATAA
1 AAAA-AAAAT-A
11073879 AAATAAAAATA
1 AAA-AAAAATA
11073890 AAAAAATAATA
1 AAAAAA-AATA
11073901 A
1 A
11073902 GATAAGGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
10 3 0.07
11 20 0.48
12 13 0.31
13 6 0.14
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:11073864 original size:6 final size:6
Alignment explanation
Indices: 11073855--11073893 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
11073845 AAAAAAATCA
11073855 AAAAAT -AAAAT AAAAAT -AAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
11073894 AATAATAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:11073875 original size:17 final size:17
Alignment explanation
Indices: 11073856--11073901 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
11073846 AAAAAATCAA
11073856 AAAAT-AAAATAAAAAT
1 AAAATAAAAATAAAAAT
11073872 AAAATAAAAATAAAAAT
1 AAAATAAAAATAAAAAT
11073889 AAAA-AAATAATAA
1 AAAATAAA-AATAA
11073902 GATAAGGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.29
17 20 0.71
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAATAAAAATAAAAAT
Found at i:11073946 original size:3 final size:3
Alignment explanation
Indices: 11073938--11073978 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
11073928 CTAATCAATA
*
11073938 AAT AAT AAT AAT AAT AAT AAT AA- AAGA AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AA
11073979 ATAAGAAAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.89
4 2 0.06
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:11073970 original size:21 final size:20
Alignment explanation
Indices: 11073944--11073986 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
11073934 AATAAATAAT
11073944 AATAATAATAATAATAAAAGA
1 AATAATAATAATAA-AAAAGA
*
11073965 AATAATAATAATAAATAAGA
1 AATAATAATAATAAAAAAGA
11073985 AA
1 AA
11073987 GAAAGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (20 bp):
AATAATAATAATAAAAAAGA
Found at i:11074478 original size:24 final size:25
Alignment explanation
Indices: 11074428--11074478 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
11074418 TCGGATTCTG
* *
11074428 AAAAATTTCCAAAAATTTTTCAGAA
1 AAAAACTTCCAAAAATTTTTCAAAA
11074453 AAAAACTT-CAAAAATTTTAT-AAAA
1 AAAAACTTCCAAAAATTTT-TCAAAA
11074477 AA
1 AA
11074479 TTCTCACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (25 bp):
AAAAACTTCCAAAAATTTTTCAAAA
Found at i:11074766 original size:3 final size:3
Alignment explanation
Indices: 11074758--11074805 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
11074748 ACCAACCAAA
*
11074758 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT CAT AAT AGAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
11074804 AA
1 AA
11074806 ATATACATTG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11074862 original size:18 final size:20
Alignment explanation
Indices: 11074816--11074876 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 20
11074806 ATATACATTG
11074816 ATAGATAAATATAAAAAAAATTA
1 ATAGAT-AA-ATAAAAAAAA-TA
11074839 ATAGATAAATAAAAAAAA-A
1 ATAGATAAATAAAAAAAATA
*
11074858 A-AGATAAATATAAAAAATA
1 ATAGATAAATAAAAAAAATA
11074877 TACATTAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
18 15 0.42
19 3 0.08
21 10 0.28
22 2 0.06
23 6 0.17
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (20 bp):
ATAGATAAATAAAAAAAATA
Found at i:11074863 original size:41 final size:45
Alignment explanation
Indices: 11074818--11074901 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 45
11074808 ATACATTGAT
11074818 AGATAAATAT-AAAAA-A-A-ATTAATAGATAAATAAAAAAAAAA
1 AGATAAATATAAAAAATATACATTAATAGATAAATAAAAAAAAAA
*
11074859 AGATAAATATAAAAAATATACATTAATAGATAAATAATAAAAA
1 AGATAAATATAAAAAATATACATTAATAGATAAATAAAAAAAA
11074902 CGTATATATA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
41 10 0.26
42 5 0.13
43 1 0.03
44 1 0.03
45 21 0.55
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.23
Consensus pattern (45 bp):
AGATAAATATAAAAAATATACATTAATAGATAAATAAAAAAAAAA
Found at i:11074889 original size:27 final size:28
Alignment explanation
Indices: 11074859--11074932 Score: 80
Period size: 33 Copynumber: 2.5 Consensus size: 28
11074849 AAAAAAAAAA
11074859 AGATAAATATAAAAA-ATATACATTAAT
1 AGATAAATATAAAAATATATACATTAAT
*
11074886 AGATAAATAATAAAAACGTATATATATATTAAT
1 AGATAAAT-AT-AAAA---ATATATACATTAAT
11074919 AGATAAATA-AAAAA
1 AGATAAATATAAAAA
11074933 GATTAGTAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
27 9 0.22
28 2 0.05
29 4 0.10
30 4 0.10
32 2 0.05
33 19 0.47
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (28 bp):
AGATAAATATAAAAATATATACATTAAT
Found at i:11074943 original size:54 final size:50
Alignment explanation
Indices: 11074880--11074981 Score: 134
Period size: 54 Copynumber: 2.0 Consensus size: 50
11074870 AAAAATATAC
*
11074880 ATTAATAGATAAATAATAA-AAACGTATATATATATTAATAGATAAATAAAAAAG
1 ATTAATAGATAAATAATAATAAA---ATATATAT-TT-ATAAATAAATAAAAAAG
*
11074934 ATTAGTAGATAAATAATAATAAAATATATATTTATAAATAAATAAAAA
1 ATTAATAGATAAATAATAATAAAATATATATTTATAAATAAATAAAAA
11074982 TAAAATTACA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
50 14 0.31
51 2 0.04
52 8 0.18
54 18 0.40
55 3 0.07
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (50 bp):
ATTAATAGATAAATAATAATAAAATATATATTTATAAATAAATAAAAAAG
Found at i:11074975 original size:29 final size:29
Alignment explanation
Indices: 11074861--11074987 Score: 90
Period size: 29 Copynumber: 4.6 Consensus size: 29
11074851 AAAAAAAAAG
* * *
11074861 ATAAAT-ATAA-AAAATATACATTAATAG
1 ATAAATAATAATAAAATATATATTTATAA
* * *
11074888 ATAAATAATAA-AAACGTATATATATATTA
1 ATAAATAATAATAAA-ATATATATTTATAA
* * *
11074917 ATAGAT-A-AATAAAA-A-AGA-TTAGTAG
1 ATAAATAATAATAAAATATATATTTA-TAA
11074942 ATAAATAATAATAAAATATATATTTATAA
1 ATAAATAATAATAAAATATATATTTATAA
*
11074971 ATAAATAAAAATAAAAT
1 ATAAATAATAATAAAAT
11074988 TACAAATGGG
Statistics
Matches: 75, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
24 2 0.03
25 8 0.11
26 2 0.03
27 15 0.20
28 12 0.16
29 33 0.44
30 3 0.04
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.31
Consensus pattern (29 bp):
ATAAATAATAATAAAATATATATTTATAA
Found at i:11074994 original size:22 final size:23
Alignment explanation
Indices: 11074951--11074994 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
11074941 GATAAATAAT
* * *
11074951 AATAAAATATATATTTATAAATA
1 AATAAAATATAAAATTACAAATA
11074974 AATAAAA-ATAAAATTACAAAT
1 AATAAAATATAAAATTACAAAT
11074995 GGGCTTACCC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
AATAAAATATAAAATTACAAATA
Found at i:11075237 original size:45 final size:43
Alignment explanation
Indices: 11075170--11075608 Score: 445
Period size: 45 Copynumber: 10.0 Consensus size: 43
11075160 TAATTTTGAT
* * * *
11075170 CAAAGCTCCTTTAAGCAAAGGCTCAACAACTTTGAGAAACATAAA
1 CAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGA-AAA-ATAAA
* * * * *
11075215 CAAAGCTCTTTTAAATAGAGGCTCAATGAATTTGAAAAATATAAA
1 CAAAGCTCCTCTAAACAGAGGCTCAACGACTTTG-AAAA-ATAAA
* * *
11075260 CAAAGCTCCTATAATCAGAGGCTCAACGA-TAAT-AAAAATAAA
1 CAAAGCTCCTCTAAACAGAGGCTCAACGACT-TTGAAAAATAAA
* *
11075302 TAAAGCTTCTCTAAACAGAGGCTCAACGACTTTTGAAAAGATAAA
1 CAAAGCTCCTCTAAACAGAGGCTCAACGAC-TTTGAAAA-ATAAA
* *
11075347 CAAAGCTCCTTTAAACAGAGGCTCAATGACTTTGAAAAATAAA
1 CAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAA
* * *
11075390 TAAATCT-CTCATAAACAGAGGCTCAATGACTTTTGAAAAGATAAA
1 CAAAGCTCCTC-TAAACAGAGGCTCAACGAC-TTTGAAAA-ATAAA
* *
11075435 CAAAGCTCCTCTAAACAAAGGCTCAACGACTTTGGAAAATAAA
1 CAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAA
* * *
11075478 TAAAGCTCCTCTAAACAGAGGCTCAATGATTTTTGAAAAATAAA
1 CAAAGCTCCTCTAAACAGAGGCTCAACGA-CTTTGAAAAATAAA
* * *
11075522 TAAAGCTCCTCTAATCAAAGGCTCAACGACTTTGAAAAAATAAA
1 CAAAGCTCCTCTAAACAGAGGCTCAACGACTTTG-AAAAATAAA
* * * * *
11075566 TAAAGCTCCTCTAGACAGAAGCTCAA-AACTTTAAAAAAGTAAA
1 CAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAA-TAAA
11075609 TGCTCATTGA
Statistics
Matches: 335, Mismatches: 46, Indels: 28
0.82 0.11 0.07
Matches are distributed among these distances:
42 37 0.11
43 78 0.23
44 98 0.29
45 118 0.35
46 4 0.01
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.23
Consensus pattern (43 bp):
CAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAA
Found at i:11075325 original size:87 final size:88
Alignment explanation
Indices: 11075170--11075591 Score: 530
Period size: 88 Copynumber: 4.8 Consensus size: 88
11075160 TAATTTTGAT
* * * * * * *
11075170 CAAAGCTCCTTTAAGCAAAGGCTCAACAACTTTGAGAAACATAAACAAAGCTCTTTTAAATAGAG
1 CAAAGCTCCTCTAAACAAAGGCTCAACGACTTTGA-AAA-ATAAATAAAGCTCCTCTAAACAGAG
* *
11075235 GCTCAATGA-ATTTGAAAAATATAAA
64 GCTCAATGACTTTTG-AAAAGATAAA
* * * * *
11075260 CAAAGCTCCTATAATCAGAGGCTCAACGA-TAAT-AAAAATAAATAAAGCTTCTCTAAACAGAGG
1 CAAAGCTCCTCTAAACAAAGGCTCAACGACT-TTGAAAAATAAATAAAGCTCCTCTAAACAGAGG
*
11075323 CTCAACGACTTTTGAAAAGATAAA
65 CTCAATGACTTTTGAAAAGATAAA
* * * *
11075347 CAAAGCTCCTTTAAACAGAGGCTCAATGACTTTGAAAAATAAATAAATCT-CTCATAAACAGAGG
1 CAAAGCTCCTCTAAACAAAGGCTCAACGACTTTGAAAAATAAATAAAGCTCCTC-TAAACAGAGG
11075411 CTCAATGACTTTTGAAAAGATAAA
65 CTCAATGACTTTTGAAAAGATAAA
*
11075435 CAAAGCTCCTCTAAACAAAGGCTCAACGACTTTGGAAAATAAATAAAGCTCCTCTAAACAGAGGC
1 CAAAGCTCCTCTAAACAAAGGCTCAACGACTTTGAAAAATAAATAAAGCTCCTCTAAACAGAGGC
*
11075500 TCAATGATTTTTGAAAA-ATAAA
66 TCAATGACTTTTGAAAAGATAAA
* * * *
11075522 TAAAGCTCCTCTAATCAAAGGCTCAACGACTTTGAAAAAATAAATAAAGCTCCTCTAGACAGAAG
1 CAAAGCTCCTCTAAACAAAGGCTCAACGACTTTG-AAAAATAAATAAAGCTCCTCTAAACAGAGG
11075587 CTCAA
65 CTCAA
11075592 AACTTTAAAA
Statistics
Matches: 295, Mismatches: 30, Indels: 16
0.87 0.09 0.05
Matches are distributed among these distances:
87 104 0.35
88 160 0.54
89 5 0.02
90 26 0.09
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.23
Consensus pattern (88 bp):
CAAAGCTCCTCTAAACAAAGGCTCAACGACTTTGAAAAATAAATAAAGCTCCTCTAAACAGAGGC
TCAATGACTTTTGAAAAGATAAA
Found at i:11076651 original size:17 final size:15
Alignment explanation
Indices: 11076631--11076673 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
11076621 TTCATTAACT
11076631 TTTTCTTTTCATTTTCA
1 TTTT-TTTTCATTTT-A
11076648 TTTTTTTTTCATTTTA
1 -TTTTTTTTCATTTTA
11076664 TTTTTTTTCA
1 TTTTTTTTCA
11076674 AGCATAGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.40
16 1 0.04
17 10 0.40
18 4 0.16
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTTTCATTTTA
Found at i:11077254 original size:185 final size:185
Alignment explanation
Indices: 11076936--11077305 Score: 654
Period size: 185 Copynumber: 2.0 Consensus size: 185
11076926 ATCATGGCAC
11076936 AATGTAATCAATATCTTTTCTTCTATGAAATTTAACTGTTCATAACGTTCTCAAATCCATTAAGC
1 AATGTAATCAATATCTTTTCTTCTATGAAATTTAACTGTTCATAACGTTCTCAAATCCATTAAGC
* *
11077001 TGTTTTCAATTCAACTTTTTTTAGAACCCTCAAGGATGGGATCTCCACTTCTACTGATAGTGCAA
66 TGCTTTCAATTCAACTTTTTTTAGAACCCTCAAGGATGGGATCTCCACTTCTACTGATAGTACAA
* * *
11077066 CTTCTATCTCATAAACCAAAGAAAATAGGATT-GCTCCAATAGAGGTACGCACTGA
131 CTTCTATCTCATAAACCAAAAAAAATAAGATTACCT-CAATAGAGGTACGCACTGA
*
11077121 AATGTAATCAATCTCTTTTCTTCTATGAAATTTAACTGTTCATAACGTTCTCAAATCCATTCAA-
1 AATGTAATCAATATCTTTTCTTCTATGAAATTTAACTGTTCATAACGTTCTCAAATCCATT-AAG
11077185 CTGCTTTCAATTCAACTTTTTTTAGAACCCTCAAGGATGGGATCTCCACTTCTACTGATAGTACA
65 CTGCTTTCAATTCAACTTTTTTTAGAACCCTCAAGGATGGGATCTCCACTTCTACTGATAGTACA
11077250 ACTTCTATCTCATAAACCAAAAAAAATAAGATTACCTCAATAGAGGTACGCACTGA
130 ACTTCTATCTCATAAACCAAAAAAAATAAGATTACCTCAATAGAGGTACGCACTGA
11077306 CGTTTGATAT
Statistics
Matches: 177, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
185 173 0.98
186 4 0.02
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (185 bp):
AATGTAATCAATATCTTTTCTTCTATGAAATTTAACTGTTCATAACGTTCTCAAATCCATTAAGC
TGCTTTCAATTCAACTTTTTTTAGAACCCTCAAGGATGGGATCTCCACTTCTACTGATAGTACAA
CTTCTATCTCATAAACCAAAAAAAATAAGATTACCTCAATAGAGGTACGCACTGA
Found at i:11078344 original size:7 final size:7
Alignment explanation
Indices: 11078332--11078365 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
11078322 CGAGTTTTGA
11078332 ATCTCTC
1 ATCTCTC
11078339 ATCTCTC
1 ATCTCTC
11078346 ATCTCTC
1 ATCTCTC
*
11078353 ATATCTC
1 ATCTCTC
11078360 AT-TCTC
1 ATCTCTC
11078366 TTTTCAACTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
6 4 0.15
7 22 0.85
ACGTcount: A:0.18, C:0.38, G:0.00, T:0.44
Consensus pattern (7 bp):
ATCTCTC
Found at i:11087366 original size:57 final size:57
Alignment explanation
Indices: 11087297--11087455 Score: 207
Period size: 58 Copynumber: 2.7 Consensus size: 57
11087287 GCTTTTATAT
*
11087297 AAGAAAAATTGATACTTTTAACTTTTTCTCAAAATATTTTTCT-G-AAACTTTAATTTC
1 AAGAAAAATTGATACTTTCAACTTTTTCTCAAAATATTTTT-TAGAAAAC-TTAATTTC
*
11087354 GAA-AAAAATTGATACTTTCAACTTTTTCTCAGAAATATTTTTTAGAAAACTTATTTTC
1 -AAGAAAAATTGATACTTTCAACTTTTTCTCA-AAATATTTTTTAGAAAACTTAATTTC
* *
11087412 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATGTTTTT
1 AAGAAAAATTGATACTTTCAACTTTTTCTC-AAAATAT-TTTTT
11087456 TTGGAATTTT
Statistics
Matches: 91, Mismatches: 4, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
57 30 0.33
58 51 0.56
59 10 0.11
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (57 bp):
AAGAAAAATTGATACTTTCAACTTTTTCTCAAAATATTTTTTAGAAAACTTAATTTC
Found at i:11087474 original size:58 final size:57
Alignment explanation
Indices: 11087289--11087478 Score: 199
Period size: 58 Copynumber: 3.3 Consensus size: 57
11087279 TACTCATTGC
* * *
11087289 TTTTATAT-AAGAAAAATTGATACTTTTAACTTTTTCTC-AAAATATTTTTCTGAAA
1 TTTTATTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAA
* * *
11087344 CTTTAATTTCGAA-AAAAATTGATACTTTCAACTTTTTCTCAGAAATATTTTTTAGAAA
1 -TTTTATTTC-AAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAA
** * * *
11087402 ACTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATGTTTTTTTGGAA
1 TTTTA-TTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATA--TTTTTTTGAAA
*
11087462 TTTTATTT-AAGGAAAAT
1 TTTTATTTCAAGAAAAAT
11087479 CAAAAAATAA
Statistics
Matches: 111, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
56 6 0.05
57 30 0.27
58 60 0.54
59 3 0.03
60 12 0.11
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.45
Consensus pattern (57 bp):
TTTTATTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAA
Found at i:11087527 original size:3 final size:3
Alignment explanation
Indices: 11087511--11087558 Score: 55
Period size: 3 Copynumber: 16.0 Consensus size: 3
11087501 TAAATAATTC
*
11087511 TAA T-A TAA TAAA TAA TAA TAA TAA TAA TAA -AA GAAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
11087556 TAA
1 TAA
11087559 ATAAGAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
2 4 0.10
3 31 0.77
4 5 0.12
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:11087532 original size:24 final size:24
Alignment explanation
Indices: 11087511--11087567 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
11087501 TAAATAATTC
* *
11087511 TAATATAATAAATAATAATAATAA
1 TAATAAAAGAAATAATAATAATAA
11087535 TAATAAAAGAAATAATAATAATAAA
1 TAATAAAAGAAATAATAATAAT-AA
*
11087560 TAAGAAAA
1 TAATAAAA
11087568 AAAAACATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 20 0.69
25 9 0.31
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (24 bp):
TAATAAAAGAAATAATAATAATAA
Found at i:11087535 original size:21 final size:21
Alignment explanation
Indices: 11087502--11087566 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
11087492 AAAGAACACT
**
11087502 AAATAATTCTAATATAATAA-
1 AAATAATAATAATATAATAAG
11087522 ATAATAATAATAATAATAA-AAG
1 A-AATAATAATAAT-ATAATAAG
11087544 AAATAATAATAATA-AATAAG
1 AAATAATAATAATATAATAAG
11087564 AAA
1 AAA
11087567 AAAAAACATT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
19 2 0.05
20 8 0.21
21 24 0.62
22 5 0.13
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.28
Consensus pattern (21 bp):
AAATAATAATAATATAATAAG
Found at i:11087642 original size:13 final size:13
Alignment explanation
Indices: 11087624--11087667 Score: 88
Period size: 13 Copynumber: 3.4 Consensus size: 13
11087614 AAAAAAGATG
11087624 GCTCGAAGACGAA
1 GCTCGAAGACGAA
11087637 GCTCGAAGACGAA
1 GCTCGAAGACGAA
11087650 GCTCGAAGACGAA
1 GCTCGAAGACGAA
11087663 GCTCG
1 GCTCG
11087668 GGGAAGTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.34, C:0.25, G:0.32, T:0.09
Consensus pattern (13 bp):
GCTCGAAGACGAA
Found at i:11088367 original size:20 final size:20
Alignment explanation
Indices: 11088344--11088383 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
11088334 GGATAAACCA
11088344 ACAAAAAAAAGAATAATAAT
1 ACAAAAAAAAGAATAATAAT
* * *
11088364 ACAATAATAATAATAATAAT
1 ACAAAAAAAAGAATAATAAT
11088384 CGTAATAGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.23
Consensus pattern (20 bp):
ACAAAAAAAAGAATAATAAT
Found at i:11088398 original size:23 final size:23
Alignment explanation
Indices: 11088355--11088462 Score: 74
Period size: 23 Copynumber: 5.0 Consensus size: 23
11088345 CAAAAAAAAG
*
11088355 AATAATAATA-CAATA-AT-AAT
1 AATAATAATAGTAATAGATAAAT
*
11088375 AATAATAATCGTAATAGATAAAT
1 AATAATAATAGTAATAGATAAAT
11088398 -ATACAT--T-G--ATAGATAAAT
1 AATA-ATAATAGTAATAGATAAAT
* *
11088416 -ATAAAAAATATTAATAGATAAAT
1 AAT-AATAATAGTAATAGATAAAT
* *
11088439 AAAAATAATAATAATAGATAAAT
1 AATAATAATAGTAATAGATAAAT
11088462 A
1 A
11088463 TAAAAAATAT
Statistics
Matches: 70, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
18 13 0.19
19 1 0.01
20 11 0.16
21 5 0.07
22 5 0.07
23 34 0.49
24 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.30
Consensus pattern (23 bp):
AATAATAATAGTAATAGATAAAT
Found at i:11088425 original size:27 final size:26
Alignment explanation
Indices: 11088394--11088573 Score: 150
Period size: 23 Copynumber: 7.0 Consensus size: 26
11088384 CGTAATAGAT
*
11088394 AAATATACATTGATAGATAAATAT-AA
1 AAATATA-ATTAATAGATAAATATAAA
11088420 AAA-AT-ATTAATAGATAAATA-AAA
1 AAATATAATTAATAGATAAATATAAA
*
11088443 ATA-ATAA-TAATAGATAAATATAAA
1 AAATATAATTAATAGATAAATATAAA
11088467 AAATATACATTAATAGATAAATAATAAA
1 AAATATA-ATTAATAGATAAAT-ATAAA
11088495 AACGTATATATATTAATAGAT-AA-AT-AA
1 AA---ATATA-ATTAATAGATAAATATAAA
*
11088522 AAA-A-GATTAATAGATAAATAATAAA
1 AAATATAATTAATAGATAAAT-ATAAA
* *
11088547 AAATATATATTTATAAATAAATA-AAA
1 AAATATA-ATTAATAGATAAATATAAA
11088573 A
1 A
11088574 TGCAAATGGG
Statistics
Matches: 129, Mismatches: 8, Indels: 34
0.75 0.05 0.20
Matches are distributed among these distances:
21 10 0.08
22 2 0.02
23 34 0.26
24 9 0.07
25 10 0.08
26 9 0.07
27 17 0.13
28 21 0.16
30 2 0.02
31 15 0.12
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (26 bp):
AAATATAATTAATAGATAAATATAAA
Found at i:11088471 original size:23 final size:24
Alignment explanation
Indices: 11088406--11088553 Score: 119
Period size: 21 Copynumber: 5.9 Consensus size: 24
11088396 ATATACATTG
*
11088406 ATAGATAAATATAAAAA-ATATTA
1 ATAGATAAATATAAAAATATAATA
11088429 ATAGAT-AA-ATAAAAATAATAATA
1 ATAGATAAATATAAAAAT-ATAATA
11088452 ATAGATAAATATAAAAAATATACATTA
1 ATAGATAAATAT-AAAAATATA-A-TA
11088479 ATAGATAAATAATAAAAACGTATATATATTA
1 ATAGATAAAT-AT-AAAA---ATATA-A-TA
*
11088510 ATAGATAAATA-AAAAAGAT--TA
1 ATAGATAAATATAAAAATATAATA
11088531 ATAGATAAATAATAAAAAATATA
1 ATAGATAAAT-AT-AAAAATATA
11088554 TATTTATAAA
Statistics
Matches: 106, Mismatches: 4, Indels: 28
0.77 0.03 0.20
Matches are distributed among these distances:
21 19 0.18
22 3 0.03
23 17 0.16
24 9 0.08
25 8 0.08
26 7 0.07
27 12 0.11
28 11 0.10
30 1 0.01
31 19 0.18
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.28
Consensus pattern (24 bp):
ATAGATAAATATAAAAATATAATA
Found at i:11088473 original size:73 final size:73
Alignment explanation
Indices: 11088348--11088573 Score: 207
Period size: 70 Copynumber: 3.1 Consensus size: 73
11088338 AAACCAACAA
* * * * * * *
11088348 AAAAAAGAATAATA-ATACAATAATAATAATAATAATCG-T-AATA-GATAAATATACATTGATA
1 AAAAAATATTAATAGATA-AATAAAAATAATAATAATAGATAAATATAAAAAATATACATTAATA
11088409 GATAAATAT
65 GATAAATAT
11088418 AAAAAATATTAATAGATAAATAAAAATAATAATAATAGATAAATATAAAAAATATACATTAATAG
1 AAAAAATATTAATAGATAAATAAAAATAATAATAATAGATAAATATAAAAAATATACATTAATAG
11088483 ATAAATAAT
66 ATAAAT-AT
11088492 AAAAACGTATATATATTAATAGATAAATAAAAA-AGAT--TAATAGATAAATAATAAAAAATATA
1 --AAA---A-A-ATATTAATAGATAAATAAAAATA-ATAATAATAGATAAAT-ATAAAAAATATA
* * *
11088554 TATTTATAAATAAATA-
57 CATTAATAGATAAATAT
11088570 AAAA
1 AAAA
11088574 TGCAAATGGG
Statistics
Matches: 132, Mismatches: 10, Indels: 25
0.79 0.06 0.15
Matches are distributed among these distances:
70 30 0.23
71 4 0.03
72 4 0.03
73 23 0.17
74 2 0.02
76 6 0.05
79 14 0.11
80 26 0.20
81 23 0.17
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (73 bp):
AAAAAATATTAATAGATAAATAAAAATAATAATAATAGATAAATATAAAAAATATACATTAATAG
ATAAATAT
Found at i:11091656 original size:2 final size:2
Alignment explanation
Indices: 11091649--11091674 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11091639 ATGTTTTAGT
11091649 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
11091675 CTCTTTTACT
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):
TA
Found at i:11092368 original size:75 final size:75
Alignment explanation
Indices: 11092285--11092436 Score: 268
Period size: 75 Copynumber: 2.0 Consensus size: 75
11092275 ACTTGTACTA
* *
11092285 AAAAAATACCCCAAAATAAAAAATATATAATAGTGATTTTTTCTAACCAGAGCCGTCCAAATCAT
1 AAAAAATACCCCAAAATAAAAAATATATAATACTGATTTTTTCTAACCAGAGCCATCCAAATCAT
11092350 CTTTTAGCCC
66 CTTTTAGCCC
*
11092360 AAAAAATACCCCAAAATAAAAAATATATAATACTGATTTTTTTTAACCAGAGCCATCCAAATCAT
1 AAAAAATACCCCAAAATAAAAAATATATAATACTGATTTTTTCTAACCAGAGCCATCCAAATCAT
*
11092425 GTTTTAGCCC
66 CTTTTAGCCC
11092435 AA
1 AA
11092437 CAATAAATAG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.28
Consensus pattern (75 bp):
AAAAAATACCCCAAAATAAAAAATATATAATACTGATTTTTTCTAACCAGAGCCATCCAAATCAT
CTTTTAGCCC
Found at i:11098230 original size:22 final size:21
Alignment explanation
Indices: 11098204--11098304 Score: 77
Period size: 22 Copynumber: 4.7 Consensus size: 21
11098194 TATTTATATA
11098204 TATTATATTATATTAATAAAAT
1 TATTAT-TTATATTAATAAAAT
*
11098226 TATTATTTAATATTTTAATTTAAA-
1 TATTATTT-ATA--TTAA-TAAAAT
11098250 -A-TATTTAT-TTAATAAAAT
1 TATTATTTATATTAATAAAAT
*
11098268 TATTATTTATGTATAATTAAAA-
1 TATTATTTATAT-TAA-TAAAAT
*
11098290 TATAATTTATATTAA
1 TATTATTTATATTAA
11098305 AAATAATATT
Statistics
Matches: 65, Mismatches: 4, Indels: 21
0.72 0.04 0.23
Matches are distributed among these distances:
17 4 0.06
18 4 0.06
19 1 0.02
20 7 0.11
21 8 0.12
22 27 0.42
23 6 0.09
24 4 0.06
25 4 0.06
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (21 bp):
TATTATTTATATTAATAAAAT
Found at i:11098298 original size:42 final size:43
Alignment explanation
Indices: 11098211--11098304 Score: 122
Period size: 42 Copynumber: 2.2 Consensus size: 43
11098201 ATATATTATA
* * *
11098211 TTATATTAATAAAATTATTATTTAATATTTTAATTTAAAATAT
1 TTATATTAATAAAATTATTATTTAATAGTATAATTAAAAATAT
11098254 TTAT-TTAATAAAATTATTATTT-AT-GTATAATTAAAATATAAT
1 TTATATTAATAAAATTATTATTTAATAGTATAATTAAAA-AT-AT
11098296 TTATATTAA
1 TTATATTAA
11098305 AAATAATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
40 9 0.20
41 4 0.09
42 24 0.53
43 8 0.18
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (43 bp):
TTATATTAATAAAATTATTATTTAATAGTATAATTAAAAATAT
Found at i:11100008 original size:18 final size:18
Alignment explanation
Indices: 11099982--11100031 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
11099972 CTTGTGCGGA
11099982 TGCTGCTGCTGCTGCATC
1 TGCTGCTGCTGCTGCATC
*
11100000 TGCAT-CTGCAT-CTGCATT
1 TGC-TGCTGC-TGCTGCATC
*
11100018 TGCTGCTGTTGCTG
1 TGCTGCTGCTGCTG
11100032 ATAGTTAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
17 2 0.08
18 22 0.85
19 2 0.08
ACGTcount: A:0.08, C:0.28, G:0.26, T:0.38
Consensus pattern (18 bp):
TGCTGCTGCTGCTGCATC
Found at i:11103462 original size:12 final size:12
Alignment explanation
Indices: 11103440--11103469 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
11103430 TAAAATTTTT
11103440 TAATCAAAATAAA
1 TAAT-AAAATAAA
11103453 TAATAAAATAAA
1 TAATAAAATAAA
11103465 TAATA
1 TAATA
11103470 TCCCTAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (12 bp):
TAATAAAATAAA
Found at i:11114195 original size:24 final size:24
Alignment explanation
Indices: 11114136--11114213 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
11114126 GTCACACGGT
* *
11114136 TATAAATATAATAATTTAAAATATAA
1 TATAAAAATAA-AATAT-AAATATAA
* * **
11114162 TATGATAATATGATATAAATATAA
1 TATAAAAATAAAATATAAATATAA
* *
11114186 TTTAAAAATAAAATATAAAAATAA
1 TATAAAAATAAAATATAAATATAA
11114210 TATA
1 TATA
11114214 GTTTAAAATT
Statistics
Matches: 39, Mismatches: 13, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
24 29 0.74
25 3 0.08
26 7 0.18
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (24 bp):
TATAAAAATAAAATATAAATATAA
Found at i:11114226 original size:24 final size:23
Alignment explanation
Indices: 11114194--11114254 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
11114184 AATTTAAAAA
11114194 TAAAA-TATAAAAATAATATAGTT
1 TAAAATTATAAAAATAATATA-TT
* *
11114217 TAAAATTATAATAATTATTATATT
1 TAAAATTATAA-AAATAATATATT
*
11114241 TAAATTTAATAAAA
1 TAAAATT-ATAAAA
11114255 TAAAAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 5 0.16
24 15 0.47
25 12 0.38
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
TAAAATTATAAAAATAATATATT
Found at i:11114338 original size:32 final size:32
Alignment explanation
Indices: 11114295--11114368 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
11114285 TATAAATTGT
*
11114295 TATATATAATTTTTATATAAAATATAATACAAA
1 TATATA-AATTTTAATATAAAATATAATACAAA
*** *
11114328 TATATAAATTTTAATATTTTATATAATATAAA
1 TATATAAATTTTAATATAAAATATAATACAAA
*
11114360 TATACAAAT
1 TATATAAAT
11114369 CATAAGATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
32 29 0.83
33 6 0.17
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (32 bp):
TATATAAATTTTAATATAAAATATAATACAAA
Found at i:11120199 original size:23 final size:23
Alignment explanation
Indices: 11120169--11120214 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
11120159 AAATCTTAAG
11120169 GAAAGGGTCATTTTGGTTTCCTT
1 GAAAGGGTCATTTTGGTTTCCTT
11120192 GAAAGGGTCATTTTGGTTTCCTT
1 GAAAGGGTCATTTTGGTTTCCTT
11120215 TAGCTCCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.13, G:0.26, T:0.43
Consensus pattern (23 bp):
GAAAGGGTCATTTTGGTTTCCTT
Found at i:11121484 original size:32 final size:36
Alignment explanation
Indices: 11121450--11121534 Score: 118
Period size: 37 Copynumber: 2.4 Consensus size: 36
11121440 CAATAAAATA
* *
11121450 TATAA-ATATTAACGTAATTTAAATTCCTTTTATAT
1 TATAATATATAAACGTAATTTAAATACCTTTTATAT
* *
11121485 TATAATATATAGAATGTAATTTAAATACCTTTTAAAT
1 TATAATATATA-AACGTAATTTAAATACCTTTTATAT
11121522 TATAATATATAAA
1 TATAATATATAAA
11121535 TTAAGCAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
35 5 0.11
36 6 0.14
37 33 0.75
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
TATAATATATAAACGTAATTTAAATACCTTTTATAT
Found at i:11122217 original size:23 final size:24
Alignment explanation
Indices: 11122185--11122234 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
11122175 ACAAATTTGT
*
11122185 AAAATATTATCTATTTTA-ATC-TA
1 AAAATATTAT-AATTTTATATCATA
*
11122208 AAAATTTTATAATTTTATATCATA
1 AAAATATTATAATTTTATATCATA
11122232 AAA
1 AAA
11122235 TGTATATTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 6 0.26
23 12 0.52
24 5 0.22
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (24 bp):
AAAATATTATAATTTTATATCATA
Found at i:11126935 original size:2 final size:2
Alignment explanation
Indices: 11126928--11126964 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11126918 TATTAGACAG
11126928 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11126965 ATCTTATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11129428 original size:2 final size:2
Alignment explanation
Indices: 11129417--11129446 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
11129407 AGACGGCCTT
*
11129417 TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
11129447 GTTGTTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:11130018 original size:12 final size:13
Alignment explanation
Indices: 11129994--11130026 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
11129984 TACATAAAAT
11129994 AATTATGATTTAA-
1 AATTAT-ATTTAAC
11130007 AATTATATTTAAC
1 AATTATATTTAAC
11130020 AATTATA
1 AATTATA
11130027 AGCCAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (13 bp):
AATTATATTTAAC
Found at i:11132352 original size:135 final size:135
Alignment explanation
Indices: 11132086--11132351 Score: 371
Period size: 135 Copynumber: 2.0 Consensus size: 135
11132076 ATAACTTCAA
*
11132086 TAATAAAAGAGAGGGTTTTAAGGAAAAGTTAAAAGTATCAAATTTCCTTAGAAAATAAAAAAATT
1 TAATAAAAAAGAGGGTTTTAAGGAAAAGTTAAAAGTATCAAATTTCCTTAGAAAATAAAAAAATT
**
11132151 TTCAAAAAATAAATTTCACAAGAAAAATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTTTAAAA
66 TTCAAAAAATAAATTTCACAAGAAAAAGATTTAAGAAAAAGTTGAAAGTATCAATTTTTTTAAAA
11132216 AAAAT
131 AAAAT
* * * * *
11132221 TAATAAAAAAGAGGGTTTTAAGGAAAAGTTGAAAGTGTCAATTTTTCTTA-AAAA-ATAAAAATT
1 TAATAAAAAAGAGGGTTTTAAGGAAAAGTTAAAAGTATCAAATTTCCTTAGAAAATAAAAAAATT
* * * *
11132284 TT-AAAAAATATATTTCA-AA-ATAAACGATTTAAGGAAACGTTGAAAGTATCAATTTTTCTTAA
66 TTCAAAAAATAAATTTCACAAGA-AAAAGATTTAAGAAAAAGTTGAAAGTATCAATTTTT-TTAA
11132346 AAAAAA
129 AAAAAA
11132352 ATCTTTTCAA
Statistics
Matches: 117, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
130 1 0.01
131 33 0.28
132 24 0.21
133 10 0.09
134 4 0.03
135 45 0.38
ACGTcount: A:0.52, C:0.05, G:0.12, T:0.31
Consensus pattern (135 bp):
TAATAAAAAAGAGGGTTTTAAGGAAAAGTTAAAAGTATCAAATTTCCTTAGAAAATAAAAAAATT
TTCAAAAAATAAATTTCACAAGAAAAAGATTTAAGAAAAAGTTGAAAGTATCAATTTTTTTAAAA
AAAAT
Found at i:11143610 original size:15 final size:15
Alignment explanation
Indices: 11143576--11143612 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
11143566 TATTAAATTT
*
11143576 ATAAAATTATTTATA
1 ATAAAAATATTTATA
11143591 A-AAAAATATTTATA
1 ATAAAAATATTTATA
11143605 ATAAAAAT
1 ATAAAAAT
11143613 TAAATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAAAATATTTATA
Found at i:11149630 original size:2 final size:2
Alignment explanation
Indices: 11149623--11149652 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
11149613 TCAATAACAA
*
11149623 AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11149653 TTGGAACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11157403 original size:26 final size:25
Alignment explanation
Indices: 11157374--11157422 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
11157364 ATTAATTAAA
*
11157374 ATTAATATATTTTTATTAAAAAATAT
1 ATTAATATATATTTA-TAAAAAATAT
11157400 ATTAATATATATTTATAAAAAAT
1 ATTAATATATATTTATAAAAAAT
11157423 TACCTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTAATATATATTTATAAAAAATAT
Found at i:11157433 original size:24 final size:26
Alignment explanation
Indices: 11157376--11157436 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
11157366 TAATTAAAAT
* *
11157376 TAATATATTTTTATTAAAAAATATAT
1 TAATATATATTTATTAAAAAATATAC
11157402 TAATATATATTTA-TAAAAAAT-TACC
1 TAATATATATTTATTAAAAAATATA-C
11157427 TAAATATATA
1 T-AATATATA
11157437 AAATAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 2 0.06
25 9 0.29
26 20 0.65
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (26 bp):
TAATATATATTTATTAAAAAATATAC
Found at i:11158589 original size:22 final size:23
Alignment explanation
Indices: 11158564--11158618 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 23
11158554 AAATAATTAT
11158564 TATATATATAAATTTAT-TTAAA
1 TATATATATAAATTTATATTAAA
*
11158586 TATAT-TA-AAATTTTTATTAAA
1 TATATATATAAATTTATATTAAA
11158607 -ATAATATATAAA
1 TAT-ATATATAAA
11158619 AAATTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 9 0.32
21 9 0.32
22 7 0.25
23 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TATATATATAAATTTATATTAAA
Found at i:11158590 original size:20 final size:21
Alignment explanation
Indices: 11158565--11158618 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
11158555 AATAATTATT
*
11158565 ATATATATAAA-TTTATTTAA
1 ATATATATAAATTTTATTAAA
11158585 ATATAT-TAAAATTTTTATTAAA
1 ATATATAT-AAA-TTTTATTAAA
11158607 ATAATATATAAA
1 AT-ATATATAAA
11158619 AAATTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 1 0.04
20 9 0.32
22 10 0.36
23 7 0.25
24 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATATATATAAATTTTATTAAA
Found at i:11158601 original size:18 final size:20
Alignment explanation
Indices: 11158565--11158601 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
11158555 AATAATTATT
*
11158565 ATATATATAAATTTATTTAA
1 ATATATATAAAATTATTTAA
11158585 ATATAT-TAAAATT-TTTA
1 ATATATATAAAATTATTTA
11158602 TTAAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.25
19 6 0.38
20 6 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATATAAAATTATTTAA
Found at i:11162402 original size:16 final size:16
Alignment explanation
Indices: 11162383--11162413 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11162373 TTAAATTATA
11162383 TTTTAAATTTTAAATT
1 TTTTAAATTTTAAATT
*
11162399 TTTTATATTTTAAAT
1 TTTTAAATTTTAAAT
11162414 AAATTAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTAAATTTTAAATT
Found at i:11162547 original size:22 final size:22
Alignment explanation
Indices: 11162521--11162569 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
11162511 TGTTTTATGT
11162521 ATTTTTTAT-TTTAT-ATTTAAA
1 ATTTTTTATATTT-TGATTTAAA
*
11162542 TTTTTTTATATTTTGATTTAAA
1 ATTTTTTATATTTTGATTTAAA
11162564 ATTTTT
1 ATTTTT
11162570 AAAATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
ATTTTTTATATTTTGATTTAAA
Found at i:11163221 original size:34 final size:33
Alignment explanation
Indices: 11163163--11163229 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
11163153 TTAATACTCA
* * *
11163163 TTTAATATGTATTTAATATATATATATATATTTT
1 TTTAATATATATTAAATATATATAT-TAAATTTT
11163197 TTTAATATATATTAAATA-ACTATATTAAATTTT
1 TTTAATATATATTAAATATA-TATATTAAATTTT
11163230 AATATCAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 8 0.28
34 21 0.72
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (33 bp):
TTTAATATATATTAAATATATATATTAAATTTT
Found at i:11165406 original size:22 final size:25
Alignment explanation
Indices: 11165381--11165431 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
11165371 TATTTTAAAT
11165381 TTTTAA-ATAATA-TATT-ATTTAA
1 TTTTAATATAATATTATTAATTTAA
*
11165403 TTTTAATTTTAATATTATTAATTTAA
1 TTTTAA-TATAATATTATTAATTTAA
11165429 TTT
1 TTT
11165432 ACTTATATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 6 0.25
24 5 0.21
25 4 0.17
26 9 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTTAATATAATATTATTAATTTAA
Found at i:11165439 original size:22 final size:22
Alignment explanation
Indices: 11165391--11165431 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
11165381 TTTTAAATAA
11165391 TATATTATTTAATTTTAATTTT
1 TATATTATTTAATTTTAATTTT
*
11165413 AATATTA-TTAA-TTTAATTT
1 TATATTATTTAATTTTAATTT
11165432 ACTTATATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 4 0.22
22 6 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATATTATTTAATTTTAATTTT
Found at i:11165476 original size:16 final size:16
Alignment explanation
Indices: 11165451--11165485 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
11165441 ATATCTAATC
11165451 AATAAAATTATTT-TT
1 AATAAAATTATTTCTT
11165466 AATATAAATTATTTCTT
1 AATA-AAATTATTTCTT
11165483 AAT
1 AAT
11165486 TATATATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 9 0.50
17 5 0.28
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
AATAAAATTATTTCTT
Found at i:11165513 original size:16 final size:16
Alignment explanation
Indices: 11165492--11165522 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11165482 TAATTATATA
*
11165492 TAAATATAAATTTTAT
1 TAAATATAAAATTTAT
11165508 TAAATATAAAATTTA
1 TAAATATAAAATTTA
11165523 AATTATATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATATAAAATTTAT
Found at i:11166467 original size:17 final size:20
Alignment explanation
Indices: 11166437--11166473 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
11166427 AATATATTAC
11166437 ATATTAATTATTTA-TAAAT
1 ATATTAATTATTTATTAAAT
11166456 ATATT-ATT-TTTATTAAAT
1 ATATTAATTATTTATTAAAT
11166474 TAAGATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.24
18 8 0.47
19 5 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATTAATTATTTATTAAAT
Found at i:11166497 original size:212 final size:213
Alignment explanation
Indices: 11166130--11166556 Score: 669
Period size: 212 Copynumber: 2.0 Consensus size: 213
11166120 GCATATAAAC
* * * *
11166130 ACAAAGCATCATGTTGATACAATGAATGAGGACAAAATAAGAGTTAAAATAAGTATAATTTATAT
1 ACAAAGCATCATGTTGACACAATGAATGAAGACAAAATAAGAGTTAAAATAAATAAAATTTATAT
* * * * * **
11166195 AATGAATGGTTGGATAGATTAATAGATTATTTATTAATTATTTATAAATATAATATTTTTATTAA
66 AATAAATGGCTAGATAAATGAATAGATTACATATTAATTATTTATAAATATAATATTTTTATTAA
11166260 ATTAAGATATTAAATAATAACTTAATTAATATATTAC-ATATATAAATATAAAATAAAATAAATA
131 ATTAAGATATTAAATAATAACTTAATTAATATATTACAATATATAAATATAAAATAAAATAAATA
*
11166324 ATTAAAAATTTTATATAT
196 ATTAAAAAATTTATATAT
* *
11166342 ACAAAGCATCATGTTGACACATTG-ATGGAAGACAGAATAAGAGTTAAAATAAATAAAATTTATA
1 ACAAAGCATCATGTTGACACAATGAAT-GAAGACAAAATAAGAGTTAAAATAAATAAAATTTATA
* *
11166406 TAATAAATGGCTAGATAAATGAATATATTACATATTAATTATTTATAAATATATTATTTTTATTA
65 TAATAAATGGCTAGATAAATGAATAGATTACATATTAATTATTTATAAATATAATATTTTTATTA
*
11166471 AATTAAGATATTAAATAATAACTTAATTAATATATTACATATATATAAATATAAAATAAAATAAT
130 AATTAAGATATTAAATAATAACTTAATTAATATATTACA-ATATATAAATATAAAATAAAATAAA
11166536 TAATTAAAAAATTTATATAT
194 TAATTAAAAAATTTATATAT
11166556 A
1 A
11166557 TTCAAGGTAA
Statistics
Matches: 195, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
211 2 0.01
212 149 0.76
214 44 0.23
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (213 bp):
ACAAAGCATCATGTTGACACAATGAATGAAGACAAAATAAGAGTTAAAATAAATAAAATTTATAT
AATAAATGGCTAGATAAATGAATAGATTACATATTAATTATTTATAAATATAATATTTTTATTAA
ATTAAGATATTAAATAATAACTTAATTAATATATTACAATATATAAATATAAAATAAAATAAATA
ATTAAAAAATTTATATAT
Found at i:11167386 original size:10 final size:9
Alignment explanation
Indices: 11167358--11167416 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
11167348 TATTTTTCTA
*
11167358 AAAAATTAT
1 AAAAATTTT
11167367 -AAAATTTT
1 AAAAATTTT
11167375 AAAAATTGTT
1 AAAAATT-TT
*
11167385 AAATA-TTT
1 AAAAATTTT
11167393 AAAAATTTT
1 AAAAATTTT
**
11167402 ATTAATTATT
1 AAAAATT-TT
11167412 AAAAA
1 AAAAA
11167417 AGGAAAAAGA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
8 13 0.33
9 15 0.38
10 11 0.28
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (9 bp):
AAAAATTTT
Found at i:11167411 original size:20 final size:18
Alignment explanation
Indices: 11167358--11167399 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
11167348 TATTTTTCTA
* *
11167358 AAAAATTATAAAAT-TTT
1 AAAAATTGTTAAATATTT
11167375 AAAAATTGTTAAATATTT
1 AAAAATTGTTAAATATTT
11167393 AAAAATT
1 AAAAATT
11167400 TTATTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
AAAAATTGTTAAATATTT
Found at i:11167792 original size:29 final size:26
Alignment explanation
Indices: 11167760--11167823 Score: 65
Period size: 29 Copynumber: 2.3 Consensus size: 26
11167750 TTATAAATTT
*
11167760 TAAAAAATCTGAAAATAATTTTAAAAAA
1 TAAAAAATAT-AAAATAA-TTTAAAAAA
*
11167788 CTAAAAAGATATAAAGTAATTTAAAAAA
1 -TAAAAA-ATATAAAATAATTTAAAAAA
*
11167816 GAAAAAAT
1 TAAAAAAT
11167824 GGCATAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 2 0.06
27 5 0.16
28 9 0.29
29 12 0.39
30 3 0.10
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.25
Consensus pattern (26 bp):
TAAAAAATATAAAATAATTTAAAAAA
Found at i:11167794 original size:20 final size:21
Alignment explanation
Indices: 11167755--11167794 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
11167745 ATTATTTATA
*
11167755 AATTTTAAAAAATCTGAAAAT
1 AATTTTAAAAAATCTAAAAAT
11167776 AATTTTAAAAAA-CTAAAAA
1 AATTTTAAAAAATCTAAAAA
11167795 GATATAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (21 bp):
AATTTTAAAAAATCTAAAAAT
Found at i:11168346 original size:22 final size:20
Alignment explanation
Indices: 11168304--11168341 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11168294 AATTTAAAAT
11168304 TTTAA-AAAATATTTATATAA
1 TTTAATAAAA-ATTTATATAA
11168324 TTTAATAAAAATTTATAT
1 TTTAATAAAAATTTATAT
11168342 TTAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAATAAAAATTTATATAA
Found at i:11168354 original size:22 final size:22
Alignment explanation
Indices: 11168289--11168356 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
11168279 AAATAAAAAT
* *
11168289 AATTTA-ATTTAAAATTTTAAAA
1 AATTTATATTTAATATATT-AAA
* * *
11168311 AATATT-TATATAATTTAATAAA
1 AAT-TTATATTTAATATATTAAA
11168333 AATTTATATTTAATATATTAAA
1 AATTTATATTTAATATATTAAA
11168355 AA
1 AA
11168357 AATTATAATA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
21 2 0.06
22 24 0.69
23 9 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATTTATATTTAATATATTAAA
Found at i:11168357 original size:24 final size:22
Alignment explanation
Indices: 11168282--11168360 Score: 67
Period size: 24 Copynumber: 3.5 Consensus size: 22
11168272 GATATAAAAA
11168282 TAAAAATAATTTA-ATTTAAAATTT
1 TAAAAA-AATTTATATTT-AAA-TT
11168306 TAAAAAATATTTATA--T-AATT
1 TAAAAAA-ATTTATATTTAAATT
11168326 TAATAAAAATTTATATTTAATATAT
1 TAA-AAAAATTTATATTTAA-AT-T
11168351 TAAAAAAATT
1 TAAAAAAATT
11168361 ATAATAAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
20 12 0.26
21 6 0.13
22 1 0.02
23 3 0.06
24 20 0.43
25 5 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAAAAAAATTTATATTTAAATT
Found at i:11169017 original size:12 final size:12
Alignment explanation
Indices: 11168961--11169021 Score: 50
Period size: 12 Copynumber: 5.1 Consensus size: 12
11168951 GAACAGAAAC
*
11168961 AACAACAACAAC
1 AACAACAACAAA
* *
11168973 AACAACATCAAG
1 AACAACAACAAA
* * *
11168985 AAGAAGAAGAAA
1 AACAACAACAAA
*
11168997 AACAGCAACAAA
1 AACAACAACAAA
*
11169009 AAGAACAACAAA
1 AACAACAACAAA
11169021 A
1 A
11169022 CCAAGGGGAA
Statistics
Matches: 36, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.69, C:0.20, G:0.10, T:0.02
Consensus pattern (12 bp):
AACAACAACAAA
Found at i:11172395 original size:364 final size:366
Alignment explanation
Indices: 11171703--11172437 Score: 1366
Period size: 364 Copynumber: 2.0 Consensus size: 366
11171693 CAAAGGCATT
11171703 TATCCTTTTTTCTCTCAAAACCCTGGAAGGACTGGCCTATGTTGACACTGGCAGACTTGCAGGAG
1 TATCCTTTTTTCTCTCAAAACCCTGGAAGGACTGGCCTATGTTGACACTGGCAGACTTGCAGGAG
*
11171768 AATTGGTCATGTATCCAATCCAAGAAGAGAATTAATTTAAATGTAATTTCTCGTTGTTTTTTTCC
66 AATTGGTCATGTATCCAATCCAAGAAGAGAATTAATTTAAATGTAATTTCTC-----TCTTTTCC
11171833 GTTTTTTGGCCAGTTTTCTTGTTGAGCAGCTTTATACAATTTTAATAGAAGAGTCTAATCAAGTC
126 GTTTTTTGGCCAGTTTTCTTGTTGAGCAGCTTTATACAATTTTAATAGAAGAGTCTAATCAAGTC
* *
11171898 ACGATTGGATTGACGTAATGAAAAGAGTCTTCTATAAAATATAGCAAATGTAAATAAATGATGAT
191 ACAATTGGATTGACGTAATGAAAAGAGTCTTCTATAAAATATAGCAAATGAAAATAAATGATGAT
*
11171963 ACATGCATTAGACAAATCTACCGTCTTTATCATAAAAAATAAAAAAAGGAAAAGCATTTTTCTTT
256 ACATGCATTAGACAAATCTACCATCTTTATCATAAAAAATAAAAAAAGGAAAAGCATTTTTCTTT
11172028 TTTACAAAGGGAAGCCGAAACCTAGAGGATTAAGAAAAAAATTATA
321 TTTACAAAGGGAAGCCGAAACCTAGAGGATTAAGAAAAAAATTATA
11172074 TATCCTTTTTTCTCTC-AAACCCTGGAAGGACTGGCCTATGTTGACACTGGCAGACTTGCAGGAG
1 TATCCTTTTTTCTCTCAAAACCCTGGAAGGACTGGCCTATGTTGACACTGGCAGACTTGCAGGAG
*
11172138 AATTGGTCATGTATCCAATTCAAGAAGAGAATTAATTTAAATGTAATTTCTC-CTTTTCCGTTTT
66 AATTGGTCATGTATCCAATCCAAGAAGAGAATTAATTTAAATGTAATTTCTCTCTTTTCCGTTTT
11172202 TTGGCCAGTTTTCTTGTTGAGCAGCTTTATACAATTTTAATAGAAGAGTCTAATCAAGTCACAAT
131 TTGGCCAGTTTTCTTGTTGAGCAGCTTTATACAATTTTAATAGAAGAGTCTAATCAAGTCACAAT
11172267 TGGATTGACGTAATGAAAAGAGTCTTCTATAAAATATAGCAAATGAAAATAAATGATGATACATG
196 TGGATTGACGTAATGAAAAGAGTCTTCTATAAAATATAGCAAATGAAAATAAATGATGATACATG
11172332 CATTAGACAAATCTACCATCTTTATCATAAAAAATAAAAAAAGGAAAAGCATTTTTCTTTTTTAC
261 CATTAGACAAATCTACCATCTTTATCATAAAAAATAAAAAAAGGAAAAGCATTTTTCTTTTTTAC
11172397 AAAGGGAAGCCGAAACCTAGAGGATTAAGAAAAAAATTATA
326 AAAGGGAAGCCGAAACCTAGAGGATTAAGAAAAAAATTATA
11172438 AGTGTTTAAT
Statistics
Matches: 359, Mismatches: 5, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
364 244 0.68
370 99 0.28
371 16 0.04
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (366 bp):
TATCCTTTTTTCTCTCAAAACCCTGGAAGGACTGGCCTATGTTGACACTGGCAGACTTGCAGGAG
AATTGGTCATGTATCCAATCCAAGAAGAGAATTAATTTAAATGTAATTTCTCTCTTTTCCGTTTT
TTGGCCAGTTTTCTTGTTGAGCAGCTTTATACAATTTTAATAGAAGAGTCTAATCAAGTCACAAT
TGGATTGACGTAATGAAAAGAGTCTTCTATAAAATATAGCAAATGAAAATAAATGATGATACATG
CATTAGACAAATCTACCATCTTTATCATAAAAAATAAAAAAAGGAAAAGCATTTTTCTTTTTTAC
AAAGGGAAGCCGAAACCTAGAGGATTAAGAAAAAAATTATA
Found at i:11177389 original size:123 final size:123
Alignment explanation
Indices: 11177142--11177387 Score: 424
Period size: 123 Copynumber: 2.0 Consensus size: 123
11177132 TACAGCTCAT
*
11177142 GATAATCCATCGATTAATTTAGCATTAGAATCATTAATATCTGTGTTATAACAGTAAACTTCAAA
1 GATAATCCATCGATTAATTTAGCATTAGAATCATTAATATCTGTGCTATAACAGTAAACTTCAAA
*
11177207 GTGCATTTGATGTGTGCACATGCTCATATGTGTGTGAATGAGTAAAGATGGATCGAGA
66 GTGCATTTGATGTGTGCACATGCTCATATGTGTGTGAACGAGTAAAGATGGATCGAGA
*
11177265 GATAATCCATCGATTAATTTAGCATTAGAATCATTAATATCTGTGCTA-AACATTAAACTTCAAA
1 GATAATCCATCGATTAATTTAGCATTAGAATCATTAATATCTGTGCTATAACAGTAAACTTCAAA
* * *
11177329 GTGCATTTGATGTGTGCACATGCTCGTATGT-TGTGAGCGAGTAATGATGGATCGAGA
66 GTGCATTTGATGTGTGCACATGCTCATATGTGTGTGAACGAGTAAAGATGGATCGAGA
11177386 GA
1 GA
11177388 GAATACCGTT
Statistics
Matches: 117, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
121 25 0.21
122 45 0.38
123 47 0.40
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (123 bp):
GATAATCCATCGATTAATTTAGCATTAGAATCATTAATATCTGTGCTATAACAGTAAACTTCAAA
GTGCATTTGATGTGTGCACATGCTCATATGTGTGTGAACGAGTAAAGATGGATCGAGA
Found at i:11181336 original size:23 final size:24
Alignment explanation
Indices: 11181310--11181361 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
11181300 AAAAATTTTG
*
11181310 ATTTTAATTCATTT-TAATATTAA
1 ATTTTAATTCATTTATAAAATTAA
**
11181333 ATTTTAATTTTTTTATAAAATTAA
1 ATTTTAATTCATTTATAAAATTAA
11181357 ATTTT
1 ATTTT
11181362 CATAATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTTTAATTCATTTATAAAATTAA
Found at i:11184774 original size:48 final size:48
Alignment explanation
Indices: 11184703--11184794 Score: 166
Period size: 48 Copynumber: 1.9 Consensus size: 48
11184693 TCTAGCAAAG
* *
11184703 TAATCTAAGTGATTAATCTGTTATCTGAGCCTAACTGTTGAACTTAAA
1 TAATCTAAGTGATTAATCTGTTATCTGAACCCAACTGTTGAACTTAAA
11184751 TAATCTAAGTGATTAATCTGTTATCTGAACCCAACTGTTGAACT
1 TAATCTAAGTGATTAATCTGTTATCTGAACCCAACTGTTGAACT
11184795 ATCTTTACTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (48 bp):
TAATCTAAGTGATTAATCTGTTATCTGAACCCAACTGTTGAACTTAAA
Found at i:11185745 original size:2 final size:2
Alignment explanation
Indices: 11185740--11185764 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11185730 TGTGTGTGTG
11185740 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
11185765 TAGTTGATTG
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:11190259 original size:2 final size:2
Alignment explanation
Indices: 11190254--11190281 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11190244 AGATTTTATT
11190254 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
11190282 AAAGAAGATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11196031 original size:2 final size:2
Alignment explanation
Indices: 11196024--11196061 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
11196014 TAAGTTTTAC
* *
11196024 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11196062 GTGGTATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:11196037 original size:8 final size:8
Alignment explanation
Indices: 11196021--11196061 Score: 64
Period size: 8 Copynumber: 5.1 Consensus size: 8
11196011 AAATAAGTTT
11196021 TACATATA
1 TACATATA
*
11196029 TATATATA
1 TACATATA
*
11196037 TATATATA
1 TACATATA
11196045 TACATATA
1 TACATATA
11196053 TACATATA
1 TACATATA
11196061 T
1 T
11196062 GTGGTATTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (8 bp):
TACATATA
Found at i:11210651 original size:18 final size:18
Alignment explanation
Indices: 11210628--11210707 Score: 61
Period size: 18 Copynumber: 4.3 Consensus size: 18
11210618 TAATTTAACT
11210628 TAAATTTACATATATATA
1 TAAATTTACATATATATA
** *
11210646 TAAATTTTTATTTATATA
1 TAAATTTACATATATATA
* * * *
11210664 TATATGTGATTATATATAAA
1 TAAAT-TTA-CATATATATA
* *
11210684 TTAATTCACATATATATA
1 TAAATTTACATATATATA
11210702 TAAATT
1 TAAATT
11210708 AAAAATAAAA
Statistics
Matches: 46, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
18 32 0.70
19 3 0.07
20 11 0.24
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.49
Consensus pattern (18 bp):
TAAATTTACATATATATA
Found at i:11210926 original size:16 final size:16
Alignment explanation
Indices: 11210905--11210935 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11210895 TAATTTTGAC
*
11210905 TTAAACTCAATCCGAT
1 TTAAACCCAATCCGAT
11210921 TTAAACCCAATCCGA
1 TTAAACCCAATCCGA
11210936 CCCATGAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.29, G:0.06, T:0.26
Consensus pattern (16 bp):
TTAAACCCAATCCGAT
Found at i:11212358 original size:72 final size:71
Alignment explanation
Indices: 11212247--11212379 Score: 164
Period size: 72 Copynumber: 1.9 Consensus size: 71
11212237 TATATCATAT
* * * *
11212247 AAAATATTAAAATTTATATATTTATATTTTATT--TTATATAAAAGTTATGTATTATAATTTTTA
1 AAAATATTAAAATATATATATTTATATTTTATTAAATATATATAA-TTAT-TATTAAAATTTTTA
11212310 TTGATACA
64 TTGATACA
*
11212318 AAAATA-TAAAATATATATATTTTTTAATTTTATTAAATATATATAATTATTATTAAAATTTT
1 AAAATATTAAAATATATATA-TTTAT-ATTTTATTAAATATATATAATTATTATTAAAATTTT
11212380 AAATTATATT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
70 12 0.23
71 10 0.19
72 19 0.36
73 4 0.08
74 8 0.15
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (71 bp):
AAAATATTAAAATATATATATTTATATTTTATTAAATATATATAATTATTATTAAAATTTTTATT
GATACA
Found at i:11212489 original size:12 final size:12
Alignment explanation
Indices: 11212472--11212499 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
11212462 CTCATGCGGT
11212472 TTTAACATAGAA
1 TTTAACATAGAA
11212484 TTTAACATAGAA
1 TTTAACATAGAA
11212496 TTTA
1 TTTA
11212500 TATTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (12 bp):
TTTAACATAGAA
Found at i:11220742 original size:2 final size:2
Alignment explanation
Indices: 11220735--11220770 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
11220725 GGTGATGTTG
11220735 AT AT AT AT AT AT AT AT A- 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
11220771 AACTGCCTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11220757 original size:17 final size:17
Alignment explanation
Indices: 11220735--11220768 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
11220725 GGTGATGTTG
11220735 ATATATATATATATATA
1 ATATATATATATATATA
11220752 ATATATATATATATATA
1 ATATATATATATATATA
11220769 TAAACTGCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:11220759 original size:19 final size:19
Alignment explanation
Indices: 11220735--11220771 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
11220725 GGTGATGTTG
11220735 ATATATATATATATATAAT
1 ATATATATATATATATAAT
11220754 ATATATATATATATATAA
1 ATATATATATATATATAA
11220772 ACTGCCTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATATATATATATATAAT
Found at i:11226471 original size:19 final size:19
Alignment explanation
Indices: 11226442--11226478 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
11226432 TTGATTATTT
11226442 TTAACTTAATAAAAATAACA
1 TTAACTTAAT-AAAATAACA
11226462 TTAA-TTAATAAAATAAC
1 TTAACTTAATAAAATAAC
11226479 TTTTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.32
Consensus pattern (19 bp):
TTAACTTAATAAAATAACA
Found at i:11226484 original size:19 final size:21
Alignment explanation
Indices: 11226440--11226484 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
11226430 ATTTGATTAT
11226440 TTTTAACTTAATAAAAATAAC
1 TTTTAACTTAATAAAAATAAC
*
11226461 -ATTAA-TTAAT-AAAATAAC
1 TTTTAACTTAATAAAAATAAC
11226479 TTTTAA
1 TTTTAA
11226485 AATTGAGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTTAACTTAATAAAAATAAC
Found at i:11232402 original size:2 final size:2
Alignment explanation
Indices: 11232363--11232392 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
11232353 ACTCATCTTC
*
11232363 TA TA TA TA AA 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
11232393 AAGAATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:11232572 original size:19 final size:19
Alignment explanation
Indices: 11232528--11232572 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
11232518 TGTAACATTG
11232528 TATATAAAAAATTATTAAA
1 TATATAAAAAATTATTAAA
* *
11232547 TAAATAAATAATTAATTAAA
1 TATATAAAAAATT-ATTAAA
11232567 -ATATAA
1 TATATAA
11232573 TTAAAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TATATAAAAAATTATTAAA
Found at i:11237471 original size:19 final size:20
Alignment explanation
Indices: 11237437--11237474 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
11237427 TTGAAATATA
*
11237437 TATATATTTTAGTTTTTATG
1 TATATATTTTAATTTTTATG
11237457 TATAT-TTTTAATTTTTAT
1 TATATATTTTAATTTTTAT
11237475 ATAATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (20 bp):
TATATATTTTAATTTTTATG
Found at i:11237532 original size:13 final size:13
Alignment explanation
Indices: 11237513--11237552 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
11237503 ATCTACTCAA
11237513 ATATATTAAAATT
1 ATATATTAAAATT
* *
11237526 TTATATTAAAATA
1 ATATATTAAAATT
*
11237539 ATATATAAAAATT
1 ATATATTAAAATT
11237552 A
1 A
11237553 AAAAAAATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATATTAAAATT
Found at i:11242897 original size:25 final size:23
Alignment explanation
Indices: 11242860--11242906 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
11242850 TCAAATCGGC
11242860 AGTTTTTATTATTAAAAAATAGAT
1 AGTTTTTATTATT-AAAAATAGAT
* *
11242884 AGTTTTTGTCTATTTAAAATAGA
1 AGTTTTTAT-TATTAAAAATAGA
11242907 CAGCTATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (23 bp):
AGTTTTTATTATTAAAAATAGAT
Found at i:11243954 original size:63 final size:62
Alignment explanation
Indices: 11243873--11244009 Score: 150
Period size: 63 Copynumber: 2.2 Consensus size: 62
11243863 ATTTAAGGCC
*** * **
11243873 TTAAATAATCCTCTTTAAAAAAATATTGGA-GATTATTTAAGGTGTTTTTGGACCAAAAACGCA
1 TTAAATAAT-CTCTTTAAAAAAATA-AAAATGATTATTTAAGGCGTTTTTCAACCAAAAACGCA
* * * *
11243936 TTAAATAATCTATTTTAAAAAAATAAAAATGATTATTTAAGGCGTTTTTCAATCAAAAATGCC
1 TTAAATAATCT-CTTTAAAAAAATAAAAATGATTATTTAAGGCGTTTTTCAACCAAAAACGCA
11243999 TTAAATAATCT
1 TTAAATAATCT
11244010 TCAATATTTT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
62 3 0.05
63 59 0.95
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (62 bp):
TTAAATAATCTCTTTAAAAAAATAAAAATGATTATTTAAGGCGTTTTTCAACCAAAAACGCA
Found at i:11244402 original size:15 final size:15
Alignment explanation
Indices: 11244382--11244424 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
11244372 AAATATTAAT
* *
11244382 AAAGGAAAGGAAATG
1 AAAGGAAAAGAAAAG
11244397 AAAGGAAAAGAAAAG
1 AAAGGAAAAGAAAAG
*
11244412 AATGGAAAAGAAA
1 AAAGGAAAAGAAA
11244425 GTTTTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.05
Consensus pattern (15 bp):
AAAGGAAAAGAAAAG
Found at i:11247123 original size:18 final size:18
Alignment explanation
Indices: 11247100--11247134 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11247090 ATAATGGCGA
*
11247100 TATTGATGCTAGTGATGC
1 TATTGATGATAGTGATGC
11247118 TATTGATGATAGTGATG
1 TATTGATGATAGTGATG
11247135 ATATCGATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.40
Consensus pattern (18 bp):
TATTGATGATAGTGATGC
Found at i:11253522 original size:21 final size:20
Alignment explanation
Indices: 11253496--11253539 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
11253486 TTTATGTATG
11253496 TATGTATGTATATATATACTA
1 TATGTATGTATATATATA-TA
*
11253517 TATGTATGTGTATATATATA
1 TATGTATGTATATATATATA
11253537 TAT
1 TAT
11253540 ATGTTTATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.50
Consensus pattern (20 bp):
TATGTATGTATATATATATA
Found at i:11259901 original size:13 final size:13
Alignment explanation
Indices: 11259868--11259910 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
11259858 TTAATGAGAT
*
11259868 TTTTCAATTTATTA
1 TTTT-AATTTTTTA
11259882 GTTTTAATTTTTTA
1 -TTTTAATTTTTTA
11259896 TTTTAA-TTTTTA
1 TTTTAATTTTTTA
11259908 TTT
1 TTT
11259911 AATAATTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 9 0.33
13 6 0.22
14 8 0.30
15 4 0.15
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (13 bp):
TTTTAATTTTTTA
Found at i:11260414 original size:18 final size:19
Alignment explanation
Indices: 11260380--11260421 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
11260370 AAAATTCTAA
11260380 AAAAATTCTAAAATTTTTTG
1 AAAAATTCT-AAATTTTTTG
*
11260400 AAAAATTCT-AATTTTTTT
1 AAAAATTCTAAATTTTTTG
11260418 AAAA
1 AAAA
11260422 TTATAGAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.57
20 9 0.43
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (19 bp):
AAAAATTCTAAATTTTTTG
Found at i:11261851 original size:85 final size:83
Alignment explanation
Indices: 11261746--11262331 Score: 250
Period size: 85 Copynumber: 6.9 Consensus size: 83
11261736 CAAACTTAGA
* * * * *
11261746 TTGATCAAAAGAGCTTGGATCTATAAAATACTTTTATAAAGGTTTAATTCGACAATACAGCTC-A
1 TTGACCAAAAGAGTTTGGATCTA-AAAATAC-TTCATAAAGGTCTAATTCGACAAAACAGCTCGA
*
11261810 TTCAAAGAGCTGGGACTCAGC
64 -TCAAAGAGCTCGGACTCAGC
* * * * * *
11261831 TTGACCGAAAGAGTTTGGATCTACAAATACCTTCATAAAAGGTCTAATTCAATAAAATAGTTCGA
1 TTGACCAAAAGAGTTTGGATCTAAAAATA-CTTCAT-AAAGGTCTAATTCGACAAAACAGCTCGA
*
11261896 TCAAAGAGCTCGGACTCAGT
64 TCAAAGAGCTCGGACTCAGC
* * * * * * *
11261916 TTGATCAAAAGAGTTTGAATTTACAAAATAACTTCATAAAGGCCTAATTCGACAAAATAACTCAA
1 TTGACCAAAAGAGTTTGGATCTA-AAAAT-ACTTCATAAAGGTCTAATTCGACAAAACAGCTCGA
* * * *
11261981 TCAAAAAACTCAGACTCGGC
64 TCAAAGAGCTCGGACTCAGC
* ** * * ** * * * * *
11262001 -TCATTTAAAAAAGCTCAGATTTACAAAATGCCTTTATAAAAGTCTAATTCGACAAAATAGCTCC
1 TTGA-CCAAAAGAGTTTGGATCTA-AAAAT-ACTTCATAAAGGTCTAATTCGACAAAACAGCT-C
* * ** *
11262065 G-TCAAATAACTTAGACTCA-A
62 GATCAAAGAGCTCGGACTCAGC
* * * * * * * **
11262085 TTCGACGAAAAGAGCTCGAATCTATAAAATACCTTAATAAAGG-CTCAATTCAACAAAATAATTC
1 TT-GACCAAAAGAGTTTGGATCTA-AAAATA-CTTCATAAAGGTCT-AATTCGACAAAACAGCTC
* * ***
11262149 GACCAAAAAGCTTAAACTCAGC
62 GATCAAAGAGCTCGGACTCAGC
* * * * * *
11262171 TCGATCAAAAGAGTTTGGATCTATAAAATGCCTTCATAAATGT-TCAATTCAACAAAATAGCTCG
1 TTGACCAAAAGAGTTTGGATCTA-AAAAT-ACTTCATAAAGGTCT-AATTCGACAAAACAGCTCG
** *
11262235 ATC-AAGTAGCTTAGACTCAAC
63 ATCAAAG-AGCTCGGACTCAGC
** * * * * * * * * *
11262256 TCAACCAATAGAGTTTGGATTTATATAATGCCTTCATAAAGGCCTAATTTGACAAAATAGCTTGG
1 TTGACCAAAAGAGTTTGGATCTA-AAAAT-ACTTCATAAAGGTCTAATTCGACAAAACAGCTCGA
*
11262321 TTAAAGAGCTC
64 TCAAAGAGCTC
11262332 ATCTCGACCA
Statistics
Matches: 389, Mismatches: 94, Indels: 36
0.75 0.18 0.07
Matches are distributed among these distances:
84 17 0.04
85 353 0.91
86 18 0.05
87 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.27
Consensus pattern (83 bp):
TTGACCAAAAGAGTTTGGATCTAAAAATACTTCATAAAGGTCTAATTCGACAAAACAGCTCGATC
AAAGAGCTCGGACTCAGC
Found at i:11262098 original size:170 final size:170
Alignment explanation
Indices: 11261848--11262314 Score: 431
Period size: 170 Copynumber: 2.7 Consensus size: 170
11261838 AAAGAGTTTG
* * * * * * **
11261848 GATCTAC-AAATACCTTCATAAAAGGTCTAATTCAATAAAATAGTTCGATCAAAGAGCTCGGACT
1 GATCTACAAAATGCCTTCATAAAAGTTC-AATTCAACAAAATAGCTCGATCAAATAACTTAGACT
** ** * * *
11261912 CAGTTTGATCAAAAGAGTTTGAATTTACAAAATAACTTCATAAAGGCCTAATTCGACAAAATAAC
65 CAACTCAACCAAAAGAGTTTGAATTTATAAAATACCTTCATAAAGGCCTAATTCGACAAAATAAC
* * * *
11261977 TCAATCAAAAAACTCAGACTCGGCTC-ATTTAAAAAAGCTCA
130 TCAACCAAAAAACTCAAACTCAGCTCGA-TCAAAAAAGCTCA
* * *
11262018 GATTTACAAAATGCCTTTATAAAAG-TCTAATTCGACAAAATAGCTCCG-TCAAATAACTTAGAC
1 GATCTACAAAATGCCTTCATAAAAGTTC-AATTCAACAAAATAGCT-CGATCAAATAACTTAGAC
* * * * * * * *
11262081 TCAATTCGACGAAAAGAGCTCGAATCTATAAAATACCTTAATAAAGG-CTCAATTCAACAAAATA
64 TCAACTCAACCAAAAGAGTTTGAATTTATAAAATACCTTCATAAAGGCCT-AATTCGACAAAATA
* * * * * * **
11262145 ATTCGACCAAAAAGCTTAAACTCAGCTCGATCAAAAGAGTTTG
128 ACTCAACCAAAAAACTCAAACTCAGCTCGATCAAAAAAGCTCA
* * * *
11262188 GATCTATAAAATGCCTTCATAAATGTTCAATTCAACAAAATAGCTCGATCAAGTAGCTTAGACTC
1 GATCTACAAAATGCCTTCATAAAAGTTCAATTCAACAAAATAGCTCGATCAAATAACTTAGACTC
* * * * *
11262253 AACTCAACCAATAGAGTTTGGATTTATATAATGCCTTCATAAAGGCCTAATTTGACAAAATA
66 AACTCAACCAAAAGAGTTTGAATTTATAAAATACCTTCATAAAGGCCTAATTCGACAAAATA
11262315 GCTTGGTTAA
Statistics
Matches: 237, Mismatches: 53, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
169 4 0.02
170 211 0.89
171 22 0.09
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (170 bp):
GATCTACAAAATGCCTTCATAAAAGTTCAATTCAACAAAATAGCTCGATCAAATAACTTAGACTC
AACTCAACCAAAAGAGTTTGAATTTATAAAATACCTTCATAAAGGCCTAATTCGACAAAATAACT
CAACCAAAAAACTCAAACTCAGCTCGATCAAAAAAGCTCA
Found at i:11262568 original size:19 final size:19
Alignment explanation
Indices: 11262546--11262584 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
11262536 AGTTTGGGTA
*
11262546 AAAAAAGCTCATCTTAGTC
1 AAAAAAGCTCATCTCAGTC
*
11262565 AAAAGAGCTCATCTCAGTC
1 AAAAAAGCTCATCTCAGTC
11262584 A
1 A
11262585 CCTTGATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.23, G:0.13, T:0.23
Consensus pattern (19 bp):
AAAAAAGCTCATCTCAGTC
Found at i:11262771 original size:102 final size:102
Alignment explanation
Indices: 11262564--11262779 Score: 247
Period size: 102 Copynumber: 2.1 Consensus size: 102
11262554 TCATCTTAGT
* * *
11262564 CAAAAGAGCTCATCTCAGTCACCTTGATTAAAGAATTTATCTCGATAAATTACCTACATAAAGGC
1 CAAAAGAGCTCATCTCAATCACCTTGATCAAAGAATTCATCTCGATAAATTACCTACATAAAGGC
* * *
11262629 TTGGCTGAGCCACATCGATCAAAGTAATTAGTTTGGC
66 TTGACTGAGCCACATCGATCAAAATAATTAGTTTGAC
* * * * *
11262666 CAAAAGAGCTCATCTCAATCACGTTGGTCAAAGAGTTCATCTTGATAAATTGCCTACATAAAGGC
1 CAAAAGAGCTCATCTCAATCACCTTGATCAAAGAATTCATCTCGATAAATTACCTACATAAAGGC
* * * * **
11262731 TTGATTGGGCCATC-TC-AGCTAAAATGATTCTTTTGAC
66 TTGACTGAGCCA-CATCGATC-AAAATAATTAGTTTGAC
11262768 CAAAAGAGCTCA
1 CAAAAGAGCTCA
11262780 GTTTGATCAA
Statistics
Matches: 95, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
101 2 0.02
102 92 0.97
103 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (102 bp):
CAAAAGAGCTCATCTCAATCACCTTGATCAAAGAATTCATCTCGATAAATTACCTACATAAAGGC
TTGACTGAGCCACATCGATCAAAATAATTAGTTTGAC
Found at i:11262790 original size:19 final size:18
Alignment explanation
Indices: 11262762--11262807 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
11262752 AAATGATTCT
*
11262762 TTTGACCAAAAGAGCTCA
1 TTTGATCAAAAGAGCTCA
*
11262780 GTTTGATCAAAGGAGCTCA
1 -TTTGATCAAAAGAGCTCA
11262799 TTTCGATCA
1 TTT-GATCA
11262808 CCTCGATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 3 0.12
19 21 0.88
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (18 bp):
TTTGATCAAAAGAGCTCA
Found at i:11263088 original size:19 final size:19
Alignment explanation
Indices: 11263066--11263112 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
11263056 TAGCTTGGCC
11263066 AAAAGAGCTCGCATCGGTT
1 AAAAGAGCTCGCATCGGTT
11263085 AAAAGAGCTCGCATCGGTT
1 AAAAGAGCTCGCATCGGTT
11263104 AAAAGAGCT
1 AAAAGAGCT
11263113 AATCTCGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (19 bp):
AAAAGAGCTCGCATCGGTT
Found at i:11264126 original size:24 final size:25
Alignment explanation
Indices: 11264099--11264189 Score: 79
Period size: 24 Copynumber: 3.8 Consensus size: 25
11264089 TATTAATTTA
**
11264099 AAATATAATATAATA-ATACGATAT
1 AAATATAATATAATATATAAAATAT
11264123 AAATATAATATAA-ATATAAAATAT
1 AAATATAATATAATATATAAAATAT
*
11264147 AAA-ATTAATATAAT-T-TAAAATTT
1 AAATA-TAATATAATATATAAAATAT
*
11264170 TAATAATAAT-T-ATATATAAA
1 AAAT-ATAATATAATATATAAA
11264190 TTTAATAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
22 2 0.04
23 13 0.23
24 40 0.71
25 1 0.02
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (25 bp):
AAATATAATATAATATATAAAATAT
Found at i:11264147 original size:13 final size:11
Alignment explanation
Indices: 11264099--11264159 Score: 54
Period size: 11 Copynumber: 5.2 Consensus size: 11
11264089 TATTAATTTA
11264099 AAATATAATAT
1 AAATATAATAT
11264110 -AATAATACGATAT
1 AAAT-ATA--ATAT
11264123 AAATATAATAT
1 AAATATAATAT
11264134 AAATATAAAATAT
1 AAATAT--AATAT
11264147 AAA-ATTAATAT
1 AAATA-TAATAT
11264158 AA
1 AA
11264160 TTTAAAATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
10 3 0.07
11 20 0.47
12 1 0.02
13 16 0.37
14 3 0.07
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (11 bp):
AAATATAATAT
Found at i:11264789 original size:23 final size:21
Alignment explanation
Indices: 11264748--11264789 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
11264738 AATTTAATTG
*
11264748 TAATCATAAAAATTTTATTCA
1 TAATCATAAAAAATTTATTCA
11264769 TAATCAATAAATAAATTTATT
1 TAATC-ATAAA-AAATTTATT
11264790 TTAAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 5 0.28
23 8 0.44
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (21 bp):
TAATCATAAAAAATTTATTCA
Found at i:11269263 original size:33 final size:30
Alignment explanation
Indices: 11269213--11269292 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
11269203 ATATAATATT
*
11269213 ATAAAATTTTA-AAATTTAATTTAAATTTGA
1 ATAAAATTTTATTAATTTAATTTAAA-TTGA
** *
11269243 ATCAATTTTTTATATAATTTAATTTGAATTGA
1 AT-AAAATTTTAT-TAATTTAATTTAAATTGA
11269275 ATAAAATTTTATTAATTT
1 ATAAAATTTTATTAATTT
11269293 TGTTTGGTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
30 8 0.20
31 15 0.37
32 6 0.15
33 12 0.29
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (30 bp):
ATAAAATTTTATTAATTTAATTTAAATTGA
Found at i:11269355 original size:13 final size:13
Alignment explanation
Indices: 11269331--11269371 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
11269321 ATTATTTTTT
11269331 TATT-TTTT-ATA
1 TATTATTTTAATA
11269342 TATTATTTTAATA
1 TATTATTTTAATA
**
11269355 TAAAATTTTAATA
1 TATTATTTTAATA
11269368 TATT
1 TATT
11269372 TAAATAAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
11 4 0.17
12 4 0.17
13 16 0.67
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTATTTTAATA
Found at i:11269444 original size:20 final size:17
Alignment explanation
Indices: 11269408--11269449 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 17
11269398 ATTTTTATTT
11269408 TATAAAAATTTAAAATA
1 TATAAAAATTTAAAATA
11269425 TATAAAAATTAATAAAAATA
1 TATAAAAATT--T-AAAATA
11269445 TATAA
1 TATAA
11269450 TTTGTTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.45
19 1 0.05
20 11 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TATAAAAATTTAAAATA
Found at i:11270052 original size:14 final size:14
Alignment explanation
Indices: 11270033--11270063 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
11270023 TGGTTTCCCT
11270033 TTCATCGCCTCCTC
1 TTCATCGCCTCCTC
11270047 TTCATCGCCTCCTC
1 TTCATCGCCTCCTC
11270061 TTC
1 TTC
11270064 TCATCTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.48, G:0.06, T:0.39
Consensus pattern (14 bp):
TTCATCGCCTCCTC
Found at i:11270656 original size:85 final size:85
Alignment explanation
Indices: 11270530--11270703 Score: 296
Period size: 85 Copynumber: 2.0 Consensus size: 85
11270520 AAGCTTTTTT
*
11270530 GCAAAAAAAAAAATCTTGTAAGTTAGCTATGCTTGCTTAATATGTAGTAACAAAAAATACTAATT
1 GCAAAAAAAAAAATCTTGTAAGTTAGCAATGCTTGCTTAATATGTAGTAACAAAAAATACTAATT
11270595 AATATTTGATGGA-TTTATGG
66 AATATTTGAT-GATTTTATGG
* * *
11270615 GCAAAAAAAAAATTGTTGTAAGTTAGCAATGCTTGCTTAATATGTAGTAGCAAAAAATACTAATT
1 GCAAAAAAAAAAATCTTGTAAGTTAGCAATGCTTGCTTAATATGTAGTAACAAAAAATACTAATT
11270680 AATATTTGATGATTTTATGG
66 AATATTTGATGATTTTATGG
11270700 GCAA
1 GCAA
11270704 TTTGGAGGTA
Statistics
Matches: 84, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
84 2 0.02
85 82 0.98
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (85 bp):
GCAAAAAAAAAAATCTTGTAAGTTAGCAATGCTTGCTTAATATGTAGTAACAAAAAATACTAATT
AATATTTGATGATTTTATGG
Found at i:11272337 original size:8 final size:8
Alignment explanation
Indices: 11272324--11272349 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
11272314 AAATGTTACT
11272324 TTTAAAGA
1 TTTAAAGA
11272332 TTTAAAGA
1 TTTAAAGA
11272340 TTTAAAGA
1 TTTAAAGA
11272348 TT
1 TT
11272350 GTACGTATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (8 bp):
TTTAAAGA
Found at i:11282613 original size:3 final size:3
Alignment explanation
Indices: 11282607--11282645 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
11282597 CAACAACAAC
11282607 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11282646 TTATACAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:11287226 original size:17 final size:17
Alignment explanation
Indices: 11287201--11287234 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11287191 GAACAAAGAC
11287201 AGCAGGCAGAAAGGCAT
1 AGCAGGCAGAAAGGCAT
*
11287218 AGCATGCAGAAAGGCAT
1 AGCAGGCAGAAAGGCAT
11287235 GAAGATAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.18, G:0.32, T:0.09
Consensus pattern (17 bp):
AGCAGGCAGAAAGGCAT
Found at i:11287229 original size:49 final size:48
Alignment explanation
Indices: 11287138--11287237 Score: 128
Period size: 49 Copynumber: 2.1 Consensus size: 48
11287128 CATGAAGGCA
* *
11287138 GAACAGAACAAAGACAGTAAAAAAAAGGCATAGCATATAGAAAAGCAT
1 GAACAGAACAAAGACAGCAAAAAAAAGGCATAGCATACAGAAAAGCAT
** * * *
11287186 GAACAGAACAAAGACAGCAGGCAGAAAGGCATAGCATGCAGAAAGGCAT
1 GAACAGAACAAAGACAGCA-AAAAAAAGGCATAGCATACAGAAAAGCAT
11287235 GAA
1 GAA
11287238 GATAGAACAG
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
48 18 0.41
49 26 0.59
ACGTcount: A:0.53, C:0.15, G:0.24, T:0.08
Consensus pattern (48 bp):
GAACAGAACAAAGACAGCAAAAAAAAGGCATAGCATACAGAAAAGCAT
Found at i:11287311 original size:34 final size:34
Alignment explanation
Indices: 11287218--11287312 Score: 109
Period size: 34 Copynumber: 2.8 Consensus size: 34
11287208 AGAAAGGCAT
* * * * * *
11287218 AGCATGCAGAAAGGCATGAAGATAGAACAGAGAT
1 AGCATGCAAAAAGGCACGAAGGTAGCACACAGAC
** *
11287252 AGCACACAAAAAGGCACGAAAGTAGCACACAGAC
1 AGCATGCAAAAAGGCACGAAGGTAGCACACAGAC
11287286 AGCATGCAAAAAGGCACGAAGGTAGCA
1 AGCATGCAAAAAGGCACGAAGGTAGCA
11287313 TGCAGTAGCT
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.47, C:0.19, G:0.26, T:0.07
Consensus pattern (34 bp):
AGCATGCAAAAAGGCACGAAGGTAGCACACAGAC
Found at i:11291756 original size:13 final size:13
Alignment explanation
Indices: 11291716--11291748 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
11291706 AAGTAAAGTT
11291716 AGTTTCTATCTTG
1 AGTTTCTATCTTG
11291729 AGTTTCTATCTTG
1 AGTTTCTATCTTG
11291742 AGTTTCT
1 AGTTTCT
11291749 GTCCTGAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (13 bp):
AGTTTCTATCTTG
Found at i:11293549 original size:9 final size:9
Alignment explanation
Indices: 11293524--11293556 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
11293514 GAAACCAATT
11293524 TTTATAAAAA
1 TTTAT-AAAA
11293534 TTT-TAAAA
1 TTTATAAAA
11293542 TTTATAAAA
1 TTTATAAAA
11293551 TTTATA
1 TTTATA
11293557 TTTCTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 7 0.32
9 12 0.55
10 3 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTTATAAAA
Found at i:11302773 original size:6 final size:6
Alignment explanation
Indices: 11302758--11302792 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
11302748 CCCTTCCATT
* *
11302758 CCTCCA CCTCCG CCTCCG CCTCCG CCTCCA CCTCC
1 CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG CCTCC
11302793 AGCCGGCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.06, C:0.69, G:0.09, T:0.17
Consensus pattern (6 bp):
CCTCCG
Done.