Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 114 of 130
Found at i:22377203 original size:19 final size:18
Alignment explanation
Indices: 22377176--22377211 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
22377166 GAGAAAGGCA
*
22377176 AAAATAAATAAATAAAAAT
1 AAAAGAAATAAA-AAAAAT
22377195 AAAAGAAATAAAAAAAA
1 AAAAGAAATAAAAAAAA
22377212 GTTTTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (18 bp):
AAAAGAAATAAAAAAAAT
Found at i:22379400 original size:3 final size:3
Alignment explanation
Indices: 22379392--22379418 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
22379382 AATTGAACTA
22379392 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
22379419 TGGAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:22383461 original size:19 final size:19
Alignment explanation
Indices: 22383437--22383474 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
22383427 TAAGCTTTAA
*
22383437 AATAAATTTAATTTAAATT
1 AATAAATATAATTTAAATT
*
22383456 AATAAATATATTTTAAATT
1 AATAAATATAATTTAAATT
22383475 TAAAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATAAATATAATTTAAATT
Found at i:22386174 original size:6 final size:6
Alignment explanation
Indices: 22386163--22386187 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
22386153 TTCTATGTGG
22386163 TGATTT TGATTT TGATTT TGATTT T
1 TGATTT TGATTT TGATTT TGATTT T
22386188 ACTTTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (6 bp):
TGATTT
Found at i:22389863 original size:16 final size:17
Alignment explanation
Indices: 22389828--22389865 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
22389818 ACACAGGCTC
* *
22389828 AAAGACAAGATAGCAAA
1 AAAGACAAGACAGAAAA
22389845 AAAGAC-AGACAGAAAA
1 AAAGACAAGACAGAAAA
22389861 AAAGA
1 AAAGA
22389866 AACAGAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.68, C:0.11, G:0.18, T:0.03
Consensus pattern (17 bp):
AAAGACAAGACAGAAAA
Found at i:22389870 original size:14 final size:17
Alignment explanation
Indices: 22389842--22389881 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
22389832 ACAAGATAGC
22389842 AAAAAAGACAGACAGA-
1 AAAAAAGACAGACAGAG
22389858 AAAAAAGA-A-ACAGAG
1 AAAAAAGACAGACAGAG
22389873 AAAATAAGA
1 AAAA-AAGA
22389882 TGGTGTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 5 0.23
15 5 0.23
16 12 0.55
ACGTcount: A:0.72, C:0.07, G:0.17, T:0.03
Consensus pattern (17 bp):
AAAAAAGACAGACAGAG
Found at i:22395859 original size:30 final size:30
Alignment explanation
Indices: 22395818--22395874 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
22395808 TTTTTTATTT
* * *
22395818 ATATATATATTTAGATAATGATATTTTTAA
1 ATATATATATTTAAAAAATAATATTTTTAA
*
22395848 ATATTTATATTTAAAAAATAATATTTT
1 ATATATATATTTAAAAAATAATATTTT
22395875 ATTAATTTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (30 bp):
ATATATATATTTAAAAAATAATATTTTTAA
Found at i:22396796 original size:18 final size:17
Alignment explanation
Indices: 22396773--22396835 Score: 67
Period size: 18 Copynumber: 3.7 Consensus size: 17
22396763 AACTTTACTT
*
22396773 ATAAATAATTTTATATTA
1 ATAAAT-ATTTTATGTTA
*
22396791 ATAAATA--ATATGTTA
1 ATAAATATTTTATGTTA
22396806 ATAAATATTATTATGTTA
1 ATAAATATT-TTATGTTA
*
22396824 ATTAATATTTTA
1 ATAAATATTTTA
22396836 ATAATATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
15 13 0.34
17 4 0.11
18 21 0.55
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
ATAAATATTTTATGTTA
Found at i:22396808 original size:11 final size:11
Alignment explanation
Indices: 22396794--22396903 Score: 74
Period size: 11 Copynumber: 10.5 Consensus size: 11
22396784 TATATTAATA
*
22396794 AATAATATGTT
1 AATAATATATT
22396805 AATAA-ATATT
1 AATAATATATT
*
22396815 -AT--TATGTT
1 AATAATATATT
*
22396823 AATTAATATTTT
1 AA-TAATATATT
22396835 AATAATATATT
1 AATAATATATT
*
22396846 AATAA-ATAAT
1 AATAATATATT
* *
22396856 -ATACTAT-TA
1 AATAATATATT
22396865 ATATAATATATT
1 A-ATAATATATT
22396877 AATAAATATATT
1 AAT-AATATATT
*
22396889 -ATAATATAAT
1 AATAATATATT
22396899 AATAA
1 AATAA
22396904 ATAGTATAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
8 4 0.05
9 6 0.08
10 18 0.23
11 32 0.42
12 17 0.22
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.45
Consensus pattern (11 bp):
AATAATATATT
Found at i:22396808 original size:15 final size:15
Alignment explanation
Indices: 22396784--22396902 Score: 92
Period size: 15 Copynumber: 8.1 Consensus size: 15
22396774 TAAATAATTT
22396784 TATATTAATAAATAA
1 TATATTAATAAATAA
*
22396799 TATGTTAATAAAT-A
1 TATATTAATAAATAA
* *
22396813 T-TATTATGTTAATTAA
1 TATATTA--ATAAATAA
22396829 TAT-TT--T-AATAA
1 TATATTAATAAATAA
22396840 TATATTAATAAATAA
1 TATATTAATAAATAA
* *
22396855 TATACTATTAATATAA
1 TATATTAATAA-ATAA
22396871 TATATTAATAAAT-A
1 TATATTAATAAATAA
22396885 TAT-TATAATATAATAA
1 TATAT-TAATA-AATAA
22396901 TA
1 TA
22396903 AATAGTATAA
Statistics
Matches: 83, Mismatches: 9, Indels: 23
0.72 0.08 0.20
Matches are distributed among these distances:
11 7 0.08
12 3 0.04
13 5 0.06
14 12 0.14
15 35 0.42
16 20 0.24
17 1 0.01
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (15 bp):
TATATTAATAAATAA
Found at i:22396825 original size:33 final size:30
Alignment explanation
Indices: 22396773--22396846 Score: 78
Period size: 33 Copynumber: 2.3 Consensus size: 30
22396763 AACTTTACTT
22396773 ATAAATAATT-TTATATTAATAAATAATATGTTA
1 ATAAAT-ATTATTATATTAAT---TAATATGTTA
* *
22396806 ATAAATATTATTATGTTAATTAATATTTTA
1 ATAAATATTATTATATTAATTAATATGTTA
22396836 ATAATATATTA
1 ATAA-ATATTA
22396847 ATAAATAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
30 13 0.35
31 6 0.16
32 3 0.08
33 15 0.41
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (30 bp):
ATAAATATTATTATATTAATTAATATGTTA
Found at i:22396841 original size:41 final size:42
Alignment explanation
Indices: 22396794--22396899 Score: 128
Period size: 41 Copynumber: 2.5 Consensus size: 42
22396784 TATATTAATA
* * * *
22396794 AATAATATGTTAATAAATATTATTA-TGTTAAT-TAATATTTT
1 AATAATATATTAATAAATAATA-TACTATTAATATAATATATT
22396835 AATAATATATTAATAAATAATATACTATTAATATAATATATT
1 AATAATATATTAATAAATAATATACTATTAATATAATATATT
22396877 AATAAATATATT-ATAATATAATA
1 AAT-AATATATTAATAA-ATAATA
22396900 ATAAATAGTA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
40 2 0.04
41 26 0.46
42 15 0.26
43 14 0.25
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (42 bp):
AATAATATATTAATAAATAATATACTATTAATATAATATATT
Found at i:22396845 original size:56 final size:53
Alignment explanation
Indices: 22396784--22396911 Score: 148
Period size: 53 Copynumber: 2.4 Consensus size: 53
22396774 TAAATAATTT
** * * * *
22396784 TATATTAATAAATAATATGTTAATAAATATTATTATGTTAATTAATATTTTAATAA
1 TATATTAATAAATAATATACT-ATAAATA-TAATATATTAATAAATATATT-ATAA
*
22396840 TATATTAATAAATAATATACTATTAATATAATATATTAATAAATATATTATAA
1 TATATTAATAAATAATATACTATAAATATAATATATTAATAAATATATTATAA
* *
22396893 TATAATAATAAATAGTATA
1 TATATTAATAAATAATATA
22396912 AAGAATAATA
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
53 21 0.33
54 17 0.27
55 6 0.10
56 19 0.30
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (53 bp):
TATATTAATAAATAATATACTATAAATATAATATATTAATAAATATATTATAA
Found at i:22396871 original size:31 final size:27
Alignment explanation
Indices: 22396836--22396899 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 27
22396826 TAATATTTTA
22396836 ATAATATATTAATAAATAATATACTATTAAT
1 ATAATATATTAATAAAT-ATAT--TA-TAAT
22396867 ATAATATATTAATAAATATATTATAAT
1 ATAATATATTAATAAATATATTATAAT
22396894 ATAATA
1 ATAATA
22396900 ATAAATAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
27 10 0.30
28 2 0.06
30 4 0.12
31 17 0.52
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
ATAATATATTAATAAATATATTATAAT
Found at i:22396895 original size:8 final size:8
Alignment explanation
Indices: 22396834--22396924 Score: 61
Period size: 8 Copynumber: 12.0 Consensus size: 8
22396824 ATTAATATTT
22396834 TAATAATA
1 TAATAATA
*
22396842 TATTAATA
1 TAATAATA
22396850 -AATAATA
1 TAATAATA
* *
22396857 TACTATTA
1 TAATAATA
22396865 -ATATAATA
1 TA-ATAATA
*
22396873 TATTAATA
1 TAATAATA
22396881 -AAT-ATA
1 TAATAATA
*
22396887 TTATAATA
1 TAATAATA
22396895 TAATAATA
1 TAATAATA
*
22396903 -AATAGTA
1 TAATAATA
22396910 TAA-AGA-A
1 TAATA-ATA
22396917 TAATAATA
1 TAATAATA
22396925 GTTTTAGTTT
Statistics
Matches: 62, Mismatches: 12, Indels: 18
0.67 0.13 0.20
Matches are distributed among these distances:
6 3 0.05
7 23 0.37
8 35 0.56
9 1 0.02
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.38
Consensus pattern (8 bp):
TAATAATA
Found at i:22396912 original size:12 final size:11
Alignment explanation
Indices: 22396834--22396924 Score: 54
Period size: 12 Copynumber: 8.5 Consensus size: 11
22396824 ATTAATATTT
22396834 TAAT-AATATA
1 TAATAAATATA
22396844 TTAATAAATA-A
1 -TAATAAATATA
*
22396855 T-AT-ACTAT-
1 TAATAAATATA
22396863 TAATATAATATA
1 TAATA-AATATA
22396875 TTAATAAATATA
1 -TAATAAATATA
*
22396887 TTAT-AATATAA
1 TAATAAATAT-A
22396898 TAATAAATAGTA
1 TAATAAATA-TA
22396910 TAA-AGAATA-A
1 TAATA-AATATA
22396920 TAATA
1 TAATA
22396925 GTTTTAGTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 24
0.70 0.04 0.26
Matches are distributed among these distances:
8 4 0.06
9 4 0.06
10 10 0.16
11 18 0.28
12 22 0.34
13 6 0.09
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.38
Consensus pattern (11 bp):
TAATAAATATA
Found at i:22397028 original size:25 final size:24
Alignment explanation
Indices: 22396997--22397054 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 24
22396987 TATAATTATT
*
22396997 TTTTAATATTAATAA-TTTTAATA
1 TTTTAATATAAATAACTTTTAATA
22397020 TACTTTAATAATAAATAACTTTTAATA
1 T--TTTAAT-ATAAATAACTTTTAATA
22397047 TTTTAATA
1 TTTTAATA
22397055 GTTATATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 1 0.03
24 1 0.03
25 12 0.40
26 7 0.23
27 9 0.30
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTTAATATAAATAACTTTTAATA
Found at i:22397122 original size:33 final size:33
Alignment explanation
Indices: 22397084--22397148 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
22397074 AAAAAAACAG
*
22397084 ATTTTTCA-AAAAACAACCAAACAATAAAAAAT
1 ATTTTTTATAAAAACAACCAAACAATAAAAAAT
* ** *
22397116 ATTTTTTATTAATTCATCCAAACAATAAAAAAT
1 ATTTTTTATAAAAACAACCAAACAATAAAAAAT
22397149 CAATTCCAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 7 0.26
33 20 0.74
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (33 bp):
ATTTTTTATAAAAACAACCAAACAATAAAAAAT
Found at i:22399016 original size:127 final size:122
Alignment explanation
Indices: 22398862--22399126 Score: 284
Period size: 127 Copynumber: 2.1 Consensus size: 122
22398852 TTCCTAATGA
*
22398862 AAATCATTTTTTTACTGTAAAAGAAATCAAATTTTATATTTAAAAAAAA-CAATATTTTAAAATT
1 AAATCATTTTTTTACTGTAAAAGAAATCAAA-CTT-TATTTAAAAAAAATCAATA-TTTAAAATT
* * *
22398926 TTTTAGAATTTTTTCT-TATTTTAAAATATTAAATTTAATATTTTTAAATATTTTTATTTTTTT
63 TTTAAGAA-ATTTTCTATATTTTAAAATATTAAATTTAAT-TTTTTAAATA--TTTAATTTTTT
* * * * * *
22398989 AAATCATATTTTTTAGTTTTAAA-AAATCAAACTTTATTTAAAAAAAATTAGTATTTCAAATTTT
1 AAATCAT-TTTTTTACTGTAAAAGAAATCAAACTTTATTTAAAAAAAATCAATATTTAAAATTTT
* * *
22399053 TAAGAAATTTTCTAGATTTTTTAAAATATTAAATTTACTTTTTTCAATATTTAATTTTTT
65 TAAGAAATTTTCT--ATATTTTAAAATATTAAATTTAATTTTTTAAATATTTAATTTTTT
22399113 AAATTTCATTTTTT
1 AAA--TCATTTTTT
22399127 GATTTTGTGC
Statistics
Matches: 118, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
124 19 0.16
125 33 0.28
126 18 0.15
127 36 0.31
128 12 0.10
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (122 bp):
AAATCATTTTTTTACTGTAAAAGAAATCAAACTTTATTTAAAAAAAATCAATATTTAAAATTTTT
AAGAAATTTTCTATATTTTAAAATATTAAATTTAATTTTTTAAATATTTAATTTTTT
Found at i:22399094 original size:22 final size:21
Alignment explanation
Indices: 22399069--22399109 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
22399059 ATTTTCTAGA
22399069 TTTTTTAAAATATTAAATTTAC
1 TTTTTT-AAATATTAAATTTAC
* *
22399091 TTTTTTCAATATTTAATTT
1 TTTTTTAAATATTAAATTT
22399110 TTTAAATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTTTAAATATTAAATTTAC
Found at i:22399118 original size:14 final size:14
Alignment explanation
Indices: 22399081--22399126 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
22399071 TTTTAAAATA
*
22399081 TTAAATTTACTTTT
1 TTAAATTTAATTTT
22399095 TTCAATATTTAATTTT
1 TT-AA-ATTTAATTTT
*
22399111 TTAAATTTCATTTT
1 TTAAATTTAATTTT
22399125 TT
1 TT
22399127 GATTTTGTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 13 0.46
15 4 0.14
16 11 0.39
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (14 bp):
TTAAATTTAATTTT
Found at i:22399257 original size:21 final size:20
Alignment explanation
Indices: 22399229--22399268 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
22399219 TATATTTTTA
* *
22399229 TTTTTATTTTTTATAAAATT
1 TTTTTATTTTATAAAAAATT
22399249 TTTTATATTTTATAAAAAAT
1 TTTT-TATTTTATAAAAAAT
22399269 CTAGAAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTATTTTATAAAAAATT
Found at i:22399262 original size:19 final size:19
Alignment explanation
Indices: 22399229--22399265 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
22399219 TATATTTTTA
*
22399229 TTTTTATTTTTTATAAAAT
1 TTTTTATATTTTATAAAAT
22399248 TTTTTATATTTTATAAAA
1 TTTTTATATTTTATAAAA
22399266 AATCTAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTTATATTTTATAAAAT
Found at i:22399528 original size:46 final size:45
Alignment explanation
Indices: 22399441--22399635 Score: 121
Period size: 45 Copynumber: 4.5 Consensus size: 45
22399431 TTGAAACAGT
22399441 AAAT-TTAGTATTTTTTAAAAATCTAAAAAAATTCTAAAAAATTCA
1 AAATATTAGTATTTTTTAAAAA-CTAAAAAAATTCTAAAAAATTCA
* * *
22399486 AAATATTAGT-TTTTTTAAAAA-TAAAATATGATTTTAATAAAATTGA
1 AAATATTAGTATTTTTTAAAAACTAAAA-A-AATTCTAA-AAAATTCA
** * * *
22399532 AATATATATA-TGATTTTTTGGAAATTAATAATA-T-TAAAAATATT--
1 AA-ATAT-TAGT-ATTTTTTAAAAACTAAAAAAATTCTAAAAA-ATTCA
* *
22399576 AAAT-TTA--ATATTTTAAAAAATAAAAAAATTCTAAAAAA-TCA
1 AAATATTAGTATTTTTTAAAAACTAAAAAAATTCTAAAAAATTCA
*
22399617 TAATA-TAG-ATTTTTTAAAA
1 AAATATTAGTATTTTTTAAAA
22399636 TTAAAATTTA
Statistics
Matches: 119, Mismatches: 15, Indels: 35
0.70 0.09 0.21
Matches are distributed among these distances:
39 16 0.13
40 2 0.02
41 13 0.11
42 11 0.09
43 7 0.06
44 3 0.03
45 24 0.20
46 20 0.17
47 6 0.05
48 3 0.03
49 10 0.08
50 4 0.03
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.41
Consensus pattern (45 bp):
AAATATTAGTATTTTTTAAAAACTAAAAAAATTCTAAAAAATTCA
Found at i:22400023 original size:118 final size:118
Alignment explanation
Indices: 22399881--22400108 Score: 303
Period size: 118 Copynumber: 1.9 Consensus size: 118
22399871 TTTTTAATGG
* * * * * ***
22399881 CAAAAAATTGATTAAGTTAGTAATTGGACTAAAATTATCAAATCAAAATAGTGCAGGTACTAAAT
1 CAAAAAATTGACTAAATTAGTAATTGAACTAAAATTATCAAATCAAAATAATACAAAAACTAAAT
* * *
22399946 TTGTATGAATTACAATATAAAGATCAAATTTCAAAATTTAACAGAACACATGA
66 ATGTATAAATTACAATATAAAGATCAAACTTCAAAATTTAACAGAACACATGA
* * * *
22399999 CAAAAATTTGACTAAATTAGTAATTGAACTAAGATTATCAAATCAAAATAATATAAAAATTAAAT
1 CAAAAAATTGACTAAATTAGTAATTGAACTAAAATTATCAAATCAAAATAATACAAAAACTAAAT
* *
22400064 ATGTATAAATTACAATATAAAGATTAAACTTCAAATTTTAACAGA
66 ATGTATAAATTACAATATAAAGATCAAACTTCAAAATTTAACAGA
22400109 GTATAAATAC
Statistics
Matches: 93, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
118 93 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (118 bp):
CAAAAAATTGACTAAATTAGTAATTGAACTAAAATTATCAAATCAAAATAATACAAAAACTAAAT
ATGTATAAATTACAATATAAAGATCAAACTTCAAAATTTAACAGAACACATGA
Found at i:22400658 original size:31 final size:31
Alignment explanation
Indices: 22400623--22400684 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
22400613 AAAAATTGAA
22400623 AGTTACACATATAAAAG-AAATATTACAATTT
1 AGTTACACAT-TAAAAGTAAATATTACAATTT
* * * *
22400654 AGTTAGAGATTAAAAGTTAATATTATAATTT
1 AGTTACACATTAAAAGTAAATATTACAATTT
22400685 TGTTTTATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.37
Consensus pattern (31 bp):
AGTTACACATTAAAAGTAAATATTACAATTT
Found at i:22405234 original size:3 final size:3
Alignment explanation
Indices: 22405226--22405271 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
22405216 TAAAAGAATA
*
22405226 AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
22405272 TCATAGAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:22406200 original size:17 final size:19
Alignment explanation
Indices: 22406178--22406230 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
22406168 ATTTGTGTAA
22406178 AAGATG-TAGAAA-AAAAC
1 AAGATGTTAGAAAGAAAAC
*
22406195 AAGATGTTAGAAAGAAAAA
1 AAGATGTTAGAAAGAAAAC
*
22406214 AAAAGTGTTAG-AAGAAA
1 AAGA-TGTTAGAAAGAAA
22406231 TAATAACAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 6 0.19
18 6 0.19
19 13 0.42
20 6 0.19
ACGTcount: A:0.62, C:0.02, G:0.21, T:0.15
Consensus pattern (19 bp):
AAGATGTTAGAAAGAAAAC
Found at i:22406222 original size:20 final size:21
Alignment explanation
Indices: 22406185--22406239 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
22406175 TAAAAGATGT
22406185 AGAAAAAAACAAGATGTTAGAA
1 AGAAAAAAACAAGATGTTAG-A
22406207 AGAAAAAAA-AAG-TGTTAGA
1 AGAAAAAAACAAGATGTTAGA
22406226 AGAAATAATAACAA
1 AGAAA-AA-AACAA
22406240 CAACAACAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.20
20 8 0.27
21 5 0.17
22 11 0.37
ACGTcount: A:0.65, C:0.04, G:0.16, T:0.15
Consensus pattern (21 bp):
AGAAAAAAACAAGATGTTAGA
Found at i:22406252 original size:15 final size:15
Alignment explanation
Indices: 22406232--22406266 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
22406222 TAGAAGAAAT
22406232 AATAACAACAACAAC
1 AATAACAACAACAAC
22406247 AATAACAACAACAAC
1 AATAACAACAACAAC
22406262 AATAA
1 AATAA
22406267 TAATAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.69, C:0.23, G:0.00, T:0.09
Consensus pattern (15 bp):
AATAACAACAACAAC
Found at i:22406268 original size:3 final size:3
Alignment explanation
Indices: 22406262--22406300 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
22406252 CAACAACAAC
22406262 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
22406301 TATTATTATT
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:22406305 original size:3 final size:3
Alignment explanation
Indices: 22406299--22406338 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
22406289 AATAATAATA
22406299 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
22406339 AAAAGAGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:22406793 original size:20 final size:20
Alignment explanation
Indices: 22406748--22406795 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
22406738 CAAAGGTAAT
* *
22406748 AAAAAATTTAAAAAAAGGTT
1 AAAAAATTGAAAAAAAGGTC
*
22406768 AAAAAATTGAAAAAAATGTC
1 AAAAAATTGAAAAAAAGGTC
22406788 ATAAAAAT
1 A-AAAAAT
22406796 GTTAGAGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (20 bp):
AAAAAATTGAAAAAAAGGTC
Found at i:22410689 original size:33 final size:32
Alignment explanation
Indices: 22410646--22410714 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
22410636 AATTAGATAT
*
22410646 TTTTGTTATTTGAGTGAATTAATGAAAAATGTA
1 TTTTATTATTT-AGTGAATTAATGAAAAATGTA
** **
22410679 TTTTATTATTTAGTGGGTTTTTGAAAAATGTA
1 TTTTATTATTTAGTGAATTAATGAAAAATGTA
22410711 TTTT
1 TTTT
22410715 TTAAAAATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
32 21 0.68
33 10 0.32
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.52
Consensus pattern (32 bp):
TTTTATTATTTAGTGAATTAATGAAAAATGTA
Found at i:22410765 original size:17 final size:18
Alignment explanation
Indices: 22410743--22410822 Score: 71
Period size: 17 Copynumber: 4.5 Consensus size: 18
22410733 TAATCCTTAA
22410743 AATATTAAAA-AATTATT
1 AATATTAAAATAATTATT
22410760 AATATTAAAATAATTA-T
1 AATATTAAAATAATTATT
*
22410777 -ATTTTAATAATAA-TATTT
1 AATATTAA-AATAATTA-TT
*
22410795 AACATTAAAAT-ATTATACT
1 AATATTAAAATAATTAT--T
22410814 AATATTAAA
1 AATATTAAA
22410823 CTTTTAAAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
16 8 0.16
17 18 0.35
18 11 0.22
19 14 0.27
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
AATATTAAAATAATTATT
Found at i:22410885 original size:28 final size:27
Alignment explanation
Indices: 22410853--22410925 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 27
22410843 ATTATATTTG
22410853 TTAATACTTTAAAATATTCAAAATAGTA
1 TTAATACTTTAAAATATTC-AAATAGTA
* *
22410881 TTAATATTCTTAAAAAATTCAAATAGTA
1 TTAATACT-TTAAAATATTCAAATAGTA
*
22410909 TTAATACTCTAAAATAT
1 TTAATACTTTAAAATAT
22410926 GATTTCTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 7 0.18
28 22 0.56
29 10 0.26
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.40
Consensus pattern (27 bp):
TTAATACTTTAAAATATTCAAATAGTA
Found at i:22411281 original size:25 final size:26
Alignment explanation
Indices: 22411251--22411319 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 26
22411241 AAATAATAAA
*
22411251 AATATTATTTACTATATTAAT-GTTT
1 AATATTATTTACTATATTAATAGTAT
*
22411276 AATATT-TATTACTAAATTAATAGTAT
1 AATATTAT-TTACTATATTAATAGTAT
*
22411302 AATACTATTTA-T-TATTAA
1 AATATTATTTACTATATTAA
22411320 AATATTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
24 6 0.16
25 19 0.51
26 11 0.30
27 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (26 bp):
AATATTATTTACTATATTAATAGTAT
Found at i:22411343 original size:24 final size:25
Alignment explanation
Indices: 22411307--22411357 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
22411297 AGTATAATAC
22411307 TATTTATTATTAA-AATATTA-AAAA
1 TATTTATTATTAATAATA-TAGAAAA
22411331 TATTTATGT-TTAATAATATAGAAAA
1 TATTTAT-TATTAATAATATAGAAAA
22411356 TA
1 TA
22411358 AAATATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (25 bp):
TATTTATTATTAATAATATAGAAAA
Found at i:22417350 original size:45 final size:45
Alignment explanation
Indices: 22417277--22417430 Score: 174
Period size: 45 Copynumber: 3.5 Consensus size: 45
22417267 GGATAGTTTG
** * * *
22417277 GCTGAGAAGACAAACAAAGAGACT-GCCATGACAGTAAATAGTTCA
1 GCTGAGAAGATGAAGAAAGAGA-TGGCCATGATAGTAAATAGCTCA
* *
22417322 GCTGAGAATATGAAGAAAGGGATGGCCATGATAGTAAATAGCTCA
1 GCTGAGAAGATGAAGAAAGAGATGGCCATGATAGTAAATAGCTCA
*
22417367 GCTGTGAAGATG-AGAAAAGAGATGG--AT-ATAGTAAATAGCTCA
1 GCTGAGAAGATGAAG-AAAGAGATGGCCATGATAGTAAATAGCTCA
*
22417409 GTTGAGAAGATGAAGAAAGAGA
1 GCTGAGAAGATGAAGAAAGAGA
22417431 CAGCAGCGGT
Statistics
Matches: 94, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
42 32 0.34
43 4 0.04
44 3 0.03
45 55 0.59
ACGTcount: A:0.44, C:0.10, G:0.28, T:0.18
Consensus pattern (45 bp):
GCTGAGAAGATGAAGAAAGAGATGGCCATGATAGTAAATAGCTCA
Found at i:22417531 original size:114 final size:114
Alignment explanation
Indices: 22417331--22417544 Score: 284
Period size: 114 Copynumber: 1.9 Consensus size: 114
22417321 AGCTGAGAAT
* ** * * * *
22417331 ATGAAGAAAGGGATGGCCATGATAGTAAATAGCTCAGCTGTGAAGATGAGAAAAGAGATGGATAT
1 ATGAAGAAAGAGACAGCCATGACAGTAAATAGCTCAGCTGAGAAGATGAGAAAAGAGACGGATAC
*
22417396 AGTAAATAGCTCAGTTGAGAAGATGAAGAAAGAGACAGCAGCGGTGAAG
66 AGTAAATAGCTCAGCTGAGAAGATGAAGAAAGAGACAGCAGCGGTGAAG
* * * * *
22417445 ATGAAGAAAGAGACAGCTATGACAGTAAATAGCTTAGCTGAGAAGATGAGAGAAGATACGGCTAC
1 ATGAAGAAAGAGACAGCCATGACAGTAAATAGCTCAGCTGAGAAGATGAGAAAAGAGACGGATAC
* * *
22417510 AGTGACTAGCTCAGCTGAGAAGATGAAGAGAGAGA
66 AGTAAATAGCTCAGCTGAGAAGATGAAGAAAGAGA
22417545 TGGCTGTGAC
Statistics
Matches: 84, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
114 84 1.00
ACGTcount: A:0.42, C:0.10, G:0.31, T:0.17
Consensus pattern (114 bp):
ATGAAGAAAGAGACAGCCATGACAGTAAATAGCTCAGCTGAGAAGATGAGAAAAGAGACGGATAC
AGTAAATAGCTCAGCTGAGAAGATGAAGAAAGAGACAGCAGCGGTGAAG
Found at i:22417558 original size:45 final size:44
Alignment explanation
Indices: 22417441--22417583 Score: 150
Period size: 45 Copynumber: 3.2 Consensus size: 44
22417431 CAGCAGCGGT
* ** * *
22417441 GAAGATGAAGAAAGAGACAGCTATGACAGTAAATAGCTTAGCTGA
1 GAAGATGAAGAGAGAGATGGCT-TGACAGTGAATAGCTCAGCTGA
*
22417486 GAAGATG-AGAGA-AGATACGGC-T-ACAGTGACTAGCTCAGCTGA
1 GAAGATGAAGAGAGAGAT--GGCTTGACAGTGAATAGCTCAGCTGA
*
22417528 GAAGATGAAGAGAGAGATGGCTGTGACAGTGAATGGCTCAGCTGA
1 GAAGATGAAGAGAGAGATGGCT-TGACAGTGAATAGCTCAGCTGA
*
22417573 GAAGACGAAGA
1 GAAGATGAAGA
22417584 AACATATGAC
Statistics
Matches: 82, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
42 27 0.33
43 9 0.11
44 9 0.11
45 37 0.45
ACGTcount: A:0.39, C:0.13, G:0.32, T:0.16
Consensus pattern (44 bp):
GAAGATGAAGAGAGAGATGGCTTGACAGTGAATAGCTCAGCTGA
Found at i:22417597 original size:45 final size:45
Alignment explanation
Indices: 22417464--22417597 Score: 123
Period size: 45 Copynumber: 3.0 Consensus size: 45
22417454 GAGACAGCTA
* * * * *
22417464 TGACAGTAAATAGCTTAGCTGAGAAGATG-AGAGA-AGAT-ACGG
1 TGACAGTGAATAGCTCAGCTGAGAAGACGAAGAAACAGATGACTG
* * * * *
22417506 CT-ACAGTGACTAGCTCAGCTGAGAAGATGAAGAGAGAGATGGCTG
1 -TGACAGTGAATAGCTCAGCTGAGAAGACGAAGAAACAGATGACTG
* *
22417551 TGACAGTGAATGGCTCAGCTGAGAAGACGAAGAAACATATGACTG
1 TGACAGTGAATAGCTCAGCTGAGAAGACGAAGAAACAGATGACTG
22417596 TG
1 TG
22417598 GTAGTTTCAA
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
42 24 0.32
43 6 0.08
44 5 0.07
45 40 0.53
ACGTcount: A:0.37, C:0.13, G:0.31, T:0.19
Consensus pattern (45 bp):
TGACAGTGAATAGCTCAGCTGAGAAGACGAAGAAACAGATGACTG
Found at i:22440026 original size:30 final size:30
Alignment explanation
Indices: 22439972--22440032 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
22439962 ATGAATTTAC
* * * *
22439972 TTCATTTATAAAGTCTAGGGGCTCTTCTAT
1 TTCAATTACAAAGTCCAGGCGCTCTTCTAT
22440002 TTCAATTACAAAGTCCAGGCGCTCTTCTAT
1 TTCAATTACAAAGTCCAGGCGCTCTTCTAT
22440032 T
1 T
22440033 AGAACTTCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (30 bp):
TTCAATTACAAAGTCCAGGCGCTCTTCTAT
Found at i:22447674 original size:22 final size:22
Alignment explanation
Indices: 22447646--22447706 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
22447636 AGCCAAAATG
22447646 CTTAAAACTCGAAACTCTAAAA
1 CTTAAAACTCGAAACTCTAAAA
* * *
22447668 CTTAAAA-TCTTAAACTTTAAAC
1 CTTAAAACTC-GAAACTCTAAAA
22447690 CTTAAAATCCTCGAAAC
1 CTTAAAA--CTCGAAAC
22447707 CTTAAAATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
21 2 0.06
22 23 0.74
24 4 0.13
25 2 0.06
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.28
Consensus pattern (22 bp):
CTTAAAACTCGAAACTCTAAAA
Found at i:22447743 original size:15 final size:15
Alignment explanation
Indices: 22447703--22447745 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
22447693 AAAATCCTCG
22447703 AAACCTTAAAATTCAA
1 AAACCTTAAAA-TCAA
* *
22447719 AATCC-AAAAATCAA
1 AAACCTTAAAATCAA
22447733 AAACCTTAAAATC
1 AAACCTTAAAATC
22447746 GACATGTAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
14 8 0.36
15 10 0.45
16 4 0.18
ACGTcount: A:0.58, C:0.21, G:0.00, T:0.21
Consensus pattern (15 bp):
AAACCTTAAAATCAA
Found at i:22458406 original size:16 final size:15
Alignment explanation
Indices: 22458377--22458457 Score: 62
Period size: 15 Copynumber: 5.4 Consensus size: 15
22458367 TTAGGGTTGT
22458377 GATTTTA-GAGTTTGG
1 GATTTTAGGA-TTTGG
22458392 AGATTTTAGGATTTGG
1 -GATTTTAGGATTTGG
22458408 G-TTTTGAGG-TTT-G
1 GATTTT-AGGATTTGG
* *
22458421 GATTTTAAGGGTTTCG
1 GATTTT-AGGATTTGG
* *
22458437 GATTTTAAGATTTTG
1 GATTTTAGGATTTGG
22458452 GATTTT
1 GATTTT
22458458 TGAATTTTAG
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
13 2 0.04
14 14 0.25
15 19 0.34
16 19 0.34
17 2 0.04
ACGTcount: A:0.20, C:0.01, G:0.30, T:0.49
Consensus pattern (15 bp):
GATTTTAGGATTTGG
Found at i:22458458 original size:16 final size:16
Alignment explanation
Indices: 22458393--22458457 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 16
22458383 AGAGTTTGGA
22458393 GATTTT-AGGA-TTTG
1 GATTTTAAGGATTTTG
* *
22458407 GGTTTTGAGG--TTTG
1 GATTTTAAGGATTTTG
* *
22458421 GATTTTAAGGGTTTCG
1 GATTTTAAGGATTTTG
22458437 GATTTTAA-GATTTTG
1 GATTTTAAGGATTTTG
22458452 GATTTT
1 GATTTT
22458458 TGAATTTTAG
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
14 17 0.40
15 14 0.33
16 11 0.26
ACGTcount: A:0.18, C:0.02, G:0.29, T:0.51
Consensus pattern (16 bp):
GATTTTAAGGATTTTG
Found at i:22458481 original size:17 final size:16
Alignment explanation
Indices: 22458455--22458500 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
22458445 GATTTTGGAT
*
22458455 TTTTGAATTTTAGGAGA
1 TTTTGGATTTTAGG-GA
*
22458472 TTTTGGATTTTAGGGG
1 TTTTGGATTTTAGGGA
*
22458488 TTTGGGATTTTAG
1 TTTTGGATTTTAG
22458501 TGGGGGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (16 bp):
TTTTGGATTTTAGGGA
Found at i:22460042 original size:3 final size:3
Alignment explanation
Indices: 22460034--22460067 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
22460024 GTCATTTTAA
*
22460034 ATT ATT ATT ATT AAT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
22460068 AAACAGTAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:22463080 original size:70 final size:70
Alignment explanation
Indices: 22463006--22463299 Score: 199
Period size: 70 Copynumber: 4.3 Consensus size: 70
22462996 TTCGATCACA
* * * * * *
22463006 TTTATTATTTGACTTGTGATTCAATCCCAATTATCTTTTTCCTTCAAC-TAGCAGTTCAATCCCG
1 TTTATTCTTTGACTCGTGACTCAATCCCAATCATCTTTATCCTTCAACTTA-CAGTTCAATCCCA
22463070 GTCATC
65 GTCATC
* * * * *
22463076 TTTATTCTTTGACTCGTGACTCAGTCCCAGTCATCTTTATCTTTTAACTTACAGTTCAATCTCAG
1 TTTATTCTTTGACTCGTGACTCAATCCCAATCATCTTTATCCTTCAACTTACAGTTCAATCCCAG
*
22463141 TCATT
66 TCATC
* * * ** *
22463146 TTTATTCTTTGA--C-TAACTGC--TCCCAGTCATCTTTATTCTTTGACTTACAGTTCAATCTCA
1 TTTATTCTTTGACTCGTGACT-CAATCCCAATCATCTTTATCCTTCAACTTACAGTTCAATCCCA
* *
22463206 ATCATT
65 GTCATC
* * * * * * * * ** *
22463212 TTTATACTCTGACTGGT-AGCTCAGTCTCAGTTATCTTTATCTTTCAACTT-GTGATTCAATCTC
1 TTTATTCTTTGACTCGTGA-CTCAATCCCAATCATCTTTATCCTTCAACTTACAG-TTCAATCCC
* *
22463275 AATTATC
64 AGTCATC
22463282 TTTATTCTTTGACTCGTG
1 TTTATTCTTTGACTCGTG
22463300 GTTTAATCCA
Statistics
Matches: 181, Mismatches: 33, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
66 52 0.29
67 4 0.02
68 4 0.02
69 4 0.02
70 115 0.64
71 2 0.01
ACGTcount: A:0.22, C:0.23, G:0.10, T:0.45
Consensus pattern (70 bp):
TTTATTCTTTGACTCGTGACTCAATCCCAATCATCTTTATCCTTCAACTTACAGTTCAATCCCAG
TCATC
Found at i:22463142 original size:35 final size:34
Alignment explanation
Indices: 22463103--22463571 Score: 143
Period size: 35 Copynumber: 13.4 Consensus size: 34
22463093 GACTCAGTCC
*
22463103 CAGTCATCTTTATCTTTTAACTTACAGTTCAATCT
1 CAGTCATCTTTAT-TTTTGACTTACAGTTCAATCT
* * * *
22463138 CAGTCATTTTTATTCTTTGAC-TA-ACTGC--TCC
1 CAGTCATCTTTATT-TTTGACTTACAGTTCAATCT
22463169 CAGTCATCTTTATTCTTTGACTTACAGTTCAATCT
1 CAGTCATCTTTATT-TTTGACTTACAGTTCAATCT
* * * * *** * *
22463204 CAATCATTTTTATACTCTGACTGGTAGCTCAGTCT
1 CAGTCATCTTTAT-TTTTGACTTACAGTTCAATCT
* ** **
22463239 CAGTTATCTTTATCTTTCAACTT-GTGATTCAATCT
1 CAGTCATCTTTAT-TTTTGACTTACAG-TTCAATCT
* * **** *
22463274 CAATTATCTTTATTCTTTGACTCGTGGTTTAATC-
1 CAGTCATCTTTATT-TTTGACTTACAGTTCAATCT
* * * *
22463308 CAGCCAT-TTTATTCTCTGACTTGCTGTTCAATC-
1 CAGTCATCTTTATT-TTTGACTTACAGTTCAATCT
* * * *
22463341 CTAATCATATTTATTTTTTGACTTATAGTTAAATCT
1 C-AGTCATCTTTA-TTTTTGACTTACAGTTCAATCT
* * * *
22463377 C-GATCATCTTTATTTTTTCACTTGCAGTTCAAACC
1 CAG-TCATCTTTA-TTTTTGACTTACAGTTCAATCT
* * *
22463412 CAGTCATCTTTATTCTTTTACTTGTGACTTGTGATTCAATCC
1 CAGTCATCTTTATT-TTTGAC-T-T-AC---AG-TTCAATCT
* * **
22463454 CAGTCATTTTTATTTTTTAACTTATGGTTCAATC-
1 CAGTCATCTTTA-TTTTTGACTTACAGTTCAATCT
* * * *
22463488 CTTGTCATATTTATTCTTTAACTTGCAGTTCAATC-
1 C-AGTCATCTTTATT-TTTGACTTACAGTTCAATCT
* * *
22463523 CTAGTCAT-TTTCATTTCTTGACTTGCAATTCAATCA
1 C-AGTCATCTTT-ATTT-TTGACTTACAGTTCAATCT
*
22463559 CAATCATCTTTAT
1 CAGTCATCTTTAT
22463572 CCCTGACGTA
Statistics
Matches: 326, Mismatches: 78, Indels: 60
0.70 0.17 0.13
Matches are distributed among these distances:
31 22 0.07
32 2 0.01
33 28 0.09
34 22 0.07
35 210 0.64
36 11 0.03
37 1 0.00
38 1 0.00
39 1 0.00
40 1 0.00
41 2 0.01
42 23 0.07
43 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (34 bp):
CAGTCATCTTTATTTTTGACTTACAGTTCAATCT
Found at i:22463200 original size:66 final size:66
Alignment explanation
Indices: 22463100--22463225 Score: 200
Period size: 66 Copynumber: 1.9 Consensus size: 66
22463090 CGTGACTCAG
* * *
22463100 TCCCAGTCATCTTTATCTTTTAACTTACAGTTCAATCTCAGTCATTTTTATTCTTTGACTAACTG
1 TCCCAGTCATCTTTATCTTTTAACTTACAGTTCAATCTCAATCATTTTTATACTCTGACTAACTG
22463165 C
66 C
*
22463166 TCCCAGTCATCTTTAT-TCTTTGACTTACAGTTCAATCTCAATCATTTTTATACTCTGACT
1 TCCCAGTCATCTTTATCT-TTTAACTTACAGTTCAATCTCAATCATTTTTATACTCTGACT
22463226 GGTAGCTCAG
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
65 1 0.02
66 54 0.98
ACGTcount: A:0.23, C:0.25, G:0.07, T:0.45
Consensus pattern (66 bp):
TCCCAGTCATCTTTATCTTTTAACTTACAGTTCAATCTCAATCATTTTTATACTCTGACTAACTG
C
Found at i:22463512 original size:112 final size:112
Alignment explanation
Indices: 22463324--22463530 Score: 274
Period size: 112 Copynumber: 1.8 Consensus size: 112
22463314 TTTTATTCTC
* * *
22463324 TGACTTGCTGTTCAATCCTAATCATATTTATTTTTTGACTTATAGTTAAATCTCGATCATCTTTA
1 TGACTTGCTGTTCAATCCCAATCATATTTATTTTTTAACTTATAGTTAAATCTCGATCATATTTA
* *
22463389 TTTTTTCACTTGCAGTTCAAACCCAGTCATCTTTATTCTTTTACTTG
66 TTCTTTAACTTGCAGTTCAAACCCAGTCATCTTTATTCTTTTACTTG
* * * * *
22463436 TGACTTG-TGATTCAATCCCAGTCATTTTTATTTTTTAACTTATGGTTCAATCCTTG-TCATATT
1 TGACTTGCTG-TTCAATCCCAATCATATTTATTTTTTAACTTATAGTTAAAT-CTCGATCATATT
* *
22463499 TATTCTTTAACTTGCAGTTCAATCCTAGTCAT
64 TATTCTTTAACTTGCAGTTCAAACCCAGTCAT
22463531 TTTCATTTCT
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
111 2 0.02
112 76 0.94
113 3 0.04
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.48
Consensus pattern (112 bp):
TGACTTGCTGTTCAATCCCAATCATATTTATTTTTTAACTTATAGTTAAATCTCGATCATATTTA
TTCTTTAACTTGCAGTTCAAACCCAGTCATCTTTATTCTTTTACTTG
Found at i:22463881 original size:18 final size:18
Alignment explanation
Indices: 22463847--22463884 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
22463837 AGCCCACTAC
*
22463847 TTTTATTTTTGTCTTTAT
1 TTTTATTTTTCTCTTTAT
22463865 TTTTATTTTTACT-TTTAT
1 TTTTATTTTT-CTCTTTAT
22463883 TT
1 TT
22463885 CATTATTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTATTTTTCTCTTTAT
Found at i:22464925 original size:8 final size:8
Alignment explanation
Indices: 22464912--22464960 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
22464902 TCAAAACTTG
22464912 AAACCTTA
1 AAACCTTA
22464920 AAACC-TA
1 AAACCTTA
22464927 AAACCTT-
1 AAACCTTA
*
22464934 AAACTTTA
1 AAACCTTA
*
22464942 AACCCTTA
1 AAACCTTA
*
22464950 AAACCCTA
1 AAACCTTA
22464958 AAA
1 AAA
22464961 TCTAAAAGCA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
7 13 0.38
8 21 0.62
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (8 bp):
AAACCTTA
Found at i:22464930 original size:15 final size:15
Alignment explanation
Indices: 22464912--22464960 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
22464902 TCAAAACTTG
22464912 AAACCTTAAAACCTA
1 AAACCTTAAAACCTA
*
22464927 AAACCTT-AAACTTTA
1 AAACCTTAAAAC-CTA
*
22464942 AACCCTTAAAACCCTA
1 AAACCTTAAAA-CCTA
22464958 AAA
1 AAA
22464961 TCTAAAAGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
14 4 0.15
15 15 0.56
16 7 0.26
17 1 0.04
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (15 bp):
AAACCTTAAAACCTA
Found at i:22468395 original size:2 final size:2
Alignment explanation
Indices: 22468388--22468413 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22468378 ACACTGCTGA
22468388 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
22468414 TAACACTTAC
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:22468483 original size:23 final size:24
Alignment explanation
Indices: 22468449--22468507 Score: 111
Period size: 23 Copynumber: 2.5 Consensus size: 24
22468439 AGAGTTTCGT
22468449 TATATATATATGTATGTATGTATG
1 TATATATATATGTATGTATGTATG
22468473 TAT-TATATATGTATGTATGTATG
1 TATATATATATGTATGTATGTATG
22468496 TATATATATATG
1 TATATATATATG
22468508 CTTTGGTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 23 0.68
24 11 0.32
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (24 bp):
TATATATATATGTATGTATGTATG
Found at i:22468487 original size:27 final size:27
Alignment explanation
Indices: 22468448--22468506 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
22468438 AAGAGTTTCG
*
22468448 TTATATATATATGTATGTATGTATGTA
1 TTATATATATATGTATGTATGTATATA
*
22468475 TTATATATGTATGTATGTATGTATATA
1 TTATATATATATGTATGTATGTATATA
22468502 -TATAT
1 TTATAT
22468507 GCTTTGGTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 5 0.17
27 25 0.83
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.53
Consensus pattern (27 bp):
TTATATATATATGTATGTATGTATATA
Found at i:22468506 original size:4 final size:4
Alignment explanation
Indices: 22468457--22468498 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
22468447 GTTATATATA
*
22468457 TATG TATG TATG TATG TAT- TATA TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
22468499 ATATATATGC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
3 3 0.08
4 33 0.92
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:22470575 original size:2 final size:2
Alignment explanation
Indices: 22470570--22470599 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
22470560 TTTCAACCAA
22470570 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
22470600 GTGCTTGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:22470778 original size:19 final size:19
Alignment explanation
Indices: 22470750--22470788 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
22470740 TAGAAACAAT
22470750 TAAGCCAATCACTTACGGA
1 TAAGCCAATCACTTACGGA
*
22470769 TAAGCTAATCACTTACGGA
1 TAAGCCAATCACTTACGGA
22470788 T
1 T
22470789 CATTAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (19 bp):
TAAGCCAATCACTTACGGA
Found at i:22473869 original size:16 final size:16
Alignment explanation
Indices: 22473813--22473872 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
22473803 TAAAATGCAA
22473813 AAACCCTCAAAACCCT
1 AAACCCTCAAAACCCT
* *
22473829 AGAA-CTTTAAAA-CCT
1 A-AACCCTCAAAACCCT
**
22473844 CAAAATCTCAAAACCCT
1 -AAACCCTCAAAACCCT
22473861 AAACCCTCAAAA
1 AAACCCTCAAAA
22473873 TTCTAAAGCC
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
15 5 0.15
16 23 0.70
17 5 0.15
ACGTcount: A:0.48, C:0.33, G:0.02, T:0.17
Consensus pattern (16 bp):
AAACCCTCAAAACCCT
Found at i:22473927 original size:16 final size:16
Alignment explanation
Indices: 22473906--22473966 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 16
22473896 CCCTAAAACA
22473906 CAAAACCTAAAAACCT
1 CAAAACCTAAAAACCT
* *
22473922 CAAAACCCAAGAACCT
1 CAAAACCTAAAAACCT
* * *
22473938 CAAAACTTTAAAA-TT
1 CAAAACCTAAAAACCT
*
22473953 CAAAACCTTAAAAC
1 CAAAACCTAAAAAC
22473967 TCCCGAACCC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
15 13 0.36
16 23 0.64
ACGTcount: A:0.54, C:0.28, G:0.02, T:0.16
Consensus pattern (16 bp):
CAAAACCTAAAAACCT
Found at i:22473957 original size:15 final size:15
Alignment explanation
Indices: 22473937--22474113 Score: 79
Period size: 15 Copynumber: 10.9 Consensus size: 15
22473927 CCCAAGAACC
*
22473937 TCAAAACTTTAAAAT
1 TCAAAACCTTAAAAT
22473952 TCAAAACCTTAAAACT
1 TCAAAACCTTAAAA-T
* ** *
22473968 CCCGAACCCTAAAAT
1 TCAAAACCTTAAAAT
* *
22473983 CCAAAACCTTAAGAT
1 TCAAAACCTTAAAAT
* *
22473998 GCTCAAATCCTAAATCTAAAAC
1 --TCAAAACC----T-TAAAAT
* *
22474020 CCTAAAATCCTTAAAAC
1 TC-AAAA-CCTTAAAAT
22474037 TCTAAAACCCTTAAAAT
1 TC-AAAA-CCTTAAAAT
*
22474054 TCAAAATCTTAAAACCT
1 TCAAAACCTTAAAA--T
*
22474071 T--AAACCTTAAATAC
1 TCAAAACCTTAAA-AT
22474085 TCAAAACCTTAAAAT
1 TCAAAACCTTAAAAT
*
22474100 TCAAAACCCTAAAA
1 TCAAAACCTTAAAA
22474114 CCCTCAAATC
Statistics
Matches: 124, Mismatches: 23, Indels: 30
0.70 0.13 0.17
Matches are distributed among these distances:
14 1 0.01
15 55 0.44
16 26 0.21
17 30 0.24
18 1 0.01
20 1 0.01
21 4 0.03
22 6 0.05
ACGTcount: A:0.49, C:0.25, G:0.02, T:0.24
Consensus pattern (15 bp):
TCAAAACCTTAAAAT
Found at i:22474113 original size:23 final size:23
Alignment explanation
Indices: 22474013--22474115 Score: 84
Period size: 23 Copynumber: 4.3 Consensus size: 23
22474003 AATCCTAAAT
* * *
22474013 CTAAAACCCTAAAATCCTTAAAACT
1 CTAAAACCTTAAAAT--TCAAAACC
*
22474038 CTAAAACCCTTAAAATTCAAAATC
1 CTAAAA-CCTTAAAATTCAAAACC
* * *
22474062 TTAAAACCTTAAACCTT-AAATACT
1 CTAAAACCTTAAA-ATTCAAA-ACC
22474086 C-AAAACCTTAAAATTCAAAACC
1 CTAAAACCTTAAAATTCAAAACC
22474108 CTAAAACC
1 CTAAAACC
22474116 CTCAAATCCT
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
22 5 0.08
23 30 0.48
24 13 0.21
25 6 0.10
26 8 0.13
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (23 bp):
CTAAAACCTTAAAATTCAAAACC
Found at i:22474153 original size:8 final size:8
Alignment explanation
Indices: 22474014--22474308 Score: 73
Period size: 8 Copynumber: 37.5 Consensus size: 8
22474004 ATCCTAAATC
*
22474014 TAAAACCC
1 TAAAACCT
22474022 TAAAATCCT
1 TAAAA-CCT
22474031 TAAAA-CT
1 TAAAACCT
22474038 CTAAAACCCT
1 -TAAAA-CCT
22474048 TAAAA--T
1 TAAAACCT
*
22474054 TCAAAATCT
1 T-AAAACCT
22474063 TAAAACCT
1 TAAAACCT
22474071 T-AAACCT
1 TAAAACCT
22474078 TAAATA-CT
1 TAAA-ACCT
*
22474086 CAAAACCT
1 TAAAACCT
22474094 TAAAA--T
1 TAAAACCT
*
22474100 TCAAAACCC
1 T-AAAACCT
22474109 TAAAACCCT
1 TAAAA-CCT
* *
22474118 CAAATCC-
1 TAAAACCT
*
22474125 TATAACC-
1 TAAAACCT
**
22474132 CCAAACCTT
1 TAAAACC-T
22474141 TAAAACCT
1 TAAAACCT
**
22474149 TAAAATAT
1 TAAAACCT
** *
22474157 CGAAACCC
1 TAAAACCT
*
22474165 T-AAA-TT
1 TAAAACCT
*
22474171 TGAAACCT
1 TAAAACCT
*
22474179 AAAAATCCT
1 TAAAA-CCT
* *
22474188 CAAAATCT
1 TAAAACCT
* *
22474196 CAAAACTT
1 TAAAACCT
*
22474204 TAAAACCG
1 TAAAACCT
*
22474212 TAAAATGC-
1 TAAAA-CCT
22474220 TAAAACAC-
1 TAAAAC-CT
*
22474228 TAAAA-CA
1 TAAAACCT
* *
22474235 TCAAACCC
1 TAAAACCT
22474243 TAAAA--T
1 TAAAACCT
22474249 TAAAACCT
1 TAAAACCT
* *
22474257 TAAAATCG
1 TAAAACCT
*
22474265 TAAAACCC
1 TAAAACCT
* *
22474273 TAAAATCA
1 TAAAACCT
*
22474281 TAAAACCC
1 TAAAACCT
22474289 TAAAACCT
1 TAAAACCT
* *
22474297 TGAAACTT
1 TAAAACCT
22474305 TAAA
1 TAAA
22474309 GCGAGACCTT
Statistics
Matches: 208, Mismatches: 54, Indels: 50
0.67 0.17 0.16
Matches are distributed among these distances:
6 11 0.05
7 36 0.17
8 125 0.60
9 34 0.16
10 2 0.01
ACGTcount: A:0.50, C:0.25, G:0.02, T:0.23
Consensus pattern (8 bp):
TAAAACCT
Found at i:22474253 original size:45 final size:46
Alignment explanation
Indices: 22474203--22474293 Score: 132
Period size: 45 Copynumber: 2.0 Consensus size: 46
22474193 TCTCAAAACT
*
22474203 TTAAAACCGTAAAAT-GCTAAAACACTAAAA-CATCAAACCCTAAAA
1 TTAAAACCGTAAAATCG-TAAAACACTAAAATCATAAAACCCTAAAA
* *
22474248 TTAAAACCTTAAAATCGTAAAACCCTAAAATCATAAAACCCTAAAA
1 TTAAAACCGTAAAATCGTAAAACACTAAAATCATAAAACCCTAAAA
22474294 CCTTGAAACT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
45 26 0.63
46 15 0.37
ACGTcount: A:0.55, C:0.22, G:0.03, T:0.20
Consensus pattern (46 bp):
TTAAAACCGTAAAATCGTAAAACACTAAAATCATAAAACCCTAAAA
Found at i:22474302 original size:16 final size:16
Alignment explanation
Indices: 22474009--22474293 Score: 105
Period size: 16 Copynumber: 18.2 Consensus size: 16
22473999 CTCAAATCCT
22474009 AAATC-TAAAACCCTA
1 AAATCTTAAAACCCTA
*
22474024 AAATCCTTAAAACTCTA
1 AAAT-CTTAAAACCCTA
* **
22474041 AAACCCTTAAAATTC-A
1 AAA-TCTTAAAACCCTA
*
22474057 AAATCTTAAAA-CCTT
1 AAATCTTAAAACCCTA
* *
22474072 AAACCTTAAATACTC-A
1 AAATCTTAAA-ACCCTA
* **
22474088 AAACCTTAAAATTC-A
1 AAATCTTAAAACCCTA
* * *
22474103 AAACCCTAAAACCCTC
1 AAATCTTAAAACCCTA
* * *
22474119 AAATCCTATAACCC-C
1 AAATCTTAAAACCCTA
* *
22474134 AAACCTTTAAAACCTTA
1 AAATC-TTAAAACCCTA
* **
22474151 AAATATCGAAACCCT-
1 AAATCTTAAAACCCTA
*
22474166 AAAT-TTGAAA-CCTAA
1 AAATCTTAAAACCCT-A
* *
22474181 AAATCCTCAAAA-TCTCA
1 AAAT-CTTAAAACCCT-A
*
22474198 AAA-CTTTAAAACCGTA
1 AAATC-TTAAAACCCTA
*
22474214 AAATGC-TAAAACACTA
1 AAAT-CTTAAAACCCTA
* *
22474230 AAA-CATCAAACCCTA
1 AAATCTTAAAACCCTA
*
22474245 AAA--TTAAAACCTTA
1 AAATCTTAAAACCCTA
*
22474259 AAATCGTAAAACCCTA
1 AAATCTTAAAACCCTA
*
22474275 AAATCATAAAACCCTA
1 AAATCTTAAAACCCTA
22474291 AAA
1 AAA
22474294 CCTTGAAACT
Statistics
Matches: 206, Mismatches: 44, Indels: 39
0.71 0.15 0.13
Matches are distributed among these distances:
13 3 0.01
14 18 0.09
15 60 0.29
16 88 0.43
17 36 0.17
18 1 0.00
ACGTcount: A:0.51, C:0.25, G:0.02, T:0.23
Consensus pattern (16 bp):
AAATCTTAAAACCCTA
Found at i:22483710 original size:24 final size:24
Alignment explanation
Indices: 22483677--22483739 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
22483667 AAACTTATTG
* *
22483677 ATAATTTTTTTTTAATTTTAAATCAT
1 ATAATTTTTATAT-ATTTT-AATCAT
* *
22483703 ATTATTTTTATATATTTTATTCAT
1 ATAATTTTTATATATTTTAATCAT
22483727 ATAATTTTTATAT
1 ATAATTTTTATAT
22483740 CGTATTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 17 0.53
25 5 0.16
26 10 0.31
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (24 bp):
ATAATTTTTATATATTTTAATCAT
Found at i:22484342 original size:13 final size:13
Alignment explanation
Indices: 22484324--22484356 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
22484314 ATTTGTTTAC
*
22484324 TAAAATTAAATGA
1 TAAAATTAAATCA
22484337 TAAAATTAAATCA
1 TAAAATTAAATCA
22484350 TAAAATT
1 TAAAATT
22484357 GGACATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (13 bp):
TAAAATTAAATCA
Found at i:22484775 original size:29 final size:29
Alignment explanation
Indices: 22484719--22484775 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
22484709 AAAATTTTTT
* * *
22484719 TTTATATTTATTAATTTTTTTTGGAATTG
1 TTTATATATATTAATTTTCTTTGCAATTG
22484748 TTTATATATATTAATTTATCTTT-CAATT
1 TTTATATATATTAATTT-TCTTTGCAATT
22484776 AAAAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.28, C:0.04, G:0.05, T:0.63
Consensus pattern (29 bp):
TTTATATATATTAATTTTCTTTGCAATTG
Found at i:22486372 original size:22 final size:22
Alignment explanation
Indices: 22486327--22486372 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
22486317 TGATTGGCGG
* **
22486327 AAGCAAGAATCAAACTCATTTC
1 AAGCAAGAATCAAACTAAAATC
*
22486349 AAGCGAGAATCAAACTAAAATC
1 AAGCAAGAATCAAACTAAAATC
22486371 AA
1 AA
22486373 ACTCAGAAGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.52, C:0.20, G:0.11, T:0.17
Consensus pattern (22 bp):
AAGCAAGAATCAAACTAAAATC
Found at i:22490188 original size:18 final size:18
Alignment explanation
Indices: 22490160--22490197 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
22490150 AATCTCTGGT
22490160 AAGTAATTT-AAATATAA
1 AAGTAATTTAAAATATAA
22490177 AAGTATATTTAAAATATAA
1 AAGTA-ATTTAAAATATAA
22490196 AA
1 AA
22490198 ATAAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 10 0.53
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (18 bp):
AAGTAATTTAAAATATAA
Found at i:22492416 original size:17 final size:16
Alignment explanation
Indices: 22492377--22492412 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
22492367 AATGATTTTC
* *
22492377 AATTAAATATAAAATT
1 AATTAAAAATAAAAAT
22492393 AATTAAAAATAAAAAT
1 AATTAAAAATAAAAAT
22492409 AATT
1 AATT
22492413 TAAACAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTAAAAATAAAAAT
Found at i:22492936 original size:30 final size:30
Alignment explanation
Indices: 22492888--22492968 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
22492878 CCATTTAAAC
*
22492888 TTTAATTTACA-CTCAAATAAATCTTTAA-T
1 TTTAATTTATATCT-AAATAAATCTTTAACT
* * *
22492917 TATTAATTTGTATCTAAATAATTTTTTAACT
1 T-TTAATTTATATCTAAATAAATCTTTAACT
*
22492948 TTTAATTTATATTTAAATAAA
1 TTTAATTTATATCTAAATAAA
22492969 CCCTTAACAT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
29 1 0.02
30 37 0.88
31 4 0.10
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (30 bp):
TTTAATTTATATCTAAATAAATCTTTAACT
Found at i:22494711 original size:15 final size:15
Alignment explanation
Indices: 22494688--22494718 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
22494678 AATTTTAGAA
*
22494688 ATTTTGGATTTTAGG
1 ATTTCGGATTTTAGG
22494703 ATTTCGGATTTTAGG
1 ATTTCGGATTTTAGG
22494718 A
1 A
22494719 GTTTAAAGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.26, T:0.48
Consensus pattern (15 bp):
ATTTCGGATTTTAGG
Found at i:22496200 original size:27 final size:25
Alignment explanation
Indices: 22496170--22496229 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 25
22496160 TTTTCTATTT
22496170 TTTTATTCTT-TTGTTTATTAATAATTA
1 TTTTATT-TTATTGTTTATT-A-AATTA
*
22496197 TTTTATTTTATTTTTTATTAAATTA
1 TTTTATTTTATTGTTTATTAAATTA
22496222 TTATTATT
1 TT-TTATT
22496230 GTTGTTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 7 0.23
26 8 0.27
27 15 0.50
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (25 bp):
TTTTATTTTATTGTTTATTAAATTA
Found at i:22496226 original size:3 final size:3
Alignment explanation
Indices: 22496193--22496270 Score: 94
Period size: 3 Copynumber: 27.7 Consensus size: 3
22496183 TTTATTAATA
* * *
22496193 ATT ATT -TT ATT -TT ATT -TT -TT ATT A-A ATT ATT ATT ATT GTT GTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
22496236 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
22496271 AGTGAAATGA
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
2 9 0.13
3 58 0.87
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:22497234 original size:25 final size:25
Alignment explanation
Indices: 22497206--22497255 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
22497196 CCAAAGACTC
* *
22497206 ACATTATCATGTACTGTCAAAAAAT
1 ACATTACCATGTACTGTAAAAAAAT
22497231 ACATTACCATGTACTGTAAAAAAAT
1 ACATTACCATGTACTGTAAAAAAAT
22497256 GGCTGCCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (25 bp):
ACATTACCATGTACTGTAAAAAAAT
Found at i:22498994 original size:69 final size:67
Alignment explanation
Indices: 22498866--22499406 Score: 565
Period size: 69 Copynumber: 7.8 Consensus size: 67
22498856 AATTTAAGGT
* * * *
22498866 TTTTATTTTCAAGAAAAATTGATACTTTTAACTTTTCCTCAAAAATACTTTTTCTTTTTTAAAAA
1 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATA-------TTTTTT--AGA
* *
22498931 AATATTTATTG
57 AATTTTTATTA
* * * *
22498942 TTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTTTGAAATTTTT
1 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATA--TTTTTTAGAAATTTTT
22499007 A-T-
64 ATTA
* *
22499009 TTTTATTTTCAATGAAAATTGATACTTTCAACTTTTTCTCAAAAATAATTTTT-GAAATTTTTAT
1 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAATTTTTAT
*
22499073 CAAAA
66 ---TA
* *
22499078 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAGAATATTTTTTTGAAATTTATT-
1 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAATTT-TTA
22499142 TTA
65 TTA
* *
22499145 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAATTTTTAT
1 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAATTTTTAT
22499210 TAAAA
66 T---A
22499215 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTT-GAAATTTTTAT
1 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAATTTTTAT
*
22499279 CAAAA
66 ---TA
* *
22499284 TTTTATTTTCAAAGAAAATTAATACTTTCAACTTTTTCTCAAAAATATTTTTTTA-AAATTTTAT
1 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATA-TTTTTTAGAAATTTT-T
**
22499348 GAAAA
64 -ATTA
* * * * *
22499353 TTTTATTTTAAAGAAAAATTGGTGCTTTTAA-TATTTTCTCAAAAATATTTTTTA
1 TTTTATTTTCAAGGAAAATTGATACTTTCAACT-TTTTCTCAAAAATATTTTTTA
22499407 TTTTAAAAGA
Statistics
Matches: 414, Mismatches: 32, Indels: 46
0.84 0.07 0.09
Matches are distributed among these distances:
64 10 0.02
65 5 0.01
66 2 0.00
67 105 0.25
68 9 0.02
69 155 0.37
70 74 0.18
71 10 0.02
72 1 0.00
76 43 0.10
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (67 bp):
TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAATTTTTAT
TA
Found at i:22499231 original size:137 final size:136
Alignment explanation
Indices: 22498866--22499405 Score: 653
Period size: 136 Copynumber: 3.9 Consensus size: 136
22498856 AATTTAAGGT
* * * *
22498866 TTTTATTTTCAAGAAAAATTGATACTTTTAACTTTTCCTCAAAAATACTTTTTCTTTTTTAAAAA
1 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATA----TT-TTTTTGAAAAT
** *** * * *
22498931 AATATTTATTGTTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTT
61 TTTA-TTAAAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATA--TTTTT
*
22498996 TTGAAATTTTTAT-
123 TTGAAATTTTTTTA
* *
22499009 TTTTATTTTCAATG-AAAATTGATACTTTCAACTTTTTCTCAAAAATA-ATTTTTGAAATTTTTA
1 TTTTATTTTCAA-GAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAAATTTTA
* *
22499072 TCAAAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAGAATATTTTTTTGAAAT
65 TTAAAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAAT
22499137 TTATTTTA
130 TT-TTTTA
*
22499145 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAATTTTTAT
1 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAAATTTTAT
22499210 TAAAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATA-TTTTTTGAAATT
66 TAAAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAATT
*
22499274 TTTATCAAAA
131 TTT-T---TA
*
22499284 TTTTATTTTCAA-AGAAAATTAATACTTTCAACTTTTTCTCAAAAATATTTTTTT-AAAATTTTA
1 TTTTATTTTCAAGA-AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAAATTTTA
* * * * * *
22499347 TGAAAATTTTATTTTAAAGAAAAATTGGTGCTTTTAA-TATTTTCTCAAAAATATTTTTT
65 TTAAAATTTTATTTTCAAGGAAAATTGATACTTTCAACT-TTTTCTCAAAAATATTTTTT
22499406 ATTTTAAAAG
Statistics
Matches: 356, Mismatches: 29, Indels: 28
0.86 0.07 0.07
Matches are distributed among these distances:
134 14 0.04
135 6 0.02
136 104 0.29
137 77 0.22
138 54 0.15
139 57 0.16
143 43 0.12
144 1 0.00
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (136 bp):
TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAAATTTTAT
TAAAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAATT
TTTTTA
Found at i:22499260 original size:206 final size:203
Alignment explanation
Indices: 22498942--22499405 Score: 682
Period size: 206 Copynumber: 2.3 Consensus size: 203
22498932 ATATTTATTG
* * * *
22498942 TTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTTTGAAATTTTT
1 TTTTATTTTAAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATA--TTTTTTTGAAATTTTT
*
22499007 ATTTTTATTTTCAATGAAAATTGATACTTTCAACTTTTTCTCAAAAATAATTTTTGAAATTTTTA
64 ATTTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATAATTTTTGAAATTTTTA
* * * *
22499072 TCAAAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAGAATATTTTTTTGAAA-
129 TCAAAATTTTATTTTCAAAGAAAATTAATACTTTCAACTTTTTCTCAAAAATATTTTTTTAAAAT
***
22499136 TTTAT-TTTA
194 TTTATGAAAA
*
22499145 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAATTTTTAT
1 TTTTATTTTAAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAATTTTTA-
*
22499210 TAAAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAATTT
65 T----TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATAATTTTTGAAATTT
22499275 TTATCAAAATTTTATTTTCAAAGAAAATTAATACTTTCAACTTTTTCTCAAAAATATTTTTTTAA
126 TTATCAAAATTTTATTTTCAAAGAAAATTAATACTTTCAACTTTTTCTCAAAAATATTTTTTTAA
22499340 AATTTTATGAAAA
191 AATTTTATGAAAA
* * *
22499353 TTTTATTTTAAAGAAAAATTGGTGCTTTTAA-TATTTTCTCAAAAATATTTTTT
1 TTTTATTTTAAAGAAAAATTGATACTTTCAACT-TTTTCTCAAAAATATTTTTT
22499406 ATTTTAAAAG
Statistics
Matches: 236, Mismatches: 17, Indels: 11
0.89 0.06 0.04
Matches are distributed among these distances:
201 17 0.07
202 1 0.00
203 43 0.18
206 121 0.51
207 6 0.03
208 48 0.20
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (203 bp):
TTTTATTTTAAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAATTTTTAT
TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATAATTTTTGAAATTTTTATC
AAAATTTTATTTTCAAAGAAAATTAATACTTTCAACTTTTTCTCAAAAATATTTTTTTAAAATTT
TATGAAAA
Found at i:22499470 original size:22 final size:22
Alignment explanation
Indices: 22499445--22499487 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
22499435 GAATGCTTAC
22499445 TCAAATAAATAAATAAATAATT
1 TCAAATAAATAAATAAATAATT
* * *
22499467 TCAATTTAATCAATAAATAAT
1 TCAAATAAATAAATAAATAAT
22499488 AATAAACAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (22 bp):
TCAAATAAATAAATAAATAATT
Found at i:22500791 original size:160 final size:159
Alignment explanation
Indices: 22500625--22501190 Score: 467
Period size: 160 Copynumber: 3.5 Consensus size: 159
22500615 ATGAAAAAAA
* * * *
22500625 AAGTCTAAAATGAATAATCTGGGCTAAACCAAAGAAGGATTCGACATAAGTCAAAATTTAAAAAT
1 AAGTCTAAAATGAATAATCTGGACTAAACCAAAGAA-GATTCGACATAAGTCGAAATCTAAAAAC
* * * * * * *
22500690 AAAATGACTTGGACGAAATCGAAGTTTGAAATGCAAGCTAAAGAAGGATCTGACATAAGTTAAAA
65 AAAATGACCTGGATGAAATCGAAGTTTGAAATGAAAGCCAAAAAAAGATCTGACATAAGTCAAAA
*
22500755 TCC-ATAACAAAATGACCTAGATTGAACCTG
130 TCCAAAAACAAAATGACCTAGATTGAACC-G
* * * * *
22500785 AAGTCTAGAATGAATAATCTAGACTAAACCAAAGAAGAATCTGGCATAGGTCGAAATCTAAAAAC
1 AAGTCTAAAATGAATAATCTGGACTAAACCAAAGAAGATTC-GACATAAGTCGAAATCTAAAAAC
* * * * *
22500850 AAGATGACCTGGATGAGATCGAAGTCT-AAAGTGAAAGCCAAAAAAAGATCTGACGTAGGTCAAA
65 AAAATGACCTGGATGAAATCGAAGTTTGAAA-TGAAAGCCAAAAAAAGATCTGACATAAGTCAAA
* *
22500914 ATCCAAAAACAAAATGACCTAGATTGTATCG
129 ATCCAAAAACAAAATGACCTAGATTGAACCG
* * * * * * * * * *
22500945 AAGTCTGAAACGAGTACT-TGGTCTAAGTCGAAAAAAGATTTGACATAAGTTGAAATCTAAAAAC
1 AAGTCTAAAATGAATAATCTGGACTAA-ACCAAAGAAGATTCGACATAAGTCGAAATCTAAAAAC
* ** * *
22501009 AAAATGACCTGGATGAAATCGAAGCTTGAAATGAATAATTTAGACTAAGCCAGAGGAGGATCTTA
65 AAAATGACCTGGATGAAATCGAAG-TT----TG-A-AA--T-GA--AAGCCAAAAAAAGATCTGA
* * * * *
22501074 CATAAATTAAAATTCAAAAACAAAATGACCGAGATTGAATCG
118 CATAAGTCAAAATCCAAAAACAAAATGACCTAGATTGAACCG
* * * * * *
22501116 AAGTCTGAACTGAATAA-CTTGGACTAGACCAAAGAAGGA-TCTAGCATATGTCGAAATCCAAAA
1 AAGTCTAAAATGAATAATC-TGGACTAAACCAAAGAA-GATTCGA-CATAAGTCGAAATCTAAAA
22501179 ACAAAATGACCT
63 ACAAAATGACCT
22501191 AAATTGAATT
Statistics
Matches: 317, Mismatches: 69, Indels: 28
0.77 0.17 0.07
Matches are distributed among these distances:
159 55 0.17
160 127 0.40
161 22 0.07
164 1 0.00
166 1 0.00
167 2 0.01
168 1 0.00
169 2 0.01
171 70 0.22
172 36 0.11
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.22
Consensus pattern (159 bp):
AAGTCTAAAATGAATAATCTGGACTAAACCAAAGAAGATTCGACATAAGTCGAAATCTAAAAACA
AAATGACCTGGATGAAATCGAAGTTTGAAATGAAAGCCAAAAAAAGATCTGACATAAGTCAAAAT
CCAAAAACAAAATGACCTAGATTGAACCG
Found at i:22501103 original size:86 final size:86
Alignment explanation
Indices: 22500909--22501404 Score: 324
Period size: 86 Copynumber: 5.8 Consensus size: 86
22500899 CTGACGTAGG
* * * * * * *
22500909 TCAAAATCCAAAAACAAAATGACCTAGATTGTATCGAAGTCTGAAACGAGT-ACTTGGTCTAAGT
1 TCAAAATTCAAAAACAAAATGACCTGGATTGAATCGAAGTCTGAAATGAATAACTTGGACTAAGC
* * *
22500973 C-GAAAAAAGAT-TTGACATAAG
66 CAG-AGAAGGATCTT-ACATAAA
** * *
22500994 TTGAAA-TCTAAAAACAAAATGACCTGGA-TGAAATCGAAG-CTTGAAATGAATAATTTAGACTA
1 TCAAAATTC-AAAAACAAAATGACCTGGATTG-AATCGAAGTC-TGAAATGAATAACTTGGACTA
*
22501056 AGCCAGAGGAGGATCTTACATAAA
63 AGCCAGAGAAGGATCTTACATAAA
* *
22501080 TTAAAATTCAAAAACAAAATGACC-GAGATTGAATCGAAGTCTGAACTGAATAACTTGGACT-AG
1 TCAAAATTCAAAAACAAAATGACCTG-GATTGAATCGAAGTCTGAAATGAATAACTTGGACTAAG
* **
22501143 ACCAAAGAAGGATC-TAGCATATG
65 -CCAGAGAAGGATCTTA-CATAAA
* * ** * * * *
22501166 TCGAAATCCAAAAACAAAATGACCTAAATTGAATTGAAGTCTGAAACGAATAGCTTGGATTAAG-
1 TCAAAATTCAAAAACAAAATGACCTGGATTGAATCGAAGTCTGAAATGAATAACTTGGACTAAGC
* *
22501230 CTGAAGAAGGAT-TTGACAGAAA
66 CAG-AGAAGGATCTT-ACATAAA
* * * *
22501252 TCAAAATAT-AAAAACAAAATAACCTGGA-TGAAACCGAAGTCTGAAATGAATAACTTGAATTAA
1 TCAAAAT-TCAAAAACAAAATGACCTGGATTG-AATCGAAGTCTGAAATGAATAACTTGGACTAA
* **
22501315 GCC-GAAGAAAGATC-TAGCATATG
64 GCCAG-AGAAGGATCTTA-CATAAA
* * * * * * * *
22501338 CCAAAA-TCTAAAAATAGAATGACCTAGATTAAATAGAAGTTTGAAATGAATAA-TCTGAACTAA
1 TCAAAATTC-AAAAACAAAATGACCTGGATTGAATCGAAGTCTGAAATGAATAACT-TGGACTAA
22501401 GCCA
64 GCCA
22501405 AAATACGTTA
Statistics
Matches: 322, Mismatches: 62, Indels: 52
0.74 0.14 0.12
Matches are distributed among these distances:
84 5 0.02
85 47 0.15
86 257 0.80
87 13 0.04
ACGTcount: A:0.46, C:0.14, G:0.18, T:0.23
Consensus pattern (86 bp):
TCAAAATTCAAAAACAAAATGACCTGGATTGAATCGAAGTCTGAAATGAATAACTTGGACTAAGC
CAGAGAAGGATCTTACATAAA
Found at i:22501390 original size:258 final size:257
Alignment explanation
Indices: 22500912--22501390 Score: 585
Period size: 258 Copynumber: 1.9 Consensus size: 257
22500902 ACGTAGGTCA
* * *
22500912 AAATCCAAAAACAAAATGACCTAGATTGTATCGAAGTCTGAAACGAGTACTTGGTCTAAGTCGAA
1 AAATCCAAAAACAAAATGACCTAAATTGAATCGAAGTCTGAAACGAATACTTGGTCTAAGTCGAA
* * ** * * *
22500977 AAAAGATTTGACATAAGTTGAAATCTAAAAACAAAATGACCTGGATGAAATCGAAGCTTGAAATG
66 AAAAGATTTGACAGAAATCAAAATATAAAAACAAAATAACCTGGATGAAACCGAAGCTTGAAATG
* * * **
22501042 AATAATTTAGACTAAGCCAGAGGAGGATCTTACATAAATTAAAATTCAAAAACAAAATGACCGAG
131 AATAATTGAGACTAAGCCAGAGAAAGATCTTACATAAACCAAAATTCAAAAACAAAATGACCGAG
* * *
22501107 ATTGAATCGAAGTCTGAACTGAATAACTTGGACTAGACCAAAGAAGGATCTAGCATATGTCG
196 ATTAAATAGAAGTCTGAAATGAATAACTTGGACTAGACCAAAGAAGGATCTAGCATATGTCG
*
22501169 AAATCCAAAAACAAAATGACCTAAATTGAATTGAAGTCTGAAACGAATAGCTTGGAT-TAAG-CT
1 AAATCCAAAAACAAAATGACCTAAATTGAATCGAAGTCTGAAACGAATA-CTTGG-TCTAAGTC-
* *
22501232 GAAGAAGGATTTGACAGAAATCAAAATATAAAAACAAAATAACCTGGATGAAACCGAAG-TCTGA
63 GAAAAAAGATTTGACAGAAATCAAAATATAAAAACAAAATAACCTGGATGAAACCGAAGCT-TGA
* ** * *
22501296 AATGAATAACTTGA-ATTAAGCC-GAAGAAAGATC-TAGCATATGCCAAAA-TCTAAAAATAGAA
127 AATGAATAA-TTGAGACTAAGCCAG-AGAAAGATCTTA-CATAAACCAAAATTC-AAAAACAAAA
* *
22501357 TGACCTAGATTAAATAGAAGTTTGAAATGAATAA
188 TGACCGAGATTAAATAGAAGTCTGAAATGAATAA
22501391 TCTGAACTAA
Statistics
Matches: 186, Mismatches: 28, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
257 52 0.28
258 130 0.70
259 4 0.02
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23
Consensus pattern (257 bp):
AAATCCAAAAACAAAATGACCTAAATTGAATCGAAGTCTGAAACGAATACTTGGTCTAAGTCGAA
AAAAGATTTGACAGAAATCAAAATATAAAAACAAAATAACCTGGATGAAACCGAAGCTTGAAATG
AATAATTGAGACTAAGCCAGAGAAAGATCTTACATAAACCAAAATTCAAAAACAAAATGACCGAG
ATTAAATAGAAGTCTGAAATGAATAACTTGGACTAGACCAAAGAAGGATCTAGCATATGTCG
Found at i:22505823 original size:19 final size:20
Alignment explanation
Indices: 22505799--22505837 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
22505789 GACAAGATGT
* *
22505799 ATGGAATGAA-AATTAAAAA
1 ATGGAAAGAAGAAATAAAAA
22505818 ATGGAAAGAAGAAATAAAAA
1 ATGGAAAGAAGAAATAAAAA
22505838 TGCATCACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (20 bp):
ATGGAAAGAAGAAATAAAAA
Found at i:22512928 original size:69 final size:66
Alignment explanation
Indices: 22512849--22513360 Score: 416
Period size: 69 Copynumber: 7.7 Consensus size: 66
22512839 TTTGATATAA
* *
22512849 AAAAATTGATACTTTCAACTTTTTCTTAAAAATCTTTTTTTTGAAATCCTTATTTTTTTTATTCT
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAAT-TTTTTTTTGAAAT--TTATTTTTTTTATTTT
22512914 CAAG
63 CAAG
* * *
22512918 AAAAATTGATACCTTCAACTTTTTCACAAAAATTTTTTTTTTGAAAATCTT-TATTGTTTTATTT
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAA-TTTTTTTTTG-AAAT-TTAT-TTTTTTTATTT
*
22512982 TTAAG
62 TCAAG
* *
22512987 AAAAATTGATACTTTCAAATTTTTTTCAAAAATATATTTTTTT-AAATTT-TTTATTTTTATTTT
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAAT-T-TTTTTTTGAAATTTATTT-TTTTTATTTT
*
22513050 TAA-
63 CAAG
* *
22513053 AAAAATTAATACTTTCAACTTTTTTCTCAAAAA--TATTTTT-AAA---A----TTTTATTTTCA
1 AAAAATTGATACTTTCAAC-TTTTTCTCAAAAATTTTTTTTTGAAATTTATTTTTTTTATTTTCA
22513108 AG
65 AG
* ** * *
22513110 AAAAATTGATACTTTCAACTTTTCCTTTAAAA-TATTTTTTGAAATTT-TTATCAAAATTTTATT
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAATTTTTTTTTGAAATTTATT-T----TTTTTATT
*
22513173 TT-AAA
61 TTCAAG
* * * *
22513178 AAAAATTGATAATTTCAACTTTTTCTCAAGAATATTTTTTTAAAATTTATTTTATTTTATTTTCA
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAATTTTTTTTTGAAATTTATTTT-TTTTATTTTCA
22513243 AG
65 AG
* * * * * * *
22513245 AAAATTTGATACTTTCAAC-TTTTCCCCAAAATATATTTTTAAAATTT-TTATGAAAATTTTATT
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAATTTTTTTTTGAAATTTATT-T----TTTTTATT
22513308 TTCAAG
61 TTCAAG
* *
22513314 GAAAATTGATACTTTCAACTTTTTCTCAAAAA-TATTTTTTGAAATTT
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAATTTTTTTTTGAAATTT
22513361 TTATCAAAAT
Statistics
Matches: 362, Mismatches: 48, Indels: 66
0.76 0.10 0.14
Matches are distributed among these distances:
56 21 0.06
57 23 0.06
58 3 0.01
63 9 0.02
65 2 0.01
66 53 0.15
67 46 0.13
68 35 0.10
69 146 0.40
70 24 0.07
ACGTcount: A:0.36, C:0.10, G:0.04, T:0.51
Consensus pattern (66 bp):
AAAAATTGATACTTTCAACTTTTTCTCAAAAATTTTTTTTTGAAATTTATTTTTTTTATTTTCAA
G
Found at i:22513129 original size:192 final size:190
Alignment explanation
Indices: 22512905--22513292 Score: 471
Period size: 192 Copynumber: 2.0 Consensus size: 190
22512895 TCCTTATTTT
* *
22512905 TTTTATTCTCAAGAAAAATTGATACCTTCAACTTTTTCACAAAAATTTTTTTTTTGAAAATCTTT
1 TTTTATTCTCAAGAAAAATTGATACCTTCAACTTTTCCACAAAAA--TATTTTTTG-AAATCTTT
** * * * *
22512970 AT-TGTTTTATTTTTAAGAAAAATTGATACTTTCAAATTTTTTTCAAAAATATATTTTTTTAAA-
63 ATAAATTTTA-TTTTAAAAAAAATTGATAATTTCAAATTTTTCTCAAAAATAT-TTTTTTAAAAT
* * *
22513033 TT-TTTTATTTTTATTTTTAA-AAAAATTAATACTTTCAACTTTTTTCTCAAAA-ATATTTTTAA
126 TTATTTTA-TTTTATTTTCAAGAAAAATTAATACTTTCAAC-TTTTCCCCAAAATATATTTTTAA
22513095 AA
189 AA
* * *** *
22513097 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTTTAAAATATTTTTTGAAATTTTTATC
1 TTTTATTCTCAAGAAAAATTGATACCTTCAACTTTTCCACAAAAATATTTTTTGAAATCTTTAT-
* *
22513162 AAAATTTTATTTTAAAAAAAATTGATAATTTCAACTTTTTCTCAAGAATATTTTTTTAAAATTTA
65 -AAATTTTATTTTAAAAAAAATTGATAATTTCAAATTTTTCTCAAAAATATTTTTTTAAAATTTA
* *
22513227 TTTTATTTTATTTTCAAGAAAATTTGATACTTTCAACTTTTCCCCAAAATATATTTTTAAAA
129 TTTTATTTTATTTTCAAGAAAAATTAATACTTTCAACTTTTCCCCAAAATATATTTTTAAAA
22513289 TTTT
1 TTTT
22513293 TATGAAAATT
Statistics
Matches: 168, Mismatches: 21, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
189 9 0.05
190 17 0.10
191 60 0.36
192 82 0.49
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.51
Consensus pattern (190 bp):
TTTTATTCTCAAGAAAAATTGATACCTTCAACTTTTCCACAAAAATATTTTTTGAAATCTTTATA
AATTTTATTTTAAAAAAAATTGATAATTTCAAATTTTTCTCAAAAATATTTTTTTAAAATTTATT
TTATTTTATTTTCAAGAAAAATTAATACTTTCAACTTTTCCCCAAAATATATTTTTAAAA
Found at i:22513145 original size:56 final size:57
Alignment explanation
Indices: 22513041--22513157 Score: 157
Period size: 57 Copynumber: 2.1 Consensus size: 57
22513031 AATTTTTTAT
* *
22513041 TTTTATTTTTAAAAAAATTAATACTTTCAACTTTTTTCTCAAAAATA-TTTTTAAAA
1 TTTTATTTTCAAAAAAATTAATACTTTCAACTTTTTCCTCAAAAATATTTTTTAAAA
* ** *
22513097 TTTTATTTTCAAGAAAAATTGATACTTTCAAC-TTTTCCTTTAAAATATTTTTTGAAA
1 TTTTATTTTCAA-AAAAATTAATACTTTCAACTTTTTCCTCAAAAATATTTTTTAAAA
22513154 TTTT
1 TTTT
22513158 TATCAAAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
56 23 0.43
57 30 0.57
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (57 bp):
TTTTATTTTCAAAAAAATTAATACTTTCAACTTTTTCCTCAAAAATATTTTTTAAAA
Found at i:22513361 original size:69 final size:69
Alignment explanation
Indices: 22513093--22513440 Score: 411
Period size: 69 Copynumber: 5.1 Consensus size: 69
22513083 AAATATTTTT
* * **
22513093 AAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTTTAAAATATTTTTTGAAATTTT
1 AAAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAATTTT
22513158 TATC
66 TATC
** * * * *
22513162 AAAATTTTATTTT-AAAAAAAATTGATAATTTCAACTTTTTCTCAAGAATATTTTTTTAAA-ATT
1 AAAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAATTTT
22513225 TAT-
66 TATC
*** * * *
22513228 TTTATTTTATTTTCAA-GAAAATTTGATACTTTCAAC-TTTTCCCCAAAATATATTTTTAAAATT
1 AAAATTTTATTTTCAAGGAAAA-TTGATACTTTCAACTTTTTCTCAAAAATAT-TTTTTGAAATT
*
22513291 TTTATG
64 TTTATC
22513297 AAAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAATTTT
1 AAAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAATTTT
22513362 TATC
66 TATC
* * * * **
22513366 AAAATGTTATTTTCAAGGGAAAA-TGATACTTTTAACTTTTCCTTAAAAATGGTTTTTGAAAATT
1 AAAATTTTATTTTCAA-GGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTG-AAATT
22513430 TTTATC
64 TTTATC
22513436 AAAAT
1 AAAAT
22513441 GTTTTTGAAA
Statistics
Matches: 239, Mismatches: 31, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
66 26 0.11
67 28 0.12
68 45 0.19
69 100 0.42
70 40 0.17
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (69 bp):
AAAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAATTTT
TATC
Found at i:22513444 original size:24 final size:25
Alignment explanation
Indices: 22513411--22513464 Score: 101
Period size: 24 Copynumber: 2.2 Consensus size: 25
22513401 CTTTTCCTTA
22513411 AAAATGGTTTTTGAAAATTTTTATC
1 AAAATGGTTTTTGAAAATTTTTATC
22513436 AAAAT-GTTTTTGAAAATTTTTATC
1 AAAATGGTTTTTGAAAATTTTTATC
22513460 AAAAT
1 AAAAT
22513465 TTTATTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (25 bp):
AAAATGGTTTTTGAAAATTTTTATC
Found at i:22513451 original size:12 final size:11
Alignment explanation
Indices: 22513418--22513467 Score: 55
Period size: 12 Copynumber: 4.3 Consensus size: 11
22513408 TTAAAAATGG
22513418 TTTTTGAAAAT
1 TTTTTGAAAAT
*
22513429 TTTTATCAAAAT
1 TTTT-TGAAAAT
22513441 GTTTTTGAAAAT
1 -TTTTTGAAAAT
*
22513453 TTTTATCAAAAT
1 TTTT-TGAAAAT
22513465 TTT
1 TTT
22513468 ATTTTAAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
11 8 0.24
12 21 0.64
13 4 0.12
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (11 bp):
TTTTTGAAAAT
Found at i:22515487 original size:15 final size:15
Alignment explanation
Indices: 22515467--22515507 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
22515457 CTAATAGATG
22515467 AAAAAATAAAAAAAT
1 AAAAAATAAAAAAAT
*
22515482 AAAAAATAAAAGAAT
1 AAAAAATAAAAAAAT
22515497 AAGAAAA-AAAA
1 AA-AAAATAAAA
22515508 TAAAAGAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (15 bp):
AAAAAATAAAAAAAT
Found at i:22515492 original size:20 final size:20
Alignment explanation
Indices: 22515476--22515516 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
22515466 GAAAAAATAA
22515476 AAAAATAAAAAATAAAAGAAT
1 AAAAA-AAAAAATAAAAGAAT
*
22515497 AAGAAAAAAAATAAAAGAAT
1 AAAAAAAAAAATAAAAGAAT
22515517 GAGAAAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.12
Consensus pattern (20 bp):
AAAAAAAAAAATAAAAGAAT
Found at i:22515510 original size:35 final size:35
Alignment explanation
Indices: 22515467--22515540 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
22515457 CTAATAGATG
22515467 AAAAAATAAAAAAAT-AAAAAATAAAAGAATAAGAA
1 AAAAAATAAAAAAATGAAAAAATAAAA-AATAAGAA
* * **
22515502 AAAAAATAAAAGAATGAGAAAATGTAAAATAAGAA
1 AAAAAATAAAAAAATGAAAAAATAAAAAATAAGAA
22515537 AAAA
1 AAAA
22515541 GGAATACTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 26 0.76
36 8 0.24
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (35 bp):
AAAAAATAAAAAAATGAAAAAATAAAAAATAAGAA
Found at i:22515512 original size:8 final size:8
Alignment explanation
Indices: 22515467--22515504 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
22515457 CTAATAGATG
22515467 AAAAAATA
1 AAAAAATA
22515475 AAAAAAT-
1 AAAAAATA
22515482 AAAAAATA
1 AAAAAATA
*
22515490 AAAGAATA
1 AAAAAATA
22515498 AGAAAAA
1 A-AAAAA
22515505 AAATAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
7 7 0.27
8 15 0.58
9 4 0.15
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (8 bp):
AAAAAATA
Found at i:22515521 original size:20 final size:20
Alignment explanation
Indices: 22515482--22515523 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
22515472 ATAAAAAAAT
22515482 AAAAAATAAAAGAATAAGAA
1 AAAAAATAAAAGAATAAGAA
*
22515502 AAAAAATAAAAGAATGAGAA
1 AAAAAATAAAAGAATAAGAA
22515522 AA
1 AA
22515524 TGTAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (20 bp):
AAAAAATAAAAGAATAAGAA
Found at i:22516366 original size:63 final size:63
Alignment explanation
Indices: 22516247--22516366 Score: 143
Period size: 63 Copynumber: 1.9 Consensus size: 63
22516237 ATCAGTGGGT
* * * *
22516247 AAAATTTATTTTGAAATGGTTAGTGCTGAGAAACATATGAATGGTGACCAAGTGATGGAGGAC
1 AAAATTTATTTTGAAATGGCTAGTACTGAGAAACATATGAATGATGACCAAATGATGGAGGAC
* * * * *
22516310 AAAATTTATTTTGCAATGGCTAGTACTGA-AAAGCCTGTGAATTATGATCAAATGATG
1 AAAATTTATTTTGAAATGGCTAGTACTGAGAAA-CATATGAATGATGACCAAATGATG
22516367 AAAATAATAT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
62 3 0.06
63 44 0.94
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.31
Consensus pattern (63 bp):
AAAATTTATTTTGAAATGGCTAGTACTGAGAAACATATGAATGATGACCAAATGATGGAGGAC
Found at i:22516841 original size:21 final size:20
Alignment explanation
Indices: 22516793--22516854 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
22516783 TGGATAAAGT
*
22516793 TTTAAATGAGAACATTTGAG
1 TTTAAATGAGAATATTTGAG
22516813 TCTTAAATGAGAATATTTGAG
1 T-TTAAATGAGAATATTTGAG
* *
22516834 TTTCAAATAAGAATCTTTGAG
1 TTT-AAATGAGAATATTTGAG
22516855 ATATAAAGCC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 3 0.08
21 34 0.92
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (20 bp):
TTTAAATGAGAATATTTGAG
Found at i:22517548 original size:122 final size:120
Alignment explanation
Indices: 22517368--22517589 Score: 295
Period size: 122 Copynumber: 1.8 Consensus size: 120
22517358 CCTCTGCTTG
** *
22517368 AAAAAGCCTTTTATTTTTTAAAGTTGTTGTGCCTCTGTTTAGAAGAGCCTTTTATTTTTCAAA-A
1 AAAAAGCCTTTTATTTTTTAAAGTTGTTAAGCCTCTATTTAGAAGAGCCTTTTATTTTTCAAACA
22517432 TTGTTAGGCCTCTGTTTAGAGGAACCTTTATTTTTTAAAGTTTTTTAGGCTTTGTCTA
66 TTG--A-GCCTCTGTTTAGAGGAACCTTTATTTTTTAAAGTTTTTTAGGCTTTGTCTA
* * * *
22517490 AAAAAGCC-TTTATTTTTTAAAGTTTTTAAGCCTCTATTTATATGAGCCTTTATTTTTTTCAAAG
1 AAAAAGCCTTTTATTTTTTAAAGTTGTTAAGCCTCTATTTAGAAGAGCCTTT-TATTTTTCAAA-
* *
22517554 CCATTGAGCCTTTGTTTAGAGGAGCCTTTATTTTTT
64 -CATTGAGCCTCTGTTTAGAGGAACCTTTATTTTTT
22517590 TCAAAGTCGT
Statistics
Matches: 87, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
121 37 0.43
122 45 0.52
123 1 0.01
125 4 0.05
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (120 bp):
AAAAAGCCTTTTATTTTTTAAAGTTGTTAAGCCTCTATTTAGAAGAGCCTTTTATTTTTCAAACA
TTGAGCCTCTGTTTAGAGGAACCTTTATTTTTTAAAGTTTTTTAGGCTTTGTCTA
Found at i:22517642 original size:41 final size:41
Alignment explanation
Indices: 22517324--22517656 Score: 275
Period size: 41 Copynumber: 8.1 Consensus size: 41
22517314 TATGTATCTA
* * * *
22517324 TTTAGAGGAGCATTTA-TTTTTCAAAGTTATTGTGCCTCTG
1 TTTAGAAGAGCCTTTATTTTTTCAAAGTTGTTGAGCCTCTG
* * *
22517364 CTT-GAAAAAGCCTTTTATTTTTT-AAAGTTGTTGTGCCTCTG
1 TTTAG-AAGAGCC-TTTATTTTTTCAAAGTTGTTGAGCCTCTG
*
22517405 TTTAGAAGAGCCTTT-TATTTTTCAAAATTGTT-AGGCCTCTG
1 TTTAGAAGAGCCTTTAT-TTTTTCAAAGTTGTTGA-GCCTCTG
* * * * * *
22517446 TTTAGAGGAACCTTTATTTTTT-AAAGTTTTTTAGGCTTTG
1 TTTAGAAGAGCCTTTATTTTTTCAAAGTTGTTGAGCCTCTG
* * * * * *
22517486 TCTAAAAAAGCCTTTATTTTTT-AAAGTTTTTAAGCCTCTA
1 TTTAGAAGAGCCTTTATTTTTTCAAAGTTGTTGAGCCTCTG
* * *** *
22517526 TTTATATGAGCCTTTATTTTTTTCAAAGCCATTGAGCCTTTG
1 TTTAGAAGAGCCTTTA-TTTTTTCAAAGTTGTTGAGCCTCTG
* * *
22517568 TTTAGAGGAGCCTTTATTTTTTTCAAAGTCGTTGAGCCTCTA
1 TTTAGAAGAGCCTTTA-TTTTTTCAAAGTTGTTGAGCCTCTG
* * *
22517610 TTTAGAAGAGCCTTTATTTTTTCAAAGTCGTTGAGCTTCTA
1 TTTAGAAGAGCCTTTATTTTTTCAAAGTTGTTGAGCCTCTG
22517651 TTTAGA
1 TTTAGA
22517657 GGAGTTTTTT
Statistics
Matches: 240, Mismatches: 42, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
39 2 0.01
40 69 0.29
41 99 0.41
42 70 0.29
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (41 bp):
TTTAGAAGAGCCTTTATTTTTTCAAAGTTGTTGAGCCTCTG
Found at i:22518140 original size:22 final size:23
Alignment explanation
Indices: 22518100--22518145 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
22518090 CCCGAAATTA
22518100 ATAAAATATTATTTTTTAAATAT
1 ATAAAATATTATTTTTTAAATAT
22518123 ATAAAATATTA-TTTTTAAATAT
1 ATAAAATATTATTTTTTAAATAT
22518145 A
1 A
22518146 AATATTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATAAAATATTATTTTTTAAATAT
Found at i:22518147 original size:28 final size:30
Alignment explanation
Indices: 22518116--22518181 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
22518106 TATTATTTTT
* *
22518116 TAAATATAT-AAAATATTATT-TTTAAATA
1 TAAATATATAAAAATATCATTATATAAATA
*
22518144 TAAATATTTAAAAATATCATTATATAAATA
1 TAAATATATAAAAATATCATTATATAAATA
*
22518174 TATATATA
1 TAAATATA
22518182 ATTAATTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 8 0.26
29 10 0.32
30 13 0.42
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (30 bp):
TAAATATATAAAAATATCATTATATAAATA
Found at i:22518689 original size:11 final size:10
Alignment explanation
Indices: 22518673--22518728 Score: 53
Period size: 11 Copynumber: 5.5 Consensus size: 10
22518663 GTCATTTCAT
22518673 TTTTTTAGGTA
1 TTTTTTA-GTA
22518684 TTTTTT-GTA
1 TTTTTTAGTA
*
22518693 -TTTTTATTTA
1 TTTTTTA-GTA
*
22518703 TTTTTTATGTT
1 TTTTTTA-GTA
22518714 TTTTTTAGTA
1 TTTTTTAGTA
22518724 TTTTT
1 TTTTT
22518729 ACATGATTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
8 5 0.13
9 3 0.08
10 9 0.24
11 21 0.55
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (10 bp):
TTTTTTAGTA
Found at i:22518697 original size:21 final size:21
Alignment explanation
Indices: 22518671--22518729 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
22518661 TAGTCATTTC
22518671 ATTTTTTTAGGTATTTTT-TGT
1 ATTTTTTTA-GTATTTTTATGT
22518692 ATTTTTATT--TATTTTTTATGT
1 ATTTTT-TTAGTA-TTTTTATGT
22518713 -TTTTTTTAGTATTTTTA
1 ATTTTTTTAGTATTTTTA
22518730 CATGATTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
19 4 0.12
20 16 0.48
21 11 0.33
22 2 0.06
ACGTcount: A:0.17, C:0.00, G:0.08, T:0.75
Consensus pattern (21 bp):
ATTTTTTTAGTATTTTTATGT
Found at i:22518706 original size:31 final size:32
Alignment explanation
Indices: 22518666--22518729 Score: 87
Period size: 30 Copynumber: 2.0 Consensus size: 32
22518656 CAACCTAGTC
22518666 ATTTCATTTTTTTAGGTATTTTTT-GTATTTTT
1 ATTTCA-TTTTTTAGGTATTTTTTAGTATTTTT
* *
22518698 ATTT-ATTTTTTATGTTTTTTTTAGTATTTTT
1 ATTTCATTTTTTAGGTATTTTTTAGTATTTTT
22518729 A
1 A
22518730 CATGATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 15 0.52
31 10 0.34
32 4 0.14
ACGTcount: A:0.17, C:0.02, G:0.08, T:0.73
Consensus pattern (32 bp):
ATTTCATTTTTTAGGTATTTTTTAGTATTTTT
Found at i:22518727 original size:19 final size:20
Alignment explanation
Indices: 22518672--22518727 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 20
22518662 AGTCATTTCA
*
22518672 TTTTTTTAGGTATTTTTTGTAT
1 TTTTTTTA-GTATTTTATG-AT
*
22518694 TTTTATTTA-TTTTTTATG-T
1 TTTT-TTTAGTATTTTATGAT
22518713 TTTTTTTAGTATTTT
1 TTTTTTTAGTATTTT
22518728 TACATGATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
18 4 0.14
19 10 0.34
21 7 0.24
22 4 0.14
23 4 0.14
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (20 bp):
TTTTTTTAGTATTTTATGAT
Found at i:22518759 original size:14 final size:14
Alignment explanation
Indices: 22518742--22518774 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
22518732 TGATTAAATT
22518742 TAAAAAAA-AAAGAA
1 TAAAAAAATAAA-AA
22518756 TAAAAAAATAAAAA
1 TAAAAAAATAAAAA
22518770 TAAAA
1 TAAAA
22518775 TTTTTTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 15 0.83
15 3 0.17
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (14 bp):
TAAAAAAATAAAAA
Found at i:22522199 original size:16 final size:16
Alignment explanation
Indices: 22522169--22522199 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22522159 TCCATGAAGG
*
22522169 TGTTGTTCCGTGAATA
1 TGTTGCTCCGTGAATA
22522185 TGTTGCTCCGTGAAT
1 TGTTGCTCCGTGAAT
22522200 GAGTTATTCC
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:0.16, C:0.16, G:0.26, T:0.42
Consensus pattern (16 bp):
TGTTGCTCCGTGAATA
Found at i:22522231 original size:15 final size:15
Alignment explanation
Indices: 22522174--22522231 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
22522164 GAAGGTGTTG
*
22522174 TTCCGTGAATATGTTG
1 TTCCGTGAATA-GTTA
*
22522190 CTCCGTGAATGAGTTA
1 TTCCGTGAAT-AGTTA
* *
22522206 TTCCTTAAATAGTTA
1 TTCCGTGAATAGTTA
*
22522221 TTTCGTGAATA
1 TTCCGTGAATA
22522232 ACTATTCTGT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
15 13 0.39
16 19 0.58
17 1 0.03
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (15 bp):
TTCCGTGAATAGTTA
Found at i:22523378 original size:6 final size:6
Alignment explanation
Indices: 22523363--22523395 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
22523353 TCAAATGTGA
22523363 TTTT-T TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
22523396 TGTTTAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTCT
Found at i:22524716 original size:27 final size:26
Alignment explanation
Indices: 22524685--22524760 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 26
22524675 AACTCTTGTA
22524685 ATAAAATTTTAATACAATATTTAAATT
1 ATAAAATTTTAATA-AATATTTAAATT
* * *
22524712 TTAAAAATTTATAATATGACATTTAAATT
1 AT-AAAATTT-TAATA-AATATTTAAATT
*
22524741 ATAAATTTATTAATAAATAT
1 ATAAAATT-TTAATAAATAT
22524761 GATATTTATT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
27 4 0.11
28 17 0.45
29 17 0.45
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (26 bp):
ATAAAATTTTAATAAATATTTAAATT
Found at i:22524794 original size:27 final size:27
Alignment explanation
Indices: 22524771--22524843 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 27
22524761 GATATTTATT
22524771 TTTAATATATTA-ATTAATAAATTTATAA
1 TTTAA-ATATTATATT-ATAAATTTATAA
*
22524799 TTTAAATATTATATTATAAATATTTAAAA
1 TTTAAATATTATATTAT-AA-ATTTATAA
*
22524828 TTTAAATATCATATTA
1 TTTAAATATTATATTA
22524844 AATATTTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 8 0.20
28 10 0.25
29 22 0.55
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (27 bp):
TTTAAATATTATATTATAAATTTATAA
Found at i:22524823 original size:29 final size:29
Alignment explanation
Indices: 22524762--22524850 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 29
22524752 AATAAATATG
*
22524762 ATATTTAT-TTTTAATATATTA-ATTA-ATA
1 ATATTTATAATTTAA-ATATTATATTATA-A
22524790 A-ATTTATAATTTAAATATTATATTATAA
1 ATATTTATAATTTAAATATTATATTATAA
* *
22524818 ATATTTAAAATTTAAATATCATA-T-TAA
1 ATATTTATAATTTAAATATTATATTATAA
22524845 ATATTT
1 ATATTT
22524851 TATTATAATT
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
27 21 0.39
28 13 0.24
29 20 0.37
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (29 bp):
ATATTTATAATTTAAATATTATATTATAA
Found at i:22524845 original size:27 final size:29
Alignment explanation
Indices: 22524791--22524850 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
22524781 TAATTAATAA
* *
22524791 ATTTATAATTTAAATATTATATTATAAAT
1 ATTTAAAATTTAAATATCATATTATAAAT
22524820 ATTTAAAATTTAAATATCATA-T-TAAAT
1 ATTTAAAATTTAAATATCATATTATAAAT
22524847 ATTT
1 ATTT
22524851 TATTATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 9 0.31
28 1 0.03
29 19 0.66
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (29 bp):
ATTTAAAATTTAAATATCATATTATAAAT
Found at i:22525622 original size:3 final size:3
Alignment explanation
Indices: 22525614--22525664 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
22525604 AAAATTACAA
22525614 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
22525662 TAT
1 TAT
22525665 AAGGTGTGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:22541293 original size:31 final size:31
Alignment explanation
Indices: 22541228--22541293 Score: 73
Period size: 30 Copynumber: 2.1 Consensus size: 31
22541218 ATTCGAGTTC
* * *
22541228 AATTAAATTTATTTTTTTGAACTTGATTTAT
1 AATTAAATTGATTTTTTTGAACTAGAATTAT
22541259 AATT-AATTGATTTTTTTGAAATCTAGAATT-T
1 AATTAAATTGATTTTTTTG-AA-CTAGAATTAT
22541290 AATT
1 AATT
22541294 GAGTTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
30 13 0.43
31 11 0.37
32 6 0.20
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.55
Consensus pattern (31 bp):
AATTAAATTGATTTTTTTGAACTAGAATTAT
Found at i:22546528 original size:15 final size:15
Alignment explanation
Indices: 22546508--22546544 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
22546498 CTAATAGATG
22546508 AAAAAATAAAAAAAT
1 AAAAAATAAAAAAAT
*
22546523 AAAAAATAAAAGAAT
1 AAAAAATAAAAAAAT
22546538 AAGAAAA
1 AA-AAAA
22546545 AAATAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (15 bp):
AAAAAATAAAAAAAT
Done.