Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 32 of 190
Found at i:5599636 original size:16 final size:17
Alignment explanation
Indices: 5599613--5599667 Score: 78
Period size: 16 Copynumber: 3.4 Consensus size: 17
5599603 TATGGCATAC
*
5599613 TATTATTAATACTATTA
1 TATTATTAATATTATTA
*
5599630 T-TTATTATTATTATTA
1 TATTATTAATATTATTA
5599646 TATTATT-ATATTATTA
1 TATTATTAATATTATTA
5599662 TATTAT
1 TATTAT
5599668 ATTTTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 28 0.82
17 6 0.18
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTATTAATATTATTA
Found at i:5599668 original size:13 final size:13
Alignment explanation
Indices: 5599628--5599670 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
5599618 TTAATACTAT
5599628 TATT-TATTATTA
1 TATTATATTATTA
5599640 TTATTATATTATTA
1 -TATTATATTATTA
5599654 TATTAT-TATATTA
1 TATTATAT-TATTA
5599667 TATT
1 TATT
5599671 TTTTTTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.04
13 19 0.68
14 8 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TATTATATTATTA
Found at i:5600635 original size:3 final size:3
Alignment explanation
Indices: 5600622--5600668 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
5600612 ATTCTACAAA
*
5600622 AAT ACT AAT AAT AAT AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5600669 CCTTTCAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5600651 original size:20 final size:20
Alignment explanation
Indices: 5600628--5600667 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5600618 CAAAAATACT
5600628 AATAATAATAATAATAATAA
1 AATAATAATAATAATAATAA
5600648 AATAATAATAATAATAATAA
1 AATAATAATAATAATAATAA
5600668 TCCTTTCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AATAATAATAATAATAATAA
Found at i:5600653 original size:17 final size:17
Alignment explanation
Indices: 5600631--5600664 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5600621 AAATACTAAT
5600631 AATAATAATAATAATAA
1 AATAATAATAATAATAA
5600648 AATAATAATAATAATAA
1 AATAATAATAATAATAA
5600665 TAATCCTTTC
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAATAATAATAATAA
Found at i:5604478 original size:58 final size:58
Alignment explanation
Indices: 5604414--5604925 Score: 540
Period size: 59 Copynumber: 8.7 Consensus size: 58
5604404 CTTGTACAGA
*
5604414 AAAAATTAATACTTTCAACTTTTTCCTAAAAATATTCTTTTGAAACTTTTA-TTTCAAG
1 AAAAATTGATACTTTCAACTTTTTCCTAAAAATATT-TTTTGAAACTTTTATTTTCAAG
* *
5604472 AAAAATTGATACTTTCAAC-TTTTCACCAAAAATATTTTTTGGAAACTTTGATTTTCAAG
1 AAAAATTGATACTTTCAACTTTTTC-CTAAAAATATTTTTT-GAAACTTTTATTTTCAAG
* * * * *
5604531 GAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTGATTTTCGAG
1 AAAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTG-AAACTTTTATTTTCAAG
* * * * *
5604590 GAAAATTGATACTCTCAAC-TTTTCCTCAAAAAATTTTTTTTGAAA-ATTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTTCCT--AAAAATATTTTTTGAAACTTTTATTTTCAAG
* *
5604648 AAAAATTGATACTTTCAACTTTTCCCTAAAAATATTCTTTTGAAACTTTTA-TTTCCAG
1 AAAAATTGATACTTTCAACTTTTTCCTAAAAATATT-TTTTGAAACTTTTATTTTCAAG
* *
5604706 AAAAATTGATACTTTCAAC-TTTTCCTCAAAAATTTATTTTTTGAAA-ATTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTTCCT-AAAAA--TATTTTTTGAAACTTTTATTTTCAAG
* * * * *
5604765 GAAAATTGATATTTTTAACTTTTTCCCAAAAATATTTTTTGAAAACTTTGATTTTCGAAG
1 AAAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTG-AAACTTTTATTTTC-AAG
* * * **
5604825 -AAAATTGATACTTTCAACTTTTTCTCAAAAAACAATCTTTTTTTGAAA-ATTTATTTTTGAG
1 AAAAATTGATACTTTCAACTTTTTC-C--TAAA-AAT-ATTTTTTGAAACTTTTATTTTCAAG
*
5604886 GAAAATTGATACTTTCAACTTTTTTCC-AAAAATATTTTTT
1 AAAAATTGATACTTTCAAC-TTTTTCCTAAAAATATTTTTT
5604926 TGGATTTTAT
Statistics
Matches: 388, Mismatches: 41, Indels: 51
0.81 0.09 0.11
Matches are distributed among these distances:
57 38 0.10
58 116 0.30
59 153 0.39
60 31 0.08
61 2 0.01
62 29 0.07
63 12 0.03
64 7 0.02
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (58 bp):
AAAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTGAAACTTTTATTTTCAAG
Found at i:5604830 original size:234 final size:237
Alignment explanation
Indices: 5604414--5604945 Score: 812
Period size: 234 Copynumber: 2.3 Consensus size: 237
5604404 CTTGTACAGA
*
5604414 AAAAATTAATACTTTCAACTTTTTCCTAAAAATATTCTTTTGAAACTTTTATTTCAAGAAAAATT
1 AAAAATTGATACTTTCAACTTTTTCCTAAAAATATTCTTTTGAAACTTTTATTTCAAGAAAAATT
*
5604479 GATACTTTCAACTTTTCACCAAAAATATTTTTTGGAAACTTTGATTTTCAAGGAAAATTGATACT
66 GATACTTTCAACTTTTCACCAAAAATATTTTTTGGAAAATTTGATTTTCAAGGAAAATTGATACT
*
5604544 TTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTGATTTTCGAGGAAAATTGATACTCTCAAC
131 TTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTGATTTTCGAAGAAAATTGATACTCTCAAC
5604609 TTTTCCTC-AAAA-AAT-TTTTTTTGAAAATTTATTTTTAAG
196 TTTTCCTCAAAAACAATCTTTTTTTGAAAATTTATTTTTAAG
* *
5604648 AAAAATTGATACTTTCAACTTTTCCCTAAAAATATTCTTTTGAAACTTTTATTTCCAGAAAAATT
1 AAAAATTGATACTTTCAACTTTTTCCTAAAAATATTCTTTTGAAACTTTTATTTCAAGAAAAATT
*
5604713 GATACTTTCAACTTTTC-CTCAAAAATTTATTTTTT-GAAAATTT-ATTTTTAAGGAAAATTGAT
66 GATACTTTCAACTTTTCAC-CAAAAA--TATTTTTTGGAAAATTTGATTTTCAAGGAAAATTGAT
* * * *
5604775 ATTTTTAACTTTTTCCCAAAAATATTTTTTGAAAACTTTGATTTTCGAAGAAAATTGATACTTTC
128 ACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTGATTTTCGAAGAAAATTGATACTCTC
* *
5604840 AACTTTTTCTCAAAAAACAATCTTTTTTTGAAAATTTATTTTTGAG
193 AACTTTTCCTC-AAAAACAATCTTTTTTTGAAAATTTATTTTTAAG
* * * *
5604886 GAAAATTGATACTTTCAACTTTTTTCC-AAAAATATTTTTTTG-GA-TTTTATTTAAAGAAAA
1 AAAAATTGATACTTTCAAC-TTTTTCCTAAAAATATTCTTTTGAAACTTTTATTTCAAGAAAA
5604946 TAAAATAATA
Statistics
Matches: 272, Mismatches: 18, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
233 1 0.00
234 173 0.64
235 7 0.03
236 26 0.10
237 4 0.01
238 55 0.20
239 6 0.02
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.44
Consensus pattern (237 bp):
AAAAATTGATACTTTCAACTTTTTCCTAAAAATATTCTTTTGAAACTTTTATTTCAAGAAAAATT
GATACTTTCAACTTTTCACCAAAAATATTTTTTGGAAAATTTGATTTTCAAGGAAAATTGATACT
TTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTGATTTTCGAAGAAAATTGATACTCTCAAC
TTTTCCTCAAAAACAATCTTTTTTTGAAAATTTATTTTTAAG
Found at i:5604960 original size:13 final size:13
Alignment explanation
Indices: 5604942--5604966 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5604932 TTATTTAAAG
5604942 AAAATAAAATAAT
1 AAAATAAAATAAT
5604955 AAAATAAAATAA
1 AAAATAAAATAA
5604967 AAGTGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:5604977 original size:22 final size:21
Alignment explanation
Indices: 5604952--5605024 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 21
5604942 AAAATAAAAT
5604952 AATAAAATAAAATAAAAGTGAA
1 AATAAAATAAAATAAAAGT-AA
* *
5604974 AATAAAAAAAAAGAAAAGTAA
1 AATAAAATAAAATAAAAGTAA
*
5604995 AACAAAAATAAAAATAAAA-TAA
1 AA-TAAAAT-AAAATAAAAGTAA
5605017 AGATAAAA
1 A-ATAAAA
5605025 GAACATTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
21 4 0.10
22 29 0.69
23 9 0.21
ACGTcount: A:0.78, C:0.01, G:0.07, T:0.14
Consensus pattern (21 bp):
AATAAAATAAAATAAAAGTAA
Found at i:5604981 original size:13 final size:12
Alignment explanation
Indices: 5604942--5605024 Score: 52
Period size: 11 Copynumber: 7.2 Consensus size: 12
5604932 TTATTTAAAG
5604942 AAAATAAAATAA
1 AAAATAAAATAA
5604954 TAAAATAAAAT-A
1 -AAAATAAAATAA
*
5604966 AAAGTGAAAAT-A
1 AAAAT-AAAATAA
*
5604978 AAAA-AAAA-GA
1 AAAATAAAATAA
* *
5604988 AAAGTAAAA-CA
1 AAAATAAAATAA
*
5604999 AAAATAAAA-AT
1 AAAATAAAATAA
5605010 AAAATAAAGATAA
1 AAAATAAA-ATAA
5605023 AA
1 AA
5605025 GAACATTAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
10 8 0.14
11 25 0.44
12 11 0.19
13 13 0.23
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.14
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:5605022 original size:6 final size:5
Alignment explanation
Indices: 5604942--5605038 Score: 72
Period size: 5 Copynumber: 18.6 Consensus size: 5
5604932 TTATTTAAAG
* *
5604942 AAAAT AAAAT --AAT AAAAT AAAAT AAAAGT GAAAAT AAAAA AAAAG AAAAGT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT AAAAT AAAA-T
* * * *
5604993 AAAACA AAAAT AAAAAT AAAAT AAAGAT AAAAG AACAT TAAAT AAA
1 AAAA-T AAAAT -AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAA
5605039 CCTAATATAA
Statistics
Matches: 73, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
3 3 0.04
5 46 0.63
6 20 0.27
7 4 0.05
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:5605022 original size:17 final size:16
Alignment explanation
Indices: 5604942--5605024 Score: 78
Period size: 17 Copynumber: 4.9 Consensus size: 16
5604932 TTATTTAAAG
5604942 AAAATAAAATAATAAAAT
1 AAAAT-AAA-AATAAAAT
*
5604960 AAAATAAAAGTGAAAAT
1 AAAATAAAAAT-AAAAT
*
5604977 AAAA-AAAAAGAAAAGT
1 AAAATAAAAATAAAA-T
*
5604993 AAAACAAAAATAAAAAT
1 AAAATAAAAAT-AAAAT
*
5605010 AAAATAAAGATAAAA
1 AAAATAAAAATAAAA
5605025 GAACATTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
15 4 0.07
16 15 0.27
17 27 0.49
18 9 0.16
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.14
Consensus pattern (16 bp):
AAAATAAAAATAAAAT
Found at i:5605618 original size:26 final size:24
Alignment explanation
Indices: 5605580--5605632 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
5605570 ACCGGAATCT
* *
5605580 AAAAATTTTCCAAAAATTTCCAGAA
1 AAAAATTTGCCAAAAATCTCCA-AA
5605605 AAAAATTTCGCCAAAAATCTCCAAA
1 AAAAATTT-GCCAAAAATCTCCAAA
5605630 AAA
1 AAA
5605633 TTTTTTTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.55, C:0.19, G:0.04, T:0.23
Consensus pattern (24 bp):
AAAAATTTGCCAAAAATCTCCAAA
Found at i:5605992 original size:22 final size:21
Alignment explanation
Indices: 5605959--5606074 Score: 98
Period size: 21 Copynumber: 5.5 Consensus size: 21
5605949 AGAAATTAAC
*
5605959 AGATAATTAAAAATAATAATA
1 AGATAAATAAAAATAATAATA
* *
5605980 AGATAAATCAAAAAT-ATTACA
1 AGATAAAT-AAAAATAATAATA
5606001 AGATAAATAAATAATAATAAT-
1 AGATAAATAAA-AATAATAATA
5606022 A-ATAAATAATAATATAATAATA
1 AGATAAATAA-AA-ATAATAATA
*
5606044 A-ATAAATTATAATATAATAATA
1 AGATAAA-TA-AAAATAATAATA
*
5606066 A-ATATATAA
1 AGATAAATAA
5606075 CTAGATAAAT
Statistics
Matches: 80, Mismatches: 7, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
20 13 0.16
21 34 0.43
22 29 0.36
23 3 0.04
24 1 0.01
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.30
Consensus pattern (21 bp):
AGATAAATAAAAATAATAATA
Found at i:5606012 original size:4 final size:4
Alignment explanation
Indices: 5606003--5606192 Score: 96
Period size: 4 Copynumber: 48.2 Consensus size: 4
5605993 ATATTACAAG
5606003 ATAA ATAA AT-A AT-A AT-A AT-A ATAA AT-A AT-A ATATA AT-A ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA-A ATAA ATAA
* * * *
5606045 ATAA ATTATA ATATA AT-A ATAA ATAT ATAA CTAG ATAA ATAAA ATAC
1 ATAA A-TA-A ATA-A ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA
* * * * * **
5606092 ATAT ATAA AT-A TTAA CAAAA ATAA ATAA ATAA ATAA ATAA AGAT ATGC
1 ATAA ATAA ATAA ATAA -ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* * * *
5606140 ATAT ATTA ATAC ATAGTA AT-A ATAA ATAA ATAA ATAA AT-A ATAA ATAC
1 ATAA ATAA ATAA ATA--A ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
5606188 ATAA A
1 ATAA A
5606193 ATACAAAGAA
Statistics
Matches: 145, Mismatches: 27, Indels: 28
0.73 0.14 0.14
Matches are distributed among these distances:
3 32 0.22
4 92 0.63
5 17 0.12
6 4 0.03
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (4 bp):
ATAA
Found at i:5606018 original size:3 final size:3
Alignment explanation
Indices: 5606010--5606066 Score: 64
Period size: 3 Copynumber: 18.7 Consensus size: 3
5606000 AAGATAAATA
*
5606010 AAT AAT AAT AAT AAT AAAT AAT AAT -AT AAT AAT AAAT AAAT TAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AAT
5606057 -AT AAT AAT AA
1 AAT AAT AAT AA
5606067 ATATATAACT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 4 0.08
3 34 0.71
4 10 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5606038 original size:12 final size:12
Alignment explanation
Indices: 5606013--5606236 Score: 84
Period size: 12 Copynumber: 19.2 Consensus size: 12
5606003 ATAAATAAAT
5606013 AATAATAATAATA
1 AATAATAAT-ATA
5606026 AATAATAATAT-
1 AATAATAATATA
5606037 AATAATAA-ATA
1 AATAATAATATA
*
5606048 AATTATAATAT-
1 AATAATAATATA
5606059 AATAATAA-ATA
1 AATAATAATATA
* *
5606070 TATAACT-AGATA
1 AATAA-TAATATA
*
5606082 AATAA-AATACA
1 AATAATAATATA
* *
5606093 TAT-ATAAATATT
1 AATAAT-AATATA
*
5606105 AACAA-AA-ATA
1 AATAATAATATA
5606115 AATAAATAA-ATA
1 AAT-AATAATATA
*
5606127 AATAA-AGATATG
1 AATAATA-ATATA
* *
5606139 CAT-ATATTAATA
1 AATAATAAT-ATA
* *
5606151 CATAGTAATAATA
1 AATAATAAT-ATA
5606164 AATAAATAA-ATA
1 AAT-AATAATATA
5606176 AATAATAA-ATA
1 AATAATAATATA
* *
5606187 CATAA-AATACA
1 AATAATAATATA
* * *
5606198 AAGAAAAAAAATA
1 AA-TAATAATATA
5606211 AAT-ATAAATATA
1 AATAAT-AATATA
*
5606223 AAAAATAATATA
1 AATAATAATATA
5606235 AA
1 AA
5606237 ATATAAAATA
Statistics
Matches: 158, Mismatches: 31, Indels: 45
0.68 0.13 0.19
Matches are distributed among these distances:
10 12 0.08
11 57 0.36
12 58 0.37
13 27 0.17
14 4 0.03
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (12 bp):
AATAATAATATA
Found at i:5606056 original size:38 final size:38
Alignment explanation
Indices: 5605969--5606131 Score: 120
Period size: 40 Copynumber: 4.2 Consensus size: 38
5605959 AGATAATTAA
* * *
5605969 AAATAATAATA-AGATAAATCAAAAATATTACAAGATAAAT
1 AAATAATAATATA-AT-AAT-AAATATATAACTAGATAAAT
5606009 AAATAATAATAATAATAA-ATAATAATATAA-TA-ATAAAT
1 AAATAATAAT-ATAATAATA-AAT-ATATAACTAGATAAAT
*
5606047 AAATTATAATATAATAATAAATATATAACTAGATAAAT
1 AAATAATAATATAATAATAAATATATAACTAGATAAAT
* * * * *
5606085 AAAATACAT-ATATAAATATTAACAAAAATAAATAAATAAAT
1 -AAATA-ATAATAT-AATAATAA-ATATATAACTAGATAAAT
5606126 AAATAA
1 AAATAA
5606132 AGATATGCAT
Statistics
Matches: 102, Mismatches: 10, Indels: 23
0.76 0.07 0.17
Matches are distributed among these distances:
36 6 0.06
37 12 0.12
38 23 0.23
39 12 0.12
40 31 0.30
41 17 0.17
42 1 0.01
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (38 bp):
AAATAATAATATAATAATAAATATATAACTAGATAAAT
Found at i:5606082 original size:22 final size:20
Alignment explanation
Indices: 5606003--5606074 Score: 87
Period size: 22 Copynumber: 3.6 Consensus size: 20
5605993 ATATTACAAG
*
5606003 ATAAATAAATAATAATAATA
1 ATAAATATATAATAATAATA
5606023 ATAAATA-ATAAT-ATAATA
1 ATAAATATATAATAATAATA
5606041 ATAAATAAATTATAAT-ATAATA
1 ATAAAT--A-TATAATAATAATA
5606063 ATAAATATATAA
1 ATAAATATATAA
5606075 CTAGATAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
18 12 0.25
19 10 0.21
20 9 0.19
22 17 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAATATATAATAATAATA
Found at i:5606225 original size:19 final size:18
Alignment explanation
Indices: 5606160--5606248 Score: 74
Period size: 19 Copynumber: 4.7 Consensus size: 18
5606150 ACATAGTAAT
5606160 AATAAATAAATAAATA-AA
1 AATAAA-AAATAAATATAA
* *
5606178 TAATAAATACATAAAATACAA
1 -AATAAA-AAAT-AAATATAA
*
5606199 AGAAAAAAAATAAATATAA
1 A-ATAAAAAATAAATATAA
5606218 ATATAAAAAAT-AATATAA
1 A-ATAAAAAATAAATATAA
*
5606236 AATATAAAATAAA
1 AATAAAAAATAAA
5606249 AGTCAAATTG
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
17 8 0.14
18 10 0.17
19 26 0.44
20 9 0.15
21 6 0.10
ACGTcount: A:0.74, C:0.02, G:0.01, T:0.22
Consensus pattern (18 bp):
AATAAAAAATAAATATAA
Found at i:5606244 original size:18 final size:19
Alignment explanation
Indices: 5606203--5606248 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
5606193 ATACAAAGAA
5606203 AAAAAATAAATATAAATAT
1 AAAAAATAAATATAAATAT
5606222 AAAAAAT-AATATAAA-AT
1 AAAAAATAAATATAAATAT
*
5606239 ATAAAATAAA
1 AAAAAATAAA
5606249 AGTCAAATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 8 0.32
18 10 0.40
19 7 0.28
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAAAATAAATATAAATAT
Found at i:5606247 original size:24 final size:23
Alignment explanation
Indices: 5606167--5606249 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 23
5606157 AATAATAAAT
* *
5606167 AAATAAATAAATAATAAATACATA
1 AAATAAA-AAATAATAAAAATATA
* *
5606191 AAATACAAAGAAAAAAAATAAATATA
1 AAATA-AAA-AATAATAA-AAATATA
5606217 AATATAAAAAATAATATAAAATATA
1 AA-ATAAAAAATAATA-AAAATATA
5606242 AAATAAAA
1 AAATAAAA
5606250 GTCAAATTGA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
24 12 0.25
25 22 0.46
26 11 0.23
27 3 0.06
ACGTcount: A:0.75, C:0.02, G:0.01, T:0.22
Consensus pattern (23 bp):
AAATAAAAAATAATAAAAATATA
Found at i:5607001 original size:59 final size:59
Alignment explanation
Indices: 5606909--5607030 Score: 201
Period size: 59 Copynumber: 2.1 Consensus size: 59
5606899 TATTAAGTTT
* *
5606909 TGAATTTTTTATAATTTTATATACAAATGAAATCTCT-TCGTTTAATTATGAAAATTATG
1 TGAATTTTTTATAATTTTATATACAAATGAAATCCCTCT-ATTTAATTATGAAAATTATG
*
5606968 TGAATTTTTTATAATTTTATATGCAAATGAAATCCCTCTATTTAATTATGAAAATTATG
1 TGAATTTTTTATAATTTTATATACAAATGAAATCCCTCTATTTAATTATGAAAATTATG
5607027 TGAA
1 TGAA
5607031 AATTACAATT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 58 0.98
60 1 0.02
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (59 bp):
TGAATTTTTTATAATTTTATATACAAATGAAATCCCTCTATTTAATTATGAAAATTATG
Found at i:5608488 original size:19 final size:19
Alignment explanation
Indices: 5608464--5608511 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
5608454 TGCCTATGAA
5608464 TTTAATTAT-TTAATTATAT
1 TTTAATTATGTTAATTA-AT
5608483 TTTAATT-TGTTAATTAAT
1 TTTAATTATGTTAATTAAT
5608501 TATTCAATTAT
1 T-TT-AATTAT
5608512 CATAACTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 4 0.16
19 16 0.64
20 4 0.16
21 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTAATTATGTTAATTAAT
Found at i:5617202 original size:10 final size:11
Alignment explanation
Indices: 5617167--5617202 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
5617157 TTAAAATTCA
5617167 CAAAAACTAAT
1 CAAAAACTAAT
5617178 C-AAAACTAAT
1 CAAAAACTAAT
5617188 -AAAAAC-AAT
1 CAAAAACTAAT
5617197 CAAAAA
1 CAAAAA
5617203 TGTTCAGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 3 0.13
10 19 0.83
11 1 0.04
ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14
Consensus pattern (11 bp):
CAAAAACTAAT
Found at i:5619550 original size:5 final size:6
Alignment explanation
Indices: 5619520--5619563 Score: 65
Period size: 6 Copynumber: 7.5 Consensus size: 6
5619510 ACAGTAAAAT
5619520 TTTAAA TTTAAA TTTAAA TTTTAAA -TTAAA -TTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTT
5619564 TTTTGTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 10 0.28
6 20 0.56
7 6 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:5619641 original size:25 final size:24
Alignment explanation
Indices: 5619607--5619655 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
5619597 AAAGTTCAAA
5619607 ATTTTTAATTGTAATTT-GATTTTG
1 ATTTTTAATT-TAATTTCGATTTTG
*
5619631 ATTTTTAAATTTAGTTTCGATTTTG
1 ATTTTT-AATTTAATTTCGATTTTG
5619656 TCATTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.24, C:0.02, G:0.12, T:0.61
Consensus pattern (24 bp):
ATTTTTAATTTAATTTCGATTTTG
Found at i:5620690 original size:10 final size:11
Alignment explanation
Indices: 5620665--5620706 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
5620655 CAATCGCAAG
* *
5620665 TTTTTGTTTTG
1 TTTTTATTTTA
5620676 TTTTTATTTTA
1 TTTTTATTTTA
5620687 -TTTTATTTTA
1 TTTTTATTTTA
5620697 TTTTTATTTT
1 TTTTTATTTT
5620707 TTATTTTTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.83
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:5620690 original size:21 final size:21
Alignment explanation
Indices: 5620666--5620706 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5620656 AATCGCAAGT
* *
5620666 TTTTGTTTTGTTTTTATTTTA
1 TTTTATTTTATTTTTATTTTA
5620687 TTTTATTTTATTTTTATTTT
1 TTTTATTTTATTTTTATTTT
5620707 TTATTTTTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.83
Consensus pattern (21 bp):
TTTTATTTTATTTTTATTTTA
Found at i:5620713 original size:5 final size:5
Alignment explanation
Indices: 5620677--5620706 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
5620667 TTTGTTTTGT
5620677 TTTTA TTTTA TTTTA TTTTA TTTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TTTT
5620707 TTATTTTTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:5620912 original size:19 final size:19
Alignment explanation
Indices: 5620848--5620917 Score: 70
Period size: 21 Copynumber: 3.5 Consensus size: 19
5620838 TGATTCATTT
*
5620848 TTGCATGATTATTAATTAA
1 TTGCATGATAATTAATTAA
* *
5620867 TTTGCATGATATTTTATCTTAA
1 -TTGCATGATA-ATTA-ATTAA
5620889 TTGCATGATAATTAA-TATA
1 TTGCATGATAATTAATTA-A
5620908 TTGCATGATA
1 TTGCATGATA
5620918 TTATATTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
18 2 0.05
19 11 0.26
20 12 0.29
21 13 0.31
22 4 0.10
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.47
Consensus pattern (19 bp):
TTGCATGATAATTAATTAA
Found at i:5620934 original size:41 final size:41
Alignment explanation
Indices: 5620847--5620935 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 41
5620837 GTGATTCATT
* * *
5620847 TTTGCATGATTATTAATTAATTTGCATGATATTTTATCTTA
1 TTTGCATGATAATTAATTAATTTGCATGATATTATATATTA
*
5620888 ATTGCATGATAATTAA-T-ATATTGCATGATATTATATTATTA
1 TTTGCATGATAATTAATTAAT-TTGCATGATATTATA-TATTA
5620929 TTTGCAT
1 TTTGCAT
5620936 AGATTATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 2 0.05
40 15 0.37
41 24 0.59
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.51
Consensus pattern (41 bp):
TTTGCATGATAATTAATTAATTTGCATGATATTATATATTA
Found at i:5620941 original size:21 final size:20
Alignment explanation
Indices: 5620847--5620942 Score: 65
Period size: 21 Copynumber: 4.7 Consensus size: 20
5620837 GTGATTCATT
*
5620847 TTTGCATGATTAT-TAATTAA
1 TTTGCATGATTATATTATT-A
*
5620867 TTTGCATGA-TATTTTATCTTA
1 TTTGCATGATTATATTA--TTA
* *
5620888 ATTGCATGA-TA-ATTAATA
1 TTTGCATGATTATATTATTA
5620906 TATTGCATGATATTATATTATTA
1 T-TTGCATG--ATTATATTATTA
5620929 TTTGCATAGATTAT
1 TTTGCAT-GATTAT
5620943 TTTGCATGGT
Statistics
Matches: 61, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
18 2 0.03
19 10 0.16
20 14 0.23
21 17 0.28
22 10 0.16
23 8 0.13
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTGCATGATTATATTATTA
Found at i:5622246 original size:20 final size:20
Alignment explanation
Indices: 5622221--5622321 Score: 73
Period size: 20 Copynumber: 5.1 Consensus size: 20
5622211 ACCCTTTGTG
5622221 TTGTTCTTTGTATTTATATA
1 TTGTTCTTTGTATTTATATA
* *
5622241 TTGTTCTTTGTATATATCATG
1 TTGTTCTTTGTATTTAT-ATA
* **** * *
5622262 TT-TACTAACCA-TT-TGTG
1 TTGTTCTTTGTATTTATATA
5622279 TTGTTCTTTGTATTTATATA
1 TTGTTCTTTGTATTTATATA
*
5622299 TTGTTCTTTGTATATATCATA
1 TTGTTCTTTGTATTTAT-ATA
5622320 TT
1 TT
5622322 TACTAACCCA
Statistics
Matches: 59, Mismatches: 17, Indels: 9
0.69 0.20 0.11
Matches are distributed among these distances:
17 4 0.07
18 5 0.08
19 3 0.05
20 38 0.64
21 9 0.15
ACGTcount: A:0.21, C:0.09, G:0.11, T:0.59
Consensus pattern (20 bp):
TTGTTCTTTGTATTTATATA
Found at i:5622269 original size:58 final size:58
Alignment explanation
Indices: 5622188--5622330 Score: 232
Period size: 58 Copynumber: 2.4 Consensus size: 58
5622178 TTTTTATTTC
* *
5622188 TTGTATATATTATTTGTATACTAACCCTTTGTGTTGTTCTTTGTATTTATATATTGTTCT
1 TTGTATATATCA--TGTTTACTAACCCTTTGTGTTGTTCTTTGTATTTATATATTGTTCT
*
5622248 TTGTATATATCATGTTTACTAACCATTTGTGTTGTTCTTTGTATTTATATATTGTTCT
1 TTGTATATATCATGTTTACTAACCCTTTGTGTTGTTCTTTGTATTTATATATTGTTCT
*
5622306 TTGTATATATCATATTTACTAACCC
1 TTGTATATATCATGTTTACTAACCC
5622331 ATTTCTTTCA
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
58 67 0.86
60 11 0.14
ACGTcount: A:0.22, C:0.12, G:0.10, T:0.55
Consensus pattern (58 bp):
TTGTATATATCATGTTTACTAACCCTTTGTGTTGTTCTTTGTATTTATATATTGTTCT
Found at i:5625901 original size:69 final size:69
Alignment explanation
Indices: 5625815--5625967 Score: 227
Period size: 69 Copynumber: 2.2 Consensus size: 69
5625805 TCCTTGATAA
* * *
5625815 TTACATTTGCATCATGGTTAGGGCATGTATTCACATTATGTACAGAACATTTGAATCATAGTAGG
1 TTACATTTGCATCATGGTTAGGGCATGCATTCACATCATGTAAAGAACATTTGAATCATAGTAGG
*
5625880 ACAT
66 AAAT
*
5625884 TTACATTTGCAAT-ATGGTTAGGGCATGCATTTACATCATGTAAAGAACATTTGAATCATAGTAG
1 TTACATTTGC-ATCATGGTTAGGGCATGCATTCACATCATGTAAAGAACATTTGAATCATAGTAG
5625948 GAAAT
65 GAAAT
* *
5625953 TTGCATTAGCATCAT
1 TTACATTTGCATCAT
5625968 TTAGTAAGAA
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
68 2 0.03
69 71 0.95
70 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (69 bp):
TTACATTTGCATCATGGTTAGGGCATGCATTCACATCATGTAAAGAACATTTGAATCATAGTAGG
AAAT
Found at i:5626487 original size:18 final size:17
Alignment explanation
Indices: 5626464--5626620 Score: 109
Period size: 18 Copynumber: 8.9 Consensus size: 17
5626454 ATCTTTTGAA
5626464 TGTGAATCATTAAATTCT
1 TGTGAATC-TTAAATTCT
5626482 TGTGAATCATTAAATTCT
1 TGTGAATC-TTAAATTCT
5626500 TGTGAAT-TTGAAATTCT
1 TGTGAATCTT-AAATTCT
*
5626517 TGTGAATCTTTAAATTTT
1 TGTGAATC-TTAAATTCT
** * *
5626535 TACGAATCTAAAAATCT
1 TGTGAATCTTAAATTCT
* *
5626552 TATGAATCTTGCAATTCT
1 TGTGAATCTT-AAATTCT
** *
5626570 TGCAAATTTTTAAATTCT
1 TGTGAA-TCTTAAATTCT
* * *
5626588 TATGAATATGAAATTCT
1 TGTGAATCTTAAATTCT
**
5626605 TGCAAATCTTTAAATT
1 TGTGAATC-TTAAATT
5626621 TTTGCAAATC
Statistics
Matches: 108, Mismatches: 25, Indels: 12
0.74 0.17 0.08
Matches are distributed among these distances:
16 2 0.02
17 41 0.38
18 60 0.56
19 5 0.05
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (17 bp):
TGTGAATCTTAAATTCT
Found at i:5626523 original size:53 final size:54
Alignment explanation
Indices: 5626464--5626620 Score: 158
Period size: 53 Copynumber: 3.0 Consensus size: 54
5626454 ATCTTTTGAA
* * *
5626464 TGTGAATCATTAAATTCTTGTGAATCATTAAATTCTTGTGAAT-TTGAAATTCT
1 TGTGAATCTTTAAATTCTTATGAATCATAAAATTCTTGTGAATCTTGAAATTCT
* * * * *
5626517 TGTGAATCTTTAAATTTTTACGAATC-TAAAAATCTTATGAATCTTGCAATTCT
1 TGTGAATCTTTAAATTCTTATGAATCATAAAATTCTTGTGAATCTTGAAATTCT
** * * ** *
5626570 TGCAAATTTTTAAATTCTTATGAAT-ATGAAATTCTTGCAAATCTTTAAATT
1 TGTGAATCTTTAAATTCTTATGAATCATAAAATTCTTGTGAATCTTGAAATT
5626621 TTTGCAAATC
Statistics
Matches: 82, Mismatches: 20, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
52 13 0.16
53 69 0.84
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (54 bp):
TGTGAATCTTTAAATTCTTATGAATCATAAAATTCTTGTGAATCTTGAAATTCT
Found at i:5626608 original size:35 final size:36
Alignment explanation
Indices: 5626468--5626620 Score: 132
Period size: 35 Copynumber: 4.3 Consensus size: 36
5626458 TTTGAATGTG
* * * **
5626468 AATCATTAAATTCTTGTGAATCATTAAATTCTTGTG
1 AATCTTTAAATTCTTATGAATCATGAAATTCTTGCA
* * * * * * *
5626504 AAT-TTGAAATTCTTGTGAATCTTTAAATTTTTACG
1 AATCTTTAAATTCTTATGAATCATGAAATTCTTGCA
* * * *
5626539 AATC-TAAAAATCTTATGAATCTTGCAATTCTTGCA
1 AATCTTTAAATTCTTATGAATCATGAAATTCTTGCA
*
5626574 AATTTTTAAATTCTTATGAAT-ATGAAATTCTTGCA
1 AATCTTTAAATTCTTATGAATCATGAAATTCTTGCA
5626609 AATCTTTAAATT
1 AATCTTTAAATT
5626621 TTTGCAAATC
Statistics
Matches: 95, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
35 78 0.82
36 17 0.18
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.44
Consensus pattern (36 bp):
AATCTTTAAATTCTTATGAATCATGAAATTCTTGCA
Found at i:5626642 original size:35 final size:35
Alignment explanation
Indices: 5626568--5626648 Score: 85
Period size: 35 Copynumber: 2.3 Consensus size: 35
5626558 TCTTGCAATT
* **
5626568 CTTGCAAATTTTTAAATTCTTATGAATATGAAATT
1 CTTGCAAATCTTTAAATTCTTATGAATATGAAAAC
*
5626603 CTTGCAAATCTTTAAATT-TT-TGCAAATCTGAAAAC
1 CTTGCAAATCTTTAAATTCTTATG--AATATGAAAAC
*
5626638 CTTGCGAATCT
1 CTTGCAAATCT
5626649 AAAAGTCTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
33 2 0.05
34 2 0.05
35 35 0.90
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41
Consensus pattern (35 bp):
CTTGCAAATCTTTAAATTCTTATGAATATGAAAAC
Found at i:5626658 original size:17 final size:17
Alignment explanation
Indices: 5626633--5626676 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
5626623 TGCAAATCTG
*
5626633 AAAAC-CTTGCGAATCT
1 AAAACTCTTGCGAACCT
* *
5626649 AAAAGTCTTGAGAACCT
1 AAAACTCTTGCGAACCT
5626666 AAAACTCTTGC
1 AAAACTCTTGC
5626677 AAGCTAGAAG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.25
Consensus pattern (17 bp):
AAAACTCTTGCGAACCT
Found at i:5626816 original size:33 final size:33
Alignment explanation
Indices: 5626755--5626819 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
5626745 AATCTGAAAA
* *
5626755 ATCTTGCAAATCTGAACCTTTTGTGAAACTTAG
1 ATCTTGCAAATCTGAACCTTTCGCGAAACTTAG
5626788 ATCTTGCAAATCTGAAACC-TTCGCGAAACTTA
1 ATCTTGCAAATCTG-AACCTTTCGCGAAACTTA
5626820 AAGAGACTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (33 bp):
ATCTTGCAAATCTGAACCTTTCGCGAAACTTAG
Found at i:5627285 original size:20 final size:20
Alignment explanation
Indices: 5627231--5627287 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 20
5627221 TTTACATGAT
*
5627231 ATGATTATATATTTTATTTGT
1 ATGATTATATA-TTTATTTGC
5627252 ATGATTGTTAATATATTTATTTGC
1 ATGA---TT-ATATATTTATTTGC
5627276 ATGATTATATAT
1 ATGATTATATAT
5627288 CATTTTGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
20 6 0.19
21 6 0.19
24 14 0.45
25 5 0.16
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.56
Consensus pattern (20 bp):
ATGATTATATATTTATTTGC
Found at i:5627396 original size:19 final size:21
Alignment explanation
Indices: 5627311--5627409 Score: 84
Period size: 21 Copynumber: 5.0 Consensus size: 21
5627301 TGATTCATTT
*
5627311 TTGCATGATTATT-A-ATTAA
1 TTGCATGATAATTAATATTAA
* * * *
5627330 TTTACATGATATTTTATCTTAA
1 -TTGCATGATAATTAATATTAA
* *
5627352 TTGCATGATAGTTTATATTAA
1 TTGCATGATAATTAATATTAA
5627373 TTGCATGATAATTAATA-T-A
1 TTGCATGATAATTAATATTAA
5627392 TTGCATGAT-ATT-ATATTA
1 TTGCATGATAATTAATATTA
5627410 TTATCTGCAT
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.05
18 4 0.06
19 10 0.15
20 11 0.17
21 34 0.52
22 4 0.06
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (21 bp):
TTGCATGATAATTAATATTAA
Found at i:5628740 original size:7 final size:7
Alignment explanation
Indices: 5628724--5628758 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
5628714 TAATATCTTA
5628724 TAAA-TT
1 TAAATTT
5628730 TAAATTT
1 TAAATTT
5628737 TAAATTT
1 TAAATTT
5628744 TAAATTT
1 TAAATTT
5628751 TAATATTT
1 TAA-ATTT
5628759 ATAATTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 4 0.15
7 19 0.70
8 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TAAATTT
Found at i:5628759 original size:14 final size:13
Alignment explanation
Indices: 5628724--5628765 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 13
5628714 TAATATCTTA
5628724 TAAATTTAAATTT
1 TAAATTTAAATTT
5628737 TAAATTTTAAATTT
1 TAAA-TTTAAATTT
5628751 TAATATTTATAATTT
1 TAA-ATTTA-AATTT
5628766 CTTTCTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.15
14 16 0.62
15 6 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TAAATTTAAATTT
Found at i:5629171 original size:26 final size:26
Alignment explanation
Indices: 5629142--5629194 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
5629132 TTTAAGTTCA
* *
5629142 AATTTTAT-TTTATATTTATTTGGTTT
1 AATTTTATGTTGA-ATTTATTTAGTTT
5629168 AATTTTATGTTGAATTTATTTAGTTT
1 AATTTTATGTTGAATTTATTTAGTTT
5629194 A
1 A
5629195 TTGATTTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.64
Consensus pattern (26 bp):
AATTTTATGTTGAATTTATTTAGTTT
Found at i:5629955 original size:38 final size:41
Alignment explanation
Indices: 5629913--5630002 Score: 107
Period size: 38 Copynumber: 2.3 Consensus size: 41
5629903 TTAAACAAAA
* *
5629913 TTAAAAATAATATTTGT-AAAGTTTGAATTT-TA-AATTTT
1 TTAAAAATAATATTTGTAAAAATTTGAATTTATATAATATT
* *
5629951 TTAAAAAT-ATATTTTTAAAAATTTTAATTTAATATAATATT
1 TTAAAAATAATATTTGTAAAAATTTGAATTT-ATATAATATT
5629992 TTAAAAATAAT
1 TTAAAAATAAT
5630003 GATCAAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
37 7 0.16
38 19 0.44
40 2 0.05
41 13 0.30
42 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (41 bp):
TTAAAAATAATATTTGTAAAAATTTGAATTTATATAATATT
Found at i:5632239 original size:18 final size:19
Alignment explanation
Indices: 5632189--5632239 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
5632179 ATGTAATAAT
*
5632189 AAATCTTATAATAATAGTA
1 AAATTTTATAATAATAGTA
*
5632208 AAATTTTATCATAATA-TA
1 AAATTTTATAATAATAGTA
5632226 AATATTTTA-AATAA
1 AA-ATTTTATAATAA
5632240 AAATCACACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (19 bp):
AAATTTTATAATAATAGTA
Found at i:5632498 original size:73 final size:73
Alignment explanation
Indices: 5632374--5632511 Score: 170
Period size: 73 Copynumber: 1.9 Consensus size: 73
5632364 ATATTTTTAA
* * * * * * *
5632374 ATATTTTTAACAAAGATCATATTTTTAATTTACAAACATCATTTTTATTGAATTTTAAAAATTAA
1 ATATTTTCAACAAAAATCACATTTTTAATTTAAAAACATCATCTTTATTGAACTCTAAAAATTAA
5632439 TTTTGTTC
66 TTTTGTTC
* * *
5632447 ATATTTTCAACAAAAATCACATTTTT-ATCTTAAAAATATTATCTTTGTTGAACTCTAAAAATTA
1 ATATTTTCAACAAAAATCACATTTTTAAT-TTAAAAACATCATCTTTATTGAACTCTAAAAATTA
5632511 A
65 A
5632512 ATAAGAATAA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
72 2 0.04
73 52 0.96
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.46
Consensus pattern (73 bp):
ATATTTTCAACAAAAATCACATTTTTAATTTAAAAACATCATCTTTATTGAACTCTAAAAATTAA
TTTTGTTC
Found at i:5634583 original size:21 final size:20
Alignment explanation
Indices: 5634551--5634598 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 20
5634541 ACTTATATCT
5634551 AAATCTATTTAAAT-ATATTAA
1 AAAT-TATTTAAATAATA-TAA
5634572 AAATTATATTAAATAATATAA
1 AAATTAT-TTAAATAATATAA
5634593 AAATTA
1 AAATTA
5634599 AATTTCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.12
21 19 0.76
22 3 0.12
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATTATTTAAATAATATAA
Found at i:5635525 original size:16 final size:17
Alignment explanation
Indices: 5635494--5635528 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5635484 ATAAGATAAT
5635494 TTATTTATTGATCAAAA
1 TTATTTATTGATCAAAA
*
5635511 TTATTT-TTTATCAAAA
1 TTATTTATTGATCAAAA
5635527 TT
1 TT
5635529 TATATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (17 bp):
TTATTTATTGATCAAAA
Found at i:5635531 original size:17 final size:18
Alignment explanation
Indices: 5635491--5635531 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
5635481 AGTATAAGAT
5635491 AATTTATTTATTGATCAA
1 AATTTATTTATTGATCAA
*
5635509 AA-TTATTT-TTTATCAA
1 AATTTATTTATTGATCAA
5635525 AATTTAT
1 AATTTAT
5635532 ATAATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 9 0.43
17 10 0.48
18 2 0.10
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (18 bp):
AATTTATTTATTGATCAA
Found at i:5639474 original size:21 final size:21
Alignment explanation
Indices: 5639450--5639494 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5639440 AAACAATAAA
* *
5639450 AAAAATGTGATTTTTCAATCT
1 AAAAATGTGATTTGTAAATCT
* *
5639471 AAAAGTTTGATTTGTAAATCT
1 AAAAATGTGATTTGTAAATCT
5639492 AAA
1 AAA
5639495 TAAAAAAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (21 bp):
AAAAATGTGATTTGTAAATCT
Found at i:5643650 original size:17 final size:17
Alignment explanation
Indices: 5643624--5643682 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
5643614 TCTATTTGTT
*
5643624 ATTTTTTTTTGTTATTA
1 ATTTTATTTTGTTATTA
5643641 ATTTTATTTT-TTATTAA
1 ATTTTATTTTGTTATT-A
* *
5643658 ATTTT-TTTGGTTTTTA
1 ATTTTATTTTGTTATTA
5643674 A-TTTATTTT
1 ATTTTATTTT
5643683 TAATTAGATA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
15 3 0.09
16 13 0.37
17 19 0.54
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (17 bp):
ATTTTATTTTGTTATTA
Found at i:5643679 original size:32 final size:33
Alignment explanation
Indices: 5643626--5643688 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
5643616 TATTTGTTAT
* *
5643626 TTTTTTTTGTTATTAATTTTATTTTTTATTAAA
1 TTTTTTTGGTTATTAATTTTATTTTTAATTAAA
*
5643659 TTTTTTTGGTTTTTAA-TTTATTTTTAATTA
1 TTTTTTTGGTTATTAATTTTATTTTTAATTA
5643689 GATAAAGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (33 bp):
TTTTTTTGGTTATTAATTTTATTTTTAATTAAA
Found at i:5646937 original size:4 final size:4
Alignment explanation
Indices: 5646920--5646994 Score: 59
Period size: 4 Copynumber: 18.5 Consensus size: 4
5646910 CAATCTCAAT
*
5646920 TAAA -AAA T-AA TAAA TAAA -AAA CAGAA TAAA TAAAA TAAA TAAA TAAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TA-AA TAAA T-AAA TAAA TAAA T-AAA
*
5646968 TAAAA TAAA -AAA TATAA AAAA TAAA TA
1 T-AAA TAAA TAAA TA-AA TAAA TAAA TA
5646995 TAAAAACCTA
Statistics
Matches: 60, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
3 12 0.20
4 29 0.48
5 19 0.32
ACGTcount: A:0.77, C:0.01, G:0.01, T:0.20
Consensus pattern (4 bp):
TAAA
Found at i:5646957 original size:5 final size:5
Alignment explanation
Indices: 5646947--5646986 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
5646937 AAAACAGAAT
*
5646947 AAATA AAAT- AAAT- AAATA AAATA AAATA AAA-A ATATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAA
5646987 AATAAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 11 0.35
5 20 0.65
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:5646958 original size:9 final size:9
Alignment explanation
Indices: 5646944--5646994 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
5646934 TAAAAAACAG
5646944 AATAAATAA
1 AATAAATAA
5646953 AATAAAT-A
1 AATAAATAA
5646961 AATAAAATAA
1 AAT-AAATAA
5646971 AAT-AA-AA
1 AATAAATAA
5646978 AATATAA-AA
1 AATA-AATAA
5646987 AATAAATA
1 AATAAATA
5646995 TAAAAACCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
7 5 0.14
8 8 0.22
9 20 0.54
10 4 0.11
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
AATAAATAA
Found at i:5646962 original size:13 final size:14
Alignment explanation
Indices: 5646944--5646998 Score: 73
Period size: 13 Copynumber: 4.1 Consensus size: 14
5646934 TAAAAAACAG
5646944 AATAAATAAA-ATA
1 AATAAATAAATATA
5646957 AATAAATAAA-ATAA
1 AATAAATAAATAT-A
5646971 AATAAA-AAATATA
1 AATAAATAAATATA
5646984 AA-AAATAAATATA
1 AATAAATAAATATA
5646997 AA
1 AA
5646999 AACCTATGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.08
13 27 0.69
14 9 0.23
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAAATAAATATA
Found at i:5648221 original size:43 final size:43
Alignment explanation
Indices: 5648131--5648228 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 43
5648121 CGACAAAGCA
5648131 TTTGAAACTTTGGAATTTTAAAATCCTCTCCCTCAACAAAATC
1 TTTGAAACTTTGGAATTTTAAAATCCTCTCCCTCAACAAAATC
* * * * **
5648174 TTTGAAATTTTGGAATTTTAAAATGCTCTTCCTTAACAGAGGT-
1 TTTGAAACTTTGGAATTTTAAAATCCTCTCCCTCAACA-AAATC
5648217 TTTGAAACTTTG
1 TTTGAAACTTTG
5648229 AAGTTTTTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 45 0.96
44 2 0.04
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (43 bp):
TTTGAAACTTTGGAATTTTAAAATCCTCTCCCTCAACAAAATC
Found at i:5648891 original size:28 final size:27
Alignment explanation
Indices: 5648859--5648920 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
5648849 TTGATGTTGG
*
5648859 TGCAAATACTTATCTCAC-CAAATAAAAA
1 TGCAAATACTT-TC-CACAAAAATAAAAA
* *
5648887 TGCAAATGCTTTCCACAAAAATGAAAA
1 TGCAAATACTTTCCACAAAAATAAAAA
5648914 TGCAAAT
1 TGCAAAT
5648921 CTCATCATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 3 0.10
27 17 0.57
28 10 0.33
ACGTcount: A:0.48, C:0.19, G:0.08, T:0.24
Consensus pattern (27 bp):
TGCAAATACTTTCCACAAAAATAAAAA
Found at i:5649042 original size:177 final size:177
Alignment explanation
Indices: 5648739--5649096 Score: 628
Period size: 177 Copynumber: 2.0 Consensus size: 177
5648729 AGTTGGGTTT
5648739 AAATCTCATCATGTGCCAACTAATCTTAAATCTTGTCTTTTTTATTCTTTCTTCACTTTAAAGTT
1 AAATCTCATCATGTGCCAACTAATCTTAAATCTTGTCTTTTTTATTCTTTCTTCACTTTAAAGTT
* * *
5648804 TGCAAAAATACAAATGTCATGATATGAATGCCAATGTATCCTACCTTGATGTTGGTGCAAATACT
66 TGCAAAAATACAAATGTCATGATATGAATGCCAATGTATCCTACCCTAATGTTGATGCAAATACT
5648869 TATCTCACCAAATAAAAATGCAAATGCTTTCCACAAAAATGAAAATGC
131 TATCTCA-CAAATAAAAATGCAAATGCTTTCCACAAAAATGAAAATGC
* *
5648917 AAATCTCATCATGTGCCAGCTAATCTTAAATCTTGTC-TTTTTGTTCTTTCTTCACTTTAAAGTT
1 AAATCTCATCATGTGCCAACTAATCTTAAATCTTGTCTTTTTTATTCTTTCTTCACTTTAAAGTT
5648981 TGCAAAAATACAAATGTCATGATATGAATGCCAATGTATCCTACCCTAATGTTGATGCAAATACT
66 TGCAAAAATACAAATGTCATGATATGAATGCCAATGTATCCTACCCTAATGTTGATGCAAATACT
* * *
5649046 TATCTCACTAATATAAATGCAAATGCTTTCCACAAAAATGAAAATGT
131 TATCTCACAAATAAAAATGCAAATGCTTTCCACAAAAATGAAAATGC
5649093 AAAT
1 AAAT
5649097 ATTTATCTCA
Statistics
Matches: 172, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
176 41 0.24
177 95 0.55
178 36 0.21
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (177 bp):
AAATCTCATCATGTGCCAACTAATCTTAAATCTTGTCTTTTTTATTCTTTCTTCACTTTAAAGTT
TGCAAAAATACAAATGTCATGATATGAATGCCAATGTATCCTACCCTAATGTTGATGCAAATACT
TATCTCACAAATAAAAATGCAAATGCTTTCCACAAAAATGAAAATGC
Found at i:5649386 original size:71 final size:69
Alignment explanation
Indices: 5649245--5649391 Score: 170
Period size: 71 Copynumber: 2.1 Consensus size: 69
5649235 TCTAATTGAG
* * * * *
5649245 ATGCAAATGCAATATTCAAACAATGATTTAGATGCTCACCAAATGACGTAAATGCATGGTACAAA
1 ATGCAAATGCAATATTAAAACAATGATTTAAATCCTCACCAAAAGACGCAAATGCATGGTA-AAA
5649310 AAATT
65 AAATT
** *
5649315 ATGCAAATGCAATATTTAAAACAATGATTTAAATCCTCATGAAAAGATGCAAATGCATGAGCT-A
1 ATGCAAATGCAATA-TTAAAACAATGATTTAAATCCTCACCAAAAGACGCAAATGCATG-G-TAA
*
5649379 AACAATT
63 AAAAATT
5649386 ATGCAA
1 ATGCAA
5649392 TTTGTAAATT
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
70 14 0.22
71 49 0.75
72 1 0.02
73 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.26
Consensus pattern (69 bp):
ATGCAAATGCAATATTAAAACAATGATTTAAATCCTCACCAAAAGACGCAAATGCATGGTAAAAA
AATT
Found at i:5649420 original size:50 final size:50
Alignment explanation
Indices: 5649361--5649490 Score: 170
Period size: 50 Copynumber: 2.6 Consensus size: 50
5649351 TCATGAAAAG
*
5649361 ATGCAAATGCATGAGCTAAACAATTATGCAATTTGTAAATTCCCTAAATA
1 ATGCAAATGCATGATCTAAACAATTATGCAATTTGTAAATTCCCTAAATA
* * *** *
5649411 ATGCAAATGCAAGATCTAAACAATTATGCAATTTTTAAATTTGTTAAATG
1 ATGCAAATGCATGATCTAAACAATTATGCAATTTGTAAATTCCCTAAATA
* * *
5649461 ATGTAAATGCATGATCCAAATAATTATGCA
1 ATGCAAATGCATGATCTAAACAATTATGCA
5649491 GATGCAATTA
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 69 1.00
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.32
Consensus pattern (50 bp):
ATGCAAATGCATGATCTAAACAATTATGCAATTTGTAAATTCCCTAAATA
Found at i:5649675 original size:21 final size:20
Alignment explanation
Indices: 5649645--5649683 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5649635 TGGTAACAAC
5649645 AATTACCCCAAATTAATAAAA
1 AATTACCCCAAA-TAATAAAA
* *
5649666 AATTATCCCACATAATAA
1 AATTACCCCAAATAATAA
5649684 TTTTTCATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.54, C:0.21, G:0.00, T:0.26
Consensus pattern (20 bp):
AATTACCCCAAATAATAAAA
Found at i:5656695 original size:24 final size:27
Alignment explanation
Indices: 5656665--5656729 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 27
5656655 ATGTAAGGAT
5656665 ATCATGCAATAAA-A-TATAAA-AAAA
1 ATCATGCAATAAATATTATAAATAAAA
* *
5656689 ATCATGCAA-AAATATTATAAATCATA
1 ATCATGCAATAAATATTATAAATAAAA
5656715 ATCATGCAAATAAAT
1 ATCATGC-AATAAAT
5656730 TAAATTCATG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 3 0.09
24 10 0.29
25 6 0.18
26 9 0.26
27 2 0.06
28 4 0.12
ACGTcount: A:0.58, C:0.11, G:0.05, T:0.26
Consensus pattern (27 bp):
ATCATGCAATAAATATTATAAATAAAA
Found at i:5656729 original size:19 final size:19
Alignment explanation
Indices: 5656705--5656743 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5656695 CAAAAATATT
5656705 ATAAATCATAA-TCATGCAA
1 ATAAATCA-AATTCATGCAA
*
5656724 ATAAATTAAATTCATGCAA
1 ATAAATCAAATTCATGCAA
5656743 A
1 A
5656744 ATTATCATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.54, C:0.13, G:0.05, T:0.28
Consensus pattern (19 bp):
ATAAATCAAATTCATGCAA
Found at i:5656731 original size:26 final size:25
Alignment explanation
Indices: 5656665--5656731 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 25
5656655 ATGTAAGGAT
*
5656665 ATCATGC-AATAAAATATAAAAAAA
1 ATCATGCAAATAAATTATAAAAAAA
* *
5656689 ATCATGCAAA-AATATTATAAATCATA
1 ATCATGCAAATAA-ATTATAAA-AAAA
5656715 ATCATGCAAATAAATTA
1 ATCATGCAAATAAATTA
5656732 AATTCATGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
24 9 0.25
25 9 0.25
26 16 0.44
27 2 0.06
ACGTcount: A:0.58, C:0.10, G:0.04, T:0.27
Consensus pattern (25 bp):
ATCATGCAAATAAATTATAAAAAAA
Found at i:5656751 original size:32 final size:29
Alignment explanation
Indices: 5656726--5656781 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
5656716 TCATGCAAAT
*
5656726 AAAT-TAAATTCATGCAAAATTATCATAC
1 AAATATAAATTCATGCAAAAATATCATAC
*
5656754 AAATATATATTCATGCAAAAATATCATA
1 AAATATAAATTCATGCAAAAATATCATA
5656782 ACATAATCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.32
Consensus pattern (29 bp):
AAATATAAATTCATGCAAAAATATCATAC
Found at i:5656772 original size:16 final size:15
Alignment explanation
Indices: 5656733--5656777 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 15
5656723 AATAAATTAA
5656733 ATTCATGCAAAAT-T
1 ATTCATGCAAAATAT
*
5656747 A-TCATACAAATATAT
1 ATTCATGCAAA-ATAT
5656762 ATTCATGCAAAA-AT
1 ATTCATGCAAAATAT
5656776 AT
1 AT
5656778 CATAACATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 8 0.31
14 7 0.27
15 3 0.12
16 8 0.31
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.33
Consensus pattern (15 bp):
ATTCATGCAAAATAT
Found at i:5656966 original size:28 final size:26
Alignment explanation
Indices: 5656927--5656979 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
5656917 ATTTTAGTTA
5656927 AAAAATAAT-AAATAGAAAATAGAAAAG
1 AAAAATAATAAAATA-AAAATA-AAAAG
5656954 AAAAATAAATAAAATAAAAATAAAAA
1 AAAAAT-AATAAAATAAAAATAAAAA
5656980 CATATGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 10 0.42
28 9 0.38
29 5 0.21
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (26 bp):
AAAAATAATAAAATAAAAATAAAAAG
Found at i:5665472 original size:14 final size:14
Alignment explanation
Indices: 5665453--5665492 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
5665443 CAAAAAATTA
5665453 TTCAAAGTTATATT
1 TTCAAAGTTATATT
5665467 TTCAAAGTTATATT
1 TTCAAAGTTATATT
5665481 TTCAAAGTTATA
1 TTCAAAGTTATA
5665493 AAGCCTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (14 bp):
TTCAAAGTTATATT
Found at i:5665672 original size:44 final size:44
Alignment explanation
Indices: 5665602--5665722 Score: 154
Period size: 44 Copynumber: 2.7 Consensus size: 44
5665592 AATGTTTAAA
* * *
5665602 TTTTTAAAAGTTATTGAGCTTCTATTTAGAGGAGCCTTTTATAT
1 TTTTTAAAAGTTGTTAAGCTTCTATTTAGAGAAGCCTTTTATAT
*
5665646 TTTTTAAAAATTGTTAAGCCTT-TATTTAGAGAAGCCTTTTATAT
1 TTTTTAAAAGTTGTTAAG-CTTCTATTTAGAGAAGCCTTTTATAT
*
5665690 TTTTCAAAAGTTGTTGTTAAGCTTCTATTTAGA
1 TTTTTAAAA---GTTGTTAAGCTTCTATTTAGA
5665723 TGAGCTTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
44 44 0.67
45 3 0.05
46 3 0.05
47 16 0.24
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.48
Consensus pattern (44 bp):
TTTTTAAAAGTTGTTAAGCTTCTATTTAGAGAAGCCTTTTATAT
Found at i:5665743 original size:47 final size:47
Alignment explanation
Indices: 5665624--5665745 Score: 121
Period size: 44 Copynumber: 2.7 Consensus size: 47
5665614 ATTGAGCTTC
* * * *
5665624 TATTTAGAGGAGCCTTTTATATTTTTTAAAA---ATTGTTAAGCCTT
1 TATTTAGAGAAGCCTTTTATATTGTTCAAAAGTTGTTGTTAAGCCTT
*
5665668 TATTTAGAGAAGCCTTTTATATTTTTCAAAAGTTGTTGTTAAG-CTT
1 TATTTAGAGAAGCCTTTTATATTGTTCAAAAGTTGTTGTTAAGCCTT
*
5665714 CTATTTAGATG-AG-CTTTTCATGTTGTTCAAAA
1 -TATTTAGA-GAAGCCTTTT-ATATTGTTCAAAA
5665746 AGTTTGAGTT
Statistics
Matches: 67, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
44 29 0.43
46 8 0.12
47 29 0.43
48 1 0.01
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.47
Consensus pattern (47 bp):
TATTTAGAGAAGCCTTTTATATTGTTCAAAAGTTGTTGTTAAGCCTT
Found at i:5667480 original size:19 final size:19
Alignment explanation
Indices: 5667449--5667489 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
5667439 TTATGCTTAT
*
5667449 TAAA-TAGATTTGAATAAA
1 TAAATTAGACTTGAATAAA
*
5667467 TAAATTAGACTTGATTAAA
1 TAAATTAGACTTGAATAAA
5667486 -AAAT
1 TAAAT
5667490 AATATCGAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.34
Consensus pattern (19 bp):
TAAATTAGACTTGAATAAA
Found at i:5668910 original size:10 final size:10
Alignment explanation
Indices: 5668895--5668924 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5668885 TAAATCGTAT
5668895 TATTTTTATA
1 TATTTTTATA
5668905 TATTTTTAT-
1 TATTTTTATA
5668914 TATTTTTATA
1 TATTTTTATA
5668924 T
1 T
5668925 TATATTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TATTTTTATA
Found at i:5668925 original size:11 final size:11
Alignment explanation
Indices: 5668892--5668938 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
5668882 TTTTAAATCG
5668892 TATTATTTTTA
1 TATTATTTTTA
5668903 TA-TA-TTTT-
1 TATTATTTTTA
5668911 TATTATTTTTA
1 TATTATTTTTA
5668922 TATTATATTATTA
1 TATTAT-TT-TTA
5668935 TATT
1 TATT
5668939 GTGTGAAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 2 0.06
9 6 0.19
10 6 0.19
11 8 0.26
12 2 0.06
13 7 0.23
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTATTTTTA
Found at i:5668932 original size:19 final size:19
Alignment explanation
Indices: 5668892--5668935 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
5668882 TTTTAAATCG
*
5668892 TATTATTTTTATATATTTT
1 TATTATTTTTATATATTAT
5668911 TATTATTTTTATAT-TATAT
1 TATTATTTTTATATAT-TAT
5668930 TATTAT
1 TATTAT
5668936 ATTGTGTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TATTATTTTTATATATTAT
Found at i:5678640 original size:9 final size:9
Alignment explanation
Indices: 5678626--5678655 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
5678616 TAATAATTTT
5678626 TAATTAAAA
1 TAATTAAAA
5678635 TAATTAAAA
1 TAATTAAAA
5678644 TATATTAAAA
1 TA-ATTAAAA
5678654 TA
1 TA
5678656 TAAAAATTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAA
Found at i:5678652 original size:10 final size:10
Alignment explanation
Indices: 5678628--5678657 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5678618 ATAATTTTTA
5678628 ATTAAAATA-
1 ATTAAAATAT
5678637 ATTAAAATAT
1 ATTAAAATAT
5678647 ATTAAAATAT
1 ATTAAAATAT
5678657 A
1 A
5678658 AAAATTCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:5679368 original size:18 final size:19
Alignment explanation
Indices: 5679332--5679374 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
5679322 TAGAATGAAA
5679332 TTATATATTTTTATTAATTT
1 TTATATATTTTTA-TAATTT
5679352 TTATATATTTTTA-AATTT
1 TTATATATTTTTATAATTT
5679370 TTATA
1 TTATA
5679375 AAATAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 10 0.43
20 13 0.57
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATATATTTTTATAATTT
Found at i:5679371 original size:8 final size:9
Alignment explanation
Indices: 5679332--5679375 Score: 54
Period size: 10 Copynumber: 4.7 Consensus size: 9
5679322 TAGAATGAAA
5679332 TTATATATTT
1 TTATA-ATTT
5679342 TTATTAATTT
1 TTA-TAATTT
5679352 TTATATATTT
1 TTATA-ATTT
5679362 TTA-AATTT
1 TTATAATTT
5679370 TTATAA
1 TTATAA
5679376 AATAAAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 7 0.23
9 5 0.16
10 17 0.55
11 2 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TTATAATTT
Found at i:5680235 original size:13 final size:13
Alignment explanation
Indices: 5680219--5680246 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5680209 TTTAAAAATT
5680219 AAAAAAAAAAAGA
1 AAAAAAAAAAAGA
5680232 AAAAAAAAAAAGA
1 AAAAAAAAAAAGA
5680245 AA
1 AA
5680247 GAAAGAAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGA
Found at i:5691659 original size:14 final size:14
Alignment explanation
Indices: 5691632--5691664 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5691622 AATTAAAAGT
5691632 AATG-ATAAAAATA
1 AATGTATAAAAATA
*
5691645 AATGTATAAATATA
1 AATGTATAAAAATA
5691659 AATGTA
1 AATGTA
5691665 ATTATGATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (14 bp):
AATGTATAAAAATA
Found at i:5706119 original size:14 final size:13
Alignment explanation
Indices: 5706100--5706141 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
5706090 CATGCCTAGA
5706100 TCATGCTAAAATAT
1 TCATGC-AAAATAT
5706114 TCATGCAAGAA-AT
1 TCATGCAA-AATAT
5706127 TCATGCAAATATAT
1 TCATGCAAA-ATAT
5706141 T
1 T
5706142 AATTATCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.04
13 13 0.52
14 11 0.44
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (13 bp):
TCATGCAAAATAT
Found at i:5706152 original size:20 final size:20
Alignment explanation
Indices: 5706123--5706182 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
5706113 TTCATGCAAG
*
5706123 AAAT-TCATGCAAATATATT
1 AAATATCATGCAAATATATA
*
5706142 AATTATCATGC-AATAATATA
1 AAATATCATGCAAAT-ATATA
*
5706162 AAATACCATGCAAATATATA
1 AAATATCATGCAAATATATA
5706182 A
1 A
5706183 TCATGAAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
19 6 0.18
20 25 0.74
21 3 0.09
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.32
Consensus pattern (20 bp):
AAATATCATGCAAATATATA
Found at i:5706305 original size:19 final size:19
Alignment explanation
Indices: 5706277--5706344 Score: 57
Period size: 19 Copynumber: 3.3 Consensus size: 19
5706267 ATATCATTCA
*
5706277 AATATAATATAAATCATGC
1 AATAAAATATAAATCATGC
5706296 AATAACATATAATATCATATCATGC
1 AATAA-A-AT-ATA--A-ATCATGC
5706321 AAT-AAATATAAAATCATGC
1 AATAAAATAT-AAATCATGC
5706340 AATAA
1 AATAA
5706345 TAATCATATA
Statistics
Matches: 40, Mismatches: 1, Indels: 15
0.71 0.02 0.27
Matches are distributed among these distances:
19 14 0.35
20 3 0.08
21 4 0.10
22 6 0.15
23 1 0.03
24 2 0.05
25 10 0.25
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.29
Consensus pattern (19 bp):
AATAAAATATAAATCATGC
Found at i:5706337 original size:24 final size:24
Alignment explanation
Indices: 5706276--5706337 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
5706266 GATATCATTC
*
5706276 AAATATAATAT-AAATCATGCAAT
1 AAATATAATATCATATCATGCAAT
5706299 AACATATAATATCATATCATGCAAT
1 AA-ATATAATATCATATCATGCAAT
*
5706324 AAATATAAAATCAT
1 AAATATAATATCAT
5706338 GCAATAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
23 2 0.06
24 20 0.57
25 13 0.37
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.31
Consensus pattern (24 bp):
AAATATAATATCATATCATGCAAT
Found at i:5706373 original size:16 final size:16
Alignment explanation
Indices: 5706324--5706374 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
5706314 ATCATGCAAT
*
5706324 AAATATAAAATCATGC
1 AAATATATAATCATGC
**
5706340 -AATA-ATAATCATAT
1 AAATATATAATCATGC
*
5706354 AAATATATAACCATGC
1 AAATATATAATCATGC
5706370 AAATA
1 AAATA
5706375 AATATATTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 7 0.26
15 8 0.30
16 12 0.44
ACGTcount: A:0.57, C:0.12, G:0.04, T:0.27
Consensus pattern (16 bp):
AAATATATAATCATGC
Found at i:5706455 original size:14 final size:14
Alignment explanation
Indices: 5706412--5706457 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
5706402 AAATAAATAA
5706412 ATTAATAATCATGC
1 ATTAATAATCATGC
5706426 AATTAAATACATCATGC
1 -ATT-AATA-ATCATGC
*
5706443 ATTAACAATCATGC
1 ATTAATAATCATGC
5706457 A
1 A
5706458 AATAAATATG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 8 0.29
15 6 0.21
16 7 0.25
17 7 0.25
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (14 bp):
ATTAATAATCATGC
Found at i:5706482 original size:20 final size:23
Alignment explanation
Indices: 5706459--5706505 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
5706449 AATCATGCAA
*
5706459 ATAAAT-ATGC-AATTA-AATAT
1 ATAAATCATGCAAATAATAATAT
5706479 AT-AATCATGCAAATAATAATAT
1 ATAAATCATGCAAATAATAATAT
5706501 ATAAA
1 ATAAA
5706506 GCAAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 3 0.14
20 6 0.27
21 4 0.18
22 7 0.32
23 2 0.09
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.32
Consensus pattern (23 bp):
ATAAATCATGCAAATAATAATAT
Found at i:5706492 original size:16 final size:16
Alignment explanation
Indices: 5706410--5706533 Score: 76
Period size: 16 Copynumber: 7.6 Consensus size: 16
5706400 ACAAATAAAT
*
5706410 AAATTAATAATCATGC
1 AAATAAATAATCATGC
*
5706426 AATTAAATACATCATGC
1 AAATAAATA-ATCATGC
* *
5706443 --ATTAACAATCATGC
1 AAATAAATAATCATGC
*
5706457 AAATAAAT-ATGCAAT-T
1 AAATAAATAAT-C-ATGC
*
5706473 AAATATATAATCATGC
1 AAATAAATAATCATGC
* *
5706489 AAATAATAATATATAAAGC
1 AAAT-A-AATA-ATCATGC
*
5706508 AAATAAATTATCATGC
1 AAATAAATAATCATGC
5706524 AAATATAATA
1 AAATA-AATA
5706534 TTAGTCATGT
Statistics
Matches: 80, Mismatches: 17, Indels: 21
0.68 0.14 0.18
Matches are distributed among these distances:
14 7 0.09
15 8 0.10
16 34 0.43
17 18 0.22
18 4 0.05
19 9 0.11
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.30
Consensus pattern (16 bp):
AAATAAATAATCATGC
Found at i:5707175 original size:12 final size:12
Alignment explanation
Indices: 5707158--5707190 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
5707148 ACTAAAAAAC
5707158 AAAATTAAACCA
1 AAAATTAAACCA
*
5707170 AAAATTAAACTA
1 AAAATTAAACCA
5707182 AAAATTAAA
1 AAAATTAAA
5707191 ATACAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAATTAAACCA
Found at i:5710117 original size:620 final size:616
Alignment explanation
Indices: 5708917--5710154 Score: 2268
Period size: 617 Copynumber: 2.0 Consensus size: 616
5708907 AAAATAGAAC
5708917 CGTAACAACCATCACAAAAAGCCTTTCAAACACCATACCTAAAACATAAATTTACAAACCACATT
1 CGTAACAACCATCACAAAAAGCCTTTCAAACACCATACCTAAAACATAAATTTACAAACCACATT
5708982 GCAAAAACTTAGTCACCAAAAAAAAAAAAGCAATTCAAAGAAAATAAAAACCTTGCAAACACCAT
66 GCAAAAACTTAGTCACCAAAAAAAAAAAAGCAATTCAAAGAAAATAAAAACCTTGCAAACACCAT
5709047 AAAAGATTCATGCATATATAAAAAATTACAAAGAAAGATAATAGTGATACTCAACAAAATCTCTA
131 AAAAGATTCATGCATATATAAAAAATTACAAAGAAAGATAATAGTGATACTCAACAAAATCTCTA
5709112 TCAATACATGTGAAGAAAAAAGCTCCATAAACACATGTAAATAGGCCGATGCATAAAAACTCATT
196 TCAATACATGTGAAGAAAAAAGCTCCATAAACACATGTAAATAGGCCGATGCATAAAAACTCATT
5709177 GTGCATCCTTAACTACAACTCTTAGCCTAACTTCATCAATGAAAAATAAAATCAACTAATAGTCA
261 GTGCATCCTTAACTACAACTCTTAGCCTAACTTCATCAATGAAAAATAAAATCAACTAATAGTCA
*
5709242 AAATACATGCACACAAAAAAAAAGGTTCATTATTTTTTACATGTTTTCTACCATTTTCAAAGTAT
326 AAAAACATGCACACAAAAAAAAAGGTTCATTATTTTTTACATGTTTTCTACCATTTTCAAAGTAT
* *
5709307 CATAATTCATATTAAAAAAAAAATCACCTGGCAAAATAAAAACTAATTAGAACCCTAATTGATTA
391 CATAATTCATAGTAAAAAAAAAATCACCTGGCAAAATAAAAACTAATTAGAACCCCAATTGATTA
5709372 AGAACGCAAACCCCAAAATCCCACTAAACTAATCAAAACCCAAATTATTTTTTTGCAAATTAAAC
456 AGAACGCAAACCCCAAAATCCCACTAAACTAATCAAAACCCAAATTATTTTTTTGCAAATTAAAC
5709437 AAATCTAAACAATACCCAAATGCCAAAACCAAGCATTTAGATAGAAAACCATAATTTTTTTTTAG
521 AAATCTAAACAATACCCAAATGCCAAAACCAAGCATTTAGATAGAAAACCATAATTTTTTTTTAG
5709502 AAAAGACATACATTACTTCTTTTCCAAACTT
586 AAAAGACATACATTACTTCTTTTCCAAACTT
* *
5709533 CGTAACAACCATCACAAAAAGCCTTTCAAACACCATGCCTAAAACATAAATTTACAACCCACATT
1 CGTAACAACCATCACAAAAAGCCTTTCAAACACCATACCTAAAACATAAATTTACAAACCACATT
*
5709598 GCAAAAACTTCGTCACCAAAAAAAAAAAAAAAGCAATTCAAAGAAAATAAAAACCTTGCAAACAC
66 GCAAAAACTTAGTCACC---AAAAAAAAAAAAGCAATTCAAAGAAAATAAAAACCTTGCAAACAC
*
5709663 TATAAAAGATTCATGCATGCATA-AAAAAATTACAAAGAAAGATAATAGTGATACTCAACAAAAT
128 CATAAAAGATTCATGCAT--ATATAAAAAATTACAAAGAAAGATAATAGTGATACTCAACAAAAT
*
5709727 CTCTATCAATACATGTGAAGAAAAAAGCTCCATAAACACATGTAAATAGGTCGATGCATAAAAAC
191 CTCTATCAATACATGTGAAGAAAAAAGCTCCATAAACACATGTAAATAGGCCGATGCATAAAAAC
5709792 TCATTGTGCATCCTTAACTACAACTCTTAGCCTAACTTCATCAATGAAAAAT-AAATCAACTAAT
256 TCATTGTGCATCCTTAACTACAACTCTTAGCCTAACTTCATCAATGAAAAATAAAATCAACTAAT
*
5709856 AGT-AAAAAACATGCACAC-AAAAAAAAGGTTCATTATTTTTTACATGTTTTTTACCATTTTCAA
321 AGTCAAAAAACATGCACACAAAAAAAAAGGTTCATTATTTTTTACATGTTTTCTACCATTTTCAA
*
5709919 AGTATCATAATTCATAGTAAAAAAAAATTCACCTGGCAAAATAAAAACTAATTAGAACCCCAATT
386 AGTATCATAATTCATAGTAAAAAAAAAATCACCTGGCAAAATAAAAACTAATTAGAACCCCAATT
* *
5709984 GATTAAGAACGCAAACCCCAAAATCCCACTAAACTAATCAAAACCCAAATTTTTTTTTCTGTAAA
451 GATTAAGAACGCAAACCCCAAAATCCCACTAAACTAATCAAAACCCAAATTATTTTTT-TGCAAA
* *
5710049 TTAAACAAATCTAAACAATACCTAAATGTCAAAACCAAGCATTTAGATAGAAAACCATAATTTTT
515 TTAAACAAATCTAAACAATACCCAAATGCCAAAACCAAGCATTTAGATAGAAAACCATAATTTTT
5710114 TTTTAGAAAAGACATACATTACTTCTTTTCCAAACTT
580 TTTTAGAAAAGACATACATTACTTCTTTTCCAAACTT
5710151 CGTA
1 CGTA
5710155 CACGCACTTT
Statistics
Matches: 602, Mismatches: 14, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
616 79 0.13
617 163 0.27
618 123 0.20
619 77 0.13
620 157 0.26
621 3 0.00
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.25
Consensus pattern (616 bp):
CGTAACAACCATCACAAAAAGCCTTTCAAACACCATACCTAAAACATAAATTTACAAACCACATT
GCAAAAACTTAGTCACCAAAAAAAAAAAAGCAATTCAAAGAAAATAAAAACCTTGCAAACACCAT
AAAAGATTCATGCATATATAAAAAATTACAAAGAAAGATAATAGTGATACTCAACAAAATCTCTA
TCAATACATGTGAAGAAAAAAGCTCCATAAACACATGTAAATAGGCCGATGCATAAAAACTCATT
GTGCATCCTTAACTACAACTCTTAGCCTAACTTCATCAATGAAAAATAAAATCAACTAATAGTCA
AAAAACATGCACACAAAAAAAAAGGTTCATTATTTTTTACATGTTTTCTACCATTTTCAAAGTAT
CATAATTCATAGTAAAAAAAAAATCACCTGGCAAAATAAAAACTAATTAGAACCCCAATTGATTA
AGAACGCAAACCCCAAAATCCCACTAAACTAATCAAAACCCAAATTATTTTTTTGCAAATTAAAC
AAATCTAAACAATACCCAAATGCCAAAACCAAGCATTTAGATAGAAAACCATAATTTTTTTTTAG
AAAAGACATACATTACTTCTTTTCCAAACTT
Found at i:5721422 original size:22 final size:21
Alignment explanation
Indices: 5721376--5721435 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 21
5721366 TTGTAAGAAT
*
5721376 TTTTATTTATTTTTATTTTAGA
1 TTTT-TTTATTTTTATTTTACA
5721398 TTTTTTTATTTTGTA-TTTATCA
1 TTTTTTTATTTT-TATTTTA-CA
*
5721420 TTTTTATTTTTTTTAT
1 TTTTT-TTATTTTTAT
5721436 GGTCTATCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 12 0.38
22 14 0.44
23 6 0.19
ACGTcount: A:0.18, C:0.02, G:0.03, T:0.77
Consensus pattern (21 bp):
TTTTTTTATTTTTATTTTACA
Found at i:5723056 original size:58 final size:58
Alignment explanation
Indices: 5722980--5723496 Score: 427
Period size: 58 Copynumber: 8.6 Consensus size: 58
5722970 ATATGTTTTG
* *
5722980 AAATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTTTTGAAAATAAGTTTTCTAAA
1 AAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTTTTGAAAATAAGTTTTCTAAA
* *
5723038 AAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGTTTTCTAAA
1 AAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTTTTGAAAATAAGTTTTCTAAA
* * ** * *
5723096 AAATATTTTTTTAGGAAAAGTAAAAAGTATCAATTTTTCTTGAAAATAA-TTTTTTAAAA
1 AAATA-TTTTTGAGAAAAAGTTGAAAGTATCAATTTTTTTTGAAAATAAGTTTTCT-AAA
* * * * *
5723155 AAAGGGTTTTTTTTAGGAAAAA-TTGAAAGTATCAATTTTTTTT-TAAATAACTTTCTTTAAA
1 AAA---TATTTTTGA-GAAAAAGTTGAAAGTATCAATTTTTTTTGAAAATAAGTTT-TCTAAA
* * * * * * *
5723216 AAAGGTTTTTTTAAGAAAAAAAAATTAAAAGTATCAATTTTCTTTGAAAATAACTTTTTTTTAAA
1 AAA--TATTTTT--G-AGAAAAAGTTGAAAGTATCAATTTTTTTTGAAAATAA--GTTTTCTAAA
* * *
5723281 AAAGGTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTCTAAA
1 AAA--TATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTTTTGAAAATAAGTTTTCTAAA
* * *
5723341 AAATATTTTCGAGAACAAGTTGAAAGTATCAATTTTCTTTGAAAATAA-TTTTCTAAA
1 AAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTTTTGAAAATAAGTTTTCTAAA
* * * ** * * *
5723398 AAAGGGTTTTTTTTTTAGGAAAAA-TTGAATGTATCAATTTTCCTCGAAATTAAAG-TTTCAAAA
1 AAA-----TATTTTTGA-GAAAAAGTTGAAAGTATCAATTTTTTTTGAAAAT-AAGTTTTCTAAA
* * *
5723461 AAACATTTTAG-GGAAAAGTTGAAAGTATCAATTTTT
1 AAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTT
5723497 CTTATACAAA
Statistics
Matches: 383, Mismatches: 52, Indels: 49
0.79 0.11 0.10
Matches are distributed among these distances:
56 5 0.01
57 28 0.07
58 107 0.28
59 44 0.11
60 26 0.07
61 34 0.09
62 74 0.19
63 38 0.10
64 6 0.02
65 18 0.05
66 3 0.01
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.41
Consensus pattern (58 bp):
AAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTTTTGAAAATAAGTTTTCTAAA
Found at i:5723106 original size:16 final size:16
Alignment explanation
Indices: 5723068--5723105 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5723058 TGAAAGTATC
*
5723068 AATTTTTCTTAAAAAT
1 AATTTTTCTAAAAAAT
*
5723084 AAGTTTTCTAAAAAAT
1 AATTTTTCTAAAAAAT
5723100 -ATTTTT
1 AATTTTT
5723106 TTAGGAAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (16 bp):
AATTTTTCTAAAAAAT
Found at i:5723412 original size:245 final size:241
Alignment explanation
Indices: 5722994--5723438 Score: 673
Period size: 245 Copynumber: 1.8 Consensus size: 241
5722984 ATTTTTGAGG
* *
5722994 AAAAGTTAAAAGTATCAATTTTTTTTGAAAATAAGTTTTCTAAAAAATATTTTTGAGAAAAAGTT
1 AAAAATTAAAAGTATCAATTTTCTTTGAAAATAAGTTTTCTAAAAAATATTTTTGAGAAAAAGTT
**
5723059 GAAAGTATCAATTTTTCTTAAAAATAAGTTTTCTAAAAAATATTTTTTTAGGAAAAGTAAAAAGT
66 GAAAGTATCAATTTTTCTTAAAAATAAGTTTTCTAAAAAATATTTTTCGAGGAAAAGTAAAAAGT
*
5723124 ATCAATTTTTCTTGAAAATAATTTTTTAAAAAAAGGGTTTTTTTTAGGAAAAATTGAAAGTATCA
131 ATCAATTTTTCTTGAAAATAATTTTCTAAAAAAAGGGTTTTTTTTAGGAAAAATTGAAAGTATCA
5723189 ATTTTTTTTTAAATAACTTTCTTTAAAAAAGGTTTTTTTAAGAAAA
196 ATTTTTTTTTAAATAACTTTCTTTAAAAAAGGTTTTTTTAAGAAAA
* * * *
5723235 AAAAATTAAAAGTATCAATTTTCTTTGAAAATAACTTTTTTTTAAAAAAGGTTTTTTTGAGGAAA
1 AAAAATTAAAAGTATCAATTTTCTTTGAAAATAA--GTTTTCTAAAAAA--TATTTTTGAGAAAA
* **
5723300 AGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTCTAAAAAATA-TTTTCGA-GAACAAGTTG
62 AGTTGAAAGTATCAATTTTTCTTAAAAATAAGTTTTCTAAAAAATATTTTTCGAGGAA-AAGTAA
5723363 AAAGTATCAA-TTTTCTTTGAAAATAATTTTCT-AAAAAAGGGTTTTTTTTTTAGGAAAAATTGA
126 AAAGTATCAATTTTTC-TTGAAAATAATTTTCTAAAAAAAGGG--TTTTTTTTAGGAAAAATTGA
*
5723426 ATGTATCAATTTT
188 AAGTATCAATTTT
5723439 CCTCGAAATT
Statistics
Matches: 183, Mismatches: 13, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
241 32 0.17
243 28 0.15
244 34 0.19
245 89 0.49
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (241 bp):
AAAAATTAAAAGTATCAATTTTCTTTGAAAATAAGTTTTCTAAAAAATATTTTTGAGAAAAAGTT
GAAAGTATCAATTTTTCTTAAAAATAAGTTTTCTAAAAAATATTTTTCGAGGAAAAGTAAAAAGT
ATCAATTTTTCTTGAAAATAATTTTCTAAAAAAAGGGTTTTTTTTAGGAAAAATTGAAAGTATCA
ATTTTTTTTTAAATAACTTTCTTTAAAAAAGGTTTTTTTAAGAAAA
Found at i:5723497 original size:120 final size:120
Alignment explanation
Indices: 5722982--5723499 Score: 510
Period size: 120 Copynumber: 4.3 Consensus size: 120
5722972 ATGTTTTGAA
* * *
5722982 ATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTT-TTTGAAAATAAGTTTTCTAAAAAA--TAT
1 ATATTTTAG-GGAAAAGTTAAAAGTATCAATTTTTCTTTGAAAATAATTTTTCTAAAAAAGGTTT
* *
5723044 TTTTGA-GAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGTTTTCTAAAAAAT
65 TTTTGAGGAAAAA-TTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTCTAAAAAAG
* *
5723100 ATTTTTTTA-GGAAAAGTAAAAAGTATCAATTTTTC-TTGAAAATAATTTTT-TAAAAAAAGGGT
1 A-TATTTTAGGGAAAAGTTAAAAGTATCAATTTTTCTTTGAAAATAATTTTTCT-AAAAAA-GGT
* ** * *
5723162 TTTTTTTAGGAAAAATTGAAAGTATCAATTTTT-TTTTAAATAACTTTCTTTAAAAAAGG
63 TTTTTTGAGGAAAAATTGAAAGTATCAATTTTTCTTGAAAATAAGTTT-TCTAAAAAA-G
* * ** * *
5723221 TTTTTTTAAGAAAAAAAAATTAAAAGTATCAA-TTTTCTTTGAAAATAACTTTTTTTTAAAAAAG
1 ATATTTT-AG--GGAAAAGTTAAAAGTATCAATTTTTCTTTGAAAATAA--TTTTTCTAAAAAAG
*
5723285 GTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTCT-AAAAA-
61 GTTTTTTTGAGGAAAAATTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTCTAAAAAAG
* * *
5723343 ATATTTTCGAGAACAAGTTGAAAGTATCAA-TTTTCTTTGAAAATAA-TTTTCTAAAAAAGGGTT
1 ATATTTTAGGGAA-AAGTTAAAAGTATCAATTTTTCTTTGAAAATAATTTTTCTAAAAAA-GG--
* * * * *
5723406 TTTTTTTTAGGAAAAATTGAATGTATCAATTTTCCTCGAAATTAAAG-TTTC-AAAAAA-
62 TTTTTTTGAGGAAAAATTGAAAGTATCAATTTTTCTTGAAAAT-AAGTTTTCTAAAAAAG
* *
5723463 ACATTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTT
1 ATATTTTAGGGAAAAGTTAAAAGTATCAATTTTTCTT
5723500 ATACAAAAGC
Statistics
Matches: 337, Mismatches: 38, Indels: 48
0.80 0.09 0.11
Matches are distributed among these distances:
116 1 0.00
117 55 0.16
118 3 0.01
119 35 0.10
120 132 0.39
121 11 0.03
122 5 0.01
123 5 0.01
124 31 0.09
125 36 0.11
126 22 0.07
127 1 0.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.41
Consensus pattern (120 bp):
ATATTTTAGGGAAAAGTTAAAAGTATCAATTTTTCTTTGAAAATAATTTTTCTAAAAAAGGTTTT
TTTGAGGAAAAATTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTCTAAAAAAG
Found at i:5738796 original size:30 final size:30
Alignment explanation
Indices: 5738757--5738851 Score: 102
Period size: 30 Copynumber: 3.2 Consensus size: 30
5738747 AAATAAATGT
* * *
5738757 TTAATTTTTAATTTATATTTAGATAAGCCA
1 TTAACTTTTAATTTATATCTAAATAAGCCA
* * *
5738787 TTAACTTTTAATTTTTATGTAAATAAGTTC-
1 TTAACTTTTAATTTATATCTAAATAAG-CCA
* *
5738817 TTAACTTTTAATTTATACCTAAATAAACCA
1 TTAACTTTTAATTTATATCTAAATAAGCCA
5738847 TTAAC
1 TTAAC
5738852 ATAAATCAGT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
29 1 0.02
30 51 0.96
31 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (30 bp):
TTAACTTTTAATTTATATCTAAATAAGCCA
Found at i:5740196 original size:14 final size:13
Alignment explanation
Indices: 5740169--5740193 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5740159 TTAATATCCC
5740169 TAAAAAAATAAAT
1 TAAAAAAATAAAT
5740182 TAAAAAAATAAA
1 TAAAAAAATAAA
5740194 ATTTATCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAAAAAATAAAT
Found at i:5749496 original size:2 final size:2
Alignment explanation
Indices: 5749489--5749519 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5749479 GTAACTAATA
5749489 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5749520 GATAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5751184 original size:27 final size:27
Alignment explanation
Indices: 5751151--5751212 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
5751141 AAATTGTATA
* * *
5751151 TATAAATTT-AATAATATATTTGATATT
1 TATAAATTTAAAAAATA-ATTAGAAATT
5751178 TATAAATTTAAAAAATAATTAGAAATT
1 TATAAATTTAAAAAATAATTAGAAATT
5751205 TATAAATT
1 TATAAATT
5751213 ATTTTTATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 25 0.81
28 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (27 bp):
TATAAATTTAAAAAATAATTAGAAATT
Found at i:5752132 original size:24 final size:24
Alignment explanation
Indices: 5752100--5752147 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5752090 CATTGAACTT
*
5752100 AAATTTTAT-CATTAACATATTTAA
1 AAATATTATGCATTAA-ATATTTAA
*
5752124 AAATATTATGCATTAAATTTTTAA
1 AAATATTATGCATTAAATATTTAA
5752148 TATTTTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (24 bp):
AAATATTATGCATTAAATATTTAA
Found at i:5752960 original size:21 final size:20
Alignment explanation
Indices: 5752935--5752979 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 20
5752925 AATTATGAAT
5752935 TTTATTTTATTTTATTT-TAAA
1 TTTA-TTTA-TTTATTTATAAA
5752956 TTTATTTATTTATTTAATAAA
1 TTTATTTATTTATTT-ATAAA
5752977 TTT
1 TTT
5752980 TAAAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.32
20 4 0.18
21 11 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATTTATTTATTTATAAA
Found at i:5753299 original size:30 final size:29
Alignment explanation
Indices: 5753265--5753347 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 29
5753255 CATTATATTT
*
5753265 AAATAAGTTCTTAATTTTTAATTTG-AATC
1 AAATAAGTTTTTAA-TTTTAATTTGTAATC
*
5753294 AAAATAA-TCTTTTAACTTTTAATTTGTATTC
1 -AAATAAGT-TTTTAA-TTTTAATTTGTAATC
5753325 AAATAAGTTTTTAATTTTAATTT
1 AAATAAGTTTTTAATTTTAATTT
5753348 ATACTTATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
29 10 0.21
30 33 0.70
31 4 0.09
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.52
Consensus pattern (29 bp):
AAATAAGTTTTTAATTTTAATTTGTAATC
Found at i:5753428 original size:60 final size:59
Alignment explanation
Indices: 5753314--5753495 Score: 215
Period size: 60 Copynumber: 3.1 Consensus size: 59
5753304 TTTAACTTTT
* * * **
5753314 AATTTGTATTCAAATAAGTTTTT-AATTTTAATTTATACTTATATAAACTTTTAACATA
1 AATTTATATCCAAATAAATTTTTAAATTTTAATTTATACTTATATAAACCCTTAACATA
* *
5753372 AATTTATATCTAAATAAATTTTTAAATTTCTAATTTAT-GTCTATATAAACCCTTAACATA
1 AATTTATATCCAAATAAATTTTTAAATTT-TAATTTATACT-TATATAAACCCTTAACATA
* * ** *
5753432 AATTTATATCCAAATAAATTTTTAAATTTTTAATTTATATTTAAATAAATTCTTAATATA
1 AATTTATATCCAAATAAATTTTTAAA-TTTTAATTTATACTTATATAAACCCTTAACATA
5753492 AATT
1 AATT
5753496 ATTTTTTCAT
Statistics
Matches: 106, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
58 19 0.18
59 6 0.06
60 77 0.73
61 4 0.04
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (59 bp):
AATTTATATCCAAATAAATTTTTAAATTTTAATTTATACTTATATAAACCCTTAACATA
Found at i:5753470 original size:31 final size:30
Alignment explanation
Indices: 5753257--5753487 Score: 147
Period size: 29 Copynumber: 7.7 Consensus size: 30
5753247 AAATAAATCA
* * * *
5753257 TTATATTTAAATAAGTTCTTAATTTTTAAT
1 TTATATCTAAATAAATTTTTAAATTTTAAT
* *
5753287 TTGA-ATCAAAAT-AATCTTTTAACTTTTAAT
1 TT-ATATCTAAATAAAT-TTTTAAATTTTAAT
* *
5753317 TTGTAT-TCAAATAAGTTTTT-AATTTTAAT
1 TTATATCT-AAATAAATTTTTAAATTTTAAT
* * *
5753346 TTATA-CTTATATAAACTTTTAACA--TAAAT
1 TTATATC-TAAATAAATTTTTAA-ATTTTAAT
5753375 TTATATCTAAATAAATTTTTAAATTTCTAAT
1 TTATATCTAAATAAATTTTTAAATTT-TAAT
* * *** *
5753406 TTATGTCTATATAAACCCTTAACA--TAAAT
1 TTATATCTAAATAAATTTTTAA-ATTTTAAT
*
5753435 TTATATCCAAATAAATTTTTAAATTTTTAAT
1 TTATATCTAAATAAATTTTTAAA-TTTTAAT
* *
5753466 TTATATTTAAATAAATTCTTAA
1 TTATATCTAAATAAATTTTTAA
5753488 TATAAATTAT
Statistics
Matches: 151, Mismatches: 33, Indels: 33
0.70 0.15 0.15
Matches are distributed among these distances:
28 2 0.01
29 64 0.42
30 37 0.25
31 47 0.31
32 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (30 bp):
TTATATCTAAATAAATTTTTAAATTTTAAT
Found at i:5753540 original size:29 final size:29
Alignment explanation
Indices: 5753506--5753571 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
5753496 ATTTTTTCAT
*
5753506 TTTATTTGCATATAATAAAAATATAAAAA
1 TTTATTTACATATAATAAAAATATAAAAA
* *
5753535 TTTATTTACATATAATTAAATTATAAAAA
1 TTTATTTACATATAATAAAAATATAAAAA
*
5753564 ATTATTTA
1 TTTATTTA
5753572 AAATAAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (29 bp):
TTTATTTACATATAATAAAAATATAAAAA
Found at i:5754327 original size:14 final size:15
Alignment explanation
Indices: 5754308--5754341 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5754298 GCATAGATTG
*
5754308 TTTTATATATTATT-
1 TTTTATAGATTATTA
5754322 TTTTATAGATTATTA
1 TTTTATAGATTATTA
5754337 TTTTA
1 TTTTA
5754342 CATAATAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTTATAGATTATTA
Found at i:5755361 original size:11 final size:11
Alignment explanation
Indices: 5755329--5755369 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
5755319 TCAATAAAAT
5755329 TAATAAATTTA
1 TAATAAATTTA
5755340 TAAATAAATTTA
1 T-AATAAATTTA
*
5755352 TAATATATTTA
1 TAATAAATTTA
*
5755363 TTATAAA
1 TAATAAA
5755370 AAAATCTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TAATAAATTTA
Found at i:5760144 original size:32 final size:32
Alignment explanation
Indices: 5760101--5760177 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 32
5760091 TGAATTTAAT
*
5760101 TTAAATAAAATTTAAATTTAAATTAA-TTATT-A
1 TTAAATTAAATTTAAA--TAAATTAATTTATTGA
*
5760133 TTAAATTAAATTTAAATAATTTAATTTATTGA
1 TTAAATTAAATTTAAATAAATTAATTTATTGA
5760165 TTAAATTAAATTT
1 TTAAATTAAATTT
5760178 GATTATTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 7 0.17
31 5 0.12
32 29 0.71
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (32 bp):
TTAAATTAAATTTAAATAAATTAATTTATTGA
Found at i:5760181 original size:15 final size:15
Alignment explanation
Indices: 5760118--5760182 Score: 51
Period size: 15 Copynumber: 4.2 Consensus size: 15
5760108 AAATTTAAAT
*
5760118 TTAAATT-AATTATTA
1 TTAAATTAAATT-TGA
*
5760133 TTAAATTAAATTTAA
1 TTAAATTAAATTTGA
* * *
5760148 ATAATTTAATTTATTGA
1 TTAAATTAA-AT-TTGA
5760165 TTAAATTAAATTTGA
1 TTAAATTAAATTTGA
5760180 TTA
1 TTA
5760183 TTTTTATATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
15 23 0.59
16 6 0.15
17 10 0.26
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
TTAAATTAAATTTGA
Found at i:5760370 original size:11 final size:11
Alignment explanation
Indices: 5760356--5760440 Score: 50
Period size: 11 Copynumber: 7.5 Consensus size: 11
5760346 TGATTTTTAT
*
5760356 TTTAAGTTAAA
1 TTTAAATTAAA
5760367 TTTAAATTAAA
1 TTTAAATTAAA
*
5760378 --AAAATTAAAA
1 TTTAAATT-AAA
**
5760388 TTT-AATCGAA
1 TTTAAATTAAA
*
5760398 TTTAAATTTAA
1 TTTAAATTAAA
5760409 TTTCAAATTTTAAA
1 TTT-AAA--TTAAA
*
5760423 TTTTAAATTGAA
1 -TTTAAATTAAA
5760435 TTTAAA
1 TTTAAA
5760441 CTCAAATTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 16
0.70 0.11 0.20
Matches are distributed among these distances:
9 5 0.09
10 8 0.14
11 27 0.47
12 7 0.12
14 7 0.12
15 3 0.05
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:5768984 original size:24 final size:25
Alignment explanation
Indices: 5768956--5769020 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
5768946 AGTTTTTTTA
* * *
5768956 AAAAATAATTATAAAATTACATAAT
1 AAAAATAATTAAAAAATCAAATAAT
**
5768981 AAAAATCTTTAAAAAATCAAATAAT
1 AAAAATAATTAAAAAATCAAATAAT
5769006 AAAAA-AATTAAAAAA
1 AAAAATAATTAAAAAA
5769021 AAAAACTTAC
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
24 8 0.24
25 25 0.76
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (25 bp):
AAAAATAATTAAAAAATCAAATAAT
Found at i:5770539 original size:32 final size:32
Alignment explanation
Indices: 5770495--5770561 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 32
5770485 AACACTTTAA
* *
5770495 AAAACTTCTCT-AACAGGAGGCTACGATATTTG
1 AAAACTTCTCTAAACA-GAGGCAACGATACTTG
*
5770527 AAAAC-TCTTCTAAACAGAGGCAATGATACTTG
1 AAAACTTC-TCTAAACAGAGGCAACGATACTTG
5770559 AAA
1 AAA
5770562 TTAAAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
31 2 0.07
32 24 0.80
33 4 0.13
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.25
Consensus pattern (32 bp):
AAAACTTCTCTAAACAGAGGCAACGATACTTG
Found at i:5770593 original size:165 final size:165
Alignment explanation
Indices: 5770311--5770630 Score: 514
Period size: 165 Copynumber: 1.9 Consensus size: 165
5770301 TTATTTAACC
* * * * * * * *
5770311 AAAGGCTATGACACTTTAAAAGAGTCCTCTAATAAAAGGCTATGATATTTGAGAACTCTTCTAAC
1 AAAGCCTATAACACTTTAAAAAACTCCTCTAACAAAAGGCTACGATATTTGAAAACTCTTCTAAA
*
5770376 CAAAGGCAATGATACTTGAAATTAAAATTTTTAAAGGTCTTATAGATTATGCCATTTTATCTTAC
66 CAAAGGCAATGATACTTGAAATTAAAATTTTTAAAGGTCTTATAGATTATGCCATTTGATCTTAC
*
5770441 AAATCATGCTTAATTTTGAAAGAGTCATCTATCCA
131 AAATCATGCCTAATTTTGAAAGAGTCATCTATCCA
* **
5770476 AAAGCCTATAACACTTTAAAAAACTTCTCTAACAGGAGGCTACGATATTTGAAAACTCTTCTAAA
1 AAAGCCTATAACACTTTAAAAAACTCCTCTAACAAAAGGCTACGATATTTGAAAACTCTTCTAAA
*
5770541 CAGAGGCAATGATACTTGAAATTAAAATTTTTAAAGGTCTTATAGATTATGCCATTTGATCTTAC
66 CAAAGGCAATGATACTTGAAATTAAAATTTTTAAAGGTCTTATAGATTATGCCATTTGATCTTAC
5770606 AAATCATGCCTAATTTTGAAAGAGT
131 AAATCATGCCTAATTTTGAAAGAGT
5770631 AATTTATTCA
Statistics
Matches: 141, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
165 141 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (165 bp):
AAAGCCTATAACACTTTAAAAAACTCCTCTAACAAAAGGCTACGATATTTGAAAACTCTTCTAAA
CAAAGGCAATGATACTTGAAATTAAAATTTTTAAAGGTCTTATAGATTATGCCATTTGATCTTAC
AAATCATGCCTAATTTTGAAAGAGTCATCTATCCA
Found at i:5771066 original size:33 final size:33
Alignment explanation
Indices: 5770989--5771075 Score: 86
Period size: 33 Copynumber: 2.6 Consensus size: 33
5770979 GATAGAGCCA
* * * *
5770989 CAAGTCGAAAATGACATGACTGAGACTGAGTTG
1 CAAGTCGAAAATGAAATGATTGAGACTAAATTG
* ** *
5771022 TAAGTAAAAAATGAGATGATTGAGACTAAATCT-
1 CAAGTCGAAAATGAAATGATTGAGACTAAAT-TG
5771055 CAAGTCGAAAATGAAATGATT
1 CAAGTCGAAAATGAAATGATT
5771076 AGGATTGAGC
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
33 41 0.98
34 1 0.02
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (33 bp):
CAAGTCGAAAATGAAATGATTGAGACTAAATTG
Found at i:5771900 original size:22 final size:22
Alignment explanation
Indices: 5771875--5771921 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5771865 TAAATTAAGT
* * *
5771875 TTAGGTGTAAGCTAATTTGGGC
1 TTAGGTGCAAGCTAATATGGAC
*
5771897 TTAGGTGCCAGCTAATATGGAC
1 TTAGGTGCAAGCTAATATGGAC
5771919 TTA
1 TTA
5771922 AAGTTCTAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.34
Consensus pattern (22 bp):
TTAGGTGCAAGCTAATATGGAC
Done.