Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007877.1 Hibiscus syriacus cultivar Beakdansim tig00110253_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 614694
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:534377 original size:20 final size:20
Alignment explanation
Indices: 534354--534391 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
534344 AAAGGATCAA
*
534354 ATAAAAAATTGTGAAATGTG
1 ATAAAAAATTGTAAAATGTG
534374 ATAAAAAATTGTAAAATG
1 ATAAAAAATTGTAAAATG
534392 GACTGAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.16, T:0.29
Consensus pattern (20 bp):
ATAAAAAATTGTAAAATGTG
Found at i:534552 original size:2 final size:2
Alignment explanation
Indices: 534545--534606 Score: 65
Period size: 2 Copynumber: 31.0 Consensus size: 2
534535 ACATTACAAG
* *
534545 TA TA TA TA TA TA TA AA GTA TA -A GTA TC TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA
*
534588 TA TA TA TA AA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA
534607 ATAAGAATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
1 2 0.04
2 46 0.92
3 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:534618 original size:21 final size:22
Alignment explanation
Indices: 534594--534652 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 22
534584 TATATATATA
534594 TAAATATAATATAAT-AAGAAT
1 TAAATATAATATAATAAAGAAT
534615 TAAAGTAT-ATA-ATATAAAGAAT
1 TAAA-TATAATATA-ATAAAGAAT
534637 TAAGTATATAATATAA
1 TAA--ATATAATATAA
534653 AGTATTAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
20 1 0.03
21 9 0.29
22 12 0.39
23 3 0.10
24 5 0.16
25 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (22 bp):
TAAATATAATATAATAAAGAAT
Found at i:534653 original size:21 final size:21
Alignment explanation
Indices: 534597--534693 Score: 117
Period size: 21 Copynumber: 4.5 Consensus size: 21
534587 ATATATATAA
534597 ATATAATATAATAAGAATTAAAGT
1 ATATAATAT-A-AAGAATT-AAGT
534621 ATATAATATAAAGAATTAAGT
1 ATATAATATAAAGAATTAAGT
*
534642 ATATAATATAAAGTATTAAGT
1 ATATAATATAAAGAATTAAGT
*
534663 ATA-AACTATAAAGTA-TAAGT
1 ATATAA-TATAAAGAATTAAGT
534683 ATATATATATA
1 ATATA-ATATA
534694 TATATATAAA
Statistics
Matches: 69, Mismatches: 1, Indels: 9
0.87 0.01 0.11
Matches are distributed among these distances:
20 10 0.14
21 41 0.59
22 8 0.12
23 1 0.01
24 9 0.13
ACGTcount: A:0.56, C:0.01, G:0.08, T:0.35
Consensus pattern (21 bp):
ATATAATATAAAGAATTAAGT
Found at i:534655 original size:14 final size:15
Alignment explanation
Indices: 534617--535115 Score: 124
Period size: 14 Copynumber: 34.4 Consensus size: 15
534607 ATAAGAATTA
534617 AAGTATATAA-TATA-
1 AAGTATA-AAGTATAT
* *
534631 AAGAATTAAGTATAT
1 AAGTATAAAGTATAT
534646 AA-TATAAAGTAT-T
1 AAGTATAAAGTATAT
*
534659 AAGTATAAACTATA-
1 AAGTATAAAGTATAT
534673 AAGTAT-AAGTATAT
1 AAGTATAAAGTATAT
*
534687 ATA-TATATA-TATAT
1 A-AGTATAAAGTATAT
*
534701 AAACTATAAAGTATAT
1 -AAGTATAAAGTATAT
534717 AA-TATAAAGTAT-T
1 AAGTATAAAGTATAT
* *
534730 AAATATATAA-TA-AA
1 AAGTATA-AAGTATAT
534744 AAGTAATAAATGTTTGGATAT
1 AAGT-ATAAA-G--T--ATAT
*
534765 AAGTATTAAGTATAT
1 AAGTATAAAGTATAT
534780 AA-TAT-AAGTAT-T
1 AAGTATAAAGTATAT
*
534792 AAATAT-AAGTATTAACAT
1 AAGTATAAAGTA-T---AT
534810 AAGTATTAAAGTATAT
1 AAGTA-TAAAGTATAT
*
534826 AAAAAGTAATAAAGTGT-T
1 ---AAGT-ATAAAGTATAT
* *
534844 -TGGAT-AAGTAT-T
1 AAGTATAAAGTATAT
*
534856 AAATATATAA--ATAT
1 AAGTATA-AAGTATAT
534870 AAGTATTAAAGTATAT
1 AAGTA-TAAAGTATAT
*
534886 -A-TATAAAGTTTTGGTAT
1 AAGTATAAAG---T-ATAT
*
534903 AAATATATACA-TATAT
1 AAGTATA-A-AGTATAT
534919 AA-TATAAAGTATAT
1 AAGTATAAAGTATAT
*
534933 AAGTATATA-TATA-
1 AAGTATAAAGTATAT
*
534946 AACTATAAAGT-T-T
1 AAGTATAAAGTATAT
534959 -AGTATAAAGTATAT
1 AAGTATAAAGTATAT
534973 ACA-TA-AAA--ATA-
1 A-AGTATAAAGTATAT
* ** *
534984 AAGTGT-TTGGATAT
1 AAGTATAAAGTATAT
*
534998 AAGTATTAAGTATAT
1 AAGTATAAAGTATAT
*
535013 AAATATAAAGTAT-T
1 AAGTATAAAGTATAT
535027 AAAGTATATAA--AT-T
1 -AAGTATA-AAGTATAT
535041 AAGTATTAAA-TATAT
1 AAGTA-TAAAGTATAT
*
535056 -A-TATAATATTATAT
1 AAGTATAA-AGTATAT
535070 AAGTAT--A-TATA-
1 AAGTATAAAGTATAT
* * *
535081 AAGTTTTAACTATAT
1 AAGTATAAAGTATAT
535096 AA-TATAAAGTATAT
1 AAGTATAAAGTATAT
535110 AAGTAT
1 AAGTAT
535116 GTTGAATCAT
Statistics
Matches: 368, Mismatches: 41, Indels: 151
0.66 0.07 0.27
Matches are distributed among these distances:
10 1 0.00
11 7 0.02
12 28 0.08
13 64 0.17
14 128 0.35
15 68 0.18
16 23 0.06
17 5 0.01
18 8 0.02
19 18 0.05
20 12 0.03
21 6 0.02
ACGTcount: A:0.52, C:0.01, G:0.10, T:0.37
Consensus pattern (15 bp):
AAGTATAAAGTATAT
Found at i:534710 original size:7 final size:6
Alignment explanation
Indices: 534548--534741 Score: 76
Period size: 6 Copynumber: 30.5 Consensus size: 6
534538 TTACAAGTAT
* * ** * * *
534548 ATATAT ATATAA AGTATAA GTATCT ATATAT ATATAT ATATAT ATATAA
1 ATATAA ATATAA A-TATAA ATATAA ATATAA ATATAA ATATAA ATATAA
* *
534597 ATAT-A ATAT-A ATA-AGA AT-TAA AGTATATA ATATAA AGAATTAA GTATATA
1 ATATAA ATATAA ATATA-A ATATAA A-TATA-A ATATAA A-TA-TAA ATATA-A
* * * *
534647 ATATAA AGTATTAA GTATAA ACTATAA AGTATAA GTAT-- ATATAT ATATAT
1 ATATAA A-TA-TAA ATATAA A-TATAA A-TATAA ATATAA ATATAA ATATAA
534697 ATATAA ACTATAA AGTATATA ATATAA AGTATTAA ATATATA ATA
1 ATATAA A-TATAA A-TATA-A ATATAA A-TA-TAA ATATA-A ATA
534742 AAAAGTAATA
Statistics
Matches: 150, Mismatches: 18, Indels: 39
0.72 0.09 0.19
Matches are distributed among these distances:
4 3 0.02
5 11 0.07
6 67 0.45
7 55 0.37
8 14 0.09
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.38
Consensus pattern (6 bp):
ATATAA
Found at i:534747 original size:92 final size:92
Alignment explanation
Indices: 534588--534838 Score: 256
Period size: 92 Copynumber: 2.8 Consensus size: 92
534578 TATATATATA
* * * *
534588 TATATATAAATATAATATAATAAGA-ATTAAAGTATATAATATAAAGAATTAAGTATATAATATA
1 TATATATATATAT-ATAT-ATAA-ATA-TAAAGTATATAATATAAAGTATTAAATATATAATAAA
*
534652 AAGT-ATTAA-GTATAAACTATAAAGTA-TAAG
62 AAGTAATAAATGTATAAA-TAT-AAGTATTAAG
534682 TATATATATATATATATATAAACTATAAAGTATATAATATAAAGTATTAAATATATAATAAAAAG
1 TATATATATATATATATATAAA-TATAAAGTATATAATATAAAGTATTAAATATATAATAAAAAG
* **
534747 TAATAAATGTTTGGATATAAGTATTAAG
65 TAATAAATGTATAAATATAAGTATTAAG
* *
534775 TATATA-ATATA-AGTAT-TAAATAT-AAGTAT-TAACAT-AAGTATTAAA-GTAT-ATAAAAAG
1 TATATATATATATA-TATATAAATATAAAGTATATAATATAAAGTATTAAATATATAATAAAAAG
534832 TAATAAA
65 TAATAAA
534839 GTGTTTGGAT
Statistics
Matches: 141, Mismatches: 10, Indels: 21
0.82 0.06 0.12
Matches are distributed among these distances:
85 15 0.11
86 3 0.02
87 10 0.07
88 5 0.04
89 6 0.04
90 3 0.02
91 6 0.04
92 55 0.39
93 22 0.16
94 16 0.11
ACGTcount: A:0.55, C:0.01, G:0.08, T:0.35
Consensus pattern (92 bp):
TATATATATATATATATATAAATATAAAGTATATAATATAAAGTATTAAATATATAATAAAAAGT
AATAAATGTATAAATATAAGTATTAAG
Found at i:534813 original size:12 final size:12
Alignment explanation
Indices: 534771--534818 Score: 69
Period size: 13 Copynumber: 3.8 Consensus size: 12
534761 ATATAAGTAT
534771 TAAGTATATAATA
1 TAAGTAT-TAATA
534784 TAAGTATTAAATA
1 TAAGTATT-AATA
*
534797 TAAGTATTAACA
1 TAAGTATTAATA
534809 TAAGTATTAA
1 TAAGTATTAA
534819 AGTATATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 14 0.42
13 19 0.58
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (12 bp):
TAAGTATTAATA
Found at i:534814 original size:25 final size:27
Alignment explanation
Indices: 534765--534824 Score: 88
Period size: 25 Copynumber: 2.3 Consensus size: 27
534755 GTTTGGATAT
*
534765 AAGTATTAAGTATATAATATAAGTATTA
1 AAGTA-TAAGTATATAACATAAGTATTA
534793 AA-TATAAGTAT-TAACATAAGTATTA
1 AAGTATAAGTATATAACATAAGTATTA
534818 AAGTATA
1 AAGTATA
534825 TAAAAAGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 15 0.50
26 11 0.37
27 2 0.07
28 2 0.07
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.37
Consensus pattern (27 bp):
AAGTATAAGTATATAACATAAGTATTA
Found at i:534871 original size:21 final size:21
Alignment explanation
Indices: 534647--534894 Score: 115
Period size: 21 Copynumber: 11.7 Consensus size: 21
534637 TAAGTATATA
534647 ATATAAAGTATTAAGTA-TAAACT
1 ATATAAA-TA-TAAGTATTAAA-T
* *
534670 ATA-AAGTATAAGTATATATAT
1 ATATAAATATAAGTAT-TAAAT
* *
534691 ATATATATATAAACTA-TAAAGT
1 ATATAAATAT-AAGTATTAAA-T
534713 ATAT-AATATAAAGTATTAAAT
1 ATATAAATAT-AAGTATTAAAT
* *
534734 ATAT-AATAAAAAGTAATAAAT
1 ATATAAAT-ATAAGTATTAAAT
* * ** *
534755 GTTTGGATATAAGTATTAAGT
1 ATATAAATATAAGTATTAAAT
534776 ATAT-AATATAAGTATTAAAT
1 ATATAAATATAAGTATTAAAT
*
534796 ATAAGTATTAACATAAGTATTAAAGT
1 AT-A-TA--AATATAAGTATTAAA-T
*
534822 ATAT-AA-A-AAGTAATAAAGT
1 ATATAAATATAAGTATTAAA-T
* ***
534841 GT-T-TGGATAAGTATTAAAT
1 ATATAAATATAAGTATTAAAT
534860 ATATAAATATAAGTATTAAAGT
1 ATATAAATATAAGTATTAAA-T
*
534882 ATATATATA-AAGT
1 ATATAAATATAAGT
534895 TTTGGTATAA
Statistics
Matches: 175, Mismatches: 31, Indels: 40
0.71 0.13 0.16
Matches are distributed among these distances:
18 1 0.01
19 15 0.09
20 33 0.19
21 69 0.39
22 31 0.18
23 7 0.04
24 1 0.01
25 15 0.09
26 3 0.02
ACGTcount: A:0.52, C:0.01, G:0.10, T:0.36
Consensus pattern (21 bp):
ATATAAATATAAGTATTAAAT
Found at i:534910 original size:85 final size:84
Alignment explanation
Indices: 534677--534911 Score: 234
Period size: 85 Copynumber: 2.8 Consensus size: 84
534667 ACTATAAAGT
* * * ** *
534677 ATAAGTATATATATATATATATATAAACTA-TAAAGTATATAATATAAAGTATTAAATATATA-A
1 ATAAGTAT-TAAATATATAAATAT-AAGTATTAAAGTATAT-ATATAAAGTATTGTATAAATATA
534740 TAAAAAGTAATAAATGTTTGGA
63 TAAAAAGTAATAAATGTTTGGA
* *
534762 TATAAGTATTAAGTATAT-AATATAAGTATTAAA-TATA-AGTATTAACA-TA-AGTATTAAAGT
1 -ATAAGTATTAAATATATAAATATAAGTATTAAAGTATATA-TA-TAA-AGTATTGTA-TAAA-T
534822 ATATAAAAAGTAATAAAGTGTTTGG-
60 ATATAAAAAGTAATAAA-TGTTTGGA
*
534847 ATAAGTATTAAATATATAAATATAAGTATTAAAGTATATATATAAAGTTTTGGTATAAATATATA
1 ATAAGTATTAAATATATAAATATAAGTATTAAAGTATATATATAAAGTATT-GTATAAATATATA
534912 CATATATAAT
Statistics
Matches: 124, Mismatches: 11, Indels: 29
0.76 0.07 0.18
Matches are distributed among these distances:
81 1 0.01
82 3 0.02
83 16 0.13
84 28 0.23
85 47 0.38
86 25 0.20
87 4 0.03
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.37
Consensus pattern (84 bp):
ATAAGTATTAAATATATAAATATAAGTATTAAAGTATATATATAAAGTATTGTATAAATATATAA
AAAGTAATAAATGTTTGGA
Found at i:534942 original size:55 final size:54
Alignment explanation
Indices: 534834--534947 Score: 153
Period size: 55 Copynumber: 2.1 Consensus size: 54
534824 ATAAAAAGTA
*
534834 ATAAAGTGTTTGGATAAGTATTAAATATATAAATATAAGTATTAAAGTATATAT
1 ATAAAGTGTTTGGATAAATATTAAATATATAAATATAAGTATTAAAGTATATAT
*
534888 ATAAAGT-TTTGGTATAAATATATACATATAT-AATATAAAGTA-TATAAGTATATAT
1 ATAAAGTGTTTGG-ATAAATAT-TAAATATATAAATAT-AAGTATTA-AAGTATATAT
534943 ATAAA
1 ATAAA
534948 CTATAAAGTT
Statistics
Matches: 54, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
53 5 0.09
54 21 0.39
55 28 0.52
ACGTcount: A:0.50, C:0.01, G:0.11, T:0.39
Consensus pattern (54 bp):
ATAAAGTGTTTGGATAAATATTAAATATATAAATATAAGTATTAAAGTATATAT
Found at i:534964 original size:21 final size:21
Alignment explanation
Indices: 534900--534973 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 21
534890 AAAGTTTTGG
534900 TATAAA-TATATACA-TATATAA
1 TATAAACTATATA-AGTATAT-A
*
534921 TATAAAGTATATAAGTATATA
1 TATAAACTATATAAGTATATA
534942 TATAAACTATA-AAGT-T-TA
1 TATAAACTATATAAGTATATA
*
534960 GTATAAAGTATATA
1 -TATAAACTATATA
534974 CATAAAAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.04
19 11 0.23
20 5 0.11
21 18 0.38
22 11 0.23
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.38
Consensus pattern (21 bp):
TATAAACTATATAAGTATATA
Found at i:535026 original size:22 final size:21
Alignment explanation
Indices: 534994--535115 Score: 103
Period size: 22 Copynumber: 5.8 Consensus size: 21
534984 AAGTGTTTGG
534994 ATATAAGTATTAAGTATATAA
1 ATATAAGTATTAAGTATATAA
535015 ATATAAAGTATTAAAGTATATAA
1 ATAT-AAGTATT-AAGTATATAA
* *
535038 AT-TAAGTATTAAATATATAT
1 ATATAAGTATTAAGTATATAA
*
535058 ATA-ATATTATATAAGTATAT--
1 ATATA-AGTAT-TAAGTATATAA
* *
535078 ATA-AAGTTTTAACTATAT-A
1 ATATAAGTATTAAGTATATAA
535097 ATATAAAGTATATAAGTAT
1 ATAT-AAGTAT-TAAGTAT
535116 GTTGAATCAT
Statistics
Matches: 83, Mismatches: 9, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
18 8 0.10
19 6 0.07
20 15 0.18
21 20 0.24
22 22 0.27
23 12 0.14
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.40
Consensus pattern (21 bp):
ATATAAGTATTAAGTATATAA
Found at i:535079 original size:147 final size:144
Alignment explanation
Indices: 534709--535103 Score: 369
Period size: 147 Copynumber: 2.7 Consensus size: 144
534699 ATAAACTATA
* * * *
534709 AAGTATAT-AATATAAAGTATTAAA-TATATAATAAAAAGTAATAAATGTTTGGATATAAGTATT
1 AAGTATATAAATATAAAGTATTAAAGTATATAA-ATAAAGTATTAAATATAT--ATATAA-TATT
* *
534772 A-AGT-ATATAATATAAGTATTAAATATAAGTATTAACATAAGTATTAAAGTATATAAAAAGTAA
62 ATA-TAATAT-ATATAAGTATTAAATATAACTATAAACATAAGTATTAAAGTATATAAAAAG-AA
534835 TAAAGTGTTTGGATAAGTATT
124 TAAAGTGTTTGGATAAGTATT
* * * ** *
534856 AAATATATAAATAT-AAGTATTAAAGTATATATATAAAGTTTTGGTATAAATATATACATATATA
1 AAGTATATAAATATAAAGTATTAAAGTATATAAATAAAGTATT-AAATATATATATA-ATAT-T-
* ** *
534920 ATATAA-AGTATATAAGTA-TATATATAAACTATAAAGTTTAGTA-TAAAGTATATACATAAA-A
62 ATATAATA-TATATAAGTATTAAATAT-AACTATAAACATAAGTATTAAAGTATATA-A-AAAGA
534981 ATAAAGTGTTTGGATATAAGTATT
123 ATAAAGTGTTTGG--ATAAGTATT
*
535005 AAGTATATAAATATAAAGTATTAAAGTATATAAATTAAGTATTAAATATATATATAATATTATAT
1 AAGTATATAAATATAAAGTATTAAAGTATATAAATAAAGTATTAAATATATATATAATATTATAT
*
535070 AAGTATATATAAAGTTTTAACTATATAA-TATAAA
66 AA-TATATAT-AAGTATTAA--ATATAACTATAAA
535104 GTATATAAGT
Statistics
Matches: 202, Mismatches: 25, Indels: 40
0.76 0.09 0.15
Matches are distributed among these distances:
146 14 0.07
147 63 0.31
148 48 0.24
149 46 0.23
150 27 0.13
151 4 0.02
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.37
Consensus pattern (144 bp):
AAGTATATAAATATAAAGTATTAAAGTATATAAATAAAGTATTAAATATATATATAATATTATAT
AATATATATAAGTATTAAATATAACTATAAACATAAGTATTAAAGTATATAAAAAGAATAAAGTG
TTTGGATAAGTATT
Found at i:535111 original size:9 final size:8
Alignment explanation
Indices: 534994--535115 Score: 63
Period size: 8 Copynumber: 16.2 Consensus size: 8
534984 AAGTGTTTGG
534994 ATATAAGT
1 ATATAAGT
535002 AT-TAAGT
1 ATATAAGT
*
535009 ATATAAAT
1 ATATAAGT
535017 ATA-AAGT
1 ATATAAGT
535024 AT-TAAAGT
1 ATAT-AAGT
535032 ATATAA--
1 ATATAAGT
535038 AT-TAAGT
1 ATATAAGT
*
535045 AT-TAAAT
1 ATATAAGT
535052 ATAT-A-T
1 ATATAAGT
*
535058 ATA-ATATT
1 ATATA-AGT
535066 ATATAAGTAT
1 ATATAAG--T
535076 ATATAAAGT
1 ATAT-AAGT
* *
535085 -TTTAACT
1 ATATAAGT
535092 ATATAA-T
1 ATATAAGT
535099 ATA-AAGT
1 ATATAAGT
535106 ATATAAGT
1 ATATAAGT
535114 AT
1 AT
535116 GTTGAATCAT
Statistics
Matches: 90, Mismatches: 7, Indels: 34
0.69 0.05 0.26
Matches are distributed among these distances:
5 3 0.03
6 8 0.09
7 33 0.37
8 35 0.39
9 3 0.03
10 5 0.06
11 3 0.03
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.40
Consensus pattern (8 bp):
ATATAAGT
Found at i:535393 original size:36 final size:36
Alignment explanation
Indices: 535308--535407 Score: 119
Period size: 36 Copynumber: 2.7 Consensus size: 36
535298 TTCGTCCTAG
* **
535308 TAGGATTCAAACTCCTAAAAATAGGATAGAATTTTGT
1 TAGGATTCAAACTCCT-AAAATAGGATAGAATTCTAC
*
535345 TAGGATTCAAACTCCTAAAATAGGATAGAGTTCTAC
1 TAGGATTCAAACTCCTAAAATAGGATAGAATTCTAC
* * *
535381 TATGATTTAAACTCTTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAA-ATAGGAT
535408 CCATAAGCAC
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
36 32 0.58
37 23 0.42
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (36 bp):
TAGGATTCAAACTCCTAAAATAGGATAGAATTCTAC
Found at i:535913 original size:20 final size:20
Alignment explanation
Indices: 535888--535925 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
535878 TTTATTATTA
535888 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
535908 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
535926 TTTACTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:535954 original size:37 final size:37
Alignment explanation
Indices: 535872--535955 Score: 93
Period size: 37 Copynumber: 2.3 Consensus size: 37
535862 ATTACTTTTG
*
535872 ATTTT-TTTTATTATTATTTTACTTATATATATATGCT
1 ATTTTCTTTT-TTATTATTTTACTCATATATATATGCT
* * *
535909 -TTTACTTTTTTATATATTTTACTCATTTATTTAT-CT
1 ATTTTCTTTTTTAT-TATTTTACTCATATATATATGCT
535945 ATTTTCTTTTT
1 ATTTTCTTTTT
535956 ATCTTTATCC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
36 9 0.23
37 30 0.77
ACGTcount: A:0.23, C:0.08, G:0.01, T:0.68
Consensus pattern (37 bp):
ATTTTCTTTTTTATTATTTTACTCATATATATATGCT
Found at i:540591 original size:17 final size:16
Alignment explanation
Indices: 540569--540616 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 16
540559 TCAGAACAAA
540569 AAAAAAAAAAAAGAAGC
1 AAAAAAAAAAAAGAA-C
540586 AAAAAAAAAAAAGAAC
1 AAAAAAAAAAAAGAAC
**
540602 AAAAATCAAAAAGAA
1 AAAAAAAAAAAAGAA
540617 AAAGGGACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.48
17 15 0.52
ACGTcount: A:0.83, C:0.06, G:0.08, T:0.02
Consensus pattern (16 bp):
AAAAAAAAAAAAGAAC
Found at i:540596 original size:23 final size:23
Alignment explanation
Indices: 540566--540633 Score: 66
Period size: 24 Copynumber: 3.0 Consensus size: 23
540556 GAATCAGAAC
*
540566 AAAAAAAAAA-AAAAAGAAGCAA
1 AAAAAAAAAAGAAAAAAAAGCAA
* *
540588 AAAAAAAAAAGAACAAAAATCAA
1 AAAAAAAAAAGAAAAAAAAGCAA
** *
540611 AAAGAAAAAGGGACAAAAAAGCA
1 AAA-AAAAAAAGAAAAAAAAGCA
540634 CATGCAAAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
22 10 0.28
23 12 0.33
24 14 0.39
ACGTcount: A:0.79, C:0.07, G:0.12, T:0.01
Consensus pattern (23 bp):
AAAAAAAAAAGAAAAAAAAGCAA
Found at i:541299 original size:22 final size:22
Alignment explanation
Indices: 541226--541302 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
541216 GCTACCCCAT
*
541226 CAAACCATTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
541248 CAAACCTATGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
541270 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
541292 CAAACCTTTGA
1 CAAACCTTTGA
541303 CCAAACATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:541522 original size:24 final size:24
Alignment explanation
Indices: 541494--541556 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
541484 GGGACAATAT
541494 TTTCAAAACTTTTAATTAAACATC
1 TTTCAAAACTTTTAATTAAACATC
** * *
541518 TTTCAAAACACTTGATTAAATATC
1 TTTCAAAACTTTTAATTAAACATC
*
541542 TTTCGAAACTCTTTA
1 TTTCAAAACT-TTTA
541557 TTGATATTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
24 28 0.93
25 2 0.07
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.41
Consensus pattern (24 bp):
TTTCAAAACTTTTAATTAAACATC
Found at i:542286 original size:106 final size:106
Alignment explanation
Indices: 542129--543177 Score: 1592
Period size: 106 Copynumber: 10.0 Consensus size: 106
542119 ATATCGTGCC
* *
542129 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
542194 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
542235 ACTCAAGACAACGTAAGTTCAACTTCACGACGAAGGGCCCGCTGGTTGTCAATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
542300 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
542341 ATTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* * *
542406 AATTTTAGACCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
542447 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAATAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
542512 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
542553 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
542618 AATTTCAGAGCCAATTTCAACTCCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
542659 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT-AATTAAATAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-TAAACAATTTCC
542723 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATA-TGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
542764 ACTCTAGACAACGCAAGTTCAACTTCATGATGAAGGGACCGCTGGTTGTCAATAAACAA-----C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
542824 ---TTC----CC-ATTTTAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
542857 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
542921 AATTTCAGAGCCAATTTCAACTTCACATCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
542962 ACTCCAGACAACGCAAGTTCAACTTCACGATGAATGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
543027 AATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGA
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* ** * * * *
543068 ACTCGAGACAATACAAGTTCAACTTCACAACGAAGGGACGGCTAGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* * *
543133 AGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
543174 ACTC
1 ACTC
543178 GGAACAATGC
Statistics
Matches: 863, Mismatches: 63, Indels: 34
0.90 0.07 0.04
Matches are distributed among these distances:
92 23 0.03
93 61 0.07
97 4 0.00
100 4 0.00
104 2 0.00
105 140 0.16
106 629 0.73
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:543944 original size:36 final size:36
Alignment explanation
Indices: 543880--543981 Score: 195
Period size: 36 Copynumber: 2.8 Consensus size: 36
543870 TTCGTCCTAC
543880 TAGGATTCAAACTCCTAAAAATAGGATAGAATTTTGT
1 TAGGATTCAAACTCCT-AAAATAGGATAGAATTTTGT
543917 TAGGATTCAAACTCCTAAAATAGGATAGAATTTTGT
1 TAGGATTCAAACTCCTAAAATAGGATAGAATTTTGT
543953 TAGGATTCAAACTCCTAAAATAGGATAGA
1 TAGGATTCAAACTCCTAAAATAGGATAGA
543982 GTTCTACTAT
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 49 0.75
37 16 0.25
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (36 bp):
TAGGATTCAAACTCCTAAAATAGGATAGAATTTTGT
Found at i:544001 original size:36 final size:36
Alignment explanation
Indices: 543876--544012 Score: 166
Period size: 36 Copynumber: 3.8 Consensus size: 36
543866 CCTTTTCGTC
543876 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCT-AAAATAGGATAGAATT
* **
543913 TTGTTAGGATTCAAACTCCTAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAATAGGATAGAATT
* ** *
543949 TTGTTAGGATTCAAACTCCTAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAATAGGATAGAATT
* * *
543985 CTACTATGATTTAAACTCTTAAAGATAG
1 CTACTAGGATTCAAACTCCTAAA-ATAG
544013 AATCCACAAG
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
36 68 0.76
37 21 0.24
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.32
Consensus pattern (36 bp):
CTACTAGGATTCAAACTCCTAAAATAGGATAGAATT
Found at i:548173 original size:43 final size:46
Alignment explanation
Indices: 548126--548234 Score: 134
Period size: 43 Copynumber: 2.4 Consensus size: 46
548116 GTAACCATGC
*
548126 AAATAAGCTTATGAGCTTACGGAA-T-AATGGCAAGTATATAGG-A
1 AAATAAGCTTACGAGCTTACGGAATTAAATGGCAAGTATATAGGTA
* * * * *
548169 AAATAAGCTTACAAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTACGGAA-TTAAATGGCAAGTATATAGGTA
548216 AAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTA
548235 TGGGATAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
43 21 0.38
45 1 0.02
46 14 0.25
47 19 0.35
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.30
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTACGGAATTAAATGGCAAGTATATAGGTA
Found at i:548225 original size:47 final size:44
Alignment explanation
Indices: 548126--548250 Score: 153
Period size: 47 Copynumber: 2.8 Consensus size: 44
548116 GTAACCATGC
* * *
548126 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATAGGA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGA
* * *
548169 AAATAAGCTTACAAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGG-A
*
548216 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
548251 AGATTTTATA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
43 21 0.30
45 12 0.17
46 14 0.20
47 23 0.33
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGA
Found at i:549996 original size:6 final size:6
Alignment explanation
Indices: 549985--550015 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
549975 TAAACCCATA
*
549985 GGTCAT GGTCAT GGTCAT GGTCAC GGTCAT G
1 GGTCAT GGTCAT GGTCAT GGTCAT GGTCAT G
550016 ATACAAGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.19, G:0.35, T:0.29
Consensus pattern (6 bp):
GGTCAT
Found at i:551118 original size:14 final size:13
Alignment explanation
Indices: 551094--551149 Score: 80
Period size: 13 Copynumber: 4.3 Consensus size: 13
551084 TATTATAAGA
551094 AGAAGAAAAAAAT
1 AGAAGAAAAAAAT
551107 AGAAGAAAAAAAT
1 AGAAGAAAAAAAT
551120 AGAAGAAAAAAAAT
1 AGAAG-AAAAAAAT
551134 AGAA-AAAGAAAA-
1 AGAAGAAA-AAAAT
551146 AGAA
1 AGAA
551150 AACGAAGAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
12 7 0.17
13 22 0.54
14 12 0.29
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (13 bp):
AGAAGAAAAAAAT
Found at i:551123 original size:26 final size:26
Alignment explanation
Indices: 551093--551149 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
551083 ATATTATAAG
551093 AAGAAG-AAAAAAATAGAAGAAA-AAA
1 AAGAAGAAAAAAAATAGAA-AAAGAAA
551118 ATAGAAGAAAAAAAATAGAAAAAGAAA
1 A-AGAAGAAAAAAAATAGAAAAAGAAA
551145 AAGAA
1 AAGAA
551150 AACGAAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
25 1 0.03
26 12 0.41
27 16 0.55
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (26 bp):
AAGAAGAAAAAAAATAGAAAAAGAAA
Found at i:551142 original size:17 final size:17
Alignment explanation
Indices: 551122--551219 Score: 71
Period size: 17 Copynumber: 5.8 Consensus size: 17
551112 AAAAAAATAG
551122 AAGAAAAAAAATAGAAA
1 AAGAAAAAAAATAGAAA
*
551139 AAGAAAAAGAAA-ACGAAG
1 AAGAAAAA-AAATA-GAAA
551157 AAG-AAAAAAAT-GAAA
1 AAGAAAAAAAATAGAAA
* *
551172 ACGAGAAAGAAA-AGAAA
1 AAGA-AAAAAAATAGAAA
*
551189 AAGAGAAAAAAAT-GAGAG
1 AAGA-AAAAAAATAGA-AA
*
551207 ATGAAAAAAAATA
1 AAGAAAAAAAATA
551220 TATTTCACTT
Statistics
Matches: 64, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
15 5 0.08
16 3 0.05
17 43 0.67
18 13 0.20
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.05
Consensus pattern (17 bp):
AAGAAAAAAAATAGAAA
Found at i:551158 original size:21 final size:22
Alignment explanation
Indices: 551134--551192 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
551124 GAAAAAAAAT
551134 AGAAAAAGAAAAAGAAAACGA-
1 AGAAAAAGAAAAAGAAAACGAG
*
551155 AGAAGAAA-AAAATGAAAACGAG
1 AGAA-AAAGAAAAAGAAAACGAG
*
551177 AAAGAAAAGAAAAAGA
1 AGA-AAAAGAAAAAGA
551193 GAAAAAAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 16 0.52
22 8 0.26
23 7 0.23
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.02
Consensus pattern (22 bp):
AGAAAAAGAAAAAGAAAACGAG
Found at i:551159 original size:35 final size:33
Alignment explanation
Indices: 551120--551203 Score: 107
Period size: 34 Copynumber: 2.5 Consensus size: 33
551110 AGAAAAAAAT
551120 AGAAGAAAAAAAATAGAAAAAGAAAAAGAAAACGA
1 AGAAGAAAAAAAAT-GAAAAAGAAAAAGAAAA-GA
* *
551155 AGAAG-AAAAAAATGAAAACGAGAAAGAAAAGA
1 AGAAGAAAAAAAATGAAAAAGAAAAAGAAAAGA
*
551187 AAAAGAGAAAAAAATGA
1 AGAAGA-AAAAAAATGA
551204 GAGATGAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
32 6 0.14
33 15 0.34
34 18 0.41
35 5 0.11
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (33 bp):
AGAAGAAAAAAAATGAAAAAGAAAAAGAAAAGA
Found at i:551160 original size:12 final size:12
Alignment explanation
Indices: 551090--551197 Score: 62
Period size: 13 Copynumber: 8.7 Consensus size: 12
551080 TATATATTAT
*
551090 AAGAAGAAGAAA
1 AAGAAAAAGAAA
551102 AA-AATAGAAGAAA
1 AAGAA-A-AAGAAA
551115 AA-AATAGAAGAAA
1 AAGAA-A-AAGAAA
*
551128 AA-AAATAGAAA
1 AAGAAAAAGAAA
551139 AAGAAAAAGAAA
1 AAGAAAAAGAAA
* *
551151 ACGAAGAAGAAAAA
1 AAGAA-AA-AGAAA
* *
551165 AATGAAAACGAGA
1 AA-GAAAAAGAAA
551178 AAG-AAAAGAAA
1 AAGAAAAAGAAA
551189 AAGAGAAAA
1 AAGA-AAAA
551198 AAATGAGAGA
Statistics
Matches: 77, Mismatches: 11, Indels: 15
0.75 0.11 0.15
Matches are distributed among these distances:
11 18 0.23
12 16 0.21
13 33 0.43
14 7 0.09
15 3 0.04
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.04
Consensus pattern (12 bp):
AAGAAAAAGAAA
Found at i:551164 original size:13 final size:12
Alignment explanation
Indices: 551090--551164 Score: 73
Period size: 13 Copynumber: 6.2 Consensus size: 12
551080 TATATATTAT
551090 AAGAAGAAGAAA
1 AAGAAGAAGAAA
*
551102 AAAATAGAAGAAA
1 AAGA-AGAAGAAA
*
551115 AAAATAGAAGAAA
1 AAGA-AGAAGAAA
551128 AA-AA-ATAGAAA
1 AAGAAGA-AGAAA
*
551139 AAGAAAAAGAAA
1 AAGAAGAAGAAA
*
551151 ACGAAGAAGAAA
1 AAGAAGAAGAAA
551163 AA
1 AA
551165 AATGAAAACG
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
10 1 0.02
11 8 0.15
12 22 0.40
13 24 0.44
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.04
Consensus pattern (12 bp):
AAGAAGAAGAAA
Found at i:551192 original size:50 final size:48
Alignment explanation
Indices: 551107--551216 Score: 125
Period size: 50 Copynumber: 2.2 Consensus size: 48
551097 AGAAAAAAAT
*
551107 AGAAGAAAAAAATAGAAGAAAAAAAATAGAAAAAGAAAAAGAAAACGA-
1 AGAAGAAAAAAATAAAAGAAAAAAAATAGAAAAAGAAAAA-AAAACGAG
* * *
551155 AGAAGAAAAAAATGAAAACGAGAAAGAAA-AGAAAAAGAGAAAAAAATGAG
1 AGAAGAAAAAAAT-AAAA-GA-AAAAAAATAGAAAAAGAAAAAAAAACGAG
*
551205 AGATGAAAAAAA
1 AGAAGAAAAAAA
551217 ATATATTTCA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
48 13 0.25
49 9 0.17
50 25 0.47
51 6 0.11
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.05
Consensus pattern (48 bp):
AGAAGAAAAAAATAAAAGAAAAAAAATAGAAAAAGAAAAAAAAACGAG
Found at i:566085 original size:3 final size:3
Alignment explanation
Indices: 566070--566175 Score: 115
Period size: 3 Copynumber: 34.7 Consensus size: 3
566060 TTCATTTAAA
*
566070 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
566115 TAT TAT AAT TAT AAT TAC TAA TAT TAT TATT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
*
566161 TAT TAAA TAT TAT TA
1 TAT T-AT TAT TAT TA
566176 CAAGCCCAAA
Statistics
Matches: 86, Mismatches: 13, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
2 1 0.01
3 79 0.92
4 6 0.07
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:566719 original size:19 final size:19
Alignment explanation
Indices: 566695--566732 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
566685 AAGCCTTGAC
566695 CATCGCCGGA-AACACTAAA
1 CATCGCCGGAGAACA-TAAA
*
566714 CATCGCTGGAGAACATAAA
1 CATCGCCGGAGAACATAAA
566733 ATACCGAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.42, C:0.26, G:0.18, T:0.13
Consensus pattern (19 bp):
CATCGCCGGAGAACATAAA
Found at i:578895 original size:17 final size:16
Alignment explanation
Indices: 578875--578932 Score: 75
Period size: 16 Copynumber: 3.6 Consensus size: 16
578865 ATTATGCTTG
578875 AAGAAAAAAAAAAGAGA
1 AAGAAAAAAAAAA-AGA
578892 AAGAGAAAAAAAAAAGA
1 AAGA-AAAAAAAAAAGA
578909 AA-AAAAAGAAAAAA-A
1 AAGAAAAA-AAAAAAGA
578924 AAGAAAAAA
1 AAGAAAAAA
578933 GAAGAAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.21
16 12 0.32
17 9 0.24
18 9 0.24
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAAAAAAGA
Found at i:578900 original size:13 final size:13
Alignment explanation
Indices: 578875--578940 Score: 66
Period size: 13 Copynumber: 5.1 Consensus size: 13
578865 ATTATGCTTG
578875 AAGAAA-AAAAAA
1 AAGAAAGAAAAAA
578887 AGAGAAAGAGAAAAA
1 A-AGAAAGA-AAAAA
578902 AA-AAAGAAAAAA
1 AAGAAAGAAAAAA
578914 AAGAAA-AAAAAA
1 AAGAAAGAAAAAA
* *
578926 GAAAAAAGAAGAAA
1 -AAGAAAGAAAAAA
578940 A
1 A
578941 TGGGGGGTCA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
12 14 0.30
13 19 0.41
14 7 0.15
15 6 0.13
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAGAAAGAAAAAA
Found at i:578903 original size:20 final size:20
Alignment explanation
Indices: 578875--578940 Score: 91
Period size: 19 Copynumber: 3.4 Consensus size: 20
578865 ATTATGCTTG
*
578875 AAGAAAAAAAAAAG-AGAAA
1 AAGAAAAAAAAAAGAAAAAA
*
578894 GAGAAAAAAAAAAGAAAAAA
1 AAGAAAAAAAAAAGAAAAAA
578914 AAG-AAAAAAAAAGAAAAAA
1 AAGAAAAAAAAAAGAAAAAA
578933 GAAGAAAA
1 -AAGAAAA
578941 TGGGGGGTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
19 29 0.71
20 9 0.22
21 3 0.07
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (20 bp):
AAGAAAAAAAAAAGAAAAAA
Found at i:580225 original size:83 final size:83
Alignment explanation
Indices: 580083--580555 Score: 829
Period size: 83 Copynumber: 5.7 Consensus size: 83
580073 ACTGGAACAA
*
580083 ATGAATGTGCTCATAGCACCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
*
580148 AATCATTGAAATTGAAAG
66 AATTATTGAAATTGAAAG
*
580166 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTGTGGCAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
*
580231 AATCATTGAAATTGAAAG
66 AATTATTGAAATTGAAAG
* *
580249 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
* *
580314 AGTTATTGAATTTGAAAG
66 AATTATTGAAATTGAAAG
580332 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
* *
580397 AGTTATTGAATTTGAAAG
66 AATTATTGAAATTGAAAG
*
580415 ATGAATGTGCTCATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
*
580480 AATTATTGAAATTGGAAG
66 AATTATTGAAATTGAAAG
*
580498 ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
580556 TATGAACCCC
Statistics
Matches: 374, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 374 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (83 bp):
ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
AATTATTGAAATTGAAAG
Found at i:581785 original size:116 final size:113
Alignment explanation
Indices: 581388--582405 Score: 1236
Period size: 113 Copynumber: 8.8 Consensus size: 113
581378 TGGCAAAGAT
* ** * ***
581388 TTAAATCCATCATTCAATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATTCATCATTTGATGGATCAGCTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
* *
581453 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTCGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * *
581501 TCAAATCCATCATTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATTCATCATTTGATGGATCAGCTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
* * * *
581566 AGAAGGAAGAATAAGTTCATAATAAGAAGAATTTGTTTAACCCTTTGGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CCTTTTGC
*
581615 TTGAATTCATCATTTGATGGATCATCAGCTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCGTC
1 TTAAATTCATCATTTGATGG---ATCAGCTTTTCCAGAGAGAGTTCATAATGAGAAGAA--C-TC
* * * * *
581680 ATCTGAAGAAAGAAAAAGAAATTCATAATGAGAAGAATTTGCTCAATCTTTTGC
60 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
581734 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATTCATCATTTGATGGATCAGCTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
* * * *
581799 AGAAGGAAGAATAAGTTCATAATAAGAAGAATTTGTTTAACCCTTTGGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CCTTTTGC
*
581848 TTGAATTCATCATTTGATGGATCATCAGCTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCGCC
1 TTAAATTCATCATTTGATGG---ATCAGCTTTTCCAGAGAGAGTTCATAATGAGAAGAACT---C
* * * * *
581913 ATCTGAAGAAAGAAAAAGAAATTCATAATGAGAAGAATTTGCTCAATCTTTTGC
60 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
581967 TCAAATCCATCATTTGATGGATCAGCTTTTCTAGA-A-AGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATTCATCATTTGATGGATCAGCTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
* *
582030 AGAAGGAAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
582078 TTAAATTCATCATTTGATGGATTAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTG
1 TTAAATTCATCATTTGATGGATCAGCTTTTCCAGAG-AGAGTTCATAATGAGAAGAACTCATCTG
* * * *
582142 AAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGT
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
582191 TTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCAT
1 TTAAATTCATCATTTGATGGATCAGCTTTTCCAGAG-AGAGTTCATAATGAGAAGAA--C-TCAT
* * * *
582255 CTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGT
62 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
582307 TTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCAT
1 TTAAATTCATCATTTGATGGATCAGCTTTTCCAGAG-AGAGTTCATAATGAGAAGAA--C-TCAT
582371 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
62 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
582406 CTAATCTGAA
Statistics
Matches: 802, Mismatches: 83, Indels: 37
0.87 0.09 0.04
Matches are distributed among these distances:
111 75 0.09
112 1 0.00
113 257 0.32
114 68 0.08
115 2 0.00
116 201 0.25
117 70 0.09
119 47 0.06
120 81 0.10
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (113 bp):
TTAAATTCATCATTTGATGGATCAGCTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:581817 original size:233 final size:231
Alignment explanation
Indices: 581425--582405 Score: 1373
Period size: 233 Copynumber: 4.3 Consensus size: 231
581415 TTTCCAGTTC
*
581425 GAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTT
1 GAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTT
* * * *
581487 GTTCAACCTTTCGCTCAAATCCATCATTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAG
66 GCTCAATCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTGCCAGAGAAAGTTCATAATGAG
*
581552 AAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATAAGAAGAATTTGTTTAACCCTTTGGCTT
131 AAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATAAGAAGAATTTGTTCAA-CCTTTGGCTT
* *
581617 GAATTCATCATTTGATGGATCATCAGCTTTTCCAGAG-A
195 GAATTCATCATTTGATGGATCAT-AGCATTGCCAG-GTA
*
581655 GAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAAGAAAAAGAAATTCATAATGAGAAGAATTT
1 GAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTT
*
581720 GCTCAATCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAG
66 GCTCAATCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTGCCAGAGAAAGTTCATAATGAG
*
581785 AAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATAAGAAGAATTTGTTTAACCCTTTGGCTT
131 AAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATAAGAAGAATTTGTTCAA-CCTTTGGCTT
* *
581850 GAATTCATCATTTGATGGATCATCAGCTTTTCCAGAG-A
195 GAATTCATCATTTGATGGATCAT-AGCATTGCCAG-GTA
* *
581888 GAGTTCATAATGAGAAGAACTCGCCATCTGAAGAAAGAAAAAGAAATTCATAATGAGAAGAATTT
1 GAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTT
* *
581953 GCTCAATCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTT-TC-TAGAAAGTTCATAATGAG
66 GCTCAATCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTGCCAGAGAAAGTTCATAATGAG
* * * *
582016 AAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTA
131 AAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATAAGAAGAATTTGTTCAACCTTTGGCTTG
*
582081 AATTCATCATTTGATGGAT--TAACATTGCCAGGTA
196 AATTCATCATTTGATGGATCATAGCATTGCCAGGTA
* * *
582115 GAGTTCATAATGAGAAGAA--C-TCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTT
1 GAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTT
* * ** * * * *
582177 GTTCAA-CTTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATG
66 GCTCAATC-TTTTGCTCAAATCCATCATTTGATGGATCAGCTTTGCCAGAG-AAAGTTCATAATG
* * * * * *
582240 AGAAGAACTCGTCATCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTT
129 AGAAGAA--C-TCATCTGAAGAAGGAAGAATAAGTTCATAATAAGAAGAATTTGTTCAACCTTTG
*
582305 GTTTGAATTCATCATTTGATGGATCA-A-CATTGCCAGGTA
191 GCTTGAATTCATCATTTGATGGATCATAGCATTGCCAGGTA
* *
582344 GAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1 GAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAA
582406 CTAATCTGAA
Statistics
Matches: 696, Mismatches: 39, Indels: 30
0.91 0.05 0.04
Matches are distributed among these distances:
223 1 0.00
224 71 0.10
225 3 0.00
226 20 0.03
227 28 0.04
228 2 0.00
229 104 0.15
230 47 0.07
231 70 0.10
232 40 0.06
233 310 0.45
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (231 bp):
GAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTT
GCTCAATCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTGCCAGAGAAAGTTCATAATGAG
AAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATAAGAAGAATTTGTTCAACCTTTGGCTTG
AATTCATCATTTGATGGATCATAGCATTGCCAGGTA
Found at i:582702 original size:3 final size:3
Alignment explanation
Indices: 582687--582784 Score: 90
Period size: 3 Copynumber: 31.7 Consensus size: 3
582677 TTCATTTAAA
* *
582687 TAT TAT T-T ATAT TAT TAT TAT TAT ATAT AAT TAT TAT TAT TAT AAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
* * * * *
582733 TAT AAT TAC TAA TAT TAT TATT TAT TAT TAA TAT TAT TAT TAAA TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT
582780 TAT TA
1 TAT TA
582785 CAAGCCCAAA
Statistics
Matches: 77, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
2 1 0.01
3 67 0.87
4 9 0.12
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:582727 original size:34 final size:34
Alignment explanation
Indices: 582687--582774 Score: 108
Period size: 34 Copynumber: 2.6 Consensus size: 34
582677 TTCATTTAAA
*
582687 TATTATTTATATTATTATTATTATATATAATTA-T
1 TATTATTTATATTATTATTACTA-ATATAATTATT
* *
582721 TATTA-TTATAATTATAATTACTAATATTATTATT
1 TATTATTTAT-ATTATTATTACTAATATAATTATT
*
582755 TATTATTAATATTATTATTA
1 TATTATTTATATTATTATTA
582775 AATATTATTA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
33 12 0.26
34 31 0.67
35 3 0.07
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (34 bp):
TATTATTTATATTATTATTACTAATATAATTATT
Found at i:587142 original size:14 final size:14
Alignment explanation
Indices: 587123--587149 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
587113 TATATAGTAT
587123 ATAATTTTAAAAAA
1 ATAATTTTAAAAAA
587137 ATAATTTTAAAAA
1 ATAATTTTAAAAA
587150 TATATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATAATTTTAAAAAA
Found at i:587253 original size:74 final size:72
Alignment explanation
Indices: 587145--587283 Score: 190
Period size: 76 Copynumber: 1.9 Consensus size: 72
587135 AAATAATTTT
* * *
587145 AAAAATATATAATATATGGTTTTTAAAACATTTTG-AAAACTTATATAATATATAGTTTTGAAAT
1 AAAAATATATAATATATAGTTTTTAAAACATTTTGAAAAACGTATATAAAATATAGTTTT-AAAT
587209 CATTTCGA
65 CATTTCGA
* *
587217 AAAAATATATAATATATAATTTCTTTAAAACCTTTTGAAAAAACGTATATAAAATATAGTTTTAA
1 AAAAATATATAATATAT-AGTT-TTTAAAACATTTTG-AAAAACGTATATAAAATATAGTTTTAA
587282 AT
63 AT
587284 TTTTTTTTGA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
72 17 0.29
73 2 0.03
74 13 0.22
75 4 0.07
76 22 0.38
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.40
Consensus pattern (72 bp):
AAAAATATATAATATATAGTTTTTAAAACATTTTGAAAAACGTATATAAAATATAGTTTTAAATC
ATTTCGA
Found at i:587258 original size:38 final size:36
Alignment explanation
Indices: 587145--587408 Score: 161
Period size: 36 Copynumber: 7.2 Consensus size: 36
587135 AAATAATTTT
*
587145 AAAAATATATAATATATGGTTTTTAAAACATTTTGA
1 AAAAATATATAATATATAGTTTTTAAAACATTTTGA
** * * *
587181 AAACTTATATAATATATAGTTTTGAAATCATTTCGA
1 AAAAATATATAATATATAGTTTTTAAAACATTTTGA
* *
587217 AAAAATATATAATATATAATTTCTTTAAAACCTTTTGA
1 AAAAATATATAATATAT-AGTT-TTTAAAACATTTTGA
* ***
587255 AAAAACGTATATAAAATATAG-TTTTAAATTTTTTTTTGA
1 AAAAA--TATATAATATATAGTTTTTAAA--ACATTTTGA
* *
587294 AAAATTATATAATATA-A-TGTTTAAAATCA-TTT-A
1 AAAAATATATAATATATAGTTTTTAAAA-CATTTTGA
*
587327 AAAAA-A-ACTAATATA-ATGTTTTTAAATCATTTTTTTG-
1 AAAAATATA-TAATATATA-GTTTTTAAAACA---TTTTGA
* ** * *
587364 AAAAA-CTATAATATATAGTTTGGAAAACTTGTTTTA
1 AAAAATATATAATATATAGTTTTTAAAACAT-TTTGA
587400 AAAAATATA
1 AAAAATATA
587409 ATATATGGTT
Statistics
Matches: 173, Mismatches: 34, Indels: 41
0.70 0.14 0.17
Matches are distributed among these distances:
31 1 0.01
32 9 0.05
33 7 0.04
34 11 0.06
35 3 0.02
36 57 0.33
37 44 0.25
38 19 0.11
39 11 0.06
40 11 0.06
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (36 bp):
AAAAATATATAATATATAGTTTTTAAAACATTTTGA
Found at i:587376 original size:37 final size:36
Alignment explanation
Indices: 587275--587378 Score: 92
Period size: 37 Copynumber: 2.9 Consensus size: 36
587265 ATAAAATATA
* *
587275 GTTTTAAAT-TTTTTTTTGAAAAATTATATAATATAAT
1 GTTTTAAATCATTTTTTTGAAAAA--CTATAATATAAT
* ***
587312 GTTTAAAATCA--TTTAAAAAAAAC--TAATATAAT
1 GTTTTAAATCATTTTTTTGAAAAACTATAATATAAT
587344 GTTTTTAAATCATTTTTTTGAAAAACTATAATATA
1 G-TTTTAAATCATTTTTTTGAAAAACTATAATATA
587379 TAGTTTGGAA
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
32 10 0.20
33 9 0.18
35 9 0.18
36 8 0.16
37 15 0.29
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (36 bp):
GTTTTAAATCATTTTTTTGAAAAACTATAATATAAT
Found at i:590055 original size:19 final size:19
Alignment explanation
Indices: 590031--590085 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
590021 AAATGCATTT
590031 CATGCACCGATGCACTCTC
1 CATGCACCGATGCACTCTC
590050 CATGCACCGATGCACTCTC
1 CATGCACCGATGCACTCTC
*
590069 CATGCATCGATGCACTC
1 CATGCACCGATGCACTC
590086 GGAATATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.22, C:0.40, G:0.16, T:0.22
Consensus pattern (19 bp):
CATGCACCGATGCACTCTC
Found at i:595941 original size:24 final size:22
Alignment explanation
Indices: 595913--595993 Score: 85
Period size: 24 Copynumber: 3.6 Consensus size: 22
595903 CATTTAACAA
595913 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCAT-CC-TTGAATG
*
595937 TGCATCGATGCATCC--GCATG
1 TGCATCGATGCATCCTTGAATG
* *
595957 ATGCACCGATGCATGCCTTGAATA
1 -TGCATCGATGCAT-CCTTGAATG
595981 TGCATCGATGCAT
1 TGCATCGATGCAT
595994 AAGACCATGC
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 4 0.08
21 12 0.25
22 2 0.04
23 14 0.29
24 16 0.33
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATG
Found at i:595948 original size:44 final size:44
Alignment explanation
Indices: 595892--595993 Score: 109
Period size: 44 Copynumber: 2.3 Consensus size: 44
595882 TTTGTGCTTC
* * *
595892 ATGCACCGATGCATTTAACA-ATGCATCGATGCATCCCTTTGAAT
1 ATGCATCGATGCATTCAACAGATGCACCGATGCATCCC-TTGAAT
* ** *
595936 GTGCATCGATGCA-TCCGCATGATGCACCGATGCATGCCTTGAAT
1 ATGCATCGATGCATTCAACA-GATGCACCGATGCATCCCTTGAAT
595980 ATGCATCGATGCAT
1 ATGCATCGATGCAT
595994 AAGACCATGC
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
43 3 0.06
44 29 0.62
45 15 0.32
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.27
Consensus pattern (44 bp):
ATGCATCGATGCATTCAACAGATGCACCGATGCATCCCTTGAAT
Found at i:597942 original size:18 final size:17
Alignment explanation
Indices: 597913--597961 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
597903 TTGTTAAACA
597913 TTTTGATTTGGATGTTT
1 TTTTGATTTGGATGTTT
*
597930 ATGTTTG-TTTGGATATTT
1 -T-TTTGATTTGGATGTTT
*
597948 TTTTGTTTTGGATG
1 TTTTGATTTGGATG
597962 CTTGGACGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 4 0.15
17 8 0.30
18 11 0.41
19 4 0.15
ACGTcount: A:0.12, C:0.00, G:0.24, T:0.63
Consensus pattern (17 bp):
TTTTGATTTGGATGTTT
Found at i:602123 original size:95 final size:94
Alignment explanation
Indices: 602009--602191 Score: 296
Period size: 95 Copynumber: 1.9 Consensus size: 94
601999 TATAATATTA
*
602009 TATATATACAATAAAGCTTGAGTTGTCCCTCT-AGAGAAATAGGTTAAACGCCCCGGCTTTATGG
1 TATATATACAATAAAGCTTGAGCTGTCCCTCTAAG-GAAATAGGTTAAACGCCCCGGCTTTATGG
* *
602073 ATAATATTCAGCTAGCCTGATAAAGGTAAT
65 ATAAGATTCAGCTAACCTGATAAAGGTAAT
* *
602103 TATACTATACAATGAAGCTTGAGCTGTCCCTCTAAGGAAATTGGTTAAACGCCCCGGCTTTATGG
1 TATA-TATACAATAAAGCTTGAGCTGTCCCTCTAAGGAAATAGGTTAAACGCCCCGGCTTTATGG
602168 ATAAGATTCAGCTAACCTGATAAA
65 ATAAGATTCAGCTAACCTGATAAA
602192 AGTGTTTATA
Statistics
Matches: 82, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
94 4 0.05
95 76 0.93
96 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (94 bp):
TATATATACAATAAAGCTTGAGCTGTCCCTCTAAGGAAATAGGTTAAACGCCCCGGCTTTATGGA
TAAGATTCAGCTAACCTGATAAAGGTAAT
Found at i:603522 original size:84 final size:84
Alignment explanation
Indices: 603370--603931 Score: 618
Period size: 84 Copynumber: 6.8 Consensus size: 84
603360 TTTTAAAGAA
* * * * * * * * *
603370 ATCAGTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTTCCAACAAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
*
603435 ACGCTCAGCTCAAAGGCAC
66 ACGCTCAGCTCCAAGGCAC
* *
603454 GA-CATCTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGAC
1 -ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGAC
*
603518 TACGCTCAGCTCCAAGGCAT
65 TACGCTCAGCTCCAAGGCAC
* * *
603538 ATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
603603 ACGCTCAGCTCCAAGGCAC
66 ACGCTCAGCTCCAAGGCAC
* * * * * *
603622 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATATG----TCAAAGACCCTCGAGTTTGATT
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* * *
603683 ACACTCAGCTTCGAGGGCAC
66 ACGCTCAGC-TCCAAGGCAC
* * * * * * * *
603703 ATCATTTACAGCATAACTCAAGGCTAGAAGAGTTATCTGTC-ACCAAAAGGCCTTCGAGTTCGAC
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGAC
* * *
603767 TACGCTCAGCTCCAACGAAT
65 TACGCTCAGCTCCAAGGCAC
* * * * * *
603787 ATCATTTGCAGCACAACTTAAGTCTAAAAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
603852 ACGCTCAGCTCCAAGGCAC
66 ACGCTCAGCTCCAAGGCAC
** * * *
603871 ATCATTTGTTGCATAGCTTAAGTCGAGAA--GATATATGCCAACCGAAGACCTTCGAGTTCGA
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGA
603932 TTACATTCAC
Statistics
Matches: 396, Mismatches: 74, Indels: 17
0.81 0.15 0.03
Matches are distributed among these distances:
80 26 0.07
81 39 0.10
82 27 0.07
83 1 0.00
84 276 0.70
85 27 0.07
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (84 bp):
ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCCAAGGCAC
Found at i:604715 original size:37 final size:36
Alignment explanation
Indices: 604627--604769 Score: 94
Period size: 40 Copynumber: 3.8 Consensus size: 36
604617 TAATTTAAAA
*
604627 AAAACATTTTG-AAAATATATAATATATGGTTTTTG
1 AAAACATTTTGAAAAATATATAATATATGCTTTTTG
* * *
604662 AAATCAATTTGAAAAAATATATAATGTATAGCTTCTTT-
1 AAAACATTTTG-AAAAATATATAATATAT-GCTT-TTTG
* * **
604700 AAAACCTTTTGAAAAAACTTATATAAAATATAG-TTTTAAA
1 AAAACATTTTG-AAAAA--TATATAATATAT-GCTTTT-TG
604740 AAAGACATTTTTGAAAAATTATATAATATA
1 AAA-ACA-TTTTGAAAAA-TATATAATATA
604770 ATGTTTAAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
35 9 0.10
37 15 0.17
38 19 0.22
39 5 0.06
40 26 0.30
41 7 0.08
42 5 0.06
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (36 bp):
AAAACATTTTGAAAAATATATAATATATGCTTTTTG
Found at i:611371 original size:89 final size:90
Alignment explanation
Indices: 611213--611377 Score: 228
Period size: 89 Copynumber: 1.8 Consensus size: 90
611203 TTAATAATTT
*
611213 TCAAATAAATTTTGGTTCGATTAACGGTAAGGAAAAATAATTTATTTTATTCAGTTAATAATTTT
1 TCAAATAAATTTTGGTTCGATTAACGGTAA-GAAAAATAATTTATTTGATTCAGTTAATAATTTT
611278 CAAATAAATTTTGATTCGATTAACAG
65 CAAATAAATTTTGATTCGATTAACAG
* * * * *
611304 TCAAAT-AATTTTGGTTCGATTAATGGTTA-AAAAAT-CTGTTGATTTGGTTCGGTTAATAATTT
1 TCAAATAAATTTTGGTTCGATTAACGGTAAGAAAAATAAT-TT-ATTTGATTCAGTTAATAATTT
611366 TCAAATAAATTT
64 TCAAATAAATTT
611378 CGGTTCGGTT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
87 1 0.02
88 8 0.12
89 30 0.45
90 21 0.32
91 6 0.09
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.42
Consensus pattern (90 bp):
TCAAATAAATTTTGGTTCGATTAACGGTAAGAAAAATAATTTATTTGATTCAGTTAATAATTTTC
AAATAAATTTTGATTCGATTAACAG
Found at i:611714 original size:94 final size:95
Alignment explanation
Indices: 611486--611700 Score: 342
Period size: 94 Copynumber: 2.3 Consensus size: 95
611476 AAGAAAAAAA
* * *
611486 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTTCTATTA
1 TTCGGTTAATAATTTTCAAATAAATTTTGGTTCAATTAACGGTCAAATAATTTCGGTTTCGATTA
* *
611551 ATGTTAAAGAAAAAAATTATGTTAATTTGG
66 ATGTTAAAGAAAAAAATTAGGTTAATTTCG
*
611581 TTCGGTTAATAATTTTCAAATAAATTTTGGTTCAATTAACTGTCAAATAATTTCGG-TTCGATTA
1 TTCGGTTAATAATTTTCAAATAAATTTTGGTTCAATTAACGGTCAAATAATTTCGGTTTCGATTA
*
611645 ATGTTAAAGAAAAAAATTCGGTTAATTTCG
66 ATGTTAAAGAAAAAAATTAGGTTAATTTCG
* *
611675 TTCGGTTTATAATTTTAAAATAAATT
1 TTCGGTTAATAATTTTCAAATAAATT
611701 ATTTTTTCCT
Statistics
Matches: 111, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
94 58 0.52
95 53 0.48
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.42
Consensus pattern (95 bp):
TTCGGTTAATAATTTTCAAATAAATTTTGGTTCAATTAACGGTCAAATAATTTCGGTTTCGATTA
ATGTTAAAGAAAAAAATTAGGTTAATTTCG
Done.