Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 63 of 126
Found at i:18440195 original size:66 final size:66
Alignment explanation
Indices: 18440080--18440226 Score: 240
Period size: 66 Copynumber: 2.2 Consensus size: 66
18440070 TCGCTGCTGC
* * *
18440080 CTCCACTTTAAGTTGTAGGTGGAGTTCTTCATATTTTTTTTGAGACTCTGCTTCTCTCACTGCAG
1 CTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTCACTGCAG
18440145 T
66 T
* * *
18440146 CTCCTCTTTAAGTTTTAGATGGAGTTCATCATATTTTTTTTGAGCCTCTGCTTCTCTCGCTGCAG
1 CTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTCACTGCAG
18440211 T
66 T
18440212 CTCCTCTTTAAGTTG
1 CTCCTCTTTAAGTTG
18440227 AGCAATTTGC
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 74 1.00
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (66 bp):
CTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTCACTGCAG
T
Found at i:18445687 original size:22 final size:22
Alignment explanation
Indices: 18445660--18445787 Score: 68
Period size: 22 Copynumber: 5.8 Consensus size: 22
18445650 TATTAATTAC
18445660 ATAATTAAATATTTAATTTAGT
1 ATAATTAAATATTTAATTTAGT
** *
18445682 ATAATTTAAATAAATAA-TTAAT
1 ATAA-TTAAATATTTAATTTAGT
* *
18445704 -TAATTAAA-A-TTAATTAATT
1 ATAATTAAATATTTAATTTAGT
* ** *
18445723 AT-ATATAATTATTTACGAAAATATT
1 ATAAT-TAAATATTT---AATTTAGT
* *
18445748 TTAATTTAATATTTAATTTAGT
1 ATAATTAAATATTTAATTTAGT
*
18445770 ATAATTAAATAATTAATT
1 ATAATTAAATATTTAATT
18445788 AATTAATTAA
Statistics
Matches: 77, Mismatches: 19, Indels: 20
0.66 0.16 0.17
Matches are distributed among these distances:
18 3 0.04
19 6 0.08
20 9 0.12
21 4 0.05
22 30 0.39
23 10 0.13
25 13 0.17
26 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (22 bp):
ATAATTAAATATTTAATTTAGT
Found at i:18445703 original size:4 final size:4
Alignment explanation
Indices: 18445696--18445810 Score: 60
Period size: 4 Copynumber: 28.5 Consensus size: 4
18445686 TTTAAATAAA
* ** * *
18445696 TAAT TAAT TAAT TAA- -AAT TAAT TAAT TATAT ATAAT TATT TACG AAAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TA-AT -TAAT TAAT TAAT TAAT
* * * *
18445744 TATTT TAATT TAA- TATT TAATT TAGT ATAAT TAAA TAAT TAAT TAAT
1 TA-AT TAA-T TAAT TAAT TAA-T TAAT -TAAT TAAT TAAT TAAT TAAT
18445791 TAAT TAA- -AAT TAAT TAAT TA
1 TAAT TAAT TAAT TAAT TAAT TA
18445811 TACATAATTA
Statistics
Matches: 84, Mismatches: 16, Indels: 22
0.69 0.13 0.18
Matches are distributed among these distances:
2 4 0.05
3 2 0.02
4 60 0.71
5 16 0.19
6 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:18445709 original size:8 final size:8
Alignment explanation
Indices: 18445651--18445810 Score: 62
Period size: 8 Copynumber: 19.5 Consensus size: 8
18445641 GGTTCTTTTT
18445651 ATTAATTA
1 ATTAATTA
18445659 CA-TAATTA
1 -ATTAATTA
* *
18445667 AATATTTA
1 ATTAATTA
*
18445675 ATTTAGTATA
1 A-TTAAT-TA
*
18445685 ATTTAAATA
1 A-TTAATTA
*
18445694 AATAATTA
1 ATTAATTA
18445702 ATTAATTA
1 ATTAATTA
18445710 A--AATTA
1 ATTAATTA
18445716 ATTAATTA
1 ATTAATTA
18445724 TATATAATTA
1 -AT-TAATTA
* ***
18445734 TTTACGAA
1 ATTAATTA
* *
18445742 AATATTTTA
1 ATTA-ATTA
18445751 ATTTAA-TA
1 A-TTAATTA
*
18445759 TTTAATTTA
1 ATTAA-TTA
*
18445768 GTATAATTA
1 AT-TAATTA
*
18445777 AATAATTA
1 ATTAATTA
18445785 ATTAATTA
1 ATTAATTA
18445793 ATTAA--A
1 ATTAATTA
18445799 ATTAATTA
1 ATTAATTA
18445807 ATTA
1 ATTA
18445811 TACATAATTA
Statistics
Matches: 113, Mismatches: 24, Indels: 29
0.68 0.14 0.17
Matches are distributed among these distances:
6 12 0.11
7 5 0.04
8 60 0.53
9 18 0.16
10 18 0.16
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (8 bp):
ATTAATTA
Found at i:18445732 original size:18 final size:17
Alignment explanation
Indices: 18445687--18446099 Score: 68
Period size: 18 Copynumber: 23.9 Consensus size: 17
18445677 TTAGTATAAT
*
18445687 TTAA-ATAAATAATTAA
1 TTAATATAATTAATTAA
*
18445703 TTAATTAAAATTAATTAA
1 TTAA-TATAATTAATTAA
*
18445721 TTATATATAATTATTTACGA
1 TTA-ATATAATTAATTA--A
* *
18445741 -AAATAT-TTTAATTTAA
1 TTAATATAATTAA-TTAA
* *
18445757 -T-ATTTAATTTAGTATAA
1 TTAATATAA-TTAAT-TAA
18445774 TTAA-ATAATTAATTAA
1 TTAATATAATTAATTAA
*
18445790 TTAATTAAAATTAATTAA
1 TTAA-TATAATTAATTAA
* *
18445808 TTATACATAATTATTTACGA
1 TTA-ATATAATTAATTA--A
* *
18445828 -AAATAT-TTTAAATTAA
1 TTAATATAATT-AATTAA
* *
18445844 AT-ATTTAATTAAATATAA
1 TTAATATAATT-AAT-TAA
18445862 TTAA-ATAATTAATTGATA
1 TTAATATAATTAATT-A-A
* *
18445880 CTGT-TTACAATTAAATACATAA
1 -T-TAATATAATT-AAT---TAA
*
18445902 TTAAACATAATTAATTAA
1 TT-AATATAATTAATTAA
*
18445920 TTTAATATAATT-ATTCAC
1 -TTAATATAATTAATT-AA
*
18445938 TTAATATAAATTAAATAA
1 TTAATAT-AATTAATTAA
18445956 TTAA-AT-ATT--TTAAA
1 TTAATATAATTAATT-AA
*
18445970 TTAAT-TATTTAATTAA
1 TTAATATAATTAATTAA
* *
18445986 TTTAAAAT-ATT-A-CAA
1 -TTAATATAATTAATTAA
18446001 TTAA-ATACA-TAATT--
1 TTAATATA-ATTAATTAA
* * *
18446015 TAAACATAATTAAATAA
1 TTAATATAATTAATTAA
* * *
18446032 TTTAAAATAATTATTTAGT
1 -TTAATATAATTAATTA-A
*
18446051 TTAATATAATTAAATAA
1 TTAATATAATTAATTAA
*
18446068 TTAA-ATATTTTAAATTAA
1 TTAATATA-ATT-AATTAA
*
18446086 TT-ATTTAATTAATT
1 TTAATATAATTAATT
18446100 GATACTGTTT
Statistics
Matches: 285, Mismatches: 56, Indels: 112
0.63 0.12 0.25
Matches are distributed among these distances:
13 3 0.01
14 16 0.06
15 19 0.07
16 28 0.10
17 54 0.19
18 130 0.46
19 11 0.04
20 9 0.03
21 7 0.02
22 6 0.02
23 1 0.00
24 1 0.00
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.45
Consensus pattern (17 bp):
TTAATATAATTAATTAA
Found at i:18445789 original size:26 final size:26
Alignment explanation
Indices: 18445760--18445810 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
18445750 AATTTAATAT
* *
18445760 TTAATTTAGTATAATTAAATAATTAA
1 TTAATTAAGTAAAATTAAATAATTAA
* *
18445786 TTAATTAATTAAAATTAATTAATTA
1 TTAATTAAGTAAAATTAAATAATTA
18445811 TACATAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
TTAATTAAGTAAAATTAAATAATTAA
Found at i:18445808 original size:87 final size:87
Alignment explanation
Indices: 18445661--18445875 Score: 367
Period size: 87 Copynumber: 2.4 Consensus size: 87
18445651 ATTAATTACA
*
18445661 TAATTAAATATTTAATTTAGTATAATTTAAATAAATAATTAATTAATTAAAATTAATTAATTATA
1 TAATTAAATATTTAATTTAGTATAA-TTAAATAATTAATTAATTAATTAAAATTAATTAATTATA
*
18445726 TATAATTATTTACGAAAATATTT
65 CATAATTATTTACGAAAATATTT
*
18445749 TAATTTAATATTTAATTTAGTATAATTAAATAATTAATTAATTAATTAAAATTAATTAATTATAC
1 TAATTAAATATTTAATTTAGTATAATTAAATAATTAATTAATTAATTAAAATTAATTAATTATAC
18445814 ATAATTATTTACGAAAATATTT
66 ATAATTATTTACGAAAATATTT
* *
18445836 TAAATTAAATATTTAATTAAATATAATTAAATAATTAATT
1 T-AATTAAATATTTAATTTAGTATAATTAAATAATTAATT
18445876 GATACTGTTT
Statistics
Matches: 120, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
87 61 0.51
88 59 0.49
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (87 bp):
TAATTAAATATTTAATTTAGTATAATTAAATAATTAATTAATTAATTAAAATTAATTAATTATAC
ATAATTATTTACGAAAATATTT
Found at i:18445820 original size:14 final size:14
Alignment explanation
Indices: 18445697--18445810 Score: 72
Period size: 14 Copynumber: 7.9 Consensus size: 14
18445687 TTAAATAAAT
18445697 AATTAATTAATTAA
1 AATTAATTAATTAA
18445711 AATTAATTAATT-A
1 AATTAATTAATTAA
* *
18445724 TATATAATTATTTACGA
1 AAT-TAATTAATTA--A
* *
18445741 AAATATTTTAATTTAA
1 AATTA-ATTAA-TTAA
* * * *
18445757 TATTTAATTTAGTAT
1 -AATTAATTAATTAA
*
18445772 AATTAAATAATT--
1 AATTAATTAATTAA
18445784 AATTAATTAATTAA
1 AATTAATTAATTAA
18445798 AATTAATTAATTA
1 AATTAATTAATTA
18445811 TACATAATTA
Statistics
Matches: 74, Mismatches: 17, Indels: 18
0.68 0.16 0.17
Matches are distributed among these distances:
12 11 0.15
13 3 0.04
14 41 0.55
15 2 0.03
16 6 0.08
17 8 0.11
18 3 0.04
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (14 bp):
AATTAATTAATTAA
Found at i:18445864 original size:10 final size:11
Alignment explanation
Indices: 18445838--18445875 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
18445828 AAATATTTTA
18445838 AATTAAATATTT
1 AATTAAATA-TT
18445850 AATTAAATA-T
1 AATTAAATATT
18445860 AATTAAATAATT
1 AATTAAAT-ATT
18445872 AATT
1 AATT
18445876 GATACTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
12 14 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
AATTAAATATT
Found at i:18445930 original size:112 final size:111
Alignment explanation
Indices: 18445814--18446639 Score: 854
Period size: 112 Copynumber: 7.6 Consensus size: 111
18445804 TTAATTATAC
** **
18445814 ATAATTATTTAC-GAAAAT-ATTTTA-AATTAAATATTTAATTAAATATAATTAAATAATTAATT
1 ATAATTATTTACTGAAAATAATTAAATAATTAAATA-TT--TTAAAT-TAATTATTTAATTAATT
*
18445876 GATACTGTTTACAATTAAATACATAATTAAACATAATTAATTAATTTAAT
62 GATACTGTTTACAATTAAATACATAATTAAACATAATTAAATAATTTAAT
* * * * *
18445926 ATAATTATTCACTTAATATAAATTAAATAATTAAATATTTTAAATTAATTATTTAATTAATTTAA
1 ATAATTATTTACTGAAAAT-AATTAAATAATTAAATATTTTAAATTAATTATTTAATTAATTGAT
* * *
18445991 AAT-ATTACAATTAAATACATAATTTAAACATAATTAAATAATTTAAA
65 ACTGTTTACAATTAAATACATAA-TTAAACATAATTAAATAATTTAAT
* * *
18446038 ATAATTATTTAGTTTAATATAATTAAATAATTAAATATTTTAAATTAATTATTTAATTAATTGAT
1 ATAATTATTTA-CTGAAAATAATTAAATAATTAAATATTTTAAATTAATTATTTAATTAATTGAT
* *
18446103 ACTGTTTATATTTAAATACATAATTAAACATAATTAAATAATTTAAT
65 ACTGTTTACAATTAAATACATAATTAAACATAATTAAATAATTTAAT
* * * *
18446150 ATAATTATTTACTTTAATATAATTACATAATTAAATATTTTAAATTAATTATTTAATTACTTGAT
1 ATAATTATTTAC-TGAAAATAATTAAATAATTAAATATTTTAAATTAATTATTTAATTAATTGAT
* *
18446215 ACTATTTAC-----AAT---TAA-T--ACATAATTAAATGATTTAAT
65 ACTGTTTACAATTAAATACATAATTAAACATAATTAAATAATTTAAT
** * * *
18446251 ATAATTATTTACT-TTAATATATTAAAATAATTAAAT-CTATAAATTAATTATTTAATTAATTTA
1 ATAATTATTTACTGAAAATA-ATT-AAATAATTAAATATTTTAAATTAATTATTTAATTAATTGA
* * * *
18446314 AAATATTTACAATTAAATACATAATTAAATATAATT-AA-AATTTAAT
64 TACTGTTTACAATTAAATACATAATTAAACATAATTAAATAATTTAAT
* * *
18446360 A-AATTATTTAGTTTAATATAATT-AATAATTAAATATTTTAAATTAATTATTTAATTAATTGAT
1 ATAATTATTTA-CTGAAAATAATTAAATAATTAAATATTTTAAATTAATTATTTAATTAATTGAT
* * * *
18446423 ACCGTTTATAATTAAATACATAATT-AA-ATTATATAAATGATTTAAT
65 ACTGTTTACAATTAAATACATAATTAAACATAAT-TAAATAATTTAAT
* *
18446469 ATAATTATTTACT----TTAA-T--ATAATT-AATTTTTTAAATTAATTA-TTAATTAATTGATA
1 ATAATTATTTACTGAAAATAATTAAATAATTAAATATTTTAAATTAATTATTTAATTAATTG--A
* *
18446525 TACTATTTACAATTAAATATATAATTAAACA-AATTAAATAATTTAAT
64 TACTGTTTACAATTAAATACATAATTAAACATAATTAAATAATTTAAT
* * * *
18446572 ATAATTATTTAGTTTAATATAATTACATAATTAAATATTTTAAATTAATTATTTAATTAATTGAT
1 ATAATTATTTA-CTGAAAATAATTAAATAATTAAATATTTTAAATTAATTATTTAATTAATTGAT
18446637 ACT
65 ACT
18446640 AAAGATAAAT
Statistics
Matches: 606, Mismatches: 66, Indels: 85
0.80 0.09 0.11
Matches are distributed among these distances:
99 3 0.00
100 35 0.06
101 53 0.09
102 17 0.03
103 53 0.09
104 9 0.01
105 7 0.01
106 4 0.01
107 17 0.03
108 62 0.10
109 23 0.04
110 14 0.02
111 36 0.06
112 214 0.35
113 44 0.07
115 6 0.01
116 9 0.01
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (111 bp):
ATAATTATTTACTGAAAATAATTAAATAATTAAATATTTTAAATTAATTATTTAATTAATTGATA
CTGTTTACAATTAAATACATAATTAAACATAATTAAATAATTTAAT
Found at i:18446120 original size:224 final size:219
Alignment explanation
Indices: 18445852--18446633 Score: 970
Period size: 224 Copynumber: 3.6 Consensus size: 219
18445842 AAATATTTAA
** * *
18445852 TTAAATATAATTAAATAATTAATTGATACTGTTTACAATTAAATACATAATTAAACATAATTAAT
1 TTAAAT-TAATTATTTAATTAATTGATACTATTTACAATTAAATACATAATTAAACATAATTAAA
*
18445917 TAATTTAATATAATTATTCA-CTTAATATAAATTAAATAATTAAATATTTTAAATTAATTATTTA
65 TAATTTAATATAATTATTTAGCTTAATAT-AATTAAATAATTAAATATTTTAAATTAATTATTTA
* *
18445981 ATTAATTTAAAATATTACAATTAAATACATAATTTAAACATAATTAAATAATTTAAAATAATTAT
129 ATTAATTT---ATATTACAATTAAATACATAA-TTAAACATAATTAAATGATTTAATATAATTAT
*
18446046 TTAGTTTAATATAATTAAATAATTAAATATT
190 TTACTTTAATATAATTAAATAATTAAAT-TT
* * *
18446077 TTAAATTAATTATTTAATTAATTGATACTGTTTATATTTAAATACATAATTAAACATAATTAAAT
1 TTAAATTAATTATTTAATTAATTGATACTATTTACAATTAAATACATAATTAAACATAATTAAAT
*
18446142 AATTTAATATAATTATTTA-CTTTAATATAATTACATAATTAAATATTTTAAATTAATTATTTAA
66 AATTTAATATAATTATTTAGC-TTAATATAATTAAATAATTAAATATTTTAAATTAATTATTTAA
* * *
18446206 TT-ACTT-GA-TACTATT---TAC--AATTAATACATAATTAAATGATTTAATATAATTATTTAC
130 TTAATTTATATTACAATTAAATACATAATTAA-ACATAATTAAATGATTTAATATAATTATTTAC
*
18446263 TTTAATAT-ATTAAAATAATTAAATCT
194 TTTAATATAATT-AAATAATTAAATTT
* * * * *
18446289 ATAAATTAATTATTTAATTAATTTAAAATATTTACAATTAAATACATAATTAAATATAATT-AA-
1 TTAAATTAATTATTTAATTAATTGATACTATTTACAATTAAATACATAATTAAACATAATTAAAT
*
18446352 AATTTAATA-AATTATTTAGTTTAATATAATT-AATAATTAAATATTTTAAATTAATTATTTAAT
66 AATTTAATATAATTATTTAGCTTAATATAATTAAATAATTAAATATTTTAAATTAATTATTTAAT
* * *
18446415 TAATTGATACCGTTTATAATTAAATACATAATT-AA-ATTATATAAATGATTTAATATAATTATT
131 TAATTTATA----TTACAATTAAATACATAATTAAACATAAT-TAAATGATTTAATATAATTATT
18446478 TACTTTAATATAA-T---TAA-T---TTT
191 TACTTTAATATAATTAAATAATTAAATTT
*
18446499 TTAAATTAATTA-TTAATTAATTGATATACTATTTACAATTAAATATATAATTAAACA-AATTAA
1 TTAAATTAATTATTTAATTAATTG--ATACTATTTACAATTAAATACATAATTAAACATAATTAA
* *
18446562 ATAATTTAATATAATTATTTAGTTTAATATAATTACATAATTAAATATTTTAAATTAATTATTTA
64 ATAATTTAATATAATTATTTAGCTTAATATAATTAAATAATTAAATATTTTAAATTAATTATTTA
18446627 ATTAATT
129 ATTAATT
18446634 GATACTAAAG
Statistics
Matches: 495, Mismatches: 38, Indels: 59
0.84 0.06 0.10
Matches are distributed among these distances:
208 32 0.06
209 32 0.06
210 27 0.05
211 32 0.06
212 70 0.14
213 74 0.15
214 39 0.08
215 8 0.02
217 4 0.01
218 44 0.09
219 3 0.01
220 4 0.01
223 3 0.01
224 110 0.22
225 13 0.03
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (219 bp):
TTAAATTAATTATTTAATTAATTGATACTATTTACAATTAAATACATAATTAAACATAATTAAAT
AATTTAATATAATTATTTAGCTTAATATAATTAAATAATTAAATATTTTAAATTAATTATTTAAT
TAATTTATATTACAATTAAATACATAATTAAACATAATTAAATGATTTAATATAATTATTTACTT
TAATATAATTAAATAATTAAATTT
Found at i:18446145 original size:18 final size:18
Alignment explanation
Indices: 18446122--18446200 Score: 70
Period size: 18 Copynumber: 4.4 Consensus size: 18
18446112 ATTTAAATAC
*
18446122 ATAATTAAACATAATTAA
1 ATAATTAAATATAATTAA
* *
18446140 ATAATTTAATATAATTAT
1 ATAATTAAATATAATTAA
* * * *
18446158 TTACTTTAATATAATTAC
1 ATAATTAAATATAATTAA
*
18446176 ATAATTAAATAT-TTTAA
1 ATAATTAAATATAATTAA
18446193 ATTAATTA
1 A-TAATTA
18446201 TTTAATTACT
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
17 4 0.08
18 45 0.92
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (18 bp):
ATAATTAAATATAATTAA
Found at i:18446160 original size:44 final size:43
Alignment explanation
Indices: 18446111--18446205 Score: 104
Period size: 44 Copynumber: 2.2 Consensus size: 43
18446101 ATACTGTTTA
18446111 TATTTAAAT-ACATAATTAAACATAATTAAATAATTT-AATATAAT
1 TATTTAAATAACATAATT--ACATAATTAAATAATTTAAAT-TAAT
** * *
18446155 TATTTACTTTAATATAATTACATAATTAAATATTTTAAATTAAT
1 TATTTA-AATAACATAATTACATAATTAAATAATTTAAATTAAT
18446199 TATTTAA
1 TATTTAA
18446206 TTACTTGATA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
44 32 0.74
45 4 0.09
46 7 0.16
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (43 bp):
TATTTAAATAACATAATTACATAATTAAATAATTTAAATTAAT
Found at i:18446495 original size:22 final size:24
Alignment explanation
Indices: 18446464--18446520 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 24
18446454 TATAAATGAT
**
18446464 TTAATATAATTATTTACTTTAA-TA
1 TTAAT-TAATTATTTAAATTAATTA
*
18446488 -TAATTAATTTTTTAAATTAATTA
1 TTAATTAATTATTTAAATTAATTA
18446511 TTAATTAATT
1 TTAATTAATT
18446521 GATATACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 13 0.46
23 6 0.21
24 9 0.32
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TTAATTAATTATTTAAATTAATTA
Found at i:18446577 original size:18 final size:18
Alignment explanation
Indices: 18446556--18446609 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
18446546 TAATTAAACA
18446556 AATTAAATAATTTAATAT
1 AATTAAATAATTTAATAT
** *
18446574 AATTATTTAGTTTAATAT
1 AATTAAATAATTTAATAT
* *
18446592 AATTACATAATTAAATAT
1 AATTAAATAATTTAATAT
18446610 TTTAAATTAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (18 bp):
AATTAAATAATTTAATAT
Found at i:18450948 original size:83 final size:82
Alignment explanation
Indices: 18450796--18451258 Score: 424
Period size: 82 Copynumber: 5.6 Consensus size: 82
18450786 TTTAAATAAA
** * * * *
18450796 TTAGCGGCGC-TTATGGGAAAGCGCCGCTAATG--CACACCTTTAGCGACGCTT-ATTAGAAAAG
1 TTAGCGGCGCTTTA-GATAAAGCGCCGCTAATGACCAGACCTTTAGCGGCGCTTGA--GGGAAAG
*
18450857 CGCCGCTAATGACCTAACCT
63 CGCCGCTAATGACCTGACCT
* * * *
18450877 TTAGCGGCGCTTTATATATAAGTGCCGCTAATGACCGGAACTTTAGCGGCGCTTGAGGGAAAGCG
1 TTAGCGGCGCTTTAGATA-AAGCGCCGCTAATGACCAGACCTTTAGCGGCGCTTGAGGGAAAGCG
*
18450942 CCGCTAATGACCCGACCTT
65 CCGCTAATGACCTGACC-T
* ** * * * *
18450961 TTAGTGGCGCTTTAGGGAAAGCGCCGCTAATGATCATACCTTTAGCGGCGCTTCAGGTAAAGCGC
1 TTAGCGGCGCTTTAGATAAAGCGCCGCTAATGACCAGACCTTTAGCGGCGCTTGAGGGAAAGCGC
* *
18451026 CACTAATTACCTGACCT
66 CGCTAATGACCTGACCT
*** * * * *
18451043 TTAGCGGCGCTTTCCCTCAAGCGCCGCTAATTACCCGACCTTTAGCGGCGCATT-AGAGAAAGCG
1 TTAGCGGCGCTTTAGATAAAGCGCCGCTAATGACCAGACCTTTAGCGGCGC-TTGAGGGAAAGCG
* *
18451107 CCGCTAATGACTTGAACT
65 CCGCTAATGACCTGACCT
*
18451125 TTAGCGGCGCTTGT-GATAAAGCGCCGCTAATGA-CATGACCTTTAGCGGCGCTTGTGGGTAAAG
1 TTAGCGGCGCTT-TAGATAAAGCGCCGCTAATGACCA-GACCTTTAGCGGCGCTTGAGGG-AAAG
* * *
18451188 TGCCGCTAATAACCCGACCT
63 CGCCGCTAATGACCTGACCT
* ** *
18451208 TTAGCGGCGCTTGT-G-TTAAGCGCCGCTAATG-CTTGACCTTTTGCGGCGCTT
1 TTAGCGGCGCTT-TAGATAAAGCGCCGCTAATGACCAGACCTTTAGCGGCGCTT
18451259 TGTTTCCAAA
Statistics
Matches: 312, Mismatches: 58, Indels: 24
0.79 0.15 0.06
Matches are distributed among these distances:
81 30 0.10
82 139 0.45
83 112 0.36
84 30 0.10
85 1 0.00
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.25
Consensus pattern (82 bp):
TTAGCGGCGCTTTAGATAAAGCGCCGCTAATGACCAGACCTTTAGCGGCGCTTGAGGGAAAGCGC
CGCTAATGACCTGACCT
Found at i:18451023 original size:41 final size:39
Alignment explanation
Indices: 18450796--18451258 Score: 344
Period size: 41 Copynumber: 11.3 Consensus size: 39
18450786 TTTAAATAAA
*
18450796 TTAGCGGCGCTTATGGGAAAGCGCCGCTAATG-CAC-ACCT
1 TTAGCGGCGCTTA-GGTAAAGCGCCGCTAATGAC-CTACCT
* * *
18450835 TTAGCGACGCTTATTAGAAAAGCGCCGCTAATGACCTAACCT
1 TTAGCGGCGCTTA--GGTAAAGCGCCGCTAATGACCT-ACCT
** * * *
18450877 TTAGCGGCGCTTTATATATAAGTGCCGCTAATGACCGGAACT
1 TTAGCGGCGC-TTAGGTA-AAGCGCCGCTAATGACC-TACCT
* *
18450919 TTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCCGACCTT
1 TTAGCGGCGCTT-AGGTAAAGCGCCGCTAATGA-CCTACC-T
* * *
18450961 TTAGTGGCGCTTTAGGGAAAGCGCCGCTAATGATCATACCT
1 TTAGCGGCGC-TTAGGTAAAGCGCCGCTAATGA-CCTACCT
* *
18451002 TTAGCGGCGCTTCAGGTAAAGCGCCACTAATTACCTGACCT
1 TTAGCGGCGCTT-AGGTAAAGCGCCGCTAATGACCT-ACCT
*** * * *
18451043 TTAGCGGCGCTTTCCCTCAAGCGCCGCTAATTACCCGACCT
1 TTAGCGGCGC-TTAGGTAAAGCGCCGCTAATGA-CCTACCT
* *
18451084 TTAGCGGCGCATTAGAG-AAAGCGCCGCTAATGACTTGAACT
1 TTAGCGGCGC-TTAG-GTAAAGCGCCGCTAATGACCT-ACCT
*
18451125 TTAGCGGCGCTT-GTGATAAAGCGCCGCTAATGACATGACCT
1 TTAGCGGCGCTTAG-G-TAAAGCGCCGCTAATGACCT-ACCT
* * * *
18451166 TTAGCGGCGCTTGTGGGTAAAGTGCCGCTAATAACCCGACCT
1 TTAGCGGCGC-T-TAGGTAAAGCGCCGCTAATGA-CCTACCT
* *
18451208 TTAGCGGCGCTT-GTGTTAAGCGCCGCTAATG-CTTGACCT
1 TTAGCGGCGCTTAG-GTAAAGCGCCGCTAATGACCT-ACCT
*
18451247 TTTGCGGCGCTT
1 TTAGCGGCGCTT
18451259 TGTTTCCAAA
Statistics
Matches: 347, Mismatches: 52, Indels: 50
0.77 0.12 0.11
Matches are distributed among these distances:
38 1 0.00
39 30 0.09
40 40 0.12
41 153 0.44
42 114 0.33
43 8 0.02
44 1 0.00
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.25
Consensus pattern (39 bp):
TTAGCGGCGCTTAGGTAAAGCGCCGCTAATGACCTACCT
Found at i:18451277 original size:123 final size:122
Alignment explanation
Indices: 18450796--18451261 Score: 484
Period size: 123 Copynumber: 3.8 Consensus size: 122
18450786 TTTAAATAAA
* * * * *
18450796 TTAGCGGCGCTTATGGGAAAGCGCCGCTAATGCAC-ACCTTTAGCGACGCTTATTAGAAAAGCGC
1 TTAGCGGCGCTTGTGGGAAAGCGCCGCTAATACCCGACCTTTAGCGGCGCTTAGTAG-AAAGCGC
* * * * * *
18450860 CGCTAATGACCTAACCTTTAGCGGCGCTTTATATATAAGTGCCGCTAATGACCGGAACT
65 CGCTAATGACTTGACCTTTAGCGGCGCTTTGTATA-AAGCGCCGCTAATGACCTGACCT
* * *
18450919 TTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCCGACCTTTTAGTGGCGCTTTAG-GGAAAGC
1 TTAGCGGCGCTTGTGGGAAAGCGCCGCTAAT-ACCCGACC-TTTAGCGGCGC-TTAGTAGAAAGC
* * * * *
18450983 GCCGCTAATGATCAT-ACCTTTAGCGGCGCTTCAG-GTAAAGCGCCACTAATTACCTGACCT
63 GCCGCTAATGA-CTTGACCTTTAGCGGCGCTT-TGTATAAAGCGCCGCTAATGACCTGACCT
****
18451043 TTAGCGGCGCTT-TCCCTCAAGCGCCGCTAATTACCCGACCTTTAGCGGCGCATTAG-AGAAAGC
1 TTAGCGGCGCTTGT-GGGAAAGCGCCGCTAA-TACCCGACCTTTAGCGGCGC-TTAGTAGAAAGC
* *
18451106 GCCGCTAATGACTTGAACTTTAGCGGCGC-TTGTGATAAAGCGCCGCTAATGACATGACCT
63 GCCGCTAATGACTTGACCTTTAGCGGCGCTTTGT-ATAAAGCGCCGCTAATGACCTGACCT
* *
18451166 TTAGCGGCGCTTGTGGGTAAAGTGCCGCTAATAACCCGACCTTTAGCGGCGCTT-GT-GTTAAGC
1 TTAGCGGCGCTTGTGGG-AAAGCGCCGCTAAT-ACCCGACCTTTAGCGGCGCTTAGTAG-AAAGC
*
18451229 GCCGCTAATG-CTTGACCTTTTGCGGCGCTTTGT
63 GCCGCTAATGACTTGACCTTTAGCGGCGCTTTGT
18451262 TTCCAAACGC
Statistics
Matches: 286, Mismatches: 40, Indels: 34
0.79 0.11 0.09
Matches are distributed among these distances:
121 1 0.00
122 21 0.07
123 128 0.45
124 83 0.29
125 38 0.13
126 12 0.04
127 3 0.01
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.25
Consensus pattern (122 bp):
TTAGCGGCGCTTGTGGGAAAGCGCCGCTAATACCCGACCTTTAGCGGCGCTTAGTAGAAAGCGCC
GCTAATGACTTGACCTTTAGCGGCGCTTTGTATAAAGCGCCGCTAATGACCTGACCT
Found at i:18452566 original size:12 final size:12
Alignment explanation
Indices: 18452498--18452566 Score: 52
Period size: 12 Copynumber: 5.7 Consensus size: 12
18452488 ATCCACAAAA
*
18452498 TAAACATTAAAT
1 TAAATATTAAAT
18452510 TAAAT-TTAATAT
1 TAAATATTAA-AT
*
18452522 TAAGATAATAAAT
1 TAA-ATATTAAAT
*
18452535 TTAATATT-AAT
1 TAAATATTAAAT
**
18452546 ATAGGTATTAAAT
1 -TAAATATTAAAT
18452559 TAAATATT
1 TAAATATT
18452567 CTTAAAACTT
Statistics
Matches: 43, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
11 7 0.16
12 24 0.56
13 9 0.21
14 3 0.07
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.42
Consensus pattern (12 bp):
TAAATATTAAAT
Found at i:18468195 original size:26 final size:26
Alignment explanation
Indices: 18468165--18468230 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 26
18468155 CTGAAGAAAT
*
18468165 TACTGAACTGGCTCGTAAGAACGATA
1 TACTGTACTGGCTCGTAAGAACGATA
18468191 TACTGTACTGG---G--AG--CGATA
1 TACTGTACTGGCTCGTAAGAACGATA
18468210 TACTGTACTGGCTCGTAAGAA
1 TACTGTACTGGCTCGTAAGAA
18468231 TTGGCTCGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 14
0.68 0.02 0.30
Matches are distributed among these distances:
19 16 0.50
21 2 0.06
22 1 0.03
23 1 0.03
24 2 0.06
26 10 0.31
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (26 bp):
TACTGTACTGGCTCGTAAGAACGATA
Found at i:18468350 original size:36 final size:36
Alignment explanation
Indices: 18468264--18468450 Score: 204
Period size: 36 Copynumber: 5.2 Consensus size: 36
18468254 GACTAGGCTT
* *
18468264 GTATGAGCTAAAATTTACTGGGAGGCTTGAAGGGCTC
1 GTATGAGCTAAAATTTACT-GGAGACTTGAAGAGCTC
* * *
18468301 ATATGAGCT-AAATTTACTGCG-GACTTGAAGATCTT
1 GTATGAGCTAAAATTTACTG-GAGACTTGAAGAGCTC
*
18468336 GTATGAGCTAAAATTTACTGGGAGACTTGAAGAGATC
1 GTATGAGCTAAAATTTACT-GGAGACTTGAAGAGCTC
18468373 GTATGAGCT-AAATTTACTAGGAGACTTGAAGAGCTC
1 GTATGAGCTAAAATTTACT-GGAGACTTGAAGAGCTC
* * *
18468409 GTATGAGCT-AAA-TTACTGGGAAAATTGAAGAGATC
1 GTATGAGCTAAAATTTACT-GGAGACTTGAAGAGCTC
*
18468444 GTTTGAG
1 GTATGAG
18468451 AAACGAATGT
Statistics
Matches: 130, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
35 44 0.34
36 57 0.44
37 29 0.22
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.29
Consensus pattern (36 bp):
GTATGAGCTAAAATTTACTGGAGACTTGAAGAGCTC
Found at i:18468378 original size:72 final size:73
Alignment explanation
Indices: 18468260--18468450 Score: 264
Period size: 72 Copynumber: 2.7 Consensus size: 73
18468250 CACTGACTAG
* * * *
18468260 GCTTGTATGAGCTAAAATTTACTGGGAGGCTTGAAGGGCTCATATGAGCTAAATTTACT-GCG-G
1 GCTTGTATGAGCTAAAATTTACTGGGAGACTTGAAGAGATCGTATGAGCTAAATTTACTAG-GAG
18468323 ACTTGAAGA
65 ACTTGAAGA
*
18468332 TCTTGTATGAGCTAAAATTTACTGGGAGACTTGAAGAGATCGTATGAGCTAAATTTACTAGGAGA
1 GCTTGTATGAGCTAAAATTTACTGGGAGACTTGAAGAGATCGTATGAGCTAAATTTACTAGGAGA
18468397 CTTGAAGA
66 CTTGAAGA
* * * *
18468405 GCTCGTATGAGCT-AAA-TTACTGGGAAAATTGAAGAGATCGTTTGAG
1 GCTTGTATGAGCTAAAATTTACTGGGAGACTTGAAGAGATCGTATGAG
18468451 AAACGAATGT
Statistics
Matches: 107, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
71 27 0.25
72 58 0.54
73 22 0.21
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (73 bp):
GCTTGTATGAGCTAAAATTTACTGGGAGACTTGAAGAGATCGTATGAGCTAAATTTACTAGGAGA
CTTGAAGA
Found at i:18473882 original size:21 final size:24
Alignment explanation
Indices: 18473857--18473908 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 24
18473847 TATAGATAAG
18473857 ATATAATCTA-TTTTCGAAA-AT-
1 ATATAATCTAGTTTTCGAAATATA
*
18473878 ATAT-ATTTAGGTTTTCGAAATATA
1 ATATAATCTA-GTTTTCGAAATATA
18473902 ATATAAT
1 ATATAAT
18473909 AAAATTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 4 0.16
21 4 0.16
22 9 0.36
23 2 0.08
24 4 0.16
25 2 0.08
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (24 bp):
ATATAATCTAGTTTTCGAAATATA
Found at i:18474982 original size:18 final size:17
Alignment explanation
Indices: 18474959--18475001 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
18474949 AATGTATTCT
18474959 AAATTATATAATATATAA
1 AAATTATATAATATA-AA
*
18474977 AAATTACATAATATAAA
1 AAATTATATAATATAAA
*
18474994 ATATTATA
1 AAATTATA
18475002 AACTTAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATTATATAATATAAA
Found at i:18475553 original size:10 final size:10
Alignment explanation
Indices: 18475538--18475562 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
18475528 TAGTAAAGAT
18475538 CAACCTCTAC
1 CAACCTCTAC
18475548 CAACCTCTAC
1 CAACCTCTAC
18475558 CAACC
1 CAACC
18475563 CTCAGAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (10 bp):
CAACCTCTAC
Found at i:18476788 original size:30 final size:30
Alignment explanation
Indices: 18476754--18477022 Score: 219
Period size: 30 Copynumber: 9.1 Consensus size: 30
18476744 TTAAAACCAA
18476754 GTCAAATTTGAATTTTTGGAAACTTTAGGG
1 GTCAAATTTGAATTTTTGGAAACTTTAGGG
*** *
18476784 GTCAAATCAAAATTTTTGGAAAATTT-GAGG
1 GTCAAATTTGAATTTTTGGAAACTTTAG-GG
* * *
18476814 GTCAAATTGGAATTTTTGGTAAC-TTCGAGG
1 GTCAAATTTGAATTTTTGGAAACTTTAG-GG
** *
18476844 GTCAAATTCAAATTTTTGGAAAATTTAGGG
1 GTCAAATTTGAATTTTTGGAAACTTTAGGG
* *
18476874 ATCAAATTTGAATTTTTTGAAA-TTTAGGG
1 GTCAAATTTGAATTTTTGGAAACTTTAGGG
* * * * *
18476903 TTCGAA-TTCAATTTTCTAGAAAGTTTAGGG
1 GTCAAATTTGAATTTT-TGGAAACTTTAGGG
** * *
18476933 GTCAAATTCAAATTTTTGGAAAGTTTAGAG
1 GTCAAATTTGAATTTTTGGAAACTTTAGGG
* * * *
18476963 GTCAAATTTGAA--ATTGAAAAGTTTGGGG
1 GTCAAATTTGAATTTTTGGAAACTTTAGGG
*
18476991 GTCAAATTTGAATTTTTTGAAAAC-TTAGGG
1 GTCAAATTTGAA-TTTTTGGAAACTTTAGGG
18477021 GT
1 GT
18477023 TAAAAATAAT
Statistics
Matches: 193, Mismatches: 37, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
28 32 0.17
29 19 0.10
30 125 0.65
31 17 0.09
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.38
Consensus pattern (30 bp):
GTCAAATTTGAATTTTTGGAAACTTTAGGG
Found at i:18477774 original size:2 final size:2
Alignment explanation
Indices: 18477761--18477804 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
18477751 ATTTATTTGA
*
18477761 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18477803 AT
1 AT
18477805 GAAATAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18479014 original size:40 final size:39
Alignment explanation
Indices: 18478959--18479073 Score: 158
Period size: 39 Copynumber: 2.9 Consensus size: 39
18478949 TTGGATTACC
*
18478959 TCAATCTGCCCCATGGTTGGGGTAAGAGATCGGATGGTCT
1 TCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGG-CT
* * * *
18478999 TCAATCTGCCCCATGGTCGAGGTAAAAGATTGGATTGCT
1 TCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGCT
* *
18479038 TTAATCTGCCCCATGGTCAGGGTAAGAGATCGGATG
1 TCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATG
18479074 ATATTTTCAT
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
39 32 0.50
40 32 0.50
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (39 bp):
TCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGCT
Found at i:18479055 original size:39 final size:39
Alignment explanation
Indices: 18478941--18479072 Score: 149
Period size: 39 Copynumber: 3.4 Consensus size: 39
18478931 AGCTTTAGGT
* * * * *
18478941 GTAAAAGATTGGATTACCTCAATCTGCCCCATGGTTGGG
1 GTAAAAGATCGGATTGCTTCAATCTGCCCCATGGTCGAG
* *
18478980 GTAAGAGATCGGATGGTCTTCAATCTGCCCCATGGTCGAG
1 GTAAAAGATCGGATTG-CTTCAATCTGCCCCATGGTCGAG
* *
18479020 GTAAAAGATTGGATTGCTTTAATCTGCCCCATGGTC-AGG
1 GTAAAAGATCGGATTGCTTCAATCTGCCCCATGGTCGA-G
*
18479059 GTAAGAGATCGGAT
1 GTAAAAGATCGGAT
18479073 GATATTTTCA
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 44 0.56
40 33 0.42
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (39 bp):
GTAAAAGATCGGATTGCTTCAATCTGCCCCATGGTCGAG
Found at i:18482707 original size:18 final size:18
Alignment explanation
Indices: 18482684--18482718 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
18482674 TAAAAGGATA
18482684 TTAATATTTTAGACTTAG
1 TTAATATTTTAGACTTAG
18482702 TTAATATTTTAGACTTA
1 TTAATATTTTAGACTTA
18482719 AAATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (18 bp):
TTAATATTTTAGACTTAG
Found at i:18487640 original size:15 final size:15
Alignment explanation
Indices: 18487603--18487650 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 15
18487593 CAATTACATG
18487603 AATAATAAATATACAA
1 AATAA-AAATATACAA
*
18487619 AAT--AAATATATAA
1 AATAAAAATATACAA
*
18487632 AATAAAAATAAACAA
1 AATAAAAATATACAA
18487647 AATA
1 AATA
18487651 CACAATGCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 12 0.44
15 12 0.44
16 3 0.11
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (15 bp):
AATAAAAATATACAA
Found at i:18487641 original size:19 final size:20
Alignment explanation
Indices: 18487603--18487643 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
18487593 CAATTACATG
18487603 AATAATAAATATACAAAATA
1 AATAATAAATATACAAAATA
18487623 AATATATAAA-ATA-AAAATA
1 AATA-ATAAATATACAAAATA
18487642 AA
1 AA
18487644 CAAAATACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 7 0.35
21 5 0.25
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (20 bp):
AATAATAAATATACAAAATA
Found at i:18487854 original size:30 final size:29
Alignment explanation
Indices: 18487813--18487955 Score: 139
Period size: 30 Copynumber: 4.8 Consensus size: 29
18487803 TAAAATGAAA
* *
18487813 TTTTGAAAAGTTTGGGGGTCAAAACTTATT
1 TTTTGAAAAGTTTAGGGGTCAAAACATA-T
* *
18487843 TTTTCAAAAGTTT-GAGGGTTAAAACATAT
1 TTTTGAAAAGTTTAG-GGGTCAAAACATAT
*
18487872 TTTTGAAAAGTTTAGGGGTCAAATCATAAT
1 TTTTGAAAAGTTTAGGGGTCAAAACAT-AT
* *
18487902 TTTTGGAAAGTTTAGGGGTC-AAATATGAAT
1 TTTTGAAAAGTTTAGGGGTCAAAACAT--AT
*
18487932 TTTT-AGATAGTTTAGGGGTCAAAA
1 TTTTGA-AAAGTTTAGGGGTCAAAA
18487956 AATAATTTCT
Statistics
Matches: 96, Mismatches: 11, Indels: 11
0.81 0.09 0.09
Matches are distributed among these distances:
29 28 0.29
30 65 0.68
31 3 0.03
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (29 bp):
TTTTGAAAAGTTTAGGGGTCAAAACATAT
Found at i:18487905 original size:59 final size:59
Alignment explanation
Indices: 18487813--18487963 Score: 162
Period size: 59 Copynumber: 2.5 Consensus size: 59
18487803 TAAAATGAAA
* * * *
18487813 TTTTGAAAAGTTTGGGGGTCAAAACTTATTTTTTCAAAAGTTTGAGGGTTAAAACAT-AT
1 TTTTGAAAAGTTTAGGGGTCAAAACATAATTTTTCAAAAGTTT-AGGGGTAAAACATAAT
* ** * *
18487872 TTTTGAAAAGTTTAGGGGTCAAATCATAATTTTTGGAAAGTTTAGGGGTCAAATATGAAT
1 TTTTGAAAAGTTTAGGGGTCAAAACATAATTTTTCAAAAGTTTAGGGGTAAAACAT-AAT
* *
18487932 TTTT-AGATAGTTTAGGGGTCAAAAAATAATTT
1 TTTTGA-AAAGTTTAGGGGTCAAAACATAATTT
18487964 CTAAATAAAA
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
58 10 0.13
59 38 0.49
60 29 0.38
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.38
Consensus pattern (59 bp):
TTTTGAAAAGTTTAGGGGTCAAAACATAATTTTTCAAAAGTTTAGGGGTAAAACATAAT
Found at i:18489793 original size:42 final size:42
Alignment explanation
Indices: 18489684--18490369 Score: 639
Period size: 42 Copynumber: 16.8 Consensus size: 42
18489674 GAGATGGTAG
* *
18489684 CTTCAATCTGCCCCACTTGATTTAGGGGTAAAAGATTGGATG--G-
1 CTTCAATCTGCCCCA--TGA--TCGGGGTAAGAGATTGGATGATGT
* * *
18489727 CTTCAATCTGCCCCATGGTTGGGGTAAGAGATTGGATGATGC
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* * *
18489769 CTTCATTCTGCCTCATGATCGGGGTAAGAGATTGGATGATTT
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* * * **
18489811 CTTTAATCTGCCTCATGATCGTGGTAAGAGATTGGATGATAC
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* * * *
18489853 CTTCAATCTGCCTCATGATCGGGGTAAGAGATTAGATAATTT
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* * *
18489895 CTTCAATTTACCCCATGATCGGGGTAAGAGATTGGATGATGC
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* *
18489937 CTTCAATCTACCCCATGATCGGGGTAAGAGATTGGATGATTT
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* * *
18489979 CTTTAATCTG---C-TCAT--GGGTAAGAGATTGGATGATGC
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* * ** *
18490015 CTTCAATTTACCCCATGATCAAGGTAAGAGATTGGATGATGC
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* *
18490057 CTTCAATCTGCCCTATGATCGGGGTAAGAGATTGGATGATTT
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* * *
18490099 CTTTAATCTACCCCATGATCGGTGTAAGAGATTGGATGATGT
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
** * ** * *
18490141 CTTCAATCTGCCCTTTAATTAGGGTAAAAGA-T-CA-GAT-T
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* ** * *
18490179 CTTCTATCTGCCTTATGCTCGAGGTAAGAGATT--A-GATG-
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
**
18490217 CTTCAATCAACCCCATGATCGGGGTAAGAGATT--A-GATG-
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
*
18490255 CTTCAATTTGCCCCATGATCGGGGTAAGAGATTGG-TG-TGT
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* * * * *
18490295 CTTCAATCTGCCCCATGATCGCGGTAAAATATTAG-T-TTGT
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* * *
18490335 CTTCAATTTACCCCATGATCGGGGTAAAAGATTGG
1 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
18490370 TGTGTAGCTT
Statistics
Matches: 536, Mismatches: 91, Indels: 35
0.81 0.14 0.05
Matches are distributed among these distances:
36 26 0.05
38 91 0.17
39 26 0.05
40 69 0.13
41 4 0.01
42 305 0.57
43 15 0.03
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (42 bp):
CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
Found at i:18490062 original size:204 final size:202
Alignment explanation
Indices: 18489708--18490369 Score: 642
Period size: 204 Copynumber: 3.3 Consensus size: 202
18489698 ACTTGATTTA
* * * * **
18489708 GGGGTAAAAGATTGGATG--G-CTTCAATCTGCCCCATGGTTGGGGTAAGAGATTGGATGATGCC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGGTAAAAGATTGGATGATTTC
* * * * * * *
18489770 TTCATTCTGCCTCATGATCGGGGTAAGAGATTGGATGATTTCTTTAATCTGCCTCATGATCGTGG
66 TTTAATCTGCCTC---ATC-GGGTAAGAGATTGGATGA-TGCTTCAATCTACCCCATGATCGAGG
*
18489835 TAAGAGATTGGATGATACCTTCAATCTGCCTCATGATCGGGGTAAGAGATTAGATAATTTCTTCA
126 TAAGAGATTGGATGATGCCTTCAATCTGCC-CATGATCGGGGTAAGAGATT-GAT-ATTTCTTCA
*
18489900 ATTTACCCCATGATC
188 ATCTACCCCATGATC
* * *
18489915 GGGGTAAGAGATTGGATGATGCCTTCAATCTACCCCATGATCGGGGTAAGAGATTGGATGATTTC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGGTAAAAGATTGGATGATTTC
* *
18489980 TTTAATCTG-CTCAT-GGGTAAGAGATTGGATGATGCCTTCAATTTACCCCATGATCAAGGTAAG
66 TTTAATCTGCCTCATCGGGTAAGAGATTGGATGATG-CTTCAATCTACCCCATGATCGAGGTAAG
*
18490043 AGATTGGATGATGCCTTCAATCTGCCCTATGATCGGGGTAAGAGATTGGATGATTTCTTTAATCT
130 AGATTGGATGATGCCTTCAATCTGCCC-ATGATCGGGGTAAGAGATT-GAT-ATTTCTTCAATCT
18490108 ACCCCATGATC
192 ACCCCATGATC
* * * ** * ** *
18490119 GGTGTAAGAGATTGGATGATGTCTTCAATCTGCCCTTTAATTAGGGTAAAAGA-T-CA-GA-TTC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGGTAAAAGATTGGATGATTTC
* * *
18490180 TTCT-ATCTGCCTTATGCTCGAGGTAAGAGATT--A-GATGCTTCAATCAACCCCATGATCGGGG
66 TT-TAATCTGCCTCA---TCG-GGTAAGAGATTGGATGATGCTTCAATCTACCCCATGATCGAGG
* * * *
18490241 TAAGAGATT--A-GATG-CTTCAATTTGCCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAAT
126 TAAGAGATTGGATGATGCCTTCAATCTG-CCCATGATCGGGGTAAGAGATTGATATTTCTTCAAT
*
18490302 CTGCCCCATGATC
190 CTACCCCATGATC
* * * * *
18490315 GCGGTAAAATATTAG-T-TTGTCTTCAATTTACCCCATGATCGGGGTAAAAGATTGG
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGGTAAAAGATTGG
18490370 TGTGTAGCTT
Statistics
Matches: 385, Mismatches: 55, Indels: 41
0.80 0.11 0.09
Matches are distributed among these distances:
194 27 0.07
195 2 0.01
196 30 0.08
197 2 0.01
198 28 0.07
199 7 0.02
200 11 0.03
201 6 0.02
202 30 0.08
203 7 0.02
204 155 0.40
205 1 0.00
206 13 0.03
207 17 0.04
209 4 0.01
210 45 0.12
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (202 bp):
GGGGTAAAAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGGTAAAAGATTGGATGATTTC
TTTAATCTGCCTCATCGGGTAAGAGATTGGATGATGCTTCAATCTACCCCATGATCGAGGTAAGA
GATTGGATGATGCCTTCAATCTGCCCATGATCGGGGTAAGAGATTGATATTTCTTCAATCTACCC
CATGATC
Found at i:18490747 original size:50 final size:50
Alignment explanation
Indices: 18490663--18490783 Score: 136
Period size: 50 Copynumber: 2.4 Consensus size: 50
18490653 GGTTCGCTGA
* * * **
18490663 TGCGACTTCAACCTTTCCC-TTTATATCTCCATGGTACAAGATTTGCCAT
1 TGCGGCTTCAATCTTTCCCATCTATATCTCCATGGTACAAGATCCGCCAT
* * * *
18490712 TGCGGCTTCAATCTTTCCCATCTATATTTCCATGGTACTAGATCCGTCGT
1 TGCGGCTTCAATCTTTCCCATCTATATCTCCATGGTACAAGATCCGCCAT
* *
18490762 TGCGGCCTCGATCTTTCCCATC
1 TGCGGCTTCAATCTTTCCCATC
18490784 ACGCCTCTAA
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
49 17 0.28
50 43 0.72
ACGTcount: A:0.18, C:0.31, G:0.15, T:0.36
Consensus pattern (50 bp):
TGCGGCTTCAATCTTTCCCATCTATATCTCCATGGTACAAGATCCGCCAT
Found at i:18490926 original size:99 final size:98
Alignment explanation
Indices: 18490759--18490971 Score: 279
Period size: 99 Copynumber: 2.2 Consensus size: 98
18490749 CTAGATCCGT
* * *
18490759 CGTTGCGGCCTCGATCTTTCCCATCACGCCTCTAAGGTACCAGGTTTACCATTACGACCTCAACC
1 CGTTGCGGCCTCAATCCTTCCCATCACGCCTCTAAGGTACCAGGTTCACCATTACGACCTCAACC
*
18490824 TTT-CCTTTCATATCTTTATGGTACCGGATTCAC
66 TTTCCCTTT-ATATCTTCATGGTACCGGATTCAC
* * * * *
18490857 CGTTGTGGCCTCAATCCTTCCCATCACATCTTCTAAGGTA-CATGGTTCACCGTTGC-ACCCTCA
1 CGTTGCGGCCTCAATCCTTCCCATCAC-GCCTCTAAGGTACCA-GGTTCACCATTACGA-CCTCA
*
18490920 ACCTTTCCCTTTATATCTTCATGGTATCGGATTCAC
63 ACCTTTCCCTTTATATCTTCATGGTACCGGATTCAC
18490956 CGTTGCGGCCTCAATC
1 CGTTGCGGCCTCAATC
18490972 TTTTCCTTTA
Statistics
Matches: 100, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
98 27 0.27
99 68 0.68
100 5 0.05
ACGTcount: A:0.19, C:0.33, G:0.15, T:0.33
Consensus pattern (98 bp):
CGTTGCGGCCTCAATCCTTCCCATCACGCCTCTAAGGTACCAGGTTCACCATTACGACCTCAACC
TTTCCCTTTATATCTTCATGGTACCGGATTCAC
Found at i:18490938 original size:50 final size:51
Alignment explanation
Indices: 18490609--18490982 Score: 170
Period size: 49 Copynumber: 7.6 Consensus size: 51
18490599 TGTGGAATTT
* * * * * *
18490609 ACCGTTGCAGCCTCAATCTTTCCCTTCATATC-TCTAAGGTATAAGG-TTC
1 ACCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCTATGGTACATGGATTC
* * * * * * * *
18490658 GCTGATGCGACTTCAACCTTTCCCTTTATATC-TCCATGGTACA-AGATTT
1 ACCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCTATGGTACATGGATTC
* * * * * * * *
18490707 GCCATTGCGGCTTCAATCTTTCCCATCTATAT-TTCCATGGTAC-TAGATCC
1 ACCGTTGCGGCCTCAACCTTTCCC-TTTATATCTTCTATGGTACATGGATTC
** * * * * ** * * *
18490757 GTCGTTGCGGCCTCGATCTTTCCCATCA-CGCCTCTAAGGTACCA-GG-TTT
1 ACCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCTATGGTA-CATGGATTC
* * * *
18490806 ACCATTACGACCTCAACCTTT-CCTTTCATATCTT-TATGGTAC-CGGATTC
1 ACCGTTGCGGCCTCAACCTTTCCCTTT-ATATCTTCTATGGTACATGGATTC
* * * * *
18490855 ACCGTTGTGGCCTCAATCC-TTCCCATCACATCTTCTAAGGTACATGG-TTC
1 ACCGTTGCGGCCTCAA-CCTTTCCCTTTATATCTTCTATGGTACATGGATTC
**
18490905 ACCGTTGCACCCTCAACCTTTCCCTTTATATCTTC-ATGGT--ATCGGATTC
1 ACCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCTATGGTACAT-GGATTC
* *
18490954 ACCGTTGCGGCCTCAATCTTTTCCTTTAT
1 ACCGTTGCGGCCTCAACCTTTCCCTTTAT
18490983 TTCCATGGTG
Statistics
Matches: 237, Mismatches: 70, Indels: 36
0.69 0.20 0.10
Matches are distributed among these distances:
47 2 0.01
48 9 0.04
49 139 0.59
50 85 0.36
51 2 0.01
ACGTcount: A:0.20, C:0.30, G:0.15, T:0.35
Consensus pattern (51 bp):
ACCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCTATGGTACATGGATTC
Found at i:18492965 original size:71 final size:71
Alignment explanation
Indices: 18492826--18492964 Score: 187
Period size: 71 Copynumber: 2.0 Consensus size: 71
18492816 ATAGATTTTC
* *
18492826 AAGATGCCCTTTGCGGGTTTTCATCTTGACTTTCTTTTTTTCTTCCTTTTTCTTTTCTTTTCTTT
1 AAGATGCCCTTTGCGGGTTTTCATATTGACTTTCTTTTTTTCTTCCTTTTTCTTTTCTTATCTTT
18492891 TTTTAA
66 TTTTAA
* *
18492897 AAGATGCCCTTTGTGGGTTTTCTTATTGACTTT-TTGTTTCTT-TT-C-TTTTCTTCTTCTTATC
1 AAGATGCCCTTTGCGGGTTTTCATATTGACTTTCTT-TTT-TTCTTCCTTTTTCTT-TTCTTATC
18492958 TTTTTTT
63 TTTTTTT
18492965 TGATCTCCTA
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
69 7 0.11
70 17 0.28
71 35 0.57
72 2 0.03
ACGTcount: A:0.09, C:0.18, G:0.11, T:0.62
Consensus pattern (71 bp):
AAGATGCCCTTTGCGGGTTTTCATATTGACTTTCTTTTTTTCTTCCTTTTTCTTTTCTTATCTTT
TTTTAA
Found at i:18495703 original size:21 final size:21
Alignment explanation
Indices: 18495661--18495704 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
18495651 GCCTTCCTCT
*
18495661 TTGCGCTTCTTTTTCTTATCC
1 TTGCGCTTCTCTTTCTTATCC
*
18495682 TTGCGCTTTCTCTTT-TTGTCC
1 TTGCGC-TTCTCTTTCTTATCC
18495703 TT
1 TT
18495705 TGAATCAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.02, C:0.27, G:0.11, T:0.59
Consensus pattern (21 bp):
TTGCGCTTCTCTTTCTTATCC
Found at i:18508247 original size:30 final size:30
Alignment explanation
Indices: 18508194--18508395 Score: 175
Period size: 30 Copynumber: 6.8 Consensus size: 30
18508184 AAAAATGAAA
* *
18508194 TTTTAGAAAGTTT-AGGGGCCAAATTCAAAT
1 TTTTGGAAAGTTTGA-GGGTCAAATTCAAAT
*
18508224 TTTTGGGAAGTTTGAGGGTCAAATTCAAAT
1 TTTTGGAAAGTTTGAGGGTCAAATTCAAAT
*
18508254 TTTTAGAAAGTTTGAGGGTCAAAACTT--AAT
1 TTTTGGAAAGTTTGAGGGTC-AAA-TTCAAAT
* * * *
18508284 TTTTGGAAATTTTGGGGGTTAAA-ACATAAT
1 TTTTGGAAAGTTTGAGGGTCAAATTCA-AAT
* *
18508314 TTTTGGAAAGTTTAAGGGTCAAA-TAATAAT
1 TTTTGGAAAGTTTGAGGGTCAAATTCA-AAT
* **
18508344 TTTTAGAAAGTTT-AGGGTCAAATTTGAAT
1 TTTTGGAAAGTTTGAGGGTCAAATTCAAAT
*
18508373 TTTTGGATAGTTT-AGGGGTCAAA
1 TTTTGGAAAGTTTGA-GGGTCAAA
18508396 AAATAATTTC
Statistics
Matches: 143, Mismatches: 21, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
29 27 0.19
30 110 0.77
31 4 0.03
32 2 0.01
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (30 bp):
TTTTGGAAAGTTTGAGGGTCAAATTCAAAT
Found at i:18508404 original size:30 final size:30
Alignment explanation
Indices: 18508180--18508404 Score: 158
Period size: 30 Copynumber: 7.5 Consensus size: 30
18508170 GGAGAAACGA
* *
18508180 GGTC-AAAAATGAAATTTTAGAAAGTTTAGG
1 GGTCAAAAAAT-AATTTTTGGAAAGTTTAGG
* ** *
18508210 GGCCAAATTCA-AATTTTTGGGAAGTTT-GAG
1 GGTCAAA-AAATAATTTTTGGAAAGTTTAG-G
** *
18508240 GGTCAAATTCA-AATTTTTAGAAAGTTT-GAG
1 GGTCAAA-AAATAATTTTTGGAAAGTTTAG-G
** * *
18508270 GGTCAAAACTTAATTTTTGGAAATTTTGGG
1 GGTCAAAAAATAATTTTTGGAAAGTTTAGG
* * *
18508300 GGTTAAAACATAATTTTTGGAAAGTTTAAG
1 GGTCAAAAAATAATTTTTGGAAAGTTTAGG
* *
18508330 GGTCAAATAATAATTTTTAGAAAGTTTA-G
1 GGTCAAAAAATAATTTTTGGAAAGTTTAGG
** *
18508359 GGTC-AAATTTGAATTTTTGGATAGTTTAGG
1 GGTCAAAAAAT-AATTTTTGGAAAGTTTAGG
18508389 GGTCAAAAAATAATTT
1 GGTCAAAAAATAATTT
18508405 CTAAATAAAA
Statistics
Matches: 158, Mismatches: 29, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
28 3 0.02
29 22 0.14
30 125 0.79
31 7 0.04
32 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.36
Consensus pattern (30 bp):
GGTCAAAAAATAATTTTTGGAAAGTTTAGG
Found at i:18514390 original size:18 final size:18
Alignment explanation
Indices: 18514367--18514413 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
18514357 CTTATGAAGT
*
18514367 TGTCGACGCAATTGCCAA
1 TGTCGACACAATTGCCAA
18514385 TGTCGACACAATTGCCAA
1 TGTCGACACAATTGCCAA
18514403 TGTCGACACAA
1 TGTCGACACAA
18514414 CCGGGTGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (18 bp):
TGTCGACACAATTGCCAA
Found at i:18521249 original size:25 final size:24
Alignment explanation
Indices: 18521219--18521268 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
18521209 GGTGTTGAAG
*
18521219 AGGAAGA-AGAGAAAAGAGAATAAGA
1 AGGAAGAGA-AGAAAAG-GAAAAAGA
18521244 AGGAAGAGAAGAAAAGGAAAAAGA
1 AGGAAGAGAAGAAAAGGAAAAAGA
18521268 A
1 A
18521269 ATTGAAGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 8 0.35
25 14 0.61
26 1 0.04
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (24 bp):
AGGAAGAGAAGAAAAGGAAAAAGA
Found at i:18521721 original size:17 final size:17
Alignment explanation
Indices: 18521679--18521713 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
18521669 ATGCATTTCA
*
18521679 TATAGTTGTCACTGCAT
1 TATACTTGTCACTGCAT
*
18521696 TATACTTGTCTCTGCAT
1 TATACTTGTCACTGCAT
18521713 T
1 T
18521714 TTATTTGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (17 bp):
TATACTTGTCACTGCAT
Found at i:18528244 original size:19 final size:19
Alignment explanation
Indices: 18528148--18528247 Score: 130
Period size: 19 Copynumber: 5.3 Consensus size: 19
18528138 CAGTATAGTA
*
18528148 TATTGCTCTTACGAGCCAG
1 TATTGCTCTTACGAGCTAG
* *
18528167 AATTGCTCTTACGAGCCAG
1 TATTGCTCTTACGAGCTAG
*
18528186 TATTGCTCTTACGAGCTAA
1 TATTGCTCTTACGAGCTAG
*
18528205 TATTGCTCTTATGAG-TCAG
1 TATTGCTCTTACGAGCT-AG
*
18528224 TATTGCTCTTACAAGCTAG
1 TATTGCTCTTACGAGCTAG
18528243 TATTG
1 TATTG
18528248 TTGATTTCTT
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
18 1 0.01
19 69 0.97
20 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (19 bp):
TATTGCTCTTACGAGCTAG
Found at i:18534002 original size:17 final size:17
Alignment explanation
Indices: 18533965--18534000 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
18533955 ACTACAATGC
*
18533965 AAATGCATTGACAAATA
1 AAATGCAGTGACAAATA
18533982 AAATGCAGTGAC-AATA
1 AAATGCAGTGACAAATA
18533998 AAA
1 AAA
18534001 ATATGATGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.56, C:0.11, G:0.14, T:0.19
Consensus pattern (17 bp):
AAATGCAGTGACAAATA
Found at i:18541794 original size:22 final size:21
Alignment explanation
Indices: 18541756--18541796 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
18541746 AAGAAAAGAA
18541756 AAAATAACTTATATATTAATT
1 AAAATAACTTATATATTAATT
* *
18541777 AAAATTACTATATTTATTAA
1 AAAATAACT-TATATATTAA
18541797 ATATTTTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAATAACTTATATATTAATT
Found at i:18552931 original size:65 final size:65
Alignment explanation
Indices: 18552822--18553015 Score: 282
Period size: 65 Copynumber: 3.0 Consensus size: 65
18552812 TACTTTTGGA
* * *
18552822 TTAATTTCATCTTTGGTCCCTTCAAATTGCTTTTTGCTTTAATTTAATTACTCTCCAGCGTTGAT
1 TTAACTTCATCTTTGGTCCCTTTAAATTGCTTTTTGCTTTAATTTAATTGCTCTCCAGCGTTGAT
* *
18552887 TTAACTTCATCTTTGGTCCCTTTAAATTGCTTTTTGCTTTAATTTAATTGCTCTCCAGTGTTGGT
1 TTAACTTCATCTTTGGTCCCTTTAAATTGCTTTTTGCTTTAATTTAATTGCTCTCCAGCGTTGAT
* * * * *
18552952 TTAACTTCATCTTTGGTCCCCTTAAATTACCTTCTGCTTTAATTTGATTGCT-TCCTAGCGTTGA
1 TTAACTTCATCTTTGGTCCCTTTAAATTGCTTTTTGCTTTAATTTAATTGCTCTCC-AGCGTTGA
18553016 ATTCTATGTG
Statistics
Matches: 116, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
64 3 0.03
65 113 0.97
ACGTcount: A:0.19, C:0.21, G:0.12, T:0.48
Consensus pattern (65 bp):
TTAACTTCATCTTTGGTCCCTTTAAATTGCTTTTTGCTTTAATTTAATTGCTCTCCAGCGTTGAT
Found at i:18558907 original size:21 final size:21
Alignment explanation
Indices: 18558870--18558921 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
18558860 ATTAACATGG
*
18558870 TTTATATTAAATATAAATA-GA
1 TTTA-ATTAAATATAAAAATGA
*
18558891 TTTAATTAAGATTTAAAAATGA
1 TTTAATTAA-ATATAAAAATGA
18558913 TTT-ATTAAA
1 TTTAATTAAA
18558922 GCTTAATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 6 0.22
21 16 0.59
22 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (21 bp):
TTTAATTAAATATAAAAATGA
Found at i:18563181 original size:20 final size:19
Alignment explanation
Indices: 18563158--18563231 Score: 60
Period size: 20 Copynumber: 3.8 Consensus size: 19
18563148 ACTATGGTGA
18563158 CTTTGTTTGCACTTTCATGC
1 CTTTGTTTGCAC-TTCATGC
* * *
18563178 CTTTGTATGAACGTCAGTG-
1 CTTTGTTTGCACTTCA-TGC
**
18563197 CTTCTGTTTGCACTTGGTGC
1 CTT-TGTTTGCACTTCATGC
*
18563217 CTTTGTTTCCACTTC
1 CTTTGTTTGCACTTC
18563232 GGTGCCTATG
Statistics
Matches: 41, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
19 18 0.44
20 23 0.56
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (19 bp):
CTTTGTTTGCACTTCATGC
Found at i:18563237 original size:20 final size:19
Alignment explanation
Indices: 18563201--18563258 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
18563191 TCAGTGCTTC
* *
18563201 TGTTTGCACTTGGTGCCTT
1 TGTTTCCACTTGGTGCCTA
18563220 TGTTTCCACTTCGGTGCCTA
1 TGTTTCCACTT-GGTGCCTA
*
18563240 TGTATCCACTATGGTGCCT
1 TGTTTCCACT-TGGTGCCT
18563259 CTATTTACAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 10 0.29
20 23 0.68
21 1 0.03
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.41
Consensus pattern (19 bp):
TGTTTCCACTTGGTGCCTA
Found at i:18563269 original size:20 final size:20
Alignment explanation
Indices: 18563246--18563285 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
18563236 CCTATGTATC
*
18563246 CACTATGGTGCCTCTATTTA
1 CACTATGGTACCTCTATTTA
18563266 CACTATGGTACCTCTATTTA
1 CACTATGGTACCTCTATTTA
18563286 GAACGTTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (20 bp):
CACTATGGTACCTCTATTTA
Found at i:18563314 original size:16 final size:16
Alignment explanation
Indices: 18563293--18563325 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
18563283 TTAGAACGTT
18563293 GGTGTTTTCTAGTGTG
1 GGTGTTTTCTAGTGTG
18563309 GGTGTTTTCTAGTGTG
1 GGTGTTTTCTAGTGTG
18563325 G
1 G
18563326 TATGGTTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.06, G:0.39, T:0.48
Consensus pattern (16 bp):
GGTGTTTTCTAGTGTG
Found at i:18583043 original size:38 final size:38
Alignment explanation
Indices: 18583000--18583083 Score: 168
Period size: 38 Copynumber: 2.2 Consensus size: 38
18582990 AGAATACATT
18583000 AAAGCAATATAAAACAACCACACATAATTCAACGCCAG
1 AAAGCAATATAAAACAACCACACATAATTCAACGCCAG
18583038 AAAGCAATATAAAACAACCACACATAATTCAACGCCAG
1 AAAGCAATATAAAACAACCACACATAATTCAACGCCAG
18583076 AAAGCAAT
1 AAAGCAAT
18583084 CAAATTAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.54, C:0.25, G:0.08, T:0.13
Consensus pattern (38 bp):
AAAGCAATATAAAACAACCACACATAATTCAACGCCAG
Found at i:18583629 original size:65 final size:65
Alignment explanation
Indices: 18583540--18583679 Score: 181
Period size: 65 Copynumber: 2.2 Consensus size: 65
18583530 ACAATATAAA
** * *
18583540 ATGAAGTTAAAACAACGCCAGAAAGCAATCAAATTAAAACAAAAGGCAATTTAAAGGGACCAAAG
1 ATGAAGTTAAAACAACGCCAGAAAGCAATCAAATTAAAACAAAAAACAATATAAAGCGACCAAAG
* ** * * *
18583605 ATGAAGTTAAATCAACGCTGGAAAGTAATTAAATTAAAGCAAAAAACAATATAAAGCGACCAAAG
1 ATGAAGTTAAAACAACGCCAGAAAGCAATCAAATTAAAACAAAAAACAATATAAAGCGACCAAAG
*
18583670 ATGAAATTAA
1 ATGAAGTTAA
18583680 GCCCAAAGTA
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.54, C:0.13, G:0.16, T:0.17
Consensus pattern (65 bp):
ATGAAGTTAAAACAACGCCAGAAAGCAATCAAATTAAAACAAAAAACAATATAAAGCGACCAAAG
Found at i:18584432 original size:18 final size:18
Alignment explanation
Indices: 18584397--18584436 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
18584387 AAATAATATT
** *
18584397 TAAAAATTATTTATTTAA
1 TAAAAATTATAAAATTAA
18584415 TAAAAATTATAAAATTAA
1 TAAAAATTATAAAATTAA
18584433 TAAA
1 TAAA
18584437 GTATATTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAAATTATAAAATTAA
Found at i:18584477 original size:2 final size:2
Alignment explanation
Indices: 18584470--18584503 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
18584460 TCATATTCAA
18584470 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18584504 ATTTTATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:18584491 original size:17 final size:17
Alignment explanation
Indices: 18584469--18584505 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
18584459 TTCATATTCA
18584469 AATATATATATATATAT
1 AATATATATATATATAT
18584486 AATATATATATATATAT
1 AATATATATATATATAT
18584503 AAT
1 AAT
18584506 TTTATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATATATATATATATAT
Found at i:18584492 original size:15 final size:15
Alignment explanation
Indices: 18584472--18584501 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
18584462 ATATTCAAAT
18584472 ATATATATATATATA
1 ATATATATATATATA
18584487 ATATATATATATATA
1 ATATATATATATATA
18584502 TAATTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:18584556 original size:23 final size:24
Alignment explanation
Indices: 18584511--18584557 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
18584501 ATAATTTTAT
**
18584511 AAAAAACATATAAAAATTTTAAAA
1 AAAAAACATATAAAAATAATAAAA
*
18584535 AAAAAACTTAT-AAAATAATAAAA
1 AAAAAACATATAAAAATAATAAAA
18584558 TTTCATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.23
Consensus pattern (24 bp):
AAAAAACATATAAAAATAATAAAA
Found at i:18584599 original size:48 final size:47
Alignment explanation
Indices: 18584542--18584634 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 47
18584532 AAAAAAAAAC
18584542 TTATAAAATAATAAAATTTCAT-TAAAAATCATAAAAAATATAAAAATA
1 TTATAAAATAATAAAATTT-ATAT-AAAATCATAAAAAATATAAAAATA
* * * * *
18584590 TTATTAAATATTAAAATTTATATAAACTTATAAAAATTATAAAAA
1 TTATAAAATAATAAAATTTATATAAAATCATAAAAAATATAAAAA
18584635 AACCTAATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
47 21 0.54
48 18 0.46
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (47 bp):
TTATAAAATAATAAAATTTATATAAAATCATAAAAAATATAAAAATA
Found at i:18584620 original size:10 final size:9
Alignment explanation
Indices: 18584519--18584634 Score: 55
Period size: 9 Copynumber: 12.9 Consensus size: 9
18584509 ATAAAAAACA
18584519 TATAAAAAT
1 TATAAAAAT
*
18584528 TTTAAAAA-
1 TATAAAAAT
*
18584536 -A-AAAACT
1 TATAAAAAT
18584543 TAT-AAAAT
1 TATAAAAAT
* *
18584551 AATAAAATT
1 TATAAAAAT
18584560 TCATTAAAAAT
1 T-A-TAAAAAT
* *
18584571 CATAAAAAA
1 TATAAAAAT
18584580 TATAAAAA-
1 TATAAAAAT
*
18584588 TATTATTAAA-
1 TA-TA-AAAAT
*
18584598 TATTAAAATT
1 TA-TAAAAAT
*
18584608 TATATAAACT
1 TATA-AAAAT
18584618 TATAAAAAT
1 TATAAAAAT
18584627 TATAAAAA
1 TATAAAAA
18584635 AACCTAATAA
Statistics
Matches: 81, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
6 4 0.05
8 9 0.11
9 42 0.52
10 20 0.25
11 6 0.07
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (9 bp):
TATAAAAAT
Found at i:18584646 original size:11 final size:11
Alignment explanation
Indices: 18584619--18584665 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
18584609 ATATAAACTT
18584619 ATAAAAAT-TA
1 ATAAAAATCTA
* *
18584629 TAAAAAAACCTA
1 -ATAAAAATCTA
*
18584641 ATAAAATTCTA
1 ATAAAAATCTA
18584652 ATAAAAATCTA
1 ATAAAAATCTA
18584663 ATA
1 ATA
18584666 TCATATCATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAAAAATCTA
Found at i:18584646 original size:21 final size:22
Alignment explanation
Indices: 18584622--18584665 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
18584612 TAAACTTATA
18584622 AAAATTATAA-AAAAACCTAAT
1 AAAATTATAATAAAAACCTAAT
* *
18584643 AAAATTCTAATAAAAATCTAAT
1 AAAATTATAATAAAAACCTAAT
18584665 A
1 A
18584666 TCATATCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAATTATAATAAAAACCTAAT
Found at i:18584768 original size:3 final size:3
Alignment explanation
Indices: 18584757--18584803 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
18584747 TATTATTAAA
18584757 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
18584804 GGTGTCAACT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:18587993 original size:14 final size:14
Alignment explanation
Indices: 18587893--18587999 Score: 72
Period size: 14 Copynumber: 7.4 Consensus size: 14
18587883 TATTTTGAAT
* *
18587893 TTTAGGGTTTTTAA
1 TTTAAGGTTTTAAA
*
18587907 TTTAAGGGTTTTGAA
1 TTTAA-GGTTTTAAA
*
18587922 TTAAAGGTTTTAAA
1 TTTAAGGTTTTAAA
**
18587936 TTTTGAAGG-TTTAGGG
1 -TTT-AAGGTTTTA-AA
*
18587952 TTTAAGGTTTTGAA
1 TTTAAGGTTTTAAA
* *
18587966 TATAAGGTTATAAA
1 TTTAAGGTTTTAAA
*
18587980 TTTAGGGTTTTAAAA
1 TTTAAGGTTTT-AAA
18587995 TTTAA
1 TTTAA
18588000 TATTTAAGGT
Statistics
Matches: 70, Mismatches: 17, Indels: 11
0.71 0.17 0.11
Matches are distributed among these distances:
14 35 0.50
15 31 0.44
16 4 0.06
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (14 bp):
TTTAAGGTTTTAAA
Found at i:18588010 original size:22 final size:21
Alignment explanation
Indices: 18587979--18588020 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
18587969 AAGGTTATAA
*
18587979 ATTTAGGGTTTTAAAATTTAAT
1 ATTTAAGG-TTTAAAATTTAAT
*
18588001 ATTTAAGGTTTAGAATTTAA
1 ATTTAAGGTTTAAAATTTAA
18588021 GTTAGTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (21 bp):
ATTTAAGGTTTAAAATTTAAT
Found at i:18590600 original size:24 final size:24
Alignment explanation
Indices: 18590573--18590620 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
18590563 ATTAAACTTA
*
18590573 TAATTAAAAT-AAATTGCAACGGAT
1 TAATGAAAATCAAATT-CAACGGAT
*
18590597 TAATGAAAATCAAATTCAAGGGAT
1 TAATGAAAATCAAATTCAACGGAT
18590621 CTGTTTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (24 bp):
TAATGAAAATCAAATTCAACGGAT
Found at i:18591550 original size:22 final size:21
Alignment explanation
Indices: 18591483--18591555 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 21
18591473 ATAATATTTG
18591483 AATTCTTCTAGAGTCAACATTA
1 AATT-TTCTAGAGTCAACATTA
* * * *
18591505 AATTTT-TATATTGC-ACTTTG
1 AATTTTCTAGAGT-CAACATTA
18591525 AATTATTCTAGAGTCAACATTA
1 AATT-TTCTAGAGTCAACATTA
18591547 AA-TTTCTAG
1 AATTTTCTAG
18591556 TCTATACATA
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
20 18 0.46
21 7 0.18
22 14 0.36
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (21 bp):
AATTTTCTAGAGTCAACATTA
Found at i:18598379 original size:21 final size:20
Alignment explanation
Indices: 18598343--18598381 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
18598333 TAACAAATGT
*
18598343 ATAAAATAATTAAATATTAA
1 ATAAAATAAATAAATATTAA
18598363 ATAAAATAAAATAAATATT
1 ATAAAAT-AAATAAATATT
18598382 TTAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAAATAAATAAATATTAA
Found at i:18602126 original size:17 final size:19
Alignment explanation
Indices: 18602099--18602137 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
18602089 GATATGGGAC
*
18602099 AAAAATGAGAA-TGAAGTG
1 AAAAATGAGAATTGAAATG
18602117 AAAAAT-AGAATTGAAATG
1 AAAAATGAGAATTGAAATG
18602135 AAA
1 AAA
18602138 CTTGATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.18
Consensus pattern (19 bp):
AAAAATGAGAATTGAAATG
Found at i:18604665 original size:32 final size:32
Alignment explanation
Indices: 18604629--18605046 Score: 480
Period size: 32 Copynumber: 13.0 Consensus size: 32
18604619 CATGAAACAA
* ** *
18604629 TGTTCACAGATTGATAGCTCTTACAAGCTTAC
1 TGTTCACAGATTAATAGCTCTTATGAGCATAC
* *
18604661 TGTTCACAGATTGATAACTCTTATGAGCATAC
1 TGTTCACAGATTAATAGCTCTTATGAGCATAC
*
18604693 TATTCACAGATTAATAGCTCTTATGAGCATAC
1 TGTTCACAGATTAATAGCTCTTATGAGCATAC
* * * * *
18604725 TGTTCATAGATTGATAGCTCTTATAATCATAT
1 TGTTCACAGATTAATAGCTCTTATGAGCATAC
* * * *
18604757 TATTCATAGATTAATAGCTCTTCTAAGCATAC
1 TGTTCACAGATTAATAGCTCTTATGAGCATAC
* * * *
18604789 TATTCACAGATTGATAGCTCTTCTAAGCATAC
1 TGTTCACAGATTAATAGCTCTTATGAGCATAC
* * * *
18604821 TGTTCACAGATTGATAGCTCTTCTAAGAATAC
1 TGTTCACAGATTAATAGCTCTTATGAGCATAC
18604853 TGTTCACAGATTAATAGCTCTTATGAGCATAC
1 TGTTCACAGATTAATAGCTCTTATGAGCATAC
18604885 TGTTCACAGATTAATAGCTCTTATGAGCATAC
1 TGTTCACAGATTAATAGCTCTTATGAGCATAC
* *
18604917 TGTTAATAGATTAATAGCTCTTATGAGCATAC
1 TGTTCACAGATTAATAGCTCTTATGAGCATAC
* * *
18604949 TGTTCACAGATTGATAGCTCTTACGAGTATAC
1 TGTTCACAGATTAATAGCTCTTATGAGCATAC
* * **
18604981 TGTTCATAGATTAATAGCTCATATGAATATAC
1 TGTTCACAGATTAATAGCTCTTATGAGCATAC
* *
18605013 TAGGT-ACTAG-TTAGTTAGCTCTTATGAGCATAC
1 T-GTTCAC-AGATTA-ATAGCTCTTATGAGCATAC
18605046 T
1 T
18605047 ATGAAAATTA
Statistics
Matches: 339, Mismatches: 44, Indels: 5
0.87 0.11 0.01
Matches are distributed among these distances:
32 319 0.94
33 20 0.06
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (32 bp):
TGTTCACAGATTAATAGCTCTTATGAGCATAC
Found at i:18613744 original size:29 final size:29
Alignment explanation
Indices: 18613698--18613757 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
18613688 ACCTCCTTAG
* *
18613698 AATTATTCAACTTTGTGACAAGGGATTCA
1 AATTATTCAACTTCGTGACAAGGAATTCA
*
18613727 AATTATTCAACTTCGTGAGAAGGAATTCA
1 AATTATTCAACTTCGTGACAAGGAATTCA
18613756 AA
1 AA
18613758 GTAATATTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (29 bp):
AATTATTCAACTTCGTGACAAGGAATTCA
Found at i:18617383 original size:24 final size:24
Alignment explanation
Indices: 18617356--18617412 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
18617346 CTGCAACTTC
18617356 TACTAC-AAGTACACAAACTACCGA
1 TACTACTAAGTACA-AAACTACCGA
* * *
18617380 TACTTCTAAGTGCAAAACTACTGA
1 TACTACTAAGTACAAAACTACCGA
18617404 TATCTACTA
1 TA-CTACTA
18617413 TGCAACTACT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 16 0.59
25 11 0.41
ACGTcount: A:0.40, C:0.25, G:0.09, T:0.26
Consensus pattern (24 bp):
TACTACTAAGTACAAAACTACCGA
Found at i:18618045 original size:23 final size:24
Alignment explanation
Indices: 18618018--18618064 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
18618008 GACAGAATTG
*
18618018 GCTCTCACGAGCCCAGA-AGGTTA
1 GCTCTCACAAGCCCAGATAGGTTA
*
18618041 GCTCTTACAAGCCCAGATAGGTTA
1 GCTCTCACAAGCCCAGATAGGTTA
18618065 ACCAGTATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (24 bp):
GCTCTCACAAGCCCAGATAGGTTA
Found at i:18619340 original size:29 final size:30
Alignment explanation
Indices: 18619293--18619351 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
18619283 TCTTACTTAA
* *
18619293 TTAACTTTAACTAACTTATAA-ATTTAAAAT
1 TTAAATTTAACTAAATTATAATA-TTAAAAT
18619323 TTAAATTTAA-TAAATTATAATATTAAAAT
1 TTAAATTTAACTAAATTATAATATTAAAAT
18619352 ATATAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (30 bp):
TTAAATTTAACTAAATTATAATATTAAAAT
Found at i:18619376 original size:16 final size:15
Alignment explanation
Indices: 18619316--18619376 Score: 63
Period size: 16 Copynumber: 4.0 Consensus size: 15
18619306 ACTTATAAAT
18619316 TTAAAATTTA-AAT-
1 TTAAAATTTATAATA
*
18619329 TTAATAAATTATAATA
1 TTAA-AATTTATAATA
*
18619345 TTAAAATATATAAATA
1 TTAAAATTTAT-AATA
18619361 TTAAATATTTATAATA
1 TTAAA-ATTTATAATA
18619377 ATTATAATCA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
13 4 0.10
14 5 0.13
15 8 0.21
16 17 0.44
17 5 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TTAAAATTTATAATA
Found at i:18626882 original size:180 final size:181
Alignment explanation
Indices: 18626569--18626931 Score: 604
Period size: 180 Copynumber: 2.0 Consensus size: 181
18626559 ATCCCCCAAA
* *
18626569 ATTGATTTTTGGGCTTCTCACAAATGCTTTTCCAAATTAGACTTGTTTTCCCTTGTTTGGACCCA
1 ATTGATTTTTGGGCTGCTCACAAATGCTTTGCCAAATTAGACTTGTTTTCCCTTGTTTGGACCCA
* * * *
18626634 ATTTGTTTACCAAACTTGTCCATCAATTGATCCATCTTTAATTGGATGAAATCAATCTCTTTATG
66 ATTTGTTTACCAAACTTGTCCATCAATTGATCCATCTTCAATTAGATGAAATCAAGCTCTTCATG
*
18626699 ACCCATTTTGCATGTGTTTTTCGTCCAAAT-AGAATGAA-TTGGGTATGTCC
131 ACCCATTTTGCATGTGTTTTTCGTCCAAATGA-AATGAATTTGGGCATGTCC
*
18626749 ATTGATTTTTGGGCTGCTCACAAATGCTTTGCCAAATTGGACTTGTTTTCCCTTGTTTGGACCCA
1 ATTGATTTTTGGGCTGCTCACAAATGCTTTGCCAAATTAGACTTGTTTTCCCTTGTTTGGACCCA
* *
18626814 ATTTGTTTACTAGACTTGTCCATCAATTGATCCATCTTCAATTAGATGAAATCAAGCTCTTCATG
66 ATTTGTTTACCAAACTTGTCCATCAATTGATCCATCTTCAATTAGATGAAATCAAGCTCTTCATG
*
18626879 ACCCATTTTGCATGTGTTTTTCGTCCATATGAAATGAATTTGGGCATGTCC
131 ACCCATTTTGCATGTGTTTTTCGTCCAAATGAAATGAATTTGGGCATGTCC
18626930 AT
1 AT
18626932 GTAACTTTAT
Statistics
Matches: 170, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
180 156 0.92
181 14 0.08
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (181 bp):
ATTGATTTTTGGGCTGCTCACAAATGCTTTGCCAAATTAGACTTGTTTTCCCTTGTTTGGACCCA
ATTTGTTTACCAAACTTGTCCATCAATTGATCCATCTTCAATTAGATGAAATCAAGCTCTTCATG
ACCCATTTTGCATGTGTTTTTCGTCCAAATGAAATGAATTTGGGCATGTCC
Found at i:18628568 original size:20 final size:20
Alignment explanation
Indices: 18628545--18628586 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
18628535 AAAATCATGG
18628545 ATAAACTACCAA-AATCACAA
1 ATAAACTACCAATAATCA-AA
*
18628565 ATAAACTACTAATAATCAAA
1 ATAAACTACCAATAATCAAA
18628585 AT
1 AT
18628587 TATGGACAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.60, C:0.19, G:0.00, T:0.21
Consensus pattern (20 bp):
ATAAACTACCAATAATCAAA
Found at i:18628571 original size:47 final size:47
Alignment explanation
Indices: 18628518--18628632 Score: 149
Period size: 47 Copynumber: 2.4 Consensus size: 47
18628508 AATAATGCAG
* * *
18628518 ATAAACTGCCAATAATCAAAATCATGGATAAACTACCAAAATCACAA
1 ATAAACTACCAATAATCAAAATCATGGACAAACCACCAAAATCACAA
* * * *
18628565 ATAAACTACTAATAATCAAAATTATGGACAAGCCACCAAAATCACAG
1 ATAAACTACCAATAATCAAAATCATGGACAAACCACCAAAATCACAA
*
18628612 ATATACTACCACATAATCAAA
1 ATAAACTACCA-ATAATCAAA
18628633 TCGTGAACAG
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
47 49 0.84
48 9 0.16
ACGTcount: A:0.52, C:0.22, G:0.06, T:0.20
Consensus pattern (47 bp):
ATAAACTACCAATAATCAAAATCATGGACAAACCACCAAAATCACAA
Found at i:18629180 original size:8 final size:8
Alignment explanation
Indices: 18629169--18629193 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
18629159 ATTTTATCCC
18629169 TTTAAAAT
1 TTTAAAAT
18629177 TTTAAAAT
1 TTTAAAAT
18629185 TTTAAAAT
1 TTTAAAAT
18629193 T
1 T
18629194 AGTAAAGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTAAAAT
Found at i:18634279 original size:17 final size:18
Alignment explanation
Indices: 18634241--18634281 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
18634231 CTTTACTTTT
* *
18634241 ATTTTATTTTACCACTGA
1 ATTTTATTTTAACACAGA
18634259 ATTTTATTTTAACA-AGA
1 ATTTTATTTTAACACAGA
18634276 ATTTTA
1 ATTTTA
18634282 GTCACCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (18 bp):
ATTTTATTTTAACACAGA
Found at i:18635784 original size:30 final size:32
Alignment explanation
Indices: 18635748--18635826 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 32
18635738 CTTTTATGTC
* *
18635748 TTAAATTTTGAATTAAAAT-TTTTAATTTA-T
1 TTAAATTTTAAATTAAAATATTTAAATTTATT
* *
18635778 TTAAA-TTTAAATTCAACTATTTAAATTTATT
1 TTAAATTTTAAATTAAAATATTTAAATTTATT
*
18635809 TTAAA-TTTAAATTTAAAT
1 TTAAATTTTAAATTAAAAT
18635827 CAAATTATGA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 10 0.24
30 14 0.34
31 17 0.41
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (32 bp):
TTAAATTTTAAATTAAAATATTTAAATTTATT
Found at i:18635785 original size:6 final size:6
Alignment explanation
Indices: 18635776--18635826 Score: 59
Period size: 6 Copynumber: 8.3 Consensus size: 6
18635766 TTTTTAATTT
* *
18635776 ATTTAA ATTTAA ATTCAA CTATTTAA ATTT-A TTTTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA --ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
18635825 AT
1 AT
18635827 CAAATTATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
5 4 0.11
6 29 0.76
8 5 0.13
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (6 bp):
ATTTAA
Found at i:18637695 original size:28 final size:28
Alignment explanation
Indices: 18637663--18637761 Score: 101
Period size: 29 Copynumber: 3.5 Consensus size: 28
18637653 AAACAGTCCT
*
18637663 AAAATTACATTTTGACCCAAAACTTTAA
1 AAAATTACATTTTGACCCAAAACTTTCA
* * *
18637691 AAAATTATATTTTGACACCGAAACTTCCA
1 AAAATTACATTTTGAC-CCAAAACTTTCA
* *
18637720 AAAATTACCATTTT-ACCTCCAAACTTTCC
1 AAAATTA-CATTTTGACC-CAAAACTTTCA
*
18637749 AAAATTCCATTTT
1 AAAATTACATTTT
18637762 TAACCCCAGT
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
28 22 0.37
29 32 0.54
30 5 0.08
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAATTACATTTTGACCCAAAACTTTCA
Found at i:18637918 original size:38 final size:37
Alignment explanation
Indices: 18637850--18637923 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 37
18637840 TATCCTGAAC
* *
18637850 TTTCTAAAATTCCATTTTAGCCCCGGTTTCACCAAAG
1 TTTCCAAAATTCCATTTTAGCCCCGATTTCACCAAAG
*
18637887 TTTCCAAAATTCCATTTTTAAG-CTCGATTTCACCAAA
1 TTTCCAAAATTCCA-TTTT-AGCCCCGATTTCACCAAA
18637924 AATTACCATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 13 0.41
38 17 0.53
39 2 0.06
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.36
Consensus pattern (37 bp):
TTTCCAAAATTCCATTTTAGCCCCGATTTCACCAAAG
Found at i:18640620 original size:2 final size:2
Alignment explanation
Indices: 18640613--18640645 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18640603 ACATTCAATT
18640613 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
18640646 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:18643897 original size:31 final size:31
Alignment explanation
Indices: 18643862--18643956 Score: 92
Period size: 31 Copynumber: 3.2 Consensus size: 31
18643852 CTGGTATTTG
18643862 AACTTGACACTTTTTCATAATTTGGTACCTA
1 AACTTGACACTTTTTCATAATTTGGTACCTA
* * * *
18643893 AACTT-----TTTTTGACTCAAATTGATACCTG
1 AACTTGACACTTTTTCA-T-AATTTGGTACCTA
*
18643921 AACTTGACACTTTTTCCTAATTTGGTACCTA
1 AACTTGACACTTTTTCATAATTTGGTACCTA
18643952 AACTT
1 AACTT
18643957 TTTTTAGACC
Statistics
Matches: 48, Mismatches: 9, Indels: 14
0.68 0.13 0.20
Matches are distributed among these distances:
26 6 0.12
27 1 0.02
28 15 0.31
31 20 0.42
32 1 0.02
33 5 0.10
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.42
Consensus pattern (31 bp):
AACTTGACACTTTTTCATAATTTGGTACCTA
Found at i:18643952 original size:59 final size:59
Alignment explanation
Indices: 18643860--18644040 Score: 218
Period size: 59 Copynumber: 3.0 Consensus size: 59
18643850 ATCTGGTATT
* * *
18643860 TGAACTTGACACTTTTTCATAATTTGGTACCTAAACTTTTTTTGACTCAAATTGATACC
1 TGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTGACTCAATTTGGTACC
* *
18643919 TGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTAGACCCAATTTGGTATC
1 TGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTT-GACTCAATTTGGTACC
* **** * * *
18643979 TAAACTTGGTGTTTTTTTTCCTAATTTGGTACCTAATCTTTTTTAGATTCAATTTGGTACC
1 TGAACTT-G-ACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTGACTCAATTTGGTACC
18644040 T
1 T
18644041 AAATTTATTA
Statistics
Matches: 104, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
59 42 0.40
60 18 0.17
61 15 0.14
62 29 0.28
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.46
Consensus pattern (59 bp):
TGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTGACTCAATTTGGTACC
Found at i:18644285 original size:31 final size:31
Alignment explanation
Indices: 18644248--18644382 Score: 93
Period size: 31 Copynumber: 4.5 Consensus size: 31
18644238 CCCCAAAAAG
* *
18644248 TTTAAGTATCAACTTAA-AAAAAAGTGTCAAA
1 TTTAAGTACCAAATTAAGAAAAAA-TGTCAAA
*
18644279 TTTAAGTACCAAATTAAGAAAAAATGTCAAG
1 TTTAAGTACCAAATTAAGAAAAAATGTCAAA
* * * *
18644310 TTTGAGAACTAAATT-AGATAAAAA---AAAA
1 TTTAAGTACCAAATTAAGA-AAAAATGTCAAA
* * *
18644338 TTTAGGTATCAAATTAA-AAAAATATATCAAA
1 TTTAAGTACCAAATTAAGAAAAA-ATGTCAAA
* *
18644369 ATCAAGTACCAAAT
1 TTTAAGTACCAAAT
18644383 ATTATATTAA
Statistics
Matches: 79, Mismatches: 18, Indels: 14
0.71 0.16 0.13
Matches are distributed among these distances:
27 4 0.05
28 14 0.18
29 1 0.01
30 3 0.04
31 51 0.65
32 6 0.08
ACGTcount: A:0.54, C:0.09, G:0.10, T:0.27
Consensus pattern (31 bp):
TTTAAGTACCAAATTAAGAAAAAATGTCAAA
Found at i:18644847 original size:18 final size:19
Alignment explanation
Indices: 18644824--18644862 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
18644814 AACCTGATTT
18644824 TTAAAATAATTTAA-AAAA
1 TTAAAATAATTTAAGAAAA
*
18644842 TTAAAATATTTTAAGAAAA
1 TTAAAATAATTTAAGAAAA
18644861 TT
1 TT
18644863 TTCAATTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TTAAAATAATTTAAGAAAA
Found at i:18648216 original size:16 final size:16
Alignment explanation
Indices: 18648193--18648226 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
18648183 AATATTACAC
18648193 TTCCATAATTATC-TT
1 TTCCATAATTATCATT
18648208 TTCCAATAATTATCATT
1 TTCC-ATAATTATCATT
18648225 TT
1 TT
18648227 ACCCCTTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 9 0.53
17 4 0.24
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (16 bp):
TTCCATAATTATCATT
Found at i:18649324 original size:21 final size:21
Alignment explanation
Indices: 18649298--18649337 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18649288 GTAATCTCAA
**
18649298 TCCTCAATTTTCAATTTTCAG
1 TCCTCAATACTCAATTTTCAG
18649319 TCCTCAATACTCAATTTTC
1 TCCTCAATACTCAATTTTC
18649338 TTTTAATTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.28, G:0.03, T:0.45
Consensus pattern (21 bp):
TCCTCAATACTCAATTTTCAG
Found at i:18654347 original size:54 final size:55
Alignment explanation
Indices: 18654239--18654348 Score: 159
Period size: 54 Copynumber: 2.0 Consensus size: 55
18654229 TTAGGTGGGC
* * *
18654239 TTCTAATGTTAATGCTAATAGGTTTGGGGTCAAATGGAAATAATAATGGTGCTTA
1 TTCTAATGCTAATGCTAATAGGTTTGGGGTCAAATAGAAATAATAATGATGCTTA
* * *
18654294 TTCTAATGCTAATGCTGATAGGTTT-GGGTCCAATAGAATTAATAATGATGCTTA
1 TTCTAATGCTAATGCTAATAGGTTTGGGGTCAAATAGAAATAATAATGATGCTTA
18654348 T
1 T
18654349 AATAGTGATA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
54 26 0.53
55 23 0.47
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (55 bp):
TTCTAATGCTAATGCTAATAGGTTTGGGGTCAAATAGAAATAATAATGATGCTTA
Found at i:18654361 original size:54 final size:55
Alignment explanation
Indices: 18654242--18654361 Score: 143
Period size: 54 Copynumber: 2.2 Consensus size: 55
18654232 GGTGGGCTTC
* * * **
18654242 TAATGTTAATGCTAATAGGTTTGGGGTCAAATGGAAATAATAATGGTGCTTATTC
1 TAATGATAATGCTAATAGGTTTGGGGTCAAATAGAAATAATAATGATGCTTATAA
* * * *
18654297 TAATGCTAATGCTGATAGGTTT-GGGTCCAATAGAATTAATAATGATGCTTATAA
1 TAATGATAATGCTAATAGGTTTGGGGTCAAATAGAAATAATAATGATGCTTATAA
*
18654351 TAGTGATAATG
1 TAATGATAATG
18654362 GACCTAGTGC
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
54 35 0.64
55 20 0.36
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (55 bp):
TAATGATAATGCTAATAGGTTTGGGGTCAAATAGAAATAATAATGATGCTTATAA
Found at i:18658275 original size:58 final size:59
Alignment explanation
Indices: 18658175--18658448 Score: 281
Period size: 59 Copynumber: 4.7 Consensus size: 59
18658165 TAAACAATAA
* * * * *
18658175 TTTTGGACACTTCG-GGGTAAAATGGTAAGTTTTAGAAA-TTTCGGGTTCAAATATGGAAT
1 TTTTGGACA-TCCGAGGGTAAAATGG-AAATTTTTGAAAGTTTCGGGGTCAAAAATGGAAT
* * *
18658234 TTTTGGACATCCG-GGATAAAATGGAAATTTTTGAAAGTTTCGAGGTCAAAAATGAAAT
1 TTTTGGACATCCGAGGGTAAAATGGAAATTTTTGAAAGTTTCGGGGTCAAAAATGGAAT
* ** * * *
18658292 TTTTGGACATCCGAGGGTAAAATGGTAATTTTCAAAAGTTTTGGGGTAAAAAATGGTAT
1 TTTTGGACATCCGAGGGTAAAATGGAAATTTTTGAAAGTTTCGGGGTCAAAAATGGAAT
* * * * * *
18658351 TTTTAGACATCCGAGGATAAAATGGTAATTTTTGAAAGTTT-GGGGGC-AAAATGGTAC
1 TTTTGGACATCCGAGGGTAAAATGGAAATTTTTGAAAGTTTCGGGGTCAAAAATGGAAT
* *
18658408 TTTTGGATATCCGAGGGTAAAAT-GATAATTTTTGGAAGTTT
1 TTTTGGACATCCGAGGGTAAAATGGA-AATTTTTGAAAGTTT
18658449 AAGGTTAAAA
Statistics
Matches: 183, Mismatches: 29, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
56 1 0.01
57 53 0.29
58 47 0.26
59 82 0.45
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.34
Consensus pattern (59 bp):
TTTTGGACATCCGAGGGTAAAATGGAAATTTTTGAAAGTTTCGGGGTCAAAAATGGAAT
Found at i:18658321 original size:29 final size:29
Alignment explanation
Indices: 18658175--18658477 Score: 117
Period size: 29 Copynumber: 10.4 Consensus size: 29
18658165 TAAACAATAA
* * *
18658175 TTTTGGACACTTCGGGGTAAAATGGTAAG
1 TTTTGGAAAGTTCGGGGTAAAATGGTAAT
* * *
18658204 TTTTAGAAATTTCGGGTTCAAATATGG-AAT
1 TTTTGGAAAGTTCGGGGT-AAA-ATGGTAAT
* * * *
18658234 TTTTGGACA-TCCGGGATAAAATGGAAAT
1 TTTTGGAAAGTTCGGGGTAAAATGGTAAT
* *
18658262 TTTT-GAAAGTTTCGAGGTCAAAAAT-GAAAT
1 TTTTGGAAAG-TTCGGGGT--AAAATGGTAAT
* *
18658292 TTTTGGACA-TCCGAGGGTAAAATGGTAA-
1 TTTTGGAAAGTTCG-GGGTAAAATGGTAAT
** *
18658320 TTTTCAAAAGTTTTGGGGTAAAAAATGGT-AT
1 TTTTGGAAAG-TTCGGGGT--AAAATGGTAAT
* * * *
18658351 TTTTAGACA-TCCGAGGATAAAATGGTAAT
1 TTTTGGAAAGTTCG-GGGTAAAATGGTAAT
* * *
18658380 TTTT-GAAAGTTTGGGGGCAAAATGGT-AC
1 TTTTGGAAAG-TTCGGGGTAAAATGGTAAT
* * *
18658408 TTTTGGATA-TCCGAGGGTAAAATGATAAT
1 TTTTGGAAAGTTCG-GGGTAAAATGGTAAT
** * *
18658437 TTTTGG-AAGTTTAAGGTTAAAATTGTAAT
1 TTTTGGAAAG-TTCGGGGTAAAATGGTAAT
*
18658466 TTTTTGAAAGTT
1 TTTTGGAAAGTT
18658478 TATGGCAAAA
Statistics
Matches: 201, Mismatches: 48, Indels: 50
0.67 0.16 0.17
Matches are distributed among these distances:
27 9 0.04
28 48 0.24
29 82 0.41
30 36 0.18
31 26 0.13
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.35
Consensus pattern (29 bp):
TTTTGGAAAGTTCGGGGTAAAATGGTAAT
Found at i:18658487 original size:29 final size:30
Alignment explanation
Indices: 18658426--18658537 Score: 140
Period size: 30 Copynumber: 3.8 Consensus size: 30
18658416 ATCCGAGGGT
* **
18658426 AAAATGATAATTTTT-GGAAGTTTAAGGTTA
1 AAAATG-TAATTTTTAGAAAGTTTAAGGACA
* * *
18658456 AAATTGTAATTTTTTGAAAGTTTATGG-CA
1 AAAATGTAATTTTTAGAAAGTTTAAGGACA
18658485 AAAATGTAA-TTTTAGAAAGTTTAAGGACA
1 AAAATGTAATTTTTAGAAAGTTTAAGGACA
18658514 AAAATGTAATTTTTAGAAAGTTTA
1 AAAATGTAATTTTTAGAAAGTTTA
18658538 GGGGTTAAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
28 15 0.21
29 28 0.39
30 29 0.40
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.39
Consensus pattern (30 bp):
AAAATGTAATTTTTAGAAAGTTTAAGGACA
Found at i:18658547 original size:29 final size:29
Alignment explanation
Indices: 18658422--18658599 Score: 137
Period size: 29 Copynumber: 6.0 Consensus size: 29
18658412 GGATATCCGA
* *
18658422 GGGTAAAATGATAATTTTT-GGAAGTTTAA
1 GGGTAAAATG-TAATTTTTAGAAAGTTTAG
* * *
18658451 GGTTAAAATTGTAATTTTTTGAAAGTTTAT
1 GGGTAAAA-TGTAATTTTTAGAAAGTTTAG
**
18658481 GGCAAAAATGTAA-TTTTAGAAAGTTTAAG
1 GGGTAAAATGTAATTTTTAGAAAGTTT-AG
***
18658510 GACAAAAATGTAATTTTTAGAAAGTTTAG
1 GGGTAAAATGTAATTTTTAGAAAGTTTAG
* *
18658539 GGGTTAAATGTAATATATTT-GAAAACTTTAG
1 GGGTAAAATGTAAT-T-TTTAG-AAAGTTTAG
* * *
18658570 GGGTTAAAATATGATTTTTAGACAGTTTAG
1 GGG-TAAAATGTAATTTTTAGAAAGTTTAG
18658600 AGACCTCTTG
Statistics
Matches: 122, Mismatches: 18, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
28 12 0.10
29 45 0.37
30 41 0.34
31 16 0.13
32 8 0.07
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.39
Consensus pattern (29 bp):
GGGTAAAATGTAATTTTTAGAAAGTTTAG
Found at i:18658548 original size:58 final size:58
Alignment explanation
Indices: 18658422--18658552 Score: 163
Period size: 58 Copynumber: 2.2 Consensus size: 58
18658412 GGATATCCGA
* * ** * * *
18658422 GGGTAAAATGATAATTTTTGGAAGTTTAAGGTTAAAATTGTAATTTTTTGAAAGTTTAT
1 GGGTAAAATG-TAATTTTAGAAAGTTTAAGGACAAAAATGTAATTTTTAGAAAGTTTAG
**
18658481 GGCAAAAATGTAATTTTAGAAAGTTTAAGGACAAAAATGTAATTTTTAGAAAGTTTAG
1 GGGTAAAATGTAATTTTAGAAAGTTTAAGGACAAAAATGTAATTTTTAGAAAGTTTAG
*
18658539 GGGTTAAATGTAAT
1 GGGTAAAATGTAAT
18658553 ATATTTGAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
58 52 0.87
59 8 0.13
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.38
Consensus pattern (58 bp):
GGGTAAAATGTAATTTTAGAAAGTTTAAGGACAAAAATGTAATTTTTAGAAAGTTTAG
Found at i:18659692 original size:13 final size:14
Alignment explanation
Indices: 18659655--18659692 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
18659645 CCTTTTTTAT
*
18659655 TATTATTTTATAAA
1 TATTATTTAATAAA
*
18659669 TATTATTTAATATA
1 TATTATTTAATAAA
18659683 T-TTATTTAAT
1 TATTATTTAAT
18659693 GCACTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTATTTAATAAA
Found at i:18661087 original size:39 final size:39
Alignment explanation
Indices: 18661028--18661290 Score: 136
Period size: 39 Copynumber: 6.8 Consensus size: 39
18661018 GATAACTGCA
*
18661028 ATCTGCCCCAAGCTTGGGGTAGGAGATTGGCTGACTGTG
1 ATCTGCCCCAAGCTTGGGGTAAGAGATTGGCTGACTGTG
* * * * * ** **
18661067 ATTTGCCCCATGCTTAGGGTAAAAGATCGAATGACTGCA
1 ATCTGCCCCAAGCTTGGGGTAAGAGATTGGCTGACTGTG
* *
18661106 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGA-TGGTG
1 ATCTGCCCCAAGCTTGGGGTAAGAGATTGGCTGACT-GTG
* * * * * * * **
18661145 ATCTGCCCCAAACTCGAGGTAAAAGATCGGATGGCTGCA
1 ATCTGCCCCAAGCTTGGGGTAAGAGATTGGCTGACTGTG
* * *** *
18661184 ATCTG-CCTAGGCTCAAGATAAGAGATTGGCTGA-TGGTG
1 ATCTGCCCCAAGCTTGGGGTAAGAGATTGGCTGACT-GTG
* ** * * * * * **
18661222 ATCTACCTTAAGCTTAGGGTAAAAGATAGGATGGCTGCA
1 ATCTGCCCCAAGCTTGGGGTAAGAGATTGGCTGACTGTG
* *
18661261 ATCTGCCCCAGGCTCGGGGTAAGAGATTGG
1 ATCTGCCCCAAGCTTGGGGTAAGAGATTGG
18661291 TCAATGATGA
Statistics
Matches: 159, Mismatches: 60, Indels: 10
0.69 0.26 0.04
Matches are distributed among these distances:
37 1 0.01
38 25 0.16
39 131 0.82
40 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (39 bp):
ATCTGCCCCAAGCTTGGGGTAAGAGATTGGCTGACTGTG
Found at i:18661152 original size:78 final size:78
Alignment explanation
Indices: 18661022--18661290 Score: 337
Period size: 78 Copynumber: 3.5 Consensus size: 78
18661012 GTTTTAGATA
* * * * *
18661022 ACTGCAATCTGCCCCAAGCTTGGGGTAGGAGATTGGCTGACT-GTGATTTGCCCCATGCTTAGGG
1 ACTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGA-TGGTGATCTGCCCCAAGCTTAGGG
*
18661086 TAAAAGATCGAATG
65 TAAAAGATCGGATG
* *
18661100 ACTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAAC-TCGAGG
1 ACTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTTAG-GG
18661164 TAAAAGATCGGATG
65 TAAAAGATCGGATG
* * ** * * **
18661178 GCTGCAATCTG-CCTAGGCTCAAGATAAGAGATTGGCTGATGGTGATCTACCTTAAGCTTAGGGT
1 ACTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTTAGGGT
*
18661242 AAAAGATAGGATG
66 AAAAGATCGGATG
*
18661255 GCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGG
1 ACTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGG
18661291 TCAATGATGA
Statistics
Matches: 164, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
77 67 0.41
78 97 0.59
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.23
Consensus pattern (78 bp):
ACTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTTAGGGT
AAAAGATCGGATG
Found at i:18661588 original size:49 final size:49
Alignment explanation
Indices: 18661535--18662771 Score: 444
Period size: 49 Copynumber: 25.2 Consensus size: 49
18661525 TTTGCTGTTT
** *
18661535 CGACTTAAATTTTTGCTTTCATGCTTCTGAGGTATAAGGTTCGTCATTG
1 CGACTTAAATTTTCCCTTTCATGCTTCTGAGGTATAAGGTTCGCCATTG
* * * *
18661584 CGACTTAAACCTTTCCCTTTGCGT-CTTC-GTGGTACT--GGATTCGCCGTTG
1 CGACTTAAA-TTTTCCCTTT-CATGCTTCTGAGGTA-TAAGG-TTCGCCATTG
* * * *
18661633 CGGCTTAAATCTTTCCCTTTCATGCTTCTAAGGTATAAGGTTCGCCACTA
1 CGACTTAAAT-TTTCCCTTTCATGCTTCTGAGGTATAAGGTTCGCCATTG
* * ** * * *
18661683 TGACTTAAACCTTTCCCTTTTGTGTCTTC-AAGGTACT--GGATTCGTCTTTG
1 CGACTTAAA-TTTTCCCTTTCATG-CTTCTGAGGTA-TAAGG-TTCGCCATTG
*
18661733 CGGCTTAAATCTTTCCC-TTCATG-TCTCTGAGGTATAAGGTTCGCCATTG
1 CGACTTAAAT-TTTCCCTTTCATGCT-TCTGAGGTATAAGGTTCGCCATTG
* * * * * *
18661782 CGACTTAAACCTTTCACTTT-GTGTCTTC-GTGGTACT--GGATTCGTCGTTG
1 CGACTTAAA-TTTTCCCTTTCATG-CTTCTGAGGTA-TAAGG-TTCGCCATTG
* * * *
18661831 CGGCTTAAATCTTTCCC-TTCACG-TCTCTAAGGTATAAGGTTCGCCATTT
1 CGACTTAAAT-TTTCCCTTTCATGCT-TCTGAGGTATAAGGTTCGCCATTG
* * * *
18661880 CGACTTAAACCTTTCCCTTT-GTGTCTTC--ATTGTACT--GGATTCGCCGTTG
1 CGACTTAAA-TTTTCCCTTTCATG-CTTCTGA-GGTA-TAAGG-TTCGCCATTG
*
18661929 CGACTTAAATCTTTCCC-TTCATG-TCTCTGAGGTATAAGGTTCGTCATTG
1 CGACTTAAAT-TTTCCCTTTCATGCT-TCTGAGGTATAAGGTTCGCCATTG
* * * * *
18661978 CGACTTAAACCTTTCCCTTTGTAT-CTTC--ATGGTACT-AGATTCGCCGTTA
1 CGACTTAAA-TTTTCCCTTT-CATGCTTCTGA-GGTA-TAAGGTTCGCCATTG
* *
18662027 CGGCTTAAATCTTTCCC-TTCATG-TCTCTGAGGTGTAAGGTTCGCCATTG
1 CGACTTAAAT-TTTCCCTTTCATGCT-TCTGAGGTATAAGGTTCGCCATTG
* * *
18662076 CGACTTAAACCTTTCCCTTT-GTGTCTTC-GTA-GTACT--GGATTCGCCGTTG
1 CGACTTAAA-TTTTCCCTTTCATG-CTTCTG-AGGTA-TAAGG-TTCGCCATTG
18662125 CGACTTAAATCTTTCCC-TTCATG-TCTCTGAGGTATAAGGTTCGCCATTG
1 CGACTTAAAT-TTTCCCTTTCATGCT-TCTGAGGTATAAGGTTCGCCATTG
* * * * *
18662174 CGACTTAAACCTTTCCCTTT-GTGTCTTC-GTGGTACT--GGATTCACCGTTG
1 CGACTTAAA-TTTTCCCTTTCATG-CTTCTGAGGTA-TAAGG-TTCGCCATTG
* **
18662223 C-AGCTTAAATCTTTCCC-TTCATG-TCTCTGAGGCATAAGGTTTTCCATTG
1 CGA-CTTAAAT-TTTCCCTTTCATGCT-TCTGAGGTATAAGGTTCGCCATTG
* * * * * *
18662272 TGACTTAAACCTTTCCCTTT-GTGTCTTC-GTGGTACT--GGATTTGCCGTTG
1 CGACTTAAA-TTTTCCCTTTCATG-CTTCTGAGGTA-TAAGG-TTCGCCATTG
*
18662321 CGGCTTAAATCTTTCCC-TTCATGTCTT-TGAGGTATAAGGTTCGCCATTG
1 CGACTTAAAT-TTTCCCTTTCATG-CTTCTGAGGTATAAGGTTCGCCATTG
* * ** * * *
18662370 CAACTTAAACCTTT-CCTTTTGTGTCTTC-GTGGTACT--GGATTAC-TCGTTG
1 CGACTTAAA-TTTTCCCTTTCATG-CTTCTGAGGTA-TAAGG-TT-CGCCATTG
* * * *
18662419 CGGCTTAAATCTTT-TCTTTCATG-TCTCTGAGGTATAAAGTTTGCCATTG
1 CGACTTAAAT-TTTCCCTTTCATGCT-TCTGAGGTATAAGGTTCGCCATTG
* * * * *
18662468 CGACTTAAACCTTTCCCTTT-GTGTCTTC-GTGGTACT--GGATTCACCGTTG
1 CGACTTAAA-TTTTCCCTTTCATG-CTTCTGAGGTA-TAAGG-TTCGCCATTG
* * * *
18662517 CGGCTTAAATCTTTCTC-TTCATGTCTT-TGAGGTATAAAGTTCACCATTG
1 CGACTTAAAT-TTTCCCTTTCATG-CTTCTGAGGTATAAGGTTCGCCATTG
* * *
18662566 CGACTTAAACCTTTCCCTTT-GTGTCTTCGTTA--TACTACA--TTCGCCATTG
1 CGACTTAAA-TTTTCCCTTTCATG-CTTC-TGAGGTA-TA-AGGTTCGCCATTG
*
18662615 CGGCTTAAATCTTTCCC-TTCATG-TCTCTGAGGTATAAGGTTCGCCATTG
1 CGACTTAAAT-TTTCCCTTTCATGCT-TCTGAGGTATAAGGTTCGCCATTG
* * * * * *
18662664 CAACTTAAACCTTTCCCTTT-GTGTCTTC-GTGGTACT-AGAG-TCACCGTTG
1 CGACTTAAA-TTTTCCCTTTCATG-CTTCTGAGGTA-TAAG-GTTCGCCATTG
* *
18662713 CGGCTTAGATCTTTTCCC-TTCATG-TCTCTGAGGTATAAGGTTCGCCATTG
1 CGACTTA-A-ATTTTCCCTTTCATGCT-TCTGAGGTATAAGGTTCGCCATTG
18662763 CGACTTAAA
1 CGACTTAAA
18662772 CCTTTCTCTT
Statistics
Matches: 874, Mismatches: 170, Indels: 289
0.66 0.13 0.22
Matches are distributed among these distances:
47 13 0.01
48 67 0.08
49 610 0.70
50 162 0.19
51 22 0.03
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (49 bp):
CGACTTAAATTTTCCCTTTCATGCTTCTGAGGTATAAGGTTCGCCATTG
Found at i:18661838 original size:98 final size:98
Alignment explanation
Indices: 18661538--18662853 Score: 1972
Period size: 98 Copynumber: 13.4 Consensus size: 98
18661528 GCTGTTTCGA
* * * *
18661538 CTTAAATTTTTGCTTTCATG-CTTCTGAGGTATAAGGTTCGTCATTGCGACTTAAACCTTTCCCT
1 CTTAAATCTTTCCCTTCATGTC-TCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCT
*
18661602 TTGCGTCTTCGTGGTACTGGATTCGCCGTTGCGG
65 TTGTGTCTTCGTGGTACTGGATTCGCCGTTGCGG
* * **
18661636 CTTAAATCTTTCCCTTTCATG-CTTCTAAGGTATAAGGTTCGCCACTATGACTTAAACCTTTCCC
1 CTTAAATCTTTCCC-TTCATGTC-TCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCC
** * *
18661700 TTTTGTGTCTTCAAGGTACTGGATTCGTCTTTGCGG
64 -TTTGTGTCTTCGTGGTACTGGATTCGCCGTTGCGG
*
18661736 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCACTT
1 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
*
18661801 TGTGTCTTCGTGGTACTGGATTCGTCGTTGCGG
66 TGTGTCTTCGTGGTACTGGATTCGCCGTTGCGG
* * *
18661834 CTTAAATCTTTCCCTTCACGTCTCTAAGGTATAAGGTTCGCCATTTCGACTTAAACCTTTCCCTT
1 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
* * *
18661899 TGTGTCTTCATTGTACTGGATTCGCCGTTGCGA
66 TGTGTCTTCGTGGTACTGGATTCGCCGTTGCGG
*
18661932 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGTCATTGCGACTTAAACCTTTCCCTT
1 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
* * * *
18661997 TGTATCTTCATGGTACTAGATTCGCCGTTACGG
66 TGTGTCTTCGTGGTACTGGATTCGCCGTTGCGG
*
18662030 CTTAAATCTTTCCCTTCATGTCTCTGAGGTGTAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
1 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
* *
18662095 TGTGTCTTCGTAGTACTGGATTCGCCGTTGCGA
66 TGTGTCTTCGTGGTACTGGATTCGCCGTTGCGG
18662128 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
1 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
* *
18662193 TGTGTCTTCGTGGTACTGGATTCACCGTTGCAG
66 TGTGTCTTCGTGGTACTGGATTCGCCGTTGCGG
* ** *
18662226 CTTAAATCTTTCCCTTCATGTCTCTGAGGCATAAGGTTTTCCATTGTGACTTAAACCTTTCCCTT
1 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
*
18662291 TGTGTCTTCGTGGTACTGGATTTGCCGTTGCGG
66 TGTGTCTTCGTGGTACTGGATTCGCCGTTGCGG
* * *
18662324 CTTAAATCTTTCCCTTCATGTCTTTGAGGTATAAGGTTCGCCATTGCAACTTAAACCTTTCCTTT
1 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
*
18662389 TGTGTCTTCGTGGTACTGGATTAC-TCGTTGCGG
66 TGTGTCTTCGTGGTACTGGATT-CGCCGTTGCGG
* * * *
18662422 CTTAAATCTTTTCTTTCATGTCTCTGAGGTATAAAGTTTGCCATTGCGACTTAAACCTTTCCCTT
1 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
*
18662487 TGTGTCTTCGTGGTACTGGATTCACCGTTGCGG
66 TGTGTCTTCGTGGTACTGGATTCGCCGTTGCGG
* * * *
18662520 CTTAAATCTTTCTCTTCATGTCTTTGAGGTATAAAGTTCACCATTGCGACTTAAACCTTTCCCTT
1 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
** ** *
18662585 TGTGTCTTCGTTATACTACATTCGCCATTGCGG
66 TGTGTCTTCGTGGTACTGGATTCGCCGTTGCGG
*
18662618 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCAACTTAAACCTTTCCCTT
1 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
* * *
18662683 TGTGTCTTCGTGGTACTAGAGTCACCGTTGCGG
66 TGTGTCTTCGTGGTACTGGATTCGCCGTTGCGG
* *
18662716 CTTAGATCTTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCTCT
1 CTTAAATC-TTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCT
* * *
18662781 TTGTGTCTTCGTGGTATTGAAGTCGCCGTTGCGG
65 TTGTGTCTTCGTGGTACTGGATTCGCCGTTGCGG
* *
18662815 CTTAAATCTTTCCCTTCATGTCTCTAAGGTATATGGTTC
1 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTC
18662854 CCTTTGTGTG
Statistics
Matches: 1104, Mismatches: 108, Indels: 12
0.90 0.09 0.01
Matches are distributed among these distances:
97 1 0.00
98 881 0.80
99 177 0.16
100 45 0.04
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.39
Consensus pattern (98 bp):
CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
TGTGTCTTCGTGGTACTGGATTCGCCGTTGCGG
Found at i:18662113 original size:294 final size:294
Alignment explanation
Indices: 18661538--18663497 Score: 2849
Period size: 294 Copynumber: 6.7 Consensus size: 294
18661528 GCTGTTTCGA
* * * *
18661538 CTTAAATTTTTGCTTTCATG-CTTCTGAGGTATAAGGTTCGTCATTGCGACTTAAACCTTTCCCT
1 CTTAAATCTTTCCCTTCATGTC-TCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCT
* *
18661602 TTGCGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTTCATG-CTTCTAAGG
65 TTGTGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCC-TTCATGTC-TCTGAGG
* ** ** * *
18661666 TATAAGGTTCGCCACTATGACTTAAACCTTTCCCTTTTGTGTCTTCAAGGTACTGGATTCGTCTT
128 TATAAGGTTCGCCATTGCGACTTAAACCTTTCCC-TTTGTGTCTTCGTGGTACTGGATTCGCCGT
18661731 TGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTT
192 TGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTT
* *
18661796 CACTTTGTGTCTTCGTGGTACTGGATTCGTCGTTGCGG
257 CCCTTTGTGTCTTCGTGGTACTGGATTCGCCGTTGCGG
* * *
18661834 CTTAAATCTTTCCCTTCACGTCTCTAAGGTATAAGGTTCGCCATTTCGACTTAAACCTTTCCCTT
1 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
* * *
18661899 TGTGTCTTCATTGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTCTCTGAGGTAT
66 TGTGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTAT
* * * * *
18661964 AAGGTTCGTCATTGCGACTTAAACCTTTCCCTTTGTATCTTCATGGTACTAGATTCGCCGTTACG
131 AAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCGTTGCG
*
18662029 GCTTAAATCTTTCCCTTCATGTCTCTGAGGTGTAAGGTTCGCCATTGCGACTTAAACCTTTCCCT
196 GCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCT
* *
18662094 TTGTGTCTTCGTAGTACTGGATTCGCCGTTGCGA
261 TTGTGTCTTCGTGGTACTGGATTCGCCGTTGCGG
18662128 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
1 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
* * *
18662193 TGTGTCTTCGTGGTACTGGATTCACCGTTGCAGCTTAAATCTTTCCCTTCATGTCTCTGAGGCAT
66 TGTGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTAT
** * *
18662258 AAGGTTTTCCATTGTGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTTGCCGTTGCG
131 AAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCGTTGCG
* * *
18662323 GCTTAAATCTTTCCCTTCATGTCTTTGAGGTATAAGGTTCGCCATTGCAACTTAAACCTTTCCTT
196 GCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCT
*
18662388 TTGTGTCTTCGTGGTACTGGATTAC-TCGTTGCGG
261 TTGTGTCTTCGTGGTACTGGATT-CGCCGTTGCGG
* * * *
18662422 CTTAAATCTTTTCTTTCATGTCTCTGAGGTATAAAGTTTGCCATTGCGACTTAAACCTTTCCCTT
1 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
* * *
18662487 TGTGTCTTCGTGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCTCTTCATGTCTTTGAGGTAT
66 TGTGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTAT
* * ** ** *
18662552 AAAGTTCACCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTTATACTACATTCGCCATTGCG
131 AAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCGTTGCG
*
18662617 GCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCAACTTAAACCTTTCCCT
196 GCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCT
* * *
18662682 TTGTGTCTTCGTGGTACTAGAGTCACCGTTGCGG
261 TTGTGTCTTCGTGGTACTGGATTCGCCGTTGCGG
* *
18662716 CTTAGATCTTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCTCT
1 CTTAAATC-TTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCT
* * * *
18662781 TTGTGTCTTCGTGGTATTGAAGTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTAAGG--
65 TTGTGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTA
*
18662844 T-A---T----A-TG-G----------TTCCCTTTGTGTGCTT-GTGGTACTGGATTCACCGTTG
130 TAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGT-CTTCGTGGTACTGGATTCGCCGTTG
* *
18662888 CGGCTTAAATCTTTCCCTTCATGTCTCTTAGGTATAAGGTTTGCCATTGCGACTTAAACCTTTCC
194 CGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCC
*
18662953 CTTTGTGTCTTCGTGGTACTGGATTCGTCGTTGCGG
259 CTTTGTGTCTTCGTGGTACTGGATTCGCCGTTGCGG
18662989 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
1 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
* *
18663054 TGTGTCTTCGTGGTACTGGAGTCGCTGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTAT
66 TGTGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTAT
* * * * *
18663119 AAGGTTCGCCATTACGACTTAAACCTTTCCCTTTGTGTCTTAGTGGTACTGGAGTCGTCGTTGTG
131 AAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCGTTGCG
* * *
18663184 GCTTAAATCTCTCCCTTCATGTTTCTAAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCT
196 GCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCT
* * ** *
18663249 TTGTGTCTTCATGGTATTGGATTCGCCACTGTGG
261 TTGTGTCTTCGTGGTACTGGATTCGCCGTTGCGG
*
18663283 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTTGCCATTGCGACTTAAACCTTTCCCTT
1 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
* *
18663348 TGTGTCTTCGTAGTACTGGATTCGCCGTTGTGGCTTAAAATCTTTCCCTTCATGTCTCTGAGGTA
66 TGTGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTT-AAATCTTTCCCTTCATGTCTCTGAGGTA
* *
18663413 TAAGGTTCGCCATTGCGACTTAAACCTTTTCGTTTGTGTCTTCGTGGTACTGGAGTT-GCCGTTG
130 TAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGA-TTCGCCGTTG
*
18663477 CTGCTTAAATCTTTCCCTTCA
194 CGGCTTAAATCTTTCCCTTCA
18663498 AATTTTCATG
Statistics
Matches: 1497, Mismatches: 136, Indels: 63
0.88 0.08 0.04
Matches are distributed among these distances:
272 114 0.08
273 128 0.09
274 4 0.00
275 1 0.00
278 1 0.00
282 1 0.00
283 2 0.00
284 3 0.00
285 1 0.00
289 1 0.00
292 1 0.00
293 5 0.00
294 881 0.59
295 252 0.17
296 101 0.07
297 1 0.00
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (294 bp):
CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
TGTGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTAT
AAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCGTTGCG
GCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCT
TTGTGTCTTCGTGGTACTGGATTCGCCGTTGCGG
Found at i:18662905 original size:76 final size:76
Alignment explanation
Indices: 18662779--18662928 Score: 230
Period size: 76 Copynumber: 2.0 Consensus size: 76
18662769 AAACCTTTCT
* *
18662779 CTTTGTGTCTTCGTGGTATTGAAGTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTAAGG
1 CTTTGTGTCTTCGTGGTACTGAAGTCACCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTAAGG
*
18662844 TATATGGTTCC
66 TATAAGGTTCC
* * *
18662855 CTTTGTGTGCTT-GTGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTTAG
1 CTTTGTGT-CTTCGTGGTACTGAAGTCACCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTAAG
18662919 GTATAAGGTT
65 GTATAAGGTT
18662929 TGCCATTGCG
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
76 64 0.96
77 3 0.04
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.41
Consensus pattern (76 bp):
CTTTGTGTCTTCGTGGTACTGAAGTCACCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTAAGG
TATAAGGTTCC
Found at i:18662944 original size:49 final size:49
Alignment explanation
Indices: 18662885--18663441 Score: 426
Period size: 49 Copynumber: 11.3 Consensus size: 49
18662875 GGATTCACCG
* * *
18662885 TTGCGGCTTAAATCTTTCCCTTCATGTCTCTTAGGTATAAGGTTTGCCA
1 TTGCGACTTAAACCTTTCCCTTCATGTCTCTTAGGTATAAGGTTCGCCA
** * * *
18662934 TTGCGACTTAAACCTTTCCCTTTGTGTCTTCGT-GGTACT--GGATTCGTCG
1 TTGCGACTTAAACCTTTCCCTTCATGTC-TCTTAGGTA-TAAGG-TTCGCCA
* * *
18662983 TTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCA
1 TTGCGACTTAAACCTTTCCCTTCATGTCTCTTAGGTATAAGGTTCGCCA
** * * **
18663032 TTGCGACTTAAACCTTTCCCTTTGTGTCTTCGT-GGTACT--GGAGTCGCTG
1 TTGCGACTTAAACCTTTCCCTTCATGTC-TCTTAGGTA-TAAGG-TTCGCCA
* * *
18663081 TTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCA
1 TTGCGACTTAAACCTTTCCCTTCATGTCTCTTAGGTATAAGGTTCGCCA
* * * * *
18663130 TTACGACTTAAACCTTTCCCTT--TGTGTCTTAGTGGTACT--GGAGTCGTCG
1 TTGCGACTTAAACCTTTCCCTTCATGTCTCTTA--GGTA-TAAGG-TTCGCCA
* * * * * *
18663179 TTGTGGCTTAAATCTCTCCCTTCATGTTTCTAAGGTATAAGGTTCGCCA
1 TTGCGACTTAAACCTTTCCCTTCATGTCTCTTAGGTATAAGGTTCGCCA
* *
18663228 TTGCGACTTAAACCTTTCCCTT--TGTGTCTTCATGGTAT-TGGATTCGCCA
1 TTGCGACTTAAACCTTTCCCTTCATGTCTCTT-A-GGTATAAGG-TTCGCCA
* * * * * *
18663277 CTGTGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTTGCCA
1 TTGCGACTTAAACCTTTCCCTTCATGTCTCTTAGGTATAAGGTTCGCCA
* * * *
18663326 TTGCGACTTAAACCTTTCCCTT--TGTGTCTT-CGTAGTACTGGATTCGCCG
1 TTGCGACTTAAACCTTTCCCTTCATGTCTCTTAGGTA-TA-AGG-TTCGCCA
* * * *
18663375 TTGTGGCTTAAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCA
1 TTGCGACTT-AAACCTTTCCCTTCATGTCTCTTAGGTATAAGGTTCGCCA
18663425 TTGCGACTTAAACCTTT
1 TTGCGACTTAAACCTTT
18663442 TCGTTTGTGT
Statistics
Matches: 387, Mismatches: 88, Indels: 66
0.72 0.16 0.12
Matches are distributed among these distances:
46 3 0.01
47 21 0.05
48 18 0.05
49 277 0.72
50 42 0.11
51 15 0.04
52 8 0.02
53 3 0.01
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (49 bp):
TTGCGACTTAAACCTTTCCCTTCATGTCTCTTAGGTATAAGGTTCGCCA
Found at i:18662967 original size:174 final size:175
Alignment explanation
Indices: 18662676--18663027 Score: 573
Period size: 174 Copynumber: 2.0 Consensus size: 175
18662666 ACTTAAACCT
*
18662676 TTCCCTTTGTGTCTTCGTGGTACTAGAGTCACCGTTGCGGCTTAGATCTTTTCCCTTCATGTCTC
1 TTCCCTTTGTGTCTTCGTGGTACTAGAGTCACCGTTGCGGCTTAAATCTTTTCCCTTCATGTCTC
* *
18662741 TGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCTCTTTGTGTCTTCGTGGTATTGAAGTCG
66 TGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGAAGTCG
*
18662806 CCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTAAGGTATATGG
131 CCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTAAGGTATAAGG
* *
18662851 TTCCCTTTGTGTGCTT-GTGGTACTGGATTCACCGTTGCGGCTTAAATC-TTTCCCTTCATGTCT
1 TTCCCTTTGTGT-CTTCGTGGTACTAGAGTCACCGTTGCGGCTTAAATCTTTTCCCTTCATGTCT
* * * *
18662914 CTTAGGTATAAGGTTTGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTC
65 CTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGAAGTC
* *
18662979 GTCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGG
130 GCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTAAGGTATAAGG
18663025 TTC
1 TTC
18663028 GCCATTGCGA
Statistics
Matches: 164, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
174 120 0.73
175 41 0.25
176 3 0.02
ACGTcount: A:0.15, C:0.23, G:0.22, T:0.40
Consensus pattern (175 bp):
TTCCCTTTGTGTCTTCGTGGTACTAGAGTCACCGTTGCGGCTTAAATCTTTTCCCTTCATGTCTC
TGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGAAGTCG
CCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTAAGGTATAAGG
Found at i:18663020 original size:98 final size:98
Alignment explanation
Indices: 18662851--18663497 Score: 1028
Period size: 98 Copynumber: 6.6 Consensus size: 98
18662841 AGGTATATGG
*
18662851 TTCCCTTTGTGTGCTT-GTGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGTCTC
1 TTCCCTTTGTGT-CTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTC
* *
18662915 TTAGGTATAAGGTTTGCCATTGCGACTTAAACCT
65 TGAGGTATAAGGTTCGCCATTGCGACTTAAACCT
*
18662949 TTCCCTTTGTGTCTTCGTGGTACTGGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCT
1 TTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCT
18663014 GAGGTATAAGGTTCGCCATTGCGACTTAAACCT
66 GAGGTATAAGGTTCGCCATTGCGACTTAAACCT
* *
18663047 TTCCCTTTGTGTCTTCGTGGTACTGGAGTCGCTGTTGCGGCTTAAATCTTTCCCTTCATGTCTCT
1 TTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCT
*
18663112 GAGGTATAAGGTTCGCCATTACGACTTAAACCT
66 GAGGTATAAGGTTCGCCATTGCGACTTAAACCT
* * * * * *
18663145 TTCCCTTTGTGTCTTAGTGGTACTGGAGTCGTCGTTGTGGCTTAAATCTCTCCCTTCATGTTTCT
1 TTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCT
*
18663210 AAGGTATAAGGTTCGCCATTGCGACTTAAACCT
66 GAGGTATAAGGTTCGCCATTGCGACTTAAACCT
* * ** *
18663243 TTCCCTTTGTGTCTTCATGGTATTGGATTCGCCACTGTGGCTTAAATCTTTCCCTTCATGTCTCT
1 TTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCT
*
18663308 GAGGTATAAGGTTTGCCATTGCGACTTAAACCT
66 GAGGTATAAGGTTCGCCATTGCGACTTAAACCT
* *
18663341 TTCCCTTTGTGTCTTCGTAGTACTGGATTCGCCGTTGTGGCTTAAAATCTTTCCCTTCATGTCTC
1 TTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTT-AAATCTTTCCCTTCATGTCTC
18663406 TGAGGTATAAGGTTCGCCATTGCGACTTAAACCT
65 TGAGGTATAAGGTTCGCCATTGCGACTTAAACCT
* * *
18663440 TTTCGTTTGTGTCTTCGTGGTACTGGAGTT-GCCGTTGCTGCTTAAATCTTTCCCTTCA
1 TTCCCTTTGTGTCTTCGTGGTACTGGA-TTCGCCGTTGCGGCTTAAATCTTTCCCTTCA
18663498 AATTTTCATG
Statistics
Matches: 508, Mismatches: 38, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
97 3 0.01
98 414 0.81
99 89 0.18
100 2 0.00
ACGTcount: A:0.16, C:0.24, G:0.21, T:0.39
Consensus pattern (98 bp):
TTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCT
GAGGTATAAGGTTCGCCATTGCGACTTAAACCT
Found at i:18664508 original size:21 final size:20
Alignment explanation
Indices: 18664451--18664518 Score: 84
Period size: 21 Copynumber: 3.4 Consensus size: 20
18664441 CGACCTCTCC
* *
18664451 TTTTCTTTTTCCGTTTTTCTA
1 TTTTCTTTTTCC-TTTTTTTT
18664472 TTTTCTTTTTCCTTTTTTATT
1 TTTTCTTTTTCCTTTTTT-TT
*
18664493 TTTTCTTTTT-TTTTTTTTT
1 TTTTCTTTTTCCTTTTTTTT
18664512 TTTTCTT
1 TTTTCTT
18664519 CATTGCATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 9 0.21
20 11 0.26
21 23 0.53
ACGTcount: A:0.03, C:0.13, G:0.01, T:0.82
Consensus pattern (20 bp):
TTTTCTTTTTCCTTTTTTTT
Found at i:18669076 original size:97 final size:97
Alignment explanation
Indices: 18668904--18669094 Score: 244
Period size: 97 Copynumber: 2.0 Consensus size: 97
18668894 CTTGGAAAAT
* * *
18668904 GATATTCAATTATCTCGGTTTGAAGAAAAATCGCACCTACTAAGTTAAGGCACAAATTTTCAGAA
1 GATATTCAATTATCTCGATTTGAAGAAAAATCGCACCTACTAAGTTAAGGCACAAATATTCAAAA
* *
18668969 TCAGAGAT-AAAGAAACATTGCCTTGATTTAAG
66 TCAGAAATAAAAG-AACATTGCCTCGATTTAAG
* * * *
18669001 GATATTCGATTAT-TCCGATTTGAATAAAAATCGCGCCTAGTAAGTTAAGGCACAAATATTCAAA
1 GATATTCAATTATCT-CGATTTGAAGAAAAATCGCACCTACTAAGTTAAGGCACAAATATTCAAA
*
18669065 ACTCA-AAATAAAAGAATATTGCCTCGATTT
65 A-TCAGAAATAAAAGAACATTGCCTCGATTT
18669095 TAAAGGTTTC
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
96 1 0.01
97 73 0.90
98 7 0.09
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (97 bp):
GATATTCAATTATCTCGATTTGAAGAAAAATCGCACCTACTAAGTTAAGGCACAAATATTCAAAA
TCAGAAATAAAAGAACATTGCCTCGATTTAAG
Found at i:18669538 original size:59 final size:59
Alignment explanation
Indices: 18669390--18669548 Score: 158
Period size: 59 Copynumber: 2.7 Consensus size: 59
18669380 TTTTAAGGTT
* * * * **
18669390 AAATGGAATTTTTGGATATCCGAGGGTAAAATGGTAATTTTTAGAAGTTTCAAGATTGA
1 AAATGGAATTTTTGGATATTCAAGGGTAAAATGGTAATTTTCAAAAGTTTCAAGATCAA
*** * *
18669449 AAATTCCATTTTTGGACA-TCTAAGGGTAAAATGGTAATTTTCAAAAGTTTCAAGGTCAA
1 AAATGGAATTTTTGGATATTC-AAGGGTAAAATGGTAATTTTCAAAAGTTTCAAGATCAA
* * * **
18669508 AAATGGTATTTTTGGGTATTCAAGGTTAAAACAGTAATTTT
1 AAATGGAATTTTTGGATATTCAAGGGTAAAATGGTAATTTT
18669549 TGGAGGATTC
Statistics
Matches: 79, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
58 1 0.01
59 76 0.96
60 2 0.03
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (59 bp):
AAATGGAATTTTTGGATATTCAAGGGTAAAATGGTAATTTTCAAAAGTTTCAAGATCAA
Found at i:18669608 original size:29 final size:28
Alignment explanation
Indices: 18669568--18669714 Score: 129
Period size: 28 Copynumber: 5.2 Consensus size: 28
18669558 CGGGGTTAAA
* * *
18669568 AAAATGATATTTTTAGATATTTGGGGAT
1 AAAATGGTATTTTTGGAAATTTGGGGAT
*
18669596 AAAATGGTAATTTTTGGAAACTTGGGGA-
1 AAAATGGT-ATTTTTGGAAATTTGGGGAT
* *
18669624 AAAATTGTATTTTTGGACATTT-GGGAGT
1 AAAATGGTATTTTTGGAAATTTGGGGA-T
* * * *
18669652 AAAATGGTAATTTTGGAAGTTTGAGGTT
1 AAAATGGTATTTTTGGAAATTTGGGGAT
* *
18669680 AAAATTGTAATTTTTGGAAAGTTTAGGGA-
1 AAAATGGT-ATTTTTGGAAA-TTTGGGGAT
18669709 AAAATG
1 AAAATG
18669715 TAATCTTGAA
Statistics
Matches: 93, Mismatches: 20, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
26 4 0.04
27 12 0.13
28 40 0.43
29 32 0.34
30 5 0.05
ACGTcount: A:0.35, C:0.01, G:0.25, T:0.38
Consensus pattern (28 bp):
AAAATGGTATTTTTGGAAATTTGGGGAT
Found at i:18669646 original size:56 final size:56
Alignment explanation
Indices: 18669566--18669795 Score: 152
Period size: 56 Copynumber: 4.0 Consensus size: 56
18669556 TTCGGGGTTA
* * *
18669566 AAAAAATGATATTTTTAGATATTTGGGGATAAAATGGTAATTTTTGGAAACTTG-GGG
1 AAAAATTG-TATTTTTGGAAATTT-GGGATAAAATGGTAATTTTTGGAAACTTGAGGG
* ** *
18669623 AAAAATTGTATTTTTGGACATTTGGGAGTAAAATGGTAA-TTTTGGAAGTTTGAGGT
1 AAAAATTGTATTTTTGGAAATTTGGGA-TAAAATGGTAATTTTTGGAAACTTGAGGG
* * * * *
18669679 TAAAATTGTAATTTTTGGAAAGTTTAGGGA-AAAAT-GTAA-TCTTGAAAAGTTCGAGGAC
1 AAAAATTGT-ATTTTTGGAAA-TTT-GGGATAAAATGGTAATTTTTGGAAACTT-GAGG-G
* *
18669737 AAAAATT-TAATTTTTGGAAAGTTTAAGGG-TCAAAAT-GTAATTTTTAGAAAGTTCGAGGG
1 AAAAATTGT-ATTTTTGGAAA-TTT--GGGAT-AAAATGGTAATTTTTGGAAACTT-GAGGG
18669796 TTAAAATATA
Statistics
Matches: 144, Mismatches: 18, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
55 15 0.10
56 46 0.32
57 43 0.30
58 13 0.09
59 13 0.09
60 14 0.10
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (56 bp):
AAAAATTGTATTTTTGGAAATTTGGGATAAAATGGTAATTTTTGGAAACTTGAGGG
Found at i:18669711 original size:28 final size:29
Alignment explanation
Indices: 18669595--18669854 Score: 157
Period size: 30 Copynumber: 9.0 Consensus size: 29
18669585 TATTTGGGGA
* * *
18669595 TAAAATGGTAATTTTTGGAAA-CTTGGGG
1 TAAAATTGTAATTTTTGGAAAGTTTAGGG
* * *
18669623 AAAAATTGT-ATTTTTGGACA-TTTGGGAG
1 TAAAATTGTAATTTTTGGAAAGTTTAGG-G
* *
18669651 TAAAATGGTAA-TTTTGG-AAGTTTGAGGT
1 TAAAATTGTAATTTTTGGAAAGTTT-AGGG
18669679 TAAAATTGTAATTTTTGGAAAGTTTAGGG
1 TAAAATTGTAATTTTTGGAAAGTTTAGGG
* * * * *
18669708 -AAAAATGTAA-TCTTGAAAAGTTCGAGGAC
1 TAAAATTGTAATTTTTGGAAAGTT-TAGG-G
*
18669737 AAAAATT-TAATTTTTGGAAAGTTTAAGGG
1 TAAAATTGTAATTTTTGGAAAGTTT-AGGG
* *
18669766 TCAAAA-TGTAATTTTTAGAAAGTTCGAGGG
1 T-AAAATTGTAATTTTTGGAAAGTT-TAGGG
* * *
18669796 TTAAAA-TATAATTTTTGAAAACTTTAGGGG
1 -TAAAATTGTAATTTTTGGAAAGTTTA-GGG
*
18669826 TCAAAA-TATAATTTTTGGACAA-TTTAGGG
1 T-AAAATTGTAATTTTTGGA-AAGTTTAGGG
18669855 ACATCTTGAG
Statistics
Matches: 184, Mismatches: 30, Indels: 35
0.74 0.12 0.14
Matches are distributed among these distances:
27 26 0.14
28 46 0.25
29 21 0.11
30 88 0.48
31 3 0.02
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.37
Consensus pattern (29 bp):
TAAAATTGTAATTTTTGGAAAGTTTAGGG
Found at i:18669729 original size:57 final size:57
Alignment explanation
Indices: 18669624--18669824 Score: 189
Period size: 57 Copynumber: 3.5 Consensus size: 57
18669614 AACTTGGGGA
* * *
18669624 AAAATTGT-ATTTTTGGACA-TTT-GGGAGTAAAATGGTAATTTTG-GAAGTTTGAGGTT
1 AAAATTGTAATTTTTGGAAAGTTTAGGGA--AAAAT-GTAATTTTGAAAAGTTCGAGGTT
* **
18669680 AAAATTGTAATTTTTGGAAAGTTTAGGGAAAAATGTAATCTTGAAAAGTTCGAGGACA
1 AAAATTGTAATTTTTGGAAAGTTTAGGGAAAAATGTAATTTTGAAAAGTTCGAGG-TT
* *
18669738 AAAATT-TAATTTTTGGAAAGTTTAAGGGTCAAAATGTAATTTTTAGAAAGTTCGAGGGTT
1 AAAATTGTAATTTTTGGAAAGTTT-AGGG-AAAAATGTAATTTTGA-AAAGTTCGA-GGTT
* * *
18669798 AAAA-TATAATTTTTGAAAACTTTAGGG
1 AAAATTGTAATTTTTGGAAAGTTTAGGG
18669825 GTCAAAATAT
Statistics
Matches: 122, Mismatches: 13, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
56 16 0.13
57 41 0.34
58 13 0.11
59 22 0.18
60 28 0.23
61 2 0.02
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.37
Consensus pattern (57 bp):
AAAATTGTAATTTTTGGAAAGTTTAGGGAAAAATGTAATTTTGAAAAGTTCGAGGTT
Found at i:18669808 original size:60 final size:60
Alignment explanation
Indices: 18669652--18669841 Score: 194
Period size: 60 Copynumber: 3.2 Consensus size: 60
18669642 ATTTGGGAGT
* * * *
18669652 AAAATGGTAA-TTTT-GGAAGTTTGA-GGTTAAAATTGTAATTTTTGGAAAGTTT-AGGG-A
1 AAAAT-GTAATTTTTAGAAAGTTCGAGGGTTAAAA-TATAATTTTTGGAAAGTTTAAGGGTC
* * *** *
18669709 AAAATGTAATCTTGA-AAAGTTCGAGGACAAAAATTTAATTTTTGGAAAGTTTAAGGGTC
1 AAAATGTAATTTTTAGAAAGTTCGAGGGTTAAAATATAATTTTTGGAAAGTTTAAGGGTC
* * *
18669768 AAAATGTAATTTTTAGAAAGTTCGAGGGTTAAAATATAATTTTTGAAAACTTTAGGGGTC
1 AAAATGTAATTTTTAGAAAGTTCGAGGGTTAAAATATAATTTTTGGAAAGTTTAAGGGTC
*
18669828 AAAATATAATTTTT
1 AAAATGTAATTTTT
18669842 GGACAATTTA
Statistics
Matches: 108, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
56 4 0.04
57 32 0.30
58 9 0.08
59 13 0.12
60 50 0.46
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.37
Consensus pattern (60 bp):
AAAATGTAATTTTTAGAAAGTTCGAGGGTTAAAATATAATTTTTGGAAAGTTTAAGGGTC
Done.