Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 68 of 210
Found at i:20388391 original size:14 final size:14
Alignment explanation
Indices: 20388352--20388395 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
20388342 GAAAAAAATA
20388352 AAAAAGTGAAAA-GG
1 AAAAAGT-AAAATGG
*
20388366 AAAAATGAAAAATGG
1 AAAAA-GTAAAATGG
20388381 AAAAAGTAAAATGG
1 AAAAAGTAAAATGG
20388395 A
1 A
20388396 GAGGCTAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 18 0.69
15 8 0.31
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (14 bp):
AAAAAGTAAAATGG
Found at i:20389765 original size:44 final size:44
Alignment explanation
Indices: 20389704--20390886 Score: 921
Period size: 44 Copynumber: 26.7 Consensus size: 44
20389694 ATACTGGTGG
**
20389704 TGAAGTAGATC-GAAGATAATGGATCTTGTCTTCATGTATTGACA
1 TGAAGTAGATCAG-AGATAACAGATCTTGTCTTCATGTATTGACA
*** * * *
20389748 TGAAGTAGATCAGAGATAGTGGATCTTGTCTTCCTGTACTGGCA
1 TGAAGTAGATCAGAGATAACAGATCTTGTCTTCATGTATTGACA
* * * *
20389792 GTGAAGTAGATC-GAAGA-AAGCAAATCTTGTCTTCCTATACTGGTGGC-
1 -TGAAGTAGATCAG-AGATAA-CAGATCTTGTCTTCATGTA-T--TGACA
* * * * *
20389839 -GAAGTAGATCAAAGA-AAGCAGATCTTATCTTCCCATACTAGT-A-G
1 TGAAGTAGATCAGAGATAA-CAGATCTTGTCTT--CAT-GTATTGACA
* *
20389883 TGAAGTAGATC-GAAGA-AAGCAGATCTTGTCTTCATGTATTGGCG
1 TGAAGTAGATCAG-AGATAA-CAGATCTTGTCTTCATGTATTGACA
** *
20389927 TGAAGTAGATC-GAAGATAACAGATCTTGTCTTCCCGTACTGGTG-GA
1 TGAAGTAGATCAG-AGATAACAGATCTTGTCTTCATGTA-T--TGACA
* *
20389973 -GAAGTAGATC-GAAGA-AAGCAGATCTTGTCTTCATGTATTGGCG
1 TGAAGTAGATCAG-AGATAA-CAGATCTTGTCTTCATGTATTGACA
* * * *
20390016 TGAAGTAGATC-GAAGATAGCAAATCTTGTCTTCATGTATTGGCG
1 TGAAGTAGATCAG-AGATAACAGATCTTGTCTTCATGTATTGACA
* * ** *
20390060 TGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGC-
1 TGAAGTAGATCAGAGATAACAGATCTTGTCTT--CAT-GTATTGACA
* *
20390106 -GAAGTAGATC-GAAGA-AAGCAGATCTTGTCTTCATGTATTGGCG
1 TGAAGTAGATCAG-AGATAA-CAGATCTTGTCTTCATGTATTGACA
** * *
20390149 TGAAGTAGATC-GAAGATAGTAGATCTTGTATTCATTTATTGACA
1 TGAAGTAGATCAG-AGATAACAGATCTTGTCTTCATGTATTGACA
* *
20390193 TGAAGTAGATC-GAGATAAAATATCTTGTCTTCATGTATTGACA
1 TGAAGTAGATCAGAGATAACAGATCTTGTCTTCATGTATTGACA
* **
20390236 TGAAGTAAATCAGAGATAATGGATCTTGTCTTCATGTATTGACA
1 TGAAGTAGATCAGAGATAACAGATCTTGTCTTCATGTATTGACA
* * * * * * *
20390280 TAAAATAGATCAAAGATAGCAGATCTTGTCTTCTCATACTAGTG--G
1 TGAAGTAGATCAGAGATAACAGATCTTGTC-T-TCAT-GTATTGACA
* * *
20390325 TGAAATATATC-GA-ATATAGCAGATCTTGTATTCATGTATTGACA
1 TGAAGTAGATCAGAGATA-A-CAGATCTTGTCTTCATGTATTGACA
*
20390369 TGAAGTAGATCAGAGATAGCAGATCTTGTCTTCATGTATTGACA
1 TGAAGTAGATCAGAGATAACAGATCTTGTCTTCATGTATTGACA
**
20390413 TGAAGTAGATCAGAGATAATGGATCTTGTCTTCATGTATTGACA
1 TGAAGTAGATCAGAGATAACAGATCTTGTCTTCATGTATTGACA
* * *** * ***
20390457 TGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGG
1 TGAAGTAGATCAGAGATAACAGATCTTGTCTTCATGTA-TTGACA
** *
20390502 TGAAGTAGATC-GAAGATAGTAGATCTTGTCTTCATGTACTGACA
1 TGAAGTAGATCAG-AGATAACAGATCTTGTCTTCATGTATTGACA
* * *
20390546 TAAAGAAGATCAGAGATAGCAGATCTTGTCTTCATGTATTGACA
1 TGAAGTAGATCAGAGATAACAGATCTTGTCTTCATGTATTGACA
**
20390590 TGAAGTAGATCAGAGATAATGGATCTTGTCTTCATGTATTGACA
1 TGAAGTAGATCAGAGATAACAGATCTTGTCTTCATGTATTGACA
* * *** * ***
20390634 TGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGG
1 TGAAGTAGATCAGAGATAACAGATCTTGTCTTCATGTA-TTGACA
*
20390679 TGAAGTAGATC-GAAGATAGCAGATCTTGTCTTCATGTATTGACA
1 TGAAGTAGATCAG-AGATAACAGATCTTGTCTTCATGTATTGACA
* **
20390723 TGATGTAGATCAGAGATAATGGATCTTGTCTTCATGTATTGACA
1 TGAAGTAGATCAGAGATAACAGATCTTGTCTTCATGTATTGACA
* * * * *** * ***
20390767 TGAAGTAGATCAAAGATAGCAAATTTTGTCTTCCCATACTGGTGG
1 TGAAGTAGATCAGAGATAACAGATCTTGTCTTCATGTA-TTGACA
**
20390812 TGAAGTAGATC-GAAGATAATGGATCTTGTCTTCATGTATTGACA
1 TGAAGTAGATCAG-AGATAACAGATCTTGTCTTCATGTATTGACA
*
20390856 TGAAGTAGATCAGAGATAGCAGATCTTGTCT
1 TGAAGTAGATCAGAGATAACAGATCTTGTCT
20390887 ACCTGTACTA
Statistics
Matches: 922, Mismatches: 165, Indels: 104
0.77 0.14 0.09
Matches are distributed among these distances:
42 14 0.02
43 49 0.05
44 557 0.60
45 273 0.30
46 10 0.01
47 13 0.01
48 6 0.01
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (44 bp):
TGAAGTAGATCAGAGATAACAGATCTTGTCTTCATGTATTGACA
Found at i:20390076 original size:133 final size:133
Alignment explanation
Indices: 20389670--20390895 Score: 1075
Period size: 133 Copynumber: 9.2 Consensus size: 133
20389660 AGCAGGTTGA
* ** *
20389670 AAAGATAACAGATATTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATG--GATCTTGT
1 AAAGATAACAGATCTTGTCTTCCTGTACTGGTGGAGAAGTAGATCGAAGA-AA-GCAGATCTTGT
* ** * * *
20389733 CTTCATGTATTGACATGAAGTAGATC-AGAGATAGTGGATCTTGTCTTCCTGTACTGGCAGTGAA
64 CTTCATGTATTGACGTGAAGTAGATCGA-AGATAGCAGATCTTGTCTTCATGTATTGACA-TGAA
20389797 GTAGATC
127 GTAGATC
* * * * * *
20389804 GAAGA-AAGCAAATCTTGTCTTCCTATACTGGTGGCGAAGTAGATCAAAGAAAGCAGATCTTATC
1 AAAGATAA-CAGATCTTGTCTTCCTGTACTGGTGGAGAAGTAGATCGAAGAAAGCAGATCTTGTC
* * * * *
20389868 TTCCCATACTAGT-A-GTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAA
65 TT--CAT-GTATTGACGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTGACATGAA
20389931 GTAGATC
127 GTAGATC
* *
20389938 GAAGATAACAGATCTTGTCTTCCCGTACTGGTGGAGAAGTAGATCGAAGAAAGCAGATCTTGTCT
1 AAAGATAACAGATCTTGTCTTCCTGTACTGGTGGAGAAGTAGATCGAAGAAAGCAGATCTTGTCT
* * * *
20390003 TCATGTATTGGCGTGAAGTAGATCGAAGATAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAG
66 TCATGTATTGACGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTGACATGAAGTAG
20390068 ATC
131 ATC
** *
20390071 AAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCT
1 AAAGATAACAGATCTTGTCTTCCTGTACTGGTGGAGAAGTAGATCGAAGAAAGCAGATCTTGTCT
* * * *
20390136 TCATGTATTGGCGTGAAGTAGATCGAAGATAGTAGATCTTGTATTCATTTATTGACATGAAGTAG
66 TCATGTATTGACGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTGACATGAAGTAG
20390201 ATC
131 ATC
* * * * * *
20390204 -GAGATAAAATATCTTGTCTTCATGTA-T--TGACATGAAGTAAATC-AGAGATAATG--GATCT
1 AAAGATAACAGATCTTGTCTTCCTGTACTGGTG-GA-GAAGTAGATCGA-AGA-AA-GCAGATCT
* * * * * * *
20390262 TGTCTTCATGTATTGACATAAAATAGATCAAAGATAGCAGATCTTGTCTTCTCATACTAGTG--G
61 TGTCTTCATGTATTGACGTGAAGTAGATCGAAGATAGCAGATCTTGTC-T-TCAT-GTATTGACA
* *
20390325 TGAAATATATC
123 TGAAGTAGATC
* * * * * * *
20390336 GAATATAGCAGATCTTGTATTCATGTA-T--TGACATGAAGTAGATC-AGAGATAGCAGATCTTG
1 AAAGATAACAGATCTTGTCTTCCTGTACTGGTG-GA-GAAGTAGATCGA-AGAAAGCAGATCTTG
* ***
20390397 TCTTCATGTATTGACATGAAGTAGATC-AGAGATAATGGATCTTGTCTTCATGTATTGACATGAA
63 TCTTCATGTATTGACGTGAAGTAGATCGA-AGATAGCAGATCTTGTCTTCATGTATTGACATGAA
20390461 GTAGATC
127 GTAGATC
* ** * * *
20390468 AAAGATAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAGTAGATCTTGTCT
1 AAAGATAACAGATCTTGTCTTCCTGTACTGGTGGAGAAGTAGATCGAAGAAAGCAGATCTTGTCT
* * * *
20390533 TCATGTACTGACATAAAGAAGATC-AGAGATAGCAGATCTTGTCTTCATGTATTGACATGAAGTA
66 TCATGTATTGACGTGAAGTAGATCGA-AGATAGCAGATCTTGTCTTCATGTATTGACATGAAGTA
20390597 GATC
130 GATC
* ** * * * *
20390601 AGAGATAATGGATCTTGTCTTCATGTA-T--TGACATGAAGTAGATCAAAGATAGCAGATCTTGT
1 AAAGATAACAGATCTTGTCTTCCTGTACTGGTG-GA-GAAGTAGATCGAAGAAAGCAGATCTTGT
*** * ** *
20390663 CTTCCCATACTGGTGGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTGACATGATG
64 CTTCATGTA-TTGACGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTGACATGAAG
20390728 TAGATC
128 TAGATC
* ** * * * * * *
20390734 AGAGATAATGGATCTTGTCTTCATGTA-T--TGACATGAAGTAGATCAAAGATAGCAAATTTTGT
1 AAAGATAACAGATCTTGTCTTCCTGTACTGGTG-GA-GAAGTAGATCGAAGAAAGCAGATCTTGT
*** * ** ***
20390796 CTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAG
64 CTTCATGTA-TTGACGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTGACATGAAG
20390861 TAGATC
128 TAGATC
* * *
20390867 AGAGATAGCAGATCTTGTCTACCTGTACT
1 AAAGATAACAGATCTTGTCTTCCTGTACT
20390896 AGTAGCGAAG
Statistics
Matches: 936, Mismatches: 123, Indels: 66
0.83 0.11 0.06
Matches are distributed among these distances:
129 2 0.00
130 7 0.01
131 67 0.07
132 102 0.11
133 584 0.62
134 126 0.13
135 40 0.04
136 5 0.01
137 3 0.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (133 bp):
AAAGATAACAGATCTTGTCTTCCTGTACTGGTGGAGAAGTAGATCGAAGAAAGCAGATCTTGTCT
TCATGTATTGACGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTGACATGAAGTAG
ATC
Found at i:20390162 original size:177 final size:175
Alignment explanation
Indices: 20389704--20390886 Score: 1145
Period size: 177 Copynumber: 6.7 Consensus size: 175
20389694 ATACTGGTGG
* ** * * * **
20389704 TGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGTG
1 TGAAGTAGATCAAAGATAACAGATCTTGTCTTCATGTAGTGACA-GAAGTAGATCAAAGAAAGCA
* * * *
20389769 GATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCGAAGAAAGCAAATCTTGTCTTCCTATACTG
65 GATCTTGTCTTCCTGTACTGGC-GTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTA-T-
* * * * * * *
20389834 GTGGC--GAAGTAGATCAAAGAAAGCAGATCTTATCTTCCCATACTAGT-A-G
127 -TGACATGAAGTAGATCAGAGATAGCAGATCTTGTCTT--CAT-GTATTGACA
* * * * *
20389883 TGAAGTAGATCGAAGA-AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAA-
1 TGAAGTAGATCAAAGATAA-CAGATCTTGTCTTCATGTAGTGAC-AGAAGTAGATCAAAGA-AAG
* * * *
20389946 CAGATCTTGTCTTCCCGTACTGGTGGAGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTAT
63 CAGATCTTGTCTTCCTGTACTGG-CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTAT
* * * * *
20390011 TGGCGTGAAGTAGATC-GAAGATAGCAAATCTTGTCTTCATGTATTGGCG
127 TGACATGAAGTAGATCAG-AGATAGCAGATCTTGTCTTCATGTATTGACA
* * * *
20390060 TGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGC-GAAGTAGATCGAAGAAAG
1 TGAAGTAGATCAAAGATAACAGATCTTGTCTT--CAT-GTAGTGACAGAAGTAGATCAAAGAAAG
* * * * *
20390124 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGTAGATCTTGTATTCATTTATT
63 CAGATCTTGTCTTCCTGTACTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATT
** *
20390189 GACATGAAGTAGATC-GAGATAAAATATCTTGTCTTCATGTATTGACA
128 GACATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCATGTATTGACA
* * ** * * * *
20390236 TGAAGTAAATCAGAGATAATGGATCTTGTCTTCATGTATTGACATAAAATAGATCAAAGATAGCA
1 TGAAGTAGATCAAAGATAACAGATCTTGTCTTCATGTAGTGACA-GAAGTAGATCAAAGAAAGCA
* * * * *
20390301 GATCTTGTCTT-CTCATACTAGTG-GTGAAATATATCGAATATAGCAGATCTTGTATTCATGTAT
65 GATCTTGTCTTCCT-GTACT-G-GCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTAT
20390364 TGACATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCATGTATTGACA
127 TGACATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCATGTATTGACA
* ** * *
20390413 TGAAGTAGATCAGAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCA
1 TGAAGTAGATCAAAGATAACAGATCTTGTCTTCATGTAGTGACA-GAAGTAGATCAAAGAAAGCA
** * * *
20390478 GATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAGTAGATCTTGTCTTCATGTACTG
65 GATCTTGTCTTCCTGTACTGG-CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTG
* *
20390543 ACATAAAGAAGATCAGAGATAGCAGATCTTGTCTTCATGTATTGACA
129 ACATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCATGTATTGACA
* ** * *
20390590 TGAAGTAGATCAGAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCA
1 TGAAGTAGATCAAAGATAACAGATCTTGTCTTCATGTAGTGACA-GAAGTAGATCAAAGAAAGCA
** *
20390655 GATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTG
65 GATCTTGTCTTCCTGTACTGG-CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTG
* ***
20390720 ACATGATGTAGATCAGAGATAATGGATCTTGTCTTCATGTATTGACA
129 ACATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCATGTATTGACA
* * * * * ** *
20390767 TGAAGTAGATCAAAGATAGCAAATTTTGTCTTCCCATACTGGTG-GTGAAGTAGATCGAAGATAA
1 TGAAGTAGATCAAAGATAACAGATCTTGTCTT--CAT-GTAGTGACAGAAGTAGATCAAAGA-AA
* * * *
20390831 TG--GATCTTGTCTTCATGTATTGACATGAAGTAGATC-AGAGATAGCAGATCTTGTCT
62 -GCAGATCTTGTCTTCCTGTACTGGCGTGAAGTAGATCGA-AGATAGCAGATCTTGTCT
20390887 ACCTGTACTA
Statistics
Matches: 870, Mismatches: 105, Indels: 60
0.84 0.10 0.06
Matches are distributed among these distances:
173 4 0.00
174 4 0.00
175 34 0.04
176 115 0.13
177 494 0.57
178 97 0.11
179 112 0.13
180 10 0.01
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (175 bp):
TGAAGTAGATCAAAGATAACAGATCTTGTCTTCATGTAGTGACAGAAGTAGATCAAAGAAAGCAG
ATCTTGTCTTCCTGTACTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTGAC
ATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCATGTATTGACA
Found at i:20390918 original size:89 final size:87
Alignment explanation
Indices: 20389725--20390886 Score: 773
Period size: 89 Copynumber: 13.1 Consensus size: 87
20389715 GAAGATAATG
* * * * *
20389725 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGTGGATCTTGTCTTCCTGTACTGG
1 GATCTTGTCTTCATGTATTGACA-GAAGTAGATCAAAGATAATGGATCTTGTCTTCATGTATTGA
*
20389790 CAGTGAAGTAGATC-GAAGAAAGCA
65 CA-TGAAGTAGATCAG-AGATAGCA
* * * * *
20389814 AATCTTGTCTTCCTATACTGGTGGC-GAAGTAGATCAAAGA-AA-GCAGATCTTATCTTCCCATA
1 GATCTTGTCTTCATGTA-T--TGACAGAAGTAGATCAAAGATAATG--GATCTTGTCTT--CAT-
* * * *
20389876 CTAGT-A-GTGAAGTAGATC-GAAGAAAGCA
58 GTATTGACATGAAGTAGATCAG-AGATAGCA
* * * ** **
20389904 GATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCTTGTCTTCCCGTACTGG
1 GATCTTGTCTTCATGTATTGAC-AGAAGTAGATCAAAGATAATGGATCTTGTCTTCATGTA-T--
* *
20389969 TG-GA-GAAGTAGATC-GAAGAAAGCA
62 TGACATGAAGTAGATCAG-AGATAGCA
* * * **** *
20389993 GATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAAATCTTGTCTTCATGTATTGG
1 GATCTTGTCTTCATGTATTGAC-AGAAGTAGATCAAAGATAATGGATCTTGTCTTCATGTATTGA
* * *
20390058 CGTGAAGTAGATCAAAGATAACA
65 CATGAAGTAGATCAGAGATAGCA
* ** * *
20390081 GATCTTGTCTTCCCATACTGGTGGC-GAAGTAGATCGAAGA-AA-GCAGATCTTGTCTTCATGTA
1 GATCTTGTCTT--CAT-GTATTGACAGAAGTAGATCAAAGATAATG--GATCTTGTCTTCATGTA
* * *
20390143 TTGGCGTGAAGTAGATC-GAAGATAGTA
61 TTGACATGAAGTAGATCAG-AGATAGCA
* * * ***
20390170 GATCTTGTATTCATTTATTGACATGAAGTAGATC-GAGATAAAATATCTTGTCTTCATGTATTGA
1 GATCTTGTCTTCATGTATTGACA-GAAGTAGATCAAAGATAATGGATCTTGTCTTCATGTATTGA
* ***
20390234 CATGAAGTAAATCAGAGATAATG
65 CATGAAGTAGATCAGAGATAGCA
* * *** * *
20390257 GATCTTGTCTTCATGTATTGACATAAAATAGATCAAAGATAGCAGATCTTGTCTTCTCATACTAG
1 GATCTTGTCTTCATGTATTGACA-GAAGTAGATCAAAGATAATGGATCTTGTC-T-TCAT-GTAT
* * * *
20390322 TG--GTGAAATATATC-GAATATAGCA
62 TGACATGAAGTAGATCAG-AGATAGCA
* * ***
20390346 GATCTTGTATTCATGTATTGACATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCATGTATTGA
1 GATCTTGTCTTCATGTATTGACA-GAAGTAGATCAAAGATAATGGATCTTGTCTTCATGTATTGA
***
20390411 CATGAAGTAGATCAGAGATAATG
65 CATGAAGTAGATCAGAGATAGCA
*** *** *
20390434 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACTGG
1 GATCTTGTCTTCATGTATTGACA-GAAGTAGATCAAAGATAATGGATCTTGTCTTCATGTA-TTG
*** *
20390499 TGGTGAAGTAGATC-GAAGATAGTA
64 ACATGAAGTAGATCAG-AGATAGCA
* * * * ***
20390523 GATCTTGTCTTCATGTACTGACATAAAGAAGATCAGAGATAGCAGATCTTGTCTTCATGTATTGA
1 GATCTTGTCTTCATGTATTGACA-GAAGTAGATCAAAGATAATGGATCTTGTCTTCATGTATTGA
***
20390588 CATGAAGTAGATCAGAGATAATG
65 CATGAAGTAGATCAGAGATAGCA
*** *** *
20390611 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACTGG
1 GATCTTGTCTTCATGTATTGACA-GAAGTAGATCAAAGATAATGGATCTTGTCTTCATGTA-TTG
***
20390676 TGGTGAAGTAGATC-GAAGATAGCA
64 ACATGAAGTAGATCAG-AGATAGCA
* *
20390700 GATCTTGTCTTCATGTATTGACATGATGTAGATCAGAGATAATGGATCTTGTCTTCATGTATTGA
1 GATCTTGTCTTCATGTATTGACA-GAAGTAGATCAAAGATAATGGATCTTGTCTTCATGTATTGA
*
20390765 CATGAAGTAGATCAAAGATAGCA
65 CATGAAGTAGATCAGAGATAGCA
* * * ** ** *
20390788 AATTTTGTCTTCCCATACTGGTG-GTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATT
1 GATCTTGTCTT--CAT-GTATTGACAGAAGTAGATCAAAGATAATGGATCTTGTCTTCATGTATT
20390852 GACATGAAGTAGATCAGAGATAGCA
63 GACATGAAGTAGATCAGAGATAGCA
20390877 GATCTTGTCT
1 GATCTTGTCT
20390887 ACCTGTACTA
Statistics
Matches: 877, Mismatches: 148, Indels: 96
0.78 0.13 0.09
Matches are distributed among these distances:
86 12 0.01
87 81 0.09
88 233 0.27
89 459 0.52
90 72 0.08
91 12 0.01
92 5 0.01
93 3 0.00
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.31
Consensus pattern (87 bp):
GATCTTGTCTTCATGTATTGACAGAAGTAGATCAAAGATAATGGATCTTGTCTTCATGTATTGAC
ATGAAGTAGATCAGAGATAGCA
Found at i:20391387 original size:22 final size:21
Alignment explanation
Indices: 20391362--20391402 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
20391352 AACAAACGCA
* *
20391362 AACAATACAACGAAGAAAAAGG
1 AACAAAACAAC-AACAAAAAGG
20391384 AACAAAACAACAACAAAAA
1 AACAAAACAACAACAAAAA
20391403 ACAAAATAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.71, C:0.17, G:0.10, T:0.02
Consensus pattern (21 bp):
AACAAAACAACAACAAAAAGG
Found at i:20396669 original size:23 final size:24
Alignment explanation
Indices: 20396641--20396693 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 24
20396631 AAAAATAATT
* *
20396641 TTAATTATTTTTAATTTTTAAAAA
1 TTAATTATTTTAAATTTTAAAAAA
20396665 -TAATT-TTTTAAATTTTAAAAAA
1 TTAATTATTTTAAATTTTAAAAAA
20396687 TTAATTA
1 TTAATTA
20396694 AATGCTTACG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTAATTATTTTAAATTTTAAAAAA
Found at i:20402540 original size:10 final size:10
Alignment explanation
Indices: 20402534--20402600 Score: 54
Period size: 10 Copynumber: 6.9 Consensus size: 10
20402524 CACATATTTA
20402534 TATATATATT
1 TATATATATT
20402544 TATAT-TATT
1 TATATATATT
20402553 T-T-TAT-TT
1 TATATATATT
*
20402560 TCATA-ATTTT
1 T-ATATATATT
20402570 TATATATATT
1 TATATATATT
*
20402580 TATATGCATATA
1 TATAT--ATATT
20402592 TATATATAT
1 TATATATAT
20402601 ACATACGTGC
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
7 4 0.09
8 2 0.04
9 11 0.23
10 21 0.45
12 9 0.19
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (10 bp):
TATATATATT
Found at i:20407868 original size:18 final size:18
Alignment explanation
Indices: 20407847--20407882 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20407837 AAAAATTGTT
20407847 AAAAAAAGAAAAAAGAAA
1 AAAAAAAGAAAAAAGAAA
* *
20407865 AAAAGAAGGAAAAAGAAA
1 AAAAAAAGAAAAAAGAAA
20407883 GAAGAAATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAAAGAAAAAAGAAA
Found at i:20409168 original size:46 final size:46
Alignment explanation
Indices: 20409101--20409494 Score: 617
Period size: 46 Copynumber: 8.5 Consensus size: 46
20409091 CAGATCAATG
* * * *
20409101 AGATAGCAGATCTTGTCTTCCTTTATTTGGCAGTGGAGTAAATTGA
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGA
* *
20409147 AGATAGCAGATCTTGTCTTCCTCTATTTGGCAGTGGAGTAGATCGA
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGA
* *
20409193 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGGTTGA
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGA
*
20409239 ATATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGA
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGA
*
20409285 AGATAGGAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGA
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGA
* * *
20409331 AGATAGGAGATCTTGTCTTCCTGTATTTGGTAGCGGGGTAGATCGA
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGA
* * *
20409377 AGATAGCAGATCCTGTCTTCCTATATTTGGCAGCAGAGTAGATCGA
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGA
* *
20409423 AGATAACAGATCTTGTCTTCCTGTATTTGGGCAGCGGAGTAGATTGA
1 AGATAGCAGATCTTGTCTTCCTGTATTT-GGCAGCGGAGTAGATCGA
20409470 AGATAGCAGATCTTGTCTTCCTGTA
1 AGATAGCAGATCTTGTCTTCCTGTA
20409495 CTGGCAGTGA
Statistics
Matches: 321, Mismatches: 26, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
46 281 0.88
47 40 0.12
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (46 bp):
AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGA
Found at i:20409684 original size:132 final size:132
Alignment explanation
Indices: 20409529--20409959 Score: 736
Period size: 132 Copynumber: 3.3 Consensus size: 132
20409519 CAACGAACCT
* *
20409529 TATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCCCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCATATTCTGTCCCCCTAAGCAGTAGTGG
* *
20409594 AGCAAATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAAATTTAAGCCATTAGT
66 AGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGT
20409659 CC
131 CC
* * *
20409661 TATCTCCCTAAACAGTAGTGGAGTAGGTCGAAGATTGCATATTTTGTCCCCCTAAGTAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCATATTCTGTCCCCCTAAGCAGTAGTGG
* * *
20409726 AGCAGATCGAAGATGGTGAATTTTATCTTCCCAAGATAATGGAGAAGCAGATTTGAGCCATTAGT
66 AGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGT
20409791 CC
131 CC
*
20409793 TATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCATATTCTGTCCCTCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCATATTCTGTCCCCCTAAGCAGTAGTGG
20409858 AGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGT
66 AGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGT
20409923 CC
131 CC
* * *
20409925 TGTCTCCCTAAGCAGTAGTGGAGTAGATAGAAGAT
1 TATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGAT
20409960 GGTGAATCTT
Statistics
Matches: 279, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 279 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (132 bp):
TATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCATATTCTGTCCCCCTAAGCAGTAGTGG
AGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGT
CC
Found at i:20409960 original size:220 final size:220
Alignment explanation
Indices: 20409705--20410117 Score: 677
Period size: 220 Copynumber: 1.9 Consensus size: 220
20409695 TTGCATATTT
* * *
20409705 TGTCCCCCTAAGTAGTAGTGGAGCAGATCGAAGATGGTGAATTTTATCTTCCCAAGATAATGGAG
1 TGTCCCCCTAAGCAGTAGTGGAGCAGATAGAAGATGGTGAATCTTATCTTCCCAAGATAATGGAG
* * *
20409770 AAGCAGATTTGAGCCA-TTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCATA
66 AAGCAGATTTAAGCCATTTA-TCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAGATTGCAGA
20409834 TTCTGTC-CCTCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGT
130 TTCTGTCTCC-CTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGT
20409898 GGAGAAGCAGATTTAAGCCATTAGTCC
194 GGAGAAGCAGATTTAAGCCATTAGTCC
* * *
20409925 TGTCTCCCTAAGCAGTAGTGGAGTAGATAGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAG
1 TGTCCCCCTAAGCAGTAGTGGAGCAGATAGAAGATGGTGAATCTTATCTTCCCAAGATAATGGAG
* * *
20409990 AAGCAGGTTTAAGCCATTTATCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTAAAGTTTGCAGAT
66 AAGCAGATTTAAGCCATTTATCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAGATTGCAGAT
*
20410055 TCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGACTCTTATCTTCCCAAGATAGT
131 TCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGT
20410118 AGGGAAGTAA
Statistics
Matches: 178, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
220 173 0.97
221 5 0.03
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (220 bp):
TGTCCCCCTAAGCAGTAGTGGAGCAGATAGAAGATGGTGAATCTTATCTTCCCAAGATAATGGAG
AAGCAGATTTAAGCCATTTATCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAGATTGCAGAT
TCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGG
AGAAGCAGATTTAAGCCATTAGTCC
Found at i:20409989 original size:42 final size:42
Alignment explanation
Indices: 20409852--20409989 Score: 113
Period size: 44 Copynumber: 3.2 Consensus size: 42
20409842 CTCTAAGCAG
*
20409852 TAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGA
1 TAGTGGAGCAGATAGAAGATGGTGAATCTTATCTTCCCAAGA
** * * *
20409894 TAGTGGAGAAGCAGATTTAAGCCAT--T-AGTCCTGTC-TCCCTAAGCA
1 TAGT-G-G-AGCAGATAGAAG--ATGGTGAATCTTATCTTCCC-AAG-A
*
20409939 GTAGTGGAGTAGATAGAAGATGGTGAATCTTATCTTCCCAAGA
1 -TAGTGGAGCAGATAGAAGATGGTGAATCTTATCTTCCCAAGA
20409982 TAGTGGAG
1 TAGTGGAG
20409990 AAGCAGGTTT
Statistics
Matches: 73, Mismatches: 11, Indels: 24
0.68 0.10 0.22
Matches are distributed among these distances:
41 2 0.03
42 12 0.16
43 16 0.22
44 20 0.27
45 17 0.23
46 4 0.05
47 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (42 bp):
TAGTGGAGCAGATAGAAGATGGTGAATCTTATCTTCCCAAGA
Found at i:20410035 original size:46 final size:45
Alignment explanation
Indices: 20409894--20410035 Score: 111
Period size: 44 Copynumber: 3.2 Consensus size: 45
20409884 CTTCCCAAGA
*
20409894 TAGTGGAGAAGCAGATTTAAGCCA-TTAGTCCTGTCTCCCTAAGCAG
1 TAGTGGAGAAGCAG-TTTAAGCCATTTA-TCCTATCTCCCTAAGCAG
* ** * *
20409940 TAGTGGAGTAG-A-TAGAAG--ATGGTGAATCTTATCTTCCC-AAG-A-
1 TAGTGGAGAAGCAGTTTAAGCCAT--T-TATCCTATC-TCCCTAAGCAG
20409982 TAGTGGAGAAGCAGGTTTAAGCCATTTATCCTATCTCCCTAAGCAG
1 TAGTGGAGAAGCA-GTTTAAGCCATTTATCCTATCTCCCTAAGCAG
20410028 TAGTGGAG
1 TAGTGGAG
20410036 TAGGTTAAAG
Statistics
Matches: 72, Mismatches: 11, Indels: 26
0.66 0.10 0.24
Matches are distributed among these distances:
41 1 0.01
42 10 0.14
43 10 0.14
44 19 0.26
45 12 0.17
46 18 0.25
47 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (45 bp):
TAGTGGAGAAGCAGTTTAAGCCATTTATCCTATCTCCCTAAGCAG
Found at i:20410036 original size:88 final size:88
Alignment explanation
Indices: 20409844--20410038 Score: 338
Period size: 88 Copynumber: 2.2 Consensus size: 88
20409834 TTCTGTCCCT
* *
20409844 CTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGA
1 CTAAGCAGTAGTGGAGTAGATAGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGA
*
20409909 TTTAAGCCATTAGTCCTGTCTCC
66 TTTAAGCCATTAGTCCTATCTCC
*
20409932 CTAAGCAGTAGTGGAGTAGATAGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGG
1 CTAAGCAGTAGTGGAGTAGATAGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGA
20409997 TTTAAGCCATTTA-TCCTATCTCC
66 TTTAAGCCA-TTAGTCCTATCTCC
20410020 CTAAGCAGTAGTGGAGTAG
1 CTAAGCAGTAGTGGAGTAG
20410039 GTTAAAGTTT
Statistics
Matches: 102, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
88 99 0.97
89 3 0.03
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (88 bp):
CTAAGCAGTAGTGGAGTAGATAGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGA
TTTAAGCCATTAGTCCTATCTCC
Found at i:20410425 original size:21 final size:20
Alignment explanation
Indices: 20410391--20410434 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 20
20410381 TGCCCACCCC
*
20410391 AAAACCCATTACAAACTAAAAA
1 AAAACCCATAAC-AAC-AAAAA
20410413 AAAACCCA-AACAACAAAAA
1 AAAACCCATAACAACAAAAA
20410432 AAA
1 AAA
20410435 CCAGCCTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
20 3 0.14
21 2 0.10
22 8 0.38
ACGTcount: A:0.70, C:0.23, G:0.00, T:0.07
Consensus pattern (20 bp):
AAAACCCATAACAACAAAAA
Found at i:20412218 original size:25 final size:24
Alignment explanation
Indices: 20412181--20412281 Score: 100
Period size: 25 Copynumber: 4.2 Consensus size: 24
20412171 TTTATTGTAT
20412181 TTTTTAATGTATTATATTAATGTG
1 TTTTTAATGTATTATATTAATGTG
* *
20412205 TTTTGGTAAT-TATTGTAATT-ATAT-
1 TTTT--TAATGTATTAT-ATTAATGTG
* *
20412229 TATTTAATGTATTATATTAATGTA
1 TTTTTAATGTATTATATTAATGTG
*
20412253 TTATTTAATGTATAATATTAATGTG
1 TT-TTTAATGTATTATATTAATGTG
20412278 TTTT
1 TTTT
20412282 GGTAATTATT
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
22 7 0.11
23 8 0.13
24 10 0.16
25 30 0.48
26 7 0.11
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (24 bp):
TTTTTAATGTATTATATTAATGTG
Found at i:20412265 original size:73 final size:75
Alignment explanation
Indices: 20412152--20412292 Score: 223
Period size: 73 Copynumber: 1.9 Consensus size: 75
20412142 TATTTTTGTA
* * * *
20412152 ATTATATTATTGTACTATATTTATTGTATTTTTTAATGTATTATATTAATGTGTTTTGGTAATTA
1 ATTATATTAATGTACTATATTTAATGTATTATTTAATGTATAATATTAATGTGTTTTGGTAATTA
20412217 TTGTAATTAT
66 TTGTAATTAT
*
20412227 ATTAT-TTAATGTATTATA-TTAATGTATTATTTAATGTATAATATTAATGTGTTTTGGTAATTA
1 ATTATATTAATGTACTATATTTAATGTATTATTTAATGTATAATATTAATGTGTTTTGGTAATTA
20412290 TTG
66 TTG
20412293 CAACAACCTA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
73 45 0.74
74 11 0.18
75 5 0.08
ACGTcount: A:0.31, C:0.01, G:0.11, T:0.57
Consensus pattern (75 bp):
ATTATATTAATGTACTATATTTAATGTATTATTTAATGTATAATATTAATGTGTTTTGGTAATTA
TTGTAATTAT
Found at i:20429948 original size:16 final size:17
Alignment explanation
Indices: 20429928--20429975 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
20429918 AAATAATATT
20429928 TATATTTTTTTATTTTA
1 TATATTTTTTTATTTTA
** *
20429945 -ATATTTAATAATTTTA
1 TATATTTTTTTATTTTA
*
20429961 TACATTTTTTTATTT
1 TATATTTTTTTATTT
20429976 ATTGAAAATT
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (17 bp):
TATATTTTTTTATTTTA
Found at i:20439864 original size:2 final size:2
Alignment explanation
Indices: 20439857--20439889 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20439847 TTGTACCTTT
20439857 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20439890 TAGATAATAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20441947 original size:35 final size:35
Alignment explanation
Indices: 20441908--20442034 Score: 148
Period size: 35 Copynumber: 3.6 Consensus size: 35
20441898 ATGGTGTCGT
* * **
20441908 TCCATAGAGCCAGTAGATCATCT-CTGTGATGCCAC
1 TCCATAAAGCCAGTAGACCAT-TACCATGATGCCAC
* * *
20441943 TCCATAGAGCCAGTAGACCATTACCATAATGCTAC
1 TCCATAAAGCCAGTAGACCATTACCATGATGCCAC
* *
20441978 TCTATAAAGCCAGTAGACCATTGCCATGATGCCAC
1 TCCATAAAGCCAGTAGACCATTACCATGATGCCAC
*
20442013 TCCATAAAGCTAGTAGACCATT
1 TCCATAAAGCCAGTAGACCATT
20442035 TATCTAACCA
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
34 1 0.01
35 78 0.99
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (35 bp):
TCCATAAAGCCAGTAGACCATTACCATGATGCCAC
Found at i:20443356 original size:25 final size:24
Alignment explanation
Indices: 20443320--20443406 Score: 104
Period size: 25 Copynumber: 3.5 Consensus size: 24
20443310 TTTAGACGTT
*
20443320 AGACACAA-TTAATGTGTCTGAACTA
1 AGAC-CAATTTAAT-TGTCTAAACTA
*
20443345 AGACCAATTTAATTTGTCAAAACTA
1 AGACCAATTTAA-TTGTCTAAACTA
*
20443370 AGTCCAATTTAATTCGTCTAAACTA
1 AGACCAATTTAATT-GTCTAAACTA
20443395 AGACCAATTTAA
1 AGACCAATTTAA
20443407 ATAATATATT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
24 5 0.09
25 48 0.89
26 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.31
Consensus pattern (24 bp):
AGACCAATTTAATTGTCTAAACTA
Found at i:20448198 original size:25 final size:25
Alignment explanation
Indices: 20448170--20448242 Score: 83
Period size: 25 Copynumber: 2.9 Consensus size: 25
20448160 ACAATTAAGG
* *
20448170 TGTCTGAACTACGACCAATTTAATT
1 TGTCTAAACTAAGACCAATTTAATT
* ***
20448195 TGTCAAAACTAATTTCAATTTAATT
1 TGTCTAAACTAAGACCAATTTAATT
*
20448220 CGTCTAAACTAAGACCAATTTAA
1 TGTCTAAACTAAGACCAATTTAA
20448243 ATCATATATT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (25 bp):
TGTCTAAACTAAGACCAATTTAATT
Found at i:20456649 original size:21 final size:21
Alignment explanation
Indices: 20456620--20456664 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
20456610 TTGGTCAAGG
20456620 AAAAAAAAAGAAA-AATAAAAT
1 AAAAAAAAAGAAAGAA-AAAAT
*
20456641 AAAAGAAAAGAAAGAAAAAAT
1 AAAAAAAAAGAAAGAAAAAAT
20456662 AAA
1 AAA
20456665 TATTTCTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.07
Consensus pattern (21 bp):
AAAAAAAAAGAAAGAAAAAAT
Found at i:20457871 original size:8 final size:8
Alignment explanation
Indices: 20457860--20457895 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
20457850 AAAATAGTTT
20457860 AGAAGAAG
1 AGAAGAAG
20457868 AGAAGAAG
1 AGAAGAAG
20457876 AGAAGAAG
1 AGAAGAAG
20457884 AGAAGAAG
1 AGAAGAAG
20457892 AGAA
1 AGAA
20457896 TGGAAGGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (8 bp):
AGAAGAAG
Found at i:20458009 original size:17 final size:17
Alignment explanation
Indices: 20457979--20458030 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
20457969 AAAAAAATAG
*
20457979 AAGA-AAAGGAAAGGAA
1 AAGAGAAAGGGAAGGAA
*
20457995 ATGAGAAAGGGAAGGAA
1 AAGAGAAAGGGAAGGAA
* *
20458012 AAGAGAATGGGAAAGAA
1 AAGAGAAAGGGAAGGAA
20458029 AA
1 AA
20458031 AGGGATTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 3 0.10
17 27 0.90
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.04
Consensus pattern (17 bp):
AAGAGAAAGGGAAGGAA
Found at i:20458009 original size:42 final size:44
Alignment explanation
Indices: 20457908--20458013 Score: 112
Period size: 45 Copynumber: 2.5 Consensus size: 44
20457898 GAAGGGAAGC
* *
20457908 AAGG-GAAAAAGAAAGAAAAAAAATAGAAGTAAAATAGGTAAAGA
1 AAGGAGAAAGAGAAGGAAAAAAAATAGAAG-AAAATAGGTAAAGA
* *
20457952 GAGGAGAATGAGAAGGAAAAAAAATAGAAG-AAA-AGG-AAAGGA
1 AAGGAGAAAGAGAAGGAAAAAAAATAGAAGAAAATAGGTAAA-GA
* *
20457994 AATGAGAAAGGGAAGGAAAA
1 AAGGAGAAAGAGAAGGAAAA
20458014 GAGAATGGGA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
41 3 0.06
42 21 0.40
43 3 0.06
44 3 0.06
45 22 0.42
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (44 bp):
AAGGAGAAAGAGAAGGAAAAAAAATAGAAGAAAATAGGTAAAGA
Found at i:20458020 original size:23 final size:22
Alignment explanation
Indices: 20457963--20458026 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
20457953 AGGAGAATGA
* *
20457963 GAAGGAAAAAAAAT-AG-AAGA
1 GAAGGAAAAGAAATGAGAAAGG
* *
20457983 AAAGGAAAGGAAATGAGAAAGG
1 GAAGGAAAAGAAATGAGAAAGG
*
20458005 GAAGGAAAAGAGAATGGGAAAG
1 GAAGGAAAAGA-AATGAGAAAG
20458027 AAAAAGGGAT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
20 11 0.32
21 2 0.06
22 12 0.35
23 9 0.26
ACGTcount: A:0.61, C:0.00, G:0.34, T:0.05
Consensus pattern (22 bp):
GAAGGAAAAGAAATGAGAAAGG
Found at i:20460608 original size:33 final size:33
Alignment explanation
Indices: 20460493--20460611 Score: 123
Period size: 33 Copynumber: 3.6 Consensus size: 33
20460483 ACCCACCATC
* * * * *
20460493 ACTGGAGTACTCTACTTCTCTTGGCCCGTATCT
1 ACTGCAGTACTCCACTCCTCTCGGCTCGTATCT
* *
20460526 ACTGCAGTACTCCATTCCTC-CTGGCTCGTATCC
1 ACTGCAGTACTCCACTCCTCTC-GGCTCGTATCT
* *
20460559 ATTGCGGTACTCCACTCCTCTCGGCTCGTATCT
1 ACTGCAGTACTCCACTCCTCTCGGCTCGTATCT
* *
20460592 ACCGTAGTACTCCACTCCTC
1 ACTGCAGTACTCCACTCCTC
20460612 CCGACTCAAG
Statistics
Matches: 69, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
33 68 0.99
34 1 0.01
ACGTcount: A:0.15, C:0.37, G:0.16, T:0.32
Consensus pattern (33 bp):
ACTGCAGTACTCCACTCCTCTCGGCTCGTATCT
Found at i:20460937 original size:48 final size:48
Alignment explanation
Indices: 20460866--20460974 Score: 157
Period size: 48 Copynumber: 2.3 Consensus size: 48
20460856 CTTTGTATTT
* **
20460866 ATTT-AATTGAGATTTATTACAACATTAAAACTTGGAACAAACTTTGTA
1 ATTTAAATT-AGATTAATTACAACATTAAAACGAGGAACAAACTTTGTA
*
20460914 ATTTAAATTAGATTAATTGCAACATTAAAACGAGGAACAAACTTTGTA
1 ATTTAAATTAGATTAATTACAACATTAAAACGAGGAACAAACTTTGTA
*
20460962 ATATAAATTAGAT
1 ATTTAAATTAGAT
20460975 ACATTAGAGT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
48 51 0.93
49 4 0.07
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (48 bp):
ATTTAAATTAGATTAATTACAACATTAAAACGAGGAACAAACTTTGTA
Found at i:20464066 original size:3 final size:3
Alignment explanation
Indices: 20463997--20464050 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
20463987 TTCTGATTGT
* *
20463997 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20464045 TTA TTA
1 TTA TTA
20464051 CAGCTTTGTA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:20467197 original size:21 final size:21
Alignment explanation
Indices: 20467173--20467212 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20467163 AGAATTGCCA
*
20467173 AAATAGTTTGAAGAGAAATGG
1 AAATAGATTGAAGAGAAATGG
*
20467194 AAATGGATTGAAGAGAAAT
1 AAATAGATTGAAGAGAAAT
20467213 TTAGGGCAAT
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:0.50, C:0.00, G:0.28, T:0.23
Consensus pattern (21 bp):
AAATAGATTGAAGAGAAATGG
Found at i:20469315 original size:18 final size:18
Alignment explanation
Indices: 20469292--20469348 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
20469282 GTTCAGATTC
20469292 AAAAAAAAATCAAAATAT
1 AAAAAAAAATCAAAATAT
*
20469310 AAAAAAAAATCAATCA-AT
1 AAAAAAAAATCAA-AATAT
20469328 -AAAAAAAAT-AAAATA-
1 AAAAAAAAATCAAAATAT
20469343 AAAAAA
1 AAAAAA
20469349 TGAAAATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
15 1 0.03
16 8 0.24
17 9 0.26
18 15 0.44
19 1 0.03
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (18 bp):
AAAAAAAAATCAAAATAT
Found at i:20469342 original size:14 final size:15
Alignment explanation
Indices: 20469293--20469402 Score: 81
Period size: 13 Copynumber: 7.3 Consensus size: 15
20469283 TTCAGATTCA
20469293 AAAAAAAATCAAAATAT
1 AAAAAAAATC-AAA-AT
20469310 AAAAAAAAATCAATCAAT
1 -AAAAAAAATCAA--AAT
20469328 AAAAAAAAT-AAAAT
1 AAAAAAAATCAAAAT
*
20469342 -AAAAAAATGAAAAT
1 AAAAAAAATCAAAAT
*
20469356 AAAAAAAA--GAAAT
1 AAAAAAAATCAAAAT
20469369 AAAAAAGAA--AAAA-
1 AAAAAA-AATCAAAAT
20469382 AGAAAAAAATCAAAAT
1 A-AAAAAAATCAAAAT
20469398 CAAAA
1 -AAAA
20469403 TCAAAATGAA
Statistics
Matches: 80, Mismatches: 2, Indels: 22
0.77 0.02 0.21
Matches are distributed among these distances:
13 21 0.26
14 18 0.22
15 11 0.14
16 5 0.06
17 12 0.15
18 12 0.15
19 1 0.01
ACGTcount: A:0.80, C:0.05, G:0.04, T:0.12
Consensus pattern (15 bp):
AAAAAAAATCAAAAT
Found at i:20469345 original size:13 final size:13
Alignment explanation
Indices: 20469329--20469402 Score: 69
Period size: 14 Copynumber: 5.4 Consensus size: 13
20469319 TCAATCAATA
20469329 AAAAAAATAAAAT
1 AAAAAAATAAAAT
20469342 AAAAAAATGAAAAT
1 AAAAAAAT-AAAAT
20469356 AAAAAAA-AGAAAT
1 AAAAAAATA-AAAT
* *
20469369 AAAAAAGAAAAAAAG
1 -AAAAA-AATAAAAT
20469384 AAAAAAATCAAAAT
1 AAAAAAAT-AAAAT
*
20469398 CAAAA
1 AAAAA
20469403 TCAAAATGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
12 1 0.02
13 14 0.27
14 30 0.59
15 5 0.10
16 1 0.02
ACGTcount: A:0.82, C:0.03, G:0.05, T:0.09
Consensus pattern (13 bp):
AAAAAAATAAAAT
Found at i:20469348 original size:8 final size:8
Alignment explanation
Indices: 20469328--20469396 Score: 52
Period size: 8 Copynumber: 8.4 Consensus size: 8
20469318 ATCAATCAAT
20469328 AAAAAA-A
1 AAAAAATA
*
20469335 ATAAAATA
1 AAAAAATA
20469343 AAAAAATGA
1 AAAAAAT-A
*
20469352 AAATAAAAA
1 AAA-AAATA
20469361 AAAGAAAT-
1 AAA-AAATA
*
20469369 AAAAAAGA
1 AAAAAATA
*
20469377 AAAAAAGA
1 AAAAAATA
20469385 AAAAAATCA
1 AAAAAAT-A
20469394 AAA
1 AAA
20469397 TCAAAATCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
7 8 0.16
8 24 0.48
9 15 0.30
10 3 0.06
ACGTcount: A:0.84, C:0.01, G:0.06, T:0.09
Consensus pattern (8 bp):
AAAAAATA
Found at i:20469359 original size:27 final size:27
Alignment explanation
Indices: 20469303--20469402 Score: 78
Period size: 27 Copynumber: 3.6 Consensus size: 27
20469293 AAAAAAAATC
* *
20469303 AAAATATAA-AAAAAAATCAATCAATAAAA
1 AAAATAAAATAAAAAAAT-AA-AAAT-AAA
*
20469332 AAAATAAAATAAAAAAATGAAAATAAA
1 AAAATAAAATAAAAAAATAAAAATAAA
* *
20469359 AAAA-AGAAATAAAAAAGAAAAAAAGAAA
1 AAAATA-AAATAAAAAA-ATAAAAATAAA
*
20469387 AAAATCAAAATCAAAA
1 AAAAT-AAAATAAAAA
20469403 TCAAAATGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
26 1 0.02
27 17 0.29
28 15 0.25
29 17 0.29
30 9 0.15
ACGTcount: A:0.80, C:0.04, G:0.04, T:0.12
Consensus pattern (27 bp):
AAAATAAAATAAAAAAATAAAAATAAA
Found at i:20469368 original size:19 final size:18
Alignment explanation
Indices: 20469332--20469396 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 18
20469322 ATCAATAAAA
20469332 AAAATAAAATAAAA-AAAT
1 AAAATAAAA-AAAAGAAAT
20469350 GAAAATAAAAAAAAGAAAT
1 -AAAATAAAAAAAAGAAAT
*
20469369 AAAAAAGAAAAAAAGAAA-
1 AAAATA-AAAAAAAGAAAT
20469387 AAAATCAAAA
1 AAAAT-AAAA
20469397 TCAAAATCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
18 16 0.39
19 25 0.61
ACGTcount: A:0.83, C:0.02, G:0.06, T:0.09
Consensus pattern (18 bp):
AAAATAAAAAAAAGAAAT
Found at i:20470317 original size:52 final size:51
Alignment explanation
Indices: 20470260--20470357 Score: 142
Period size: 52 Copynumber: 1.9 Consensus size: 51
20470250 GAGAAGGGAT
* *
20470260 CAAGGTGAAAACCCGCAAAGAGCACTTTGATTCCTAAAAAAAAAAAAGAGAC
1 CAAGGTGAAAACCCACAAAGAGCACTTTGAGTCC-AAAAAAAAAAAAGAGAC
* * *
20470312 CAAGGTGAAAACCTACAAAGGGCACTTTGAGTCCAAAAAATAAAAA
1 CAAGGTGAAAACCCACAAAGAGCACTTTGAGTCCAAAAAAAAAAAA
20470358 TAAATCAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
51 11 0.27
52 30 0.73
ACGTcount: A:0.50, C:0.18, G:0.17, T:0.14
Consensus pattern (51 bp):
CAAGGTGAAAACCCACAAAGAGCACTTTGAGTCCAAAAAAAAAAAAGAGAC
Found at i:20470452 original size:84 final size:84
Alignment explanation
Indices: 20470306--20470479 Score: 321
Period size: 84 Copynumber: 2.1 Consensus size: 84
20470296 AAAAAAAAAA
* *
20470306 AGAGACCAAGGTGAAAACCTACAAAGGGCACTTTGAGTCCAAAAAATAAAAATAAATCAAAAACA
1 AGAGGCCAAGGTGAAAACCCACAAAGGGCACTTTGAGTCCAAAAAATAAAAATAAATCAAAAACA
20470371 AAAAAAGAAAAGAAAATGG
66 AAAAAAGAAAAGAAAATGG
*
20470390 AGAGGCCAAGGTGAAAACCCGCAAAGGGCACTTTGAGTCCAAAAAATAAAAATAAATCAAAAACA
1 AGAGGCCAAGGTGAAAACCCACAAAGGGCACTTTGAGTCCAAAAAATAAAAATAAATCAAAAACA
20470455 AAAAAAGAAAAGAAAATGG
66 AAAAAAGAAAAGAAAATGG
20470474 AGAGGC
1 AGAGGC
20470480 GCTTTGAGAG
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 87 1.00
ACGTcount: A:0.56, C:0.14, G:0.19, T:0.11
Consensus pattern (84 bp):
AGAGGCCAAGGTGAAAACCCACAAAGGGCACTTTGAGTCCAAAAAATAAAAATAAATCAAAAACA
AAAAAAGAAAAGAAAATGG
Found at i:20471907 original size:44 final size:44
Alignment explanation
Indices: 20471843--20472141 Score: 413
Period size: 44 Copynumber: 6.8 Consensus size: 44
20471833 ATACCAATTA
* *
20471843 TATCTCCCTAGG-CAGTAGTGGAATAGGTTGAATATTGTAAGTCC
1 TATCTCCCT-GGACAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
20471887 TATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
1 TATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* *
20471931 TATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTATAAGCCC
1 TATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* * *
20471975 TATCTCCCTGGACAACAGTGGAATAGGATGAAGATTGTAAGCCC
1 TATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* * *
20472019 TATCTCTCTGGACAGCAGCGGAATAGGTTAAAGATTGTAAGTCC
1 TATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
*
20472063 TATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGT-AGATCA
1 TATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTAAG-TCC
* ** * * *
20472107 TGTCTCCCTAAACAGTAGTGGAATAGATCGAAGAT
1 TATCTCCCTGGACAGCAGTGGAATAGGTTGAAGAT
20472142 GACAAATCTT
Statistics
Matches: 230, Mismatches: 23, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
43 4 0.02
44 226 0.98
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (44 bp):
TATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
Found at i:20472219 original size:50 final size:50
Alignment explanation
Indices: 20472146--20472810 Score: 449
Period size: 50 Copynumber: 13.7 Consensus size: 50
20472136 GAAGATGACA
* * * *
20472146 AATCTTACTTCCCTGGCAGTGCAGTTGAACAGATTGAAGCTACAACGGCA
1 AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* * * * *
20472196 AATTTTGCTTCCCTGACAATGCAGTTAAAAAGATTAAAGCTACAACAGCG
1 AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* * * * *** * * * * *
20472246 AATCTTACCTCTCAGGTGGTGTAGTGGAACAGATTAAAGCCACAAGGGTG
1 AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* *
20472296 AATCTTGCTTTCCC-GACATTGCAGTT-AA-AGATTAAAGCTACAACAGCG
1 AATCTTGC-TTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* * ** * * *
20472344 AATCTT-ATTTCCTGGTAGTGTAGTGGAACAGATTAAAGCCACAACGGCG
1 AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* * *
20472393 AATCTTGCTT-CCTCGATATTGCAGTT-AA-AGATTAAAGCTACAACAGCG
1 AATCTTGCTTCCCT-GACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* * * * * * *
20472441 AATCTT-ATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAAAGGTG
1 AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* * *
20472490 AATCTTGCTTCCCCGACATTGCAGTT-AA-AGATTAAAGCTACAACAGCG
1 AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* * * * * * *
20472538 AATCTT-ATTTCCTGGCAGTGCAATGGAACAGATTAAAGCCACAACGGTG
1 AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* *
20472587 AATCTTGCTTCCC---CA--ACA-TTG--CAG-TTAAAGCTACAACAGCG
1 AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* * * * * * *
20472628 AATATT-ATTTCCTGGA-AGTACAATGGAACAGATTAAAGCTACAACGGTG
1 AATCTTGCTTCCCT-GACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* * * * * ** *
20472677 AATCTTGCTTCCCCGACATTGCAGTTAAAAATATTAAAGCTACAACAACA
1 AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* * * * * *
20472727 AATATT-ATTTCCTGGCAGTGCAGTGGAACAGATTAAAGTTACAACGGCG
1 AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* * * *
20472776 AATCTTGTTTCCCCGACATTGCAGTTAAACAGATT
1 AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATT
20472811 GAAGACAGTA
Statistics
Matches: 455, Mismatches: 134, Indels: 52
0.71 0.21 0.08
Matches are distributed among these distances:
40 4 0.01
41 19 0.04
42 3 0.01
43 1 0.00
44 2 0.00
45 5 0.01
46 6 0.01
47 31 0.07
48 80 0.18
49 135 0.30
50 166 0.36
51 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (50 bp):
AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
Found at i:20472381 original size:49 final size:49
Alignment explanation
Indices: 20472146--20472787 Score: 423
Period size: 49 Copynumber: 13.2 Consensus size: 49
20472136 GAAGATGACA
* * * * *
20472146 AATCTTACTTCCCTGGCAGTGCAGTTGAACAGATTGAAGCTACAACGGCA
1 AATCTTA-TTTCCTGGCAGTGCAGTGGAACAGATTAAAGCTACAACAGCG
* * * * * ** *
20472196 AATTTTGCTTCCCTGACAATGCAGTTAAAAAGATTAAAGCTACAACAGCG
1 AATCTT-ATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCTACAACAGCG
** * ** * * ** *
20472246 AATCTTACCTCTCAGGTGGTGTAGTGGAACAGATTAAAGCCACAAGGGTG
1 AATCTTATTTC-CTGGCAGTGCAGTGGAACAGATTAAAGCTACAACAGCG
* * * * *
20472296 AATCTTGCTTTCCCGACATTGCAGT-TAA-AGATTAAAGCTACAACAGCG
1 AATCTT-ATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCTACAACAGCG
* * * *
20472344 AATCTTATTTCCTGGTAGTGTAGTGGAACAGATTAAAGCCACAACGGCG
1 AATCTTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCTACAACAGCG
** ** * *
20472393 AATCTTGCTTCCTCGATATTGCAGT-TAA-AGATTAAAGCTACAACAGCG
1 AATCTTATTTCCT-GGCAGTGCAGTGGAACAGATTAAAGCTACAACAGCG
* *
20472441 AATCTTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAA-AGGTG
1 AATCTTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCTACAACA-GCG
* * * * * *
20472490 AATCTTGCTTCCCCGACATTGCAGT-TAA-AGATTAAAGCTACAACAGCG
1 AATCTT-ATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCTACAACAGCG
* * * *
20472538 AATCTTATTTCCTGGCAGTGCAATGGAACAGATTAAAGCCACAACGGTG
1 AATCTTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCTACAACAGCG
** * * *
20472587 AATCTTGCTTCC--CCA--ACA-TTG--CAG-TTAAAGCTACAACAGCG
1 AATCTTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCTACAACAGCG
* * * * * *
20472628 AATATTATTTCCTGGAAGTACAATGGAACAGATTAAAGCTACAACGGTG
1 AATCTTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCTACAACAGCG
* * * * * ** * * * *
20472677 AATCTTGCTTCCCCGACATTGCAGTTAAAAATATTAAAGCTACAACAACA
1 AATCTT-ATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCTACAACAGCG
* * *
20472727 AATATTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGTTACAACGGCG
1 AATCTTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCTACAACAGCG
*
20472776 AATCTTGTTTCC
1 AATCTTATTTCC
20472788 CCGACATTGC
Statistics
Matches: 437, Mismatches: 133, Indels: 45
0.71 0.22 0.07
Matches are distributed among these distances:
41 23 0.05
42 3 0.01
43 1 0.00
44 2 0.00
45 5 0.01
46 2 0.00
47 34 0.08
48 83 0.19
49 146 0.33
50 136 0.31
51 2 0.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (49 bp):
AATCTTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCTACAACAGCG
Found at i:20472396 original size:97 final size:97
Alignment explanation
Indices: 20472146--20472804 Score: 834
Period size: 97 Copynumber: 6.8 Consensus size: 97
20472136 GAAGATGACA
* * * * ** *
20472146 AATCTTACTTCCCTGGCAGTGCAGTTGAACAGATTGAAGCTACAACGGCAAATTTTGC-TTCCCT
1 AATCTTA-TTTCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTTCCC-
*
20472210 GACAATGCAGTTAAAAAGATTAAAGCTACAACAGCG
64 GACATTGCAGTT--AAAGATTAAAGCTACAACAGCG
** * ** * *
20472246 AATCTTACCTCTCAGGTGGTGTAGTGGAACAGATTAAAGCCACAAGGGTGAATCTTGCTTTCCCG
1 AATCTTATTTC-CTGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTTCCCG
20472311 ACATTGCAGTTAAAGATTAAAGCTACAACAGCG
65 ACATTGCAGTTAAAGATTAAAGCTACAACAGCG
* * *
20472344 AATCTTATTTCCTGGTAGTGTAGTGGAACAGATTAAAGCCACAACGGCGAATCTTGC-TTCCTCG
1 AATCTTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTTCC-CG
*
20472408 ATATTGCAGTTAAAGATTAAAGCTACAACAGCG
65 ACATTGCAGTTAAAGATTAAAGCTACAACAGCG
* *
20472441 AATCTTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAAAGGTGAATCTTGCTTCCCCGA
1 AATCTTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTTCCCGA
20472506 CATTGCAGTTAAAGATTAAAGCTACAACAGCG
66 CATTGCAGTTAAAGATTAAAGCTACAACAGCG
* * *
20472538 AATCTTATTTCCTGGCAGTGCAATGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCAA
1 AATCTTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTTCCCGA
20472603 CATTGC------AG-TTAAAGCTACAACAGCG
66 CATTGCAGTTAAAGATTAAAGCTACAACAGCG
* * * * * *
20472628 AATATTATTTCCTGGAAGTACAATGGAACAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGA
1 AATCTTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTTCCCGA
* * *
20472693 CATTGCAGTTAAAAATATTAAAGCTACAACAACA
66 CATTGCAGTT--AAAGATTAAAGCTACAACAGCG
* ** *
20472727 AATATTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGTTACAACGGCGAATCTTG-TTTCCCCG
1 AATCTTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTT-CCCG
20472791 ACATTGCAGTTAAA
65 ACATTGCAGTTAAA
20472805 CAGATTGAAG
Statistics
Matches: 500, Mismatches: 45, Indels: 31
0.87 0.08 0.05
Matches are distributed among these distances:
90 83 0.17
91 2 0.00
96 4 0.01
97 234 0.47
98 37 0.07
99 82 0.16
100 53 0.11
101 5 0.01
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (97 bp):
AATCTTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTTCCCGA
CATTGCAGTTAAAGATTAAAGCTACAACAGCG
Found at i:20472674 original size:90 final size:90
Alignment explanation
Indices: 20472521--20472804 Score: 388
Period size: 90 Copynumber: 3.1 Consensus size: 90
20472511 CAGTTAAAGA
* *
20472521 TTAAAGCTACAACAGCGAATCTTATTTCCTGGCAGTGCAATGGAACAGATTAAAGCCACAACGGT
1 TTAAAGCTACAACAGCGAATATTATTTCCTGGCAGTGCAATGGAACAGATTAAAGCTACAACGGT
*
20472586 GAATCTTGCTTCCCCAACATTGCAG
66 GAATCTTGCTTCCCCGACATTGCAG
* *
20472611 TTAAAGCTACAACAGCGAATATTATTTCCTGGAAGTACAATGGAACAGATTAAAGCTACAACGGT
1 TTAAAGCTACAACAGCGAATATTATTTCCTGGCAGTGCAATGGAACAGATTAAAGCTACAACGGT
20472676 GAATCTTGCTTCCCCGACATTGCAG
66 GAATCTTGCTTCCCCGACATTGCAG
* * * *
20472701 TTAAAAATATTAAAGCTACAACAACAAATATTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGT
1 ---------TTAAAGCTACAACAGCGAATATTATTTCCTGGCAGTGCAATGGAACAGATTAAAGC
* *
20472766 TACAACGGCGAATCTTGTTTCCCCGACATTGCAG
57 TACAACGGTGAATCTTGCTTCCCCGACATTGCAG
20472800 TTAAA
1 TTAAA
20472805 CAGATTGAAG
Statistics
Matches: 172, Mismatches: 13, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
90 90 0.52
99 82 0.48
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (90 bp):
TTAAAGCTACAACAGCGAATATTATTTCCTGGCAGTGCAATGGAACAGATTAAAGCTACAACGGT
GAATCTTGCTTCCCCGACATTGCAG
Found at i:20477947 original size:113 final size:114
Alignment explanation
Indices: 20477748--20477954 Score: 310
Period size: 113 Copynumber: 1.8 Consensus size: 114
20477738 TAATAGTTAC
*
20477748 TAACAAAATAACTTTAAAATAAATTAAAAAAATAATAAAAGATTACATTCATAACCTAACAGATC
1 TAACAAAATAACTTTAAAATAAATTAAAAAAATAATAAAAGATTACATTCATAACCTAACAAATC
20477813 ACCATAAACATTAAACCAAACAAACAATTAACCGAGTCACAAAAATTAA
66 ACCATAAACATTAAACCAAACAAACAATTAACCGAGTCACAAAAATTAA
* * *
20477862 TAACAAAATGACTTTAAAATAAATT-AAAAATTTATAAAA-ATTTACATTCATAACCTAACAAAT
1 TAACAAAATAACTTTAAAATAAATTAAAAAAATAATAAAAGA-TTACATTCATAACCTAACAAAT
** * * *
20477925 CTTCATCAACATTAAACTAAACAAGCAATT
65 CACCATAAACATTAAACCAAACAAACAATT
20477955 TATAATAGTT
Statistics
Matches: 83, Mismatches: 9, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
112 1 0.01
113 58 0.70
114 24 0.29
ACGTcount: A:0.56, C:0.16, G:0.03, T:0.26
Consensus pattern (114 bp):
TAACAAAATAACTTTAAAATAAATTAAAAAAATAATAAAAGATTACATTCATAACCTAACAAATC
ACCATAAACATTAAACCAAACAAACAATTAACCGAGTCACAAAAATTAA
Found at i:20478092 original size:18 final size:17
Alignment explanation
Indices: 20478060--20478117 Score: 75
Period size: 18 Copynumber: 3.4 Consensus size: 17
20478050 CTCATCATAA
20478060 TCCTTCTTT-TTTCTTC
1 TCCTTCTTTCTTTCTTC
20478076 TCCATTCTTTCTTTCTTC
1 TCC-TTCTTTCTTTCTTC
*
20478094 TCCCTCTCTTCTTTCTTC
1 TCCTTCT-TTCTTTCTTC
20478112 T-CTTCT
1 TCCTTCT
20478118 GATATCTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
16 3 0.08
17 13 0.35
18 21 0.57
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (17 bp):
TCCTTCTTTCTTTCTTC
Found at i:20486685 original size:20 final size:20
Alignment explanation
Indices: 20486662--20486707 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
20486652 TGTTAATATT
*
20486662 TTGTTATTTATTCAAATAGG
1 TTGTTACTTATTCAAATAGG
*
20486682 TTGTTACTTATTTAAATAGG
1 TTGTTACTTATTCAAATAGG
20486702 TTGTTA
1 TTGTTA
20486708 AGCTTTACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.04, G:0.15, T:0.52
Consensus pattern (20 bp):
TTGTTACTTATTCAAATAGG
Found at i:20491929 original size:19 final size:18
Alignment explanation
Indices: 20491893--20491932 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
20491883 AAGTCTACCA
20491893 ATTTAAGGTTTTTTTAGT
1 ATTTAAGGTTTTTTTAGT
20491911 ATTT-AGGTTTCTATTTAGT
1 ATTTAAGGTTT-T-TTTAGT
20491930 ATT
1 ATT
20491933 ACTTTTGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 5 0.25
19 9 0.45
ACGTcount: A:0.23, C:0.03, G:0.15, T:0.60
Consensus pattern (18 bp):
ATTTAAGGTTTTTTTAGT
Found at i:20494762 original size:6 final size:6
Alignment explanation
Indices: 20494751--20494781 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
20494741 TCTGTGTGTT
20494751 GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA G
1 GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA G
20494782 GTGGAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (6 bp):
GAAAGA
Found at i:20500628 original size:24 final size:24
Alignment explanation
Indices: 20500599--20500644 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
20500589 CAAGCCAGGT
*
20500599 ACAAAAAAGAAATAGAAGAAAACA
1 ACAAAAAAGAAATAAAAGAAAACA
*
20500623 ACAAAAAAGAAGTAAAAGAAAA
1 ACAAAAAAGAAATAAAAGAAAA
20500645 GAAATTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.76, C:0.07, G:0.13, T:0.04
Consensus pattern (24 bp):
ACAAAAAAGAAATAAAAGAAAACA
Found at i:20504765 original size:27 final size:27
Alignment explanation
Indices: 20504710--20504765 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
20504700 TATTTTCTCG
* * ** *
20504710 AAATTTTATTAGGGGTAAAATGGTTAA
1 AAATTTTATCAGAGGTAAAATCATCAA
20504737 AAATTTTATCAGAGGTAAAATCATCAA
1 AAATTTTATCAGAGGTAAAATCATCAA
20504764 AA
1 AA
20504766 TTTATTGAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.46, C:0.05, G:0.16, T:0.32
Consensus pattern (27 bp):
AAATTTTATCAGAGGTAAAATCATCAA
Found at i:20507981 original size:50 final size:50
Alignment explanation
Indices: 20507882--20507981 Score: 137
Period size: 50 Copynumber: 2.0 Consensus size: 50
20507872 GGACACACCA
* *
20507882 CAGCTCTTATGAGCTTCCCGATACTCAGCTCACATAAGCTTCCTATTATT
1 CAGCTCGTATGAGCTTCCCGATACTCAGCTCACATAAGCTTCCCATTATT
* * * * *
20507932 CAGCTCGTATGAGCTTCCCGTTATTCAGCTCGCATGAGCTTCCCGTTATT
1 CAGCTCGTATGAGCTTCCCGATACTCAGCTCACATAAGCTTCCCATTATT
20507982 TAACTCGGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.34
Consensus pattern (50 bp):
CAGCTCGTATGAGCTTCCCGATACTCAGCTCACATAAGCTTCCCATTATT
Found at i:20507988 original size:25 final size:25
Alignment explanation
Indices: 20507890--20507981 Score: 121
Period size: 25 Copynumber: 3.7 Consensus size: 25
20507880 CACAGCTCTT
* * *
20507890 ATGAGCTTCCCGATACTCAGCTCAC
1 ATGAGCTTCCCGTTATTCAGCTCGC
* ** *
20507915 ATAAGCTTCCTATTATTCAGCTCGT
1 ATGAGCTTCCCGTTATTCAGCTCGC
20507940 ATGAGCTTCCCGTTATTCAGCTCGC
1 ATGAGCTTCCCGTTATTCAGCTCGC
20507965 ATGAGCTTCCCGTTATT
1 ATGAGCTTCCCGTTATT
20507982 TAACTCGGAA
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 56 1.00
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATTCAGCTCGC
Found at i:20507995 original size:25 final size:25
Alignment explanation
Indices: 20507892--20507997 Score: 79
Period size: 25 Copynumber: 4.2 Consensus size: 25
20507882 CAGCTCTTAT
* * * *
20507892 GAGCTTCCCGATACTCAGCTCACATA
1 GAGCTTCCCGTTATTCAACTCGCA-A
** * * *
20507918 -AGCTTCCTATTATTCAGCTCGTAT
1 GAGCTTCCCGTTATTCAACTCGCAA
* *
20507942 GAGCTTCCCGTTATTCAGCTCGCAT
1 GAGCTTCCCGTTATTCAACTCGCAA
* *
20507967 GAGCTTCCCGTTATTTAACTCGGAA
1 GAGCTTCCCGTTATTCAACTCGCAA
20507992 GAGCTT
1 GAGCTT
20507998 ATTGTTTATA
Statistics
Matches: 65, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
25 65 1.00
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.32
Consensus pattern (25 bp):
GAGCTTCCCGTTATTCAACTCGCAA
Found at i:20507996 original size:50 final size:50
Alignment explanation
Indices: 20507892--20507997 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 50
20507882 CAGCTCTTAT
* * * *
20507892 GAGCTTCCCGATACTCAGCTCACATAAGCTTCCTATTATTCAGCTCGTAT
1 GAGCTTCCCGATACTCAGCTCACATAAGCTTCCCATTATTCAACTCGGAA
* * * * * *
20507942 GAGCTTCCCGTTATTCAGCTCGCATGAGCTTCCCGTTATTTAACTCGGAA
1 GAGCTTCCCGATACTCAGCTCACATAAGCTTCCCATTATTCAACTCGGAA
20507992 GAGCTT
1 GAGCTT
20507998 ATTGTTTATA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.32
Consensus pattern (50 bp):
GAGCTTCCCGATACTCAGCTCACATAAGCTTCCCATTATTCAACTCGGAA
Found at i:20513881 original size:56 final size:56
Alignment explanation
Indices: 20513795--20513908 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
20513785 GAAAGTTCTT
20513795 TGGTTCGGTCGTAAAGGAAAGCTGAGTCCGCGATTTATTAGGCCATATGAGATTAC
1 TGGTTCGGTCGTAAAGGAAAGCTGAGTCCGCGATTTATTAGGCCATATGAGATTAC
20513851 TGGTTCGGTCGTAAAGGAAAGCTGAGTCCGCGATTTATTAGGCCATATGAGATTAC
1 TGGTTCGGTCGTAAAGGAAAGCTGAGTCCGCGATTTATTAGGCCATATGAGATTAC
20513907 TG
1 TG
20513909 AGAGAATCAG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (56 bp):
TGGTTCGGTCGTAAAGGAAAGCTGAGTCCGCGATTTATTAGGCCATATGAGATTAC
Found at i:20515354 original size:25 final size:25
Alignment explanation
Indices: 20515326--20515395 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
20515316 ACTCAAGTCA
*
20515326 CATGAGCTTCCCGTTATTCGGCTCG
1 CATGAGCTTCCCGTTATTCAGCTCG
20515351 CATGAGCTTCCCGTTATTCAGCTCG
1 CATGAGCTTCCCGTTATTCAGCTCG
*
20515376 CATGAGCTTCTCGTTATTCA
1 CATGAGCTTCCCGTTATTCA
20515396 ACTCAGAAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.16, C:0.30, G:0.20, T:0.34
Consensus pattern (25 bp):
CATGAGCTTCCCGTTATTCAGCTCG
Found at i:20517426 original size:45 final size:45
Alignment explanation
Indices: 20517302--20517427 Score: 144
Period size: 45 Copynumber: 2.8 Consensus size: 45
20517292 TGTTCTGAGG
* * * **
20517302 ATGCCATAGTATCTTTCAGCCATGGTCTTACACATTCCCAATATA
1 ATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTCCCAATATA
* * * * * *
20517347 ATGCCATAATGTCTTTCAATTATGGTCTTGTTCATTTCCGATTTA
1 ATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTCCCAATATA
*
20517392 TTGCCATAGTGTCTTTCAACTATGGTCTTATTCATT
1 ATGCCATAGTGTCTTTCAACTATGGTCTTATTCATT
20517428 AAAGCTTGGC
Statistics
Matches: 66, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 66 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (45 bp):
ATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTCCCAATATA
Found at i:20517554 original size:17 final size:17
Alignment explanation
Indices: 20517531--20517579 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
20517521 TTTTATTAAT
20517531 ATTTTAACATATAAAATC
1 ATTTTAA-ATATAAAATC
*
20517549 -TTTTAAAT-TAAAAAC
1 ATTTTAAATATAAAATC
*
20517564 ATTTTAAACATAAAAT
1 ATTTTAAATATAAAAT
20517580 TTCATACTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 6 0.23
16 9 0.35
17 11 0.42
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTTTAAATATAAAATC
Found at i:20521327 original size:15 final size:15
Alignment explanation
Indices: 20521309--20521339 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20521299 GGTTGGAGCC
20521309 TTAGTCTACTAAGCA
1 TTAGTCTACTAAGCA
20521324 TTAGTCTACTAAGCA
1 TTAGTCTACTAAGCA
20521339 T
1 T
20521340 GTTAGAACGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35
Consensus pattern (15 bp):
TTAGTCTACTAAGCA
Found at i:20522132 original size:10 final size:11
Alignment explanation
Indices: 20522108--20522150 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
20522098 CCTCTTCCTA
*
20522108 TTTCTTTTGGT
1 TTTCTTTTTGT
20522119 TTTCTTTTTG-
1 TTTCTTTTTGT
*
20522129 TTTCTTTTTCT
1 TTTCTTTTTGT
20522140 TTTCTATTTTG
1 TTTCT-TTTTG
20522151 AAAATAGAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 9 0.33
11 14 0.52
12 4 0.15
ACGTcount: A:0.02, C:0.12, G:0.09, T:0.77
Consensus pattern (11 bp):
TTTCTTTTTGT
Found at i:20522132 original size:21 final size:22
Alignment explanation
Indices: 20522108--20522150 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
20522098 CCTCTTCCTA
*
20522108 TTTCTTTTGGTTTTCT-TTTTG
1 TTTCTTTTGCTTTTCTATTTTG
*
20522129 TTTCTTTTTCTTTTCTATTTTG
1 TTTCTTTTGCTTTTCTATTTTG
20522151 AAAATAGAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.02, C:0.12, G:0.09, T:0.77
Consensus pattern (22 bp):
TTTCTTTTGCTTTTCTATTTTG
Found at i:20522935 original size:18 final size:17
Alignment explanation
Indices: 20522893--20522937 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
20522883 TGTCATTCGT
*
20522893 TTTCAAAACATTATCCA
1 TTTCAAAACATTATCAA
*
20522910 TTTACAAATCATTATTCAA
1 TTT-CAAAACATTA-TCAA
20522929 TTTCAAAAC
1 TTTCAAAAC
20522938 TTTTTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 3 0.13
18 14 0.61
19 6 0.26
ACGTcount: A:0.42, C:0.20, G:0.00, T:0.38
Consensus pattern (17 bp):
TTTCAAAACATTATCAA
Found at i:20528630 original size:22 final size:22
Alignment explanation
Indices: 20528592--20528637 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
20528582 GGATTTGTAA
* *
20528592 TGGATTTGATTTATTTTGTGTT
1 TGGATTTGATTGATTTTGGGTT
*
20528614 TGGATTTGATTGGTTTTGGGTT
1 TGGATTTGATTGATTTTGGGTT
20528636 TG
1 TG
20528638 TCTCTATTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.11, C:0.00, G:0.30, T:0.59
Consensus pattern (22 bp):
TGGATTTGATTGATTTTGGGTT
Found at i:20531974 original size:25 final size:25
Alignment explanation
Indices: 20531946--20531994 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
20531936 TATAGTCTAT
*
20531946 CTATAGTAGTCTC-AGTATATACTAC
1 CTATAGCAGTCTCAAG-ATATACTAC
*
20531971 CTATAGCAGTTTCAAGATATACTA
1 CTATAGCAGTCTCAAGATATACTA
20531995 TCAAAGACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (25 bp):
CTATAGCAGTCTCAAGATATACTAC
Found at i:20539713 original size:46 final size:46
Alignment explanation
Indices: 20539630--20539726 Score: 142
Period size: 46 Copynumber: 2.1 Consensus size: 46
20539620 ATGGCAAGAA
* *
20539630 AATATTATTATATTTTTTATTTTAATTAATATAATTATTAAGTTGTT
1 AATAGTATTATATTTTTTACTTT-ATTAATATAATTATTAAGTTGTT
*
20539677 AATAGTATTATATTTTTTTACTTT-TTAATATCATTATTAAGTTGTT
1 AATAGTATTATA-TTTTTTACTTTATTAATATAATTATTAAGTTGTT
20539723 AATA
1 AATA
20539727 ATTATTGTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
46 25 0.54
47 11 0.24
48 10 0.22
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (46 bp):
AATAGTATTATATTTTTTACTTTATTAATATAATTATTAAGTTGTT
Found at i:20541562 original size:57 final size:59
Alignment explanation
Indices: 20541475--20541596 Score: 194
Period size: 58 Copynumber: 2.1 Consensus size: 59
20541465 ATAAAAATGG
* *
20541475 TGAAAATGGAGAAATTGGAAACATTTGGAAATTATTATGGTTTTCT-CCAAAATGAAAA
1 TGAAAATGGAGAAATTGGAAACATTTGGAAATGAATATGGTTTTCTCCCAAAATGAAAA
* *
20541533 TGAAAATGGAGAAA-TGGAATCATTTGGAAATGAATGTGGTTTTCTCCCAAAATGAAAA
1 TGAAAATGGAGAAATTGGAAACATTTGGAAATGAATATGGTTTTCTCCCAAAATGAAAA
20541591 TGAAAA
1 TGAAAA
20541597 ATAAAAATAA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
57 27 0.46
58 32 0.54
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.29
Consensus pattern (59 bp):
TGAAAATGGAGAAATTGGAAACATTTGGAAATGAATATGGTTTTCTCCCAAAATGAAAA
Found at i:20545195 original size:16 final size:16
Alignment explanation
Indices: 20545161--20545195 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
20545151 AATTTAATAC
**
20545161 TTATCTTAATATTTTA
1 TTATCTTAATATTAAA
20545177 TTATCTTAATATTAAA
1 TTATCTTAATATTAAA
20545193 TTA
1 TTA
20545196 AATTAAATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATCTTAATATTAAA
Found at i:20545294 original size:58 final size:61
Alignment explanation
Indices: 20545182--20545297 Score: 175
Period size: 61 Copynumber: 2.0 Consensus size: 61
20545172 TTTTATTATC
*
20545182 TTAATATTAAATTAAATTAAATACTTATCTTATAGATAAGTATTCTATTAATTTAATAGAT
1 TTAATATTAAATTAAATTAAATACTTATCTTATAGATAAGTATTATATTAATTTAATAGAT
* * *
20545243 TTAATATTAAATTTAATTTAATATTTATC-T-T-GATAAGTATTATATTAATTTAATA
1 TTAATATTAAATTAAATTAAATACTTATCTTATAGATAAGTATTATATTAATTTAATA
20545298 TTAAAGTGGT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 23 0.45
59 1 0.02
60 1 0.02
61 26 0.51
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.49
Consensus pattern (61 bp):
TTAATATTAAATTAAATTAAATACTTATCTTATAGATAAGTATTATATTAATTTAATAGAT
Found at i:20552062 original size:30 final size:28
Alignment explanation
Indices: 20552026--20552092 Score: 89
Period size: 30 Copynumber: 2.3 Consensus size: 28
20552016 TTATTGATTT
* *
20552026 TTTCAAATTTAATCCAACGACCTATTTTTC
1 TTTCAAATTTAATCAAACGA-CTA-TTTTA
*
20552056 TTTCAAATTTAATCAAATGACTATTTTA
1 TTTCAAATTTAATCAAACGACTATTTTA
20552084 TTTCAAATT
1 TTTCAAATT
20552093 AATAACATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 13 0.38
29 3 0.09
30 18 0.53
ACGTcount: A:0.34, C:0.16, G:0.03, T:0.46
Consensus pattern (28 bp):
TTTCAAATTTAATCAAACGACTATTTTA
Found at i:20553682 original size:179 final size:180
Alignment explanation
Indices: 20553365--20553725 Score: 654
Period size: 179 Copynumber: 2.0 Consensus size: 180
20553355 CCATGAAGCT
20553365 TTGTCATATTTCTTCGTTTTCTGTTCAATTTGTTGTTCATGTTTCATTCGTGTGTTCAAGATTTT
1 TTGTCATATTTCTTCGTTTTCTGTTCAATTTGTTGTTCATGTTTCATTCGTGTGTTCAAGATTTT
20553430 CCTTACCAAACATTTGTACTATCAATTTTATGGTTATATTATCATGATGACTACTACAATACATG
66 CCTTACCAAACATTTGTACTATCAATTTTATGGTTATATTATCATGATGACTACTACAATACATG
*
20553495 AAAGTGGAACACTAAG-GAAATTGGCTTTAAACTTTTCCAAACTTGATCGG
131 AAAGTGGAACACTAAGAG-AATTGGCTTTAAACTTTGCCAAACTTGATCGG
**
20553545 TTGTCATATTTCTTCGTTTTCTGTTCAATTTGTTGTTCATGTTTCATTCGTGTGTTTGAGATTTT
1 TTGTCATATTTCTTCGTTTTCTGTTCAATTTGTTGTTCATGTTTCATTCGTGTGTTCAAGATTTT
*
20553610 CC-TACCGAACATTTGTACTATCAATTTTATGGTTATATTATCATGATGACTACTACAATACATG
66 CCTTACCAAACATTTGTACTATCAATTTTATGGTTATATTATCATGATGACTACTACAATACATG
*
20553674 AAAGTGGAACACTAAGAGAGTTGGCTTTAAACTTTGCCAAACTTGATCGG
131 AAAGTGGAACACTAAGAGAATTGGCTTTAAACTTTGCCAAACTTGATCGG
20553724 TT
1 TT
20553726 TGATGGTGGA
Statistics
Matches: 175, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
179 109 0.62
180 66 0.38
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (180 bp):
TTGTCATATTTCTTCGTTTTCTGTTCAATTTGTTGTTCATGTTTCATTCGTGTGTTCAAGATTTT
CCTTACCAAACATTTGTACTATCAATTTTATGGTTATATTATCATGATGACTACTACAATACATG
AAAGTGGAACACTAAGAGAATTGGCTTTAAACTTTGCCAAACTTGATCGG
Found at i:20561411 original size:3 final size:3
Alignment explanation
Indices: 20561403--20561440 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
20561393 AAGGAAATTT
20561403 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
20561441 GAGCGGGAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:20561544 original size:12 final size:11
Alignment explanation
Indices: 20561517--20561551 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
20561507 ATAAATAAAA
20561517 AAGGAAAGGA-
1 AAGGAAAGGAG
20561527 AAGGAAAGGAGG
1 AAGGAAAGGA-G
20561539 AAGGAAAGGAG
1 AAGGAAAGGAG
20561550 AA
1 AA
20561552 ATTGTGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.43
11 3 0.13
12 10 0.43
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (11 bp):
AAGGAAAGGAG
Found at i:20563516 original size:14 final size:14
Alignment explanation
Indices: 20563490--20563524 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
20563480 GACATTTTTT
*
20563490 TTCTAATGATACTA
1 TTCTAACGATACTA
*
20563504 TTTTAACGATACTA
1 TTCTAACGATACTA
20563518 TTCTAAC
1 TTCTAAC
20563525 ATGTAATTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (14 bp):
TTCTAACGATACTA
Found at i:20566684 original size:22 final size:21
Alignment explanation
Indices: 20566656--20566707 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
20566646 TAGCTTATCC
* *
20566656 TTCTTTCTTTCTCTTTTTCTTT
1 TTCTTTCTTTC-CCTTTTCTGT
20566678 TTCTTTCTTTCCCTTTTCTGT
1 TTCTTTCTTTCCCTTTTCTGT
20566699 TTCGTTTCT
1 TTC-TTTCT
20566708 AAATTTGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.00, C:0.25, G:0.04, T:0.71
Consensus pattern (21 bp):
TTCTTTCTTTCCCTTTTCTGT
Found at i:20567180 original size:33 final size:34
Alignment explanation
Indices: 20567097--20567185 Score: 83
Period size: 33 Copynumber: 2.7 Consensus size: 34
20567087 CGTGTCATTA
*
20567097 CACCGCAGTACAACACTCCTCC-CGGTCCGTATC
1 CACCACAGTACAACACTCCTCCTCGGTCCGTATC
* * ** *
20567130 CACCGCATTACTCCACTCCTCCTGGGT-CGTATC
1 CACCACAGTACAACACTCCTCCTCGGTCCGTATC
* * *
20567163 CACTATAGTACAACACTCATCCT
1 CACCACAGTACAACACTCCTCCT
20567186 AGCTCAAGTT
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
33 41 0.93
34 3 0.07
ACGTcount: A:0.22, C:0.42, G:0.12, T:0.24
Consensus pattern (34 bp):
CACCACAGTACAACACTCCTCCTCGGTCCGTATC
Found at i:20567566 original size:49 final size:49
Alignment explanation
Indices: 20567444--20567634 Score: 242
Period size: 49 Copynumber: 3.8 Consensus size: 49
20567434 GTATTTATTT
* *
20567444 AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTTTGTGGTCTGGTCATA
1 AATTAGATTAATTACAACATTAAAACTTGGAACAAAC--T-T--TATGGTCATA
20567498 AATTAGATTAATTACAACATTAAAACTTGGAACAAACTTTATGGTCATA
1 AATTAGATTAATTACAACATTAAAACTTGGAACAAACTTTATGGTCATA
** * **
20567547 AATTAGATTAATTGGAACATTAAAACTTGGAACAAACATTATAAT-ATA
1 AATTAGATTAATTACAACATTAAAACTTGGAACAAACTTTATGGTCATA
*
20567595 AATTA-AATACATTACAACATTAAAACTTGGAACAAACTTT
1 AATTAGATTA-ATTACAACATTAAAACTTGGAACAAACTTT
20567635 GCAATATAAA
Statistics
Matches: 125, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
47 3 0.02
48 35 0.28
49 49 0.39
51 1 0.01
52 1 0.01
54 36 0.29
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (49 bp):
AATTAGATTAATTACAACATTAAAACTTGGAACAAACTTTATGGTCATA
Found at i:20567632 original size:97 final size:100
Alignment explanation
Indices: 20567444--20567634 Score: 264
Period size: 97 Copynumber: 1.9 Consensus size: 100
20567434 GTATTTATTT
* * ** *
20567444 AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTTTGTGGTCTGGTCATAAATTAGATTAA
1 AATTAGATTAATTGCAACATTAAAACTTGGAACAAAC--TAT-GTATAATCATAAATTAGAATAA
20567509 TTACAACATTAAAACTTGGAACAAACTTTATGGTCATA
63 TTACAACATTAAAACTTGGAACAAACTTTATGGTCATA
*
20567547 AATTAGATTAATTGGAACATTAAAACTTGGAACAAAC-AT-TATAAT-ATAAATTA-AATACATT
1 AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTATGTATAATCATAAATTAGAATA-ATT
20567608 ACAACATTAAAACTTGGAACAAACTTT
65 ACAACATTAAAACTTGGAACAAACTTT
20567635 GCAATATAAA
Statistics
Matches: 81, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
96 3 0.04
97 38 0.47
98 3 0.04
100 1 0.01
103 36 0.44
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (100 bp):
AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTATGTATAATCATAAATTAGAATAATTA
CAACATTAAAACTTGGAACAAACTTTATGGTCATA
Found at i:20571032 original size:27 final size:26
Alignment explanation
Indices: 20570957--20571032 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 26
20570947 GGGATTTGGT
20570957 ACTGGTGCCGCCTATCAGATAAGGGTC
1 ACTGGTGCCGCCTATCAGAT-AGGGTC
*** *
20570984 ACCAATGTCGCCTATCAGATAGGGATC
1 ACTGGTGCCGCCTATCAGATAGGG-TC
20571011 ACTGGTGCCGCCTATCAGATAG
1 ACTGGTGCCGCCTATCAGATAG
20571033 ACACCATAGC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 4 0.10
27 36 0.90
ACGTcount: A:0.25, C:0.26, G:0.26, T:0.22
Consensus pattern (26 bp):
ACTGGTGCCGCCTATCAGATAGGGTC
Found at i:20578741 original size:22 final size:22
Alignment explanation
Indices: 20578714--20578760 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
20578704 TAAAACTTGA
20578714 ATTAAATCCTAAAAAAGTTAGC
1 ATTAAATCCTAAAAAAGTTAGC
20578736 ATTAAATCCTAAAAAAGTTAGC
1 ATTAAATCCTAAAAAAGTTAGC
20578758 ATT
1 ATT
20578761 GTTATGGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.30
Consensus pattern (22 bp):
ATTAAATCCTAAAAAAGTTAGC
Found at i:20587802 original size:14 final size:16
Alignment explanation
Indices: 20587767--20587805 Score: 55
Period size: 14 Copynumber: 2.5 Consensus size: 16
20587757 ATGATAAAAA
20587767 TATAATTTCATTATTT
1 TATAATTTCATTATTT
20587783 TAATAATTT-A-TATTT
1 T-ATAATTTCATTATTT
20587798 TATAATTT
1 TATAATTT
20587806 TTAAAGGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.32
15 6 0.27
16 2 0.09
17 7 0.32
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TATAATTTCATTATTT
Found at i:20587846 original size:29 final size:33
Alignment explanation
Indices: 20587797--20587864 Score: 90
Period size: 30 Copynumber: 2.2 Consensus size: 33
20587787 AATTTATATT
*
20587797 TTATAATTTTTAAAGGATT-AAAT-TAA-TTTA
1 TTATTATTTTTAAAGGATTAAAATATAATTTTA
*
20587827 TTATTATTTTTAGAGG-TTAAAATATAATTTTA
1 TTATTATTTTTAAAGGATTAAAATATAATTTTA
20587859 TTATTA
1 TTATTA
20587865 ATTTAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 2 0.06
30 18 0.55
31 3 0.09
32 10 0.30
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (33 bp):
TTATTATTTTTAAAGGATTAAAATATAATTTTA
Found at i:20588864 original size:22 final size:23
Alignment explanation
Indices: 20588837--20588880 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
20588827 TTAACGAACA
20588837 AAATATATAAATAT-AAATAAAC
1 AAATATATAAATATAAAATAAAC
* *
20588859 AAATATTTATATATAAAATAAA
1 AAATATATAAATATAAAATAAA
20588881 ATATAAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
AAATATATAAATATAAAATAAAC
Found at i:20588882 original size:20 final size:21
Alignment explanation
Indices: 20588836--20588885 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
20588826 ATTAACGAAC
20588836 AAAATATATAAATATAAATAA
1 AAAATATATAAATATAAATAA
* * *
20588857 ACAAATATTTATATATAAA-AT
1 A-AAATATATAAATATAAATAA
20588878 AAAATATA
1 AAAATATA
20588886 AATTGAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 6 0.25
21 3 0.12
22 15 0.62
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAATATATAAATATAAATAA
Found at i:20589514 original size:22 final size:22
Alignment explanation
Indices: 20589489--20589531 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
20589479 TAGTCATATA
20589489 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
20589511 ATAATTTATTATTTTAATAAA
1 ATAAATTATTAATATAATAAA
20589532 ATATTTAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:20589568 original size:13 final size:14
Alignment explanation
Indices: 20589552--20589593 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
20589542 TTTCAATTTT
20589552 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
20589565 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
20589580 ATTTTAAATAATAT
1 ATTTT-AATAATAT
20589594 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:20589578 original size:16 final size:16
Alignment explanation
Indices: 20589556--20589592 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
20589546 AATTTTATTT
20589556 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
20589573 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
20589588 TAATA
1 TAATA
20589593 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:20591086 original size:2 final size:2
Alignment explanation
Indices: 20591079--20591114 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
20591069 TGTCTTTTTA
20591079 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
20591115 TATTTAGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20593201 original size:18 final size:16
Alignment explanation
Indices: 20593169--20593204 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
20593159 ACAAATGAAT
20593169 AATAAAAAAATATTTA
1 AATAAAAAAATATTTA
20593185 AATAAAAAATATAATTTA
1 AATAAAAAA-AT-ATTTA
20593203 AA
1 AA
20593205 ATTAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 2 0.11
18 7 0.39
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AATAAAAAAATATTTA
Found at i:20600094 original size:18 final size:19
Alignment explanation
Indices: 20600071--20600111 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
20600061 ATTAAGTTAA
*
20600071 TTTTAAAGTATTTT-ATTT
1 TTTTAAAATATTTTAATTT
20600089 TTTTAAAATATTTTAATTT
1 TTTTAAAATATTTTAATTT
20600108 TTTT
1 TTTT
20600112 GTCGATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTAAAATATTTTAATTT
Found at i:20614629 original size:22 final size:22
Alignment explanation
Indices: 20614580--20614631 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
20614570 CAGTTTAAAC
20614580 CCTAACCCTAACAAAAAAAAAA
1 CCTAACCCTAACAAAAAAAAAA
* * * *
20614602 CACTAACCTTAACCATAAAAAAT
1 C-CTAACCCTAACAAAAAAAAAA
20614625 CCTAACC
1 CCTAACC
20614632 ATAAGAGAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (22 bp):
CCTAACCCTAACAAAAAAAAAA
Found at i:20620178 original size:30 final size:28
Alignment explanation
Indices: 20620120--20620226 Score: 83
Period size: 30 Copynumber: 3.6 Consensus size: 28
20620110 AAAAGGGTAC
* * *
20620120 AAAA-TATATACATGTACATATATAAAA
1 AAAATTATATACATATATATAGATAAAA
20620147 AAAATTATATACATATATATAGATTATAAA
1 AAAATTATATACATATATATAGA-TA-AAA
* *
20620177 AAAGATAAT-TACATATATATATATAAACA
1 AAA-ATTATATACATATATATAGATAAA-A
*
20620206 AATAATAATAATTACATATAT
1 AA-AATTAT-A-TACATATAT
20620227 TAAAATTAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
27 4 0.06
28 17 0.26
29 12 0.18
30 20 0.30
31 4 0.06
32 9 0.14
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAATTATATACATATATATAGATAAAA
Found at i:20620267 original size:26 final size:25
Alignment explanation
Indices: 20620238--20620289 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
20620228 AAAATTAATT
20620238 AATTTA-GAAAAATATATATATAAAAA
1 AATTTATGAAAAATA-ATATA-AAAAA
*
20620264 AATTTATGAAGAATAATATAAAAAA
1 AATTTATGAAAAATAATATAAAAAA
20620289 A
1 A
20620290 CATACGTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 6 0.25
26 11 0.46
27 7 0.29
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (25 bp):
AATTTATGAAAAATAATATAAAAAA
Found at i:20620386 original size:17 final size:17
Alignment explanation
Indices: 20620364--20620407 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
20620354 TAGGAAATAA
20620364 AAAATGTATATGTATAT
1 AAAATGTATATGTATAT
*
20620381 AAAATGTAAATGTATAT
1 AAAATGTATATGTATAT
*
20620398 -ATATGTATAT
1 AAAATGTATAT
20620408 AAAAGTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAATGTATATGTATAT
Found at i:20620544 original size:3 final size:3
Alignment explanation
Indices: 20620536--20620574 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
20620526 GTATATATAG
* *
20620536 TAA TAA TAA TAA TGA TAA TAA TAA CAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20620575 CTTAATAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:20620939 original size:21 final size:21
Alignment explanation
Indices: 20620890--20620987 Score: 121
Period size: 21 Copynumber: 4.7 Consensus size: 21
20620880 AAATTAAATC
*
20620890 TCTAAGATTACA-AAATCATA
1 TCTAAGATTGCATAAATCATA
20620910 TCTTCTAAGATTGCATAAATCATA
1 ---TCTAAGATTGCATAAATCATA
*
20620934 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATAAATCATA
20620955 TCTAAGATTGCAT--ATCATA
1 TCTAAGATTGCATAAATCATA
*
20620974 TCTAAGATTACATA
1 TCTAAGATTGCATA
20620988 TCCTTGAAGA
Statistics
Matches: 70, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
19 18 0.26
21 33 0.47
23 11 0.16
24 8 0.11
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (21 bp):
TCTAAGATTGCATAAATCATA
Found at i:20624157 original size:22 final size:23
Alignment explanation
Indices: 20624131--20624179 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
20624121 GAAGTTTCAG
*
20624131 TCTCTAACTTTCACTCAG-ACAA
1 TCTCTAACTTTAACTCAGTACAA
*
20624153 TCTCTAACTTTAACTCAGTACAG
1 TCTCTAACTTTAACTCAGTACAA
20624176 TCTC
1 TCTC
20624180 ATAAAGTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.35
Consensus pattern (23 bp):
TCTCTAACTTTAACTCAGTACAA
Found at i:20624589 original size:18 final size:20
Alignment explanation
Indices: 20624566--20624606 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
20624556 ACAACGAAAG
20624566 TTTAGAAA-CC-GTTTATAT
1 TTTAGAAATCCAGTTTATAT
*
20624584 TTTAGAAATCCAGTTTGTAT
1 TTTAGAAATCCAGTTTATAT
20624604 TTT
1 TTT
20624607 TGGAAAACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 2 0.10
20 10 0.50
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (20 bp):
TTTAGAAATCCAGTTTATAT
Found at i:20626278 original size:8 final size:8
Alignment explanation
Indices: 20626265--20626298 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
20626255 ATCCCAACTC
20626265 CCCACTAA
1 CCCACTAA
*
20626273 CTCACTAA
1 CCCACTAA
*
20626281 CCCATTAA
1 CCCACTAA
20626289 CCCACTAA
1 CCCACTAA
20626297 CC
1 CC
20626299 AACAACTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.35, C:0.47, G:0.00, T:0.18
Consensus pattern (8 bp):
CCCACTAA
Found at i:20637674 original size:44 final size:44
Alignment explanation
Indices: 20637625--20637807 Score: 120
Period size: 44 Copynumber: 4.2 Consensus size: 44
20637615 CTTTGATTTG
*
20637625 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTA
1 CTCCACTACTGCTCAGGGAGATAAGATCTGTAATCTTCAATCTA
* ** * * * *
20637669 TTCCACTGTTGCCCAGGGAGAT-AGAAC--TACTGGCTTCAATGTA
1 CTCCACTACTGCTCAGGGAGATAAGATCTGTAAT--CTTCAATCTA
* ** * * **** ** *
20637712 CTCCACTGCAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTG
1 CTCCACTAC-TGCTCAGGGAGATAAGATCTGTAATCTTCAATCTA
*
20637757 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTA
1 CTCCACTACTGCTCAGGGAGATAAGATCTGTAATCTTCAATCTA
*
20637801 TTCCACT
1 CTCCACT
20637808 GTGCCCAGGA
Statistics
Matches: 96, Mismatches: 37, Indels: 12
0.66 0.26 0.08
Matches are distributed among these distances:
41 3 0.03
43 20 0.21
44 55 0.57
45 17 0.18
47 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (44 bp):
CTCCACTACTGCTCAGGGAGATAAGATCTGTAATCTTCAATCTA
Found at i:20637730 original size:132 final size:131
Alignment explanation
Indices: 20637533--20637824 Score: 523
Period size: 132 Copynumber: 2.2 Consensus size: 131
20637523 ATTTCTTCTG
* * *
20637533 TCTATTCCATTGTTGCCCTAGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGG
1 TCTATTCCACTGTTGCCC-AGGAGATAGAACTACTGGCTTCAATGTACTCCACTGCAACCTCAGG
*
20637598 GAGGTAAAATCCACCATCTTTGATTTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTC
65 GAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTC
20637663 AA
130 AA
20637665 TCTATTCCACTGTTGCCCAGGGAGATAGAACTACTGGCTTCAATGTACTCCACTGCAACCTCAGG
1 TCTATTCCACTGTTGCCCA-GGAGATAGAACTACTGGCTTCAATGTACTCCACTGCAACCTCAGG
20637730 GAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTC
65 GAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTC
20637795 AA
130 AA
20637797 TCTATTCCACTG-TGCCCAGGAGATAGAA
1 TCTATTCCACTGTTGCCCAGGAGATAGAA
20637825 TGNNNNNNNN
Statistics
Matches: 155, Mismatches: 4, Indels: 4
0.95 0.02 0.02
Matches are distributed among these distances:
130 10 0.06
131 7 0.05
132 138 0.89
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (131 bp):
TCTATTCCACTGTTGCCCAGGAGATAGAACTACTGGCTTCAATGTACTCCACTGCAACCTCAGGG
AGGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
A
Found at i:20638877 original size:99 final size:100
Alignment explanation
Indices: 20638704--20638965 Score: 445
Period size: 99 Copynumber: 2.6 Consensus size: 100
20638694 NNNNNNNNNN
* *
20638704 ATCAGGGAAATCAGATCCGTCGTCGTAGCTTCAATCCGTTCCACTGCACTGCTAAGGAAGTAAGA
1 ATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCCGTTCCACTGCACTGCTAAGGAAGTAAGA
*
20638769 TCCGCCGTTGCGGCTTTAATCTT-TTAATTGCAAT
66 TCCGCCGTTGCGGCTTCAATCTTGTTAATTGCAAT
20638803 ATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCCGTTCCACTGCACTGCTAAGGAAGTAAGA
1 ATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCCGTTCCACTGCACTGCTAAGGAAGTAAGA
* *
20638868 TCCGTCGTTGTGGCTTCAATCTTGTTAATTGCAAT
66 TCCGCCGTTGCGGCTTCAATCTTGTTAATTGCAAT
* * *
20638903 ATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTACTAATGAAGTAA
1 ATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCCGTTCCACTGCACTGCTAAGGAAGTAA
20638966 AATCTATGGT
Statistics
Matches: 154, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
99 83 0.54
100 71 0.46
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.27
Consensus pattern (100 bp):
ATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCCGTTCCACTGCACTGCTAAGGAAGTAAGA
TCCGCCGTTGCGGCTTCAATCTTGTTAATTGCAAT
Found at i:20638919 original size:50 final size:50
Alignment explanation
Indices: 20638766--20638939 Score: 165
Period size: 50 Copynumber: 3.5 Consensus size: 50
20638756 TAAGGAAGTA
* ** *
20638766 AGATCCGCCGTTGCGGCTTTAATCTT-TTAATTGCAATATCAGGGAAACC
1 AGATCCGCCGTCGTAGCTTCAATCTTGTTAATTGCAATATCAGGGAAACC
* * * * * * ***
20638815 AGATCCGCCGTCGTAGCTTCAATC-CGTTCCACTGCACT-GCTAAGGAAGTA
1 AGATCCGCCGTCGTAGCTTCAATCTTGTT-AATTGCAATATC-AGGGAAACC
* * *
20638865 AGATCCGTCGTTGTGGCTTCAATCTTGTTAATTGCAATATCAGGGAAACC
1 AGATCCGCCGTCGTAGCTTCAATCTTGTTAATTGCAATATCAGGGAAACC
20638915 AGATCCGCCGTCGTAGCTTCAATCT
1 AGATCCGCCGTCGTAGCTTCAATCT
20638940 GTTCCACTGC
Statistics
Matches: 92, Mismatches: 28, Indels: 9
0.71 0.22 0.07
Matches are distributed among these distances:
49 23 0.25
50 65 0.71
51 4 0.04
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (50 bp):
AGATCCGCCGTCGTAGCTTCAATCTTGTTAATTGCAATATCAGGGAAACC
Found at i:20652349 original size:151 final size:151
Alignment explanation
Indices: 20652075--20652356 Score: 372
Period size: 151 Copynumber: 1.9 Consensus size: 151
20652065 TAAATTACAC
* *
20652075 TTTCTTAAAATCAAAACTTTATTTCGAAAAAGTTAAAAAATATCAAAGTTTTATTTTAAAAAATT
1 TTTCTTAAAATCAAAACTTTATTTCGAAAAAGTTAAAAAAGATCAAAATTTTATTTTAAAAAATT
* ** * ***
20652140 TAAATTTGTTCCTTAAAATGACTAAAAGGCAGATTTTTATTTTAAAAATCTAAACTTTCACTTTT
66 TAAACTTGTTCCTTAAAATGACTAAAAAACAAATTTTTAAAATAAAAATCTAAACTTTCACTTTT
20652205 TTTTAAAAACAAATCACTGTT
131 TTTTAAAAACAAATCACTGTT
* * *
20652226 TTTCTTAAAAATCAAAACTTTATTTC-AAAATAGTTGAAAAAGATCAAAATTTTGTTTT-AAGAA
1 TTTCTT-AAAATCAAAACTTTATTTCGAAAA-AGTTAAAAAAGATCAAAATTTTATTTTAAAAAA
* * * *
20652289 TTTAAACTT-TTCTTTTAATATGACTAAAAAATAAATTTTTAAAATAAAAATCTAAACTTTCTCT
64 TTTAAACTTGTTC-CTTAAAATGACTAAAAAACAAATTTTTAAAATAAAAATCTAAACTTTCACT
20652353 TTTT
128 TTTT
20652357 AAAAAAAAAA
Statistics
Matches: 112, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
150 3 0.03
151 67 0.60
152 42 0.38
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.42
Consensus pattern (151 bp):
TTTCTTAAAATCAAAACTTTATTTCGAAAAAGTTAAAAAAGATCAAAATTTTATTTTAAAAAATT
TAAACTTGTTCCTTAAAATGACTAAAAAACAAATTTTTAAAATAAAAATCTAAACTTTCACTTTT
TTTTAAAAACAAATCACTGTT
Found at i:20654800 original size:17 final size:16
Alignment explanation
Indices: 20654760--20654801 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
20654750 AGATTAAGGG
20654760 AATAAAAAAAATAAAT
1 AATAAAAAAAATAAAT
*
20654776 AATGAAAAGAAATAAAT
1 AAT-AAAAAAAATAAAT
20654793 AAATAAAAA
1 -AATAAAAA
20654802 TAAGCAAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 3 0.14
17 16 0.73
18 3 0.14
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (16 bp):
AATAAAAAAAATAAAT
Found at i:20654814 original size:27 final size:27
Alignment explanation
Indices: 20654755--20654819 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
20654745 AGAATAGATT
*
20654755 AAGGGAATAAA-AAAAATAAATAATGA
1 AAGGAAATAAATAAAAATAAATAATGA
*
20654781 AAAGAAATAAATAAATAA-AAATAA-GCA
1 AAGGAAATAAATAAA-AATAAATAATG-A
20654808 AAGGAAATAAAT
1 AAGGAAATAAAT
20654820 TGATAAATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 10 0.30
27 21 0.64
28 2 0.06
ACGTcount: A:0.71, C:0.02, G:0.12, T:0.15
Consensus pattern (27 bp):
AAGGAAATAAATAAAAATAAATAATGA
Found at i:20666102 original size:6 final size:6
Alignment explanation
Indices: 20666091--20666116 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
20666081 AATTGGGAAC
20666091 AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
20666117 TAAACAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:20666932 original size:23 final size:23
Alignment explanation
Indices: 20666902--20666957 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
20666892 CACCAGCCTT
20666902 TACACACCATCTCCGTCCAACCC
1 TACACACCATCTCCGTCCAACCC
20666925 TACACACCATCTCCGTCCAACCC
1 TACACACCATCTCCGTCCAACCC
20666948 TACACACCAT
1 TACACACCAT
20666958 GTGGGGATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.29, C:0.50, G:0.04, T:0.18
Consensus pattern (23 bp):
TACACACCATCTCCGTCCAACCC
Found at i:20674448 original size:14 final size:14
Alignment explanation
Indices: 20674429--20674466 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
20674419 ATTAAGGGTG
20674429 TAAAAATAAATAAA
1 TAAAAATAAATAAA
*
20674443 TAAAAATAAACAAA
1 TAAAAATAAATAAA
*
20674457 T-GAAATAAAT
1 TAAAAATAAAT
20674467 CGATAAACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (14 bp):
TAAAAATAAATAAA
Found at i:20677954 original size:24 final size:26
Alignment explanation
Indices: 20677911--20677970 Score: 79
Period size: 24 Copynumber: 2.4 Consensus size: 26
20677901 TTTTTTTTCT
**
20677911 TTTTACAATAATTT-GTAAA-AAGAA
1 TTTTACAATAATTTAAAAAATAAGAA
*
20677935 TTTTACAATAATTTAAAAAATAATAA
1 TTTTACAATAATTTAAAAAATAAGAA
20677961 TTTTACAATA
1 TTTTACAATA
20677971 TTTTTAAGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 14 0.45
25 3 0.10
26 14 0.45
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (26 bp):
TTTTACAATAATTTAAAAAATAAGAA
Found at i:20686466 original size:30 final size:30
Alignment explanation
Indices: 20686402--20686470 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
20686392 AAGTGTAGAA
20686402 AACCTCTC-TCTATCCACTTTTGATCCACC
1 AACCTCTCTTCTATCCACTTTTGATCCACC
* * *
20686431 AACCTCTCTTCATATCTACTTTT-ATCTATC
1 AACCTCTCTTC-TATCCACTTTTGATCCACC
20686461 AACCTCTCTT
1 AACCTCTCTT
20686471 TCTTTGTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 8 0.23
30 17 0.49
31 10 0.29
ACGTcount: A:0.22, C:0.36, G:0.01, T:0.41
Consensus pattern (30 bp):
AACCTCTCTTCTATCCACTTTTGATCCACC
Found at i:20690666 original size:40 final size:40
Alignment explanation
Indices: 20690611--20690686 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
20690601 GCTCAGCTCG
20690611 AAGGCTCGTTTGAAAATTGAGAGGGTTTGAATAAAAATAT
1 AAGGCTCGTTTGAAAATTGAGAGGGTTTGAATAAAAATAT
20690651 AAGGCTCGTTTGAAAATTGAGAGGGTTTGAATAAAA
1 AAGGCTCGTTTGAAAATTGAGAGGGTTTGAATAAAA
20690687 TAGACCTGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.29
Consensus pattern (40 bp):
AAGGCTCGTTTGAAAATTGAGAGGGTTTGAATAAAAATAT
Found at i:20691566 original size:16 final size:16
Alignment explanation
Indices: 20691545--20691616 Score: 99
Period size: 16 Copynumber: 4.5 Consensus size: 16
20691535 CGTTTGGTTC
20691545 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
20691561 GCTGTAATTGAATAGA
1 GCTGTAATGGAATAGA
* *
20691577 GCTATAATGGAACAGA
1 GCTGTAATGGAATAGA
*
20691593 GGTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
20691609 ACTGTAAT
1 GCTGTAAT
20691617 AGTAATTCAA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.39, C:0.07, G:0.28, T:0.26
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:20691656 original size:45 final size:44
Alignment explanation
Indices: 20691598--20691690 Score: 143
Period size: 44 Copynumber: 2.1 Consensus size: 44
20691588 ACAGAGGTGT
20691598 AATGGAATAGAACTGTAATAGTAATTCAAT-TGTTTGATTGAATAG
1 AATGGAATAGAACTGTAATAGT-ATTC-ATGTGTTTGATTGAATAG
* *
20691643 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATAG
1 AATGGAATAGAACTGTAATAGTATTCATGTGTTTGATTGAATAG
20691687 AATG
1 AATG
20691691 ATGTTGTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.49
45 22 0.49
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCATGTGTTTGATTGAATAG
Found at i:20691912 original size:55 final size:54
Alignment explanation
Indices: 20691803--20691919 Score: 128
Period size: 55 Copynumber: 2.1 Consensus size: 54
20691793 TATTATTAAT
* *
20691803 ATAAATAATAAATAATTTAATCATATTTGAACATAATTATTATTAAATATAATTTA
1 ATAAA-AATAAATAATTTAATAAAATTTGAACATAATTATTATT-AATATAATTTA
* * * *
20691859 ATAAAAATATATAATTTAATAAAATTCTTAATATAATTATTCTT-ATATGAATTTA
1 ATAAAAATAAATAATTTAATAAAATT-TGAACATAATTATTATTAATAT-AATTTA
*
20691914 CTAAAA
1 ATAAAA
20691920 TCATAATATA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
54 4 0.08
55 29 0.56
56 19 0.37
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (54 bp):
ATAAAAATAAATAATTTAATAAAATTTGAACATAATTATTATTAATATAATTTA
Found at i:20695077 original size:25 final size:25
Alignment explanation
Indices: 20695049--20695098 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
20695039 TGAAGGAAAA
20695049 GATGAAGCTGAGGGCAGAAAAGTTT
1 GATGAAGCTGAGGGCAGAAAAGTTT
20695074 GATGAAGCTGAGGGCAGAAAAGTTT
1 GATGAAGCTGAGGGCAGAAAAGTTT
20695099 CTAACTACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.08, G:0.36, T:0.20
Consensus pattern (25 bp):
GATGAAGCTGAGGGCAGAAAAGTTT
Found at i:20697085 original size:51 final size:51
Alignment explanation
Indices: 20697009--20697110 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
20696999 CAACTTAAAC
*
20697009 ACCGAGATGTTCTGTTCTTGGTTTCTTTGTAGGTCTCTTGAATCTTGCTTT
1 ACCGAGATGTTCTGTTCTTGGTTTCTTTGTAGGTCTCTTGAATCTCGCTTT
*
20697060 ACCGAGATGTTCTGTTCTTGGTTTCTTTGTAGGTCTTTTGAATCTCGCTTT
1 ACCGAGATGTTCTGTTCTTGGTTTCTTTGTAGGTCTCTTGAATCTCGCTTT
20697111 CTTTCTTCCA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.49
Consensus pattern (51 bp):
ACCGAGATGTTCTGTTCTTGGTTTCTTTGTAGGTCTCTTGAATCTCGCTTT
Found at i:20697448 original size:21 final size:21
Alignment explanation
Indices: 20697375--20697579 Score: 123
Period size: 21 Copynumber: 9.5 Consensus size: 21
20697365 TGTTACTGAA
20697375 TTTGTTGTTTTAAATCGATTC
1 TTTGTTGTTTTAAATCGATTC
* * *
20697396 TTT-TAT-TCTTTGAATCAATTG
1 TTTGT-TGT-TTTAAATCGATTC
*
20697417 TTTGTTGTTTTAAATTGATTC
1 TTTGTTGTTTTAAATCGATTC
* *
20697438 TTTGCTT-TTTTGAAGCGATTC
1 TTTG-TTGTTTTAAATCGATTC
* * *
20697459 ATGATTTTTGTTTTAAATTGATCC
1 -T--TTGTTGTTTTAAATCGATTC
*
20697483 ATGATTGTTGTTTTAAATCGATTA
1 -T--TTGTTGTTTTAAATCGATTC
* * *
20697507 TTTGCTT-CTTTAAATTGATTTT
1 TTTG-TTGTTTTAAATCGA-TTC
20697529 TTTGTTGTTTTAAATCGATTC
1 TTTGTTGTTTTAAATCGATTC
* * * *
20697550 ATTATT-ATTTGAATCGATTC
1 TTTGTTGTTTTAAATCGATTC
20697570 TTTGTTGTTT
1 TTTGTTGTTT
20697580 AGCTTGATTC
Statistics
Matches: 139, Mismatches: 32, Indels: 26
0.71 0.16 0.13
Matches are distributed among these distances:
20 18 0.13
21 64 0.46
22 22 0.16
23 3 0.02
24 32 0.23
ACGTcount: A:0.21, C:0.08, G:0.14, T:0.57
Consensus pattern (21 bp):
TTTGTTGTTTTAAATCGATTC
Found at i:20700544 original size:29 final size:29
Alignment explanation
Indices: 20700512--20700644 Score: 149
Period size: 29 Copynumber: 4.6 Consensus size: 29
20700502 TCACACGGCT
* *
20700512 GACCACACACCCGTGTGGTGCACATGATC
1 GACCACACGCCCGTGTGGTGCACATGACC
* * * * *
20700541 GACCACACGCTCATGTAGTGAACATGACA
1 GACCACACGCCCGTGTGGTGCACATGACC
* * * *
20700570 AACTACATGCCTGTGTGGTGCACATGACC
1 GACCACACGCCCGTGTGGTGCACATGACC
*
20700599 GACCACACGCCTGTGTGGTGCACATGACC
1 GACCACACGCCCGTGTGGTGCACATGACC
*
20700628 GACCACATGCCCGTGTG
1 GACCACACGCCCGTGTG
20700645 ACGCAGTGTA
Statistics
Matches: 83, Mismatches: 21, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 83 1.00
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.19
Consensus pattern (29 bp):
GACCACACGCCCGTGTGGTGCACATGACC
Done.