Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 58 of 145
Found at i:20082884 original size:21 final size:22
Alignment explanation
Indices: 20082846--20082894 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
20082836 ATGAAATGAA
*
20082846 AAAAAT-AAAAAAGTGAAAAGG
1 AAAAATGAAAAAAGTGAAAAAG
*
20082867 AAAAATGAAAAATG-GAAAAAG
1 AAAAATGAAAAAAGTGAAAAAG
*
20082888 TAAAATG
1 AAAAATG
20082895 GAGAGGCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.69, C:0.00, G:0.18, T:0.12
Consensus pattern (22 bp):
AAAAATGAAAAAAGTGAAAAAG
Found at i:20082892 original size:14 final size:14
Alignment explanation
Indices: 20082853--20082896 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
20082843 GAAAAAAATA
20082853 AAAAAGTGAAAA-GG
1 AAAAAGT-AAAATGG
*
20082867 AAAAATGAAAAATGG
1 AAAAA-GTAAAATGG
20082882 AAAAAGTAAAATGG
1 AAAAAGTAAAATGG
20082896 A
1 A
20082897 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:20084663 original size:177 final size:174
Alignment explanation
Indices: 20084205--20085431 Score: 1274
Period size: 177 Copynumber: 6.9 Consensus size: 174
20084195 ATACTGGTGG
* * *
20084205 TGAAGTAGATC-GAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGT
1 TGAAGTAGATCAG-AGATAATGGATCTTGTCTTCATGTATTGACA-GAAGTAGATCAAAGAAAGC
* * * *
20084269 GGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCCTATACT
64 AGATCTTGTCTTCCTGTACTGGC-GTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTA-T
* * * * * *
20084334 GGTGGC--GAAGTAGATCAAAGAAAGCAGATCTTATCTTCCCATACTAGT-A-G
127 --TGACATGAAGTAGATC-AAGATAGCAGATCTTGTCTT--CAT-GTATTGACA
* * * * *
20084384 TGAAGTAGATC-GA-AAAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAA
1 TGAAGTAGATCAGAGATAATG--GATCTTGTCTTCATGTATTGAC-AGAAGTAGATCAAAGA-AA
* * * *
20084447 -CAGATCTTGTCTTCCCGTACTGGTGGAGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTA
62 GCAGATCTTGTCTTCCTGTACTGG-CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTA
* * * * *
20084511 TTGGCGTGAAGTAGATCGAAGATAGCAAATCTTGTCTTCATGTATTGGCG
126 TTGACATGAAGTAGATC-AAGATAGCAGATCTTGTCTTCATGTATTGACA
* ** * ** * *
20084561 TGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGC-GAAGTAGATCGAAGAAAG
1 TGAAGTAGATCAGAGATAATGGATCTTGTCTT--CAT-GTATTGACAGAAGTAGATCAAAGAAAG
* * * *
20084625 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGTAGATCTTGTCTTCATTTATT
63 CAGATCTTGTCTTCCTGTACTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATT
* ** *
20084690 GACATGAAGTAGATCGAGATAAAATATCTTGTCTTCATGTATTGACA
128 GACATGAAGTAGATCAAGATAGCAGATCTTGTCTTCATGTATTGACA
* * * *
20084737 TGAAGTAAATCAGAGATAATGGATCTTGTCTTCATGTATTGACATAAAATAGATCAAAGATAGCA
1 TGAAGTAGATCAGAGATAATGGATCTTGTCTTCATGTATTGACA-GAAGTAGATCAAAGAAAGCA
* * * * *
20084802 GATCTTGTCTT-CTCATACTAGTG-GTGAAATATATCGAATATAGCAGATCTTGTATTCATGTAT
65 GATCTTGTCTTCCT-GTACT-G-GCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTAT
20084865 TGACATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCATGTATTGACA
127 TGACATGAAGTAGATCA-AGATAGCAGATCTTGTCTTCATGTATTGACA
* *
20084914 TGAAGTAGATCAGAGATAATGGATCTTGTCTTCATGTATTGACATAAAGTAGATCAAAGATAGCA
1 TGAAGTAGATCAGAGATAATGGATCTTGTCTTCATGTATTGACA-GAAGTAGATCAAAGAAAGCA
** * *
20084979 GATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAGTAGATCTTGTCTTCATGTATTG
65 GATCTTGTCTTCCTGTACTGG-CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTG
* *
20085044 ACATAAAGAAGATCAGAGATAGCAGATCTTGTCTTCATGTATTGACA
129 ACATGAAGTAGATCA-AGATAGCAGATCTTGTCTTCATGTATTGACA
*
20085091 TGAAGTAGATCAGAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATG
1 TGAAGTAGATCAGAGATAATGGATCTTGTCTTCATGTATTGACA-GAAGTAGATCAAAGA-AA-G
* * * * * * * * ***
20085156 --GATCTTGTCTTCATGTATTGACATAAAGTAGATCAAAGATAGCAAATTTTGTCTTCCCATACT
63 CAGATCTTGTCTTCCTGTACTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTA-T
* ***
20085219 GGTGGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTGACA
127 TGACATGAAGTAGATC-AAGATAGCAGATCTTGTCTTCATGTATTGACA
* *
20085268 TGATGTAGATCAGAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCA
1 TGAAGTAGATCAGAGATAATGGATCTTGTCTTCATGTATTGACA-GAAGTAGATCAAAGAAAGCA
* * ** * ***
20085333 AATTTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTG
65 GATCTTGTCTTCCTGTACTGG-CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTG
20085398 ACATGAAGTAGATCAGAGATAGCAGATCTTGTCT
129 ACATGAAGTAGATCA-AGATAGCAGATCTTGTCT
20085432 ACCTGTACTA
Statistics
Matches: 887, Mismatches: 129, Indels: 66
0.82 0.12 0.06
Matches are distributed among these distances:
173 4 0.00
174 4 0.00
175 35 0.04
176 145 0.16
177 488 0.55
178 96 0.11
179 109 0.12
180 6 0.01
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (174 bp):
TGAAGTAGATCAGAGATAATGGATCTTGTCTTCATGTATTGACAGAAGTAGATCAAAGAAAGCAG
ATCTTGTCTTCCTGTACTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTGAC
ATGAAGTAGATCAAGATAGCAGATCTTGTCTTCATGTATTGACA
Found at i:20085426 original size:44 final size:44
Alignment explanation
Indices: 20084226--20085431 Score: 1034
Period size: 44 Copynumber: 27.2 Consensus size: 44
20084216 GAAGATAATG
**
20084226 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGTG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCA
* * * *
20084270 GATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATC-GAAGAAAGCA
1 GATCTTGTCTTCATGTATTGACA-TGAAGTAGATCAG-AGATAGCA
* * * * *
20084315 GATCTTGTCTTCCTATACTGGTGGC--GAAGTAGATCAAAGAAAGCA
1 GATCTTGTCTTCATGTA-T--TGACATGAAGTAGATCAGAGATAGCA
* * * * * *
20084360 GATCTTATCTTCCCATACTAGT-A-GTGAAGTAGATC-GAAAAAAGCA
1 GATCTTGTCTT--CAT-GTATTGACATGAAGTAGATCAG-AGATAGCA
* * *
20084405 GATCTTGTCTTCATGTATTGGCGTGAAGTAGATC-GAAGATAACA
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAGCA
** * *
20084449 GATCTTGTCTTCCCGTACTGGTG-GA-GAAGTAGATC-GAAGAAAGCA
1 GATCTTGTCTTCATGTA-T--TGACATGAAGTAGATCAG-AGATAGCA
* *
20084494 GATCTTGTCTTCATGTATTGGCGTGAAGTAGATC-GAAGATAGCA
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAGCA
* * * * *
20084538 AATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAACA
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCA
* ** * *
20084582 GATCTTGTCTTCCCATACTGGTGGC--GAAGTAGATC-GAAGAAAGCA
1 GATCTTGTCTT--CAT-GTATTGACATGAAGTAGATCAG-AGATAGCA
* * *
20084627 GATCTTGTCTTCATGTATTGGCGTGAAGTAGATC-GAAGATAGTA
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAGCA
* **
20084671 GATCTTGTCTTCATTTATTGACATGAAGTAGATC-GAGATAAAA
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCA
* * ***
20084714 TATCTTGTCTTCATGTATTGACATGAAGTAAATCAGAGATAATG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCA
* * *
20084758 GATCTTGTCTTCATGTATTGACATAAAATAGATCAAAGATAGCA
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCA
* * * * * *
20084802 GATCTTGTCTTCTCATACTAGTG--GTGAAATATATC-GAATATAGCA
1 GATCTTGTC-T-TCAT-GTATTGACATGAAGTAGATCAG-AGATAGCA
*
20084847 GATCTTGTATTCATGTATTGACATGAAGTAGATCAGAGATAGCA
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCA
***
20084891 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCA
* *
20084935 GATCTTGTCTTCATGTATTGACATAAAGTAGATCAAAGATAGCA
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCA
*** * *** *
20084979 GATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC-GAAGATAGTA
1 GATCTTGTCTTCATGTA-TTGACATGAAGTAGATCAG-AGATAGCA
* *
20085024 GATCTTGTCTTCATGTATTGACATAAAGAAGATCAGAGATAGCA
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCA
***
20085068 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCA
***
20085112 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCA
* *
20085156 GATCTTGTCTTCATGTATTGACATAAAGTAGATCAAAGATAGCA
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCA
* * *** * ***
20085200 AATTTTGTCTTCCCATACTGGTGGTGAAGTAGATC-GAAGATAGCA
1 GATCTTGTCTTCATGTA-TTGACATGAAGTAGATCAG-AGATAGCA
* ***
20085245 GATCTTGTCTTCATGTATTGACATGATGTAGATCAGAGATAATG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCA
*
20085289 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCA
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCA
* * *** * *** ***
20085333 AATTTTGTCTTCCCATACTGGTGGTGAAGTAGATC-GAAGATAATG
1 GATCTTGTCTTCATGTA-TTGACATGAAGTAGATCAG-AGATAGCA
20085378 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCA
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCA
20085422 GATCTTGTCT
1 GATCTTGTCT
20085432 ACCTGTACTA
Statistics
Matches: 945, Mismatches: 174, Indels: 86
0.78 0.14 0.07
Matches are distributed among these distances:
42 14 0.01
43 47 0.05
44 585 0.62
45 273 0.29
46 7 0.01
47 13 0.01
48 6 0.01
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (44 bp):
GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCA
Found at i:20085426 original size:133 final size:133
Alignment explanation
Indices: 20084226--20085431 Score: 1142
Period size: 133 Copynumber: 9.1 Consensus size: 133
20084216 GAAGATAATG
* ** *
20084226 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGTGGATCTTGTCTTCCTGTACTGG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCAGATCTTGTCTTCATGTACTGG
* * * *
20084291 -CAGTGAAGTAGATCGAAGA-AAGCAGATCTTGTCTTCCTATACTGGTGGC--GAAGTAGATCAA
66 AC-GTGAAGTAGATCGAAGATAA-CAGATCTTGTCTTCATGTA-T--TGACATGAAGTAGATCAG
*
20084352 AGAAAGCA
126 AGATAGCA
* * * * *
20084360 GATCTTATCTTCCCATACTAGT-A-GTGAAGTAGATCGAAA-AAAGCAGATCTTGTCTTCATGTA
1 GATCTTGTCTT--CAT-GTATTGACATGAAGTAGATC-AAAGATAGCAGATCTTGTCTTCATGTA
* ** *
20084422 TTGG-CGTGAAGTAGATCGAAGATAACAGATCTTGTCTTCCCGTACTGGTG-GA-GAAGTAGATC
62 CTGGACGTGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTA-T--TGACATGAAGTAGATC
*
20084484 -GAAGAAAGCA
124 AG-AGATAGCA
* * * * *
20084494 GATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAAATCTTGTCTTCATGTATTGG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCAGATCTTGTCTTCATGTACTGG
* * ** *
20084559 -CGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGC--GAAGTAGATC-GAA
66 ACGTGAAGTAGATCGAAGATAACAGATCTTGTCTT--CAT-GTATTGACATGAAGTAGATCAG-A
*
20084620 GAAAGCA
127 GATAGCA
* * * * * *
20084627 GATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGTAGATCTTGTCTTCATTTA-TTG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCAGATCTTGTCTTCATGTACTGG
* * * *
20084691 ACATGAAGTAGATCG-AGATAAAATATCTTGTCTTCATGTATTGACATGAAGTAAATCAGAGATA
66 ACGTGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATA
***
20084755 ATG
131 GCA
* * * *
20084758 GATCTTGTCTTCATGTATTGACATAAAATAGATCAAAGATAGCAGATCTTGTCTTC-TCATACTA
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCAGATCTTGTCTTCAT-GTACTG
** * * * * *
20084822 GTGGTGAAATATATCGAATATAGCAGATCTTGTATTCATGTATTGACATGAAGTAGATCAGAGAT
65 GACGTGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGAT
20084887 AGCA
130 AGCA
* *** *
20084891 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATGGATCTTGTCTTCATGTA-TTG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCAGATCTTGTCTTCATGTACTGG
* * * * *** * ***
20084955 ACATAAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC-GAAGA
66 ACGTGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTA-TTGACATGAAGTAGATCAG-AGA
*
20085019 TAGTA
129 TAGCA
* * * *
20085024 GATCTTGTCTTCATGTATTGACATAAAGAAGATCAGAGATAGCAGATCTTGTCTTCATGTA-TTG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCAGATCTTGTCTTCATGTACTGG
* **
20085088 ACATGAAGTAGATC-AGAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGAT
66 ACGTGAAGTAGATCGA-AGATAACAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGAT
***
20085152 AATG
130 AGCA
* * * ***
20085156 GATCTTGTCTTCATGTATTGACATAAAGTAGATCAAAGATAGCAAATTTTGTCTTCCCATACTGG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCAGATCTTGTCTTCATGTACTGG
** * *
20085221 TGGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTGACATGATGTAGATCAGAGATA
66 ACGTGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATA
***
20085286 ATG
131 GCA
* * ***
20085289 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCAAATTTTGTCTTCCCATACTGG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCAGATCTTGTCTTCATGTACTGG
** **
20085354 TGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATA
66 ACGTGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATA
20085419 GCA
131 GCA
20085422 GATCTTGTCT
1 GATCTTGTCT
20085432 ACCTGTACTA
Statistics
Matches: 911, Mismatches: 133, Indels: 57
0.83 0.12 0.05
Matches are distributed among these distances:
129 4 0.00
130 4 0.00
131 68 0.07
132 143 0.16
133 565 0.62
134 80 0.09
135 37 0.04
136 7 0.01
137 3 0.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (133 bp):
GATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCAGATCTTGTCTTCATGTACTGG
ACGTGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATA
GCA
Found at i:20085958 original size:22 final size:21
Alignment explanation
Indices: 20085933--20085973 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
20085923 AACAAACGCA
* *
20085933 AACAATACAACGAAGAAAAAGG
1 AACAAAACAAC-AACAAAAAGG
20085955 AACAAAACAACAACAAAAA
1 AACAAAACAACAACAAAAA
20085974 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:20091229 original size:22 final size:23
Alignment explanation
Indices: 20091180--20091229 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
20091170 ATTTAAAAAA
* *
20091180 TATTAAAAATATTTTTTATATAC
1 TATTAAAAATAATTTTAATATAC
*
20091203 T-TTAAAAATAATTTTAAT-TAT
1 TATTAAAAATAATTTTAATATAC
20091224 TATTAA
1 TATTAA
20091230 TTTTTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 3 0.13
22 19 0.83
23 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTAAAAATAATTTTAATATAC
Found at i:20091255 original size:21 final size:23
Alignment explanation
Indices: 20091217--20091260 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
20091207 AAAATAATTT
*
20091217 TAATTATTATTAATTTTTAAAAA
1 TAATTATTATTAAATTTTAAAAA
20091240 TAATT-TT-TTAAATTTTAAAAA
1 TAATTATTATTAAATTTTAAAAA
20091261 ATTAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 13 0.65
22 2 0.10
23 5 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATTATTATTAAATTTTAAAAA
Found at i:20092775 original size:14 final size:13
Alignment explanation
Indices: 20092755--20092784 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
20092745 ATTTAAAGGC
*
20092755 TAAAAAAAAAGAT
1 TAAAAAAAAAAAT
20092768 TAAAAAAAAAAAT
1 TAAAAAAAAAAAT
20092781 TAAA
1 TAAA
20092785 CGAGAAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (13 bp):
TAAAAAAAAAAAT
Found at i:20102283 original size:7 final size:7
Alignment explanation
Indices: 20102271--20102329 Score: 57
Period size: 7 Copynumber: 8.0 Consensus size: 7
20102261 AAAATTGTTA
20102271 AAAAAAG
1 AAAAAAG
20102278 AAAAAAG
1 AAAAAAG
20102285 AAAAAAAG
1 -AAAAAAG
20102293 AAGGAAAAAG
1 -A--AAAAAG
*
20102303 AAAGAAG
1 AAAAAAG
20102310 -AAAAAG
1 AAAAAAG
20102316 AAAAAAG
1 AAAAAAG
*
20102323 AGAAAAG
1 AAAAAAG
20102330 GAGAGGCCAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
6 5 0.11
7 24 0.53
8 9 0.20
9 1 0.02
10 6 0.13
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:20102288 original size:13 final size:13
Alignment explanation
Indices: 20102272--20102329 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
20102262 AAATTGTTAA
20102272 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
* *
20102285 AAAAA-AAGAAGG
1 AAAAAGAAAAAAG
*
20102297 AAAAAGAAAGAAG
1 AAAAAGAAAAAAG
20102310 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
20102323 AGAAAAG
1 A-AAAAG
20102330 GAGAGGCCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
12 10 0.27
13 22 0.59
14 5 0.14
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:20102884 original size:212 final size:213
Alignment explanation
Indices: 20102511--20102902 Score: 741
Period size: 212 Copynumber: 1.8 Consensus size: 213
20102501 CAGGAAAGGG
20102511 TAGGCGACATCTTGGGGCATCGACAAAGTCCTGTAGATCTCCTAAACACATGTCAAACTCAGAAT
1 TAGGCGACATCTTGGGGCATCGACAAAGTCCTGTAGATCTCCTAAACACATGTCAAACTCAGAAT
*
20102576 GGTCTTCAGAAAGTTTGTACAGAGAAGTTCAAGCTGCGATATCTGGGGCATCTAGTCCTCATACT
66 GGTCTTCAGAAAATTTGTACAGAGAAGTTCAAGCTGCGATATCTGGGGCATCTAGTCCTCATACT
*
20102641 ATTTATATTGAATTTTTTGCTCTTGGAATACTTCATT-ATTTTCAAGATATTTGAGTTGAAAACC
131 ATTTATATTAAATTTTTTGCTCTTGGAATACTTCATTCATTTTCAAGATATTTGAGTTGAAAACC
20102705 TGAAAAGGGCGAAAATGT
196 TGAAAAGGGCGAAAATGT
20102723 TAGGCGACATCTTGGGGCATCGACAAAGTCCTGTAGATCTCCTAAACACATGTCAAACTCAGAAT
1 TAGGCGACATCTTGGGGCATCGACAAAGTCCTGTAGATCTCCTAAACACATGTCAAACTCAGAAT
20102788 GGTCTTCAGAAAATTTGTACAGAGAAGTTCAAGCTGCGATATCTGGGGCATCTAGTCCTCATACT
66 GGTCTTCAGAAAATTTGTACAGAGAAGTTCAAGCTGCGATATCTGGGGCATCTAGTCCTCATACT
* *
20102853 ATTTATATTAAATTTTTTGCTCTTTGAATACTTCATTCTTTTTCAAGATA
131 ATTTATATTAAATTTTTTGCTCTTGGAATACTTCATTCATTTTCAAGATA
20102903 CGTGTTCCCA
Statistics
Matches: 175, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
212 164 0.94
213 11 0.06
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (213 bp):
TAGGCGACATCTTGGGGCATCGACAAAGTCCTGTAGATCTCCTAAACACATGTCAAACTCAGAAT
GGTCTTCAGAAAATTTGTACAGAGAAGTTCAAGCTGCGATATCTGGGGCATCTAGTCCTCATACT
ATTTATATTAAATTTTTTGCTCTTGGAATACTTCATTCATTTTCAAGATATTTGAGTTGAAAACC
TGAAAAGGGCGAAAATGT
Found at i:20103805 original size:46 final size:46
Alignment explanation
Indices: 20103738--20104085 Score: 525
Period size: 46 Copynumber: 7.5 Consensus size: 46
20103728 CAGATCAATG
* * * **
20103738 AGATAGCAGATCTTGTCTTCCTTTATTTGGCAGTGGAGTAAATTAA
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGA
* *
20103784 AGATAGCAGATCTTGTCTTCCTCTATTTGGCAGTGGAGTAGATCGA
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGA
* *
20103830 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGGTTGA
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGA
*
20103876 ATATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGA
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGA
* * *
20103922 AGATAGGAGATCTTGTCTTCCTGTATTTGGTAGCGGGGTAGATCGA
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGA
* * *
20103968 AGATAGCAGATCCTGTCTTCCTATATTTGGCAGCAGAGTAGATCGA
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGA
* *
20104014 AGATAACAGATCTTGTCTTCCTGTATTTGGGCAGCGGAGTAGATTGA
1 AGATAGCAGATCTTGTCTTCCTGTATTT-GGCAGCGGAGTAGATCGA
20104061 AGATAGCAGATCTTGTCTTCCTGTA
1 AGATAGCAGATCTTGTCTTCCTGTA
20104086 CTGGCAGTGA
Statistics
Matches: 274, Mismatches: 27, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
46 234 0.85
47 40 0.15
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (46 bp):
AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGA
Found at i:20104275 original size:132 final size:132
Alignment explanation
Indices: 20104120--20104550 Score: 736
Period size: 132 Copynumber: 3.3 Consensus size: 132
20104110 CAACGAACCT
* *
20104120 TATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCCCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCATATTCTGTCCCCCTAAGCAGTAGTGG
* *
20104185 AGCAAATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAAATTTAAGCCATTAGT
66 AGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGT
20104250 CC
131 CC
* * *
20104252 TATCTCCCTAAACAGTAGTGGAGTAGGTCGAAGATTGCATATTTTGTCCCCCTAAGTAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCATATTCTGTCCCCCTAAGCAGTAGTGG
* * *
20104317 AGCAGATCGAAGATGGTGAATTTTATCTTCCCAAGATAATGGAGAAGCAGATTTGAGCCATTAGT
66 AGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGT
20104382 CC
131 CC
*
20104384 TATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCATATTCTGTCCCTCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCATATTCTGTCCCCCTAAGCAGTAGTGG
20104449 AGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGT
66 AGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGT
20104514 CC
131 CC
* * *
20104516 TGTCTCCCTAAGCAGTAGTGGAGTAGATAGAAGAT
1 TATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGAT
20104551 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:20104551 original size:220 final size:220
Alignment explanation
Indices: 20104296--20104708 Score: 686
Period size: 220 Copynumber: 1.9 Consensus size: 220
20104286 TTGCATATTT
* * *
20104296 TGTCCCCCTAAGTAGTAGTGGAGCAGATCGAAGATGGTGAATTTTATCTTCCCAAGATAATGGAG
1 TGTCCCCCTAAGCAGTAGTGGAGCAGATAGAAGATGGTGAATCTTATCTTCCCAAGATAATGGAG
* * *
20104361 AAGCAGATTTGAGCCA-TTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCATA
66 AAGCAGATTTAAGCCATTTA-TCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAGATTGCAGA
20104425 TTCTGTC-CCTCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGT
130 TTCTGTCTCC-CTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGT
20104489 GGAGAAGCAGATTTAAGCCATTAGTCC
194 GGAGAAGCAGATTTAAGCCATTAGTCC
* * *
20104516 TGTCTCCCTAAGCAGTAGTGGAGTAGATAGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAG
1 TGTCCCCCTAAGCAGTAGTGGAGCAGATAGAAGATGGTGAATCTTATCTTCCCAAGATAATGGAG
* * *
20104581 AAGCAGGTTTAAGCCATTTATCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTAAAGTTTGCAGAT
66 AAGCAGATTTAAGCCATTTATCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAGATTGCAGAT
20104646 TCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGT
131 TCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGT
20104709 AGGGAAGTAA
Statistics
Matches: 179, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
220 174 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:20104580 original size:42 final size:42
Alignment explanation
Indices: 20104443--20104580 Score: 113
Period size: 44 Copynumber: 3.2 Consensus size: 42
20104433 CTCTAAGCAG
*
20104443 TAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGA
1 TAGTGGAGCAGATAGAAGATGGTGAATCTTATCTTCCCAAGA
** * * *
20104485 TAGTGGAGAAGCAGATTTAAGCCAT--T-AGTCCTGTC-TCCCTAAGCA
1 TAGT-G-G-AGCAGATAGAAG--ATGGTGAATCTTATCTTCCC-AAG-A
*
20104530 GTAGTGGAGTAGATAGAAGATGGTGAATCTTATCTTCCCAAGA
1 -TAGTGGAGCAGATAGAAGATGGTGAATCTTATCTTCCCAAGA
20104573 TAGTGGAG
1 TAGTGGAG
20104581 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:20104626 original size:46 final size:45
Alignment explanation
Indices: 20104485--20104626 Score: 111
Period size: 44 Copynumber: 3.2 Consensus size: 45
20104475 CTTCCCAAGA
*
20104485 TAGTGGAGAAGCAGATTTAAGCCA-TTAGTCCTGTCTCCCTAAGCAG
1 TAGTGGAGAAGCAG-TTTAAGCCATTTA-TCCTATCTCCCTAAGCAG
* ** * *
20104531 TAGTGGAGTAG-A-TAGAAG--ATGGTGAATCTTATCTTCCC-AAG-A-
1 TAGTGGAGAAGCAGTTTAAGCCAT--T-TATCCTATC-TCCCTAAGCAG
20104573 TAGTGGAGAAGCAGGTTTAAGCCATTTATCCTATCTCCCTAAGCAG
1 TAGTGGAGAAGCA-GTTTAAGCCATTTATCCTATCTCCCTAAGCAG
20104619 TAGTGGAG
1 TAGTGGAG
20104627 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:20104627 original size:88 final size:88
Alignment explanation
Indices: 20104435--20104629 Score: 338
Period size: 88 Copynumber: 2.2 Consensus size: 88
20104425 TTCTGTCCCT
* *
20104435 CTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGA
1 CTAAGCAGTAGTGGAGTAGATAGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGA
*
20104500 TTTAAGCCATTAGTCCTGTCTCC
66 TTTAAGCCATTAGTCCTATCTCC
*
20104523 CTAAGCAGTAGTGGAGTAGATAGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGG
1 CTAAGCAGTAGTGGAGTAGATAGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGA
20104588 TTTAAGCCATTTA-TCCTATCTCC
66 TTTAAGCCA-TTAGTCCTATCTCC
20104611 CTAAGCAGTAGTGGAGTAG
1 CTAAGCAGTAGTGGAGTAG
20104630 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:20105016 original size:21 final size:20
Alignment explanation
Indices: 20104982--20105025 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 20
20104972 TGCCCACCCC
*
20104982 AAAACCCATTACAAACTAAAAA
1 AAAACCCATAAC-AAC-AAAAA
20105004 AAAACCCA-AACAACAAAAA
1 AAAACCCATAACAACAAAAA
20105023 AAA
1 AAA
20105026 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:20106809 original size:25 final size:24
Alignment explanation
Indices: 20106772--20106872 Score: 100
Period size: 25 Copynumber: 4.2 Consensus size: 24
20106762 TTTATTGTAT
20106772 TTTTTAATGTATTATATTAATGTG
1 TTTTTAATGTATTATATTAATGTG
* *
20106796 TTTTGGTAAT-TATTGTAATT-ATAT-
1 TTTT--TAATGTATTAT-ATTAATGTG
* *
20106820 TATTTAATGTATTATATTAATGTA
1 TTTTTAATGTATTATATTAATGTG
*
20106844 TTATTTAATGTATAATATTAATGTG
1 TT-TTTAATGTATTATATTAATGTG
20106869 TTTT
1 TTTT
20106873 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:20106856 original size:73 final size:75
Alignment explanation
Indices: 20106743--20106883 Score: 223
Period size: 73 Copynumber: 1.9 Consensus size: 75
20106733 TATTTTTGTA
* * * *
20106743 ATTATATTATTGTACTATATTTATTGTATTTTTTAATGTATTATATTAATGTGTTTTGGTAATTA
1 ATTATATTAATGTACTATATTTAATGTATTATTTAATGTATAATATTAATGTGTTTTGGTAATTA
20106808 TTGTAATTAT
66 TTGTAATTAT
*
20106818 ATTAT-TTAATGTATTATA-TTAATGTATTATTTAATGTATAATATTAATGTGTTTTGGTAATTA
1 ATTATATTAATGTACTATATTTAATGTATTATTTAATGTATAATATTAATGTGTTTTGGTAATTA
20106881 TTG
66 TTG
20106884 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:20114440 original size:2 final size:2
Alignment explanation
Indices: 20114427--20114459 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
20114417 AACCAGAACA
*
20114427 AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20114460 AAATTTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:20120197 original size:24 final size:24
Alignment explanation
Indices: 20120165--20120236 Score: 135
Period size: 24 Copynumber: 3.0 Consensus size: 24
20120155 TTTTGCTGGA
*
20120165 AAAATATGAAAAAATTTAGTTTTC
1 AAAATATGAAAAAATTCAGTTTTC
20120189 AAAATATGAAAAAATTCAGTTTTC
1 AAAATATGAAAAAATTCAGTTTTC
20120213 AAAATATGAAAAAATTCAGTTTTC
1 AAAATATGAAAAAATTCAGTTTTC
20120237 TTTTTCCTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.35
Consensus pattern (24 bp):
AAAATATGAAAAAATTCAGTTTTC
Found at i:20121324 original size:27 final size:27
Alignment explanation
Indices: 20121286--20121350 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
20121276 TCTGTCAGGT
20121286 AGGCGCCAATGAATGTGCCTCATAGAG
1 AGGCGCCAATGAATGTGCCTCATAGAG
*
20121313 AGGCGCCAATGAATGTGCCTCATAGGG
1 AGGCGCCAATGAATGTGCCTCATAGAG
20121340 AGGCGCCAATG
1 AGGCGCCAATG
20121351 GTGGCCTTCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.28, C:0.23, G:0.32, T:0.17
Consensus pattern (27 bp):
AGGCGCCAATGAATGTGCCTCATAGAG
Found at i:20127282 original size:2 final size:2
Alignment explanation
Indices: 20127263--20127309 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
20127253 AATTACACAA
* * *
20127263 TC TC TT TC TC TC TT TC TC TC TC TC TT TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
20127305 TC TC T
1 TC TC T
20127310 TCTTTTATCA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (2 bp):
TC
Found at i:20127286 original size:12 final size:12
Alignment explanation
Indices: 20127269--20127314 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
20127259 ACAATCTCTT
20127269 TCTCTCTTTCTC
1 TCTCTCTTTCTC
20127281 TCTCTCTTTCTC
1 TCTCTCTTTCTC
*
20127293 TCTCTCTCTCTC
1 TCTCTCTTTCTC
20127305 TCTCTTCTTT
1 TCTC-TCTTT
20127315 TATCATGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 27 0.87
13 4 0.13
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (12 bp):
TCTCTCTTTCTC
Found at i:20142054 original size:35 final size:35
Alignment explanation
Indices: 20142015--20142141 Score: 148
Period size: 35 Copynumber: 3.6 Consensus size: 35
20142005 ATGGTGTCGT
* * **
20142015 TCCATAGAGCCAGTAGATCATCT-CTGTGATGCCAC
1 TCCATAAAGCCAGTAGACCAT-TACCATGATGCCAC
* * *
20142050 TCCATAGAGCCAGTAGACCATTACCATAATGCTAC
1 TCCATAAAGCCAGTAGACCATTACCATGATGCCAC
* *
20142085 TCTATAAAGCCAGTAGACCATTGCCATGATGCCAC
1 TCCATAAAGCCAGTAGACCATTACCATGATGCCAC
*
20142120 TCCATAAAGCTAGTAGACCATT
1 TCCATAAAGCCAGTAGACCATT
20142142 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:20143463 original size:25 final size:24
Alignment explanation
Indices: 20143427--20143513 Score: 104
Period size: 25 Copynumber: 3.5 Consensus size: 24
20143417 TTTAGACGTT
*
20143427 AGACACAA-TTAATGTGTCTGAACTA
1 AGAC-CAATTTAAT-TGTCTAAACTA
*
20143452 AGACCAATTTAATTTGTCAAAACTA
1 AGACCAATTTAA-TTGTCTAAACTA
*
20143477 AGTCCAATTTAATTCGTCTAAACTA
1 AGACCAATTTAATT-GTCTAAACTA
20143502 AGACCAATTTAA
1 AGACCAATTTAA
20143514 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:20148298 original size:25 final size:24
Alignment explanation
Indices: 20148276--20148348 Score: 83
Period size: 25 Copynumber: 3.0 Consensus size: 24
20148266 ACAATTAAGG
*
20148276 TGTCTGAACTAAGACCAATTTAATT
1 TGTCTAAACTAAGACCAATTTAA-T
* ***
20148301 TGTCAAAACTAATTTCAATTTAAT
1 TGTCTAAACTAAGACCAATTTAAT
20148325 TCGTCTAAACTAAGACCAATTTAA
1 T-GTCTAAACTAAGACCAATTTAA
20148349 ATCATATATT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
24 2 0.05
25 36 0.95
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (24 bp):
TGTCTAAACTAAGACCAATTTAAT
Found at i:20156755 original size:21 final size:21
Alignment explanation
Indices: 20156726--20156770 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
20156716 TGGTCAAGGA
20156726 AAAAAAAAAGAAA-AATAAAAT
1 AAAAAAAAAGAAAGAA-AAAAT
*
20156747 AAAAGAAAAGAAAGAAAAAAT
1 AAAAAAAAAGAAAGAAAAAAT
20156768 AAA
1 AAA
20156771 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:20157977 original size:8 final size:8
Alignment explanation
Indices: 20157966--20158001 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
20157956 AAAATAGTTT
20157966 AGAAGAAG
1 AGAAGAAG
20157974 AGAAGAAG
1 AGAAGAAG
20157982 AGAAGAAG
1 AGAAGAAG
20157990 AGAAGAAG
1 AGAAGAAG
20157998 AGAA
1 AGAA
20158002 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:20158115 original size:17 final size:17
Alignment explanation
Indices: 20158085--20158136 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
20158075 AAAAAAATAG
*
20158085 AAGA-AAAGGAAAGGAA
1 AAGAGAAAGGGAAGGAA
*
20158101 ATGAGAAAGGGAAGGAA
1 AAGAGAAAGGGAAGGAA
* *
20158118 AAGAGAATGGGAAAGAA
1 AAGAGAAAGGGAAGGAA
20158135 AA
1 AA
20158137 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:20158115 original size:42 final size:44
Alignment explanation
Indices: 20158014--20158119 Score: 112
Period size: 45 Copynumber: 2.5 Consensus size: 44
20158004 GAAGGGAAGC
* *
20158014 AAGG-GAAAAAGAAAGAAAAAAAATAGAAGTAAAATAGGTAAAGA
1 AAGGAGAAAGAGAAGGAAAAAAAATAGAAG-AAAATAGGTAAAGA
* *
20158058 GAGGAGAATGAGAAGGAAAAAAAATAGAAG-AAA-AGG-AAAGGA
1 AAGGAGAAAGAGAAGGAAAAAAAATAGAAGAAAATAGGTAAA-GA
* *
20158100 AATGAGAAAGGGAAGGAAAA
1 AAGGAGAAAGAGAAGGAAAA
20158120 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:20158126 original size:23 final size:22
Alignment explanation
Indices: 20158069--20158132 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
20158059 AGGAGAATGA
* *
20158069 GAAGGAAAAAAAAT-AG-AAGA
1 GAAGGAAAAGAAATGAGAAAGG
* *
20158089 AAAGGAAAGGAAATGAGAAAGG
1 GAAGGAAAAGAAATGAGAAAGG
*
20158111 GAAGGAAAAGAGAATGGGAAAG
1 GAAGGAAAAGA-AATGAGAAAG
20158133 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:20160714 original size:33 final size:33
Alignment explanation
Indices: 20160599--20160717 Score: 123
Period size: 33 Copynumber: 3.6 Consensus size: 33
20160589 ACCCACCATC
* * * * *
20160599 ACTGGAGTACTCTACTTCTCTTGGCCCGTATCT
1 ACTGCAGTACTCCACTCCTCTCGGCTCGTATCT
* *
20160632 ACTGCAGTACTCCATTCCTC-CTGGCTCGTATCC
1 ACTGCAGTACTCCACTCCTCTC-GGCTCGTATCT
* *
20160665 ATTGCGGTACTCCACTCCTCTCGGCTCGTATCT
1 ACTGCAGTACTCCACTCCTCTCGGCTCGTATCT
* *
20160698 ACCGTAGTACTCCACTCCTC
1 ACTGCAGTACTCCACTCCTC
20160718 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:20161043 original size:48 final size:48
Alignment explanation
Indices: 20160972--20161080 Score: 157
Period size: 48 Copynumber: 2.3 Consensus size: 48
20160962 CTTTGTATTT
* **
20160972 ATTT-AATTGAGATTTATTACAACATTAAAACTTGGAACAAACTTTGTA
1 ATTTAAATT-AGATTAATTACAACATTAAAACGAGGAACAAACTTTGTA
*
20161020 ATTTAAATTAGATTAATTGCAACATTAAAACGAGGAACAAACTTTGTA
1 ATTTAAATTAGATTAATTACAACATTAAAACGAGGAACAAACTTTGTA
*
20161068 ATATAAATTAGAT
1 ATTTAAATTAGAT
20161081 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:20164175 original size:3 final size:3
Alignment explanation
Indices: 20164103--20164159 Score: 96
Period size: 3 Copynumber: 19.0 Consensus size: 3
20164093 TTCTGATTGT
* *
20164103 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20164151 TTA TTA TTA
1 TTA TTA TTA
20164160 CAGCTTTGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:20173738 original size:21 final size:21
Alignment explanation
Indices: 20173714--20173753 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20173704 AGAATTGCCA
*
20173714 AAATAGTTTGAAGAGAAATGG
1 AAATAGATTGAAGAGAAATGG
*
20173735 AAATGGATTGAAGAGAAAT
1 AAATAGATTGAAGAGAAAT
20173754 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:20175859 original size:18 final size:18
Alignment explanation
Indices: 20175836--20175889 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
20175826 CAGATTCAAT
20175836 AAAAAATCAAAATATAAA
1 AAAAAATCAAAATATAAA
*
20175854 AAAAAATCAATCA-AT-AA
1 AAAAAATCAA-AATATAAA
20175871 AAAAAAT-AAAATA-AAA
1 AAAAAATCAAAATATAAA
20175887 AAA
1 AAA
20175890 TGAAAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 1 0.03
16 8 0.26
17 9 0.29
18 12 0.39
19 1 0.03
ACGTcount: A:0.80, C:0.06, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAAAATCAAAATATAAA
Found at i:20175864 original size:29 final size:30
Alignment explanation
Indices: 20175844--20175915 Score: 89
Period size: 28 Copynumber: 2.5 Consensus size: 30
20175834 ATAAAAAATC
*
20175844 AAAATATAA-AAAAAAATCAATCAATAAAA
1 AAAATAAAATAAAAAAATCAATCAATAAAA
*
20175873 AAAATAAAATAAAAAAATGAA--AATAAAA
1 AAAATAAAATAAAAAAATCAATCAATAAAA
*
20175901 AAAA-GAAATAAAAAA
1 AAAATAAAATAAAAAA
20175916 GAAAAAAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
27 10 0.26
28 11 0.28
29 8 0.21
30 10 0.26
ACGTcount: A:0.81, C:0.03, G:0.03, T:0.14
Consensus pattern (30 bp):
AAAATAAAATAAAAAAATCAATCAATAAAA
Found at i:20175883 original size:14 final size:15
Alignment explanation
Indices: 20175836--20175943 Score: 77
Period size: 13 Copynumber: 7.1 Consensus size: 15
20175826 CAGATTCAAT
20175836 AAAAAATCAAAATATAAA
1 AAAAAATC-AAA-AT-AA
20175854 AAAAAATCAATCAATAA
1 AAAAAATCAA--AATAA
20175871 AAAAAAT-AAAAT-A
1 AAAAAATCAAAATAA
*
20175884 AAAAAATGAAAATAA
1 AAAAAATCAAAATAA
*
20175899 AAAAAA--GAAATAA
1 AAAAAATCAAAATAA
20175912 AAAAGAA--AAAA-AGA
1 AAAA-AATCAAAATA-A
20175926 AAAAAATCAAAATCAA
1 AAAAAATCAAAAT-AA
20175942 AA
1 AA
20175944 TGAAAAAAGA
Statistics
Matches: 78, Mismatches: 2, Indels: 22
0.76 0.02 0.22
Matches are distributed among these distances:
13 21 0.27
14 18 0.23
15 11 0.14
16 5 0.06
17 12 0.15
18 10 0.13
19 1 0.01
ACGTcount: A:0.80, C:0.05, G:0.04, T:0.12
Consensus pattern (15 bp):
AAAAAATCAAAATAA
Found at i:20175886 original size:13 final size:13
Alignment explanation
Indices: 20175870--20175943 Score: 69
Period size: 14 Copynumber: 5.4 Consensus size: 13
20175860 TCAATCAATA
20175870 AAAAAAATAAAAT
1 AAAAAAATAAAAT
20175883 AAAAAAATGAAAAT
1 AAAAAAAT-AAAAT
20175897 AAAAAAA-AGAAAT
1 AAAAAAATA-AAAT
* *
20175910 AAAAAAGAAAAAAAG
1 -AAAAA-AATAAAAT
20175925 AAAAAAATCAAAAT
1 AAAAAAAT-AAAAT
*
20175939 CAAAA
1 AAAAA
20175944 TGAAAAAAGA
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:20175895 original size:19 final size:18
Alignment explanation
Indices: 20175873--20175937 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 18
20175863 ATCAATAAAA
20175873 AAAATAAAATAAAA-AAAT
1 AAAATAAAA-AAAAGAAAT
20175891 GAAAATAAAAAAAAGAAAT
1 -AAAATAAAAAAAAGAAAT
*
20175910 AAAAAAGAAAAAAAGAAA-
1 AAAATA-AAAAAAAGAAAT
20175928 AAAATCAAAA
1 AAAAT-AAAA
20175938 TCAAAATGAA
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:20175921 original size:47 final size:47
Alignment explanation
Indices: 20175836--20175967 Score: 130
Period size: 48 Copynumber: 2.8 Consensus size: 47
20175826 CAGATTCAAT
* * *
20175836 AAAAAATCAAAATATAAAAAA-AAATCAATCAATA-AAAAAAATAAAATA
1 AAAAAATCAAAATAAAAAAAAGAAAT-AA-CAAAAGAAAAAAAGAAAA-A
*
20175884 AAAAAATGAAAATAAAAAAAAGAAATAA-AAAAGAAAAAAAGAAAAA
1 AAAAAATCAAAATAAAAAAAAGAAATAACAAAAGAAAAAAAGAAAAA
* *
20175930 AATCAAAATCAAAAT-GAAAAAAGAAA-AAGAAAAGAAAA
1 AA--AAAATCAAAATAAAAAAAAGAAATAACAAAAGAAAA
20175968 GGAAAGGCCA
Statistics
Matches: 73, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
46 8 0.11
47 30 0.41
48 31 0.42
49 4 0.05
ACGTcount: A:0.80, C:0.04, G:0.06, T:0.11
Consensus pattern (47 bp):
AAAAAATCAAAATAAAAAAAAGAAATAACAAAAGAAAAAAAGAAAAA
Found at i:20175921 original size:48 final size:47
Alignment explanation
Indices: 20175836--20175967 Score: 128
Period size: 47 Copynumber: 2.8 Consensus size: 47
20175826 CAGATTCAAT
* * * *
20175836 AAAAAATCAAAATATAAAAAA-AAATCAATCAATA-AAAAAAATAAAATA
1 AAAAAATCAAAATAAAAAAAAGAAAT-AA--AAAAGAAAAAAAGAAAAAA
*
20175884 AAAAAATGAAAATAAAAAAAAGAAATAAAAAAGAAAAAAAGAAAAAA
1 AAAAAATCAAAATAAAAAAAAGAAATAAAAAAGAAAAAAAGAAAAAA
* *
20175931 ATCAAAATCAAAAT-GAAAAAAGAAA-AAGAAAAGAAAA
1 A-AAAAATCAAAATAAAAAAAAGAAATAA-AAAAGAAAA
20175968 GGAAAGGCCA
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
46 5 0.07
47 32 0.44
48 31 0.43
49 4 0.06
ACGTcount: A:0.80, C:0.04, G:0.06, T:0.11
Consensus pattern (47 bp):
AAAAAATCAAAATAAAAAAAAGAAATAAAAAAGAAAAAAAGAAAAAA
Found at i:20175923 original size:28 final size:28
Alignment explanation
Indices: 20175871--20175957 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
20175861 CAATCAATAA
*
20175871 AAAAAATAAAATAAAAAAATGAAAATA-A
1 AAAAAATAAAA-AAAAAAATGAAAAAAGA
* *
20175899 AAAAAA-GAAATAAAAAA-GAAAAAAAGA
1 AAAAAATAAAAAAAAAAATG-AAAAAAGA
* **
20175926 AAAAAATCAAAATCAAAATGAAAAAAGA
1 AAAAAATAAAAAAAAAAATGAAAAAAGA
20175954 AAAA
1 AAAA
20175958 GAAAAGAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
25 1 0.02
26 11 0.23
27 10 0.21
28 25 0.52
29 1 0.02
ACGTcount: A:0.82, C:0.02, G:0.07, T:0.09
Consensus pattern (28 bp):
AAAAAATAAAAAAAAAAATGAAAAAAGA
Found at i:20175951 original size:8 final size:7
Alignment explanation
Indices: 20175833--20175922 Score: 55
Period size: 7 Copynumber: 13.3 Consensus size: 7
20175823 GTTCAGATTC
20175833 AATAAAA
1 AATAAAA
20175840 AATCAAAA
1 AAT-AAAA
*
20175848 TATAAAA
1 AATAAAA
*
20175855 AA-AAATC
1 AATAAA-A
* *
20175862 AATCAAT
1 AATAAAA
20175869 AA-AAAA
1 AATAAAA
20175875 AATAAAA
1 AATAAAA
*
20175882 TA-AAAA
1 AATAAAA
*
20175888 AAT-GAA
1 AATAAAA
20175894 AATAAAA
1 AATAAAA
*
20175901 AA-AAGA
1 AATAAAA
20175907 AATAAAA
1 AATAAAA
*
20175914 AAGAAAA
1 AATAAAA
20175921 AA
1 AA
20175923 AGAAAAAAAT
Statistics
Matches: 62, Mismatches: 14, Indels: 14
0.69 0.16 0.16
Matches are distributed among these distances:
6 22 0.35
7 32 0.52
8 8 0.13
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.13
Consensus pattern (7 bp):
AATAAAA
Found at i:20176852 original size:52 final size:51
Alignment explanation
Indices: 20176795--20176892 Score: 142
Period size: 52 Copynumber: 1.9 Consensus size: 51
20176785 GAGAAGGGAT
* *
20176795 CAAGGTGAAAACCCGCAAAGAGCACTTTGATTCCTAAAAAAAAAAAAGAGAC
1 CAAGGTGAAAACCCACAAAGAGCACTTTGAGTCC-AAAAAAAAAAAAGAGAC
* * *
20176847 CAAGGTGAAAACCTACAAAGGGCACTTTGAGTCCAAAAAATAAAAA
1 CAAGGTGAAAACCCACAAAGAGCACTTTGAGTCCAAAAAAAAAAAA
20176893 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:20176987 original size:84 final size:84
Alignment explanation
Indices: 20176841--20177014 Score: 321
Period size: 84 Copynumber: 2.1 Consensus size: 84
20176831 AAAAAAAAAA
* *
20176841 AGAGACCAAGGTGAAAACCTACAAAGGGCACTTTGAGTCCAAAAAATAAAAATAAATCAAAAACA
1 AGAGGCCAAGGTGAAAACCCACAAAGGGCACTTTGAGTCCAAAAAATAAAAATAAATCAAAAACA
20176906 AAAAAAGAAAAGAAAATGG
66 AAAAAAGAAAAGAAAATGG
*
20176925 AGAGGCCAAGGTGAAAACCCGCAAAGGGCACTTTGAGTCCAAAAAATAAAAATAAATCAAAAACA
1 AGAGGCCAAGGTGAAAACCCACAAAGGGCACTTTGAGTCCAAAAAATAAAAATAAATCAAAAACA
20176990 AAAAAAGAAAAGAAAATGG
66 AAAAAAGAAAAGAAAATGG
20177009 AGAGGC
1 AGAGGC
20177015 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:20178441 original size:44 final size:44
Alignment explanation
Indices: 20178377--20178675 Score: 413
Period size: 44 Copynumber: 6.8 Consensus size: 44
20178367 ATACCAATTA
* *
20178377 TATCTCCCTAGG-CAGTAGTGGAATAGGTTGAATATTGTAAGTCC
1 TATCTCCCT-GGACAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
20178421 TATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
1 TATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* *
20178465 TATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTATAAGCCC
1 TATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* * *
20178509 TATCTCCCTGGACAACAGTGGAATAGGATGAAGATTGTAAGCCC
1 TATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* * *
20178553 TATCTCTCTGGACAGCAGCGGAATAGGTTAAAGATTGTAAGTCC
1 TATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
*
20178597 TATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGT-AGATCA
1 TATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTAAG-TCC
* ** * * *
20178641 TGTCTCCCTAAACAGTAGTGGAATAGATCGAAGAT
1 TATCTCCCTGGACAGCAGTGGAATAGGTTGAAGAT
20178676 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:20178753 original size:50 final size:50
Alignment explanation
Indices: 20178680--20179345 Score: 442
Period size: 50 Copynumber: 13.7 Consensus size: 50
20178670 GAAGATGACA
* * * *
20178680 AATCTTACTTCCCTGGCAGTGCAGTTGAACAGATTGAAGCTACAACGGCA
1 AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* * * * *
20178730 AATTTTGCTTCCCTGACAATGCAGTTAAAAAGATTAAAGCTACAACAGCG
1 AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* * * * *** * * * * *
20178780 AATCTTACCTCTCAGGTGGTGTAGTGGAACAGATTAAAGCCACAAGGGTG
1 AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* *
20178830 AATCTTGCTTTCCC-GACATTGCAGTT-AA-AGATTAAAGCTACAACAGCG
1 AATCTTGC-TTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* * ** * * *
20178878 AATCTT-ATTTCCTGGTAGTGTAGTGGAACAGATTAAAGCCACAACGGCG
1 AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* * *
20178927 AATCTTGCTT-CCTCGATATTGCAGTT-AA-AGATTAAAGCTACAACAGCG
1 AATCTTGCTTCCCT-GACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* * * * * * *
20178975 AATCTT-ATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAAAGGTG
1 AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* * *
20179024 AATCTTGCTTCCCCGACATTGCAGTT-AA-AGATTAAAGCTACAACAGCG
1 AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* * * * * * *
20179072 AATCTT-ATTTCCTGGCAGTGCAATGGAACAGATTAAAGCCACAACGGTG
1 AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* *
20179121 AATCTTGCTTCCC---CA--ACA-TTG--CAG-TTAAAGCTACAACAGCG
1 AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* * * * * * *
20179162 AATATT-ATTTCCTGGA-AGTACAATGGAACAGATTAAAGCTACAACGGTG
1 AATCTTGCTTCCCT-GACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* * * * * ** *
20179211 AATCTTGCTTCCCCGACATTGCAGTTAAAAATATTAAAGCTACAACAACA
1 AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
* * * * * *
20179261 AATATT-ATTTCCTGGCAGTGCAGTGGAAACAGATTAAAGTTACAACGGCG
1 AATCTTGCTTCCCTGACAGTGCAGTTG-AACAGATTAAAGCTACAACGGCG
* * * *
20179311 AATCTTGTTTCCCCGACATTGCAGTTAAACAGATT
1 AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATT
20179346 GAAGACAGTA
Statistics
Matches: 455, Mismatches: 134, Indels: 54
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
49 113 0.25
50 175 0.38
51 16 0.04
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (50 bp):
AATCTTGCTTCCCTGACAGTGCAGTTGAACAGATTAAAGCTACAACGGCG
Found at i:20178930 original size:97 final size:97
Alignment explanation
Indices: 20178680--20179339 Score: 827
Period size: 97 Copynumber: 6.8 Consensus size: 97
20178670 GAAGATGACA
* * * * ** *
20178680 AATCTTACTTCCCTGGCAGTGCAGTTGAACAGATTGAAGCTACAACGGCAAATTTTGC-TTCCCT
1 AATCTTA-TTTCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTTCCC-
*
20178744 GACAATGCAGTTAAAAAGATTAAAGCTACAACAGCG
64 GACATTGCAGTT--AAAGATTAAAGCTACAACAGCG
** * ** * *
20178780 AATCTTACCTCTCAGGTGGTGTAGTGGAACAGATTAAAGCCACAAGGGTGAATCTTGCTTTCCCG
1 AATCTTATTTC-CTGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTTCCCG
20178845 ACATTGCAGTTAAAGATTAAAGCTACAACAGCG
65 ACATTGCAGTTAAAGATTAAAGCTACAACAGCG
* * *
20178878 AATCTTATTTCCTGGTAGTGTAGTGGAACAGATTAAAGCCACAACGGCGAATCTTGC-TTCCTCG
1 AATCTTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTTCC-CG
*
20178942 ATATTGCAGTTAAAGATTAAAGCTACAACAGCG
65 ACATTGCAGTTAAAGATTAAAGCTACAACAGCG
* *
20178975 AATCTTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAAAGGTGAATCTTGCTTCCCCGA
1 AATCTTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTTCCCGA
20179040 CATTGCAGTTAAAGATTAAAGCTACAACAGCG
66 CATTGCAGTTAAAGATTAAAGCTACAACAGCG
* * *
20179072 AATCTTATTTCCTGGCAGTGCAATGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCAA
1 AATCTTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTTCCCGA
20179137 CATTGC------AG-TTAAAGCTACAACAGCG
66 CATTGCAGTTAAAGATTAAAGCTACAACAGCG
* * * * * *
20179162 AATATTATTTCCTGGAAGTACAATGGAACAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGA
1 AATCTTATTTCCTGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTTCCCGA
* * *
20179227 CATTGCAGTTAAAAATATTAAAGCTACAACAACA
66 CATTGCAGTT--AAAGATTAAAGCTACAACAGCG
* ** *
20179261 AATATTATTTCCTGGCAGTGCAGTGGAAACAGATTAAAGTTACAACGGCGAATCTTG-TTTCCCC
1 AATCTTATTTCCTGGCAGTGCAGTGG-AACAGATTAAAGCCACAACGGTGAATCTTGCTTT-CCC
20179325 GACATTGCAGTTAAA
64 GACATTGCAGTTAAA
20179340 CAGATTGAAG
Statistics
Matches: 500, Mismatches: 45, Indels: 32
0.87 0.08 0.06
Matches are distributed among these distances:
90 83 0.17
91 2 0.00
96 4 0.01
97 231 0.46
98 38 0.08
99 41 0.08
100 96 0.19
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:20179208 original size:90 final size:90
Alignment explanation
Indices: 20179055--20179339 Score: 381
Period size: 90 Copynumber: 3.1 Consensus size: 90
20179045 CAGTTAAAGA
* *
20179055 TTAAAGCTACAACAGCGAATCTTATTTCCTGGCAGTGCAATGGAACAGATTAAAGCCACAACGGT
1 TTAAAGCTACAACAGCGAATATTATTTCCTGGCAGTGCAATGGAACAGATTAAAGCTACAACGGT
*
20179120 GAATCTTGCTTCCCCAACATTGCAG
66 GAATCTTGCTTCCCCGACATTGCAG
* *
20179145 TTAAAGCTACAACAGCGAATATTATTTCCTGGAAGTACAATGGAACAGATTAAAGCTACAACGGT
1 TTAAAGCTACAACAGCGAATATTATTTCCTGGCAGTGCAATGGAACAGATTAAAGCTACAACGGT
20179210 GAATCTTGCTTCCCCGACATTGCAG
66 GAATCTTGCTTCCCCGACATTGCAG
* * *
20179235 TTAAAAATATTAAAGCTACAACAACAAATATTATTTCCTGGCAGTGCAGTGGAAACAGATTAAAG
1 ---------TTAAAGCTACAACAGCGAATATTATTTCCTGGCAGTGCAATGG-AACAGATTAAAG
* * *
20179300 TTACAACGGCGAATCTTGTTTCCCCGACATTGCAG
56 CTACAACGGTGAATCTTGCTTCCCCGACATTGCAG
20179335 TTAAA
1 TTAAA
20179340 CAGATTGAAG
Statistics
Matches: 172, Mismatches: 13, Indels: 19
0.84 0.06 0.09
Matches are distributed among these distances:
90 85 0.49
91 5 0.03
99 38 0.22
100 44 0.26
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (90 bp):
TTAAAGCTACAACAGCGAATATTATTTCCTGGCAGTGCAATGGAACAGATTAAAGCTACAACGGT
GAATCTTGCTTCCCCGACATTGCAG
Found at i:20184482 original size:113 final size:114
Alignment explanation
Indices: 20184283--20184489 Score: 310
Period size: 113 Copynumber: 1.8 Consensus size: 114
20184273 TAATAGTTAC
*
20184283 TAACAAAATAACTTTAAAATAAATTAAAAAAATAATAAAAGATTACATTCATAACCTAACAGATC
1 TAACAAAATAACTTTAAAATAAATTAAAAAAATAATAAAAGATTACATTCATAACCTAACAAATC
20184348 ACCATAAACATTAAACCAAACAAACAATTAACCGAGTCACAAAAATTAA
66 ACCATAAACATTAAACCAAACAAACAATTAACCGAGTCACAAAAATTAA
* * *
20184397 TAACAAAATGACTTTAAAATAAATT-AAAAATTTATAAAA-ATTTACATTCATAACCTAACAAAT
1 TAACAAAATAACTTTAAAATAAATTAAAAAAATAATAAAAGA-TTACATTCATAACCTAACAAAT
** * * *
20184460 CTTCATCAACATTAAACTAAACAAGCAATT
65 CACCATAAACATTAAACCAAACAAACAATT
20184490 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:20184627 original size:18 final size:17
Alignment explanation
Indices: 20184595--20184652 Score: 75
Period size: 18 Copynumber: 3.4 Consensus size: 17
20184585 CTCATCATAA
20184595 TCCTTCTTT-TTTCTTC
1 TCCTTCTTTCTTTCTTC
20184611 TCCATTCTTTCTTTCTTC
1 TCC-TTCTTTCTTTCTTC
*
20184629 TCCCTCTCTTCTTTCTTC
1 TCCTTCT-TTCTTTCTTC
20184647 T-CTTCT
1 TCCTTCT
20184653 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:20193224 original size:20 final size:20
Alignment explanation
Indices: 20193199--20193244 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
20193189 GTTAATATTT
*
20193199 TTGTTATTTATTCAAATAGG
1 TTGTTACTTATTCAAATAGG
*
20193219 TTGTTACTTATTTAAATAGG
1 TTGTTACTTATTCAAATAGG
20193239 TTGTTA
1 TTGTTA
20193245 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:20198466 original size:19 final size:18
Alignment explanation
Indices: 20198430--20198469 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
20198420 AAGTCTACCA
20198430 ATTTAAGGTTTTTTTAGT
1 ATTTAAGGTTTTTTTAGT
20198448 ATTT-AGGTTTCTATTTAGT
1 ATTTAAGGTTT-T-TTTAGT
20198467 ATT
1 ATT
20198470 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:20201293 original size:6 final size:6
Alignment explanation
Indices: 20201282--20201306 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
20201272 TCTGTGTGTT
20201282 GAAAGA GAAAGA GAAAGA GAAAGA G
1 GAAAGA GAAAGA GAAAGA GAAAGA G
20201307 GTGGAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (6 bp):
GAAAGA
Found at i:20207151 original size:24 final size:24
Alignment explanation
Indices: 20207122--20207167 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
20207112 CAAGCCAGGT
*
20207122 ACAAAAAAGAAATAGAAGAAAACA
1 ACAAAAAAGAAATAAAAGAAAACA
*
20207146 ACAAAAAAGAAGTAAAAGAAAA
1 ACAAAAAAGAAATAAAAGAAAA
20207168 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:20211155 original size:27 final size:27
Alignment explanation
Indices: 20211100--20211155 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
20211090 TATTTTCTCG
* * ** *
20211100 AAATTTTATTAGGGGTAAAATGGTTAA
1 AAATTTTATCAGAGGTAAAATCATCAA
20211127 AAATTTTATCAGAGGTAAAATCATCAA
1 AAATTTTATCAGAGGTAAAATCATCAA
20211154 AA
1 AA
20211156 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:20214373 original size:50 final size:50
Alignment explanation
Indices: 20214274--20214373 Score: 137
Period size: 50 Copynumber: 2.0 Consensus size: 50
20214264 GGACACACCA
* *
20214274 CAGCTCTTATGAGCTTCCCGATACTCAGCTCACATAAGCTTCCTATTATT
1 CAGCTCGTATGAGCTTCCCGATACTCAGCTCACATAAGCTTCCCATTATT
* * * * *
20214324 CAGCTCGTATGAGCTTCCCGTTATTCAGCTCGCATGAGCTTCCCGTTATT
1 CAGCTCGTATGAGCTTCCCGATACTCAGCTCACATAAGCTTCCCATTATT
20214374 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:20214380 original size:25 final size:25
Alignment explanation
Indices: 20214282--20214373 Score: 121
Period size: 25 Copynumber: 3.7 Consensus size: 25
20214272 CACAGCTCTT
* * *
20214282 ATGAGCTTCCCGATACTCAGCTCAC
1 ATGAGCTTCCCGTTATTCAGCTCGC
* ** *
20214307 ATAAGCTTCCTATTATTCAGCTCGT
1 ATGAGCTTCCCGTTATTCAGCTCGC
20214332 ATGAGCTTCCCGTTATTCAGCTCGC
1 ATGAGCTTCCCGTTATTCAGCTCGC
20214357 ATGAGCTTCCCGTTATT
1 ATGAGCTTCCCGTTATT
20214374 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:20214387 original size:25 final size:25
Alignment explanation
Indices: 20214284--20214389 Score: 79
Period size: 25 Copynumber: 4.2 Consensus size: 25
20214274 CAGCTCTTAT
* * * *
20214284 GAGCTTCCCGATACTCAGCTCACATA
1 GAGCTTCCCGTTATTCAACTCGCA-A
** * * *
20214310 -AGCTTCCTATTATTCAGCTCGTAT
1 GAGCTTCCCGTTATTCAACTCGCAA
* *
20214334 GAGCTTCCCGTTATTCAGCTCGCAT
1 GAGCTTCCCGTTATTCAACTCGCAA
* *
20214359 GAGCTTCCCGTTATTTAACTCGGAA
1 GAGCTTCCCGTTATTCAACTCGCAA
20214384 GAGCTT
1 GAGCTT
20214390 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:20214388 original size:50 final size:50
Alignment explanation
Indices: 20214284--20214389 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 50
20214274 CAGCTCTTAT
* * * *
20214284 GAGCTTCCCGATACTCAGCTCACATAAGCTTCCTATTATTCAGCTCGTAT
1 GAGCTTCCCGATACTCAGCTCACATAAGCTTCCCATTATTCAACTCGGAA
* * * * * *
20214334 GAGCTTCCCGTTATTCAGCTCGCATGAGCTTCCCGTTATTTAACTCGGAA
1 GAGCTTCCCGATACTCAGCTCACATAAGCTTCCCATTATTCAACTCGGAA
20214384 GAGCTT
1 GAGCTT
20214390 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:20220273 original size:56 final size:56
Alignment explanation
Indices: 20220187--20220300 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
20220177 GAAAGTTCTT
20220187 TGGTTCGGTCGTAAAGGAAAGCTGAGTCCGCGATTTATTAGGCCATATGAGATTAC
1 TGGTTCGGTCGTAAAGGAAAGCTGAGTCCGCGATTTATTAGGCCATATGAGATTAC
20220243 TGGTTCGGTCGTAAAGGAAAGCTGAGTCCGCGATTTATTAGGCCATATGAGATTAC
1 TGGTTCGGTCGTAAAGGAAAGCTGAGTCCGCGATTTATTAGGCCATATGAGATTAC
20220299 TG
1 TG
20220301 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:20221746 original size:25 final size:25
Alignment explanation
Indices: 20221718--20221787 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
20221708 ACTCAAGTCA
*
20221718 CATGAGCTTCCCGTTATTCGGCTCG
1 CATGAGCTTCCCGTTATTCAGCTCG
20221743 CATGAGCTTCCCGTTATTCAGCTCG
1 CATGAGCTTCCCGTTATTCAGCTCG
*
20221768 CATGAGCTTCTCGTTATTCA
1 CATGAGCTTCCCGTTATTCA
20221788 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:20223818 original size:45 final size:45
Alignment explanation
Indices: 20223694--20223819 Score: 135
Period size: 45 Copynumber: 2.8 Consensus size: 45
20223684 TGTTCTGAGG
* * * **
20223694 ATGCCATAGTATCTTTCAGCCATGGTCTTACACATTCCCAATATA
1 ATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTCCCAATATA
* * * * * *
20223739 ATGCCATAATGTCTTTCAATTATGGTCTTGTTCATTTCCGATTTA
1 ATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTCCCAATATA
* *
20223784 TTGCCATAGTGTCTTTCAACTATAGTCTTATTCATT
1 ATGCCATAGTGTCTTTCAACTATGGTCTTATTCATT
20223820 AAAGCTTGGC
Statistics
Matches: 65, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
45 65 1.00
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (45 bp):
ATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTCCCAATATA
Found at i:20223946 original size:17 final size:17
Alignment explanation
Indices: 20223923--20223971 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
20223913 TTTTATTAAT
20223923 ATTTTAACATATAAAATC
1 ATTTTAA-ATATAAAATC
*
20223941 -TTTTAAAT-TAAAAAC
1 ATTTTAAATATAAAATC
*
20223956 ATTTTAAACATAAAAT
1 ATTTTAAATATAAAAT
20223972 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:20228509 original size:10 final size:11
Alignment explanation
Indices: 20228485--20228527 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
20228475 CCTCTTCCTA
*
20228485 TTTCTTTTGGT
1 TTTCTTTTTGT
20228496 TTTCTTTTTG-
1 TTTCTTTTTGT
*
20228506 TTTCTTTTTCT
1 TTTCTTTTTGT
20228517 TTTCTATTTTG
1 TTTCT-TTTTG
20228528 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:20228509 original size:21 final size:22
Alignment explanation
Indices: 20228485--20228527 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
20228475 CCTCTTCCTA
*
20228485 TTTCTTTTGGTTTTCT-TTTTG
1 TTTCTTTTGCTTTTCTATTTTG
*
20228506 TTTCTTTTTCTTTTCTATTTTG
1 TTTCTTTTGCTTTTCTATTTTG
20228528 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:20235010 original size:22 final size:22
Alignment explanation
Indices: 20234972--20235017 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
20234962 GGATTTGTAA
* *
20234972 TGGATTTGATTTATTTTGTGTT
1 TGGATTTGATTGATTTTGGGTT
*
20234994 TGGATTTGATTGGTTTTGGGTT
1 TGGATTTGATTGATTTTGGGTT
20235016 TG
1 TG
20235018 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:20238355 original size:25 final size:25
Alignment explanation
Indices: 20238327--20238375 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
20238317 TATAGTCTAT
*
20238327 CTATAGTAGTCTC-AGTATATACTAC
1 CTATAGCAGTCTCAAG-ATATACTAC
*
20238352 CTATAGCAGTTTCAAGATATACTA
1 CTATAGCAGTCTCAAGATATACTA
20238376 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:20246096 original size:46 final size:46
Alignment explanation
Indices: 20246013--20246109 Score: 142
Period size: 46 Copynumber: 2.1 Consensus size: 46
20246003 ATGGCAAGAA
* *
20246013 AATATTATTATATTTTTTATTTTAATTAATATAATTATTAAGTTGTT
1 AATAGTATTATATTTTTTACTTT-ATTAATATAATTATTAAGTTGTT
*
20246060 AATAGTATTATATTTTTTTACTTT-TTAATATCATTATTAAGTTGTT
1 AATAGTATTATA-TTTTTTACTTTATTAATATAATTATTAAGTTGTT
20246106 AATA
1 AATA
20246110 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:20247922 original size:57 final size:59
Alignment explanation
Indices: 20247835--20247956 Score: 194
Period size: 58 Copynumber: 2.1 Consensus size: 59
20247825 ATAAAAATGG
* *
20247835 TGAAAATGGAGAAATTGGAAACATTTGGAAATTATTATGGTTTTCT-CCAAAATGAAAA
1 TGAAAATGGAGAAATTGGAAACATTTGGAAATGAATATGGTTTTCTCCCAAAATGAAAA
* *
20247893 TGAAAATGGAGAAA-TGGAATCATTTGGAAATGAATGTGGTTTTCTCCCAAAATGAAAA
1 TGAAAATGGAGAAATTGGAAACATTTGGAAATGAATATGGTTTTCTCCCAAAATGAAAA
20247951 TGAAAA
1 TGAAAA
20247957 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:20251578 original size:16 final size:16
Alignment explanation
Indices: 20251544--20251578 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
20251534 AATTTAATAC
**
20251544 TTATCTTAATATTTTA
1 TTATCTTAATATTAAA
20251560 TTATCTTAATATTAAA
1 TTATCTTAATATTAAA
20251576 TTA
1 TTA
20251579 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:20251633 original size:61 final size:58
Alignment explanation
Indices: 20251565--20251676 Score: 161
Period size: 61 Copynumber: 1.9 Consensus size: 58
20251555 TTTTATTATC
*
20251565 TTAATATTAAATTAAATTAAATACTTATCTTATAGATAAGTATTCTATTAATTTAATAGAT
1 TTAATATTAAATTAAATTAAATACTTATC-T-T-GATAAGTATTATATTAATTTAATAGAT
* * *
20251626 TTAATATTAAATTTAATTTAATATTTATCTTGATAAGTATTATATTAATTT
1 TTAATATTAAATTAAATTAAATACTTATCTTGATAAGTATTATATTAATTT
20251677 TTAATATTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
58 19 0.40
59 1 0.02
60 1 0.02
61 26 0.55
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (58 bp):
TTAATATTAAATTAAATTAAATACTTATCTTGATAAGTATTATATTAATTTAATAGAT
Found at i:20258205 original size:30 final size:28
Alignment explanation
Indices: 20258169--20258235 Score: 89
Period size: 30 Copynumber: 2.3 Consensus size: 28
20258159 TTATTGATTT
* *
20258169 TTTCAAATTTAATCCAACGACCTATTTTTC
1 TTTCAAATTTAATCAAACGA-CTA-TTTTA
*
20258199 TTTCAAATTTAATCAAATGACTATTTTA
1 TTTCAAATTTAATCAAACGACTATTTTA
20258227 TTTCAAATT
1 TTTCAAATT
20258236 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:20259825 original size:179 final size:180
Alignment explanation
Indices: 20259508--20259868 Score: 654
Period size: 179 Copynumber: 2.0 Consensus size: 180
20259498 CCATGAAGCT
20259508 TTGTCATATTTCTTCGTTTTCTGTTCAATTTGTTGTTCATGTTTCATTCGTGTGTTCAAGATTTT
1 TTGTCATATTTCTTCGTTTTCTGTTCAATTTGTTGTTCATGTTTCATTCGTGTGTTCAAGATTTT
20259573 CCTTACCAAACATTTGTACTATCAATTTTATGGTTATATTATCATGATGACTACTACAATACATG
66 CCTTACCAAACATTTGTACTATCAATTTTATGGTTATATTATCATGATGACTACTACAATACATG
*
20259638 AAAGTGGAACACTAAG-GAAATTGGCTTTAAACTTTTCCAAACTTGATCGG
131 AAAGTGGAACACTAAGAG-AATTGGCTTTAAACTTTGCCAAACTTGATCGG
**
20259688 TTGTCATATTTCTTCGTTTTCTGTTCAATTTGTTGTTCATGTTTCATTCGTGTGTTTGAGATTTT
1 TTGTCATATTTCTTCGTTTTCTGTTCAATTTGTTGTTCATGTTTCATTCGTGTGTTCAAGATTTT
*
20259753 CC-TACCGAACATTTGTACTATCAATTTTATGGTTATATTATCATGATGACTACTACAATACATG
66 CCTTACCAAACATTTGTACTATCAATTTTATGGTTATATTATCATGATGACTACTACAATACATG
*
20259817 AAAGTGGAACACTAAGAGAGTTGGCTTTAAACTTTGCCAAACTTGATCGG
131 AAAGTGGAACACTAAGAGAATTGGCTTTAAACTTTGCCAAACTTGATCGG
20259867 TT
1 TT
20259869 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:20267663 original size:12 final size:11
Alignment explanation
Indices: 20267636--20267670 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
20267626 ATAAATAAAA
20267636 AAGGAAAGGA-
1 AAGGAAAGGAG
20267646 AAGGAAAGGAGG
1 AAGGAAAGGA-G
20267658 AAGGAAAGGAG
1 AAGGAAAGGAG
20267669 AA
1 AA
20267671 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:20269633 original size:14 final size:14
Alignment explanation
Indices: 20269607--20269641 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
20269597 GACATTTTTT
*
20269607 TTCTAATGATACTA
1 TTCTAACGATACTA
*
20269621 TTTTAACGATACTA
1 TTCTAACGATACTA
20269635 TTCTAAC
1 TTCTAAC
20269642 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:20272587 original size:476 final size:477
Alignment explanation
Indices: 20271685--20272638 Score: 1901
Period size: 476 Copynumber: 2.0 Consensus size: 477
20271675 TTCTATCTTC
20271685 AATTCACTATTTCACTTCCATTTCTCATATCATATCATTTCAATATCAATTGTAAGACTTTATCA
1 AATTCACTATTTCACTTCCATTTCTCATATCATATCATTTCAATATCAATTGTAAGACTTTATCA
20271750 TTCATTTACCCGTATTAACACGACTCGGACTTGAACGGATACACGGATCCAACCAAAACACACCA
66 TTCATTTACCCGTATTAACACGACTCGGACTTGAACGGATACACGGATCCAACCAAAACACACCA
20271815 GTTTGGCACCTAGTGCCTCATCGGATAATTCGAAGTAATAATTTGACACCGAGTCTCTCATCGGC
131 GTTTGGCACCTAGTGCCTCATCGGATAATTCGAAGTAATAATTTGACACCGAGTCTCTCATCGGC
20271880 TAAACCAAAGTAAATTGGAACCCAGTGCCTCATCGAATTAATTCGAAGTAGTAAATTAACACCCA
196 TAAACCAAAGTAAATTGGAACCCAGTGCCTCATCGAATTAATTCGAAGTAGTAAATTAACACCCA
20271945 GTGTCTCATCAACTCGAAGTCGAAGAAATCCCTGAACTCTTCCAATCCTATGGCATGCCATCTAT
261 GTGTCTCATCAACTCGAAGTCGAAGAAATCCCTGAACTCTTCCAATCCTATGGCATGCCATCTAT
20272010 ATCCGACTCAGCTCGATACAGTTAATAGGTTTCAATTCACTTTCCAAATGCAACAAATATCCAAT
326 ATCCGACTCAGCTCGATACAGTTAATAGGTTTCAATTCACTTTCCAAATGCAACAAATATCCAAT
20272075 ATTCAAATTTCACATTAATCACATATACATATAAATTCAATTCAATATCAAAATGCTAAATTCTC
391 ATTCAAATTTCACATTAATCACATATACATATAAATTCAATTCAATATCAAAATGCTAAATTCTC
20272140 ACCTCAACCACTTACCATAAAT
456 ACCTCAACCACTTACCATAAAT
20272162 AATTCACTA-TTCACTTCCATTTCTCATATCATATCATTTCAATATCAATTGTAAGACTTTATCA
1 AATTCACTATTTCACTTCCATTTCTCATATCATATCATTTCAATATCAATTGTAAGACTTTATCA
20272226 TTCATTTACCCGTATTAACACGACTCGGACTTGAACGGATACACGGATCCAACCAAAACACACCA
66 TTCATTTACCCGTATTAACACGACTCGGACTTGAACGGATACACGGATCCAACCAAAACACACCA
20272291 GTTTGGCACCTAGTGCCTCATCGGATAATTCGAAGTAATAATTTGACACCGAGTCTCTCATCGGC
131 GTTTGGCACCTAGTGCCTCATCGGATAATTCGAAGTAATAATTTGACACCGAGTCTCTCATCGGC
20272356 TAAACCAAAGTAAATTGGAACCCAGTGCCTCATCGAATTAATTCGAAGTAGTAAATTAACACCCA
196 TAAACCAAAGTAAATTGGAACCCAGTGCCTCATCGAATTAATTCGAAGTAGTAAATTAACACCCA
20272421 GTGTCTCATCAACTCGAAGTCGAAGAAATCCCTGAACTCTTCCAATCCTATGGCATGCCATCTAT
261 GTGTCTCATCAACTCGAAGTCGAAGAAATCCCTGAACTCTTCCAATCCTATGGCATGCCATCTAT
20272486 ATCCGACTCAGCTCGATACAGTTAATAGGTTTCAATTCACTTTCCAAATGCAACAAATATCCAAT
326 ATCCGACTCAGCTCGATACAGTTAATAGGTTTCAATTCACTTTCCAAATGCAACAAATATCCAAT
20272551 ATTCAAATTTCACATTAATCACATATACATATAAATTCAATTCAATATCAAAATGCTAAATTCTC
391 ATTCAAATTTCACATTAATCACATATACATATAAATTCAATTCAATATCAAAATGCTAAATTCTC
20272616 ACCTCAACCACTTACCATAAAT
456 ACCTCAACCACTTACCATAAAT
20272638 A
1 A
20272639 TTTAATCAAA
Statistics
Matches: 477, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
476 468 0.98
477 9 0.02
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.29
Consensus pattern (477 bp):
AATTCACTATTTCACTTCCATTTCTCATATCATATCATTTCAATATCAATTGTAAGACTTTATCA
TTCATTTACCCGTATTAACACGACTCGGACTTGAACGGATACACGGATCCAACCAAAACACACCA
GTTTGGCACCTAGTGCCTCATCGGATAATTCGAAGTAATAATTTGACACCGAGTCTCTCATCGGC
TAAACCAAAGTAAATTGGAACCCAGTGCCTCATCGAATTAATTCGAAGTAGTAAATTAACACCCA
GTGTCTCATCAACTCGAAGTCGAAGAAATCCCTGAACTCTTCCAATCCTATGGCATGCCATCTAT
ATCCGACTCAGCTCGATACAGTTAATAGGTTTCAATTCACTTTCCAAATGCAACAAATATCCAAT
ATTCAAATTTCACATTAATCACATATACATATAAATTCAATTCAATATCAAAATGCTAAATTCTC
ACCTCAACCACTTACCATAAAT
Found at i:20273277 original size:22 final size:21
Alignment explanation
Indices: 20273249--20273300 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
20273239 TAGCTTATCC
* *
20273249 TTCTTTCTTTCTCTTTTTCTTT
1 TTCTTTCTTTC-CCTTTTCTGT
20273271 TTCTTTCTTTCCCTTTTCTGT
1 TTCTTTCTTTCCCTTTTCTGT
20273292 TTCGTTTCT
1 TTC-TTTCT
20273301 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:20273773 original size:33 final size:34
Alignment explanation
Indices: 20273690--20273778 Score: 83
Period size: 33 Copynumber: 2.7 Consensus size: 34
20273680 CGTGTCATTA
*
20273690 CACCGCAGTACAACACTCCTCC-CGGTCCGTATC
1 CACCACAGTACAACACTCCTCCTCGGTCCGTATC
* * ** *
20273723 CACCGCATTACTCCACTCCTCCTGGGT-CGTATC
1 CACCACAGTACAACACTCCTCCTCGGTCCGTATC
* * *
20273756 CACTATAGTACAACACTCATCCT
1 CACCACAGTACAACACTCCTCCT
20273779 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:20274159 original size:49 final size:49
Alignment explanation
Indices: 20274037--20274227 Score: 242
Period size: 49 Copynumber: 3.8 Consensus size: 49
20274027 GTATTTATTT
* *
20274037 AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTTTGTGGTCTGGTCATA
1 AATTAGATTAATTACAACATTAAAACTTGGAACAAAC--T-T--TATGGTCATA
20274091 AATTAGATTAATTACAACATTAAAACTTGGAACAAACTTTATGGTCATA
1 AATTAGATTAATTACAACATTAAAACTTGGAACAAACTTTATGGTCATA
** * **
20274140 AATTAGATTAATTGGAACATTAAAACTTGGAACAAACATTATAAT-ATA
1 AATTAGATTAATTACAACATTAAAACTTGGAACAAACTTTATGGTCATA
*
20274188 AATTA-AATACATTACAACATTAAAACTTGGAACAAACTTT
1 AATTAGATTA-ATTACAACATTAAAACTTGGAACAAACTTT
20274228 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:20274225 original size:97 final size:100
Alignment explanation
Indices: 20274037--20274227 Score: 264
Period size: 97 Copynumber: 1.9 Consensus size: 100
20274027 GTATTTATTT
* * ** *
20274037 AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTTTGTGGTCTGGTCATAAATTAGATTAA
1 AATTAGATTAATTGCAACATTAAAACTTGGAACAAAC--TAT-GTATAATCATAAATTAGAATAA
20274102 TTACAACATTAAAACTTGGAACAAACTTTATGGTCATA
63 TTACAACATTAAAACTTGGAACAAACTTTATGGTCATA
*
20274140 AATTAGATTAATTGGAACATTAAAACTTGGAACAAAC-AT-TATAAT-ATAAATTA-AATACATT
1 AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTATGTATAATCATAAATTAGAATA-ATT
20274201 ACAACATTAAAACTTGGAACAAACTTT
65 ACAACATTAAAACTTGGAACAAACTTT
20274228 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:20277622 original size:27 final size:26
Alignment explanation
Indices: 20277550--20277624 Score: 98
Period size: 26 Copynumber: 2.8 Consensus size: 26
20277540 GGGATTTGGT
20277550 ACTGGTGCCGCCTATCAGATAAGGGTC
1 ACTGGTGCCGCCTATCAGAT-AGGGTC
** *
20277577 AC-AATGTCGCCTATCAGATAGGGATC
1 ACTGGTGCCGCCTATCAGATAGGG-TC
20277603 ACTGGTGCCGCCTATCAGATAG
1 ACTGGTGCCGCCTATCAGATAG
20277625 ACACCATAGC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 4 0.10
26 18 0.45
27 18 0.45
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (26 bp):
ACTGGTGCCGCCTATCAGATAGGGTC
Found at i:20285355 original size:22 final size:22
Alignment explanation
Indices: 20285328--20285374 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
20285318 TAAAACTTGA
20285328 ATTAAATCCTAAAAAAGTTAGC
1 ATTAAATCCTAAAAAAGTTAGC
20285350 ATTAAATCCTAAAAAAGTTAGC
1 ATTAAATCCTAAAAAAGTTAGC
20285372 ATT
1 ATT
20285375 GCTATGGTTA
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:20295402 original size:22 final size:23
Alignment explanation
Indices: 20295375--20295418 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
20295365 TTAACGAACA
20295375 AAATATATAAATAT-AAATAAAC
1 AAATATATAAATATAAAATAAAC
* *
20295397 AAATATTTAGATATAAAATAAA
1 AAATATATAAATATAAAATAAA
20295419 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:0.02, T:0.30
Consensus pattern (23 bp):
AAATATATAAATATAAAATAAAC
Found at i:20295420 original size:20 final size:21
Alignment explanation
Indices: 20295374--20295423 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
20295364 ATTAACGAAC
20295374 AAAATATATAAATATAAATAA
1 AAAATATATAAATATAAATAA
* * *
20295395 ACAAATATTTAGATATAAA-AT
1 A-AAATATATAAATATAAATAA
20295416 AAAATATA
1 AAAATATA
20295424 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:0.02, T:0.30
Consensus pattern (21 bp):
AAAATATATAAATATAAATAA
Found at i:20297140 original size:2 final size:2
Alignment explanation
Indices: 20297133--20297158 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20297123 TGTCTTTTTA
20297133 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
20297159 TTATTTAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20324360 original size:18 final size:19
Alignment explanation
Indices: 20324337--20324377 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
20324327 ATTAAGTTAA
*
20324337 TTTTAAAGTATTTT-ATTT
1 TTTTAAAATATTTTAATTT
20324355 TTTTAAAATATTTTAATTT
1 TTTTAAAATATTTTAATTT
20324374 TTTT
1 TTTT
20324378 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:20327623 original size:14 final size:14
Alignment explanation
Indices: 20327604--20327637 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
20327594 TTAATCCGAG
20327604 ACCAATCCAACACA
1 ACCAATCCAACACA
20327618 ACCAATCCAACACA
1 ACCAATCCAACACA
20327632 ACCAAT
1 ACCAAT
20327638 TCATTTCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.50, C:0.41, G:0.00, T:0.09
Consensus pattern (14 bp):
ACCAATCCAACACA
Found at i:20337445 original size:51 final size:52
Alignment explanation
Indices: 20337393--20337561 Score: 134
Period size: 52 Copynumber: 3.2 Consensus size: 52
20337383 AAATTAAAGC
20337393 TTCAATTTTAGGCTATTTCATCATAAAATTCCACAACATATTGATAGCAGCT
1 TTCAATTTTAGGCTATTTCATCATAAAATTCCACAACATATTGATAGCAGCT
* ** ** * *
20337445 TTCAATTTCATTCATAAAATCAAAAACTAATGAAAATCATCC-CAAACAAATT-A-A--AGC-
1 TTCAATTTTAGGC-T-ATTTC----A-TCAT-AAAAT--TCCAC-AACATATTGATAGCAGCT
20337502 TTCAATTTTAGGCTATTTCATCATAAAATTCCACAACATATTGATAGCAGCT
1 TTCAATTTTAGGCTATTTCATCATAAAATTCCACAACATATTGATAGCAGCT
20337554 TTCAATTT
1 TTCAATTT
20337562 CATTCACATA
Statistics
Matches: 86, Mismatches: 14, Indels: 34
0.64 0.10 0.25
Matches are distributed among these distances:
47 10 0.12
48 2 0.02
49 6 0.07
50 3 0.03
51 4 0.05
52 18 0.21
53 1 0.01
54 3 0.03
55 3 0.03
56 1 0.01
57 10 0.12
58 4 0.05
59 3 0.03
60 6 0.07
61 2 0.02
62 10 0.12
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.34
Consensus pattern (52 bp):
TTCAATTTTAGGCTATTTCATCATAAAATTCCACAACATATTGATAGCAGCT
Found at i:20337506 original size:109 final size:110
Alignment explanation
Indices: 20337366--20337587 Score: 403
Period size: 109 Copynumber: 2.0 Consensus size: 110
20337356 ATTACCTAGT
20337366 AAAATCATCCCATAAACAAATTAAAGCTTCAATTTTAGGCTATTTCATCATAAAATTCCACAACA
1 AAAATCATCCCA-AAACAAATTAAAGCTTCAATTTTAGGCTATTTCATCATAAAATTCCACAACA
*
20337431 TATTGATAGCAGCTTTCAATTTCATTCATA-AAATCAAAAACTAATG
65 TATTGATAGCAGCTTTCAATTTCATTCACATAAA-CAAAAACTAATG
20337477 AAAATCATCCC-AAACAAATTAAAGCTTCAATTTTAGGCTATTTCATCATAAAATTCCACAACAT
1 AAAATCATCCCAAAACAAATTAAAGCTTCAATTTTAGGCTATTTCATCATAAAATTCCACAACAT
20337541 ATTGATAGCAGCTTTCAATTTCATTCACATAAACAAAAACTAATG
66 ATTGATAGCAGCTTTCAATTTCATTCACATAAACAAAAACTAATG
20337586 AA
1 AA
20337588 TTTAGTAATA
Statistics
Matches: 109, Mismatches: 1, Indels: 4
0.96 0.01 0.04
Matches are distributed among these distances:
109 95 0.87
110 3 0.03
111 11 0.10
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (110 bp):
AAAATCATCCCAAAACAAATTAAAGCTTCAATTTTAGGCTATTTCATCATAAAATTCCACAACAT
ATTGATAGCAGCTTTCAATTTCATTCACATAAACAAAAACTAATG
Found at i:20338012 original size:92 final size:92
Alignment explanation
Indices: 20337855--20338042 Score: 351
Period size: 92 Copynumber: 2.0 Consensus size: 92
20337845 AATATCTCCT
20337855 TTTTGGGTTTATTACAGTTTATGTCCCTCCTCATTTAACAATTGAATTATTTAATCCTTCTAGTA
1 TTTTGGGTTTATTACAGTTTATGTCCCTCCTCATTTAACAATTGAATTATTTAATCCTTCTAGTA
20337920 ACTTTTACAACTTTTTCAATTTAGTCC
66 ACTTTTACAACTTTTTCAATTTAGTCC
20337947 TTTTGGG-TTATTTACAGTTTATGTCCCTCCTCATTTAACAATTGAATTATTTAATCCTTCTAGT
1 TTTTGGGTTTA-TTACAGTTTATGTCCCTCCTCATTTAACAATTGAATTATTTAATCCTTCTAGT
*
20338011 AACTTTTACAACTTTTTCAATTTTGTCC
65 AACTTTTACAACTTTTTCAATTTAGTCC
20338039 TTTT
1 TTTT
20338043 CACTTAATTG
Statistics
Matches: 94, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
91 3 0.03
92 91 0.97
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.49
Consensus pattern (92 bp):
TTTTGGGTTTATTACAGTTTATGTCCCTCCTCATTTAACAATTGAATTATTTAATCCTTCTAGTA
ACTTTTACAACTTTTTCAATTTAGTCC
Found at i:20339741 original size:132 final size:132
Alignment explanation
Indices: 20339504--20339771 Score: 536
Period size: 132 Copynumber: 2.0 Consensus size: 132
20339494 TGAATAAACT
20339504 CTTAAGATTTTTTTGTCTGATGATAATGCAGAAAAATAAAGAGAATTCTAGATATTCCAATTTTT
1 CTTAAGATTTTTTTGTCTGATGATAATGCAGAAAAATAAAGAGAATTCTAGATATTCCAATTTTT
20339569 AATGTTAGTAAAATTTGTTATTTTTCCATTTTACCCTTATTTCGCCAATTCTCCTGATTTTTCTC
66 AATGTTAGTAAAATTTGTTATTTTTCCATTTTACCCTTATTTCGCCAATTCTCCTGATTTTTCTC
20339634 AG
131 AG
20339636 CTTAAGATTTTTTTGTCTGATGATAATGCAGAAAAATAAAGAGAATTCTAGATATTCCAATTTTT
1 CTTAAGATTTTTTTGTCTGATGATAATGCAGAAAAATAAAGAGAATTCTAGATATTCCAATTTTT
20339701 AATGTTAGTAAAATTTGTTATTTTTCCATTTTACCCTTATTTCGCCAATTCTCCTGATTTTTCTC
66 AATGTTAGTAAAATTTGTTATTTTTCCATTTTACCCTTATTTCGCCAATTCTCCTGATTTTTCTC
20339766 AG
131 AG
20339768 CTTA
1 CTTA
20339772 TGCCGCCCAA
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
132 136 1.00
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (132 bp):
CTTAAGATTTTTTTGTCTGATGATAATGCAGAAAAATAAAGAGAATTCTAGATATTCCAATTTTT
AATGTTAGTAAAATTTGTTATTTTTCCATTTTACCCTTATTTCGCCAATTCTCCTGATTTTTCTC
AG
Found at i:20340712 original size:22 final size:22
Alignment explanation
Indices: 20340687--20340741 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
20340677 TTCGCAGTTT
20340687 AAACCCTAACCCTAACAAAAAA
1 AAACCCTAACCCTAACAAAAAA
* * * *
20340709 AAACACTAACCTTAACCATAAA
1 AAACCCTAACCCTAACAAAAAA
*
20340731 AAATCCTAACC
1 AAACCCTAACC
20340742 ATAAGAGAGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.55, C:0.31, G:0.00, T:0.15
Consensus pattern (22 bp):
AAACCCTAACCCTAACAAAAAA
Found at i:20346510 original size:3 final size:3
Alignment explanation
Indices: 20346502--20346540 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
20346492 GTATATATAG
* *
20346502 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
20346541 CAACTTAATA
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:20346908 original size:21 final size:21
Alignment explanation
Indices: 20346859--20346956 Score: 112
Period size: 21 Copynumber: 4.7 Consensus size: 21
20346849 AAATTAAATC
*
20346859 TCTAAGATTACA-AAATCATA
1 TCTAAGATTGCATAAATCATA
20346879 TCTTCTAAGATTGCATAAATCATA
1 ---TCTAAGATTGCATAAATCATA
*
20346903 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATAAATCATA
*
20346924 TCTAAGATTG--TATATCATA
1 TCTAAGATTGCATAAATCATA
*
20346943 TCTAAGATTACATA
1 TCTAAGATTGCATA
20346957 TCCTTGAATG
Statistics
Matches: 69, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
19 18 0.26
21 32 0.46
23 11 0.16
24 8 0.12
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (21 bp):
TCTAAGATTGCATAAATCATA
Found at i:20348073 original size:88 final size:88
Alignment explanation
Indices: 20347965--20348183 Score: 368
Period size: 88 Copynumber: 2.5 Consensus size: 88
20347955 GTTGGGGTCA
* * *
20347965 TCGATCTGATTCGCTGTCGGTCCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCA-CTGCAA
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCT-CAGCTACAA
20348029 CCCAGGGAGGCAAGGCTGGTGTCT
65 CCCAGGGAGGCAAGGCTGGTGTCT
*
20348053 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACTTGCTCAGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCAGCTACAAC
*
20348118 CCAGGGAGGCAAGGTTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
*
20348141 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATTTGCTAT
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTAT
20348184 CTTCGATCTA
Statistics
Matches: 124, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
87 2 0.02
88 122 0.98
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCAGCTACAAC
CCAGGGAGGCAAGGCTGGTGTCT
Found at i:20348084 original size:44 final size:44
Alignment explanation
Indices: 20348031--20348174 Score: 114
Period size: 44 Copynumber: 3.3 Consensus size: 44
20348021 CACTGCAACC
*
20348031 CAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
* * * ** * * ****
20348075 CAGGAAGGCAAGATCTGCTAT-TTTTAACTTGC-TCAGCT-ACAACC
1 CAGGAAGGCAAG-GCTGGTGTCTTCGATC-TGCTTC-GCTGTCGGTG
* *
20348119 CAGGGAGGCAAGGTTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
20348163 CAGGAAGGCAAG
1 CAGGAAGGCAAG
20348175 ATTTGCTATC
Statistics
Matches: 68, Mismatches: 26, Indels: 12
0.64 0.25 0.11
Matches are distributed among these distances:
43 10 0.15
44 47 0.69
45 11 0.16
ACGTcount: A:0.19, C:0.22, G:0.33, T:0.26
Consensus pattern (44 bp):
CAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
Found at i:20348189 original size:45 final size:45
Alignment explanation
Indices: 20348050--20348197 Score: 124
Period size: 44 Copynumber: 3.3 Consensus size: 45
20348040 AAGGCTGGTG
*
20348050 TCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTA
1 TCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATTTGCTA
** * * **** * * * *
20348095 T-TTTTAACTTGC-TCAGCT-ACAACCCAGGGAGGCAAG-GTTGGTG
1 TCTTCGATC-TGCTTC-GCTGTCGGTGCAGGAAGGCAAGATTTGCTA
20348138 TCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATTTGCTA
1 TCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATTTGCTA
*
20348183 TCTTCGATCTACTTC
1 TCTTCGATCTGCTTC
20348198 ACGCCAATAC
Statistics
Matches: 71, Mismatches: 26, Indels: 12
0.65 0.24 0.11
Matches are distributed among these distances:
43 10 0.14
44 36 0.51
45 25 0.35
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.31
Consensus pattern (45 bp):
TCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATTTGCTA
Found at i:20348231 original size:44 final size:44
Alignment explanation
Indices: 20348163--20348401 Score: 232
Period size: 44 Copynumber: 5.4 Consensus size: 44
20348153 GCTGTCGGTG
* * *
20348163 CAGGAAGGCAAGATTTGCTATCTTCGATCTACTTCACGCCAATA
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATA
* * * *
20348207 CATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTA
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACCAATA
** * *
20348252 TGGGAAGACAAGATTTGC-ATCTTCGATCCACTTC-CTACCAATA
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATA
* * * *
20348295 TAGGAAGACATGACCTGCTATCTTCGATCTACTTCACGA-CTATA
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATA
* * * *
20348339 CATGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCCACCAATA
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACCAATA
**
20348384 TGGGAAGACAAGATCTGC
1 CAGGAAGACAAGATCTGC
20348402 ATGTTCCTAC
Statistics
Matches: 157, Mismatches: 32, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
42 1 0.01
43 20 0.13
44 94 0.60
45 42 0.27
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (44 bp):
CAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATA
Found at i:20350069 original size:17 final size:17
Alignment explanation
Indices: 20350047--20350086 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
20350037 CGATAGAGTC
*
20350047 TTTTTTCACGCCATCTT
1 TTTTTTCACACCATCTT
**
20350064 TTTTTTTGCACCATCTT
1 TTTTTTCACACCATCTT
20350081 TTTTTT
1 TTTTTT
20350087 TGGGTAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.10, C:0.23, G:0.05, T:0.62
Consensus pattern (17 bp):
TTTTTTCACACCATCTT
Found at i:20354299 original size:21 final size:20
Alignment explanation
Indices: 20354273--20354347 Score: 116
Period size: 21 Copynumber: 3.7 Consensus size: 20
20354263 AATCATATCT
20354273 TCTAAGATTGCATAAATCATA
1 TCTAAGATTGCAT-AATCATA
20354294 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATA-ATCATA
20354315 TCTAAGATTGCAT-ATCATA
1 TCTAAGATTGCATAATCATA
*
20354334 TCTAAGATTACATA
1 TCTAAGATTGCATA
20354348 TCCTTGAAGA
Statistics
Matches: 51, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
19 18 0.35
20 1 0.02
21 32 0.63
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (20 bp):
TCTAAGATTGCATAATCATA
Found at i:20356008 original size:537 final size:537
Alignment explanation
Indices: 20354995--20356068 Score: 2148
Period size: 537 Copynumber: 2.0 Consensus size: 537
20354985 TGTGCCCCAG
20354995 AAAAGTTACCTCTCGCAACCAGAACTCACACTTGCTCAACTTAGCGTAGAGCTGTTTCTCTCAAA
1 AAAAGTTACCTCTCGCAACCAGAACTCACACTTGCTCAACTTAGCGTAGAGCTGTTTCTCTCAAA
20355060 GTATCTGAAGCACTACTCTAAGATGCTCATCCTCAGTCTTAGAGTCAACCAGAATATCATCGATG
66 GTATCTGAAGCACTACTCTAAGATGCTCATCCTCAGTCTTAGAGTCAACCAGAATATCATCGATG
20355125 AAGACCACGATAAACTGATCCAGATAAGGCTGAAAAACTCGGTTCATCAGATCCATGAATGCAAC
131 AAGACCACGATAAACTGATCCAGATAAGGCTGAAAAACTCGGTTCATCAGATCCATGAATGCAAC
20355190 TGGAGCATTGGTCAATCCAAAGGGAATAACTAGGAACTAGTAATGCCAATAACGAGTCCTAAATG
196 TGGAGCATTGGTCAATCCAAAGGGAATAACTAGGAACTAGTAATGCCAATAACGAGTCCTAAATG
20355255 TCGTCTTATGATCTTTTCTTAACTCTAAGCTGATGATACCCAAAATGAAGATCTATTTTTGAGAA
261 TCGTCTTATGATCTTTTCTTAACTCTAAGCTGATGATACCCAAAATGAAGATCTATTTTTGAGAA
20355320 CATTGAAACCCCTAGAAATTGATCAAACAAATCATCGATCCTCGAAATTGGATACTTATTTTTCA
326 CATTGAAACCCCTAGAAATTGATCAAACAAATCATCGATCCTCGAAATTGGATACTTATTTTTCA
20355385 CTATTCAACTACCGGTAGTCGATGTACATCCTTATGGTACCATCTTTTTTCTTTACAAACAGAAC
391 CTATTCAACTACCGGTAGTCGATGTACATCCTTATGGTACCATCTTTTTTCTTTACAAACAGAAC
20355450 CGATGCCCCCCACGGAGACACACTAGGATGGATGAAACCATGATCCAGAAGCTCTTGAAGTTGAG
456 CGATGCCCCCCACGGAGACACACTAGGATGGATGAAACCATGATCCAGAAGCTCTTGAAGTTGAG
20355515 CCTTAAGCTCCTTCGGT
521 CCTTAAGCTCCTTCGGT
20355532 AAAAGTTACCTCTCGCAACCAGAACTCACACTTGCTCAACTTAGCGTAGAGCTGTTTCTCTCAAA
1 AAAAGTTACCTCTCGCAACCAGAACTCACACTTGCTCAACTTAGCGTAGAGCTGTTTCTCTCAAA
20355597 GTATCTGAAGCACTACTCTAAGATGCTCATCCTCAGTCTTAGAGTCAACCAGAATATCATCGATG
66 GTATCTGAAGCACTACTCTAAGATGCTCATCCTCAGTCTTAGAGTCAACCAGAATATCATCGATG
20355662 AAGACCACGATAAACTGATCCAGATAAGGCTGAAAAACTCGGTTCATCAGATCCATGAATGCAAC
131 AAGACCACGATAAACTGATCCAGATAAGGCTGAAAAACTCGGTTCATCAGATCCATGAATGCAAC
20355727 TGGAGCATTGGTCAATCCAAAGGGAATAACTAGGAACTAGTAATGCCAATAACGAGTCCTAAATG
196 TGGAGCATTGGTCAATCCAAAGGGAATAACTAGGAACTAGTAATGCCAATAACGAGTCCTAAATG
20355792 TCGTCTTATGATCTTTTCTTAACTCTAAGCTGATGATACCCAAAATGAAGATCTATTTTTGAGAA
261 TCGTCTTATGATCTTTTCTTAACTCTAAGCTGATGATACCCAAAATGAAGATCTATTTTTGAGAA
20355857 CATTGAAACCCCTAGAAATTGATCAAACAAATCATCGATCCTCGAAATTGGATACTTATTTTTCA
326 CATTGAAACCCCTAGAAATTGATCAAACAAATCATCGATCCTCGAAATTGGATACTTATTTTTCA
20355922 CTATTCAACTACCGGTAGTCGATGTACATCCTTATGGTACCATCTTTTTTCTTTACAAACAGAAC
391 CTATTCAACTACCGGTAGTCGATGTACATCCTTATGGTACCATCTTTTTTCTTTACAAACAGAAC
20355987 CGATGCCCCCCACGGAGACACACTAGGATGGATGAAACCATGATCCAGAAGCTCTTGAAGTTGAG
456 CGATGCCCCCCACGGAGACACACTAGGATGGATGAAACCATGATCCAGAAGCTCTTGAAGTTGAG
20356052 CCTTAAGCTCCTTCGGT
521 CCTTAAGCTCCTTCGGT
20356069 GCCATTCGGT
Statistics
Matches: 537, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
537 537 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (537 bp):
AAAAGTTACCTCTCGCAACCAGAACTCACACTTGCTCAACTTAGCGTAGAGCTGTTTCTCTCAAA
GTATCTGAAGCACTACTCTAAGATGCTCATCCTCAGTCTTAGAGTCAACCAGAATATCATCGATG
AAGACCACGATAAACTGATCCAGATAAGGCTGAAAAACTCGGTTCATCAGATCCATGAATGCAAC
TGGAGCATTGGTCAATCCAAAGGGAATAACTAGGAACTAGTAATGCCAATAACGAGTCCTAAATG
TCGTCTTATGATCTTTTCTTAACTCTAAGCTGATGATACCCAAAATGAAGATCTATTTTTGAGAA
CATTGAAACCCCTAGAAATTGATCAAACAAATCATCGATCCTCGAAATTGGATACTTATTTTTCA
CTATTCAACTACCGGTAGTCGATGTACATCCTTATGGTACCATCTTTTTTCTTTACAAACAGAAC
CGATGCCCCCCACGGAGACACACTAGGATGGATGAAACCATGATCCAGAAGCTCTTGAAGTTGAG
CCTTAAGCTCCTTCGGT
Found at i:20358054 original size:22 final size:23
Alignment explanation
Indices: 20358028--20358076 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
20358018 GAAGTTTCAG
*
20358028 TCTCTAACTTTCACTCAG-ACAA
1 TCTCTAACTTTAACTCAGTACAA
*
20358050 TCTCTAACTTTAACTCAGTACAG
1 TCTCTAACTTTAACTCAGTACAA
20358073 TCTC
1 TCTC
20358077 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:20358486 original size:18 final size:20
Alignment explanation
Indices: 20358463--20358503 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
20358453 ACAACGAAAG
20358463 TTTAGAAA-CC-GTTTATAT
1 TTTAGAAATCCAGTTTATAT
*
20358481 TTTAGAAATCCAGTTTGTAT
1 TTTAGAAATCCAGTTTATAT
20358501 TTT
1 TTT
20358504 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:20365680 original size:9 final size:8
Alignment explanation
Indices: 20365661--20365714 Score: 65
Period size: 9 Copynumber: 6.5 Consensus size: 8
20365651 ATATATAGAA
*
20365661 AATATAGT
1 AATATAAT
20365669 AATAGTAAT
1 AATA-TAAT
20365678 AATA-AAT
1 AATATAAT
20365685 AATAATAAT
1 AAT-ATAAT
20365694 AATATAAT
1 AATATAAT
20365702 AATAATAAT
1 AAT-ATAAT
20365711 AATA
1 AATA
20365715 GAAAATCGTG
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
7 6 0.15
8 14 0.34
9 21 0.51
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (8 bp):
AATATAAT
Found at i:20365682 original size:3 final size:3
Alignment explanation
Indices: 20365668--20365714 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
20365658 GAAAATATAG
*
20365668 TAA TAG TAA TAA TAAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20365713 TA
1 TA
20365715 GAAAATCGTG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:20365702 original size:14 final size:14
Alignment explanation
Indices: 20365674--20365711 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
20365664 ATAGTAATAG
20365674 TAATAATAA-ATAA
1 TAATAATAATATAA
20365687 TAATAATAATATAA
1 TAATAATAATATAA
20365701 TAATAATAATA
1 TAATAATAATA
20365712 ATAGAAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAATAATAATATAA
Found at i:20366129 original size:19 final size:18
Alignment explanation
Indices: 20366098--20366135 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
20366088 TTTAAACTAA
20366098 ATTTTAACAAAAAAAAAC
1 ATTTTAACAAAAAAAAAC
*
20366116 ATTTATAACTAAAAAAAAC
1 ATTT-TAACAAAAAAAAAC
20366135 A
1 A
20366136 AAAAAAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.24
Consensus pattern (18 bp):
ATTTTAACAAAAAAAAAC
Found at i:20373023 original size:151 final size:151
Alignment explanation
Indices: 20372749--20373030 Score: 372
Period size: 151 Copynumber: 1.9 Consensus size: 151
20372739 TAAATTACAC
* *
20372749 TTTCTTAAAATCAAAACTTTATTTCGAAAAAGTTAAAAAATATCAAAGTTTTATTTTAAAAAATT
1 TTTCTTAAAATCAAAACTTTATTTCGAAAAAGTTAAAAAAGATCAAAATTTTATTTTAAAAAATT
* ** * ***
20372814 TAAATTTGTTCCTTAAAATGACTAAAAGGCAGATTTTTATTTTAAAAATCTAAACTTTCACTTTT
66 TAAACTTGTTCCTTAAAATGACTAAAAAACAAATTTTTAAAATAAAAATCTAAACTTTCACTTTT
20372879 TTTTAAAAACAAATCACTGTT
131 TTTTAAAAACAAATCACTGTT
* * *
20372900 TTTCTTAAAAATCAAAACTTTATTTC-AAAATAGTTGAAAAAGATCAAAATTTTGTTTT-AAGAA
1 TTTCTT-AAAATCAAAACTTTATTTCGAAAA-AGTTAAAAAAGATCAAAATTTTATTTTAAAAAA
* * * *
20372963 TTTAAACTT-TTCTTTTAATATGACTAAAAAATAAATTTTTAAAATAAAAATCTAAACTTTCTCT
64 TTTAAACTTGTTC-CTTAAAATGACTAAAAAACAAATTTTTAAAATAAAAATCTAAACTTTCACT
20373027 TTTT
128 TTTT
20373031 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:20375474 original size:17 final size:16
Alignment explanation
Indices: 20375434--20375475 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
20375424 AGATTAAGGG
20375434 AATAAAAAAAATAAAT
1 AATAAAAAAAATAAAT
*
20375450 AATGAAAAGAAATAAAT
1 AAT-AAAAAAAATAAAT
20375467 AAATAAAAA
1 -AATAAAAA
20375476 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:20375488 original size:27 final size:27
Alignment explanation
Indices: 20375429--20375493 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
20375419 AGAATAGATT
*
20375429 AAGGGAATAAA-AAAAATAAATAATGA
1 AAGGAAATAAATAAAAATAAATAATGA
*
20375455 AAAGAAATAAATAAATAA-AAATAA-GCA
1 AAGGAAATAAATAAA-AATAAATAATG-A
20375482 AAGGAAATAAAT
1 AAGGAAATAAAT
20375494 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:20379531 original size:2 final size:2
Alignment explanation
Indices: 20379524--20379551 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20379514 TTTACACTTC
20379524 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
20379552 TAAAAAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:20386774 original size:6 final size:6
Alignment explanation
Indices: 20386763--20386788 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
20386753 AATTGGGAAC
20386763 AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
20386789 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:20387604 original size:23 final size:23
Alignment explanation
Indices: 20387574--20387629 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
20387564 CACCAGCCTT
20387574 TACACACCATCTCCGTCCAACCC
1 TACACACCATCTCCGTCCAACCC
20387597 TACACACCATCTCCGTCCAACCC
1 TACACACCATCTCCGTCCAACCC
20387620 TACACACCAT
1 TACACACCAT
20387630 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:20395122 original size:14 final size:14
Alignment explanation
Indices: 20395103--20395140 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
20395093 ATTAAGGGTG
20395103 TAAAAATAAATAAA
1 TAAAAATAAATAAA
*
20395117 TAAAAATAAACAAA
1 TAAAAATAAATAAA
*
20395131 T-GAAATAAAT
1 TAAAAATAAAT
20395141 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:20398627 original size:24 final size:26
Alignment explanation
Indices: 20398584--20398643 Score: 79
Period size: 24 Copynumber: 2.4 Consensus size: 26
20398574 TTTTTTTTCT
**
20398584 TTTTACAATAATTT-GTAAA-AAGAA
1 TTTTACAATAATTTAAAAAATAAGAA
*
20398608 TTTTACAATAATTTAAAAAATAATAA
1 TTTTACAATAATTTAAAAAATAAGAA
20398634 TTTTACAATA
1 TTTTACAATA
20398644 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
Done.