Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 153 of 290
Found at i:52037070 original size:11 final size:11
Alignment explanation
Indices: 52037047--52037079 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
52037037 CAAATAGAGG
52037047 TATAACAAA-AT
1 TATAA-AAATAT
52037058 TATAAAAATAT
1 TATAAAAATAT
52037069 TATAAAAATAT
1 TATAAAAATAT
52037080 GATATTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 3 0.14
11 18 0.86
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
TATAAAAATAT
Found at i:52037275 original size:52 final size:52
Alignment explanation
Indices: 52037215--52037322 Score: 207
Period size: 52 Copynumber: 2.1 Consensus size: 52
52037205 ATGATTTAAT
*
52037215 AAAAATATAACAACCTTATAAAAAATAGAAAAGGAAAGAAAAGAACAATGTA
1 AAAAATATAACAACCTTATAAAAAATAGAAAAGAAAAGAAAAGAACAATGTA
52037267 AAAAATATAACAACCTTATAAAAAATAGAAAAGAAAAGAAAAGAACAATGTA
1 AAAAATATAACAACCTTATAAAAAATAGAAAAGAAAAGAAAAGAACAATGTA
52037319 AAAA
1 AAAA
52037323 GTGACAATAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.68, C:0.07, G:0.10, T:0.15
Consensus pattern (52 bp):
AAAAATATAACAACCTTATAAAAAATAGAAAAGAAAAGAAAAGAACAATGTA
Found at i:52038912 original size:21 final size:21
Alignment explanation
Indices: 52038888--52038933 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
52038878 CAGACATGGT
* *
52038888 CGTGTGGCTACTCCACATGCC
1 CGTGTGACTACTCCAAATGCC
52038909 CGTGTGACTACTCCAAATGCC
1 CGTGTGACTACTCCAAATGCC
52038930 CGTG
1 CGTG
52038934 CGCTCACCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.17, C:0.35, G:0.24, T:0.24
Consensus pattern (21 bp):
CGTGTGACTACTCCAAATGCC
Found at i:52041314 original size:16 final size:16
Alignment explanation
Indices: 52041293--52041327 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
52041283 AGTCCTTGTA
52041293 ATTTTA-TCACTTTAAC
1 ATTTTAGTC-CTTTAAC
52041309 ATTTTAGTCCTTTAAC
1 ATTTTAGTCCTTTAAC
52041325 ATT
1 ATT
52041328 AAAATTACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.29, C:0.17, G:0.03, T:0.51
Consensus pattern (16 bp):
ATTTTAGTCCTTTAAC
Found at i:52044539 original size:24 final size:25
Alignment explanation
Indices: 52044506--52044558 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 25
52044496 GTAAGGTGAG
52044506 TTATAATTGATTAAGTGAGTTGAAA
1 TTATAATTGATTAAGTGAGTTGAAA
52044531 TTAT-ATTGATTAAGTGAGTTGAAA
1 TTATAATTGATTAAGTGAGTTGAAA
52044555 TTAT
1 TTAT
52044559 GTGATTGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (25 bp):
TTATAATTGATTAAGTGAGTTGAAA
Found at i:52045197 original size:9 final size:9
Alignment explanation
Indices: 52045168--52045204 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
52045158 TGAGTTTTCG
52045168 AATTCGAAT
1 AATTCGAAT
*
52045177 AACTCGAAT
1 AATTCGAAT
52045186 AATTCGAAT
1 AATTCGAAT
*
52045195 AATTTGAAT
1 AATTCGAAT
52045204 A
1 A
52045205 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:52045591 original size:17 final size:17
Alignment explanation
Indices: 52045564--52045625 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
52045554 ACTCCCCCTA
*
52045564 TTTACTTCCCCTCAAACT
1 TTTACTTCCCC-AAAACT
52045582 TTTA-TTCCCCAAAACTT
1 TTTACTTCCCCAAAAC-T
* *
52045599 TTTATTTTTCCCCTAAACT
1 TTTA--CTTCCCCAAAACT
52045618 TTTACTTC
1 TTTACTTC
52045626 TCATCCTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 4 0.11
17 14 0.38
18 4 0.11
19 5 0.14
20 10 0.27
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTACTTCCCCAAAACT
Found at i:52046048 original size:5 final size:5
Alignment explanation
Indices: 52046031--52046061 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
52046021 GAACAAATAT
*
52046031 ATTCG ATTTG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
52046062 ATTCCATCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (5 bp):
ATTCG
Found at i:52058077 original size:25 final size:25
Alignment explanation
Indices: 52058049--52058100 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
52058039 CTCTCACGTA
*
52058049 TACATACTTTAATAACTCACAAGTC
1 TACATACTTTAATAACTCACAACTC
52058074 TACATACTTTAATAACTCACAACTC
1 TACATACTTTAATAACTCACAACTC
52058099 TA
1 TA
52058101 GCTTATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.40, C:0.25, G:0.02, T:0.33
Consensus pattern (25 bp):
TACATACTTTAATAACTCACAACTC
Found at i:52059868 original size:48 final size:48
Alignment explanation
Indices: 52059655--52059927 Score: 195
Period size: 48 Copynumber: 5.7 Consensus size: 48
52059645 AGAGTAAATA
* * * * ** *
52059655 CCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATCCATCAAGT-
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGACACCTATAT-ACGTG
* * * * * *
52059703 -CGATGTCATGTCCCAGACATGGTCTTACATTGACTATCGAAAT-CGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGAC-ACCTATATACG-TG
* * * * * *
52059751 CCGACGCCATGTCCCAAACTTGGTCTTACACTAGTTCTCAC-ATATCCGTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACT-G-ACAC-CTATATACGTG
* *
52059801 CCGATGCCATGTCCTAGACATGGTCTTACACTGACACCTTTATACGTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGACACCTATATACGTG
* *
52059849 CCGATGCCATGTCCCAGACATGGTCTTATACTGACA-C-ATTTA-GTAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGACACCTATATACGT-G
* *
52059895 TCGATG-CATGTCCTAGACAT-GTCTTACACTGAC
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGAC
52059928 TTACATCTCG
Statistics
Matches: 178, Mismatches: 37, Indels: 24
0.74 0.15 0.10
Matches are distributed among these distances:
44 12 0.07
45 15 0.08
46 10 0.06
47 32 0.18
48 45 0.25
49 27 0.15
50 33 0.19
51 4 0.02
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (48 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGACACCTATATACGTG
Found at i:52067516 original size:46 final size:45
Alignment explanation
Indices: 52067433--52067553 Score: 156
Period size: 46 Copynumber: 2.6 Consensus size: 45
52067423 TTATATGTGC
*
52067433 CGATGCCATGTGCCAAACATGGTCTTACAC-TGATACATCTCGTA-GT
1 CGATG-CATGTCCCAAACAT-GTCTTACACTTGATACATCTCG-AGGT
* *
52067479 CGATGCATGTCCCAGACATGTCTTACACTTGCTTACATCTCGAGGT
1 CGATGCATGTCCCAAACATGTCTTACACTTG-ATACATCTCGAGGT
*
52067525 CGATGCATGTCCCAAATATGTCTTACACT
1 CGATGCATGTCCCAAACATGTCTTACACT
52067554 AGCTATCGTC
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
44 9 0.13
45 15 0.22
46 43 0.64
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (45 bp):
CGATGCATGTCCCAAACATGTCTTACACTTGATACATCTCGAGGT
Found at i:52073249 original size:7 final size:7
Alignment explanation
Indices: 52073237--52073263 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
52073227 GGGCTTACAA
52073237 AAAGGTG
1 AAAGGTG
52073244 AAAGGTG
1 AAAGGTG
52073251 AAAGGTG
1 AAAGGTG
52073258 AAAGGT
1 AAAGGT
52073264 TAATTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.41, T:0.15
Consensus pattern (7 bp):
AAAGGTG
Found at i:52082024 original size:13 final size:13
Alignment explanation
Indices: 52082006--52082030 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52081996 TGTGGGTGCA
52082006 CACGGCCGTGTCG
1 CACGGCCGTGTCG
52082019 CACGGCCGTGTC
1 CACGGCCGTGTC
52082031 TGTCTTCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.40, G:0.36, T:0.16
Consensus pattern (13 bp):
CACGGCCGTGTCG
Found at i:52089075 original size:19 final size:18
Alignment explanation
Indices: 52089027--52089080 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
52089017 TTTTATTGCA
52089027 TTTTATTTTATTTT-TAT
1 TTTTATTTTATTTTCTAT
52089044 TTTTAATTCTTATTTTCTAAT
1 TTTT-ATT-TTATTTTCT-AT
*
52089065 TTTTCTTTTATTTTCT
1 TTTTATTTTATTTTCT
52089081 TCTGGCAGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 4 0.12
18 3 0.09
19 16 0.50
20 3 0.09
21 6 0.19
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTATTTTATTTTCTAT
Found at i:52095662 original size:15 final size:15
Alignment explanation
Indices: 52095637--52095674 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
52095627 TCTCCCATTG
52095637 CCCTCCCTTTTT-TT
1 CCCTCCCTTTTTCTT
52095651 CCCTCTCCTTTTTCTT
1 CCCTC-CCTTTTTCTT
*
52095667 CCTTCCCT
1 CCCTCCCT
52095675 ATCCCTATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 5 0.24
15 10 0.48
16 6 0.29
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (15 bp):
CCCTCCCTTTTTCTT
Found at i:52097647 original size:6 final size:6
Alignment explanation
Indices: 52097638--52097713 Score: 107
Period size: 6 Copynumber: 12.5 Consensus size: 6
52097628 TTTTATTTCC
*
52097638 TTTTAT TTTTAT TTTTAT TTTTAT TATTAGT TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-T TTTTAT TTTTAT TTTTAT
* * *
52097687 TTTTAT TTTTCT ATTTAT TTGTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT
52097714 CCTAGACTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
6 56 0.92
7 5 0.08
ACGTcount: A:0.17, C:0.01, G:0.03, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:52097677 original size:25 final size:24
Alignment explanation
Indices: 52097640--52097711 Score: 99
Period size: 25 Copynumber: 3.0 Consensus size: 24
52097630 TTATTTCCTT
52097640 TTATTTTTATTTTTATTTTTATTA
1 TTATTTTTATTTTTATTTTTATTA
*
52097664 TTAGTTTTTATTTTTATTTTTATTT
1 TTA-TTTTTATTTTTATTTTTATTA
* * *
52097689 TTATTTTTCTATTTATTTGTATT
1 TTATTTTTATTTTTATTTTTATT
52097712 TTCCTAGACT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 20 0.47
25 23 0.53
ACGTcount: A:0.18, C:0.01, G:0.03, T:0.78
Consensus pattern (24 bp):
TTATTTTTATTTTTATTTTTATTA
Found at i:52106130 original size:15 final size:16
Alignment explanation
Indices: 52106110--52106139 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52106100 CAACTTGATC
52106110 GCCATC-CATTTTTTT
1 GCCATCTCATTTTTTT
52106125 GCCATCTCATTTTTT
1 GCCATCTCATTTTTT
52106140 CCGCATAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.13, C:0.27, G:0.07, T:0.53
Consensus pattern (16 bp):
GCCATCTCATTTTTTT
Found at i:52110767 original size:39 final size:36
Alignment explanation
Indices: 52110724--52110796 Score: 83
Period size: 39 Copynumber: 1.9 Consensus size: 36
52110714 AATGAATTTT
*
52110724 AAAATTTAAAAAATAAATTAATAAAATTTCTTAAAAATA
1 AAAATATAAAAAATAAATT-AT-AAATTT-TTAAAAATA
** *
52110763 AAAATATAAGGAATAAATTCTAAATTTTTAAAAA
1 AAAATATAAAAAATAAATTATAAATTTTTAAAAA
52110797 CCATGTAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
36 7 0.23
37 6 0.20
38 1 0.03
39 16 0.53
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (36 bp):
AAAATATAAAAAATAAATTATAAATTTTTAAAAATA
Found at i:52118446 original size:19 final size:19
Alignment explanation
Indices: 52118422--52118465 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
52118412 AATCTTTAAG
52118422 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
52118441 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
52118460 GATATG
1 GATATG
52118466 ATATGATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:52118478 original size:29 final size:31
Alignment explanation
Indices: 52118436--52118493 Score: 102
Period size: 29 Copynumber: 1.9 Consensus size: 31
52118426 TGCAATCTTA
52118436 GATATGATATGCAATC-TT-AGATATGATAT
1 GATATGATATGCAATCTTTAAGATATGATAT
52118465 GATATGATATGCAATCTTTAAGATATGAT
1 GATATGATATGCAATCTTTAAGATATGAT
52118494 TTTGTAATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 16 0.59
30 2 0.07
31 9 0.33
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (31 bp):
GATATGATATGCAATCTTTAAGATATGATAT
Found at i:52126258 original size:44 final size:44
Alignment explanation
Indices: 52126198--52126648 Score: 280
Period size: 44 Copynumber: 10.2 Consensus size: 44
52126188 CAAAGAAACA
* *
52126198 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
1 AGATCTGGCATTCCTGTGTTTATAGGGAACAGATCGAAGATAGC
* * * * **
52126242 AGATCTGACATTCCTGTGCTTACAGCGAAGCAGATCGAAGATTTC
1 AGATCTGGCATTCCTGTGTTTATAGGGAA-CAGATCGAAGATAGC
* * *
52126287 AG--CATGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGT
1 AGATC-TGGCATTCCTGTGTTTATAGGGAACAGA-TCGAAGATAGC
* **
52126330 AGATTTGGCA-TCCTTGTGTTTATAGGGAACAGATCGAAGATAAT
1 AGATCTGGCATTCC-TGTGTTTATAGGGAACAGATCGAAGATAGC
* * * * * * * **
52126374 AGATCTGACACTCCTATGCTTACAGCGAAGCAGATCGAGGATTTC
1 AGATCTGGCATTCCTGTGTTTATAGGGAA-CAGATCGAAGATAGC
* *
52126419 AG--CATGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGC
1 AGATC-TGGCATTCCTGTGTTTATAGGGAACAGA-TCGAAGATAGC
* * * *
52126462 AGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAAC
1 AGATCTGGCATTCCTGTGTTTATAGGGAACAGATCGAAGATAGC
* * * * * * * **
52126506 AGATCTGACACTCCTATGCTTACAGCGAAGCAGATCGAGGATTTC
1 AGATCTGGCATTCCTGTGTTTATAGGGAA-CAGATCGAAGATAGC
*
52126551 AG--CATGGCA-TCCTTGTGTTTATAGGGAACA-AGTTGAAGATAGC
1 AGATC-TGGCATTCC-TGTGTTTATAGGGAACAGA-TCGAAGATAGC
* * * * * *
52126594 AGATTTGGCA-TCTCTGTATTGT-CAGAGAGCAGATCGAAGATACC
1 AGATCTGGCATTC-CTGTGTT-TATAGGGAACAGATCGAAGATAGC
*
52126638 AGATTTGGCAT
1 AGATCTGGCAT
52126649 CTCTGTATTG
Statistics
Matches: 311, Mismatches: 72, Indels: 47
0.72 0.17 0.11
Matches are distributed among these distances:
42 3 0.01
43 41 0.13
44 217 0.70
45 50 0.16
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (44 bp):
AGATCTGGCATTCCTGTGTTTATAGGGAACAGATCGAAGATAGC
Found at i:52126435 original size:132 final size:132
Alignment explanation
Indices: 52126198--52126641 Score: 737
Period size: 132 Copynumber: 3.4 Consensus size: 132
52126188 CAAAGAAACA
* * *
52126198 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCTATGCTT
*
52126263 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAGGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
*
52126328 GT
131 GC
* *
52126330 AGATTTGGCATCCTTGTGTTTATAGGGAACAGATCGAAGATAATAGATCTGACACTCCTATGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCTATGCTT
52126395 ACAGCGAAGCAGATCGAGGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAGGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
52126460 GC
131 GC
*
52126462 AGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCTATGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCTATGCTT
*
52126527 ACAGCGAAGCAGATCGAGGATTTCAGCATGGCATCCTTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAGGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
52126592 GC
131 GC
* * * * * *
52126594 AGATTTGGCATCTCTGTATTGT-CAGAGAGCAGATCGAAGATACCAGAT
1 AGATTTGGCATCCCTGTGTT-TATAGGGAACAGATCGAAGATAACAGAT
52126642 TTGGCATCTC
Statistics
Matches: 293, Mismatches: 18, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
132 292 1.00
133 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (132 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCTATGCTT
ACAGCGAAGCAGATCGAGGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
GC
Found at i:52126580 original size:88 final size:86
Alignment explanation
Indices: 52126202--52126654 Score: 323
Period size: 88 Copynumber: 5.2 Consensus size: 86
52126192 GAAACAAGAT
52126202 TTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAG
1 TTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACA-TCCTGTGCTTACAG
*
52126267 CGAAGCAGATCGAAGATTTCAGCA
65 CGAA-CAGATCGAAGATATCAG-A
* * * * * *
52126291 -TGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGTAGATTTGGCATCCTTGTGTTTATA
1 TTGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCTGACATCC-TGTGCTTACA
*
52126354 GGGAACAGATCGAAGATAAT-AGA
64 GCGAACAGATCGAAGAT-ATCAGA
* * * * * * ** * *
52126377 TCTGACA-CTCCTATGCTTACAGCGAAGCAGATCGAGGATTTCAG--CATGGCATCCCTGTGTTT
1 T-TGGCATC-CCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATC-TGACAT-CCTGTGCTT
* * * *
52126439 ATAGGGAACA-AGTTGAAGATAGCAGA
61 ACAGCGAACAGA-TCGAAGATATCAGA
* * *
52126465 TTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCTATGCTTACA
1 -TTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACA-TCCTGTGCTTACA
* *
52126530 GCGAAGCAGATCGAGGATTTCAGCA
64 GCGAA-CAGATCGAAGATATCAG-A
* * * * * *
52126555 -TGGCATCCTTGTGTTTATAGGGAACA-AGTTGAAGATAGCAGATTTGGCATCTCTGT-ATTGTC
1 TTGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCTGACATC-CTGTGCTT-AC
* * *
52126617 AGAGAGCAGATCGAAGATACCAGA
63 AGCGAACAGATCGAAGATATCAGA
*
52126641 TTTGGCATCTCTGT
1 -TTGGCATCCCTGT
52126655 ATTGGCAGAG
Statistics
Matches: 286, Mismatches: 53, Indels: 51
0.73 0.14 0.13
Matches are distributed among these distances:
86 2 0.01
87 54 0.19
88 200 0.70
89 27 0.09
90 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (86 bp):
TTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACATCCTGTGCTTACAGC
GAACAGATCGAAGATATCAGA
Found at i:52126649 original size:44 final size:44
Alignment explanation
Indices: 52126585--52126677 Score: 168
Period size: 44 Copynumber: 2.1 Consensus size: 44
52126575 GGAACAAGTT
* *
52126585 GAAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATC
1 GAAGATACCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATC
52126629 GAAGATACCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATC
1 GAAGATACCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATC
52126673 GAAGA
1 GAAGA
52126678 CATAGCTAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (44 bp):
GAAGATACCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATC
Found at i:52126985 original size:44 final size:44
Alignment explanation
Indices: 52126931--52127045 Score: 230
Period size: 44 Copynumber: 2.6 Consensus size: 44
52126921 AATCTAAGAT
52126931 GATTTGGCATCTCTGTATTGTCAGAGAGCAGATTGAAGATACCA
1 GATTTGGCATCTCTGTATTGTCAGAGAGCAGATTGAAGATACCA
52126975 GATTTGGCATCTCTGTATTGTCAGAGAGCAGATTGAAGATACCA
1 GATTTGGCATCTCTGTATTGTCAGAGAGCAGATTGAAGATACCA
52127019 GATTTGGCATCTCTGTATTGTCAGAGA
1 GATTTGGCATCTCTGTATTGTCAGAGA
52127046 ACAAATCGAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 71 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (44 bp):
GATTTGGCATCTCTGTATTGTCAGAGAGCAGATTGAAGATACCA
Found at i:52127247 original size:202 final size:203
Alignment explanation
Indices: 52127019--52127463 Score: 775
Period size: 205 Copynumber: 2.2 Consensus size: 203
52127009 GAAGATACCA
* *
52127019 GATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCT-CTTTGACGGAGTGCAG
1 GATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCTTCGACGGAGGGCAG
* * *
52127083 ACACATAGCAGATCCAAACTTCAGATGTTTATACTGAAGTAGATCCAAGATGGTTTGGCATCCTT
66 ACACATAGCACATCCAAACTTCAGATGTTTATACTGAAGCAGATCCAAGATAGTTTGGCATCCTT
* *
52127148 GTGCTTACAAGGAGCAAATCGAATACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAA
131 GTGCTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTAAAGCAAA
52127213 TCTAAGAT
196 TCTAAGAT
52127221 GATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCGACGGAGGGC
1 GATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCT-C-CTTCGACGGAGGGC
*
52127286 AGACACATAGCACATCCAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATAGTTTGGCATCC
64 AGACACATAGCACATCCAAACTTCAGATGTTTATACTGAAGCAGATCCAAGATAGTTTGGCATCC
52127351 TTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTAAAGCA
129 TTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTAAAGCA
*
52127416 AATCTATGAT
194 AATCTAAGAT
*
52127426 GATTTGGCATCTCTGTATTGTCAGGGAACAAATCGAAG
1 GATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAG
52127464 AAGCAGATTT
Statistics
Matches: 230, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
202 48 0.21
205 182 0.79
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (203 bp):
GATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCTTCGACGGAGGGCAG
ACACATAGCACATCCAAACTTCAGATGTTTATACTGAAGCAGATCCAAGATAGTTTGGCATCCTT
GTGCTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTAAAGCAAA
TCTAAGAT
Found at i:52128027 original size:19 final size:19
Alignment explanation
Indices: 52128003--52128046 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
52127993 AATCTTTAAG
52128003 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
52128022 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
52128041 GATATG
1 GATATG
52128047 ATATGATATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:52128061 original size:29 final size:30
Alignment explanation
Indices: 52128017--52128074 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 30
52128007 TGCAATCTTA
*
52128017 GATATGATATGTAATCTT-AGATATGATAT
1 GATATGATATGCAATCTTAAGATATGATAT
52128046 GATATGATATGCAATCTTGAAGATATGAT
1 GATATGATATGCAATCTT-AAGATATGAT
52128075 TTTGTAATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 17 0.65
31 9 0.35
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (30 bp):
GATATGATATGCAATCTTAAGATATGATAT
Found at i:52130262 original size:4 final size:4
Alignment explanation
Indices: 52130253--52130299 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
52130243 AAAATAAACA
** *
52130253 TAAT TAAT TAAT T--T TAAT TAAT TAAT TAAT TTTT TAAT TAAA TAAT
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
52130299 T
1 T
52130300 TTCTCAACCC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
2 2 0.06
4 33 0.94
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (4 bp):
TAAT
Found at i:52130272 original size:14 final size:14
Alignment explanation
Indices: 52130253--52130279 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52130243 AAAATAAACA
52130253 TAATTAATTAATTT
1 TAATTAATTAATTT
52130267 TAATTAATTAATT
1 TAATTAATTAATT
52130280 AATTTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAATTAATTAATTT
Found at i:52131007 original size:22 final size:21
Alignment explanation
Indices: 52130961--52131009 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
52130951 TAATACAATG
* *
52130961 TCTTTTTTTTAAAATGATAAT
1 TCTTTTTTTCAAAATGATAAA
52130982 TCTTTTTTTACAAACATG-TAAA
1 TCTTTTTTT-CAAA-ATGATAAA
52131004 TCTTTT
1 TCTTTT
52131010 ATCGGTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.38
22 12 0.50
23 3 0.12
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.55
Consensus pattern (21 bp):
TCTTTTTTTCAAAATGATAAA
Found at i:52131711 original size:49 final size:50
Alignment explanation
Indices: 52131616--52131711 Score: 117
Period size: 49 Copynumber: 1.9 Consensus size: 50
52131606 AATTCTAAAA
* **
52131616 AAATATAAAAATACATAAATATTTTCAAAAAATATAATAATGAATTTGAG
1 AAATATAAAAATACATAAATATTTTCAAAAAACATAATAAAAAATTTGAG
*
52131666 AAATATATAAAA-ACA-AAA-ATTATTTAAAAAACATAATAAAAAATTT
1 AAATATA-AAAATACATAAATATT-TTCAAAAAACATAATAAAAAATTT
52131712 AAATTTAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
48 3 0.08
49 23 0.57
50 10 0.25
51 4 0.10
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.30
Consensus pattern (50 bp):
AAATATAAAAATACATAAATATTTTCAAAAAACATAATAAAAAATTTGAG
Found at i:52132552 original size:24 final size:22
Alignment explanation
Indices: 52132506--52132552 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
52132496 CAATATTTTT
**
52132506 TTTATTTTTATATATTTTTAAA
1 TTTATTTTTATATATTTGAAAA
52132528 TTTATTATTATATATATTTGAAAA
1 TTTATT-TT-TATATATTTGAAAA
52132552 T
1 T
52132553 ATTTATGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 2 0.10
24 13 0.62
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTATTTTTATATATTTGAAAA
Found at i:52132555 original size:22 final size:22
Alignment explanation
Indices: 52132508--52132555 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
52132498 ATATTTTTTT
* * *
52132508 TATTTTTATATATTTTTAAATT
1 TATTATTATATATTTTGAAATA
52132530 TATTATTATATATATTTGAAA-A
1 TATTATTATATAT-TTTGAAATA
52132552 TATT
1 TATT
52132556 TATGTATTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TATTATTATATATTTTGAAATA
Found at i:52139212 original size:26 final size:26
Alignment explanation
Indices: 52139182--52139237 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
52139172 TGAAATTCCC
52139182 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
52139208 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
52139234 ATCA
1 ATCA
52139238 ATTTGTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:52150014 original size:9 final size:9
Alignment explanation
Indices: 52150000--52150024 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
52149990 GGACTAAATC
52150000 GTAAAAGCT
1 GTAAAAGCT
52150009 GTAAAAGCT
1 GTAAAAGCT
52150018 GTAAAAG
1 GTAAAAG
52150025 TTGATTGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.08, G:0.24, T:0.20
Consensus pattern (9 bp):
GTAAAAGCT
Found at i:52161816 original size:39 final size:38
Alignment explanation
Indices: 52161733--52161832 Score: 112
Period size: 39 Copynumber: 2.6 Consensus size: 38
52161723 GAAATCCTTG
* *
52161733 TTATAATTATTGTAATTATAATTTAGGATCAAATATTA
1 TTATAATTATTCTAATTATAATTTAGGATCAAACATTA
* * *
52161771 TCATAATTATTCTAATTGTAATTTTTTGG-TCAAACATTA
1 TTATAATTATTCTAATTATAA--TTTAGGATCAAACATTA
**
52161810 TTATAATTATGGTAATTATAATT
1 TTATAATTATTCTAATTATAATT
52161833 ATTATATTCG
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
37 2 0.04
38 18 0.35
39 26 0.51
40 5 0.10
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (38 bp):
TTATAATTATTCTAATTATAATTTAGGATCAAACATTA
Found at i:52168507 original size:34 final size:30
Alignment explanation
Indices: 52168471--52168533 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
52168461 CATAGAAAAT
52168471 TTAATTTAAATAATA-TTTTTTATTTATAC
1 TTAATTTAAATAATATTTTTTTATTTATAC
52168500 TTAATTTAAATAATATTTTTTTATTTATAC
1 TTAATTTAAATAATATTTTTTTATTTATAC
52168530 TTAA
1 TTAA
52168534 AAGTATATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 15 0.45
30 18 0.55
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (30 bp):
TTAATTTAAATAATATTTTTTTATTTATAC
Found at i:52168917 original size:13 final size:13
Alignment explanation
Indices: 52168901--52168927 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52168891 TAATTAAAGG
52168901 GTTAAAATTTAAA
1 GTTAAAATTTAAA
52168914 GTTAAAATTTAAA
1 GTTAAAATTTAAA
52168927 G
1 G
52168928 ATGATAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (13 bp):
GTTAAAATTTAAA
Found at i:52169001 original size:9 final size:9
Alignment explanation
Indices: 52168979--52169055 Score: 68
Period size: 9 Copynumber: 8.6 Consensus size: 9
52168969 AACTTTGGAT
*
52168979 CATAAGTTA
1 CATAACTTA
52168988 CATAACTTA
1 CATAACTTA
*
52168997 TATAACTTA
1 CATAACTTA
52169006 CATAACTTA
1 CATAACTTA
52169015 CATAA--TA
1 CATAACTTA
*
52169022 CATAAATATA
1 CATAACT-TA
* * *
52169032 TATATCATA
1 CATAACTTA
52169041 TCATAACTTA
1 -CATAACTTA
52169051 CATAA
1 CATAA
52169056 AACTTTGGAT
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
7 7 0.13
9 36 0.67
10 11 0.20
ACGTcount: A:0.48, C:0.16, G:0.01, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:52191144 original size:26 final size:26
Alignment explanation
Indices: 52191115--52191284 Score: 331
Period size: 26 Copynumber: 6.5 Consensus size: 26
52191105 CATGAAATTT
52191115 CTAACCTATTATCATGGAACATTTAC
1 CTAACCTATTATCATGGAACATTTAC
52191141 CTAACCTATTATCATGGAACATTTAC
1 CTAACCTATTATCATGGAACATTTAC
52191167 CTAACCTATTATCATGGAACATTTAC
1 CTAACCTATTATCATGGAACATTTAC
52191193 CTAACCTATTATCATGGAACATTTAC
1 CTAACCTATTATCATGGAACATTTAC
52191219 CTAACCTATTATCATGGAACATTTAC
1 CTAACCTATTATCATGGAACATTTAC
52191245 CTAACCTATTATCATGGAACATTTAC
1 CTAACCTATTATCATGGAACATTTAC
*
52191271 CTAACCCATTATCA
1 CTAACCTATTATCA
52191285 ATTTGTATCA
Statistics
Matches: 143, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 143 1.00
ACGTcount: A:0.35, C:0.24, G:0.07, T:0.34
Consensus pattern (26 bp):
CTAACCTATTATCATGGAACATTTAC
Found at i:52198441 original size:27 final size:27
Alignment explanation
Indices: 52198401--52198541 Score: 173
Period size: 27 Copynumber: 5.2 Consensus size: 27
52198391 AGGAAGCGTC
*
52198401 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
52198428 CTGGTGGCTCTGCCGC-ATATATCTG-T
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
52198454 CCTGGTGGCTATGCCACAATTATCTGAT
1 -CTGGTGGCTCTGCCACAATTATCTGAT
*
52198482 CTGGTGGCTCTGCCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
52198509 CTAGTGGCTCTGCCACAA-TATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
52198536 CTGGTG
1 CTGGTG
52198542 ACTTCGTCAC
Statistics
Matches: 98, Mismatches: 9, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
26 11 0.11
27 83 0.85
28 4 0.04
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:52198480 original size:54 final size:54
Alignment explanation
Indices: 52198398--52198541 Score: 236
Period size: 54 Copynumber: 2.7 Consensus size: 54
52198388 TGGAGGAAGC
*
52198398 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCGCATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
52198452 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
* * *
52198506 GTTCTAGTGGCTCTGCCACAA-TATCTGTATCTGGTG
1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTG
52198542 ACTTCGTCAC
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
53 6 0.07
54 79 0.93
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.34
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
Found at i:52198553 original size:81 final size:80
Alignment explanation
Indices: 52198401--52198559 Score: 198
Period size: 81 Copynumber: 2.0 Consensus size: 80
52198391 AGGAAGCGTC
* * *
52198401 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCGCATATATCTGTCCTGGTGGCTAT
1 CTGGTGGCTATGCCACAATTATCTGATCTAGTGGCTCTGCCACATATATCTGTCCTGGTGACTAT
52198466 GCCACAATTATCTGAT
66 GCCACAA-TATCTGAT
* * *
52198482 CTGGTGGCTCTGCCAC-ATATATCTGTTCTAGTGGCTCTGCCACA-ATATCTGTATCTGGTGACT
1 CTGGTGGCTATGCCACAAT-TATCTGATCTAGTGGCTCTGCCACATATATCTGT-CCTGGTGACT
*
52198545 -TCGTCACAATATCTG
64 AT-GCCACAATATCTG
52198560 GCAGCCTCGC
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
80 17 0.25
81 51 0.75
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (80 bp):
CTGGTGGCTATGCCACAATTATCTGATCTAGTGGCTCTGCCACATATATCTGTCCTGGTGACTAT
GCCACAATATCTGAT
Found at i:52206423 original size:27 final size:27
Alignment explanation
Indices: 52206383--52206521 Score: 171
Period size: 27 Copynumber: 5.2 Consensus size: 27
52206373 AGGAAGCGTC
*
52206383 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
52206410 CTGGTGGCTCTGCCAC-ATATATCT--C
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
52206435 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
52206462 CTGGTGGCTCTGCCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
52206489 CTGATGGCTCTGCCACAA-TATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
52206516 CTGGTG
1 CTGGTG
52206522 ACTTCGTCAC
Statistics
Matches: 96, Mismatches: 9, Indels: 14
0.81 0.08 0.12
Matches are distributed among these distances:
25 20 0.21
26 12 0.12
27 63 0.66
28 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:52206459 original size:52 final size:53
Alignment explanation
Indices: 52206379--52206521 Score: 227
Period size: 52 Copynumber: 2.7 Consensus size: 53
52206369 ATGGAGGAAG
52206379 CGTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATAT
1 CGTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATAT
52206432 C-TCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATAT
1 CGTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATAT
* * *
52206484 CTGTTCTGATGGCTCTGCCACAA-TATCTGTATCTGGTG
1 C-GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTG
52206522 ACTTCGTCAC
Statistics
Matches: 84, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
52 52 0.62
53 7 0.08
54 25 0.30
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (53 bp):
CGTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATAT
Found at i:52209025 original size:137 final size:137
Alignment explanation
Indices: 52208779--52209065 Score: 484
Period size: 137 Copynumber: 2.1 Consensus size: 137
52208769 TATTGGGCCT
** **
52208779 AAGCCCATTCCGGTAACAGTGGTACTGGACCAGAGCCCTTTTCCGATTACAACAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGACCAGAGCCCTTTTCAAATTACAACAAACTGGGCCTT
* * *
52208844 AGCCCCTTATTTAGATAACAGTATGGCCCATAGGCCTATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAACACATGCAACATCAGTAAA
52208909 CATATGC
131 CATATGC
* * *
52208916 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAAATTACAATATACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGACCAGAGCCCTTTTCAAATTACAACAAACTGGGCCTT
52208981 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAACACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAACACATGCAACATCAGTAAA
52209046 CATATGC
131 CATATGC
52209053 AAGCCCATTTGGG
1 AAGCCCATTTGGG
52209066 GAGACTACTC
Statistics
Matches: 140, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
137 140 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGACCAGAGCCCTTTTCAAATTACAACAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAACACATGCAACATCAGTAAA
CATATGC
Found at i:52209342 original size:26 final size:26
Alignment explanation
Indices: 52209313--52209365 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
52209303 TCAAACATGC
52209313 ATTTAAGTCAATTTAAC-CCTAGGGGT
1 ATTTAAGT-AATTTAACTCCTAGGGGT
** *
52209339 ATTTCGGTAATTTATCTCCTAGGGGT
1 ATTTAAGTAATTTAACTCCTAGGGGT
52209365 A
1 A
52209366 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (26 bp):
ATTTAAGTAATTTAACTCCTAGGGGT
Found at i:52210521 original size:26 final size:26
Alignment explanation
Indices: 52210484--52210699 Score: 387
Period size: 26 Copynumber: 8.3 Consensus size: 26
52210474 GACATGAAAT
*
52210484 TATTATCATGAAACATTTACCTAACC
1 TATTATCATGGAACATTTACCTAACC
* *
52210510 CATTATCATGAAACATTTACCTAACC
1 TATTATCATGGAACATTTACCTAACC
*
52210536 CATTATCATGGAACATTTACCTAACC
1 TATTATCATGGAACATTTACCTAACC
52210562 TATTATCATGGAACATTTACCTAACC
1 TATTATCATGGAACATTTACCTAACC
52210588 TATTATCATGGAACATTTACCTAACC
1 TATTATCATGGAACATTTACCTAACC
52210614 TATTATCATGGAACATTTACCTAACC
1 TATTATCATGGAACATTTACCTAACC
52210640 TATTATCATGGAACATTTACCTAACC
1 TATTATCATGGAACATTTACCTAACC
52210666 TATTATCATGGAACATTTACCTAACC
1 TATTATCATGGAACATTTACCTAACC
*
52210692 CATTATCA
1 TATTATCA
52210700 ATTTGTATCA
Statistics
Matches: 186, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 186 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (26 bp):
TATTATCATGGAACATTTACCTAACC
Found at i:52214477 original size:266 final size:266
Alignment explanation
Indices: 52214003--52214533 Score: 999
Period size: 266 Copynumber: 2.0 Consensus size: 266
52213993 TGCATACCGC
52214003 AATTGCCACACCTTAACGTCATGGATATTTCTAGGAAACTGATTTGATTACGTCATTTTTAGGAA
1 AATTGCCACACCTTAACGTCATGGATATTTCTAGGAAACTGATTTGATTACGTCATTTTTAGGAA
52214068 AAGTGATTAATTTTGGAAAATACTTTCATTGCGGAAGCTTTGCTTGTTGTCGTGTTATTTTGAAA
66 AAGTGATTAATTTTGGAAAATACTTTCATTGCGGAAGCTTTGCTTGTTGTCGTGTTATTTTGAAA
*
52214133 TCAACTATTGTTTTTGAAGACGCGCCCTAAAGCTATCCAATTTCAACAGTTAAAATAAGTAATAC
131 TCAACTATTGTTTTTGAAAACGCGCCCTAAAGCTATCCAATTTCAACAGTTAAAATAAGTAATAC
52214198 CTATCTTAGTAATACATATTAAAACCATCAAAAATAATTAAGCGGCCTTATTACATTTAAAAACC
196 CTATCTTAGTAATACATATTAAAACCATCAAAAATAATTAAGCGGCCTTATTACATTTAAAAACC
52214263 CAAAAT
261 CAAAAT
52214269 AATTGCCACACCTTAACGTCATGGATATTTCTAGGAAACTGATTTGATTACGTCATTTTTAGGAA
1 AATTGCCACACCTTAACGTCATGGATATTTCTAGGAAACTGATTTGATTACGTCATTTTTAGGAA
52214334 AAGTGATTAATTTTGGAAAATACTTTCATTGCGGAAGCTTTGCTTGTTGTCGTGTTATTTTGAAA
66 AAGTGATTAATTTTGGAAAATACTTTCATTGCGGAAGCTTTGCTTGTTGTCGTGTTATTTTGAAA
* * * *
52214399 TCAATTGTTGTTTTTGAAAACGTGCCCTAAAGCTATCCAATTTCAACAGTTAAAATAAGTATTAC
131 TCAACTATTGTTTTTGAAAACGCGCCCTAAAGCTATCCAATTTCAACAGTTAAAATAAGTAATAC
* *
52214464 CTATCTTAGTAATACATATTAAAACCATCAAAAATAATTAAGCGGCCTTATTATATTTAAAAGCC
196 CTATCTTAGTAATACATATTAAAACCATCAAAAATAATTAAGCGGCCTTATTACATTTAAAAACC
52214529 CAAAA
261 CAAAA
52214534 ACTTCAAACG
Statistics
Matches: 258, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
266 258 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (266 bp):
AATTGCCACACCTTAACGTCATGGATATTTCTAGGAAACTGATTTGATTACGTCATTTTTAGGAA
AAGTGATTAATTTTGGAAAATACTTTCATTGCGGAAGCTTTGCTTGTTGTCGTGTTATTTTGAAA
TCAACTATTGTTTTTGAAAACGCGCCCTAAAGCTATCCAATTTCAACAGTTAAAATAAGTAATAC
CTATCTTAGTAATACATATTAAAACCATCAAAAATAATTAAGCGGCCTTATTACATTTAAAAACC
CAAAAT
Found at i:52216945 original size:9 final size:9
Alignment explanation
Indices: 52216931--52216955 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
52216921 ATGTTCTCTA
52216931 AGGTTGCAC
1 AGGTTGCAC
52216940 AGGTTGCAC
1 AGGTTGCAC
52216949 AGGTTGC
1 AGGTTGC
52216956 CTAAGTTGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.36, T:0.24
Consensus pattern (9 bp):
AGGTTGCAC
Found at i:52218012 original size:21 final size:18
Alignment explanation
Indices: 52217975--52218013 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
52217965 ACTTTTTCTC
52217975 TTTGTACTGAAGTTATTA
1 TTTGTACTGAAGTTATTA
*
52217993 TTTGTACTGAAGTTGTTA
1 TTTGTACTGAAGTTATTA
52218011 TTT
1 TTT
52218014 CATTAGGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.18, T:0.54
Consensus pattern (18 bp):
TTTGTACTGAAGTTATTA
Found at i:52221620 original size:45 final size:45
Alignment explanation
Indices: 52221542--52221857 Score: 171
Period size: 45 Copynumber: 6.8 Consensus size: 45
52221532 GATTTGCTCT
* *
52221542 ACTGCAACTTCAAGGAGATAAGA-TCTGCCATCTTCAGTCTACTCC
1 ACTGCAACTTCAGGGAGATAAGACT-TGCTATCTTCAGTCTACTCC
* * *
52221587 ACTGCAGCTTCAGGGAGATAAGACTTGCTATCTT-AGATTTAATTTGACC
1 ACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAG-TCT-A-CT--CC
* * * * * *
52221636 TACTGCAACTTCAGAGAGATATGA-TCTGTTTAT-TTATAGGTTCAATATGTTTC
1 -ACTGCAACTTCAGGGAGATAAGACT-TG-CTATCTT-CA-G-TC--TA--CTCC
* * * * * * *
52221689 ACTGCATCTTTAGGGAAATAAGA-TTCACTAACTTCAGCCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGACTT-GCTATCTTCAGTCTACTCC
* **
52221734 ACTGCAACTTCAGGGAGATAAGACTTACTA-CTTCAACCTACTCC
1 ACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAGTCTACTCC
* * * * *
52221778 ACTGCAACTTTAGGGAGATAAGGTCTT-CAATCTTCAGTCTGCTCT
1 ACTGCAACTTCAGGGAGATAA-GACTTGCTATCTTCAGTCTACTCC
*
52221823 ACTGCAACTTCAGGGGGATAAGACTTGCTA-CTTCA
1 ACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCA
52221858 ACTTGCTTCA
Statistics
Matches: 208, Mismatches: 42, Indels: 43
0.71 0.14 0.15
Matches are distributed among these distances:
44 45 0.22
45 92 0.44
46 4 0.02
47 2 0.01
49 4 0.02
50 25 0.12
51 7 0.03
52 22 0.11
53 3 0.01
54 1 0.00
55 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (45 bp):
ACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAGTCTACTCC
Found at i:52221782 original size:44 final size:44
Alignment explanation
Indices: 52221688--52221875 Score: 182
Period size: 45 Copynumber: 4.2 Consensus size: 44
52221678 CAATATGTTT
* * * *
52221688 CACTGCATCTTTAGGGAAATAAGA-TTCACTAACTTCAGCCTGCTC
1 CACTGCAACTTCAGGGAGATAAGACTT-ACT-ACTTCAACCTGCTC
*
52221733 CACTGCAACTTCAGGGAGATAAGACTTACTACTTCAACCTACTC
1 CACTGCAACTTCAGGGAGATAAGACTTACTACTTCAACCTGCTC
* * * **
52221777 CACTGCAACTTTAGGGAGATAAGGTCTT-CAATCTTCAGTCTGCTC
1 CACTGCAACTTCAGGGAGATAA-GACTTACTA-CTTCAACCTGCTC
* * * * *
52221822 TACTGCAACTTCAGGGGGATAAGACTTGCTACTTCAACTTGCTT
1 CACTGCAACTTCAGGGAGATAAGACTTACTACTTCAACCTGCTC
*
52221866 CACTACAACT
1 CACTGCAACT
52221876 GCTTCACTGC
Statistics
Matches: 117, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
44 56 0.48
45 59 0.50
46 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (44 bp):
CACTGCAACTTCAGGGAGATAAGACTTACTACTTCAACCTGCTC
Found at i:52221880 original size:14 final size:14
Alignment explanation
Indices: 52221856--52221889 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
52221846 CTTGCTACTT
52221856 CAACTTGCTTCACTA
1 CAAC-TGCTTCACTA
*
52221871 CAACTGCTTCACTG
1 CAACTGCTTCACTA
52221885 CAACT
1 CAACT
52221890 TTAGGGGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.26, C:0.35, G:0.09, T:0.29
Consensus pattern (14 bp):
CAACTGCTTCACTA
Found at i:52232835 original size:19 final size:19
Alignment explanation
Indices: 52232811--52232849 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
52232801 TAAAAAAGAA
52232811 TGTATAAAATTTTCATTCT
1 TGTATAAAATTTTCATTCT
52232830 TGTATAAAATTTTCATTCT
1 TGTATAAAATTTTCATTCT
52232849 T
1 T
52232850 CCTTTTACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.54
Consensus pattern (19 bp):
TGTATAAAATTTTCATTCT
Found at i:52235094 original size:15 final size:14
Alignment explanation
Indices: 52235074--52235115 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
52235064 CACACACATG
*
52235074 AAAAAAAATAAAAGT
1 AAAAAAAATAAAA-C
52235089 AAAAAAAATAAAAC
1 AAAAAAAATAAAAC
52235103 AAAAAAAATAAAA
1 AAAAAAAATAAAA
52235116 TTTTTTTACC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.86, C:0.02, G:0.02, T:0.10
Consensus pattern (14 bp):
AAAAAAAATAAAAC
Found at i:52235876 original size:24 final size:24
Alignment explanation
Indices: 52235826--52236046 Score: 160
Period size: 23 Copynumber: 9.3 Consensus size: 24
52235816 TATTAATGGT
52235826 TATTTTTAATAT-TATTAT-TAT-
1 TATTTTTAATATATATTATGTATG
* *
52235847 CATTTTGAATATATA-TATTGTATG
1 TATTTTTAATATATATTA-TGTATG
* *
52235871 TGTTTTTCATATATATTATGTATG
1 TATTTTTAATATATATTATGTATG
*
52235895 TATTTTTAATAT-TATTAAT-TATA
1 TATTTTTAATATATATT-ATGTATG
52235918 TATTTTT-ATATATATTATGTATG
1 TATTTTTAATATATATTATGTATG
* *
52235941 TATTTTTAAATATCATACTAT-TCATA
1 TATTTTT-AATAT-ATATTATGT-ATG
* *
52235967 TATTTTT-ATGT-TATCTCATGTATA
1 TATTTTTAATATATAT-T-ATGTATG
*
52235991 TATTTTTAATAT-TATTA-GTTATA
1 TATTTTTAATATATATTATG-TATG
* * *
52236014 TATTTTTTATACTATTTTATGTATA
1 TATTTTTAATA-TATATTATGTATG
52236039 TATTTTTA
1 TATTTTTA
52236047 TATTATCCTT
Statistics
Matches: 162, Mismatches: 18, Indels: 36
0.75 0.08 0.17
Matches are distributed among these distances:
21 12 0.07
22 12 0.07
23 47 0.29
24 46 0.28
25 29 0.18
26 16 0.10
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.59
Consensus pattern (24 bp):
TATTTTTAATATATATTATGTATG
Found at i:52236065 original size:23 final size:23
Alignment explanation
Indices: 52235873--52236052 Score: 129
Period size: 24 Copynumber: 7.5 Consensus size: 23
52235863 ATTGTATGTG
*
52235873 TTTTTCATA-TATATTATGTATGTA
1 TTTTT-ATATTAT-TTATGTATATA
*
52235897 TTTTTAATATTATTAAT-TATATA
1 TTTTT-ATATTATTTATGTATATA
*
52235920 TTTTTATA-TATATTATGTATGTA
1 TTTTTATATTAT-TTATGTATATA
* *
52235943 TTTTTAAATATCATACTAT-TCATATA
1 TTTTT--ATATTAT-TTATGT-ATATA
* *
52235969 TTTTTATGTTATCTCATGTATATA
1 TTTTTATATTAT-TTATGTATATA
52235993 TTTTTAATATTA-TTA-GTTATATA
1 TTTTT-ATATTATTTATG-TATATA
*
52236016 TTTTTTATACTATTTTATGTATATA
1 -TTTTTATATTA-TTTATGTATATA
52236041 TTTTTATATTAT
1 TTTTTATATTAT
52236053 CCTTATTATT
Statistics
Matches: 125, Mismatches: 17, Indels: 29
0.73 0.10 0.17
Matches are distributed among these distances:
21 3 0.02
22 7 0.06
23 34 0.27
24 43 0.34
25 22 0.18
26 16 0.13
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTTATATTATTTATGTATATA
Found at i:52236083 original size:48 final size:48
Alignment explanation
Indices: 52235887--52236083 Score: 124
Period size: 48 Copynumber: 4.1 Consensus size: 48
52235877 TCATATATAT
* * *
52235887 TATGTATGTATTTTTAATATTATTAATTATATATT-TTTATA-TA-TA
1 TATGTATATATTTTTAATATTATTAGTTATATATTATTGATACTAGTA
* * * ** *
52235932 TTATGTATGTATTTTTAAATATCATACTA-TTCATATATT-TTTATGTTA-TC
1 -TATGTATATATTTTT-AATAT--TATTAGTT-ATATATTATTGATACTAGTA
* * * *
52235982 TCATGTATATATTTTTAATATTATTAGTTATATATTTTTTATACTATTT
1 T-ATGTATATATTTTTAATATTATTAGTTATATATTATTGATACTAGTA
*
52236031 TATGTATATATTTTT-ATATTATCCTTA-TTAT-TATTATTGATATTAGTA
1 TATGTATATATTTTTAATATTA---TTAGTTATATATTATTGATACTAGTA
52236079 TATGT
1 TATGT
52236084 TTTATTATAT
Statistics
Matches: 126, Mismatches: 13, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
46 15 0.12
47 22 0.17
48 42 0.33
49 28 0.22
50 19 0.15
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59
Consensus pattern (48 bp):
TATGTATATATTTTTAATATTATTAGTTATATATTATTGATACTAGTA
Found at i:52236108 original size:21 final size:20
Alignment explanation
Indices: 52236076--52236126 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
52236066 ATTGATATTA
* *
52236076 GTATATGTTTTATTATATAT
1 GTATATATTTTAATATATAT
52236096 GTATATATCTTTAATATATAT
1 GTATATAT-TTTAATATATAT
52236117 GTATATATTT
1 GTATATATTT
52236127 ATGTAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (20 bp):
GTATATATTTTAATATATAT
Found at i:52236227 original size:24 final size:23
Alignment explanation
Indices: 52236174--52236230 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
52236164 TTCTAATATG
*
52236174 TATATATTATGTAGATATTTTAA
1 TATATATTATATAGATATTTTAA
*
52236197 TATTATATTATATATGCAT-TTTTTA
1 TA-TATATTATATA-G-ATATTTTAA
52236222 TATATATTA
1 TATATATTA
52236231 CGTATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 2 0.07
24 17 0.59
25 8 0.28
26 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (23 bp):
TATATATTATATAGATATTTTAA
Found at i:52236381 original size:25 final size:25
Alignment explanation
Indices: 52236265--52236386 Score: 90
Period size: 25 Copynumber: 4.9 Consensus size: 25
52236255 TATTTTTATA
* * * *
52236265 TATATCATGTATATATTTTGAATAC
1 TATATTATGTATATATTTTTAACAT
52236290 TATATTA--TATAT-TTTTT-ACAT
1 TATATTATGTATATATTTTTAACAT
* *
52236311 TATCTTATGTATATATTTTTTAATAACT
1 TATATTATGTATATA-TTTTTAA-CA-T
* * *
52236339 ATATATTATTTTTGTATTTTTAACAT
1 -TATATTATGTATATATTTTTAACAT
*
52236365 TATATTATGTACATATTTTTAA
1 TATATTATGTATATATTTTTAA
52236387 TACTATGTAT
Statistics
Matches: 74, Mismatches: 15, Indels: 16
0.70 0.14 0.15
Matches are distributed among these distances:
21 8 0.11
22 4 0.05
23 10 0.14
25 29 0.39
26 2 0.03
27 2 0.03
28 8 0.11
29 11 0.15
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.57
Consensus pattern (25 bp):
TATATTATGTATATATTTTTAACAT
Found at i:52236395 original size:20 final size:21
Alignment explanation
Indices: 52236370--52236413 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
52236360 AACATTATAT
*
52236370 TATGTACATA-TTTTTAATAC
1 TATGTACATACTTTGTAATAC
*
52236390 TATGTATATACTTTGTAATAC
1 TATGTACATACTTTGTAATAC
52236411 TAT
1 TAT
52236414 TATTATGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.50
Consensus pattern (21 bp):
TATGTACATACTTTGTAATAC
Found at i:52251631 original size:155 final size:155
Alignment explanation
Indices: 52251349--52252191 Score: 1641
Period size: 155 Copynumber: 5.4 Consensus size: 155
52251339 TTCTATTTTC
52251349 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
52251414 TGTCTTTCAAAAAAATCAACTCATATTATGAGAGTGAGTTGAGCCTCGGAACACACTGAGGTATT
66 TGTCTTTCAAAAAAATCAACTCATATTATGAGAGTGAGTTGAGCCTCGGAACACACTGAGGTATT
52251479 TCTTTTCAATTTCTGCTTTTCAAAA
131 TCTTTTCAATTTCTGCTTTTCAAAA
52251504 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
52251569 TGTCTTTCAAAAAAATCAACTCATATTATGAGAGTGAGTTGAGCCTCGGAACACACTGAGGTATT
66 TGTCTTTCAAAAAAATCAACTCATATTATGAGAGTGAGTTGAGCCTCGGAACACACTGAGGTATT
52251634 TCTTTTCAATTTCTGCTTTTCAAAA
131 TCTTTTCAATTTCTGCTTTTCAAAA
52251659 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
52251724 TGTCTTTCAAAAAAATCAACTCATATTATGAGAGTGAGTTGAGCCTCGGAACACACTGAGGTATT
66 TGTCTTTCAAAAAAATCAACTCATATTATGAGAGTGAGTTGAGCCTCGGAACACACTGAGGTATT
52251789 TCTTTTCAATTTCTGCTTTTCAAAA
131 TCTTTTCAATTTCTGCTTTTCAAAA
52251814 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
52251879 TGTCTTTCAAAAAAATCAACTCATATTATGAGAGTGAGTTGAGCCTCGGAACACACTGAGGTATT
66 TGTCTTTCAAAAAAATCAACTCATATTATGAGAGTGAGTTGAGCCTCGGAACACACTGAGGTATT
52251944 TCTTTTCAATTTCTGCTTTTCAAAA
131 TCTTTTCAATTTCTGCTTTTCAAAA
52251969 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
52252034 TGTCTTTCAAAAAAATCAACTCATATTATGAGAGTGAGTTGAGCCTCGGAACACACTGAGGTATT
66 TGTCTTTCAAAAAAATCAACTCATATTATGAGAGTGAGTTGAGCCTCGGAACACACTGAGGTATT
52252099 TCTTTTCAATTTCTGCTTTTCAAAA
131 TCTTTTCAATTTCTGCTTTTCAAAA
* * * * *
52252124 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTAAGGTATTTTTAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
52252189 TGT
66 TGT
52252192 TTTTTCAATT
Statistics
Matches: 683, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
155 683 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (155 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
TGTCTTTCAAAAAAATCAACTCATATTATGAGAGTGAGTTGAGCCTCGGAACACACTGAGGTATT
TCTTTTCAATTTCTGCTTTTCAAAA
Found at i:52252209 original size:14 final size:14
Alignment explanation
Indices: 52252178--52252213 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
52252168 TGCTAAGGTA
*
52252178 TTTTTAATTTCTGT
1 TTTTTAATTTATGT
52252192 TTTTTCAATTTATGT
1 TTTTT-AATTTATGT
52252207 TTTTTAA
1 TTTTTAA
52252214 AAATGTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (14 bp):
TTTTTAATTTATGT
Found at i:52264683 original size:81 final size:79
Alignment explanation
Indices: 52264478--52264768 Score: 398
Period size: 79 Copynumber: 3.7 Consensus size: 79
52264468 TTCTATTTTC
* *
52264478 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTA----TTTTCAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTCTTTTCAA
52264539 TTTCTG-TCTTTCAA
66 TTTCTGCT-TTTCAA
** *
52264553 AAAAATCAACTCATATTATGAGA-GTGAGTTGAGCCTC-GGAACACACTGAGGTATTTCTTTTCA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACGCTGAGGTATTTCTTTTCA
52264616 ATTTCTGCTTTTCAAAA
65 ATTTCTGCTTTTC--AA
* *
52264633 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACATGCTGAGGTATTTCTTTTCAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTCTTTTCAA
* *
52264698 TTTTTTCTTTTCAA
66 TTTCTGCTTTTCAA
* *
52264712 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTAAGGTATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTT
52264769 TTAATTTCTG
Statistics
Matches: 193, Mismatches: 13, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
73 1 0.01
74 25 0.13
75 21 0.11
78 17 0.09
79 58 0.30
80 23 0.12
81 46 0.24
82 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Consensus pattern (79 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTCTTTTCAA
TTTCTGCTTTTCAA
Found at i:52264797 original size:14 final size:14
Alignment explanation
Indices: 52264766--52264801 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
52264756 TGCTAAGGTA
*
52264766 TTTTTAATTTCTGT
1 TTTTTAATTTATGT
52264780 TTTTTCAATTTATGT
1 TTTTT-AATTTATGT
52264795 TTTTTAA
1 TTTTTAA
52264802 AAATCAACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (14 bp):
TTTTTAATTTATGT
Found at i:52264892 original size:88 final size:88
Alignment explanation
Indices: 52264712--52265024 Score: 375
Period size: 88 Copynumber: 3.6 Consensus size: 88
52264702 TTCTTTTCAA
* ** * *
52264712 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACATGCTAAGGTATTTTTAATT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGGTCACATGCTGAGGTATTTTCAATT
* *
52264775 TCTGTTTTTTCAATTTATGTTTTTT
66 TCTG-TTTTTCAATATCTG-TTTTT
*
52264800 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGGTCACATG-TCGAGGTATTTTCAAA
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGGTCACATGCT-GAGGTATTTTCAAT
* * *
52264864 ATCTGTTTTTCAAAATCTGTTTTC
65 TTCTGTTTTTCAATATCTGTTTTT
* * * *
52264888 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGGTCACATGCTGAGGTATTTTCAATT
*
52264953 TCTGTTTTT-AATGTCTGTTTTT
66 TCTGTTTTTCAATATCTGTTTTT
* * *
52264975 AAAGAGTCAACTCATATTGCAAGAAGTGAGTTGAG-CTTAGGATCACATGC
1 AAA-AATCAACTCATATTGCGAGAAGTGAGTTGAGCCTT-GGGTCACATGC
52265025 CGAGTAAAGA
Statistics
Matches: 194, Mismatches: 25, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
87 16 0.08
88 145 0.75
89 13 0.07
90 20 0.10
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (88 bp):
AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGGTCACATGCTGAGGTATTTTCAATT
TCTGTTTTTCAATATCTGTTTTT
Found at i:52264894 original size:14 final size:14
Alignment explanation
Indices: 52264856--52264891 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
52264846 TGTCGAGGTA
52264856 TTTTCAAAATCTGT
1 TTTTCAAAATCTGT
52264870 TTTTCAAAATCTG-
1 TTTTCAAAATCTGT
52264883 TTTTCAAAA
1 TTTTCAAAA
52264892 ATCAACTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (14 bp):
TTTTCAAAATCTGT
Found at i:52265970 original size:141 final size:141
Alignment explanation
Indices: 52265716--52265996 Score: 517
Period size: 141 Copynumber: 2.0 Consensus size: 141
52265706 GGCCACCTGT
*
52265716 CCTCTGACGCCTCTGCCACCACCCATCGCCACCTGCTCCATTGCCACTTGCACCTGCAAATGAAG
1 CCTCTGACGCCTCTGCCACCACCCATCGCCACCTGCTCCATCGCCACTTGCACCTGCAAATGAAG
* *
52265781 AAAAGATATAAACAATAAAAAAATACTTTGTAAACGACTATTTAAGCCTTGCAAATATTTTGTAT
66 AAAAGACATAAACAATAAAAAAATACTTTGTAAACGACTATATAAGCCTTGCAAATATTTTGTAT
52265846 TTTACGTTCTC
131 TTTACGTTCTC
*
52265857 CCTCTGACGCCTCTGCCACCACCCATCGCCACCTGCTCCATCGCCACTTGCATCTGCAAATGAAG
1 CCTCTGACGCCTCTGCCACCACCCATCGCCACCTGCTCCATCGCCACTTGCACCTGCAAATGAAG
*
52265922 AAAAGACATAAACAATAAAAAAATACTTTGTAAATGACTATATAAGCCTTGCAAATATTTTGTAT
66 AAAAGACATAAACAATAAAAAAATACTTTGTAAACGACTATATAAGCCTTGCAAATATTTTGTAT
52265987 TTTACGTTCT
131 TTTACGTTCT
52265997 TTGGACAAGA
Statistics
Matches: 135, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
141 135 1.00
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.28
Consensus pattern (141 bp):
CCTCTGACGCCTCTGCCACCACCCATCGCCACCTGCTCCATCGCCACTTGCACCTGCAAATGAAG
AAAAGACATAAACAATAAAAAAATACTTTGTAAACGACTATATAAGCCTTGCAAATATTTTGTAT
TTTACGTTCTC
Found at i:52266096 original size:61 final size:61
Alignment explanation
Indices: 52266029--52266145 Score: 234
Period size: 61 Copynumber: 1.9 Consensus size: 61
52266019 AAAGAAAGAA
52266029 TAGATTCAAATACTAAAAACATAGCAAGCTGATCAAAAACCAATTCATCATACAAAGGTCT
1 TAGATTCAAATACTAAAAACATAGCAAGCTGATCAAAAACCAATTCATCATACAAAGGTCT
52266090 TAGATTCAAATACTAAAAACATAGCAAGCTGATCAAAAACCAATTCATCATACAAA
1 TAGATTCAAATACTAAAAACATAGCAAGCTGATCAAAAACCAATTCATCATACAAA
52266146 TATCCTGTTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.50, C:0.20, G:0.09, T:0.22
Consensus pattern (61 bp):
TAGATTCAAATACTAAAAACATAGCAAGCTGATCAAAAACCAATTCATCATACAAAGGTCT
Found at i:52266276 original size:15 final size:14
Alignment explanation
Indices: 52266256--52266297 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
52266246 CACACACATG
*
52266256 AAAAAAAATAAAAGT
1 AAAAAAAATAAAA-C
52266271 AAAAAAAATAAAAC
1 AAAAAAAATAAAAC
52266285 AAAAAAAATAAAA
1 AAAAAAAATAAAA
52266298 TTTTTTTACC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.86, C:0.02, G:0.02, T:0.10
Consensus pattern (14 bp):
AAAAAAAATAAAAC
Found at i:52273182 original size:17 final size:16
Alignment explanation
Indices: 52273162--52273200 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
52273152 GAGGGAAAGC
*
52273162 AGAGAAAGAAATAGAAT
1 AGAGAAAGAAA-AGAAA
52273179 AGAGAAAAGAAAAGAAA
1 AGAG-AAAGAAAAGAAA
52273196 AGAGA
1 AGAGA
52273201 GTCGTACCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 12 0.60
18 7 0.35
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.05
Consensus pattern (16 bp):
AGAGAAAGAAAAGAAA
Found at i:52274314 original size:16 final size:15
Alignment explanation
Indices: 52274293--52274325 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
52274283 CTAACATATT
52274293 AAATAAAACATAAATA
1 AAATAAAACA-AAATA
52274309 AAATAAAACAAAATA
1 AAATAAAACAAAATA
52274324 AA
1 AA
52274326 TATTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (15 bp):
AAATAAAACAAAATA
Found at i:52282041 original size:29 final size:29
Alignment explanation
Indices: 52281998--52282076 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
52281988 CTTAATAATC
52281998 AACCACGCACACTTAGTGCCATGTAATTT-A
1 AACC-CGCACACTTAGTGCCATG-AATTTCA
* *
52282028 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGAATTTCA
* *
52282057 AGCCCGCACACTTAATGCCA
1 AACCCGCACACTTAGTGCCA
52282077 ATCTCACAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 4 0.09
29 36 0.84
30 3 0.07
ACGTcount: A:0.30, C:0.32, G:0.14, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGAATTTCA
Found at i:52289020 original size:33 final size:33
Alignment explanation
Indices: 52288983--52289049 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
52288973 TTTTCAGCAT
52288983 ATTCATCCATGGAAAAATTTTCATAATTTGATA
1 ATTCATCCATGGAAAAATTTTCATAATTTGATA
*
52289016 ATTCATCCATGGAAAAATTTTCATACTTTGATA
1 ATTCATCCATGGAAAAATTTTCATAATTTGATA
52289049 A
1 A
52289050 CTTTTCAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (33 bp):
ATTCATCCATGGAAAAATTTTCATAATTTGATA
Found at i:52294568 original size:28 final size:29
Alignment explanation
Indices: 52294536--52294650 Score: 137
Period size: 29 Copynumber: 4.0 Consensus size: 29
52294526 TACCTGTATT
* *
52294536 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* *
52294564 TGGCCCATTAGGCCCAAATCACCTGT-AAA
1 TGGCCCATTAGGCCCAAATCACAT-TCATA
*
52294593 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* *
52294622 TGGCCCGTTAGGCCC-AGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
52294650 T
1 T
52294651 TCATGCTCAC
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
28 27 0.36
29 47 0.63
30 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.26
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:52294598 original size:57 final size:58
Alignment explanation
Indices: 52294527--52294637 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 58
52294517 AATTTCACAT
** *
52294527 ACCTGTATTTGGCCCATTAAGCCC-AATCATATTCATATGGCCCATTAGGCCCAAATC
1 ACCTGTAAATGGCCCATTAAGCCCAAATCACATTCATATGGCCCATTAGGCCCAAATC
* * *
52294584 ACCTGTAAATGGCCCATTAGGCCCAAATCACATTTATATGGCCCGTTAGGCCCA
1 ACCTGTAAATGGCCCATTAAGCCCAAATCACATTCATATGGCCCATTAGGCCCA
52294638 GTCACATTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 21 0.45
58 26 0.55
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (58 bp):
ACCTGTAAATGGCCCATTAAGCCCAAATCACATTCATATGGCCCATTAGGCCCAAATC
Found at i:52296146 original size:15 final size:15
Alignment explanation
Indices: 52296126--52296155 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
52296116 AGTTCAGGAT
52296126 TTCGGGATTTTTGGG
1 TTCGGGATTTTTGGG
52296141 TTCGGGATTTTTGGG
1 TTCGGGATTTTTGGG
52296156 GCGTTACAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.40, T:0.47
Consensus pattern (15 bp):
TTCGGGATTTTTGGG
Found at i:52300573 original size:47 final size:47
Alignment explanation
Indices: 52300519--52301015 Score: 904
Period size: 47 Copynumber: 10.6 Consensus size: 47
52300509 TATTTGAATA
52300519 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
52300566 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
52300613 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
52300660 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
52300707 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
52300754 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
52300801 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
52300848 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
52300895 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * * *
52300942 AATGTGAAAGTGTATATATGTAACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
52300989 GATGTGAAACTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
52301016 TCCCGAAGGG
Statistics
Matches: 437, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 437 1.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:52304787 original size:41 final size:41
Alignment explanation
Indices: 52304730--52304816 Score: 156
Period size: 41 Copynumber: 2.1 Consensus size: 41
52304720 TTGTTATTAC
52304730 AGTGATGCATTATTAAATGGGATTAGATTGTGATTTGATGT
1 AGTGATGCATTATTAAATGGGATTAGATTGTGATTTGATGT
* *
52304771 AGTGATGTATTATTAAATGGGATTAGATTGTGATTTTATGT
1 AGTGATGCATTATTAAATGGGATTAGATTGTGATTTGATGT
52304812 AGTGA
1 AGTGA
52304817 GACAAAGCAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.30, C:0.01, G:0.26, T:0.43
Consensus pattern (41 bp):
AGTGATGCATTATTAAATGGGATTAGATTGTGATTTGATGT
Found at i:52310605 original size:39 final size:39
Alignment explanation
Indices: 52310539--52310754 Score: 301
Period size: 39 Copynumber: 5.5 Consensus size: 39
52310529 CAAAGCATGT
* * * *
52310539 GGGACTTTAAGCCCGAATATAATACCAGCAC-AAAGCCTAC
1 GGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTTC
52310579 GGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTTC
1 GGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTTC
* * * *
52310619 GGGGCTTAACTC-GATATAACACGAGCACGAATGCCTTC
1 GGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTC
*
52310657 GGGGCTTAGCCCGGATATAACACCAGCACGAATGCCTTC
1 GGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTC
*
52310696 GAGACTTAGCCCGGATATAACACCAGCACGAATGCCTTC
1 GGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTC
52310735 GGGACTTAGCCCGGATATAA
1 GGGACTTAGCCCGGATATAA
52310755 TTCTCCATTA
Statistics
Matches: 160, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
38 35 0.22
39 106 0.66
40 19 0.12
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (39 bp):
GGGACTTAGCCCGGATATAACACCAGCACGAATGCCTTC
Found at i:52312848 original size:15 final size:16
Alignment explanation
Indices: 52312821--52312850 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
52312811 AGGGCTATTA
52312821 CACATATTATGTTAAC
1 CACATATTATGTTAAC
52312837 CACATA-TATGTTAA
1 CACATATTATGTTAA
52312851 GTAGTTGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.37
Consensus pattern (16 bp):
CACATATTATGTTAAC
Found at i:52315694 original size:29 final size:29
Alignment explanation
Indices: 52315627--52315734 Score: 94
Period size: 29 Copynumber: 3.8 Consensus size: 29
52315617 TTCACATACC
* * *
52315627 TGTATCTGGCCCATTAAGCCC-AATCATA
1 TGTATATGGCCCATTAGGCCCAAATCACA
* * *
52315655 T-TCATAGGGCCCATTAGTCCCAAATCACC
1 TGT-ATATGGCCCATTAGGCCCAAATCACA
* * *
52315684 TGTATCTGGCCTATCAGGCCCAAATCACA
1 TGTATATGGCCCATTAGGCCCAAATCACA
* *
52315713 TTTATATGGCCCACTAGGCCCA
1 TGTATATGGCCCATTAGGCCCA
52315735 GTCACATTCA
Statistics
Matches: 60, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
27 1 0.02
28 15 0.25
29 43 0.72
30 1 0.02
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (29 bp):
TGTATATGGCCCATTAGGCCCAAATCACA
Found at i:52315705 original size:57 final size:58
Alignment explanation
Indices: 52315624--52315734 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 58
52315614 AAATTCACAT
* * * *
52315624 ACCTGTATCTGGCCCATTAAGCCC-AATCATATTCATAGGGCCCATTAGTCCCAAATC
1 ACCTGTATCTGGCCCATCAAGCCCAAATCACATTCATAGGGCCCACTAGGCCCAAATC
* * * *
52315681 ACCTGTATCTGGCCTATCAGGCCCAAATCACATTTATATGGCCCACTAGGCCCA
1 ACCTGTATCTGGCCCATCAAGCCCAAATCACATTCATAGGGCCCACTAGGCCCA
52315735 GTCACATTCA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
57 21 0.47
58 24 0.53
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.25
Consensus pattern (58 bp):
ACCTGTATCTGGCCCATCAAGCCCAAATCACATTCATAGGGCCCACTAGGCCCAAATC
Found at i:52320582 original size:18 final size:18
Alignment explanation
Indices: 52320561--52320595 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52320551 GAGGCATTAA
52320561 CAAACAAAAACACATTTT
1 CAAACAAAAACACATTTT
**
52320579 CAAACAACCACACATTT
1 CAAACAAAAACACATTT
52320596 ATACAAGTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (18 bp):
CAAACAAAAACACATTTT
Found at i:52320695 original size:17 final size:19
Alignment explanation
Indices: 52320659--52320704 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
52320649 TGATTTTTTT
*
52320659 AATCATAATATAATATATA
1 AATCATAATATAAAATATA
52320678 AATCAT-AT-TAAAATATA
1 AATCATAATATAAAATATA
52320695 AATCAATAAT
1 AATC-ATAAT
52320705 GAACCTCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 12 0.50
18 4 0.17
19 8 0.33
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATCATAATATAAAATATA
Found at i:52323250 original size:28 final size:28
Alignment explanation
Indices: 52323218--52323282 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
52323208 ATTTACTAGA
* *
52323218 ATACCCCTTTGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
52323246 ATACCCCTATGTGTGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
52323274 ATACCCCTA
1 ATACCCCTA
52323283 GGGTTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:52323928 original size:19 final size:19
Alignment explanation
Indices: 52323904--52323942 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
52323894 TTTTAATTAT
* *
52323904 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
52323923 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
52323942 T
1 T
52323943 ATGAAGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:52337519 original size:76 final size:76
Alignment explanation
Indices: 52337433--52337586 Score: 272
Period size: 76 Copynumber: 2.0 Consensus size: 76
52337423 GTAGAGTCTG
* *
52337433 ATTCAGAGTTGATAACGATGATTTCTTGAGATTTTGAGATCAAATTTGTATTCTAAGAAATCCAG
1 ATTCAGAGTTGATAAAGATGATTTCTTGAGATTTTGAGATCAAATTTGTATTCCAAGAAATCCAG
52337498 AGTTAATTCAA
66 AGTTAATTCAA
* *
52337509 ATTCAGAGTTGATAAAGATGATTTCTTGAGATTTTGAGATCGAATTTGTATTCCGAGAAATCCAG
1 ATTCAGAGTTGATAAAGATGATTTCTTGAGATTTTGAGATCAAATTTGTATTCCAAGAAATCCAG
52337574 AGTTAATTCAA
66 AGTTAATTCAA
52337585 AT
1 AT
52337587 GATTCTAGGT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.36
Consensus pattern (76 bp):
ATTCAGAGTTGATAAAGATGATTTCTTGAGATTTTGAGATCAAATTTGTATTCCAAGAAATCCAG
AGTTAATTCAA
Found at i:52342141 original size:29 final size:28
Alignment explanation
Indices: 52342053--52342167 Score: 113
Period size: 29 Copynumber: 4.0 Consensus size: 28
52342043 TTCATGTATC
* * *
52342053 TGGCCCATTAAGCCCAATCATATTCATA
1 TGGCCCATTAGGCCCAATCACATTTATA
* * *
52342081 TGGCCCATTAGGCTCAAATCACCTGTATA
1 TGGCCCATTAGGC-CCAATCACATTTATA
*
52342110 TGGCCCATTAGGCCCAAATCACATTTAAA
1 TGGCCCATTAGGCCC-AATCACATTTATA
* * * *
52342139 TGGACCGTTAGGCCCAGTCACATTCATA
1 TGGCCCATTAGGCCCAATCACATTTATA
52342167 T
1 T
52342168 TCATGCTCAC
Statistics
Matches: 70, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
28 24 0.34
29 46 0.66
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.27
Consensus pattern (28 bp):
TGGCCCATTAGGCCCAATCACATTTATA
Found at i:52346634 original size:29 final size:29
Alignment explanation
Indices: 52346577--52346676 Score: 121
Period size: 29 Copynumber: 3.5 Consensus size: 29
52346567 TACCTATATT
* * *
52346577 TGGCCCATTAAGCCC-AATCATATTTATA
1 TGGCCCATTAGGCCCAAATCACATGTATA
* * *
52346605 TGGCTCATTAGGCCCGAATCACCTGTATA
1 TGGCCCATTAGGCCCAAATCACATGTATA
*
52346634 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATGTATA
*
52346663 TGGCCCGTTAGGCC
1 TGGCCCATTAGGCC
52346677 TAGTCACATT
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
28 13 0.21
29 48 0.79
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATGTATA
Found at i:52346641 original size:57 final size:58
Alignment explanation
Indices: 52346568--52346676 Score: 157
Period size: 58 Copynumber: 1.9 Consensus size: 58
52346558 AGATTCACAT
* * *
52346568 ACCTATATTTGGCCCATTAAGCCC-AATCATATTTATATGGCTCATTAGGCCCGAATC
1 ACCTATATATGGCCCATTAAGCCCAAATCACATTTATATGGCCCATTAGGCCCGAATC
* * *
52346625 ACCTGTATATGGCCCATTAGGCCCAAATCACATTTATATGGCCCGTTAGGCC
1 ACCTATATATGGCCCATTAAGCCCAAATCACATTTATATGGCCCATTAGGCC
52346677 TAGTCACATT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
57 21 0.47
58 24 0.53
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.29
Consensus pattern (58 bp):
ACCTATATATGGCCCATTAAGCCCAAATCACATTTATATGGCCCATTAGGCCCGAATC
Found at i:52347669 original size:40 final size:40
Alignment explanation
Indices: 52347645--52347807 Score: 245
Period size: 40 Copynumber: 4.1 Consensus size: 40
52347635 AGCCCAGATG
*
52347645 TAACAACCAGCACAAATGCCTTCGAGACTTAACCCGGAAA
1 TAACAACCAGCACGAATGCCTTCGAGACTTAACCCGGAAA
* * *
52347685 TAGCAACCAGCATGAATGCCTTCGGGACTTAACCCGGAAA
1 TAACAACCAGCACGAATGCCTTCGAGACTTAACCCGGAAA
* *
52347725 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGAAAA
1 TAACAACCAGCACGAATGCCTTCGAGACTTAACCCGGAAA
* * *
52347765 TAACAACCAGCATGAATGCCTTCGGGACTTAACCCGGATA
1 TAACAACCAGCACGAATGCCTTCGAGACTTAACCCGGAAA
52347805 TAA
1 TAA
52347808 TCCTTAATTG
Statistics
Matches: 113, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 113 1.00
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.17
Consensus pattern (40 bp):
TAACAACCAGCACGAATGCCTTCGAGACTTAACCCGGAAA
Found at i:52347778 original size:80 final size:80
Alignment explanation
Indices: 52347645--52347807 Score: 281
Period size: 80 Copynumber: 2.0 Consensus size: 80
52347635 AGCCCAGATG
* *
52347645 TAACAACCAGCACAAATGCCTTCGAGACTTAACCCGGAAATAGCAACCAGCATGAATGCCTTCGG
1 TAACAACCAGCACAAATGCCTTCGAGACTTAACCCGAAAATAACAACCAGCATGAATGCCTTCGG
52347710 GACTTAACCCGGAAA
66 GACTTAACCCGGAAA
* *
52347725 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGAAAATAACAACCAGCATGAATGCCTTCGG
1 TAACAACCAGCACAAATGCCTTCGAGACTTAACCCGAAAATAACAACCAGCATGAATGCCTTCGG
*
52347790 GACTTAACCCGGATA
66 GACTTAACCCGGAAA
52347805 TAA
1 TAA
52347808 TCCTTAATTG
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.17
Consensus pattern (80 bp):
TAACAACCAGCACAAATGCCTTCGAGACTTAACCCGAAAATAACAACCAGCATGAATGCCTTCGG
GACTTAACCCGGAAA
Found at i:52350140 original size:24 final size:24
Alignment explanation
Indices: 52350111--52350161 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
52350101 GTACCCAAAC
* *
52350111 TTTCGGCTTTTCGGCATTTCAACT
1 TTTCGGCATTTCGACATTTCAACT
*
52350135 TTTCGGCATTTCGACATTTCAGCT
1 TTTCGGCATTTCGACATTTCAACT
52350159 TTT
1 TTT
52350162 GCTGATTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.14, C:0.24, G:0.16, T:0.47
Consensus pattern (24 bp):
TTTCGGCATTTCGACATTTCAACT
Found at i:52350154 original size:16 final size:16
Alignment explanation
Indices: 52350119--52350154 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
52350109 ACTTTCGGCT
*
52350119 TTTCGGCATTTCAACT
1 TTTCGGCATTTCAACA
*
52350135 TTTCGGCATTTCGACA
1 TTTCGGCATTTCAACA
52350151 TTTC
1 TTTC
52350155 AGCTTTTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.25, G:0.14, T:0.44
Consensus pattern (16 bp):
TTTCGGCATTTCAACA
Found at i:52355229 original size:43 final size:43
Alignment explanation
Indices: 52355180--52355270 Score: 105
Period size: 42 Copynumber: 2.1 Consensus size: 43
52355170 TCTTATATGT
52355180 AATCAAATATCGATACC-ACTGTACCAAACAAGGTCTTACACG-A
1 AATCAAATA-CGATACCGA-TGTACCAAACAAGGTCTTACACGTA
* * * * *
52355223 AATCAAATACGATGCCGATGTCCCAGATATGGTCTTACACGTA
1 AATCAAATACGATACCGATGTACCAAACAAGGTCTTACACGTA
52355266 AATCA
1 AATCA
52355271 TAAATCAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
42 25 0.61
43 16 0.39
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.23
Consensus pattern (43 bp):
AATCAAATACGATACCGATGTACCAAACAAGGTCTTACACGTA
Found at i:52355291 original size:44 final size:42
Alignment explanation
Indices: 52355145--52355310 Score: 138
Period size: 43 Copynumber: 3.9 Consensus size: 42
52355135 AAAAAGCTCG
* * * *
52355145 TACAATGCCAACGTCCCAGACCTGGTCTTATATGTAATCAAA
1 TACAATGCCAACGTCCCAGACATGGTCTTACACGAAATCAAA
* * * * *
52355187 TATCGATACC-ACTGTACCAAACAAGGTCTTACACGAAATCAAA
1 TA-CAATGCCAAC-GTCCCAGACATGGTCTTACACGAAATCAAA
* * * *
52355230 TACGATGCCGATGTCCCAGATATGGTCTTACACGTAAATCATAA
1 TACAATGCCAACGTCCCAGACATGGTCTTACACG-AAATCA-AA
* *
52355274 -ATCAATGCCAACGTCCCAGACGTGATCTTACACGAAA
1 TA-CAATGCCAACGTCCCAGACATGGTCTTACACGAAA
52355311 ACACATATCG
Statistics
Matches: 97, Mismatches: 21, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
42 28 0.29
43 41 0.42
44 28 0.29
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (42 bp):
TACAATGCCAACGTCCCAGACATGGTCTTACACGAAATCAAA
Found at i:52363360 original size:20 final size:20
Alignment explanation
Indices: 52363335--52363380 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
52363325 GAAACATTGC
*
52363335 ACACGCCCGTGTGCTTTGGG
1 ACACGCCCATGTGCTTTGGG
52363355 ACACGCCCATGTGCTTTGGG
1 ACACGCCCATGTGCTTTGGG
52363375 ACACGC
1 ACACGC
52363381 ATGTGTCCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.33, G:0.30, T:0.22
Consensus pattern (20 bp):
ACACGCCCATGTGCTTTGGG
Found at i:52363385 original size:18 final size:19
Alignment explanation
Indices: 52363344--52363385 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
52363334 CACACGCCCG
52363344 TGTGCTTTGGGACACGCCCA
1 TGTGCTTTGGGACACG-CCA
52363364 TGTGCTTTGGGACACG-CA
1 TGTGCTTTGGGACACGCCA
52363382 TGTG
1 TGTG
52363386 TCCCCTACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 6 0.27
20 16 0.73
ACGTcount: A:0.14, C:0.24, G:0.33, T:0.29
Consensus pattern (19 bp):
TGTGCTTTGGGACACGCCA
Found at i:52385073 original size:21 final size:21
Alignment explanation
Indices: 52385047--52385089 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
52385037 TTTCCATCCT
52385047 TTGTAGTCCCGCCAAGCTAGC
1 TTGTAGTCCCGCCAAGCTAGC
*
52385068 TTGTAGTTCCGCCAAGCTAGC
1 TTGTAGTCCCGCCAAGCTAGC
52385089 T
1 T
52385090 CGGGGATCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.30, G:0.23, T:0.28
Consensus pattern (21 bp):
TTGTAGTCCCGCCAAGCTAGC
Found at i:52389063 original size:12 final size:12
Alignment explanation
Indices: 52389046--52389072 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
52389036 ATTCCGAAGT
52389046 ATATATATATAC
1 ATATATATATAC
52389058 ATATATATATAC
1 ATATATATATAC
52389070 ATA
1 ATA
52389073 AGTATGCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:52389603 original size:27 final size:28
Alignment explanation
Indices: 52389519--52389613 Score: 129
Period size: 28 Copynumber: 3.4 Consensus size: 28
52389509 CATGAGATTG
* * * *
52389519 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
52389548 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
52389576 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
52389603 GCACTGAGTGT
1 GCACTAAGTGT
52389614 ACGGACTTAA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 21 0.34
28 22 0.36
29 18 0.30
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:52389627 original size:27 final size:27
Alignment explanation
Indices: 52389547--52389629 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
52389537 TAAATTGTAC
* * *
52389547 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTACGA-CTTGAATATAT
* * *
52389575 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTACGACTTGAATATAT
*
52389602 AGCACTGAGTGTACGGACTT-AATATAT
1 AGCACTAAGTGTAC-GACTTGAATATAT
52389629 A
1 A
52389630 CTTTTGAATC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
27 29 0.59
28 20 0.41
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTACGACTTGAATATAT
Found at i:52393681 original size:46 final size:47
Alignment explanation
Indices: 52393630--52393724 Score: 174
Period size: 46 Copynumber: 2.0 Consensus size: 47
52393620 TTAAAGAAGA
52393630 GAAAATTTTCATTTTTCACACCATAAAT-AGTCTTTTCTAGTTTTGT
1 GAAAATTTTCATTTTTCACACCATAAATAAGTCTTTTCTAGTTTTGT
52393676 GAAAATTTTCATTTTTCACACCATAAATAAAGTCTTTTCTAGTTTTGT
1 GAAAATTTTCATTTTTCACACCATAAAT-AAGTCTTTTCTAGTTTTGT
52393724 G
1 G
52393725 TTTTGATTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 28 0.60
48 19 0.40
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.46
Consensus pattern (47 bp):
GAAAATTTTCATTTTTCACACCATAAATAAGTCTTTTCTAGTTTTGT
Found at i:52396507 original size:27 final size:26
Alignment explanation
Indices: 52396463--52396514 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
52396453 CTTGCTGCAA
*
52396463 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
52396490 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
52396515 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:52396578 original size:67 final size:67
Alignment explanation
Indices: 52396444--52396581 Score: 188
Period size: 67 Copynumber: 2.1 Consensus size: 67
52396434 GAGGAAGCGT
* * * * *
52396444 TCTGGCAGCCTTGCTGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATATATGTTCTGGTGACCTAGTCAAAA
52396509 TA
66 TA
* * *
52396511 TCTGGCAGCCTCGCTGCAATCTGGTGGCTTCGCCACATATATATGTTCTTGTGGCCTAG-CTAAA
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATATATGTTCTGGTGACCTAGTC-AAA
52396575 ATA
65 ATA
52396578 TCTG
1 TCTG
52396582 TATCTGGTGA
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 1 0.02
67 61 0.98
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.32
Consensus pattern (67 bp):
TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATATATGTTCTGGTGACCTAGTCAAAA
TA
Found at i:52403737 original size:33 final size:32
Alignment explanation
Indices: 52403688--52403751 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
52403678 CTCGCTGCAA
* *
52403688 TCTAGTGGCTTCGCCACATATATATATATCTGT
1 TCTAGTGGCCTAGCCACA-ATATATATATCTGT
* *
52403721 TCTAGTGGCCTAGCCACAATATCTGTATCTG
1 TCTAGTGGCCTAGCCACAATATATATATCTG
52403752 GTGACTTTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.36
Consensus pattern (32 bp):
TCTAGTGGCCTAGCCACAATATATATATCTGT
Found at i:52404623 original size:22 final size:20
Alignment explanation
Indices: 52404593--52404638 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
52404583 TGAAATTTTA
52404593 ATTAGTATTATGAGATAAAATT
1 ATTAGTATTATGAGA-AAAA-T
* *
52404615 ATTATTATTATTAGAAAAAT
1 ATTAGTATTATGAGAAAAAT
52404635 ATTA
1 ATTA
52404639 CTGTATGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 4 0.18
22 13 0.59
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (20 bp):
ATTAGTATTATGAGAAAAAT
Found at i:52409774 original size:27 final size:27
Alignment explanation
Indices: 52409743--52409794 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
52409733 ACAAGTGAGG
52409743 AAAAAGAAAAAGAGAATGAAAAAGAGC
1 AAAAAGAAAAAGAGAATGAAAAAGAGC
* ** *
52409770 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAAGAGAATGAAAAAGA
52409795 ATGTGAAACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAATGAAAAAGAGC
Found at i:52412245 original size:31 final size:31
Alignment explanation
Indices: 52412204--52412299 Score: 156
Period size: 31 Copynumber: 3.1 Consensus size: 31
52412194 GGCTGTTACA
52412204 TACCTGATCAGTGAAAAGTGGTAGCTCCGGC
1 TACCTGATCAGTGAAAAGTGGTAGCTCCGGC
* *
52412235 TACCTAATCAGTGAAAAATGGTAGCTCCGGC
1 TACCTGATCAGTGAAAAGTGGTAGCTCCGGC
* *
52412266 TACCTGATCAGTGAATAGTGGTAGCTTCGGC
1 TACCTGATCAGTGAAAAGTGGTAGCTCCGGC
52412297 TAC
1 TAC
52412300 AAGTGACAAG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (31 bp):
TACCTGATCAGTGAAAAGTGGTAGCTCCGGC
Found at i:52412394 original size:47 final size:48
Alignment explanation
Indices: 52412324--52412449 Score: 170
Period size: 47 Copynumber: 2.7 Consensus size: 48
52412314 AAGTGATTTC
*
52412324 CGTATAAGACCATATCTGGGATATGGCATCGATGTGATATATG-GTACT
1 CGTATAAGACCATATCTGGGATATGGCATCGATGTGAGATATGTG-ACT
*
52412372 -GTATAAGACCATATCTGGGATATGGCATC-A-GTGAGATATGTGATT
1 CGTATAAGACCATATCTGGGATATGGCATCGATGTGAGATATGTGACT
* * *
52412417 CGTGTAAGACCATAGCTGGGCTATGGCATCGAT
1 CGTATAAGACCATATCTGGGATATGGCATCGAT
52412450 ATATGAATAT
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
45 11 0.16
46 28 0.41
47 30 0.43
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (48 bp):
CGTATAAGACCATATCTGGGATATGGCATCGATGTGAGATATGTGACT
Found at i:52412526 original size:42 final size:42
Alignment explanation
Indices: 52412418--52412532 Score: 144
Period size: 42 Copynumber: 2.7 Consensus size: 42
52412408 TATGTGATTC
*
52412418 GTGTAAGACCATAGCTGGGCTATGGCATCGATATATGAATAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATATATGAAGAT
* * *
52412460 GTGTAAGACCATAGCAGGGCTATGGCAT-TATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGA-TATATGAAGAT
* *
52412502 GTGTAAGACCATAGTTGAAG-TATGGCATCGA
1 GTGTAAGACCATAGCTG-GGCTATGGCATCGA
52412533 GAAAACGAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
41 1 0.02
42 59 0.95
43 2 0.03
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (42 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCGATATATGAAGAT
Found at i:52416964 original size:50 final size:50
Alignment explanation
Indices: 52416860--52416985 Score: 175
Period size: 50 Copynumber: 2.5 Consensus size: 50
52416850 CCATGGCAAC
* *
52416860 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGAAAAGTGA
1 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGACCAAGGAAAAGTGA
*
52416910 AAGTGATAAGTGATAGCTTC-GCTACACTTATCTGACCAATGACAAA-TGA
1 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGACCAAGGA-AAAGTGA
* *
52416959 GAAGTGAAAAGTGGTAGCTTCAGCTAC
1 -AAGTGATAAGTGATAGCTTCAGCTAC
52416986 TTGATCAGTG
Statistics
Matches: 69, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
49 23 0.33
50 41 0.59
51 5 0.07
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGACCAAGGAAAAGTGA
Found at i:52416999 original size:31 final size:31
Alignment explanation
Indices: 52416961--52417140 Score: 238
Period size: 31 Copynumber: 5.8 Consensus size: 31
52416951 ACAAATGAGA
* *
52416961 AGTGAAAAGTGGTAGCTTCAGCTACTTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
52416992 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
52417023 AGTGAAAAGTAGTAG-TTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTT-CGGCTACCTGATC
* *
52417054 AGTGAAAAGTTGTAG-TTGCGGCTACCTAATC
1 AGTGAAAAGTGGTAGCTT-CGGCTACCTGATC
* *
52417085 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
52417116 AATGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
52417141 AAGTGACAAG
Statistics
Matches: 132, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
30 2 0.02
31 129 0.98
32 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:52417233 original size:47 final size:47
Alignment explanation
Indices: 52417164--52417287 Score: 151
Period size: 47 Copynumber: 2.7 Consensus size: 47
52417154 CAAGTGATTT
* * * *
52417164 CTGTATAAGACAATATCTGGGATATGGCATCGGTGTGATATATGCTA
1 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* *
52417211 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATT
1 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* * * *
52417258 C-GTGTAAGACCATAACTGAGCTATGGCATC
1 CTGTATAAGACCATATCTGGGATATGGCATC
52417288 TGTAATGCCC
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
46 25 0.37
47 42 0.63
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (47 bp):
CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
Found at i:52418715 original size:40 final size:40
Alignment explanation
Indices: 52418641--52418742 Score: 147
Period size: 40 Copynumber: 2.6 Consensus size: 40
52418631 AACCCAAGTA
*
52418641 CCTTCGGGAT-TTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGG-TCTTAGCCCGGATATAGCAACTAGCACAAATG
52418680 CCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATG
1 CCTTCGGGTCTTAGCCCGGATATAG-CAACTAGCACAAATG
*
52418720 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGTCTTAGCCCGGATAT
52418743 CATTCGAATA
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
38 1 0.02
39 12 0.21
40 44 0.76
41 1 0.02
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CCTTCGGGTCTTAGCCCGGATATAGCAACTAGCACAAATG
Done.