Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001547.1 Hibiscus syriacus cultivar Beakdansim tig00003041_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10425128
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 51
Found at i:376298 original size:235 final size:235
Alignment explanation
Indices: 375821--376399 Score: 758
Period size: 235 Copynumber: 2.5 Consensus size: 235
375811 AAAATTTACT
* * *
375821 TTGATGGATTTGAGTAAAA-GTTCGAACAAATTCTTCTCATTATGAACTCCTTCCCCCTCTTCCG
1 TTGATGGATTTGAGTAAAAGGTT-GAACAAATTCTTCTCATTATGAACTTCTTCTCCCTCTTCAG
* * * * *
375885 ATGAGTCCTTTTCCTTATGAACTTTCCATTGAAAATGACGTTCCACCTTCTTCTGTGATGGATTT
65 ATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGACGATCCACCTTCTTCTGTGATGGATTT
* * *
375950 AAGTAAAATGTCGAACAAATTCTTCTCATTATGAATTTTTTCCCCTCATCGAACGAGTCATTCTC
130 AAGTAAAAGGTCGAACAAATTCTTCTCATTATGAATTCTTTCCCCTCATCGAACGAGTCATCCTC
* * * *
376015 ATTATGAACTCTCCATTTAAAATGTCGATCTACCTCCTTCA
195 ATTATGAACTCTCCAATGAAAATGTCGATCCACCTCATTCA
** * * *
376056 TTGATGGATTTCTGTAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTCACTCTTCGGA
1 TTGATGGATTTGAGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTCTTCAGA
*
376121 TGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGATGATCCACC-TCATTCTGTGAT-GATTT
66 TGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGACGATCCACCTTC-TTCTGTGATGGATTT
* * * * * *
376184 GAGTAAAAGGTCGAACAAGTTCTTCTTATTATGAACTTCTTTCTCCCTCTTCGGATGAGTTC-TC
130 AAGTAAAAGGTCGAACAAATTCTTCTCATTATGAA-TTCTTTC-CCCTCATCGAACGAG-TCATC
376248 CTCATTATGAACTCTCCAATGAAAATGAT-GATCCA-CTCATTC-
192 CTCATTATGAACTCTCCAATGAAAATG-TCGATCCACCTCATTCA
*
376290 TGTGATGGATTTGAGTAAAAGGTCGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTCTTCAG
1 T-TGATGGATTTGAGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTCTTCAG
* * **
376355 ATGAATTTTTCTCATTACAAACTCTCCATTGAAAATGACGATCCA
65 ATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGACGATCCA
376400 TGTAAAATCC
Statistics
Matches: 300, Mismatches: 37, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
234 39 0.13
235 212 0.71
236 46 0.15
237 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.37
Consensus pattern (235 bp):
TTGATGGATTTGAGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTCTTCAGA
TGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGACGATCCACCTTCTTCTGTGATGGATTTA
AGTAAAAGGTCGAACAAATTCTTCTCATTATGAATTCTTTCCCCTCATCGAACGAGTCATCCTCA
TTATGAACTCTCCAATGAAAATGTCGATCCACCTCATTCA
Found at i:377736 original size:22 final size:22
Alignment explanation
Indices: 377711--377779 Score: 120
Period size: 22 Copynumber: 3.1 Consensus size: 22
377701 GAGTCGAGGG
377711 ATATACAGTGGTCATTCGGGAC
1 ATATACAGTGGTCATTCGGGAC
*
377733 ATATATAGTGGTCATTCGGGAC
1 ATATACAGTGGTCATTCGGGAC
*
377755 ATATACAGTGGTCCTTCGGGAC
1 ATATACAGTGGTCATTCGGGAC
377777 ATA
1 ATA
377780 GTGGTCCTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (22 bp):
ATATACAGTGGTCATTCGGGAC
Found at i:377784 original size:18 final size:19
Alignment explanation
Indices: 377717--377788 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 19
377707 AGGGATATAC
*
377717 AGTGGTCATTCGGGACATATAT
1 AGTGGTCCTTCGGGAC--A-AT
*
377739 AGTGGTCATTCGGGACATAT
1 AGTGGTCCTTCGGGACA-AT
377759 ACAGTGGTCCTTCGGGAC-AT
1 --AGTGGTCCTTCGGGACAAT
377779 AGTGGTCCTT
1 AGTGGTCCTT
377789 TGGAACAAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
18 10 0.21
20 6 0.13
22 31 0.66
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (19 bp):
AGTGGTCCTTCGGGACAAT
Found at i:380270 original size:117 final size:118
Alignment explanation
Indices: 380041--380582 Score: 695
Period size: 117 Copynumber: 4.6 Consensus size: 118
380031 GGGTGTTACA
* * * * *
380041 ATCCACCTCCTTCTGTGATGGATTTGAGTAAAAAGTCGAACAAGCTCTTCTCATTATAAACTTAT
1 ATCCACCTCATTCTGTGATGGATTTGAGTAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCT
* *
380106 TCTCCCT-TCTCGGACGAGTCCTTCTCATTATGAACTCTCCATTGAAAATTAAG
66 TCTCCCTCT-TCGGACGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGAAG
* * * *
380159 ATCCACCTCATTCTATGATGAATTTAAGTAAAAGGTCGAACAAGTTCTTCTCA-TAAGAACTTCT
1 ATCCACCTCATTCTGTGATGGATTTGAGTAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCT
* * * * *
380223 TCTCTCTCTTCAGACGAGTTCTTTTCATTATGACCTCTTCATTGAAAATGACA-
66 TCTCCCTCTTCGGACGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGA-AG
* *
380276 ATCCACCTCATTCTGTGATGGATTTGAGTAAAAGGTCGAACAAATTCTTCTCATTATGAACTTTT
1 ATCCACCTCATTCTGTGATGGATTTGAGTAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCT
* * *
380341 TCTCCCTCATCGGACGAGTTCTTCTCATTATGAAATCTCCATTGAAAATGAGG
66 TCTCCCTCTTCGGACGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGAAG
** * *
380394 ATCCACCAT-ATTCTGTGATAAATTTGAGTAAAA-ATCGAACAAATTCTTCTCATTATGAACTTC
1 ATCCACC-TCATTCTGTGATGGATTTGAGTAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTC
* * * ** * *
380457 TTTTCCCTCGTCGAACGAGTTCTTCTCATTATGAACTCTTAATTGAATATGATG
65 TTCTCCCTCTTCGGACGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGAAG
* *
380511 ATCCACCTC---CTGTGATGGATTTGAGTAAAAGGTCGAATAAGTTATTCTCATTATGAACTTCT
1 ATCCACCTCATTCTGTGATGGATTTGAGTAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCT
380573 TCTCCCTCTT
66 TCTCCCTCTT
380583 TTGTGACGTA
Statistics
Matches: 367, Mismatches: 50, Indels: 17
0.85 0.12 0.04
Matches are distributed among these distances:
114 19 0.05
115 35 0.10
116 1 0.00
117 180 0.49
118 131 0.36
119 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.36
Consensus pattern (118 bp):
ATCCACCTCATTCTGTGATGGATTTGAGTAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCT
TCTCCCTCTTCGGACGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGAAG
Found at i:380456 original size:235 final size:233
Alignment explanation
Indices: 380038--380581 Score: 747
Period size: 235 Copynumber: 2.3 Consensus size: 233
380028 TTGGGGTGTT
* * *
380038 ACAATCCACCTCCTTCTGTGATGGATTTGAGTAAAAAGTCGAACAAGCTCTTCTCATTATAAACT
1 ACAATCCACCT-CTTCTGTGATGGATTTGAGTAAAAGGTCGAACAAGTTCTTCTCATTATGAACT
* *
380103 TATTCTCCCTTCTCGGACGAGTCCTTCTCATTATGAACTCTCCATTGAAAATTAAGATCCACCTC
65 TATTCTCCC-TCTCGGACGAGTCCTTCTCATTATGAAATCTCCATTGAAAATGAAGATCCACCTC
* * * * *
380168 ATTCTATGATGAATTTAAGTAAAAGGTCGAACAAGTTCTTCTCATAAGAACTTCTTCTCTCTCTT
129 ATTCTATGATAAATTTAAGTAAAAGATCGAACAAATTCTTCTCATAAGAACTTCTTCTCCCTCGT
* * *
380233 C-AGACGAGTTCTTTTCATTATGACCTCTTCATTGAAAATG
194 CGA-ACGAGTTCTTCTCATTATGAACTCTTAATTGAAAATG
*
380273 ACAATCCACCTCATTCTGTGATGGATTTGAGTAAAAGGTCGAACAAATTCTTCTCATTATGAACT
1 ACAATCCACCTC-TTCTGTGATGGATTTGAGTAAAAGGTCGAACAAGTTCTTCTCATTATGAACT
* * *
380338 TTTTCTCCCTCATCGGACGAGTTCTTCTCATTATGAAATCTCCATTGAAAATGAGGATCCACCAT
65 TATTCTCCCTC-TCGGACGAGTCCTTCTCATTATGAAATCTCCATTGAAAATGAAGATCCACC-T
* * * *
380403 -ATTCTGTGATAAATTTGAGTAAAA-ATCGAACAAATTCTTCTCATTATGAACTTCTTTTCCCTC
128 CATTCTATGATAAATTTAAGTAAAAGATCGAACAAATTCTTCTCA-TAAGAACTTCTTCTCCCTC
*
380466 GTCGAACGAGTTCTTCTCATTATGAACTCTTAATTGAATATG
192 GTCGAACGAGTTCTTCTCATTATGAACTCTTAATTGAAAATG
** * *
380508 ATGATCCACCTC--CTGTGATGGATTTGAGTAAAAGGTCGAATAAGTTATTCTCATTATGAACTT
1 ACAATCCACCTCTTCTGTGATGGATTTGAGTAAAAGGTCGAACAAGTTCTTCTCATTATGAACTT
*
380571 CTTCTCCCTCT
66 ATTCTCCCTCT
380582 TTTGTGACGT
Statistics
Matches: 276, Mismatches: 28, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
231 1 0.00
232 57 0.21
234 20 0.07
235 196 0.71
236 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (233 bp):
ACAATCCACCTCTTCTGTGATGGATTTGAGTAAAAGGTCGAACAAGTTCTTCTCATTATGAACTT
ATTCTCCCTCTCGGACGAGTCCTTCTCATTATGAAATCTCCATTGAAAATGAAGATCCACCTCAT
TCTATGATAAATTTAAGTAAAAGATCGAACAAATTCTTCTCATAAGAACTTCTTCTCCCTCGTCG
AACGAGTTCTTCTCATTATGAACTCTTAATTGAAAATG
Found at i:380607 original size:63 final size:62
Alignment explanation
Indices: 380529--380646 Score: 173
Period size: 63 Copynumber: 1.9 Consensus size: 62
380519 CCTGTGATGG
* * * *
380529 ATTTGAGTAAAAGGTCGAATAAGTTATTCTCATTATGAACTTCTTCTCCCTCTTTTGTGACGT
1 ATTTAAGTAAAAGGTCAAACAAATTATTCTCATTATGAACTTCTTCTCCCT-TTTTGTGACGT
* *
380592 ATTTAAGTAAAAGGTCAAACAAATTCTTCTCATTATGAGCTTCTTCTCCCTTTTT
1 ATTTAAGTAAAAGGTCAAACAAATTATTCTCATTATGAACTTCTTCTCCCTTTTT
380647 AGACAAGTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
62 4 0.08
63 45 0.92
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.42
Consensus pattern (62 bp):
ATTTAAGTAAAAGGTCAAACAAATTATTCTCATTATGAACTTCTTCTCCCTTTTTGTGACGT
Found at i:380805 original size:118 final size:119
Alignment explanation
Indices: 380592--381069 Score: 604
Period size: 118 Copynumber: 4.1 Consensus size: 119
380582 TTTGTGACGT
* * * * *
380592 ATTTAAGTAAAAGGTCAAACAAATTCTTCTCATTATGAGCTTCTTCTCCCT-TTTTAGACAAGTT
1 ATTTGAGTAAAAGGTCGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTCTTTCAGACGAGTT
* * * * *
380656 CTTCTCTTTACGAACTCTCCATTGAAAATGATGATCCACCTCATTATGTTATGG
66 CTTCTCATTACGAACTCTCCATTGAAAATGACGATCCACCTCATTCTATGATGG
* * * *
380710 ATTTGAGTAAAAGGTCGAGCAAATTCTTCTCATTATGAACTTCTTCTCCCTCATT-GGATGAGTT
1 ATTTGAGTAAAAGGTCGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTCTTTCAGACGAGTT
* * * * *
380774 CTTCTCATTACAAACTCTCTATTGAATATGATGATCCACCTCTTTCTATGATGG
66 CTTCTCATTACGAACTCTCCATTGAAAATGACGATCCACCTCATTCTATGATGG
* * *
380828 ATTTGAGTAAAATGTCGAACAAATTCTTCTCATTATGAATTTCTTCTCCCT-TTTCAGACGAGTC
1 ATTTGAGTAAAAGGTCGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTCTTTCAGACGAGTT
* * ** *
380892 CTTCTTATTATGAACTCTCCATTGAAAATGACGATTTACCTCCTTCTATGATGG
66 CTTCTCATTACGAACTCTCCATTGAAAATGACGATCCACCTCATTCTATGATGG
* ** * * *
380946 ATTTGAGTAAAAGTTTTAACAAATGCTTCTCATTATGAACTTATTCTCCCTC-TTCGGACGAGTT
1 ATTTGAGTAAAAGGTCGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTCTTTCAGACGAGTT
* * *
381010 CTTCTCATTATGAACTCTCCATTGAAAATGACAATCCACCTCATTCTGTGATGG
66 CTTCTCATTACGAACTCTCCATTGAAAATGACGATCCACCTCATTCTATGATGG
381064 ATTTGA
1 ATTTGA
381070 ATTTCAAAGT
Statistics
Matches: 310, Mismatches: 47, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
117 2 0.01
118 306 0.99
119 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (119 bp):
ATTTGAGTAAAAGGTCGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTCTTTCAGACGAGTT
CTTCTCATTACGAACTCTCCATTGAAAATGACGATCCACCTCATTCTATGATGG
Found at i:382829 original size:21 final size:21
Alignment explanation
Indices: 382803--382966 Score: 80
Period size: 21 Copynumber: 8.0 Consensus size: 21
382793 CCTCATTCCA
382803 ATTTTCTTTTCTCTCTTTTTT
1 ATTTTCTTTTCTCTCTTTTTT
* *
382824 ATTTTCATTTC-CTTCATTTTT
1 ATTTTCTTTTCTC-TCTTTTTT
* *
382845 CTCTCTCTTTTCTCT-TTTTTCT
1 AT-TTTCTTTTCTCTCTTTTT-T
* * * *
382867 CATTTT-TCTTCATTTCTTATTC
1 -ATTTTCTTTTC-TCTCTTTTTT
*
382889 ATTTTCTTTTCTTTCTTTTTCT
1 ATTTTCTTTTCTCTCTTTTT-T
382911 -TTTTCTTTT-TCT-TTTTTT
1 ATTTTCTTTTCTCTCTTTTTT
*
382929 -TTCTT-TTTT-TTTCTTTTTT
1 ATT-TTCTTTTCTCTCTTTTTT
* *
382948 CTTTT-TTTT-TCTATTTTTT
1 ATTTTCTTTTCTCTCTTTTTT
382967 CTCTCTCTCT
Statistics
Matches: 112, Mismatches: 19, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
18 9 0.08
19 27 0.24
20 5 0.04
21 48 0.43
22 17 0.15
23 6 0.05
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.76
Consensus pattern (21 bp):
ATTTTCTTTTCTCTCTTTTTT
Found at i:382855 original size:11 final size:9
Alignment explanation
Indices: 382840--382970 Score: 67
Period size: 9 Copynumber: 14.1 Consensus size: 9
382830 ATTTCCTTCA
382840 TTTTTCTCTC
1 TTTTT-TCTC
*
382850 TCTTTTCTC
1 TTTTTTCTC
382859 TTTTTTCTC
1 TTTTTTCTC
*
382868 ATTTTTCTTC
1 TTTTTTC-TC
382878 ATTTCTTAT-TC
1 -TTT-TT-TCTC
*
382889 ATTTTCTTTTC
1 -TTTT-TTCTC
*
382900 TTTCTTTTTC
1 TTT-TTTCTC
382910 -TTTTTCT-
1 TTTTTTCTC
382917 TTTTCTT-T-
1 TTTT-TTCTC
382925 TTTTTTCT-
1 TTTTTTCTC
*
382933 TTTTTTTTC
1 TTTTTTCTC
*
382942 TTTTTTCTTT
1 TTTTTTC-TC
*
382952 TTTTTTCTA
1 TTTTTTCTC
382961 TTTTTTCTC
1 TTTTTTCTC
382970 T
1 T
382971 CTCTCTTCAA
Statistics
Matches: 99, Mismatches: 10, Indels: 25
0.74 0.07 0.19
Matches are distributed among these distances:
7 2 0.02
8 20 0.20
9 38 0.38
10 24 0.24
11 12 0.12
12 2 0.02
13 1 0.01
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTTCTC
Found at i:382910 original size:10 final size:10
Alignment explanation
Indices: 382891--382968 Score: 74
Period size: 10 Copynumber: 8.1 Consensus size: 10
382881 TCTTATTCAT
382891 TTTC-TTTTC
1 TTTCTTTTTC
382900 TTTCTTTTTC
1 TTTCTTTTTC
*
382910 TTT-TTCTT-
1 TTTCTTTTTC
*
382918 TTTCTTTTTT
1 TTTCTTTTTC
*
382928 TTTCTTTTTT
1 TTTCTTTTTC
382938 TTTCTTTTTTC
1 TTTC-TTTTTC
*
382949 TTTTTTTTTC
1 TTTCTTTTTC
*
382959 TAT-TTTTTC
1 TTTCTTTTTC
382968 T
1 T
382969 CTCTCTCTTC
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
8 3 0.05
9 19 0.32
10 30 0.50
11 8 0.13
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:382911 original size:6 final size:6
Alignment explanation
Indices: 382869--382957 Score: 77
Period size: 6 Copynumber: 15.7 Consensus size: 6
382859 TTTTTTCTCA
* *
382869 TTTTTC TTCATTTC TTATTC ATTTTC -TTTTC --TTTC TTTTTC TTTTTC
1 TTTTTC TT--TTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
382916 TTTTTC -TTTT- TTTTTC -TTTT- TTTTTC TTTTTTC TTTTT- TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC -TTTTTC TTTTTC TTTT
382958 CTATTTTTTC
Statistics
Matches: 71, Mismatches: 3, Indels: 19
0.76 0.03 0.20
Matches are distributed among these distances:
4 4 0.06
5 25 0.35
6 30 0.42
7 6 0.08
8 6 0.08
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:382920 original size:27 final size:27
Alignment explanation
Indices: 382805--382964 Score: 92
Period size: 27 Copynumber: 5.6 Consensus size: 27
382795 TCATTCCAAT
* *
382805 TTTCTTTTCTCTCTTTTTTATTTTCATTTC
1 TTTCTTTT-TCT-TTTTCT-TTTTCTTTTC
* * *
382835 CTTCATTTTTCTCTCTCTTTTCTCTTTT-
1 TTTC-TTTTTCTTTTTCTTTT-TCTTTTC
*
382863 TTCTCATTTTTCTTCATTTCTTATTCATTTTC
1 TT-TC-TTTTTCTT--TTTCTTTTTC-TTTTC
*
382895 TTT-TCTTTCTTTTTCTTTTTCTTTTTC
1 TTTCTTTTTCTTTTTCTTTTTC-TTTTC
* *
382922 TTTTTTTTTCTTTTT-TTTTCTTTTTTC
1 TTTCTTTTTCTTTTTCTTTT-TCTTTTC
*
382949 TTTTTTTTTCTATTTT
1 TTTCTTTTTCT-TTTT
382965 TTCTCTCTCT
Statistics
Matches: 106, Mismatches: 14, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
27 37 0.35
28 19 0.18
29 25 0.24
30 8 0.08
31 15 0.14
32 2 0.02
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (27 bp):
TTTCTTTTTCTTTTTCTTTTTCTTTTC
Found at i:382946 original size:17 final size:17
Alignment explanation
Indices: 382895--382965 Score: 101
Period size: 16 Copynumber: 4.2 Consensus size: 17
382885 ATTCATTTTC
*
382895 TTTTCTTTCTTTTTC-T
1 TTTTCTTTTTTTTTCTT
*
382911 TTTTCTTTTTCTTT-TT
1 TTTTCTTTTTTTTTCTT
382927 TTTTCTTTTTTTTTCTT
1 TTTTCTTTTTTTTTCTT
382944 TTTTCTTTTTTTTTCTAT
1 TTTTCTTTTTTTTTCT-T
382962 TTTT
1 TTTT
382966 TCTCTCTCTC
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
16 26 0.53
17 18 0.37
18 5 0.10
ACGTcount: A:0.01, C:0.13, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTCTTTTTTTTTCTT
Found at i:382965 original size:27 final size:26
Alignment explanation
Indices: 382910--382966 Score: 96
Period size: 27 Copynumber: 2.2 Consensus size: 26
382900 TTTCTTTTTC
*
382910 TTTTTCTTTTTCTTTTTTTTTCTTTT
1 TTTTTCTTTTTCTTTTTTTTTCTATT
382936 TTTTTCTTTTTTCTTTTTTTTTCTATT
1 TTTTTC-TTTTTCTTTTTTTTTCTATT
382963 TTTT
1 TTTT
382967 CTCTCTCTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 6 0.21
27 23 0.79
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.88
Consensus pattern (26 bp):
TTTTTCTTTTTCTTTTTTTTTCTATT
Found at i:382966 original size:1 final size:1
Alignment explanation
Indices: 382890--382957 Score: 55
Period size: 1 Copynumber: 68.0 Consensus size: 1
382880 TTCTTATTCA
* * * * * * * * *
382890 TTTTCTTTTCTTTCTTTTTCTTTTTCTTTTTCTTTTTTTTTCTTTTTTTTTCTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
382955 TTT
1 TTT
382958 CTATTTTTTC
Statistics
Matches: 49, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:385683 original size:3 final size:3
Alignment explanation
Indices: 385665--385922 Score: 148
Period size: 3 Copynumber: 87.3 Consensus size: 3
385655 TGTAAATAGC
* * * *
385665 AAT AAG AAT AAT -AT AAT AA- AAT AAT AAT CAT AAT CAT AAT CAT AACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T
* *
385712 AAT AAT AAT AA- AGAT AAT AAA AAT AAT -AT AAT AAT AAT AAA AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
385756 AATT AAT AA- AAT AAG AGT AAT AAT AA- AAT AAC ATT AAAT AAT AAT
1 AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
* * * *
385801 TAT AAT AAT AA- GAT AAT AAG AA- AAT AAT AAAT GAT AA- ATAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT A-AT AAT
* * *
385845 AAT AAT AA- AGT AAT AGT AA- AAT GAT AAT AAGT ACA- AAT AAT ACAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T A-AT AAT AAT A-AT
* * *
385890 AA- AAT AAT AGT AAT -AT ATAT ACT AAA AAT AAT A
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT A
385923 GTATATGGCA
Statistics
Matches: 192, Mismatches: 39, Indels: 48
0.69 0.14 0.17
Matches are distributed among these distances:
2 23 0.12
3 147 0.77
4 21 0.11
5 1 0.01
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:385730 original size:9 final size:8
Alignment explanation
Indices: 385671--385852 Score: 75
Period size: 8 Copynumber: 21.2 Consensus size: 8
385661 TAGCAATAAG
*
385671 AATAATAT
1 AATAAAAT
385679 AATAAAAT
1 AATAAAAT
*
385687 AATAATCAT
1 AATAA-AAT
385696 AATCATAATCAT
1 AAT-A-AA--AT
385708 AACTAATAAT
1 AA-TAA-AAT
385718 AATAAAGAT
1 AATAAA-AT
385727 AATAAAAAT
1 AAT-AAAAT
*
385736 AATATAAT
1 AATAAAAT
*
385744 AATAATAAA
1 AATAA-AAT
*
385753 AAT-AATT
1 AATAAAAT
385760 AATAAAAT
1 AATAAAAT
* *
385768 AAGAGTAAT
1 AATA-AAAT
385777 AATAAAAT
1 AATAAAAT
*
385785 AACATTAAAT
1 -A-ATAAAAT
385795 AAT--AAT
1 AATAAAAT
*
385801 TATAATAAT
1 AATAA-AAT
* *
385810 AAGATAAT
1 AATAAAAT
*
385818 AAGAAAAT
1 AATAAAAT
385826 AAT-AAAT
1 AATAAAAT
*
385833 GATAAATAT
1 AATAAA-AT
385842 AATAATAAT
1 AATAA-AAT
385851 AA
1 AA
385853 AGTAATAGTA
Statistics
Matches: 132, Mismatches: 22, Indels: 39
0.68 0.11 0.20
Matches are distributed among these distances:
6 5 0.04
7 10 0.08
8 47 0.36
9 46 0.35
10 15 0.11
11 2 0.02
12 6 0.05
13 1 0.01
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (8 bp):
AATAAAAT
Found at i:385778 original size:41 final size:41
Alignment explanation
Indices: 385665--385920 Score: 145
Period size: 41 Copynumber: 6.1 Consensus size: 41
385655 TGTAAATAGC
* * * *
385665 AATAAGAATAATATAATAAAATAATAATCATAATCATAATCAT
1 AATAAAAATAAT-TAATAAAATAATAGTAATAAT-ATAATAAT
**
385708 AACT---AATAA-TAATAAAGATAATAAAAATAATATAATAAT
1 AA-TAAAAATAATTAATAAA-ATAATAGTAATAATATAATAAT
* * *
385747 AATAAAAATAATTAATAAAATAAGAGTAATAATAAAATAAC
1 AATAAAAATAATTAATAAAATAATAGTAATAATATAATAAT
* * * *
385788 ATTAAATAATAATT-ATAATAATAAGA-TAATAAGAAAATAAT
1 AATAAA-AATAATTAATAA-AATAATAGTAATAATATAATAAT
*
385829 AAATGATAAATATAATAATAATAAAGTAATAGTAA-AATGATAAT-A-
1 -AAT-A-AAA-ATAAT--TAATAAAATAATAGTAATAAT-ATAATAAT
* * * *
385874 AGTACAAATAA-TACATAAAATAATAGTAATATATATACTAAA
1 AATAAAAATAATTA-ATAAAATAATAGTAATA-ATATAATAAT
385916 AATAA
1 AATAA
385921 TAGTATATGG
Statistics
Matches: 169, Mismatches: 22, Indels: 45
0.72 0.09 0.19
Matches are distributed among these distances:
38 3 0.02
39 30 0.18
40 17 0.10
41 56 0.33
42 28 0.17
43 5 0.03
44 10 0.06
46 9 0.05
47 11 0.07
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.29
Consensus pattern (41 bp):
AATAAAAATAATTAATAAAATAATAGTAATAATATAATAAT
Found at i:385832 original size:38 final size:37
Alignment explanation
Indices: 385711--385849 Score: 126
Period size: 38 Copynumber: 3.7 Consensus size: 37
385701 TAATCATAAC
* *
385711 TAAT-AATAATAAAGATAATAA-AA-ATAATATAATAA
1 TAATAAATAATAAATATAATAATAAGATAATA-AAAAA
*
385746 TAATAAA-AATAATTAATAA-AATAAGAGTAATAATAAAA
1 TAATAAATAATAAAT-ATAATAATAAGA-TAATAA-AAAA
*
385784 TAACATTAAATAATAATTATAATAATAAGATAATAAGAAAA
1 T-A-A-TAAATAATAAATATAATAATAAGATAATAA-AAAA
*
385825 TAATAAATGATAAATATAATAATAA
1 TAATAAATAATAAATATAATAATAA
385850 TAAAGTAATA
Statistics
Matches: 87, Mismatches: 6, Indels: 19
0.78 0.05 0.17
Matches are distributed among these distances:
35 11 0.13
36 8 0.09
37 2 0.02
38 29 0.33
39 2 0.02
40 2 0.02
41 19 0.22
42 14 0.16
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (37 bp):
TAATAAATAATAAATATAATAATAAGATAATAAAAAA
Found at i:394163 original size:19 final size:20
Alignment explanation
Indices: 394126--394164 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
394116 ATTTTTAAAA
394126 TATTAAAATAATTTATTTAT
1 TATTAAAATAATTTATTTAT
*
394146 TATTAAAAT-ATTTTTTTAT
1 TATTAAAATAATTTATTTAT
394165 AATTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTAAAATAATTTATTTAT
Found at i:394264 original size:5 final size:5
Alignment explanation
Indices: 394254--394352 Score: 58
Period size: 5 Copynumber: 18.8 Consensus size: 5
394244 AGTAATAGTG
* ** *
394254 TTATA TTATA TTATA TTTTAA AAATA TTATA TCTTATA TTATTA TAATA
1 TTATA TTATA TTATA TTAT-A TTATA TTATA --TTATA TTA-TA TTATA
* * *
394303 TAATTGA TTATT TTATTA TTATA TTA-A -AATA TTATA TTATA TTATA
1 TTA-T-A TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA
394349 TTAT
1 TTAT
394353 TAGAAATATT
Statistics
Matches: 73, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
3 1 0.01
4 2 0.03
5 50 0.68
6 12 0.16
7 8 0.11
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (5 bp):
TTATA
Found at i:394267 original size:31 final size:29
Alignment explanation
Indices: 394224--394353 Score: 89
Period size: 28 Copynumber: 4.5 Consensus size: 29
394214 GTATTATAAA
*
394224 TTATTTTA-ATTATTTATTAAAGTAATAGTG
1 TTATATTATATTATTTATTAAA-TAATA-TG
394254 TTATATTATATTATATT-TTAAA-AATAT-
1 TTATATTATATTAT-TTATTAAATAATATG
*
394281 TATATCTTATATTA-TTA-TAATATAAT-TG
1 T-TATATTATATTATTTATTAA-ATAATATG
* *
394309 ATTAT-TT-TATTATTATATTAAAATATTATA
1 -TTATATTATATTATT-TATT-AAATAATATG
394339 TTATATTATATTATT
1 TTATATTATATTATT
394354 AGAAATATTA
Statistics
Matches: 81, Mismatches: 4, Indels: 29
0.71 0.04 0.25
Matches are distributed among these distances:
26 10 0.12
27 6 0.07
28 20 0.25
29 14 0.17
30 12 0.15
31 17 0.21
32 2 0.02
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (29 bp):
TTATATTATATTATTTATTAAATAATATG
Found at i:394283 original size:26 final size:26
Alignment explanation
Indices: 394254--394379 Score: 93
Period size: 26 Copynumber: 4.8 Consensus size: 26
394244 AGTAATAGTG
394254 TTATATTATATTATATTTTAAAAATA
1 TTATATTATATTATATTTTAAAAATA
** * *
394280 TTATATCTTATATTATTATAATATAATTGA
1 TTATA--TTATATTA-TATTTTAAAAAT-A
*
394310 TTAT-TT-TATTATTATATT-AAAATA
1 TTATATTATATTA-TATTTTAAAAATA
*
394334 TTATATTATATTATATTATTAGAAATA
1 TTATATTATATTATATT-TTAAAAATA
*
394361 TTA-A-TA-AATATATTTTAAA
1 TTATATTATATTATATTTTAAA
394380 TATTTTAATA
Statistics
Matches: 81, Mismatches: 11, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
23 4 0.05
24 12 0.15
25 10 0.12
26 24 0.30
27 10 0.12
28 8 0.10
29 8 0.10
30 5 0.06
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (26 bp):
TTATATTATATTATATTTTAAAAATA
Found at i:394302 original size:23 final size:23
Alignment explanation
Indices: 394260--394352 Score: 75
Period size: 23 Copynumber: 4.0 Consensus size: 23
394250 AGTGTTATAT
*
394260 TATATTATATT-TTAAAAATATTA
1 TATATTATATTATT-ATAATATTA
* *
394283 TATCTTATATTATTATAATATAA
1 TATATTATATTATTATAATATTA
* *
394306 T-TGATTATTTTATTATTATATTAA
1 TAT-ATTATATTATTATAATATT-A
* *
394330 AATATTATATTA-TATTATATTA
1 TATATTATATTATTATAATATTA
394352 T
1 T
394353 TAGAAATATT
Statistics
Matches: 56, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
22 2 0.04
23 42 0.75
24 11 0.20
25 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (23 bp):
TATATTATATTATTATAATATTA
Found at i:394322 original size:8 final size:8
Alignment explanation
Indices: 394278--394354 Score: 52
Period size: 8 Copynumber: 9.6 Consensus size: 8
394268 ATTTTAAAAA
394278 TATTATA-
1 TATTATAT
*
394285 TCTTATAT
1 TATTATAT
*
394293 TATTATAA
1 TATTATAT
*
394301 TATAATTGAT
1 TATTA-T-AT
*
394311 TATTTTAT
1 TATTATAT
394319 TATTATAT
1 TATTATAT
**
394327 TAAAATAT
1 TATTATAT
394335 TA-TAT-T
1 TATTATAT
394341 ATATTATAT
1 -TATTATAT
394350 TATTA
1 TATTA
394355 GAAATATTAA
Statistics
Matches: 53, Mismatches: 11, Indels: 11
0.71 0.15 0.15
Matches are distributed among these distances:
6 1 0.02
7 10 0.19
8 35 0.66
9 3 0.06
10 4 0.08
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (8 bp):
TATTATAT
Found at i:394575 original size:22 final size:22
Alignment explanation
Indices: 394550--394601 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
394540 AGGAGATTTT
*
394550 GTTGATCAGTAAAATGTTTTAC
1 GTTGATCAGGAAAATGTTTTAC
394572 GTTGATCAGGAAAATGTTTTAC
1 GTTGATCAGGAAAATGTTTTAC
*
394594 ATTGATCA
1 GTTGATCA
394602 ACCGGTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (22 bp):
GTTGATCAGGAAAATGTTTTAC
Found at i:398605 original size:4 final size:4
Alignment explanation
Indices: 398596--398628 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
398586 AAGTACATAC
*
398596 GTAT GTAT GTAT GTAT GTAT GTAT GTAC GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
398629 AATGGCATGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.24, C:0.03, G:0.27, T:0.45
Consensus pattern (4 bp):
GTAT
Found at i:400902 original size:17 final size:17
Alignment explanation
Indices: 400880--400913 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
400870 GACTGCTTTT
400880 ACTAACTCTCTTCGATC
1 ACTAACTCTCTTCGATC
400897 ACTAACTCTCTTCGATC
1 ACTAACTCTCTTCGATC
400914 CATCCTTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.35, G:0.06, T:0.35
Consensus pattern (17 bp):
ACTAACTCTCTTCGATC
Found at i:403744 original size:3 final size:3
Alignment explanation
Indices: 403736--403812 Score: 106
Period size: 3 Copynumber: 26.7 Consensus size: 3
403726 AAGTCCGTTG
403736 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
403782 TTA ATA CTA ATA TT- TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
403813 TTGTTTTTTC
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
2 6 0.09
3 61 0.91
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:404811 original size:21 final size:21
Alignment explanation
Indices: 404781--404824 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
404771 TAGAAATAGG
*
404781 AAAAAAAGAAAAAT-GAGGAA
1 AAAAAAAGAAAAATAGAAGAA
404801 AAAATAAAGAAAAATAGAAGAA
1 AAAA-AAAGAAAAATAGAAGAA
404823 AA
1 AA
404825 TGAAATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 10 0.48
22 7 0.33
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (21 bp):
AAAAAAAGAAAAATAGAAGAA
Found at i:405542 original size:52 final size:51
Alignment explanation
Indices: 405372--405570 Score: 245
Period size: 51 Copynumber: 3.9 Consensus size: 51
405362 TGTGTTGTAT
* * * * *
405372 TTTAATTTATACATTTTAGTCACTATTTATTTCTGATTTGTCTATTGATCA
1 TTTAATTTATGCATTTTAGTCACTGTTTATTTCTGATTTGGCTATTGTTCC
405423 TTTAATTTATGCATTTTAGTCACTGTTTATTTCTGATTTGGCTATTGTTCC
1 TTTAATTTATGCATTTTAGTCACTGTTTATTTCTGATTTGGCTATTGTTCC
* * * * *
405474 TTTAATTTATGTATTTTAGTCACCGTTTATTTTTTTATTTGGCTACTGTTCC
1 TTTAATTTATGCATTTTAGTCACTGTTTA-TTTCTGATTTGGCTATTGTTCC
* * * ** *
405526 TTTATTTTGTGCATTTTAGTCATTGCCTATTTCTAATTTGGCTAT
1 TTTAATTTATGCATTTTAGTCACTGTTTATTTCTGATTTGGCTAT
405571 GTTTTTTTAT
Statistics
Matches: 127, Mismatches: 20, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
51 86 0.68
52 41 0.32
ACGTcount: A:0.20, C:0.13, G:0.12, T:0.56
Consensus pattern (51 bp):
TTTAATTTATGCATTTTAGTCACTGTTTATTTCTGATTTGGCTATTGTTCC
Found at i:405565 original size:103 final size:102
Alignment explanation
Indices: 405372--405570 Score: 245
Period size: 103 Copynumber: 1.9 Consensus size: 102
405362 TGTGTTGTAT
* * *
405372 TTTAATTTATACATTTTAGTCACTATTTATTTCTGATTTGTCTATTGATCATTTAATTTATGCAT
1 TTTAATTTATACATTTTAGTCACCATTTATTTCTGATTTGGCTACTGATCATTTAATTTATGCAT
** *
405437 TTTAGTCACTGTTTATTTCTGATTTGGCTATTGTTCC
66 TTTAGTCACTGCCTATTTCTAATTTGGCTATTGTTCC
** * * * * * * *
405474 TTTAATTTATGTATTTTAGTCACCGTTTATTTTTTTATTTGGCTACTGTTCCTTTATTTTGTGCA
1 TTTAATTTATACATTTTAGTCACCATTTA-TTTCTGATTTGGCTACTGATCATTTAATTTATGCA
*
405539 TTTTAGTCATTGCCTATTTCTAATTTGGCTAT
65 TTTTAGTCACTGCCTATTTCTAATTTGGCTAT
405571 GTTTTTTTAT
Statistics
Matches: 80, Mismatches: 16, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
102 25 0.31
103 55 0.69
ACGTcount: A:0.20, C:0.13, G:0.12, T:0.56
Consensus pattern (102 bp):
TTTAATTTATACATTTTAGTCACCATTTATTTCTGATTTGGCTACTGATCATTTAATTTATGCAT
TTTAGTCACTGCCTATTTCTAATTTGGCTATTGTTCC
Found at i:406465 original size:129 final size:128
Alignment explanation
Indices: 406218--406611 Score: 511
Period size: 131 Copynumber: 3.0 Consensus size: 128
406208 ATAAGTAACA
* * * * * *
406218 CTCGAATCAGTATTGATTTTTAATATGAAGTAGTGATATCTCCTCATTTCAGCTGGAGTAATAAA
1 CTCGAATTAATATTGATTTTTAAGATGAAATAGTGATATCT-CTCATTTCGGTTGGAGTAAT--A
**
406283 TGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATCATTAGATATTATCATTTTC
63 TGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATCATTAGATATTATTGTTTTC
406348 T
128 T
406349 CTCGAATTAATATTGATTTTTAAGATGAAATAGTGATATCTGCTCATTTCGGTTGGAGTAATATG
1 CTCGAATTAATATTGATTTTTAAGATGAAATAGTGATATCT-CTCATTTCGGTTGGAGTAATATG
*
406414 ACTACTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATCATTAGATATTATTGTTTTCT
65 ACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATCATTAGATATTATTGTTTTCT
* * * * * *
406478 CTTGAATTAATATTGAATTTTAAGACGAAAAAGTGATATCTCTTACTTTCGATTGGGGTAGTAAT
1 CTCGAATTAATATTGATTTTTAAGATGAAATAGTGATATCTCTCA-TTTCGGTT--GG-AGTAAT
* * * * ** *
406543 -TGATTGCTTTAAGGCATGCGAGGTTATTTATTTTCGATTATAAATAATTAGATATTATTGTTTT
62 ATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATCATTAGATATTATTGTTTT
406607 CT
127 CT
406609 CTC
1 CTC
406612 TTAGAATTTT
Statistics
Matches: 234, Mismatches: 25, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
128 3 0.01
129 108 0.46
131 117 0.50
132 6 0.03
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (128 bp):
CTCGAATTAATATTGATTTTTAAGATGAAATAGTGATATCTCTCATTTCGGTTGGAGTAATATGA
CTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATCATTAGATATTATTGTTTTCT
Found at i:406602 original size:131 final size:129
Alignment explanation
Indices: 406249--406611 Score: 480
Period size: 129 Copynumber: 2.8 Consensus size: 129
406239 AATATGAAGT
* *
406249 AGTGATATCTCCTCATTTC-AGCTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTA
1 AGTGATATCTGCTCATTTCGA-TTGGAGTAAT--ATGACTGCTTTAAGGCATGAGAGGTCATTTA
** * *
406313 TTCTCGATTGGAAATCATTAGATATTATCATTTTCTCTCGAATTAATATTGATTTTTAAGATGAA
63 TTCTCGATTGGAAATCATTAGATATTATTGTTTTCTCTCGAATTAATATTGAATTTTAAGACGAA
*
406378 AT
128 AA
* *
406380 AGTGATATCTGCTCATTTCGGTTGGAGTAATATGACTACTTTAAGGCATGAGAGGTCATTTATTC
1 AGTGATATCTGCTCATTTCGATTGGAGTAATATGACTGCTTTAAGGCATGAGAGGTCATTTATTC
*
406445 TCGATTGGAAATCATTAGATATTATTGTTTTCTCTTGAATTAATATTGAATTTTAAGACGAAAA
66 TCGATTGGAAATCATTAGATATTATTGTTTTCTCTCGAATTAATATTGAATTTTAAGACGAAAA
* * * *
406509 AGTGATATCT-CTTACTTTCGATTGGGGTAGTAAT-TGATTGCTTTAAGGCATGCGAGGTTATTT
1 AGTGATATCTGCTCA-TTTCGATT--GG-AGTAATATGACTGCTTTAAGGCATGAGAGGTCATTT
* ** *
406572 ATTTTCGATTATAAATAATTAGATATTATTGTTTTCTCTC
62 ATTCTCGATTGGAAATCATTAGATATTATTGTTTTCTCTC
406612 TTAGAATTTT
Statistics
Matches: 206, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
128 3 0.01
129 108 0.52
131 89 0.43
132 6 0.03
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (129 bp):
AGTGATATCTGCTCATTTCGATTGGAGTAATATGACTGCTTTAAGGCATGAGAGGTCATTTATTC
TCGATTGGAAATCATTAGATATTATTGTTTTCTCTCGAATTAATATTGAATTTTAAGACGAAAA
Found at i:409995 original size:8 final size:7
Alignment explanation
Indices: 409937--410025 Score: 51
Period size: 7 Copynumber: 12.7 Consensus size: 7
409927 AGTCGACAAT
409937 AAAGAAA
1 AAAGAAA
409944 GAAA-AAA
1 -AAAGAAA
*
409951 AATGAAA
1 AAAGAAA
*
409958 AGAGAGAA
1 AAAGA-AA
*
409966 TAAGAAA
1 AAAGAAA
*
409973 AAA-AAT
1 AAAGAAA
*
409979 AAAG-TA
1 AAAGAAA
*
409985 ATAGAAA
1 AAAGAAA
*
409992 AATAGAAG
1 AA-AGAAA
410000 AAA-AAA
1 AAAGAAA
410006 AAAGAAAA
1 AAAG-AAA
410014 AAAGAAA
1 AAAGAAA
410021 AAAGA
1 AAAGA
410026 TGAAAAAAGA
Statistics
Matches: 60, Mismatches: 14, Indels: 15
0.67 0.16 0.17
Matches are distributed among these distances:
6 15 0.25
7 24 0.40
8 21 0.35
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.07
Consensus pattern (7 bp):
AAAGAAA
Found at i:410020 original size:18 final size:18
Alignment explanation
Indices: 409997--410043 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
409987 AGAAAAATAG
409997 AAGAAAAAAAAAGAAAAA
1 AAGAAAAAAAAAGAAAAA
* *
410015 AAGAAAAAAGATGAAAAA
1 AAGAAAAAAAAAGAAAAA
410033 AGAGAAGAAAA
1 A-AGAA-AAAA
410044 TAGATCAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 17 0.68
19 4 0.16
20 4 0.16
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (18 bp):
AAGAAAAAAAAAGAAAAA
Found at i:412593 original size:239 final size:242
Alignment explanation
Indices: 412166--412836 Score: 933
Period size: 241 Copynumber: 2.8 Consensus size: 242
412156 ATCAAGTTTG
* *
412166 ATTTCCAAAGTTTCTTACTTAGTAAATCCTT-TGGGTCATCAGTAAGTCTTTCGAGCATGATGTT
1 ATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCTGGGCCATCAGTAAGTCTTTCGAGCATGATGTT
** * * * *
412230 TAAATTATTCGGGTCTTCTATAAGTCTTCCGAGCAAGATGATAAGTCATTTGGGCCATCCATAAG
66 TAAATCCTTCGGGTCATCTATAAGTCTTTCGAGAAAGATGATAAGTCATTTGGACCATCCATAAG
* * * *
412295 ACCTTCGGGTAGGGCATTTTCAT-AAGATTTCAAAATATGAGAAAAAGATTTCCAAAGTTTCTCA
131 ACCTTCGGGTAGGACGTTTTC-TCAAGATTTCAAAAGATGAGAAAATGATTTCCAAAGTTTCTCA
* * * *
412359 GTTAAA-CTTTTTCTGAAATTTGGTTTCTTTTGAAAA-TGAGAAAACA
195 CTCAAACCTTTTTCTGAAAATTGGTTTCTTTTGAAAAGTAAGAAAACA
*
412405 ATTTCCAAAGTTTCTTACTTAGTAAGT-CTTCTGGGCCATCAGTAAGTCTTTTGAGCATGATGTT
1 ATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCTGGGCCATCAGTAAGTCTTTCGAGCATGATGTT
* * *
412469 TAAATCCTTCGGGTCATCTATAAGTCTTTCAAGAAAAATGATAAGTCATTTGGACCATCTATAAG
66 TAAATCCTTCGGGTCATCTATAAGTCTTTCGAGAAAGATGATAAGTCATTTGGACCATCCATAAG
** * * *
412534 ACCTTCGGGTATAATGTTTTCTCAAGATTTCAAAAGATAAGAAAATGATTTCTAAAGTTTCTCAC
131 ACCTTCGGGTAGGACGTTTTCTCAAGATTTCAAAAGATGAGAAAATGATTTCCAAAGTTTCTCAC
*
412599 TCAAACCTTTTTTTGAAAATTGGTTTCTTTTGAAAAGTAAGAAAACA
196 TCAAACCTTTTTCTGAAAATTGGTTTCTTTTGAAAAGTAAGAAAACA
* *
412646 ATTTCCAAAGTTTCTTACTTAGTAAGTCCTTC-GGACCATCAGTAAGTCTTTCGAGCATGATGCT
1 ATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCTGGGCCATCAGTAAGTCTTTCGAGCATGATGTT
* ** **
412710 TAAATCCTTCAGGTCATCCGTAAGTCTTTCGAGAAAGATGATAAGTTC-TTCAGACCATCCATAA
66 TAAATCCTTCGGGTCATCTATAAGTCTTTCGAGAAAGATGATAAG-TCATTTGGACCATCCATAA
* * ** *
412774 GACTTTCGGGCAGGACGTTTTGACAATATTTCAAAAGATGAGAAAATGATTTCCAAAGTTTCT
130 GACCTTCGGGTAGGACGTTTTCTCAAGATTTCAAAAGATGAGAAAATGATTTCCAAAGTTTCT
412837 TACCTAGTAA
Statistics
Matches: 379, Mismatches: 47, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
238 4 0.01
239 170 0.45
240 28 0.07
241 171 0.45
242 6 0.02
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (242 bp):
ATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCTGGGCCATCAGTAAGTCTTTCGAGCATGATGTT
TAAATCCTTCGGGTCATCTATAAGTCTTTCGAGAAAGATGATAAGTCATTTGGACCATCCATAAG
ACCTTCGGGTAGGACGTTTTCTCAAGATTTCAAAAGATGAGAAAATGATTTCCAAAGTTTCTCAC
TCAAACCTTTTTCTGAAAATTGGTTTCTTTTGAAAAGTAAGAAAACA
Found at i:413328 original size:260 final size:262
Alignment explanation
Indices: 412806--413438 Score: 725
Period size: 260 Copynumber: 2.4 Consensus size: 262
412796 ACAATATTTC
* *
412806 AAAAGA-TGAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAATTATTTCCAAAATTGGTAAGAC
1 AAAAGAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAATTATTTCCAAAATTGGTAAGTC
*
412870 CTTCAGGTCATCAGTAA-TTCTTTTGAGCATGATGATTAAATCCTTCGAGTCATCTATAAGTCTT
66 CTTCAGGTCATCAGTAAGTTCTTTCGAGCATGATGATTAAATCCTTCGAGTCATCTATAAGTCTT
* * * *
412934 TCGAACAAGATGATAAATCTTTTGAGCCATCCGTAAGACCTTCGGACAGAATGTTTTCACATGAT
131 TCGAACAAGATGATAAACCCTTCGAGCCATCCATAAGACCTTCGGACAGAATGTTTTCACATGAT
* * * * * *
412999 TTCAAAATATGAGAAAATGATTTTCAAAATTTCTCATTTAAATTTTTTCTAAAAACTAGTTTCTT
196 TTCAAAAAACGAGAAAATAATTTCCAAAATTTCTCAATTAAATATTTTCTAAAAACTAG-TTCTT
413064 TTG
260 TTG
* * * *
413067 -AAA-AGTAAGAAGATGATTTTCAAAGTTTTTTGCCTAGTAAATTATTTCCAAAATTGGTAAGTC
1 AAAAGAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAATTATTTCCAAAATTGGTAAGTC
* ** * ** *
413130 ATTTGGGTCATCAGTAAGTTC-TTCGAGCATGATGCTTAAATGTTTC-AGGTCATCTGTAAGTCT
66 CTTCAGGTCATCAGTAAGTTCTTTCGAGCATGATGATTAAATCCTTCGA-GTCATCTATAAGTCT
** * * *
413193 TAT-GAGTAAGATGATAAGCCCTTCGGGCCATCTATAAGACCTTCAGG-CATG-ATGTTTTCACA
130 T-TCGAACAAGATGATAAACCCTTCGAGCCATCCATAAGACCTTC-GGACA-GAATGTTTTCACA
* * * **
413255 TGTTTTTCAAAAAACGAGAAAATAATTTCCAAAGTTTCTCAATTAAATATTTTCTGAAAGTTGCA
192 TG-ATTTCAAAAAACGAGAAAATAATTTCCAAAATTTCTCAATTAAATATTTTCTAAAAACT--A
413320 G-T-TTTTG
254 GTTCTTTTG
** * *
413327 AAAAGTAGTAAGAAAACAATTCCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGT
1 AAAAG-AGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAATTATTTCCAAAATTGGTAAGT
* * *
413392 CCTTCAGGCCATTAGTAAG-TCTTTCGAGCATGATGA-TAAGTCCTTCG
65 CCTTCAGGTCATCAGTAAGTTCTTTCGAGCATGATGATTAAATCCTTCG
413439 GGCCATCCAT
Statistics
Matches: 307, Mismatches: 51, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
259 2 0.01
260 157 0.51
261 59 0.19
262 9 0.03
263 80 0.26
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (262 bp):
AAAAGAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAATTATTTCCAAAATTGGTAAGTC
CTTCAGGTCATCAGTAAGTTCTTTCGAGCATGATGATTAAATCCTTCGAGTCATCTATAAGTCTT
TCGAACAAGATGATAAACCCTTCGAGCCATCCATAAGACCTTCGGACAGAATGTTTTCACATGAT
TTCAAAAAACGAGAAAATAATTTCCAAAATTTCTCAATTAAATATTTTCTAAAAACTAGTTCTTT
TG
Found at i:414211 original size:134 final size:132
Alignment explanation
Indices: 413989--414435 Score: 515
Period size: 134 Copynumber: 3.3 Consensus size: 132
413979 ATCAAACTCA
* * *
413989 ATTCAATCTTCCCTAAAGAATAGTGGAATGAATCAACA-TTCCGAGATCTGATTTTTCCTAAAGA
1 ATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAACATTTCC-AGATCTGATTTTACCTGAA-A
*
414053 AGCAGTGAAACAGATCCCTCTTTTTTCCAGATTTGATATTCCCTGAGGAACAGTGGAACAAGTCT
64 AGCAGTG-AACAGAT-CCTCTTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGTCT
*
414118 GCCTTG
127 GCCTCG
* *
414124 ATTCAATGTT-CCTGAAGAATAGTGGAATGAATCAACACTTCCAGATCTGATTTTACCTGAATAA
1 ATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAACATTTCCAGATCTGATTTTACCTGAA-AA
* * * * * *
414188 GAAGCTGAACATATCCATTTTTTTTCCAGATTTTATCTTCCCTAAGGAACAGTGGAACAAGTTTG
65 GCAG-TGAACAGATCC-TCTTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGTCTG
414253 CCTCG
128 CCTCG
* * * * * *
414258 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAATATTTCCAAATTTGATTTTCCCTGAAGAG
1 ATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAACATTTCCAGATCTGATTTTACCTGAAAAG
* * * * *
414323 CAGTGGAATAGATCGCTCTTTTTTCTAGATTTGATCTTCCATGAAGAAGTAGTGGAACAAGTCTG
66 CAGT-GAACAGATC-CTCTTTTTTCCAGATTTGATCTTCCCTGAGGAA-CAGTGGAACAAGTCTG
414388 CCTCG
128 CCTCG
* * * *
414393 ATTTAATCCT-CCT-AATGAATAATGGAATGAACCAACATTTCCA
1 ATTCAATCTTCCCTGAA-GAATAGTGGAATGAATCAACATTTCCA
414436 TATTATAGTC
Statistics
Matches: 266, Mismatches: 38, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
133 5 0.02
134 173 0.65
135 88 0.33
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Consensus pattern (132 bp):
ATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAACATTTCCAGATCTGATTTTACCTGAAAAG
CAGTGAACAGATCCTCTTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGTCTGCCT
CG
Found at i:414677 original size:3 final size:3
Alignment explanation
Indices: 414669--414726 Score: 75
Period size: 3 Copynumber: 20.0 Consensus size: 3
414659 TCCGAAGTCC
* * *
414669 ATT ATT ATT ATT ATT ATT ATT -TT AAT ACT AAT ATT -TT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
414715 ATT ATT ATT ATT
1 ATT ATT ATT ATT
414727 TTGTTTTTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 4 0.08
3 45 0.92
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:415497 original size:1 final size:1
Alignment explanation
Indices: 415487--415521 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
415477 GAAATAGGGG
* *
415487 AAAAATAAAAAAAAAAAAAAAAAAATAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
415522 GAAGAAAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.94, C:0.00, G:0.00, T:0.06
Consensus pattern (1 bp):
A
Found at i:415506 original size:10 final size:10
Alignment explanation
Indices: 415487--415521 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
415477 GAAATAGGGG
415487 AAAAATAAAA
1 AAAAATAAAA
*
415497 AAAAAAAAAA
1 AAAAATAAAA
415507 AAAAATAAAA
1 AAAAATAAAA
415517 AAAAA
1 AAAAA
415522 GAAGAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.94, C:0.00, G:0.00, T:0.06
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:415810 original size:166 final size:169
Alignment explanation
Indices: 415536--415869 Score: 638
Period size: 166 Copynumber: 2.0 Consensus size: 169
415526 AAAATGGAAT
415536 ATATAGGCTACCCGAACAGCGTCGTTTCGGTCTCAGTCCTATGCGTTTTGAGATTGAAGGGTATA
1 ATATAGGCTACCCGAACAGCGTCGTTTCGGTCTCAGTCCTATGCGTTTTGAGATTGAAGGGTATA
415601 ATGCCTCCCGCTATCCCCATCTTTTTATCATTTACAATTTGGTCAC-T-TTTTGTGATAAACTTC
66 ATGCCTCCCGCTATCCCCATCTTTTTATCATTTACAATTTGGTCACTTATTTTGTGATAAACTTC
*
415664 TTATTTGTTTCAATTGTTTGCCTTTATTT-TTAATTTTC
131 TTATTTGTTTCAATTGTTTGCCTTTATTTAATAATTTTC
415702 ATATAGGCTACCCGAACAGCGTCGTTTCGGTCTCAGTCCTATGCGTTTTGAGATTGAAGGGTATA
1 ATATAGGCTACCCGAACAGCGTCGTTTCGGTCTCAGTCCTATGCGTTTTGAGATTGAAGGGTATA
415767 ATGCCTCCCGCTATCCCCATCTTTTTATCATTTACAATTTGGTCACTTATTTTGTGATAAACTTC
66 ATGCCTCCCGCTATCCCCATCTTTTTATCATTTACAATTTGGTCACTTATTTTGTGATAAACTTC
415832 TTATTTGTTTCAATTGTTTGCCTTTATTTAATAATTTT
131 TTATTTGTTTCAATTGTTTGCCTTTATTTAATAATTTT
415870 TCCATTTCAT
Statistics
Matches: 164, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
166 111 0.68
167 1 0.01
168 45 0.27
169 7 0.04
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.43
Consensus pattern (169 bp):
ATATAGGCTACCCGAACAGCGTCGTTTCGGTCTCAGTCCTATGCGTTTTGAGATTGAAGGGTATA
ATGCCTCCCGCTATCCCCATCTTTTTATCATTTACAATTTGGTCACTTATTTTGTGATAAACTTC
TTATTTGTTTCAATTGTTTGCCTTTATTTAATAATTTTC
Found at i:416280 original size:51 final size:51
Alignment explanation
Indices: 416250--416448 Score: 299
Period size: 51 Copynumber: 3.9 Consensus size: 51
416240 GTGTTGTATT
*
416250 TTTAATTTATGCATTTTAGCCACTCTTTATTTCTGATTTGGCTATTGTTCC
1 TTTAATTTATGCATTTTAGTCACTCTTTATTTCTGATTTGGCTATTGTTCC
*
416301 TTTAATTTATGCATTTTAGTCACTGTTTATTTCTGATTTGGCTATTGTTCC
1 TTTAATTTATGCATTTTAGTCACTCTTTATTTCTGATTTGGCTATTGTTCC
* * * * * *
416352 TTTAATTTATGTATTTTAGTCACTTTTTATTTTTTATTTGGGTATTGTTCT
1 TTTAATTTATGCATTTTAGTCACTCTTTATTTCTGATTTGGCTATTGTTCC
* * *
416403 TTTATTTTATGCATTTTAGTCACTGTCTATTTCTGATTTGGCTATT
1 TTTAATTTATGCATTTTAGTCACTCTTTATTTCTGATTTGGCTATT
416449 TTTTTTATCT
Statistics
Matches: 133, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 133 1.00
ACGTcount: A:0.18, C:0.13, G:0.13, T:0.57
Consensus pattern (51 bp):
TTTAATTTATGCATTTTAGTCACTCTTTATTTCTGATTTGGCTATTGTTCC
Found at i:417282 original size:131 final size:131
Alignment explanation
Indices: 417098--417493 Score: 485
Period size: 131 Copynumber: 3.0 Consensus size: 131
417088 ATAAGTAACA
* * * **
417098 CTCGAATCAATAATACTTTTTAAGATGAAATAGTGATATCTCCTCATTTCGGTTGGAGTTATAAA
1 CTCGAATAAATATTAATTTTTAAGACAAAATAGTGATATCTCCTCATTTCGGTTGGAGTTATAAA
*
417163 TTACTGCTTTAAGGCATGAGAGGTCATTTATTCTTGATTGGAAATCATTAGATATTATCGATTTC
66 TTACTGCTTTAAGACATGAGAGGTCATTTATTCTTGATTGGAAATCATTAGATATTATCGATTTC
417228 T
131 T
* * * * * * * *
417229 CTCGAATCAGTATTGATTTTTAAGACCAAATAGTAATATCACCTCATTTCGGTTGCAGTAATAAA
1 CTCGAATAAATATTAATTTTTAAGACAAAATAGTGATATCTCCTCATTTCGGTTGGAGTTATAAA
* * * *
417294 TGATTGCTTTAAGACATGAGAGGTCATTTATTCTCGATTGAAAATCATTAGATATTATC-ATTTT
66 TTACTGCTTTAAGACATGAGAGGTCATTTATTCTTGATTGGAAATCATTAGATATTATCGA-TTT
417358 CT
130 CT
* * * * * *
417360 CTTGAATAAATATTAAGTTTTAAGACAAAATAGTGATATCTCTTCCTTTTGATTGTG-G-TAGT-
1 CTCGAATAAATATTAATTTTTAAGACAAAATAGTGATATCTCCTCATTTCGGTTG-GAGTTA-TA
* * *
417422 AATTGACTGCTTTAAGACATGAGAGGTCATTTATTCTTGATTGGAAATAATTAGATACTATCGTT
64 AATT-ACTGCTTTAAGACATGAGAGGTCATTTATTCTTGATTGGAAATCATTAGATATTATCGAT
417487 TTCT
128 TTCT
417491 CTC
1 CTC
417494 TTAGAATTAT
Statistics
Matches: 223, Mismatches: 37, Indels: 10
0.83 0.14 0.04
Matches are distributed among these distances:
130 5 0.02
131 218 0.98
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (131 bp):
CTCGAATAAATATTAATTTTTAAGACAAAATAGTGATATCTCCTCATTTCGGTTGGAGTTATAAA
TTACTGCTTTAAGACATGAGAGGTCATTTATTCTTGATTGGAAATCATTAGATATTATCGATTTC
T
Found at i:420904 original size:7 final size:7
Alignment explanation
Indices: 420887--420943 Score: 64
Period size: 7 Copynumber: 8.0 Consensus size: 7
420877 ACATGTGTAT
420887 ATATATA
1 ATATATA
420894 ATATA-A
1 ATATATA
420900 TATATATA
1 -ATATATA
420908 ATATA-A
1 ATATATA
*
420914 TATATATT
1 -ATATATA
420922 ATATATA
1 ATATATA
420929 ATATATA
1 ATATATA
420936 TATATATA
1 -ATATATA
420944 TAGATGGATA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
6 2 0.05
7 33 0.77
8 8 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
ATATATA
Found at i:420904 original size:14 final size:15
Alignment explanation
Indices: 420884--420943 Score: 95
Period size: 16 Copynumber: 3.9 Consensus size: 15
420874 AGAACATGTG
420884 TATATATATAATATAA
1 TATATATAT-ATATAA
420900 TATATATA-ATATAA
1 TATATATATATATAA
420914 TATATATTATATATAA
1 TATATA-TATATATAA
420930 TATATATATATATA
1 TATATATATATATA
420944 TAGATGGATA
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
14 12 0.29
15 10 0.24
16 20 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATATATATATAA
Found at i:420906 original size:9 final size:9
Alignment explanation
Indices: 420884--420945 Score: 76
Period size: 9 Copynumber: 6.9 Consensus size: 9
420874 AGAACATGTG
420884 TATATAT-A
1 TATATATAA
420892 TA-ATATAA
1 TATATATAA
420900 TATATATAA
1 TATATATAA
420909 TATAATATATA
1 TAT-ATATA-A
420920 TTATATATAA
1 -TATATATAA
420930 TATATAT-A
1 TATATATAA
420938 TATATATA
1 TATATATA
420946 GATGGATATA
Statistics
Matches: 48, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
7 4 0.08
8 13 0.27
9 16 0.33
10 6 0.12
11 6 0.12
12 3 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TATATATAA
Found at i:420956 original size:2 final size:2
Alignment explanation
Indices: 420884--420945 Score: 82
Period size: 2 Copynumber: 34.0 Consensus size: 2
420874 AGAACATGTG
420884 TA TA TA TA TA -A TA TA -A TA TA TA TA -A TA TA -A TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
420921 TA TA TA TA -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
420946 GATGGATATA
Statistics
Matches: 54, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
1 6 0.11
2 48 0.89
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:424650 original size:42 final size:42
Alignment explanation
Indices: 424586--424722 Score: 238
Period size: 42 Copynumber: 3.3 Consensus size: 42
424576 GAAACTTGCT
* * *
424586 TCAAGATCTTTCTCCTTGTTTCTTGAATCGGCAAGGAGGCTC
1 TCAAGATCTTTCACCTTGTTTCTTGAATCAGCAAGGAGGGTC
*
424628 TCAAAATCTTTCACCTTGTTTCTTGAATCAGCAAGGAGGGTC
1 TCAAGATCTTTCACCTTGTTTCTTGAATCAGCAAGGAGGGTC
424670 TCAAGATCTTTCACCTTGTTTCTTGAATCAGCAAGGAGGGTC
1 TCAAGATCTTTCACCTTGTTTCTTGAATCAGCAAGGAGGGTC
424712 TCAAGATCTTT
1 TCAAGATCTTT
424723 TATCCTTATC
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 90 1.00
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (42 bp):
TCAAGATCTTTCACCTTGTTTCTTGAATCAGCAAGGAGGGTC
Found at i:428434 original size:30 final size:32
Alignment explanation
Indices: 428371--428437 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
428361 TCTTATTTTG
428371 TATATATATACATATTTTCATTTTATTATTAC
1 TATATATATACATATTTTCATTTTATTATTAC
* *
428403 TATATATATATAT-TTATTTATTTT-TTA-TAC
1 TATATATATACATATT-TTCATTTTATTATTAC
428433 TATAT
1 TATAT
428438 CTATCATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 8 0.25
31 5 0.16
32 19 0.59
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (32 bp):
TATATATATACATATTTTCATTTTATTATTAC
Found at i:428436 original size:28 final size:28
Alignment explanation
Indices: 428357--428437 Score: 69
Period size: 30 Copynumber: 2.8 Consensus size: 28
428347 ATTATTTTAT
*
428357 TTTATCTTATTTTGTATA-TATATACATA
1 TTTAT-TTATTTTTTATACTATATACATA
* *
428385 -TT-TTCATTTTATTATTACTATATATATATA
1 TTTATTTATTTT-TTA-TAC--TATATACATA
428415 TTTATTTATTTTTTATACTATAT
1 TTTATTTATTTTTTATACTATAT
428438 CTATCATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
25 6 0.14
26 3 0.07
27 4 0.10
28 5 0.12
30 12 0.29
31 5 0.12
32 7 0.17
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62
Consensus pattern (28 bp):
TTTATTTATTTTTTATACTATATACATA
Found at i:428475 original size:19 final size:21
Alignment explanation
Indices: 428451--428495 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
428441 TCATTATTAT
*
428451 TATTTAATTA-TAT-TTTTTC
1 TATTTAATTACTATATTTCTC
*
428470 TATTTATTTACTATATTTCTC
1 TATTTAATTACTATATTTCTC
428491 TATTT
1 TATTT
428496 TTGGTCTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 9 0.41
20 3 0.14
21 10 0.45
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTTAATTACTATATTTCTC
Found at i:428559 original size:25 final size:26
Alignment explanation
Indices: 428519--428586 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 26
428509 ATTTATATTA
428519 TATT-TATTAT-TATTTTCTATATATG
1 TATTGTATTATAT-TTTTCTATATATG
* * *
428544 TATTTTA-TATATTTTTC-ATGTATT
1 TATTGTATTATATTTTTCTATATATG
428568 TATTGTATTATATTTTTCT
1 TATTGTATTATATTTTTCT
428587 TATGTACATT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
24 11 0.31
25 22 0.61
26 3 0.08
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.66
Consensus pattern (26 bp):
TATTGTATTATATTTTTCTATATATG
Found at i:428599 original size:15 final size:15
Alignment explanation
Indices: 428579--428620 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
428569 ATTGTATTAT
*
428579 ATTTTTCTTATGTAC
1 ATTTTTCTTATATAC
*
428594 ATTTTTCTTATATAT
1 ATTTTTCTTATATAC
428609 ATTTTTACTTAT
1 ATTTTT-CTTAT
428621 TATTTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.24, C:0.10, G:0.02, T:0.64
Consensus pattern (15 bp):
ATTTTTCTTATATAC
Found at i:428785 original size:16 final size:16
Alignment explanation
Indices: 428742--428791 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
428732 TTTATTTCCT
*
428742 TTATTTATTCATTTT-
1 TTATTTATTCTTTTTA
428757 TTATTT-TGGTCTTTTTA
1 TTATTTAT--TCTTTTTA
*
428774 TTATTTATTCTTTATA
1 TTATTTATTCTTTTTA
428790 TT
1 TT
428792 GCATTGTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 1 0.03
15 6 0.21
16 15 0.52
17 6 0.21
18 1 0.03
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.72
Consensus pattern (16 bp):
TTATTTATTCTTTTTA
Found at i:439060 original size:66 final size:66
Alignment explanation
Indices: 438949--439076 Score: 177
Period size: 66 Copynumber: 1.9 Consensus size: 66
438939 ATACTTCGCC
* * *
438949 TAGGATGAAAACCCGAAAGGACGTCCTAAGTCGAAGAAAGAAAAAGAAAAAA-AGGAAAAAAACG
1 TAGGATGAAAACCCGAAAGGACGCCCTAAATCGAAAAAAGAAAAAGAAAAAATA-GAAAAAAACG
439013 TT
65 TT
* * * *
439015 TAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAATAAAAAGAAAAAATAGAAAAAAA
1 TAGGATGAAAACCCGAAAGGACGCCCTAAATCGAAAAAAGAAAAAGAAAAAATAGAAAAAAA
439077 GAAGAAAGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 53 0.98
67 1 0.02
ACGTcount: A:0.56, C:0.12, G:0.21, T:0.11
Consensus pattern (66 bp):
TAGGATGAAAACCCGAAAGGACGCCCTAAATCGAAAAAAGAAAAAGAAAAAATAGAAAAAAACGT
T
Found at i:439065 original size:7 final size:7
Alignment explanation
Indices: 439055--439111 Score: 51
Period size: 7 Copynumber: 7.6 Consensus size: 7
439045 TTGAAAAAAT
439055 AAAAAGAA
1 AAAAAG-A
439063 AAAATAGAA
1 AAAA-AG-A
439072 AAAAAGA
1 AAAAAGA
*
439079 AGAAAGA
1 AAAAAGA
*
439086 ACAAAAGG
1 A-AAAAGA
439094 AAAAAGA
1 AAAAAGA
*
439101 GAAAAGA
1 AAAAAGA
439108 AAAA
1 AAAA
439112 TAAGGTGGGT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
7 22 0.54
8 11 0.27
9 8 0.20
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (7 bp):
AAAAAGA
Found at i:439071 original size:9 final size:8
Alignment explanation
Indices: 439055--439105 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
439045 TTGAAAAAAT
439055 AAAAAGAA
1 AAAAAGAA
439063 AAAATAGAA
1 AAAA-AGAA
439072 AAAAAG-A
1 AAAAAGAA
*
439079 AGAAAGAA
1 AAAAAGAA
*
439087 CAAAAGGAA
1 -AAAAAGAA
*
439096 AAAGAGAA
1 AAAAAGAA
439104 AA
1 AA
439106 GAAAAATAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 15 0.43
9 14 0.40
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (8 bp):
AAAAAGAA
Found at i:441080 original size:23 final size:24
Alignment explanation
Indices: 441041--441086 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
441031 TGTATATGTT
441041 AATGTGATATTATTTATAGTATAC
1 AATGTGATATTATTTATAGTATAC
*
441065 AATGT-ATATGTA-TTATATTATA
1 AATGTGATAT-TATTTATAGTATA
441087 AATACATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (24 bp):
AATGTGATATTATTTATAGTATAC
Found at i:441091 original size:27 final size:25
Alignment explanation
Indices: 441048--441100 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 25
441038 GTTAATGTGA
*
441048 TATTATTTATAGTATACAATGTATATG
1 TATTATTTATAGAATAC-ATGT-TATG
441075 TATTATATTATA-AATACATGTTATG
1 TATTAT-TTATAGAATACATGTTATG
441100 T
1 T
441101 TACATACTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 5 0.21
26 4 0.17
27 10 0.42
28 5 0.21
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (25 bp):
TATTATTTATAGAATACATGTTATG
Found at i:442252 original size:10 final size:9
Alignment explanation
Indices: 442224--442282 Score: 50
Period size: 9 Copynumber: 6.3 Consensus size: 9
442214 CCTTTTTTTA
*
442224 TATTTTGTT
1 TATTTTATT
442233 TATTTCTATT
1 TATTT-TATT
442243 TAGTTTTA-T
1 TA-TTTTATT
442252 TATTATTA-T
1 TATT-TTATT
442261 TATTTTATTT
1 TATTTTA-TT
*
442271 TATCTTATT
1 TATTTTATT
442280 TAT
1 TAT
442283 ATACATATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
8 5 0.12
9 21 0.49
10 14 0.33
11 3 0.07
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.71
Consensus pattern (9 bp):
TATTTTATT
Found at i:442311 original size:21 final size:21
Alignment explanation
Indices: 442254--442311 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
442244 AGTTTTATTA
* *
442254 TTATTATTATTTTATTTTATC
1 TTATTATTACTATATTTTATC
442275 TTATTTATATAC-ATATTTTCAT-
1 TTA-TTAT-TACTATATTTT-ATC
442297 TTATTATTACTATAT
1 TTATTATTACTATAT
442312 ATATATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
20 3 0.10
21 11 0.35
22 13 0.42
23 4 0.13
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (21 bp):
TTATTATTACTATATTTTATC
Found at i:443709 original size:2 final size:2
Alignment explanation
Indices: 443692--443743 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
443682 ATGTGAAATT
*
443692 TA TA TA TG TA TA -A TA TA TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
443732 TA TA TA TA TA TA
1 TA TA TA TA TA TA
443744 AAAGAAGTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:445561 original size:30 final size:30
Alignment explanation
Indices: 445523--445594 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
445513 TATCAAATTT
445523 CTCATGTCATATTCTCATATGATCACATAA
1 CTCATGTCATATTCTCATATGATCACATAA
* * * *
445553 CTCGTGTCACT-TTCTCATGTGGTCACATAG
1 CTCATGTCA-TATTCTCATATGATCACATAA
445583 CTCATGTCATAT
1 CTCATGTCATAT
445595 AATCTCTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 1 0.03
30 33 0.94
31 1 0.03
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (30 bp):
CTCATGTCATATTCTCATATGATCACATAA
Found at i:445707 original size:17 final size:17
Alignment explanation
Indices: 445685--445717 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
445675 CATATACCAT
*
445685 AACATATATTTATATCA
1 AACATATACTTATATCA
445702 AACATATACTTATATC
1 AACATATACTTATATC
445718 TACTAATTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.39
Consensus pattern (17 bp):
AACATATACTTATATCA
Found at i:446235 original size:114 final size:120
Alignment explanation
Indices: 446047--446283 Score: 423
Period size: 114 Copynumber: 2.0 Consensus size: 120
446037 TAGGGTACCG
446047 ATACCCTACCCTGGTATCGATACCAAAATTAGCTTCGATGTTCCCTAGTATCGATACTCATTCCT
1 ATACCCTACCCTGGTATCGATACCAAAATTAGCTTCGATGTTCCCTA-TATCGATACTCATTCCT
446112 TATGATATCGATACTTTTCATACAGGTACTGATACCCCATGCGTAATTTTCTCATA
65 TATGATATCGATACTTTTCATACAGGTACTGATACCCCATGCGTAATTTTCTCATA
446168 ATACCCTACCCTGGTA-CGATACCAAAATTA-CTTCGATGTTCCCT-TA-CGA-ACT-ATTCCTT
1 ATACCCTACCCTGGTATCGATACCAAAATTAGCTTCGATGTTCCCTATATCGATACTCATTCCTT
446227 ATGATATCGATACTTTTCATACAGGTACTGATACCCCATGCGTAATTTTCTCATA
66 ATGATATCGATACTTTTCATACAGGTACTGATACCCCATGCGTAATTTTCTCATA
446282 AT
1 AT
446284 TTGCCTTGTA
Statistics
Matches: 116, Mismatches: 0, Indels: 7
0.94 0.00 0.06
Matches are distributed among these distances:
114 64 0.55
115 3 0.03
116 3 0.03
117 2 0.02
119 14 0.12
120 14 0.12
121 16 0.14
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.35
Consensus pattern (120 bp):
ATACCCTACCCTGGTATCGATACCAAAATTAGCTTCGATGTTCCCTATATCGATACTCATTCCTT
ATGATATCGATACTTTTCATACAGGTACTGATACCCCATGCGTAATTTTCTCATA
Found at i:447255 original size:17 final size:18
Alignment explanation
Indices: 447227--447280 Score: 74
Period size: 17 Copynumber: 3.0 Consensus size: 18
447217 TTTTTATCTA
447227 AAATAAATATTTAATTATT
1 AAAT-AATATTTAATTATT
*
447246 AAATAA-ATTTAATTACT
1 AAATAATATTTAATTATT
*
447263 AAGTAATATTTAATTATT
1 AAATAATATTTAATTATT
447281 TGAATCACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.48
18 12 0.39
19 4 0.13
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (18 bp):
AAATAATATTTAATTATT
Found at i:452708 original size:60 final size:60
Alignment explanation
Indices: 452592--452724 Score: 155
Period size: 60 Copynumber: 2.2 Consensus size: 60
452582 AAAGTTGGGT
* * *
452592 AAAG-TACATAAATGGTCCCTTGACTATAGTATATTATTTTATTAATTCTTATGACTATTA
1 AAAGTTACA-AAATGGTCCCTTGACTATAGTATATTAATTTATTAAGTCTTACGACTATTA
* * *
452652 AAAGTTACAAAATGGTCCCTTGACTATAAG-ATGTTAATTTGTTGAGTCTCT-CGACTATTA
1 AAAGTTACAAAATGGTCCCTTGACTAT-AGTATATTAATTTATTAAGTCT-TACGACTATTA
*
452712 TAAGTTACAAAAT
1 AAAGTTACAAAAT
452725 AGTTACCGAC
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
60 56 0.89
61 7 0.11
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (60 bp):
AAAGTTACAAAATGGTCCCTTGACTATAGTATATTAATTTATTAAGTCTTACGACTATTA
Found at i:454228 original size:23 final size:23
Alignment explanation
Indices: 454202--454256 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
454192 CGCTTATATT
*
454202 ATACGTTTTCATCTCCCTTTATG
1 ATACGTTTTCATATCCCTTTATG
* *
454225 ATACGTTTTTTATATGCCTTTATG
1 ATACG-TTTTCATATCCCTTTATG
*
454249 ACACGTTT
1 ATACGTTT
454257 ATTATGCCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 8 0.30
24 19 0.70
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.49
Consensus pattern (23 bp):
ATACGTTTTCATATCCCTTTATG
Found at i:454265 original size:22 final size:24
Alignment explanation
Indices: 454217--454267 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
454207 TTTTCATCTC
* *
454217 CCTTTATGATACGTTTTTTATATG
1 CCTTTATGACACGTTTTATATATG
454241 CCTTTATGACACG-TTTAT-TATG
1 CCTTTATGACACGTTTTATATATG
454263 CCTTT
1 CCTTT
454268 TGGTATGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.36
23 4 0.16
24 12 0.48
ACGTcount: A:0.20, C:0.18, G:0.12, T:0.51
Consensus pattern (24 bp):
CCTTTATGACACGTTTTATATATG
Found at i:454896 original size:2 final size:2
Alignment explanation
Indices: 454889--454932 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
454879 AATCAAAGTG
454889 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
454931 AT
1 AT
454933 TATTAAGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:455740 original size:21 final size:21
Alignment explanation
Indices: 455710--455825 Score: 73
Period size: 21 Copynumber: 5.6 Consensus size: 21
455700 GATTTATATA
*
455710 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
* * *
455731 TTCGCGTTGCGA-ATTTCCAAA
1 TTCGCGTTGCGATA-GTCGAAG
*
455752 TT--CATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
* *
455771 TTCGCGTTGCGATTTATTAC-AAA
1 TTCGCGTTGCGA--TAGT-CGAAG
455794 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
* *
455813 TTTGTGTTGCGAT
1 TTCGCGTTGCGAT
455826 TTATTCCAAA
Statistics
Matches: 71, Mismatches: 14, Indels: 20
0.68 0.13 0.19
Matches are distributed among these distances:
18 1 0.01
19 20 0.28
20 2 0.03
21 40 0.56
23 7 0.10
24 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCGAAG
Found at i:455807 original size:42 final size:42
Alignment explanation
Indices: 455716--455850 Score: 211
Period size: 42 Copynumber: 3.3 Consensus size: 42
455706 TATATTCGCA
* *
455716 TTGCGATAGTCGAAGTTCGCGTTGCGA-AT-TTCCAAATTCA
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
455756 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
455798 TTGCGATAGTCGAAGTTTGTGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
455840 TTGCGATAGTC
1 TTGCGATAGTC
455851 CAAAATCGCA
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
40 27 0.31
41 1 0.01
42 59 0.68
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:455842 original size:21 final size:21
Alignment explanation
Indices: 455775--455846 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
455765 TCGAAGTTCG
*
455775 CGTTGCGATTTATTACAAATT
1 CGTTGCGATTTATTCCAAATT
* * *
455796 CGTTGCGA--TAGTCGAAGTTT
1 CGTTGCGATTTATTCCAA-ATT
*
455816 GTGTTGCGATTTATTCCAAATT
1 -CGTTGCGATTTATTCCAAATT
455838 CGTTGCGAT
1 CGTTGCGAT
455847 AGTCCAAAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
19 5 0.13
20 2 0.05
21 23 0.61
22 2 0.05
23 6 0.16
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.40
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATT
Found at i:456548 original size:23 final size:23
Alignment explanation
Indices: 456520--456565 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
456510 CAAATGCAAT
*
456520 TTTGGAATAAATCGCAACGCGAA
1 TTTGGAATAAATCGCAACACGAA
456543 TTTGGAATAAATCGCAACACGAA
1 TTTGGAATAAATCGCAACACGAA
456566 CTTCGACTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (23 bp):
TTTGGAATAAATCGCAACACGAA
Found at i:467961 original size:26 final size:26
Alignment explanation
Indices: 467926--467983 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
467916 GGACACTTAC
* *
467926 TGCA-TATGGTGGGCATGACCTTGTG
1 TGCATTATGGTGGGCACGACCTTATG
467951 TGCATTATGGTGGGCACGACCTTATG
1 TGCATTATGGTGGGCACGACCTTATG
*
467977 TGTATTA
1 TGCATTA
467984 GCACTTCGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 4 0.14
26 25 0.86
ACGTcount: A:0.19, C:0.16, G:0.31, T:0.34
Consensus pattern (26 bp):
TGCATTATGGTGGGCACGACCTTATG
Found at i:468379 original size:15 final size:15
Alignment explanation
Indices: 468359--468387 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
468349 ACCTATCAAG
468359 GATTATATCTCCAGA
1 GATTATATCTCCAGA
468374 GATTATATCTCCAG
1 GATTATATCTCCAG
468388 TATCAGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (15 bp):
GATTATATCTCCAGA
Found at i:473673 original size:26 final size:26
Alignment explanation
Indices: 473633--473695 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
473623 ATAAAGGACA
*
473633 CTTA-GTGCA-TATGGTGGGCATGAC
1 CTTATGTGCATTATGGTGGGCACGAC
*
473657 CTTGTGTGCATTATGGTGGGCACGAC
1 CTTATGTGCATTATGGTGGGCACGAC
*
473683 CTTATGTGTATTA
1 CTTATGTGCATTA
473696 GCACTTCGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 3 0.09
25 5 0.15
26 25 0.76
ACGTcount: A:0.19, C:0.16, G:0.30, T:0.35
Consensus pattern (26 bp):
CTTATGTGCATTATGGTGGGCACGAC
Found at i:474092 original size:15 final size:15
Alignment explanation
Indices: 474072--474100 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
474062 ACCTATCGAG
474072 GATTATATCTCCAGA
1 GATTATATCTCCAGA
474087 GATTATATCTCCAG
1 GATTATATCTCCAG
474101 TATCAGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (15 bp):
GATTATATCTCCAGA
Found at i:479791 original size:26 final size:26
Alignment explanation
Indices: 479751--479813 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
479741 ATAAAGGACA
*
479751 CTTA-GTGCA-TATGGTGGGCATGAC
1 CTTATGTGCATTATGGTGGGCACGAC
*
479775 CTTGTGTGCATTATGGTGGGCACGAC
1 CTTATGTGCATTATGGTGGGCACGAC
*
479801 CTTATGTGTATTA
1 CTTATGTGCATTA
479814 GCACTTCGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 3 0.09
25 5 0.15
26 25 0.76
ACGTcount: A:0.19, C:0.16, G:0.30, T:0.35
Consensus pattern (26 bp):
CTTATGTGCATTATGGTGGGCACGAC
Found at i:480210 original size:15 final size:15
Alignment explanation
Indices: 480190--480218 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
480180 ACCTATCGAG
480190 GATTATATCTCCAGA
1 GATTATATCTCCAGA
480205 GATTATATCTCCAG
1 GATTATATCTCCAG
480219 TATCAGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (15 bp):
GATTATATCTCCAGA
Found at i:485924 original size:26 final size:26
Alignment explanation
Indices: 485884--485946 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
485874 ATAAAGGACA
*
485884 CTTA-GTGCA-TATGGTGGGCATGAC
1 CTTATGTGCATTATGGTGGGCACGAC
*
485908 CTTGTGTGCATTATGGTGGGCACGAC
1 CTTATGTGCATTATGGTGGGCACGAC
*
485934 CTTATGTGTATTA
1 CTTATGTGCATTA
485947 GCACTTCGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 3 0.09
25 5 0.15
26 25 0.76
ACGTcount: A:0.19, C:0.16, G:0.30, T:0.35
Consensus pattern (26 bp):
CTTATGTGCATTATGGTGGGCACGAC
Found at i:486333 original size:15 final size:15
Alignment explanation
Indices: 486313--486341 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
486303 ACCTATCGAG
486313 GATTATATCTCCAGA
1 GATTATATCTCCAGA
486328 GATTATATCTCCAG
1 GATTATATCTCCAG
486342 TATCAGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (15 bp):
GATTATATCTCCAGA
Found at i:492089 original size:26 final size:26
Alignment explanation
Indices: 492013--492091 Score: 115
Period size: 26 Copynumber: 3.0 Consensus size: 26
492003 CCTTAGGGCA
**
492013 TATGGTGGGCACAACCTTATGTGT-T
1 TATGGTGGGCATGACCTTATGTGTAT
*
492038 ATATGGTGGGCATGACTTTATGTGTAT
1 -TATGGTGGGCATGACCTTATGTGTAT
492065 TATGGTGGGCATGACCTTATGTGTAT
1 TATGGTGGGCATGACCTTATGTGTAT
492091 T
1 T
492092 TGCACTTCGG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
26 47 0.98
27 1 0.02
ACGTcount: A:0.20, C:0.11, G:0.29, T:0.39
Consensus pattern (26 bp):
TATGGTGGGCATGACCTTATGTGTAT
Found at i:492419 original size:31 final size:31
Alignment explanation
Indices: 492381--492444 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
492371 ACTAAGTGTA
*
492381 TACTTAGTATGCGATGATTCTTACTTGTAGG
1 TACTTAGTATGCGATGATTCTCACTTGTAGG
492412 TACTTAGTATGCGATGATTCTCACTTGTAGG
1 TACTTAGTATGCGATGATTCTCACTTGTAGG
492443 TA
1 TA
492445 AAAAGCAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.23, C:0.14, G:0.22, T:0.41
Consensus pattern (31 bp):
TACTTAGTATGCGATGATTCTCACTTGTAGG
Found at i:493924 original size:14 final size:15
Alignment explanation
Indices: 493900--493930 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
493890 AACACCACGA
493900 AAAGAAGAAGAAAAT
1 AAAGAAGAAGAAAAT
493915 AAAGAA-AAGAAAAT
1 AAAGAAGAAGAAAAT
493929 AA
1 AA
493931 TGGAGCTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.06
Consensus pattern (15 bp):
AAAGAAGAAGAAAAT
Found at i:494067 original size:39 final size:39
Alignment explanation
Indices: 493995--494188 Score: 255
Period size: 39 Copynumber: 4.9 Consensus size: 39
493985 TTATACTAAA
* * *
493995 AATAAAAGACTCTCCAACTTCCAAGAG-CTCTTAAATTCAC
1 AATAAAA-A-TCTCTAACTCCCAAAAGACTCTTAAATTCAC
*
494035 AATAAAAATCTCTAACTCTCAAAAGACTCTTAAATTCAC
1 AATAAAAATCTCTAACTCCCAAAAGACTCTTAAATTCAC
* *
494074 AATAAAAATCTATAACTCCCAATAGACTCTTAAATTCAC
1 AATAAAAATCTCTAACTCCCAAAAGACTCTTAAATTCAC
* * * *
494113 AATAAAAATATCTAACTCCTAAAAAACTCTTAAATTCAG
1 AATAAAAATCTCTAACTCCCAAAAGACTCTTAAATTCAC
* *
494152 AATAAAAATCTCTAACTCCCAAAATACTCTTCAATTC
1 AATAAAAATCTCTAACTCCCAAAAGACTCTTAAATTC
494189 CCCCTTAAAT
Statistics
Matches: 136, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
38 13 0.10
39 116 0.85
40 7 0.05
ACGTcount: A:0.45, C:0.24, G:0.03, T:0.28
Consensus pattern (39 bp):
AATAAAAATCTCTAACTCCCAAAAGACTCTTAAATTCAC
Found at i:497886 original size:20 final size:20
Alignment explanation
Indices: 497860--497912 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
497850 TGATTCAAGT
497860 GGTATCGATACCAAGAGG-G
1 GGTATCGATACCAAGAGGAG
* * *
497879 GAGTATCGATACTATGAGGAT
1 G-GTATCGATACCAAGAGGAG
497900 GGTATCGATACCA
1 GGTATCGATACCA
497913 TTGTTAACAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.23
Consensus pattern (20 bp):
GGTATCGATACCAAGAGGAG
Found at i:498410 original size:55 final size:55
Alignment explanation
Indices: 498326--498579 Score: 287
Period size: 55 Copynumber: 4.6 Consensus size: 55
498316 AAATAGGTTC
* *
498326 TATGTATGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACAGGCAA
1 TATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACAAGCAA
* * * * * *
498381 TATGTGTGCAAAACCATGGAATTCATCATGAGTTTATGAATAACCGTA-TAGACAC
1 TATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACAAG-CAA
* * *
498436 TATGTGTGTAAATCCACGAAATTCATCATTAGTTGATGAATAACCATACAAG-AA
1 TATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACAAGCAA
* * * * *
498490 CTTTGTGCGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCTTACAAGCAC
1 -TATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACAAGCAA
* * * * *
498546 TATATATACAAATCCATGAAATTCATCAAGAGTT
1 TATGTGTGCAAATCCACGAAATTCATCATGAGTT
498580 AATTGATATT
Statistics
Matches: 163, Mismatches: 32, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
54 2 0.01
55 158 0.97
56 3 0.02
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (55 bp):
TATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACAAGCAA
Found at i:498518 original size:110 final size:110
Alignment explanation
Indices: 498325--498579 Score: 334
Period size: 110 Copynumber: 2.3 Consensus size: 110
498315 CAAATAGGTT
* * *
498325 CTATGTATGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACAGGCAATATGTGTGC
1 CTATGTATGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCATACAAGCAATATGTGCGC
* *
498390 AAAACCATGGAATTCATCATGAGTTTATGAATAACCGTATAGACA
66 AAAACCACGGAATTCATCATGAGTTGATGAATAACCGTATAGACA
* * * *
498435 CTATGTGTGTAAATCCACGAAATTCATCATTAGTTGATGAATAACCATACAAG-AACTTTGTGCG
1 CTATGTATGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCATACAAGCAA-TATGTGCG
* * *
498499 CAAATCCACGGAATTCATCATGAGTTGATGAATAACCTTACA-AGCA
65 CAAAACCACGGAATTCATCATGAGTTGATGAATAACCGTATAGA-CA
* * * *
498545 CTATATATACAAATCCATGAAATTCATCAAGAGTT
1 CTATGTATGCAAATCCACGAAATTCATCATGAGTT
498580 AATTGATATT
Statistics
Matches: 124, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
109 3 0.02
110 121 0.98
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (110 bp):
CTATGTATGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCATACAAGCAATATGTGCGC
AAAACCACGGAATTCATCATGAGTTGATGAATAACCGTATAGACA
Found at i:498933 original size:45 final size:45
Alignment explanation
Indices: 498884--499104 Score: 203
Period size: 45 Copynumber: 4.8 Consensus size: 45
498874 GCATAACATT
* *
498884 GTATAAAATGCATGAAAGGATGCCATAAATGAAATGTATAATTGA
1 GTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGA
* *
498929 GTATAAAAAAAGGGCATGAAAGTATGCCATAAATGAAATGTATAATAGT
1 GTAT---AAAA-GGCATGAAAGGATGCCATAAATGAAATGTATAATAGA
* * * *
498978 TTATAAAAGGGCATGAAATGATTCCATAAATGAAATGTATAATAGC
1 GTATAAAA-GGCATGAAAGGATGCCATAAATGAAATGTATAATAGA
* * * * *
499024 GTATAAAAGGCTTAAAAGGATGCTATAAATAAAATGCAT-AT-GA
1 GTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGA
* ** * *
499067 GTGCATTATCGACATGAAAGGATGCCATAATTGAAATG
1 GT--ATAAAAGGCATGAAAGGATGCCATAAATGAAATG
499105 CATATGGGTG
Statistics
Matches: 143, Mismatches: 27, Indels: 12
0.79 0.15 0.07
Matches are distributed among these distances:
43 3 0.02
44 2 0.01
45 53 0.37
46 45 0.31
48 4 0.03
49 36 0.25
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.26
Consensus pattern (45 bp):
GTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGA
Found at i:498956 original size:49 final size:49
Alignment explanation
Indices: 498893--499031 Score: 187
Period size: 46 Copynumber: 2.9 Consensus size: 49
498883 TGTATAAAAT
*
498893 GCATGAAAGGATGCCATAAATGAAATGTATAATTGAGTATAAAAAAAGG
1 GCATGAAAGTATGCCATAAATGAAATGTATAATTGAGTATAAAAAAAGG
* *
498942 GCATGAAAGTATGCCATAAATGAAATGTATAA-T-AGT-TTATAAAAGG
1 GCATGAAAGTATGCCATAAATGAAATGTATAATTGAGTATAAAAAAAGG
* * *
498988 GCATGAAA-TGATTCCATAAATGAAATGTATAATAGCGTATAAAA
1 GCATGAAAGT-ATGCCATAAATGAAATGTATAATTGAGTATAAAA
499032 GGCTTAAAAG
Statistics
Matches: 78, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
45 1 0.01
46 37 0.47
47 3 0.04
48 3 0.04
49 34 0.44
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.26
Consensus pattern (49 bp):
GCATGAAAGTATGCCATAAATGAAATGTATAATTGAGTATAAAAAAAGG
Found at i:499005 original size:46 final size:45
Alignment explanation
Indices: 498885--499059 Score: 183
Period size: 46 Copynumber: 3.8 Consensus size: 45
498875 CATAACATTG
*
498885 TATAAAA-TGCATGAAAGGATGCCATAAATGAAATGTATAATTGAGTAT
1 TATAAAAGGGCATGAAA-GATGCCATAAATGAAATGTATAA-T-AGT-T
* *
498933 AAAAAAAGGGCATGAAAGTATGCCATAAATGAAATGTATAATAGTT
1 TATAAAAGGGCATGAAAG-ATGCCATAAATGAAATGTATAATAGTT
* **
498979 TATAAAAGGGCATGAAATGATTCCATAAATGAAATGTATAATAGCG
1 TATAAAAGGGCATGAAA-GATGCCATAAATGAAATGTATAATAGTT
* * * *
499025 TATAAAA-GGCTTAAAAGGATGCTATAAATAAAATG
1 TATAAAAGGGCATGAAA-GATGCCATAAATGAAATG
499060 CATATGAGTG
Statistics
Matches: 110, Mismatches: 14, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
45 22 0.20
46 47 0.43
47 4 0.04
48 7 0.06
49 30 0.27
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.26
Consensus pattern (45 bp):
TATAAAAGGGCATGAAAGATGCCATAAATGAAATGTATAATAGTT
Found at i:499105 original size:45 final size:44
Alignment explanation
Indices: 499038--499255 Score: 292
Period size: 45 Copynumber: 4.8 Consensus size: 44
499028 AAAAGGCTTA
* * * *
499038 AAAGGATGCTATAAATAAAATGCATATGAGTGCATTATCGACATG
1 AAAGGATGCCATAATTGAAATGCATATG-GTGCATTATCGGCATG
499083 AAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGGCATG
1 AAAGGATGCCATAATTGAAATGCATAT-GGTGCATTATCGGCATG
* *
499128 AAAAGATGCCATAATTGAAATGCATATGGGTGCATTATTGGCATG
1 AAAGGATGCCATAATTGAAATGCATAT-GGTGCATTATCGGCATG
* * *
499173 AAAGGATGCCATAATTAAAATACATATGGTGCATTATTGGCATG
1 AAAGGATGCCATAATTGAAATGCATATGGTGCATTATCGGCATG
* *
499217 AAAGAATGCCATAAATGAAAATGCATAATGGTGCATTAT
1 AAAGGATGCCATAATTG-AAATGCAT-ATGGTGCATTAT
499256 AAGTATGATT
Statistics
Matches: 157, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
44 31 0.20
45 113 0.72
46 13 0.08
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (44 bp):
AAAGGATGCCATAATTGAAATGCATATGGTGCATTATCGGCATG
Found at i:506670 original size:121 final size:122
Alignment explanation
Indices: 506453--506688 Score: 348
Period size: 121 Copynumber: 1.9 Consensus size: 122
506443 CCCAAGCCTG
* * * *
506453 GGTCTTTGATACGCCTGCGGAGATGTCGTTGTCTCAATCGTGAAACCCAGCACGCGCCGTCTCGG
1 GGTCTTTGATACGCCTGCGGAGATGCCGTCGCCTCAATCGTGAAACCCAGCACGCCCCGTCTCGG
* **
506518 CGTGCTTCGGCATTGGCGTGCTCAGGACGTCGGCCTGCGGG-TCCCCATCAGGCTCA
66 CGTGCTTCGACATCAGCGTGCTCAGGACGTCGGCCTGCGGGCTCCCCATCAGGCTCA
* ** *
506574 GGTCTTTGATACGCCTGCGGATATGCCGTCGCCTTGATCGTGGAACCCAGCACGCCCCGTCTCGG
1 GGTCTTTGATACGCCTGCGGAGATGCCGTCGCCTCAATCGTGAAACCCAGCACGCCCCGTCTCGG
* *
506639 CGTGTTTCGACATCAGCGTGCTCAGGGCGTCGGCCTGCGGGCTCCCCATC
66 CGTGCTTCGACATCAGCGTGCTCAGGACGTCGGCCTGCGGGCTCCCCATC
506689 CTGCCCGTCT
Statistics
Matches: 101, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
121 93 0.92
122 8 0.08
ACGTcount: A:0.13, C:0.33, G:0.31, T:0.23
Consensus pattern (122 bp):
GGTCTTTGATACGCCTGCGGAGATGCCGTCGCCTCAATCGTGAAACCCAGCACGCCCCGTCTCGG
CGTGCTTCGACATCAGCGTGCTCAGGACGTCGGCCTGCGGGCTCCCCATCAGGCTCA
Found at i:512411 original size:19 final size:19
Alignment explanation
Indices: 512387--512430 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
512377 GGTGTGCATG
512387 CTGACCGG-TCTGAACAGGT
1 CTGACCGGTTC-GAACAGGT
*
512406 CTGACCGGTTCGAACCGGT
1 CTGACCGGTTCGAACAGGT
512425 CTGACC
1 CTGACC
512431 CGACACGACC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 21 0.91
20 2 0.09
ACGTcount: A:0.18, C:0.32, G:0.30, T:0.20
Consensus pattern (19 bp):
CTGACCGGTTCGAACAGGT
Found at i:512618 original size:86 final size:87
Alignment explanation
Indices: 512468--512688 Score: 304
Period size: 86 Copynumber: 2.5 Consensus size: 87
512458 TGACCCGACC
*
512468 CGGTGATATTTTGGTAATTATTTTTAAAATGGTGATATTTTGGTAATTATTATTAAAACAGTGAT
1 CGGTGATATTTTGGTAATTATTTTTAAAAAGGTGATATTTTGGTAATTATTATTAAAACAGTGAT
512533 ATTTT-GGTAATTATTTTT-AAA
66 ATTTTAGG-AATTATTTTTAAAA
* * *
512554 CGGTGATATTTTGGGAATTATTTTTAAAAAGGTGATATTTTAGG-AATTATTTTTAAAACGGTGA
1 CGGTGATATTTTGGTAATTATTTTTAAAAAGGTGATATTTT-GGTAATTATTATTAAAACAGTGA
512618 TATTTTAGGAATTATTTTTAAAA
65 TATTTTAGGAATTATTTTTAAAA
* * * * * *
512641 GGGAGATATTTTTGTAAATATTTTTAAAAACGGTGCTATTTTCGTAAT
1 CGGTGATATTTTGGTAATTATTTTTAAAAA-GGTGATATTTTGGTAAT
512689 AATTGCTGTG
Statistics
Matches: 119, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
86 73 0.61
87 33 0.28
88 13 0.11
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.46
Consensus pattern (87 bp):
CGGTGATATTTTGGTAATTATTTTTAAAAAGGTGATATTTTGGTAATTATTATTAAAACAGTGAT
ATTTTAGGAATTATTTTTAAAA
Found at i:512689 original size:29 final size:29
Alignment explanation
Indices: 512468--512688 Score: 295
Period size: 29 Copynumber: 7.6 Consensus size: 29
512458 TGACCCGACC
512468 CGGTGATATTTTGGTAATTATTTTTAAAA
1 CGGTGATATTTTGGTAATTATTTTTAAAA
* *
512497 TGGTGATATTTTGGTAATTATTATTAAAA
1 CGGTGATATTTTGGTAATTATTTTTAAAA
*
512526 CAGTGATATTTTGGTAATTATTTTT-AAA
1 CGGTGATATTTTGGTAATTATTTTTAAAA
*
512554 CGGTGATATTTTGGGAATTATTTTTAAAA
1 CGGTGATATTTTGGTAATTATTTTTAAAA
*
512583 AGGTGATATTTTAGG-AATTATTTTTAAAA
1 CGGTGATATTTT-GGTAATTATTTTTAAAA
512612 CGGTGATATTTTAGG-AATTATTTTTAAAA
1 CGGTGATATTTT-GGTAATTATTTTTAAAA
* * * *
512641 GGGAGATATTTTTGTAAATATTTTTAAAAA
1 CGGTGATATTTTGGTAATTATTTTT-AAAA
* *
512671 CGGTGCTATTTTCGTAAT
1 CGGTGATATTTTGGTAAT
512689 AATTGCTGTG
Statistics
Matches: 170, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
28 27 0.16
29 124 0.73
30 19 0.11
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.46
Consensus pattern (29 bp):
CGGTGATATTTTGGTAATTATTTTTAAAA
Found at i:515000 original size:22 final size:21
Alignment explanation
Indices: 514971--515014 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
514961 CAATATTGTA
*
514971 ATAGAGTATCGGTACCATGGT
1 ATAGAGTATCGATACCATGGT
514992 ATAGTAGTATCGATACCATGGT
1 ATAG-AGTATCGATACCATGGT
515014 A
1 A
515015 GGGTTATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (21 bp):
ATAGAGTATCGATACCATGGT
Found at i:515439 original size:55 final size:55
Alignment explanation
Indices: 515354--515684 Score: 384
Period size: 55 Copynumber: 6.1 Consensus size: 55
515344 GCAAATAGGT
** * * * *
515354 ACTATGTGTGCAAATCCATTGAATTTATCATGACTTGGTTAATAACCGTACAGGC
1 ACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGC
* *
515409 ACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACAGGA
1 ACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGC
* ** * * *
515464 AC--TGTTTAAAAATACACGGAATTCATTATGAGTTGATGAATAACCGTACAGAC
1 ACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGC
* * * *
515517 ACTGTGTGTGTAAATCCACGGAATTCATCATGAGTTGATGAATAACTGTACATGC
1 ACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGC
* *
515572 ACTATCG-GTGCAAATCCACGGAATTCATCATTAGTTGATGAATAACCGTACAGGT
1 ACTAT-GTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGC
* * ** *
515627 ACGATGTGTGC-AACCCACAAAATTCATCATGAGTTGATGAACT-ACCGTATAGGC
1 ACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAA-TAACCGTACAGGC
515681 ACTA
1 ACTA
515685 CGTGCGCATC
Statistics
Matches: 234, Mismatches: 37, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
53 45 0.19
54 39 0.17
55 149 0.64
56 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Consensus pattern (55 bp):
ACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGC
Found at i:515568 original size:108 final size:108
Alignment explanation
Indices: 515374--515684 Score: 349
Period size: 108 Copynumber: 2.9 Consensus size: 108
515364 CAAATCCATT
* * * * *
515374 GAATTTATCATGACTTGGTTAATAACCGTACAGGCACTATGTGTGCAAATCCACAGAATTCATCA
1 GAATTCATCATGAGTTGATGAATAACCGTACAGGCACTGTGTGTG-AAATCCACAGAATTCATCA
* *
515439 TGAGTTGATGAATAACCGTACAGGAACTGT-TTAAAAATACACG
65 TGAGTTGATGAATAACCGTACAGGAACTATCGTAAAAATACACG
* * *
515482 GAATTCATTATGAGTTGATGAATAACCGTACAGACACTGTGTGTGTAAATCCACGGAATTCATCA
1 GAATTCATCATGAGTTGATGAATAACCGTACAGGCACTGTGTGTG-AAATCCACAGAATTCATCA
* * * ** *
515547 TGAGTTGATGAATAACTGTACATGCACTATCGGTGCAAATCCACG
65 TGAGTTGATGAATAACCGTACAGGAACTATC-GTAAAAATACACG
* * * * *
515592 GAATTCATCATTAGTTGATGAATAACCGTACAGGTAC-GATGTGTGCAACCCACAAAATTCATCA
1 GAATTCATCATGAGTTGATGAATAACCGTACAGGCACTG-TGTGTGAAATCCACAGAATTCATCA
* *
515656 TGAGTTGATGAACT-ACCGTATAGGCACTA
65 TGAGTTGATGAA-TAACCGTACAGGAACTA
515685 CGTGCGCATC
Statistics
Matches: 171, Mismatches: 28, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
108 82 0.48
109 40 0.23
110 49 0.29
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (108 bp):
GAATTCATCATGAGTTGATGAATAACCGTACAGGCACTGTGTGTGAAATCCACAGAATTCATCAT
GAGTTGATGAATAACCGTACAGGAACTATCGTAAAAATACACG
Found at i:515979 original size:68 final size:68
Alignment explanation
Indices: 515846--515979 Score: 187
Period size: 68 Copynumber: 2.0 Consensus size: 68
515836 GATTAATAGT
* * * * *
515846 CTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
1 CTAGCTGTGCATTTGACAGAAAAGTGTCAATTATACCAGTTAGATGAAAGGCTAAATACCGTTGA
515911 GGC
66 GGC
* * * *
515914 CTAGCTGTGCATTTGATAGAAATGTGTCAATTATACCAGTTAGATGAGAGGCTAAATATCGTTGA
1 CTAGCTGTGCATTTGACAGAAAAGTGTCAATTATACCAGTTAGATGAAAGGCTAAATACCGTTGA
515979 G
66 G
515980 TAAAAGATTA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 57 1.00
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (68 bp):
CTAGCTGTGCATTTGACAGAAAAGTGTCAATTATACCAGTTAGATGAAAGGCTAAATACCGTTGA
GGC
Found at i:516214 original size:46 final size:45
Alignment explanation
Indices: 516076--516253 Score: 234
Period size: 46 Copynumber: 3.8 Consensus size: 45
516066 GACTAGTTGT
*
516076 ATGACAATGTATAA-CGTTGTATAAAAGGCATGAAAGGATACCATAA
1 ATGA-AATGTATAATAG-TGTATAAAAGGCATGAAAGGATACCATAA
* *
516122 ATGAAATGTATAATA-TCGTATAAAAAAGTGCATGAAAAGATGCCATAA
1 ATGAAATGTATAATAGT-GTAT--AAAAG-GCATGAAAGGATACCATAA
516170 ATGAAATGTATAATAGTGTATAAAAGGGCATGAAAGGATACCATAA
1 ATGAAATGTATAATAGTGTATAAAA-GGCATGAAAGGATACCATAA
* *
516216 ATGAAATGTATAATAGCGTATAAAAGGCATAAAAGGAT
1 ATGAAATGTATAATAGTGTATAAAAGGCATGAAAGGAT
516254 GTCATAAACA
Statistics
Matches: 118, Mismatches: 7, Indels: 15
0.84 0.05 0.11
Matches are distributed among these distances:
44 1 0.01
45 25 0.21
46 49 0.42
47 6 0.05
48 36 0.31
49 1 0.01
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (45 bp):
ATGAAATGTATAATAGTGTATAAAAGGCATGAAAGGATACCATAA
Found at i:516290 original size:45 final size:45
Alignment explanation
Indices: 516241--516453 Score: 266
Period size: 45 Copynumber: 4.7 Consensus size: 45
516231 GCGTATAAAA
* * ** * *
516241 GGCATAAAAGGATGTCATAAACAAATTGCATATGGGTACATTATC
1 GGCATGAAAGGATGCCATAATGAAAATGCATATGGGTGCATTATC
* *
516286 GGCATGAAAGGATGCCATAATTG-AAATGCATAAGGGTGCTTTATC
1 GGCATGAAAGGATGCCATAA-TGAAAATGCATATGGGTGCATTATC
* *
516331 GACATGAAAGGATGCCATAATTAAAATGCATATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAATGAAAATGCATATGGGTGCATTATC
* * * *
516376 GGCATAAAATGATGCCATAATTAAAATGCATATGGGTGCATTATT
1 GGCATGAAAGGATGCCATAATGAAAATGCATATGGGTGCATTATC
*
516421 GGCATGAAAGAATGCCATAAATGAAAATGCATA
1 GGCATGAAAGGATGCCAT-AATGAAAATGCATA
516454 ATGGTACATT
Statistics
Matches: 145, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
44 1 0.01
45 131 0.90
46 13 0.09
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (45 bp):
GGCATGAAAGGATGCCATAATGAAAATGCATATGGGTGCATTATC
Found at i:528379 original size:19 final size:19
Alignment explanation
Indices: 528342--528379 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
528332 TGATCATTTC
*
528342 ATGTTGTTTGCATTGTTAT
1 ATGTTGTTGGCATTGTTAT
528361 ATGTTGTTAGGCATT-TTAT
1 ATGTTGTT-GGCATTGTTAT
528380 TTTAGAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.18, C:0.05, G:0.21, T:0.55
Consensus pattern (19 bp):
ATGTTGTTGGCATTGTTAT
Found at i:534319 original size:77 final size:79
Alignment explanation
Indices: 534230--534378 Score: 187
Period size: 77 Copynumber: 1.9 Consensus size: 79
534220 TTAATAAATT
**
534230 TCTTATTTAATTAGTCCAAATTAAATAT-ACATT-AAAGACTTATAATCTGAATTACAATC-TCT
1 TCTTATTTAATTAGTCCAAATTAAATATCA-ATTAAAAGACTTATAATCAAAATTACAATCTTCT
534292 AATGTTTATTTAAAA
65 AATGTTTATTTAAAA
* ** * * * *
534307 TCTTATTTAATTATTCTGAATTAAATATCAATTAAAAGAGTTGTAATCAAAATTACATTCTTTTA
1 TCTTATTTAATTAGTCCAAATTAAATATCAATTAAAAGACTTATAATCAAAATTACAATCTTCTA
534372 ATGTTTA
66 ATGTTTA
534379 CTTACTATAT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
77 28 0.47
78 22 0.37
79 10 0.17
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (79 bp):
TCTTATTTAATTAGTCCAAATTAAATATCAATTAAAAGACTTATAATCAAAATTACAATCTTCTA
ATGTTTATTTAAAA
Found at i:537975 original size:746 final size:747
Alignment explanation
Indices: 536543--537981 Score: 2628
Period size: 746 Copynumber: 1.9 Consensus size: 747
536533 GATAAGCCCT
*
536543 TAATGGACCAAGTGCATGTCTATAAAGGATTGTCTCTGACATTCTAGATGAAGGGATGAAAATGT
1 TAATGGACCAAGTGCATGTCTATAAAGGATTATCTCTGACATTCTAGATGAAGGGATGAAAATGT
* *
536608 GAGACATTCTCCAAGCGAATATGTTAATTGAAAAACTACCCAAGTCATAGTCTGATTTACACAAA
66 GAGACATTCCCCAAGCGAATATGTTAATTGAAAAACTACCCAAGTCATAGTCCGATTTACACAAA
* *
536673 AAAAGAGTTATTTCCATGGAAGAGCATATTTACCGCATGAAAATCGAGAAAGCAAATCGTCTTAA
131 AAAAGAGTTATTTCCATGGAAGAGCATATTTACCACATGAAAACCGAGAAAGCAAATCGTCTTAA
536738 AGATAAGGATTTTATTCCTATAAATGAATTATCATTTAAAGCTAATCTTGTAGAATCTTCATACG
196 AGATAAGGATTTTATTCCTATAAATGAATTATCATTTAAAGCTAATCTTGTAGAATCTTCATACG
*
536803 GTGCAAATCATAATAGGTTCAAGAATACTTCTAGCCTAAAGAAAAAAAAGTAACTCTAAACAAAA
261 GTGCAAATCATAATAGGTTCAAGAATACTTCTAGCCCAAAGAAAAAAAAGTAACTCTAAACAAAA
*
536868 GAAGGTAACAACCTTCAAAAAGACGGGAACCAAACATAAAGAAAATAACTCGGTGAGTTGCTATG
326 GAAGGTAACAACCTTCAAAAAGACGGGAACCAAACATAAAGAAAATAACTCGATGAGTTGCTATG
*
536933 TATGTGGAATGTCGGGACACAAAGCATGCCAATGTTTTCATTGCTCTGATCTCCACAAGCATCAT
391 TATGTGGAATGTCGGGACACAAAGCATGCCAATGTTTTCATTGCTCTGATCGCCACAAGCATCAT
* *
536998 AATCAAAATGAGAATAAACCACAAGTAAAATTGATCGAGAATCCAGACGAGGTGATTGTTGTTTT
456 AATCAAAATGAGAATAAACCACAAGCAAAATTGATCGAGAATCCAGACGAGGTGATTGTTATTTT
537063 GGTCTCTGAGGTCAGTTTGGTGGAAAACCACACTAAGTGTGTCACACCCCAAATTTTACTTAAAA
521 GGTCTCTGAGGTCAGTTTGGTGGAAAACCACACTAAGTGTGTCACACCCCAAATTTTACTTAAAA
*
537128 ATAATAATTTAATTAATTAATTAAGGGGCCAAAATGAATAATTCTGGGTCAAATTCAAATGTGGA
586 ATAATAATTTAATTAATTAATTAAGGGGCCAAAATGAATAATTCTGGGTCAAATTCAAATCTGGA
537193 AGAACTTTAGGGACCCAACCTGAGATTTTCCCATTATCTACCTTTAGAGAAAAAAAATGAAATAA
651 AGAACTTTAGGGACCCAACCTGAGATTTTCCCATTATCTACCTTTAGAGAAAAAAAATGAAATAA
537258 GGAATGGTTGGCACGATTTGAAGCCAAGCCAA
716 GGAATGGTTGGCACGATTTGAAGCCAAGCCAA
*
537290 TAATGGACCAAGTGCATGTCTATAAAGGATTATCTCTGATATTCTAGATGAAGGGATGAAAATGT
1 TAATGGACCAAGTGCATGTCTATAAAGGATTATCTCTGACATTCTAGATGAAGGGATGAAAATGT
* *
537355 GAGACATTCCCCAAGCGAATATGTTGATTGAAAAACTACCCAGGTCATAGTCCGATTTACACAAA
66 GAGACATTCCCCAAGCGAATATGTTAATTGAAAAACTACCCAAGTCATAGTCCGATTTACACAAA
* *
537420 AAATGAGTTATTTCCATGGAAGAGCCTATTTACCACATGAAAACCGAGAAAGCAAATCGTCTTAA
131 AAAAGAGTTATTTCCATGGAAGAGCATATTTACCACATGAAAACCGAGAAAGCAAATCGTCTTAA
* *
537485 AGATAAGGATTTTATTCCTATAAATGAATTATCATTTAAGGCTAATCTTGTAGAATCTTCCTACG
196 AGATAAGGATTTTATTCCTATAAATGAATTATCATTTAAAGCTAATCTTGTAGAATCTTCATACG
*
537550 GTGCAAATCATAATAGGTTCAAGAATACTTCTAGCCCAAAG-AAAAAAAGTAACTCTAAACCAAA
261 GTGCAAATCATAATAGGTTCAAGAATACTTCTAGCCCAAAGAAAAAAAAGTAACTCTAAACAAAA
537614 GAAGGTAACAACCTTCAAAAAGACGGGAACCAAACATAAAGAAAATAACTCGATGAGTTGCTATG
326 GAAGGTAACAACCTTCAAAAAGACGGGAACCAAACATAAAGAAAATAACTCGATGAGTTGCTATG
*
537679 TATGTGGAATGTCGTGACACAAAGCATGCCAATGTTTTCATTGCTCTGATCGCCACAAGCATCAT
391 TATGTGGAATGTCGGGACACAAAGCATGCCAATGTTTTCATTGCTCTGATCGCCACAAGCATCAT
*
537744 AATCAAAATGAGAATAAACCGCAAGCAAAATTGATCGAGAATCCAGACGAGGTGATTGTTATTTT
456 AATCAAAATGAGAATAAACCACAAGCAAAATTGATCGAGAATCCAGACGAGGTGATTGTTATTTT
*
537809 GGTCTCTGAGGTCAGTTTGGTGGAAAACCACACTAAGTGTGTCACACCTCAAATTTTACTTAAAA
521 GGTCTCTGAGGTCAGTTTGGTGGAAAACCACACTAAGTGTGTCACACCCCAAATTTTACTTAAAA
* *
537874 ATAATAATTTAATTAATTAATTAAGGGGCCAAAATGAATAATTCTGGGTTAAATTCAAATCTGTA
586 ATAATAATTTAATTAATTAATTAAGGGGCCAAAATGAATAATTCTGGGTCAAATTCAAATCTGGA
* * *
537939 AGAAGTTTAGGGACCTAACTTGAGATTTTCCCATTATCTACCT
651 AGAACTTTAGGGACCCAACCTGAGATTTTCCCATTATCTACCT
537982 GTTCGCGTGT
Statistics
Matches: 665, Mismatches: 27, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
746 377 0.57
747 288 0.43
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.27
Consensus pattern (747 bp):
TAATGGACCAAGTGCATGTCTATAAAGGATTATCTCTGACATTCTAGATGAAGGGATGAAAATGT
GAGACATTCCCCAAGCGAATATGTTAATTGAAAAACTACCCAAGTCATAGTCCGATTTACACAAA
AAAAGAGTTATTTCCATGGAAGAGCATATTTACCACATGAAAACCGAGAAAGCAAATCGTCTTAA
AGATAAGGATTTTATTCCTATAAATGAATTATCATTTAAAGCTAATCTTGTAGAATCTTCATACG
GTGCAAATCATAATAGGTTCAAGAATACTTCTAGCCCAAAGAAAAAAAAGTAACTCTAAACAAAA
GAAGGTAACAACCTTCAAAAAGACGGGAACCAAACATAAAGAAAATAACTCGATGAGTTGCTATG
TATGTGGAATGTCGGGACACAAAGCATGCCAATGTTTTCATTGCTCTGATCGCCACAAGCATCAT
AATCAAAATGAGAATAAACCACAAGCAAAATTGATCGAGAATCCAGACGAGGTGATTGTTATTTT
GGTCTCTGAGGTCAGTTTGGTGGAAAACCACACTAAGTGTGTCACACCCCAAATTTTACTTAAAA
ATAATAATTTAATTAATTAATTAAGGGGCCAAAATGAATAATTCTGGGTCAAATTCAAATCTGGA
AGAACTTTAGGGACCCAACCTGAGATTTTCCCATTATCTACCTTTAGAGAAAAAAAATGAAATAA
GGAATGGTTGGCACGATTTGAAGCCAAGCCAA
Found at i:538323 original size:17 final size:16
Alignment explanation
Indices: 538301--538334 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
538291 TAAAAATAGT
538301 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
538318 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
538334 A
1 A
538335 TCCTCACGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:548561 original size:17 final size:16
Alignment explanation
Indices: 548539--548572 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
548529 TAAAAACAGT
548539 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
548556 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
548572 A
1 A
548573 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:559994 original size:29 final size:30
Alignment explanation
Indices: 559954--560019 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
559944 TTAGTTTAAA
* * *
559954 TTTTAATAAAAA-TATAATTAGTTA-ATATT
1 TTTTATTAAAAATTATAATT-GATATAGATT
559983 TTTTATTAAAAATTATAATTGATATAGATT
1 TTTTATTAAAAATTATAATTGATATAGATT
560013 TTTTATT
1 TTTTATT
560020 TGTTTAGGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (30 bp):
TTTTATTAAAAATTATAATTGATATAGATT
Found at i:561152 original size:3 final size:3
Alignment explanation
Indices: 561144--561196 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
561134 TTTATATAAA
* **
561144 ATT ATT ATT ATT ATT ATT ATT CTT -TT ATAT ACA ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
561189 ATT ATT AT
1 ATT ATT AT
561197 AAAATTCAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:561169 original size:33 final size:33
Alignment explanation
Indices: 561132--561196 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
561122 AGGACACAAC
561132 CTTTTATATAAAATTATTATTATTATTATTATT
1 CTTTTATATAAAATTATTATTATTATTATTATT
*
561165 CTTTTATATACAATTATTATTATTATTATTAT
1 CTTTTATATAAAATTATTATTATTATTATTAT
561197 AAAATTCAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (33 bp):
CTTTTATATAAAATTATTATTATTATTATTATT
Found at i:561440 original size:18 final size:19
Alignment explanation
Indices: 561410--561446 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
561400 AAGTATAGTG
561410 ATTTATTTCAAA-TTAATT
1 ATTTATTTCAAATTTAATT
561428 ATTTA-TTCAAAATTTAATT
1 ATTTATTTC-AAATTTAATT
561447 TTAATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.18
18 8 0.47
19 6 0.35
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTATTTCAAATTTAATT
Found at i:561745 original size:35 final size:35
Alignment explanation
Indices: 561699--561771 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
561689 ACTGGGACGA
561699 GCGACGGTTGGGGATGGTTCTCCAAAGGTCAACGG
1 GCGACGGTTGGGGATGGTTCTCCAAAGGTCAACGG
*
561734 GCGACGGTTGGGGATGGTTCTCCGAAGGTCAACGG
1 GCGACGGTTGGGGATGGTTCTCCAAAGGTCAACGG
561769 GCG
1 GCG
561772 TTAAAAATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.18, C:0.21, G:0.42, T:0.19
Consensus pattern (35 bp):
GCGACGGTTGGGGATGGTTCTCCAAAGGTCAACGG
Found at i:567078 original size:20 final size:19
Alignment explanation
Indices: 567053--567105 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
567043 AAAAGCTTGA
*
567053 GTGCATCGATGCATGGTCTT
1 GTGCATCGATGCATGGT-AT
567073 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
*
567092 GTCCATCGATGCAT
1 GTGCATCGATGCAT
567106 AAAATGCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.32
Consensus pattern (19 bp):
GTGCATCGATGCATGGTAT
Found at i:567100 original size:19 final size:20
Alignment explanation
Indices: 567056--567105 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
567046 AGCTTGAGTG
* *
567056 CATCGATGCATGGTCTTGTG
1 CATCGATGCATGGTCATGTC
567076 CATCGATGCATGGT-ATGTC
1 CATCGATGCATGGTCATGTC
567095 CATCGATGCAT
1 CATCGATGCAT
567106 AAAATGCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.32
Consensus pattern (20 bp):
CATCGATGCATGGTCATGTC
Found at i:567141 original size:84 final size:84
Alignment explanation
Indices: 567015--567170 Score: 210
Period size: 84 Copynumber: 1.9 Consensus size: 84
567005 AGAGTACATT
** ** *
567015 GATGCATAAAATGCATTCGATGTTTTGAAAAAGCTTGAGTGCATCGATGCATGG-TCTTGTGCAT
1 GATGCATAAAATGCATTCGATGTTTCAAAAAAAATTGAGTGCATCGATGCATGGAT-TGGTGCAT
567079 CGATGCATGGTATGTCCATC
65 CGATGCATGGTATGTCCATC
567099 GATGCATAAAATGCATTCGATG-TTCAAAATAATAATTG-GTGCATCGATGCATGGATTGGTGCA
1 GATGCATAAAATGCATTCGATGTTTCAAAA-AA-AATTGAGTGCATCGATGCATGGATTGGTGCA
*
567162 TCGGTGCAT
64 TCGATGCAT
567171 CACTTTGAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
83 5 0.08
84 54 0.86
85 4 0.06
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.31
Consensus pattern (84 bp):
GATGCATAAAATGCATTCGATGTTTCAAAAAAAATTGAGTGCATCGATGCATGGATTGGTGCATC
GATGCATGGTATGTCCATC
Found at i:567158 original size:20 final size:20
Alignment explanation
Indices: 567133--567170 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
567123 CAAAATAATA
567133 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
567153 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
567171 CACTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:575830 original size:45 final size:46
Alignment explanation
Indices: 575749--575839 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
575739 TTGAAAAAGC
* * *
575749 CTGAGTGCATCGATACATTGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATACATGGTCATGTGCATCGATGCATAAAATGCA
*
575795 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATACATGGTCATGTGCATCGATGCATAAAATGCA
575840 TTCGATGTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 22 0.54
46 19 0.46
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (46 bp):
CTGAGTGCATCGATACATGGTCATGTGCATCGATGCATAAAATGCA
Done.