Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008806.1 Hibiscus syriacus cultivar Beakdansim tig00111959_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: 454619
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:185671 original size:38 final size:37
Alignment explanation
Indices: 185608--185713 Score: 108
Period size: 38 Copynumber: 2.8 Consensus size: 37
185598 TATATTTTCA
* * *
185608 AAAAAATTATATATATTATATATGTTTTCAAAAACCCTTT
1 AAAAAACTATATATA-T-TACATGTTTTCAAAAA-CATTT
*
185648 AAAAAACTATATATATTACATGTTTTCAAAAATATTT
1 AAAAAACTATATATATTACATGTTTTCAAAAACATTT
** *
185685 TCAAAACTATAT-TA-TACACGTTTTCAAAA
1 AAAAAACTATATATATTACATGTTTTCAAAA
185714 CCATACGTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
35 14 0.24
36 2 0.03
37 13 0.22
38 15 0.25
39 1 0.02
40 14 0.24
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.40
Consensus pattern (37 bp):
AAAAAACTATATATATTACATGTTTTCAAAAACATTT
Found at i:185761 original size:37 final size:37
Alignment explanation
Indices: 185716--185910 Score: 269
Period size: 35 Copynumber: 5.4 Consensus size: 37
185706 TTTCAAAACC
* *
185716 ATACGTTTTCAAAAATGCTTTCAAAATCATATATTAT
1 ATACGTTTTCAAAAATGTTTTCAAAACCATATATTAT
*
185753 ATACGTTTTCAAAAATGTTTTCAAGACCATATATTAT
1 ATACGTTTTCAAAAATGTTTTCAAAACCATATATTAT
*
185790 ATAAGTTTTCAAAAAAATGTTTTCAAAACCATATA-T-T
1 ATACGTTTTC--AAAAATGTTTTCAAAACCATATATTAT
*
185827 ATACGTTTTCAAACATGTTTTCAAAACCATATATTAT
1 ATACGTTTTCAAAAATGTTTTCAAAACCATATATTAT
185864 AT--GTTTTCAAAAATGTTATT-AAAACCATATA-T-T
1 ATACGTTTTCAAAAATGTT-TTCAAAACCATATATTAT
185897 ATACGTTTTCAAAA
1 ATACGTTTTCAAAA
185911 TTATCAAAAA
Statistics
Matches: 143, Mismatches: 8, Indels: 16
0.86 0.05 0.10
Matches are distributed among these distances:
33 3 0.02
34 1 0.01
35 57 0.40
36 3 0.02
37 56 0.39
38 1 0.01
39 22 0.15
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.40
Consensus pattern (37 bp):
ATACGTTTTCAAAAATGTTTTCAAAACCATATATTAT
Found at i:185802 original size:74 final size:69
Alignment explanation
Indices: 185720--185910 Score: 265
Period size: 74 Copynumber: 2.6 Consensus size: 69
185710 AAAACCATAC
* *
185720 GTTTTCAAAAATGCTTTCAAAATCATATATTATATACGTTTTCAAAAATGTTTTCAAGACCATAT
1 GTTTTCAAAAATG-TTTCAAAACCATATA-T-TATACGTTTTCAAAAATGTTTTCAAAACCATAT
185785 ATTATAT
63 ATTATAT
*
185792 AAGTTTTCAAAAAAATGTTTTCAAAACCATATATTATACGTTTTCAAACATGTTTTCAAAACCAT
1 --GTTTTC--AAAAATG-TTTCAAAACCATATATTATACGTTTTCAAAAATGTTTTCAAAACCAT
185857 ATATTATAT
61 ATATTATAT
*
185866 GTTTTCAAAAATGTTATTAAAACCATATATTATACGTTTTCAAAA
1 GTTTTCAAAAATGTT-TCAAAACCATATATTATACGTTTTCAAAA
185911 TTATCAAAAA
Statistics
Matches: 108, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
69 2 0.02
70 34 0.31
72 6 0.06
74 44 0.41
75 1 0.01
76 21 0.19
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.40
Consensus pattern (69 bp):
GTTTTCAAAAATGTTTCAAAACCATATATTATACGTTTTCAAAAATGTTTTCAAAACCATATATT
ATAT
Found at i:185812 original size:88 final size:87
Alignment explanation
Indices: 185629--185817 Score: 213
Period size: 88 Copynumber: 2.1 Consensus size: 87
185619 TATATTATAT
185629 ATGTTTTCAAAAACCCTTTAAAAAACTATATATATTACATGTTTTCAAAAATATTTTCAAAACTA
1 ATGTTTTCAAAAACCCTTTAAAAAACTATATATATTACA-GTTTTCAAAAATATTTTCAAAACTA
* *
185694 TATTATACACGTTTTCAAAACCAT
65 TATTATACAAGTTTTCAAAA-CAA
* ** * * * *
185718 ACGTTTTCAAAAATGCTTTCAAAATC-ATATATTATATAC-GTTTTCAAAAATGTTTTCAAGACC
1 ATGTTTTCAAAAACCCTTTAAAAAACTATATA-TAT-TACAGTTTTCAAAAATATTTTCAA-AAC
*
185781 ATATATTATATAAGTTTTCAAAA-AA
63 -TATATTATACAAGTTTTCAAAACAA
185806 ATGTTTTCAAAA
1 ATGTTTTCAAAA
185818 CCATATATTA
Statistics
Matches: 85, Mismatches: 11, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
88 36 0.42
89 26 0.31
90 23 0.27
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.39
Consensus pattern (87 bp):
ATGTTTTCAAAAACCCTTTAAAAAACTATATATATTACAGTTTTCAAAAATATTTTCAAAACTAT
ATTATACAAGTTTTCAAAACAA
Found at i:194792 original size:26 final size:25
Alignment explanation
Indices: 194763--194841 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 25
194753 TAAAAAGTCA
194763 AAAATAAAGTTAAATAATAAAAT-ATT
1 AAAA-AAA-TTAAATAATAAAATAATT
*
194789 AAAAATATTAAA-AATAAAATAATT
1 AAAAAAATTAAATAATAAAATAATT
*
194813 AAAAGAAAATTCAAAT--TAAAATGATT
1 -AAA-AAAATT-AAATAATAAAATAATT
194839 AAA
1 AAA
194842 TTGAAAATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
23 8 0.18
24 8 0.18
25 8 0.18
26 18 0.40
27 3 0.07
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (25 bp):
AAAAAAATTAAATAATAAAATAATT
Found at i:194854 original size:15 final size:15
Alignment explanation
Indices: 194804--194856 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 15
194794 TATTAAAAAT
*
194804 AAAATAATTAAA-AG
1 AAAATAATTAAATTG
*
194818 AAAAT--TCAAATT-
1 AAAATAATTAAATTG
*
194830 AAAATGATTAAATTG
1 AAAATAATTAAATTG
194845 AAAATAATTAAA
1 AAAATAATTAAA
194857 AGTCAAGGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
12 9 0.29
14 11 0.35
15 11 0.35
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (15 bp):
AAAATAATTAAATTG
Found at i:196002 original size:17 final size:17
Alignment explanation
Indices: 195959--196032 Score: 87
Period size: 17 Copynumber: 4.3 Consensus size: 17
195949 TAAAACCAAA
* *
195959 AATAATAAAATAAATA-
1 AATAAAAAAATAAAAAT
*
195975 AATGAACAAAATAAAAAT
1 AAT-AAAAAAATAAAAAT
*
195993 AATAAAAAAATTAAAAT
1 AATAAAAAAATAAAAAT
196010 AATAAAAATAATAAAAAT
1 AATAAAAA-AATAAAAAT
196028 AATAA
1 AATAA
196033 TATAATATGT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
16 3 0.06
17 31 0.62
18 16 0.32
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.22
Consensus pattern (17 bp):
AATAAAAAAATAAAAAT
Found at i:196013 original size:26 final size:26
Alignment explanation
Indices: 195959--196039 Score: 87
Period size: 26 Copynumber: 3.2 Consensus size: 26
195949 TAAAACCAAA
* * *
195959 AATAATAA-AATAAATAAATGAACAA-
1 AATAAAAATAATAAAAAAATTAA-AAT
195984 AATAAAAATAATAAAAAAATTAAAAT
1 AATAAAAATAATAAAAAAATTAAAAT
*
196010 AATAAAAATAATAAAAATAA-TAATAT
1 AATAAAAATAATAAAAA-AATTAAAAT
196036 AATA
1 AATA
196040 TGTATTATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
25 9 0.18
26 38 0.78
27 2 0.04
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.23
Consensus pattern (26 bp):
AATAAAAATAATAAAAAAATTAAAAT
Found at i:196037 original size:17 final size:17
Alignment explanation
Indices: 195956--196039 Score: 84
Period size: 17 Copynumber: 5.1 Consensus size: 17
195946 ACCTAAAACC
195956 AAAAATAATAAAATAA-
1 AAAAATAATAAAATAAT
* * *
195972 ATAAATGA-ACAA-AAT
1 AAAAATAATAAAATAAT
*
195987 AAAAATAATAAAAAAAT
1 AAAAATAATAAAATAAT
*
196004 TAAAATAATAAAAATAAT
1 AAAAATAAT-AAAATAAT
*
196022 AAAAATAATAATATAAT
1 AAAAATAATAAAATAAT
196039 A
1 A
196040 TGTATTATAT
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
14 2 0.04
15 9 0.17
16 9 0.17
17 19 0.35
18 15 0.28
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.23
Consensus pattern (17 bp):
AAAAATAATAAAATAAT
Found at i:196102 original size:27 final size:26
Alignment explanation
Indices: 196046--196099 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 26
196036 AATATGTATT
196046 ATATATTTATTTAAAAACTATATAAC
1 ATATATTTATTTAAAAACTATATAAC
196072 ATATATTGTATTTTCAAAAACTATATAA
1 ATATATT-TA-TTT-AAAAACTATATAA
196100 TATGTTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 7 0.28
27 2 0.08
28 3 0.12
29 13 0.52
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (26 bp):
ATATATTTATTTAAAAACTATATAAC
Found at i:196120 original size:22 final size:23
Alignment explanation
Indices: 196082--196125 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
196072 ATATATTGTA
*
196082 TTTTCAAAAACTATATA-ATATG
1 TTTTCAAAAAATATATATATATG
196104 TTTTCAAAAAA-ATTATATATAT
1 TTTTCAAAAAATA-TATATATAT
196126 TATATATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 1 0.05
22 14 0.74
23 4 0.21
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (23 bp):
TTTTCAAAAAATATATATATATG
Found at i:196163 original size:42 final size:41
Alignment explanation
Indices: 196103--196229 Score: 119
Period size: 35 Copynumber: 3.2 Consensus size: 41
196093 TATATAATAT
* *
196103 GTTTTCAAAAAAATTATATATATTATATATGTTTTCAAAAACC
1 GTTTTCAAAAAAACTATATATA-T-TACATGTTTTCAAAAACC
* *
196146 GTTTT-AAAAACACTATATATATTACATGTTTTCAAAAA-T
1 GTTTTCAAAAAAACTATATATATTACATGTTTTCAAAAACC
*
196185 ATTTTC---AAAACTATAT-TATATAC--GTTTTCAAAAA-C
1 GTTTTCAAAAAAACTATATATAT-TACATGTTTTCAAAAACC
196220 GTTTTCAAAA
1 GTTTTCAAAA
196230 CCATGCGTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 15
0.76 0.09 0.16
Matches are distributed among these distances:
35 16 0.23
36 3 0.04
37 12 0.17
38 1 0.01
39 4 0.06
40 15 0.21
41 1 0.01
42 14 0.20
43 5 0.07
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (41 bp):
GTTTTCAAAAAAACTATATATATTACATGTTTTCAAAAACC
Found at i:196200 original size:35 final size:35
Alignment explanation
Indices: 196119--196463 Score: 312
Period size: 35 Copynumber: 9.7 Consensus size: 35
196109 AAAAAAATTA
* *
196119 TATATATTATATATGTTTTCAAAAACCGTTTTAAAAACAC
1 TATATA-T-TATATGTTTTCAAAAA-TGTTTT-CAAA-AC
* *
196159 TATATATATTACATGTTTTCAAAAATATTTTCAAAAC
1 --TATATATTATATGTTTTCAAAAATGTTTTCAAAAC
* *
196196 TATAT-TATATACGTTTTCAAAAACGTTTTCAAAAC
1 TATATAT-TATATGTTTTCAAAAATGTTTTCAAAAC
* ** *
196231 -------CATGCGTTTTCAAAAATGCTTTCAAAAC
1 TATATATTATATGTTTTCAAAAATGTTTTCAAAAC
* *
196259 CATATATTATAAACGTTTTCAAAAATGTTTTCAAAA-
1 TATATATTAT--ATGTTTTCAAAAATGTTTTCAAAAC
*
196295 TCATATATTATATAGGTTTTCAAAAATATTTTCAAAAC
1 T-ATATATTATAT--GTTTTCAAAAATGTTTTCAAAAC
*
196333 TATATATTATATGTGTTTTCAAAAATGTTTTCAAAGC
1 TATATATTATA--TGTTTTCAAAAATGTTTTCAAAAC
* * *
196370 CATATATTATAAGTTTTCAAACATGTTTTCAAAAC
1 TATATATTATATGTTTTCAAAAATGTTTTCAAAAC
* *
196405 CATATATTATACGTTTTCAAAAATGTTTTCAAAAC
1 TATATATTATATGTTTTCAAAAATGTTTTCAAAAC
*
196440 CATATATTATATGTTTTCAAAAAT
1 TATATATTATATGTTTTCAAAAAT
196464 ATGTTAAAAA
Statistics
Matches: 260, Mismatches: 27, Indels: 39
0.80 0.08 0.12
Matches are distributed among these distances:
28 24 0.09
34 1 0.00
35 109 0.42
37 95 0.37
38 4 0.02
39 5 0.02
40 15 0.06
41 1 0.00
42 6 0.02
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (35 bp):
TATATATTATATGTTTTCAAAAATGTTTTCAAAAC
Found at i:196205 original size:40 final size:40
Alignment explanation
Indices: 196117--196219 Score: 101
Period size: 40 Copynumber: 2.6 Consensus size: 40
196107 TCAAAAAAAT
* *
196117 TATATATATTATATATGTTTTCAAAAACCGTTTTAAAAACAC
1 TATATATA-T-TACATGTTTTCAAAAACCATTTTAAAAACAC
* *
196159 TATATATATTACATGTTTTCAAAAA-TATTTT-CAAA-AC
1 TATATATATTACATGTTTTCAAAAACCATTTTAAAAACAC
196196 TATAT-TATATAC--GTTTTCAAAAAC
1 TATATATAT-TACATGTTTTCAAAAAC
196220 GTTTTCAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
35 11 0.20
36 3 0.05
37 10 0.18
38 3 0.05
39 4 0.07
40 15 0.27
41 1 0.02
42 8 0.15
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.42
Consensus pattern (40 bp):
TATATATATTACATGTTTTCAAAAACCATTTTAAAAACAC
Found at i:196223 original size:12 final size:12
Alignment explanation
Indices: 196206--196294 Score: 63
Period size: 12 Copynumber: 7.0 Consensus size: 12
196196 TATATTATAT
196206 ACGTTTTCAAAA
1 ACGTTTTCAAAA
196218 ACGTTTTCAAAA
1 ACGTTTTCAAAA
196230 CCATGCGTTTTCAAAA
1 --A--CGTTTTCAAAA
* *
196246 ATGCTTTCAAAA
1 ACGTTTTCAAAA
* * *
196258 CCATATATT-ATAA
1 ACGT-T-TTCAAAA
196271 ACGTTTTCAAAA
1 ACGTTTTCAAAA
*
196283 ATGTTTTCAAAA
1 ACGTTTTCAAAA
196295 TCATATATTA
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
11 2 0.03
12 36 0.61
13 6 0.10
14 4 0.07
16 11 0.19
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (12 bp):
ACGTTTTCAAAA
Found at i:196240 original size:16 final size:16
Alignment explanation
Indices: 196219--196261 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
196209 TTTTCAAAAA
196219 CGTTTTCAAAACCATG
1 CGTTTTCAAAACCATG
196235 CGTTTTCAAAA--ATG
1 CGTTTTCAAAACCATG
196249 C--TTTCAAAACCAT
1 CGTTTTCAAAACCAT
196262 ATATTATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 8 0.32
14 6 0.24
16 11 0.44
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (16 bp):
CGTTTTCAAAACCATG
Found at i:196253 original size:28 final size:28
Alignment explanation
Indices: 196207--196261 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
196197 ATATTATATA
*
196207 CGTTTTCAAAAACGTTTTCAAAACCATG
1 CGTTTTCAAAAACGCTTTCAAAACCATG
*
196235 CGTTTTCAAAAATGCTTTCAAAACCAT
1 CGTTTTCAAAAACGCTTTCAAAACCAT
196262 ATATTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (28 bp):
CGTTTTCAAAAACGCTTTCAAAACCATG
Found at i:196282 original size:65 final size:63
Alignment explanation
Indices: 196173--196294 Score: 190
Period size: 65 Copynumber: 1.9 Consensus size: 63
196163 TATATTACAT
* *
196173 GTTTTCAAAAATATTTTCAAAACTATATTATATACGTTTTCAAAAACGTTTTCAAAACCATGC
1 GTTTTCAAAAATACTTTCAAAACTATATTATAAACGTTTTCAAAAACGTTTTCAAAACCATGC
* *
196236 GTTTTCAAAAATGCTTTCAAAACCATATATTATAAACGTTTTCAAAAATGTTTTCAAAA
1 GTTTTCAAAAATACTTTCAAAA-C-TATATTATAAACGTTTTCAAAAACGTTTTCAAAA
196295 TCATATATTA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
63 20 0.38
64 1 0.02
65 32 0.60
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.38
Consensus pattern (63 bp):
GTTTTCAAAAATACTTTCAAAACTATATTATAAACGTTTTCAAAAACGTTTTCAAAACCATGC
Found at i:196468 original size:37 final size:35
Alignment explanation
Indices: 196236--196486 Score: 324
Period size: 37 Copynumber: 7.0 Consensus size: 35
196226 AAAACCATGC
* *
196236 GTTTTCAAAAATGCTTTCAAAACCATATATTATAAAC
1 GTTTTCAAAAATGTTTTCAAAACCATATATTAT--AT
*
196273 GTTTTCAAAAATGTTTTCAAAATCATATATTATAT
1 GTTTTCAAAAATGTTTTCAAAACCATATATTATAT
* *
196308 AGGTTTTCAAAAATATTTTCAAAACTATATATTATATGT
1 --GTTTTCAAAAATGTTTTCAAAACCATATATTATA--T
* *
196347 GTTTTCAAAAATGTTTTCAAAGCCATATATTATAA
1 GTTTTCAAAAATGTTTTCAAAACCATATATTATAT
* *
196382 GTTTTCAAACATGTTTTCAAAACCATATATTATAC
1 GTTTTCAAAAATGTTTTCAAAACCATATATTATAT
196417 GTTTTCAAAAATGTTTTCAAAACCATATATTATAT
1 GTTTTCAAAAATGTTTTCAAAACCATATATTATAT
* * * *
196452 GTTTTCAAAAATATGTTAAAAAAC-TATATTATAT
1 GTTTTCAAAAATGTTTTCAAAACCATATATTATAT
196486 G
1 G
196487 ATTATATATA
Statistics
Matches: 191, Mismatches: 19, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
34 11 0.06
35 86 0.45
37 93 0.49
39 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (35 bp):
GTTTTCAAAAATGTTTTCAAAACCATATATTATAT
Found at i:197190 original size:23 final size:23
Alignment explanation
Indices: 197160--197224 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
197150 ATTTTGTATA
197160 TGTTGCACGTTTATCTCTATC-TG
1 TGTTGCACGTTTATCTCT-TCATG
* * *
197183 TGTTGCACGTTTATTTGTTCATT
1 TGTTGCACGTTTATCTCTTCATG
*
197206 TGTGGCACGTTTATCTCTT
1 TGTTGCACGTTTATCTCTT
197225 ACTTTGTGGC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 2 0.06
23 33 0.94
ACGTcount: A:0.12, C:0.18, G:0.18, T:0.51
Consensus pattern (23 bp):
TGTTGCACGTTTATCTCTTCATG
Found at i:197230 original size:23 final size:23
Alignment explanation
Indices: 197164--197235 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
197154 TGTATATGTT
* *
197164 GCACGTTTATCTC-TATCTGTGTT
1 GCACGTTTATCTCTTA-CTTTGTG
* *
197187 GCACGTTTATTTGTT-CATTTGTG
1 GCACGTTTATCTCTTAC-TTTGTG
197210 GCACGTTTATCTCTTACTTTGTG
1 GCACGTTTATCTCTTACTTTGTG
197233 GCA
1 GCA
197236 TGCTTTTCGA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
22 1 0.03
23 37 0.93
24 2 0.05
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.47
Consensus pattern (23 bp):
GCACGTTTATCTCTTACTTTGTG
Found at i:207263 original size:29 final size:29
Alignment explanation
Indices: 207243--207307 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
207233 ATACTAGAAT
* * *
207243 TTAAAGTACTGAAATATAAATGCTGAAAA
1 TTAAAGAACTGAAATAGAAATACTGAAAA
*
207272 TTAAAGAACTGAAATGGAAATACTGAAAAA
1 TTAAAGAACTGAAATAGAAATACTG-AAAA
207302 TTAAAG
1 TTAAAG
207308 TCAAAAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 21 0.68
30 10 0.32
ACGTcount: A:0.54, C:0.06, G:0.15, T:0.25
Consensus pattern (29 bp):
TTAAAGAACTGAAATAGAAATACTGAAAA
Found at i:208802 original size:25 final size:25
Alignment explanation
Indices: 208761--208842 Score: 137
Period size: 25 Copynumber: 3.3 Consensus size: 25
208751 CTATGGGCTG
*
208761 GCTCAACAAACTGATCAAGTTGACA
1 GCTCAACAAGCTGATCAAGTTGACA
*
208786 GCTCAACAAGCTAATCAAGTTGACA
1 GCTCAACAAGCTGATCAAGTTGACA
208811 GCTCAACAAGCTGATCAAGTTGACA
1 GCTCAACAAGCTGATCAAGTTGACA
*
208836 GCCCAAC
1 GCTCAAC
208843 TACAGTAATG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.18
Consensus pattern (25 bp):
GCTCAACAAGCTGATCAAGTTGACA
Found at i:209186 original size:59 final size:60
Alignment explanation
Indices: 209087--209204 Score: 148
Period size: 59 Copynumber: 2.0 Consensus size: 60
209077 ATTTGACACT
* * * * * *
209087 ATGCCATCAAGCTCTAGGGGGAGGCATTCAATTGCGAGCTTCTTCGACCTCAATGTCGAG
1 ATGCCATCAAGCTCTAGGGGAAGGCATGCAACTACCAGCTTCTTCGACCTAAATGTCGAG
* * *
209147 ATGCCTTCAAGTTC-AGGGGAAGGCATGCAACTACCAGCTTGTTCGACCTAAATGTCGA
1 ATGCCATCAAGCTCTAGGGGAAGGCATGCAACTACCAGCTTCTTCGACCTAAATGTCGA
209205 CAGCATGGAG
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
59 37 0.76
60 12 0.24
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (60 bp):
ATGCCATCAAGCTCTAGGGGAAGGCATGCAACTACCAGCTTCTTCGACCTAAATGTCGAG
Found at i:209765 original size:23 final size:21
Alignment explanation
Indices: 209714--209791 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 21
209704 AGGGTGTCAA
*
209714 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTAC
209735 AGTGCATCCATGCACCTGCC-AC
1 AGTGCATCCATGCACC--CCTAC
* * **
209757 TAGTGCATCGATGCA-CCATGT
1 -AGTGCATCCATGCACCCCTAC
209778 AGTGCATCCATGCA
1 AGTGCATCCATGCA
209792 TTCCATTTCG
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
20 14 0.30
21 16 0.34
22 2 0.04
23 15 0.32
ACGTcount: A:0.23, C:0.35, G:0.21, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:209837 original size:20 final size:20
Alignment explanation
Indices: 209812--209864 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
209802 AATGCAATTA
209812 GTGCATCGATGCATCCTGT-T
1 GTGCATCGATGCATCCT-TCT
209832 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
*
209852 GTGCATCCATGCA
1 GTGCATCGATGCA
209865 CCAAGGCTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.32
Consensus pattern (20 bp):
GTGCATCGATGCATCCTTCT
Found at i:212977 original size:21 final size:21
Alignment explanation
Indices: 212938--212976 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
212928 AAACAATTGG
212938 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
*
212959 TAACAATTGGTAT-ATTTT
1 TAACAATTGATATCATTTT
212977 TCATTAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:213226 original size:21 final size:21
Alignment explanation
Indices: 213202--213301 Score: 112
Period size: 21 Copynumber: 4.7 Consensus size: 21
213192 AGGGTGTCGA
213202 AGTGCATCCATGCACCCCTGT
1 AGTGCATCCATGCACCCCTGT
* * *
213223 AGTGTATCCATGTACCCCTGC
1 AGTGCATCCATGCACCCCTGT
**
213244 AGTGCATCCATGCACCTGCCACT
1 AGTGCATCCATGCACC--CCTGT
* *
213267 AGTGCATCGATGCA-CCATGT
1 AGTGCATCCATGCACCCCTGT
213287 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
213302 TCCATTTCGA
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
20 15 0.24
21 32 0.51
22 1 0.02
23 15 0.24
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGT
Found at i:216528 original size:7 final size:8
Alignment explanation
Indices: 216491--216534 Score: 72
Period size: 8 Copynumber: 5.6 Consensus size: 8
216481 TGAAAACCCT
216491 AGTTTTAG
1 AGTTTTAG
216499 AGTTTTAG
1 AGTTTTAG
216507 AGTTTTAG
1 AGTTTTAG
216515 AGTTTTAG
1 AGTTTTAG
216523 -GTTTTAG
1 AGTTTTAG
*
216530 GGTTT
1 AGTTT
216535 AGTGTTTGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.20
8 28 0.80
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.52
Consensus pattern (8 bp):
AGTTTTAG
Found at i:219119 original size:15 final size:15
Alignment explanation
Indices: 219098--219132 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
219088 TGTCGTGGTC
219098 CAGCAGGGTCATCTG
1 CAGCAGGGTCATCTG
* *
219113 TAGCAGGGTTATCTG
1 CAGCAGGGTCATCTG
219128 CAGCA
1 CAGCA
219133 ATGTGTGGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (15 bp):
CAGCAGGGTCATCTG
Found at i:219438 original size:20 final size:20
Alignment explanation
Indices: 219409--219451 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
219399 ATTGCACCAC
*
219409 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
219429 ATGCAGCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
219449 ATG
1 ATG
219452 GGCTCTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:227197 original size:2 final size:2
Alignment explanation
Indices: 227190--227220 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
227180 ATTAAACCAT
227190 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
227221 TGGAGTGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:229013 original size:23 final size:23
Alignment explanation
Indices: 228982--229036 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
228972 ATAAACAGAC
* *
228982 GAACGTAAACGAACACAATAAAT
1 GAACATAAACGAACAAAATAAAT
*
229005 GAACATAAACGAACAAAATAAGT
1 GAACATAAACGAACAAAATAAAT
229028 GAACATAAA
1 GAACATAAA
229037 TGAATTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.60, C:0.15, G:0.13, T:0.13
Consensus pattern (23 bp):
GAACATAAACGAACAAAATAAAT
Found at i:236867 original size:34 final size:32
Alignment explanation
Indices: 236801--236870 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
236791 CCTTACAAAC
* * *
236801 TCCCTAGTTTTTCCGGGCTAAACTATAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
236833 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
236867 TCCC
1 TCCC
236871 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:237179 original size:21 final size:21
Alignment explanation
Indices: 237153--237194 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
237143 CCAGAATGGG
*
237153 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
237174 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
237195 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:237324 original size:19 final size:19
Alignment explanation
Indices: 237300--237355 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
237290 GAGCCTCGGG
*
237300 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAACAGTAAT
* *
237319 TTACTGTTTAAATAGTAAT
1 TTACTGTTCAAACAGTAAT
*
237338 TTACTGTTCAAATAGTAA
1 TTACTGTTCAAACAGTAA
237356 ATTCTATTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAT
Found at i:237488 original size:31 final size:31
Alignment explanation
Indices: 237422--237518 Score: 155
Period size: 31 Copynumber: 3.2 Consensus size: 31
237412 ATTTTTGTAA
*
237422 ATTTTGAATAATTCAATT-AAGTCC-AAAA-C
1 ATTTTGTA-AATTCAATTCAAGTCCAAAAACC
237451 ATTTTGTAAATTCAATTCAAGTCCAAAAACC
1 ATTTTGTAAATTCAATTCAAGTCCAAAAACC
237482 ATTTTGTAAATTCAATTCAAGTCCAAAAACC
1 ATTTTGTAAATTCAATTCAAGTCCAAAAACC
237513 ATTTTG
1 ATTTTG
237519 CCTTAAATTG
Statistics
Matches: 64, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
28 9 0.14
29 13 0.20
30 4 0.06
31 38 0.59
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.35
Consensus pattern (31 bp):
ATTTTGTAAATTCAATTCAAGTCCAAAAACC
Found at i:239063 original size:2 final size:2
Alignment explanation
Indices: 239007--239052 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
238997 TTCATCTATC
239007 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A T- TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
239046 TA TA TA T
1 TA TA TA T
239053 TAAAATATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:243793 original size:23 final size:22
Alignment explanation
Indices: 243763--243805 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
243753 TTGTGGTAGT
243763 AAATTTGAACATTGATGTTTACC
1 AAATTTGAACATTGA-GTTTACC
243786 AAATTTGAACATTGAGTTTA
1 AAATTTGAACATTGAGTTTA
243806 TGCGTTACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (22 bp):
AAATTTGAACATTGAGTTTACC
Found at i:244047 original size:24 final size:24
Alignment explanation
Indices: 244010--244073 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
244000 GGCCTTTTCA
*
244010 AGCTTCAATCGAGCTCGAGTCTTG
1 AGCTTCAATCGAGCTCGAGTCTCG
* *
244034 AGCTTTAATTGAGCTCGAGTCTCG
1 AGCTTCAATCGAGCTCGAGTCTCG
244058 AGCTTCAATCGAGCTC
1 AGCTTCAATCGAGCTC
244074 CTAAAATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
AGCTTCAATCGAGCTCGAGTCTCG
Found at i:244106 original size:16 final size:16
Alignment explanation
Indices: 244081--244111 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
244071 CTCCTAAAAT
*
244081 TTTTTTGAGTTCGAGC
1 TTTTTCGAGTTCGAGC
244097 TTTTTCGAGTTCGAG
1 TTTTTCGAGTTCGAG
244112 TTGAGTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.13, G:0.26, T:0.48
Consensus pattern (16 bp):
TTTTTCGAGTTCGAGC
Found at i:246711 original size:29 final size:28
Alignment explanation
Indices: 246679--246841 Score: 159
Period size: 29 Copynumber: 5.7 Consensus size: 28
246669 TAAAAATATA
* *
246679 AAATTATAATAAAGGCCTAAACTTTTTAG
1 AAATTATAATAAAGGAC-AAACTTTTTAT
* * * *
246708 AAATCATATTAAAGGACAAA-TGTGTTAG
1 AAATTATAATAAAGGACAAACT-TTTTAT
* *
246736 GAATTAAAATAAAGGACCAAACTTTTTAT
1 AAATTATAATAAAGGA-CAAACTTTTTAT
*
246765 AAATTATTATAAAGGACAAAGCTTTTTAT
1 AAATTATAATAAAGGACAAA-CTTTTTAT
* *
246794 AAATTATAATAAGGGACAAGGCTTTTTAT
1 AAATTATAATAAAGGACAA-ACTTTTTAT
*
246823 AAATTACAATAAAGG-CAAA
1 AAATTATAATAAAGGACAAA
246842 AAAAATTACA
Statistics
Matches: 110, Mismatches: 19, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
27 1 0.01
28 27 0.25
29 81 0.74
30 1 0.01
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (28 bp):
AAATTATAATAAAGGACAAACTTTTTAT
Found at i:246880 original size:28 final size:29
Alignment explanation
Indices: 246821--246894 Score: 123
Period size: 28 Copynumber: 2.6 Consensus size: 29
246811 AAGGCTTTTT
*
246821 ATAAATTACAATAAAGGCAAAAAAAATTAC
1 ATAAATTACAAT-AATGCAAAAAAAATTAC
246851 ATAAATTACAATAATGC-AAAAAAATTAC
1 ATAAATTACAATAATGCAAAAAAAATTAC
246879 ATAAATTACAATAATG
1 ATAAATTACAATAATG
246895 GCATACATAT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
28 27 0.63
29 4 0.09
30 12 0.28
ACGTcount: A:0.61, C:0.09, G:0.05, T:0.24
Consensus pattern (29 bp):
ATAAATTACAATAATGCAAAAAAAATTAC
Found at i:246922 original size:29 final size:29
Alignment explanation
Indices: 246881--246953 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 29
246871 AAAATTACAT
*
246881 AAATTACAATAATGGCATACATA-TTTTAA
1 AAATTATAATAATGGC-TACATACTTTTAA
*
246910 AAATTATAATAATGG-TACGTACTTTTAA
1 AAATTATAATAATGGCTACATACTTTTAA
246938 AAATTATAATAATGGC
1 AAATTATAATAATGGC
246954 CCAAAATGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 5 0.12
28 21 0.52
29 14 0.35
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.36
Consensus pattern (29 bp):
AAATTATAATAATGGCTACATACTTTTAA
Found at i:248252 original size:27 final size:28
Alignment explanation
Indices: 248148--248249 Score: 100
Period size: 28 Copynumber: 3.6 Consensus size: 28
248138 GCACGGGCTG
* * *
248148 TTAAGGAATGGAGGTGTTGCCGCTGCCG
1 TTAAGGAATGGAGGTGTTGCTGCTTCCA
* *
248176 TTAAGGACTGGAGGTG-TGTTGCTATCGCCA
1 TTAAGGAATGGAGGTGTTGCTGCT-T--CCA
*
248206 CTAA-GAATGGAGGTGTTGCTGCTTCCA
1 TTAAGGAATGGAGGTGTTGCTGCTTCCA
*
248233 TTAAGGAATGAAGGTGT
1 TTAAGGAATGGAGGTGT
248250 GCTACTTAAG
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
27 11 0.19
28 26 0.44
29 11 0.19
30 11 0.19
ACGTcount: A:0.23, C:0.15, G:0.34, T:0.28
Consensus pattern (28 bp):
TTAAGGAATGGAGGTGTTGCTGCTTCCA
Found at i:249219 original size:6 final size:6
Alignment explanation
Indices: 249208--249240 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
249198 GATCATAAAT
*
249208 ATATAC ATATAC ATATA- ATATAC ATGTAC ATAT
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATAT
249241 TAACCAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.36
Consensus pattern (6 bp):
ATATAC
Found at i:249230 original size:11 final size:12
Alignment explanation
Indices: 249208--249240 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
249198 GATCATAAAT
249208 ATATACATATAC
1 ATATACATATAC
249220 ATATA-ATATAC
1 ATATACATATAC
*
249231 ATGTACATAT
1 ATATACATAT
249241 TAACCAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.36
Consensus pattern (12 bp):
ATATACATATAC
Found at i:249230 original size:17 final size:17
Alignment explanation
Indices: 249208--249240 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
249198 GATCATAAAT
249208 ATATACATATACATATA
1 ATATACATATACATATA
*
249225 ATATACATGTACATAT
1 ATATACATATACATAT
249241 TAACCAAAAA
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:0.48, C:0.12, G:0.03, T:0.36
Consensus pattern (17 bp):
ATATACATATACATATA
Found at i:250936 original size:198 final size:203
Alignment explanation
Indices: 250596--250997 Score: 760
Period size: 198 Copynumber: 2.0 Consensus size: 203
250586 CTACTAAATT
250596 GGAGAATGACTTTCGATTAGAGGACATATGATAAGTGCAACATGAATATAATATTTACTCATCTA
1 GGAGAATGACTTTCGATTAGAGGACATATGATAAGTGCAACATGAATATAATATTTACTCATCTA
250661 AATGGAATGTTGATGATGAAGCAACCAATGATATGTCAGATTAACTAACATCATGCTTTGTAACA
66 AATGGAATGTTGATGATGAAGCAACCAATGATATGTCAGATTAACTAACATCATGCTTTGTAACA
250726 CATGCATATGGAGTAGGTTT-TTTCTTCTTCAGCTTC-GGTAATCTTTCTTCCAATGGAATTTC-
131 CATGCATATGGAGTAGGTTTATTTCTTCTTCAGCTTCGGGTAATCTTTCTTCCAATGGAATTTCT
250788 CATGACAA
196 CATGACAA
250796 GGAGAATGACTTTCGATTAGAGGACATATGATAAG-GCAACATGAATATAATATTTACTCATCTA
1 GGAGAATGACTTTCGATTAGAGGACATATGATAAGTGCAACATGAATATAATATTTACTCATCTA
250860 AAT-GAATGTTGATGATGAAGCAACCAATGATATGTCAGATTAACTAACATCATGCTTTGTAACA
66 AATGGAATGTTGATGATGAAGCAACCAATGATATGTCAGATTAACTAACATCATGCTTTGTAACA
250924 CATGCATATGGAGTAGGTTTCATTTCTTCTTCAGCTTCGGGTAATCTTTCTTCCAATGGAATTTC
131 CATGCATATGGAGTAGGTTT-ATTTCTTCTTCAGCTTCGGGTAATCTTTCTTCCAATGGAATTTC
250989 TCATGACAA
195 TCATGACAA
250998 AAGGTACATT
Statistics
Matches: 198, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
198 81 0.41
199 32 0.16
200 51 0.26
201 26 0.13
202 8 0.04
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (203 bp):
GGAGAATGACTTTCGATTAGAGGACATATGATAAGTGCAACATGAATATAATATTTACTCATCTA
AATGGAATGTTGATGATGAAGCAACCAATGATATGTCAGATTAACTAACATCATGCTTTGTAACA
CATGCATATGGAGTAGGTTTATTTCTTCTTCAGCTTCGGGTAATCTTTCTTCCAATGGAATTTCT
CATGACAA
Found at i:252952 original size:31 final size:30
Alignment explanation
Indices: 252889--252978 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 30
252879 ACTAATAAAT
* ** *
252889 TTTGATAAGTTTAAGGACCATTTTGTAGTAG
1 TTTGATAAGTTTAATGAATATTTTATA-TAG
252920 TTTGATAAGTTTAATGAATATTTTATGATAG
1 TTTGATAAGTTTAATGAATATTTTAT-ATAG
* *
252951 TTTGACAATATTTAATG-ATAATTTTATA
1 TTTGATAA-GTTTAATGAAT-ATTTTATA
252979 AATATTTTGT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
31 35 0.70
32 15 0.30
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.47
Consensus pattern (30 bp):
TTTGATAAGTTTAATGAATATTTTATATAG
Found at i:253422 original size:42 final size:42
Alignment explanation
Indices: 253370--253514 Score: 156
Period size: 42 Copynumber: 3.5 Consensus size: 42
253360 TGCCACAAAA
*
253370 TGATACTTTAGCGGCGTTTTTCCAACAAACGCCACAATAGAG
1 TGATATTTTAGCGGCGTTTTTCCAACAAACGCCACAATAGAG
* ** *
253412 TGATAATTTAGCGGCGTTTGTAGC-ACAAACGCCAGAATAGAG
1 TGATATTTTAGCGGCGTTT-TTCCAACAAACGCCACAATAGAG
* *
253454 T--TATTTATAGTGGC-TTTTTTCAACAAACGCCACAATAGA-
1 TGATATTT-TAGCGGCGTTTTTCCAACAAACGCCACAATAGAG
*
253493 TTAGTATTTTAGCGGCGTTTTT
1 TGA-TATTTTAGCGGCGTTTTT
253515 ATACAAATAC
Statistics
Matches: 86, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
39 3 0.03
40 23 0.27
41 12 0.14
42 46 0.53
43 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (42 bp):
TGATATTTTAGCGGCGTTTTTCCAACAAACGCCACAATAGAG
Found at i:254175 original size:21 final size:21
Alignment explanation
Indices: 254151--254197 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
254141 GTGTTTTTCT
254151 GCTTTCGAATAGAAAA-ATATA
1 GCTTTCGAATAGAAAATA-ATA
*
254172 GCTTTCGAATAGGAAATAATA
1 GCTTTCGAATAGAAAATAATA
254193 GCTTT
1 GCTTT
254198 TGAAAACATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (21 bp):
GCTTTCGAATAGAAAATAATA
Found at i:257585 original size:89 final size:87
Alignment explanation
Indices: 257431--257603 Score: 274
Period size: 89 Copynumber: 2.0 Consensus size: 87
257421 AGACCTAACC
* *
257431 TCCTTTTATAGCCAAGTTACTCTAATCATATAGGGTTTTATTATTTCAAATTAATTAAATCTATA
1 TCCTCTTATAGCCAAGTTACACTAATCATATAGGGTTTTATTATTTCAAATTAATTAAATCTATA
*
257496 TTTAATTAATGGAATTTAATAA
66 TTTAATTAATGGAAATTAATAA
* *
257518 TCCTCTTATATCCAAGTTACACTAATCATATTGGGGATTTTATTATTTCAAATTAATTAAATCTA
1 TCCTCTTATAGCCAAGTTACACTAATCATA-TAGGG-TTTTATTATTTCAAATTAATTAAATCTA
*
257583 TATTTAATTAATTGAAATTAA
64 TATTTAATTAATGGAAATTAA
257604 ATATTCGGGA
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
87 27 0.35
88 4 0.05
89 47 0.60
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.45
Consensus pattern (87 bp):
TCCTCTTATAGCCAAGTTACACTAATCATATAGGGTTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATGGAAATTAATAA
Found at i:265717 original size:44 final size:44
Alignment explanation
Indices: 265652--265757 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
265642 ACAATACCGA
* *
265652 CATTTGTA-ACAAAAAACGCCGCTATATACCAGACCTTTTGTC-G
1 CATTTGTACCCAAAAAATGCCGCTATATACCAGACCTTTTG-CGG
* *
265695 CATTTGTATCCGAAAAATGCCGCTATATACCAGACCTTTTGCGG
1 CATTTGTACCCAAAAAATGCCGCTATATACCAGACCTTTTGCGG
*
265739 CGTTTGTACCCAAAAAATG
1 CATTTGTACCCAAAAAATG
265758 ACGTTAAATG
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
43 9 0.16
44 46 0.84
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (44 bp):
CATTTGTACCCAAAAAATGCCGCTATATACCAGACCTTTTGCGG
Found at i:267170 original size:18 final size:18
Alignment explanation
Indices: 267147--267194 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
267137 TTTCAAATAG
267147 TTGAGATGGAGGATAAAT
1 TTGAGATGGAGGATAAAT
*
267165 TTGAGAAT-GAGGATACAT
1 TTGAG-ATGGAGGATAAAT
* *
267183 GTGAGGTGGAGG
1 TTGAGATGGAGG
267195 TGGGTGATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 22 0.88
19 2 0.08
ACGTcount: A:0.33, C:0.02, G:0.40, T:0.25
Consensus pattern (18 bp):
TTGAGATGGAGGATAAAT
Found at i:277970 original size:21 final size:21
Alignment explanation
Indices: 277919--277971 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
277909 ATTATGACTA
277919 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
277940 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
277961 TCGCAATGCGA
1 TCGCAATGCGA
277972 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:277986 original size:20 final size:21
Alignment explanation
Indices: 277961--278012 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
277951 TTTTCCCAAT
*
277961 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
277981 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
278002 TCGCAATGCGA
1 TCGCAATGCGA
278013 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:277991 original size:41 final size:41
Alignment explanation
Indices: 277946--278177 Score: 132
Period size: 41 Copynumber: 5.7 Consensus size: 41
277936 AATTTCGCGT
*
277946 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * *
277987 TGCGAATTTGGAAAATCGCAATGCG-AT-ACTGACTATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGT-A-AATCGCAA
* * * * * **
278028 TGCAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCCTAATTCGCAATGCGA-ATAAGTAAATCGCAA
* * *
278069 TGCGATTTTCATAATTTGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * *
278110 CGCGA-TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAA-TAAGTAAATCGCAA
* * * *
278151 TGCGA-ATACGTAAATCGCAATGCGAAT
1 TGCGATTTTCCTAATTCGCAATGCGAAT
278178 CTTACTATCG
Statistics
Matches: 144, Mismatches: 40, Indels: 15
0.72 0.20 0.08
Matches are distributed among these distances:
39 2 0.01
40 25 0.17
41 115 0.80
43 1 0.01
44 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (41 bp):
TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
Found at i:278056 original size:21 final size:21
Alignment explanation
Indices: 278022--278094 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
278012 ATACTGACTA
* *
278022 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
278043 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
278063 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
*
278084 TTGCAATGCGA
1 TCGCAATGCGA
278095 ATACGTAAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 17 0.41
21 24 0.59
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:278192 original size:20 final size:20
Alignment explanation
Indices: 278086--278177 Score: 130
Period size: 20 Copynumber: 4.5 Consensus size: 20
278076 TTCATAATTT
278086 GCAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
* * *
278106 GCAACGCGATTAAGTAAATC
1 GCAATGCGAATACGTAAATC
* *
278126 GCAATGCGAATTAGGAAAATC
1 GCAATGCGAA-TACGTAAATC
278147 GCAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
278167 GCAATGCGAAT
1 GCAATGCGAAT
278178 CTTACTATCG
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 44 0.71
21 18 0.29
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.20
Consensus pattern (20 bp):
GCAATGCGAATACGTAAATC
Found at i:278774 original size:19 final size:19
Alignment explanation
Indices: 278750--278794 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
278740 GCAACAAGAG
*
278750 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
278769 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
278788 AATCGCA
1 AATCGCA
278795 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:278831 original size:14 final size:14
Alignment explanation
Indices: 278812--278867 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
278802 TTTCATTTCG
278812 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
278826 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
278845 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
278859 CGTTGCGAT
1 CGTTGCGAT
278868 AGTCATTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 2 0.06
19 11 0.31
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:278841 original size:33 final size:33
Alignment explanation
Indices: 278795--278876 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
278785 CAAAATCGCA
**
278795 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
278828 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
278861 TTGCGATAGTCATTTC
1 TTGCGATAGTCATTTC
278877 AACCAAAAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
Found at i:278850 original size:19 final size:17
Alignment explanation
Indices: 278803--278855 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 17
278793 CATTGCGATT
278803 TTCATTTCGCGTTGCGA
1 TTCATTTCGCGTTGCGA
*
278820 TTC---TCTCGTTGCGA
1 TTCATTTCGCGTTGCGA
278834 TAGTCATTTCGCGTTGCGA
1 T--TCATTTCGCGTTGCGA
278853 TTC
1 TTC
278856 TCTCGTTGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 11 0.38
16 2 0.07
17 5 0.17
19 11 0.38
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.42
Consensus pattern (17 bp):
TTCATTTCGCGTTGCGA
Found at i:281047 original size:21 final size:21
Alignment explanation
Indices: 281023--281089 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
281013 TCATTCCTCG
281023 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
281044 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
281065 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
281086 AGAG
1 AGAG
281090 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:281047 original size:42 final size:42
Alignment explanation
Indices: 280971--281089 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
280961 GACTCGCCTG
* * * * * * *
280971 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
281013 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
281055 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
281090 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:282458 original size:14 final size:14
Alignment explanation
Indices: 282439--282474 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
282429 ATTGTTTAAT
282439 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
282453 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
282467 TGATTTGT
1 TGATTTGT
282475 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:282618 original size:14 final size:14
Alignment explanation
Indices: 282599--282655 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
282589 GCGAAATGAA
282599 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
282613 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
282632 AATCGCAACGAGAG
1 AATCGCAACGAGAG
282646 AATCGCAACG
1 AATCGCAACG
282656 TGAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:282626 original size:33 final size:33
Alignment explanation
Indices: 282581--282671 Score: 146
Period size: 33 Copynumber: 2.8 Consensus size: 33
282571 AAAAAGTACT
*
282581 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
282614 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* * *
282647 ATCGCAACGTGAAATTAAATTCGCA
1 ATCGCAACGCGAAATGAAAATCGCA
282672 TTGTGATTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:282640 original size:19 final size:19
Alignment explanation
Indices: 282581--282641 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
282571 AAAAAGTACT
*
282581 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
282600 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
282614 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
282633 ATCGCAACG
1 ATCGCAACG
282642 AGAGAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:282688 original size:19 final size:19
Alignment explanation
Indices: 282666--282730 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
282656 TGAAATTAAA
*
282666 TTCGCATTGTGATTTTCAT
1 TTCGCATTGCGATTTTCAT
282685 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
282701 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
282718 TTCGCATTGCGAT
1 TTCGCATTGCGAT
282731 AGTAATTTCC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 6 0.16
16 7 0.18
17 7 0.18
19 18 0.47
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:282738 original size:19 final size:20
Alignment explanation
Indices: 282716--282757 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
282706 TGCGATTTTC
*
282716 ATTT-CGCATTGCGATAGTA
1 ATTTCCGCATTGCGATAGAA
*
282735 ATTTCCGCGTTGCGATAGAA
1 ATTTCCGCATTGCGATAGAA
282755 ATT
1 ATT
282758 AAGATGATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGAA
Found at i:285251 original size:24 final size:24
Alignment explanation
Indices: 285217--285270 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
285207 CTGAAACATC
*
285217 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
285241 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
285265 ATCAAA
1 ATCAAA
285271 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:286181 original size:20 final size:20
Alignment explanation
Indices: 286092--286183 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
286082 TGCGAATTTG
* *
286092 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
286112 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
286132 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
286153 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
286173 GAAAATCGCAA
1 GAAAATCGCAA
286184 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:286422 original size:20 final size:20
Alignment explanation
Indices: 286397--286464 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
286387 CAACGGGGAA
*
286397 ATCGCAACGCGAAAATGGCT
1 ATCGCAACACGAAAATGGCT
** ***
286417 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACACGAAAATG-GCT
286437 ATCGCAACACGAAAATGGCT
1 ATCGCAACACGAAAATGGCT
286457 ATCGCAAC
1 ATCGCAAC
286465 TAGAAAATCG
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (20 bp):
ATCGCAACACGAAAATGGCT
Found at i:286470 original size:20 final size:20
Alignment explanation
Indices: 286397--286472 Score: 57
Period size: 20 Copynumber: 3.8 Consensus size: 20
286387 CAACGGGGAA
**
286397 ATCGCAACGCGAAAATGGCT
1 ATCGCAACTAGAAAATGGCT
* * ***
286417 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACTAGAAAATG-GCT
286437 ATCGCAAC-ACGAAAATGGCT
1 ATCGCAACTA-GAAAATGGCT
286457 ATCGCAACTAGAAAAT
1 ATCGCAACTAGAAAAT
286473 CGCAATGCAA
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
19 5 0.12
20 31 0.74
21 6 0.14
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.17
Consensus pattern (20 bp):
ATCGCAACTAGAAAATGGCT
Found at i:286536 original size:19 final size:19
Alignment explanation
Indices: 286514--286558 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
286504 TTCTCGTTGT
286514 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
286533 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
286552 GATTTTC
1 GATTTTC
286559 TCGTTGCGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.49
Consensus pattern (19 bp):
GATTTTCATTTCGCATTGC
Found at i:288194 original size:41 final size:42
Alignment explanation
Indices: 288140--288231 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
288130 CCTCTTCAAC
* *
288140 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* *
288181 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
*
288223 AATGACAGG
1 GATGACAGG
288232 TGAGTCGGAC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 20 0.45
42 24 0.55
ACGTcount: A:0.22, C:0.15, G:0.41, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:288594 original size:20 final size:20
Alignment explanation
Indices: 288569--288621 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
288559 GAAGAATAGT
*
288569 TTACTTTCGTAACACGAAAC
1 TTACTTTCGCAACACGAAAC
* *
288589 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAC
* *
288609 TGACTATCGCAAC
1 TTACTTTCGCAAC
288622 GCGGAAATGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.26
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAC
Found at i:288622 original size:20 final size:20
Alignment explanation
Indices: 288595--288657 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
288585 AAACTTACTT
*
288595 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
288615 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
288635 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
288655 TCG
1 TCG
288658 TAGTGCGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:288736 original size:19 final size:18
Alignment explanation
Indices: 288712--288803 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
288702 ACAAATCGCA
288712 TTGCGATTTTCATTTCACG
1 TTGCGATTTTCATTTC-CG
*
288731 TTGCGA-TTT--TGT-CG
1 TTGCGATTTTCATTTCCG
*
288745 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTC-CG
*
288764 TTGCGA-TTT--TGT-CG
1 TTGCGATTTTCATTTCCG
*
288778 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTC-CG
288797 TTGCGAT
1 TTGCGAT
288804 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 7, Indels: 20
0.67 0.08 0.24
Matches are distributed among these distances:
14 15 0.27
15 6 0.11
16 4 0.07
17 4 0.07
18 6 0.11
19 21 0.38
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (18 bp):
TTGCGATTTTCATTTCCG
Found at i:288748 original size:14 final size:14
Alignment explanation
Indices: 288729--288787 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
288719 TTTCATTTCA
288729 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
288743 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
288760 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
288776 CGTTGCGATTTT
1 CGTTGCGATTTT
288788 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:288754 original size:33 final size:33
Alignment explanation
Indices: 288712--288803 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
288702 ACAAATCGCA
* *
288712 TTGCGATTTTCATTTCACGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
288745 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
288778 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
288804 AGCCATTTCC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:288842 original size:20 final size:20
Alignment explanation
Indices: 288788--288831 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
288778 TTGCGATTTT
288788 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
*
288807 CATTTCCGCATTGCGATAGT
1 CATTTCCGCATTGCGATAGC
288827 CATTT
1 CATTT
288832 TCGTGTTGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:289412 original size:18 final size:18
Alignment explanation
Indices: 289389--289436 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
289379 CGGGTCGATC
289389 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
289407 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
289425 AGGTGATGGCTC
1 AGGTGATGGCTC
289437 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:290781 original size:20 final size:20
Alignment explanation
Indices: 290756--290798 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
290746 AATAGTTTCT
*
290756 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAACCGCAACAC
290776 GAAAATGAAAACCGCAACAC
1 GAAAATGAAAACCGCAACAC
290796 GAA
1 GAA
290799 TTTGACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.56, C:0.21, G:0.16, T:0.07
Consensus pattern (20 bp):
GAAAATGAAAACCGCAACAC
Found at i:291104 original size:22 final size:22
Alignment explanation
Indices: 291078--291121 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
291068 GATAGAGATA
291078 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
291100 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
291122 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:291336 original size:20 final size:20
Alignment explanation
Indices: 291311--291377 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
291301 GTATTATCTC
* *
291311 GTTGCGAAAGTCAGTATTGA
1 GTTGCGAAAGTAAGTATCGA
*
291331 GTTGCGAAATTAAGTATCGA
1 GTTGCGAAAGTAAGTATCGA
*
291351 GTTGCGAAAGTAAGTATCGC
1 GTTGCGAAAGTAAGTATCGA
291371 GTTGCGA
1 GTTGCGA
291378 TTTTGTATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.28
Consensus pattern (20 bp):
GTTGCGAAAGTAAGTATCGA
Found at i:291413 original size:41 final size:41
Alignment explanation
Indices: 291285--291463 Score: 157
Period size: 41 Copynumber: 4.4 Consensus size: 41
291275 CGCTTTGAAA
* * * *
291285 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCATTGCGAAAGTCAGT
* * ** * * *
291326 ATTGAGTTGCGAAATT-AAGTATCG-AGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATTTTGTATTATCGCA-TTGCGAAAGTCAGT
*
291366 ATCGCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCATTGCGAAAGTCAGT
* ** * *
291407 ACCGCGTTGCGATTTTCCA-AATTCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTA-TCGCATTGCGAAAGTCAGT
*
291448 ATCGCATTGCGATTTT
1 ATCGCGTTGCGATTTT
291464 CCAAATTCGC
Statistics
Matches: 109, Mismatches: 25, Indels: 8
0.77 0.18 0.06
Matches are distributed among these distances:
40 31 0.28
41 77 0.71
42 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCATTGCGAAAGTCAGT
Found at i:291439 original size:21 final size:21
Alignment explanation
Indices: 291413--291478 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
291403 CAGTACCGCG
291413 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
** *
291434 TTGCGATAGT-C-AGTATCGCA
1 TTGCGATTTTCCAAAT-TCGCA
291454 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
291475 TTGC
1 TTGC
291479 AAATTGGGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
19 2 0.06
20 14 0.39
21 18 0.50
22 2 0.06
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCA
Found at i:291454 original size:20 final size:20
Alignment explanation
Indices: 291285--291460 Score: 83
Period size: 20 Copynumber: 8.7 Consensus size: 20
291275 CGCTTTGAAA
*
291285 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
291306 ATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
291326 ATTG-AGTTGCGAAATTAAGT
1 ATCGCA-TTGCGATAGTCAGT
* *
291346 ATCG-AGTTGCGAAAGTAAGT
1 ATCGCA-TTGCGATAGTCAGT
* * *
291366 ATCGCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
291387 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * ** *
291407 ACCGCGTTGCGATTTTCCA-A
1 ATCGCATTGCGATAGT-CAGT
291427 ATTCGCATTGCGATAGTCAGT
1 A-TCGCATTGCGATAGTCAGT
291448 ATCGCATTGCGAT
1 ATCGCATTGCGAT
291461 TTTCCAAATT
Statistics
Matches: 118, Mismatches: 28, Indels: 19
0.72 0.17 0.12
Matches are distributed among these distances:
19 5 0.04
20 74 0.63
21 37 0.31
22 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:291464 original size:41 final size:41
Alignment explanation
Indices: 291352--291478 Score: 175
Period size: 41 Copynumber: 3.1 Consensus size: 41
291342 AAGTATCGAG
* * ** *
291352 TTGCGAAAGTAAGTATCGCGTTGCGATTTT-GTATTATCGCA
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAAT-TCGCA
*
291393 TTGCGATAGTCAGTACCGCGTTGCGATTTTCCAAATTCGCA
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAATTCGCA
*
291434 TTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCGCA
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAATTCGCA
291475 TTGC
1 TTGC
291479 AAATTGGGAA
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
41 75 0.97
42 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAATTCGCA
Found at i:291505 original size:21 final size:21
Alignment explanation
Indices: 291470--291543 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
291460 TTTTCCAAAT
* *
291470 TCGCATTGCAAATTGGGAAAA
1 TCGCAATGCGAATTGGGAAAA
*
291491 TTGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATTGGGAAAA
*
291512 TCGCAACGCGAAATT-GGAAAA
1 TCGCAATGCG-AATTGGGAAAA
*
291533 TCGCATTGCGA
1 TCGCAATGCGA
291544 TAGTCATAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
20 1 0.02
21 40 0.89
22 4 0.09
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTGGGAAAA
Found at i:293413 original size:14 final size:14
Alignment explanation
Indices: 293394--293420 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
293384 TTGTTGAATA
293394 TTTAAAATATAATC
1 TTTAAAATATAATC
293408 TTTAAAATATAAT
1 TTTAAAATATAAT
293421 TTATAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTAAAATATAATC
Found at i:293522 original size:24 final size:24
Alignment explanation
Indices: 293488--293548 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
293478 AAATAATATT
*
293488 AAATAAAATTATT-TTAAAATTAAA
1 AAATAATATTATTGTT-AAATTAAA
* * *
293512 AAATATTATTATTGTTATATTAAT
1 AAATAATATTATTGTTAAATTAAA
293536 AAATAATATTATT
1 AAATAATATTATT
293549 CATTGTATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 29 0.94
25 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
AAATAATATTATTGTTAAATTAAA
Found at i:297190 original size:26 final size:26
Alignment explanation
Indices: 297154--297207 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
297144 ATTAAATGCA
297154 TATGGTGGGCA-TGACCTTATGTGTAT
1 TATGGTGGGCACT-ACCTTATGTGTAT
297180 TATGGTGGGCACTACCTTATGTGTAT
1 TATGGTGGGCACTACCTTATGTGTAT
297206 TA
1 TA
297208 GCACTTTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 26 0.96
27 1 0.04
ACGTcount: A:0.20, C:0.13, G:0.28, T:0.39
Consensus pattern (26 bp):
TATGGTGGGCACTACCTTATGTGTAT
Found at i:299376 original size:17 final size:16
Alignment explanation
Indices: 299303--299378 Score: 59
Period size: 16 Copynumber: 4.8 Consensus size: 16
299293 AATTATTCCC
**
299303 ATTTTATATGTGCTTT
1 ATTTTATATGTTATTT
*
299319 ATTTTAATAACGTT-TTT
1 ATTTT-AT-ATGTTATTT
* *
299336 ATATAATATG--ATTT
1 ATTTTATATGTTATTT
299350 ATTTTATATGTTATTT
1 ATTTTATATGTTATTT
299366 ATTTTATTATGTT
1 ATTTTA-TATGTT
299379 GTCTCACTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
14 11 0.23
15 2 0.04
16 17 0.36
17 14 0.30
18 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (16 bp):
ATTTTATATGTTATTT
Found at i:300964 original size:20 final size:19
Alignment explanation
Indices: 300939--300978 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
300929 TTGGGGCCTG
300939 ATGGTATCGATACTATGTAT
1 ATGGTATCGATACTAT-TAT
300959 ATGGTATCGATACTATTAT
1 ATGGTATCGATACTATTAT
300978 A
1 A
300979 CAAAGTAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (19 bp):
ATGGTATCGATACTATTAT
Found at i:311027 original size:18 final size:18
Alignment explanation
Indices: 310988--311075 Score: 117
Period size: 18 Copynumber: 4.9 Consensus size: 18
310978 ATTGAATATT
310988 TGTCCCGAA-AGA-CACTA
1 TGTCCCGAAGA-ACCACTA
311005 TGTCCCGAAGAACCACTA
1 TGTCCCGAAGAACCACTA
* * *
311023 CGTCCCAAAGGACCACTA
1 TGTCCCGAAGAACCACTA
311041 TGTCCCGAAGAACCACTA
1 TGTCCCGAAGAACCACTA
*
311059 TGTCCCGAAGGACCACT
1 TGTCCCGAAGAACCACT
311076 CATAATCCCT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
17 10 0.16
18 52 0.84
ACGTcount: A:0.32, C:0.34, G:0.18, T:0.16
Consensus pattern (18 bp):
TGTCCCGAAGAACCACTA
Found at i:311040 original size:36 final size:36
Alignment explanation
Indices: 311000--311075 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
310990 TCCCGAAAGA
311000 CACTATGTCCCGAAGAACCACTACGTCCCAAAGGAC
1 CACTATGTCCCGAAGAACCACTACGTCCCAAAGGAC
* *
311036 CACTATGTCCCGAAGAACCACTATGTCCCGAAGGAC
1 CACTATGTCCCGAAGAACCACTACGTCCCAAAGGAC
311072 CACT
1 CACT
311076 CATAATCCCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.32, C:0.36, G:0.17, T:0.16
Consensus pattern (36 bp):
CACTATGTCCCGAAGAACCACTACGTCCCAAAGGAC
Found at i:311360 original size:8 final size:8
Alignment explanation
Indices: 311323--311361 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
311313 ACTATAACCA
311323 ATATGTAT
1 ATATGTAT
*
311331 ATATATAT
1 ATATGTAT
*
311339 ATATATAT
1 ATATGTAT
311347 ATATGTAT
1 ATATGTAT
*
311355 ACATGTA
1 ATATGTA
311362 CATGAATATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (8 bp):
ATATGTAT
Found at i:319178 original size:20 final size:19
Alignment explanation
Indices: 319153--319192 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
319143 TTGGGGCCTG
*
319153 ATGGTATCGATACTATGTAT
1 ATGGTATCAATACTAT-TAT
319173 ATGGTATCAATACTATTAT
1 ATGGTATCAATACTATTAT
319192 A
1 A
319193 CAAAGTAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (19 bp):
ATGGTATCAATACTATTAT
Found at i:336417 original size:25 final size:24
Alignment explanation
Indices: 336400--336457 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 24
336390 CCCGATCTGA
336400 AATGACCCAACCCGACCCCGACCCG
1 AATGACCCAACCCGA-CCCGACCCG
336425 AATGACCCAACCCGACCCCGACCCG
1 AATGACCCAACCCGA-CCCGACCCG
336450 AATGACCC
1 AATGACCC
336458 GATTGCCATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.29, C:0.50, G:0.16, T:0.05
Consensus pattern (24 bp):
AATGACCCAACCCGACCCGACCCG
Found at i:337396 original size:22 final size:21
Alignment explanation
Indices: 337370--337410 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
337360 GCTGCAAAAT
337370 TGATGGTC-TTGATGGATGAAGA
1 TGATGG-CGTTGAT-GATGAAGA
337392 TGATGGCGTTGATGATGAA
1 TGATGGCGTTGATGATGAA
337411 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.27, C:0.05, G:0.37, T:0.32
Consensus pattern (21 bp):
TGATGGCGTTGATGATGAAGA
Found at i:338413 original size:25 final size:24
Alignment explanation
Indices: 338385--338464 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 24
338375 ATTTAAATTA
338385 AACTACTTAGTAGTTATCCTTATCT
1 AACTACTTAGTAGTTAT-CTTATCT
* * *
338410 AACTTTCTAAG-AGTTAAT-TTAAACT
1 AAC-TACTTAGTAGTT-ATCTT-ATCT
338435 AAACTACTTAGTAGTTATCTTTATCT
1 -AACTACTTAGTAGTTATC-TTATCT
338461 AACT
1 AACT
338465 TTCTAAGAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
24 2 0.05
25 21 0.50
26 17 0.40
27 2 0.05
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.42
Consensus pattern (24 bp):
AACTACTTAGTAGTTATCTTATCT
Found at i:338448 original size:51 final size:51
Alignment explanation
Indices: 338372--338513 Score: 203
Period size: 51 Copynumber: 2.8 Consensus size: 51
338362 GAACAAGTAT
338372 TTAATTTAAATTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
1 TTAATTTAAATTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
* *
338423 TTAATTTAAACTAAACTACTTAGTAGTTATCTTTATCTAACTTTCTAAGAG
1 TTAATTTAAATTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
* * * * * *
338474 TTAGTGTTATATTAAAATACTAATTAATTATCCTTATCTA
1 TTAAT-TTAAATTAAACTACTTAGTAGTTATCCTTATCTA
338514 TCGCATAACC
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
51 53 0.66
52 27 0.34
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (51 bp):
TTAATTTAAATTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
Found at i:338450 original size:26 final size:26
Alignment explanation
Indices: 338367--338451 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
338357 GGTGAGAACA
* *
338367 AGTATTTAATTTAAATTAAACTACTT
1 AGTAGTTAATTTAAACTAAACTACTT
* * *
338393 AGTAGTT-ATCCTT-ATCT-AACTTTCTA
1 AGTAGTTAAT--TTAAACTAAAC-TACTT
338419 AG-AGTTAATTTAAACTAAACTACTT
1 AGTAGTTAATTTAAACTAAACTACTT
338444 AGTAGTTA
1 AGTAGTTA
338452 TCTTTATCTA
Statistics
Matches: 44, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
24 2 0.05
25 17 0.39
26 23 0.52
27 2 0.05
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
AGTAGTTAATTTAAACTAAACTACTT
Found at i:338462 original size:26 final size:26
Alignment explanation
Indices: 338383--338462 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 26
338373 TAATTTAAAT
*
338383 TAAACTACTTAGTAGTTATCCTTATC
1 TAAACTACTTAGTAGTTATCTTTATC
* * * *
338409 T-AACTTTCTAAG-AGTTAAT-TTAAAC
1 TAAAC-TACTTAGTAGTT-ATCTTTATC
338434 TAAACTACTTAGTAGTTATCTTTATC
1 TAAACTACTTAGTAGTTATCTTTATC
338460 TAA
1 TAA
338463 CTTTCTAAGA
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
25 18 0.45
26 22 0.55
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.42
Consensus pattern (26 bp):
TAAACTACTTAGTAGTTATCTTTATC
Found at i:338475 original size:25 final size:25
Alignment explanation
Indices: 338396--338476 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
338386 ACTACTTAGT
*
338396 AGTTATCCTTATCTAACTTTCTAAG
1 AGTTATCTTTATCTAACTTTCTAAG
* * * *
338421 AGTTAAT-TTAAACTAAAC-TACTTAG
1 AGTT-ATCTTTATCT-AACTTTCTAAG
338446 TAGTTATCTTTATCTAACTTTCTAAG
1 -AGTTATCTTTATCTAACTTTCTAAG
338472 AGTTA
1 AGTTA
338477 GTGTTATATT
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
25 23 0.55
26 19 0.45
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (25 bp):
AGTTATCTTTATCTAACTTTCTAAG
Found at i:340119 original size:23 final size:21
Alignment explanation
Indices: 340077--340123 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
340067 TTTGCAATTC
340077 TTTTATCTTTTATTTATCTTG
1 TTTTATCTTTTATTTATCTTG
*
340098 TTTTAATCTTATTTTTTATCTTG
1 TTTT-ATCTT-TTATTTATCTTG
340121 TTT
1 TTT
340124 CCAGCACCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.17
22 5 0.22
23 14 0.61
ACGTcount: A:0.15, C:0.09, G:0.04, T:0.72
Consensus pattern (21 bp):
TTTTATCTTTTATTTATCTTG
Found at i:344950 original size:12 final size:11
Alignment explanation
Indices: 344890--344952 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
344880 TATATAAGAC
*
344890 TAAAATAATAA
1 TAAAATAATAT
344901 TAAAATAATAAT
1 TAAAATAAT-AT
*
344913 T--AA-AGTAT
1 TAAAATAATAT
*
344921 TAAAAGTAATAA
1 TAAAA-TAATAT
344933 TAAAATAATAT
1 TAAAATAATAT
344944 TACAAATAA
1 TA-AAATAA
344953 ATAATGAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
8 3 0.07
9 2 0.05
10 4 0.10
11 16 0.39
12 16 0.39
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (11 bp):
TAAAATAATAT
Found at i:347268 original size:113 final size:112
Alignment explanation
Indices: 347009--347577 Score: 621
Period size: 113 Copynumber: 5.0 Consensus size: 112
346999 AAATTAAGGT
* *
347009 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTA
* * * ** *
347073 TGAACACT-TCTGGAAATGTTGATGTTGATCTATCTTCTTCTGTGAT-AGAGTCAAAC-A
66 TGAACTCTACCTGG--A-----ATGTTGATC---CATC--GAGTGATGA-ATTCAAACAA
*
347130 AAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTA
* *
347194 TGAACTCTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAA
66 TGAACTCTAC-CTGG-AATGTTGATCCATCGAGTGATGAATTCAAACAA
* * * * *
347243 AAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCATATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTA
* * * *
347308 TGAACTCTACCTGGTAATGATGATCCATCAAATGATGAATTCAAATAA
66 TGAACTCTACCTGG-AATGTTGATCCATCGAGTGATGAATTCAAACAA
*
347356 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTA
* * * *
347421 TGAACT-TTCTCTGGCAATGCTAATCCATCGGGTGATGAATT-AAAGCAA
66 TGAACTCTAC-CTGG-AATGTTGATCCATCGAGTGATGAATTCAAA-CAA
* * * *
347469 AAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTA
* * * *
347534 TGAACTCTACCTGGCATGTTGATCCATTGAGTAATGGATTCAAA
66 TGAACTCTACCTGGAATGTTGATCCATCGAGTGATGAATTCAAA
347578 TCTTTGCTAA
Statistics
Matches: 390, Mismatches: 48, Indels: 28
0.84 0.10 0.06
Matches are distributed among these distances:
112 36 0.09
113 237 0.61
114 36 0.09
117 8 0.02
121 64 0.16
122 5 0.01
123 4 0.01
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (112 bp):
AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTA
TGAACTCTACCTGGAATGTTGATCCATCGAGTGATGAATTCAAACAA
Found at i:347433 original size:226 final size:225
Alignment explanation
Indices: 347012--347560 Score: 687
Period size: 226 Copynumber: 2.4 Consensus size: 225
347002 TTAAGGTAAG
*
347012 GTTGAACAAATTCTTCTCATTATGAATTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * * *** * *
347076 ACACT-TCTGGAAATGTTGATGTTGATCTATCTTCTTCTG-TGATAGAGTCAAA-CAAAGGTTGA
66 ACTCTACCTGG-AA---TGA---TGATC---CATCAAATGATG--A-ATTCAAATAAAAGGTTGA
*
347138 ACAAATTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTCTT
118 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTCTT
* *
347203 CTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA-CAAAAA
183 CTCTGGAAAAGCTAATCCATCGAGTGATGAATT-AAAGCAAAAA
* * *
347246 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCATATGAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
*
347311 ACTCTACCTGGTAATGATGATCCATCAAATGATGAATTCAAATAAAAGGTTGAACAAGTTCTTCT
66 ACTCTACCTGG-AATGATGATCCATCAAATGATGAATTCAAATAAAAGGTTGAACAAATTCTTCT
* *
347376 CATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACT-TTCTCTGGCAATG
130 CATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTCTTCTCTGGAAAAG
* *
347440 CTAATCCATCGGGTGATGAATTAAAGCAAAAG
194 CTAATCCATCGAGTGATGAATTAAAGCAAAAA
* * *
347472 GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* *
347537 ACTCTACCTGGCATGTTGATCCAT
66 ACTCTACCTGGAATGATGATCCAT
347561 TGAGTAATGG
Statistics
Matches: 282, Mismatches: 27, Indels: 21
0.85 0.08 0.06
Matches are distributed among these distances:
225 20 0.07
226 145 0.51
227 35 0.12
228 2 0.01
230 5 0.02
233 3 0.01
234 33 0.12
235 33 0.12
236 6 0.02
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (225 bp):
GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACTCTACCTGGAATGATGATCCATCAAATGATGAATTCAAATAAAAGGTTGAACAAATTCTTCTC
ATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTCTTCTCTGGAAAAGCT
AATCCATCGAGTGATGAATTAAAGCAAAAA
Found at i:347992 original size:22 final size:22
Alignment explanation
Indices: 347937--347992 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
347927 TAAAGCTTTT
* * *
347937 ATCTTTGAAAATAGAATCTATC
1 ATCTTTGAAGAGAGAATATATC
*
347959 ATCTTTGGAGAGAGAATATATC
1 ATCTTTGAAGAGAGAATATATC
347981 ATCTTTGAAGAG
1 ATCTTTGAAGAG
347993 TATAGATGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Consensus pattern (22 bp):
ATCTTTGAAGAGAGAATATATC
Found at i:349426 original size:36 final size:36
Alignment explanation
Indices: 349346--349438 Score: 107
Period size: 36 Copynumber: 2.6 Consensus size: 36
349336 TCTTGTTGAG
* * *
349346 ATGAGCCTCCAAGAATG-CCCAAATATTCATATTGCC
1 ATGAGCCTTCAA-AATGCCCCAAATATTCATACTGAC
*
349382 GTGAGCCTTCAAAATGCCCCAAATATTCATACTGAC
1 ATGAGCCTTCAAAATGCCCCAAATATTCATACTGAC
* **
349418 ATGGGCCTTCAGGATGCCCCA
1 ATGAGCCTTCAAAATGCCCCA
349439 CATGAATAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 4 0.08
36 44 0.92
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (36 bp):
ATGAGCCTTCAAAATGCCCCAAATATTCATACTGAC
Found at i:354087 original size:25 final size:26
Alignment explanation
Indices: 354026--354088 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 26
354016 TTATGCAAAT
* *
354026 ATGCAAATG-CAAAAATGAAATATAA
1 ATGCAAATGTAAAAAATGAAATAAAA
** *
354051 ATATAAACGTAAAAAATGAAA-AAAA
1 ATGCAAATGTAAAAAATGAAATAAAA
354076 ATGCAAATGTAAA
1 ATGCAAATGTAAA
354089 TATGTGAATG
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
25 19 0.66
26 10 0.34
ACGTcount: A:0.63, C:0.06, G:0.11, T:0.19
Consensus pattern (26 bp):
ATGCAAATGTAAAAAATGAAATAAAA
Found at i:355218 original size:15 final size:17
Alignment explanation
Indices: 355188--355220 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
355178 AAAAAAAGGG
355188 AAAAAATCAAATAAATT
1 AAAAAATCAAATAAATT
355205 AAAAAA-CAAA-AAATT
1 AAAAAATCAAATAAATT
355220 A
1 A
355221 GAACTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 4 0.25
17 6 0.38
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAAAATCAAATAAATT
Found at i:355617 original size:23 final size:23
Alignment explanation
Indices: 355591--355644 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
355581 TTAACACTTG
355591 AAAATAA-A-ATAAAGATATTAATA
1 AAAATAATATATAAA-ATATT-ATA
*
355614 AAAA-AATATATAAAATATTATG
1 AAAATAATATATAAAATATTATA
355636 AAAATAATA
1 AAAATAATA
355645 AGTATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 8 0.30
23 14 0.52
24 5 0.19
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.28
Consensus pattern (23 bp):
AAAATAATATATAAAATATTATA
Found at i:358262 original size:3 final size:3
Alignment explanation
Indices: 358256--358311 Score: 69
Period size: 3 Copynumber: 18.3 Consensus size: 3
358246 GCCTGTAAAT
*
358256 ATA ATA AT- ATCA ATTA ATA ATA ATA ATA ATA ATT ATA ATA ATA ATA
1 ATA ATA ATA AT-A A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
358302 AAA ATA ATA A
1 ATA ATA ATA A
358312 AACGGGATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.04
3 40 0.87
4 3 0.07
5 1 0.02
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:358578 original size:26 final size:25
Alignment explanation
Indices: 358549--358629 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 25
358539 TTAATTTAAA
358549 CTAAACTACTTAGTAGTTATCCTTAT
1 CTAAACTACTTAGTAGTTAT-CTTAT
* * *
358575 CT-AACTTTCTAAG-AGTTAAT-TTAAA
1 CTAAAC-TACTTAGTAGTT-ATCTT-AT
358600 CTAAACTACTTAGTAGTTATCTTTAT
1 CTAAACTACTTAGTAGTTATC-TTAT
358626 CTAA
1 CTAA
358630 CTTTCTAAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
24 2 0.05
25 17 0.40
26 21 0.50
27 2 0.05
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (25 bp):
CTAAACTACTTAGTAGTTATCTTAT
Done.