Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008192.1 Hibiscus syriacus cultivar Beakdansim tig00110809_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: 1702141
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:165885 original size:12 final size:11
Alignment explanation
Indices: 165870--165899 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
165860 TAAATAATAA
165870 AATAATACAAG
1 AATAATACAAG
165881 TAATAATACAAG
1 -AATAATACAAG
165893 AATAATA
1 AATAATA
165900 AAAAGAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (11 bp):
AATAATACAAG
Found at i:165938 original size:14 final size:14
Alignment explanation
Indices: 165915--165947 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
165905 AAAGAGAAAG
165915 TAAA-AAAATATAA
1 TAAATAAAATATAA
165928 TAAATAAAATATAA
1 TAAATAAAATATAA
*
165942 AAAATA
1 TAAATA
165948 TACATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAATAAAATATAA
Found at i:165960 original size:22 final size:22
Alignment explanation
Indices: 165917--165964 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
165907 AGAGAAAGTA
165917 AAAAAATATAATAAATAAAATAT
1 AAAAAATATAAT-AATAAAATAT
*
165940 AAAAAATATACAT-ATATAATAT
1 AAAAAATATA-ATAATAAAATAT
165962 AAA
1 AAA
165965 TAAGTAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 11 0.48
23 10 0.43
24 2 0.09
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAAAATATAATAATAAAATAT
Found at i:166000 original size:14 final size:13
Alignment explanation
Indices: 165942--166023 Score: 59
Period size: 13 Copynumber: 6.5 Consensus size: 13
165932 TAAAATATAA
165942 AAAATATACATA-T
1 AAAATATA-ATAGT
*
165955 ATAATATAAATAAGT
1 AAAATAT-AAT-AGT
* *
165970 AGAATA-AA-AGG
1 AAAATATAATAGT
165981 AAAATATAATAGT
1 AAAATATAATAGT
165994 AAAA-ATAATA-T
1 AAAATATAATAGT
166005 -AAATATAATAGT
1 AAAATATAATAGT
166017 AATAATA
1 AA-AATA
166024 AAAATGCAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 17
0.71 0.06 0.22
Matches are distributed among these distances:
10 3 0.05
11 14 0.25
12 9 0.16
13 17 0.31
14 6 0.11
15 6 0.11
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.28
Consensus pattern (13 bp):
AAAATATAATAGT
Found at i:166012 original size:11 final size:11
Alignment explanation
Indices: 165927--166014 Score: 51
Period size: 11 Copynumber: 8.1 Consensus size: 11
165917 AAAAAATATA
*
165927 ATAAATAAAAT
1 ATAAATATAAT
165938 ATAAA-A-AAT
1 ATAAATATAAT
165947 ATACATATATAAT
1 ATA-A-ATATAAT
*
165960 ATAAATA-AGT
1 ATAAATATAAT
* * *
165970 A-GAATAAAAGG
1 ATAAATATAA-T
165981 A-AAATATAAT
1 ATAAATATAAT
*
165991 AGTAAAAATAAT
1 A-TAAATATAAT
166003 ATAAATATAAT
1 ATAAATATAAT
166014 A
1 A
166015 GTAATAATAA
Statistics
Matches: 60, Mismatches: 9, Indels: 16
0.71 0.11 0.19
Matches are distributed among these distances:
9 10 0.17
10 7 0.12
11 26 0.43
12 11 0.18
13 6 0.10
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.27
Consensus pattern (11 bp):
ATAAATATAAT
Found at i:166647 original size:37 final size:36
Alignment explanation
Indices: 166593--166697 Score: 111
Period size: 37 Copynumber: 2.8 Consensus size: 36
166583 GTGCTTGTGG
* * *
166593 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTAT-TTTAAGAGTTTGAATCCTAGTAGAACTCT
* * *
166630 ATCCTACTTTTAAGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTA-TTTTAAGAGTTTGAATCCTAGTAGAACTCT
* *
166667 ATCATATTTTTATGAGTTTGAATCCTAGTAG
1 ATCCTA-TTTTAAGAGTTTGAATCCTAGTAG
166698 GACGAAAAGG
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
37 55 0.98
38 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (36 bp):
ATCCTATTTTAAGAGTTTGAATCCTAGTAGAACTCT
Found at i:167290 original size:91 final size:88
Alignment explanation
Indices: 167179--167352 Score: 233
Period size: 91 Copynumber: 1.9 Consensus size: 88
167169 TAACTTTTAT
** * *
167179 AATAACACTTTTTATTTTTATAATTCATACCGTTAATTTTTTCGATTTCACTTTTTTATATTTAT
1 AATAACACTTTTTACCTTTATAATTCATACCGTTAATTTTTT--AATTCAC-TTTTTATATTTAA
167244 AATTGATGA-CTCTAATTTTTTTTTTC
63 AATTGAT-ACCTCTAATTTTTTTTTTC
* * * *
167270 AATATCACTTTTTACCTTTATAATTGATACCTTTAATTTTTTAATTCACTTTTTATCTTTAAAAT
1 AATAACACTTTTTACCTTTATAATTCATACCGTTAATTTTTTAATTCACTTTTTATATTTAAAAT
167335 TGATACCTCTAATTTTTT
66 TGATACCTCTAATTTTTT
167353 AATACCATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
87 1 0.01
88 30 0.41
89 6 0.08
91 37 0.50
ACGTcount: A:0.28, C:0.13, G:0.03, T:0.56
Consensus pattern (88 bp):
AATAACACTTTTTACCTTTATAATTCATACCGTTAATTTTTTAATTCACTTTTTATATTTAAAAT
TGATACCTCTAATTTTTTTTTTC
Found at i:167310 original size:42 final size:42
Alignment explanation
Indices: 167179--167420 Score: 173
Period size: 41 Copynumber: 5.6 Consensus size: 42
167169 TAACTTTTAT
* ** * *
167179 AATAACACTTTTTATTTTTATAATTCATACCGTTAATTTTTTC
1 AATATCACTTTTTACCTTTATAATTGATACCTTTAA-TTTTTC
* * ** **
167222 GATTTCACTTTTTTATATTTATAATTGATGACTCTAATTTTTTTTTTC
1 AATATCAC-TTTTTACCTTTATAATTGAT-AC-C---TTTAATTTTTC
*
167270 AATATCACTTTTTACCTTTATAATTGATACCTTTAATTTTTT
1 AATATCACTTTTTACCTTTATAATTGATACCTTTAATTTTTC
* * * *
167312 AAT-TCACTTTTTATCTTTAAAATTGATACCTCTAATTTTTT
1 AATATCACTTTTTACCTTTATAATTGATACCTTTAATTTTTC
* * * ** **
167353 AATACCATTTTTTACCTTTAAAATTGAGGCCCCTAAGTTTTTC
1 AATATCACTTTTTACCTTTATAATTGATACCTTTAA-TTTTTC
*
167396 AATCAT-ACTTTTTACTTTTATAATT
1 AAT-ATCACTTTTTACCTTTATAATT
167421 TAAACCCCTA
Statistics
Matches: 161, Mismatches: 29, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
41 38 0.24
42 37 0.23
43 29 0.18
44 19 0.12
45 3 0.02
46 3 0.02
47 18 0.11
48 12 0.07
49 2 0.01
ACGTcount: A:0.28, C:0.14, G:0.04, T:0.53
Consensus pattern (42 bp):
AATATCACTTTTTACCTTTATAATTGATACCTTTAATTTTTC
Found at i:167322 original size:41 final size:43
Alignment explanation
Indices: 167102--167420 Score: 208
Period size: 42 Copynumber: 7.4 Consensus size: 43
167092 TATATTATAT
* * * *
167102 TTTTTATTTTTATAATTGAGT-CCTTTTATTTTTTCAATTTTA-
1 TTTTTATCTTTATAATTGA-TACCTTTAATTTTTTCAATATCAC
* * * * *
167144 TTTTTATATGTATTATTGAGGTACC--TAACTTTTAT-AATAACAC
1 TTTTTATCTTTATAATTGA--TACCTTTAA-TTTTTTCAATATCAC
* * * * *
167187 TTTTTATTTTTATAATTCATACCGTTAATTTTTTCGATTTCAC
1 TTTTTATCTTTATAATTGATACCTTTAATTTTTTCAATATCAC
* **
167230 TTTTTTATATTTATAATTGATGACTCTAATTTTTTTTTTCAATATCAC
1 -TTTTTATCTTTATAATTGAT-AC-CT--TTAATTTTTTCAATATCAC
*
167278 TTTTTACCTTTATAATTGATACCTTTAATTTTTT-AAT-TCAC
1 TTTTTATCTTTATAATTGATACCTTTAATTTTTTCAATATCAC
* * * *
167319 TTTTTATCTTTAAAATTGATACCTCTAATTTTTT-AATACCAT
1 TTTTTATCTTTATAATTGATACCTTTAATTTTTTCAATATCAC
* * ** ** *
167361 TTTTTACCTTTAAAATTGAGGCCCCTAAGTTTTTCAATCAT-AC
1 TTTTTATCTTTATAATTGATACCTTTAATTTTTTCAAT-ATCAC
167404 TTTTTA-CTTTTATAATT
1 TTTTTATC-TTTATAATT
167421 TAAACCCCTA
Statistics
Matches: 221, Mismatches: 40, Indels: 31
0.76 0.14 0.11
Matches are distributed among these distances:
41 42 0.19
42 62 0.28
43 56 0.25
44 21 0.10
45 4 0.02
46 3 0.01
47 18 0.08
48 15 0.07
ACGTcount: A:0.27, C:0.13, G:0.05, T:0.55
Consensus pattern (43 bp):
TTTTTATCTTTATAATTGATACCTTTAATTTTTTCAATATCAC
Found at i:168944 original size:18 final size:19
Alignment explanation
Indices: 168921--168958 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
168911 AACAATATAT
168921 TTAAAA-ACATAAAATAAA
1 TTAAAACACATAAAATAAA
*
168939 TTAAAACATATAAAATAAA
1 TTAAAACACATAAAATAAA
168958 T
1 T
168959 GACTAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (19 bp):
TTAAAACACATAAAATAAA
Found at i:169819 original size:28 final size:29
Alignment explanation
Indices: 169775--169830 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
169765 ATTTTCTCTG
*
169775 TTTTTTTTCTATGTCTCTTTCTC-TTCTT
1 TTTTTTTTCTATGTCTCTATCTCGTTCTT
* *
169803 TTTTTTTTCTGTTTCTCTATCTCGTTCT
1 TTTTTTTTCTATGTCTCTATCTCGTTCT
169831 ATCTCTCTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.04, C:0.21, G:0.05, T:0.70
Consensus pattern (29 bp):
TTTTTTTTCTATGTCTCTATCTCGTTCTT
Found at i:170359 original size:3 final size:3
Alignment explanation
Indices: 170342--170457 Score: 171
Period size: 3 Copynumber: 38.7 Consensus size: 3
170332 TTTAATATAT
* *
170342 TAA TAA T-A TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
170389 TATA TAA TAA TAA TAA TGA TAA TAG TAA TAA TAA TAA TAA TAA TAA
1 TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
170435 TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
170458 TGGATAAAAA
Statistics
Matches: 101, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
2 2 0.02
3 97 0.96
4 2 0.02
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:171018 original size:113 final size:113
Alignment explanation
Indices: 170774--171182 Score: 716
Period size: 113 Copynumber: 3.6 Consensus size: 113
170764 GAATTATGCC
* * *
170774 AAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
170838 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGT
*
170885 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAA
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
170950 TATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGT
170998 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
171063 TATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGT
*
171111 AAAAGGTTGAAC-AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTCCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
171175 TATGAACT
66 TATGAACT
171183 CGAACTGGAA
Statistics
Matches: 286, Mismatches: 10, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
111 4 0.01
112 122 0.43
113 160 0.56
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGT
Found at i:171181 original size:225 final size:224
Alignment explanation
Indices: 170774--171182 Score: 712
Period size: 225 Copynumber: 1.8 Consensus size: 224
170764 GAATTATGCC
* * *
170774 AAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
170839 ATGAACTTCTCCGGAAAAGATAATCCATCAATTGATGGATTCAGGTAAAAGGTTGAACAAATTCT
66 ATGAACTTCTCCGGAAAAGATAATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCT
*
170904 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAATATGAACTTTCTCTGGAAA
131 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTCCTCAATATGAACTTTCTCTGGAAA
170969 AGATGATCCACCAAATGATGGATTCAGGT
196 AGATGATCCACCAAATGATGGATTCAGGT
170998 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
171063 TATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAAC-AATT
65 TATGAAC-TTCTCCGGAAAAGATAATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
*
171127 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTCCTCATTATGAACT
129 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTCCTCAATATGAACT
171183 CGAACTGGAA
Statistics
Matches: 174, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
224 4 0.02
225 122 0.70
226 48 0.28
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (224 bp):
AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTCTCCGGAAAAGATAATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCT
TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTCCTCAATATGAACTTTCTCTGGAAA
AGATGATCCACCAAATGATGGATTCAGGT
Found at i:172079 original size:83 final size:84
Alignment explanation
Indices: 171943--172407 Score: 857
Period size: 84 Copynumber: 5.6 Consensus size: 84
171933 CCTACTGAAT
* *
171943 CAGATCAGATAACTCAAAGAACACCTCCAGAAGATGCTA-TGAACACATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCCAAATTCA
*
172007 ATGATTGGTTTTGTCAAAT
66 ATGATTGGTTTTGTCAAAC
172026 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCCAAATTCA
172090 ATGATTGGTTTTGTCAAAC
66 ATGATTGGTTTTGTCAAAC
172109 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TG-GCACATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCCAAATTCA
172172 ATGATTGGTTTTGTCAAAC
66 ATGATTGGTTTTGTCAAAC
*
172191 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGAGCACATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCCAAATTCA
172256 ATGATTGGTTTTGTCAAAC
66 ATGATTGGTTTTGTCAAAC
*
172275 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGAGCACATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCCAAATTCA
172340 ATGATTGGTTTTGTCAAAC
66 ATGATTGGTTTTGTCAAAC
172359 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACAT
172408 ATAAAAGGTT
Statistics
Matches: 374, Mismatches: 5, Indels: 5
0.97 0.01 0.01
Matches are distributed among these distances:
82 82 0.22
83 117 0.31
84 175 0.47
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (84 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCCAAATTCA
ATGATTGGTTTTGTCAAAC
Found at i:172240 original size:166 final size:167
Alignment explanation
Indices: 171943--172407 Score: 871
Period size: 166 Copynumber: 2.8 Consensus size: 167
171933 CCTACTGAAT
* *
171943 CAGATCAGATAACTCAAAGAACACCTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAA
*
172008 TGATTGGTTTTGTCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAC
66 TGATTGGTTTTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAC
172072 ATTCATCTTCCAAATTCAATGATTGGTTTTGTCAAAC
131 ATTCATCTTCCAAATTCAATGATTGGTTTTGTCAAAC
172109 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG-GCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAA
*
172173 TGATTGGTTTTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGAGCAC
66 TGATTGGTTTTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAC
172238 ATTCATCTTCCAAATTCAATGATTGGTTTTGTCAAAC
131 ATTCATCTTCCAAATTCAATGATTGGTTTTGTCAAAC
172275 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGAGCACATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT-GAGCACATTCATCTTCCAAATTCA
172340 ATGATTGGTTTTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCA
65 ATGATTGGTTTTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCA
172405 CAT
130 CAT
172408 ATAAAAGGTT
Statistics
Matches: 291, Mismatches: 5, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
165 80 0.27
166 121 0.42
167 1 0.00
168 89 0.31
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (167 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAA
TGATTGGTTTTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAC
ATTCATCTTCCAAATTCAATGATTGGTTTTGTCAAAC
Found at i:173549 original size:1 final size:1
Alignment explanation
Indices: 173538--173610 Score: 101
Period size: 1 Copynumber: 73.0 Consensus size: 1
173528 TTGACCCACC
* * * * *
173538 TTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTCTTTTCTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
173603 TTTTTTTT
1 TTTTTTTT
173611 CTTTCTTCAA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:173566 original size:23 final size:23
Alignment explanation
Indices: 173538--173614 Score: 113
Period size: 22 Copynumber: 3.4 Consensus size: 23
173528 TTGACCCACC
173538 TTTTTTC-TTTTTTTTTTTTTTT
1 TTTTTTCTTTTTTTTTTTTTTTT
173560 TTTTTT-TTTTTTTTTTTTTTTT
1 TTTTTTCTTTTTTTTTTTTTTTT
* * *
173582 TTTTTTCTTTTCTTTTCTCTTTT
1 TTTTTTCTTTTTTTTTTTTTTTT
173605 TTTTTTCTTT
1 TTTTTTCTTT
173615 CTTCAAGCAT
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
22 27 0.54
23 23 0.46
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (23 bp):
TTTTTTCTTTTTTTTTTTTTTTT
Found at i:184436 original size:19 final size:19
Alignment explanation
Indices: 184415--184450 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
184405 AATATATTTA
184415 AAAACA-ATAAAATAAATT
1 AAAACATATAAAATAAATT
184433 AAAACATATAAAATAAAT
1 AAAACATATAAAATAAAT
184451 GACTAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAACATATAAAATAAATT
Found at i:185543 original size:20 final size:19
Alignment explanation
Indices: 185503--185562 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 19
185493 GGGCCTGTAA
* *
185503 TTATATATTTTTTAT-TAT
1 TTATATATATTTAATATAT
* *
185521 TTATTTATTTTTAATAATAT
1 TTATATATATTTAAT-ATAT
*
185541 TTATATGTATTTAATATAT
1 TTATATATATTTAATATAT
185560 TTA
1 TTA
185563 ATAATAATAG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 13 0.37
19 7 0.20
20 15 0.43
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TTATATATATTTAATATAT
Found at i:185552 original size:26 final size:30
Alignment explanation
Indices: 185513--185568 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
185503 TTATATATTT
*
185513 TTTATTATTTATTT-AT-T-TTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
185540 TTTA-TATGTATTTAATATATTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
185569 ATAGTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 8 0.32
27 6 0.24
28 1 0.04
29 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTATTATGTATTTAATATATTTAATAATA
Found at i:185569 original size:3 final size:3
Alignment explanation
Indices: 185561--185664 Score: 172
Period size: 3 Copynumber: 34.7 Consensus size: 3
185551 TTAATATATT
*
185561 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
185609 TAA TGA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
185657 TAA TAA TA
1 TAA TAA TA
185665 TGGATAAAAA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 93 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:187232 original size:5 final size:5
Alignment explanation
Indices: 187222--187246 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
187212 TTTATGTCAA
187222 TTAAT TTAAT TTAAT TTAAT TTAAT
1 TTAAT TTAAT TTAAT TTAAT TTAAT
187247 AGTAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTAAT
Found at i:192797 original size:20 final size:21
Alignment explanation
Indices: 192772--192823 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
192762 TTTTCCCAAT
*
192772 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
192792 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
192813 TCGCAATGCGA
1 TCGCAATGCGA
192824 TAATACAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:192859 original size:20 final size:20
Alignment explanation
Indices: 192834--192886 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
192824 TAATACAAAA
192834 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
* *
192854 TCGCAATGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
*
192874 TCGCAACGAGATA
1 TCGCAACGCGATA
192887 ATACAGAATC
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:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:193059 original size:12 final size:12
Alignment explanation
Indices: 193040--193073 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
193030 CTCTCTGGCG
193040 ACATCCGTTCCT
1 ACATCCGTTCCT
*
193052 ATATCCGTTCCT
1 ACATCCGTTCCT
193064 ACATCC-TTCC
1 ACATCCGTTCC
193074 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:193655 original size:24 final size:24
Alignment explanation
Indices: 193628--193681 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
193618 GTATTCGAAA
*
193628 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
193652 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
193676 TTTGAT
1 TTTGAT
193682 GATGTTTCAG
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:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:193873 original size:12 final size:12
Alignment explanation
Indices: 193856--193880 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
193846 ATATAATCCT
193856 GAAGAAGAAAAA
1 GAAGAAGAAAAA
193868 GAAGAAGAAAAA
1 GAAGAAGAAAAA
193880 G
1 G
193881 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:196214 original size:33 final size:33
Alignment explanation
Indices: 196172--196298 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
196162 GGAAATTACT
*
196172 ATCGCAATGCAAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
196205 ATCGCAATGCGAAATGAAAATCGCAACGCGA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
196237 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
196271 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
196299 CGAATTTAAT
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
32 1 0.01
33 84 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:196279 original size:66 final size:66
Alignment explanation
Indices: 196173--196305 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
196163 GAAATTACTA
196173 TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
196238 T
66 T
* *
196239 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
196304 T
66 T
196305 T
1 T
196306 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.16
Consensus pattern (66 bp):
TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:196301 original size:19 final size:19
Alignment explanation
Indices: 196172--196302 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
196162 GGAAATTACT
*
196172 ATCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
196191 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
196205 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
196224 ATCGCAACGCG-AAT----
1 ATCGCAATGCGAAATGAAA
*
196238 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
196257 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
196271 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
196290 ATCGCAACGCGAA
1 ATCGCAATGCGAA
196303 TTTAATTTCG
Statistics
Matches: 85, Mismatches: 12, Indels: 30
0.67 0.09 0.24
Matches are distributed among these distances:
14 28 0.33
15 5 0.06
16 4 0.05
17 3 0.04
18 5 0.06
19 40 0.47
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:196330 original size:14 final size:14
Alignment explanation
Indices: 196313--196369 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
196303 TTTAATTTCG
196313 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
196327 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
196346 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
196360 CGTTGCGATT
1 CGTTGCGATT
196370 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:196349 original size:33 final size:33
Alignment explanation
Indices: 196298--196387 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
196288 AAATCGCAAC
* *
196298 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
196331 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
196364 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
196388 AGTATTTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.43
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:196351 original size:19 final size:19
Alignment explanation
Indices: 196327--196387 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
196317 GCGATTCTCT
196327 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
196346 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
196360 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
196379 CATTGCGAT
1 CGTTGCGAT
196388 AGTATTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:196513 original size:14 final size:14
Alignment explanation
Indices: 196494--196530 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
196484 CATCAATTAA
196494 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
196508 ACAAATCACCTTTT
1 ACAAATCAACTTTT
196522 ACAAATCAA
1 ACAAATCAA
196531 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:197945 original size:21 final size:21
Alignment explanation
Indices: 197879--197945 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
197869 GTGAATCGGG
*
197879 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
197899 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
197921 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
197942 CTCT
1 CTCT
197946 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:197964 original size:42 final size:41
Alignment explanation
Indices: 197879--198001 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
197869 GTGAATCGGG
* * * *
197879 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
197921 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
197963 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
198002 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:198398 original size:91 final size:93
Alignment explanation
Indices: 198219--198403 Score: 306
Period size: 91 Copynumber: 2.0 Consensus size: 93
198209 ATTTCAAACT
198219 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
198284 AGAATTGGCAGCAACCGAATAAATTTAC
66 AGAATTGGCAGCAACCGAATAAATTTAC
*
198312 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAA-ACA-A-TTTA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
*
198373 GCAGTATTGGCAGCAACCGAATAAATTTAC
64 GCAGAATTGGCAGCAACCGAATAAATTTAC
198403 T
1 T
198404 AAGCAATTTA
Statistics
Matches: 88, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
91 34 0.39
92 1 0.01
93 22 0.25
94 4 0.05
95 27 0.31
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.22
Consensus pattern (93 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
AGAATTGGCAGCAACCGAATAAATTTAC
Found at i:200138 original size:19 final size:19
Alignment explanation
Indices: 200087--200217 Score: 146
Period size: 19 Copynumber: 7.1 Consensus size: 19
200077 TCTTTTGGTT
*
200087 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
200106 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
200126 GAAATGACTATCGCGA--C
1 GAAATGAAAATCGCAACGC
*
200143 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
200159 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
200178 GAAATGAAAATCGTAACGC
1 GAAATGAAAATCGCAACGC
*
200197 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
200216 GA
1 GA
200218 TTTTGGTTTC
Statistics
Matches: 94, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
14 8 0.09
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 63 0.67
20 17 0.18
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:200246 original size:19 final size:19
Alignment explanation
Indices: 200213--200279 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
200203 AAAATCGCAA
**
200213 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
200232 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
200251 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
200271 TGCGATTTT
1 TGCGATTTT
200280 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:200824 original size:20 final size:20
Alignment explanation
Indices: 200799--200848 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
200789 GCGCTATGTA
200799 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
200819 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
200839 TATCTCGTTG
1 AATCGCGTTG
200849 AGATTTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:200885 original size:20 final size:20
Alignment explanation
Indices: 200860--200913 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
200850 GATTTTGTAT
200860 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
200880 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
200900 TATCGCATTGCGAT
1 TATCGCATTGCGAT
200914 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:200915 original size:61 final size:61
Alignment explanation
Indices: 200800--200916 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
200790 CGCTATGTAA
* * * * *
200800 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGAGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGAGATTTTGTATT
* * * *
200861 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGAGATTTT
200917 CCCAATTCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGAGATTTTGTATT
Found at i:200932 original size:61 final size:61
Alignment explanation
Indices: 200800--200934 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
200790 CGCTATGTAA
* * * * * ** *
200800 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGAGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGAGATTTTCCAAT
* * * *
200861 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGAGATTTT-CCAAT
200923 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
200935 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGAGATTTTCCAAT
Found at i:203379 original size:22 final size:21
Alignment explanation
Indices: 203351--203401 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
203341 TTAGGACAAC
*
203351 ATCGATACCCTAG-CACTAGAGT
1 ATCGATACCC-AGTC-CAAGAGT
*
203373 ATCGATACTCAGTCCAAGAGT
1 ATCGATACCCAGTCCAAGAGT
203394 ATCGATAC
1 ATCGATAC
203402 TACCATCCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (21 bp):
ATCGATACCCAGTCCAAGAGT
Found at i:205252 original size:111 final size:111
Alignment explanation
Indices: 205058--205280 Score: 403
Period size: 111 Copynumber: 2.0 Consensus size: 111
205048 TTTTTTAATA
205058 AAAAAACATGTTATTTTAAAAAAATTGAAATAACGGAATAATAGAGGAATAACGATCCGCTATTG
1 AAAAAACATGTTATTTTAAAAAAATTGAAATAACGGAATAATAGAGGAATAACGATCCGCTATTG
* *
205123 CTGTGAGTGGCCGCAATCTTCCGCTATTGGTGTGATCCAGCTTCAC
66 CCGTGAGTGGCCGCAATCTGCCGCTATTGGTGTGATCCAGCTTCAC
*
205169 AAAAAACATGTT-TTTTAAAAAAAATTGAAATAACGGAATAATAGAGGAATAACGGTCCGCTATT
1 AAAAAACATGTTATTTT-AAAAAAATTGAAATAACGGAATAATAGAGGAATAACGATCCGCTATT
205233 GCCGTGAGTGGCCGCAATCTGCCGCTATTGGTGTGATCCAGCTTCAC
65 GCCGTGAGTGGCCGCAATCTGCCGCTATTGGTGTGATCCAGCTTCAC
205280 A
1 A
205281 CCGTTACTTT
Statistics
Matches: 108, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
110 4 0.04
111 104 0.96
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (111 bp):
AAAAAACATGTTATTTTAAAAAAATTGAAATAACGGAATAATAGAGGAATAACGATCCGCTATTG
CCGTGAGTGGCCGCAATCTGCCGCTATTGGTGTGATCCAGCTTCAC
Found at i:212746 original size:13 final size:13
Alignment explanation
Indices: 212730--212795 Score: 69
Period size: 13 Copynumber: 5.1 Consensus size: 13
212720 TGGTTTGACC
212730 AACTAATTTGATT
1 AACTAATTTGATT
**
212743 AACTAATTTGAGA
1 AACTAATTTGATT
*
212756 AACTGATTTGATT
1 AACTAATTTGATT
* **
212769 AGCTAATTTGAGA
1 AACTAATTTGATT
*
212782 AACTGATTTGATT
1 AACTAATTTGATT
212795 A
1 A
212796 GTTGTTTGTA
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (13 bp):
AACTAATTTGATT
Found at i:212796 original size:26 final size:26
Alignment explanation
Indices: 212730--212796 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
212720 TGGTTTGACC
* *
212730 AACTAATTTGATTAACTAATTTGAGA
1 AACTGATTTGATTAGCTAATTTGAGA
212756 AACTGATTTGATTAGCTAATTTGAGA
1 AACTGATTTGATTAGCTAATTTGAGA
212782 AACTGATTTGATTAG
1 AACTGATTTGATTAG
212797 TTGTTTGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.39
Consensus pattern (26 bp):
AACTGATTTGATTAGCTAATTTGAGA
Found at i:213613 original size:2 final size:2
Alignment explanation
Indices: 213608--213640 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
213598 ACACACACAC
213608 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
213641 CAATTATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:213816 original size:3 final size:3
Alignment explanation
Indices: 213808--213839 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
213798 GGATACTATC
213808 ATT ATT ATT ATT ATT A-T ATT ATT -TT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
213840 ATAATAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:214529 original size:20 final size:20
Alignment explanation
Indices: 214506--214560 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
214496 GCACTAACTC
214506 TATTATACT-GCCACCACTAA
1 TATT-TACTGGCCACCACTAA
*
214526 TATTTGCTGGCCACCACTAA
1 TATTTACTGGCCACCACTAA
*
214546 TATTTGCTGGCCACC
1 TATTTACTGGCCACC
214561 CATGTTTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.25, C:0.31, G:0.13, T:0.31
Consensus pattern (20 bp):
TATTTACTGGCCACCACTAA
Found at i:215172 original size:146 final size:146
Alignment explanation
Indices: 214899--215173 Score: 336
Period size: 146 Copynumber: 1.9 Consensus size: 146
214889 TCTCGCCGGA
* *
214899 GATCGGGATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATA
1 GATCGGAATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCAACACGAACAACATA
* ** * ** * *
214964 TTGAAAATTCAAGACGATCGGACAGTGGACGGTGACGGATCGGAGAAAACATATCCGGACGGTTT
66 TTGAAAAATCAAGACGATCGGACAGTGGACGACGACAGATCAAAGAAAACACATCCGAACGGTTT
215029 TTAGCCTCTTGCTGGT
131 TTAGCCTCTTGCTGGT
* * * * * *
215045 GATCGGAATCTTCGATCAATATTCCGAACGGTGAAAAGTTGTGTG-ATGCCAACACGAACAACCT
1 GATCGGAATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCG-GAAGGCCAACACGAACAACAT
* * * * * *
215109 ATTGAAAAATCAGGACGATCGGACGGTGGATGACGGCAGATCAAAGAAAATACATTCGAACGGTT
65 ATTGAAAAATCAAGACGATCGGACAGTGGACGACGACAGATCAAAGAAAACACATCCGAACGGTT
215174 ATCTTTGTAT
Statistics
Matches: 106, Mismatches: 22, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
146 105 0.99
147 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (146 bp):
GATCGGAATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCAACACGAACAACATA
TTGAAAAATCAAGACGATCGGACAGTGGACGACGACAGATCAAAGAAAACACATCCGAACGGTTT
TTAGCCTCTTGCTGGT
Found at i:221538 original size:3 final size:3
Alignment explanation
Indices: 221530--221561 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
221520 CTTTAGTATT
221530 GAA GAA GAA GAA GAA GAA GAA GAA GATA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA G
221562 GCCTTGGTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.34, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:222690 original size:9 final size:9
Alignment explanation
Indices: 222676--222802 Score: 69
Period size: 10 Copynumber: 13.1 Consensus size: 9
222666 GGTTTTGCTT
222676 AAAAATAAA
1 AAAAATAAA
*
222685 AAAAAT--G
1 AAAAATAAA
*
222692 AAAAATGAA
1 AAAAATAAA
222701 AAAAATGAAA
1 AAAAAT-AAA
*
222711 AAAAATGAA
1 AAAAATAAA
222720 AAAAATGAAATA
1 AAAAAT--AA-A
*
222732 GAAAAATAGA
1 -AAAAATAAA
*
222742 AAAAATGGAA
1 AAAAAT-AAA
222752 AAAAATAAAA
1 AAAAAT-AAA
*
222762 AAAAAGAAGAA
1 AAAAA-TA-AA
*
222773 AAAAAGAAGA
1 AAAAATAA-A
*
222783 AAAAAAACAA
1 AAAAATA-AA
222793 AAAAATAAA
1 AAAAATAAA
222802 A
1 A
222803 GGGGGGTTCA
Statistics
Matches: 92, Mismatches: 14, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
7 6 0.07
9 30 0.33
10 39 0.42
11 10 0.11
12 1 0.01
13 6 0.07
ACGTcount: A:0.80, C:0.01, G:0.10, T:0.09
Consensus pattern (9 bp):
AAAAATAAA
Found at i:222695 original size:8 final size:8
Alignment explanation
Indices: 222684--222755 Score: 53
Period size: 9 Copynumber: 8.8 Consensus size: 8
222674 TTAAAAATAA
222684 AAAAAATG
1 AAAAAATG
222692 -AAAAATG
1 AAAAAATG
222699 AAAAAAATG
1 -AAAAAATG
222708 AAAAAAAATG
1 --AAAAAATG
222718 AAAAAAATG
1 -AAAAAATG
*
222727 -AAATA-G
1 AAAAAATG
222733 -AAAAATAG
1 AAAAAAT-G
222741 AAAAAATGG
1 AAAAAAT-G
222750 AAAAAA
1 AAAAAA
222756 ATAAAAAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
6 5 0.09
7 11 0.20
8 1 0.02
9 29 0.53
10 9 0.16
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:222721 original size:16 final size:15
Alignment explanation
Indices: 222676--222775 Score: 57
Period size: 19 Copynumber: 6.3 Consensus size: 15
222666 GGTTTTGCTT
222676 AAAAATAAAAAAAATG
1 AAAAAT-AAAAAAATG
222692 AAAAATGAAAAAAATG
1 AAAAAT-AAAAAAATG
222708 AAAAAAAATGAAAAAAATG
1 ---AAAAAT-AAAAAAATG
*
222727 --AAATAGAAAAATAG
1 AAAAATAAAAAAAT-G
222741 AAAAAATGGAAAAAAAT-
1 -AAAAAT--AAAAAAATG
*
222758 AAAAA-AAAAGAA-G
1 AAAAATAAAAAAATG
222771 AAAAA
1 AAAAA
222776 AAGAAGAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 23
0.72 0.04 0.24
Matches are distributed among these distances:
13 18 0.26
14 5 0.07
16 20 0.29
17 4 0.06
19 23 0.33
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.10
Consensus pattern (15 bp):
AAAAATAAAAAAATG
Found at i:222737 original size:41 final size:40
Alignment explanation
Indices: 222687--222765 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 40
222677 AAAATAAAAA
*
222687 AAATGAAAAAT-GAAAAAAATGAAAAAAAATGAAAAAAATG
1 AAATGAAAAATAG-AAAAAATGAAAAAAAATAAAAAAAATG
*
222727 AAATAGAAAAATAGAAAAAATGGAAAAAAATAAAAAAAA
1 AAAT-GAAAAATAGAAAAAATGAAAAAAAATAAAAAAAA
222766 AGAAGAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
40 4 0.11
41 30 0.86
42 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (40 bp):
AAATGAAAAATAGAAAAAATGAAAAAAAATAAAAAAAATG
Found at i:222761 original size:8 final size:8
Alignment explanation
Indices: 222676--222802 Score: 61
Period size: 8 Copynumber: 15.2 Consensus size: 8
222666 GGTTTTGCTT
222676 AAAAATAA
1 AAAAATAA
*
222684 AAAAA-ATG
1 AAAAATA-A
222692 AAAAATGAA
1 AAAAAT-AA
222701 AAAAATGAAA
1 AAAAAT--AA
222711 AAAAATGAA
1 AAAAAT-AA
222720 AAAAAT--
1 AAAAATAA
* *
222726 -GAAATAG
1 AAAAATAA
222733 AAAAATAGA
1 AAAAATA-A
222742 AAAAATGGAA
1 AAAAAT--AA
222752 AAAAATAA
1 AAAAATAA
222760 AAAAA-AA
1 AAAAATAA
222767 GAAGAAA-AA
1 -AA-AAATAA
222776 AAGAAGA-AA
1 AA-AA-ATAA
*
222785 AAAAACAA
1 AAAAATAA
222793 AAAAATAA
1 AAAAATAA
222801 AA
1 AA
222803 GGGGGGTTCA
Statistics
Matches: 97, Mismatches: 8, Indels: 28
0.73 0.06 0.21
Matches are distributed among these distances:
5 4 0.04
7 4 0.04
8 42 0.43
9 30 0.31
10 16 0.16
11 1 0.01
ACGTcount: A:0.80, C:0.01, G:0.10, T:0.09
Consensus pattern (8 bp):
AAAAATAA
Found at i:222784 original size:41 final size:41
Alignment explanation
Indices: 222675--222802 Score: 113
Period size: 41 Copynumber: 3.1 Consensus size: 41
222665 GGGTTTTGCT
* *
222675 TAAAAATAAAAAAAAT-G-AAAAATGAAAAAAATGAAAAAAAA
1 TAAAAA-AAAAGAAATAGAAAAAAAG-AAAAAATGAAAAAAAA
* * * *
222716 TGAAAAAAATGAAATAGAAAAATAGAAAAAATGGAAAAAAA
1 TAAAAAAAAAGAAATAGAAAAAAAGAAAAAATGAAAAAAAA
*
222757 TAAAAAAAAAGAAGA-A-AAAAAGAAGAAAAAA-AACAAAAAAA
1 TAAAAAAAAAGAA-ATAGAAAAA-AAGAAAAAATGA-AAAAAAA
222798 TAAAA
1 TAAAA
222803 GGGGGGTTCA
Statistics
Matches: 71, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
40 12 0.17
41 53 0.75
42 6 0.08
ACGTcount: A:0.80, C:0.01, G:0.10, T:0.09
Consensus pattern (41 bp):
TAAAAAAAAAGAAATAGAAAAAAAGAAAAAATGAAAAAAAA
Found at i:222796 original size:11 final size:11
Alignment explanation
Indices: 222758--222797 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
222748 GGAAAAAAAT
222758 AAAAAAAAAGA
1 AAAAAAAAAGA
*
222769 AGAAAAAAAGA
1 AAAAAAAAAGA
*
222780 AGAAAAAAAACA
1 A-AAAAAAAAGA
222792 AAAAAA
1 AAAAAA
222798 TAAAAGGGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.88, C:0.03, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:224285 original size:108 final size:110
Alignment explanation
Indices: 224082--224364 Score: 489
Period size: 108 Copynumber: 2.6 Consensus size: 110
224072 TGAAGCAAAA
224082 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
*
224147 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
66 CGAGTCTTATACTCTATGAAGAAATAGGGGGCAGACGCGATTGAT
* *
224192 GAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
* *
224255 CGAGTCTTATACTCTATGAATAAATAGGGGGCAGACGCGATTGTT
66 CGAGTCTTATACTCTATGAAGAAATAGGGGGCAGACGCGATTGAT
* *
224300 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTGGGAGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
224365 GTTCGAGTTC
Statistics
Matches: 162, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
108 100 0.62
109 6 0.04
110 56 0.35
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (110 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
CGAGTCTTATACTCTATGAAGAAATAGGGGGCAGACGCGATTGAT
Found at i:224361 original size:55 final size:55
Alignment explanation
Indices: 224082--224353 Score: 467
Period size: 55 Copynumber: 5.0 Consensus size: 55
224072 TGAAGCAAAA
224082 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
224137 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
224192 GAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
224245 GAAGATTGTTCGAGTCTTATACTCTATGAATAAATAGGGGGCAGACGCGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
224300 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGT
224354 GGGAGATTAT
Statistics
Matches: 201, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
53 47 0.23
54 6 0.03
55 148 0.74
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.28
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
Found at i:224417 original size:52 final size:52
Alignment explanation
Indices: 224357--224805 Score: 783
Period size: 52 Copynumber: 8.6 Consensus size: 52
224347 CGATCGTGGG
224357 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
224409 AGATTATTGTTCGAGATT-TAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAG-TTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
224461 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
224513 AGATTATTGTTCGAGTTCTAGTCCTTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
224565 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
224617 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
224669 AGATTATTGTTCGAGTTCTAGTCCTTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * *
224721 AGATTATTTTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
224773 AGATTATCGTTCGAGTTCTACTCCCTGAAGAAA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAA
224806 TAGAGAGCGA
Statistics
Matches: 377, Mismatches: 18, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
51 2 0.01
52 373 0.99
53 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (52 bp):
AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
Found at i:224888 original size:55 final size:53
Alignment explanation
Indices: 224466--224876 Score: 165
Period size: 52 Copynumber: 7.8 Consensus size: 53
224456 TAGGAAGATT
* * ** **
224466 ATTGTTCGAGTTCTAGTCCCTGAAGAAAATTG-G-GC-AGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAA-AGAGAGCGA-ACCCGTAAAAAGAAG
* * * ** **
224518 ATTGTTCGAGTTCTAGTCCTTGAAGAAAATTG-G-GC-AGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAA-AGAGAGCGA-ACCCGTAAAAAGAAG
* * * * ** **
224570 ATTGTTCGAGTTCTAGTCCCTGAAGAAAATTG-G-GC-AGTCTCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAA-AGAGAGCGA-ACCCGTAAAAAGAAG
* * ** **
224622 ATTGTTCGAGTTCTAGTCCCTGAAGAAAATTG-G-GC-AGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAA-AGAGAGCGA-ACCCGTAAAAAGAAG
* * * ** **
224674 ATTGTTCGAGTTCTAGTCCTTGAAGAAAATTG-G-GC-AGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAA-AGAGAGCGA-ACCCGTAAAAAGAAG
* * * * * ** **
224726 ATTTTTCGAGTTCTAGTCCCTGAAGAAAATTG-G-GC-AGTCTCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAA-AGAGAGCGA-ACCCGTAAAAAGAAG
* *
224778 ATCGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAACCCGTAAAAAGAAG
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGAACCCGTAAAAAGAAG
224831 ATTGTTCGAGTTCTATACTCCCTGAAGAAAAAGAGAGCGAACCCGT
1 ATTGTTCGAGTTC--TACTCCCTGAAGAAAAAGAGAGCGAACCCGT
224877 TTGCAGAAGA
Statistics
Matches: 330, Mismatches: 24, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
51 1 0.00
52 275 0.83
53 23 0.07
54 1 0.00
55 30 0.09
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (53 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGAACCCGTAAAAAGAAG
Found at i:225071 original size:3 final size:3
Alignment explanation
Indices: 225063--225097 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
225053 GGATACTATC
225063 ATT ATT ATT ATT ATT ATT A-T ATT ATT -TT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
225098 ATAATAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:225789 original size:20 final size:20
Alignment explanation
Indices: 225766--225820 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
225756 GCACTAACTC
225766 TATTATACT-GCCACCACTAA
1 TATT-TACTGGCCACCACTAA
*
225786 TATTTGCTGGCCACCACTAA
1 TATTTACTGGCCACCACTAA
*
225806 TATTTGCTGGCCACC
1 TATTTACTGGCCACC
225821 CATGTTTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.25, C:0.31, G:0.13, T:0.31
Consensus pattern (20 bp):
TATTTACTGGCCACCACTAA
Found at i:226428 original size:146 final size:146
Alignment explanation
Indices: 226158--226432 Score: 345
Period size: 146 Copynumber: 1.9 Consensus size: 146
226148 TCTCGCCGGA
* **
226158 GATCGGGATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCATTACGAACAACATA
1 GATCGGAATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCAACACGAACAACATA
* ** * ** *
226223 TTGAAAATTCAAGACGATCGGACGGTGGACGGTGACGGATCGGAGAAAACATATCCGGACGGTTT
66 TTGAAAAATCAAGACGATCGGACGGTGGACGACGACAGATCAAAGAAAACACATCCGGACGGTTT
226288 TTAGCCTCTTGCTGGT
131 TTAGCCTCTTGCTGGT
* * * * * *
226304 GATCGGAATCTTCGATCAATATTCCGAACGGTGAAAAGTTGTGTG-ATGCCAACACGAACAACCT
1 GATCGGAATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCG-GAAGGCCAACACGAACAACAT
* * * * *
226368 ATTGAAAAATCAGGACGATCGGACGGTGGATGACGGCAGATCAAAGAAAATACATTCGGACGGTT
65 ATTGAAAAATCAAGACGATCGGACGGTGGACGACGACAGATCAAAGAAAACACATCCGGACGGTT
226433 ATCTTTGTAT
Statistics
Matches: 107, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
146 106 0.99
147 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21
Consensus pattern (146 bp):
GATCGGAATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCAACACGAACAACATA
TTGAAAAATCAAGACGATCGGACGGTGGACGACGACAGATCAAAGAAAACACATCCGGACGGTTT
TTAGCCTCTTGCTGGT
Found at i:228704 original size:26 final size:26
Alignment explanation
Indices: 228652--228705 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
228642 AAAAGCACTA
*
228652 TATTAAAAGAGATTTATTTCCTATTT
1 TATTAAAAGAGATTTATTACCTATTT
* * *
228678 TATTAGAAGAGATTTATTAGCTCTTT
1 TATTAAAAGAGATTTATTACCTATTT
228704 TA
1 TA
228706 GTGCAATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.48
Consensus pattern (26 bp):
TATTAAAAGAGATTTATTACCTATTT
Found at i:230357 original size:39 final size:37
Alignment explanation
Indices: 230275--230678 Score: 373
Period size: 37 Copynumber: 11.2 Consensus size: 37
230265 TATACATAAC
* * * *
230275 ATATATAATAAATAGTGTTGAAAGCATTTTTTTTGAAAGT
1 ATATATAATATATAGTTTTGAAAACA---TTTTTGAAAAT
230315 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTG--AAAAT
*
230354 ATATATAATATATAGTTTTGAAAACATTTTTAAAAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTT--GAAAAT
* * *
230393 TTATATAATATATAGTTTTGAAAACATTTTCGAAAGT
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
* * ***
230430 ATATATAATATATAGTCTT-AAAACGTTTTT-TTGA-
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
* * *
230464 A-A-ATAATATATAGTTTTAAAAATATTTTTGAAAAC
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
*
230499 ATATATAATATATAGTTTGGAAAACATTTTTGAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
230536 ATATAT-ATAATATAGTTTTGAAAACATTTTTG-----
1 ATATATAAT-ATATAGTTTTGAAAACATTTTTGAAAAT
*
230568 A-ATAT-ATATATAGTTTTGAAAATATTTTTCG---A-
1 ATATATAATATATAGTTTTGAAAACATTTTT-GAAAAT
* *
230600 A-A-AT-ATATATAGTTTTGAAAATATTTTTCGAATAT
1 ATATATAATATATAGTTTTGAAAACATTTTT-GAAAAT
*
230635 ATATATAATATATAGTTTT-AAAACGTTTTTGAAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTG-AAAAT
230672 ATATATA
1 ATATATA
230679 TAGTTTATAT
Statistics
Matches: 312, Mismatches: 32, Indels: 43
0.81 0.08 0.11
Matches are distributed among these distances:
30 21 0.07
31 35 0.11
32 17 0.05
33 10 0.03
34 3 0.01
35 2 0.01
36 14 0.04
37 106 0.34
38 12 0.04
39 69 0.22
40 23 0.07
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (37 bp):
ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
Found at i:230505 original size:30 final size:32
Alignment explanation
Indices: 230434--230505 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
230424 GAAAGTATAT
* *
230434 ATAATATATAGTCTTAAAACGTTTTTTTGAAA
1 ATAATATATAGTCTTAAAACATATTTTTGAAA
*
230466 ATAATATATAGTTTTAAAA-ATATTTTTGAAA
1 ATAATATATAGTCTTAAAACATATTTTTGAAA
*
230497 A-CATATATA
1 ATAATATATA
230506 ATATATAGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
30 7 0.19
31 11 0.31
32 18 0.50
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (32 bp):
ATAATATATAGTCTTAAAACATATTTTTGAAA
Found at i:230573 original size:31 final size:31
Alignment explanation
Indices: 230538--230641 Score: 174
Period size: 31 Copynumber: 3.4 Consensus size: 31
230528 TTGAAAATAT
*
230538 ATATATAATATAGTTTTGAAAACATTTTT-GA
1 ATATAT-ATATAGTTTTGAAAATATTTTTCGA
230569 ATATATATATAGTTTTGAAAATATTTTTCGA
1 ATATATATATAGTTTTGAAAATATTTTTCGA
*
230600 AAATATATATAGTTTTGAAAATATTTTTCGA
1 ATATATATATAGTTTTGAAAATATTTTTCGA
230631 ATATATATATA
1 ATATATATATA
230642 ATATATAGTT
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
30 21 0.30
31 48 0.70
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (31 bp):
ATATATATATAGTTTTGAAAATATTTTTCGA
Found at i:242376 original size:20 final size:21
Alignment explanation
Indices: 242322--242384 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
242312 GATTCCCCTG
242322 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
242346 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
242366 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
242385 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:246234 original size:22 final size:21
Alignment explanation
Indices: 246192--246231 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
246182 GAGTTTGTTT
*
246192 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
246213 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
246232 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:254499 original size:24 final size:23
Alignment explanation
Indices: 254467--254521 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
254457 GTAATAAGAA
* *
254467 TTTTT-TGTTTTCCTAACATGTTT
1 TTTTTCTGTTTTCATAACAT-ATT
*
254490 TTTTTCTGTTTTCATAGCATATT
1 TTTTTCTGTTTTCATAACATATT
254513 TTTTTCTGT
1 TTTTTCTGT
254522 CTTTTGATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 16 0.57
24 12 0.43
ACGTcount: A:0.13, C:0.13, G:0.09, T:0.65
Consensus pattern (23 bp):
TTTTTCTGTTTTCATAACATATT
Found at i:254537 original size:23 final size:22
Alignment explanation
Indices: 254486--254538 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
254476 TTCCTAACAT
254486 GTTTTTTTTCTGTTTTCATAGC
1 GTTTTTTTTCTGTTTTCATAGC
* *
254508 ATATTTTTTTCTGTCTTTTGATA-C
1 GT-TTTTTTTCTG--TTTTCATAGC
254532 GTTTTTT
1 GTTTTTT
254539 ATTTTCTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 1 0.04
23 15 0.60
24 2 0.08
25 7 0.28
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.66
Consensus pattern (22 bp):
GTTTTTTTTCTGTTTTCATAGC
Found at i:256334 original size:19 final size:17
Alignment explanation
Indices: 256288--256335 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
256278 TTAAGATTCA
*
256288 GATTATATTTTTTTTAT
1 GATTTTATTTTTTTTAT
*
256305 GATTTTAATTTTTTTTGT
1 GATTTT-ATTTTTTTTAT
256323 GACTTTGTATTTT
1 GA-TTT-TATTTT
256336 CTAATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 5 0.19
18 12 0.46
19 8 0.31
20 1 0.04
ACGTcount: A:0.19, C:0.02, G:0.10, T:0.69
Consensus pattern (17 bp):
GATTTTATTTTTTTTAT
Found at i:256378 original size:27 final size:28
Alignment explanation
Indices: 256346--256408 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 28
256336 CTAATTATTT
* *
256346 TTTATAAAATTTTATT-TTTAAATATAA
1 TTTATAAAATATTATTATTTAAAAATAA
256373 TTTAT---ATATTATTATTTAAAAATAA
1 TTTATAAAATATTATTATTTAAAAATAA
*
256398 TTTAAAAAATA
1 TTTATAAAATA
256409 AAAATATTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
24 7 0.24
25 14 0.48
27 5 0.17
28 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTATAAAATATTATTATTTAAAAATAA
Found at i:261482 original size:12 final size:12
Alignment explanation
Indices: 261454--261490 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
261444 TTTGGTAATC
261454 CCCGCCCCGATTA
1 CCCGCCCCGA-TA
261467 CCCGCCCCGATA
1 CCCGCCCCGATA
*
261479 CCCGTCCCGATA
1 CCCGCCCCGATA
261491 AATATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.16, C:0.54, G:0.16, T:0.14
Consensus pattern (12 bp):
CCCGCCCCGATA
Found at i:261513 original size:2 final size:2
Alignment explanation
Indices: 261506--261569 Score: 112
Period size: 2 Copynumber: 32.5 Consensus size: 2
261496 TAAAAATAAT
261506 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
*
261548 TA TA TA TA TA TA CA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
261570 TAATGAATTT
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:270201 original size:96 final size:96
Alignment explanation
Indices: 270037--270231 Score: 275
Period size: 96 Copynumber: 2.0 Consensus size: 96
270027 TAAGATAATG
* * **
270037 TTGGGGCACGATTGAACCCCCATCATTTTGAAATGACAAGATTCAGACAAAGAAGGCATCAAGAA
1 TTGGGGCACGACTGAACCCACATCATGATGAAATGACAAGATTCAGACAAAGAAGGCATCAAGAA
*
270102 TGAGCCTTACAATTTGAGATGA-TGGGGCATT
66 TGAGCCTTACAATTTGAGAT-ATTGAGGCATT
* * * **
270133 TTGGGGCGCGACTGAACCCACATCATGATGAAATTACAAGATTCAGACCAAGAAGGCATTGAGAA
1 TTGGGGCACGACTGAACCCACATCATGATGAAATGACAAGATTCAGACAAAGAAGGCATCAAGAA
*
270198 TGAGCCTTATAATTTGAGATATTGAGGCATT
66 TGAGCCTTACAATTTGAGATATTGAGGCATT
270229 TTG
1 TTG
270232 AAGGCCCGTA
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
95 1 0.01
96 86 0.99
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (96 bp):
TTGGGGCACGACTGAACCCACATCATGATGAAATGACAAGATTCAGACAAAGAAGGCATCAAGAA
TGAGCCTTACAATTTGAGATATTGAGGCATT
Found at i:271501 original size:36 final size:36
Alignment explanation
Indices: 271461--271695 Score: 194
Period size: 36 Copynumber: 6.5 Consensus size: 36
271451 AAGTCAATCT
271461 TAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCC
1 TAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCC
* *
271497 TAAGCCTTCACCGGAGAGTAGTGAAGCAAACCAT-C
1 TAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCC
* * *
271532 TGAAGCCTTCACCGGAGA-ATAGTGAAGCAATCAAT-C
1 T-AAGCCTTCACCGAAGAGA-AGTGAAGCAAACCATCC
* * *
271568 TGAAGCCTTCACCGGAGA-ATAGTGAAGCAAACAATCA
1 T-AAGCCTTCACCGAAGAGA-AGTGAAGCAAACCATCC
* * *
271605 TAAGTCTTCACC-AGAGAGTAGTGAAGCAAACCATCT
1 TAAGCCTTCACCGA-AGAGAAGTGAAGCAAACCATCC
* * * * **
271641 TAAGTCC-TCACCAAAAAGTAGTGAAGCAGATCCATTT
1 TAAG-CCTTCACCGAAGAGAAGTGAAGCA-AACCATCC
* *
271678 TAAGCCTTCTCAGAAGAG
1 TAAGCCTTCACCGAAGAG
271696 TGTTGGAACA
Statistics
Matches: 170, Mismatches: 20, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
35 2 0.01
36 148 0.87
37 20 0.12
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.19
Consensus pattern (36 bp):
TAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCC
Found at i:271539 original size:72 final size:72
Alignment explanation
Indices: 271457--271695 Score: 252
Period size: 72 Copynumber: 3.3 Consensus size: 72
271447 GAGCAAGTCA
271457 ATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCCTAAGCCTTCACCGGAGAGTAGTGAA
1 ATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCCTAAGCCTTCACCGGAGAGTAGTGAA
271522 GCAAACC
66 GCAAACC
* * * * *
271529 ATCTGAAGCCTTCACCGGAGA-ATAGTGAAGCAATCAAT-CTGAAGCCTTCACCGGAGAATAGTG
1 ATCTTAAGCCTTCACCGAAGAGA-AGTGAAGCAAACCATCCT-AAGCCTTCACCGGAGAGTAGTG
*
271592 AAGCAAACA
64 AAGCAAACC
* * * * ** *
271601 ATCATAAGTCTTCACC-AGAGAGTAGTGAAGCAAACCATCTTAAGTCC-TCACCAAAAAGTAGTG
1 ATCTTAAGCCTTCACCGA-AGAGAAGTGAAGCAAACCATCCTAAG-CCTTCACCGGAGAGTAGTG
*
271664 AAGCAGATCC
64 AAGCA-AACC
* * *
271674 ATTTTAAGCCTTCTCAGAAGAG
1 ATCTTAAGCCTTCACCGAAGAG
271696 TGTTGGAACA
Statistics
Matches: 134, Mismatches: 25, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
71 3 0.02
72 110 0.82
73 20 0.15
74 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (72 bp):
ATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCCTAAGCCTTCACCGGAGAGTAGTGAA
GCAAACC
Found at i:271663 original size:108 final size:108
Alignment explanation
Indices: 271448--271695 Score: 313
Period size: 108 Copynumber: 2.3 Consensus size: 108
271438 ATGAGATTGG
* * *
271448 AGCAAGTCAATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCCTAAGCCTTCACCGGAG
1 AGCAA-TCAATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACAATCATAAGCCTTCACCAGAG
* *
271513 AGTAGTGAAGCAAACCATCTGAAGCCTTCACCGGAGAATAGTGA
65 AGTAGTGAAGCAAACCATCTGAAGCCTTCACCGAAAAATAGTGA
* * *
271557 AGCAATCAATCTGAAGCCTTCACCGGAGA-ATAGTGAAGCAAACAATCATAAGTCTTCACCAGAG
1 AGCAATCAATCTTAAGCCTTCACCGAAGAGA-AGTGAAGCAAACAATCATAAGCCTTCACCAGAG
*
271621 AGTAGTGAAGCAAACCATCTTAAGTCC-TCACC-AAAAAGTAGTGA
65 AGTAGTGAAGCAAACCATCTGAAG-CCTTCACCGAAAAA-TAGTGA
* * * *
271665 AGCAGATCCATTTTAAGCCTTCTCAGAAGAG
1 AGCA-ATCAATCTTAAGCCTTCACCGAAGAG
271696 TGTTGGAACA
Statistics
Matches: 119, Mismatches: 15, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
107 4 0.03
108 89 0.75
109 26 0.22
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.19
Consensus pattern (108 bp):
AGCAATCAATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACAATCATAAGCCTTCACCAGAGA
GTAGTGAAGCAAACCATCTGAAGCCTTCACCGAAAAATAGTGA
Found at i:272150 original size:51 final size:51
Alignment explanation
Indices: 272066--272416 Score: 508
Period size: 51 Copynumber: 6.8 Consensus size: 51
272056 TGAAAATATG
*
272066 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
*
272117 CGAGGTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGA-GATGT
1 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATG-T-T
* * * *
272169 CTAAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCAG-TTGAAGATGTT
1 C-GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCC-GTTTGAAGATGTT
* *
272221 CGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
*
272272 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
*
272323 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
* * * * * *
272374 CGAGTTCTATACTCCCTAGAGAAATAGGGAGCGAACCCATTTG
1 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG
272417 TTGAAGATTG
Statistics
Matches: 277, Mismatches: 17, Indels: 12
0.91 0.06 0.04
Matches are distributed among these distances:
50 2 0.01
51 229 0.83
52 4 0.01
53 40 0.14
54 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.23
Consensus pattern (51 bp):
CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
Found at i:272442 original size:55 final size:55
Alignment explanation
Indices: 272189--272954 Score: 505
Period size: 55 Copynumber: 14.3 Consensus size: 55
272179 TACTCCCTAG
* * * *
272189 AGAAAGAGGGAGCGA-ACCCA--GTTGAAGA-TGTTCGAGT-TCCATACTCCCTAA
1 AGAAATAGGGAGCGAGACCCATTGTTGAAGATTGTTCGAGTCT-TATACTCTCTGA
* * *
272240 AGAAAGAGGGAGCGA-ACCC-GT-TTGAAGA-TGTTCGAGT-TCTATACTC-CTTAA
1 AGAAATAGGGAGCGAGACCCATTGTTGAAGATTGTTCGAGTCT-TATACTCTC-TGA
* * * *
272291 AGAAAGAAGGAGCGA-ACCC-GT-TTGAAGA-TGTTCGAGT-TCTATACTC-CTTAA
1 AGAAATAGGGAGCGAGACCCATTGTTGAAGATTGTTCGAGTCT-TATACTCTC-TGA
* * * *
272342 AGAAAGAAGGAGCGA-ACCC-GT-TTGAAGA-TGTTCGAGT-TCTATACTCCCT-A
1 AGAAATAGGGAGCGAGACCCATTGTTGAAGATTGTTCGAGTCT-TATACTCTCTGA
272392 GAGAAATAGGGAGCGA-ACCCATTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
1 -AGAAATAGGGAGCGAGACCCA-TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * *
272448 AGAAATAGGG-G-GTAGACGCAATCGTTGAAGATTGTTCGGGTCTTATACTCTCTGA
1 AGAAATAGGGAGCG-AGAC-CCATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * * *
272503 AGAAGTAGGGGGC-AGACGCGATTGATGAAGATTG-T-GAGTCTTATACTCTCTGA
1 AGAAATAGGGAGCGAGAC-CCATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * *
272556 AGAAATAGGGGGC-AGACGCAATTGATGAAGATTG-T-GAGTCTTATACTCTCTGA
1 AGAAATAGGGAGCGAGAC-CCATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * *
272609 AGAAATAGGGGGC-AGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
1 AGAAATAGGGAGCGAGAC-CCATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * *
272664 AGAAATAGGGGGC-AGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
1 AGAAATAGGGAGCGAGAC-CCATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * *
272719 AGAAATAGGG-GC-AGACGCGATTGATGAAGATT-AT-G-GTTCTTATACTCTCTGA
1 AGAAATAGGGAGCGAGAC-CCATTGTTGAAGATTGTTCGAG-TCTTATACTCTCTGA
* * * *
272771 AGAAATAGGGGGC-AGA-CAAGTTTGTTGAAGA-TGATTCAAGTCTTATACCCTCTGA
1 AGAAATAGGGAGCGAGACCCA--TTGTTGAAGATTG-TTCGAGTCTTATACTCTCTGA
* * * *
272826 AGAAATAGGGAGCGA-ACCCATTTTTCTGAAGATT-TATTGAAT-TCTATACTCCCTGA
1 AGAAATAGGGAGCGAGACCCA-TTGT-TGAAGATTGT-TCGAGTCT-TATACTCTCTGA
* * * * ** *
272882 AAAGAATAAGGAGCAAGTACGC--TGATTGAAGATTAATCGAGTCCTATACTCTCTGA
1 AGA-AATAGGGAGCGAG-ACCCATTG-TTGAAGATTGTTCGAGTCTTATACTCTCTGA
272938 A-AGAATAGGGAGC-AGAC
1 AGA-AATAGGGAGCGAGAC
272955 ATTTTTTTTC
Statistics
Matches: 631, Mismatches: 46, Indels: 74
0.84 0.06 0.10
Matches are distributed among these distances:
50 2 0.00
51 163 0.26
52 28 0.04
53 119 0.19
54 33 0.05
55 216 0.34
56 55 0.09
57 12 0.02
59 3 0.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (55 bp):
AGAAATAGGGAGCGAGACCCATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
Found at i:272451 original size:153 final size:153
Alignment explanation
Indices: 272066--272442 Score: 494
Period size: 155 Copynumber: 2.4 Consensus size: 153
272056 TGAAAATATG
* * * * *
272066 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGGTCCATACTC
1 CGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTC
*
272131 CTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTAAGTTCCATACTCCCTAGAGAAAGA
66 CTT--AGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTAAGTTCCATACTCCCTAAAGAAAGA
*
272196 GGGAGCGAACCCAGTTGAAGATGTT
129 AGGAGCGAACCCAGTTGAAGATGTT
272221 CGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTC
1 CGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTC
* * *
272286 CTTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGT-TCGAGTTCTATACTCCTTAAAGAAAG
66 CTT--AGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT-AAGTTCCATACTCCCTAAAGAAAG
272348 AAGGAGCGAACCC-GTTTGAAGATGTT
128 AAGGAGCGAACCCAG-TTGAAGATGTT
* * * *
272374 CGAGTTCTATACTCCCTAGAGAAATAGGGAGCGAACCCATTTGTTGAAGATTGTTCGAG-TCTTA
1 CGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCC--GT-TTGAAGA-TGTTCGAGTTC-TA
272438 TACTC
61 TACTC
272443 TCTGAAGAAA
Statistics
Matches: 201, Mismatches: 14, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
152 2 0.01
153 84 0.42
154 1 0.00
155 90 0.45
156 9 0.04
157 15 0.07
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.24
Consensus pattern (153 bp):
CGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTC
CTTAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTAAGTTCCATACTCCCTAAAGAAAGAAG
GAGCGAACCCAGTTGAAGATGTT
Found at i:272565 original size:53 final size:55
Alignment explanation
Indices: 272363--272835 Score: 616
Period size: 55 Copynumber: 8.7 Consensus size: 55
272353 GCGAACCCGT
* * * *
272363 TTGAAGA-TGTTCGAGT-TCTATACTCCCT-AGAGAAATAGGGAGC-GAACCCATTTG
1 TTGAAGATTGTTCGAGTCT-TATACTCTCTGA-AGAAATAGGGGGCAG-ACGCAATTG
* *
272417 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGTAGACGCAATCG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTG
* * *
272472 TTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAGTAGGGGGCAGACGCGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTG
*
272527 ATGAAGATTG-T-GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTG
* *
272580 ATGAAGATTG-T-GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTG
*
272633 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTG
*
272688 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATA-GGGGCAGACGCGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTG
* *
272742 ATGAAGATT-AT-G-GTTCTTATACTCTCTGAAGAAATAGGGGGCAGA--CAAGTTTG
1 TTGAAGATTGTTCGAG-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAA--TTG
* *
272795 TTGAAGA-TGATTCAAGTCTTATACCCTCTGAAGAAATAGGG
1 TTGAAGATTG-TTCGAGTCTTATACTCTCTGAAGAAATAGGG
272836 AGCGAACCCA
Statistics
Matches: 379, Mismatches: 26, Indels: 27
0.88 0.06 0.06
Matches are distributed among these distances:
51 3 0.01
52 24 0.06
53 118 0.31
54 32 0.08
55 198 0.52
56 4 0.01
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (55 bp):
TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTG
Found at i:272610 original size:161 final size:162
Alignment explanation
Indices: 272364--272835 Score: 640
Period size: 161 Copynumber: 2.9 Consensus size: 162
272354 CGAACCCGTT
* * * *
272364 TGAAGA-TGTTCGAGT-TCTATACTCCCT-AGAGAAATAGGGAGC-GAACCCATTTGTTGAAGAT
1 TGAAGATTGTTCGAGTCT-TATACTCTCTGA-AGAAATAGGG-GCAG-ACGCAATTGATGAAGAT
* *
272425 TGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGTAGACGCAATCGTTGAAGATTGTTCGGGTC
62 TG-T-GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTC
* * *
272490 TTATACTCTCTGAAGAAGTAGGGGGCAGACGCGATTGA
125 TTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGA
272528 TGAAGATTG-T-GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTGATGAAGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATA-GGGGCAGACGCAATTGATGAAGATTGT
272591 GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATA
65 GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATA
*
272656 CTCTCTGAAGAAATAGGGGGCAGACGCAATCGT
130 CTCTCTGAAGAAATAGGGGGCAGACGCAATCGA
* *
272689 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGCAGACGCGATTGATGAAGATTATG
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGCAGACGCAATTGATGAAGATTGTG
* *
272754 -GTTCTTATACTCTCTGAAGAAATAGGGGGCAGA--CAAGTTTGTTGAAGA-TGATTCAAGTCTT
66 AG-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAA--TCGTTGAAGATTG-TTCGAGTCTT
*
272815 ATACCCTCTGAAGAAATAGGG
127 ATACTCTCTGAAGAAATAGGG
272836 AGCGAACCCA
Statistics
Matches: 282, Mismatches: 15, Indels: 24
0.88 0.05 0.07
Matches are distributed among these distances:
160 3 0.01
161 104 0.37
162 97 0.34
163 63 0.22
164 13 0.05
165 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (162 bp):
TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGCAGACGCAATTGATGAAGATTGTG
AGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATAC
TCTCTGAAGAAATAGGGGGCAGACGCAATCGA
Found at i:272615 original size:216 final size:215
Alignment explanation
Indices: 272393--272859 Score: 710
Period size: 216 Copynumber: 2.2 Consensus size: 215
272383 TACTCCCTAG
272393 AGAAATAGGGAGCGAACCCATTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG
1 AGAAATAGGGAGCGAACCCATTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG
* * *
272458 GGTAGACGCAATCGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAGTAGGGGGCAGACGCG
66 GGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATA-GGGGCAGACGCG
*
272523 ATTGATGAAGATTGTGAG-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAA-TTGATGAAG
130 ATTGATGAAGATTATG-GTTCTTATACTCTCTGAAGAAATAGGGGGCAGA--CAAGTTGATGAAG
* *
272586 ATTG-T-GAGTCTTATACTCTCTGA
192 A-TGATCAAGTCTTATACCCTCTGA
* * * *
272609 AGAAATAGGGGGC-AGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGG
1 AGAAATAGGGAGCGA-ACCCATTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGG
272673 GGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGCAGACGCG
65 GGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGCAGACGCG
*
272738 ATTGATGAAGATTATGGTTCTTATACTCTCTGAAGAAATAGGGGGCAGACAAGTTTGTTGAAGAT
130 ATTGATGAAGATTATGGTTCTTATACTCTCTGAAGAAATAGGGGGCAGACAAG-TTGATGAAGAT
272803 GATTCAAGTCTTATACCCTCTGA
194 GA-TCAAGTCTTATACCCTCTGA
*
272826 AGAAATAGGGAGCGAACCCATTTTTCTGAAGATT
1 AGAAATAGGGAGCGAACCCATTTGT-TGAAGATT
272860 TATTGAATTC
Statistics
Matches: 226, Mismatches: 16, Indels: 16
0.88 0.06 0.06
Matches are distributed among these distances:
213 3 0.01
214 3 0.01
215 68 0.30
216 109 0.48
217 34 0.15
218 9 0.04
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (215 bp):
AGAAATAGGGAGCGAACCCATTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG
GGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGCAGACGCGA
TTGATGAAGATTATGGTTCTTATACTCTCTGAAGAAATAGGGGGCAGACAAGTTGATGAAGATGA
TCAAGTCTTATACCCTCTGA
Found at i:277929 original size:20 final size:20
Alignment explanation
Indices: 277898--277955 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
277888 TTAGATTCAC
*
277898 AGAATCTAAGATTATCAGT-
1 AGAATATAAGATTATCAGTG
* *
277917 AGAAATGTAAGATTATCGGTG
1 AG-AATATAAGATTATCAGTG
*
277938 AGAATATAAAATTATCAG
1 AGAATATAAGATTATCAG
277956 GGAATAGGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.45, C:0.07, G:0.19, T:0.29
Consensus pattern (20 bp):
AGAATATAAGATTATCAGTG
Found at i:278778 original size:31 final size:31
Alignment explanation
Indices: 278735--278796 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
278725 TAACTTAAGT
* * *
278735 AGGCAAAATATAATTAATCATAGAAACTGAG
1 AGGCAAAATATAACTAACCATAGAAAATGAG
* *
278766 AGGCAAAGTATAACTAACCATATAAAATGAG
1 AGGCAAAATATAACTAACCATAGAAAATGAG
278797 GGGGTAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.52, C:0.11, G:0.16, T:0.21
Consensus pattern (31 bp):
AGGCAAAATATAACTAACCATAGAAAATGAG
Found at i:279485 original size:17 final size:18
Alignment explanation
Indices: 279463--279496 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
279453 TGATATCAAC
279463 TTGAT-ATTAATTTTGAT
1 TTGATAATTAATTTTGAT
*
279480 TTGATAATTTATTTTGA
1 TTGATAATTAATTTTGA
279497 ACCGAGGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (18 bp):
TTGATAATTAATTTTGAT
Found at i:280307 original size:10 final size:10
Alignment explanation
Indices: 280292--280333 Score: 57
Period size: 10 Copynumber: 3.9 Consensus size: 10
280282 TAATATTATC
280292 AAAATTAATA
1 AAAATTAATA
280302 AAAATTAATA
1 AAAATTAATA
280312 AAAATTAAGTA
1 AAAATTAA-TA
280323 TCAAAATTAAT
1 --AAAATTAAT
280334 GGGTAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 18 0.62
11 2 0.07
12 1 0.03
13 8 0.28
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (10 bp):
AAAATTAATA
Found at i:284637 original size:24 final size:26
Alignment explanation
Indices: 284610--284658 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
284600 TCACCCGCAT
284610 CATCCATCCACCCAT-TA-ATATATC
1 CATCCATCCACCCATATATATATATC
* *
284634 CATCCCTCCATCCATATATATATAT
1 CATCCATCCACCCATATATATATAT
284659 ATTATTCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 13 0.62
25 2 0.10
26 6 0.29
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (26 bp):
CATCCATCCACCCATATATATATATC
Found at i:284763 original size:14 final size:14
Alignment explanation
Indices: 284744--284786 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
284734 TTTAGATTTT
*
284744 TTAAAATTACATTA
1 TTAAAAATACATTA
*
284758 TTAAAAATATA-TA
1 TTAAAAATACATTA
*
284771 TTAAAAATGCATTA
1 TTAAAAATACATTA
284785 TT
1 TT
284787 GATAATTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:287517 original size:21 final size:21
Alignment explanation
Indices: 287474--287560 Score: 61
Period size: 20 Copynumber: 4.2 Consensus size: 21
287464 TATCGCATTA
***
287474 CGATTTTCTAAATTCGTGTTG
1 CGATTTTCTAAATTCGCAATG
*
287495 CGATTTTCTGAATTCGCAATG
1 CGATTTTCTAAATTCGCAATG
* * * *
287516 CGAATATGTAAA-TCACAATG
1 CGATTTTCTAAATTCGCAATG
* * *
287536 CGAATATGTAAA-TCGCAATG
1 CGATTTTCTAAATTCGCAATG
287556 CGATT
1 CGATT
287561 ATGACTATCG
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
20 30 0.55
21 25 0.45
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Consensus pattern (21 bp):
CGATTTTCTAAATTCGCAATG
Found at i:287570 original size:20 final size:20
Alignment explanation
Indices: 287508--287633 Score: 112
Period size: 20 Copynumber: 6.3 Consensus size: 20
287498 TTTTCTGAAT
* *
287508 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTATG-ACTA
* * *
287528 TCACAATGCGAATATGTA-AA
1 TCGCAATGCGATTATG-ACTA
287548 TCGCAATGCGATTATGACTA
1 TCGCAATGCGATTATGACTA
* *
287568 TCGCAATGTGATTCTGACTA
1 TCGCAATGCGATTATGACTA
* * *
287588 TCGCAACGCGATTCTGATTA
1 TCGCAATGCGATTATGACTA
* *
287608 TCGCAATGAGATTCTGACTA
1 TCGCAATGCGATTATGACTA
287628 TCGCAA
1 TCGCAA
287634 CGTGATTTTG
Statistics
Matches: 93, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
19 1 0.01
20 92 0.99
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (20 bp):
TCGCAATGCGATTATGACTA
Found at i:287634 original size:40 final size:40
Alignment explanation
Indices: 287547--287646 Score: 146
Period size: 40 Copynumber: 2.5 Consensus size: 40
287537 GAATATGTAA
* *
287547 ATCGCAATGCGATTATGACTATCGCAATGTGATTCTGACT
1 ATCGCAACGCGATTATGACTATCGCAATGAGATTCTGACT
* *
287587 ATCGCAACGCGATTCTGATTATCGCAATGAGATTCTGACT
1 ATCGCAACGCGATTATGACTATCGCAATGAGATTCTGACT
* *
287627 ATCGCAACGTGATTTTGACT
1 ATCGCAACGCGATTATGACT
287647 GTCGTAACAC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (40 bp):
ATCGCAACGCGATTATGACTATCGCAATGAGATTCTGACT
Found at i:287646 original size:20 final size:20
Alignment explanation
Indices: 287547--287633 Score: 129
Period size: 20 Copynumber: 4.3 Consensus size: 20
287537 GAATATGTAA
*
287547 ATCGCAATGCGATTATGACT
1 ATCGCAATGCGATTCTGACT
*
287567 ATCGCAATGTGATTCTGACT
1 ATCGCAATGCGATTCTGACT
* *
287587 ATCGCAACGCGATTCTGATT
1 ATCGCAATGCGATTCTGACT
*
287607 ATCGCAATGAGATTCTGACT
1 ATCGCAATGCGATTCTGACT
287627 ATCGCAA
1 ATCGCAA
287634 CGTGATTTTG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (20 bp):
ATCGCAATGCGATTCTGACT
Found at i:290793 original size:18 final size:18
Alignment explanation
Indices: 290770--290804 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
290760 AGAAAAAGGC
*
290770 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
290788 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
290805 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:291000 original size:20 final size:20
Alignment explanation
Indices: 290975--291119 Score: 89
Period size: 20 Copynumber: 7.8 Consensus size: 20
290965 TTACACATTC
290975 ATTTGAATATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
290995 ATTTGATTATCGCAACTC-A
1 ATTTGAATATCGCAACGCGA
291014 A----AA-ATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
*
291029 ATTTGACTATCGCAA--CGA
1 ATTTGAATATCGCAACGCGA
*
291047 A----AAAATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* * *
291063 ATTTGACTATCACAACGTGA
1 ATTTGAATATCGCAACGCGA
* * * *
291083 ATTTGATTATCGAAACGGGT
1 ATTTGAATATCGCAACGCGA
* *
291103 ATTCGACTATCGCAACG
1 ATTTGAATATCGCAACG
291120 AGAAAATCGC
Statistics
Matches: 94, Mismatches: 19, Indels: 24
0.69 0.14 0.18
Matches are distributed among these distances:
14 17 0.18
15 3 0.03
16 4 0.04
18 4 0.04
19 3 0.03
20 63 0.67
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (20 bp):
ATTTGAATATCGCAACGCGA
Found at i:291026 original size:34 final size:34
Alignment explanation
Indices: 290983--291153 Score: 162
Period size: 34 Copynumber: 4.9 Consensus size: 34
290973 TCATTTGAAT
* **
290983 ATCGCAACGCGAATTTGATTATCGCAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGAAAAA
291017 ATCGCAACGCGAATTTGACTATCGCAACGAAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGAAAAA
* **
291051 ATCGCAACGCGAATTTGACTATCACAACGTGAATTTGATT
1 ATCGCAACGCGAATTTGACTATCGCAAC--GAA----AAA
* * * * *
291091 ATCGAAACGGGTATTCGACTATCGCAACGAGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGAAAAA
* * *
291125 ATCGCAAAGCGTATTAGACTATCGCAACG
1 ATCGCAACGCGAATTTGACTATCGCAACG
291154 CGAATTGACT
Statistics
Matches: 113, Mismatches: 18, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
34 84 0.74
36 3 0.03
38 2 0.02
40 24 0.21
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCGCAACGAAAAA
Found at i:291168 original size:19 final size:20
Alignment explanation
Indices: 291125--291168 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
291115 CAACGAGAAA
*
291125 ATCGCAAAGCGTATTAGACT
1 ATCGCAAAGCGAATTAGACT
*
291145 ATCGCAACGCGAATT-GACT
1 ATCGCAAAGCGAATTAGACT
*
291164 TTCGC
1 ATCGC
291169 GTTGCGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAAAGCGAATTAGACT
Found at i:292859 original size:42 final size:41
Alignment explanation
Indices: 292752--292863 Score: 100
Period size: 42 Copynumber: 2.7 Consensus size: 41
292742 TCTAGAATGT
* * * *
292752 TGGGAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGATGG-CCTCTTGAACGATGACAGGGGCCTCTTGAACGA
* * ** *
292794 TGGGATGGGACTTTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAT-GGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
292836 TAGGGGAT-GCCTCTTGAACGATGACAGG
1 T--GGGATGGCCTCTTGAACGATGACAGG
292864 TGAGTTGGGC
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
42 46 0.87
43 2 0.04
44 5 0.09
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
TGGGATGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:293379 original size:18 final size:19
Alignment explanation
Indices: 293353--293395 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
293343 CTTAAAATCA
*
293353 CAACACGAA-TGACTATCG
1 CAACGCGAATTGACTATCG
293371 CAACGCGAATTTGACTATCG
1 CAACGCGAA-TTGACTATCG
293391 CAACG
1 CAACG
293396 AGAGAATCGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.36
20 14 0.64
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.19
Consensus pattern (19 bp):
CAACGCGAATTGACTATCG
Found at i:293503 original size:20 final size:20
Alignment explanation
Indices: 293438--293503 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
293428 GCGATTCTTT
**
293438 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCATTTTCA
* **
293458 CGTTGTGATAGTCATTTTTG
1 CGTTGCGATAGTCATTTTCA
*
293478 CATTGCGATAGTCATTTTCA
1 CGTTGCGATAGTCATTTTCA
293498 CGTTGC
1 CGTTGC
293504 AAAAGTAAAC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCA
Found at i:293676 original size:18 final size:18
Alignment explanation
Indices: 293653--293720 Score: 118
Period size: 18 Copynumber: 3.8 Consensus size: 18
293643 TTTACTAAGC
293653 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
*
293671 AATCTAATTGAAATGGTT
1 AATCTAAGTGAAATGGTT
*
293689 AATCTAAGTGAAAAGGTT
1 AATCTAAGTGAAATGGTT
293707 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
293721 TACGAGTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:295469 original size:20 final size:20
Alignment explanation
Indices: 295446--295541 Score: 104
Period size: 20 Copynumber: 4.8 Consensus size: 20
295436 TCTGAAACTT
295446 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
295466 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
295486 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** * *
295506 ACTATTGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
295525 AAAATCGCAACACGAAA
1 AAAATCGCAACACGAAA
295542 CTAAAATTGC
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
19 13 0.21
20 50 0.79
ACGTcount: A:0.47, C:0.22, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:295965 original size:22 final size:22
Alignment explanation
Indices: 295938--295980 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
295928 GAGATAGATG
295938 GATTTCGCCGGAGATGGGGACT
1 GATTTCGCCGGAGATGGGGACT
**
295960 GATTTCGTTGGAGATGGGGAC
1 GATTTCGCCGGAGATGGGGAC
295981 GAATGTCGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.14, G:0.42, T:0.26
Consensus pattern (22 bp):
GATTTCGCCGGAGATGGGGACT
Found at i:296183 original size:20 final size:20
Alignment explanation
Indices: 296155--296227 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
296145 GCGTTTTGAA
*
296155 AATCACGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
296175 AATCGCGTTGCGATGGTCAG
1 AATCGCGTTGCGATAGTCAG
296195 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
296215 AATCGCATTGCGA
1 AATCGCGTTGCGA
296228 ATTCGGAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:296344 original size:19 final size:19
Alignment explanation
Indices: 296320--296367 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
296310 TACCGGAGAT
296320 CGCGTTGCGAATTATCGGA
1 CGCGTTGCGAATTATCGGA
296339 CGCGTTGCGAATTATCGGA
1 CGCGTTGCGAATTATCGGA
*
296358 CGCATTGCGA
1 CGCGTTGCGA
296368 TTTAGTTGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.21, C:0.23, G:0.31, T:0.25
Consensus pattern (19 bp):
CGCGTTGCGAATTATCGGA
Found at i:296695 original size:15 final size:15
Alignment explanation
Indices: 296675--296730 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
296665 TAACCGGTTT
296675 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
**
296690 CGGTTTTTTTTAAAAAC
1 CGG--TTTTAAAAAAAC
*
296707 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
296722 CGATTTTAA
1 CGGTTTTAA
296731 TATTATTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 19 0.59
17 13 0.41
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:297425 original size:13 final size:13
Alignment explanation
Indices: 297404--297458 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
297394 AAGTTCGATA
*
297404 AATTCAAATACTT
1 AATTGAAATACTT
297417 AATTGAAATACTT
1 AATTGAAATACTT
* *
297430 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
297444 AATTGAAATACTT
1 AATTGAAATACTT
297457 AA
1 AA
297459 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:297540 original size:32 final size:33
Alignment explanation
Indices: 297444--297542 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
297434 AACTCAACAT
* * *
297444 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
297477 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
*
297510 AATTCAAATGCTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
297542 A
1 A
297543 TTGAAACAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 12 0.19
33 50 0.81
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:297561 original size:21 final size:21
Alignment explanation
Indices: 297537--297578 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
297527 ACTTCAAGTT
297537 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
297558 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
297579 AAAATAAACT
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:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:299852 original size:13 final size:13
Alignment explanation
Indices: 299834--299858 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
299824 TTTTTCTCCA
299834 AACCGGTTAAAAT
1 AACCGGTTAAAAT
299847 AACCGGTTAAAA
1 AACCGGTTAAAA
299859 AAAATCTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (13 bp):
AACCGGTTAAAAT
Found at i:303013 original size:2 final size:2
Alignment explanation
Indices: 303002--303039 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
302992 TTGAATTATT
303002 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
303040 ATTTTAACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:303218 original size:28 final size:26
Alignment explanation
Indices: 303186--303244 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
303176 ACATGTTTAG
*
303186 TATTTCAACT-ATTATTTTTGTTTCAGTT
1 TATTT-AACTAATTA-TTTT-TTTAAGTT
*
303214 TATTTATCTAATTATTTTTTTAAGTT
1 TATTTAACTAATTATTTTTTTAAGTT
303240 TATTT
1 TATTT
303245 TTGAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 12 0.43
27 7 0.25
28 9 0.32
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.64
Consensus pattern (26 bp):
TATTTAACTAATTATTTTTTTAAGTT
Found at i:304531 original size:2 final size:2
Alignment explanation
Indices: 304524--304577 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
304514 GATGTGCATA
304524 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
304566 AT AT AT AT AT AT
1 AT AT AT AT AT AT
304578 GTACGCATGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:305843 original size:2 final size:2
Alignment explanation
Indices: 305832--305863 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
305822 TTGAATTATT
305832 TA TA -A TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
305864 ATTTTAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.