Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 85 of 343
Found at i:28123786 original size:42 final size:42
Alignment explanation
Indices: 28123726--28123806 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
28123716 TATATATATT
**
28123726 TATATAGCCGAAGCTATCTTGATCTCGCACACTAAGTGCAAA
1 TATATAGCCGAAGCTATCTCAATCTCGCACACTAAGTGCAAA
* * *
28123768 TATATAGCCGAAGTTATCTCAATTTTGCACACTAAGTGC
1 TATATAGCCGAAGCTATCTCAATCTCGCACACTAAGTGC
28123807 CTAAAATTAG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (42 bp):
TATATAGCCGAAGCTATCTCAATCTCGCACACTAAGTGCAAA
Found at i:28136101 original size:37 final size:37
Alignment explanation
Indices: 28136051--28136126 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
28136041 TTTGACCAAT
28136051 TTCTAAGTCTATGGACAAAAATTGGACATGGATGGAA
1 TTCTAAGTCTATGGACAAAAATTGGACATGGATGGAA
28136088 TTCTAAGTCTATGGACAAAAATTGGACATGGATGGAA
1 TTCTAAGTCTATGGACAAAAATTGGACATGGATGGAA
28136125 TT
1 TT
28136127 TTTGGAAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.29
Consensus pattern (37 bp):
TTCTAAGTCTATGGACAAAAATTGGACATGGATGGAA
Found at i:28153484 original size:20 final size:19
Alignment explanation
Indices: 28153452--28153491 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
28153442 AGCACATGTA
*
28153452 TTCACAAAATTCAGAACTT
1 TTCACAAAATTCACAACTT
*
28153471 TTCATCAAATTTCACAACTT
1 TTCA-CAAAATTCACAACTT
28153491 T
1 T
28153492 ATGATTTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.38
Consensus pattern (19 bp):
TTCACAAAATTCACAACTT
Found at i:28179838 original size:49 final size:47
Alignment explanation
Indices: 28179705--28180126 Score: 573
Period size: 48 Copynumber: 8.7 Consensus size: 47
28179695 GAAATGATAG
*
28179705 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGT-ATATATGTGA
* *
28179753 TAAGGCCTAATAGCAGATGCGATGAATGTGAAAGTGTATATATGTGGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGT-GA
* *
28179801 TAAGGCCTAATAGCCGAAGTGGATGAATGTGAAAGTGTATATGTGGTGGA
1 TAAGGCCTAATAGCCGATGT-GATGAATGTGAAAGTGTATATAT-GT-GA
*
28179851 TCAACGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAATATGTGA
1 T-AA-GGCCTAATAGCCGATGTGATGAATGTGAAAGTGTAT-ATATGTGA
* *
28179901 TAAGGCCTAAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCT-AATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
28179949 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
28179996 T-AGG-CTAATAGCCGATGTGATGAA--TGAAAGTGTAATATATGTAA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGT-ATATATGTGA
*
28180040 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTGAATATATAGTAA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGT--ATATAT-GTGA
*
28180090 TAAGGGCCTAAGTGGCCGATGTGATGCAATGTGAAAG
1 TAA-GGCCTAA-TAGCCGATGTGATG-AATGTGAAAG
28180127 GTGTCCGAAT
Statistics
Matches: 342, Mismatches: 15, Indels: 29
0.89 0.04 0.08
Matches are distributed among these distances:
43 9 0.03
44 10 0.03
45 23 0.07
46 23 0.07
47 46 0.13
48 82 0.24
49 62 0.18
50 16 0.05
51 30 0.09
52 31 0.09
53 10 0.03
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:28179959 original size:148 final size:141
Alignment explanation
Indices: 28179707--28180126 Score: 587
Period size: 148 Copynumber: 2.9 Consensus size: 141
28179697 AATGATAGTA
*
28179707 AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAATATATGTGATAAGGCCTAATAGCAGATG
1 AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAATATATGTGATAAGGCCTAATAGCCGATG
* *
28179772 CGATGAATGTGAAAGTGTATATATGTGGATAAGGCCTAATAGCCGAAGTGGATGAATGTGAAAGT
66 TGATGAATGTGAAAGTGTATATATGT-GATAAGGCCTAATAGCCGATGT-GATGAATGTGAAAGT
*
28179837 GTATATGTGGTGGAT
129 GTATATAT-GT-GAT
*
28179852 CAACGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT-ATAATATGTGATAAGGCCTAAATGGC
1 --A-GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAAT-ATATGTGATAAGGCCT-AATAGC
*
28179916 CGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
61 CGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
28179981 AGTGTATATATGTGAT
126 AGTGTATATATGTGAT
* *
28179997 AGG-CTAATAGCCGATGTGATGAA--TGAAAGTGTAATATATGTAATAAGGCCTAATAGCCGATG
1 AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAATATATGTGATAAGGCCTAATAGCCGATG
* *
28180059 TGATGAATGTGAAAGTGTGAATATATAGTAATAAGGGCCTAAGTGGCCGATGTGATGCAATGTGA
66 TGATGAATGTGAAAGTGT--ATATAT-GTGATAA-GGCCTAA-TAGCCGATGTGATG-AATGTGA
28180124 AAG
125 AAG
28180127 GTGTCCGAAT
Statistics
Matches: 251, Mismatches: 12, Indels: 23
0.88 0.04 0.08
Matches are distributed among these distances:
138 28 0.11
139 24 0.10
140 7 0.03
141 25 0.10
142 9 0.04
143 14 0.06
144 10 0.04
145 3 0.01
146 2 0.01
147 25 0.10
148 71 0.28
149 33 0.13
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.28
Consensus pattern (141 bp):
AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAATATATGTGATAAGGCCTAATAGCCGATG
TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGT
ATATATGTGAT
Found at i:28180380 original size:36 final size:36
Alignment explanation
Indices: 28180325--28180401 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
28180315 CCGAGCTCTA
* * *
28180325 AAGACCCGATGACTACGTGTGGGAATTTTGT-CGGGT
1 AAGACCCGATAACTACGTGTGAG-ATTATGTCCGGGT
*
28180361 AAGACCCGATAACTTCGTGTGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGAGATTATGTCCGGGT
28180397 AAGAC
1 AAGAC
28180402 TTCGTAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
35 6 0.17
36 30 0.83
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (36 bp):
AAGACCCGATAACTACGTGTGAGATTATGTCCGGGT
Found at i:28182120 original size:28 final size:27
Alignment explanation
Indices: 28182053--28182122 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 27
28182043 AGAATATGAT
* *
28182053 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTAACCATGCA
* *
28182080 GCACTAAGTGTGCGAATCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TAACCATGCA
*
28182108 GCACTAAGGGTGCGA
1 GCACTAAGTGTGCGA
28182123 TTTGATTACG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 17 0.46
28 20 0.54
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTAACCATGCA
Found at i:28182138 original size:55 final size:53
Alignment explanation
Indices: 28181998--28182149 Score: 178
Period size: 55 Copynumber: 2.8 Consensus size: 53
28181988 TAAATTGTAC
* *
28181998 AGCACTAAGTGTGCGATTCGATTATGTTGCACTAAGTGTGCGAAAAGAATATG
1 AGCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGAAAAGAATATG
* ** * ***
28182051 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAATCTAACTATG
1 A-GCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGAAAAGAA-TATG
* *
28182106 TAGCACTAAGGGTGCGATTTGATTACGTGGCACTAAGTGTGCGA
1 -AGCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGA
28182150 GTTGAGTGAA
Statistics
Matches: 81, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
53 1 0.01
54 39 0.48
55 40 0.49
56 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (53 bp):
AGCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGAAAAGAATATG
Found at i:28182154 original size:27 final size:27
Alignment explanation
Indices: 28181999--28182154 Score: 145
Period size: 27 Copynumber: 5.7 Consensus size: 27
28181989 AAATTGTACA
* *
28181999 GCACTAAGTGTGCG-ATTCGATTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
** *
28182026 GCACTAAGTGTGCGAAAAGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
28182053 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* *
28182080 GCACTAAGTGTGCGAATCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * * *
28182108 GCACTAAGGGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
28182135 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
28182155 GTGAATAGCA
Statistics
Matches: 105, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
27 82 0.78
28 23 0.22
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:28184811 original size:109 final size:109
Alignment explanation
Indices: 28184676--28184994 Score: 528
Period size: 101 Copynumber: 3.0 Consensus size: 109
28184666 GGAATTAACG
28184676 GCCGACCAATATGCATGGATTAATGACTTGAATTATTTATTATGTTTTATGGCATTATGGTATAC
1 GCCGACCAATATGCATGGATTAATGACTTGAATTATTTATTATGTTTTATGGCATTATGGTATAC
28184741 TTTAATATATGTTAATATATTATATTTAATAAAAGATGAAAGTA
66 TTTAATATATGTTAATATATTATATTTAATAAAAGATGAAAGTA
28184785 GCCGACCAATATGCATGGATTAATGACTTGAATTATTTATTATGTTTTATGGCATTATGGTATAC
1 GCCGACCAATATGCATGGATTAATGACTTGAATTATTTATTATGTTTTATGGCATTATGGTATAC
28184850 -TTAATATATG-T--TA-A-TATA-TT-ATAAAAGATGAAAGTA
66 TTTAATATATGTTAATATATTATATTTAATAAAAGATGAAAGTA
* *
28184886 GCCGACCAATATGCATGGATTAATGACTTGAATTGTTTATTATATTTTATGGCATTATGGTATAC
1 GCCGACCAATATGCATGGATTAATGACTTGAATTATTTATTATGTTTTATGGCATTATGGTATAC
* * * *
28184951 TTTAATATATGTTAATATATTATGTTTAAGAAGAGAGGAAAGTA
66 TTTAATATATGTTAATATATTATATTTAATAAAAGATGAAAGTA
28184995 TTCATCTTTC
Statistics
Matches: 196, Mismatches: 6, Indels: 16
0.90 0.03 0.07
Matches are distributed among these distances:
101 79 0.40
102 12 0.06
103 5 0.03
104 1 0.01
105 4 0.02
106 1 0.01
107 4 0.02
108 12 0.06
109 78 0.40
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (109 bp):
GCCGACCAATATGCATGGATTAATGACTTGAATTATTTATTATGTTTTATGGCATTATGGTATAC
TTTAATATATGTTAATATATTATATTTAATAAAAGATGAAAGTA
Found at i:28185398 original size:28 final size:28
Alignment explanation
Indices: 28185358--28185427 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
28185348 TATGAGATTG
*
28185358 GCACTAAGTGTGCGAGTTTAATT-GTATA
1 GCACTAAGTGTGCGAGTTTAATTATTA-A
*
28185386 GCACTAAGTGTGCGAGTTTGATTATTAA
1 GCACTAAGTGTGCGAGTTTAATTATTAA
28185414 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
28185428 GACTTACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 37 0.95
29 2 0.05
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATTAA
Found at i:28186382 original size:4 final size:4
Alignment explanation
Indices: 28186373--28186399 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
28186363 GTCAAGTCTG
28186373 ATTT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT
28186400 AGCCAATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:28190209 original size:40 final size:39
Alignment explanation
Indices: 28190049--28190304 Score: 227
Period size: 39 Copynumber: 6.5 Consensus size: 39
28190039 AAATCACGTA
* * * **
28190049 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCAAATG
1 CCTTCGGGACTTAACCCGGATTTAG-TACTCGCACAAATG
* * * *
28190088 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATG
1 CCTTCGGGACTTAACCCGGATTTAGT-ACTCGCACAAATG
* *
28190127 CCTTCGGGACTTAACCCGGATTTAATACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAATG
*
28190166 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGTA-CTCGCACAAATG
*
28190206 CCTTCGGG-CTTAACCCGGAACTT-GTATCTCGCACAAATG
1 CCTTCGGGACTTAACCCGG-ATTTAGTA-CTCGCACAAATG
** * * *
28190245 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAA-G
1 CCTTCGGGA-CTTAACCCGGATTTAGT-AC-TCGCACAAATG
*
28190285 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
28190305 CAGCATTCAA
Statistics
Matches: 180, Mismatches: 26, Indels: 21
0.79 0.11 0.09
Matches are distributed among these distances:
38 9 0.05
39 100 0.56
40 59 0.33
41 12 0.07
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (39 bp):
CCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAATG
Found at i:28190313 original size:41 final size:41
Alignment explanation
Indices: 28190236--28190313 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
28190226 CTTGTATCTC
* * *
28190236 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
28190277 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
28190314 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:28198118 original size:40 final size:39
Alignment explanation
Indices: 28197958--28198213 Score: 227
Period size: 39 Copynumber: 6.5 Consensus size: 39
28197948 AAATCACGTA
* * * **
28197958 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCAAATG
1 CCTTCGGGACTTAACCCGGATTTAG-TACTCGCACAAATG
* * * *
28197997 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATG
1 CCTTCGGGACTTAACCCGGATTTAGT-ACTCGCACAAATG
* *
28198036 CCTTCGGGACTTAACCCGGATTTAATACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAATG
*
28198075 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGTA-CTCGCACAAATG
*
28198115 CCTTCGGG-CTTAACCCGGAACTT-GTATCTCGCACAAATG
1 CCTTCGGGACTTAACCCGG-ATTTAGTA-CTCGCACAAATG
** * * *
28198154 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAA-G
1 CCTTCGGGA-CTTAACCCGGATTTAGT-AC-TCGCACAAATG
*
28198194 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
28198214 CAGCATTCAA
Statistics
Matches: 180, Mismatches: 26, Indels: 21
0.79 0.11 0.09
Matches are distributed among these distances:
38 9 0.05
39 100 0.56
40 59 0.33
41 12 0.07
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (39 bp):
CCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAATG
Found at i:28198222 original size:41 final size:41
Alignment explanation
Indices: 28198145--28198222 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
28198135 CTTGTATCTC
* * *
28198145 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
28198186 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
28198223 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:28203681 original size:25 final size:25
Alignment explanation
Indices: 28203652--28203699 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28203642 TTATAACATG
* * *
28203652 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTGTACCCCTAGGTA
28203677 AAAATGACCATTGTACCCCTAGG
1 AAAATGACCATTGTACCCCTAGG
28203700 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTGTACCCCTAGGTA
Found at i:28203909 original size:46 final size:47
Alignment explanation
Indices: 28203842--28203937 Score: 158
Period size: 47 Copynumber: 2.1 Consensus size: 47
28203832 AGGAAGTGAA
28203842 AAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTGTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTGTGCCCCAGTTATT
* * *
28203888 AAAGGGCTTATGCCCTAGTTATTAAAAGGGCTTTTGCCCTAGTTATT
1 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTGTGCCCCAGTTATT
28203935 AAA
1 AAA
28203938 AGAGGCTAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
46 22 0.48
47 24 0.52
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (47 bp):
AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTGTGCCCCAGTTATT
Found at i:28203920 original size:24 final size:24
Alignment explanation
Indices: 28203841--28203944 Score: 149
Period size: 23 Copynumber: 4.4 Consensus size: 24
28203831 AAGGAAGTGA
28203841 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
28203865 -AAAGGGCTTGTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
28203888 -AAAGGGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
28203911 AAAAGGGCTTTTGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
28203935 AAAAGAGGCT
1 AAAAG-GGCT
28203945 AGGCCTCCAG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
23 43 0.58
24 27 0.36
25 4 0.05
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:28209534 original size:40 final size:40
Alignment explanation
Indices: 28209479--28209563 Score: 170
Period size: 40 Copynumber: 2.1 Consensus size: 40
28209469 AAATTTAAAG
28209479 TCAATTTTAGAGGTCATCTTACCTCGAGTTGAATCAAGTT
1 TCAATTTTAGAGGTCATCTTACCTCGAGTTGAATCAAGTT
28209519 TCAATTTTAGAGGTCATCTTACCTCGAGTTGAATCAAGTT
1 TCAATTTTAGAGGTCATCTTACCTCGAGTTGAATCAAGTT
28209559 TCAAT
1 TCAAT
28209564 CACGTTTACG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (40 bp):
TCAATTTTAGAGGTCATCTTACCTCGAGTTGAATCAAGTT
Found at i:28210640 original size:23 final size:23
Alignment explanation
Indices: 28210597--28210646 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
28210587 TTTCTATTAA
* *
28210597 TTAAATAATAAAAAATTATAATT
1 TTAAATAATAAAAAATAATAAAT
*
28210620 TTAAAT-ATAACATAATAATAAAT
1 TTAAATAATAA-AAAATAATAAAT
28210643 TTAA
1 TTAA
28210647 CTCTCAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TTAAATAATAAAAAATAATAAAT
Found at i:28214360 original size:15 final size:15
Alignment explanation
Indices: 28214340--28214369 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28214330 TTAATTTTAT
28214340 ATTTTAATTTTGAGA
1 ATTTTAATTTTGAGA
28214355 ATTTTAATTTTGAGA
1 ATTTTAATTTTGAGA
28214370 CATTGAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (15 bp):
ATTTTAATTTTGAGA
Found at i:28215140 original size:19 final size:19
Alignment explanation
Indices: 28215088--28215131 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 19
28215078 TTTTTCATAT
28215088 TTTAAACAAAAAATTTAAAAA
1 TTTAAA-AAAAAA-TTAAAAA
28215109 TTTAAAAAAAAATTAAAAA
1 TTTAAAAAAAAATTAAAAA
28215128 TTTA
1 TTTA
28215132 TGAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 11 0.48
20 6 0.26
21 6 0.26
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
TTTAAAAAAAAATTAAAAA
Found at i:28216415 original size:22 final size:21
Alignment explanation
Indices: 28216367--28216420 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
28216357 ATTTCCACAG
28216367 TTTTAATTTATAAACCCTAAA
1 TTTTAATTTATAAACCCTAAA
* * *
28216388 TATTTAATTTATACACCCATCAC
1 T-TTTAATTTATAAACCC-TAAA
28216411 TTTTAATTTA
1 TTTTAATTTA
28216421 CACCTAAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.04
22 24 0.86
23 3 0.11
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTTAATTTATAAACCCTAAA
Found at i:28217074 original size:19 final size:20
Alignment explanation
Indices: 28217036--28217074 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28217026 TTGGGGGTAA
* *
28217036 AGGGTGAAAAGTAAATATTT
1 AGGGGGAAAAGTAAAAATTT
28217056 AGGGGGAAAA-TAAAAATTT
1 AGGGGGAAAAGTAAAAATTT
28217075 TTTAGGGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.26, T:0.26
Consensus pattern (20 bp):
AGGGGGAAAAGTAAAAATTT
Found at i:28221482 original size:43 final size:43
Alignment explanation
Indices: 28221330--28221494 Score: 176
Period size: 43 Copynumber: 3.8 Consensus size: 43
28221320 TTTCGACATG
* *
28221330 TGATTTCGTGTAAGACCACGTCTGGGAAATTGGCATCGACT-TGA
1 TGATTACGTGTAAGACCACGTCTGGGACATTGGCATCGA-TAT-A
* *
28221374 -GATTTACGTGTAAGACCATGTCTGGGACATAGGCATCG-TATA
1 TGA-TTACGTGTAAGACCACGTCTGGGACATTGGCATCGATATA
* * *
28221416 TGATTTCGTGTAAGACC-CTGTCTGGGACAGTGGCATCGATATT
1 TGATTACGTGTAAGACCAC-GTCTGGGACATTGGCATCGATATA
** *
28221459 TGATTACAAGTAAGACCACGTCTGAGACATTGGCAT
1 TGATTACGTGTAAGACCACGTCTGGGACATTGGCAT
28221495 TGTACGAGCT
Statistics
Matches: 101, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
42 32 0.32
43 37 0.37
44 32 0.32
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (43 bp):
TGATTACGTGTAAGACCACGTCTGGGACATTGGCATCGATATA
Found at i:28233602 original size:32 final size:32
Alignment explanation
Indices: 28233566--28233628 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
28233556 AAGTTGAGAA
28233566 CTATATGGTTTAAATTAATATGGTCTTATGCG
1 CTATATGGTTTAAATTAATATGGTCTTATGCG
*
28233598 CTATATGGTTTAAGTTAATATGGTCTTATGC
1 CTATATGGTTTAAATTAATATGGTCTTATGC
28233629 ACATAGTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (32 bp):
CTATATGGTTTAAATTAATATGGTCTTATGCG
Found at i:28237174 original size:15 final size:17
Alignment explanation
Indices: 28237156--28237193 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
28237146 TTGCTCTCTA
28237156 TCTTTTTA-TTTC-TTC
1 TCTTTTTATTTTCTTTC
28237171 TCTTTTTATTTTCTTTC
1 TCTTTTTATTTTCTTTC
28237188 TCTTTT
1 TCTTTT
28237194 CTTTACACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 8 0.38
16 4 0.19
17 9 0.43
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.76
Consensus pattern (17 bp):
TCTTTTTATTTTCTTTC
Found at i:28251098 original size:55 final size:55
Alignment explanation
Indices: 28251011--28251117 Score: 178
Period size: 55 Copynumber: 1.9 Consensus size: 55
28251001 CATGATTGGA
* *
28251011 AATACCTTATAACCCTAATCCGGTGACGGATACGGGCTAGGGATGTTATACTGGT
1 AATACCTTATAACCCTAATCCAGTGACAGATACGGGCTAGGGATGTTATACTGGT
* *
28251066 AATACCTTATAACCTTAATCCAGTGACAGATACGGGTTAGGGATGTTATACT
1 AATACCTTATAACCCTAATCCAGTGACAGATACGGGCTAGGGATGTTATACT
28251118 AATGACATGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (55 bp):
AATACCTTATAACCCTAATCCAGTGACAGATACGGGCTAGGGATGTTATACTGGT
Found at i:28254721 original size:40 final size:39
Alignment explanation
Indices: 28254524--28254707 Score: 203
Period size: 40 Copynumber: 4.6 Consensus size: 39
28254514 CGAATGATGT
* * * *
28254524 CCGGGCTAAGTTCCGAAGGC-TTTGTGCTAAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-AA
* * *
28254564 CCGGACTAAGAT-TCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-A
*
28254604 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28254642 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
28254683 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
28254708 AACGAGTTGC
Statistics
Matches: 125, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
39 34 0.27
40 81 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28254729 original size:79 final size:79
Alignment explanation
Indices: 28254577--28254730 Score: 213
Period size: 79 Copynumber: 1.9 Consensus size: 79
28254567 GACTAAGATT
* **
28254577 CGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
1 CGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
28254642 TCCGGGTTAAGTCC
66 TCCGGGTTAAGTCC
* * *
28254656 CGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAGTTGCTA
1 CGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTACTA
*
28254720 TATCC-GGTTAA
64 AATCCGGGTTAA
28254731 ATTCTGAAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
78 2 0.03
79 38 0.58
80 26 0.39
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (79 bp):
CGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
TCCGGGTTAAGTCC
Found at i:28254740 original size:79 final size:77
Alignment explanation
Indices: 28254557--28254740 Score: 208
Period size: 79 Copynumber: 2.3 Consensus size: 77
28254547 GTGCTAAGTG
* *
28254557 ACTATATCCGGACTAAGATTCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGG
1 ACTATATCCGG-TTAA-ATTCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGG
**
28254622 CATTGGTGCGAGTT
64 CATTGGAACGAGTT
* * * *
28254636 ACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAA
1 ACTATATCC-GGTTAAAT-TCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAA
*
28254700 GGCATTTGAACGAGTT
62 GGCATTGGAACGAGTT
*
28254716 GCTATATCCGGTTAAATTCTGAAGG
1 ACTATATCCGGTTAAATTC-GAAGG
28254741 TATGTGATTC
Statistics
Matches: 87, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
78 4 0.05
79 55 0.63
80 28 0.32
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (77 bp):
ACTATATCCGGTTAAATTCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCA
TTGGAACGAGTT
Found at i:28258057 original size:37 final size:39
Alignment explanation
Indices: 28257957--28258178 Score: 240
Period size: 40 Copynumber: 5.6 Consensus size: 39
28257947 TTGAATGATG
* *
28257957 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
28257996 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
28258037 TCC-GGCTAAG-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* *
28258074 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* *
28258113 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
* *
28258152 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAG-CCCGAAGGCATTTG
28258179 AACGAGTAGC
Statistics
Matches: 162, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
37 30 0.19
38 7 0.04
39 42 0.26
40 71 0.44
41 11 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:28265974 original size:40 final size:38
Alignment explanation
Indices: 28265890--28266109 Score: 250
Period size: 40 Copynumber: 5.7 Consensus size: 38
28265880 TTGAATGATG
* * *
28265890 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTA-A
* * *
28265930 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAA
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA
28265969 TTCCGGGCTAAGCCCGAAGGCATTT-TGCGAG-TACTAA
1 -TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
28266006 TCC-GGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACT-AA
*
28266044 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-A
* *
28266084 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAG-CCCGAAGGCATTTG
28266110 AACGAGTAGC
Statistics
Matches: 159, Mismatches: 13, Indels: 16
0.85 0.07 0.09
Matches are distributed among these distances:
35 20 0.13
36 9 0.06
37 10 0.06
38 11 0.07
39 20 0.13
40 82 0.52
41 7 0.04
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (38 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:28269680 original size:40 final size:39
Alignment explanation
Indices: 28269653--28269818 Score: 194
Period size: 39 Copynumber: 4.2 Consensus size: 39
28269643 TTTTGGGACA
*
28269653 TAGCCCGGTTATAGTAACTCGTACAAATGCCTTCGGGACT
1 TAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGG-CT
* * *
28269693 TAACCCGGATT-TAGTAACTCGCACCAATGCCTTCAGGCT
1 TAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGCT
*
28269732 TAGCCCGG-AATTAGTAACTCGCACAAATGCCTTCGGGCT
1 TAGCCCGGTTA-TAGTAACTCGCACAAATGCCTTCGGGCT
* * *
28269771 TAGCCCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACT
1 TAGCCCGGTTATAGTAAC-TCGCACAAATGCCTTCGGG-CT
28269811 TAGCCCGG
1 TAGCCCGG
28269819 ACATTATTCG
Statistics
Matches: 109, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
39 58 0.53
40 49 0.45
41 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (39 bp):
TAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGCT
Found at i:28269736 original size:79 final size:79
Alignment explanation
Indices: 28269664--28269824 Score: 218
Period size: 79 Copynumber: 2.0 Consensus size: 79
28269654 AGCCCGGTTA
* * * *
28269664 TAGTAACTCGTACAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC-TCGCACCAATGCCTTCA
1 TAGTAACTCGCACAAATGCCTTCGGG-CTTAACCCGGATATAGTAACTTAGCA-CAAAGCCTTCA
28269728 GG-CTTAGCCCGGAAT
64 GGACTTAGCCCGGAAT
* * *
28269743 TAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGATATAGTCACTTAGCACAAAGCCTTCGGG
1 TAGTAACTCGCACAAATGCCTTCGGGCTTAACCCGGATATAGTAACTTAGCACAAAGCCTTCAGG
28269808 ACTTAGCCCGGACAT
66 ACTTAGCCCGGA-AT
28269823 TA
1 TA
28269825 TTCGAATAAC
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
78 28 0.39
79 40 0.56
80 4 0.06
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (79 bp):
TAGTAACTCGCACAAATGCCTTCGGGCTTAACCCGGATATAGTAACTTAGCACAAAGCCTTCAGG
ACTTAGCCCGGAAT
Found at i:28269819 original size:40 final size:40
Alignment explanation
Indices: 28269617--28269819 Score: 227
Period size: 40 Copynumber: 5.1 Consensus size: 40
28269607 CGGAATTTAA
** * * *
28269617 CCGGATATAGCT-ACTCGTTCAAATGCTTTTGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
28269657 CCGGTTATAGTAACTCGTACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
28269697 CCGGATTTAGTAACTCGCACCAATGCCTTCAGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
28269736 CCGGA-ATTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
28269775 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
28269815 CCGGA
1 CCGGA
28269820 CATTATTCGA
Statistics
Matches: 141, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
39 61 0.43
40 80 0.57
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:28277158 original size:40 final size:39
Alignment explanation
Indices: 28277074--28277258 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 39
28277064 TCGAATGATG
* *
28277074 TCCGGGCTAAGTTCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGC-GAGTTACTAAT
*
28277113 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
28277154 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAT
*
28277193 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAT
* *
28277232 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGT-CCGAAGGCATTTG
28277259 AAAAAGTTGC
Statistics
Matches: 126, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
39 36 0.29
40 81 0.64
41 9 0.07
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:28277210 original size:79 final size:81
Alignment explanation
Indices: 28277074--28277256 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
28277064 TCGAATGATG
* * *
28277074 TCCGGGCTAAGTTCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATT
28277138 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * **
28277153 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGAT-CCGAAGGCA
28277215 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
28277233 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
28277257 TGAAAAAGTT
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:28277280 original size:79 final size:79
Alignment explanation
Indices: 28277127--28277291 Score: 190
Period size: 79 Copynumber: 2.1 Consensus size: 79
28277117 GGACTAAGAT
* ****
28277127 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAAAAAGTTACTAA
*
28277192 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
28277206 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAAAAAGTTGCT
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAAAAAGTTACT
* * *
28277270 ATATTC-GGTTAAATT
64 AAATCCGGGTTAAATC
28277285 CCGAAGG
1 CCGAAGG
28277292 TACGTGATTC
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
78 2 0.03
79 47 0.65
80 23 0.32
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAAAAAGTTACTAA
ATCCGGGTTAAATC
Found at i:28280321 original size:49 final size:49
Alignment explanation
Indices: 28280268--28280499 Score: 275
Period size: 49 Copynumber: 4.7 Consensus size: 49
28280258 CTGGTACGCA
* * *
28280268 TAGTAGCCTACACTTAGTACTTCACATGTGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
** * *
28280317 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCCGGTACACG
* ** * * *
28280367 TAGTAGCCTGCACTTAGTCCTACACACGTGATTGAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCCGGTACACG
* * * *
28280418 TAGTAGCTTGCACTTAGTACTACACATGCGACCAATTATTCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
*
28280467 TAGTAGCCTGCACTTAGTATTACACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC
28280500 TCGCAATGGA
Statistics
Matches: 150, Mismatches: 30, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
49 69 0.46
50 46 0.31
51 35 0.23
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
Found at i:28280766 original size:27 final size:27
Alignment explanation
Indices: 28280726--28280779 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
28280716 TGGTACAACC
* *
28280726 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
28280753 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
28280780 TCAAATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:28284546 original size:18 final size:18
Alignment explanation
Indices: 28284518--28284564 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
28284508 TACGTATGGT
28284518 CAAATTCATAATAATAATA
1 CAAA-TCATAATAATAATA
*
28284537 CATATCATAATAATAATA
1 CAAATCATAATAATAATA
28284555 CAAATCATAA
1 CAAATCATAA
28284565 ACAAACTTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 23 0.88
19 3 0.12
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (18 bp):
CAAATCATAATAATAATA
Found at i:28287981 original size:31 final size:31
Alignment explanation
Indices: 28287943--28288002 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
28287933 TTGTGAACTA
*
28287943 TACTATGT-ATATTTTTGATT-AAATTGAATGT
1 TACTATGTGA-ATTTTT-ATTGAAAATGAATGT
28287974 TACTATGTGAATTTTTATTGAAAATGAAT
1 TACTATGTGAATTTTTATTGAAAATGAAT
28288003 CGATATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 3 0.12
31 22 0.85
32 1 0.04
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.48
Consensus pattern (31 bp):
TACTATGTGAATTTTTATTGAAAATGAATGT
Found at i:28292612 original size:27 final size:27
Alignment explanation
Indices: 28292571--28292624 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
28292561 TGTCATGTGA
* *
28292571 AATTGAATGGCAAATTATTGTTACATG
1 AATTGAATGGCAAATTACTATTACATG
**
28292598 AATTGAATGTTAAATTACTATTACATG
1 AATTGAATGGCAAATTACTATTACATG
28292625 GGTTGTACCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (27 bp):
AATTGAATGGCAAATTACTATTACATG
Found at i:28292930 original size:49 final size:50
Alignment explanation
Indices: 28292850--28293079 Score: 257
Period size: 49 Copynumber: 4.6 Consensus size: 50
28292840 ATCTATTGTG
* *
28292850 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * ** *
28292900 -GGTCGCATGTGTAGTACAAAGTGCAGGCTACTATGCATACCCGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * * * * * **
28292950 CGATCACGTGTGTAGTACTAAGTGCAGGTTACTACGTGTATCTGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
28293000 AGGTCACATGTGTAGTACTAAATGCTGGCTACTACGTGTACTAGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
*
28293050 -GGTCGCATGTGTAGTACTAAGTGCAGGCTA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTA
28293080 TTATGCGTGC
Statistics
Matches: 145, Mismatches: 33, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
49 67 0.46
50 43 0.30
51 35 0.24
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:28300583 original size:45 final size:45
Alignment explanation
Indices: 28300534--28300656 Score: 156
Period size: 45 Copynumber: 2.7 Consensus size: 45
28300524 ATCTAGACCG
* *
28300534 ATGAGTTGTTTATCCACAACATACTAGTAGCTTTTATCTGCACCA
1 ATGAGTGGTTTATCCACAACATACTAGCAGCTTTTATCTGCACCA
* ** * **
28300579 ATGAGTGGTTTCTCCACAATGTACTAGCAGATTTTATCTGCACTG
1 ATGAGTGGTTTATCCACAACATACTAGCAGCTTTTATCTGCACCA
* *
28300624 ATGAGTGGTTTATCCATACCATACTAGCAGCTT
1 ATGAGTGGTTTATCCACAACATACTAGCAGCTT
28300657 ATTTGCAAAC
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 64 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (45 bp):
ATGAGTGGTTTATCCACAACATACTAGCAGCTTTTATCTGCACCA
Found at i:28316056 original size:23 final size:23
Alignment explanation
Indices: 28316026--28316091 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
28316016 GCTTTACCGA
28316026 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
* * *
28316049 TCAGGCACCTCATGTGTTGT-TT
1 TCAGGCACTTTATGTGTCGTATT
*
28316071 T-AGGCACTTTATGTGCCGTAT
1 TCAGGCACTTTATGTGTCGTAT
28316092 ACTGATCAGG
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
21 14 0.40
22 4 0.11
23 17 0.49
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.41
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:28319295 original size:55 final size:53
Alignment explanation
Indices: 28319176--28319356 Score: 231
Period size: 55 Copynumber: 3.4 Consensus size: 53
28319166 ATTGCCATGT
*
28319176 CTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAACTCAGCAATGCCATAC
1 CTTGACATGGTCTTACATGGTA-CCTTGCCTTATAGAACTCATCAATGCCATAC
* *
28319229 CTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAATGCCAT-C
1 CTTGACATGGTCTTACATGGTACC-TTGCCTTATAG-AACTCATCAATGCCATAC
* * * *
28319283 TCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAATGCCATGC
1 -CTTGACATGGTCTTACATG-GTACCTTGCCTTATAGAACTCATCAATGCCATAC
*
28319338 CTTGGCATGGTCTTACATG
1 CTTGACATGGTCTTACATG
28319357 ATATTCTTGT
Statistics
Matches: 113, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
52 2 0.02
53 29 0.26
54 35 0.31
55 45 0.40
56 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.35
Consensus pattern (53 bp):
CTTGACATGGTCTTACATGGTACCTTGCCTTATAGAACTCATCAATGCCATAC
Found at i:28319398 original size:47 final size:47
Alignment explanation
Indices: 28319343--28319464 Score: 190
Period size: 47 Copynumber: 2.6 Consensus size: 47
28319333 CATGCCTTGG
* *
28319343 CATGGTCTTACATGATATTCTTGTCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
* * * *
28319390 CATGGTCTTACATGGTACCCTTGTCTTACCAAATGTCATGTTTCGAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
28319437 CATGGTCTTACATGGTATCCTTGTCTTA
1 CATGGTCTTACATGGTATCCTTGTCTTA
28319465 GTGCCAATGC
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 68 1.00
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.38
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
Found at i:28319540 original size:47 final size:46
Alignment explanation
Indices: 28319436--28319599 Score: 168
Period size: 45 Copynumber: 3.5 Consensus size: 46
28319426 CATGTTTCGA
* * *
28319436 ACATGGTCTTACATGGTATCCTTGTCTTAGTGCCAATGCCACATCTTG
1 ACATGGTCTTACATGGTATCCTTATC--AATGCCAATGCCATATCTTG
** * * *
28319484 ATGTGGTCTTACATGGAATCCTTAATCAATGCCGATGCCATGTCTTG
1 ACATGGTCTTACATGGTATCCTT-ATCAATGCCAATGCCATATCTTG
* * * ** *
28319531 ACATGGTCTTACACGGGATCCTT-GCCTTACCAATGCCATATCTTG
1 ACATGGTCTTACATGGTATCCTTATCAATGCCAATGCCATATCTTG
28319576 ACATGGTCTTACATGGTATCCTTA
1 ACATGGTCTTACATGGTATCCTTA
28319600 ACTGTCAATT
Statistics
Matches: 94, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
45 37 0.39
47 35 0.37
48 20 0.21
49 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (46 bp):
ACATGGTCTTACATGGTATCCTTATCAATGCCAATGCCATATCTTG
Found at i:28320871 original size:27 final size:27
Alignment explanation
Indices: 28320839--28320890 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
28320829 ATAATAGTCC
*
28320839 AATTAATAAATAAATACATCCACTTCT
1 AATTAATAAATAAAGACATCCACTTCT
28320866 AATTAATAAATAAAGACATCCACTT
1 AATTAATAAATAAAGACATCCACTT
28320891 TAAGAACACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.31
Consensus pattern (27 bp):
AATTAATAAATAAAGACATCCACTTCT
Found at i:28324270 original size:22 final size:22
Alignment explanation
Indices: 28324245--28324308 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
28324235 AGTTACAATT
* * *
28324245 AAATTAAAATAAAAATCTAACA
1 AAATTATAATAAAAATATAAAA
*
28324267 AAATTATAA-AAAATTATAAAA
1 AAATTATAATAAAAATATAAAA
28324288 AATATTATAATAAAAA-ATAAA
1 AA-ATTATAATAAAAATATAAA
28324309 GTAAACTACA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 11 0.31
22 20 0.57
23 4 0.11
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATTATAATAAAAATATAAAA
Found at i:28324294 original size:12 final size:11
Alignment explanation
Indices: 28324266--28324303 Score: 51
Period size: 10 Copynumber: 3.4 Consensus size: 11
28324256 AAAATCTAAC
28324266 AAAATTAT-AA
1 AAAATTATAAA
28324276 AAAATTATAAA
1 AAAATTATAAA
28324287 AAATATTATAATA
1 AAA-ATTATAA-A
28324300 AAAA
1 AAAA
28324304 ATAAAGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 8 0.32
11 5 0.20
12 8 0.32
13 4 0.16
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAATTATAAA
Found at i:28324693 original size:2 final size:2
Alignment explanation
Indices: 28324686--28324718 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
28324676 TTCCTTTCAT
*
28324686 GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
28324719 GGAATAGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:28339657 original size:15 final size:15
Alignment explanation
Indices: 28339620--28339648 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28339610 CAACTAATCA
28339620 AAAAAGAAAAAAACG
1 AAAAAGAAAAAAACG
28339635 AAAAAGAAAAAAAC
1 AAAAAGAAAAAAAC
28339649 AGAGAAGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAACG
Found at i:28347856 original size:12 final size:12
Alignment explanation
Indices: 28347839--28347871 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
28347829 CGGCCTACCC
28347839 ATATTAATTTTT
1 ATATTAATTTTT
28347851 ATATT-ATTTTT
1 ATATTAATTTTT
28347862 ATA-TAATTTT
1 ATATTAATTTT
28347872 AAAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:28348693 original size:32 final size:32
Alignment explanation
Indices: 28348650--28348710 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
28348640 GACTTAAAAA
* *
28348650 AACATATTTTTATTTTTTAAAATCTAAACTTT
1 AACAGATTTTTATTTTTCAAAATCTAAACTTT
28348682 AACAGATTTTTATTTTTCAAAATCTAAAC
1 AACAGATTTTTATTTTTCAAAATCTAAAC
28348711 CTTTTCCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (32 bp):
AACAGATTTTTATTTTTCAAAATCTAAACTTT
Found at i:28348797 original size:53 final size:51
Alignment explanation
Indices: 28348740--28348956 Score: 138
Period size: 53 Copynumber: 4.1 Consensus size: 51
28348730 ATTTTTTTTC
* * *
28348740 TTAAAGATTAAAGCTTTTATTTTGAAGTAGTTAAAAAAAATCAAAACTTTGTT
1 TTAAAGATTAAA-CTTTTACTTTGAAATAATTAAAAAAAAT-AAAACTTTGTT
* * * * * * *
28348793 TTAAAAATTTAAAC-TTTCCTTTAAAATAACTAAAAAAAATAGAATTTTATTT
1 TTAAAGA-TTAAACTTTTACTTTGAAATAATTAAAAAAAATAAAACTTT-GTT
* * * *
28348845 TTCAAACACTAAACTTTCT-CTTTTTTAAA-AA-TAAAAAAAA-AAACACTATTTTT
1 TT-AAAGATTAAACTTT-TAC--TTTGAAATAATTAAAAAAAATAAA-ACT-TTGTT
* *
28348898 CTTAAAGATTAAAACTTTTACTTTGAAATAGTTAAAAAATATCAAAACTTTGTT
1 -TTAAAGATT-AAACTTTTACTTTGAAATAATTAAAAAAAAT-AAAACTTTGTT
28348952 TTAAA
1 TTAAA
28348957 AATTTAAAAT
Statistics
Matches: 127, Mismatches: 21, Indels: 32
0.71 0.12 0.18
Matches are distributed among these distances:
51 6 0.05
52 37 0.29
53 40 0.31
54 32 0.25
55 9 0.07
56 3 0.02
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.39
Consensus pattern (51 bp):
TTAAAGATTAAACTTTTACTTTGAAATAATTAAAAAAAATAAAACTTTGTT
Found at i:28348827 original size:52 final size:51
Alignment explanation
Indices: 28348771--28348989 Score: 167
Period size: 52 Copynumber: 4.2 Consensus size: 51
28348761 TTGAAGTAGT
28348771 TAAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAAC
1 TAAAAAAAAT-AAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAAC
* * * * * *
28348823 TAAAAAAAATAGAATTTTATTTTTCAAACA-CTAAACTTTCTCTTTTTTAAA-AA-
1 TAAAAAAAATAAAACTTT-GTTTT-AAAAATTTAAACTTTC-C--TTTAAAATAAC
* * * * * **
28348876 TAAAAAAAA-AAACACTATTTTTCTTAAAGATTAAAACTTTTACTTTGAAATAGT
1 TAAAAAAAATAAA-ACT-TTGTT-TTAAAAATTTAAAC-TTTCCTTTAAAATAAC
* * *
28348930 TAAAAAATATCAAAACTTTGTTTTAAAAATTTAAAATTCCCTTTAAAATAAC
1 TAAAAAAAAT-AAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAAC
28348982 TAAAAAAA
1 TAAAAAAA
28348990 CATATTTTTA
Statistics
Matches: 128, Mismatches: 25, Indels: 28
0.71 0.14 0.15
Matches are distributed among these distances:
51 6 0.05
52 49 0.38
53 35 0.27
54 23 0.18
55 12 0.09
56 3 0.02
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.37
Consensus pattern (51 bp):
TAAAAAAAATAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAAC
Found at i:28348900 original size:159 final size:158
Alignment explanation
Indices: 28348734--28349033 Score: 469
Period size: 159 Copynumber: 1.9 Consensus size: 158
28348724 AAAAATATTT
* * *
28348734 TTTTTCTTAAAGATTAAAGCTTTTATTTTGAAGTAGTTAAAAAAAATCAAAACTTTGTTTTAAAA
1 TTTTTCTTAAAGATTAAAACTTTTACTTTGAAATAGTTAAAAAAAATCAAAACTTTGTTTTAAAA
* * *
28348799 ATTTAAACTTTCCTTTAAAATAACTAAAAAAA-ATAGAATTTTATTTTTCAAACA-CTAAACTTT
66 ATTTAAAATTCCCTTTAAAATAACTAAAAAAACAT--AATTTTATTTTTCAAAAATCTAAACTTT
*
28348862 CTCTTTTTTAAAAATAAAAAAAAAAACACTA
129 CTC-CTTTTAAAAATAAAAAAAAAAACACTA
*
28348893 TTTTTCTTAAAGATTAAAACTTTTACTTTGAAATAGTTAAAAAATATCAAAACTTTGTTTTAAAA
1 TTTTTCTTAAAGATTAAAACTTTTACTTTGAAATAGTTAAAAAAAATCAAAACTTTGTTTTAAAA
* *
28348958 ATTTAAAATTCCCTTTAAAATAACTAAAAAAACATATTTTTATTTTTTAAAAATCTAAACTTTCT
66 ATTTAAAATTCCCTTTAAAATAACTAAAAAAACATAATTTTATTTTTCAAAAATCTAAACTTTCT
28349023 CCTTTTAAAAA
131 CCTTTTAAAAA
28349034 GATACTATTT
Statistics
Matches: 129, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
158 24 0.19
159 103 0.80
160 2 0.02
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (158 bp):
TTTTTCTTAAAGATTAAAACTTTTACTTTGAAATAGTTAAAAAAAATCAAAACTTTGTTTTAAAA
ATTTAAAATTCCCTTTAAAATAACTAAAAAAACATAATTTTATTTTTCAAAAATCTAAACTTTCT
CCTTTTAAAAATAAAAAAAAAAACACTA
Found at i:28350329 original size:13 final size:13
Alignment explanation
Indices: 28350311--28350335 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28350301 GTTATTTTTA
28350311 GTTTGGAATCTTC
1 GTTTGGAATCTTC
28350324 GTTTGGAATCTT
1 GTTTGGAATCTT
28350336 ATTGTTGTTT
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:0.16, C:0.12, G:0.24, T:0.48
Consensus pattern (13 bp):
GTTTGGAATCTTC
Found at i:28351299 original size:35 final size:35
Alignment explanation
Indices: 28351245--28351322 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
28351235 TTACACATCC
* *
28351245 GTATCTGTATCTGAGATGGGCTTAGGCCCGAATCT
1 GTATCTGTATCTGAAATGGGCGTAGGCCCGAATCT
* * *
28351280 GTATTTGTATCTGAAATGGGCGTAGGCCCTAATTT
1 GTATCTGTATCTGAAATGGGCGTAGGCCCGAATCT
28351315 GTATCTGT
1 GTATCTGT
28351323 CTGATGTTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.36
Consensus pattern (35 bp):
GTATCTGTATCTGAAATGGGCGTAGGCCCGAATCT
Found at i:28352110 original size:42 final size:42
Alignment explanation
Indices: 28351949--28352403 Score: 586
Period size: 42 Copynumber: 11.0 Consensus size: 42
28351939 AAGTAAACTA
* * *
28351949 GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAA--CTA-
1 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
* * * *
28351988 GAAAAGTAAACGGACCTCCACACCTGGGCCTCTAAA--CTA-
1 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
* * *
28352027 GAAAAGTAAACGGACCT-C-CAGCTGGGTCTCTAAATGCAAT
1 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
* *
28352067 GAAAAGTGAATGGACCTCCACACCTAGATCTCTAAATGCAAT
1 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
* * *
28352109 GAAAGGTGAATGG-CATCCACACCTGGGTCTCTAGATGCAAT
1 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
* * **
28352150 GAAAAGTGAATGGACCTCCACACTTGGGTATCTAAATATAAT
1 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
* * *
28352192 GAAAAGTGAATGAACCTCCACACTTAGGTCTCTAAATGCAAT
1 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
*
28352234 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATACAAT
1 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
* *
28352276 GAAAAGTGAATGGACCTCCACACCTGGGTTTCTAGATGCAAT
1 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
* *
28352318 GGAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATACAAT
1 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
* *
28352360 GGAAAGTAAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
1 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
28352402 GA
1 GA
28352404 TTGTTTTCCT
Statistics
Matches: 370, Mismatches: 40, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
37 14 0.04
38 1 0.00
39 57 0.15
40 15 0.04
41 37 0.10
42 246 0.66
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.21
Consensus pattern (42 bp):
GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
Found at i:28357797 original size:24 final size:24
Alignment explanation
Indices: 28357747--28357800 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
28357737 AATCGAATTT
*
28357747 GCACACATAGTGCTCGTCACACTC
1 GCACACATAGTGCTAGTCACACTC
28357771 GCACACATAGTGCCATAGT-ACAC-C
1 GCACACATAGTG-C-TAGTCACACTC
28357795 GCACAC
1 GCACAC
28357801 TCAGTGCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 19 0.70
25 5 0.19
26 3 0.11
ACGTcount: A:0.30, C:0.37, G:0.17, T:0.17
Consensus pattern (24 bp):
GCACACATAGTGCTAGTCACACTC
Found at i:28371582 original size:14 final size:14
Alignment explanation
Indices: 28371551--28371589 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
28371541 ATGAGTCTTC
28371551 AAAAATAAATAGAAAT
1 AAAAATAAA-A-AAAT
*
28371567 AAAAGTAAAAAAAT
1 AAAAATAAAAAAAT
28371581 AAAAATAAA
1 AAAAATAAA
28371590 GTAAGTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 1 0.05
16 8 0.38
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (14 bp):
AAAAATAAAAAAAT
Found at i:28371586 original size:20 final size:20
Alignment explanation
Indices: 28371552--28371593 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
28371542 TGAGTCTTCA
*
28371552 AAAATAAATAGAAATAAAAGT
1 AAAATAAATAAAAAT-AAAGT
28371573 AAAA-AAATAAAAATAAAGT
1 AAAATAAATAAAAATAAAGT
28371592 AA
1 AA
28371594 GTTTAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 9 0.45
21 4 0.20
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (20 bp):
AAAATAAATAAAAATAAAGT
Found at i:28380629 original size:14 final size:14
Alignment explanation
Indices: 28380598--28380636 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
28380588 ACGAGTCTTC
28380598 AAAAATAAATAGAAAT
1 AAAAATAAA-A-AAAT
*
28380614 AAAAGTAAAAAAAT
1 AAAAATAAAAAAAT
28380628 AAAAATAAA
1 AAAAATAAA
28380637 GCGAGTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 1 0.05
16 8 0.38
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (14 bp):
AAAAATAAAAAAAT
Found at i:28392786 original size:4 final size:4
Alignment explanation
Indices: 28392779--28392809 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
28392769 ATAAACGAAC
*
28392779 GAAT GAAT GAAT GGAT GAAT GAAT GAAT GAA
1 GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAA
28392810 ATTGGGGCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.23
Consensus pattern (4 bp):
GAAT
Found at i:28399655 original size:50 final size:49
Alignment explanation
Indices: 28399545--28399720 Score: 181
Period size: 50 Copynumber: 3.5 Consensus size: 49
28399535 CTGGTACGCA
* * * * ** *
28399545 TAGTAGCCTGCACATAGTACTATACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACCATCCGATACACG
*
28399594 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AACCATCCGATACACG
**** * * * *
28399644 TAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAACCATCCGATACACG
28399695 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
28399721 TGCGACCTCA
Statistics
Matches: 108, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
49 29 0.27
50 43 0.40
51 35 0.32
52 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAACCATCCGATACACG
Found at i:28399728 original size:101 final size:99
Alignment explanation
Indices: 28399545--28399728 Score: 251
Period size: 101 Copynumber: 1.8 Consensus size: 99
28399535 CTGGTACGCA
* * *
28399545 TAGTAGCCTGCACATAGTACTATACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACATAGTACTACACACGCGACCAATTATCCGGTACACATAGTAGCCTGCACTTA
*
28399610 GTACTACACACGTGACCTAACCATCTGATACACG
66 GTACTACACACGCGACCTAACCATCTGATACACG
* * * * * *
28399644 TAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACATAGTACTACACACGCGA-C-CAATTATCCGGTACACATAGTAGCCTGCACT
*
28399709 TAGTACTACACATGCGACCT
64 TAGTACTACACACGCGACCT
28399729 CACAATAGAT
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
99 27 0.38
100 1 0.01
101 44 0.61
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTGCACATAGTACTACACACGCGACCAATTATCCGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCTAACCATCTGATACACG
Found at i:28404610 original size:40 final size:39
Alignment explanation
Indices: 28404573--28404757 Score: 232
Period size: 40 Copynumber: 4.6 Consensus size: 39
28404563 GCTACTCGTT
*
28404573 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTA-CCCGGATT-TAGTAACTCGCA
28404613 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTT-ACCCGGATTTAGTAACTCGCA
28404653 CAAATGCCTTCGGGACTTACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTACCCGGATTTAGTAACTCGCA
* * * * *
28404692 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTA-CCCGGATTTAGTAAC-TCGCA
28404733 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTA-CCCGGA
28404758 CATCATTCAA
Statistics
Matches: 132, Mismatches: 7, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
38 3 0.02
39 36 0.27
40 79 0.60
41 14 0.11
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTACCCGGATTTAGTAACTCGCA
Found at i:28404688 original size:79 final size:82
Alignment explanation
Indices: 28404573--28404757 Score: 256
Period size: 79 Copynumber: 2.3 Consensus size: 82
28404563 GCTACTCGTT
*
28404573 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
28404636 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
**
28404653 CAAATGCCTTCGGGACTTA-CCCGGATT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
28404716 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
28404733 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28404758 CATCATTCAA
Statistics
Matches: 94, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
78 3 0.03
79 57 0.61
80 34 0.36
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:28412660 original size:40 final size:40
Alignment explanation
Indices: 28412597--28412779 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
28412587 AGCTACTCTT
*
28412597 CAAATGCC-TCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
28412636 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
28412676 CAAATGCCTTCAGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * *
28412716 CAAATGCCTTC-GGATCTT-GTCCGGATAT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
28412755 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28412780 CATCATTCAA
Statistics
Matches: 129, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
38 13 0.10
39 35 0.27
40 79 0.61
41 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:28426091 original size:46 final size:46
Alignment explanation
Indices: 28426041--28426213 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
28426031 TGGTTGAGCA
*
28426041 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
28426087 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* * *
28426134 TCCGAACTCATTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
28426180 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
28426214 GGGGCGGGTT
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 60 0.57
47 28 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:28426197 original size:93 final size:93
Alignment explanation
Indices: 28426038--28426208 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
28426028 GGATGGTTGA
* * *
28426038 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
28426103 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
28426131 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
28426196 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
28426209 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:28426473 original size:19 final size:20
Alignment explanation
Indices: 28426436--28426473 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
28426426 ATAAGGTGGT
28426436 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
28426456 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
28426474 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:28428884 original size:28 final size:28
Alignment explanation
Indices: 28428847--28428948 Score: 168
Period size: 28 Copynumber: 3.6 Consensus size: 28
28428837 TTTAAATTGC
*
28428847 ATAGCACTAAGTGTGCAAGTTTGATTAT
1 ATAGCACTAAGTGTGCGAGTTTGATTAT
28428875 ATAGCACTAAGTGTGCGAGTTTGATTAT
1 ATAGCACTAAGTGTGCGAGTTTGATTAT
*
28428903 GTAAGCACTAAGTGTGCGAGTTTGATTAT
1 AT-AGCACTAAGTGTGCGAGTTTGATTAT
*
28428932 ATAACACTAAGTGTGCG
1 ATAGCACTAAGTGTGCG
28428949 GACTTACTAT
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
28 42 0.61
29 27 0.39
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (28 bp):
ATAGCACTAAGTGTGCGAGTTTGATTAT
Found at i:28430616 original size:41 final size:41
Alignment explanation
Indices: 28430559--28430654 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
28430549 GGGGTGTTAC
*
28430559 ATCTGCTGTAGCTTCGATTAATCCACTAAAACTTCAAGGAG
1 ATCTGCTGTAGCTTCGATTAATCCAATAAAACTTCAAGGAG
*
28430600 ATCTGCTGTAGCTTCGATTAATCCAATGAAACTTCAAGGAG
1 ATCTGCTGTAGCTTCGATTAATCCAATAAAACTTCAAGGAG
*
28430641 ATCTGCTGTGGCTT
1 ATCTGCTGTAGCTT
28430655 TTAGCTGCTC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (41 bp):
ATCTGCTGTAGCTTCGATTAATCCAATAAAACTTCAAGGAG
Found at i:28430897 original size:87 final size:87
Alignment explanation
Indices: 28430701--28431044 Score: 440
Period size: 87 Copynumber: 4.0 Consensus size: 87
28430691 TGATTTTCAA
* * ** ** *
28430701 CCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTCATCAGT-GATCTGTTTCCCTACTGCTTAG
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCA-CCTTCAATCTGTTTCCCTACTGCTTAG
* * * *
28430765 GTGTTTAAGATCTTGTAAAATCAG
65 GGGGTTAAGATC-TGTAAATTTAG
* * * *
28430789 CCTGTTACCCTACTACTTAGGGGTTTAAGGCTCATCGCCTTCGATCTGTTTCCCTACTGCTTAGG
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCACCTTCAATCTGTTTCCCTACTGCTTAGG
28430854 GGGTTAAGATCTGTAAATTTAG
66 GGGTTAAGATCTGTAAATTTAG
* * * *
28430876 TCTGTTACCCTACTGCTTAGGGTTTTAAGACTCATCATCTTCAATCTGCTTCCCTACTGCTTAGG
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCACCTTCAATCTGTTTCCCTACTGCTTAGG
* * *
28430941 GGGTTGAGGTCTATAAATTTAG
66 GGGTTAAGATCTGTAAATTTAG
*
28430963 CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCATCTTCAATCTGTTTCCCT-CTGCTTAGG
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCACCTTCAATCTGTTTCCCTACTGCTTAGG
*
28431027 GGGTTGAGATCTGTAAAT
66 GGGTTAAGATCTGTAAAT
28431045 CTTCAATCTG
Statistics
Matches: 228, Mismatches: 27, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
86 25 0.11
87 139 0.61
88 64 0.28
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (87 bp):
CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCACCTTCAATCTGTTTCCCTACTGCTTAGG
GGGTTAAGATCTGTAAATTTAG
Found at i:28431047 original size:44 final size:44
Alignment explanation
Indices: 28430696--28431054 Score: 213
Period size: 44 Copynumber: 8.2 Consensus size: 44
28430686 ATATTTGATT
* * * *
28430696 TTCAACCTGTTACCCTACTGCTTAGGGGGTTAAG-GCTT--GTC
1 TTCAATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTAAATC
* * *
28430737 ATCAGTGATCTGTTTCCCTACTGCTTAGGTGTTTAAGATCTTGTAAA--
1 TTCA---ATCTGTTTCCCTACTGCTTAGGGGGTTAAGATC-T-TAAATC
* ** * * * * * ***
28430784 ATCAGCCTGTTACCCTACTACTTAGGGGTTTAAG-GCTCATCGCC
1 TTCAATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTA-AATC
*
28430828 TTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAAT-
1 TTCAATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCT-TAAATC
* * ** * *
28430872 TT-AGTCTGTTACCCTACTGCTTAGGGTTTTAAGA-CTCATCATC
1 TTCAATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTA-AATC
* * *
28430915 TTCAATCTGCTTCCCTACTGCTTAGGGGGTTGAGGTCTATAAAT-
1 TTCAATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCT-TAAATC
** * * * *
28430959 TT-AGCCTGTTACCCTACTGCTTAGGGGTTTAAGA-CTCATCATC
1 TTCAATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTA-AATC
*
28431002 TTCAATCTGTTTCCCT-CTGCTTAGGGGGTTGAGATCTGTAAATC
1 TTCAATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCT-TAAATC
28431046 TTCAATCTG
1 TTCAATCTG
28431055 CTTCACTGCA
Statistics
Matches: 235, Mismatches: 60, Indels: 43
0.70 0.18 0.13
Matches are distributed among these distances:
41 6 0.03
42 9 0.04
43 73 0.31
44 131 0.56
45 8 0.03
46 3 0.01
47 5 0.02
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (44 bp):
TTCAATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTAAATC
Found at i:28431291 original size:88 final size:87
Alignment explanation
Indices: 28431148--28431307 Score: 239
Period size: 88 Copynumber: 1.8 Consensus size: 87
28431138 CAGCCTATTA
* * * * *
28431148 CCCTACTACTTAGGGGGTTAAGGTCTGTAAATTTGGCTTGTTACCCTATTGCTTAGGGGGTTAAA
1 CCCTACTACTTAGGGGGATAAGATCTATAAATTTAGCTTGTTACCCTACTGCTTAGGGGGTTAAA
28431213 GCTCATTATTTTCGATCTGTTT
66 GCTCATTATTTTCGATCTGTTT
* * *
28431235 CCCTACTGCTTAGGGTGATAAGATCTATGAACTTTAGCTTGTTACCCTACTGCTTAGGGGGTTAA
1 CCCTACTACTTAGGGGGATAAGATCTAT-AAATTTAGCTTGTTACCCTACTGCTTAGGGGGTTAA
28431300 AGCTCATT
65 AGCTCATT
28431308 GCCTACGGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
87 23 0.36
88 41 0.64
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (87 bp):
CCCTACTACTTAGGGGGATAAGATCTATAAATTTAGCTTGTTACCCTACTGCTTAGGGGGTTAAA
GCTCATTATTTTCGATCTGTTT
Found at i:28437690 original size:29 final size:28
Alignment explanation
Indices: 28437647--28437770 Score: 124
Period size: 28 Copynumber: 4.4 Consensus size: 28
28437637 AGATTGGCAG
* *
28437647 TAAGTGTGCGGGTTTAAATTGCATAGCAC
1 TAAGTGTGCGAGTTT-AATTGTATAGCAC
* * *
28437676 TAAGTGTGCAAGTTTGATTATATAGCAC
1 TAAGTGTGCGAGTTTAATTGTATAGCAC
*
28437704 TAAGTGTGCGAGTTTGATTATGTA-AGCAC
1 TAAGTGTGCGAGTTT-AAT-TGTATAGCAC
* * * *
28437733 TAAGTGTGCGAGTTTGATTATATAACAT
1 TAAGTGTGCGAGTTTAATTGTATAGCAC
28437761 TAAGTGTGCG
1 TAAGTGTGCG
28437771 GACTTACTAT
Statistics
Matches: 78, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
27 3 0.04
28 38 0.49
29 34 0.44
30 3 0.04
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.35
Consensus pattern (28 bp):
TAAGTGTGCGAGTTTAATTGTATAGCAC
Found at i:28437709 original size:28 final size:28
Alignment explanation
Indices: 28437669--28437770 Score: 159
Period size: 28 Copynumber: 3.6 Consensus size: 28
28437659 TTTAAATTGC
*
28437669 ATAGCACTAAGTGTGCAAGTTTGATTAT
1 ATAGCACTAAGTGTGCGAGTTTGATTAT
28437697 ATAGCACTAAGTGTGCGAGTTTGATTAT
1 ATAGCACTAAGTGTGCGAGTTTGATTAT
*
28437725 GTAAGCACTAAGTGTGCGAGTTTGATTAT
1 AT-AGCACTAAGTGTGCGAGTTTGATTAT
* *
28437754 ATAACATTAAGTGTGCG
1 ATAGCACTAAGTGTGCG
28437771 GACTTACTAT
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
28 41 0.60
29 27 0.40
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (28 bp):
ATAGCACTAAGTGTGCGAGTTTGATTAT
Found at i:28439438 original size:41 final size:41
Alignment explanation
Indices: 28439381--28439476 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
28439371 GGGGTGTTAC
*
28439381 ATCTGCTGTAGCTTCGATTAATCCACTAAAACTTCAAGGAG
1 ATCTGCTGTAGCTTCGATTAATCCAATAAAACTTCAAGGAG
*
28439422 ATCTGCTGTAGCTTCGATTAATCCAATGAAACTTCAAGGAG
1 ATCTGCTGTAGCTTCGATTAATCCAATAAAACTTCAAGGAG
*
28439463 ATCTGCTGTGGCTT
1 ATCTGCTGTAGCTT
28439477 TTAGCTGCTC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (41 bp):
ATCTGCTGTAGCTTCGATTAATCCAATAAAACTTCAAGGAG
Found at i:28439578 original size:44 final size:43
Alignment explanation
Indices: 28439524--28439854 Score: 149
Period size: 44 Copynumber: 7.6 Consensus size: 43
28439514 GATTTTCAAC
28439524 CTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTCATCAGTGAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTCATCA-TGAT
* * * * * *
28439568 CTGTTTCCCTACTGCTTAGGTGTTTAAGATCTTGTAAAATCA-G-C
1 CTGTTACCCTACTGCTTAGGGGGTTAAG-GCTTGT--CATCATGAT
* * ** ** *
28439612 CTGTTACCCTACTACTTAGGGGTTTAAGGCTCATCGCCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTCATCAT-GAT
* * * *
28439656 CTGTTTCCCTACTGCTTAGGGGGTTAA-GATCTGT-A-AATTTAGT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGGCT-TGTCATCA-TGA-T
** * ** * *
28439699 CTGTTACCCTACTGCTTAGGGTTTTAAGACTCATCATCTTCAAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTCATCAT-GAT
* * * * *
28439743 CTGCTT-CCCTACTGCTTAGGGGGTTGAGG--TCT-ATAAATTTAGC
1 CTG-TTACCCTACTGCTTAGGGGGTTAAGGCTTGTCAT-CA-TGA-T
* * ** * *
28439786 CTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCATCTTCAAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTCATCAT-GAT
*
28439830 CTGTTTCCCTACTGCTTAGGGGGTT
1 CTGTTACCCTACTGCTTAGGGGGTT
28439855 GAGATCTGTA
Statistics
Matches: 207, Mismatches: 58, Indels: 44
0.67 0.19 0.14
Matches are distributed among these distances:
41 3 0.01
42 5 0.02
43 57 0.28
44 125 0.60
45 11 0.05
46 2 0.01
47 4 0.02
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (43 bp):
CTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTCATCATGAT
Found at i:28439719 original size:87 final size:87
Alignment explanation
Indices: 28439523--28439867 Score: 449
Period size: 87 Copynumber: 4.0 Consensus size: 87
28439513 TGATTTTCAA
* * ** ** *
28439523 CCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTCATCAGT-GATCTGTTTCCCTACTGCTTAG
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCA-CCTTCAATCTGTTTCCCTACTGCTTAG
* * * *
28439587 GTGTTTAAGATCTTGTAAAATCAG
65 GGGGTTAAGATC-TGTAAATTTAG
* * * *
28439611 CCTGTTACCCTACTACTTAGGGGTTTAAGGCTCATCGCCTTCGATCTGTTTCCCTACTGCTTAGG
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCACCTTCAATCTGTTTCCCTACTGCTTAGG
28439676 GGGTTAAGATCTGTAAATTTAG
66 GGGTTAAGATCTGTAAATTTAG
* * * *
28439698 TCTGTTACCCTACTGCTTAGGGTTTTAAGACTCATCATCTTCAATCTGCTTCCCTACTGCTTAGG
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCACCTTCAATCTGTTTCCCTACTGCTTAGG
* * *
28439763 GGGTTGAGGTCTATAAATTTAG
66 GGGTTAAGATCTGTAAATTTAG
*
28439785 CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCATCTTCAATCTGTTTCCCTACTGCTTAGG
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCACCTTCAATCTGTTTCCCTACTGCTTAGG
*
28439850 GGGTTGAGATCTGTAAAT
66 GGGTTAAGATCTGTAAAT
28439868 CTTCAATCTG
Statistics
Matches: 229, Mismatches: 27, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
87 165 0.72
88 64 0.28
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (87 bp):
CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCACCTTCAATCTGTTTCCCTACTGCTTAGG
GGGTTAAGATCTGTAAATTTAG
Found at i:28440114 original size:88 final size:86
Alignment explanation
Indices: 28439965--28440175 Score: 262
Period size: 88 Copynumber: 2.4 Consensus size: 86
28439955 AATTTTCAGC
* * * * *
28439965 CTATTACCCTACTACTTAGGGGGTTAAGGTCTGT-AAATTTGGCTTGTTACCCTATTGCTTAGGG
1 CTATTCCCCTACTGCTTA-GGGG-TAAGATCTGTGAAATTTAGCTTGTTACCCTACTGCTTAGGG
**
28440029 GGTTAAAGCTCATTATTTTCGAT
64 GGTTAAAGCTCATTACCTTCGAT
* * * *
28440052 CTGTTTCCCTACTGCTTAGGGTGATAAGATCTATGAACTTTAGCTTGTTACCCTACTGCTTAGGG
1 CTATTCCCCTACTGCTTAGGG-G-TAAGATCTGTGAAATTTAGCTTGTTACCCTACTGCTTAGGG
*
28440117 GGTTAAAGCTCATTGCCTTCGAT
64 GGTTAAAGCTCATTACCTTCGAT
28440140 CTATTCCCCTACTGCTTATGGGGTAAGATCTGTGAA
1 CTATTCCCCTACTGCTTA-GGGGTAAGATCTGTGAA
28440176 TTCACTAATT
Statistics
Matches: 106, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
86 3 0.03
87 36 0.34
88 64 0.60
89 3 0.03
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (86 bp):
CTATTCCCCTACTGCTTAGGGGTAAGATCTGTGAAATTTAGCTTGTTACCCTACTGCTTAGGGGG
TTAAAGCTCATTACCTTCGAT
Found at i:28440150 original size:44 final size:44
Alignment explanation
Indices: 28440009--28440163 Score: 138
Period size: 44 Copynumber: 3.5 Consensus size: 44
28439999 AAATTTGGCT
* *
28440009 TGTTACCCTATTGCTTAGGGGGTTAAAGCTCATT-ATTTTCGATC
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCTCATTGA-CTTCGATC
* * * * * *
28440053 TGTTTCCCTACTGCTTAGGGTGAT-AAGATC-TATGAACTT-TAGC
1 TGTTACCCTACTGCTTAGGGGGTTAAAGCTCAT-TG-ACTTCGATC
*
28440096 TTGTTACCCTACTGCTTAGGGGGTTAAAGCTCATTGCCTTCGATC
1 -TGTTACCCTACTGCTTAGGGGGTTAAAGCTCATTGACTTCGATC
* * *
28440141 TATTCCCCTACTGCTTATGGGGT
1 TGTTACCCTACTGCTTAGGGGGT
28440164 AAGATCTGTG
Statistics
Matches: 86, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
42 1 0.01
43 8 0.09
44 66 0.77
45 10 0.12
46 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (44 bp):
TGTTACCCTACTGCTTAGGGGGTTAAAGCTCATTGACTTCGATC
Found at i:28448242 original size:19 final size:19
Alignment explanation
Indices: 28448200--28448246 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
28448190 AGTGAAATTT
*
28448200 TAATGCAAATGTTTCAATG
1 TAATGCAAATGTTGCAATG
*
28448219 TAATGCAAATGTATGGAATG
1 TAATGCAAATGT-TGCAATG
28448239 -AATGCAAA
1 TAATGCAAA
28448247 AGAAAGGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.30
Consensus pattern (19 bp):
TAATGCAAATGTTGCAATG
Found at i:28451076 original size:3 final size:3
Alignment explanation
Indices: 28451068--28451145 Score: 56
Period size: 3 Copynumber: 25.3 Consensus size: 3
28451058 TATATAGAAT
28451068 ATA ATA ATA AT- ATAA ATA ATA ATA TATA CATGA GA-A ATA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA -ATA -AT-A -ATA ATA ATA ATA
* *
28451113 ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA A
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA A
28451146 AAAAATAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
2 7 0.11
3 43 0.70
4 9 0.15
5 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:28451087 original size:12 final size:12
Alignment explanation
Indices: 28451065--28451146 Score: 71
Period size: 12 Copynumber: 6.7 Consensus size: 12
28451055 GCATATATAG
28451065 AATAT-AATAAT
1 AATATAAATAAT
28451076 AATATAAATAAT
1 AATATAAATAAT
28451088 AATATATACATGAGA-
1 AATATA-A-AT-A-AT
28451103 AATA-ATAATAAT
1 AATATA-AATAAT
28451115 AATATAAATAAT
1 AATATAAATAAT
* *
28451127 AGTAAAAATAAT
1 AATATAAATAAT
*
28451139 AAAATAAA
1 AATATAAA
28451147 AAAATAAAAC
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
11 6 0.10
12 38 0.64
13 4 0.07
14 5 0.08
15 5 0.08
16 1 0.02
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (12 bp):
AATATAAATAAT
Found at i:28451089 original size:18 final size:18
Alignment explanation
Indices: 28451059--28451141 Score: 87
Period size: 18 Copynumber: 4.4 Consensus size: 18
28451049 GAGAGGGCAT
28451059 ATATAGAAT-ATAATAATA
1 ATATA-AATAATAATAATA
28451077 ATATAAATAATAATATATA
1 ATATAAATAATAATA-ATA
*
28451096 CATGAGAAATAATAATAATA
1 -AT-ATAAATAATAATAATA
* *
28451116 ATATAAATAATAGTAAAA
1 ATATAAATAATAATAATA
28451134 ATAATAAA
1 AT-ATAAA
28451142 ATAAAAAAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
17 3 0.05
18 26 0.46
19 10 0.18
20 5 0.09
21 12 0.21
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.30
Consensus pattern (18 bp):
ATATAAATAATAATAATA
Found at i:28461861 original size:46 final size:45
Alignment explanation
Indices: 28461811--28461986 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 45
28461801 TGGTTGAGCA
28461811 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGGATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGGA-G
* * *
28461857 TCCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATGTAACTAGGCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C--GG-AG
*
28461904 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGGA-G
*
28461950 CCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28461987 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 8, Indels: 22
0.79 0.06 0.16
Matches are distributed among these distances:
43 4 0.04
44 1 0.01
45 3 0.03
46 65 0.59
47 29 0.26
48 4 0.04
49 1 0.01
50 4 0.04
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGGAG
Found at i:28461967 original size:93 final size:93
Alignment explanation
Indices: 28461808--28461978 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
28461798 GGATGGTTGA
* * *
28461808 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGGATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
28461873 TGAGTCTGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
28461901 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28461966 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
28461979 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:28474597 original size:55 final size:55
Alignment explanation
Indices: 28474507--28474626 Score: 134
Period size: 55 Copynumber: 2.2 Consensus size: 55
28474497 TATATGGGCC
* *
28474507 CACGCCCATGTTAATTTAACAGGTTCGACCACGGGTGCTAGACACGAGCATGTCG
1 CACGCCCGTGTTAATTTAACAGGTTCGACCACGGGTGCAAGACACGAGCATGTCG
* * * * * * *
28474562 CACGCCCGTGTTAATTTGATAGGTTC-AGCCGCGGGTTCAAGGCACGGGCGTGTCG
1 CACGCCCGTGTTAATTTAACAGGTTCGA-CCACGGGTGCAAGACACGAGCATGTCG
*
28474617 CACACCCGTG
1 CACGCCCGTG
28474627 CTGTTTTGGT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 1 0.02
55 53 0.98
ACGTcount: A:0.21, C:0.28, G:0.29, T:0.22
Consensus pattern (55 bp):
CACGCCCGTGTTAATTTAACAGGTTCGACCACGGGTGCAAGACACGAGCATGTCG
Found at i:28481498 original size:29 final size:29
Alignment explanation
Indices: 28481403--28481490 Score: 131
Period size: 29 Copynumber: 3.0 Consensus size: 29
28481393 TGGCCCATCT
* *
28481403 CATTCATATGGCCCATCAGGCCCAATTCA
1 CATTCATATGGCCCATTAGGCCCAAATCA
*
28481432 CATTCATATGGCCCATTAGGCCCAAAACA
1 CATTCATATGGCCCATTAGGCCCAAATCA
* *
28481461 TATTCATATGGCCCATTAGGCCTAAATCA
1 CATTCATATGGCCCATTAGGCCCAAATCA
28481490 C
1 C
28481491 CTTTATATTC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.31, C:0.31, G:0.14, T:0.25
Consensus pattern (29 bp):
CATTCATATGGCCCATTAGGCCCAAATCA
Found at i:28483013 original size:16 final size:16
Alignment explanation
Indices: 28482988--28483019 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28482978 AAATTCAAGT
28482988 TTTCGAGATTTTTGGG
1 TTTCGAGATTTTTGGG
*
28483004 TTTCGGGATTTTTGGG
1 TTTCGAGATTTTTGGG
28483020 GCGTTACAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.06, G:0.34, T:0.50
Consensus pattern (16 bp):
TTTCGAGATTTTTGGG
Found at i:28483058 original size:10 final size:10
Alignment explanation
Indices: 28483043--28483074 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
28483033 AATGTCCAAA
28483043 ATATGGATAG
1 ATATGGATAG
28483053 ATATGGATAG
1 ATATGGATAG
28483063 ATATGGATAG
1 ATATGGATAG
28483073 AT
1 AT
28483075 CATGTTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (10 bp):
ATATGGATAG
Found at i:28489409 original size:68 final size:68
Alignment explanation
Indices: 28489272--28489428 Score: 174
Period size: 68 Copynumber: 2.3 Consensus size: 68
28489262 TTAACTGTGA
* * * * *
28489272 AATC-AACAGATTCGGACAGCTACATTAACTAAATAAAACAGCATATATGGTATTGCATCGAACA
1 AATCTAACACATTCGGACAGCTACATTAACCAAATAAAACAACATAAATGATATTGCATCGAACA
28489336 ATG
66 ATG
* * * * * *
28489339 AATTTAACACATTCGGATAGCTACATTTACCAAATAAAACAACATAAATGATGA-TGCTTTGAAT
1 AATCTAACACATTCGGACAGCTACATTAACCAAATAAAACAACATAAATGAT-ATTGCATCGAAC
*
28489403 AGTG
65 AATG
*
28489407 AATCTAACACATTCGAACAGCT
1 AATCTAACACATTCGGACAGCT
28489429 TAATTTTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
67 3 0.04
68 69 0.95
69 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (68 bp):
AATCTAACACATTCGGACAGCTACATTAACCAAATAAAACAACATAAATGATATTGCATCGAACA
ATG
Found at i:28491817 original size:57 final size:58
Alignment explanation
Indices: 28491748--28491886 Score: 226
Period size: 58 Copynumber: 2.4 Consensus size: 58
28491738 GTGCCCACTG
*
28491748 ACCGATCTTGCACACATAGTGCTCGGTTGAA-GAACTCGCACACACAGTGCCTCAATA
1 ACCGATCTTGCACACATAGTGCTCGGTTAAAGGAACTCGCACACACAGTGCCTCAATA
* *
28491805 ACCGATCTTGCACACATAGTGCTCGGTTAAAGGAATTCGCACACACAGTGCCTCAATT
1 ACCGATCTTGCACACATAGTGCTCGGTTAAAGGAACTCGCACACACAGTGCCTCAATA
* *
28491863 ACCGATCTCGCACACATAATGCTC
1 ACCGATCTTGCACACATAGTGCTC
28491887 ATATTCATTC
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
57 30 0.39
58 46 0.61
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.22
Consensus pattern (58 bp):
ACCGATCTTGCACACATAGTGCTCGGTTAAAGGAACTCGCACACACAGTGCCTCAATA
Found at i:28491819 original size:29 final size:29
Alignment explanation
Indices: 28491782--28491878 Score: 99
Period size: 29 Copynumber: 3.3 Consensus size: 29
28491772 GGTTGAAGAA
28491782 CTCGCACACACAGTGCCTCAATAACCGAT
1 CTCGCACACACAGTGCCTCAATAACCGAT
* * ** **
28491811 CTTGCACACATAGTG-CTCGGTTAAAGGAAT
1 CTCGCACACACAGTGCCTC-AATAACCG-AT
*
28491841 -TCGCACACACAGTGCCTCAATTACCGAT
1 CTCGCACACACAGTGCCTCAATAACCGAT
28491869 CTCGCACACA
1 CTCGCACACA
28491879 TAATGCTCAT
Statistics
Matches: 51, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
28 5 0.10
29 41 0.80
30 5 0.10
ACGTcount: A:0.30, C:0.33, G:0.16, T:0.21
Consensus pattern (29 bp):
CTCGCACACACAGTGCCTCAATAACCGAT
Found at i:28492093 original size:43 final size:43
Alignment explanation
Indices: 28492032--28492147 Score: 178
Period size: 43 Copynumber: 2.7 Consensus size: 43
28492022 AGCATTATGT
* **
28492032 TAGGCACGAAGACCCGAATACACATCATTGGCACGAAGCCTAC
1 TAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTAC
* *
28492075 TAGGCACGAAGGCCCGAATACACATCACCGGTACGAAGCCTGC
1 TAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTAC
*
28492118 TAGGCACAAAGGCCCGAATACACATCACCG
1 TAGGCACGAAGGCCCGAATACACATCACCG
28492148 AGTTTCATGC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 67 1.00
ACGTcount: A:0.34, C:0.32, G:0.22, T:0.12
Consensus pattern (43 bp):
TAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTAC
Found at i:28494995 original size:68 final size:68
Alignment explanation
Indices: 28494858--28495014 Score: 201
Period size: 68 Copynumber: 2.3 Consensus size: 68
28494848 TTAACTGTGA
* * * *
28494858 AATC-AACAGATTCGGACAGCTACATTTACTAAATAAAACAGCATATATGGTAGTGCATCGAACA
1 AATCTAACACATTCGGACAGCTACATTTACCAAATAAAACAGCATAAATGATAGTGCATCGAACA
28494922 ATG
66 ATG
* * * *
28494925 AATTTAACACATTCGGACAGCTACATTTACCAAATAAAACAGCATAAATGAT-GATGCTTTGAAT
1 AATCTAACACATTCGGACAGCTACATTTACCAAATAAAACAGCATAAATGATAG-TGCATCGAAC
*
28494989 AGTG
65 AATG
*
28494993 AATCTAACACATTCGAACAGCT
1 AATCTAACACATTCGGACAGCT
28495015 TAATTTTAAG
Statistics
Matches: 77, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
67 4 0.05
68 73 0.95
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.25
Consensus pattern (68 bp):
AATCTAACACATTCGGACAGCTACATTTACCAAATAAAACAGCATAAATGATAGTGCATCGAACA
ATG
Found at i:28497407 original size:29 final size:28
Alignment explanation
Indices: 28497370--28497466 Score: 90
Period size: 29 Copynumber: 3.4 Consensus size: 28
28497360 GGTTGAAGAA
28497370 CTCGCACACACAGTGCCTCAACTACCAAT
1 CTCGCACACACAGTGCCTCAA-TACCAAT
* * **
28497399 CTCGCACACATAGTGCTCGGTTAA-AGGAAT
1 CTCGCACACACAGTGC-C--TCAATACCAAT
*
28497429 -TCACACACACAGTGCCTCAATTACCAAT
1 CTCGCACACACAGTGCCTCAA-TACCAAT
28497457 CTCGCACACA
1 CTCGCACACA
28497467 TAATGCTCAT
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
26 3 0.06
28 5 0.10
29 36 0.69
30 5 0.10
32 3 0.06
ACGTcount: A:0.32, C:0.35, G:0.13, T:0.20
Consensus pattern (28 bp):
CTCGCACACACAGTGCCTCAATACCAAT
Found at i:28497454 original size:58 final size:57
Alignment explanation
Indices: 28497314--28497474 Score: 209
Period size: 58 Copynumber: 2.8 Consensus size: 57
28497304 TGAATCTCAT
** * * *
28497314 TTCACACACTTAGTGCC-C-ATTGACCGATCTTGCACACATAGTGCTCGGTTGAAGAA
1 TTCACACACACAGTGCCTCAATT-ACCAATCTCGCACACATAGTGCTCGGTTAAAGAA
* * *
28497370 CTCGCACACACAGTGCCTCAACTACCAATCTCGCACACATAGTGCTCGGTTAAAGGAA
1 TTCACACACACAGTGCCTCAATTACCAATCTCGCACACATAGTGCTCGGTTAAA-GAA
*
28497428 TTCACACACACAGTGCCTCAATTACCAATCTCGCACACATAATGCTC
1 TTCACACACACAGTGCCTCAATTACCAATCTCGCACACATAGTGCTC
28497475 ATATTCATTC
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
56 13 0.14
57 29 0.32
58 48 0.53
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.23
Consensus pattern (57 bp):
TTCACACACACAGTGCCTCAATTACCAATCTCGCACACATAGTGCTCGGTTAAAGAA
Found at i:28497667 original size:43 final size:43
Alignment explanation
Indices: 28497619--28497735 Score: 198
Period size: 43 Copynumber: 2.7 Consensus size: 43
28497609 CAGCATTATG
* *
28497619 CTAGGCACGAAGACCCGAATACACATCACTGGCACGAAGCCTA
1 CTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTA
*
28497662 CTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTG
1 CTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTA
*
28497705 CTAGGCACAAAGGCCCGAATACACATCACCG
1 CTAGGCACGAAGGCCCGAATACACATCACCG
28497736 AGTTTCATGC
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.33, C:0.34, G:0.22, T:0.10
Consensus pattern (43 bp):
CTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTA
Found at i:28500298 original size:40 final size:40
Alignment explanation
Indices: 28500248--28500432 Score: 193
Period size: 40 Copynumber: 4.7 Consensus size: 40
28500238 TCGAGTGATG
* *
28500248 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTG-TAAGTTACTATA
* *
28500288 TCCGGACTAAGAT-CCGAAGGCATTTGTGTGAGTTACTA-A
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGTAAGTTACTATA
*
28500327 TTCCGGGCTAAG-CCCGAAGGCA-TTG-GTACGAGTTACTAAA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGTA--AGTTACTATA
* **
28500367 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGTAAGTTACTATA
* *
28500407 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28500433 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 13, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
37 2 0.02
38 3 0.02
39 28 0.23
40 78 0.64
41 10 0.08
42 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGTAAGTTACTATA
Found at i:28500384 original size:79 final size:79
Alignment explanation
Indices: 28500301--28500455 Score: 208
Period size: 79 Copynumber: 2.0 Consensus size: 79
28500291 GGACTAAGAT
* * *
28500301 CCGAAGGCATTTGTGTGAGTTACTA-ATTCCGGGCTAAG-CCCGAAGGCATTGGTACGAGTTA-C
1 CCGAAGGCATTTGTGCGAGTTACTATA-ACCGGGCTAAGTCCCGAAGGCATTGGAACGAG-TAGC
28500363 TAAATCCGGGTTAAGTC
64 TAAATCC-GGTTAAGTC
* *
28500380 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTA
1 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTGGAACGAGTAGCTA
*
28500445 TATCCGGTTAA
66 AATCCGGTTAA
28500456 ATTCTGAAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
79 41 0.61
80 26 0.39
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTGGAACGAGTAGCTA
AATCCGGTTAAGTC
Found at i:28508400 original size:39 final size:41
Alignment explanation
Indices: 28508299--28508482 Score: 204
Period size: 40 Copynumber: 4.6 Consensus size: 41
28508289 TCGAATGATG
* * *
28508299 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAATA
*
28508339 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAATA
* *
28508379 TCCGGGCTAAG-CCCGAAGGCATTGGTACGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
* *
28508418 TCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
* *
28508458 ACC-GGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28508483 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
39 54 0.44
40 58 0.48
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
Found at i:28508489 original size:39 final size:38
Alignment explanation
Indices: 28508303--28508489 Score: 155
Period size: 39 Copynumber: 4.8 Consensus size: 38
28508293 ATGATGTCCG
* * * * *
28508303 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCC
1 GGCTAAGTCCCGAAGGCATTTGTAC-GAGTTACTA-AACC
* *
28508342 GGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAATTCC
1 GG-CTAAG-TCCCGAAGGCATTTGTACGAGTTACTAA-ACC
* *
28508382 GGGCTAAG-CCCGAAGGCATTGGTACGAGTTACTAAATCTG
1 -GGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAA-C-C
* *
28508422 GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
1 GGCTAAGTCCCGAAGGCATTTGTACGAGTTACTA-AACC
* *
28508461 GGCTATGTCCCGAAGGCATTTGAACGAGT
1 GGCTAAGTCCCGAAGGCATTTGTACGAGT
28508490 AGCTATATCC
Statistics
Matches: 123, Mismatches: 15, Indels: 20
0.78 0.09 0.13
Matches are distributed among these distances:
39 59 0.48
40 52 0.42
41 12 0.10
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (38 bp):
GGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAACC
Found at i:28511880 original size:67 final size:68
Alignment explanation
Indices: 28511752--28511900 Score: 169
Period size: 67 Copynumber: 2.2 Consensus size: 68
28511742 TTAACTGTGA
* * * * ** *
28511752 AATC-AACAGATTCAGACAGCTACATTTACTAAATAAAATAGCATATCTGGTAGTGCATTGAATA
1 AATCGAACACATTCGGATAGCTACATTTACCAAATAAAATAGCATAAATGATAGTGCATTGAATA
28511816 ATG
66 ATG
** *
28511819 AATTTAACACATTCGGATAGCTACA-TTACCAAATAAAATAGCATAAATGAT-GATGCTTTGAAT
1 AATCGAACACATTCGGATAGCTACATTTACCAAATAAAATAGCATAAATGATAG-TGCATTGAAT
*
28511882 AGTG
65 AATG
28511886 AATCGAACACATTCG
1 AATCGAACACATTCG
28511901 AACAGCTTAA
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
66 1 0.01
67 50 0.74
68 17 0.25
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (68 bp):
AATCGAACACATTCGGATAGCTACATTTACCAAATAAAATAGCATAAATGATAGTGCATTGAATA
ATG
Found at i:28514681 original size:11 final size:11
Alignment explanation
Indices: 28514665--28514690 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28514655 CGAAGCCCAC
28514665 ATCACAATAAT
1 ATCACAATAAT
28514676 ATCACAATAAT
1 ATCACAATAAT
28514687 ATCA
1 ATCA
28514691 TACATGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (11 bp):
ATCACAATAAT
Found at i:28515180 original size:27 final size:27
Alignment explanation
Indices: 28515150--28515224 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 27
28515140 GCAAAACAGT
*
28515150 CATTTTACCCTACAAGGGTATGTCAGC
1 CATTTTACACTACAAGGGTATGTCAGC
* * *
28515177 CATTTTACACTACAAGGGTATTTCGGT
1 CATTTTACACTACAAGGGTATGTCAGC
* *
28515204 AATTTTACACTATAAGGGTAT
1 CATTTTACACTACAAGGGTAT
28515225 TTCGATAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (27 bp):
CATTTTACACTACAAGGGTATGTCAGC
Found at i:28515225 original size:27 final size:26
Alignment explanation
Indices: 28515190--28515343 Score: 173
Period size: 27 Copynumber: 5.7 Consensus size: 26
28515180 TTTACACTAC
*
28515190 AAGGGTATTTCGGTAATTTTACACTAT
1 AAGGGTATTTCGGTAATTTTACA-AAT
*
28515217 AAGGGTATTTCGATAATTTTACAAAT
1 AAGGGTATTTCGGTAATTTTACAAAT
* *
28515243 CAGGGGTGTTTCGGTAATTTTACAAAT
1 -AAGGGTATTTCGGTAATTTTACAAAT
* *
28515270 CGAGGGTATTTCAGTAATTTTACAAAT
1 -AAGGGTATTTCGGTAATTTTACAAAT
* *
28515297 CGAGGGTATTTTGGTAATTTTACAAATT
1 -AAGGGTATTTCGGTAATTTTACAAA-T
* *
28515325 GAGGGTATTTTGGTAATTT
1 AAGGGTATTTCGGTAATTT
28515344 CTCTTTATTA
Statistics
Matches: 114, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
26 2 0.02
27 111 0.97
28 1 0.01
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.40
Consensus pattern (26 bp):
AAGGGTATTTCGGTAATTTTACAAAT
Found at i:28515236 original size:54 final size:54
Alignment explanation
Indices: 28515162--28515343 Score: 190
Period size: 54 Copynumber: 3.4 Consensus size: 54
28515152 TTTTACCCTA
* ** * *
28515162 CAAGGGTATGTCAGCCATTTTAC-ACTACAAGGGTATTTCGGTAATTTTACACTAT
1 CAAGGGTATTTCAGTAATTTTACAAAT-CAAGGGTATTTCGGTAATTTTACA-AAT
* *
28515217 -AAGGGTATTTC-GATAATTTTACAAATCAGGGGTGTTTCGGTAATTTTACAAAT
1 CAAGGGTATTTCAG-TAATTTTACAAATCAAGGGTATTTCGGTAATTTTACAAAT
* * *
28515270 CGAGGGTATTTCAGTAATTTTACAAATCGAGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTCAGTAATTTTACAAATCAAGGGTATTTCGGTAATTTTACAAAT
** **
28515324 TGAGGGTATTTTGGTAATTT
1 CAAGGGTATTTCAGTAATTT
28515344 CTCTTTATTA
Statistics
Matches: 108, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
53 3 0.03
54 102 0.94
55 3 0.03
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (54 bp):
CAAGGGTATTTCAGTAATTTTACAAATCAAGGGTATTTCGGTAATTTTACAAAT
Found at i:28515340 original size:81 final size:81
Alignment explanation
Indices: 28515191--28515343 Score: 202
Period size: 81 Copynumber: 1.9 Consensus size: 81
28515181 TTACACTACA
* * *
28515191 AGGGTATTTCGGTAATTTTACACTATAAGGGTATTTCGATAATTTTACAAATCAGGGGTGTTTCG
1 AGGGTATTTCAGTAATTTTACACAATAAGGGTATTTCGATAATTTTACAAATCAGGGGTATTTCG
28515256 GTAATTTTACAAATCG
66 GTAATTTTACAAATCG
* * * *
28515272 AGGGTATTTCAGTAATTTTACA-AATCGAGGGTATTTTGGTAATTTTACAAAT-TGAGGGTATTT
1 AGGGTATTTCAGTAATTTTACACAAT-AAGGGTATTTCGATAATTTTACAAATCAG-GGGTATTT
*
28515335 TGGTAATTT
64 CGGTAATTT
28515344 CTCTTTATTA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
80 3 0.05
81 59 0.95
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (81 bp):
AGGGTATTTCAGTAATTTTACACAATAAGGGTATTTCGATAATTTTACAAATCAGGGGTATTTCG
GTAATTTTACAAATCG
Found at i:28515714 original size:32 final size:32
Alignment explanation
Indices: 28515660--28515723 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
28515650 GGGCCCCTTT
* * *
28515660 AGGCCCAATCTCGCTCACATGGCCTATCAGGC
1 AGGCCCAATCACACTCACATGGCCCATCAGGC
* *
28515692 AGGCCCAATCACATTCATATGGCCCATCAGGC
1 AGGCCCAATCACACTCACATGGCCCATCAGGC
28515724 CCAACTACTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.25, C:0.36, G:0.20, T:0.19
Consensus pattern (32 bp):
AGGCCCAATCACACTCACATGGCCCATCAGGC
Found at i:28526328 original size:43 final size:42
Alignment explanation
Indices: 28526266--28526380 Score: 108
Period size: 42 Copynumber: 2.7 Consensus size: 42
28526256 TACAACGTCG
* * *
28526266 ATGTCCCGGAC-GTGGTCTTACATGTAATTCA-ATATTGATGCCT
1 ATGTCCCAGACAG-GGTCTTACA-GTAATTCAGATA-CGATGCCA
* ** *
28526309 CTGTCCCAGACAGGGTCTTACACAAAATCAGATACGATGCCA
1 ATGTCCCAGACAGGGTCTTACAGTAATTCAGATACGATGCCA
*
28526351 ATGTCCCAGACATGGTCTTACACGTAATTC
1 ATGTCCCAGACAGGGTCTTACA-GTAATTC
28526381 TCAAATCGAG
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
42 31 0.54
43 25 0.44
44 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (42 bp):
ATGTCCCAGACAGGGTCTTACAGTAATTCAGATACGATGCCA
Found at i:28528705 original size:20 final size:20
Alignment explanation
Indices: 28528680--28528717 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28528670 GTCACATATA
28528680 TCATGAACTCAGACCACAAC
1 TCATGAACTCAGACCACAAC
* *
28528700 TCATGAGCTCAGATCACA
1 TCATGAACTCAGACCACA
28528718 TAGTTCCTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.32, G:0.13, T:0.18
Consensus pattern (20 bp):
TCATGAACTCAGACCACAAC
Done.