Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 121 of 144
Found at i:28584886 original size:22 final size:20
Alignment explanation
Indices: 28584821--28584872 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
28584811 GAGAGAATTC
* * *
28584821 AAAAATATAATGAAATATTAA
1 AAAAATATGAGGAAATA-CAA
28584842 AAAAATATGAGGAAATACAA
1 AAAAATATGAGGAAATACAA
*
28584862 AAAATTATGAG
1 AAAAATATGAG
28584873 AGAATATCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.23
Consensus pattern (20 bp):
AAAAATATGAGGAAATACAA
Found at i:28586925 original size:29 final size:29
Alignment explanation
Indices: 28586891--28587085 Score: 146
Period size: 30 Copynumber: 6.6 Consensus size: 29
28586881 TAAATTGTCC
*
28586891 AAAATTATATATTAACCCT-AAACTTTTT
1 AAAATTATATTTTAACCCTAAAACTTTTT
* *
28586919 CAAAATTATTTTTTAACCCTAAAACTTTCT
1 -AAAATTATATTTTAACCCTAAAACTTTTT
* *
28586949 ATAAATTACATTTTGACCCCT-AAACTTTTGT
1 A-AAATTATATTTT-AACCCTAAAACTTTT-T
*
28586980 AAATTTAT-TTTTAA-CCTAAAACTTTTT
1 AAAATTATATTTTAACCCTAAAACTTTTT
* * *
28587007 ATAAATTACATTTTGACCCCTAAAAATTTTT
1 A-AAATTATATTTT-AACCCTAAAACTTTTT
* * * * *
28587038 GAAATTATCTTCTAACCCCCAAAACTTTCT
1 AAAATTATATTTTAA-CCCTAAAACTTTTT
* * *
28587068 AAAACTACATTTTTACCC
1 AAAATTATATTTTAACCC
28587086 CCAAGTTTTC
Statistics
Matches: 128, Mismatches: 28, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
27 5 0.04
28 14 0.11
29 30 0.23
30 60 0.47
31 19 0.15
ACGTcount: A:0.37, C:0.19, G:0.02, T:0.42
Consensus pattern (29 bp):
AAAATTATATTTTAACCCTAAAACTTTTT
Found at i:28586975 original size:60 final size:59
Alignment explanation
Indices: 28586906--28587086 Score: 224
Period size: 58 Copynumber: 3.1 Consensus size: 59
28586896 TATATATTAA
28586906 CCCTAAACTTTTTCAAAATTATTTTTTAACCCTAAAACTTTCTATAAATTACATTTTGAC
1 CCCTAAACTTTTT-AAAATTATTTTTTAACCCTAAAACTTTCTATAAATTACATTTTGAC
* *
28586966 CCCTAAACTTTTGTAAATTTA-TTTTTAA-CCTAAAACTTTTTATAAATTACATTTTGAC
1 CCCTAAACTTTT-TAAAATTATTTTTTAACCCTAAAACTTTCTATAAATTACATTTTGAC
* * * * * * *
28587024 CCCTAAAAATTTTTGAAATTATCTTCTAACCCCCAAAACTTTCTA-AAACTACATTTTTAC
1 CCCT-AAACTTTTTAAAATTATTTTTTAA-CCCTAAAACTTTCTATAAATTACATTTTGAC
28587084 CCC
1 CCC
28587087 CAAGTTTTCA
Statistics
Matches: 105, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
58 39 0.37
59 19 0.18
60 34 0.32
61 13 0.12
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.41
Consensus pattern (59 bp):
CCCTAAACTTTTTAAAATTATTTTTTAACCCTAAAACTTTCTATAAATTACATTTTGAC
Found at i:28587240 original size:28 final size:28
Alignment explanation
Indices: 28587075--28587337 Score: 176
Period size: 28 Copynumber: 9.4 Consensus size: 28
28587065 TCTAAAACTA
* *
28587075 CATTTTTACCCCCAAGTTTT-CATAATTC
1 CATTTTTACCCCGAA-TTTTCCAAAATTC
28587103 CATTTTTGACCCC-AATTTTACCAAAATTAC
1 CATTTTT-ACCCCGAATTTT-CCAAAATT-C
* *
28587133 CA-TTTTACCTCCGAACTTTCTAAAATT-
1 CATTTTTACC-CCGAATTTTCCAAAATTC
28587160 CA-TTTTACCCCCG-A-TTTCACAAAATTAC
1 CATTTTTA-CCCCGAATTTTC-CAAAATT-C
* *
28587188 CA--TTT-CCCTCGAACTTTCTAAAATTC
1 CATTTTTACCC-CGAATTTTCCAAAATTC
28587214 CATTTTTACCCCG-ATTTTACCAAAATTAC
1 CATTTTTACCCCGAATTTT-CCAAAATT-C
* *
28587243 CATTTTAACCCTGAATTTTCCAAAATTC
1 CATTTTTACCCCGAATTTTCCAAAATTC
* * *
28587271 CATTTTAACTCC--ATTTTACCAAAATTA
1 CATTTTTACCCCGAATTTT-CCAAAATTC
* * *
28587298 C-TATTTTCCCCCGAACTTTCTAAAATTC
1 CAT-TTTTACCCCGAATTTTCCAAAATTC
28587326 CATTTTTGACCC
1 CATTTTT-ACCC
28587338 TAATTTCATC
Statistics
Matches: 191, Mismatches: 19, Indels: 49
0.74 0.07 0.19
Matches are distributed among these distances:
25 7 0.04
26 18 0.09
27 43 0.23
28 55 0.29
29 55 0.29
30 13 0.07
ACGTcount: A:0.30, C:0.28, G:0.03, T:0.39
Consensus pattern (28 bp):
CATTTTTACCCCGAATTTTCCAAAATTC
Found at i:28587323 original size:139 final size:137
Alignment explanation
Indices: 28587060--28587330 Score: 297
Period size: 139 Copynumber: 2.0 Consensus size: 137
28587050 TAACCCCCAA
* *
28587060 AACTTTCTAAAACTACATTTTTACCCCCAAGTTTTCATAATTCCATTTTTGACCCCAATTTTACC
1 AACTTTCTAAAACTACATTTTTACCCCCAAGTTTTCAAAATTCCATTTTTAACCCCAATTTTACC
* *
28587125 AAAATTACCATTTTACCTCCGAACTTTCTAAAATTCATTTTACCCCCGATTTCACAAAATTACCA
66 AAAATTACCATTTTAACTCC-AACTTTCCAAAATTCATTTTACCCCCGATTTCACAAAATT-CCA
28587190 TTTCCCTCG
129 TTTCCCTCG
* * * *
28587199 AACTTTCTAAAATTCCATTTTTA-CCCCGA-TTTTACCAAAATTACCA-TTTTAACCCTGAATTT
1 AACTTTCTAAAACTACATTTTTACCCCCAAGTTTT--CAAAATT-CCATTTTTAACCC-CAATTT
* *
28587261 T-CCAAAATT-CCATTTTAACTCC-ATTTTACCAAAATTACTATTTT-CCCCCGAACTTTC-TAA
62 TACCAAAATTACCATTTTAACTCCAACTTT-CCAAAATT-C-ATTTTACCCCCG-A-TTTCACAA
28587321 AATTCCATTT
122 AATTCCATTT
28587331 TTGACCCTAA
Statistics
Matches: 113, Mismatches: 10, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
136 4 0.04
137 11 0.10
138 30 0.27
139 55 0.49
140 13 0.12
ACGTcount: A:0.31, C:0.27, G:0.03, T:0.39
Consensus pattern (137 bp):
AACTTTCTAAAACTACATTTTTACCCCCAAGTTTTCAAAATTCCATTTTTAACCCCAATTTTACC
AAAATTACCATTTTAACTCCAACTTTCCAAAATTCATTTTACCCCCGATTTCACAAAATTCCATT
TCCCTCG
Found at i:28587352 original size:56 final size:57
Alignment explanation
Indices: 28587098--28587368 Score: 324
Period size: 56 Copynumber: 4.8 Consensus size: 57
28587088 AAGTTTTCAT
*
28587098 AATTCCATTTTTGACCCCAATTTTACCAAAATTACCATTTTACCTCCGAACTTTCTAA
1 AATTCCATTTTT-ACCCCAATTTTACCAAAATTACCATTTTACCCCCGAACTTTCTAA
* * *
28587156 AATT-CA-TTTTACCCCCGATTTCA-CAAAATTACCA-TTT-CCCTCGAACTTTCTAA
1 AATTCCATTTTTA-CCCCAATTTTACCAAAATTACCATTTTACCCCCGAACTTTCTAA
* * * * *
28587209 AATTCCATTTTTACCCCGATTTTACCAAAATTACCATTTTAACCCTGAATTTTCCAA
1 AATTCCATTTTTACCCCAATTTTACCAAAATTACCATTTTACCCCCGAACTTTCTAA
* * *
28587266 AATTCCATTTTAACTCC-ATTTTACCAAAATTACTATTTT-CCCCCGAACTTTCTAA
1 AATTCCATTTTTACCCCAATTTTACCAAAATTACCATTTTACCCCCGAACTTTCTAA
* * *
28587321 AATTCCATTTTTGACCCTAATTTCATC-AAATTACCATTTTACCCCCGA
1 AATTCCATTTTT-ACCCCAATTTTACCAAAATTACCATTTTACCCCCGA
28587369 GTATTCGTTT
Statistics
Matches: 181, Mismatches: 23, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
53 18 0.10
54 15 0.08
55 51 0.28
56 52 0.29
57 41 0.23
58 4 0.02
ACGTcount: A:0.31, C:0.28, G:0.03, T:0.38
Consensus pattern (57 bp):
AATTCCATTTTTACCCCAATTTTACCAAAATTACCATTTTACCCCCGAACTTTCTAA
Found at i:28587404 original size:16 final size:17
Alignment explanation
Indices: 28587383--28587418 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
28587373 TCGTTTCATT
*
28587383 TTTGCTC-ATCGTTTTA
1 TTTGCTCAATCATTTTA
28587399 TTTGCTCAATCATTTTA
1 TTTGCTCAATCATTTTA
28587416 TTT
1 TTT
28587419 CGTGTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.17, C:0.17, G:0.08, T:0.58
Consensus pattern (17 bp):
TTTGCTCAATCATTTTA
Found at i:28591146 original size:24 final size:24
Alignment explanation
Indices: 28591110--28591155 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
28591100 ATCAGAGAAT
* * *
28591110 AGAAAGGCTAGAGCAGTTGCAAAA
1 AGAAAAGCAAGAGCAGATGCAAAA
*
28591134 AGAAAAGCAAGAGTAGATGCAA
1 AGAAAAGCAAGAGCAGATGCAA
28591156 GCTCAGTTAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.28, T:0.11
Consensus pattern (24 bp):
AGAAAAGCAAGAGCAGATGCAAAA
Found at i:28599351 original size:92 final size:92
Alignment explanation
Indices: 28599192--28600365 Score: 1329
Period size: 92 Copynumber: 12.5 Consensus size: 92
28599182 CAGATCAAAA
28599192 ATAACAAGCCTTTATCTCTCTGAAGTTAGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAATCT
1 ATAACAAGCCTTTATCTCTCTGAAGTT-GTAGTAAGAGCAAGATGAAGCTTCAAACATCAAATCT
*
28599257 TATCCCCTTGAAGTTGCAGTAAAGTTGG
65 TATCCTCTTGAAGTTGCAGTAAAGTTGG
* * *
28599285 ATAACAAGCCTTTATCTCTCTAAAGTTGTAGTAGGAGCAAGATGAAGCTTCAAACATCAAAACTT
1 ATAACAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAATCTT
28599350 ATCCTCTTGAAGTTGCAGTAAAGTTGG
66 ATCCTCTTGAAGTTGCAGTAAAGTTGG
*
28599377 ATAACAAGCCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTTAAACATCAAATCT
1 ATAACAAG-CCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAATCT
28599442 TATCCTCTTGAAGTTGCAGTAAAGTTGG
65 TATCCTCTTGAAGTTGCAGTAAAGTTGG
*
28599470 ATAACAAGCCTCTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAATCTT
1 ATAACAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAATCTT
* *
28599535 ATCCTTTTGAGGTTGCAGTAAAGTTGG
66 ATCCTCTTGAAGTTGCAGTAAAGTTGG
* * *
28599562 ATAACAAGCCTTTATCTTTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACATTAAATCTT
1 ATAACAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAATCTT
28599627 ATCCTCTTGAAGTTGCAGTAAAGTTGG
66 ATCCTCTTGAAGTTGCAGTAAAGTTGG
* * **** * * **
28599654 ATAACAAGCTTTTATC-CAGT-TGGATAACAAGCTTTTA-T-CCCTCTGAAGTTGTAG-TAGGAG
1 ATAACAAGCCTTTATCTC--TCT-G-----AAG-TTGTAGTAAGAGC--AAGATGAAGCT-TCA-
* * * * *** * * *
28599714 CAAGAT-GAAGCTTCAAACATCAAATCTT-ATCCT-C-TTGAAGTTGC
53 -AACATCAAATCTT-----ATC--CTCTTGAAGTTGCAGTAAAGTTGG
* * * ** * * ** *
28599758 AGT-A-AAG--TTGGATAACAAGC-CTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAATCT
1 A-TAACAAGCCTT---TATC--TCTC-TGA--AGT-TGTAG-T-AAG-AGCA---AGATGAAGCT
* * *
28599818 TTAAACATCAAAACTTATTCTCTTGAAGTTGCAGTAAAGTTGG
50 TCAAACATCAAATCTTATCCTCTTGAAGTTGCAGTAAAGTTGG
* *
28599861 ATAACAAGCCTTT-TCTCTCTGAAGTTGTAGTAGGAGCAAGATGAAGCTTCAAACATCAAAACTT
1 ATAACAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAATCTT
28599925 ATCCTCTTGAAGTTGCAGT-AAGTTGG
66 ATCCTCTTGAAGTTGCAGTAAAGTTGG
* *
28599951 ATAACAAGCCTTTTTCTCTCTGAAGTTGTAGTAGGAGCAAGATGAAGCTTCAAACATCAAATCTT
1 ATAACAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAATCTT
28600016 ATCCTCTTGAAGTTGCAGTAAAGTTGG
66 ATCCTCTTGAAGTTGCAGTAAAGTTGG
* *
28600043 ATAACAAGCCTTTATCTCTCTGAAGTTTTAGTAAGAGCAAGATGAAGCTTCAAACATCAAAACTT
1 ATAACAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAATCTT
28600108 ATCCTCTTGAAGTTGCAGTAAAGTTGG
66 ATCCTCTTGAAGTTGCAGTAAAGTTGG
* *
28600135 ATAACAAGCCTTTATCTTTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAAACTT
1 ATAACAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAATCTT
28600200 ATCCTCTTGAAGTTGCAGTAAAGTTGG
66 ATCCTCTTGAAGTTGCAGTAAAGTTGG
*
28600227 ATAACAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAAGATCAAATCTT
1 ATAACAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAATCTT
*
28600292 ATCCTCTTGAAGTTGCAGTAAAATTGG
66 ATCCTCTTGAAGTTGCAGTAAAGTTGG
* * * * * * *
28600319 ATAGCAAGTCTTTATTTCTC-CAAGTTGTAATAAGAGCAGGATAAAGC
1 ATAACAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGC
28600366 CTCGAAGTCA
Statistics
Matches: 930, Mismatches: 97, Indels: 110
0.82 0.09 0.10
Matches are distributed among these distances:
90 20 0.02
91 134 0.14
92 542 0.58
93 116 0.12
94 2 0.00
95 1 0.00
96 1 0.00
97 5 0.01
98 6 0.01
99 12 0.01
100 13 0.01
101 10 0.01
102 7 0.01
103 13 0.01
104 16 0.02
105 6 0.01
106 9 0.01
107 10 0.01
108 6 0.01
109 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (92 bp):
ATAACAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAATCTT
ATCCTCTTGAAGTTGCAGTAAAGTTGG
Found at i:28599678 original size:23 final size:23
Alignment explanation
Indices: 28599648--28599693 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
28599638 GTTGCAGTAA
28599648 AGTTGGATAACAAGCTTTTATCC
1 AGTTGGATAACAAGCTTTTATCC
28599671 AGTTGGATAACAAGCTTTTATCC
1 AGTTGGATAACAAGCTTTTATCC
28599694 CTCTGAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (23 bp):
AGTTGGATAACAAGCTTTTATCC
Found at i:28599758 original size:115 final size:115
Alignment explanation
Indices: 28599556--28599784 Score: 395
Period size: 115 Copynumber: 2.0 Consensus size: 115
28599546 GTTGCAGTAA
** *
28599556 AGTTGGATAACAAGCCTTTATCTTTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACATTA
1 AGTTGGATAACAAGCCTTTATCCCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACATCA
*
28599621 AATCTTATCCTCTTGAAGTTGCAGTAAAGTTGGATAACAAGCTTTTATCC
66 AATCTTATCCTCTTGAAGTTGCAGTAAAGTTGGATAACAAGCCTTTATCC
* * *
28599671 AGTTGGATAACAAGCTTTTATCCCTCTGAAGTTGTAGTAGGAGCAAGATGAAGCTTCAAACATCA
1 AGTTGGATAACAAGCCTTTATCCCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACATCA
28599736 AATCTTATCCTCTTGAAGTTGCAGTAAAGTTGGATAACAAGCCTTTATC
66 AATCTTATCCTCTTGAAGTTGCAGTAAAGTTGGATAACAAGCCTTTATC
28599785 TCTCTGAAGT
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
115 107 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (115 bp):
AGTTGGATAACAAGCCTTTATCCCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACATCA
AATCTTATCCTCTTGAAGTTGCAGTAAAGTTGGATAACAAGCCTTTATCC
Found at i:28599843 original size:207 final size:208
Alignment explanation
Indices: 28599464--28599874 Score: 698
Period size: 207 Copynumber: 2.0 Consensus size: 208
28599454 GTTGCAGTAA
*
28599464 AGTTGGATAACAAGCCTCTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCA
1 AGTTGGATAACAAGCCTCTATCCCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCA
* * *
28599529 AATCTTATCCTTTTGAGGTTGCAGTAAAGTTGGATAACAAGCCTTTATCTTTCTGAAGTTATAGT
66 AATCTTATCCTCTTGAAGTTGCAGTAAAGTTGGATAACAAGCCTTTATCTCTCTGAAGTTATAGT
* *
28599594 AAGAGCAAGATGAAGCTTCAAACATTAAATCTTATCCTCTTGAAGTTGCAGTAAAGTTGGATAAC
131 AAGAGCAAGATGAAGCTTCAAACATCAAAACTTATCCTCTTGAAGTTGCAGTAAAGTTGGATAAC
28599659 AAG-CTTTTATCC
196 AAGCCTTTTATCC
* * *
28599671 AGTTGGATAACAAGCTTTTATCCCTCTGAAGTTGTAGTAGGAGCAAGATGAAGCTTCAAACATCA
1 AGTTGGATAACAAGCCTCTATCCCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCA
*
28599736 AATCTTATCCTCTTGAAGTTGCAGTAAAGTTGGATAACAAGCCTTTATCTCTCTGAAGTTGTAGT
66 AATCTTATCCTCTTGAAGTTGCAGTAAAGTTGGATAACAAGCCTTTATCTCTCTGAAGTTATAGT
* * *
28599801 AAGAGCAAGATGAATCTTTAAACATCAAAACTTATTCTCTTGAAGTTGCAGTAAAGTTGGATAAC
131 AAGAGCAAGATGAAGCTTCAAACATCAAAACTTATCCTCTTGAAGTTGCAGTAAAGTTGGATAAC
28599866 AAGCCTTTT
196 AAGCCTTTT
28599875 CTCTCTGAAG
Statistics
Matches: 190, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
207 185 0.97
208 5 0.03
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Consensus pattern (208 bp):
AGTTGGATAACAAGCCTCTATCCCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCA
AATCTTATCCTCTTGAAGTTGCAGTAAAGTTGGATAACAAGCCTTTATCTCTCTGAAGTTATAGT
AAGAGCAAGATGAAGCTTCAAACATCAAAACTTATCCTCTTGAAGTTGCAGTAAAGTTGGATAAC
AAGCCTTTTATCC
Found at i:28602471 original size:30 final size:28
Alignment explanation
Indices: 28602433--28602638 Score: 205
Period size: 30 Copynumber: 6.9 Consensus size: 28
28602423 CCCTAGAGGT
*
28602433 CCCTAAACTATCCAAAAATTATATTTTAA
1 CCCTAAACTTTCC-AAAATTATATTTTAA
*
28602462 CCTCTAAACTTTTCCAAAATTATATTTTGA
1 CC-CTAAAC-TTTCCAAAATTATATTTTAA
* * *
28602492 CCCTAAAACTTTCTATAAATTACATTTTGA
1 CCCT-AAACTTTCCA-AAATTATATTTTAA
* *
28602522 CCCTTAAACTTTGGCAAATTTATATTTTAA
1 CCC-TAAACTTT-CCAAAATTATATTTTAA
* *
28602552 CCCTAAAACTTTCTATAAATTACATTTTAA
1 CCCT-AAACTTTCCA-AAATTATATTTTAA
28602582 CCCCTAAACTTTTCCAAAATTATATTTTAA
1 -CCCTAAAC-TTTCCAAAATTATATTTTAA
* *
28602612 CCCTAAAACTTTCTAAAATTACATTTT
1 CCCT-AAACTTTCCAAAATTATATTTT
28602639 TTACCCCCAA
Statistics
Matches: 149, Mismatches: 17, Indels: 22
0.79 0.09 0.12
Matches are distributed among these distances:
29 31 0.21
30 103 0.69
31 15 0.10
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.40
Consensus pattern (28 bp):
CCCTAAACTTTCCAAAATTATATTTTAA
Found at i:28602645 original size:60 final size:60
Alignment explanation
Indices: 28602448--28602638 Score: 303
Period size: 60 Copynumber: 3.2 Consensus size: 60
28602438 AACTATCCAA
* * *
28602448 AAATTATATTTTAACCTCTAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTTCTAT
1 AAATTACATTTTAACCCCTAAACTTTTCCAAAATTATATTTTAACCCTAAAACTTTCTAT
* * ** *
28602508 AAATTACATTTTGACCCTTAAACTTTGGCAAATTTATATTTTAACCCTAAAACTTTCTAT
1 AAATTACATTTTAACCCCTAAACTTTTCCAAAATTATATTTTAACCCTAAAACTTTCTAT
28602568 AAATTACATTTTAACCCCTAAACTTTTCCAAAATTATATTTTAACCCTAAAACTTTCTA-
1 AAATTACATTTTAACCCCTAAACTTTTCCAAAATTATATTTTAACCCTAAAACTTTCTAT
28602627 AAATTACATTTT
1 AAATTACATTTT
28602639 TTACCCCCAA
Statistics
Matches: 118, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
59 12 0.10
60 106 0.90
ACGTcount: A:0.37, C:0.19, G:0.02, T:0.42
Consensus pattern (60 bp):
AAATTACATTTTAACCCCTAAACTTTTCCAAAATTATATTTTAACCCTAAAACTTTCTAT
Found at i:28602673 original size:60 final size:58
Alignment explanation
Indices: 28602448--28602661 Score: 241
Period size: 60 Copynumber: 3.6 Consensus size: 58
28602438 AACTATCCAA
* * * *
28602448 AAATTATATTTTAACCTCTAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTTCTAT
1 AAATTACATTTTAACC-CCAAACTTTTAC-AAATTATATTTTAACCCTAAAACTTTCTAT
* * **
28602508 AAATTACATTTTGACCCTTAAACTTTGGCAAATTTATATTTTAACCCTAAAACTTTCTAT
1 AAATTACATTTTAACCC-CAAACTTTTACAAA-TTATATTTTAACCCTAAAACTTTCTAT
*
28602568 AAATTACATTTTAACCCCTAAACTTTTCCAAAATTATATTTTAACCCTAAAACTTTCTA-
1 AAATTACATTTTAACCCC-AAACTTTTAC-AAATTATATTTTAACCCTAAAACTTTCTAT
* * *
28602627 AAATTACATTTTTTACCCCCAAGTTTTACATAATT
1 AAATTACA-TTTTAACCCCAAACTTTTACA-AATT
28602662 CCATTTTTAA
Statistics
Matches: 135, Mismatches: 13, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
58 1 0.01
59 23 0.17
60 108 0.80
61 3 0.02
ACGTcount: A:0.36, C:0.20, G:0.02, T:0.42
Consensus pattern (58 bp):
AAATTACATTTTAACCCCAAACTTTTACAAATTATATTTTAACCCTAAAACTTTCTAT
Found at i:28602717 original size:29 final size:28
Alignment explanation
Indices: 28602685--28602989 Score: 130
Period size: 29 Copynumber: 10.6 Consensus size: 28
28602675 TAATTTTACC
28602685 AAAATTTCCATTTTACCCCCAAACTTTCT
1 AAAATTTCCATTTTACCCCC-AACTTTCT
* *
28602714 AAAA-TTCCTTTTTACCCCCGA-TTTCAT
1 AAAATTTCCATTTTACCCCCAACTTTC-T
* *
28602741 CAAAATTACCATTTTACCTCCGAACTTTCT
1 -AAAATTTCCATTTTACC-CCCAACTTTCT
* * *
28602771 AAAA-TTCCATTTTTGCCCCCGA-TTTCACC
1 AAAATTTCCA-TTTTACCCCCAACTTT--CT
* * **
28602800 AAAATTGCCATTTTTCCCTGAACTTTCT
1 AAAATTTCCATTTTACCCCCAACTTTCT
* * * *
28602828 AAAA-TTCCATTTTTA-CCTCGATTTTACC
1 AAAATTTCCA-TTTTACCCCCAACTTT-CT
* * *
28602856 AAAATTGCCATTTTACCCCCGAATTTTCC
1 AAAATTTCCATTTTACCCCC-AACTTTCT
* * * *
28602885 AAAATTT-CATTTTAACCCCGATTTTACCA
1 AAAATTTCCATTTTACCCCCAACTTT--CT
*
28602914 AAAATTAT-CATATTT-CCCTCGAACTTTCT
1 AAAATT-TCCAT-TTTACCC-CCAACTTTCT
*
28602943 AAAA-TTCCATTTTTGA-CCCTAA-TTTCAT
1 AAAATTTCCA-TTTT-ACCCCCAACTTTC-T
*
28602971 CAAAATTACCATTTTACCC
1 -AAAATTTCCATTTTACCC
28602990 TCGGGTATCT
Statistics
Matches: 211, Mismatches: 37, Indels: 56
0.69 0.12 0.18
Matches are distributed among these distances:
26 4 0.02
27 26 0.12
28 66 0.31
29 77 0.36
30 26 0.12
31 12 0.06
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.39
Consensus pattern (28 bp):
AAAATTTCCATTTTACCCCCAACTTTCT
Found at i:28602720 original size:58 final size:58
Alignment explanation
Indices: 28602637--28602989 Score: 369
Period size: 57 Copynumber: 6.1 Consensus size: 58
28602627 AAATTACATT
* *** * *
28602637 TTTTACCCCC-AAGTTT-TACATAATTCCATTTTTAACCTTAATTTTACCAAAATTTCCA
1 TTTTACCCCCGAACTTTCTA-A-AATTCCATTTTTAACCCCGATTTCACCAAAATTACCA
* * *
28602695 TTTTACCCCCAAACTTTCTAAAATTCC-TTTTTACCCCCGATTTCATCAAAATTACCA
1 TTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAATTACCA
* ** *
28602752 TTTTACCTCCGAACTTTCTAAAATTCCATTTTTGCCCCCGATTTCACCAAAATTGCCA
1 TTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAATTACCA
* * * * *
28602810 TTTT-TCCCTGAACTTTCTAAAATTCCATTTTT-ACCTCGATTTTACCAAAATTGCCA
1 TTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAATTACCA
* * * * *
28602866 TTTTACCCCCGAATTTTCCAAAATTTCA-TTTTAACCCCGATTTTACCAAAAATTATCA
1 TTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACC-AAAATTACCA
* * ** *
28602924 TATTT-CCCTCGAACTTTCTAAAATTCCATTTTTGACCCTAATTTCATCAAAATTACCA
1 T-TTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAATTACCA
28602982 TTTTACCC
1 TTTTACCC
28602990 TCGGGTATCT
Statistics
Matches: 249, Mismatches: 37, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
56 29 0.12
57 107 0.43
58 88 0.35
59 23 0.09
60 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.04, T:0.40
Consensus pattern (58 bp):
TTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAATTACCA
Found at i:28603003 original size:172 final size:172
Alignment explanation
Indices: 28602658--28602990 Score: 454
Period size: 172 Copynumber: 1.9 Consensus size: 172
28602648 AGTTTTACAT
* * * *
28602658 AATTCCATTTTTAACCTTAATTTTACCAAAATTTCCATTTTACCCCCAAACTTTCTAAAATTCCT
1 AATTCCATTTTTAACCTCAATTTTACCAAAATTGCCATTTTACCCCCAAACTTTCCAAAATTCCA
* * *
28602723 TTTTACCCCCGATTTCATCAAAATTACCATTTTACCTCCGAACTTTCTAAAATTCCATTTTTGCC
66 TTTTAACCCCGATTTCACCAAAATTACCATTTTACCTCCGAACTTTCTAAAATTCCATTTTTGAC
* * * *
28602788 CCCGATTTCACCAAAATTGCCATTTTTCCCTGAACTTTCTAA
131 CCCAATTTCACCAAAATTACCATTTTACCCTGAACTATCTAA
* * * *
28602830 AATTCCATTTTT-ACCTCGATTTTACCAAAATTGCCATTTTACCCCCGAATTTTCCAAAATTTCA
1 AATTCCATTTTTAACCTCAATTTTACCAAAATTGCCATTTTACCCCCAAACTTTCCAAAATTCCA
* * *
28602894 TTTTAACCCCGATTTTACCAAAAATTATCATATTTCCCT-CGAACTTTCTAAAATTCCATTTTTG
66 TTTTAACCCCGATTTCACC-AAAATTACCAT-TTTACCTCCGAACTTTCTAAAATTCCATTTTTG
* *
28602958 ACCCTAATTTCATCAAAATTACCATTTTACCCT
129 ACCCCAATTTCACCAAAATTACCATTTTACCCT
28602991 CGGGTATCTA
Statistics
Matches: 140, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
171 60 0.43
172 74 0.53
173 6 0.04
ACGTcount: A:0.29, C:0.27, G:0.04, T:0.40
Consensus pattern (172 bp):
AATTCCATTTTTAACCTCAATTTTACCAAAATTGCCATTTTACCCCCAAACTTTCCAAAATTCCA
TTTTAACCCCGATTTCACCAAAATTACCATTTTACCTCCGAACTTTCTAAAATTCCATTTTTGAC
CCCAATTTCACCAAAATTACCATTTTACCCTGAACTATCTAA
Found at i:28603123 original size:16 final size:17
Alignment explanation
Indices: 28603102--28603137 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
28603092 TCATTTCGTT
28603102 TTTGCTT-ATCATTTTA
1 TTTGCTTAATCATTTTA
*
28603118 TTTGCTTAATTATTTTA
1 TTTGCTTAATCATTTTA
28603135 TTT
1 TTT
28603138 CGTGTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTGCTTAATCATTTTA
Found at i:28603969 original size:20 final size:20
Alignment explanation
Indices: 28603946--28604063 Score: 96
Period size: 20 Copynumber: 5.9 Consensus size: 20
28603936 CCAAATAAAT
28603946 AGGAAGTACAAAAAATTATG
1 AGGAAGTACAAAAAATTATG
* *
28603966 AGGATGTACAGAAAATTATG
1 AGGAAGTACAAAAAATTATG
* * *
28603986 ATGAAATACTAAGAAA-TATG
1 AGGAAGTAC-AAAAAATTATG
* * *
28604006 AGAAAGTACCAAATATTATG
1 AGGAAGTACAAAAAATTATG
* *
28604026 AGGAAATACCAAAAAAAT-TG
1 AGGAAGTA-CAAAAAATTATG
**
28604046 AAAAAGTACAAAAAATTA
1 AGGAAGTACAAAAAATTA
28604064 AAAGGGGATA
Statistics
Matches: 72, Mismatches: 22, Indels: 8
0.71 0.22 0.08
Matches are distributed among these distances:
19 11 0.15
20 51 0.71
21 10 0.14
ACGTcount: A:0.56, C:0.07, G:0.16, T:0.21
Consensus pattern (20 bp):
AGGAAGTACAAAAAATTATG
Found at i:28604052 original size:40 final size:40
Alignment explanation
Indices: 28603946--28604063 Score: 112
Period size: 40 Copynumber: 3.0 Consensus size: 40
28603936 CCAAATAAAT
* * ** * *
28603946 AGGAAGTACAAAAAATTATGAGGATGTACAGAAAATTATG
1 AGGAAATACAAAAAAATATGAAAAAGTACAAAAAATTATG
* * * * * *
28603986 ATGAAATACTAAGAAATATGAGAAAGTACCAAATATTATG
1 AGGAAATACAAAAAAATATGAAAAAGTACAAAAAATTATG
28604026 AGGAAATACCAAAAAAAT-TGAAAAAGTACAAAAAATTA
1 AGGAAATA-CAAAAAAATATGAAAAAGTACAAAAAATTA
28604064 AAAGGGGATA
Statistics
Matches: 61, Mismatches: 16, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
40 54 0.89
41 7 0.11
ACGTcount: A:0.56, C:0.07, G:0.16, T:0.21
Consensus pattern (40 bp):
AGGAAATACAAAAAAATATGAAAAAGTACAAAAAATTATG
Found at i:28615667 original size:23 final size:23
Alignment explanation
Indices: 28615628--28615671 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
28615618 GTGTAAATAC
*
28615628 ATTTTAACTTTAGCCATTGATGT
1 ATTTTAACTGTAGCCATTGATGT
28615651 ATTTTAATCTGTA-CCATTGAT
1 ATTTTAA-CTGTAGCCATTGAT
28615672 TTTGGGAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.27, C:0.14, G:0.11, T:0.48
Consensus pattern (23 bp):
ATTTTAACTGTAGCCATTGATGT
Found at i:28617790 original size:28 final size:28
Alignment explanation
Indices: 28617738--28617908 Score: 120
Period size: 29 Copynumber: 5.9 Consensus size: 28
28617728 GGACATCCGG
*
28617738 GGGT-AAAATGGTAA-TTTCGAGAGTTCTA
1 GGGTCAAAATGG-AATTTTTGA-AGTTCTA
*
28617766 GGGTCAAAATGGAATTTTTGAAGTT-TG
1 GGGTCAAAATGGAATTTTTGAAGTTCTA
*
28617793 GGGTCAAAAATGGAATTTTTGGAAG--CTC
1 GGGTC-AAAATGGAATTTTT-GAAGTTCTA
*
28617821 GGAGTCAAAAATGGAATTTTTGGAAGTTCGA
1 GG-GTC-AAAATGGAATTTTT-GAAGTTCTA
* * *
28617852 GGGTATAAAATGTAATTTTTGAAAGTT-TT
1 GGGT-CAAAATGGAATTTTTG-AAGTTCTA
* *
28617881 GAGGTCAAAATGTAATTTCTAGAAGTTC
1 G-GGTCAAAATGGAATTT-TTGAAGTTC
28617909 GGGGGCTAAA
Statistics
Matches: 119, Mismatches: 11, Indels: 24
0.77 0.07 0.16
Matches are distributed among these distances:
27 6 0.05
28 27 0.23
29 58 0.49
30 25 0.21
31 3 0.03
ACGTcount: A:0.33, C:0.06, G:0.26, T:0.34
Consensus pattern (28 bp):
GGGTCAAAATGGAATTTTTGAAGTTCTA
Found at i:28617827 original size:29 final size:29
Alignment explanation
Indices: 28617766--28617937 Score: 154
Period size: 29 Copynumber: 5.9 Consensus size: 29
28617756 GAGAGTTCTA
*
28617766 GGGTC-AAAATGGAATTTTT-GAAGTTTG
1 GGGTCAAAAATGGAATTTTTGGAAGTTCG
*
28617793 GGGTCAAAAATGGAATTTTTGGAAGCTCG
1 GGGTCAAAAATGGAATTTTTGGAAGTTCG
*
28617822 GAGTCAAAAATGGAATTTTTGGAAGTTCG
1 GGGTCAAAAATGGAATTTTTGGAAGTTCG
* * *
28617851 AGGGT-ATAAAATGTAATTTTTGAAAGTTTTG
1 -GGGTCA-AAAATGGAATTTTTGGAAG-TTCG
* * * *
28617882 AGGTC-AAAATGTAATTTCTAGAAGTTCG
1 GGGTCAAAAATGGAATTTTTGGAAGTTCG
* * **
28617910 GGGGCTAAAATATAATTTTTGGATAGTT
1 GGGTCAAAAATGGAATTTTTGGA-AGTT
28617938 TAGGGACCTC
Statistics
Matches: 119, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
27 5 0.04
28 20 0.17
29 64 0.54
30 27 0.23
31 3 0.03
ACGTcount: A:0.33, C:0.06, G:0.26, T:0.35
Consensus pattern (29 bp):
GGGTCAAAAATGGAATTTTTGGAAGTTCG
Found at i:28617920 original size:88 final size:88
Alignment explanation
Indices: 28617771--28617937 Score: 203
Period size: 88 Copynumber: 1.9 Consensus size: 88
28617761 TTCTAGGGTC
* * * * *
28617771 AAAATGGAATTTTTGAAGTTTGGGGTCAAAAATGGAATTTTTGGAAGCTCGGAGTCAAAAATGGA
1 AAAATGGAATTTTTGAAGTTTGAGGTCAAAAATGGAATTTCTAGAAGCTCGGAGGCAAAAATAGA
28617836 ATTTTTGGA-AGTTCGAGGGTAT
66 ATTTTTGGATAGTTCGAGGGTAT
* * * * *
28617858 AAAATGTAATTTTTGAAAGTTTTGAGGTC-AAAATGTAATTTCTAGAAGTTCGGGGGCTAAAATA
1 AAAATGGAATTTTTG-AAG-TTTGAGGTCAAAAATGGAATTTCTAGAAGCTCGGAGGCAAAAATA
*
28617922 TAATTTTTGGATAGTT
64 GAATTTTTGGATAGTT
28617938 TAGGGACCTC
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
87 14 0.21
88 40 0.61
89 12 0.18
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.35
Consensus pattern (88 bp):
AAAATGGAATTTTTGAAGTTTGAGGTCAAAAATGGAATTTCTAGAAGCTCGGAGGCAAAAATAGA
ATTTTTGGATAGTTCGAGGGTAT
Found at i:28617938 original size:59 final size:57
Alignment explanation
Indices: 28617767--28617938 Score: 175
Period size: 59 Copynumber: 2.9 Consensus size: 57
28617757 AGAGTTCTAG
* * * * * *
28617767 GGTCAAAATGGAATTTTTGAAGTTTGGGGTCAAAAATGGAATTTTTGGAAGCTCGGA
1 GGTCAAAATGGAATTTTAGAAGTTCGGGGTCTAAAATGTAATTTTTGGAAGTTTGGA
* * * *
28617824 -GTCAAAAATGGAATTTTTGGAAGTTCGAGGGTATAAAATGTAATTTTTGAAAGTTTTGA
1 GGTC-AAAATGGAA-TTTTAGAAGTTCG-GGGTCTAAAATGTAATTTTTGGAAGTTTGGA
* * *
28617883 GGTCAAAATGTAATTTCTAGAAGTTCGGGGGCTAAAATATAATTTTTGGATAGTTT
1 GGTCAAAATGGAATTT-TAGAAGTTCGGGGTCTAAAATGTAATTTTTGGA-AGTTT
28617939 AGGGACCTCT
Statistics
Matches: 94, Mismatches: 15, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
56 3 0.03
57 9 0.10
58 33 0.35
59 46 0.49
60 3 0.03
ACGTcount: A:0.33, C:0.06, G:0.26, T:0.35
Consensus pattern (57 bp):
GGTCAAAATGGAATTTTAGAAGTTCGGGGTCTAAAATGTAATTTTTGGAAGTTTGGA
Found at i:28619662 original size:28 final size:25
Alignment explanation
Indices: 28619621--28619684 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
28619611 TTGCAGGTAA
* *
28619621 TGGTGGTAGCAG-AGTAAGGTGGAGC
1 TGGTGGTGGCAGCAG-AGGGTGGAGC
* * *
28619646 TGTTGGTGGCAGGAGAGGTTGGAGC
1 TGGTGGTGGCAGCAGAGGGTGGAGC
28619671 TGGTGGTGGCAGCA
1 TGGTGGTGGCAGCA
28619685 ATCAGCAGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 30 0.94
26 2 0.06
ACGTcount: A:0.19, C:0.09, G:0.50, T:0.22
Consensus pattern (25 bp):
TGGTGGTGGCAGCAGAGGGTGGAGC
Found at i:28620945 original size:41 final size:42
Alignment explanation
Indices: 28620869--28620952 Score: 161
Period size: 41 Copynumber: 2.0 Consensus size: 42
28620859 TCCAATTACC
28620869 TGAAAGAGGTAGGTTAGGAGCAATAACAAGCTGTCTTTTGAG
1 TGAAAGAGGTAGGTTAGGAGCAATAACAAGCTGTCTTTTGAG
28620911 TGAAAGAGGTAGGTTAGG-GCAATAACAAGCTGTCTTTTGAG
1 TGAAAGAGGTAGGTTAGGAGCAATAACAAGCTGTCTTTTGAG
28620952 T
1 T
28620953 TAAATCAAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 24 0.57
42 18 0.43
ACGTcount: A:0.32, C:0.10, G:0.31, T:0.27
Consensus pattern (42 bp):
TGAAAGAGGTAGGTTAGGAGCAATAACAAGCTGTCTTTTGAG
Found at i:28622460 original size:19 final size:18
Alignment explanation
Indices: 28622417--28622460 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
28622407 TTAAATAACA
28622417 TTAATTATATTTTATTAT
1 TTAATTATATTTTATTAT
*
28622435 TTAAATTTTATTTTATTAT
1 TT-AATTATATTTTATTAT
28622454 TATAATT
1 T-TAATT
28622461 CGCCAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 20 0.87
20 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTAATTATATTTTATTAT
Found at i:28623338 original size:6 final size:6
Alignment explanation
Indices: 28623329--28623402 Score: 60
Period size: 6 Copynumber: 12.0 Consensus size: 6
28623319 TTTTAATTTT
* *
28623329 ATTTAA ATTTAA ATTTAA TTATTTAA ATTT-A CTTTAA ATTAAA ATTTAA
1 ATTTAA ATTTAA ATTTAA --ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
** * *
28623378 ATAAAA ATTAAA ACATTAA ATTTAA
1 ATTTAA ATTTAA A-TTTAA ATTTAA
28623403 CATTAAAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
5 4 0.07
6 40 0.74
7 4 0.07
8 6 0.11
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:28623352 original size:20 final size:20
Alignment explanation
Indices: 28623327--28623379 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
28623317 ATTTTTAATT
28623327 TTATTTAAATTTAAATTTAA
1 TTATTTAAATTTAAATTTAA
*
28623347 TTATTTAAATTT-ACTTTAA
1 TTATTTAAATTTAAATTTAA
*
28623366 --ATTAAAATTTAAAT
1 TTATTTAAATTTAAAT
28623380 AAAAATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 9 0.31
18 2 0.07
19 6 0.21
20 12 0.41
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATTTAAATTTAAATTTAA
Found at i:28623382 original size:11 final size:12
Alignment explanation
Indices: 28623333--28623410 Score: 52
Period size: 12 Copynumber: 6.2 Consensus size: 12
28623323 AATTTTATTT
28623333 AAATTTAAATTTA
1 AAATTTAAA-TTA
*
28623346 ATTATTTAAATT-
1 A-AATTTAAATTA
* *
28623358 TACTTTAAATTA
1 AAATTTAAATTA
*
28623370 AAATTTAAATAA
1 AAATTTAAATTA
*
28623382 AAATTAAAACATT-
1 AAATT-TAA-ATTA
28623395 AAATTTAACATTA
1 AAATTTAA-ATTA
28623408 AAA
1 AAA
28623411 AATTAAAAGT
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
11 8 0.16
12 20 0.40
13 13 0.26
14 9 0.18
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (12 bp):
AAATTTAAATTA
Found at i:28625225 original size:18 final size:18
Alignment explanation
Indices: 28625202--28625251 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 18
28625192 CAAAACTTTT
28625202 CCTAAATTACATTTTGAC
1 CCTAAATTACATTTTGAC
28625220 CCTAAA--AC-TTTT---
1 CCTAAATTACATTTTGAC
28625232 CCTAAATTACATTTTGAC
1 CCTAAATTACATTTTGAC
28625250 CC
1 CC
28625252 CAAAACTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
12 6 0.23
14 2 0.08
15 8 0.31
16 2 0.08
18 8 0.31
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (18 bp):
CCTAAATTACATTTTGAC
Found at i:28625229 original size:30 final size:30
Alignment explanation
Indices: 28625193--28625291 Score: 164
Period size: 30 Copynumber: 3.3 Consensus size: 30
28625183 TCTAAGCCCC
28625193 AAAACTTTTCCTAAATTACATTTTGACCCT
1 AAAACTTTTCCTAAATTACATTTTGACCCT
*
28625223 AAAACTTTTCCTAAATTACATTTTGACCCC
1 AAAACTTTTCCTAAATTACATTTTGACCCT
*
28625253 AAAACTTTT-TTGAAATTACATTTTGACCCT
1 AAAACTTTTCCT-AAATTACATTTTGACCCT
28625283 AAAACTTTT
1 AAAACTTTT
28625292 AAAAATTACC
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
29 1 0.02
30 64 0.98
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.40
Consensus pattern (30 bp):
AAAACTTTTCCTAAATTACATTTTGACCCT
Found at i:28625282 original size:60 final size:59
Alignment explanation
Indices: 28625189--28625326 Score: 183
Period size: 60 Copynumber: 2.3 Consensus size: 59
28625179 GCTTTCTAAG
**
28625189 CCCCAAAACTTTTCCTAAATTACATTTTGACCCTAAAACTTTTCCTAAATTA-CATTTTGA
1 CCCCAAAACTTTTCCTAAATTACATTTTGACCCTAAAACTTTT-AAAAATTACCATTTT-A
*
28625249 CCCCAAAACTTTT-TTGAAATTACATTTTGACCCTAAAACTTTTAAAAATTACCATTTTA
1 CCCCAAAACTTTTCCT-AAATTACATTTTGACCCTAAAACTTTTAAAAATTACCATTTTA
* *
28625308 CCCCCAAAC-TTCCCTAAAT
1 CCCCAAAACTTTTCCTAAAT
28625327 CCCATTTTAA
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
58 6 0.09
59 17 0.25
60 46 0.67
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (59 bp):
CCCCAAAACTTTTCCTAAATTACATTTTGACCCTAAAACTTTTAAAAATTACCATTTTA
Found at i:28625326 original size:29 final size:29
Alignment explanation
Indices: 28625189--28625326 Score: 152
Period size: 30 Copynumber: 4.7 Consensus size: 29
28625179 GCTTTCTAAG
28625189 CCCCAAAACTTTTCCTAAATTACATTTTGA
1 CCCCAAAAC-TTTCCTAAATTACATTTTGA
*
28625219 CCCTAAAACTTTTCCTAAATTACATTTTGA
1 CCCCAAAAC-TTTCCTAAATTACATTTTGA
**
28625249 CCCCAAAACTTTTTTGAAATTACATTTTGA
1 CCCCAAAACTTTCCT-AAATTACATTTTGA
* ***
28625279 CCCTAAAACTTTTAAAAATTACCATTTT-A
1 CCCCAAAACTTTCCTAAATTA-CATTTTGA
* *
28625308 CCCCCAAACTTCCCTAAAT
1 CCCCAAAACTTTCCTAAAT
28625327 CCCATTTTAA
Statistics
Matches: 93, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
29 24 0.26
30 69 0.74
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
CCCCAAAACTTTCCTAAATTACATTTTGA
Found at i:28634594 original size:25 final size:26
Alignment explanation
Indices: 28634549--28634601 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
28634539 AAATTTAAAT
*
28634549 TATTTTATAAAAATT-CCAAAATTTA
1 TATTTTATAAAAATTACAAAAATTTA
*
28634574 TATTTTCA-AAAAATTATAAAAATTTA
1 TATTTT-ATAAAAATTACAAAAATTTA
28634600 TA
1 TA
28634602 AAAAATCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (26 bp):
TATTTTATAAAAATTACAAAAATTTA
Found at i:28635462 original size:32 final size:27
Alignment explanation
Indices: 28635410--28635475 Score: 69
Period size: 31 Copynumber: 2.2 Consensus size: 27
28635400 ATTGTATTCA
*
28635410 TAAAATTTATTAAAAATATTTTTATATT
1 TAAAATTTATTAAAAATA-TTTGATATT
28635438 TAAAATTTATTTAAACGAATTATTTGATATT
1 TAAAATTTA-TTAAA--AA-TATTTGATATT
28635469 TATAAAT
1 TA-AAAT
28635476 AATTTATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 9 0.28
29 5 0.16
31 12 0.38
32 6 0.19
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (27 bp):
TAAAATTTATTAAAAATATTTGATATT
Found at i:28643384 original size:58 final size:58
Alignment explanation
Indices: 28643335--28643444 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
28643325 ATCACTTTAA
* * * * *
28643335 TATTAAATTAATATAATACT-TGT-CAAGATAAATATTAGATTAAATTTAATAAATCT
1 TATTAAATTAATAGAATACTATCTGCAAAATAAACATTAAATTAAATTTAATAAATCT
*
28643391 TATTAAATTAATAGAATATTATCTGCAAAATAAACATTAAATTAAATTTAATAA
1 TATTAAATTAATAGAATACTATCTGCAAAATAAACATTAAATTAAATTTAATAA
28643445 TAAGGTAATC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
56 18 0.39
57 2 0.04
58 26 0.57
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (58 bp):
TATTAAATTAATAGAATACTATCTGCAAAATAAACATTAAATTAAATTTAATAAATCT
Found at i:28643412 original size:19 final size:19
Alignment explanation
Indices: 28643362--28643412 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
28643352 ACTTGTCAAG
28643362 ATAAATATTAGATTAAATTTA
1 ATAAATATT--ATTAAATTTA
*
28643383 ATAAATCTTATTAAA-TTA
1 ATAAATATTATTAAATTTA
28643401 ATAGAATATTAT
1 ATA-AATATTAT
28643413 CTGCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 6 0.22
19 13 0.48
21 8 0.30
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (19 bp):
ATAAATATTATTAAATTTA
Found at i:28645430 original size:6 final size:6
Alignment explanation
Indices: 28645419--28645477 Score: 109
Period size: 6 Copynumber: 9.8 Consensus size: 6
28645409 TATAAGCACA
28645419 ATGGGG ATGGGG ATGGGG ATGGGG ATGGGG ATGGGG ATGGGG ATGGGG
1 ATGGGG ATGGGG ATGGGG ATGGGG ATGGGG ATGGGG ATGGGG ATGGGG
*
28645467 ATGGGA ATGGG
1 ATGGGG ATGGG
28645478 TGGGAATTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.19, C:0.00, G:0.64, T:0.17
Consensus pattern (6 bp):
ATGGGG
Found at i:28646883 original size:16 final size:16
Alignment explanation
Indices: 28646862--28646899 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
28646852 TTAGTTTGGT
*
28646862 CCAATTTGTTAATAGC
1 CCAATTTATTAATAGC
28646878 CCAATTTATTAATAGC
1 CCAATTTATTAATAGC
28646894 CCAATT
1 CCAATT
28646900 AATAAGCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (16 bp):
CCAATTTATTAATAGC
Found at i:28646991 original size:46 final size:46
Alignment explanation
Indices: 28646921--28647037 Score: 117
Period size: 46 Copynumber: 2.5 Consensus size: 46
28646911 TCAAATTAAA
* * * * * *
28646921 TTGTCTTTCATAATTTCAAAGATTTATTTGACTAAGTTATTGGCAT
1 TTGTCTTCCATAATTTTAAGGATTTATTTGACTAAATTATAGGAAT
* ** *
28646967 TTGTCTTCCATAATTTTAGGGATTTATTTGGTTAAATTGTAGGAAT
1 TTGTCTTCCATAATTTTAAGGATTTATTTGACTAAATTATAGGAAT
* * *
28647013 TTTTCTTCCACAATTTTATGGATTT
1 TTGTCTTCCATAATTTTAAGGATTT
28647038 GTTTATCTTT
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.26, C:0.10, G:0.15, T:0.50
Consensus pattern (46 bp):
TTGTCTTCCATAATTTTAAGGATTTATTTGACTAAATTATAGGAAT
Found at i:28649163 original size:30 final size:31
Alignment explanation
Indices: 28649126--28649198 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
28649116 ATCAAATTGA
*
28649126 AAAACTCAAGTAAC-AACTAAACATTGAAAC
1 AAAACTCAAGTAACAAACTAAACATTAAAAC
* * *
28649156 CAAACTCAAGT-ACTAAATTGAACATTAAAAC
1 AAAACTCAAGTAAC-AAACTAAACATTAAAAC
28649187 AAAACTCAAGTA
1 AAAACTCAAGTA
28649199 CTAAATAGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 2 0.06
30 10 0.29
31 23 0.66
ACGTcount: A:0.55, C:0.19, G:0.07, T:0.19
Consensus pattern (31 bp):
AAAACTCAAGTAACAAACTAAACATTAAAAC
Found at i:28649192 original size:31 final size:31
Alignment explanation
Indices: 28649145--28649204 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
28649135 GTAACAACTA
* *
28649145 AACATTGAAACCAAACTCAAGTACTAAATTG
1 AACATTAAAACAAAACTCAAGTACTAAATTG
28649176 AACATTAAAACAAAACTCAAGTACTAAAT
1 AACATTAAAACAAAACTCAAGTACTAAAT
28649205 AGTATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.53, C:0.18, G:0.07, T:0.22
Consensus pattern (31 bp):
AACATTAAAACAAAACTCAAGTACTAAATTG
Found at i:28651511 original size:2 final size:2
Alignment explanation
Indices: 28651504--28651541 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
28651494 GGGCTTTTTA
28651504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28651542 TGGCTCATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28653936 original size:24 final size:27
Alignment explanation
Indices: 28653893--28653945 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 27
28653883 AGTATTTCCT
*
28653893 CTCTTCTCTTCCTCCT-C-CACTCTCC
1 CTCTTCTCCTCCTCCTCCACACTCTCC
28653918 CTCTTCTCCT-CTCCTCCACACTCTCC
1 CTCTTCTCCTCCTCCTCCACACTCTCC
28653944 CT
1 CT
28653946 TGGCTTCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 5 0.20
25 10 0.40
26 10 0.40
ACGTcount: A:0.06, C:0.57, G:0.00, T:0.38
Consensus pattern (27 bp):
CTCTTCTCCTCCTCCTCCACACTCTCC
Found at i:28655084 original size:2 final size:2
Alignment explanation
Indices: 28655077--28655121 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
28655067 TAGTACACTC
*
28655077 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28655119 AT A
1 AT A
28655122 ATTAGAAGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28656561 original size:25 final size:23
Alignment explanation
Indices: 28656531--28656577 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
28656521 TGGTTAATTA
28656531 TCAAATTTAACTAAAAAAATATAAT
1 TCAAA-TTAAC-AAAAAAATATAAT
*
28656556 TCAAATTGACAAAAAAATATAA
1 TCAAATTAACAAAAAAATATAA
28656578 ACGTTGGGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.57
24 4 0.19
25 5 0.24
ACGTcount: A:0.62, C:0.09, G:0.02, T:0.28
Consensus pattern (23 bp):
TCAAATTAACAAAAAAATATAAT
Found at i:28658546 original size:3 final size:3
Alignment explanation
Indices: 28658538--28658564 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
28658528 TTAAAAAACC
28658538 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
28658565 AAGAAACACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:28660170 original size:13 final size:13
Alignment explanation
Indices: 28660152--28660178 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28660142 TAAAATACAC
28660152 AAATAATTTGCTT
1 AAATAATTTGCTT
28660165 AAATAATTTGCTT
1 AAATAATTTGCTT
28660178 A
1 A
28660179 TCAAAATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (13 bp):
AAATAATTTGCTT
Found at i:28663932 original size:16 final size:17
Alignment explanation
Indices: 28663893--28663936 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
28663883 TTAGATTGTA
28663893 TTTTTTTTACTCTTCTTC
1 TTTTTTTTA-TCTTCTTC
*
28663911 CTTTTTTT-TCTTCTTC
1 TTTTTTTTATCTTCTTC
28663927 TTTTTTTTAT
1 TTTTTTTTAT
28663937 TGCCCAACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 15 0.65
17 1 0.04
18 7 0.30
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTTTTATCTTCTTC
Found at i:28664774 original size:13 final size:13
Alignment explanation
Indices: 28664756--28664780 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28664746 TTCAATAAAA
28664756 TTTTAAATTTAGT
1 TTTTAAATTTAGT
28664769 TTTTAAATTTAG
1 TTTTAAATTTAG
28664781 ATTTGGTTCG
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:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (13 bp):
TTTTAAATTTAGT
Found at i:28666170 original size:15 final size:15
Alignment explanation
Indices: 28666152--28666185 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28666142 CAAAACTAAG
*
28666152 ATTTTTAAAATATTT
1 ATTTTTAAAATATTC
*
28666167 ATTTTTACAATATTC
1 ATTTTTAAAATATTC
28666182 ATTT
1 ATTT
28666186 GTTCTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTTAAAATATTC
Found at i:28667231 original size:24 final size:24
Alignment explanation
Indices: 28667186--28667232 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
28667176 TTAGTTTAAG
**
28667186 TTTTAACTAGAAAAATGTAAATAA
1 TTTTAACTAGAAAAATACAAATAA
28667210 TTTTAACATA-AAAAATACAAATA
1 TTTTAAC-TAGAAAAATACAAATA
28667233 CACATAGGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.32
Consensus pattern (24 bp):
TTTTAACTAGAAAAATACAAATAA
Found at i:28668196 original size:21 final size:21
Alignment explanation
Indices: 28668172--28668211 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
28668162 TAAAACGTCG
28668172 TAGTTTT-ATCTTTTAACTTAA
1 TAGTTTTAAT-TTTTAACTTAA
28668193 TAGTTTTAATTTTTAACTT
1 TAGTTTTAATTTTTAACTT
28668212 TAGAAAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (21 bp):
TAGTTTTAATTTTTAACTTAA
Found at i:28672945 original size:50 final size:50
Alignment explanation
Indices: 28672880--28673044 Score: 177
Period size: 50 Copynumber: 3.3 Consensus size: 50
28672870 TACAGGATAA
* * * *
28672880 GTGTCATCGTCCACAGTGAAGCCGTTCAAAATTACGCAAAGTGATGAAAG
1 GTGTCATCGTTCACAGTGAAGCCGTTCAGAATTATGCAAAATGATGAAAG
* * * * * *
28672930 GTGTCATAGTTCACAGTGGAGCTGTTCAGAATTATGCAAATTTGAAGAGAG
1 GTGTCATCGTTCACAGTGAAGCCGTTCAGAATTATGCAAA-ATGATGAAAG
* ** * * *
28672981 GTGTCTTCGTTCATGGTGAAACCGTTTAGAATTATGCAAAATGATGAATG
1 GTGTCATCGTTCACAGTGAAGCCGTTCAGAATTATGCAAAATGATGAAAG
28673031 GTGTCATCGTTCAC
1 GTGTCATCGTTCAC
28673045 GACAAAGTCA
Statistics
Matches: 91, Mismatches: 23, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
50 52 0.57
51 39 0.43
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (50 bp):
GTGTCATCGTTCACAGTGAAGCCGTTCAGAATTATGCAAAATGATGAAAG
Found at i:28680234 original size:33 final size:34
Alignment explanation
Indices: 28680186--28680252 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
28680176 AAGACTTTCT
* *
28680186 CTCTCTTCTTTTTTTTTTTTCTCTAAATCAAATA
1 CTCTCTTCTTTTTTTTCTCTCTCTAAATCAAATA
* *
28680220 CTCTC-TCTTTTTTTTCTCTCTTTGAATCAAATA
1 CTCTCTTCTTTTTTTTCTCTCTCTAAATCAAATA
28680253 AGAGAGAGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 24 0.83
34 5 0.17
ACGTcount: A:0.19, C:0.22, G:0.01, T:0.57
Consensus pattern (34 bp):
CTCTCTTCTTTTTTTTCTCTCTCTAAATCAAATA
Found at i:28681622 original size:13 final size:14
Alignment explanation
Indices: 28681596--28681624 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
28681586 TTTTATATTT
28681596 ATTTTAATAAAAAA
1 ATTTTAATAAAAAA
28681610 ATTTTAA-AAAAAA
1 ATTTTAATAAAAAA
28681623 AT
1 AT
28681625 CTATAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATTTTAATAAAAAA
Found at i:28687776 original size:2 final size:2
Alignment explanation
Indices: 28687769--28687805 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
28687759 AACTACATTT
28687769 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28687806 GCCCTGTGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28688092 original size:25 final size:23
Alignment explanation
Indices: 28688064--28688110 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
28688054 CGATATATGT
*
28688064 GTTATAATATTTTATTGATGTTGAC
1 GTTAAAATA-TTTATTG-TGTTGAC
28688089 GTTAAAATATTTATTGTGTTGA
1 GTTAAAATATTTATTGTGTTGA
28688111 TGAAATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 7 0.33
25 8 0.38
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.51
Consensus pattern (23 bp):
GTTAAAATATTTATTGTGTTGAC
Found at i:28693910 original size:3 final size:3
Alignment explanation
Indices: 28693902--28693927 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28693892 TATCTATCTG
28693902 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
28693928 AACTCATCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28699267 original size:22 final size:21
Alignment explanation
Indices: 28699215--28699267 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
28699205 TTTAAAACAG
28699215 TAATAAAAT-TAATAATAAAA
1 TAATAAAATATAATAATAAAA
* * *
28699235 TAAGAATAATATAATATTCAAA
1 TAATAA-AATATAATAATAAAA
28699257 TAATAACAATA
1 TAATAA-AATA
28699268 ACATAGTAGC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 5 0.19
21 3 0.12
22 18 0.69
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (21 bp):
TAATAAAATATAATAATAAAA
Found at i:28703267 original size:26 final size:25
Alignment explanation
Indices: 28703207--28703267 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
28703197 AAATATTTAT
*
28703207 AATATATAATATATAAATTAATAAAA
1 AATATA-AAAATATAAATTAATAAAA
*
28703233 AATAAAAAAATATAAACTTAA-ACAAA
1 AATATAAAAATATAAA-TTAATA-AAA
*
28703259 CATATAAAA
1 AATATAAAA
28703268 GAAATAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 10 0.34
26 19 0.66
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (25 bp):
AATATAAAAATATAAATTAATAAAA
Found at i:28706530 original size:90 final size:91
Alignment explanation
Indices: 28706377--28706560 Score: 307
Period size: 90 Copynumber: 2.0 Consensus size: 91
28706367 GGATGTAAAA
* *
28706377 ATGTATGGTGTTATAGTCAAATGATTAGGCAGATAATGATCATCTAATACGACTATATTCCTAAA
1 ATGTATGATGTTATAGTCAAATGATTAGGCAAATAATGATCATCTAATACGACTATATTCCTAAA
* *
28706442 ATATATG-AAAAACCCTTAAATGTGT
66 ATAAATGAAAAAACCCTTAAACGTGT
*
28706467 ATGTATGATGTTATAGTCAAATGATTAGGCAAATAATGATCATTTAATACGACTATATTCCTAAA
1 ATGTATGATGTTATAGTCAAATGATTAGGCAAATAATGATCATCTAATACGACTATATTCCTAAA
*
28706532 ATAAATGAAAAAACCCTTATACGTGT
66 ATAAATGAAAAAACCCTTAAACGTGT
28706558 ATG
1 ATG
28706561 ATTTGTTGAG
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
90 68 0.78
91 19 0.22
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (91 bp):
ATGTATGATGTTATAGTCAAATGATTAGGCAAATAATGATCATCTAATACGACTATATTCCTAAA
ATAAATGAAAAAACCCTTAAACGTGT
Found at i:28707008 original size:26 final size:26
Alignment explanation
Indices: 28706979--28707056 Score: 156
Period size: 26 Copynumber: 3.0 Consensus size: 26
28706969 AATTGGGTGG
28706979 CCTGTATTTCCTGAGTGTTGTGGACA
1 CCTGTATTTCCTGAGTGTTGTGGACA
28707005 CCTGTATTTCCTGAGTGTTGTGGACA
1 CCTGTATTTCCTGAGTGTTGTGGACA
28707031 CCTGTATTTCCTGAGTGTTGTGGACA
1 CCTGTATTTCCTGAGTGTTGTGGACA
28707057 AGGTCGGAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.15, C:0.19, G:0.27, T:0.38
Consensus pattern (26 bp):
CCTGTATTTCCTGAGTGTTGTGGACA
Found at i:28712347 original size:35 final size:34
Alignment explanation
Indices: 28712301--28712718 Score: 141
Period size: 35 Copynumber: 12.1 Consensus size: 34
28712291 GCATTTAAAA
* *
28712301 TTTGCTTTGCTTTGCTTTATATTATTTTATATTGT
1 TTTGCTTTGCTTTGCTTTATATTATTTGAT-TTGC
* *
28712336 TTTGCTTTGCTTTGCTTTATATTGCTTTGCTTTGC
1 TTTGCTTTGCTTTGCTTTATATT-ATTTGATTTGC
* * * *
28712371 TTTACTTTACTTTGCTTTATATTACTTTGCTTT-A
1 TTTGCTTTGCTTTGCTTTATATTA-TTTGATTTGC
* * * *
28712405 TATTACTTTGTTTTGCTTTATATTGCTTTGCTTTGC
1 T-TTGCTTTGCTTTGCTTTATATT-ATTTGATTTGC
* * * * *
28712441 TTT-ATATTACTTTGGTTTATATTGCTTTGCTTTGC
1 TTTGCT-TTGCTTTGCTTTATATT-ATTTGATTTGC
* *
28712476 TTT-ATATGGCTTTGC-TT-TA-TA--T-A---GC
1 TTTGCT-TTGCTTTGCTTTATATTATTTGATTTGC
* *
28712501 TTTGCTTTGCTTTGCTTTATATTGCTTTGCTTTGC
1 TTTGCTTTGCTTTGCTTTATATT-ATTTGATTTGC
* *
28712536 TTTATATGGCTTTGCTTTGCTTTATATTGCTTTGCTTTGC
1 --T-T-T-GCTTTGCTTTGCTTTATATT-ATTTGATTTGC
* * * ** *
28712576 TGT-ATATAGCTTTGCTTTATATGGCTTTGCTTTGC
1 TTTGCT-TTGCTTTGCTTTATAT-TATTTGATTTGC
* * * *
28712611 TTT-ATATTGCTTTGCTTTCTATTGCTTT-ATATAGC
1 TTTGCT-TTGCTTTGCTTTATATT-ATTTGAT-TTGC
* * * * *
28712646 TTTTCTTTTCTTTGCTTTGCT-TTGCTTT-ATATTAC
1 TTTGCTTTGCTTTGCTTT-ATATT-ATTTGAT-TTGC
* *
28712681 TTTGCTTTGCTTTGCTTTATGTTACTTTGCTTTGC
1 TTTGCTTTGCTTTGCTTTATATTA-TTTGATTTGC
28712716 TTT
1 TTT
28712719 ATATAGCTTT
Statistics
Matches: 307, Mismatches: 45, Indels: 62
0.74 0.11 0.15
Matches are distributed among these distances:
25 13 0.04
26 3 0.01
27 2 0.01
28 1 0.00
29 1 0.00
31 1 0.00
32 1 0.00
33 2 0.01
34 7 0.02
35 230 0.75
36 10 0.03
37 1 0.00
38 2 0.01
39 1 0.00
40 32 0.10
ACGTcount: A:0.12, C:0.14, G:0.14, T:0.60
Consensus pattern (34 bp):
TTTGCTTTGCTTTGCTTTATATTATTTGATTTGC
Found at i:28712390 original size:60 final size:59
Alignment explanation
Indices: 28712302--28712863 Score: 277
Period size: 60 Copynumber: 9.3 Consensus size: 59
28712292 CATTTAAAAT
28712302 TTGCTTTGCTTTGCTTTA--TA-TTAT--TTTATATTGTTTTGCTTTGCTTTGCTTTATA
1 TTGCTTTGCTTTGCTTTATTTACTT-TGCTTTATATTGTTTTGCTTTGCTTTGCTTTATA
* *
28712357 TTGCTTTGCTTTGCTTTACTTTACTTTGCTTTATATTACTTTGCTTTATATTACTTTGTTTTGCT
1 TTGCTTTGCTTTGCTTTA-TTTACTTTGC-TT-TA-TA--TTG---T-T-TTGCTTTGCTTTGCT
28712422 TTATA
55 TTATA
*
28712427 TTGCTTTGCTTTGCTTTATATTACTTTGGTTTATA-----TTGCTTTGCTTTGCTTTATA
1 TTGCTTTGCTTTGCTTTAT-TTACTTTGCTTTATATTGTTTTGCTTTGCTTTGCTTTATA
* * * * * * *
28712482 TGGCTTTGCTTT-ATATAGCTTTGCTTTGCTTTGCT-TTATATTGCTTTGCTTTGCTTTATA
1 TTGCTTTGCTTTGCTTTA--TTTACTTTGCTTT-ATATTGTTTTGCTTTGCTTTGCTTTATA
* * ** * * *
28712542 TGGCTTTGCTTTGCTTTATATTGCTTTGC-TT-TGCTG-TAT--ATAGCTTTGCTTTATA
1 TTGCTTTGCTTTGCTTTAT-TTACTTTGCTTTATATTGTTTTGCTTTGCTTTGCTTTATA
* * * * * * * *
28712597 TGGCTTTGCTTTGCTTTATATTGCTTTGCTTTCTATTGCTTT-ATATAGCTTTTCTTT-TCT
1 TTGCTTTGCTTTGCTTTAT-TTACTTTGCTTTATATTGTTTTGCT-TTGCTTTGCTTTAT-A
*
28712657 TTGCTTTGCTTTGCTTTATATTACTTTGCTTTGCT-TTGCTTTATGTTACTTTGCTTTGCTTTAT
1 TTGCTTTGCTTTGCTTTAT-TTACTTTGCTTT-ATATTG-TTT-TG---CTTTGCTTTGCTTTAT
28712721 A
59 A
* * * * * *
28712722 TAGCTTTTCTTTTCTTTTCTTTGCTTTGCTTTGATTTATAT-TACTTTGCTTTGCTTTACTTTAT
1 TTGCTTTGCTTTGC-TTTATTTACTTTGCTTT-A--TAT-TGT--TTTGCTTTGCTTTGCTTTAT
28712786 A
59 A
* * * ** *
28712787 TTACTTTGCTTTGCTTTATATAGCTTTGATTTATATTACTTTGCTTT-ATATTGCTTTATA
1 TTGCTTTGCTTTGCTTTATTTA-CTTTGCTTTATATTGTTTTGCTTTGCT-TTGCTTTATA
* * *
28712847 TAGCTTTTCTTTTCTTT
1 TTGCTTTGCTTTGCTTT
28712864 GCTTTGCTTT
Statistics
Matches: 401, Mismatches: 54, Indels: 99
0.72 0.10 0.18
Matches are distributed among these distances:
54 3 0.01
55 100 0.25
56 4 0.01
57 5 0.01
58 6 0.01
59 7 0.02
60 115 0.29
61 10 0.02
62 6 0.01
63 2 0.00
64 6 0.01
65 70 0.17
66 6 0.01
67 4 0.01
68 6 0.01
69 7 0.02
70 44 0.11
ACGTcount: A:0.13, C:0.14, G:0.13, T:0.60
Consensus pattern (59 bp):
TTGCTTTGCTTTGCTTTATTTACTTTGCTTTATATTGTTTTGCTTTGCTTTGCTTTATA
Found at i:28712672 original size:25 final size:25
Alignment explanation
Indices: 28712644--28712803 Score: 103
Period size: 25 Copynumber: 6.2 Consensus size: 25
28712634 GCTTTATATA
28712644 GCTTTTCTTTTCTTTGCTTTGCTTT
1 GCTTTTCTTTTCTTTGCTTTGCTTT
* *
28712669 GCTTTAT-ATTACTTTGCTTTGCTTT
1 GCTTT-TCTTTTCTTTGCTTTGCTTT
* *
28712694 GCTTTAT-GTTACTTTGCTTTGCTTTATAT
1 GCTTT-TCTTTTCTTTGCTTTGC--T-T-T
*
28712723 AGCTTTTCTTTTCTTTTCTTTGCTTT
1 -GCTTTTCTTTTCTTTGCTTTGCTTT
** * *
28712749 GCTTTGATTTAT-ATTACTTTGCTTT
1 GCTTTTCTTT-TCTTTGCTTTGCTTT
* * *
28712774 GCTTTACTTTAT-ATTACTTTGCTTT
1 GCTTTTCTTT-TCTTTGCTTTGCTTT
28712799 GCTTT
1 GCTTT
28712804 ATATAGCTTT
Statistics
Matches: 115, Mismatches: 12, Indels: 16
0.80 0.08 0.11
Matches are distributed among these distances:
25 89 0.77
26 3 0.03
27 2 0.02
28 2 0.02
29 2 0.02
30 17 0.15
ACGTcount: A:0.10, C:0.16, G:0.11, T:0.62
Consensus pattern (25 bp):
GCTTTTCTTTTCTTTGCTTTGCTTT
Found at i:28712804 original size:25 final size:24
Alignment explanation
Indices: 28712740--28712805 Score: 114
Period size: 25 Copynumber: 2.7 Consensus size: 24
28712730 CTTTTCTTTT
28712740 CTTTGCTTTGCTTTGATTTATATTA
1 CTTTGCTTTGCTTT-ATTTATATTA
28712765 CTTTGCTTTGCTTTACTTTATATTA
1 CTTTGCTTTGCTTTA-TTTATATTA
28712790 CTTTGCTTTGCTTTAT
1 CTTTGCTTTGCTTTAT
28712806 ATAGCTTTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
24 2 0.05
25 38 0.95
ACGTcount: A:0.14, C:0.15, G:0.11, T:0.61
Consensus pattern (24 bp):
CTTTGCTTTGCTTTATTTATATTA
Found at i:28712833 original size:20 final size:20
Alignment explanation
Indices: 28712337--28712814 Score: 387
Period size: 20 Copynumber: 24.4 Consensus size: 20
28712327 TTATATTGTT
28712337 TTGCTTTGCTTTGCTTTATA
1 TTGCTTTGCTTTGCTTTATA
28712357 TTGCTTTGCTTTGC-TT-TA
1 TTGCTTTGCTTTGCTTTATA
*
28712375 ---CTTTACTTTGCTTTATA
1 TTGCTTTGCTTTGCTTTATA
*
28712392 -----TTACTTTGCTTTATA
1 TTGCTTTGCTTTGCTTTATA
* *
28712407 TTACTTTGTTTTGCTTTATA
1 TTGCTTTGCTTTGCTTTATA
28712427 TTGCTTTGCTTTGCTTTATA
1 TTGCTTTGCTTTGCTTTATA
*
28712447 TTACTTTG----G-TTTATA
1 TTGCTTTGCTTTGCTTTATA
28712462 TTGCTTTGCTTTGCTTTATA
1 TTGCTTTGCTTTGCTTTATA
* * *
28712482 TGGCTTTGCTTT-ATATAGCT-
1 TTGCTTTGCTTTGCTTTA--TA
28712502 TTGCTTTGCTTTGCTTTATA
1 TTGCTTTGCTTTGCTTTATA
28712522 TTGCTTTGCTTTGCTTTATA
1 TTGCTTTGCTTTGCTTTATA
*
28712542 TGGCTTTGCTTTGCTTTATA
1 TTGCTTTGCTTTGCTTTATA
*
28712562 TTGCTTTGCTTTGCTGTATA
1 TTGCTTTGCTTTGCTTTATA
*
28712582 -----TAGCTTTGCTTTATA
1 TTGCTTTGCTTTGCTTTATA
*
28712597 TGGCTTTGCTTTGCTTTATA
1 TTGCTTTGCTTTGCTTTATA
28712617 TTGCTTTGCTTTCTATTGCTTTATA
1 TTGCTTTG----CT-TTGCTTTATA
* * * *
28712642 TAGCTTTTCTTTTCTTTGCT-
1 TTGCTTTGCTTTGCTTT-ATA
*
28712662 TTGCTTTGCTTT-ATATTACT-
1 TTGCTTTGCTTTGCT-TTA-TA
*
28712682 TTGCTTTGCTTTGCTTTATG
1 TTGCTTTGCTTTGCTTTATA
*
28712702 TTACTTTGCTTTGCTTTATA
1 TTGCTTTGCTTTGCTTTATA
* * * *
28712722 TAGCTTTTCTTTTCTTT-TCT
1 TTGCTTTGCTTTGCTTTAT-A
*
28712742 TTGCTTTGCTTTGATTTATATTA
1 TTGCTTTGCTTTG-CTT-TA-TA
*
28712765 CTTTGCTTTGCTTTACTTTATA
1 --TTGCTTTGCTTTGCTTTATA
*
28712787 TTACTTTGCTTTGCTTTATA
1 TTGCTTTGCTTTGCTTTATA
*
28712807 TAGCTTTG
1 TTGCTTTG
28712815 ATTTATATTA
Statistics
Matches: 373, Mismatches: 47, Indels: 76
0.75 0.09 0.15
Matches are distributed among these distances:
15 51 0.14
16 3 0.01
17 2 0.01
18 2 0.01
19 10 0.03
20 257 0.69
21 10 0.03
22 3 0.01
23 2 0.01
24 5 0.01
25 28 0.08
ACGTcount: A:0.12, C:0.15, G:0.14, T:0.59
Consensus pattern (20 bp):
TTGCTTTGCTTTGCTTTATA
Found at i:28712858 original size:15 final size:15
Alignment explanation
Indices: 28712794--28712843 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
28712784 ATATTACTTT
28712794 GCTTTGCTTTATATA
1 GCTTTGCTTTATATA
*
28712809 GCTTTGATTTATATTA
1 GCTTTGCTTTATA-TA
*
28712825 -CTTTGCTTTATATT
1 GCTTTGCTTTATATA
28712839 GCTTT
1 GCTTT
28712844 ATATAGCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 1 0.03
15 27 0.90
16 2 0.07
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.58
Consensus pattern (15 bp):
GCTTTGCTTTATATA
Found at i:28712910 original size:15 final size:15
Alignment explanation
Indices: 28712890--28713399 Score: 149
Period size: 15 Copynumber: 33.7 Consensus size: 15
28712880 ATAGCAAAGC
*
28712890 AAAGCAAAGTAATAT
1 AAAGCAAAGCAATAT
*
28712905 AAAGCAAAACAATAT
1 AAAGCAAAGCAATAT
28712920 AAAGCAAAGCAAGGCAATAT
1 AAAGC--A--AA-GCAATAT
* *
28712940 AAAGCAAAACAA-AGC
1 AAAGCAAAGCAATA-T
* *
28712955 AAAGTAATA-TAATAT
1 AAAGCAA-AGCAATAT
*
28712970 GAAGCAAAGCAATAT
1 AAAGCAAAGCAATAT
*
28712985 AAAGAAAAGC-----
1 AAAGCAAAGCAATAT
* *
28712995 AAAGTAAAGTAATAT
1 AAAGCAAAGCAATAT
* * *
28713010 AAAGCAATGTAA-AGC
1 AAAGCAAAGCAATA-T
* *
28713025 AAAGCAATGCAA-AG
1 AAAGCAAAGCAATAT
**
28713039 AAATATAAAGCAATAT
1 AAA-GCAAAGCAATAT
*
28713055 AAAGCAAAGCAA-AGA
1 AAAGCAAAGCAATA-T
* *
28713070 AAAGTAATA-TAATAT
1 AAAGCAA-AGCAATAT
*
28713085 AAAGCAAAGTAATAT
1 AAAGCAAAGCAATAT
*
28713100 AAAGAAAAGCAAAGTAAAGT
1 AAAGCAAAGC-AA-T--A-T
*
28713120 AAAGCAAAGTAATAT
1 AAAGCAAAGCAATAT
*
28713135 AAAGCAAAGCAA-AGC
1 AAAGCAAAGCAATA-T
*
28713150 AAAGCAAAGAAATAT
1 AAAGCAAAGCAATAT
*
28713165 AAAGCAATATAAAGCAA-AGC
1 AAAGC-----AAAGCAATA-T
28713185 AAAGCAAAGCAATAT
1 AAAGCAAAGCAATAT
* *
28713200 AAAGCAATA-TAA-AGC
1 AAAGCAA-AGCAATA-T
*
28713215 AAAGCAAAGTAATAT
1 AAAGCAAAGCAATAT
*
28713230 AATA-TAAAGCAATAT
1 AA-AGCAAAGCAATAT
*
28713245 AAAGCAATGC-----
1 AAAGCAAAGCAATAT
*
28713255 AAAGCAAAGTAATAT
1 AAAGCAAAGCAATAT
*
28713270 AAAGAAAAGCAA-AGT
1 AAAGCAAAGCAATA-T
*
28713285 AAAACAAAGCAA-AGT
1 AAAGCAAAGCAATA-T
* *
28713300 AATA-TAAAGCAA-AGC
1 AA-AGCAAAGCAATA-T
*
28713315 AAAGCAAAGTAATAT
1 AAAGCAAAGCAATAT
* *
28713330 AAAGCAATGCAA-AGC
1 AAAGCAAAGCAATA-T
*
28713345 AAAGCAAAGAAATAT
1 AAAGCAAAGCAATAT
* *
28713360 AAAGCAATA-TAA-AGC
1 AAAGCAA-AGCAATA-T
28713375 AAAGCAAAGCAATAT
1 AAAGCAAAGCAATAT
28713390 AAAGCAAAGC
1 AAAGCAAAGC
28713400 TTCTTTGATA
Statistics
Matches: 369, Mismatches: 70, Indels: 112
0.67 0.13 0.20
Matches are distributed among these distances:
10 16 0.04
14 17 0.05
15 272 0.74
16 23 0.06
17 2 0.01
18 2 0.01
19 6 0.02
20 31 0.08
ACGTcount: A:0.61, C:0.11, G:0.15, T:0.14
Consensus pattern (15 bp):
AAAGCAAAGCAATAT
Found at i:28712910 original size:20 final size:20
Alignment explanation
Indices: 28712885--28713399 Score: 222
Period size: 20 Copynumber: 26.5 Consensus size: 20
28712875 GTTTGATAGC
28712885 AAAGCAAAGCAAAGTAATAT
1 AAAGCAAAGCAAAGTAATAT
*
28712905 AAAGC--A--AAA-CAATAT
1 AAAGCAAAGCAAAGTAATAT
* *
28712920 AAAGCAAAGCAAGGCAATAT
1 AAAGCAAAGCAAAGTAATAT
28712940 AAAGCAAAACAAAGCAAAGTAATAT
1 AAAG-----CAAAGCAAAGTAATAT
*
28712965 AATATG--AAGCAAAGCAATAT
1 AA-A-GCAAAGCAAAGTAATAT
*
28712985 AAAGAAAAGCAAAGTAA-AGT
1 AAAGCAAAGCAAAGTAATA-T
* * *
28713005 AATA-TAAAGCAATGTAA-AGC
1 AA-AGCAAAGCAAAGTAATA-T
* *
28713025 AAAGCAATGCAAAGAAATAT
1 AAAGCAAAGCAAAGTAATAT
* *
28713045 AAAGC--A--ATA-TAA-AGC
1 AAAGCAAAGCAAAGTAATA-T
*
28713060 AAAGCAAAGAAAAGTAATAT
1 AAAGCAAAGCAAAGTAATAT
*
28713080 AATA-TAAAGCAAAGTAATAT
1 AA-AGCAAAGCAAAGTAATAT
*
28713100 AAAGAAAAGCAAAG-----T
1 AAAGCAAAGCAAAGTAATAT
*
28713115 AAAGTAAAGCAAAGTAATAT
1 AAAGCAAAGCAAAGTAATAT
* *
28713135 AAAGCAAAGCAAAGCAA-AGC
1 AAAGCAAAGCAAAGTAATA-T
** *
28713155 AAAG-AAATATAAAGCAATAT
1 AAAGCAAA-GCAAAGTAATAT
*
28713175 AAAGCAAAGCAAAG-----C
1 AAAGCAAAGCAAAGTAATAT
* *
28713190 AAAGCAATA-TAAAGCAATAT
1 AAAGCAA-AGCAAAGTAATAT
28713210 AAAGCAAAGCAAAGTAATAT
1 AAAGCAAAGCAAAGTAATAT
* *
28713230 AATA-TAAAGCAATA-TAA-AGC
1 AA-AGCAAAGCAA-AGTAATA-T
*
28713250 AATGCAAAGCAAAGTAATAT
1 AAAGCAAAGCAAAGTAATAT
* * *
28713270 AAAGAAAAGCAAAGTAAAAC
1 AAAGCAAAGCAAAGTAATAT
* *
28713290 AAAGCAAAGTAATA-TAA-AGC
1 AAAGCAAAGCAA-AGTAATA-T
28713310 AAAGCAAAGCAAAGTAATAT
1 AAAGCAAAGCAAAGTAATAT
* * *
28713330 AAAGCAATGCAAAGCAA-AGC
1 AAAGCAAAGCAAAGTAATA-T
** *
28713350 AAAG-AAATATAAAGCAATAT
1 AAAGCAAA-GCAAAGTAATAT
*
28713370 AAAGCAAAGCAAAGCAATAT
1 AAAGCAAAGCAAAGTAATAT
28713390 AAAGCAAAGC
1 AAAGCAAAGC
28713400 TTCTTTGATA
Statistics
Matches: 379, Mismatches: 59, Indels: 114
0.69 0.11 0.21
Matches are distributed among these distances:
14 1 0.00
15 42 0.11
16 6 0.02
17 2 0.01
18 2 0.01
19 20 0.05
20 271 0.72
21 17 0.04
25 16 0.04
26 1 0.00
27 1 0.00
ACGTcount: A:0.61, C:0.11, G:0.15, T:0.14
Consensus pattern (20 bp):
AAAGCAAAGCAAAGTAATAT
Found at i:28712931 original size:35 final size:35
Alignment explanation
Indices: 28712885--28713312 Score: 226
Period size: 35 Copynumber: 12.8 Consensus size: 35
28712875 GTTTGATAGC
28712885 AAAGCAAAGCAAAGTAATATAAAGCAAAACAATAT
1 AAAGCAAAGCAAAGTAATATAAAGCAAAACAATAT
* *
28712920 AAAGCAAAGCAAGGCAATATAAAGCAAAAC-----
1 AAAGCAAAGCAAAGTAATATAAAGCAAAACAATAT
* * *
28712950 AAAGCAAAGTAATA-TAATATGAAGCAAAGCAATAT
1 AAAGCAAAGCAA-AGTAATATAAAGCAAAACAATAT
* * * *
28712985 AAAGAAAAGCAAAGTAA-AGTAATA-TAAAGCAATGT
1 AAAGCAAAGCAAAGTAATA-TAA-AGCAAAACAATAT
* * * *
28713020 AAAGCAAAGCAATGCAA-AGAAA-TATAAAGCAATAT
1 AAAGCAAAGCAAAGTAATATAAAGCA-AAA-CAATAT
* * *
28713055 AAAGCAAAGCAAAG----A-AAAGTAATATAATAT
1 AAAGCAAAGCAAAGTAATATAAAGCAAAACAATAT
28713085 -----AAAGCAAAGTAATATAAAG-AAAAGCAA-AGT
1 AAAGCAAAGCAAAGTAATATAAAGCAAAA-CAATA-T
* *
28713115 AAAGTAAAGCAAAGTAATATAAAGCAAAGC-----
1 AAAGCAAAGCAAAGTAATATAAAGCAAAACAATAT
* * * *
28713145 AAAGCAAAGCAAAGAAATATAAAGCAATATAA-AGC
1 AAAGCAAAGCAAAGTAATATAAAGCAAAACAATA-T
*
28713180 AAAGCAAAGCAAAGCAATATAAAG-----CAATAT
1 AAAGCAAAGCAAAGTAATATAAAGCAAAACAATAT
* *
28713210 AAAGCAAAGCAAAGTAATATAATA-TAAAGCAATAT
1 AAAGCAAAGCAAAGTAATATAA-AGCAAAACAATAT
28713245 AAAGCAATGCAAAGCAAAGTAATATAAAG-AAAAGCAA-AGT
1 --A--AA-GCAAAGCAAAGTAATATAAAGCAAAA-CAATA-T
*
28713285 AAAACAAAGCAAAGTAATATAAAGCAAA
1 AAAGCAAAGCAAAGTAATATAAAGCAAA
28713313 GCAAAGCAAA
Statistics
Matches: 312, Mismatches: 35, Indels: 91
0.71 0.08 0.21
Matches are distributed among these distances:
25 9 0.03
29 5 0.02
30 84 0.27
31 7 0.02
32 3 0.01
33 3 0.01
34 6 0.02
35 154 0.49
36 9 0.03
37 1 0.00
38 1 0.00
39 7 0.02
40 23 0.07
ACGTcount: A:0.61, C:0.10, G:0.14, T:0.14
Consensus pattern (35 bp):
AAAGCAAAGCAAAGTAATATAAAGCAAAACAATAT
Found at i:28712955 original size:60 final size:60
Alignment explanation
Indices: 28712882--28713397 Score: 271
Period size: 65 Copynumber: 8.1 Consensus size: 60
28712872 TTGGTTTGAT
* *
28712882 AGCAAAGCAAAGCAAAGTAATATAAAGCAAAACAATATAAAGCAAAGCAAGGCAATATAA
1 AGCAAAACAAAGCAAAGTAATATAAAGCAAAACAATATAAAGCAAAGCAAAGCAATATAA
* * *
28712942 AGCAAAACAAAGCAAAGTAATATAATATGAAGCAAAGCAATATAAAGAAAAGCAAAGTAAAGTAA
1 AGCAAAACAAAGCAAAGT-A-AT-ATA--AAGCAAAACAATAT-----AAAGCAAAGCAAAGCAA
28713007 TATAA
56 TATAA
*** * * ** *
28713012 AGCAATGTAAAGCAAAGCAATGCAAAGAAATATAAAGCAATATAAAGCAAAGCAAAG-AAAAGTA
1 AGCAAAACAAAGCAAAGTAAT--ATA-AAGCA-AAA-CAATATAAAGCAAAGCAAAGCAATA-TA
28713076 A
60 A
* * * * *
28713077 TA-TAATATAAAGCAAAGTAATATAAAG-AAAAGCAA-AGTAAAGTAAAGCAAAGTAATATAA
1 -AGCAAAACAAAGCAAAGTAATATAAAGCAAAA-CAATA-TAAAGCAAAGCAAAGCAATATAA
* * * *
28713137 AGCAAAGCAAAGCAAAGCAAAGAAATATAAAGCAATATAA-AGCAAAGCAAAGCAAAGCAATATA
1 AGC--A--AAA-CAAAGCAAAGTAATATAAAGCAAAACAATA-TAAAGCAAAGCAAAGCAATATA
28713201 A
60 A
* * *
28713202 AGCAATATAAAGCAAAGCAAAGTAATATAATA-TAAAGCAATATAAAGCAATGCAAAGCAA-AGT
1 AGC---A-AAA-CAAAGCAAAGTAATATAA-AGCAAAACAATATAAAGCAAAGCAAAGCAATA-T
28713265 AA
59 AA
* * * **
28713267 TA-TAAAGA-AAAGCAAAGTAAAACAAAGCAAAGTAATATAAAGCAAAGCAAAGCAAAGTAATAT
1 -AGCAAA-ACAAAGCAAAGTAATATAAAGCAAAACAATATAAAGCAAAGCAAAGC-----AATAT
28713330 AA
59 AA
** * * *
28713332 AGCAATGCAAAGCAAAGCAA-AGAAA-TATAAAGCAATATAAAGCAAAGCAAAGCAATATAA
1 AGCAAAACAAAGCAAAGTAATATAAAGCA-AAA-CAATATAAAGCAAAGCAAAGCAATATAA
28713392 AGCAAA
1 AGCAAA
28713398 GCTTCTTTGA
Statistics
Matches: 359, Mismatches: 56, Indels: 82
0.72 0.11 0.16
Matches are distributed among these distances:
59 3 0.01
60 91 0.25
61 7 0.02
62 7 0.02
63 6 0.02
64 13 0.04
65 172 0.48
66 10 0.03
68 6 0.02
69 5 0.01
70 39 0.11
ACGTcount: A:0.61, C:0.11, G:0.15, T:0.14
Consensus pattern (60 bp):
AGCAAAACAAAGCAAAGTAATATAAAGCAAAACAATATAAAGCAAAGCAAAGCAATATAA
Found at i:28712956 original size:45 final size:45
Alignment explanation
Indices: 28712905--28713386 Score: 207
Period size: 45 Copynumber: 11.2 Consensus size: 45
28712895 AAAGTAATAT
** *
28712905 AAAGCAAAACAATATAAAGCAAAGCAAGGCAATATAAAGCAAAA-C
1 AAAGCAAAGTAATATAAAGCAAAGCAAAGCAATATAAAG-AAAAGC
28712950 AAAGCAAAGTAATATAATATG--AAGCAAAGCAATATAAAGAAAAGC
1 AAAGCAAAGTAATATAA-A-GCAAAGCAAAGCAATATAAAGAAAAGC
* * * * * *
28712995 AAAGTAAAGTAATATAAAGCAATGTAAAGCAA-AGCAATGCAAAG-
1 AAAGCAAAGTAATATAAAGCAAAGCAAAGCAATA-TAAAGAAAAGC
** * * * * *
28713039 AAATATAAAGCAATATAAAGCAAAGCAAAG-AAAAGTAATATAATA-T
1 AAA-GCAAAGTAATATAAAGCAAAGCAAAGCAATA-TAA-AGAAAAGC
* *
28713085 AAAGCAAAGTAATATAAAG---A--AAAGC-----AAAGTAAAGT
1 AAAGCAAAGTAATATAAAGCAAAGCAAAGCAATATAAAGAAAAGC
* *
28713120 AAAGCAAAGTAATATAAAGCAAAGCAAAGCAA-AGCAAAGAAATA-T
1 AAAGCAAAGTAATATAAAGCAAAGCAAAGCAATA-TAAAGAAA-AGC
*
28713165 AAAGCAATA-TAA-AGCAAAGCAAAGCAAAGCAATATAAAGCAATATAAAGC
1 AAAGCAA-AGTAATA-TAAAGCAAAGCAAAGCAATATAAAG----A-AAAGC
* * * *
28713215 AAAGCAAAGTAATAT--A--ATA-TAAAGCAATATAAAGCAATGC
1 AAAGCAAAGTAATATAAAGCAAAGCAAAGCAATATAAAGAAAAGC
*
28713255 AAAGCAAAGTAATATAAAGAAAAGCAAAG-----T----AAAA-C
1 AAAGCAAAGTAATATAAAGCAAAGCAAAGCAATATAAAGAAAAGC
*
28713290 AAAGCAAAGTAATATAAAGCAAAGCAAAGCAA-AGTAATA-TAAAGC
1 AAAGCAAAGTAATATAAAGCAAAGCAAAGCAATA-TAA-AGAAAAGC
* * * ** *
28713335 AATGCAAAGCAA-AGCAAAG-AAATATAAAGCAATATAAAGCAAAGC
1 AAAGCAAAGTAATA-TAAAGCAAA-GCAAAGCAATATAAAGAAAAGC
28713380 AAAGCAA
1 AAAGCAA
28713387 TATAAAGCAA
Statistics
Matches: 338, Mismatches: 46, Indels: 106
0.69 0.09 0.22
Matches are distributed among these distances:
34 3 0.01
35 51 0.15
36 2 0.01
38 1 0.00
40 30 0.09
42 2 0.01
43 1 0.00
44 22 0.07
45 196 0.58
46 12 0.04
47 1 0.00
48 1 0.00
49 3 0.01
50 12 0.04
51 1 0.00
ACGTcount: A:0.61, C:0.11, G:0.15, T:0.14
Consensus pattern (45 bp):
AAAGCAAAGTAATATAAAGCAAAGCAAAGCAATATAAAGAAAAGC
Found at i:28712977 original size:25 final size:25
Alignment explanation
Indices: 28712905--28712981 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
28712895 AAAGTAATAT
* * *
28712905 AAAGCAAAACAATATAAAGCAAAGC
1 AAAGCAATATAATATGAAGCAAAGC
* *
28712930 AAGGCAATATAA-A-GCAAAACAAAGC
1 AAAGCAATATAATATG--AAGCAAAGC
*
28712955 AAAGTAATATAATATGAAGCAAAGC
1 AAAGCAATATAATATGAAGCAAAGC
28712980 AA
1 AA
28712982 TATAAAGAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
24 1 0.03
25 37 0.93
26 1 0.03
27 1 0.03
ACGTcount: A:0.61, C:0.13, G:0.14, T:0.12
Consensus pattern (25 bp):
AAAGCAATATAATATGAAGCAAAGC
Found at i:28712998 original size:10 final size:10
Alignment explanation
Indices: 28712985--28713398 Score: 128
Period size: 10 Copynumber: 42.4 Consensus size: 10
28712975 AAAGCAATAT
*
28712985 AAAGAAAAGC
1 AAAGTAAAGC
*
28712995 AAAGTAAAGT
1 AAAGTAAAGC
28713005 AATA-TAAAGC
1 AA-AGTAAAGC
*
28713015 AATGTAAAGC
1 AAAGTAAAGC
* *
28713025 AAAGCAATGC
1 AAAGTAAAGC
28713035 AAAG--AA--
1 AAAGTAAAGC
*
28713041 ATA-TAAAGC
1 AAAGTAAAGC
28713050 AATA-TAAAGC
1 AA-AGTAAAGC
* *
28713060 AAAGCAAAGA
1 AAAGTAAAGC
*
28713070 AAAGTAATA-T
1 AAAGTAA-AGC
28713080 AATA-TAAAGC
1 AA-AGTAAAGC
*
28713090 AAAGTAATA-T
1 AAAGTAA-AGC
*
28713100 AAAGAAAAGC
1 AAAGTAAAGC
*
28713110 AAAGTAAAGT
1 AAAGTAAAGC
* *
28713120 AAAGCAAAGT
1 AAAGTAAAGC
28713130 AATA-TAAAGC
1 AA-AGTAAAGC
*
28713140 AAAGCAAAGC
1 AAAGTAAAGC
*
28713150 AAAGCAAAG-
1 AAAGTAAAGC
*
28713159 AAATATAAAGC
1 AAA-GTAAAGC
28713170 AATA-TAAAGC
1 AA-AGTAAAGC
*
28713180 AAAGCAAAGC
1 AAAGTAAAGC
* *
28713190 AAAGCAATA-T
1 AAAGTAA-AGC
* *
28713200 AAAGCAATA-T
1 AAAGTAA-AGC
*
28713210 AAAGCAAAGC
1 AAAGTAAAGC
*
28713220 AAAGTAATA-T
1 AAAGTAA-AGC
28713230 AATA-TAAAGC
1 AA-AGTAAAGC
28713240 AATA-TAAAGC
1 AA-AGTAAAGC
* *
28713250 AATGCAAAGC
1 AAAGTAAAGC
*
28713260 AAAGTAATA-T
1 AAAGTAA-AGC
*
28713270 AAAGAAAAGC
1 AAAGTAAAGC
*
28713280 AAAGTAAAAC
1 AAAGTAAAGC
* *
28713290 AAAGCAAAGT
1 AAAGTAAAGC
28713300 AATA-TAAAGC
1 AA-AGTAAAGC
*
28713310 AAAGCAAAGC
1 AAAGTAAAGC
28713320 AAAGT--A--
1 AAAGTAAAGC
*
28713326 ATA-TAAAGC
1 AAAGTAAAGC
* *
28713335 AATGCAAAGC
1 AAAGTAAAGC
*
28713345 AAAGCAAAG-
1 AAAGTAAAGC
*
28713354 AAATATAAAGC
1 AAA-GTAAAGC
28713365 AATA-TAAAGC
1 AA-AGTAAAGC
*
28713375 AAAGCAAAGC
1 AAAGTAAAGC
28713385 AATA-TAAAGC
1 AA-AGTAAAGC
28713395 AAAG
1 AAAG
28713399 CTTCTTTGAT
Statistics
Matches: 306, Mismatches: 57, Indels: 82
0.69 0.13 0.18
Matches are distributed among these distances:
5 1 0.00
6 4 0.01
7 3 0.01
8 2 0.01
9 20 0.07
10 259 0.85
11 15 0.05
12 2 0.01
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.14
Consensus pattern (10 bp):
AAAGTAAAGC
Found at i:28713009 original size:25 final size:25
Alignment explanation
Indices: 28712920--28713351 Score: 180
Period size: 25 Copynumber: 17.7 Consensus size: 25
28712910 AAAACAATAT
*
28712920 AAAGCAAAGCAAGGCAATATAAAGC
1 AAAGCAAAGCAAAGCAATATAAAGC
* *
28712945 AAAACAAAGCAAAGTAATAT-AA--
1 AAAGCAAAGCAAAGCAATATAAAGC
* * *
28712967 TATG--AAGCAAAGCAATATAAAGA
1 AAAGCAAAGCAAAGCAATATAAAGC
* *
28712990 AAAGCAAAGTAAAGTAATATAAAGC
1 AAAGCAAAGCAAAGCAATATAAAGC
* *
28713015 AATGTAAAGCAAAGC-A-AT---GC
1 AAAGCAAAGCAAAGCAATATAAAGC
**
28713035 AAAG-AAATATAAAGCAATATAAAGC
1 AAAGCAAA-GCAAAGCAATATAAAGC
* * *
28713060 AAAGCAAAGAAAAGTAATATAATA-T
1 AAAGCAAAGCAAAGCAATATAA-AGC
* ** *
28713085 AAAGCAAAGTAATATAAAGA-AAAGC
1 AAAGCAAAGCAA-AGCAATATAAAGC
* *
28713110 AAAGTAAAGTAAAGCAAAGTAATATAAAGC
1 AAAGCAAAGCAAAGC-----AATATAAAGC
* **
28713140 AAAGCAAAGCAAAGCAA-AGAAATAT
1 AAAGCAAAGCAAAGCAATATAAA-GC
* *
28713165 AAAGCAATA-TAAAGCAA-AGCAAAGC
1 AAAGCAA-AGCAAAGCAATA-TAAAGC
*
28713190 AAAGCAATA-TAAAGCAATATAAAGC
1 AAAGCAA-AGCAAAGCAATATAAAGC
* *
28713215 AAAGCAAAGTAATA-TAATATAAAGC
1 AAAGCAAAGCAA-AGCAATATAAAGC
* * * *
28713240 AATA-TAAAGCAATGCAA-AGCAAAGT
1 AA-AGCAAAGCAAAGCAATA-TAAAGC
* *
28713265 AATA-TAAAGAAAAGCAA-AGT--A--
1 AA-AGCAAAGCAAAGCAATA-TAAAGC
*
28713286 AAA-CAAAGCAAAGTAATATAAAGC
1 AAAGCAAAGCAAAGCAATATAAAGC
*
28713310 AAAGCAAAGCAAAGTAATATAAAGC
1 AAAGCAAAGCAAAGCAATATAAAGC
*
28713335 AATGCAAAGCAAAGCAA
1 AAAGCAAAGCAAAGCAA
28713352 AGAAATATAA
Statistics
Matches: 314, Mismatches: 57, Indels: 72
0.71 0.13 0.16
Matches are distributed among these distances:
19 3 0.01
20 35 0.11
21 6 0.02
22 4 0.01
23 5 0.02
24 14 0.04
25 211 0.67
26 15 0.05
29 3 0.01
30 18 0.06
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.14
Consensus pattern (25 bp):
AAAGCAAAGCAAAGCAATATAAAGC
Found at i:28713108 original size:5 final size:5
Alignment explanation
Indices: 28713100--28713399 Score: 115
Period size: 5 Copynumber: 60.0 Consensus size: 5
28713090 AAAGTAATAT
* * * * *
28713100 AAAGA AAAGC AAAGT AAAGT AAAGC AAAGT AATA-T AAAGC AAAGC AAAGC
1 AAAGC AAAGC AAAGC AAAGC AAAGC AAAGC AA-AGC AAAGC AAAGC AAAGC
** * *
28713150 AAAGC AAAG- AAATAT AAAGC AATA-T AAAGC AAAGC AAAGC AAAGC AATA-T
1 AAAGC AAAGC AAA-GC AAAGC AA-AGC AAAGC AAAGC AAAGC AAAGC AA-AGC
* * * * *
28713200 AAAGC AATA-T AAAGC AAAGC AAAGT AATA-T AATA-T AAAGC AATA-T
1 AAAGC AA-AGC AAAGC AAAGC AAAGC AA-AGC AA-AGC AAAGC AA-AGC
* * * * * *
28713245 AAAGC AATGC AAAGC AAAGT AATA-T AAAGA AAAGC AAAGT AAAAC AAAGC
1 AAAGC AAAGC AAAGC AAAGC AA-AGC AAAGC AAAGC AAAGC AAAGC AAAGC
* * * * *
28713295 AAAGT AATA-T AAAGC AAAGC AAAGC AAAGT AATA-T AAAGC AATGC AAAGC
1 AAAGC AA-AGC AAAGC AAAGC AAAGC AAAGC AA-AGC AAAGC AAAGC AAAGC
** * *
28713345 AAAGC AAAG- AAATAT AAAGC AATA-T AAAGC AAAGC AAAGC AATA-T
1 AAAGC AAAGC AAA-GC AAAGC AA-AGC AAAGC AAAGC AAAGC AA-AGC
28713390 AAAGC AAAGC
1 AAAGC AAAGC
28713400 TTCTTTGATA
Statistics
Matches: 229, Mismatches: 40, Indels: 52
0.71 0.12 0.16
Matches are distributed among these distances:
4 17 0.07
5 195 0.85
6 17 0.07
ACGTcount: A:0.61, C:0.11, G:0.15, T:0.13
Consensus pattern (5 bp):
AAAGC
Found at i:28713314 original size:35 final size:35
Alignment explanation
Indices: 28713085--28713386 Score: 276
Period size: 35 Copynumber: 8.9 Consensus size: 35
28713075 AATATAATAT
* * *
28713085 AAAGCAAAGTAATATAAAGAAAAGCAAAGTAAAGT
1 AAAGCAAAGTAATATAAAGCAAAGCAAAGCAAAGC
28713120 AAAGCAAAGTAATATAAAGCAAAGCAAAGCAAAGC
1 AAAGCAAAGTAATATAAAGCAAAGCAAAGCAAAGC
*
28713155 AAAG---A--AATATAAAGCAATA-TAAAGCAAAGC
1 AAAGCAAAGTAATATAAAGCAA-AGCAAAGCAAAGC
* *
28713185 AAAGCAAAGCAATATAAAGCAATA-TAAAGCAAAGC
1 AAAGCAAAGTAATATAAAGCAA-AGCAAAGCAAAGC
* * *
28713220 AAAGTAATA-TAATATAAAGCAATA-TAAAGCAATGC
1 AAAGCAA-AGTAATATAAAGCAA-AGCAAAGCAAAGC
* * *
28713255 AAAGCAAAGTAATATAAAGAAAAGCAAAGTAAAAC
1 AAAGCAAAGTAATATAAAGCAAAGCAAAGCAAAGC
*
28713290 AAAGCAAAGTAATATAAAGCAAAGCAAAGCAAAGT
1 AAAGCAAAGTAATATAAAGCAAAGCAAAGCAAAGC
* *
28713325 AATA-TAAAG-CA-AT---GCAAAGCAAAGCAAAG-
1 AA-AGCAAAGTAATATAAAGCAAAGCAAAGCAAAGC
** *
28713354 AAATATAAAGCAATATAAAGCAAAGCAAAGCAA
1 AAA-GCAAAGTAATATAAAGCAAAGCAAAGCAA
28713387 TATAAAGCAA
Statistics
Matches: 230, Mismatches: 20, Indels: 34
0.81 0.07 0.12
Matches are distributed among these distances:
28 1 0.00
29 2 0.01
30 47 0.20
31 2 0.01
32 3 0.01
33 3 0.01
34 3 0.01
35 167 0.73
36 2 0.01
ACGTcount: A:0.61, C:0.11, G:0.15, T:0.13
Consensus pattern (35 bp):
AAAGCAAAGTAATATAAAGCAAAGCAAAGCAAAGC
Found at i:28714089 original size:110 final size:107
Alignment explanation
Indices: 28713798--28714196 Score: 649
Period size: 106 Copynumber: 3.7 Consensus size: 107
28713788 TGGAAATATG
*
28713798 CCTTATTTTTTAGAAACTCCTAATTAATCAGAAAAATATTAGAAATCCTTCTAACAGACAAAAAA
1 CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAATATTAGAAATCCTTCTAACAGACAAAAAA
* * *
28713863 TATTAAGCTATTAAGCATCATCGTGAT-AACCATTTTCTTTT
66 TATGAAGCTATTAAGCATCATCCTGATGAACCCTTTTCTTTT
* *
28713904 CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAATTATTAGAAATCCTTCTAACAAACAAAAAA
1 CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAATATTAGAAATCCTTCTAACAGACAAAAAA
* *
28713969 TATGAAGCTATTAAGCATCATCCTCATGAACCCTTTTTTTTTTT
66 TATGAAGCTATTAAGCATCATCCTGATGAACCC--TTTTCTTTT
28714013 CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAACTATTAGAAATCCTTCTAACAGACAAAAA
1 CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAA-TATTAGAAATCCTTCTAACAGACAAAAA
28714078 ATATGAAGCTATTAAGCATCATCCTGATGAACCC-TTTCTTTT
65 ATATGAAGCTATTAAGCATCATCCTGATGAACCCTTTTCTTTT
* *
28714120 CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAATATTAGAAATCCTACTCACAGACAAAAAA
1 CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAATATTAGAAATCCTTCTAACAGAC-AAAAA
*
28714185 ATATGAATCTAT
65 ATATGAAGCTAT
28714197 CACCATAGAG
Statistics
Matches: 273, Mismatches: 15, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
106 107 0.39
107 63 0.23
109 43 0.16
110 60 0.22
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.35
Consensus pattern (107 bp):
CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAATATTAGAAATCCTTCTAACAGACAAAAAA
TATGAAGCTATTAAGCATCATCCTGATGAACCCTTTTCTTTT
Found at i:28714183 original size:216 final size:216
Alignment explanation
Indices: 28713798--28714196 Score: 685
Period size: 216 Copynumber: 1.8 Consensus size: 216
28713788 TGGAAATATG
*
28713798 CCTTATTTTTTAGAAACTCCTAATTAATCAGAAAAATATTAGAAATCCTTCTAACAGACAAAAAA
1 CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAATATTAGAAATCCTTCTAACAGACAAAAAA
* * *
28713863 TATTAAGCTATTAAGCATCATCGTGATAACCATTTTCTTTTCCTTATTTTTTAGAAAATCCTAAT
66 TATGAAGCTATTAAGCATCATCCTGATAACCACTTTCTTTTCCTTATTTTTTAGAAAATCCTAAT
* *
28713928 TAATCAGAAAATTATTAGAAATCCTTCTAACAAAC-AAAAAATATGAAGCTATTAAGCATCATCC
131 TAATCAGAAAAATATTAGAAATCCTACTAACAAACAAAAAAATATGAAGCTATTAAGCATCATCC
28713992 TCATGAACCCTTTTTTTTTTT
196 TCATGAACCCTTTTTTTTTTT
28714013 CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAACTATTAGAAATCCTTCTAACAGACAAAAA
1 CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAA-TATTAGAAATCCTTCTAACAGACAAAAA
28714078 ATATGAAGCTATTAAGCATCATCCTGATGAACC-CTTTCTTTTCCTTATTTTTTAGAAAATCCTA
65 ATATGAAGCTATTAAGCATCATCCTGAT-AACCACTTTCTTTTCCTTATTTTTTAGAAAATCCTA
* * *
28714142 ATTAATCAGAAAAATATTAGAAATCCTACTCACAGACAAAAAAATATGAATCTAT
129 ATTAATCAGAAAAATATTAGAAATCCTACTAACAAACAAAAAAATATGAAGCTAT
28714197 CACCATAGAG
Statistics
Matches: 172, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
215 35 0.20
216 117 0.68
217 20 0.12
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.35
Consensus pattern (216 bp):
CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAATATTAGAAATCCTTCTAACAGACAAAAAA
TATGAAGCTATTAAGCATCATCCTGATAACCACTTTCTTTTCCTTATTTTTTAGAAAATCCTAAT
TAATCAGAAAAATATTAGAAATCCTACTAACAAACAAAAAAATATGAAGCTATTAAGCATCATCC
TCATGAACCCTTTTTTTTTTT
Found at i:28714827 original size:105 final size:107
Alignment explanation
Indices: 28714529--28714841 Score: 531
Period size: 110 Copynumber: 2.9 Consensus size: 107
28714519 TGGAGATATG
28714529 CCTTATTTTTTTAGAAAATCCTAATTAATCAGAAAAATATTAGAAATCCTTCTAACAGACAAAAA
1 CCTTA-TTTTTTAGAAAATCCTAATTAATCAGAAAAATATTAGAAATCCTTCTAACAGACAAAAA
* *
28714594 ATATGAAGCTATTAAGCATCAACCTGATGAACCCTTTTTTTTTTTT
65 ATATGAAGCTATTAAGCATCATCCTGATGAACCC---TTTTCTTTT
28714640 CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAATATTAGAAATCCTTCTAACAGACAAAAAA
1 CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAATATTAGAAATCCTTCTAACAGACAAAAAA
*
28714705 TATGAAGCTATTGAGCATCATCCTGATGAACCC-TTTCTTTT
66 TATGAAGCTATTAAGCATCATCCTGATGAACCCTTTTCTTTT
* *
28714746 CCTTATTTTTTAG-AAATTCTAATTAATCAGAAAAATATTAGAAATCCTTCTCACAGACAAAAAA
1 CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAATATTAGAAATCCTTCTAACAGACAAAAAA
28714810 TATGAAGCTATTAAGCATCATCCTGATGAACC
66 TATGAAGCTATTAAGCATCATCCTGATGAACC
28714842 AATTTTTGAT
Statistics
Matches: 196, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
105 80 0.41
106 20 0.10
110 91 0.46
111 5 0.03
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (107 bp):
CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAATATTAGAAATCCTTCTAACAGACAAAAAA
TATGAAGCTATTAAGCATCATCCTGATGAACCCTTTTCTTTT
Found at i:28719831 original size:20 final size:20
Alignment explanation
Indices: 28719808--28719882 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
28719798 TATTGCTTGG
28719808 CTTTCCTTTATATTACTTTC
1 CTTTCCTTTATATTACTTTC
* *
28719828 CTTTGCTTTACTTTATATTGCTTTG
1 CTTT-C----CTTTATATTACTTTC
*
28719853 CTTTGCTTTATATTACTTTC
1 CTTTCCTTTATATTACTTTC
*
28719873 CTTTGCTTTA
1 CTTTCCTTTA
28719883 CTTTATATTG
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
20 27 0.60
21 1 0.02
25 17 0.38
ACGTcount: A:0.13, C:0.20, G:0.07, T:0.60
Consensus pattern (20 bp):
CTTTCCTTTATATTACTTTC
Found at i:28719841 original size:25 final size:25
Alignment explanation
Indices: 28719807--28719902 Score: 112
Period size: 25 Copynumber: 4.0 Consensus size: 25
28719797 ATATTGCTTG
*
28719807 GCTTTCCTTTATATTACTTTCCTTT
1 GCTTTACTTTATATTACTTTCCTTT
*
28719832 GCTTTAC-TT-TA-TA--TTGCTTT
1 GCTTTACTTTATATTACTTTCCTTT
*
28719852 GCTTTGCTTTATATTACTTTCCTTT
1 GCTTTACTTTATATTACTTTCCTTT
* *
28719877 GCTTTACTTTATATTGCTTTGCTTT
1 GCTTTACTTTATATTACTTTCCTTT
28719902 G
1 G
28719903 TTGTGCTGTG
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
20 12 0.20
21 2 0.03
22 4 0.07
23 4 0.07
24 2 0.03
25 35 0.59
ACGTcount: A:0.12, C:0.19, G:0.09, T:0.59
Consensus pattern (25 bp):
GCTTTACTTTATATTACTTTCCTTT
Found at i:28719918 original size:25 final size:24
Alignment explanation
Indices: 28719890--28721282 Score: 267
Period size: 27 Copynumber: 55.1 Consensus size: 24
28719880 TTACTTTATA
*
28719890 TTGCTTTGCTTTGTTGTGCTGTGCT
1 TTGCTTTGCTTTGTT-TGCTTTGCT
* **
28719915 TTGCTTTGCTTTGCTGTGCTTTTTAT
1 TTGCTTTGCTTTG-TTTGC-TTTGCT
* * *
28719941 ATTGCTTTGCTTTATATTACTTTACT
1 -TTGCTTTGCTTTGT-TTGCTTTGCT
*
28719967 TTGCTTTGCTTTATATTGCTTTGCT
1 TTGCTTTGCTTTGT-TTGCTTTGCT
* *
28719992 GTGCATTGCTTTGTTTTGCTTTGCTT
1 TTGCTTTGCTTTG-TTTGCTTTGC-T
**
28720018 TTTATATTGCTTTGGTTTGCTTTGCT
1 TTGCT-TTGCTTT-GTTTGCTTTGCT
* * *
28720044 GTGCTTT-TTATATGCTTTGCTCTTTGTT
1 TTGCTTTGCT-T-TG-TTTG--CTTTGCT
* *
28720072 TTGCTGTGCTTT-TTAT--ATTGCT
1 TTGCTTTGCTTTGTT-TGCTTTGCT
28720094 TTGC-TT--TTTGTATTGCTTTGCT
1 TTGCTTTGCTTTGT-TTGCTTTGCT
* **
28720116 TTGTTTTGCTTTGCTTTTTATATTGCT
1 TTGCTTTGCTTTG--TTTGCT-TTGCT
* *
28720143 TTGCTTT--TTAT-ATTGCTTTGGT
1 TTGCTTTGCTT-TGTTTGCTTTGCT
* * * *
28720165 TT-ATATGCTTTG-CT-CTTTGTT
1 TTGCTTTGCTTTGTTTGCTTTGCT
* *
28720186 TTGCTGTGCTTT-TTAT--ATTGCT
1 TTGCTTTGCTTTGTT-TGCTTTGCT
28720208 TTGC-TT--TTTGTATTGCTTTGCT
1 TTGCTTTGCTTTGT-TTGCTTTGCT
* * **
28720230 TTGTTTTGCTGTGCTTTTTATATTGCT
1 TTGCTTTGCTTTG--TTTGCT-TTGCT
* **
28720257 TTGCTTTGTTTTGTTGTGCTTTTTAT
1 TTGCTTTGCTTTGTT-TGC-TTTGCT
* *
28720283 ATTGCTTTGCTTTATATTACTTTAG-T
1 -TTGCTTTGCTTTGT-TTGCTTT-GCT
*
28720309 TTGCTTTGCTTTATATTGCTTTGCT
1 TTGCTTTGCTTTGT-TTGCTTTGCT
* *
28720334 GTGCATTGCTTTGTTTTGCTTTGCTT
1 TTGCTTTGCTTTG-TTTGCTTTGC-T
** *
28720360 TTTATATTGCTTTGCTTTGTTTTGCT
1 TTGCT-TTGCTTTG-TTTGCTTTGCT
** *
28720386 TTGCTTTTTATATTGCTTTGGTTTGCT
1 TTGC-TTTGCT-TTG-TTTGCTTTGCT
* *
28720413 TTGCTGTGCTTTTTATATTGCTTTGCT
1 TTGCTTTGC--TTTGT-TTGCTTTGCT
* *
28720440 TTGTTTTGCTTTG-CT-CTTTG-T
1 TTGCTTTGCTTTGTTTGCTTTGCT
*
28720461 ATTGCTTTGCTTTGTTTTGCTGTGCTT
1 -TTGCTTTGCTTTG-TTTGCTTTGC-T
**
28720488 TTTATATTGCTTTGCTTT-CTTTTGCT
1 TTGCT-TTGCTTTG-TTTGC-TTTGCT
* **
28720514 TTGCTTTGTTTTGCTTTGCTTTTATAT
1 TTGCTTTGCTTTG-TTTGC-TTT-GCT
28720541 TTGCCTTT-CTTTGTTTTGCTTTGCTCT
1 TTG-CTTTGCTTTG-TTTGCTTTG--CT
* *
28720568 TTG-TATTACTTTGCTTTGTTTTGCT
1 TTGCT-TTGCTTTG-TTTGCTTTGCT
* ** *
28720593 GTGCTTTTTATATTGCTTTGCTTTGTT
1 TTGC-TTTGCT-TTG-TTTGCTTTGCT
*
28720620 TTGCTTTGCTTT-TTAT-ATTTGCT
1 TTGCTTTGCTTTGTT-TGCTTTGCT
* *
28720643 TTGCTTTGTTTTGCTGTGCTTT--T
1 TTGCTTTGCTTTG-TTTGCTTTGCT
* *
28720666 TAT-ATTTGCTTTGCTTTTGCTGTGCTT
1 T-TGCTTTGCTTTG--TTTGCTTTGC-T
** * *
28720693 TTTATATTGTTTTGCTTTGCTTTGTT
1 TTGCT-TTGCTTTG-TTTGCTTTGCT
* *
28720719 TTGCTGTGCTTTTATATTGCTTTGCT
1 TTGCTTTGC-TTTGT-TTGCTTTGCT
* * **
28720745 TTGCTCTTTGTTTTGCTGTGCTTTTTAT
1 TTG--CTTTGCTTTG-TTTGC-TTTGCT
* *
28720773 ATTGCTGTGCTTT-TTAT-ATTTGCT
1 -TTGCTTTGCTTTGTT-TGCTTTGCT
* ** *
28720797 TTGCTTTTGCTGTGCTTTTTATATTGTT
1 TTGC-TTTGCTTTG--TTTGCT-TTGCT
*
28720825 TTGCTTTGCTTTGTTTTGCTGTGCTT
1 TTGCTTTGCTTTG-TTTGCTTTGC-T
** *
28720851 TTTATATTGCTTTGCTTTGCTCTTTGTT
1 TTGCT-TTGCTTTG-TTTG--CTTTGCT
* *
28720879 TTGCTGTGCTTT-TTAT--ATTGCT
1 TTGCTTTGCTTTGTT-TGCTTTGCT
* *
28720901 GTGCTTT--TTATATTTGCTTTGCTT
1 TTGCTTTGCTT-TGTTTGCTTTGC-T
* * *
28720925 TTGCTGTGCTTTTTATATTGTTTTGCT
1 TTGCTTTGC--TTTGT-TTGCTTTGCT
* * **
28720952 TTGCTTTGTTTTGCTGTGCTTTTTAT
1 TTGCTTTGCTTTG-TTTGC-TTTGCT
*
28720978 ATTGCTTTGCTTTGTTTTGCTGTGCTT
1 -TTGCTTTGCTTTG-TTTGCTTTGC-T
** *
28721005 TTTATATTGCTTTGCTTTGTTTTGCT
1 TTGCT-TTGCTTTG-TTTGCTTTGCT
28721031 TTGCTTTGCTTTGTTTTGCTTTGCT
1 TTGCTTTGCTTTG-TTTGCTTTGCT
* *
28721056 TT--TTAT-ATTTGCCTTT-CTTTGTT
1 TTGCTT-TGCTTTG--TTTGCTTTGCT
*
28721079 TTGCTTTGCTCTTTGTATTACTTTGCT
1 TTGCTTTG--CTTTGT-TTGCTTTGCT
* * * *
28721106 TTGTTTTGCTGTGCTT--TTT-AT
1 TTGCTTTGCTTTGTTTGCTTTGCT
28721127 ATTGCTTTGCTTTGTTTTGCTTTGCTTT
1 -TTGCTTTGCTTTG-TTTGCTTTGC--T
** *
28721155 TTATATTTGCTTTGCTTTGTTTTGCT
1 TT-GCTTTGCTTTG-TTTGCTTTGCT
* *
28721181 GTGCTTT--TTATATTTGCTTTGCTT
1 TTGCTTTGCTT-TGTTTGCTTTGC-T
* * *
28721205 TTGCTGTGCTTTTTATATTGTTTTGCT
1 TTGCTTTGC--TTTGT-TTGCTTTGCT
* *
28721232 GTGCTTT--TTAT-ATTGCTTTGCT
1 TTGCTTTGCTT-TGTTTGCTTTGCT
*
28721254 TTGCTTTGCTCTTTGTTTTGCTGTGCT
1 TTGCTTTG--CTTTG-TTTGCTTTGCT
28721281 TT
1 TT
28721283 TTATATTGCT
Statistics
Matches: 994, Mismatches: 224, Indels: 298
0.66 0.15 0.20
Matches are distributed among these distances:
19 6 0.01
20 6 0.01
21 18 0.02
22 104 0.10
23 76 0.08
24 43 0.04
25 192 0.19
26 125 0.13
27 330 0.33
28 86 0.09
29 8 0.01
ACGTcount: A:0.07, C:0.13, G:0.18, T:0.62
Consensus pattern (24 bp):
TTGCTTTGCTTTGTTTGCTTTGCT
Found at i:28720049 original size:32 final size:32
Alignment explanation
Indices: 28719997--28721299 Score: 774
Period size: 32 Copynumber: 40.2 Consensus size: 32
28719987 TTGCTGTGCA
*
28719997 TTGCTTTGTTTTGCTTTGCTTTTTATATTGCT
1 TTGCTTTGTTTTGCTGTGCTTTTTATATTGCT
* *
28720029 TTGGTTTGCTTTGCTGTGCTTTTTATA-TGCT
1 TTGCTTTGTTTTGCTGTGCTTTTTATATTGCT
28720060 TTGCTCTTTGTTTTGCTGTGCTTTTTATATTGCT
1 TTG--CTTTGTTTTGCTGTGCTTTTTATATTGCT
* * *
28720094 TTGCTTTTTGTATTGCTTTGCTTTGT-T-TTGCT
1 TTGC--TTTGTTTTGCTGTGCTTTTTATATTGCT
* *
28720126 TTGCTTTTTATATTGCTTTGCTTTTTATATTGCT
1 TTGCTTTGT-T-TTGCTGTGCTTTTTATATTGCT
* * * * * * *
28720160 TTGGTTT-ATATGCTTTGCTCTTTGTTTTGCT
1 TTGCTTTGTTTTGCTGTGCTTTTTATATTGCT
* * * *
28720191 GTGCTTTTTATATTGCTTTGCTTTTTGTATTGCT
1 TTGCTTTGT-T-TTGCTGTGCTTTTTATATTGCT
28720225 TTGCTTTGTTTTGCTGTGCTTTTTATATTGCT
1 TTGCTTTGTTTTGCTGTGCTTTTTATATTGCT
*
28720257 TTGCTTTGTTTTGTTGTGCTTTTTATATTGCT
1 TTGCTTTGTTTTGCTGTGCTTTTTATATTGCT
* * * * **
28720289 TTGCTTTATATTACTTTAG--TTTGCT-TTGCT
1 TTGCTTTGTTTTGCTGT-GCTTTTTATATTGCT
* * * *
28720319 TT-ATATTGCTTTGCTGTGCATTGCTTTGTTTTGCT
1 TTGCT-TTGTTTTGCTGTGC-TT--TTTATATTGCT
* * *
28720354 TTGCTTTTTATATTGCTTTGCTTTGT-T-TTGCT
1 TTGCTTTGT-T-TTGCTGTGCTTTTTATATTGCT
* * * **
28720386 TTGCTTTTTATATTGCTTTG-GTTTGCT-TTGCT
1 TTGCTTTGT-T-TTGCTGTGCTTTTTATATTGCT
* * * *
28720418 GTGCTTTTTATATTGCTTTGCTTTGT-T-TTGCT
1 TTGCTTTGT-T-TTGCTGTGCTTTTTATATTGCT
* * *
28720450 TTGCTCTTTGTATTGCTTTGCTTTGT-T-TTGCT
1 TTG--CTTTGTTTTGCTGTGCTTTTTATATTGCT
* * * *
28720482 GTGCTTTTTATATTGCTTTGCTTTCT-T-TTGCT
1 TTGCTTTGT-T-TTGCTGTGCTTTTTATATTGCT
*
28720514 TTGCTTTGTTTTGCTTTGC-TTTTATATTTGCCT
1 TTGCTTTGTTTTGCTGTGCTTTTTATA-TTG-CT
* * * *
28720547 TT-CTTTGTTTTGCTTTGCTCTTTGTATTACT
1 TTGCTTTGTTTTGCTGTGCTTTTTATATTGCT
28720578 TTGCTTTGTTTTGCTGTGCTTTTTATATTGCT
1 TTGCTTTGTTTTGCTGTGCTTTTTATATTGCT
*
28720610 TTGCTTTGTTTTGCTTTGCTTTTTATATTTGCT
1 TTGCTTTGTTTTGCTGTGCTTTTTATA-TTGCT
28720643 TTGCTTTGTTTTGCTGTGCTTTTTATA----T
1 TTGCTTTGTTTTGCTGTGCTTTTTATATTGCT
28720671 TTGCTTTGCTTTTGCTGTGCTTTTTATATTGTTTTGCT
1 TTGCTTTG-TTTTGCTGTGCTTTTTATA-----TTGCT
*
28720709 TTGCTTTGTTTTGCTGTGCTTTTATATTGCTTTGCT
1 TTGCTTTGTTTTGCTGTGCTTTT-TA-T--ATTGCT
28720745 TTGCTCTTTGTTTTGCTGTGCTTTTTATATTGCT
1 TTG--CTTTGTTTTGCTGTGCTTTTTATATTGCT
* * * ** *
28720779 GTGCTTTTTATATTTGCTTTGCTTTTGCT-GTGCTT
1 TTGC--TTTGT-TTTGCTGTGCTTTTTATATTGC-T
** * *
28720814 TTTATATTGTTTTGCTTTGCTTTGT-T-TTGCT
1 TTGCT-TTGTTTTGCTGTGCTTTTTATATTGCT
* * * **
28720845 GTGCTTT-TTAT-AT-TGC-TTTGCT-TTGC-
1 TTGCTTTGTTTTGCTGTGCTTTTTATATTGCT
28720871 -T-CTTTGTTTTGCTGTGCTTTTTATATTGCT
1 TTGCTTTGTTTTGCTGTGCTTTTTATATTGCT
* * * ** *
28720901 GTGCTTTTTATATTTGCTTTGCTTTTGCT-GTGCTT
1 TTGC--TTTGT-TTTGCTGTGCTTTTTATATTGC-T
** * *
28720936 TTTATATTGTTTTGCTTTGCTTTGT-T-TTGCT
1 TTGCT-TTGTTTTGCTGTGCTTTTTATATTGCT
* * * *
28720967 GTGCTTTTTATATTGCTTTGCTTTGT-T-TTGCT
1 TTGCTTTGT-T-TTGCTGTGCTTTTTATATTGCT
* * * * *
28720999 GTGCTTTTTATATTGCTTTGCTTTGTTTTGCTTTGCT
1 TTGCTTTGT-T-TTGCTGTGCTTT-TTAT--ATTGCT
*
28721036 TTGCTTTGTTTTGCTTTGCTTTTTATATTTGCCT
1 TTGCTTTGTTTTGCTGTGCTTTTTATA-TTG-CT
* * * *
28721070 TT-CTTTGTTTTGCTTTGCTCTTTGTATTACT
1 TTGCTTTGTTTTGCTGTGCTTTTTATATTGCT
28721101 TTGCTTTGTTTTGCTGTGCTTTTTATATTGCT
1 TTGCTTTGTTTTGCTGTGCTTTTTATATTGCT
*
28721133 TTGCTTTGTTTTGCTTTGCTTTTTATATTTGCT
1 TTGCTTTGTTTTGCTGTGCTTTTTATA-TTGCT
28721166 TTGCTTTGTTTTGCTGTGCTTTTTATA----T
1 TTGCTTTGTTTTGCTGTGCTTTTTATATTGCT
*
28721194 TTGCTTTGCTTTTGCTGTGCTTTTTATATTGTT
1 TTGCTTTG-TTTTGCTGTGCTTTTTATATTGCT
* ** * **
28721227 TTGCTGTGCTTTTTATATTGC-TTTGCT-TTGCT
1 TTGCTTTG-TTTTGCT-GTGCTTTTTATATTGCT
28721259 TTGCTCTTTGTTTTGCTGTGCTTTTTATATTGCT
1 TTG--CTTTGTTTTGCTGTGCTTTTTATATTGCT
*
28721293 GTGCTTT
1 TTGCTTT
28721300 TTATATTTGC
Statistics
Matches: 1035, Mismatches: 144, Indels: 184
0.76 0.11 0.13
Matches are distributed among these distances:
24 4 0.00
25 4 0.00
26 3 0.00
27 11 0.01
28 23 0.02
29 50 0.05
30 38 0.04
31 53 0.05
32 411 0.40
33 182 0.18
34 120 0.12
35 53 0.05
36 14 0.01
37 37 0.04
38 31 0.03
39 1 0.00
ACGTcount: A:0.06, C:0.13, G:0.17, T:0.63
Consensus pattern (32 bp):
TTGCTTTGTTTTGCTGTGCTTTTTATATTGCT
Found at i:28721297 original size:22 final size:22
Alignment explanation
Indices: 28721199--28721479 Score: 133
Period size: 22 Copynumber: 12.9 Consensus size: 22
28721189 TATATTTGCT
28721199 TTGCTTTTGCTGTGCTTTTTATA
1 TTGC-TTTGCTGTGCTTTTTATA
*
28721222 TTGTTTTGCTGTGCTTTTTATA
1 TTGCTTTGCTGTGCTTTTTATA
* * *
28721244 TTGCTTTGCTTTGCTTTGCTCT-
1 TTGCTTTGCTGTGCTTT-TTATA
*
28721266 TTGTTTTGCTGTGCTTTTTATA
1 TTGCTTTGCTGTGCTTTTTATA
* ** *
28721288 TTGCTGTGCT-TTTTATATTTGCT-
1 TTGCTTTGCTGTGCT-T-TTT-ATA
28721311 TTGCTTTTGCTGTGCTTTTTATA
1 TTGC-TTTGCTGTGCTTTTTATA
**
28721334 TTG--TT--T-TGC-TTTGCT-
1 TTGCTTTGCTGTGCTTTTTATA
*
28721349 TTGTTTTGCTGTGCTTTTTATA
1 TTGCTTTGCTGTGCTTTTTATA
* **
28721371 TTGCTTTGCTTTG-TTTTGCT-
1 TTGCTTTGCTGTGCTTTTTATA
* ** * * *
28721391 GTGCTTTTTATATTGCTTTGCTCT-
1 TTGC-TTTGCT-GTGCTTT-TTATA
*
28721415 TTGTTTTGCTGTGCTTTTTATA
1 TTGCTTTGCTGTGCTTTTTATA
* *
28721437 TTGCTTTGCTGT-TTATATTTGCT-
1 TTGCTTTGCTGTGCT-T-TTT-ATA
28721460 TTGCTTTGCTGTGCTTTTTA
1 TTGCTTTGCTGTGCTTTTTA
28721480 ATATAGACAT
Statistics
Matches: 191, Mismatches: 43, Indels: 50
0.67 0.15 0.18
Matches are distributed among these distances:
15 3 0.02
16 4 0.02
17 5 0.03
18 1 0.01
19 1 0.01
20 8 0.04
21 20 0.10
22 93 0.49
23 41 0.21
24 13 0.07
25 2 0.01
ACGTcount: A:0.07, C:0.13, G:0.18, T:0.62
Consensus pattern (22 bp):
TTGCTTTGCTGTGCTTTTTATA
Found at i:28721380 original size:32 final size:32
Alignment explanation
Indices: 28720039--28721466 Score: 760
Period size: 32 Copynumber: 43.8 Consensus size: 32
28720029 TTGGTTTGCT
* * * *
28720039 TTGCTGTGCTTT-TTATATGCTTTGCTCTTTGTT
1 TTGCTTTGCTTTGTT-T-TGCTTTGCTTTTTATA
* * *
28720072 TTGCTGTGCTTTTTATATTGCTTTGCTTTTTGTA
1 TTGCTTTGCTTTGT-T-TTGCTTTGCTTTTTATA
28720106 TTGCTTTGCTTTGTTTTGCTTTGCTTTTTATA
1 TTGCTTTGCTTTGTTTTGCTTTGCTTTTTATA
* *
28720138 TTGCTTTGCTTTTTATATTGCTTTG--GTTTATA
1 TTGCTTTGCTTTGT-T-TTGCTTTGCTTTTTATA
*
28720170 -TGCTTTGCTCTTTGTTTTGCTGTGCTTTTTATA
1 TTGCTTTG--CTTTGTTTTGCTTTGCTTTTTATA
* *
28720203 TTGCTTTGCTTTTTGTATTGCTTTGCTTTGT-T-
1 TTGCTTTGC--TTTGTTTTGCTTTGCTTTTTATA
* * *
28720235 TTGCTGTGCTTTTTATATTGCTTTGCTTTGT-T-
1 TTGCTTTGCTTTGT-T-TTGCTTTGCTTTTTATA
*
28720267 TTG-TTGTGCTTTTTATATTGCTTTGC--TTTATA
1 TTGCTT-TGCTTTGT-T-TTGCTTTGCTTTTTATA
* *
28720299 TTAC--T--TTAG-TTTGCTTTGC--TTTATA
1 TTGCTTTGCTTTGTTTTGCTTTGCTTTTTATA
* *
28720324 TTGCTTTGC--TG---TGCATTGCTTTGT-T-
1 TTGCTTTGCTTTGTTTTGCTTTGCTTTTTATA
* *
28720349 TTGCTTTGCTTTTTATATTGCTTTGCTTTGT-T-
1 TTGCTTTGCTTTGT-T-TTGCTTTGCTTTTTATA
* * **
28720381 TTGCTTTGCTTTTTATATTGCTTTG-GTTTGCT-
1 TTGCTTTGCTTTGT-T-TTGCTTTGCTTTTTATA
* * *
28720413 TTGCTGTGCTTTTTATATTGCTTTGCTTTGT-T-
1 TTGCTTTGCTTTGT-T-TTGCTTTGCTTTTTATA
* *
28720445 TTGCTTTGCTCTTTGTATTGCTTTGCTTTGT-T-
1 TTGCTTTG--CTTTGTTTTGCTTTGCTTTTTATA
* * *
28720477 TTGCTGTGCTTTTTATATTGCTTTGCTTTCT-T-
1 TTGCTTTGCTTTGT-T-TTGCTTTGCTTTTTATA
28720509 TTGCTTTGCTTTGTTTTGCTTTGC-TTTTATA
1 TTGCTTTGCTTTGTTTTGCTTTGCTTTTTATA
* *
28720540 TTTGCCTTT-CTTTGTTTTGCTTTGCTCTTTGTA
1 -TTG-CTTTGCTTTGTTTTGCTTTGCTTTTTATA
* *
28720573 TTACTTTGCTTTGTTTTGCTGTGCTTTTTATA
1 TTGCTTTGCTTTGTTTTGCTTTGCTTTTTATA
28720605 TTGCTTTGCTTTGTTTTGCTTTGCTTTTTATA
1 TTGCTTTGCTTTGTTTTGCTTTGCTTTTTATA
*
28720637 TTTGCTTTGCTTTGTTTTGCTGTGCTTTTTATA
1 -TTGCTTTGCTTTGTTTTGCTTTGCTTTTTATA
* * * *
28720670 TTTGCTTTGCTTTTGCTGTGCTTT--TTATATTGTT
1 -TTGCTTTGC-TTTGTTTTGCTTTGCTT-T-TTATA
* *
28720704 TTGCTTTGCTTTGTTTTGCTGTGCTTTTATATTGCT
1 TTGCTTTGCTTTGTTTTGCTTTGCTTTT-TA-T--A
*
28720740 TTGCTTTGCTCTTTGTTTTGCTGTGCTTTTTATA
1 TTGCTTTG--CTTTGTTTTGCTTTGCTTTTTATA
* * **
28720774 TTGCTGTGCTTTTTATATTTGCTTTGCTTTTGCT-
1 TTGCTTTGC--TTTGT-TTTGCTTTGCTTTTTATA
* ** * *
28720808 GTGCTTTTTATATTGTTTTGCTTTGCTTTGTTTTGC
1 TTGC-TTTGCT-TTGTTTTGCTTTGCTTT-TTAT-A
** * * * *
28720844 TGTGCTTTTTATATTGCTTTGCTTTGCTCTTTGTT
1 T-TGC-TTTGCT-TTGTTTTGCTTTGCTTTTTATA
* * *
28720879 TTGCTGTGCTTTTTATATTGCTGTGCTTTTTATA
1 TTGCTTTGCTTTGT-T-TTGCTTTGCTTTTTATA
* * * *
28720913 TTTGCTTTGCTTTTGCTGTGCTTT--TTATATTGTT
1 -TTGCTTTGC-TTTGTTTTGCTTTGCTT-T-TTATA
*
28720947 TTGCTTTGCTTTGTTTTGCTGTGCTTTTTATA
1 TTGCTTTGCTTTGTTTTGCTTTGCTTTTTATA
*
28720979 TTGCTTTGCTTTGTTTTGCTGTGCTTTTTATA
1 TTGCTTTGCTTTGTTTTGCTTTGCTTTTTATA
* *
28721011 TTGCTTTGCTTTGTTTTGCTTTGCTTTGCTTTGTT
1 TTGCTTTGCTTTGTTTTGCTTTGC-TT--TTTATA
* *
28721046 TTGCTTTGCTTTTTATATTTGCCTTT-CTTTGT-T-
1 TTGCTTTGC--TTTGT-TTTG-CTTTGCTTTTTATA
* * *
28721079 TTGCTTTGCTCTTTGTATTACTTTGCTTTGT-T-
1 TTGCTTTG--CTTTGTTTTGCTTTGCTTTTTATA
* * *
28721111 TTGCTGTGCTTTTTATATTGCTTTGCTTTGT-T-
1 TTGCTTTGCTTTGT-T-TTGCTTTGCTTTTTATA
* *
28721143 TTGCTTTGCTTTTTATATTTGCTTTGCTTTGT-T-
1 TTGCTTTGC--TTTGT-TTTGCTTTGCTTTTTATA
* * **
28721176 TTGCTGTGCTTTTTATATTTGCTTTGCTTTTGCT-
1 TTGCTTTGC--TTTGT-TTTGCTTTGCTTTTTATA
* ** *
28721210 GTGCTTTTTATATTGTTTTGCTGTGCTTTTTATA
1 TTGC-TTTGCT-TTGTTTTGCTTTGCTTTTTATA
* *
28721244 TTGCTTTGCTTTGCTTTGC--T-CTTTGT-T-
1 TTGCTTTGCTTTGTTTTGCTTTGCTTTTTATA
* * *
28721271 TTGCTGTGCTTTTTATATTGCTGTGCTTTTTATA
1 TTGCTTTGCTTTGT-T-TTGCTTTGCTTTTTATA
* * * *
28721305 TTTGCTTTGCTTTTGCTGTGCTTT--TTATATTGTT
1 -TTGCTTTGC-TTTGTTTTGCTTTGCTT-T-TTATA
*
28721339 TTGCTTTGCTTTGTTTTGCTGTGCTTTTTATA
1 TTGCTTTGCTTTGTTTTGCTTTGCTTTTTATA
*
28721371 TTGCTTTGCTTTGTTTTGCTGTGCTTTTTATA
1 TTGCTTTGCTTTGTTTTGCTTTGCTTTTTATA
*
28721403 TTGCTTTGCTCTTTGTTTTGCTGTGCTTTTTATA
1 TTGCTTTG--CTTTGTTTTGCTTTGCTTTTTATA
*
28721437 TTGCTTTGCTGTTTATATTTGCTTTGCTTT
1 TTGCTTTGC--TTTGT-TTTGCTTTGCTTT
28721467 GCTGTGCTTT
Statistics
Matches: 1139, Mismatches: 149, Indels: 212
0.76 0.10 0.14
Matches are distributed among these distances:
25 34 0.03
26 2 0.00
27 16 0.01
28 4 0.00
29 12 0.01
30 28 0.02
31 28 0.02
32 469 0.41
33 208 0.18
34 188 0.17
35 68 0.06
36 19 0.02
37 34 0.03
38 25 0.02
39 4 0.00
ACGTcount: A:0.07, C:0.13, G:0.17, T:0.63
Consensus pattern (32 bp):
TTGCTTTGCTTTGTTTTGCTTTGCTTTTTATA
Found at i:28721446 original size:5 final size:5
Alignment explanation
Indices: 28719823--28721397 Score: 430
Period size: 5 Copynumber: 301.8 Consensus size: 5
28719813 CTTTATATTA
* * * * * *
28719823 CTTTC CTTTG CTTTA CTTT- ATATTG CTTTG CTTTG CTTT- ATATTA CTTTC
1 CTTTG CTTTG CTTTG CTTTG CT-TTG CTTTG CTTTG CTTTG CT-TTG CTTTG
* * *
28719873 CTTTG CTTTA CTTT- ATATTG CTTTG CTTTG -TTGTG CTGTG CTTTG CTTTG
1 CTTTG CTTTG CTTTG CT-TTG CTTTG CTTTG CTT-TG CTTTG CTTTG CTTTG
* * * * * *
28719923 CTTTG CTGTG CTTTTT ATATTG CTTTG CTTT- ATATTA CTTTA CTTTG
1 CTTTG CTTTG C-TTTG CT-TTG CTTTG CTTTG CT-TTG CTTTG CTTTG
* * * * *
28719970 CTTTG CTTT- ATATTG CTTTG CTGTG CATTG CTTTG TTTTG CTTTG CTTTTT
1 CTTTG CTTTG CT-TTG CTTTG CTTTG CTTTG CTTTG CTTTG CTTTG C-TTTG
* * * *
28720021 ATATTG CTTTG GTTTG CTTTG CTGTG CTTT- TTATATG CTTTG CTCTTTG
1 CT-TTG CTTTG CTTTG CTTTG CTTTG CTTTG CT-T-TG CTTTG --CTTTG
* * * *
28720070 TTTTG CTGTG CTTTTT ATATTG CTTTG CTTTTTG -TATTG CTTTG CTTTG
1 CTTTG CTTTG C-TTTG CT-TTG CTTTG C--TTTG CT-TTG CTTTG CTTTG
* * * * * *
28720119 TTTTG CTTTG CTTTTT ATATTG CTTTG CTTTTT ATATTG CTTTG GTTT-
1 CTTTG CTTTG C-TTTG CT-TTG CTTTG C-TTTG CT-TTG CTTTG CTTTG
* * * * * *
28720167 ATATG CTTTG CTCTTTG TTTTG CTGTG CTTTTT ATATTG CTTTG CTTTTTG
1 CTTTG CTTTG --CTTTG CTTTG CTTTG C-TTTG CT-TTG CTTTG C--TTTG
* * * *
28720218 -TATTG CTTTG CTTTG TTTTG CTGTG CTTTTT ATATTG CTTTG CTTTG
1 CT-TTG CTTTG CTTTG CTTTG CTTTG C-TTTG CT-TTG CTTTG CTTTG
* * * * *
28720265 TTTTG -TTGTG CTTTTT ATATTG CTTTG CTTT- ATATTA CTTTAG -TTTG
1 CTTTG CTT-TG C-TTTG CT-TTG CTTTG CTTTG CT-TTG CTTT-G CTTTG
* * * * *
28720312 CTTTG CTTT- ATATTG CTTTG CTGTG CATTG CTTTG TTTTG CTTTG CTTTTT
1 CTTTG CTTTG CT-TTG CTTTG CTTTG CTTTG CTTTG CTTTG CTTTG C-TTTG
* * * * *
28720363 ATATTG CTTTG CTTTG TTTTG CTTTG CTTTTT ATATTG CTTTG GTTTG
1 CT-TTG CTTTG CTTTG CTTTG CTTTG C-TTTG CT-TTG CTTTG CTTTG
* * * *
28720411 CTTTG CTGTG CTTTTT ATATTG CTTTG CTTTG TTTTG CTTTG CTCTTTG
1 CTTTG CTTTG C-TTTG CT-TTG CTTTG CTTTG CTTTG CTTTG --CTTTG
* * * *
28720460 -TATTG CTTTG CTTTG TTTTG CTGTG CTTTTT ATATTG CTTTG CTTT-
1 CT-TTG CTTTG CTTTG CTTTG CTTTG C-TTTG CT-TTG CTTTG CTTTG
* * *
28720506 CTTTTG CTTTG CTTTG TTTTG CTTTG CTTTTAT ATTTG CCTTT- CTTTG
1 C-TTTG CTTTG CTTTG CTTTG CTTTG C-TTT-G CTTTG -CTTTG CTTTG
* * * * *
28720554 TTTTG CTTTG CTCTTTG -TATTA CTTTG CTTTG TTTTG CTGTG CTTTTT
1 CTTTG CTTTG --CTTTG CT-TTG CTTTG CTTTG CTTTG CTTTG C-TTTG
* * *
28720602 ATATTG CTTTG CTTTG TTTTG CTTTG CTTT- -TTAT- ATTTG CTTTG CTTTG
1 CT-TTG CTTTG CTTTG CTTTG CTTTG CTTTG CTT-TG CTTTG CTTTG CTTTG
* * * * *
28720651 TTTTG CTGTG CTTT- -TTAT- ATTTG CTTTG CTTTTG CTGTG CTTTTT
1 CTTTG CTTTG CTTTG CTT-TG CTTTG CTTTG C-TTTG CTTTG C-TTTG
* * * * * *
28720696 ATATTG TTTTG CTTTG CTTTG TTTTG CTGTG CTTTT ATATTG CTTTG CTTTG
1 CT-TTG CTTTG CTTTG CTTTG CTTTG CTTTG CTTTG CT-TTG CTTTG CTTTG
* * * * * *
28720748 CTCTTTG TTTTG CTGTG CTTTTT ATATTG CTGTG CTTT- -TTAT- ATTTG
1 --CTTTG CTTTG CTTTG C-TTTG CT-TTG CTTTG CTTTG CTT-TG CTTTG
* * * * *
28720795 CTTTG CTTTTG CTGTG CTTTTT ATATTG TTTTG CTTTG CTTTG TTTTG
1 CTTTG C-TTTG CTTTG C-TTTG CT-TTG CTTTG CTTTG CTTTG CTTTG
* * * * * *
28720843 CTGTG CTTTTT ATATTG CTTTG CTTTG CTCTTTG TTTTG CTGTG CTTTTT
1 CTTTG C-TTTG CT-TTG CTTTG CTTTG --CTTTG CTTTG CTTTG C-TTTG
* * * * *
28720893 ATATTG CTGTG CTTT- -TTAT- ATTTG CTTTG CTTTTG CTGTG CTTTTT
1 CT-TTG CTTTG CTTTG CTT-TG CTTTG CTTTG C-TTTG CTTTG C-TTTG
* * * * * *
28720939 ATATTG TTTTG CTTTG CTTTG TTTTG CTGTG CTTTTT ATATTG CTTTG
1 CT-TTG CTTTG CTTTG CTTTG CTTTG CTTTG C-TTTG CT-TTG CTTTG
* * * * *
28720987 CTTTG TTTTG CTGTG CTTTTT ATATTG CTTTG CTTTG TTTTG CTTTG CTTTG
1 CTTTG CTTTG CTTTG C-TTTG CT-TTG CTTTG CTTTG CTTTG CTTTG CTTTG
* * *
28721039 CTTTG TTTTG CTTTG CTTT- -TTAT- ATTTG CCTTT- CTTTG TTTTG CTTTG
1 CTTTG CTTTG CTTTG CTTTG CTT-TG CTTTG -CTTTG CTTTG CTTTG CTTTG
* * * * *
28721087 CTCTTTG -TATTA CTTTG CTTTG TTTTG CTGTG CTTTTT ATATTG CTTTG
1 --CTTTG CT-TTG CTTTG CTTTG CTTTG CTTTG C-TTTG CT-TTG CTTTG
* * * *
28721136 CTTTG TTTTG CTTTG CTTT- -TTAT- ATTTG CTTTG CTTTG TTTTG CTGTG
1 CTTTG CTTTG CTTTG CTTTG CTT-TG CTTTG CTTTG CTTTG CTTTG CTTTG
* * * * *
28721184 CTTT- -TTAT- ATTTG CTTTG CTTTTG CTGTG CTTTTT ATATTG TTTTG
1 CTTTG CTT-TG CTTTG CTTTG C-TTTG CTTTG C-TTTG CT-TTG CTTTG
* * * * *
28721230 CTGTG CTTTTT ATATTG CTTTG CTTTG CTTTG CTCTTTG TTTTG CTGTG
1 CTTTG C-TTTG CT-TTG CTTTG CTTTG CTTTG --CTTTG CTTTG CTTTG
* * * * *
28721279 CTTTTT ATATTG CTGTG CTTT- -TTAT- ATTTG CTTTG CTTTTG CTGTG
1 C-TTTG CT-TTG CTTTG CTTTG CTT-TG CTTTG CTTTG C-TTTG CTTTG
* * * * * * *
28721325 CTTTTT ATATTG TTTTG CTTTG CTTTG TTTTG CTGTG CTTTTT ATATTG
1 C-TTTG CT-TTG CTTTG CTTTG CTTTG CTTTG CTTTG C-TTTG CT-TTG
* *
28721374 CTTTG CTTTG TTTTG CTGTG CTTT
1 CTTTG CTTTG CTTTG CTTTG CTTT
28721398 TTATATTGCT
Statistics
Matches: 1132, Mismatches: 292, Indels: 292
0.66 0.17 0.17
Matches are distributed among these distances:
3 16 0.01
4 45 0.04
5 825 0.73
6 195 0.17
7 51 0.05
ACGTcount: A:0.07, C:0.14, G:0.17, T:0.62
Consensus pattern (5 bp):
CTTTG
Found at i:28723642 original size:20 final size:20
Alignment explanation
Indices: 28723617--28724384 Score: 259
Period size: 20 Copynumber: 39.4 Consensus size: 20
28723607 AGTACTTGAA
*
28723617 TTGCTTTGCTCTATATTGCT
1 TTGCTTTGCTTTATATTGCT
* *
28723637 TTGCTTTGCTTTTTATTACT
1 TTGCTTTGCTTTATATTGCT
28723657 TTGCTTTGCTTTATATTGATTTGCT
1 TTGCTTTGC-TT-TA-T-A-TTGCT
*
28723682 ATGCTTTGCTTTATATTGCT
1 TTGCTTTGCTTTATATTGCT
*
28723702 ATGCTTTGCTTTATATTGCT
1 TTGCTTTGCTTTATATTGCT
*
28723722 TTGC-TT-C---ATATTACT
1 TTGCTTTGCTTTATATTGCT
* *
28723737 TTGCTTTGTTTTATATTTCT
1 TTGCTTTGCTTTATATTGCT
* *
28723757 TTGCTTTTCTTTATATTACTTT
1 TTGCTTTGCTTTATATTGC--T
28723779 ACTCTGCTTTGCTTTATATTGCT
1 --T-TGCTTTGCTTTATATTGCT
* ** * **
28723802 TTGCTGTGCTGTGCTTTTTAT
1 TTGCTTTGCT-TTATATTGCT
*
28723823 ATTGCTTTGCTTTGT-TCTGCT
1 -TTGCTTTGCTTTATAT-TGCT
*
28723844 GTGC-TT--TTTATATTGCT
1 TTGCTTTGCTTTATATTGCT
* *
28723861 TTGCTTTGTTTTGCT-TTGCT
1 TTGCTTTGCTTT-ATATTGCT
*
28723881 TTGCTGTGCTTTTTATATTGCT
1 TTGCTTTGC--TTTATATTGCT
*
28723903 TTGCTTTG-TTT-TGTTG--
1 TTGCTTTGCTTTATATTGCT
28723919 -TGC-TT--TTTATATTGCT
1 TTGCTTTGCTTTATATTGCT
* *
28723935 TTGCTTTGTTTTGCT-TTGCT
1 TTGCTTTGCTTT-ATATTGCT
*
28723955 TTGCTGTGCTTTTTATATTGCT
1 TTGCTTTGC--TTTATATTGCT
*
28723977 TTGCTTTG-TTT-TGCTGTGCTTT
1 TTGCTTTGCTTTAT-AT-TGC--T
* *
28723999 TTG-TATTGCTTTGCT-TTGTT
1 TTGCT-TTGCTTT-ATATTGCT
*
28724019 TTGCTGTGCAATTTATATTGCT
1 TTGCTTTGC--TTTATATTGCT
* *
28724041 TTGCTTTGTTTTGCT-TTGCT
1 TTGCTTTGCTTT-ATATTGCT
* *
28724061 TTCCTGTGCTTTTTATATTGCT
1 TTGCTTTGC--TTTATATTGCT
** * **
28724083 TTGCTTTGCTGTGCTTTTTAT
1 TTGCTTTGCT-TTATATTGCT
* * *
28724104 ATTGCTTTACTTTGTTTTGCT
1 -TTGCTTTGCTTTATATTGCT
* *
28724125 TTGC--T-CTTTGTTTTGCT
1 TTGCTTTGCTTTATATTGCT
*
28724142 GTGC-TT--TTTATATTGCT
1 TTGCTTTGCTTTATATTGCT
*
28724159 TTGC-TT--TTTATATTGTT
1 TTGCTTTGCTTTATATTGCT
* *
28724176 TTGCTTTGCTTTGTTTTGCT
1 TTGCTTTGCTTTATATTGCT
*
28724196 GTGC-TT--TTTATATTGCT
1 TTGCTTTGCTTTATATTGCT
* *
28724213 TTGC--T-CTTTGTTTTGCT
1 TTGCTTTGCTTTATATTGCT
*
28724230 GTGC-TT--TTTATATTGCT
1 TTGCTTTGCTTTATATTGCT
*
28724247 TTGC-TT--TTTATATTGTT
1 TTGCTTTGCTTTATATTGCT
*
28724264 TTGCTGTGCTTTTTATATTGCT
1 TTGCTTTGC--TTTATATTGCT
* *
28724286 TTGCTTT--TTT-TTTTGGT
1 TTGCTTTGCTTTATATTGCT
*
28724303 TTGC-TT--TTTATATTTGTT
1 TTGCTTTGCTTTATA-TTGCT
28724321 TTGCTTTG---T-T-TTGCT
1 TTGCTTTGCTTTATATTGCT
28724336 TTGC-TT--TTTATATTTGCT
1 TTGCTTTGCTTTATA-TTGCT
*
28724354 TTGCTTTGGCTCTTTGTATTGCT
1 TTGCTTT-G--CTTTATATTGCT
28724377 TTGCTTTG
1 TTGCTTTG
28724385 TTTTGCTGTG
Statistics
Matches: 574, Mismatches: 93, Indels: 160
0.69 0.11 0.19
Matches are distributed among these distances:
13 3 0.01
14 8 0.01
15 23 0.04
16 9 0.02
17 120 0.21
18 38 0.07
19 17 0.03
20 159 0.28
21 33 0.06
22 106 0.18
23 20 0.03
24 9 0.02
25 29 0.05
ACGTcount: A:0.08, C:0.14, G:0.17, T:0.62
Consensus pattern (20 bp):
TTGCTTTGCTTTATATTGCT
Found at i:28723680 original size:35 final size:35
Alignment explanation
Indices: 28723637--28724580 Score: 135
Period size: 32 Copynumber: 27.4 Consensus size: 35
28723627 CTATATTGCT
28723637 TTGCTTTGCTTTTTATTACTTTGCTTTGCTTTATA
1 TTGCTTTGCTTTTTATTACTTTGCTTTGCTTTATA
* * * *
28723672 TTGATTTGC----TA-TGCTTTGCTTT-ATATTGCTA
1 TTGCTTTGCTTTTTATTACTTTGCTTTGCT-TT-ATA
* *
28723703 -TGCTTTGCTTTATATTGCTTTGC-TT-CATATTACT-
1 TTGCTTTGCTTTTTATTACTTTGCTTTGC-T-TTA-TA
* *
28723737 TTGCTTTG-TTTTATATTTCTTTGCTTTTCTTTATA
1 TTGCTTTGCTTTT-TATTACTTTGCTTTGCTTTATA
* * ** * * *
28723772 TTACTTTACTCTGCT-TTGCTTT-ATATTGCTTTGCT-
1 TTGCTTTGCT-TTTTATTACTTTGCT-TTGCTTT-ATA
* * *
28723807 GTGCTGTGCTTTTTA-TA--TTGCTTTGCTTTGT-
1 TTGCTTTGCTTTTTATTACTTTGCTTTGCTTTATA
* * * *
28723838 TCTGCTGTGCTTTTTATATTGCTTTGCTTTGTTTTGCT-
1 T-TGCTTTGC-TTTT-TATTACTTTGCTTTGCTTT-ATA
* *
28723876 TTGCTTTGCTGTGCTTT-TTA-TATTGCTTTGCTTTGTT
1 TTGCTTTGCT-T--TTTATTACT-TTGCTTTGCTTTATA
* * *
28723913 TTG-TTGTGCTTTTTATATTGCTTTGCTTTGTTTTGCT-
1 TTGCTT-TGC-TTTT-TATTACTTTGCTTTGCTTT-ATA
* *
28723950 TTGCTTTGCTGTGCTTT-TTA-TATTGCTTTGCTTTGTT
1 TTGCTTTGCT-T--TTTATTACT-TTGCTTTGCTTTATA
* * * *
28723987 TTGCTGTGCTTTTT-GTA--TTGCTTTGCTTTGTT
1 TTGCTTTGCTTTTTATTACTTTGCTTTGCTTTATA
* ** * *
28724019 TTGCTGTGCAATTTA-TA--TTGCTTTGCTTTGTT
1 TTGCTTTGCTTTTTATTACTTTGCTTTGCTTTATA
* * * ** *
28724051 TTGCTTTGCTTTCCT-GTGCTTTTTATATTGCTTTGCT-
1 TTGCTTTGCTTT-TTATTAC-TTTGCT-TTGCTTT-ATA
* * * *
28724088 TTGCTGTGCTTTTTA-TA--TTGCTTTACTTTGTT
1 TTGCTTTGCTTTTTATTACTTTGCTTTGCTTTATA
* * *
28724120 TTGCTTTGCTCTTT-GT--TTTGCTGTGCTTTTTATA
1 TTGCTTTGCTTTTTATTACTTTGCTTTGC--TTTATA
** * *
28724154 TTGCTTTGCTTTTTATATTGTTTTGCTTTGCTTTGTT
1 TTGCTTTGC-TTTT-TATTACTTTGCTTTGCTTTATA
* * *
28724191 TTGCTGTGCTTTTTA-TA--TTGCTTTGCTCTTTGTT
1 TTGCTTTGCTTTTTATTACTTTGCTTTG--CTTTATA
*
28724225 TTGCTGTGCTTTTTA-TA--TTGCTTTGCTTTTTATA
1 TTGCTTTGCTTTTTATTACTTTGCTTTGC--TTTATA
* * *
28724259 TTGTTTTGCTGTGCTTT-TTA-TATTGCTTTGCTTTTTTTT
1 TTGCTTTGCT-T--TTTATTACT-TTGCTTTGC--TTTATA
* * * *
28724298 TTGGTTTGCTTTTTA-TA-TTTGTTTTGCTTTGTT
1 TTGCTTTGCTTTTTATTACTTTGCTTTGCTTTATA
* *
28724331 TTGCTTTGCTTTTTATATTTGCTTTGCTTTGGCTCTTTGTA
1 TTGCTTTGC-TTTT-TA-TTACTTTGCTTT-G--CTTTATA
* *
28724372 TTGCTTTGCTTTGTT-TTGCTGTGC-TT--TTTATA
1 TTGCTTTGCTTT-TTATTACTTTGCTTTGCTTTATA
*
28724404 TTGCTTTGCTTTCTT-TTGCTTTGC-TT--TTTATA
1 TTGCTTTGCTTT-TTATTACTTTGCTTTGCTTTATA
* *
28724436 TTTGCTTTGCTTTGTT-TTGCTTTGC--T-CTTTGTA
1 -TTGCTTTGCTTT-TTATTACTTTGCTTTGCTTTATA
* * *
28724469 CTGCTTTGCTTTGTT-TTGCTGTGC-TT--TTTATA
1 TTGCTTTGCTTT-TTATTACTTTGCTTTGCTTTATA
*
28724501 TTTGCTTTGCTTTCTT-TTGCTTTGC-TT--TTTATA
1 -TTGCTTTGCTTT-TTATTACTTTGCTTTGCTTTATA
* *
28724534 TTTGCTTTGCTTTCTT-TTGCTGTGC-TT--TTTATA
1 -TTGCTTTGCTTT-TTATTACTTTGCTTTGCTTTATA
28724567 TTTGCTTTGCTTTT
1 -TTGCTTTGCTTTT
28724581 GCTGTGCTTT
Statistics
Matches: 724, Mismatches: 98, Indels: 177
0.72 0.10 0.18
Matches are distributed among these distances:
29 1 0.00
30 19 0.03
31 6 0.01
32 169 0.23
33 126 0.17
34 81 0.11
35 84 0.12
36 32 0.04
37 122 0.17
38 26 0.04
39 38 0.05
40 4 0.01
41 16 0.02
ACGTcount: A:0.07, C:0.14, G:0.16, T:0.62
Consensus pattern (35 bp):
TTGCTTTGCTTTTTATTACTTTGCTTTGCTTTATA
Found at i:28723834 original size:32 final size:32
Alignment explanation
Indices: 28723797--28724653 Score: 482
Period size: 32 Copynumber: 26.9 Consensus size: 32
28723787 TTGCTTTATA
* *
28723797 TTGCTTTGCTGTGCTGTGCTTTTTATATTGCT
1 TTGCTTTGTTCTGCTGTGCTTTTTATATTGCT
28723829 TTGCTTTGTTCTGCTGTGCTTTTTATATTGCT
1 TTGCTTTGTTCTGCTGTGCTTTTTATATTGCT
* * ** *
28723861 TTGCTTTGTTTTGCTTTGC-TTTGCT-GTGCTT
1 TTGCTTTGTTCTGCTGTGCTTTTTATATTGC-T
** * *
28723892 TTTATATTGCTT-TGCTTTG-TTTTGT-T-GTGCTT
1 TTGCT-TTG-TTCTGCTGTGCTTTT-TATATTGC-T
** * **
28723924 TTTATATTGCTT-TGCTTTG-TTTTGCT-TTGCT
1 TTGCT-TTG-TTCTGCTGTGCTTTTTATATTGCT
28723955 TTGC--TG---TGC--T--TTT-TATATTGCT
1 TTGCTTTGTTCTGCTGTGCTTTTTATATTGCT
* *
28723977 TTGCTTTGTTTTGCTGTGCTTTTTGTATTGCT
1 TTGCTTTGTTCTGCTGTGCTTTTTATATTGCT
* **
28724009 TTGCTTTGTTTTGCTGTGCAATTTATATTGCT
1 TTGCTTTGTTCTGCTGTGCTTTTTATATTGCT
* * * * **
28724041 TTGCTTTGTTTTGCTTTGCTTTCCTGTGCTTTTTAT
1 TTGCTTTGTTCTGCTGTGCTTT--T-T-ATATTGCT
28724077 ATTGCTTTGCTT-TGCTGTGCTTTTTATATTGCT
1 -TTGCTTTG-TTCTGCTGTGCTTTTTATATTGCT
* * * * * *
28724110 TTACTTTGTTTTGCTTTGCTCTTTGTTTTGCT
1 TTGCTTTGTTCTGCTGTGCTTTTTATATTGCT
* * * *
28724142 GTGCTTTTTATATTGCTTTGCTTTTTATATTGTTTTGCT
1 TTGCTTTGT-T-CTGCTGTGCTTTTTATA-----TTGCT
*
28724181 TTGCTTTGTTTTGCTGTGCTTTTTATATTGCT
1 TTGCTTTGTTCTGCTGTGCTTTTTATATTGCT
*
28724213 TTGCTCTTTGTTTTGCTGTGCTTTTTATATTGCT
1 TTG--CTTTGTTCTGCTGTGCTTTTTATATTGCT
*
28724247 TTGCTTTTTATATTGTTTTGCTGTGCTTTTTATATTGCT
1 TTGC------T-TTGTTCTGCTGTGCTTTTTATATTGCT
* * * * *
28724286 TTGCTTTTTTTTTTGGTTTGCTTTTTATATTTGTT
1 TTGC--TTTGTTCTGCTGTGCTTTTTATA-TTGCT
* *
28724321 TTGCTTTGTTTTGCTTTGCTTTTTATATTTGCT
1 TTGCTTTGTTCTGCTGTGCTTTTTATA-TTGCT
* * * **
28724354 TTGCTTTG-GCT-CTTTG-TATTGCT-TTGCT
1 TTGCTTTGTTCTGCTGTGCTTTTTATATTGCT
28724382 TTG---T-TT-TGCTGTGCTTTTTATATTGCT
1 TTGCTTTGTTCTGCTGTGCTTTTTATATTGCT
* * *
28724409 TTGCTTTCTTTTGCTTTGCTTTTTATATTTGCT
1 TTGCTTTGTTCTGCTGTGCTTTTTATA-TTGCT
* * * * *
28724442 TTGCTTTGTTTTGCTTTGCTCTTTGTACTGCT
1 TTGCTTTGTTCTGCTGTGCTTTTTATATTGCT
*
28724474 TTGCTTTGTTTTGCTGTGCTTTTTATATTTGCT
1 TTGCTTTGTTCTGCTGTGCTTTTTATA-TTGCT
* * *
28724507 TTGCTTTCTTTTGCTTTGCTTTTTATATTTGCT
1 TTGCTTTGTTCTGCTGTGCTTTTTATA-TTGCT
* *
28724540 TTGCTTTCTTTTGCTGTGCTTTTTATATTTGCT
1 TTGCTTTGTTCTGCTGTGCTTTTTATA-TTGCT
*
28724573 TTGC--T-TT-TGCTGTGCTTTTTATATTACT
1 TTGCTTTGTTCTGCTGTGCTTTTTATATTGCT
*
28724601 TTGC--T-TT-TGCTGTGCTTTTTATATTGGT
1 TTGCTTTGTTCTGCTGTGCTTTTTATATTGCT
28724629 TTGC--T-TT-TGCTGTGCTTTTTATATT
1 TTGCTTTGTTCTGCTGTGCTTTTTATATT
28724654 TACCAAAGCA
Statistics
Matches: 694, Mismatches: 79, Indels: 108
0.79 0.09 0.12
Matches are distributed among these distances:
21 1 0.00
22 12 0.02
23 1 0.00
24 3 0.00
25 8 0.01
26 4 0.01
27 11 0.02
28 65 0.09
29 17 0.02
30 10 0.01
31 24 0.03
32 233 0.34
33 141 0.20
34 67 0.10
35 12 0.02
36 4 0.01
37 34 0.05
38 4 0.01
39 43 0.06
ACGTcount: A:0.06, C:0.13, G:0.17, T:0.63
Consensus pattern (32 bp):
TTGCTTTGTTCTGCTGTGCTTTTTATATTGCT
Found at i:28723874 original size:42 final size:42
Alignment explanation
Indices: 28723828--28724430 Score: 343
Period size: 42 Copynumber: 14.3 Consensus size: 42
28723818 TTTATATTGC
28723828 TTTGCTTTG-TTCTGCTGTGCTTTTTATATTGCTTTGCTTTGT
1 TTTGCTTTGCTT-TGCTGTGCTTTTTATATTGCTTTGCTTTGT
28723870 TTTGCTTTGCTTTGCTGTGCTTTTTATATTGCTTTGCTTTG-
1 TTTGCTTTGCTTTGCTGTGCTTTTTATATTGCTTTGCTTTGT
28723911 --T--TTTG---T--TGTGCTTTTTATATTGCTTTGCTTTGT
1 TTTGCTTTGCTTTGCTGTGCTTTTTATATTGCTTTGCTTTGT
28723944 TTTGCTTTGCTTTGCTGTGCTTTTTATATTGCTTTGCTTTGT
1 TTTGCTTTGCTTTGCTGTGCTTTTTATATTGCTTTGCTTTGT
* * ** * *
28723986 TTTGCTGTGCTTT--T-TG-TATTGCT-TTGCTTTGTTTTGC
1 TTTGCTTTGCTTTGCTGTGCTTTTTATATTGCTTTGCTTTGT
* * * * * *
28724023 TGTGCAATTT-ATATTGCTTTGCTTTGTTTTGCTTTGCTTTCCTGTGCTTTTT
1 TTTGC--TTTGCT-TTGCTGTGCTTT-TTAT--ATTGC--T--T-TGCTTTGT
*
28724075 ATATTGCTTTGCTTTGCTGTGCTTTTTATATTGCTTTACTTTGT
1 -T-TTGCTTTGCTTTGCTGTGCTTTTTATATTGCTTTGCTTTGT
*
28724119 TTTGCTTTGCTCTTTGTTTTGCTGTGCTTTTTATATTGCTTTGCTTTTT
1 TTTGCTTTG--C-----TTTGCTGTGCTTTTTATATTGCTTTGCTTTGT
* * ** * ** *
28724168 ATATTGTTTTGCTTTGCTTTG-TTTTGCT-GTGCTTTTTATATTGC
1 -T-TTGCTTTGCTTTGCTGTGCTTTTTATATTGC-TTTGCT-TTGT
*
28724212 TTTGCTCTTTGTTTTGCTGTGCTTTTTATATTGCTTTGCTTT-T
1 TTTG--CTTTGCTTTGCTGTGCTTTTTATATTGCTTTGCTTTGT
* * *
28724255 TAT--ATTGTTTTGCTGTGCTTTTTATATTGCTTTGCTTT-T
1 TTTGCTTTGCTTTGCTGTGCTTTTTATATTGCTTTGCTTTGT
* * *
28724294 TTT--TTTGGTTTGCT-T--TTTATAT-TTGTTTTGCTTTGT
1 TTTGCTTTGCTTTGCTGTGCTTTTTATATTGCTTTGCTTTGT
** * * * *
28724330 TTTGCTTTGCTTTTTATATTTGCTTTGCT-T-TGGCTCTTTG-TATTGC
1 TTTGCTTTGC--TTT-GCTGTGCTTT-TTATATTG--CTTTGCT-TTGT
* *
28724376 TTTGCTTTGTTTTGCTGTGCTTTTTATATTGCTTTGCTTTCT
1 TTTGCTTTGCTTTGCTGTGCTTTTTATATTGCTTTGCTTTGT
28724418 TTTGCTTTGCTTT
1 TTTGCTTTGCTTT
28724431 TTATATTTGC
Statistics
Matches: 435, Mismatches: 65, Indels: 122
0.70 0.10 0.20
Matches are distributed among these distances:
32 26 0.06
34 1 0.00
35 12 0.03
36 10 0.02
37 24 0.06
38 10 0.02
39 53 0.12
40 5 0.01
41 2 0.00
42 114 0.26
43 26 0.06
44 44 0.10
45 12 0.03
46 19 0.04
47 5 0.01
49 36 0.08
50 1 0.00
51 11 0.03
52 19 0.04
53 2 0.00
54 3 0.01
ACGTcount: A:0.06, C:0.13, G:0.18, T:0.63
Consensus pattern (42 bp):
TTTGCTTTGCTTTGCTGTGCTTTTTATATTGCTTTGCTTTGT
Found at i:28723886 original size:74 final size:74
Alignment explanation
Indices: 28723783--28724607 Score: 644
Period size: 74 Copynumber: 11.1 Consensus size: 74
28723773 TACTTTACTC
* * * *
28723783 TGCTTTGCTTTATATTGCTTTGCTGTGCTGTGCTTTTTATATTGCTTTGCTTTGTTCTGCTGTGC
1 TGCTTTGCTTTGTTTTGCTTTGCTTTGCTGTGCTTTTTATATTGCTTTGCTTTGTTTTGCTGTGC
28723848 TTTTTATAT
66 TTTTTATAT
*
28723857 TGCTTTGCTTTGTTTTGCTTTGCTTTGCTGTGCTTTTTATATTGCTTTGCTTTGTTTTGTTGTGC
1 TGCTTTGCTTTGTTTTGCTTTGCTTTGCTGTGCTTTTTATATTGCTTTGCTTTGTTTTGCTGTGC
28723922 TTTTTATAT
66 TTTTTATAT
28723931 TGCTTTGCTTTGTTTTGCTTTGCTTTGCTGTGCTTTTTATATTGCTTTGCTTTGTTTTGCTGTGC
1 TGCTTTGCTTTGTTTTGCTTTGCTTTGCTGTGCTTTTTATATTGCTTTGCTTTGTTTTGCTGTGC
*
28723996 TTTTTGTAT
66 TTTTTATAT
* * * ** * * *
28724005 TGCTTTGCTTTGTTTTGCTGTGCAATTT-ATATTGC-TTTGCT-TTGTTTTGCTTTGCTTTCCTG
1 TGCTTTGCTTTGTTTTGCTTTGC--TTTGCT-GTGCTTTTTATATTGCTTTGCTTTGTTTTGCTG
28724067 TGCTTTTTATAT
63 TGCTTTTTATAT
* * ** * * *
28724079 TGCTTTGCTTTGCTGTGCTTTTTATATTGCTTTACTTTGT-T-TTGCTTTGCTCTTTGTTTTGCT
1 TGCTTTGCTTTGTTTTGC-TTTGCT-TTGCTGTGCTTTTTATATTGCTTTG--CTTTGTTTTGCT
28724142 GTGCTTTTTATAT
62 GTGCTTTTTATAT
28724155 TGCTTTGCTTTTTATATTGTTTTGCTTTGCTTTGTTTTGCTGTGCTTTTTATATTGCTTTGCTCT
1 TGCTTTGC------T-TTGTTTTGCTTTGC-----TTTGCTGTGCTTTTTATATTGCTTTG--CT
28724220 TTGTTTTGCTGTGCTTTTTATAT
52 TTGTTTTGCTGTGCTTTTTATAT
* * * * * *
28724243 TGCTTTGCTTT-TTAT--ATTGTTTTGCTGTGCTTTTTATATTGCTTTGCTTTTTTTTTTGGTTT
1 TGCTTTGCTTTGTTTTGCTTTGCTTTGCTGTGCTTTTTATATTGCTTTGC--TTTGTTTTGCTGT
28724305 GCTTTTTATATT
64 GCTTTTTATA-T
* * ** *
28724317 TGTTTTGCTTTGTTTTGCTTTGCTTT--T-T-ATATTTGCT-TTGCTTTGGCTCTTTGTATTGCT
1 TGCTTTGCTTTGTTTTGCTTTGCTTTGCTGTGCT-TTTTATATTGCTTT-G--CTTTGTTTTGCT
* *
28724377 TTGCTTTGT-T-T
62 GTGCTTTTTATAT
* * *
28724388 TGCTGTGCTTTTTATATTGCTTTGCTTTCTTTTGCTTTGCTTTTTATATTTGCTTTGCTTTGTTT
1 TGCTTTGCTTTGT-T-TTGCTTTG----C-TTTGCTGTGCTTTTTATA-TTGCTTTGCTTTGTTT
* * * *
28724453 TGCTTTGCTCTTTGTAC
58 TGCTGTGCTTTTTATAT
* * *
28724470 TGCTTTGCTTTGTTTTGC--TG---TGCT-T--TTTATAT-TTGCTTTGCTTTCTTTTGCTTTGC
1 TGCTTTGCTTTGTTTTGCTTTGCTTTGCTGTGCTTTTTATATTGCTTTGCTTTGTTTTGCTGTGC
28724526 TTTTTATA-
66 TTTTTATAT
*
28724534 ---TTTGCTTTGCTTT-C--T--TTTGCTGTGCTTTTTATATTTGCTTTGCTTT----TGCTGTG
1 TGCTTTGCTTTGTTTTGCTTTGCTTTGCTGTGCTTTTTATA-TTGCTTTGCTTTGTTTTGCTGTG
28724587 CTTTTTATAT
65 CTTTTTATAT
*
28724597 TACTTTGCTTT
1 TGCTTTGCTTT
28724608 TGCTGTGCTT
Statistics
Matches: 621, Mismatches: 71, Indels: 126
0.76 0.09 0.15
Matches are distributed among these distances:
60 2 0.00
61 16 0.03
62 16 0.03
64 6 0.01
65 29 0.05
66 20 0.03
67 6 0.01
69 1 0.00
70 4 0.01
71 12 0.02
72 1 0.00
73 64 0.10
74 254 0.41
75 14 0.02
76 38 0.06
77 7 0.01
78 8 0.01
80 26 0.04
81 9 0.01
82 18 0.03
83 14 0.02
86 11 0.02
87 2 0.00
88 43 0.07
ACGTcount: A:0.06, C:0.14, G:0.17, T:0.63
Consensus pattern (74 bp):
TGCTTTGCTTTGTTTTGCTTTGCTTTGCTGTGCTTTTTATATTGCTTTGCTTTGTTTTGCTGTGC
TTTTTATAT
Found at i:28724179 original size:22 final size:22
Alignment explanation
Indices: 28724132--28724187 Score: 68
Period size: 17 Copynumber: 2.8 Consensus size: 22
28724122 GCTTTGCTCT
*
28724132 TTGTTTTGCTGTGCTTTTTATA
1 TTGTTTTGCTTTGCTTTTTATA
28724154 -----TTGCTTTGCTTTTTATA
1 TTGTTTTGCTTTGCTTTTTATA
28724171 TTGTTTTGCTTTGCTTT
1 TTGTTTTGCTTTGCTTT
28724188 GTTTTGCTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 10
0.72 0.03 0.26
Matches are distributed among these distances:
17 16 0.57
22 12 0.43
ACGTcount: A:0.07, C:0.11, G:0.16, T:0.66
Consensus pattern (22 bp):
TTGTTTTGCTTTGCTTTTTATA
Found at i:28724214 original size:88 final size:87
Alignment explanation
Indices: 28724087--28724580 Score: 430
Period size: 88 Copynumber: 5.7 Consensus size: 87
28724077 ATTGCTTTGC
* * * *
28724087 TTTGCTGTGCTTTTTATATTGCTTTACTTTGTT-TTGCTTTGCTCTTTGTTTTGCTGTGCTTTTT
1 TTTGCTTTGCTTTGT-T-TTGCTTTGCTTTTTTATTGCTTTGCTCTTTGTTTTGCTGTGCTTTTT
28724151 ATATTGCTTTGCTTTTTATATTGT
64 ATATTGCTTTGCTTTTTATATTGT
*
28724175 TTTGCTTTGCTTTGTTTTGCTGTGCTTTTTATATTGCTTTGCTCTTTGTTTTGCTGTGCTTTTTA
1 TTTGCTTTGCTTTGTTTTGCTTTGCTTTTT-TATTGCTTTGCTCTTTGTTTTGCTGTGCTTTTTA
28724240 TATTGCTTTGCTTTTTATATTGT
65 TATTGCTTTGCTTTTTATATTGT
* * * * * * * *
28724263 TTTGCTGTGCTTTTTATATTGCTTTGCTTTTTTTTTTGGTTTGCTTTTTATATTTGTTTTGCTTT
1 TTTGCTTTGCTTTGT-T-TTGCTTTGC-TTTTTTATTGCTTTGCTCTTTGT-TTTGCTGTGCTTT
* *
28724328 GT-T-TTGCTTTGCTTTTTATATTTGC
62 TTATATTGCTTTGCTTTTTATA-TTGT
* * * * * * * *
28724353 TTTGCTTTGGCTCTTTGTATTGCTTTGCTTTGTT-TTGCTGTGCTTTTTATATTGCTTTGCTTTC
1 TTTGCTTT-G--CTTTGTTTTGCTTTGCTTTTTTATTGCTTTGCTCTTTGTTTTGCTGTGCTTTT
28724417 T-T-TTGCTTTGCTTTTTATA----
63 TATATTGCTTTGCTTTTTATATTGT
* *
28724436 TTTGCTTTGCTTTGTTTTGCTTTGCTCTTTGTACTGCTTTG--CTTTGTTTTGCTGTGCTTTTTA
1 TTTGCTTTGCTTTGTTTTGCTTTGCT-TTTTTATTGCTTTGCTCTTTGTTTTGCTGTGCTTTTTA
* *
28724499 TATTTGCTTTGCTTTCT-T-TTGC
65 TA-TTGCTTTGCTTTTTATATTGT
* * * * * *
28724521 TTTGCTTT--TTAT-ATTTGCTTTGCTTTCTT-TTGCTGTGCTTTTTATATTTGCTTTGCTTTT
1 TTTGCTTTGCTT-TGTTTTGCTTTGCTTTTTTATTGCTTTGCTCTTTGT-TTTGCTGTGCTTTT
28724581 GCTGTGCTTT
Statistics
Matches: 339, Mismatches: 44, Indels: 50
0.78 0.10 0.12
Matches are distributed among these distances:
80 32 0.09
81 10 0.03
82 11 0.03
83 38 0.11
84 14 0.04
85 8 0.02
86 11 0.03
87 2 0.01
88 111 0.33
89 32 0.09
90 38 0.11
91 27 0.08
93 5 0.01
ACGTcount: A:0.06, C:0.13, G:0.16, T:0.64
Consensus pattern (87 bp):
TTTGCTTTGCTTTGTTTTGCTTTGCTTTTTTATTGCTTTGCTCTTTGTTTTGCTGTGCTTTTTAT
ATTGCTTTGCTTTTTATATTGT
Found at i:28724298 original size:22 final size:22
Alignment explanation
Indices: 28723919--28724388 Score: 147
Period size: 22 Copynumber: 22.3 Consensus size: 22
28723909 TGTTTTGTTG
28723919 TGCTTTTTATATTGCTTTGCTT
1 TGCTTTTTATATTGCTTTGCTT
** *
28723941 TG-TTTTGCT-TTGCTTTGCTG
1 TGCTTTTTATATTGCTTTGCTT
28723961 TGCTTTTTATATTGCTTTGCTT
1 TGCTTTTTATATTGCTTTGCTT
** *
28723983 TG-TTTTGCT-GTGCTTTTTG-TAT
1 TGCTTTTTATATTGC--TTTGCT-T
** * *
28724005 TGC-TTTGCT-TTGTTTTGCTG
1 TGCTTTTTATATTGCTTTGCTT
**
28724025 TGCAATTTATATTGCTTTGCTT
1 TGCTTTTTATATTGCTTTGCTT
** * *
28724047 TG-TTTTGCT-TTGCTTTCCTG
1 TGCTTTTTATATTGCTTTGCTT
28724067 TGCTTTTTATATTGCTTTGCTTTGCT
1 TGCTTTTTATATTGCTTTGC--T--T
*
28724093 GTGCTTTTTATATTGCTTTACTT
1 -TGCTTTTTATATTGCTTTGCTT
** *
28724116 TG-TTTTGCT-TTGCTCTTTGTTT
1 TGCTTTTTATATTG--CTTTGCTT
* *
28724138 TGCTGTGCTTTTTA-T--ATTGCTT
1 TGCT-T--TTTATATTGCTTTGCTT
*
28724160 TGCTTTTTATATTGTTTTGCTT
1 TGCTTTTTATATTGCTTTGCTT
*
28724182 TGCTTTGT-T-TTGC--TG---
1 TGCTTTTTATATTGCTTTGCTT
28724197 TGCTTTTTATATTGCTTTGC--
1 TGCTTTTTATATTGCTTTGCTT
* *
28724217 T-CTTTGT-T-TTGCTGTGCTT
1 TGCTTTTTATATTGCTTTGCTT
28724236 T-----TTATATTGCTTT----
1 TGCTTTTTATATTGCTTTGCTT
* *
28724249 -GCTTTTTATATTGTTTTGCTG
1 TGCTTTTTATATTGCTTTGCTT
28724270 TGCTTTTTATATTGCTTTGCTT
1 TGCTTTTTATATTGCTTTGCTT
** * **
28724292 TTTTTTTTGGT-TTGCTTTTTATATT
1 TGCTTTTT-ATATTGC--TTT-GCTT
** *
28724317 TG-TTTTGCT-TTGTTTTGCTT
1 TGCTTTTTATATTGCTTTGCTT
28724337 TGCTTTTTATATTTGCTTTGCTT
1 TGCTTTTTATA-TTGCTTTGCTT
* *
28724360 TGGCTCTTTGTATTGCTTTGCTT
1 T-GCTTTTTATATTGCTTTGCTT
28724383 TG-TTTT
1 TGCTTTT
28724389 GCTGTGCTTT
Statistics
Matches: 330, Mismatches: 65, Indels: 107
0.66 0.13 0.21
Matches are distributed among these distances:
15 8 0.02
16 2 0.01
17 29 0.09
18 3 0.01
19 13 0.04
20 45 0.14
21 46 0.14
22 110 0.33
23 30 0.09
24 17 0.05
25 4 0.01
26 4 0.01
27 19 0.06
ACGTcount: A:0.07, C:0.13, G:0.17, T:0.63
Consensus pattern (22 bp):
TGCTTTTTATATTGCTTTGCTT
Found at i:28724446 original size:33 final size:32
Alignment explanation
Indices: 28724370--28724653 Score: 349
Period size: 33 Copynumber: 9.1 Consensus size: 32
28724360 TGGCTCTTTG
*
28724370 TATTGCTTTGCTTTGTTTTGCTGTGCTTTTTA
1 TATTGCTTTGCTTTCTTTTGCTGTGCTTTTTA
*
28724402 TATTGCTTTGCTTTCTTTTGCTTTGCTTTTTA
1 TATTGCTTTGCTTTCTTTTGCTGTGCTTTTTA
* * * *
28724434 TATTTGCTTTGCTTTGTTTTGCTTTGCTCTTTG
1 TA-TTGCTTTGCTTTCTTTTGCTGTGCTTTTTA
* *
28724467 TACTGCTTTGCTTTGTTTTGCTGTGCTTTTTA
1 TATTGCTTTGCTTTCTTTTGCTGTGCTTTTTA
*
28724499 TATTTGCTTTGCTTTCTTTTGCTTTGCTTTTTA
1 TA-TTGCTTTGCTTTCTTTTGCTGTGCTTTTTA
28724532 TATTTGCTTTGCTTTCTTTTGCTGTGCTTTTTA
1 TA-TTGCTTTGCTTTCTTTTGCTGTGCTTTTTA
28724565 TA----TTTGCTTTGCTTTTGCTGTGCTTTTTA
1 TATTGCTTTGCTTT-CTTTTGCTGTGCTTTTTA
*
28724594 TATTACTTTG----CTTTTGCTGTGCTTTTTA
1 TATTGCTTTGCTTTCTTTTGCTGTGCTTTTTA
*
28724622 TATTGGTTTG----CTTTTGCTGTGCTTTTTA
1 TATTGCTTTGCTTTCTTTTGCTGTGCTTTTTA
28724650 TATT
1 TATT
28724654 TACCAAAGCA
Statistics
Matches: 230, Mismatches: 15, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
28 56 0.24
29 20 0.09
32 60 0.26
33 94 0.41
ACGTcount: A:0.07, C:0.14, G:0.16, T:0.63
Consensus pattern (32 bp):
TATTGCTTTGCTTTCTTTTGCTGTGCTTTTTA
Found at i:28724521 original size:28 final size:28
Alignment explanation
Indices: 28724302--28724654 Score: 139
Period size: 28 Copynumber: 11.6 Consensus size: 28
28724292 TTTTTTTTGG
* *
28724302 TTTGCTTTTTATATTTGTTTTGCTTTGT
1 TTTGCTTTTTATATTTGCTTTGCTTTCT
*
28724330 TTTGCTTTGCTT-T-TTAT-ATTTGCTTTGCT
1 TTTGCTTT--TTATATT-TGCTTTGCTTT-CT
* * * *
28724359 TTGGCTCTTTGTA-TTGCTTTGCTTTGT
1 TTTGCTTTTTATATTTGCTTTGCTTTCT
*
28724386 TTTGCTGTGCTTTTTATATTGCTTTGCTTTCTTTT
1 TTTGCT-T--TTTATAT-TTGCTTTGCTTTC---T
*
28724421 GCTTTGCTTTTTATATTTGCTTTGCTTTGT
1 --TTTGCTTTTTATATTTGCTTTGCTTTCT
* * * *
28724451 TTTGCTTTGCTCTTTGTACTGCTTTGCTTTGTTT
1 TTTGCTTT--T-TATAT-TTGCTTTGC-TT-TCT
28724485 TGCTGTGCTTTTTATATTTGCTTTGCTTTCTTTT
1 T--T-TGCTTTTTATATTTGCTTTGCTTTC---T
28724519 GCTTTGCTTTTTATATTTGCTTTGCTTTCTTT
1 --TTTGCTTTTTATATTTGCTTTGCTTTC--T
28724551 TGCTGTGCTTTTTATATTTGCTTTGCTTT-T
1 T--T-TGCTTTTTATATTTGCTTTGCTTTCT
* *
28724581 GCTGTGCTTTTTATA-TTACTTTGCTTT-T
1 --TTTGCTTTTTATATTTGCTTTGCTTTCT
* *
28724609 GCTGTGCTTTTTATA-TTGGTTTGCTTT-T
1 --TTTGCTTTTTATATTTGCTTTGCTTTCT
*
28724637 GCTGTGCTTTTTATATTT
1 --TTTGCTTTTTATATTT
28724655 ACCAAAGCAA
Statistics
Matches: 264, Mismatches: 24, Indels: 73
0.73 0.07 0.20
Matches are distributed among these distances:
27 9 0.03
28 89 0.34
29 22 0.08
30 11 0.04
31 4 0.02
32 27 0.10
33 71 0.27
34 14 0.05
35 2 0.01
36 3 0.01
37 12 0.05
ACGTcount: A:0.07, C:0.14, G:0.16, T:0.64
Consensus pattern (28 bp):
TTTGCTTTTTATATTTGCTTTGCTTTCT
Found at i:28724607 original size:5 final size:5
Alignment explanation
Indices: 28723632--28724590 Score: 223
Period size: 5 Copynumber: 186.4 Consensus size: 5
28723622 TTGCTCTATA
* * * *
28723632 TTGCT TTGCT TTGCT TT-TT ATTACT TTGCT TTGCT TT-AT ATTGAT TTGCT
1 TTGCT TTGCT TTGCT TTGCT -TTGCT TTGCT TTGCT TTGCT -TTGCT TTGCT
* * * *
28723682 ATGCT TTGCT TT-AT ATTGCT ATGCT TTGCT TT-AT ATTGCT TTGC- TT-CAT
1 TTGCT TTGCT TTGCT -TTGCT TTGCT TTGCT TTGCT -TTGCT TTGCT TTGC-T
* ** * * * *
28723731 ATTACT TTGCT TTG-T TTTAT ATTTCT TTGCT TTTCT TT-AT ATTACT
1 -TTGCT TTGCT TTGCT TTGCT -TTGCT TTGCT TTGCT TTGCT -TTGCT
* * * * * **
28723777 TTACT CTGCT TTGCT TT-AT ATTGCT TTGCT GTGCT GTGCTT TTTAT ATTGCT
1 TTGCT TTGCT TTGCT TTGCT -TTGCT TTGCT TTGCT TTGC-T TTGCT -TTGCT
* ** *
28723829 TTGCT TTG-T TCTGCT GTGCTT TTTAT ATTGCT TTGCT TTGTT TTGCT
1 TTGCT TTGCT T-TGCT TTGC-T TTGCT -TTGCT TTGCT TTGCT TTGCT
* ** *
28723876 TTGCT TTGCT GTGCTT TTTAT ATTGCT TTGCT TTGTT TTG-T TGTGCTT
1 TTGCT TTGCT TTGC-T TTGCT -TTGCT TTGCT TTGCT TTGCT T-TGC-T
** * * **
28723924 TTTAT ATTGCT TTGCT TTGTT TTGCT TTGCT TTGCT GTGCTT TTTAT ATTGCT
1 TTGCT -TTGCT TTGCT TTGCT TTGCT TTGCT TTGCT TTGC-T TTGCT -TTGCT
* * *
28723977 TTGCT TTGTT TTGCT GTGCTTT TTG-T ATTGCT TTGCT TTGTT TTGCT
1 TTGCT TTGCT TTGCT TTGC--T TTGCT -TTGCT TTGCT TTGCT TTGCT
* * * * *
28724024 GTGCAAT TT-AT ATTGCT TTGCT TTGTT TTGCT TTGCT TTCCT GTGCTT
1 TTGC--T TTGCT -TTGCT TTGCT TTGCT TTGCT TTGCT TTGCT TTGC-T
** * ** * *
28724072 TTTAT ATTGCT TTGCT TTGCT GTGCTT TTTAT ATTGCT TTACT TTGTT
1 TTGCT -TTGCT TTGCT TTGCT TTGC-T TTGCT -TTGCT TTGCT TTGCT
* * ** **
28724120 TTGCT TTGCTCT TTGTT TTGCT GTGCTT TTTAT ATTGCT TTGCTT TTTAT
1 TTGCT TTG--CT TTGCT TTGCT TTGC-T TTGCT -TTGCT TTGC-T TTGCT
* * * **
28724170 ATTGTT TTGCT TTGCT TTGTT TTGCT GTGCTT TTTAT ATTGCT TTGCTCT
1 -TTGCT TTGCT TTGCT TTGCT TTGCT TTGC-T TTGCT -TTGCT TTG--CT
* * ** ** *
28724220 TTGTT TTGCT GTGCTT TTTAT ATTGCT TTGCTT TTTAT ATTGTT TTGCT
1 TTGCT TTGCT TTGC-T TTGCT -TTGCT TTGC-T TTGCT -TTGCT TTGCT
* ** * * *
28724269 GTGCTT TTTAT ATTGCT TTGCT TT--T TT-TT TTGGT TTGCT TT--T TAT-AT
1 TTGC-T TTGCT -TTGCT TTGCT TTGCT TTGCT TTGCT TTGCT TTGCT T-TGCT
* * *
28724316 TTGTT TTGCT TTGTT TTGCT TTGCT TT--T TAT-AT TTGCT TTGCT TTGGCTCT
1 TTGCT TTGCT TTGCT TTGCT TTGCT TTGCT T-TGCT TTGCT TTGCT TT-G--CT
* * **
28724367 TTG-T ATTGCT TTGCT TTGTT TTGCT GTGCTT TTTAT ATTGCT TTGCT
1 TTGCT -TTGCT TTGCT TTGCT TTGCT TTGC-T TTGCT -TTGCT TTGCT
* *
28724414 TT-CTT TTGCT TTGCT TT--T TAT-AT TTGCT TTGCT TTGTT TTGCT TTGCTCT
1 TTGC-T TTGCT TTGCT TTGCT T-TGCT TTGCT TTGCT TTGCT TTGCT TTG--CT
* * * *
28724464 TTG-T ACTGCT TTGCT TTGTT TTGCT GTGCT TT--T TAT-AT TTGCT TTGCT
1 TTGCT -TTGCT TTGCT TTGCT TTGCT TTGCT TTGCT T-TGCT TTGCT TTGCT
*
28724512 TT-CTT TTGCT TTGCT TT--T TAT-AT TTGCT TTGCT TT-CTT TTGCT
1 TTGC-T TTGCT TTGCT TTGCT T-TGCT TTGCT TTGCT TTGC-T TTGCT
* * *
28724555 GTGCT TT--T TAT-AT TTGCT TTGCTT TTGCT GTGCT TT
1 TTGCT TTGCT T-TGCT TTGCT TTGC-T TTGCT TTGCT TT
28724591 TTATATTACT
Statistics
Matches: 697, Mismatches: 159, Indels: 196
0.66 0.15 0.19
Matches are distributed among these distances:
3 16 0.02
4 37 0.05
5 517 0.74
6 99 0.14
7 24 0.03
8 4 0.01
ACGTcount: A:0.07, C:0.14, G:0.16, T:0.62
Consensus pattern (5 bp):
TTGCT
Found at i:28725358 original size:43 final size:43
Alignment explanation
Indices: 28725310--28725402 Score: 186
Period size: 43 Copynumber: 2.2 Consensus size: 43
28725300 AAAGCAGAAG
28725310 CAACTTAACTTGAGGTAAAACAATAGTCATGATACAACTTTAT
1 CAACTTAACTTGAGGTAAAACAATAGTCATGATACAACTTTAT
28725353 CAACTTAACTTGAGGTAAAACAATAGTCATGATACAACTTTAT
1 CAACTTAACTTGAGGTAAAACAATAGTCATGATACAACTTTAT
28725396 CAACTTA
1 CAACTTA
28725403 TGATACCACA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (43 bp):
CAACTTAACTTGAGGTAAAACAATAGTCATGATACAACTTTAT
Found at i:28727703 original size:43 final size:43
Alignment explanation
Indices: 28727655--28727747 Score: 186
Period size: 43 Copynumber: 2.2 Consensus size: 43
28727645 AAAGCAGAAG
28727655 CAACTTAACTTGAGGTAAAACAATAGTCATGATACAACTTTAT
1 CAACTTAACTTGAGGTAAAACAATAGTCATGATACAACTTTAT
28727698 CAACTTAACTTGAGGTAAAACAATAGTCATGATACAACTTTAT
1 CAACTTAACTTGAGGTAAAACAATAGTCATGATACAACTTTAT
28727741 CAACTTA
1 CAACTTA
28727748 TGATACCACA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (43 bp):
CAACTTAACTTGAGGTAAAACAATAGTCATGATACAACTTTAT
Found at i:28743738 original size:26 final size:26
Alignment explanation
Indices: 28743709--28743758 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
28743699 GACTGATAGT
*
28743709 TGATTGTAGTGATTGATTTGATCACC
1 TGATTGTAGTAATTGATTTGATCACC
* *
28743735 TGATTTTATTAATTGATTTGATCA
1 TGATTGTAGTAATTGATTTGATCA
28743759 ACTAATTCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.48
Consensus pattern (26 bp):
TGATTGTAGTAATTGATTTGATCACC
Found at i:28743770 original size:26 final size:26
Alignment explanation
Indices: 28743720--28743774 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
28743710 GATTGTAGTG
* * *
28743720 ATTGATTTGATCACCTGATTTTATTA
1 ATTGATTTGATCAACTAATTCTATTA
28743746 ATTGATTTGATCAACTAATTCTATTA
1 ATTGATTTGATCAACTAATTCTATTA
28743772 ATT
1 ATT
28743775 AATTATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (26 bp):
ATTGATTTGATCAACTAATTCTATTA
Found at i:28748074 original size:35 final size:35
Alignment explanation
Indices: 28748027--28748096 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
28748017 ATATTAAAAT
* * *
28748027 TGATCATGGATTAGGTTATTCGTTCAGATTCGAAA
1 TGATCATCGATTAGGTTATTCGCTCAGATCCGAAA
28748062 TGATCATCGATTAGGTTATTCGCTCAGATCCGAAA
1 TGATCATCGATTAGGTTATTCGCTCAGATCCGAAA
28748097 GCTCGTTAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (35 bp):
TGATCATCGATTAGGTTATTCGCTCAGATCCGAAA
Found at i:28754774 original size:22 final size:21
Alignment explanation
Indices: 28754738--28754778 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
28754728 CGTCTTTGAA
*
28754738 TTTAGTTTTTTTATTTTAATT
1 TTTAGTTTTTGTATTTTAATT
28754759 TTTATGTTTTTGTATTTTAA
1 TTTA-GTTTTTGTATTTTAA
28754779 AATTTCAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (21 bp):
TTTAGTTTTTGTATTTTAATT
Found at i:28762614 original size:5 final size:5
Alignment explanation
Indices: 28762604--28762628 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28762594 AACGAAGAGC
28762604 ATGTG ATGTG ATGTG ATGTG ATGTG
1 ATGTG ATGTG ATGTG ATGTG ATGTG
28762629 CTGTTTAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
ATGTG
Found at i:28763871 original size:28 final size:29
Alignment explanation
Indices: 28763840--28763897 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
28763830 TTTTTCTTTT
*
28763840 ATAAAAAAATTAAAATTAAA-TCTAAAAA
1 ATAAAAAAATTAAAATAAAATTCTAAAAA
*
28763868 ATAAAAAAATTAAAATAAAATTTTAAAAA
1 ATAAAAAAATTAAAATAAAATTCTAAAAA
28763897 A
1 A
28763898 GTTAAATGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (29 bp):
ATAAAAAAATTAAAATAAAATTCTAAAAA
Found at i:28764134 original size:15 final size:15
Alignment explanation
Indices: 28764113--28764148 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
28764103 AATTATTTAG
28764113 TTTTTAATAAA-TAT
1 TTTTTAATAAATTAT
28764127 TATTTTAATAAATTAT
1 T-TTTTAATAAATTAT
28764143 TTTTTA
1 TTTTTA
28764149 TTGTATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 1 0.05
15 15 0.75
16 4 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTTAATAAATTAT
Found at i:28769114 original size:2 final size:2
Alignment explanation
Indices: 28769065--28769096 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28769055 AAGGGGACTT
28769065 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
28769097 TACAGGGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:28772198 original size:21 final size:22
Alignment explanation
Indices: 28772174--28772216 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
28772164 AATGTACATT
*
28772174 ACTCAAAACCCCGAATA-CAAA
1 ACTCAAAACCCCAAATAGCAAA
*
28772195 ACTCAAAATCCCAAATAGCAAA
1 ACTCAAAACCCCAAATAGCAAA
28772217 TCGATAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.53, C:0.30, G:0.05, T:0.12
Consensus pattern (22 bp):
ACTCAAAACCCCAAATAGCAAA
Found at i:28780056 original size:21 final size:23
Alignment explanation
Indices: 28780030--28780074 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
28780020 TAACTCAACT
*
28780030 AATTA-TTTTATAT-ATAATATA
1 AATTATTTTTACATAATAATATA
28780051 AATTATTTTTACATAATAATATA
1 AATTATTTTTACATAATAATATA
28780074 A
1 A
28780075 GTCTAGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 7 0.33
23 9 0.43
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
AATTATTTTTACATAATAATATA
Found at i:28780068 original size:20 final size:21
Alignment explanation
Indices: 28780030--28780068 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28780020 TAACTCAACT
*
28780030 AATTATTTTATATATAATATA
1 AATTATTTTATACATAATATA
28780051 AATTATTTT-TACATAATA
1 AATTATTTTATACATAATA
28780069 ATATAAGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTATTTTATACATAATATA
Found at i:28792482 original size:2 final size:2
Alignment explanation
Indices: 28792465--28792500 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
28792455 TAGCTGTGAG
* *
28792465 AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28792501 TCTTTTTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:28794606 original size:14 final size:14
Alignment explanation
Indices: 28794564--28794608 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
28794554 GTATTATTAA
28794564 TAATTTTCTAATAT
1 TAATTTTCTAATAT
* *
28794578 TAATTAAT-TATTAT
1 TAATT-TTCTAATAT
28794592 TAATTTTCTAATAT
1 TAATTTTCTAATAT
28794606 TAA
1 TAA
28794609 CTGGTTAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 1 0.04
14 23 0.92
15 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (14 bp):
TAATTTTCTAATAT
Found at i:28794623 original size:28 final size:27
Alignment explanation
Indices: 28794556--28794610 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
28794546 AATTTATCGT
*
28794556 ATTATTAATAATTTTCTAATATTAATTA
1 ATTATT-ATAATTTTCTAATATTAACTA
28794584 ATTATTATTAATTTTCTAATATTAACT
1 ATTATTA-TAATTTTCTAATATTAACT
28794611 GGTTAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 1 0.04
28 24 0.96
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (27 bp):
ATTATTATAATTTTCTAATATTAACTA
Found at i:28801234 original size:27 final size:25
Alignment explanation
Indices: 28801186--28801235 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
28801176 ATTTTCCTAT
**
28801186 AAAAGTATAAAAAATATTTCATCAA
1 AAAAGTATAAAAAATAAATCATCAA
28801211 AAAATGTATAAAAAAATAAATCATC
1 AAAA-GTAT-AAAAAATAAATCATC
28801236 TAAACTTTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 4 0.19
27 13 0.62
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.26
Consensus pattern (25 bp):
AAAAGTATAAAAAATAAATCATCAA
Done.