Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold472
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: 529027
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:157510 original size:122 final size:119
Alignment explanation
Indices: 157228--157591 Score: 330
Period size: 116 Copynumber: 3.0 Consensus size: 119
157218 AGCATGATGC
* * * *
157228 CTTTTAAAGCCTACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAAGACACCTTTTCCTT
1 CTTTCAAAGCCTACACAAGTTGGTGGCAC-TTTCCAGTCCTCAAAGAGCAGGA-AGCTTTTCCTT
* * * * *
157293 TTAAAGCCCACACAAGTTCGTGGCATTTTCTAGTCCTT-AAAGAGTAGGA--C--GC-
64 TTAAAGACCAC-CAAGTTGGTGGCACTTTCTAGT-CTTCAAAGAGCAGGATGCTTTCT
* * * * *
157345 CTTTCAAAACCTACACAAGTTGGTGGCATTTTTCAGCCCTCAAAGAGCAGGATGCTTTCTCCTTT
1 CTTTCAAAGCCTACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGAAGCTTT-TCCTTT
*
157410 TAAAGACCACTCGAGTTGGTGGCACTTTCCT-GTCTTCAAAGAGCAGGATGCTTTCT
65 TAAAGACCAC-CAAGTTGGTGGCACTTT-CTAGTCTTCAAAGAGCAGGATGCTTTCT
* * * * *
157466 CTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCTTCAAAGAGTAGGACGCATTTT-CTT
1 CTTT-CAAAGCCTACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGAAGC-TTTTCCTT
** * * * * *
157530 TTCAAAGTTCACAAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAAGATGCCTTTTT
64 TT-AAAGACCACCAAGTTGGTGGCACTTTCTAGTCTTCAAAGAGCAGGATG-CTTTCT
157588 CTTT
1 CTTT
157592 TCTCCTTTAT
Statistics
Matches: 201, Mismatches: 33, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
115 7 0.03
116 60 0.30
117 28 0.14
118 1 0.00
120 2 0.01
121 41 0.20
122 59 0.29
123 3 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (119 bp):
CTTTCAAAGCCTACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGAAGCTTTTCCTTTT
AAAGACCACCAAGTTGGTGGCACTTTCTAGTCTTCAAAGAGCAGGATGCTTTCT
Found at i:157653 original size:45 final size:43
Alignment explanation
Indices: 157586--157751 Score: 180
Period size: 45 Copynumber: 3.9 Consensus size: 43
157576 AGATGCCTTT
*
157586 TTCTTTTCTCCTTTATCCTCAAAGAGCAGGACACACTTCATATCC
1 TTCTTTTC-CCTTTGTCCTCAAAGAGCAGGACACACTTCAT-TCC
* * * *
157631 TTCTTTTCCCTTTTGTCTTCAAAGAGTAAGACGC-CTT--TTCC
1 TTCTTTTCCC-TTTGTCCTCAAAGAGCAGGACACACTTCATTCC
*
157672 TT-TTCT-CCTTTGTCCTCAAAGAGCAGGACACACTTCATTCCC
1 TTCTTTTCCCTTTGTCCTCAAAGAGCAGGACACACTTCATT-CC
* *
157714 TTCTTTTCCCTTTCGTCCTCAAAGAGTAGGACGCACTT
1 TTCTTTTCCCTTT-GTCCTCAAAGAGCAGGACACACTT
157752 TATTTTCCTC
Statistics
Matches: 100, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
38 19 0.19
39 5 0.05
40 3 0.03
41 7 0.07
42 5 0.05
43 3 0.03
44 10 0.10
45 48 0.48
ACGTcount: A:0.20, C:0.30, G:0.12, T:0.37
Consensus pattern (43 bp):
TTCTTTTCCCTTTGTCCTCAAAGAGCAGGACACACTTCATTCC
Found at i:157705 original size:83 final size:83
Alignment explanation
Indices: 157557--157752 Score: 295
Period size: 83 Copynumber: 2.3 Consensus size: 83
157547 TGGTGGCACT
* * *
157557 TTTTAGTCCTCAAAGAGCAAGATGCCTTTTTCTTTTCTCCTTTATCCTCAAAGAGCAGGACACAC
1 TTTT-GTCCTCAAAGAGTAAGACGCCTTTTCCTTTTCTCCTTTATCCTCAAAGAGCAGGACACAC
157622 TTCATAT-CCTTCTTTTCCC
65 TTCAT-TCCCTTCTTTTCCC
* *
157641 TTTTGTCTTCAAAGAGTAAGACGCCTTTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACACT
1 TTTTGTCCTCAAAGAGTAAGACGCCTTTTCCTTTTCTCCTTTATCCTCAAAGAGCAGGACACACT
157706 TCATTCCCTTCTTTTCCC
66 TCATTCCCTTCTTTTCCC
* *
157724 TTTCGTCCTCAAAGAGTAGGACGCACTTT
1 TTTTGTCCTCAAAGAGTAAGACGC-CTTT
157753 ATTTTCCTCT
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
82 1 0.01
83 93 0.91
84 8 0.08
ACGTcount: A:0.21, C:0.29, G:0.13, T:0.37
Consensus pattern (83 bp):
TTTTGTCCTCAAAGAGTAAGACGCCTTTTCCTTTTCTCCTTTATCCTCAAAGAGCAGGACACACT
TCATTCCCTTCTTTTCCC
Found at i:160831 original size:79 final size:78
Alignment explanation
Indices: 160695--160916 Score: 257
Period size: 78 Copynumber: 2.8 Consensus size: 78
160685 TCTTCATCTC
* * * * *
160695 GGGGATACTCCAACCCTGGTTTTATTTCC-AAAACATCAATTTTTCATAATCGAGGATACTCTAA
1 GGGGATACTCCAACCCCGATTTTA-TTCCTAAAACACCAATTTTTCACAATCGGGGATACTCTAA
* * *
160759 TCCCGTTATTTCCGA
65 CCCCATCATTT-CGA
* * * * *
160774 GGGGATACTCTAACCCCGATTTTATTCCTAAAACACCAGTTTTTCGCAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTCCTAAAACACCAATTTTTCACAATCGGGGATACTCTAAC
160839 CCCATCATTTCGA
66 CCCATCATTTCGA
** * * *
160852 GGGGATACTCCAACCCCGATTTTATTTTTGAAACACCAATTCTCCACAATCGGGGATACTCTAAC
1 GGGGATACTCCAACCCCGATTTTATTCCTAAAACACCAATTTTTCACAATCGGGGATACTCTAAC
160917 TCCGATTTTA
Statistics
Matches: 119, Mismatches: 23, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
78 62 0.52
79 57 0.48
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.31
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGATTTTATTCCTAAAACACCAATTTTTCACAATCGGGGATACTCTAAC
CCCATCATTTCGA
Found at i:160886 original size:78 final size:79
Alignment explanation
Indices: 160695--160912 Score: 258
Period size: 79 Copynumber: 2.8 Consensus size: 79
160685 TCTTCATCTC
* * * * * * * *
160695 GGGGATACTCCAACCCTGGTTTTATTTCCAAAACATCAATTTTTCATAATCGAGGATACTCTAAT
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
* *
160760 CCCGTTATTTCCGA
66 CCCATCATTTCCGA
* * * * *
160774 GGGGATACTCTAACCCCGATTTTATTCCTAAAACACCAGTTTTTCGCAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
160839 CCCATCATTT-CGA
66 CCCATCATTTCCGA
* * * *
160852 GGGGATACTCCAACCCCGATTTTATTTTTGAAACACCAATTCTCCACAATCGGGGATACTC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATACTC
160913 TAACTCCGAT
Statistics
Matches: 115, Mismatches: 24, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
78 55 0.48
79 60 0.52
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.31
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
CCCATCATTTCCGA
Found at i:160928 original size:51 final size:51
Alignment explanation
Indices: 160852--160971 Score: 159
Period size: 51 Copynumber: 2.4 Consensus size: 51
160842 ATCATTTCGA
***
160852 GGGGATACTCCAACCCCGATTTTATTTTTGAAACACCAATTCTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATC
* * * * *
160903 GGGGATACTCTAACTCCGATTTTATTTCCAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATC
*
160954 GGAGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
160972 TTATTTCATC
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.29
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATC
Found at i:160983 original size:28 final size:27
Alignment explanation
Indices: 160951--161026 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 27
160941 ATTTTTCACA
*
160951 ATCGGAGATACTCCAACCCCGTTATTT
1 ATCGGGGATACTCCAACCCCGTTATTT
**
160978 CATCGGGGATACTCCAACCCTATTATTT
1 -ATCGGGGATACTCCAACCCCGTTATTT
161006 -TCAGGGGATACTCCAACCCCG
1 ATC-GGGGATACTCCAACCCCG
161027 GATTTATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 2 0.05
27 16 0.38
28 24 0.57
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTATTT
Found at i:160989 original size:157 final size:156
Alignment explanation
Indices: 160825--161156 Score: 393
Period size: 157 Copynumber: 2.1 Consensus size: 156
160815 TTTCGCAATT
*
160825 GGGGATACTCCAACCCCATCA-TTTCGAGGGGATACTCCAACCCC-GATTTTATTTTTGAAACAC
1 GGGGATACTCCAACCCCATCATTTTC-AGGGGATACTCCAACCCCGGA-TTTATTTTTAAAACAC
* * * ** *
160888 CAA-TTCTCCACAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAATACCAA-TTTTTCACA
64 CAATTTCT-CACAATCGGGGATACTCCAACCCCAACCTTATTTCCAAAACACCAATTTTTTCACA
160951 ATCGGAGATACTCCAACCCCGTTATTTCATC
128 ATCGGAGATACTCCAACCCCGTTATTT--TC
* * * ***
160982 GGGGATACTCCAACCCTATTATTTTCAGGGGATACTCCAACCCCGGATTTATTTTTAAAATATTG
1 GGGGATACTCCAACCCCATCATTTTCAGGGGATACTCCAACCCCGGATTTATTTTTAAAACACCA
* * * *
161047 ATTTCTCACAATTGGGGATACTCCAACCCCAACCTTATTTCTAAAGCATCAATTTTTTCACAATC
66 ATTTCTCACAATCGGGGATACTCCAACCCCAACCTTATTTCCAAAACACCAATTTTTTCACAATC
* * *
161112 GGGGATACTCCAATCCTGTTATTTTC
131 GGAGATACTCCAACCCCGTTATTTTC
161138 GAGGAGATACTCCAACCCC
1 G-GG-GATACTCCAACCCC
161157 GATTTTATTT
Statistics
Matches: 148, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
156 3 0.02
157 89 0.60
158 56 0.38
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (156 bp):
GGGGATACTCCAACCCCATCATTTTCAGGGGATACTCCAACCCCGGATTTATTTTTAAAACACCA
ATTTCTCACAATCGGGGATACTCCAACCCCAACCTTATTTCCAAAACACCAATTTTTTCACAATC
GGAGATACTCCAACCCCGTTATTTTC
Found at i:161020 original size:27 final size:27
Alignment explanation
Indices: 160957--161025 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 27
160947 CACAATCGGA
*
160957 GATACTCCAACCCCGTTATTTCATCGGG
1 GATACTCCAACCCCATTATTTCA-CGGG
*
160985 GATACTCCAACCCTATTATTTTCA-GGG
1 GATACTCCAACCCCATTA-TTTCACGGG
161012 GATACTCCAACCCC
1 GATACTCCAACCCC
161026 GGATTTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 16 0.43
28 16 0.43
29 5 0.14
ACGTcount: A:0.25, C:0.33, G:0.14, T:0.28
Consensus pattern (27 bp):
GATACTCCAACCCCATTATTTCACGGG
Found at i:161085 original size:51 final size:52
Alignment explanation
Indices: 161009--161124 Score: 128
Period size: 51 Copynumber: 2.2 Consensus size: 52
160999 ATTATTTTCA
* * * * ** *
161009 GGGGATACTCCAACCCCGGATTTATTTTTAAAATATTGA-TTTCTCACAATT
1 GGGGATACTCCAACCCCGAACTTATTTCTAAAACATCAATTTTCTCACAATC
* *
161060 GGGGATACTCCAACCCC-AACCTTATTTCTAAAGCATCAATTTTTTCACAATC
1 GGGGATACTCCAACCCCGAA-CTTATTTCTAAAACATCAATTTTCTCACAATC
161112 GGGGATACTCCAA
1 GGGGATACTCCAA
161125 TCCTGTTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
50 1 0.02
51 30 0.56
52 23 0.43
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGAACTTATTTCTAAAACATCAATTTTCTCACAATC
Found at i:161278 original size:79 final size:79
Alignment explanation
Indices: 161063--161279 Score: 254
Period size: 79 Copynumber: 2.7 Consensus size: 79
161053 CACAATTGGG
* ** * * * * * * *
161063 GATACTCCAACCCCAACCTTATTTCTAAAGCATCAATTTTTTCACAATCGGGGATACTCCAATCC
1 GATACTCCAACCCCGATTTTATTTCCAAAACACCGA-TTTTCCATAATCGGGGATACTCCAACCC
*
161128 TGTTATTTTCGAGGA
65 TGTTATTTTCAAGGA
* * * ** *
161143 GATACTCCAACCCCGATTTTATTTTCAAAATACCGATTTTCTATAATCAAGAATACTCCAACCCT
1 GATACTCCAACCCCGATTTTATTTCCAAAACACCGATTTTCCATAATCGGGGATACTCCAACCCT
*
161208 GTTATTTTCAAGGG
66 GTTATTTTCAAGGA
*
161222 GATACTCCAACCCCGATTTTATTTCCAGAACACCGATTTTCCATAATCGGGGATACTC
1 GATACTCCAACCCCGATTTTATTTCCAAAACACCGATTTTCCATAATCGGGGATACTC
161280 TAGCCCCGTT
Statistics
Matches: 112, Mismatches: 25, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
79 85 0.76
80 27 0.24
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (79 bp):
GATACTCCAACCCCGATTTTATTTCCAAAACACCGATTTTCCATAATCGGGGATACTCCAACCCT
GTTATTTTCAAGGA
Found at i:164880 original size:11 final size:11
Alignment explanation
Indices: 164864--164923 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
164854 ACTAAACTTT
164864 ATAGGTCTATG
1 ATAGGTCTATG
164875 ATAGGT-TCATTG
1 ATAGGTCT-A-TG
* * *
164887 TTA-CTCAATG
1 ATAGGTCTATG
164897 ATAGGTCTATG
1 ATAGGTCTATG
*
164908 ATAGGTTTATG
1 ATAGGTCTATG
164919 ATAGG
1 ATAGG
164924 ATGGGATCTT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
10 5 0.13
11 29 0.76
12 4 0.11
ACGTcount: A:0.28, C:0.08, G:0.25, T:0.38
Consensus pattern (11 bp):
ATAGGTCTATG
Found at i:165072 original size:207 final size:207
Alignment explanation
Indices: 164717--165095 Score: 731
Period size: 207 Copynumber: 1.8 Consensus size: 207
164707 CAAACAAAGC
164717 ATGGGATCTTCATCAATCAAGCCAAATATACAAAAAAGCTACTCAAAAGGTTTCAAATGGATCAA
1 ATGGGATCTTCATCAATCAAGCCAAATATACAAAAAAGCTACTCAAAAGGTTTCAAATGGATCAA
164782 GTCCAACCGTGTGAAACACCGATGAGTACTACAACAAAGCTTGAAAAGGATGAAGGAGGTAATTT
66 GTCCAACCGTGTGAAACACCGATGAGTACTACAACAAAGCTTGAAAAGGATGAAGGAGGTAATTT
*
164847 TATTGATACTAAACTTTATAGGTCTATGATAGGTTCATTGTTACTCAATGATAGGTCTATGATAG
131 TATCGATACTAAACTTTATAGGTCTATGATAGGTTCATTGTTACTCAATGATAGGTCTATGATAG
164912 GTTTATGATAGG
196 GTTTATGATAGG
164924 ATGGGATCTTCATCAATCAAGCCAAATATACAAAAAAGCTACTCAAAAGGTTTCAAATGGATCAA
1 ATGGGATCTTCATCAATCAAGCCAAATATACAAAAAAGCTACTCAAAAGGTTTCAAATGGATCAA
**
164989 GTCCAACCGTGTGAAACACCGATGAGTACTACATTAAAGCTTGAAAAGGATGAAGGAGGTAATTT
66 GTCCAACCGTGTGAAACACCGATGAGTACTACAACAAAGCTTGAAAAGGATGAAGGAGGTAATTT
165054 TATCGATACTAAACTTTATAGGTCTATGATAGGTTCATTGTT
131 TATCGATACTAAACTTTATAGGTCTATGATAGGTTCATTGTT
165096 GTATCTTACC
Statistics
Matches: 169, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
207 169 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.28
Consensus pattern (207 bp):
ATGGGATCTTCATCAATCAAGCCAAATATACAAAAAAGCTACTCAAAAGGTTTCAAATGGATCAA
GTCCAACCGTGTGAAACACCGATGAGTACTACAACAAAGCTTGAAAAGGATGAAGGAGGTAATTT
TATCGATACTAAACTTTATAGGTCTATGATAGGTTCATTGTTACTCAATGATAGGTCTATGATAG
GTTTATGATAGG
Found at i:167163 original size:34 final size:35
Alignment explanation
Indices: 167125--167191 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
167115 CCTTACAACA
167125 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
167159 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
167192 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:167682 original size:19 final size:20
Alignment explanation
Indices: 167642--167682 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
167632 TGAACAGTGA
**
167642 TGTATCGATACTATTTATAG
1 TGTATCGATACTATGAATAG
167662 TGTATCGATAC-ATGAATAG
1 TGTATCGATACTATGAATAG
167681 TG
1 TG
167683 ATGAACAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.39
Consensus pattern (20 bp):
TGTATCGATACTATGAATAG
Found at i:170932 original size:15 final size:15
Alignment explanation
Indices: 170912--170949 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
170902 AAGAATATTT
*
170912 ATTTATTTTTAATTA
1 ATTTATTTGTAATTA
*
170927 ATTTATTTGTATTTA
1 ATTTATTTGTAATTA
170942 ATTTATTT
1 ATTTATTT
170950 AATTTTGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
ATTTATTTGTAATTA
Found at i:170932 original size:19 final size:19
Alignment explanation
Indices: 170908--170950 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
170898 TGATAAGAAT
*
170908 ATTTATTTATTTTTAATTA
1 ATTTATTTATATTTAATTA
* *
170927 ATTTATTTGTATTTAATTT
1 ATTTATTTATATTTAATTA
170946 ATTTA
1 ATTTA
170951 ATTTTGCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTATTTATATTTAATTA
Found at i:174116 original size:93 final size:93
Alignment explanation
Indices: 174002--174182 Score: 290
Period size: 93 Copynumber: 1.9 Consensus size: 93
173992 AATTCCCTGC
* * **
174002 ATGTATCGATATATTTGGGTTAAAAACCCAGAATATATCGATAAAATGAGAAATGTATTGATACA
1 ATGTATCAATATATTTAGGTTAAAAACCCAGAATATATCGATAAAATGAGAAATGTATCAATACA
174067 TTACAAACATATATTGATACATTGAAGA
66 TTACAAACATATATTGATACATTGAAGA
*
174095 ATGTATCAATATATTTAGGTTAAAAACCCAGAATATATCGATATAATGAGAAATGTATCAATACA
1 ATGTATCAATATATTTAGGTTAAAAACCCAGAATATATCGATAAAATGAGAAATGTATCAATACA
* * *
174160 TTGCAAGCATGTATTGATACATT
66 TTACAAACATATATTGATACATT
174183 CACTTACGTA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 80 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.32
Consensus pattern (93 bp):
ATGTATCAATATATTTAGGTTAAAAACCCAGAATATATCGATAAAATGAGAAATGTATCAATACA
TTACAAACATATATTGATACATTGAAGA
Found at i:174268 original size:20 final size:20
Alignment explanation
Indices: 174243--174312 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
174233 ATGGTCCAAG
*
174243 ATTGATGCATTCACTTATGT
1 ATTGATACATTCACTTATGT
174263 ATTGATACATTCACTTATGT
1 ATTGATACATTCACTTATGT
* * *
174283 ATCGATACATTAACTTGTTGT
1 ATTGATACATTCACTT-ATGT
*
174304 ATCGATACA
1 ATTGATACA
174313 AATTGTAGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 33 0.73
21 12 0.27
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (20 bp):
ATTGATACATTCACTTATGT
Found at i:177248 original size:13 final size:13
Alignment explanation
Indices: 177208--177259 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
177198 CCGTTTGAAG
177208 CAATGTATCGATA
1 CAATGTATCGATA
177221 CAA--T-TC-AT-
1 CAATGTATCGATA
177229 C-ATGTATCGATA
1 CAATGTATCGATA
*
177241 CAATGTATCAATA
1 CAATGTATCGATA
177254 CAATGT
1 CAATGT
177260 GCCATGTATC
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 19 0.59
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:177255 original size:33 final size:33
Alignment explanation
Indices: 177208--177276 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
177198 CCGTTTGAAG
*
177208 CAATGTATCGATACAAT-T-CATCATGTATCGATA
1 CAATGTATCAATACAATGTGC--CATGTATCGATA
177241 CAATGTATCAATACAATGTGCCATGTATCGATA
1 CAATGTATCAATACAATGTGCCATGTATCGATA
177274 CAA
1 CAA
177277 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
33 31 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (33 bp):
CAATGTATCAATACAATGTGCCATGTATCGATA
Found at i:179888 original size:13 final size:13
Alignment explanation
Indices: 179869--179908 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
179859 ATAGTAACCC
*
179869 ATGTATCGATATA
1 ATGTATCGATACA
* *
179882 TTGTATCGATGCA
1 ATGTATCGATACA
179895 ATGTATCGATACA
1 ATGTATCGATACA
179908 A
1 A
179909 AAAATATTGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:186200 original size:20 final size:19
Alignment explanation
Indices: 186175--186228 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
186165 CTGCCATTTT
* **
186175 CATGTATCGATATAATTGTC
1 CATGTATCGATACAA-TGAA
*
186195 CATGTATCAATACAATGAA
1 CATGTATCGATACAATGAA
186214 CATGTATCGATACAA
1 CATGTATCGATACAA
186229 AGCATAATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:193851 original size:52 final size:52
Alignment explanation
Indices: 193766--193890 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
193756 ATATGAAAAG
* *
193766 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
193818 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
193870 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
193891 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:193903 original size:52 final size:51
Alignment explanation
Indices: 193766--193910 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 51
193756 ATATGAAAAG
*
193766 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
193818 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
193870 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
193911 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:193917 original size:13 final size:13
Alignment explanation
Indices: 193899--193923 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
193889 CAAAGATCAG
193899 TGTATCGATACAA
1 TGTATCGATACAA
193912 TGTATCGATACA
1 TGTATCGATACA
193924 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:194007 original size:33 final size:33
Alignment explanation
Indices: 193965--194034 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
193955 GGCAGTAGCT
193965 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
193998 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
194031 TACA
1 TACA
194035 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:194008 original size:13 final size:13
Alignment explanation
Indices: 193990--194014 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
193980 CAAAAAAATA
193990 TGTATCGATACAT
1 TGTATCGATACAT
194003 TGTATCGATACA
1 TGTATCGATACA
194015 ACATTTTATG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:197155 original size:33 final size:33
Alignment explanation
Indices: 197111--197176 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
197101 GCCAAGGAAA
*
197111 TGTATCCATACATT-ATTCAATGTATCGATACAT
1 TGTATCAATACATTGA-TCAATGTATCGATACAT
**
197144 TGTATCAATACATTGATCTTTGTATCGATACAT
1 TGTATCAATACATTGATCAATGTATCGATACAT
197177 CTGGGAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.41
Consensus pattern (33 bp):
TGTATCAATACATTGATCAATGTATCGATACAT
Found at i:197711 original size:12 final size:12
Alignment explanation
Indices: 197694--197719 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
197684 GACCCAGGCT
197694 AACCCAAATGCC
1 AACCCAAATGCC
197706 AACCCAAATGCC
1 AACCCAAATGCC
197718 AA
1 AA
197720 TAATGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.38, G:0.08, T:0.08
Consensus pattern (12 bp):
AACCCAAATGCC
Found at i:200035 original size:8 final size:8
Alignment explanation
Indices: 200022--200051 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
200012 TTGTGTTGTA
200022 ATCATAAC
1 ATCATAAC
200030 ATCATAAC
1 ATCATAAC
200038 ATCAATAAC
1 ATC-ATAAC
200047 ATCAT
1 ATCAT
200052 TATTTGCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (8 bp):
ATCATAAC
Found at i:200257 original size:31 final size:31
Alignment explanation
Indices: 200154--200322 Score: 159
Period size: 30 Copynumber: 5.4 Consensus size: 31
200144 CAATCTCTTT
* *
200154 TTTCTAAGTCCACGACTCAGTGGAATCCTTTTC
1 TTTCAAAGTCCACGACTCAGTGGCAT--TTTTC
* * *
200187 -TTCCAAGTCCATGACTCAGTGGCA--TCTC
1 TTTCAAAGTCCACGACTCAGTGGCATTTTTC
*
200215 TTCCCAAAGTCCACGACTCAGTGGCATTTTTC
1 TT-TCAAAGTCCACGACTCAGTGGCATTTTTC
*
200247 TTTCAAAGTCCACGACTCAGTGGCATTTCT-
1 TTTCAAAGTCCACGACTCAGTGGCATTTTTC
* *
200277 TTTCTAAGTCCACGACT-ATATGGCACCTTTTTC
1 TTTCAAAGTCCACGACTCA-GTGGCA--TTTTTC
200310 TTTTCAAAGTCCA
1 -TTTCAAAGTCCA
200323 TAACTTTGTG
Statistics
Matches: 113, Mismatches: 14, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
28 3 0.03
29 2 0.02
30 41 0.36
31 26 0.23
32 30 0.27
34 11 0.10
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.34
Consensus pattern (31 bp):
TTTCAAAGTCCACGACTCAGTGGCATTTTTC
Found at i:200270 original size:61 final size:61
Alignment explanation
Indices: 200159--200322 Score: 188
Period size: 61 Copynumber: 2.6 Consensus size: 61
200149 TCTTTTTTCT
* * *
200159 AAGTCCACGACTCAGTGGAATCCTTTTC-TTCCAAGTCCATGACTCAGTGGCATCTCTTCCCA
1 AAGTCCACGACTCAGTGGCAT--TTTTCTTTCAAAGTCCACGACTCAGTGGCATCTCTTCCCA
* ** *
200221 AAGTCCACGACTCAGTGGCATTTTTCTTTCAAAGTCCACGACTCAGTGGCATTTCTTTTCT
1 AAGTCCACGACTCAGTGGCATTTTTCTTTCAAAGTCCACGACTCAGTGGCATCTCTTCCCA
*
200282 AAGTCCACGACT-ATATGGCACCTTTTTCTTTTCAAAGTCCA
1 AAGTCCACGACTCA-GTGGCA--TTTTTC-TTTCAAAGTCCA
200323 TAACTTTGTG
Statistics
Matches: 89, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
60 6 0.07
61 45 0.51
62 20 0.22
63 6 0.07
64 12 0.13
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.33
Consensus pattern (61 bp):
AAGTCCACGACTCAGTGGCATTTTTCTTTCAAAGTCCACGACTCAGTGGCATCTCTTCCCA
Found at i:200335 original size:34 final size:34
Alignment explanation
Indices: 200219--200881 Score: 288
Period size: 34 Copynumber: 20.7 Consensus size: 34
200209 CATCTCTTCC
* *
200219 CAAAGTCCACGACTCAGTGGCA--TTTTTC-TTT
1 CAAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
* *
200250 CAAAGTCCACGACTCAGTGGCA----TTTCTTTT
1 CAAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
* * * *
200280 CTAAGTCCACGACTATATGGCACCTTTTTCTTTT
1 CAAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
* * *
200314 CAAAGTCCATAACTTTGTGGCA-----TCCTTTT
1 CAAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
* ** *
200343 --ATGTCCACAACTCCATGGCACCTTGTTCCTTTT
1 CAAAGTCCACAACTCTGTGGCACCTT-TTTCTTTT
*
200376 -AAAGTCCACAACTCCGTGGCACTCTTTTTCTTTT
1 CAAAGTCCACAACTCTGTGGCAC-CTTTTTCTTTT
200410 CAAAGTCCACAACTCTGTGGCACC-----CTTTT
1 CAAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
* *
200439 --AAGCCCACAACTCTGTGGCACTCTTCTTCCTTTT
1 CAAAGTCCACAACTCTGTGGCAC-CTT-TTTCTTTT
* *
200473 --AAGTCCACAACTCCGTGGCACCTTGTTCCTTTT
1 CAAAGTCCACAACTCTGTGGCACCTT-TTTCTTTT
* *
200506 --AAGCCCACAACTCTGTGGCACTTTTTTTCCTTTT
1 CAAAGTCCACAACTCTGTGGCAC-CTTTTT-CTTTT
* * **
200540 --AAGCCCATAACTCCATGGCACTCTTTTTCCTTTT
1 CAAAGTCCACAACTCTGTGGCAC-CTTTTT-CTTTT
*
200574 --AAGTCCACAACTCCGTGGCACTCTTTTTTCCTTTT
1 CAAAGTCCACAACTCTGTGGCAC-C-TTTTT-CTTTT
*
200609 --AAGCCCACAACT-TCGTGGCACTCTTTTTCCTTTT
1 CAAAGTCCACAACTCT-GTGGCAC-CTTTTT-CTTTT
*
200643 --AAGCCCACAACTCTGTGGCACC-----C-TTT
1 CAAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
200669 -AAAG-CTCACAACTCTGTGGCACTCTTTTTCCTTTT
1 CAAAGTC-CACAACTCTGTGGCAC-CTTTTT-CTTTT
*
200704 --AAGTCCACAACTCTATGGCACC-----CTTTT
1 CAAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
* * *
200731 --AAGCCCACAACTAC-ATGGTACTCTTTTTCCTTTT
1 CAAAGTCCACAACT-CTGTGGCAC-CTTTTT-CTTTT
200765 --AAGTCCACAACTCTGTGGCACC-----CTTTT
1 CAAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
* *
200792 --AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
1 CAAAGTCCACAACTCTGTGGCAC-CTTTTT-CTTTT
* *
200826 --AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
1 CAAAGTCCACAACTCTGTGGCAC-CTTTTT-CTTTT
* *
200860 --AATTCCACAACTCCGTGGCACC
1 CAAAGTCCACAACTCTGTGGCACC
200882 CACAACTTCG
Statistics
Matches: 533, Mismatches: 46, Indels: 104
0.78 0.07 0.15
Matches are distributed among these distances:
26 4 0.01
27 101 0.19
28 5 0.01
29 15 0.03
30 21 0.04
31 22 0.04
33 44 0.08
34 261 0.49
35 60 0.11
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.35
Consensus pattern (34 bp):
CAAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
Found at i:200395 original size:61 final size:62
Alignment explanation
Indices: 200252--200845 Score: 453
Period size: 61 Copynumber: 9.3 Consensus size: 62
200242 TTTTCTTTCA
* * * * * ***
200252 AAGTCCACGACTCAGTGGCATTTCTTTTCTAAGTCCACGACTATATGGCAC-CTTTTT-CTTTT
1 AAGTCCACAACTCTGTGGCA-TTCCTTT-TAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * * * * *
200314 CAAAGTCCATAACTTTGTGGCA-TCCTTTTATGTCCACAACTCCATGGCAC-CTTGTTCCTTTT
1 --AAGTCCACAACTCTGTGGCATTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * * *
200376 AAAGTCCACAACTCCGTGGCACTCTTTTTCTTTTCAAAGTCCACAACTCTGTGGCA--C-----C
1 -AAGTCCACAACTCTGTGGCA-----TTCCTTTT--AAGCCCACAACTCCGTGGCACTCTTTTTC
200434 CTTTT
58 CTTTT
* * *
200439 AAGCCCACAACTCTGTGGCACTCTTCTTCCTTTTAAGTCCACAACTCCGTGGCAC-CTTGTTCCT
1 AAGTCCACAACTCTGTGGCA------TTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCT
200503 TTT
60 TTT
* * *
200506 AAGCCCACAACTCTGTGGCACTTTTTTTCCTTTTAAGCCCATAACTCCATGGCACTCTTTTTCCT
1 AAGTCCACAACTCTGTGGCA------TTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCT
200571 TTT
60 TTT
* *
200574 AAGTCCACAACTCCGTGGCACTCTTTTTTCCTTTTAAGCCCACAACTTCGTGGCACTCTTTTTCC
1 AAGTCCACAACTCTGTGGCA-------TTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCC
200639 TTTT
59 TTTT
* * * * *
200643 AAGCCCACAACTCTGTGGCA-CCCTTTAAAGCTCACAACTCTGTGGCACTCTTTTTCCTTTT
1 AAGTCCACAACTCTGTGGCATTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * * * *
200704 AAGTCCACAACTCTATGGCA-CCCTTTTAAGCCCACAACTACATGGTACTCTTTTTCCTTTT
1 AAGTCCACAACTCTGTGGCATTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
*
200765 AAGTCCACAACTCTGTGGCA-CCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
1 AAGTCCACAACTCTGTGGCATTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
* *
200826 AAGCCCACAACTCCGTGGCA
1 AAGTCCACAACTCTGTGGCA
200846 CTCTTTTTCC
Statistics
Matches: 453, Mismatches: 59, Indels: 39
0.82 0.11 0.07
Matches are distributed among these distances:
61 224 0.49
62 29 0.06
63 14 0.03
64 16 0.04
67 62 0.14
68 30 0.07
69 78 0.17
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.35
Consensus pattern (62 bp):
AAGTCCACAACTCTGTGGCATTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
Found at i:200417 original size:96 final size:94
Alignment explanation
Indices: 200297--201056 Score: 550
Period size: 95 Copynumber: 8.1 Consensus size: 94
200287 CACGACTATA
* * * *
200297 TGGCAC-CTTTTTCTTTTCAAAGTCCATAACTTTGTGGCATCCTTTTATGTCCACAACTCCATGG
1 TGGCACTCTTTTTCTTTT--AAGTCCACAACTCTGTGGCATCCTTTTAAGCCCACAACTCCATGG
*
200361 CAC-CTTGTTCCTTTTAAAGTCCACAACTCCG
64 CACTCTTTTTCCTTTT-AAGTCCACAACTCCG
* **
200392 TGGCACTCTTTTTCTTTTCAAAGTCCACAACTCTGTGGCACCCTTTTAAGCCCACAACTCTGTGG
1 TGGCACTCTTTTTCTTTT--AAGTCCACAACTCTGTGGCATCCTTTTAAGCCCACAACTCCATGG
*
200457 CACTCTTCTTCCTTTTAAGTCCACAACTCCG
64 CACTCTTTTTCCTTTTAAGTCCACAACTCCG
* * *
200488 TGGCAC-CTTGTTCCTTTTAAGCCCACAACTCTGTGGCACTTTTTTTCCTTTTAAGCCCATAACT
1 TGGCACTCTT-TTTCTTTTAAGTCCACAACTCTGTGGCA-------TCCTTTTAAGCCCACAACT
200552 CCATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCG
58 CCATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCG
*
200589 TGGCACTCTTTTTTCCTTTTAAGCCCACAACT-TCGTGGCACTCTTTTTCCTTTTAAGCCCACAA
1 TGGCACTC-TTTTT-CTTTTAAGTCCACAACTCT-GTGGCA-------TCCTTTTAAGCCCACAA
** * *
200653 CTCTGTGGCA--C-----CCTTTAAAG-CTCACAACTCTG
56 CTCCATGGCACTCTTTTTCCTTTTAAGTC-CACAACTCCG
* * * *
200685 TGGCACTCTTTTTCCTTTTAAGTCCACAACTCTATGGCACCCTTTTAAGCCCACAACTACATGGT
1 TGGCACTCTTTTT-CTTTTAAGTCCACAACTCTGTGGCATCCTTTTAAGCCCACAACTCCATGGC
*
200750 ACTCTTTTTCCTTTTAAGTCCACAACTCTG
65 ACTCTTTTTCCTTTTAAGTCCACAACTCCG
* *
200780 TGGCAC-C-----CTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTC
1 TGGCACTCTTTTTCTTTTAAGTCCACAACTCTGTGGCA-------TCCTTTTAAGCCCACAACTC
* *
200839 CGTGGCACTCTTTTTCCTTTTAATTCCACAACTCCG
59 CATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCG
***** * ** ** **
200875 TGGCAC-CCACAAC--TT-CGT-GGC-ACTCT-T--TTTCCTTTTAAGCCCACAACTCTGTGGCA
1 TGGCACTCTTTTTCTTTTAAGTCCACAACTCTGTGGCATCCTTTTAAGCCCACAACTCCATGGCA
*
200931 CTCTTTTTCCTTTTAAGCCCACAACTCCG
66 CTCTTTTTCCTTTTAAGTCCACAACTCCG
* * * *
200960 TGGCACTCTTTTTCCTTTTAATTCCACAACTCCGTGG----C-----A-CCCACAACTTCGTGGC
1 TGGCACTCTTTTT-CTTTTAAGTCCACAACTCTGTGGCATCCTTTTAAGCCCACAACTCCATGGC
*
201015 ACTCTTTTTCCTTTTAAGTCCACAACTCTG
65 ACTCTTTTTCCTTTTAAGTCCACAACTCCG
* *
201045 TGGGACCCTTTT
1 TGGCACTCTTTT
201057 AAGCCCACAA
Statistics
Matches: 554, Mismatches: 65, Indels: 102
0.77 0.09 0.14
Matches are distributed among these distances:
85 111 0.20
86 2 0.00
87 1 0.00
88 44 0.08
89 2 0.00
90 2 0.00
91 2 0.00
92 4 0.01
93 1 0.00
94 21 0.04
95 122 0.22
96 110 0.20
97 12 0.02
98 2 0.00
100 1 0.00
101 58 0.10
102 4 0.01
103 55 0.10
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.36
Consensus pattern (94 bp):
TGGCACTCTTTTTCTTTTAAGTCCACAACTCTGTGGCATCCTTTTAAGCCCACAACTCCATGGCA
CTCTTTTTCCTTTTAAGTCCACAACTCCG
Found at i:200668 original size:27 final size:27
Alignment explanation
Indices: 200637--200818 Score: 141
Period size: 27 Copynumber: 6.2 Consensus size: 27
200627 CACTCTTTTT
200637 CCTTTTAAGCCCACAACTCTGTGGCAC
1 CCTTTTAAGCCCACAACTCTGTGGCAC
* *
200664 CCTTTAAAGCTCACAACTCTGTGGCACTC
1 CCTTTTAAGCCCACAACTCTGTGGCA--C
* *
200693 TTTTTCCTTTTAAGTCCACAACTCTATGGCAC
1 -----CCTTTTAAGCCCACAACTCTGTGGCAC
* *
200725 CCTTTTAAGCCCACAACTACATG-GTACTC
1 CCTTTTAAGCCCACAACT-C-TGTG-GCAC
*
200754 TTTTTCCTTTTAAGTCCACAACTCTGTGGCAC
1 -----CCTTTTAAGCCCACAACTCTGTGGCAC
*
200786 CCTTTTAAGCCCACAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCTGTGGCAC
*
200813 TCTTTT
1 CCTTTT
200819 TCCTTTTAAG
Statistics
Matches: 123, Mismatches: 16, Indels: 32
0.72 0.09 0.19
Matches are distributed among these distances:
27 71 0.58
28 2 0.02
29 4 0.03
32 5 0.04
33 2 0.02
34 39 0.32
ACGTcount: A:0.22, C:0.33, G:0.12, T:0.33
Consensus pattern (27 bp):
CCTTTTAAGCCCACAACTCTGTGGCAC
Found at i:200886 original size:17 final size:17
Alignment explanation
Indices: 200864--200897 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
200854 CCTTTTAATT
200864 CCACAACTCCGTGGCAC
1 CCACAACTCCGTGGCAC
*
200881 CCACAACTTCGTGGCAC
1 CCACAACTCCGTGGCAC
200898 TCTTTTTCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.44, G:0.18, T:0.15
Consensus pattern (17 bp):
CCACAACTCCGTGGCAC
Found at i:200896 original size:85 final size:85
Alignment explanation
Indices: 200795--201286 Score: 329
Period size: 85 Copynumber: 5.5 Consensus size: 85
200785 CCCTTTTAAG
200795 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
**
200860 AATTCCACAACTCCGTGGCA
66 AAGCCCACAACTCCGTGGCA
* *
200880 CCCACAACTTCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTT
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
200945 AAGCCCACAACTCCGTGGCA
66 AAGCCCACAACTCCGTGGCA
* **** * *** * **** * *** *
200965 CTC-TTTTTCCTTTTAATTCCACAACTCCGTGGCA-CCCACAACTTCGTGGCACTCTTTTTCCTT
1 CCCACAACTCCGTGGCACT-C-TTTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTT
* *
201028 TTAAGTCCACAACTCTGTGGGACCCTTTTAA
64 TTAAGCCCACAACTCCGT-GG---C-----A
* *
201059 GCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCA--C-----CCTTT
1 -CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTT
* *
201117 TAAGTCCACAACTCCATGGCACCCTTTTAA
65 TAAGCCCACAACTCCGTGG----C-----A
*
201147 GCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAG-CCATAACTCCGTGGCACTCTTTTTCCTTT
1 -CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTT
* *
201211 TAAGTCCACAACTCTGTGGCACCCTTTTAA
65 TAAGCCCACAACTCCGTGG----C-----A
*
201241 GCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCC
1 -CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCC
201287 ATGGTACCCT
Statistics
Matches: 329, Mismatches: 55, Indels: 36
0.78 0.13 0.09
Matches are distributed among these distances:
84 5 0.02
85 127 0.39
86 7 0.02
87 16 0.05
88 65 0.20
89 2 0.01
93 1 0.00
94 74 0.22
95 26 0.08
96 6 0.02
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.34
Consensus pattern (85 bp):
CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
AAGCCCACAACTCCGTGGCA
Found at i:200905 original size:51 final size:51
Alignment explanation
Indices: 200829--200931 Score: 170
Period size: 51 Copynumber: 2.0 Consensus size: 51
200819 TCCTTTTAAG
**
200829 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAATTCCACAACTCCGTGGCA
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCA
* *
200880 CCCACAACTTCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCTGTGGCA
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCA
200931 C
1 C
200932 TCTTTTTCCT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.19, C:0.37, G:0.13, T:0.31
Consensus pattern (51 bp):
CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCA
Found at i:200929 original size:34 final size:34
Alignment explanation
Indices: 200880--201454 Score: 345
Period size: 34 Copynumber: 17.7 Consensus size: 34
200870 CTCCGTGGCA
*
200880 CCCACAACTTCGTGGCACTCTTTTTCCTTTTAAG
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAG
*
200914 CCCACAACTCTGTGGCACTCTTTTTCCTTTTAAG
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAG
*
200948 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAT
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAG
* * ** **
200982 TCCACAACTCCGTGGCACCCACAACTTCGTGGCACTCTTT-TT
1 CCCACAACTCCGTGG----CAC-TCTT--TTTC-CT-TTTAAG
*** * * ***
201024 CCTTTTAAGTCC---ACAACTCTGTGGGACCCTTTTAAG
1 CC-CACAACTCCGTGGC-ACTCT-T--TTTCCTTTTAAG
201060 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAG
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAG
* *
201094 TCCACAACTCTGTGGCA--C-----CCTTTTAAG
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAG
* *
201121 TCCACAACTCCATGGCA--C-----CCTTTTAAG
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAG
201148 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAG
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAG
*
201182 -CCATAACTCCGTGGCACTCTTTTTCCTTTTAAG
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAG
* *
201215 TCCACAACTCTGTGGCA--C-----CCTTTTAAG
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAG
201242 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAG
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAG
* * *
201276 TCCACAACTCCATGGTA--C-----CCTTTTAAG
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAG
* * * * *
201303 TCCACAATTTCGTGGTACT-TTTTTCTTTTTGAAG
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTT-AAG
201337 CCCACAACTCCGTGGCACTCTTTTTTCCTTTTAAG
1 CCCACAACTCCGTGGCACTC-TTTTTCCTTTTAAG
* *
201372 TCCACAACTCTGTGGCA--C-----CCTTTTAAG
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAG
* * *
201399 TCCATAACTCCGTGGCA-TCTTTCTCCTTTTAAG
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAG
* * *
201432 CCCA-AAGTCAGTGGCACCCTTTT
1 CCCACAACTCCGTGGCACTCTTTT
201455 CAAAAGTCCA
Statistics
Matches: 431, Mismatches: 62, Indels: 97
0.73 0.11 0.16
Matches are distributed among these distances:
27 120 0.28
28 1 0.00
29 2 0.00
32 13 0.03
33 54 0.13
34 166 0.39
35 26 0.06
36 18 0.04
37 10 0.02
38 4 0.01
39 3 0.01
41 2 0.00
42 4 0.01
43 8 0.02
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.35
Consensus pattern (34 bp):
CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAG
Found at i:200950 original size:119 final size:119
Alignment explanation
Indices: 200786--201234 Score: 605
Period size: 119 Copynumber: 3.8 Consensus size: 119
200776 TCTGTGGCAC
200786 CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTT
1 CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTT
*
200851 TTTCCTTTTAATTCCACAACTCCGTGGCACCCACAACTTCGTGGCACTCTTTTT
66 TTTCCTTTTAAGTCCACAACTCCGTGGCACCCACAACTTCGTGGCACTCTTTTT
*
200905 CCTTTTAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTT
1 CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTT
*
200970 TTTCCTTTTAATTCCACAACTCCGTGGCACCCACAACTTCGTGGCACTCTTTTT
66 TTTCCTTTTAAGTCCACAACTCCGTGGCACCCACAACTTCGTGGCACTCTTTTT
* * *
201024 CCTTTTAAGTCCACAACTCTGTGGGA--C-----CCTTTTAAGCCCACAACTCCGTGGCACTCTT
1 CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTT
* ** * ** ****
201082 TTTCCTTTTAAGTCCACAACTCTGTGGCA-CC-C-TTTTAAGTCCACAACTCCATGGCAC
66 TTTCCTTTTAAGTCCACAACTCCGTGGCACCCACAACTT-CGT-GGC-ACT-C-T-TTTT
*
201139 CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAG-CCATAACTCCGTGGCACTCTT
1 CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTT
*
201203 TTTCCTTTTAAGTCCACAACTCTGTGGCACCC
66 TTTCCTTTTAAGTCCACAACTCCGTGGCACCC
201235 TTTTAAGCCC
Statistics
Matches: 298, Mismatches: 18, Indels: 25
0.87 0.05 0.07
Matches are distributed among these distances:
109 2 0.01
110 3 0.01
111 3 0.01
112 61 0.20
113 1 0.00
114 1 0.00
115 23 0.08
117 2 0.01
119 142 0.48
121 49 0.16
122 11 0.04
ACGTcount: A:0.19, C:0.35, G:0.12, T:0.34
Consensus pattern (119 bp):
CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTT
TTTCCTTTTAAGTCCACAACTCCGTGGCACCCACAACTTCGTGGCACTCTTTTT
Found at i:201005 original size:17 final size:17
Alignment explanation
Indices: 200983--201016 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
200973 CCTTTTAATT
200983 CCACAACTCCGTGGCAC
1 CCACAACTCCGTGGCAC
*
201000 CCACAACTTCGTGGCAC
1 CCACAACTCCGTGGCAC
201017 TCTTTTTCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.44, G:0.18, T:0.15
Consensus pattern (17 bp):
CCACAACTCCGTGGCAC
Found at i:201024 original size:51 final size:51
Alignment explanation
Indices: 200948--201113 Score: 215
Period size: 51 Copynumber: 3.1 Consensus size: 51
200938 TCCTTTTAAG
* *
200948 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAATTCCACAACTCCGTGGCA
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCA
*
200999 CCCACAACTTCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGGACCCTTTTAA
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGT-GG---C-----A
201059 GCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCA
1 -CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCA
201111 CCC
1 CCC
201114 TTTTAAGTCC
Statistics
Matches: 101, Mismatches: 4, Indels: 20
0.81 0.03 0.16
Matches are distributed among these distances:
51 47 0.47
52 3 0.03
55 1 0.01
57 1 0.01
60 3 0.03
61 46 0.46
ACGTcount: A:0.19, C:0.36, G:0.13, T:0.32
Consensus pattern (51 bp):
CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCA
Found at i:201055 original size:27 final size:27
Alignment explanation
Indices: 201024--201415 Score: 228
Period size: 27 Copynumber: 13.0 Consensus size: 27
201014 CACTCTTTTT
* *
201024 CCTTTTAAGTCCACAACTCTGTGGGAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
201051 CCTTTTAAGCCCACAACTCCGTGGCACTC
1 CCTTTTAAGTCCACAACTCCGTGGCA--C
*
201080 TTTTTCCTTTTAAGTCCACAACTCTGTGGCAC
1 -----CCTTTTAAGTCCACAACTCCGTGGCAC
*
201112 CCTTTTAAGTCCACAACTCCATGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
201139 CCTTTTAAGCCCACAACTCCGTGGCACTC
1 CCTTTTAAGTCCACAACTCCGTGGCA--C
*
201168 TTTTTCCTTTTAAG-CCATAACTCCGTGGCACTC
1 -----CCTTTTAAGTCCACAACTCCGTGGCA--C
*
201201 TTTTTCCTTTTAAGTCCACAACTCTGTGGCAC
1 -----CCTTTTAAGTCCACAACTCCGTGGCAC
*
201233 CCTTTTAAGCCCACAACTCCGTGGCACTC
1 CCTTTTAAGTCCACAACTCCGTGGCA--C
* *
201262 TTTTTCCTTTTAAGTCCACAACTCCATGGTAC
1 -----CCTTTTAAGTCCACAACTCCGTGGCAC
* * *
201294 CCTTTTAAGTCCACAATTTCGTGGTAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
* *
201321 TTTTTTCTTTTTGAAGCCCACAACTCCGTGGCACTC
1 ------CCTTTT-AAGTCCACAACTCCGTGGCA--C
*
201357 TTTTTTCCTTTTAAGTCCACAACTCTGTGGCAC
1 ------CCTTTTAAGTCCACAACTCCGTGGCAC
*
201390 CCTTTTAAGTCCATAACTCCGTGGCA
1 CCTTTTAAGTCCACAACTCCGTGGCA
201416 TCTTTCTCCT
Statistics
Matches: 304, Mismatches: 30, Indels: 62
0.77 0.08 0.16
Matches are distributed among these distances:
27 144 0.47
29 3 0.01
32 3 0.01
33 38 0.12
34 86 0.28
35 18 0.06
36 12 0.04
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.34
Consensus pattern (27 bp):
CCTTTTAAGTCCACAACTCCGTGGCAC
Found at i:201075 original size:61 final size:61
Alignment explanation
Indices: 200999--201360 Score: 427
Period size: 61 Copynumber: 6.0 Consensus size: 61
200989 CTCCGTGGCA
* * *
200999 CCCACAACTTCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGGACCCTTTTAAG
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAG
*
201060 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAG
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAG
* * *
201121 TCCACAACTCCATGGCA--C-----CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA--C-----CCTTTT
201179 AAG
59 AAG
* *
201182 -CCATAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAG
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAG
* *
201242 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCATGGTACCCTTTTAAG
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAG
* * * * * * *
201303 TCCACAATTTCGTGGTACT-TTTTTCTTTTTGAAGCCCACAACTCCGTGGCACTCTTTT
1 CCCACAACTCCGTGGCACTCTTTTTCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT
201361 TTCCTTTTAA
Statistics
Matches: 262, Mismatches: 23, Indels: 32
0.83 0.07 0.10
Matches are distributed among these distances:
54 24 0.09
56 1 0.00
59 1 0.00
60 33 0.13
61 177 0.68
62 1 0.00
65 1 0.00
67 24 0.09
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.35
Consensus pattern (61 bp):
CCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAG
Found at i:201241 original size:182 final size:186
Alignment explanation
Indices: 201000--201395 Score: 602
Period size: 182 Copynumber: 2.1 Consensus size: 186
200990 TCCGTGGCAC
* *
201000 CCACAACTTCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGGACCCTTTTAAGCCCAC
1 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGCCCAC
**
201065 AACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACT
66 AACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCATGGCACCCTTTTAAGTCCACAACT
201130 CCATGGCAC-CCTTTT-AAGCCCACAACTCCGTGGCACTC-TTTTTCCTTTTAAG-
131 CCATGGCACTCCTTTTGAAGCCCACAACTCCGTGGCACTCTTTTTTCCTTTTAAGT
*
201182 CCATAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGCCCAC
1 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGCCCAC
* *
201247 AACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCATGGTACCCTTTTAAGTCCACAATT
66 AACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCATGGCACCCTTTTAAGTCCACAACT
* * * *
201312 TCGTGGTACTTTTTTCTTTTTGAAGCCCACAACTCCGTGGCACTCTTTTTTCCTTTTAAGT
131 CCATGGCAC-----TCCTTTTGAAGCCCACAACTCCGTGGCACTCTTTTTTCCTTTTAAGT
* *
201373 CCACAACTCTGTGGCACCCTTTT
1 CCACAACTCCGTGGCACTCTTTT
201396 AAGTCCATAA
Statistics
Matches: 191, Mismatches: 14, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
182 129 0.68
188 5 0.03
189 23 0.12
190 14 0.07
191 20 0.10
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.35
Consensus pattern (186 bp):
CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGCCCAC
AACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCATGGCACCCTTTTAAGTCCACAACT
CCATGGCACTCCTTTTGAAGCCCACAACTCCGTGGCACTCTTTTTTCCTTTTAAGT
Found at i:201253 original size:94 final size:93
Alignment explanation
Indices: 201000--201395 Score: 474
Period size: 88 Copynumber: 4.2 Consensus size: 93
200990 TCCGTGGCAC
* *
201000 CCACAACTTCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGGACCCTTTTAAGCCCAC
1 CCACAACTCCGTGGCAC-C-TTTTCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGCCCAC
201065 AACTCCGTGGCACTCTTTTTCCTTTTAAGT
64 AACTCCGTGGCACTCTTTTTCCTTTTAAGT
* **
201095 CCACAACTCTGTGGCA-C----CCTTTTAAGTCCACAACTCCATGGCACCCTTTTAAGCCCACAA
1 CCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGCCCACAA
201155 CTCCGTGGCACTCTTTTTCCTTTTAAG-
66 CTCCGTGGCACTCTTTTTCCTTTTAAGT
*
201182 CCATAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGCCCAC
1 CCACAACTCCGTGGCAC-C-TTTTCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGCCCAC
201247 AACTCCGTGGCACTCTTTTTCCTTTTAAGT
64 AACTCCGTGGCACTCTTTTTCCTTTTAAGT
* * * * *
201277 CCACAACTCCATGGTA-C----CCTTTTAAGTCCACAA-TTTCGTGGTACTTTTTTCTTTTTGAA
1 CCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACTCT-GTGGCAC------CCTTTT-AA
201336 GCCCACAACTCCGTGGCACTCTTTTTTCCTTTTAAGT
58 GCCCACAACTCCGTGGCACTC-TTTTTCCTTTTAAGT
*
201373 CCACAACTCTGTGGCACCCTTTT
1 CCACAACTCCGTGGCA-CCTTTT
201396 AAGTCCATAA
Statistics
Matches: 260, Mismatches: 18, Indels: 39
0.82 0.06 0.12
Matches are distributed among these distances:
87 16 0.06
88 89 0.34
89 1 0.00
93 2 0.01
94 73 0.28
95 50 0.19
96 28 0.11
98 1 0.00
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.35
Consensus pattern (93 bp):
CCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGCCCACAA
CTCCGTGGCACTCTTTTTCCTTTTAAGT
Found at i:201377 original size:35 final size:34
Alignment explanation
Indices: 201294--201454 Score: 117
Period size: 27 Copynumber: 5.0 Consensus size: 34
201284 TCCATGGTAC
* * *
201294 CCTTTTAAGTCCACAATTTCGTGGTA-CTTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTTT
* *
201327 CTTTTTGAAGCCCACAACTCCGTGGCACTCTTTTTT
1 CCTTTT-AAGTCCACAACTCCGTGGCAC-CTTTTTT
*
201363 CCTTTTAAGTCCACAACTCTGTGGCA-C------
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTTT
* * *
201390 CCTTTTAAGTCCATAACTCCGTGGCATC-TTTCT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTTT
* * * *
201423 CCTTTTAAGCCCA-AAGTCAGTGGCACCCTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
201455 CAAAAGTCCA
Statistics
Matches: 103, Mismatches: 15, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
27 24 0.23
28 1 0.01
32 11 0.11
33 21 0.20
34 16 0.16
35 18 0.17
36 12 0.12
ACGTcount: A:0.19, C:0.29, G:0.14, T:0.38
Consensus pattern (34 bp):
CCTTTTAAGTCCACAACTCCGTGGCACCTTTTTT
Found at i:201476 original size:62 final size:62
Alignment explanation
Indices: 201329--201478 Score: 171
Period size: 62 Copynumber: 2.4 Consensus size: 62
201319 ACTTTTTTCT
* * * *
201329 TTTTGAAGCCCACAACTCCGTGGCACTCTTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACTCTTTTCTCCTTTTAAGCCCACAACTCAGTGGCACCC
* *
201392 TTTTAAGTCCATAACTCCGTGGCA-TC-TTTCTCCTTTTAAGCCCA-AAGTCAGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACTCTTTTCTCCTTTTAAGCCCACAACTCAGTGGCACCC
* *
201451 TTTTCAAAAGTCCACAAGTCGGTGGCAC
1 TTTT---AAGTCCACAACTCCGTGGCAC
201479 CCCTCTCAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
59 17 0.23
60 16 0.22
61 2 0.03
62 35 0.47
63 4 0.05
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (62 bp):
TTTTAAGTCCACAACTCCGTGGCACTCTTTTCTCCTTTTAAGCCCACAACTCAGTGGCACCC
Found at i:201504 original size:29 final size:30
Alignment explanation
Indices: 201429--201563 Score: 127
Period size: 29 Copynumber: 4.6 Consensus size: 30
201419 TTCTCCTTTT
** *
201429 AAGCCCA-AAGTCAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTTGGTGGCACCCCTTTCAA
* * *
201458 AAGTCCACAAGTCGGTGGCACCCCTCTC-A
1 AAGCCCACAAGTTGGTGGCACCCCTTTCAA
* *
201487 AAGCCCACAAGTTAGTGGCA-ACC-TTCAA
1 AAGCCCACAAGTTGGTGGCACCCCTTTCAA
* *
201515 AAGCACACAAGTTGGT-GCAACCCTTTCAA
1 AAGCCCACAAGTTGGTGGCACCCCTTTCAA
201544 AAGGCCACACAAGTTGGTGG
1 AA-GCC-CACAAGTTGGTGG
201564 TGTCTTCTTC
Statistics
Matches: 86, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
27 5 0.06
28 19 0.22
29 31 0.36
30 19 0.22
31 11 0.13
32 1 0.01
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.19
Consensus pattern (30 bp):
AAGCCCACAAGTTGGTGGCACCCCTTTCAA
Found at i:201524 original size:57 final size:58
Alignment explanation
Indices: 201429--201563 Score: 143
Period size: 59 Copynumber: 2.3 Consensus size: 58
201419 TTCTCCTTTT
* * *
201429 AAGCCCA-AAGTCAGTGGCACCCTTTTCAAAAGTCCACAAGTCGGTGGCACCCCTCTC-A
1 AAGCCCACAAGTTAGTGGCAACC-TTTCAAAAGTCCACAAGTCGGT-GCAACCCTCTCAA
* *
201487 AAGCCCACAAGTTAGTGGCAACC-TTCAAAAG-CACACAAGTTGGTGCAACCCTTTCAA
1 AAGCCCACAAGTTAGTGGCAACCTTTCAAAAGTC-CACAAGTCGGTGCAACCCTCTCAA
*
201544 AAGGCCACACAAGTTGGTGG
1 AA-GCC-CACAAGTTAGTGG
201564 TGTCTTCTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
56 10 0.15
57 21 0.32
58 10 0.15
59 25 0.38
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.19
Consensus pattern (58 bp):
AAGCCCACAAGTTAGTGGCAACCTTTCAAAAGTCCACAAGTCGGTGCAACCCTCTCAA
Found at i:201687 original size:39 final size:39
Alignment explanation
Indices: 201622--202086 Score: 275
Period size: 39 Copynumber: 11.0 Consensus size: 39
201612 ACCTTGTCTC
*
201622 TAAGACCAA-AGTCGCTGGCCTTGAATCAGCACATTGACA
1 TAAGACCAATA-TCGCTGGCCTTGAATCAGCACATTGGCA
* * *
201661 TAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCA
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
* * *
201700 CCTTGTCTCTAAGACCAATGTCGCTAGCCTTGAATCAGCATATTGGCA
1 ---------TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
* * *
201748 TAAGCCCAATATCGCTGGCTTTGAATCAGCATATTGGCA
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
* *
201787 CCTTGTCTTTAAGACTAATGTCGCTGGCCTTGAATCAGCACATTGGCA
1 ---------TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
* * * * * *
201835 TAAGCCCAATATTGCTAGCCCTAAATCAGCATATTGGCA
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
* *
201874 CCTTGTCTTTAAGACCAATATCGCTGACCTTGAATTAGCACATTGGCA
1 ---------TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
* * * * *
201922 CAAGTCCAATATCGTTGACCTTGAATTAGCACATTGGCA
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
* * *
201961 CAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
* ** *
202000 CCTTGTCTTTAAGACTAATGCCACTGGCCTTGAATCAGCACATTGGCA
1 ---------TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
* * *
202048 TAAGCCCAATGTCGCTGGCCTTGACTCAGCACATTGGCA
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
202087 CTTTATCCAT
Statistics
Matches: 339, Mismatches: 50, Indels: 74
0.73 0.11 0.16
Matches are distributed among these distances:
39 204 0.60
40 1 0.00
48 134 0.40
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (39 bp):
TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
Found at i:201730 original size:87 final size:87
Alignment explanation
Indices: 201574--201961 Score: 553
Period size: 87 Copynumber: 4.5 Consensus size: 87
201564 TGTCTTCTTC
* * * *
201574 TAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAAAGTCGCTG
1 TAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTG
*
201639 GCCTTGAATCAGCACATTGACA
66 GCCTTGAATCAGCACATTGGCA
*
201661 TAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTA
1 TAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTG
*
201726 GCCTTGAATCAGCATATTGGCA
66 GCCTTGAATCAGCACATTGGCA
* * * *
201748 TAAGCCCAATATCGCTGGCTTTGAATCAGCATATTGGCACCTTGTCTTTAAGACTAATGTCGCTG
1 TAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTG
201813 GCCTTGAATCAGCACATTGGCA
66 GCCTTGAATCAGCACATTGGCA
* * * * *
201835 TAAGCCCAATATTGCTAGCCCTAAATCAGCATATTGGCACCTTGTCTTTAAGACCAATATCGCTG
1 TAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTG
* *
201900 ACCTTGAATTAGCACATTGGCA
66 GCCTTGAATCAGCACATTGGCA
* * * * *
201922 CAAGTCCAATATCG-TTGACCTTGAATTAGCACATTGGCAC
1 TAAGCCCAATATCGCTAG-CCTTGAATCAGCATATTGGCAC
201962 AAGTCCAATA
Statistics
Matches: 270, Mismatches: 30, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
86 2 0.01
87 268 0.99
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (87 bp):
TAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTG
GCCTTGAATCAGCACATTGGCA
Found at i:201959 original size:126 final size:126
Alignment explanation
Indices: 201807--202087 Score: 382
Period size: 126 Copynumber: 2.2 Consensus size: 126
201797 AAGACTAATG
* * *
201807 TCGCTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATTGCTAGCCCTAAATCAGCATATTGG
1 TCGCTGACCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTAGCCCTAAATCAGCATATTGG
* * * *
201872 CACCTTGTCTTTAAGACCAATATCGCTGACCTTGAATTAGCACATTGGCACAAGTCCAATA
66 CACCTTGTCTTTAAGACCAATACCACTGACCTTGAATCAGCACATTGGCACAAGCCCAATA
* * * * * *
201933 TCGTTGACCTTGAATTAGCACATTGGCACAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
1 TCGCTGACCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTAGCCCTAAATCAGCATATTGG
* * * * *
201998 CACCTTGTCTTTAAGACTAATGCCACTGGCCTTGAATCAGCACATTGGCATAAGCCCAATG
66 CACCTTGTCTTTAAGACCAATACCACTGACCTTGAATCAGCACATTGGCACAAGCCCAATA
* *
202059 TCGCTGGCCTTGACTCAGCACATTGGCAC
1 TCGCTGACCTTGAATCAGCACATTGGCAC
202088 TTTATCCATC
Statistics
Matches: 133, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
126 133 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (126 bp):
TCGCTGACCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTAGCCCTAAATCAGCATATTGG
CACCTTGTCTTTAAGACCAATACCACTGACCTTGAATCAGCACATTGGCACAAGCCCAATA
Found at i:202086 original size:87 final size:90
Alignment explanation
Indices: 201940--202324 Score: 280
Period size: 98 Copynumber: 4.1 Consensus size: 90
201930 ATATCGTTGA
* * *
201940 CCTTGAATTAGCACATTGGCACAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC-CT-
1 CCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTCTA
* * *
202003 T-GTCTTTAAGACTAATGCCACTGG
66 TCATCTTTAAGACCAATACCACTGG
* * * *
202027 CCTTGAATCAGCACATTGGCATAAGCCCAATGTCGCTGGCCTTGACTCAGCACATTGGCACTTTA
1 CCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTCTA
* * *
202092 TCCATCTTTAAGTCCAATATCATTGG
66 T-CATCTTTAAGACCAATACCACTGG
** * *
202118 CCTTGAATCAGCACATTGGCGTCTTCATCCTTAAGTTCAATATCGTTGGCCTTGAATCAGCATAT
1 CCTTGAATCAGCACATT-G-G----CA--C--AAGCCCAATATCGCTGGCCTTGAATCAGCACAT
** **
202183 TGGCA-TCT-TCATCTTTAAGACCAATGTCGTTGG
56 TGGCACTCTATCATCTTTAAGACCAATACCACTGG
* * * **
202216 CCTTGAATCAGCACAATGGCATCTTCATCTTTAAGTCCAATATCGATGGCCTTGAATCAGCATGT
1 CCTTGAATCAGCACATTGG------CA-C---AAGCCCAATATCGCTGGCCTTGAATCAGCACAT
**
202281 TGGCA-TCT-TCATCTTTAAGACCAATGTCACTGG
56 TGGCACTCTATCATCTTTAAGACCAATACCACTGG
202314 CCTTGAATCAG
1 CCTTGAATCAG
202325 AACAATTGCA
Statistics
Matches: 250, Mismatches: 31, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
87 55 0.22
88 1 0.00
89 1 0.00
91 34 0.14
92 1 0.00
93 1 0.00
96 1 0.00
97 4 0.02
98 117 0.47
99 1 0.00
100 2 0.01
101 32 0.13
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (90 bp):
CCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTCTA
TCATCTTTAAGACCAATACCACTGG
Found at i:202171 original size:49 final size:49
Alignment explanation
Indices: 202048--202441 Score: 405
Period size: 49 Copynumber: 7.9 Consensus size: 49
202038 CACATTGGCA
* * * *
202048 TAAGCCCAATGTCGCTGGCCTTGACTCAGCACATTGGCACTTTATCCATCTT
1 TAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCA-TCT-T-CATCTT
* * * *
202100 TAAGTCCAATATCATTGGCCTTGAATCAGCACATTGGCGTCTTCATCCT
1 TAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * *
202149 TAAGTTCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* *
202198 TAAGACCAATGTCGTTGGCCTTGAATCAGCACAATGGCATCTTCATCTT
1 TAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * **
202247 TAAGTCCAATATCGATGGCCTTGAATCAGCATGTTGGCATCTTCATCTT
1 TAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* ** * *
202296 TAAGACCAATGTCACTGGCCTTGAATCAGAACAATT-GCACCTTCATCTT
1 TAAGTCCAATGTCGTTGGCCTTGAATCAGCAC-ATTGGCATCTTCATCTT
* * * * * * *
202345 TAAGTCCGATGTCATTGTCCTTGAATTAGCATATTGGCATCTTTAACATT
1 TAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCATC-TT
* **
202395 CCTAAG-CCTAATGTCGCTGGCCTTGTCTCAGCACATTGGCATTCTTC
1 --TAAGTCC-AATGTCGTTGGCCTTGAATCAGCACATTGGCA-TCTTC
202442 TCCAATTCTG
Statistics
Matches: 284, Mismatches: 51, Indels: 13
0.82 0.15 0.04
Matches are distributed among these distances:
48 3 0.01
49 207 0.73
50 5 0.02
51 4 0.01
52 61 0.21
53 4 0.01
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (49 bp):
TAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
Found at i:208879 original size:19 final size:20
Alignment explanation
Indices: 208836--208886 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
208826 TACAAGCTAA
**
208836 TGTATCGATACATTTTATGG
1 TGTATCGATACATACTATGG
*
208856 TGTATCGATACATACTGT-G
1 TGTATCGATACATACTATGG
208875 TGTATCGATACA
1 TGTATCGATACA
208887 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATACTATGG
Found at i:209608 original size:23 final size:23
Alignment explanation
Indices: 209578--209622 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
209568 CCCCTTAATC
209578 ATAAGCACTTATCTTTTTCTCCA
1 ATAAGCACTTATCTTTTTCTCCA
209601 ATAAGCACTTATCTTTTTCTCC
1 ATAAGCACTTATCTTTTTCTCC
209623 CCCTTAAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.24, C:0.27, G:0.04, T:0.44
Consensus pattern (23 bp):
ATAAGCACTTATCTTTTTCTCCA
Found at i:209801 original size:20 final size:22
Alignment explanation
Indices: 209760--209802 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
209750 TTATAGATTA
*
209760 AAACTCAAAGTACAATGCAAAT
1 AAACACAAAGTACAATGCAAAT
209782 AAACACAAAGT-CAA-GCAAAT
1 AAACACAAAGTACAATGCAAAT
209802 A
1 A
209803 CATTAATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 3 0.15
22 10 0.50
ACGTcount: A:0.58, C:0.19, G:0.09, T:0.14
Consensus pattern (22 bp):
AAACACAAAGTACAATGCAAAT
Found at i:210966 original size:21 final size:22
Alignment explanation
Indices: 210942--210986 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
210932 GTGTGGGGGC
* *
210942 TGCCCGGTTGCGACCTGG-GAG
1 TGCCCAGTCGCGACCTGGTGAG
210963 TG-CCAGTCGCGACCTGGTGAG
1 TGCCCAGTCGCGACCTGGTGAG
210984 TGC
1 TGC
210987 TGCCTAGGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.11, C:0.29, G:0.40, T:0.20
Consensus pattern (22 bp):
TGCCCAGTCGCGACCTGGTGAG
Found at i:211279 original size:20 final size:21
Alignment explanation
Indices: 211250--211290 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
211240 TGATTTTGAA
211250 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
211269 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
211291 AAGAATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:211444 original size:13 final size:13
Alignment explanation
Indices: 211424--211460 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
211414 AATCCCCCTA
*
211424 TATCGATACAGTG
1 TATCGATACAATG
*
211437 TATTGATACAATG
1 TATCGATACAATG
211450 TATCGATACAA
1 TATCGATACAA
211461 AGAATGCTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:217796 original size:20 final size:20
Alignment explanation
Indices: 217754--217803 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
217744 TATTTTTCAA
*
217754 GTATCGATACAATGCAACAT
1 GTATCGATACAATGAAACAT
* **
217774 GTATCGATACAATTAAATGT
1 GTATCGATACAATGAAACAT
217794 GTATCGATAC
1 GTATCGATAC
217804 TTTTTAGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACAATGAAACAT
Found at i:227784 original size:21 final size:21
Alignment explanation
Indices: 227743--227786 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
227733 TTTTCTTTTA
* *
227743 ATCATCTTTATGGGTTTAAAC
1 ATCATCTTTATGGCTTGAAAC
227764 ATCATCTTCT-TGGCTTGAAAC
1 ATCATCTT-TATGGCTTGAAAC
227785 AT
1 AT
227787 TTTAAAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (21 bp):
ATCATCTTTATGGCTTGAAAC
Found at i:229619 original size:50 final size:51
Alignment explanation
Indices: 229511--229630 Score: 161
Period size: 50 Copynumber: 2.4 Consensus size: 51
229501 CTCGGAATTG
* * *
229511 ATGGGGTTGGAGTATCCCCAAGATGAAAATTTTAATATTTTGGAAATAAAA
1 ATGGGGTTGGAGTATCCCCAAAAAGAAAATATTAATATTTTGGAAATAAAA
** *
229562 ACAGGGTTGGAGTATCCCCAAAAAGAAAA-ATTAATATTTTGGAATTAAAA
1 ATGGGGTTGGAGTATCCCCAAAAAGAAAATATTAATATTTTGGAAATAAAA
* *
229612 GTGGGGTTTGAGTATCCCC
1 ATGGGGTTGGAGTATCCCC
229631 TCGAATTGAT
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
50 34 0.58
51 25 0.42
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.29
Consensus pattern (51 bp):
ATGGGGTTGGAGTATCCCCAAAAAGAAAATATTAATATTTTGGAAATAAAA
Found at i:229739 original size:80 final size:79
Alignment explanation
Indices: 229565--229770 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 79
229555 AATAAAAACA
* * * * ** *
229565 GGGTTGGAGTATCCCCAAAAAG-AAAAATTAATATTTTGG-AATTAAAAGTGGGGTTTGAGTATC
1 GGGTTAGAGTATCCCCAAAATGAAAAAATTAATATTTTGGAAATAAAAAATGGAATTGGAGTATC
229628 CCCTCGAATTGATC
66 CCCTCGAATTGATC
* * *
229642 GGGTTACAGTATCCCCAAGATGAAAAAATTAATATTTTGGAAATAAAAAATGGAATTGGAGTATT
1 GGGTTAGAGTATCCCCAAAATGAAAAAATTAATATTTTGGAAATAAAAAATGGAATTGGAGTATC
*
229707 CCCTCAGAATTGATG
66 CCCTC-GAATTGATC
* * *
229722 GGGTTTGAGTATCCCCAAAAT-AAAAATTTTAATATTTTGAAAATAAAAA
1 GGGTTAGAGTATCCCCAAAATGAAAAA-ATTAATATTTTGGAAATAAAAA
229771 CGGGGTCGAA
Statistics
Matches: 109, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
77 18 0.17
78 17 0.16
79 28 0.26
80 46 0.42
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.30
Consensus pattern (79 bp):
GGGTTAGAGTATCCCCAAAATGAAAAAATTAATATTTTGGAAATAAAAAATGGAATTGGAGTATC
CCCTCGAATTGATC
Found at i:229811 original size:79 final size:78
Alignment explanation
Indices: 229565--229895 Score: 306
Period size: 79 Copynumber: 4.2 Consensus size: 78
229555 AATAAAAACA
* * * *
229565 GGGTTGGAGTATCCCCAAAA-AGAAAAATTAATATTTTGGAATTAAAAGTGGGGTTTGAGTATCC
1 GGGTTGGAGTATCCCCAAAATA-AAAAATTAATATTTTGAAAATAAAAATGGGGTTGGAGTATCC
* * * *
229629 CCTC-GAATTGATC
65 CCTCAAAAATAATG
** * * ** *
229642 GGGTTACAGTATCCCCAAGATGAAAAAATTAATATTTTGGAAATAAAAAATGGAATTGGAGTATT
1 GGGTTGGAGTATCCCCAAAAT-AAAAAATTAATATTTTGAAAAT-AAAAATGGGGTTGGAGTATC
* * *
229707 CCCTCAGAATTGATG
64 CCCTCAAAAATAATG
* * * * *
229722 GGGTTTGAGTATCCCCAAAATAAAAATTTTAATATTTTGAAAATAAAAACGGGGTCGAAGTATCC
1 GGGTTGGAGTATCCCCAAAATAAAAA-ATTAATATTTTGAAAATAAAAATGGGGTTGGAGTATCC
*
229787 CTTCAAAAATAATG
65 CCTCAAAAATAATG
* ** * * *
229801 GGGTTGGAGTATCTCTGAGATAAAAATTTTAATATTTTAAAAATAAAAATGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCAAAATAAAAA-ATTAATATTTTGAAAATAAAAATGGGGTTGGAGTATCC
* *
229866 CCTCGAAAATAACG
65 CCTCAAAAATAATG
*
229880 GGGTTGGAATATCCCC
1 GGGTTGGAGTATCCCC
229896 GAGATGAAGA
Statistics
Matches: 209, Mismatches: 40, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
77 17 0.08
78 20 0.10
79 131 0.63
80 41 0.20
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.29
Consensus pattern (78 bp):
GGGTTGGAGTATCCCCAAAATAAAAAATTAATATTTTGAAAATAAAAATGGGGTTGGAGTATCCC
CTCAAAAATAATG
Found at i:233033 original size:28 final size:26
Alignment explanation
Indices: 232988--233039 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
232978 AATTAAAAAT
232988 AAAATAAAATAAAGAATATAAATATAA
1 AAAATAAAATAAAGAATA-AAATATAA
**
233015 AAAATTAAAATAATTAATAAAATAT
1 AAAA-TAAAATAAAGAATAAAATAT
233040 TTTTAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (26 bp):
AAAATAAAATAAAGAATAAAATATAA
Found at i:233386 original size:19 final size:20
Alignment explanation
Indices: 233364--233402 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
233354 AATGATAATT
233364 TTTAAAA-TAAAT-TTTAAAA
1 TTTAAAACT-AATCTTTAAAA
233383 TTTAAAACTAATCTTTAAAA
1 TTTAAAACTAATCTTTAAAA
233403 AAAAACTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTAAAACTAATCTTTAAAA
Found at i:239199 original size:43 final size:43
Alignment explanation
Indices: 239133--239772 Score: 623
Period size: 42 Copynumber: 15.0 Consensus size: 43
239123 GGCAGTTTTT
* * * *
239133 AAGGTCAAAGTCGACAGGTAGATTGAGGGATAGAGAAGTCTCC
1 AAGGTCAAAGCCGACAGGCAGACTAAGGGATAGAGAAGTCTCC
* * * *
239176 AAGGTCAAAGCCGACAGGCAGATTGAGAGATAGAAAAGTCTCC
1 AAGGTCAAAGCCGACAGGCAGACTAAGGGATAGAGAAGTCTCC
* * * * *
239219 ATGGTCAAAGCCAACAGGCAAACTTTAGAGATA-AGAAAGTCTCC
1 AAGGTCAAAGCCGACAGGCAGAC-TAAGGGATAGAG-AAGTCTCC
*
239263 AGGGTCAAAGCCGACAGGCAGACTAAGGG-TA-AGAAAGTCTCC
1 AAGGTCAAAGCCGACAGGCAGACTAAGGGATAGAG-AAGTCTCC
* * *
239305 AGGGTCAAAGCCGACTGGCAGACTAA-GGATAGAAAAGTCTCC
1 AAGGTCAAAGCCGACAGGCAGACTAAGGGATAGAGAAGTCTCC
* * * *
239347 AAGATCAAAGCCGACAGGCAGACTGAGGGAAAGA-AAGTCTTC
1 AAGGTCAAAGCCGACAGGCAGACTAAGGGATAGAGAAGTCTCC
*
239389 AAGGTCAAAGCCGACAGGCAGACTGAGGGA-AG-GAAAGTCTCC
1 AAGGTCAAAGCCGACAGGCAGACTAAGGGATAGAG-AAGTCTCC
* * *
239431 -AGAGTCAAAGCGGATAGGCAGACTAAGGGATAG-GAAAGTATCC
1 AAG-GTCAAAGCCGACAGGCAGACTAAGGGATAGAG-AAGTCTCC
* *
239474 GAGGTCAAAGCCGACAGGCAGACTAAGGGATAG-GCAAGTATCC
1 AAGGTCAAAGCCGACAGGCAGACTAAGGGATAGAG-AAGTCTCC
**
239517 GGGGTCAAAGCCGACAGGCAGACTAAGGGATAG-GAAAGTCTCC
1 AAGGTCAAAGCCGACAGGCAGACTAAGGGATAGAG-AAGTCTCC
** * *
239560 AAGGTCAAAGATGATAGACAGACTAAGGG-TAG-GATAGTCTCC
1 AAGGTCAAAGCCGACAGGCAGACTAAGGGATAGAGA-AGTCTCC
* * * * * *
239602 AGGGTCAAAGCTGACAGGCAAACTGAGGGAAAGA-AAGTCTTC
1 AAGGTCAAAGCCGACAGGCAGACTAAGGGATAGAGAAGTCTCC
* *
239644 -AGGATCAAAGCTGACAGGCAGACTAAGGGA-AGAAAAGTCTCC
1 AAGG-TCAAAGCCGACAGGCAGACTAAGGGATAGAGAAGTCTCC
* * * *
239686 AAGGTCAAAGCCGACTGGCAAACTAAGAGATAGAAAAGTCTCC
1 AAGGTCAAAGCCGACAGGCAGACTAAGGGATAGAGAAGTCTCC
* * *
239729 AAGATCAAAGCCAACAGGCAGACTAAAGG-TA-AGAAAGTCTCC
1 AAGGTCAAAGCCGACAGGCAGACTAAGGGATAGAG-AAGTCTCC
239771 AA
1 AA
239773 AAGTTTAATG
Statistics
Matches: 515, Mismatches: 64, Indels: 37
0.84 0.10 0.06
Matches are distributed among these distances:
41 13 0.03
42 242 0.47
43 222 0.43
44 38 0.07
ACGTcount: A:0.38, C:0.19, G:0.29, T:0.14
Consensus pattern (43 bp):
AAGGTCAAAGCCGACAGGCAGACTAAGGGATAGAGAAGTCTCC
Found at i:239585 original size:255 final size:253
Alignment explanation
Indices: 239133--239771 Score: 804
Period size: 255 Copynumber: 2.5 Consensus size: 253
239123 GGCAGTTTTT
* * * *
239133 AAGGTCAAAGTCGACAGGTAGATTGAGGGATA-GAGAAGTCTCCAAGGTCAAAGCCGACAGGCAG
1 AAGGTCAAAGCCGACAGGCAGACTGAGGGA-AGGA-AAGTCTCCAAGGTCAAAGCCGATAGGCAG
* * * * *
239197 ATTGAGAGATAGAAAAGTCTCCATGGTCAAAGCCAACAGGCAAACTTTAGAGATAAGAAAGTCTC
64 ACTAAGAGATAGAAAAGTCTCCA-GGTCAAAGCCAACAGGCAGAC-TAAGAGATAAGAAAGTATC
* * *
239262 CAGGGTCAAAGCCGACAGGCAGACTAAGGGTAAGAAAGTCTCCAGGGTCAAAGCCGACTGGCAGA
127 CAGGGTCAAAGCCGACAGGCAGACTAAGGGTAAGAAAGTCTCCAAGGTCAAAGACGACTGACAGA
*
239327 CTAAGGATAGAAAAGTCTCCAAGATCAAAGCCGACAGGCAGACTGAGGGAAAGAAAGTCTTC
192 CTAAGGATAGAAAAGTCTCCAAGATCAAAGCCGACAGGCAAACTGAGGGAAAGAAAGTCTTC
*
239389 AAGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAAAGTCTCC-AGAGTCAAAGCGGATAGGCAGA
1 AAGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAAAGTCTCCAAG-GTCAAAGCCGATAGGCAGA
* * * * * * * *
239453 CTAAGGGATAGGAAAGTATCCGAGGTCAAAGCCGACAGGCAGACTAAGGGATAGGCAAGTATCCG
65 CTAAGAGATAGAAAAGTCTCC-AGGTCAAAGCCAACAGGCAGACTAAGAGATAAGAAAGTATCCA
* *
239518 GGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAAGGTCAAAGATGA-TAGACAGA
129 GGGTCAAAGCCGACAGGCAGACTAAGGG-TAAGAAAGTCTCCAAGGTCAAAGACGACT-GACAGA
* * * * * *
239582 CTAAGGGTAGGATAGTCTCCAGGGTCAAAGCTGACAGGCAAACTGAGGGAAAGAAAGTCTTC
192 CTAAGGATAGAAAAGTCTCCAAGATCAAAGCCGACAGGCAAACTGAGGGAAAGAAAGTCTTC
* * * *
239644 -AGGATCAAAGCTGACAGGCAGACTAAGGGAAGAAAAGTCTCCAAGGTCAAAGCCGACT-GGCAA
1 AAGG-TCAAAGCCGACAGGCAGACTGAGGGAAGGAAAGTCTCCAAGGTCAAAGCCGA-TAGGCAG
* * *
239707 ACTAAGAGATAGAAAAGTCTCCAAGATCAAAGCCAACAGGCAGACTAA-AGGTAAGAAAGTCTCC
64 ACTAAGAGATAGAAAAGTCTCC-AGGTCAAAGCCAACAGGCAGACTAAGAGATAAGAAAGTATCC
239771 A
128 A
239772 AAAGTTTAAT
Statistics
Matches: 328, Mismatches: 47, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
254 60 0.18
255 235 0.72
256 33 0.10
ACGTcount: A:0.38, C:0.19, G:0.29, T:0.14
Consensus pattern (253 bp):
AAGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAAAGTCTCCAAGGTCAAAGCCGATAGGCAGAC
TAAGAGATAGAAAAGTCTCCAGGTCAAAGCCAACAGGCAGACTAAGAGATAAGAAAGTATCCAGG
GTCAAAGCCGACAGGCAGACTAAGGGTAAGAAAGTCTCCAAGGTCAAAGACGACTGACAGACTAA
GGATAGAAAAGTCTCCAAGATCAAAGCCGACAGGCAAACTGAGGGAAAGAAAGTCTTC
Found at i:252962 original size:47 final size:47
Alignment explanation
Indices: 252832--252962 Score: 190
Period size: 47 Copynumber: 2.8 Consensus size: 47
252822 GCTGTGCTCG
* * *
252832 TGGAGTTACTGCCGGTTGTTCGTGGAAGTTGCTGCTACCGTGGAAGC
1 TGGAGTTACTGCCGGTTGCTCGTGGAAGCTGCTGCTGCCGTGGAAGC
* * * *
252879 TTGAGTTACTGTCGGTTGCTCGTGGAAACTACTGCTGCCGTGGAAGC
1 TGGAGTTACTGCCGGTTGCTCGTGGAAGCTGCTGCTGCCGTGGAAGC
*
252926 TGGAGTTGCTGCCGGTTGCTCGTGGAAGCTGCTGCTG
1 TGGAGTTACTGCCGGTTGCTCGTGGAAGCTGCTGCTG
252963 GTGGATGCTG
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.14, C:0.21, G:0.36, T:0.30
Consensus pattern (47 bp):
TGGAGTTACTGCCGGTTGCTCGTGGAAGCTGCTGCTGCCGTGGAAGC
Found at i:253615 original size:20 final size:21
Alignment explanation
Indices: 253590--253633 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
253580 TCATGATGAT
253590 TTTTTTTACTTTT-ATTTTTA
1 TTTTTTTACTTTTGATTTTTA
253610 TTTTTTTACTTTTGATTTTTA
1 TTTTTTTACTTTTGATTTTTA
253631 TTT
1 TTT
253634 ATTATTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTTTTACTTTTGATTTTTA
Found at i:255966 original size:2 final size:2
Alignment explanation
Indices: 255959--255985 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
255949 ATAAAGTGAT
255959 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
255986 CAAGCAAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:257552 original size:17 final size:17
Alignment explanation
Indices: 257525--257557 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
257515 AACTTTTATT
257525 ATTTGTTCCTTGTTTTCA
1 ATTTGTTCCTT-TTTTCA
257543 ATTT-TTCCTTTTTTC
1 ATTTGTTCCTTTTTTC
257558 TTTAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.09, C:0.18, G:0.06, T:0.67
Consensus pattern (17 bp):
ATTTGTTCCTTTTTTCA
Found at i:257880 original size:12 final size:11
Alignment explanation
Indices: 257863--257890 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
257853 AAGAGCAAAT
257863 AAAAAAAAAAC
1 AAAAAAAAAAC
257874 AAAAAAAAAAC
1 AAAAAAAAAAC
257885 AAAAAA
1 AAAAAA
257891 CAAATCTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:260086 original size:21 final size:21
Alignment explanation
Indices: 260062--260102 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
260052 AATTAAAAAA
260062 ATAT-TTTTA-TATTAAATTT
1 ATATATTTTATTATTAAATTT
260081 ATATATTTTATTATTAAATTT
1 ATATATTTTATTATTAAATTT
260102 A
1 A
260103 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.20
20 5 0.25
21 11 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATATTTTATTATTAAATTT
Found at i:269914 original size:21 final size:21
Alignment explanation
Indices: 269881--269921 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
269871 CTAAGTAAAA
269881 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
269902 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
269922 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:269986 original size:20 final size:20
Alignment explanation
Indices: 269960--270031 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
269950 AACTCTGAAA
269960 AGTATCGATACACATTTAAAT
1 AGTATCGATACACA-TTAAAT
* **
269981 -GTATCGATACAGATTGCAT
1 AGTATCGATACACATTAAAT
*
270000 AGTATCGATACACA-CAAAT
1 AGTATCGATACACATTAAAT
*
270019 ATTTATCGATACA
1 A-GTATCGATACA
270032 GGTCATTGGT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
19 7 0.17
20 34 0.83
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (20 bp):
AGTATCGATACACATTAAAT
Found at i:270127 original size:10 final size:10
Alignment explanation
Indices: 270108--270157 Score: 75
Period size: 10 Copynumber: 5.1 Consensus size: 10
270098 AATCTCATTT
*
270108 TCACTGTTCA
1 TCACTATTCA
270118 TCACTATTCA
1 TCACTATTCA
270128 TCACTATTCA
1 TCACTATTCA
270138 TCACTATTCA
1 TCACTATTCA
*
270148 -CACTGTTCA
1 TCACTATTCA
270157 T
1 T
270158 GTATCACTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
9 8 0.22
10 29 0.78
ACGTcount: A:0.26, C:0.30, G:0.04, T:0.40
Consensus pattern (10 bp):
TCACTATTCA
Found at i:270137 original size:20 final size:20
Alignment explanation
Indices: 270108--270157 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
270098 AATCTCATTT
270108 TCACTGTTCATCACTATTCA
1 TCACTGTTCATCACTATTCA
*
270128 TCACTATTCATCACTATTCA
1 TCACTGTTCATCACTATTCA
270148 -CACTGTTCAT
1 TCACTGTTCAT
270158 GTATCACTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 9 0.32
20 19 0.68
ACGTcount: A:0.26, C:0.30, G:0.04, T:0.40
Consensus pattern (20 bp):
TCACTGTTCATCACTATTCA
Found at i:270223 original size:13 final size:13
Alignment explanation
Indices: 270205--270242 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
270195 TCACTATTCA
270205 TGTATCGATACAG
1 TGTATCGATACAG
270218 TGTATCGATACAG
1 TGTATCGATACAG
270231 TGTATCGATACA
1 TGTATCGATACA
270243 TCATAAATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:272591 original size:22 final size:22
Alignment explanation
Indices: 272563--272605 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
272553 AGAAAGTGAC
272563 ATACTTAGACATCATGACAAAT
1 ATACTTAGACATCATGACAAAT
*
272585 ATACTTAGATATCATGACAAA
1 ATACTTAGACATCATGACAAA
272606 CAGGTTCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28
Consensus pattern (22 bp):
ATACTTAGACATCATGACAAAT
Found at i:273990 original size:17 final size:17
Alignment explanation
Indices: 273968--274004 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
273958 AATTATTTTT
*
273968 AGTTGTGTGAGATCGAA
1 AGTTGTATGAGATCGAA
273985 AGTTGTATGAGATCGAA
1 AGTTGTATGAGATCGAA
274002 AGT
1 AGT
274005 GGCTGCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.30
Consensus pattern (17 bp):
AGTTGTATGAGATCGAA
Found at i:277564 original size:10 final size:9
Alignment explanation
Indices: 277546--277587 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
277536 GTTAGTGTTA
277546 TAAATTAAT
1 TAAATTAAT
277555 TAATATTAAT
1 TAA-ATTAAT
277565 TAAATTAA-
1 TAAATTAAT
*
277573 TAAA-AAAT
1 TAAATTAAT
277581 TAAATTA
1 TAAATTA
277588 CAAAATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
7 2 0.07
8 8 0.29
9 9 0.32
10 9 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
TAAATTAAT
Found at i:285315 original size:13 final size:13
Alignment explanation
Indices: 285297--285321 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
285287 ACAACAAGTA
285297 TGTATCGATACAT
1 TGTATCGATACAT
285310 TGTATCGATACA
1 TGTATCGATACA
285322 CAAAAAATTG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:287529 original size:21 final size:21
Alignment explanation
Indices: 287496--287540 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
287486 TTGCAAGTTG
*
287496 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
287518 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
287538 AAA
1 AAA
287541 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:289363 original size:15 final size:15
Alignment explanation
Indices: 289343--289373 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
289333 TAAAAATGTC
*
289343 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
289358 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
289373 C
1 C
289374 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:291470 original size:13 final size:13
Alignment explanation
Indices: 291452--291490 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
291442 ACATTTTTCT
291452 TTGTATCGATACA
1 TTGTATCGATACA
*
291465 TTGTATCGATATA
1 TTGTATCGATACA
291478 TTGTATCGATACA
1 TTGTATCGATACA
291491 GGGTGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:294040 original size:13 final size:13
Alignment explanation
Indices: 294022--294047 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
294012 TACAGCAAGT
294022 ATGTATCGATACA
1 ATGTATCGATACA
294035 ATGTATCGATACA
1 ATGTATCGATACA
294048 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:298792 original size:65 final size:65
Alignment explanation
Indices: 298688--298817 Score: 251
Period size: 65 Copynumber: 2.0 Consensus size: 65
298678 ATACAGTCAC
*
298688 TGCACCAACCTTTTCAATCCAATCGTGGATTGTTATAATCCCTGCACAATTTGAAGTGTTGTTGA
1 TGCACCAACCTTTTCAATCCAATCGTAGATTGTTATAATCCCTGCACAATTTGAAGTGTTGTTGA
298753 TGCACCAACCTTTTCAATCCAATCGTAGATTGTTATAATCCCTGCACAATTTGAAGTGTTGTTGA
1 TGCACCAACCTTTTCAATCCAATCGTAGATTGTTATAATCCCTGCACAATTTGAAGTGTTGTTGA
298818 CAAACTGCGT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (65 bp):
TGCACCAACCTTTTCAATCCAATCGTAGATTGTTATAATCCCTGCACAATTTGAAGTGTTGTTGA
Found at i:299565 original size:30 final size:31
Alignment explanation
Indices: 299529--299596 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
299519 TAATTTTAAA
* **
299529 TTAAATTT-TATTTAATAAT-ATTTATTTATT
1 TTAAATTTATATTTAA-AATCAATTATAAATT
299559 TTAAATTTATATTTAAAATCAATTATAAATT
1 TTAAATTTATATTTAAAATCAATTATAAATT
299590 TTAAATT
1 TTAAATT
299597 GATCCACTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 11 0.33
31 22 0.67
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (31 bp):
TTAAATTTATATTTAAAATCAATTATAAATT
Found at i:305226 original size:16 final size:15
Alignment explanation
Indices: 305205--305234 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
305195 CATTTTACAA
305205 TATTTTTATAATTTTT
1 TATTTTTAT-ATTTTT
305221 TATTTTTATATTTT
1 TATTTTTATATTTT
305235 ATGAAAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TATTTTTATATTTTT
Found at i:305294 original size:2 final size:2
Alignment explanation
Indices: 305289--305322 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
305279 TTATTTCTTA
*
305289 AT AT AT AT AT AT AT AT AT AT AT TT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
305323 ACAAGGTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:306544 original size:26 final size:26
Alignment explanation
Indices: 306483--306546 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
306473 GATAAAAATG
*
306483 TTAA-ATTTTAAA-TTAAATGAATTA
1 TTAATATTTTAAATTTAAATAAATTA
* *
306507 TTAATATATTAAATTTATATAAA-TA
1 TTAATATTTTAAATTTAAATAAATTA
306532 TATAATATTTTAAAT
1 T-TAATATTTTAAAT
306547 ATGATTATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 4 0.12
25 10 0.30
26 19 0.58
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
TTAATATTTTAAATTTAAATAAATTA
Found at i:308485 original size:37 final size:36
Alignment explanation
Indices: 308444--308550 Score: 107
Period size: 34 Copynumber: 3.1 Consensus size: 36
308434 ATTAATTATT
308444 AATTTTTTATTAAAAATAAAAATTAATTAAATTTAAA
1 AATTTTTTATTAAAAATAAAAATT-ATTAAATTTAAA
* * **
308481 AATTTTATATTGAAAAATTAAAA-TATT-AA-TTATT
1 AATTTTTTATT-AAAAATAAAAATTATTAAATTTAAA
* *
308515 AATTTTTTAAT-AAAATAAAAATT-TTAAATTAAAA
1 AATTTTTTATTAAAAATAAAAATTATTAAATTTAAA
308549 AA
1 AA
308551 ATTAAAAAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
32 11 0.20
33 3 0.05
34 16 0.29
35 2 0.04
36 3 0.05
37 11 0.20
38 10 0.18
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (36 bp):
AATTTTTTATTAAAAATAAAAATTATTAAATTTAAA
Found at i:308531 original size:70 final size:69
Alignment explanation
Indices: 308385--308553 Score: 218
Period size: 69 Copynumber: 2.5 Consensus size: 69
308375 TGGATAAAAT
* * * *
308385 TAAAAATAAAATTTAATTAAATTAAAAAAATTCATGTTAAAATCGAAGTATTAATTATTAATTTT
1 TAAAAATAAAAATTAATTAAATTAAAAAAATTCATATTAAAATCAAAATATTAATTATTAATTTT
*
308450 TTAT
66 TTAA
* * * *
308454 TAAAAATAAAAATTAATTAAATTTAAAAATTTTATATTGAAAAATTAAAATATTAATTATTAATT
1 TAAAAATAAAAATTAATTAAATTAAAAAAATTCATATT--AAAATCAAAATATTAATTATTAATT
308519 TTTTAA
64 TTTTAA
308525 T-AAAATAAAAATT--TTAAATTAAAAAAATT
1 TAAAAATAAAAATTAATTAAATTAAAAAAATT
308554 AAAAAATAAG
Statistics
Matches: 87, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
68 14 0.16
69 33 0.38
70 12 0.14
71 28 0.32
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (69 bp):
TAAAAATAAAAATTAATTAAATTAAAAAAATTCATATTAAAATCAAAATATTAATTATTAATTTT
TTAA
Found at i:308926 original size:27 final size:26
Alignment explanation
Indices: 308895--308955 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
308885 TGTAAAATTA
*
308895 ATTTGATTAAATGTATTATTTATTTTT
1 ATTTGATTAAATGTA-AATTTATTTTT
* *
308922 ATTTG-TAGAAATTTAAATTTATTTTT
1 ATTTGAT-TAAATGTAAATTTATTTTT
308948 -TTTGATTA
1 ATTTGATTA
308956 TACGAATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
25 5 0.18
26 12 0.43
27 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (26 bp):
ATTTGATTAAATGTAAATTTATTTTT
Found at i:309078 original size:21 final size:21
Alignment explanation
Indices: 309052--309092 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
309042 TTGGGAAACT
309052 ACATGAAATT-CTCTAAAAATC
1 ACATGAAATTCCT-TAAAAATC
309073 ACATGAAATTCCTTAAAAAT
1 ACATGAAATTCCTTAAAAAT
309093 TTCAAGATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.29
Consensus pattern (21 bp):
ACATGAAATTCCTTAAAAATC
Found at i:309669 original size:23 final size:22
Alignment explanation
Indices: 309643--309685 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
309633 AATTATTATT
*
309643 AATTATAAATTTTGTAAATAATA
1 AATTATAAACTTT-TAAATAATA
*
309666 AATTATTAACTTTTAAATAA
1 AATTATAAACTTTTAAATAA
309686 GATACTCTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
AATTATAAACTTTTAAATAATA
Found at i:309789 original size:20 final size:20
Alignment explanation
Indices: 309764--309817 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
309754 TTTCAGAAGC
*
309764 TATATATTAAATAAAGAAATA
1 TATATATT-AATAAAGAAAAA
309785 T-TATA-TAATACAAGAAAAA
1 TATATATTAATA-AAGAAAAA
309804 TATATATTAATAAA
1 TATATATTAATAAA
309818 AGAAGAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 4 0.14
19 9 0.31
20 10 0.34
21 6 0.21
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (20 bp):
TATATATTAATAAAGAAAAA
Found at i:309806 original size:21 final size:21
Alignment explanation
Indices: 309764--309821 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 21
309754 TTTCAGAAGC
*
309764 TATATATTAA-ATAAAGAAATA
1 TATATATTAATA-AAAGAAAAA
*
309785 T-TATA-TAATACAAGAAAAA
1 TATATATTAATAAAAGAAAAA
309804 TATATATTAATAAAAGAA
1 TATATATTAATAAAAGAA
309822 GAAAGACAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 11 0.35
20 9 0.29
21 11 0.35
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (21 bp):
TATATATTAATAAAAGAAAAA
Found at i:310289 original size:68 final size:69
Alignment explanation
Indices: 310158--310294 Score: 179
Period size: 71 Copynumber: 2.0 Consensus size: 69
310148 TTTTAATTTT
** * *
310158 TTTATTTTATTAAAAATTAATAATTAATATTTTAATTTTTTAATATAAATTTTTTCAAATTTAAT
1 TTTATTTTATTAAAAATTAATAATTAATACATTAA-TTCTTAACATAAATTTTTTCAAATTTAAT
310223 TAAAA
65 TAAAA
* * *
310228 TTTATTTTTATTAAAAATTGATAATTAATACATTGA-TCTTAACAT-AATTTTTTTAAATTTAAT
1 TTTA-TTTTATTAAAAATTAATAATTAATACATTAATTCTTAACATAAATTTTTTCAAATTTAAT
310291 TAAA
65 TAAA
310295 TTAAATTTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
68 21 0.36
69 7 0.12
70 4 0.07
71 27 0.46
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (69 bp):
TTTATTTTATTAAAAATTAATAATTAATACATTAATTCTTAACATAAATTTTTTCAAATTTAATT
AAAA
Found at i:311324 original size:3 final size:3
Alignment explanation
Indices: 311312--311341 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
311302 GTCTTTTATT
311312 TTC TTC -TC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
311342 CTTTTCCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:316043 original size:31 final size:31
Alignment explanation
Indices: 316005--316065 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
315995 AAAAATGAAG
* *
316005 AGTTGGAGCAACATATGTAGATGGTAGTGGA
1 AGTTGGAGCAACATAGGTAGATGGAAGTGGA
316036 AGTTGGAGCAACATAGGTAGATGGAAGTGG
1 AGTTGGAGCAACATAGGTAGATGGAAGTGG
316066 GGGCAGGGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.07, G:0.38, T:0.23
Consensus pattern (31 bp):
AGTTGGAGCAACATAGGTAGATGGAAGTGGA
Found at i:319012 original size:23 final size:23
Alignment explanation
Indices: 318985--319029 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
318975 GTCATTTTAA
*
318985 ATTCAAGTTAATTGGGTTTGATC
1 ATTCAAGTCAATTGGGTTTGATC
319008 ATTCAAGTCAATTGGGTTTGAT
1 ATTCAAGTCAATTGGGTTTGAT
319030 ATTTTAGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (23 bp):
ATTCAAGTCAATTGGGTTTGATC
Found at i:335671 original size:51 final size:50
Alignment explanation
Indices: 335608--335722 Score: 158
Period size: 51 Copynumber: 2.3 Consensus size: 50
335598 AATTAACTAG
* * *
335608 ATGTATCAATACATTGAAAATTATATCGATATATCTAGGTAAAAAAACAGA
1 ATGTATCGATACATTGAAAAATATATCGATACATCTAGGT-AAAAAACAGA
* * * *
335659 ATGTATCGATACATTGAAAAATGTATCGATACATTTGGGTAAAAATCAGA
1 ATGTATCGATACATTGAAAAATATATCGATACATCTAGGTAAAAAACAGA
335709 ATGTATCGATACAT
1 ATGTATCGATACAT
335723 GTACTGTTCA
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
50 23 0.40
51 34 0.60
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.30
Consensus pattern (50 bp):
ATGTATCGATACATTGAAAAATATATCGATACATCTAGGTAAAAAACAGA
Found at i:336452 original size:18 final size:18
Alignment explanation
Indices: 336429--336465 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
336419 GTTTATTTGG
336429 TTTTTTCTATTTTCTCTC
1 TTTTTTCTATTTTCTCTC
* *
336447 TTTTTTCTTTTTTTTCTC
1 TTTTTTCTATTTTCTCTC
336465 T
1 T
336466 ACTTGCTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTCTATTTTCTCTC
Found at i:337120 original size:163 final size:164
Alignment explanation
Indices: 336951--337298 Score: 393
Period size: 163 Copynumber: 2.1 Consensus size: 164
336941 TAATTTAAAA
* *
336951 TTTTCAAAACTGATTTAATATAAAT-TGAATGACAATATTAGACAAATTATAAAAATTTTAAACC
1 TTTTCAAAACTGATTTAATATAAGTGT-AATGACAATATTAGACAAATTATAAAAAATTTAAACC
* * *
337015 AAGAAAAATTTTTCC-AAAAACATTTATGGAATAAAAAATTCAGTTTTTGAGAAATAG-GAGAAT
65 AAG-AAAATTCTCCCGAAAAACATTTAGGGAAT-AAAAATTCAGTTTTTGAGAAATAGAG-GAAT
*
337078 TT-A-AAAAAAATGAAAAACTTATGAAAATAA-ATGAAT
127 TTAAGAAAAAAATGAAAAACTGATG-AAATAACATGAAT
* * * * ** * * *
337114 TTTTCAAAATTGATTTAAAATGAGTGTAATGACAATGTTAGATGAATTTTAAAAAATTTGAATCA
1 TTTTCAAAACTGATTTAATATAAGTGTAATGACAATATTAGACAAATTATAAAAAATTTAAACCA
* * *
337179 AGAAAATTCTCCCGAAAAACATTTAGGGAATGAAAATTCAGTTTTTTAGAAATAGAGGCATTTCA
66 AGAAAATTCTCCCGAAAAACATTTAGGGAATAAAAATTCAGTTTTTGAGAAATAGAGGAATTT-A
** *
337244 AGGAAAAAAATGAAAATGTGATGAAATAACTTGAAT
130 A-GAAAAAAATGAAAAACTGATGAAATAACATGAAT
*
337280 TTTTCAAAACTGGTTTAAT
1 TTTTCAAAACTGATTTAAT
337299 GATGATTACA
Statistics
Matches: 153, Mismatches: 24, Indels: 13
0.81 0.13 0.07
Matches are distributed among these distances:
162 36 0.24
163 71 0.46
164 2 0.01
165 6 0.04
166 38 0.25
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.32
Consensus pattern (164 bp):
TTTTCAAAACTGATTTAATATAAGTGTAATGACAATATTAGACAAATTATAAAAAATTTAAACCA
AGAAAATTCTCCCGAAAAACATTTAGGGAATAAAAATTCAGTTTTTGAGAAATAGAGGAATTTAA
GAAAAAAATGAAAAACTGATGAAATAACATGAAT
Found at i:337330 original size:166 final size:163
Alignment explanation
Indices: 336951--337343 Score: 379
Period size: 163 Copynumber: 2.4 Consensus size: 163
336941 TAATTTAAAA
* * * * * * *
336951 TTTTCAAAACTGATTTAATATAAAT-TGAATGACAATATTAGACAAATTATAAAAATTTTAAACC
1 TTTTCAAAACTGATTTAAAATGAGTGT-AATAACAATATTAGATAAATTTTAAAAAATTTAAACC
* * *
337015 AAGAAAAATTTTTCCAAAAACATTTATGGAATAAAAAATTCAGTTTTTGAGAAATAGGAGAATTT
65 AAGAAAAATTCTCCCAAAAACATTTAGGGAATAAAAAATTCAGTTTTTGAGAAATAGGAGAATTT
*
337080 AAAAAAAATGAAAAACTTATGAAAATAAATGAAT
130 AAAAAAAATGAAAAACTGATGAAAATAAATGAAT
* * * * * *
337114 TTTTCAAAATTGATTTAAAATGAGTGTAATGACAATGTTAGATGAATTTTAAAAAATTTGAATCA
1 TTTTCAAAACTGATTTAAAATGAGTGTAATAACAATATTAGATAAATTTTAAAAAATTTAAACCA
* * *
337179 AG-AAAATTCTCCCGAAAAACATTTAGGGAAT-GAAAATTCAGTTTTTTAGAAATA-GAGGCATT
66 AGAAAAATTCTCCC-AAAAACATTTAGGGAATAAAAAATTCAGTTTTTGAGAAATAGGA-GAATT
** *
337241 TCAAGGAAAAAAATGAAAATGTGATG-AAATAACTTGAAT
129 T--A--AAAAAAATGAAAAACTGATGAAAATAA-ATGAAT
* * * * *
337280 TTTTCAAAACTGGTTTAATGATGA-T-TACATAATAATATTCA-ATAAATTTTAAATATTTTAAA
1 TTTTCAAAACTGATTTAA-AATGAGTGTA-ATAACAATATT-AGATAAATTTTAAAAAATTTAAA
337342 CC
63 CC
337344 GTTGAAAATC
Statistics
Matches: 187, Mismatches: 32, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
161 2 0.01
162 35 0.19
163 70 0.37
164 2 0.01
165 8 0.04
166 65 0.35
167 5 0.03
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.33
Consensus pattern (163 bp):
TTTTCAAAACTGATTTAAAATGAGTGTAATAACAATATTAGATAAATTTTAAAAAATTTAAACCA
AGAAAAATTCTCCCAAAAACATTTAGGGAATAAAAAATTCAGTTTTTGAGAAATAGGAGAATTTA
AAAAAAATGAAAAACTGATGAAAATAAATGAAT
Found at i:339043 original size:85 final size:85
Alignment explanation
Indices: 338894--339077 Score: 212
Period size: 85 Copynumber: 2.2 Consensus size: 85
338884 GCGGTTAGGT
* * *
338894 CAACAAAGGATAAAAAGGATTACCTAAAACTAAGCCAATAGGTAGATAAAGGATACAAACGTTGA
1 CAACAAAGGATAAAAAGGATTACCTAAAACTAAGCCAACAGGTAAACAAAGGATACAAACGTTGA
* *
338959 TCGAGGTTAAACCGATAAGC
66 TCGAGATTAAACCAATAAGC
* * * * *
338979 CAACAAAGGATAAAAA-GATTTACCTGAGACTAGGTCAACAGGTAAACAAGGGATGA-AAGA-GT
1 CAACAAAGGATAAAAAGGA-TTACCTAAAACTAAGCCAACAGGTAAACAAAGGAT-ACAA-ACGT
* *
339041 TGATCGAGATTAAACTAATAAGT
63 TGATCGAGATTAAACCAATAAGC
339064 CAACAAAGGATAAA
1 CAACAAAGGATAAA
339078 TGGATTTATC
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
84 2 0.02
85 80 0.95
86 2 0.02
ACGTcount: A:0.48, C:0.14, G:0.21, T:0.18
Consensus pattern (85 bp):
CAACAAAGGATAAAAAGGATTACCTAAAACTAAGCCAACAGGTAAACAAAGGATACAAACGTTGA
TCGAGATTAAACCAATAAGC
Found at i:339221 original size:85 final size:83
Alignment explanation
Indices: 339094--339297 Score: 230
Period size: 85 Copynumber: 2.4 Consensus size: 83
339084 TATCTGGGAT
* * * *
339094 TAAGCCGAAGGTAAATAAAGGATAAAAGGGTTGACCAGGATTGAACTGGCAAGTTAACAAAAGAT
1 TAAGCCGAAAGTAAACAAAGGATAAAAGGGTTGACCAAGATTGAACTGACAAGTTAACAAAAGAT
339159 GAAAAGTGTTACCTAAGAC
66 -AAAAGTGTTACCTAAGAC
* * **
339178 TAAGCCGATAAGTAAACAAGGGATGAAAGGGTTGGTCAAGATTGAACTGACAAGTTAACAAAAGA
1 TAAGCCGA-AAGTAAACAAAGGATAAAAGGGTTGACCAAGATTGAACTGACAAGTTAACAAAAGA
* *
339243 TAAAAG-GATTTACCCAGGAC
65 TAAAAGTG--TTACCTAAGAC
* * * *
339263 TAAGCTGACAGGTAAACAAACGATAAAAAGGTTGA
1 TAAGCCGA-AAGTAAACAAAGGATAAAAGGGTTGA
339298 TTGAGAATAA
Statistics
Matches: 99, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
83 1 0.01
84 13 0.13
85 85 0.86
ACGTcount: A:0.45, C:0.12, G:0.25, T:0.19
Consensus pattern (83 bp):
TAAGCCGAAAGTAAACAAAGGATAAAAGGGTTGACCAAGATTGAACTGACAAGTTAACAAAAGAT
AAAAGTGTTACCTAAGAC
Found at i:339423 original size:39 final size:39
Alignment explanation
Indices: 339374--339487 Score: 158
Period size: 39 Copynumber: 2.9 Consensus size: 39
339364 AGGTTAAAAG
* *
339374 GGTTGACCAGGGCAAAATCGATAAAGTCAACCAATTGGA
1 GGTTGGCCAGGGCAAAATCGATAAAGTCAACCAATTGAA
* *
339413 GGTTGGCCAGGGCGAAATCGATAAAGTCAACCAATTTAA
1 GGTTGGCCAGGGCAAAATCGATAAAGTCAACCAATTGAA
* *
339452 GGTTGGCTAGGGCAAAA-CTGATAAAGTCAACAAATT
1 GGTTGGCCAGGGCAAAATC-GATAAAGTCAACCAATT
339488 AAAAGGGTTG
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 1 0.01
39 66 0.99
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (39 bp):
GGTTGGCCAGGGCAAAATCGATAAAGTCAACCAATTGAA
Found at i:339736 original size:45 final size:46
Alignment explanation
Indices: 339525--339760 Score: 221
Period size: 46 Copynumber: 5.2 Consensus size: 46
339515 AAAGTTAATG
* * * * * *
339525 AGAATGAAAAGGGTTTGACTAGGGTGGTAA--AAAATAGTCAAACA
1 AGAATGAAAAGGGTTTGACTAAGGTGATAACCGATACAATCAAACA
** *
339569 AGAATGAAAAAAGTTTGACTAAGGTGATAACCGATACAATTAAACA
1 AGAATGAAAAGGGTTTGACTAAGGTGATAACCGATACAATCAAACA
* * * * * *
339615 CGGATGAAAATGGTTTGACTAAGGTGGTAACTGATATAATCAAACA
1 AGAATGAAAAGGGTTTGACTAAGGTGATAACCGATACAATCAAACA
* * * **
339661 AGAATAAAAAGGGTTTGAATAGGGTGATAACTAATACAATCAAACA
1 AGAATGAAAAGGGTTTGACTAAGGTGATAACCGATACAATCAAACA
* *
339707 AGAATGAAAA-GGTTTGAC-CAGTGTGATAACCGATACAGTCAAACA
1 AGAATGAAAAGGGTTTGACTAAG-GTGATAACCGATACAATCAAACA
339752 A-AGATGAAA
1 AGA-ATGAAA
339761 CTGGTTTATT
Statistics
Matches: 155, Mismatches: 33, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
44 28 0.18
45 34 0.22
46 93 0.60
ACGTcount: A:0.46, C:0.10, G:0.22, T:0.22
Consensus pattern (46 bp):
AGAATGAAAAGGGTTTGACTAAGGTGATAACCGATACAATCAAACA
Found at i:340633 original size:92 final size:92
Alignment explanation
Indices: 340524--340703 Score: 254
Period size: 92 Copynumber: 2.0 Consensus size: 92
340514 ACAATCAAGC
* *
340524 TTTGTGATGCATCAATACCATCTAGTGGTCAGATGAAGAGGATACGATTG-GAAATGTATGGTCT
1 TTTGTGATGCATAAATACCATCTAGTGGTCAGATGAAGAGGATACGATTGAG-AATGTATGATCT
* *
340588 GGATGTCCTTACCCCAAGGAAATCAGGT
65 GGATATCCCTACCCCAAGGAAATCAGGT
** * * *
340616 TTTGTGATGCATAAATACCATCTAGTGGTTGGATGAAGGGGATATGATTGAGAATGTGTGATCTG
1 TTTGTGATGCATAAATACCATCTAGTGGTCAGATGAAGAGGATACGATTGAGAATGTATGATCTG
*
340681 GATATCCCTACCCTAAGGAAATC
66 GATATCCCTACCCCAAGGAAATC
340704 GGGCAAAAGA
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
92 76 0.99
93 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (92 bp):
TTTGTGATGCATAAATACCATCTAGTGGTCAGATGAAGAGGATACGATTGAGAATGTATGATCTG
GATATCCCTACCCCAAGGAAATCAGGT
Found at i:353655 original size:13 final size:13
Alignment explanation
Indices: 353637--353662 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
353627 TACACCAAGT
353637 ATGTATCGATACA
1 ATGTATCGATACA
353650 ATGTATCGATACA
1 ATGTATCGATACA
353663 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:353660 original size:32 final size:33
Alignment explanation
Indices: 353619--353682 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
353609 TAGCCAAACT
* **
353619 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
353651 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
353683 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:355918 original size:21 final size:21
Alignment explanation
Indices: 355885--355929 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
355875 TTGCAAGTTG
*
355885 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
355907 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
355927 AAA
1 AAA
355930 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:359840 original size:13 final size:13
Alignment explanation
Indices: 359822--359846 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
359812 GGAAATTCAA
359822 TGTATCGATACAT
1 TGTATCGATACAT
359835 TGTATCGATACA
1 TGTATCGATACA
359847 GGGTGATTAT
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Done.