Multiple sequence alignment - TraesCS7A01G071500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7A01G071500 chr7A 100.000 5580 0 0 1 5580 37111343 37116922 0.000000e+00 10305.0
1 TraesCS7A01G071500 chr7A 97.368 342 8 1 1 341 96084883 96084542 1.040000e-161 580.0
2 TraesCS7A01G071500 chr7A 86.126 382 37 9 4592 4968 37121687 37122057 1.130000e-106 398.0
3 TraesCS7A01G071500 chr3D 95.283 4282 138 30 912 5161 25398740 25394491 0.000000e+00 6730.0
4 TraesCS7A01G071500 chr3D 86.858 2298 264 21 2493 4761 40009627 40007339 0.000000e+00 2536.0
5 TraesCS7A01G071500 chr3D 93.692 539 29 4 340 878 25399276 25398743 0.000000e+00 802.0
6 TraesCS7A01G071500 chr3D 93.763 465 27 2 5118 5580 25394442 25393978 0.000000e+00 697.0
7 TraesCS7A01G071500 chr3D 85.855 608 69 9 955 1558 40011402 40010808 1.020000e-176 630.0
8 TraesCS7A01G071500 chr3D 82.031 128 13 7 1957 2077 40010188 40010064 3.560000e-17 100.0
9 TraesCS7A01G071500 chr3D 95.455 44 2 0 5118 5161 25394488 25394445 2.790000e-08 71.3
10 TraesCS7A01G071500 chr7D 95.209 4279 138 32 912 5161 37800337 37804577 0.000000e+00 6704.0
11 TraesCS7A01G071500 chr7D 91.887 530 26 4 340 869 37799813 37800325 0.000000e+00 725.0
12 TraesCS7A01G071500 chr7D 93.978 465 26 2 5118 5580 37804626 37805090 0.000000e+00 702.0
13 TraesCS7A01G071500 chr7D 85.714 203 28 1 4612 4813 37833969 37834171 4.380000e-51 213.0
14 TraesCS7A01G071500 chr7D 95.455 44 2 0 5118 5161 37804580 37804623 2.790000e-08 71.3
15 TraesCS7A01G071500 chr4A 96.155 3615 107 9 1977 5580 687181457 687177864 0.000000e+00 5877.0
16 TraesCS7A01G071500 chr4A 93.386 1270 71 5 667 1924 687182727 687181459 0.000000e+00 1868.0
17 TraesCS7A01G071500 chr4A 98.230 339 6 0 1 339 595382403 595382741 1.340000e-165 593.0
18 TraesCS7A01G071500 chr4A 94.424 269 12 1 340 608 687183240 687182975 1.450000e-110 411.0
19 TraesCS7A01G071500 chr4A 86.624 157 18 1 4616 4772 687154136 687153983 2.670000e-38 171.0
20 TraesCS7A01G071500 chr3B 86.664 2302 264 23 2493 4761 63410614 63408323 0.000000e+00 2510.0
21 TraesCS7A01G071500 chr3B 85.238 630 72 12 935 1558 63412219 63411605 3.670000e-176 628.0
22 TraesCS7A01G071500 chr3B 78.041 296 40 17 4990 5262 222196430 222196723 4.470000e-36 163.0
23 TraesCS7A01G071500 chr3B 77.119 236 34 15 1853 2077 63411275 63411049 9.820000e-23 119.0
24 TraesCS7A01G071500 chr3A 86.554 2298 271 21 2493 4761 51472160 51469872 0.000000e+00 2497.0
25 TraesCS7A01G071500 chr3A 85.783 626 74 7 935 1558 51473778 51473166 0.000000e+00 649.0
26 TraesCS7A01G071500 chr3A 97.345 339 7 2 3 339 626025680 626025342 4.850000e-160 575.0
27 TraesCS7A01G071500 chr2A 98.235 340 5 1 1 339 88975046 88975385 1.340000e-165 593.0
28 TraesCS7A01G071500 chr5A 97.953 342 5 2 1 340 601714420 601714079 4.810000e-165 592.0
29 TraesCS7A01G071500 chr5A 98.225 338 5 1 3 339 399457125 399457462 1.730000e-164 590.0
30 TraesCS7A01G071500 chr5A 97.935 339 5 2 4 340 590096010 590095672 2.240000e-163 586.0
31 TraesCS7A01G071500 chr2B 97.947 341 6 1 1 340 213244823 213244483 1.730000e-164 590.0
32 TraesCS7A01G071500 chr1A 97.654 341 6 2 1 339 537981507 537981847 8.060000e-163 584.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G071500 chr7A 37111343 37116922 5579 False 10305.000000 10305 100.000000 1 5580 1 chr7A.!!$F1 5579
1 TraesCS7A01G071500 chr3D 25393978 25399276 5298 True 2075.075000 6730 94.548250 340 5580 4 chr3D.!!$R1 5240
2 TraesCS7A01G071500 chr3D 40007339 40011402 4063 True 1088.666667 2536 84.914667 955 4761 3 chr3D.!!$R2 3806
3 TraesCS7A01G071500 chr7D 37799813 37805090 5277 False 2050.575000 6704 94.132250 340 5580 4 chr7D.!!$F2 5240
4 TraesCS7A01G071500 chr4A 687177864 687183240 5376 True 2718.666667 5877 94.655000 340 5580 3 chr4A.!!$R2 5240
5 TraesCS7A01G071500 chr3B 63408323 63412219 3896 True 1085.666667 2510 83.007000 935 4761 3 chr3B.!!$R1 3826
6 TraesCS7A01G071500 chr3A 51469872 51473778 3906 True 1573.000000 2497 86.168500 935 4761 2 chr3A.!!$R2 3826

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
397 398 0.825840 ATGCCCCTAGACTCGAGAGC 60.826 60.0 21.68 10.7 0.00 4.09 F
1619 1835 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.0 0.00 0.0 0.00 3.82 F
2962 3602 0.451383 CCATCGCGAAAGGATTTGCA 59.549 50.0 22.31 0.0 44.81 4.08 F
3262 3902 1.094785 CCTATTCACAGGTTTGGCGG 58.905 55.0 0.00 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2227 2854 0.179156 GGCACGCAATCAGAACATGG 60.179 55.000 0.00 0.0 0.00 3.66 R
3181 3821 0.674581 CCTTCGGCTTGAGTGATGCA 60.675 55.000 0.00 0.0 0.00 3.96 R
3811 4451 1.082117 CGGCCGCACGAGTAAAATCT 61.082 55.000 14.67 0.0 35.47 2.40 R
5108 5813 1.152777 CCAAGTGAACCTGCACCCA 60.153 57.895 0.00 0.0 39.59 4.51 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 9.444600 AAACTTATATGTATTCCACAAGAACGT 57.555 29.630 0.00 0.00 41.55 3.99
69 70 8.420374 ACTTATATGTATTCCACAAGAACGTG 57.580 34.615 0.00 0.00 41.55 4.49
70 71 8.255206 ACTTATATGTATTCCACAAGAACGTGA 58.745 33.333 0.00 0.00 41.55 4.35
71 72 9.261180 CTTATATGTATTCCACAAGAACGTGAT 57.739 33.333 0.00 0.00 41.55 3.06
74 75 7.915293 ATGTATTCCACAAGAACGTGATAAA 57.085 32.000 0.00 0.00 41.55 1.40
75 76 7.915293 TGTATTCCACAAGAACGTGATAAAT 57.085 32.000 0.00 0.00 39.34 1.40
76 77 8.330466 TGTATTCCACAAGAACGTGATAAATT 57.670 30.769 0.00 0.00 39.34 1.82
77 78 8.788806 TGTATTCCACAAGAACGTGATAAATTT 58.211 29.630 0.00 0.00 39.34 1.82
78 79 9.274065 GTATTCCACAAGAACGTGATAAATTTC 57.726 33.333 0.00 0.00 39.34 2.17
79 80 5.922546 TCCACAAGAACGTGATAAATTTCG 58.077 37.500 0.00 0.00 39.34 3.46
80 81 5.467399 TCCACAAGAACGTGATAAATTTCGT 59.533 36.000 0.00 0.00 39.34 3.85
81 82 5.788531 CCACAAGAACGTGATAAATTTCGTC 59.211 40.000 0.00 0.00 39.34 4.20
82 83 5.499955 CACAAGAACGTGATAAATTTCGTCG 59.500 40.000 0.00 0.00 39.34 5.12
83 84 5.403166 ACAAGAACGTGATAAATTTCGTCGA 59.597 36.000 0.00 0.00 35.49 4.20
84 85 6.074195 ACAAGAACGTGATAAATTTCGTCGAA 60.074 34.615 2.90 2.90 35.49 3.71
85 86 6.456447 AGAACGTGATAAATTTCGTCGAAA 57.544 33.333 21.74 21.74 35.94 3.46
86 87 6.879962 AGAACGTGATAAATTTCGTCGAAAA 58.120 32.000 23.11 8.64 35.11 2.29
87 88 7.346695 AGAACGTGATAAATTTCGTCGAAAAA 58.653 30.769 23.11 12.66 35.11 1.94
88 89 8.013378 AGAACGTGATAAATTTCGTCGAAAAAT 58.987 29.630 23.11 16.33 35.11 1.82
89 90 7.473691 ACGTGATAAATTTCGTCGAAAAATG 57.526 32.000 23.11 12.34 35.11 2.32
90 91 7.073265 ACGTGATAAATTTCGTCGAAAAATGT 58.927 30.769 23.11 13.33 35.11 2.71
91 92 7.588488 ACGTGATAAATTTCGTCGAAAAATGTT 59.412 29.630 23.11 16.17 35.11 2.71
92 93 7.880757 CGTGATAAATTTCGTCGAAAAATGTTG 59.119 33.333 23.11 7.05 35.11 3.33
93 94 8.687301 GTGATAAATTTCGTCGAAAAATGTTGT 58.313 29.630 23.11 13.08 35.11 3.32
94 95 8.686418 TGATAAATTTCGTCGAAAAATGTTGTG 58.314 29.630 23.11 0.00 35.11 3.33
95 96 8.789881 ATAAATTTCGTCGAAAAATGTTGTGA 57.210 26.923 23.11 4.65 35.11 3.58
96 97 7.692908 AAATTTCGTCGAAAAATGTTGTGAT 57.307 28.000 23.11 1.18 35.11 3.06
97 98 7.692908 AATTTCGTCGAAAAATGTTGTGATT 57.307 28.000 23.11 7.19 35.11 2.57
98 99 7.692908 ATTTCGTCGAAAAATGTTGTGATTT 57.307 28.000 23.11 0.47 35.11 2.17
99 100 6.489469 TTCGTCGAAAAATGTTGTGATTTG 57.511 33.333 4.91 0.00 0.00 2.32
100 101 5.574082 TCGTCGAAAAATGTTGTGATTTGT 58.426 33.333 0.00 0.00 0.00 2.83
101 102 6.716438 TCGTCGAAAAATGTTGTGATTTGTA 58.284 32.000 0.00 0.00 0.00 2.41
102 103 6.848800 TCGTCGAAAAATGTTGTGATTTGTAG 59.151 34.615 0.00 0.00 0.00 2.74
103 104 6.086241 CGTCGAAAAATGTTGTGATTTGTAGG 59.914 38.462 0.00 0.00 0.00 3.18
104 105 5.918011 TCGAAAAATGTTGTGATTTGTAGGC 59.082 36.000 0.00 0.00 0.00 3.93
105 106 5.920273 CGAAAAATGTTGTGATTTGTAGGCT 59.080 36.000 0.00 0.00 0.00 4.58
106 107 6.129115 CGAAAAATGTTGTGATTTGTAGGCTG 60.129 38.462 0.00 0.00 0.00 4.85
107 108 5.789643 AAATGTTGTGATTTGTAGGCTGT 57.210 34.783 0.00 0.00 0.00 4.40
108 109 6.892658 AAATGTTGTGATTTGTAGGCTGTA 57.107 33.333 0.00 0.00 0.00 2.74
109 110 5.880054 ATGTTGTGATTTGTAGGCTGTAC 57.120 39.130 0.00 0.00 0.00 2.90
110 111 4.709250 TGTTGTGATTTGTAGGCTGTACA 58.291 39.130 0.00 0.00 0.00 2.90
111 112 5.126779 TGTTGTGATTTGTAGGCTGTACAA 58.873 37.500 0.00 0.00 35.84 2.41
113 114 6.095580 TGTTGTGATTTGTAGGCTGTACAAAA 59.904 34.615 21.14 9.41 46.38 2.44
114 115 6.701145 TGTGATTTGTAGGCTGTACAAAAA 57.299 33.333 21.14 13.64 46.38 1.94
115 116 7.283625 TGTGATTTGTAGGCTGTACAAAAAT 57.716 32.000 21.14 11.24 46.38 1.82
116 117 8.397575 TGTGATTTGTAGGCTGTACAAAAATA 57.602 30.769 21.14 12.47 46.38 1.40
117 118 8.851145 TGTGATTTGTAGGCTGTACAAAAATAA 58.149 29.630 21.14 10.52 46.38 1.40
118 119 9.124807 GTGATTTGTAGGCTGTACAAAAATAAC 57.875 33.333 21.14 15.13 46.38 1.89
119 120 8.851145 TGATTTGTAGGCTGTACAAAAATAACA 58.149 29.630 21.14 15.20 46.38 2.41
120 121 9.685828 GATTTGTAGGCTGTACAAAAATAACAA 57.314 29.630 21.14 3.75 46.38 2.83
127 128 9.260002 AGGCTGTACAAAAATAACAAATTTCTG 57.740 29.630 0.00 0.00 0.00 3.02
128 129 8.495148 GGCTGTACAAAAATAACAAATTTCTGG 58.505 33.333 0.00 0.00 0.00 3.86
129 130 8.009409 GCTGTACAAAAATAACAAATTTCTGGC 58.991 33.333 0.00 0.00 0.00 4.85
130 131 8.371770 TGTACAAAAATAACAAATTTCTGGCC 57.628 30.769 0.00 0.00 0.00 5.36
131 132 6.875948 ACAAAAATAACAAATTTCTGGCCC 57.124 33.333 0.00 0.00 0.00 5.80
132 133 6.360618 ACAAAAATAACAAATTTCTGGCCCA 58.639 32.000 0.00 0.00 0.00 5.36
133 134 6.830838 ACAAAAATAACAAATTTCTGGCCCAA 59.169 30.769 0.00 0.00 0.00 4.12
134 135 7.505248 ACAAAAATAACAAATTTCTGGCCCAAT 59.495 29.630 0.00 0.00 0.00 3.16
135 136 9.007901 CAAAAATAACAAATTTCTGGCCCAATA 57.992 29.630 0.00 0.00 0.00 1.90
136 137 9.579932 AAAAATAACAAATTTCTGGCCCAATAA 57.420 25.926 0.00 0.00 0.00 1.40
137 138 8.560355 AAATAACAAATTTCTGGCCCAATAAC 57.440 30.769 0.00 0.00 0.00 1.89
138 139 5.559148 AACAAATTTCTGGCCCAATAACA 57.441 34.783 0.00 0.00 0.00 2.41
139 140 5.559148 ACAAATTTCTGGCCCAATAACAA 57.441 34.783 0.00 0.00 0.00 2.83
140 141 5.934781 ACAAATTTCTGGCCCAATAACAAA 58.065 33.333 0.00 0.00 0.00 2.83
141 142 6.360618 ACAAATTTCTGGCCCAATAACAAAA 58.639 32.000 0.00 0.00 0.00 2.44
142 143 6.830838 ACAAATTTCTGGCCCAATAACAAAAA 59.169 30.769 0.00 0.00 0.00 1.94
143 144 7.505248 ACAAATTTCTGGCCCAATAACAAAAAT 59.495 29.630 0.00 0.00 0.00 1.82
144 145 9.007901 CAAATTTCTGGCCCAATAACAAAAATA 57.992 29.630 0.00 0.00 0.00 1.40
145 146 9.579932 AAATTTCTGGCCCAATAACAAAAATAA 57.420 25.926 0.00 0.00 0.00 1.40
146 147 9.579932 AATTTCTGGCCCAATAACAAAAATAAA 57.420 25.926 0.00 0.00 0.00 1.40
147 148 8.980481 TTTCTGGCCCAATAACAAAAATAAAA 57.020 26.923 0.00 0.00 0.00 1.52
148 149 8.614469 TTCTGGCCCAATAACAAAAATAAAAG 57.386 30.769 0.00 0.00 0.00 2.27
149 150 7.164803 TCTGGCCCAATAACAAAAATAAAAGG 58.835 34.615 0.00 0.00 0.00 3.11
150 151 5.707764 TGGCCCAATAACAAAAATAAAAGGC 59.292 36.000 0.00 0.00 34.75 4.35
151 152 6.189677 GCCCAATAACAAAAATAAAAGGCC 57.810 37.500 0.00 0.00 0.00 5.19
152 153 5.124776 GCCCAATAACAAAAATAAAAGGCCC 59.875 40.000 0.00 0.00 0.00 5.80
153 154 6.241645 CCCAATAACAAAAATAAAAGGCCCA 58.758 36.000 0.00 0.00 0.00 5.36
154 155 6.889177 CCCAATAACAAAAATAAAAGGCCCAT 59.111 34.615 0.00 0.00 0.00 4.00
155 156 7.395772 CCCAATAACAAAAATAAAAGGCCCATT 59.604 33.333 0.00 0.00 0.00 3.16
156 157 9.454859 CCAATAACAAAAATAAAAGGCCCATTA 57.545 29.630 0.00 0.00 0.00 1.90
165 166 8.932434 AAATAAAAGGCCCATTAAAAATGTGT 57.068 26.923 0.00 0.00 0.00 3.72
169 170 8.932434 AAAAGGCCCATTAAAAATGTGTATTT 57.068 26.923 0.00 0.00 38.11 1.40
170 171 7.920160 AAGGCCCATTAAAAATGTGTATTTG 57.080 32.000 0.00 0.00 36.65 2.32
171 172 7.014988 AGGCCCATTAAAAATGTGTATTTGT 57.985 32.000 0.00 0.00 36.65 2.83
172 173 7.102993 AGGCCCATTAAAAATGTGTATTTGTC 58.897 34.615 0.00 0.00 36.65 3.18
173 174 7.038373 AGGCCCATTAAAAATGTGTATTTGTCT 60.038 33.333 0.00 0.00 36.65 3.41
174 175 7.606073 GGCCCATTAAAAATGTGTATTTGTCTT 59.394 33.333 0.00 0.00 36.65 3.01
175 176 8.998377 GCCCATTAAAAATGTGTATTTGTCTTT 58.002 29.630 0.00 0.00 36.65 2.52
182 183 9.665719 AAAAATGTGTATTTGTCTTTTTCCTGT 57.334 25.926 0.00 0.00 36.65 4.00
184 185 9.965824 AAATGTGTATTTGTCTTTTTCCTGTAG 57.034 29.630 0.00 0.00 35.26 2.74
185 186 7.504924 TGTGTATTTGTCTTTTTCCTGTAGG 57.495 36.000 0.00 0.00 0.00 3.18
186 187 6.016610 TGTGTATTTGTCTTTTTCCTGTAGGC 60.017 38.462 0.00 0.00 34.44 3.93
187 188 5.475564 TGTATTTGTCTTTTTCCTGTAGGCC 59.524 40.000 0.00 0.00 34.44 5.19
188 189 3.586470 TTGTCTTTTTCCTGTAGGCCA 57.414 42.857 5.01 0.00 34.44 5.36
189 190 2.858745 TGTCTTTTTCCTGTAGGCCAC 58.141 47.619 5.01 1.31 34.44 5.01
190 191 2.173782 TGTCTTTTTCCTGTAGGCCACA 59.826 45.455 5.01 6.68 35.30 4.17
191 192 3.181434 TGTCTTTTTCCTGTAGGCCACAT 60.181 43.478 5.01 0.00 36.29 3.21
192 193 3.191371 GTCTTTTTCCTGTAGGCCACATG 59.809 47.826 5.01 4.92 36.29 3.21
193 194 2.969821 TTTTCCTGTAGGCCACATGT 57.030 45.000 5.01 0.00 36.29 3.21
194 195 4.042311 TCTTTTTCCTGTAGGCCACATGTA 59.958 41.667 5.01 0.00 36.29 2.29
195 196 4.374689 TTTTCCTGTAGGCCACATGTAA 57.625 40.909 5.01 2.38 36.29 2.41
196 197 4.374689 TTTCCTGTAGGCCACATGTAAA 57.625 40.909 5.01 5.80 36.29 2.01
197 198 3.343941 TCCTGTAGGCCACATGTAAAC 57.656 47.619 5.01 0.00 36.29 2.01
198 199 2.006888 CCTGTAGGCCACATGTAAACG 58.993 52.381 5.01 0.00 36.29 3.60
199 200 2.614481 CCTGTAGGCCACATGTAAACGT 60.614 50.000 5.01 0.00 36.29 3.99
200 201 3.368635 CCTGTAGGCCACATGTAAACGTA 60.369 47.826 5.01 0.00 36.29 3.57
201 202 4.439057 CTGTAGGCCACATGTAAACGTAT 58.561 43.478 5.01 0.00 36.29 3.06
202 203 5.452216 CCTGTAGGCCACATGTAAACGTATA 60.452 44.000 5.01 0.00 36.29 1.47
203 204 5.975282 TGTAGGCCACATGTAAACGTATAA 58.025 37.500 5.01 0.00 30.04 0.98
204 205 6.584488 TGTAGGCCACATGTAAACGTATAAT 58.416 36.000 5.01 0.00 30.04 1.28
205 206 7.724287 TGTAGGCCACATGTAAACGTATAATA 58.276 34.615 5.01 0.00 30.04 0.98
206 207 7.652909 TGTAGGCCACATGTAAACGTATAATAC 59.347 37.037 5.01 0.00 30.04 1.89
207 208 6.823497 AGGCCACATGTAAACGTATAATACT 58.177 36.000 5.01 0.00 0.00 2.12
208 209 6.704493 AGGCCACATGTAAACGTATAATACTG 59.296 38.462 5.01 0.00 0.00 2.74
209 210 6.480981 GGCCACATGTAAACGTATAATACTGT 59.519 38.462 0.00 0.00 0.00 3.55
210 211 7.342194 GCCACATGTAAACGTATAATACTGTG 58.658 38.462 0.00 15.91 33.46 3.66
211 212 7.223193 GCCACATGTAAACGTATAATACTGTGA 59.777 37.037 19.73 1.38 34.40 3.58
212 213 9.089601 CCACATGTAAACGTATAATACTGTGAA 57.910 33.333 19.73 1.15 34.40 3.18
220 221 9.900710 AAACGTATAATACTGTGAAATTTTGCA 57.099 25.926 0.00 0.00 0.00 4.08
241 242 9.717942 TTTGCATATACATAGTATACATGTGCA 57.282 29.630 21.34 18.72 37.22 4.57
242 243 9.889128 TTGCATATACATAGTATACATGTGCAT 57.111 29.630 18.65 12.92 37.22 3.96
243 244 9.316730 TGCATATACATAGTATACATGTGCATG 57.683 33.333 21.34 21.28 44.15 4.06
293 294 8.480643 TTTTTCGTGCTCCAGAAAAATAAAAA 57.519 26.923 10.76 0.00 45.59 1.94
312 313 3.904136 AAATGAAAACGAGCTCACTGG 57.096 42.857 15.40 0.00 0.00 4.00
313 314 2.839486 ATGAAAACGAGCTCACTGGA 57.161 45.000 15.40 0.00 0.00 3.86
314 315 2.154854 TGAAAACGAGCTCACTGGAG 57.845 50.000 15.40 0.00 44.33 3.86
322 323 3.073735 CTCACTGGAGCTCGGCCT 61.074 66.667 7.83 0.00 33.67 5.19
323 324 3.071206 TCACTGGAGCTCGGCCTC 61.071 66.667 7.83 0.00 0.00 4.70
338 339 2.024918 CCTCCGATGGCATTTTCCG 58.975 57.895 0.00 0.00 0.00 4.30
358 359 2.112815 GGGGTGCGCAGGTTATGTC 61.113 63.158 12.22 0.00 0.00 3.06
366 367 3.202906 GCGCAGGTTATGTCTCCAATTA 58.797 45.455 0.30 0.00 0.00 1.40
367 368 3.248602 GCGCAGGTTATGTCTCCAATTAG 59.751 47.826 0.30 0.00 0.00 1.73
368 369 4.442706 CGCAGGTTATGTCTCCAATTAGT 58.557 43.478 0.00 0.00 0.00 2.24
397 398 0.825840 ATGCCCCTAGACTCGAGAGC 60.826 60.000 21.68 10.70 0.00 4.09
423 424 1.367840 GGAACGTCTGCCACTGAGT 59.632 57.895 0.00 0.00 0.00 3.41
574 576 4.087892 GCCAGCTGCCTCTCCGAA 62.088 66.667 8.66 0.00 0.00 4.30
762 960 4.517952 TGCCAACTTGTCATACAATTGG 57.482 40.909 10.83 19.03 37.48 3.16
769 967 8.303156 CCAACTTGTCATACAATTGGTGAATTA 58.697 33.333 10.83 2.07 37.48 1.40
853 1051 1.000938 CTTGGAGCCTCTTGTTTGCAC 60.001 52.381 0.00 0.00 0.00 4.57
862 1060 5.244626 AGCCTCTTGTTTGCACAATTATTCT 59.755 36.000 0.00 0.00 42.21 2.40
869 1067 9.844790 CTTGTTTGCACAATTATTCTATGAAGA 57.155 29.630 0.00 0.00 42.21 2.87
893 1091 9.950496 AGAGAAAATGAATTATATATGCGGAGT 57.050 29.630 0.00 0.00 0.00 3.85
910 1108 4.037565 GCGGAGTTAAATATTTGAAGGGGG 59.962 45.833 11.05 0.00 0.00 5.40
1133 1343 1.918253 GGGAGATGCCACTGGACAT 59.082 57.895 0.00 1.94 38.95 3.06
1324 1534 4.076175 AGTACAGGGGAGAACAGGTATT 57.924 45.455 0.00 0.00 0.00 1.89
1329 1539 4.019231 ACAGGGGAGAACAGGTATTTCTTC 60.019 45.833 0.00 0.00 33.30 2.87
1384 1594 7.609097 TCATCTAGAAGAGCCAATATCAAGT 57.391 36.000 0.00 0.00 0.00 3.16
1464 1678 4.074970 CACTGGAGCTTCCACTGTTAAAT 58.925 43.478 1.25 0.00 42.67 1.40
1530 1744 4.537015 CAAAAACAAGTAGGTGCTACTGC 58.463 43.478 0.00 0.00 45.28 4.40
1597 1813 7.010830 CACATTATACTCAATGGTCTCTGTGTG 59.989 40.741 1.36 0.00 39.71 3.82
1619 1835 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1648 1864 7.611855 CAGGGTATCCAAAAGTAACAAGAAGAT 59.388 37.037 0.00 0.00 34.83 2.40
1649 1865 8.170730 AGGGTATCCAAAAGTAACAAGAAGATT 58.829 33.333 0.00 0.00 34.83 2.40
1660 1876 8.635765 AGTAACAAGAAGATTCCAAATGCTAA 57.364 30.769 0.00 0.00 0.00 3.09
1710 1989 2.559698 TTTCAATCAGCCAAGACCGA 57.440 45.000 0.00 0.00 0.00 4.69
1861 2154 8.670521 ACAGGAAATTCAGAATCCCTATTTTT 57.329 30.769 13.79 0.00 33.55 1.94
1887 2183 6.506500 AATGTAGCCTTTCTTCAGTCAATG 57.493 37.500 0.00 0.00 0.00 2.82
1925 2221 1.818642 AGAGGTGCAGATTGTCAAGC 58.181 50.000 0.00 0.00 0.00 4.01
1985 2464 4.624125 GCTGGAGTATTTAGTTCTGCCACT 60.624 45.833 0.00 0.00 0.00 4.00
2080 2564 9.961265 ATAGCATCATTTTGTCTATGAAACATG 57.039 29.630 0.00 0.00 35.77 3.21
2106 2650 9.593134 GTCATATCTTCACTAATTTCTGTCTGT 57.407 33.333 0.00 0.00 0.00 3.41
2129 2754 5.129320 GTCCCTTCCTTTCAATTATGGCAAT 59.871 40.000 0.00 0.00 0.00 3.56
2137 2762 8.266473 TCCTTTCAATTATGGCAATTGCTAATT 58.734 29.630 28.42 24.89 41.70 1.40
2201 2828 1.002792 GTTTCCCGTGACACTTTCTGC 60.003 52.381 3.68 0.00 0.00 4.26
2227 2854 7.429340 CAGTTCGCATAGTTATTTGAATGGTTC 59.571 37.037 0.00 0.00 0.00 3.62
2352 2981 9.981114 CAGATTTGTTTTTATGAACCCTACTTT 57.019 29.630 0.00 0.00 0.00 2.66
2403 3034 7.455953 TGTTAGTTCATCATAGATAGATGCCCT 59.544 37.037 0.00 0.00 41.98 5.19
2408 3039 7.180322 TCATCATAGATAGATGCCCTTCTTC 57.820 40.000 0.00 0.00 41.98 2.87
2426 3057 3.449377 TCTTCCAGCCACATGATTACGTA 59.551 43.478 0.00 0.00 0.00 3.57
2479 3110 7.601130 TGCACGATTACTTTACTTGTAGATTGT 59.399 33.333 0.00 0.00 0.00 2.71
2480 3111 9.079833 GCACGATTACTTTACTTGTAGATTGTA 57.920 33.333 0.00 0.00 0.00 2.41
2579 3214 6.857437 AGGGATTTTCAACTAGAATTTGGG 57.143 37.500 0.00 0.00 35.83 4.12
2589 3224 4.839121 ACTAGAATTTGGGCGTGATGTTA 58.161 39.130 0.00 0.00 0.00 2.41
2821 3461 5.682234 ATGCATATGATGGTTCGGAGATA 57.318 39.130 6.97 0.00 35.04 1.98
2962 3602 0.451383 CCATCGCGAAAGGATTTGCA 59.549 50.000 22.31 0.00 44.81 4.08
3181 3821 2.550830 AGGAGAAACTGCGTGTGAAT 57.449 45.000 0.00 0.00 0.00 2.57
3262 3902 1.094785 CCTATTCACAGGTTTGGCGG 58.905 55.000 0.00 0.00 0.00 6.13
3487 4127 2.034221 AAGGTTCCGCTCAAGGCC 59.966 61.111 0.00 0.00 37.74 5.19
3719 4359 4.456911 CACATGTGTTTGAAGATAGCCACT 59.543 41.667 18.03 0.00 0.00 4.00
3811 4451 3.570125 AGATAAGAGATGCGATGGTCGAA 59.430 43.478 3.20 0.00 43.74 3.71
3949 4589 1.078759 GGTCAGATGCCGTCTTCACG 61.079 60.000 0.00 0.00 46.29 4.35
4213 4858 2.193536 GTTTGAAGTGCGGGGCAGT 61.194 57.895 0.00 0.00 44.78 4.40
4351 4996 7.715657 TCTACGACTACTGTTCCAAGTTTTTA 58.284 34.615 0.00 0.00 0.00 1.52
4429 5074 6.096846 ACATGGATACCTTTGATTTTAGTGCC 59.903 38.462 0.00 0.00 0.00 5.01
4474 5119 2.355197 CCACGCACATCAGATAAACCA 58.645 47.619 0.00 0.00 0.00 3.67
4488 5133 8.202461 TCAGATAAACCAAGAAGAAAGAGGTA 57.798 34.615 0.00 0.00 31.10 3.08
4543 5188 2.898933 TAGCAGGTGCAAGCAGGCT 61.899 57.895 16.51 16.51 46.35 4.58
4791 5454 3.866883 ATTGTAATGAAACAAGCCCCG 57.133 42.857 0.00 0.00 42.33 5.73
4831 5494 0.249120 TGGATAGTTGAGGGTGCACG 59.751 55.000 11.45 0.00 0.00 5.34
4871 5534 6.156775 TGGAGTTCAGGATATGATTTGACTCA 59.843 38.462 8.75 0.00 41.12 3.41
5108 5813 7.095816 GCTTGGCTAATCAAACAACGTTTTTAT 60.096 33.333 0.00 0.00 0.00 1.40
5163 5960 4.020218 TGAAAGAGAGTTCATGGTAGTGGG 60.020 45.833 0.00 0.00 32.56 4.61
5164 5961 1.834263 AGAGAGTTCATGGTAGTGGGC 59.166 52.381 0.00 0.00 0.00 5.36
5172 5969 2.965831 TCATGGTAGTGGGCTCTGTATC 59.034 50.000 0.00 0.00 0.00 2.24
5177 5974 4.106502 TGGTAGTGGGCTCTGTATCTAGAT 59.893 45.833 10.73 10.73 0.00 1.98
5252 6050 5.306160 AGGGTGTAACTTAAGTTCTGTAGCA 59.694 40.000 23.76 11.48 39.31 3.49
5281 6079 3.439154 AGAGATGATGATCCGGTGCTAT 58.561 45.455 0.00 0.00 0.00 2.97
5297 6095 2.164422 TGCTATCTTCTGGACAGTGTCG 59.836 50.000 16.89 4.56 32.65 4.35
5449 6247 2.315925 TAGCAGCTGTCTATTGTGGC 57.684 50.000 16.64 0.00 0.00 5.01
5461 6259 2.610438 ATTGTGGCCAGGATCACTTT 57.390 45.000 5.11 0.00 35.15 2.66
5513 6312 3.969287 TCTGCTGGGATCATGTATAGC 57.031 47.619 0.00 0.00 0.00 2.97
5540 6339 9.624373 AGATAATAATGATTCTGTGAGCACTTT 57.376 29.630 1.99 0.00 0.00 2.66
5560 6359 9.277783 GCACTTTGGAAGTATATACATTCTCAT 57.722 33.333 15.18 0.00 40.46 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 9.444600 ACGTTCTTGTGGAATACATATAAGTTT 57.555 29.630 0.00 0.00 39.48 2.66
43 44 8.879759 CACGTTCTTGTGGAATACATATAAGTT 58.120 33.333 0.00 0.00 39.48 2.66
44 45 8.255206 TCACGTTCTTGTGGAATACATATAAGT 58.745 33.333 0.00 0.00 39.48 2.24
45 46 8.642908 TCACGTTCTTGTGGAATACATATAAG 57.357 34.615 0.00 0.00 39.48 1.73
48 49 9.607988 TTTATCACGTTCTTGTGGAATACATAT 57.392 29.630 0.00 0.00 39.48 1.78
49 50 9.607988 ATTTATCACGTTCTTGTGGAATACATA 57.392 29.630 0.00 0.00 39.48 2.29
50 51 7.915293 TTTATCACGTTCTTGTGGAATACAT 57.085 32.000 0.00 0.00 39.48 2.29
51 52 7.915293 ATTTATCACGTTCTTGTGGAATACA 57.085 32.000 0.00 0.00 40.31 2.29
52 53 9.274065 GAAATTTATCACGTTCTTGTGGAATAC 57.726 33.333 0.00 0.00 40.31 1.89
53 54 8.172484 CGAAATTTATCACGTTCTTGTGGAATA 58.828 33.333 0.00 0.00 40.31 1.75
54 55 7.021196 CGAAATTTATCACGTTCTTGTGGAAT 58.979 34.615 0.00 0.00 40.31 3.01
55 56 6.017770 ACGAAATTTATCACGTTCTTGTGGAA 60.018 34.615 0.00 0.00 40.31 3.53
56 57 5.467399 ACGAAATTTATCACGTTCTTGTGGA 59.533 36.000 0.00 0.00 40.31 4.02
57 58 5.685841 ACGAAATTTATCACGTTCTTGTGG 58.314 37.500 0.00 0.00 40.31 4.17
58 59 5.499955 CGACGAAATTTATCACGTTCTTGTG 59.500 40.000 4.42 0.00 39.04 3.33
59 60 5.403166 TCGACGAAATTTATCACGTTCTTGT 59.597 36.000 0.00 0.00 39.04 3.16
60 61 5.839188 TCGACGAAATTTATCACGTTCTTG 58.161 37.500 0.00 0.00 39.04 3.02
61 62 6.456447 TTCGACGAAATTTATCACGTTCTT 57.544 33.333 8.05 0.00 39.04 2.52
62 63 6.456447 TTTCGACGAAATTTATCACGTTCT 57.544 33.333 18.66 0.00 39.04 3.01
63 64 7.523889 TTTTTCGACGAAATTTATCACGTTC 57.476 32.000 22.62 0.00 39.04 3.95
64 65 7.588488 ACATTTTTCGACGAAATTTATCACGTT 59.412 29.630 22.62 0.00 39.04 3.99
65 66 7.073265 ACATTTTTCGACGAAATTTATCACGT 58.927 30.769 22.62 9.49 41.57 4.49
66 67 7.473691 ACATTTTTCGACGAAATTTATCACG 57.526 32.000 22.62 8.95 31.34 4.35
67 68 8.687301 ACAACATTTTTCGACGAAATTTATCAC 58.313 29.630 22.62 0.00 31.34 3.06
68 69 8.686418 CACAACATTTTTCGACGAAATTTATCA 58.314 29.630 22.62 5.01 31.34 2.15
69 70 8.897809 TCACAACATTTTTCGACGAAATTTATC 58.102 29.630 22.62 0.00 31.34 1.75
70 71 8.789881 TCACAACATTTTTCGACGAAATTTAT 57.210 26.923 22.62 13.70 31.34 1.40
71 72 8.789881 ATCACAACATTTTTCGACGAAATTTA 57.210 26.923 22.62 12.16 31.34 1.40
72 73 7.692908 ATCACAACATTTTTCGACGAAATTT 57.307 28.000 22.62 11.08 31.34 1.82
73 74 7.692908 AATCACAACATTTTTCGACGAAATT 57.307 28.000 22.62 11.77 31.34 1.82
74 75 7.221838 ACAAATCACAACATTTTTCGACGAAAT 59.778 29.630 22.62 7.21 31.34 2.17
75 76 6.528423 ACAAATCACAACATTTTTCGACGAAA 59.472 30.769 18.66 18.66 0.00 3.46
76 77 6.030849 ACAAATCACAACATTTTTCGACGAA 58.969 32.000 6.10 6.10 0.00 3.85
77 78 5.574082 ACAAATCACAACATTTTTCGACGA 58.426 33.333 0.00 0.00 0.00 4.20
78 79 5.864830 ACAAATCACAACATTTTTCGACG 57.135 34.783 0.00 0.00 0.00 5.12
79 80 6.129194 GCCTACAAATCACAACATTTTTCGAC 60.129 38.462 0.00 0.00 0.00 4.20
80 81 5.918011 GCCTACAAATCACAACATTTTTCGA 59.082 36.000 0.00 0.00 0.00 3.71
81 82 5.920273 AGCCTACAAATCACAACATTTTTCG 59.080 36.000 0.00 0.00 0.00 3.46
82 83 6.701400 ACAGCCTACAAATCACAACATTTTTC 59.299 34.615 0.00 0.00 0.00 2.29
83 84 6.581712 ACAGCCTACAAATCACAACATTTTT 58.418 32.000 0.00 0.00 0.00 1.94
84 85 6.160576 ACAGCCTACAAATCACAACATTTT 57.839 33.333 0.00 0.00 0.00 1.82
85 86 5.789643 ACAGCCTACAAATCACAACATTT 57.210 34.783 0.00 0.00 0.00 2.32
86 87 5.767665 TGTACAGCCTACAAATCACAACATT 59.232 36.000 0.00 0.00 0.00 2.71
87 88 5.312895 TGTACAGCCTACAAATCACAACAT 58.687 37.500 0.00 0.00 0.00 2.71
88 89 4.709250 TGTACAGCCTACAAATCACAACA 58.291 39.130 0.00 0.00 0.00 3.33
89 90 5.682943 TTGTACAGCCTACAAATCACAAC 57.317 39.130 0.00 0.00 34.84 3.32
90 91 6.701145 TTTTGTACAGCCTACAAATCACAA 57.299 33.333 14.83 1.77 44.00 3.33
91 92 6.701145 TTTTTGTACAGCCTACAAATCACA 57.299 33.333 14.83 2.05 44.00 3.58
92 93 9.124807 GTTATTTTTGTACAGCCTACAAATCAC 57.875 33.333 14.83 8.22 44.00 3.06
93 94 8.851145 TGTTATTTTTGTACAGCCTACAAATCA 58.149 29.630 14.83 8.09 44.00 2.57
94 95 9.685828 TTGTTATTTTTGTACAGCCTACAAATC 57.314 29.630 14.83 7.29 44.00 2.17
101 102 9.260002 CAGAAATTTGTTATTTTTGTACAGCCT 57.740 29.630 0.00 0.00 0.00 4.58
102 103 8.495148 CCAGAAATTTGTTATTTTTGTACAGCC 58.505 33.333 0.00 0.00 0.00 4.85
103 104 8.009409 GCCAGAAATTTGTTATTTTTGTACAGC 58.991 33.333 0.00 0.00 0.00 4.40
104 105 8.495148 GGCCAGAAATTTGTTATTTTTGTACAG 58.505 33.333 0.00 0.00 0.00 2.74
105 106 7.442666 GGGCCAGAAATTTGTTATTTTTGTACA 59.557 33.333 4.39 0.00 0.00 2.90
106 107 7.442666 TGGGCCAGAAATTTGTTATTTTTGTAC 59.557 33.333 0.00 0.00 0.00 2.90
107 108 7.509546 TGGGCCAGAAATTTGTTATTTTTGTA 58.490 30.769 0.00 0.00 0.00 2.41
108 109 6.360618 TGGGCCAGAAATTTGTTATTTTTGT 58.639 32.000 0.00 0.00 0.00 2.83
109 110 6.874288 TGGGCCAGAAATTTGTTATTTTTG 57.126 33.333 0.00 0.00 0.00 2.44
110 111 9.579932 TTATTGGGCCAGAAATTTGTTATTTTT 57.420 25.926 6.23 0.00 0.00 1.94
111 112 9.008965 GTTATTGGGCCAGAAATTTGTTATTTT 57.991 29.630 6.23 0.00 0.00 1.82
112 113 8.160106 TGTTATTGGGCCAGAAATTTGTTATTT 58.840 29.630 6.23 0.00 0.00 1.40
113 114 7.684529 TGTTATTGGGCCAGAAATTTGTTATT 58.315 30.769 6.23 0.00 0.00 1.40
114 115 7.251321 TGTTATTGGGCCAGAAATTTGTTAT 57.749 32.000 6.23 0.00 0.00 1.89
115 116 6.672266 TGTTATTGGGCCAGAAATTTGTTA 57.328 33.333 6.23 0.00 0.00 2.41
116 117 5.559148 TGTTATTGGGCCAGAAATTTGTT 57.441 34.783 6.23 0.00 0.00 2.83
117 118 5.559148 TTGTTATTGGGCCAGAAATTTGT 57.441 34.783 6.23 0.00 0.00 2.83
118 119 6.874288 TTTTGTTATTGGGCCAGAAATTTG 57.126 33.333 6.23 0.00 0.00 2.32
119 120 9.579932 TTATTTTTGTTATTGGGCCAGAAATTT 57.420 25.926 6.23 0.00 29.23 1.82
120 121 9.579932 TTTATTTTTGTTATTGGGCCAGAAATT 57.420 25.926 6.23 2.65 29.23 1.82
121 122 9.579932 TTTTATTTTTGTTATTGGGCCAGAAAT 57.420 25.926 6.23 0.00 30.78 2.17
122 123 8.980481 TTTTATTTTTGTTATTGGGCCAGAAA 57.020 26.923 6.23 1.95 0.00 2.52
123 124 7.663493 CCTTTTATTTTTGTTATTGGGCCAGAA 59.337 33.333 6.23 2.09 0.00 3.02
124 125 7.164803 CCTTTTATTTTTGTTATTGGGCCAGA 58.835 34.615 6.23 0.00 0.00 3.86
125 126 6.128035 GCCTTTTATTTTTGTTATTGGGCCAG 60.128 38.462 6.23 0.00 0.00 4.85
126 127 5.707764 GCCTTTTATTTTTGTTATTGGGCCA 59.292 36.000 0.00 0.00 0.00 5.36
127 128 5.124776 GGCCTTTTATTTTTGTTATTGGGCC 59.875 40.000 0.00 0.00 45.71 5.80
128 129 5.124776 GGGCCTTTTATTTTTGTTATTGGGC 59.875 40.000 0.84 0.00 35.98 5.36
129 130 6.241645 TGGGCCTTTTATTTTTGTTATTGGG 58.758 36.000 4.53 0.00 0.00 4.12
130 131 7.936496 ATGGGCCTTTTATTTTTGTTATTGG 57.064 32.000 4.53 0.00 0.00 3.16
139 140 9.360901 ACACATTTTTAATGGGCCTTTTATTTT 57.639 25.926 10.21 0.00 0.00 1.82
140 141 8.932434 ACACATTTTTAATGGGCCTTTTATTT 57.068 26.923 10.21 0.00 0.00 1.40
144 145 8.791675 CAAATACACATTTTTAATGGGCCTTTT 58.208 29.630 10.21 3.79 31.82 2.27
145 146 7.941790 ACAAATACACATTTTTAATGGGCCTTT 59.058 29.630 4.53 7.62 31.82 3.11
146 147 7.457561 ACAAATACACATTTTTAATGGGCCTT 58.542 30.769 4.53 0.00 31.82 4.35
147 148 7.014988 ACAAATACACATTTTTAATGGGCCT 57.985 32.000 4.53 0.00 31.82 5.19
148 149 7.102993 AGACAAATACACATTTTTAATGGGCC 58.897 34.615 0.00 0.00 31.82 5.80
149 150 8.546597 AAGACAAATACACATTTTTAATGGGC 57.453 30.769 1.71 0.00 31.82 5.36
156 157 9.665719 ACAGGAAAAAGACAAATACACATTTTT 57.334 25.926 0.00 0.00 31.82 1.94
158 159 9.965824 CTACAGGAAAAAGACAAATACACATTT 57.034 29.630 0.00 0.00 34.60 2.32
159 160 8.576442 CCTACAGGAAAAAGACAAATACACATT 58.424 33.333 0.00 0.00 37.39 2.71
160 161 7.309194 GCCTACAGGAAAAAGACAAATACACAT 60.309 37.037 0.00 0.00 37.39 3.21
161 162 6.016610 GCCTACAGGAAAAAGACAAATACACA 60.017 38.462 0.00 0.00 37.39 3.72
162 163 6.379386 GCCTACAGGAAAAAGACAAATACAC 58.621 40.000 0.00 0.00 37.39 2.90
163 164 5.475564 GGCCTACAGGAAAAAGACAAATACA 59.524 40.000 0.00 0.00 37.39 2.29
164 165 5.475564 TGGCCTACAGGAAAAAGACAAATAC 59.524 40.000 3.32 0.00 37.39 1.89
165 166 5.475564 GTGGCCTACAGGAAAAAGACAAATA 59.524 40.000 3.32 0.00 37.39 1.40
166 167 4.280929 GTGGCCTACAGGAAAAAGACAAAT 59.719 41.667 3.32 0.00 37.39 2.32
167 168 3.634910 GTGGCCTACAGGAAAAAGACAAA 59.365 43.478 3.32 0.00 37.39 2.83
168 169 3.219281 GTGGCCTACAGGAAAAAGACAA 58.781 45.455 3.32 0.00 37.39 3.18
169 170 2.173782 TGTGGCCTACAGGAAAAAGACA 59.826 45.455 3.32 0.00 37.39 3.41
170 171 2.858745 TGTGGCCTACAGGAAAAAGAC 58.141 47.619 3.32 0.00 37.39 3.01
171 172 3.181434 ACATGTGGCCTACAGGAAAAAGA 60.181 43.478 21.36 0.00 43.52 2.52
172 173 3.157087 ACATGTGGCCTACAGGAAAAAG 58.843 45.455 21.36 6.30 43.52 2.27
173 174 3.237268 ACATGTGGCCTACAGGAAAAA 57.763 42.857 21.36 0.00 43.52 1.94
174 175 2.969821 ACATGTGGCCTACAGGAAAA 57.030 45.000 21.36 0.00 43.52 2.29
175 176 4.076394 GTTTACATGTGGCCTACAGGAAA 58.924 43.478 21.36 14.53 43.52 3.13
176 177 3.681593 GTTTACATGTGGCCTACAGGAA 58.318 45.455 21.36 10.72 43.52 3.36
177 178 2.354303 CGTTTACATGTGGCCTACAGGA 60.354 50.000 21.36 6.38 43.52 3.86
178 179 2.006888 CGTTTACATGTGGCCTACAGG 58.993 52.381 9.11 15.38 46.10 4.00
179 180 2.695359 ACGTTTACATGTGGCCTACAG 58.305 47.619 9.11 4.13 43.80 2.74
180 181 2.843401 ACGTTTACATGTGGCCTACA 57.157 45.000 9.11 7.45 44.87 2.74
181 182 7.869429 AGTATTATACGTTTACATGTGGCCTAC 59.131 37.037 9.11 0.69 0.00 3.18
182 183 7.868922 CAGTATTATACGTTTACATGTGGCCTA 59.131 37.037 9.11 0.00 0.00 3.93
183 184 6.704493 CAGTATTATACGTTTACATGTGGCCT 59.296 38.462 9.11 0.00 0.00 5.19
184 185 6.480981 ACAGTATTATACGTTTACATGTGGCC 59.519 38.462 9.11 0.00 0.00 5.36
185 186 7.223193 TCACAGTATTATACGTTTACATGTGGC 59.777 37.037 9.11 0.00 36.02 5.01
186 187 8.637281 TCACAGTATTATACGTTTACATGTGG 57.363 34.615 9.11 0.00 36.02 4.17
194 195 9.900710 TGCAAAATTTCACAGTATTATACGTTT 57.099 25.926 0.00 0.00 0.00 3.60
215 216 9.717942 TGCACATGTATACTATGTATATGCAAA 57.282 29.630 18.15 6.65 36.67 3.68
216 217 9.889128 ATGCACATGTATACTATGTATATGCAA 57.111 29.630 21.07 12.83 37.36 4.08
217 218 9.316730 CATGCACATGTATACTATGTATATGCA 57.683 33.333 20.32 20.32 37.84 3.96
268 269 8.480643 TTTTTATTTTTCTGGAGCACGAAAAA 57.519 26.923 17.05 17.05 46.68 1.94
290 291 4.338118 TCCAGTGAGCTCGTTTTCATTTTT 59.662 37.500 9.64 0.00 0.00 1.94
291 292 3.882888 TCCAGTGAGCTCGTTTTCATTTT 59.117 39.130 9.64 0.00 0.00 1.82
292 293 3.476552 TCCAGTGAGCTCGTTTTCATTT 58.523 40.909 9.64 0.00 0.00 2.32
293 294 3.070018 CTCCAGTGAGCTCGTTTTCATT 58.930 45.455 9.64 0.00 0.00 2.57
294 295 2.693069 CTCCAGTGAGCTCGTTTTCAT 58.307 47.619 9.64 0.00 0.00 2.57
295 296 2.154854 CTCCAGTGAGCTCGTTTTCA 57.845 50.000 9.64 0.00 0.00 2.69
305 306 3.073735 AGGCCGAGCTCCAGTGAG 61.074 66.667 8.47 0.00 41.84 3.51
306 307 3.071206 GAGGCCGAGCTCCAGTGA 61.071 66.667 8.47 0.00 0.00 3.41
307 308 4.154347 GGAGGCCGAGCTCCAGTG 62.154 72.222 8.47 0.00 39.45 3.66
320 321 1.447317 CCGGAAAATGCCATCGGAGG 61.447 60.000 0.00 0.00 42.94 4.30
321 322 1.447317 CCCGGAAAATGCCATCGGAG 61.447 60.000 0.73 0.00 42.94 4.63
322 323 1.453015 CCCGGAAAATGCCATCGGA 60.453 57.895 0.73 0.00 42.94 4.55
323 324 2.489275 CCCCGGAAAATGCCATCGG 61.489 63.158 0.73 0.00 40.32 4.18
324 325 2.489275 CCCCCGGAAAATGCCATCG 61.489 63.158 0.73 0.00 0.00 3.84
325 326 3.537388 CCCCCGGAAAATGCCATC 58.463 61.111 0.73 0.00 0.00 3.51
358 359 7.495606 GGGGCATTTTTGAAATACTAATTGGAG 59.504 37.037 0.00 0.00 0.00 3.86
366 367 6.494059 AGTCTAGGGGCATTTTTGAAATACT 58.506 36.000 0.00 0.00 0.00 2.12
367 368 6.458342 CGAGTCTAGGGGCATTTTTGAAATAC 60.458 42.308 0.00 0.00 0.00 1.89
368 369 5.588648 CGAGTCTAGGGGCATTTTTGAAATA 59.411 40.000 0.00 0.00 0.00 1.40
397 398 1.801771 TGGCAGACGTTCCGTAATTTG 59.198 47.619 0.00 0.00 41.37 2.32
423 424 3.709653 AGGGAGGAAAGTGCGAATATACA 59.290 43.478 0.00 0.00 0.00 2.29
702 893 0.244721 GCAACAGAGGGGTGCAATTC 59.755 55.000 0.00 0.00 0.00 2.17
769 967 8.255905 GGTTGGATTGAAGATGAAATTTCAGAT 58.744 33.333 24.17 13.37 41.08 2.90
885 1083 5.301805 CCCCTTCAAATATTTAACTCCGCAT 59.698 40.000 0.00 0.00 0.00 4.73
1133 1343 2.619931 TGGACACCTCATCCTTGAAGA 58.380 47.619 0.00 0.00 37.13 2.87
1324 1534 6.482308 GGCTACACAAAACAGTAGAAGAAGAA 59.518 38.462 0.00 0.00 40.02 2.52
1329 1539 6.619801 AAAGGCTACACAAAACAGTAGAAG 57.380 37.500 0.00 0.00 40.02 2.85
1384 1594 4.926140 AATGTCAGTCGCATCAGAGATA 57.074 40.909 0.00 0.00 0.00 1.98
1464 1678 2.171237 CACCCTGTGCATTAGATCCAGA 59.829 50.000 0.00 0.00 0.00 3.86
1597 1813 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1619 1835 4.913784 TGTTACTTTTGGATACCCTGGAC 58.086 43.478 0.00 0.00 0.00 4.02
1648 1864 1.539388 CAGCACCGTTAGCATTTGGAA 59.461 47.619 0.00 0.00 0.00 3.53
1649 1865 1.164411 CAGCACCGTTAGCATTTGGA 58.836 50.000 0.00 0.00 0.00 3.53
1660 1876 2.546494 GCTTGAACTGCAGCACCGT 61.546 57.895 15.27 0.00 0.00 4.83
1710 1989 8.786826 TCGTTGTAATCATTTAAAGTCTCCAT 57.213 30.769 0.00 0.00 0.00 3.41
1861 2154 8.514594 CATTGACTGAAGAAAGGCTACATTAAA 58.485 33.333 0.00 0.00 0.00 1.52
1887 2183 8.722394 GCACCTCTTTAAGTAGGCATATATTTC 58.278 37.037 9.34 0.00 36.24 2.17
1911 2207 1.241165 CCACAGCTTGACAATCTGCA 58.759 50.000 16.94 0.00 0.00 4.41
2079 2563 9.591792 CAGACAGAAATTAGTGAAGATATGACA 57.408 33.333 0.00 0.00 0.00 3.58
2080 2564 9.593134 ACAGACAGAAATTAGTGAAGATATGAC 57.407 33.333 0.00 0.00 0.00 3.06
2106 2650 4.329638 TGCCATAATTGAAAGGAAGGGA 57.670 40.909 0.00 0.00 0.00 4.20
2129 2754 8.750298 GGGCTACTAGTAGATATGAATTAGCAA 58.250 37.037 30.09 0.00 35.21 3.91
2142 2767 6.659668 CAGCTATAACATGGGCTACTAGTAGA 59.340 42.308 30.09 12.50 35.21 2.59
2201 2828 6.785191 ACCATTCAAATAACTATGCGAACTG 58.215 36.000 0.00 0.00 0.00 3.16
2211 2838 7.451255 TCAGAACATGGAACCATTCAAATAACT 59.549 33.333 3.35 0.00 33.90 2.24
2227 2854 0.179156 GGCACGCAATCAGAACATGG 60.179 55.000 0.00 0.00 0.00 3.66
2280 2909 6.037830 GGAACAACAAAAGTAGCAGTAACAGA 59.962 38.462 0.00 0.00 0.00 3.41
2352 2981 7.118245 CAGTTCACTAAGCATTAACTGATCACA 59.882 37.037 7.56 0.00 46.29 3.58
2403 3034 3.270027 CGTAATCATGTGGCTGGAAGAA 58.730 45.455 0.00 0.00 34.07 2.52
2408 3039 5.237815 ACATATACGTAATCATGTGGCTGG 58.762 41.667 15.82 0.00 30.64 4.85
2426 3057 5.123227 CAGTCCAACCAACGGATAACATAT 58.877 41.667 0.00 0.00 34.32 1.78
2480 3111 9.981460 AAGTAAAATGATTGATCCTTAGTCCTT 57.019 29.630 0.00 0.00 0.00 3.36
2481 3112 9.401058 CAAGTAAAATGATTGATCCTTAGTCCT 57.599 33.333 0.00 0.00 0.00 3.85
2482 3113 9.178758 ACAAGTAAAATGATTGATCCTTAGTCC 57.821 33.333 0.00 0.00 0.00 3.85
2483 3114 9.994432 CACAAGTAAAATGATTGATCCTTAGTC 57.006 33.333 0.00 0.00 0.00 2.59
2484 3115 9.739276 TCACAAGTAAAATGATTGATCCTTAGT 57.261 29.630 0.00 0.00 0.00 2.24
2579 3214 0.878416 TGGCAAAGGTAACATCACGC 59.122 50.000 0.00 0.00 41.41 5.34
2589 3224 1.829533 CAGCTGTGGTGGCAAAGGT 60.830 57.895 5.25 0.00 0.00 3.50
2744 3384 0.996462 CAAAAGCCATGCAAGCATCG 59.004 50.000 13.87 0.00 33.90 3.84
2821 3461 5.742743 AGTTCCTGGGGAGGATCTATTATT 58.257 41.667 0.00 0.00 36.53 1.40
2995 3635 1.134220 TCCCCAACACACTTCACAGTC 60.134 52.381 0.00 0.00 0.00 3.51
3181 3821 0.674581 CCTTCGGCTTGAGTGATGCA 60.675 55.000 0.00 0.00 0.00 3.96
3262 3902 1.267121 TCTGTGCCACTTCTCTACCC 58.733 55.000 0.00 0.00 0.00 3.69
3487 4127 4.036734 ACCAGCAACTTGTACTCATTTGTG 59.963 41.667 0.00 0.00 0.00 3.33
3719 4359 9.223099 CATGATATGATGTAAACAGAAGGCATA 57.777 33.333 0.00 0.00 0.00 3.14
3811 4451 1.082117 CGGCCGCACGAGTAAAATCT 61.082 55.000 14.67 0.00 35.47 2.40
4213 4858 8.948631 TTGCAAGATTAACAACAAAAATACCA 57.051 26.923 0.00 0.00 0.00 3.25
4474 5119 7.928873 TGTTGGGATTATACCTCTTTCTTCTT 58.071 34.615 0.00 0.00 0.00 2.52
4488 5133 5.253096 AGAGTGGTTACCTTGTTGGGATTAT 59.747 40.000 2.07 0.00 41.11 1.28
4561 5206 4.244425 TGTCTACAGAAGAGCTTCACAC 57.756 45.455 12.32 2.69 41.84 3.82
4763 5426 7.489113 GGGCTTGTTTCATTACAATAATCACTG 59.511 37.037 0.00 0.00 37.39 3.66
4791 5454 4.224433 CACATTGATGTTTGAGTCAGTGC 58.776 43.478 0.00 0.00 39.39 4.40
4831 5494 6.980397 CCTGAACTCCAATACCATTTAATTGC 59.020 38.462 0.00 0.00 32.79 3.56
5108 5813 1.152777 CCAAGTGAACCTGCACCCA 60.153 57.895 0.00 0.00 39.59 4.51
5163 5960 4.083003 CGTCCTTCCATCTAGATACAGAGC 60.083 50.000 4.54 0.00 0.00 4.09
5164 5961 4.457603 CCGTCCTTCCATCTAGATACAGAG 59.542 50.000 4.54 1.76 0.00 3.35
5172 5969 4.827835 TGTTATCTCCGTCCTTCCATCTAG 59.172 45.833 0.00 0.00 0.00 2.43
5177 5974 1.475280 CGTGTTATCTCCGTCCTTCCA 59.525 52.381 0.00 0.00 0.00 3.53
5252 6050 4.465660 CCGGATCATCATCTCTAGTCCATT 59.534 45.833 0.00 0.00 0.00 3.16
5281 6079 1.609072 CAGTCGACACTGTCCAGAAGA 59.391 52.381 19.50 0.00 44.63 2.87
5297 6095 4.859798 CCATCGACTACTCTGTTTTCAGTC 59.140 45.833 0.00 0.00 46.98 3.51
5449 6247 5.416013 GGACTAAAAGGAAAAGTGATCCTGG 59.584 44.000 0.00 0.00 46.65 4.45
5461 6259 5.278957 GCAAAGCTTGATGGACTAAAAGGAA 60.279 40.000 0.00 0.00 0.00 3.36
5513 6312 8.604640 AGTGCTCACAGAATCATTATTATCTG 57.395 34.615 2.63 0.00 43.79 2.90
5528 6327 7.041721 TGTATATACTTCCAAAGTGCTCACAG 58.958 38.462 13.89 0.00 42.84 3.66
5540 6339 9.860898 CGAATCATGAGAATGTATATACTTCCA 57.139 33.333 13.89 13.09 0.00 3.53


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.