Multiple sequence alignment - TraesCS6D01G265000

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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 TraesCS6D01G265000 chr6D 100.000 5532 0 0 1 5532 374110413 374104882 0.000000e+00 10216.0
1 TraesCS6D01G265000 chr6D 82.454 701 90 28 2313 2999 373424268 373423587 2.870000e-162 582.0
2 TraesCS6D01G265000 chr6D 77.308 899 136 38 1366 2225 373425648 373424779 8.390000e-128 468.0
3 TraesCS6D01G265000 chr6D 86.932 352 36 8 3100 3448 373423070 373422726 2.420000e-103 387.0
4 TraesCS6D01G265000 chr6D 90.714 140 11 2 169 308 464487024 464487161 9.460000e-43 185.0
5 TraesCS6D01G265000 chr6A 93.340 4234 206 34 822 5014 516162148 516157950 0.000000e+00 6187.0
6 TraesCS6D01G265000 chr6A 82.749 713 95 23 2253 2952 515673272 515672575 1.320000e-170 610.0
7 TraesCS6D01G265000 chr6A 81.818 638 95 12 3885 4514 515669545 515668921 2.950000e-142 516.0
8 TraesCS6D01G265000 chr6A 80.349 631 90 20 1615 2225 515674364 515673748 1.090000e-121 448.0
9 TraesCS6D01G265000 chr6A 86.895 351 38 6 3100 3448 515672047 515671703 2.420000e-103 387.0
10 TraesCS6D01G265000 chr6A 92.473 186 11 3 5347 5532 516157664 516157482 4.250000e-66 263.0
11 TraesCS6D01G265000 chr6A 86.784 227 18 6 302 527 516164122 516163907 5.540000e-60 243.0
12 TraesCS6D01G265000 chr6A 81.155 329 20 21 5033 5331 516157966 516157650 5.580000e-55 226.0
13 TraesCS6D01G265000 chr6A 85.345 116 5 9 68 181 516164222 516164117 5.860000e-20 110.0
14 TraesCS6D01G265000 chr6B 98.769 2193 25 2 1584 3774 561275684 561273492 0.000000e+00 3899.0
15 TraesCS6D01G265000 chr6B 95.433 1073 33 8 523 1586 561276823 561275758 0.000000e+00 1696.0
16 TraesCS6D01G265000 chr6B 94.793 941 41 2 3977 4909 561258519 561257579 0.000000e+00 1459.0
17 TraesCS6D01G265000 chr6B 81.365 762 106 27 2253 3000 561151965 561151226 6.170000e-164 588.0
18 TraesCS6D01G265000 chr6B 81.077 650 102 12 3885 4526 561148108 561147472 2.980000e-137 499.0
19 TraesCS6D01G265000 chr6B 80.442 634 85 25 1615 2225 561153057 561152440 1.090000e-121 448.0
20 TraesCS6D01G265000 chr6B 86.857 350 39 5 3100 3448 561150808 561150465 8.690000e-103 385.0
21 TraesCS6D01G265000 chr6B 99.061 213 2 0 3767 3979 561271074 561270862 3.130000e-102 383.0
22 TraesCS6D01G265000 chr6B 87.660 235 15 4 305 527 561277104 561276872 1.530000e-65 261.0
23 TraesCS6D01G265000 chr6B 84.483 116 15 3 68 181 561277216 561277102 1.630000e-20 111.0
24 TraesCS6D01G265000 chr2D 90.780 141 11 1 166 306 286778374 286778236 2.630000e-43 187.0
25 TraesCS6D01G265000 chr2D 91.176 136 10 2 171 306 386707529 386707662 3.400000e-42 183.0
26 TraesCS6D01G265000 chr2D 82.011 189 20 5 5033 5209 77634179 77633993 1.240000e-31 148.0
27 TraesCS6D01G265000 chrUn 90.000 140 14 0 173 312 263461949 263461810 1.220000e-41 182.0
28 TraesCS6D01G265000 chr5D 90.441 136 13 0 178 313 269087869 269087734 4.400000e-41 180.0
29 TraesCS6D01G265000 chr7B 91.473 129 11 0 179 307 104514631 104514759 1.580000e-40 178.0
30 TraesCS6D01G265000 chr2A 91.473 129 11 0 179 307 425829942 425830070 1.580000e-40 178.0
31 TraesCS6D01G265000 chr7A 91.406 128 11 0 179 306 42992961 42993088 5.700000e-40 176.0
32 TraesCS6D01G265000 chr7A 84.354 147 23 0 2567 2713 186641565 186641419 1.610000e-30 145.0
33 TraesCS6D01G265000 chr7A 83.000 100 17 0 4914 5013 675402907 675402808 2.120000e-14 91.6
34 TraesCS6D01G265000 chr3D 89.855 138 13 1 179 316 565073622 565073758 5.700000e-40 176.0
35 TraesCS6D01G265000 chr3D 84.962 133 8 6 5089 5209 311542296 311542428 2.090000e-24 124.0
36 TraesCS6D01G265000 chr7D 84.049 163 24 2 2552 2713 184099039 184099200 7.420000e-34 156.0
37 TraesCS6D01G265000 chr7D 88.235 119 13 1 5089 5207 584280517 584280400 2.080000e-29 141.0
38 TraesCS6D01G265000 chr7D 87.826 115 14 0 5089 5203 467511621 467511507 9.670000e-28 135.0
39 TraesCS6D01G265000 chr7D 92.857 84 6 0 5124 5207 517306721 517306638 7.530000e-24 122.0
40 TraesCS6D01G265000 chr3A 89.256 121 13 0 5089 5209 186204359 186204479 9.600000e-33 152.0
41 TraesCS6D01G265000 chr1B 90.351 114 11 0 5096 5209 553972109 553972222 3.450000e-32 150.0
42 TraesCS6D01G265000 chr1B 86.885 122 12 4 5090 5207 173971163 173971284 3.480000e-27 134.0
43 TraesCS6D01G265000 chr1D 79.897 194 22 8 5033 5209 229605758 229605565 5.820000e-25 126.0


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 TraesCS6D01G265000 chr6D 374104882 374110413 5531 True 10216.00 10216 100.000000 1 5532 1 chr6D.!!$R1 5531
1 TraesCS6D01G265000 chr6D 373422726 373425648 2922 True 479.00 582 82.231333 1366 3448 3 chr6D.!!$R2 2082
2 TraesCS6D01G265000 chr6A 516157482 516164222 6740 True 1405.80 6187 87.819400 68 5532 5 chr6A.!!$R2 5464
3 TraesCS6D01G265000 chr6A 515668921 515674364 5443 True 490.25 610 82.952750 1615 4514 4 chr6A.!!$R1 2899
4 TraesCS6D01G265000 chr6B 561257579 561258519 940 True 1459.00 1459 94.793000 3977 4909 1 chr6B.!!$R1 932
5 TraesCS6D01G265000 chr6B 561270862 561277216 6354 True 1270.00 3899 93.081200 68 3979 5 chr6B.!!$R3 3911
6 TraesCS6D01G265000 chr6B 561147472 561153057 5585 True 480.00 588 82.435250 1615 4526 4 chr6B.!!$R2 2911

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
108 110 0.040204 CCACCCCATTGCTTCTTCCT 59.960 55.0 0.00 0.0 0.00 3.36 F
579 659 0.101759 AATCATTCAGTGGCATGCGC 59.898 50.0 12.44 0.0 37.44 6.09 F
1017 2638 0.661187 CGATGTGCAATTATGGCGGC 60.661 55.0 0.00 0.0 0.00 6.53 F
1624 3340 0.679002 TCTTCTCTGCTTGCCATGCC 60.679 55.0 0.00 0.0 0.00 4.40 F
2661 4866 0.607489 ACTGGTCTGCATTGAGTGGC 60.607 55.0 0.00 0.0 0.00 5.01 F
3773 10513 0.041535 AATTGGCATCCTTCAGGGCA 59.958 50.0 0.00 0.0 35.41 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1084 2705 1.751927 CTCCTTGCTCATGGTGCCC 60.752 63.158 8.67 0.00 0.00 5.36 R
2565 4770 1.624336 AATTTCTCAGCTGCAGGCAA 58.376 45.000 17.12 5.26 44.79 4.52 R
2661 4866 5.100259 ACGTTCATAAGTTCAGTATCCACG 58.900 41.667 0.00 0.00 0.00 4.94 R
3462 6108 2.553602 AGCAATGCGACAAGATCACAAA 59.446 40.909 0.00 0.00 0.00 2.83 R
3773 10513 0.610232 GAGGGGCATGTGCAAGACTT 60.610 55.000 7.36 0.00 44.36 3.01 R
4847 11911 0.389757 TGTGCGGTGCTGTAACAGTA 59.610 50.000 0.00 0.00 33.43 2.74 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
28 29 8.836268 TTTTTACACGTCACTAAATATGTCCT 57.164 30.769 0.00 0.00 0.00 3.85
29 30 8.836268 TTTTACACGTCACTAAATATGTCCTT 57.164 30.769 0.00 0.00 0.00 3.36
30 31 8.836268 TTTACACGTCACTAAATATGTCCTTT 57.164 30.769 0.00 0.00 0.00 3.11
31 32 8.836268 TTACACGTCACTAAATATGTCCTTTT 57.164 30.769 0.00 0.00 0.00 2.27
32 33 7.129109 ACACGTCACTAAATATGTCCTTTTG 57.871 36.000 0.00 0.00 0.00 2.44
33 34 6.932400 ACACGTCACTAAATATGTCCTTTTGA 59.068 34.615 0.00 0.00 0.00 2.69
34 35 7.606456 ACACGTCACTAAATATGTCCTTTTGAT 59.394 33.333 0.00 0.00 0.00 2.57
35 36 8.450964 CACGTCACTAAATATGTCCTTTTGATT 58.549 33.333 0.00 0.00 0.00 2.57
36 37 8.665685 ACGTCACTAAATATGTCCTTTTGATTC 58.334 33.333 0.00 0.00 0.00 2.52
37 38 8.122952 CGTCACTAAATATGTCCTTTTGATTCC 58.877 37.037 0.00 0.00 0.00 3.01
38 39 8.122952 GTCACTAAATATGTCCTTTTGATTCCG 58.877 37.037 0.00 0.00 0.00 4.30
39 40 7.827236 TCACTAAATATGTCCTTTTGATTCCGT 59.173 33.333 0.00 0.00 0.00 4.69
40 41 8.122952 CACTAAATATGTCCTTTTGATTCCGTC 58.877 37.037 0.00 0.00 0.00 4.79
41 42 5.734855 AATATGTCCTTTTGATTCCGTCG 57.265 39.130 0.00 0.00 0.00 5.12
42 43 2.823924 TGTCCTTTTGATTCCGTCGA 57.176 45.000 0.00 0.00 0.00 4.20
43 44 3.114668 TGTCCTTTTGATTCCGTCGAA 57.885 42.857 0.00 0.00 0.00 3.71
44 45 3.064207 TGTCCTTTTGATTCCGTCGAAG 58.936 45.455 0.00 0.00 31.88 3.79
45 46 3.243941 TGTCCTTTTGATTCCGTCGAAGA 60.244 43.478 0.00 0.00 31.88 2.87
46 47 3.368236 GTCCTTTTGATTCCGTCGAAGAG 59.632 47.826 0.00 0.00 36.95 2.85
47 48 2.094417 CCTTTTGATTCCGTCGAAGAGC 59.906 50.000 0.00 0.00 36.95 4.09
48 49 1.346365 TTTGATTCCGTCGAAGAGCG 58.654 50.000 0.00 0.00 36.95 5.03
108 110 0.040204 CCACCCCATTGCTTCTTCCT 59.960 55.000 0.00 0.00 0.00 3.36
139 152 4.593864 GCTCCGCTCCCGTCCATC 62.594 72.222 0.00 0.00 0.00 3.51
140 153 2.835431 CTCCGCTCCCGTCCATCT 60.835 66.667 0.00 0.00 0.00 2.90
142 155 1.076559 TCCGCTCCCGTCCATCTAA 60.077 57.895 0.00 0.00 0.00 2.10
143 156 1.067582 CCGCTCCCGTCCATCTAAC 59.932 63.158 0.00 0.00 0.00 2.34
144 157 1.392710 CCGCTCCCGTCCATCTAACT 61.393 60.000 0.00 0.00 0.00 2.24
145 158 0.249073 CGCTCCCGTCCATCTAACTG 60.249 60.000 0.00 0.00 0.00 3.16
175 188 0.179240 CTGACGAGCACGCAAACATC 60.179 55.000 2.62 0.00 43.96 3.06
181 195 2.094258 CGAGCACGCAAACATCAATACT 59.906 45.455 0.00 0.00 0.00 2.12
182 196 3.674423 GAGCACGCAAACATCAATACTC 58.326 45.455 0.00 0.00 0.00 2.59
183 197 3.338249 AGCACGCAAACATCAATACTCT 58.662 40.909 0.00 0.00 0.00 3.24
184 198 3.372206 AGCACGCAAACATCAATACTCTC 59.628 43.478 0.00 0.00 0.00 3.20
185 199 3.372206 GCACGCAAACATCAATACTCTCT 59.628 43.478 0.00 0.00 0.00 3.10
186 200 4.493220 GCACGCAAACATCAATACTCTCTC 60.493 45.833 0.00 0.00 0.00 3.20
187 201 4.033358 CACGCAAACATCAATACTCTCTCC 59.967 45.833 0.00 0.00 0.00 3.71
188 202 3.243877 CGCAAACATCAATACTCTCTCCG 59.756 47.826 0.00 0.00 0.00 4.63
189 203 4.184629 GCAAACATCAATACTCTCTCCGT 58.815 43.478 0.00 0.00 0.00 4.69
190 204 4.631813 GCAAACATCAATACTCTCTCCGTT 59.368 41.667 0.00 0.00 0.00 4.44
191 205 5.122396 GCAAACATCAATACTCTCTCCGTTT 59.878 40.000 0.00 0.00 0.00 3.60
192 206 6.673316 GCAAACATCAATACTCTCTCCGTTTC 60.673 42.308 0.00 0.00 0.00 2.78
193 207 5.661056 ACATCAATACTCTCTCCGTTTCA 57.339 39.130 0.00 0.00 0.00 2.69
194 208 6.037786 ACATCAATACTCTCTCCGTTTCAA 57.962 37.500 0.00 0.00 0.00 2.69
195 209 6.464222 ACATCAATACTCTCTCCGTTTCAAA 58.536 36.000 0.00 0.00 0.00 2.69
196 210 6.934645 ACATCAATACTCTCTCCGTTTCAAAA 59.065 34.615 0.00 0.00 0.00 2.44
197 211 7.607991 ACATCAATACTCTCTCCGTTTCAAAAT 59.392 33.333 0.00 0.00 0.00 1.82
198 212 9.098355 CATCAATACTCTCTCCGTTTCAAAATA 57.902 33.333 0.00 0.00 0.00 1.40
199 213 8.475331 TCAATACTCTCTCCGTTTCAAAATAC 57.525 34.615 0.00 0.00 0.00 1.89
200 214 8.311836 TCAATACTCTCTCCGTTTCAAAATACT 58.688 33.333 0.00 0.00 0.00 2.12
201 215 8.936864 CAATACTCTCTCCGTTTCAAAATACTT 58.063 33.333 0.00 0.00 0.00 2.24
202 216 6.787085 ACTCTCTCCGTTTCAAAATACTTG 57.213 37.500 0.00 0.00 0.00 3.16
203 217 6.522054 ACTCTCTCCGTTTCAAAATACTTGA 58.478 36.000 0.00 0.00 0.00 3.02
204 218 6.424207 ACTCTCTCCGTTTCAAAATACTTGAC 59.576 38.462 0.00 0.00 0.00 3.18
205 219 6.522054 TCTCTCCGTTTCAAAATACTTGACT 58.478 36.000 0.00 0.00 0.00 3.41
206 220 6.990349 TCTCTCCGTTTCAAAATACTTGACTT 59.010 34.615 0.00 0.00 0.00 3.01
207 221 7.497909 TCTCTCCGTTTCAAAATACTTGACTTT 59.502 33.333 0.00 0.00 0.00 2.66
208 222 7.636326 TCTCCGTTTCAAAATACTTGACTTTC 58.364 34.615 0.00 0.00 0.00 2.62
209 223 7.281324 TCTCCGTTTCAAAATACTTGACTTTCA 59.719 33.333 0.00 0.00 0.00 2.69
210 224 7.936584 TCCGTTTCAAAATACTTGACTTTCAT 58.063 30.769 0.00 0.00 0.00 2.57
211 225 8.410141 TCCGTTTCAAAATACTTGACTTTCATT 58.590 29.630 0.00 0.00 0.00 2.57
212 226 9.030301 CCGTTTCAAAATACTTGACTTTCATTT 57.970 29.630 0.00 0.00 0.00 2.32
213 227 9.833894 CGTTTCAAAATACTTGACTTTCATTTG 57.166 29.630 0.00 0.00 0.00 2.32
281 295 9.382275 ACATTTATATTTTGACAAATGGAAGGC 57.618 29.630 0.50 0.00 40.85 4.35
282 296 9.381033 CATTTATATTTTGACAAATGGAAGGCA 57.619 29.630 0.50 0.00 35.63 4.75
284 298 8.945481 TTATATTTTGACAAATGGAAGGCATG 57.055 30.769 0.50 0.00 34.29 4.06
285 299 4.686191 TTTTGACAAATGGAAGGCATGT 57.314 36.364 0.50 0.00 0.00 3.21
286 300 5.798125 TTTTGACAAATGGAAGGCATGTA 57.202 34.783 0.50 0.00 0.00 2.29
287 301 5.999205 TTTGACAAATGGAAGGCATGTAT 57.001 34.783 0.00 0.00 0.00 2.29
288 302 5.999205 TTGACAAATGGAAGGCATGTATT 57.001 34.783 0.00 0.00 0.00 1.89
289 303 5.327616 TGACAAATGGAAGGCATGTATTG 57.672 39.130 0.00 0.00 0.00 1.90
290 304 4.771577 TGACAAATGGAAGGCATGTATTGT 59.228 37.500 0.00 0.00 32.89 2.71
291 305 5.075858 ACAAATGGAAGGCATGTATTGTG 57.924 39.130 0.00 0.00 0.00 3.33
292 306 4.771577 ACAAATGGAAGGCATGTATTGTGA 59.228 37.500 0.00 0.00 0.00 3.58
293 307 5.245751 ACAAATGGAAGGCATGTATTGTGAA 59.754 36.000 0.00 0.00 0.00 3.18
294 308 5.999205 AATGGAAGGCATGTATTGTGAAA 57.001 34.783 0.00 0.00 0.00 2.69
295 309 6.549433 AATGGAAGGCATGTATTGTGAAAT 57.451 33.333 0.00 0.00 0.00 2.17
296 310 7.658525 AATGGAAGGCATGTATTGTGAAATA 57.341 32.000 0.00 0.00 0.00 1.40
297 311 6.698008 TGGAAGGCATGTATTGTGAAATAG 57.302 37.500 0.00 0.00 0.00 1.73
298 312 6.422333 TGGAAGGCATGTATTGTGAAATAGA 58.578 36.000 0.00 0.00 0.00 1.98
299 313 6.543465 TGGAAGGCATGTATTGTGAAATAGAG 59.457 38.462 0.00 0.00 0.00 2.43
300 314 6.016777 GGAAGGCATGTATTGTGAAATAGAGG 60.017 42.308 0.00 0.00 0.00 3.69
301 315 5.380043 AGGCATGTATTGTGAAATAGAGGG 58.620 41.667 0.00 0.00 0.00 4.30
302 316 5.132648 AGGCATGTATTGTGAAATAGAGGGA 59.867 40.000 0.00 0.00 0.00 4.20
303 317 5.471456 GGCATGTATTGTGAAATAGAGGGAG 59.529 44.000 0.00 0.00 0.00 4.30
304 318 6.058183 GCATGTATTGTGAAATAGAGGGAGT 58.942 40.000 0.00 0.00 0.00 3.85
305 319 7.217200 GCATGTATTGTGAAATAGAGGGAGTA 58.783 38.462 0.00 0.00 0.00 2.59
306 320 7.171678 GCATGTATTGTGAAATAGAGGGAGTAC 59.828 40.741 0.00 0.00 0.00 2.73
307 321 7.727578 TGTATTGTGAAATAGAGGGAGTACA 57.272 36.000 0.00 0.00 0.00 2.90
314 328 8.160765 TGTGAAATAGAGGGAGTACAAAATTGA 58.839 33.333 0.00 0.00 0.00 2.57
337 351 6.209986 TGAAAATTAGTCTACTGTTCGGGAGA 59.790 38.462 0.00 0.00 0.00 3.71
385 404 2.540101 CTGACGAACAGTTTCTCACACC 59.460 50.000 0.00 0.00 41.30 4.16
509 536 3.128845 GAATTTTCCCCGCGGCGA 61.129 61.111 25.92 15.74 0.00 5.54
573 653 1.728490 GCGGGGAATCATTCAGTGGC 61.728 60.000 0.00 0.00 0.00 5.01
579 659 0.101759 AATCATTCAGTGGCATGCGC 59.898 50.000 12.44 0.00 37.44 6.09
612 692 1.880675 TGGCGGAAAATTGCGTTCTTA 59.119 42.857 8.78 0.00 44.21 2.10
667 754 1.551145 GCTCTCTGTTCGATCCGTTC 58.449 55.000 0.00 0.00 0.00 3.95
744 831 5.581126 TCATGTTTGCTTATGATTGTCCC 57.419 39.130 0.00 0.00 0.00 4.46
835 2455 5.470098 AGATTTGTAGTAACTGCTGTTGTGG 59.530 40.000 18.22 0.00 37.59 4.17
875 2495 1.971357 ACTTGTGGACTGGTGTAGGAG 59.029 52.381 0.00 0.00 0.00 3.69
887 2507 1.550976 GTGTAGGAGGTGCTAGCTGTT 59.449 52.381 17.23 0.31 0.00 3.16
929 2549 2.357034 GTCGTTTCGGCTGGAGCA 60.357 61.111 0.20 0.00 44.36 4.26
957 2578 2.430332 CTGATGGTGGTGGTGTTTGTTT 59.570 45.455 0.00 0.00 0.00 2.83
959 2580 3.118956 TGATGGTGGTGGTGTTTGTTTTC 60.119 43.478 0.00 0.00 0.00 2.29
978 2599 2.907634 TCTTTACAGGTTTGTGACGCA 58.092 42.857 0.00 0.00 38.23 5.24
979 2600 2.610374 TCTTTACAGGTTTGTGACGCAC 59.390 45.455 3.44 3.44 38.23 5.34
1017 2638 0.661187 CGATGTGCAATTATGGCGGC 60.661 55.000 0.00 0.00 0.00 6.53
1064 2685 1.758936 TCTGATACGGATGACCACGT 58.241 50.000 0.00 0.00 46.17 4.49
1084 2705 2.126071 AAGACACGGGCGATGACG 60.126 61.111 0.00 0.00 42.93 4.35
1139 2760 6.813293 TTTAGACCTGGATGATGAAGATCA 57.187 37.500 0.00 0.00 42.92 2.92
1217 2838 1.453155 AAGCCTACGCAAGATTGGTG 58.547 50.000 0.00 0.00 43.62 4.17
1338 2959 7.011482 GGATTCGATTATGTAGCTCTGTTTGTT 59.989 37.037 0.00 0.00 0.00 2.83
1624 3340 0.679002 TCTTCTCTGCTTGCCATGCC 60.679 55.000 0.00 0.00 0.00 4.40
1852 3582 8.494347 CAAGCTGTGATGCTCTAAATAGTTATC 58.506 37.037 0.00 0.00 43.24 1.75
2098 3833 9.832445 AGTTTTCTGTCTAGATGTTTCTAACAA 57.168 29.630 0.00 0.00 45.86 2.83
2385 4573 7.812648 TGGAGAAACTTTTACCGTATGAATTG 58.187 34.615 0.00 0.00 0.00 2.32
2661 4866 0.607489 ACTGGTCTGCATTGAGTGGC 60.607 55.000 0.00 0.00 0.00 5.01
3773 10513 0.041535 AATTGGCATCCTTCAGGGCA 59.958 50.000 0.00 0.00 35.41 5.36
4111 11166 8.588290 AATGCTGATTTGTAATTAAGTGGGTA 57.412 30.769 0.00 0.00 0.00 3.69
4145 11201 0.656259 CTGGATGCAGACGCTTCATG 59.344 55.000 8.85 0.00 42.61 3.07
4268 11324 1.140052 TGAGAAACCTGTCGAAAGCCA 59.860 47.619 0.00 0.00 0.00 4.75
4568 11628 0.107831 GCTGTTCCCCCGCATGTATA 59.892 55.000 0.00 0.00 0.00 1.47
4657 11717 1.150827 TGTGTGCTTCATTGCTCTCG 58.849 50.000 0.00 0.00 0.00 4.04
4662 11722 1.012841 GCTTCATTGCTCTCGGGAAG 58.987 55.000 0.00 0.00 38.34 3.46
4797 11861 5.139001 TCTCTGATCATGCTCACTATCTGT 58.861 41.667 0.00 0.00 0.00 3.41
4817 11881 3.632604 TGTAGTCTATGGAAGAAGCGGAG 59.367 47.826 0.00 0.00 35.47 4.63
4828 11892 1.808945 AGAAGCGGAGTGATTGCAAAG 59.191 47.619 1.71 0.00 0.00 2.77
4829 11893 0.242017 AAGCGGAGTGATTGCAAAGC 59.758 50.000 1.71 0.00 0.00 3.51
4830 11894 0.607489 AGCGGAGTGATTGCAAAGCT 60.607 50.000 1.71 1.41 30.31 3.74
4831 11895 0.455633 GCGGAGTGATTGCAAAGCTG 60.456 55.000 1.71 0.00 30.31 4.24
4832 11896 0.877071 CGGAGTGATTGCAAAGCTGT 59.123 50.000 1.71 0.00 30.31 4.40
4833 11897 1.135859 CGGAGTGATTGCAAAGCTGTC 60.136 52.381 1.71 0.00 30.31 3.51
4834 11898 1.881973 GGAGTGATTGCAAAGCTGTCA 59.118 47.619 1.71 0.00 30.31 3.58
4835 11899 2.490903 GGAGTGATTGCAAAGCTGTCAT 59.509 45.455 1.71 0.00 30.31 3.06
4836 11900 3.057033 GGAGTGATTGCAAAGCTGTCATT 60.057 43.478 1.71 0.00 30.31 2.57
4837 11901 4.156556 GGAGTGATTGCAAAGCTGTCATTA 59.843 41.667 1.71 0.00 30.31 1.90
4838 11902 5.051891 AGTGATTGCAAAGCTGTCATTAC 57.948 39.130 1.71 0.00 30.31 1.89
4839 11903 4.763793 AGTGATTGCAAAGCTGTCATTACT 59.236 37.500 1.71 0.00 30.31 2.24
4840 11904 5.939883 AGTGATTGCAAAGCTGTCATTACTA 59.060 36.000 1.71 0.00 30.31 1.82
4841 11905 6.600822 AGTGATTGCAAAGCTGTCATTACTAT 59.399 34.615 1.71 0.00 30.31 2.12
4842 11906 7.121759 AGTGATTGCAAAGCTGTCATTACTATT 59.878 33.333 1.71 0.00 30.31 1.73
4843 11907 7.219535 GTGATTGCAAAGCTGTCATTACTATTG 59.780 37.037 1.71 0.00 30.31 1.90
4844 11908 4.985413 TGCAAAGCTGTCATTACTATTGC 58.015 39.130 5.67 5.67 0.00 3.56
4845 11909 4.458642 TGCAAAGCTGTCATTACTATTGCA 59.541 37.500 10.24 10.24 0.00 4.08
4846 11910 5.048154 TGCAAAGCTGTCATTACTATTGCAA 60.048 36.000 11.54 0.00 0.00 4.08
4847 11911 6.038356 GCAAAGCTGTCATTACTATTGCAAT 58.962 36.000 17.56 17.56 0.00 3.56
4861 11945 4.701956 ATTGCAATACTGTTACAGCACC 57.298 40.909 11.02 0.00 34.37 5.01
4888 11972 3.981071 AGGATTCCAGATGAAACACGA 57.019 42.857 5.29 0.00 36.33 4.35
4913 11998 8.934023 AATTACAACCAGTCATTCCTTCTTTA 57.066 30.769 0.00 0.00 0.00 1.85
4934 12019 9.817809 TCTTTAAGAGCATGGTTAATAGTACAG 57.182 33.333 0.00 0.00 0.00 2.74
4936 12021 5.878406 AGAGCATGGTTAATAGTACAGCT 57.122 39.130 0.00 0.00 0.00 4.24
4946 12031 3.951775 ATAGTACAGCTAGCTGATGGC 57.048 47.619 43.42 28.89 46.30 4.40
4966 12051 6.916360 TGGCTATATGATACTGTCATGTCA 57.084 37.500 0.00 0.00 46.85 3.58
4970 12055 8.907885 GGCTATATGATACTGTCATGTCATCTA 58.092 37.037 0.00 0.00 46.85 1.98
4982 12067 8.533569 TGTCATGTCATCTATAGTCAACCTTA 57.466 34.615 0.00 0.00 0.00 2.69
4988 12073 9.368416 TGTCATCTATAGTCAACCTTATAGCTT 57.632 33.333 0.00 0.00 0.00 3.74
5001 12086 8.338259 CAACCTTATAGCTTGCAAGTACAATAG 58.662 37.037 26.55 16.12 0.00 1.73
5082 12167 7.393515 ACTTTATTAAAACATGGTCCACCTCTC 59.606 37.037 0.00 0.00 36.82 3.20
5083 12168 4.715534 TTAAAACATGGTCCACCTCTCA 57.284 40.909 0.00 0.00 36.82 3.27
5091 12176 1.208293 GGTCCACCTCTCATTCTCACC 59.792 57.143 0.00 0.00 0.00 4.02
5093 12178 2.093764 GTCCACCTCTCATTCTCACCTG 60.094 54.545 0.00 0.00 0.00 4.00
5094 12179 1.905215 CCACCTCTCATTCTCACCTGT 59.095 52.381 0.00 0.00 0.00 4.00
5114 12217 3.503363 TGTTGCAGTTGGCTCTTATTCTG 59.497 43.478 0.00 0.00 45.15 3.02
5127 12230 5.877564 GCTCTTATTCTGTAGCCAGTTTCTT 59.122 40.000 0.00 0.00 39.82 2.52
5139 12254 3.680490 CCAGTTTCTTTTCTCTCCCCTC 58.320 50.000 0.00 0.00 0.00 4.30
5146 12261 2.342406 TTTCTCTCCCCTCCATGTCA 57.658 50.000 0.00 0.00 0.00 3.58
5148 12263 0.689080 TCTCTCCCCTCCATGTCAGC 60.689 60.000 0.00 0.00 0.00 4.26
5217 12332 6.533819 TTGTACTTGTTCTAAACATGACCG 57.466 37.500 0.00 0.00 41.79 4.79
5218 12333 4.449743 TGTACTTGTTCTAAACATGACCGC 59.550 41.667 0.00 1.98 41.79 5.68
5219 12334 2.478894 ACTTGTTCTAAACATGACCGCG 59.521 45.455 0.00 0.00 41.79 6.46
5221 12336 2.756829 TGTTCTAAACATGACCGCGAA 58.243 42.857 8.23 0.00 36.25 4.70
5222 12337 3.331150 TGTTCTAAACATGACCGCGAAT 58.669 40.909 8.23 0.00 36.25 3.34
5223 12338 4.496360 TGTTCTAAACATGACCGCGAATA 58.504 39.130 8.23 0.00 36.25 1.75
5224 12339 5.113383 TGTTCTAAACATGACCGCGAATAT 58.887 37.500 8.23 0.00 36.25 1.28
5225 12340 5.006261 TGTTCTAAACATGACCGCGAATATG 59.994 40.000 8.23 11.21 36.25 1.78
5226 12341 4.939271 TCTAAACATGACCGCGAATATGA 58.061 39.130 8.23 0.00 0.00 2.15
5227 12342 3.944422 AAACATGACCGCGAATATGAC 57.056 42.857 8.23 0.00 0.00 3.06
5228 12343 2.595124 ACATGACCGCGAATATGACA 57.405 45.000 8.23 0.00 0.00 3.58
5229 12344 2.201732 ACATGACCGCGAATATGACAC 58.798 47.619 8.23 0.00 0.00 3.67
5230 12345 2.200899 CATGACCGCGAATATGACACA 58.799 47.619 8.23 0.00 0.00 3.72
5231 12346 2.371910 TGACCGCGAATATGACACAA 57.628 45.000 8.23 0.00 0.00 3.33
5232 12347 2.267426 TGACCGCGAATATGACACAAG 58.733 47.619 8.23 0.00 0.00 3.16
5233 12348 2.094442 TGACCGCGAATATGACACAAGA 60.094 45.455 8.23 0.00 0.00 3.02
5272 12387 1.481772 GAGAAGCTCAGGATGCTGTCT 59.518 52.381 14.43 9.34 41.03 3.41
5290 12405 1.065709 TCTCCGACCATAACTTTGCCC 60.066 52.381 0.00 0.00 0.00 5.36
5294 12409 1.472480 CGACCATAACTTTGCCCAAGG 59.528 52.381 0.00 0.00 36.72 3.61
5316 12431 1.377856 GCAAGGGGAAGAGTGCCTC 60.378 63.158 0.00 0.00 35.06 4.70
5317 12432 1.301293 CAAGGGGAAGAGTGCCTCC 59.699 63.158 0.00 0.00 35.06 4.30
5318 12433 1.925972 AAGGGGAAGAGTGCCTCCC 60.926 63.158 0.00 0.00 41.57 4.30
5319 12434 2.285743 GGGGAAGAGTGCCTCCCT 60.286 66.667 7.08 0.00 41.96 4.20
5320 12435 1.925972 GGGGAAGAGTGCCTCCCTT 60.926 63.158 7.08 0.00 41.96 3.95
5321 12436 1.301293 GGGAAGAGTGCCTCCCTTG 59.699 63.158 0.00 0.00 39.27 3.61
5322 12437 1.201429 GGGAAGAGTGCCTCCCTTGA 61.201 60.000 0.00 0.00 39.27 3.02
5323 12438 0.915364 GGAAGAGTGCCTCCCTTGAT 59.085 55.000 0.00 0.00 0.00 2.57
5324 12439 1.283321 GGAAGAGTGCCTCCCTTGATT 59.717 52.381 0.00 0.00 0.00 2.57
5325 12440 2.291217 GGAAGAGTGCCTCCCTTGATTT 60.291 50.000 0.00 0.00 0.00 2.17
5326 12441 2.503895 AGAGTGCCTCCCTTGATTTG 57.496 50.000 0.00 0.00 0.00 2.32
5327 12442 1.988107 AGAGTGCCTCCCTTGATTTGA 59.012 47.619 0.00 0.00 0.00 2.69
5328 12443 2.026449 AGAGTGCCTCCCTTGATTTGAG 60.026 50.000 0.00 0.00 0.00 3.02
5329 12444 1.707427 AGTGCCTCCCTTGATTTGAGT 59.293 47.619 0.00 0.00 0.00 3.41
5330 12445 2.108952 AGTGCCTCCCTTGATTTGAGTT 59.891 45.455 0.00 0.00 0.00 3.01
5331 12446 2.893489 GTGCCTCCCTTGATTTGAGTTT 59.107 45.455 0.00 0.00 0.00 2.66
5332 12447 3.321968 GTGCCTCCCTTGATTTGAGTTTT 59.678 43.478 0.00 0.00 0.00 2.43
5333 12448 3.966665 TGCCTCCCTTGATTTGAGTTTTT 59.033 39.130 0.00 0.00 0.00 1.94
5385 12500 2.178235 GGCAACTAACGGGATCGGC 61.178 63.158 0.00 0.00 41.39 5.54
5388 12503 3.728279 AACTAACGGGATCGGCGCC 62.728 63.158 19.07 19.07 41.39 6.53
5459 12574 1.152383 GATCTTCAACCGCGGTAGCC 61.152 60.000 34.44 15.90 41.18 3.93
5478 12593 0.867746 CGATGTTGATATGGTGGCCG 59.132 55.000 0.00 0.00 0.00 6.13
5480 12595 2.571212 GATGTTGATATGGTGGCCGAA 58.429 47.619 0.00 0.00 0.00 4.30
5495 12610 1.292223 CGAAGGGCGAAGGAAGACA 59.708 57.895 0.00 0.00 44.57 3.41
5514 12629 0.524862 AAAGCATCCAAGCGAGCTTG 59.475 50.000 25.92 25.92 45.73 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.836268 AGGACATATTTAGTGACGTGTAAAAA 57.164 30.769 0.00 0.00 0.00 1.94
5 6 8.836268 AAAGGACATATTTAGTGACGTGTAAA 57.164 30.769 0.00 0.00 0.00 2.01
6 7 8.714179 CAAAAGGACATATTTAGTGACGTGTAA 58.286 33.333 0.00 0.00 0.00 2.41
7 8 8.089597 TCAAAAGGACATATTTAGTGACGTGTA 58.910 33.333 0.00 0.00 0.00 2.90
8 9 6.932400 TCAAAAGGACATATTTAGTGACGTGT 59.068 34.615 0.00 0.00 0.00 4.49
9 10 7.359262 TCAAAAGGACATATTTAGTGACGTG 57.641 36.000 0.00 0.00 0.00 4.49
10 11 8.561738 AATCAAAAGGACATATTTAGTGACGT 57.438 30.769 0.00 0.00 0.00 4.34
11 12 8.122952 GGAATCAAAAGGACATATTTAGTGACG 58.877 37.037 0.00 0.00 0.00 4.35
12 13 8.122952 CGGAATCAAAAGGACATATTTAGTGAC 58.877 37.037 0.00 0.00 0.00 3.67
13 14 7.827236 ACGGAATCAAAAGGACATATTTAGTGA 59.173 33.333 0.00 0.00 0.00 3.41
14 15 7.985476 ACGGAATCAAAAGGACATATTTAGTG 58.015 34.615 0.00 0.00 0.00 2.74
15 16 7.011109 CGACGGAATCAAAAGGACATATTTAGT 59.989 37.037 0.00 0.00 0.00 2.24
16 17 7.223971 TCGACGGAATCAAAAGGACATATTTAG 59.776 37.037 0.00 0.00 0.00 1.85
17 18 7.042950 TCGACGGAATCAAAAGGACATATTTA 58.957 34.615 0.00 0.00 0.00 1.40
18 19 5.878116 TCGACGGAATCAAAAGGACATATTT 59.122 36.000 0.00 0.00 0.00 1.40
19 20 5.424757 TCGACGGAATCAAAAGGACATATT 58.575 37.500 0.00 0.00 0.00 1.28
20 21 5.018539 TCGACGGAATCAAAAGGACATAT 57.981 39.130 0.00 0.00 0.00 1.78
21 22 4.459390 TCGACGGAATCAAAAGGACATA 57.541 40.909 0.00 0.00 0.00 2.29
22 23 3.328382 TCGACGGAATCAAAAGGACAT 57.672 42.857 0.00 0.00 0.00 3.06
23 24 2.823924 TCGACGGAATCAAAAGGACA 57.176 45.000 0.00 0.00 0.00 4.02
24 25 3.323243 TCTTCGACGGAATCAAAAGGAC 58.677 45.455 0.00 0.00 0.00 3.85
25 26 3.585862 CTCTTCGACGGAATCAAAAGGA 58.414 45.455 0.00 0.00 0.00 3.36
26 27 2.094417 GCTCTTCGACGGAATCAAAAGG 59.906 50.000 0.00 0.00 0.00 3.11
27 28 2.222596 CGCTCTTCGACGGAATCAAAAG 60.223 50.000 0.00 0.00 41.67 2.27
28 29 1.724623 CGCTCTTCGACGGAATCAAAA 59.275 47.619 0.00 0.00 41.67 2.44
29 30 1.068125 TCGCTCTTCGACGGAATCAAA 60.068 47.619 0.00 0.00 43.16 2.69
30 31 0.524414 TCGCTCTTCGACGGAATCAA 59.476 50.000 0.00 0.00 43.16 2.57
31 32 2.177044 TCGCTCTTCGACGGAATCA 58.823 52.632 0.00 0.00 43.16 2.57
39 40 1.792006 GAAACCCTTTCGCTCTTCGA 58.208 50.000 0.00 0.00 46.88 3.71
48 49 3.547413 CGTTCCTGTTTCGAAACCCTTTC 60.547 47.826 32.14 20.09 38.11 2.62
49 50 2.356695 CGTTCCTGTTTCGAAACCCTTT 59.643 45.455 32.14 0.00 38.11 3.11
50 51 1.944709 CGTTCCTGTTTCGAAACCCTT 59.055 47.619 32.14 0.00 38.11 3.95
51 52 1.589803 CGTTCCTGTTTCGAAACCCT 58.410 50.000 32.14 0.00 38.11 4.34
52 53 0.589708 CCGTTCCTGTTTCGAAACCC 59.410 55.000 32.14 14.05 38.11 4.11
53 54 1.003223 CACCGTTCCTGTTTCGAAACC 60.003 52.381 32.14 18.32 38.11 3.27
54 55 1.935199 TCACCGTTCCTGTTTCGAAAC 59.065 47.619 29.72 29.72 39.33 2.78
55 56 1.935199 GTCACCGTTCCTGTTTCGAAA 59.065 47.619 6.47 6.47 0.00 3.46
56 57 1.574134 GTCACCGTTCCTGTTTCGAA 58.426 50.000 0.00 0.00 0.00 3.71
57 58 0.249573 GGTCACCGTTCCTGTTTCGA 60.250 55.000 0.00 0.00 0.00 3.71
58 59 1.554042 CGGTCACCGTTCCTGTTTCG 61.554 60.000 8.54 0.00 42.73 3.46
59 60 2.231820 CGGTCACCGTTCCTGTTTC 58.768 57.895 8.54 0.00 42.73 2.78
60 61 4.449391 CGGTCACCGTTCCTGTTT 57.551 55.556 8.54 0.00 42.73 2.83
127 140 1.112113 TCAGTTAGATGGACGGGAGC 58.888 55.000 0.00 0.00 0.00 4.70
128 141 2.873133 GTCAGTTAGATGGACGGGAG 57.127 55.000 0.00 0.00 0.00 4.30
134 147 2.167662 TCAGTGCGTCAGTTAGATGGA 58.832 47.619 0.00 0.00 33.68 3.41
135 148 2.654749 TCAGTGCGTCAGTTAGATGG 57.345 50.000 0.00 0.00 33.68 3.51
136 149 3.366121 CAGTTCAGTGCGTCAGTTAGATG 59.634 47.826 0.00 0.00 36.29 2.90
138 151 2.621526 TCAGTTCAGTGCGTCAGTTAGA 59.378 45.455 0.00 0.00 0.00 2.10
139 152 2.726760 GTCAGTTCAGTGCGTCAGTTAG 59.273 50.000 0.00 0.00 0.00 2.34
140 153 2.739292 GTCAGTTCAGTGCGTCAGTTA 58.261 47.619 0.00 0.00 0.00 2.24
142 155 0.595053 CGTCAGTTCAGTGCGTCAGT 60.595 55.000 0.00 0.00 0.00 3.41
143 156 0.317854 TCGTCAGTTCAGTGCGTCAG 60.318 55.000 0.00 0.00 0.00 3.51
144 157 0.317854 CTCGTCAGTTCAGTGCGTCA 60.318 55.000 0.00 0.00 0.00 4.35
145 158 1.609840 GCTCGTCAGTTCAGTGCGTC 61.610 60.000 0.00 0.00 0.00 5.19
175 188 8.480643 AGTATTTTGAAACGGAGAGAGTATTG 57.519 34.615 0.00 0.00 0.00 1.90
181 195 6.522054 AGTCAAGTATTTTGAAACGGAGAGA 58.478 36.000 0.00 0.00 0.00 3.10
182 196 6.787085 AGTCAAGTATTTTGAAACGGAGAG 57.213 37.500 0.00 0.00 0.00 3.20
183 197 7.281324 TGAAAGTCAAGTATTTTGAAACGGAGA 59.719 33.333 0.00 0.00 0.00 3.71
184 198 7.414436 TGAAAGTCAAGTATTTTGAAACGGAG 58.586 34.615 0.00 0.00 0.00 4.63
185 199 7.323049 TGAAAGTCAAGTATTTTGAAACGGA 57.677 32.000 0.00 0.00 0.00 4.69
186 200 8.574196 AATGAAAGTCAAGTATTTTGAAACGG 57.426 30.769 0.00 0.00 0.00 4.44
187 201 9.833894 CAAATGAAAGTCAAGTATTTTGAAACG 57.166 29.630 0.00 0.00 28.22 3.60
255 269 9.382275 GCCTTCCATTTGTCAAAATATAAATGT 57.618 29.630 1.31 0.00 38.30 2.71
256 270 9.381033 TGCCTTCCATTTGTCAAAATATAAATG 57.619 29.630 1.31 0.00 39.19 2.32
258 272 9.381033 CATGCCTTCCATTTGTCAAAATATAAA 57.619 29.630 1.31 0.00 34.14 1.40
259 273 8.538701 ACATGCCTTCCATTTGTCAAAATATAA 58.461 29.630 1.31 0.00 34.14 0.98
260 274 8.076910 ACATGCCTTCCATTTGTCAAAATATA 57.923 30.769 1.31 0.00 34.14 0.86
261 275 6.949715 ACATGCCTTCCATTTGTCAAAATAT 58.050 32.000 1.31 0.00 34.14 1.28
262 276 6.357579 ACATGCCTTCCATTTGTCAAAATA 57.642 33.333 1.31 0.00 34.14 1.40
263 277 5.231702 ACATGCCTTCCATTTGTCAAAAT 57.768 34.783 1.31 0.00 36.39 1.82
264 278 4.686191 ACATGCCTTCCATTTGTCAAAA 57.314 36.364 1.31 0.00 29.71 2.44
265 279 5.999205 ATACATGCCTTCCATTTGTCAAA 57.001 34.783 0.00 0.00 29.71 2.69
266 280 5.245751 ACAATACATGCCTTCCATTTGTCAA 59.754 36.000 0.00 0.00 30.42 3.18
267 281 4.771577 ACAATACATGCCTTCCATTTGTCA 59.228 37.500 0.00 0.00 30.42 3.58
268 282 5.104374 CACAATACATGCCTTCCATTTGTC 58.896 41.667 0.00 0.00 32.71 3.18
269 283 4.771577 TCACAATACATGCCTTCCATTTGT 59.228 37.500 0.00 0.00 34.39 2.83
270 284 5.327616 TCACAATACATGCCTTCCATTTG 57.672 39.130 0.00 0.00 29.71 2.32
271 285 5.999205 TTCACAATACATGCCTTCCATTT 57.001 34.783 0.00 0.00 29.71 2.32
272 286 5.999205 TTTCACAATACATGCCTTCCATT 57.001 34.783 0.00 0.00 29.71 3.16
273 287 7.062322 TCTATTTCACAATACATGCCTTCCAT 58.938 34.615 0.00 0.00 33.39 3.41
274 288 6.422333 TCTATTTCACAATACATGCCTTCCA 58.578 36.000 0.00 0.00 0.00 3.53
275 289 6.016777 CCTCTATTTCACAATACATGCCTTCC 60.017 42.308 0.00 0.00 0.00 3.46
276 290 6.016777 CCCTCTATTTCACAATACATGCCTTC 60.017 42.308 0.00 0.00 0.00 3.46
277 291 5.829924 CCCTCTATTTCACAATACATGCCTT 59.170 40.000 0.00 0.00 0.00 4.35
278 292 5.132648 TCCCTCTATTTCACAATACATGCCT 59.867 40.000 0.00 0.00 0.00 4.75
279 293 5.376625 TCCCTCTATTTCACAATACATGCC 58.623 41.667 0.00 0.00 0.00 4.40
280 294 6.058183 ACTCCCTCTATTTCACAATACATGC 58.942 40.000 0.00 0.00 0.00 4.06
281 295 8.204160 TGTACTCCCTCTATTTCACAATACATG 58.796 37.037 0.00 0.00 0.00 3.21
282 296 8.319057 TGTACTCCCTCTATTTCACAATACAT 57.681 34.615 0.00 0.00 0.00 2.29
283 297 7.727578 TGTACTCCCTCTATTTCACAATACA 57.272 36.000 0.00 0.00 0.00 2.29
284 298 9.444600 TTTTGTACTCCCTCTATTTCACAATAC 57.555 33.333 0.00 0.00 0.00 1.89
286 300 9.533831 AATTTTGTACTCCCTCTATTTCACAAT 57.466 29.630 0.00 0.00 0.00 2.71
287 301 8.792633 CAATTTTGTACTCCCTCTATTTCACAA 58.207 33.333 0.00 0.00 0.00 3.33
288 302 8.160765 TCAATTTTGTACTCCCTCTATTTCACA 58.839 33.333 0.00 0.00 0.00 3.58
289 303 8.561738 TCAATTTTGTACTCCCTCTATTTCAC 57.438 34.615 0.00 0.00 0.00 3.18
290 304 9.581289 TTTCAATTTTGTACTCCCTCTATTTCA 57.419 29.630 0.00 0.00 0.00 2.69
296 310 9.588096 ACTAATTTTCAATTTTGTACTCCCTCT 57.412 29.630 0.00 0.00 0.00 3.69
297 311 9.841880 GACTAATTTTCAATTTTGTACTCCCTC 57.158 33.333 0.00 0.00 0.00 4.30
298 312 9.588096 AGACTAATTTTCAATTTTGTACTCCCT 57.412 29.630 0.00 0.00 0.00 4.20
307 321 9.893305 CCGAACAGTAGACTAATTTTCAATTTT 57.107 29.630 8.93 0.00 0.00 1.82
314 328 6.436532 TCTCTCCCGAACAGTAGACTAATTTT 59.563 38.462 0.00 0.00 0.00 1.82
318 332 4.224594 TCTCTCTCCCGAACAGTAGACTAA 59.775 45.833 0.00 0.00 0.00 2.24
337 351 2.495669 CGGCTTCTTCCTTCTCTTCTCT 59.504 50.000 0.00 0.00 0.00 3.10
371 390 3.989104 CGGAGGTGTGAGAAACTGT 57.011 52.632 0.00 0.00 0.00 3.55
385 404 0.614979 TGGGTTCTCTTCTCCCGGAG 60.615 60.000 8.30 8.30 43.75 4.63
521 548 1.619669 CCCCAAACCCTAGGAGCCT 60.620 63.158 11.48 0.00 0.00 4.58
550 630 3.649986 GAATGATTCCCCGCGCCG 61.650 66.667 0.00 0.00 0.00 6.46
553 633 1.439353 CCACTGAATGATTCCCCGCG 61.439 60.000 0.00 0.00 0.00 6.46
554 634 1.728490 GCCACTGAATGATTCCCCGC 61.728 60.000 2.26 0.00 0.00 6.13
555 635 0.394216 TGCCACTGAATGATTCCCCG 60.394 55.000 2.26 0.00 0.00 5.73
556 636 1.684983 CATGCCACTGAATGATTCCCC 59.315 52.381 2.26 0.00 0.00 4.81
557 637 1.068127 GCATGCCACTGAATGATTCCC 59.932 52.381 6.36 0.00 0.00 3.97
573 653 1.008194 CAAATCGGGGATGCGCATG 60.008 57.895 30.76 13.79 0.00 4.06
579 659 2.480610 CCGCCACAAATCGGGGATG 61.481 63.158 0.00 0.00 41.82 3.51
598 678 5.812652 TGAAACGAGTAAGAACGCAATTTT 58.187 33.333 0.00 0.00 0.00 1.82
603 683 3.047796 GACTGAAACGAGTAAGAACGCA 58.952 45.455 0.00 0.00 0.00 5.24
676 763 0.370273 GTGGAATTCGCTAGCACACG 59.630 55.000 16.45 0.00 0.00 4.49
744 831 4.629200 GGCTCTGAACATCTGAACACTTAG 59.371 45.833 0.00 0.00 0.00 2.18
875 2495 0.951040 ACGCAAGAACAGCTAGCACC 60.951 55.000 18.83 2.51 43.62 5.01
929 2549 1.600636 CACCACCATCAGCAACGGT 60.601 57.895 0.00 0.00 0.00 4.83
957 2578 3.064271 GTGCGTCACAAACCTGTAAAGAA 59.936 43.478 5.30 0.00 33.22 2.52
959 2580 2.612212 AGTGCGTCACAAACCTGTAAAG 59.388 45.455 11.58 0.00 36.74 1.85
1017 2638 2.944557 CAGTCATCGACGTCGCCG 60.945 66.667 32.19 23.86 37.67 6.46
1064 2685 2.180769 CATCGCCCGTGTCTTCGA 59.819 61.111 0.00 0.00 35.34 3.71
1084 2705 1.751927 CTCCTTGCTCATGGTGCCC 60.752 63.158 8.67 0.00 0.00 5.36
1217 2838 6.972901 GCTAACCCAATAAGAAGTGCATTTAC 59.027 38.462 0.00 0.00 0.00 2.01
1624 3340 8.964420 ACGGAACAATAGAAACATTTTACATG 57.036 30.769 0.00 0.00 0.00 3.21
1852 3582 4.090090 TGACTCTAAACAGAGAAGGAGGG 58.910 47.826 8.60 0.00 39.14 4.30
1895 3628 3.688694 TTTCTTTTCTAGTGGGCGCTA 57.311 42.857 7.64 0.00 0.00 4.26
2098 3833 7.482169 TTCCTGTTCTAAGACATGTATCAGT 57.518 36.000 0.00 0.00 0.00 3.41
2385 4573 6.515272 TTGCAAAGATCCCTGAACTAATTC 57.485 37.500 0.00 0.00 35.18 2.17
2403 4591 4.910195 AGACACATAATCAGGACTTGCAA 58.090 39.130 0.00 0.00 0.00 4.08
2565 4770 1.624336 AATTTCTCAGCTGCAGGCAA 58.376 45.000 17.12 5.26 44.79 4.52
2661 4866 5.100259 ACGTTCATAAGTTCAGTATCCACG 58.900 41.667 0.00 0.00 0.00 4.94
2798 5008 8.983724 GCTTCTGTAATAAGAGATCCATAACAC 58.016 37.037 0.00 0.00 0.00 3.32
3417 6047 8.672815 CCAGCTTTCCAAAACAAATAAAAGAAA 58.327 29.630 0.00 0.00 0.00 2.52
3460 6106 3.922240 GCAATGCGACAAGATCACAAAAT 59.078 39.130 0.00 0.00 0.00 1.82
3462 6108 2.553602 AGCAATGCGACAAGATCACAAA 59.446 40.909 0.00 0.00 0.00 2.83
3531 6177 2.652857 AGGGTACAAAAGTAAGCCCCAT 59.347 45.455 0.00 0.00 36.86 4.00
3773 10513 0.610232 GAGGGGCATGTGCAAGACTT 60.610 55.000 7.36 0.00 44.36 3.01
4111 11166 5.263599 TGCATCCAGAATAAGAAATGGTGT 58.736 37.500 0.00 0.00 34.32 4.16
4268 11324 2.357154 GGTTGCCCTTCAGTACATGGAT 60.357 50.000 0.00 0.00 0.00 3.41
4568 11628 4.349342 AGTTCTGTTCAAGACTTCTGGGAT 59.651 41.667 0.00 0.00 33.46 3.85
4629 11689 6.732154 AGCAATGAAGCACACATGTATATTC 58.268 36.000 0.00 1.81 36.85 1.75
4635 11695 2.486982 GAGAGCAATGAAGCACACATGT 59.513 45.455 0.00 0.00 36.85 3.21
4657 11717 0.890996 CACCTCAGTGCCAACTTCCC 60.891 60.000 0.00 0.00 37.14 3.97
4768 11832 0.759959 AGCATGATCAGAGAGGCTGG 59.240 55.000 0.09 0.00 44.98 4.85
4797 11861 3.632604 CACTCCGCTTCTTCCATAGACTA 59.367 47.826 0.00 0.00 30.90 2.59
4817 11881 5.051891 AGTAATGACAGCTTTGCAATCAC 57.948 39.130 0.00 0.00 29.93 3.06
4828 11892 7.251704 ACAGTATTGCAATAGTAATGACAGC 57.748 36.000 23.19 7.25 32.15 4.40
4830 11894 9.660180 TGTAACAGTATTGCAATAGTAATGACA 57.340 29.630 23.19 19.57 32.15 3.58
4832 11896 8.826710 GCTGTAACAGTATTGCAATAGTAATGA 58.173 33.333 23.19 8.20 33.43 2.57
4833 11897 8.611757 TGCTGTAACAGTATTGCAATAGTAATG 58.388 33.333 23.19 18.30 33.43 1.90
4834 11898 8.612619 GTGCTGTAACAGTATTGCAATAGTAAT 58.387 33.333 23.19 17.39 33.43 1.89
4835 11899 7.065324 GGTGCTGTAACAGTATTGCAATAGTAA 59.935 37.037 23.19 11.40 33.43 2.24
4836 11900 6.537301 GGTGCTGTAACAGTATTGCAATAGTA 59.463 38.462 23.19 8.50 33.43 1.82
4837 11901 5.354234 GGTGCTGTAACAGTATTGCAATAGT 59.646 40.000 19.41 19.25 33.43 2.12
4838 11902 5.502382 CGGTGCTGTAACAGTATTGCAATAG 60.502 44.000 19.41 11.28 33.43 1.73
4839 11903 4.331443 CGGTGCTGTAACAGTATTGCAATA 59.669 41.667 15.21 15.21 33.43 1.90
4840 11904 3.126858 CGGTGCTGTAACAGTATTGCAAT 59.873 43.478 17.56 17.56 33.43 3.56
4841 11905 2.482336 CGGTGCTGTAACAGTATTGCAA 59.518 45.455 0.00 0.00 33.43 4.08
4842 11906 2.073056 CGGTGCTGTAACAGTATTGCA 58.927 47.619 0.00 0.00 33.43 4.08
4843 11907 1.202031 GCGGTGCTGTAACAGTATTGC 60.202 52.381 0.00 0.00 33.43 3.56
4844 11908 2.073056 TGCGGTGCTGTAACAGTATTG 58.927 47.619 0.00 0.00 33.43 1.90
4845 11909 2.073816 GTGCGGTGCTGTAACAGTATT 58.926 47.619 0.00 0.00 33.43 1.89
4846 11910 1.001520 TGTGCGGTGCTGTAACAGTAT 59.998 47.619 0.00 0.00 33.43 2.12
4847 11911 0.389757 TGTGCGGTGCTGTAACAGTA 59.610 50.000 0.00 0.00 33.43 2.74
4857 11941 1.212751 GGAATCCTTTGTGCGGTGC 59.787 57.895 0.00 0.00 0.00 5.01
4861 11945 2.358957 TCATCTGGAATCCTTTGTGCG 58.641 47.619 0.00 0.00 0.00 5.34
4888 11972 7.839680 AAAGAAGGAATGACTGGTTGTAATT 57.160 32.000 0.00 0.00 32.51 1.40
4913 11998 6.240549 AGCTGTACTATTAACCATGCTCTT 57.759 37.500 0.00 0.00 0.00 2.85
4936 12021 6.891908 TGACAGTATCATATAGCCATCAGCTA 59.108 38.462 0.00 0.00 45.14 3.32
4956 12041 7.048629 AGGTTGACTATAGATGACATGACAG 57.951 40.000 6.78 0.00 0.00 3.51
4960 12045 9.579768 GCTATAAGGTTGACTATAGATGACATG 57.420 37.037 6.78 0.00 0.00 3.21
5066 12151 2.915604 AGAATGAGAGGTGGACCATGTT 59.084 45.455 0.00 0.00 38.89 2.71
5070 12155 1.902508 GTGAGAATGAGAGGTGGACCA 59.097 52.381 0.00 0.00 38.89 4.02
5091 12176 3.755378 AGAATAAGAGCCAACTGCAACAG 59.245 43.478 0.00 0.00 44.83 3.16
5093 12178 3.503748 ACAGAATAAGAGCCAACTGCAAC 59.496 43.478 0.00 0.00 44.83 4.17
5094 12179 3.754965 ACAGAATAAGAGCCAACTGCAA 58.245 40.909 0.00 0.00 44.83 4.08
5114 12217 4.004314 GGGAGAGAAAAGAAACTGGCTAC 58.996 47.826 0.00 0.00 0.00 3.58
5127 12230 2.191400 CTGACATGGAGGGGAGAGAAA 58.809 52.381 0.00 0.00 0.00 2.52
5200 12315 2.756829 TCGCGGTCATGTTTAGAACAA 58.243 42.857 6.13 0.00 45.86 2.83
5203 12318 5.233476 GTCATATTCGCGGTCATGTTTAGAA 59.767 40.000 6.13 0.00 0.00 2.10
5210 12325 2.200899 TGTGTCATATTCGCGGTCATG 58.799 47.619 6.13 7.33 0.00 3.07
5216 12331 4.081761 GTGTTTCTTGTGTCATATTCGCG 58.918 43.478 0.00 0.00 0.00 5.87
5217 12332 5.029650 TGTGTTTCTTGTGTCATATTCGC 57.970 39.130 0.00 0.00 0.00 4.70
5218 12333 6.742718 GGATTGTGTTTCTTGTGTCATATTCG 59.257 38.462 0.00 0.00 0.00 3.34
5219 12334 6.742718 CGGATTGTGTTTCTTGTGTCATATTC 59.257 38.462 0.00 0.00 0.00 1.75
5221 12336 5.123820 CCGGATTGTGTTTCTTGTGTCATAT 59.876 40.000 0.00 0.00 0.00 1.78
5222 12337 4.454161 CCGGATTGTGTTTCTTGTGTCATA 59.546 41.667 0.00 0.00 0.00 2.15
5223 12338 3.253188 CCGGATTGTGTTTCTTGTGTCAT 59.747 43.478 0.00 0.00 0.00 3.06
5224 12339 2.616376 CCGGATTGTGTTTCTTGTGTCA 59.384 45.455 0.00 0.00 0.00 3.58
5225 12340 2.616842 ACCGGATTGTGTTTCTTGTGTC 59.383 45.455 9.46 0.00 0.00 3.67
5226 12341 2.616842 GACCGGATTGTGTTTCTTGTGT 59.383 45.455 9.46 0.00 0.00 3.72
5227 12342 2.878406 AGACCGGATTGTGTTTCTTGTG 59.122 45.455 9.46 0.00 0.00 3.33
5228 12343 3.208747 AGACCGGATTGTGTTTCTTGT 57.791 42.857 9.46 0.00 0.00 3.16
5229 12344 3.563808 TCAAGACCGGATTGTGTTTCTTG 59.436 43.478 9.46 14.52 40.78 3.02
5230 12345 3.815401 CTCAAGACCGGATTGTGTTTCTT 59.185 43.478 9.46 0.14 0.00 2.52
5231 12346 3.071023 TCTCAAGACCGGATTGTGTTTCT 59.929 43.478 9.46 0.00 0.00 2.52
5232 12347 3.399330 TCTCAAGACCGGATTGTGTTTC 58.601 45.455 9.46 0.00 0.00 2.78
5233 12348 3.071023 TCTCTCAAGACCGGATTGTGTTT 59.929 43.478 9.46 0.00 0.00 2.83
5272 12387 0.693622 TGGGCAAAGTTATGGTCGGA 59.306 50.000 0.00 0.00 0.00 4.55
5290 12405 1.607467 CTTCCCCTTGCCCACCTTG 60.607 63.158 0.00 0.00 0.00 3.61
5294 12409 1.303643 CACTCTTCCCCTTGCCCAC 60.304 63.158 0.00 0.00 0.00 4.61
5340 12455 0.698818 ACTCCAATCAAGGGTCACCC 59.301 55.000 3.85 3.85 45.90 4.61
5341 12456 2.162681 CAACTCCAATCAAGGGTCACC 58.837 52.381 0.00 0.00 0.00 4.02
5342 12457 2.162681 CCAACTCCAATCAAGGGTCAC 58.837 52.381 0.00 0.00 0.00 3.67
5343 12458 2.061848 TCCAACTCCAATCAAGGGTCA 58.938 47.619 0.00 0.00 0.00 4.02
5344 12459 2.879103 TCCAACTCCAATCAAGGGTC 57.121 50.000 0.00 0.00 0.00 4.46
5345 12460 4.386761 CCATATCCAACTCCAATCAAGGGT 60.387 45.833 0.00 0.00 0.00 4.34
5385 12500 4.738998 TGGGGTTGATGCCTGGCG 62.739 66.667 14.98 0.00 0.00 5.69
5388 12503 2.757099 GGCTGGGGTTGATGCCTG 60.757 66.667 0.00 0.00 41.92 4.85
5405 12520 3.555956 GTCTTCGGTATGCCACTACATTG 59.444 47.826 0.00 0.00 34.09 2.82
5453 12568 3.067106 CACCATATCAACATCGGCTACC 58.933 50.000 0.00 0.00 0.00 3.18
5459 12574 0.867746 CGGCCACCATATCAACATCG 59.132 55.000 2.24 0.00 0.00 3.84
5478 12593 1.807142 CTTTGTCTTCCTTCGCCCTTC 59.193 52.381 0.00 0.00 0.00 3.46
5480 12595 0.606673 GCTTTGTCTTCCTTCGCCCT 60.607 55.000 0.00 0.00 0.00 5.19
5495 12610 0.524862 CAAGCTCGCTTGGATGCTTT 59.475 50.000 20.87 0.00 46.88 3.51


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

AutoCloner maintained by Alex Coulton.