Multiple sequence alignment - TraesCS4A01G273100

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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 TraesCS4A01G273100 chr4A 100.000 3314 0 0 1 3314 583971798 583968485 0.000000e+00 6120.0
1 TraesCS4A01G273100 chr4A 86.525 141 13 5 187 327 501300681 501300815 2.060000e-32 150.0
2 TraesCS4A01G273100 chr4A 100.000 53 0 0 2866 2918 583968875 583968823 7.570000e-17 99.0
3 TraesCS4A01G273100 chr4A 100.000 53 0 0 2924 2976 583968933 583968881 7.570000e-17 99.0
4 TraesCS4A01G273100 chr4D 91.437 2756 97 55 625 3314 16542573 16545255 0.000000e+00 3653.0
5 TraesCS4A01G273100 chr4D 90.573 541 42 6 326 864 16542038 16542571 0.000000e+00 708.0
6 TraesCS4A01G273100 chr4D 84.946 186 23 5 5 186 16541731 16541915 2.030000e-42 183.0
7 TraesCS4A01G273100 chr4D 89.076 119 11 2 70 186 16541922 16542040 2.660000e-31 147.0
8 TraesCS4A01G273100 chr4D 100.000 64 0 0 2928 2991 16544759 16544822 5.810000e-23 119.0
9 TraesCS4A01G273100 chr4B 93.896 2310 98 21 625 2918 28408444 28410726 0.000000e+00 3445.0
10 TraesCS4A01G273100 chr4B 90.485 536 46 4 330 864 28407911 28408442 0.000000e+00 702.0
11 TraesCS4A01G273100 chr2B 84.690 1339 201 4 996 2332 198542776 198541440 0.000000e+00 1334.0
12 TraesCS4A01G273100 chr2B 93.750 48 3 0 2847 2894 765391295 765391248 4.590000e-09 73.1
13 TraesCS4A01G273100 chr2A 84.690 1339 201 4 996 2332 161272035 161270699 0.000000e+00 1334.0
14 TraesCS4A01G273100 chr2A 91.289 287 22 2 1220 1505 682728037 682727753 4.010000e-104 388.0
15 TraesCS4A01G273100 chr2A 87.047 193 22 3 1771 1962 682727755 682727565 7.200000e-52 215.0
16 TraesCS4A01G273100 chr2A 93.878 49 3 0 2847 2895 416923055 416923007 1.280000e-09 75.0
17 TraesCS4A01G273100 chr2D 84.099 1327 202 8 996 2317 139741213 139742535 0.000000e+00 1273.0
18 TraesCS4A01G273100 chr2D 93.878 49 3 0 2847 2895 317589439 317589487 1.280000e-09 75.0
19 TraesCS4A01G273100 chr5B 89.091 55 4 2 2845 2899 471403185 471403133 2.130000e-07 67.6
20 TraesCS4A01G273100 chr1A 95.122 41 2 0 2847 2887 532891511 532891551 7.680000e-07 65.8
21 TraesCS4A01G273100 chr1A 94.872 39 2 0 2845 2883 15521544 15521582 9.930000e-06 62.1
22 TraesCS4A01G273100 chr3D 93.023 43 3 0 2850 2892 563445324 563445366 2.760000e-06 63.9


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 TraesCS4A01G273100 chr4A 583968485 583971798 3313 True 2106.0 6120 100.0000 1 3314 3 chr4A.!!$R1 3313
1 TraesCS4A01G273100 chr4D 16541731 16545255 3524 False 962.0 3653 91.2064 5 3314 5 chr4D.!!$F1 3309
2 TraesCS4A01G273100 chr4B 28407911 28410726 2815 False 2073.5 3445 92.1905 330 2918 2 chr4B.!!$F1 2588
3 TraesCS4A01G273100 chr2B 198541440 198542776 1336 True 1334.0 1334 84.6900 996 2332 1 chr2B.!!$R1 1336
4 TraesCS4A01G273100 chr2A 161270699 161272035 1336 True 1334.0 1334 84.6900 996 2332 1 chr2A.!!$R1 1336
5 TraesCS4A01G273100 chr2D 139741213 139742535 1322 False 1273.0 1273 84.0990 996 2317 1 chr2D.!!$F1 1321

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
311 316 0.036388 ACTTATGCGGGATATGCGGG 60.036 55.0 4.01 0.0 34.24 6.13 F
640 647 0.107703 TCATCACGTGATTCCTGGGC 60.108 55.0 28.04 0.0 31.21 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1515 1768 0.462759 GCTTCTTGGGGAGATCCACG 60.463 60.0 0.47 0.0 44.25 4.94 R
2623 2884 0.779997 AGATGGGCAAAACAGGAGGT 59.220 50.0 0.00 0.0 0.00 3.85 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
18 19 3.306206 GCTCCCGTAATTTTGTGCG 57.694 52.632 0.00 0.00 0.00 5.34
19 20 0.796870 GCTCCCGTAATTTTGTGCGC 60.797 55.000 0.00 0.00 0.00 6.09
21 22 1.153920 CCCGTAATTTTGTGCGCCC 60.154 57.895 4.18 0.00 0.00 6.13
22 23 1.153920 CCGTAATTTTGTGCGCCCC 60.154 57.895 4.18 0.00 0.00 5.80
23 24 1.591504 CCGTAATTTTGTGCGCCCCT 61.592 55.000 4.18 0.00 0.00 4.79
24 25 0.242555 CGTAATTTTGTGCGCCCCTT 59.757 50.000 4.18 0.00 0.00 3.95
31 32 3.373565 GTGCGCCCCTTTCCCTTG 61.374 66.667 4.18 0.00 0.00 3.61
33 34 4.678743 GCGCCCCTTTCCCTTGGT 62.679 66.667 0.00 0.00 0.00 3.67
37 38 1.202770 CGCCCCTTTCCCTTGGTATAG 60.203 57.143 0.00 0.00 0.00 1.31
42 43 3.490348 CCTTTCCCTTGGTATAGGCATG 58.510 50.000 0.00 0.00 33.73 4.06
47 48 4.562767 TCCCTTGGTATAGGCATGTTCTA 58.437 43.478 0.00 0.00 33.73 2.10
62 63 4.274602 TGTTCTAATCGGTTTGTGCCTA 57.725 40.909 0.00 0.00 0.00 3.93
63 64 4.839121 TGTTCTAATCGGTTTGTGCCTAT 58.161 39.130 0.00 0.00 0.00 2.57
64 65 4.873827 TGTTCTAATCGGTTTGTGCCTATC 59.126 41.667 0.00 0.00 0.00 2.08
65 66 3.713288 TCTAATCGGTTTGTGCCTATCG 58.287 45.455 0.00 0.00 0.00 2.92
67 68 0.539986 ATCGGTTTGTGCCTATCGGT 59.460 50.000 0.00 0.00 0.00 4.69
68 69 0.108520 TCGGTTTGTGCCTATCGGTC 60.109 55.000 0.00 0.00 0.00 4.79
69 70 1.087771 CGGTTTGTGCCTATCGGTCC 61.088 60.000 0.00 0.00 0.00 4.46
70 71 0.252197 GGTTTGTGCCTATCGGTCCT 59.748 55.000 0.00 0.00 0.00 3.85
72 73 2.104281 GGTTTGTGCCTATCGGTCCTAT 59.896 50.000 0.00 0.00 0.00 2.57
82 86 5.995897 GCCTATCGGTCCTATTTTACATTGT 59.004 40.000 0.00 0.00 0.00 2.71
84 88 7.012989 GCCTATCGGTCCTATTTTACATTGTTT 59.987 37.037 0.00 0.00 0.00 2.83
100 104 7.849322 ACATTGTTTAAGTATGTTTTCCCCT 57.151 32.000 0.00 0.00 0.00 4.79
103 107 5.707495 TGTTTAAGTATGTTTTCCCCTGGT 58.293 37.500 0.00 0.00 0.00 4.00
119 124 2.422519 CCTGGTGCTGGCTAGATTTGAT 60.423 50.000 0.00 0.00 0.00 2.57
186 191 8.150945 ACTCACAATTGTACAGTTCTATGTCTT 58.849 33.333 11.53 0.00 34.56 3.01
187 192 9.639601 CTCACAATTGTACAGTTCTATGTCTTA 57.360 33.333 11.53 0.00 34.56 2.10
189 194 8.873830 CACAATTGTACAGTTCTATGTCTTAGG 58.126 37.037 11.53 0.00 34.56 2.69
190 195 8.041323 ACAATTGTACAGTTCTATGTCTTAGGG 58.959 37.037 9.97 0.00 34.56 3.53
192 197 5.586877 TGTACAGTTCTATGTCTTAGGGGT 58.413 41.667 0.00 0.00 34.56 4.95
193 198 5.421056 TGTACAGTTCTATGTCTTAGGGGTG 59.579 44.000 0.00 0.00 34.56 4.61
194 199 3.197983 ACAGTTCTATGTCTTAGGGGTGC 59.802 47.826 0.00 0.00 0.00 5.01
195 200 2.772515 AGTTCTATGTCTTAGGGGTGCC 59.227 50.000 0.00 0.00 0.00 5.01
197 202 2.398588 TCTATGTCTTAGGGGTGCCAG 58.601 52.381 0.00 0.00 0.00 4.85
198 203 2.023404 TCTATGTCTTAGGGGTGCCAGA 60.023 50.000 0.00 0.00 0.00 3.86
199 204 1.207791 ATGTCTTAGGGGTGCCAGAG 58.792 55.000 0.00 0.00 0.00 3.35
200 205 1.222113 GTCTTAGGGGTGCCAGAGC 59.778 63.158 0.00 0.00 40.48 4.09
201 206 2.187946 CTTAGGGGTGCCAGAGCG 59.812 66.667 0.00 0.00 44.31 5.03
202 207 3.391665 CTTAGGGGTGCCAGAGCGG 62.392 68.421 0.00 0.00 44.31 5.52
221 226 4.162690 GTCCGATCCGCCCAGCTT 62.163 66.667 0.00 0.00 0.00 3.74
222 227 3.399181 TCCGATCCGCCCAGCTTT 61.399 61.111 0.00 0.00 0.00 3.51
223 228 3.204827 CCGATCCGCCCAGCTTTG 61.205 66.667 0.00 0.00 0.00 2.77
225 230 1.153449 CGATCCGCCCAGCTTTGTA 60.153 57.895 0.00 0.00 0.00 2.41
227 232 0.107654 GATCCGCCCAGCTTTGTAGT 60.108 55.000 0.00 0.00 0.00 2.73
228 233 1.138266 GATCCGCCCAGCTTTGTAGTA 59.862 52.381 0.00 0.00 0.00 1.82
229 234 1.200519 TCCGCCCAGCTTTGTAGTAT 58.799 50.000 0.00 0.00 0.00 2.12
230 235 2.390696 TCCGCCCAGCTTTGTAGTATA 58.609 47.619 0.00 0.00 0.00 1.47
231 236 2.767394 TCCGCCCAGCTTTGTAGTATAA 59.233 45.455 0.00 0.00 0.00 0.98
232 237 3.198200 TCCGCCCAGCTTTGTAGTATAAA 59.802 43.478 0.00 0.00 0.00 1.40
233 238 3.311596 CCGCCCAGCTTTGTAGTATAAAC 59.688 47.826 0.00 0.00 0.00 2.01
234 239 3.936453 CGCCCAGCTTTGTAGTATAAACA 59.064 43.478 0.00 0.00 0.00 2.83
235 240 4.034048 CGCCCAGCTTTGTAGTATAAACAG 59.966 45.833 0.00 0.00 0.00 3.16
237 242 5.823045 GCCCAGCTTTGTAGTATAAACAGAT 59.177 40.000 0.00 0.00 0.00 2.90
238 243 6.017852 GCCCAGCTTTGTAGTATAAACAGATC 60.018 42.308 0.00 0.00 0.00 2.75
239 244 7.047891 CCCAGCTTTGTAGTATAAACAGATCA 58.952 38.462 0.00 0.00 0.00 2.92
240 245 7.011482 CCCAGCTTTGTAGTATAAACAGATCAC 59.989 40.741 0.00 0.00 0.00 3.06
241 246 7.254117 CCAGCTTTGTAGTATAAACAGATCACG 60.254 40.741 0.00 0.00 0.00 4.35
242 247 7.275779 CAGCTTTGTAGTATAAACAGATCACGT 59.724 37.037 0.00 0.00 0.00 4.49
243 248 7.817962 AGCTTTGTAGTATAAACAGATCACGTT 59.182 33.333 0.00 0.00 0.00 3.99
244 249 9.079833 GCTTTGTAGTATAAACAGATCACGTTA 57.920 33.333 0.00 0.00 0.00 3.18
256 261 7.948278 ACAGATCACGTTAGCTATAATTTCC 57.052 36.000 0.00 0.00 0.00 3.13
257 262 7.727181 ACAGATCACGTTAGCTATAATTTCCT 58.273 34.615 0.00 0.00 0.00 3.36
258 263 7.868415 ACAGATCACGTTAGCTATAATTTCCTC 59.132 37.037 0.00 0.00 0.00 3.71
259 264 7.867909 CAGATCACGTTAGCTATAATTTCCTCA 59.132 37.037 0.00 0.00 0.00 3.86
260 265 8.589338 AGATCACGTTAGCTATAATTTCCTCAT 58.411 33.333 0.00 0.00 0.00 2.90
261 266 8.764524 ATCACGTTAGCTATAATTTCCTCATC 57.235 34.615 0.00 0.00 0.00 2.92
262 267 7.152645 TCACGTTAGCTATAATTTCCTCATCC 58.847 38.462 0.00 0.00 0.00 3.51
263 268 6.929049 CACGTTAGCTATAATTTCCTCATCCA 59.071 38.462 0.00 0.00 0.00 3.41
265 270 7.990886 ACGTTAGCTATAATTTCCTCATCCAAA 59.009 33.333 0.00 0.00 0.00 3.28
266 271 9.003658 CGTTAGCTATAATTTCCTCATCCAAAT 57.996 33.333 0.00 0.00 0.00 2.32
278 283 8.650143 TTCCTCATCCAAATTTAGCTTAGTTT 57.350 30.769 0.00 0.00 0.00 2.66
280 285 6.753744 CCTCATCCAAATTTAGCTTAGTTTGC 59.246 38.462 13.41 0.00 31.87 3.68
282 287 7.090173 TCATCCAAATTTAGCTTAGTTTGCAC 58.910 34.615 13.41 0.00 31.87 4.57
284 289 7.753309 TCCAAATTTAGCTTAGTTTGCACTA 57.247 32.000 13.41 0.00 34.06 2.74
285 290 8.348285 TCCAAATTTAGCTTAGTTTGCACTAT 57.652 30.769 13.41 0.00 35.32 2.12
286 291 8.802267 TCCAAATTTAGCTTAGTTTGCACTATT 58.198 29.630 13.41 0.00 35.32 1.73
289 294 9.639601 AAATTTAGCTTAGTTTGCACTATTTCC 57.360 29.630 0.00 0.00 35.32 3.13
291 296 4.923415 AGCTTAGTTTGCACTATTTCCCT 58.077 39.130 0.00 0.00 35.32 4.20
292 297 6.062258 AGCTTAGTTTGCACTATTTCCCTA 57.938 37.500 0.00 0.00 35.32 3.53
293 298 5.880887 AGCTTAGTTTGCACTATTTCCCTAC 59.119 40.000 0.00 0.00 35.32 3.18
294 299 5.880887 GCTTAGTTTGCACTATTTCCCTACT 59.119 40.000 0.00 0.00 35.32 2.57
295 300 6.374613 GCTTAGTTTGCACTATTTCCCTACTT 59.625 38.462 0.00 0.00 35.32 2.24
296 301 7.551617 GCTTAGTTTGCACTATTTCCCTACTTA 59.448 37.037 0.00 0.00 35.32 2.24
297 302 9.614792 CTTAGTTTGCACTATTTCCCTACTTAT 57.385 33.333 0.00 0.00 35.32 1.73
298 303 7.865706 AGTTTGCACTATTTCCCTACTTATG 57.134 36.000 0.00 0.00 0.00 1.90
299 304 6.318900 AGTTTGCACTATTTCCCTACTTATGC 59.681 38.462 0.00 0.00 0.00 3.14
301 306 3.746492 GCACTATTTCCCTACTTATGCGG 59.254 47.826 0.00 0.00 0.00 5.69
302 307 4.315803 CACTATTTCCCTACTTATGCGGG 58.684 47.826 0.00 0.00 39.41 6.13
303 308 4.039973 CACTATTTCCCTACTTATGCGGGA 59.960 45.833 0.00 0.00 45.02 5.14
304 309 4.844655 ACTATTTCCCTACTTATGCGGGAT 59.155 41.667 7.00 0.00 45.91 3.85
308 313 2.500098 TCCCTACTTATGCGGGATATGC 59.500 50.000 0.00 0.00 41.95 3.14
309 314 2.540515 CCTACTTATGCGGGATATGCG 58.459 52.381 2.91 0.00 34.24 4.73
310 315 2.540515 CTACTTATGCGGGATATGCGG 58.459 52.381 0.00 0.00 34.24 5.69
311 316 0.036388 ACTTATGCGGGATATGCGGG 60.036 55.000 4.01 0.00 34.24 6.13
312 317 0.249120 CTTATGCGGGATATGCGGGA 59.751 55.000 4.01 1.11 34.24 5.14
313 318 0.908910 TTATGCGGGATATGCGGGAT 59.091 50.000 12.68 12.68 34.24 3.85
314 319 0.177836 TATGCGGGATATGCGGGATG 59.822 55.000 16.54 0.00 34.24 3.51
315 320 3.127533 GCGGGATATGCGGGATGC 61.128 66.667 4.01 0.00 46.70 3.91
316 321 2.436646 CGGGATATGCGGGATGCC 60.437 66.667 0.00 0.00 45.60 4.40
317 322 2.044946 GGGATATGCGGGATGCCC 60.045 66.667 0.00 6.52 45.60 5.36
318 323 2.756400 GGATATGCGGGATGCCCA 59.244 61.111 0.00 0.00 45.83 5.36
319 324 1.675641 GGATATGCGGGATGCCCAC 60.676 63.158 0.00 0.00 45.83 4.61
320 325 1.376466 GATATGCGGGATGCCCACT 59.624 57.895 0.00 0.00 45.83 4.00
321 326 0.250901 GATATGCGGGATGCCCACTT 60.251 55.000 0.00 0.00 45.83 3.16
322 327 0.538057 ATATGCGGGATGCCCACTTG 60.538 55.000 0.00 0.00 45.83 3.16
349 354 2.265367 TGTTGGAGGCTTGGTCTATCA 58.735 47.619 0.00 0.00 0.00 2.15
388 393 4.346129 GCACATGCTATTTGTTAGTGCTC 58.654 43.478 0.00 0.00 45.24 4.26
389 394 4.581493 CACATGCTATTTGTTAGTGCTCG 58.419 43.478 0.00 0.00 0.00 5.03
390 395 4.093408 CACATGCTATTTGTTAGTGCTCGT 59.907 41.667 0.00 0.00 0.00 4.18
391 396 5.290885 CACATGCTATTTGTTAGTGCTCGTA 59.709 40.000 0.00 0.00 0.00 3.43
392 397 5.291128 ACATGCTATTTGTTAGTGCTCGTAC 59.709 40.000 0.00 0.00 0.00 3.67
509 515 3.378339 GCCACGTAGCGTATGTTTAGAT 58.622 45.455 0.00 0.00 38.32 1.98
526 532 8.110860 TGTTTAGATTCAATTTTGAGGACCTC 57.889 34.615 15.13 15.13 38.61 3.85
530 536 5.412904 AGATTCAATTTTGAGGACCTCGAAC 59.587 40.000 21.92 10.08 38.61 3.95
547 553 4.389576 CGCCACACGCTTTCTGCC 62.390 66.667 0.00 0.00 38.78 4.85
640 647 0.107703 TCATCACGTGATTCCTGGGC 60.108 55.000 28.04 0.00 31.21 5.36
663 670 2.417516 CCGAATCGGCCGACTCAT 59.582 61.111 33.05 19.29 41.17 2.90
664 671 1.658114 CCGAATCGGCCGACTCATA 59.342 57.895 33.05 11.13 41.17 2.15
697 704 1.610363 TACCGTTGCTGGCATTTTCA 58.390 45.000 0.00 0.00 0.00 2.69
786 793 8.576442 AGATCACGTGTTGGATTTAATTCTTTT 58.424 29.630 16.51 0.00 0.00 2.27
791 798 8.626526 ACGTGTTGGATTTAATTCTTTTAGTGT 58.373 29.630 0.00 0.00 0.00 3.55
857 864 3.371168 GTTGTCGTGTTGCATTGAATGT 58.629 40.909 7.05 0.00 0.00 2.71
864 871 2.160219 TGTTGCATTGAATGTCTCGCTC 59.840 45.455 7.05 0.00 0.00 5.03
870 1123 4.556523 GCATTGAATGTCTCGCTCTTTTTC 59.443 41.667 7.05 0.00 0.00 2.29
884 1137 5.622007 CGCTCTTTTTCCCATGCAAAATCTA 60.622 40.000 0.00 0.00 0.00 1.98
887 1140 7.173047 GCTCTTTTTCCCATGCAAAATCTAAAA 59.827 33.333 0.00 0.00 0.00 1.52
892 1145 9.517868 TTTTCCCATGCAAAATCTAAAATCAAT 57.482 25.926 0.00 0.00 0.00 2.57
893 1146 9.517868 TTTCCCATGCAAAATCTAAAATCAATT 57.482 25.926 0.00 0.00 0.00 2.32
894 1147 9.517868 TTCCCATGCAAAATCTAAAATCAATTT 57.482 25.926 0.00 0.00 34.92 1.82
896 1149 9.777575 CCCATGCAAAATCTAAAATCAATTTTC 57.222 29.630 4.07 0.00 40.24 2.29
900 1153 9.881529 TGCAAAATCTAAAATCAATTTTCTTGC 57.118 25.926 4.07 11.76 40.24 4.01
901 1154 9.881529 GCAAAATCTAAAATCAATTTTCTTGCA 57.118 25.926 4.07 0.00 40.24 4.08
904 1157 9.498176 AAATCTAAAATCAATTTTCTTGCAGCT 57.502 25.926 4.07 0.00 40.24 4.24
905 1158 8.699283 ATCTAAAATCAATTTTCTTGCAGCTC 57.301 30.769 4.07 0.00 40.24 4.09
906 1159 7.889469 TCTAAAATCAATTTTCTTGCAGCTCT 58.111 30.769 4.07 0.00 40.24 4.09
907 1160 8.362639 TCTAAAATCAATTTTCTTGCAGCTCTT 58.637 29.630 4.07 0.00 40.24 2.85
908 1161 9.630098 CTAAAATCAATTTTCTTGCAGCTCTTA 57.370 29.630 4.07 0.00 40.24 2.10
909 1162 8.530269 AAAATCAATTTTCTTGCAGCTCTTAG 57.470 30.769 0.00 0.00 35.18 2.18
910 1163 7.458409 AATCAATTTTCTTGCAGCTCTTAGA 57.542 32.000 0.00 0.00 0.00 2.10
911 1164 6.246420 TCAATTTTCTTGCAGCTCTTAGAC 57.754 37.500 0.00 0.00 0.00 2.59
912 1165 6.000219 TCAATTTTCTTGCAGCTCTTAGACT 59.000 36.000 0.00 0.00 0.00 3.24
913 1166 6.148480 TCAATTTTCTTGCAGCTCTTAGACTC 59.852 38.462 0.00 0.00 0.00 3.36
924 1177 5.304101 CAGCTCTTAGACTCCCATCACTTAT 59.696 44.000 0.00 0.00 0.00 1.73
925 1178 5.538433 AGCTCTTAGACTCCCATCACTTATC 59.462 44.000 0.00 0.00 0.00 1.75
926 1179 5.303078 GCTCTTAGACTCCCATCACTTATCA 59.697 44.000 0.00 0.00 0.00 2.15
927 1180 6.516527 GCTCTTAGACTCCCATCACTTATCAG 60.517 46.154 0.00 0.00 0.00 2.90
935 1188 2.871022 CCATCACTTATCAGCACTCTGC 59.129 50.000 0.00 0.00 45.46 4.26
952 1205 5.698089 CACTCTGCTCATTTCTTACACTTGA 59.302 40.000 0.00 0.00 0.00 3.02
956 1209 7.615403 TCTGCTCATTTCTTACACTTGATAGT 58.385 34.615 0.00 0.00 34.00 2.12
1143 1396 0.388649 ATCAAGTCTCGCGTGTGACC 60.389 55.000 23.34 9.30 38.97 4.02
1338 1591 9.764363 AAGGAAAAGAAGGTTACAATTGATTTC 57.236 29.630 13.59 7.98 0.00 2.17
1515 1768 3.968649 TGAAGTGCTTCACAAATTCAGC 58.031 40.909 10.26 0.00 43.90 4.26
1845 2099 8.976986 AAATTCTAGCAAATGTGAAGTTCATC 57.023 30.769 9.18 3.86 0.00 2.92
2081 2335 1.338105 CCAGAGCAACTTCCGTGATCA 60.338 52.381 0.00 0.00 0.00 2.92
2337 2591 3.638860 ACCAATCAATCACATGCCTGAT 58.361 40.909 0.00 0.00 31.84 2.90
2339 2593 3.383505 CCAATCAATCACATGCCTGATGT 59.616 43.478 0.00 0.00 46.98 3.06
2363 2617 4.142773 GGTCGCGGTTAAATCTGAATTTGA 60.143 41.667 6.13 0.00 35.84 2.69
2408 2662 3.251972 CCTCAAAGAAGCTGTGAGTTTCC 59.748 47.826 12.31 0.00 42.56 3.13
2424 2681 5.532406 TGAGTTTCCTCATATGCAATTAGCC 59.468 40.000 0.00 0.00 42.80 3.93
2425 2682 4.829492 AGTTTCCTCATATGCAATTAGCCC 59.171 41.667 0.00 0.00 44.83 5.19
2434 2694 3.290948 TGCAATTAGCCCGTAATTCCT 57.709 42.857 0.00 0.00 44.83 3.36
2457 2717 6.816640 CCTTTGTCATTTGCATGATTTCTGAT 59.183 34.615 0.00 0.00 41.64 2.90
2511 2771 4.530857 GGCGCGGGTCAGCTACAT 62.531 66.667 8.83 0.00 34.40 2.29
2512 2772 2.415843 GCGCGGGTCAGCTACATA 59.584 61.111 8.83 0.00 34.40 2.29
2513 2773 1.006102 GCGCGGGTCAGCTACATAT 60.006 57.895 8.83 0.00 34.40 1.78
2563 2824 6.827586 ACAACCGCAATTCCTCTATTAAAA 57.172 33.333 0.00 0.00 0.00 1.52
2570 2831 6.035650 CGCAATTCCTCTATTAAAAGACGTCA 59.964 38.462 19.50 0.00 0.00 4.35
2601 2862 5.282055 TCCTAAATCGCAATGATGACTCT 57.718 39.130 0.00 0.00 37.39 3.24
2608 2869 2.604914 CGCAATGATGACTCTGTGTACC 59.395 50.000 0.00 0.00 0.00 3.34
2618 2879 1.343465 CTCTGTGTACCGAACCTTGGT 59.657 52.381 0.00 0.00 43.62 3.67
2619 2880 1.764134 TCTGTGTACCGAACCTTGGTT 59.236 47.619 4.52 4.52 40.96 3.67
2620 2881 1.871039 CTGTGTACCGAACCTTGGTTG 59.129 52.381 10.04 0.00 40.96 3.77
2621 2882 1.209990 TGTGTACCGAACCTTGGTTGT 59.790 47.619 10.04 5.38 40.96 3.32
2622 2883 2.291365 GTGTACCGAACCTTGGTTGTT 58.709 47.619 10.04 0.00 40.96 2.83
2623 2884 3.118482 TGTGTACCGAACCTTGGTTGTTA 60.118 43.478 10.04 0.00 40.96 2.41
2624 2885 3.248363 GTGTACCGAACCTTGGTTGTTAC 59.752 47.826 10.04 8.35 40.96 2.50
2625 2886 1.971481 ACCGAACCTTGGTTGTTACC 58.029 50.000 10.04 0.00 45.26 2.85
2626 2887 1.491754 ACCGAACCTTGGTTGTTACCT 59.508 47.619 10.04 0.00 45.27 3.08
2627 2888 2.148768 CCGAACCTTGGTTGTTACCTC 58.851 52.381 10.04 0.00 45.27 3.85
2628 2889 2.148768 CGAACCTTGGTTGTTACCTCC 58.851 52.381 10.04 0.00 45.27 4.30
2629 2890 2.224450 CGAACCTTGGTTGTTACCTCCT 60.224 50.000 10.04 0.00 45.27 3.69
2630 2891 2.951229 ACCTTGGTTGTTACCTCCTG 57.049 50.000 0.00 0.00 45.27 3.86
2631 2892 2.132686 ACCTTGGTTGTTACCTCCTGT 58.867 47.619 0.00 0.00 45.27 4.00
2632 2893 2.512476 ACCTTGGTTGTTACCTCCTGTT 59.488 45.455 0.00 0.00 45.27 3.16
2633 2894 3.053170 ACCTTGGTTGTTACCTCCTGTTT 60.053 43.478 0.00 0.00 45.27 2.83
2634 2895 3.958147 CCTTGGTTGTTACCTCCTGTTTT 59.042 43.478 0.00 0.00 45.27 2.43
2635 2896 4.202111 CCTTGGTTGTTACCTCCTGTTTTG 60.202 45.833 0.00 0.00 45.27 2.44
2636 2897 2.691011 TGGTTGTTACCTCCTGTTTTGC 59.309 45.455 0.00 0.00 45.27 3.68
2637 2898 2.035449 GGTTGTTACCTCCTGTTTTGCC 59.965 50.000 0.00 0.00 41.53 4.52
2638 2899 1.989706 TGTTACCTCCTGTTTTGCCC 58.010 50.000 0.00 0.00 0.00 5.36
2639 2900 1.215673 TGTTACCTCCTGTTTTGCCCA 59.784 47.619 0.00 0.00 0.00 5.36
2640 2901 2.158385 TGTTACCTCCTGTTTTGCCCAT 60.158 45.455 0.00 0.00 0.00 4.00
2641 2902 2.492088 GTTACCTCCTGTTTTGCCCATC 59.508 50.000 0.00 0.00 0.00 3.51
2722 3012 1.896220 TTAGCAACTTGTCTGCCCTG 58.104 50.000 0.00 0.00 40.86 4.45
2763 3053 1.888512 TCTGCCCTGAATTTGAGTTGC 59.111 47.619 0.00 0.00 0.00 4.17
2868 3158 4.014406 ACCTCCGTCCCAAATTATTTGTC 58.986 43.478 15.40 5.99 38.98 3.18
2918 3208 6.865834 ATCTGTCTGGACAAATCTAAGTCT 57.134 37.500 4.94 0.00 41.33 3.24
2919 3209 6.274157 TCTGTCTGGACAAATCTAAGTCTC 57.726 41.667 4.94 0.00 41.33 3.36
2920 3210 5.060662 TGTCTGGACAAATCTAAGTCTCG 57.939 43.478 0.51 0.00 38.56 4.04
2921 3211 4.765339 TGTCTGGACAAATCTAAGTCTCGA 59.235 41.667 0.51 0.00 38.56 4.04
2922 3212 5.243060 TGTCTGGACAAATCTAAGTCTCGAA 59.757 40.000 0.51 0.00 38.56 3.71
2961 3271 9.639563 ATCTAGGTATGGATGTATATCTGTCTG 57.360 37.037 0.00 0.00 33.68 3.51
2962 3272 8.055790 TCTAGGTATGGATGTATATCTGTCTGG 58.944 40.741 0.00 0.00 33.68 3.86
2963 3273 6.805150 AGGTATGGATGTATATCTGTCTGGA 58.195 40.000 0.00 0.00 33.68 3.86
3070 3380 2.158827 TCTGCAGTACAAAGAGCACCAA 60.159 45.455 14.67 0.00 32.87 3.67
3080 3390 1.177256 AGAGCACCAAAAGCAGCTGG 61.177 55.000 17.12 0.00 37.48 4.85
3125 3476 1.656652 CGCATGTCTCCTACCTTTGG 58.343 55.000 0.00 0.00 0.00 3.28
3137 3488 2.042831 CCTTTGGAAGCGCTCCTGG 61.043 63.158 12.06 13.13 45.64 4.45
3188 3540 0.677288 TCGATCTTCACACCGTGGTT 59.323 50.000 3.03 0.00 33.87 3.67
3217 3584 3.716006 CTGCAACGGAGGTGCACG 61.716 66.667 11.45 1.16 34.61 5.34
3225 3592 1.509004 GGAGGTGCACGAGTCTCTC 59.491 63.158 11.45 10.19 0.00 3.20
3277 3644 2.548178 CGAGTGGACTTGCTGCAAT 58.452 52.632 16.38 6.29 0.00 3.56
3278 3645 0.167470 CGAGTGGACTTGCTGCAATG 59.833 55.000 16.38 12.16 0.00 2.82
3281 3648 1.153524 TGGACTTGCTGCAATGGGT 59.846 52.632 16.38 10.47 0.00 4.51
3286 3653 0.597568 CTTGCTGCAATGGGTCGAAA 59.402 50.000 16.38 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.796870 GCGCACAAAATTACGGGAGC 60.797 55.000 0.30 0.00 0.00 4.70
1 2 0.179174 GGCGCACAAAATTACGGGAG 60.179 55.000 10.83 0.00 0.00 4.30
2 3 1.587933 GGGCGCACAAAATTACGGGA 61.588 55.000 10.83 0.00 0.00 5.14
3 4 1.153920 GGGCGCACAAAATTACGGG 60.154 57.895 10.83 0.00 0.00 5.28
8 9 0.034756 GGAAAGGGGCGCACAAAATT 59.965 50.000 13.89 0.00 0.00 1.82
11 12 2.915137 GGGAAAGGGGCGCACAAA 60.915 61.111 13.89 0.00 0.00 2.83
18 19 1.145119 CCTATACCAAGGGAAAGGGGC 59.855 57.143 0.00 0.00 32.55 5.80
19 20 1.145119 GCCTATACCAAGGGAAAGGGG 59.855 57.143 5.42 0.00 37.11 4.79
21 22 3.117512 ACATGCCTATACCAAGGGAAAGG 60.118 47.826 0.00 0.00 40.73 3.11
22 23 4.170468 ACATGCCTATACCAAGGGAAAG 57.830 45.455 0.00 0.00 40.73 2.62
23 24 4.229582 AGAACATGCCTATACCAAGGGAAA 59.770 41.667 0.00 0.00 40.73 3.13
24 25 3.785887 AGAACATGCCTATACCAAGGGAA 59.214 43.478 0.00 0.00 40.73 3.97
31 32 5.148651 ACCGATTAGAACATGCCTATACC 57.851 43.478 0.00 0.00 0.00 2.73
33 34 6.481976 CACAAACCGATTAGAACATGCCTATA 59.518 38.462 0.00 0.00 0.00 1.31
37 38 3.758300 CACAAACCGATTAGAACATGCC 58.242 45.455 0.00 0.00 0.00 4.40
42 43 4.025979 CGATAGGCACAAACCGATTAGAAC 60.026 45.833 0.00 0.00 33.69 3.01
62 63 9.457436 ACTTAAACAATGTAAAATAGGACCGAT 57.543 29.630 0.00 0.00 0.00 4.18
63 64 8.851541 ACTTAAACAATGTAAAATAGGACCGA 57.148 30.769 0.00 0.00 0.00 4.69
82 86 4.525100 GCACCAGGGGAAAACATACTTAAA 59.475 41.667 0.00 0.00 0.00 1.52
84 88 3.332485 AGCACCAGGGGAAAACATACTTA 59.668 43.478 0.00 0.00 0.00 2.24
91 95 2.574018 GCCAGCACCAGGGGAAAAC 61.574 63.158 0.00 0.00 0.00 2.43
92 96 1.431195 TAGCCAGCACCAGGGGAAAA 61.431 55.000 0.00 0.00 0.00 2.29
96 100 1.639635 AATCTAGCCAGCACCAGGGG 61.640 60.000 0.00 0.00 0.00 4.79
97 101 0.257039 AAATCTAGCCAGCACCAGGG 59.743 55.000 0.00 0.00 0.00 4.45
100 104 2.646930 CATCAAATCTAGCCAGCACCA 58.353 47.619 0.00 0.00 0.00 4.17
103 107 2.723322 AGCATCAAATCTAGCCAGCA 57.277 45.000 0.00 0.00 0.00 4.41
119 124 3.190079 GTGCTTCTCATCGAACATAGCA 58.810 45.455 8.05 8.05 29.76 3.49
167 172 6.672657 ACCCCTAAGACATAGAACTGTACAAT 59.327 38.462 0.00 0.00 33.04 2.71
169 174 5.421056 CACCCCTAAGACATAGAACTGTACA 59.579 44.000 0.00 0.00 33.04 2.90
176 181 2.771943 CTGGCACCCCTAAGACATAGAA 59.228 50.000 0.00 0.00 33.04 2.10
204 209 3.682292 AAAGCTGGGCGGATCGGAC 62.682 63.158 4.16 0.00 0.00 4.79
205 210 3.399181 AAAGCTGGGCGGATCGGA 61.399 61.111 4.16 0.00 0.00 4.55
207 212 1.153449 TACAAAGCTGGGCGGATCG 60.153 57.895 0.00 0.00 0.00 3.69
208 213 0.107654 ACTACAAAGCTGGGCGGATC 60.108 55.000 0.00 0.00 0.00 3.36
210 215 1.200519 ATACTACAAAGCTGGGCGGA 58.799 50.000 0.00 0.00 0.00 5.54
211 216 2.902705 TATACTACAAAGCTGGGCGG 57.097 50.000 0.00 0.00 0.00 6.13
212 217 3.936453 TGTTTATACTACAAAGCTGGGCG 59.064 43.478 0.00 0.00 0.00 6.13
213 218 5.183228 TCTGTTTATACTACAAAGCTGGGC 58.817 41.667 0.00 0.00 0.00 5.36
214 219 7.011482 GTGATCTGTTTATACTACAAAGCTGGG 59.989 40.741 0.00 0.00 0.00 4.45
215 220 7.254117 CGTGATCTGTTTATACTACAAAGCTGG 60.254 40.741 0.00 0.00 0.00 4.85
216 221 7.275779 ACGTGATCTGTTTATACTACAAAGCTG 59.724 37.037 0.00 0.00 0.00 4.24
217 222 7.321153 ACGTGATCTGTTTATACTACAAAGCT 58.679 34.615 0.00 0.00 0.00 3.74
218 223 7.521509 ACGTGATCTGTTTATACTACAAAGC 57.478 36.000 0.00 0.00 0.00 3.51
221 226 8.464404 AGCTAACGTGATCTGTTTATACTACAA 58.536 33.333 8.80 0.00 0.00 2.41
222 227 7.993101 AGCTAACGTGATCTGTTTATACTACA 58.007 34.615 8.80 0.00 0.00 2.74
230 235 8.827677 GGAAATTATAGCTAACGTGATCTGTTT 58.172 33.333 0.00 0.00 0.00 2.83
231 236 8.204836 AGGAAATTATAGCTAACGTGATCTGTT 58.795 33.333 0.00 8.59 0.00 3.16
232 237 7.727181 AGGAAATTATAGCTAACGTGATCTGT 58.273 34.615 0.00 0.00 0.00 3.41
233 238 7.867909 TGAGGAAATTATAGCTAACGTGATCTG 59.132 37.037 0.00 0.00 0.00 2.90
234 239 7.952671 TGAGGAAATTATAGCTAACGTGATCT 58.047 34.615 0.00 0.00 0.00 2.75
235 240 8.764524 ATGAGGAAATTATAGCTAACGTGATC 57.235 34.615 0.00 0.00 0.00 2.92
237 242 7.152645 GGATGAGGAAATTATAGCTAACGTGA 58.847 38.462 0.00 0.00 0.00 4.35
238 243 6.929049 TGGATGAGGAAATTATAGCTAACGTG 59.071 38.462 0.00 0.00 0.00 4.49
239 244 7.062749 TGGATGAGGAAATTATAGCTAACGT 57.937 36.000 0.00 0.00 0.00 3.99
240 245 7.962964 TTGGATGAGGAAATTATAGCTAACG 57.037 36.000 0.00 0.00 0.00 3.18
250 255 9.259832 ACTAAGCTAAATTTGGATGAGGAAATT 57.740 29.630 8.82 0.00 34.04 1.82
251 256 8.829373 ACTAAGCTAAATTTGGATGAGGAAAT 57.171 30.769 8.82 0.00 0.00 2.17
253 258 8.522830 CAAACTAAGCTAAATTTGGATGAGGAA 58.477 33.333 8.82 0.00 0.00 3.36
254 259 7.362920 GCAAACTAAGCTAAATTTGGATGAGGA 60.363 37.037 8.82 0.00 33.55 3.71
255 260 6.753744 GCAAACTAAGCTAAATTTGGATGAGG 59.246 38.462 8.82 0.00 33.55 3.86
256 261 7.274250 GTGCAAACTAAGCTAAATTTGGATGAG 59.726 37.037 5.63 4.09 35.31 2.90
257 262 7.039784 AGTGCAAACTAAGCTAAATTTGGATGA 60.040 33.333 5.63 0.00 35.31 2.92
258 263 7.092716 AGTGCAAACTAAGCTAAATTTGGATG 58.907 34.615 5.63 0.00 35.31 3.51
259 264 7.232118 AGTGCAAACTAAGCTAAATTTGGAT 57.768 32.000 5.63 0.00 35.31 3.41
260 265 6.648879 AGTGCAAACTAAGCTAAATTTGGA 57.351 33.333 5.63 10.91 33.55 3.53
261 266 8.986477 AATAGTGCAAACTAAGCTAAATTTGG 57.014 30.769 14.74 0.00 33.55 3.28
263 268 9.639601 GGAAATAGTGCAAACTAAGCTAAATTT 57.360 29.630 0.00 0.00 0.00 1.82
265 270 7.615757 AGGGAAATAGTGCAAACTAAGCTAAAT 59.384 33.333 0.00 0.00 0.00 1.40
266 271 6.946009 AGGGAAATAGTGCAAACTAAGCTAAA 59.054 34.615 0.00 0.00 0.00 1.85
267 272 6.481643 AGGGAAATAGTGCAAACTAAGCTAA 58.518 36.000 0.00 0.00 0.00 3.09
268 273 6.062258 AGGGAAATAGTGCAAACTAAGCTA 57.938 37.500 0.00 0.00 0.00 3.32
269 274 4.923415 AGGGAAATAGTGCAAACTAAGCT 58.077 39.130 0.00 0.00 0.00 3.74
270 275 5.880887 AGTAGGGAAATAGTGCAAACTAAGC 59.119 40.000 0.00 0.00 0.00 3.09
273 278 7.497909 GCATAAGTAGGGAAATAGTGCAAACTA 59.502 37.037 0.00 0.00 0.00 2.24
274 279 6.318900 GCATAAGTAGGGAAATAGTGCAAACT 59.681 38.462 0.00 0.00 0.00 2.66
275 280 6.495706 GCATAAGTAGGGAAATAGTGCAAAC 58.504 40.000 0.00 0.00 0.00 2.93
278 283 4.377021 CGCATAAGTAGGGAAATAGTGCA 58.623 43.478 0.00 0.00 0.00 4.57
289 294 2.540515 CGCATATCCCGCATAAGTAGG 58.459 52.381 0.00 0.00 0.00 3.18
291 296 1.206132 CCCGCATATCCCGCATAAGTA 59.794 52.381 0.00 0.00 0.00 2.24
292 297 0.036388 CCCGCATATCCCGCATAAGT 60.036 55.000 0.00 0.00 0.00 2.24
293 298 0.249120 TCCCGCATATCCCGCATAAG 59.751 55.000 0.00 0.00 0.00 1.73
294 299 0.908910 ATCCCGCATATCCCGCATAA 59.091 50.000 0.00 0.00 0.00 1.90
295 300 0.177836 CATCCCGCATATCCCGCATA 59.822 55.000 0.00 0.00 0.00 3.14
296 301 1.078214 CATCCCGCATATCCCGCAT 60.078 57.895 0.00 0.00 0.00 4.73
297 302 2.347114 CATCCCGCATATCCCGCA 59.653 61.111 0.00 0.00 0.00 5.69
298 303 3.127533 GCATCCCGCATATCCCGC 61.128 66.667 0.00 0.00 41.79 6.13
299 304 2.436646 GGCATCCCGCATATCCCG 60.437 66.667 0.00 0.00 45.17 5.14
314 319 1.406539 CCAACATAGATGCAAGTGGGC 59.593 52.381 0.00 0.00 0.00 5.36
315 320 2.947652 CTCCAACATAGATGCAAGTGGG 59.052 50.000 0.00 0.00 0.00 4.61
316 321 2.947652 CCTCCAACATAGATGCAAGTGG 59.052 50.000 0.00 0.00 0.00 4.00
317 322 2.357009 GCCTCCAACATAGATGCAAGTG 59.643 50.000 0.00 0.00 0.00 3.16
318 323 2.240667 AGCCTCCAACATAGATGCAAGT 59.759 45.455 0.00 0.00 0.00 3.16
319 324 2.928334 AGCCTCCAACATAGATGCAAG 58.072 47.619 0.00 0.00 0.00 4.01
320 325 3.018856 CAAGCCTCCAACATAGATGCAA 58.981 45.455 0.00 0.00 0.00 4.08
321 326 2.646930 CAAGCCTCCAACATAGATGCA 58.353 47.619 0.00 0.00 0.00 3.96
322 327 1.952296 CCAAGCCTCCAACATAGATGC 59.048 52.381 0.00 0.00 0.00 3.91
323 328 3.118112 AGACCAAGCCTCCAACATAGATG 60.118 47.826 0.00 0.00 0.00 2.90
324 329 3.118531 AGACCAAGCCTCCAACATAGAT 58.881 45.455 0.00 0.00 0.00 1.98
349 354 7.211966 GCATGTGCTCAAGAATAGGAAATAT 57.788 36.000 0.00 0.00 38.21 1.28
371 376 5.068234 AGTACGAGCACTAACAAATAGCA 57.932 39.130 0.00 0.00 34.78 3.49
378 383 6.652481 ACTTCTTACTAGTACGAGCACTAACA 59.348 38.462 0.91 0.00 30.77 2.41
388 393 4.334759 TGCAGGCTACTTCTTACTAGTACG 59.665 45.833 0.91 0.37 0.00 3.67
389 394 5.357596 ACTGCAGGCTACTTCTTACTAGTAC 59.642 44.000 19.93 0.00 0.00 2.73
390 395 5.507637 ACTGCAGGCTACTTCTTACTAGTA 58.492 41.667 19.93 0.00 0.00 1.82
391 396 4.345854 ACTGCAGGCTACTTCTTACTAGT 58.654 43.478 19.93 0.00 0.00 2.57
392 397 4.993029 ACTGCAGGCTACTTCTTACTAG 57.007 45.455 19.93 0.00 0.00 2.57
509 515 3.496884 CGTTCGAGGTCCTCAAAATTGAA 59.503 43.478 19.15 9.69 36.64 2.69
565 571 6.707608 TCTGCGTATCATATCAAGCAAGAAAT 59.292 34.615 0.00 0.00 34.04 2.17
571 577 3.006217 AGCTCTGCGTATCATATCAAGCA 59.994 43.478 0.00 0.00 0.00 3.91
572 578 3.583806 AGCTCTGCGTATCATATCAAGC 58.416 45.455 0.00 0.00 0.00 4.01
621 627 0.107703 GCCCAGGAATCACGTGATGA 60.108 55.000 30.57 4.63 43.13 2.92
622 628 0.107508 AGCCCAGGAATCACGTGATG 60.108 55.000 30.57 19.47 36.62 3.07
663 670 9.221933 CCAGCAACGGTAAAAATACCATATATA 57.778 33.333 5.91 0.00 40.08 0.86
664 671 7.308951 GCCAGCAACGGTAAAAATACCATATAT 60.309 37.037 5.91 0.00 40.08 0.86
697 704 8.879427 AACCACCTAAGCTCTACAATTTAATT 57.121 30.769 0.00 0.00 0.00 1.40
765 772 8.626526 ACACTAAAAGAATTAAATCCAACACGT 58.373 29.630 0.00 0.00 0.00 4.49
786 793 6.018832 GCACGGTCACTTTACTTAAAACACTA 60.019 38.462 0.00 0.00 0.00 2.74
791 798 4.260866 GCTGCACGGTCACTTTACTTAAAA 60.261 41.667 0.00 0.00 0.00 1.52
844 851 2.417933 AGAGCGAGACATTCAATGCAAC 59.582 45.455 0.00 0.00 0.00 4.17
857 864 1.271325 TGCATGGGAAAAAGAGCGAGA 60.271 47.619 0.00 0.00 0.00 4.04
864 871 9.001542 TGATTTTAGATTTTGCATGGGAAAAAG 57.998 29.630 0.00 0.00 35.03 2.27
870 1123 9.777575 GAAAATTGATTTTAGATTTTGCATGGG 57.222 29.630 1.93 0.00 39.86 4.00
884 1137 8.362639 TCTAAGAGCTGCAAGAAAATTGATTTT 58.637 29.630 1.02 1.54 42.24 1.82
887 1140 6.658391 AGTCTAAGAGCTGCAAGAAAATTGAT 59.342 34.615 1.02 0.00 34.07 2.57
892 1145 4.319177 GGAGTCTAAGAGCTGCAAGAAAA 58.681 43.478 1.02 0.00 34.07 2.29
893 1146 3.307059 GGGAGTCTAAGAGCTGCAAGAAA 60.307 47.826 1.02 0.00 34.07 2.52
894 1147 2.234908 GGGAGTCTAAGAGCTGCAAGAA 59.765 50.000 1.02 0.00 34.07 2.52
896 1149 1.552337 TGGGAGTCTAAGAGCTGCAAG 59.448 52.381 1.02 0.00 0.00 4.01
897 1150 1.644509 TGGGAGTCTAAGAGCTGCAA 58.355 50.000 1.02 0.00 0.00 4.08
898 1151 1.759445 GATGGGAGTCTAAGAGCTGCA 59.241 52.381 1.02 0.00 0.00 4.41
899 1152 1.759445 TGATGGGAGTCTAAGAGCTGC 59.241 52.381 0.00 0.00 0.00 5.25
900 1153 3.030291 AGTGATGGGAGTCTAAGAGCTG 58.970 50.000 0.00 0.00 0.00 4.24
901 1154 3.396685 AGTGATGGGAGTCTAAGAGCT 57.603 47.619 0.00 0.00 0.00 4.09
902 1155 5.303078 TGATAAGTGATGGGAGTCTAAGAGC 59.697 44.000 0.00 0.00 0.00 4.09
903 1156 6.516527 GCTGATAAGTGATGGGAGTCTAAGAG 60.517 46.154 0.00 0.00 0.00 2.85
904 1157 5.303078 GCTGATAAGTGATGGGAGTCTAAGA 59.697 44.000 0.00 0.00 0.00 2.10
905 1158 5.069648 TGCTGATAAGTGATGGGAGTCTAAG 59.930 44.000 0.00 0.00 0.00 2.18
906 1159 4.962362 TGCTGATAAGTGATGGGAGTCTAA 59.038 41.667 0.00 0.00 0.00 2.10
907 1160 4.342378 GTGCTGATAAGTGATGGGAGTCTA 59.658 45.833 0.00 0.00 0.00 2.59
908 1161 3.133721 GTGCTGATAAGTGATGGGAGTCT 59.866 47.826 0.00 0.00 0.00 3.24
909 1162 3.133721 AGTGCTGATAAGTGATGGGAGTC 59.866 47.826 0.00 0.00 0.00 3.36
910 1163 3.110705 AGTGCTGATAAGTGATGGGAGT 58.889 45.455 0.00 0.00 0.00 3.85
911 1164 3.387374 AGAGTGCTGATAAGTGATGGGAG 59.613 47.826 0.00 0.00 0.00 4.30
912 1165 3.133542 CAGAGTGCTGATAAGTGATGGGA 59.866 47.826 0.00 0.00 45.17 4.37
913 1166 3.464907 CAGAGTGCTGATAAGTGATGGG 58.535 50.000 0.00 0.00 45.17 4.00
927 1180 3.999663 AGTGTAAGAAATGAGCAGAGTGC 59.000 43.478 0.00 0.00 45.46 4.40
952 1205 6.299805 TCACCTGCAGAATACAGAAACTAT 57.700 37.500 17.39 0.00 37.32 2.12
956 1209 4.756642 CAGTTCACCTGCAGAATACAGAAA 59.243 41.667 17.39 0.00 37.32 2.52
1143 1396 5.595542 ACCATATTCATCACCCAACATCTTG 59.404 40.000 0.00 0.00 0.00 3.02
1338 1591 0.749091 TGATGGGCTTGAATGGCTCG 60.749 55.000 0.00 0.00 31.94 5.03
1515 1768 0.462759 GCTTCTTGGGGAGATCCACG 60.463 60.000 0.47 0.00 44.25 4.94
1845 2099 3.055819 TCCCGATCAACTTCTTCTCTTGG 60.056 47.826 0.00 0.00 0.00 3.61
2081 2335 6.951971 ACTTCTAACTCAGCATTGGTAGATT 58.048 36.000 0.00 0.00 0.00 2.40
2337 2591 1.001068 TCAGATTTAACCGCGACCACA 59.999 47.619 8.23 0.00 0.00 4.17
2339 2593 2.459060 TTCAGATTTAACCGCGACCA 57.541 45.000 8.23 0.00 0.00 4.02
2340 2594 4.095610 CAAATTCAGATTTAACCGCGACC 58.904 43.478 8.23 0.00 33.78 4.79
2363 2617 0.892755 TCCGGAGCAAATAGTCACGT 59.107 50.000 0.00 0.00 0.00 4.49
2408 2662 6.403636 GGAATTACGGGCTAATTGCATATGAG 60.404 42.308 6.97 0.00 40.93 2.90
2424 2681 4.804108 TGCAAATGACAAAGGAATTACGG 58.196 39.130 0.00 0.00 0.00 4.02
2425 2682 6.092092 TCATGCAAATGACAAAGGAATTACG 58.908 36.000 0.00 0.00 0.00 3.18
2434 2694 6.091577 GCATCAGAAATCATGCAAATGACAAA 59.908 34.615 0.00 0.00 44.18 2.83
2457 2717 5.745312 TCTGAAAATAGAACAGGAGAGCA 57.255 39.130 0.00 0.00 33.19 4.26
2563 2824 6.918569 CGATTTAGGATAACATCTTGACGTCT 59.081 38.462 17.92 0.00 0.00 4.18
2570 2831 8.509690 CATCATTGCGATTTAGGATAACATCTT 58.490 33.333 0.00 0.00 29.21 2.40
2601 2862 1.209990 ACAACCAAGGTTCGGTACACA 59.790 47.619 0.51 0.00 34.99 3.72
2608 2869 2.148768 GGAGGTAACAACCAAGGTTCG 58.851 52.381 0.51 1.16 36.00 3.95
2618 2879 2.312390 GGGCAAAACAGGAGGTAACAA 58.688 47.619 0.00 0.00 41.41 2.83
2619 2880 1.215673 TGGGCAAAACAGGAGGTAACA 59.784 47.619 0.00 0.00 41.41 2.41
2620 2881 1.989706 TGGGCAAAACAGGAGGTAAC 58.010 50.000 0.00 0.00 0.00 2.50
2621 2882 2.378547 AGATGGGCAAAACAGGAGGTAA 59.621 45.455 0.00 0.00 0.00 2.85
2622 2883 1.992557 AGATGGGCAAAACAGGAGGTA 59.007 47.619 0.00 0.00 0.00 3.08
2623 2884 0.779997 AGATGGGCAAAACAGGAGGT 59.220 50.000 0.00 0.00 0.00 3.85
2624 2885 1.928868 AAGATGGGCAAAACAGGAGG 58.071 50.000 0.00 0.00 0.00 4.30
2625 2886 4.341366 AAAAAGATGGGCAAAACAGGAG 57.659 40.909 0.00 0.00 0.00 3.69
2647 2933 1.596934 GACGCATGAGTTCCTGGGA 59.403 57.895 2.82 0.00 0.00 4.37
2659 2945 0.599991 TTCAGACAACAGCGACGCAT 60.600 50.000 23.70 6.71 0.00 4.73
2722 3012 4.641989 AGACATTTGCCATGTTCTACCATC 59.358 41.667 0.44 0.00 31.52 3.51
2749 3039 5.368256 AGCTTACAGCAACTCAAATTCAG 57.632 39.130 0.00 0.00 45.56 3.02
2763 3053 8.083462 TGACAACAACAATAAGTAGCTTACAG 57.917 34.615 0.00 0.00 0.00 2.74
2774 3064 3.149981 TCCCGCATGACAACAACAATAA 58.850 40.909 0.00 0.00 0.00 1.40
2948 3258 9.201989 ACTTAGATTTGTCCAGACAGATATACA 57.798 33.333 3.99 0.00 42.94 2.29
2949 3259 9.685828 GACTTAGATTTGTCCAGACAGATATAC 57.314 37.037 3.99 0.00 42.94 1.47
2950 3260 9.421399 TGACTTAGATTTGTCCAGACAGATATA 57.579 33.333 3.99 3.20 42.94 0.86
2951 3261 8.311395 TGACTTAGATTTGTCCAGACAGATAT 57.689 34.615 3.99 4.10 42.94 1.63
2952 3262 7.718334 TGACTTAGATTTGTCCAGACAGATA 57.282 36.000 3.99 0.00 42.94 1.98
2953 3263 6.611613 TGACTTAGATTTGTCCAGACAGAT 57.388 37.500 3.65 3.65 42.94 2.90
2954 3264 6.438741 AGATGACTTAGATTTGTCCAGACAGA 59.561 38.462 0.09 0.00 42.94 3.41
2955 3265 6.638610 AGATGACTTAGATTTGTCCAGACAG 58.361 40.000 0.09 0.00 42.94 3.51
2956 3266 6.211384 TGAGATGACTTAGATTTGTCCAGACA 59.789 38.462 0.00 0.00 39.98 3.41
2957 3267 6.634805 TGAGATGACTTAGATTTGTCCAGAC 58.365 40.000 0.00 0.00 32.67 3.51
2958 3268 6.857437 TGAGATGACTTAGATTTGTCCAGA 57.143 37.500 0.00 0.00 32.67 3.86
2959 3269 7.042858 CGAATGAGATGACTTAGATTTGTCCAG 60.043 40.741 0.00 0.00 32.67 3.86
2960 3270 6.758416 CGAATGAGATGACTTAGATTTGTCCA 59.242 38.462 0.00 0.00 32.67 4.02
2961 3271 6.980978 TCGAATGAGATGACTTAGATTTGTCC 59.019 38.462 0.00 0.00 32.67 4.02
2962 3272 7.918033 TCTCGAATGAGATGACTTAGATTTGTC 59.082 37.037 0.00 0.00 46.25 3.18
2963 3273 7.776107 TCTCGAATGAGATGACTTAGATTTGT 58.224 34.615 0.00 0.00 46.25 2.83
3054 3364 3.287222 TGCTTTTGGTGCTCTTTGTACT 58.713 40.909 0.00 0.00 0.00 2.73
3055 3365 3.632189 CTGCTTTTGGTGCTCTTTGTAC 58.368 45.455 0.00 0.00 0.00 2.90
3056 3366 2.034558 GCTGCTTTTGGTGCTCTTTGTA 59.965 45.455 0.00 0.00 0.00 2.41
3057 3367 1.202452 GCTGCTTTTGGTGCTCTTTGT 60.202 47.619 0.00 0.00 0.00 2.83
3058 3368 1.068127 AGCTGCTTTTGGTGCTCTTTG 59.932 47.619 0.00 0.00 0.00 2.77
3059 3369 1.068127 CAGCTGCTTTTGGTGCTCTTT 59.932 47.619 0.00 0.00 33.03 2.52
3060 3370 0.672342 CAGCTGCTTTTGGTGCTCTT 59.328 50.000 0.00 0.00 33.03 2.85
3061 3371 1.177256 CCAGCTGCTTTTGGTGCTCT 61.177 55.000 8.66 0.00 33.03 4.09
3062 3372 1.288127 CCAGCTGCTTTTGGTGCTC 59.712 57.895 8.66 0.00 33.03 4.26
3080 3390 3.322706 AAAATCGAACGCAGCCGGC 62.323 57.895 21.89 21.89 39.22 6.13
3088 3398 1.573156 GCGCTTTAGCAAAATCGAACG 59.427 47.619 0.00 0.00 42.21 3.95
3089 3399 2.580589 TGCGCTTTAGCAAAATCGAAC 58.419 42.857 9.73 0.00 45.06 3.95
3090 3400 2.979401 TGCGCTTTAGCAAAATCGAA 57.021 40.000 9.73 0.00 45.06 3.71
3125 3476 2.821810 GCCTTCCAGGAGCGCTTC 60.822 66.667 13.26 10.56 37.67 3.86
3161 3512 3.062639 CGGTGTGAAGATCGAAAGGAATG 59.937 47.826 0.00 0.00 0.00 2.67
3162 3513 3.262420 CGGTGTGAAGATCGAAAGGAAT 58.738 45.455 0.00 0.00 0.00 3.01
3176 3528 0.756294 ATCTGTGAACCACGGTGTGA 59.244 50.000 7.45 0.00 41.12 3.58
3207 3559 1.509004 GAGAGACTCGTGCACCTCC 59.491 63.158 12.15 2.91 0.00 4.30
3217 3584 2.102252 GTGGTCATCCATGGAGAGACTC 59.898 54.545 32.44 25.92 46.20 3.36
3243 3610 4.326766 CGCCGGTGTTGCAACCTG 62.327 66.667 26.14 20.22 38.14 4.00
3277 3644 1.371183 CAGCTCTGGTTTCGACCCA 59.629 57.895 3.16 3.16 0.00 4.51
3278 3645 1.376037 CCAGCTCTGGTTTCGACCC 60.376 63.158 7.75 0.00 45.53 4.46


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

AutoCloner maintained by Alex Coulton.