Multiple sequence alignment - TraesCS5D01G030700

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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 TraesCS5D01G030700 chr5D 100.000 3695 0 0 1 3695 28023131 28026825 0.000000e+00 6824.0
1 TraesCS5D01G030700 chr5D 93.119 1831 68 19 959 2757 27861727 27859923 0.000000e+00 2630.0
2 TraesCS5D01G030700 chr5D 87.413 286 30 4 2906 3190 27857247 27856967 1.280000e-84 324.0
3 TraesCS5D01G030700 chr5D 87.395 238 15 7 634 866 27862146 27861919 3.660000e-65 259.0
4 TraesCS5D01G030700 chr5D 89.714 175 10 2 1 167 27883780 27883606 2.230000e-52 217.0
5 TraesCS5D01G030700 chr5D 96.512 86 3 0 466 551 560280907 560280822 3.850000e-30 143.0
6 TraesCS5D01G030700 chr5D 86.861 137 5 4 2786 2909 27859867 27859731 1.380000e-29 141.0
7 TraesCS5D01G030700 chr5D 95.402 87 4 0 466 552 443898231 443898317 4.980000e-29 139.0
8 TraesCS5D01G030700 chr5D 91.000 100 7 2 460 559 258647911 258648008 2.320000e-27 134.0
9 TraesCS5D01G030700 chr5D 80.503 159 14 12 306 462 27862874 27862731 5.050000e-19 106.0
10 TraesCS5D01G030700 chr5D 82.857 105 7 2 2816 2909 27857392 27857288 2.360000e-12 84.2
11 TraesCS5D01G030700 chr5A 94.623 2213 93 17 713 2909 19066954 19069156 0.000000e+00 3404.0
12 TraesCS5D01G030700 chr5A 88.184 457 18 2 48 504 19172799 19173219 2.540000e-141 512.0
13 TraesCS5D01G030700 chr5A 82.069 290 19 13 2906 3191 19069194 19069454 2.230000e-52 217.0
14 TraesCS5D01G030700 chr5A 88.816 152 11 2 55 206 19066237 19066382 8.150000e-42 182.0
15 TraesCS5D01G030700 chr4B 90.901 2286 129 36 652 2909 575770518 575772752 0.000000e+00 2996.0
16 TraesCS5D01G030700 chr4B 80.156 640 96 19 1174 1805 11433605 11434221 2.020000e-122 449.0
17 TraesCS5D01G030700 chr4B 95.714 70 3 0 1945 2014 11434376 11434445 3.020000e-21 113.0
18 TraesCS5D01G030700 chr4B 87.368 95 7 3 2977 3071 575772789 575772878 1.820000e-18 104.0
19 TraesCS5D01G030700 chr6D 89.961 518 31 16 3189 3695 59025214 59025721 0.000000e+00 649.0
20 TraesCS5D01G030700 chr7A 88.201 517 40 16 3192 3695 171260428 171260936 6.830000e-167 597.0
21 TraesCS5D01G030700 chr7A 86.266 466 47 12 3192 3649 572137948 572137492 1.190000e-134 490.0
22 TraesCS5D01G030700 chr3D 87.597 516 49 10 3189 3695 599433121 599433630 5.320000e-163 584.0
23 TraesCS5D01G030700 chrUn 87.379 515 51 8 3189 3695 408731866 408731358 2.470000e-161 579.0
24 TraesCS5D01G030700 chr1A 86.024 508 55 13 3192 3695 430240513 430241008 7.030000e-147 531.0
25 TraesCS5D01G030700 chr4A 80.655 641 94 19 1174 1805 597052603 597053222 1.550000e-128 470.0
26 TraesCS5D01G030700 chr4A 91.000 100 8 1 462 561 381476895 381476993 2.320000e-27 134.0
27 TraesCS5D01G030700 chr4A 77.103 214 33 12 2977 3189 46084485 46084287 3.900000e-20 110.0
28 TraesCS5D01G030700 chr4A 92.857 70 5 0 1945 2014 597053383 597053452 6.530000e-18 102.0
29 TraesCS5D01G030700 chr3A 84.086 509 58 14 3192 3695 686540391 686539901 1.550000e-128 470.0
30 TraesCS5D01G030700 chr3A 85.408 466 48 14 3192 3650 374358536 374358988 2.010000e-127 466.0
31 TraesCS5D01G030700 chr3A 95.745 94 4 0 466 559 512320213 512320120 6.390000e-33 152.0
32 TraesCS5D01G030700 chr3A 79.221 154 29 3 2991 3144 494719282 494719432 1.820000e-18 104.0
33 TraesCS5D01G030700 chr4D 80.156 640 96 21 1174 1805 6283777 6284393 2.020000e-122 449.0
34 TraesCS5D01G030700 chr4D 89.011 91 10 0 1924 2014 6284527 6284617 3.020000e-21 113.0
35 TraesCS5D01G030700 chr7B 82.081 519 62 20 3191 3695 681580821 681581322 7.380000e-112 414.0
36 TraesCS5D01G030700 chr7D 95.402 87 4 0 466 552 75800766 75800852 4.980000e-29 139.0
37 TraesCS5D01G030700 chr7D 90.000 70 7 0 1945 2014 406314832 406314763 1.410000e-14 91.6
38 TraesCS5D01G030700 chr2A 92.632 95 7 0 466 560 748960881 748960975 1.790000e-28 137.0
39 TraesCS5D01G030700 chr2A 93.333 90 6 0 466 555 715471644 715471555 2.320000e-27 134.0
40 TraesCS5D01G030700 chr6A 92.553 94 4 3 466 557 566634996 566634904 8.330000e-27 132.0
41 TraesCS5D01G030700 chr3B 91.429 70 6 0 1945 2014 722586169 722586100 3.040000e-16 97.1
42 TraesCS5D01G030700 chr3B 92.308 65 4 1 3099 3163 487043008 487043071 1.410000e-14 91.6
43 TraesCS5D01G030700 chr1B 91.429 70 6 0 1945 2014 409833553 409833484 3.040000e-16 97.1
44 TraesCS5D01G030700 chr5B 98.039 51 1 0 3643 3693 421558485 421558435 5.080000e-14 89.8


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 TraesCS5D01G030700 chr5D 28023131 28026825 3694 False 6824.000000 6824 100.000000 1 3695 1 chr5D.!!$F1 3694
1 TraesCS5D01G030700 chr5D 27856967 27862874 5907 True 590.700000 2630 86.358000 306 3190 6 chr5D.!!$R3 2884
2 TraesCS5D01G030700 chr5A 19066237 19069454 3217 False 1267.666667 3404 88.502667 55 3191 3 chr5A.!!$F2 3136
3 TraesCS5D01G030700 chr4B 575770518 575772878 2360 False 1550.000000 2996 89.134500 652 3071 2 chr4B.!!$F2 2419
4 TraesCS5D01G030700 chr4B 11433605 11434445 840 False 281.000000 449 87.935000 1174 2014 2 chr4B.!!$F1 840
5 TraesCS5D01G030700 chr6D 59025214 59025721 507 False 649.000000 649 89.961000 3189 3695 1 chr6D.!!$F1 506
6 TraesCS5D01G030700 chr7A 171260428 171260936 508 False 597.000000 597 88.201000 3192 3695 1 chr7A.!!$F1 503
7 TraesCS5D01G030700 chr3D 599433121 599433630 509 False 584.000000 584 87.597000 3189 3695 1 chr3D.!!$F1 506
8 TraesCS5D01G030700 chrUn 408731358 408731866 508 True 579.000000 579 87.379000 3189 3695 1 chrUn.!!$R1 506
9 TraesCS5D01G030700 chr4A 597052603 597053452 849 False 286.000000 470 86.756000 1174 2014 2 chr4A.!!$F2 840
10 TraesCS5D01G030700 chr4D 6283777 6284617 840 False 281.000000 449 84.583500 1174 2014 2 chr4D.!!$F1 840
11 TraesCS5D01G030700 chr7B 681580821 681581322 501 False 414.000000 414 82.081000 3191 3695 1 chr7B.!!$F1 504

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
72 73 0.817229 GGCAGCAGGCTAATCACCTC 60.817 60.000 0.00 0.0 44.01 3.85 F
948 1592 1.003597 CTGTGCCTCAGCTGAGCTT 60.004 57.895 34.09 0.0 40.75 3.74 F
1838 2518 1.439679 GGCAGCACCTACACAAGTAC 58.560 55.000 0.00 0.0 34.51 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1838 2518 1.373570 GAGGTCATCGGAAGGCTTTG 58.626 55.0 0.00 0.0 0.00 2.77 R
2479 3216 0.612732 TCCACCGGGATCTTGTACGT 60.613 55.0 6.32 0.0 38.64 3.57 R
3254 6534 0.463295 ACATGGCGAATGGCTGAGAG 60.463 55.0 0.00 0.0 40.94 3.20 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
22 23 5.319140 TCCACATCAATCAAGCAGAAATG 57.681 39.130 0.00 0.00 0.00 2.32
23 24 3.863424 CCACATCAATCAAGCAGAAATGC 59.137 43.478 0.00 0.00 0.00 3.56
24 25 4.490743 CACATCAATCAAGCAGAAATGCA 58.509 39.130 2.73 0.00 37.25 3.96
25 26 4.926832 CACATCAATCAAGCAGAAATGCAA 59.073 37.500 2.73 0.00 37.25 4.08
26 27 5.580691 CACATCAATCAAGCAGAAATGCAAT 59.419 36.000 2.73 0.00 37.25 3.56
27 28 5.580691 ACATCAATCAAGCAGAAATGCAATG 59.419 36.000 2.73 1.80 37.25 2.82
28 29 3.930229 TCAATCAAGCAGAAATGCAATGC 59.070 39.130 0.00 0.00 40.29 3.56
29 30 3.603158 ATCAAGCAGAAATGCAATGCA 57.397 38.095 11.44 11.44 44.86 3.96
30 31 3.388345 TCAAGCAGAAATGCAATGCAA 57.612 38.095 13.45 0.00 43.62 4.08
31 32 3.729966 TCAAGCAGAAATGCAATGCAAA 58.270 36.364 13.45 0.00 43.62 3.68
32 33 3.495377 TCAAGCAGAAATGCAATGCAAAC 59.505 39.130 13.45 6.78 43.62 2.93
33 34 3.114668 AGCAGAAATGCAATGCAAACA 57.885 38.095 13.45 0.00 43.62 2.83
34 35 2.803956 AGCAGAAATGCAATGCAAACAC 59.196 40.909 13.45 4.53 43.62 3.32
35 36 2.803956 GCAGAAATGCAATGCAAACACT 59.196 40.909 13.45 6.87 43.62 3.55
36 37 3.363575 GCAGAAATGCAATGCAAACACTG 60.364 43.478 13.45 18.60 43.62 3.66
37 38 4.052608 CAGAAATGCAATGCAAACACTGA 58.947 39.130 13.45 0.00 43.62 3.41
38 39 4.688879 CAGAAATGCAATGCAAACACTGAT 59.311 37.500 13.45 0.00 43.62 2.90
39 40 4.927425 AGAAATGCAATGCAAACACTGATC 59.073 37.500 13.45 2.27 43.62 2.92
40 41 2.334971 TGCAATGCAAACACTGATCG 57.665 45.000 5.01 0.00 34.76 3.69
41 42 1.608109 TGCAATGCAAACACTGATCGT 59.392 42.857 5.01 0.00 34.76 3.73
42 43 2.605097 TGCAATGCAAACACTGATCGTG 60.605 45.455 5.01 13.71 41.96 4.35
43 44 5.095419 TGCAATGCAAACACTGATCGTGT 62.095 43.478 5.01 14.77 46.17 4.49
44 45 6.834795 TGCAATGCAAACACTGATCGTGTC 62.835 45.833 18.93 10.57 44.22 3.67
52 53 3.692791 CACTGATCGTGTCCTAATCGA 57.307 47.619 8.84 0.00 38.84 3.59
53 54 3.622828 CACTGATCGTGTCCTAATCGAG 58.377 50.000 8.84 0.00 38.84 4.04
71 72 1.225704 GGCAGCAGGCTAATCACCT 59.774 57.895 0.00 0.00 44.01 4.00
72 73 0.817229 GGCAGCAGGCTAATCACCTC 60.817 60.000 0.00 0.00 44.01 3.85
75 76 2.286872 CAGCAGGCTAATCACCTCTTG 58.713 52.381 0.00 0.00 34.42 3.02
83 84 4.141846 GGCTAATCACCTCTTGATCTGACA 60.142 45.833 0.00 0.00 44.86 3.58
117 118 2.536365 CTAATTGCTTCGTACTCGCCA 58.464 47.619 0.00 0.00 36.96 5.69
140 141 3.999001 CTGAGTTGTCAGCTATCTGCAAA 59.001 43.478 5.43 0.00 43.89 3.68
167 168 5.521010 GCAATTGCAATTGTACTGTATGCAT 59.479 36.000 38.75 3.79 45.41 3.96
176 177 1.086696 ACTGTATGCATTGCGTGTCC 58.913 50.000 13.63 2.36 0.00 4.02
182 183 1.175654 TGCATTGCGTGTCCATGATT 58.824 45.000 3.84 0.00 0.00 2.57
221 229 8.781196 GCATCATCAATGTTCTACATGACTAAT 58.219 33.333 0.00 0.00 37.97 1.73
226 234 8.662781 TCAATGTTCTACATGACTAATTAGGC 57.337 34.615 16.73 14.39 37.97 3.93
227 235 8.486210 TCAATGTTCTACATGACTAATTAGGCT 58.514 33.333 19.12 1.89 37.97 4.58
231 270 8.486210 TGTTCTACATGACTAATTAGGCTCATT 58.514 33.333 19.12 10.97 30.79 2.57
236 275 7.220030 ACATGACTAATTAGGCTCATTGGTAG 58.780 38.462 19.12 8.66 30.79 3.18
242 281 6.759497 AATTAGGCTCATTGGTAGAACAAC 57.241 37.500 0.00 0.00 32.39 3.32
245 284 5.700402 AGGCTCATTGGTAGAACAACTAT 57.300 39.130 0.00 0.00 33.39 2.12
257 296 7.819415 TGGTAGAACAACTATTCAGACAAGATG 59.181 37.037 0.00 0.00 33.39 2.90
263 302 6.370994 ACAACTATTCAGACAAGATGAGCAAG 59.629 38.462 0.00 0.00 0.00 4.01
264 303 5.426504 ACTATTCAGACAAGATGAGCAAGG 58.573 41.667 0.00 0.00 0.00 3.61
266 305 3.606595 TCAGACAAGATGAGCAAGGAG 57.393 47.619 0.00 0.00 0.00 3.69
267 306 3.168292 TCAGACAAGATGAGCAAGGAGA 58.832 45.455 0.00 0.00 0.00 3.71
268 307 3.773667 TCAGACAAGATGAGCAAGGAGAT 59.226 43.478 0.00 0.00 0.00 2.75
269 308 3.872182 CAGACAAGATGAGCAAGGAGATG 59.128 47.826 0.00 0.00 0.00 2.90
270 309 3.773667 AGACAAGATGAGCAAGGAGATGA 59.226 43.478 0.00 0.00 0.00 2.92
271 310 4.409574 AGACAAGATGAGCAAGGAGATGAT 59.590 41.667 0.00 0.00 0.00 2.45
274 313 5.221682 ACAAGATGAGCAAGGAGATGATAGG 60.222 44.000 0.00 0.00 0.00 2.57
275 314 4.749820 AGATGAGCAAGGAGATGATAGGA 58.250 43.478 0.00 0.00 0.00 2.94
276 315 5.343715 AGATGAGCAAGGAGATGATAGGAT 58.656 41.667 0.00 0.00 0.00 3.24
277 316 5.786457 AGATGAGCAAGGAGATGATAGGATT 59.214 40.000 0.00 0.00 0.00 3.01
278 317 5.480642 TGAGCAAGGAGATGATAGGATTC 57.519 43.478 0.00 0.00 0.00 2.52
279 318 4.285517 TGAGCAAGGAGATGATAGGATTCC 59.714 45.833 0.00 0.00 0.00 3.01
280 319 3.586618 AGCAAGGAGATGATAGGATTCCC 59.413 47.826 0.00 0.00 0.00 3.97
281 320 3.586618 GCAAGGAGATGATAGGATTCCCT 59.413 47.826 0.00 0.00 46.62 4.20
282 321 4.323409 GCAAGGAGATGATAGGATTCCCTC 60.323 50.000 0.00 0.00 43.14 4.30
283 322 4.774243 AGGAGATGATAGGATTCCCTCA 57.226 45.455 7.75 7.75 43.14 3.86
284 323 5.302746 AGGAGATGATAGGATTCCCTCAT 57.697 43.478 14.98 14.98 43.14 2.90
285 324 6.429239 AGGAGATGATAGGATTCCCTCATA 57.571 41.667 15.02 0.00 43.14 2.15
286 325 6.820205 AGGAGATGATAGGATTCCCTCATAA 58.180 40.000 15.02 0.00 43.14 1.90
287 326 7.437572 AGGAGATGATAGGATTCCCTCATAAT 58.562 38.462 15.02 9.28 43.14 1.28
288 327 7.911106 AGGAGATGATAGGATTCCCTCATAATT 59.089 37.037 15.02 7.22 43.14 1.40
289 328 9.218525 GGAGATGATAGGATTCCCTCATAATTA 57.781 37.037 15.02 0.00 43.14 1.40
298 337 8.727149 AGGATTCCCTCATAATTATTCTGAACA 58.273 33.333 0.00 0.00 38.86 3.18
299 338 9.525826 GGATTCCCTCATAATTATTCTGAACAT 57.474 33.333 0.00 0.00 0.00 2.71
301 340 8.607441 TTCCCTCATAATTATTCTGAACATCG 57.393 34.615 0.00 0.00 0.00 3.84
302 341 7.161404 TCCCTCATAATTATTCTGAACATCGG 58.839 38.462 0.00 0.00 0.00 4.18
303 342 6.128172 CCCTCATAATTATTCTGAACATCGGC 60.128 42.308 0.00 0.00 0.00 5.54
304 343 6.427853 CCTCATAATTATTCTGAACATCGGCA 59.572 38.462 0.00 0.00 0.00 5.69
357 396 3.820777 CATGCATGCAGATCTCATCAG 57.179 47.619 26.69 1.84 0.00 2.90
358 397 3.403038 CATGCATGCAGATCTCATCAGA 58.597 45.455 26.69 0.00 0.00 3.27
359 398 3.771577 TGCATGCAGATCTCATCAGAT 57.228 42.857 18.46 0.00 42.59 2.90
381 420 4.161102 TCAGATCAGATCAGCATGGAGAT 58.839 43.478 13.14 0.00 36.16 2.75
383 422 4.932799 CAGATCAGATCAGCATGGAGATTC 59.067 45.833 13.14 0.00 36.16 2.52
385 424 2.697229 TCAGATCAGCATGGAGATTCGT 59.303 45.455 0.00 0.00 36.16 3.85
413 453 2.318908 TGGCTTGGAACATCAGCTTTT 58.681 42.857 0.00 0.00 39.30 2.27
440 480 5.541953 CAGATGATTCTGTGGTATCCTCA 57.458 43.478 0.00 0.00 43.73 3.86
442 482 6.531923 CAGATGATTCTGTGGTATCCTCATT 58.468 40.000 0.00 0.00 43.73 2.57
446 486 3.266510 TCTGTGGTATCCTCATTGTGC 57.733 47.619 0.00 0.00 0.00 4.57
447 487 2.571202 TCTGTGGTATCCTCATTGTGCA 59.429 45.455 0.00 0.00 0.00 4.57
449 489 3.949754 CTGTGGTATCCTCATTGTGCAAT 59.050 43.478 0.00 0.00 0.00 3.56
450 490 3.947196 TGTGGTATCCTCATTGTGCAATC 59.053 43.478 0.00 0.00 0.00 2.67
451 491 4.202441 GTGGTATCCTCATTGTGCAATCT 58.798 43.478 0.00 0.00 0.00 2.40
452 492 4.274459 GTGGTATCCTCATTGTGCAATCTC 59.726 45.833 0.00 0.00 0.00 2.75
453 493 3.817647 GGTATCCTCATTGTGCAATCTCC 59.182 47.826 0.00 0.00 0.00 3.71
454 494 3.947612 ATCCTCATTGTGCAATCTCCT 57.052 42.857 0.00 0.00 0.00 3.69
455 495 2.995283 TCCTCATTGTGCAATCTCCTG 58.005 47.619 0.00 0.00 0.00 3.86
456 496 2.306805 TCCTCATTGTGCAATCTCCTGT 59.693 45.455 0.00 0.00 0.00 4.00
457 497 3.087031 CCTCATTGTGCAATCTCCTGTT 58.913 45.455 0.00 0.00 0.00 3.16
458 498 3.119602 CCTCATTGTGCAATCTCCTGTTG 60.120 47.826 0.00 0.00 0.00 3.33
459 499 3.753815 TCATTGTGCAATCTCCTGTTGA 58.246 40.909 0.00 0.00 0.00 3.18
460 500 4.338012 TCATTGTGCAATCTCCTGTTGAT 58.662 39.130 0.00 0.00 0.00 2.57
464 504 4.401022 TGTGCAATCTCCTGTTGATTTCT 58.599 39.130 0.00 0.00 32.47 2.52
465 505 5.559770 TGTGCAATCTCCTGTTGATTTCTA 58.440 37.500 0.00 0.00 32.47 2.10
466 506 5.412594 TGTGCAATCTCCTGTTGATTTCTAC 59.587 40.000 0.00 0.00 32.47 2.59
467 507 5.412594 GTGCAATCTCCTGTTGATTTCTACA 59.587 40.000 0.00 0.00 32.47 2.74
468 508 5.412594 TGCAATCTCCTGTTGATTTCTACAC 59.587 40.000 0.00 0.00 32.47 2.90
473 513 6.100004 TCTCCTGTTGATTTCTACACGAATC 58.900 40.000 0.00 0.00 0.00 2.52
474 514 6.037786 TCCTGTTGATTTCTACACGAATCT 57.962 37.500 0.00 0.00 0.00 2.40
475 515 6.464222 TCCTGTTGATTTCTACACGAATCTT 58.536 36.000 0.00 0.00 0.00 2.40
476 516 6.590292 TCCTGTTGATTTCTACACGAATCTTC 59.410 38.462 0.00 0.00 0.00 2.87
499 746 7.971004 TCGCGTAAGATCAATGATATATGAC 57.029 36.000 5.77 0.00 43.02 3.06
500 747 7.762382 TCGCGTAAGATCAATGATATATGACT 58.238 34.615 5.77 0.00 43.02 3.41
520 767 8.613060 ATGACTTAGATGTGCAATACTTATGG 57.387 34.615 0.00 0.00 0.00 2.74
563 810 9.615295 TTAGCAAAATTGTAATTCTTAACCGAC 57.385 29.630 0.00 0.00 0.00 4.79
564 811 7.653647 AGCAAAATTGTAATTCTTAACCGACA 58.346 30.769 0.00 0.00 0.00 4.35
565 812 8.303876 AGCAAAATTGTAATTCTTAACCGACAT 58.696 29.630 0.00 0.00 0.00 3.06
567 814 8.859156 CAAAATTGTAATTCTTAACCGACATGG 58.141 33.333 0.00 0.00 46.41 3.66
568 815 7.931578 AATTGTAATTCTTAACCGACATGGA 57.068 32.000 0.00 0.00 42.00 3.41
569 816 8.519799 AATTGTAATTCTTAACCGACATGGAT 57.480 30.769 0.00 0.00 42.00 3.41
570 817 7.548196 TTGTAATTCTTAACCGACATGGATC 57.452 36.000 0.00 0.00 42.00 3.36
586 833 4.737578 ATGGATCCATGAAGCTAATTGCT 58.262 39.130 26.78 0.00 44.14 3.91
610 1065 6.426980 TCGGAATCAAGATGATGAGTTTTG 57.573 37.500 0.00 0.00 37.15 2.44
619 1074 2.037901 TGATGAGTTTTGGGCTTGCAA 58.962 42.857 0.00 0.00 0.00 4.08
623 1078 2.170187 TGAGTTTTGGGCTTGCAATTGT 59.830 40.909 7.40 0.00 0.00 2.71
701 1177 4.091549 ACATTCCATCACTCCAAAAGCAT 58.908 39.130 0.00 0.00 0.00 3.79
745 1230 2.917971 CGTCACGAGGAAGAAGAATGAC 59.082 50.000 0.00 0.00 33.30 3.06
754 1239 2.758736 AGAAGAATGACGCAGCTTCT 57.241 45.000 15.33 15.33 41.48 2.85
825 1315 4.092383 ACACAAAGTCACAAACGTACTCAC 59.908 41.667 0.00 0.00 0.00 3.51
826 1316 4.328983 CACAAAGTCACAAACGTACTCACT 59.671 41.667 0.00 0.00 0.00 3.41
827 1317 4.565564 ACAAAGTCACAAACGTACTCACTC 59.434 41.667 0.00 0.00 0.00 3.51
828 1318 4.380841 AAGTCACAAACGTACTCACTCA 57.619 40.909 0.00 0.00 0.00 3.41
869 1513 1.732941 TTGATTTGATCACGGACCGG 58.267 50.000 20.00 0.00 39.39 5.28
924 1568 3.533105 CCATGCATGGCGCCACAT 61.533 61.111 35.50 28.15 41.75 3.21
925 1569 2.497293 CATGCATGGCGCCACATT 59.503 55.556 35.50 14.65 41.33 2.71
934 1578 2.013400 TGGCGCCACATTATTACTGTG 58.987 47.619 29.03 7.09 42.88 3.66
948 1592 1.003597 CTGTGCCTCAGCTGAGCTT 60.004 57.895 34.09 0.00 40.75 3.74
967 1618 2.410785 TCACCGCCGTATTCGATTAG 57.589 50.000 0.00 0.00 39.71 1.73
1086 1744 2.814341 CTGCTGCTCCTGCTCGTG 60.814 66.667 0.00 0.00 40.48 4.35
1838 2518 1.439679 GGCAGCACCTACACAAGTAC 58.560 55.000 0.00 0.00 34.51 2.73
2185 2916 4.056125 TGCGACTCCTGTGGCTCG 62.056 66.667 4.96 0.00 46.05 5.03
2337 3074 3.000819 TCCCTCGGCGACATGGTT 61.001 61.111 4.99 0.00 0.00 3.67
2346 3083 2.726691 CGACATGGTTGCGGACGTC 61.727 63.158 7.13 7.13 0.00 4.34
2583 3326 3.934962 GCGAGGGGGATGAGGCTC 61.935 72.222 7.79 7.79 0.00 4.70
2690 3433 2.831565 AGATTCTCTCCTGCCAAGACT 58.168 47.619 0.00 0.00 0.00 3.24
3006 6285 5.927819 AGGTGGAAGATCTCTCAATCAATC 58.072 41.667 0.00 0.00 0.00 2.67
3021 6300 8.260818 TCTCAATCAATCGAGGTCTCTAATTTT 58.739 33.333 0.00 0.00 0.00 1.82
3071 6350 4.156190 TCAACGCTTTGTAGTTTTGTGGAA 59.844 37.500 2.56 0.00 34.02 3.53
3082 6361 5.649782 AGTTTTGTGGAATTATCTGCTGG 57.350 39.130 0.00 0.00 0.00 4.85
3163 6443 3.026694 ACAATTTCAAGAGCCCATAGCC 58.973 45.455 0.00 0.00 45.47 3.93
3167 6447 1.056700 TCAAGAGCCCATAGCCCTCC 61.057 60.000 0.00 0.00 45.47 4.30
3176 6456 0.815615 CATAGCCCTCCGGAGTTTGC 60.816 60.000 29.25 25.80 0.00 3.68
3184 6464 2.151202 CTCCGGAGTTTGCTTTGCTTA 58.849 47.619 24.04 0.00 0.00 3.09
3219 6499 2.230750 ACTAGTTAACGAGCGCTCCTTT 59.769 45.455 30.66 24.45 0.00 3.11
3233 6513 1.379044 CCTTTGGGAGCCTCGCAAT 60.379 57.895 22.78 0.00 46.38 3.56
3249 6529 1.089112 CAATGATCAGCGCCACTTGA 58.911 50.000 2.29 0.40 0.00 3.02
3271 6553 1.525535 GCTCTCAGCCATTCGCCAT 60.526 57.895 0.00 0.00 38.78 4.40
3340 6633 2.530700 CGCGTTTTCGGCTTTTTAAACA 59.469 40.909 0.00 0.00 44.29 2.83
3345 6638 6.173044 CGTTTTCGGCTTTTTAAACAGTTTC 58.827 36.000 0.48 0.00 39.94 2.78
3354 6647 8.388103 GGCTTTTTAAACAGTTTCTTTCCTTTC 58.612 33.333 0.48 0.00 0.00 2.62
3355 6648 8.388103 GCTTTTTAAACAGTTTCTTTCCTTTCC 58.612 33.333 0.48 0.00 0.00 3.13
3467 6766 1.808411 TTTTCTTTCGCGAGAGGCAT 58.192 45.000 24.53 0.00 43.84 4.40
3488 6787 2.297880 TGGTTGTGCTTTAGCGAGAGTA 59.702 45.455 0.00 0.00 45.83 2.59
3598 6904 2.802816 GTTGTGCTTTCGTGAGAGTCAT 59.197 45.455 0.00 0.00 43.69 3.06
3632 6940 3.193056 TCGGAAAGGGAAAAACAAAACGT 59.807 39.130 0.00 0.00 0.00 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.381185 GCATTTCTGCTTGATTGATGTGGA 60.381 41.667 0.00 0.00 45.32 4.02
1 2 3.863424 GCATTTCTGCTTGATTGATGTGG 59.137 43.478 0.00 0.00 45.32 4.17
15 16 4.052608 TCAGTGTTTGCATTGCATTTCTG 58.947 39.130 12.95 16.69 38.76 3.02
16 17 4.325028 TCAGTGTTTGCATTGCATTTCT 57.675 36.364 12.95 6.29 38.76 2.52
17 18 4.201551 CGATCAGTGTTTGCATTGCATTTC 60.202 41.667 12.95 6.71 38.76 2.17
18 19 3.676172 CGATCAGTGTTTGCATTGCATTT 59.324 39.130 12.95 0.00 38.76 2.32
19 20 3.247442 CGATCAGTGTTTGCATTGCATT 58.753 40.909 12.95 0.00 38.76 3.56
20 21 2.229543 ACGATCAGTGTTTGCATTGCAT 59.770 40.909 12.95 0.00 38.76 3.96
21 22 1.608109 ACGATCAGTGTTTGCATTGCA 59.392 42.857 7.38 7.38 36.47 4.08
22 23 1.980844 CACGATCAGTGTTTGCATTGC 59.019 47.619 0.46 0.46 45.51 3.56
33 34 3.972950 CTCGATTAGGACACGATCAGT 57.027 47.619 0.00 0.00 35.58 3.41
45 46 0.676184 TAGCCTGCTGCCTCGATTAG 59.324 55.000 0.97 0.00 42.71 1.73
46 47 1.119684 TTAGCCTGCTGCCTCGATTA 58.880 50.000 0.97 0.00 42.71 1.75
47 48 0.471617 ATTAGCCTGCTGCCTCGATT 59.528 50.000 0.97 0.00 42.71 3.34
48 49 0.034616 GATTAGCCTGCTGCCTCGAT 59.965 55.000 0.97 0.00 42.71 3.59
49 50 1.329913 TGATTAGCCTGCTGCCTCGA 61.330 55.000 0.97 0.00 42.71 4.04
50 51 1.144716 TGATTAGCCTGCTGCCTCG 59.855 57.895 0.97 0.00 42.71 4.63
51 52 0.817229 GGTGATTAGCCTGCTGCCTC 60.817 60.000 0.97 0.00 42.71 4.70
52 53 1.225704 GGTGATTAGCCTGCTGCCT 59.774 57.895 0.97 0.00 42.71 4.75
53 54 0.817229 GAGGTGATTAGCCTGCTGCC 60.817 60.000 0.97 0.00 42.71 4.85
71 72 4.262335 CCATCGATCCATGTCAGATCAAGA 60.262 45.833 0.00 0.00 40.17 3.02
72 73 3.995048 CCATCGATCCATGTCAGATCAAG 59.005 47.826 0.00 0.00 40.17 3.02
75 76 3.847542 CTCCATCGATCCATGTCAGATC 58.152 50.000 0.00 0.00 37.39 2.75
83 84 3.341823 GCAATTAGCTCCATCGATCCAT 58.658 45.455 0.00 0.00 41.15 3.41
117 118 2.564504 TGCAGATAGCTGACAACTCAGT 59.435 45.455 13.26 0.00 45.30 3.41
150 151 4.496539 CACGCAATGCATACAGTACAATTG 59.503 41.667 5.91 3.24 0.00 2.32
152 153 3.689161 ACACGCAATGCATACAGTACAAT 59.311 39.130 5.91 0.00 0.00 2.71
153 154 3.070748 ACACGCAATGCATACAGTACAA 58.929 40.909 5.91 0.00 0.00 2.41
154 155 2.670905 GACACGCAATGCATACAGTACA 59.329 45.455 5.91 0.00 0.00 2.90
155 156 2.030457 GGACACGCAATGCATACAGTAC 59.970 50.000 5.91 0.00 0.00 2.73
156 157 2.276201 GGACACGCAATGCATACAGTA 58.724 47.619 5.91 0.00 0.00 2.74
157 158 1.086696 GGACACGCAATGCATACAGT 58.913 50.000 5.91 0.00 0.00 3.55
158 159 1.085893 TGGACACGCAATGCATACAG 58.914 50.000 5.91 0.00 0.00 2.74
159 160 1.401199 CATGGACACGCAATGCATACA 59.599 47.619 5.91 0.00 0.00 2.29
160 161 1.670295 TCATGGACACGCAATGCATAC 59.330 47.619 5.91 0.00 0.00 2.39
161 162 2.035530 TCATGGACACGCAATGCATA 57.964 45.000 5.91 0.00 0.00 3.14
162 163 1.395635 ATCATGGACACGCAATGCAT 58.604 45.000 5.91 0.00 0.00 3.96
167 168 1.199789 GCAGAAATCATGGACACGCAA 59.800 47.619 0.00 0.00 0.00 4.85
176 177 5.761726 TGATGCTACTTAGGCAGAAATCATG 59.238 40.000 0.00 0.00 43.15 3.07
182 183 5.357742 TTGATGATGCTACTTAGGCAGAA 57.642 39.130 0.00 0.00 43.15 3.02
221 229 5.499004 AGTTGTTCTACCAATGAGCCTAA 57.501 39.130 0.00 0.00 0.00 2.69
222 230 6.808321 ATAGTTGTTCTACCAATGAGCCTA 57.192 37.500 0.00 0.00 0.00 3.93
223 231 5.700402 ATAGTTGTTCTACCAATGAGCCT 57.300 39.130 0.00 0.00 0.00 4.58
224 232 5.880332 TGAATAGTTGTTCTACCAATGAGCC 59.120 40.000 0.00 0.00 0.00 4.70
225 233 6.818644 TCTGAATAGTTGTTCTACCAATGAGC 59.181 38.462 0.00 0.00 0.00 4.26
226 234 7.819415 TGTCTGAATAGTTGTTCTACCAATGAG 59.181 37.037 0.00 0.00 0.00 2.90
227 235 7.676004 TGTCTGAATAGTTGTTCTACCAATGA 58.324 34.615 0.00 0.00 0.00 2.57
231 270 7.297936 TCTTGTCTGAATAGTTGTTCTACCA 57.702 36.000 0.00 0.00 0.00 3.25
236 275 6.369890 TGCTCATCTTGTCTGAATAGTTGTTC 59.630 38.462 0.00 0.00 0.00 3.18
242 281 5.668471 TCCTTGCTCATCTTGTCTGAATAG 58.332 41.667 0.00 0.00 0.00 1.73
245 284 3.580022 TCTCCTTGCTCATCTTGTCTGAA 59.420 43.478 0.00 0.00 0.00 3.02
257 296 4.323409 GGGAATCCTATCATCTCCTTGCTC 60.323 50.000 0.00 0.00 0.00 4.26
263 302 7.688918 ATTATGAGGGAATCCTATCATCTCC 57.311 40.000 18.91 0.00 45.05 3.71
275 314 9.224267 CGATGTTCAGAATAATTATGAGGGAAT 57.776 33.333 0.00 0.00 0.00 3.01
276 315 7.661437 CCGATGTTCAGAATAATTATGAGGGAA 59.339 37.037 0.00 0.00 0.00 3.97
277 316 7.161404 CCGATGTTCAGAATAATTATGAGGGA 58.839 38.462 0.00 0.00 0.00 4.20
278 317 6.128172 GCCGATGTTCAGAATAATTATGAGGG 60.128 42.308 0.00 0.00 0.00 4.30
279 318 6.427853 TGCCGATGTTCAGAATAATTATGAGG 59.572 38.462 0.00 0.00 0.00 3.86
280 319 7.172190 ACTGCCGATGTTCAGAATAATTATGAG 59.828 37.037 0.00 0.00 34.57 2.90
281 320 6.992123 ACTGCCGATGTTCAGAATAATTATGA 59.008 34.615 0.00 0.00 34.57 2.15
282 321 7.194607 ACTGCCGATGTTCAGAATAATTATG 57.805 36.000 0.00 0.00 34.57 1.90
283 322 8.150945 ACTACTGCCGATGTTCAGAATAATTAT 58.849 33.333 0.00 0.00 34.57 1.28
284 323 7.497595 ACTACTGCCGATGTTCAGAATAATTA 58.502 34.615 0.00 0.00 34.57 1.40
285 324 6.349300 ACTACTGCCGATGTTCAGAATAATT 58.651 36.000 0.00 0.00 34.57 1.40
286 325 5.918608 ACTACTGCCGATGTTCAGAATAAT 58.081 37.500 0.00 0.00 34.57 1.28
287 326 5.339008 ACTACTGCCGATGTTCAGAATAA 57.661 39.130 0.00 0.00 34.57 1.40
288 327 5.109210 CAACTACTGCCGATGTTCAGAATA 58.891 41.667 0.00 0.00 34.57 1.75
289 328 3.895232 ACTACTGCCGATGTTCAGAAT 57.105 42.857 0.00 0.00 34.57 2.40
290 329 3.325870 CAACTACTGCCGATGTTCAGAA 58.674 45.455 0.00 0.00 34.57 3.02
291 330 2.353704 CCAACTACTGCCGATGTTCAGA 60.354 50.000 0.00 0.00 34.57 3.27
292 331 2.002586 CCAACTACTGCCGATGTTCAG 58.997 52.381 0.00 0.00 36.45 3.02
293 332 1.621317 TCCAACTACTGCCGATGTTCA 59.379 47.619 0.00 0.00 0.00 3.18
294 333 2.271800 CTCCAACTACTGCCGATGTTC 58.728 52.381 0.00 0.00 0.00 3.18
295 334 1.623811 ACTCCAACTACTGCCGATGTT 59.376 47.619 0.00 0.00 0.00 2.71
296 335 1.204941 GACTCCAACTACTGCCGATGT 59.795 52.381 0.00 0.00 0.00 3.06
297 336 1.204704 TGACTCCAACTACTGCCGATG 59.795 52.381 0.00 0.00 0.00 3.84
298 337 1.557099 TGACTCCAACTACTGCCGAT 58.443 50.000 0.00 0.00 0.00 4.18
299 338 1.000506 GTTGACTCCAACTACTGCCGA 59.999 52.381 0.00 0.00 46.84 5.54
300 339 1.429463 GTTGACTCCAACTACTGCCG 58.571 55.000 0.00 0.00 46.84 5.69
319 358 3.611113 GCATGCACACAGAATTAAGCAAG 59.389 43.478 14.21 0.00 35.45 4.01
321 360 2.557490 TGCATGCACACAGAATTAAGCA 59.443 40.909 18.46 0.00 36.34 3.91
348 387 6.127451 GCTGATCTGATCTGATCTGATGAGAT 60.127 42.308 35.17 30.72 45.12 2.75
349 388 5.184287 GCTGATCTGATCTGATCTGATGAGA 59.816 44.000 35.17 25.86 45.12 3.27
350 389 5.047660 TGCTGATCTGATCTGATCTGATGAG 60.048 44.000 33.89 30.88 45.10 2.90
351 390 4.833380 TGCTGATCTGATCTGATCTGATGA 59.167 41.667 33.89 25.75 44.64 2.92
352 391 5.140747 TGCTGATCTGATCTGATCTGATG 57.859 43.478 33.89 22.96 44.64 3.07
353 392 5.337975 CCATGCTGATCTGATCTGATCTGAT 60.338 44.000 33.89 28.98 46.44 2.90
354 393 4.021016 CCATGCTGATCTGATCTGATCTGA 60.021 45.833 33.89 23.67 41.72 3.27
355 394 4.021016 TCCATGCTGATCTGATCTGATCTG 60.021 45.833 30.92 30.11 42.30 2.90
356 395 4.161102 TCCATGCTGATCTGATCTGATCT 58.839 43.478 30.92 16.25 42.30 2.75
357 396 4.221041 TCTCCATGCTGATCTGATCTGATC 59.779 45.833 27.10 27.10 42.19 2.92
358 397 4.161102 TCTCCATGCTGATCTGATCTGAT 58.839 43.478 23.55 14.33 0.00 2.90
359 398 3.573695 TCTCCATGCTGATCTGATCTGA 58.426 45.455 23.55 4.63 0.00 3.27
381 420 1.732917 CAAGCCAACCTGCAACGAA 59.267 52.632 0.00 0.00 0.00 3.85
383 422 1.733402 TTCCAAGCCAACCTGCAACG 61.733 55.000 0.00 0.00 0.00 4.10
385 424 0.685785 TGTTCCAAGCCAACCTGCAA 60.686 50.000 0.00 0.00 0.00 4.08
427 467 2.989909 TGCACAATGAGGATACCACAG 58.010 47.619 0.00 0.00 37.17 3.66
434 474 3.053842 ACAGGAGATTGCACAATGAGGAT 60.054 43.478 0.00 0.00 0.00 3.24
440 480 5.479375 AGAAATCAACAGGAGATTGCACAAT 59.521 36.000 0.00 0.00 35.96 2.71
442 482 4.401022 AGAAATCAACAGGAGATTGCACA 58.599 39.130 0.00 0.00 35.96 4.57
446 486 5.869344 TCGTGTAGAAATCAACAGGAGATTG 59.131 40.000 0.00 0.00 35.96 2.67
447 487 6.037786 TCGTGTAGAAATCAACAGGAGATT 57.962 37.500 0.00 0.00 37.30 2.40
449 489 5.462530 TTCGTGTAGAAATCAACAGGAGA 57.537 39.130 0.00 0.00 35.61 3.71
450 490 6.102663 AGATTCGTGTAGAAATCAACAGGAG 58.897 40.000 0.00 0.00 42.91 3.69
451 491 6.037786 AGATTCGTGTAGAAATCAACAGGA 57.962 37.500 0.00 0.00 42.91 3.86
452 492 6.454318 CGAAGATTCGTGTAGAAATCAACAGG 60.454 42.308 6.81 0.00 45.09 4.00
453 493 6.461816 CGAAGATTCGTGTAGAAATCAACAG 58.538 40.000 6.81 0.00 45.09 3.16
454 494 6.389622 CGAAGATTCGTGTAGAAATCAACA 57.610 37.500 6.81 0.00 45.09 3.33
473 513 8.527488 GTCATATATCATTGATCTTACGCGAAG 58.473 37.037 15.93 12.57 36.38 3.79
474 514 8.244113 AGTCATATATCATTGATCTTACGCGAA 58.756 33.333 15.93 1.35 0.00 4.70
475 515 7.762382 AGTCATATATCATTGATCTTACGCGA 58.238 34.615 15.93 0.00 0.00 5.87
476 516 7.977490 AGTCATATATCATTGATCTTACGCG 57.023 36.000 3.53 3.53 0.00 6.01
495 742 7.173907 GCCATAAGTATTGCACATCTAAGTCAT 59.826 37.037 0.00 0.00 0.00 3.06
499 746 6.866010 TGCCATAAGTATTGCACATCTAAG 57.134 37.500 0.00 0.00 30.49 2.18
540 787 7.861176 TGTCGGTTAAGAATTACAATTTTGC 57.139 32.000 0.00 0.00 0.00 3.68
541 788 8.859156 CCATGTCGGTTAAGAATTACAATTTTG 58.141 33.333 0.00 0.00 0.00 2.44
542 789 8.798402 TCCATGTCGGTTAAGAATTACAATTTT 58.202 29.630 0.00 0.00 35.57 1.82
543 790 8.343168 TCCATGTCGGTTAAGAATTACAATTT 57.657 30.769 0.00 0.00 35.57 1.82
544 791 7.931578 TCCATGTCGGTTAAGAATTACAATT 57.068 32.000 0.00 0.00 35.57 2.32
545 792 7.228706 GGATCCATGTCGGTTAAGAATTACAAT 59.771 37.037 6.95 0.00 35.57 2.71
546 793 6.540914 GGATCCATGTCGGTTAAGAATTACAA 59.459 38.462 6.95 0.00 35.57 2.41
550 797 5.110814 TGGATCCATGTCGGTTAAGAATT 57.889 39.130 11.44 0.00 35.57 2.17
560 807 8.695374 GCAATTAGCTTCATGGATCCATGTCG 62.695 46.154 40.60 33.29 45.60 4.35
561 808 5.564259 GCAATTAGCTTCATGGATCCATGTC 60.564 44.000 40.60 31.51 45.60 3.06
563 810 4.806330 GCAATTAGCTTCATGGATCCATG 58.194 43.478 38.71 38.71 46.16 3.66
577 824 4.882671 TCTTGATTCCGAAGCAATTAGC 57.117 40.909 12.01 0.00 46.19 3.09
579 826 6.767423 TCATCATCTTGATTCCGAAGCAATTA 59.233 34.615 12.01 4.80 34.28 1.40
582 829 4.516323 TCATCATCTTGATTCCGAAGCAA 58.484 39.130 11.16 11.16 34.28 3.91
583 830 4.124970 CTCATCATCTTGATTCCGAAGCA 58.875 43.478 0.00 0.00 34.28 3.91
584 831 4.125703 ACTCATCATCTTGATTCCGAAGC 58.874 43.478 0.00 0.00 34.28 3.86
585 832 6.674694 AAACTCATCATCTTGATTCCGAAG 57.325 37.500 0.00 0.00 34.28 3.79
586 833 6.127925 CCAAAACTCATCATCTTGATTCCGAA 60.128 38.462 0.00 0.00 34.28 4.30
587 834 5.355071 CCAAAACTCATCATCTTGATTCCGA 59.645 40.000 0.00 0.00 34.28 4.55
588 835 5.449588 CCCAAAACTCATCATCTTGATTCCG 60.450 44.000 0.00 0.00 34.28 4.30
590 837 5.126707 AGCCCAAAACTCATCATCTTGATTC 59.873 40.000 0.00 0.00 34.28 2.52
593 840 4.038271 AGCCCAAAACTCATCATCTTGA 57.962 40.909 0.00 0.00 0.00 3.02
653 1127 4.174704 TCTTCCATGCCATTGAGCTTAT 57.825 40.909 0.00 0.00 0.00 1.73
701 1177 1.875157 GCAGCCATGTCATCGCATAGA 60.875 52.381 5.18 0.00 0.00 1.98
707 1192 3.945434 GCGGCAGCCATGTCATCG 61.945 66.667 13.30 0.00 37.42 3.84
708 1193 3.945434 CGCGGCAGCCATGTCATC 61.945 66.667 13.30 0.00 41.18 2.92
709 1194 4.783621 ACGCGGCAGCCATGTCAT 62.784 61.111 13.30 0.00 41.18 3.06
745 1230 2.611292 CAGATCCCTTTTAGAAGCTGCG 59.389 50.000 0.00 0.00 0.00 5.18
754 1239 2.681976 GCAGCTGAGCAGATCCCTTTTA 60.682 50.000 20.43 0.00 0.00 1.52
825 1315 1.402456 GCTTTTGTGGCTGCAGATGAG 60.402 52.381 20.43 5.66 0.00 2.90
826 1316 0.599558 GCTTTTGTGGCTGCAGATGA 59.400 50.000 20.43 0.00 0.00 2.92
827 1317 0.315886 TGCTTTTGTGGCTGCAGATG 59.684 50.000 20.43 0.00 0.00 2.90
828 1318 1.042229 TTGCTTTTGTGGCTGCAGAT 58.958 45.000 20.43 0.00 36.75 2.90
869 1513 0.727398 GTCTTGTAGCATTGGTCGGC 59.273 55.000 0.00 0.00 0.00 5.54
934 1578 1.744741 GGTGAAGCTCAGCTGAGGC 60.745 63.158 37.86 29.79 41.34 4.70
948 1592 1.948834 TCTAATCGAATACGGCGGTGA 59.051 47.619 13.24 1.20 40.21 4.02
1059 1717 2.932194 AGCAGCAGGAAGGAGGCA 60.932 61.111 0.00 0.00 0.00 4.75
1086 1744 4.527583 CGCAGGGAGAGGCAGAGC 62.528 72.222 0.00 0.00 0.00 4.09
1087 1745 4.527583 GCGCAGGGAGAGGCAGAG 62.528 72.222 0.30 0.00 0.00 3.35
1297 1958 3.406200 CCACCAGAGCCCCTCCTG 61.406 72.222 0.00 0.00 0.00 3.86
1828 2508 3.069872 TCGGAAGGCTTTGTACTTGTGTA 59.930 43.478 0.00 0.00 0.00 2.90
1838 2518 1.373570 GAGGTCATCGGAAGGCTTTG 58.626 55.000 0.00 0.00 0.00 2.77
2168 2899 4.056125 CGAGCCACAGGAGTCGCA 62.056 66.667 0.00 0.00 34.00 5.10
2434 3171 3.645660 TGCCATCGACAGCCCCAA 61.646 61.111 6.08 0.00 0.00 4.12
2479 3216 0.612732 TCCACCGGGATCTTGTACGT 60.613 55.000 6.32 0.00 38.64 3.57
2690 3433 4.371624 AATCCAACAGTCCTCAATCACA 57.628 40.909 0.00 0.00 0.00 3.58
2784 3556 1.822990 CAAGCCAGCATCCATCACTTT 59.177 47.619 0.00 0.00 0.00 2.66
2785 3557 1.471119 CAAGCCAGCATCCATCACTT 58.529 50.000 0.00 0.00 0.00 3.16
2922 6198 4.571919 TGTACCTGTACTTTACATGGCAC 58.428 43.478 8.75 0.00 38.15 5.01
2976 6255 5.384336 TGAGAGATCTTCCACCTCTATGAG 58.616 45.833 0.00 0.00 37.40 2.90
2979 6258 6.380414 TGATTGAGAGATCTTCCACCTCTAT 58.620 40.000 0.00 0.89 37.40 1.98
2983 6262 5.453057 CGATTGATTGAGAGATCTTCCACCT 60.453 44.000 0.00 0.00 0.00 4.00
2992 6271 5.139727 AGAGACCTCGATTGATTGAGAGAT 58.860 41.667 9.37 0.00 40.12 2.75
3006 6285 6.631962 ACCAAGTCTAAAATTAGAGACCTCG 58.368 40.000 13.46 6.19 42.62 4.63
3021 6300 4.039973 AGTCAAAATCGTGGACCAAGTCTA 59.960 41.667 7.33 0.00 32.47 2.59
3055 6334 8.081633 CAGCAGATAATTCCACAAAACTACAAA 58.918 33.333 0.00 0.00 0.00 2.83
3060 6339 5.047802 CACCAGCAGATAATTCCACAAAACT 60.048 40.000 0.00 0.00 0.00 2.66
3071 6350 1.202976 GCCCATCCACCAGCAGATAAT 60.203 52.381 0.00 0.00 0.00 1.28
3082 6361 1.463674 CTACCAACAAGCCCATCCAC 58.536 55.000 0.00 0.00 0.00 4.02
3167 6447 4.798574 AGAAATAAGCAAAGCAAACTCCG 58.201 39.130 0.00 0.00 0.00 4.63
3176 6456 4.789012 TGCTCCCAAGAAATAAGCAAAG 57.211 40.909 0.00 0.00 39.83 2.77
3184 6464 5.411669 CGTTAACTAGTTGCTCCCAAGAAAT 59.588 40.000 18.56 0.00 0.00 2.17
3219 6499 1.146930 GATCATTGCGAGGCTCCCA 59.853 57.895 9.32 2.72 0.00 4.37
3233 6513 1.737735 CGTCAAGTGGCGCTGATCA 60.738 57.895 7.64 0.00 35.94 2.92
3249 6529 2.510238 GAATGGCTGAGAGCGCGT 60.510 61.111 8.43 0.00 43.62 6.01
3253 6533 1.525535 ATGGCGAATGGCTGAGAGC 60.526 57.895 0.00 0.00 42.94 4.09
3254 6534 0.463295 ACATGGCGAATGGCTGAGAG 60.463 55.000 0.00 0.00 40.94 3.20
3271 6553 4.700365 CGTCCAGAGCGCGACACA 62.700 66.667 12.10 0.00 0.00 3.72
3306 6599 3.602062 CGAAAACGCGTGCAGAAAAATAT 59.398 39.130 14.98 0.00 0.00 1.28
3363 6656 1.112950 GGGGGAAAACCAAAACGTCA 58.887 50.000 0.00 0.00 42.91 4.35
3467 6766 1.070134 ACTCTCGCTAAAGCACAACCA 59.930 47.619 2.44 0.00 42.21 3.67
3539 6841 2.468532 AAAACCGTGACTTGCGAAAG 57.531 45.000 0.10 0.10 0.00 2.62
3540 6842 2.937799 AGTAAAACCGTGACTTGCGAAA 59.062 40.909 0.00 0.00 0.00 3.46
3543 6845 2.349155 GGAAGTAAAACCGTGACTTGCG 60.349 50.000 0.00 0.00 33.61 4.85
3544 6846 2.349155 CGGAAGTAAAACCGTGACTTGC 60.349 50.000 0.00 0.00 43.53 4.01
3545 6847 3.515071 CGGAAGTAAAACCGTGACTTG 57.485 47.619 0.00 0.00 43.53 3.16


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

AutoCloner maintained by Alex Coulton.