Multiple sequence alignment - TraesCS3A01G357800

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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 TraesCS3A01G357800 chr3A 100.000 2756 0 0 1 2756 605982623 605979868 0.000000e+00 5090
1 TraesCS3A01G357800 chr3B 90.028 1775 94 43 807 2561 615632963 615631252 0.000000e+00 2220
2 TraesCS3A01G357800 chr3B 78.631 599 65 33 27 620 615633833 615633293 3.400000e-89 339
3 TraesCS3A01G357800 chr3D 90.630 1270 55 34 753 2008 462839186 462837967 0.000000e+00 1628
4 TraesCS3A01G357800 chr3D 91.500 400 27 5 1377 1772 308763771 308764167 6.710000e-151 544
5 TraesCS3A01G357800 chr3D 93.578 218 14 0 2347 2564 462837552 462837335 2.650000e-85 326
6 TraesCS3A01G357800 chr3D 89.873 158 8 5 613 764 462840590 462840435 2.170000e-46 196
7 TraesCS3A01G357800 chr3D 76.000 450 49 39 1683 2107 462833522 462833107 7.840000e-41 178
8 TraesCS3A01G357800 chrUn 91.667 600 41 8 1168 1763 248128717 248129311 0.000000e+00 822
9 TraesCS3A01G357800 chr2B 91.000 600 46 7 1169 1763 654705386 654705982 0.000000e+00 802
10 TraesCS3A01G357800 chr2B 91.015 601 43 8 1168 1763 654655282 654655876 0.000000e+00 800
11 TraesCS3A01G357800 chr2B 91.000 600 45 8 1168 1763 654683554 654684148 0.000000e+00 800
12 TraesCS3A01G357800 chr2B 90.516 601 49 7 1168 1763 654734311 654734908 0.000000e+00 787
13 TraesCS3A01G357800 chr4B 85.864 573 51 15 2011 2561 576406126 576405562 1.420000e-162 582
14 TraesCS3A01G357800 chr2A 85.325 477 45 13 1970 2428 32341191 32341660 1.160000e-128 470
15 TraesCS3A01G357800 chr2A 87.054 224 12 7 2212 2418 32346618 32346841 1.280000e-58 237
16 TraesCS3A01G357800 chr1A 94.521 146 8 0 1110 1255 513745291 513745146 2.760000e-55 226
17 TraesCS3A01G357800 chr1A 94.231 104 3 1 1669 1772 551828427 551828527 3.670000e-34 156
18 TraesCS3A01G357800 chr4A 94.521 146 7 1 1110 1255 398506171 398506027 9.930000e-55 224
19 TraesCS3A01G357800 chr4A 87.719 171 21 0 1356 1526 398505991 398505821 1.670000e-47 200
20 TraesCS3A01G357800 chr5A 82.464 211 23 12 1110 1319 562487269 562487466 3.650000e-39 172


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 TraesCS3A01G357800 chr3A 605979868 605982623 2755 True 5090.0 5090 100.00000 1 2756 1 chr3A.!!$R1 2755
1 TraesCS3A01G357800 chr3B 615631252 615633833 2581 True 1279.5 2220 84.32950 27 2561 2 chr3B.!!$R1 2534
2 TraesCS3A01G357800 chr3D 462833107 462840590 7483 True 582.0 1628 87.52025 613 2564 4 chr3D.!!$R1 1951
3 TraesCS3A01G357800 chrUn 248128717 248129311 594 False 822.0 822 91.66700 1168 1763 1 chrUn.!!$F1 595
4 TraesCS3A01G357800 chr2B 654705386 654705982 596 False 802.0 802 91.00000 1169 1763 1 chr2B.!!$F3 594
5 TraesCS3A01G357800 chr2B 654655282 654655876 594 False 800.0 800 91.01500 1168 1763 1 chr2B.!!$F1 595
6 TraesCS3A01G357800 chr2B 654683554 654684148 594 False 800.0 800 91.00000 1168 1763 1 chr2B.!!$F2 595
7 TraesCS3A01G357800 chr2B 654734311 654734908 597 False 787.0 787 90.51600 1168 1763 1 chr2B.!!$F4 595
8 TraesCS3A01G357800 chr4B 576405562 576406126 564 True 582.0 582 85.86400 2011 2561 1 chr4B.!!$R1 550

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
297 299 0.025898 CACATCTTCGCGTGCATCAG 59.974 55.0 5.77 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2167 3839 0.249447 TCGAGCAGTGGTGTGAACTG 60.249 55.0 0.0 0.0 46.39 3.16 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 3.989167 TGTACGTAATTCAACAGTTCCCG 59.011 43.478 0.00 0.00 0.00 5.14
23 24 3.116079 ACGTAATTCAACAGTTCCCGT 57.884 42.857 0.00 0.00 0.00 5.28
24 25 4.255833 ACGTAATTCAACAGTTCCCGTA 57.744 40.909 0.00 0.00 0.00 4.02
25 26 4.630111 ACGTAATTCAACAGTTCCCGTAA 58.370 39.130 0.00 0.00 0.00 3.18
26 27 5.240121 ACGTAATTCAACAGTTCCCGTAAT 58.760 37.500 0.00 0.00 0.00 1.89
27 28 5.121142 ACGTAATTCAACAGTTCCCGTAATG 59.879 40.000 0.00 0.00 0.00 1.90
28 29 5.349270 CGTAATTCAACAGTTCCCGTAATGA 59.651 40.000 0.00 0.00 0.00 2.57
29 30 6.036735 CGTAATTCAACAGTTCCCGTAATGAT 59.963 38.462 0.00 0.00 0.00 2.45
30 31 6.834168 AATTCAACAGTTCCCGTAATGATT 57.166 33.333 0.00 0.00 0.00 2.57
31 32 6.834168 ATTCAACAGTTCCCGTAATGATTT 57.166 33.333 0.00 0.00 0.00 2.17
32 33 7.931578 ATTCAACAGTTCCCGTAATGATTTA 57.068 32.000 0.00 0.00 0.00 1.40
35 36 6.938030 TCAACAGTTCCCGTAATGATTTAAGT 59.062 34.615 0.00 0.00 0.00 2.24
46 47 8.936864 CCGTAATGATTTAAGTGAAAAGAGAGT 58.063 33.333 0.00 0.00 0.00 3.24
93 94 6.094603 GCACAATGTAGAAATGATTGAGAGGT 59.905 38.462 0.00 0.00 32.47 3.85
104 105 6.754702 ATGATTGAGAGGTCATTTTGAGTG 57.245 37.500 0.00 0.00 31.26 3.51
106 107 3.423539 TGAGAGGTCATTTTGAGTGGG 57.576 47.619 0.00 0.00 0.00 4.61
107 108 2.087646 GAGAGGTCATTTTGAGTGGGC 58.912 52.381 0.00 0.00 0.00 5.36
108 109 1.425066 AGAGGTCATTTTGAGTGGGCA 59.575 47.619 0.00 0.00 0.00 5.36
109 110 2.042162 AGAGGTCATTTTGAGTGGGCAT 59.958 45.455 0.00 0.00 0.00 4.40
110 111 3.266772 AGAGGTCATTTTGAGTGGGCATA 59.733 43.478 0.00 0.00 0.00 3.14
111 112 3.624777 AGGTCATTTTGAGTGGGCATAG 58.375 45.455 0.00 0.00 0.00 2.23
112 113 2.099756 GGTCATTTTGAGTGGGCATAGC 59.900 50.000 0.00 0.00 0.00 2.97
126 128 3.314635 GGGCATAGCTCAACAAATCTCAG 59.685 47.826 0.00 0.00 0.00 3.35
129 131 5.298777 GGCATAGCTCAACAAATCTCAGAAT 59.701 40.000 0.00 0.00 0.00 2.40
130 132 6.484643 GGCATAGCTCAACAAATCTCAGAATA 59.515 38.462 0.00 0.00 0.00 1.75
131 133 7.351223 GCATAGCTCAACAAATCTCAGAATAC 58.649 38.462 0.00 0.00 0.00 1.89
132 134 7.226325 GCATAGCTCAACAAATCTCAGAATACT 59.774 37.037 0.00 0.00 0.00 2.12
133 135 9.107177 CATAGCTCAACAAATCTCAGAATACTT 57.893 33.333 0.00 0.00 0.00 2.24
157 159 1.000274 AGTGCAAATTTTGGCTCGTCC 60.000 47.619 10.96 0.00 0.00 4.79
179 181 5.475220 TCCAAAGCGGAAATGTAGAATTCAA 59.525 36.000 8.44 0.00 42.52 2.69
184 186 6.324819 AGCGGAAATGTAGAATTCAATGTTG 58.675 36.000 8.44 0.00 0.00 3.33
187 189 7.116233 GCGGAAATGTAGAATTCAATGTTGTTT 59.884 33.333 8.44 0.00 0.00 2.83
188 190 8.638565 CGGAAATGTAGAATTCAATGTTGTTTC 58.361 33.333 8.44 8.22 0.00 2.78
192 194 8.955061 ATGTAGAATTCAATGTTGTTTCTTCG 57.045 30.769 8.44 0.00 35.25 3.79
193 195 7.925993 TGTAGAATTCAATGTTGTTTCTTCGT 58.074 30.769 8.44 0.00 35.25 3.85
194 196 8.402472 TGTAGAATTCAATGTTGTTTCTTCGTT 58.598 29.630 8.44 0.00 35.25 3.85
195 197 9.233232 GTAGAATTCAATGTTGTTTCTTCGTTT 57.767 29.630 8.44 0.00 35.25 3.60
196 198 8.702163 AGAATTCAATGTTGTTTCTTCGTTTT 57.298 26.923 8.44 0.00 32.18 2.43
197 199 9.150348 AGAATTCAATGTTGTTTCTTCGTTTTT 57.850 25.926 8.44 0.00 32.18 1.94
198 200 9.408731 GAATTCAATGTTGTTTCTTCGTTTTTC 57.591 29.630 0.00 0.00 0.00 2.29
199 201 6.547493 TCAATGTTGTTTCTTCGTTTTTCG 57.453 33.333 0.00 0.00 41.41 3.46
218 220 8.627428 GTTTTTCGAGTGTTATTTATGCACTTC 58.373 33.333 0.00 0.00 42.71 3.01
225 227 7.620880 AGTGTTATTTATGCACTTCCTCACTA 58.379 34.615 0.00 0.00 40.13 2.74
233 235 5.856126 TGCACTTCCTCACTAAAAATACG 57.144 39.130 0.00 0.00 0.00 3.06
234 236 4.153475 TGCACTTCCTCACTAAAAATACGC 59.847 41.667 0.00 0.00 0.00 4.42
235 237 4.153475 GCACTTCCTCACTAAAAATACGCA 59.847 41.667 0.00 0.00 0.00 5.24
256 258 6.366877 ACGCAATTTCAAATCCAATTCTCTTG 59.633 34.615 0.00 0.00 0.00 3.02
278 280 8.736244 TCTTGTTTCTATTTATTTGCACCTACC 58.264 33.333 0.00 0.00 0.00 3.18
281 283 7.448777 TGTTTCTATTTATTTGCACCTACCACA 59.551 33.333 0.00 0.00 0.00 4.17
288 290 0.391130 TGCACCTACCACATCTTCGC 60.391 55.000 0.00 0.00 0.00 4.70
293 295 0.735978 CTACCACATCTTCGCGTGCA 60.736 55.000 5.77 0.00 0.00 4.57
297 299 0.025898 CACATCTTCGCGTGCATCAG 59.974 55.000 5.77 0.00 0.00 2.90
315 317 5.496387 CATCAGATTACATGCGTCAAACTC 58.504 41.667 0.00 0.00 0.00 3.01
316 318 4.565022 TCAGATTACATGCGTCAAACTCA 58.435 39.130 0.00 0.00 0.00 3.41
318 320 3.935203 AGATTACATGCGTCAAACTCAGG 59.065 43.478 0.00 0.00 0.00 3.86
319 321 1.438651 TACATGCGTCAAACTCAGGC 58.561 50.000 0.00 0.00 0.00 4.85
321 323 0.167470 CATGCGTCAAACTCAGGCAG 59.833 55.000 0.00 0.00 38.01 4.85
324 326 0.040958 GCGTCAAACTCAGGCAGTTG 60.041 55.000 0.00 0.00 45.32 3.16
325 327 0.040958 CGTCAAACTCAGGCAGTTGC 60.041 55.000 0.00 0.00 45.32 4.17
326 328 1.312815 GTCAAACTCAGGCAGTTGCT 58.687 50.000 3.88 0.00 45.32 3.91
344 346 5.721876 TTGCTGTCATTGCAAAAGAAAAG 57.278 34.783 1.71 7.42 45.81 2.27
345 347 5.008619 TGCTGTCATTGCAAAAGAAAAGA 57.991 34.783 1.71 0.00 37.51 2.52
348 350 6.370994 TGCTGTCATTGCAAAAGAAAAGAAAA 59.629 30.769 1.71 0.00 37.51 2.29
349 351 6.903479 GCTGTCATTGCAAAAGAAAAGAAAAG 59.097 34.615 1.71 0.00 0.00 2.27
351 353 8.545229 TGTCATTGCAAAAGAAAAGAAAAGAA 57.455 26.923 1.71 0.00 0.00 2.52
352 354 8.997323 TGTCATTGCAAAAGAAAAGAAAAGAAA 58.003 25.926 1.71 0.00 0.00 2.52
353 355 9.481800 GTCATTGCAAAAGAAAAGAAAAGAAAG 57.518 29.630 1.71 0.00 0.00 2.62
363 365 6.490381 AGAAAAGAAAAGAAAGGGTAATCGCT 59.510 34.615 0.00 0.00 38.50 4.93
366 368 4.938226 AGAAAAGAAAGGGTAATCGCTGAG 59.062 41.667 0.00 0.00 36.95 3.35
372 374 1.004277 AGGGTAATCGCTGAGCCAAAA 59.996 47.619 0.00 0.00 35.59 2.44
373 375 1.132453 GGGTAATCGCTGAGCCAAAAC 59.868 52.381 0.00 0.00 33.26 2.43
374 376 1.810151 GGTAATCGCTGAGCCAAAACA 59.190 47.619 0.00 0.00 0.00 2.83
375 377 2.414161 GGTAATCGCTGAGCCAAAACAC 60.414 50.000 0.00 0.00 0.00 3.32
376 378 1.609208 AATCGCTGAGCCAAAACACT 58.391 45.000 0.00 0.00 0.00 3.55
377 379 1.609208 ATCGCTGAGCCAAAACACTT 58.391 45.000 0.00 0.00 0.00 3.16
378 380 0.662619 TCGCTGAGCCAAAACACTTG 59.337 50.000 0.00 0.00 0.00 3.16
379 381 0.936297 CGCTGAGCCAAAACACTTGC 60.936 55.000 0.00 0.00 0.00 4.01
380 382 0.386838 GCTGAGCCAAAACACTTGCT 59.613 50.000 0.00 0.00 36.62 3.91
384 386 3.443099 GAGCCAAAACACTTGCTCTTT 57.557 42.857 0.00 0.00 45.21 2.52
385 387 3.785486 GAGCCAAAACACTTGCTCTTTT 58.215 40.909 0.00 0.00 45.21 2.27
386 388 3.524541 AGCCAAAACACTTGCTCTTTTG 58.475 40.909 0.00 0.00 35.52 2.44
387 389 3.055891 AGCCAAAACACTTGCTCTTTTGT 60.056 39.130 0.00 0.00 34.44 2.83
388 390 3.684305 GCCAAAACACTTGCTCTTTTGTT 59.316 39.130 0.00 0.00 34.44 2.83
389 391 4.867608 GCCAAAACACTTGCTCTTTTGTTA 59.132 37.500 0.00 0.00 34.44 2.41
390 392 5.220397 GCCAAAACACTTGCTCTTTTGTTAC 60.220 40.000 0.00 0.00 34.44 2.50
391 393 5.866633 CCAAAACACTTGCTCTTTTGTTACA 59.133 36.000 0.00 0.00 34.44 2.41
392 394 6.367422 CCAAAACACTTGCTCTTTTGTTACAA 59.633 34.615 0.00 0.00 34.44 2.41
393 395 7.095439 CCAAAACACTTGCTCTTTTGTTACAAA 60.095 33.333 6.41 6.41 34.44 2.83
394 396 7.581011 AAACACTTGCTCTTTTGTTACAAAG 57.419 32.000 10.51 5.92 31.92 2.77
395 397 5.650543 ACACTTGCTCTTTTGTTACAAAGG 58.349 37.500 12.79 12.79 0.00 3.11
396 398 5.185056 ACACTTGCTCTTTTGTTACAAAGGT 59.815 36.000 17.25 0.00 0.00 3.50
397 399 5.743872 CACTTGCTCTTTTGTTACAAAGGTC 59.256 40.000 17.25 11.85 0.00 3.85
398 400 5.417580 ACTTGCTCTTTTGTTACAAAGGTCA 59.582 36.000 17.25 13.77 0.00 4.02
399 401 6.096846 ACTTGCTCTTTTGTTACAAAGGTCAT 59.903 34.615 17.25 3.69 0.00 3.06
400 402 6.463995 TGCTCTTTTGTTACAAAGGTCATT 57.536 33.333 17.25 0.00 0.00 2.57
424 426 2.079170 TGAAATGGAGGCAAACCACA 57.921 45.000 0.00 0.00 40.36 4.17
430 432 1.070786 GAGGCAAACCACACCTCGA 59.929 57.895 0.00 0.00 40.59 4.04
436 438 2.858260 GCAAACCACACCTCGATGTTTG 60.858 50.000 8.60 8.60 45.21 2.93
438 440 2.631160 ACCACACCTCGATGTTTGAA 57.369 45.000 8.35 0.00 0.00 2.69
440 442 3.486383 ACCACACCTCGATGTTTGAAAT 58.514 40.909 8.35 0.00 0.00 2.17
441 443 3.253188 ACCACACCTCGATGTTTGAAATG 59.747 43.478 8.35 0.00 0.00 2.32
442 444 3.366273 CCACACCTCGATGTTTGAAATGG 60.366 47.826 8.35 0.00 0.00 3.16
444 446 3.753272 ACACCTCGATGTTTGAAATGGAG 59.247 43.478 0.00 0.00 31.69 3.86
445 447 3.753272 CACCTCGATGTTTGAAATGGAGT 59.247 43.478 0.00 0.00 30.36 3.85
447 449 4.935808 ACCTCGATGTTTGAAATGGAGTAC 59.064 41.667 0.00 0.00 30.36 2.73
448 450 4.935205 CCTCGATGTTTGAAATGGAGTACA 59.065 41.667 0.00 0.00 30.36 2.90
449 451 5.411361 CCTCGATGTTTGAAATGGAGTACAA 59.589 40.000 0.00 0.00 30.36 2.41
450 452 6.402550 CCTCGATGTTTGAAATGGAGTACAAG 60.403 42.308 0.00 0.00 30.36 3.16
451 453 6.227522 TCGATGTTTGAAATGGAGTACAAGA 58.772 36.000 0.00 0.00 0.00 3.02
452 454 6.708502 TCGATGTTTGAAATGGAGTACAAGAA 59.291 34.615 0.00 0.00 0.00 2.52
453 455 7.227711 TCGATGTTTGAAATGGAGTACAAGAAA 59.772 33.333 0.00 0.00 0.00 2.52
454 456 7.860373 CGATGTTTGAAATGGAGTACAAGAAAA 59.140 33.333 0.00 0.00 0.00 2.29
455 457 8.871686 ATGTTTGAAATGGAGTACAAGAAAAC 57.128 30.769 0.00 0.00 0.00 2.43
456 458 8.062065 TGTTTGAAATGGAGTACAAGAAAACT 57.938 30.769 0.00 0.00 0.00 2.66
457 459 9.179909 TGTTTGAAATGGAGTACAAGAAAACTA 57.820 29.630 0.00 0.00 0.00 2.24
502 504 6.458342 GGCCAATCTAAACTTTATCGACTTGG 60.458 42.308 0.00 0.00 34.06 3.61
504 506 6.038271 CCAATCTAAACTTTATCGACTTGGGG 59.962 42.308 0.00 0.00 0.00 4.96
507 509 6.771573 TCTAAACTTTATCGACTTGGGGAAA 58.228 36.000 0.00 0.00 0.00 3.13
524 526 3.471680 GGAAATGAGGCACATCTCCTAC 58.528 50.000 9.70 0.00 41.51 3.18
533 535 2.482839 GCACATCTCCTACCTCTGCTTC 60.483 54.545 0.00 0.00 0.00 3.86
538 540 4.974645 TCTCCTACCTCTGCTTCAAAAA 57.025 40.909 0.00 0.00 0.00 1.94
539 541 4.899502 TCTCCTACCTCTGCTTCAAAAAG 58.100 43.478 0.00 0.00 35.47 2.27
541 543 5.071788 TCTCCTACCTCTGCTTCAAAAAGAA 59.928 40.000 0.00 0.00 34.14 2.52
542 544 5.690865 TCCTACCTCTGCTTCAAAAAGAAA 58.309 37.500 0.00 0.00 35.40 2.52
543 545 5.765182 TCCTACCTCTGCTTCAAAAAGAAAG 59.235 40.000 0.00 0.00 35.40 2.62
544 546 5.532779 CCTACCTCTGCTTCAAAAAGAAAGT 59.467 40.000 0.00 0.00 35.40 2.66
545 547 5.921962 ACCTCTGCTTCAAAAAGAAAGTT 57.078 34.783 0.00 0.00 35.40 2.66
546 548 7.228706 CCTACCTCTGCTTCAAAAAGAAAGTTA 59.771 37.037 0.00 0.00 35.40 2.24
547 549 6.796426 ACCTCTGCTTCAAAAAGAAAGTTAC 58.204 36.000 0.00 0.00 35.40 2.50
565 567 7.631717 AAGTTACTCTTTCAAAGCTTTCACT 57.368 32.000 9.23 0.00 31.57 3.41
566 568 7.020914 AGTTACTCTTTCAAAGCTTTCACTG 57.979 36.000 9.23 0.00 0.00 3.66
567 569 4.298744 ACTCTTTCAAAGCTTTCACTGC 57.701 40.909 9.23 0.00 0.00 4.40
575 577 4.397730 TCAAAGCTTTCACTGCACAAAGTA 59.602 37.500 9.23 0.00 32.96 2.24
582 584 3.599343 TCACTGCACAAAGTATAGCCAG 58.401 45.455 0.00 0.00 0.00 4.85
592 594 4.970860 AAGTATAGCCAGCACATCATCT 57.029 40.909 0.00 0.00 0.00 2.90
599 601 3.767673 AGCCAGCACATCATCTTTTTGAT 59.232 39.130 0.00 0.00 36.79 2.57
715 804 3.696051 TCTAGGGAAACATCATTTGCAGC 59.304 43.478 0.00 0.00 0.00 5.25
724 813 2.477845 TCATTTGCAGCTGCTCACTA 57.522 45.000 36.61 16.02 42.66 2.74
758 847 3.134804 ACACAAGACACAAGCTACTCCTT 59.865 43.478 0.00 0.00 0.00 3.36
769 2118 5.163301 ACAAGCTACTCCTTCAGAAGTTTCA 60.163 40.000 9.41 0.00 0.00 2.69
771 2120 5.486526 AGCTACTCCTTCAGAAGTTTCATG 58.513 41.667 9.41 0.00 0.00 3.07
842 2255 1.112916 CCCCAAAGACCAAACCGCTT 61.113 55.000 0.00 0.00 0.00 4.68
853 2266 4.814294 ACCGCTTCCGCCGATCAC 62.814 66.667 0.00 0.00 0.00 3.06
854 2267 4.812476 CCGCTTCCGCCGATCACA 62.812 66.667 0.00 0.00 0.00 3.58
855 2268 3.554692 CGCTTCCGCCGATCACAC 61.555 66.667 0.00 0.00 0.00 3.82
856 2269 3.195698 GCTTCCGCCGATCACACC 61.196 66.667 0.00 0.00 0.00 4.16
857 2270 2.511600 CTTCCGCCGATCACACCC 60.512 66.667 0.00 0.00 0.00 4.61
890 2303 9.190317 AGTCCAATCCAAAATCTCCTATAAAAC 57.810 33.333 0.00 0.00 0.00 2.43
900 2313 5.093849 TCTCCTATAAAACGACCCCAAAG 57.906 43.478 0.00 0.00 0.00 2.77
910 2323 2.356667 CCCCAAAGCCCTCTCACC 59.643 66.667 0.00 0.00 0.00 4.02
911 2324 2.538141 CCCCAAAGCCCTCTCACCA 61.538 63.158 0.00 0.00 0.00 4.17
913 2326 1.676967 CCAAAGCCCTCTCACCAGC 60.677 63.158 0.00 0.00 0.00 4.85
920 2333 2.519622 CCTCTCACCAGCCACCACA 61.520 63.158 0.00 0.00 0.00 4.17
921 2334 1.004080 CTCTCACCAGCCACCACAG 60.004 63.158 0.00 0.00 0.00 3.66
922 2335 1.762522 CTCTCACCAGCCACCACAGT 61.763 60.000 0.00 0.00 0.00 3.55
948 2387 2.628657 AGTCCACAGTCTACTGACCAAC 59.371 50.000 16.74 8.74 46.59 3.77
954 2397 4.278669 CACAGTCTACTGACCAACTAGTGT 59.721 45.833 16.74 0.00 46.59 3.55
955 2398 4.278669 ACAGTCTACTGACCAACTAGTGTG 59.721 45.833 16.74 0.00 46.59 3.82
957 2400 2.561419 TCTACTGACCAACTAGTGTGCC 59.439 50.000 0.00 0.00 0.00 5.01
958 2401 0.033504 ACTGACCAACTAGTGTGCCG 59.966 55.000 0.00 0.00 0.00 5.69
968 2411 2.563179 ACTAGTGTGCCGAGAATTCAGT 59.437 45.455 8.44 0.00 0.00 3.41
973 2416 0.391661 TGCCGAGAATTCAGTGAGCC 60.392 55.000 8.44 0.00 0.00 4.70
974 2417 1.092345 GCCGAGAATTCAGTGAGCCC 61.092 60.000 8.44 0.00 0.00 5.19
975 2418 0.807667 CCGAGAATTCAGTGAGCCCG 60.808 60.000 8.44 0.00 0.00 6.13
976 2419 1.424493 CGAGAATTCAGTGAGCCCGC 61.424 60.000 8.44 0.00 0.00 6.13
977 2420 0.107945 GAGAATTCAGTGAGCCCGCT 60.108 55.000 8.44 0.00 0.00 5.52
978 2421 1.137086 GAGAATTCAGTGAGCCCGCTA 59.863 52.381 8.44 0.00 0.00 4.26
979 2422 1.137872 AGAATTCAGTGAGCCCGCTAG 59.862 52.381 8.44 0.00 0.00 3.42
980 2423 0.462759 AATTCAGTGAGCCCGCTAGC 60.463 55.000 4.06 4.06 0.00 3.42
982 2425 0.683179 TTCAGTGAGCCCGCTAGCTA 60.683 55.000 13.93 0.00 45.15 3.32
983 2426 1.103987 TCAGTGAGCCCGCTAGCTAG 61.104 60.000 16.84 16.84 45.15 3.42
984 2427 2.028337 GTGAGCCCGCTAGCTAGC 59.972 66.667 31.88 31.88 45.15 3.42
985 2428 2.123683 TGAGCCCGCTAGCTAGCT 60.124 61.111 36.02 23.12 45.15 3.32
986 2429 1.150764 TGAGCCCGCTAGCTAGCTA 59.849 57.895 36.02 22.85 45.15 3.32
987 2430 0.891449 TGAGCCCGCTAGCTAGCTAG 60.891 60.000 37.09 37.09 45.15 3.42
1029 2472 1.138661 CCTAAGCTTCTCCTCCTGCTG 59.861 57.143 0.00 0.00 35.79 4.41
1401 2848 1.065928 CGACCAGTCGTCCTATGGC 59.934 63.158 11.94 0.00 46.99 4.40
1431 2878 3.047877 GACGGCTTCAACGTGGGG 61.048 66.667 0.00 0.00 45.68 4.96
1440 2887 4.309950 AACGTGGGGCTGTCGGTC 62.310 66.667 0.00 0.00 0.00 4.79
1763 3224 2.822561 TCTTCTGCCACTAGACTGAGTG 59.177 50.000 0.00 0.00 45.43 3.51
1773 3234 2.355946 GACTGAGTGAGTCCAGCCA 58.644 57.895 0.00 0.00 44.95 4.75
1774 3235 0.246086 GACTGAGTGAGTCCAGCCAG 59.754 60.000 0.00 0.00 44.95 4.85
1775 3236 1.190833 ACTGAGTGAGTCCAGCCAGG 61.191 60.000 0.00 0.00 39.47 4.45
1815 3279 2.963854 CGGCCGTCAGCAGCTATG 60.964 66.667 19.50 0.00 46.50 2.23
1816 3280 2.501128 GGCCGTCAGCAGCTATGA 59.499 61.111 0.00 0.00 46.50 2.15
1817 3281 1.884926 GGCCGTCAGCAGCTATGAC 60.885 63.158 17.35 17.35 46.50 3.06
1818 3282 1.142748 GCCGTCAGCAGCTATGACT 59.857 57.895 22.16 1.61 43.95 3.41
1819 3283 1.150567 GCCGTCAGCAGCTATGACTG 61.151 60.000 22.16 18.38 43.95 3.51
1852 3317 1.256376 GATCGATTAGTGCAGTGCGTG 59.744 52.381 11.20 0.00 0.00 5.34
1853 3318 0.038618 TCGATTAGTGCAGTGCGTGT 60.039 50.000 11.20 0.00 0.00 4.49
1854 3319 0.366871 CGATTAGTGCAGTGCGTGTC 59.633 55.000 11.20 3.42 0.00 3.67
1855 3320 1.428448 GATTAGTGCAGTGCGTGTCA 58.572 50.000 11.20 0.00 0.00 3.58
1867 3332 1.545582 TGCGTGTCAGTCATCTCATCA 59.454 47.619 0.00 0.00 0.00 3.07
1888 3353 3.461061 AGTCATGTGTGAGTGAGTGTTG 58.539 45.455 0.00 0.00 36.66 3.33
1908 3373 2.239654 TGGATTAGGCTTTGGAGACTGG 59.760 50.000 0.00 0.00 42.75 4.00
1916 3381 3.557903 TTGGAGACTGGCAGGCTGC 62.558 63.158 32.53 32.53 42.74 5.25
1969 3434 1.199558 GCGTTCACCTCTCGTCTAGTT 59.800 52.381 0.00 0.00 0.00 2.24
1987 3452 3.338249 AGTTGTATGGTGTTAGCTGCTG 58.662 45.455 13.43 0.00 0.00 4.41
2043 3710 0.037326 TGATCTGGTCACTTGGTCGC 60.037 55.000 0.00 0.00 0.00 5.19
2044 3711 0.037326 GATCTGGTCACTTGGTCGCA 60.037 55.000 0.00 0.00 0.00 5.10
2053 3720 3.862845 GTCACTTGGTCGCAAATGTTTTT 59.137 39.130 0.00 0.00 0.00 1.94
2064 3731 7.806014 GGTCGCAAATGTTTTTAATCACTTCTA 59.194 33.333 0.00 0.00 0.00 2.10
2080 3747 7.977789 TCACTTCTATTGTGCATTTGAGTTA 57.022 32.000 0.00 0.00 35.58 2.24
2083 3750 9.121517 CACTTCTATTGTGCATTTGAGTTAAAG 57.878 33.333 0.00 0.00 0.00 1.85
2157 3829 4.080919 AGCAACATGTGTAAGGCAGATCTA 60.081 41.667 0.00 0.00 0.00 1.98
2158 3830 4.272018 GCAACATGTGTAAGGCAGATCTAG 59.728 45.833 0.00 0.00 0.00 2.43
2168 3840 2.680312 GCAGATCTAGTGCCTTCACA 57.320 50.000 0.00 0.00 45.49 3.58
2169 3841 2.548875 GCAGATCTAGTGCCTTCACAG 58.451 52.381 0.00 0.00 45.49 3.66
2185 3857 0.530650 ACAGTTCACACCACTGCTCG 60.531 55.000 0.00 0.00 44.85 5.03
2210 3882 4.271049 CATGTATGGGACGTGAATTCTCAC 59.729 45.833 7.05 0.00 46.53 3.51
2243 3915 5.627499 ACACTTACAACATGGTAATGCTG 57.373 39.130 0.00 0.00 37.29 4.41
2355 4044 3.181475 CCATGAACTCTACACCGCATACT 60.181 47.826 0.00 0.00 0.00 2.12
2433 4122 5.830457 CCCTTTCTCCTTTCAGTTTTCTCTT 59.170 40.000 0.00 0.00 0.00 2.85
2459 4152 1.568025 GCCGTGTCCTTTTCGTCAC 59.432 57.895 0.00 0.00 0.00 3.67
2546 4239 2.107953 GAGGCTAGGAGCGGCTTG 59.892 66.667 2.97 0.00 43.62 4.01
2561 4254 3.791175 CGGCTTGTCAGTAAAAACGTAC 58.209 45.455 0.00 0.00 0.00 3.67
2586 4305 4.378459 CGAAATAAACAGAGTGCCTTCCAC 60.378 45.833 0.00 0.00 45.01 4.02
2606 4325 6.169800 TCCACGATGAAGTAAATCACATCAA 58.830 36.000 0.00 0.00 38.30 2.57
2609 4328 7.970061 CCACGATGAAGTAAATCACATCAAAAT 59.030 33.333 0.00 0.00 38.30 1.82
2610 4329 9.986833 CACGATGAAGTAAATCACATCAAAATA 57.013 29.630 0.00 0.00 38.30 1.40
2622 4341 7.943079 TCACATCAAAATATTGGATGTGAGT 57.057 32.000 34.73 16.71 45.76 3.41
2623 4342 8.352137 TCACATCAAAATATTGGATGTGAGTT 57.648 30.769 34.73 16.47 45.76 3.01
2624 4343 9.460019 TCACATCAAAATATTGGATGTGAGTTA 57.540 29.630 34.73 24.41 45.76 2.24
2699 4419 1.478105 GATCAATCACACCCCCTTTGC 59.522 52.381 0.00 0.00 0.00 3.68
2700 4420 0.893270 TCAATCACACCCCCTTTGCG 60.893 55.000 0.00 0.00 0.00 4.85
2719 4439 2.034053 GCGTTTGTGGGTTTTCAGATGA 59.966 45.455 0.00 0.00 0.00 2.92
2723 4443 3.593442 TGTGGGTTTTCAGATGAACCT 57.407 42.857 13.29 0.00 43.78 3.50
2725 4445 3.636300 TGTGGGTTTTCAGATGAACCTTG 59.364 43.478 13.29 0.00 43.78 3.61
2726 4446 3.888930 GTGGGTTTTCAGATGAACCTTGA 59.111 43.478 13.29 0.37 43.78 3.02
2735 4455 3.933955 CAGATGAACCTTGAGAGCTGAAG 59.066 47.826 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 6.978343 TCACTTAAATCATTACGGGAACTG 57.022 37.500 0.00 0.00 42.99 3.16
15 16 7.989416 TTTCACTTAAATCATTACGGGAACT 57.011 32.000 0.00 0.00 33.78 3.01
16 17 8.508875 TCTTTTCACTTAAATCATTACGGGAAC 58.491 33.333 0.00 0.00 33.78 3.62
17 18 8.624367 TCTTTTCACTTAAATCATTACGGGAA 57.376 30.769 0.00 0.00 32.61 3.97
18 19 8.098286 TCTCTTTTCACTTAAATCATTACGGGA 58.902 33.333 0.00 0.00 0.00 5.14
19 20 8.263940 TCTCTTTTCACTTAAATCATTACGGG 57.736 34.615 0.00 0.00 0.00 5.28
20 21 8.936864 ACTCTCTTTTCACTTAAATCATTACGG 58.063 33.333 0.00 0.00 0.00 4.02
21 22 9.746711 CACTCTCTTTTCACTTAAATCATTACG 57.253 33.333 0.00 0.00 0.00 3.18
26 27 9.832445 ACTTACACTCTCTTTTCACTTAAATCA 57.168 29.630 0.00 0.00 0.00 2.57
35 36 8.677148 AGCATAAAACTTACACTCTCTTTTCA 57.323 30.769 0.00 0.00 0.00 2.69
46 47 7.737972 TGCTTGTCTTAGCATAAAACTTACA 57.262 32.000 0.00 0.00 45.72 2.41
62 63 7.175467 TCAATCATTTCTACATTGTGCTTGTCT 59.825 33.333 0.00 0.00 0.00 3.41
70 71 7.397221 TGACCTCTCAATCATTTCTACATTGT 58.603 34.615 0.00 0.00 0.00 2.71
71 72 7.854557 TGACCTCTCAATCATTTCTACATTG 57.145 36.000 0.00 0.00 0.00 2.82
93 94 3.282021 GAGCTATGCCCACTCAAAATGA 58.718 45.455 0.00 0.00 0.00 2.57
98 99 1.350684 TGTTGAGCTATGCCCACTCAA 59.649 47.619 0.75 0.75 45.56 3.02
100 101 2.113860 TTGTTGAGCTATGCCCACTC 57.886 50.000 0.00 0.00 0.00 3.51
103 104 3.282021 GAGATTTGTTGAGCTATGCCCA 58.718 45.455 0.00 0.00 0.00 5.36
104 105 3.282021 TGAGATTTGTTGAGCTATGCCC 58.718 45.455 0.00 0.00 0.00 5.36
106 107 5.808042 TTCTGAGATTTGTTGAGCTATGC 57.192 39.130 0.00 0.00 0.00 3.14
107 108 8.659925 AGTATTCTGAGATTTGTTGAGCTATG 57.340 34.615 0.00 0.00 0.00 2.23
110 111 9.160496 CTTAAGTATTCTGAGATTTGTTGAGCT 57.840 33.333 0.00 0.00 0.00 4.09
111 112 9.155975 TCTTAAGTATTCTGAGATTTGTTGAGC 57.844 33.333 1.63 0.00 0.00 4.26
126 128 7.814587 AGCCAAAATTTGCACTCTTAAGTATTC 59.185 33.333 1.63 0.00 33.25 1.75
129 131 6.567701 CGAGCCAAAATTTGCACTCTTAAGTA 60.568 38.462 18.31 0.00 33.25 2.24
130 132 5.532557 GAGCCAAAATTTGCACTCTTAAGT 58.467 37.500 15.32 0.00 35.60 2.24
131 133 4.618489 CGAGCCAAAATTTGCACTCTTAAG 59.382 41.667 18.31 0.00 33.02 1.85
132 134 4.037446 ACGAGCCAAAATTTGCACTCTTAA 59.963 37.500 18.31 0.00 33.02 1.85
133 135 3.568007 ACGAGCCAAAATTTGCACTCTTA 59.432 39.130 18.31 0.00 33.02 2.10
157 159 6.808212 ACATTGAATTCTACATTTCCGCTTTG 59.192 34.615 7.05 0.00 0.00 2.77
162 164 8.519492 AAACAACATTGAATTCTACATTTCCG 57.481 30.769 7.05 0.00 0.00 4.30
163 165 9.696917 AGAAACAACATTGAATTCTACATTTCC 57.303 29.630 7.05 0.00 36.70 3.13
173 175 8.107564 CGAAAAACGAAGAAACAACATTGAATT 58.892 29.630 0.00 0.00 45.77 2.17
174 176 7.608755 CGAAAAACGAAGAAACAACATTGAAT 58.391 30.769 0.00 0.00 45.77 2.57
191 193 6.795114 AGTGCATAAATAACACTCGAAAAACG 59.205 34.615 0.00 0.00 40.56 3.60
192 194 8.502161 AAGTGCATAAATAACACTCGAAAAAC 57.498 30.769 0.00 0.00 43.63 2.43
193 195 7.806014 GGAAGTGCATAAATAACACTCGAAAAA 59.194 33.333 0.00 0.00 43.63 1.94
194 196 7.174253 AGGAAGTGCATAAATAACACTCGAAAA 59.826 33.333 0.00 0.00 43.63 2.29
195 197 6.653320 AGGAAGTGCATAAATAACACTCGAAA 59.347 34.615 0.00 0.00 43.63 3.46
196 198 6.170506 AGGAAGTGCATAAATAACACTCGAA 58.829 36.000 0.00 0.00 43.63 3.71
197 199 5.730550 AGGAAGTGCATAAATAACACTCGA 58.269 37.500 0.00 0.00 43.63 4.04
198 200 5.580691 TGAGGAAGTGCATAAATAACACTCG 59.419 40.000 0.00 0.00 43.63 4.18
199 201 6.595716 AGTGAGGAAGTGCATAAATAACACTC 59.404 38.462 0.00 0.00 43.63 3.51
200 202 6.476378 AGTGAGGAAGTGCATAAATAACACT 58.524 36.000 0.00 0.00 46.27 3.55
201 203 6.743575 AGTGAGGAAGTGCATAAATAACAC 57.256 37.500 0.00 0.00 34.48 3.32
202 204 8.856153 TTTAGTGAGGAAGTGCATAAATAACA 57.144 30.769 0.00 0.00 0.00 2.41
218 220 8.514136 TTTGAAATTGCGTATTTTTAGTGAGG 57.486 30.769 0.00 0.00 36.59 3.86
225 227 9.824534 GAATTGGATTTGAAATTGCGTATTTTT 57.175 25.926 0.00 0.00 36.59 1.94
233 235 7.662604 ACAAGAGAATTGGATTTGAAATTGC 57.337 32.000 0.00 0.00 0.00 3.56
249 251 9.077885 AGGTGCAAATAAATAGAAACAAGAGAA 57.922 29.630 0.00 0.00 0.00 2.87
256 258 7.822658 TGTGGTAGGTGCAAATAAATAGAAAC 58.177 34.615 0.00 0.00 0.00 2.78
278 280 0.025898 CTGATGCACGCGAAGATGTG 59.974 55.000 15.93 0.00 38.23 3.21
281 283 1.945387 AATCTGATGCACGCGAAGAT 58.055 45.000 15.93 8.14 0.00 2.40
288 290 1.594397 ACGCATGTAATCTGATGCACG 59.406 47.619 0.00 0.00 44.39 5.34
293 295 5.178061 TGAGTTTGACGCATGTAATCTGAT 58.822 37.500 0.00 0.00 0.00 2.90
297 299 3.485877 GCCTGAGTTTGACGCATGTAATC 60.486 47.826 0.00 0.00 0.00 1.75
315 317 0.388134 GCAATGACAGCAACTGCCTG 60.388 55.000 0.00 0.00 43.38 4.85
316 318 0.824595 TGCAATGACAGCAACTGCCT 60.825 50.000 0.00 0.00 43.38 4.75
318 320 3.573569 TTGCAATGACAGCAACTGC 57.426 47.368 0.00 0.00 46.13 4.40
323 325 5.008619 TCTTTTCTTTTGCAATGACAGCA 57.991 34.783 0.00 0.00 40.85 4.41
324 326 5.971895 TTCTTTTCTTTTGCAATGACAGC 57.028 34.783 0.00 0.00 0.00 4.40
325 327 8.188531 TCTTTTCTTTTCTTTTGCAATGACAG 57.811 30.769 0.00 1.60 0.00 3.51
326 328 8.545229 TTCTTTTCTTTTCTTTTGCAATGACA 57.455 26.923 0.00 0.00 0.00 3.58
344 346 4.437524 GCTCAGCGATTACCCTTTCTTTTC 60.438 45.833 0.00 0.00 0.00 2.29
345 347 3.440522 GCTCAGCGATTACCCTTTCTTTT 59.559 43.478 0.00 0.00 0.00 2.27
348 350 1.134371 GGCTCAGCGATTACCCTTTCT 60.134 52.381 0.00 0.00 0.00 2.52
349 351 1.300481 GGCTCAGCGATTACCCTTTC 58.700 55.000 0.00 0.00 0.00 2.62
351 353 0.618458 TTGGCTCAGCGATTACCCTT 59.382 50.000 0.00 0.00 0.00 3.95
352 354 0.618458 TTTGGCTCAGCGATTACCCT 59.382 50.000 0.00 0.00 0.00 4.34
353 355 1.132453 GTTTTGGCTCAGCGATTACCC 59.868 52.381 0.00 0.00 0.00 3.69
360 362 0.936297 GCAAGTGTTTTGGCTCAGCG 60.936 55.000 0.00 0.00 0.00 5.18
366 368 3.931285 CAAAAGAGCAAGTGTTTTGGC 57.069 42.857 0.00 0.00 42.85 4.52
372 374 5.185056 ACCTTTGTAACAAAAGAGCAAGTGT 59.815 36.000 3.21 0.00 39.12 3.55
373 375 5.650543 ACCTTTGTAACAAAAGAGCAAGTG 58.349 37.500 3.21 0.00 39.12 3.16
374 376 5.417580 TGACCTTTGTAACAAAAGAGCAAGT 59.582 36.000 3.21 0.00 39.12 3.16
375 377 5.890334 TGACCTTTGTAACAAAAGAGCAAG 58.110 37.500 3.21 0.00 39.12 4.01
376 378 5.906113 TGACCTTTGTAACAAAAGAGCAA 57.094 34.783 3.21 0.00 39.12 3.91
377 379 6.463995 AATGACCTTTGTAACAAAAGAGCA 57.536 33.333 3.21 2.04 39.12 4.26
378 380 7.165427 CAAATGACCTTTGTAACAAAAGAGC 57.835 36.000 3.21 0.00 39.12 4.09
391 393 6.290605 CCTCCATTTCAAACAAATGACCTTT 58.709 36.000 8.35 0.00 39.36 3.11
392 394 5.742838 GCCTCCATTTCAAACAAATGACCTT 60.743 40.000 8.35 0.00 39.36 3.50
393 395 4.262592 GCCTCCATTTCAAACAAATGACCT 60.263 41.667 8.35 0.00 39.36 3.85
394 396 3.996363 GCCTCCATTTCAAACAAATGACC 59.004 43.478 8.35 0.00 39.36 4.02
395 397 4.630111 TGCCTCCATTTCAAACAAATGAC 58.370 39.130 8.35 0.00 39.36 3.06
396 398 4.952071 TGCCTCCATTTCAAACAAATGA 57.048 36.364 8.35 0.00 39.36 2.57
397 399 5.277925 GGTTTGCCTCCATTTCAAACAAATG 60.278 40.000 15.83 4.81 46.66 2.32
398 400 4.821260 GGTTTGCCTCCATTTCAAACAAAT 59.179 37.500 15.83 0.00 46.66 2.32
399 401 4.195416 GGTTTGCCTCCATTTCAAACAAA 58.805 39.130 15.83 0.00 46.66 2.83
400 402 3.198635 TGGTTTGCCTCCATTTCAAACAA 59.801 39.130 15.83 5.07 46.66 2.83
411 413 1.966451 CGAGGTGTGGTTTGCCTCC 60.966 63.158 0.00 0.00 44.32 4.30
424 426 4.021102 ACTCCATTTCAAACATCGAGGT 57.979 40.909 0.00 0.00 0.00 3.85
428 430 6.480524 TCTTGTACTCCATTTCAAACATCG 57.519 37.500 0.00 0.00 0.00 3.84
430 432 8.695456 AGTTTTCTTGTACTCCATTTCAAACAT 58.305 29.630 0.00 0.00 0.00 2.71
441 443 9.968743 CGAATAAACATAGTTTTCTTGTACTCC 57.031 33.333 0.03 0.00 0.00 3.85
453 455 9.730420 GCCATATTTGTTCGAATAAACATAGTT 57.270 29.630 20.37 7.93 38.83 2.24
454 456 8.349983 GGCCATATTTGTTCGAATAAACATAGT 58.650 33.333 20.37 8.57 38.83 2.12
455 457 8.349245 TGGCCATATTTGTTCGAATAAACATAG 58.651 33.333 20.37 10.32 38.83 2.23
456 458 8.226819 TGGCCATATTTGTTCGAATAAACATA 57.773 30.769 20.37 11.56 38.83 2.29
457 459 7.106439 TGGCCATATTTGTTCGAATAAACAT 57.894 32.000 20.37 13.04 38.83 2.71
458 460 6.516739 TGGCCATATTTGTTCGAATAAACA 57.483 33.333 20.37 11.25 37.37 2.83
466 468 6.795399 AGTTTAGATTGGCCATATTTGTTCG 58.205 36.000 6.09 0.00 0.00 3.95
470 472 9.398170 CGATAAAGTTTAGATTGGCCATATTTG 57.602 33.333 6.09 0.00 0.00 2.32
502 504 1.685148 GGAGATGTGCCTCATTTCCC 58.315 55.000 13.81 4.45 46.14 3.97
504 506 3.135530 AGGTAGGAGATGTGCCTCATTTC 59.864 47.826 0.00 2.39 36.83 2.17
507 509 2.090831 AGAGGTAGGAGATGTGCCTCAT 60.091 50.000 9.50 0.00 45.92 2.90
524 526 7.012799 AGAGTAACTTTCTTTTTGAAGCAGAGG 59.987 37.037 0.00 0.00 35.89 3.69
541 543 7.475840 CAGTGAAAGCTTTGAAAGAGTAACTT 58.524 34.615 18.30 0.00 40.98 2.66
542 544 6.458888 GCAGTGAAAGCTTTGAAAGAGTAACT 60.459 38.462 18.30 0.00 0.00 2.24
543 545 5.683302 GCAGTGAAAGCTTTGAAAGAGTAAC 59.317 40.000 18.30 0.00 0.00 2.50
544 546 5.356751 TGCAGTGAAAGCTTTGAAAGAGTAA 59.643 36.000 18.30 0.00 0.00 2.24
545 547 4.881273 TGCAGTGAAAGCTTTGAAAGAGTA 59.119 37.500 18.30 0.00 0.00 2.59
546 548 3.696051 TGCAGTGAAAGCTTTGAAAGAGT 59.304 39.130 18.30 0.00 0.00 3.24
547 549 4.040376 GTGCAGTGAAAGCTTTGAAAGAG 58.960 43.478 18.30 2.67 0.00 2.85
558 560 4.455533 TGGCTATACTTTGTGCAGTGAAAG 59.544 41.667 10.02 10.02 35.64 2.62
561 563 3.599343 CTGGCTATACTTTGTGCAGTGA 58.401 45.455 0.00 0.00 0.00 3.41
562 564 2.096496 GCTGGCTATACTTTGTGCAGTG 59.904 50.000 0.00 0.00 0.00 3.66
565 567 2.083774 GTGCTGGCTATACTTTGTGCA 58.916 47.619 0.00 0.00 0.00 4.57
566 568 2.083774 TGTGCTGGCTATACTTTGTGC 58.916 47.619 0.00 0.00 0.00 4.57
567 569 3.940852 TGATGTGCTGGCTATACTTTGTG 59.059 43.478 0.00 0.00 0.00 3.33
575 577 4.951715 TCAAAAAGATGATGTGCTGGCTAT 59.048 37.500 0.00 0.00 0.00 2.97
582 584 9.962759 GTGAAATTTATCAAAAAGATGATGTGC 57.037 29.630 0.00 0.00 40.21 4.57
698 765 1.997606 GCAGCTGCAAATGATGTTTCC 59.002 47.619 33.36 0.00 41.59 3.13
700 767 2.297880 TGAGCAGCTGCAAATGATGTTT 59.702 40.909 38.24 15.47 45.16 2.83
715 804 3.733224 GTGATACGCTGATTAGTGAGCAG 59.267 47.826 4.89 0.00 44.59 4.24
724 813 3.679980 GTGTCTTGTGTGATACGCTGATT 59.320 43.478 0.00 0.00 0.00 2.57
758 847 2.156917 CAGGCAGCATGAAACTTCTGA 58.843 47.619 0.00 0.00 39.69 3.27
769 2118 3.354948 TTGAGATAACACAGGCAGCAT 57.645 42.857 0.00 0.00 0.00 3.79
771 2120 2.615912 GGATTGAGATAACACAGGCAGC 59.384 50.000 0.00 0.00 0.00 5.25
853 2266 2.499303 GATTGGACTGGGGTGGGGTG 62.499 65.000 0.00 0.00 0.00 4.61
854 2267 2.121042 ATTGGACTGGGGTGGGGT 60.121 61.111 0.00 0.00 0.00 4.95
855 2268 2.683475 GATTGGACTGGGGTGGGG 59.317 66.667 0.00 0.00 0.00 4.96
856 2269 1.799157 TTGGATTGGACTGGGGTGGG 61.799 60.000 0.00 0.00 0.00 4.61
857 2270 0.114168 TTTGGATTGGACTGGGGTGG 59.886 55.000 0.00 0.00 0.00 4.61
890 2303 2.269241 GAGAGGGCTTTGGGGTCG 59.731 66.667 0.00 0.00 0.00 4.79
900 2313 4.416738 GGTGGCTGGTGAGAGGGC 62.417 72.222 0.00 0.00 0.00 5.19
910 2323 1.598962 CTGTGGACTGTGGTGGCTG 60.599 63.158 0.00 0.00 0.00 4.85
911 2324 2.044806 GACTGTGGACTGTGGTGGCT 62.045 60.000 0.00 0.00 0.00 4.75
913 2326 1.071471 GGACTGTGGACTGTGGTGG 59.929 63.158 0.00 0.00 0.00 4.61
920 2333 2.158445 AGTAGACTGTGGACTGTGGACT 60.158 50.000 0.00 0.00 0.00 3.85
921 2334 2.029828 CAGTAGACTGTGGACTGTGGAC 60.030 54.545 9.47 0.00 39.09 4.02
922 2335 2.158519 TCAGTAGACTGTGGACTGTGGA 60.159 50.000 14.82 0.00 44.12 4.02
948 2387 2.926200 CACTGAATTCTCGGCACACTAG 59.074 50.000 7.05 0.00 0.00 2.57
954 2397 0.391661 GGCTCACTGAATTCTCGGCA 60.392 55.000 7.05 0.00 0.00 5.69
955 2398 1.092345 GGGCTCACTGAATTCTCGGC 61.092 60.000 7.05 4.32 0.00 5.54
957 2400 1.424493 GCGGGCTCACTGAATTCTCG 61.424 60.000 7.05 0.49 0.00 4.04
958 2401 0.107945 AGCGGGCTCACTGAATTCTC 60.108 55.000 7.05 0.00 0.00 2.87
984 2427 1.301244 CATGGCGGTGGCTAGCTAG 60.301 63.158 16.84 16.84 39.81 3.42
985 2428 2.807107 CCATGGCGGTGGCTAGCTA 61.807 63.158 15.72 5.44 39.81 3.32
986 2429 4.181010 CCATGGCGGTGGCTAGCT 62.181 66.667 15.72 0.00 39.81 3.32
1815 3279 0.618968 ATCCCAGACCCAGACCAGTC 60.619 60.000 0.00 0.00 0.00 3.51
1816 3280 0.618968 GATCCCAGACCCAGACCAGT 60.619 60.000 0.00 0.00 0.00 4.00
1817 3281 1.680522 CGATCCCAGACCCAGACCAG 61.681 65.000 0.00 0.00 0.00 4.00
1818 3282 1.685765 CGATCCCAGACCCAGACCA 60.686 63.158 0.00 0.00 0.00 4.02
1819 3283 0.760945 ATCGATCCCAGACCCAGACC 60.761 60.000 0.00 0.00 0.00 3.85
1852 3317 4.804665 CACATGACTGATGAGATGACTGAC 59.195 45.833 0.00 0.00 35.80 3.51
1853 3318 4.465305 ACACATGACTGATGAGATGACTGA 59.535 41.667 0.00 0.00 35.80 3.41
1854 3319 4.567159 CACACATGACTGATGAGATGACTG 59.433 45.833 0.00 0.00 35.80 3.51
1855 3320 4.465305 TCACACATGACTGATGAGATGACT 59.535 41.667 0.00 0.00 35.80 3.41
1867 3332 3.461061 CAACACTCACTCACACATGACT 58.539 45.455 0.00 0.00 0.00 3.41
1888 3353 2.924421 CCAGTCTCCAAAGCCTAATCC 58.076 52.381 0.00 0.00 0.00 3.01
1916 3381 2.031919 TACAGCAAGCACACCGGG 59.968 61.111 6.32 0.00 0.00 5.73
1921 3386 1.217001 CACGAACTACAGCAAGCACA 58.783 50.000 0.00 0.00 0.00 4.57
1929 3394 2.732597 GCCTACAGAGCACGAACTACAG 60.733 54.545 0.00 0.00 0.00 2.74
1969 3434 2.831526 TCTCAGCAGCTAACACCATACA 59.168 45.455 0.00 0.00 0.00 2.29
1987 3452 7.856145 ACATGTTATTTCAGACTGGAATCTC 57.144 36.000 12.46 7.82 0.00 2.75
2053 3720 8.565896 ACTCAAATGCACAATAGAAGTGATTA 57.434 30.769 0.00 0.00 39.30 1.75
2064 3731 6.655078 AGGACTTTAACTCAAATGCACAAT 57.345 33.333 0.00 0.00 0.00 2.71
2080 3747 5.431731 AGGAAAAATGGGGAAAAAGGACTTT 59.568 36.000 0.00 0.00 0.00 2.66
2083 3750 4.593206 AGAGGAAAAATGGGGAAAAAGGAC 59.407 41.667 0.00 0.00 0.00 3.85
2157 3829 1.668419 GTGTGAACTGTGAAGGCACT 58.332 50.000 0.00 0.00 45.36 4.40
2158 3830 0.663153 GGTGTGAACTGTGAAGGCAC 59.337 55.000 0.00 0.00 45.35 5.01
2162 3834 1.331756 GCAGTGGTGTGAACTGTGAAG 59.668 52.381 5.55 0.00 45.58 3.02
2163 3835 1.065491 AGCAGTGGTGTGAACTGTGAA 60.065 47.619 0.00 0.00 45.58 3.18
2164 3836 0.541392 AGCAGTGGTGTGAACTGTGA 59.459 50.000 0.00 0.00 45.58 3.58
2165 3837 0.940126 GAGCAGTGGTGTGAACTGTG 59.060 55.000 0.00 0.00 45.58 3.66
2166 3838 0.530650 CGAGCAGTGGTGTGAACTGT 60.531 55.000 0.00 0.00 45.58 3.55
2167 3839 0.249447 TCGAGCAGTGGTGTGAACTG 60.249 55.000 0.00 0.00 46.39 3.16
2168 3840 0.249489 GTCGAGCAGTGGTGTGAACT 60.249 55.000 0.00 0.00 0.00 3.01
2169 3841 0.529773 TGTCGAGCAGTGGTGTGAAC 60.530 55.000 0.00 0.00 0.00 3.18
2185 3857 4.442706 AGAATTCACGTCCCATACATGTC 58.557 43.478 0.00 0.00 0.00 3.06
2243 3915 4.025145 CGTTCTGTTCAAGTTCAACCCTAC 60.025 45.833 0.00 0.00 0.00 3.18
2290 3962 3.459232 TTCCTGCTGGTATCGATTGAG 57.541 47.619 1.71 0.00 34.23 3.02
2355 4044 3.242446 CGAGAGACATCGAATCGAACAGA 60.242 47.826 10.12 0.00 45.56 3.41
2459 4152 1.064166 AGACAAGCCAATCCCAGGATG 60.064 52.381 0.00 0.00 34.70 3.51
2533 4226 1.103803 TACTGACAAGCCGCTCCTAG 58.896 55.000 0.00 0.00 0.00 3.02
2546 4239 3.751570 TTCGCGTACGTTTTTACTGAC 57.248 42.857 17.90 0.00 41.18 3.51
2561 4254 1.732259 AGGCACTCTGTTTATTTCGCG 59.268 47.619 0.00 0.00 0.00 5.87
2617 4336 9.477484 CCCAACATGTCTTATACTATAACTCAC 57.523 37.037 0.00 0.00 0.00 3.51
2631 4350 9.838339 CTCTATTATTAGAACCCAACATGTCTT 57.162 33.333 0.00 0.00 34.06 3.01
2632 4351 9.213777 TCTCTATTATTAGAACCCAACATGTCT 57.786 33.333 0.00 0.00 34.06 3.41
2633 4352 9.832445 TTCTCTATTATTAGAACCCAACATGTC 57.168 33.333 0.00 0.00 34.06 3.06
2667 4386 7.286316 GGGGTGTGATTGATCAAGATTTCTTAT 59.714 37.037 14.54 0.00 38.75 1.73
2671 4390 4.098501 GGGGGTGTGATTGATCAAGATTTC 59.901 45.833 14.54 7.04 38.75 2.17
2682 4401 1.178534 ACGCAAAGGGGGTGTGATTG 61.179 55.000 0.00 0.00 41.74 2.67
2687 4407 1.380650 ACAAACGCAAAGGGGGTGT 60.381 52.632 0.00 0.00 42.62 4.16
2690 4410 2.733945 CCACAAACGCAAAGGGGG 59.266 61.111 0.00 0.00 0.00 5.40
2699 4419 3.980646 TCATCTGAAAACCCACAAACG 57.019 42.857 0.00 0.00 0.00 3.60
2700 4420 4.099419 AGGTTCATCTGAAAACCCACAAAC 59.901 41.667 17.05 0.00 44.98 2.93
2735 4455 0.822811 TGCTCTCTCATCTGTCCAGC 59.177 55.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.