Multiple sequence alignment - TraesCS4A01G301400

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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 TraesCS4A01G301400 chr4A 100.000 2264 0 0 1 2264 598515610 598517873 0.000000e+00 4181.0
1 TraesCS4A01G301400 chr5D 92.096 1379 83 14 592 1945 527486551 527487928 0.000000e+00 1919.0
2 TraesCS4A01G301400 chr5D 82.191 1269 136 52 990 2214 384428886 384430108 0.000000e+00 1009.0
3 TraesCS4A01G301400 chr5D 88.430 242 27 1 1 241 527486231 527486472 7.910000e-75 291.0
4 TraesCS4A01G301400 chr5A 90.861 1313 90 7 473 1768 588455417 588454118 0.000000e+00 1733.0
5 TraesCS4A01G301400 chr5A 87.356 261 29 4 4 261 588455731 588455472 1.700000e-76 296.0
6 TraesCS4A01G301400 chr1A 91.778 1119 76 6 586 1691 259893551 259892436 0.000000e+00 1543.0
7 TraesCS4A01G301400 chr3D 92.033 1092 74 3 613 1691 230694418 230695509 0.000000e+00 1522.0
8 TraesCS4A01G301400 chr3D 83.220 590 82 10 1680 2254 230710896 230711483 1.990000e-145 525.0
9 TraesCS4A01G301400 chr3D 82.833 600 80 13 1680 2264 230695571 230696162 1.200000e-142 516.0
10 TraesCS4A01G301400 chr3D 80.126 317 45 17 584 886 552286048 552285736 1.050000e-53 220.0
11 TraesCS4A01G301400 chr3D 82.308 260 36 7 2015 2264 486671365 486671106 1.360000e-52 217.0
12 TraesCS4A01G301400 chr3D 81.197 234 30 12 138 364 486682736 486682962 2.310000e-40 176.0
13 TraesCS4A01G301400 chr3D 72.872 564 109 30 1700 2243 230711627 230711088 1.080000e-33 154.0
14 TraesCS4A01G301400 chr3D 86.207 116 13 3 191 305 486682889 486682776 3.050000e-24 122.0
15 TraesCS4A01G301400 chr7B 82.075 1802 246 44 505 2254 65835491 65837267 0.000000e+00 1467.0
16 TraesCS4A01G301400 chr7B 91.509 212 18 0 1680 1891 685957158 685957369 2.200000e-75 292.0
17 TraesCS4A01G301400 chr7B 85.600 250 31 5 1 247 685906716 685906963 8.020000e-65 257.0
18 TraesCS4A01G301400 chr7B 77.391 230 44 7 4 229 48440129 48440354 1.820000e-26 130.0
19 TraesCS4A01G301400 chr2B 85.097 1389 166 25 331 1691 40122181 40123556 0.000000e+00 1380.0
20 TraesCS4A01G301400 chr2B 84.480 1250 144 29 331 1538 609250956 609252197 0.000000e+00 1188.0
21 TraesCS4A01G301400 chr2B 86.266 233 18 7 662 882 622710216 622710446 8.080000e-60 241.0
22 TraesCS4A01G301400 chr2B 82.278 158 28 0 1 158 609250514 609250671 1.090000e-28 137.0
23 TraesCS4A01G301400 chr2B 76.349 241 48 7 4 241 411506561 411506795 1.100000e-23 121.0
24 TraesCS4A01G301400 chr2B 89.041 73 5 2 550 621 773718860 773718930 1.110000e-13 87.9
25 TraesCS4A01G301400 chr1D 88.178 1125 84 21 582 1691 407181389 407180299 0.000000e+00 1295.0
26 TraesCS4A01G301400 chr1D 84.463 354 50 3 1680 2029 465921430 465921782 5.990000e-91 344.0
27 TraesCS4A01G301400 chr1D 81.571 331 30 11 584 886 12498730 12499057 6.250000e-61 244.0
28 TraesCS4A01G301400 chr1D 84.170 259 32 4 2015 2264 465921798 465922056 2.250000e-60 243.0
29 TraesCS4A01G301400 chr6D 91.978 723 58 0 969 1691 43206470 43205748 0.000000e+00 1014.0
30 TraesCS4A01G301400 chr6D 81.681 595 88 9 1680 2264 43205686 43205103 2.030000e-130 475.0
31 TraesCS4A01G301400 chr7A 83.474 593 84 7 1680 2259 188643644 188644235 7.110000e-150 540.0
32 TraesCS4A01G301400 chr7A 76.102 590 104 22 1680 2254 729018056 729018623 7.970000e-70 274.0
33 TraesCS4A01G301400 chr1B 81.757 592 83 9 1680 2264 642719639 642720212 2.630000e-129 472.0
34 TraesCS4A01G301400 chr7D 82.583 333 52 4 1700 2028 564725356 564725686 2.850000e-74 289.0
35 TraesCS4A01G301400 chr7D 81.419 296 43 7 1700 1990 530707108 530707396 4.860000e-57 231.0
36 TraesCS4A01G301400 chr5B 85.477 241 30 5 4 241 415419566 415419328 1.740000e-61 246.0
37 TraesCS4A01G301400 chr5B 85.135 74 8 2 552 624 272829691 272829620 3.120000e-09 73.1
38 TraesCS4A01G301400 chr3B 78.008 241 45 7 4 241 104406428 104406193 6.520000e-31 145.0
39 TraesCS4A01G301400 chr3B 78.049 205 39 5 34 235 678011110 678011311 8.490000e-25 124.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G301400 chr4A 598515610 598517873 2263 False 4181.0 4181 100.0000 1 2264 1 chr4A.!!$F1 2263
1 TraesCS4A01G301400 chr5D 527486231 527487928 1697 False 1105.0 1919 90.2630 1 1945 2 chr5D.!!$F2 1944
2 TraesCS4A01G301400 chr5D 384428886 384430108 1222 False 1009.0 1009 82.1910 990 2214 1 chr5D.!!$F1 1224
3 TraesCS4A01G301400 chr5A 588454118 588455731 1613 True 1014.5 1733 89.1085 4 1768 2 chr5A.!!$R1 1764
4 TraesCS4A01G301400 chr1A 259892436 259893551 1115 True 1543.0 1543 91.7780 586 1691 1 chr1A.!!$R1 1105
5 TraesCS4A01G301400 chr3D 230694418 230696162 1744 False 1019.0 1522 87.4330 613 2264 2 chr3D.!!$F3 1651
6 TraesCS4A01G301400 chr3D 230710896 230711483 587 False 525.0 525 83.2200 1680 2254 1 chr3D.!!$F1 574
7 TraesCS4A01G301400 chr7B 65835491 65837267 1776 False 1467.0 1467 82.0750 505 2254 1 chr7B.!!$F2 1749
8 TraesCS4A01G301400 chr2B 40122181 40123556 1375 False 1380.0 1380 85.0970 331 1691 1 chr2B.!!$F1 1360
9 TraesCS4A01G301400 chr2B 609250514 609252197 1683 False 662.5 1188 83.3790 1 1538 2 chr2B.!!$F5 1537
10 TraesCS4A01G301400 chr1D 407180299 407181389 1090 True 1295.0 1295 88.1780 582 1691 1 chr1D.!!$R1 1109
11 TraesCS4A01G301400 chr1D 465921430 465922056 626 False 293.5 344 84.3165 1680 2264 2 chr1D.!!$F2 584
12 TraesCS4A01G301400 chr6D 43205103 43206470 1367 True 744.5 1014 86.8295 969 2264 2 chr6D.!!$R1 1295
13 TraesCS4A01G301400 chr7A 188643644 188644235 591 False 540.0 540 83.4740 1680 2259 1 chr7A.!!$F1 579
14 TraesCS4A01G301400 chr7A 729018056 729018623 567 False 274.0 274 76.1020 1680 2254 1 chr7A.!!$F2 574
15 TraesCS4A01G301400 chr1B 642719639 642720212 573 False 472.0 472 81.7570 1680 2264 1 chr1B.!!$F1 584

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
434 768 0.179116 CTCTCTGGACTGGCATGTCG 60.179 60.0 9.81 0.0 37.81 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1477 1918 0.038526 TCTCGTTTCTTCCGCTCCAC 60.039 55.0 0.0 0.0 0.0 4.02 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
58 59 9.657419 TTATGATTATGTGACATAGTATGCCAG 57.343 33.333 10.16 0.00 0.00 4.85
80 81 3.879892 GCCACAAAACCCAAAAAGCATTA 59.120 39.130 0.00 0.00 0.00 1.90
81 82 4.518590 GCCACAAAACCCAAAAAGCATTAT 59.481 37.500 0.00 0.00 0.00 1.28
103 104 5.151297 TGTATGTGAAATCAGCAGACAGA 57.849 39.130 8.39 0.00 31.16 3.41
130 442 2.040544 CAGGGGTAAGGCGTTGCAG 61.041 63.158 9.43 0.00 0.00 4.41
132 444 1.196104 AGGGGTAAGGCGTTGCAGTA 61.196 55.000 9.43 0.00 0.00 2.74
146 458 3.955291 CAGTATCTAGTGCAGCGCT 57.045 52.632 14.22 14.22 0.00 5.92
179 512 1.821216 CCGCACACTGGAAAACCTAT 58.179 50.000 0.00 0.00 0.00 2.57
184 517 3.057526 GCACACTGGAAAACCTATTGGAC 60.058 47.826 0.00 0.00 37.04 4.02
229 563 4.783621 TCCAGATGTGCAGCGCCC 62.784 66.667 2.29 0.00 0.00 6.13
232 566 2.749044 AGATGTGCAGCGCCCAAG 60.749 61.111 2.29 0.00 0.00 3.61
243 577 3.971702 GCCCAAGGGACAGGCACT 61.972 66.667 9.92 0.00 46.34 4.40
257 591 4.034258 CACTGCACTTGGGCGCTG 62.034 66.667 7.64 0.00 36.28 5.18
262 596 3.367743 CACTTGGGCGCTGCACAT 61.368 61.111 7.64 0.00 43.39 3.21
263 597 3.058160 ACTTGGGCGCTGCACATC 61.058 61.111 7.64 0.00 43.39 3.06
264 598 2.749044 CTTGGGCGCTGCACATCT 60.749 61.111 7.64 0.00 43.39 2.90
265 599 3.047718 CTTGGGCGCTGCACATCTG 62.048 63.158 7.64 0.00 43.39 2.90
267 601 4.783621 GGGCGCTGCACATCTGGA 62.784 66.667 7.64 0.00 0.00 3.86
268 602 3.503363 GGCGCTGCACATCTGGAC 61.503 66.667 7.64 0.00 0.00 4.02
269 603 2.743538 GCGCTGCACATCTGGACA 60.744 61.111 0.00 0.00 0.00 4.02
270 604 2.327343 GCGCTGCACATCTGGACAA 61.327 57.895 0.00 0.00 0.00 3.18
271 605 1.792301 CGCTGCACATCTGGACAAG 59.208 57.895 0.00 0.00 0.00 3.16
272 606 1.505353 GCTGCACATCTGGACAAGC 59.495 57.895 0.00 0.00 0.00 4.01
273 607 0.959372 GCTGCACATCTGGACAAGCT 60.959 55.000 0.00 0.00 0.00 3.74
274 608 1.676916 GCTGCACATCTGGACAAGCTA 60.677 52.381 0.00 0.00 0.00 3.32
275 609 2.277969 CTGCACATCTGGACAAGCTAG 58.722 52.381 0.00 0.00 0.00 3.42
276 610 1.625315 TGCACATCTGGACAAGCTAGT 59.375 47.619 0.00 0.00 0.00 2.57
277 611 2.275318 GCACATCTGGACAAGCTAGTC 58.725 52.381 0.00 0.00 37.80 2.59
285 619 2.577449 GACAAGCTAGTCCAGAGAGC 57.423 55.000 0.00 0.00 36.42 4.09
286 620 1.821753 GACAAGCTAGTCCAGAGAGCA 59.178 52.381 0.00 0.00 38.73 4.26
287 621 2.232452 GACAAGCTAGTCCAGAGAGCAA 59.768 50.000 0.00 0.00 38.73 3.91
288 622 2.028567 ACAAGCTAGTCCAGAGAGCAAC 60.029 50.000 0.00 0.00 38.73 4.17
289 623 1.930251 AGCTAGTCCAGAGAGCAACA 58.070 50.000 0.00 0.00 38.73 3.33
290 624 1.548269 AGCTAGTCCAGAGAGCAACAC 59.452 52.381 0.00 0.00 38.73 3.32
291 625 1.273606 GCTAGTCCAGAGAGCAACACA 59.726 52.381 0.00 0.00 36.20 3.72
292 626 2.289072 GCTAGTCCAGAGAGCAACACAA 60.289 50.000 0.00 0.00 36.20 3.33
293 627 2.540265 AGTCCAGAGAGCAACACAAG 57.460 50.000 0.00 0.00 0.00 3.16
294 628 0.871057 GTCCAGAGAGCAACACAAGC 59.129 55.000 0.00 0.00 0.00 4.01
295 629 0.469494 TCCAGAGAGCAACACAAGCA 59.531 50.000 0.00 0.00 0.00 3.91
296 630 1.072806 TCCAGAGAGCAACACAAGCAT 59.927 47.619 0.00 0.00 0.00 3.79
297 631 1.884579 CCAGAGAGCAACACAAGCATT 59.115 47.619 0.00 0.00 0.00 3.56
298 632 2.095364 CCAGAGAGCAACACAAGCATTC 60.095 50.000 0.00 0.00 0.00 2.67
299 633 2.095364 CAGAGAGCAACACAAGCATTCC 60.095 50.000 0.00 0.00 0.00 3.01
300 634 1.881973 GAGAGCAACACAAGCATTCCA 59.118 47.619 0.00 0.00 0.00 3.53
301 635 1.884579 AGAGCAACACAAGCATTCCAG 59.115 47.619 0.00 0.00 0.00 3.86
302 636 1.610522 GAGCAACACAAGCATTCCAGT 59.389 47.619 0.00 0.00 0.00 4.00
303 637 2.813754 GAGCAACACAAGCATTCCAGTA 59.186 45.455 0.00 0.00 0.00 2.74
304 638 2.816087 AGCAACACAAGCATTCCAGTAG 59.184 45.455 0.00 0.00 0.00 2.57
305 639 2.095059 GCAACACAAGCATTCCAGTAGG 60.095 50.000 0.00 0.00 0.00 3.18
306 640 3.149196 CAACACAAGCATTCCAGTAGGT 58.851 45.455 0.00 0.00 35.89 3.08
307 641 3.508845 ACACAAGCATTCCAGTAGGTT 57.491 42.857 0.00 0.00 35.89 3.50
308 642 3.832527 ACACAAGCATTCCAGTAGGTTT 58.167 40.909 0.00 0.00 35.89 3.27
309 643 4.215109 ACACAAGCATTCCAGTAGGTTTT 58.785 39.130 0.00 0.00 35.89 2.43
310 644 4.278419 ACACAAGCATTCCAGTAGGTTTTC 59.722 41.667 0.00 0.00 35.89 2.29
311 645 3.826729 ACAAGCATTCCAGTAGGTTTTCC 59.173 43.478 0.00 0.00 41.05 3.13
312 646 3.087370 AGCATTCCAGTAGGTTTTCCC 57.913 47.619 0.00 0.00 41.86 3.97
314 648 3.017442 GCATTCCAGTAGGTTTTCCCTC 58.983 50.000 0.00 0.00 44.81 4.30
315 649 3.621558 CATTCCAGTAGGTTTTCCCTCC 58.378 50.000 0.00 0.00 44.81 4.30
316 650 1.272807 TCCAGTAGGTTTTCCCTCCG 58.727 55.000 0.00 0.00 44.81 4.63
317 651 1.203212 TCCAGTAGGTTTTCCCTCCGA 60.203 52.381 0.00 0.00 44.81 4.55
318 652 1.838077 CCAGTAGGTTTTCCCTCCGAT 59.162 52.381 0.00 0.00 44.81 4.18
319 653 3.036091 CCAGTAGGTTTTCCCTCCGATA 58.964 50.000 0.00 0.00 44.81 2.92
320 654 3.453353 CCAGTAGGTTTTCCCTCCGATAA 59.547 47.826 0.00 0.00 44.81 1.75
321 655 4.102681 CCAGTAGGTTTTCCCTCCGATAAT 59.897 45.833 0.00 0.00 44.81 1.28
322 656 5.397559 CCAGTAGGTTTTCCCTCCGATAATT 60.398 44.000 0.00 0.00 44.81 1.40
323 657 6.120220 CAGTAGGTTTTCCCTCCGATAATTT 58.880 40.000 0.00 0.00 44.81 1.82
324 658 6.602009 CAGTAGGTTTTCCCTCCGATAATTTT 59.398 38.462 0.00 0.00 44.81 1.82
325 659 6.827251 AGTAGGTTTTCCCTCCGATAATTTTC 59.173 38.462 0.00 0.00 44.81 2.29
326 660 5.827756 AGGTTTTCCCTCCGATAATTTTCT 58.172 37.500 0.00 0.00 40.71 2.52
327 661 6.965607 AGGTTTTCCCTCCGATAATTTTCTA 58.034 36.000 0.00 0.00 40.71 2.10
328 662 7.407729 AGGTTTTCCCTCCGATAATTTTCTAA 58.592 34.615 0.00 0.00 40.71 2.10
329 663 7.556635 AGGTTTTCCCTCCGATAATTTTCTAAG 59.443 37.037 0.00 0.00 40.71 2.18
335 669 7.562454 TCCCTCCGATAATTTTCTAAGTGTCTA 59.438 37.037 0.00 0.00 0.00 2.59
349 683 1.142748 GTCTAGTGCAGCGCCTGAT 59.857 57.895 2.29 0.00 32.44 2.90
350 684 1.142531 TCTAGTGCAGCGCCTGATG 59.857 57.895 2.29 0.00 32.44 3.07
376 710 1.674817 GCGCTGCACCCTAACTTAGAA 60.675 52.381 0.00 0.00 0.00 2.10
379 713 3.500680 CGCTGCACCCTAACTTAGAAAAA 59.499 43.478 0.00 0.00 0.00 1.94
382 716 6.455647 GCTGCACCCTAACTTAGAAAAATTT 58.544 36.000 0.00 0.00 0.00 1.82
383 717 6.586463 GCTGCACCCTAACTTAGAAAAATTTC 59.414 38.462 0.00 0.00 37.45 2.17
385 719 6.090783 GCACCCTAACTTAGAAAAATTTCGG 58.909 40.000 0.00 0.00 41.92 4.30
386 720 6.072342 GCACCCTAACTTAGAAAAATTTCGGA 60.072 38.462 0.00 0.00 41.92 4.55
387 721 7.527457 CACCCTAACTTAGAAAAATTTCGGAG 58.473 38.462 0.00 5.46 41.92 4.63
414 748 5.499004 AACCTACTGGAATGCTTCTGTTA 57.501 39.130 0.00 0.00 37.04 2.41
424 758 3.944055 TGCTTCTGTTACTCTCTGGAC 57.056 47.619 0.00 0.00 0.00 4.02
425 759 3.501349 TGCTTCTGTTACTCTCTGGACT 58.499 45.455 0.00 0.00 0.00 3.85
427 761 3.367910 GCTTCTGTTACTCTCTGGACTGG 60.368 52.174 0.00 0.00 0.00 4.00
434 768 0.179116 CTCTCTGGACTGGCATGTCG 60.179 60.000 9.81 0.00 37.81 4.35
439 773 1.184970 TGGACTGGCATGTCGAGACA 61.185 55.000 8.48 8.48 46.44 3.41
449 783 4.819761 TCGAGACATGCAGCGCCC 62.820 66.667 2.29 0.00 0.00 6.13
485 883 0.757188 ACTATCTAGTGCAGCGCCCT 60.757 55.000 2.29 0.00 34.72 5.19
545 948 2.113860 TGAAGCATTCCAGTAGCCAC 57.886 50.000 0.00 0.00 46.93 5.01
567 970 4.758692 GCTATGCAGCGCCTAAGA 57.241 55.556 2.29 0.00 38.22 2.10
642 1045 2.942376 CTGTGTGTCACTTAGGTTGCAA 59.058 45.455 4.27 0.00 35.11 4.08
683 1102 1.076339 CCCCACACACACAAACCCT 60.076 57.895 0.00 0.00 0.00 4.34
757 1196 6.520272 AGATTTTGTCTATGGATCTCGAAGG 58.480 40.000 0.00 0.00 34.69 3.46
766 1205 1.120530 GATCTCGAAGGCAACCCCTA 58.879 55.000 0.00 0.00 45.62 3.53
834 1273 8.548025 TGAATTCTCACATTACCTCAAATCCTA 58.452 33.333 7.05 0.00 0.00 2.94
1048 1487 3.149196 CCACTGTGTGCTAACCAAGAAT 58.851 45.455 7.08 0.00 31.34 2.40
1086 1525 1.464997 GAGGACGCATCTTTGGACAAC 59.535 52.381 0.00 0.00 0.00 3.32
1089 1528 2.063266 GACGCATCTTTGGACAACGTA 58.937 47.619 0.00 0.00 31.13 3.57
1136 1575 4.078537 CCATGTTGGTGTGGAGATGTTTA 58.921 43.478 0.00 0.00 37.72 2.01
1149 1588 5.308497 TGGAGATGTTTACAAGGTGAAGGTA 59.692 40.000 0.00 0.00 0.00 3.08
1152 1591 7.259088 AGATGTTTACAAGGTGAAGGTATCT 57.741 36.000 0.00 0.00 0.00 1.98
1198 1637 5.163332 ACGGAAGGGAGGAGATATTTTGTAC 60.163 44.000 0.00 0.00 0.00 2.90
1320 1761 7.617533 ACACTAACAAAAATTTCGTATGCAC 57.382 32.000 0.00 0.00 0.00 4.57
1335 1776 2.888863 CACTCACCGCCTCCTCTC 59.111 66.667 0.00 0.00 0.00 3.20
1337 1778 0.394488 CACTCACCGCCTCCTCTCTA 60.394 60.000 0.00 0.00 0.00 2.43
1348 1789 3.382227 GCCTCCTCTCTACAAGTACTTCC 59.618 52.174 4.77 0.00 0.00 3.46
1401 1842 5.710099 TGTCCAAAAGGACCAATATCAAGAC 59.290 40.000 11.79 0.00 38.04 3.01
1403 1844 7.110155 GTCCAAAAGGACCAATATCAAGACTA 58.890 38.462 3.27 0.00 33.21 2.59
1407 1848 9.050601 CAAAAGGACCAATATCAAGACTATCTC 57.949 37.037 0.00 0.00 0.00 2.75
1410 1851 7.301420 AGGACCAATATCAAGACTATCTCAGA 58.699 38.462 0.00 0.00 0.00 3.27
1477 1918 1.014564 GCGTCGTCAAAAGGAGAGGG 61.015 60.000 0.00 0.00 0.00 4.30
1571 2012 3.825160 TTGCAAAGGCTCGCGAGGT 62.825 57.895 35.10 0.80 41.91 3.85
1587 2030 1.556911 GAGGTGCAAGAGGAGGATTCA 59.443 52.381 0.00 0.00 0.00 2.57
1605 2048 1.699083 TCAGCACATGACAAGAAGGGA 59.301 47.619 0.00 0.00 31.12 4.20
1698 2214 4.342772 GGTATTTGTCATGAATGTGTCGC 58.657 43.478 0.00 0.00 0.00 5.19
1744 2260 6.229936 TGTTGGTGAACTCTTAGTAGTGTT 57.770 37.500 0.00 0.00 39.94 3.32
1768 2309 4.011058 ACTTGTGTTTGCGAAGTTGTAC 57.989 40.909 0.00 0.00 0.00 2.90
1815 2356 7.054855 GATGAACTCATCGGCATATTACTTC 57.945 40.000 4.02 0.00 42.66 3.01
1820 2361 5.986135 ACTCATCGGCATATTACTTCTGTTC 59.014 40.000 0.00 0.00 0.00 3.18
1867 2408 9.515020 CAAGTTATTGTAAGTGTTGTGATGTTT 57.485 29.630 0.00 0.00 0.00 2.83
1874 2415 6.480651 TGTAAGTGTTGTGATGTTTACGTGAT 59.519 34.615 0.00 0.00 0.00 3.06
1886 2427 6.984740 TGTTTACGTGATTTGAAATTGCTC 57.015 33.333 0.00 0.00 0.00 4.26
1893 2447 6.925165 ACGTGATTTGAAATTGCTCTCAAAAT 59.075 30.769 7.02 0.00 42.96 1.82
1900 2454 6.615088 TGAAATTGCTCTCAAAATAGCTCAC 58.385 36.000 0.00 0.00 39.53 3.51
1932 2486 5.565259 CAGTTTTGCAGTTAATAGAAGTGCG 59.435 40.000 11.37 0.00 46.62 5.34
1961 2515 2.366916 GGACTGAGGCACTGCACTATAT 59.633 50.000 2.82 0.00 41.55 0.86
1965 2519 4.405680 ACTGAGGCACTGCACTATATTGTA 59.594 41.667 2.82 0.00 41.55 2.41
1990 2547 0.888736 CCCAATCAGGCGTCACACAA 60.889 55.000 0.00 0.00 35.39 3.33
1992 2549 1.135603 CCAATCAGGCGTCACACAATG 60.136 52.381 0.00 0.00 0.00 2.82
2011 2568 1.301401 TAGTGCAACGCCTGTGTCC 60.301 57.895 0.00 0.00 45.86 4.02
2046 2634 7.306574 GCACACTAACTTAGAAATTTTTGGCAC 60.307 37.037 2.65 0.00 0.00 5.01
2052 2641 7.637709 ACTTAGAAATTTTTGGCACGAAATC 57.362 32.000 8.07 0.23 0.00 2.17
2064 2653 1.267806 CACGAAATCCTGCTGCAAAGT 59.732 47.619 3.02 0.00 0.00 2.66
2068 2657 2.712057 AATCCTGCTGCAAAGTTTCG 57.288 45.000 3.02 0.00 0.00 3.46
2085 2674 1.227089 CGGTTGCTCTCTGGATCCG 60.227 63.158 7.39 2.06 41.56 4.18
2106 2697 0.107312 ATCCAGATGTGCAGCACCTC 60.107 55.000 23.06 21.43 32.73 3.85
2110 2701 0.689055 AGATGTGCAGCACCTCAGAA 59.311 50.000 26.80 8.34 32.77 3.02
2148 2739 0.747852 TGTGTGACGCCTGACTGTTA 59.252 50.000 0.00 0.00 0.00 2.41
2175 2766 4.262036 GCTGCATAGTATAGTGTAGTGCCA 60.262 45.833 0.00 0.00 31.73 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.755123 GCACATACAGTAGTCCAAAACACT 59.245 41.667 0.00 0.00 0.00 3.55
58 59 1.743996 TGCTTTTTGGGTTTTGTGGC 58.256 45.000 0.00 0.00 0.00 5.01
80 81 5.737860 TCTGTCTGCTGATTTCACATACAT 58.262 37.500 0.00 0.00 0.00 2.29
81 82 5.151297 TCTGTCTGCTGATTTCACATACA 57.849 39.130 0.00 0.00 0.00 2.29
130 442 0.308068 TCGAGCGCTGCACTAGATAC 59.692 55.000 18.48 0.00 0.00 2.24
132 444 1.064946 GTCGAGCGCTGCACTAGAT 59.935 57.895 18.48 0.00 0.00 1.98
158 470 2.335011 GTTTTCCAGTGTGCGGCC 59.665 61.111 0.00 0.00 0.00 6.13
161 473 2.095263 CCAATAGGTTTTCCAGTGTGCG 60.095 50.000 0.00 0.00 43.73 5.34
179 512 0.761187 AGAGCAACAGAGCAGTCCAA 59.239 50.000 0.00 0.00 36.85 3.53
184 517 0.607112 TCCAGAGAGCAACAGAGCAG 59.393 55.000 0.00 0.00 36.85 4.24
229 563 2.113774 TGCAGTGCCTGTCCCTTG 59.886 61.111 13.72 0.00 33.43 3.61
232 566 2.113986 AAGTGCAGTGCCTGTCCC 59.886 61.111 13.72 0.00 33.43 4.46
245 579 3.332493 GATGTGCAGCGCCCAAGTG 62.332 63.158 2.29 0.00 0.00 3.16
246 580 3.058160 GATGTGCAGCGCCCAAGT 61.058 61.111 2.29 0.00 0.00 3.16
247 581 2.749044 AGATGTGCAGCGCCCAAG 60.749 61.111 2.29 0.00 0.00 3.61
248 582 3.057548 CAGATGTGCAGCGCCCAA 61.058 61.111 2.29 0.00 0.00 4.12
250 584 4.783621 TCCAGATGTGCAGCGCCC 62.784 66.667 2.29 0.00 0.00 6.13
251 585 3.503363 GTCCAGATGTGCAGCGCC 61.503 66.667 2.29 0.00 0.00 6.53
252 586 2.249557 CTTGTCCAGATGTGCAGCGC 62.250 60.000 0.00 0.00 0.00 5.92
253 587 1.792301 CTTGTCCAGATGTGCAGCG 59.208 57.895 0.00 0.00 0.00 5.18
254 588 0.959372 AGCTTGTCCAGATGTGCAGC 60.959 55.000 0.00 0.00 0.00 5.25
255 589 2.277969 CTAGCTTGTCCAGATGTGCAG 58.722 52.381 0.00 0.00 0.00 4.41
256 590 1.625315 ACTAGCTTGTCCAGATGTGCA 59.375 47.619 0.00 0.00 0.00 4.57
257 591 2.275318 GACTAGCTTGTCCAGATGTGC 58.725 52.381 16.35 0.00 0.00 4.57
266 600 1.821753 TGCTCTCTGGACTAGCTTGTC 59.178 52.381 18.55 18.55 37.16 3.18
267 601 1.930251 TGCTCTCTGGACTAGCTTGT 58.070 50.000 0.00 0.00 37.16 3.16
268 602 2.028658 TGTTGCTCTCTGGACTAGCTTG 60.029 50.000 0.00 0.00 37.16 4.01
269 603 2.028567 GTGTTGCTCTCTGGACTAGCTT 60.029 50.000 0.00 0.00 37.16 3.74
270 604 1.548269 GTGTTGCTCTCTGGACTAGCT 59.452 52.381 0.00 0.00 37.16 3.32
271 605 1.273606 TGTGTTGCTCTCTGGACTAGC 59.726 52.381 0.00 0.00 36.77 3.42
272 606 3.583806 CTTGTGTTGCTCTCTGGACTAG 58.416 50.000 0.00 0.00 0.00 2.57
273 607 2.289072 GCTTGTGTTGCTCTCTGGACTA 60.289 50.000 0.00 0.00 0.00 2.59
274 608 1.542108 GCTTGTGTTGCTCTCTGGACT 60.542 52.381 0.00 0.00 0.00 3.85
275 609 0.871057 GCTTGTGTTGCTCTCTGGAC 59.129 55.000 0.00 0.00 0.00 4.02
276 610 0.469494 TGCTTGTGTTGCTCTCTGGA 59.531 50.000 0.00 0.00 0.00 3.86
277 611 1.531423 ATGCTTGTGTTGCTCTCTGG 58.469 50.000 0.00 0.00 0.00 3.86
278 612 2.095364 GGAATGCTTGTGTTGCTCTCTG 60.095 50.000 0.00 0.00 0.00 3.35
279 613 2.157738 GGAATGCTTGTGTTGCTCTCT 58.842 47.619 0.00 0.00 0.00 3.10
280 614 1.881973 TGGAATGCTTGTGTTGCTCTC 59.118 47.619 0.00 0.00 0.00 3.20
281 615 1.884579 CTGGAATGCTTGTGTTGCTCT 59.115 47.619 0.00 0.00 0.00 4.09
282 616 1.610522 ACTGGAATGCTTGTGTTGCTC 59.389 47.619 0.00 0.00 0.00 4.26
283 617 1.696063 ACTGGAATGCTTGTGTTGCT 58.304 45.000 0.00 0.00 0.00 3.91
284 618 2.095059 CCTACTGGAATGCTTGTGTTGC 60.095 50.000 0.00 0.00 34.57 4.17
285 619 3.149196 ACCTACTGGAATGCTTGTGTTG 58.851 45.455 0.00 0.00 37.04 3.33
286 620 3.508845 ACCTACTGGAATGCTTGTGTT 57.491 42.857 0.00 0.00 37.04 3.32
287 621 3.508845 AACCTACTGGAATGCTTGTGT 57.491 42.857 0.00 0.00 37.04 3.72
288 622 4.321230 GGAAAACCTACTGGAATGCTTGTG 60.321 45.833 0.00 0.00 37.04 3.33
289 623 3.826729 GGAAAACCTACTGGAATGCTTGT 59.173 43.478 0.00 0.00 37.04 3.16
290 624 3.193479 GGGAAAACCTACTGGAATGCTTG 59.807 47.826 0.00 0.00 37.04 4.01
291 625 3.431415 GGGAAAACCTACTGGAATGCTT 58.569 45.455 0.00 0.00 37.04 3.91
292 626 3.087370 GGGAAAACCTACTGGAATGCT 57.913 47.619 0.00 0.00 37.04 3.79
304 638 7.338703 ACTTAGAAAATTATCGGAGGGAAAACC 59.661 37.037 0.00 0.00 40.67 3.27
305 639 8.182227 CACTTAGAAAATTATCGGAGGGAAAAC 58.818 37.037 0.00 0.00 0.00 2.43
306 640 7.886446 ACACTTAGAAAATTATCGGAGGGAAAA 59.114 33.333 0.00 0.00 0.00 2.29
307 641 7.399634 ACACTTAGAAAATTATCGGAGGGAAA 58.600 34.615 0.00 0.00 0.00 3.13
308 642 6.954232 ACACTTAGAAAATTATCGGAGGGAA 58.046 36.000 0.00 0.00 0.00 3.97
309 643 6.383147 AGACACTTAGAAAATTATCGGAGGGA 59.617 38.462 0.00 0.00 0.00 4.20
310 644 6.583562 AGACACTTAGAAAATTATCGGAGGG 58.416 40.000 0.00 0.00 0.00 4.30
311 645 8.414778 ACTAGACACTTAGAAAATTATCGGAGG 58.585 37.037 0.00 0.00 0.00 4.30
312 646 9.239002 CACTAGACACTTAGAAAATTATCGGAG 57.761 37.037 0.00 0.00 0.00 4.63
313 647 7.705325 GCACTAGACACTTAGAAAATTATCGGA 59.295 37.037 0.00 0.00 0.00 4.55
314 648 7.491372 TGCACTAGACACTTAGAAAATTATCGG 59.509 37.037 0.00 0.00 0.00 4.18
315 649 8.407457 TGCACTAGACACTTAGAAAATTATCG 57.593 34.615 0.00 0.00 0.00 2.92
316 650 8.331742 GCTGCACTAGACACTTAGAAAATTATC 58.668 37.037 0.00 0.00 0.00 1.75
317 651 7.010552 CGCTGCACTAGACACTTAGAAAATTAT 59.989 37.037 0.00 0.00 0.00 1.28
318 652 6.310467 CGCTGCACTAGACACTTAGAAAATTA 59.690 38.462 0.00 0.00 0.00 1.40
319 653 5.120830 CGCTGCACTAGACACTTAGAAAATT 59.879 40.000 0.00 0.00 0.00 1.82
320 654 4.627467 CGCTGCACTAGACACTTAGAAAAT 59.373 41.667 0.00 0.00 0.00 1.82
321 655 3.987868 CGCTGCACTAGACACTTAGAAAA 59.012 43.478 0.00 0.00 0.00 2.29
322 656 3.575630 CGCTGCACTAGACACTTAGAAA 58.424 45.455 0.00 0.00 0.00 2.52
323 657 2.671351 GCGCTGCACTAGACACTTAGAA 60.671 50.000 0.00 0.00 0.00 2.10
324 658 1.135373 GCGCTGCACTAGACACTTAGA 60.135 52.381 0.00 0.00 0.00 2.10
325 659 1.272781 GCGCTGCACTAGACACTTAG 58.727 55.000 0.00 0.00 0.00 2.18
326 660 0.108804 GGCGCTGCACTAGACACTTA 60.109 55.000 7.64 0.00 0.00 2.24
327 661 1.374758 GGCGCTGCACTAGACACTT 60.375 57.895 7.64 0.00 0.00 3.16
328 662 2.262915 GGCGCTGCACTAGACACT 59.737 61.111 7.64 0.00 0.00 3.55
329 663 2.097038 CAGGCGCTGCACTAGACAC 61.097 63.158 7.64 0.00 0.00 3.67
358 692 5.644977 ATTTTTCTAAGTTAGGGTGCAGC 57.355 39.130 7.55 7.55 0.00 5.25
364 698 6.095021 CCCTCCGAAATTTTTCTAAGTTAGGG 59.905 42.308 10.02 0.00 35.07 3.53
365 699 6.882678 TCCCTCCGAAATTTTTCTAAGTTAGG 59.117 38.462 10.02 0.00 35.07 2.69
367 701 8.694581 TTTCCCTCCGAAATTTTTCTAAGTTA 57.305 30.769 0.00 0.00 35.49 2.24
368 702 7.591421 TTTCCCTCCGAAATTTTTCTAAGTT 57.409 32.000 0.00 0.00 35.49 2.66
376 710 5.243060 CAGTAGGTTTTCCCTCCGAAATTTT 59.757 40.000 0.00 0.00 44.81 1.82
379 713 3.308188 CCAGTAGGTTTTCCCTCCGAAAT 60.308 47.826 0.00 0.00 44.81 2.17
382 716 1.203212 TCCAGTAGGTTTTCCCTCCGA 60.203 52.381 0.00 0.00 44.81 4.55
383 717 1.272807 TCCAGTAGGTTTTCCCTCCG 58.727 55.000 0.00 0.00 44.81 4.63
385 719 3.017442 GCATTCCAGTAGGTTTTCCCTC 58.983 50.000 0.00 0.00 44.81 4.30
386 720 4.811063 GAAGCATTCCAGTAGGTTTTCCCT 60.811 45.833 0.00 0.00 42.96 4.20
387 721 3.087370 AGCATTCCAGTAGGTTTTCCC 57.913 47.619 0.00 0.00 41.86 3.97
414 748 0.901124 GACATGCCAGTCCAGAGAGT 59.099 55.000 0.00 0.00 32.36 3.24
434 768 2.747460 TTGGGCGCTGCATGTCTC 60.747 61.111 7.64 0.00 0.00 3.36
449 783 2.032528 TGAAGCGCCTGTCCCTTG 59.967 61.111 2.29 0.00 0.00 3.61
526 924 1.630369 AGTGGCTACTGGAATGCTTCA 59.370 47.619 0.13 0.00 35.34 3.02
580 983 1.072666 GGCGCTGCACATTAAAGCAC 61.073 55.000 7.64 0.00 36.73 4.40
581 984 1.212490 GGCGCTGCACATTAAAGCA 59.788 52.632 7.64 0.00 36.73 3.91
583 986 1.331756 CCTAGGCGCTGCACATTAAAG 59.668 52.381 7.64 0.00 0.00 1.85
669 1088 2.092646 TGAGCTTAGGGTTTGTGTGTGT 60.093 45.455 0.00 0.00 0.00 3.72
683 1102 0.978146 GAGGGGAGGCACTGAGCTTA 60.978 60.000 0.00 0.00 41.55 3.09
1048 1487 0.687920 TCCCACTTGTTCGGCATGTA 59.312 50.000 0.00 0.00 34.26 2.29
1086 1525 7.254795 GGGATGTTGACATATTTCTCCTTTACG 60.255 40.741 0.00 0.00 36.57 3.18
1089 1528 5.590259 CGGGATGTTGACATATTTCTCCTTT 59.410 40.000 0.00 0.00 36.57 3.11
1136 1575 4.019591 GGTTGGTAGATACCTTCACCTTGT 60.020 45.833 10.30 0.00 46.58 3.16
1149 1588 4.884668 TGACTTCTTTCGGTTGGTAGAT 57.115 40.909 0.00 0.00 0.00 1.98
1152 1591 3.325425 TCCATGACTTCTTTCGGTTGGTA 59.675 43.478 0.00 0.00 0.00 3.25
1198 1637 2.148916 TCATAAGCATAGTTCGGGCG 57.851 50.000 0.00 0.00 0.00 6.13
1311 1752 2.183300 GGCGGTGAGTGCATACGA 59.817 61.111 0.00 0.00 31.60 3.43
1312 1753 1.878522 GAGGCGGTGAGTGCATACG 60.879 63.158 0.00 0.00 0.00 3.06
1320 1761 0.394488 TGTAGAGAGGAGGCGGTGAG 60.394 60.000 0.00 0.00 0.00 3.51
1335 1776 4.885907 TCTATCCACGGGAAGTACTTGTAG 59.114 45.833 14.14 6.08 34.34 2.74
1337 1778 3.705051 TCTATCCACGGGAAGTACTTGT 58.295 45.455 14.14 1.66 34.34 3.16
1348 1789 3.062763 GCACTTCATGATCTATCCACGG 58.937 50.000 0.00 0.00 0.00 4.94
1401 1842 1.000385 CTCCGCTGGCTTCTGAGATAG 60.000 57.143 0.00 0.00 0.00 2.08
1403 1844 1.684386 CCTCCGCTGGCTTCTGAGAT 61.684 60.000 0.00 0.00 0.00 2.75
1407 1848 1.743252 GAACCTCCGCTGGCTTCTG 60.743 63.158 0.00 0.00 0.00 3.02
1410 1851 0.890996 CTTTGAACCTCCGCTGGCTT 60.891 55.000 0.00 0.00 0.00 4.35
1477 1918 0.038526 TCTCGTTTCTTCCGCTCCAC 60.039 55.000 0.00 0.00 0.00 4.02
1526 1967 0.043183 TGCCCTCTCCTCCTCATGAA 59.957 55.000 0.00 0.00 0.00 2.57
1571 2012 0.986527 TGCTGAATCCTCCTCTTGCA 59.013 50.000 0.00 0.00 0.00 4.08
1587 2030 2.957402 TTCCCTTCTTGTCATGTGCT 57.043 45.000 0.00 0.00 0.00 4.40
1605 2048 0.741221 GAGTCGAGCGAGGCCATTTT 60.741 55.000 5.01 0.00 0.00 1.82
1676 2119 4.342772 GCGACACATTCATGACAAATACC 58.657 43.478 0.00 0.00 0.00 2.73
1698 2214 6.535150 ACATATCACATAACCTCACAAGTTCG 59.465 38.462 0.00 0.00 0.00 3.95
1744 2260 3.936453 ACAACTTCGCAAACACAAGTAGA 59.064 39.130 0.00 0.00 30.00 2.59
1815 2356 5.799936 ACTTCACAACAATTTGAACGAACAG 59.200 36.000 2.79 0.00 36.48 3.16
1820 2361 6.307800 ACTTGAACTTCACAACAATTTGAACG 59.692 34.615 2.79 0.00 36.48 3.95
1867 2408 6.552859 TTGAGAGCAATTTCAAATCACGTA 57.447 33.333 0.00 0.00 30.84 3.57
1869 2410 6.752335 TTTTGAGAGCAATTTCAAATCACG 57.248 33.333 4.34 0.00 41.42 4.35
1874 2415 7.596248 GTGAGCTATTTTGAGAGCAATTTCAAA 59.404 33.333 0.00 0.00 41.36 2.69
1886 2427 4.083855 TGCAGAAACGTGAGCTATTTTGAG 60.084 41.667 0.00 0.00 0.00 3.02
1893 2447 2.526304 AACTGCAGAAACGTGAGCTA 57.474 45.000 23.35 0.00 0.00 3.32
1945 2499 4.693283 TGTACAATATAGTGCAGTGCCTC 58.307 43.478 13.72 5.96 30.52 4.70
1950 2504 3.869246 GGCGTTGTACAATATAGTGCAGT 59.131 43.478 12.26 0.00 35.57 4.40
1961 2515 1.529226 CCTGATTGGGCGTTGTACAA 58.471 50.000 3.59 3.59 0.00 2.41
1990 2547 0.250295 ACACAGGCGTTGCACTACAT 60.250 50.000 0.00 0.00 0.00 2.29
1992 2549 1.566018 GGACACAGGCGTTGCACTAC 61.566 60.000 0.00 0.00 0.00 2.73
2046 2634 2.712057 AACTTTGCAGCAGGATTTCG 57.288 45.000 0.00 0.00 0.00 3.46
2052 2641 0.385390 AACCGAAACTTTGCAGCAGG 59.615 50.000 0.00 0.00 0.00 4.85
2064 2653 1.066143 GGATCCAGAGAGCAACCGAAA 60.066 52.381 6.95 0.00 0.00 3.46
2068 2657 1.522580 GCGGATCCAGAGAGCAACC 60.523 63.158 13.41 0.00 0.00 3.77
2085 2674 1.432251 GTGCTGCACATCTGGATGC 59.568 57.895 26.70 0.00 42.39 3.91
2106 2697 4.581824 AGTATAGTGCAATGCCCATTTCTG 59.418 41.667 1.53 0.00 0.00 3.02
2110 2701 3.633525 CACAGTATAGTGCAATGCCCATT 59.366 43.478 7.51 0.00 32.04 3.16
2148 2739 1.964223 ACACTATACTATGCAGCGCCT 59.036 47.619 2.29 0.00 0.00 5.52
2175 2766 2.900546 AGTTAACAGCAGTGTAGCCTCT 59.099 45.455 8.61 0.00 35.08 3.69
2217 2816 7.267128 TGAATTGAAATTGCTGTCAAAAGAGT 58.733 30.769 0.00 0.00 37.31 3.24


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

AutoCloner maintained by Alex Coulton.