Multiple sequence alignment - TraesCS5A01G278600

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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 TraesCS5A01G278600 chr5A 100.000 2267 0 0 1 2267 487985907 487983641 0.000000e+00 4187.0
1 TraesCS5A01G278600 chr5A 81.581 1569 129 78 781 2265 488009080 488007588 0.000000e+00 1149.0
2 TraesCS5A01G278600 chr5A 88.772 570 47 7 781 1349 487949178 487948625 0.000000e+00 682.0
3 TraesCS5A01G278600 chr5A 87.973 582 44 13 781 1343 487918875 487918301 0.000000e+00 664.0
4 TraesCS5A01G278600 chr5A 87.984 516 41 10 868 1377 487940963 487940463 6.970000e-165 590.0
5 TraesCS5A01G278600 chr5A 83.422 567 58 19 1697 2230 487940265 487939702 5.630000e-136 494.0
6 TraesCS5A01G278600 chr5A 84.314 459 49 14 1794 2235 487918171 487917719 5.790000e-116 427.0
7 TraesCS5A01G278600 chr5A 89.610 308 19 3 388 693 487943352 487943056 1.640000e-101 379.0
8 TraesCS5A01G278600 chr5A 87.879 330 29 5 373 693 488016585 488016912 5.910000e-101 377.0
9 TraesCS5A01G278600 chr5A 92.000 225 15 2 373 596 487926691 487926469 1.690000e-81 313.0
10 TraesCS5A01G278600 chr5A 90.385 156 12 2 541 693 487919348 487919193 3.820000e-48 202.0
11 TraesCS5A01G278600 chr5A 97.368 38 0 1 781 817 487925118 487925081 1.880000e-06 63.9
12 TraesCS5A01G278600 chr5D 86.934 1569 103 33 781 2267 386058317 386056769 0.000000e+00 1668.0
13 TraesCS5A01G278600 chr5D 93.258 534 36 0 781 1314 386046292 386045759 0.000000e+00 787.0
14 TraesCS5A01G278600 chr5D 85.946 740 59 25 781 1498 386067601 386066885 0.000000e+00 749.0
15 TraesCS5A01G278600 chr5D 87.697 634 43 10 781 1405 386036064 386035457 0.000000e+00 706.0
16 TraesCS5A01G278600 chr5D 87.544 562 37 17 868 1405 385978682 385978130 8.900000e-174 619.0
17 TraesCS5A01G278600 chr5D 86.531 542 43 9 1749 2265 386066656 386066120 9.090000e-159 569.0
18 TraesCS5A01G278600 chr5D 92.073 328 15 3 373 700 386061026 386060710 3.430000e-123 451.0
19 TraesCS5A01G278600 chr5D 89.571 326 27 4 373 693 386100366 386100689 7.540000e-110 407.0
20 TraesCS5A01G278600 chr5D 88.150 346 19 6 432 758 386046624 386046282 2.110000e-105 392.0
21 TraesCS5A01G278600 chr5D 87.387 333 25 8 376 693 386036724 386036394 1.280000e-97 366.0
22 TraesCS5A01G278600 chr5D 84.341 364 30 10 1926 2267 386035241 386034883 4.670000e-87 331.0
23 TraesCS5A01G278600 chr5B 82.589 1522 127 64 781 2229 463945299 463943843 0.000000e+00 1216.0
24 TraesCS5A01G278600 chr5B 92.362 563 36 3 781 1343 463937932 463937377 0.000000e+00 795.0
25 TraesCS5A01G278600 chr5B 92.769 484 25 3 868 1349 463912520 463912045 0.000000e+00 691.0
26 TraesCS5A01G278600 chr5B 85.831 614 58 14 781 1367 463918922 463918311 1.910000e-175 625.0
27 TraesCS5A01G278600 chr5B 92.308 403 11 6 373 758 463938321 463937922 2.540000e-154 555.0
28 TraesCS5A01G278600 chr5B 85.214 514 49 10 1777 2267 463918231 463917722 9.350000e-139 503.0
29 TraesCS5A01G278600 chr5B 85.106 470 49 8 1817 2267 463937375 463936908 5.710000e-126 460.0
30 TraesCS5A01G278600 chr5B 88.073 327 30 5 373 693 463969947 463970270 1.640000e-101 379.0
31 TraesCS5A01G278600 chr5B 95.000 40 2 0 712 751 463918952 463918913 1.880000e-06 63.9
32 TraesCS5A01G278600 chr2A 97.043 372 10 1 3 373 82049343 82049714 1.910000e-175 625.0
33 TraesCS5A01G278600 chr6A 96.791 374 11 1 1 373 94308335 94308708 6.880000e-175 623.0
34 TraesCS5A01G278600 chr7A 94.638 373 19 1 1 372 697093399 697093771 5.430000e-161 577.0
35 TraesCS5A01G278600 chr3A 93.103 377 18 8 1 373 660755897 660756269 1.530000e-151 545.0
36 TraesCS5A01G278600 chr3A 92.225 373 28 1 1 372 702075617 702075989 5.550000e-146 527.0
37 TraesCS5A01G278600 chr3A 91.979 374 27 3 1 372 701704634 701705006 2.580000e-144 521.0
38 TraesCS5A01G278600 chr3A 91.711 374 28 3 1 372 41140394 41140766 1.200000e-142 516.0
39 TraesCS5A01G278600 chr3A 91.689 373 29 2 1 372 92889496 92889867 1.200000e-142 516.0
40 TraesCS5A01G278600 chrUn 92.513 374 27 1 1 373 65047235 65047608 3.310000e-148 534.0


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 TraesCS5A01G278600 chr5A 487983641 487985907 2266 True 4187.000000 4187 100.000000 1 2267 1 chr5A.!!$R2 2266
1 TraesCS5A01G278600 chr5A 488007588 488009080 1492 True 1149.000000 1149 81.581000 781 2265 1 chr5A.!!$R3 1484
2 TraesCS5A01G278600 chr5A 487948625 487949178 553 True 682.000000 682 88.772000 781 1349 1 chr5A.!!$R1 568
3 TraesCS5A01G278600 chr5A 487939702 487943352 3650 True 487.666667 590 87.005333 388 2230 3 chr5A.!!$R6 1842
4 TraesCS5A01G278600 chr5A 487917719 487919348 1629 True 431.000000 664 87.557333 541 2235 3 chr5A.!!$R4 1694
5 TraesCS5A01G278600 chr5D 386056769 386061026 4257 True 1059.500000 1668 89.503500 373 2267 2 chr5D.!!$R4 1894
6 TraesCS5A01G278600 chr5D 386066120 386067601 1481 True 659.000000 749 86.238500 781 2265 2 chr5D.!!$R5 1484
7 TraesCS5A01G278600 chr5D 385978130 385978682 552 True 619.000000 619 87.544000 868 1405 1 chr5D.!!$R1 537
8 TraesCS5A01G278600 chr5D 386045759 386046624 865 True 589.500000 787 90.704000 432 1314 2 chr5D.!!$R3 882
9 TraesCS5A01G278600 chr5D 386034883 386036724 1841 True 467.666667 706 86.475000 376 2267 3 chr5D.!!$R2 1891
10 TraesCS5A01G278600 chr5B 463943843 463945299 1456 True 1216.000000 1216 82.589000 781 2229 1 chr5B.!!$R2 1448
11 TraesCS5A01G278600 chr5B 463936908 463938321 1413 True 603.333333 795 89.925333 373 2267 3 chr5B.!!$R4 1894
12 TraesCS5A01G278600 chr5B 463917722 463918952 1230 True 397.300000 625 88.681667 712 2267 3 chr5B.!!$R3 1555

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
144 145 0.249868 CAGTCGTTGGGCAGACTTGA 60.25 55.0 0.0 0.0 44.46 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1459 5987 0.178967 TGCATCTGGGGCAGAAACAA 60.179 50.0 0.0 0.0 44.04 2.83 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
17 18 3.956377 ATAGCCCTGGTCCACGAG 58.044 61.111 0.00 0.00 0.00 4.18
18 19 2.435693 ATAGCCCTGGTCCACGAGC 61.436 63.158 0.00 0.00 0.00 5.03
19 20 3.897681 TAGCCCTGGTCCACGAGCA 62.898 63.158 5.95 0.00 37.74 4.26
58 59 3.896133 GCCTATGCCGACGGTCGA 61.896 66.667 30.33 13.11 43.74 4.20
59 60 2.331805 CCTATGCCGACGGTCGAG 59.668 66.667 30.33 20.52 43.74 4.04
60 61 2.353607 CTATGCCGACGGTCGAGC 60.354 66.667 30.33 27.94 43.74 5.03
61 62 3.825833 CTATGCCGACGGTCGAGCC 62.826 68.421 30.33 17.92 43.74 4.70
79 80 2.520686 CCGTCGGCATAGTTTTTGAC 57.479 50.000 0.00 0.00 0.00 3.18
80 81 2.073816 CCGTCGGCATAGTTTTTGACT 58.926 47.619 0.00 0.00 42.55 3.41
81 82 3.255725 CCGTCGGCATAGTTTTTGACTA 58.744 45.455 0.00 0.00 44.62 2.59
82 83 3.680937 CCGTCGGCATAGTTTTTGACTAA 59.319 43.478 0.00 0.00 43.76 2.24
83 84 4.201685 CCGTCGGCATAGTTTTTGACTAAG 60.202 45.833 0.00 0.00 43.76 2.18
87 88 4.939509 GCATAGTTTTTGACTAAGCCGA 57.060 40.909 2.88 0.00 45.34 5.54
88 89 4.648970 GCATAGTTTTTGACTAAGCCGAC 58.351 43.478 2.88 0.00 45.34 4.79
89 90 4.724036 GCATAGTTTTTGACTAAGCCGACG 60.724 45.833 2.88 0.00 45.34 5.12
90 91 2.140717 AGTTTTTGACTAAGCCGACGG 58.859 47.619 10.29 10.29 36.65 4.79
91 92 3.693697 AGTTTTTGACTAAGCCGACGGC 61.694 50.000 31.49 31.49 42.77 5.68
113 114 4.910585 CCGTCGGCATAGGGGTGC 62.911 72.222 0.00 0.00 44.31 5.01
119 120 2.824041 GCATAGGGGTGCCACGTG 60.824 66.667 9.08 9.08 39.18 4.49
120 121 2.124736 CATAGGGGTGCCACGTGG 60.125 66.667 30.66 30.66 38.53 4.94
142 143 1.071471 CCAGTCGTTGGGCAGACTT 59.929 57.895 0.00 0.00 44.46 3.01
143 144 1.230635 CCAGTCGTTGGGCAGACTTG 61.231 60.000 0.00 0.00 44.46 3.16
144 145 0.249868 CAGTCGTTGGGCAGACTTGA 60.250 55.000 0.00 0.00 44.46 3.02
145 146 0.249911 AGTCGTTGGGCAGACTTGAC 60.250 55.000 0.00 0.00 44.46 3.18
146 147 1.300620 TCGTTGGGCAGACTTGACG 60.301 57.895 0.00 0.00 30.88 4.35
147 148 2.317609 CGTTGGGCAGACTTGACGG 61.318 63.158 0.00 0.00 30.88 4.79
148 149 2.281484 TTGGGCAGACTTGACGGC 60.281 61.111 0.00 0.00 30.88 5.68
149 150 4.680237 TGGGCAGACTTGACGGCG 62.680 66.667 4.80 4.80 30.88 6.46
173 174 0.928229 CCGTTAGGCGTGATAGTTGC 59.072 55.000 0.00 0.00 39.32 4.17
177 178 3.395669 GGCGTGATAGTTGCCGAC 58.604 61.111 0.00 0.00 39.30 4.79
178 179 2.514013 GGCGTGATAGTTGCCGACG 61.514 63.158 0.00 0.00 39.30 5.12
179 180 2.514013 GCGTGATAGTTGCCGACGG 61.514 63.158 10.29 10.29 0.00 4.79
204 205 3.087638 CCGTCGGCATAGATGTACG 57.912 57.895 0.00 0.00 33.53 3.67
205 206 0.386858 CCGTCGGCATAGATGTACGG 60.387 60.000 14.44 14.44 40.96 4.02
206 207 1.002250 CGTCGGCATAGATGTACGGC 61.002 60.000 8.24 6.23 33.76 5.68
207 208 0.666577 GTCGGCATAGATGTACGGCC 60.667 60.000 0.00 0.00 41.20 6.13
208 209 1.374252 CGGCATAGATGTACGGCCC 60.374 63.158 0.00 0.00 41.58 5.80
209 210 1.003718 GGCATAGATGTACGGCCCC 60.004 63.158 0.00 0.00 38.70 5.80
210 211 1.003718 GCATAGATGTACGGCCCCC 60.004 63.158 0.00 0.00 0.00 5.40
223 224 3.612681 CCCCCGTCGGCGTATCAT 61.613 66.667 9.28 0.00 36.15 2.45
224 225 2.270257 CCCCCGTCGGCGTATCATA 61.270 63.158 9.28 0.00 36.15 2.15
225 226 1.601419 CCCCCGTCGGCGTATCATAT 61.601 60.000 9.28 0.00 36.15 1.78
226 227 1.097232 CCCCGTCGGCGTATCATATA 58.903 55.000 9.28 0.00 36.15 0.86
227 228 1.679680 CCCCGTCGGCGTATCATATAT 59.320 52.381 9.28 0.00 36.15 0.86
228 229 2.543031 CCCCGTCGGCGTATCATATATG 60.543 54.545 9.28 6.36 36.15 1.78
229 230 2.117137 CCGTCGGCGTATCATATATGC 58.883 52.381 9.28 3.06 36.15 3.14
230 231 2.117137 CGTCGGCGTATCATATATGCC 58.883 52.381 16.81 16.81 44.13 4.40
234 235 2.117137 GGCGTATCATATATGCCGACG 58.883 52.381 20.43 20.43 39.49 5.12
235 236 2.117137 GCGTATCATATATGCCGACGG 58.883 52.381 23.39 10.29 31.85 4.79
305 306 3.204827 GCCGTCGGCGTAGGTCTA 61.205 66.667 22.50 0.00 39.62 2.59
306 307 2.550101 GCCGTCGGCGTAGGTCTAT 61.550 63.158 22.50 0.00 39.62 1.98
307 308 1.573436 CCGTCGGCGTAGGTCTATC 59.427 63.158 9.28 0.00 36.15 2.08
308 309 1.573436 CGTCGGCGTAGGTCTATCC 59.427 63.158 6.85 0.00 0.00 2.59
309 310 1.849976 CGTCGGCGTAGGTCTATCCC 61.850 65.000 6.85 0.00 36.75 3.85
310 311 1.598962 TCGGCGTAGGTCTATCCCG 60.599 63.158 6.85 10.81 36.75 5.14
311 312 1.598962 CGGCGTAGGTCTATCCCGA 60.599 63.158 0.00 0.00 35.19 5.14
312 313 1.849976 CGGCGTAGGTCTATCCCGAC 61.850 65.000 0.00 0.00 35.19 4.79
313 314 1.573436 GCGTAGGTCTATCCCGACG 59.427 63.158 8.25 8.25 44.12 5.12
314 315 1.849976 GCGTAGGTCTATCCCGACGG 61.850 65.000 6.99 6.99 42.61 4.79
315 316 1.233285 CGTAGGTCTATCCCGACGGG 61.233 65.000 27.86 27.86 46.11 5.28
327 328 2.521224 GACGGGACTCGGGCCTAT 60.521 66.667 0.84 0.00 44.45 2.57
328 329 2.838225 ACGGGACTCGGGCCTATG 60.838 66.667 0.84 0.00 44.45 2.23
329 330 4.301027 CGGGACTCGGGCCTATGC 62.301 72.222 0.84 0.00 34.75 3.14
330 331 4.301027 GGGACTCGGGCCTATGCG 62.301 72.222 0.84 0.00 38.85 4.73
331 332 4.301027 GGACTCGGGCCTATGCGG 62.301 72.222 0.84 0.00 38.85 5.69
332 333 3.224324 GACTCGGGCCTATGCGGA 61.224 66.667 0.84 0.00 38.85 5.54
333 334 3.501458 GACTCGGGCCTATGCGGAC 62.501 68.421 0.84 0.00 41.67 4.79
334 335 4.647615 CTCGGGCCTATGCGGACG 62.648 72.222 0.84 0.00 44.30 4.79
340 341 4.609018 CCTATGCGGACGGCCCTG 62.609 72.222 0.00 0.00 42.61 4.45
341 342 4.609018 CTATGCGGACGGCCCTGG 62.609 72.222 0.00 0.00 42.61 4.45
364 365 2.034221 GGCATAGGGGGCGATTCC 59.966 66.667 0.00 0.00 0.00 3.01
365 366 2.358737 GCATAGGGGGCGATTCCG 60.359 66.667 0.00 0.00 39.16 4.30
366 367 2.347490 CATAGGGGGCGATTCCGG 59.653 66.667 0.00 0.00 36.06 5.14
367 368 2.122547 ATAGGGGGCGATTCCGGT 60.123 61.111 0.00 0.00 36.06 5.28
368 369 1.156803 ATAGGGGGCGATTCCGGTA 59.843 57.895 0.00 0.00 36.06 4.02
369 370 0.903454 ATAGGGGGCGATTCCGGTAG 60.903 60.000 0.00 0.00 36.06 3.18
370 371 2.302517 TAGGGGGCGATTCCGGTAGT 62.303 60.000 0.00 0.00 36.06 2.73
371 372 2.108362 GGGGCGATTCCGGTAGTG 59.892 66.667 0.00 0.00 36.06 2.74
386 387 2.597520 GTAGTGAACGGAAGCTCTCAC 58.402 52.381 0.00 0.00 38.77 3.51
427 431 2.044123 GATTGGAATCCAGGCGTTCT 57.956 50.000 0.86 0.00 33.81 3.01
428 432 1.943340 GATTGGAATCCAGGCGTTCTC 59.057 52.381 0.86 0.00 33.81 2.87
429 433 0.984230 TTGGAATCCAGGCGTTCTCT 59.016 50.000 0.86 0.00 33.81 3.10
430 434 1.860641 TGGAATCCAGGCGTTCTCTA 58.139 50.000 0.00 0.00 0.00 2.43
483 501 3.891366 CTCCTTTTCCTCTGCCAAAAAGA 59.109 43.478 8.06 0.00 40.69 2.52
498 516 3.744940 AAAAGAGCATCCCATTCCAGA 57.255 42.857 0.00 0.00 33.66 3.86
499 517 3.967467 AAAGAGCATCCCATTCCAGAT 57.033 42.857 0.00 0.00 33.66 2.90
556 577 4.473520 CACCCGCCACCCTAGCTG 62.474 72.222 0.00 0.00 0.00 4.24
702 3076 0.817654 CCGGATAGAGTGTGCAGACA 59.182 55.000 17.22 0.00 0.00 3.41
744 5112 8.301720 TCATCCAAAAAGTTCAGAATCAGAATG 58.698 33.333 0.00 0.00 37.54 2.67
745 5113 7.587037 TCCAAAAAGTTCAGAATCAGAATGT 57.413 32.000 0.00 0.00 37.40 2.71
748 5116 9.918630 CCAAAAAGTTCAGAATCAGAATGTAAT 57.081 29.630 0.00 0.00 37.40 1.89
772 5140 5.914898 AATTGAGCTGTTTTATGGTACCC 57.085 39.130 10.07 0.00 0.00 3.69
773 5141 4.650972 TTGAGCTGTTTTATGGTACCCT 57.349 40.909 10.07 1.30 0.00 4.34
774 5142 3.950397 TGAGCTGTTTTATGGTACCCTG 58.050 45.455 10.07 0.00 0.00 4.45
775 5143 3.279434 GAGCTGTTTTATGGTACCCTGG 58.721 50.000 10.07 0.00 0.00 4.45
776 5144 2.025321 AGCTGTTTTATGGTACCCTGGG 60.025 50.000 12.28 12.28 0.00 4.45
777 5145 2.948600 GCTGTTTTATGGTACCCTGGGG 60.949 54.545 18.88 7.87 42.03 4.96
839 5211 1.202879 TGGCAATCCCGATACCATTCC 60.203 52.381 0.00 0.00 35.87 3.01
859 5240 4.636435 CAACAAGGCCGTCGGGGT 62.636 66.667 14.38 0.00 38.44 4.95
903 5284 3.225798 GGCACCCAAGCAGCACAA 61.226 61.111 0.00 0.00 35.83 3.33
958 5339 5.811613 TCAAGTGCAAAAACCATCAGAAAAG 59.188 36.000 0.00 0.00 0.00 2.27
961 5342 3.134442 TGCAAAAACCATCAGAAAAGGCT 59.866 39.130 0.00 0.00 0.00 4.58
1233 5669 4.995058 TCCGGCAGGGTCCCCTTT 62.995 66.667 3.51 0.00 45.70 3.11
1268 5710 0.394899 CAGGGGGCTTGGAACTGATC 60.395 60.000 0.00 0.00 0.00 2.92
1293 5737 4.810345 TCAATCAAGGTAACCAAAACCCT 58.190 39.130 0.00 0.00 37.77 4.34
1294 5738 4.586841 TCAATCAAGGTAACCAAAACCCTG 59.413 41.667 0.00 0.00 37.77 4.45
1296 5740 1.000717 CAAGGTAACCAAAACCCTGCG 60.001 52.381 0.00 0.00 37.77 5.18
1343 5799 6.765989 AGTTTATAAGTGTGAAGTGTCAGCAA 59.234 34.615 0.00 0.00 33.27 3.91
1351 5815 2.224137 TGAAGTGTCAGCAAGTCCTCAG 60.224 50.000 0.00 0.00 0.00 3.35
1352 5816 1.418334 AGTGTCAGCAAGTCCTCAGT 58.582 50.000 0.00 0.00 0.00 3.41
1360 5826 4.056740 CAGCAAGTCCTCAGTGCTATATG 58.943 47.826 0.00 0.00 46.66 1.78
1419 5940 4.079253 TGCCCTAGATTGACAAAGAAACC 58.921 43.478 0.00 0.00 0.00 3.27
1441 5965 1.135527 CAATGGAATGCCGCTTGTCAT 59.864 47.619 0.00 0.00 36.79 3.06
1459 5987 3.256631 GTCATTGCTGTCAATTCCTTGGT 59.743 43.478 0.00 0.00 40.74 3.67
1469 5997 3.069443 TCAATTCCTTGGTTGTTTCTGCC 59.931 43.478 0.00 0.00 32.95 4.85
1483 6011 4.746309 TGCCCCAGATGCACTGCC 62.746 66.667 9.88 3.27 44.52 4.85
1487 6015 2.693762 CCCAGATGCACTGCCAACG 61.694 63.158 9.88 0.00 44.52 4.10
1497 6025 2.143122 CACTGCCAACGTTAGTGTGAT 58.857 47.619 17.69 0.00 37.59 3.06
1498 6026 2.096268 CACTGCCAACGTTAGTGTGATG 60.096 50.000 17.69 0.00 37.59 3.07
1499 6027 1.464608 CTGCCAACGTTAGTGTGATGG 59.535 52.381 0.00 0.00 0.00 3.51
1500 6028 1.202710 TGCCAACGTTAGTGTGATGGT 60.203 47.619 0.00 0.00 29.50 3.55
1501 6029 1.196808 GCCAACGTTAGTGTGATGGTG 59.803 52.381 0.00 0.00 29.50 4.17
1502 6030 2.761559 CCAACGTTAGTGTGATGGTGA 58.238 47.619 0.00 0.00 0.00 4.02
1503 6031 3.334691 CCAACGTTAGTGTGATGGTGAT 58.665 45.455 0.00 0.00 0.00 3.06
1504 6032 3.751175 CCAACGTTAGTGTGATGGTGATT 59.249 43.478 0.00 0.00 0.00 2.57
1505 6033 4.142902 CCAACGTTAGTGTGATGGTGATTC 60.143 45.833 0.00 0.00 0.00 2.52
1506 6034 3.596214 ACGTTAGTGTGATGGTGATTCC 58.404 45.455 0.00 0.00 0.00 3.01
1536 6066 7.680442 TGCACTATTATTACACAAGCAAAGA 57.320 32.000 0.00 0.00 0.00 2.52
1572 6102 1.742308 TTAAGCCTGGACCTGGAACT 58.258 50.000 21.06 6.66 0.00 3.01
1675 6235 4.035675 AGTCTGTTTTGCACACTCTTTAGC 59.964 41.667 0.00 0.00 0.00 3.09
1746 6328 7.681939 TTACAGAACATAGAAAATCCACACC 57.318 36.000 0.00 0.00 0.00 4.16
1752 6349 5.393866 ACATAGAAAATCCACACCCTTTGT 58.606 37.500 0.00 0.00 39.97 2.83
1768 6367 3.128242 CCTTTGTCAAGCCTAGCATTCAG 59.872 47.826 0.00 0.00 0.00 3.02
1774 6373 2.409948 AGCCTAGCATTCAGACAACC 57.590 50.000 0.00 0.00 0.00 3.77
1775 6374 1.630369 AGCCTAGCATTCAGACAACCA 59.370 47.619 0.00 0.00 0.00 3.67
1815 6424 5.371526 GGCATGATTCTCCTACTGAAATGA 58.628 41.667 0.00 0.00 0.00 2.57
1853 6467 5.765182 TCCCAGTTCTTGATTTGAGAAGTTC 59.235 40.000 0.00 0.00 35.23 3.01
1854 6468 5.334414 CCCAGTTCTTGATTTGAGAAGTTCG 60.334 44.000 0.00 0.00 35.23 3.95
1857 6471 5.178438 AGTTCTTGATTTGAGAAGTTCGAGC 59.822 40.000 0.00 0.00 34.04 5.03
1860 6474 5.527214 TCTTGATTTGAGAAGTTCGAGCAAA 59.473 36.000 17.62 17.62 33.59 3.68
1899 6514 7.190920 ACCTCTCTCGTTGTATTTTTCTTTG 57.809 36.000 0.00 0.00 0.00 2.77
1924 6579 3.500014 GAGCAAAGCTTCTGAATTCTGC 58.500 45.455 7.05 3.07 39.88 4.26
1984 6641 4.972568 TCCTTAGCTGGGACCATGTTATTA 59.027 41.667 0.00 0.00 0.00 0.98
2140 6807 8.458843 GGTAGCATGTATTTTTCATTGTGTACT 58.541 33.333 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.435693 GCTCGTGGACCAGGGCTAT 61.436 63.158 14.05 0.00 0.00 2.97
1 2 3.075005 GCTCGTGGACCAGGGCTA 61.075 66.667 14.05 0.00 0.00 3.93
3 4 4.767255 CTGCTCGTGGACCAGGGC 62.767 72.222 14.05 15.33 0.00 5.19
4 5 4.767255 GCTGCTCGTGGACCAGGG 62.767 72.222 14.05 6.36 0.00 4.45
41 42 3.825833 CTCGACCGTCGGCATAGGC 62.826 68.421 20.35 0.00 40.88 3.93
42 43 2.331805 CTCGACCGTCGGCATAGG 59.668 66.667 20.35 0.00 40.88 2.57
43 44 2.353607 GCTCGACCGTCGGCATAG 60.354 66.667 20.35 11.42 40.88 2.23
44 45 3.896133 GGCTCGACCGTCGGCATA 61.896 66.667 25.50 7.94 40.88 3.14
58 59 5.979451 AGTCAAAAACTATGCCGACGGCT 62.979 47.826 36.54 24.49 42.72 5.52
59 60 3.757925 AGTCAAAAACTATGCCGACGGC 61.758 50.000 31.85 31.85 42.64 5.68
60 61 2.073816 AGTCAAAAACTATGCCGACGG 58.926 47.619 10.29 10.29 36.07 4.79
61 62 4.882447 CTTAGTCAAAAACTATGCCGACG 58.118 43.478 0.00 0.00 40.18 5.12
67 68 4.201685 CCGTCGGCTTAGTCAAAAACTATG 60.202 45.833 0.00 0.00 40.18 2.23
68 69 3.930848 CCGTCGGCTTAGTCAAAAACTAT 59.069 43.478 0.00 0.00 40.18 2.12
69 70 3.319755 CCGTCGGCTTAGTCAAAAACTA 58.680 45.455 0.00 0.00 39.55 2.24
70 71 2.140717 CCGTCGGCTTAGTCAAAAACT 58.859 47.619 0.00 0.00 42.33 2.66
71 72 1.399343 GCCGTCGGCTTAGTCAAAAAC 60.399 52.381 28.98 0.00 46.69 2.43
72 73 0.869730 GCCGTCGGCTTAGTCAAAAA 59.130 50.000 28.98 0.00 46.69 1.94
73 74 2.535588 GCCGTCGGCTTAGTCAAAA 58.464 52.632 28.98 0.00 46.69 2.44
74 75 4.272100 GCCGTCGGCTTAGTCAAA 57.728 55.556 28.98 0.00 46.69 2.69
96 97 4.910585 GCACCCCTATGCCGACGG 62.911 72.222 10.29 10.29 39.86 4.79
102 103 2.824041 CACGTGGCACCCCTATGC 60.824 66.667 12.86 0.00 45.34 3.14
103 104 2.124736 CCACGTGGCACCCCTATG 60.125 66.667 24.02 0.00 0.00 2.23
122 123 1.668151 GTCTGCCCAACGACTGGTC 60.668 63.158 7.39 0.00 44.76 4.02
123 124 1.696097 AAGTCTGCCCAACGACTGGT 61.696 55.000 7.39 0.00 44.76 4.00
124 125 1.071471 AAGTCTGCCCAACGACTGG 59.929 57.895 0.00 0.00 45.97 4.00
125 126 0.249868 TCAAGTCTGCCCAACGACTG 60.250 55.000 0.00 0.00 40.18 3.51
126 127 0.249911 GTCAAGTCTGCCCAACGACT 60.250 55.000 0.00 0.00 41.97 4.18
127 128 1.557443 CGTCAAGTCTGCCCAACGAC 61.557 60.000 0.00 0.00 32.17 4.34
128 129 1.300620 CGTCAAGTCTGCCCAACGA 60.301 57.895 0.00 0.00 32.17 3.85
129 130 2.317609 CCGTCAAGTCTGCCCAACG 61.318 63.158 0.00 0.00 0.00 4.10
130 131 2.617274 GCCGTCAAGTCTGCCCAAC 61.617 63.158 0.00 0.00 0.00 3.77
131 132 2.281484 GCCGTCAAGTCTGCCCAA 60.281 61.111 0.00 0.00 0.00 4.12
132 133 4.680237 CGCCGTCAAGTCTGCCCA 62.680 66.667 0.00 0.00 0.00 5.36
156 157 0.928229 CGGCAACTATCACGCCTAAC 59.072 55.000 0.00 0.00 43.95 2.34
157 158 0.818938 TCGGCAACTATCACGCCTAA 59.181 50.000 0.00 0.00 43.95 2.69
158 159 0.101759 GTCGGCAACTATCACGCCTA 59.898 55.000 0.00 0.00 43.95 3.93
159 160 1.153628 GTCGGCAACTATCACGCCT 60.154 57.895 0.00 0.00 43.95 5.52
160 161 2.514013 CGTCGGCAACTATCACGCC 61.514 63.158 0.00 0.00 42.64 5.68
161 162 2.514013 CCGTCGGCAACTATCACGC 61.514 63.158 0.00 0.00 0.00 5.34
162 163 3.688136 CCGTCGGCAACTATCACG 58.312 61.111 0.00 0.00 0.00 4.35
186 187 0.386858 CCGTACATCTATGCCGACGG 60.387 60.000 10.29 10.29 41.85 4.79
187 188 1.002250 GCCGTACATCTATGCCGACG 61.002 60.000 0.00 5.36 33.90 5.12
188 189 0.666577 GGCCGTACATCTATGCCGAC 60.667 60.000 0.00 0.00 31.55 4.79
189 190 1.663739 GGCCGTACATCTATGCCGA 59.336 57.895 0.00 0.00 31.55 5.54
190 191 1.374252 GGGCCGTACATCTATGCCG 60.374 63.158 0.00 0.00 43.09 5.69
191 192 1.003718 GGGGCCGTACATCTATGCC 60.004 63.158 0.00 0.00 41.42 4.40
192 193 1.003718 GGGGGCCGTACATCTATGC 60.004 63.158 0.00 0.00 0.00 3.14
193 194 1.292223 CGGGGGCCGTACATCTATG 59.708 63.158 0.00 0.00 42.73 2.23
194 195 3.787394 CGGGGGCCGTACATCTAT 58.213 61.111 0.00 0.00 42.73 1.98
207 208 1.097232 TATATGATACGCCGACGGGG 58.903 55.000 27.56 27.56 46.04 5.73
208 209 2.727777 CATATATGATACGCCGACGGG 58.272 52.381 17.22 8.43 46.04 5.28
209 210 2.117137 GCATATATGATACGCCGACGG 58.883 52.381 17.10 10.29 46.04 4.79
214 215 2.117137 CGTCGGCATATATGATACGCC 58.883 52.381 17.10 8.78 39.45 5.68
215 216 2.117137 CCGTCGGCATATATGATACGC 58.883 52.381 17.10 11.26 31.72 4.42
288 289 2.455183 GATAGACCTACGCCGACGGC 62.455 65.000 29.10 29.10 46.75 5.68
289 290 1.573436 GATAGACCTACGCCGACGG 59.427 63.158 10.29 10.29 46.04 4.79
290 291 1.573436 GGATAGACCTACGCCGACG 59.427 63.158 0.00 0.00 39.61 5.12
291 292 1.849976 CGGGATAGACCTACGCCGAC 61.850 65.000 0.00 0.00 38.98 4.79
292 293 1.598962 CGGGATAGACCTACGCCGA 60.599 63.158 0.00 0.00 38.98 5.54
293 294 1.598962 TCGGGATAGACCTACGCCG 60.599 63.158 0.00 0.00 38.98 6.46
294 295 1.849976 CGTCGGGATAGACCTACGCC 61.850 65.000 0.00 0.00 39.53 5.68
295 296 1.573436 CGTCGGGATAGACCTACGC 59.427 63.158 0.00 0.00 39.53 4.42
296 297 2.242113 CCGTCGGGATAGACCTACG 58.758 63.158 2.34 2.75 42.78 3.51
310 311 2.521224 ATAGGCCCGAGTCCCGTC 60.521 66.667 0.00 0.00 36.31 4.79
311 312 2.838225 CATAGGCCCGAGTCCCGT 60.838 66.667 0.00 0.00 36.31 5.28
312 313 4.301027 GCATAGGCCCGAGTCCCG 62.301 72.222 0.00 0.00 38.18 5.14
313 314 4.301027 CGCATAGGCCCGAGTCCC 62.301 72.222 0.00 0.00 36.38 4.46
314 315 4.301027 CCGCATAGGCCCGAGTCC 62.301 72.222 0.00 0.00 36.38 3.85
315 316 3.224324 TCCGCATAGGCCCGAGTC 61.224 66.667 0.00 0.00 40.77 3.36
316 317 3.537874 GTCCGCATAGGCCCGAGT 61.538 66.667 0.00 0.00 40.77 4.18
317 318 4.647615 CGTCCGCATAGGCCCGAG 62.648 72.222 0.00 0.00 40.77 4.63
323 324 4.609018 CAGGGCCGTCCGCATAGG 62.609 72.222 0.00 0.00 41.52 2.57
324 325 4.609018 CCAGGGCCGTCCGCATAG 62.609 72.222 0.00 0.00 41.52 2.23
344 345 3.178540 AATCGCCCCCTATGCCGAC 62.179 63.158 0.00 0.00 32.07 4.79
345 346 2.847234 AATCGCCCCCTATGCCGA 60.847 61.111 0.00 0.00 0.00 5.54
346 347 2.358737 GAATCGCCCCCTATGCCG 60.359 66.667 0.00 0.00 0.00 5.69
347 348 2.034221 GGAATCGCCCCCTATGCC 59.966 66.667 0.00 0.00 0.00 4.40
348 349 2.358737 CGGAATCGCCCCCTATGC 60.359 66.667 0.00 0.00 0.00 3.14
349 350 1.189524 TACCGGAATCGCCCCCTATG 61.190 60.000 9.46 0.00 34.56 2.23
350 351 0.903454 CTACCGGAATCGCCCCCTAT 60.903 60.000 9.46 0.00 34.56 2.57
351 352 1.532316 CTACCGGAATCGCCCCCTA 60.532 63.158 9.46 0.00 34.56 3.53
352 353 2.842936 CTACCGGAATCGCCCCCT 60.843 66.667 9.46 0.00 34.56 4.79
353 354 3.159347 ACTACCGGAATCGCCCCC 61.159 66.667 9.46 0.00 34.56 5.40
354 355 1.963464 TTCACTACCGGAATCGCCCC 61.963 60.000 9.46 0.00 34.56 5.80
355 356 0.808847 GTTCACTACCGGAATCGCCC 60.809 60.000 9.46 0.00 34.56 6.13
356 357 1.143969 CGTTCACTACCGGAATCGCC 61.144 60.000 9.46 0.00 34.56 5.54
357 358 2.285154 CGTTCACTACCGGAATCGC 58.715 57.895 9.46 0.00 34.56 4.58
363 364 0.458025 GAGCTTCCGTTCACTACCGG 60.458 60.000 0.00 0.00 45.55 5.28
364 365 0.526662 AGAGCTTCCGTTCACTACCG 59.473 55.000 0.00 0.00 0.00 4.02
365 366 1.544691 TGAGAGCTTCCGTTCACTACC 59.455 52.381 0.00 0.00 0.00 3.18
366 367 2.030185 TGTGAGAGCTTCCGTTCACTAC 60.030 50.000 13.55 0.00 40.36 2.73
367 368 2.235891 TGTGAGAGCTTCCGTTCACTA 58.764 47.619 13.55 3.17 40.36 2.74
368 369 1.040646 TGTGAGAGCTTCCGTTCACT 58.959 50.000 13.55 0.00 40.36 3.41
369 370 2.086054 ATGTGAGAGCTTCCGTTCAC 57.914 50.000 0.00 0.00 40.17 3.18
370 371 2.612972 GGAATGTGAGAGCTTCCGTTCA 60.613 50.000 0.00 0.00 29.96 3.18
371 372 2.003301 GGAATGTGAGAGCTTCCGTTC 58.997 52.381 0.00 0.45 29.96 3.95
379 380 1.028868 GGTGCCTGGAATGTGAGAGC 61.029 60.000 0.00 0.00 0.00 4.09
386 387 0.037975 GCAAGTTGGTGCCTGGAATG 60.038 55.000 4.75 0.00 38.66 2.67
422 426 3.182967 GGCTGAAGTGATGTAGAGAACG 58.817 50.000 0.00 0.00 0.00 3.95
423 427 4.180057 CTGGCTGAAGTGATGTAGAGAAC 58.820 47.826 0.00 0.00 0.00 3.01
424 428 3.196469 CCTGGCTGAAGTGATGTAGAGAA 59.804 47.826 0.00 0.00 0.00 2.87
425 429 2.762887 CCTGGCTGAAGTGATGTAGAGA 59.237 50.000 0.00 0.00 0.00 3.10
426 430 2.762887 TCCTGGCTGAAGTGATGTAGAG 59.237 50.000 0.00 0.00 0.00 2.43
427 431 2.820178 TCCTGGCTGAAGTGATGTAGA 58.180 47.619 0.00 0.00 0.00 2.59
428 432 3.834489 ATCCTGGCTGAAGTGATGTAG 57.166 47.619 0.00 0.00 0.00 2.74
429 433 3.519107 TGAATCCTGGCTGAAGTGATGTA 59.481 43.478 0.00 0.00 0.00 2.29
430 434 2.306805 TGAATCCTGGCTGAAGTGATGT 59.693 45.455 0.00 0.00 0.00 3.06
483 501 3.813240 GCACATATCTGGAATGGGATGCT 60.813 47.826 0.00 0.00 28.60 3.79
556 577 2.911552 ACTAGCTAGGGAGATAGGGC 57.088 55.000 24.35 0.00 44.52 5.19
702 3076 2.703007 GGATGAAGGAGCTGGTGACTAT 59.297 50.000 0.00 0.00 0.00 2.12
770 5138 5.074746 AGGCTAATTAATTTACCCCAGGG 57.925 43.478 5.91 0.00 42.03 4.45
771 5139 5.535030 GTGAGGCTAATTAATTTACCCCAGG 59.465 44.000 5.91 0.00 0.00 4.45
772 5140 6.263168 CAGTGAGGCTAATTAATTTACCCCAG 59.737 42.308 5.91 0.00 0.00 4.45
773 5141 6.069323 TCAGTGAGGCTAATTAATTTACCCCA 60.069 38.462 5.91 2.91 0.00 4.96
774 5142 6.262496 GTCAGTGAGGCTAATTAATTTACCCC 59.738 42.308 5.91 0.25 0.00 4.95
775 5143 6.262496 GGTCAGTGAGGCTAATTAATTTACCC 59.738 42.308 5.91 4.89 0.00 3.69
776 5144 7.054751 AGGTCAGTGAGGCTAATTAATTTACC 58.945 38.462 5.91 8.37 0.00 2.85
777 5145 8.507524 AAGGTCAGTGAGGCTAATTAATTTAC 57.492 34.615 5.91 0.00 0.00 2.01
778 5146 9.174166 GAAAGGTCAGTGAGGCTAATTAATTTA 57.826 33.333 5.91 0.00 0.00 1.40
779 5147 7.669722 TGAAAGGTCAGTGAGGCTAATTAATTT 59.330 33.333 5.91 0.00 0.00 1.82
780 5148 7.175104 TGAAAGGTCAGTGAGGCTAATTAATT 58.825 34.615 5.89 5.89 0.00 1.40
781 5149 6.721318 TGAAAGGTCAGTGAGGCTAATTAAT 58.279 36.000 0.00 0.00 0.00 1.40
782 5150 6.121776 TGAAAGGTCAGTGAGGCTAATTAA 57.878 37.500 0.00 0.00 0.00 1.40
783 5151 5.734720 CTGAAAGGTCAGTGAGGCTAATTA 58.265 41.667 0.00 0.00 45.44 1.40
784 5152 4.583871 CTGAAAGGTCAGTGAGGCTAATT 58.416 43.478 0.00 0.00 45.44 1.40
839 5211 3.726517 CCGACGGCCTTGTTGCTG 61.727 66.667 0.00 0.00 43.44 4.41
892 5273 1.465777 TGATGATCGTTGTGCTGCTTG 59.534 47.619 0.00 0.00 0.00 4.01
903 5284 3.945285 GGTGGTTATGGTTTGATGATCGT 59.055 43.478 0.00 0.00 0.00 3.73
958 5339 1.132640 CTACGTTTGCGCTGAAGCC 59.867 57.895 9.73 0.00 42.83 4.35
961 5342 1.614227 CGAGCTACGTTTGCGCTGAA 61.614 55.000 9.73 0.00 42.83 3.02
1083 5519 2.024305 CCGTAGTAGGCGAGTGCG 59.976 66.667 5.99 5.99 44.10 5.34
1230 5666 2.884639 CTGGGTGTTGTACTTGGGAAAG 59.115 50.000 0.00 0.00 0.00 2.62
1233 5669 0.768622 CCTGGGTGTTGTACTTGGGA 59.231 55.000 0.00 0.00 0.00 4.37
1268 5710 5.478407 GGTTTTGGTTACCTTGATTGATGG 58.522 41.667 2.07 0.00 32.75 3.51
1293 5737 1.344438 ACAAGAGACAAGGATCACGCA 59.656 47.619 0.00 0.00 0.00 5.24
1294 5738 1.996191 GACAAGAGACAAGGATCACGC 59.004 52.381 0.00 0.00 0.00 5.34
1296 5740 5.047660 ACTGTAGACAAGAGACAAGGATCAC 60.048 44.000 0.00 0.00 0.00 3.06
1343 5799 3.916035 TCACCATATAGCACTGAGGACT 58.084 45.455 0.00 0.00 0.00 3.85
1381 5885 4.881157 AGGGCATGGTCTACCTTTATTT 57.119 40.909 0.02 0.00 36.82 1.40
1419 5940 1.874915 CAAGCGGCATTCCATTGCG 60.875 57.895 1.45 0.00 43.71 4.85
1441 5965 3.030291 ACAACCAAGGAATTGACAGCAA 58.970 40.909 0.00 0.00 38.60 3.91
1459 5987 0.178967 TGCATCTGGGGCAGAAACAA 60.179 50.000 0.00 0.00 44.04 2.83
1469 5997 2.693762 CGTTGGCAGTGCATCTGGG 61.694 63.158 18.61 0.00 43.78 4.45
1483 6011 4.142902 GGAATCACCATCACACTAACGTTG 60.143 45.833 11.99 3.57 38.79 4.10
1487 6015 3.370978 CACGGAATCACCATCACACTAAC 59.629 47.826 0.00 0.00 38.90 2.34
1497 6025 1.164411 GTGCAATCACGGAATCACCA 58.836 50.000 0.00 0.00 38.90 4.17
1498 6026 3.996825 GTGCAATCACGGAATCACC 57.003 52.632 0.00 0.00 32.98 4.02
1536 6066 3.821033 GCTTAAATTATGTGCCGGATCCT 59.179 43.478 5.05 0.00 0.00 3.24
1572 6102 1.666599 GCGTGCATGATGCTGTTCAAA 60.667 47.619 19.19 0.00 45.31 2.69
1738 6320 1.620822 GCTTGACAAAGGGTGTGGAT 58.379 50.000 0.00 0.00 41.96 3.41
1746 6328 3.084039 TGAATGCTAGGCTTGACAAAGG 58.916 45.455 0.00 0.00 33.68 3.11
1752 6349 3.338249 GTTGTCTGAATGCTAGGCTTGA 58.662 45.455 0.00 0.00 0.00 3.02
1768 6367 5.163416 CCCCATTTCTTTGGATATGGTTGTC 60.163 44.000 12.11 0.00 44.29 3.18
1774 6373 3.307506 TGCCCCCATTTCTTTGGATATG 58.692 45.455 0.00 0.00 39.25 1.78
1775 6374 3.704545 TGCCCCCATTTCTTTGGATAT 57.295 42.857 0.00 0.00 39.25 1.63
1839 6451 5.947228 ATTTGCTCGAACTTCTCAAATCA 57.053 34.783 0.00 0.00 33.58 2.57
1853 6467 6.370718 AGGTACCTTGTAAGTTAATTTGCTCG 59.629 38.462 9.21 0.00 0.00 5.03
1854 6468 7.606839 AGAGGTACCTTGTAAGTTAATTTGCTC 59.393 37.037 17.53 0.00 0.00 4.26
1857 6471 9.152595 GAGAGAGGTACCTTGTAAGTTAATTTG 57.847 37.037 17.53 0.00 0.00 2.32
1860 6474 6.662663 ACGAGAGAGGTACCTTGTAAGTTAAT 59.337 38.462 17.53 0.00 0.00 1.40
1899 6514 1.242076 TTCAGAAGCTTTGCTCCTGC 58.758 50.000 0.00 0.00 40.83 4.85
1960 6617 1.207791 ACATGGTCCCAGCTAAGGAG 58.792 55.000 4.90 0.00 32.84 3.69
1984 6641 6.693315 ACGGTACATAATTATGCTTGCTTT 57.307 33.333 22.66 6.55 37.19 3.51
2140 6807 5.533154 CACTGATGTTTACCCCAAAACTACA 59.467 40.000 1.67 0.00 39.57 2.74
2193 6880 7.944729 ATTCTACCAGCACAAGTTCATAAAT 57.055 32.000 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.