Multiple sequence alignment - TraesCS3A01G530800

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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 TraesCS3A01G530800 chr3A 100.000 2780 0 0 1 2780 743987064 743989843 0.000000e+00 5134
1 TraesCS3A01G530800 chr3A 86.154 650 31 34 967 1592 744266446 744267060 0.000000e+00 647
2 TraesCS3A01G530800 chr3A 79.657 934 137 36 1866 2754 475469710 475468785 8.460000e-175 623
3 TraesCS3A01G530800 chr3A 85.088 570 56 16 2207 2754 714623779 714623217 3.130000e-154 555
4 TraesCS3A01G530800 chr3A 82.734 695 48 46 961 1614 744286715 744287378 1.130000e-153 553
5 TraesCS3A01G530800 chr3A 79.586 725 71 53 820 1510 744262039 744262720 5.460000e-122 448
6 TraesCS3A01G530800 chr3A 83.379 367 53 8 1866 2230 652219929 652219569 1.600000e-87 333
7 TraesCS3A01G530800 chr3B 90.784 1454 81 28 446 1870 821835935 821837364 0.000000e+00 1893
8 TraesCS3A01G530800 chr3B 82.254 834 48 54 821 1596 822038936 822039727 1.820000e-176 628
9 TraesCS3A01G530800 chr3B 82.134 834 49 53 821 1596 822067026 822067817 8.460000e-175 623
10 TraesCS3A01G530800 chr3B 80.729 851 63 60 820 1614 822094411 822095216 1.120000e-158 569
11 TraesCS3A01G530800 chr3B 90.698 301 22 3 1 298 821835445 821835742 2.010000e-106 396
12 TraesCS3A01G530800 chr3B 88.321 137 15 1 316 451 786144025 786143889 2.220000e-36 163
13 TraesCS3A01G530800 chr3D 86.594 1380 84 40 539 1858 610138469 610139807 0.000000e+00 1430
14 TraesCS3A01G530800 chr3D 88.151 903 84 14 1865 2749 330209483 330210380 0.000000e+00 1053
15 TraesCS3A01G530800 chr3D 85.675 719 81 16 1866 2566 542952716 542952002 0.000000e+00 737
16 TraesCS3A01G530800 chr3D 79.393 922 122 37 1876 2754 576786982 576787878 3.080000e-164 588
17 TraesCS3A01G530800 chr3D 80.779 822 52 58 828 1589 610186662 610187437 1.880000e-151 545
18 TraesCS3A01G530800 chr3D 79.310 870 84 63 807 1614 610190074 610190909 3.170000e-144 521
19 TraesCS3A01G530800 chr3D 93.220 118 7 1 332 448 337959625 337959508 3.680000e-39 172
20 TraesCS3A01G530800 chr3D 91.870 123 8 2 327 447 607000532 607000654 1.320000e-38 171
21 TraesCS3A01G530800 chr3D 88.489 139 14 2 331 468 504224478 504224341 1.710000e-37 167
22 TraesCS3A01G530800 chr3D 86.957 115 14 1 221 334 610138277 610138391 8.080000e-26 128
23 TraesCS3A01G530800 chr4D 85.371 916 107 21 1859 2754 456263617 456264525 0.000000e+00 924
24 TraesCS3A01G530800 chr7B 85.525 905 104 20 1866 2754 491974065 491974958 0.000000e+00 920
25 TraesCS3A01G530800 chr6A 84.885 913 105 22 1866 2754 584006016 584005113 0.000000e+00 891
26 TraesCS3A01G530800 chr6A 73.947 641 110 35 1859 2461 597036104 597035483 3.630000e-49 206
27 TraesCS3A01G530800 chr6D 83.529 935 92 38 1859 2754 27410966 27410055 0.000000e+00 817
28 TraesCS3A01G530800 chr6D 94.068 118 6 1 331 447 348647455 348647338 7.910000e-41 178
29 TraesCS3A01G530800 chr2B 83.989 737 90 17 2037 2754 16222188 16222915 0.000000e+00 682
30 TraesCS3A01G530800 chr1B 80.745 966 104 46 1859 2773 598294299 598295233 0.000000e+00 678
31 TraesCS3A01G530800 chr1B 85.030 167 16 7 1859 2021 42322977 42322816 7.970000e-36 161
32 TraesCS3A01G530800 chr1B 91.579 95 8 0 1851 1945 636034641 636034547 6.250000e-27 132
33 TraesCS3A01G530800 chr2D 84.188 702 98 11 2057 2752 634169662 634170356 0.000000e+00 669
34 TraesCS3A01G530800 chr2D 87.898 157 11 6 1859 2008 607998669 607998514 7.910000e-41 178
35 TraesCS3A01G530800 chr5A 84.977 659 74 16 2115 2753 672753367 672754020 0.000000e+00 645
36 TraesCS3A01G530800 chr2A 78.664 928 147 36 1861 2754 768453244 768454154 1.120000e-158 569
37 TraesCS3A01G530800 chr2A 91.870 123 8 2 329 450 495957820 495957941 1.320000e-38 171
38 TraesCS3A01G530800 chr2A 91.200 125 10 1 332 455 175483472 175483348 4.760000e-38 169
39 TraesCS3A01G530800 chr7A 79.252 588 86 15 1865 2435 583561980 583561412 7.270000e-101 377
40 TraesCS3A01G530800 chrUn 80.962 478 30 35 821 1260 459077283 459077737 3.450000e-84 322
41 TraesCS3A01G530800 chrUn 82.288 271 15 17 1340 1596 478839170 478838919 1.310000e-48 204
42 TraesCS3A01G530800 chrUn 93.407 91 6 0 1859 1949 43412731 43412821 4.830000e-28 135
43 TraesCS3A01G530800 chr1A 92.000 125 8 2 329 451 23098988 23099112 1.020000e-39 174
44 TraesCS3A01G530800 chr4A 92.373 118 8 1 331 447 188631964 188632081 1.710000e-37 167


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 TraesCS3A01G530800 chr3A 743987064 743989843 2779 False 5134.0 5134 100.0000 1 2780 1 chr3A.!!$F1 2779
1 TraesCS3A01G530800 chr3A 475468785 475469710 925 True 623.0 623 79.6570 1866 2754 1 chr3A.!!$R1 888
2 TraesCS3A01G530800 chr3A 714623217 714623779 562 True 555.0 555 85.0880 2207 2754 1 chr3A.!!$R3 547
3 TraesCS3A01G530800 chr3A 744286715 744287378 663 False 553.0 553 82.7340 961 1614 1 chr3A.!!$F2 653
4 TraesCS3A01G530800 chr3A 744262039 744267060 5021 False 547.5 647 82.8700 820 1592 2 chr3A.!!$F3 772
5 TraesCS3A01G530800 chr3B 821835445 821837364 1919 False 1144.5 1893 90.7410 1 1870 2 chr3B.!!$F4 1869
6 TraesCS3A01G530800 chr3B 822038936 822039727 791 False 628.0 628 82.2540 821 1596 1 chr3B.!!$F1 775
7 TraesCS3A01G530800 chr3B 822067026 822067817 791 False 623.0 623 82.1340 821 1596 1 chr3B.!!$F2 775
8 TraesCS3A01G530800 chr3B 822094411 822095216 805 False 569.0 569 80.7290 820 1614 1 chr3B.!!$F3 794
9 TraesCS3A01G530800 chr3D 330209483 330210380 897 False 1053.0 1053 88.1510 1865 2749 1 chr3D.!!$F1 884
10 TraesCS3A01G530800 chr3D 610138277 610139807 1530 False 779.0 1430 86.7755 221 1858 2 chr3D.!!$F4 1637
11 TraesCS3A01G530800 chr3D 542952002 542952716 714 True 737.0 737 85.6750 1866 2566 1 chr3D.!!$R3 700
12 TraesCS3A01G530800 chr3D 576786982 576787878 896 False 588.0 588 79.3930 1876 2754 1 chr3D.!!$F2 878
13 TraesCS3A01G530800 chr3D 610186662 610190909 4247 False 533.0 545 80.0445 807 1614 2 chr3D.!!$F5 807
14 TraesCS3A01G530800 chr4D 456263617 456264525 908 False 924.0 924 85.3710 1859 2754 1 chr4D.!!$F1 895
15 TraesCS3A01G530800 chr7B 491974065 491974958 893 False 920.0 920 85.5250 1866 2754 1 chr7B.!!$F1 888
16 TraesCS3A01G530800 chr6A 584005113 584006016 903 True 891.0 891 84.8850 1866 2754 1 chr6A.!!$R1 888
17 TraesCS3A01G530800 chr6A 597035483 597036104 621 True 206.0 206 73.9470 1859 2461 1 chr6A.!!$R2 602
18 TraesCS3A01G530800 chr6D 27410055 27410966 911 True 817.0 817 83.5290 1859 2754 1 chr6D.!!$R1 895
19 TraesCS3A01G530800 chr2B 16222188 16222915 727 False 682.0 682 83.9890 2037 2754 1 chr2B.!!$F1 717
20 TraesCS3A01G530800 chr1B 598294299 598295233 934 False 678.0 678 80.7450 1859 2773 1 chr1B.!!$F1 914
21 TraesCS3A01G530800 chr2D 634169662 634170356 694 False 669.0 669 84.1880 2057 2752 1 chr2D.!!$F1 695
22 TraesCS3A01G530800 chr5A 672753367 672754020 653 False 645.0 645 84.9770 2115 2753 1 chr5A.!!$F1 638
23 TraesCS3A01G530800 chr2A 768453244 768454154 910 False 569.0 569 78.6640 1861 2754 1 chr2A.!!$F2 893
24 TraesCS3A01G530800 chr7A 583561412 583561980 568 True 377.0 377 79.2520 1865 2435 1 chr7A.!!$R1 570

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
664 837 0.320771 GGCATCATCGGTTATCGGCT 60.321 55.0 0.0 0.0 39.77 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2626 10764 1.00358 GGAGTCACTGGGCTGAATGAA 59.996 52.381 0.0 0.0 0.0 2.57 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
29 30 4.318949 TTGCTGCGAGCTGCCTCA 62.319 61.111 21.05 5.69 45.60 3.86
38 39 1.744798 CGAGCTGCCTCATGGAATTGA 60.745 52.381 0.00 0.00 38.00 2.57
41 42 2.693591 AGCTGCCTCATGGAATTGAATG 59.306 45.455 0.00 0.00 34.57 2.67
51 52 7.859377 CCTCATGGAATTGAATGATAGTTTTCG 59.141 37.037 0.00 0.00 32.56 3.46
59 60 5.427378 TGAATGATAGTTTTCGGAGCATGA 58.573 37.500 0.00 0.00 0.00 3.07
61 62 5.936686 ATGATAGTTTTCGGAGCATGATG 57.063 39.130 0.00 0.00 0.00 3.07
68 69 3.836365 TTCGGAGCATGATGAATGGTA 57.164 42.857 0.00 0.00 46.95 3.25
80 81 5.748402 TGATGAATGGTAGAGCAACAGATT 58.252 37.500 0.00 0.00 0.00 2.40
143 147 6.460953 CCAAAAACTGTTGTGGTTATAGCTGT 60.461 38.462 12.97 0.00 37.35 4.40
153 157 8.893727 GTTGTGGTTATAGCTGTTAGAAATCAT 58.106 33.333 0.00 0.00 0.00 2.45
185 189 5.326200 AGTTGGGTTAGAAGTCATAGTCG 57.674 43.478 0.00 0.00 0.00 4.18
205 209 5.247792 AGTCGAATTGGTAGTTATATCCCCC 59.752 44.000 0.00 0.00 0.00 5.40
206 210 4.221262 TCGAATTGGTAGTTATATCCCCCG 59.779 45.833 0.00 0.00 0.00 5.73
211 215 3.181452 TGGTAGTTATATCCCCCGCAAAC 60.181 47.826 0.00 0.00 0.00 2.93
212 216 3.181452 GGTAGTTATATCCCCCGCAAACA 60.181 47.826 0.00 0.00 0.00 2.83
213 217 3.655615 AGTTATATCCCCCGCAAACAA 57.344 42.857 0.00 0.00 0.00 2.83
214 218 3.551846 AGTTATATCCCCCGCAAACAAG 58.448 45.455 0.00 0.00 0.00 3.16
219 223 1.710816 TCCCCCGCAAACAAGAAAAT 58.289 45.000 0.00 0.00 0.00 1.82
231 235 8.424731 CGCAAACAAGAAAATAATTGGTAGTTC 58.575 33.333 0.00 0.00 0.00 3.01
269 274 9.226345 CAAAAATATAAGAGAGAATTTGGACGC 57.774 33.333 0.00 0.00 0.00 5.19
271 276 7.954788 AATATAAGAGAGAATTTGGACGCTC 57.045 36.000 0.00 0.00 34.20 5.03
300 464 6.013379 TGGAGATGGAAATGACTAAGAAGTGT 60.013 38.462 0.00 0.00 35.56 3.55
334 498 7.540474 ACATGATAAACCATACGGAGATACT 57.460 36.000 0.00 0.00 35.59 2.12
335 499 7.603651 ACATGATAAACCATACGGAGATACTC 58.396 38.462 0.00 0.00 35.59 2.59
336 500 6.585695 TGATAAACCATACGGAGATACTCC 57.414 41.667 7.65 7.65 46.44 3.85
345 509 1.611519 GGAGATACTCCCTCCGTCTG 58.388 60.000 6.54 0.00 44.36 3.51
346 510 1.611519 GAGATACTCCCTCCGTCTGG 58.388 60.000 0.00 0.00 0.00 3.86
347 511 1.143277 GAGATACTCCCTCCGTCTGGA 59.857 57.143 0.00 0.00 43.88 3.86
348 512 1.569548 AGATACTCCCTCCGTCTGGAA 59.430 52.381 0.00 0.00 45.87 3.53
349 513 2.024273 AGATACTCCCTCCGTCTGGAAA 60.024 50.000 0.00 0.00 45.87 3.13
350 514 2.544844 TACTCCCTCCGTCTGGAAAT 57.455 50.000 0.00 0.00 45.87 2.17
351 515 2.544844 ACTCCCTCCGTCTGGAAATA 57.455 50.000 0.00 0.00 45.87 1.40
352 516 2.108970 ACTCCCTCCGTCTGGAAATAC 58.891 52.381 0.00 0.00 45.87 1.89
353 517 2.292323 ACTCCCTCCGTCTGGAAATACT 60.292 50.000 0.00 0.00 45.87 2.12
354 518 2.766828 CTCCCTCCGTCTGGAAATACTT 59.233 50.000 0.00 0.00 45.87 2.24
355 519 2.500098 TCCCTCCGTCTGGAAATACTTG 59.500 50.000 0.00 0.00 45.87 3.16
356 520 2.236395 CCCTCCGTCTGGAAATACTTGT 59.764 50.000 0.00 0.00 45.87 3.16
357 521 3.522553 CCTCCGTCTGGAAATACTTGTC 58.477 50.000 0.00 0.00 45.87 3.18
358 522 3.179830 CTCCGTCTGGAAATACTTGTCG 58.820 50.000 0.00 0.00 45.87 4.35
359 523 2.559668 TCCGTCTGGAAATACTTGTCGT 59.440 45.455 0.00 0.00 42.85 4.34
360 524 3.758023 TCCGTCTGGAAATACTTGTCGTA 59.242 43.478 0.00 0.00 42.85 3.43
361 525 4.103357 CCGTCTGGAAATACTTGTCGTAG 58.897 47.826 0.00 0.00 37.49 3.51
362 526 4.103357 CGTCTGGAAATACTTGTCGTAGG 58.897 47.826 0.00 0.00 0.00 3.18
363 527 4.142534 CGTCTGGAAATACTTGTCGTAGGA 60.143 45.833 0.00 0.00 0.00 2.94
364 528 5.620654 CGTCTGGAAATACTTGTCGTAGGAA 60.621 44.000 0.00 0.00 0.00 3.36
365 529 6.338937 GTCTGGAAATACTTGTCGTAGGAAT 58.661 40.000 0.00 0.00 0.00 3.01
366 530 6.255887 GTCTGGAAATACTTGTCGTAGGAATG 59.744 42.308 0.00 0.00 0.00 2.67
367 531 6.045072 TGGAAATACTTGTCGTAGGAATGT 57.955 37.500 0.00 0.00 0.00 2.71
368 532 7.123098 TCTGGAAATACTTGTCGTAGGAATGTA 59.877 37.037 0.00 0.00 0.00 2.29
369 533 7.788026 TGGAAATACTTGTCGTAGGAATGTAT 58.212 34.615 0.00 0.00 0.00 2.29
370 534 8.916062 TGGAAATACTTGTCGTAGGAATGTATA 58.084 33.333 6.64 0.00 0.00 1.47
371 535 9.189723 GGAAATACTTGTCGTAGGAATGTATAC 57.810 37.037 0.00 0.00 0.00 1.47
372 536 9.740239 GAAATACTTGTCGTAGGAATGTATACA 57.260 33.333 8.27 8.27 0.00 2.29
376 540 8.420374 ACTTGTCGTAGGAATGTATACAAATG 57.580 34.615 10.14 0.00 0.00 2.32
377 541 7.494625 ACTTGTCGTAGGAATGTATACAAATGG 59.505 37.037 10.14 0.00 0.00 3.16
378 542 7.114866 TGTCGTAGGAATGTATACAAATGGA 57.885 36.000 10.14 0.00 0.00 3.41
379 543 7.732025 TGTCGTAGGAATGTATACAAATGGAT 58.268 34.615 10.14 0.00 0.00 3.41
380 544 7.655732 TGTCGTAGGAATGTATACAAATGGATG 59.344 37.037 10.14 2.00 0.00 3.51
381 545 7.656137 GTCGTAGGAATGTATACAAATGGATGT 59.344 37.037 10.14 0.00 37.32 3.06
382 546 8.862085 TCGTAGGAATGTATACAAATGGATGTA 58.138 33.333 10.14 0.00 39.91 2.29
383 547 9.653287 CGTAGGAATGTATACAAATGGATGTAT 57.347 33.333 10.14 5.41 45.81 2.29
423 587 9.553064 ACATCTAGATACATTCATTTCTTGGAC 57.447 33.333 4.54 0.00 0.00 4.02
424 588 9.551734 CATCTAGATACATTCATTTCTTGGACA 57.448 33.333 4.54 0.00 0.00 4.02
426 590 9.605275 TCTAGATACATTCATTTCTTGGACAAG 57.395 33.333 5.72 5.72 39.71 3.16
427 591 9.388506 CTAGATACATTCATTTCTTGGACAAGT 57.611 33.333 11.44 0.00 39.38 3.16
429 593 9.911788 AGATACATTCATTTCTTGGACAAGTAT 57.088 29.630 11.44 4.73 39.38 2.12
433 597 9.696917 ACATTCATTTCTTGGACAAGTATTTTC 57.303 29.630 11.44 0.00 39.38 2.29
434 598 8.853345 CATTCATTTCTTGGACAAGTATTTTCG 58.147 33.333 11.44 0.00 39.38 3.46
435 599 7.737972 TCATTTCTTGGACAAGTATTTTCGA 57.262 32.000 11.44 0.00 39.38 3.71
436 600 7.581476 TCATTTCTTGGACAAGTATTTTCGAC 58.419 34.615 11.44 0.00 39.38 4.20
437 601 5.585500 TTCTTGGACAAGTATTTTCGACG 57.415 39.130 11.44 0.00 39.38 5.12
438 602 3.991773 TCTTGGACAAGTATTTTCGACGG 59.008 43.478 11.44 0.00 39.38 4.79
439 603 3.663995 TGGACAAGTATTTTCGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
440 604 3.581755 TGGACAAGTATTTTCGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
441 605 2.928116 GGACAAGTATTTTCGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
442 606 2.928116 GACAAGTATTTTCGACGGAGGG 59.072 50.000 0.00 0.00 0.00 4.30
443 607 2.564062 ACAAGTATTTTCGACGGAGGGA 59.436 45.455 0.00 0.00 0.00 4.20
444 608 3.187700 CAAGTATTTTCGACGGAGGGAG 58.812 50.000 0.00 0.00 0.00 4.30
445 609 2.454538 AGTATTTTCGACGGAGGGAGT 58.545 47.619 0.00 0.00 0.00 3.85
446 610 3.624777 AGTATTTTCGACGGAGGGAGTA 58.375 45.455 0.00 0.00 0.00 2.59
494 662 4.827835 GTCTGCTGGAGATACTATACCACA 59.172 45.833 1.19 0.00 31.63 4.17
502 670 5.291905 AGATACTATACCACACCCTTTGC 57.708 43.478 0.00 0.00 0.00 3.68
503 671 2.396590 ACTATACCACACCCTTTGCG 57.603 50.000 0.00 0.00 0.00 4.85
510 678 3.683937 CACCCTTTGCGCCCCTTG 61.684 66.667 4.18 0.00 0.00 3.61
514 682 1.379843 CCTTTGCGCCCCTTGGTAT 60.380 57.895 4.18 0.00 0.00 2.73
515 683 0.970427 CCTTTGCGCCCCTTGGTATT 60.970 55.000 4.18 0.00 0.00 1.89
587 756 8.684386 TTGGTTCAAATTTGACTCACATACTA 57.316 30.769 20.35 9.28 36.83 1.82
624 797 9.064706 AGAGATAAGATTGTTCCTGCAATAATG 57.935 33.333 0.00 0.00 38.98 1.90
646 819 7.934855 ATGCCTAAATCTTGAAGCATATAGG 57.065 36.000 0.00 8.07 39.07 2.57
664 837 0.320771 GGCATCATCGGTTATCGGCT 60.321 55.000 0.00 0.00 39.77 5.52
668 841 0.673985 TCATCGGTTATCGGCTGAGG 59.326 55.000 0.00 0.00 39.77 3.86
670 843 1.120530 ATCGGTTATCGGCTGAGGTT 58.879 50.000 0.00 0.00 39.77 3.50
737 910 4.421131 AGGTATAGCTAGATTCCCACAGG 58.579 47.826 1.70 0.00 0.00 4.00
741 914 1.834263 AGCTAGATTCCCACAGGTGAC 59.166 52.381 0.00 0.00 0.00 3.67
796 969 9.579768 AAGAAAGAAAGAAAGAAAGAAAGAAGC 57.420 29.630 0.00 0.00 0.00 3.86
826 999 7.381789 AGTGTAGTAGAGATATGGACAGAGA 57.618 40.000 0.00 0.00 0.00 3.10
847 1020 6.069789 AGAGAGAATCAAATTGGGTGATGAGA 60.070 38.462 0.00 0.00 35.87 3.27
1070 1298 0.807667 CATCTCCGAAGCTCCAACCG 60.808 60.000 0.00 0.00 0.00 4.44
1408 9355 0.179081 CTGCTGCAGCTGCTAGATCA 60.179 55.000 36.61 23.81 42.66 2.92
1409 9356 0.468648 TGCTGCAGCTGCTAGATCAT 59.531 50.000 36.61 0.00 42.66 2.45
1410 9357 1.134189 TGCTGCAGCTGCTAGATCATT 60.134 47.619 36.61 0.00 42.66 2.57
1480 9466 8.039538 TCGATCTACTACTACCATACCATGTAG 58.960 40.741 0.00 0.00 37.29 2.74
1484 9470 1.968493 ACTACCATACCATGTAGCCGG 59.032 52.381 0.00 0.00 0.00 6.13
1508 9501 3.370104 CCTGATCGAGGGCCTTATCTAT 58.630 50.000 22.85 8.48 38.36 1.98
1548 9542 2.758327 CAGGTGCCATGCCATGCT 60.758 61.111 0.00 0.00 0.00 3.79
1586 9580 4.170053 CCCCCTAAATAAAATCTCCCTGGT 59.830 45.833 0.00 0.00 0.00 4.00
1597 9593 9.774413 ATAAAATCTCCCTGGTTTAACTATACG 57.226 33.333 0.00 0.00 0.00 3.06
1610 9607 2.942710 ACTATACGTGTGTGTCTGTGC 58.057 47.619 0.00 0.00 0.00 4.57
1646 9643 9.755804 ATCATCACCTTCTTTTTCTTTTTCTTC 57.244 29.630 0.00 0.00 0.00 2.87
1647 9644 8.971073 TCATCACCTTCTTTTTCTTTTTCTTCT 58.029 29.630 0.00 0.00 0.00 2.85
1648 9645 9.591792 CATCACCTTCTTTTTCTTTTTCTTCTT 57.408 29.630 0.00 0.00 0.00 2.52
1649 9646 9.809096 ATCACCTTCTTTTTCTTTTTCTTCTTC 57.191 29.630 0.00 0.00 0.00 2.87
1650 9647 9.025041 TCACCTTCTTTTTCTTTTTCTTCTTCT 57.975 29.630 0.00 0.00 0.00 2.85
1658 9655 6.966534 TTCTTTTTCTTCTTCTTCATGGCT 57.033 33.333 0.00 0.00 0.00 4.75
1699 9696 4.152607 GCTGAGAGCGTTGAGAAAATTT 57.847 40.909 0.00 0.00 0.00 1.82
1735 9737 6.981762 AGCAGAAGATTAAGATGTTGTGAG 57.018 37.500 0.00 0.00 33.28 3.51
1742 9745 6.681777 AGATTAAGATGTTGTGAGTTTTGCC 58.318 36.000 0.00 0.00 0.00 4.52
1752 9755 4.440880 TGTGAGTTTTGCCCAAGAAAATG 58.559 39.130 0.00 0.00 0.00 2.32
1761 9764 9.651913 GTTTTGCCCAAGAAAATGAATATCTAA 57.348 29.630 0.00 0.00 0.00 2.10
1949 9962 4.870221 AATAATTTTCGTACGTCCCAGC 57.130 40.909 16.05 0.00 0.00 4.85
1950 9983 1.073177 AATTTTCGTACGTCCCAGCG 58.927 50.000 16.05 0.00 37.94 5.18
1980 10037 3.125316 CCGATTCCTTTCTGTCCGAAAAG 59.875 47.826 0.00 0.00 40.87 2.27
2085 10161 6.780457 ATAAATACTGCACTGCAAGGAATT 57.220 33.333 4.99 0.37 38.41 2.17
2126 10206 0.457851 ACGCTAAGAGTGCTAGCCAG 59.542 55.000 13.29 1.02 33.56 4.85
2198 10279 1.334239 GGTAGCAGTCACGCGAGATAG 60.334 57.143 15.93 8.54 36.85 2.08
2213 10297 5.049336 CGCGAGATAGTGAGAGGAAAAGATA 60.049 44.000 0.00 0.00 0.00 1.98
2538 10676 7.851822 ACTTGGCGAATATTTTAAATATGCG 57.148 32.000 25.56 25.56 36.40 4.73
2548 10686 4.566545 TTTAAATATGCGCACCTGATGG 57.433 40.909 14.90 0.00 39.83 3.51
2626 10764 3.549299 CGTCTTCACGTACTACCAGTT 57.451 47.619 0.00 0.00 41.42 3.16
2630 10768 5.467705 GTCTTCACGTACTACCAGTTTCAT 58.532 41.667 0.00 0.00 0.00 2.57
2633 10771 5.456548 TCACGTACTACCAGTTTCATTCA 57.543 39.130 0.00 0.00 0.00 2.57
2660 10798 3.342377 TGACTCCCGTCAAAATGCATA 57.658 42.857 0.00 0.00 46.61 3.14
2761 10902 4.145052 CAGTGCTTTTTCCTACTCCCTTT 58.855 43.478 0.00 0.00 0.00 3.11
2770 10911 6.713731 TTTCCTACTCCCTTTGTTCCTAAT 57.286 37.500 0.00 0.00 0.00 1.73
2771 10912 7.817910 TTTCCTACTCCCTTTGTTCCTAATA 57.182 36.000 0.00 0.00 0.00 0.98
2772 10913 8.401955 TTTCCTACTCCCTTTGTTCCTAATAT 57.598 34.615 0.00 0.00 0.00 1.28
2774 10915 8.401955 TCCTACTCCCTTTGTTCCTAATATTT 57.598 34.615 0.00 0.00 0.00 1.40
2775 10916 8.272173 TCCTACTCCCTTTGTTCCTAATATTTG 58.728 37.037 0.00 0.00 0.00 2.32
2776 10917 8.053355 CCTACTCCCTTTGTTCCTAATATTTGT 58.947 37.037 0.00 0.00 0.00 2.83
2777 10918 7.939784 ACTCCCTTTGTTCCTAATATTTGTC 57.060 36.000 0.00 0.00 0.00 3.18
2778 10919 7.699878 ACTCCCTTTGTTCCTAATATTTGTCT 58.300 34.615 0.00 0.00 0.00 3.41
2779 10920 8.170730 ACTCCCTTTGTTCCTAATATTTGTCTT 58.829 33.333 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 7.469181 GCTCCGAAAACTATCATTCAATTCCAT 60.469 37.037 0.00 0.00 0.00 3.41
38 39 6.057533 TCATCATGCTCCGAAAACTATCATT 58.942 36.000 0.00 0.00 0.00 2.57
41 42 5.991328 TTCATCATGCTCCGAAAACTATC 57.009 39.130 0.00 0.00 0.00 2.08
51 52 3.072944 GCTCTACCATTCATCATGCTCC 58.927 50.000 0.00 0.00 0.00 4.70
80 81 2.884997 ATATTGAGTTGGCGCCCGCA 62.885 55.000 26.77 14.94 44.11 5.69
82 83 1.648720 CATATTGAGTTGGCGCCCG 59.351 57.895 26.77 0.00 0.00 6.13
97 98 2.742053 GTTTCACGGAAGCAGAAGCATA 59.258 45.455 0.00 0.00 45.49 3.14
176 180 9.570488 GGATATAACTACCAATTCGACTATGAC 57.430 37.037 0.00 0.00 0.00 3.06
185 189 4.259356 GCGGGGGATATAACTACCAATTC 58.741 47.826 0.00 0.00 0.00 2.17
201 205 3.669251 TTATTTTCTTGTTTGCGGGGG 57.331 42.857 0.00 0.00 0.00 5.40
205 209 7.867445 ACTACCAATTATTTTCTTGTTTGCG 57.133 32.000 0.00 0.00 0.00 4.85
206 210 9.476202 AGAACTACCAATTATTTTCTTGTTTGC 57.524 29.630 0.00 0.00 0.00 3.68
271 276 3.482156 AGTCATTTCCATCTCCATCGG 57.518 47.619 0.00 0.00 0.00 4.18
334 498 2.500098 CAAGTATTTCCAGACGGAGGGA 59.500 50.000 0.00 0.00 44.10 4.20
335 499 2.236395 ACAAGTATTTCCAGACGGAGGG 59.764 50.000 0.00 0.00 44.10 4.30
336 500 3.522553 GACAAGTATTTCCAGACGGAGG 58.477 50.000 0.00 0.00 44.10 4.30
337 501 3.179830 CGACAAGTATTTCCAGACGGAG 58.820 50.000 0.00 0.00 44.10 4.63
339 503 2.955614 ACGACAAGTATTTCCAGACGG 58.044 47.619 0.00 0.00 0.00 4.79
341 505 5.320549 TCCTACGACAAGTATTTCCAGAC 57.679 43.478 0.00 0.00 34.34 3.51
342 506 5.988310 TTCCTACGACAAGTATTTCCAGA 57.012 39.130 0.00 0.00 34.34 3.86
343 507 6.106673 ACATTCCTACGACAAGTATTTCCAG 58.893 40.000 0.00 0.00 34.34 3.86
344 508 6.045072 ACATTCCTACGACAAGTATTTCCA 57.955 37.500 0.00 0.00 34.34 3.53
345 509 9.189723 GTATACATTCCTACGACAAGTATTTCC 57.810 37.037 0.00 0.00 34.34 3.13
346 510 9.740239 TGTATACATTCCTACGACAAGTATTTC 57.260 33.333 0.08 0.00 34.34 2.17
350 514 9.524106 CATTTGTATACATTCCTACGACAAGTA 57.476 33.333 6.36 0.00 0.00 2.24
351 515 7.494625 CCATTTGTATACATTCCTACGACAAGT 59.505 37.037 6.36 0.00 0.00 3.16
352 516 7.709182 TCCATTTGTATACATTCCTACGACAAG 59.291 37.037 6.36 0.00 0.00 3.16
353 517 7.557724 TCCATTTGTATACATTCCTACGACAA 58.442 34.615 6.36 0.00 0.00 3.18
354 518 7.114866 TCCATTTGTATACATTCCTACGACA 57.885 36.000 6.36 0.00 0.00 4.35
355 519 7.656137 ACATCCATTTGTATACATTCCTACGAC 59.344 37.037 6.36 0.00 0.00 4.34
356 520 7.732025 ACATCCATTTGTATACATTCCTACGA 58.268 34.615 6.36 0.00 0.00 3.43
357 521 7.962964 ACATCCATTTGTATACATTCCTACG 57.037 36.000 6.36 0.00 0.00 3.51
397 561 9.553064 GTCCAAGAAATGAATGTATCTAGATGT 57.447 33.333 15.79 0.00 0.00 3.06
398 562 9.551734 TGTCCAAGAAATGAATGTATCTAGATG 57.448 33.333 15.79 0.00 0.00 2.90
400 564 9.605275 CTTGTCCAAGAAATGAATGTATCTAGA 57.395 33.333 0.61 0.00 40.79 2.43
401 565 9.388506 ACTTGTCCAAGAAATGAATGTATCTAG 57.611 33.333 13.69 0.00 40.79 2.43
403 567 9.911788 ATACTTGTCCAAGAAATGAATGTATCT 57.088 29.630 13.69 0.00 40.79 1.98
407 571 9.696917 GAAAATACTTGTCCAAGAAATGAATGT 57.303 29.630 13.69 0.00 40.79 2.71
408 572 8.853345 CGAAAATACTTGTCCAAGAAATGAATG 58.147 33.333 13.69 0.00 40.79 2.67
409 573 8.792633 TCGAAAATACTTGTCCAAGAAATGAAT 58.207 29.630 13.69 0.00 40.79 2.57
410 574 8.073768 GTCGAAAATACTTGTCCAAGAAATGAA 58.926 33.333 13.69 0.00 40.79 2.57
411 575 7.570507 CGTCGAAAATACTTGTCCAAGAAATGA 60.571 37.037 13.69 0.49 40.79 2.57
412 576 6.519761 CGTCGAAAATACTTGTCCAAGAAATG 59.480 38.462 13.69 0.00 40.79 2.32
413 577 6.348213 CCGTCGAAAATACTTGTCCAAGAAAT 60.348 38.462 13.69 4.36 40.79 2.17
414 578 5.049954 CCGTCGAAAATACTTGTCCAAGAAA 60.050 40.000 13.69 2.26 40.79 2.52
415 579 4.449743 CCGTCGAAAATACTTGTCCAAGAA 59.550 41.667 13.69 0.00 40.79 2.52
416 580 3.991773 CCGTCGAAAATACTTGTCCAAGA 59.008 43.478 13.69 0.00 40.79 3.02
417 581 3.991773 TCCGTCGAAAATACTTGTCCAAG 59.008 43.478 5.51 5.51 43.79 3.61
418 582 3.991773 CTCCGTCGAAAATACTTGTCCAA 59.008 43.478 0.00 0.00 0.00 3.53
419 583 3.581755 CTCCGTCGAAAATACTTGTCCA 58.418 45.455 0.00 0.00 0.00 4.02
420 584 2.928116 CCTCCGTCGAAAATACTTGTCC 59.072 50.000 0.00 0.00 0.00 4.02
421 585 2.928116 CCCTCCGTCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
422 586 2.564062 TCCCTCCGTCGAAAATACTTGT 59.436 45.455 0.00 0.00 0.00 3.16
423 587 3.187700 CTCCCTCCGTCGAAAATACTTG 58.812 50.000 0.00 0.00 0.00 3.16
424 588 2.830321 ACTCCCTCCGTCGAAAATACTT 59.170 45.455 0.00 0.00 0.00 2.24
425 589 2.454538 ACTCCCTCCGTCGAAAATACT 58.545 47.619 0.00 0.00 0.00 2.12
426 590 2.955477 ACTCCCTCCGTCGAAAATAC 57.045 50.000 0.00 0.00 0.00 1.89
427 591 3.624777 ACTACTCCCTCCGTCGAAAATA 58.375 45.455 0.00 0.00 0.00 1.40
428 592 2.454538 ACTACTCCCTCCGTCGAAAAT 58.545 47.619 0.00 0.00 0.00 1.82
429 593 1.915141 ACTACTCCCTCCGTCGAAAA 58.085 50.000 0.00 0.00 0.00 2.29
430 594 2.290260 TGTACTACTCCCTCCGTCGAAA 60.290 50.000 0.00 0.00 0.00 3.46
431 595 1.278985 TGTACTACTCCCTCCGTCGAA 59.721 52.381 0.00 0.00 0.00 3.71
432 596 0.904649 TGTACTACTCCCTCCGTCGA 59.095 55.000 0.00 0.00 0.00 4.20
433 597 1.964552 ATGTACTACTCCCTCCGTCG 58.035 55.000 0.00 0.00 0.00 5.12
434 598 4.455190 GTCATATGTACTACTCCCTCCGTC 59.545 50.000 1.90 0.00 0.00 4.79
435 599 4.141321 TGTCATATGTACTACTCCCTCCGT 60.141 45.833 1.90 0.00 0.00 4.69
436 600 4.395625 TGTCATATGTACTACTCCCTCCG 58.604 47.826 1.90 0.00 0.00 4.63
437 601 5.386924 ACTGTCATATGTACTACTCCCTCC 58.613 45.833 1.90 0.00 0.00 4.30
438 602 8.638629 AATACTGTCATATGTACTACTCCCTC 57.361 38.462 1.90 0.00 0.00 4.30
439 603 9.435570 AAAATACTGTCATATGTACTACTCCCT 57.564 33.333 1.90 0.00 0.00 4.20
440 604 9.477484 CAAAATACTGTCATATGTACTACTCCC 57.523 37.037 1.90 0.00 0.00 4.30
441 605 9.477484 CCAAAATACTGTCATATGTACTACTCC 57.523 37.037 1.90 0.00 0.00 3.85
444 608 8.965172 CGTCCAAAATACTGTCATATGTACTAC 58.035 37.037 1.90 0.00 0.00 2.73
445 609 8.139350 CCGTCCAAAATACTGTCATATGTACTA 58.861 37.037 1.90 0.00 0.00 1.82
446 610 6.984474 CCGTCCAAAATACTGTCATATGTACT 59.016 38.462 1.90 0.00 0.00 2.73
494 662 4.994756 CCAAGGGGCGCAAAGGGT 62.995 66.667 10.83 0.00 0.00 4.34
528 696 9.847224 AACTTGAGGAAGAAAATACTGTTTCTA 57.153 29.630 0.89 0.00 45.09 2.10
530 698 9.803315 AAAACTTGAGGAAGAAAATACTGTTTC 57.197 29.630 0.00 0.00 37.70 2.78
624 797 5.707298 TGCCTATATGCTTCAAGATTTAGGC 59.293 40.000 19.77 19.77 43.87 3.93
640 813 4.501571 GCCGATAACCGATGATGCCTATAT 60.502 45.833 0.00 0.00 41.76 0.86
641 814 3.181479 GCCGATAACCGATGATGCCTATA 60.181 47.826 0.00 0.00 41.76 1.31
646 819 0.792640 CAGCCGATAACCGATGATGC 59.207 55.000 0.00 0.00 41.76 3.91
664 837 3.262151 TGTCGGTGGAAATATCAACCTCA 59.738 43.478 1.18 0.00 46.22 3.86
668 841 5.123186 TCATGTTGTCGGTGGAAATATCAAC 59.877 40.000 0.00 0.00 35.68 3.18
670 843 4.837972 TCATGTTGTCGGTGGAAATATCA 58.162 39.130 0.00 0.00 0.00 2.15
717 890 4.833380 TCACCTGTGGGAATCTAGCTATAC 59.167 45.833 0.00 0.00 36.25 1.47
720 893 3.031736 GTCACCTGTGGGAATCTAGCTA 58.968 50.000 0.00 0.00 36.25 3.32
721 894 1.834263 GTCACCTGTGGGAATCTAGCT 59.166 52.381 0.00 0.00 36.25 3.32
737 910 7.506328 ACAAGGAACTATAACCAAAAGTCAC 57.494 36.000 0.00 0.00 38.49 3.67
792 965 6.702716 ATCTCTACTACACTACCTTGCTTC 57.297 41.667 0.00 0.00 0.00 3.86
793 966 7.231722 CCATATCTCTACTACACTACCTTGCTT 59.768 40.741 0.00 0.00 0.00 3.91
794 967 6.717540 CCATATCTCTACTACACTACCTTGCT 59.282 42.308 0.00 0.00 0.00 3.91
795 968 6.715718 TCCATATCTCTACTACACTACCTTGC 59.284 42.308 0.00 0.00 0.00 4.01
796 969 7.720074 TGTCCATATCTCTACTACACTACCTTG 59.280 40.741 0.00 0.00 0.00 3.61
826 999 4.637534 CGTCTCATCACCCAATTTGATTCT 59.362 41.667 0.00 0.00 30.98 2.40
847 1020 2.158143 AGAGGAATAAGGATAGGGCCGT 60.158 50.000 2.24 2.24 0.00 5.68
984 1202 0.764890 TGAGGAATAATGGAGGGGCG 59.235 55.000 0.00 0.00 0.00 6.13
1070 1298 1.363744 CAGCAAGACATCCTCGGTTC 58.636 55.000 0.00 0.00 0.00 3.62
1480 9466 2.728817 CCTCGATCAGGTACCGGC 59.271 66.667 7.24 0.00 37.53 6.13
1484 9470 1.700955 TAAGGCCCTCGATCAGGTAC 58.299 55.000 0.00 0.00 41.51 3.34
1548 9542 3.135027 GGGGGCCTGTTTACAACAA 57.865 52.632 0.84 0.00 41.61 2.83
1584 9578 5.922544 ACAGACACACACGTATAGTTAAACC 59.077 40.000 0.00 0.00 0.00 3.27
1586 9580 5.403166 GCACAGACACACACGTATAGTTAAA 59.597 40.000 0.00 0.00 0.00 1.52
1597 9593 1.511850 TGCATAGCACAGACACACAC 58.488 50.000 0.00 0.00 31.71 3.82
1640 9637 6.713762 TTTTGAGCCATGAAGAAGAAGAAA 57.286 33.333 0.00 0.00 0.00 2.52
1670 9667 4.081972 TCTCAACGCTCTCAGCTCTTAAAT 60.082 41.667 0.00 0.00 39.60 1.40
1671 9668 3.255888 TCTCAACGCTCTCAGCTCTTAAA 59.744 43.478 0.00 0.00 39.60 1.52
1679 9676 5.348418 TCAAATTTTCTCAACGCTCTCAG 57.652 39.130 0.00 0.00 0.00 3.35
1716 9716 7.327032 GGCAAAACTCACAACATCTTAATCTTC 59.673 37.037 0.00 0.00 0.00 2.87
1723 9723 3.030291 TGGGCAAAACTCACAACATCTT 58.970 40.909 0.00 0.00 0.00 2.40
1735 9737 9.651913 TTAGATATTCATTTTCTTGGGCAAAAC 57.348 29.630 0.00 0.00 0.00 2.43
1761 9764 6.090358 CGTTCAGGTACGTCTTCAACATTTAT 59.910 38.462 0.00 0.00 36.80 1.40
1950 9983 3.010420 CAGAAAGGAATCGGGAGAAACC 58.990 50.000 0.00 0.00 45.37 3.27
1980 10037 1.191096 CTGTGCGTGCTGTGTTTTTC 58.809 50.000 0.00 0.00 0.00 2.29
2085 10161 2.032528 CTTGAGCGGCAGGGTTCA 59.967 61.111 1.45 0.00 0.00 3.18
2126 10206 3.003480 CACCAAGGCTTGCTTAGTCTAC 58.997 50.000 21.77 0.00 38.03 2.59
2231 10322 3.959385 GCAAATTTTTCGCGTTCCAAAAG 59.041 39.130 5.77 0.00 0.00 2.27
2236 10327 3.000825 ACTTTGCAAATTTTTCGCGTTCC 59.999 39.130 13.23 0.00 0.00 3.62
2525 10663 5.301551 TCCATCAGGTGCGCATATTTAAAAT 59.698 36.000 15.91 0.00 35.89 1.82
2529 10667 3.483808 TCCATCAGGTGCGCATATTTA 57.516 42.857 15.91 0.00 35.89 1.40
2538 10676 5.048083 TGAACTAAAACAATCCATCAGGTGC 60.048 40.000 0.00 0.00 35.89 5.01
2580 10718 6.402983 CGACAGAGAAAAAGATTCCTTCCATG 60.403 42.308 0.00 0.00 0.00 3.66
2619 10757 2.375174 ACTGGGCTGAATGAAACTGGTA 59.625 45.455 0.00 0.00 0.00 3.25
2626 10764 1.003580 GGAGTCACTGGGCTGAATGAA 59.996 52.381 0.00 0.00 0.00 2.57
2630 10768 2.583441 CGGGAGTCACTGGGCTGAA 61.583 63.158 0.00 0.00 0.00 3.02
2660 10798 5.316987 CATGAAACCTTAGTTGGACTCCTT 58.683 41.667 0.00 0.00 35.97 3.36
2732 10872 3.923017 AGGAAAAAGCACTGCACATAC 57.077 42.857 3.30 0.00 0.00 2.39


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

AutoCloner maintained by Alex Coulton.