Multiple sequence alignment - TraesCS6A01G398900

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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 TraesCS6A01G398900 chr6A 100.000 3686 0 0 1 3686 609164440 609160755 0.000000e+00 6807.0
1 TraesCS6A01G398900 chr6A 76.650 818 142 33 1089 1872 595489838 595489036 1.230000e-109 407.0
2 TraesCS6A01G398900 chr6A 79.062 640 95 23 2134 2752 595663709 595663088 1.590000e-108 403.0
3 TraesCS6A01G398900 chr6A 76.712 292 45 13 2907 3191 595487667 595487392 1.380000e-29 141.0
4 TraesCS6A01G398900 chr6D 94.391 3120 122 25 606 3686 452083202 452080097 0.000000e+00 4743.0
5 TraesCS6A01G398900 chr6D 94.349 2088 83 17 1622 3686 462409647 462407572 0.000000e+00 3169.0
6 TraesCS6A01G398900 chr6D 77.311 1071 173 29 1050 2064 449844486 449843430 5.340000e-158 568.0
7 TraesCS6A01G398900 chr6D 78.891 649 96 22 2134 2761 450168065 450167437 5.730000e-108 401.0
8 TraesCS6A01G398900 chr6D 78.311 438 85 6 2242 2676 450211248 450210818 1.300000e-69 274.0
9 TraesCS6A01G398900 chr6D 84.906 265 31 3 3 265 452084202 452083945 3.650000e-65 259.0
10 TraesCS6A01G398900 chr6D 91.579 190 13 1 110 296 462409837 462409648 3.650000e-65 259.0
11 TraesCS6A01G398900 chr6B 92.509 3137 148 33 606 3686 704862489 704859384 0.000000e+00 4410.0
12 TraesCS6A01G398900 chr6B 77.135 1089 176 30 1034 2064 682417946 682419019 6.910000e-157 564.0
13 TraesCS6A01G398900 chr6B 79.620 579 102 13 1304 1871 681930434 681929861 5.730000e-108 401.0
14 TraesCS6A01G398900 chr6B 78.594 640 98 23 2134 2752 682660970 682660349 1.610000e-103 387.0
15 TraesCS6A01G398900 chr6B 79.258 458 85 5 2223 2676 682707560 682707109 9.940000e-81 311.0
16 TraesCS6A01G398900 chr6B 88.832 197 17 4 1871 2064 681929748 681929554 1.710000e-58 237.0
17 TraesCS6A01G398900 chr6B 83.810 105 15 1 2223 2325 682741501 682741397 8.420000e-17 99.0
18 TraesCS6A01G398900 chr6B 85.915 71 6 4 1116 1184 69959108 69959040 5.110000e-09 73.1
19 TraesCS6A01G398900 chr5D 88.710 124 10 4 400 521 480470554 480470433 8.250000e-32 148.0
20 TraesCS6A01G398900 chr5D 88.136 118 13 1 400 517 67699165 67699281 4.960000e-29 139.0
21 TraesCS6A01G398900 chr7B 90.476 105 10 0 414 518 39380271 39380167 4.960000e-29 139.0
22 TraesCS6A01G398900 chr3A 90.385 104 10 0 414 517 125494746 125494849 1.790000e-28 137.0
23 TraesCS6A01G398900 chr3A 85.366 123 15 3 397 518 80100849 80100729 1.390000e-24 124.0
24 TraesCS6A01G398900 chr2A 84.426 122 18 1 397 518 75637123 75637243 6.470000e-23 119.0
25 TraesCS6A01G398900 chr2D 84.746 118 17 1 400 517 155730889 155731005 2.330000e-22 117.0
26 TraesCS6A01G398900 chr2B 83.465 127 20 1 391 517 767419763 767419888 2.330000e-22 117.0
27 TraesCS6A01G398900 chr2B 87.755 98 11 1 200 296 568557902 568557805 3.010000e-21 113.0
28 TraesCS6A01G398900 chr1A 84.298 121 16 3 400 519 532730501 532730619 8.360000e-22 115.0


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 TraesCS6A01G398900 chr6A 609160755 609164440 3685 True 6807 6807 100.0000 1 3686 1 chr6A.!!$R2 3685
1 TraesCS6A01G398900 chr6A 595663088 595663709 621 True 403 403 79.0620 2134 2752 1 chr6A.!!$R1 618
2 TraesCS6A01G398900 chr6A 595487392 595489838 2446 True 274 407 76.6810 1089 3191 2 chr6A.!!$R3 2102
3 TraesCS6A01G398900 chr6D 452080097 452084202 4105 True 2501 4743 89.6485 3 3686 2 chr6D.!!$R4 3683
4 TraesCS6A01G398900 chr6D 462407572 462409837 2265 True 1714 3169 92.9640 110 3686 2 chr6D.!!$R5 3576
5 TraesCS6A01G398900 chr6D 449843430 449844486 1056 True 568 568 77.3110 1050 2064 1 chr6D.!!$R1 1014
6 TraesCS6A01G398900 chr6D 450167437 450168065 628 True 401 401 78.8910 2134 2761 1 chr6D.!!$R2 627
7 TraesCS6A01G398900 chr6B 704859384 704862489 3105 True 4410 4410 92.5090 606 3686 1 chr6B.!!$R5 3080
8 TraesCS6A01G398900 chr6B 682417946 682419019 1073 False 564 564 77.1350 1034 2064 1 chr6B.!!$F1 1030
9 TraesCS6A01G398900 chr6B 682660349 682660970 621 True 387 387 78.5940 2134 2752 1 chr6B.!!$R2 618
10 TraesCS6A01G398900 chr6B 681929554 681930434 880 True 319 401 84.2260 1304 2064 2 chr6B.!!$R6 760

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
298 304 0.036388 GGTGGTGATCAAAGAGGCGA 60.036 55.0 0.0 0.0 0.0 5.54 F
507 513 0.372334 CGGGCAAGTATTTTCGGACG 59.628 55.0 0.0 0.0 0.0 4.79 F
798 1364 0.423956 TCCCTACCCCAAGAATCCCA 59.576 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1581 2173 0.529833 TACGACGGCGGGTTTTATCA 59.470 50.000 18.49 0.0 43.17 2.15 R
2456 3562 2.203070 GCAGGAGGTACATGGCGG 60.203 66.667 0.00 0.0 0.00 6.13 R
2819 3941 9.269453 GTGTAGAAATGGTGAAAAACTAGTACT 57.731 33.333 0.00 0.0 0.00 2.73 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
41 42 7.701539 TTAATGCAGATGGTGTAGTCAAATT 57.298 32.000 0.00 0.00 0.00 1.82
48 49 5.711976 AGATGGTGTAGTCAAATTTTCAGGG 59.288 40.000 0.00 0.00 0.00 4.45
54 55 0.878416 TCAAATTTTCAGGGCGGACG 59.122 50.000 0.00 0.00 0.00 4.79
60 61 3.881019 TTCAGGGCGGACGAGGAGT 62.881 63.158 0.00 0.00 0.00 3.85
65 66 2.707849 GGCGGACGAGGAGTTGCTA 61.708 63.158 0.00 0.00 35.63 3.49
68 69 0.179161 CGGACGAGGAGTTGCTACTG 60.179 60.000 5.27 0.00 33.84 2.74
78 79 1.138859 AGTTGCTACTGCTGTGTGTCA 59.861 47.619 6.48 0.00 40.48 3.58
91 92 4.439974 GCTGTGTGTCAGGATCAAAACAAA 60.440 41.667 0.00 0.00 43.78 2.83
101 102 8.081633 GTCAGGATCAAAACAAAACATACATGA 58.918 33.333 0.00 0.00 0.00 3.07
102 103 8.298854 TCAGGATCAAAACAAAACATACATGAG 58.701 33.333 0.00 0.00 0.00 2.90
103 104 8.298854 CAGGATCAAAACAAAACATACATGAGA 58.701 33.333 0.00 0.00 0.00 3.27
104 105 9.028284 AGGATCAAAACAAAACATACATGAGAT 57.972 29.630 0.00 0.00 0.00 2.75
105 106 9.294030 GGATCAAAACAAAACATACATGAGATC 57.706 33.333 0.00 0.00 0.00 2.75
108 109 9.288576 TCAAAACAAAACATACATGAGATCTCT 57.711 29.630 22.95 6.25 0.00 3.10
148 149 2.746277 GGTGTCACCGATGTGGCC 60.746 66.667 6.18 0.00 46.74 5.36
203 206 3.609853 CCTTTAGCAACTGACTATGGCA 58.390 45.455 0.00 0.00 0.00 4.92
287 293 0.179045 GGAGCTAATGCGGTGGTGAT 60.179 55.000 0.00 0.00 45.42 3.06
296 302 1.648467 GCGGTGGTGATCAAAGAGGC 61.648 60.000 0.00 0.00 0.00 4.70
297 303 1.361668 CGGTGGTGATCAAAGAGGCG 61.362 60.000 0.00 0.00 0.00 5.52
298 304 0.036388 GGTGGTGATCAAAGAGGCGA 60.036 55.000 0.00 0.00 0.00 5.54
299 305 1.610624 GGTGGTGATCAAAGAGGCGAA 60.611 52.381 0.00 0.00 0.00 4.70
310 316 4.199804 AGGCGAACCTCACTGAGT 57.800 55.556 5.32 0.00 46.34 3.41
312 318 0.889306 AGGCGAACCTCACTGAGTAC 59.111 55.000 5.32 0.00 46.34 2.73
319 325 5.679906 CGAACCTCACTGAGTACAATTTTG 58.320 41.667 5.32 0.00 0.00 2.44
322 328 6.867662 ACCTCACTGAGTACAATTTTGAAG 57.132 37.500 5.32 0.00 0.00 3.02
327 333 6.483307 TCACTGAGTACAATTTTGAAGAGTGG 59.517 38.462 0.00 0.00 0.00 4.00
329 335 4.213270 TGAGTACAATTTTGAAGAGTGGCG 59.787 41.667 0.00 0.00 0.00 5.69
331 337 2.306847 ACAATTTTGAAGAGTGGCGGT 58.693 42.857 0.00 0.00 0.00 5.68
340 346 0.802494 AGAGTGGCGGTTTATTTGCG 59.198 50.000 0.00 0.00 0.00 4.85
343 349 0.519961 GTGGCGGTTTATTTGCGAGT 59.480 50.000 0.00 0.00 0.00 4.18
345 351 1.084289 GGCGGTTTATTTGCGAGTCT 58.916 50.000 0.00 0.00 0.00 3.24
347 353 2.284417 GGCGGTTTATTTGCGAGTCTAG 59.716 50.000 0.00 0.00 0.00 2.43
349 355 3.802685 GCGGTTTATTTGCGAGTCTAGAT 59.197 43.478 0.00 0.00 0.00 1.98
371 377 8.121305 AGATGTAGAAACTATGAGCTGATAGG 57.879 38.462 22.06 6.62 31.15 2.57
416 422 9.893634 TTTATTTATTACTCACCTTCATTCGGA 57.106 29.630 0.00 0.00 0.00 4.55
417 423 9.893634 TTATTTATTACTCACCTTCATTCGGAA 57.106 29.630 0.00 0.00 0.00 4.30
418 424 8.801882 ATTTATTACTCACCTTCATTCGGAAA 57.198 30.769 0.00 0.00 34.44 3.13
419 425 8.801882 TTTATTACTCACCTTCATTCGGAAAT 57.198 30.769 0.00 0.00 34.44 2.17
420 426 9.893634 TTTATTACTCACCTTCATTCGGAAATA 57.106 29.630 0.00 0.00 34.44 1.40
422 428 8.980481 ATTACTCACCTTCATTCGGAAATATT 57.020 30.769 0.00 0.00 34.44 1.28
423 429 8.801882 TTACTCACCTTCATTCGGAAATATTT 57.198 30.769 0.00 0.00 34.44 1.40
424 430 7.088589 ACTCACCTTCATTCGGAAATATTTG 57.911 36.000 5.17 0.00 34.44 2.32
425 431 6.659242 ACTCACCTTCATTCGGAAATATTTGT 59.341 34.615 5.17 0.00 34.44 2.83
426 432 7.083875 TCACCTTCATTCGGAAATATTTGTC 57.916 36.000 5.17 0.00 34.44 3.18
427 433 5.965334 CACCTTCATTCGGAAATATTTGTCG 59.035 40.000 5.17 9.46 34.44 4.35
428 434 5.646360 ACCTTCATTCGGAAATATTTGTCGT 59.354 36.000 5.17 0.00 34.44 4.34
429 435 6.819649 ACCTTCATTCGGAAATATTTGTCGTA 59.180 34.615 5.17 4.17 34.44 3.43
430 436 7.011109 ACCTTCATTCGGAAATATTTGTCGTAG 59.989 37.037 5.17 4.90 34.44 3.51
431 437 7.223971 CCTTCATTCGGAAATATTTGTCGTAGA 59.776 37.037 5.17 6.77 34.44 2.59
432 438 8.481974 TTCATTCGGAAATATTTGTCGTAGAA 57.518 30.769 5.17 11.19 31.77 2.10
433 439 8.481974 TCATTCGGAAATATTTGTCGTAGAAA 57.518 30.769 5.17 1.19 39.69 2.52
434 440 9.104965 TCATTCGGAAATATTTGTCGTAGAAAT 57.895 29.630 5.17 3.24 39.69 2.17
435 441 9.158364 CATTCGGAAATATTTGTCGTAGAAATG 57.842 33.333 5.17 10.41 39.69 2.32
436 442 8.481974 TTCGGAAATATTTGTCGTAGAAATGA 57.518 30.769 5.17 0.00 39.69 2.57
437 443 8.481974 TCGGAAATATTTGTCGTAGAAATGAA 57.518 30.769 5.17 0.00 39.69 2.57
438 444 9.104965 TCGGAAATATTTGTCGTAGAAATGAAT 57.895 29.630 5.17 0.00 39.69 2.57
489 495 9.613957 AATACATCTAGATACATTCGTTCTTCG 57.386 33.333 4.54 0.00 41.41 3.79
490 496 6.439599 ACATCTAGATACATTCGTTCTTCGG 58.560 40.000 4.54 0.00 40.32 4.30
491 497 5.434352 TCTAGATACATTCGTTCTTCGGG 57.566 43.478 0.00 0.00 40.32 5.14
492 498 2.822764 AGATACATTCGTTCTTCGGGC 58.177 47.619 0.00 0.00 40.32 6.13
493 499 2.167693 AGATACATTCGTTCTTCGGGCA 59.832 45.455 0.00 0.00 40.32 5.36
494 500 2.459060 TACATTCGTTCTTCGGGCAA 57.541 45.000 0.00 0.00 40.32 4.52
495 501 1.156736 ACATTCGTTCTTCGGGCAAG 58.843 50.000 0.00 0.00 40.32 4.01
496 502 1.156736 CATTCGTTCTTCGGGCAAGT 58.843 50.000 0.00 0.00 40.32 3.16
497 503 2.289195 ACATTCGTTCTTCGGGCAAGTA 60.289 45.455 0.00 0.00 40.32 2.24
498 504 2.754946 TTCGTTCTTCGGGCAAGTAT 57.245 45.000 0.00 0.00 40.32 2.12
499 505 2.754946 TCGTTCTTCGGGCAAGTATT 57.245 45.000 0.00 0.00 40.32 1.89
500 506 3.048337 TCGTTCTTCGGGCAAGTATTT 57.952 42.857 0.00 0.00 40.32 1.40
501 507 3.404899 TCGTTCTTCGGGCAAGTATTTT 58.595 40.909 0.00 0.00 40.32 1.82
502 508 3.434299 TCGTTCTTCGGGCAAGTATTTTC 59.566 43.478 0.00 0.00 40.32 2.29
503 509 3.723835 CGTTCTTCGGGCAAGTATTTTCG 60.724 47.826 0.00 0.00 35.71 3.46
504 510 2.352388 TCTTCGGGCAAGTATTTTCGG 58.648 47.619 0.00 0.00 33.27 4.30
505 511 2.027929 TCTTCGGGCAAGTATTTTCGGA 60.028 45.455 0.00 0.00 33.27 4.55
506 512 1.729284 TCGGGCAAGTATTTTCGGAC 58.271 50.000 0.00 0.00 0.00 4.79
507 513 0.372334 CGGGCAAGTATTTTCGGACG 59.628 55.000 0.00 0.00 0.00 4.79
508 514 0.730840 GGGCAAGTATTTTCGGACGG 59.269 55.000 0.00 0.00 0.00 4.79
509 515 1.676615 GGGCAAGTATTTTCGGACGGA 60.677 52.381 0.00 0.00 0.00 4.69
510 516 1.664151 GGCAAGTATTTTCGGACGGAG 59.336 52.381 0.00 0.00 0.00 4.63
511 517 2.613691 GCAAGTATTTTCGGACGGAGA 58.386 47.619 0.00 0.00 0.00 3.71
512 518 2.603560 GCAAGTATTTTCGGACGGAGAG 59.396 50.000 0.00 0.00 0.00 3.20
513 519 3.675228 GCAAGTATTTTCGGACGGAGAGA 60.675 47.826 0.00 0.00 0.00 3.10
514 520 4.106197 CAAGTATTTTCGGACGGAGAGAG 58.894 47.826 0.00 0.00 0.00 3.20
515 521 3.354467 AGTATTTTCGGACGGAGAGAGT 58.646 45.455 0.00 0.00 0.00 3.24
516 522 4.521146 AGTATTTTCGGACGGAGAGAGTA 58.479 43.478 0.00 0.00 0.00 2.59
517 523 5.131784 AGTATTTTCGGACGGAGAGAGTAT 58.868 41.667 0.00 0.00 0.00 2.12
526 532 2.766263 ACGGAGAGAGTATTTGATGCCA 59.234 45.455 0.00 0.00 0.00 4.92
563 569 3.618351 CTTGGAGCCACATGATCTTCTT 58.382 45.455 0.00 0.00 0.00 2.52
564 570 3.726557 TGGAGCCACATGATCTTCTTT 57.273 42.857 0.00 0.00 0.00 2.52
565 571 4.038271 TGGAGCCACATGATCTTCTTTT 57.962 40.909 0.00 0.00 0.00 2.27
566 572 4.410099 TGGAGCCACATGATCTTCTTTTT 58.590 39.130 0.00 0.00 0.00 1.94
602 1157 2.357637 GCGATACCCTTTAGCATTTGCA 59.642 45.455 5.20 0.00 45.16 4.08
603 1158 3.548818 GCGATACCCTTTAGCATTTGCAG 60.549 47.826 5.20 0.00 45.16 4.41
604 1159 3.627577 CGATACCCTTTAGCATTTGCAGT 59.372 43.478 5.20 0.00 45.16 4.40
679 1237 2.185350 CCAACGAGCTCGCCTCAT 59.815 61.111 34.83 13.48 44.43 2.90
764 1322 2.125912 CCTCGGAACTCACTGCGG 60.126 66.667 0.00 0.00 0.00 5.69
798 1364 0.423956 TCCCTACCCCAAGAATCCCA 59.576 55.000 0.00 0.00 0.00 4.37
799 1365 1.203635 TCCCTACCCCAAGAATCCCAA 60.204 52.381 0.00 0.00 0.00 4.12
801 1367 2.358195 CCCTACCCCAAGAATCCCAAAG 60.358 54.545 0.00 0.00 0.00 2.77
851 1421 0.522180 CTAGTTGACTCCGTCACGCT 59.478 55.000 0.00 1.68 42.60 5.07
903 1474 5.046304 CCCATCCGGTGATAGATATTCTTGT 60.046 44.000 0.00 0.00 0.00 3.16
904 1475 6.154534 CCCATCCGGTGATAGATATTCTTGTA 59.845 42.308 0.00 0.00 0.00 2.41
908 1479 6.776116 TCCGGTGATAGATATTCTTGTACAGT 59.224 38.462 0.00 0.00 0.00 3.55
951 1522 4.332543 ACCCGCTCCCTTCCCTGA 62.333 66.667 0.00 0.00 0.00 3.86
1016 1587 1.339055 CGAAATGTCCAGGAGGCTGAA 60.339 52.381 0.00 0.00 33.74 3.02
1026 1597 3.316573 GAGGCTGAACGAGGTGGGG 62.317 68.421 0.00 0.00 0.00 4.96
1081 1652 4.671590 TCCCGGACGACCTGCTGA 62.672 66.667 0.73 0.00 0.00 4.26
1167 1738 2.282958 TCGCTCTGGAGGTCCGTT 60.283 61.111 0.00 0.00 39.43 4.44
1287 1858 3.513912 ACCTATGTGACATCTGTTCCGAA 59.486 43.478 0.00 0.00 0.00 4.30
1475 2067 5.472820 AGTTCAAAGGCTCTCTGAATTTCAG 59.527 40.000 18.49 18.49 45.59 3.02
1503 2095 3.093814 TCGGGTGCTAGATGTGTTAGAA 58.906 45.455 0.00 0.00 0.00 2.10
1640 2232 3.603532 TCAGCTTGAAACTAGCTCCATG 58.396 45.455 4.93 0.00 45.52 3.66
1853 2548 3.197549 TGCTCCCATTTTTGCTAATTCCC 59.802 43.478 0.00 0.00 0.00 3.97
1909 2797 6.934083 TGTCAGTACAAGCATATTGAACAAGA 59.066 34.615 0.00 0.00 30.91 3.02
1978 2871 5.891451 TGATGTTTCTATGTACTCGTCTGG 58.109 41.667 0.00 0.00 0.00 3.86
2744 3866 7.856145 ACCAGTCTTCATGATTATGTCTTTC 57.144 36.000 0.00 0.00 35.73 2.62
2819 3941 3.753272 GACCTAGTTTGAAGCAGCATTCA 59.247 43.478 0.00 0.00 37.41 2.57
2858 3992 6.159751 ACCATTTCTACACCCACCATAATAGT 59.840 38.462 0.00 0.00 0.00 2.12
2954 4088 0.975887 TGGTCACACTAGCAGATGCA 59.024 50.000 7.68 0.00 45.16 3.96
3164 4299 9.646522 ATGTTAATAGCAAACTATCCTTCCAAT 57.353 29.630 0.00 0.00 38.18 3.16
3223 4366 7.253422 CAATGACCTTCCAATCAGTGAATAAC 58.747 38.462 0.00 0.00 42.13 1.89
3230 4373 6.566079 TCCAATCAGTGAATAACCTCTCAT 57.434 37.500 0.00 0.00 0.00 2.90
3231 4374 7.675161 TCCAATCAGTGAATAACCTCTCATA 57.325 36.000 0.00 0.00 0.00 2.15
3232 4375 7.730084 TCCAATCAGTGAATAACCTCTCATAG 58.270 38.462 0.00 0.00 0.00 2.23
3233 4376 7.345653 TCCAATCAGTGAATAACCTCTCATAGT 59.654 37.037 0.00 0.00 0.00 2.12
3234 4377 7.655328 CCAATCAGTGAATAACCTCTCATAGTC 59.345 40.741 0.00 0.00 0.00 2.59
3235 4378 8.420222 CAATCAGTGAATAACCTCTCATAGTCT 58.580 37.037 0.00 0.00 0.00 3.24
3236 4379 7.575414 TCAGTGAATAACCTCTCATAGTCTC 57.425 40.000 0.00 0.00 0.00 3.36
3237 4380 7.119387 TCAGTGAATAACCTCTCATAGTCTCA 58.881 38.462 0.00 0.00 0.00 3.27
3248 4391 6.549364 CCTCTCATAGTCTCATACAGTTTCCT 59.451 42.308 0.00 0.00 0.00 3.36
3280 4423 0.111253 ACTGCTTCTTCCAACCTGGG 59.889 55.000 0.00 0.00 38.32 4.45
3281 4424 0.111253 CTGCTTCTTCCAACCTGGGT 59.889 55.000 0.00 0.00 38.32 4.51
3313 4456 6.624352 TCTCATTGTTTCCTCTGTTTTCTG 57.376 37.500 0.00 0.00 0.00 3.02
3390 4533 1.332375 TGCTGCGTTTTTGTCTACCAC 59.668 47.619 0.00 0.00 0.00 4.16
3440 4583 9.640963 GTGTCCTGTTCATATATATGACCTTAC 57.359 37.037 22.38 17.92 42.00 2.34
3548 4691 5.124457 GCTTTATGCTCATTTCCTCAACTCA 59.876 40.000 0.00 0.00 38.95 3.41
3555 4698 0.603707 TTTCCTCAACTCAGCGGCAG 60.604 55.000 1.45 0.00 0.00 4.85
3583 4726 4.025040 ACTGCCAAGATGATGTTTCAGA 57.975 40.909 7.88 0.00 34.73 3.27
3674 4820 2.103263 GCTAGGATCGGTTTCCAGATGT 59.897 50.000 0.00 0.00 38.32 3.06
3675 4821 3.321111 GCTAGGATCGGTTTCCAGATGTA 59.679 47.826 0.00 0.00 38.32 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.716799 ACACCATCTGCATTAATTTTTAGGA 57.283 32.000 0.00 0.00 0.00 2.94
15 16 7.701539 TTTGACTACACCATCTGCATTAATT 57.298 32.000 0.00 0.00 0.00 1.40
21 22 5.534278 TGAAAATTTGACTACACCATCTGCA 59.466 36.000 0.00 0.00 0.00 4.41
41 42 2.602267 TCCTCGTCCGCCCTGAAA 60.602 61.111 0.00 0.00 0.00 2.69
48 49 1.516603 GTAGCAACTCCTCGTCCGC 60.517 63.158 0.00 0.00 0.00 5.54
54 55 1.001406 ACACAGCAGTAGCAACTCCTC 59.999 52.381 0.00 0.00 45.49 3.71
60 61 1.541015 CCTGACACACAGCAGTAGCAA 60.541 52.381 0.00 0.00 44.52 3.91
63 64 2.232208 TGATCCTGACACACAGCAGTAG 59.768 50.000 0.00 0.00 44.52 2.57
65 66 1.051008 TGATCCTGACACACAGCAGT 58.949 50.000 0.00 0.00 44.52 4.40
68 69 2.618241 TGTTTTGATCCTGACACACAGC 59.382 45.455 0.00 0.00 44.52 4.40
78 79 8.408043 TCTCATGTATGTTTTGTTTTGATCCT 57.592 30.769 0.00 0.00 0.00 3.24
91 92 7.836479 TGAGATCAGAGATCTCATGTATGTT 57.164 36.000 27.12 8.59 46.66 2.71
148 149 3.166657 GCATGCTAAAGCTTCAAAGACG 58.833 45.455 11.37 0.00 42.66 4.18
296 302 5.465390 TCAAAATTGTACTCAGTGAGGTTCG 59.535 40.000 23.79 0.00 33.35 3.95
297 303 6.861065 TCAAAATTGTACTCAGTGAGGTTC 57.139 37.500 23.79 13.37 33.35 3.62
298 304 7.054124 TCTTCAAAATTGTACTCAGTGAGGTT 58.946 34.615 23.79 6.79 33.35 3.50
299 305 6.591935 TCTTCAAAATTGTACTCAGTGAGGT 58.408 36.000 23.79 11.91 33.35 3.85
306 312 4.213270 CGCCACTCTTCAAAATTGTACTCA 59.787 41.667 0.00 0.00 0.00 3.41
307 313 4.378459 CCGCCACTCTTCAAAATTGTACTC 60.378 45.833 0.00 0.00 0.00 2.59
310 316 3.482436 ACCGCCACTCTTCAAAATTGTA 58.518 40.909 0.00 0.00 0.00 2.41
312 318 3.369546 AACCGCCACTCTTCAAAATTG 57.630 42.857 0.00 0.00 0.00 2.32
319 325 2.727916 CGCAAATAAACCGCCACTCTTC 60.728 50.000 0.00 0.00 0.00 2.87
322 328 0.800012 TCGCAAATAAACCGCCACTC 59.200 50.000 0.00 0.00 0.00 3.51
327 333 3.184541 TCTAGACTCGCAAATAAACCGC 58.815 45.455 0.00 0.00 0.00 5.68
329 335 7.201145 TCTACATCTAGACTCGCAAATAAACC 58.799 38.462 0.00 0.00 0.00 3.27
331 337 9.084164 GTTTCTACATCTAGACTCGCAAATAAA 57.916 33.333 0.00 0.00 0.00 1.40
340 346 8.289618 CAGCTCATAGTTTCTACATCTAGACTC 58.710 40.741 0.00 0.00 0.00 3.36
343 349 8.932434 ATCAGCTCATAGTTTCTACATCTAGA 57.068 34.615 0.00 0.00 0.00 2.43
345 351 9.237187 CCTATCAGCTCATAGTTTCTACATCTA 57.763 37.037 3.77 0.00 0.00 1.98
347 353 7.891561 ACCTATCAGCTCATAGTTTCTACATC 58.108 38.462 3.77 0.00 0.00 3.06
349 355 7.661536 AACCTATCAGCTCATAGTTTCTACA 57.338 36.000 3.77 0.00 0.00 2.74
392 398 9.893634 TTTCCGAATGAAGGTGAGTAATAAATA 57.106 29.630 0.00 0.00 33.63 1.40
393 399 8.801882 TTTCCGAATGAAGGTGAGTAATAAAT 57.198 30.769 0.00 0.00 33.63 1.40
394 400 8.801882 ATTTCCGAATGAAGGTGAGTAATAAA 57.198 30.769 0.00 0.00 33.63 1.40
397 403 8.980481 AATATTTCCGAATGAAGGTGAGTAAT 57.020 30.769 0.00 0.00 33.63 1.89
398 404 8.673711 CAAATATTTCCGAATGAAGGTGAGTAA 58.326 33.333 0.00 0.00 33.63 2.24
399 405 7.827236 ACAAATATTTCCGAATGAAGGTGAGTA 59.173 33.333 0.00 0.00 33.63 2.59
400 406 6.659242 ACAAATATTTCCGAATGAAGGTGAGT 59.341 34.615 0.00 0.00 33.63 3.41
401 407 7.088589 ACAAATATTTCCGAATGAAGGTGAG 57.911 36.000 0.00 0.00 33.63 3.51
402 408 6.183360 CGACAAATATTTCCGAATGAAGGTGA 60.183 38.462 11.89 0.00 33.63 4.02
403 409 5.965334 CGACAAATATTTCCGAATGAAGGTG 59.035 40.000 11.89 0.00 33.63 4.00
404 410 5.646360 ACGACAAATATTTCCGAATGAAGGT 59.354 36.000 20.06 4.03 33.63 3.50
405 411 6.119144 ACGACAAATATTTCCGAATGAAGG 57.881 37.500 20.06 1.30 33.63 3.46
406 412 8.126871 TCTACGACAAATATTTCCGAATGAAG 57.873 34.615 20.06 11.68 33.63 3.02
407 413 8.481974 TTCTACGACAAATATTTCCGAATGAA 57.518 30.769 20.06 16.64 0.00 2.57
408 414 8.481974 TTTCTACGACAAATATTTCCGAATGA 57.518 30.769 20.06 13.44 0.00 2.57
409 415 9.158364 CATTTCTACGACAAATATTTCCGAATG 57.842 33.333 20.06 15.63 0.00 2.67
410 416 9.104965 TCATTTCTACGACAAATATTTCCGAAT 57.895 29.630 20.06 10.32 0.00 3.34
411 417 8.481974 TCATTTCTACGACAAATATTTCCGAA 57.518 30.769 20.06 8.97 0.00 4.30
412 418 8.481974 TTCATTTCTACGACAAATATTTCCGA 57.518 30.769 20.06 8.13 0.00 4.55
463 469 9.613957 CGAAGAACGAATGTATCTAGATGTATT 57.386 33.333 15.79 14.21 45.77 1.89
464 470 8.237949 CCGAAGAACGAATGTATCTAGATGTAT 58.762 37.037 15.79 6.61 45.77 2.29
465 471 7.308408 CCCGAAGAACGAATGTATCTAGATGTA 60.308 40.741 15.79 4.44 45.77 2.29
466 472 6.439599 CCGAAGAACGAATGTATCTAGATGT 58.560 40.000 15.79 0.32 45.77 3.06
467 473 5.859114 CCCGAAGAACGAATGTATCTAGATG 59.141 44.000 15.79 0.00 45.77 2.90
468 474 5.565045 GCCCGAAGAACGAATGTATCTAGAT 60.565 44.000 10.73 10.73 45.77 1.98
469 475 4.261489 GCCCGAAGAACGAATGTATCTAGA 60.261 45.833 0.00 0.00 45.77 2.43
470 476 3.982058 GCCCGAAGAACGAATGTATCTAG 59.018 47.826 0.00 0.00 45.77 2.43
471 477 3.382227 TGCCCGAAGAACGAATGTATCTA 59.618 43.478 0.00 0.00 45.77 1.98
472 478 2.167693 TGCCCGAAGAACGAATGTATCT 59.832 45.455 0.00 0.00 45.77 1.98
473 479 2.546778 TGCCCGAAGAACGAATGTATC 58.453 47.619 0.00 0.00 45.77 2.24
474 480 2.684001 TGCCCGAAGAACGAATGTAT 57.316 45.000 0.00 0.00 45.77 2.29
475 481 2.289195 ACTTGCCCGAAGAACGAATGTA 60.289 45.455 0.00 0.00 45.77 2.29
476 482 1.156736 CTTGCCCGAAGAACGAATGT 58.843 50.000 0.00 0.00 45.77 2.71
477 483 1.156736 ACTTGCCCGAAGAACGAATG 58.843 50.000 0.00 0.00 45.77 2.67
478 484 2.754946 TACTTGCCCGAAGAACGAAT 57.245 45.000 0.00 0.00 45.77 3.34
479 485 2.754946 ATACTTGCCCGAAGAACGAA 57.245 45.000 0.00 0.00 45.77 3.85
480 486 2.754946 AATACTTGCCCGAAGAACGA 57.245 45.000 0.00 0.00 45.77 3.85
481 487 3.723835 CGAAAATACTTGCCCGAAGAACG 60.724 47.826 0.00 0.00 42.18 3.95
482 488 3.425758 CCGAAAATACTTGCCCGAAGAAC 60.426 47.826 0.00 0.00 35.42 3.01
483 489 2.745281 CCGAAAATACTTGCCCGAAGAA 59.255 45.455 0.00 0.00 35.42 2.52
484 490 2.027929 TCCGAAAATACTTGCCCGAAGA 60.028 45.455 0.00 0.00 35.42 2.87
485 491 2.095372 GTCCGAAAATACTTGCCCGAAG 59.905 50.000 0.00 0.00 37.73 3.79
486 492 2.078392 GTCCGAAAATACTTGCCCGAA 58.922 47.619 0.00 0.00 0.00 4.30
487 493 1.729284 GTCCGAAAATACTTGCCCGA 58.271 50.000 0.00 0.00 0.00 5.14
488 494 0.372334 CGTCCGAAAATACTTGCCCG 59.628 55.000 0.00 0.00 0.00 6.13
489 495 0.730840 CCGTCCGAAAATACTTGCCC 59.269 55.000 0.00 0.00 0.00 5.36
490 496 1.664151 CTCCGTCCGAAAATACTTGCC 59.336 52.381 0.00 0.00 0.00 4.52
491 497 2.603560 CTCTCCGTCCGAAAATACTTGC 59.396 50.000 0.00 0.00 0.00 4.01
492 498 4.106029 TCTCTCCGTCCGAAAATACTTG 57.894 45.455 0.00 0.00 0.00 3.16
493 499 3.762823 ACTCTCTCCGTCCGAAAATACTT 59.237 43.478 0.00 0.00 0.00 2.24
494 500 3.354467 ACTCTCTCCGTCCGAAAATACT 58.646 45.455 0.00 0.00 0.00 2.12
495 501 3.779271 ACTCTCTCCGTCCGAAAATAC 57.221 47.619 0.00 0.00 0.00 1.89
496 502 6.095860 TCAAATACTCTCTCCGTCCGAAAATA 59.904 38.462 0.00 0.00 0.00 1.40
497 503 5.105473 TCAAATACTCTCTCCGTCCGAAAAT 60.105 40.000 0.00 0.00 0.00 1.82
498 504 4.219070 TCAAATACTCTCTCCGTCCGAAAA 59.781 41.667 0.00 0.00 0.00 2.29
499 505 3.760151 TCAAATACTCTCTCCGTCCGAAA 59.240 43.478 0.00 0.00 0.00 3.46
500 506 3.349927 TCAAATACTCTCTCCGTCCGAA 58.650 45.455 0.00 0.00 0.00 4.30
501 507 2.995283 TCAAATACTCTCTCCGTCCGA 58.005 47.619 0.00 0.00 0.00 4.55
502 508 3.633235 CATCAAATACTCTCTCCGTCCG 58.367 50.000 0.00 0.00 0.00 4.79
503 509 3.385577 GCATCAAATACTCTCTCCGTCC 58.614 50.000 0.00 0.00 0.00 4.79
504 510 3.181475 TGGCATCAAATACTCTCTCCGTC 60.181 47.826 0.00 0.00 0.00 4.79
505 511 2.766263 TGGCATCAAATACTCTCTCCGT 59.234 45.455 0.00 0.00 0.00 4.69
506 512 3.181471 ACTGGCATCAAATACTCTCTCCG 60.181 47.826 0.00 0.00 0.00 4.63
507 513 4.414337 ACTGGCATCAAATACTCTCTCC 57.586 45.455 0.00 0.00 0.00 3.71
508 514 5.537188 CCTACTGGCATCAAATACTCTCTC 58.463 45.833 0.00 0.00 0.00 3.20
509 515 5.543507 CCTACTGGCATCAAATACTCTCT 57.456 43.478 0.00 0.00 0.00 3.10
534 540 3.497115 TGGCTCCAAGGGCACACA 61.497 61.111 0.00 0.00 36.85 3.72
541 547 2.092538 AGAAGATCATGTGGCTCCAAGG 60.093 50.000 0.00 0.00 0.00 3.61
566 572 7.292713 AGGGTATCGCTTTTTCCTTTAAAAA 57.707 32.000 0.00 0.00 43.20 1.94
567 573 6.904463 AGGGTATCGCTTTTTCCTTTAAAA 57.096 33.333 0.00 0.00 35.24 1.52
568 574 6.904463 AAGGGTATCGCTTTTTCCTTTAAA 57.096 33.333 0.00 0.00 32.78 1.52
569 575 6.904463 AAAGGGTATCGCTTTTTCCTTTAA 57.096 33.333 0.00 0.00 42.49 1.52
570 576 6.094464 GCTAAAGGGTATCGCTTTTTCCTTTA 59.906 38.462 14.80 10.65 42.49 1.85
571 577 5.105877 GCTAAAGGGTATCGCTTTTTCCTTT 60.106 40.000 14.80 9.62 42.49 3.11
572 578 4.398358 GCTAAAGGGTATCGCTTTTTCCTT 59.602 41.667 14.80 0.00 42.49 3.36
573 579 3.945921 GCTAAAGGGTATCGCTTTTTCCT 59.054 43.478 14.80 0.00 42.49 3.36
574 580 3.692593 TGCTAAAGGGTATCGCTTTTTCC 59.307 43.478 14.80 6.77 42.49 3.13
575 581 4.957759 TGCTAAAGGGTATCGCTTTTTC 57.042 40.909 14.80 9.12 42.49 2.29
578 1133 4.440112 GCAAATGCTAAAGGGTATCGCTTT 60.440 41.667 14.21 14.21 45.87 3.51
583 1138 5.582689 AACTGCAAATGCTAAAGGGTATC 57.417 39.130 6.97 0.00 42.66 2.24
585 1140 5.537188 CAAAACTGCAAATGCTAAAGGGTA 58.463 37.500 6.97 0.00 42.66 3.69
748 1306 2.125912 CCCGCAGTGAGTTCCGAG 60.126 66.667 0.00 0.00 0.00 4.63
764 1322 4.048470 GGAGACTTGGGGGTGGCC 62.048 72.222 0.00 0.00 0.00 5.36
776 1342 1.769465 GGATTCTTGGGGTAGGGAGAC 59.231 57.143 0.00 0.00 0.00 3.36
779 1345 0.423956 TGGGATTCTTGGGGTAGGGA 59.576 55.000 0.00 0.00 0.00 4.20
798 1364 0.321653 AAGTGGGAGCGCGATTCTTT 60.322 50.000 12.10 0.00 0.00 2.52
799 1365 0.741221 GAAGTGGGAGCGCGATTCTT 60.741 55.000 12.10 7.54 0.00 2.52
801 1367 1.153549 AGAAGTGGGAGCGCGATTC 60.154 57.895 12.10 0.00 0.00 2.52
903 1474 3.442625 CACACCGGAGAAGATGTACTGTA 59.557 47.826 9.46 0.00 0.00 2.74
904 1475 2.231478 CACACCGGAGAAGATGTACTGT 59.769 50.000 9.46 0.00 0.00 3.55
908 1479 0.535335 GGCACACCGGAGAAGATGTA 59.465 55.000 9.46 0.00 0.00 2.29
930 1501 4.344865 GGAAGGGAGCGGGTGCAA 62.345 66.667 0.21 0.00 46.23 4.08
951 1522 0.104855 TGCAGAGTTCAGCTGACGTT 59.895 50.000 18.03 4.55 35.39 3.99
1081 1652 1.201647 CAGGAACGACATCAGGTACGT 59.798 52.381 0.00 0.00 40.64 3.57
1287 1858 1.271379 TCGCAGTGAAAGGTGTCGTAT 59.729 47.619 0.00 0.00 0.00 3.06
1475 2067 4.162690 CTAGCACCCGACAGCCCC 62.163 72.222 0.00 0.00 0.00 5.80
1581 2173 0.529833 TACGACGGCGGGTTTTATCA 59.470 50.000 18.49 0.00 43.17 2.15
1640 2232 2.584391 AACGGAGTCAGACCCTGGC 61.584 63.158 0.00 0.00 45.00 4.85
1853 2548 4.436050 GGATACAGATGACAAACAGCAACG 60.436 45.833 0.00 0.00 37.37 4.10
1909 2797 7.118101 GGTGAAAACAACAATGCACATAATGAT 59.882 33.333 0.00 0.00 0.00 2.45
1978 2871 8.037758 AGTATCAAGTAGAGGTATGCATATTGC 58.962 37.037 10.16 2.33 45.29 3.56
2080 2981 2.489971 TCCGAAGTTGTACTTTGCCAG 58.510 47.619 0.00 0.00 38.80 4.85
2140 3222 9.753674 TTCTGGTGGTTCTTATTTTTCATAGAT 57.246 29.630 0.00 0.00 0.00 1.98
2456 3562 2.203070 GCAGGAGGTACATGGCGG 60.203 66.667 0.00 0.00 0.00 6.13
2819 3941 9.269453 GTGTAGAAATGGTGAAAAACTAGTACT 57.731 33.333 0.00 0.00 0.00 2.73
2858 3992 2.098934 GTGCCACGGATTGAAATGCATA 59.901 45.455 0.00 0.00 0.00 3.14
2941 4075 4.437930 GCCTTTAGTTTGCATCTGCTAGTG 60.438 45.833 3.53 0.00 42.66 2.74
2954 4088 0.961753 GTGCTGCCTGCCTTTAGTTT 59.038 50.000 0.00 0.00 42.00 2.66
3164 4299 5.221722 GCCACTTGATCTAGTCATGGGAATA 60.222 44.000 6.86 0.00 37.54 1.75
3206 4349 6.373005 TGAGAGGTTATTCACTGATTGGAA 57.627 37.500 0.00 0.00 0.00 3.53
3223 4366 6.549364 AGGAAACTGTATGAGACTATGAGAGG 59.451 42.308 0.00 0.00 41.13 3.69
3230 4373 5.016831 TGCAGAGGAAACTGTATGAGACTA 58.983 41.667 0.00 0.00 44.43 2.59
3231 4374 3.834813 TGCAGAGGAAACTGTATGAGACT 59.165 43.478 0.00 0.00 44.43 3.24
3232 4375 4.193826 TGCAGAGGAAACTGTATGAGAC 57.806 45.455 0.00 0.00 44.43 3.36
3233 4376 4.713814 AGATGCAGAGGAAACTGTATGAGA 59.286 41.667 0.00 0.00 44.43 3.27
3234 4377 5.021033 AGATGCAGAGGAAACTGTATGAG 57.979 43.478 0.00 0.00 44.43 2.90
3235 4378 6.552725 AGATAGATGCAGAGGAAACTGTATGA 59.447 38.462 0.00 0.00 44.43 2.15
3236 4379 6.757237 AGATAGATGCAGAGGAAACTGTATG 58.243 40.000 0.00 0.00 44.43 2.39
3237 4380 6.992664 AGATAGATGCAGAGGAAACTGTAT 57.007 37.500 0.00 0.00 44.43 2.29
3248 4391 5.010516 GGAAGAAGCAGTAGATAGATGCAGA 59.989 44.000 0.00 0.00 42.45 4.26
3280 4423 6.429385 AGAGGAAACAATGAGAACATGAGAAC 59.571 38.462 0.00 0.00 36.79 3.01
3281 4424 6.429078 CAGAGGAAACAATGAGAACATGAGAA 59.571 38.462 0.00 0.00 36.79 2.87
3313 4456 2.560105 AGCTCAAAATGGAAGCCTGAAC 59.440 45.455 0.00 0.00 0.00 3.18
3440 4583 7.776933 AGACATACATACAGCTGTTTACATG 57.223 36.000 27.06 23.23 0.00 3.21
3548 4691 4.711949 CAGTTCAGGCCTGCCGCT 62.712 66.667 28.91 20.74 41.95 5.52
3583 4726 2.368875 CAACCAACACTAGACAGGGTCT 59.631 50.000 0.00 4.13 45.54 3.85
3637 4783 5.755409 TCCTAGCCACAAGACAGAATTTA 57.245 39.130 0.00 0.00 0.00 1.40
3639 4785 4.681781 CGATCCTAGCCACAAGACAGAATT 60.682 45.833 0.00 0.00 0.00 2.17
3640 4786 3.181471 CGATCCTAGCCACAAGACAGAAT 60.181 47.826 0.00 0.00 0.00 2.40
3641 4787 2.166459 CGATCCTAGCCACAAGACAGAA 59.834 50.000 0.00 0.00 0.00 3.02
3642 4788 1.751351 CGATCCTAGCCACAAGACAGA 59.249 52.381 0.00 0.00 0.00 3.41
3643 4789 1.202463 CCGATCCTAGCCACAAGACAG 60.202 57.143 0.00 0.00 0.00 3.51
3644 4790 0.824109 CCGATCCTAGCCACAAGACA 59.176 55.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.