Multiple sequence alignment - TraesCS6D01G228000

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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 TraesCS6D01G228000 chr6D 100.000 3832 0 0 1 3832 319054099 319050268 0.000000e+00 7077.0
1 TraesCS6D01G228000 chr6D 95.495 111 5 0 399 509 319053582 319053472 1.250000e-40 178.0
2 TraesCS6D01G228000 chr6D 95.495 111 5 0 518 628 319053701 319053591 1.250000e-40 178.0
3 TraesCS6D01G228000 chr6D 100.000 70 0 0 4289 4358 319049811 319049742 3.540000e-26 130.0
4 TraesCS6D01G228000 chr6D 100.000 29 0 0 2991 3019 124596697 124596725 2.000000e-03 54.7
5 TraesCS6D01G228000 chr6A 96.142 3214 81 20 651 3832 457020500 457017298 0.000000e+00 5208.0
6 TraesCS6D01G228000 chr6B 95.325 1861 67 10 527 2371 504157691 504159547 0.000000e+00 2937.0
7 TraesCS6D01G228000 chr6B 97.741 1151 19 3 2368 3515 504159627 504160773 0.000000e+00 1975.0
8 TraesCS6D01G228000 chr6B 88.889 405 40 5 1 404 504156006 504156406 1.090000e-135 494.0
9 TraesCS6D01G228000 chr6B 92.857 308 17 3 3530 3832 504166090 504166397 4.000000e-120 442.0
10 TraesCS6D01G228000 chr6B 92.537 67 5 0 4289 4355 504166465 504166531 3.590000e-16 97.1
11 TraesCS6D01G228000 chr6B 100.000 28 0 0 2991 3018 219571324 219571351 8.000000e-03 52.8
12 TraesCS6D01G228000 chr2B 77.882 963 184 18 1084 2030 614398820 614397871 4.890000e-159 571.0
13 TraesCS6D01G228000 chr2B 79.234 809 147 14 1084 1880 614503778 614502979 1.070000e-150 544.0
14 TraesCS6D01G228000 chr2B 85.156 128 19 0 1461 1588 613902342 613902469 9.830000e-27 132.0
15 TraesCS6D01G228000 chr2D 77.709 969 187 18 1078 2030 521410911 521411866 2.270000e-157 566.0
16 TraesCS6D01G228000 chr2D 74.058 451 87 20 1448 1880 521568141 521567703 1.620000e-34 158.0
17 TraesCS6D01G228000 chr2D 83.582 134 22 0 1461 1594 521587732 521587599 4.580000e-25 126.0
18 TraesCS6D01G228000 chr2A 77.547 962 189 16 1084 2030 666292870 666291921 4.920000e-154 555.0
19 TraesCS6D01G228000 chr4A 85.955 178 25 0 3655 3832 581919450 581919273 1.600000e-44 191.0
20 TraesCS6D01G228000 chr3A 83.708 178 25 3 3655 3832 712633004 712632831 9.700000e-37 165.0
21 TraesCS6D01G228000 chr3A 90.110 91 9 0 3742 3832 313495959 313496049 7.660000e-23 119.0
22 TraesCS6D01G228000 chr7D 97.500 40 0 1 4289 4327 96456916 96456877 2.810000e-07 67.6
23 TraesCS6D01G228000 chr4D 84.286 70 9 2 4290 4358 101443707 101443775 2.810000e-07 67.6
24 TraesCS6D01G228000 chrUn 100.000 30 0 0 4298 4327 89914390 89914419 6.090000e-04 56.5
25 TraesCS6D01G228000 chrUn 100.000 30 0 0 4298 4327 89982918 89982889 6.090000e-04 56.5


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 TraesCS6D01G228000 chr6D 319049742 319054099 4357 True 1890.75 7077 97.7475 1 4358 4 chr6D.!!$R1 4357
1 TraesCS6D01G228000 chr6A 457017298 457020500 3202 True 5208.00 5208 96.1420 651 3832 1 chr6A.!!$R1 3181
2 TraesCS6D01G228000 chr6B 504156006 504160773 4767 False 1802.00 2937 93.9850 1 3515 3 chr6B.!!$F2 3514
3 TraesCS6D01G228000 chr2B 614397871 614398820 949 True 571.00 571 77.8820 1084 2030 1 chr2B.!!$R1 946
4 TraesCS6D01G228000 chr2B 614502979 614503778 799 True 544.00 544 79.2340 1084 1880 1 chr2B.!!$R2 796
5 TraesCS6D01G228000 chr2D 521410911 521411866 955 False 566.00 566 77.7090 1078 2030 1 chr2D.!!$F1 952
6 TraesCS6D01G228000 chr2A 666291921 666292870 949 True 555.00 555 77.5470 1084 2030 1 chr2A.!!$R1 946

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
494 495 0.102481 AAGCCGCACCACGTATCTAG 59.898 55.0 0.0 0.0 41.42 2.43 F
964 2147 0.108585 TGCATATTTCTCTCGGCCCC 59.891 55.0 0.0 0.0 0.00 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2384 3662 1.067060 CGTACGCCATGATCTTCTCCA 59.933 52.381 0.52 0.0 0.00 3.86 R
3437 4718 0.680061 TGTACCATACACACCACGCA 59.320 50.000 0.00 0.0 32.89 5.24 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
33 34 0.240945 AGAATTTGCAAGTTCGCCCG 59.759 50.000 23.81 0.00 0.00 6.13
42 43 4.415332 GTTCGCCCGTCGCTGAGA 62.415 66.667 0.00 0.00 38.27 3.27
45 46 4.838486 CGCCCGTCGCTGAGAGTC 62.838 72.222 0.00 0.00 34.21 3.36
46 47 4.500116 GCCCGTCGCTGAGAGTCC 62.500 72.222 0.00 0.00 0.00 3.85
72 73 2.026262 AGTGGAGGTGCGGAATATTTGT 60.026 45.455 0.00 0.00 0.00 2.83
77 78 2.676342 AGGTGCGGAATATTTGTCGAAC 59.324 45.455 9.80 9.13 0.00 3.95
104 105 0.538516 TTGCATGGCGGTGGTAAGTT 60.539 50.000 0.00 0.00 0.00 2.66
139 140 2.569134 GGTCAGTCGCGAGAAGCT 59.431 61.111 10.24 0.00 45.01 3.74
154 155 3.854459 GCTAGAGCCAACGCACGC 61.854 66.667 0.00 0.00 37.52 5.34
155 156 3.545481 CTAGAGCCAACGCACGCG 61.545 66.667 10.36 10.36 46.03 6.01
178 179 1.427419 GCAATATCGGTGCGTTGCA 59.573 52.632 9.48 0.00 44.63 4.08
195 196 0.248377 GCAAGTCGCAGATGCCAATC 60.248 55.000 0.00 0.00 36.62 2.67
225 226 6.605594 TGAGTTTGTACAATCTGGAAAACCTT 59.394 34.615 21.09 0.00 0.00 3.50
237 238 9.933723 AATCTGGAAAACCTTAATGAATTCAAG 57.066 29.630 13.09 5.43 0.00 3.02
239 240 6.155827 TGGAAAACCTTAATGAATTCAAGCG 58.844 36.000 13.09 2.95 0.00 4.68
264 265 7.962373 CGATGCTTATTCAAATGTTACAACTCA 59.038 33.333 0.00 0.00 0.00 3.41
276 277 8.798859 AATGTTACAACTCAGCATAGAATCTT 57.201 30.769 0.00 0.00 0.00 2.40
281 282 9.719355 TTACAACTCAGCATAGAATCTTTTGTA 57.281 29.630 0.00 0.00 0.00 2.41
311 312 9.847224 ATTTATACTCTTATGTTCCCGTCAAAT 57.153 29.630 0.00 0.00 0.00 2.32
319 320 9.675464 TCTTATGTTCCCGTCAAATTTTATAGT 57.325 29.630 0.00 0.00 0.00 2.12
345 346 6.508030 TTCCTACCTATGTAATCCATGCAA 57.492 37.500 0.00 0.00 34.86 4.08
353 354 7.345392 ACCTATGTAATCCATGCAATTTCCTTT 59.655 33.333 0.00 0.00 34.86 3.11
355 356 6.357579 TGTAATCCATGCAATTTCCTTTGT 57.642 33.333 0.00 0.00 0.00 2.83
361 362 6.767456 TCCATGCAATTTCCTTTGTTTATGT 58.233 32.000 0.00 0.00 0.00 2.29
366 367 8.359060 TGCAATTTCCTTTGTTTATGTTGTAC 57.641 30.769 0.00 0.00 0.00 2.90
371 372 6.922247 TCCTTTGTTTATGTTGTACGACAA 57.078 33.333 19.71 6.97 35.42 3.18
393 394 8.340618 ACAATTTGATGTGTGCTAGATTACTT 57.659 30.769 2.79 0.00 30.82 2.24
404 405 4.065789 GCTAGATTACTTGTGGGTATGCC 58.934 47.826 0.00 0.00 0.00 4.40
406 407 2.504175 AGATTACTTGTGGGTATGCCGT 59.496 45.455 0.00 0.00 34.97 5.68
407 408 2.863132 TTACTTGTGGGTATGCCGTT 57.137 45.000 0.00 0.00 34.97 4.44
408 409 2.863132 TACTTGTGGGTATGCCGTTT 57.137 45.000 0.00 0.00 34.97 3.60
409 410 1.243902 ACTTGTGGGTATGCCGTTTG 58.756 50.000 0.00 0.00 34.97 2.93
410 411 1.202830 ACTTGTGGGTATGCCGTTTGA 60.203 47.619 0.00 0.00 34.97 2.69
412 413 2.208132 TGTGGGTATGCCGTTTGAAT 57.792 45.000 0.00 0.00 34.97 2.57
413 414 2.520069 TGTGGGTATGCCGTTTGAATT 58.480 42.857 0.00 0.00 34.97 2.17
414 415 2.894126 TGTGGGTATGCCGTTTGAATTT 59.106 40.909 0.00 0.00 34.97 1.82
415 416 4.079970 TGTGGGTATGCCGTTTGAATTTA 58.920 39.130 0.00 0.00 34.97 1.40
416 417 4.082679 TGTGGGTATGCCGTTTGAATTTAC 60.083 41.667 0.00 0.00 34.97 2.01
417 418 3.127203 TGGGTATGCCGTTTGAATTTACG 59.873 43.478 0.00 0.00 37.50 3.18
437 438 9.978044 ATTTACGGTACTTAATAATGGAGACTC 57.022 33.333 0.00 0.00 0.00 3.36
439 440 7.598759 ACGGTACTTAATAATGGAGACTCAT 57.401 36.000 4.53 0.00 0.00 2.90
440 441 7.434492 ACGGTACTTAATAATGGAGACTCATG 58.566 38.462 4.53 0.00 0.00 3.07
441 442 7.069578 ACGGTACTTAATAATGGAGACTCATGT 59.930 37.037 4.53 0.00 0.00 3.21
442 443 8.573885 CGGTACTTAATAATGGAGACTCATGTA 58.426 37.037 4.53 0.00 0.00 2.29
449 450 5.563876 AATGGAGACTCATGTATGATGCT 57.436 39.130 4.53 0.00 36.02 3.79
450 451 4.597404 TGGAGACTCATGTATGATGCTC 57.403 45.455 4.53 12.18 36.73 4.26
452 453 2.985809 GAGACTCATGTATGATGCTCGC 59.014 50.000 0.00 0.00 36.02 5.03
453 454 2.627221 AGACTCATGTATGATGCTCGCT 59.373 45.455 0.00 0.00 36.02 4.93
454 455 2.985809 GACTCATGTATGATGCTCGCTC 59.014 50.000 0.00 0.00 36.02 5.03
455 456 2.627221 ACTCATGTATGATGCTCGCTCT 59.373 45.455 0.00 0.00 36.02 4.09
456 457 3.069300 ACTCATGTATGATGCTCGCTCTT 59.931 43.478 0.00 0.00 36.02 2.85
457 458 4.056740 CTCATGTATGATGCTCGCTCTTT 58.943 43.478 0.00 0.00 36.02 2.52
458 459 4.053983 TCATGTATGATGCTCGCTCTTTC 58.946 43.478 0.00 0.00 0.00 2.62
459 460 2.463876 TGTATGATGCTCGCTCTTTCG 58.536 47.619 0.00 0.00 0.00 3.46
460 461 2.099098 TGTATGATGCTCGCTCTTTCGA 59.901 45.455 0.00 0.00 36.94 3.71
466 467 3.056458 TCGCTCTTTCGAGGGCAA 58.944 55.556 0.00 0.00 46.52 4.52
467 468 1.596934 TCGCTCTTTCGAGGGCAAT 59.403 52.632 0.00 0.00 46.52 3.56
469 470 1.431036 GCTCTTTCGAGGGCAATGC 59.569 57.895 0.00 0.00 37.75 3.56
470 471 1.717937 CTCTTTCGAGGGCAATGCG 59.282 57.895 0.00 0.00 33.51 4.73
471 472 2.100991 CTTTCGAGGGCAATGCGC 59.899 61.111 14.75 14.75 41.91 6.09
472 473 3.723364 CTTTCGAGGGCAATGCGCG 62.723 63.158 16.46 11.50 46.18 6.86
473 474 4.751093 TTCGAGGGCAATGCGCGA 62.751 61.111 12.10 13.59 46.18 5.87
476 477 3.430862 GAGGGCAATGCGCGACAA 61.431 61.111 12.10 0.00 46.18 3.18
477 478 3.386867 GAGGGCAATGCGCGACAAG 62.387 63.158 12.10 6.16 46.18 3.16
490 491 1.740296 GACAAGCCGCACCACGTAT 60.740 57.895 0.00 0.00 41.42 3.06
491 492 1.693083 GACAAGCCGCACCACGTATC 61.693 60.000 0.00 0.00 41.42 2.24
492 493 1.447838 CAAGCCGCACCACGTATCT 60.448 57.895 0.00 0.00 41.42 1.98
494 495 0.102481 AAGCCGCACCACGTATCTAG 59.898 55.000 0.00 0.00 41.42 2.43
495 496 1.035932 AGCCGCACCACGTATCTAGT 61.036 55.000 0.00 0.00 41.42 2.57
496 497 0.664761 GCCGCACCACGTATCTAGTA 59.335 55.000 0.00 0.00 41.42 1.82
497 498 1.598924 GCCGCACCACGTATCTAGTAC 60.599 57.143 0.00 0.00 41.42 2.73
498 499 1.945394 CCGCACCACGTATCTAGTACT 59.055 52.381 0.00 0.00 41.42 2.73
499 500 3.133691 CCGCACCACGTATCTAGTACTA 58.866 50.000 1.89 1.89 41.42 1.82
502 503 4.689812 CGCACCACGTATCTAGTACTATCT 59.310 45.833 2.33 0.00 36.87 1.98
504 505 5.122082 GCACCACGTATCTAGTACTATCTCC 59.878 48.000 2.33 0.00 0.00 3.71
505 506 5.348179 CACCACGTATCTAGTACTATCTCCG 59.652 48.000 2.33 6.81 0.00 4.63
506 507 5.011533 ACCACGTATCTAGTACTATCTCCGT 59.988 44.000 2.33 7.41 0.00 4.69
507 508 5.576384 CCACGTATCTAGTACTATCTCCGTC 59.424 48.000 2.33 0.00 0.00 4.79
508 509 6.389091 CACGTATCTAGTACTATCTCCGTCT 58.611 44.000 2.33 0.00 0.00 4.18
509 510 6.867816 CACGTATCTAGTACTATCTCCGTCTT 59.132 42.308 2.33 0.00 0.00 3.01
510 511 8.026026 CACGTATCTAGTACTATCTCCGTCTTA 58.974 40.741 2.33 0.00 0.00 2.10
511 512 8.580720 ACGTATCTAGTACTATCTCCGTCTTAA 58.419 37.037 2.33 0.00 0.00 1.85
512 513 9.416794 CGTATCTAGTACTATCTCCGTCTTAAA 57.583 37.037 2.33 0.00 0.00 1.52
516 517 9.842775 TCTAGTACTATCTCCGTCTTAAAATGA 57.157 33.333 2.33 0.00 0.00 2.57
518 519 8.522542 AGTACTATCTCCGTCTTAAAATGAGT 57.477 34.615 0.00 0.00 0.00 3.41
519 520 9.624373 AGTACTATCTCCGTCTTAAAATGAGTA 57.376 33.333 0.00 0.00 0.00 2.59
523 524 5.972935 TCTCCGTCTTAAAATGAGTATGCA 58.027 37.500 0.00 0.00 0.00 3.96
524 525 6.042777 TCTCCGTCTTAAAATGAGTATGCAG 58.957 40.000 0.00 0.00 0.00 4.41
536 1699 8.673626 AAATGAGTATGCAGTTTGAATTTACG 57.326 30.769 0.00 0.00 0.00 3.18
540 1703 7.068692 AGTATGCAGTTTGAATTTACGGTAC 57.931 36.000 0.00 0.00 0.00 3.34
559 1722 8.928270 ACGGTACTTAATAATGAAGACTCAAG 57.072 34.615 0.00 0.00 34.49 3.02
568 1731 4.833478 ATGAAGACTCAAGTATGGTGCT 57.167 40.909 0.00 0.00 34.49 4.40
569 1732 4.193826 TGAAGACTCAAGTATGGTGCTC 57.806 45.455 0.00 0.00 0.00 4.26
571 1734 1.134965 AGACTCAAGTATGGTGCTCGC 60.135 52.381 0.00 0.00 0.00 5.03
573 1736 1.134965 ACTCAAGTATGGTGCTCGCTC 60.135 52.381 0.00 0.00 0.00 5.03
574 1737 1.135915 CTCAAGTATGGTGCTCGCTCT 59.864 52.381 0.00 0.00 0.00 4.09
586 1749 1.596934 TCGCTCTTTCGAGGGCAAT 59.403 52.632 0.00 0.00 46.52 3.56
588 1751 1.431036 GCTCTTTCGAGGGCAATGC 59.569 57.895 0.00 0.00 37.75 3.56
623 1786 4.754114 CACCACGTATCTAGTACTACCTCC 59.246 50.000 0.00 0.00 0.00 4.30
624 1787 3.993081 CCACGTATCTAGTACTACCTCCG 59.007 52.174 0.00 2.53 0.00 4.63
625 1788 4.502259 CCACGTATCTAGTACTACCTCCGT 60.502 50.000 0.00 3.14 0.00 4.69
626 1789 4.683781 CACGTATCTAGTACTACCTCCGTC 59.316 50.000 0.00 0.00 0.00 4.79
627 1790 4.586841 ACGTATCTAGTACTACCTCCGTCT 59.413 45.833 0.00 0.00 0.00 4.18
628 1791 5.160641 CGTATCTAGTACTACCTCCGTCTC 58.839 50.000 0.00 0.00 0.00 3.36
646 1809 5.050769 CCGTCTCGTCTCAAAATATGAATGG 60.051 44.000 0.00 0.00 37.67 3.16
710 1886 2.149494 CGCGTTGAAATCGATCTCTACG 59.851 50.000 24.81 24.81 41.59 3.51
714 1890 4.561606 CGTTGAAATCGATCTCTACGGTTT 59.438 41.667 22.49 1.61 44.74 3.27
780 1956 2.096496 CGGCATTTCCATCTCAGTGTTC 59.904 50.000 0.00 0.00 34.01 3.18
887 2067 1.200020 CAAACAGTCCGCCTCAAATCC 59.800 52.381 0.00 0.00 0.00 3.01
916 2096 2.028045 CGTTGCTATATTAGGCGCATCG 59.972 50.000 10.83 0.00 38.61 3.84
959 2142 4.034510 GGGACAAGTTGCATATTTCTCTCG 59.965 45.833 1.81 0.00 0.00 4.04
960 2143 4.034510 GGACAAGTTGCATATTTCTCTCGG 59.965 45.833 1.81 0.00 0.00 4.63
963 2146 1.604278 GTTGCATATTTCTCTCGGCCC 59.396 52.381 0.00 0.00 0.00 5.80
964 2147 0.108585 TGCATATTTCTCTCGGCCCC 59.891 55.000 0.00 0.00 0.00 5.80
966 2149 1.059913 CATATTTCTCTCGGCCCCCT 58.940 55.000 0.00 0.00 0.00 4.79
967 2150 1.421646 CATATTTCTCTCGGCCCCCTT 59.578 52.381 0.00 0.00 0.00 3.95
968 2151 0.837272 TATTTCTCTCGGCCCCCTTG 59.163 55.000 0.00 0.00 0.00 3.61
969 2152 1.926426 ATTTCTCTCGGCCCCCTTGG 61.926 60.000 0.00 0.00 37.09 3.61
1253 2442 1.609555 CCTCATCTACTCCTACCGCAC 59.390 57.143 0.00 0.00 0.00 5.34
1638 2833 3.455469 GGGATCGACGACCCGGTT 61.455 66.667 16.37 0.00 36.56 4.44
2221 3416 1.066430 AGCAAGTCGCCGGAAAGATAA 60.066 47.619 5.05 0.00 44.04 1.75
2223 3418 2.286418 GCAAGTCGCCGGAAAGATAATG 60.286 50.000 5.05 3.32 32.94 1.90
2384 3662 3.074412 CGCAAGTAGAATCCAAGTGGTT 58.926 45.455 0.00 0.00 36.34 3.67
3435 4716 3.618997 CGGTGGGTTTGTAAGCAGTAGAT 60.619 47.826 0.00 0.00 0.00 1.98
3436 4717 4.382254 CGGTGGGTTTGTAAGCAGTAGATA 60.382 45.833 0.00 0.00 0.00 1.98
3437 4718 5.681639 GGTGGGTTTGTAAGCAGTAGATAT 58.318 41.667 0.00 0.00 0.00 1.63
3452 4734 3.111853 AGATATGCGTGGTGTGTATGG 57.888 47.619 0.00 0.00 0.00 2.74
3496 4778 4.532834 TGGTAAAGTTCTGGCAAAACTCT 58.467 39.130 6.68 0.00 35.96 3.24
3497 4779 4.578928 TGGTAAAGTTCTGGCAAAACTCTC 59.421 41.667 6.68 1.03 35.96 3.20
3524 4806 0.809385 GCTACGCAGGTGACTACTGA 59.191 55.000 0.00 0.00 40.21 3.41
3525 4807 1.202200 GCTACGCAGGTGACTACTGAG 60.202 57.143 0.00 0.00 40.21 3.35
3526 4808 2.357075 CTACGCAGGTGACTACTGAGA 58.643 52.381 3.30 0.00 40.21 3.27
3528 4810 2.171840 ACGCAGGTGACTACTGAGAAT 58.828 47.619 3.30 0.00 40.21 2.40
3565 4864 0.605319 TTTGAAGGCTACGCAGGTGG 60.605 55.000 0.00 0.00 0.00 4.61
3696 4998 5.949952 AGTCGCCTAAAAATAGAATTTGGGT 59.050 36.000 3.82 0.00 39.73 4.51
3713 5015 6.588719 TTTGGGTCAGTCAATTTTCATAGG 57.411 37.500 0.00 0.00 0.00 2.57
3719 5021 7.281100 GGGTCAGTCAATTTTCATAGGAAGTAG 59.719 40.741 0.00 0.00 33.82 2.57
3721 5023 8.874816 GTCAGTCAATTTTCATAGGAAGTAGAC 58.125 37.037 0.00 0.00 33.82 2.59
3779 5081 0.767375 GGAGAAGCTGCCCCATGATA 59.233 55.000 0.00 0.00 0.00 2.15
3787 5089 5.627182 AGCTGCCCCATGATATATCTTAG 57.373 43.478 13.79 1.15 0.00 2.18
3792 5094 4.141390 GCCCCATGATATATCTTAGGGTGG 60.141 50.000 23.96 15.19 34.44 4.61
3796 5098 4.826274 TGATATATCTTAGGGTGGCAGC 57.174 45.455 13.79 8.47 0.00 5.25
3814 5116 3.741249 CAGCTTGCCACATGATCTATCT 58.259 45.455 0.00 0.00 0.00 1.98
4330 5632 4.382541 GGTTGGGGGAGGGCCAAG 62.383 72.222 6.18 0.00 35.15 3.61
4331 5633 3.590574 GTTGGGGGAGGGCCAAGT 61.591 66.667 6.18 0.00 35.15 3.16
4332 5634 3.589542 TTGGGGGAGGGCCAAGTG 61.590 66.667 6.18 0.00 35.15 3.16
4350 5652 4.735132 GCGAGGCTGGCACGTGTA 62.735 66.667 18.38 5.94 0.00 2.90
4351 5653 2.507102 CGAGGCTGGCACGTGTAG 60.507 66.667 18.38 16.35 0.00 2.74
4352 5654 2.815647 GAGGCTGGCACGTGTAGC 60.816 66.667 27.75 27.75 36.74 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.358851 CGAACTTGCAAATTCTGGTTTGA 58.641 39.130 17.60 0.00 40.64 2.69
33 34 1.271102 ACTTCTTGGACTCTCAGCGAC 59.729 52.381 0.00 0.00 0.00 5.19
46 47 0.250295 TTCCGCACCTCCACTTCTTG 60.250 55.000 0.00 0.00 0.00 3.02
59 60 2.933906 GAGGTTCGACAAATATTCCGCA 59.066 45.455 0.00 0.00 0.00 5.69
72 73 2.954684 ATGCAAGCCCGAGGTTCGA 61.955 57.895 0.00 0.00 43.74 3.71
111 112 4.265056 ACTGACCCACAACGCCCC 62.265 66.667 0.00 0.00 0.00 5.80
117 118 1.740332 TTCTCGCGACTGACCCACAA 61.740 55.000 3.71 0.00 0.00 3.33
119 120 1.444553 CTTCTCGCGACTGACCCAC 60.445 63.158 3.71 0.00 0.00 4.61
154 155 1.154599 GCACCGATATTGCGATGCG 60.155 57.895 0.00 0.35 41.46 4.73
155 156 4.826600 GCACCGATATTGCGATGC 57.173 55.556 0.00 0.00 44.39 3.91
160 161 0.179176 TTGCAACGCACCGATATTGC 60.179 50.000 0.00 0.94 46.08 3.56
161 162 1.130373 ACTTGCAACGCACCGATATTG 59.870 47.619 0.00 0.00 38.71 1.90
178 179 0.749454 GGGATTGGCATCTGCGACTT 60.749 55.000 0.00 0.00 43.26 3.01
185 186 1.293062 ACTCACTGGGATTGGCATCT 58.707 50.000 0.00 0.00 0.00 2.90
195 196 3.753272 CCAGATTGTACAAACTCACTGGG 59.247 47.826 24.62 16.71 36.71 4.45
237 238 6.747280 AGTTGTAACATTTGAATAAGCATCGC 59.253 34.615 0.00 0.00 0.00 4.58
239 240 9.282247 CTGAGTTGTAACATTTGAATAAGCATC 57.718 33.333 0.00 0.00 0.00 3.91
257 258 8.798859 ATACAAAAGATTCTATGCTGAGTTGT 57.201 30.769 0.00 0.00 0.00 3.32
281 282 9.490379 GACGGGAACATAAGAGTATAAATGAAT 57.510 33.333 0.00 0.00 0.00 2.57
318 319 8.100791 TGCATGGATTACATAGGTAGGAAATAC 58.899 37.037 0.00 0.00 37.84 1.89
319 320 8.213489 TGCATGGATTACATAGGTAGGAAATA 57.787 34.615 0.00 0.00 37.84 1.40
320 321 7.090319 TGCATGGATTACATAGGTAGGAAAT 57.910 36.000 0.00 0.00 37.84 2.17
324 325 7.094205 GGAAATTGCATGGATTACATAGGTAGG 60.094 40.741 0.00 0.00 37.84 3.18
333 334 7.671495 AAACAAAGGAAATTGCATGGATTAC 57.329 32.000 0.00 0.00 33.52 1.89
335 336 7.884354 ACATAAACAAAGGAAATTGCATGGATT 59.116 29.630 0.00 0.00 33.52 3.01
341 342 7.168302 CGTACAACATAAACAAAGGAAATTGCA 59.832 33.333 0.00 0.00 33.52 4.08
345 346 7.932335 TGTCGTACAACATAAACAAAGGAAAT 58.068 30.769 0.00 0.00 0.00 2.17
353 354 8.346300 ACATCAAATTGTCGTACAACATAAACA 58.654 29.630 0.00 0.00 41.40 2.83
355 356 8.346300 ACACATCAAATTGTCGTACAACATAAA 58.654 29.630 0.00 0.00 41.40 1.40
361 362 4.274705 AGCACACATCAAATTGTCGTACAA 59.725 37.500 0.00 3.49 42.95 2.41
366 367 4.926860 TCTAGCACACATCAAATTGTCG 57.073 40.909 0.00 0.00 0.00 4.35
371 372 7.148188 CCACAAGTAATCTAGCACACATCAAAT 60.148 37.037 0.00 0.00 0.00 2.32
393 394 2.208132 ATTCAAACGGCATACCCACA 57.792 45.000 0.00 0.00 0.00 4.17
412 413 8.970020 TGAGTCTCCATTATTAAGTACCGTAAA 58.030 33.333 0.00 0.00 0.00 2.01
413 414 8.523915 TGAGTCTCCATTATTAAGTACCGTAA 57.476 34.615 0.00 0.00 0.00 3.18
414 415 8.573885 CATGAGTCTCCATTATTAAGTACCGTA 58.426 37.037 0.00 0.00 0.00 4.02
415 416 7.069578 ACATGAGTCTCCATTATTAAGTACCGT 59.930 37.037 0.00 0.00 0.00 4.83
416 417 7.434492 ACATGAGTCTCCATTATTAAGTACCG 58.566 38.462 0.00 0.00 0.00 4.02
422 423 9.440773 GCATCATACATGAGTCTCCATTATTAA 57.559 33.333 0.00 0.00 40.64 1.40
423 424 8.819845 AGCATCATACATGAGTCTCCATTATTA 58.180 33.333 0.00 0.00 40.64 0.98
424 425 7.687388 AGCATCATACATGAGTCTCCATTATT 58.313 34.615 0.00 0.00 40.64 1.40
425 426 7.255199 AGCATCATACATGAGTCTCCATTAT 57.745 36.000 0.00 0.00 40.64 1.28
426 427 6.571150 CGAGCATCATACATGAGTCTCCATTA 60.571 42.308 0.00 0.00 40.64 1.90
427 428 5.549347 GAGCATCATACATGAGTCTCCATT 58.451 41.667 0.00 0.00 40.64 3.16
428 429 4.321824 CGAGCATCATACATGAGTCTCCAT 60.322 45.833 0.00 0.00 40.64 3.41
429 430 3.005155 CGAGCATCATACATGAGTCTCCA 59.995 47.826 0.00 0.00 40.64 3.86
430 431 3.573598 CGAGCATCATACATGAGTCTCC 58.426 50.000 0.00 2.92 40.64 3.71
431 432 2.985809 GCGAGCATCATACATGAGTCTC 59.014 50.000 0.00 10.88 40.64 3.36
432 433 2.627221 AGCGAGCATCATACATGAGTCT 59.373 45.455 0.00 0.00 40.64 3.24
434 435 2.627221 AGAGCGAGCATCATACATGAGT 59.373 45.455 0.00 0.00 40.64 3.41
436 437 3.740631 AAGAGCGAGCATCATACATGA 57.259 42.857 0.00 0.00 41.70 3.07
437 438 3.121092 CGAAAGAGCGAGCATCATACATG 60.121 47.826 0.00 0.00 33.17 3.21
439 440 2.099098 TCGAAAGAGCGAGCATCATACA 59.901 45.455 0.00 0.00 35.01 2.29
440 441 2.732366 TCGAAAGAGCGAGCATCATAC 58.268 47.619 0.00 0.00 35.01 2.39
453 454 2.398554 GCGCATTGCCCTCGAAAGA 61.399 57.895 0.30 0.00 37.76 2.52
454 455 2.100991 GCGCATTGCCCTCGAAAG 59.899 61.111 0.30 0.00 37.76 2.62
455 456 3.798650 CGCGCATTGCCCTCGAAA 61.799 61.111 8.75 0.00 42.08 3.46
456 457 4.751093 TCGCGCATTGCCCTCGAA 62.751 61.111 8.75 0.00 42.08 3.71
459 460 3.386867 CTTGTCGCGCATTGCCCTC 62.387 63.158 8.75 0.00 42.08 4.30
460 461 3.434319 CTTGTCGCGCATTGCCCT 61.434 61.111 8.75 0.00 42.08 5.19
472 473 1.693083 GATACGTGGTGCGGCTTGTC 61.693 60.000 0.00 0.00 46.52 3.18
473 474 1.740296 GATACGTGGTGCGGCTTGT 60.740 57.895 0.00 0.00 46.52 3.16
474 475 0.179121 TAGATACGTGGTGCGGCTTG 60.179 55.000 0.00 0.00 46.52 4.01
475 476 0.102481 CTAGATACGTGGTGCGGCTT 59.898 55.000 0.00 0.00 46.52 4.35
476 477 1.035932 ACTAGATACGTGGTGCGGCT 61.036 55.000 0.00 0.00 46.52 5.52
477 478 0.664761 TACTAGATACGTGGTGCGGC 59.335 55.000 0.00 0.00 46.52 6.53
478 479 1.945394 AGTACTAGATACGTGGTGCGG 59.055 52.381 0.00 0.00 46.52 5.69
480 481 5.122082 GGAGATAGTACTAGATACGTGGTGC 59.878 48.000 8.85 0.00 38.97 5.01
482 483 5.011533 ACGGAGATAGTACTAGATACGTGGT 59.988 44.000 20.73 3.17 38.97 4.16
483 484 5.477510 ACGGAGATAGTACTAGATACGTGG 58.522 45.833 20.73 4.68 38.97 4.94
485 486 6.588719 AGACGGAGATAGTACTAGATACGT 57.411 41.667 21.26 21.26 38.97 3.57
490 491 9.842775 TCATTTTAAGACGGAGATAGTACTAGA 57.157 33.333 8.85 0.00 0.00 2.43
492 493 9.624373 ACTCATTTTAAGACGGAGATAGTACTA 57.376 33.333 4.77 4.77 0.00 1.82
496 497 7.868415 GCATACTCATTTTAAGACGGAGATAGT 59.132 37.037 0.00 0.00 0.00 2.12
497 498 7.867909 TGCATACTCATTTTAAGACGGAGATAG 59.132 37.037 0.00 0.00 0.00 2.08
498 499 7.722363 TGCATACTCATTTTAAGACGGAGATA 58.278 34.615 0.00 0.00 0.00 1.98
499 500 6.582636 TGCATACTCATTTTAAGACGGAGAT 58.417 36.000 0.00 0.00 0.00 2.75
502 503 5.730550 ACTGCATACTCATTTTAAGACGGA 58.269 37.500 0.00 0.00 0.00 4.69
504 505 7.518161 TCAAACTGCATACTCATTTTAAGACG 58.482 34.615 0.00 0.00 0.00 4.18
505 506 9.846248 ATTCAAACTGCATACTCATTTTAAGAC 57.154 29.630 0.00 0.00 0.00 3.01
510 511 9.128107 CGTAAATTCAAACTGCATACTCATTTT 57.872 29.630 0.00 0.00 0.00 1.82
511 512 7.754924 CCGTAAATTCAAACTGCATACTCATTT 59.245 33.333 0.00 0.00 0.00 2.32
512 513 7.094377 ACCGTAAATTCAAACTGCATACTCATT 60.094 33.333 0.00 0.00 0.00 2.57
514 515 5.703592 ACCGTAAATTCAAACTGCATACTCA 59.296 36.000 0.00 0.00 0.00 3.41
515 516 6.178239 ACCGTAAATTCAAACTGCATACTC 57.822 37.500 0.00 0.00 0.00 2.59
516 517 6.877322 AGTACCGTAAATTCAAACTGCATACT 59.123 34.615 0.00 0.00 0.00 2.12
517 518 7.068692 AGTACCGTAAATTCAAACTGCATAC 57.931 36.000 0.00 0.00 0.00 2.39
518 519 7.675962 AAGTACCGTAAATTCAAACTGCATA 57.324 32.000 0.00 0.00 0.00 3.14
519 520 6.569179 AAGTACCGTAAATTCAAACTGCAT 57.431 33.333 0.00 0.00 0.00 3.96
520 521 7.493743 TTAAGTACCGTAAATTCAAACTGCA 57.506 32.000 0.00 0.00 0.00 4.41
558 1721 1.469940 CGAAAGAGCGAGCACCATACT 60.470 52.381 0.00 0.00 0.00 2.12
559 1722 0.924090 CGAAAGAGCGAGCACCATAC 59.076 55.000 0.00 0.00 0.00 2.39
573 1736 2.100991 GCGCATTGCCCTCGAAAG 59.899 61.111 0.30 0.00 37.76 2.62
574 1737 3.798650 CGCGCATTGCCCTCGAAA 61.799 61.111 8.75 0.00 42.08 3.46
606 1769 5.160641 CGAGACGGAGGTAGTACTAGATAC 58.839 50.000 1.87 0.00 0.00 2.24
623 1786 5.748630 TCCATTCATATTTTGAGACGAGACG 59.251 40.000 0.00 0.00 35.27 4.18
624 1787 6.535150 TGTCCATTCATATTTTGAGACGAGAC 59.465 38.462 0.00 0.00 35.27 3.36
625 1788 6.535150 GTGTCCATTCATATTTTGAGACGAGA 59.465 38.462 0.00 0.00 35.27 4.04
626 1789 6.238211 GGTGTCCATTCATATTTTGAGACGAG 60.238 42.308 0.00 0.00 35.27 4.18
627 1790 5.584649 GGTGTCCATTCATATTTTGAGACGA 59.415 40.000 0.00 0.00 35.27 4.20
628 1791 5.353956 TGGTGTCCATTCATATTTTGAGACG 59.646 40.000 0.00 0.00 35.27 4.18
646 1809 8.506437 CATTATGGTGTACATTCATATGGTGTC 58.494 37.037 17.07 9.62 41.03 3.67
710 1886 6.183360 CCAACTATTGATCGTTCCTACAAACC 60.183 42.308 0.00 0.00 0.00 3.27
714 1890 4.468510 ACCCAACTATTGATCGTTCCTACA 59.531 41.667 0.00 0.00 0.00 2.74
826 2006 0.029035 GCTTCATTCGAGCATGGCAG 59.971 55.000 0.00 0.00 39.89 4.85
916 2096 0.030638 AAACTTGTGCATGCGTGGTC 59.969 50.000 14.09 1.67 0.00 4.02
944 2127 1.476833 GGGGCCGAGAGAAATATGCAA 60.477 52.381 0.00 0.00 0.00 4.08
945 2128 0.108585 GGGGCCGAGAGAAATATGCA 59.891 55.000 0.00 0.00 0.00 3.96
952 2135 3.009115 CCAAGGGGGCCGAGAGAA 61.009 66.667 0.00 0.00 0.00 2.87
963 2146 1.127343 CTAGAGAGGAAGGCCAAGGG 58.873 60.000 5.01 0.00 36.29 3.95
964 2147 0.467804 GCTAGAGAGGAAGGCCAAGG 59.532 60.000 5.01 0.00 36.29 3.61
966 2149 1.958288 AAGCTAGAGAGGAAGGCCAA 58.042 50.000 5.01 0.00 36.29 4.52
967 2150 1.958288 AAAGCTAGAGAGGAAGGCCA 58.042 50.000 5.01 0.00 36.29 5.36
968 2151 2.637947 CAAAAGCTAGAGAGGAAGGCC 58.362 52.381 0.00 0.00 0.00 5.19
969 2152 2.013400 GCAAAAGCTAGAGAGGAAGGC 58.987 52.381 0.00 0.00 0.00 4.35
1135 2324 1.682982 CTCGACACGGTCTTGTACAC 58.317 55.000 0.00 0.00 0.00 2.90
1188 2377 2.932194 AGCTGCTCCTTGGCCTGA 60.932 61.111 3.32 0.00 0.00 3.86
1230 2419 1.814634 CGGTAGGAGTAGATGAGGCGT 60.815 57.143 0.00 0.00 0.00 5.68
1638 2833 2.885113 CTGTCGTCGATGGGCAGA 59.115 61.111 18.79 0.00 0.00 4.26
2223 3418 3.880846 CCGCCGGAGATGCAAAGC 61.881 66.667 5.05 0.00 0.00 3.51
2384 3662 1.067060 CGTACGCCATGATCTTCTCCA 59.933 52.381 0.52 0.00 0.00 3.86
3435 4716 2.496470 TGTACCATACACACCACGCATA 59.504 45.455 0.00 0.00 32.89 3.14
3436 4717 1.276705 TGTACCATACACACCACGCAT 59.723 47.619 0.00 0.00 32.89 4.73
3437 4718 0.680061 TGTACCATACACACCACGCA 59.320 50.000 0.00 0.00 32.89 5.24
3452 4734 7.096551 ACCAAGGCAATTCATACATTTTGTAC 58.903 34.615 0.00 0.00 35.42 2.90
3565 4864 1.385409 GGCAATTTTGAGTTTACGCGC 59.615 47.619 5.73 0.00 0.00 6.86
3646 4948 7.187824 ACATTTAGCTATTGTGAAGAGAGGA 57.812 36.000 8.59 0.00 0.00 3.71
3647 4949 8.948631 TTACATTTAGCTATTGTGAAGAGAGG 57.051 34.615 16.25 0.00 0.00 3.69
3696 4998 8.593679 TGTCTACTTCCTATGAAAATTGACTGA 58.406 33.333 0.00 0.00 30.08 3.41
3713 5015 1.623359 CTGCAGCGACTGTCTACTTC 58.377 55.000 0.00 0.00 33.43 3.01
3719 5021 1.739562 CTTCCCTGCAGCGACTGTC 60.740 63.158 8.66 0.00 33.43 3.51
3721 5023 2.435586 CCTTCCCTGCAGCGACTG 60.436 66.667 8.66 0.86 34.12 3.51
3779 5081 2.487986 GCAAGCTGCCACCCTAAGATAT 60.488 50.000 0.00 0.00 37.42 1.63
3792 5094 1.671979 TAGATCATGTGGCAAGCTGC 58.328 50.000 0.00 0.00 44.08 5.25
3796 5098 5.243981 CCCTAAGATAGATCATGTGGCAAG 58.756 45.833 0.00 0.00 0.00 4.01
3814 5116 3.595664 CACCCCCAACACCCCTAA 58.404 61.111 0.00 0.00 0.00 2.69
4313 5615 4.382541 CTTGGCCCTCCCCCAACC 62.383 72.222 0.00 0.00 37.43 3.77
4314 5616 3.590574 ACTTGGCCCTCCCCCAAC 61.591 66.667 0.00 0.00 37.43 3.77
4315 5617 3.589542 CACTTGGCCCTCCCCCAA 61.590 66.667 0.00 0.00 39.91 4.12
4333 5635 4.735132 TACACGTGCCAGCCTCGC 62.735 66.667 17.22 0.00 0.00 5.03
4334 5636 2.507102 CTACACGTGCCAGCCTCG 60.507 66.667 17.22 3.48 0.00 4.63
4335 5637 2.815647 GCTACACGTGCCAGCCTC 60.816 66.667 24.91 5.18 0.00 4.70
4336 5638 4.742201 CGCTACACGTGCCAGCCT 62.742 66.667 27.54 8.03 36.87 4.58


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

AutoCloner maintained by Alex Coulton.