Multiple sequence alignment - TraesCS1A01G288900

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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 TraesCS1A01G288900 chr1A 100.000 4652 0 0 1 4652 486329977 486334628 0.000000e+00 8591
1 TraesCS1A01G288900 chr1D 96.827 3719 92 13 657 4364 386420939 386424642 0.000000e+00 6191
2 TraesCS1A01G288900 chr1D 94.909 550 21 5 1 550 386420404 386420946 0.000000e+00 854
3 TraesCS1A01G288900 chr1B 97.587 2279 55 0 660 2938 518799756 518802034 0.000000e+00 3904
4 TraesCS1A01G288900 chr1B 94.968 1709 62 14 2947 4635 518802257 518803961 0.000000e+00 2658
5 TraesCS1A01G288900 chr1B 89.266 354 21 5 1 350 518799172 518799512 1.200000e-115 427
6 TraesCS1A01G288900 chr1B 92.562 242 13 1 299 540 518799517 518799753 4.460000e-90 342


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 TraesCS1A01G288900 chr1A 486329977 486334628 4651 False 8591.00 8591 100.00000 1 4652 1 chr1A.!!$F1 4651
1 TraesCS1A01G288900 chr1D 386420404 386424642 4238 False 3522.50 6191 95.86800 1 4364 2 chr1D.!!$F1 4363
2 TraesCS1A01G288900 chr1B 518799172 518803961 4789 False 1832.75 3904 93.59575 1 4635 4 chr1B.!!$F1 4634

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
938 1002 0.107410 TCTGTTTGCCCACGTCACTT 60.107 50.000 0.00 0.0 0.00 3.16 F
2115 2179 0.868406 GAAGTCCCAGTGTTTCAGCG 59.132 55.000 0.00 0.0 0.00 5.18 F
2268 2332 1.067916 CAACCAGCAACCTTGTGCC 59.932 57.895 0.00 0.0 46.14 5.01 F
3090 3368 2.493278 GCATGTTGGAACACCTATGCTT 59.507 45.455 8.06 0.0 42.51 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2772 2836 0.729116 CCATACCAAGCGCAGAACTG 59.271 55.000 11.47 0.0 0.00 3.16 R
3329 3609 1.536709 GGCAAGGTGAAGCAAACACAG 60.537 52.381 0.00 0.0 39.65 3.66 R
3549 3829 2.901042 CCTCTGGTAGGGTTCCGC 59.099 66.667 0.00 0.0 42.32 5.54 R
4381 4675 0.612732 TTGAGCATGCAAAGAGGGGG 60.613 55.000 21.98 0.0 0.00 5.40 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
37 38 3.358076 CTCTCCGTTCCCTGTCCGC 62.358 68.421 0.00 0.00 0.00 5.54
172 175 1.295423 GTCGCTGGTAAGGAAGCCA 59.705 57.895 0.00 0.00 35.98 4.75
377 438 4.938756 TGAACCCCTGTGCCCCCT 62.939 66.667 0.00 0.00 0.00 4.79
383 444 2.677228 CCTGTGCCCCCTGGTTAG 59.323 66.667 0.00 0.00 0.00 2.34
397 459 1.266178 GGTTAGGCCTGCCATTTGTT 58.734 50.000 17.99 0.00 38.92 2.83
418 480 1.546773 GGTGGCTTGGTGGTTGTGATA 60.547 52.381 0.00 0.00 0.00 2.15
433 495 3.462199 GATACCTGAGTGCCGGCCC 62.462 68.421 26.77 14.03 0.00 5.80
475 537 2.173519 CTTGGCTGTGGTTCCATGATT 58.826 47.619 0.00 0.00 31.37 2.57
491 553 5.066893 TCCATGATTGCAGATTAGTCTTTGC 59.933 40.000 0.00 0.00 30.42 3.68
532 594 2.488153 GTGTTCTAGGTTGTGATTGGGC 59.512 50.000 0.00 0.00 0.00 5.36
540 602 0.665835 TTGTGATTGGGCGACACAAC 59.334 50.000 0.00 0.00 45.35 3.32
542 604 0.238289 GTGATTGGGCGACACAACTG 59.762 55.000 0.00 0.00 35.06 3.16
543 605 0.107643 TGATTGGGCGACACAACTGA 59.892 50.000 0.00 0.00 0.00 3.41
544 606 0.798776 GATTGGGCGACACAACTGAG 59.201 55.000 0.00 0.00 0.00 3.35
545 607 0.108585 ATTGGGCGACACAACTGAGT 59.891 50.000 0.00 0.00 0.00 3.41
546 608 0.813610 TTGGGCGACACAACTGAGTG 60.814 55.000 0.00 0.00 44.93 3.51
563 625 6.377327 CTGAGTGTCAGTTTTGTTGGTATT 57.623 37.500 0.00 0.00 39.58 1.89
564 626 7.490962 CTGAGTGTCAGTTTTGTTGGTATTA 57.509 36.000 0.00 0.00 39.58 0.98
565 627 7.254227 TGAGTGTCAGTTTTGTTGGTATTAC 57.746 36.000 0.00 0.00 0.00 1.89
566 628 7.051623 TGAGTGTCAGTTTTGTTGGTATTACT 58.948 34.615 0.00 0.00 0.00 2.24
567 629 8.205512 TGAGTGTCAGTTTTGTTGGTATTACTA 58.794 33.333 0.00 0.00 0.00 1.82
568 630 8.374327 AGTGTCAGTTTTGTTGGTATTACTAC 57.626 34.615 0.00 0.00 0.00 2.73
569 631 8.208903 AGTGTCAGTTTTGTTGGTATTACTACT 58.791 33.333 0.00 0.00 0.00 2.57
570 632 8.833493 GTGTCAGTTTTGTTGGTATTACTACTT 58.167 33.333 0.00 0.00 0.00 2.24
571 633 9.398538 TGTCAGTTTTGTTGGTATTACTACTTT 57.601 29.630 0.00 0.00 0.00 2.66
572 634 9.874215 GTCAGTTTTGTTGGTATTACTACTTTC 57.126 33.333 0.00 0.00 0.00 2.62
573 635 9.841295 TCAGTTTTGTTGGTATTACTACTTTCT 57.159 29.630 0.00 0.00 0.00 2.52
574 636 9.878599 CAGTTTTGTTGGTATTACTACTTTCTG 57.121 33.333 0.00 0.00 0.00 3.02
575 637 9.623000 AGTTTTGTTGGTATTACTACTTTCTGT 57.377 29.630 0.00 0.00 0.00 3.41
589 651 5.476091 ACTTTCTGTAGCATATAGGGAGC 57.524 43.478 0.00 0.00 29.89 4.70
590 652 5.151454 ACTTTCTGTAGCATATAGGGAGCT 58.849 41.667 0.00 0.00 42.14 4.09
591 653 5.011533 ACTTTCTGTAGCATATAGGGAGCTG 59.988 44.000 0.00 0.00 39.30 4.24
592 654 4.119556 TCTGTAGCATATAGGGAGCTGT 57.880 45.455 0.00 0.00 39.30 4.40
593 655 5.256806 TCTGTAGCATATAGGGAGCTGTA 57.743 43.478 0.00 0.00 39.30 2.74
594 656 5.010933 TCTGTAGCATATAGGGAGCTGTAC 58.989 45.833 0.00 0.00 39.30 2.90
595 657 4.999310 TGTAGCATATAGGGAGCTGTACT 58.001 43.478 0.00 0.00 39.30 2.73
596 658 4.767409 TGTAGCATATAGGGAGCTGTACTG 59.233 45.833 0.00 0.00 39.30 2.74
597 659 3.850752 AGCATATAGGGAGCTGTACTGT 58.149 45.455 0.00 0.00 37.20 3.55
598 660 4.227197 AGCATATAGGGAGCTGTACTGTT 58.773 43.478 0.00 0.00 37.20 3.16
599 661 4.039730 AGCATATAGGGAGCTGTACTGTTG 59.960 45.833 0.00 0.00 37.20 3.33
600 662 4.202264 GCATATAGGGAGCTGTACTGTTGT 60.202 45.833 0.00 0.00 0.00 3.32
601 663 5.533482 CATATAGGGAGCTGTACTGTTGTC 58.467 45.833 0.00 0.00 0.00 3.18
602 664 0.977395 AGGGAGCTGTACTGTTGTCC 59.023 55.000 0.00 5.70 0.00 4.02
603 665 0.685097 GGGAGCTGTACTGTTGTCCA 59.315 55.000 15.07 0.00 0.00 4.02
604 666 1.279271 GGGAGCTGTACTGTTGTCCAT 59.721 52.381 15.07 0.00 0.00 3.41
605 667 2.290323 GGGAGCTGTACTGTTGTCCATT 60.290 50.000 15.07 0.00 0.00 3.16
606 668 2.744202 GGAGCTGTACTGTTGTCCATTG 59.256 50.000 0.00 0.00 0.00 2.82
607 669 3.557054 GGAGCTGTACTGTTGTCCATTGA 60.557 47.826 0.00 0.00 0.00 2.57
608 670 4.256920 GAGCTGTACTGTTGTCCATTGAT 58.743 43.478 0.00 0.00 0.00 2.57
609 671 4.256920 AGCTGTACTGTTGTCCATTGATC 58.743 43.478 1.46 0.00 0.00 2.92
610 672 4.002982 GCTGTACTGTTGTCCATTGATCA 58.997 43.478 0.00 0.00 0.00 2.92
611 673 4.093998 GCTGTACTGTTGTCCATTGATCAG 59.906 45.833 0.00 0.00 0.00 2.90
612 674 5.227569 TGTACTGTTGTCCATTGATCAGT 57.772 39.130 0.00 0.00 39.11 3.41
613 675 6.353404 TGTACTGTTGTCCATTGATCAGTA 57.647 37.500 0.00 0.00 37.35 2.74
614 676 6.398095 TGTACTGTTGTCCATTGATCAGTAG 58.602 40.000 0.00 0.00 38.48 2.57
615 677 5.745312 ACTGTTGTCCATTGATCAGTAGA 57.255 39.130 0.00 0.00 34.95 2.59
616 678 5.482908 ACTGTTGTCCATTGATCAGTAGAC 58.517 41.667 9.36 9.36 34.95 2.59
617 679 4.494484 TGTTGTCCATTGATCAGTAGACG 58.506 43.478 11.11 0.00 0.00 4.18
618 680 3.165058 TGTCCATTGATCAGTAGACGC 57.835 47.619 11.11 0.00 0.00 5.19
619 681 2.495669 TGTCCATTGATCAGTAGACGCA 59.504 45.455 11.11 0.00 0.00 5.24
620 682 3.132824 TGTCCATTGATCAGTAGACGCAT 59.867 43.478 11.11 0.00 0.00 4.73
621 683 4.122776 GTCCATTGATCAGTAGACGCATT 58.877 43.478 1.34 0.00 0.00 3.56
622 684 4.572389 GTCCATTGATCAGTAGACGCATTT 59.428 41.667 1.34 0.00 0.00 2.32
623 685 5.065218 GTCCATTGATCAGTAGACGCATTTT 59.935 40.000 1.34 0.00 0.00 1.82
624 686 5.647658 TCCATTGATCAGTAGACGCATTTTT 59.352 36.000 0.00 0.00 0.00 1.94
625 687 5.967674 CCATTGATCAGTAGACGCATTTTTC 59.032 40.000 0.00 0.00 0.00 2.29
626 688 6.403527 CCATTGATCAGTAGACGCATTTTTCA 60.404 38.462 0.00 0.00 0.00 2.69
627 689 5.784750 TGATCAGTAGACGCATTTTTCAG 57.215 39.130 0.00 0.00 0.00 3.02
628 690 5.478407 TGATCAGTAGACGCATTTTTCAGA 58.522 37.500 0.00 0.00 0.00 3.27
629 691 5.578336 TGATCAGTAGACGCATTTTTCAGAG 59.422 40.000 0.00 0.00 0.00 3.35
630 692 4.883083 TCAGTAGACGCATTTTTCAGAGT 58.117 39.130 0.00 0.00 0.00 3.24
631 693 6.020971 TCAGTAGACGCATTTTTCAGAGTA 57.979 37.500 0.00 0.00 0.00 2.59
632 694 5.862323 TCAGTAGACGCATTTTTCAGAGTAC 59.138 40.000 0.00 0.00 0.00 2.73
633 695 5.062308 CAGTAGACGCATTTTTCAGAGTACC 59.938 44.000 0.00 0.00 0.00 3.34
634 696 2.993899 AGACGCATTTTTCAGAGTACCG 59.006 45.455 0.00 0.00 0.00 4.02
635 697 2.991190 GACGCATTTTTCAGAGTACCGA 59.009 45.455 0.00 0.00 0.00 4.69
636 698 3.596214 ACGCATTTTTCAGAGTACCGAT 58.404 40.909 0.00 0.00 0.00 4.18
637 699 4.751060 ACGCATTTTTCAGAGTACCGATA 58.249 39.130 0.00 0.00 0.00 2.92
638 700 5.357257 ACGCATTTTTCAGAGTACCGATAT 58.643 37.500 0.00 0.00 0.00 1.63
639 701 5.815740 ACGCATTTTTCAGAGTACCGATATT 59.184 36.000 0.00 0.00 0.00 1.28
640 702 6.129393 CGCATTTTTCAGAGTACCGATATTG 58.871 40.000 0.00 0.00 0.00 1.90
641 703 6.019075 CGCATTTTTCAGAGTACCGATATTGA 60.019 38.462 0.00 0.00 0.00 2.57
642 704 7.307396 CGCATTTTTCAGAGTACCGATATTGAT 60.307 37.037 0.00 0.00 0.00 2.57
643 705 8.012241 GCATTTTTCAGAGTACCGATATTGATC 58.988 37.037 0.00 0.00 0.00 2.92
644 706 8.499162 CATTTTTCAGAGTACCGATATTGATCC 58.501 37.037 0.00 0.00 0.00 3.36
645 707 6.724893 TTTCAGAGTACCGATATTGATCCA 57.275 37.500 0.00 0.00 0.00 3.41
646 708 6.724893 TTCAGAGTACCGATATTGATCCAA 57.275 37.500 0.00 0.00 0.00 3.53
647 709 6.332735 TCAGAGTACCGATATTGATCCAAG 57.667 41.667 0.00 0.00 0.00 3.61
648 710 5.243954 TCAGAGTACCGATATTGATCCAAGG 59.756 44.000 0.00 0.00 0.00 3.61
649 711 5.011125 CAGAGTACCGATATTGATCCAAGGT 59.989 44.000 0.00 0.00 30.88 3.50
650 712 6.208797 CAGAGTACCGATATTGATCCAAGGTA 59.791 42.308 0.00 0.00 29.29 3.08
651 713 6.208994 AGAGTACCGATATTGATCCAAGGTAC 59.791 42.308 12.41 12.41 41.86 3.34
652 714 6.075984 AGTACCGATATTGATCCAAGGTACT 58.924 40.000 16.00 16.00 44.16 2.73
653 715 5.470047 ACCGATATTGATCCAAGGTACTC 57.530 43.478 0.00 0.00 38.49 2.59
654 716 4.283722 ACCGATATTGATCCAAGGTACTCC 59.716 45.833 0.00 0.00 38.49 3.85
655 717 4.283467 CCGATATTGATCCAAGGTACTCCA 59.717 45.833 0.00 0.00 38.49 3.86
672 734 3.245229 ACTCCAGAGTGTCATCTCTCAGT 60.245 47.826 0.00 5.45 42.10 3.41
677 739 4.157472 CAGAGTGTCATCTCTCAGTTAGCA 59.843 45.833 2.95 0.00 42.10 3.49
713 775 2.095059 CCGCTAGTCTTTTGCTTTGCAT 60.095 45.455 0.00 0.00 38.76 3.96
742 806 3.825308 AGCATGCGAATGTTGTTTACTG 58.175 40.909 13.01 0.00 0.00 2.74
775 839 2.069273 CCAGCGTGTAGGTTCTTCAAG 58.931 52.381 0.00 0.00 0.00 3.02
778 842 4.304110 CAGCGTGTAGGTTCTTCAAGTTA 58.696 43.478 0.00 0.00 0.00 2.24
813 877 2.097954 TCGATGTCGGCGTGTTAGTATT 59.902 45.455 6.85 0.00 40.29 1.89
938 1002 0.107410 TCTGTTTGCCCACGTCACTT 60.107 50.000 0.00 0.00 0.00 3.16
1234 1298 2.615912 GCTGTTGGTCTGATCCTATTGC 59.384 50.000 0.00 0.00 0.00 3.56
1248 1312 6.875726 TGATCCTATTGCTGTGCTTCATATAC 59.124 38.462 0.00 0.00 0.00 1.47
1501 1565 3.973657 AGCAAGCTTGTTCACAATGAAG 58.026 40.909 26.55 0.00 37.00 3.02
1712 1776 8.220755 AGTAGAGACAGAGTTAAGATCATCAC 57.779 38.462 0.00 0.00 0.00 3.06
1859 1923 4.576463 GGTGACATTTGAGACTGACAAAGT 59.424 41.667 0.00 0.00 43.85 2.66
1956 2020 8.926374 TCTGGTTATGGATTAAATGATGCATTT 58.074 29.630 0.00 9.93 44.74 2.32
1959 2023 8.981647 GGTTATGGATTAAATGATGCATTTGAC 58.018 33.333 13.90 6.49 42.91 3.18
2115 2179 0.868406 GAAGTCCCAGTGTTTCAGCG 59.132 55.000 0.00 0.00 0.00 5.18
2142 2206 1.074566 ACAGGAAAAGAGAAGCAGGGG 59.925 52.381 0.00 0.00 0.00 4.79
2160 2224 2.508526 GGGACAGCTGTTGAACTGATT 58.491 47.619 22.65 0.00 37.35 2.57
2166 2230 1.619654 CTGTTGAACTGATTGGGGCA 58.380 50.000 0.00 0.00 0.00 5.36
2255 2319 2.622942 GTTCTGGACTTGATTGCAACCA 59.377 45.455 0.00 0.00 31.58 3.67
2256 2320 2.507484 TCTGGACTTGATTGCAACCAG 58.493 47.619 20.21 20.21 44.01 4.00
2268 2332 1.067916 CAACCAGCAACCTTGTGCC 59.932 57.895 0.00 0.00 46.14 5.01
2367 2431 5.690464 ATTTGACTCCTGATGCTACTCTT 57.310 39.130 0.00 0.00 0.00 2.85
2370 2434 4.600062 TGACTCCTGATGCTACTCTTGTA 58.400 43.478 0.00 0.00 0.00 2.41
2394 2458 4.884247 ACGTTCTAAAAAGAGGTCAGGAG 58.116 43.478 0.00 0.00 0.00 3.69
2541 2605 4.376340 CCAAGTGATAATTGGTTCAGGC 57.624 45.455 0.20 0.00 41.94 4.85
2881 2945 5.845985 TCGAGCTTTCATCTTGTGTTTAG 57.154 39.130 0.00 0.00 0.00 1.85
2898 2962 7.833786 TGTGTTTAGTCCTCTATCGTGTAAAT 58.166 34.615 0.00 0.00 0.00 1.40
3031 3309 8.837788 ATTTGTTACACCACTTAACCTACTAC 57.162 34.615 0.00 0.00 0.00 2.73
3032 3310 7.601705 TTGTTACACCACTTAACCTACTACT 57.398 36.000 0.00 0.00 0.00 2.57
3066 3344 5.752892 AGAAGCAGCATCACATAGAAATG 57.247 39.130 0.00 0.00 39.17 2.32
3090 3368 2.493278 GCATGTTGGAACACCTATGCTT 59.507 45.455 8.06 0.00 42.51 3.91
3225 3505 7.377766 TGCTGTTCTATCAAAATCAGTAACC 57.622 36.000 0.00 0.00 0.00 2.85
3284 3564 6.060028 TGTAGTCAAACAATCTTGCAAGTC 57.940 37.500 25.19 6.76 0.00 3.01
3549 3829 5.645067 TCAGATGCAGTTTTCTAGTGGATTG 59.355 40.000 0.00 0.00 38.24 2.67
3989 4282 0.538057 CCAGCTCAGTTCTTTGGCCA 60.538 55.000 0.00 0.00 0.00 5.36
4006 4299 2.102578 GCCACAAACATCCAAGGCTAT 58.897 47.619 0.00 0.00 39.02 2.97
4033 4326 4.466827 TCATGATATTGCTGCAACCATCT 58.533 39.130 26.26 13.14 0.00 2.90
4121 4414 4.802876 AAAGATAGCTATGTTCTTGCGC 57.197 40.909 15.83 0.00 30.41 6.09
4260 4554 7.503902 GCCCTTATTTAGATGGAAATTGAGACT 59.496 37.037 0.00 0.00 31.51 3.24
4294 4588 8.837389 AGTAATTCGTTTGCCCTTATTTAGATC 58.163 33.333 0.00 0.00 0.00 2.75
4347 4641 7.446625 AGTTCATCTGCACAACTTATTTCTTCT 59.553 33.333 0.00 0.00 0.00 2.85
4380 4674 3.578688 AGCTTTTCATCGGTGCAATTTC 58.421 40.909 0.00 0.00 0.00 2.17
4381 4675 2.667969 GCTTTTCATCGGTGCAATTTCC 59.332 45.455 0.00 0.00 0.00 3.13
4382 4676 3.253230 CTTTTCATCGGTGCAATTTCCC 58.747 45.455 0.00 0.00 0.00 3.97
4408 4709 5.336213 CCTCTTTGCATGCTCAAATAACACT 60.336 40.000 20.33 0.00 35.64 3.55
4418 4719 5.704978 TGCTCAAATAACACTGTGCATCTTA 59.295 36.000 7.90 0.00 37.19 2.10
4446 4750 9.507280 ACAAATTCAAATAGAACATTAGCATCG 57.493 29.630 0.00 0.00 39.49 3.84
4483 4787 4.378046 GCAACTTGTCCTGTATTTACCACG 60.378 45.833 0.00 0.00 0.00 4.94
4522 4826 4.087182 AGTCGAAAGGATCAGTACCTTCA 58.913 43.478 0.00 0.00 45.55 3.02
4532 4836 3.674997 TCAGTACCTTCAACTTGGATGC 58.325 45.455 0.00 0.00 0.00 3.91
4554 4858 7.490962 TGCGGTATAACATAAATTTCTCCTG 57.509 36.000 0.00 0.00 0.00 3.86
4572 4876 5.837438 TCTCCTGAGATCTGCATCTGATTTA 59.163 40.000 0.00 0.00 39.71 1.40
4579 4883 8.591072 TGAGATCTGCATCTGATTTATGATACA 58.409 33.333 0.00 0.00 39.71 2.29
4582 4886 7.916914 TCTGCATCTGATTTATGATACATGG 57.083 36.000 0.00 0.00 0.00 3.66
4618 4922 3.181445 TGAAAGGCTTAGAGCAACTCCAA 60.181 43.478 0.00 0.00 44.75 3.53
4624 4928 4.994217 GGCTTAGAGCAACTCCAATAGATC 59.006 45.833 2.04 0.00 44.75 2.75
4635 4939 4.202684 ACTCCAATAGATCCCGTATCCTCA 60.203 45.833 0.00 0.00 34.90 3.86
4636 4940 4.747583 TCCAATAGATCCCGTATCCTCAA 58.252 43.478 0.00 0.00 34.90 3.02
4637 4941 5.152193 TCCAATAGATCCCGTATCCTCAAA 58.848 41.667 0.00 0.00 34.90 2.69
4638 4942 5.785423 TCCAATAGATCCCGTATCCTCAAAT 59.215 40.000 0.00 0.00 34.90 2.32
4639 4943 6.070767 TCCAATAGATCCCGTATCCTCAAATC 60.071 42.308 0.00 0.00 34.90 2.17
4640 4944 6.295859 CCAATAGATCCCGTATCCTCAAATCA 60.296 42.308 0.00 0.00 34.90 2.57
4641 4945 7.334090 CAATAGATCCCGTATCCTCAAATCAT 58.666 38.462 0.00 0.00 34.90 2.45
4642 4946 5.832539 AGATCCCGTATCCTCAAATCATT 57.167 39.130 0.00 0.00 34.90 2.57
4643 4947 6.935240 AGATCCCGTATCCTCAAATCATTA 57.065 37.500 0.00 0.00 34.90 1.90
4644 4948 7.316393 AGATCCCGTATCCTCAAATCATTAA 57.684 36.000 0.00 0.00 34.90 1.40
4645 4949 7.745717 AGATCCCGTATCCTCAAATCATTAAA 58.254 34.615 0.00 0.00 34.90 1.52
4646 4950 8.217799 AGATCCCGTATCCTCAAATCATTAAAA 58.782 33.333 0.00 0.00 34.90 1.52
4647 4951 8.760980 ATCCCGTATCCTCAAATCATTAAAAA 57.239 30.769 0.00 0.00 0.00 1.94
4648 4952 8.220755 TCCCGTATCCTCAAATCATTAAAAAG 57.779 34.615 0.00 0.00 0.00 2.27
4649 4953 8.050325 TCCCGTATCCTCAAATCATTAAAAAGA 58.950 33.333 0.00 0.00 0.00 2.52
4650 4954 8.129211 CCCGTATCCTCAAATCATTAAAAAGAC 58.871 37.037 0.00 0.00 0.00 3.01
4651 4955 8.893727 CCGTATCCTCAAATCATTAAAAAGACT 58.106 33.333 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
172 175 5.010282 AGACAAAAACCAAAGCGGAGATAT 58.990 37.500 0.00 0.00 38.63 1.63
246 251 3.001736 GCGATCGATTTGGAGAAGAAAGG 59.998 47.826 21.57 0.00 0.00 3.11
377 438 0.114168 ACAAATGGCAGGCCTAACCA 59.886 50.000 24.92 24.92 43.14 3.67
380 441 1.265236 CCAACAAATGGCAGGCCTAA 58.735 50.000 3.98 0.00 43.80 2.69
397 459 1.756172 CACAACCACCAAGCCACCA 60.756 57.895 0.00 0.00 0.00 4.17
433 495 0.721718 GCCGACTTTCCATTGACTCG 59.278 55.000 0.00 0.00 0.00 4.18
439 501 1.156736 CAAGACGCCGACTTTCCATT 58.843 50.000 0.00 0.00 0.00 3.16
475 537 4.144297 ACTTTGGCAAAGACTAATCTGCA 58.856 39.130 38.62 3.16 41.02 4.41
491 553 3.308053 CACACAGCGATATCTGACTTTGG 59.692 47.826 0.34 0.00 37.51 3.28
542 604 7.492352 AGTAATACCAACAAAACTGACACTC 57.508 36.000 0.00 0.00 0.00 3.51
543 605 8.208903 AGTAGTAATACCAACAAAACTGACACT 58.791 33.333 0.00 0.00 0.00 3.55
544 606 8.374327 AGTAGTAATACCAACAAAACTGACAC 57.626 34.615 0.00 0.00 0.00 3.67
545 607 8.967664 AAGTAGTAATACCAACAAAACTGACA 57.032 30.769 0.00 0.00 0.00 3.58
546 608 9.874215 GAAAGTAGTAATACCAACAAAACTGAC 57.126 33.333 0.00 0.00 0.00 3.51
547 609 9.841295 AGAAAGTAGTAATACCAACAAAACTGA 57.159 29.630 0.00 0.00 0.00 3.41
548 610 9.878599 CAGAAAGTAGTAATACCAACAAAACTG 57.121 33.333 0.00 0.00 0.00 3.16
549 611 9.623000 ACAGAAAGTAGTAATACCAACAAAACT 57.377 29.630 0.00 0.00 0.00 2.66
566 628 6.209589 CAGCTCCCTATATGCTACAGAAAGTA 59.790 42.308 0.00 0.00 35.05 2.24
567 629 5.011533 CAGCTCCCTATATGCTACAGAAAGT 59.988 44.000 0.00 0.00 35.05 2.66
568 630 5.011533 ACAGCTCCCTATATGCTACAGAAAG 59.988 44.000 0.00 0.00 35.05 2.62
569 631 4.901849 ACAGCTCCCTATATGCTACAGAAA 59.098 41.667 0.00 0.00 35.05 2.52
570 632 4.483950 ACAGCTCCCTATATGCTACAGAA 58.516 43.478 0.00 0.00 35.05 3.02
571 633 4.119556 ACAGCTCCCTATATGCTACAGA 57.880 45.455 0.00 0.00 35.05 3.41
572 634 5.013547 AGTACAGCTCCCTATATGCTACAG 58.986 45.833 0.00 0.00 35.05 2.74
573 635 4.767409 CAGTACAGCTCCCTATATGCTACA 59.233 45.833 0.00 0.00 35.05 2.74
574 636 4.767928 ACAGTACAGCTCCCTATATGCTAC 59.232 45.833 0.00 0.00 35.05 3.58
575 637 4.999310 ACAGTACAGCTCCCTATATGCTA 58.001 43.478 0.00 0.00 35.05 3.49
576 638 3.850752 ACAGTACAGCTCCCTATATGCT 58.149 45.455 0.00 0.00 37.56 3.79
577 639 4.202264 ACAACAGTACAGCTCCCTATATGC 60.202 45.833 0.00 0.00 0.00 3.14
578 640 5.509840 GGACAACAGTACAGCTCCCTATATG 60.510 48.000 0.00 0.00 0.00 1.78
579 641 4.589374 GGACAACAGTACAGCTCCCTATAT 59.411 45.833 0.00 0.00 0.00 0.86
580 642 3.958798 GGACAACAGTACAGCTCCCTATA 59.041 47.826 0.00 0.00 0.00 1.31
581 643 2.766828 GGACAACAGTACAGCTCCCTAT 59.233 50.000 0.00 0.00 0.00 2.57
582 644 2.176889 GGACAACAGTACAGCTCCCTA 58.823 52.381 0.00 0.00 0.00 3.53
583 645 0.977395 GGACAACAGTACAGCTCCCT 59.023 55.000 0.00 0.00 0.00 4.20
584 646 0.685097 TGGACAACAGTACAGCTCCC 59.315 55.000 0.00 0.00 0.00 4.30
585 647 2.744202 CAATGGACAACAGTACAGCTCC 59.256 50.000 0.00 0.00 27.58 4.70
586 648 3.664107 TCAATGGACAACAGTACAGCTC 58.336 45.455 0.00 0.00 27.58 4.09
587 649 3.769739 TCAATGGACAACAGTACAGCT 57.230 42.857 0.00 0.00 27.58 4.24
588 650 4.002982 TGATCAATGGACAACAGTACAGC 58.997 43.478 0.00 0.00 27.58 4.40
589 651 5.240891 ACTGATCAATGGACAACAGTACAG 58.759 41.667 0.00 0.00 35.24 2.74
590 652 5.227569 ACTGATCAATGGACAACAGTACA 57.772 39.130 0.00 0.00 35.24 2.90
591 653 6.531948 GTCTACTGATCAATGGACAACAGTAC 59.468 42.308 14.82 0.00 36.93 2.73
592 654 6.625081 CGTCTACTGATCAATGGACAACAGTA 60.625 42.308 18.80 0.00 36.93 2.74
593 655 5.482908 GTCTACTGATCAATGGACAACAGT 58.517 41.667 14.82 0.00 38.18 3.55
594 656 4.564372 CGTCTACTGATCAATGGACAACAG 59.436 45.833 18.80 1.00 0.00 3.16
595 657 4.494484 CGTCTACTGATCAATGGACAACA 58.506 43.478 18.80 0.00 0.00 3.33
596 658 3.307242 GCGTCTACTGATCAATGGACAAC 59.693 47.826 18.80 7.93 0.00 3.32
597 659 3.056179 TGCGTCTACTGATCAATGGACAA 60.056 43.478 18.80 5.41 0.00 3.18
598 660 2.495669 TGCGTCTACTGATCAATGGACA 59.504 45.455 18.80 0.00 0.00 4.02
599 661 3.165058 TGCGTCTACTGATCAATGGAC 57.835 47.619 10.30 10.30 0.00 4.02
600 662 4.406648 AATGCGTCTACTGATCAATGGA 57.593 40.909 0.00 0.00 0.00 3.41
601 663 5.490139 AAAATGCGTCTACTGATCAATGG 57.510 39.130 0.00 0.00 0.00 3.16
602 664 6.545508 TGAAAAATGCGTCTACTGATCAATG 58.454 36.000 0.00 0.00 0.00 2.82
603 665 6.595326 TCTGAAAAATGCGTCTACTGATCAAT 59.405 34.615 0.00 0.00 0.00 2.57
604 666 5.931724 TCTGAAAAATGCGTCTACTGATCAA 59.068 36.000 0.00 0.00 0.00 2.57
605 667 5.478407 TCTGAAAAATGCGTCTACTGATCA 58.522 37.500 0.00 0.00 0.00 2.92
606 668 5.578727 ACTCTGAAAAATGCGTCTACTGATC 59.421 40.000 0.00 0.00 0.00 2.92
607 669 5.482908 ACTCTGAAAAATGCGTCTACTGAT 58.517 37.500 0.00 0.00 0.00 2.90
608 670 4.883083 ACTCTGAAAAATGCGTCTACTGA 58.117 39.130 0.00 0.00 0.00 3.41
609 671 5.062308 GGTACTCTGAAAAATGCGTCTACTG 59.938 44.000 0.00 0.00 0.00 2.74
610 672 5.169295 GGTACTCTGAAAAATGCGTCTACT 58.831 41.667 0.00 0.00 0.00 2.57
611 673 4.031426 CGGTACTCTGAAAAATGCGTCTAC 59.969 45.833 0.00 0.00 0.00 2.59
612 674 4.082625 TCGGTACTCTGAAAAATGCGTCTA 60.083 41.667 0.00 0.00 0.00 2.59
613 675 2.993899 CGGTACTCTGAAAAATGCGTCT 59.006 45.455 0.00 0.00 0.00 4.18
614 676 2.991190 TCGGTACTCTGAAAAATGCGTC 59.009 45.455 0.00 0.00 0.00 5.19
615 677 3.034721 TCGGTACTCTGAAAAATGCGT 57.965 42.857 0.00 0.00 0.00 5.24
616 678 5.907197 ATATCGGTACTCTGAAAAATGCG 57.093 39.130 0.00 0.00 32.29 4.73
617 679 7.246674 TCAATATCGGTACTCTGAAAAATGC 57.753 36.000 0.00 0.00 32.29 3.56
618 680 8.499162 GGATCAATATCGGTACTCTGAAAAATG 58.501 37.037 0.00 0.00 32.44 2.32
619 681 8.210946 TGGATCAATATCGGTACTCTGAAAAAT 58.789 33.333 0.00 0.00 32.44 1.82
620 682 7.561251 TGGATCAATATCGGTACTCTGAAAAA 58.439 34.615 0.00 0.00 32.44 1.94
621 683 7.119709 TGGATCAATATCGGTACTCTGAAAA 57.880 36.000 0.00 0.00 32.44 2.29
622 684 6.724893 TGGATCAATATCGGTACTCTGAAA 57.275 37.500 0.00 0.00 32.44 2.69
623 685 6.239317 CCTTGGATCAATATCGGTACTCTGAA 60.239 42.308 0.00 0.00 32.44 3.02
624 686 5.243954 CCTTGGATCAATATCGGTACTCTGA 59.756 44.000 0.00 0.00 32.44 3.27
625 687 5.011125 ACCTTGGATCAATATCGGTACTCTG 59.989 44.000 0.00 0.00 32.44 3.35
626 688 5.148502 ACCTTGGATCAATATCGGTACTCT 58.851 41.667 0.00 0.00 32.44 3.24
627 689 5.470047 ACCTTGGATCAATATCGGTACTC 57.530 43.478 0.00 0.00 32.44 2.59
628 690 6.075984 AGTACCTTGGATCAATATCGGTACT 58.924 40.000 16.76 16.76 44.12 2.73
629 691 6.342338 AGTACCTTGGATCAATATCGGTAC 57.658 41.667 14.08 14.08 41.84 3.34
630 692 5.479375 GGAGTACCTTGGATCAATATCGGTA 59.521 44.000 0.00 0.00 32.44 4.02
631 693 4.283722 GGAGTACCTTGGATCAATATCGGT 59.716 45.833 0.00 0.00 32.44 4.69
632 694 4.283467 TGGAGTACCTTGGATCAATATCGG 59.717 45.833 0.00 0.00 37.04 4.18
633 695 5.243954 TCTGGAGTACCTTGGATCAATATCG 59.756 44.000 0.00 0.00 37.04 2.92
634 696 6.268847 ACTCTGGAGTACCTTGGATCAATATC 59.731 42.308 0.95 0.00 40.43 1.63
635 697 6.042552 CACTCTGGAGTACCTTGGATCAATAT 59.957 42.308 2.75 0.00 40.20 1.28
636 698 5.363868 CACTCTGGAGTACCTTGGATCAATA 59.636 44.000 2.75 0.00 40.20 1.90
637 699 4.163078 CACTCTGGAGTACCTTGGATCAAT 59.837 45.833 2.75 0.00 40.20 2.57
638 700 3.515502 CACTCTGGAGTACCTTGGATCAA 59.484 47.826 2.75 0.00 40.20 2.57
639 701 3.099905 CACTCTGGAGTACCTTGGATCA 58.900 50.000 2.75 0.00 40.20 2.92
640 702 3.100671 ACACTCTGGAGTACCTTGGATC 58.899 50.000 2.75 0.00 40.20 3.36
641 703 3.100671 GACACTCTGGAGTACCTTGGAT 58.899 50.000 2.75 0.00 40.20 3.41
642 704 2.158370 TGACACTCTGGAGTACCTTGGA 60.158 50.000 2.75 0.00 40.20 3.53
643 705 2.248248 TGACACTCTGGAGTACCTTGG 58.752 52.381 2.75 0.00 40.20 3.61
644 706 3.766591 AGATGACACTCTGGAGTACCTTG 59.233 47.826 2.75 0.00 40.20 3.61
645 707 4.020543 GAGATGACACTCTGGAGTACCTT 58.979 47.826 2.75 0.00 40.20 3.50
646 708 3.268334 AGAGATGACACTCTGGAGTACCT 59.732 47.826 2.75 0.00 44.29 3.08
647 709 3.626930 AGAGATGACACTCTGGAGTACC 58.373 50.000 2.75 0.00 44.29 3.34
648 710 4.265893 TGAGAGATGACACTCTGGAGTAC 58.734 47.826 10.94 2.34 45.69 2.73
649 711 4.018870 ACTGAGAGATGACACTCTGGAGTA 60.019 45.833 10.94 0.00 45.69 2.59
650 712 3.245229 ACTGAGAGATGACACTCTGGAGT 60.245 47.826 10.94 9.69 45.69 3.85
651 713 3.355378 ACTGAGAGATGACACTCTGGAG 58.645 50.000 10.94 9.24 45.69 3.86
652 714 3.448093 ACTGAGAGATGACACTCTGGA 57.552 47.619 10.94 0.36 45.69 3.86
653 715 4.439974 GCTAACTGAGAGATGACACTCTGG 60.440 50.000 10.94 7.31 45.69 3.86
654 716 4.157472 TGCTAACTGAGAGATGACACTCTG 59.843 45.833 10.94 0.00 45.69 3.35
672 734 7.361457 AGCGGCTAGGATAATATTATGCTAA 57.639 36.000 27.00 16.29 41.49 3.09
677 739 8.770010 AAGACTAGCGGCTAGGATAATATTAT 57.230 34.615 33.50 14.04 38.30 1.28
713 775 2.698803 ACATTCGCATGCTCAGTACAA 58.301 42.857 17.13 0.00 33.05 2.41
742 806 2.744202 ACACGCTGGACATTCAGAAATC 59.256 45.455 0.00 0.00 36.93 2.17
775 839 9.275231 CCGACATCGAATAGATAACACTATAAC 57.725 37.037 2.09 0.00 43.02 1.89
778 842 6.323266 GCCGACATCGAATAGATAACACTAT 58.677 40.000 2.09 0.00 43.02 2.12
938 1002 4.718940 TCACTGACAATGAGCGATAAGA 57.281 40.909 0.00 0.00 0.00 2.10
1234 1298 5.291858 TCAAAGAAGCGTATATGAAGCACAG 59.708 40.000 0.00 0.00 34.56 3.66
1248 1312 6.259608 AGACATGGAAATATCTCAAAGAAGCG 59.740 38.462 0.00 0.00 0.00 4.68
1438 1502 1.800681 GTTGATAGGCACGCCCAAC 59.199 57.895 3.95 8.53 36.58 3.77
1501 1565 4.708177 TCTATTGCCTTCTTCATACCAGC 58.292 43.478 0.00 0.00 0.00 4.85
1712 1776 5.048224 CCATAATAAGCTTCTTCCATGCCAG 60.048 44.000 0.00 0.00 0.00 4.85
1859 1923 1.745890 CCTGTGTCACCTTGGACGA 59.254 57.895 0.00 0.00 40.72 4.20
1890 1954 9.166173 CTAAGTTGATGATTGACAGAACCAATA 57.834 33.333 0.00 0.00 34.67 1.90
1956 2020 2.815503 CAGATGTGCCACAGATTTGTCA 59.184 45.455 3.00 0.00 34.62 3.58
1959 2023 2.094906 CACCAGATGTGCCACAGATTTG 60.095 50.000 3.00 0.00 38.34 2.32
2115 2179 4.576463 TGCTTCTCTTTTCCTGTTGTCTTC 59.424 41.667 0.00 0.00 0.00 2.87
2142 2206 2.227388 CCCAATCAGTTCAACAGCTGTC 59.773 50.000 21.95 7.57 34.57 3.51
2160 2224 2.067932 CTTTCCACTGAGGTGCCCCA 62.068 60.000 0.00 0.00 41.75 4.96
2166 2230 4.593206 TCACTACATTCTTTCCACTGAGGT 59.407 41.667 0.00 0.00 39.02 3.85
2255 2319 2.501602 GCAAGGGCACAAGGTTGCT 61.502 57.895 3.54 0.00 41.69 3.91
2256 2320 2.029518 GCAAGGGCACAAGGTTGC 59.970 61.111 0.00 0.00 42.18 4.17
2268 2332 1.305930 GCGGAAAGGTACTGGCAAGG 61.306 60.000 0.00 0.00 40.86 3.61
2367 2431 6.395426 TGACCTCTTTTTAGAACGTCTACA 57.605 37.500 0.00 0.00 0.00 2.74
2370 2434 4.587684 TCCTGACCTCTTTTTAGAACGTCT 59.412 41.667 0.00 0.00 0.00 4.18
2541 2605 4.248859 CACCAAGAGTCCAAGTGATACTG 58.751 47.826 0.00 0.00 0.00 2.74
2772 2836 0.729116 CCATACCAAGCGCAGAACTG 59.271 55.000 11.47 0.00 0.00 3.16
2881 2945 3.491267 GCAGCATTTACACGATAGAGGAC 59.509 47.826 0.00 0.00 41.38 3.85
2898 2962 1.608055 ACAACACTAGCATTGCAGCA 58.392 45.000 11.91 0.00 36.85 4.41
2945 3223 6.311735 AGCTTGGAAGTCCTAAAAATGGTAA 58.688 36.000 0.00 0.00 36.82 2.85
2963 3241 8.739972 AGCGGGATAATAAATTAAATAGCTTGG 58.260 33.333 0.00 0.00 0.00 3.61
3066 3344 3.836949 CATAGGTGTTCCAACATGCAAC 58.163 45.455 0.00 0.00 41.59 4.17
3086 3364 7.067615 TGGAGTACAGTGAAACAATAAAAAGCA 59.932 33.333 0.00 0.00 41.43 3.91
3225 3505 7.487189 GCAAATATCTTCACATTCTCCAACAAG 59.513 37.037 0.00 0.00 0.00 3.16
3329 3609 1.536709 GGCAAGGTGAAGCAAACACAG 60.537 52.381 0.00 0.00 39.65 3.66
3549 3829 2.901042 CCTCTGGTAGGGTTCCGC 59.099 66.667 0.00 0.00 42.32 5.54
3989 4282 4.574674 TCTGATAGCCTTGGATGTTTGT 57.425 40.909 0.00 0.00 0.00 2.83
4006 4299 4.517832 GGTTGCAGCAATATCATGATCTGA 59.482 41.667 20.63 3.10 38.53 3.27
4033 4326 4.401519 CCTTTGAAGAGTATACGAGTCCCA 59.598 45.833 0.00 0.00 0.00 4.37
4121 4414 9.485206 TGACAAGATGATACATCAATGATAGTG 57.515 33.333 17.58 0.00 40.69 2.74
4260 4554 4.748102 GGGCAAACGAATTACTGATCGATA 59.252 41.667 0.00 0.00 41.43 2.92
4294 4588 3.123804 CCGAAACAGATTCATACGGAGG 58.876 50.000 0.00 0.00 41.09 4.30
4347 4641 5.277779 CCGATGAAAAGCTTGTAGACAAACA 60.278 40.000 0.00 0.00 35.15 2.83
4381 4675 0.612732 TTGAGCATGCAAAGAGGGGG 60.613 55.000 21.98 0.00 0.00 5.40
4382 4676 1.259609 TTTGAGCATGCAAAGAGGGG 58.740 50.000 21.98 0.00 33.16 4.79
4389 4683 4.548494 CACAGTGTTATTTGAGCATGCAA 58.452 39.130 21.98 5.86 0.00 4.08
4391 4685 2.919229 GCACAGTGTTATTTGAGCATGC 59.081 45.455 10.51 10.51 32.26 4.06
4433 4734 1.004927 GCACCGACGATGCTAATGTTC 60.005 52.381 7.03 0.00 40.08 3.18
4434 4735 1.006832 GCACCGACGATGCTAATGTT 58.993 50.000 7.03 0.00 40.08 2.71
4436 4737 1.006086 TTGCACCGACGATGCTAATG 58.994 50.000 16.59 0.00 43.77 1.90
4483 4787 8.656849 CCTTTCGACTTGTATAATATATGCACC 58.343 37.037 0.00 0.00 0.00 5.01
4522 4826 7.817418 ATTTATGTTATACCGCATCCAAGTT 57.183 32.000 0.00 0.00 0.00 2.66
4532 4836 9.712305 ATCTCAGGAGAAATTTATGTTATACCG 57.288 33.333 2.68 0.00 41.36 4.02
4554 4858 8.999220 TGTATCATAAATCAGATGCAGATCTC 57.001 34.615 0.00 0.00 36.75 2.75
4602 4906 4.994217 GGATCTATTGGAGTTGCTCTAAGC 59.006 45.833 0.00 0.00 42.82 3.09
4606 4910 2.366916 CGGGATCTATTGGAGTTGCTCT 59.633 50.000 0.00 0.00 0.00 4.09
4618 4922 7.502060 AATGATTTGAGGATACGGGATCTAT 57.498 36.000 0.00 0.00 46.39 1.98
4624 4928 8.129211 GTCTTTTTAATGATTTGAGGATACGGG 58.871 37.037 0.00 0.00 46.39 5.28


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

AutoCloner maintained by Alex Coulton.