Multiple sequence alignment - TraesCS6D01G188300

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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 TraesCS6D01G188300 chr6D 100.000 5417 0 0 1 5417 256315278 256320694 0.000000e+00 10004.0
1 TraesCS6D01G188300 chr6D 89.552 67 5 2 4150 4215 305190126 305190191 3.480000e-12 84.2
2 TraesCS6D01G188300 chr6A 98.111 4023 66 5 733 4752 340042919 340046934 0.000000e+00 6999.0
3 TraesCS6D01G188300 chr6A 86.802 591 65 12 4833 5417 473579132 473579715 0.000000e+00 647.0
4 TraesCS6D01G188300 chr6A 86.624 157 11 1 554 710 340042077 340042223 1.210000e-36 165.0
5 TraesCS6D01G188300 chr6A 83.721 86 12 2 4153 4237 1412757 1412841 4.500000e-11 80.5
6 TraesCS6D01G188300 chr6A 92.105 38 2 1 641 678 519688361 519688325 1.000000e-02 52.8
7 TraesCS6D01G188300 chr6B 97.364 3983 62 11 798 4752 345466284 345470251 0.000000e+00 6734.0
8 TraesCS6D01G188300 chr6B 90.054 553 49 5 8 555 570142760 570142209 0.000000e+00 712.0
9 TraesCS6D01G188300 chr6B 89.661 561 48 7 7 560 716582101 716581544 0.000000e+00 706.0
10 TraesCS6D01G188300 chr6B 94.118 68 4 0 711 778 345465927 345465994 2.670000e-18 104.0
11 TraesCS6D01G188300 chr6B 92.308 39 1 1 651 689 482170919 482170883 3.000000e-03 54.7
12 TraesCS6D01G188300 chr6B 92.105 38 2 1 641 678 628183995 628184031 1.000000e-02 52.8
13 TraesCS6D01G188300 chr1B 93.898 590 30 3 4833 5417 635795526 635794938 0.000000e+00 885.0
14 TraesCS6D01G188300 chr1B 87.069 116 12 3 2449 2563 674622788 674622675 1.580000e-25 128.0
15 TraesCS6D01G188300 chr1B 92.105 38 2 1 641 678 331037846 331037882 1.000000e-02 52.8
16 TraesCS6D01G188300 chr1B 92.105 38 2 1 641 678 664317057 664317021 1.000000e-02 52.8
17 TraesCS6D01G188300 chr5D 95.290 552 26 0 4 555 300951576 300951025 0.000000e+00 876.0
18 TraesCS6D01G188300 chr5D 93.443 549 36 0 7 555 300950321 300949773 0.000000e+00 815.0
19 TraesCS6D01G188300 chr5D 87.201 586 66 7 4833 5417 431901650 431901073 0.000000e+00 658.0
20 TraesCS6D01G188300 chr5D 94.186 86 4 1 4152 4236 297499911 297499826 4.400000e-26 130.0
21 TraesCS6D01G188300 chr5B 93.116 552 38 0 4 555 344282731 344283282 0.000000e+00 809.0
22 TraesCS6D01G188300 chr5B 89.966 588 50 8 4833 5417 213247015 213246434 0.000000e+00 750.0
23 TraesCS6D01G188300 chr5B 89.562 594 52 3 4833 5417 514044591 514045183 0.000000e+00 745.0
24 TraesCS6D01G188300 chr5B 95.294 85 4 0 4152 4236 337831162 337831078 9.460000e-28 135.0
25 TraesCS6D01G188300 chr1D 90.681 558 40 9 4 555 320637548 320638099 0.000000e+00 732.0
26 TraesCS6D01G188300 chr1D 87.069 116 12 3 2449 2563 484393364 484393251 1.580000e-25 128.0
27 TraesCS6D01G188300 chr1D 92.105 38 2 1 641 678 383873152 383873188 1.000000e-02 52.8
28 TraesCS6D01G188300 chr2A 89.964 558 52 3 4 557 19923501 19924058 0.000000e+00 717.0
29 TraesCS6D01G188300 chr2A 94.048 84 4 1 4154 4236 102688124 102688041 5.700000e-25 126.0
30 TraesCS6D01G188300 chrUn 90.381 551 41 5 9 555 77775122 77775664 0.000000e+00 713.0
31 TraesCS6D01G188300 chrUn 87.059 85 8 2 4153 4236 11032398 11032316 5.780000e-15 93.5
32 TraesCS6D01G188300 chr2D 90.090 555 41 7 4 555 297179935 297179392 0.000000e+00 708.0
33 TraesCS6D01G188300 chr7A 87.946 589 62 9 4833 5417 660548398 660547815 0.000000e+00 686.0
34 TraesCS6D01G188300 chr7A 87.905 587 59 6 4833 5417 710956056 710956632 0.000000e+00 680.0
35 TraesCS6D01G188300 chr2B 87.053 587 70 6 4833 5417 477155390 477154808 0.000000e+00 658.0
36 TraesCS6D01G188300 chr3A 86.735 588 72 6 4833 5417 154983439 154984023 0.000000e+00 649.0
37 TraesCS6D01G188300 chr3A 81.319 91 14 3 4147 4236 521635886 521635798 2.710000e-08 71.3
38 TraesCS6D01G188300 chr3A 92.857 42 0 3 651 690 544786561 544786601 2.110000e-04 58.4
39 TraesCS6D01G188300 chr1A 87.069 116 12 3 2449 2563 581573220 581573107 1.580000e-25 128.0
40 TraesCS6D01G188300 chr7B 92.105 38 2 1 641 678 677157832 677157868 1.000000e-02 52.8
41 TraesCS6D01G188300 chr3D 92.105 38 2 1 641 678 545366388 545366352 1.000000e-02 52.8


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 TraesCS6D01G188300 chr6D 256315278 256320694 5416 False 10004.0 10004 100.0000 1 5417 1 chr6D.!!$F1 5416
1 TraesCS6D01G188300 chr6A 340042077 340046934 4857 False 3582.0 6999 92.3675 554 4752 2 chr6A.!!$F3 4198
2 TraesCS6D01G188300 chr6A 473579132 473579715 583 False 647.0 647 86.8020 4833 5417 1 chr6A.!!$F2 584
3 TraesCS6D01G188300 chr6B 345465927 345470251 4324 False 3419.0 6734 95.7410 711 4752 2 chr6B.!!$F2 4041
4 TraesCS6D01G188300 chr6B 570142209 570142760 551 True 712.0 712 90.0540 8 555 1 chr6B.!!$R2 547
5 TraesCS6D01G188300 chr6B 716581544 716582101 557 True 706.0 706 89.6610 7 560 1 chr6B.!!$R3 553
6 TraesCS6D01G188300 chr1B 635794938 635795526 588 True 885.0 885 93.8980 4833 5417 1 chr1B.!!$R1 584
7 TraesCS6D01G188300 chr5D 300949773 300951576 1803 True 845.5 876 94.3665 4 555 2 chr5D.!!$R3 551
8 TraesCS6D01G188300 chr5D 431901073 431901650 577 True 658.0 658 87.2010 4833 5417 1 chr5D.!!$R2 584
9 TraesCS6D01G188300 chr5B 344282731 344283282 551 False 809.0 809 93.1160 4 555 1 chr5B.!!$F1 551
10 TraesCS6D01G188300 chr5B 213246434 213247015 581 True 750.0 750 89.9660 4833 5417 1 chr5B.!!$R1 584
11 TraesCS6D01G188300 chr5B 514044591 514045183 592 False 745.0 745 89.5620 4833 5417 1 chr5B.!!$F2 584
12 TraesCS6D01G188300 chr1D 320637548 320638099 551 False 732.0 732 90.6810 4 555 1 chr1D.!!$F1 551
13 TraesCS6D01G188300 chr2A 19923501 19924058 557 False 717.0 717 89.9640 4 557 1 chr2A.!!$F1 553
14 TraesCS6D01G188300 chrUn 77775122 77775664 542 False 713.0 713 90.3810 9 555 1 chrUn.!!$F1 546
15 TraesCS6D01G188300 chr2D 297179392 297179935 543 True 708.0 708 90.0900 4 555 1 chr2D.!!$R1 551
16 TraesCS6D01G188300 chr7A 660547815 660548398 583 True 686.0 686 87.9460 4833 5417 1 chr7A.!!$R1 584
17 TraesCS6D01G188300 chr7A 710956056 710956632 576 False 680.0 680 87.9050 4833 5417 1 chr7A.!!$F1 584
18 TraesCS6D01G188300 chr2B 477154808 477155390 582 True 658.0 658 87.0530 4833 5417 1 chr2B.!!$R1 584
19 TraesCS6D01G188300 chr3A 154983439 154984023 584 False 649.0 649 86.7350 4833 5417 1 chr3A.!!$F1 584

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
116 117 0.038892 CCATGTTGGCAAGCAGTGAC 60.039 55.000 0.0 0.0 34.82 3.67 F
404 411 0.401356 TGAATCAGCACCTGCCAAGA 59.599 50.000 0.0 0.0 43.38 3.02 F
412 419 1.102809 CACCTGCCAAGACAAGCACA 61.103 55.000 0.0 0.0 34.68 4.57 F
981 1957 1.412710 GAGCGGAGAGAGAGAGAGAGA 59.587 57.143 0.0 0.0 0.00 3.10 F
983 1959 1.412710 GCGGAGAGAGAGAGAGAGAGA 59.587 57.143 0.0 0.0 0.00 3.10 F
984 1960 2.546795 GCGGAGAGAGAGAGAGAGAGAG 60.547 59.091 0.0 0.0 0.00 3.20 F
3531 5036 1.154814 GCCTAAGTGCTTCTAGGCGC 61.155 60.000 12.7 0.0 44.52 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 2801 1.327460 CATGGAATTGCCTCGTGTACG 59.673 52.381 0.00 0.00 37.63 3.67 R
2190 3695 7.095017 GGCAGCATTACATATTCTAAAGAGTCC 60.095 40.741 0.00 0.00 0.00 3.85 R
2956 4461 8.434661 GCATTAAAAGAAACACAATGTACCATG 58.565 33.333 0.00 0.00 0.00 3.66 R
3286 4791 5.687770 TTTCAATTCTCTTGCGTTCATCA 57.312 34.783 0.00 0.00 0.00 3.07 R
3531 5036 9.385902 CAAAATATCTTGTATAGAAACATGGCG 57.614 33.333 0.00 0.00 36.22 5.69 R
4046 5553 4.648762 TGTTTTGCTTCAGAAATTCTGGGA 59.351 37.500 21.35 10.62 44.39 4.37 R
4940 6456 0.459585 TCATAGTTCACCGCCGAAGC 60.460 55.000 0.00 0.00 0.00 3.86 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
51 52 4.839550 AGAGCATAGTCATCATCCATCACT 59.160 41.667 0.00 0.00 0.00 3.41
76 77 1.373497 GCTAGATCGCCCATGTCGG 60.373 63.158 0.00 0.00 0.00 4.79
89 90 1.037579 ATGTCGGGAGCTCATCGTGA 61.038 55.000 22.12 13.49 0.00 4.35
115 116 0.178995 TCCATGTTGGCAAGCAGTGA 60.179 50.000 0.00 0.74 37.47 3.41
116 117 0.038892 CCATGTTGGCAAGCAGTGAC 60.039 55.000 0.00 0.00 34.82 3.67
259 266 2.754552 TGCCTGAGTGATTTGTTATGCC 59.245 45.455 0.00 0.00 0.00 4.40
404 411 0.401356 TGAATCAGCACCTGCCAAGA 59.599 50.000 0.00 0.00 43.38 3.02
412 419 1.102809 CACCTGCCAAGACAAGCACA 61.103 55.000 0.00 0.00 34.68 4.57
473 481 1.544759 GGGAGAAAAACCAGCGGAAGA 60.545 52.381 1.50 0.00 0.00 2.87
544 553 3.199946 CAGGCTACCAACTCCTCCATTAA 59.800 47.826 0.00 0.00 0.00 1.40
620 629 2.811431 CCTGCACAATGAAAACGGACTA 59.189 45.455 0.00 0.00 0.00 2.59
633 642 5.488645 AAACGGACTAAAACAACAACGAT 57.511 34.783 0.00 0.00 0.00 3.73
634 643 4.461992 ACGGACTAAAACAACAACGATG 57.538 40.909 0.00 0.00 0.00 3.84
635 644 4.121317 ACGGACTAAAACAACAACGATGA 58.879 39.130 0.00 0.00 0.00 2.92
636 645 4.753107 ACGGACTAAAACAACAACGATGAT 59.247 37.500 0.00 0.00 0.00 2.45
637 646 5.079406 CGGACTAAAACAACAACGATGATG 58.921 41.667 0.00 0.00 35.60 3.07
638 647 5.333798 CGGACTAAAACAACAACGATGATGT 60.334 40.000 2.67 2.67 43.56 3.06
639 648 6.077838 GGACTAAAACAACAACGATGATGTC 58.922 40.000 8.96 0.00 41.18 3.06
657 666 2.169144 TGTCGGCTGATGTCAGATGAAT 59.831 45.455 13.94 0.00 46.59 2.57
669 678 8.048514 TGATGTCAGATGAATGAGACCAAATTA 58.951 33.333 0.00 0.00 0.00 1.40
681 690 7.734924 TGAGACCAAATTATATCTCATGTGC 57.265 36.000 10.05 0.00 41.99 4.57
700 709 8.217111 TCATGTGCACTCCCTATGAATAAAATA 58.783 33.333 19.41 0.00 0.00 1.40
706 715 8.560374 GCACTCCCTATGAATAAAATACTTGTC 58.440 37.037 0.00 0.00 0.00 3.18
728 744 4.988540 TCGCCGAGAAAATCCTTGTATATG 59.011 41.667 0.00 0.00 0.00 1.78
981 1957 1.412710 GAGCGGAGAGAGAGAGAGAGA 59.587 57.143 0.00 0.00 0.00 3.10
982 1958 1.414181 AGCGGAGAGAGAGAGAGAGAG 59.586 57.143 0.00 0.00 0.00 3.20
983 1959 1.412710 GCGGAGAGAGAGAGAGAGAGA 59.587 57.143 0.00 0.00 0.00 3.10
984 1960 2.546795 GCGGAGAGAGAGAGAGAGAGAG 60.547 59.091 0.00 0.00 0.00 3.20
1516 2497 5.294306 TGAGTGCACTATATAGCTGTTTTGC 59.706 40.000 21.73 10.97 0.00 3.68
1591 2573 9.309516 TGACATACTTAACACGATTCTTTATCC 57.690 33.333 0.00 0.00 0.00 2.59
1671 2653 4.356405 TGCATGCAGCCATTAGTATACT 57.644 40.909 18.46 10.87 44.83 2.12
2042 3545 4.514441 CAGTCATGGAAATGTATGCCTCTC 59.486 45.833 0.00 0.00 0.00 3.20
2080 3583 8.836268 ATCATGTGCTTGTTTATTTTGTGATT 57.164 26.923 0.00 0.00 0.00 2.57
2190 3695 6.122277 TCTGTTATTAAAATGCCCTCTCTGG 58.878 40.000 0.00 0.00 0.00 3.86
2956 4461 5.858581 GCGATGATATATTTGGCAAAGAACC 59.141 40.000 18.61 7.83 0.00 3.62
2987 4492 8.130307 ACATTGTGTTTCTTTTAATGCACTTC 57.870 30.769 0.00 0.00 33.28 3.01
3028 4533 3.438781 ACCAACACATTGCAGTTATACGG 59.561 43.478 0.00 0.00 34.17 4.02
3081 4586 9.334947 CTTCATGTGATGATTATTGTTCTACCT 57.665 33.333 0.00 0.00 39.39 3.08
3531 5036 1.154814 GCCTAAGTGCTTCTAGGCGC 61.155 60.000 12.70 0.00 44.52 6.53
4046 5553 5.128919 GTCATAATTCTCACCCTGAATGCT 58.871 41.667 0.00 0.00 34.74 3.79
4138 5645 5.625311 GTGCTTACATTCTAAGTGCAACAAC 59.375 40.000 0.00 0.00 41.43 3.32
4152 5659 5.121142 AGTGCAACAACGCGTAACTTTATAT 59.879 36.000 14.46 0.00 41.43 0.86
4153 5660 6.310956 AGTGCAACAACGCGTAACTTTATATA 59.689 34.615 14.46 0.00 41.43 0.86
4557 6064 4.320608 TTGATTCTTTCCTTTGTGTGGC 57.679 40.909 0.00 0.00 0.00 5.01
4780 6287 2.028420 TGGAAGATCCAGCATCAACG 57.972 50.000 0.00 0.00 42.67 4.10
4781 6288 1.278985 TGGAAGATCCAGCATCAACGT 59.721 47.619 0.00 0.00 42.67 3.99
4782 6289 2.499693 TGGAAGATCCAGCATCAACGTA 59.500 45.455 0.00 0.00 42.67 3.57
4783 6290 3.055458 TGGAAGATCCAGCATCAACGTAA 60.055 43.478 0.00 0.00 42.67 3.18
4784 6291 3.938963 GGAAGATCCAGCATCAACGTAAA 59.061 43.478 0.00 0.00 36.28 2.01
4785 6292 4.394920 GGAAGATCCAGCATCAACGTAAAA 59.605 41.667 0.00 0.00 36.28 1.52
4786 6293 4.946784 AGATCCAGCATCAACGTAAAAC 57.053 40.909 0.00 0.00 33.29 2.43
4787 6294 4.323417 AGATCCAGCATCAACGTAAAACA 58.677 39.130 0.00 0.00 33.29 2.83
4788 6295 4.759693 AGATCCAGCATCAACGTAAAACAA 59.240 37.500 0.00 0.00 33.29 2.83
4789 6296 4.217754 TCCAGCATCAACGTAAAACAAC 57.782 40.909 0.00 0.00 0.00 3.32
4790 6297 3.628032 TCCAGCATCAACGTAAAACAACA 59.372 39.130 0.00 0.00 0.00 3.33
4791 6298 4.096532 TCCAGCATCAACGTAAAACAACAA 59.903 37.500 0.00 0.00 0.00 2.83
4792 6299 4.440758 CCAGCATCAACGTAAAACAACAAG 59.559 41.667 0.00 0.00 0.00 3.16
4793 6300 4.440758 CAGCATCAACGTAAAACAACAAGG 59.559 41.667 0.00 0.00 0.00 3.61
4794 6301 4.097286 AGCATCAACGTAAAACAACAAGGT 59.903 37.500 0.00 0.00 0.00 3.50
4795 6302 4.206200 GCATCAACGTAAAACAACAAGGTG 59.794 41.667 0.00 0.00 0.00 4.00
4796 6303 4.358494 TCAACGTAAAACAACAAGGTGG 57.642 40.909 0.00 0.00 0.00 4.61
4797 6304 3.757493 TCAACGTAAAACAACAAGGTGGT 59.243 39.130 0.00 0.00 0.00 4.16
4798 6305 3.768468 ACGTAAAACAACAAGGTGGTG 57.232 42.857 0.00 0.00 41.80 4.17
4799 6306 3.345414 ACGTAAAACAACAAGGTGGTGA 58.655 40.909 0.00 0.00 37.20 4.02
4800 6307 3.757493 ACGTAAAACAACAAGGTGGTGAA 59.243 39.130 0.00 0.00 37.20 3.18
4801 6308 4.142556 ACGTAAAACAACAAGGTGGTGAAG 60.143 41.667 0.00 0.00 37.20 3.02
4802 6309 3.885724 AAAACAACAAGGTGGTGAAGG 57.114 42.857 0.00 0.00 37.20 3.46
4803 6310 2.525105 AACAACAAGGTGGTGAAGGT 57.475 45.000 0.00 0.00 37.20 3.50
4804 6311 2.052782 ACAACAAGGTGGTGAAGGTC 57.947 50.000 0.00 0.00 37.20 3.85
4805 6312 1.318576 CAACAAGGTGGTGAAGGTCC 58.681 55.000 0.00 0.00 37.20 4.46
4806 6313 1.133792 CAACAAGGTGGTGAAGGTCCT 60.134 52.381 0.00 0.00 37.20 3.85
4807 6314 2.105821 CAACAAGGTGGTGAAGGTCCTA 59.894 50.000 0.00 0.00 37.20 2.94
4808 6315 1.978580 ACAAGGTGGTGAAGGTCCTAG 59.021 52.381 0.00 0.00 0.00 3.02
4809 6316 2.257207 CAAGGTGGTGAAGGTCCTAGA 58.743 52.381 0.00 0.00 0.00 2.43
4810 6317 2.637872 CAAGGTGGTGAAGGTCCTAGAA 59.362 50.000 0.00 0.00 0.00 2.10
4811 6318 2.258109 AGGTGGTGAAGGTCCTAGAAC 58.742 52.381 0.00 0.00 0.00 3.01
4812 6319 1.278413 GGTGGTGAAGGTCCTAGAACC 59.722 57.143 9.63 9.63 39.80 3.62
4813 6320 1.975680 GTGGTGAAGGTCCTAGAACCA 59.024 52.381 13.71 13.71 42.12 3.67
4814 6321 2.370849 GTGGTGAAGGTCCTAGAACCAA 59.629 50.000 17.62 4.56 42.12 3.67
4815 6322 3.050089 TGGTGAAGGTCCTAGAACCAAA 58.950 45.455 14.86 0.00 42.12 3.28
4816 6323 3.655777 TGGTGAAGGTCCTAGAACCAAAT 59.344 43.478 14.86 0.00 42.12 2.32
4817 6324 4.010349 GGTGAAGGTCCTAGAACCAAATG 58.990 47.826 0.00 0.00 42.12 2.32
4818 6325 4.263331 GGTGAAGGTCCTAGAACCAAATGA 60.263 45.833 0.00 0.00 42.12 2.57
4819 6326 4.695928 GTGAAGGTCCTAGAACCAAATGAC 59.304 45.833 0.00 0.00 42.12 3.06
4820 6327 4.262617 GAAGGTCCTAGAACCAAATGACC 58.737 47.826 0.00 1.62 42.12 4.02
4821 6328 2.576648 AGGTCCTAGAACCAAATGACCC 59.423 50.000 0.00 0.00 42.53 4.46
4822 6329 2.629051 GTCCTAGAACCAAATGACCCG 58.371 52.381 0.00 0.00 0.00 5.28
4823 6330 2.235402 GTCCTAGAACCAAATGACCCGA 59.765 50.000 0.00 0.00 0.00 5.14
4824 6331 2.907696 TCCTAGAACCAAATGACCCGAA 59.092 45.455 0.00 0.00 0.00 4.30
4825 6332 3.055385 TCCTAGAACCAAATGACCCGAAG 60.055 47.826 0.00 0.00 0.00 3.79
4826 6333 3.055385 CCTAGAACCAAATGACCCGAAGA 60.055 47.826 0.00 0.00 0.00 2.87
4827 6334 3.721087 AGAACCAAATGACCCGAAGAT 57.279 42.857 0.00 0.00 0.00 2.40
4828 6335 3.610911 AGAACCAAATGACCCGAAGATC 58.389 45.455 0.00 0.00 0.00 2.75
4829 6336 3.009033 AGAACCAAATGACCCGAAGATCA 59.991 43.478 0.00 0.00 0.00 2.92
4830 6337 3.433306 ACCAAATGACCCGAAGATCAA 57.567 42.857 0.00 0.00 0.00 2.57
4831 6338 3.761897 ACCAAATGACCCGAAGATCAAA 58.238 40.909 0.00 0.00 0.00 2.69
4894 6409 8.478775 AAAGAAAGAAAAACAGCCCTAATAGT 57.521 30.769 0.00 0.00 0.00 2.12
4927 6443 5.876357 ACACTCCATACAAACCACACTAAT 58.124 37.500 0.00 0.00 0.00 1.73
4940 6456 2.545526 CACACTAATAATGCAGCTCCGG 59.454 50.000 0.00 0.00 0.00 5.14
4994 6511 2.107041 TTGGCGTCACGAAGGACCAT 62.107 55.000 0.00 0.00 34.24 3.55
5107 6628 1.673033 CGAACATGCCGGAGAAGAAGT 60.673 52.381 5.05 0.00 0.00 3.01
5150 6671 0.032678 CGCCTCCGATATTGCTCACT 59.967 55.000 0.00 0.00 36.29 3.41
5209 6730 1.001633 GTCGTAGGAAGCACCAAAGGA 59.998 52.381 2.96 0.00 42.04 3.36
5316 6838 4.351874 TTTCACCCGAAAGACTTGATCT 57.648 40.909 0.00 0.00 40.46 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.523968 TACACACGCCGACTATTCGC 60.524 55.000 0.00 0.00 44.43 4.70
1 2 1.186030 GTACACACGCCGACTATTCG 58.814 55.000 0.00 0.00 45.44 3.34
2 3 2.267188 TGTACACACGCCGACTATTC 57.733 50.000 0.00 0.00 0.00 1.75
51 52 1.141019 GGGCGATCTAGCGTTCACA 59.859 57.895 0.00 0.00 38.18 3.58
76 77 2.349886 GACAACAATCACGATGAGCTCC 59.650 50.000 12.15 0.00 0.00 4.70
89 90 2.548493 GCTTGCCAACATGGACAACAAT 60.548 45.455 0.00 0.00 40.96 2.71
115 116 0.456221 CTCTCAACGACATAGCCGGT 59.544 55.000 1.90 0.00 0.00 5.28
116 117 0.872021 GCTCTCAACGACATAGCCGG 60.872 60.000 0.00 0.00 0.00 6.13
259 266 7.489113 CCTTCCAAAACAAAATCAGATATTCCG 59.511 37.037 0.00 0.00 0.00 4.30
379 386 2.429610 GGCAGGTGCTGATTCAATTCAT 59.570 45.455 1.26 0.00 41.70 2.57
404 411 2.365293 GGGGATCTTGTTTTGTGCTTGT 59.635 45.455 0.00 0.00 0.00 3.16
473 481 0.898789 CGTACCACCTCTCACCACCT 60.899 60.000 0.00 0.00 0.00 4.00
512 520 0.625316 TGGTAGCCTGGTACGGTCTA 59.375 55.000 0.00 0.00 0.00 2.59
544 553 9.692325 AGGCTAATTTTTCATCATCTCTACTTT 57.308 29.630 0.00 0.00 0.00 2.66
605 614 7.387945 GTTGTTGTTTTAGTCCGTTTTCATTG 58.612 34.615 0.00 0.00 0.00 2.82
633 642 1.185315 TCTGACATCAGCCGACATCA 58.815 50.000 3.88 0.00 43.46 3.07
634 643 2.133553 CATCTGACATCAGCCGACATC 58.866 52.381 3.88 0.00 43.46 3.06
635 644 1.758862 TCATCTGACATCAGCCGACAT 59.241 47.619 3.88 0.00 43.46 3.06
636 645 1.185315 TCATCTGACATCAGCCGACA 58.815 50.000 3.88 0.00 43.46 4.35
637 646 2.299993 TTCATCTGACATCAGCCGAC 57.700 50.000 3.88 0.00 43.46 4.79
638 647 2.431782 TCATTCATCTGACATCAGCCGA 59.568 45.455 3.88 0.58 43.46 5.54
639 648 2.801111 CTCATTCATCTGACATCAGCCG 59.199 50.000 3.88 0.00 43.46 5.52
640 649 3.808726 GTCTCATTCATCTGACATCAGCC 59.191 47.826 3.88 0.00 43.46 4.85
641 650 3.808726 GGTCTCATTCATCTGACATCAGC 59.191 47.826 3.88 0.00 43.46 4.26
642 651 5.019785 TGGTCTCATTCATCTGACATCAG 57.980 43.478 2.24 2.24 45.08 2.90
669 678 5.089434 TCATAGGGAGTGCACATGAGATAT 58.911 41.667 21.04 6.56 0.00 1.63
672 681 2.750814 TCATAGGGAGTGCACATGAGA 58.249 47.619 21.04 4.49 0.00 3.27
678 687 8.345565 CAAGTATTTTATTCATAGGGAGTGCAC 58.654 37.037 9.40 9.40 0.00 4.57
681 690 8.765219 CGACAAGTATTTTATTCATAGGGAGTG 58.235 37.037 0.00 0.00 0.00 3.51
700 709 1.002087 AGGATTTTCTCGGCGACAAGT 59.998 47.619 4.99 0.00 0.00 3.16
706 715 4.750098 ACATATACAAGGATTTTCTCGGCG 59.250 41.667 0.00 0.00 0.00 6.46
981 1957 2.611800 TCATGGCTGGGTGGCTCT 60.612 61.111 0.00 0.00 42.34 4.09
982 1958 1.992519 ATCTCATGGCTGGGTGGCTC 61.993 60.000 0.00 0.00 42.34 4.70
983 1959 2.005266 ATCTCATGGCTGGGTGGCT 61.005 57.895 0.00 0.00 42.34 4.75
984 1960 1.826921 CATCTCATGGCTGGGTGGC 60.827 63.158 0.00 0.00 42.18 5.01
1516 2497 4.578928 CCTAAGAAATGATAAACCACGGGG 59.421 45.833 0.00 0.00 41.29 5.73
1671 2653 1.546923 CACATTGCAGCTCCATTTGGA 59.453 47.619 0.00 0.00 43.08 3.53
1819 2801 1.327460 CATGGAATTGCCTCGTGTACG 59.673 52.381 0.00 0.00 37.63 3.67
2042 3545 7.191551 ACAAGCACATGATAAATTTCAGATCG 58.808 34.615 0.00 0.00 0.00 3.69
2190 3695 7.095017 GGCAGCATTACATATTCTAAAGAGTCC 60.095 40.741 0.00 0.00 0.00 3.85
2956 4461 8.434661 GCATTAAAAGAAACACAATGTACCATG 58.565 33.333 0.00 0.00 0.00 3.66
2987 4492 8.769891 GTGTTGGTGGGAAAATATTTTGTAAAG 58.230 33.333 17.98 0.00 0.00 1.85
3081 4586 7.014988 AGCCTTGCCATTTTCCTTAAATAAA 57.985 32.000 0.00 0.00 34.69 1.40
3286 4791 5.687770 TTTCAATTCTCTTGCGTTCATCA 57.312 34.783 0.00 0.00 0.00 3.07
3531 5036 9.385902 CAAAATATCTTGTATAGAAACATGGCG 57.614 33.333 0.00 0.00 36.22 5.69
4046 5553 4.648762 TGTTTTGCTTCAGAAATTCTGGGA 59.351 37.500 21.35 10.62 44.39 4.37
4138 5645 7.579726 ACAGAGGTAGTATATAAAGTTACGCG 58.420 38.462 3.53 3.53 0.00 6.01
4408 5915 2.697751 GCTGTAGTCCATCTCATCCTGT 59.302 50.000 0.00 0.00 0.00 4.00
4557 6064 7.710896 ACAATTCTCAAAAGAGAAAAGGTCTG 58.289 34.615 11.46 5.92 43.44 3.51
4687 6194 3.689161 CCGTTGGATAGATGCAGTTGAAA 59.311 43.478 0.00 0.00 0.00 2.69
4761 6268 1.278985 ACGTTGATGCTGGATCTTCCA 59.721 47.619 10.56 0.00 45.98 3.53
4762 6269 2.029838 ACGTTGATGCTGGATCTTCC 57.970 50.000 10.56 0.00 36.96 3.46
4763 6270 5.106712 TGTTTTACGTTGATGCTGGATCTTC 60.107 40.000 10.56 3.05 31.55 2.87
4764 6271 4.759693 TGTTTTACGTTGATGCTGGATCTT 59.240 37.500 10.56 0.00 31.55 2.40
4765 6272 4.323417 TGTTTTACGTTGATGCTGGATCT 58.677 39.130 10.56 0.00 31.55 2.75
4766 6273 4.678509 TGTTTTACGTTGATGCTGGATC 57.321 40.909 1.79 1.79 0.00 3.36
4767 6274 4.277174 TGTTGTTTTACGTTGATGCTGGAT 59.723 37.500 0.00 0.00 0.00 3.41
4768 6275 3.628032 TGTTGTTTTACGTTGATGCTGGA 59.372 39.130 0.00 0.00 0.00 3.86
4769 6276 3.958704 TGTTGTTTTACGTTGATGCTGG 58.041 40.909 0.00 0.00 0.00 4.85
4770 6277 4.440758 CCTTGTTGTTTTACGTTGATGCTG 59.559 41.667 0.00 0.00 0.00 4.41
4771 6278 4.097286 ACCTTGTTGTTTTACGTTGATGCT 59.903 37.500 0.00 0.00 0.00 3.79
4772 6279 4.206200 CACCTTGTTGTTTTACGTTGATGC 59.794 41.667 0.00 0.00 0.00 3.91
4773 6280 4.737765 CCACCTTGTTGTTTTACGTTGATG 59.262 41.667 0.00 0.00 0.00 3.07
4774 6281 4.399934 ACCACCTTGTTGTTTTACGTTGAT 59.600 37.500 0.00 0.00 0.00 2.57
4775 6282 3.757493 ACCACCTTGTTGTTTTACGTTGA 59.243 39.130 0.00 0.00 0.00 3.18
4776 6283 3.854809 CACCACCTTGTTGTTTTACGTTG 59.145 43.478 0.00 0.00 0.00 4.10
4777 6284 3.757493 TCACCACCTTGTTGTTTTACGTT 59.243 39.130 0.00 0.00 0.00 3.99
4778 6285 3.345414 TCACCACCTTGTTGTTTTACGT 58.655 40.909 0.00 0.00 0.00 3.57
4779 6286 4.347813 CTTCACCACCTTGTTGTTTTACG 58.652 43.478 0.00 0.00 0.00 3.18
4780 6287 4.158949 ACCTTCACCACCTTGTTGTTTTAC 59.841 41.667 0.00 0.00 0.00 2.01
4781 6288 4.345854 ACCTTCACCACCTTGTTGTTTTA 58.654 39.130 0.00 0.00 0.00 1.52
4782 6289 3.169908 ACCTTCACCACCTTGTTGTTTT 58.830 40.909 0.00 0.00 0.00 2.43
4783 6290 2.758423 GACCTTCACCACCTTGTTGTTT 59.242 45.455 0.00 0.00 0.00 2.83
4784 6291 2.375146 GACCTTCACCACCTTGTTGTT 58.625 47.619 0.00 0.00 0.00 2.83
4785 6292 1.409661 GGACCTTCACCACCTTGTTGT 60.410 52.381 0.00 0.00 0.00 3.32
4786 6293 1.133792 AGGACCTTCACCACCTTGTTG 60.134 52.381 0.00 0.00 0.00 3.33
4787 6294 1.222567 AGGACCTTCACCACCTTGTT 58.777 50.000 0.00 0.00 0.00 2.83
4788 6295 1.978580 CTAGGACCTTCACCACCTTGT 59.021 52.381 0.00 0.00 34.42 3.16
4789 6296 2.257207 TCTAGGACCTTCACCACCTTG 58.743 52.381 0.00 0.00 34.42 3.61
4790 6297 2.638363 GTTCTAGGACCTTCACCACCTT 59.362 50.000 0.00 0.00 34.42 3.50
4791 6298 2.258109 GTTCTAGGACCTTCACCACCT 58.742 52.381 0.00 0.00 36.65 4.00
4792 6299 1.278413 GGTTCTAGGACCTTCACCACC 59.722 57.143 13.55 0.00 36.73 4.61
4793 6300 1.975680 TGGTTCTAGGACCTTCACCAC 59.024 52.381 21.31 0.00 40.47 4.16
4794 6301 2.409064 TGGTTCTAGGACCTTCACCA 57.591 50.000 21.31 12.90 40.47 4.17
4795 6302 3.782656 TTTGGTTCTAGGACCTTCACC 57.217 47.619 21.31 4.36 40.47 4.02
4796 6303 4.695928 GTCATTTGGTTCTAGGACCTTCAC 59.304 45.833 21.31 7.10 40.47 3.18
4797 6304 4.263331 GGTCATTTGGTTCTAGGACCTTCA 60.263 45.833 21.31 5.44 41.17 3.02
4798 6305 4.262617 GGTCATTTGGTTCTAGGACCTTC 58.737 47.826 21.31 5.30 41.17 3.46
4799 6306 3.010250 GGGTCATTTGGTTCTAGGACCTT 59.990 47.826 21.31 3.52 43.30 3.50
4800 6307 2.576648 GGGTCATTTGGTTCTAGGACCT 59.423 50.000 21.31 0.00 43.30 3.85
4801 6308 2.679930 CGGGTCATTTGGTTCTAGGACC 60.680 54.545 13.97 13.97 43.10 4.46
4802 6309 2.235402 TCGGGTCATTTGGTTCTAGGAC 59.765 50.000 0.00 0.00 0.00 3.85
4803 6310 2.542550 TCGGGTCATTTGGTTCTAGGA 58.457 47.619 0.00 0.00 0.00 2.94
4804 6311 3.055385 TCTTCGGGTCATTTGGTTCTAGG 60.055 47.826 0.00 0.00 0.00 3.02
4805 6312 4.202245 TCTTCGGGTCATTTGGTTCTAG 57.798 45.455 0.00 0.00 0.00 2.43
4806 6313 4.224147 TGATCTTCGGGTCATTTGGTTCTA 59.776 41.667 0.00 0.00 0.00 2.10
4807 6314 3.009033 TGATCTTCGGGTCATTTGGTTCT 59.991 43.478 0.00 0.00 0.00 3.01
4808 6315 3.343617 TGATCTTCGGGTCATTTGGTTC 58.656 45.455 0.00 0.00 0.00 3.62
4809 6316 3.433306 TGATCTTCGGGTCATTTGGTT 57.567 42.857 0.00 0.00 0.00 3.67
4810 6317 3.433306 TTGATCTTCGGGTCATTTGGT 57.567 42.857 0.00 0.00 0.00 3.67
4811 6318 4.009675 TCTTTGATCTTCGGGTCATTTGG 58.990 43.478 0.00 0.00 0.00 3.28
4812 6319 5.392380 CCTTCTTTGATCTTCGGGTCATTTG 60.392 44.000 0.00 0.00 0.00 2.32
4813 6320 4.702131 CCTTCTTTGATCTTCGGGTCATTT 59.298 41.667 0.00 0.00 0.00 2.32
4814 6321 4.263506 ACCTTCTTTGATCTTCGGGTCATT 60.264 41.667 0.00 0.00 0.00 2.57
4815 6322 3.264450 ACCTTCTTTGATCTTCGGGTCAT 59.736 43.478 0.00 0.00 0.00 3.06
4816 6323 2.637872 ACCTTCTTTGATCTTCGGGTCA 59.362 45.455 0.00 0.00 0.00 4.02
4817 6324 3.263261 GACCTTCTTTGATCTTCGGGTC 58.737 50.000 0.00 0.00 35.85 4.46
4818 6325 2.027100 GGACCTTCTTTGATCTTCGGGT 60.027 50.000 0.00 0.00 0.00 5.28
4819 6326 2.237392 AGGACCTTCTTTGATCTTCGGG 59.763 50.000 0.00 0.00 0.00 5.14
4820 6327 3.618690 AGGACCTTCTTTGATCTTCGG 57.381 47.619 0.00 0.00 0.00 4.30
4821 6328 4.402793 TCCTAGGACCTTCTTTGATCTTCG 59.597 45.833 7.62 0.00 0.00 3.79
4822 6329 5.666462 GTCCTAGGACCTTCTTTGATCTTC 58.334 45.833 28.87 0.00 39.08 2.87
4823 6330 5.685520 GTCCTAGGACCTTCTTTGATCTT 57.314 43.478 28.87 0.00 39.08 2.40
4894 6409 1.879380 GTATGGAGTGTTGTGCTGCAA 59.121 47.619 2.77 0.00 37.81 4.08
4940 6456 0.459585 TCATAGTTCACCGCCGAAGC 60.460 55.000 0.00 0.00 0.00 3.86
4946 6462 4.567159 CCTAGTTTCTTCATAGTTCACCGC 59.433 45.833 0.00 0.00 0.00 5.68
4994 6511 2.336088 GACCGGTGGTTCGTTCGA 59.664 61.111 14.63 0.00 35.25 3.71
5043 6564 0.664466 CTGTGAAGTCGAAGCTGCGA 60.664 55.000 14.32 14.32 38.07 5.10
5047 6568 1.221414 GTTGCTGTGAAGTCGAAGCT 58.779 50.000 6.14 0.00 36.60 3.74
5107 6628 0.687920 TTTGGTCATGGTAGTCGGCA 59.312 50.000 0.00 0.00 0.00 5.69
5150 6671 3.047280 GTGGCAACGATGACGGCA 61.047 61.111 0.00 0.00 44.46 5.69
5209 6730 4.991687 GGAGTCGTCTTGAAGACTTTGATT 59.008 41.667 21.61 9.56 46.52 2.57
5246 6768 1.007336 GGCGTCGTCTTCAACATCGT 61.007 55.000 0.00 0.00 0.00 3.73
5316 6838 1.077169 TCTTCACAGCCTCTACTCCCA 59.923 52.381 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.