Multiple sequence alignment - TraesCS7A01G196200

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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 TraesCS7A01G196200 chr7A 100.000 6753 0 0 1 6753 156101788 156108540 0.000000e+00 12471
1 TraesCS7A01G196200 chr7B 94.883 5335 193 33 1476 6753 116372529 116377840 0.000000e+00 8266
2 TraesCS7A01G196200 chr7B 95.885 802 20 7 686 1487 116371719 116372507 0.000000e+00 1286
3 TraesCS7A01G196200 chr7B 84.286 630 88 8 59 680 107765456 107764830 7.490000e-169 604
4 TraesCS7A01G196200 chr7B 81.675 633 105 8 59 684 374773143 374772515 3.610000e-142 516
5 TraesCS7A01G196200 chr7D 95.356 3359 101 21 2787 6103 154177320 154180665 0.000000e+00 5288
6 TraesCS7A01G196200 chr7D 94.813 1793 57 14 687 2473 154174832 154176594 0.000000e+00 2763
7 TraesCS7A01G196200 chr7D 95.086 753 28 5 6010 6753 154180664 154181416 0.000000e+00 1177
8 TraesCS7A01G196200 chr7D 83.072 638 90 13 59 683 51783829 51784461 1.270000e-156 564
9 TraesCS7A01G196200 chr7D 97.048 271 5 2 2521 2788 154176892 154177162 2.870000e-123 453
10 TraesCS7A01G196200 chr6A 84.751 623 86 7 60 675 438026754 438026134 3.460000e-172 616
11 TraesCS7A01G196200 chr2D 84.395 628 84 10 60 679 429082295 429081674 7.490000e-169 604
12 TraesCS7A01G196200 chr5B 82.775 627 96 10 62 679 635099718 635099095 3.560000e-152 549
13 TraesCS7A01G196200 chr5B 82.692 624 98 7 59 675 72078325 72077705 4.610000e-151 545
14 TraesCS7A01G196200 chr1A 82.343 623 101 6 60 675 563185122 563184502 3.590000e-147 532
15 TraesCS7A01G196200 chr4B 82.297 627 96 9 60 675 606635046 606635668 4.640000e-146 529


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 TraesCS7A01G196200 chr7A 156101788 156108540 6752 False 12471.00 12471 100.00000 1 6753 1 chr7A.!!$F1 6752
1 TraesCS7A01G196200 chr7B 116371719 116377840 6121 False 4776.00 8266 95.38400 686 6753 2 chr7B.!!$F1 6067
2 TraesCS7A01G196200 chr7B 107764830 107765456 626 True 604.00 604 84.28600 59 680 1 chr7B.!!$R1 621
3 TraesCS7A01G196200 chr7B 374772515 374773143 628 True 516.00 516 81.67500 59 684 1 chr7B.!!$R2 625
4 TraesCS7A01G196200 chr7D 154174832 154181416 6584 False 2420.25 5288 95.57575 687 6753 4 chr7D.!!$F2 6066
5 TraesCS7A01G196200 chr7D 51783829 51784461 632 False 564.00 564 83.07200 59 683 1 chr7D.!!$F1 624
6 TraesCS7A01G196200 chr6A 438026134 438026754 620 True 616.00 616 84.75100 60 675 1 chr6A.!!$R1 615
7 TraesCS7A01G196200 chr2D 429081674 429082295 621 True 604.00 604 84.39500 60 679 1 chr2D.!!$R1 619
8 TraesCS7A01G196200 chr5B 635099095 635099718 623 True 549.00 549 82.77500 62 679 1 chr5B.!!$R2 617
9 TraesCS7A01G196200 chr5B 72077705 72078325 620 True 545.00 545 82.69200 59 675 1 chr5B.!!$R1 616
10 TraesCS7A01G196200 chr1A 563184502 563185122 620 True 532.00 532 82.34300 60 675 1 chr1A.!!$R1 615
11 TraesCS7A01G196200 chr4B 606635046 606635668 622 False 529.00 529 82.29700 60 675 1 chr4B.!!$F1 615

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
502 509 0.385598 CGTGCACGAAGACTTCTCGA 60.386 55.000 34.93 0.0 43.02 4.04 F
938 951 1.153549 GCTCGCTCGATTCCCACTT 60.154 57.895 0.00 0.0 0.00 3.16 F
1637 1686 0.105593 ATGCGCCTACCATGTCAGAG 59.894 55.000 4.18 0.0 0.00 3.35 F
1923 1974 1.509072 ACCGGGGGTACTATAATCCCA 59.491 52.381 6.32 0.0 42.71 4.37 F
2480 2534 2.360483 TGTTTTGCACATACCCACACAG 59.640 45.455 0.00 0.0 0.00 3.66 F
3961 4433 2.369203 TGACACGAGTTCCAACCCATAA 59.631 45.455 0.00 0.0 0.00 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1356 1373 0.447801 CAGGTTGCGGAATGTAGCAC 59.552 55.000 0.00 0.00 43.69 4.40 R
1923 1974 3.272551 AGGAGGGTGTATTGACTAGTCCT 59.727 47.826 20.11 7.79 0.00 3.85 R
3234 3705 1.804151 CGGGATATGGTAACGGCATTG 59.196 52.381 0.00 0.00 42.51 2.82 R
3575 4046 2.461695 TCCACCTCTAGAGCTTTCTGG 58.538 52.381 14.73 11.96 0.00 3.86 R
4218 4697 1.908619 TGGCCTTGCAATCTCTCTACA 59.091 47.619 3.32 0.00 0.00 2.74 R
5799 6313 1.114722 CCAAAACAAGCTCTGGGCCA 61.115 55.000 5.85 5.85 43.05 5.36 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
19 20 2.629336 CTAGCCCAGAAGAACCATCC 57.371 55.000 0.00 0.00 0.00 3.51
20 21 1.141858 CTAGCCCAGAAGAACCATCCC 59.858 57.143 0.00 0.00 0.00 3.85
21 22 0.551131 AGCCCAGAAGAACCATCCCT 60.551 55.000 0.00 0.00 0.00 4.20
22 23 1.213296 GCCCAGAAGAACCATCCCTA 58.787 55.000 0.00 0.00 0.00 3.53
23 24 1.564348 GCCCAGAAGAACCATCCCTAA 59.436 52.381 0.00 0.00 0.00 2.69
24 25 2.684038 GCCCAGAAGAACCATCCCTAAC 60.684 54.545 0.00 0.00 0.00 2.34
25 26 2.846827 CCCAGAAGAACCATCCCTAACT 59.153 50.000 0.00 0.00 0.00 2.24
26 27 3.118223 CCCAGAAGAACCATCCCTAACTC 60.118 52.174 0.00 0.00 0.00 3.01
27 28 3.777522 CCAGAAGAACCATCCCTAACTCT 59.222 47.826 0.00 0.00 0.00 3.24
28 29 4.383552 CCAGAAGAACCATCCCTAACTCTG 60.384 50.000 0.00 0.00 0.00 3.35
29 30 4.467795 CAGAAGAACCATCCCTAACTCTGA 59.532 45.833 0.00 0.00 0.00 3.27
30 31 5.046304 CAGAAGAACCATCCCTAACTCTGAA 60.046 44.000 0.00 0.00 0.00 3.02
31 32 5.728741 AGAAGAACCATCCCTAACTCTGAAT 59.271 40.000 0.00 0.00 0.00 2.57
32 33 6.216456 AGAAGAACCATCCCTAACTCTGAATT 59.784 38.462 0.00 0.00 0.00 2.17
33 34 5.995446 AGAACCATCCCTAACTCTGAATTC 58.005 41.667 0.00 0.00 0.00 2.17
34 35 5.488919 AGAACCATCCCTAACTCTGAATTCA 59.511 40.000 8.12 8.12 0.00 2.57
35 36 5.983333 ACCATCCCTAACTCTGAATTCAT 57.017 39.130 8.96 0.00 0.00 2.57
36 37 7.348274 AGAACCATCCCTAACTCTGAATTCATA 59.652 37.037 8.96 0.36 0.00 2.15
37 38 7.639062 ACCATCCCTAACTCTGAATTCATAT 57.361 36.000 8.96 0.00 0.00 1.78
38 39 8.742125 ACCATCCCTAACTCTGAATTCATATA 57.258 34.615 8.96 0.00 0.00 0.86
39 40 9.343994 ACCATCCCTAACTCTGAATTCATATAT 57.656 33.333 8.96 0.00 0.00 0.86
40 41 9.610705 CCATCCCTAACTCTGAATTCATATATG 57.389 37.037 8.96 6.36 0.00 1.78
44 45 9.593134 CCCTAACTCTGAATTCATATATGTAGC 57.407 37.037 8.96 1.18 0.00 3.58
51 52 9.573133 TCTGAATTCATATATGTAGCACATACG 57.427 33.333 8.96 0.00 43.13 3.06
52 53 9.573133 CTGAATTCATATATGTAGCACATACGA 57.427 33.333 8.96 6.18 43.13 3.43
53 54 9.353999 TGAATTCATATATGTAGCACATACGAC 57.646 33.333 12.42 0.00 43.13 4.34
54 55 9.353999 GAATTCATATATGTAGCACATACGACA 57.646 33.333 12.42 0.00 43.13 4.35
55 56 9.705290 AATTCATATATGTAGCACATACGACAA 57.295 29.630 12.42 0.00 43.13 3.18
56 57 8.515473 TTCATATATGTAGCACATACGACAAC 57.485 34.615 12.42 0.00 43.13 3.32
57 58 7.653647 TCATATATGTAGCACATACGACAACA 58.346 34.615 12.42 0.00 43.13 3.33
83 84 1.563410 CTTTCCTCTCTCCCAAGGCAT 59.437 52.381 0.00 0.00 32.37 4.40
116 117 2.203082 CCTCCCATCGATCTCCGCA 61.203 63.158 0.00 0.00 38.37 5.69
310 314 2.886523 TCCTCCTCAAGTTCGTTCGTTA 59.113 45.455 0.00 0.00 0.00 3.18
364 368 4.020617 CAGCTCCTTGGGGCGACA 62.021 66.667 5.81 0.00 0.00 4.35
377 381 1.612676 GGCGACAAGGTTAGGGTTTT 58.387 50.000 0.00 0.00 0.00 2.43
385 389 4.131596 CAAGGTTAGGGTTTTCTCGTTGA 58.868 43.478 0.00 0.00 0.00 3.18
387 391 3.390311 AGGTTAGGGTTTTCTCGTTGAGT 59.610 43.478 0.00 0.00 0.00 3.41
408 412 3.536837 GTGTACGCAACAACGATATTTGC 59.463 43.478 0.39 0.00 40.63 3.68
502 509 0.385598 CGTGCACGAAGACTTCTCGA 60.386 55.000 34.93 0.00 43.02 4.04
520 527 1.200252 CGACTGTCATCGACAAGGTCT 59.800 52.381 8.73 0.00 45.13 3.85
530 537 3.710722 CAAGGTCTGGCCGGCTCT 61.711 66.667 28.56 13.16 43.70 4.09
571 578 1.870458 CGCGTCGATGGCTCGTTTA 60.870 57.895 6.79 0.00 45.25 2.01
644 657 1.968493 AGAGGTGCTTTGTACTTCCGA 59.032 47.619 0.00 0.00 0.00 4.55
747 760 1.630244 CGCACAGCTTCCTTCCTTCG 61.630 60.000 0.00 0.00 0.00 3.79
768 781 2.165301 GCCACGCCTACAGCTAACG 61.165 63.158 0.00 0.00 40.39 3.18
776 789 3.185797 CGCCTACAGCTAACGAACTTTTT 59.814 43.478 0.00 0.00 40.39 1.94
778 791 5.107375 CGCCTACAGCTAACGAACTTTTTAA 60.107 40.000 0.00 0.00 40.39 1.52
781 794 5.428496 ACAGCTAACGAACTTTTTAACCC 57.572 39.130 0.00 0.00 0.00 4.11
782 795 4.883006 ACAGCTAACGAACTTTTTAACCCA 59.117 37.500 0.00 0.00 0.00 4.51
783 796 5.533528 ACAGCTAACGAACTTTTTAACCCAT 59.466 36.000 0.00 0.00 0.00 4.00
784 797 6.084277 CAGCTAACGAACTTTTTAACCCATC 58.916 40.000 0.00 0.00 0.00 3.51
785 798 5.182570 AGCTAACGAACTTTTTAACCCATCC 59.817 40.000 0.00 0.00 0.00 3.51
786 799 4.859304 AACGAACTTTTTAACCCATCCC 57.141 40.909 0.00 0.00 0.00 3.85
862 875 7.320443 TCAATCAATTAAACTAAGCTCGCAT 57.680 32.000 0.00 0.00 0.00 4.73
938 951 1.153549 GCTCGCTCGATTCCCACTT 60.154 57.895 0.00 0.00 0.00 3.16
1178 1195 1.351017 GAACTGGTGGATGTTCTCCCA 59.649 52.381 0.00 0.00 44.23 4.37
1356 1373 1.519455 GACGGAGAACATGGCTCGG 60.519 63.158 17.79 17.79 38.30 4.63
1372 1389 1.017177 TCGGTGCTACATTCCGCAAC 61.017 55.000 0.00 0.00 43.35 4.17
1378 1395 0.392998 CTACATTCCGCAACCTGGCT 60.393 55.000 0.00 0.00 0.00 4.75
1502 1551 9.528018 AAATTAATGTTGTGTTCTTCGACAAAT 57.472 25.926 0.00 0.00 33.96 2.32
1529 1578 6.775939 TCGTAGTTGTACATCTACTATCCG 57.224 41.667 28.71 20.36 36.93 4.18
1547 1596 3.656559 TCCGTCAACTTGCTTTAGTACC 58.343 45.455 0.00 0.00 0.00 3.34
1549 1598 4.000988 CCGTCAACTTGCTTTAGTACCAT 58.999 43.478 0.00 0.00 0.00 3.55
1637 1686 0.105593 ATGCGCCTACCATGTCAGAG 59.894 55.000 4.18 0.00 0.00 3.35
1678 1727 5.404366 CGAACTACACATCGAGAAGGAAAAA 59.596 40.000 0.00 0.00 41.43 1.94
1728 1778 3.034635 CTCTGTGGGCTATTACTCACCT 58.965 50.000 0.00 0.00 0.00 4.00
1731 1781 2.500098 TGTGGGCTATTACTCACCTGAC 59.500 50.000 0.00 0.00 0.00 3.51
1790 1840 3.055021 TCCGTTTATCAATGTGTAGGCCA 60.055 43.478 5.01 0.00 0.00 5.36
1923 1974 1.509072 ACCGGGGGTACTATAATCCCA 59.491 52.381 6.32 0.00 42.71 4.37
2043 2096 5.008514 GCTTGAGGGAATGAAAGCTATCTTC 59.991 44.000 0.00 0.00 41.41 2.87
2201 2255 4.626081 ACGCCTGCTCGCTTTGGT 62.626 61.111 0.00 0.00 0.00 3.67
2258 2312 8.510243 TCATAAATGCAACTATGTGTTCATCT 57.490 30.769 14.66 0.00 36.63 2.90
2278 2332 3.625764 TCTCAAGTTCAAAGTTGGTTCGG 59.374 43.478 9.75 0.00 39.30 4.30
2302 2356 8.603181 CGGATGTTCATGAAAACTTTTCTTTTT 58.397 29.630 10.35 0.00 0.00 1.94
2446 2500 6.543465 CAGGCAATATCAGTTCATCAGGTAAA 59.457 38.462 0.00 0.00 0.00 2.01
2469 2523 3.857549 TTACTGTTGCTGTTTTGCACA 57.142 38.095 0.00 0.00 43.20 4.57
2480 2534 2.360483 TGTTTTGCACATACCCACACAG 59.640 45.455 0.00 0.00 0.00 3.66
2491 2545 6.203530 CACATACCCACACAGTATCAATGATC 59.796 42.308 0.00 0.00 0.00 2.92
2492 2546 4.156455 ACCCACACAGTATCAATGATCC 57.844 45.455 0.00 0.00 0.00 3.36
2493 2547 3.117888 ACCCACACAGTATCAATGATCCC 60.118 47.826 0.00 0.00 0.00 3.85
2494 2548 3.480470 CCACACAGTATCAATGATCCCC 58.520 50.000 0.00 0.00 0.00 4.81
2495 2549 3.480470 CACACAGTATCAATGATCCCCC 58.520 50.000 0.00 0.00 0.00 5.40
2545 2849 6.995686 TCACTCTGTTGTTTTAATTAGCCTCA 59.004 34.615 0.00 0.00 0.00 3.86
2724 3031 8.124823 CAGTTGTTACATGCAAATAGACTATGG 58.875 37.037 0.00 0.00 0.00 2.74
2961 3430 8.919777 AATCCGTATCCTCTTTATAAAAAGGG 57.080 34.615 16.03 10.05 42.05 3.95
3049 3518 4.342378 AGACTCTCACTTCACAGCAAGTTA 59.658 41.667 0.00 0.00 34.17 2.24
3074 3543 8.635765 AGAGCAAGAGGATTGTAAACATTTTA 57.364 30.769 0.00 0.00 0.00 1.52
3122 3593 8.099364 TCTTTCAGTTTTGCTGGTCTAATTAG 57.901 34.615 6.11 6.11 45.08 1.73
3125 3596 7.672983 TCAGTTTTGCTGGTCTAATTAGAAG 57.327 36.000 16.73 12.42 45.08 2.85
3129 3600 9.131791 AGTTTTGCTGGTCTAATTAGAAGAAAA 57.868 29.630 16.73 14.65 33.47 2.29
3130 3601 9.744468 GTTTTGCTGGTCTAATTAGAAGAAAAA 57.256 29.630 20.17 20.17 30.64 1.94
3234 3705 7.268586 TCTGGTTTATCTTCTAACAGATCTGC 58.731 38.462 22.83 1.24 35.08 4.26
3377 3848 9.757227 ATCTTAGTCTTATGTGTTGATAGCTTC 57.243 33.333 0.00 0.00 0.00 3.86
3575 4046 9.036671 GTAGCCTTGTAAGTAATCTCTGATTTC 57.963 37.037 0.00 0.00 0.00 2.17
3810 4281 7.397192 ACTTCAGGTATTGCCATTTTCTATTGT 59.603 33.333 0.00 0.00 40.61 2.71
3961 4433 2.369203 TGACACGAGTTCCAACCCATAA 59.631 45.455 0.00 0.00 0.00 1.90
3972 4451 7.056635 AGTTCCAACCCATAAGAGATACAATG 58.943 38.462 0.00 0.00 0.00 2.82
3993 4472 9.035607 ACAATGAAGAAGCTATAACTATGTTCG 57.964 33.333 0.00 0.00 0.00 3.95
3994 4473 9.035607 CAATGAAGAAGCTATAACTATGTTCGT 57.964 33.333 0.00 0.00 0.00 3.85
3995 4474 9.601217 AATGAAGAAGCTATAACTATGTTCGTT 57.399 29.630 0.00 0.00 0.00 3.85
3999 4478 5.986004 AGCTATAACTATGTTCGTTTGCC 57.014 39.130 0.00 0.00 0.00 4.52
4012 4491 5.163499 TGTTCGTTTGCCAGGTTTCTTATTT 60.163 36.000 0.00 0.00 0.00 1.40
4218 4697 7.524717 AATACAAGAAACTGGTGCATTACTT 57.475 32.000 0.00 0.00 0.00 2.24
4233 4712 6.092670 GTGCATTACTTGTAGAGAGATTGCAA 59.907 38.462 0.00 0.00 35.28 4.08
4254 4733 1.820906 CCACATGCCCCATCTGTCG 60.821 63.158 0.00 0.00 0.00 4.35
4448 4927 7.447374 TGTATCGTCAAATTCATTTTCCTGT 57.553 32.000 0.00 0.00 0.00 4.00
4591 5072 7.273381 GTCTAATGTTGAAAAATGTTCCATCCG 59.727 37.037 0.00 0.00 0.00 4.18
4608 5089 2.358957 TCCGAATCAAATGCTGTCCAG 58.641 47.619 0.00 0.00 0.00 3.86
4624 5105 5.979517 GCTGTCCAGTCAAATATATTTTGCC 59.020 40.000 8.01 0.08 0.00 4.52
4627 5108 8.133024 TGTCCAGTCAAATATATTTTGCCTTT 57.867 30.769 8.01 0.00 0.00 3.11
4628 5109 8.250332 TGTCCAGTCAAATATATTTTGCCTTTC 58.750 33.333 8.01 0.00 0.00 2.62
4629 5110 8.250332 GTCCAGTCAAATATATTTTGCCTTTCA 58.750 33.333 8.01 0.00 0.00 2.69
4630 5111 8.469200 TCCAGTCAAATATATTTTGCCTTTCAG 58.531 33.333 8.01 0.00 0.00 3.02
4778 5262 6.835819 TTCAAGCGCAGGACTAGTATATAT 57.164 37.500 11.47 0.00 0.00 0.86
4915 5399 4.872691 CAGAAACTTCTCATCGCAGGTAAT 59.127 41.667 0.00 0.00 34.74 1.89
4953 5437 8.670135 TGTTTTATTTGATTCCGTGTATAGGTG 58.330 33.333 0.00 0.00 0.00 4.00
5013 5497 7.517614 TGTAAACCATTCATAAGCAAAGACA 57.482 32.000 0.00 0.00 0.00 3.41
5026 5510 2.287849 GCAAAGACACTTCTTGAAGGCC 60.288 50.000 13.97 0.00 41.56 5.19
5121 5605 4.676196 GCAACACCAGGAATGCTCTAATTG 60.676 45.833 0.00 0.00 35.93 2.32
5136 5620 5.023533 TCTAATTGTATGTGCTCCACTCC 57.976 43.478 0.00 0.00 35.11 3.85
5198 5682 4.262335 CCAGTTCCGTACTAAAGGTGACTT 60.262 45.833 0.00 0.00 44.47 3.01
5255 5739 8.978874 TGGCACACATGATAAAGAATATTACT 57.021 30.769 0.00 0.00 0.00 2.24
5286 5770 6.808829 AGAATTTTGAATGAAAGTCTGCACA 58.191 32.000 0.26 0.00 40.99 4.57
5641 6155 7.505585 ACAATAGAGTGGAAGGAATTTGAAACA 59.494 33.333 0.00 0.00 0.00 2.83
5662 6176 9.651718 GAAACAAGAGTAAACAAACTCATACAG 57.348 33.333 6.76 0.00 46.89 2.74
5773 6287 7.403312 TTGAGACATTTTGGAAGTTTCTTGA 57.597 32.000 0.00 0.00 0.00 3.02
5776 6290 5.595952 AGACATTTTGGAAGTTTCTTGAGCT 59.404 36.000 0.00 0.00 0.00 4.09
5783 6297 5.437060 TGGAAGTTTCTTGAGCTTGTAACT 58.563 37.500 0.00 0.00 0.00 2.24
5799 6313 5.097742 TGTAACTGTATTATGCAGCCAGT 57.902 39.130 10.13 0.00 37.96 4.00
5864 6378 2.233271 AGCACCACTGGAATCAACTTG 58.767 47.619 0.71 0.00 0.00 3.16
5882 6396 1.909700 TGGAGATTGGGTGACAAAGC 58.090 50.000 0.00 0.00 43.46 3.51
5908 6422 4.947388 TCACTTTAAGCTGAACAACAACCT 59.053 37.500 0.00 0.00 0.00 3.50
5992 6506 2.772568 TCAGTTTGACATTGCGTTGG 57.227 45.000 0.00 0.00 0.00 3.77
6014 6528 4.276926 GGATTTGGATTGTGGTAGATCAGC 59.723 45.833 0.00 0.00 0.00 4.26
6228 6838 4.162698 AGCATGCCATATCAATTGTGGTTT 59.837 37.500 15.66 1.51 35.44 3.27
6256 6866 6.376978 CATCATTTGTTGAGTCAAGTTCTCC 58.623 40.000 5.62 0.00 37.89 3.71
6261 6871 4.442706 TGTTGAGTCAAGTTCTCCAACTC 58.557 43.478 5.62 0.00 42.45 3.01
6278 6888 4.024048 CCAACTCGCTGTACATTTTGTTCT 60.024 41.667 0.00 0.00 0.00 3.01
6333 6943 5.039333 ACGAGCCGTACATATTGTAAGTTC 58.961 41.667 0.00 0.00 38.73 3.01
6627 7242 6.203530 TGAACAGTTGCTTGAGATTACTGAAG 59.796 38.462 0.00 0.00 39.65 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.141858 GGGATGGTTCTTCTGGGCTAG 59.858 57.143 0.00 0.00 0.00 3.42
3 4 1.213296 TAGGGATGGTTCTTCTGGGC 58.787 55.000 0.00 0.00 0.00 5.36
5 6 3.777522 AGAGTTAGGGATGGTTCTTCTGG 59.222 47.826 0.00 0.00 0.00 3.86
6 7 4.467795 TCAGAGTTAGGGATGGTTCTTCTG 59.532 45.833 0.00 0.00 0.00 3.02
7 8 4.689062 TCAGAGTTAGGGATGGTTCTTCT 58.311 43.478 0.00 0.00 0.00 2.85
8 9 5.422214 TTCAGAGTTAGGGATGGTTCTTC 57.578 43.478 0.00 0.00 0.00 2.87
9 10 6.012508 TGAATTCAGAGTTAGGGATGGTTCTT 60.013 38.462 3.38 0.00 0.00 2.52
10 11 5.488919 TGAATTCAGAGTTAGGGATGGTTCT 59.511 40.000 3.38 0.00 0.00 3.01
11 12 5.745227 TGAATTCAGAGTTAGGGATGGTTC 58.255 41.667 3.38 0.00 0.00 3.62
12 13 5.779241 TGAATTCAGAGTTAGGGATGGTT 57.221 39.130 3.38 0.00 0.00 3.67
13 14 5.983333 ATGAATTCAGAGTTAGGGATGGT 57.017 39.130 14.54 0.00 0.00 3.55
14 15 9.610705 CATATATGAATTCAGAGTTAGGGATGG 57.389 37.037 14.54 0.00 0.00 3.51
18 19 9.593134 GCTACATATATGAATTCAGAGTTAGGG 57.407 37.037 19.63 3.08 0.00 3.53
25 26 9.573133 CGTATGTGCTACATATATGAATTCAGA 57.427 33.333 19.63 10.02 42.39 3.27
26 27 9.573133 TCGTATGTGCTACATATATGAATTCAG 57.427 33.333 19.63 2.20 42.39 3.02
27 28 9.353999 GTCGTATGTGCTACATATATGAATTCA 57.646 33.333 19.63 11.26 42.39 2.57
28 29 9.353999 TGTCGTATGTGCTACATATATGAATTC 57.646 33.333 19.63 0.00 42.39 2.17
29 30 9.705290 TTGTCGTATGTGCTACATATATGAATT 57.295 29.630 19.63 0.00 42.39 2.17
30 31 9.140286 GTTGTCGTATGTGCTACATATATGAAT 57.860 33.333 19.63 0.31 42.39 2.57
31 32 8.138712 TGTTGTCGTATGTGCTACATATATGAA 58.861 33.333 19.63 0.00 42.39 2.57
32 33 7.593644 GTGTTGTCGTATGTGCTACATATATGA 59.406 37.037 19.63 2.59 42.39 2.15
33 34 7.595130 AGTGTTGTCGTATGTGCTACATATATG 59.405 37.037 11.29 11.29 42.39 1.78
34 35 7.658261 AGTGTTGTCGTATGTGCTACATATAT 58.342 34.615 10.74 0.00 42.39 0.86
35 36 7.034685 AGTGTTGTCGTATGTGCTACATATA 57.965 36.000 10.74 2.90 42.39 0.86
36 37 5.902681 AGTGTTGTCGTATGTGCTACATAT 58.097 37.500 10.74 0.00 42.39 1.78
37 38 5.319140 AGTGTTGTCGTATGTGCTACATA 57.681 39.130 5.28 5.28 39.88 2.29
38 39 4.188247 AGTGTTGTCGTATGTGCTACAT 57.812 40.909 6.93 6.93 42.35 2.29
39 40 3.653539 AGTGTTGTCGTATGTGCTACA 57.346 42.857 0.00 0.00 0.00 2.74
40 41 4.985044 AAAGTGTTGTCGTATGTGCTAC 57.015 40.909 0.00 0.00 0.00 3.58
41 42 5.294356 AGAAAAGTGTTGTCGTATGTGCTA 58.706 37.500 0.00 0.00 0.00 3.49
42 43 4.127171 AGAAAAGTGTTGTCGTATGTGCT 58.873 39.130 0.00 0.00 0.00 4.40
43 44 4.468095 AGAAAAGTGTTGTCGTATGTGC 57.532 40.909 0.00 0.00 0.00 4.57
44 45 5.907391 GGAAAGAAAAGTGTTGTCGTATGTG 59.093 40.000 0.00 0.00 0.00 3.21
45 46 5.820947 AGGAAAGAAAAGTGTTGTCGTATGT 59.179 36.000 0.00 0.00 0.00 2.29
46 47 6.202954 AGAGGAAAGAAAAGTGTTGTCGTATG 59.797 38.462 0.00 0.00 0.00 2.39
47 48 6.289064 AGAGGAAAGAAAAGTGTTGTCGTAT 58.711 36.000 0.00 0.00 0.00 3.06
48 49 5.667466 AGAGGAAAGAAAAGTGTTGTCGTA 58.333 37.500 0.00 0.00 0.00 3.43
49 50 4.514401 AGAGGAAAGAAAAGTGTTGTCGT 58.486 39.130 0.00 0.00 0.00 4.34
50 51 4.811557 AGAGAGGAAAGAAAAGTGTTGTCG 59.188 41.667 0.00 0.00 0.00 4.35
51 52 5.237561 GGAGAGAGGAAAGAAAAGTGTTGTC 59.762 44.000 0.00 0.00 0.00 3.18
52 53 5.126779 GGAGAGAGGAAAGAAAAGTGTTGT 58.873 41.667 0.00 0.00 0.00 3.32
53 54 4.517075 GGGAGAGAGGAAAGAAAAGTGTTG 59.483 45.833 0.00 0.00 0.00 3.33
54 55 4.166144 TGGGAGAGAGGAAAGAAAAGTGTT 59.834 41.667 0.00 0.00 0.00 3.32
55 56 3.716872 TGGGAGAGAGGAAAGAAAAGTGT 59.283 43.478 0.00 0.00 0.00 3.55
56 57 4.357918 TGGGAGAGAGGAAAGAAAAGTG 57.642 45.455 0.00 0.00 0.00 3.16
57 58 4.202514 CCTTGGGAGAGAGGAAAGAAAAGT 60.203 45.833 0.00 0.00 34.91 2.66
104 105 0.320247 GATTGCCTGCGGAGATCGAT 60.320 55.000 5.10 0.00 42.43 3.59
189 192 2.088423 CTATCTACTAGCAGGAGCCGG 58.912 57.143 0.00 0.00 43.56 6.13
310 314 3.180507 GGAGCTCCATCTAATCCATCCT 58.819 50.000 28.43 0.00 35.64 3.24
364 368 4.141551 ACTCAACGAGAAAACCCTAACCTT 60.142 41.667 0.00 0.00 33.32 3.50
377 381 1.065851 TGTTGCGTACACTCAACGAGA 59.934 47.619 9.83 0.00 42.61 4.04
385 389 4.668177 GCAAATATCGTTGTTGCGTACACT 60.668 41.667 0.00 0.00 38.39 3.55
387 391 3.738399 GCAAATATCGTTGTTGCGTACA 58.262 40.909 0.00 0.00 38.39 2.90
408 412 9.311916 CTTGAATAGATCTAAAGAACCTGACAG 57.688 37.037 6.52 0.00 0.00 3.51
502 509 1.273606 CCAGACCTTGTCGATGACAGT 59.726 52.381 0.00 0.00 43.69 3.55
520 527 3.479203 CCATACCAGAGCCGGCCA 61.479 66.667 26.15 1.31 0.00 5.36
530 537 3.845259 GTCGCCGCTCCCATACCA 61.845 66.667 0.00 0.00 0.00 3.25
589 596 0.741326 ACATCGAGATGACCACGGAG 59.259 55.000 18.76 0.00 41.20 4.63
592 599 5.718649 AAAATTACATCGAGATGACCACG 57.281 39.130 18.76 0.00 41.20 4.94
620 633 4.560919 CGGAAGTACAAAGCACCTCTAACT 60.561 45.833 0.00 0.00 0.00 2.24
624 637 1.968493 TCGGAAGTACAAAGCACCTCT 59.032 47.619 0.00 0.00 0.00 3.69
685 698 4.036852 CGTGCTTCTTCCTCCTTTTCTTTT 59.963 41.667 0.00 0.00 0.00 2.27
694 707 1.016653 GTGAGCGTGCTTCTTCCTCC 61.017 60.000 0.00 0.00 0.00 4.30
722 735 4.373116 GGAAGCTGTGCGGACGGA 62.373 66.667 21.18 0.00 0.00 4.69
768 781 3.767673 GGGAGGGATGGGTTAAAAAGTTC 59.232 47.826 0.00 0.00 0.00 3.01
776 789 0.267960 GAGGAGGGAGGGATGGGTTA 59.732 60.000 0.00 0.00 0.00 2.85
778 791 2.706071 GAGGAGGGAGGGATGGGT 59.294 66.667 0.00 0.00 0.00 4.51
781 794 0.902516 GATCGGAGGAGGGAGGGATG 60.903 65.000 0.00 0.00 0.00 3.51
782 795 1.077298 AGATCGGAGGAGGGAGGGAT 61.077 60.000 0.00 0.00 0.00 3.85
783 796 1.701757 AGATCGGAGGAGGGAGGGA 60.702 63.158 0.00 0.00 0.00 4.20
784 797 1.532794 CAGATCGGAGGAGGGAGGG 60.533 68.421 0.00 0.00 0.00 4.30
785 798 2.206536 GCAGATCGGAGGAGGGAGG 61.207 68.421 0.00 0.00 0.00 4.30
786 799 1.456518 TGCAGATCGGAGGAGGGAG 60.457 63.158 0.00 0.00 0.00 4.30
833 846 9.941664 CGAGCTTAGTTTAATTGATTGATTGAT 57.058 29.630 0.00 0.00 0.00 2.57
834 847 7.910162 GCGAGCTTAGTTTAATTGATTGATTGA 59.090 33.333 0.00 0.00 0.00 2.57
835 848 7.697710 TGCGAGCTTAGTTTAATTGATTGATTG 59.302 33.333 0.00 0.00 0.00 2.67
836 849 7.761409 TGCGAGCTTAGTTTAATTGATTGATT 58.239 30.769 0.00 0.00 0.00 2.57
938 951 1.856873 AGGCAGGGGATTTGGTGGA 60.857 57.895 0.00 0.00 0.00 4.02
972 989 1.146041 CGGCCGGATTTGGATCTCA 59.854 57.895 20.10 0.00 32.66 3.27
1356 1373 0.447801 CAGGTTGCGGAATGTAGCAC 59.552 55.000 0.00 0.00 43.69 4.40
1372 1389 2.562738 CCCTCTTAACCAAAAAGCCAGG 59.437 50.000 0.00 0.00 0.00 4.45
1378 1395 6.584488 GGCTAAAAACCCTCTTAACCAAAAA 58.416 36.000 0.00 0.00 0.00 1.94
1487 1504 5.571778 ACGAAGTATTTGTCGAAGAACAC 57.428 39.130 0.00 0.00 38.69 3.32
1502 1551 9.265901 GGATAGTAGATGTACAACTACGAAGTA 57.734 37.037 27.64 18.88 45.11 2.24
1529 1578 6.554334 TCAATGGTACTAAAGCAAGTTGAC 57.446 37.500 7.16 0.00 39.48 3.18
1547 1596 2.746362 GAGTGGGTTTCTGAGCTCAATG 59.254 50.000 18.85 7.29 0.00 2.82
1549 1598 2.037772 GAGAGTGGGTTTCTGAGCTCAA 59.962 50.000 18.85 6.19 0.00 3.02
1728 1778 6.710278 TGTGAATAATGTCTGATCCAAGTCA 58.290 36.000 0.00 0.00 0.00 3.41
1731 1781 5.587443 TGCTGTGAATAATGTCTGATCCAAG 59.413 40.000 0.00 0.00 0.00 3.61
1923 1974 3.272551 AGGAGGGTGTATTGACTAGTCCT 59.727 47.826 20.11 7.79 0.00 3.85
2258 2312 3.611970 TCCGAACCAACTTTGAACTTGA 58.388 40.909 0.00 0.00 0.00 3.02
2302 2356 7.767198 GCCTAGGTGATTAACAGTACACATTAA 59.233 37.037 11.31 0.00 35.33 1.40
2446 2500 4.383850 TGCAAAACAGCAACAGTAATGT 57.616 36.364 0.00 0.00 42.46 2.71
2469 2523 5.221925 GGGATCATTGATACTGTGTGGGTAT 60.222 44.000 8.76 0.00 33.22 2.73
2497 2551 8.197439 GTGATAAATCATAAAACAAAGAGGGGG 58.803 37.037 0.00 0.00 39.30 5.40
2545 2849 6.002082 GGTTCCCTCTGTAGTTAACAAACAT 58.998 40.000 8.61 0.00 37.74 2.71
2657 2962 9.102453 ACTAAAACCTTGAGGACTAAATAGAGT 57.898 33.333 3.59 0.00 38.94 3.24
2724 3031 5.051153 ACGAAGAAAACAGAGTCTTCTTCC 58.949 41.667 19.65 8.27 46.46 3.46
2859 3325 8.088463 TGAAATGCATTAAATTTATGACCCCT 57.912 30.769 13.39 0.00 0.00 4.79
2921 3390 6.201044 GGATACGGATTCAACACAGAACATAG 59.799 42.308 0.00 0.00 0.00 2.23
3049 3518 7.530426 AAAATGTTTACAATCCTCTTGCTCT 57.470 32.000 0.00 0.00 0.00 4.09
3129 3600 7.060421 TGAACTGTAGTTTCCTTCCAAGATTT 58.940 34.615 0.00 0.00 38.56 2.17
3130 3601 6.601332 TGAACTGTAGTTTCCTTCCAAGATT 58.399 36.000 0.00 0.00 38.56 2.40
3131 3602 6.187727 TGAACTGTAGTTTCCTTCCAAGAT 57.812 37.500 0.00 0.00 38.56 2.40
3132 3603 5.623956 TGAACTGTAGTTTCCTTCCAAGA 57.376 39.130 0.00 0.00 38.56 3.02
3133 3604 5.278022 GCTTGAACTGTAGTTTCCTTCCAAG 60.278 44.000 13.15 13.15 38.56 3.61
3134 3605 4.578928 GCTTGAACTGTAGTTTCCTTCCAA 59.421 41.667 0.00 0.00 38.56 3.53
3135 3606 4.134563 GCTTGAACTGTAGTTTCCTTCCA 58.865 43.478 0.00 0.00 38.56 3.53
3136 3607 4.390264 AGCTTGAACTGTAGTTTCCTTCC 58.610 43.478 0.00 0.00 38.56 3.46
3234 3705 1.804151 CGGGATATGGTAACGGCATTG 59.196 52.381 0.00 0.00 42.51 2.82
3575 4046 2.461695 TCCACCTCTAGAGCTTTCTGG 58.538 52.381 14.73 11.96 0.00 3.86
3850 4321 5.829924 ACAATGTTTGAAGAGAACTCATGGT 59.170 36.000 4.64 0.00 0.00 3.55
3918 4390 3.328382 AGCTCTGGTATGCGTTTTGTA 57.672 42.857 0.00 0.00 0.00 2.41
3972 4451 7.846592 GCAAACGAACATAGTTATAGCTTCTTC 59.153 37.037 0.00 0.00 0.00 2.87
3992 4471 5.048713 AGAGAAATAAGAAACCTGGCAAACG 60.049 40.000 0.00 0.00 0.00 3.60
3993 4472 6.152379 CAGAGAAATAAGAAACCTGGCAAAC 58.848 40.000 0.00 0.00 0.00 2.93
3994 4473 5.833131 ACAGAGAAATAAGAAACCTGGCAAA 59.167 36.000 0.00 0.00 0.00 3.68
3995 4474 5.385198 ACAGAGAAATAAGAAACCTGGCAA 58.615 37.500 0.00 0.00 0.00 4.52
3999 4478 6.936900 TCAGGAACAGAGAAATAAGAAACCTG 59.063 38.462 0.00 0.00 40.56 4.00
4012 4491 3.582647 TGTGGCTAAATCAGGAACAGAGA 59.417 43.478 0.00 0.00 0.00 3.10
4218 4697 1.908619 TGGCCTTGCAATCTCTCTACA 59.091 47.619 3.32 0.00 0.00 2.74
4254 4733 6.867550 ACCTAAAAGATTATCTTGCAAAGGC 58.132 36.000 8.34 0.00 46.24 4.35
4448 4927 5.551305 TGTCCTCTTGATTTCTGTCAGAA 57.449 39.130 11.36 11.36 31.28 3.02
4591 5072 4.771590 TTGACTGGACAGCATTTGATTC 57.228 40.909 0.00 0.00 0.00 2.52
4641 5125 6.300354 ACAATAGTTGGACTTTCAGAAACG 57.700 37.500 0.00 0.00 34.12 3.60
4778 5262 5.655974 TCCATAAATTTCAGCACCTGCAATA 59.344 36.000 0.00 0.00 45.16 1.90
4945 5429 9.646427 TTTGTTTGCATAATTTTCCACCTATAC 57.354 29.630 0.00 0.00 0.00 1.47
4953 5437 7.693020 ACAACACTTTGTTTGCATAATTTTCC 58.307 30.769 0.00 0.00 43.89 3.13
5026 5510 2.289694 CCATACCCATCCGAGGCTTAAG 60.290 54.545 0.00 0.00 0.00 1.85
5121 5605 2.290323 ACCTTTGGAGTGGAGCACATAC 60.290 50.000 0.00 0.00 36.74 2.39
5136 5620 1.880819 GCCCACATGAGCCACCTTTG 61.881 60.000 0.00 0.00 0.00 2.77
5198 5682 7.593273 GTGGTTCGAATTTGAATTTCACACATA 59.407 33.333 21.64 1.70 32.05 2.29
5286 5770 5.513233 AGGTTCCACTTCTTTATCATGCAT 58.487 37.500 0.00 0.00 0.00 3.96
5641 6155 7.801716 TTGCTGTATGAGTTTGTTTACTCTT 57.198 32.000 0.00 0.00 43.92 2.85
5662 6176 3.753272 TCTCATGGACTTGCTTAGTTTGC 59.247 43.478 0.00 0.00 37.17 3.68
5773 6287 4.576463 GGCTGCATAATACAGTTACAAGCT 59.424 41.667 0.50 0.00 37.47 3.74
5776 6290 5.353956 CACTGGCTGCATAATACAGTTACAA 59.646 40.000 0.50 0.00 40.14 2.41
5783 6297 1.679139 GCCACTGGCTGCATAATACA 58.321 50.000 13.28 0.00 46.69 2.29
5799 6313 1.114722 CCAAAACAAGCTCTGGGCCA 61.115 55.000 5.85 5.85 43.05 5.36
5864 6378 2.087646 GAGCTTTGTCACCCAATCTCC 58.912 52.381 0.00 0.00 31.81 3.71
5882 6396 5.991328 TGTTGTTCAGCTTAAAGTGAGAG 57.009 39.130 0.00 0.00 0.00 3.20
5908 6422 5.655974 TGCTGGAACCATATTTAGAATGCAA 59.344 36.000 0.00 0.00 0.00 4.08
5977 6491 3.068732 TCCAAATCCAACGCAATGTCAAA 59.931 39.130 0.00 0.00 0.00 2.69
5992 6506 4.883585 TGCTGATCTACCACAATCCAAATC 59.116 41.667 0.00 0.00 0.00 2.17
6014 6528 6.467047 CGTAGCTCAGATGCAAAAATTAGTTG 59.533 38.462 0.00 0.00 34.99 3.16
6195 6805 1.731433 ATGGCATGCTCCAATCGCAC 61.731 55.000 18.92 0.00 40.65 5.34
6228 6838 5.132502 ACTTGACTCAACAAATGATGGACA 58.867 37.500 0.00 0.00 37.44 4.02
6256 6866 5.095691 AGAACAAAATGTACAGCGAGTTG 57.904 39.130 0.33 3.78 0.00 3.16
6261 6871 5.088739 GGAATGAGAACAAAATGTACAGCG 58.911 41.667 0.33 0.00 0.00 5.18
6278 6888 5.640147 ACATTACCCACTGAAAAGGAATGA 58.360 37.500 0.99 0.00 0.00 2.57
6333 6943 3.509575 TGCTAACTTTGCCCTTTGGTATG 59.490 43.478 0.00 0.00 0.00 2.39
6415 7025 1.150567 CGTCCTCATAGCAGCAGCAC 61.151 60.000 3.17 0.00 45.49 4.40
6627 7242 5.880341 AGCTAACAACAAAGTGACTGAAAC 58.120 37.500 0.00 0.00 0.00 2.78
6641 7256 5.922544 AGATGCAAATCACAAAGCTAACAAC 59.077 36.000 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.