Multiple sequence alignment - TraesCS3D01G522800

Loading Multiple Alignment...

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 TraesCS3D01G522800 chr3D 100.000 7525 0 0 1 7525 603746655 603739131 0.000000e+00 13897.0
1 TraesCS3D01G522800 chr3D 85.823 2497 243 59 4365 6810 568432134 568429698 0.000000e+00 2547.0
2 TraesCS3D01G522800 chr3D 84.383 762 86 16 1542 2287 568434108 568433364 0.000000e+00 717.0
3 TraesCS3D01G522800 chr3D 82.157 779 46 37 6775 7525 568429762 568429049 3.910000e-162 582.0
4 TraesCS3D01G522800 chr3D 100.000 34 0 0 1483 1516 603745137 603745104 6.300000e-06 63.9
5 TraesCS3D01G522800 chr3D 100.000 34 0 0 1519 1552 603745173 603745140 6.300000e-06 63.9
6 TraesCS3D01G522800 chr5A 96.957 6014 131 22 671 6649 31514576 31508580 0.000000e+00 10045.0
7 TraesCS3D01G522800 chr5A 96.859 573 13 2 1 568 31515198 31514626 0.000000e+00 953.0
8 TraesCS3D01G522800 chr5A 87.457 877 40 21 6644 7467 31508354 31507495 0.000000e+00 946.0
9 TraesCS3D01G522800 chr5A 98.246 57 1 0 589 645 31514630 31514574 4.800000e-17 100.0
10 TraesCS3D01G522800 chr5A 100.000 34 0 0 1483 1516 31513724 31513691 6.300000e-06 63.9
11 TraesCS3D01G522800 chr5A 100.000 34 0 0 1519 1552 31513760 31513727 6.300000e-06 63.9
12 TraesCS3D01G522800 chr3A 98.152 4167 73 4 1622 5787 645999511 645995348 0.000000e+00 7265.0
13 TraesCS3D01G522800 chr3A 93.659 962 24 6 671 1629 646003783 646002856 0.000000e+00 1404.0
14 TraesCS3D01G522800 chr3A 88.296 1068 41 24 5780 6810 645994696 645993676 0.000000e+00 1203.0
15 TraesCS3D01G522800 chr3A 96.667 570 11 3 1 568 646004387 646003824 0.000000e+00 941.0
16 TraesCS3D01G522800 chr3A 85.283 761 61 27 6775 7515 645993740 645993011 0.000000e+00 737.0
17 TraesCS3D01G522800 chr3A 97.778 45 1 0 589 633 646003828 646003784 2.250000e-10 78.7
18 TraesCS3D01G522800 chr3A 100.000 34 0 0 1519 1552 646003002 646002969 6.300000e-06 63.9
19 TraesCS3D01G522800 chr6B 83.158 95 16 0 6330 6424 527578286 527578380 3.740000e-13 87.9
20 TraesCS3D01G522800 chr6B 86.111 72 7 2 5966 6037 527574491 527574559 2.910000e-09 75.0
21 TraesCS3D01G522800 chr6D 88.732 71 7 1 5967 6037 351746649 351746580 1.350000e-12 86.1
22 TraesCS3D01G522800 chr6D 81.818 99 16 1 6330 6428 351746198 351746102 1.740000e-11 82.4
23 TraesCS3D01G522800 chr6A 90.000 60 6 0 6330 6389 491571167 491571226 2.250000e-10 78.7
24 TraesCS3D01G522800 chr6A 85.915 71 7 2 5967 6037 491570718 491570785 1.050000e-08 73.1


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 TraesCS3D01G522800 chr3D 603739131 603746655 7524 True 4674.933333 13897 100.000000 1 7525 3 chr3D.!!$R2 7524
1 TraesCS3D01G522800 chr3D 568429049 568434108 5059 True 1282.000000 2547 84.121000 1542 7525 3 chr3D.!!$R1 5983
2 TraesCS3D01G522800 chr5A 31507495 31515198 7703 True 2028.633333 10045 96.586500 1 7467 6 chr5A.!!$R1 7466
3 TraesCS3D01G522800 chr3A 645993011 646004387 11376 True 1670.371429 7265 94.262143 1 7515 7 chr3A.!!$R1 7514

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
661 665 0.035739 TACGGAGTTGGGCAGTTTCC 59.964 55.000 0.00 0.0 37.78 3.13 F
892 905 0.107508 CACGCCCATCTCTCCATGTT 60.108 55.000 0.00 0.0 0.00 2.71 F
923 936 0.609662 AGGGATGTTGGCATGCAAAC 59.390 50.000 27.90 27.9 44.00 2.93 F
2554 5954 2.430694 ACCAGCCCTTTGTTTCTGTTTC 59.569 45.455 0.00 0.0 0.00 2.78 F
3281 6698 1.002011 GGAGCCTTGGAGGTGAACC 60.002 63.158 0.00 0.0 37.80 3.62 F
3691 7108 0.179171 AGTGCCGTAGACGAACATCG 60.179 55.000 3.07 0.0 46.93 3.84 F
3842 7259 3.009723 CAAAACTATGGCGATGAGGTGT 58.990 45.455 0.00 0.0 0.00 4.16 F
5038 8544 3.133542 AGGGGTAAGGCTCAAACGTATAC 59.866 47.826 0.00 0.0 0.00 1.47 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1867 5248 2.868583 CAAGACGATAATCTGGGTGCAG 59.131 50.000 0.00 0.00 0.00 4.41 R
2912 6329 5.968387 ACTTTCGGCAATCTAGTTATTCG 57.032 39.130 0.00 0.00 0.00 3.34 R
2973 6390 1.300481 TCGGCAATTCACGTTGTTCA 58.700 45.000 0.00 0.00 0.00 3.18 R
3666 7083 1.080772 CGTCTACGGCACTGCTTCA 60.081 57.895 0.00 0.00 35.37 3.02 R
5084 8590 0.793861 GTATCAAAACGTCGGCTGCA 59.206 50.000 0.50 0.00 0.00 4.41 R
5378 8884 1.679153 TCCGCCTTCCTTTTGTTGTTC 59.321 47.619 0.00 0.00 0.00 3.18 R
5536 9042 9.780186 ATGGAGAATTAGTTACCTTAATGTAGC 57.220 33.333 0.00 0.00 0.00 3.58 R
6611 10854 0.036105 TCGTCAGTTCCATGCATGCT 60.036 50.000 21.69 10.26 0.00 3.79 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
57 58 4.761058 AGCGAAGAGGGCTCCCGA 62.761 66.667 0.00 0.00 41.95 5.14
97 98 4.849310 GCGGAGGCGGCATTGGTA 62.849 66.667 13.08 0.00 0.00 3.25
164 165 0.873312 CGTGCCGATCATCACTCCTG 60.873 60.000 11.17 0.00 0.00 3.86
204 205 0.531532 CGCAGCCTATCAGGAACAGG 60.532 60.000 0.00 0.00 37.67 4.00
224 225 2.342648 GGCTCCCAAGTTCGTCGT 59.657 61.111 0.00 0.00 0.00 4.34
227 228 1.285023 CTCCCAAGTTCGTCGTCGT 59.715 57.895 1.33 0.00 38.33 4.34
230 231 1.369689 CCAAGTTCGTCGTCGTCGT 60.370 57.895 11.41 0.00 38.33 4.34
558 562 6.545504 TTGCTACAGATCTCAAAAGACAAC 57.454 37.500 0.00 0.00 33.32 3.32
559 563 5.858381 TGCTACAGATCTCAAAAGACAACT 58.142 37.500 0.00 0.00 33.32 3.16
560 564 6.291377 TGCTACAGATCTCAAAAGACAACTT 58.709 36.000 0.00 0.00 38.05 2.66
561 565 6.203530 TGCTACAGATCTCAAAAGACAACTTG 59.796 38.462 0.00 0.00 36.39 3.16
563 567 7.254932 GCTACAGATCTCAAAAGACAACTTGTT 60.255 37.037 0.00 0.00 36.39 2.83
565 569 7.253422 ACAGATCTCAAAAGACAACTTGTTTG 58.747 34.615 0.00 0.00 41.49 2.93
566 570 6.694411 CAGATCTCAAAAGACAACTTGTTTGG 59.306 38.462 0.00 0.00 39.84 3.28
567 571 4.743493 TCTCAAAAGACAACTTGTTTGGC 58.257 39.130 0.00 0.00 44.76 4.52
574 578 4.519191 GACAACTTGTTTGGCAATTGTG 57.481 40.909 17.96 6.60 43.70 3.33
575 579 3.932089 GACAACTTGTTTGGCAATTGTGT 59.068 39.130 17.96 9.28 43.70 3.72
576 580 3.683822 ACAACTTGTTTGGCAATTGTGTG 59.316 39.130 13.64 5.79 39.84 3.82
577 581 3.883830 ACTTGTTTGGCAATTGTGTGA 57.116 38.095 7.40 0.00 36.36 3.58
578 582 4.199432 ACTTGTTTGGCAATTGTGTGAA 57.801 36.364 7.40 0.00 36.36 3.18
579 583 4.183101 ACTTGTTTGGCAATTGTGTGAAG 58.817 39.130 7.40 5.19 36.36 3.02
580 584 3.176552 TGTTTGGCAATTGTGTGAAGG 57.823 42.857 7.40 0.00 0.00 3.46
581 585 2.499289 TGTTTGGCAATTGTGTGAAGGT 59.501 40.909 7.40 0.00 0.00 3.50
582 586 3.123050 GTTTGGCAATTGTGTGAAGGTC 58.877 45.455 7.40 0.00 0.00 3.85
583 587 2.363306 TGGCAATTGTGTGAAGGTCT 57.637 45.000 7.40 0.00 0.00 3.85
584 588 2.665165 TGGCAATTGTGTGAAGGTCTT 58.335 42.857 7.40 0.00 0.00 3.01
585 589 3.826524 TGGCAATTGTGTGAAGGTCTTA 58.173 40.909 7.40 0.00 0.00 2.10
586 590 3.820467 TGGCAATTGTGTGAAGGTCTTAG 59.180 43.478 7.40 0.00 0.00 2.18
587 591 3.366374 GGCAATTGTGTGAAGGTCTTAGC 60.366 47.826 7.40 0.00 0.00 3.09
626 630 1.134250 TGTGCTTCACTTGCTGTACCA 60.134 47.619 0.00 0.00 35.11 3.25
645 649 4.879598 ACCAGAGTACCTTTTCAACTACG 58.120 43.478 0.00 0.00 0.00 3.51
646 650 4.243270 CCAGAGTACCTTTTCAACTACGG 58.757 47.826 0.00 0.00 0.00 4.02
647 651 4.021719 CCAGAGTACCTTTTCAACTACGGA 60.022 45.833 0.00 0.00 0.00 4.69
648 652 5.162075 CAGAGTACCTTTTCAACTACGGAG 58.838 45.833 0.00 0.00 0.00 4.63
657 661 2.448749 AACTACGGAGTTGGGCAGT 58.551 52.632 13.53 0.00 44.50 4.40
658 662 0.763035 AACTACGGAGTTGGGCAGTT 59.237 50.000 13.53 0.00 44.50 3.16
659 663 0.763035 ACTACGGAGTTGGGCAGTTT 59.237 50.000 0.00 0.00 37.78 2.66
660 664 1.270678 ACTACGGAGTTGGGCAGTTTC 60.271 52.381 0.00 0.00 37.78 2.78
661 665 0.035739 TACGGAGTTGGGCAGTTTCC 59.964 55.000 0.00 0.00 37.78 3.13
662 666 1.971695 CGGAGTTGGGCAGTTTCCC 60.972 63.158 0.00 0.00 46.73 3.97
663 667 1.606601 GGAGTTGGGCAGTTTCCCC 60.607 63.158 0.00 0.00 45.97 4.81
664 668 1.606601 GAGTTGGGCAGTTTCCCCC 60.607 63.158 0.00 0.00 45.97 5.40
665 669 2.081585 GAGTTGGGCAGTTTCCCCCT 62.082 60.000 0.00 0.00 45.97 4.79
666 670 1.908299 GTTGGGCAGTTTCCCCCTG 60.908 63.158 0.00 0.00 45.97 4.45
673 677 0.676782 CAGTTTCCCCCTGCCTTACG 60.677 60.000 0.00 0.00 0.00 3.18
680 684 0.177373 CCCCTGCCTTACGAGTTACC 59.823 60.000 0.00 0.00 0.00 2.85
695 699 4.620803 CGAGTTACCAAGCCTGACTAATGT 60.621 45.833 0.00 0.00 0.00 2.71
733 737 7.096885 CGAAAACTTGTTGTTGCTTCAGATTAG 60.097 37.037 0.00 0.00 39.13 1.73
892 905 0.107508 CACGCCCATCTCTCCATGTT 60.108 55.000 0.00 0.00 0.00 2.71
923 936 0.609662 AGGGATGTTGGCATGCAAAC 59.390 50.000 27.90 27.90 44.00 2.93
967 980 5.221402 ACACACACATCCTCTGATATGCTAG 60.221 44.000 0.00 0.00 27.93 3.42
968 981 4.898265 ACACACATCCTCTGATATGCTAGT 59.102 41.667 0.00 0.00 27.93 2.57
969 982 6.015940 CACACACATCCTCTGATATGCTAGTA 60.016 42.308 0.00 0.00 27.93 1.82
970 983 6.551227 ACACACATCCTCTGATATGCTAGTAA 59.449 38.462 0.00 0.00 27.93 2.24
1163 1176 6.089685 GTCGAACAAGATACAGAACTTCCTTC 59.910 42.308 0.00 0.00 0.00 3.46
1392 1405 5.880332 ACTTCTTTTTATCGGCTGAAGCATA 59.120 36.000 0.00 0.00 44.36 3.14
1636 5002 4.721977 CGCGGTATTTTTCTTATGACAACG 59.278 41.667 0.00 0.00 0.00 4.10
1673 5039 2.615912 CTGTCAAGGCCATTAAGCTAGC 59.384 50.000 6.62 6.62 0.00 3.42
1708 5083 7.456725 AGACTTCCTTTCTGATTTTCATGAGA 58.543 34.615 0.00 0.00 0.00 3.27
1741 5116 4.081917 CCTTCTTCAGAGGAACCTACACTC 60.082 50.000 0.00 0.00 0.00 3.51
1783 5158 5.692115 TTGCCTCTTGAAGTGGTATGATA 57.308 39.130 14.10 0.00 31.72 2.15
1867 5248 4.635765 TGGTGTTGCAGAATATCTACAAGC 59.364 41.667 0.00 0.00 30.97 4.01
2554 5954 2.430694 ACCAGCCCTTTGTTTCTGTTTC 59.569 45.455 0.00 0.00 0.00 2.78
2830 6247 6.098124 TGGAACACTTCATTCAAATTCCTTGT 59.902 34.615 0.00 0.00 36.04 3.16
2912 6329 4.002906 TGAACATGTGAACTGTCCCTAC 57.997 45.455 0.00 0.00 0.00 3.18
2973 6390 4.510167 AGTATAAGGCCAACTTCAGCAT 57.490 40.909 5.01 0.00 40.64 3.79
3281 6698 1.002011 GGAGCCTTGGAGGTGAACC 60.002 63.158 0.00 0.00 37.80 3.62
3639 7056 2.906354 CCTAATGGACCTTTCTGACCG 58.094 52.381 0.00 0.00 34.57 4.79
3666 7083 1.342574 GGTGGAAGACCTCCTCTAGCT 60.343 57.143 0.00 0.00 45.64 3.32
3682 7099 1.079819 GCTGAAGCAGTGCCGTAGA 60.080 57.895 12.58 0.00 41.59 2.59
3691 7108 0.179171 AGTGCCGTAGACGAACATCG 60.179 55.000 3.07 0.00 46.93 3.84
3842 7259 3.009723 CAAAACTATGGCGATGAGGTGT 58.990 45.455 0.00 0.00 0.00 4.16
4763 8266 9.987272 CAGATAGGATTTTCTTTTTGGAAAAGT 57.013 29.630 11.60 0.00 44.75 2.66
4819 8322 9.976511 AAAATTAATCTTGCATGTAGATGATGG 57.023 29.630 3.61 0.00 32.82 3.51
4880 8384 8.220755 ACATTAACATATGCGACCTTTATGTT 57.779 30.769 1.58 11.08 42.07 2.71
5038 8544 3.133542 AGGGGTAAGGCTCAAACGTATAC 59.866 47.826 0.00 0.00 0.00 1.47
5346 8852 3.213206 TGTGTCAGGAGCTGAAAACAT 57.787 42.857 0.00 0.00 42.46 2.71
5378 8884 4.686972 TGATGGAAAGAGCGAACATAGAG 58.313 43.478 0.00 0.00 0.00 2.43
5536 9042 1.922570 CATTTCTCCACGTACCCTCG 58.077 55.000 0.00 0.00 0.00 4.63
5817 9982 3.550820 TGCTTACATGGTCTTGTGTTGT 58.449 40.909 0.00 0.00 0.00 3.32
5867 10032 3.071479 GGTTTCTGAAAGGCGTATGTGA 58.929 45.455 2.48 0.00 0.00 3.58
6152 10355 7.179516 TGTCAAATGTCCTGACCTAGTACATTA 59.820 37.037 0.00 0.00 42.13 1.90
6214 10417 2.028130 CAGAGAGTAGAATCAGGCGGT 58.972 52.381 0.00 0.00 0.00 5.68
6217 10420 2.028130 AGAGTAGAATCAGGCGGTCAG 58.972 52.381 0.00 0.00 0.00 3.51
6273 10476 3.330267 CTTTTGGTCCAGTGAGCTAGTC 58.670 50.000 0.00 0.00 39.75 2.59
6300 10503 1.896220 CTGCTGTAAACTCTGCCCAA 58.104 50.000 0.00 0.00 0.00 4.12
6301 10504 1.808945 CTGCTGTAAACTCTGCCCAAG 59.191 52.381 0.00 0.00 0.00 3.61
6384 10589 3.709653 AGTCAAGTGAGACCACAACCTTA 59.290 43.478 0.00 0.00 45.54 2.69
6426 10631 6.995686 GGGTGTCCTTTGTTCCAAAATTTTAT 59.004 34.615 2.44 0.00 0.00 1.40
6555 10792 4.351054 GTGGTGGTGGAGGCAGGG 62.351 72.222 0.00 0.00 0.00 4.45
6582 10825 0.700564 ATTGCAAGCAAGGAGGAGGA 59.299 50.000 13.35 0.00 39.47 3.71
6604 10847 2.233922 TGGAAGCAACGTTTTTGGGAAA 59.766 40.909 0.00 0.00 0.00 3.13
6606 10849 3.874543 GGAAGCAACGTTTTTGGGAAATT 59.125 39.130 0.00 0.00 0.00 1.82
6607 10850 4.025229 GGAAGCAACGTTTTTGGGAAATTC 60.025 41.667 0.00 0.00 0.00 2.17
6608 10851 4.130286 AGCAACGTTTTTGGGAAATTCA 57.870 36.364 0.00 0.00 0.00 2.57
6609 10852 4.119136 AGCAACGTTTTTGGGAAATTCAG 58.881 39.130 0.00 0.00 0.00 3.02
6610 10853 3.868661 GCAACGTTTTTGGGAAATTCAGT 59.131 39.130 0.00 0.00 0.00 3.41
6611 10854 5.044558 GCAACGTTTTTGGGAAATTCAGTA 58.955 37.500 0.00 0.00 0.00 2.74
6612 10855 5.174943 GCAACGTTTTTGGGAAATTCAGTAG 59.825 40.000 0.00 0.00 0.00 2.57
6613 10856 4.866921 ACGTTTTTGGGAAATTCAGTAGC 58.133 39.130 0.00 0.00 0.00 3.58
6614 10857 4.339814 ACGTTTTTGGGAAATTCAGTAGCA 59.660 37.500 0.00 0.00 0.00 3.49
6615 10858 5.010617 ACGTTTTTGGGAAATTCAGTAGCAT 59.989 36.000 0.00 0.00 0.00 3.79
6738 11234 6.824305 ACACCTGATCTTTTTGTAAGATGG 57.176 37.500 4.85 4.13 37.14 3.51
6804 11300 4.273318 AGTGTAATTTTCTGGATGGGAGC 58.727 43.478 0.00 0.00 0.00 4.70
6805 11301 3.065371 GTGTAATTTTCTGGATGGGAGCG 59.935 47.826 0.00 0.00 0.00 5.03
6806 11302 1.106285 AATTTTCTGGATGGGAGCGC 58.894 50.000 0.00 0.00 0.00 5.92
6807 11303 0.257039 ATTTTCTGGATGGGAGCGCT 59.743 50.000 11.27 11.27 0.00 5.92
6808 11304 0.677731 TTTTCTGGATGGGAGCGCTG 60.678 55.000 18.48 0.00 0.00 5.18
6809 11305 2.541547 TTTCTGGATGGGAGCGCTGG 62.542 60.000 18.48 0.00 0.00 4.85
6810 11306 3.790437 CTGGATGGGAGCGCTGGT 61.790 66.667 18.48 0.00 0.00 4.00
6829 11325 3.500680 TGGTCGCTGGAAGTGTAATTTTC 59.499 43.478 0.00 0.00 46.69 2.29
6832 11328 4.213482 GTCGCTGGAAGTGTAATTTTCTGT 59.787 41.667 0.00 0.00 46.69 3.41
6835 11331 6.092122 TCGCTGGAAGTGTAATTTTCTGTATG 59.908 38.462 0.00 0.00 46.69 2.39
6836 11332 6.555315 GCTGGAAGTGTAATTTTCTGTATGG 58.445 40.000 0.00 0.00 35.30 2.74
6838 11334 5.417580 TGGAAGTGTAATTTTCTGTATGGGC 59.582 40.000 0.00 0.00 0.00 5.36
6895 11392 1.134521 AGATTTGGCTGAATACCGCGA 60.135 47.619 8.23 0.00 0.00 5.87
6896 11393 1.668751 GATTTGGCTGAATACCGCGAA 59.331 47.619 8.23 0.00 0.00 4.70
6942 11439 3.952675 CGGATGATTTGGCCGCCG 61.953 66.667 4.58 0.00 38.46 6.46
6957 11458 4.120085 CCGGCCGGATTCTGTAAC 57.880 61.111 41.82 0.00 37.50 2.50
6983 11484 4.339872 TGCTACGAGTAGGAACCAAAAA 57.660 40.909 11.69 0.00 33.87 1.94
7005 11506 6.923928 AAACATGGATTTGGTCTTGTTTTG 57.076 33.333 0.00 0.00 38.64 2.44
7014 11515 4.712122 TGGTCTTGTTTTGTTCTGTTCC 57.288 40.909 0.00 0.00 0.00 3.62
7027 11528 6.570672 TGTTCTGTTCCTGTACTAGTGTAG 57.429 41.667 5.39 3.46 0.00 2.74
7030 11531 4.458295 TCTGTTCCTGTACTAGTGTAGTGC 59.542 45.833 5.39 0.00 39.81 4.40
7056 11561 1.228245 GGCTGTCAGCAACCTTCCA 60.228 57.895 25.68 0.00 44.75 3.53
7059 11564 0.249868 CTGTCAGCAACCTTCCACGA 60.250 55.000 0.00 0.00 0.00 4.35
7093 11598 3.348647 GGGGATCCCAACCAAATTTTG 57.651 47.619 32.07 1.99 44.65 2.44
7101 11609 2.411409 CCAACCAAATTTTGCGAATCGG 59.589 45.455 4.35 0.00 0.00 4.18
7107 11615 1.895051 ATTTTGCGAATCGGCGAAAG 58.105 45.000 15.93 9.56 46.37 2.62
7135 11643 3.891366 ACCAAAAACACCATGAGAGAAGG 59.109 43.478 0.00 0.00 0.00 3.46
7181 11692 5.045286 CCTAGGGAATTAGAAGGATGGATGG 60.045 48.000 0.00 0.00 0.00 3.51
7189 11700 2.978278 AGAAGGATGGATGGGATGAGAC 59.022 50.000 0.00 0.00 0.00 3.36
7223 11734 0.598680 CTCATCCATCGTTCTCGGCC 60.599 60.000 0.00 0.00 37.69 6.13
7439 11992 2.438795 AGGAGAGGAGGACGCGTC 60.439 66.667 30.67 30.67 0.00 5.19
7440 11993 2.438795 GGAGAGGAGGACGCGTCT 60.439 66.667 35.50 22.76 35.87 4.18
7442 11995 1.438562 GGAGAGGAGGACGCGTCTAC 61.439 65.000 35.50 27.39 33.55 2.59
7443 11996 0.462403 GAGAGGAGGACGCGTCTACT 60.462 60.000 35.50 28.76 33.55 2.57
7445 11998 1.202557 AGAGGAGGACGCGTCTACTAG 60.203 57.143 35.50 0.00 31.79 2.57
7446 11999 0.540923 AGGAGGACGCGTCTACTAGT 59.459 55.000 35.50 14.61 0.00 2.57
7447 12000 1.759445 AGGAGGACGCGTCTACTAGTA 59.241 52.381 35.50 1.89 0.00 1.82
7449 12002 2.482839 GGAGGACGCGTCTACTAGTACT 60.483 54.545 35.50 22.38 0.00 2.73
7450 12003 3.243569 GGAGGACGCGTCTACTAGTACTA 60.244 52.174 35.50 1.89 0.00 1.82
7451 12004 3.976169 AGGACGCGTCTACTAGTACTAG 58.024 50.000 35.50 25.30 39.04 2.57
7452 12005 2.474735 GGACGCGTCTACTAGTACTAGC 59.525 54.545 35.50 13.44 36.66 3.42
7453 12006 2.833614 CGCGTCTACTAGTACTAGCG 57.166 55.000 26.54 21.77 40.37 4.26
7517 12070 3.068560 AGATCGACCGCATCTACTAGTC 58.931 50.000 0.00 0.00 0.00 2.59
7518 12071 1.590932 TCGACCGCATCTACTAGTCC 58.409 55.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
164 165 1.760192 ATGCTGCTCCAAATCAGTCC 58.240 50.000 0.00 0.00 33.09 3.85
204 205 4.699522 ACGAACTTGGGAGCCGGC 62.700 66.667 21.89 21.89 0.00 6.13
294 298 1.205893 CCAGCAAGTGTAGAGGAGGAC 59.794 57.143 0.00 0.00 0.00 3.85
558 562 3.556775 CCTTCACACAATTGCCAAACAAG 59.443 43.478 5.05 0.91 42.87 3.16
559 563 3.055530 ACCTTCACACAATTGCCAAACAA 60.056 39.130 5.05 0.00 44.01 2.83
560 564 2.499289 ACCTTCACACAATTGCCAAACA 59.501 40.909 5.05 0.00 0.00 2.83
561 565 3.123050 GACCTTCACACAATTGCCAAAC 58.877 45.455 5.05 0.00 0.00 2.93
563 567 2.665165 AGACCTTCACACAATTGCCAA 58.335 42.857 5.05 0.00 0.00 4.52
565 569 3.366374 GCTAAGACCTTCACACAATTGCC 60.366 47.826 5.05 0.00 0.00 4.52
566 570 3.503748 AGCTAAGACCTTCACACAATTGC 59.496 43.478 5.05 0.00 0.00 3.56
567 571 5.695851 AAGCTAAGACCTTCACACAATTG 57.304 39.130 3.24 3.24 0.00 2.32
568 572 5.412904 GCTAAGCTAAGACCTTCACACAATT 59.587 40.000 0.00 0.00 0.00 2.32
569 573 4.938226 GCTAAGCTAAGACCTTCACACAAT 59.062 41.667 0.00 0.00 0.00 2.71
570 574 4.315803 GCTAAGCTAAGACCTTCACACAA 58.684 43.478 0.00 0.00 0.00 3.33
571 575 3.306780 GGCTAAGCTAAGACCTTCACACA 60.307 47.826 0.00 0.00 0.00 3.72
572 576 3.055747 AGGCTAAGCTAAGACCTTCACAC 60.056 47.826 0.00 0.00 0.00 3.82
573 577 3.173965 AGGCTAAGCTAAGACCTTCACA 58.826 45.455 0.00 0.00 0.00 3.58
574 578 3.897141 AGGCTAAGCTAAGACCTTCAC 57.103 47.619 0.00 0.00 0.00 3.18
575 579 3.961408 CCTAGGCTAAGCTAAGACCTTCA 59.039 47.826 0.00 0.00 31.79 3.02
576 580 3.962063 ACCTAGGCTAAGCTAAGACCTTC 59.038 47.826 9.30 0.00 31.79 3.46
577 581 3.996957 ACCTAGGCTAAGCTAAGACCTT 58.003 45.455 9.30 0.00 31.79 3.50
578 582 3.691698 ACCTAGGCTAAGCTAAGACCT 57.308 47.619 9.30 0.00 34.42 3.85
579 583 4.081031 ACAAACCTAGGCTAAGCTAAGACC 60.081 45.833 9.30 0.00 0.00 3.85
580 584 4.870991 CACAAACCTAGGCTAAGCTAAGAC 59.129 45.833 9.30 0.00 0.00 3.01
581 585 4.530946 ACACAAACCTAGGCTAAGCTAAGA 59.469 41.667 9.30 0.00 0.00 2.10
582 586 4.833390 ACACAAACCTAGGCTAAGCTAAG 58.167 43.478 9.30 0.00 0.00 2.18
583 587 4.903045 ACACAAACCTAGGCTAAGCTAA 57.097 40.909 9.30 0.00 0.00 3.09
584 588 4.903045 AACACAAACCTAGGCTAAGCTA 57.097 40.909 9.30 0.00 0.00 3.32
585 589 3.790089 AACACAAACCTAGGCTAAGCT 57.210 42.857 9.30 0.00 0.00 3.74
586 590 3.568430 ACAAACACAAACCTAGGCTAAGC 59.432 43.478 9.30 0.00 0.00 3.09
587 591 4.556699 GCACAAACACAAACCTAGGCTAAG 60.557 45.833 9.30 0.00 0.00 2.18
626 630 4.831710 ACTCCGTAGTTGAAAAGGTACTCT 59.168 41.667 0.00 0.00 29.35 3.24
642 646 0.035739 GGAAACTGCCCAACTCCGTA 59.964 55.000 0.00 0.00 0.00 4.02
643 647 1.228154 GGAAACTGCCCAACTCCGT 60.228 57.895 0.00 0.00 0.00 4.69
644 648 3.668386 GGAAACTGCCCAACTCCG 58.332 61.111 0.00 0.00 0.00 4.63
654 658 0.676782 CGTAAGGCAGGGGGAAACTG 60.677 60.000 0.00 0.00 38.95 3.16
655 659 0.838987 TCGTAAGGCAGGGGGAAACT 60.839 55.000 0.00 0.00 38.47 2.66
656 660 0.392595 CTCGTAAGGCAGGGGGAAAC 60.393 60.000 0.00 0.00 38.47 2.78
657 661 0.838987 ACTCGTAAGGCAGGGGGAAA 60.839 55.000 0.00 0.00 38.47 3.13
658 662 0.838987 AACTCGTAAGGCAGGGGGAA 60.839 55.000 0.00 0.00 38.47 3.97
659 663 0.041535 TAACTCGTAAGGCAGGGGGA 59.958 55.000 0.00 0.00 38.47 4.81
660 664 0.177373 GTAACTCGTAAGGCAGGGGG 59.823 60.000 0.00 0.00 38.47 5.40
661 665 0.177373 GGTAACTCGTAAGGCAGGGG 59.823 60.000 0.00 0.00 38.47 4.79
662 666 0.899720 TGGTAACTCGTAAGGCAGGG 59.100 55.000 0.00 0.00 38.47 4.45
663 667 2.618053 CTTGGTAACTCGTAAGGCAGG 58.382 52.381 0.00 0.00 38.47 4.85
664 668 2.000447 GCTTGGTAACTCGTAAGGCAG 59.000 52.381 0.00 0.00 38.47 4.85
665 669 1.338389 GGCTTGGTAACTCGTAAGGCA 60.338 52.381 0.00 0.00 42.97 4.75
666 670 1.066358 AGGCTTGGTAACTCGTAAGGC 60.066 52.381 0.00 0.00 43.55 4.35
667 671 2.232941 TCAGGCTTGGTAACTCGTAAGG 59.767 50.000 0.00 0.00 38.47 2.69
668 672 3.056749 AGTCAGGCTTGGTAACTCGTAAG 60.057 47.826 0.00 0.00 37.61 2.34
669 673 2.895404 AGTCAGGCTTGGTAACTCGTAA 59.105 45.455 0.00 0.00 37.61 3.18
673 677 4.631813 CACATTAGTCAGGCTTGGTAACTC 59.368 45.833 0.00 0.00 37.61 3.01
680 684 2.237143 TCCTCCACATTAGTCAGGCTTG 59.763 50.000 0.00 0.00 0.00 4.01
695 699 2.270352 AGTTTTCGCATGTTCCTCCA 57.730 45.000 0.00 0.00 0.00 3.86
825 838 3.803368 GCCAACAAAGGAAAATGGAGTGG 60.803 47.826 0.00 0.00 32.82 4.00
830 843 2.485038 GCATGCCAACAAAGGAAAATGG 59.515 45.455 6.36 0.00 0.00 3.16
892 905 9.829507 CATGCCAACATCCCTAAAAATAAATAA 57.170 29.630 0.00 0.00 32.87 1.40
923 936 3.314913 TGTGTGTGTGTCTTTAATGCTGG 59.685 43.478 0.00 0.00 0.00 4.85
969 982 9.804758 GCAATGTGTAGAGTAGAGTATAAAGTT 57.195 33.333 0.00 0.00 0.00 2.66
970 983 8.967918 TGCAATGTGTAGAGTAGAGTATAAAGT 58.032 33.333 0.00 0.00 0.00 2.66
978 991 5.316327 TGTCTGCAATGTGTAGAGTAGAG 57.684 43.478 0.00 0.00 39.72 2.43
1146 1159 5.188751 CCTCTTGGAAGGAAGTTCTGTATCT 59.811 44.000 2.25 0.00 38.87 1.98
1152 1165 2.057922 TGCCTCTTGGAAGGAAGTTCT 58.942 47.619 2.25 0.00 38.87 3.01
1163 1176 6.375455 AGTGTTTATATGTCTTTGCCTCTTGG 59.625 38.462 0.00 0.00 0.00 3.61
1358 1371 6.628844 GCCGATAAAAAGAAGTGGGAGTAGTA 60.629 42.308 0.00 0.00 0.00 1.82
1359 1372 5.731591 CCGATAAAAAGAAGTGGGAGTAGT 58.268 41.667 0.00 0.00 0.00 2.73
1360 1373 4.571176 GCCGATAAAAAGAAGTGGGAGTAG 59.429 45.833 0.00 0.00 0.00 2.57
1361 1374 4.224370 AGCCGATAAAAAGAAGTGGGAGTA 59.776 41.667 0.00 0.00 0.00 2.59
1603 1617 4.157289 AGAAAAATACCGCGAGTAGAGTGA 59.843 41.667 8.23 0.00 33.42 3.41
1741 5116 4.256920 CAATCAGTGGTGAAACTCCCTAG 58.743 47.826 0.00 0.00 35.88 3.02
1783 5158 6.539103 AGCGAAGAAAGAACTTTGTCTTTAGT 59.461 34.615 4.48 0.00 45.67 2.24
1867 5248 2.868583 CAAGACGATAATCTGGGTGCAG 59.131 50.000 0.00 0.00 0.00 4.41
2912 6329 5.968387 ACTTTCGGCAATCTAGTTATTCG 57.032 39.130 0.00 0.00 0.00 3.34
2973 6390 1.300481 TCGGCAATTCACGTTGTTCA 58.700 45.000 0.00 0.00 0.00 3.18
3091 6508 1.305201 GGGAAGCTTGTCGTTTGTCA 58.695 50.000 2.10 0.00 0.00 3.58
3281 6698 1.595466 TTTGCCAAGCCAATTTGCTG 58.405 45.000 4.56 0.02 41.80 4.41
3666 7083 1.080772 CGTCTACGGCACTGCTTCA 60.081 57.895 0.00 0.00 35.37 3.02
3691 7108 1.856265 CTCGGTCAAAGGCAGCCAAC 61.856 60.000 15.80 5.97 0.00 3.77
3842 7259 3.300962 ACCCTCCCCTCCCCATCA 61.301 66.667 0.00 0.00 0.00 3.07
3967 7384 4.496840 CCAAACCCACTCGAAAGTAACAAC 60.497 45.833 0.00 0.00 33.25 3.32
4819 8322 5.637006 TTTTGGGTGCACATACTTGTATC 57.363 39.130 20.43 0.00 33.76 2.24
5038 8544 9.702726 CACATAGTTTCACATATAGTTTTTCCG 57.297 33.333 0.00 0.00 0.00 4.30
5084 8590 0.793861 GTATCAAAACGTCGGCTGCA 59.206 50.000 0.50 0.00 0.00 4.41
5085 8591 0.793861 TGTATCAAAACGTCGGCTGC 59.206 50.000 0.00 0.00 0.00 5.25
5346 8852 7.447374 TCGCTCTTTCCATCATTTCTTTTAA 57.553 32.000 0.00 0.00 0.00 1.52
5378 8884 1.679153 TCCGCCTTCCTTTTGTTGTTC 59.321 47.619 0.00 0.00 0.00 3.18
5536 9042 9.780186 ATGGAGAATTAGTTACCTTAATGTAGC 57.220 33.333 0.00 0.00 0.00 3.58
5962 10127 6.278363 TGGTCAGACTACACAAGACTAAAAC 58.722 40.000 0.00 0.00 0.00 2.43
6214 10417 3.004090 AGCATGATGCCTGGCTGA 58.996 55.556 21.03 0.00 46.52 4.26
6217 10420 1.751544 TCACAGCATGATGCCTGGC 60.752 57.895 14.72 12.87 46.52 4.85
6261 10464 0.457509 CAGGCACGACTAGCTCACTG 60.458 60.000 0.00 0.00 0.00 3.66
6582 10825 2.035632 TCCCAAAAACGTTGCTTCCAT 58.964 42.857 0.00 0.00 0.00 3.41
6604 10847 3.630769 CAGTTCCATGCATGCTACTGAAT 59.369 43.478 33.64 16.31 38.68 2.57
6606 10849 2.236893 TCAGTTCCATGCATGCTACTGA 59.763 45.455 34.56 34.56 40.79 3.41
6607 10850 2.353889 GTCAGTTCCATGCATGCTACTG 59.646 50.000 32.48 32.48 38.20 2.74
6608 10851 2.636830 GTCAGTTCCATGCATGCTACT 58.363 47.619 21.69 20.72 0.00 2.57
6609 10852 1.328680 CGTCAGTTCCATGCATGCTAC 59.671 52.381 21.69 18.94 0.00 3.58
6610 10853 1.206849 TCGTCAGTTCCATGCATGCTA 59.793 47.619 21.69 8.51 0.00 3.49
6611 10854 0.036105 TCGTCAGTTCCATGCATGCT 60.036 50.000 21.69 10.26 0.00 3.79
6612 10855 0.376152 CTCGTCAGTTCCATGCATGC 59.624 55.000 21.69 11.82 0.00 4.06
6613 10856 1.931841 CTCTCGTCAGTTCCATGCATG 59.068 52.381 20.19 20.19 0.00 4.06
6614 10857 1.741732 GCTCTCGTCAGTTCCATGCAT 60.742 52.381 0.00 0.00 0.00 3.96
6615 10858 0.390340 GCTCTCGTCAGTTCCATGCA 60.390 55.000 0.00 0.00 0.00 3.96
6738 11234 0.663153 ACACTTCCAGCGCAGTTTTC 59.337 50.000 11.47 0.00 0.00 2.29
6806 11302 2.386661 ATTACACTTCCAGCGACCAG 57.613 50.000 0.00 0.00 0.00 4.00
6807 11303 2.851263 AATTACACTTCCAGCGACCA 57.149 45.000 0.00 0.00 0.00 4.02
6808 11304 3.751698 AGAAAATTACACTTCCAGCGACC 59.248 43.478 0.00 0.00 0.00 4.79
6809 11305 4.213482 ACAGAAAATTACACTTCCAGCGAC 59.787 41.667 0.00 0.00 0.00 5.19
6810 11306 4.385825 ACAGAAAATTACACTTCCAGCGA 58.614 39.130 0.00 0.00 0.00 4.93
6829 11325 4.529219 TCCAGCGCGCCCATACAG 62.529 66.667 30.33 8.87 0.00 2.74
6832 11328 3.781307 ACTTCCAGCGCGCCCATA 61.781 61.111 30.33 10.58 0.00 2.74
6938 11435 3.726595 TTACAGAATCCGGCCGGCG 62.727 63.158 39.89 24.69 34.68 6.46
6939 11436 2.178235 GTTACAGAATCCGGCCGGC 61.178 63.158 39.89 25.50 34.68 6.13
6940 11437 1.523032 GGTTACAGAATCCGGCCGG 60.523 63.158 39.13 39.13 0.00 6.13
6941 11438 0.391927 TTGGTTACAGAATCCGGCCG 60.392 55.000 21.04 21.04 0.00 6.13
6942 11439 1.828979 TTTGGTTACAGAATCCGGCC 58.171 50.000 0.00 0.00 0.00 6.13
6957 11458 3.195661 GGTTCCTACTCGTAGCATTTGG 58.804 50.000 0.00 0.00 31.95 3.28
6983 11484 5.988287 ACAAAACAAGACCAAATCCATGTT 58.012 33.333 0.00 0.00 38.74 2.71
7005 11506 6.380190 CACTACACTAGTACAGGAACAGAAC 58.620 44.000 0.00 0.00 37.23 3.01
7014 11515 3.008330 ACCTCGCACTACACTAGTACAG 58.992 50.000 0.00 0.00 37.23 2.74
7027 11528 1.845809 CTGACAGCCAAACCTCGCAC 61.846 60.000 0.00 0.00 0.00 5.34
7030 11531 1.165907 TTGCTGACAGCCAAACCTCG 61.166 55.000 24.33 0.00 41.51 4.63
7093 11598 2.321400 GAGCTTTCGCCGATTCGC 59.679 61.111 0.00 0.00 36.60 4.70
7101 11609 1.858458 GTTTTTGGTTGGAGCTTTCGC 59.142 47.619 0.00 0.00 0.00 4.70
7107 11615 2.102252 TCATGGTGTTTTTGGTTGGAGC 59.898 45.455 0.00 0.00 0.00 4.70
7117 11625 2.716424 TCCCCTTCTCTCATGGTGTTTT 59.284 45.455 0.00 0.00 0.00 2.43
7135 11643 4.575236 GGTTTGGATCTTCTTATCGTTCCC 59.425 45.833 0.00 0.00 0.00 3.97
7181 11692 2.049985 CGATCGGCCGTCTCATCC 60.050 66.667 27.15 6.56 0.00 3.51
7189 11700 1.590610 ATGAGATCCTCGATCGGCCG 61.591 60.000 22.12 22.12 43.17 6.13
7223 11734 1.358402 CAGCCGAGGAGATGAGACG 59.642 63.158 0.00 0.00 0.00 4.18
7327 11857 2.671177 GGCGCCATCGATCGGAATG 61.671 63.158 24.80 12.29 38.10 2.67
7439 11992 4.213694 CACATCCCACGCTAGTACTAGTAG 59.786 50.000 26.76 22.62 35.65 2.57
7440 11993 4.132336 CACATCCCACGCTAGTACTAGTA 58.868 47.826 26.76 0.00 35.65 1.82
7442 11995 2.293677 CCACATCCCACGCTAGTACTAG 59.706 54.545 23.25 23.25 36.29 2.57
7443 11996 2.304092 CCACATCCCACGCTAGTACTA 58.696 52.381 1.89 1.89 0.00 1.82
7445 11998 0.529992 GCCACATCCCACGCTAGTAC 60.530 60.000 0.00 0.00 0.00 2.73
7446 11999 1.820581 GCCACATCCCACGCTAGTA 59.179 57.895 0.00 0.00 0.00 1.82
7447 12000 2.584608 GCCACATCCCACGCTAGT 59.415 61.111 0.00 0.00 0.00 2.57
7449 12002 3.387091 ACGCCACATCCCACGCTA 61.387 61.111 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.