Multiple sequence alignment - TraesCS7B01G133300

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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 TraesCS7B01G133300 chr7B 100.000 3376 0 0 1 3376 162115803 162112428 0.000000e+00 6235
1 TraesCS7B01G133300 chr7D 93.161 2047 96 19 576 2601 197878172 197876149 0.000000e+00 2964
2 TraesCS7B01G133300 chr7D 97.390 498 12 1 1 498 197878665 197878169 0.000000e+00 846
3 TraesCS7B01G133300 chr7D 83.268 765 70 23 2645 3376 370161059 370161798 0.000000e+00 651
4 TraesCS7B01G133300 chr7A 94.095 1321 59 9 576 1888 206937775 206936466 0.000000e+00 1989
5 TraesCS7B01G133300 chr7A 90.691 709 41 11 1926 2628 206936469 206935780 0.000000e+00 920
6 TraesCS7B01G133300 chr7A 96.982 497 15 0 2 498 206938268 206937772 0.000000e+00 835
7 TraesCS7B01G133300 chr2D 88.661 732 66 9 2648 3376 192187858 192187141 0.000000e+00 876
8 TraesCS7B01G133300 chr2D 86.156 744 63 16 2648 3376 638393266 638392548 0.000000e+00 767
9 TraesCS7B01G133300 chr2D 88.190 525 58 4 2648 3170 448519652 448519130 1.030000e-174 623
10 TraesCS7B01G133300 chr2D 94.059 101 4 1 489 587 25037976 25037876 5.830000e-33 152
11 TraesCS7B01G133300 chr2D 90.826 109 6 3 482 586 87247313 87247205 3.510000e-30 143
12 TraesCS7B01G133300 chr4B 86.821 736 81 8 2645 3376 562616300 562617023 0.000000e+00 808
13 TraesCS7B01G133300 chr4B 93.814 97 3 2 486 580 519258910 519259005 3.510000e-30 143
14 TraesCS7B01G133300 chr6D 86.885 732 70 9 2645 3376 414103349 414104054 0.000000e+00 797
15 TraesCS7B01G133300 chr6D 86.230 748 81 12 2645 3376 141140518 141141259 0.000000e+00 791
16 TraesCS7B01G133300 chr6D 84.104 692 92 13 2649 3335 297521431 297522109 0.000000e+00 652
17 TraesCS7B01G133300 chr5A 86.096 748 64 24 2645 3376 676883092 676883815 0.000000e+00 769
18 TraesCS7B01G133300 chr5A 85.208 480 62 5 2645 3124 488040729 488041199 5.060000e-133 484
19 TraesCS7B01G133300 chr1D 85.363 731 87 12 2648 3374 410251780 410251066 0.000000e+00 739
20 TraesCS7B01G133300 chr1D 93.269 104 2 3 487 586 415987236 415987134 7.550000e-32 148
21 TraesCS7B01G133300 chr4D 83.880 732 82 19 2648 3376 383822789 383823487 0.000000e+00 665
22 TraesCS7B01G133300 chr1B 82.950 739 88 21 2648 3376 553454111 553453401 1.710000e-177 632
23 TraesCS7B01G133300 chr5B 81.114 736 108 23 2648 3375 432322081 432321369 8.180000e-156 560
24 TraesCS7B01G133300 chr2B 85.235 149 21 1 2501 2648 226711559 226711411 5.830000e-33 152
25 TraesCS7B01G133300 chr2B 96.703 91 3 0 490 580 782178846 782178756 5.830000e-33 152
26 TraesCS7B01G133300 chr4A 96.629 89 1 1 494 580 712733707 712733795 2.710000e-31 147
27 TraesCS7B01G133300 chrUn 93.684 95 4 1 494 586 94846969 94847063 1.260000e-29 141
28 TraesCS7B01G133300 chr2A 89.908 109 7 3 482 586 87445073 87444965 1.630000e-28 137
29 TraesCS7B01G133300 chr3B 90.476 105 6 3 477 579 728904943 728905045 5.880000e-28 135


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 TraesCS7B01G133300 chr7B 162112428 162115803 3375 True 6235 6235 100.000000 1 3376 1 chr7B.!!$R1 3375
1 TraesCS7B01G133300 chr7D 197876149 197878665 2516 True 1905 2964 95.275500 1 2601 2 chr7D.!!$R1 2600
2 TraesCS7B01G133300 chr7D 370161059 370161798 739 False 651 651 83.268000 2645 3376 1 chr7D.!!$F1 731
3 TraesCS7B01G133300 chr7A 206935780 206938268 2488 True 1248 1989 93.922667 2 2628 3 chr7A.!!$R1 2626
4 TraesCS7B01G133300 chr2D 192187141 192187858 717 True 876 876 88.661000 2648 3376 1 chr2D.!!$R3 728
5 TraesCS7B01G133300 chr2D 638392548 638393266 718 True 767 767 86.156000 2648 3376 1 chr2D.!!$R5 728
6 TraesCS7B01G133300 chr2D 448519130 448519652 522 True 623 623 88.190000 2648 3170 1 chr2D.!!$R4 522
7 TraesCS7B01G133300 chr4B 562616300 562617023 723 False 808 808 86.821000 2645 3376 1 chr4B.!!$F2 731
8 TraesCS7B01G133300 chr6D 414103349 414104054 705 False 797 797 86.885000 2645 3376 1 chr6D.!!$F3 731
9 TraesCS7B01G133300 chr6D 141140518 141141259 741 False 791 791 86.230000 2645 3376 1 chr6D.!!$F1 731
10 TraesCS7B01G133300 chr6D 297521431 297522109 678 False 652 652 84.104000 2649 3335 1 chr6D.!!$F2 686
11 TraesCS7B01G133300 chr5A 676883092 676883815 723 False 769 769 86.096000 2645 3376 1 chr5A.!!$F2 731
12 TraesCS7B01G133300 chr1D 410251066 410251780 714 True 739 739 85.363000 2648 3374 1 chr1D.!!$R1 726
13 TraesCS7B01G133300 chr4D 383822789 383823487 698 False 665 665 83.880000 2648 3376 1 chr4D.!!$F1 728
14 TraesCS7B01G133300 chr1B 553453401 553454111 710 True 632 632 82.950000 2648 3376 1 chr1B.!!$R1 728
15 TraesCS7B01G133300 chr5B 432321369 432322081 712 True 560 560 81.114000 2648 3375 1 chr5B.!!$R1 727

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
511 512 0.257039 GTAGTACTCCCTCCGTCCCA 59.743 60.0 0.0 0.0 0.0 4.37 F
984 999 0.671781 CTCACGGGCACAGGAAGAAG 60.672 60.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1731 1749 0.110238 CGTCCATGGCAAACGTCTTG 60.11 55.0 14.6 0.0 0.0 3.02 R
2827 2863 0.109723 GCAGCGGGGGATATGGTTTA 59.89 55.0 0.0 0.0 0.0 2.01 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
59 60 6.866770 TGAATGTAGCGCATTAATAGGTACTC 59.133 38.462 22.09 16.39 46.90 2.59
194 195 6.881602 GGTTAGTGAAAATCCTTCATGAGACT 59.118 38.462 0.00 0.00 0.00 3.24
197 198 5.182760 AGTGAAAATCCTTCATGAGACTTGC 59.817 40.000 0.00 0.00 0.00 4.01
203 204 4.245660 TCCTTCATGAGACTTGCTTTACG 58.754 43.478 0.00 0.00 0.00 3.18
227 228 7.171337 ACGCAAATGCTTGAAAATTCATTTAGT 59.829 29.630 3.63 0.00 37.03 2.24
495 496 2.531206 GCGGCTCAAGTTGTAGAGTAG 58.469 52.381 2.11 0.00 34.39 2.57
496 497 2.094649 GCGGCTCAAGTTGTAGAGTAGT 60.095 50.000 2.11 0.00 34.39 2.73
497 498 3.128242 GCGGCTCAAGTTGTAGAGTAGTA 59.872 47.826 2.11 0.00 34.39 1.82
498 499 4.660105 CGGCTCAAGTTGTAGAGTAGTAC 58.340 47.826 2.11 0.00 34.39 2.73
499 500 4.395542 CGGCTCAAGTTGTAGAGTAGTACT 59.604 45.833 1.37 1.37 34.39 2.73
500 501 5.447548 CGGCTCAAGTTGTAGAGTAGTACTC 60.448 48.000 20.73 20.73 45.38 2.59
501 502 5.163632 GGCTCAAGTTGTAGAGTAGTACTCC 60.164 48.000 23.82 12.09 46.18 3.85
502 503 5.163632 GCTCAAGTTGTAGAGTAGTACTCCC 60.164 48.000 23.82 16.17 46.18 4.30
503 504 6.137104 TCAAGTTGTAGAGTAGTACTCCCT 57.863 41.667 23.82 11.24 46.18 4.20
504 505 6.179040 TCAAGTTGTAGAGTAGTACTCCCTC 58.821 44.000 23.82 15.46 46.18 4.30
505 506 5.114764 AGTTGTAGAGTAGTACTCCCTCC 57.885 47.826 23.82 11.54 46.18 4.30
506 507 3.834489 TGTAGAGTAGTACTCCCTCCG 57.166 52.381 23.82 0.00 46.18 4.63
507 508 3.110705 TGTAGAGTAGTACTCCCTCCGT 58.889 50.000 23.82 9.26 46.18 4.69
508 509 3.133721 TGTAGAGTAGTACTCCCTCCGTC 59.866 52.174 23.82 9.36 46.18 4.79
509 510 1.490069 AGAGTAGTACTCCCTCCGTCC 59.510 57.143 23.82 0.00 46.18 4.79
510 511 0.550432 AGTAGTACTCCCTCCGTCCC 59.450 60.000 0.00 0.00 0.00 4.46
511 512 0.257039 GTAGTACTCCCTCCGTCCCA 59.743 60.000 0.00 0.00 0.00 4.37
512 513 1.133544 GTAGTACTCCCTCCGTCCCAT 60.134 57.143 0.00 0.00 0.00 4.00
513 514 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
514 515 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
515 516 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
516 517 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
517 518 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
518 519 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
519 520 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
520 521 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
521 522 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
522 523 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
524 525 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
525 526 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
526 527 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
527 528 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
528 529 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
571 572 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
572 573 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
573 574 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
574 575 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
575 576 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
796 804 9.741168 CTATATTTACACGTGCAGTTATAATGC 57.259 33.333 17.22 10.94 44.11 3.56
823 831 5.619625 ATCAGTAGTCTGCTTGCTTTTTC 57.380 39.130 0.00 0.00 41.10 2.29
845 853 3.134804 CGGTCCTCTCCTTTATGTCCAAT 59.865 47.826 0.00 0.00 0.00 3.16
848 856 5.221742 GGTCCTCTCCTTTATGTCCAATAGG 60.222 48.000 0.00 0.00 0.00 2.57
854 862 8.618240 TCTCCTTTATGTCCAATAGGTAGAAA 57.382 34.615 0.00 0.00 35.89 2.52
856 864 7.280356 TCCTTTATGTCCAATAGGTAGAAAGC 58.720 38.462 0.00 0.00 33.85 3.51
861 870 6.061022 TGTCCAATAGGTAGAAAGCATGAA 57.939 37.500 0.00 0.00 35.89 2.57
970 984 1.080230 CAGGAGTCACAGCCTCACG 60.080 63.158 0.00 0.00 30.41 4.35
984 999 0.671781 CTCACGGGCACAGGAAGAAG 60.672 60.000 0.00 0.00 0.00 2.85
1304 1319 8.152246 TCTTCGATTTACTCTTCTTTTTGGGTA 58.848 33.333 0.00 0.00 0.00 3.69
1319 1334 5.693769 TTTGGGTATGGTTTTTGGTTTCA 57.306 34.783 0.00 0.00 0.00 2.69
1411 1427 1.073125 TCGGTTCTTTCCCTTGCATCA 59.927 47.619 0.00 0.00 0.00 3.07
1461 1479 1.074775 GTTCAGGGCCATGACCACA 59.925 57.895 21.89 1.67 29.21 4.17
1683 1701 3.331478 AGAACATCAGTGCTTCAGAGG 57.669 47.619 0.00 0.00 24.49 3.69
1695 1713 1.347707 CTTCAGAGGTACAGGTTGCCA 59.652 52.381 0.00 0.00 0.00 4.92
1728 1746 1.244019 GGGAGTGTGTTCACCATGCC 61.244 60.000 0.37 0.73 44.83 4.40
1731 1749 2.983030 TGTGTTCACCATGCCGGC 60.983 61.111 22.73 22.73 39.03 6.13
1732 1750 2.983030 GTGTTCACCATGCCGGCA 60.983 61.111 34.80 34.80 39.03 5.69
1773 1791 4.012895 CTTGGAAGCGCGCACGTT 62.013 61.111 35.10 19.67 42.83 3.99
1825 1844 1.646447 TCCAGGTAGTCCAGATGGTCT 59.354 52.381 4.10 4.10 37.37 3.85
1826 1845 2.035632 CCAGGTAGTCCAGATGGTCTC 58.964 57.143 1.74 0.00 35.30 3.36
1833 1852 3.515562 AGTCCAGATGGTCTCAGTTTCT 58.484 45.455 0.00 0.00 36.34 2.52
1834 1853 3.513515 AGTCCAGATGGTCTCAGTTTCTC 59.486 47.826 0.00 0.00 36.34 2.87
1837 1856 3.594134 CAGATGGTCTCAGTTTCTCACC 58.406 50.000 0.00 0.00 0.00 4.02
1838 1857 2.232452 AGATGGTCTCAGTTTCTCACCG 59.768 50.000 0.00 0.00 0.00 4.94
1840 1859 1.613925 TGGTCTCAGTTTCTCACCGAG 59.386 52.381 0.00 0.00 0.00 4.63
1842 1861 1.000163 GTCTCAGTTTCTCACCGAGCA 60.000 52.381 0.00 0.00 0.00 4.26
1844 1863 2.094494 TCTCAGTTTCTCACCGAGCATC 60.094 50.000 0.00 0.00 0.00 3.91
1870 1889 2.800629 GCAGTGCAGCTGTTTGAAACAT 60.801 45.455 16.64 0.00 46.64 2.71
1899 1918 7.668886 CCAGGGATCTTAATCTGCTGAATATTT 59.331 37.037 0.00 0.00 32.12 1.40
1900 1919 9.075678 CAGGGATCTTAATCTGCTGAATATTTT 57.924 33.333 0.00 0.00 32.12 1.82
1901 1920 9.652114 AGGGATCTTAATCTGCTGAATATTTTT 57.348 29.630 0.00 0.00 32.12 1.94
1902 1921 9.688592 GGGATCTTAATCTGCTGAATATTTTTG 57.311 33.333 0.00 0.00 32.12 2.44
1903 1922 9.189723 GGATCTTAATCTGCTGAATATTTTTGC 57.810 33.333 0.00 0.00 32.12 3.68
1904 1923 9.962783 GATCTTAATCTGCTGAATATTTTTGCT 57.037 29.630 0.00 0.00 0.00 3.91
1905 1924 9.745880 ATCTTAATCTGCTGAATATTTTTGCTG 57.254 29.630 0.00 8.41 0.00 4.41
1906 1925 8.959548 TCTTAATCTGCTGAATATTTTTGCTGA 58.040 29.630 14.78 14.78 36.40 4.26
1907 1926 9.745880 CTTAATCTGCTGAATATTTTTGCTGAT 57.254 29.630 16.78 16.78 41.61 2.90
1914 1933 9.872721 TGCTGAATATTTTTGCTGATTTATTCA 57.127 25.926 0.00 0.00 35.73 2.57
1924 1943 5.572211 TGCTGATTTATTCATTCGACTTGC 58.428 37.500 0.00 0.00 32.72 4.01
1928 1947 7.305820 GCTGATTTATTCATTCGACTTGCAATG 60.306 37.037 0.00 0.00 32.72 2.82
1946 1965 2.670934 GCAGGTGGCTGTGGAGTG 60.671 66.667 0.00 0.00 40.25 3.51
1947 1966 2.670934 CAGGTGGCTGTGGAGTGC 60.671 66.667 0.00 0.00 0.00 4.40
1974 1993 0.036732 TGAACTGCATCCACTGGGTC 59.963 55.000 0.00 0.00 34.93 4.46
2016 2035 3.554692 GAGTTCATGGCGCGTCCG 61.555 66.667 8.89 0.00 37.80 4.79
2038 2057 4.659172 CCAAGGAAGGGCACGGCA 62.659 66.667 0.00 0.00 0.00 5.69
2082 2101 4.595538 AAGGACGTGTTCGCGGCA 62.596 61.111 13.44 2.72 42.62 5.69
2124 2143 1.375140 CGAGAAGCAGGAGCAGCAA 60.375 57.895 0.00 0.00 45.49 3.91
2127 2146 0.619505 AGAAGCAGGAGCAGCAAGAT 59.380 50.000 0.00 0.00 45.49 2.40
2142 2161 1.984288 AAGATAGTTCCAGGGGCGCC 61.984 60.000 21.18 21.18 0.00 6.53
2168 2187 6.448006 ACGGTAGTATATTCAGCTGTTCATC 58.552 40.000 14.67 1.84 0.00 2.92
2249 2270 0.467290 TGTTTGCAGGGGGTGAAGAC 60.467 55.000 0.00 0.00 0.00 3.01
2357 2378 0.615850 GGTTGGGAGACTGGAGGAAG 59.384 60.000 0.00 0.00 0.00 3.46
2418 2439 4.836175 TGGTTAGTGATGGTGTGAAGACTA 59.164 41.667 0.00 0.00 0.00 2.59
2425 2446 4.041567 TGATGGTGTGAAGACTACAACCAT 59.958 41.667 4.87 4.87 39.92 3.55
2431 2452 5.405571 GTGTGAAGACTACAACCATACACTG 59.594 44.000 0.00 0.00 34.63 3.66
2468 2489 5.047519 ACGTGCTGTAATACCTGGGATATAC 60.048 44.000 0.00 1.87 0.00 1.47
2495 2519 3.476552 TGGAAGATGACACAGAACAACC 58.523 45.455 0.00 0.00 0.00 3.77
2535 2567 6.677781 TCTCGCCCAACTTTATTAATTCAG 57.322 37.500 0.00 0.00 0.00 3.02
2579 2613 1.216064 TGGATCATGAGGTTCCCCAG 58.784 55.000 10.65 0.00 34.92 4.45
2601 2635 4.345257 AGCCAAATATGACGACCTATGTCT 59.655 41.667 0.00 0.00 39.47 3.41
2620 2654 5.109210 TGTCTAGATTACATGCGAACTTGG 58.891 41.667 0.00 0.00 0.00 3.61
2628 2662 0.729116 ATGCGAACTTGGCGAGATTG 59.271 50.000 9.20 1.33 0.00 2.67
2629 2663 1.226128 GCGAACTTGGCGAGATTGC 60.226 57.895 9.20 8.71 31.36 3.56
2630 2664 1.059369 CGAACTTGGCGAGATTGCG 59.941 57.895 9.20 2.60 35.06 4.85
2631 2665 1.351430 CGAACTTGGCGAGATTGCGA 61.351 55.000 9.20 0.00 35.06 5.10
2632 2666 0.371645 GAACTTGGCGAGATTGCGAG 59.628 55.000 9.20 0.00 35.06 5.03
2633 2667 1.639298 AACTTGGCGAGATTGCGAGC 61.639 55.000 9.20 0.00 35.06 5.03
2634 2668 1.812922 CTTGGCGAGATTGCGAGCT 60.813 57.895 0.00 0.00 35.06 4.09
2635 2669 1.364626 CTTGGCGAGATTGCGAGCTT 61.365 55.000 0.00 0.00 35.06 3.74
2636 2670 1.361668 TTGGCGAGATTGCGAGCTTC 61.362 55.000 0.00 0.00 35.06 3.86
2637 2671 1.811266 GGCGAGATTGCGAGCTTCA 60.811 57.895 0.00 0.00 35.06 3.02
2638 2672 1.361668 GGCGAGATTGCGAGCTTCAA 61.362 55.000 0.00 5.07 35.06 2.69
2639 2673 0.443869 GCGAGATTGCGAGCTTCAAA 59.556 50.000 0.00 0.00 0.00 2.69
2640 2674 1.135972 GCGAGATTGCGAGCTTCAAAA 60.136 47.619 0.00 0.00 0.00 2.44
2641 2675 2.476854 GCGAGATTGCGAGCTTCAAAAT 60.477 45.455 0.00 0.00 0.00 1.82
2642 2676 3.751621 CGAGATTGCGAGCTTCAAAATT 58.248 40.909 0.00 0.00 0.00 1.82
2643 2677 4.727734 GCGAGATTGCGAGCTTCAAAATTA 60.728 41.667 0.00 0.00 0.00 1.40
2646 2680 6.021939 CGAGATTGCGAGCTTCAAAATTAAAG 60.022 38.462 0.00 0.00 0.00 1.85
2739 2773 2.231478 GCTAGAATAGAGCCCGCATACA 59.769 50.000 0.00 0.00 42.77 2.29
2740 2774 3.118956 GCTAGAATAGAGCCCGCATACAT 60.119 47.826 0.00 0.00 42.77 2.29
2757 2791 1.826487 ATGCCCGGCCCGTAAATTC 60.826 57.895 7.03 0.00 0.00 2.17
2770 2805 0.885196 TAAATTCTTTTGCCGCGGCT 59.115 45.000 45.79 27.46 42.51 5.52
2809 2845 4.023450 CCGACTGCTATATCTACGGTTTCA 60.023 45.833 0.00 0.00 35.21 2.69
2821 2857 2.023601 GTTTCACGGCGCGTTTGT 59.976 55.556 6.90 0.27 38.32 2.83
2869 2911 2.676471 AGCCACGCAATTCCCCAC 60.676 61.111 0.00 0.00 0.00 4.61
2896 2942 0.321564 CTCCACATTTCTCGCCACCA 60.322 55.000 0.00 0.00 0.00 4.17
2910 2957 4.640690 ACCAGCGACCACCTCCCT 62.641 66.667 0.00 0.00 0.00 4.20
3132 3199 4.070552 GTCCTCTGCCGCCTCGTT 62.071 66.667 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
197 198 6.875753 TGAATTTTCAAGCATTTGCGTAAAG 58.124 32.000 4.68 0.00 38.03 1.85
227 228 4.030913 AGGCACACTCCTTAGCTGTAATA 58.969 43.478 0.00 0.00 30.82 0.98
402 403 3.713764 CCATCCTTCACTACTCCCTCAAT 59.286 47.826 0.00 0.00 0.00 2.57
495 496 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
496 497 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
497 498 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
498 499 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
499 500 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
500 501 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
501 502 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
502 503 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
503 504 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
546 547 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
547 548 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
548 549 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
549 550 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
550 551 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
552 553 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
553 554 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
554 555 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
555 556 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
556 557 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
557 558 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
558 559 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
559 560 2.492940 CCTACTCCCTCCGTCCCATAAT 60.493 54.545 0.00 0.00 0.00 1.28
560 561 1.133262 CCTACTCCCTCCGTCCCATAA 60.133 57.143 0.00 0.00 0.00 1.90
561 562 0.481567 CCTACTCCCTCCGTCCCATA 59.518 60.000 0.00 0.00 0.00 2.74
562 563 1.233369 CCTACTCCCTCCGTCCCAT 59.767 63.158 0.00 0.00 0.00 4.00
563 564 1.294426 ATCCTACTCCCTCCGTCCCA 61.294 60.000 0.00 0.00 0.00 4.37
564 565 0.776176 TATCCTACTCCCTCCGTCCC 59.224 60.000 0.00 0.00 0.00 4.46
565 566 2.903375 ATATCCTACTCCCTCCGTCC 57.097 55.000 0.00 0.00 0.00 4.79
566 567 4.208746 CCATATATCCTACTCCCTCCGTC 58.791 52.174 0.00 0.00 0.00 4.79
567 568 3.596956 ACCATATATCCTACTCCCTCCGT 59.403 47.826 0.00 0.00 0.00 4.69
568 569 4.208746 GACCATATATCCTACTCCCTCCG 58.791 52.174 0.00 0.00 0.00 4.63
569 570 4.233287 AGGACCATATATCCTACTCCCTCC 59.767 50.000 6.00 0.00 45.18 4.30
570 571 5.475398 AGGACCATATATCCTACTCCCTC 57.525 47.826 6.00 0.00 45.18 4.30
571 572 5.594777 CAAGGACCATATATCCTACTCCCT 58.405 45.833 7.90 0.00 46.36 4.20
572 573 4.162509 GCAAGGACCATATATCCTACTCCC 59.837 50.000 7.90 0.00 46.36 4.30
573 574 5.026790 AGCAAGGACCATATATCCTACTCC 58.973 45.833 7.90 0.00 46.36 3.85
574 575 5.105146 CCAGCAAGGACCATATATCCTACTC 60.105 48.000 7.90 2.25 46.36 2.59
575 576 4.780021 CCAGCAAGGACCATATATCCTACT 59.220 45.833 7.90 6.52 46.36 2.57
796 804 6.674694 AAGCAAGCAGACTACTGATATTTG 57.325 37.500 0.00 0.00 46.03 2.32
823 831 2.108168 TGGACATAAAGGAGAGGACCG 58.892 52.381 0.00 0.00 34.73 4.79
970 984 0.402121 AGGTTCTTCTTCCTGTGCCC 59.598 55.000 0.00 0.00 32.29 5.36
984 999 3.149196 TGCCATTTCTCACTTCAGGTTC 58.851 45.455 0.00 0.00 0.00 3.62
1304 1319 9.492973 CTGAATTTCTATGAAACCAAAAACCAT 57.507 29.630 0.00 0.00 0.00 3.55
1347 1363 5.751243 ACAGTTGCTATTTGTCGAGTTTT 57.249 34.783 0.00 0.00 0.00 2.43
1348 1364 5.751243 AACAGTTGCTATTTGTCGAGTTT 57.249 34.783 0.00 0.00 0.00 2.66
1349 1365 5.751243 AAACAGTTGCTATTTGTCGAGTT 57.249 34.783 0.00 0.00 0.00 3.01
1359 1375 4.893424 AACACGACAAAACAGTTGCTAT 57.107 36.364 0.00 0.00 0.00 2.97
1360 1376 5.110598 TCTAACACGACAAAACAGTTGCTA 58.889 37.500 0.00 0.00 0.00 3.49
1411 1427 9.479549 AATACCAATTCACAGTTTAGATTCCAT 57.520 29.630 0.00 0.00 0.00 3.41
1461 1479 1.580845 GCCTCATTCAGCAACAGCGT 61.581 55.000 0.00 0.00 0.00 5.07
1568 1586 3.555966 CCCATTCCAAGAACTGTATCCC 58.444 50.000 0.00 0.00 0.00 3.85
1613 1631 4.641541 CCTATGCATTTGTTCTCATCCACA 59.358 41.667 3.54 0.00 0.00 4.17
1659 1677 4.707105 TCTGAAGCACTGATGTTCTTTGA 58.293 39.130 0.00 0.00 30.23 2.69
1669 1687 1.895798 CCTGTACCTCTGAAGCACTGA 59.104 52.381 0.00 0.00 0.00 3.41
1695 1713 1.487976 CACTCCCTACATCCTGCACAT 59.512 52.381 0.00 0.00 0.00 3.21
1731 1749 0.110238 CGTCCATGGCAAACGTCTTG 60.110 55.000 14.60 0.00 0.00 3.02
1732 1750 0.250124 TCGTCCATGGCAAACGTCTT 60.250 50.000 20.20 0.00 37.64 3.01
1773 1791 0.878523 CGTCGCCAAACTGGACTTCA 60.879 55.000 0.00 0.00 40.96 3.02
1825 1844 1.402852 CGATGCTCGGTGAGAAACTGA 60.403 52.381 0.00 0.00 42.13 3.41
1826 1845 0.994995 CGATGCTCGGTGAGAAACTG 59.005 55.000 0.00 0.00 36.00 3.16
1837 1856 3.561213 CACTGCTGCCGATGCTCG 61.561 66.667 0.00 0.00 40.07 5.03
1838 1857 3.873883 GCACTGCTGCCGATGCTC 61.874 66.667 11.28 0.00 37.45 4.26
1840 1859 4.175489 CTGCACTGCTGCCGATGC 62.175 66.667 11.55 11.55 43.51 3.91
1854 1873 4.418392 CTGGATATGTTTCAAACAGCTGC 58.582 43.478 15.27 4.47 45.95 5.25
1855 1874 4.142315 CCCTGGATATGTTTCAAACAGCTG 60.142 45.833 13.48 13.48 45.95 4.24
1870 1889 5.406163 TCAGCAGATTAAGATCCCTGGATA 58.594 41.667 0.00 0.00 34.97 2.59
1899 1918 6.527722 GCAAGTCGAATGAATAAATCAGCAAA 59.472 34.615 3.77 0.00 42.53 3.68
1900 1919 6.029607 GCAAGTCGAATGAATAAATCAGCAA 58.970 36.000 3.77 0.00 42.53 3.91
1901 1920 5.123661 TGCAAGTCGAATGAATAAATCAGCA 59.876 36.000 3.77 0.00 42.53 4.41
1902 1921 5.572211 TGCAAGTCGAATGAATAAATCAGC 58.428 37.500 3.77 0.00 42.53 4.26
1903 1922 7.166970 CCATTGCAAGTCGAATGAATAAATCAG 59.833 37.037 4.94 0.00 42.53 2.90
1904 1923 6.974048 CCATTGCAAGTCGAATGAATAAATCA 59.026 34.615 4.94 0.00 43.67 2.57
1905 1924 6.074676 GCCATTGCAAGTCGAATGAATAAATC 60.075 38.462 4.94 0.00 37.47 2.17
1906 1925 5.750067 GCCATTGCAAGTCGAATGAATAAAT 59.250 36.000 4.94 0.00 37.47 1.40
1907 1926 5.101628 GCCATTGCAAGTCGAATGAATAAA 58.898 37.500 4.94 0.00 37.47 1.40
1908 1927 4.157472 TGCCATTGCAAGTCGAATGAATAA 59.843 37.500 4.94 0.00 46.66 1.40
1909 1928 3.693578 TGCCATTGCAAGTCGAATGAATA 59.306 39.130 4.94 0.00 46.66 1.75
1910 1929 2.492881 TGCCATTGCAAGTCGAATGAAT 59.507 40.909 4.94 0.00 46.66 2.57
1911 1930 1.885233 TGCCATTGCAAGTCGAATGAA 59.115 42.857 4.94 0.00 46.66 2.57
1912 1931 1.532523 TGCCATTGCAAGTCGAATGA 58.467 45.000 4.94 0.00 46.66 2.57
1924 1943 2.642254 CCACAGCCACCTGCCATTG 61.642 63.158 0.00 0.00 43.02 2.82
1928 1947 3.958860 ACTCCACAGCCACCTGCC 61.959 66.667 0.00 0.00 43.02 4.85
1946 1965 1.930908 GATGCAGTTCACAGGGCAGC 61.931 60.000 0.00 0.00 39.95 5.25
1947 1966 1.310933 GGATGCAGTTCACAGGGCAG 61.311 60.000 0.00 0.00 39.95 4.85
2082 2101 1.302832 CTTGGCGAAGTTCCTGGCT 60.303 57.895 0.00 0.00 0.00 4.75
2124 2143 2.444256 GGCGCCCCTGGAACTATCT 61.444 63.158 18.11 0.00 0.00 1.98
2127 2146 2.931105 TTGGCGCCCCTGGAACTA 60.931 61.111 26.77 0.00 0.00 2.24
2142 2161 6.040247 TGAACAGCTGAATATACTACCGTTG 58.960 40.000 23.35 0.00 0.00 4.10
2168 2187 2.233922 ACATGGTTCTCAGTTCGTAGGG 59.766 50.000 0.00 0.00 0.00 3.53
2219 2238 4.244862 CCCCTGCAAACATTGTACAAATC 58.755 43.478 13.23 0.00 0.00 2.17
2220 2239 3.007831 CCCCCTGCAAACATTGTACAAAT 59.992 43.478 13.23 0.77 0.00 2.32
2223 2242 1.133325 ACCCCCTGCAAACATTGTACA 60.133 47.619 0.00 0.00 0.00 2.90
2224 2243 1.272212 CACCCCCTGCAAACATTGTAC 59.728 52.381 0.00 0.00 0.00 2.90
2249 2270 3.423154 GCCGTTTCAGCCTCCACG 61.423 66.667 0.00 0.00 0.00 4.94
2357 2378 1.542492 TCTACCTGTCTGTTCCGGAC 58.458 55.000 1.83 0.00 39.93 4.79
2425 2446 2.095110 CGTCGTACAACATCCCAGTGTA 60.095 50.000 0.00 0.00 0.00 2.90
2431 2452 0.389426 AGCACGTCGTACAACATCCC 60.389 55.000 0.00 0.00 0.00 3.85
2468 2489 6.401394 TGTTCTGTGTCATCTTCCATCTTAG 58.599 40.000 0.00 0.00 0.00 2.18
2508 2537 9.179909 TGAATTAATAAAGTTGGGCGAGAATTA 57.820 29.630 0.00 0.00 0.00 1.40
2535 2567 5.127031 ACCATTGTACCTATGGACATTTTGC 59.873 40.000 23.64 0.00 44.36 3.68
2579 2613 4.992381 GACATAGGTCGTCATATTTGGC 57.008 45.455 0.00 0.00 33.68 4.52
2601 2635 2.863740 CGCCAAGTTCGCATGTAATCTA 59.136 45.455 0.00 0.00 0.00 1.98
2608 2642 0.729116 AATCTCGCCAAGTTCGCATG 59.271 50.000 0.00 0.00 0.00 4.06
2620 2654 0.443869 TTTGAAGCTCGCAATCTCGC 59.556 50.000 3.18 0.00 0.00 5.03
2628 2662 5.734963 GCTAGACTTTAATTTTGAAGCTCGC 59.265 40.000 0.00 0.00 0.00 5.03
2629 2663 6.831769 TGCTAGACTTTAATTTTGAAGCTCG 58.168 36.000 0.00 0.00 0.00 5.03
2630 2664 7.960195 GTCTGCTAGACTTTAATTTTGAAGCTC 59.040 37.037 0.00 0.00 41.88 4.09
2631 2665 7.094592 GGTCTGCTAGACTTTAATTTTGAAGCT 60.095 37.037 13.59 0.00 44.46 3.74
2632 2666 7.024171 GGTCTGCTAGACTTTAATTTTGAAGC 58.976 38.462 13.59 0.00 44.46 3.86
2633 2667 7.362142 GGGGTCTGCTAGACTTTAATTTTGAAG 60.362 40.741 13.59 0.00 44.46 3.02
2634 2668 6.433093 GGGGTCTGCTAGACTTTAATTTTGAA 59.567 38.462 13.59 0.00 44.46 2.69
2635 2669 5.944007 GGGGTCTGCTAGACTTTAATTTTGA 59.056 40.000 13.59 0.00 44.46 2.69
2636 2670 5.163754 CGGGGTCTGCTAGACTTTAATTTTG 60.164 44.000 13.59 0.00 44.46 2.44
2637 2671 4.941873 CGGGGTCTGCTAGACTTTAATTTT 59.058 41.667 13.59 0.00 44.46 1.82
2638 2672 4.019591 ACGGGGTCTGCTAGACTTTAATTT 60.020 41.667 13.59 0.00 44.46 1.82
2639 2673 3.518303 ACGGGGTCTGCTAGACTTTAATT 59.482 43.478 13.59 0.00 44.46 1.40
2640 2674 3.105283 ACGGGGTCTGCTAGACTTTAAT 58.895 45.455 13.59 0.00 44.46 1.40
2641 2675 2.532843 ACGGGGTCTGCTAGACTTTAA 58.467 47.619 13.59 0.00 44.46 1.52
2642 2676 2.226962 ACGGGGTCTGCTAGACTTTA 57.773 50.000 13.59 0.00 44.46 1.85
2643 2677 2.226962 TACGGGGTCTGCTAGACTTT 57.773 50.000 13.59 2.50 44.46 2.66
2646 2680 2.494870 TCTTTTACGGGGTCTGCTAGAC 59.505 50.000 0.00 7.52 44.32 2.59
2686 2720 3.470888 AAGCCCGCATACTCGCCT 61.471 61.111 0.00 0.00 0.00 5.52
2739 2773 1.826487 GAATTTACGGGCCGGGCAT 60.826 57.895 31.78 19.51 0.00 4.40
2740 2774 2.438795 GAATTTACGGGCCGGGCA 60.439 61.111 31.78 13.52 0.00 5.36
2821 2857 2.424793 GGGGGATATGGTTTAGACCCA 58.575 52.381 0.00 0.00 45.92 4.51
2827 2863 0.109723 GCAGCGGGGGATATGGTTTA 59.890 55.000 0.00 0.00 0.00 2.01
3076 3142 1.377725 GTCGTACTCCCCCGTCTCA 60.378 63.158 0.00 0.00 0.00 3.27
3084 3150 4.185059 GCCGACGGTCGTACTCCC 62.185 72.222 26.72 6.35 38.40 4.30
3127 3194 4.856607 GCCGCGGAGGAGAACGAG 62.857 72.222 33.48 0.00 45.00 4.18
3132 3199 4.877619 ATCTCGCCGCGGAGGAGA 62.878 66.667 35.83 35.83 46.87 3.71
3286 3399 4.011517 TCTTCCGGCCCAACGACC 62.012 66.667 0.00 0.00 35.47 4.79


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

AutoCloner maintained by Alex Coulton.