Multiple sequence alignment - TraesCS6A01G323400

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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 TraesCS6A01G323400 chr6A 100.000 2632 0 0 1 2632 556886281 556888912 0.000000e+00 4861.0
1 TraesCS6A01G323400 chr6A 73.814 569 95 31 2082 2628 106694480 106693944 2.690000e-40 176.0
2 TraesCS6A01G323400 chr6B 88.812 1305 76 39 813 2073 619728453 619729731 0.000000e+00 1537.0
3 TraesCS6A01G323400 chr6B 81.468 545 68 12 2108 2632 51135718 51135187 1.460000e-112 416.0
4 TraesCS6A01G323400 chr6B 84.065 433 48 9 2101 2519 619732809 619733234 5.280000e-107 398.0
5 TraesCS6A01G323400 chr6B 87.952 83 2 2 2550 2632 619733229 619733303 1.000000e-14 91.6
6 TraesCS6A01G323400 chr6D 93.648 1039 39 11 636 1661 411921574 411922598 0.000000e+00 1528.0
7 TraesCS6A01G323400 chr6D 84.029 407 30 18 1652 2042 411922621 411923008 2.490000e-95 359.0
8 TraesCS6A01G323400 chr2A 98.311 592 10 0 1 592 126650524 126649933 0.000000e+00 1038.0
9 TraesCS6A01G323400 chr2A 94.924 591 25 5 1 590 197229725 197230311 0.000000e+00 920.0
10 TraesCS6A01G323400 chr5A 97.800 591 9 4 1 590 481091127 481091714 0.000000e+00 1016.0
11 TraesCS6A01G323400 chr5A 78.070 570 77 19 2082 2626 654558776 654559322 1.520000e-82 316.0
12 TraesCS6A01G323400 chr3A 96.376 607 18 4 1 604 263166523 263165918 0.000000e+00 996.0
13 TraesCS6A01G323400 chr3A 96.796 593 18 1 1 593 722239858 722240449 0.000000e+00 989.0
14 TraesCS6A01G323400 chr3A 95.939 591 23 1 1 590 728544012 728543422 0.000000e+00 957.0
15 TraesCS6A01G323400 chr3A 95.932 590 20 4 1 589 54836003 54835417 0.000000e+00 953.0
16 TraesCS6A01G323400 chr3A 95.763 590 23 2 1 589 728594901 728594313 0.000000e+00 950.0
17 TraesCS6A01G323400 chr3A 95.586 589 24 2 1 588 728574472 728573885 0.000000e+00 942.0
18 TraesCS6A01G323400 chr3B 82.194 556 63 11 2098 2632 694178681 694178141 1.860000e-121 446.0
19 TraesCS6A01G323400 chr3B 78.897 526 82 10 2082 2587 46088150 46088666 1.950000e-86 329.0
20 TraesCS6A01G323400 chr3B 77.954 567 73 24 2090 2632 576020234 576019696 9.150000e-80 307.0
21 TraesCS6A01G323400 chr3D 79.510 571 80 13 2082 2632 581084231 581083678 3.200000e-99 372.0
22 TraesCS6A01G323400 chr2B 79.130 575 85 14 2076 2632 727310934 727311491 5.350000e-97 364.0
23 TraesCS6A01G323400 chr2B 78.374 578 86 21 2076 2632 349932104 349932663 3.240000e-89 339.0
24 TraesCS6A01G323400 chr5D 78.609 575 88 18 2076 2632 530850195 530850752 5.390000e-92 348.0
25 TraesCS6A01G323400 chr7A 77.058 571 94 27 2076 2632 715930428 715930975 7.120000e-76 294.0
26 TraesCS6A01G323400 chr7B 76.522 575 94 21 2082 2632 491915922 491915365 2.580000e-70 276.0
27 TraesCS6A01G323400 chr7D 76.481 540 91 22 2117 2632 468507633 468507106 7.230000e-66 261.0


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 TraesCS6A01G323400 chr6A 556886281 556888912 2631 False 4861.000000 4861 100.0000 1 2632 1 chr6A.!!$F1 2631
1 TraesCS6A01G323400 chr6B 619728453 619733303 4850 False 675.533333 1537 86.9430 813 2632 3 chr6B.!!$F1 1819
2 TraesCS6A01G323400 chr6B 51135187 51135718 531 True 416.000000 416 81.4680 2108 2632 1 chr6B.!!$R1 524
3 TraesCS6A01G323400 chr6D 411921574 411923008 1434 False 943.500000 1528 88.8385 636 2042 2 chr6D.!!$F1 1406
4 TraesCS6A01G323400 chr2A 126649933 126650524 591 True 1038.000000 1038 98.3110 1 592 1 chr2A.!!$R1 591
5 TraesCS6A01G323400 chr2A 197229725 197230311 586 False 920.000000 920 94.9240 1 590 1 chr2A.!!$F1 589
6 TraesCS6A01G323400 chr5A 481091127 481091714 587 False 1016.000000 1016 97.8000 1 590 1 chr5A.!!$F1 589
7 TraesCS6A01G323400 chr5A 654558776 654559322 546 False 316.000000 316 78.0700 2082 2626 1 chr5A.!!$F2 544
8 TraesCS6A01G323400 chr3A 263165918 263166523 605 True 996.000000 996 96.3760 1 604 1 chr3A.!!$R2 603
9 TraesCS6A01G323400 chr3A 722239858 722240449 591 False 989.000000 989 96.7960 1 593 1 chr3A.!!$F1 592
10 TraesCS6A01G323400 chr3A 728543422 728544012 590 True 957.000000 957 95.9390 1 590 1 chr3A.!!$R3 589
11 TraesCS6A01G323400 chr3A 54835417 54836003 586 True 953.000000 953 95.9320 1 589 1 chr3A.!!$R1 588
12 TraesCS6A01G323400 chr3A 728594313 728594901 588 True 950.000000 950 95.7630 1 589 1 chr3A.!!$R5 588
13 TraesCS6A01G323400 chr3A 728573885 728574472 587 True 942.000000 942 95.5860 1 588 1 chr3A.!!$R4 587
14 TraesCS6A01G323400 chr3B 694178141 694178681 540 True 446.000000 446 82.1940 2098 2632 1 chr3B.!!$R2 534
15 TraesCS6A01G323400 chr3B 46088150 46088666 516 False 329.000000 329 78.8970 2082 2587 1 chr3B.!!$F1 505
16 TraesCS6A01G323400 chr3B 576019696 576020234 538 True 307.000000 307 77.9540 2090 2632 1 chr3B.!!$R1 542
17 TraesCS6A01G323400 chr3D 581083678 581084231 553 True 372.000000 372 79.5100 2082 2632 1 chr3D.!!$R1 550
18 TraesCS6A01G323400 chr2B 727310934 727311491 557 False 364.000000 364 79.1300 2076 2632 1 chr2B.!!$F2 556
19 TraesCS6A01G323400 chr2B 349932104 349932663 559 False 339.000000 339 78.3740 2076 2632 1 chr2B.!!$F1 556
20 TraesCS6A01G323400 chr5D 530850195 530850752 557 False 348.000000 348 78.6090 2076 2632 1 chr5D.!!$F1 556
21 TraesCS6A01G323400 chr7A 715930428 715930975 547 False 294.000000 294 77.0580 2076 2632 1 chr7A.!!$F1 556
22 TraesCS6A01G323400 chr7B 491915365 491915922 557 True 276.000000 276 76.5220 2082 2632 1 chr7B.!!$R1 550
23 TraesCS6A01G323400 chr7D 468507106 468507633 527 True 261.000000 261 76.4810 2117 2632 1 chr7D.!!$R1 515

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
892 898 0.179129 CCAGCCTTTTATTGCCAGCG 60.179 55.0 0.0 0.0 0.0 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1877 1958 0.037046 CCAAACCAAAGCATCAGCCC 60.037 55.0 0.0 0.0 43.56 5.19 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
593 598 3.403968 GGCGAATAGGATTTTCCTCCTC 58.596 50.000 0.00 0.00 45.66 3.71
594 599 3.181454 GGCGAATAGGATTTTCCTCCTCA 60.181 47.826 0.00 0.00 45.66 3.86
595 600 4.061596 GCGAATAGGATTTTCCTCCTCAG 58.938 47.826 0.00 0.00 45.66 3.35
596 601 4.443598 GCGAATAGGATTTTCCTCCTCAGT 60.444 45.833 0.00 0.00 45.66 3.41
597 602 5.675538 CGAATAGGATTTTCCTCCTCAGTT 58.324 41.667 0.00 0.00 45.66 3.16
598 603 6.685620 GCGAATAGGATTTTCCTCCTCAGTTA 60.686 42.308 0.00 0.00 45.66 2.24
599 604 6.926272 CGAATAGGATTTTCCTCCTCAGTTAG 59.074 42.308 0.00 0.00 45.66 2.34
600 605 7.418025 CGAATAGGATTTTCCTCCTCAGTTAGT 60.418 40.741 0.00 0.00 45.66 2.24
601 606 7.757242 ATAGGATTTTCCTCCTCAGTTAGTT 57.243 36.000 0.00 0.00 45.66 2.24
602 607 5.810095 AGGATTTTCCTCCTCAGTTAGTTG 58.190 41.667 0.00 0.00 45.66 3.16
603 608 4.396478 GGATTTTCCTCCTCAGTTAGTTGC 59.604 45.833 0.00 0.00 32.53 4.17
604 609 4.706842 TTTTCCTCCTCAGTTAGTTGCT 57.293 40.909 0.00 0.00 0.00 3.91
605 610 3.963428 TTCCTCCTCAGTTAGTTGCTC 57.037 47.619 0.00 0.00 0.00 4.26
606 611 2.180276 TCCTCCTCAGTTAGTTGCTCC 58.820 52.381 0.00 0.00 0.00 4.70
607 612 1.208293 CCTCCTCAGTTAGTTGCTCCC 59.792 57.143 0.00 0.00 0.00 4.30
608 613 0.895530 TCCTCAGTTAGTTGCTCCCG 59.104 55.000 0.00 0.00 0.00 5.14
609 614 0.608640 CCTCAGTTAGTTGCTCCCGT 59.391 55.000 0.00 0.00 0.00 5.28
610 615 1.822990 CCTCAGTTAGTTGCTCCCGTA 59.177 52.381 0.00 0.00 0.00 4.02
611 616 2.232941 CCTCAGTTAGTTGCTCCCGTAA 59.767 50.000 0.00 0.00 0.00 3.18
612 617 3.118738 CCTCAGTTAGTTGCTCCCGTAAT 60.119 47.826 0.00 0.00 0.00 1.89
613 618 3.857052 TCAGTTAGTTGCTCCCGTAATG 58.143 45.455 0.00 0.00 0.00 1.90
614 619 3.259876 TCAGTTAGTTGCTCCCGTAATGT 59.740 43.478 0.00 0.00 0.00 2.71
615 620 4.000988 CAGTTAGTTGCTCCCGTAATGTT 58.999 43.478 0.00 0.00 0.00 2.71
616 621 4.000988 AGTTAGTTGCTCCCGTAATGTTG 58.999 43.478 0.00 0.00 0.00 3.33
617 622 1.165270 AGTTGCTCCCGTAATGTTGC 58.835 50.000 0.00 0.00 0.00 4.17
618 623 0.878416 GTTGCTCCCGTAATGTTGCA 59.122 50.000 0.00 0.00 0.00 4.08
619 624 1.472480 GTTGCTCCCGTAATGTTGCAT 59.528 47.619 0.00 0.00 0.00 3.96
620 625 1.378531 TGCTCCCGTAATGTTGCATC 58.621 50.000 0.00 0.00 0.00 3.91
621 626 1.339535 TGCTCCCGTAATGTTGCATCA 60.340 47.619 0.00 0.00 0.00 3.07
622 627 1.742831 GCTCCCGTAATGTTGCATCAA 59.257 47.619 0.75 0.00 0.00 2.57
623 628 2.477863 GCTCCCGTAATGTTGCATCAAC 60.478 50.000 0.75 2.96 43.78 3.18
624 629 1.735018 TCCCGTAATGTTGCATCAACG 59.265 47.619 12.82 12.82 46.13 4.10
625 630 1.735018 CCCGTAATGTTGCATCAACGA 59.265 47.619 18.83 0.00 46.13 3.85
626 631 2.223021 CCCGTAATGTTGCATCAACGAG 60.223 50.000 18.83 6.40 46.13 4.18
627 632 2.223021 CCGTAATGTTGCATCAACGAGG 60.223 50.000 18.83 9.77 46.13 4.63
628 633 2.670905 CGTAATGTTGCATCAACGAGGA 59.329 45.455 14.06 0.00 46.13 3.71
629 634 3.483574 CGTAATGTTGCATCAACGAGGAC 60.484 47.826 14.06 0.00 46.13 3.85
630 635 1.078709 ATGTTGCATCAACGAGGACG 58.921 50.000 0.75 0.00 46.13 4.79
631 636 0.948623 TGTTGCATCAACGAGGACGG 60.949 55.000 0.00 0.00 46.13 4.79
632 637 1.375396 TTGCATCAACGAGGACGGG 60.375 57.895 0.00 0.00 44.46 5.28
633 638 3.195698 GCATCAACGAGGACGGGC 61.196 66.667 0.00 0.00 44.46 6.13
634 639 2.579201 CATCAACGAGGACGGGCT 59.421 61.111 0.00 0.00 44.46 5.19
650 655 2.200337 GCTCCCGTGCCCTGTTTTT 61.200 57.895 0.00 0.00 0.00 1.94
673 678 2.434774 GAGGCCGTCCCAAAAGGT 59.565 61.111 0.00 0.00 36.75 3.50
689 694 6.667848 CCCAAAAGGTCCATTAGTCCTTAAAT 59.332 38.462 0.00 0.00 40.18 1.40
690 695 7.837187 CCCAAAAGGTCCATTAGTCCTTAAATA 59.163 37.037 0.00 0.00 40.18 1.40
691 696 9.421399 CCAAAAGGTCCATTAGTCCTTAAATAT 57.579 33.333 0.00 0.00 40.18 1.28
695 700 7.526918 AGGTCCATTAGTCCTTAAATATTGGG 58.473 38.462 0.00 0.00 0.00 4.12
696 701 6.208797 GGTCCATTAGTCCTTAAATATTGGGC 59.791 42.308 0.00 0.00 0.00 5.36
698 703 5.183140 CCATTAGTCCTTAAATATTGGGCCG 59.817 44.000 0.00 0.00 0.00 6.13
739 745 7.072454 AGTGTAAGATAGGCCCATTCTCAATTA 59.928 37.037 0.00 0.00 0.00 1.40
740 746 7.173390 GTGTAAGATAGGCCCATTCTCAATTAC 59.827 40.741 0.00 0.00 0.00 1.89
742 748 5.874093 AGATAGGCCCATTCTCAATTACAG 58.126 41.667 0.00 0.00 0.00 2.74
744 750 2.243221 AGGCCCATTCTCAATTACAGCT 59.757 45.455 0.00 0.00 0.00 4.24
747 753 3.065925 GCCCATTCTCAATTACAGCTGTC 59.934 47.826 25.56 0.00 0.00 3.51
753 759 0.748005 CAATTACAGCTGTCCCCGGG 60.748 60.000 25.56 15.80 0.00 5.73
892 898 0.179129 CCAGCCTTTTATTGCCAGCG 60.179 55.000 0.00 0.00 0.00 5.18
918 926 1.694882 TATCCCCTCCAAACCCCCG 60.695 63.158 0.00 0.00 0.00 5.73
921 929 4.426313 CCCTCCAAACCCCCGCTC 62.426 72.222 0.00 0.00 0.00 5.03
922 930 3.646715 CCTCCAAACCCCCGCTCA 61.647 66.667 0.00 0.00 0.00 4.26
941 952 1.448540 CATCCATCCCTATCGCCGC 60.449 63.158 0.00 0.00 0.00 6.53
985 996 4.179599 CTCCCTCCCCTCCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
1241 1261 2.507992 CGACGAGGCCAAGCTCAG 60.508 66.667 5.01 0.00 0.00 3.35
1327 1347 3.129502 TCGACGACGCCTACCAGG 61.130 66.667 1.48 0.00 39.58 4.45
1420 1440 3.763902 CGGTAGATCGATAGCCAATCTG 58.236 50.000 0.00 0.00 32.25 2.90
1513 1541 3.732849 GGTGGAGAGGGCCAAGGG 61.733 72.222 6.18 0.00 40.20 3.95
1543 1571 2.507992 CGTGAGCAAGCTCCGGAG 60.508 66.667 27.83 27.83 42.09 4.63
1631 1659 6.663523 GGATCAAATCCCTCTTTGGAAAGTAA 59.336 38.462 0.00 0.00 43.88 2.24
1636 1695 5.112129 TCCCTCTTTGGAAAGTAATAGGC 57.888 43.478 0.00 0.00 38.35 3.93
1639 1698 4.192317 CTCTTTGGAAAGTAATAGGCGCT 58.808 43.478 7.64 0.00 37.31 5.92
1640 1699 4.189231 TCTTTGGAAAGTAATAGGCGCTC 58.811 43.478 7.64 0.00 37.31 5.03
1643 1702 2.504175 TGGAAAGTAATAGGCGCTCCTT 59.496 45.455 7.64 0.35 40.66 3.36
1644 1703 3.132160 GGAAAGTAATAGGCGCTCCTTC 58.868 50.000 7.64 0.00 40.66 3.46
1645 1704 3.181464 GGAAAGTAATAGGCGCTCCTTCT 60.181 47.826 7.64 0.00 40.66 2.85
1646 1705 3.460857 AAGTAATAGGCGCTCCTTCTG 57.539 47.619 7.64 0.00 40.66 3.02
1653 1712 2.873288 CGCTCCTTCTGCCAAAGC 59.127 61.111 0.00 0.00 40.48 3.51
1701 1760 3.815401 GTGTGGCTTGTACAGTTCAATCT 59.185 43.478 0.00 0.00 0.00 2.40
1702 1761 4.994852 GTGTGGCTTGTACAGTTCAATCTA 59.005 41.667 0.00 0.00 0.00 1.98
1703 1762 5.120830 GTGTGGCTTGTACAGTTCAATCTAG 59.879 44.000 0.00 0.00 0.00 2.43
1718 1777 6.296365 TCAATCTAGTAGTATGTTCGTCGG 57.704 41.667 0.00 0.00 0.00 4.79
1744 1803 6.664816 TGCAGGGAATCTGAAGAATATGTTTT 59.335 34.615 0.00 0.00 46.18 2.43
1757 1816 7.481275 AGAATATGTTTTTGCTTGTTTGTGG 57.519 32.000 0.00 0.00 0.00 4.17
1766 1833 1.196127 GCTTGTTTGTGGCGTAGGTAC 59.804 52.381 0.00 0.00 0.00 3.34
1770 1837 2.224329 TGTTTGTGGCGTAGGTACATGT 60.224 45.455 2.69 2.69 0.00 3.21
1797 1864 4.196193 CAGAATAATCTGTTTGCCGGGTA 58.804 43.478 2.18 0.00 46.60 3.69
1848 1925 2.183478 TGCTTGCTCGGATTCAGAAA 57.817 45.000 0.00 0.00 0.00 2.52
1849 1926 2.715046 TGCTTGCTCGGATTCAGAAAT 58.285 42.857 0.00 0.00 0.00 2.17
1850 1927 2.679837 TGCTTGCTCGGATTCAGAAATC 59.320 45.455 0.00 0.00 40.56 2.17
1851 1928 2.679837 GCTTGCTCGGATTCAGAAATCA 59.320 45.455 1.05 0.00 42.66 2.57
1852 1929 3.242673 GCTTGCTCGGATTCAGAAATCAG 60.243 47.826 1.05 0.00 42.66 2.90
1853 1930 3.893326 TGCTCGGATTCAGAAATCAGA 57.107 42.857 1.05 1.55 42.66 3.27
1854 1931 4.206477 TGCTCGGATTCAGAAATCAGAA 57.794 40.909 3.31 0.00 42.83 3.02
1877 1958 3.624300 CATGCTCGCTCGGCTTCG 61.624 66.667 4.86 0.00 0.00 3.79
1889 1970 2.048603 GGCTTCGGGCTGATGCTTT 61.049 57.895 27.12 0.00 44.81 3.51
1890 1971 1.138247 GCTTCGGGCTGATGCTTTG 59.862 57.895 22.87 0.96 42.77 2.77
1891 1972 1.805254 CTTCGGGCTGATGCTTTGG 59.195 57.895 0.00 0.00 39.59 3.28
1920 2001 3.452627 GTGATGGATCCTGGTGTCTACTT 59.547 47.826 14.23 0.00 0.00 2.24
1935 2016 6.404954 GGTGTCTACTTTGTTTTGCCTGTAAA 60.405 38.462 0.00 0.00 0.00 2.01
1936 2017 7.030768 GTGTCTACTTTGTTTTGCCTGTAAAA 58.969 34.615 0.00 0.00 0.00 1.52
1937 2018 7.704899 GTGTCTACTTTGTTTTGCCTGTAAAAT 59.295 33.333 0.00 0.00 32.71 1.82
1938 2019 7.704472 TGTCTACTTTGTTTTGCCTGTAAAATG 59.296 33.333 0.00 0.00 32.71 2.32
1939 2020 7.169140 GTCTACTTTGTTTTGCCTGTAAAATGG 59.831 37.037 0.00 0.00 32.71 3.16
1966 2047 0.116342 TGACAGGGCTGGAAGGTCTA 59.884 55.000 0.00 0.00 34.19 2.59
1985 2066 1.153349 GGGGCGTCCAGAGATTGTC 60.153 63.158 9.07 0.00 35.00 3.18
2018 2099 0.376852 CGGACTGTGGTGTGTTTGTG 59.623 55.000 0.00 0.00 0.00 3.33
2033 2114 1.702886 TTGTGTGTTTGGTTGTTGCG 58.297 45.000 0.00 0.00 0.00 4.85
2050 2134 0.512952 GCGCTTTGATGTATAGCCGG 59.487 55.000 0.00 0.00 0.00 6.13
2067 2151 2.665185 GCAGCCCGAGTGAACGTT 60.665 61.111 0.00 0.00 0.00 3.99
2080 2177 0.780002 GAACGTTCGCTTGCTACGAA 59.220 50.000 13.36 5.18 46.45 3.85
2098 2195 2.222027 GAATAGGCGTGCCATAGCTTT 58.778 47.619 14.29 0.00 40.80 3.51
2101 2198 4.819105 ATAGGCGTGCCATAGCTTTATA 57.181 40.909 14.29 0.00 40.80 0.98
2103 2200 4.819105 AGGCGTGCCATAGCTTTATATA 57.181 40.909 14.29 0.00 40.80 0.86
2104 2201 5.359194 AGGCGTGCCATAGCTTTATATAT 57.641 39.130 14.29 0.00 40.80 0.86
2105 2202 5.118990 AGGCGTGCCATAGCTTTATATATG 58.881 41.667 14.29 0.00 40.80 1.78
2106 2203 5.104941 AGGCGTGCCATAGCTTTATATATGA 60.105 40.000 14.29 0.00 40.80 2.15
2160 5292 4.203950 TCACAATGAACAACAAGCGTAC 57.796 40.909 0.00 0.00 0.00 3.67
2161 5293 3.874543 TCACAATGAACAACAAGCGTACT 59.125 39.130 0.00 0.00 0.00 2.73
2196 5333 1.340248 TCTCGAACAAGTCCACAGACC 59.660 52.381 0.00 0.00 44.72 3.85
2207 5344 0.250295 CCACAGACCGACAACACCAT 60.250 55.000 0.00 0.00 0.00 3.55
2208 5345 1.001520 CCACAGACCGACAACACCATA 59.998 52.381 0.00 0.00 0.00 2.74
2212 5349 3.070446 ACAGACCGACAACACCATAAAGA 59.930 43.478 0.00 0.00 0.00 2.52
2218 5355 4.023193 CCGACAACACCATAAAGAAAAGCT 60.023 41.667 0.00 0.00 0.00 3.74
2220 5357 6.077838 CGACAACACCATAAAGAAAAGCTAC 58.922 40.000 0.00 0.00 0.00 3.58
2221 5358 6.073222 CGACAACACCATAAAGAAAAGCTACT 60.073 38.462 0.00 0.00 0.00 2.57
2236 5373 8.903820 AGAAAAGCTACTTACAACACAAAAGAT 58.096 29.630 0.00 0.00 0.00 2.40
2246 5383 9.099454 CTTACAACACAAAAGATCCTATCCTAC 57.901 37.037 0.00 0.00 0.00 3.18
2258 5402 3.018856 CCTATCCTACACACACACCGTA 58.981 50.000 0.00 0.00 0.00 4.02
2296 5442 1.070786 GCTCCGAAGACCAACACCA 59.929 57.895 0.00 0.00 0.00 4.17
2306 5452 2.635915 AGACCAACACCATCCGTAGAAA 59.364 45.455 0.00 0.00 0.00 2.52
2312 5458 1.597663 CACCATCCGTAGAAAATCGCC 59.402 52.381 0.00 0.00 0.00 5.54
2317 5463 1.546923 TCCGTAGAAAATCGCCTGTCA 59.453 47.619 0.00 0.00 0.00 3.58
2319 5465 2.936498 CCGTAGAAAATCGCCTGTCAAT 59.064 45.455 0.00 0.00 0.00 2.57
2323 5469 2.756760 AGAAAATCGCCTGTCAATGCAT 59.243 40.909 0.00 0.00 0.00 3.96
2427 5595 5.620205 GCATACATAGTGTCATAGAGGACCG 60.620 48.000 0.00 0.00 36.97 4.79
2437 5605 0.107312 TAGAGGACCGGAAGAGGACG 60.107 60.000 9.46 0.00 34.73 4.79
2454 5622 2.281484 GGCAGCAAACACCGGAGA 60.281 61.111 9.46 0.00 0.00 3.71
2459 5627 0.035458 AGCAAACACCGGAGAAGAGG 59.965 55.000 9.46 0.00 0.00 3.69
2482 5650 0.763223 AAGGACCCAACCGTGTCTCT 60.763 55.000 0.00 0.00 34.73 3.10
2542 5710 1.727511 CGCCAATGTGCCGATCCAAT 61.728 55.000 0.00 0.00 0.00 3.16
2587 5755 2.237392 AGATAGCCACCAACTCCAAGTC 59.763 50.000 0.00 0.00 0.00 3.01
2588 5756 1.729586 TAGCCACCAACTCCAAGTCT 58.270 50.000 0.00 0.00 0.00 3.24
2589 5757 0.398318 AGCCACCAACTCCAAGTCTC 59.602 55.000 0.00 0.00 0.00 3.36
2590 5758 0.606673 GCCACCAACTCCAAGTCTCC 60.607 60.000 0.00 0.00 0.00 3.71
2591 5759 0.764890 CCACCAACTCCAAGTCTCCA 59.235 55.000 0.00 0.00 0.00 3.86
2592 5760 1.142870 CCACCAACTCCAAGTCTCCAA 59.857 52.381 0.00 0.00 0.00 3.53
2593 5761 2.498167 CACCAACTCCAAGTCTCCAAG 58.502 52.381 0.00 0.00 0.00 3.61
2594 5762 2.127708 ACCAACTCCAAGTCTCCAAGT 58.872 47.619 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
397 401 6.653320 TCTGCTTCTTTTTCGGCTTTCTATTA 59.347 34.615 0.00 0.00 0.00 0.98
418 422 5.607119 TTTCCTGTATCGTTTCTTTCTGC 57.393 39.130 0.00 0.00 0.00 4.26
593 598 3.596214 ACATTACGGGAGCAACTAACTG 58.404 45.455 0.00 0.00 0.00 3.16
594 599 3.975168 ACATTACGGGAGCAACTAACT 57.025 42.857 0.00 0.00 0.00 2.24
595 600 3.425758 GCAACATTACGGGAGCAACTAAC 60.426 47.826 0.00 0.00 0.00 2.34
596 601 2.745281 GCAACATTACGGGAGCAACTAA 59.255 45.455 0.00 0.00 0.00 2.24
597 602 2.289756 TGCAACATTACGGGAGCAACTA 60.290 45.455 0.00 0.00 0.00 2.24
598 603 1.165270 GCAACATTACGGGAGCAACT 58.835 50.000 0.00 0.00 0.00 3.16
599 604 0.878416 TGCAACATTACGGGAGCAAC 59.122 50.000 0.00 0.00 0.00 4.17
600 605 1.742831 GATGCAACATTACGGGAGCAA 59.257 47.619 0.00 0.00 35.45 3.91
601 606 1.339535 TGATGCAACATTACGGGAGCA 60.340 47.619 0.00 0.00 36.34 4.26
602 607 1.378531 TGATGCAACATTACGGGAGC 58.621 50.000 0.00 0.00 0.00 4.70
603 608 2.223021 CGTTGATGCAACATTACGGGAG 60.223 50.000 11.97 0.00 43.70 4.30
604 609 1.735018 CGTTGATGCAACATTACGGGA 59.265 47.619 11.97 0.00 43.70 5.14
605 610 1.735018 TCGTTGATGCAACATTACGGG 59.265 47.619 17.61 0.00 43.70 5.28
606 611 2.223021 CCTCGTTGATGCAACATTACGG 60.223 50.000 17.61 10.36 43.70 4.02
607 612 2.670905 TCCTCGTTGATGCAACATTACG 59.329 45.455 13.23 13.23 43.70 3.18
608 613 3.483574 CGTCCTCGTTGATGCAACATTAC 60.484 47.826 10.48 0.00 43.70 1.89
609 614 2.670905 CGTCCTCGTTGATGCAACATTA 59.329 45.455 10.48 0.00 43.70 1.90
610 615 1.464608 CGTCCTCGTTGATGCAACATT 59.535 47.619 10.48 0.00 43.70 2.71
611 616 1.078709 CGTCCTCGTTGATGCAACAT 58.921 50.000 10.48 0.00 43.70 2.71
612 617 0.948623 CCGTCCTCGTTGATGCAACA 60.949 55.000 10.48 0.00 43.70 3.33
613 618 1.635663 CCCGTCCTCGTTGATGCAAC 61.636 60.000 0.00 0.00 40.54 4.17
614 619 1.375396 CCCGTCCTCGTTGATGCAA 60.375 57.895 0.00 0.00 35.01 4.08
615 620 2.264480 CCCGTCCTCGTTGATGCA 59.736 61.111 0.00 0.00 35.01 3.96
616 621 3.195698 GCCCGTCCTCGTTGATGC 61.196 66.667 0.00 0.00 35.01 3.91
617 622 1.519455 GAGCCCGTCCTCGTTGATG 60.519 63.158 0.00 0.00 35.01 3.07
618 623 2.722201 GGAGCCCGTCCTCGTTGAT 61.722 63.158 0.00 0.00 42.99 2.57
619 624 3.379445 GGAGCCCGTCCTCGTTGA 61.379 66.667 0.00 0.00 42.99 3.18
620 625 4.452733 GGGAGCCCGTCCTCGTTG 62.453 72.222 0.00 0.00 46.06 4.10
632 637 2.142357 GAAAAACAGGGCACGGGAGC 62.142 60.000 0.00 0.00 0.00 4.70
633 638 0.821711 TGAAAAACAGGGCACGGGAG 60.822 55.000 0.00 0.00 0.00 4.30
634 639 0.821711 CTGAAAAACAGGGCACGGGA 60.822 55.000 0.00 0.00 42.39 5.14
650 655 4.631740 TGGGACGGCCTCACCTGA 62.632 66.667 7.57 0.00 35.61 3.86
658 663 2.675423 GGACCTTTTGGGACGGCC 60.675 66.667 0.00 0.00 46.08 6.13
673 678 6.311735 GGCCCAATATTTAAGGACTAATGGA 58.688 40.000 0.00 0.00 0.00 3.41
713 719 4.298626 TGAGAATGGGCCTATCTTACACT 58.701 43.478 0.34 0.00 0.00 3.55
820 826 4.891168 ACGTTGGGACCAAGATTAAAAGTT 59.109 37.500 3.57 0.00 36.52 2.66
879 885 0.459489 GGATGGCGCTGGCAATAAAA 59.541 50.000 7.64 0.00 42.43 1.52
892 898 0.772124 TTGGAGGGGATAGGGATGGC 60.772 60.000 0.00 0.00 0.00 4.40
918 926 1.674221 GCGATAGGGATGGATGTGAGC 60.674 57.143 0.00 0.00 0.00 4.26
921 929 0.390340 CGGCGATAGGGATGGATGTG 60.390 60.000 0.00 0.00 0.00 3.21
922 930 1.975327 CGGCGATAGGGATGGATGT 59.025 57.895 0.00 0.00 0.00 3.06
1148 1168 1.374758 CAGGTCTCGTTCAGCACCC 60.375 63.158 0.00 0.00 0.00 4.61
1241 1261 1.079336 GGCACGTAGAACCTGACCC 60.079 63.158 0.00 0.00 0.00 4.46
1420 1440 2.187946 CACACCCCGGCAGAGATC 59.812 66.667 0.00 0.00 0.00 2.75
1513 1541 1.509923 CTCACGTCGTACCCTTCCC 59.490 63.158 0.00 0.00 0.00 3.97
1616 1644 3.312697 GCGCCTATTACTTTCCAAAGAGG 59.687 47.826 6.05 3.58 39.31 3.69
1631 1659 1.626356 TTGGCAGAAGGAGCGCCTAT 61.626 55.000 10.31 0.00 46.28 2.57
1636 1695 1.968017 TGCTTTGGCAGAAGGAGCG 60.968 57.895 10.12 0.00 44.28 5.03
1645 1704 1.592400 GCATCTCTGCTGCTTTGGCA 61.592 55.000 0.00 0.00 45.32 4.92
1646 1705 1.139095 GCATCTCTGCTGCTTTGGC 59.861 57.895 0.00 0.00 45.32 4.52
1684 1743 9.239002 CATACTACTAGATTGAACTGTACAAGC 57.761 37.037 0.00 0.00 34.47 4.01
1701 1760 3.009026 TGCACCGACGAACATACTACTA 58.991 45.455 0.00 0.00 0.00 1.82
1702 1761 1.814394 TGCACCGACGAACATACTACT 59.186 47.619 0.00 0.00 0.00 2.57
1703 1762 2.182825 CTGCACCGACGAACATACTAC 58.817 52.381 0.00 0.00 0.00 2.73
1718 1777 5.128919 ACATATTCTTCAGATTCCCTGCAC 58.871 41.667 0.00 0.00 42.62 4.57
1744 1803 0.665835 CCTACGCCACAAACAAGCAA 59.334 50.000 0.00 0.00 0.00 3.91
1757 1816 1.927174 CTGCAGAACATGTACCTACGC 59.073 52.381 8.42 1.48 0.00 4.42
1791 1858 2.291043 ACAGCCAGACCTTACCCGG 61.291 63.158 0.00 0.00 0.00 5.73
1797 1864 2.224548 GGTAAGAACACAGCCAGACCTT 60.225 50.000 0.00 0.00 0.00 3.50
1807 1874 5.526111 GCAACAGTCTTAAGGTAAGAACACA 59.474 40.000 1.85 0.00 45.56 3.72
1877 1958 0.037046 CCAAACCAAAGCATCAGCCC 60.037 55.000 0.00 0.00 43.56 5.19
1883 1964 2.037511 CCATCACACCAAACCAAAGCAT 59.962 45.455 0.00 0.00 0.00 3.79
1884 1965 1.411977 CCATCACACCAAACCAAAGCA 59.588 47.619 0.00 0.00 0.00 3.91
1885 1966 1.686052 TCCATCACACCAAACCAAAGC 59.314 47.619 0.00 0.00 0.00 3.51
1886 1967 3.056607 GGATCCATCACACCAAACCAAAG 60.057 47.826 6.95 0.00 0.00 2.77
1887 1968 2.896685 GGATCCATCACACCAAACCAAA 59.103 45.455 6.95 0.00 0.00 3.28
1889 1970 1.710244 AGGATCCATCACACCAAACCA 59.290 47.619 15.82 0.00 0.00 3.67
1890 1971 2.094675 CAGGATCCATCACACCAAACC 58.905 52.381 15.82 0.00 0.00 3.27
1891 1972 2.094675 CCAGGATCCATCACACCAAAC 58.905 52.381 15.82 0.00 0.00 2.93
1920 2001 4.446371 CACCCATTTTACAGGCAAAACAA 58.554 39.130 0.00 0.00 30.57 2.83
1935 2016 1.603455 CCTGTCAACGCCACCCATT 60.603 57.895 0.00 0.00 0.00 3.16
1936 2017 2.034066 CCTGTCAACGCCACCCAT 59.966 61.111 0.00 0.00 0.00 4.00
1937 2018 4.263572 CCCTGTCAACGCCACCCA 62.264 66.667 0.00 0.00 0.00 4.51
1939 2020 4.643387 AGCCCTGTCAACGCCACC 62.643 66.667 0.00 0.00 0.00 4.61
1966 2047 1.613630 ACAATCTCTGGACGCCCCT 60.614 57.895 0.00 0.00 35.38 4.79
1985 2066 0.179100 AGTCCGCGACCATCATGAAG 60.179 55.000 8.23 0.00 32.18 3.02
2018 2099 1.060409 CAAAGCGCAACAACCAAACAC 59.940 47.619 11.47 0.00 0.00 3.32
2033 2114 1.532868 CTGCCGGCTATACATCAAAGC 59.467 52.381 29.70 0.00 35.47 3.51
2050 2134 2.665185 AACGTTCACTCGGGCTGC 60.665 61.111 0.00 0.00 34.94 5.25
2057 2141 1.124477 GTAGCAAGCGAACGTTCACTC 59.876 52.381 26.71 15.05 0.00 3.51
2058 2142 1.137513 GTAGCAAGCGAACGTTCACT 58.862 50.000 26.71 20.18 0.00 3.41
2059 2143 0.179282 CGTAGCAAGCGAACGTTCAC 60.179 55.000 26.71 18.14 32.16 3.18
2067 2151 0.594028 CGCCTATTCGTAGCAAGCGA 60.594 55.000 0.00 0.00 44.51 4.93
2073 2157 0.600255 ATGGCACGCCTATTCGTAGC 60.600 55.000 9.92 0.00 41.21 3.58
2074 2158 2.596452 CTATGGCACGCCTATTCGTAG 58.404 52.381 9.92 0.00 41.21 3.51
2080 2177 3.703001 ATAAAGCTATGGCACGCCTAT 57.297 42.857 9.92 4.14 41.70 2.57
2160 5292 1.335964 CGAGAGTGGTGTGGTGTGTAG 60.336 57.143 0.00 0.00 0.00 2.74
2161 5293 0.671796 CGAGAGTGGTGTGGTGTGTA 59.328 55.000 0.00 0.00 0.00 2.90
2196 5333 5.108385 AGCTTTTCTTTATGGTGTTGTCG 57.892 39.130 0.00 0.00 0.00 4.35
2208 5345 9.353999 CTTTTGTGTTGTAAGTAGCTTTTCTTT 57.646 29.630 0.00 0.00 0.00 2.52
2212 5349 8.135529 GGATCTTTTGTGTTGTAAGTAGCTTTT 58.864 33.333 0.00 0.00 0.00 2.27
2218 5355 8.822805 AGGATAGGATCTTTTGTGTTGTAAGTA 58.177 33.333 0.00 0.00 0.00 2.24
2220 5357 9.099454 GTAGGATAGGATCTTTTGTGTTGTAAG 57.901 37.037 0.00 0.00 0.00 2.34
2221 5358 8.598916 TGTAGGATAGGATCTTTTGTGTTGTAA 58.401 33.333 0.00 0.00 0.00 2.41
2236 5373 2.097036 CGGTGTGTGTGTAGGATAGGA 58.903 52.381 0.00 0.00 0.00 2.94
2246 5383 1.614385 GTCGAGATACGGTGTGTGTG 58.386 55.000 0.00 0.00 42.82 3.82
2258 5402 2.437895 TCAGGCGTCGGTCGAGAT 60.438 61.111 0.00 0.00 42.86 2.75
2278 5422 0.321653 ATGGTGTTGGTCTTCGGAGC 60.322 55.000 0.00 0.00 42.25 4.70
2296 5442 2.167693 TGACAGGCGATTTTCTACGGAT 59.832 45.455 0.00 0.00 0.00 4.18
2306 5452 1.753930 TGATGCATTGACAGGCGATT 58.246 45.000 0.00 0.00 0.00 3.34
2312 5458 3.312697 CAGAGTGGATGATGCATTGACAG 59.687 47.826 0.00 0.00 0.00 3.51
2317 5463 2.941064 CGTTCAGAGTGGATGATGCATT 59.059 45.455 0.00 0.00 0.00 3.56
2319 5465 2.008543 GCGTTCAGAGTGGATGATGCA 61.009 52.381 0.00 0.00 32.02 3.96
2323 5469 1.847328 TAGGCGTTCAGAGTGGATGA 58.153 50.000 0.00 0.00 0.00 2.92
2413 5581 2.656002 CTCTTCCGGTCCTCTATGACA 58.344 52.381 0.00 0.00 36.97 3.58
2427 5595 1.302511 TTTGCTGCCGTCCTCTTCC 60.303 57.895 0.00 0.00 0.00 3.46
2437 5605 1.856265 CTTCTCCGGTGTTTGCTGCC 61.856 60.000 0.00 0.00 0.00 4.85
2454 5622 2.238898 CGGTTGGGTCCTTATTCCTCTT 59.761 50.000 0.00 0.00 0.00 2.85
2459 5627 2.027469 AGACACGGTTGGGTCCTTATTC 60.027 50.000 0.00 0.00 34.58 1.75
2482 5650 3.093814 TCTATTGGGAGCTTCGTGTGTA 58.906 45.455 0.00 0.00 0.00 2.90
2489 5657 5.047660 ACATCGTATCTCTATTGGGAGCTTC 60.048 44.000 0.00 0.00 33.70 3.86
2587 5755 2.581354 CCCCTCGCTCACTTGGAG 59.419 66.667 0.00 0.00 46.93 3.86
2588 5756 3.706373 GCCCCTCGCTCACTTGGA 61.706 66.667 0.00 0.00 0.00 3.53
2589 5757 3.335356 ATGCCCCTCGCTCACTTGG 62.335 63.158 0.00 0.00 38.78 3.61
2590 5758 2.110967 CATGCCCCTCGCTCACTTG 61.111 63.158 0.00 0.00 38.78 3.16
2591 5759 2.270205 CATGCCCCTCGCTCACTT 59.730 61.111 0.00 0.00 38.78 3.16
2592 5760 3.790437 CCATGCCCCTCGCTCACT 61.790 66.667 0.00 0.00 38.78 3.41


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

AutoCloner maintained by Alex Coulton.