Multiple sequence alignment - TraesCS3D01G510100

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 TraesCS3D01G510100 chr3D 100.000 4479 0 0 1 4479 595113384 595108906 0.000000e+00 8272
1 TraesCS3D01G510100 chr3D 91.915 235 17 2 1147 1381 595187912 595187680 1.200000e-85 327
2 TraesCS3D01G510100 chr3A 95.974 3825 103 29 673 4479 726142370 726138579 0.000000e+00 6163
3 TraesCS3D01G510100 chr3A 93.103 203 9 2 1184 1381 726146066 726145864 4.380000e-75 292
4 TraesCS3D01G510100 chr3A 93.103 203 9 2 1184 1381 726147452 726147250 4.380000e-75 292
5 TraesCS3D01G510100 chr3A 93.103 203 9 2 1184 1381 726148838 726148636 4.380000e-75 292
6 TraesCS3D01G510100 chr3B 97.514 3017 65 7 1119 4132 798551829 798548820 0.000000e+00 5147
7 TraesCS3D01G510100 chr3B 85.780 2806 311 48 1093 3867 251181599 251184347 0.000000e+00 2891
8 TraesCS3D01G510100 chr3B 84.944 2783 324 48 1129 3867 251267577 251270308 0.000000e+00 2730
9 TraesCS3D01G510100 chr3B 89.302 215 13 4 1176 1381 798557347 798557134 1.240000e-65 261
10 TraesCS3D01G510100 chr2D 97.387 574 15 0 1 574 116762804 116762231 0.000000e+00 977
11 TraesCS3D01G510100 chr5A 95.122 574 28 0 1 574 79274096 79273523 0.000000e+00 905
12 TraesCS3D01G510100 chr6A 94.948 574 29 0 1 574 510873146 510872573 0.000000e+00 900
13 TraesCS3D01G510100 chr2A 94.948 574 29 0 1 574 769613911 769613338 0.000000e+00 900
14 TraesCS3D01G510100 chr2A 94.077 574 34 0 1 574 596375074 596375647 0.000000e+00 872
15 TraesCS3D01G510100 chr6B 94.774 574 30 0 1 574 119508458 119509031 0.000000e+00 894
16 TraesCS3D01G510100 chr6B 94.435 575 29 3 1 574 218017380 218017952 0.000000e+00 881
17 TraesCS3D01G510100 chr6B 93.391 575 36 2 1 574 522024069 522024642 0.000000e+00 850
18 TraesCS3D01G510100 chr4A 93.728 574 35 1 1 574 660343052 660342480 0.000000e+00 859
19 TraesCS3D01G510100 chr1B 88.172 93 11 0 4387 4479 242739340 242739248 1.320000e-20 111


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 TraesCS3D01G510100 chr3D 595108906 595113384 4478 True 8272.00 8272 100.00000 1 4479 1 chr3D.!!$R1 4478
1 TraesCS3D01G510100 chr3A 726138579 726148838 10259 True 1759.75 6163 93.82075 673 4479 4 chr3A.!!$R1 3806
2 TraesCS3D01G510100 chr3B 798548820 798551829 3009 True 5147.00 5147 97.51400 1119 4132 1 chr3B.!!$R1 3013
3 TraesCS3D01G510100 chr3B 251181599 251184347 2748 False 2891.00 2891 85.78000 1093 3867 1 chr3B.!!$F1 2774
4 TraesCS3D01G510100 chr3B 251267577 251270308 2731 False 2730.00 2730 84.94400 1129 3867 1 chr3B.!!$F2 2738
5 TraesCS3D01G510100 chr2D 116762231 116762804 573 True 977.00 977 97.38700 1 574 1 chr2D.!!$R1 573
6 TraesCS3D01G510100 chr5A 79273523 79274096 573 True 905.00 905 95.12200 1 574 1 chr5A.!!$R1 573
7 TraesCS3D01G510100 chr6A 510872573 510873146 573 True 900.00 900 94.94800 1 574 1 chr6A.!!$R1 573
8 TraesCS3D01G510100 chr2A 769613338 769613911 573 True 900.00 900 94.94800 1 574 1 chr2A.!!$R1 573
9 TraesCS3D01G510100 chr2A 596375074 596375647 573 False 872.00 872 94.07700 1 574 1 chr2A.!!$F1 573
10 TraesCS3D01G510100 chr6B 119508458 119509031 573 False 894.00 894 94.77400 1 574 1 chr6B.!!$F1 573
11 TraesCS3D01G510100 chr6B 218017380 218017952 572 False 881.00 881 94.43500 1 574 1 chr6B.!!$F2 573
12 TraesCS3D01G510100 chr6B 522024069 522024642 573 False 850.00 850 93.39100 1 574 1 chr6B.!!$F3 573
13 TraesCS3D01G510100 chr4A 660342480 660343052 572 True 859.00 859 93.72800 1 574 1 chr4A.!!$R1 573

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
612 613 0.108377 CAGGTACGCCAGCATGTACA 60.108 55.000 0.00 0.00 42.09 2.90 F
613 614 0.830648 AGGTACGCCAGCATGTACAT 59.169 50.000 1.41 1.41 42.09 2.29 F
618 619 0.937304 CGCCAGCATGTACATACACC 59.063 55.000 8.32 0.00 39.30 4.16 F
684 6481 1.006832 GTTGCAGGTACGCCAGTATG 58.993 55.000 0.00 0.00 37.19 2.39 F
794 6596 1.069765 CTCTGGCACAACGACTGGT 59.930 57.895 0.00 0.00 38.70 4.00 F
2976 8796 0.701731 TGGTCAACCCCATCGGAATT 59.298 50.000 0.00 0.00 34.64 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2025 7842 0.121197 TGGGTTCCTCCTCTCCCAAT 59.879 55.000 0.00 0.0 45.66 3.16 R
2745 8565 4.516698 GGTGGAACTACTTGCATATGATGG 59.483 45.833 6.97 0.0 36.74 3.51 R
2759 8579 4.719273 TGGACATCATATGTGGTGGAACTA 59.281 41.667 7.68 0.0 45.03 2.24 R
2838 8658 7.366461 GGGATATTACTTGGCATATGACCCATA 60.366 40.741 5.99 0.0 0.00 2.74 R
3075 8895 1.050204 GCTCAGCTGGGATCAGAGAT 58.950 55.000 20.53 0.0 43.49 2.75 R
4289 10135 1.478631 TGTTGACCAAACACATGCCA 58.521 45.000 0.00 0.0 43.96 4.92 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
323 324 2.743928 GTCACCAGCTTGGCTCGG 60.744 66.667 2.50 0.00 42.67 4.63
394 395 3.634448 AGAGGATGTAGATCAGGTCGTTG 59.366 47.826 1.87 0.00 0.00 4.10
574 575 3.418047 CTCGTAAAACCCTCCACCAAAT 58.582 45.455 0.00 0.00 0.00 2.32
575 576 3.414269 TCGTAAAACCCTCCACCAAATC 58.586 45.455 0.00 0.00 0.00 2.17
576 577 3.150767 CGTAAAACCCTCCACCAAATCA 58.849 45.455 0.00 0.00 0.00 2.57
577 578 3.570550 CGTAAAACCCTCCACCAAATCAA 59.429 43.478 0.00 0.00 0.00 2.57
578 579 4.038162 CGTAAAACCCTCCACCAAATCAAA 59.962 41.667 0.00 0.00 0.00 2.69
579 580 5.279256 CGTAAAACCCTCCACCAAATCAAAT 60.279 40.000 0.00 0.00 0.00 2.32
581 582 3.541242 ACCCTCCACCAAATCAAATCA 57.459 42.857 0.00 0.00 0.00 2.57
582 583 4.065214 ACCCTCCACCAAATCAAATCAT 57.935 40.909 0.00 0.00 0.00 2.45
584 585 4.845796 ACCCTCCACCAAATCAAATCATTT 59.154 37.500 0.00 0.00 0.00 2.32
586 587 6.500049 ACCCTCCACCAAATCAAATCATTTTA 59.500 34.615 0.00 0.00 0.00 1.52
587 588 6.818142 CCCTCCACCAAATCAAATCATTTTAC 59.182 38.462 0.00 0.00 0.00 2.01
589 590 7.546667 CCTCCACCAAATCAAATCATTTTACTG 59.453 37.037 0.00 0.00 0.00 2.74
590 591 7.961351 TCCACCAAATCAAATCATTTTACTGT 58.039 30.769 0.00 0.00 0.00 3.55
591 592 8.428063 TCCACCAAATCAAATCATTTTACTGTT 58.572 29.630 0.00 0.00 0.00 3.16
592 593 8.497554 CCACCAAATCAAATCATTTTACTGTTG 58.502 33.333 0.00 0.00 0.00 3.33
594 595 7.714377 ACCAAATCAAATCATTTTACTGTTGCA 59.286 29.630 0.00 0.00 0.00 4.08
597 598 6.403866 TCAAATCATTTTACTGTTGCAGGT 57.596 33.333 1.08 0.00 35.51 4.00
598 599 7.517614 TCAAATCATTTTACTGTTGCAGGTA 57.482 32.000 1.08 0.00 35.51 3.08
599 600 7.367285 TCAAATCATTTTACTGTTGCAGGTAC 58.633 34.615 1.08 0.00 35.51 3.34
600 601 5.545658 ATCATTTTACTGTTGCAGGTACG 57.454 39.130 1.08 0.00 35.51 3.67
601 602 3.187637 TCATTTTACTGTTGCAGGTACGC 59.812 43.478 1.08 0.00 35.51 4.42
602 603 1.515081 TTTACTGTTGCAGGTACGCC 58.485 50.000 1.08 0.00 35.51 5.68
603 604 0.393448 TTACTGTTGCAGGTACGCCA 59.607 50.000 1.08 0.00 35.51 5.69
605 606 2.668212 TGTTGCAGGTACGCCAGC 60.668 61.111 0.00 0.00 46.14 4.85
609 610 2.436646 GCAGGTACGCCAGCATGT 60.437 61.111 0.00 0.00 45.38 3.21
610 611 1.153449 GCAGGTACGCCAGCATGTA 60.153 57.895 0.00 0.00 45.38 2.29
611 612 1.429148 GCAGGTACGCCAGCATGTAC 61.429 60.000 0.00 0.73 45.38 2.90
612 613 0.108377 CAGGTACGCCAGCATGTACA 60.108 55.000 0.00 0.00 42.09 2.90
613 614 0.830648 AGGTACGCCAGCATGTACAT 59.169 50.000 1.41 1.41 42.09 2.29
614 615 2.036387 AGGTACGCCAGCATGTACATA 58.964 47.619 8.32 0.00 42.09 2.29
615 616 2.132762 GGTACGCCAGCATGTACATAC 58.867 52.381 8.32 2.44 42.09 2.39
616 617 2.482316 GGTACGCCAGCATGTACATACA 60.482 50.000 8.32 0.00 42.09 2.29
618 619 0.937304 CGCCAGCATGTACATACACC 59.063 55.000 8.32 0.00 39.30 4.16
619 620 1.742071 CGCCAGCATGTACATACACCA 60.742 52.381 8.32 0.00 39.30 4.17
620 621 2.364632 GCCAGCATGTACATACACCAA 58.635 47.619 8.32 0.00 39.30 3.67
621 622 2.752354 GCCAGCATGTACATACACCAAA 59.248 45.455 8.32 0.00 39.30 3.28
622 623 3.381272 GCCAGCATGTACATACACCAAAT 59.619 43.478 8.32 0.00 39.30 2.32
623 624 4.498009 GCCAGCATGTACATACACCAAATC 60.498 45.833 8.32 0.00 39.30 2.17
624 625 4.639755 CCAGCATGTACATACACCAAATCA 59.360 41.667 8.32 0.00 39.30 2.57
625 626 5.125257 CCAGCATGTACATACACCAAATCAA 59.875 40.000 8.32 0.00 39.30 2.57
626 627 6.350027 CCAGCATGTACATACACCAAATCAAA 60.350 38.462 8.32 0.00 39.30 2.69
627 628 7.259882 CAGCATGTACATACACCAAATCAAAT 58.740 34.615 8.32 0.00 39.30 2.32
628 629 7.433131 CAGCATGTACATACACCAAATCAAATC 59.567 37.037 8.32 0.00 39.30 2.17
629 630 7.122501 AGCATGTACATACACCAAATCAAATCA 59.877 33.333 8.32 0.00 39.30 2.57
630 631 7.922278 GCATGTACATACACCAAATCAAATCAT 59.078 33.333 8.32 0.00 39.30 2.45
631 632 9.806203 CATGTACATACACCAAATCAAATCATT 57.194 29.630 8.32 0.00 39.30 2.57
633 634 9.241919 TGTACATACACCAAATCAAATCATTCT 57.758 29.630 0.00 0.00 0.00 2.40
636 637 9.466497 ACATACACCAAATCAAATCATTCTACT 57.534 29.630 0.00 0.00 0.00 2.57
638 639 7.161773 ACACCAAATCAAATCATTCTACTGG 57.838 36.000 0.00 0.00 0.00 4.00
639 640 6.038356 CACCAAATCAAATCATTCTACTGGC 58.962 40.000 0.00 0.00 0.00 4.85
640 641 5.716228 ACCAAATCAAATCATTCTACTGGCA 59.284 36.000 0.00 0.00 0.00 4.92
644 645 5.378230 TCAAATCATTCTACTGGCAGGAT 57.622 39.130 20.34 7.63 0.00 3.24
645 646 6.499106 TCAAATCATTCTACTGGCAGGATA 57.501 37.500 20.34 0.00 0.00 2.59
646 647 7.083062 TCAAATCATTCTACTGGCAGGATAT 57.917 36.000 20.34 4.00 0.00 1.63
647 648 7.520798 TCAAATCATTCTACTGGCAGGATATT 58.479 34.615 20.34 5.68 0.00 1.28
648 649 8.000709 TCAAATCATTCTACTGGCAGGATATTT 58.999 33.333 20.34 10.93 0.00 1.40
649 650 7.756395 AATCATTCTACTGGCAGGATATTTG 57.244 36.000 20.34 9.08 0.00 2.32
650 651 6.499106 TCATTCTACTGGCAGGATATTTGA 57.501 37.500 20.34 11.21 0.00 2.69
651 652 6.528321 TCATTCTACTGGCAGGATATTTGAG 58.472 40.000 20.34 0.00 0.00 3.02
652 653 5.957771 TTCTACTGGCAGGATATTTGAGT 57.042 39.130 20.34 0.00 0.00 3.41
653 654 5.282055 TCTACTGGCAGGATATTTGAGTG 57.718 43.478 20.34 0.00 0.00 3.51
654 655 4.716784 TCTACTGGCAGGATATTTGAGTGT 59.283 41.667 20.34 0.00 0.00 3.55
656 657 2.947652 CTGGCAGGATATTTGAGTGTGG 59.052 50.000 6.61 0.00 0.00 4.17
659 660 4.210331 GGCAGGATATTTGAGTGTGGATT 58.790 43.478 0.00 0.00 0.00 3.01
660 661 4.276926 GGCAGGATATTTGAGTGTGGATTC 59.723 45.833 0.00 0.00 0.00 2.52
662 663 6.291377 GCAGGATATTTGAGTGTGGATTCTA 58.709 40.000 0.00 0.00 0.00 2.10
663 664 6.203723 GCAGGATATTTGAGTGTGGATTCTAC 59.796 42.308 0.00 0.00 0.00 2.59
664 665 7.504403 CAGGATATTTGAGTGTGGATTCTACT 58.496 38.462 1.69 0.00 0.00 2.57
665 666 7.440556 CAGGATATTTGAGTGTGGATTCTACTG 59.559 40.741 1.69 0.00 0.00 2.74
666 667 7.126421 AGGATATTTGAGTGTGGATTCTACTGT 59.874 37.037 1.69 0.00 0.00 3.55
667 668 7.770897 GGATATTTGAGTGTGGATTCTACTGTT 59.229 37.037 1.69 0.00 0.00 3.16
670 671 3.070878 TGAGTGTGGATTCTACTGTTGCA 59.929 43.478 1.69 0.00 0.00 4.08
671 672 3.668447 AGTGTGGATTCTACTGTTGCAG 58.332 45.455 1.69 0.00 37.52 4.41
672 673 2.744202 GTGTGGATTCTACTGTTGCAGG 59.256 50.000 1.69 0.00 35.51 4.85
673 674 2.371841 TGTGGATTCTACTGTTGCAGGT 59.628 45.455 1.69 0.00 35.51 4.00
674 675 3.580895 TGTGGATTCTACTGTTGCAGGTA 59.419 43.478 1.69 0.00 35.51 3.08
675 676 3.933332 GTGGATTCTACTGTTGCAGGTAC 59.067 47.826 1.08 0.00 35.51 3.34
676 677 3.187700 GGATTCTACTGTTGCAGGTACG 58.812 50.000 1.08 0.00 35.51 3.67
684 6481 1.006832 GTTGCAGGTACGCCAGTATG 58.993 55.000 0.00 0.00 37.19 2.39
689 6486 2.417651 GCAGGTACGCCAGTATGTACAA 60.418 50.000 0.00 0.00 42.09 2.41
701 6498 6.350110 GCCAGTATGTACAAACACCAAATCAT 60.350 38.462 0.00 0.00 38.78 2.45
766 6568 8.907222 AAGAAAAATGAAAATGTGCTACCAAT 57.093 26.923 0.00 0.00 0.00 3.16
767 6569 8.907222 AGAAAAATGAAAATGTGCTACCAATT 57.093 26.923 0.00 0.00 0.00 2.32
768 6570 9.995003 AGAAAAATGAAAATGTGCTACCAATTA 57.005 25.926 0.00 0.00 0.00 1.40
770 6572 8.546597 AAAATGAAAATGTGCTACCAATTACC 57.453 30.769 0.00 0.00 0.00 2.85
771 6573 6.849085 ATGAAAATGTGCTACCAATTACCA 57.151 33.333 0.00 0.00 0.00 3.25
772 6574 6.656632 TGAAAATGTGCTACCAATTACCAA 57.343 33.333 0.00 0.00 0.00 3.67
773 6575 7.055667 TGAAAATGTGCTACCAATTACCAAA 57.944 32.000 0.00 0.00 0.00 3.28
776 6578 2.823154 TGTGCTACCAATTACCAAAGCC 59.177 45.455 0.00 0.00 0.00 4.35
777 6579 3.089284 GTGCTACCAATTACCAAAGCCT 58.911 45.455 0.00 0.00 0.00 4.58
778 6580 3.128764 GTGCTACCAATTACCAAAGCCTC 59.871 47.826 0.00 0.00 0.00 4.70
779 6581 3.010138 TGCTACCAATTACCAAAGCCTCT 59.990 43.478 0.00 0.00 0.00 3.69
781 6583 2.807676 ACCAATTACCAAAGCCTCTGG 58.192 47.619 0.00 0.00 40.05 3.86
792 6594 3.957260 CCTCTGGCACAACGACTG 58.043 61.111 0.00 0.00 38.70 3.51
793 6595 1.669115 CCTCTGGCACAACGACTGG 60.669 63.158 0.00 0.00 38.70 4.00
794 6596 1.069765 CTCTGGCACAACGACTGGT 59.930 57.895 0.00 0.00 38.70 4.00
840 6642 2.434359 CCCGACTTCGACTTGGGC 60.434 66.667 0.00 0.00 43.02 5.36
841 6643 2.657237 CCGACTTCGACTTGGGCT 59.343 61.111 0.00 0.00 43.02 5.19
845 6647 2.113243 GACTTCGACTTGGGCTGGGT 62.113 60.000 0.00 0.00 0.00 4.51
880 6682 1.305046 TCCAACCGACCTCCTCTCC 60.305 63.158 0.00 0.00 0.00 3.71
893 6695 3.023832 CTCCTCTCCTCTCTTCACCTTC 58.976 54.545 0.00 0.00 0.00 3.46
900 6702 3.264450 TCCTCTCTTCACCTTCCCAAATC 59.736 47.826 0.00 0.00 0.00 2.17
942 6744 3.739613 GATCCCCACCCACCCACC 61.740 72.222 0.00 0.00 0.00 4.61
986 6788 2.588439 GAAACCCTAGACCCCGCC 59.412 66.667 0.00 0.00 0.00 6.13
987 6789 3.381333 GAAACCCTAGACCCCGCCG 62.381 68.421 0.00 0.00 0.00 6.46
2049 7866 1.127343 GAGAGGAGGAACCCATGGAG 58.873 60.000 15.22 5.95 40.05 3.86
2976 8796 0.701731 TGGTCAACCCCATCGGAATT 59.298 50.000 0.00 0.00 34.64 2.17
3015 8835 2.669569 CCTCCACAACCACCTGCG 60.670 66.667 0.00 0.00 0.00 5.18
3075 8895 1.558294 AGGCAGAGAACAGATGATGCA 59.442 47.619 0.00 0.00 35.40 3.96
3105 8925 1.303155 AGCTGAGCAGTTCCTTGCC 60.303 57.895 7.39 0.00 45.18 4.52
3157 8977 4.963628 ACTTCCACTCTAATCCCCTACTTC 59.036 45.833 0.00 0.00 0.00 3.01
3298 9118 4.870636 AGATCTCTGTCCAATCACTCTCT 58.129 43.478 0.00 0.00 0.00 3.10
3316 9136 0.032678 CTGACACAGTCGGCAGTCTT 59.967 55.000 8.39 0.00 34.95 3.01
3617 9452 3.894759 AGTCCAGCACTATGATTTGCAT 58.105 40.909 0.00 0.00 41.48 3.96
3999 9845 0.697658 TGGGTGATGGCTGATGTTCA 59.302 50.000 0.00 0.00 0.00 3.18
4175 10021 1.036707 GCCCTTTGTTGTGGTTGCTA 58.963 50.000 0.00 0.00 0.00 3.49
4201 10047 6.106673 CGGTCATAAGTTGATTTCTGTAGGT 58.893 40.000 0.00 0.00 36.54 3.08
4229 10075 8.471361 TGCATTTATTTTCATGTTTATTGCGA 57.529 26.923 0.00 0.00 0.00 5.10
4289 10135 4.985538 TGCTTTCCAGTTATTCTGAAGGT 58.014 39.130 0.00 0.00 46.27 3.50
4292 10138 3.350219 TCCAGTTATTCTGAAGGTGGC 57.650 47.619 0.00 0.00 46.27 5.01
4328 10174 7.862372 GTCAACATAGGCATATATGGTTGTTTG 59.138 37.037 21.22 7.73 37.45 2.93
4332 10178 5.396057 AGGCATATATGGTTGTTTGGGTA 57.604 39.130 14.51 0.00 0.00 3.69
4349 10195 7.094420 TGTTTGGGTACTGATAATGATTGTGTG 60.094 37.037 0.00 0.00 0.00 3.82
4350 10196 6.061022 TGGGTACTGATAATGATTGTGTGT 57.939 37.500 0.00 0.00 0.00 3.72
4389 10237 4.695455 ACCGACTTGTTCCATTGTCAATAG 59.305 41.667 0.00 0.00 0.00 1.73
4404 10253 7.531857 TTGTCAATAGTAAATGAAGGGCAAA 57.468 32.000 0.00 0.00 0.00 3.68
4416 10265 2.080654 AGGGCAAAAGTAGGCACAAA 57.919 45.000 0.00 0.00 35.37 2.83
4435 10284 5.001232 ACAAATAAGTTATGGTGCGACACT 58.999 37.500 9.31 0.00 34.40 3.55
4436 10285 5.106712 ACAAATAAGTTATGGTGCGACACTG 60.107 40.000 9.31 0.05 34.40 3.66
4473 10322 6.936335 TCACAGAAGTGTCATTATGATTGTGT 59.064 34.615 0.00 1.36 46.01 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
279 280 1.467342 GTGGGCTATTTGGACGTCAAC 59.533 52.381 18.91 0.81 34.67 3.18
323 324 2.824341 TCCCAAGTTCTCTAAGTCCGAC 59.176 50.000 0.00 0.00 0.00 4.79
352 353 5.928839 CCTCTAACATGGTCAAAGGATATCG 59.071 44.000 0.00 0.00 0.00 2.92
394 395 0.958876 CCCGGTTTGGCTTGAGGTAC 60.959 60.000 0.00 0.00 35.87 3.34
447 448 3.322369 ACATGTTGCATGCATTGTTGAG 58.678 40.909 23.37 10.42 0.00 3.02
574 575 6.403866 ACCTGCAACAGTAAAATGATTTGA 57.596 33.333 0.00 0.00 0.00 2.69
575 576 6.305399 CGTACCTGCAACAGTAAAATGATTTG 59.695 38.462 0.00 0.00 0.00 2.32
576 577 6.378582 CGTACCTGCAACAGTAAAATGATTT 58.621 36.000 0.00 0.00 0.00 2.17
577 578 5.619086 GCGTACCTGCAACAGTAAAATGATT 60.619 40.000 0.00 0.00 34.15 2.57
578 579 4.142687 GCGTACCTGCAACAGTAAAATGAT 60.143 41.667 0.00 0.00 34.15 2.45
579 580 3.187637 GCGTACCTGCAACAGTAAAATGA 59.812 43.478 0.00 0.00 34.15 2.57
581 582 2.486592 GGCGTACCTGCAACAGTAAAAT 59.513 45.455 0.00 0.00 36.28 1.82
582 583 1.874872 GGCGTACCTGCAACAGTAAAA 59.125 47.619 0.00 0.00 36.28 1.52
584 585 0.393448 TGGCGTACCTGCAACAGTAA 59.607 50.000 0.00 0.00 36.63 2.24
586 587 1.301716 CTGGCGTACCTGCAACAGT 60.302 57.895 0.00 0.00 36.63 3.55
587 588 3.566261 CTGGCGTACCTGCAACAG 58.434 61.111 0.00 0.00 36.63 3.16
594 595 0.830648 ATGTACATGCTGGCGTACCT 59.169 50.000 7.78 0.00 37.73 3.08
597 598 2.482316 GGTGTATGTACATGCTGGCGTA 60.482 50.000 22.21 0.86 38.63 4.42
598 599 1.651987 GTGTATGTACATGCTGGCGT 58.348 50.000 22.21 0.00 38.63 5.68
599 600 0.937304 GGTGTATGTACATGCTGGCG 59.063 55.000 22.21 0.00 38.63 5.69
600 601 2.036958 TGGTGTATGTACATGCTGGC 57.963 50.000 22.21 13.15 38.63 4.85
601 602 4.639755 TGATTTGGTGTATGTACATGCTGG 59.360 41.667 22.21 0.00 38.63 4.85
602 603 5.816449 TGATTTGGTGTATGTACATGCTG 57.184 39.130 22.21 0.00 38.63 4.41
603 604 6.832520 TTTGATTTGGTGTATGTACATGCT 57.167 33.333 22.21 3.44 38.63 3.79
605 606 9.806203 AATGATTTGATTTGGTGTATGTACATG 57.194 29.630 18.81 0.00 38.63 3.21
607 608 9.241919 AGAATGATTTGATTTGGTGTATGTACA 57.758 29.630 0.00 0.00 0.00 2.90
610 611 9.466497 AGTAGAATGATTTGATTTGGTGTATGT 57.534 29.630 0.00 0.00 0.00 2.29
611 612 9.726232 CAGTAGAATGATTTGATTTGGTGTATG 57.274 33.333 0.00 0.00 0.00 2.39
612 613 8.906867 CCAGTAGAATGATTTGATTTGGTGTAT 58.093 33.333 0.00 0.00 0.00 2.29
613 614 7.148086 GCCAGTAGAATGATTTGATTTGGTGTA 60.148 37.037 0.00 0.00 0.00 2.90
614 615 6.350445 GCCAGTAGAATGATTTGATTTGGTGT 60.350 38.462 0.00 0.00 0.00 4.16
615 616 6.038356 GCCAGTAGAATGATTTGATTTGGTG 58.962 40.000 0.00 0.00 0.00 4.17
616 617 5.716228 TGCCAGTAGAATGATTTGATTTGGT 59.284 36.000 0.00 0.00 0.00 3.67
618 619 6.095860 TCCTGCCAGTAGAATGATTTGATTTG 59.904 38.462 0.00 0.00 0.00 2.32
619 620 6.189859 TCCTGCCAGTAGAATGATTTGATTT 58.810 36.000 0.00 0.00 0.00 2.17
620 621 5.759059 TCCTGCCAGTAGAATGATTTGATT 58.241 37.500 0.00 0.00 0.00 2.57
621 622 5.378230 TCCTGCCAGTAGAATGATTTGAT 57.622 39.130 0.00 0.00 0.00 2.57
622 623 4.842531 TCCTGCCAGTAGAATGATTTGA 57.157 40.909 0.00 0.00 0.00 2.69
623 624 7.756395 AATATCCTGCCAGTAGAATGATTTG 57.244 36.000 0.00 0.00 0.00 2.32
624 625 8.000709 TCAAATATCCTGCCAGTAGAATGATTT 58.999 33.333 0.00 0.00 0.00 2.17
625 626 7.520798 TCAAATATCCTGCCAGTAGAATGATT 58.479 34.615 0.00 0.00 0.00 2.57
626 627 7.083062 TCAAATATCCTGCCAGTAGAATGAT 57.917 36.000 0.00 0.00 0.00 2.45
627 628 6.100279 ACTCAAATATCCTGCCAGTAGAATGA 59.900 38.462 0.00 0.00 0.00 2.57
628 629 6.204301 CACTCAAATATCCTGCCAGTAGAATG 59.796 42.308 0.00 0.00 0.00 2.67
629 630 6.126652 ACACTCAAATATCCTGCCAGTAGAAT 60.127 38.462 0.00 0.00 0.00 2.40
630 631 5.189736 ACACTCAAATATCCTGCCAGTAGAA 59.810 40.000 0.00 0.00 0.00 2.10
631 632 4.716784 ACACTCAAATATCCTGCCAGTAGA 59.283 41.667 0.00 0.00 0.00 2.59
632 633 4.813161 CACACTCAAATATCCTGCCAGTAG 59.187 45.833 0.00 0.00 0.00 2.57
633 634 4.384098 CCACACTCAAATATCCTGCCAGTA 60.384 45.833 0.00 0.00 0.00 2.74
634 635 3.614092 CACACTCAAATATCCTGCCAGT 58.386 45.455 0.00 0.00 0.00 4.00
635 636 2.947652 CCACACTCAAATATCCTGCCAG 59.052 50.000 0.00 0.00 0.00 4.85
636 637 2.575735 TCCACACTCAAATATCCTGCCA 59.424 45.455 0.00 0.00 0.00 4.92
638 639 5.128919 AGAATCCACACTCAAATATCCTGC 58.871 41.667 0.00 0.00 0.00 4.85
639 640 7.440556 CAGTAGAATCCACACTCAAATATCCTG 59.559 40.741 0.00 0.00 0.00 3.86
640 641 7.126421 ACAGTAGAATCCACACTCAAATATCCT 59.874 37.037 0.00 0.00 0.00 3.24
644 645 6.371548 GCAACAGTAGAATCCACACTCAAATA 59.628 38.462 0.00 0.00 0.00 1.40
645 646 5.182001 GCAACAGTAGAATCCACACTCAAAT 59.818 40.000 0.00 0.00 0.00 2.32
646 647 4.515191 GCAACAGTAGAATCCACACTCAAA 59.485 41.667 0.00 0.00 0.00 2.69
647 648 4.065088 GCAACAGTAGAATCCACACTCAA 58.935 43.478 0.00 0.00 0.00 3.02
648 649 3.070878 TGCAACAGTAGAATCCACACTCA 59.929 43.478 0.00 0.00 0.00 3.41
649 650 3.664107 TGCAACAGTAGAATCCACACTC 58.336 45.455 0.00 0.00 0.00 3.51
650 651 3.557898 CCTGCAACAGTAGAATCCACACT 60.558 47.826 0.00 0.00 0.00 3.55
651 652 2.744202 CCTGCAACAGTAGAATCCACAC 59.256 50.000 0.00 0.00 0.00 3.82
652 653 2.371841 ACCTGCAACAGTAGAATCCACA 59.628 45.455 0.00 0.00 0.00 4.17
653 654 3.059352 ACCTGCAACAGTAGAATCCAC 57.941 47.619 0.00 0.00 0.00 4.02
654 655 3.368013 CGTACCTGCAACAGTAGAATCCA 60.368 47.826 0.00 0.00 0.00 3.41
656 657 2.603560 GCGTACCTGCAACAGTAGAATC 59.396 50.000 0.00 0.00 34.15 2.52
659 660 0.245539 GGCGTACCTGCAACAGTAGA 59.754 55.000 0.00 0.00 36.28 2.59
660 661 0.037697 TGGCGTACCTGCAACAGTAG 60.038 55.000 0.00 0.00 36.63 2.57
662 663 1.301716 CTGGCGTACCTGCAACAGT 60.302 57.895 0.00 0.00 36.63 3.55
663 664 0.037697 TACTGGCGTACCTGCAACAG 60.038 55.000 0.00 0.00 38.43 3.16
664 665 0.611200 ATACTGGCGTACCTGCAACA 59.389 50.000 0.00 0.00 38.43 3.33
665 666 1.006832 CATACTGGCGTACCTGCAAC 58.993 55.000 0.00 0.00 38.43 4.17
666 667 0.611200 ACATACTGGCGTACCTGCAA 59.389 50.000 0.00 0.00 38.43 4.08
667 668 1.135527 GTACATACTGGCGTACCTGCA 59.864 52.381 0.00 0.00 38.43 4.41
670 671 3.258872 TGTTTGTACATACTGGCGTACCT 59.741 43.478 16.00 0.00 37.73 3.08
671 672 3.368843 GTGTTTGTACATACTGGCGTACC 59.631 47.826 16.00 0.00 37.73 3.34
672 673 3.368843 GGTGTTTGTACATACTGGCGTAC 59.631 47.826 16.00 6.05 38.76 3.67
673 674 3.006644 TGGTGTTTGTACATACTGGCGTA 59.993 43.478 16.00 0.00 36.50 4.42
674 675 2.224329 TGGTGTTTGTACATACTGGCGT 60.224 45.455 16.00 0.00 36.50 5.68
675 676 2.418692 TGGTGTTTGTACATACTGGCG 58.581 47.619 16.00 0.00 36.50 5.69
676 677 4.839668 TTTGGTGTTTGTACATACTGGC 57.160 40.909 16.00 7.54 36.50 4.85
718 6517 3.886505 TCCCCGTATATTTGATTTGGTGC 59.113 43.478 0.00 0.00 0.00 5.01
730 6529 9.816354 CATTTTCATTTTTCTTTCCCCGTATAT 57.184 29.630 0.00 0.00 0.00 0.86
733 6532 6.926272 CACATTTTCATTTTTCTTTCCCCGTA 59.074 34.615 0.00 0.00 0.00 4.02
735 6534 5.334028 GCACATTTTCATTTTTCTTTCCCCG 60.334 40.000 0.00 0.00 0.00 5.73
776 6578 0.317160 TACCAGTCGTTGTGCCAGAG 59.683 55.000 0.00 0.00 0.00 3.35
777 6579 0.032952 GTACCAGTCGTTGTGCCAGA 59.967 55.000 0.00 0.00 0.00 3.86
778 6580 0.033504 AGTACCAGTCGTTGTGCCAG 59.966 55.000 0.00 0.00 0.00 4.85
779 6581 0.249699 CAGTACCAGTCGTTGTGCCA 60.250 55.000 0.00 0.00 0.00 4.92
781 6583 1.137513 GTCAGTACCAGTCGTTGTGC 58.862 55.000 0.00 0.00 0.00 4.57
783 6585 1.266175 CGAGTCAGTACCAGTCGTTGT 59.734 52.381 10.26 0.00 32.94 3.32
784 6586 1.534163 TCGAGTCAGTACCAGTCGTTG 59.466 52.381 15.67 0.00 37.83 4.10
785 6587 1.805345 CTCGAGTCAGTACCAGTCGTT 59.195 52.381 15.67 0.00 37.83 3.85
786 6588 1.440708 CTCGAGTCAGTACCAGTCGT 58.559 55.000 15.67 0.00 37.83 4.34
787 6589 0.097325 GCTCGAGTCAGTACCAGTCG 59.903 60.000 15.13 11.70 37.94 4.18
788 6590 0.452585 GGCTCGAGTCAGTACCAGTC 59.547 60.000 13.26 0.00 0.00 3.51
789 6591 1.306642 CGGCTCGAGTCAGTACCAGT 61.307 60.000 18.62 0.00 0.00 4.00
790 6592 1.025113 TCGGCTCGAGTCAGTACCAG 61.025 60.000 18.62 0.00 0.00 4.00
791 6593 1.002990 TCGGCTCGAGTCAGTACCA 60.003 57.895 18.62 0.00 0.00 3.25
792 6594 3.900855 TCGGCTCGAGTCAGTACC 58.099 61.111 18.62 6.14 0.00 3.34
817 6619 2.126031 GTCGAAGTCGGGCTGGTC 60.126 66.667 0.11 0.00 40.29 4.02
820 6622 1.738099 CCAAGTCGAAGTCGGGCTG 60.738 63.158 0.11 0.00 40.29 4.85
821 6623 2.657237 CCAAGTCGAAGTCGGGCT 59.343 61.111 0.11 0.00 40.29 5.19
822 6624 2.434359 CCCAAGTCGAAGTCGGGC 60.434 66.667 0.11 0.00 40.29 6.13
825 6627 1.738099 CCAGCCCAAGTCGAAGTCG 60.738 63.158 0.00 0.00 41.45 4.18
826 6628 1.376037 CCCAGCCCAAGTCGAAGTC 60.376 63.158 0.00 0.00 0.00 3.01
827 6629 0.834687 TACCCAGCCCAAGTCGAAGT 60.835 55.000 0.00 0.00 0.00 3.01
828 6630 0.391263 GTACCCAGCCCAAGTCGAAG 60.391 60.000 0.00 0.00 0.00 3.79
830 6632 2.288025 GGTACCCAGCCCAAGTCGA 61.288 63.158 0.00 0.00 0.00 4.20
831 6633 2.267961 GGTACCCAGCCCAAGTCG 59.732 66.667 0.00 0.00 0.00 4.18
840 6642 2.496291 GGATCGGACCGGTACCCAG 61.496 68.421 12.38 4.64 0.00 4.45
841 6643 2.442643 GGATCGGACCGGTACCCA 60.443 66.667 12.38 1.74 0.00 4.51
845 6647 1.039233 GGACTTGGATCGGACCGGTA 61.039 60.000 15.25 0.00 0.00 4.02
851 6653 0.901114 TCGGTTGGACTTGGATCGGA 60.901 55.000 0.00 0.00 0.00 4.55
880 6682 4.260170 CAGATTTGGGAAGGTGAAGAGAG 58.740 47.826 0.00 0.00 0.00 3.20
940 6742 0.974010 TCGGAAGCGATTGTAGGGGT 60.974 55.000 0.00 0.00 0.00 4.95
942 6744 1.341531 AGATCGGAAGCGATTGTAGGG 59.658 52.381 0.00 0.00 0.00 3.53
943 6745 2.398498 CAGATCGGAAGCGATTGTAGG 58.602 52.381 0.00 0.00 0.00 3.18
944 6746 1.789464 GCAGATCGGAAGCGATTGTAG 59.211 52.381 0.00 0.00 0.00 2.74
945 6747 1.538204 GGCAGATCGGAAGCGATTGTA 60.538 52.381 0.00 0.00 0.00 2.41
1347 7149 1.515736 GACGCGGTGCTGGTAGTAC 60.516 63.158 12.47 0.00 0.00 2.73
2025 7842 0.121197 TGGGTTCCTCCTCTCCCAAT 59.879 55.000 0.00 0.00 45.66 3.16
2745 8565 4.516698 GGTGGAACTACTTGCATATGATGG 59.483 45.833 6.97 0.00 36.74 3.51
2759 8579 4.719273 TGGACATCATATGTGGTGGAACTA 59.281 41.667 7.68 0.00 45.03 2.24
2838 8658 7.366461 GGGATATTACTTGGCATATGACCCATA 60.366 40.741 5.99 0.00 0.00 2.74
3075 8895 1.050204 GCTCAGCTGGGATCAGAGAT 58.950 55.000 20.53 0.00 43.49 2.75
3105 8925 1.414181 AGAGACATTACCGGATGCTGG 59.586 52.381 9.46 0.00 35.68 4.85
3149 8969 9.267084 GCAGAATAATAAGAAAGAGAAGTAGGG 57.733 37.037 0.00 0.00 0.00 3.53
3157 8977 6.256539 TGACAGCGCAGAATAATAAGAAAGAG 59.743 38.462 11.47 0.00 0.00 2.85
3298 9118 1.324383 TAAGACTGCCGACTGTGTCA 58.676 50.000 0.00 0.00 32.09 3.58
3435 9255 3.237746 TCCCTCAGAGCTAGATTGATGG 58.762 50.000 0.00 1.43 0.00 3.51
3617 9452 5.407387 GCATAGACAAGTCCGAAAACTACAA 59.593 40.000 0.00 0.00 0.00 2.41
3999 9845 7.318141 CCATGCTATTCTGTCAACAAGATTTT 58.682 34.615 0.00 0.00 0.00 1.82
4175 10021 4.579869 ACAGAAATCAACTTATGACCGCT 58.420 39.130 0.00 0.00 41.93 5.52
4212 10058 8.357796 TGAAAACATCGCAATAAACATGAAAA 57.642 26.923 0.00 0.00 0.00 2.29
4227 10073 7.827819 TTAGTCACTTAGGATGAAAACATCG 57.172 36.000 0.00 0.00 32.60 3.84
4274 10120 4.012374 ACATGCCACCTTCAGAATAACTG 58.988 43.478 0.00 0.00 46.97 3.16
4289 10135 1.478631 TGTTGACCAAACACATGCCA 58.521 45.000 0.00 0.00 43.96 4.92
4328 10174 7.391148 AAACACACAATCATTATCAGTACCC 57.609 36.000 0.00 0.00 0.00 3.69
4357 10203 3.623960 TGGAACAAGTCGGTTAACAACAG 59.376 43.478 8.10 4.96 31.92 3.16
4389 10237 4.219725 TGCCTACTTTTGCCCTTCATTTAC 59.780 41.667 0.00 0.00 0.00 2.01
4404 10253 6.127730 GCACCATAACTTATTTGTGCCTACTT 60.128 38.462 16.05 0.00 42.33 2.24
4416 10265 3.932710 CACAGTGTCGCACCATAACTTAT 59.067 43.478 0.00 0.00 34.49 1.73
4435 10284 2.049888 TCTGTGACATGGCAAACACA 57.950 45.000 0.58 18.32 40.22 3.72
4436 10285 2.358898 ACTTCTGTGACATGGCAAACAC 59.641 45.455 0.58 12.68 0.00 3.32


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

AutoCloner maintained by Alex Coulton.