Multiple sequence alignment - TraesCS7A01G466200

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 TraesCS7A01G466200 chr7A 100.000 2444 0 0 1 2444 663455543 663453100 0.000000e+00 4514.0
1 TraesCS7A01G466200 chr7A 94.797 615 29 2 1 615 107015550 107014939 0.000000e+00 955.0
2 TraesCS7A01G466200 chr7A 93.333 615 38 2 1 615 175071303 175071914 0.000000e+00 905.0
3 TraesCS7A01G466200 chr7A 89.533 621 44 7 2 615 3037107 3036501 0.000000e+00 767.0
4 TraesCS7A01G466200 chr7A 89.577 614 46 4 2 615 17716031 17715436 0.000000e+00 763.0
5 TraesCS7A01G466200 chr7A 80.782 614 105 5 1004 1604 647917453 647916840 3.680000e-128 468.0
6 TraesCS7A01G466200 chr7A 78.957 537 92 13 1004 1525 647862856 647862326 1.800000e-91 346.0
7 TraesCS7A01G466200 chr7A 82.447 376 62 3 1004 1375 647307616 647307241 2.340000e-85 326.0
8 TraesCS7A01G466200 chr7A 85.586 111 13 3 1665 1775 661945448 661945555 1.990000e-21 113.0
9 TraesCS7A01G466200 chr7A 92.308 65 5 0 1603 1667 663498054 663497990 2.590000e-15 93.5
10 TraesCS7A01G466200 chr7A 86.111 72 10 0 1603 1674 647306523 647306452 7.250000e-11 78.7
11 TraesCS7A01G466200 chr7A 86.111 72 10 0 1603 1674 647306979 647306908 7.250000e-11 78.7
12 TraesCS7A01G466200 chr7B 92.295 1194 64 14 849 2019 632271279 632270091 0.000000e+00 1670.0
13 TraesCS7A01G466200 chr7B 94.855 311 14 2 2018 2327 632269886 632269577 3.650000e-133 484.0
14 TraesCS7A01G466200 chr7B 90.798 163 10 2 695 856 632271596 632271438 1.900000e-51 213.0
15 TraesCS7A01G466200 chr7B 81.757 148 25 2 1676 1823 630311068 630311213 3.300000e-24 122.0
16 TraesCS7A01G466200 chr7B 84.685 111 14 3 1665 1775 630139211 630139318 9.240000e-20 108.0
17 TraesCS7A01G466200 chr7B 81.560 141 10 11 2307 2443 632269566 632269438 4.300000e-18 102.0
18 TraesCS7A01G466200 chr7B 88.889 72 8 0 1603 1674 632337339 632337268 3.350000e-14 89.8
19 TraesCS7A01G466200 chr7D 91.571 1222 56 18 1264 2443 573462092 573460876 0.000000e+00 1642.0
20 TraesCS7A01G466200 chr7D 90.750 627 44 5 2 615 629192578 629193203 0.000000e+00 824.0
21 TraesCS7A01G466200 chr7D 92.035 452 36 0 849 1300 573462548 573462097 9.530000e-179 636.0
22 TraesCS7A01G466200 chr7D 89.895 287 27 2 330 615 40197196 40196911 3.840000e-98 368.0
23 TraesCS7A01G466200 chr7D 80.000 440 84 4 1007 1442 562257249 562256810 3.030000e-84 322.0
24 TraesCS7A01G466200 chr7D 90.625 128 12 0 712 839 573462949 573462822 1.160000e-38 171.0
25 TraesCS7A01G466200 chr7D 79.730 222 37 5 1676 1895 573622039 573621824 1.170000e-33 154.0
26 TraesCS7A01G466200 chr7D 76.471 289 50 9 1676 1956 573460472 573460194 9.110000e-30 141.0
27 TraesCS7A01G466200 chr7D 82.993 147 23 2 1676 1822 572757762 572757906 5.480000e-27 132.0
28 TraesCS7A01G466200 chr7D 85.455 110 13 3 1666 1775 572723841 572723947 7.140000e-21 111.0
29 TraesCS7A01G466200 chr7D 88.889 72 8 0 1603 1674 573622151 573622080 3.350000e-14 89.8
30 TraesCS7A01G466200 chr7D 86.111 72 10 0 1603 1674 562148470 562148399 7.250000e-11 78.7
31 TraesCS7A01G466200 chr7D 86.111 72 10 0 1603 1674 562148926 562148855 7.250000e-11 78.7
32 TraesCS7A01G466200 chr7D 88.889 54 6 0 1687 1740 573460689 573460636 1.570000e-07 67.6
33 TraesCS7A01G466200 chr6A 94.309 615 33 2 1 615 49843574 49842962 0.000000e+00 941.0
34 TraesCS7A01G466200 chr6A 82.271 361 60 3 1004 1360 55709405 55709765 2.360000e-80 309.0
35 TraesCS7A01G466200 chr6A 86.301 73 6 4 1700 1769 490998981 490998910 2.610000e-10 76.8
36 TraesCS7A01G466200 chr3A 92.520 615 30 5 1 615 141875547 141874949 0.000000e+00 867.0
37 TraesCS7A01G466200 chr1A 92.058 617 27 4 1 617 159528735 159529329 0.000000e+00 848.0
38 TraesCS7A01G466200 chr1A 94.888 313 16 0 1 313 589609704 589609392 7.850000e-135 490.0
39 TraesCS7A01G466200 chr3D 89.984 629 40 8 2 622 569884180 569884793 0.000000e+00 791.0
40 TraesCS7A01G466200 chr3D 89.199 287 29 2 330 615 558269458 558269743 8.310000e-95 357.0
41 TraesCS7A01G466200 chrUn 79.024 615 114 9 1004 1604 20705501 20706114 8.140000e-110 407.0
42 TraesCS7A01G466200 chrUn 81.167 377 67 3 1002 1374 20430137 20430513 1.420000e-77 300.0
43 TraesCS7A01G466200 chr6D 83.133 83 14 0 1676 1758 351987016 351987098 2.610000e-10 76.8
44 TraesCS7A01G466200 chr6B 81.443 97 14 4 1676 1769 526797780 526797685 2.610000e-10 76.8


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 TraesCS7A01G466200 chr7A 663453100 663455543 2443 True 4514.00 4514 100.0000 1 2444 1 chr7A.!!$R6 2443
1 TraesCS7A01G466200 chr7A 107014939 107015550 611 True 955.00 955 94.7970 1 615 1 chr7A.!!$R3 614
2 TraesCS7A01G466200 chr7A 175071303 175071914 611 False 905.00 905 93.3330 1 615 1 chr7A.!!$F1 614
3 TraesCS7A01G466200 chr7A 3036501 3037107 606 True 767.00 767 89.5330 2 615 1 chr7A.!!$R1 613
4 TraesCS7A01G466200 chr7A 17715436 17716031 595 True 763.00 763 89.5770 2 615 1 chr7A.!!$R2 613
5 TraesCS7A01G466200 chr7A 647916840 647917453 613 True 468.00 468 80.7820 1004 1604 1 chr7A.!!$R5 600
6 TraesCS7A01G466200 chr7A 647862326 647862856 530 True 346.00 346 78.9570 1004 1525 1 chr7A.!!$R4 521
7 TraesCS7A01G466200 chr7B 632269438 632271596 2158 True 617.25 1670 89.8770 695 2443 4 chr7B.!!$R2 1748
8 TraesCS7A01G466200 chr7D 629192578 629193203 625 False 824.00 824 90.7500 2 615 1 chr7D.!!$F3 613
9 TraesCS7A01G466200 chr7D 573460194 573462949 2755 True 531.52 1642 87.9182 712 2443 5 chr7D.!!$R4 1731
10 TraesCS7A01G466200 chr6A 49842962 49843574 612 True 941.00 941 94.3090 1 615 1 chr6A.!!$R1 614
11 TraesCS7A01G466200 chr3A 141874949 141875547 598 True 867.00 867 92.5200 1 615 1 chr3A.!!$R1 614
12 TraesCS7A01G466200 chr1A 159528735 159529329 594 False 848.00 848 92.0580 1 617 1 chr1A.!!$F1 616
13 TraesCS7A01G466200 chr3D 569884180 569884793 613 False 791.00 791 89.9840 2 622 1 chr3D.!!$F2 620
14 TraesCS7A01G466200 chrUn 20705501 20706114 613 False 407.00 407 79.0240 1004 1604 1 chrUn.!!$F2 600

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
662 701 0.036875 GTTAGTTCTGGGCCTGCTGT 59.963 55.0 4.53 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1667 2045 0.179097 GTCATCGAGCTGTCCTTCCC 60.179 60.0 0.0 0.0 0.0 3.97 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
31 32 0.765510 AGTTTTCTGCCCGTCCTCTT 59.234 50.000 0.00 0.00 0.00 2.85
109 132 4.640789 AACAAACATAGTGGCGACAAAA 57.359 36.364 0.00 0.00 46.06 2.44
343 373 2.558359 AGAATTCTTGGTTTGGCCTTCG 59.442 45.455 3.32 0.00 38.35 3.79
513 552 9.146984 CGAAATATGTCGGGTTGTATAATATGT 57.853 33.333 7.45 0.00 37.37 2.29
519 558 6.126997 TGTCGGGTTGTATAATATGTCCAACT 60.127 38.462 0.00 0.00 36.52 3.16
521 560 8.092687 GTCGGGTTGTATAATATGTCCAACTAT 58.907 37.037 0.00 0.00 36.52 2.12
530 569 1.959710 TGTCCAACTATAGCCCCACA 58.040 50.000 0.00 0.00 0.00 4.17
531 570 2.270858 TGTCCAACTATAGCCCCACAA 58.729 47.619 0.00 0.00 0.00 3.33
544 583 3.096092 GCCCCACAAGGATGAAAATACA 58.904 45.455 0.00 0.00 38.24 2.29
545 584 3.706086 GCCCCACAAGGATGAAAATACAT 59.294 43.478 0.00 0.00 38.24 2.29
565 604 1.223598 TCCATCCCCGTCCCCTAATAA 59.776 52.381 0.00 0.00 0.00 1.40
618 657 2.489619 GCCCCATTGCCATCTTGATCTA 60.490 50.000 0.00 0.00 0.00 1.98
621 660 3.418995 CCATTGCCATCTTGATCTAGGG 58.581 50.000 4.29 0.22 0.00 3.53
622 661 2.645838 TTGCCATCTTGATCTAGGGC 57.354 50.000 14.47 14.47 41.70 5.19
623 662 1.811778 TGCCATCTTGATCTAGGGCT 58.188 50.000 19.44 0.00 41.86 5.19
624 663 1.419012 TGCCATCTTGATCTAGGGCTG 59.581 52.381 19.44 9.39 41.86 4.85
625 664 1.881498 GCCATCTTGATCTAGGGCTGC 60.881 57.143 14.20 0.00 38.37 5.25
626 665 1.698532 CCATCTTGATCTAGGGCTGCT 59.301 52.381 4.29 0.00 0.00 4.24
627 666 2.289569 CCATCTTGATCTAGGGCTGCTC 60.290 54.545 4.29 0.00 0.00 4.26
628 667 2.165357 TCTTGATCTAGGGCTGCTCA 57.835 50.000 0.74 0.00 0.00 4.26
629 668 2.470990 TCTTGATCTAGGGCTGCTCAA 58.529 47.619 0.74 0.77 0.00 3.02
630 669 3.044156 TCTTGATCTAGGGCTGCTCAAT 58.956 45.455 0.74 0.00 0.00 2.57
631 670 4.226384 TCTTGATCTAGGGCTGCTCAATA 58.774 43.478 0.74 0.00 0.00 1.90
632 671 4.282957 TCTTGATCTAGGGCTGCTCAATAG 59.717 45.833 0.74 0.00 0.00 1.73
633 672 3.849527 TGATCTAGGGCTGCTCAATAGA 58.150 45.455 0.74 1.20 0.00 1.98
634 673 4.423913 TGATCTAGGGCTGCTCAATAGAT 58.576 43.478 10.17 10.17 36.23 1.98
635 674 4.842948 TGATCTAGGGCTGCTCAATAGATT 59.157 41.667 11.31 0.00 34.24 2.40
636 675 5.309020 TGATCTAGGGCTGCTCAATAGATTT 59.691 40.000 11.31 0.00 34.24 2.17
637 676 4.965814 TCTAGGGCTGCTCAATAGATTTG 58.034 43.478 0.74 0.00 0.00 2.32
638 677 2.941480 AGGGCTGCTCAATAGATTTGG 58.059 47.619 0.74 0.00 0.00 3.28
639 678 1.959282 GGGCTGCTCAATAGATTTGGG 59.041 52.381 0.00 0.00 0.00 4.12
640 679 1.339291 GGCTGCTCAATAGATTTGGGC 59.661 52.381 3.27 3.27 45.71 5.36
641 680 1.339291 GCTGCTCAATAGATTTGGGCC 59.661 52.381 7.66 0.00 44.94 5.80
642 681 1.605710 CTGCTCAATAGATTTGGGCCG 59.394 52.381 7.66 0.00 44.94 6.13
643 682 0.954452 GCTCAATAGATTTGGGCCGG 59.046 55.000 0.00 0.00 39.90 6.13
644 683 1.750682 GCTCAATAGATTTGGGCCGGT 60.751 52.381 1.90 0.00 39.90 5.28
645 684 2.654863 CTCAATAGATTTGGGCCGGTT 58.345 47.619 1.90 0.00 0.00 4.44
646 685 3.815809 CTCAATAGATTTGGGCCGGTTA 58.184 45.455 1.90 0.00 0.00 2.85
647 686 3.815401 CTCAATAGATTTGGGCCGGTTAG 59.185 47.826 1.90 0.00 0.00 2.34
648 687 3.201266 TCAATAGATTTGGGCCGGTTAGT 59.799 43.478 1.90 0.00 0.00 2.24
649 688 3.945640 ATAGATTTGGGCCGGTTAGTT 57.054 42.857 1.90 0.00 0.00 2.24
650 689 2.124277 AGATTTGGGCCGGTTAGTTC 57.876 50.000 1.90 0.00 0.00 3.01
651 690 1.633945 AGATTTGGGCCGGTTAGTTCT 59.366 47.619 1.90 0.00 0.00 3.01
652 691 1.743394 GATTTGGGCCGGTTAGTTCTG 59.257 52.381 1.90 0.00 0.00 3.02
653 692 0.250989 TTTGGGCCGGTTAGTTCTGG 60.251 55.000 1.90 0.00 36.96 3.86
654 693 2.132089 TTGGGCCGGTTAGTTCTGGG 62.132 60.000 1.90 0.00 34.64 4.45
656 695 2.437895 GCCGGTTAGTTCTGGGCC 60.438 66.667 1.90 0.00 37.82 5.80
657 696 2.967946 GCCGGTTAGTTCTGGGCCT 61.968 63.158 4.53 0.00 37.82 5.19
658 697 1.078426 CCGGTTAGTTCTGGGCCTG 60.078 63.158 4.53 4.06 0.00 4.85
659 698 1.745489 CGGTTAGTTCTGGGCCTGC 60.745 63.158 4.53 0.00 0.00 4.85
660 699 1.685820 GGTTAGTTCTGGGCCTGCT 59.314 57.895 4.53 0.02 0.00 4.24
661 700 0.678048 GGTTAGTTCTGGGCCTGCTG 60.678 60.000 4.53 0.00 0.00 4.41
662 701 0.036875 GTTAGTTCTGGGCCTGCTGT 59.963 55.000 4.53 0.00 0.00 4.40
663 702 0.771127 TTAGTTCTGGGCCTGCTGTT 59.229 50.000 4.53 0.00 0.00 3.16
664 703 0.771127 TAGTTCTGGGCCTGCTGTTT 59.229 50.000 4.53 0.00 0.00 2.83
665 704 0.771127 AGTTCTGGGCCTGCTGTTTA 59.229 50.000 4.53 0.00 0.00 2.01
666 705 1.355720 AGTTCTGGGCCTGCTGTTTAT 59.644 47.619 4.53 0.00 0.00 1.40
667 706 2.171003 GTTCTGGGCCTGCTGTTTATT 58.829 47.619 4.53 0.00 0.00 1.40
668 707 1.838112 TCTGGGCCTGCTGTTTATTG 58.162 50.000 4.53 0.00 0.00 1.90
669 708 0.174162 CTGGGCCTGCTGTTTATTGC 59.826 55.000 4.53 0.00 0.00 3.56
670 709 1.139520 GGGCCTGCTGTTTATTGCG 59.860 57.895 0.84 0.00 0.00 4.85
671 710 1.139520 GGCCTGCTGTTTATTGCGG 59.860 57.895 0.00 0.00 35.50 5.69
672 711 1.517039 GCCTGCTGTTTATTGCGGC 60.517 57.895 0.00 0.00 39.82 6.53
673 712 1.882311 CCTGCTGTTTATTGCGGCA 59.118 52.632 0.00 0.00 44.88 5.69
674 713 0.457035 CCTGCTGTTTATTGCGGCAT 59.543 50.000 2.28 0.00 45.75 4.40
675 714 1.534595 CCTGCTGTTTATTGCGGCATC 60.535 52.381 2.28 0.00 45.75 3.91
676 715 1.132834 CTGCTGTTTATTGCGGCATCA 59.867 47.619 2.28 0.00 45.75 3.07
677 716 1.132834 TGCTGTTTATTGCGGCATCAG 59.867 47.619 2.28 8.99 42.57 2.90
678 717 1.401552 GCTGTTTATTGCGGCATCAGA 59.598 47.619 2.28 0.00 38.08 3.27
679 718 2.033801 GCTGTTTATTGCGGCATCAGAT 59.966 45.455 2.28 0.00 38.08 2.90
680 719 3.250762 GCTGTTTATTGCGGCATCAGATA 59.749 43.478 2.28 0.00 38.08 1.98
681 720 4.083110 GCTGTTTATTGCGGCATCAGATAT 60.083 41.667 2.28 0.00 38.08 1.63
682 721 5.563475 GCTGTTTATTGCGGCATCAGATATT 60.563 40.000 2.28 0.00 38.08 1.28
683 722 6.348458 GCTGTTTATTGCGGCATCAGATATTA 60.348 38.462 2.28 0.00 38.08 0.98
684 723 7.503521 TGTTTATTGCGGCATCAGATATTAA 57.496 32.000 2.28 0.00 0.00 1.40
685 724 8.109705 TGTTTATTGCGGCATCAGATATTAAT 57.890 30.769 2.28 0.00 0.00 1.40
686 725 8.236586 TGTTTATTGCGGCATCAGATATTAATC 58.763 33.333 2.28 0.00 0.00 1.75
687 726 5.824904 ATTGCGGCATCAGATATTAATCC 57.175 39.130 2.28 0.00 31.98 3.01
688 727 4.284829 TGCGGCATCAGATATTAATCCA 57.715 40.909 0.00 0.00 31.98 3.41
689 728 4.002982 TGCGGCATCAGATATTAATCCAC 58.997 43.478 0.00 0.00 31.98 4.02
690 729 3.062639 GCGGCATCAGATATTAATCCACG 59.937 47.826 0.00 0.00 31.98 4.94
691 730 4.494484 CGGCATCAGATATTAATCCACGA 58.506 43.478 0.00 0.00 31.98 4.35
692 731 5.111989 CGGCATCAGATATTAATCCACGAT 58.888 41.667 0.00 0.00 31.98 3.73
693 732 5.233050 CGGCATCAGATATTAATCCACGATC 59.767 44.000 0.00 0.00 31.98 3.69
694 733 6.344500 GGCATCAGATATTAATCCACGATCT 58.656 40.000 0.00 0.00 31.98 2.75
695 734 6.257411 GGCATCAGATATTAATCCACGATCTG 59.743 42.308 14.93 14.93 43.16 2.90
696 735 6.257411 GCATCAGATATTAATCCACGATCTGG 59.743 42.308 18.59 9.53 42.42 3.86
697 736 5.724328 TCAGATATTAATCCACGATCTGGC 58.276 41.667 18.59 0.00 42.42 4.85
698 737 5.481824 TCAGATATTAATCCACGATCTGGCT 59.518 40.000 18.59 0.00 42.42 4.75
709 748 4.452455 CCACGATCTGGCTTTATAATGGAC 59.548 45.833 0.00 0.00 31.36 4.02
710 749 4.452455 CACGATCTGGCTTTATAATGGACC 59.548 45.833 0.00 0.00 0.00 4.46
714 753 5.048846 TCTGGCTTTATAATGGACCCTTC 57.951 43.478 1.00 0.00 0.00 3.46
720 759 5.127031 GCTTTATAATGGACCCTTCTTGCAA 59.873 40.000 0.00 0.00 0.00 4.08
776 815 7.336931 TCCTAACAGAGATTATTGCCTTTTCAC 59.663 37.037 0.00 0.00 0.00 3.18
861 1176 4.336280 ACTCCCTTGAACTAAAATGCTCC 58.664 43.478 0.00 0.00 0.00 4.70
887 1202 7.148836 CGTTTGCAATTTTCAGTTATGCATACA 60.149 33.333 5.74 0.00 45.41 2.29
921 1236 2.699954 ACATTAGTGCCCTTTGTCTCG 58.300 47.619 0.00 0.00 0.00 4.04
937 1252 0.652592 CTCGTGGCTTTGCTAATCGG 59.347 55.000 0.00 0.00 0.00 4.18
942 1257 3.120130 CGTGGCTTTGCTAATCGGTTTAA 60.120 43.478 0.00 0.00 0.00 1.52
993 1308 7.750903 GTGACTTATCCTGCTTTGTTGTAATTC 59.249 37.037 0.00 0.00 0.00 2.17
997 1312 3.572255 TCCTGCTTTGTTGTAATTCCCAC 59.428 43.478 0.00 0.00 0.00 4.61
1033 1348 2.028876 TCTTCGTGAAGACACTCACCA 58.971 47.619 8.19 0.00 42.34 4.17
1092 1407 2.165641 AGTCGACAATGTGAAGGCGATA 59.834 45.455 19.50 0.00 0.00 2.92
1164 1479 0.964358 GCAAGCAGCTTGAGGATGGT 60.964 55.000 34.93 0.00 43.42 3.55
1175 1490 0.108138 GAGGATGGTCGGACACTTGG 60.108 60.000 10.76 0.00 0.00 3.61
1229 1544 4.792804 GGTGCTCAGGCTCAGGGC 62.793 72.222 0.00 0.00 39.59 5.19
1239 1554 0.037877 GGCTCAGGGCTGATATGCAT 59.962 55.000 3.79 3.79 39.13 3.96
1240 1555 1.547223 GGCTCAGGGCTGATATGCATT 60.547 52.381 3.54 0.00 39.13 3.56
1281 1596 4.954202 ACTGGCAAGATCATCATGTTTGAT 59.046 37.500 11.89 11.89 43.51 2.57
1282 1597 5.067413 ACTGGCAAGATCATCATGTTTGATC 59.933 40.000 22.79 22.79 46.42 2.92
1366 1727 0.323178 CAGCAGGGCCTCATCTTTGT 60.323 55.000 0.95 0.00 0.00 2.83
1587 1965 2.102578 AGCAGTGGTTGATATTTGCCC 58.897 47.619 0.00 0.00 32.21 5.36
1619 1997 1.077429 GGACCATCACCTTGGAGGC 60.077 63.158 0.00 0.00 39.63 4.70
1658 2036 2.063266 TGACAACGTGAAGGCGAATAC 58.937 47.619 0.00 0.00 35.59 1.89
1667 2045 2.280628 GAAGGCGAATACCCAAGACAG 58.719 52.381 0.00 0.00 0.00 3.51
1683 2071 0.616111 ACAGGGAAGGACAGCTCGAT 60.616 55.000 0.00 0.00 0.00 3.59
1758 2146 2.927580 GCTCCGTCTTCGTGGTGGA 61.928 63.158 0.00 0.00 35.01 4.02
1762 2150 2.022129 CGTCTTCGTGGTGGACAGC 61.022 63.158 0.00 0.00 0.00 4.40
1780 2168 1.177401 GCGAATTTCTTTGGGCTCCT 58.823 50.000 0.00 0.00 0.00 3.69
1782 2170 2.436417 CGAATTTCTTTGGGCTCCTGA 58.564 47.619 0.00 0.00 0.00 3.86
1785 2173 4.261994 CGAATTTCTTTGGGCTCCTGAAAA 60.262 41.667 0.96 0.00 31.71 2.29
1830 2218 0.034896 GGTGGCCTCTTCTTTCGTCA 59.965 55.000 3.32 0.00 0.00 4.35
1836 2224 2.862921 GCCTCTTCTTTCGTCAACGTCT 60.863 50.000 2.09 0.00 40.80 4.18
1913 2303 4.232221 GTGCAATTTGTGAGAACATCTGG 58.768 43.478 0.00 0.00 0.00 3.86
2028 2624 5.471797 TGGTCGTTTTTGCTATCAAAGATCA 59.528 36.000 0.00 0.00 42.50 2.92
2045 2641 7.394077 TCAAAGATCATAACTTCAGATTTGGCA 59.606 33.333 0.00 0.00 0.00 4.92
2057 2653 5.239351 TCAGATTTGGCATTTCCATGTTTG 58.761 37.500 0.00 0.00 46.04 2.93
2219 2816 2.612567 GCACACCGGCGTGATTTCA 61.613 57.895 26.37 0.00 43.14 2.69
2227 2824 2.476185 CCGGCGTGATTTCATCTGAAAC 60.476 50.000 6.01 3.67 45.55 2.78
2255 2852 5.467035 AAGTTGGGTGATTGTTGTATTGG 57.533 39.130 0.00 0.00 0.00 3.16
2345 2976 1.089920 CACTAGGGCATCAACACTGC 58.910 55.000 0.00 0.00 38.93 4.40
2360 2991 1.608590 CACTGCCCATCAAAACGAACT 59.391 47.619 0.00 0.00 0.00 3.01
2387 3018 1.270094 ACATTCGTGGACGCTTTCTCA 60.270 47.619 0.00 0.00 39.60 3.27
2400 3031 3.436704 CGCTTTCTCAAAATAGGCTCACA 59.563 43.478 0.00 0.00 0.00 3.58
2413 3045 2.092914 AGGCTCACACCCTGCTTTATAC 60.093 50.000 0.00 0.00 0.00 1.47
2440 3072 2.285602 GCAAACATCATAGTACACGGCG 60.286 50.000 4.80 4.80 0.00 6.46
2441 3073 3.183754 CAAACATCATAGTACACGGCGA 58.816 45.455 16.62 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 132 7.551035 TTGTTTTGCTGCTGAAATGTTATTT 57.449 28.000 0.00 0.00 0.00 1.40
184 207 7.212976 ACACTCTATATAGCTGTTGAACCATG 58.787 38.462 4.75 0.00 0.00 3.66
365 398 1.791103 GCTATCGAGCCTGAGCGACT 61.791 60.000 0.00 0.00 46.67 4.18
513 552 1.843851 CCTTGTGGGGCTATAGTTGGA 59.156 52.381 0.84 0.00 0.00 3.53
519 558 4.871871 TTTTCATCCTTGTGGGGCTATA 57.128 40.909 0.00 0.00 35.33 1.31
521 560 3.756082 ATTTTCATCCTTGTGGGGCTA 57.244 42.857 0.00 0.00 35.33 3.93
544 583 0.196118 ATTAGGGGACGGGGATGGAT 59.804 55.000 0.00 0.00 0.00 3.41
545 584 0.868894 TATTAGGGGACGGGGATGGA 59.131 55.000 0.00 0.00 0.00 3.41
565 604 2.034532 CCCCGCGGGTTTTTACCT 59.965 61.111 40.52 0.00 38.25 3.08
618 657 2.423947 CCCAAATCTATTGAGCAGCCCT 60.424 50.000 0.00 0.00 0.00 5.19
621 660 1.339291 GGCCCAAATCTATTGAGCAGC 59.661 52.381 0.00 0.00 0.00 5.25
622 661 1.605710 CGGCCCAAATCTATTGAGCAG 59.394 52.381 0.00 0.00 0.00 4.24
623 662 1.679139 CGGCCCAAATCTATTGAGCA 58.321 50.000 0.00 0.00 0.00 4.26
624 663 0.954452 CCGGCCCAAATCTATTGAGC 59.046 55.000 0.00 0.00 0.00 4.26
625 664 2.348411 ACCGGCCCAAATCTATTGAG 57.652 50.000 0.00 0.00 0.00 3.02
626 665 2.818751 AACCGGCCCAAATCTATTGA 57.181 45.000 0.00 0.00 0.00 2.57
627 666 3.551846 ACTAACCGGCCCAAATCTATTG 58.448 45.455 0.00 0.00 0.00 1.90
628 667 3.945640 ACTAACCGGCCCAAATCTATT 57.054 42.857 0.00 0.00 0.00 1.73
629 668 3.458487 AGAACTAACCGGCCCAAATCTAT 59.542 43.478 0.00 0.00 0.00 1.98
630 669 2.841881 AGAACTAACCGGCCCAAATCTA 59.158 45.455 0.00 0.00 0.00 1.98
631 670 1.633945 AGAACTAACCGGCCCAAATCT 59.366 47.619 0.00 0.00 0.00 2.40
632 671 1.743394 CAGAACTAACCGGCCCAAATC 59.257 52.381 0.00 0.00 0.00 2.17
633 672 1.615919 CCAGAACTAACCGGCCCAAAT 60.616 52.381 0.00 0.00 0.00 2.32
634 673 0.250989 CCAGAACTAACCGGCCCAAA 60.251 55.000 0.00 0.00 0.00 3.28
635 674 1.377229 CCAGAACTAACCGGCCCAA 59.623 57.895 0.00 0.00 0.00 4.12
636 675 2.598787 CCCAGAACTAACCGGCCCA 61.599 63.158 0.00 0.00 0.00 5.36
637 676 2.271173 CCCAGAACTAACCGGCCC 59.729 66.667 0.00 0.00 0.00 5.80
638 677 2.437895 GCCCAGAACTAACCGGCC 60.438 66.667 0.00 0.00 33.30 6.13
639 678 2.437895 GGCCCAGAACTAACCGGC 60.438 66.667 0.00 0.00 38.96 6.13
640 679 1.078426 CAGGCCCAGAACTAACCGG 60.078 63.158 0.00 0.00 0.00 5.28
641 680 1.745489 GCAGGCCCAGAACTAACCG 60.745 63.158 0.00 0.00 0.00 4.44
642 681 0.678048 CAGCAGGCCCAGAACTAACC 60.678 60.000 0.00 0.00 0.00 2.85
643 682 0.036875 ACAGCAGGCCCAGAACTAAC 59.963 55.000 0.00 0.00 0.00 2.34
644 683 0.771127 AACAGCAGGCCCAGAACTAA 59.229 50.000 0.00 0.00 0.00 2.24
645 684 0.771127 AAACAGCAGGCCCAGAACTA 59.229 50.000 0.00 0.00 0.00 2.24
646 685 0.771127 TAAACAGCAGGCCCAGAACT 59.229 50.000 0.00 0.00 0.00 3.01
647 686 1.839424 ATAAACAGCAGGCCCAGAAC 58.161 50.000 0.00 0.00 0.00 3.01
648 687 2.170166 CAATAAACAGCAGGCCCAGAA 58.830 47.619 0.00 0.00 0.00 3.02
649 688 1.838112 CAATAAACAGCAGGCCCAGA 58.162 50.000 0.00 0.00 0.00 3.86
650 689 0.174162 GCAATAAACAGCAGGCCCAG 59.826 55.000 0.00 0.00 0.00 4.45
651 690 1.594194 CGCAATAAACAGCAGGCCCA 61.594 55.000 0.00 0.00 0.00 5.36
652 691 1.139520 CGCAATAAACAGCAGGCCC 59.860 57.895 0.00 0.00 0.00 5.80
653 692 1.139520 CCGCAATAAACAGCAGGCC 59.860 57.895 0.00 0.00 0.00 5.19
654 693 1.517039 GCCGCAATAAACAGCAGGC 60.517 57.895 0.00 0.00 36.08 4.85
655 694 0.457035 ATGCCGCAATAAACAGCAGG 59.543 50.000 0.00 0.00 36.80 4.85
656 695 1.132834 TGATGCCGCAATAAACAGCAG 59.867 47.619 0.00 0.00 36.80 4.24
657 696 1.132834 CTGATGCCGCAATAAACAGCA 59.867 47.619 0.00 0.00 37.94 4.41
658 697 1.401552 TCTGATGCCGCAATAAACAGC 59.598 47.619 0.00 0.00 0.00 4.40
659 698 3.976793 ATCTGATGCCGCAATAAACAG 57.023 42.857 0.00 3.20 0.00 3.16
660 699 7.503521 TTAATATCTGATGCCGCAATAAACA 57.496 32.000 0.00 0.00 0.00 2.83
661 700 7.698130 GGATTAATATCTGATGCCGCAATAAAC 59.302 37.037 0.00 0.00 0.00 2.01
662 701 7.392953 TGGATTAATATCTGATGCCGCAATAAA 59.607 33.333 0.00 0.00 0.00 1.40
663 702 6.883756 TGGATTAATATCTGATGCCGCAATAA 59.116 34.615 0.00 0.00 0.00 1.40
664 703 6.316140 GTGGATTAATATCTGATGCCGCAATA 59.684 38.462 0.00 0.00 0.00 1.90
665 704 5.124457 GTGGATTAATATCTGATGCCGCAAT 59.876 40.000 0.00 0.00 0.00 3.56
666 705 4.455533 GTGGATTAATATCTGATGCCGCAA 59.544 41.667 0.00 0.00 0.00 4.85
667 706 4.002982 GTGGATTAATATCTGATGCCGCA 58.997 43.478 0.00 0.00 0.00 5.69
668 707 3.062639 CGTGGATTAATATCTGATGCCGC 59.937 47.826 0.00 0.00 0.00 6.53
669 708 4.494484 TCGTGGATTAATATCTGATGCCG 58.506 43.478 0.00 0.00 0.00 5.69
670 709 6.257411 CAGATCGTGGATTAATATCTGATGCC 59.743 42.308 15.64 0.23 44.01 4.40
671 710 7.231705 CAGATCGTGGATTAATATCTGATGC 57.768 40.000 15.64 2.58 44.01 3.91
672 711 7.847235 AGCCAGATCGTGGATTAATATCTGATG 60.847 40.741 19.89 10.03 45.28 3.07
673 712 6.155910 AGCCAGATCGTGGATTAATATCTGAT 59.844 38.462 19.89 8.78 45.28 2.90
674 713 5.481824 AGCCAGATCGTGGATTAATATCTGA 59.518 40.000 19.89 5.04 45.28 3.27
675 714 5.728471 AGCCAGATCGTGGATTAATATCTG 58.272 41.667 14.42 14.42 45.28 2.90
687 726 4.452455 GGTCCATTATAAAGCCAGATCGTG 59.548 45.833 0.00 0.00 0.00 4.35
688 727 4.505039 GGGTCCATTATAAAGCCAGATCGT 60.505 45.833 0.00 0.00 0.00 3.73
689 728 4.003648 GGGTCCATTATAAAGCCAGATCG 58.996 47.826 0.00 0.00 0.00 3.69
690 729 5.248380 AGGGTCCATTATAAAGCCAGATC 57.752 43.478 6.64 0.00 32.95 2.75
691 730 5.373854 AGAAGGGTCCATTATAAAGCCAGAT 59.626 40.000 6.64 0.00 32.95 2.90
692 731 4.726825 AGAAGGGTCCATTATAAAGCCAGA 59.273 41.667 6.64 0.00 32.95 3.86
693 732 5.053978 AGAAGGGTCCATTATAAAGCCAG 57.946 43.478 6.64 0.00 32.95 4.85
694 733 5.200483 CAAGAAGGGTCCATTATAAAGCCA 58.800 41.667 6.64 0.00 32.95 4.75
695 734 4.038042 GCAAGAAGGGTCCATTATAAAGCC 59.962 45.833 0.00 0.00 0.00 4.35
696 735 4.644685 TGCAAGAAGGGTCCATTATAAAGC 59.355 41.667 0.00 0.00 0.00 3.51
697 736 6.773976 TTGCAAGAAGGGTCCATTATAAAG 57.226 37.500 0.00 0.00 0.00 1.85
698 737 6.951198 TCTTTGCAAGAAGGGTCCATTATAAA 59.049 34.615 0.00 0.00 33.83 1.40
709 748 2.444421 AGCAGATCTTTGCAAGAAGGG 58.556 47.619 9.38 0.00 46.47 3.95
710 749 5.633830 TTAAGCAGATCTTTGCAAGAAGG 57.366 39.130 9.38 0.00 46.47 3.46
737 776 9.661954 AATCTCTGTTAGGATCTATTTCCAGTA 57.338 33.333 0.00 0.00 38.32 2.74
776 815 5.633182 ACAAATAACAACCGCATAGCAAAAG 59.367 36.000 0.00 0.00 0.00 2.27
861 1176 5.573296 TGCATAACTGAAAATTGCAAACG 57.427 34.783 1.71 0.00 40.11 3.60
887 1202 8.166061 AGGGCACTAATGTAAATGATGTGATAT 58.834 33.333 0.00 0.00 0.00 1.63
902 1217 2.416547 CACGAGACAAAGGGCACTAATG 59.583 50.000 0.00 0.00 0.00 1.90
921 1236 4.082949 AGTTAAACCGATTAGCAAAGCCAC 60.083 41.667 0.00 0.00 0.00 5.01
937 1252 8.613482 GGAAGAGGCTTACATGAATAGTTAAAC 58.387 37.037 0.00 0.00 0.00 2.01
942 1257 6.352516 CAAGGAAGAGGCTTACATGAATAGT 58.647 40.000 0.00 0.00 0.00 2.12
997 1312 9.349981 CTTCACGAAGATCTGCATCTGCATAAG 62.350 44.444 5.16 0.00 44.61 1.73
1033 1348 2.277969 CTCAAGCGTGATGATCTTGCT 58.722 47.619 1.88 6.24 37.64 3.91
1092 1407 4.439860 GGATACCCTCCTTATCCTGGAAT 58.560 47.826 0.00 0.00 41.32 3.01
1164 1479 3.755112 TTGTAATCACCAAGTGTCCGA 57.245 42.857 0.00 0.00 34.79 4.55
1175 1490 8.421784 TGGACTCCTTCTGTATATTGTAATCAC 58.578 37.037 0.00 0.00 0.00 3.06
1229 1544 7.431376 GTGTCATCACAAAGAAATGCATATCAG 59.569 37.037 0.00 0.00 43.37 2.90
1232 1547 7.121611 TGAGTGTCATCACAAAGAAATGCATAT 59.878 33.333 0.00 0.00 46.01 1.78
1281 1596 3.744238 TCAATTGTGTCGGAGAACAGA 57.256 42.857 5.13 0.00 39.69 3.41
1282 1597 6.481134 CATTATCAATTGTGTCGGAGAACAG 58.519 40.000 5.13 0.00 39.69 3.16
1286 1646 4.512484 TGCATTATCAATTGTGTCGGAGA 58.488 39.130 5.13 0.00 0.00 3.71
1366 1727 1.614903 CATCTTCCAGTTGCTTGCCAA 59.385 47.619 0.00 0.00 0.00 4.52
1431 1792 2.680805 GCATAAGCCTCAGCACAAGGTA 60.681 50.000 1.63 0.00 43.56 3.08
1587 1965 1.165907 TGGTCCTCAAGTTGCTTGCG 61.166 55.000 0.00 0.00 40.84 4.85
1619 1997 0.459585 AATGGTGTCCGACGATTCCG 60.460 55.000 0.00 0.00 42.50 4.30
1667 2045 0.179097 GTCATCGAGCTGTCCTTCCC 60.179 60.000 0.00 0.00 0.00 3.97
1683 2071 4.980805 GCAAGGGTGCGTCCGTCA 62.981 66.667 0.00 0.00 41.93 4.35
1758 2146 1.541588 GAGCCCAAAGAAATTCGCTGT 59.458 47.619 0.00 0.00 0.00 4.40
1762 2150 2.436417 TCAGGAGCCCAAAGAAATTCG 58.564 47.619 0.00 0.00 0.00 3.34
1780 2168 4.202101 ACAGACATGCGAACCAAATTTTCA 60.202 37.500 0.00 0.00 0.00 2.69
1782 2170 4.320608 ACAGACATGCGAACCAAATTTT 57.679 36.364 0.00 0.00 0.00 1.82
1785 2173 2.884012 TCAACAGACATGCGAACCAAAT 59.116 40.909 0.00 0.00 0.00 2.32
1823 2211 4.932268 ACAAAAGAAGACGTTGACGAAA 57.068 36.364 10.87 0.00 43.02 3.46
1830 2218 5.349543 ACTTCACGTAACAAAAGAAGACGTT 59.650 36.000 14.33 0.00 43.72 3.99
1836 2224 6.670233 ACACAAACTTCACGTAACAAAAGAA 58.330 32.000 0.00 0.00 0.00 2.52
1930 2320 9.632638 AACTTATTCATAACATAGACCAAGCAT 57.367 29.630 0.00 0.00 0.00 3.79
2028 2624 6.855763 TGGAAATGCCAAATCTGAAGTTAT 57.144 33.333 0.00 0.00 45.87 1.89
2045 2641 3.233507 ACTGACCAGCAAACATGGAAAT 58.766 40.909 0.00 0.00 40.51 2.17
2057 2653 2.508526 AGATGTTTGGAACTGACCAGC 58.491 47.619 0.00 0.00 41.19 4.85
2219 2816 9.533831 AATCACCCAACTTATTTAGTTTCAGAT 57.466 29.630 0.00 0.00 44.73 2.90
2345 2976 1.904287 TGGGAGTTCGTTTTGATGGG 58.096 50.000 0.00 0.00 0.00 4.00
2360 2991 1.231221 CGTCCACGAATGTTTTGGGA 58.769 50.000 0.00 0.00 43.02 4.37
2387 3018 1.355720 AGCAGGGTGTGAGCCTATTTT 59.644 47.619 0.00 0.00 45.88 1.82
2400 3031 6.379703 TGTTTGCATTATGTATAAAGCAGGGT 59.620 34.615 12.46 0.00 44.46 4.34
2413 3045 7.071414 CCGTGTACTATGATGTTTGCATTATG 58.929 38.462 0.00 0.00 35.07 1.90


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

AutoCloner maintained by Alex Coulton.