Multiple sequence alignment - TraesCS4D01G152800

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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 TraesCS4D01G152800 chr4D 100.000 2859 0 0 1 2859 188961636 188964494 0.000000e+00 5280.0
1 TraesCS4D01G152800 chr4D 97.106 691 20 0 1 691 416378979 416378289 0.000000e+00 1166.0
2 TraesCS4D01G152800 chr4D 96.948 688 21 0 1 688 340246789 340247476 0.000000e+00 1155.0
3 TraesCS4D01G152800 chr4D 84.219 640 29 15 1128 1766 146028915 146028347 8.950000e-155 556.0
4 TraesCS4D01G152800 chr4D 83.000 200 30 4 1423 1620 338368087 338368284 8.140000e-41 178.0
5 TraesCS4D01G152800 chr2D 98.395 2056 17 3 804 2859 288163633 288161594 0.000000e+00 3600.0
6 TraesCS4D01G152800 chr2D 96.961 691 21 0 1 691 20734614 20733924 0.000000e+00 1160.0
7 TraesCS4D01G152800 chr2D 96.961 691 21 0 1 691 29984216 29983526 0.000000e+00 1160.0
8 TraesCS4D01G152800 chr2D 96.948 688 21 0 1 688 369876783 369877470 0.000000e+00 1155.0
9 TraesCS4D01G152800 chr2D 89.313 524 44 8 2338 2859 33338379 33337866 0.000000e+00 647.0
10 TraesCS4D01G152800 chr2D 92.255 439 26 4 1199 1629 36535194 36535632 1.460000e-172 616.0
11 TraesCS4D01G152800 chr2D 95.050 101 5 0 1728 1828 36535688 36535788 2.950000e-35 159.0
12 TraesCS4D01G152800 chr2D 94.667 75 3 1 688 761 46167660 46167734 6.470000e-22 115.0
13 TraesCS4D01G152800 chr2D 94.667 75 2 2 688 761 620304478 620304405 6.470000e-22 115.0
14 TraesCS4D01G152800 chr5D 97.238 688 19 0 1 688 509128392 509129079 0.000000e+00 1166.0
15 TraesCS4D01G152800 chr5D 92.402 487 27 4 1858 2341 148236531 148236052 0.000000e+00 686.0
16 TraesCS4D01G152800 chr5D 89.313 524 47 7 2338 2859 10495568 10495052 0.000000e+00 649.0
17 TraesCS4D01G152800 chr7D 97.093 688 20 0 1 688 522237844 522238531 0.000000e+00 1160.0
18 TraesCS4D01G152800 chr7D 89.122 524 48 7 2338 2859 2872942 2872426 0.000000e+00 643.0
19 TraesCS4D01G152800 chr7D 94.667 75 1 2 688 761 64431210 64431138 2.330000e-21 113.0
20 TraesCS4D01G152800 chr7D 92.000 75 4 2 688 761 528078421 528078348 1.400000e-18 104.0
21 TraesCS4D01G152800 chr3D 97.093 688 20 0 1 688 334829881 334830568 0.000000e+00 1160.0
22 TraesCS4D01G152800 chr3D 96.948 688 21 0 1 688 320811715 320812402 0.000000e+00 1155.0
23 TraesCS4D01G152800 chr3D 86.022 93 11 2 688 780 101854306 101854216 6.520000e-17 99.0
24 TraesCS4D01G152800 chr5B 95.018 562 28 0 2298 2859 634279310 634278749 0.000000e+00 883.0
25 TraesCS4D01G152800 chr5B 92.935 552 35 4 1129 1678 634280302 634279753 0.000000e+00 800.0
26 TraesCS4D01G152800 chr5B 87.048 525 58 8 2338 2859 76158356 76158873 4.100000e-163 584.0
27 TraesCS4D01G152800 chr5B 90.066 302 28 1 834 1135 634280649 634280350 9.600000e-105 390.0
28 TraesCS4D01G152800 chr5B 94.059 101 6 0 1757 1857 634279755 634279655 1.370000e-33 154.0
29 TraesCS4D01G152800 chr5B 93.333 75 4 1 688 761 17591966 17592040 3.010000e-20 110.0
30 TraesCS4D01G152800 chr6D 95.385 520 24 0 2325 2844 443355392 443355911 0.000000e+00 828.0
31 TraesCS4D01G152800 chr6D 94.636 522 26 1 2325 2844 443464573 443465094 0.000000e+00 808.0
32 TraesCS4D01G152800 chr6D 85.491 448 57 4 688 1135 23362095 23362534 7.220000e-126 460.0
33 TraesCS4D01G152800 chr6D 90.459 283 27 0 841 1123 462917924 462918206 9.670000e-100 374.0
34 TraesCS4D01G152800 chr2B 89.032 620 42 17 1225 1828 62546746 62547355 0.000000e+00 745.0
35 TraesCS4D01G152800 chrUn 89.216 612 37 8 1156 1766 427445403 427445986 0.000000e+00 737.0
36 TraesCS4D01G152800 chrUn 82.769 325 47 4 688 1012 465772958 465772643 6.030000e-72 281.0
37 TraesCS4D01G152800 chr1A 89.552 603 34 8 1165 1766 514433969 514433395 0.000000e+00 737.0
38 TraesCS4D01G152800 chr1A 89.552 603 34 8 1165 1766 514503255 514502681 0.000000e+00 737.0
39 TraesCS4D01G152800 chr1A 85.106 611 59 16 1221 1828 236303444 236302863 1.900000e-166 595.0
40 TraesCS4D01G152800 chr2A 87.418 612 57 13 1221 1828 40537623 40538218 0.000000e+00 686.0
41 TraesCS4D01G152800 chr2A 90.574 488 40 5 1858 2341 142697551 142698036 2.400000e-180 641.0
42 TraesCS4D01G152800 chr2A 90.798 326 28 2 810 1135 191876807 191877130 4.370000e-118 435.0
43 TraesCS4D01G152800 chr2A 84.058 207 13 6 929 1135 14901197 14901383 6.290000e-42 182.0
44 TraesCS4D01G152800 chr2A 93.333 75 4 1 688 761 17866767 17866841 3.010000e-20 110.0
45 TraesCS4D01G152800 chr6A 92.165 485 33 4 1858 2338 603055825 603056308 0.000000e+00 680.0
46 TraesCS4D01G152800 chr3A 91.598 488 36 4 1858 2341 589831379 589831865 0.000000e+00 669.0
47 TraesCS4D01G152800 chr3A 88.571 525 46 8 2338 2859 107617928 107617415 2.420000e-175 625.0
48 TraesCS4D01G152800 chr3A 95.111 225 11 0 902 1126 21101199 21101423 3.500000e-94 355.0
49 TraesCS4D01G152800 chr3A 84.946 93 11 3 688 780 513543166 513543077 1.090000e-14 91.6
50 TraesCS4D01G152800 chr7B 91.529 484 37 3 1858 2338 81406373 81406855 0.000000e+00 664.0
51 TraesCS4D01G152800 chr7A 90.984 488 39 4 1858 2341 461943568 461943082 0.000000e+00 652.0
52 TraesCS4D01G152800 chr7A 90.574 488 41 4 1858 2341 461938440 461937954 2.400000e-180 641.0
53 TraesCS4D01G152800 chr5A 90.984 488 38 5 1858 2341 37147125 37146640 0.000000e+00 652.0
54 TraesCS4D01G152800 chr4A 85.458 612 52 8 1156 1766 410685096 410684521 1.130000e-168 603.0
55 TraesCS4D01G152800 chr4A 84.889 450 55 8 688 1135 690154233 690154671 2.610000e-120 442.0
56 TraesCS4D01G152800 chr4A 82.297 209 33 4 1423 1629 133841656 133841450 8.140000e-41 178.0
57 TraesCS4D01G152800 chr1D 90.964 332 28 2 805 1135 78365496 78365166 2.020000e-121 446.0
58 TraesCS4D01G152800 chr4B 83.500 200 29 4 1423 1620 417351923 417352120 1.750000e-42 183.0
59 TraesCS4D01G152800 chr1B 98.413 63 1 0 688 750 80959005 80959067 8.370000e-21 111.0


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 TraesCS4D01G152800 chr4D 188961636 188964494 2858 False 5280.00 5280 100.0000 1 2859 1 chr4D.!!$F1 2858
1 TraesCS4D01G152800 chr4D 416378289 416378979 690 True 1166.00 1166 97.1060 1 691 1 chr4D.!!$R2 690
2 TraesCS4D01G152800 chr4D 340246789 340247476 687 False 1155.00 1155 96.9480 1 688 1 chr4D.!!$F3 687
3 TraesCS4D01G152800 chr4D 146028347 146028915 568 True 556.00 556 84.2190 1128 1766 1 chr4D.!!$R1 638
4 TraesCS4D01G152800 chr2D 288161594 288163633 2039 True 3600.00 3600 98.3950 804 2859 1 chr2D.!!$R4 2055
5 TraesCS4D01G152800 chr2D 20733924 20734614 690 True 1160.00 1160 96.9610 1 691 1 chr2D.!!$R1 690
6 TraesCS4D01G152800 chr2D 29983526 29984216 690 True 1160.00 1160 96.9610 1 691 1 chr2D.!!$R2 690
7 TraesCS4D01G152800 chr2D 369876783 369877470 687 False 1155.00 1155 96.9480 1 688 1 chr2D.!!$F2 687
8 TraesCS4D01G152800 chr2D 33337866 33338379 513 True 647.00 647 89.3130 2338 2859 1 chr2D.!!$R3 521
9 TraesCS4D01G152800 chr2D 36535194 36535788 594 False 387.50 616 93.6525 1199 1828 2 chr2D.!!$F3 629
10 TraesCS4D01G152800 chr5D 509128392 509129079 687 False 1166.00 1166 97.2380 1 688 1 chr5D.!!$F1 687
11 TraesCS4D01G152800 chr5D 10495052 10495568 516 True 649.00 649 89.3130 2338 2859 1 chr5D.!!$R1 521
12 TraesCS4D01G152800 chr7D 522237844 522238531 687 False 1160.00 1160 97.0930 1 688 1 chr7D.!!$F1 687
13 TraesCS4D01G152800 chr7D 2872426 2872942 516 True 643.00 643 89.1220 2338 2859 1 chr7D.!!$R1 521
14 TraesCS4D01G152800 chr3D 334829881 334830568 687 False 1160.00 1160 97.0930 1 688 1 chr3D.!!$F2 687
15 TraesCS4D01G152800 chr3D 320811715 320812402 687 False 1155.00 1155 96.9480 1 688 1 chr3D.!!$F1 687
16 TraesCS4D01G152800 chr5B 76158356 76158873 517 False 584.00 584 87.0480 2338 2859 1 chr5B.!!$F2 521
17 TraesCS4D01G152800 chr5B 634278749 634280649 1900 True 556.75 883 93.0195 834 2859 4 chr5B.!!$R1 2025
18 TraesCS4D01G152800 chr6D 443355392 443355911 519 False 828.00 828 95.3850 2325 2844 1 chr6D.!!$F2 519
19 TraesCS4D01G152800 chr6D 443464573 443465094 521 False 808.00 808 94.6360 2325 2844 1 chr6D.!!$F3 519
20 TraesCS4D01G152800 chr2B 62546746 62547355 609 False 745.00 745 89.0320 1225 1828 1 chr2B.!!$F1 603
21 TraesCS4D01G152800 chrUn 427445403 427445986 583 False 737.00 737 89.2160 1156 1766 1 chrUn.!!$F1 610
22 TraesCS4D01G152800 chr1A 514433395 514433969 574 True 737.00 737 89.5520 1165 1766 1 chr1A.!!$R2 601
23 TraesCS4D01G152800 chr1A 514502681 514503255 574 True 737.00 737 89.5520 1165 1766 1 chr1A.!!$R3 601
24 TraesCS4D01G152800 chr1A 236302863 236303444 581 True 595.00 595 85.1060 1221 1828 1 chr1A.!!$R1 607
25 TraesCS4D01G152800 chr2A 40537623 40538218 595 False 686.00 686 87.4180 1221 1828 1 chr2A.!!$F3 607
26 TraesCS4D01G152800 chr3A 107617415 107617928 513 True 625.00 625 88.5710 2338 2859 1 chr3A.!!$R1 521
27 TraesCS4D01G152800 chr4A 410684521 410685096 575 True 603.00 603 85.4580 1156 1766 1 chr4A.!!$R2 610

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
742 743 0.167251 CGCGGTTTATTTTCGCTGGT 59.833 50.0 0.0 0.0 46.23 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2363 2500 0.898789 TGGAAGAGGAGGACGGTGAC 60.899 60.0 0.0 0.0 0.0 3.67 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
158 159 8.469309 TCTTCCTCATTTTCTTCAAATTCAGT 57.531 30.769 0.00 0.00 32.24 3.41
159 160 8.917088 TCTTCCTCATTTTCTTCAAATTCAGTT 58.083 29.630 0.00 0.00 32.24 3.16
202 203 0.392998 GAATGCCCGAGCCTTCTTGA 60.393 55.000 0.00 0.00 39.67 3.02
331 332 4.832823 TCTTCTTTGATTCCTTTTCCCACC 59.167 41.667 0.00 0.00 0.00 4.61
387 388 3.132646 TGCATTTGTGACAAAGCCTCTTT 59.867 39.130 16.43 0.00 0.00 2.52
453 454 0.603569 AGCGACCACGTCTTGAGAAT 59.396 50.000 0.00 0.00 41.98 2.40
470 471 9.305555 TCTTGAGAATTTCTGGAATTTCTTCAT 57.694 29.630 16.43 1.73 39.61 2.57
476 477 6.653526 TTTCTGGAATTTCTTCATGAGCAA 57.346 33.333 0.00 0.00 32.70 3.91
497 498 3.920231 TGCTAGATCATGGCTCAGTTT 57.080 42.857 0.00 0.00 36.12 2.66
530 531 1.055040 AGGCTGCTGTCAGAGTCTTT 58.945 50.000 3.32 0.00 42.95 2.52
688 689 2.337583 TGTAATCAGCACGCTCTTGTC 58.662 47.619 0.00 0.00 0.00 3.18
691 692 0.894141 ATCAGCACGCTCTTGTCTCT 59.106 50.000 0.00 0.00 0.00 3.10
692 693 1.534729 TCAGCACGCTCTTGTCTCTA 58.465 50.000 0.00 0.00 0.00 2.43
693 694 1.200252 TCAGCACGCTCTTGTCTCTAC 59.800 52.381 0.00 0.00 0.00 2.59
694 695 1.201181 CAGCACGCTCTTGTCTCTACT 59.799 52.381 0.00 0.00 0.00 2.57
695 696 1.470890 AGCACGCTCTTGTCTCTACTC 59.529 52.381 0.00 0.00 0.00 2.59
696 697 1.468395 GCACGCTCTTGTCTCTACTCC 60.468 57.143 0.00 0.00 0.00 3.85
697 698 2.088423 CACGCTCTTGTCTCTACTCCT 58.912 52.381 0.00 0.00 0.00 3.69
698 699 3.271729 CACGCTCTTGTCTCTACTCCTA 58.728 50.000 0.00 0.00 0.00 2.94
699 700 3.690139 CACGCTCTTGTCTCTACTCCTAA 59.310 47.826 0.00 0.00 0.00 2.69
700 701 4.336993 CACGCTCTTGTCTCTACTCCTAAT 59.663 45.833 0.00 0.00 0.00 1.73
701 702 4.336993 ACGCTCTTGTCTCTACTCCTAATG 59.663 45.833 0.00 0.00 0.00 1.90
702 703 4.261405 CGCTCTTGTCTCTACTCCTAATGG 60.261 50.000 0.00 0.00 0.00 3.16
703 704 4.890581 GCTCTTGTCTCTACTCCTAATGGA 59.109 45.833 0.00 0.00 40.69 3.41
704 705 5.221165 GCTCTTGTCTCTACTCCTAATGGAC 60.221 48.000 0.00 0.00 37.46 4.02
705 706 4.882427 TCTTGTCTCTACTCCTAATGGACG 59.118 45.833 0.00 0.00 37.46 4.79
706 707 4.498894 TGTCTCTACTCCTAATGGACGA 57.501 45.455 0.00 0.00 37.46 4.20
707 708 4.197750 TGTCTCTACTCCTAATGGACGAC 58.802 47.826 0.00 0.00 37.46 4.34
708 709 4.080469 TGTCTCTACTCCTAATGGACGACT 60.080 45.833 0.00 0.00 37.46 4.18
709 710 4.883006 GTCTCTACTCCTAATGGACGACTT 59.117 45.833 0.00 0.00 37.46 3.01
710 711 4.882427 TCTCTACTCCTAATGGACGACTTG 59.118 45.833 0.00 0.00 37.46 3.16
711 712 4.851843 TCTACTCCTAATGGACGACTTGA 58.148 43.478 0.00 0.00 37.46 3.02
712 713 5.446860 TCTACTCCTAATGGACGACTTGAT 58.553 41.667 0.00 0.00 37.46 2.57
713 714 4.392921 ACTCCTAATGGACGACTTGATG 57.607 45.455 0.00 0.00 37.46 3.07
714 715 4.023980 ACTCCTAATGGACGACTTGATGA 58.976 43.478 0.00 0.00 37.46 2.92
715 716 4.466370 ACTCCTAATGGACGACTTGATGAA 59.534 41.667 0.00 0.00 37.46 2.57
716 717 5.129485 ACTCCTAATGGACGACTTGATGAAT 59.871 40.000 0.00 0.00 37.46 2.57
717 718 6.323996 ACTCCTAATGGACGACTTGATGAATA 59.676 38.462 0.00 0.00 37.46 1.75
718 719 6.749139 TCCTAATGGACGACTTGATGAATAG 58.251 40.000 0.00 0.00 37.46 1.73
719 720 6.323996 TCCTAATGGACGACTTGATGAATAGT 59.676 38.462 0.00 0.00 37.46 2.12
720 721 6.642950 CCTAATGGACGACTTGATGAATAGTC 59.357 42.308 0.00 0.00 35.43 2.59
721 722 5.860941 ATGGACGACTTGATGAATAGTCT 57.139 39.130 0.00 0.00 38.86 3.24
722 723 5.661056 TGGACGACTTGATGAATAGTCTT 57.339 39.130 0.00 0.00 38.86 3.01
723 724 5.651530 TGGACGACTTGATGAATAGTCTTC 58.348 41.667 0.00 0.00 38.86 2.87
724 725 4.735822 GGACGACTTGATGAATAGTCTTCG 59.264 45.833 0.00 0.00 39.33 3.79
725 726 4.106197 ACGACTTGATGAATAGTCTTCGC 58.894 43.478 0.00 0.00 38.86 4.70
726 727 3.178618 CGACTTGATGAATAGTCTTCGCG 59.821 47.826 0.00 0.00 38.86 5.87
727 728 3.448686 ACTTGATGAATAGTCTTCGCGG 58.551 45.455 6.13 0.00 31.94 6.46
728 729 3.119101 ACTTGATGAATAGTCTTCGCGGT 60.119 43.478 6.13 0.00 31.94 5.68
729 730 3.520290 TGATGAATAGTCTTCGCGGTT 57.480 42.857 6.13 0.00 31.94 4.44
730 731 3.857052 TGATGAATAGTCTTCGCGGTTT 58.143 40.909 6.13 0.00 31.94 3.27
731 732 5.001237 TGATGAATAGTCTTCGCGGTTTA 57.999 39.130 6.13 0.00 31.94 2.01
732 733 5.597806 TGATGAATAGTCTTCGCGGTTTAT 58.402 37.500 6.13 0.00 31.94 1.40
733 734 6.046593 TGATGAATAGTCTTCGCGGTTTATT 58.953 36.000 6.13 4.24 31.94 1.40
734 735 6.537301 TGATGAATAGTCTTCGCGGTTTATTT 59.463 34.615 6.13 0.00 31.94 1.40
735 736 6.730960 TGAATAGTCTTCGCGGTTTATTTT 57.269 33.333 6.13 0.00 0.00 1.82
736 737 6.768078 TGAATAGTCTTCGCGGTTTATTTTC 58.232 36.000 6.13 3.85 0.00 2.29
737 738 3.717350 AGTCTTCGCGGTTTATTTTCG 57.283 42.857 6.13 0.00 0.00 3.46
738 739 2.159747 AGTCTTCGCGGTTTATTTTCGC 60.160 45.455 6.13 0.00 45.15 4.70
739 740 2.070783 TCTTCGCGGTTTATTTTCGCT 58.929 42.857 6.13 0.00 46.23 4.93
740 741 2.159761 TCTTCGCGGTTTATTTTCGCTG 60.160 45.455 6.13 0.00 46.23 5.18
741 742 0.444651 TCGCGGTTTATTTTCGCTGG 59.555 50.000 6.13 0.00 46.23 4.85
742 743 0.167251 CGCGGTTTATTTTCGCTGGT 59.833 50.000 0.00 0.00 46.23 4.00
743 744 1.400500 CGCGGTTTATTTTCGCTGGTT 60.400 47.619 0.00 0.00 46.23 3.67
744 745 2.668250 GCGGTTTATTTTCGCTGGTTT 58.332 42.857 0.00 0.00 45.16 3.27
745 746 3.054166 GCGGTTTATTTTCGCTGGTTTT 58.946 40.909 0.00 0.00 45.16 2.43
746 747 3.491639 GCGGTTTATTTTCGCTGGTTTTT 59.508 39.130 0.00 0.00 45.16 1.94
762 763 2.761160 TTTTTCGGCTCCTCCCCC 59.239 61.111 0.00 0.00 0.00 5.40
763 764 3.262448 TTTTTCGGCTCCTCCCCCG 62.262 63.158 0.00 0.00 45.64 5.73
783 784 4.802051 CCACCCCATCCCACGCAG 62.802 72.222 0.00 0.00 0.00 5.18
784 785 4.802051 CACCCCATCCCACGCAGG 62.802 72.222 0.00 0.00 37.03 4.85
793 794 4.323477 CCACGCAGGGACCCGAAA 62.323 66.667 4.40 0.00 0.00 3.46
794 795 2.281208 CACGCAGGGACCCGAAAA 60.281 61.111 4.40 0.00 0.00 2.29
795 796 1.894756 CACGCAGGGACCCGAAAAA 60.895 57.895 4.40 0.00 0.00 1.94
810 811 2.948448 AAAAACCCCACCCCTCCC 59.052 61.111 0.00 0.00 0.00 4.30
963 964 1.678970 GGGCAGGACGGCTTGAATT 60.679 57.895 3.68 0.00 40.90 2.17
1381 1445 1.667722 CAAAAGTCCCTGGCCAAGC 59.332 57.895 7.01 0.00 0.00 4.01
1416 1480 1.140816 GCTCTCTCAACGTGTTCACC 58.859 55.000 0.00 0.00 0.00 4.02
1921 2054 2.186826 GTCAAATCCCCATCCCGCG 61.187 63.158 0.00 0.00 0.00 6.46
2220 2357 0.554792 CCTGGGATTCATCAAGGGCT 59.445 55.000 0.00 0.00 31.86 5.19
2252 2389 4.569564 ACGTTTAATCTCGGTATTCTTGGC 59.430 41.667 0.00 0.00 0.00 4.52
2708 2849 5.776716 ACAAGATCATTGGTTCCATTCTGTT 59.223 36.000 0.00 0.00 0.00 3.16
2793 2936 3.564027 GCTTCATTCGCGGACCGG 61.564 66.667 17.22 0.00 37.59 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 112 2.216898 GAGGCATTTGAGGATTCCGAG 58.783 52.381 0.00 0.00 0.00 4.63
158 159 3.157087 GGCAAGGAAATGGACTCTGAAA 58.843 45.455 0.00 0.00 0.00 2.69
159 160 2.108075 TGGCAAGGAAATGGACTCTGAA 59.892 45.455 0.00 0.00 0.00 3.02
202 203 3.007723 TCATCTCACAAGAAGAGCAGCTT 59.992 43.478 0.00 0.00 40.25 3.74
331 332 5.171476 ACACTACATTCAAGATTGTCCTCG 58.829 41.667 1.30 0.00 0.00 4.63
387 388 5.248248 TGATTCCTCATCCAGTGACTACAAA 59.752 40.000 0.00 0.00 32.22 2.83
453 454 6.653526 TTGCTCATGAAGAAATTCCAGAAA 57.346 33.333 0.00 0.00 0.00 2.52
470 471 2.105993 AGCCATGATCTAGCATTGCTCA 59.894 45.455 15.81 7.62 41.72 4.26
476 477 4.434545 AAACTGAGCCATGATCTAGCAT 57.565 40.909 0.00 0.00 0.00 3.79
497 498 1.887956 GCAGCCTTGGTGATCCTGAAA 60.888 52.381 0.00 0.00 32.22 2.69
530 531 4.774726 AGGCAGTTTCTGAGTCTGAAGATA 59.225 41.667 11.68 0.00 32.44 1.98
688 689 4.882427 TCAAGTCGTCCATTAGGAGTAGAG 59.118 45.833 0.00 0.00 46.92 2.43
691 692 5.198207 TCATCAAGTCGTCCATTAGGAGTA 58.802 41.667 0.00 0.00 46.92 2.59
692 693 4.023980 TCATCAAGTCGTCCATTAGGAGT 58.976 43.478 0.00 0.00 46.92 3.85
693 694 4.655762 TCATCAAGTCGTCCATTAGGAG 57.344 45.455 0.00 0.00 46.92 3.69
694 695 5.614324 ATTCATCAAGTCGTCCATTAGGA 57.386 39.130 0.00 0.00 43.21 2.94
695 696 6.516718 ACTATTCATCAAGTCGTCCATTAGG 58.483 40.000 0.00 0.00 0.00 2.69
696 697 7.429633 AGACTATTCATCAAGTCGTCCATTAG 58.570 38.462 0.00 0.00 45.47 1.73
697 698 7.348080 AGACTATTCATCAAGTCGTCCATTA 57.652 36.000 0.00 0.00 45.47 1.90
698 699 6.227298 AGACTATTCATCAAGTCGTCCATT 57.773 37.500 0.00 0.00 45.47 3.16
699 700 5.860941 AGACTATTCATCAAGTCGTCCAT 57.139 39.130 0.00 0.00 45.47 3.41
700 701 5.651530 GAAGACTATTCATCAAGTCGTCCA 58.348 41.667 7.03 0.00 45.47 4.02
701 702 4.735822 CGAAGACTATTCATCAAGTCGTCC 59.264 45.833 11.13 0.00 43.78 4.79
702 703 4.205385 GCGAAGACTATTCATCAAGTCGTC 59.795 45.833 7.93 7.93 45.47 4.20
703 704 4.106197 GCGAAGACTATTCATCAAGTCGT 58.894 43.478 0.00 0.00 45.47 4.34
704 705 3.178618 CGCGAAGACTATTCATCAAGTCG 59.821 47.826 0.00 0.00 45.47 4.18
705 706 3.487574 CCGCGAAGACTATTCATCAAGTC 59.512 47.826 8.23 0.00 42.02 3.01
706 707 3.119101 ACCGCGAAGACTATTCATCAAGT 60.119 43.478 8.23 0.00 0.00 3.16
707 708 3.448686 ACCGCGAAGACTATTCATCAAG 58.551 45.455 8.23 0.00 0.00 3.02
708 709 3.520290 ACCGCGAAGACTATTCATCAA 57.480 42.857 8.23 0.00 0.00 2.57
709 710 3.520290 AACCGCGAAGACTATTCATCA 57.480 42.857 8.23 0.00 0.00 3.07
710 711 6.526566 AATAAACCGCGAAGACTATTCATC 57.473 37.500 8.23 0.00 0.00 2.92
711 712 6.920569 AAATAAACCGCGAAGACTATTCAT 57.079 33.333 8.23 0.00 0.00 2.57
712 713 6.454583 CGAAAATAAACCGCGAAGACTATTCA 60.455 38.462 8.23 0.00 0.00 2.57
713 714 5.894807 CGAAAATAAACCGCGAAGACTATTC 59.105 40.000 8.23 3.85 0.00 1.75
714 715 5.725864 GCGAAAATAAACCGCGAAGACTATT 60.726 40.000 8.23 0.32 39.54 1.73
715 716 4.260091 GCGAAAATAAACCGCGAAGACTAT 60.260 41.667 8.23 0.00 39.54 2.12
716 717 3.061161 GCGAAAATAAACCGCGAAGACTA 59.939 43.478 8.23 0.00 39.54 2.59
717 718 2.159747 GCGAAAATAAACCGCGAAGACT 60.160 45.455 8.23 0.00 39.54 3.24
718 719 2.163638 GCGAAAATAAACCGCGAAGAC 58.836 47.619 8.23 0.00 39.54 3.01
719 720 2.513964 GCGAAAATAAACCGCGAAGA 57.486 45.000 8.23 0.00 39.54 2.87
745 746 2.761160 GGGGGAGGAGCCGAAAAA 59.239 61.111 0.00 0.00 37.63 1.94
746 747 3.712907 CGGGGGAGGAGCCGAAAA 61.713 66.667 0.00 0.00 37.63 2.29
766 767 4.802051 CTGCGTGGGATGGGGTGG 62.802 72.222 0.00 0.00 0.00 4.61
767 768 4.802051 CCTGCGTGGGATGGGGTG 62.802 72.222 0.00 0.00 0.00 4.61
776 777 3.835790 TTTTCGGGTCCCTGCGTGG 62.836 63.158 6.29 0.00 0.00 4.94
777 778 1.894756 TTTTTCGGGTCCCTGCGTG 60.895 57.895 6.29 0.00 0.00 5.34
778 779 2.511900 TTTTTCGGGTCCCTGCGT 59.488 55.556 6.29 0.00 0.00 5.24
793 794 2.797075 GGGGAGGGGTGGGGTTTTT 61.797 63.158 0.00 0.00 0.00 1.94
794 795 3.197895 GGGGAGGGGTGGGGTTTT 61.198 66.667 0.00 0.00 0.00 2.43
915 916 4.680537 AGCGGTGTCTCCCCTCGT 62.681 66.667 0.00 0.00 0.00 4.18
963 964 1.906824 GGCGATCCCGGTGATAGGA 60.907 63.158 0.00 0.00 32.41 2.94
1416 1480 3.838795 GCGTTGTACTCCGCTGCG 61.839 66.667 16.34 16.34 46.08 5.18
1950 2083 1.212751 GCACACCGGAAAGAATGCC 59.787 57.895 9.46 0.00 0.00 4.40
2220 2357 2.159894 CGAGATTAAACGTTCGCTTGCA 60.160 45.455 0.00 0.00 0.00 4.08
2252 2389 3.057104 TGCTTCAAATCATTCAGGCACAG 60.057 43.478 0.00 0.00 0.00 3.66
2363 2500 0.898789 TGGAAGAGGAGGACGGTGAC 60.899 60.000 0.00 0.00 0.00 3.67
2708 2849 3.731136 GCAGAGCGGTGTCACAAA 58.269 55.556 5.12 0.00 0.00 2.83
2793 2936 1.227853 ACACTTCCCACGGTGCTTC 60.228 57.895 1.68 0.00 36.99 3.86


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

AutoCloner maintained by Alex Coulton.