Multiple sequence alignment - TraesCS3A01G141700

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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 TraesCS3A01G141700 chr3A 100.000 3347 0 0 1 3347 121316301 121319647 0.000000e+00 6181.0
1 TraesCS3A01G141700 chr3A 97.858 1587 22 8 804 2384 121235377 121236957 0.000000e+00 2732.0
2 TraesCS3A01G141700 chr3A 84.942 1202 143 15 1053 2230 121479401 121480588 0.000000e+00 1182.0
3 TraesCS3A01G141700 chr3A 93.333 480 29 2 1 477 121234599 121235078 0.000000e+00 706.0
4 TraesCS3A01G141700 chr3A 85.068 221 24 4 2018 2230 121482464 121482683 2.020000e-52 217.0
5 TraesCS3A01G141700 chr3D 92.144 1884 91 21 828 2664 109271730 109269857 0.000000e+00 2606.0
6 TraesCS3A01G141700 chr3D 87.869 643 72 1 1594 2230 108953888 108953246 0.000000e+00 750.0
7 TraesCS3A01G141700 chr3D 90.750 400 23 9 93 479 109273246 109272848 3.830000e-144 521.0
8 TraesCS3A01G141700 chr3D 85.714 490 61 4 1053 1539 108954447 108953964 2.980000e-140 508.0
9 TraesCS3A01G141700 chr3D 91.304 161 13 1 2710 2870 109269858 109269699 5.620000e-53 219.0
10 TraesCS3A01G141700 chr3D 90.909 88 8 0 1 88 109273659 109273572 5.870000e-23 119.0
11 TraesCS3A01G141700 chr3B 93.991 1481 52 9 820 2263 160641236 160639756 0.000000e+00 2207.0
12 TraesCS3A01G141700 chr3B 84.909 1206 145 22 1053 2230 160368133 160366937 0.000000e+00 1184.0
13 TraesCS3A01G141700 chr3B 91.498 494 30 3 1 482 160642848 160642355 0.000000e+00 669.0
14 TraesCS3A01G141700 chr3B 81.658 736 80 34 2573 3288 160634614 160633914 8.110000e-156 560.0
15 TraesCS3A01G141700 chr3B 91.156 147 7 2 2248 2394 160639739 160639599 9.480000e-46 195.0
16 TraesCS3A01G141700 chr3B 92.982 57 4 0 3291 3347 160633887 160633831 2.140000e-12 84.2
17 TraesCS3A01G141700 chr5D 86.207 1247 136 24 988 2202 27540048 27541290 0.000000e+00 1317.0
18 TraesCS3A01G141700 chr5B 82.703 925 120 23 969 1858 20628697 20627778 0.000000e+00 785.0
19 TraesCS3A01G141700 chr5B 90.141 355 35 0 1854 2208 20627556 20627202 2.350000e-126 462.0
20 TraesCS3A01G141700 chr5A 82.857 910 111 29 988 1858 18857122 18858025 0.000000e+00 774.0
21 TraesCS3A01G141700 chr5A 90.196 357 35 0 1854 2210 18858240 18858596 1.820000e-127 466.0
22 TraesCS3A01G141700 chrUn 83.388 614 83 8 1599 2204 329101084 329100482 4.880000e-153 551.0
23 TraesCS3A01G141700 chrUn 83.388 614 83 8 1599 2204 380933078 380932476 4.880000e-153 551.0


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 TraesCS3A01G141700 chr3A 121316301 121319647 3346 False 6181.000000 6181 100.00000 1 3347 1 chr3A.!!$F1 3346
1 TraesCS3A01G141700 chr3A 121234599 121236957 2358 False 1719.000000 2732 95.59550 1 2384 2 chr3A.!!$F2 2383
2 TraesCS3A01G141700 chr3A 121479401 121482683 3282 False 699.500000 1182 85.00500 1053 2230 2 chr3A.!!$F3 1177
3 TraesCS3A01G141700 chr3D 109269699 109273659 3960 True 866.250000 2606 91.27675 1 2870 4 chr3D.!!$R2 2869
4 TraesCS3A01G141700 chr3D 108953246 108954447 1201 True 629.000000 750 86.79150 1053 2230 2 chr3D.!!$R1 1177
5 TraesCS3A01G141700 chr3B 160366937 160368133 1196 True 1184.000000 1184 84.90900 1053 2230 1 chr3B.!!$R1 1177
6 TraesCS3A01G141700 chr3B 160639599 160642848 3249 True 1023.666667 2207 92.21500 1 2394 3 chr3B.!!$R3 2393
7 TraesCS3A01G141700 chr3B 160633831 160634614 783 True 322.100000 560 87.32000 2573 3347 2 chr3B.!!$R2 774
8 TraesCS3A01G141700 chr5D 27540048 27541290 1242 False 1317.000000 1317 86.20700 988 2202 1 chr5D.!!$F1 1214
9 TraesCS3A01G141700 chr5B 20627202 20628697 1495 True 623.500000 785 86.42200 969 2208 2 chr5B.!!$R1 1239
10 TraesCS3A01G141700 chr5A 18857122 18858596 1474 False 620.000000 774 86.52650 988 2210 2 chr5A.!!$F1 1222
11 TraesCS3A01G141700 chrUn 329100482 329101084 602 True 551.000000 551 83.38800 1599 2204 1 chrUn.!!$R1 605
12 TraesCS3A01G141700 chrUn 380932476 380933078 602 True 551.000000 551 83.38800 1599 2204 1 chrUn.!!$R2 605

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
429 766 0.909623 AACCCGAGGGATGTCGATTT 59.090 50.0 16.26 0.0 42.85 2.17 F
606 1092 2.456073 ATACTACTCACGCCTCCCTT 57.544 50.0 0.00 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 2953 1.019673 CCAGCATGACACTGCCATAC 58.980 55.000 0.0 0.0 43.33 2.39 R
2579 4562 1.747206 CGGTGAAATCCCAGATCCCAC 60.747 57.143 0.0 0.0 0.00 4.61 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
134 456 7.393234 TCACTTTTTCCTCAAGAAAGAACAAGA 59.607 33.333 11.97 0.00 45.11 3.02
164 487 7.875041 AGCAATCACTAGCATATTCGATAACTT 59.125 33.333 0.00 0.00 0.00 2.66
186 509 9.444600 AACTTTAAAGAGGCATAATCTAAACGA 57.555 29.630 21.92 0.00 0.00 3.85
301 629 3.760684 ACTATCGAACGTCTGGGTTAGTT 59.239 43.478 0.00 0.00 0.00 2.24
304 632 1.790623 CGAACGTCTGGGTTAGTTGTG 59.209 52.381 0.00 0.00 0.00 3.33
305 633 2.544277 CGAACGTCTGGGTTAGTTGTGA 60.544 50.000 0.00 0.00 0.00 3.58
306 634 2.521105 ACGTCTGGGTTAGTTGTGAC 57.479 50.000 0.00 0.00 0.00 3.67
307 635 1.069668 ACGTCTGGGTTAGTTGTGACC 59.930 52.381 0.00 0.00 35.14 4.02
308 636 1.343465 CGTCTGGGTTAGTTGTGACCT 59.657 52.381 0.00 0.00 36.18 3.85
412 749 2.099098 CGGAATAATGCCTCAACCCAAC 59.901 50.000 0.00 0.00 0.00 3.77
429 766 0.909623 AACCCGAGGGATGTCGATTT 59.090 50.000 16.26 0.00 42.85 2.17
457 794 4.925068 ACGCATGCCTCATAATTTTCTTC 58.075 39.130 13.15 0.00 0.00 2.87
466 803 6.017109 GCCTCATAATTTTCTTCGAATAGGCA 60.017 38.462 0.00 0.00 43.20 4.75
467 804 7.579726 CCTCATAATTTTCTTCGAATAGGCAG 58.420 38.462 0.00 0.00 0.00 4.85
468 805 7.442364 CCTCATAATTTTCTTCGAATAGGCAGA 59.558 37.037 0.00 0.00 0.00 4.26
469 806 8.731275 TCATAATTTTCTTCGAATAGGCAGAA 57.269 30.769 0.00 0.00 0.00 3.02
470 807 9.173021 TCATAATTTTCTTCGAATAGGCAGAAA 57.827 29.630 0.00 0.53 34.23 2.52
471 808 9.226345 CATAATTTTCTTCGAATAGGCAGAAAC 57.774 33.333 7.12 0.00 35.48 2.78
472 809 7.454260 AATTTTCTTCGAATAGGCAGAAACT 57.546 32.000 7.12 0.87 35.48 2.66
473 810 6.877611 TTTTCTTCGAATAGGCAGAAACTT 57.122 33.333 7.12 0.00 35.48 2.66
474 811 7.972832 TTTTCTTCGAATAGGCAGAAACTTA 57.027 32.000 7.12 0.00 35.48 2.24
475 812 7.972832 TTTCTTCGAATAGGCAGAAACTTAA 57.027 32.000 0.00 0.00 31.70 1.85
476 813 7.972832 TTCTTCGAATAGGCAGAAACTTAAA 57.027 32.000 0.00 0.00 0.00 1.52
477 814 7.972832 TCTTCGAATAGGCAGAAACTTAAAA 57.027 32.000 0.00 0.00 0.00 1.52
478 815 8.385898 TCTTCGAATAGGCAGAAACTTAAAAA 57.614 30.769 0.00 0.00 0.00 1.94
479 816 8.504005 TCTTCGAATAGGCAGAAACTTAAAAAG 58.496 33.333 0.00 0.00 0.00 2.27
480 817 7.739498 TCGAATAGGCAGAAACTTAAAAAGT 57.261 32.000 0.00 0.00 45.46 2.66
533 870 7.923414 AAGTTCACTATCCCAACATAGTTTC 57.077 36.000 0.00 0.00 37.47 2.78
534 871 7.259088 AGTTCACTATCCCAACATAGTTTCT 57.741 36.000 0.00 0.00 37.47 2.52
546 883 7.254898 CCCAACATAGTTTCTGTACATATGCAG 60.255 40.741 11.58 3.31 39.75 4.41
558 895 7.709182 TCTGTACATATGCAGCGTAAAAATACT 59.291 33.333 1.58 0.00 38.37 2.12
559 896 8.874744 TGTACATATGCAGCGTAAAAATACTA 57.125 30.769 1.58 0.00 0.00 1.82
606 1092 2.456073 ATACTACTCACGCCTCCCTT 57.544 50.000 0.00 0.00 0.00 3.95
612 1098 4.523558 ACTACTCACGCCTCCCTTAATATC 59.476 45.833 0.00 0.00 0.00 1.63
613 1099 3.577919 ACTCACGCCTCCCTTAATATCT 58.422 45.455 0.00 0.00 0.00 1.98
617 1103 4.654262 TCACGCCTCCCTTAATATCTTCTT 59.346 41.667 0.00 0.00 0.00 2.52
618 1104 5.836898 TCACGCCTCCCTTAATATCTTCTTA 59.163 40.000 0.00 0.00 0.00 2.10
619 1105 6.325545 TCACGCCTCCCTTAATATCTTCTTAA 59.674 38.462 0.00 0.00 0.00 1.85
621 1107 8.311836 CACGCCTCCCTTAATATCTTCTTAATA 58.688 37.037 0.00 0.00 0.00 0.98
665 1845 6.333416 TGAGACAGAGATAGTACATGTTTGC 58.667 40.000 2.30 0.00 0.00 3.68
674 1856 4.514781 AGTACATGTTTGCGTACTCTCA 57.485 40.909 2.30 0.00 43.76 3.27
676 1858 3.386768 ACATGTTTGCGTACTCTCACT 57.613 42.857 0.00 0.00 0.00 3.41
682 1864 4.743151 TGTTTGCGTACTCTCACTGTAAAG 59.257 41.667 0.00 0.00 0.00 1.85
688 1870 5.392165 GCGTACTCTCACTGTAAAGTGATCT 60.392 44.000 16.22 4.64 46.24 2.75
689 1871 6.183360 GCGTACTCTCACTGTAAAGTGATCTA 60.183 42.308 16.22 4.73 46.24 1.98
691 1873 8.399425 CGTACTCTCACTGTAAAGTGATCTAAT 58.601 37.037 16.22 3.91 46.24 1.73
693 1875 8.354711 ACTCTCACTGTAAAGTGATCTAATCA 57.645 34.615 16.22 0.00 46.24 2.57
694 1876 8.976353 ACTCTCACTGTAAAGTGATCTAATCAT 58.024 33.333 16.22 0.00 46.24 2.45
721 1903 9.891828 TTTTATGCAGTATTTGTTTACAGAGTG 57.108 29.630 0.00 0.00 0.00 3.51
731 1913 7.684062 TTTGTTTACAGAGTGAGTACGTAAC 57.316 36.000 0.00 0.00 0.00 2.50
806 1988 7.701924 GCTTGATCATTGGAAACGAATCATAAA 59.298 33.333 0.00 0.00 0.00 1.40
813 2037 5.708948 TGGAAACGAATCATAAAGCCTTTG 58.291 37.500 0.00 0.00 0.00 2.77
818 2042 4.887071 ACGAATCATAAAGCCTTTGCCATA 59.113 37.500 0.00 0.00 38.69 2.74
822 2046 8.081633 CGAATCATAAAGCCTTTGCCATATTTA 58.918 33.333 0.00 0.00 38.69 1.40
823 2047 9.196552 GAATCATAAAGCCTTTGCCATATTTAC 57.803 33.333 0.00 0.00 38.69 2.01
824 2048 7.652524 TCATAAAGCCTTTGCCATATTTACA 57.347 32.000 0.00 0.00 38.69 2.41
825 2049 7.488322 TCATAAAGCCTTTGCCATATTTACAC 58.512 34.615 0.00 0.00 38.69 2.90
826 2050 4.736126 AAGCCTTTGCCATATTTACACC 57.264 40.909 0.00 0.00 38.69 4.16
827 2051 3.707316 AGCCTTTGCCATATTTACACCA 58.293 40.909 0.00 0.00 38.69 4.17
828 2052 4.093011 AGCCTTTGCCATATTTACACCAA 58.907 39.130 0.00 0.00 38.69 3.67
829 2053 4.530161 AGCCTTTGCCATATTTACACCAAA 59.470 37.500 0.00 0.00 38.69 3.28
1570 2923 3.375299 GCTCAGGTTCATATGTTGGTCAC 59.625 47.826 1.90 0.00 0.00 3.67
1588 2941 5.475909 TGGTCACTTCTTGTAGAGTAACGAT 59.524 40.000 0.00 0.00 0.00 3.73
1589 2942 6.656270 TGGTCACTTCTTGTAGAGTAACGATA 59.344 38.462 0.00 0.00 0.00 2.92
1590 2943 7.338703 TGGTCACTTCTTGTAGAGTAACGATAT 59.661 37.037 0.00 0.00 0.00 1.63
1591 2944 7.644551 GGTCACTTCTTGTAGAGTAACGATATG 59.355 40.741 0.00 0.00 0.00 1.78
1592 2945 8.182881 GTCACTTCTTGTAGAGTAACGATATGT 58.817 37.037 0.00 0.00 0.00 2.29
2401 4373 9.474313 AAATTAATAGTTGGGCAATCAGTAAGA 57.526 29.630 0.00 0.00 0.00 2.10
2402 4374 9.474313 AATTAATAGTTGGGCAATCAGTAAGAA 57.526 29.630 0.00 0.00 0.00 2.52
2403 4375 8.871629 TTAATAGTTGGGCAATCAGTAAGAAA 57.128 30.769 0.00 0.00 0.00 2.52
2407 4379 5.416952 AGTTGGGCAATCAGTAAGAAAGATG 59.583 40.000 0.00 0.00 0.00 2.90
2409 4381 3.067320 GGGCAATCAGTAAGAAAGATGGC 59.933 47.826 0.00 0.00 37.86 4.40
2411 4383 4.036144 GGCAATCAGTAAGAAAGATGGCTC 59.964 45.833 0.00 0.00 38.48 4.70
2412 4384 4.036144 GCAATCAGTAAGAAAGATGGCTCC 59.964 45.833 0.00 0.00 36.12 4.70
2413 4385 5.188434 CAATCAGTAAGAAAGATGGCTCCA 58.812 41.667 0.00 0.00 0.00 3.86
2414 4386 4.478206 TCAGTAAGAAAGATGGCTCCAG 57.522 45.455 0.00 0.00 0.00 3.86
2416 4388 3.937706 CAGTAAGAAAGATGGCTCCAGTG 59.062 47.826 0.00 0.00 0.00 3.66
2417 4389 3.584848 AGTAAGAAAGATGGCTCCAGTGT 59.415 43.478 0.00 0.00 0.00 3.55
2431 4414 5.010719 GGCTCCAGTGTACTATATACTTGCA 59.989 44.000 0.00 0.00 0.00 4.08
2437 4420 7.360361 CAGTGTACTATATACTTGCATCGACA 58.640 38.462 0.00 0.00 0.00 4.35
2470 4453 3.507233 ACATTTCAACATGGCGTGATCTT 59.493 39.130 14.82 0.00 0.00 2.40
2473 4456 6.542005 ACATTTCAACATGGCGTGATCTTATA 59.458 34.615 14.82 0.00 0.00 0.98
2480 4463 6.705302 ACATGGCGTGATCTTATATCAGAAT 58.295 36.000 14.82 0.00 0.00 2.40
2514 4497 0.109272 GCGTAAGGGGAAGCAAAAGC 60.109 55.000 0.00 0.00 38.28 3.51
2517 4500 3.078837 CGTAAGGGGAAGCAAAAGCTTA 58.921 45.455 0.00 0.00 0.00 3.09
2524 4507 4.202212 GGGGAAGCAAAAGCTTACTGAAAA 60.202 41.667 11.78 0.00 31.67 2.29
2565 4548 1.141881 CGGCCTGAAGCGTCATAGT 59.858 57.895 1.88 0.00 45.17 2.12
2666 4733 4.349663 TTCATTAAAATTGGACTCGCCG 57.650 40.909 0.00 0.00 40.66 6.46
2667 4734 3.340034 TCATTAAAATTGGACTCGCCGT 58.660 40.909 0.00 0.00 40.66 5.68
2668 4735 3.126171 TCATTAAAATTGGACTCGCCGTG 59.874 43.478 0.00 0.00 40.66 4.94
2669 4736 2.459060 TAAAATTGGACTCGCCGTGA 57.541 45.000 0.00 0.00 40.66 4.35
2670 4737 0.872388 AAAATTGGACTCGCCGTGAC 59.128 50.000 0.00 0.00 40.66 3.67
2671 4738 0.250124 AAATTGGACTCGCCGTGACA 60.250 50.000 0.00 0.00 40.66 3.58
2672 4739 0.949105 AATTGGACTCGCCGTGACAC 60.949 55.000 0.00 0.00 40.66 3.67
2674 4741 4.736896 GGACTCGCCGTGACACCC 62.737 72.222 0.00 0.00 0.00 4.61
2753 4821 2.350522 GAACTCGGCAATGTCTCACAT 58.649 47.619 0.00 0.00 41.31 3.21
2776 4844 7.394923 ACATTCCTCGAGTTCCTCCTAATATAG 59.605 40.741 12.31 0.00 0.00 1.31
2785 4853 9.095700 GAGTTCCTCCTAATATAGACTTGGAAT 57.904 37.037 0.00 0.00 34.27 3.01
2860 4932 1.054406 CCCCACAGACGACCCCATAT 61.054 60.000 0.00 0.00 0.00 1.78
2864 4936 1.613925 CACAGACGACCCCATATCGAT 59.386 52.381 2.16 2.16 42.25 3.59
2876 4948 6.833041 ACCCCATATCGATGTTACATGTTTA 58.167 36.000 8.54 0.00 0.00 2.01
2878 4950 6.708502 CCCCATATCGATGTTACATGTTTACA 59.291 38.462 8.54 9.82 0.00 2.41
2887 4959 7.148869 CGATGTTACATGTTTACAGAAACTCGA 60.149 37.037 18.79 0.00 44.52 4.04
2892 4964 6.888430 ACATGTTTACAGAAACTCGACAATC 58.112 36.000 0.00 0.00 44.52 2.67
2898 4970 8.734030 GTTTACAGAAACTCGACAATCTTTTTG 58.266 33.333 0.00 0.00 41.55 2.44
2899 4971 5.273944 ACAGAAACTCGACAATCTTTTTGC 58.726 37.500 0.00 0.00 0.00 3.68
2900 4972 5.163663 ACAGAAACTCGACAATCTTTTTGCA 60.164 36.000 0.00 0.00 0.00 4.08
2901 4973 5.916883 CAGAAACTCGACAATCTTTTTGCAT 59.083 36.000 0.00 0.00 0.00 3.96
2903 4975 7.591057 CAGAAACTCGACAATCTTTTTGCATTA 59.409 33.333 0.00 0.00 0.00 1.90
2906 5037 8.452989 AACTCGACAATCTTTTTGCATTATTC 57.547 30.769 0.00 0.00 0.00 1.75
2919 5050 8.873215 TTTTGCATTATTCTTTTTGTTACGGA 57.127 26.923 0.00 0.00 0.00 4.69
2934 5065 6.730960 TGTTACGGAAATTCCATAAGTCAC 57.269 37.500 13.04 4.33 35.91 3.67
2935 5066 6.231951 TGTTACGGAAATTCCATAAGTCACA 58.768 36.000 13.04 6.74 35.91 3.58
2936 5067 6.370442 TGTTACGGAAATTCCATAAGTCACAG 59.630 38.462 13.04 0.00 35.91 3.66
2937 5068 4.906618 ACGGAAATTCCATAAGTCACAGT 58.093 39.130 13.04 0.00 35.91 3.55
2950 5081 0.608130 TCACAGTTATGCCGAGCACT 59.392 50.000 0.50 0.00 43.04 4.40
2951 5082 1.002366 CACAGTTATGCCGAGCACTC 58.998 55.000 0.50 0.00 43.04 3.51
2966 5097 2.987149 AGCACTCGTGTAAATGAACTCG 59.013 45.455 0.00 0.00 37.62 4.18
2970 5101 4.443063 CACTCGTGTAAATGAACTCGACAA 59.557 41.667 0.00 0.00 39.60 3.18
2982 5113 5.830912 TGAACTCGACAATCATTTTGCTTT 58.169 33.333 0.00 0.00 0.00 3.51
3011 5816 9.932207 TTATTAGAAAATTCAAGGAGTCACGTA 57.068 29.630 0.00 0.00 0.00 3.57
3023 5828 3.194861 GAGTCACGTATATGCCAAGCAA 58.805 45.455 0.00 0.00 43.62 3.91
3025 5830 2.031683 GTCACGTATATGCCAAGCAACC 59.968 50.000 0.00 0.00 43.62 3.77
3026 5831 2.013400 CACGTATATGCCAAGCAACCA 58.987 47.619 0.00 0.00 43.62 3.67
3027 5832 2.618241 CACGTATATGCCAAGCAACCAT 59.382 45.455 0.00 0.00 43.62 3.55
3055 5860 9.991388 GAGATATACTCGGTAAACAGCTAATAG 57.009 37.037 0.00 0.00 35.84 1.73
3080 5885 2.346803 GCCTGTGTGACACGTATCAAT 58.653 47.619 11.51 0.00 37.14 2.57
3092 5897 5.093457 ACACGTATCAATGACTAACTGACG 58.907 41.667 0.00 0.00 0.00 4.35
3099 5904 0.034337 TGACTAACTGACGGTTGGCC 59.966 55.000 10.03 0.00 39.56 5.36
3115 5920 1.069935 GCCTTCCTATGCCGAGGTC 59.930 63.158 1.19 0.00 37.88 3.85
3134 5939 1.533731 TCGAAAACTAGGCAAAAGGCG 59.466 47.619 0.00 0.00 46.16 5.52
3145 5950 2.064573 CAAAAGGCGGACCATTTGTC 57.935 50.000 4.97 0.00 45.41 3.18
3163 5968 0.545787 TCCACTTAAAGGGGAGCGGA 60.546 55.000 0.00 0.00 44.45 5.54
3201 6103 4.643387 ACGCAAAAGCCCTCGCCT 62.643 61.111 0.00 0.00 34.57 5.52
3203 6105 2.985847 GCAAAAGCCCTCGCCTGT 60.986 61.111 0.00 0.00 34.57 4.00
3207 6109 1.198759 AAAAGCCCTCGCCTGTCCTA 61.199 55.000 0.00 0.00 34.57 2.94
3208 6110 1.617947 AAAGCCCTCGCCTGTCCTAG 61.618 60.000 0.00 0.00 34.57 3.02
3210 6112 2.443016 CCCTCGCCTGTCCTAGCT 60.443 66.667 0.00 0.00 0.00 3.32
3217 6119 0.972983 GCCTGTCCTAGCTGTCTCCA 60.973 60.000 0.00 0.00 0.00 3.86
3219 6121 2.114616 CCTGTCCTAGCTGTCTCCATT 58.885 52.381 0.00 0.00 0.00 3.16
3224 6126 3.198853 GTCCTAGCTGTCTCCATTTCCTT 59.801 47.826 0.00 0.00 0.00 3.36
3233 6135 4.120589 GTCTCCATTTCCTTCGATACACC 58.879 47.826 0.00 0.00 0.00 4.16
3236 6138 3.055675 TCCATTTCCTTCGATACACCGTT 60.056 43.478 0.00 0.00 0.00 4.44
3243 6145 2.162754 CGATACACCGTTGCCGTCC 61.163 63.158 0.00 0.00 0.00 4.79
3262 6164 3.535962 GCCGCCCTCTCTCCTCAG 61.536 72.222 0.00 0.00 0.00 3.35
3264 6166 3.535962 CGCCCTCTCTCCTCAGCC 61.536 72.222 0.00 0.00 0.00 4.85
3266 6168 2.433994 GCCCTCTCTCCTCAGCCTG 61.434 68.421 0.00 0.00 0.00 4.85
3271 6174 1.682854 CTCTCTCCTCAGCCTGTCATC 59.317 57.143 0.00 0.00 0.00 2.92
3276 6179 1.508545 CTCAGCCTGTCATCGTCGT 59.491 57.895 0.00 0.00 0.00 4.34
3288 6191 1.270826 CATCGTCGTATGGATCTGGCT 59.729 52.381 0.00 0.00 0.00 4.75
3289 6192 0.952280 TCGTCGTATGGATCTGGCTC 59.048 55.000 0.00 0.00 0.00 4.70
3338 6317 8.588472 TGTATAACTAGAACATGCAGCTGATAT 58.412 33.333 20.43 8.07 0.00 1.63
3339 6318 9.429359 GTATAACTAGAACATGCAGCTGATATT 57.571 33.333 20.43 5.20 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 7.147811 TGCAGTAAGTTCATAAACTGGGTTTTT 60.148 33.333 5.18 0.00 45.07 1.94
105 427 6.683974 TCTTTCTTGAGGAAAAAGTGACTG 57.316 37.500 0.00 0.00 42.52 3.51
134 456 4.445718 CGAATATGCTAGTGATTGCTCGTT 59.554 41.667 0.00 0.00 0.00 3.85
292 620 5.772393 AATATCAGGTCACAACTAACCCA 57.228 39.130 0.00 0.00 36.11 4.51
294 622 8.958119 TCATAAATATCAGGTCACAACTAACC 57.042 34.615 0.00 0.00 35.69 2.85
301 629 6.829849 TGCATCTCATAAATATCAGGTCACA 58.170 36.000 0.00 0.00 0.00 3.58
304 632 5.936372 TGCTGCATCTCATAAATATCAGGTC 59.064 40.000 0.00 0.00 0.00 3.85
305 633 5.704515 GTGCTGCATCTCATAAATATCAGGT 59.295 40.000 5.27 0.00 0.00 4.00
306 634 5.163884 CGTGCTGCATCTCATAAATATCAGG 60.164 44.000 5.27 0.00 0.00 3.86
307 635 5.636543 TCGTGCTGCATCTCATAAATATCAG 59.363 40.000 5.27 0.00 0.00 2.90
308 636 5.540911 TCGTGCTGCATCTCATAAATATCA 58.459 37.500 5.27 0.00 0.00 2.15
391 728 2.051334 TGGGTTGAGGCATTATTCCG 57.949 50.000 0.00 0.00 0.00 4.30
412 749 1.299541 CAAAATCGACATCCCTCGGG 58.700 55.000 0.00 0.00 34.27 5.14
429 766 2.682155 TATGAGGCATGCGTACACAA 57.318 45.000 13.78 3.38 0.00 3.33
533 870 7.851508 AGTATTTTTACGCTGCATATGTACAG 58.148 34.615 0.33 5.35 36.96 2.74
534 871 7.780008 AGTATTTTTACGCTGCATATGTACA 57.220 32.000 4.29 0.00 0.00 2.90
586 932 3.589951 AAGGGAGGCGTGAGTAGTATA 57.410 47.619 0.00 0.00 0.00 1.47
590 936 4.767928 AGATATTAAGGGAGGCGTGAGTAG 59.232 45.833 0.00 0.00 0.00 2.57
593 939 4.282195 AGAAGATATTAAGGGAGGCGTGAG 59.718 45.833 0.00 0.00 0.00 3.51
596 942 6.742559 TTAAGAAGATATTAAGGGAGGCGT 57.257 37.500 0.00 0.00 0.00 5.68
643 1823 5.105716 ACGCAAACATGTACTATCTCTGTCT 60.106 40.000 0.00 0.00 0.00 3.41
655 1835 4.234574 CAGTGAGAGTACGCAAACATGTA 58.765 43.478 0.00 0.00 0.00 2.29
657 1837 3.059884 ACAGTGAGAGTACGCAAACATG 58.940 45.455 0.00 0.00 0.00 3.21
701 1883 6.787085 ACTCACTCTGTAAACAAATACTGC 57.213 37.500 0.00 0.00 0.00 4.40
702 1884 7.594015 ACGTACTCACTCTGTAAACAAATACTG 59.406 37.037 0.00 0.00 0.00 2.74
703 1885 7.655490 ACGTACTCACTCTGTAAACAAATACT 58.345 34.615 0.00 0.00 0.00 2.12
704 1886 7.864307 ACGTACTCACTCTGTAAACAAATAC 57.136 36.000 0.00 0.00 0.00 1.89
705 1887 9.398170 GTTACGTACTCACTCTGTAAACAAATA 57.602 33.333 0.00 0.00 0.00 1.40
710 1892 7.433425 AGTTTGTTACGTACTCACTCTGTAAAC 59.567 37.037 0.00 0.00 0.00 2.01
720 1902 4.984161 GGCACTAAGTTTGTTACGTACTCA 59.016 41.667 0.00 0.00 0.00 3.41
721 1903 4.984161 TGGCACTAAGTTTGTTACGTACTC 59.016 41.667 0.00 0.00 0.00 2.59
785 1967 6.322201 AGGCTTTATGATTCGTTTCCAATGAT 59.678 34.615 0.00 0.00 0.00 2.45
789 1971 5.975693 AAGGCTTTATGATTCGTTTCCAA 57.024 34.783 0.00 0.00 0.00 3.53
806 1988 3.707316 TGGTGTAAATATGGCAAAGGCT 58.293 40.909 0.00 0.00 40.87 4.58
1556 2902 7.039011 ACTCTACAAGAAGTGACCAACATATGA 60.039 37.037 10.38 0.00 0.00 2.15
1588 2941 6.818142 GCATGACACTGCCATACATATACATA 59.182 38.462 0.00 0.00 36.10 2.29
1589 2942 5.645067 GCATGACACTGCCATACATATACAT 59.355 40.000 0.00 0.00 36.10 2.29
1590 2943 4.996758 GCATGACACTGCCATACATATACA 59.003 41.667 0.00 0.00 36.10 2.29
1591 2944 5.121298 CAGCATGACACTGCCATACATATAC 59.879 44.000 0.00 0.00 43.33 1.47
1592 2945 5.240121 CAGCATGACACTGCCATACATATA 58.760 41.667 0.00 0.00 43.33 0.86
1597 2953 1.019673 CCAGCATGACACTGCCATAC 58.980 55.000 0.00 0.00 43.33 2.39
2259 4105 2.719556 CCGTACGATCGATGCACTAAAG 59.280 50.000 24.34 0.56 0.00 1.85
2388 4360 3.950395 AGCCATCTTTCTTACTGATTGCC 59.050 43.478 0.00 0.00 31.73 4.52
2398 4370 3.584848 AGTACACTGGAGCCATCTTTCTT 59.415 43.478 0.00 0.00 0.00 2.52
2400 4372 3.618690 AGTACACTGGAGCCATCTTTC 57.381 47.619 0.00 0.00 0.00 2.62
2401 4373 7.730784 AGTATATAGTACACTGGAGCCATCTTT 59.269 37.037 0.00 0.00 0.00 2.52
2402 4374 7.242359 AGTATATAGTACACTGGAGCCATCTT 58.758 38.462 0.00 0.00 0.00 2.40
2403 4375 6.795590 AGTATATAGTACACTGGAGCCATCT 58.204 40.000 0.00 0.00 0.00 2.90
2407 4379 5.010719 TGCAAGTATATAGTACACTGGAGCC 59.989 44.000 0.00 0.00 0.00 4.70
2409 4381 7.024171 CGATGCAAGTATATAGTACACTGGAG 58.976 42.308 0.00 0.00 0.00 3.86
2411 4383 6.802348 GTCGATGCAAGTATATAGTACACTGG 59.198 42.308 0.00 0.00 0.00 4.00
2412 4384 7.360361 TGTCGATGCAAGTATATAGTACACTG 58.640 38.462 0.00 0.00 0.00 3.66
2413 4385 7.506328 TGTCGATGCAAGTATATAGTACACT 57.494 36.000 0.00 0.00 0.00 3.55
2414 4386 8.570096 TTTGTCGATGCAAGTATATAGTACAC 57.430 34.615 0.00 0.00 0.00 2.90
2431 4414 8.755018 GTTGAAATGTGAAAAGATTTTGTCGAT 58.245 29.630 0.00 0.00 0.00 3.59
2437 4420 7.518689 CGCCATGTTGAAATGTGAAAAGATTTT 60.519 33.333 0.00 0.00 0.00 1.82
2470 4453 5.359756 AGCTGCGTGTTTCATTCTGATATA 58.640 37.500 0.00 0.00 0.00 0.86
2473 4456 2.430465 AGCTGCGTGTTTCATTCTGAT 58.570 42.857 0.00 0.00 0.00 2.90
2565 4548 2.402182 TCCCACTAGTGTTGGTACCA 57.598 50.000 21.18 11.60 31.54 3.25
2579 4562 1.747206 CGGTGAAATCCCAGATCCCAC 60.747 57.143 0.00 0.00 0.00 4.61
2615 4674 4.500499 AATAGATCACTCTGCCAAGCTT 57.500 40.909 0.00 0.00 32.66 3.74
2657 4724 4.736896 GGGTGTCACGGCGAGTCC 62.737 72.222 16.62 10.38 0.00 3.85
2666 4733 1.098712 TTTGCCGAGTTGGGTGTCAC 61.099 55.000 0.00 0.00 38.63 3.67
2667 4734 1.098712 GTTTGCCGAGTTGGGTGTCA 61.099 55.000 0.00 0.00 38.63 3.58
2668 4735 0.818040 AGTTTGCCGAGTTGGGTGTC 60.818 55.000 0.00 0.00 38.63 3.67
2669 4736 0.395173 AAGTTTGCCGAGTTGGGTGT 60.395 50.000 0.00 0.00 38.63 4.16
2670 4737 0.310854 GAAGTTTGCCGAGTTGGGTG 59.689 55.000 0.00 0.00 38.63 4.61
2671 4738 0.106918 TGAAGTTTGCCGAGTTGGGT 60.107 50.000 0.00 0.00 38.63 4.51
2672 4739 1.247567 ATGAAGTTTGCCGAGTTGGG 58.752 50.000 0.00 0.00 38.63 4.12
2674 4741 3.354089 ACAATGAAGTTTGCCGAGTTG 57.646 42.857 0.00 0.00 0.00 3.16
2743 4811 3.118956 GGAACTCGAGGAATGTGAGACAT 60.119 47.826 18.41 0.00 41.31 3.06
2776 4844 6.738114 TGAAAATGTCAGTCAATTCCAAGTC 58.262 36.000 0.00 0.00 0.00 3.01
2818 4890 4.806625 GCCCATCTATCAGTCATTGCAGAT 60.807 45.833 0.00 0.00 32.02 2.90
2833 4905 2.063979 CGTCTGTGGGGCCCATCTA 61.064 63.158 31.48 17.30 35.28 1.98
2860 4932 7.148869 CGAGTTTCTGTAAACATGTAACATCGA 60.149 37.037 19.38 11.16 46.18 3.59
2864 4936 6.757478 TGTCGAGTTTCTGTAAACATGTAACA 59.243 34.615 12.07 12.07 46.18 2.41
2876 4948 5.163663 TGCAAAAAGATTGTCGAGTTTCTGT 60.164 36.000 0.00 0.00 0.00 3.41
2878 4950 5.499139 TGCAAAAAGATTGTCGAGTTTCT 57.501 34.783 0.00 0.00 0.00 2.52
2892 4964 9.579610 CCGTAACAAAAAGAATAATGCAAAAAG 57.420 29.630 0.00 0.00 0.00 2.27
2898 4970 9.952341 GAATTTCCGTAACAAAAAGAATAATGC 57.048 29.630 0.00 0.00 0.00 3.56
2906 5037 9.124807 GACTTATGGAATTTCCGTAACAAAAAG 57.875 33.333 21.20 16.04 41.68 2.27
2911 5042 6.231951 TGTGACTTATGGAATTTCCGTAACA 58.768 36.000 21.20 16.70 41.68 2.41
2912 5043 6.370718 ACTGTGACTTATGGAATTTCCGTAAC 59.629 38.462 21.20 14.81 41.68 2.50
2915 5046 4.906618 ACTGTGACTTATGGAATTTCCGT 58.093 39.130 14.45 14.45 40.17 4.69
2916 5047 5.880054 AACTGTGACTTATGGAATTTCCG 57.120 39.130 10.79 0.00 40.17 4.30
2919 5050 6.183360 CGGCATAACTGTGACTTATGGAATTT 60.183 38.462 6.68 0.00 33.75 1.82
2928 5059 1.001974 TGCTCGGCATAACTGTGACTT 59.998 47.619 0.00 0.00 31.71 3.01
2950 5081 5.224135 TGATTGTCGAGTTCATTTACACGA 58.776 37.500 0.00 0.00 38.48 4.35
2951 5082 5.509605 TGATTGTCGAGTTCATTTACACG 57.490 39.130 0.00 0.00 34.16 4.49
2955 5086 7.592938 AGCAAAATGATTGTCGAGTTCATTTA 58.407 30.769 21.24 0.00 44.89 1.40
2960 5091 6.753897 AAAAGCAAAATGATTGTCGAGTTC 57.246 33.333 0.00 0.00 0.00 3.01
2999 5804 3.741388 GCTTGGCATATACGTGACTCCTT 60.741 47.826 0.00 0.00 0.00 3.36
3011 5816 4.712051 TCTCTATGGTTGCTTGGCATAT 57.288 40.909 0.00 0.00 38.76 1.78
3013 5818 3.589951 ATCTCTATGGTTGCTTGGCAT 57.410 42.857 0.00 0.00 38.76 4.40
3023 5828 7.094291 GCTGTTTACCGAGTATATCTCTATGGT 60.094 40.741 0.00 8.33 40.75 3.55
3025 5830 8.046294 AGCTGTTTACCGAGTATATCTCTATG 57.954 38.462 0.00 0.00 40.75 2.23
3026 5831 9.736414 TTAGCTGTTTACCGAGTATATCTCTAT 57.264 33.333 0.00 0.00 40.75 1.98
3027 5832 9.736414 ATTAGCTGTTTACCGAGTATATCTCTA 57.264 33.333 0.00 0.00 40.75 2.43
3042 5847 3.570912 GGCCCACCTATTAGCTGTTTA 57.429 47.619 0.00 0.00 0.00 2.01
3055 5860 2.594592 GTGTCACACAGGCCCACC 60.595 66.667 2.00 0.00 34.08 4.61
3058 5863 0.739813 GATACGTGTCACACAGGCCC 60.740 60.000 9.06 0.00 37.49 5.80
3063 5868 4.251543 AGTCATTGATACGTGTCACACA 57.748 40.909 15.10 0.71 33.40 3.72
3080 5885 0.034337 GGCCAACCGTCAGTTAGTCA 59.966 55.000 0.00 0.00 36.18 3.41
3099 5904 0.744874 TTCGACCTCGGCATAGGAAG 59.255 55.000 10.37 4.20 39.15 3.46
3115 5920 1.401018 CCGCCTTTTGCCTAGTTTTCG 60.401 52.381 0.00 0.00 36.24 3.46
3145 5950 0.392595 GTCCGCTCCCCTTTAAGTGG 60.393 60.000 0.00 0.00 43.20 4.00
3217 6119 2.676342 GCAACGGTGTATCGAAGGAAAT 59.324 45.455 0.66 0.00 0.00 2.17
3219 6121 1.673626 GGCAACGGTGTATCGAAGGAA 60.674 52.381 0.66 0.00 0.00 3.36
3248 6150 2.042025 AGGCTGAGGAGAGAGGGC 60.042 66.667 0.00 0.00 0.00 5.19
3260 6162 1.481240 CATACGACGATGACAGGCTG 58.519 55.000 14.16 14.16 0.00 4.85
3261 6163 0.385751 CCATACGACGATGACAGGCT 59.614 55.000 0.00 0.00 0.00 4.58
3262 6164 0.384309 TCCATACGACGATGACAGGC 59.616 55.000 0.00 0.00 0.00 4.85
3264 6166 3.559504 CAGATCCATACGACGATGACAG 58.440 50.000 0.00 0.00 0.00 3.51
3266 6168 2.922758 GCCAGATCCATACGACGATGAC 60.923 54.545 0.00 0.00 0.00 3.06
3271 6174 0.039074 GGAGCCAGATCCATACGACG 60.039 60.000 0.00 0.00 39.34 5.12
3296 6199 3.751246 CAACCAGGCATGCCACGG 61.751 66.667 37.18 34.72 38.92 4.94
3299 6202 2.025416 AGTTATACAACCAGGCATGCCA 60.025 45.455 37.18 16.40 35.31 4.92
3300 6203 2.654863 AGTTATACAACCAGGCATGCC 58.345 47.619 30.12 30.12 35.05 4.40
3301 6204 4.703897 TCTAGTTATACAACCAGGCATGC 58.296 43.478 9.90 9.90 35.05 4.06


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

AutoCloner maintained by Alex Coulton.