Multiple sequence alignment - TraesCS2B01G138400

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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 TraesCS2B01G138400 chr2B 100.000 4977 0 0 1 4977 105536612 105541588 0.000000e+00 9191.0
1 TraesCS2B01G138400 chr2B 93.322 614 33 3 4299 4905 106166214 106165602 0.000000e+00 900.0
2 TraesCS2B01G138400 chr2B 96.000 75 2 1 4902 4976 106165307 106165234 2.430000e-23 121.0
3 TraesCS2B01G138400 chr2D 94.203 3381 141 23 953 4299 65692901 65689542 0.000000e+00 5107.0
4 TraesCS2B01G138400 chr2D 90.290 587 37 10 90 668 65695864 65695290 0.000000e+00 750.0
5 TraesCS2B01G138400 chr2D 82.898 421 42 15 3579 3996 65685964 65685571 7.930000e-93 351.0
6 TraesCS2B01G138400 chr2D 100.000 29 0 0 3239 3267 121704705 121704677 3.000000e-03 54.7
7 TraesCS2B01G138400 chr2A 94.361 3210 124 27 953 4124 68878278 68881468 0.000000e+00 4872.0
8 TraesCS2B01G138400 chr2A 88.758 596 41 12 45 638 68876074 68876645 0.000000e+00 706.0
9 TraesCS2B01G138400 chr2A 87.879 198 17 3 3579 3776 68886245 68886435 5.010000e-55 226.0
10 TraesCS2B01G138400 chr2A 96.226 53 2 0 905 957 755693042 755693094 2.470000e-13 87.9
11 TraesCS2B01G138400 chrUn 94.797 615 26 6 4296 4905 377801742 377802355 0.000000e+00 953.0
12 TraesCS2B01G138400 chrUn 94.737 38 2 0 3232 3269 35540818 35540781 5.380000e-05 60.2
13 TraesCS2B01G138400 chrUn 94.737 38 2 0 3232 3269 244207322 244207359 5.380000e-05 60.2
14 TraesCS2B01G138400 chr4A 94.788 614 27 5 4296 4905 730573852 730574464 0.000000e+00 952.0
15 TraesCS2B01G138400 chr4A 94.910 609 28 2 4299 4905 657083490 657082883 0.000000e+00 950.0
16 TraesCS2B01G138400 chr4A 94.634 615 27 6 4296 4905 730494524 730495137 0.000000e+00 948.0
17 TraesCS2B01G138400 chr4A 94.634 615 27 6 4296 4905 730626306 730626919 0.000000e+00 948.0
18 TraesCS2B01G138400 chr4A 77.368 190 31 7 3234 3417 532794403 532794586 8.810000e-18 102.0
19 TraesCS2B01G138400 chr4A 96.364 55 2 0 903 957 374633415 374633361 1.910000e-14 91.6
20 TraesCS2B01G138400 chr4A 84.524 84 11 2 3616 3698 532796845 532796927 1.150000e-11 82.4
21 TraesCS2B01G138400 chr1B 94.745 609 30 2 4299 4905 623676725 623676117 0.000000e+00 946.0
22 TraesCS2B01G138400 chr1B 92.308 78 6 0 3346 3423 687278426 687278349 1.460000e-20 111.0
23 TraesCS2B01G138400 chr1B 77.895 190 30 7 3234 3417 222209479 222209662 1.890000e-19 108.0
24 TraesCS2B01G138400 chr6B 93.137 612 39 3 4296 4905 148406099 148406709 0.000000e+00 894.0
25 TraesCS2B01G138400 chr6B 92.822 613 40 4 4296 4905 148479577 148480188 0.000000e+00 885.0
26 TraesCS2B01G138400 chr6B 97.333 75 2 0 4902 4976 288657993 288658067 1.450000e-25 128.0
27 TraesCS2B01G138400 chr6B 97.333 75 2 0 4902 4976 617111072 617110998 1.450000e-25 128.0
28 TraesCS2B01G138400 chr6B 93.333 75 5 0 4902 4976 217153413 217153339 1.460000e-20 111.0
29 TraesCS2B01G138400 chr6B 96.364 55 2 0 903 957 681374498 681374552 1.910000e-14 91.6
30 TraesCS2B01G138400 chr3D 74.380 847 167 40 2942 3755 143459409 143460238 2.890000e-82 316.0
31 TraesCS2B01G138400 chr7B 97.333 75 2 0 4902 4976 26649197 26649271 1.450000e-25 128.0
32 TraesCS2B01G138400 chr7B 75.000 192 34 7 3355 3545 376934845 376934667 5.340000e-10 76.8
33 TraesCS2B01G138400 chr3B 97.333 75 2 0 4902 4976 752910421 752910495 1.450000e-25 128.0
34 TraesCS2B01G138400 chr3B 94.545 55 3 0 903 957 566393412 566393466 8.880000e-13 86.1
35 TraesCS2B01G138400 chr7D 96.000 75 3 0 4902 4976 487869312 487869238 6.770000e-24 122.0
36 TraesCS2B01G138400 chr7D 94.737 38 2 0 3232 3269 176160394 176160431 5.380000e-05 60.2
37 TraesCS2B01G138400 chr5B 94.667 75 4 0 4902 4976 661910263 661910337 3.150000e-22 117.0
38 TraesCS2B01G138400 chr5B 86.747 83 5 4 3618 3697 11771812 11771733 2.470000e-13 87.9
39 TraesCS2B01G138400 chr7A 93.333 75 5 0 4902 4976 502248455 502248381 1.460000e-20 111.0
40 TraesCS2B01G138400 chr7A 94.828 58 3 0 900 957 641014086 641014143 1.910000e-14 91.6
41 TraesCS2B01G138400 chr7A 96.296 54 2 0 904 957 674005776 674005829 6.860000e-14 89.8
42 TraesCS2B01G138400 chr7A 94.545 55 3 0 903 957 573129633 573129687 8.880000e-13 86.1
43 TraesCS2B01G138400 chr1A 92.308 78 6 0 3346 3423 592530824 592530747 1.460000e-20 111.0
44 TraesCS2B01G138400 chr1A 86.585 82 7 3 3618 3697 99868409 99868330 2.470000e-13 87.9
45 TraesCS2B01G138400 chr1D 91.026 78 7 0 3346 3423 494011709 494011632 6.810000e-19 106.0
46 TraesCS2B01G138400 chr5A 93.846 65 3 1 894 957 671198535 671198599 4.100000e-16 97.1
47 TraesCS2B01G138400 chr4B 98.182 55 1 0 903 957 10516429 10516375 4.100000e-16 97.1
48 TraesCS2B01G138400 chr5D 87.654 81 8 2 3618 3697 11950020 11949941 5.300000e-15 93.5
49 TraesCS2B01G138400 chr3A 94.828 58 2 1 900 957 439913218 439913274 6.860000e-14 89.8
50 TraesCS2B01G138400 chr3A 94.595 37 2 0 3233 3269 10500664 10500700 1.940000e-04 58.4
51 TraesCS2B01G138400 chr4D 85.542 83 10 2 3616 3697 397094311 397094230 8.880000e-13 86.1
52 TraesCS2B01G138400 chr4D 81.818 99 16 2 3616 3713 63585447 63585350 1.150000e-11 82.4


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 TraesCS2B01G138400 chr2B 105536612 105541588 4976 False 9191.000000 9191 100.000000 1 4977 1 chr2B.!!$F1 4976
1 TraesCS2B01G138400 chr2B 106165234 106166214 980 True 510.500000 900 94.661000 4299 4976 2 chr2B.!!$R1 677
2 TraesCS2B01G138400 chr2D 65685571 65695864 10293 True 2069.333333 5107 89.130333 90 4299 3 chr2D.!!$R2 4209
3 TraesCS2B01G138400 chr2A 68876074 68881468 5394 False 2789.000000 4872 91.559500 45 4124 2 chr2A.!!$F3 4079
4 TraesCS2B01G138400 chrUn 377801742 377802355 613 False 953.000000 953 94.797000 4296 4905 1 chrUn.!!$F2 609
5 TraesCS2B01G138400 chr4A 730573852 730574464 612 False 952.000000 952 94.788000 4296 4905 1 chr4A.!!$F2 609
6 TraesCS2B01G138400 chr4A 657082883 657083490 607 True 950.000000 950 94.910000 4299 4905 1 chr4A.!!$R2 606
7 TraesCS2B01G138400 chr4A 730494524 730495137 613 False 948.000000 948 94.634000 4296 4905 1 chr4A.!!$F1 609
8 TraesCS2B01G138400 chr4A 730626306 730626919 613 False 948.000000 948 94.634000 4296 4905 1 chr4A.!!$F3 609
9 TraesCS2B01G138400 chr1B 623676117 623676725 608 True 946.000000 946 94.745000 4299 4905 1 chr1B.!!$R1 606
10 TraesCS2B01G138400 chr6B 148406099 148406709 610 False 894.000000 894 93.137000 4296 4905 1 chr6B.!!$F1 609
11 TraesCS2B01G138400 chr6B 148479577 148480188 611 False 885.000000 885 92.822000 4296 4905 1 chr6B.!!$F2 609
12 TraesCS2B01G138400 chr3D 143459409 143460238 829 False 316.000000 316 74.380000 2942 3755 1 chr3D.!!$F1 813

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
934 3718 0.031721 ACGACCCGTTTGTGAGAGAC 59.968 55.0 0.0 0.0 36.35 3.36 F
1230 4041 0.033991 TCCTCCTCTCCAACCTCTCG 60.034 60.0 0.0 0.0 0.00 4.04 F
3090 5901 1.106944 CCGTGAAAAAGCTGTGGGGT 61.107 55.0 0.0 0.0 0.00 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2413 5224 0.038251 GTGGACACATCAGCGAGTGA 60.038 55.0 7.65 0.0 40.38 3.41 R
3122 5933 0.036388 GTCCTTCATGCCGTCCTTGA 60.036 55.0 0.00 0.0 0.00 3.02 R
4021 6881 1.019278 AAGTGTGGCGATGCTAACCG 61.019 55.0 0.00 0.0 0.00 4.44 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
21 22 3.990092 TGAACTAGTAGTGCAAGTGTGG 58.010 45.455 8.66 0.00 28.77 4.17
22 23 2.457366 ACTAGTAGTGCAAGTGTGGC 57.543 50.000 0.85 0.00 0.00 5.01
23 24 1.691976 ACTAGTAGTGCAAGTGTGGCA 59.308 47.619 0.85 0.00 39.32 4.92
28 29 2.439338 TGCAAGTGTGGCACGGTT 60.439 55.556 13.77 5.78 39.64 4.44
29 30 1.153147 TGCAAGTGTGGCACGGTTA 60.153 52.632 13.77 0.00 39.64 2.85
30 31 0.748367 TGCAAGTGTGGCACGGTTAA 60.748 50.000 13.77 0.00 39.64 2.01
31 32 0.382515 GCAAGTGTGGCACGGTTAAA 59.617 50.000 13.77 0.00 39.64 1.52
32 33 1.000717 GCAAGTGTGGCACGGTTAAAT 60.001 47.619 13.77 0.00 39.64 1.40
33 34 2.544903 GCAAGTGTGGCACGGTTAAATT 60.545 45.455 13.77 0.00 39.64 1.82
34 35 3.712187 CAAGTGTGGCACGGTTAAATTT 58.288 40.909 13.77 0.00 39.64 1.82
35 36 4.116238 CAAGTGTGGCACGGTTAAATTTT 58.884 39.130 13.77 0.00 39.64 1.82
36 37 3.972403 AGTGTGGCACGGTTAAATTTTC 58.028 40.909 13.77 0.00 39.64 2.29
37 38 3.634910 AGTGTGGCACGGTTAAATTTTCT 59.365 39.130 13.77 0.00 39.64 2.52
38 39 4.822896 AGTGTGGCACGGTTAAATTTTCTA 59.177 37.500 13.77 0.00 39.64 2.10
39 40 4.913345 GTGTGGCACGGTTAAATTTTCTAC 59.087 41.667 13.77 0.00 0.00 2.59
40 41 4.822896 TGTGGCACGGTTAAATTTTCTACT 59.177 37.500 13.77 0.00 0.00 2.57
41 42 5.049267 TGTGGCACGGTTAAATTTTCTACTC 60.049 40.000 13.77 0.00 0.00 2.59
42 43 5.180680 GTGGCACGGTTAAATTTTCTACTCT 59.819 40.000 0.00 0.00 0.00 3.24
43 44 6.369615 GTGGCACGGTTAAATTTTCTACTCTA 59.630 38.462 0.00 0.00 0.00 2.43
44 45 7.065443 GTGGCACGGTTAAATTTTCTACTCTAT 59.935 37.037 0.00 0.00 0.00 1.98
45 46 8.259411 TGGCACGGTTAAATTTTCTACTCTATA 58.741 33.333 0.00 0.00 0.00 1.31
46 47 9.269453 GGCACGGTTAAATTTTCTACTCTATAT 57.731 33.333 0.00 0.00 0.00 0.86
135 136 2.492484 ACCACGATCTAGTTCACACTCC 59.508 50.000 0.00 0.00 34.06 3.85
326 328 4.378774 TGTGTCCCAAATCAAAATGCAAG 58.621 39.130 0.00 0.00 0.00 4.01
336 339 8.347035 CCAAATCAAAATGCAAGTTTTTCAGAT 58.653 29.630 0.00 0.00 27.89 2.90
389 392 1.271871 TGTCCTCCAAAATCACGGCAT 60.272 47.619 0.00 0.00 0.00 4.40
467 477 5.989551 AATTGACATGGCAAAACAAGTTC 57.010 34.783 19.96 0.00 0.00 3.01
476 486 4.932200 TGGCAAAACAAGTTCGAAAAATGT 59.068 33.333 0.00 2.47 0.00 2.71
531 541 6.356757 TGCTTTAAGTTTTCATGGCAAAAC 57.643 33.333 12.55 12.55 43.73 2.43
542 552 8.490355 GTTTTCATGGCAAAACTGAATCTTTAG 58.510 33.333 12.98 0.00 41.28 1.85
547 557 6.664515 TGGCAAAACTGAATCTTTAGTAACG 58.335 36.000 0.00 0.00 0.00 3.18
555 565 6.823689 ACTGAATCTTTAGTAACGATGGCAAT 59.176 34.615 2.87 0.00 0.00 3.56
567 577 5.384063 ACGATGGCAATATGTTTTTGTGA 57.616 34.783 0.00 0.00 0.00 3.58
570 580 6.035217 CGATGGCAATATGTTTTTGTGATCA 58.965 36.000 0.00 0.00 0.00 2.92
617 627 2.225091 GCCATGGGGATAATGGATGTGA 60.225 50.000 15.13 0.00 46.44 3.58
643 653 0.175760 TACTGGCGCTGAGATGGTTC 59.824 55.000 7.64 0.00 0.00 3.62
652 662 2.420642 CTGAGATGGTTCGGGCATATG 58.579 52.381 0.00 0.00 0.00 1.78
656 666 0.183492 ATGGTTCGGGCATATGCAGT 59.817 50.000 28.07 3.69 44.36 4.40
661 671 2.549198 CGGGCATATGCAGTGCAGG 61.549 63.158 28.07 15.86 43.65 4.85
665 675 1.389609 GCATATGCAGTGCAGGCCTT 61.390 55.000 24.20 8.73 43.65 4.35
668 678 0.677731 TATGCAGTGCAGGCCTTCAC 60.678 55.000 26.00 26.00 43.65 3.18
670 680 2.623915 GCAGTGCAGGCCTTCACAG 61.624 63.158 32.73 26.90 35.76 3.66
671 681 2.282040 AGTGCAGGCCTTCACAGC 60.282 61.111 32.73 20.18 35.76 4.40
672 682 3.730761 GTGCAGGCCTTCACAGCG 61.731 66.667 27.92 5.10 33.63 5.18
673 683 3.939939 TGCAGGCCTTCACAGCGA 61.940 61.111 0.00 0.00 0.00 4.93
674 684 3.123620 GCAGGCCTTCACAGCGAG 61.124 66.667 0.00 0.00 0.00 5.03
683 2662 3.782244 CACAGCGAGCTTCACGGC 61.782 66.667 0.00 0.00 0.00 5.68
764 2743 4.703899 ACGAAATCTTGTACGTGTTCAC 57.296 40.909 0.00 0.00 37.58 3.18
771 2750 5.654603 TCTTGTACGTGTTCACTATGGAT 57.345 39.130 0.00 0.00 0.00 3.41
774 2753 4.993905 TGTACGTGTTCACTATGGATCTG 58.006 43.478 0.00 0.00 0.00 2.90
775 2754 2.893637 ACGTGTTCACTATGGATCTGC 58.106 47.619 0.00 0.00 0.00 4.26
808 2787 9.360093 TGTGTTTAAAAGTTTACAGTGATTTGG 57.640 29.630 0.00 0.00 0.00 3.28
845 2826 1.185315 CAAAATCCCTGCCGACCAAT 58.815 50.000 0.00 0.00 0.00 3.16
846 2827 2.291282 ACAAAATCCCTGCCGACCAATA 60.291 45.455 0.00 0.00 0.00 1.90
881 3660 1.269569 TGAGAGCTTCGCGAAGAACAA 60.270 47.619 43.98 26.18 40.79 2.83
884 3663 0.861837 AGCTTCGCGAAGAACAACAG 59.138 50.000 43.98 22.42 40.79 3.16
894 3678 3.303791 CGAAGAACAACAGTTAAGCCCAC 60.304 47.826 0.00 0.00 0.00 4.61
895 3679 2.583143 AGAACAACAGTTAAGCCCACC 58.417 47.619 0.00 0.00 0.00 4.61
896 3680 1.611977 GAACAACAGTTAAGCCCACCC 59.388 52.381 0.00 0.00 0.00 4.61
897 3681 0.178973 ACAACAGTTAAGCCCACCCC 60.179 55.000 0.00 0.00 0.00 4.95
898 3682 0.178975 CAACAGTTAAGCCCACCCCA 60.179 55.000 0.00 0.00 0.00 4.96
899 3683 0.178973 AACAGTTAAGCCCACCCCAC 60.179 55.000 0.00 0.00 0.00 4.61
900 3684 1.674322 CAGTTAAGCCCACCCCACG 60.674 63.158 0.00 0.00 0.00 4.94
901 3685 1.844289 AGTTAAGCCCACCCCACGA 60.844 57.895 0.00 0.00 0.00 4.35
902 3686 1.073548 GTTAAGCCCACCCCACGAA 59.926 57.895 0.00 0.00 0.00 3.85
903 3687 0.958876 GTTAAGCCCACCCCACGAAG 60.959 60.000 0.00 0.00 0.00 3.79
904 3688 2.132089 TTAAGCCCACCCCACGAAGG 62.132 60.000 0.00 0.00 37.03 3.46
908 3692 4.323477 CCACCCCACGAAGGCGAA 62.323 66.667 0.00 0.00 41.64 4.70
909 3693 2.046314 CACCCCACGAAGGCGAAT 60.046 61.111 0.00 0.00 41.64 3.34
910 3694 2.106683 CACCCCACGAAGGCGAATC 61.107 63.158 0.00 0.00 41.64 2.52
911 3695 2.513897 CCCCACGAAGGCGAATCC 60.514 66.667 0.00 0.00 41.64 3.01
913 3697 1.815421 CCCACGAAGGCGAATCCTG 60.815 63.158 0.00 0.00 46.94 3.86
914 3698 1.079127 CCACGAAGGCGAATCCTGT 60.079 57.895 0.00 0.00 46.94 4.00
915 3699 0.174845 CCACGAAGGCGAATCCTGTA 59.825 55.000 0.00 0.00 46.94 2.74
916 3700 1.278238 CACGAAGGCGAATCCTGTAC 58.722 55.000 0.00 0.00 46.94 2.90
917 3701 0.179145 ACGAAGGCGAATCCTGTACG 60.179 55.000 0.00 0.00 46.94 3.67
918 3702 0.099968 CGAAGGCGAATCCTGTACGA 59.900 55.000 0.00 0.00 46.94 3.43
919 3703 1.557651 GAAGGCGAATCCTGTACGAC 58.442 55.000 0.00 0.00 46.94 4.34
920 3704 0.175073 AAGGCGAATCCTGTACGACC 59.825 55.000 0.00 0.00 46.94 4.79
921 3705 1.227176 GGCGAATCCTGTACGACCC 60.227 63.158 0.00 0.00 0.00 4.46
922 3706 1.588139 GCGAATCCTGTACGACCCG 60.588 63.158 0.00 0.00 0.00 5.28
923 3707 1.805254 CGAATCCTGTACGACCCGT 59.195 57.895 0.00 0.00 44.35 5.28
924 3708 0.171903 CGAATCCTGTACGACCCGTT 59.828 55.000 0.00 0.00 41.54 4.44
925 3709 1.403249 CGAATCCTGTACGACCCGTTT 60.403 52.381 0.00 0.00 41.54 3.60
926 3710 1.997606 GAATCCTGTACGACCCGTTTG 59.002 52.381 0.00 0.00 41.54 2.93
927 3711 0.971386 ATCCTGTACGACCCGTTTGT 59.029 50.000 0.00 0.00 41.54 2.83
928 3712 0.032403 TCCTGTACGACCCGTTTGTG 59.968 55.000 0.00 0.00 41.54 3.33
929 3713 0.032403 CCTGTACGACCCGTTTGTGA 59.968 55.000 0.00 0.00 41.54 3.58
930 3714 1.415374 CTGTACGACCCGTTTGTGAG 58.585 55.000 0.00 0.00 41.54 3.51
931 3715 1.001048 CTGTACGACCCGTTTGTGAGA 60.001 52.381 0.00 0.00 41.54 3.27
932 3716 1.001048 TGTACGACCCGTTTGTGAGAG 60.001 52.381 0.00 0.00 41.54 3.20
933 3717 1.267806 GTACGACCCGTTTGTGAGAGA 59.732 52.381 0.00 0.00 41.54 3.10
934 3718 0.031721 ACGACCCGTTTGTGAGAGAC 59.968 55.000 0.00 0.00 36.35 3.36
935 3719 0.666577 CGACCCGTTTGTGAGAGACC 60.667 60.000 0.00 0.00 0.00 3.85
936 3720 0.680061 GACCCGTTTGTGAGAGACCT 59.320 55.000 0.00 0.00 0.00 3.85
937 3721 0.680061 ACCCGTTTGTGAGAGACCTC 59.320 55.000 0.00 0.00 39.86 3.85
938 3722 0.388649 CCCGTTTGTGAGAGACCTCG 60.389 60.000 0.00 0.00 42.33 4.63
939 3723 0.314302 CCGTTTGTGAGAGACCTCGT 59.686 55.000 0.00 0.00 42.33 4.18
940 3724 1.666311 CCGTTTGTGAGAGACCTCGTC 60.666 57.143 0.00 0.00 42.33 4.20
941 3725 1.687628 GTTTGTGAGAGACCTCGTCG 58.312 55.000 0.00 0.00 42.33 5.12
942 3726 1.001597 GTTTGTGAGAGACCTCGTCGT 60.002 52.381 0.00 0.00 42.33 4.34
943 3727 0.591659 TTGTGAGAGACCTCGTCGTG 59.408 55.000 0.00 0.00 42.33 4.35
944 3728 1.235281 TGTGAGAGACCTCGTCGTGG 61.235 60.000 11.71 11.71 42.33 4.94
945 3729 1.674651 TGAGAGACCTCGTCGTGGG 60.675 63.158 17.11 11.08 42.33 4.61
946 3730 2.361357 AGAGACCTCGTCGTGGGG 60.361 66.667 17.11 8.79 37.67 4.96
947 3731 3.450115 GAGACCTCGTCGTGGGGG 61.450 72.222 17.11 6.54 37.67 5.40
948 3732 4.296729 AGACCTCGTCGTGGGGGT 62.297 66.667 17.11 9.41 37.67 4.95
949 3733 4.065281 GACCTCGTCGTGGGGGTG 62.065 72.222 17.11 0.00 31.60 4.61
950 3734 4.608774 ACCTCGTCGTGGGGGTGA 62.609 66.667 17.11 0.00 0.00 4.02
951 3735 4.065281 CCTCGTCGTGGGGGTGAC 62.065 72.222 5.40 0.00 0.00 3.67
983 3773 1.671901 CCTCCACTTCTCCGCTCTCC 61.672 65.000 0.00 0.00 0.00 3.71
984 3774 1.999071 CTCCACTTCTCCGCTCTCCG 61.999 65.000 0.00 0.00 0.00 4.63
985 3775 2.344203 CCACTTCTCCGCTCTCCGT 61.344 63.158 0.00 0.00 34.38 4.69
1011 3810 0.754217 CCAATGCCATGACTCCCCTG 60.754 60.000 0.00 0.00 0.00 4.45
1013 3812 2.578586 AATGCCATGACTCCCCTGCC 62.579 60.000 0.00 0.00 0.00 4.85
1089 3888 2.266055 GACTTCACCCGCCTCCTG 59.734 66.667 0.00 0.00 0.00 3.86
1230 4041 0.033991 TCCTCCTCTCCAACCTCTCG 60.034 60.000 0.00 0.00 0.00 4.04
1392 4203 1.684049 CTTCTCCGGAGAGGTGCCT 60.684 63.158 31.81 0.00 40.83 4.75
1495 4306 1.817099 GCCAATGTCAGCTCCCTCG 60.817 63.158 0.00 0.00 0.00 4.63
1630 4441 1.134220 GGATACCGTCTTCCATTGGCA 60.134 52.381 0.00 0.00 31.99 4.92
1695 4506 2.519780 GGCGAGATCCCGGAGAGT 60.520 66.667 0.73 0.00 0.00 3.24
2322 5133 4.910195 TGCTGATATCAGACAACCACTTT 58.090 39.130 32.38 0.00 46.59 2.66
2325 5136 4.910195 TGATATCAGACAACCACTTTGCT 58.090 39.130 0.00 0.00 39.01 3.91
2463 5274 4.095610 GGCTTGATTTACGGAACAATTCG 58.904 43.478 0.00 0.00 0.00 3.34
2505 5316 1.144276 TGTTCGACGGTGGCAGAAA 59.856 52.632 0.00 0.00 0.00 2.52
2562 5373 1.519455 GAACATCCCGTCGGAGCTG 60.519 63.158 14.39 9.36 43.12 4.24
2598 5409 2.416747 CTGAATTCGCTTGACCTGTCA 58.583 47.619 0.04 0.00 37.91 3.58
2667 5478 2.497138 CTGAGCATGTTCAACCTGTCA 58.503 47.619 13.57 0.00 0.00 3.58
2903 5714 2.039405 GCCAGAGCCAGCACAAGAG 61.039 63.158 0.00 0.00 0.00 2.85
3078 5889 2.024868 CGATGTCGTGGCCGTGAAA 61.025 57.895 0.00 0.00 35.01 2.69
3089 5900 1.659794 CCGTGAAAAAGCTGTGGGG 59.340 57.895 0.00 0.00 0.00 4.96
3090 5901 1.106944 CCGTGAAAAAGCTGTGGGGT 61.107 55.000 0.00 0.00 0.00 4.95
3121 5932 1.374252 GCGGCGAAGAGGAAAGACA 60.374 57.895 12.98 0.00 0.00 3.41
3122 5933 0.741221 GCGGCGAAGAGGAAAGACAT 60.741 55.000 12.98 0.00 0.00 3.06
3199 6022 1.873591 GGCACAAGAACATCGTGAAGT 59.126 47.619 0.37 0.00 32.23 3.01
3577 6400 7.254556 CGGTTCTTTATCCCGGACTTTATTAAC 60.255 40.741 0.73 0.00 38.09 2.01
3597 6421 2.289631 ACTTGCCGATGAACTGATGACA 60.290 45.455 0.00 0.00 0.00 3.58
3736 6575 2.657237 CTCGGCGACAAGGACCTT 59.343 61.111 4.99 0.00 0.00 3.50
4062 6922 8.765219 CACTTACTTACCATGCAGAATACATAC 58.235 37.037 0.00 0.00 0.00 2.39
4063 6923 8.705594 ACTTACTTACCATGCAGAATACATACT 58.294 33.333 0.00 0.00 0.00 2.12
4064 6924 9.197694 CTTACTTACCATGCAGAATACATACTC 57.802 37.037 0.00 0.00 0.00 2.59
4065 6925 6.525629 ACTTACCATGCAGAATACATACTCC 58.474 40.000 0.00 0.00 0.00 3.85
4066 6926 6.099701 ACTTACCATGCAGAATACATACTCCA 59.900 38.462 0.00 0.00 0.00 3.86
4067 6927 5.573380 ACCATGCAGAATACATACTCCAT 57.427 39.130 0.00 0.00 0.00 3.41
4095 6955 7.123247 AGGTGTGAAATCTTAATGCAGCTTAAT 59.877 33.333 0.00 0.00 30.45 1.40
4120 6980 0.621571 AGCAGGGGACTCCATTAGCA 60.622 55.000 0.00 0.00 40.21 3.49
4154 7014 8.828751 TCTAGGGCTATAAAAACTCCTTTGTAA 58.171 33.333 0.00 0.00 0.00 2.41
4155 7015 7.698506 AGGGCTATAAAAACTCCTTTGTAAC 57.301 36.000 0.00 0.00 0.00 2.50
4157 7017 7.948447 AGGGCTATAAAAACTCCTTTGTAACTT 59.052 33.333 0.00 0.00 0.00 2.66
4186 7046 4.355543 TTCTCTTGTTGTTGCTGTTGTC 57.644 40.909 0.00 0.00 0.00 3.18
4262 7122 2.610694 CGGATAGCATGGCAAGCCG 61.611 63.158 11.59 5.01 39.42 5.52
4279 7139 3.077359 AGCCGATTTCAGAAGAAAGTGG 58.923 45.455 0.00 0.00 46.13 4.00
4281 7141 3.077359 CCGATTTCAGAAGAAAGTGGCT 58.923 45.455 0.00 0.00 46.13 4.75
4282 7142 3.126000 CCGATTTCAGAAGAAAGTGGCTC 59.874 47.826 0.00 0.00 46.13 4.70
4283 7143 3.748048 CGATTTCAGAAGAAAGTGGCTCA 59.252 43.478 0.00 0.00 46.13 4.26
4288 7148 4.152647 TCAGAAGAAAGTGGCTCACTAGA 58.847 43.478 8.07 0.00 44.62 2.43
4348 7306 3.550561 CGTGCGCTAAAAACTGATTTGA 58.449 40.909 9.73 0.00 0.00 2.69
4735 10906 1.337823 CGGTGAAGAACGACCTTCCAT 60.338 52.381 15.18 0.00 41.29 3.41
4773 10944 2.667874 TGCTCGTTCGCCAATGCA 60.668 55.556 0.00 0.00 37.32 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.737252 GCCACACTTGCACTACTAGTTC 59.263 50.000 0.00 0.00 31.53 3.01
2 3 2.104111 TGCCACACTTGCACTACTAGTT 59.896 45.455 0.00 0.00 31.53 2.24
4 5 2.455674 TGCCACACTTGCACTACTAG 57.544 50.000 0.00 0.00 32.85 2.57
11 12 0.748367 TTAACCGTGCCACACTTGCA 60.748 50.000 0.00 0.00 36.12 4.08
12 13 0.382515 TTTAACCGTGCCACACTTGC 59.617 50.000 0.00 0.00 31.34 4.01
13 14 3.363341 AATTTAACCGTGCCACACTTG 57.637 42.857 0.00 0.00 31.34 3.16
14 15 4.098807 AGAAAATTTAACCGTGCCACACTT 59.901 37.500 0.00 0.00 31.34 3.16
15 16 3.634910 AGAAAATTTAACCGTGCCACACT 59.365 39.130 0.00 0.00 31.34 3.55
16 17 3.972403 AGAAAATTTAACCGTGCCACAC 58.028 40.909 0.00 0.00 0.00 3.82
17 18 4.822896 AGTAGAAAATTTAACCGTGCCACA 59.177 37.500 0.00 0.00 0.00 4.17
18 19 5.180680 AGAGTAGAAAATTTAACCGTGCCAC 59.819 40.000 0.00 0.00 0.00 5.01
19 20 5.310451 AGAGTAGAAAATTTAACCGTGCCA 58.690 37.500 0.00 0.00 0.00 4.92
20 21 5.874895 AGAGTAGAAAATTTAACCGTGCC 57.125 39.130 0.00 0.00 0.00 5.01
60 61 6.881065 CAGGGACAGTAGATGAATTTTTCTCA 59.119 38.462 0.00 0.00 0.00 3.27
69 70 2.166459 CGCTTCAGGGACAGTAGATGAA 59.834 50.000 0.00 0.00 0.00 2.57
77 78 1.572085 CTGCAACGCTTCAGGGACAG 61.572 60.000 0.00 0.00 0.00 3.51
135 136 2.892334 CGACACCCACAGTTTGGCG 61.892 63.158 0.00 0.00 45.37 5.69
446 456 4.050553 CGAACTTGTTTTGCCATGTCAAT 58.949 39.130 0.00 0.00 0.00 2.57
452 462 5.584251 ACATTTTTCGAACTTGTTTTGCCAT 59.416 32.000 0.00 0.00 0.00 4.40
467 477 3.913548 TGTCACCCATCACATTTTTCG 57.086 42.857 0.00 0.00 0.00 3.46
476 486 8.256605 CCATGTTAATTAAAATGTCACCCATCA 58.743 33.333 21.65 3.89 30.57 3.07
520 530 6.899393 ACTAAAGATTCAGTTTTGCCATGA 57.101 33.333 0.00 0.00 0.00 3.07
531 541 6.662414 TTGCCATCGTTACTAAAGATTCAG 57.338 37.500 0.00 0.00 0.00 3.02
542 552 6.804295 TCACAAAAACATATTGCCATCGTTAC 59.196 34.615 0.00 0.00 0.00 2.50
547 557 7.707464 TGATGATCACAAAAACATATTGCCATC 59.293 33.333 0.00 0.00 31.66 3.51
555 565 6.527057 TGCCATGATGATCACAAAAACATA 57.473 33.333 0.00 0.00 0.00 2.29
587 597 1.288508 ATCCCCATGGCAGCCACTTA 61.289 55.000 19.10 0.73 35.80 2.24
592 602 0.901580 CCATTATCCCCATGGCAGCC 60.902 60.000 6.09 3.66 34.98 4.85
600 610 2.104111 GACGTCACATCCATTATCCCCA 59.896 50.000 11.55 0.00 0.00 4.96
643 653 2.549198 CCTGCACTGCATATGCCCG 61.549 63.158 24.54 17.28 42.69 6.13
652 662 2.595463 TGTGAAGGCCTGCACTGC 60.595 61.111 38.16 18.17 36.05 4.40
656 666 3.889134 CTCGCTGTGAAGGCCTGCA 62.889 63.158 10.33 10.33 0.00 4.41
661 671 1.669115 TGAAGCTCGCTGTGAAGGC 60.669 57.895 0.00 0.00 0.00 4.35
665 675 2.049156 CCGTGAAGCTCGCTGTGA 60.049 61.111 0.00 0.00 0.00 3.58
744 2723 4.966850 AGTGAACACGTACAAGATTTCG 57.033 40.909 0.00 0.00 36.20 3.46
783 2762 9.575783 TCCAAATCACTGTAAACTTTTAAACAC 57.424 29.630 0.00 0.00 0.00 3.32
786 2765 9.308318 GCTTCCAAATCACTGTAAACTTTTAAA 57.692 29.630 0.00 0.00 0.00 1.52
788 2767 8.134895 CAGCTTCCAAATCACTGTAAACTTTTA 58.865 33.333 0.00 0.00 0.00 1.52
789 2768 6.980397 CAGCTTCCAAATCACTGTAAACTTTT 59.020 34.615 0.00 0.00 0.00 2.27
795 2774 3.253188 GTGCAGCTTCCAAATCACTGTAA 59.747 43.478 0.00 0.00 0.00 2.41
853 2834 3.207677 CGAAGCTCTCAACTGCACT 57.792 52.632 0.00 0.00 0.00 4.40
881 3660 1.458927 GTGGGGTGGGCTTAACTGT 59.541 57.895 0.00 0.00 0.00 3.55
884 3663 0.958876 CTTCGTGGGGTGGGCTTAAC 60.959 60.000 0.00 0.00 0.00 2.01
903 3687 1.227176 GGGTCGTACAGGATTCGCC 60.227 63.158 0.00 0.00 0.00 5.54
904 3688 1.588139 CGGGTCGTACAGGATTCGC 60.588 63.158 0.00 0.00 0.00 4.70
905 3689 0.171903 AACGGGTCGTACAGGATTCG 59.828 55.000 0.00 0.00 39.99 3.34
906 3690 1.997606 CAAACGGGTCGTACAGGATTC 59.002 52.381 0.00 0.00 39.99 2.52
907 3691 1.345415 ACAAACGGGTCGTACAGGATT 59.655 47.619 0.00 0.00 39.99 3.01
908 3692 0.971386 ACAAACGGGTCGTACAGGAT 59.029 50.000 0.00 0.00 39.99 3.24
909 3693 0.032403 CACAAACGGGTCGTACAGGA 59.968 55.000 0.00 0.00 39.99 3.86
910 3694 0.032403 TCACAAACGGGTCGTACAGG 59.968 55.000 0.00 0.00 39.99 4.00
911 3695 1.001048 TCTCACAAACGGGTCGTACAG 60.001 52.381 0.00 0.00 39.99 2.74
912 3696 1.001048 CTCTCACAAACGGGTCGTACA 60.001 52.381 0.00 0.00 39.99 2.90
913 3697 1.267806 TCTCTCACAAACGGGTCGTAC 59.732 52.381 0.00 0.00 39.99 3.67
914 3698 1.267806 GTCTCTCACAAACGGGTCGTA 59.732 52.381 0.00 0.00 39.99 3.43
915 3699 0.031721 GTCTCTCACAAACGGGTCGT 59.968 55.000 0.00 0.00 43.97 4.34
916 3700 0.666577 GGTCTCTCACAAACGGGTCG 60.667 60.000 0.00 0.00 0.00 4.79
917 3701 0.680061 AGGTCTCTCACAAACGGGTC 59.320 55.000 0.00 0.00 0.00 4.46
918 3702 0.680061 GAGGTCTCTCACAAACGGGT 59.320 55.000 0.00 0.00 39.74 5.28
919 3703 0.388649 CGAGGTCTCTCACAAACGGG 60.389 60.000 0.00 0.00 39.95 5.28
920 3704 0.314302 ACGAGGTCTCTCACAAACGG 59.686 55.000 0.00 0.00 39.95 4.44
921 3705 1.687628 GACGAGGTCTCTCACAAACG 58.312 55.000 0.00 0.00 39.95 3.60
922 3706 1.001597 ACGACGAGGTCTCTCACAAAC 60.002 52.381 0.00 0.00 39.95 2.93
923 3707 1.001706 CACGACGAGGTCTCTCACAAA 60.002 52.381 0.00 0.00 39.95 2.83
924 3708 0.591659 CACGACGAGGTCTCTCACAA 59.408 55.000 0.00 0.00 39.95 3.33
925 3709 1.235281 CCACGACGAGGTCTCTCACA 61.235 60.000 0.00 0.00 39.95 3.58
926 3710 1.502640 CCACGACGAGGTCTCTCAC 59.497 63.158 0.00 0.00 39.95 3.51
927 3711 1.674651 CCCACGACGAGGTCTCTCA 60.675 63.158 10.51 0.00 39.95 3.27
928 3712 2.408241 CCCCACGACGAGGTCTCTC 61.408 68.421 10.51 0.00 36.69 3.20
929 3713 2.361357 CCCCACGACGAGGTCTCT 60.361 66.667 10.51 0.00 0.00 3.10
930 3714 3.450115 CCCCCACGACGAGGTCTC 61.450 72.222 10.51 0.00 0.00 3.36
931 3715 4.296729 ACCCCCACGACGAGGTCT 62.297 66.667 10.51 0.00 0.00 3.85
932 3716 4.065281 CACCCCCACGACGAGGTC 62.065 72.222 10.51 0.00 0.00 3.85
933 3717 4.608774 TCACCCCCACGACGAGGT 62.609 66.667 10.51 4.42 0.00 3.85
934 3718 4.065281 GTCACCCCCACGACGAGG 62.065 72.222 0.00 2.17 0.00 4.63
935 3719 4.065281 GGTCACCCCCACGACGAG 62.065 72.222 0.00 0.00 32.74 4.18
947 3731 2.430367 GGAGTGGTGGTGGGTCAC 59.570 66.667 0.00 0.00 36.95 3.67
948 3732 2.852075 GGGAGTGGTGGTGGGTCA 60.852 66.667 0.00 0.00 0.00 4.02
949 3733 2.529389 AGGGAGTGGTGGTGGGTC 60.529 66.667 0.00 0.00 0.00 4.46
950 3734 2.529389 GAGGGAGTGGTGGTGGGT 60.529 66.667 0.00 0.00 0.00 4.51
951 3735 3.330720 GGAGGGAGTGGTGGTGGG 61.331 72.222 0.00 0.00 0.00 4.61
963 3747 1.671901 GAGAGCGGAGAAGTGGAGGG 61.672 65.000 0.00 0.00 0.00 4.30
983 3773 1.678635 ATGGCATTGGTGTGGGACG 60.679 57.895 0.00 0.00 0.00 4.79
984 3774 0.611618 TCATGGCATTGGTGTGGGAC 60.612 55.000 0.00 0.00 0.00 4.46
985 3775 0.611618 GTCATGGCATTGGTGTGGGA 60.612 55.000 0.00 0.00 0.00 4.37
1013 3812 3.086600 GGAGGAGGCACAGGAGGG 61.087 72.222 0.00 0.00 0.00 4.30
1201 4012 3.844090 GAGGAGGAGCGAGGCCAC 61.844 72.222 5.01 0.00 0.00 5.01
1203 4014 3.223589 GAGAGGAGGAGCGAGGCC 61.224 72.222 0.00 0.00 0.00 5.19
1479 4290 0.179089 CCTCGAGGGAGCTGACATTG 60.179 60.000 24.62 0.00 39.06 2.82
1695 4506 1.143183 GTTCTCCAAGCGCCCGATA 59.857 57.895 2.29 0.00 0.00 2.92
1781 4592 1.433534 GTCCAAGAACCTCAGCTTCG 58.566 55.000 0.00 0.00 0.00 3.79
2278 5089 3.716006 CGACAGGTTGTGCGCCAG 61.716 66.667 4.18 0.00 0.00 4.85
2284 5095 2.941333 CAGCTGCGACAGGTTGTG 59.059 61.111 0.00 0.00 40.40 3.33
2413 5224 0.038251 GTGGACACATCAGCGAGTGA 60.038 55.000 7.65 0.00 40.38 3.41
2505 5316 1.605712 GCAAGGTCGAGCTGTGTAAGT 60.606 52.381 19.39 0.00 0.00 2.24
2598 5409 1.768112 CGCCGGTGAACTCGTTGTTT 61.768 55.000 10.20 0.00 39.30 2.83
3075 5886 0.310854 CGACACCCCACAGCTTTTTC 59.689 55.000 0.00 0.00 0.00 2.29
3078 5889 2.113139 CCGACACCCCACAGCTTT 59.887 61.111 0.00 0.00 0.00 3.51
3121 5932 0.911769 TCCTTCATGCCGTCCTTGAT 59.088 50.000 0.00 0.00 0.00 2.57
3122 5933 0.036388 GTCCTTCATGCCGTCCTTGA 60.036 55.000 0.00 0.00 0.00 3.02
3577 6400 2.349590 TGTCATCAGTTCATCGGCAAG 58.650 47.619 0.00 0.00 0.00 4.01
3597 6421 3.763360 CTCTGGAGTTCAGACAGATCACT 59.237 47.826 0.00 0.00 46.71 3.41
3603 6427 3.126171 CGAGTACTCTGGAGTTCAGACAG 59.874 52.174 20.34 0.00 46.71 3.51
4021 6881 1.019278 AAGTGTGGCGATGCTAACCG 61.019 55.000 0.00 0.00 0.00 4.44
4062 6922 7.067372 TGCATTAAGATTTCACACCTAATGGAG 59.933 37.037 0.00 0.00 37.04 3.86
4063 6923 6.889177 TGCATTAAGATTTCACACCTAATGGA 59.111 34.615 0.00 0.00 37.04 3.41
4064 6924 7.099266 TGCATTAAGATTTCACACCTAATGG 57.901 36.000 0.00 0.00 39.83 3.16
4065 6925 6.694411 GCTGCATTAAGATTTCACACCTAATG 59.306 38.462 0.00 0.00 0.00 1.90
4066 6926 6.604795 AGCTGCATTAAGATTTCACACCTAAT 59.395 34.615 1.02 0.00 0.00 1.73
4067 6927 5.945784 AGCTGCATTAAGATTTCACACCTAA 59.054 36.000 1.02 0.00 0.00 2.69
4095 6955 1.995626 GGAGTCCCCTGCTGGCTAA 60.996 63.158 3.63 0.00 0.00 3.09
4120 6980 7.873195 AGTTTTTATAGCCCTAGATCAACCTT 58.127 34.615 0.00 0.00 0.00 3.50
4154 7014 8.903820 AGCAACAACAAGAGAAAAATACTAAGT 58.096 29.630 0.00 0.00 0.00 2.24
4155 7015 9.173939 CAGCAACAACAAGAGAAAAATACTAAG 57.826 33.333 0.00 0.00 0.00 2.18
4157 7017 8.220755 ACAGCAACAACAAGAGAAAAATACTA 57.779 30.769 0.00 0.00 0.00 1.82
4186 7046 5.664457 ACGGATCTATGTATATGTGCCATG 58.336 41.667 0.00 0.00 0.00 3.66
4262 7122 4.759183 AGTGAGCCACTTTCTTCTGAAATC 59.241 41.667 2.38 0.00 42.59 2.17
4281 7141 8.540730 GAGATGCTCTCAGTACACTTCTAGTGA 61.541 44.444 13.35 0.00 44.42 3.41
4282 7142 6.458206 GAGATGCTCTCAGTACACTTCTAGTG 60.458 46.154 5.33 5.33 45.65 2.74
4283 7143 5.505780 AGATGCTCTCAGTACACTTCTAGT 58.494 41.667 0.00 0.00 0.00 2.57
4288 7148 3.435275 TGGAGATGCTCTCAGTACACTT 58.565 45.455 13.06 0.00 45.12 3.16
4329 7287 3.550561 CGTCAAATCAGTTTTTAGCGCA 58.449 40.909 11.47 0.00 0.00 6.09
4607 10387 6.127810 AGTTTCTATCGCTGTATGTCGTAA 57.872 37.500 0.00 0.00 0.00 3.18
4735 10906 2.029020 AGTGCGACATAGTTTCAGCAGA 60.029 45.455 0.00 0.00 35.15 4.26
4773 10944 4.814294 GACCGGCGTCAGCGGAAT 62.814 66.667 6.01 0.00 45.20 3.01


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

AutoCloner maintained by Alex Coulton.