Multiple sequence alignment - TraesCS5A01G222800

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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 TraesCS5A01G222800 chr5A 100.000 3461 0 0 1 3461 438822315 438825775 0.000000e+00 6392.0
1 TraesCS5A01G222800 chr5A 97.720 921 21 0 2541 3461 438832827 438833747 0.000000e+00 1585.0
2 TraesCS5A01G222800 chr5A 93.913 920 52 4 2544 3460 315509637 315508719 0.000000e+00 1386.0
3 TraesCS5A01G222800 chr5A 93.608 923 54 5 2542 3460 206740277 206739356 0.000000e+00 1373.0
4 TraesCS5A01G222800 chr5A 95.745 611 25 1 1 611 440801333 440800724 0.000000e+00 983.0
5 TraesCS5A01G222800 chr5A 94.165 617 35 1 1 616 438800911 438801527 0.000000e+00 939.0
6 TraesCS5A01G222800 chr5B 92.051 1648 92 15 922 2547 396432118 396433748 0.000000e+00 2281.0
7 TraesCS5A01G222800 chr5B 87.582 153 14 4 740 888 396430944 396431095 4.590000e-39 172.0
8 TraesCS5A01G222800 chr2B 84.573 1640 168 38 945 2528 158431039 158432649 0.000000e+00 1548.0
9 TraesCS5A01G222800 chr6A 93.601 922 54 5 2542 3461 319338915 319337997 0.000000e+00 1371.0
10 TraesCS5A01G222800 chr6A 93.943 908 52 3 2555 3460 125731033 125731939 0.000000e+00 1369.0
11 TraesCS5A01G222800 chr6A 91.993 612 47 2 1 611 473007095 473007705 0.000000e+00 857.0
12 TraesCS5A01G222800 chr7A 93.290 924 55 7 2542 3461 534511946 534511026 0.000000e+00 1356.0
13 TraesCS5A01G222800 chr7A 92.796 930 60 7 2535 3460 321563181 321564107 0.000000e+00 1339.0
14 TraesCS5A01G222800 chr7A 91.993 612 47 2 1 611 151126462 151127072 0.000000e+00 857.0
15 TraesCS5A01G222800 chr4A 93.081 925 55 9 2542 3460 465774305 465775226 0.000000e+00 1345.0
16 TraesCS5A01G222800 chr4A 91.993 612 46 3 1 611 160465816 160465207 0.000000e+00 856.0
17 TraesCS5A01G222800 chr2A 92.981 926 57 8 2541 3461 382361841 382362763 0.000000e+00 1343.0
18 TraesCS5A01G222800 chr2A 86.545 1204 134 15 922 2110 104787345 104788535 0.000000e+00 1301.0
19 TraesCS5A01G222800 chr2A 91.993 612 47 2 1 611 130821845 130822455 0.000000e+00 857.0
20 TraesCS5A01G222800 chr2A 91.993 612 46 2 1 611 563966736 563966127 0.000000e+00 856.0
21 TraesCS5A01G222800 chr2A 85.618 445 42 9 2103 2528 104788559 104789000 6.810000e-122 448.0
22 TraesCS5A01G222800 chr5D 89.507 1096 61 13 1471 2547 337681641 337682701 0.000000e+00 1338.0
23 TraesCS5A01G222800 chr5D 93.097 507 29 4 922 1423 337681138 337681643 0.000000e+00 737.0
24 TraesCS5A01G222800 chr5D 90.909 77 3 1 739 815 337680967 337681039 2.200000e-17 100.0
25 TraesCS5A01G222800 chr2D 86.789 1196 135 12 922 2105 108769888 108771072 0.000000e+00 1312.0
26 TraesCS5A01G222800 chr2D 85.393 445 43 9 2103 2528 108771101 108771542 3.170000e-120 442.0
27 TraesCS5A01G222800 chr1A 92.787 610 42 2 1 609 87717190 87717798 0.000000e+00 881.0
28 TraesCS5A01G222800 chr3A 92.157 612 46 2 1 611 588660957 588661567 0.000000e+00 863.0
29 TraesCS5A01G222800 chr7D 96.721 61 2 0 660 720 562813512 562813452 6.110000e-18 102.0
30 TraesCS5A01G222800 chr1D 96.721 61 2 0 660 720 47982811 47982751 6.110000e-18 102.0
31 TraesCS5A01G222800 chr7B 93.651 63 2 2 660 720 618414444 618414382 3.680000e-15 93.5
32 TraesCS5A01G222800 chr4D 91.304 69 4 2 653 720 46761131 46761064 3.680000e-15 93.5
33 TraesCS5A01G222800 chr4D 93.651 63 2 1 660 720 49808532 49808594 3.680000e-15 93.5


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 TraesCS5A01G222800 chr5A 438822315 438825775 3460 False 6392.0 6392 100.0000 1 3461 1 chr5A.!!$F2 3460
1 TraesCS5A01G222800 chr5A 438832827 438833747 920 False 1585.0 1585 97.7200 2541 3461 1 chr5A.!!$F3 920
2 TraesCS5A01G222800 chr5A 315508719 315509637 918 True 1386.0 1386 93.9130 2544 3460 1 chr5A.!!$R2 916
3 TraesCS5A01G222800 chr5A 206739356 206740277 921 True 1373.0 1373 93.6080 2542 3460 1 chr5A.!!$R1 918
4 TraesCS5A01G222800 chr5A 440800724 440801333 609 True 983.0 983 95.7450 1 611 1 chr5A.!!$R3 610
5 TraesCS5A01G222800 chr5A 438800911 438801527 616 False 939.0 939 94.1650 1 616 1 chr5A.!!$F1 615
6 TraesCS5A01G222800 chr5B 396430944 396433748 2804 False 1226.5 2281 89.8165 740 2547 2 chr5B.!!$F1 1807
7 TraesCS5A01G222800 chr2B 158431039 158432649 1610 False 1548.0 1548 84.5730 945 2528 1 chr2B.!!$F1 1583
8 TraesCS5A01G222800 chr6A 319337997 319338915 918 True 1371.0 1371 93.6010 2542 3461 1 chr6A.!!$R1 919
9 TraesCS5A01G222800 chr6A 125731033 125731939 906 False 1369.0 1369 93.9430 2555 3460 1 chr6A.!!$F1 905
10 TraesCS5A01G222800 chr6A 473007095 473007705 610 False 857.0 857 91.9930 1 611 1 chr6A.!!$F2 610
11 TraesCS5A01G222800 chr7A 534511026 534511946 920 True 1356.0 1356 93.2900 2542 3461 1 chr7A.!!$R1 919
12 TraesCS5A01G222800 chr7A 321563181 321564107 926 False 1339.0 1339 92.7960 2535 3460 1 chr7A.!!$F2 925
13 TraesCS5A01G222800 chr7A 151126462 151127072 610 False 857.0 857 91.9930 1 611 1 chr7A.!!$F1 610
14 TraesCS5A01G222800 chr4A 465774305 465775226 921 False 1345.0 1345 93.0810 2542 3460 1 chr4A.!!$F1 918
15 TraesCS5A01G222800 chr4A 160465207 160465816 609 True 856.0 856 91.9930 1 611 1 chr4A.!!$R1 610
16 TraesCS5A01G222800 chr2A 382361841 382362763 922 False 1343.0 1343 92.9810 2541 3461 1 chr2A.!!$F2 920
17 TraesCS5A01G222800 chr2A 104787345 104789000 1655 False 874.5 1301 86.0815 922 2528 2 chr2A.!!$F3 1606
18 TraesCS5A01G222800 chr2A 130821845 130822455 610 False 857.0 857 91.9930 1 611 1 chr2A.!!$F1 610
19 TraesCS5A01G222800 chr2A 563966127 563966736 609 True 856.0 856 91.9930 1 611 1 chr2A.!!$R1 610
20 TraesCS5A01G222800 chr5D 337680967 337682701 1734 False 725.0 1338 91.1710 739 2547 3 chr5D.!!$F1 1808
21 TraesCS5A01G222800 chr2D 108769888 108771542 1654 False 877.0 1312 86.0910 922 2528 2 chr2D.!!$F1 1606
22 TraesCS5A01G222800 chr1A 87717190 87717798 608 False 881.0 881 92.7870 1 609 1 chr1A.!!$F1 608
23 TraesCS5A01G222800 chr3A 588660957 588661567 610 False 863.0 863 92.1570 1 611 1 chr3A.!!$F1 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
820 827 0.190815 ACCAAGCCCACCCATCTTTT 59.809 50.0 0.0 0.0 0.0 2.27 F
1173 2188 0.107081 TCTCCCTCGATCTCTCCGTC 59.893 60.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 2829 0.179215 CAAAGTCCGTGCTTGATCGC 60.179 55.0 0.0 0.0 0.0 4.58 R
3010 4106 0.761187 TGCAGCTCCATCTCATACCC 59.239 55.0 0.0 0.0 0.0 3.69 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
33 34 1.827969 GGTGATCACTGTAGCCTCACT 59.172 52.381 24.50 0.00 37.11 3.41
201 203 2.501128 CAGCCCGTCGTGGATGAT 59.499 61.111 11.20 0.00 44.65 2.45
255 257 1.692749 AGGTCATGGCCACCCGTAT 60.693 57.895 20.74 0.00 33.96 3.06
309 311 1.064685 GGGTGGCAGGCTTTACTGTAT 60.065 52.381 0.00 0.00 40.59 2.29
310 312 2.620627 GGGTGGCAGGCTTTACTGTATT 60.621 50.000 0.00 0.00 40.59 1.89
535 537 3.490348 CCATGTCTTGGTTTCTTGAGGT 58.510 45.455 0.00 0.00 40.99 3.85
549 551 4.115199 AGGTCCGGATGGGCTTGC 62.115 66.667 7.81 0.00 40.80 4.01
552 554 1.754234 GTCCGGATGGGCTTGCAAT 60.754 57.895 7.81 0.00 36.72 3.56
612 616 4.944930 CCCATGGTTATTTACTCCGACAAA 59.055 41.667 11.73 0.00 0.00 2.83
616 620 7.334921 CCATGGTTATTTACTCCGACAAAAGTA 59.665 37.037 2.57 0.00 0.00 2.24
617 621 8.889717 CATGGTTATTTACTCCGACAAAAGTAT 58.110 33.333 0.00 0.00 0.00 2.12
618 622 8.851541 TGGTTATTTACTCCGACAAAAGTATT 57.148 30.769 0.00 0.00 0.00 1.89
619 623 8.938906 TGGTTATTTACTCCGACAAAAGTATTC 58.061 33.333 0.00 0.00 0.00 1.75
620 624 9.159364 GGTTATTTACTCCGACAAAAGTATTCT 57.841 33.333 0.00 0.00 0.00 2.40
650 654 9.968743 ATTAGTGATTTCGTCGTTTAGATTTTC 57.031 29.630 0.00 0.00 0.00 2.29
651 655 6.828672 AGTGATTTCGTCGTTTAGATTTTCC 58.171 36.000 0.00 0.00 0.00 3.13
652 656 6.649557 AGTGATTTCGTCGTTTAGATTTTCCT 59.350 34.615 0.00 0.00 0.00 3.36
653 657 7.816031 AGTGATTTCGTCGTTTAGATTTTCCTA 59.184 33.333 0.00 0.00 0.00 2.94
654 658 8.437742 GTGATTTCGTCGTTTAGATTTTCCTAA 58.562 33.333 0.00 0.00 0.00 2.69
655 659 9.158233 TGATTTCGTCGTTTAGATTTTCCTAAT 57.842 29.630 0.00 0.00 0.00 1.73
658 662 9.859427 TTTCGTCGTTTAGATTTTCCTAATAGA 57.141 29.630 0.00 0.00 0.00 1.98
690 694 4.487714 AGGAACTCGCCATCTTTATTCA 57.512 40.909 0.00 0.00 0.00 2.57
691 695 4.843728 AGGAACTCGCCATCTTTATTCAA 58.156 39.130 0.00 0.00 0.00 2.69
692 696 4.636206 AGGAACTCGCCATCTTTATTCAAC 59.364 41.667 0.00 0.00 0.00 3.18
693 697 4.201920 GGAACTCGCCATCTTTATTCAACC 60.202 45.833 0.00 0.00 0.00 3.77
694 698 3.950397 ACTCGCCATCTTTATTCAACCA 58.050 40.909 0.00 0.00 0.00 3.67
695 699 4.331968 ACTCGCCATCTTTATTCAACCAA 58.668 39.130 0.00 0.00 0.00 3.67
696 700 4.764823 ACTCGCCATCTTTATTCAACCAAA 59.235 37.500 0.00 0.00 0.00 3.28
697 701 5.106157 ACTCGCCATCTTTATTCAACCAAAG 60.106 40.000 0.00 0.00 33.86 2.77
698 702 3.859386 CGCCATCTTTATTCAACCAAAGC 59.141 43.478 0.00 0.00 32.84 3.51
699 703 4.617995 CGCCATCTTTATTCAACCAAAGCA 60.618 41.667 0.00 0.00 32.84 3.91
700 704 5.237048 GCCATCTTTATTCAACCAAAGCAA 58.763 37.500 0.00 0.00 32.84 3.91
701 705 5.700373 GCCATCTTTATTCAACCAAAGCAAA 59.300 36.000 0.00 0.00 32.84 3.68
702 706 6.204495 GCCATCTTTATTCAACCAAAGCAAAA 59.796 34.615 0.00 0.00 32.84 2.44
703 707 7.571798 GCCATCTTTATTCAACCAAAGCAAAAG 60.572 37.037 0.00 0.00 32.84 2.27
704 708 7.442062 CCATCTTTATTCAACCAAAGCAAAAGT 59.558 33.333 0.00 0.00 32.84 2.66
705 709 8.490355 CATCTTTATTCAACCAAAGCAAAAGTC 58.510 33.333 0.00 0.00 32.84 3.01
706 710 7.551585 TCTTTATTCAACCAAAGCAAAAGTCA 58.448 30.769 0.00 0.00 32.84 3.41
707 711 8.203485 TCTTTATTCAACCAAAGCAAAAGTCAT 58.797 29.630 0.00 0.00 32.84 3.06
708 712 9.474920 CTTTATTCAACCAAAGCAAAAGTCATA 57.525 29.630 0.00 0.00 0.00 2.15
709 713 9.474920 TTTATTCAACCAAAGCAAAAGTCATAG 57.525 29.630 0.00 0.00 0.00 2.23
710 714 5.452078 TCAACCAAAGCAAAAGTCATAGG 57.548 39.130 0.00 0.00 0.00 2.57
711 715 4.892934 TCAACCAAAGCAAAAGTCATAGGT 59.107 37.500 0.00 0.00 0.00 3.08
712 716 6.065374 TCAACCAAAGCAAAAGTCATAGGTA 58.935 36.000 0.00 0.00 0.00 3.08
713 717 5.959618 ACCAAAGCAAAAGTCATAGGTAC 57.040 39.130 0.00 0.00 0.00 3.34
714 718 5.381757 ACCAAAGCAAAAGTCATAGGTACA 58.618 37.500 0.00 0.00 0.00 2.90
715 719 5.830991 ACCAAAGCAAAAGTCATAGGTACAA 59.169 36.000 0.00 0.00 0.00 2.41
716 720 6.016276 ACCAAAGCAAAAGTCATAGGTACAAG 60.016 38.462 0.00 0.00 0.00 3.16
717 721 6.381801 CAAAGCAAAAGTCATAGGTACAAGG 58.618 40.000 0.00 0.00 0.00 3.61
718 722 5.242795 AGCAAAAGTCATAGGTACAAGGT 57.757 39.130 0.00 0.00 0.00 3.50
719 723 5.631119 AGCAAAAGTCATAGGTACAAGGTT 58.369 37.500 0.00 0.00 0.00 3.50
720 724 6.775708 AGCAAAAGTCATAGGTACAAGGTTA 58.224 36.000 0.00 0.00 0.00 2.85
721 725 6.879458 AGCAAAAGTCATAGGTACAAGGTTAG 59.121 38.462 0.00 0.00 0.00 2.34
722 726 6.653740 GCAAAAGTCATAGGTACAAGGTTAGT 59.346 38.462 0.00 0.00 0.00 2.24
723 727 7.174426 GCAAAAGTCATAGGTACAAGGTTAGTT 59.826 37.037 0.00 0.00 0.00 2.24
724 728 9.715121 CAAAAGTCATAGGTACAAGGTTAGTTA 57.285 33.333 0.00 0.00 0.00 2.24
728 732 9.263446 AGTCATAGGTACAAGGTTAGTTAATCA 57.737 33.333 0.00 0.00 0.00 2.57
729 733 9.530633 GTCATAGGTACAAGGTTAGTTAATCAG 57.469 37.037 0.00 0.00 0.00 2.90
730 734 9.483489 TCATAGGTACAAGGTTAGTTAATCAGA 57.517 33.333 0.00 0.00 0.00 3.27
731 735 9.530633 CATAGGTACAAGGTTAGTTAATCAGAC 57.469 37.037 0.00 0.00 0.00 3.51
732 736 6.944096 AGGTACAAGGTTAGTTAATCAGACC 58.056 40.000 0.00 0.00 0.00 3.85
733 737 6.499350 AGGTACAAGGTTAGTTAATCAGACCA 59.501 38.462 0.00 0.00 32.81 4.02
734 738 6.592994 GGTACAAGGTTAGTTAATCAGACCAC 59.407 42.308 0.00 0.00 32.81 4.16
735 739 6.435292 ACAAGGTTAGTTAATCAGACCACT 57.565 37.500 0.00 0.00 32.81 4.00
736 740 6.465084 ACAAGGTTAGTTAATCAGACCACTC 58.535 40.000 0.00 0.00 32.81 3.51
737 741 6.042781 ACAAGGTTAGTTAATCAGACCACTCA 59.957 38.462 0.00 0.00 32.81 3.41
754 758 2.168106 ACTCACAGATGCACTCCTCATC 59.832 50.000 0.00 0.00 40.34 2.92
760 764 4.040217 ACAGATGCACTCCTCATCTAATCC 59.960 45.833 5.32 0.00 46.31 3.01
815 819 2.604382 GCAACCAAGCCCACCCAT 60.604 61.111 0.00 0.00 0.00 4.00
820 827 0.190815 ACCAAGCCCACCCATCTTTT 59.809 50.000 0.00 0.00 0.00 2.27
842 849 4.678743 GTTGAGCCCACCCACCCC 62.679 72.222 0.00 0.00 0.00 4.95
845 852 3.672503 GAGCCCACCCACCCCATT 61.673 66.667 0.00 0.00 0.00 3.16
852 859 4.092574 CCCACCCCATTGGCCCAT 62.093 66.667 0.00 0.00 37.83 4.00
853 860 2.709756 CCCACCCCATTGGCCCATA 61.710 63.158 0.00 0.00 37.83 2.74
863 870 4.547367 GGCCCATAAGCCGCGACT 62.547 66.667 8.23 0.00 44.57 4.18
867 874 2.411701 CATAAGCCGCGACTCCGA 59.588 61.111 8.23 0.00 38.22 4.55
892 899 1.591394 CGTAGGCGCGAAAAATAGCAC 60.591 52.381 12.10 0.00 0.00 4.40
895 902 2.285083 AGGCGCGAAAAATAGCACATA 58.715 42.857 12.10 0.00 0.00 2.29
896 903 2.878406 AGGCGCGAAAAATAGCACATAT 59.122 40.909 12.10 0.00 0.00 1.78
898 905 3.664025 GGCGCGAAAAATAGCACATATTC 59.336 43.478 12.10 0.00 32.71 1.75
899 906 3.664025 GCGCGAAAAATAGCACATATTCC 59.336 43.478 12.10 0.00 32.71 3.01
900 907 4.788201 GCGCGAAAAATAGCACATATTCCA 60.788 41.667 12.10 0.00 32.71 3.53
901 908 4.905866 CGCGAAAAATAGCACATATTCCAG 59.094 41.667 0.00 0.00 32.71 3.86
941 1937 3.001406 AAACCGTCTCCCCCTCCG 61.001 66.667 0.00 0.00 0.00 4.63
1173 2188 0.107081 TCTCCCTCGATCTCTCCGTC 59.893 60.000 0.00 0.00 0.00 4.79
1237 2252 0.822532 GGCCATCATCTGCCTTGAGG 60.823 60.000 0.00 0.00 44.46 3.86
1285 2300 1.444553 CTCCAAGTGCTCGACGGAC 60.445 63.158 0.00 0.00 0.00 4.79
1289 2304 2.856628 AAGTGCTCGACGGACTGCA 61.857 57.895 9.14 0.67 44.21 4.41
1304 2319 0.890683 CTGCACATTTGGAGGTTCCC 59.109 55.000 0.00 0.00 37.53 3.97
1369 2386 2.189594 TGAGCAGGTTTCAGGTGATG 57.810 50.000 0.00 0.00 0.00 3.07
1469 2486 1.086696 CCTTGGTGTCAAGTATGCCG 58.913 55.000 5.56 0.00 46.65 5.69
1475 2492 1.468520 GTGTCAAGTATGCCGCATTGT 59.531 47.619 11.97 0.00 0.00 2.71
1476 2493 1.468127 TGTCAAGTATGCCGCATTGTG 59.532 47.619 11.97 7.62 0.00 3.33
1483 2500 0.244450 ATGCCGCATTGTGTTTCTGG 59.756 50.000 0.00 0.00 0.00 3.86
1510 2527 6.869388 TCACTAATTCATACGTGCAAGTAACA 59.131 34.615 16.44 3.48 0.00 2.41
1571 2588 0.251121 TGGATGTGCGTGAATTGGGT 60.251 50.000 0.00 0.00 0.00 4.51
1656 2673 4.461198 CTCCCTTTGGTAGTTCTGTTGTT 58.539 43.478 0.00 0.00 0.00 2.83
1657 2674 4.457466 TCCCTTTGGTAGTTCTGTTGTTC 58.543 43.478 0.00 0.00 0.00 3.18
1658 2675 4.165372 TCCCTTTGGTAGTTCTGTTGTTCT 59.835 41.667 0.00 0.00 0.00 3.01
1659 2676 4.275936 CCCTTTGGTAGTTCTGTTGTTCTG 59.724 45.833 0.00 0.00 0.00 3.02
1660 2677 4.261197 CCTTTGGTAGTTCTGTTGTTCTGC 60.261 45.833 0.00 0.00 0.00 4.26
1702 2720 5.476254 TGTTGATGTCTGGTTATGCAATTGA 59.524 36.000 10.34 0.00 0.00 2.57
1703 2721 6.153170 TGTTGATGTCTGGTTATGCAATTGAT 59.847 34.615 10.34 2.74 0.00 2.57
1811 2829 1.078214 TGCATTGCCTCCTTCTCGG 60.078 57.895 6.12 0.00 0.00 4.63
1812 2830 2.476320 GCATTGCCTCCTTCTCGGC 61.476 63.158 0.00 0.00 46.46 5.54
1816 2834 2.028337 GCCTCCTTCTCGGCGATC 59.972 66.667 11.27 0.00 36.45 3.69
1817 2835 2.786495 GCCTCCTTCTCGGCGATCA 61.786 63.158 11.27 0.00 36.45 2.92
1818 2836 1.816537 CCTCCTTCTCGGCGATCAA 59.183 57.895 11.27 5.60 0.00 2.57
1819 2837 0.249238 CCTCCTTCTCGGCGATCAAG 60.249 60.000 11.27 15.33 0.00 3.02
1820 2838 0.873743 CTCCTTCTCGGCGATCAAGC 60.874 60.000 11.27 0.00 0.00 4.01
1821 2839 1.153568 CCTTCTCGGCGATCAAGCA 60.154 57.895 11.27 0.00 39.27 3.91
1822 2840 1.424493 CCTTCTCGGCGATCAAGCAC 61.424 60.000 11.27 0.00 39.27 4.40
1899 2929 4.142600 GGCATAAGGTGACAACAGAATCAC 60.143 45.833 0.00 0.00 43.75 3.06
1906 2940 7.027778 AGGTGACAACAGAATCACTAAAAAC 57.972 36.000 4.53 0.00 43.91 2.43
1907 2941 6.601613 AGGTGACAACAGAATCACTAAAAACA 59.398 34.615 4.53 0.00 43.91 2.83
1952 2986 5.458779 GGAAGCGTATAAATGATTTGTTGCC 59.541 40.000 0.00 0.00 0.00 4.52
2039 3073 2.760650 TGTGTGGTACATCTAGCTCTGG 59.239 50.000 0.00 0.00 44.52 3.86
2061 3095 6.709281 TGGATTTACAACGGTAATGGACTTA 58.291 36.000 0.00 0.00 39.15 2.24
2125 3190 8.607441 TCTCACATATACATGTTTAGATTGGC 57.393 34.615 2.30 0.00 42.98 4.52
2188 3253 2.838736 CAGGTTTCGACATCTATGGGG 58.161 52.381 0.00 0.00 0.00 4.96
2209 3274 5.984233 GGGACCTTTGTTTTGATGTTTTC 57.016 39.130 0.00 0.00 0.00 2.29
2446 3529 2.845586 TCAGGGGATGACAATGATGACA 59.154 45.455 0.00 0.00 35.75 3.58
2528 3612 8.889000 GTTAGTTGTGAAATTCATGACGTAAAC 58.111 33.333 0.00 5.71 0.00 2.01
2626 3710 1.535028 TGTAAGCAATGTCGCAAGTGG 59.465 47.619 0.00 0.00 39.48 4.00
2628 3712 0.823356 AAGCAATGTCGCAAGTGGGT 60.823 50.000 0.00 0.00 39.48 4.51
2797 3886 3.165071 CCCAAAAGCTACACAAATCCCT 58.835 45.455 0.00 0.00 0.00 4.20
3010 4106 9.420551 CTATTTAAGCTTATAGGAAGGGTAACG 57.579 37.037 7.08 0.00 37.60 3.18
3064 4162 4.513692 GCATATTTGGTGGCTAACATACGA 59.486 41.667 0.00 0.00 0.00 3.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.354704 CCCATTAAGGAGACAAGACGCA 60.355 50.000 0.00 0.00 41.22 5.24
201 203 2.130821 TTGCCACGTTGCCCCTGATA 62.131 55.000 9.38 0.00 0.00 2.15
309 311 2.047655 GATGTGACGGGGCGTGAA 60.048 61.111 0.00 0.00 41.37 3.18
310 312 4.429212 CGATGTGACGGGGCGTGA 62.429 66.667 0.00 0.00 41.37 4.35
535 537 0.614415 AAATTGCAAGCCCATCCGGA 60.614 50.000 6.61 6.61 0.00 5.14
624 628 9.968743 GAAAATCTAAACGACGAAATCACTAAT 57.031 29.630 0.00 0.00 0.00 1.73
625 629 8.437742 GGAAAATCTAAACGACGAAATCACTAA 58.562 33.333 0.00 0.00 0.00 2.24
626 630 7.816031 AGGAAAATCTAAACGACGAAATCACTA 59.184 33.333 0.00 0.00 0.00 2.74
627 631 6.649557 AGGAAAATCTAAACGACGAAATCACT 59.350 34.615 0.00 0.00 0.00 3.41
628 632 6.828672 AGGAAAATCTAAACGACGAAATCAC 58.171 36.000 0.00 0.00 0.00 3.06
629 633 8.537049 TTAGGAAAATCTAAACGACGAAATCA 57.463 30.769 0.00 0.00 0.00 2.57
632 636 9.859427 TCTATTAGGAAAATCTAAACGACGAAA 57.141 29.630 0.00 0.00 33.54 3.46
661 665 2.631160 TGGCGAGTTCCTCTCAAAAA 57.369 45.000 0.00 0.00 42.88 1.94
662 666 2.303022 AGATGGCGAGTTCCTCTCAAAA 59.697 45.455 0.00 0.00 42.88 2.44
663 667 1.902508 AGATGGCGAGTTCCTCTCAAA 59.097 47.619 0.00 0.00 42.88 2.69
664 668 1.561643 AGATGGCGAGTTCCTCTCAA 58.438 50.000 0.00 0.00 42.88 3.02
665 669 1.561643 AAGATGGCGAGTTCCTCTCA 58.438 50.000 0.00 0.00 42.88 3.27
666 670 2.682155 AAAGATGGCGAGTTCCTCTC 57.318 50.000 0.00 0.00 39.62 3.20
667 671 4.162320 TGAATAAAGATGGCGAGTTCCTCT 59.838 41.667 0.00 0.00 0.00 3.69
668 672 4.442706 TGAATAAAGATGGCGAGTTCCTC 58.557 43.478 0.00 0.00 0.00 3.71
669 673 4.487714 TGAATAAAGATGGCGAGTTCCT 57.512 40.909 0.00 0.00 0.00 3.36
670 674 4.201920 GGTTGAATAAAGATGGCGAGTTCC 60.202 45.833 0.00 0.00 0.00 3.62
671 675 4.394920 TGGTTGAATAAAGATGGCGAGTTC 59.605 41.667 0.00 0.00 0.00 3.01
672 676 4.331968 TGGTTGAATAAAGATGGCGAGTT 58.668 39.130 0.00 0.00 0.00 3.01
673 677 3.950397 TGGTTGAATAAAGATGGCGAGT 58.050 40.909 0.00 0.00 0.00 4.18
674 678 4.963276 TTGGTTGAATAAAGATGGCGAG 57.037 40.909 0.00 0.00 0.00 5.03
675 679 4.380444 GCTTTGGTTGAATAAAGATGGCGA 60.380 41.667 8.45 0.00 36.29 5.54
676 680 3.859386 GCTTTGGTTGAATAAAGATGGCG 59.141 43.478 8.45 0.00 36.29 5.69
677 681 4.819769 TGCTTTGGTTGAATAAAGATGGC 58.180 39.130 8.45 0.00 36.29 4.40
678 682 7.442062 ACTTTTGCTTTGGTTGAATAAAGATGG 59.558 33.333 8.45 0.00 36.29 3.51
679 683 8.369218 ACTTTTGCTTTGGTTGAATAAAGATG 57.631 30.769 8.45 0.00 36.29 2.90
680 684 8.203485 TGACTTTTGCTTTGGTTGAATAAAGAT 58.797 29.630 8.45 0.00 36.29 2.40
681 685 7.551585 TGACTTTTGCTTTGGTTGAATAAAGA 58.448 30.769 8.45 0.00 36.29 2.52
682 686 7.769272 TGACTTTTGCTTTGGTTGAATAAAG 57.231 32.000 0.00 0.00 37.06 1.85
683 687 9.474920 CTATGACTTTTGCTTTGGTTGAATAAA 57.525 29.630 0.00 0.00 0.00 1.40
684 688 8.087750 CCTATGACTTTTGCTTTGGTTGAATAA 58.912 33.333 0.00 0.00 0.00 1.40
685 689 7.232534 ACCTATGACTTTTGCTTTGGTTGAATA 59.767 33.333 0.00 0.00 0.00 1.75
686 690 6.041979 ACCTATGACTTTTGCTTTGGTTGAAT 59.958 34.615 0.00 0.00 0.00 2.57
687 691 5.362430 ACCTATGACTTTTGCTTTGGTTGAA 59.638 36.000 0.00 0.00 0.00 2.69
688 692 4.892934 ACCTATGACTTTTGCTTTGGTTGA 59.107 37.500 0.00 0.00 0.00 3.18
689 693 5.200368 ACCTATGACTTTTGCTTTGGTTG 57.800 39.130 0.00 0.00 0.00 3.77
690 694 5.830991 TGTACCTATGACTTTTGCTTTGGTT 59.169 36.000 0.00 0.00 0.00 3.67
691 695 5.381757 TGTACCTATGACTTTTGCTTTGGT 58.618 37.500 0.00 0.00 0.00 3.67
692 696 5.957842 TGTACCTATGACTTTTGCTTTGG 57.042 39.130 0.00 0.00 0.00 3.28
693 697 6.016276 ACCTTGTACCTATGACTTTTGCTTTG 60.016 38.462 0.00 0.00 0.00 2.77
694 698 6.068670 ACCTTGTACCTATGACTTTTGCTTT 58.931 36.000 0.00 0.00 0.00 3.51
695 699 5.631119 ACCTTGTACCTATGACTTTTGCTT 58.369 37.500 0.00 0.00 0.00 3.91
696 700 5.242795 ACCTTGTACCTATGACTTTTGCT 57.757 39.130 0.00 0.00 0.00 3.91
697 701 5.959618 AACCTTGTACCTATGACTTTTGC 57.040 39.130 0.00 0.00 0.00 3.68
698 702 8.617290 AACTAACCTTGTACCTATGACTTTTG 57.383 34.615 0.00 0.00 0.00 2.44
702 706 9.263446 TGATTAACTAACCTTGTACCTATGACT 57.737 33.333 0.00 0.00 0.00 3.41
703 707 9.530633 CTGATTAACTAACCTTGTACCTATGAC 57.469 37.037 0.00 0.00 0.00 3.06
704 708 9.483489 TCTGATTAACTAACCTTGTACCTATGA 57.517 33.333 0.00 0.00 0.00 2.15
705 709 9.530633 GTCTGATTAACTAACCTTGTACCTATG 57.469 37.037 0.00 0.00 0.00 2.23
706 710 8.702819 GGTCTGATTAACTAACCTTGTACCTAT 58.297 37.037 0.00 0.00 0.00 2.57
707 711 7.675195 TGGTCTGATTAACTAACCTTGTACCTA 59.325 37.037 0.00 0.00 0.00 3.08
708 712 6.499350 TGGTCTGATTAACTAACCTTGTACCT 59.501 38.462 0.00 0.00 0.00 3.08
709 713 6.592994 GTGGTCTGATTAACTAACCTTGTACC 59.407 42.308 0.00 0.00 0.00 3.34
710 714 7.384477 AGTGGTCTGATTAACTAACCTTGTAC 58.616 38.462 0.00 0.00 0.00 2.90
711 715 7.233962 TGAGTGGTCTGATTAACTAACCTTGTA 59.766 37.037 0.00 0.00 0.00 2.41
712 716 6.042781 TGAGTGGTCTGATTAACTAACCTTGT 59.957 38.462 0.00 0.00 0.00 3.16
713 717 6.369065 GTGAGTGGTCTGATTAACTAACCTTG 59.631 42.308 0.00 0.00 0.00 3.61
714 718 6.042781 TGTGAGTGGTCTGATTAACTAACCTT 59.957 38.462 0.00 0.00 0.00 3.50
715 719 5.542635 TGTGAGTGGTCTGATTAACTAACCT 59.457 40.000 0.00 0.00 0.00 3.50
716 720 5.790593 TGTGAGTGGTCTGATTAACTAACC 58.209 41.667 0.00 0.00 0.00 2.85
717 721 6.688578 TCTGTGAGTGGTCTGATTAACTAAC 58.311 40.000 0.00 0.00 0.00 2.34
718 722 6.911250 TCTGTGAGTGGTCTGATTAACTAA 57.089 37.500 0.00 0.00 0.00 2.24
719 723 6.628175 GCATCTGTGAGTGGTCTGATTAACTA 60.628 42.308 0.00 0.00 0.00 2.24
720 724 5.728471 CATCTGTGAGTGGTCTGATTAACT 58.272 41.667 0.00 0.00 0.00 2.24
721 725 4.331168 GCATCTGTGAGTGGTCTGATTAAC 59.669 45.833 0.00 0.00 0.00 2.01
722 726 4.020307 TGCATCTGTGAGTGGTCTGATTAA 60.020 41.667 0.00 0.00 0.00 1.40
723 727 3.515104 TGCATCTGTGAGTGGTCTGATTA 59.485 43.478 0.00 0.00 0.00 1.75
724 728 2.303890 TGCATCTGTGAGTGGTCTGATT 59.696 45.455 0.00 0.00 0.00 2.57
725 729 1.904537 TGCATCTGTGAGTGGTCTGAT 59.095 47.619 0.00 0.00 0.00 2.90
726 730 1.001293 GTGCATCTGTGAGTGGTCTGA 59.999 52.381 0.00 0.00 0.00 3.27
727 731 1.001746 AGTGCATCTGTGAGTGGTCTG 59.998 52.381 0.00 0.00 0.00 3.51
728 732 1.274728 GAGTGCATCTGTGAGTGGTCT 59.725 52.381 0.00 0.00 0.00 3.85
729 733 1.674221 GGAGTGCATCTGTGAGTGGTC 60.674 57.143 0.00 0.00 0.00 4.02
730 734 0.322975 GGAGTGCATCTGTGAGTGGT 59.677 55.000 0.00 0.00 0.00 4.16
731 735 0.612229 AGGAGTGCATCTGTGAGTGG 59.388 55.000 0.00 0.00 0.00 4.00
732 736 1.274447 TGAGGAGTGCATCTGTGAGTG 59.726 52.381 0.00 0.00 0.00 3.51
733 737 1.637338 TGAGGAGTGCATCTGTGAGT 58.363 50.000 0.00 0.00 0.00 3.41
734 738 2.823984 GATGAGGAGTGCATCTGTGAG 58.176 52.381 0.00 0.00 39.18 3.51
735 739 2.975732 GATGAGGAGTGCATCTGTGA 57.024 50.000 0.00 0.00 39.18 3.58
754 758 1.471676 GCTGGTGAGTGGTCGGATTAG 60.472 57.143 0.00 0.00 0.00 1.73
760 764 3.625897 TGGGCTGGTGAGTGGTCG 61.626 66.667 0.00 0.00 0.00 4.79
820 827 1.479757 GGTGGGTGGGCTCAACTAAAA 60.480 52.381 0.00 0.00 27.90 1.52
847 854 2.967615 GAGTCGCGGCTTATGGGC 60.968 66.667 17.37 0.00 37.12 5.36
852 859 2.488355 CTTCGGAGTCGCGGCTTA 59.512 61.111 17.37 0.00 36.13 3.09
853 860 4.436998 CCTTCGGAGTCGCGGCTT 62.437 66.667 17.37 0.00 36.13 4.35
892 899 2.937469 TGTTTTGGCGCTGGAATATG 57.063 45.000 7.64 0.00 0.00 1.78
895 902 1.066929 GGATTGTTTTGGCGCTGGAAT 60.067 47.619 7.64 0.00 0.00 3.01
896 903 0.316841 GGATTGTTTTGGCGCTGGAA 59.683 50.000 7.64 0.00 0.00 3.53
898 905 1.444212 CGGATTGTTTTGGCGCTGG 60.444 57.895 7.64 0.00 0.00 4.85
899 906 0.039617 TTCGGATTGTTTTGGCGCTG 60.040 50.000 7.64 0.00 0.00 5.18
900 907 0.671251 TTTCGGATTGTTTTGGCGCT 59.329 45.000 7.64 0.00 0.00 5.92
901 908 1.191425 GTTTTCGGATTGTTTTGGCGC 59.809 47.619 0.00 0.00 0.00 6.53
991 1996 3.349006 CATGTCCATAGCCGCCGC 61.349 66.667 0.00 0.00 0.00 6.53
1047 2058 3.294493 GCCTTGCGCACAAAGGGA 61.294 61.111 24.31 2.13 34.74 4.20
1173 2188 1.539341 CAGCATCAGAGACACGTACG 58.461 55.000 15.01 15.01 0.00 3.67
1304 2319 1.299316 CATGCCTTAAATGCCGGCG 60.299 57.895 23.90 6.39 46.67 6.46
1311 2326 2.026262 ACGGGTCAGACATGCCTTAAAT 60.026 45.455 2.17 0.00 0.00 1.40
1323 2340 1.760613 AGACAAAACAGACGGGTCAGA 59.239 47.619 1.17 0.00 0.00 3.27
1369 2386 1.084370 CCGCCTCTGACCGATCAAAC 61.084 60.000 0.00 0.00 33.30 2.93
1392 2409 1.063642 TCTCCGACATCCCACTCATCT 60.064 52.381 0.00 0.00 0.00 2.90
1469 2486 3.715628 AGTGAACCAGAAACACAATGC 57.284 42.857 0.00 0.00 37.05 3.56
1475 2492 6.932400 ACGTATGAATTAGTGAACCAGAAACA 59.068 34.615 0.00 0.00 0.00 2.83
1476 2493 7.234384 CACGTATGAATTAGTGAACCAGAAAC 58.766 38.462 0.00 0.00 36.79 2.78
1483 2500 6.165659 ACTTGCACGTATGAATTAGTGAAC 57.834 37.500 0.00 0.00 36.79 3.18
1510 2527 2.439507 ACCGCTCCATTCATCAATACCT 59.560 45.455 0.00 0.00 0.00 3.08
1656 2673 2.229792 CAAGTTAACCTTGCAGGCAGA 58.770 47.619 0.88 0.00 43.84 4.26
1657 2674 2.712057 CAAGTTAACCTTGCAGGCAG 57.288 50.000 0.88 0.00 43.84 4.85
1669 2686 4.460263 ACCAGACATCAACAGCAAGTTAA 58.540 39.130 0.00 0.00 38.74 2.01
1702 2720 3.509442 TCCAAAACTTTGCATCCCAGAT 58.491 40.909 0.00 0.00 36.86 2.90
1703 2721 2.956132 TCCAAAACTTTGCATCCCAGA 58.044 42.857 0.00 0.00 36.86 3.86
1811 2829 0.179215 CAAAGTCCGTGCTTGATCGC 60.179 55.000 0.00 0.00 0.00 4.58
1812 2830 0.443869 CCAAAGTCCGTGCTTGATCG 59.556 55.000 0.00 0.00 0.00 3.69
1813 2831 1.464997 GACCAAAGTCCGTGCTTGATC 59.535 52.381 0.00 0.00 37.00 2.92
1814 2832 1.523758 GACCAAAGTCCGTGCTTGAT 58.476 50.000 0.00 0.00 37.00 2.57
1815 2833 0.878523 CGACCAAAGTCCGTGCTTGA 60.879 55.000 0.00 0.00 40.12 3.02
1816 2834 1.569493 CGACCAAAGTCCGTGCTTG 59.431 57.895 0.00 0.00 40.12 4.01
1817 2835 1.597027 CCGACCAAAGTCCGTGCTT 60.597 57.895 0.00 0.00 40.12 3.91
1818 2836 2.030562 CCGACCAAAGTCCGTGCT 59.969 61.111 0.00 0.00 40.12 4.40
1819 2837 3.723348 GCCGACCAAAGTCCGTGC 61.723 66.667 0.00 0.00 40.12 5.34
1820 2838 3.047877 GGCCGACCAAAGTCCGTG 61.048 66.667 0.00 0.00 40.12 4.94
1821 2839 3.552384 TGGCCGACCAAAGTCCGT 61.552 61.111 0.00 0.00 45.37 4.69
1899 2929 5.750067 AGCATGCAAAGTGAACTGTTTTTAG 59.250 36.000 21.98 0.00 0.00 1.85
1906 2940 3.088194 ACAAGCATGCAAAGTGAACTG 57.912 42.857 21.98 5.04 0.00 3.16
1907 2941 3.450578 CAACAAGCATGCAAAGTGAACT 58.549 40.909 21.98 0.00 0.00 3.01
2061 3095 9.577110 CAACTGTCTGCAAATATATGACAAATT 57.423 29.630 4.52 0.56 37.24 1.82
2073 3107 2.026641 AGTGCACAACTGTCTGCAAAT 58.973 42.857 21.04 4.75 37.88 2.32
2092 3126 5.791666 ACATGTATATGTGAGATGCAGGAG 58.208 41.667 4.06 0.00 45.54 3.69
2105 3139 6.073058 ACAGCGCCAATCTAAACATGTATATG 60.073 38.462 2.29 0.00 40.24 1.78
2125 3190 5.569059 GTCAAAACAGGATAATGAAACAGCG 59.431 40.000 0.00 0.00 0.00 5.18
2188 3253 4.506288 CCGAAAACATCAAAACAAAGGTCC 59.494 41.667 0.00 0.00 0.00 4.46
2209 3274 1.414158 TCTTCTCCTTGGCTATCCCG 58.586 55.000 0.00 0.00 35.87 5.14
2346 3411 8.386606 TCAACAATTGCAAATTACAAGTTGTTC 58.613 29.630 14.90 0.00 37.04 3.18
2351 3416 6.482641 TGCATCAACAATTGCAAATTACAAGT 59.517 30.769 1.71 0.00 45.30 3.16
2427 3510 3.894759 CTTGTCATCATTGTCATCCCCT 58.105 45.455 0.00 0.00 0.00 4.79
2446 3529 2.971330 AGCAGGCTCATACATCTAGCTT 59.029 45.455 0.00 0.00 36.48 3.74
2528 3612 3.304190 GGGCGTTACAAAACACTTGTAGG 60.304 47.826 0.00 0.00 36.40 3.18
2626 3710 4.522789 ACATGGGTTGTGTGAAGATTAACC 59.477 41.667 0.00 0.00 37.11 2.85
2628 3712 8.952278 GTATTACATGGGTTGTGTGAAGATTAA 58.048 33.333 0.00 0.00 39.48 1.40
2725 3812 6.797454 AGTCGAACCTTGATTGTATCTAGAC 58.203 40.000 0.00 0.00 34.67 2.59
3010 4106 0.761187 TGCAGCTCCATCTCATACCC 59.239 55.000 0.00 0.00 0.00 3.69
3064 4162 4.502962 CCTTCTCTTCTCGCTCTCATTTT 58.497 43.478 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.