Multiple sequence alignment - TraesCS5B01G297600

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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 TraesCS5B01G297600 chr5B 100.000 7621 0 0 1 7621 480286543 480294163 0.000000e+00 14074.0
1 TraesCS5B01G297600 chr5B 89.263 624 52 11 1 617 66994093 66994708 0.000000e+00 767.0
2 TraesCS5B01G297600 chr5D 95.801 3739 76 27 2332 6031 400275235 400278931 0.000000e+00 5960.0
3 TraesCS5B01G297600 chr5D 90.288 1596 71 33 772 2335 400269534 400271077 0.000000e+00 2012.0
4 TraesCS5B01G297600 chr5D 97.579 1074 18 2 6556 7621 400279836 400280909 0.000000e+00 1832.0
5 TraesCS5B01G297600 chr5D 96.744 645 20 1 5916 6560 400278908 400279551 0.000000e+00 1074.0
6 TraesCS5B01G297600 chr5A 92.607 2002 86 26 743 2704 505605939 505607918 0.000000e+00 2820.0
7 TraesCS5B01G297600 chr5A 93.728 1690 48 17 3081 4723 505607919 505609597 0.000000e+00 2481.0
8 TraesCS5B01G297600 chr5A 92.622 1613 68 16 4958 6560 505609730 505611301 0.000000e+00 2272.0
9 TraesCS5B01G297600 chr5A 92.030 1079 45 23 6553 7621 505611583 505612630 0.000000e+00 1478.0
10 TraesCS5B01G297600 chr5A 89.985 689 48 11 1 684 617905845 617905173 0.000000e+00 870.0
11 TraesCS5B01G297600 chr5A 96.364 55 2 0 4722 4776 505609679 505609733 2.930000e-14 91.6
12 TraesCS5B01G297600 chr3B 93.632 691 42 2 1 690 602479081 602478392 0.000000e+00 1031.0
13 TraesCS5B01G297600 chr2B 93.218 693 29 10 1 690 426888183 426887506 0.000000e+00 1003.0
14 TraesCS5B01G297600 chr2B 89.428 577 48 11 1 569 56925828 56925257 0.000000e+00 715.0
15 TraesCS5B01G297600 chr2B 94.231 52 3 0 7568 7619 698084995 698085046 6.340000e-11 80.5
16 TraesCS5B01G297600 chr7B 91.607 560 39 7 1 556 710734404 710734959 0.000000e+00 767.0
17 TraesCS5B01G297600 chr7B 81.325 166 31 0 7456 7621 228363203 228363368 1.330000e-27 135.0
18 TraesCS5B01G297600 chr1B 89.217 575 51 11 1 569 182167402 182166833 0.000000e+00 708.0
19 TraesCS5B01G297600 chr4A 89.927 546 45 9 1 541 673751926 673752466 0.000000e+00 695.0
20 TraesCS5B01G297600 chr4A 85.981 107 15 0 7457 7563 590278419 590278525 1.740000e-21 115.0
21 TraesCS5B01G297600 chr4A 83.721 86 11 3 611 695 727714422 727714339 2.280000e-10 78.7
22 TraesCS5B01G297600 chr4B 85.714 665 78 14 9 669 2338638 2339289 0.000000e+00 686.0
23 TraesCS5B01G297600 chr4B 86.916 107 14 0 7457 7563 22274004 22274110 3.740000e-23 121.0
24 TraesCS5B01G297600 chr4D 90.654 107 10 0 7457 7563 12410896 12410790 7.970000e-30 143.0
25 TraesCS5B01G297600 chr7D 81.928 166 30 0 7456 7621 251374464 251374629 2.870000e-29 141.0
26 TraesCS5B01G297600 chr7D 94.231 52 3 0 7570 7621 77075437 77075386 6.340000e-11 80.5
27 TraesCS5B01G297600 chr7A 81.928 166 30 0 7456 7621 270043206 270043041 2.870000e-29 141.0
28 TraesCS5B01G297600 chr2A 94.231 52 3 0 7568 7619 66913105 66913156 6.340000e-11 80.5
29 TraesCS5B01G297600 chr2A 82.716 81 12 1 609 689 733536529 733536607 3.820000e-08 71.3
30 TraesCS5B01G297600 chr1A 94.231 52 3 0 7568 7619 459594190 459594139 6.340000e-11 80.5
31 TraesCS5B01G297600 chr3D 90.196 51 5 0 639 689 154611891 154611941 4.940000e-07 67.6


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 TraesCS5B01G297600 chr5B 480286543 480294163 7620 False 14074.000000 14074 100.0000 1 7621 1 chr5B.!!$F2 7620
1 TraesCS5B01G297600 chr5B 66994093 66994708 615 False 767.000000 767 89.2630 1 617 1 chr5B.!!$F1 616
2 TraesCS5B01G297600 chr5D 400275235 400280909 5674 False 2955.333333 5960 96.7080 2332 7621 3 chr5D.!!$F2 5289
3 TraesCS5B01G297600 chr5D 400269534 400271077 1543 False 2012.000000 2012 90.2880 772 2335 1 chr5D.!!$F1 1563
4 TraesCS5B01G297600 chr5A 505605939 505612630 6691 False 1828.520000 2820 93.4702 743 7621 5 chr5A.!!$F1 6878
5 TraesCS5B01G297600 chr5A 617905173 617905845 672 True 870.000000 870 89.9850 1 684 1 chr5A.!!$R1 683
6 TraesCS5B01G297600 chr3B 602478392 602479081 689 True 1031.000000 1031 93.6320 1 690 1 chr3B.!!$R1 689
7 TraesCS5B01G297600 chr2B 426887506 426888183 677 True 1003.000000 1003 93.2180 1 690 1 chr2B.!!$R2 689
8 TraesCS5B01G297600 chr2B 56925257 56925828 571 True 715.000000 715 89.4280 1 569 1 chr2B.!!$R1 568
9 TraesCS5B01G297600 chr7B 710734404 710734959 555 False 767.000000 767 91.6070 1 556 1 chr7B.!!$F2 555
10 TraesCS5B01G297600 chr1B 182166833 182167402 569 True 708.000000 708 89.2170 1 569 1 chr1B.!!$R1 568
11 TraesCS5B01G297600 chr4A 673751926 673752466 540 False 695.000000 695 89.9270 1 541 1 chr4A.!!$F2 540
12 TraesCS5B01G297600 chr4B 2338638 2339289 651 False 686.000000 686 85.7140 9 669 1 chr4B.!!$F1 660

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
798 825 0.034767 CACATGATGACCAGCCCAGT 60.035 55.0 0.00 0.0 0.00 4.00 F
1748 1828 0.108281 GCTACTTTGGACTCCGACCC 60.108 60.0 0.00 0.0 0.00 4.46 F
3029 3120 1.428448 TGTCGACAGCATTTCTTCCG 58.572 50.0 15.76 0.0 0.00 4.30 F
3700 3795 0.686769 CCGTCCCTACAGTAAGGCCT 60.687 60.0 0.00 0.0 35.09 5.19 F
5211 5445 2.154567 ACATCTGGCCGTACCTAAGA 57.845 50.0 0.00 0.0 40.22 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 2159 1.064134 CGCATCGATCTGACGGTCA 59.936 57.895 10.88 10.88 0.00 4.02 R
3340 3435 4.830600 GGTGGAACAAAGGGATAAGTTTGA 59.169 41.667 1.98 0.00 44.16 2.69 R
4333 4448 2.209838 ATGTACACGGAGCTTGATCG 57.790 50.000 0.00 0.00 0.00 3.69 R
5298 5532 0.742281 CCCAGTTGCTCGGATGACAG 60.742 60.000 0.00 0.00 0.00 3.51 R
7143 7789 0.320421 GGTGTAGTTTCCAGCTCGCA 60.320 55.000 0.00 0.00 0.00 5.10 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
471 486 6.316319 TGTTCTCTGTTTTAACAAACGTTCC 58.684 36.000 0.00 0.00 44.76 3.62
617 644 1.530720 GCCAAGAAAAACAATTGGGCG 59.469 47.619 10.83 0.00 43.06 6.13
690 717 1.233369 GGCAGGTAGGAGCTCCCTA 59.767 63.158 29.54 17.22 45.48 3.53
708 735 2.567049 GCGAGCGGCGTATAGGAT 59.433 61.111 9.37 0.00 43.41 3.24
709 736 1.080705 GCGAGCGGCGTATAGGATT 60.081 57.895 9.37 0.00 43.41 3.01
710 737 0.666577 GCGAGCGGCGTATAGGATTT 60.667 55.000 9.37 0.00 43.41 2.17
711 738 1.779569 CGAGCGGCGTATAGGATTTT 58.220 50.000 9.37 0.00 34.64 1.82
712 739 1.719780 CGAGCGGCGTATAGGATTTTC 59.280 52.381 9.37 0.00 34.64 2.29
713 740 2.067013 GAGCGGCGTATAGGATTTTCC 58.933 52.381 9.37 0.00 36.58 3.13
714 741 1.414919 AGCGGCGTATAGGATTTTCCA 59.585 47.619 9.37 0.00 39.61 3.53
715 742 1.529865 GCGGCGTATAGGATTTTCCAC 59.470 52.381 9.37 0.00 39.61 4.02
716 743 2.828877 CGGCGTATAGGATTTTCCACA 58.171 47.619 0.00 0.00 39.61 4.17
717 744 3.399330 CGGCGTATAGGATTTTCCACAT 58.601 45.455 0.00 0.00 39.61 3.21
718 745 4.562082 CGGCGTATAGGATTTTCCACATA 58.438 43.478 0.00 0.00 39.61 2.29
719 746 4.387862 CGGCGTATAGGATTTTCCACATAC 59.612 45.833 0.00 3.08 39.61 2.39
720 747 5.302360 GGCGTATAGGATTTTCCACATACA 58.698 41.667 13.95 0.00 39.61 2.29
721 748 5.178809 GGCGTATAGGATTTTCCACATACAC 59.821 44.000 13.95 7.74 39.61 2.90
722 749 5.756347 GCGTATAGGATTTTCCACATACACA 59.244 40.000 13.95 0.00 39.61 3.72
723 750 6.292703 GCGTATAGGATTTTCCACATACACAC 60.293 42.308 13.95 4.59 39.61 3.82
724 751 6.759356 CGTATAGGATTTTCCACATACACACA 59.241 38.462 13.95 0.00 39.61 3.72
725 752 7.441157 CGTATAGGATTTTCCACATACACACAT 59.559 37.037 13.95 0.00 39.61 3.21
726 753 9.120538 GTATAGGATTTTCCACATACACACATT 57.879 33.333 10.87 0.00 39.61 2.71
728 755 9.693739 ATAGGATTTTCCACATACACACATTAA 57.306 29.630 0.00 0.00 39.61 1.40
729 756 8.055279 AGGATTTTCCACATACACACATTAAG 57.945 34.615 0.00 0.00 39.61 1.85
730 757 7.669722 AGGATTTTCCACATACACACATTAAGT 59.330 33.333 0.00 0.00 39.61 2.24
731 758 7.754924 GGATTTTCCACATACACACATTAAGTG 59.245 37.037 0.00 0.00 44.58 3.16
738 765 3.918544 CACATTAAGTGGCCGGGG 58.081 61.111 2.18 0.00 44.69 5.73
739 766 2.044352 ACATTAAGTGGCCGGGGC 60.044 61.111 14.65 14.65 41.06 5.80
740 767 2.044451 CATTAAGTGGCCGGGGCA 60.044 61.111 20.63 20.63 44.11 5.36
741 768 1.455587 CATTAAGTGGCCGGGGCAT 60.456 57.895 27.04 14.20 44.11 4.40
742 769 1.042559 CATTAAGTGGCCGGGGCATT 61.043 55.000 27.04 20.06 44.11 3.56
743 770 0.325203 ATTAAGTGGCCGGGGCATTT 60.325 50.000 29.16 29.16 44.11 2.32
744 771 0.543174 TTAAGTGGCCGGGGCATTTT 60.543 50.000 30.83 25.47 44.11 1.82
745 772 0.543174 TAAGTGGCCGGGGCATTTTT 60.543 50.000 30.83 23.41 44.11 1.94
775 802 0.589708 AAAACGAACAGGCCGTAAGC 59.410 50.000 0.00 0.00 39.57 3.09
791 818 2.760634 AAGCGTACACATGATGACCA 57.239 45.000 0.00 0.00 0.00 4.02
798 825 0.034767 CACATGATGACCAGCCCAGT 60.035 55.000 0.00 0.00 0.00 4.00
803 830 0.811616 GATGACCAGCCCAGTTAGCG 60.812 60.000 0.00 0.00 34.64 4.26
811 838 2.436646 CCAGTTAGCGTGGGCCAG 60.437 66.667 6.40 1.95 41.24 4.85
828 855 2.622436 CCAGGAAGATTCGAACTGACC 58.378 52.381 12.79 12.32 0.00 4.02
920 958 0.609131 AATGAAGGCCGTTGACCTGG 60.609 55.000 0.00 0.00 37.67 4.45
955 997 0.817654 CCGAGCTCACATCCACAGTA 59.182 55.000 15.40 0.00 0.00 2.74
986 1034 4.637489 CTCGCCTGATCGCCTCCG 62.637 72.222 0.00 0.00 0.00 4.63
992 1040 1.826054 CTGATCGCCTCCGGTCTCT 60.826 63.158 0.00 0.00 44.75 3.10
996 1044 4.200283 CGCCTCCGGTCTCTGCTC 62.200 72.222 0.00 0.00 0.00 4.26
1064 1112 3.560251 ATTCCCATCCGCCTCCCG 61.560 66.667 0.00 0.00 0.00 5.14
1333 1400 0.917533 AGGTCAGCTTGGATGCATCT 59.082 50.000 25.28 2.94 34.99 2.90
1400 1468 0.543410 AGGGGTACGTGTGGATGTCA 60.543 55.000 0.00 0.00 0.00 3.58
1463 1531 1.376942 CAAGCAGCTGTGGGAGGAG 60.377 63.158 16.64 0.00 0.00 3.69
1525 1593 0.602562 GAGAGCCTCGGATGGATGAG 59.397 60.000 0.00 0.00 0.00 2.90
1546 1614 1.732259 GACAGGTAAAGCCATGTGACG 59.268 52.381 0.00 0.00 40.61 4.35
1569 1637 4.792189 GGTTGTCTATAAGTCGTTGACTCG 59.208 45.833 0.00 0.00 42.59 4.18
1651 1723 9.629878 ACAGAGTACAGTAGCAGTATATTTAGT 57.370 33.333 0.00 0.00 0.00 2.24
1652 1724 9.885934 CAGAGTACAGTAGCAGTATATTTAGTG 57.114 37.037 0.00 0.00 32.75 2.74
1653 1725 9.629878 AGAGTACAGTAGCAGTATATTTAGTGT 57.370 33.333 0.00 0.00 34.85 3.55
1713 1793 6.282199 TCTGGTCCAGTAGATTTCACTAAC 57.718 41.667 18.65 0.00 32.61 2.34
1748 1828 0.108281 GCTACTTTGGACTCCGACCC 60.108 60.000 0.00 0.00 0.00 4.46
1914 2000 7.437862 TGCTTGTTTTGTTAAGGAAGCTTATTG 59.562 33.333 0.00 0.00 37.34 1.90
2046 2132 1.853319 CGCACTCTGTGTCGGAAAC 59.147 57.895 0.00 0.00 35.75 2.78
2073 2159 4.384208 GGTGGTGCTATGTTCTTACCTGAT 60.384 45.833 0.00 0.00 32.68 2.90
2082 2168 3.056821 TGTTCTTACCTGATGACCGTCAG 60.057 47.826 7.41 11.30 44.12 3.51
2100 2186 2.203070 ATCGATGCGTTCCAGGCC 60.203 61.111 0.00 0.00 0.00 5.19
2126 2212 7.044052 CGTGTCTTTGATTGAAAAGGTTTCTTC 60.044 37.037 2.68 1.31 37.67 2.87
2355 2443 2.113860 TCAGGCTACTGGAATTGCAC 57.886 50.000 0.00 0.00 44.99 4.57
2390 2478 7.818493 TCTATAATTAGCTTGACGATGATGC 57.182 36.000 0.00 0.00 0.00 3.91
2456 2544 8.174733 AGCCATTTCCATTCTTCTGTATTATG 57.825 34.615 0.00 0.00 0.00 1.90
2462 2551 7.864108 TCCATTCTTCTGTATTATGGTGTTG 57.136 36.000 0.00 0.00 37.58 3.33
2609 2698 7.669722 TGCATAGTTTCTTAGGACCAAATTCTT 59.330 33.333 0.00 0.00 0.00 2.52
2723 2814 5.163854 CCTGGCATTCTCGTAGTAAAAAGTG 60.164 44.000 0.00 0.00 0.00 3.16
2775 2866 6.735678 AACAAACTGGGATGAAACAAAAAC 57.264 33.333 0.00 0.00 0.00 2.43
2792 2883 7.360113 ACAAAAACATCCACTCTTTATGGTT 57.640 32.000 0.00 0.00 38.47 3.67
2876 2967 8.731605 TCTGTGACACTGTTTTGTATTTTAACA 58.268 29.630 7.20 0.00 0.00 2.41
2971 3062 6.115446 CAGCACTCAAAACTATCCTATGGAA 58.885 40.000 0.00 0.00 34.34 3.53
3004 3095 8.518430 TTATGCTAGCTCAAAATAAACCATGA 57.482 30.769 17.23 0.00 0.00 3.07
3029 3120 1.428448 TGTCGACAGCATTTCTTCCG 58.572 50.000 15.76 0.00 0.00 4.30
3054 3145 7.910162 CGTAATATAATATTTGCATGCTGGTCC 59.090 37.037 20.33 0.00 0.00 4.46
3055 3146 8.960591 GTAATATAATATTTGCATGCTGGTCCT 58.039 33.333 20.33 2.25 0.00 3.85
3056 3147 8.426569 AATATAATATTTGCATGCTGGTCCTT 57.573 30.769 20.33 8.05 0.00 3.36
3057 3148 6.736110 ATAATATTTGCATGCTGGTCCTTT 57.264 33.333 20.33 6.67 0.00 3.11
3078 3169 9.333724 TCCTTTCTTCGTGTTATTTAAGAACTT 57.666 29.630 4.11 0.00 37.61 2.66
3700 3795 0.686769 CCGTCCCTACAGTAAGGCCT 60.687 60.000 0.00 0.00 35.09 5.19
4272 4387 5.452496 GCAGAATGAGGCTGTACTTAGATGA 60.452 44.000 0.00 0.00 39.69 2.92
4333 4448 2.758009 AGGCATTTTCATGTTGTGCAC 58.242 42.857 10.75 10.75 37.53 4.57
4404 4544 5.438761 AGTAGCTCAAAACATTGTTGACC 57.561 39.130 2.13 0.00 31.78 4.02
4466 4606 5.449725 GCTTGCTCCCTTGATTGAATAGAAC 60.450 44.000 0.00 0.00 0.00 3.01
4467 4607 5.178096 TGCTCCCTTGATTGAATAGAACA 57.822 39.130 0.00 0.00 0.00 3.18
4468 4608 5.569355 TGCTCCCTTGATTGAATAGAACAA 58.431 37.500 0.00 0.00 0.00 2.83
4469 4609 5.415701 TGCTCCCTTGATTGAATAGAACAAC 59.584 40.000 0.00 0.00 0.00 3.32
4470 4610 5.415701 GCTCCCTTGATTGAATAGAACAACA 59.584 40.000 0.00 0.00 0.00 3.33
4471 4611 6.071952 GCTCCCTTGATTGAATAGAACAACAA 60.072 38.462 0.00 0.00 0.00 2.83
4472 4612 7.452880 TCCCTTGATTGAATAGAACAACAAG 57.547 36.000 0.00 0.00 36.86 3.16
4473 4613 7.004086 TCCCTTGATTGAATAGAACAACAAGT 58.996 34.615 0.00 0.00 36.25 3.16
4521 4662 6.270815 TGGTCGACTAAATACAGTTATGAGC 58.729 40.000 16.46 0.00 0.00 4.26
4536 4677 9.155975 ACAGTTATGAGCTTTACACATTCTTAG 57.844 33.333 0.00 0.00 31.51 2.18
4643 4785 3.181479 CGCTAGGTACTGCTGAAATGGTA 60.181 47.826 0.00 0.00 41.52 3.25
4965 5190 5.455326 GGCTGTCACCCTGATTTATATCTGT 60.455 44.000 0.00 0.00 0.00 3.41
5047 5281 2.535534 CGCGTATCAGTTCATTGCACAG 60.536 50.000 0.00 0.00 0.00 3.66
5199 5433 4.156739 GTGCTTTTCTTCCCTTACATCTGG 59.843 45.833 0.00 0.00 0.00 3.86
5211 5445 2.154567 ACATCTGGCCGTACCTAAGA 57.845 50.000 0.00 0.00 40.22 2.10
5298 5532 2.075338 CTGCTTCTGCTTCAGGAACTC 58.925 52.381 0.00 0.00 36.82 3.01
5802 6036 6.125327 TGTTGTTGATTTACGCTTCTTTCA 57.875 33.333 0.00 0.00 0.00 2.69
5809 6043 5.298276 TGATTTACGCTTCTTTCAAGGTGTT 59.702 36.000 0.00 0.00 0.00 3.32
5878 6112 3.326588 GGGGGAAAGCAGGTAATTTTTGT 59.673 43.478 0.00 0.00 0.00 2.83
5883 6117 6.589907 GGGAAAGCAGGTAATTTTTGTATGTG 59.410 38.462 0.00 0.00 0.00 3.21
5884 6118 6.090763 GGAAAGCAGGTAATTTTTGTATGTGC 59.909 38.462 0.00 0.00 0.00 4.57
5885 6119 5.072040 AGCAGGTAATTTTTGTATGTGCC 57.928 39.130 0.00 0.00 0.00 5.01
5989 6315 9.396022 CTAGCTTAAAATTTCCTTGGACTCATA 57.604 33.333 0.00 0.00 0.00 2.15
6021 6347 6.647067 GGATAAATGGTGTCTACAGTATCAGC 59.353 42.308 7.66 7.66 0.00 4.26
6058 6384 6.017109 GCAAGGTCAACTTTCTTGAGATACAA 60.017 38.462 6.49 0.00 39.97 2.41
6077 6403 9.182214 AGATACAACAGCATTAAGTGATCAATT 57.818 29.630 13.58 13.58 0.00 2.32
6078 6404 9.793252 GATACAACAGCATTAAGTGATCAATTT 57.207 29.630 14.34 6.35 0.00 1.82
6428 6754 1.009829 GCATTTAGACTCGTGCCAGG 58.990 55.000 0.00 0.00 0.00 4.45
6476 6802 6.646653 CACTGCTAAGTACTCAATTGTGAGAA 59.353 38.462 14.16 0.00 43.84 2.87
6485 6811 3.443052 TCAATTGTGAGAAATGCCCCAT 58.557 40.909 5.13 0.00 0.00 4.00
6495 6821 1.856629 AATGCCCCATGAAGTTCCAG 58.143 50.000 0.00 0.00 0.00 3.86
6500 6826 2.440409 CCCCATGAAGTTCCAGTTCAG 58.560 52.381 0.00 0.00 40.49 3.02
6570 7187 6.301169 ACCCCTCTAAATGCATATAGTAGC 57.699 41.667 0.00 0.00 0.00 3.58
7054 7700 9.981114 GGTTTCCCAATAATACCATGAAATAAG 57.019 33.333 0.00 0.00 0.00 1.73
7055 7701 9.476202 GTTTCCCAATAATACCATGAAATAAGC 57.524 33.333 0.00 0.00 0.00 3.09
7056 7702 8.774546 TTCCCAATAATACCATGAAATAAGCA 57.225 30.769 0.00 0.00 0.00 3.91
7057 7703 8.774546 TCCCAATAATACCATGAAATAAGCAA 57.225 30.769 0.00 0.00 0.00 3.91
7058 7704 9.206690 TCCCAATAATACCATGAAATAAGCAAA 57.793 29.630 0.00 0.00 0.00 3.68
7080 7726 3.492102 TTGCAGGAGTAGCAAACTTCT 57.508 42.857 0.00 0.00 45.79 2.85
7081 7727 4.617253 TTGCAGGAGTAGCAAACTTCTA 57.383 40.909 0.01 0.00 42.70 2.10
7122 7768 4.548494 TGTAGCAAATTTGTGAGTGCATG 58.452 39.130 19.03 0.00 39.50 4.06
7143 7789 1.846007 TGTGTTTGTTTGGCCTGTCT 58.154 45.000 3.32 0.00 0.00 3.41
7159 7805 1.336887 TGTCTGCGAGCTGGAAACTAC 60.337 52.381 0.00 0.00 0.00 2.73
7309 7955 4.207165 ACTTGATTTCACCCCGGATTATG 58.793 43.478 0.73 0.00 0.00 1.90
7315 7961 0.396811 CACCCCGGATTATGGACTCC 59.603 60.000 0.73 0.00 0.00 3.85
7405 8058 1.064463 GGAGGAATGGACCTGCATTCA 60.064 52.381 18.00 0.00 45.58 2.57
7410 8063 4.105217 AGGAATGGACCTGCATTCATCATA 59.895 41.667 18.00 0.00 39.01 2.15
7412 8065 4.719026 ATGGACCTGCATTCATCATACT 57.281 40.909 0.00 0.00 0.00 2.12
7423 8078 5.587844 GCATTCATCATACTGAAGAAGGTGT 59.412 40.000 8.07 0.00 37.92 4.16
7424 8079 6.457934 GCATTCATCATACTGAAGAAGGTGTG 60.458 42.308 8.07 0.99 37.92 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 49 7.227049 TCCAGAACAACTTTTTGAAAACTCT 57.773 32.000 0.00 0.00 36.48 3.24
226 231 8.364129 TGGAAGCATGAACAATTCTTTAAAAC 57.636 30.769 0.00 0.00 0.00 2.43
331 344 3.386402 ACAAATTTGGGACCACGAACAAT 59.614 39.130 21.74 0.00 0.00 2.71
598 625 2.142319 CCGCCCAATTGTTTTTCTTGG 58.858 47.619 4.43 0.00 39.31 3.61
690 717 1.524863 AATCCTATACGCCGCTCGCT 61.525 55.000 0.00 0.00 43.23 4.93
691 718 0.666577 AAATCCTATACGCCGCTCGC 60.667 55.000 0.00 0.00 43.23 5.03
692 719 1.719780 GAAAATCCTATACGCCGCTCG 59.280 52.381 0.00 0.00 45.38 5.03
693 720 2.067013 GGAAAATCCTATACGCCGCTC 58.933 52.381 0.00 0.00 32.53 5.03
694 721 1.414919 TGGAAAATCCTATACGCCGCT 59.585 47.619 0.00 0.00 37.46 5.52
695 722 1.529865 GTGGAAAATCCTATACGCCGC 59.470 52.381 0.00 0.00 37.46 6.53
696 723 2.828877 TGTGGAAAATCCTATACGCCG 58.171 47.619 0.00 0.00 37.46 6.46
697 724 5.178809 GTGTATGTGGAAAATCCTATACGCC 59.821 44.000 17.51 9.77 37.46 5.68
698 725 5.756347 TGTGTATGTGGAAAATCCTATACGC 59.244 40.000 19.48 19.48 37.46 4.42
699 726 6.759356 TGTGTGTATGTGGAAAATCCTATACG 59.241 38.462 14.10 0.00 37.46 3.06
700 727 8.677148 ATGTGTGTATGTGGAAAATCCTATAC 57.323 34.615 13.03 13.03 37.46 1.47
702 729 9.693739 TTAATGTGTGTATGTGGAAAATCCTAT 57.306 29.630 0.00 0.00 37.46 2.57
703 730 9.173021 CTTAATGTGTGTATGTGGAAAATCCTA 57.827 33.333 0.00 0.00 37.46 2.94
704 731 7.669722 ACTTAATGTGTGTATGTGGAAAATCCT 59.330 33.333 0.00 0.00 37.46 3.24
705 732 7.754924 CACTTAATGTGTGTATGTGGAAAATCC 59.245 37.037 0.00 0.00 41.53 3.01
706 733 7.754924 CCACTTAATGTGTGTATGTGGAAAATC 59.245 37.037 9.70 0.00 44.08 2.17
707 734 7.601856 CCACTTAATGTGTGTATGTGGAAAAT 58.398 34.615 9.70 0.00 44.08 1.82
708 735 6.515862 GCCACTTAATGTGTGTATGTGGAAAA 60.516 38.462 16.47 0.00 44.08 2.29
709 736 5.048364 GCCACTTAATGTGTGTATGTGGAAA 60.048 40.000 16.47 0.00 44.08 3.13
710 737 4.457603 GCCACTTAATGTGTGTATGTGGAA 59.542 41.667 16.47 0.00 44.08 3.53
711 738 4.006989 GCCACTTAATGTGTGTATGTGGA 58.993 43.478 16.47 0.00 44.08 4.02
712 739 3.128589 GGCCACTTAATGTGTGTATGTGG 59.871 47.826 0.00 10.57 44.81 4.17
713 740 3.181511 CGGCCACTTAATGTGTGTATGTG 60.182 47.826 2.24 0.00 44.81 3.21
714 741 3.006940 CGGCCACTTAATGTGTGTATGT 58.993 45.455 2.24 0.00 44.81 2.29
715 742 2.354510 CCGGCCACTTAATGTGTGTATG 59.645 50.000 2.24 0.00 44.81 2.39
716 743 2.639065 CCGGCCACTTAATGTGTGTAT 58.361 47.619 2.24 0.00 44.81 2.29
717 744 1.339247 CCCGGCCACTTAATGTGTGTA 60.339 52.381 2.24 0.00 44.81 2.90
718 745 0.608035 CCCGGCCACTTAATGTGTGT 60.608 55.000 2.24 0.00 44.81 3.72
719 746 1.312371 CCCCGGCCACTTAATGTGTG 61.312 60.000 2.24 0.00 44.81 3.82
720 747 1.001393 CCCCGGCCACTTAATGTGT 60.001 57.895 2.24 0.00 44.81 3.72
721 748 2.414785 GCCCCGGCCACTTAATGTG 61.415 63.158 2.24 0.00 45.80 3.21
722 749 2.044352 GCCCCGGCCACTTAATGT 60.044 61.111 2.24 0.00 34.56 2.71
723 750 1.042559 AATGCCCCGGCCACTTAATG 61.043 55.000 2.24 0.00 41.09 1.90
724 751 0.325203 AAATGCCCCGGCCACTTAAT 60.325 50.000 2.24 0.00 41.09 1.40
725 752 0.543174 AAAATGCCCCGGCCACTTAA 60.543 50.000 2.24 0.00 41.09 1.85
726 753 0.543174 AAAAATGCCCCGGCCACTTA 60.543 50.000 2.24 0.00 41.09 2.24
727 754 1.841103 AAAAATGCCCCGGCCACTT 60.841 52.632 2.24 0.00 41.09 3.16
728 755 2.203773 AAAAATGCCCCGGCCACT 60.204 55.556 2.24 0.00 41.09 4.00
759 786 1.865788 TACGCTTACGGCCTGTTCGT 61.866 55.000 0.00 12.74 46.04 3.85
770 797 3.517602 TGGTCATCATGTGTACGCTTAC 58.482 45.455 8.10 0.00 0.00 2.34
775 802 1.290203 GGCTGGTCATCATGTGTACG 58.710 55.000 0.00 0.00 0.00 3.67
798 825 1.271840 ATCTTCCTGGCCCACGCTAA 61.272 55.000 0.00 0.00 34.44 3.09
803 830 0.035439 TTCGAATCTTCCTGGCCCAC 60.035 55.000 0.00 0.00 0.00 4.61
811 838 1.407025 GGGGGTCAGTTCGAATCTTCC 60.407 57.143 0.00 2.59 0.00 3.46
828 855 1.080298 GGCCGTATTCGTATCGGGG 60.080 63.158 12.27 0.23 43.77 5.73
920 958 3.403558 GGGAGGAGGGAGTGGCAC 61.404 72.222 10.29 10.29 0.00 5.01
986 1034 1.758514 TCCATCGGGAGCAGAGACC 60.759 63.158 0.00 0.00 38.64 3.85
1333 1400 6.139679 ACAAAATCAATCAGAACCCTAGGA 57.860 37.500 11.48 0.00 0.00 2.94
1514 1582 1.704641 TACCTGTCCTCATCCATCCG 58.295 55.000 0.00 0.00 0.00 4.18
1517 1585 2.173569 GGCTTTACCTGTCCTCATCCAT 59.826 50.000 0.00 0.00 34.51 3.41
1525 1593 2.084546 GTCACATGGCTTTACCTGTCC 58.915 52.381 0.00 0.00 40.22 4.02
1546 1614 4.792189 CGAGTCAACGACTTATAGACAACC 59.208 45.833 0.00 0.00 43.53 3.77
1616 1688 7.830201 ACTGCTACTGTACTCTGTAGTTATTCT 59.170 37.037 16.52 0.00 43.37 2.40
1630 1702 9.609950 GCTACACTAAATATACTGCTACTGTAC 57.390 37.037 0.00 0.00 0.00 2.90
1651 1723 3.603158 TTACTGCCATTTCGAGCTACA 57.397 42.857 0.00 0.00 0.00 2.74
1652 1724 4.201822 CCTTTTACTGCCATTTCGAGCTAC 60.202 45.833 0.00 0.00 0.00 3.58
1653 1725 3.938963 CCTTTTACTGCCATTTCGAGCTA 59.061 43.478 0.00 0.00 0.00 3.32
1654 1726 2.749621 CCTTTTACTGCCATTTCGAGCT 59.250 45.455 0.00 0.00 0.00 4.09
1655 1727 2.488153 ACCTTTTACTGCCATTTCGAGC 59.512 45.455 0.00 0.00 0.00 5.03
1914 2000 4.004314 GCTCTTTAGAGGTTCTTCCAACC 58.996 47.826 8.73 0.00 42.29 3.77
2046 2132 2.315925 AGAACATAGCACCACCATCG 57.684 50.000 0.00 0.00 0.00 3.84
2073 2159 1.064134 CGCATCGATCTGACGGTCA 59.936 57.895 10.88 10.88 0.00 4.02
2082 2168 2.247437 GGCCTGGAACGCATCGATC 61.247 63.158 0.00 0.00 0.00 3.69
2100 2186 6.265577 AGAAACCTTTTCAATCAAAGACACG 58.734 36.000 1.72 0.00 36.03 4.49
2149 2235 9.384764 GCAAGGATTCTTCTAACTACACTTATT 57.615 33.333 0.00 0.00 0.00 1.40
2158 2244 4.021016 AGACGTGCAAGGATTCTTCTAACT 60.021 41.667 4.26 0.00 0.00 2.24
2315 2401 1.571460 GCTGGTGCTCTTGTTCACG 59.429 57.895 0.00 0.00 34.20 4.35
2355 2443 9.547753 TCAAGCTAATTATAGAAGCTACTTTGG 57.452 33.333 0.19 0.00 45.61 3.28
2390 2478 4.940046 GCATCCTAACATGGTGATGGATAG 59.060 45.833 11.79 9.00 36.09 2.08
2402 2490 9.822185 GAAATAAATGAAAAGGCATCCTAACAT 57.178 29.630 0.00 0.00 31.13 2.71
2456 2544 5.768317 TCTGCATAAAGTAAAAGCAACACC 58.232 37.500 0.00 0.00 34.45 4.16
2462 2551 6.317391 ACCTCTGATCTGCATAAAGTAAAAGC 59.683 38.462 0.00 0.00 0.00 3.51
2775 2866 7.039784 TGGAAAGAAAACCATAAAGAGTGGATG 60.040 37.037 0.00 0.00 39.12 3.51
2876 2967 6.942976 TCTGGTTTGGTATTAGAACGAAGAT 58.057 36.000 0.00 0.00 0.00 2.40
2949 3040 7.094377 TGTTTTCCATAGGATAGTTTTGAGTGC 60.094 37.037 0.00 0.00 0.00 4.40
3004 3095 5.335191 GGAAGAAATGCTGTCGACAATTTCT 60.335 40.000 33.00 33.00 39.25 2.52
3029 3120 8.960591 AGGACCAGCATGCAAATATTATATTAC 58.039 33.333 21.98 0.00 31.97 1.89
3340 3435 4.830600 GGTGGAACAAAGGGATAAGTTTGA 59.169 41.667 1.98 0.00 44.16 2.69
3773 3868 6.541278 TGAAACAGATGAGGCATTTCTATCAG 59.459 38.462 0.00 0.00 31.86 2.90
4272 4387 3.071023 TGGTCGAAATTCACCAGAGTCTT 59.929 43.478 11.42 0.00 37.78 3.01
4333 4448 2.209838 ATGTACACGGAGCTTGATCG 57.790 50.000 0.00 0.00 0.00 3.69
4404 4544 5.618056 ATGTCTGTTATGTCACTGCAAAG 57.382 39.130 0.00 0.00 0.00 2.77
4466 4606 4.159377 ACTGTGTGTTGTTGACTTGTTG 57.841 40.909 0.00 0.00 0.00 3.33
4467 4607 4.846779 AACTGTGTGTTGTTGACTTGTT 57.153 36.364 0.00 0.00 37.52 2.83
4521 4662 6.001460 TCCCAACCACTAAGAATGTGTAAAG 58.999 40.000 0.00 0.00 33.92 1.85
4536 4677 5.652452 AGCAGTAGAAATTTATCCCAACCAC 59.348 40.000 0.00 0.00 0.00 4.16
4643 4785 5.192522 AGGGTCACCAAGAATCATATCTGTT 59.807 40.000 0.00 0.00 40.13 3.16
4805 5030 6.430451 GCGTGAAATATCAGTCCTAATTTGG 58.570 40.000 0.00 0.00 35.88 3.28
5047 5281 7.308830 GCATTCCAATTTCCATCCAGTATACTC 60.309 40.741 1.26 0.00 0.00 2.59
5199 5433 6.081872 ACATACTAATGTCTTAGGTACGGC 57.918 41.667 0.00 0.00 42.92 5.68
5298 5532 0.742281 CCCAGTTGCTCGGATGACAG 60.742 60.000 0.00 0.00 0.00 3.51
5802 6036 7.176589 TGACAAAAGGAAATTACAACACCTT 57.823 32.000 0.00 0.00 41.83 3.50
5876 6110 0.250945 TGAAAAGGGCGGCACATACA 60.251 50.000 12.47 2.13 0.00 2.29
5878 6112 0.037590 AGTGAAAAGGGCGGCACATA 59.962 50.000 12.47 0.00 33.85 2.29
5883 6117 1.460273 TTTCCAGTGAAAAGGGCGGC 61.460 55.000 0.00 0.00 37.53 6.53
5884 6118 0.313987 GTTTCCAGTGAAAAGGGCGG 59.686 55.000 0.00 0.00 41.92 6.13
5885 6119 1.001378 CTGTTTCCAGTGAAAAGGGCG 60.001 52.381 0.00 0.00 41.92 6.13
5914 6148 9.014297 CCATTTTAAATCCTGAAACTGTAGACT 57.986 33.333 0.00 0.00 0.00 3.24
5989 6315 8.884323 ACTGTAGACACCATTTATCCATATCAT 58.116 33.333 0.00 0.00 0.00 2.45
6021 6347 5.535333 AGTTGACCTTGCTGATTTTGAATG 58.465 37.500 0.00 0.00 0.00 2.67
6283 6609 7.497595 AGTTTGTGACAGTCTTACTTCACATA 58.502 34.615 17.59 13.36 41.31 2.29
6362 6688 6.752351 ACGAGCTACATTATGTTCTAACACAG 59.248 38.462 2.23 0.00 42.51 3.66
6428 6754 4.457257 GGCACATATCTAGCTTTCCCAATC 59.543 45.833 0.00 0.00 0.00 2.67
6476 6802 1.077663 ACTGGAACTTCATGGGGCATT 59.922 47.619 0.00 0.00 0.00 3.56
6485 6811 4.058124 CGTCATTCTGAACTGGAACTTCA 58.942 43.478 0.00 0.00 0.00 3.02
6495 6821 2.996621 AGTTAGCAGCGTCATTCTGAAC 59.003 45.455 0.00 0.00 33.54 3.18
6500 6826 7.537306 TGAAAAATAAAGTTAGCAGCGTCATTC 59.463 33.333 0.00 0.00 0.00 2.67
6570 7187 2.072298 GCTGTTAGAAGCTGTGAGTGG 58.928 52.381 0.00 0.00 40.20 4.00
7060 7706 3.492102 AGAAGTTTGCTACTCCTGCAA 57.508 42.857 0.00 0.00 46.90 4.08
7061 7707 3.617531 GCTAGAAGTTTGCTACTCCTGCA 60.618 47.826 0.00 0.00 35.54 4.41
7062 7708 2.933260 GCTAGAAGTTTGCTACTCCTGC 59.067 50.000 0.00 0.00 35.54 4.85
7063 7709 4.193826 TGCTAGAAGTTTGCTACTCCTG 57.806 45.455 0.00 0.00 35.54 3.86
7064 7710 4.284746 ACTTGCTAGAAGTTTGCTACTCCT 59.715 41.667 1.04 0.00 35.54 3.69
7065 7711 4.570930 ACTTGCTAGAAGTTTGCTACTCC 58.429 43.478 1.04 0.00 35.54 3.85
7066 7712 6.546972 AAACTTGCTAGAAGTTTGCTACTC 57.453 37.500 21.79 0.00 45.58 2.59
7122 7768 2.094234 AGACAGGCCAAACAAACACAAC 60.094 45.455 5.01 0.00 0.00 3.32
7143 7789 0.320421 GGTGTAGTTTCCAGCTCGCA 60.320 55.000 0.00 0.00 0.00 5.10
7410 8063 4.455606 CTTCTTTCCACACCTTCTTCAGT 58.544 43.478 0.00 0.00 0.00 3.41
7412 8065 3.214328 GCTTCTTTCCACACCTTCTTCA 58.786 45.455 0.00 0.00 0.00 3.02
7423 8078 3.891366 CCTTTCTTCCTTGCTTCTTTCCA 59.109 43.478 0.00 0.00 0.00 3.53
7424 8079 3.305676 GCCTTTCTTCCTTGCTTCTTTCC 60.306 47.826 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.