Multiple sequence alignment - TraesCS3B01G327500

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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 TraesCS3B01G327500 chr3B 100.000 7379 0 0 1 7379 528146314 528138936 0.000000e+00 13627.0
1 TraesCS3B01G327500 chr3A 96.297 7049 175 41 248 7252 523553258 523546252 0.000000e+00 11492.0
2 TraesCS3B01G327500 chr3A 96.078 102 2 1 7278 7379 523546258 523546159 1.650000e-36 165.0
3 TraesCS3B01G327500 chr3D 97.136 6249 127 21 546 6783 402692196 402685989 0.000000e+00 10501.0
4 TraesCS3B01G327500 chr3D 92.045 616 36 8 6767 7379 402685667 402685062 0.000000e+00 854.0
5 TraesCS3B01G327500 chr3D 89.860 572 28 16 1 561 402692776 402692224 0.000000e+00 708.0
6 TraesCS3B01G327500 chr2B 80.672 119 23 0 1511 1629 716053033 716052915 7.880000e-15 93.5
7 TraesCS3B01G327500 chr2A 80.374 107 21 0 1523 1629 725420258 725420152 1.710000e-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 TraesCS3B01G327500 chr3B 528138936 528146314 7378 True 13627.0 13627 100.000000 1 7379 1 chr3B.!!$R1 7378
1 TraesCS3B01G327500 chr3A 523546159 523553258 7099 True 5828.5 11492 96.187500 248 7379 2 chr3A.!!$R1 7131
2 TraesCS3B01G327500 chr3D 402685062 402692776 7714 True 4021.0 10501 93.013667 1 7379 3 chr3D.!!$R1 7378

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
952 1030 0.035915 TTCGCCGGAAATGATGGTGA 60.036 50.000 5.05 0.0 40.34 4.02 F
1671 1770 0.032130 TCGATATTGAGACAGGGCGC 59.968 55.000 0.00 0.0 0.00 6.53 F
2751 2850 0.834612 TTACAGGGGCACTTATCGGG 59.165 55.000 0.00 0.0 0.00 5.14 F
4002 4101 1.006758 AGGGGTCAGACCTTATCACGA 59.993 52.381 19.57 0.0 38.64 4.35 F
5124 5226 0.518636 CAATGCTGGTGGTCTTGACG 59.481 55.000 0.00 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 2043 0.613260 AGCTGCGGTAGACATTCCAA 59.387 50.000 0.00 0.00 0.00 3.53 R
3195 3294 0.174389 CAGCACATCGCCTGTACTCT 59.826 55.000 0.00 0.00 44.04 3.24 R
4497 4599 1.337167 GCATGGTTCTGGTTTTCAGGC 60.337 52.381 0.00 0.00 43.53 4.85 R
5160 5262 0.902048 CAGCCTCCAGACCACTCAGA 60.902 60.000 0.00 0.00 0.00 3.27 R
7098 7546 0.306533 GTCACGAAAAGCTTTCCGCA 59.693 50.000 18.31 1.52 42.61 5.69 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
27 28 1.374560 CCCAAACACAAGTGTCACGA 58.625 50.000 6.28 0.00 44.13 4.35
32 33 0.248012 ACACAAGTGTCACGACCACA 59.752 50.000 0.00 0.00 40.24 4.17
37 38 0.104304 AGTGTCACGACCACAGGTTC 59.896 55.000 0.00 0.00 35.25 3.62
85 86 2.539142 GCGACAGATACTCTACACCACG 60.539 54.545 0.00 0.00 0.00 4.94
89 90 4.333690 ACAGATACTCTACACCACGAACT 58.666 43.478 0.00 0.00 0.00 3.01
121 126 4.543689 TCTTCCGCCTTTATCTCCTCTAA 58.456 43.478 0.00 0.00 0.00 2.10
122 127 5.148502 TCTTCCGCCTTTATCTCCTCTAAT 58.851 41.667 0.00 0.00 0.00 1.73
157 162 2.804421 TGCGATATTGCTTCACGTTG 57.196 45.000 15.98 0.00 35.36 4.10
160 165 2.847254 GCGATATTGCTTCACGTTGCTC 60.847 50.000 7.76 0.00 0.00 4.26
174 179 9.907576 CTTCACGTTGCTCTTAATCTTAATAAG 57.092 33.333 0.00 0.00 0.00 1.73
224 229 2.917701 TTCATTTGGCTACATGTGCG 57.082 45.000 9.11 0.16 0.00 5.34
225 230 1.093972 TCATTTGGCTACATGTGCGG 58.906 50.000 9.11 0.00 0.00 5.69
226 231 0.526096 CATTTGGCTACATGTGCGGC 60.526 55.000 9.11 12.22 0.00 6.53
227 232 0.680921 ATTTGGCTACATGTGCGGCT 60.681 50.000 19.29 2.76 0.00 5.52
228 233 1.585267 TTTGGCTACATGTGCGGCTG 61.585 55.000 19.29 0.00 0.00 4.85
229 234 3.880846 GGCTACATGTGCGGCTGC 61.881 66.667 11.65 11.65 43.20 5.25
272 277 0.668535 GGTCTGGTTGTTTCAGTGGC 59.331 55.000 0.00 0.00 34.15 5.01
276 285 1.067516 CTGGTTGTTTCAGTGGCAAGG 59.932 52.381 0.00 0.00 0.00 3.61
280 289 1.152830 GTTTCAGTGGCAAGGGGGA 59.847 57.895 0.00 0.00 0.00 4.81
399 408 9.443283 CAAATCTCCGAATATTAAAAGCTCTTG 57.557 33.333 0.00 0.00 0.00 3.02
466 475 0.463833 TCCGCTCATCTCGTCTGCTA 60.464 55.000 0.00 0.00 0.00 3.49
467 476 0.040514 CCGCTCATCTCGTCTGCTAG 60.041 60.000 0.00 0.00 0.00 3.42
468 477 0.660488 CGCTCATCTCGTCTGCTAGT 59.340 55.000 0.00 0.00 0.00 2.57
469 478 1.867865 CGCTCATCTCGTCTGCTAGTA 59.132 52.381 0.00 0.00 0.00 1.82
528 537 2.076863 GCACGCCTATATTGATCACCC 58.923 52.381 0.00 0.00 0.00 4.61
532 541 4.214119 CACGCCTATATTGATCACCCAAAG 59.786 45.833 0.00 0.00 0.00 2.77
533 542 4.102524 ACGCCTATATTGATCACCCAAAGA 59.897 41.667 0.00 0.00 0.00 2.52
534 543 5.221925 ACGCCTATATTGATCACCCAAAGAT 60.222 40.000 0.00 0.00 0.00 2.40
536 545 7.050377 CGCCTATATTGATCACCCAAAGATAT 58.950 38.462 0.00 0.00 0.00 1.63
537 546 7.225538 CGCCTATATTGATCACCCAAAGATATC 59.774 40.741 0.00 0.00 0.00 1.63
538 547 8.270744 GCCTATATTGATCACCCAAAGATATCT 58.729 37.037 0.00 0.00 0.00 1.98
551 608 5.455849 CCAAAGATATCTATACGCGAATCCG 59.544 44.000 15.93 0.00 39.16 4.18
584 641 3.333680 TCCCCTAGATTTTCCAAACAGCT 59.666 43.478 0.00 0.00 0.00 4.24
607 664 0.957395 CAGCCGAGTGCCAATTCTGT 60.957 55.000 0.00 0.00 42.71 3.41
648 705 4.674475 GAGACGAAACCTAGGATCAGAAC 58.326 47.826 17.98 1.25 0.00 3.01
667 724 5.050499 CAGAACTTAGAACTGCTGTTGAGTG 60.050 44.000 14.22 4.49 36.39 3.51
668 725 4.408182 ACTTAGAACTGCTGTTGAGTGT 57.592 40.909 14.22 5.07 36.39 3.55
670 727 4.572389 ACTTAGAACTGCTGTTGAGTGTTG 59.428 41.667 14.22 0.80 36.39 3.33
671 728 3.266510 AGAACTGCTGTTGAGTGTTGA 57.733 42.857 14.22 0.00 36.39 3.18
672 729 3.201290 AGAACTGCTGTTGAGTGTTGAG 58.799 45.455 14.22 0.00 36.39 3.02
673 730 2.698855 ACTGCTGTTGAGTGTTGAGT 57.301 45.000 0.00 0.00 0.00 3.41
674 731 2.991250 ACTGCTGTTGAGTGTTGAGTT 58.009 42.857 0.00 0.00 0.00 3.01
676 733 3.127548 ACTGCTGTTGAGTGTTGAGTTTG 59.872 43.478 0.00 0.00 0.00 2.93
677 734 3.081061 TGCTGTTGAGTGTTGAGTTTGT 58.919 40.909 0.00 0.00 0.00 2.83
678 735 4.257731 TGCTGTTGAGTGTTGAGTTTGTA 58.742 39.130 0.00 0.00 0.00 2.41
680 737 4.332819 GCTGTTGAGTGTTGAGTTTGTAGT 59.667 41.667 0.00 0.00 0.00 2.73
681 738 5.522460 GCTGTTGAGTGTTGAGTTTGTAGTA 59.478 40.000 0.00 0.00 0.00 1.82
718 779 6.144563 TCTCGTTCATTCATCATTCTTATCGC 59.855 38.462 0.00 0.00 0.00 4.58
768 833 0.666577 GCACGGAAACACTAGCGAGT 60.667 55.000 0.00 0.00 35.80 4.18
769 834 1.337821 CACGGAAACACTAGCGAGTC 58.662 55.000 0.00 0.00 31.73 3.36
770 835 0.109873 ACGGAAACACTAGCGAGTCG 60.110 55.000 8.54 8.54 31.73 4.18
771 836 0.167470 CGGAAACACTAGCGAGTCGA 59.833 55.000 18.61 0.00 31.73 4.20
772 837 1.790838 CGGAAACACTAGCGAGTCGAG 60.791 57.143 18.61 8.30 31.73 4.04
773 838 1.261097 GAAACACTAGCGAGTCGAGC 58.739 55.000 18.61 0.00 31.73 5.03
775 840 1.296755 AACACTAGCGAGTCGAGCGA 61.297 55.000 18.61 0.00 40.04 4.93
776 841 1.011684 CACTAGCGAGTCGAGCGAG 60.012 63.158 18.61 7.64 41.93 5.03
778 843 2.814238 CTAGCGAGTCGAGCGAGCA 61.814 63.158 18.61 0.00 40.04 4.26
816 887 2.542595 CCAGAAGCAAAGCAAAGCAAAG 59.457 45.455 0.00 0.00 0.00 2.77
817 888 2.033151 CAGAAGCAAAGCAAAGCAAAGC 60.033 45.455 0.00 0.00 0.00 3.51
818 889 1.935199 GAAGCAAAGCAAAGCAAAGCA 59.065 42.857 0.00 0.00 0.00 3.91
819 890 2.027003 AGCAAAGCAAAGCAAAGCAA 57.973 40.000 0.00 0.00 0.00 3.91
820 891 2.358015 AGCAAAGCAAAGCAAAGCAAA 58.642 38.095 0.00 0.00 0.00 3.68
868 940 3.554524 CAGACAAACGTCGCATGATTTT 58.445 40.909 0.00 0.00 38.51 1.82
875 947 1.025041 GTCGCATGATTTTCCCCTCC 58.975 55.000 0.00 0.00 0.00 4.30
877 949 0.106519 CGCATGATTTTCCCCTCCCT 60.107 55.000 0.00 0.00 0.00 4.20
908 986 0.807667 CCGCCTCATGTGTGTAGAGC 60.808 60.000 0.00 0.00 0.00 4.09
912 990 0.174389 CTCATGTGTGTAGAGCGCCT 59.826 55.000 2.29 3.28 0.00 5.52
913 991 0.173481 TCATGTGTGTAGAGCGCCTC 59.827 55.000 2.29 0.45 0.00 4.70
914 992 0.807667 CATGTGTGTAGAGCGCCTCC 60.808 60.000 2.29 0.00 0.00 4.30
915 993 0.972983 ATGTGTGTAGAGCGCCTCCT 60.973 55.000 2.29 1.09 0.00 3.69
916 994 1.139947 GTGTGTAGAGCGCCTCCTC 59.860 63.158 2.29 0.00 0.00 3.71
917 995 2.052690 TGTGTAGAGCGCCTCCTCC 61.053 63.158 2.29 0.00 32.17 4.30
918 996 2.829003 TGTAGAGCGCCTCCTCCG 60.829 66.667 2.29 0.00 32.17 4.63
919 997 3.597728 GTAGAGCGCCTCCTCCGG 61.598 72.222 2.29 0.00 32.17 5.14
920 998 3.805497 TAGAGCGCCTCCTCCGGA 61.805 66.667 2.93 2.93 32.17 5.14
921 999 3.134703 TAGAGCGCCTCCTCCGGAT 62.135 63.158 3.57 0.00 32.17 4.18
922 1000 3.984749 GAGCGCCTCCTCCGGATC 61.985 72.222 3.57 0.00 0.00 3.36
926 1004 2.597805 GCCTCCTCCGGATCGCTA 60.598 66.667 3.57 0.00 0.00 4.26
927 1005 2.921797 GCCTCCTCCGGATCGCTAC 61.922 68.421 3.57 0.00 0.00 3.58
928 1006 2.269529 CCTCCTCCGGATCGCTACC 61.270 68.421 3.57 0.00 0.00 3.18
929 1007 1.228306 CTCCTCCGGATCGCTACCT 60.228 63.158 3.57 0.00 0.00 3.08
949 1027 3.304659 CCTTAATTCGCCGGAAATGATGG 60.305 47.826 5.05 5.30 35.40 3.51
950 1028 1.762708 AATTCGCCGGAAATGATGGT 58.237 45.000 5.05 0.00 35.40 3.55
952 1030 0.035915 TTCGCCGGAAATGATGGTGA 60.036 50.000 5.05 0.00 40.34 4.02
953 1031 0.742990 TCGCCGGAAATGATGGTGAC 60.743 55.000 5.05 0.00 37.37 3.67
954 1032 0.744414 CGCCGGAAATGATGGTGACT 60.744 55.000 5.05 0.00 35.26 3.41
955 1033 1.472552 CGCCGGAAATGATGGTGACTA 60.473 52.381 5.05 0.00 35.26 2.59
956 1034 2.213499 GCCGGAAATGATGGTGACTAG 58.787 52.381 5.05 0.00 0.00 2.57
957 1035 2.420129 GCCGGAAATGATGGTGACTAGT 60.420 50.000 5.05 0.00 0.00 2.57
958 1036 3.181469 GCCGGAAATGATGGTGACTAGTA 60.181 47.826 5.05 0.00 0.00 1.82
1671 1770 0.032130 TCGATATTGAGACAGGGCGC 59.968 55.000 0.00 0.00 0.00 6.53
1758 1857 3.068881 CTCAAGGCCGAGGTGGAA 58.931 61.111 0.00 0.00 42.00 3.53
1944 2043 2.543777 TTGTAGAGCAGCGGTCTTTT 57.456 45.000 13.79 0.00 40.94 2.27
1965 2064 1.003118 TGGAATGTCTACCGCAGCTTT 59.997 47.619 0.00 0.00 0.00 3.51
1980 2079 1.074889 AGCTTTGACCGGTTATGGGTT 59.925 47.619 9.42 0.00 38.07 4.11
2175 2274 1.133407 GTGTCGAGGGAGACTAAGCTG 59.867 57.143 0.00 0.00 41.47 4.24
2184 2283 4.167113 AGGGAGACTAAGCTGATCTCTGTA 59.833 45.833 17.20 0.00 39.12 2.74
2397 2496 4.101645 TCCTTGGGTTCGGAATTTTACA 57.898 40.909 0.00 0.00 0.00 2.41
2409 2508 6.731164 TCGGAATTTTACAGAGAAAACCAAC 58.269 36.000 0.00 0.00 31.35 3.77
2601 2700 3.941483 CCACGAAGACAATATTCAGCCTT 59.059 43.478 0.00 0.00 0.00 4.35
2751 2850 0.834612 TTACAGGGGCACTTATCGGG 59.165 55.000 0.00 0.00 0.00 5.14
3090 3189 5.125739 AGTTGTTTGGAAAATTCGTGTGGTA 59.874 36.000 0.00 0.00 0.00 3.25
3195 3294 5.016352 ACACTGGGGTAGGATATCTAGCATA 59.984 44.000 2.05 0.00 45.57 3.14
3317 3416 4.397103 TCAGCTGTTCCTTGCATTTGATAG 59.603 41.667 14.67 0.00 0.00 2.08
3319 3418 3.129988 GCTGTTCCTTGCATTTGATAGCT 59.870 43.478 0.00 0.00 0.00 3.32
3346 3445 5.428253 TGGAATACGGGAAATTCTCTGAAG 58.572 41.667 0.00 0.00 34.43 3.02
3420 3519 4.214332 GTGGAACTGCTACTGAAGGAAAAG 59.786 45.833 0.00 0.00 0.00 2.27
3453 3552 3.820467 CCAAGATAGTCAACACCTTGCAA 59.180 43.478 0.00 0.00 34.51 4.08
3491 3590 6.159299 TGCAGTTCATGATTTTCCAAAGAA 57.841 33.333 0.00 0.00 0.00 2.52
3574 3673 1.538047 GTTGCTCTTTGAGGATGCCA 58.462 50.000 0.00 0.00 28.56 4.92
3593 3692 3.633986 GCCATAAAATTCCCTGGTGAGAG 59.366 47.826 0.00 0.00 0.00 3.20
3840 3939 3.920446 TCGTCGTGAAAATGAAGATGGA 58.080 40.909 0.00 0.00 0.00 3.41
4002 4101 1.006758 AGGGGTCAGACCTTATCACGA 59.993 52.381 19.57 0.00 38.64 4.35
4168 4267 1.478510 ACAATGGTTTGCAACAACGGA 59.521 42.857 0.00 0.00 36.22 4.69
4374 4473 4.669965 CGTGTTGCTTATGTTGATGAGGTG 60.670 45.833 0.00 0.00 0.00 4.00
4375 4474 3.191162 TGTTGCTTATGTTGATGAGGTGC 59.809 43.478 0.00 0.00 0.00 5.01
4376 4475 3.070476 TGCTTATGTTGATGAGGTGCA 57.930 42.857 0.00 0.00 0.00 4.57
4377 4476 3.623703 TGCTTATGTTGATGAGGTGCAT 58.376 40.909 0.00 0.00 40.77 3.96
4497 4599 4.757149 CCACTGAAACTTGGAGAAGGTAAG 59.243 45.833 0.00 0.00 34.46 2.34
4536 4638 4.508551 TGCCATCATATTCACAAGAGGT 57.491 40.909 0.00 0.00 0.00 3.85
4746 4848 2.750237 GTTACCCTTGGGCAGCGG 60.750 66.667 5.46 0.00 0.00 5.52
5028 5130 6.703607 GTGAACAGACATTGAGTAGGGATATG 59.296 42.308 0.00 0.00 0.00 1.78
5037 5139 6.961360 TTGAGTAGGGATATGTACAGACTG 57.039 41.667 0.33 0.00 0.00 3.51
5124 5226 0.518636 CAATGCTGGTGGTCTTGACG 59.481 55.000 0.00 0.00 0.00 4.35
5160 5262 3.866582 GGGCGCCTGTATCTGGCT 61.867 66.667 28.56 0.00 44.56 4.75
5190 5292 1.454663 GGAGGCTGGAATTCAGGGC 60.455 63.158 7.93 11.03 43.54 5.19
5211 5313 4.201822 GGCAGTGCTAATGCTACTAACAAC 60.202 45.833 16.11 0.00 43.35 3.32
5355 5457 5.771153 TCACAATGCAGATGAACTTTTCA 57.229 34.783 9.10 0.00 45.01 2.69
5424 5526 2.415893 CCGAACAATTCTTCATGGTGGC 60.416 50.000 0.00 0.00 0.00 5.01
5827 5929 6.097412 CCTTTGGGGAAAGATTTTGGAGATAG 59.903 42.308 0.00 0.00 37.23 2.08
6105 6207 6.240145 TCAAATCATTGACATCTTCACTGGA 58.760 36.000 0.00 0.00 40.59 3.86
6373 6475 2.719798 CTGGCAAGAAAACGAACACAG 58.280 47.619 0.00 0.00 0.00 3.66
6447 6549 9.271828 CAATGTACTGTGCATCCACTTATATTA 57.728 33.333 11.78 0.00 42.54 0.98
6448 6550 9.494271 AATGTACTGTGCATCCACTTATATTAG 57.506 33.333 11.78 0.00 42.54 1.73
6449 6551 8.018537 TGTACTGTGCATCCACTTATATTAGT 57.981 34.615 0.00 0.00 42.54 2.24
6450 6552 9.138596 TGTACTGTGCATCCACTTATATTAGTA 57.861 33.333 0.00 0.00 42.54 1.82
6451 6553 9.627395 GTACTGTGCATCCACTTATATTAGTAG 57.373 37.037 0.00 0.00 42.54 2.57
6452 6554 8.478775 ACTGTGCATCCACTTATATTAGTAGA 57.521 34.615 0.00 0.00 42.54 2.59
6453 6555 8.361139 ACTGTGCATCCACTTATATTAGTAGAC 58.639 37.037 0.00 0.00 42.54 2.59
6454 6556 8.478775 TGTGCATCCACTTATATTAGTAGACT 57.521 34.615 0.00 0.00 42.54 3.24
6455 6557 8.924303 TGTGCATCCACTTATATTAGTAGACTT 58.076 33.333 0.00 0.00 42.54 3.01
6485 6587 5.722263 TGGCATCTTTACATTGAATTGTGG 58.278 37.500 0.00 0.00 0.00 4.17
6486 6588 5.245751 TGGCATCTTTACATTGAATTGTGGT 59.754 36.000 0.00 0.00 0.00 4.16
6495 6597 1.619654 TGAATTGTGGTGCTTCTGGG 58.380 50.000 0.00 0.00 0.00 4.45
6506 6608 0.957888 GCTTCTGGGAGCAGTGGAAC 60.958 60.000 0.00 0.00 42.25 3.62
6555 6657 8.929827 TCATACTATTTTGACAAATGGCATTG 57.070 30.769 14.47 10.40 34.88 2.82
6583 6685 5.246307 AGTCTAAACTTGCCGCTTTCTAAT 58.754 37.500 0.00 0.00 28.74 1.73
6640 6742 7.992754 AGCTCCATTGATGATTTAGATTACC 57.007 36.000 0.00 0.00 0.00 2.85
6674 6776 5.412594 TGGTGTCACTGATGAGCTTAAATTC 59.587 40.000 2.35 0.00 34.75 2.17
6816 7256 1.814429 TCCCCTTTTCTGTCTGTCCA 58.186 50.000 0.00 0.00 0.00 4.02
6854 7294 3.347216 AGTTTCACTCAGCACAACAGTT 58.653 40.909 0.00 0.00 0.00 3.16
6925 7368 5.163426 TGGTGTCTTTGCATGAAATTCAAGT 60.163 36.000 0.00 0.00 0.00 3.16
6936 7379 7.094248 TGCATGAAATTCAAGTTAGCATGTAGT 60.094 33.333 0.00 0.00 35.38 2.73
6937 7380 8.397906 GCATGAAATTCAAGTTAGCATGTAGTA 58.602 33.333 0.00 0.00 35.38 1.82
7016 7459 4.762251 AGAGATGTAACTGCTGGGTTTTTC 59.238 41.667 0.00 0.00 0.00 2.29
7094 7542 1.410517 CCGGTCATCTCTGTACAGCAT 59.589 52.381 18.45 9.44 0.00 3.79
7098 7546 4.701765 GGTCATCTCTGTACAGCATCAAT 58.298 43.478 18.45 4.06 0.00 2.57
7179 7627 6.640518 TGGCGATTTCTCTAGTTTAGATGTT 58.359 36.000 0.00 0.00 33.66 2.71
7180 7628 6.757010 TGGCGATTTCTCTAGTTTAGATGTTC 59.243 38.462 0.00 0.00 33.66 3.18
7201 7649 6.312918 TGTTCTCAGATTCGTATAACTTTGGC 59.687 38.462 0.00 0.00 0.00 4.52
7208 7656 8.495949 CAGATTCGTATAACTTTGGCGATTTAT 58.504 33.333 0.00 0.00 0.00 1.40
7240 7689 1.927895 GCACTAGCTGCGTGTTAGAT 58.072 50.000 16.27 0.00 35.72 1.98
7268 7717 0.378610 GATTGCGCTTCAGCTTACCC 59.621 55.000 9.73 0.00 39.32 3.69
7269 7718 1.369091 ATTGCGCTTCAGCTTACCCG 61.369 55.000 9.73 0.00 39.32 5.28
7274 7723 0.037232 GCTTCAGCTTACCCGTGAGT 60.037 55.000 0.00 0.00 38.21 3.41
7280 7729 2.093973 CAGCTTACCCGTGAGTTCTGAT 60.094 50.000 0.00 0.00 0.00 2.90
7281 7730 2.093973 AGCTTACCCGTGAGTTCTGATG 60.094 50.000 0.00 0.00 0.00 3.07
7282 7731 2.094182 GCTTACCCGTGAGTTCTGATGA 60.094 50.000 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.930310 CTGTGGTCGTGACACTTGTG 59.070 55.000 3.68 0.00 39.52 3.33
68 69 7.375384 CGAAAGTTCGTGGTGTAGAGTATCTG 61.375 46.154 5.28 0.00 45.64 2.90
100 101 4.939052 TTAGAGGAGATAAAGGCGGAAG 57.061 45.455 0.00 0.00 0.00 3.46
104 105 9.495572 AGAAATTTATTAGAGGAGATAAAGGCG 57.504 33.333 0.00 0.00 32.89 5.52
111 116 8.722422 AGGCTGAAGAAATTTATTAGAGGAGAT 58.278 33.333 0.00 0.00 0.00 2.75
112 117 8.095452 AGGCTGAAGAAATTTATTAGAGGAGA 57.905 34.615 0.00 0.00 0.00 3.71
121 126 5.841957 ATCGCAAGGCTGAAGAAATTTAT 57.158 34.783 0.00 0.00 38.47 1.40
122 127 6.942532 ATATCGCAAGGCTGAAGAAATTTA 57.057 33.333 0.00 0.00 38.47 1.40
133 138 1.672881 GTGAAGCAATATCGCAAGGCT 59.327 47.619 0.00 0.00 36.13 4.58
181 186 9.559958 GAATCAACATCAATATCTCGTTTGTTT 57.440 29.630 0.00 0.00 0.00 2.83
182 187 8.729756 TGAATCAACATCAATATCTCGTTTGTT 58.270 29.630 0.00 0.00 0.00 2.83
183 188 8.267620 TGAATCAACATCAATATCTCGTTTGT 57.732 30.769 0.00 0.00 0.00 2.83
184 189 9.726232 AATGAATCAACATCAATATCTCGTTTG 57.274 29.630 0.00 0.00 0.00 2.93
186 191 9.726232 CAAATGAATCAACATCAATATCTCGTT 57.274 29.630 0.00 0.00 0.00 3.85
187 192 8.347771 CCAAATGAATCAACATCAATATCTCGT 58.652 33.333 0.00 0.00 0.00 4.18
188 193 7.325338 GCCAAATGAATCAACATCAATATCTCG 59.675 37.037 0.00 0.00 0.00 4.04
201 206 4.674885 CGCACATGTAGCCAAATGAATCAA 60.675 41.667 0.00 0.00 0.00 2.57
272 277 2.983592 GTGCGGTGTTCCCCCTTG 60.984 66.667 0.00 0.00 0.00 3.61
347 356 4.124970 CCATATGGCATATGAGTCCATCG 58.875 47.826 37.08 20.23 44.19 3.84
399 408 2.622942 TGAATTGTGGGTGAGAAAGCAC 59.377 45.455 0.00 0.00 38.05 4.40
466 475 3.421844 GTTTCAGCCCATTTCCAGTACT 58.578 45.455 0.00 0.00 0.00 2.73
467 476 2.161609 CGTTTCAGCCCATTTCCAGTAC 59.838 50.000 0.00 0.00 0.00 2.73
468 477 2.432444 CGTTTCAGCCCATTTCCAGTA 58.568 47.619 0.00 0.00 0.00 2.74
469 478 1.247567 CGTTTCAGCCCATTTCCAGT 58.752 50.000 0.00 0.00 0.00 4.00
528 537 6.483851 CGGATTCGCGTATAGATATCTTTG 57.516 41.667 11.25 0.00 0.00 2.77
551 608 9.143155 TGGAAAATCTAGGGGATTAATTTTAGC 57.857 33.333 0.00 0.00 43.17 3.09
584 641 0.613260 AATTGGCACTCGGCTGACTA 59.387 50.000 0.00 0.00 44.01 2.59
591 648 0.523072 CCAACAGAATTGGCACTCGG 59.477 55.000 0.00 0.00 32.18 4.63
607 664 1.304381 GGTGAAGCCATGGAGCCAA 60.304 57.895 18.40 0.00 37.17 4.52
648 705 4.811024 TCAACACTCAACAGCAGTTCTAAG 59.189 41.667 0.00 0.00 35.28 2.18
667 724 6.854496 TTGGTGATGTACTACAAACTCAAC 57.146 37.500 0.00 0.00 0.00 3.18
668 725 7.254227 GTTTGGTGATGTACTACAAACTCAA 57.746 36.000 16.55 0.91 44.36 3.02
672 729 6.128902 CGAGAGTTTGGTGATGTACTACAAAC 60.129 42.308 16.29 16.29 46.70 2.93
673 730 5.924254 CGAGAGTTTGGTGATGTACTACAAA 59.076 40.000 0.00 0.00 0.00 2.83
674 731 5.010314 ACGAGAGTTTGGTGATGTACTACAA 59.990 40.000 0.00 0.00 46.40 2.41
676 733 5.056894 ACGAGAGTTTGGTGATGTACTAC 57.943 43.478 0.00 0.00 46.40 2.73
718 779 1.608025 CCGGTGGGATAATGATGACGG 60.608 57.143 0.00 0.00 34.06 4.79
768 833 4.103103 CCACGACTGCTCGCTCGA 62.103 66.667 7.42 0.00 44.33 4.04
769 834 3.898627 AACCACGACTGCTCGCTCG 62.899 63.158 0.00 0.00 44.33 5.03
770 835 2.049063 AACCACGACTGCTCGCTC 60.049 61.111 0.00 0.00 44.33 5.03
771 836 2.356313 CAACCACGACTGCTCGCT 60.356 61.111 0.00 0.00 44.33 4.93
772 837 3.414700 CCAACCACGACTGCTCGC 61.415 66.667 0.00 0.00 44.33 5.03
773 838 0.878523 TTTCCAACCACGACTGCTCG 60.879 55.000 0.00 0.00 46.06 5.03
775 840 2.702847 GTTTCCAACCACGACTGCT 58.297 52.632 0.00 0.00 0.00 4.24
816 887 1.458588 TGGGGTTTGAGGGGTTTGC 60.459 57.895 0.00 0.00 0.00 3.68
817 888 1.460273 CGTGGGGTTTGAGGGGTTTG 61.460 60.000 0.00 0.00 0.00 2.93
818 889 1.152631 CGTGGGGTTTGAGGGGTTT 60.153 57.895 0.00 0.00 0.00 3.27
819 890 2.518933 CGTGGGGTTTGAGGGGTT 59.481 61.111 0.00 0.00 0.00 4.11
820 891 4.280019 GCGTGGGGTTTGAGGGGT 62.280 66.667 0.00 0.00 0.00 4.95
891 969 1.424493 GCGCTCTACACACATGAGGC 61.424 60.000 0.00 0.00 0.00 4.70
914 992 3.576648 GAATTAAGGTAGCGATCCGGAG 58.423 50.000 11.34 0.00 0.00 4.63
915 993 2.030540 CGAATTAAGGTAGCGATCCGGA 60.031 50.000 6.61 6.61 0.00 5.14
916 994 2.325761 CGAATTAAGGTAGCGATCCGG 58.674 52.381 0.00 0.00 0.00 5.14
917 995 1.719780 GCGAATTAAGGTAGCGATCCG 59.280 52.381 0.00 0.00 0.00 4.18
918 996 2.067013 GGCGAATTAAGGTAGCGATCC 58.933 52.381 0.00 0.00 0.00 3.36
919 997 1.719780 CGGCGAATTAAGGTAGCGATC 59.280 52.381 0.00 0.00 0.00 3.69
920 998 1.604693 CCGGCGAATTAAGGTAGCGAT 60.605 52.381 9.30 0.00 0.00 4.58
921 999 0.249155 CCGGCGAATTAAGGTAGCGA 60.249 55.000 9.30 0.00 0.00 4.93
922 1000 0.249155 TCCGGCGAATTAAGGTAGCG 60.249 55.000 9.30 0.00 0.00 4.26
923 1001 1.944032 TTCCGGCGAATTAAGGTAGC 58.056 50.000 9.30 0.00 0.00 3.58
924 1002 4.124238 TCATTTCCGGCGAATTAAGGTAG 58.876 43.478 9.30 0.00 0.00 3.18
925 1003 4.139859 TCATTTCCGGCGAATTAAGGTA 57.860 40.909 9.30 0.00 0.00 3.08
926 1004 2.993937 TCATTTCCGGCGAATTAAGGT 58.006 42.857 9.30 0.00 0.00 3.50
927 1005 3.304659 CCATCATTTCCGGCGAATTAAGG 60.305 47.826 9.30 0.00 0.00 2.69
928 1006 3.315191 ACCATCATTTCCGGCGAATTAAG 59.685 43.478 9.30 0.00 0.00 1.85
929 1007 3.066064 CACCATCATTTCCGGCGAATTAA 59.934 43.478 9.30 0.00 0.00 1.40
949 1027 5.220758 GGAGGCGTTAGTACTTACTAGTCAC 60.221 48.000 10.09 0.00 39.69 3.67
950 1028 4.878397 GGAGGCGTTAGTACTTACTAGTCA 59.122 45.833 10.09 0.00 39.69 3.41
952 1030 5.109500 AGGAGGCGTTAGTACTTACTAGT 57.891 43.478 10.09 0.00 39.69 2.57
953 1031 4.514816 GGAGGAGGCGTTAGTACTTACTAG 59.485 50.000 10.09 0.00 39.69 2.57
954 1032 4.164988 AGGAGGAGGCGTTAGTACTTACTA 59.835 45.833 10.09 0.00 37.73 1.82
955 1033 3.053768 AGGAGGAGGCGTTAGTACTTACT 60.054 47.826 10.09 0.00 40.24 2.24
956 1034 3.066481 CAGGAGGAGGCGTTAGTACTTAC 59.934 52.174 0.00 0.20 0.00 2.34
957 1035 3.285484 CAGGAGGAGGCGTTAGTACTTA 58.715 50.000 0.00 0.00 0.00 2.24
958 1036 2.100989 CAGGAGGAGGCGTTAGTACTT 58.899 52.381 0.00 0.00 0.00 2.24
1077 1176 3.555795 CCTGGATCGGGATGATGTTGTAG 60.556 52.174 0.00 0.00 37.47 2.74
1758 1857 2.044946 GTCCCATTCCGGCTTGCT 60.045 61.111 0.00 0.00 0.00 3.91
1867 1966 2.242043 CACAAAGAAGCCCCTTGATGT 58.758 47.619 0.00 0.00 0.00 3.06
1900 1999 1.228124 TCTTCCCAACACGGCCAAG 60.228 57.895 2.24 0.00 0.00 3.61
1944 2043 0.613260 AGCTGCGGTAGACATTCCAA 59.387 50.000 0.00 0.00 0.00 3.53
1965 2064 1.841277 AGCATAACCCATAACCGGTCA 59.159 47.619 8.04 0.00 31.48 4.02
1980 2079 6.179756 TGCCTGAAAGAACAGAATAAGCATA 58.820 36.000 0.00 0.00 39.94 3.14
2175 2274 1.683917 AGCACCATCCGTACAGAGATC 59.316 52.381 0.00 0.00 0.00 2.75
2184 2283 2.045926 GCCTTGAGCACCATCCGT 60.046 61.111 0.00 0.00 42.97 4.69
2397 2496 5.946486 AGAATTCTCCAGTTGGTTTTCTCT 58.054 37.500 0.88 0.00 36.34 3.10
2409 2508 5.931146 GGTGAGCACATATAGAATTCTCCAG 59.069 44.000 12.24 3.54 0.00 3.86
2448 2547 1.302192 ACGGCCTACAAATGTGCGT 60.302 52.632 0.00 0.00 0.00 5.24
2505 2604 4.444022 GCAAGAAGGCAGATCCAGAATAGA 60.444 45.833 0.00 0.00 37.29 1.98
2601 2700 2.159296 CCAGTTACGTCGGATGTCATGA 60.159 50.000 6.05 0.00 0.00 3.07
2751 2850 1.379642 CCCCCAGATGCGAGAAAAGC 61.380 60.000 0.00 0.00 0.00 3.51
3195 3294 0.174389 CAGCACATCGCCTGTACTCT 59.826 55.000 0.00 0.00 44.04 3.24
3317 3416 4.580580 AGAATTTCCCGTATTCCATTGAGC 59.419 41.667 0.00 0.00 33.45 4.26
3319 3418 5.822519 CAGAGAATTTCCCGTATTCCATTGA 59.177 40.000 0.00 0.00 33.45 2.57
3346 3445 4.705991 AGGTAACAAGTCTAGCCTGTAGTC 59.294 45.833 0.00 0.00 41.41 2.59
3420 3519 7.064016 GTGTTGACTATCTTGGTCTGATCTTTC 59.936 40.741 0.00 0.00 35.04 2.62
3453 3552 4.284490 TGAACTGCAAGGACATAGAGAGTT 59.716 41.667 0.00 0.00 39.30 3.01
3491 3590 2.644798 AGCTGTTCAATACCCTTCCTGT 59.355 45.455 0.00 0.00 0.00 4.00
3574 3673 5.779241 TCACTCTCACCAGGGAATTTTAT 57.221 39.130 0.00 0.00 0.00 1.40
4002 4101 7.691993 ATAGTACATCATTCCCCTAACAGTT 57.308 36.000 0.00 0.00 0.00 3.16
4168 4267 3.181450 CCTCTGTTCAACCTCCTTTGAGT 60.181 47.826 0.00 0.00 36.84 3.41
4374 4473 3.694364 ATCACCCATCTCGTGATGC 57.306 52.632 19.56 0.00 46.61 3.91
4377 4476 7.718334 ATATTGTATATCACCCATCTCGTGA 57.282 36.000 0.00 0.00 44.00 4.35
4497 4599 1.337167 GCATGGTTCTGGTTTTCAGGC 60.337 52.381 0.00 0.00 43.53 4.85
4536 4638 3.181478 TGTCAATTGTTTGCACTGCATCA 60.181 39.130 4.10 5.03 38.76 3.07
4746 4848 3.462021 CTTCAGTGGATTAGCTAGCACC 58.538 50.000 18.83 14.36 0.00 5.01
5028 5130 4.705507 TCAGTTCTATGACCCAGTCTGTAC 59.294 45.833 0.00 0.00 33.15 2.90
5124 5226 3.734463 CCCCCAAACAAATGTGTAAACC 58.266 45.455 0.00 0.00 36.80 3.27
5160 5262 0.902048 CAGCCTCCAGACCACTCAGA 60.902 60.000 0.00 0.00 0.00 3.27
5190 5292 6.480524 TTGTTGTTAGTAGCATTAGCACTG 57.519 37.500 0.00 0.00 45.49 3.66
5211 5313 1.364901 CACAGCACCCAAGGCTTTG 59.635 57.895 0.68 0.68 40.23 2.77
5349 5451 9.604626 GAAAATGTGTAGAAGACAGATGAAAAG 57.395 33.333 0.00 0.00 41.05 2.27
5355 5457 6.600822 CCATGGAAAATGTGTAGAAGACAGAT 59.399 38.462 5.56 0.00 43.68 2.90
5424 5526 1.209128 CAGTAGCCCGATACTTTGCG 58.791 55.000 0.00 0.00 33.68 4.85
5682 5784 5.966636 TGAAATCCTCGAAATCATACACG 57.033 39.130 0.00 0.00 0.00 4.49
6105 6207 4.463891 CCAGTAGGAATGAATGCCAAAAGT 59.536 41.667 0.00 0.00 36.89 2.66
6396 6498 6.978080 GCAAATAGGCCAGATAAATCGAAAAA 59.022 34.615 5.01 0.00 0.00 1.94
6448 6550 5.855740 AAGATGCCAGTAGGTAAGTCTAC 57.144 43.478 0.00 0.00 39.76 2.59
6449 6551 6.893554 TGTAAAGATGCCAGTAGGTAAGTCTA 59.106 38.462 0.00 0.00 37.19 2.59
6450 6552 5.720041 TGTAAAGATGCCAGTAGGTAAGTCT 59.280 40.000 0.00 0.00 37.19 3.24
6451 6553 5.974108 TGTAAAGATGCCAGTAGGTAAGTC 58.026 41.667 0.00 0.00 37.19 3.01
6452 6554 6.561519 ATGTAAAGATGCCAGTAGGTAAGT 57.438 37.500 0.00 0.00 37.19 2.24
6453 6555 7.047891 TCAATGTAAAGATGCCAGTAGGTAAG 58.952 38.462 0.00 0.00 37.19 2.34
6454 6556 6.953101 TCAATGTAAAGATGCCAGTAGGTAA 58.047 36.000 0.00 0.00 37.19 2.85
6455 6557 6.553953 TCAATGTAAAGATGCCAGTAGGTA 57.446 37.500 0.00 0.00 37.19 3.08
6456 6558 5.435686 TCAATGTAAAGATGCCAGTAGGT 57.564 39.130 0.00 0.00 37.19 3.08
6457 6559 6.949352 ATTCAATGTAAAGATGCCAGTAGG 57.051 37.500 0.00 0.00 38.23 3.18
6485 6587 1.673665 CCACTGCTCCCAGAAGCAC 60.674 63.158 0.00 0.00 47.00 4.40
6495 6597 0.615850 AGCCCTAAGTTCCACTGCTC 59.384 55.000 0.00 0.00 0.00 4.26
6506 6608 3.706594 TCACCATGAGACTAAGCCCTAAG 59.293 47.826 0.00 0.00 0.00 2.18
6541 6643 2.964464 ACTTGTCCAATGCCATTTGTCA 59.036 40.909 0.00 0.00 0.00 3.58
6583 6685 5.413309 ACTGAAAACACCAATTGGACAAA 57.587 34.783 31.22 8.36 38.94 2.83
6640 6742 2.203139 TGACACCAGCCCAACACG 60.203 61.111 0.00 0.00 0.00 4.49
6674 6776 3.362304 GCAGCATTTTTCGTTTTCAGCAG 60.362 43.478 0.00 0.00 0.00 4.24
6747 6849 6.226787 CACTCATCCCATTAGACAAGGATAC 58.773 44.000 0.00 0.00 36.99 2.24
6816 7256 0.963962 ACTTGGTGGTATCGACACGT 59.036 50.000 0.00 0.00 39.69 4.49
6925 7368 4.466370 AGAACAGGCTGTACTACATGCTAA 59.534 41.667 22.37 0.00 0.00 3.09
6955 7398 6.200665 GCACAATTTGATACTTTTTCAGTGCA 59.799 34.615 2.79 0.00 39.46 4.57
6962 7405 8.819974 CAGAAAGTGCACAATTTGATACTTTTT 58.180 29.630 21.04 5.59 40.95 1.94
6975 7418 4.707105 TCTCTGAATCAGAAAGTGCACAA 58.293 39.130 21.04 0.00 40.18 3.33
7030 7475 1.350019 ACAACCTGGTTAGTACCTGCC 59.650 52.381 12.53 0.00 45.27 4.85
7094 7542 1.606668 ACGAAAAGCTTTCCGCATTGA 59.393 42.857 18.31 0.00 42.61 2.57
7098 7546 0.306533 GTCACGAAAAGCTTTCCGCA 59.693 50.000 18.31 1.52 42.61 5.69
7108 7556 4.181578 GGAGCTAAGCTATGTCACGAAAA 58.818 43.478 0.00 0.00 39.88 2.29
7111 7559 2.375146 TGGAGCTAAGCTATGTCACGA 58.625 47.619 0.00 0.00 39.88 4.35
7150 7598 4.657436 AACTAGAGAAATCGCCAGTAGG 57.343 45.455 0.00 0.00 38.23 3.18
7179 7627 5.041287 CGCCAAAGTTATACGAATCTGAGA 58.959 41.667 0.00 0.00 0.00 3.27
7180 7628 5.041287 TCGCCAAAGTTATACGAATCTGAG 58.959 41.667 0.00 0.00 0.00 3.35
7192 7640 6.127758 ACTCAATGCATAAATCGCCAAAGTTA 60.128 34.615 0.00 0.00 0.00 2.24
7201 7649 4.912214 TGCAAGACTCAATGCATAAATCG 58.088 39.130 0.00 0.00 46.87 3.34
7232 7681 6.146837 AGCGCAATCATCATCTAATCTAACAC 59.853 38.462 11.47 0.00 0.00 3.32
7240 7689 3.249320 GCTGAAGCGCAATCATCATCTAA 59.751 43.478 11.47 0.00 0.00 2.10
7268 7717 8.278408 CCAACAAATATATCATCAGAACTCACG 58.722 37.037 0.00 0.00 0.00 4.35
7269 7718 8.072567 GCCAACAAATATATCATCAGAACTCAC 58.927 37.037 0.00 0.00 0.00 3.51
7274 7723 6.491062 CCAGGCCAACAAATATATCATCAGAA 59.509 38.462 5.01 0.00 0.00 3.02
7280 7729 4.183223 AGCCAGGCCAACAAATATATCA 57.817 40.909 8.22 0.00 0.00 2.15
7281 7730 5.560724 TCTAGCCAGGCCAACAAATATATC 58.439 41.667 8.22 0.00 0.00 1.63
7282 7731 5.582950 TCTAGCCAGGCCAACAAATATAT 57.417 39.130 8.22 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.