Multiple sequence alignment - TraesCS2B01G301400

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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 TraesCS2B01G301400 chr2B 100.000 4892 0 0 1 4892 424325637 424330528 0.000000e+00 9034
1 TraesCS2B01G301400 chr2B 100.000 2640 0 0 5216 7855 424330852 424333491 0.000000e+00 4876
2 TraesCS2B01G301400 chr2B 78.429 1451 281 22 1108 2539 54545157 54546594 0.000000e+00 917
3 TraesCS2B01G301400 chr2B 88.060 134 16 0 5592 5725 54548848 54548981 8.160000e-35 159
4 TraesCS2B01G301400 chr2A 95.574 4293 130 19 632 4892 477002624 477006888 0.000000e+00 6820
5 TraesCS2B01G301400 chr2A 92.769 2434 90 28 5231 7593 477007023 477009441 0.000000e+00 3441
6 TraesCS2B01G301400 chr2A 92.171 281 15 5 7573 7852 477009453 477009727 2.660000e-104 390
7 TraesCS2B01G301400 chr2A 88.806 134 15 0 5592 5725 36051539 36051672 1.750000e-36 165
8 TraesCS2B01G301400 chr2D 95.469 4282 109 24 650 4892 356526442 356530677 0.000000e+00 6754
9 TraesCS2B01G301400 chr2D 93.210 2327 92 27 5231 7508 356530812 356533121 0.000000e+00 3362
10 TraesCS2B01G301400 chr2D 96.486 626 22 0 1 626 453734538 453735163 0.000000e+00 1035
11 TraesCS2B01G301400 chr2D 92.476 319 12 6 7537 7852 356533117 356533426 5.590000e-121 446
12 TraesCS2B01G301400 chr2D 87.313 134 17 0 5592 5725 32802255 32802388 3.800000e-33 154
13 TraesCS2B01G301400 chr6B 96.486 626 22 0 1 626 143645631 143646256 0.000000e+00 1035
14 TraesCS2B01G301400 chr6B 96.486 626 22 0 1 626 273229499 273230124 0.000000e+00 1035
15 TraesCS2B01G301400 chr6B 96.486 626 22 0 1 626 455421903 455421278 0.000000e+00 1035
16 TraesCS2B01G301400 chr6A 96.486 626 22 0 1 626 234188240 234188865 0.000000e+00 1035
17 TraesCS2B01G301400 chr5B 96.326 626 23 0 1 626 287777145 287776520 0.000000e+00 1029
18 TraesCS2B01G301400 chr4B 96.326 626 23 0 1 626 669601905 669602530 0.000000e+00 1029
19 TraesCS2B01G301400 chr4A 96.326 626 23 0 1 626 624980534 624981159 0.000000e+00 1029
20 TraesCS2B01G301400 chr3B 96.326 626 23 0 1 626 588665970 588665345 0.000000e+00 1029


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 TraesCS2B01G301400 chr2B 424325637 424333491 7854 False 6955.000000 9034 100.000000 1 7855 2 chr2B.!!$F2 7854
1 TraesCS2B01G301400 chr2B 54545157 54548981 3824 False 538.000000 917 83.244500 1108 5725 2 chr2B.!!$F1 4617
2 TraesCS2B01G301400 chr2A 477002624 477009727 7103 False 3550.333333 6820 93.504667 632 7852 3 chr2A.!!$F2 7220
3 TraesCS2B01G301400 chr2D 356526442 356533426 6984 False 3520.666667 6754 93.718333 650 7852 3 chr2D.!!$F3 7202
4 TraesCS2B01G301400 chr2D 453734538 453735163 625 False 1035.000000 1035 96.486000 1 626 1 chr2D.!!$F2 625
5 TraesCS2B01G301400 chr6B 143645631 143646256 625 False 1035.000000 1035 96.486000 1 626 1 chr6B.!!$F1 625
6 TraesCS2B01G301400 chr6B 273229499 273230124 625 False 1035.000000 1035 96.486000 1 626 1 chr6B.!!$F2 625
7 TraesCS2B01G301400 chr6B 455421278 455421903 625 True 1035.000000 1035 96.486000 1 626 1 chr6B.!!$R1 625
8 TraesCS2B01G301400 chr6A 234188240 234188865 625 False 1035.000000 1035 96.486000 1 626 1 chr6A.!!$F1 625
9 TraesCS2B01G301400 chr5B 287776520 287777145 625 True 1029.000000 1029 96.326000 1 626 1 chr5B.!!$R1 625
10 TraesCS2B01G301400 chr4B 669601905 669602530 625 False 1029.000000 1029 96.326000 1 626 1 chr4B.!!$F1 625
11 TraesCS2B01G301400 chr4A 624980534 624981159 625 False 1029.000000 1029 96.326000 1 626 1 chr4A.!!$F1 625
12 TraesCS2B01G301400 chr3B 588665345 588665970 625 True 1029.000000 1029 96.326000 1 626 1 chr3B.!!$R1 625


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
589 590 0.756903 TAGCTTGAAGCCGGTATCCC 59.243 55.000 14.45 0.00 43.77 3.85 F
616 617 1.181786 CTTCGCCTTCTGTCCTCTCT 58.818 55.000 0.00 0.00 0.00 3.10 F
758 759 2.624846 TATCCCCATCCTCCCCTTTT 57.375 50.000 0.00 0.00 0.00 2.27 F
2202 2210 0.700564 ATGGAAGCTTCTCAGGGCAA 59.299 50.000 25.05 2.89 0.00 4.52 F
2551 2559 0.762418 CAAGGTACTGTCCACACCCA 59.238 55.000 0.00 0.00 40.86 4.51 F
3231 3405 1.956477 GGTGAAGCCATGACAACACTT 59.044 47.619 0.00 0.00 37.17 3.16 F
4736 5114 0.244721 GCCCAGGTTGCAAAGATGTC 59.755 55.000 0.00 0.00 0.00 3.06 F
6523 6974 1.003118 TGATCCAGTACACTTGTGGGC 59.997 52.381 5.72 0.00 31.70 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2079 2087 1.066573 ACAGGATCGACTGCTTCCAAG 60.067 52.381 4.88 0.00 42.21 3.61 R
2202 2210 2.303022 CAGGGTCTCATACACAACACCT 59.697 50.000 0.00 0.00 31.97 4.00 R
2415 2423 3.123620 CTCCACTCCGCAGCAAGC 61.124 66.667 0.00 0.00 40.87 4.01 R
3881 4065 2.176045 TGGCTAAGGACGAATGTCTGA 58.824 47.619 0.00 0.00 44.83 3.27 R
3994 4178 2.294979 CATGTCTGCTACACATGCCAT 58.705 47.619 9.38 0.00 43.48 4.40 R
4810 5189 3.914312 TGTGTAAGAGCTACTTCACAGC 58.086 45.455 16.94 0.00 39.34 4.40 R
6734 7207 0.772124 ATGGGGCCCTTCCGACATAT 60.772 55.000 25.93 1.65 33.20 1.78 R
7437 7939 0.109532 TTCTCGTTGTTGGATGCCCA 59.890 50.000 0.00 0.00 41.64 5.36 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
103 104 1.686052 CTTCCCTTCTCGAGAGGATGG 59.314 57.143 24.81 17.82 0.00 3.51
256 257 1.799258 GATGCCATAGCCAAAGCCCG 61.799 60.000 0.00 0.00 41.25 6.13
331 332 2.955660 CCTCCTACGAAGAGCTTCTCAT 59.044 50.000 8.44 0.00 37.44 2.90
360 361 3.594603 ACACTCCTAACCATGTCTTCG 57.405 47.619 0.00 0.00 0.00 3.79
384 385 1.988846 CCTTCCCAGAACTCCCTCTTT 59.011 52.381 0.00 0.00 0.00 2.52
418 419 1.524961 CCTACTTGCGGGGCATACA 59.475 57.895 0.00 0.00 38.76 2.29
438 439 7.413000 GCATACACGTTGATAACATTGAGAACT 60.413 37.037 0.00 0.00 0.00 3.01
441 442 8.373048 ACACGTTGATAACATTGAGAACTAAA 57.627 30.769 0.00 0.00 0.00 1.85
452 453 9.793259 AACATTGAGAACTAAATCCTCAACTAA 57.207 29.630 0.00 0.00 45.92 2.24
528 529 4.660168 ACTTGAGGCTCTTGTTGATCAAT 58.340 39.130 16.72 0.00 35.35 2.57
560 561 2.057137 TTTCTGTTTGCAGCTGTCCT 57.943 45.000 16.64 0.00 42.29 3.85
563 564 2.180131 CTGTTTGCAGCTGTCCTCGC 62.180 60.000 16.64 0.00 35.77 5.03
564 565 2.110835 TTTGCAGCTGTCCTCGCA 59.889 55.556 16.64 2.29 0.00 5.10
589 590 0.756903 TAGCTTGAAGCCGGTATCCC 59.243 55.000 14.45 0.00 43.77 3.85
616 617 1.181786 CTTCGCCTTCTGTCCTCTCT 58.818 55.000 0.00 0.00 0.00 3.10
626 627 6.576442 GCCTTCTGTCCTCTCTATTTGGTTTA 60.576 42.308 0.00 0.00 0.00 2.01
627 628 6.819146 CCTTCTGTCCTCTCTATTTGGTTTAC 59.181 42.308 0.00 0.00 0.00 2.01
628 629 7.310734 CCTTCTGTCCTCTCTATTTGGTTTACT 60.311 40.741 0.00 0.00 0.00 2.24
629 630 8.660295 TTCTGTCCTCTCTATTTGGTTTACTA 57.340 34.615 0.00 0.00 0.00 1.82
630 631 8.294954 TCTGTCCTCTCTATTTGGTTTACTAG 57.705 38.462 0.00 0.00 0.00 2.57
631 632 7.894364 TCTGTCCTCTCTATTTGGTTTACTAGT 59.106 37.037 0.00 0.00 0.00 2.57
632 633 8.064336 TGTCCTCTCTATTTGGTTTACTAGTC 57.936 38.462 0.00 0.00 0.00 2.59
633 634 7.123847 TGTCCTCTCTATTTGGTTTACTAGTCC 59.876 40.741 0.00 0.00 0.00 3.85
634 635 7.123847 GTCCTCTCTATTTGGTTTACTAGTCCA 59.876 40.741 0.00 0.00 0.00 4.02
635 636 7.123847 TCCTCTCTATTTGGTTTACTAGTCCAC 59.876 40.741 0.00 0.00 0.00 4.02
636 637 6.860080 TCTCTATTTGGTTTACTAGTCCACG 58.140 40.000 0.00 0.00 0.00 4.94
637 638 6.435277 TCTCTATTTGGTTTACTAGTCCACGT 59.565 38.462 0.00 0.00 0.00 4.49
638 639 7.611467 TCTCTATTTGGTTTACTAGTCCACGTA 59.389 37.037 0.00 0.00 0.00 3.57
639 640 8.121305 TCTATTTGGTTTACTAGTCCACGTAA 57.879 34.615 0.00 0.00 0.00 3.18
641 642 6.403866 TTTGGTTTACTAGTCCACGTAAGA 57.596 37.500 0.00 0.00 43.62 2.10
642 643 5.633830 TGGTTTACTAGTCCACGTAAGAG 57.366 43.478 0.00 0.00 43.62 2.85
643 644 5.316167 TGGTTTACTAGTCCACGTAAGAGA 58.684 41.667 0.00 0.00 43.62 3.10
644 645 5.769662 TGGTTTACTAGTCCACGTAAGAGAA 59.230 40.000 0.00 0.00 43.62 2.87
645 646 6.072286 TGGTTTACTAGTCCACGTAAGAGAAG 60.072 42.308 0.00 0.00 43.62 2.85
646 647 6.072230 GGTTTACTAGTCCACGTAAGAGAAGT 60.072 42.308 0.00 0.00 43.62 3.01
647 648 7.119846 GGTTTACTAGTCCACGTAAGAGAAGTA 59.880 40.741 0.00 0.00 43.62 2.24
648 649 8.672815 GTTTACTAGTCCACGTAAGAGAAGTAT 58.327 37.037 0.00 0.00 43.62 2.12
665 666 7.497249 AGAGAAGTATGATGAACAATTAGCACC 59.503 37.037 0.00 0.00 0.00 5.01
754 755 2.706190 CGAATATATCCCCATCCTCCCC 59.294 54.545 0.00 0.00 0.00 4.81
758 759 2.624846 TATCCCCATCCTCCCCTTTT 57.375 50.000 0.00 0.00 0.00 2.27
776 777 5.163652 CCCTTTTATCCACGTCCATCTTTTC 60.164 44.000 0.00 0.00 0.00 2.29
886 887 4.517832 ACGAACCCTAACTTGTTTGGATTC 59.482 41.667 13.89 11.81 31.42 2.52
934 935 7.560368 TCTAATTCTCTGTTTCTCTTGGATCC 58.440 38.462 4.20 4.20 0.00 3.36
962 964 2.663852 CCGTCCAGTTTTCCGCGT 60.664 61.111 4.92 0.00 0.00 6.01
1008 1010 6.096282 GGAAATTCGATCTGAAAATGGGGTTA 59.904 38.462 4.52 0.00 40.71 2.85
2079 2087 3.123050 GTTGGTTGCAAATCCAAGTCAC 58.877 45.455 18.96 7.19 43.16 3.67
2202 2210 0.700564 ATGGAAGCTTCTCAGGGCAA 59.299 50.000 25.05 2.89 0.00 4.52
2292 2300 2.746904 TGTGGTCAATAATCAGGTTGCG 59.253 45.455 0.00 0.00 0.00 4.85
2415 2423 2.744202 GGCTGTGGTTCATACTTGTGAG 59.256 50.000 0.00 0.00 0.00 3.51
2551 2559 0.762418 CAAGGTACTGTCCACACCCA 59.238 55.000 0.00 0.00 40.86 4.51
2708 2848 9.866655 TTGGAACTCTGGCTAATTATCATTTAT 57.133 29.630 0.00 0.00 0.00 1.40
2731 2881 9.595823 TTATTAGACATAACTGTGAGCCTTAAC 57.404 33.333 0.00 0.00 35.14 2.01
3231 3405 1.956477 GGTGAAGCCATGACAACACTT 59.044 47.619 0.00 0.00 37.17 3.16
3583 3757 8.164070 ACATGGGTTACTTCAGTTAGATTTCTT 58.836 33.333 0.00 0.00 0.00 2.52
3584 3758 9.667107 CATGGGTTACTTCAGTTAGATTTCTTA 57.333 33.333 0.00 0.00 0.00 2.10
3659 3833 8.433421 TCAGCTAGTTTAGTTATAATGTTGGC 57.567 34.615 0.00 0.00 0.00 4.52
3679 3853 7.119116 TGTTGGCTTTATGTTGTACATAGTGAG 59.881 37.037 0.00 0.00 41.56 3.51
3753 3927 4.996758 TCAGTATTTGACAGTGGACACATG 59.003 41.667 5.14 0.00 0.00 3.21
3818 4002 8.107196 AGAATTGACAATACCCTAAGGAGAAT 57.893 34.615 0.00 0.00 36.73 2.40
3870 4054 8.970859 AGTATTACTGAAGATGCAATTTAGCT 57.029 30.769 0.00 0.00 34.99 3.32
3884 4068 5.574443 GCAATTTAGCTTGCTAAGGTTTCAG 59.426 40.000 13.72 5.25 46.32 3.02
3886 4070 5.941948 TTTAGCTTGCTAAGGTTTCAGAC 57.058 39.130 13.72 0.00 40.27 3.51
3890 4074 4.457257 AGCTTGCTAAGGTTTCAGACATTC 59.543 41.667 0.00 0.00 35.27 2.67
3953 4137 5.114780 GTCATGATCTTTTAGCAGCTGAGA 58.885 41.667 20.43 11.45 0.00 3.27
3994 4178 1.002576 CGTTGAATTGAGCAGCACACA 60.003 47.619 0.00 0.00 0.00 3.72
4030 4214 1.064906 ACATGTTGCTCAGGGATGGAG 60.065 52.381 0.00 0.00 35.47 3.86
4042 4226 2.173569 AGGGATGGAGTCATGGCTAAAC 59.826 50.000 0.00 0.00 32.98 2.01
4184 4371 9.793252 GTTGATTTCTACATGCTCATAATTGTT 57.207 29.630 0.00 0.00 0.00 2.83
4303 4490 1.880027 GACTACTTGGGGTGCACTTTG 59.120 52.381 17.98 5.65 0.00 2.77
4736 5114 0.244721 GCCCAGGTTGCAAAGATGTC 59.755 55.000 0.00 0.00 0.00 3.06
4741 5119 2.485426 CAGGTTGCAAAGATGTCGACAT 59.515 45.455 30.37 30.37 39.70 3.06
4750 5128 7.041721 TGCAAAGATGTCGACATAAGTATCTT 58.958 34.615 30.04 23.88 36.57 2.40
4755 5133 6.918569 AGATGTCGACATAAGTATCTTTTCCG 59.081 38.462 30.04 0.00 36.57 4.30
4810 5189 4.125703 GGAACATATGAGGAGAGCACTTG 58.874 47.826 10.38 0.00 0.00 3.16
4883 5262 2.325583 ACTGCCATAACCATACACCG 57.674 50.000 0.00 0.00 0.00 4.94
5267 5718 4.386652 GCAACATTTGTATTGTGCTTCCTG 59.613 41.667 0.00 0.00 0.00 3.86
5283 5734 4.021894 GCTTCCTGTACTTCTGAGTTCTGA 60.022 45.833 0.00 0.00 37.33 3.27
5408 5859 6.655078 AGTATTGGTGAAGCATTTTGAAGT 57.345 33.333 0.00 0.00 0.00 3.01
5602 6053 4.877823 TGTCCATTATTGCAGATGAGTGAC 59.122 41.667 7.99 7.56 0.00 3.67
5756 6207 2.285144 AACCTCCCTACCCCCACG 60.285 66.667 0.00 0.00 0.00 4.94
5774 6225 2.606587 GCCTTCCTCCTGCCCTTCA 61.607 63.158 0.00 0.00 0.00 3.02
5775 6226 1.931007 GCCTTCCTCCTGCCCTTCAT 61.931 60.000 0.00 0.00 0.00 2.57
5788 6239 3.054728 TGCCCTTCATAACCATCTTTCGA 60.055 43.478 0.00 0.00 0.00 3.71
6079 6530 4.501071 GGAAGCTATACGTCCAACAAAGA 58.499 43.478 0.00 0.00 45.49 2.52
6088 6539 3.130340 ACGTCCAACAAAGATGCAAACTT 59.870 39.130 0.00 0.00 0.00 2.66
6185 6636 4.848357 AGAAGTCGGATTCCAATGATGTT 58.152 39.130 3.09 0.00 0.00 2.71
6262 6713 6.212955 GTGAGCTGAAGAGATATCCAAGTAC 58.787 44.000 0.00 0.00 0.00 2.73
6301 6752 4.671377 TGCTCAAATATTTCCATTGCGTC 58.329 39.130 0.00 0.00 0.00 5.19
6375 6826 7.418483 GCATGTAGGGAGAGAAACTCTTCTATT 60.418 40.741 6.96 0.00 42.19 1.73
6427 6878 5.407407 ACAGAACAATAGGAAGTGATCGT 57.593 39.130 0.00 0.00 28.96 3.73
6430 6881 6.102663 CAGAACAATAGGAAGTGATCGTTCT 58.897 40.000 7.38 0.00 41.75 3.01
6438 6889 4.641094 AGGAAGTGATCGTTCTAGTAGTGG 59.359 45.833 7.38 0.00 0.00 4.00
6448 6899 4.023878 CGTTCTAGTAGTGGAGGACTATGC 60.024 50.000 0.00 0.00 39.44 3.14
6482 6933 7.138054 ACCAGGATACCTATTTCTAGTTTGG 57.862 40.000 0.00 0.00 29.64 3.28
6483 6934 6.906901 ACCAGGATACCTATTTCTAGTTTGGA 59.093 38.462 0.00 0.00 29.64 3.53
6484 6935 7.404980 ACCAGGATACCTATTTCTAGTTTGGAA 59.595 37.037 0.00 0.00 29.64 3.53
6485 6936 8.272173 CCAGGATACCTATTTCTAGTTTGGAAA 58.728 37.037 0.00 0.00 35.57 3.13
6521 6972 3.738982 TGTTGATCCAGTACACTTGTGG 58.261 45.455 5.72 0.00 0.00 4.17
6523 6974 1.003118 TGATCCAGTACACTTGTGGGC 59.997 52.381 5.72 0.00 31.70 5.36
6530 6982 2.371841 AGTACACTTGTGGGCATGAGAA 59.628 45.455 0.00 0.00 0.00 2.87
6734 7207 4.692155 CGTGGCAGCATAGATGATATCAAA 59.308 41.667 9.99 0.00 0.00 2.69
6809 7282 2.684843 GCAGGAGCAAACCGAGCTG 61.685 63.158 0.00 0.00 43.58 4.24
6849 7322 0.252284 AGACCCCATCAAGTCTCCGT 60.252 55.000 0.00 0.00 39.08 4.69
6851 7324 1.003233 GACCCCATCAAGTCTCCGTTT 59.997 52.381 0.00 0.00 0.00 3.60
6882 7355 6.301486 TGTAGATTCTTTGCATAGCCATCAT 58.699 36.000 14.33 6.34 0.00 2.45
6918 7391 4.278170 CCTACCATGCAGAAAAACAACAGA 59.722 41.667 0.00 0.00 0.00 3.41
6961 7435 5.583061 AGCATTTGGTGAATAATCGTTACGA 59.417 36.000 10.62 10.62 41.13 3.43
6974 7448 2.295629 TCGTTACGAATGTGTGGTACCA 59.704 45.455 11.60 11.60 31.06 3.25
7001 7475 3.938289 GTTAGAAACGGTCTGAGGTCT 57.062 47.619 1.40 0.00 37.12 3.85
7098 7572 3.238108 ACAAGCTGTATCCAGTTCTCG 57.762 47.619 0.00 0.00 41.02 4.04
7099 7573 2.563179 ACAAGCTGTATCCAGTTCTCGT 59.437 45.455 0.00 0.00 41.02 4.18
7155 7629 3.541996 TGTATGTCCTACGAGACGGTA 57.458 47.619 0.00 0.00 39.77 4.02
7157 7631 2.408271 ATGTCCTACGAGACGGTACA 57.592 50.000 0.00 0.00 39.77 2.90
7160 7634 2.093288 TGTCCTACGAGACGGTACATCT 60.093 50.000 0.00 0.00 39.77 2.90
7207 7682 5.325239 TCCAGTCTGTCTCTCTGAAATACA 58.675 41.667 0.00 0.00 0.00 2.29
7223 7724 7.448161 TCTGAAATACATGGAAAGAAGAAGCAA 59.552 33.333 0.00 0.00 0.00 3.91
7250 7751 5.044919 CACCATCTCCCAGGCCAATTATATA 60.045 44.000 5.01 0.00 0.00 0.86
7426 7928 7.839680 AAATTTCAATCTTGTAACCCTCACT 57.160 32.000 0.00 0.00 0.00 3.41
7427 7929 6.824305 ATTTCAATCTTGTAACCCTCACTG 57.176 37.500 0.00 0.00 0.00 3.66
7437 7939 3.710722 CCTCACTGGGAGCGCCTT 61.711 66.667 2.29 0.00 42.62 4.35
7514 8027 1.227973 GCCATAGCACTACCAGGCC 60.228 63.158 0.00 0.00 39.53 5.19
7542 8063 0.721483 GAACGCGCACTTACACAAGC 60.721 55.000 5.73 0.00 34.94 4.01
7555 8076 7.856459 ACTTACACAAGCAAAAGGACACCCT 62.856 44.000 0.00 0.00 38.85 4.34
7556 8077 1.338020 CACAAGCAAAAGGACACCCTC 59.662 52.381 0.00 0.00 43.48 4.30
7557 8078 1.064017 ACAAGCAAAAGGACACCCTCA 60.064 47.619 0.00 0.00 43.48 3.86
7559 8080 1.986882 AGCAAAAGGACACCCTCAAG 58.013 50.000 0.00 0.00 43.48 3.02
7577 8134 5.221521 CCTCAAGGGAAAAGAAAGGGAAAAG 60.222 44.000 0.00 0.00 37.23 2.27
7599 8156 1.227002 GATCCCACGCTTCGACTCC 60.227 63.158 0.00 0.00 0.00 3.85
7600 8157 2.630592 GATCCCACGCTTCGACTCCC 62.631 65.000 0.00 0.00 0.00 4.30
7845 8402 2.045926 GCTCCGTGGGTGCATCTT 60.046 61.111 0.00 0.00 41.27 2.40
7852 8409 2.086869 CGTGGGTGCATCTTCAGATTT 58.913 47.619 0.00 0.00 31.21 2.17
7853 8410 3.270027 CGTGGGTGCATCTTCAGATTTA 58.730 45.455 0.00 0.00 31.21 1.40
7854 8411 3.310774 CGTGGGTGCATCTTCAGATTTAG 59.689 47.826 0.00 0.00 31.21 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 5.506982 GCCAACATTCTAGCCAGATTGATTC 60.507 44.000 10.40 0.00 36.23 2.52
120 121 4.760204 GTGACTTTTAGTAGTGGCCAACAT 59.240 41.667 7.24 0.00 0.00 2.71
256 257 1.737735 GTTTTGAAGGGGCGCATGC 60.738 57.895 10.83 7.91 41.71 4.06
317 318 2.793790 CCGATTGATGAGAAGCTCTTCG 59.206 50.000 4.19 0.00 43.97 3.79
331 332 3.433343 TGGTTAGGAGTGTACCGATTGA 58.567 45.455 0.00 0.00 34.62 2.57
360 361 1.604915 GGAGTTCTGGGAAGGCCTC 59.395 63.158 5.23 0.00 0.00 4.70
384 385 2.371841 AGTAGGCCACAATGAGAACACA 59.628 45.455 5.01 0.00 0.00 3.72
418 419 8.665685 GGATTTAGTTCTCAATGTTATCAACGT 58.334 33.333 0.00 0.00 0.00 3.99
438 439 5.938125 GGTCAAGCTGTTAGTTGAGGATTTA 59.062 40.000 0.00 0.00 33.37 1.40
441 442 3.327757 TGGTCAAGCTGTTAGTTGAGGAT 59.672 43.478 0.00 0.00 33.37 3.24
452 453 2.158900 CGGATTATCCTGGTCAAGCTGT 60.159 50.000 9.78 0.00 33.30 4.40
560 561 2.483876 GCTTCAAGCTATGGTATGCGA 58.516 47.619 0.71 0.00 38.45 5.10
563 564 2.146342 CCGGCTTCAAGCTATGGTATG 58.854 52.381 9.83 0.00 41.99 2.39
564 565 1.768870 ACCGGCTTCAAGCTATGGTAT 59.231 47.619 16.66 0.00 41.99 2.73
589 590 2.269241 GAAGGCGAAGGAGGTGGG 59.731 66.667 0.00 0.00 0.00 4.61
616 617 8.121305 TCTTACGTGGACTAGTAAACCAAATA 57.879 34.615 0.00 0.00 35.40 1.40
626 627 6.413052 TCATACTTCTCTTACGTGGACTAGT 58.587 40.000 0.00 0.00 0.00 2.57
627 628 6.922247 TCATACTTCTCTTACGTGGACTAG 57.078 41.667 0.00 0.00 0.00 2.57
628 629 7.052248 TCATCATACTTCTCTTACGTGGACTA 58.948 38.462 0.00 0.00 0.00 2.59
629 630 5.886474 TCATCATACTTCTCTTACGTGGACT 59.114 40.000 0.00 0.00 0.00 3.85
630 631 6.132791 TCATCATACTTCTCTTACGTGGAC 57.867 41.667 0.00 0.00 0.00 4.02
631 632 6.152154 TGTTCATCATACTTCTCTTACGTGGA 59.848 38.462 0.00 0.00 0.00 4.02
632 633 6.330278 TGTTCATCATACTTCTCTTACGTGG 58.670 40.000 0.00 0.00 0.00 4.94
633 634 7.812309 TTGTTCATCATACTTCTCTTACGTG 57.188 36.000 0.00 0.00 0.00 4.49
638 639 8.887717 GTGCTAATTGTTCATCATACTTCTCTT 58.112 33.333 0.00 0.00 0.00 2.85
639 640 7.497249 GGTGCTAATTGTTCATCATACTTCTCT 59.503 37.037 0.00 0.00 0.00 3.10
640 641 7.517417 CGGTGCTAATTGTTCATCATACTTCTC 60.517 40.741 0.00 0.00 0.00 2.87
641 642 6.258727 CGGTGCTAATTGTTCATCATACTTCT 59.741 38.462 0.00 0.00 0.00 2.85
642 643 6.422223 CGGTGCTAATTGTTCATCATACTTC 58.578 40.000 0.00 0.00 0.00 3.01
643 644 5.296780 CCGGTGCTAATTGTTCATCATACTT 59.703 40.000 0.00 0.00 0.00 2.24
644 645 4.816385 CCGGTGCTAATTGTTCATCATACT 59.184 41.667 0.00 0.00 0.00 2.12
645 646 4.814234 TCCGGTGCTAATTGTTCATCATAC 59.186 41.667 0.00 0.00 0.00 2.39
646 647 5.029807 TCCGGTGCTAATTGTTCATCATA 57.970 39.130 0.00 0.00 0.00 2.15
647 648 3.884895 TCCGGTGCTAATTGTTCATCAT 58.115 40.909 0.00 0.00 0.00 2.45
648 649 3.342377 TCCGGTGCTAATTGTTCATCA 57.658 42.857 0.00 0.00 0.00 3.07
665 666 5.681639 AGAATACTATTTTGGGTCCTTCCG 58.318 41.667 0.00 0.00 37.00 4.30
754 755 5.163652 GGGAAAAGATGGACGTGGATAAAAG 60.164 44.000 0.00 0.00 0.00 2.27
758 759 3.112263 AGGGAAAAGATGGACGTGGATA 58.888 45.455 0.00 0.00 0.00 2.59
847 848 6.776744 AGGGTTCGTTACCTAGAAAAGAAAT 58.223 36.000 8.88 0.00 46.86 2.17
848 849 6.178607 AGGGTTCGTTACCTAGAAAAGAAA 57.821 37.500 8.88 0.00 46.86 2.52
849 850 5.813513 AGGGTTCGTTACCTAGAAAAGAA 57.186 39.130 8.88 0.00 46.86 2.52
850 851 6.494835 AGTTAGGGTTCGTTACCTAGAAAAGA 59.505 38.462 8.88 0.00 46.86 2.52
851 852 6.695429 AGTTAGGGTTCGTTACCTAGAAAAG 58.305 40.000 8.88 0.00 46.86 2.27
852 853 6.670695 AGTTAGGGTTCGTTACCTAGAAAA 57.329 37.500 8.88 0.00 46.86 2.29
853 854 6.041979 ACAAGTTAGGGTTCGTTACCTAGAAA 59.958 38.462 8.88 0.00 46.86 2.52
854 855 5.539955 ACAAGTTAGGGTTCGTTACCTAGAA 59.460 40.000 8.88 0.49 46.86 2.10
855 856 5.079643 ACAAGTTAGGGTTCGTTACCTAGA 58.920 41.667 8.88 0.00 46.86 2.43
856 857 5.397142 ACAAGTTAGGGTTCGTTACCTAG 57.603 43.478 8.88 0.00 46.86 3.02
886 887 3.386078 TCATCAGGAGAAAAGATCGGAGG 59.614 47.826 0.00 0.00 0.00 4.30
934 935 3.305177 CTGGACGGGTTGGGGTACG 62.305 68.421 0.00 0.00 0.00 3.67
962 964 0.744874 CTCCCGACGCCAAATCTAGA 59.255 55.000 0.00 0.00 0.00 2.43
1455 1463 4.803088 CGATCCAAATCAGACTCAGAGAAC 59.197 45.833 3.79 0.00 31.76 3.01
2079 2087 1.066573 ACAGGATCGACTGCTTCCAAG 60.067 52.381 4.88 0.00 42.21 3.61
2202 2210 2.303022 CAGGGTCTCATACACAACACCT 59.697 50.000 0.00 0.00 31.97 4.00
2292 2300 4.355437 CTGACATCGGATCAGTAGTGAAC 58.645 47.826 3.93 1.39 39.04 3.18
2415 2423 3.123620 CTCCACTCCGCAGCAAGC 61.124 66.667 0.00 0.00 40.87 4.01
2551 2559 3.966543 CCTTTGGGAGCGGGGTGT 61.967 66.667 0.00 0.00 33.58 4.16
2681 2821 7.573968 AATGATAATTAGCCAGAGTTCCAAC 57.426 36.000 0.00 0.00 0.00 3.77
2708 2848 7.241042 AGTTAAGGCTCACAGTTATGTCTAA 57.759 36.000 0.00 0.00 37.65 2.10
2854 3004 9.163894 TCCTAATCACCTGATTCAGATAGAAAT 57.836 33.333 15.36 6.20 43.17 2.17
3231 3405 4.594970 TGTGAGGTTTGAAAGTTTCTGGA 58.405 39.130 16.33 0.63 0.00 3.86
3593 3767 7.230849 TCTGCTTATGGTGATTTCATGTTTT 57.769 32.000 0.00 0.00 0.00 2.43
3818 4002 6.519213 GCCCCAATTTGTTTATGTTCTAACCA 60.519 38.462 0.00 0.00 0.00 3.67
3867 4051 3.492102 TGTCTGAAACCTTAGCAAGCT 57.508 42.857 0.00 0.00 0.00 3.74
3870 4054 4.385825 ACGAATGTCTGAAACCTTAGCAA 58.614 39.130 0.00 0.00 0.00 3.91
3879 4063 3.007506 TGGCTAAGGACGAATGTCTGAAA 59.992 43.478 0.00 0.00 44.83 2.69
3881 4065 2.176045 TGGCTAAGGACGAATGTCTGA 58.824 47.619 0.00 0.00 44.83 3.27
3884 4068 6.619801 ATTATTTGGCTAAGGACGAATGTC 57.380 37.500 0.00 0.00 44.72 3.06
3886 4070 6.208644 CCAATTATTTGGCTAAGGACGAATG 58.791 40.000 3.53 0.00 45.71 2.67
3938 4122 5.065602 TGTTGCATATCTCAGCTGCTAAAAG 59.934 40.000 9.47 0.15 36.84 2.27
3953 4137 3.442273 CGGGTACAAACCTTGTTGCATAT 59.558 43.478 0.00 0.00 45.95 1.78
3994 4178 2.294979 CATGTCTGCTACACATGCCAT 58.705 47.619 9.38 0.00 43.48 4.40
4030 4214 4.503741 ACAACATGTGTTTAGCCATGAC 57.496 40.909 0.00 0.00 40.70 3.06
4042 4226 7.795431 ATGCTACGAAATTAAACAACATGTG 57.205 32.000 0.00 0.00 0.00 3.21
4061 4245 8.384693 AGATCATCCCAGAACATATAATGCTA 57.615 34.615 0.00 0.00 0.00 3.49
4113 4300 6.697641 GGGTCTACCAATTATTCCAGGATA 57.302 41.667 0.81 0.00 39.85 2.59
4184 4371 7.425606 GCTTCAGATTTTCTTAACAGTTCCAA 58.574 34.615 0.00 0.00 0.00 3.53
4303 4490 4.033358 CAGATGACAAGGTTATGACTTCGC 59.967 45.833 0.00 0.00 0.00 4.70
4380 4738 6.599244 GGAAACACATCAGGAGATAACATCAA 59.401 38.462 0.00 0.00 31.88 2.57
4393 4751 7.885297 TCAATTAAGAAAGGGAAACACATCAG 58.115 34.615 0.00 0.00 0.00 2.90
4400 4758 7.468141 ACCAGATCAATTAAGAAAGGGAAAC 57.532 36.000 0.00 0.00 0.00 2.78
4730 5108 6.918569 CGGAAAAGATACTTATGTCGACATCT 59.081 38.462 33.11 21.12 37.76 2.90
4736 5114 9.685005 CTTTAAACGGAAAAGATACTTATGTCG 57.315 33.333 1.45 0.00 36.27 4.35
4810 5189 3.914312 TGTGTAAGAGCTACTTCACAGC 58.086 45.455 16.94 0.00 39.34 4.40
5243 5694 4.039004 AGGAAGCACAATACAAATGTTGCA 59.961 37.500 9.77 0.00 30.35 4.08
5267 5718 7.878036 ACTTTCTAGTCAGAACTCAGAAGTAC 58.122 38.462 0.00 0.00 40.54 2.73
5283 5734 5.031066 TGGTGTAGTTGCAACTTTCTAGT 57.969 39.130 35.20 13.57 40.37 2.57
5368 5819 5.010012 CCAATACTACATGGATTTTGGCTCC 59.990 44.000 0.00 0.00 39.12 4.70
5467 5918 3.518634 TTTGTTGGTTCTGCAGGTTTC 57.481 42.857 15.13 2.19 0.00 2.78
5586 6037 5.289595 GGTTATCGTCACTCATCTGCAATA 58.710 41.667 0.00 0.00 0.00 1.90
5602 6053 6.662234 TCTCAGGTATAACATAGGGGTTATCG 59.338 42.308 2.15 0.00 41.68 2.92
5756 6207 1.931007 ATGAAGGGCAGGAGGAAGGC 61.931 60.000 0.00 0.00 0.00 4.35
5788 6239 4.406003 AGAGGAAGATACAGGTTAACGCAT 59.594 41.667 0.00 0.00 0.00 4.73
6079 6530 4.401925 AGGTGAAGAAGCTAAGTTTGCAT 58.598 39.130 11.84 0.00 33.90 3.96
6185 6636 3.796844 GCTGCTCAACTCTACATATCGCA 60.797 47.826 0.00 0.00 0.00 5.10
6301 6752 6.670233 AGAAAAAGGACTACTCGATATAGCG 58.330 40.000 3.47 3.47 0.00 4.26
6427 6878 5.125367 TGCATAGTCCTCCACTACTAGAA 57.875 43.478 0.00 0.00 40.60 2.10
6430 6881 6.808321 AAAATGCATAGTCCTCCACTACTA 57.192 37.500 0.00 0.00 40.60 1.82
6438 6889 7.719633 TCCTGGTTAATAAAATGCATAGTCCTC 59.280 37.037 0.00 0.00 0.00 3.71
6492 6943 6.738114 AGTGTACTGGATCAACAAAAATGTG 58.262 36.000 0.00 0.00 0.00 3.21
6530 6982 4.215109 GGTGGGCAAACAATATGAGGTAT 58.785 43.478 0.00 0.00 0.00 2.73
6734 7207 0.772124 ATGGGGCCCTTCCGACATAT 60.772 55.000 25.93 1.65 33.20 1.78
6809 7282 2.669569 TGCAGCGCCTTCTTCACC 60.670 61.111 2.29 0.00 0.00 4.02
6849 7322 9.844790 CTATGCAAAGAATCTACATGTTCAAAA 57.155 29.630 2.30 0.00 0.00 2.44
6851 7324 7.415541 GGCTATGCAAAGAATCTACATGTTCAA 60.416 37.037 2.30 0.00 0.00 2.69
6882 7355 4.962362 TGCATGGTAGGAGATCAGAAGTTA 59.038 41.667 0.00 0.00 0.00 2.24
6918 7391 8.680903 CAAATGCTGAAGAGGTGTAATTTAGAT 58.319 33.333 0.00 0.00 0.00 1.98
6981 7455 3.938289 AGACCTCAGACCGTTTCTAAC 57.062 47.619 0.00 0.00 31.12 2.34
7098 7572 5.924254 GGGTACACTTCTTTATTGGCAAAAC 59.076 40.000 3.01 0.00 0.00 2.43
7099 7573 5.598830 TGGGTACACTTCTTTATTGGCAAAA 59.401 36.000 3.01 0.00 0.00 2.44
7157 7631 1.833630 TGCTAGGCACAGCAGTAAGAT 59.166 47.619 9.45 0.00 46.41 2.40
7207 7682 3.319122 GGTGTGTTGCTTCTTCTTTCCAT 59.681 43.478 0.00 0.00 0.00 3.41
7223 7724 2.606587 GGCCTGGGAGATGGTGTGT 61.607 63.158 0.00 0.00 0.00 3.72
7250 7751 0.523072 GACGAAAGCATGTGCCACAT 59.477 50.000 4.03 4.03 43.38 3.21
7362 7863 3.827008 TGGATCTATCAGGCAAGTCAC 57.173 47.619 0.00 0.00 0.00 3.67
7437 7939 0.109532 TTCTCGTTGTTGGATGCCCA 59.890 50.000 0.00 0.00 41.64 5.36
7555 8076 4.653801 CCTTTTCCCTTTCTTTTCCCTTGA 59.346 41.667 0.00 0.00 0.00 3.02
7556 8077 4.653801 TCCTTTTCCCTTTCTTTTCCCTTG 59.346 41.667 0.00 0.00 0.00 3.61
7557 8078 4.654262 GTCCTTTTCCCTTTCTTTTCCCTT 59.346 41.667 0.00 0.00 0.00 3.95
7559 8080 3.005472 CGTCCTTTTCCCTTTCTTTTCCC 59.995 47.826 0.00 0.00 0.00 3.97
7562 8083 4.523173 GGATCGTCCTTTTCCCTTTCTTTT 59.477 41.667 0.00 0.00 32.53 2.27
7563 8084 4.079970 GGATCGTCCTTTTCCCTTTCTTT 58.920 43.478 0.00 0.00 32.53 2.52
7564 8085 3.561528 GGGATCGTCCTTTTCCCTTTCTT 60.562 47.826 0.00 0.00 44.86 2.52
7565 8086 2.026169 GGGATCGTCCTTTTCCCTTTCT 60.026 50.000 0.00 0.00 44.86 2.52
7577 8134 2.582498 CGAAGCGTGGGATCGTCC 60.582 66.667 0.00 0.00 35.23 4.79
7586 8143 0.941542 TTTTTGGGAGTCGAAGCGTG 59.058 50.000 0.00 0.00 0.00 5.34
7614 8171 1.323412 TCAAGCGGCTTTTTAGGCAA 58.677 45.000 13.53 0.00 0.00 4.52
7615 8172 1.202114 CATCAAGCGGCTTTTTAGGCA 59.798 47.619 13.53 0.00 0.00 4.75
7616 8173 1.202348 ACATCAAGCGGCTTTTTAGGC 59.798 47.619 13.53 0.00 0.00 3.93
7617 8174 3.575965 AACATCAAGCGGCTTTTTAGG 57.424 42.857 13.53 6.08 0.00 2.69
7618 8175 6.378582 TCTTAAACATCAAGCGGCTTTTTAG 58.621 36.000 13.53 7.98 0.00 1.85
7619 8176 6.320494 TCTTAAACATCAAGCGGCTTTTTA 57.680 33.333 13.53 12.19 0.00 1.52
7623 8180 3.568007 TGTTCTTAAACATCAAGCGGCTT 59.432 39.130 9.94 9.94 40.45 4.35
7625 8182 3.492313 CTGTTCTTAAACATCAAGCGGC 58.508 45.455 0.00 0.00 44.18 6.53
7626 8183 3.751175 TCCTGTTCTTAAACATCAAGCGG 59.249 43.478 0.00 0.00 44.18 5.52



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

AutoCloner maintained by Alex Coulton.