Multiple sequence alignment - TraesCS3D01G353400

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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 TraesCS3D01G353400 chr3D 100.000 3233 0 0 1 3233 464046757 464049989 0.000000e+00 5971.0
1 TraesCS3D01G353400 chr3D 86.154 65 8 1 564 627 394184407 394184343 5.790000e-08 69.4
2 TraesCS3D01G353400 chr3B 90.342 2371 114 36 331 2634 617414719 617417041 0.000000e+00 3003.0
3 TraesCS3D01G353400 chr3B 93.023 387 19 5 2847 3230 617417146 617417527 2.820000e-155 558.0
4 TraesCS3D01G353400 chr3B 89.954 219 8 1 121 339 617414410 617414614 1.480000e-68 270.0
5 TraesCS3D01G353400 chr3B 97.810 137 3 0 2645 2781 617417018 617417154 1.500000e-58 237.0
6 TraesCS3D01G353400 chr3A 93.179 1950 81 13 718 2633 607062453 607064384 0.000000e+00 2817.0
7 TraesCS3D01G353400 chr3A 88.142 506 35 13 2645 3139 607064363 607064854 2.160000e-161 579.0
8 TraesCS3D01G353400 chr3A 90.489 368 21 5 114 477 607061849 607062206 1.050000e-129 473.0
9 TraesCS3D01G353400 chr3A 88.554 166 15 2 462 627 607062221 607062382 7.070000e-47 198.0
10 TraesCS3D01G353400 chr3A 95.506 89 4 0 18 106 607061697 607061785 3.360000e-30 143.0
11 TraesCS3D01G353400 chr3A 95.652 46 1 1 582 627 718376640 718376684 4.470000e-09 73.1
12 TraesCS3D01G353400 chr5D 100.000 41 0 0 587 627 539481162 539481202 3.460000e-10 76.8
13 TraesCS3D01G353400 chr5B 100.000 41 0 0 587 627 681134210 681134250 3.460000e-10 76.8
14 TraesCS3D01G353400 chr4A 100.000 41 0 0 587 627 628924498 628924458 3.460000e-10 76.8
15 TraesCS3D01G353400 chr2B 100.000 41 0 0 587 627 39188642 39188602 3.460000e-10 76.8
16 TraesCS3D01G353400 chr2A 100.000 41 0 0 587 627 24307380 24307420 3.460000e-10 76.8


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 TraesCS3D01G353400 chr3D 464046757 464049989 3232 False 5971 5971 100.00000 1 3233 1 chr3D.!!$F1 3232
1 TraesCS3D01G353400 chr3B 617414410 617417527 3117 False 1017 3003 92.78225 121 3230 4 chr3B.!!$F1 3109
2 TraesCS3D01G353400 chr3A 607061697 607064854 3157 False 842 2817 91.17400 18 3139 5 chr3A.!!$F2 3121

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
533 737 0.179094 TTCAAGGTCACGCAACGAGT 60.179 50.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2439 2692 2.034685 TCTCGCTGCACATACATCTACC 59.965 50.0 0.0 0.0 0.0 3.18 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
36 37 6.128227 TGGGTTTATTATTCGTCGGACAAAAG 60.128 38.462 9.10 0.00 0.00 2.27
50 51 0.673644 CAAAAGTGGCGATCGGGACT 60.674 55.000 18.30 0.00 0.00 3.85
92 93 3.781162 GTGCCCGCGACGTTAACC 61.781 66.667 8.23 0.00 0.00 2.85
112 113 1.597663 CGCTATCCGGAAATGAACACC 59.402 52.381 9.01 0.00 0.00 4.16
116 173 1.732941 TCCGGAAATGAACACCATCG 58.267 50.000 0.00 0.00 33.53 3.84
185 246 1.922570 TAAGATTTGCGCTCTCGGAC 58.077 50.000 9.73 0.00 35.25 4.79
238 299 0.749818 TGCGAAAAGGGTGTGCTTGA 60.750 50.000 0.00 0.00 0.00 3.02
371 545 7.320443 TGACGATATTCCTTTCCATTCTTTG 57.680 36.000 0.00 0.00 0.00 2.77
372 546 7.109501 TGACGATATTCCTTTCCATTCTTTGA 58.890 34.615 0.00 0.00 0.00 2.69
374 548 8.348285 ACGATATTCCTTTCCATTCTTTGAAA 57.652 30.769 0.00 0.00 0.00 2.69
382 556 8.362639 TCCTTTCCATTCTTTGAAAAGATCTTG 58.637 33.333 9.17 5.47 43.92 3.02
386 560 8.924511 TCCATTCTTTGAAAAGATCTTGTAGT 57.075 30.769 9.17 0.00 43.92 2.73
388 562 9.403110 CCATTCTTTGAAAAGATCTTGTAGTTG 57.597 33.333 9.17 1.72 43.92 3.16
389 563 9.403110 CATTCTTTGAAAAGATCTTGTAGTTGG 57.597 33.333 9.17 0.00 43.92 3.77
452 626 5.598769 ACTAATAGTGCCCAAGTTCGTATC 58.401 41.667 0.00 0.00 0.00 2.24
477 651 4.962995 ACTGAGCAAGTAGTATATGGTGGT 59.037 41.667 0.00 0.00 37.36 4.16
478 652 6.040504 CACTGAGCAAGTAGTATATGGTGGTA 59.959 42.308 0.00 0.00 36.83 3.25
528 732 3.994392 GAGTAGATTTCAAGGTCACGCAA 59.006 43.478 0.00 0.00 0.00 4.85
529 733 3.746492 AGTAGATTTCAAGGTCACGCAAC 59.254 43.478 0.00 0.00 0.00 4.17
530 734 1.531149 AGATTTCAAGGTCACGCAACG 59.469 47.619 0.00 0.00 0.00 4.10
531 735 1.529438 GATTTCAAGGTCACGCAACGA 59.471 47.619 0.00 0.00 0.00 3.85
532 736 0.934496 TTTCAAGGTCACGCAACGAG 59.066 50.000 0.00 0.00 0.00 4.18
533 737 0.179094 TTCAAGGTCACGCAACGAGT 60.179 50.000 0.00 0.00 0.00 4.18
534 738 0.669619 TCAAGGTCACGCAACGAGTA 59.330 50.000 0.00 0.00 0.00 2.59
535 739 1.067364 TCAAGGTCACGCAACGAGTAA 59.933 47.619 0.00 0.00 0.00 2.24
536 740 1.191647 CAAGGTCACGCAACGAGTAAC 59.808 52.381 0.00 0.00 0.00 2.50
585 794 9.995003 AATGATTAACCTTTCAGTGCATTTTAA 57.005 25.926 0.00 0.00 0.00 1.52
634 863 4.680237 CGCAAGGCTCCACGACCA 62.680 66.667 0.00 0.00 0.00 4.02
637 866 1.227823 CAAGGCTCCACGACCACAA 60.228 57.895 0.00 0.00 0.00 3.33
695 924 5.373812 TTTTGTTTCCTTCCTGAGACTCT 57.626 39.130 3.68 0.00 0.00 3.24
696 925 6.494666 TTTTGTTTCCTTCCTGAGACTCTA 57.505 37.500 3.68 0.00 0.00 2.43
697 926 5.730296 TTGTTTCCTTCCTGAGACTCTAG 57.270 43.478 3.68 0.00 0.00 2.43
701 930 2.310349 TCCTTCCTGAGACTCTAGCAGT 59.690 50.000 3.68 0.00 38.45 4.40
713 942 5.358442 AGACTCTAGCAGTACACATTACCTG 59.642 44.000 0.00 0.00 34.41 4.00
738 967 3.138304 CGAACTGGAAATGGTGAGTGAA 58.862 45.455 0.00 0.00 0.00 3.18
769 1013 2.919494 GCTCCACAAAACCAGGGCG 61.919 63.158 0.00 0.00 0.00 6.13
806 1050 2.926586 GCTCAAAACGAATCCCCAAAGC 60.927 50.000 0.00 0.00 0.00 3.51
807 1051 2.558359 CTCAAAACGAATCCCCAAAGCT 59.442 45.455 0.00 0.00 0.00 3.74
808 1052 2.556622 TCAAAACGAATCCCCAAAGCTC 59.443 45.455 0.00 0.00 0.00 4.09
809 1053 1.545841 AAACGAATCCCCAAAGCTCC 58.454 50.000 0.00 0.00 0.00 4.70
810 1054 0.698818 AACGAATCCCCAAAGCTCCT 59.301 50.000 0.00 0.00 0.00 3.69
811 1055 0.698818 ACGAATCCCCAAAGCTCCTT 59.301 50.000 0.00 0.00 0.00 3.36
812 1056 1.340114 ACGAATCCCCAAAGCTCCTTC 60.340 52.381 0.00 0.00 0.00 3.46
852 1096 3.244353 ACACAACAGATCAGGAGGAACAG 60.244 47.826 0.00 0.00 0.00 3.16
854 1098 3.392616 ACAACAGATCAGGAGGAACAGTT 59.607 43.478 0.00 0.00 29.97 3.16
857 1101 3.257393 CAGATCAGGAGGAACAGTTTCG 58.743 50.000 0.00 0.00 31.78 3.46
869 1113 1.947456 ACAGTTTCGTTTCTGGCCTTC 59.053 47.619 3.32 0.00 36.17 3.46
888 1132 0.999406 CAATCCTACGTCCAACTGCG 59.001 55.000 0.00 0.00 0.00 5.18
889 1133 0.739813 AATCCTACGTCCAACTGCGC 60.740 55.000 0.00 0.00 0.00 6.09
890 1134 1.884075 ATCCTACGTCCAACTGCGCA 61.884 55.000 10.98 10.98 0.00 6.09
891 1135 1.666553 CCTACGTCCAACTGCGCAA 60.667 57.895 13.05 0.00 0.00 4.85
939 1192 1.142060 TCGATGACCCACCAACAACTT 59.858 47.619 0.00 0.00 0.00 2.66
940 1193 1.266718 CGATGACCCACCAACAACTTG 59.733 52.381 0.00 0.00 0.00 3.16
944 1197 2.291282 TGACCCACCAACAACTTGAACT 60.291 45.455 0.00 0.00 0.00 3.01
969 1222 3.503748 CACTCCAGAAAGGGTAGCAAAAG 59.496 47.826 0.00 0.00 38.24 2.27
984 1237 2.031120 CAAAAGCCCTGTCAGGTGAAA 58.969 47.619 17.85 0.00 31.93 2.69
989 1242 1.067060 GCCCTGTCAGGTGAAACAAAC 59.933 52.381 17.85 0.00 39.98 2.93
1236 1489 2.358737 GTCACCTTCACCGCCCTG 60.359 66.667 0.00 0.00 0.00 4.45
1407 1660 3.122323 TTCGACGAAATGCCCGCC 61.122 61.111 8.05 0.00 0.00 6.13
1560 1813 1.348064 TCAACCTCCTTGTCGATGGT 58.652 50.000 0.00 0.00 0.00 3.55
1563 1816 3.000727 CAACCTCCTTGTCGATGGTTAC 58.999 50.000 0.00 0.00 38.76 2.50
1620 1873 1.138671 CAACCAAATAAGGGCGGCG 59.861 57.895 0.51 0.51 0.00 6.46
1732 1985 0.179089 CATGAAGGAGCGAGGACTGG 60.179 60.000 0.00 0.00 0.00 4.00
1755 2008 2.879103 CCACAAATGGGACCTACACT 57.121 50.000 0.00 0.00 43.04 3.55
1902 2155 3.708121 GCATGGAAGGGAAAATGAAGGAT 59.292 43.478 0.00 0.00 0.00 3.24
1951 2204 3.135994 GAGAAAGGTGTTAAGGCGAACA 58.864 45.455 4.20 4.20 36.98 3.18
1968 2221 4.568359 GCGAACAGTGTGATCTATGACATT 59.432 41.667 0.00 0.00 0.00 2.71
2106 2359 7.850982 CGTAGTCTTTGTAATGATGGTAAATGC 59.149 37.037 0.00 0.00 0.00 3.56
2252 2505 2.431782 AGGCAGTCAAGCATGTGTTTTT 59.568 40.909 0.00 0.00 35.83 1.94
2404 2657 1.000394 CCAAAACTTAACCAAGGGCGG 60.000 52.381 0.00 0.00 35.97 6.13
2439 2692 8.336806 TGATAAGCAAATTCAAAGCAACAAAAG 58.663 29.630 0.00 0.00 0.00 2.27
2478 2750 3.126831 GAGATAAAGGTCAGTGCATCCG 58.873 50.000 0.00 0.00 0.00 4.18
2500 2772 8.145316 TCCGTACTTGTATAATTTATGTTGGC 57.855 34.615 0.00 0.00 0.00 4.52
2507 2779 9.935682 CTTGTATAATTTATGTTGGCTGTGTAG 57.064 33.333 0.00 0.00 0.00 2.74
2508 2780 8.445275 TGTATAATTTATGTTGGCTGTGTAGG 57.555 34.615 0.00 0.00 0.00 3.18
2522 2794 4.274950 GCTGTGTAGGTACATTTGTGTTGT 59.725 41.667 0.00 0.00 38.63 3.32
2523 2795 5.467399 GCTGTGTAGGTACATTTGTGTTGTA 59.533 40.000 0.00 0.00 38.63 2.41
2524 2796 6.148811 GCTGTGTAGGTACATTTGTGTTGTAT 59.851 38.462 0.00 0.00 38.63 2.29
2525 2797 7.428282 TGTGTAGGTACATTTGTGTTGTATG 57.572 36.000 0.00 0.00 38.63 2.39
2588 2860 5.125578 GGTTTCTTCTTTTCCGGATGCTAAT 59.874 40.000 4.15 0.00 0.00 1.73
2622 2902 7.700505 TGCTATATGAATGCTTTCTTTCTGTG 58.299 34.615 12.96 0.74 32.78 3.66
2623 2903 7.337689 TGCTATATGAATGCTTTCTTTCTGTGT 59.662 33.333 12.96 0.00 32.78 3.72
2624 2904 8.186821 GCTATATGAATGCTTTCTTTCTGTGTT 58.813 33.333 12.96 0.00 32.78 3.32
2627 2907 9.768662 ATATGAATGCTTTCTTTCTGTGTTTTT 57.231 25.926 12.96 0.00 32.78 1.94
2779 3128 6.756221 ACGTAGTTTTTCTTACCTCTGTGAT 58.244 36.000 0.00 0.00 37.78 3.06
2780 3129 6.645415 ACGTAGTTTTTCTTACCTCTGTGATG 59.355 38.462 0.00 0.00 37.78 3.07
2781 3130 5.948992 AGTTTTTCTTACCTCTGTGATGC 57.051 39.130 0.00 0.00 0.00 3.91
2782 3131 5.625150 AGTTTTTCTTACCTCTGTGATGCT 58.375 37.500 0.00 0.00 0.00 3.79
2783 3132 5.471456 AGTTTTTCTTACCTCTGTGATGCTG 59.529 40.000 0.00 0.00 0.00 4.41
2784 3133 4.890158 TTTCTTACCTCTGTGATGCTGA 57.110 40.909 0.00 0.00 0.00 4.26
2785 3134 5.426689 TTTCTTACCTCTGTGATGCTGAT 57.573 39.130 0.00 0.00 0.00 2.90
2786 3135 5.426689 TTCTTACCTCTGTGATGCTGATT 57.573 39.130 0.00 0.00 0.00 2.57
2787 3136 5.426689 TCTTACCTCTGTGATGCTGATTT 57.573 39.130 0.00 0.00 0.00 2.17
2788 3137 5.181009 TCTTACCTCTGTGATGCTGATTTG 58.819 41.667 0.00 0.00 0.00 2.32
2789 3138 3.708403 ACCTCTGTGATGCTGATTTGA 57.292 42.857 0.00 0.00 0.00 2.69
2790 3139 3.341823 ACCTCTGTGATGCTGATTTGAC 58.658 45.455 0.00 0.00 0.00 3.18
2791 3140 3.244665 ACCTCTGTGATGCTGATTTGACA 60.245 43.478 0.00 0.00 0.00 3.58
2792 3141 3.374367 CCTCTGTGATGCTGATTTGACAG 59.626 47.826 0.00 0.00 40.43 3.51
2800 3149 1.817357 CTGATTTGACAGCTGAGGCA 58.183 50.000 23.35 12.50 41.70 4.75
2801 3150 2.366533 CTGATTTGACAGCTGAGGCAT 58.633 47.619 23.35 6.83 41.70 4.40
2802 3151 2.753452 CTGATTTGACAGCTGAGGCATT 59.247 45.455 23.35 0.00 41.70 3.56
2803 3152 2.490509 TGATTTGACAGCTGAGGCATTG 59.509 45.455 23.35 0.00 41.70 2.82
2804 3153 2.275134 TTTGACAGCTGAGGCATTGA 57.725 45.000 23.35 0.00 41.70 2.57
2805 3154 2.502142 TTGACAGCTGAGGCATTGAT 57.498 45.000 23.35 0.00 41.70 2.57
2806 3155 2.034104 TGACAGCTGAGGCATTGATC 57.966 50.000 23.35 4.34 41.70 2.92
2807 3156 1.307097 GACAGCTGAGGCATTGATCC 58.693 55.000 23.35 0.00 41.70 3.36
2808 3157 0.917533 ACAGCTGAGGCATTGATCCT 59.082 50.000 23.35 0.00 41.70 3.24
2814 3163 2.547299 GAGGCATTGATCCTCTGGAG 57.453 55.000 2.01 0.00 45.13 3.86
2815 3164 2.045524 GAGGCATTGATCCTCTGGAGA 58.954 52.381 2.01 0.00 45.13 3.71
2816 3165 2.037511 GAGGCATTGATCCTCTGGAGAG 59.962 54.545 2.01 0.00 45.13 3.20
2817 3166 2.045524 GGCATTGATCCTCTGGAGAGA 58.954 52.381 5.17 0.00 44.74 3.10
2818 3167 2.437281 GGCATTGATCCTCTGGAGAGAA 59.563 50.000 5.17 0.00 44.74 2.87
2819 3168 3.465871 GCATTGATCCTCTGGAGAGAAC 58.534 50.000 5.17 0.00 44.74 3.01
2820 3169 3.134442 GCATTGATCCTCTGGAGAGAACT 59.866 47.826 5.17 0.00 44.74 3.01
2821 3170 4.695396 CATTGATCCTCTGGAGAGAACTG 58.305 47.826 5.17 0.00 44.74 3.16
2822 3171 2.744760 TGATCCTCTGGAGAGAACTGG 58.255 52.381 5.17 0.00 44.74 4.00
2823 3172 2.043664 TGATCCTCTGGAGAGAACTGGT 59.956 50.000 5.17 0.00 44.74 4.00
2824 3173 3.269643 TGATCCTCTGGAGAGAACTGGTA 59.730 47.826 5.17 0.00 44.74 3.25
2825 3174 3.088789 TCCTCTGGAGAGAACTGGTAC 57.911 52.381 5.17 0.00 44.74 3.34
2826 3175 2.104170 CCTCTGGAGAGAACTGGTACC 58.896 57.143 4.43 4.43 44.74 3.34
2827 3176 2.291930 CCTCTGGAGAGAACTGGTACCT 60.292 54.545 14.36 0.00 44.74 3.08
2828 3177 2.757868 CTCTGGAGAGAACTGGTACCTG 59.242 54.545 16.66 16.66 44.74 4.00
2829 3178 1.827969 CTGGAGAGAACTGGTACCTGG 59.172 57.143 21.46 12.77 0.00 4.45
2830 3179 0.537653 GGAGAGAACTGGTACCTGGC 59.462 60.000 21.46 13.29 0.00 4.85
2831 3180 0.173708 GAGAGAACTGGTACCTGGCG 59.826 60.000 21.46 6.63 0.00 5.69
2832 3181 1.448013 GAGAACTGGTACCTGGCGC 60.448 63.158 21.46 0.00 0.00 6.53
2833 3182 2.436115 GAACTGGTACCTGGCGCC 60.436 66.667 22.73 22.73 0.00 6.53
2834 3183 2.928396 AACTGGTACCTGGCGCCT 60.928 61.111 29.70 10.43 0.00 5.52
2835 3184 2.854187 GAACTGGTACCTGGCGCCTC 62.854 65.000 29.70 8.76 0.00 4.70
2836 3185 3.390521 CTGGTACCTGGCGCCTCA 61.391 66.667 29.70 7.24 0.00 3.86
2837 3186 3.665675 CTGGTACCTGGCGCCTCAC 62.666 68.421 29.70 18.49 0.00 3.51
2838 3187 3.702048 GGTACCTGGCGCCTCACA 61.702 66.667 29.70 5.90 0.00 3.58
2839 3188 2.584608 GTACCTGGCGCCTCACAT 59.415 61.111 29.70 11.13 0.00 3.21
2840 3189 1.521681 GTACCTGGCGCCTCACATC 60.522 63.158 29.70 10.03 0.00 3.06
2841 3190 2.731571 TACCTGGCGCCTCACATCC 61.732 63.158 29.70 0.00 0.00 3.51
2842 3191 3.790437 CCTGGCGCCTCACATCCT 61.790 66.667 29.70 0.00 0.00 3.24
2843 3192 2.270205 CTGGCGCCTCACATCCTT 59.730 61.111 29.70 0.00 0.00 3.36
2844 3193 2.046023 TGGCGCCTCACATCCTTG 60.046 61.111 29.70 0.00 0.00 3.61
2845 3194 2.268920 GGCGCCTCACATCCTTGA 59.731 61.111 22.15 0.00 0.00 3.02
2846 3195 1.153086 GGCGCCTCACATCCTTGAT 60.153 57.895 22.15 0.00 0.00 2.57
2847 3196 1.162800 GGCGCCTCACATCCTTGATC 61.163 60.000 22.15 0.00 0.00 2.92
2848 3197 0.179062 GCGCCTCACATCCTTGATCT 60.179 55.000 0.00 0.00 0.00 2.75
2849 3198 1.745141 GCGCCTCACATCCTTGATCTT 60.745 52.381 0.00 0.00 0.00 2.40
2850 3199 1.938577 CGCCTCACATCCTTGATCTTG 59.061 52.381 0.00 0.00 0.00 3.02
2851 3200 2.419159 CGCCTCACATCCTTGATCTTGA 60.419 50.000 0.00 0.00 0.00 3.02
2908 3258 2.441750 GGATGCTGGTTTCCCTGGTATA 59.558 50.000 0.00 0.00 0.00 1.47
2974 3325 3.982576 AAAACGAGGGTTGCTTACTTG 57.017 42.857 0.00 0.00 36.25 3.16
3025 3376 6.439375 GGGTAAAGAAAAATACCAACCCATCT 59.561 38.462 2.36 0.00 43.95 2.90
3049 3400 2.436292 GACTCTGCAGGCTGCCAG 60.436 66.667 34.58 29.70 44.23 4.85
3057 3408 1.025041 GCAGGCTGCCAGTTATTACC 58.975 55.000 28.87 0.00 37.42 2.85
3103 3461 1.152652 ACACCATTTTGGGCGTCCA 60.153 52.632 3.51 3.51 43.37 4.02
3182 3540 3.376234 CCCTTGCATACATTGACACTGAG 59.624 47.826 0.00 0.00 0.00 3.35
3184 3542 2.358957 TGCATACATTGACACTGAGGC 58.641 47.619 0.00 1.35 0.00 4.70
3218 3576 2.003658 AAGTTGGTGTTGGCGCAGTG 62.004 55.000 10.83 0.00 0.00 3.66
3223 3581 2.030412 TGTTGGCGCAGTGACGAT 59.970 55.556 10.83 0.00 34.06 3.73
3230 3588 0.721154 GCGCAGTGACGATCATCAAA 59.279 50.000 0.30 0.00 34.06 2.69
3231 3589 1.328680 GCGCAGTGACGATCATCAAAT 59.671 47.619 0.30 0.00 34.06 2.32
3232 3590 2.539688 GCGCAGTGACGATCATCAAATA 59.460 45.455 0.30 0.00 34.06 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.094881 CGAATAATAAACCCATCACCACAAGT 59.905 38.462 0.00 0.00 0.00 3.16
1 2 6.094881 ACGAATAATAAACCCATCACCACAAG 59.905 38.462 0.00 0.00 0.00 3.16
2 3 5.946972 ACGAATAATAAACCCATCACCACAA 59.053 36.000 0.00 0.00 0.00 3.33
3 4 5.502079 ACGAATAATAAACCCATCACCACA 58.498 37.500 0.00 0.00 0.00 4.17
4 5 5.277154 CGACGAATAATAAACCCATCACCAC 60.277 44.000 0.00 0.00 0.00 4.16
5 6 4.812091 CGACGAATAATAAACCCATCACCA 59.188 41.667 0.00 0.00 0.00 4.17
6 7 4.212636 CCGACGAATAATAAACCCATCACC 59.787 45.833 0.00 0.00 0.00 4.02
7 8 5.050567 GTCCGACGAATAATAAACCCATCAC 60.051 44.000 0.00 0.00 0.00 3.06
8 9 5.051816 GTCCGACGAATAATAAACCCATCA 58.948 41.667 0.00 0.00 0.00 3.07
9 10 5.051816 TGTCCGACGAATAATAAACCCATC 58.948 41.667 0.00 0.00 0.00 3.51
10 11 5.026038 TGTCCGACGAATAATAAACCCAT 57.974 39.130 0.00 0.00 0.00 4.00
11 12 4.468765 TGTCCGACGAATAATAAACCCA 57.531 40.909 0.00 0.00 0.00 4.51
12 13 5.799681 TTTGTCCGACGAATAATAAACCC 57.200 39.130 0.00 0.00 0.00 4.11
13 14 6.739550 CACTTTTGTCCGACGAATAATAAACC 59.260 38.462 1.90 0.00 0.00 3.27
14 15 6.739550 CCACTTTTGTCCGACGAATAATAAAC 59.260 38.462 1.90 0.00 0.00 2.01
15 16 6.621164 GCCACTTTTGTCCGACGAATAATAAA 60.621 38.462 1.90 0.00 0.00 1.40
16 17 5.163834 GCCACTTTTGTCCGACGAATAATAA 60.164 40.000 1.90 0.00 0.00 1.40
36 37 1.359475 GACTAGTCCCGATCGCCAC 59.641 63.158 12.13 8.09 0.00 5.01
50 51 0.616395 TTGGGCATGACGAGGGACTA 60.616 55.000 0.00 0.00 41.55 2.59
55 56 2.390599 CGTGTTGGGCATGACGAGG 61.391 63.158 0.00 0.00 36.21 4.63
92 93 1.597663 GGTGTTCATTTCCGGATAGCG 59.402 52.381 4.15 0.00 0.00 4.26
106 107 2.040544 CCACTGGCCGATGGTGTTC 61.041 63.158 15.55 0.00 0.00 3.18
107 108 2.034066 CCACTGGCCGATGGTGTT 59.966 61.111 15.55 0.00 0.00 3.32
108 109 4.722700 GCCACTGGCCGATGGTGT 62.723 66.667 22.60 1.84 44.06 4.16
142 202 3.244596 GGAAGGATCCGGAATAAAGGGAG 60.245 52.174 9.01 0.00 35.59 4.30
185 246 1.740025 GAACCAAGGGAAAGCGATCAG 59.260 52.381 0.00 0.00 0.00 2.90
238 299 4.080015 TGGAGGGGATTTGACGTTATTCAT 60.080 41.667 0.00 0.00 0.00 2.57
276 337 2.346541 GCCTCCCCTTTGCAGCTTC 61.347 63.158 0.00 0.00 0.00 3.86
371 545 7.201767 CCATGATCCCAACTACAAGATCTTTTC 60.202 40.741 4.86 0.00 36.82 2.29
372 546 6.604795 CCATGATCCCAACTACAAGATCTTTT 59.395 38.462 4.86 1.64 36.82 2.27
374 548 5.192522 ACCATGATCCCAACTACAAGATCTT 59.807 40.000 0.88 0.88 36.82 2.40
379 553 3.282021 CCACCATGATCCCAACTACAAG 58.718 50.000 0.00 0.00 0.00 3.16
382 556 1.064758 TGCCACCATGATCCCAACTAC 60.065 52.381 0.00 0.00 0.00 2.73
384 558 0.632835 ATGCCACCATGATCCCAACT 59.367 50.000 0.00 0.00 0.00 3.16
385 559 1.488390 AATGCCACCATGATCCCAAC 58.512 50.000 0.00 0.00 0.00 3.77
386 560 2.250921 AAATGCCACCATGATCCCAA 57.749 45.000 0.00 0.00 0.00 4.12
388 562 3.233507 ACATAAATGCCACCATGATCCC 58.766 45.455 0.00 0.00 0.00 3.85
389 563 5.622914 GCATACATAAATGCCACCATGATCC 60.623 44.000 0.00 0.00 45.31 3.36
452 626 5.292765 CACCATATACTACTTGCTCAGTGG 58.707 45.833 0.00 0.00 39.91 4.00
477 651 3.125316 CCGAAAGAAAACTGGTCGTGTA 58.875 45.455 0.00 0.00 0.00 2.90
478 652 1.937899 CCGAAAGAAAACTGGTCGTGT 59.062 47.619 0.00 0.00 0.00 4.49
481 655 1.191647 CGTCCGAAAGAAAACTGGTCG 59.808 52.381 0.00 0.00 0.00 4.79
483 657 1.139455 TCCGTCCGAAAGAAAACTGGT 59.861 47.619 0.00 0.00 0.00 4.00
564 773 7.598493 GCTGATTAAAATGCACTGAAAGGTTAA 59.402 33.333 0.00 0.00 39.30 2.01
585 794 1.144936 GCTAGACGGGCTTGCTGAT 59.855 57.895 10.13 0.00 41.33 2.90
634 863 1.603455 CAATGGTCGCCCACCTTGT 60.603 57.895 0.00 0.00 46.98 3.16
637 866 0.469144 AAAACAATGGTCGCCCACCT 60.469 50.000 0.00 0.00 46.98 4.00
685 914 3.348119 TGTGTACTGCTAGAGTCTCAGG 58.652 50.000 12.20 0.00 35.96 3.86
690 919 5.357314 TCAGGTAATGTGTACTGCTAGAGTC 59.643 44.000 0.00 0.00 35.96 3.36
695 924 5.047872 TCGTTTCAGGTAATGTGTACTGCTA 60.048 40.000 0.00 0.00 0.00 3.49
696 925 3.994392 CGTTTCAGGTAATGTGTACTGCT 59.006 43.478 0.00 0.00 0.00 4.24
697 926 3.991773 TCGTTTCAGGTAATGTGTACTGC 59.008 43.478 0.00 0.00 0.00 4.40
701 930 4.992319 CCAGTTCGTTTCAGGTAATGTGTA 59.008 41.667 0.00 0.00 0.00 2.90
713 942 3.564225 ACTCACCATTTCCAGTTCGTTTC 59.436 43.478 0.00 0.00 0.00 2.78
738 967 6.152831 GGTTTTGTGGAGCCTAAAGTTCATAT 59.847 38.462 0.00 0.00 0.00 1.78
806 1050 6.491714 TTATGATGAGGAAGAAGGAAGGAG 57.508 41.667 0.00 0.00 0.00 3.69
807 1051 6.215431 TGTTTATGATGAGGAAGAAGGAAGGA 59.785 38.462 0.00 0.00 0.00 3.36
808 1052 6.317391 GTGTTTATGATGAGGAAGAAGGAAGG 59.683 42.308 0.00 0.00 0.00 3.46
809 1053 6.881065 TGTGTTTATGATGAGGAAGAAGGAAG 59.119 38.462 0.00 0.00 0.00 3.46
810 1054 6.778821 TGTGTTTATGATGAGGAAGAAGGAA 58.221 36.000 0.00 0.00 0.00 3.36
811 1055 6.373005 TGTGTTTATGATGAGGAAGAAGGA 57.627 37.500 0.00 0.00 0.00 3.36
812 1056 6.430925 TGTTGTGTTTATGATGAGGAAGAAGG 59.569 38.462 0.00 0.00 0.00 3.46
852 1096 3.565516 GATTGAAGGCCAGAAACGAAAC 58.434 45.455 5.01 0.00 0.00 2.78
854 1098 2.159382 GGATTGAAGGCCAGAAACGAA 58.841 47.619 5.01 0.00 0.00 3.85
857 1101 2.678336 CGTAGGATTGAAGGCCAGAAAC 59.322 50.000 5.01 0.00 0.00 2.78
869 1113 0.999406 CGCAGTTGGACGTAGGATTG 59.001 55.000 0.00 0.00 0.00 2.67
889 1133 3.716006 CACGGCCAGCAGACGTTG 61.716 66.667 4.72 0.00 39.02 4.10
890 1134 4.235762 ACACGGCCAGCAGACGTT 62.236 61.111 4.72 0.00 39.02 3.99
891 1135 4.969196 CACACGGCCAGCAGACGT 62.969 66.667 2.24 1.22 42.17 4.34
939 1192 2.106511 CCCTTTCTGGAGTGGAAGTTCA 59.893 50.000 5.01 0.00 38.35 3.18
940 1193 2.106684 ACCCTTTCTGGAGTGGAAGTTC 59.893 50.000 0.00 0.00 38.35 3.01
944 1197 1.628846 GCTACCCTTTCTGGAGTGGAA 59.371 52.381 0.00 0.00 38.35 3.53
969 1222 1.067060 GTTTGTTTCACCTGACAGGGC 59.933 52.381 25.34 10.19 40.58 5.19
973 1226 4.873746 TTTTGGTTTGTTTCACCTGACA 57.126 36.364 0.00 0.00 35.07 3.58
974 1227 4.390603 GGTTTTTGGTTTGTTTCACCTGAC 59.609 41.667 0.00 0.00 35.07 3.51
984 1237 2.101750 GGACATCGGGTTTTTGGTTTGT 59.898 45.455 0.00 0.00 0.00 2.83
989 1242 1.211709 GCGGACATCGGGTTTTTGG 59.788 57.895 0.00 0.00 39.69 3.28
1236 1489 2.264794 ACGAAGTGGCCGTGGATC 59.735 61.111 0.00 0.00 42.51 3.36
1282 1535 2.660572 CCTCCTCATCTCCTCGAAGAA 58.339 52.381 0.00 0.00 34.09 2.52
1284 1537 1.327303 CCCTCCTCATCTCCTCGAAG 58.673 60.000 0.00 0.00 0.00 3.79
1456 1709 3.594775 CTTGCCGTGCCTGCACAA 61.595 61.111 21.01 8.04 46.47 3.33
1539 1792 2.305927 ACCATCGACAAGGAGGTTGAAT 59.694 45.455 7.33 0.00 38.60 2.57
1560 1813 3.918253 CTGCCCAGCCTTGCCGTAA 62.918 63.158 0.00 0.00 0.00 3.18
1563 1816 4.809496 ATCTGCCCAGCCTTGCCG 62.809 66.667 0.00 0.00 0.00 5.69
1755 2008 4.081406 GGGCCAATGCATCAATCAGTATA 58.919 43.478 4.39 0.00 40.13 1.47
1902 2155 3.249805 TGGAACAGCTTCCTGGCA 58.750 55.556 6.03 0.00 45.87 4.92
1968 2221 5.924356 TCTCGTCCATAGCCAAAAATCATA 58.076 37.500 0.00 0.00 0.00 2.15
2252 2505 5.904941 ACATCTGAATTTGCACAGAAACAA 58.095 33.333 8.62 0.00 44.47 2.83
2271 2524 8.345565 ACTTTCTCAAGACAAACATACAACATC 58.654 33.333 0.00 0.00 33.72 3.06
2404 2657 9.638300 CTTTGAATTTGCTTATCACTATCGTAC 57.362 33.333 0.00 0.00 0.00 3.67
2439 2692 2.034685 TCTCGCTGCACATACATCTACC 59.965 50.000 0.00 0.00 0.00 3.18
2478 2750 9.716507 CACAGCCAACATAAATTATACAAGTAC 57.283 33.333 0.00 0.00 0.00 2.73
2500 2772 7.172532 ACATACAACACAAATGTACCTACACAG 59.827 37.037 0.00 0.00 38.45 3.66
2507 2779 8.203937 TGCTATACATACAACACAAATGTACC 57.796 34.615 0.00 0.00 38.45 3.34
2508 2780 7.850982 GCTGCTATACATACAACACAAATGTAC 59.149 37.037 0.00 0.00 38.45 2.90
2522 2794 4.665833 AACTTGGTCGCTGCTATACATA 57.334 40.909 0.00 0.00 0.00 2.29
2523 2795 3.543680 AACTTGGTCGCTGCTATACAT 57.456 42.857 0.00 0.00 0.00 2.29
2524 2796 4.665833 ATAACTTGGTCGCTGCTATACA 57.334 40.909 0.00 0.00 0.00 2.29
2525 2797 5.062308 GCATATAACTTGGTCGCTGCTATAC 59.938 44.000 0.00 0.00 0.00 1.47
2643 2923 8.655970 CCTCAAAAACGAAAAACAGAAAGAAAT 58.344 29.630 0.00 0.00 0.00 2.17
2644 2924 7.359681 GCCTCAAAAACGAAAAACAGAAAGAAA 60.360 33.333 0.00 0.00 0.00 2.52
2645 2925 6.090223 GCCTCAAAAACGAAAAACAGAAAGAA 59.910 34.615 0.00 0.00 0.00 2.52
2646 2926 5.575218 GCCTCAAAAACGAAAAACAGAAAGA 59.425 36.000 0.00 0.00 0.00 2.52
2647 2927 5.347364 TGCCTCAAAAACGAAAAACAGAAAG 59.653 36.000 0.00 0.00 0.00 2.62
2648 2928 5.230942 TGCCTCAAAAACGAAAAACAGAAA 58.769 33.333 0.00 0.00 0.00 2.52
2649 2929 4.810790 TGCCTCAAAAACGAAAAACAGAA 58.189 34.783 0.00 0.00 0.00 3.02
2650 2930 4.442375 TGCCTCAAAAACGAAAAACAGA 57.558 36.364 0.00 0.00 0.00 3.41
2651 2931 5.523013 TTTGCCTCAAAAACGAAAAACAG 57.477 34.783 0.00 0.00 29.89 3.16
2652 2932 7.009723 GTCTATTTGCCTCAAAAACGAAAAACA 59.990 33.333 0.00 0.00 36.90 2.83
2653 2933 7.009723 TGTCTATTTGCCTCAAAAACGAAAAAC 59.990 33.333 0.00 0.00 36.90 2.43
2654 2934 7.036220 TGTCTATTTGCCTCAAAAACGAAAAA 58.964 30.769 0.00 0.00 36.90 1.94
2765 3045 5.046376 TCAAATCAGCATCACAGAGGTAAGA 60.046 40.000 0.00 0.00 0.00 2.10
2770 3050 3.340928 TGTCAAATCAGCATCACAGAGG 58.659 45.455 0.00 0.00 0.00 3.69
2781 3130 1.817357 TGCCTCAGCTGTCAAATCAG 58.183 50.000 14.67 1.13 40.80 2.90
2782 3131 2.490509 CAATGCCTCAGCTGTCAAATCA 59.509 45.455 14.67 5.11 40.80 2.57
2783 3132 2.751259 TCAATGCCTCAGCTGTCAAATC 59.249 45.455 14.67 0.00 40.80 2.17
2784 3133 2.799017 TCAATGCCTCAGCTGTCAAAT 58.201 42.857 14.67 1.30 40.80 2.32
2785 3134 2.275134 TCAATGCCTCAGCTGTCAAA 57.725 45.000 14.67 0.00 40.80 2.69
2786 3135 2.362736 GATCAATGCCTCAGCTGTCAA 58.637 47.619 14.67 0.00 40.80 3.18
2787 3136 1.407851 GGATCAATGCCTCAGCTGTCA 60.408 52.381 14.67 10.76 40.80 3.58
2788 3137 1.134159 AGGATCAATGCCTCAGCTGTC 60.134 52.381 14.67 5.07 40.80 3.51
2789 3138 0.917533 AGGATCAATGCCTCAGCTGT 59.082 50.000 14.67 0.00 40.80 4.40
2790 3139 3.802862 AGGATCAATGCCTCAGCTG 57.197 52.632 7.63 7.63 40.80 4.24
2796 3145 2.048601 CTCTCCAGAGGATCAATGCCT 58.951 52.381 0.00 0.00 38.48 4.75
2797 3146 2.045524 TCTCTCCAGAGGATCAATGCC 58.954 52.381 3.72 0.00 42.30 4.40
2798 3147 3.134442 AGTTCTCTCCAGAGGATCAATGC 59.866 47.826 3.72 0.00 42.30 3.56
2799 3148 4.443175 CCAGTTCTCTCCAGAGGATCAATG 60.443 50.000 3.72 0.00 42.30 2.82
2800 3149 3.710677 CCAGTTCTCTCCAGAGGATCAAT 59.289 47.826 3.72 0.00 42.30 2.57
2801 3150 3.102972 CCAGTTCTCTCCAGAGGATCAA 58.897 50.000 3.72 0.00 42.30 2.57
2802 3151 2.043664 ACCAGTTCTCTCCAGAGGATCA 59.956 50.000 3.72 0.00 42.30 2.92
2803 3152 2.745968 ACCAGTTCTCTCCAGAGGATC 58.254 52.381 3.72 0.00 42.30 3.36
2804 3153 2.938428 ACCAGTTCTCTCCAGAGGAT 57.062 50.000 3.72 0.00 42.30 3.24
2805 3154 2.291670 GGTACCAGTTCTCTCCAGAGGA 60.292 54.545 7.15 0.00 42.30 3.71
2806 3155 2.104170 GGTACCAGTTCTCTCCAGAGG 58.896 57.143 7.15 0.00 42.30 3.69
2807 3156 2.757868 CAGGTACCAGTTCTCTCCAGAG 59.242 54.545 15.94 0.00 43.36 3.35
2808 3157 2.557676 CCAGGTACCAGTTCTCTCCAGA 60.558 54.545 15.94 0.00 0.00 3.86
2809 3158 1.827969 CCAGGTACCAGTTCTCTCCAG 59.172 57.143 15.94 0.00 0.00 3.86
2810 3159 1.938585 CCAGGTACCAGTTCTCTCCA 58.061 55.000 15.94 0.00 0.00 3.86
2811 3160 0.537653 GCCAGGTACCAGTTCTCTCC 59.462 60.000 15.94 0.00 0.00 3.71
2812 3161 0.173708 CGCCAGGTACCAGTTCTCTC 59.826 60.000 15.94 0.00 0.00 3.20
2813 3162 1.889530 GCGCCAGGTACCAGTTCTCT 61.890 60.000 15.94 0.00 0.00 3.10
2814 3163 1.448013 GCGCCAGGTACCAGTTCTC 60.448 63.158 15.94 0.00 0.00 2.87
2815 3164 2.663196 GCGCCAGGTACCAGTTCT 59.337 61.111 15.94 0.00 0.00 3.01
2816 3165 2.436115 GGCGCCAGGTACCAGTTC 60.436 66.667 24.80 0.00 0.00 3.01
2817 3166 2.928396 AGGCGCCAGGTACCAGTT 60.928 61.111 31.54 0.00 0.00 3.16
2818 3167 3.391382 GAGGCGCCAGGTACCAGT 61.391 66.667 31.54 3.33 0.00 4.00
2819 3168 3.390521 TGAGGCGCCAGGTACCAG 61.391 66.667 31.54 5.89 0.00 4.00
2820 3169 3.702048 GTGAGGCGCCAGGTACCA 61.702 66.667 31.54 13.04 0.00 3.25
2821 3170 2.925162 GATGTGAGGCGCCAGGTACC 62.925 65.000 31.54 2.73 0.00 3.34
2822 3171 1.521681 GATGTGAGGCGCCAGGTAC 60.522 63.158 31.54 20.75 0.00 3.34
2823 3172 2.731571 GGATGTGAGGCGCCAGGTA 61.732 63.158 31.54 12.85 0.00 3.08
2824 3173 4.101448 GGATGTGAGGCGCCAGGT 62.101 66.667 31.54 8.11 0.00 4.00
2825 3174 3.335356 AAGGATGTGAGGCGCCAGG 62.335 63.158 31.54 0.00 0.00 4.45
2826 3175 2.110967 CAAGGATGTGAGGCGCCAG 61.111 63.158 31.54 0.60 0.00 4.85
2827 3176 1.913951 ATCAAGGATGTGAGGCGCCA 61.914 55.000 31.54 8.23 0.00 5.69
2828 3177 1.153086 ATCAAGGATGTGAGGCGCC 60.153 57.895 21.89 21.89 0.00 6.53
2829 3178 0.179062 AGATCAAGGATGTGAGGCGC 60.179 55.000 0.00 0.00 0.00 6.53
2830 3179 1.938577 CAAGATCAAGGATGTGAGGCG 59.061 52.381 0.00 0.00 0.00 5.52
2831 3180 3.272574 TCAAGATCAAGGATGTGAGGC 57.727 47.619 0.00 0.00 0.00 4.70
2848 3197 6.149308 CCTGCACTAACATTTGACTACATCAA 59.851 38.462 0.00 0.00 45.92 2.57
2849 3198 5.643348 CCTGCACTAACATTTGACTACATCA 59.357 40.000 0.00 0.00 34.65 3.07
2850 3199 5.643777 ACCTGCACTAACATTTGACTACATC 59.356 40.000 0.00 0.00 0.00 3.06
2851 3200 5.560724 ACCTGCACTAACATTTGACTACAT 58.439 37.500 0.00 0.00 0.00 2.29
2908 3258 8.885494 TCTAGCATGTTAAAAGCAACAAAAAT 57.115 26.923 0.00 0.00 41.50 1.82
2974 3325 6.456181 CCATTCTTAGATTGTTCGAAGCTGAC 60.456 42.308 0.00 0.00 35.32 3.51
3025 3376 3.470709 GCAGCCTGCAGAGTCATTATTA 58.529 45.455 17.39 0.00 44.26 0.98
3049 3400 4.119442 TCAGGAACGCTCAGGTAATAAC 57.881 45.455 0.00 0.00 0.00 1.89
3057 3408 1.734465 GGTTTCATCAGGAACGCTCAG 59.266 52.381 0.00 0.00 34.56 3.35
3182 3540 4.368315 CAACTTAGAAAAACAACCAGGCC 58.632 43.478 0.00 0.00 0.00 5.19
3184 3542 5.105513 ACACCAACTTAGAAAAACAACCAGG 60.106 40.000 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.