Multiple sequence alignment - TraesCS7D01G386700

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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 TraesCS7D01G386700 chr7D 100.000 2786 0 0 1 2786 500965582 500962797 0.000000e+00 5145.0
1 TraesCS7D01G386700 chr7D 100.000 65 0 0 2980 3044 500962603 500962539 1.480000e-23 121.0
2 TraesCS7D01G386700 chr7D 88.000 100 10 1 2409 2508 500930857 500930760 1.920000e-22 117.0
3 TraesCS7D01G386700 chr7D 89.831 59 6 0 2983 3041 296610839 296610781 3.250000e-10 76.8
4 TraesCS7D01G386700 chr7A 91.514 2180 106 30 257 2412 567445096 567442972 0.000000e+00 2928.0
5 TraesCS7D01G386700 chr7A 93.585 265 10 1 2409 2666 567442935 567442671 3.680000e-104 388.0
6 TraesCS7D01G386700 chr7A 93.750 240 9 1 1 240 567445375 567445142 3.730000e-94 355.0
7 TraesCS7D01G386700 chr7A 87.611 113 13 1 2665 2776 92001439 92001551 2.460000e-26 130.0
8 TraesCS7D01G386700 chr7A 94.444 36 2 0 3007 3042 648363034 648362999 4.240000e-04 56.5
9 TraesCS7D01G386700 chr7B 90.380 2183 99 33 257 2412 529949447 529947349 0.000000e+00 2765.0
10 TraesCS7D01G386700 chr7B 89.641 251 11 3 2409 2659 529947313 529947078 3.810000e-79 305.0
11 TraesCS7D01G386700 chr7B 89.627 241 10 6 1 240 529949719 529949493 2.970000e-75 292.0
12 TraesCS7D01G386700 chr7B 92.222 180 11 2 2487 2666 529842734 529842558 5.040000e-63 252.0
13 TraesCS7D01G386700 chr7B 87.826 115 13 1 2665 2778 368205873 368205759 1.900000e-27 134.0
14 TraesCS7D01G386700 chr7B 88.000 100 10 2 2409 2508 529825590 529825493 1.920000e-22 117.0
15 TraesCS7D01G386700 chr7B 90.000 70 7 0 2439 2508 529849382 529849313 1.160000e-14 91.6
16 TraesCS7D01G386700 chr4B 87.179 117 10 4 2665 2778 64813234 64813120 8.860000e-26 128.0
17 TraesCS7D01G386700 chr4B 87.179 117 10 4 2665 2778 65137840 65137726 8.860000e-26 128.0
18 TraesCS7D01G386700 chr2A 87.850 107 12 1 2665 2770 20013031 20013137 1.150000e-24 124.0
19 TraesCS7D01G386700 chr2A 91.071 56 5 0 2980 3035 384845112 384845167 3.250000e-10 76.8
20 TraesCS7D01G386700 chr2A 88.889 54 6 0 2989 3042 229678818 229678765 1.960000e-07 67.6
21 TraesCS7D01G386700 chr3D 86.207 116 13 3 2665 2778 13703259 13703145 4.120000e-24 122.0
22 TraesCS7D01G386700 chr3D 86.667 60 8 0 2983 3042 13702551 13702492 1.960000e-07 67.6
23 TraesCS7D01G386700 chr5D 87.619 105 11 2 2665 2769 282145090 282145192 1.480000e-23 121.0
24 TraesCS7D01G386700 chr2D 86.087 115 13 3 2665 2778 537235608 537235496 1.480000e-23 121.0
25 TraesCS7D01G386700 chr1D 82.946 129 15 6 2665 2786 60945401 60945273 3.210000e-20 110.0
26 TraesCS7D01G386700 chr6A 85.714 63 9 0 2980 3042 400038766 400038828 1.960000e-07 67.6
27 TraesCS7D01G386700 chr5A 86.667 60 8 0 2983 3042 526508411 526508352 1.960000e-07 67.6
28 TraesCS7D01G386700 chr1B 86.441 59 8 0 2984 3042 1475492 1475434 7.040000e-07 65.8


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 TraesCS7D01G386700 chr7D 500962539 500965582 3043 True 2633.000000 5145 100.000000 1 3044 2 chr7D.!!$R3 3043
1 TraesCS7D01G386700 chr7A 567442671 567445375 2704 True 1223.666667 2928 92.949667 1 2666 3 chr7A.!!$R2 2665
2 TraesCS7D01G386700 chr7B 529947078 529949719 2641 True 1120.666667 2765 89.882667 1 2659 3 chr7B.!!$R5 2658

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
577 619 0.105760 ACCAAACCCATCCAACTGCA 60.106 50.0 0.0 0.0 0.00 4.41 F
1761 1816 0.183492 TTGATATGCAGGAGCCCACC 59.817 55.0 0.0 0.0 41.13 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1888 1943 0.827089 TGCCCACATTGTCCAACAGG 60.827 55.0 0.00 0.00 0.0 4.00 R
2983 3098 0.037326 TGACACAGGATCCTCAACGC 60.037 55.0 12.69 1.14 0.0 4.84 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 4.735132 CAGGGACGCGCCGAGAAA 62.735 66.667 5.73 0.00 37.63 2.52
28 29 4.436998 AGGGACGCGCCGAGAAAG 62.437 66.667 5.73 0.00 37.63 2.62
29 30 4.430765 GGGACGCGCCGAGAAAGA 62.431 66.667 5.73 0.00 37.63 2.52
30 31 2.431942 GGACGCGCCGAGAAAGAA 60.432 61.111 5.73 0.00 0.00 2.52
31 32 2.025418 GGACGCGCCGAGAAAGAAA 61.025 57.895 5.73 0.00 0.00 2.52
32 33 1.562575 GGACGCGCCGAGAAAGAAAA 61.563 55.000 5.73 0.00 0.00 2.29
240 241 0.871057 GACTGCTGCTTCTCCACAAC 59.129 55.000 0.00 0.00 0.00 3.32
242 243 1.311859 CTGCTGCTTCTCCACAACAA 58.688 50.000 0.00 0.00 0.00 2.83
243 244 1.677576 CTGCTGCTTCTCCACAACAAA 59.322 47.619 0.00 0.00 0.00 2.83
247 248 3.558505 CTGCTTCTCCACAACAAATTCG 58.441 45.455 0.00 0.00 0.00 3.34
249 250 3.629855 TGCTTCTCCACAACAAATTCGAA 59.370 39.130 0.00 0.00 0.00 3.71
250 251 4.278170 TGCTTCTCCACAACAAATTCGAAT 59.722 37.500 4.39 4.39 0.00 3.34
251 252 4.618489 GCTTCTCCACAACAAATTCGAATG 59.382 41.667 12.25 4.12 0.00 2.67
252 253 5.762045 CTTCTCCACAACAAATTCGAATGT 58.238 37.500 12.25 2.41 0.00 2.71
254 255 6.236017 TCTCCACAACAAATTCGAATGTAC 57.764 37.500 12.25 0.00 0.00 2.90
255 256 5.024768 TCCACAACAAATTCGAATGTACG 57.975 39.130 12.25 5.67 0.00 3.67
261 291 7.633281 CACAACAAATTCGAATGTACGTATACC 59.367 37.037 12.25 0.00 34.70 2.73
284 316 5.357032 CCTATTTTTGGTAGGTTCAGCGAAT 59.643 40.000 0.00 0.00 35.12 3.34
305 337 1.602377 AGGCAAACGGAAAGAACTTCG 59.398 47.619 0.00 0.00 34.56 3.79
363 395 2.048222 TACACGAGCACAGCTGGC 60.048 61.111 19.93 18.01 39.88 4.85
395 427 1.592223 CCAGGAGACCGAGTTGACC 59.408 63.158 0.00 0.00 0.00 4.02
418 450 2.406616 CCAAGAACGCATTCCGGGG 61.407 63.158 0.00 0.00 42.52 5.73
469 501 2.237393 AAGCTCTCATTCGGCATCTC 57.763 50.000 0.00 0.00 0.00 2.75
518 560 3.877508 CTGAAAAGAGGAACCGTCAAGTT 59.122 43.478 0.00 0.00 0.00 2.66
523 565 2.561858 AGAGGAACCGTCAAGTTAGTCC 59.438 50.000 0.00 0.00 0.00 3.85
551 593 0.892755 AAGCCGAATCAGTGTACCGA 59.107 50.000 0.00 0.00 0.00 4.69
552 594 0.456221 AGCCGAATCAGTGTACCGAG 59.544 55.000 0.00 0.00 0.00 4.63
553 595 0.172803 GCCGAATCAGTGTACCGAGT 59.827 55.000 0.00 0.00 0.00 4.18
554 596 1.402968 GCCGAATCAGTGTACCGAGTA 59.597 52.381 0.00 0.00 0.00 2.59
555 597 2.793933 GCCGAATCAGTGTACCGAGTAC 60.794 54.545 7.11 7.11 39.24 2.73
556 598 2.223433 CCGAATCAGTGTACCGAGTACC 60.223 54.545 10.45 4.19 38.14 3.34
557 599 2.538333 CGAATCAGTGTACCGAGTACCG 60.538 54.545 10.45 0.00 38.14 4.02
558 600 2.408271 ATCAGTGTACCGAGTACCGA 57.592 50.000 10.45 6.28 41.76 4.69
568 610 0.248289 CGAGTACCGACCAAACCCAT 59.752 55.000 0.00 0.00 41.76 4.00
573 615 0.538746 ACCGACCAAACCCATCCAAC 60.539 55.000 0.00 0.00 0.00 3.77
574 616 0.251165 CCGACCAAACCCATCCAACT 60.251 55.000 0.00 0.00 0.00 3.16
575 617 0.881118 CGACCAAACCCATCCAACTG 59.119 55.000 0.00 0.00 0.00 3.16
576 618 0.603065 GACCAAACCCATCCAACTGC 59.397 55.000 0.00 0.00 0.00 4.40
577 619 0.105760 ACCAAACCCATCCAACTGCA 60.106 50.000 0.00 0.00 0.00 4.41
578 620 1.047002 CCAAACCCATCCAACTGCAA 58.953 50.000 0.00 0.00 0.00 4.08
579 621 1.001181 CCAAACCCATCCAACTGCAAG 59.999 52.381 0.00 0.00 42.29 4.01
619 661 3.367932 TCGAAAGTCGAATCATGTGCTTC 59.632 43.478 0.00 0.00 46.90 3.86
670 713 2.049618 TGCGAATGGTTTTGCCGC 60.050 55.556 0.00 0.00 40.93 6.53
735 778 2.280254 CGGCGGTGGTGTAACACA 60.280 61.111 0.00 0.00 43.08 3.72
737 780 1.964373 GGCGGTGGTGTAACACAGG 60.964 63.158 0.74 0.00 43.08 4.00
738 781 1.227734 GCGGTGGTGTAACACAGGT 60.228 57.895 0.74 0.00 43.08 4.00
820 863 1.177401 TCGTCTGGGAGTCTGATGTG 58.823 55.000 0.00 0.00 33.64 3.21
821 864 0.891373 CGTCTGGGAGTCTGATGTGT 59.109 55.000 0.00 0.00 0.00 3.72
822 865 2.092323 CGTCTGGGAGTCTGATGTGTA 58.908 52.381 0.00 0.00 0.00 2.90
823 866 2.492088 CGTCTGGGAGTCTGATGTGTAA 59.508 50.000 0.00 0.00 0.00 2.41
824 867 3.056821 CGTCTGGGAGTCTGATGTGTAAA 60.057 47.826 0.00 0.00 0.00 2.01
825 868 4.246458 GTCTGGGAGTCTGATGTGTAAAC 58.754 47.826 0.00 0.00 0.00 2.01
826 869 3.901222 TCTGGGAGTCTGATGTGTAAACA 59.099 43.478 0.00 0.00 0.00 2.83
827 870 4.532126 TCTGGGAGTCTGATGTGTAAACAT 59.468 41.667 0.00 0.00 0.00 2.71
828 871 4.832248 TGGGAGTCTGATGTGTAAACATC 58.168 43.478 17.79 17.79 44.89 3.06
829 872 3.865745 GGGAGTCTGATGTGTAAACATCG 59.134 47.826 19.02 14.13 46.93 3.84
830 873 4.495422 GGAGTCTGATGTGTAAACATCGT 58.505 43.478 19.02 5.79 46.93 3.73
831 874 4.563184 GGAGTCTGATGTGTAAACATCGTC 59.437 45.833 19.02 12.96 46.93 4.20
832 875 5.392767 AGTCTGATGTGTAAACATCGTCT 57.607 39.130 19.02 13.98 46.93 4.18
833 876 5.164233 AGTCTGATGTGTAAACATCGTCTG 58.836 41.667 19.02 10.43 46.93 3.51
834 877 4.327357 GTCTGATGTGTAAACATCGTCTGG 59.673 45.833 19.02 8.38 46.93 3.86
835 878 3.595173 TGATGTGTAAACATCGTCTGGG 58.405 45.455 19.02 0.00 46.93 4.45
836 879 3.259625 TGATGTGTAAACATCGTCTGGGA 59.740 43.478 19.02 0.00 46.93 4.37
837 880 3.313012 TGTGTAAACATCGTCTGGGAG 57.687 47.619 0.00 0.00 0.00 4.30
838 881 2.631062 TGTGTAAACATCGTCTGGGAGT 59.369 45.455 0.00 0.00 0.00 3.85
839 882 3.251571 GTGTAAACATCGTCTGGGAGTC 58.748 50.000 0.00 0.00 0.00 3.36
840 883 3.056749 GTGTAAACATCGTCTGGGAGTCT 60.057 47.826 0.00 0.00 0.00 3.24
841 884 2.751166 AAACATCGTCTGGGAGTCTG 57.249 50.000 0.00 0.00 0.00 3.51
842 885 1.924731 AACATCGTCTGGGAGTCTGA 58.075 50.000 0.00 0.00 0.00 3.27
843 886 2.151502 ACATCGTCTGGGAGTCTGAT 57.848 50.000 0.00 0.00 0.00 2.90
844 887 3.298686 ACATCGTCTGGGAGTCTGATA 57.701 47.619 0.00 0.00 0.00 2.15
845 888 3.632333 ACATCGTCTGGGAGTCTGATAA 58.368 45.455 0.00 0.00 0.00 1.75
851 894 5.125097 TCGTCTGGGAGTCTGATAAGTAAAC 59.875 44.000 0.00 0.00 0.00 2.01
854 897 6.981559 GTCTGGGAGTCTGATAAGTAAACATC 59.018 42.308 0.00 0.00 0.00 3.06
857 900 5.978322 GGGAGTCTGATAAGTAAACATCGTC 59.022 44.000 0.00 0.00 0.00 4.20
860 903 6.565234 AGTCTGATAAGTAAACATCGTCTGG 58.435 40.000 0.00 0.00 0.00 3.86
861 904 5.749109 GTCTGATAAGTAAACATCGTCTGGG 59.251 44.000 0.00 0.00 0.00 4.45
862 905 5.655090 TCTGATAAGTAAACATCGTCTGGGA 59.345 40.000 0.00 0.00 0.00 4.37
907 954 7.872138 ACCATTACTTTAGATCAAATGGAGGA 58.128 34.615 16.93 0.00 46.21 3.71
990 1037 2.745728 GCTTGTTGCATGCATCCAC 58.254 52.632 23.37 17.46 42.31 4.02
991 1038 1.074319 GCTTGTTGCATGCATCCACG 61.074 55.000 23.37 18.57 42.31 4.94
992 1039 1.074319 CTTGTTGCATGCATCCACGC 61.074 55.000 23.37 8.38 0.00 5.34
1129 1178 2.576615 AGGGACAAACTTTGAGCACTC 58.423 47.619 8.55 0.00 0.00 3.51
1217 1266 1.141657 AGTACAGATGCGGCATTCCAT 59.858 47.619 17.78 6.11 0.00 3.41
1273 1322 2.698803 CCAATGAGGTGTCGAATGTCA 58.301 47.619 0.00 0.00 0.00 3.58
1284 1333 5.175126 GGTGTCGAATGTCACTATAAATCCG 59.825 44.000 4.18 0.00 34.99 4.18
1332 1381 3.735591 TCCCTTTCCTGTTCGTTAGTTG 58.264 45.455 0.00 0.00 0.00 3.16
1490 1543 0.321919 TGCTCCTGAGTGTTCATGCC 60.322 55.000 0.00 0.00 31.68 4.40
1511 1566 4.660168 CCAGAGCTATATGGCCTTTCATT 58.340 43.478 7.54 0.00 29.32 2.57
1563 1618 1.654954 GGCACAGGCATGCTCTTCTG 61.655 60.000 18.92 17.81 45.38 3.02
1613 1668 3.471680 ACTCTTTGTTCTCAGAGTTGCC 58.528 45.455 0.00 0.00 38.32 4.52
1631 1686 2.355837 GACGGCAACTGACAGCGA 60.356 61.111 1.25 0.00 0.00 4.93
1684 1739 2.935849 GCAAGGGGTTGTCAAAAACTTG 59.064 45.455 15.01 15.01 37.48 3.16
1690 1745 4.888823 GGGGTTGTCAAAAACTTGTAGGTA 59.111 41.667 0.00 0.00 0.00 3.08
1761 1816 0.183492 TTGATATGCAGGAGCCCACC 59.817 55.000 0.00 0.00 41.13 4.61
1769 1824 2.358737 GGAGCCCACCGTTGACAG 60.359 66.667 0.00 0.00 0.00 3.51
1776 1831 1.002659 CCCACCGTTGACAGAACCATA 59.997 52.381 0.00 0.00 0.00 2.74
1790 1845 4.878397 CAGAACCATAACAGATGAGGGAAC 59.122 45.833 0.00 0.00 0.00 3.62
1888 1943 2.669364 CAAGCTCAGGTGCAAAACATC 58.331 47.619 0.00 0.00 34.99 3.06
2044 2099 0.036306 CCCGCCCAAGAACAACTAGT 59.964 55.000 0.00 0.00 0.00 2.57
2045 2100 1.156736 CCGCCCAAGAACAACTAGTG 58.843 55.000 0.00 0.00 0.00 2.74
2061 2116 5.272405 ACTAGTGGTGGATAGGGTATAGG 57.728 47.826 0.00 0.00 0.00 2.57
2181 2236 5.295787 GTGTTGTGTTTCTCCTGTGTCATAA 59.704 40.000 0.00 0.00 0.00 1.90
2182 2237 6.017109 GTGTTGTGTTTCTCCTGTGTCATAAT 60.017 38.462 0.00 0.00 0.00 1.28
2307 2365 5.424121 ACTGACACACTAACATTTTCTGC 57.576 39.130 0.00 0.00 0.00 4.26
2416 2524 5.363580 AGTGTGAAATTTGTCCAATTCCACT 59.636 36.000 0.00 3.27 35.47 4.00
2447 2555 9.060347 CATTCACAAGGAAATATACATAGCAGT 57.940 33.333 0.00 0.00 39.39 4.40
2460 2568 2.134201 TAGCAGTCAACGTGTGTCAG 57.866 50.000 0.00 0.00 0.00 3.51
2558 2673 0.251653 AGTGACTTCGGTAGGAGGCA 60.252 55.000 0.00 0.00 0.00 4.75
2659 2774 8.364142 CCAATTGGTTTGAAGTTCCAAGTATTA 58.636 33.333 16.90 0.00 43.12 0.98
2669 2784 9.871238 TGAAGTTCCAAGTATTATTCTGTAGTC 57.129 33.333 0.00 0.00 0.00 2.59
2670 2785 9.871238 GAAGTTCCAAGTATTATTCTGTAGTCA 57.129 33.333 0.00 0.00 0.00 3.41
2673 2788 9.262358 GTTCCAAGTATTATTCTGTAGTCATCC 57.738 37.037 0.00 0.00 0.00 3.51
2674 2789 7.658261 TCCAAGTATTATTCTGTAGTCATCCG 58.342 38.462 0.00 0.00 0.00 4.18
2675 2790 7.287005 TCCAAGTATTATTCTGTAGTCATCCGT 59.713 37.037 0.00 0.00 0.00 4.69
2676 2791 7.382488 CCAAGTATTATTCTGTAGTCATCCGTG 59.618 40.741 0.00 0.00 0.00 4.94
2677 2792 6.982852 AGTATTATTCTGTAGTCATCCGTGG 58.017 40.000 0.00 0.00 0.00 4.94
2678 2793 2.604046 ATTCTGTAGTCATCCGTGGC 57.396 50.000 0.00 0.00 0.00 5.01
2679 2794 0.172578 TTCTGTAGTCATCCGTGGCG 59.827 55.000 0.00 0.00 34.36 5.69
2680 2795 0.963856 TCTGTAGTCATCCGTGGCGT 60.964 55.000 0.00 0.00 34.36 5.68
2681 2796 0.736636 CTGTAGTCATCCGTGGCGTA 59.263 55.000 0.00 0.00 34.36 4.42
2682 2797 0.736636 TGTAGTCATCCGTGGCGTAG 59.263 55.000 0.00 0.00 34.36 3.51
2701 2816 3.419759 GCGAGCTCGGGCGAAAAA 61.420 61.111 35.10 0.00 44.37 1.94
2702 2817 2.750888 GCGAGCTCGGGCGAAAAAT 61.751 57.895 35.10 0.00 44.37 1.82
2703 2818 1.060937 CGAGCTCGGGCGAAAAATG 59.939 57.895 28.40 0.00 44.37 2.32
2704 2819 1.226407 GAGCTCGGGCGAAAAATGC 60.226 57.895 0.00 0.00 44.37 3.56
2712 2827 3.306206 GCGAAAAATGCCTGTACGG 57.694 52.632 0.00 0.00 0.00 4.02
2713 2828 0.179174 GCGAAAAATGCCTGTACGGG 60.179 55.000 17.09 17.09 0.00 5.28
2714 2829 1.161843 CGAAAAATGCCTGTACGGGT 58.838 50.000 21.95 0.32 0.00 5.28
2715 2830 1.135803 CGAAAAATGCCTGTACGGGTG 60.136 52.381 21.95 0.00 0.00 4.61
2716 2831 0.601057 AAAAATGCCTGTACGGGTGC 59.399 50.000 21.95 9.17 0.00 5.01
2717 2832 1.582610 AAAATGCCTGTACGGGTGCG 61.583 55.000 21.95 0.00 0.00 5.34
2718 2833 3.969250 AATGCCTGTACGGGTGCGG 62.969 63.158 21.95 0.00 0.00 5.69
2721 2836 4.752879 CCTGTACGGGTGCGGGTG 62.753 72.222 13.06 0.00 37.02 4.61
2722 2837 3.687102 CTGTACGGGTGCGGGTGA 61.687 66.667 0.00 0.00 0.00 4.02
2723 2838 3.927163 CTGTACGGGTGCGGGTGAC 62.927 68.421 0.00 0.00 0.00 3.67
2741 2856 4.814294 CGGACCGGCTACAGGCAC 62.814 72.222 5.81 0.00 44.01 5.01
2742 2857 4.468689 GGACCGGCTACAGGCACC 62.469 72.222 0.00 0.07 44.01 5.01
2743 2858 4.814294 GACCGGCTACAGGCACCG 62.814 72.222 0.00 0.00 46.50 4.94
2996 3111 3.077556 AGCGGCGTTGAGGATCCT 61.078 61.111 16.13 16.13 0.00 3.24
2997 3112 2.892425 GCGGCGTTGAGGATCCTG 60.892 66.667 22.02 5.61 0.00 3.86
2998 3113 2.579201 CGGCGTTGAGGATCCTGT 59.421 61.111 22.02 0.00 0.00 4.00
2999 3114 1.811266 CGGCGTTGAGGATCCTGTG 60.811 63.158 22.02 6.88 0.00 3.66
3000 3115 1.296715 GGCGTTGAGGATCCTGTGT 59.703 57.895 22.02 0.00 0.00 3.72
3001 3116 0.741221 GGCGTTGAGGATCCTGTGTC 60.741 60.000 22.02 5.24 0.00 3.67
3002 3117 0.037326 GCGTTGAGGATCCTGTGTCA 60.037 55.000 22.02 8.32 0.00 3.58
3003 3118 1.714794 CGTTGAGGATCCTGTGTCAC 58.285 55.000 22.02 3.64 0.00 3.67
3004 3119 1.673033 CGTTGAGGATCCTGTGTCACC 60.673 57.143 22.02 2.28 0.00 4.02
3005 3120 0.608130 TTGAGGATCCTGTGTCACCG 59.392 55.000 22.02 0.00 0.00 4.94
3006 3121 1.257750 TGAGGATCCTGTGTCACCGG 61.258 60.000 22.02 7.09 0.00 5.28
3007 3122 1.229209 AGGATCCTGTGTCACCGGT 60.229 57.895 15.29 0.00 0.00 5.28
3008 3123 1.079127 GGATCCTGTGTCACCGGTG 60.079 63.158 29.26 29.26 0.00 4.94
3009 3124 1.541310 GGATCCTGTGTCACCGGTGA 61.541 60.000 33.23 33.23 37.24 4.02
3022 3137 2.047179 GGTGACGGGAGGAACAGC 60.047 66.667 0.00 0.00 0.00 4.40
3023 3138 2.047179 GTGACGGGAGGAACAGCC 60.047 66.667 0.00 0.00 0.00 4.85
3024 3139 3.691342 TGACGGGAGGAACAGCCG 61.691 66.667 0.00 0.00 43.43 5.52
3025 3140 4.452733 GACGGGAGGAACAGCCGG 62.453 72.222 0.00 0.00 43.43 6.13
3030 3145 2.686106 GAGGAACAGCCGGGGGTA 60.686 66.667 2.18 0.00 43.43 3.69
3031 3146 3.007323 AGGAACAGCCGGGGGTAC 61.007 66.667 2.18 0.00 43.43 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.009389 CCGTCGCTTCTCGCTTTTCT 61.009 55.000 0.00 0.00 38.27 2.52
28 29 1.416434 CCGTCGCTTCTCGCTTTTC 59.584 57.895 0.00 0.00 38.27 2.29
29 30 2.027625 CCCGTCGCTTCTCGCTTTT 61.028 57.895 0.00 0.00 38.27 2.27
30 31 2.432628 CCCGTCGCTTCTCGCTTT 60.433 61.111 0.00 0.00 38.27 3.51
160 161 0.804989 AGCTCTTGCGTTTACCATGC 59.195 50.000 0.00 0.00 45.42 4.06
163 164 2.244000 GCAGCTCTTGCGTTTACCA 58.756 52.632 0.00 0.00 44.09 3.25
261 291 5.873179 TTCGCTGAACCTACCAAAAATAG 57.127 39.130 0.00 0.00 0.00 1.73
284 316 2.803956 CGAAGTTCTTTCCGTTTGCCTA 59.196 45.455 0.56 0.00 31.82 3.93
363 395 1.002868 CCTGGGACTTCAGGCTGTG 60.003 63.158 15.27 11.18 46.47 3.66
369 401 0.612174 TCGGTCTCCTGGGACTTCAG 60.612 60.000 12.89 0.00 36.55 3.02
395 427 0.721718 GGAATGCGTTCTTGGAGACG 59.278 55.000 17.88 0.00 34.68 4.18
518 560 1.214589 GGCTTTCGAGCGTGGACTA 59.785 57.895 0.00 0.00 35.24 2.59
543 585 0.881118 TTGGTCGGTACTCGGTACAC 59.119 55.000 13.76 6.41 40.41 2.90
551 593 0.616891 GGATGGGTTTGGTCGGTACT 59.383 55.000 0.00 0.00 0.00 2.73
552 594 0.325602 TGGATGGGTTTGGTCGGTAC 59.674 55.000 0.00 0.00 0.00 3.34
553 595 1.065647 TTGGATGGGTTTGGTCGGTA 58.934 50.000 0.00 0.00 0.00 4.02
554 596 0.538746 GTTGGATGGGTTTGGTCGGT 60.539 55.000 0.00 0.00 0.00 4.69
555 597 0.251165 AGTTGGATGGGTTTGGTCGG 60.251 55.000 0.00 0.00 0.00 4.79
556 598 0.881118 CAGTTGGATGGGTTTGGTCG 59.119 55.000 0.00 0.00 0.00 4.79
557 599 0.603065 GCAGTTGGATGGGTTTGGTC 59.397 55.000 0.00 0.00 0.00 4.02
558 600 0.105760 TGCAGTTGGATGGGTTTGGT 60.106 50.000 0.00 0.00 0.00 3.67
576 618 1.595489 GCGTCAACTGTTGCAGACTTG 60.595 52.381 15.52 0.00 35.18 3.16
577 619 0.657840 GCGTCAACTGTTGCAGACTT 59.342 50.000 15.52 0.00 35.18 3.01
578 620 0.179073 AGCGTCAACTGTTGCAGACT 60.179 50.000 15.52 7.37 35.18 3.24
579 621 0.233332 GAGCGTCAACTGTTGCAGAC 59.767 55.000 15.52 8.04 35.18 3.51
580 622 1.215014 CGAGCGTCAACTGTTGCAGA 61.215 55.000 15.52 0.00 35.18 4.26
619 661 2.104792 TGGTCAGTTTTCAGAGGTGGAG 59.895 50.000 0.00 0.00 0.00 3.86
670 713 1.642037 TAGGAGTGAACGCTCGTCGG 61.642 60.000 12.61 0.00 43.86 4.79
735 778 1.230635 GCAAGATCGCACACACACCT 61.231 55.000 0.00 0.00 0.00 4.00
737 780 1.154599 CGCAAGATCGCACACACAC 60.155 57.895 0.00 0.00 43.02 3.82
738 781 1.594021 ACGCAAGATCGCACACACA 60.594 52.632 0.00 0.00 43.62 3.72
742 785 3.776849 CGCACGCAAGATCGCACA 61.777 61.111 0.00 0.00 43.62 4.57
778 821 4.639171 GCAAACAACCGGTGGCGG 62.639 66.667 8.52 0.00 0.00 6.13
820 863 3.192844 TCAGACTCCCAGACGATGTTTAC 59.807 47.826 0.00 0.00 0.00 2.01
821 864 3.427573 TCAGACTCCCAGACGATGTTTA 58.572 45.455 0.00 0.00 0.00 2.01
822 865 2.248248 TCAGACTCCCAGACGATGTTT 58.752 47.619 0.00 0.00 0.00 2.83
823 866 1.924731 TCAGACTCCCAGACGATGTT 58.075 50.000 0.00 0.00 0.00 2.71
824 867 2.151502 ATCAGACTCCCAGACGATGT 57.848 50.000 0.00 0.00 0.00 3.06
825 868 3.634448 ACTTATCAGACTCCCAGACGATG 59.366 47.826 0.00 0.00 0.00 3.84
826 869 3.904717 ACTTATCAGACTCCCAGACGAT 58.095 45.455 0.00 0.00 0.00 3.73
827 870 3.367646 ACTTATCAGACTCCCAGACGA 57.632 47.619 0.00 0.00 0.00 4.20
828 871 5.105877 TGTTTACTTATCAGACTCCCAGACG 60.106 44.000 0.00 0.00 0.00 4.18
829 872 6.282199 TGTTTACTTATCAGACTCCCAGAC 57.718 41.667 0.00 0.00 0.00 3.51
830 873 6.183360 CGATGTTTACTTATCAGACTCCCAGA 60.183 42.308 0.00 0.00 0.00 3.86
831 874 5.980116 CGATGTTTACTTATCAGACTCCCAG 59.020 44.000 0.00 0.00 0.00 4.45
832 875 5.421056 ACGATGTTTACTTATCAGACTCCCA 59.579 40.000 0.00 0.00 0.00 4.37
833 876 5.903810 ACGATGTTTACTTATCAGACTCCC 58.096 41.667 0.00 0.00 0.00 4.30
834 877 6.693545 CAGACGATGTTTACTTATCAGACTCC 59.306 42.308 0.00 0.00 0.00 3.85
835 878 6.693545 CCAGACGATGTTTACTTATCAGACTC 59.306 42.308 0.00 0.00 0.00 3.36
836 879 6.405953 CCCAGACGATGTTTACTTATCAGACT 60.406 42.308 0.00 0.00 0.00 3.24
837 880 5.749109 CCCAGACGATGTTTACTTATCAGAC 59.251 44.000 0.00 0.00 0.00 3.51
838 881 5.655090 TCCCAGACGATGTTTACTTATCAGA 59.345 40.000 0.00 0.00 0.00 3.27
839 882 5.902681 TCCCAGACGATGTTTACTTATCAG 58.097 41.667 0.00 0.00 0.00 2.90
840 883 5.421056 ACTCCCAGACGATGTTTACTTATCA 59.579 40.000 0.00 0.00 0.00 2.15
841 884 5.903810 ACTCCCAGACGATGTTTACTTATC 58.096 41.667 0.00 0.00 0.00 1.75
842 885 5.934402 ACTCCCAGACGATGTTTACTTAT 57.066 39.130 0.00 0.00 0.00 1.73
843 886 5.163723 CGTACTCCCAGACGATGTTTACTTA 60.164 44.000 0.00 0.00 41.60 2.24
844 887 4.380233 CGTACTCCCAGACGATGTTTACTT 60.380 45.833 0.00 0.00 41.60 2.24
845 888 3.128242 CGTACTCCCAGACGATGTTTACT 59.872 47.826 0.00 0.00 41.60 2.24
851 894 0.809385 ACACGTACTCCCAGACGATG 59.191 55.000 0.89 0.00 41.60 3.84
854 897 0.594602 TCAACACGTACTCCCAGACG 59.405 55.000 0.00 0.00 44.57 4.18
857 900 2.609737 GGTTCTCAACACGTACTCCCAG 60.610 54.545 0.00 0.00 0.00 4.45
860 903 2.295349 TCTGGTTCTCAACACGTACTCC 59.705 50.000 0.00 0.00 0.00 3.85
861 904 3.637998 TCTGGTTCTCAACACGTACTC 57.362 47.619 0.00 0.00 0.00 2.59
862 905 3.492137 GGTTCTGGTTCTCAACACGTACT 60.492 47.826 0.00 0.00 0.00 2.73
907 954 0.041386 AACCTAGGGCTTCGACCTCT 59.959 55.000 14.81 0.00 35.03 3.69
1129 1178 4.665833 TGAGTATATTCACGTCCTTGGG 57.334 45.455 0.00 0.00 0.00 4.12
1217 1266 4.865761 GCACGTATCTCCCGCGCA 62.866 66.667 8.75 0.00 33.83 6.09
1222 1271 0.462047 CCTTGTGGCACGTATCTCCC 60.462 60.000 13.77 0.00 0.00 4.30
1273 1322 3.322254 CACTGAGAGGGCGGATTTATAGT 59.678 47.826 0.00 0.00 0.00 2.12
1332 1381 3.978373 CGAGTATGTCGGTCGTGC 58.022 61.111 0.00 0.00 45.58 5.34
1470 1523 1.681166 GGCATGAACACTCAGGAGCAT 60.681 52.381 0.00 0.00 35.30 3.79
1475 1528 1.735386 CTCTGGCATGAACACTCAGG 58.265 55.000 0.00 0.00 36.42 3.86
1490 1543 4.391216 CGAATGAAAGGCCATATAGCTCTG 59.609 45.833 5.01 0.00 0.00 3.35
1511 1566 7.603651 ACTATAAGAAAGAAAAGAGCAGTCGA 58.396 34.615 0.00 0.00 0.00 4.20
1563 1618 7.515684 GCATGTCAGAGTTTTGTTCAAAATCAC 60.516 37.037 12.71 8.25 41.16 3.06
1613 1668 3.767230 CGCTGTCAGTTGCCGTCG 61.767 66.667 0.93 0.00 0.00 5.12
1623 1678 2.041115 CGGTCCTCTCTCGCTGTCA 61.041 63.158 0.00 0.00 0.00 3.58
1631 1686 0.905337 CCTGGTTTCCGGTCCTCTCT 60.905 60.000 0.00 0.00 0.00 3.10
1684 1739 6.604735 AGTGCATTTCATCGAAATACCTAC 57.395 37.500 1.83 0.90 39.82 3.18
1690 1745 4.319766 GCGGATAGTGCATTTCATCGAAAT 60.320 41.667 0.00 0.00 42.14 2.17
1761 1816 4.929211 TCATCTGTTATGGTTCTGTCAACG 59.071 41.667 0.00 0.00 0.00 4.10
1769 1824 4.200092 GGTTCCCTCATCTGTTATGGTTC 58.800 47.826 0.00 0.00 0.00 3.62
1776 1831 2.290577 GCTTCTGGTTCCCTCATCTGTT 60.291 50.000 0.00 0.00 0.00 3.16
1790 1845 1.241165 TGTCAGTGCATTGCTTCTGG 58.759 50.000 23.30 12.22 34.34 3.86
1888 1943 0.827089 TGCCCACATTGTCCAACAGG 60.827 55.000 0.00 0.00 0.00 4.00
2044 2099 3.666116 AGCTACCTATACCCTATCCACCA 59.334 47.826 0.00 0.00 0.00 4.17
2045 2100 4.334208 AGCTACCTATACCCTATCCACC 57.666 50.000 0.00 0.00 0.00 4.61
2061 2116 6.401047 AAAAAGGTAAGGGAAACAAGCTAC 57.599 37.500 0.00 0.00 0.00 3.58
2157 2212 3.006940 TGACACAGGAGAAACACAACAC 58.993 45.455 0.00 0.00 0.00 3.32
2307 2365 5.615289 AGAACGAGGGAATATCAAATCCAG 58.385 41.667 0.00 0.00 37.46 3.86
2416 2524 8.821686 ATGTATATTTCCTTGTGAATGTGGAA 57.178 30.769 0.00 0.00 36.87 3.53
2447 2555 2.607038 CCTCGATTCTGACACACGTTGA 60.607 50.000 5.01 0.00 0.00 3.18
2460 2568 2.168521 TCCACTGAATCCACCTCGATTC 59.831 50.000 4.70 4.70 45.59 2.52
2582 2697 2.223502 GCATATCTGTTCACCTCGACGA 60.224 50.000 0.00 0.00 0.00 4.20
2659 2774 1.202417 CGCCACGGATGACTACAGAAT 60.202 52.381 0.00 0.00 0.00 2.40
2666 2781 2.494918 GCTACGCCACGGATGACT 59.505 61.111 0.00 0.00 0.00 3.41
2667 2782 2.954868 CGCTACGCCACGGATGAC 60.955 66.667 0.00 0.00 0.00 3.06
2684 2799 2.750888 ATTTTTCGCCCGAGCTCGC 61.751 57.895 30.49 16.74 38.18 5.03
2685 2800 1.060937 CATTTTTCGCCCGAGCTCG 59.939 57.895 29.06 29.06 36.60 5.03
2686 2801 1.226407 GCATTTTTCGCCCGAGCTC 60.226 57.895 2.73 2.73 36.60 4.09
2687 2802 2.700773 GGCATTTTTCGCCCGAGCT 61.701 57.895 0.00 0.00 44.22 4.09
2688 2803 2.202610 GGCATTTTTCGCCCGAGC 60.203 61.111 0.00 0.00 44.22 5.03
2694 2809 0.179174 CCCGTACAGGCATTTTTCGC 60.179 55.000 0.00 0.00 39.21 4.70
2695 2810 1.135803 CACCCGTACAGGCATTTTTCG 60.136 52.381 0.00 0.00 39.21 3.46
2696 2811 1.402325 GCACCCGTACAGGCATTTTTC 60.402 52.381 0.00 0.00 39.21 2.29
2697 2812 0.601057 GCACCCGTACAGGCATTTTT 59.399 50.000 0.00 0.00 39.21 1.94
2698 2813 1.582610 CGCACCCGTACAGGCATTTT 61.583 55.000 0.00 0.00 39.21 1.82
2699 2814 2.038269 CGCACCCGTACAGGCATTT 61.038 57.895 0.00 0.00 39.21 2.32
2700 2815 2.435938 CGCACCCGTACAGGCATT 60.436 61.111 0.00 0.00 39.21 3.56
2701 2816 4.467084 CCGCACCCGTACAGGCAT 62.467 66.667 0.00 0.00 39.21 4.40
2704 2819 4.752879 CACCCGCACCCGTACAGG 62.753 72.222 0.00 0.00 40.63 4.00
2705 2820 3.687102 TCACCCGCACCCGTACAG 61.687 66.667 0.00 0.00 0.00 2.74
2706 2821 3.993584 GTCACCCGCACCCGTACA 61.994 66.667 0.00 0.00 0.00 2.90
2707 2822 4.747529 GGTCACCCGCACCCGTAC 62.748 72.222 0.00 0.00 0.00 3.67
2724 2839 4.814294 GTGCCTGTAGCCGGTCCG 62.814 72.222 3.60 3.60 42.71 4.79
2725 2840 4.468689 GGTGCCTGTAGCCGGTCC 62.469 72.222 1.90 0.00 42.71 4.46
2726 2841 4.814294 CGGTGCCTGTAGCCGGTC 62.814 72.222 1.90 0.00 42.71 4.79
2979 3094 3.077556 AGGATCCTCAACGCCGCT 61.078 61.111 9.02 0.00 0.00 5.52
2980 3095 2.892425 CAGGATCCTCAACGCCGC 60.892 66.667 12.69 0.00 0.00 6.53
2981 3096 1.811266 CACAGGATCCTCAACGCCG 60.811 63.158 12.69 0.73 0.00 6.46
2982 3097 0.741221 GACACAGGATCCTCAACGCC 60.741 60.000 12.69 0.00 0.00 5.68
2983 3098 0.037326 TGACACAGGATCCTCAACGC 60.037 55.000 12.69 1.14 0.00 4.84
2984 3099 1.673033 GGTGACACAGGATCCTCAACG 60.673 57.143 12.69 2.85 0.00 4.10
2985 3100 1.673033 CGGTGACACAGGATCCTCAAC 60.673 57.143 12.69 9.08 0.00 3.18
2986 3101 0.608130 CGGTGACACAGGATCCTCAA 59.392 55.000 12.69 0.00 0.00 3.02
2987 3102 1.257750 CCGGTGACACAGGATCCTCA 61.258 60.000 18.91 4.01 35.32 3.86
2988 3103 1.258445 ACCGGTGACACAGGATCCTC 61.258 60.000 28.57 0.81 36.90 3.71
2989 3104 1.229209 ACCGGTGACACAGGATCCT 60.229 57.895 28.57 9.02 36.90 3.24
2990 3105 1.079127 CACCGGTGACACAGGATCC 60.079 63.158 31.31 2.48 36.90 3.36
2991 3106 1.972198 TCACCGGTGACACAGGATC 59.028 57.895 33.23 0.24 36.90 3.36
2992 3107 4.208426 TCACCGGTGACACAGGAT 57.792 55.556 33.23 11.94 36.90 3.24
3004 3119 2.261671 CTGTTCCTCCCGTCACCG 59.738 66.667 0.00 0.00 0.00 4.94
3005 3120 2.047179 GCTGTTCCTCCCGTCACC 60.047 66.667 0.00 0.00 0.00 4.02
3006 3121 2.047179 GGCTGTTCCTCCCGTCAC 60.047 66.667 0.00 0.00 0.00 3.67
3007 3122 3.691342 CGGCTGTTCCTCCCGTCA 61.691 66.667 0.00 0.00 37.36 4.35
3008 3123 4.452733 CCGGCTGTTCCTCCCGTC 62.453 72.222 0.00 0.00 40.38 4.79
3013 3128 2.686106 TACCCCCGGCTGTTCCTC 60.686 66.667 0.00 0.00 0.00 3.71
3014 3129 3.007323 GTACCCCCGGCTGTTCCT 61.007 66.667 0.00 0.00 0.00 3.36
3015 3130 4.105553 GGTACCCCCGGCTGTTCC 62.106 72.222 0.00 0.00 0.00 3.62
3016 3131 3.007323 AGGTACCCCCGGCTGTTC 61.007 66.667 8.74 0.00 38.74 3.18
3017 3132 3.327404 CAGGTACCCCCGGCTGTT 61.327 66.667 8.74 0.00 38.74 3.16
3018 3133 2.752036 TAACAGGTACCCCCGGCTGT 62.752 60.000 8.74 1.88 38.74 4.40
3019 3134 1.555477 TTAACAGGTACCCCCGGCTG 61.555 60.000 8.74 1.15 38.74 4.85
3020 3135 0.841594 TTTAACAGGTACCCCCGGCT 60.842 55.000 8.74 0.00 38.74 5.52
3021 3136 0.038021 TTTTAACAGGTACCCCCGGC 59.962 55.000 8.74 0.00 38.74 6.13
3022 3137 1.073603 TGTTTTAACAGGTACCCCCGG 59.926 52.381 8.74 0.00 38.74 5.73
3023 3138 2.565046 TGTTTTAACAGGTACCCCCG 57.435 50.000 8.74 0.00 38.74 5.73


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

AutoCloner maintained by Alex Coulton.