Multiple sequence alignment - TraesCS5A01G420500

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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 TraesCS5A01G420500 chr5A 100.000 3916 0 0 1 3916 606961564 606957649 0.000000e+00 7232
1 TraesCS5A01G420500 chr5D 88.449 4043 254 98 1 3916 486445208 486441252 0.000000e+00 4682
2 TraesCS5A01G420500 chr5B 92.597 2391 140 19 971 3335 597855581 597853202 0.000000e+00 3400
3 TraesCS5A01G420500 chr5B 86.310 935 67 23 4 924 597860081 597859194 0.000000e+00 961
4 TraesCS5A01G420500 chr5B 83.263 472 50 11 3471 3916 597853132 597852664 1.310000e-109 407
5 TraesCS5A01G420500 chr5B 84.247 146 15 5 502 639 676300729 676300584 6.830000e-28 135
6 TraesCS5A01G420500 chr2B 86.301 146 12 5 502 639 764724457 764724312 6.780000e-33 152
7 TraesCS5A01G420500 chr2B 84.138 145 16 4 502 639 40808108 40808252 2.450000e-27 134
8 TraesCS5A01G420500 chr4A 85.235 149 11 4 504 651 133946724 133946862 4.080000e-30 143
9 TraesCS5A01G420500 chr7B 84.828 145 15 5 502 639 689375648 689375504 5.280000e-29 139
10 TraesCS5A01G420500 chr7B 83.673 147 14 5 502 639 604533877 604533732 3.180000e-26 130
11 TraesCS5A01G420500 chr4B 88.889 117 6 4 530 639 402224160 402224044 1.900000e-28 137
12 TraesCS5A01G420500 chr3B 88.793 116 7 3 530 639 710462767 710462652 1.900000e-28 137
13 TraesCS5A01G420500 chr1B 82.192 146 18 5 502 639 41211391 41211246 6.870000e-23 119


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 TraesCS5A01G420500 chr5A 606957649 606961564 3915 True 7232.000000 7232 100.000 1 3916 1 chr5A.!!$R1 3915
1 TraesCS5A01G420500 chr5D 486441252 486445208 3956 True 4682.000000 4682 88.449 1 3916 1 chr5D.!!$R1 3915
2 TraesCS5A01G420500 chr5B 597852664 597860081 7417 True 1589.333333 3400 87.390 4 3916 3 chr5B.!!$R2 3912

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
65 66 0.101040 CACATAAGCCAACATGCGGG 59.899 55.0 4.06 1.55 36.02 6.13 F
229 253 0.106708 AACGAGCCTGAAGTCAAGCA 59.893 50.0 4.79 0.00 35.83 3.91 F
1887 5544 0.179067 TCTTGGTGTGTTCGGTGTCC 60.179 55.0 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 5544 0.656259 CAGCATCAGCATCAACCTCG 59.344 55.0 0.0 0.0 45.49 4.63 R
2150 5807 0.464373 TGAAATGCCAGGATCGAGCC 60.464 55.0 13.0 13.0 0.00 4.70 R
3401 7093 0.251564 TCCCAAACCATCGCCACATT 60.252 50.0 0.0 0.0 0.00 2.71 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 7.872113 AAGGAAGAGCTAATGTCATTTTAGG 57.128 36.000 2.79 0.00 0.00 2.69
28 29 5.825151 AGGAAGAGCTAATGTCATTTTAGGC 59.175 40.000 2.79 4.28 0.00 3.93
29 30 5.825151 GGAAGAGCTAATGTCATTTTAGGCT 59.175 40.000 2.79 8.65 0.00 4.58
31 32 5.128919 AGAGCTAATGTCATTTTAGGCTGG 58.871 41.667 2.79 0.00 0.00 4.85
32 33 4.860022 AGCTAATGTCATTTTAGGCTGGT 58.140 39.130 2.79 0.00 0.00 4.00
33 34 6.001449 AGCTAATGTCATTTTAGGCTGGTA 57.999 37.500 2.79 0.00 0.00 3.25
34 35 6.058183 AGCTAATGTCATTTTAGGCTGGTAG 58.942 40.000 2.79 0.00 0.00 3.18
37 38 7.254932 GCTAATGTCATTTTAGGCTGGTAGAAG 60.255 40.741 2.79 0.00 0.00 2.85
65 66 0.101040 CACATAAGCCAACATGCGGG 59.899 55.000 4.06 1.55 36.02 6.13
79 80 1.284715 GCGGGTTAAGTTGGTGTGC 59.715 57.895 0.00 0.00 0.00 4.57
107 111 3.600388 CCAAGACCACATAACTCAGACC 58.400 50.000 0.00 0.00 0.00 3.85
120 124 5.779241 AACTCAGACCCAATTAATCCTGA 57.221 39.130 0.00 0.00 0.00 3.86
130 154 7.344134 ACCCAATTAATCCTGAAACCTAGTAC 58.656 38.462 0.00 0.00 0.00 2.73
139 163 5.887598 TCCTGAAACCTAGTACGTAATAGCA 59.112 40.000 21.57 13.92 0.00 3.49
156 180 5.977489 ATAGCAAACCCTGAACTTTTACC 57.023 39.130 0.00 0.00 0.00 2.85
159 183 3.243737 GCAAACCCTGAACTTTTACCTGG 60.244 47.826 0.00 0.00 0.00 4.45
161 185 3.503800 ACCCTGAACTTTTACCTGGTC 57.496 47.619 0.63 0.00 0.00 4.02
164 188 3.412386 CCTGAACTTTTACCTGGTCCAG 58.588 50.000 12.40 12.40 0.00 3.86
169 193 6.001460 TGAACTTTTACCTGGTCCAGTATTG 58.999 40.000 17.85 4.79 0.00 1.90
170 194 5.578157 ACTTTTACCTGGTCCAGTATTGT 57.422 39.130 17.85 10.49 0.00 2.71
171 195 5.313712 ACTTTTACCTGGTCCAGTATTGTG 58.686 41.667 17.85 3.69 0.00 3.33
179 203 6.208599 ACCTGGTCCAGTATTGTGTTAAATTG 59.791 38.462 17.85 0.00 0.00 2.32
199 223 3.000041 TGCAACAAGTCTATTAGGCACG 59.000 45.455 0.00 0.00 0.00 5.34
201 225 3.682858 GCAACAAGTCTATTAGGCACGAA 59.317 43.478 0.00 0.00 0.00 3.85
224 248 4.213482 ACACATTTAAACGAGCCTGAAGTC 59.787 41.667 0.00 0.00 0.00 3.01
226 250 4.819630 ACATTTAAACGAGCCTGAAGTCAA 59.180 37.500 0.00 0.00 0.00 3.18
227 251 5.049405 ACATTTAAACGAGCCTGAAGTCAAG 60.049 40.000 0.00 0.00 0.00 3.02
228 252 1.230324 AAACGAGCCTGAAGTCAAGC 58.770 50.000 0.00 0.00 33.65 4.01
229 253 0.106708 AACGAGCCTGAAGTCAAGCA 59.893 50.000 4.79 0.00 35.83 3.91
230 254 0.320247 ACGAGCCTGAAGTCAAGCAG 60.320 55.000 4.79 1.27 35.83 4.24
234 258 3.547567 CCTGAAGTCAAGCAGGGAG 57.452 57.895 0.00 0.00 46.24 4.30
264 288 1.071471 CACCTTGGGCGTGAAGAGT 59.929 57.895 0.00 0.00 32.77 3.24
408 432 4.640690 ACCTCCTCCACCACCGCT 62.641 66.667 0.00 0.00 0.00 5.52
456 480 1.550524 TCCACCTCCGTCTTCATCTTG 59.449 52.381 0.00 0.00 0.00 3.02
533 567 4.508128 GCGAATCGACGGGGAGCA 62.508 66.667 6.91 0.00 0.00 4.26
775 834 3.086282 GGTTTTGGAGGATTTAGCGGAA 58.914 45.455 0.00 0.00 0.00 4.30
779 838 2.467880 TGGAGGATTTAGCGGAAGAGT 58.532 47.619 0.00 0.00 0.00 3.24
817 876 2.128853 CTCGCGGCAGAGGAGATCTC 62.129 65.000 14.75 14.75 42.75 2.75
850 909 2.645567 CGGAGCGAGTGTGTGACT 59.354 61.111 0.00 0.00 37.76 3.41
851 910 1.730902 CGGAGCGAGTGTGTGACTG 60.731 63.158 0.00 0.00 33.83 3.51
852 911 1.373497 GGAGCGAGTGTGTGACTGG 60.373 63.158 0.00 0.00 33.83 4.00
855 914 4.436515 CGAGTGTGTGACTGGCAA 57.563 55.556 0.00 0.00 33.83 4.52
856 915 2.229039 CGAGTGTGTGACTGGCAAG 58.771 57.895 0.00 0.00 33.83 4.01
857 916 1.835483 CGAGTGTGTGACTGGCAAGC 61.835 60.000 0.00 0.00 33.83 4.01
893 952 3.389002 AGGCGGGTTACGTATTCCTAAAT 59.611 43.478 14.19 1.01 46.52 1.40
896 955 5.177511 GGCGGGTTACGTATTCCTAAATTAC 59.822 44.000 14.19 0.00 46.52 1.89
897 956 5.107875 GCGGGTTACGTATTCCTAAATTACG 60.108 44.000 14.19 9.74 46.52 3.18
898 957 5.107875 CGGGTTACGTATTCCTAAATTACGC 60.108 44.000 14.19 5.77 37.63 4.42
900 959 5.985530 GGTTACGTATTCCTAAATTACGCCT 59.014 40.000 0.00 0.00 37.63 5.52
903 962 5.287226 ACGTATTCCTAAATTACGCCTCTG 58.713 41.667 0.00 0.00 37.63 3.35
904 963 5.068198 ACGTATTCCTAAATTACGCCTCTGA 59.932 40.000 0.00 0.00 37.63 3.27
905 964 5.981315 CGTATTCCTAAATTACGCCTCTGAA 59.019 40.000 0.00 0.00 0.00 3.02
906 965 6.074463 CGTATTCCTAAATTACGCCTCTGAAC 60.074 42.308 0.00 0.00 0.00 3.18
936 4584 3.060895 GTGTTCTTCATTCTACGCCTTCG 59.939 47.826 0.00 0.00 42.43 3.79
941 4589 0.179145 CATTCTACGCCTTCGGTCGT 60.179 55.000 7.33 7.33 40.69 4.34
950 4598 1.129811 GCCTTCGGTCGTTTAATGTGG 59.870 52.381 0.00 0.00 0.00 4.17
951 4599 2.690786 CCTTCGGTCGTTTAATGTGGA 58.309 47.619 0.00 0.00 0.00 4.02
952 4600 3.267483 CCTTCGGTCGTTTAATGTGGAT 58.733 45.455 0.00 0.00 0.00 3.41
953 4601 3.308866 CCTTCGGTCGTTTAATGTGGATC 59.691 47.826 0.00 0.00 0.00 3.36
954 4602 2.896168 TCGGTCGTTTAATGTGGATCC 58.104 47.619 4.20 4.20 0.00 3.36
955 4603 1.591158 CGGTCGTTTAATGTGGATCCG 59.409 52.381 7.39 0.00 0.00 4.18
956 4604 2.624636 GGTCGTTTAATGTGGATCCGT 58.375 47.619 7.39 0.00 0.00 4.69
957 4605 2.350498 GGTCGTTTAATGTGGATCCGTG 59.650 50.000 7.39 0.00 0.00 4.94
958 4606 3.255725 GTCGTTTAATGTGGATCCGTGA 58.744 45.455 7.39 0.00 0.00 4.35
959 4607 3.306166 GTCGTTTAATGTGGATCCGTGAG 59.694 47.826 7.39 0.00 0.00 3.51
1449 5106 2.741211 GTCGGCTTCGGGGTGTTC 60.741 66.667 0.00 0.00 34.13 3.18
1512 5169 3.049674 CTGGTGAACGCGGTGCAT 61.050 61.111 12.47 0.00 0.00 3.96
1623 5280 3.394606 GGGCTTTGGAGGATATGAGGTTA 59.605 47.826 0.00 0.00 0.00 2.85
1647 5304 1.134946 GGATGGAAGCCGGATTTTGTG 59.865 52.381 6.32 0.00 24.31 3.33
1751 5408 2.807247 GTGTTGCACCAAGGAAGGT 58.193 52.632 0.00 0.00 44.48 3.50
1857 5514 3.788797 GCGATTTCCCAATTGATGACGAC 60.789 47.826 7.12 0.00 0.00 4.34
1875 5532 2.155732 CGACGTGTTGAATCTCTTGGTG 59.844 50.000 0.00 0.00 0.00 4.17
1887 5544 0.179067 TCTTGGTGTGTTCGGTGTCC 60.179 55.000 0.00 0.00 0.00 4.02
1908 5565 1.035932 AGGTTGATGCTGATGCTGCC 61.036 55.000 0.00 0.00 40.48 4.85
2005 5662 1.533513 TGCAAGAATGGCAAGGGCA 60.534 52.632 0.00 0.00 46.27 5.36
2150 5807 9.672673 TGTGATAAAGGAGATAAAAAGGAAGAG 57.327 33.333 0.00 0.00 0.00 2.85
2154 5811 5.366482 AGGAGATAAAAAGGAAGAGGCTC 57.634 43.478 6.34 6.34 0.00 4.70
2230 5887 2.769095 CTCCTTAGGCCTGCTAAGAAGT 59.231 50.000 17.99 0.00 36.74 3.01
2544 6201 5.539193 AGGTATTCCTGTCCTCGTTATTAGG 59.461 44.000 0.00 0.00 43.33 2.69
2545 6202 5.303845 GGTATTCCTGTCCTCGTTATTAGGT 59.696 44.000 0.00 0.00 35.48 3.08
2546 6203 6.491403 GGTATTCCTGTCCTCGTTATTAGGTA 59.509 42.308 0.00 0.00 35.48 3.08
2547 6204 7.178097 GGTATTCCTGTCCTCGTTATTAGGTAT 59.822 40.741 0.00 0.00 35.48 2.73
2548 6205 7.613551 ATTCCTGTCCTCGTTATTAGGTATT 57.386 36.000 0.00 0.00 35.48 1.89
2549 6206 8.716674 ATTCCTGTCCTCGTTATTAGGTATTA 57.283 34.615 0.00 0.00 35.48 0.98
2556 6213 6.872020 TCCTCGTTATTAGGTATTATTGCTGC 59.128 38.462 0.00 0.00 35.48 5.25
2561 6218 9.807386 CGTTATTAGGTATTATTGCTGCTTTAC 57.193 33.333 0.00 0.00 0.00 2.01
2572 6229 6.833342 ATTGCTGCTTTACTTTTTCTGTTG 57.167 33.333 0.00 0.00 0.00 3.33
2588 6245 8.740123 TTTTCTGTTGTCTCCTTGTAAATGTA 57.260 30.769 0.00 0.00 0.00 2.29
2589 6246 8.740123 TTTCTGTTGTCTCCTTGTAAATGTAA 57.260 30.769 0.00 0.00 0.00 2.41
2665 6323 5.700373 GTCTTCCATCCAATATTGAGAGCTC 59.300 44.000 17.23 5.27 0.00 4.09
2678 6336 3.930336 TGAGAGCTCGAATTCACATGTT 58.070 40.909 8.37 0.00 0.00 2.71
2714 6372 5.183904 GTGCCTAACAGATGTTGAGGAAATT 59.816 40.000 17.85 0.00 38.90 1.82
2729 6387 5.539574 TGAGGAAATTGAAATGGCTTCTGAA 59.460 36.000 0.00 0.00 34.86 3.02
2834 6492 1.494721 AGCCTTCAACCTGTCAGGAAA 59.505 47.619 26.18 14.34 37.67 3.13
2891 6549 1.753073 GAAGTTGGCCCATGGATGAAG 59.247 52.381 15.22 0.00 0.00 3.02
2923 6581 6.879276 AGATGATTATGCTTGAATCACAGG 57.121 37.500 9.65 0.00 44.03 4.00
2941 6599 7.135591 TCACAGGTTCAATGGTCATATCATA 57.864 36.000 0.00 0.00 0.00 2.15
2942 6600 7.748677 TCACAGGTTCAATGGTCATATCATAT 58.251 34.615 0.00 0.00 0.00 1.78
2973 6631 2.367894 TGTCCATTTTGCCAAGAATGCA 59.632 40.909 0.00 0.00 36.84 3.96
2975 6633 2.367894 TCCATTTTGCCAAGAATGCACA 59.632 40.909 0.00 0.00 38.72 4.57
2978 6636 4.319911 CCATTTTGCCAAGAATGCACAAAG 60.320 41.667 0.00 0.00 38.72 2.77
2983 6641 2.035066 GCCAAGAATGCACAAAGTGTCT 59.965 45.455 0.00 0.00 35.75 3.41
2989 6647 4.274459 AGAATGCACAAAGTGTCTTGAGAC 59.726 41.667 4.20 4.20 44.97 3.36
3030 6688 3.753272 AGTGCATTACTTCACAAAGCGAT 59.247 39.130 0.00 0.00 35.67 4.58
3045 6703 5.992217 ACAAAGCGATATTGATACTTCCCTC 59.008 40.000 0.00 0.00 0.00 4.30
3054 6712 4.613925 TGATACTTCCCTCTGATGCATC 57.386 45.455 20.14 20.14 0.00 3.91
3055 6713 4.229639 TGATACTTCCCTCTGATGCATCT 58.770 43.478 26.32 6.41 0.00 2.90
3075 6734 7.496920 TGCATCTAGTTCTCAGAATTACCAATG 59.503 37.037 0.00 0.00 0.00 2.82
3077 6736 9.258826 CATCTAGTTCTCAGAATTACCAATGAG 57.741 37.037 0.00 0.00 40.42 2.90
3094 6753 6.127897 ACCAATGAGAAAATGACCGAGATTTC 60.128 38.462 0.00 0.00 33.13 2.17
3096 6755 6.674694 ATGAGAAAATGACCGAGATTTCTG 57.325 37.500 4.50 0.00 41.00 3.02
3125 6786 5.426689 TCTGGTTTGTGCTGATCTATTCT 57.573 39.130 0.00 0.00 0.00 2.40
3135 6796 4.347292 TGCTGATCTATTCTGAGCAATCCT 59.653 41.667 0.00 0.00 36.74 3.24
3153 6816 6.319658 GCAATCCTGAGGTATCATTTCTTTCA 59.680 38.462 0.00 0.00 34.12 2.69
3159 6822 7.201679 CCTGAGGTATCATTTCTTTCACATCAC 60.202 40.741 0.00 0.00 34.12 3.06
3175 6838 6.273071 TCACATCACCATTTACTGTAGATCG 58.727 40.000 0.00 0.00 0.00 3.69
3183 6846 9.745880 CACCATTTACTGTAGATCGTTAGTATT 57.254 33.333 6.77 0.00 0.00 1.89
3219 6890 9.793252 ATGATTATGTGACTTCTGTAATTTTGC 57.207 29.630 0.00 0.00 0.00 3.68
3220 6891 8.791675 TGATTATGTGACTTCTGTAATTTTGCA 58.208 29.630 0.00 0.00 0.00 4.08
3235 6918 1.323271 TTGCACCTTTTCGCCCACAA 61.323 50.000 0.00 0.00 0.00 3.33
3249 6932 3.303329 CGCCCACAAATATCATCAAGACG 60.303 47.826 0.00 0.00 0.00 4.18
3254 6937 6.018425 CCCACAAATATCATCAAGACGAAGAG 60.018 42.308 0.00 0.00 0.00 2.85
3283 6972 8.518430 AGTTGTCATTTGTGCACCATATTATA 57.482 30.769 15.69 0.00 0.00 0.98
3284 6973 9.135189 AGTTGTCATTTGTGCACCATATTATAT 57.865 29.630 15.69 0.00 0.00 0.86
3305 6994 9.942850 TTATATGGAAATTATTCATCTCAGCGA 57.057 29.630 0.00 0.00 37.29 4.93
3308 6997 5.879777 TGGAAATTATTCATCTCAGCGACAA 59.120 36.000 0.00 0.00 37.29 3.18
3310 6999 6.854892 GGAAATTATTCATCTCAGCGACAATG 59.145 38.462 0.00 0.00 37.29 2.82
3329 7018 2.023673 TGTCTTCTGGTTGCAGGTTTG 58.976 47.619 0.00 0.00 0.00 2.93
3334 7023 3.625897 GGTTGCAGGTTTGGGGCC 61.626 66.667 0.00 0.00 0.00 5.80
3355 7044 4.095036 GCCACTGTTCTATTTTGCTCCTAC 59.905 45.833 0.00 0.00 0.00 3.18
3382 7074 7.118971 TGCAAAATAAATCTGGTGTTTATTGGC 59.881 33.333 14.60 14.60 39.53 4.52
3384 7076 6.865834 AATAAATCTGGTGTTTATTGGCCA 57.134 33.333 0.00 0.00 39.19 5.36
3407 7099 2.653726 TGCTTGGCTGGTATAATGTGG 58.346 47.619 0.00 0.00 0.00 4.17
3416 7108 3.882888 CTGGTATAATGTGGCGATGGTTT 59.117 43.478 0.00 0.00 0.00 3.27
3488 7180 3.879295 ACTTCATTATGATGGTTCTGCCG 59.121 43.478 11.83 0.00 41.21 5.69
3493 7185 0.833287 ATGATGGTTCTGCCGCTACT 59.167 50.000 0.00 0.00 41.21 2.57
3508 7200 2.654863 GCTACTGTGGGTATGCCAATT 58.345 47.619 1.04 0.00 36.17 2.32
3514 7206 1.034838 TGGGTATGCCAATTGCGGTC 61.035 55.000 1.04 0.00 45.60 4.79
3519 7217 0.683828 ATGCCAATTGCGGTCATGGA 60.684 50.000 0.00 0.00 45.60 3.41
3610 7308 3.760151 TCAAGGCAATTCTTGTCCATCTG 59.240 43.478 6.74 0.00 43.25 2.90
3620 7318 2.094100 TGTCCATCTGATCTCCTCCC 57.906 55.000 0.00 0.00 0.00 4.30
3635 7339 1.305633 TCCCCCTCAGAGACTGCTG 60.306 63.158 0.00 0.00 37.24 4.41
3644 7348 3.987547 TCAGAGACTGCTGAAAGTTCTG 58.012 45.455 0.00 3.34 41.65 3.02
3660 7388 1.898574 CTGTGAGGGTTGGTGGCAC 60.899 63.158 9.70 9.70 0.00 5.01
3681 7409 2.309528 TTCACGATGGCATCCTACAC 57.690 50.000 21.20 0.00 0.00 2.90
3684 7412 1.134699 CACGATGGCATCCTACACTGT 60.135 52.381 21.20 8.81 0.00 3.55
3727 7457 6.040054 TGGATTCAGCTTGATTTATGTCATGG 59.960 38.462 0.00 0.00 0.00 3.66
3765 7495 4.634199 CTGCACTCCATTTTTGGAATTGT 58.366 39.130 0.00 0.00 37.55 2.71
3766 7496 5.782047 CTGCACTCCATTTTTGGAATTGTA 58.218 37.500 0.00 0.00 37.55 2.41
3785 7515 4.055360 TGTACATCGAGTTTCTGTGGTTG 58.945 43.478 0.00 0.00 0.00 3.77
3788 7518 1.124780 TCGAGTTTCTGTGGTTGGGA 58.875 50.000 0.00 0.00 0.00 4.37
3836 7566 3.186909 TGTCGACATTTTAGATGCCTCG 58.813 45.455 15.76 0.00 0.00 4.63
3837 7567 2.540101 GTCGACATTTTAGATGCCTCGG 59.460 50.000 11.55 0.00 0.00 4.63
3858 7588 4.489810 GGTAGATTGTCCATAGATGCTCG 58.510 47.826 0.00 0.00 0.00 5.03
3859 7589 4.021894 GGTAGATTGTCCATAGATGCTCGT 60.022 45.833 0.00 0.00 0.00 4.18
3869 7599 1.267121 AGATGCTCGTAGGTGTGGTT 58.733 50.000 0.00 0.00 0.00 3.67
3877 7607 2.028476 TCGTAGGTGTGGTTCTGGATTG 60.028 50.000 0.00 0.00 0.00 2.67
3912 7642 8.251750 TGTTACTCAAGCATGTTGTATACTTC 57.748 34.615 4.17 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.884164 ACCAGCCTAAAATGACATTAGCTC 59.116 41.667 0.00 0.00 0.00 4.09
24 25 0.323999 TCCGCACTTCTACCAGCCTA 60.324 55.000 0.00 0.00 0.00 3.93
25 26 1.192146 TTCCGCACTTCTACCAGCCT 61.192 55.000 0.00 0.00 0.00 4.58
27 28 1.291132 GATTCCGCACTTCTACCAGC 58.709 55.000 0.00 0.00 0.00 4.85
28 29 2.271800 GTGATTCCGCACTTCTACCAG 58.728 52.381 0.00 0.00 35.91 4.00
29 30 1.621317 TGTGATTCCGCACTTCTACCA 59.379 47.619 0.00 0.00 39.49 3.25
31 32 4.025647 GCTTATGTGATTCCGCACTTCTAC 60.026 45.833 0.00 0.00 39.49 2.59
32 33 4.119862 GCTTATGTGATTCCGCACTTCTA 58.880 43.478 0.00 0.00 39.49 2.10
33 34 2.939103 GCTTATGTGATTCCGCACTTCT 59.061 45.455 0.00 0.00 39.49 2.85
34 35 2.032178 GGCTTATGTGATTCCGCACTTC 59.968 50.000 0.00 0.00 39.49 3.01
37 38 1.378531 TGGCTTATGTGATTCCGCAC 58.621 50.000 0.00 0.00 39.22 5.34
79 80 2.556622 GTTATGTGGTCTTGGGTGTTGG 59.443 50.000 0.00 0.00 0.00 3.77
107 111 7.046033 ACGTACTAGGTTTCAGGATTAATTGG 58.954 38.462 0.00 0.00 0.00 3.16
120 124 6.070596 AGGGTTTGCTATTACGTACTAGGTTT 60.071 38.462 18.37 0.00 0.00 3.27
130 154 5.622770 AAAGTTCAGGGTTTGCTATTACG 57.377 39.130 0.00 0.00 0.00 3.18
135 159 4.825085 CAGGTAAAAGTTCAGGGTTTGCTA 59.175 41.667 0.00 0.00 0.00 3.49
137 161 3.243737 CCAGGTAAAAGTTCAGGGTTTGC 60.244 47.826 0.00 0.00 0.00 3.68
139 163 4.212716 GACCAGGTAAAAGTTCAGGGTTT 58.787 43.478 0.00 0.00 0.00 3.27
156 180 6.092748 GCAATTTAACACAATACTGGACCAG 58.907 40.000 20.45 20.45 37.52 4.00
159 183 6.920758 TGTTGCAATTTAACACAATACTGGAC 59.079 34.615 0.59 0.00 33.43 4.02
161 185 7.437862 ACTTGTTGCAATTTAACACAATACTGG 59.562 33.333 0.59 0.00 37.73 4.00
164 188 8.574196 AGACTTGTTGCAATTTAACACAATAC 57.426 30.769 0.59 0.00 37.73 1.89
169 193 9.341899 CCTAATAGACTTGTTGCAATTTAACAC 57.658 33.333 0.59 0.00 37.73 3.32
170 194 8.026607 GCCTAATAGACTTGTTGCAATTTAACA 58.973 33.333 0.59 0.00 36.34 2.41
171 195 8.026607 TGCCTAATAGACTTGTTGCAATTTAAC 58.973 33.333 0.59 0.00 0.00 2.01
179 203 3.259064 TCGTGCCTAATAGACTTGTTGC 58.741 45.455 0.00 0.00 0.00 4.17
199 223 4.742438 TCAGGCTCGTTTAAATGTGTTC 57.258 40.909 7.28 3.04 0.00 3.18
201 225 4.134563 ACTTCAGGCTCGTTTAAATGTGT 58.865 39.130 7.28 0.00 0.00 3.72
228 252 1.186200 TGCTACTACTGCACTCCCTG 58.814 55.000 0.00 0.00 35.31 4.45
229 253 3.691820 TGCTACTACTGCACTCCCT 57.308 52.632 0.00 0.00 35.31 4.20
237 261 0.460284 CGCCCAAGGTGCTACTACTG 60.460 60.000 0.00 0.00 0.00 2.74
238 262 0.903454 ACGCCCAAGGTGCTACTACT 60.903 55.000 0.00 0.00 36.54 2.57
239 263 0.739813 CACGCCCAAGGTGCTACTAC 60.740 60.000 0.00 0.00 36.54 2.73
240 264 0.901114 TCACGCCCAAGGTGCTACTA 60.901 55.000 0.00 0.00 36.54 1.82
244 268 2.281761 CTTCACGCCCAAGGTGCT 60.282 61.111 0.00 0.00 36.54 4.40
264 288 0.324738 AGATCCTCTTCACCGAGCCA 60.325 55.000 0.00 0.00 0.00 4.75
430 454 0.114560 AAGACGGAGGTGGAGGAGAA 59.885 55.000 0.00 0.00 0.00 2.87
456 480 2.300967 TGGTCAGGTGATGCCCTCC 61.301 63.158 0.00 0.00 38.26 4.30
533 567 0.257328 TGAGTCGCCAGATCTCCTCT 59.743 55.000 0.00 0.00 33.14 3.69
775 834 2.545810 CTTCTTCTTCCTCCCCACTCT 58.454 52.381 0.00 0.00 0.00 3.24
779 838 1.203364 AGAGCTTCTTCTTCCTCCCCA 60.203 52.381 0.00 0.00 0.00 4.96
875 934 5.177511 GGCGTAATTTAGGAATACGTAACCC 59.822 44.000 15.41 11.97 36.63 4.11
893 952 4.213270 CACTTTCATTGTTCAGAGGCGTAA 59.787 41.667 0.00 0.00 0.00 3.18
896 955 2.549754 ACACTTTCATTGTTCAGAGGCG 59.450 45.455 0.00 0.00 0.00 5.52
897 956 4.574599 AACACTTTCATTGTTCAGAGGC 57.425 40.909 0.00 0.00 31.30 4.70
904 963 8.070171 CGTAGAATGAAGAACACTTTCATTGTT 58.930 33.333 15.52 8.10 39.94 2.83
905 964 7.576236 CGTAGAATGAAGAACACTTTCATTGT 58.424 34.615 15.52 14.07 33.72 2.71
906 965 6.521133 GCGTAGAATGAAGAACACTTTCATTG 59.479 38.462 15.52 5.18 33.72 2.82
918 4566 2.579207 CCGAAGGCGTAGAATGAAGA 57.421 50.000 0.00 0.00 46.14 2.87
936 4584 2.350498 CACGGATCCACATTAAACGACC 59.650 50.000 13.41 0.00 0.00 4.79
941 4589 2.026729 TGCCTCACGGATCCACATTAAA 60.027 45.455 13.41 0.00 0.00 1.52
1449 5106 3.114616 CTGCCCACACTCTTCGCG 61.115 66.667 0.00 0.00 0.00 5.87
1501 5158 3.195002 CCGATGATGCACCGCGTT 61.195 61.111 4.92 0.00 0.00 4.84
1512 5169 0.690744 TGATCAAGCCCTCCCGATGA 60.691 55.000 0.00 0.00 0.00 2.92
1581 5238 1.607509 CGCCAAGCATCCTCTATCCTG 60.608 57.143 0.00 0.00 0.00 3.86
1623 5280 1.910580 AATCCGGCTTCCATCCACGT 61.911 55.000 0.00 0.00 0.00 4.49
1647 5304 1.082117 CGGACACAATCCTGTACGCC 61.082 60.000 0.00 0.00 46.69 5.68
1751 5408 2.972713 AGCAAAACCTCTCTGTAGTCCA 59.027 45.455 0.00 0.00 0.00 4.02
1857 5514 2.872245 ACACACCAAGAGATTCAACACG 59.128 45.455 0.00 0.00 0.00 4.49
1887 5544 0.656259 CAGCATCAGCATCAACCTCG 59.344 55.000 0.00 0.00 45.49 4.63
1908 5565 8.074370 CCTATCATGAACTTGCAGAACATAATG 58.926 37.037 0.00 0.00 0.00 1.90
2005 5662 7.121759 CACTCTAAACATTTCCCACATCTCATT 59.878 37.037 0.00 0.00 0.00 2.57
2150 5807 0.464373 TGAAATGCCAGGATCGAGCC 60.464 55.000 13.00 13.00 0.00 4.70
2154 5811 4.067192 TGTATGATGAAATGCCAGGATCG 58.933 43.478 0.00 0.00 0.00 3.69
2230 5887 2.374839 TGGTGAACATCTCATCCCACAA 59.625 45.455 0.00 0.00 33.80 3.33
2258 5915 3.902881 AGGTCTGCAGATTTGGACTAG 57.097 47.619 21.47 0.00 0.00 2.57
2365 6022 5.027460 TGTGTATGTTGTACTATCTGGGGT 58.973 41.667 0.00 0.00 0.00 4.95
2367 6024 6.816136 TGATGTGTATGTTGTACTATCTGGG 58.184 40.000 0.00 0.00 0.00 4.45
2544 6201 9.626045 ACAGAAAAAGTAAAGCAGCAATAATAC 57.374 29.630 0.00 0.00 0.00 1.89
2546 6203 8.981647 CAACAGAAAAAGTAAAGCAGCAATAAT 58.018 29.630 0.00 0.00 0.00 1.28
2547 6204 7.978975 ACAACAGAAAAAGTAAAGCAGCAATAA 59.021 29.630 0.00 0.00 0.00 1.40
2548 6205 7.488322 ACAACAGAAAAAGTAAAGCAGCAATA 58.512 30.769 0.00 0.00 0.00 1.90
2549 6206 6.340522 ACAACAGAAAAAGTAAAGCAGCAAT 58.659 32.000 0.00 0.00 0.00 3.56
2556 6213 7.762382 ACAAGGAGACAACAGAAAAAGTAAAG 58.238 34.615 0.00 0.00 0.00 1.85
2561 6218 8.190784 ACATTTACAAGGAGACAACAGAAAAAG 58.809 33.333 0.00 0.00 0.00 2.27
2564 6221 8.740123 TTACATTTACAAGGAGACAACAGAAA 57.260 30.769 0.00 0.00 0.00 2.52
2572 6229 7.110155 TCCAAGGATTACATTTACAAGGAGAC 58.890 38.462 0.00 0.00 0.00 3.36
2619 6277 3.153369 TGACATAACACCCAATGCTGT 57.847 42.857 0.00 0.00 0.00 4.40
2665 6323 8.017373 ACTTCAACAGAATAACATGTGAATTCG 58.983 33.333 20.29 17.91 35.30 3.34
2714 6372 6.265196 ACTTTATGTGTTCAGAAGCCATTTCA 59.735 34.615 0.89 0.00 38.31 2.69
2729 6387 5.086104 AGCGTCTAATCCACTTTATGTGT 57.914 39.130 0.00 0.00 44.81 3.72
2834 6492 7.557719 CCCTGAGAATGTAAATAACAGACCAAT 59.442 37.037 0.00 0.00 42.70 3.16
2923 6581 9.671279 TGGTATCATATGATATGACCATTGAAC 57.329 33.333 25.33 13.63 36.37 3.18
2941 6599 4.160252 GGCAAAATGGACAAGTGGTATCAT 59.840 41.667 0.00 0.00 0.00 2.45
2942 6600 3.509575 GGCAAAATGGACAAGTGGTATCA 59.490 43.478 0.00 0.00 0.00 2.15
2983 6641 2.501723 GCCTGACCTCCAATAGTCTCAA 59.498 50.000 0.00 0.00 34.02 3.02
2989 6647 2.503356 ACTGAAGCCTGACCTCCAATAG 59.497 50.000 0.00 0.00 0.00 1.73
3030 6688 6.499699 AGATGCATCAGAGGGAAGTATCAATA 59.500 38.462 27.81 0.00 38.35 1.90
3045 6703 7.384660 GGTAATTCTGAGAACTAGATGCATCAG 59.615 40.741 27.81 22.52 36.38 2.90
3075 6734 7.596749 TTACAGAAATCTCGGTCATTTTCTC 57.403 36.000 0.00 0.00 36.54 2.87
3077 6736 8.029642 TCTTTACAGAAATCTCGGTCATTTTC 57.970 34.615 0.00 0.00 31.90 2.29
3094 6753 4.756642 TCAGCACAAACCAGATCTTTACAG 59.243 41.667 0.00 0.00 0.00 2.74
3096 6755 5.645497 AGATCAGCACAAACCAGATCTTTAC 59.355 40.000 0.00 0.00 41.82 2.01
3125 6786 5.131642 AGAAATGATACCTCAGGATTGCTCA 59.868 40.000 0.00 0.00 34.12 4.26
3135 6796 6.599244 GGTGATGTGAAAGAAATGATACCTCA 59.401 38.462 0.00 0.00 35.41 3.86
3153 6816 6.222038 ACGATCTACAGTAAATGGTGATGT 57.778 37.500 0.00 0.00 0.00 3.06
3219 6890 3.192422 TGATATTTGTGGGCGAAAAGGTG 59.808 43.478 0.00 0.00 0.00 4.00
3220 6891 3.426615 TGATATTTGTGGGCGAAAAGGT 58.573 40.909 0.00 0.00 0.00 3.50
3249 6932 5.466728 TGCACAAATGACAACTAGACTCTTC 59.533 40.000 0.00 0.00 0.00 2.87
3254 6937 3.563808 TGGTGCACAAATGACAACTAGAC 59.436 43.478 20.43 0.00 0.00 2.59
3283 6972 6.057533 TGTCGCTGAGATGAATAATTTCCAT 58.942 36.000 0.00 0.00 0.00 3.41
3284 6973 5.427378 TGTCGCTGAGATGAATAATTTCCA 58.573 37.500 0.00 0.00 0.00 3.53
3291 6980 5.268118 AGACATTGTCGCTGAGATGAATA 57.732 39.130 11.01 0.00 37.67 1.75
3304 6993 2.227388 CCTGCAACCAGAAGACATTGTC 59.773 50.000 8.82 8.82 41.77 3.18
3305 6994 2.233271 CCTGCAACCAGAAGACATTGT 58.767 47.619 0.00 0.00 41.77 2.71
3308 6997 2.624838 CAAACCTGCAACCAGAAGACAT 59.375 45.455 0.00 0.00 41.77 3.06
3310 6999 1.338020 CCAAACCTGCAACCAGAAGAC 59.662 52.381 0.00 0.00 41.77 3.01
3329 7018 1.204704 GCAAAATAGAACAGTGGCCCC 59.795 52.381 0.00 0.00 0.00 5.80
3334 7023 5.163814 GCAGTAGGAGCAAAATAGAACAGTG 60.164 44.000 0.00 0.00 0.00 3.66
3355 7044 8.658609 CCAATAAACACCAGATTTATTTTGCAG 58.341 33.333 1.01 0.00 39.22 4.41
3361 7053 6.865834 TGGCCAATAAACACCAGATTTATT 57.134 33.333 0.61 0.00 40.98 1.40
3382 7074 5.012239 ACATTATACCAGCCAAGCATATGG 58.988 41.667 4.56 0.00 43.70 2.74
3384 7076 5.012239 CCACATTATACCAGCCAAGCATAT 58.988 41.667 0.00 0.00 0.00 1.78
3401 7093 0.251564 TCCCAAACCATCGCCACATT 60.252 50.000 0.00 0.00 0.00 2.71
3407 7099 3.380004 TCAATGTAATCCCAAACCATCGC 59.620 43.478 0.00 0.00 0.00 4.58
3416 7108 1.209261 TGCTCGCTCAATGTAATCCCA 59.791 47.619 0.00 0.00 0.00 4.37
3467 7159 3.304257 GCGGCAGAACCATCATAATGAAG 60.304 47.826 0.00 0.00 39.03 3.02
3488 7180 2.348411 ATTGGCATACCCACAGTAGC 57.652 50.000 0.00 0.00 45.34 3.58
3493 7185 1.318886 CCGCAATTGGCATACCCACA 61.319 55.000 7.72 0.00 45.34 4.17
3508 7200 0.687427 TCTGATCCTCCATGACCGCA 60.687 55.000 0.00 0.00 0.00 5.69
3514 7206 7.769507 CCATATAACTCATTCTGATCCTCCATG 59.230 40.741 0.00 0.00 0.00 3.66
3519 7217 7.512058 AGTCACCATATAACTCATTCTGATCCT 59.488 37.037 0.00 0.00 0.00 3.24
3543 7241 4.593206 TGGTCAGTTTCAGAATCCACTAGT 59.407 41.667 0.00 0.00 0.00 2.57
3572 7270 5.001232 TGCCTTGACCTTCTATAACACAAC 58.999 41.667 0.00 0.00 0.00 3.32
3610 7308 0.856982 TCTCTGAGGGGGAGGAGATC 59.143 60.000 4.59 0.00 31.02 2.75
3620 7318 1.622811 ACTTTCAGCAGTCTCTGAGGG 59.377 52.381 4.59 0.00 43.23 4.30
3635 7339 2.618709 CACCAACCCTCACAGAACTTTC 59.381 50.000 0.00 0.00 0.00 2.62
3644 7348 0.755327 AAAGTGCCACCAACCCTCAC 60.755 55.000 0.00 0.00 0.00 3.51
3660 7388 2.609459 GTGTAGGATGCCATCGTGAAAG 59.391 50.000 10.04 0.00 0.00 2.62
3681 7409 4.383118 CCACAACAGGGACCTTAGATACAG 60.383 50.000 0.00 0.00 0.00 2.74
3684 7412 4.069312 TCCACAACAGGGACCTTAGATA 57.931 45.455 0.00 0.00 0.00 1.98
3727 7457 1.923227 GCAGCCTACGCCCTTGTTTC 61.923 60.000 0.00 0.00 34.57 2.78
3741 7471 0.968405 TCCAAAAATGGAGTGCAGCC 59.032 50.000 0.00 0.00 33.38 4.85
3765 7495 3.556213 CCCAACCACAGAAACTCGATGTA 60.556 47.826 0.00 0.00 0.00 2.29
3766 7496 2.494059 CCAACCACAGAAACTCGATGT 58.506 47.619 0.00 0.00 0.00 3.06
3795 7525 5.120830 CGACAAAACACCCTTAATCAGAGAG 59.879 44.000 0.00 0.00 0.00 3.20
3808 7538 5.342259 GCATCTAAAATGTCGACAAAACACC 59.658 40.000 24.13 2.24 0.00 4.16
3836 7566 4.021894 ACGAGCATCTATGGACAATCTACC 60.022 45.833 0.00 0.00 0.00 3.18
3837 7567 5.127693 ACGAGCATCTATGGACAATCTAC 57.872 43.478 0.00 0.00 0.00 2.59
3858 7588 2.304761 TCCAATCCAGAACCACACCTAC 59.695 50.000 0.00 0.00 0.00 3.18
3859 7589 2.304761 GTCCAATCCAGAACCACACCTA 59.695 50.000 0.00 0.00 0.00 3.08
3869 7599 1.216064 CAGATGGGGTCCAATCCAGA 58.784 55.000 0.88 0.00 36.95 3.86
3877 7607 2.681097 GCTTGAGTAACAGATGGGGTCC 60.681 54.545 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.