Multiple sequence alignment - TraesCS5D01G148100

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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 TraesCS5D01G148100 chr5D 100.000 6684 0 0 1 6684 234851984 234845301 0.000000e+00 12344.0
1 TraesCS5D01G148100 chr5A 95.557 4456 156 26 2241 6684 319228158 319232583 0.000000e+00 7094.0
2 TraesCS5D01G148100 chr5A 89.591 1979 118 33 317 2240 319226134 319228079 0.000000e+00 2433.0
3 TraesCS5D01G148100 chr5A 89.630 135 4 6 1 134 319226010 319226135 5.360000e-36 163.0
4 TraesCS5D01G148100 chr5B 94.488 2703 103 8 3987 6684 269977007 269979668 0.000000e+00 4124.0
5 TraesCS5D01G148100 chr5B 95.570 1264 34 12 2734 3993 269975738 269976983 0.000000e+00 2004.0
6 TraesCS5D01G148100 chr5B 91.595 1047 65 12 970 2010 269973400 269974429 0.000000e+00 1424.0
7 TraesCS5D01G148100 chr5B 94.720 644 25 8 2008 2646 269974518 269975157 0.000000e+00 992.0
8 TraesCS5D01G148100 chr5B 91.693 313 18 5 515 826 269973083 269973388 1.720000e-115 427.0
9 TraesCS5D01G148100 chr5B 84.138 290 23 11 238 520 269964131 269964404 6.650000e-65 259.0
10 TraesCS5D01G148100 chr5B 87.773 229 8 6 1 228 269963535 269963744 4.000000e-62 250.0
11 TraesCS5D01G148100 chr5B 90.798 163 15 0 6369 6531 366049597 366049435 1.130000e-52 219.0
12 TraesCS5D01G148100 chr5B 94.792 96 4 1 2644 2739 269975238 269975332 1.500000e-31 148.0
13 TraesCS5D01G148100 chr3A 91.411 163 14 0 6369 6531 600920855 600921017 2.430000e-54 224.0
14 TraesCS5D01G148100 chr4D 90.909 165 14 1 6366 6530 100229492 100229655 3.140000e-53 220.0
15 TraesCS5D01G148100 chr4B 90.909 165 13 2 6366 6530 142520898 142521060 3.140000e-53 220.0
16 TraesCS5D01G148100 chr4B 90.798 163 15 0 6369 6531 406390841 406391003 1.130000e-52 219.0
17 TraesCS5D01G148100 chr2A 89.349 169 18 0 6362 6530 135473221 135473389 5.250000e-51 213.0
18 TraesCS5D01G148100 chr2A 92.453 106 6 1 3745 3850 587158357 587158254 4.180000e-32 150.0
19 TraesCS5D01G148100 chr2A 97.561 41 1 0 107 147 543576545 543576585 3.340000e-08 71.3
20 TraesCS5D01G148100 chr1A 87.432 183 20 3 6350 6530 59114477 59114658 2.440000e-49 207.0
21 TraesCS5D01G148100 chr7D 93.396 106 7 0 3743 3848 190163117 190163222 2.500000e-34 158.0
22 TraesCS5D01G148100 chr7B 93.396 106 7 0 3744 3849 237489311 237489416 2.500000e-34 158.0
23 TraesCS5D01G148100 chr3B 93.333 105 7 0 3737 3841 256253815 256253711 8.970000e-34 156.0
24 TraesCS5D01G148100 chr1B 93.269 104 7 0 3745 3848 359902144 359902041 3.230000e-33 154.0
25 TraesCS5D01G148100 chrUn 92.523 107 6 2 3744 3849 362465900 362465795 1.160000e-32 152.0
26 TraesCS5D01G148100 chr4A 93.204 103 7 0 3742 3844 492942341 492942239 1.160000e-32 152.0
27 TraesCS5D01G148100 chr2D 86.275 51 5 2 3591 3640 635853184 635853135 3.000000e-03 54.7


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 TraesCS5D01G148100 chr5D 234845301 234851984 6683 True 12344.000000 12344 100.000000 1 6684 1 chr5D.!!$R1 6683
1 TraesCS5D01G148100 chr5A 319226010 319232583 6573 False 3230.000000 7094 91.592667 1 6684 3 chr5A.!!$F1 6683
2 TraesCS5D01G148100 chr5B 269973083 269979668 6585 False 1519.833333 4124 93.809667 515 6684 6 chr5B.!!$F2 6169
3 TraesCS5D01G148100 chr5B 269963535 269964404 869 False 254.500000 259 85.955500 1 520 2 chr5B.!!$F1 519

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
224 226 0.175760 AGTAGTAGGTGGCATGCGTG 59.824 55.000 12.44 0.09 0.00 5.34 F
1175 1597 0.326618 ACCCACCTCTATCACCCAGG 60.327 60.000 0.00 0.00 0.00 4.45 F
1505 1942 0.107654 GCGTTCCTACTGGATTGCCT 60.108 55.000 0.00 0.00 42.81 4.75 F
1582 2019 0.321653 ATTCCCAGTTCTGCGGTGAC 60.322 55.000 0.00 0.00 0.00 3.67 F
1727 2169 0.389948 CACCACCTACCTGCTTCGTC 60.390 60.000 0.00 0.00 0.00 4.20 F
2286 2905 0.530744 TCAGTACACGGCTCCATGTC 59.469 55.000 0.00 0.00 0.00 3.06 F
2559 3183 1.069513 TGGGGTTTGTACAGTCGACAG 59.930 52.381 19.50 12.96 0.00 3.51 F
3129 4246 2.612721 GGGGCACAACATGTTTTCATCC 60.613 50.000 8.77 7.21 38.64 3.51 F
4663 5815 0.960364 GTTTCAGGATTCCGGCAGCA 60.960 55.000 0.00 0.00 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1306 1733 0.033011 CGGAAGAGGAGGAGGAGGAA 60.033 60.000 0.00 0.00 0.00 3.36 R
2268 2887 0.460284 GGACATGGAGCCGTGTACTG 60.460 60.000 15.38 0.00 45.11 2.74 R
2540 3164 1.607251 CCTGTCGACTGTACAAACCCC 60.607 57.143 17.92 0.00 0.00 4.95 R
2653 3359 2.119801 AGAGCATGTTTAGCCCACAG 57.880 50.000 0.00 0.00 0.00 3.66 R
2752 3868 3.880490 TGAAAACACTCACGGTAGCAAAT 59.120 39.130 0.00 0.00 0.00 2.32 R
4219 5371 4.574421 GCCTTCCATTTTCTCTAGCTTCTC 59.426 45.833 0.00 0.00 0.00 2.87 R
4428 5580 7.515586 TCTGAGGAGATGCAGATTTGAAATAT 58.484 34.615 0.00 0.00 36.31 1.28 R
5037 6189 1.000163 ACTCCACAGAACTGTACAGCG 60.000 52.381 22.90 11.18 42.83 5.18 R
5877 7033 1.064017 AGTGTTCTGGCAGGAAACCAA 60.064 47.619 12.71 0.00 36.56 3.67 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
58 59 0.612174 TCCCTCAGCTAGCTTGACGT 60.612 55.000 16.46 0.00 0.00 4.34
89 91 1.445716 GCCTGTGAGCATGGCATCTC 61.446 60.000 15.60 15.60 45.46 2.75
90 92 0.818445 CCTGTGAGCATGGCATCTCC 60.818 60.000 18.14 12.55 0.00 3.71
91 93 1.153309 TGTGAGCATGGCATCTCCG 60.153 57.895 18.14 2.20 37.80 4.63
92 94 1.890979 GTGAGCATGGCATCTCCGG 60.891 63.158 18.14 0.00 37.80 5.14
93 95 2.369633 TGAGCATGGCATCTCCGGT 61.370 57.895 18.14 5.88 37.80 5.28
94 96 1.890979 GAGCATGGCATCTCCGGTG 60.891 63.158 0.00 0.00 37.80 4.94
95 97 3.589881 GCATGGCATCTCCGGTGC 61.590 66.667 6.98 6.98 40.33 5.01
96 98 2.191375 CATGGCATCTCCGGTGCT 59.809 61.111 14.45 0.00 42.16 4.40
97 99 1.452651 CATGGCATCTCCGGTGCTT 60.453 57.895 14.45 1.38 42.16 3.91
162 164 3.508012 CCCTATCGATCGTCCTCTGATTT 59.492 47.826 15.94 0.00 0.00 2.17
171 173 1.636003 GTCCTCTGATTTTGGTCCCCT 59.364 52.381 0.00 0.00 0.00 4.79
173 175 1.341383 CCTCTGATTTTGGTCCCCTGG 60.341 57.143 0.00 0.00 0.00 4.45
174 176 0.704076 TCTGATTTTGGTCCCCTGGG 59.296 55.000 5.50 5.50 0.00 4.45
175 177 0.972471 CTGATTTTGGTCCCCTGGGC 60.972 60.000 7.39 0.00 34.68 5.36
176 178 1.685765 GATTTTGGTCCCCTGGGCC 60.686 63.158 7.39 4.64 34.68 5.80
177 179 2.168272 GATTTTGGTCCCCTGGGCCT 62.168 60.000 7.39 0.00 34.20 5.19
178 180 2.460476 ATTTTGGTCCCCTGGGCCTG 62.460 60.000 7.39 3.68 34.20 4.85
206 208 1.673168 GCCCCTAGCATGAACAAGAG 58.327 55.000 0.00 0.00 42.97 2.85
224 226 0.175760 AGTAGTAGGTGGCATGCGTG 59.824 55.000 12.44 0.09 0.00 5.34
236 238 3.364442 TGCGTGGGGAGCATTTTG 58.636 55.556 0.00 0.00 40.01 2.44
253 632 7.577979 AGCATTTTGTTTGTTTGCAATATCAG 58.422 30.769 0.00 0.00 35.79 2.90
255 634 7.856894 GCATTTTGTTTGTTTGCAATATCAGTT 59.143 29.630 0.00 0.00 34.18 3.16
284 663 7.116376 GGAAACTATTTTGTTAGCCTGCTTTTC 59.884 37.037 0.00 0.00 0.00 2.29
286 665 4.846779 ATTTTGTTAGCCTGCTTTTCGA 57.153 36.364 0.00 0.00 0.00 3.71
302 681 0.617935 TCGAGGATGGGCAATTCACA 59.382 50.000 0.00 0.00 0.00 3.58
304 683 1.818060 CGAGGATGGGCAATTCACAAA 59.182 47.619 0.00 0.00 0.00 2.83
306 685 2.562298 GAGGATGGGCAATTCACAAACA 59.438 45.455 0.00 0.00 0.00 2.83
335 716 2.795231 ACTGGAGACCACAATGATGG 57.205 50.000 0.00 0.00 46.10 3.51
348 729 6.389906 CCACAATGATGGTTTTCTTCTTACC 58.610 40.000 0.00 0.00 34.77 2.85
354 735 3.219281 TGGTTTTCTTCTTACCAGTGCC 58.781 45.455 0.00 0.00 37.04 5.01
380 765 5.866207 AGAAAAAGATAAAGGTCGGTCACT 58.134 37.500 0.00 0.00 0.00 3.41
412 797 2.919229 CCTAATTTACTGCGTCGAACGT 59.081 45.455 0.00 0.00 44.73 3.99
413 798 4.097714 CCTAATTTACTGCGTCGAACGTA 58.902 43.478 0.00 4.20 44.73 3.57
414 799 3.959609 AATTTACTGCGTCGAACGTAC 57.040 42.857 0.00 0.00 44.73 3.67
457 842 6.936279 ACTACTACAATGCAATAGTGTCTGT 58.064 36.000 15.36 10.67 38.71 3.41
462 847 4.279169 ACAATGCAATAGTGTCTGTGCTTT 59.721 37.500 0.00 0.00 30.55 3.51
465 862 4.609947 TGCAATAGTGTCTGTGCTTTTTG 58.390 39.130 0.00 0.00 37.87 2.44
471 868 7.755582 ATAGTGTCTGTGCTTTTTGTTTTTC 57.244 32.000 0.00 0.00 0.00 2.29
472 869 4.929211 AGTGTCTGTGCTTTTTGTTTTTCC 59.071 37.500 0.00 0.00 0.00 3.13
501 898 2.967076 CGGTGAAGTGCGTGTGCT 60.967 61.111 0.00 0.00 43.34 4.40
574 973 3.876914 TCCATGTTCACACACTTTCTCAC 59.123 43.478 0.00 0.00 35.03 3.51
614 1013 2.570415 TCCAAATTTACCGGACAGCA 57.430 45.000 9.46 0.00 0.00 4.41
617 1016 2.094752 CCAAATTTACCGGACAGCAAGG 60.095 50.000 9.46 0.00 0.00 3.61
704 1107 7.986553 AAAGAAAGATCAATAGGAGGAGAGA 57.013 36.000 0.00 0.00 0.00 3.10
789 1192 4.651503 TCCACTCTCAAGTCTCAAGTCTTT 59.348 41.667 0.00 0.00 31.71 2.52
791 1194 5.221422 CCACTCTCAAGTCTCAAGTCTTTCT 60.221 44.000 0.00 0.00 31.71 2.52
793 1196 6.420604 CACTCTCAAGTCTCAAGTCTTTCTTC 59.579 42.308 0.00 0.00 31.07 2.87
1167 1589 2.188817 GGTCAGTGAACCCACCTCTAT 58.811 52.381 0.00 0.00 44.22 1.98
1169 1591 2.832129 GTCAGTGAACCCACCTCTATCA 59.168 50.000 0.00 0.00 44.22 2.15
1170 1592 2.832129 TCAGTGAACCCACCTCTATCAC 59.168 50.000 0.00 0.00 44.22 3.06
1171 1593 2.093447 CAGTGAACCCACCTCTATCACC 60.093 54.545 0.00 0.00 44.22 4.02
1173 1595 1.203376 TGAACCCACCTCTATCACCCA 60.203 52.381 0.00 0.00 0.00 4.51
1174 1596 1.486726 GAACCCACCTCTATCACCCAG 59.513 57.143 0.00 0.00 0.00 4.45
1175 1597 0.326618 ACCCACCTCTATCACCCAGG 60.327 60.000 0.00 0.00 0.00 4.45
1215 1637 4.838152 TTGCCTCCGCGGATCTGC 62.838 66.667 31.19 29.07 38.08 4.26
1312 1740 0.528684 CGCACTCGGATTCTTCCTCC 60.529 60.000 0.00 0.00 40.17 4.30
1321 1749 2.090775 GGATTCTTCCTCCTCCTCCTCT 60.091 54.545 0.00 0.00 39.14 3.69
1370 1803 2.225727 AGTTTCCGAATTTTCTGACGGC 59.774 45.455 0.00 0.00 44.19 5.68
1474 1911 3.005554 CTGCTCAAGGTACAATGTCCTG 58.994 50.000 5.40 1.98 33.97 3.86
1475 1912 2.371841 TGCTCAAGGTACAATGTCCTGT 59.628 45.455 5.40 0.00 33.97 4.00
1476 1913 3.003480 GCTCAAGGTACAATGTCCTGTC 58.997 50.000 5.40 0.00 33.97 3.51
1477 1914 3.600388 CTCAAGGTACAATGTCCTGTCC 58.400 50.000 5.40 0.00 33.97 4.02
1478 1915 3.248024 TCAAGGTACAATGTCCTGTCCT 58.752 45.455 5.40 0.00 33.97 3.85
1505 1942 0.107654 GCGTTCCTACTGGATTGCCT 60.108 55.000 0.00 0.00 42.81 4.75
1507 1944 2.803492 GCGTTCCTACTGGATTGCCTAG 60.803 54.545 0.00 0.00 42.81 3.02
1511 1948 3.838565 TCCTACTGGATTGCCTAGAGAG 58.161 50.000 0.00 0.00 37.46 3.20
1525 1962 4.692228 CCTAGAGAGAAGATGGCAACTTC 58.308 47.826 24.96 24.96 42.53 3.01
1548 1985 4.664640 CGCATCACATTTTTGTGCATTCAC 60.665 41.667 0.00 0.00 43.40 3.18
1570 2007 5.124457 CACATTTTCTGACTACCATTCCCAG 59.876 44.000 0.00 0.00 0.00 4.45
1582 2019 0.321653 ATTCCCAGTTCTGCGGTGAC 60.322 55.000 0.00 0.00 0.00 3.67
1709 2151 1.962822 CTGCTTGCTGACGGCTTCA 60.963 57.895 7.96 0.00 42.39 3.02
1727 2169 0.389948 CACCACCTACCTGCTTCGTC 60.390 60.000 0.00 0.00 0.00 4.20
1730 2172 0.888619 CACCTACCTGCTTCGTCAGA 59.111 55.000 4.22 0.00 36.19 3.27
1752 2194 1.209747 GAGGGGTCGGTTGCTATTCTT 59.790 52.381 0.00 0.00 0.00 2.52
1758 2205 2.094417 GTCGGTTGCTATTCTTGTCTGC 59.906 50.000 0.00 0.00 0.00 4.26
1830 2277 2.034687 CTTGTGGTGCTCAGGGGG 59.965 66.667 0.00 0.00 0.00 5.40
1874 2321 4.218200 TGTTGTGCAAATCCCAAGTGATAG 59.782 41.667 0.00 0.00 0.00 2.08
1875 2322 4.032960 TGTGCAAATCCCAAGTGATAGT 57.967 40.909 0.00 0.00 0.00 2.12
1878 2325 4.335594 GTGCAAATCCCAAGTGATAGTACC 59.664 45.833 0.00 0.00 0.00 3.34
1882 2329 6.625081 GCAAATCCCAAGTGATAGTACCAAAC 60.625 42.308 0.00 0.00 0.00 2.93
1931 2381 8.030106 AGTACTAATTCTCACAGCTAGTCAAAC 58.970 37.037 0.00 0.00 0.00 2.93
1933 2383 3.728076 TTCTCACAGCTAGTCAAACGT 57.272 42.857 0.00 0.00 0.00 3.99
1967 2417 4.016444 GGTATCACTTCTGCCAAATTGGA 58.984 43.478 17.47 0.00 40.96 3.53
1986 2436 2.871633 GGATTTTGTTGGCTTGGTTGTG 59.128 45.455 0.00 0.00 0.00 3.33
2010 2460 8.173130 GTGGTAATCATTACGGTTTTAGTTCAG 58.827 37.037 1.33 0.00 37.00 3.02
2212 2752 5.458041 ACAATGACACATCCAAAAAGAGG 57.542 39.130 0.00 0.00 0.00 3.69
2225 2765 4.283212 CCAAAAAGAGGGGTAAGAAATGCA 59.717 41.667 0.00 0.00 0.00 3.96
2264 2883 1.068333 GCATGCCATCACGTTGACTTT 60.068 47.619 6.36 0.00 0.00 2.66
2268 2887 2.483877 TGCCATCACGTTGACTTTGATC 59.516 45.455 0.00 0.00 0.00 2.92
2284 2903 1.136891 TGATCAGTACACGGCTCCATG 59.863 52.381 0.00 0.00 0.00 3.66
2285 2904 1.137086 GATCAGTACACGGCTCCATGT 59.863 52.381 0.00 0.00 0.00 3.21
2286 2905 0.530744 TCAGTACACGGCTCCATGTC 59.469 55.000 0.00 0.00 0.00 3.06
2299 2922 3.384668 CTCCATGTCCTTACTGTATGCG 58.615 50.000 0.00 0.00 0.00 4.73
2375 2998 8.538701 GTCATGGAGATCAATGGTAAGAGATAT 58.461 37.037 0.00 0.00 0.00 1.63
2378 3001 9.956640 ATGGAGATCAATGGTAAGAGATATTTC 57.043 33.333 0.00 0.00 0.00 2.17
2409 3033 6.061441 TCTCTTCTGTTGGCAAATGTTTAGA 58.939 36.000 0.00 0.00 0.00 2.10
2559 3183 1.069513 TGGGGTTTGTACAGTCGACAG 59.930 52.381 19.50 12.96 0.00 3.51
2580 3204 3.007940 AGGATTTTCAGGACGTCACATGA 59.992 43.478 18.91 14.81 0.00 3.07
2602 3226 9.401873 CATGATAAATGCCAAATGTATGTGTAG 57.598 33.333 0.00 0.00 0.00 2.74
2620 3244 4.616802 GTGTAGGAACATTGTTGCATTTCG 59.383 41.667 21.04 0.00 38.08 3.46
2752 3868 9.883142 CACCCTTCAAAATTGCCTATTAAATAA 57.117 29.630 0.00 0.00 0.00 1.40
2772 3888 4.911514 AATTTGCTACCGTGAGTGTTTT 57.088 36.364 0.00 0.00 0.00 2.43
2929 4046 7.816995 TGCTACATTTTGTCCCATGATAAAAAC 59.183 33.333 0.00 0.00 42.45 2.43
2931 4048 9.874205 CTACATTTTGTCCCATGATAAAAACAT 57.126 29.630 0.00 0.00 42.45 2.71
2932 4049 8.550710 ACATTTTGTCCCATGATAAAAACATG 57.449 30.769 0.00 0.00 42.45 3.21
2933 4050 8.156165 ACATTTTGTCCCATGATAAAAACATGT 58.844 29.630 0.00 0.00 42.45 3.21
3004 4121 7.582719 TCCCTGGTTGATTATTATGCTTTAGT 58.417 34.615 0.00 0.00 0.00 2.24
3022 4139 6.291796 GCTTTAGTTGTCTTGACAAATGCAAC 60.292 38.462 21.61 15.53 37.18 4.17
3129 4246 2.612721 GGGGCACAACATGTTTTCATCC 60.613 50.000 8.77 7.21 38.64 3.51
3184 4302 3.440522 GGCCATTTGGAACTGTTCTAGTC 59.559 47.826 19.05 4.29 35.36 2.59
3864 4984 6.299141 ACTACATATTTGCTGACCCTATTGG 58.701 40.000 0.00 0.00 41.37 3.16
3993 5145 7.280876 TGCATCTCTAAATGTGGATAAGTGTTC 59.719 37.037 0.00 0.00 0.00 3.18
4004 5156 5.364157 GTGGATAAGTGTTCTCTCCCTGTAT 59.636 44.000 0.00 0.00 0.00 2.29
4034 5186 5.119931 TGTTTTCTTGTACATGCATCACC 57.880 39.130 0.00 0.00 0.00 4.02
4428 5580 5.665916 TGAGCATGAGATTGACAGTAGAA 57.334 39.130 0.00 0.00 0.00 2.10
4585 5737 5.342866 ACTCCAAGGTATACTGTCCTTTCT 58.657 41.667 2.25 0.00 41.44 2.52
4656 5808 3.871594 CCTACGACATGTTTCAGGATTCC 59.128 47.826 12.80 0.00 0.00 3.01
4663 5815 0.960364 GTTTCAGGATTCCGGCAGCA 60.960 55.000 0.00 0.00 0.00 4.41
4850 6002 3.199677 AGGAATTTCGTGTCACGTTTCA 58.800 40.909 23.82 2.72 43.14 2.69
5037 6189 7.224297 TCAATATGGGAGACAAAGTAATAGGC 58.776 38.462 0.00 0.00 0.00 3.93
5193 6345 1.674441 ACCAGCTTGCATGATCAATCG 59.326 47.619 0.00 0.00 0.00 3.34
5209 6361 3.882888 TCAATCGCTTCAAAAGGTCAGTT 59.117 39.130 0.00 0.00 0.00 3.16
5226 6378 4.154918 GTCAGTTAACTTGCCATTCCTCTG 59.845 45.833 5.07 0.00 0.00 3.35
5440 6595 6.137794 AGTTCGGTATCACATAGACTTGAG 57.862 41.667 0.00 0.00 0.00 3.02
5540 6695 6.153170 TGGATACGATTATGGAATTAGCCGTA 59.847 38.462 0.00 0.00 42.51 4.02
5545 6700 5.229469 CGATTATGGAATTAGCCGTATCGAC 59.771 44.000 0.00 0.00 35.20 4.20
5768 6924 3.389741 GCATGAACTTGCTTCCACG 57.610 52.632 0.00 0.00 39.57 4.94
5856 7012 3.418913 TGGCACCGCGTCAATTCG 61.419 61.111 4.92 0.00 0.00 3.34
5871 7027 6.622028 GCGTCAATTCGAGGAAGGAAAATAAA 60.622 38.462 0.00 0.00 0.00 1.40
5880 7036 8.736244 TCGAGGAAGGAAAATAAACTAAATTGG 58.264 33.333 0.00 0.00 0.00 3.16
6072 7228 1.484240 GCAAGAGCTACACTGAGGGAT 59.516 52.381 0.00 0.00 37.91 3.85
6101 7257 0.665068 CAGTGCTACACGGCGTGTAA 60.665 55.000 41.05 30.12 46.35 2.41
6118 7274 4.213270 CGTGTAAAGAGAACAAATGCCTCA 59.787 41.667 0.00 0.00 0.00 3.86
6153 7309 5.042463 TCGCTTTGTTATTATGGGATGGA 57.958 39.130 0.00 0.00 0.00 3.41
6196 7352 9.373750 GATGACATCATAAATGTATGTTTGTCG 57.626 33.333 22.57 3.83 44.32 4.35
6215 7371 2.425312 TCGGCACTGTCATGTTTTTGTT 59.575 40.909 0.00 0.00 0.00 2.83
6377 7534 8.165397 GGAACTCATATAAGTAGTACTCCCTCT 58.835 40.741 2.58 0.00 0.00 3.69
6479 7636 9.053840 AGATTCACTCATTTTGCTCTGTATATG 57.946 33.333 0.00 0.00 0.00 1.78
6490 7647 4.830600 TGCTCTGTATATGGTCCGTATTGA 59.169 41.667 8.95 5.30 0.00 2.57
6507 7664 9.367444 TCCGTATTGAAATCTCTAAAAAGACTC 57.633 33.333 0.00 0.00 0.00 3.36
6524 7681 9.454859 AAAAAGACTCATATTTAGGAACAGAGG 57.545 33.333 0.00 0.00 0.00 3.69
6677 7835 5.643339 GAACACTTCGGAAGCTACATATG 57.357 43.478 17.37 8.85 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 2.703416 CTCACAGGCATACAGCTTCAA 58.297 47.619 0.00 0.00 44.79 2.69
89 91 3.710722 AGCTGGAGGAAGCACCGG 61.711 66.667 0.00 0.00 46.08 5.28
90 92 2.435586 CAGCTGGAGGAAGCACCG 60.436 66.667 5.57 0.00 46.08 4.94
91 93 0.250901 TTTCAGCTGGAGGAAGCACC 60.251 55.000 15.13 0.00 46.08 5.01
92 94 0.877743 GTTTCAGCTGGAGGAAGCAC 59.122 55.000 15.13 0.00 46.08 4.40
93 95 0.250901 GGTTTCAGCTGGAGGAAGCA 60.251 55.000 15.13 0.00 46.08 3.91
94 96 0.250901 TGGTTTCAGCTGGAGGAAGC 60.251 55.000 15.13 13.24 43.88 3.86
95 97 1.349026 TCTGGTTTCAGCTGGAGGAAG 59.651 52.381 15.13 7.06 40.69 3.46
96 98 1.072331 GTCTGGTTTCAGCTGGAGGAA 59.928 52.381 15.13 0.00 40.69 3.36
97 99 0.687354 GTCTGGTTTCAGCTGGAGGA 59.313 55.000 15.13 0.00 40.69 3.71
184 186 0.392461 TTGTTCATGCTAGGGGCGAC 60.392 55.000 0.00 0.00 45.43 5.19
206 208 0.810031 CCACGCATGCCACCTACTAC 60.810 60.000 13.15 0.00 0.00 2.73
224 226 2.290367 GCAAACAAACAAAATGCTCCCC 59.710 45.455 0.00 0.00 34.29 4.81
228 230 7.227116 ACTGATATTGCAAACAAACAAAATGCT 59.773 29.630 1.71 0.00 39.77 3.79
229 231 7.354257 ACTGATATTGCAAACAAACAAAATGC 58.646 30.769 1.71 0.00 39.77 3.56
232 234 9.039870 CCTAACTGATATTGCAAACAAACAAAA 57.960 29.630 1.71 0.00 39.77 2.44
233 235 7.655328 CCCTAACTGATATTGCAAACAAACAAA 59.345 33.333 1.71 0.00 39.77 2.83
234 236 7.014711 TCCCTAACTGATATTGCAAACAAACAA 59.985 33.333 1.71 0.00 39.77 2.83
235 237 6.491745 TCCCTAACTGATATTGCAAACAAACA 59.508 34.615 1.71 0.00 39.77 2.83
236 238 6.919721 TCCCTAACTGATATTGCAAACAAAC 58.080 36.000 1.71 0.00 39.77 2.93
253 632 7.535997 CAGGCTAACAAAATAGTTTCCCTAAC 58.464 38.462 0.00 0.00 32.78 2.34
255 634 5.650703 GCAGGCTAACAAAATAGTTTCCCTA 59.349 40.000 0.00 0.00 32.78 3.53
284 663 1.462616 TTGTGAATTGCCCATCCTCG 58.537 50.000 0.00 0.00 0.00 4.63
286 665 2.607499 TGTTTGTGAATTGCCCATCCT 58.393 42.857 0.00 0.00 0.00 3.24
302 681 4.020485 GGTCTCCAGTACTGTGGTATGTTT 60.020 45.833 21.18 0.00 38.88 2.83
304 683 3.097614 GGTCTCCAGTACTGTGGTATGT 58.902 50.000 21.18 0.00 38.88 2.29
306 685 3.097614 GTGGTCTCCAGTACTGTGGTAT 58.902 50.000 21.18 0.00 38.88 2.73
335 716 4.911514 TTGGCACTGGTAAGAAGAAAAC 57.088 40.909 0.00 0.00 0.00 2.43
348 729 6.515832 ACCTTTATCTTTTTCTTTGGCACTG 58.484 36.000 0.00 0.00 0.00 3.66
354 735 6.856426 GTGACCGACCTTTATCTTTTTCTTTG 59.144 38.462 0.00 0.00 0.00 2.77
438 823 4.578871 AGCACAGACACTATTGCATTGTA 58.421 39.130 0.00 0.00 37.44 2.41
440 825 4.430137 AAGCACAGACACTATTGCATTG 57.570 40.909 0.00 0.00 37.44 2.82
494 891 1.200948 TCAGATCAGTCAGAGCACACG 59.799 52.381 0.00 0.00 34.30 4.49
501 898 6.740681 GCACCATAATCATCAGATCAGTCAGA 60.741 42.308 0.00 0.00 31.90 3.27
635 1034 0.396060 CCCTATCTTCTCTGCCTGCC 59.604 60.000 0.00 0.00 0.00 4.85
636 1035 0.396060 CCCCTATCTTCTCTGCCTGC 59.604 60.000 0.00 0.00 0.00 4.85
637 1036 0.396060 GCCCCTATCTTCTCTGCCTG 59.604 60.000 0.00 0.00 0.00 4.85
638 1037 1.118356 CGCCCCTATCTTCTCTGCCT 61.118 60.000 0.00 0.00 0.00 4.75
704 1107 5.536916 TCTTCTTCTCTCTCGAGTTCCTTTT 59.463 40.000 13.13 0.00 38.45 2.27
789 1192 0.888619 CAGCGGTAGTGGACAGAAGA 59.111 55.000 0.00 0.00 0.00 2.87
791 1194 1.541310 CCCAGCGGTAGTGGACAGAA 61.541 60.000 0.00 0.00 37.23 3.02
793 1196 2.579201 CCCAGCGGTAGTGGACAG 59.421 66.667 0.00 0.00 37.23 3.51
914 1327 7.148474 CGTGTGCTGGTGATTAGTTTTATAAGT 60.148 37.037 0.00 0.00 0.00 2.24
915 1328 7.180079 CGTGTGCTGGTGATTAGTTTTATAAG 58.820 38.462 0.00 0.00 0.00 1.73
916 1329 6.402766 GCGTGTGCTGGTGATTAGTTTTATAA 60.403 38.462 0.00 0.00 38.39 0.98
1305 1732 1.788229 GGAAGAGGAGGAGGAGGAAG 58.212 60.000 0.00 0.00 0.00 3.46
1306 1733 0.033011 CGGAAGAGGAGGAGGAGGAA 60.033 60.000 0.00 0.00 0.00 3.36
1307 1734 1.615814 CGGAAGAGGAGGAGGAGGA 59.384 63.158 0.00 0.00 0.00 3.71
1312 1740 1.219393 GCAACCGGAAGAGGAGGAG 59.781 63.158 9.46 0.00 34.73 3.69
1370 1803 2.598192 CACAAACACCGCACAGAAAAAG 59.402 45.455 0.00 0.00 0.00 2.27
1474 1911 4.501921 CAGTAGGAACGCGTAATTTAGGAC 59.498 45.833 14.46 3.02 0.00 3.85
1475 1912 4.440525 CCAGTAGGAACGCGTAATTTAGGA 60.441 45.833 14.46 0.00 36.89 2.94
1476 1913 3.800506 CCAGTAGGAACGCGTAATTTAGG 59.199 47.826 14.46 6.09 36.89 2.69
1477 1914 4.675510 TCCAGTAGGAACGCGTAATTTAG 58.324 43.478 14.46 0.00 42.23 1.85
1478 1915 4.717233 TCCAGTAGGAACGCGTAATTTA 57.283 40.909 14.46 0.00 42.23 1.40
1505 1942 3.429547 GCGAAGTTGCCATCTTCTCTCTA 60.430 47.826 12.39 0.00 39.08 2.43
1507 1944 1.663135 GCGAAGTTGCCATCTTCTCTC 59.337 52.381 12.39 0.64 39.08 3.20
1511 1948 1.739466 TGATGCGAAGTTGCCATCTTC 59.261 47.619 5.59 5.59 38.22 2.87
1525 1962 3.429207 TGAATGCACAAAAATGTGATGCG 59.571 39.130 12.80 0.00 42.02 4.73
1548 1985 5.256474 ACTGGGAATGGTAGTCAGAAAATG 58.744 41.667 0.00 0.00 0.00 2.32
1558 1995 1.656652 CGCAGAACTGGGAATGGTAG 58.343 55.000 12.43 0.00 45.10 3.18
1570 2007 0.318762 AGGAAGAGTCACCGCAGAAC 59.681 55.000 0.00 0.00 0.00 3.01
1582 2019 3.685139 TGTAGAAACCAGCAGGAAGAG 57.315 47.619 0.35 0.00 38.69 2.85
1709 2151 0.830444 TGACGAAGCAGGTAGGTGGT 60.830 55.000 0.00 0.00 0.00 4.16
1727 2169 1.376037 GCAACCGACCCCTCTTCTG 60.376 63.158 0.00 0.00 0.00 3.02
1730 2172 1.209747 GAATAGCAACCGACCCCTCTT 59.790 52.381 0.00 0.00 0.00 2.85
1752 2194 2.356673 CACGCAGCAGAGCAGACA 60.357 61.111 0.00 0.00 0.00 3.41
1758 2205 4.383861 TGAGGCCACGCAGCAGAG 62.384 66.667 5.01 0.00 0.00 3.35
1772 2219 4.572909 TCATCAGAGACAAATGGTGTGAG 58.427 43.478 0.00 0.00 41.96 3.51
1874 2321 9.691362 ACACAATTTGATTTATCTGTTTGGTAC 57.309 29.630 2.79 0.00 0.00 3.34
1878 2325 9.372541 GCAAACACAATTTGATTTATCTGTTTG 57.627 29.630 22.39 22.39 45.09 2.93
1882 2329 8.301730 ACTGCAAACACAATTTGATTTATCTG 57.698 30.769 2.79 5.87 0.00 2.90
1931 2381 6.980978 AGAAGTGATACCAAATAGATGACACG 59.019 38.462 0.00 0.00 0.00 4.49
1933 2383 6.763135 GCAGAAGTGATACCAAATAGATGACA 59.237 38.462 0.00 0.00 0.00 3.58
1967 2417 2.238395 ACCACAACCAAGCCAACAAAAT 59.762 40.909 0.00 0.00 0.00 1.82
1986 2436 8.483307 TCTGAACTAAAACCGTAATGATTACC 57.517 34.615 9.55 0.00 32.49 2.85
2010 2460 9.286946 CATCAAATAGACAAATGAAGAGCTTTC 57.713 33.333 0.00 0.00 0.00 2.62
2212 2752 5.859205 ATTTGATCCTGCATTTCTTACCC 57.141 39.130 0.00 0.00 0.00 3.69
2225 2765 9.038072 TGGCATGCATTATATTTATTTGATCCT 57.962 29.630 21.36 0.00 0.00 3.24
2264 2883 1.136891 CATGGAGCCGTGTACTGATCA 59.863 52.381 0.00 0.00 0.00 2.92
2268 2887 0.460284 GGACATGGAGCCGTGTACTG 60.460 60.000 15.38 0.00 45.11 2.74
2284 2903 3.123804 CACCATCGCATACAGTAAGGAC 58.876 50.000 0.00 0.00 0.00 3.85
2285 2904 2.764010 ACACCATCGCATACAGTAAGGA 59.236 45.455 0.00 0.00 0.00 3.36
2286 2905 3.179443 ACACCATCGCATACAGTAAGG 57.821 47.619 0.00 0.00 0.00 2.69
2299 2922 5.525378 GTGTATGAGATCCTGAAACACCATC 59.475 44.000 0.00 0.00 31.77 3.51
2344 2967 4.927049 ACCATTGATCTCCATGACAAGTT 58.073 39.130 0.00 0.00 0.00 2.66
2375 2998 5.593909 TGCCAACAGAAGAGAAAAGATGAAA 59.406 36.000 0.00 0.00 0.00 2.69
2378 3001 5.443185 TTGCCAACAGAAGAGAAAAGATG 57.557 39.130 0.00 0.00 0.00 2.90
2391 3014 5.046910 ACGATCTAAACATTTGCCAACAG 57.953 39.130 0.00 0.00 0.00 3.16
2409 3033 1.798813 GGAAAGTGAAACGCAGACGAT 59.201 47.619 0.00 0.00 45.86 3.73
2540 3164 1.607251 CCTGTCGACTGTACAAACCCC 60.607 57.143 17.92 0.00 0.00 4.95
2544 3168 5.361427 TGAAAATCCTGTCGACTGTACAAA 58.639 37.500 17.92 0.00 0.00 2.83
2559 3183 3.334691 TCATGTGACGTCCTGAAAATCC 58.665 45.455 14.12 0.00 0.00 3.01
2580 3204 8.413229 GTTCCTACACATACATTTGGCATTTAT 58.587 33.333 0.00 0.00 0.00 1.40
2602 3226 2.730928 CACCGAAATGCAACAATGTTCC 59.269 45.455 0.00 0.00 0.00 3.62
2620 3244 6.096695 ACAAAATTATTATTGACGCCACACC 58.903 36.000 6.79 0.00 0.00 4.16
2653 3359 2.119801 AGAGCATGTTTAGCCCACAG 57.880 50.000 0.00 0.00 0.00 3.66
2752 3868 3.880490 TGAAAACACTCACGGTAGCAAAT 59.120 39.130 0.00 0.00 0.00 2.32
2772 3888 6.975772 GCGTTTATTTATTGCCACCTAATTGA 59.024 34.615 0.00 0.00 0.00 2.57
3022 4139 4.177165 TGCTGCTTGATAACAATGGTTG 57.823 40.909 0.00 0.00 37.88 3.77
3129 4246 7.370383 ACAAACATACTGGACATTTAAGCAAG 58.630 34.615 0.00 0.00 0.00 4.01
3184 4302 9.965824 AACAAATTCAGTGTTTTATGGTAGAAG 57.034 29.630 0.00 0.00 35.70 2.85
3394 4512 9.941664 CTTCAGTTTTGCAATACTAGGATAATG 57.058 33.333 20.12 8.35 0.00 1.90
3962 5082 8.750515 TTATCCACATTTAGAGATGCATTCAA 57.249 30.769 0.00 0.00 0.00 2.69
4096 5248 9.712305 GTATACTCCATTGCTTGATACAAGTAT 57.288 33.333 12.07 0.00 0.00 2.12
4097 5249 8.700973 TGTATACTCCATTGCTTGATACAAGTA 58.299 33.333 12.07 5.88 0.00 2.24
4098 5250 7.564793 TGTATACTCCATTGCTTGATACAAGT 58.435 34.615 12.07 0.00 0.00 3.16
4187 5339 5.070001 TGAAAACAGTAAGCAGCCATTAGT 58.930 37.500 0.00 0.00 0.00 2.24
4219 5371 4.574421 GCCTTCCATTTTCTCTAGCTTCTC 59.426 45.833 0.00 0.00 0.00 2.87
4428 5580 7.515586 TCTGAGGAGATGCAGATTTGAAATAT 58.484 34.615 0.00 0.00 36.31 1.28
4656 5808 1.337074 ACATGGAAAACAATGCTGCCG 60.337 47.619 0.00 0.00 0.00 5.69
4663 5815 5.475220 TGTCGGTGAATACATGGAAAACAAT 59.525 36.000 0.00 0.00 0.00 2.71
4722 5874 7.985184 ACATTAGCGTCCAAATATGAGTTTCTA 59.015 33.333 0.00 0.00 0.00 2.10
4850 6002 3.260380 CCGGAGAGGCTGAGAATGATTAT 59.740 47.826 0.00 0.00 0.00 1.28
5037 6189 1.000163 ACTCCACAGAACTGTACAGCG 60.000 52.381 22.90 11.18 42.83 5.18
5193 6345 4.740205 GCAAGTTAACTGACCTTTTGAAGC 59.260 41.667 9.34 0.00 0.00 3.86
5209 6361 4.365514 TTGTCAGAGGAATGGCAAGTTA 57.634 40.909 0.00 0.00 39.75 2.24
5226 6378 7.365840 ACAGTTTTCTTTCGATAGGATTGTC 57.634 36.000 2.93 0.00 0.00 3.18
5440 6595 2.468915 AGTAAACCTCTAGGGAGTGCC 58.531 52.381 0.20 0.00 40.27 5.01
5540 6695 1.139058 AGCCGCCTTTTCTATGTCGAT 59.861 47.619 0.00 0.00 0.00 3.59
5545 6700 3.126831 CAGAGTAGCCGCCTTTTCTATG 58.873 50.000 0.00 0.00 0.00 2.23
5689 6844 2.493675 ACTGTGCTACGTCTCATGTCAT 59.506 45.455 0.00 0.00 0.00 3.06
5784 6940 3.914426 AATACTGCATCCCGTTTCTCT 57.086 42.857 0.00 0.00 0.00 3.10
5871 7027 4.112634 TCTGGCAGGAAACCAATTTAGT 57.887 40.909 15.73 0.00 36.56 2.24
5877 7033 1.064017 AGTGTTCTGGCAGGAAACCAA 60.064 47.619 12.71 0.00 36.56 3.67
5880 7036 2.808543 CTGTAGTGTTCTGGCAGGAAAC 59.191 50.000 15.73 11.90 0.00 2.78
6072 7228 1.879380 GTGTAGCACTGAACATTGGCA 59.121 47.619 0.00 0.00 0.00 4.92
6101 7257 2.165998 GGCTGAGGCATTTGTTCTCTT 58.834 47.619 0.00 0.00 40.87 2.85
6137 7293 8.780616 ATCAACAATTCCATCCCATAATAACA 57.219 30.769 0.00 0.00 0.00 2.41
6153 7309 7.392393 TGATGTCATCAACAGAGATCAACAATT 59.608 33.333 13.25 0.00 41.17 2.32
6196 7352 2.284952 GCAACAAAAACATGACAGTGCC 59.715 45.455 0.00 0.00 0.00 5.01
6237 7393 1.337703 GGATTGCACAGCACACAAGAA 59.662 47.619 0.00 0.00 38.71 2.52
6287 7444 1.800586 CTGAGGAACAACCATGTGACG 59.199 52.381 0.00 0.00 40.46 4.35
6479 7636 8.388853 GTCTTTTTAGAGATTTCAATACGGACC 58.611 37.037 0.00 0.00 0.00 4.46
6507 7664 6.268847 AGCTACTCCCTCTGTTCCTAAATATG 59.731 42.308 0.00 0.00 0.00 1.78
6517 7674 3.648545 AGTTGAAAGCTACTCCCTCTGTT 59.351 43.478 0.00 0.00 0.00 3.16
6520 7677 3.904339 TGAAGTTGAAAGCTACTCCCTCT 59.096 43.478 0.00 0.00 29.75 3.69
6524 7681 5.751243 TGTTTGAAGTTGAAAGCTACTCC 57.249 39.130 0.00 0.00 29.75 3.85


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

AutoCloner maintained by Alex Coulton.