Multiple sequence alignment - TraesCS7A01G184800

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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 TraesCS7A01G184800 chr7A 100.000 3041 0 0 1 3041 139097656 139100696 0.000000e+00 5616.0
1 TraesCS7A01G184800 chr7A 94.444 36 2 0 2500 2535 139100048 139100083 4.240000e-04 56.5
2 TraesCS7A01G184800 chr7A 94.444 36 2 0 2393 2428 139100155 139100190 4.240000e-04 56.5
3 TraesCS7A01G184800 chr7B 95.995 1523 40 7 1532 3041 104322501 104324015 0.000000e+00 2455.0
4 TraesCS7A01G184800 chr7B 95.424 590 23 1 943 1532 104321850 104322435 0.000000e+00 937.0
5 TraesCS7A01G184800 chr7B 88.435 147 15 2 2201 2347 227592453 227592309 3.120000e-40 176.0
6 TraesCS7A01G184800 chr7B 78.409 176 31 5 1562 1737 21230453 21230285 1.150000e-19 108.0
7 TraesCS7A01G184800 chr7B 93.443 61 2 2 1681 1740 104322710 104322769 4.180000e-14 89.8
8 TraesCS7A01G184800 chr7B 97.222 36 1 0 2393 2428 104323478 104323513 9.100000e-06 62.1
9 TraesCS7A01G184800 chr7B 94.444 36 2 0 2500 2535 104323371 104323406 4.240000e-04 56.5
10 TraesCS7A01G184800 chr7D 87.173 842 106 2 86 925 588426584 588427425 0.000000e+00 955.0
11 TraesCS7A01G184800 chr4D 93.814 97 2 3 1 97 421459363 421459271 3.160000e-30 143.0
12 TraesCS7A01G184800 chr2A 94.624 93 2 2 1 93 559691210 559691121 1.140000e-29 141.0
13 TraesCS7A01G184800 chr4B 81.215 181 26 6 746 923 491048415 491048240 4.090000e-29 139.0
14 TraesCS7A01G184800 chr5D 92.857 98 1 4 1 95 55708280 55708186 1.470000e-28 137.0
15 TraesCS7A01G184800 chr3D 92.784 97 3 2 1 96 157671319 157671226 1.470000e-28 137.0
16 TraesCS7A01G184800 chr3D 95.455 88 1 1 1 88 349198360 349198444 1.470000e-28 137.0
17 TraesCS7A01G184800 chr3D 91.262 103 3 3 1 100 159849533 159849632 5.290000e-28 135.0
18 TraesCS7A01G184800 chr2D 92.000 100 3 3 1 99 475650430 475650525 5.290000e-28 135.0
19 TraesCS7A01G184800 chr2D 91.089 101 5 3 1 101 26781352 26781256 1.900000e-27 134.0
20 TraesCS7A01G184800 chr6A 90.385 104 6 2 1 103 488120812 488120912 1.900000e-27 134.0


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 TraesCS7A01G184800 chr7A 139097656 139100696 3040 False 1909.666667 5616 96.2960 1 3041 3 chr7A.!!$F1 3040
1 TraesCS7A01G184800 chr7B 104321850 104324015 2165 False 720.080000 2455 95.3056 943 3041 5 chr7B.!!$F1 2098
2 TraesCS7A01G184800 chr7D 588426584 588427425 841 False 955.000000 955 87.1730 86 925 1 chr7D.!!$F1 839

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
669 672 0.038159 CCTCGGACTCGAAGCAAGTT 60.038 55.0 0.0 0.0 45.47 2.66 F
1210 1213 0.169009 GGTGCGTCCAATTTCTGCTC 59.831 55.0 0.0 0.0 35.97 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 1821 0.811915 CTTCATCCACCTCGTCGTCT 59.188 55.0 0.00 0.00 0.0 4.18 R
2894 2975 1.027357 ACTGCAGTTTGGCAAGACAG 58.973 50.0 15.25 15.04 44.4 3.51 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
43 44 9.746457 TGTGTAATAATAATAGCCCATAATGCA 57.254 29.630 0.00 0.00 0.00 3.96
54 55 8.978874 ATAGCCCATAATGCAATAAATATCGA 57.021 30.769 0.00 0.00 0.00 3.59
55 56 7.886629 AGCCCATAATGCAATAAATATCGAT 57.113 32.000 2.16 2.16 0.00 3.59
56 57 8.978874 AGCCCATAATGCAATAAATATCGATA 57.021 30.769 7.75 7.75 0.00 2.92
57 58 9.578576 AGCCCATAATGCAATAAATATCGATAT 57.421 29.630 12.25 12.25 0.00 1.63
80 81 9.897744 ATATAAAAGTATGATGCAAAATGGACG 57.102 29.630 0.00 0.00 0.00 4.79
81 82 5.643379 AAAGTATGATGCAAAATGGACGT 57.357 34.783 0.00 0.00 0.00 4.34
82 83 6.751514 AAAGTATGATGCAAAATGGACGTA 57.248 33.333 0.00 0.00 0.00 3.57
83 84 6.942532 AAGTATGATGCAAAATGGACGTAT 57.057 33.333 0.00 0.00 0.00 3.06
84 85 6.545504 AGTATGATGCAAAATGGACGTATC 57.454 37.500 0.00 0.00 0.00 2.24
91 92 4.335315 TGCAAAATGGACGTATCAGGATTC 59.665 41.667 0.00 0.00 0.00 2.52
92 93 4.335315 GCAAAATGGACGTATCAGGATTCA 59.665 41.667 0.00 0.00 0.00 2.57
104 105 0.184451 AGGATTCATGGCGGCATTCT 59.816 50.000 23.47 9.58 0.00 2.40
119 120 3.127721 GGCATTCTTTACTTGAGTGCTCC 59.872 47.826 10.16 0.00 43.58 4.70
122 123 5.675575 GCATTCTTTACTTGAGTGCTCCATG 60.676 44.000 0.00 0.00 41.75 3.66
124 125 3.327757 TCTTTACTTGAGTGCTCCATGGT 59.672 43.478 12.58 0.00 0.00 3.55
125 126 3.788227 TTACTTGAGTGCTCCATGGTT 57.212 42.857 12.58 0.00 0.00 3.67
126 127 1.901591 ACTTGAGTGCTCCATGGTTG 58.098 50.000 12.58 7.38 0.00 3.77
146 147 2.604079 TGCATTTGGGCCCTGGTG 60.604 61.111 25.70 18.86 0.00 4.17
155 156 4.424711 GCCCTGGTGGATGGCGAA 62.425 66.667 0.00 0.00 35.08 4.70
176 177 0.592637 TGGCAGAACATCTTTGTGCG 59.407 50.000 0.65 0.00 36.41 5.34
200 201 3.294493 GAGCCCAGCGCCAAACAA 61.294 61.111 2.29 0.00 38.78 2.83
263 264 2.370519 TGTTAGGCTTGCTGTGACCTTA 59.629 45.455 0.00 0.00 33.60 2.69
266 267 1.630369 AGGCTTGCTGTGACCTTATGA 59.370 47.619 0.00 0.00 0.00 2.15
279 280 1.949525 CCTTATGAGCGATTTGGTGGG 59.050 52.381 0.00 0.00 0.00 4.61
281 282 0.546122 TATGAGCGATTTGGTGGGCT 59.454 50.000 0.00 0.00 38.70 5.19
311 312 5.552870 AAGCCATACACGAGGAGATATTT 57.447 39.130 0.00 0.00 0.00 1.40
319 320 4.080863 ACACGAGGAGATATTTCAAAGCCT 60.081 41.667 0.00 0.00 0.00 4.58
321 322 3.812053 CGAGGAGATATTTCAAAGCCTGG 59.188 47.826 0.00 0.00 0.00 4.45
323 324 3.203934 AGGAGATATTTCAAAGCCTGGCT 59.796 43.478 17.22 17.22 42.56 4.75
338 339 2.357009 CCTGGCTGCTACACATCAATTC 59.643 50.000 0.00 0.00 0.00 2.17
342 343 4.576053 TGGCTGCTACACATCAATTCATAC 59.424 41.667 0.00 0.00 0.00 2.39
366 367 1.909302 GGTTCATTGAGGACCTGGAGA 59.091 52.381 0.00 0.00 0.00 3.71
368 369 3.539604 GTTCATTGAGGACCTGGAGATG 58.460 50.000 0.00 0.00 0.00 2.90
371 372 0.907486 TTGAGGACCTGGAGATGCTG 59.093 55.000 0.00 0.00 0.00 4.41
383 384 3.022406 GGAGATGCTGCCAAAGAAGATT 58.978 45.455 0.00 0.00 0.00 2.40
384 385 3.181489 GGAGATGCTGCCAAAGAAGATTG 60.181 47.826 0.00 0.00 0.00 2.67
385 386 2.165845 AGATGCTGCCAAAGAAGATTGC 59.834 45.455 0.00 0.00 0.00 3.56
388 389 1.001181 GCTGCCAAAGAAGATTGCCAA 59.999 47.619 0.00 0.00 0.00 4.52
410 411 3.515286 CCGGCTCCGCGAGAAGTA 61.515 66.667 8.23 0.00 38.24 2.24
417 418 0.394762 TCCGCGAGAAGTAAGGGCTA 60.395 55.000 8.23 0.00 0.00 3.93
420 421 1.945394 CGCGAGAAGTAAGGGCTACTA 59.055 52.381 0.00 0.00 40.14 1.82
439 440 4.426112 GCCAAAGGCGCTTCCTGC 62.426 66.667 7.64 1.17 46.94 4.85
447 448 2.662596 CGCTTCCTGCTGGGTACA 59.337 61.111 10.07 0.00 40.11 2.90
466 467 4.647424 ACACCAAAATTCATGTTGACGT 57.353 36.364 0.00 0.00 0.00 4.34
487 488 5.162075 CGTTAGTCTGTCTAGGAACCAAAG 58.838 45.833 0.00 0.00 0.00 2.77
488 489 5.278858 CGTTAGTCTGTCTAGGAACCAAAGT 60.279 44.000 0.00 0.00 0.00 2.66
491 492 5.145564 AGTCTGTCTAGGAACCAAAGTACA 58.854 41.667 0.00 0.00 0.00 2.90
492 493 5.601313 AGTCTGTCTAGGAACCAAAGTACAA 59.399 40.000 0.00 0.00 0.00 2.41
494 495 5.836898 TCTGTCTAGGAACCAAAGTACAAGA 59.163 40.000 0.00 0.00 0.00 3.02
496 497 5.836898 TGTCTAGGAACCAAAGTACAAGAGA 59.163 40.000 0.00 0.00 0.00 3.10
497 498 6.497259 TGTCTAGGAACCAAAGTACAAGAGAT 59.503 38.462 0.00 0.00 0.00 2.75
499 500 5.825593 AGGAACCAAAGTACAAGAGATGA 57.174 39.130 0.00 0.00 0.00 2.92
500 501 6.380079 AGGAACCAAAGTACAAGAGATGAT 57.620 37.500 0.00 0.00 0.00 2.45
503 504 5.171339 ACCAAAGTACAAGAGATGATGCT 57.829 39.130 0.00 0.00 0.00 3.79
511 512 2.605837 AGAGATGATGCTGCTGTCTG 57.394 50.000 0.00 0.00 0.00 3.51
518 519 3.029570 TGATGCTGCTGTCTGTAGAGAT 58.970 45.455 0.00 0.00 0.00 2.75
530 531 4.220821 GTCTGTAGAGATGAACAAGGGACA 59.779 45.833 0.00 0.00 0.00 4.02
538 539 6.789457 AGAGATGAACAAGGGACATATATGGA 59.211 38.462 16.96 0.00 0.00 3.41
540 541 7.456725 AGATGAACAAGGGACATATATGGAAG 58.543 38.462 16.96 3.59 0.00 3.46
541 542 5.376625 TGAACAAGGGACATATATGGAAGC 58.623 41.667 16.96 3.61 0.00 3.86
542 543 5.132648 TGAACAAGGGACATATATGGAAGCT 59.867 40.000 16.96 0.00 0.00 3.74
543 544 5.234466 ACAAGGGACATATATGGAAGCTC 57.766 43.478 16.96 4.89 0.00 4.09
546 547 4.100373 AGGGACATATATGGAAGCTCCTC 58.900 47.826 16.96 8.16 37.46 3.71
574 576 0.522626 TTCATGGCGTTGCTGATGTG 59.477 50.000 0.00 0.00 0.00 3.21
580 582 1.021390 GCGTTGCTGATGTGCCTACT 61.021 55.000 0.00 0.00 0.00 2.57
594 597 3.319405 GTGCCTACTCTTGAGCTATAGCA 59.681 47.826 26.07 3.93 45.16 3.49
600 603 3.634448 ACTCTTGAGCTATAGCATGTCGT 59.366 43.478 26.07 12.48 45.16 4.34
625 628 2.268920 TGGCGTTGGCAGAGGATC 59.731 61.111 0.00 0.00 42.47 3.36
645 648 7.568349 AGGATCTGCAGATAAACAGTTTCATA 58.432 34.615 28.78 0.00 34.37 2.15
659 662 2.930682 GTTTCATAGTTGCCTCGGACTC 59.069 50.000 0.00 0.00 0.00 3.36
669 672 0.038159 CCTCGGACTCGAAGCAAGTT 60.038 55.000 0.00 0.00 45.47 2.66
673 676 4.439700 CCTCGGACTCGAAGCAAGTTATTA 60.440 45.833 0.00 0.00 45.47 0.98
675 678 3.243177 CGGACTCGAAGCAAGTTATTAGC 59.757 47.826 0.00 0.00 39.00 3.09
696 699 8.818141 TTAGCGATATTGAAAGAGGTATGAAG 57.182 34.615 0.00 0.00 0.00 3.02
705 708 2.399580 AGAGGTATGAAGGGTGGCTAC 58.600 52.381 0.00 0.00 0.00 3.58
775 778 7.712204 TGTTCTTTTACTTTTGAAGGGAGTT 57.288 32.000 0.00 0.00 0.00 3.01
793 796 4.202223 GGAGTTCCTCAAATATAGACGCCA 60.202 45.833 0.00 0.00 31.08 5.69
797 800 7.155328 AGTTCCTCAAATATAGACGCCAATAG 58.845 38.462 0.00 0.00 0.00 1.73
803 806 7.959175 TCAAATATAGACGCCAATAGGTTAGT 58.041 34.615 0.00 0.00 37.19 2.24
812 815 5.533528 ACGCCAATAGGTTAGTCAAGTTTTT 59.466 36.000 0.00 0.00 37.19 1.94
813 816 5.856455 CGCCAATAGGTTAGTCAAGTTTTTG 59.144 40.000 0.00 0.00 37.19 2.44
820 823 7.939784 AGGTTAGTCAAGTTTTTGAACTCTT 57.060 32.000 0.00 0.00 44.49 2.85
837 840 5.819825 ACTCTTTTGTTCAGGAAAGACAC 57.180 39.130 0.00 0.00 37.06 3.67
864 867 0.994247 TGTTGAGCCCACATGATCCT 59.006 50.000 0.00 0.00 0.00 3.24
873 876 4.646492 AGCCCACATGATCCTTTTTGTATC 59.354 41.667 0.00 0.00 0.00 2.24
883 886 5.796502 TCCTTTTTGTATCCCTCTCCATT 57.203 39.130 0.00 0.00 0.00 3.16
907 910 8.865590 TTTGGAGTTTGAGTAATAAAACTTGC 57.134 30.769 7.09 0.00 44.53 4.01
909 912 8.911918 TGGAGTTTGAGTAATAAAACTTGCTA 57.088 30.769 7.09 0.00 44.53 3.49
953 956 3.161450 TAGCCACGCCTCATCCCC 61.161 66.667 0.00 0.00 0.00 4.81
960 963 1.764054 CGCCTCATCCCCTCCTCTT 60.764 63.158 0.00 0.00 0.00 2.85
1076 1079 1.377202 TTGCCGGACAGATGAAGCC 60.377 57.895 5.05 0.00 0.00 4.35
1080 1083 0.673644 CCGGACAGATGAAGCCGTTT 60.674 55.000 0.00 0.00 42.08 3.60
1117 1120 1.513586 CTGTTCCGCGACTACGACC 60.514 63.158 8.23 0.00 42.66 4.79
1120 1123 2.743752 TTCCGCGACTACGACCTCG 61.744 63.158 8.23 0.00 46.33 4.63
1152 1155 1.657181 CGCGTTGGCCAAAGTTGTC 60.657 57.895 28.54 13.60 35.02 3.18
1157 1160 2.539274 CGTTGGCCAAAGTTGTCAATTG 59.461 45.455 22.47 0.00 0.00 2.32
1181 1184 2.541178 CGTACGAGGTACAGATGGAAGC 60.541 54.545 10.44 0.00 38.77 3.86
1191 1194 4.213564 ACAGATGGAAGCCTTCACTAAG 57.786 45.455 6.80 0.00 31.13 2.18
1207 1210 3.074412 ACTAAGGTGCGTCCAATTTCTG 58.926 45.455 0.75 0.00 39.02 3.02
1208 1211 0.598065 AAGGTGCGTCCAATTTCTGC 59.402 50.000 0.75 0.00 39.02 4.26
1209 1212 0.250901 AGGTGCGTCCAATTTCTGCT 60.251 50.000 0.75 0.00 39.02 4.24
1210 1213 0.169009 GGTGCGTCCAATTTCTGCTC 59.831 55.000 0.00 0.00 35.97 4.26
1211 1214 1.160137 GTGCGTCCAATTTCTGCTCT 58.840 50.000 0.00 0.00 0.00 4.09
1254 1257 3.248602 GGTTCATCCGATTTGATCCTTCG 59.751 47.826 0.00 0.00 32.51 3.79
1302 1305 2.683933 CCAGTCGGTGGCTAGGGT 60.684 66.667 0.00 0.00 40.39 4.34
1357 1360 3.458487 AGTCTTAAAGTTCTGGTGGTGGT 59.542 43.478 0.00 0.00 0.00 4.16
1417 1420 3.543537 CAGAGGTAGCCGCTGGAT 58.456 61.111 2.16 0.00 45.47 3.41
1428 1431 1.871080 CCGCTGGATAAGATGGTGAC 58.129 55.000 0.00 0.00 0.00 3.67
1487 1490 4.760047 GACCAGATGGCGCCGTGT 62.760 66.667 29.48 21.43 39.32 4.49
1721 1802 2.293118 TGGTGGATGAAGATGAGGAGGA 60.293 50.000 0.00 0.00 0.00 3.71
1740 1821 2.354704 GGACGTGGTGGATGAAGATGAA 60.355 50.000 0.00 0.00 0.00 2.57
1743 1824 2.932614 CGTGGTGGATGAAGATGAAGAC 59.067 50.000 0.00 0.00 0.00 3.01
1745 1826 2.831526 TGGTGGATGAAGATGAAGACGA 59.168 45.455 0.00 0.00 0.00 4.20
1748 1829 2.752903 TGGATGAAGATGAAGACGACGA 59.247 45.455 0.00 0.00 0.00 4.20
1771 1852 2.103941 GTGGATGAAGATGAGGAGGACC 59.896 54.545 0.00 0.00 0.00 4.46
1778 1859 1.006043 AGATGAGGAGGACCGTGAAGA 59.994 52.381 0.00 0.00 41.83 2.87
1811 1892 8.692710 TGATGAGATACTGACGGTAATTAAAGT 58.307 33.333 0.00 0.00 33.74 2.66
1877 1958 7.259882 TGGCAGAACTTATTAGATTGCATTTG 58.740 34.615 0.00 0.00 31.80 2.32
1884 1965 9.880157 AACTTATTAGATTGCATTTGATTTGCT 57.120 25.926 0.00 0.00 40.77 3.91
1886 1967 8.564648 TTATTAGATTGCATTTGATTTGCTCG 57.435 30.769 0.00 0.00 40.77 5.03
2075 2156 9.410556 GATTTATGTGTAAGCACTTGTTCATTT 57.589 29.630 0.00 0.00 45.44 2.32
2183 2264 7.713764 AAAAAGTTTGATCTTGCATACCAAC 57.286 32.000 0.00 0.00 0.00 3.77
2184 2265 6.403866 AAAGTTTGATCTTGCATACCAACA 57.596 33.333 0.00 0.00 0.00 3.33
2185 2266 5.633830 AGTTTGATCTTGCATACCAACAG 57.366 39.130 0.00 0.00 0.00 3.16
2186 2267 5.072741 AGTTTGATCTTGCATACCAACAGT 58.927 37.500 0.00 0.00 0.00 3.55
2189 2270 7.230510 AGTTTGATCTTGCATACCAACAGTAAA 59.769 33.333 0.00 0.00 33.70 2.01
2193 2274 6.952773 TCTTGCATACCAACAGTAAAAGTT 57.047 33.333 0.00 0.00 33.70 2.66
2247 2328 6.609237 TTCAGTTGAACATTCACTTCTCAG 57.391 37.500 0.00 0.00 36.83 3.35
2362 2443 9.849166 GATGTCTTGTTATAGAATAGCTAGACC 57.151 37.037 16.40 5.24 31.33 3.85
2369 2450 8.222637 TGTTATAGAATAGCTAGACCCAGTGTA 58.777 37.037 0.00 0.00 31.33 2.90
2428 2509 3.737559 ATGGTGATAGTTTTGAGCCCA 57.262 42.857 0.00 0.00 0.00 5.36
2447 2528 4.139786 CCCATACATGTAGCTTTCATGCT 58.860 43.478 22.73 15.60 44.26 3.79
2528 2609 7.985184 TCCAATGTGTAGTATGGTGATAGTTTC 59.015 37.037 0.00 0.00 34.50 2.78
2537 2618 3.371034 TGGTGATAGTTTCGATCCCTGA 58.629 45.455 0.00 0.00 0.00 3.86
2546 2627 5.080337 AGTTTCGATCCCTGAGATGCTATA 58.920 41.667 0.00 0.00 34.42 1.31
2551 2632 4.037803 CGATCCCTGAGATGCTATATGGAG 59.962 50.000 0.00 0.00 34.42 3.86
2589 2670 1.136110 TGAGCTCACCGATTATGCGAA 59.864 47.619 13.74 0.00 0.00 4.70
2609 2690 8.310406 TGCGAACCTATTATATTGAATCACAG 57.690 34.615 0.00 0.00 0.00 3.66
2660 2741 5.984725 TCGTACCATAATTCCAAGTGTGAT 58.015 37.500 0.00 0.00 0.00 3.06
2661 2742 5.815222 TCGTACCATAATTCCAAGTGTGATG 59.185 40.000 0.00 0.00 0.00 3.07
2662 2743 5.584649 CGTACCATAATTCCAAGTGTGATGT 59.415 40.000 0.00 0.00 0.00 3.06
2663 2744 6.093495 CGTACCATAATTCCAAGTGTGATGTT 59.907 38.462 0.00 0.00 0.00 2.71
2713 2794 5.664294 TGCTTATTCATTGAGCATGGTTT 57.336 34.783 0.00 0.00 41.15 3.27
2716 2797 6.152492 TGCTTATTCATTGAGCATGGTTTACA 59.848 34.615 0.00 0.00 41.15 2.41
2767 2848 6.879276 AGAAGGGTTTAGTAAAGAAGTTGC 57.121 37.500 0.00 0.00 0.00 4.17
2931 3012 8.086143 ACTGCAGTAGGAAAACTATATGGTAA 57.914 34.615 20.16 0.00 33.43 2.85
2947 3028 4.040936 TGGTAATGCCATTGTGGTAAGT 57.959 40.909 0.00 0.00 43.61 2.24
2958 3039 5.527582 CCATTGTGGTAAGTCCTAATGCTAC 59.472 44.000 0.00 0.00 38.68 3.58
2960 3041 5.950544 TGTGGTAAGTCCTAATGCTACAT 57.049 39.130 0.00 0.00 37.07 2.29
2997 3078 8.006298 TCCAATTGTTATTAGTATTTGGCCTG 57.994 34.615 3.32 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 9.746457 TGCATTATGGGCTATTATTATTACACA 57.254 29.630 0.00 0.00 0.00 3.72
28 29 9.407380 TCGATATTTATTGCATTATGGGCTATT 57.593 29.630 0.00 0.00 0.00 1.73
29 30 8.978874 TCGATATTTATTGCATTATGGGCTAT 57.021 30.769 0.00 0.00 0.00 2.97
30 31 8.978874 ATCGATATTTATTGCATTATGGGCTA 57.021 30.769 0.00 0.00 0.00 3.93
31 32 7.886629 ATCGATATTTATTGCATTATGGGCT 57.113 32.000 0.00 0.00 0.00 5.19
54 55 9.897744 CGTCCATTTTGCATCATACTTTTATAT 57.102 29.630 0.00 0.00 0.00 0.86
55 56 8.898761 ACGTCCATTTTGCATCATACTTTTATA 58.101 29.630 0.00 0.00 0.00 0.98
56 57 7.771183 ACGTCCATTTTGCATCATACTTTTAT 58.229 30.769 0.00 0.00 0.00 1.40
57 58 7.151999 ACGTCCATTTTGCATCATACTTTTA 57.848 32.000 0.00 0.00 0.00 1.52
58 59 6.024552 ACGTCCATTTTGCATCATACTTTT 57.975 33.333 0.00 0.00 0.00 2.27
59 60 5.643379 ACGTCCATTTTGCATCATACTTT 57.357 34.783 0.00 0.00 0.00 2.66
60 61 6.542005 TGATACGTCCATTTTGCATCATACTT 59.458 34.615 0.00 0.00 0.00 2.24
61 62 6.054941 TGATACGTCCATTTTGCATCATACT 58.945 36.000 0.00 0.00 0.00 2.12
62 63 6.299023 TGATACGTCCATTTTGCATCATAC 57.701 37.500 0.00 0.00 0.00 2.39
63 64 5.469760 CCTGATACGTCCATTTTGCATCATA 59.530 40.000 0.00 0.00 0.00 2.15
64 65 4.276678 CCTGATACGTCCATTTTGCATCAT 59.723 41.667 0.00 0.00 0.00 2.45
65 66 3.627123 CCTGATACGTCCATTTTGCATCA 59.373 43.478 0.00 0.00 0.00 3.07
66 67 3.876914 TCCTGATACGTCCATTTTGCATC 59.123 43.478 0.00 0.00 0.00 3.91
67 68 3.884895 TCCTGATACGTCCATTTTGCAT 58.115 40.909 0.00 0.00 0.00 3.96
68 69 3.342377 TCCTGATACGTCCATTTTGCA 57.658 42.857 0.00 0.00 0.00 4.08
69 70 4.335315 TGAATCCTGATACGTCCATTTTGC 59.665 41.667 0.00 0.00 0.00 3.68
70 71 6.432936 CATGAATCCTGATACGTCCATTTTG 58.567 40.000 0.00 0.00 0.00 2.44
71 72 5.532406 CCATGAATCCTGATACGTCCATTTT 59.468 40.000 0.00 0.00 0.00 1.82
72 73 5.065914 CCATGAATCCTGATACGTCCATTT 58.934 41.667 0.00 0.00 0.00 2.32
73 74 4.645535 CCATGAATCCTGATACGTCCATT 58.354 43.478 0.00 0.00 0.00 3.16
74 75 3.557898 GCCATGAATCCTGATACGTCCAT 60.558 47.826 0.00 0.00 0.00 3.41
75 76 2.224281 GCCATGAATCCTGATACGTCCA 60.224 50.000 0.00 0.00 0.00 4.02
76 77 2.417719 GCCATGAATCCTGATACGTCC 58.582 52.381 0.00 0.00 0.00 4.79
77 78 2.061773 CGCCATGAATCCTGATACGTC 58.938 52.381 0.00 0.00 0.00 4.34
78 79 1.270305 CCGCCATGAATCCTGATACGT 60.270 52.381 0.00 0.00 0.00 3.57
79 80 1.432514 CCGCCATGAATCCTGATACG 58.567 55.000 0.00 0.00 0.00 3.06
80 81 1.160137 GCCGCCATGAATCCTGATAC 58.840 55.000 0.00 0.00 0.00 2.24
81 82 0.764271 TGCCGCCATGAATCCTGATA 59.236 50.000 0.00 0.00 0.00 2.15
82 83 0.111832 ATGCCGCCATGAATCCTGAT 59.888 50.000 0.00 0.00 0.00 2.90
83 84 0.106569 AATGCCGCCATGAATCCTGA 60.107 50.000 0.00 0.00 0.00 3.86
84 85 0.313043 GAATGCCGCCATGAATCCTG 59.687 55.000 0.00 0.00 0.00 3.86
91 92 2.423185 TCAAGTAAAGAATGCCGCCATG 59.577 45.455 0.00 0.00 0.00 3.66
92 93 2.684881 CTCAAGTAAAGAATGCCGCCAT 59.315 45.455 0.00 0.00 0.00 4.40
104 105 3.788227 ACCATGGAGCACTCAAGTAAA 57.212 42.857 21.47 0.00 0.00 2.01
119 120 0.036199 CCCAAATGCACCCAACCATG 60.036 55.000 0.00 0.00 0.00 3.66
122 123 2.347114 GCCCAAATGCACCCAACC 59.653 61.111 0.00 0.00 0.00 3.77
124 125 2.927317 GGGCCCAAATGCACCCAA 60.927 61.111 19.95 0.00 42.33 4.12
125 126 3.926214 AGGGCCCAAATGCACCCA 61.926 61.111 27.56 0.00 45.45 4.51
126 127 3.393106 CAGGGCCCAAATGCACCC 61.393 66.667 27.56 0.00 43.17 4.61
146 147 1.377202 TTCTGCCAGTTCGCCATCC 60.377 57.895 0.00 0.00 0.00 3.51
152 153 2.549754 ACAAAGATGTTCTGCCAGTTCG 59.450 45.455 0.00 0.00 35.91 3.95
155 156 1.610522 GCACAAAGATGTTCTGCCAGT 59.389 47.619 0.00 0.00 37.82 4.00
197 198 9.376075 GTATCAATCATCGAGAATATCCATTGT 57.624 33.333 0.00 0.00 0.00 2.71
234 235 0.961753 GCAAGCCTAACAAAGCCAGT 59.038 50.000 0.00 0.00 0.00 4.00
236 237 0.961019 CAGCAAGCCTAACAAAGCCA 59.039 50.000 0.00 0.00 0.00 4.75
238 239 1.608590 TCACAGCAAGCCTAACAAAGC 59.391 47.619 0.00 0.00 0.00 3.51
254 255 3.270027 CCAAATCGCTCATAAGGTCACA 58.730 45.455 0.00 0.00 0.00 3.58
263 264 0.546122 TAGCCCACCAAATCGCTCAT 59.454 50.000 0.00 0.00 32.76 2.90
266 267 1.224592 CCTAGCCCACCAAATCGCT 59.775 57.895 0.00 0.00 35.34 4.93
279 280 2.803492 CGTGTATGGCTTTCCTCCTAGC 60.803 54.545 0.00 0.00 36.66 3.42
281 282 2.693591 CTCGTGTATGGCTTTCCTCCTA 59.306 50.000 0.00 0.00 0.00 2.94
311 312 0.606401 GTGTAGCAGCCAGGCTTTGA 60.606 55.000 12.86 0.00 42.71 2.69
319 320 3.070476 TGAATTGATGTGTAGCAGCCA 57.930 42.857 0.00 0.00 31.34 4.75
321 322 5.525012 TGAGTATGAATTGATGTGTAGCAGC 59.475 40.000 0.00 0.00 0.00 5.25
323 324 6.051074 CCTGAGTATGAATTGATGTGTAGCA 58.949 40.000 0.00 0.00 0.00 3.49
338 339 4.163078 AGGTCCTCAATGAACCTGAGTATG 59.837 45.833 5.86 0.00 41.83 2.39
366 367 2.667473 GCAATCTTCTTTGGCAGCAT 57.333 45.000 0.00 0.00 0.00 3.79
400 401 0.739561 AGTAGCCCTTACTTCTCGCG 59.260 55.000 0.00 0.00 39.64 5.87
433 434 4.322681 TGGTGTACCCAGCAGGAA 57.677 55.556 0.00 0.00 43.78 3.36
437 438 2.950781 TGAATTTTGGTGTACCCAGCA 58.049 42.857 0.00 0.00 46.31 4.41
438 439 3.258123 ACATGAATTTTGGTGTACCCAGC 59.742 43.478 0.00 0.00 46.31 4.85
439 440 5.010516 TCAACATGAATTTTGGTGTACCCAG 59.989 40.000 0.00 0.00 46.31 4.45
447 448 6.262273 AGACTAACGTCAACATGAATTTTGGT 59.738 34.615 0.00 0.00 42.73 3.67
461 462 3.755378 GGTTCCTAGACAGACTAACGTCA 59.245 47.826 0.00 0.00 42.73 4.35
466 467 6.779049 TGTACTTTGGTTCCTAGACAGACTAA 59.221 38.462 0.00 0.00 0.00 2.24
475 476 6.936279 TCATCTCTTGTACTTTGGTTCCTAG 58.064 40.000 0.00 0.00 0.00 3.02
476 477 6.928348 TCATCTCTTGTACTTTGGTTCCTA 57.072 37.500 0.00 0.00 0.00 2.94
487 488 3.529533 ACAGCAGCATCATCTCTTGTAC 58.470 45.455 0.00 0.00 0.00 2.90
488 489 3.450096 AGACAGCAGCATCATCTCTTGTA 59.550 43.478 0.00 0.00 0.00 2.41
491 492 2.236644 ACAGACAGCAGCATCATCTCTT 59.763 45.455 0.00 0.00 0.00 2.85
492 493 1.832366 ACAGACAGCAGCATCATCTCT 59.168 47.619 0.00 0.00 0.00 3.10
494 495 3.029570 TCTACAGACAGCAGCATCATCT 58.970 45.455 0.00 0.00 0.00 2.90
496 497 3.029570 TCTCTACAGACAGCAGCATCAT 58.970 45.455 0.00 0.00 0.00 2.45
497 498 2.450476 TCTCTACAGACAGCAGCATCA 58.550 47.619 0.00 0.00 0.00 3.07
499 500 3.029570 TCATCTCTACAGACAGCAGCAT 58.970 45.455 0.00 0.00 0.00 3.79
500 501 2.450476 TCATCTCTACAGACAGCAGCA 58.550 47.619 0.00 0.00 0.00 4.41
503 504 4.322273 CCTTGTTCATCTCTACAGACAGCA 60.322 45.833 0.00 0.00 0.00 4.41
511 512 8.037758 CCATATATGTCCCTTGTTCATCTCTAC 58.962 40.741 11.73 0.00 0.00 2.59
518 519 5.132648 AGCTTCCATATATGTCCCTTGTTCA 59.867 40.000 11.73 0.00 0.00 3.18
530 531 9.554053 AATTACTAGTGAGGAGCTTCCATATAT 57.446 33.333 5.39 0.00 39.61 0.86
538 539 5.686124 GCCATGAATTACTAGTGAGGAGCTT 60.686 44.000 5.39 0.00 0.00 3.74
540 541 4.061596 GCCATGAATTACTAGTGAGGAGC 58.938 47.826 5.39 0.00 0.00 4.70
541 542 4.202161 ACGCCATGAATTACTAGTGAGGAG 60.202 45.833 5.39 0.00 0.00 3.69
542 543 3.704566 ACGCCATGAATTACTAGTGAGGA 59.295 43.478 5.39 0.00 0.00 3.71
543 544 4.060038 ACGCCATGAATTACTAGTGAGG 57.940 45.455 5.39 0.00 0.00 3.86
546 547 3.623060 AGCAACGCCATGAATTACTAGTG 59.377 43.478 5.39 0.00 0.00 2.74
574 576 4.021544 ACATGCTATAGCTCAAGAGTAGGC 60.022 45.833 24.61 0.00 42.66 3.93
580 582 3.632145 TCACGACATGCTATAGCTCAAGA 59.368 43.478 24.61 11.64 42.66 3.02
594 597 2.029288 CGCCAGTGCTTCACGACAT 61.029 57.895 0.00 0.00 39.64 3.06
600 603 3.286751 GCCAACGCCAGTGCTTCA 61.287 61.111 0.00 0.00 34.43 3.02
618 621 5.690464 AACTGTTTATCTGCAGATCCTCT 57.310 39.130 31.92 12.33 36.05 3.69
624 627 7.361201 GCAACTATGAAACTGTTTATCTGCAGA 60.361 37.037 20.79 20.79 36.62 4.26
625 628 6.744537 GCAACTATGAAACTGTTTATCTGCAG 59.255 38.462 7.63 7.63 38.58 4.41
659 662 7.105494 TCAATATCGCTAATAACTTGCTTCG 57.895 36.000 0.00 0.00 0.00 3.79
673 676 6.226787 CCTTCATACCTCTTTCAATATCGCT 58.773 40.000 0.00 0.00 0.00 4.93
675 678 6.425114 CACCCTTCATACCTCTTTCAATATCG 59.575 42.308 0.00 0.00 0.00 2.92
692 695 0.251922 AGTACCGTAGCCACCCTTCA 60.252 55.000 0.00 0.00 0.00 3.02
693 696 1.767759 TAGTACCGTAGCCACCCTTC 58.232 55.000 0.00 0.00 0.00 3.46
696 699 1.696063 TGATAGTACCGTAGCCACCC 58.304 55.000 0.00 0.00 0.00 4.61
775 778 5.542635 ACCTATTGGCGTCTATATTTGAGGA 59.457 40.000 4.55 0.00 36.63 3.71
784 787 5.363005 ACTTGACTAACCTATTGGCGTCTAT 59.637 40.000 10.50 0.00 36.63 1.98
789 792 5.622770 AAAACTTGACTAACCTATTGGCG 57.377 39.130 0.00 0.00 36.63 5.69
793 796 9.628500 AGAGTTCAAAAACTTGACTAACCTATT 57.372 29.630 0.00 0.00 45.80 1.73
797 800 8.860128 CAAAAGAGTTCAAAAACTTGACTAACC 58.140 33.333 0.00 0.00 45.80 2.85
813 816 6.258899 GTGTCTTTCCTGAACAAAAGAGTTC 58.741 40.000 0.00 0.00 46.22 3.01
820 823 3.126171 CACACGTGTCTTTCCTGAACAAA 59.874 43.478 20.49 0.00 0.00 2.83
830 833 2.418628 CTCAACAACCACACGTGTCTTT 59.581 45.455 20.49 11.89 0.00 2.52
837 840 1.821759 TGGGCTCAACAACCACACG 60.822 57.895 0.00 0.00 0.00 4.49
864 867 5.898120 TCCAAATGGAGAGGGATACAAAAA 58.102 37.500 0.00 0.00 39.78 1.94
883 886 8.232913 AGCAAGTTTTATTACTCAAACTCCAA 57.767 30.769 0.00 0.00 41.42 3.53
925 928 0.675522 GCGTGGCTAGGGTTTGCTAA 60.676 55.000 0.00 0.00 0.00 3.09
926 929 1.078708 GCGTGGCTAGGGTTTGCTA 60.079 57.895 0.00 0.00 0.00 3.49
927 930 2.359975 GCGTGGCTAGGGTTTGCT 60.360 61.111 0.00 0.00 0.00 3.91
928 931 3.440415 GGCGTGGCTAGGGTTTGC 61.440 66.667 0.00 0.00 0.00 3.68
929 932 1.745489 GAGGCGTGGCTAGGGTTTG 60.745 63.158 0.00 0.00 0.00 2.93
930 933 1.562672 ATGAGGCGTGGCTAGGGTTT 61.563 55.000 0.00 0.00 0.00 3.27
931 934 1.972660 GATGAGGCGTGGCTAGGGTT 61.973 60.000 0.00 0.00 0.00 4.11
932 935 2.365635 ATGAGGCGTGGCTAGGGT 60.366 61.111 0.00 0.00 0.00 4.34
933 936 2.423446 GATGAGGCGTGGCTAGGG 59.577 66.667 0.00 0.00 0.00 3.53
934 937 2.423446 GGATGAGGCGTGGCTAGG 59.577 66.667 0.00 0.00 0.00 3.02
935 938 2.423446 GGGATGAGGCGTGGCTAG 59.577 66.667 0.00 0.00 0.00 3.42
936 939 3.161450 GGGGATGAGGCGTGGCTA 61.161 66.667 0.00 0.00 0.00 3.93
938 941 4.554036 GAGGGGATGAGGCGTGGC 62.554 72.222 0.00 0.00 0.00 5.01
939 942 3.866582 GGAGGGGATGAGGCGTGG 61.867 72.222 0.00 0.00 0.00 4.94
940 943 2.765807 AGGAGGGGATGAGGCGTG 60.766 66.667 0.00 0.00 0.00 5.34
941 944 2.444895 GAGGAGGGGATGAGGCGT 60.445 66.667 0.00 0.00 0.00 5.68
953 956 4.856607 GTCGGCGGCGAAGAGGAG 62.857 72.222 36.31 2.23 0.00 3.69
1076 1079 1.274596 AATAGCGTACGCAGGAAACG 58.725 50.000 38.58 3.40 44.88 3.60
1080 1083 0.313043 GGCTAATAGCGTACGCAGGA 59.687 55.000 38.58 24.70 43.62 3.86
1144 1147 3.805422 TCGTACGAGCAATTGACAACTTT 59.195 39.130 15.28 0.00 0.00 2.66
1152 1155 2.852413 CTGTACCTCGTACGAGCAATTG 59.148 50.000 34.54 23.95 41.41 2.32
1157 1160 1.002684 CCATCTGTACCTCGTACGAGC 60.003 57.143 34.54 23.18 41.41 5.03
1191 1194 0.169009 GAGCAGAAATTGGACGCACC 59.831 55.000 0.00 0.00 39.54 5.01
1198 1201 4.553323 CAAACAGGAAGAGCAGAAATTGG 58.447 43.478 0.00 0.00 0.00 3.16
1207 1210 2.039879 TCTTACCCCAAACAGGAAGAGC 59.960 50.000 0.00 0.00 41.22 4.09
1208 1211 4.576330 ATCTTACCCCAAACAGGAAGAG 57.424 45.455 0.00 0.00 41.22 2.85
1209 1212 5.076873 CAAATCTTACCCCAAACAGGAAGA 58.923 41.667 0.00 0.00 41.22 2.87
1210 1213 4.220602 CCAAATCTTACCCCAAACAGGAAG 59.779 45.833 0.00 0.00 41.22 3.46
1211 1214 4.156477 CCAAATCTTACCCCAAACAGGAA 58.844 43.478 0.00 0.00 41.22 3.36
1254 1257 0.666577 CCCAAACAGACTCGTCGACC 60.667 60.000 10.58 0.00 34.09 4.79
1302 1305 6.127366 CGGTTAACCCCTAACACTAATCACTA 60.127 42.308 19.09 0.00 41.60 2.74
1357 1360 0.395311 CGGCCCACTACCTCAGTCTA 60.395 60.000 0.00 0.00 34.26 2.59
1417 1420 0.824109 CAGCCGAGGTCACCATCTTA 59.176 55.000 0.00 0.00 0.00 2.10
1487 1490 3.245016 ACATGATTGCCTTCTGTCCTCAA 60.245 43.478 0.00 0.00 0.00 3.02
1721 1802 2.567169 TCTTCATCTTCATCCACCACGT 59.433 45.455 0.00 0.00 0.00 4.49
1740 1821 0.811915 CTTCATCCACCTCGTCGTCT 59.188 55.000 0.00 0.00 0.00 4.18
1743 1824 1.405463 TCATCTTCATCCACCTCGTCG 59.595 52.381 0.00 0.00 0.00 5.12
1745 1826 1.759445 CCTCATCTTCATCCACCTCGT 59.241 52.381 0.00 0.00 0.00 4.18
1748 1829 2.022625 TCCTCCTCATCTTCATCCACCT 60.023 50.000 0.00 0.00 0.00 4.00
1771 1852 7.326547 CAGTATCTCATCATCTTCATCTTCACG 59.673 40.741 0.00 0.00 0.00 4.35
1778 1859 5.538053 ACCGTCAGTATCTCATCATCTTCAT 59.462 40.000 0.00 0.00 0.00 2.57
1847 1928 4.755266 TCTAATAAGTTCTGCCAGGACC 57.245 45.455 0.00 0.00 0.00 4.46
1877 1958 7.535489 AGTAAGTATAACAACCGAGCAAATC 57.465 36.000 0.00 0.00 0.00 2.17
1884 1965 8.114331 TCAGAAGAAGTAAGTATAACAACCGA 57.886 34.615 0.00 0.00 0.00 4.69
1921 2002 5.355071 CAGTAGCAGGCTTATTGTGATCAAA 59.645 40.000 0.00 0.00 37.11 2.69
2075 2156 5.017490 TGGAAGAAACAAGGTTACCACAAA 58.983 37.500 3.51 0.00 0.00 2.83
2164 2245 5.376854 ACTGTTGGTATGCAAGATCAAAC 57.623 39.130 0.00 0.00 0.00 2.93
2165 2246 7.517614 TTTACTGTTGGTATGCAAGATCAAA 57.482 32.000 0.00 0.00 0.00 2.69
2247 2328 1.913403 GATGTGCAGCATTAACGCAAC 59.087 47.619 0.00 0.00 38.06 4.17
2369 2450 7.981225 ACTTTGCTGATGTTGTTTCAATAAACT 59.019 29.630 3.01 0.00 44.44 2.66
2428 2509 6.426328 GCTTCTAGCATGAAAGCTACATGTAT 59.574 38.462 24.59 18.77 44.50 2.29
2447 2528 8.596781 AACTAGAGAACCAGATTAAGCTTCTA 57.403 34.615 0.00 0.00 0.00 2.10
2528 2609 3.956848 TCCATATAGCATCTCAGGGATCG 59.043 47.826 0.00 0.00 31.27 3.69
2537 2618 7.341769 GGACAGAGTTATCTCCATATAGCATCT 59.658 40.741 0.00 0.00 41.26 2.90
2546 2627 4.651503 ACAATCGGACAGAGTTATCTCCAT 59.348 41.667 0.00 0.00 41.26 3.41
2551 2632 3.799420 GCTCACAATCGGACAGAGTTATC 59.201 47.826 0.00 0.00 0.00 1.75
2741 2822 7.660617 GCAACTTCTTTACTAAACCCTTCTACT 59.339 37.037 0.00 0.00 0.00 2.57
2767 2848 2.158986 AGATTCTGGACCTCGCATTCTG 60.159 50.000 0.00 0.00 0.00 3.02
2894 2975 1.027357 ACTGCAGTTTGGCAAGACAG 58.973 50.000 15.25 15.04 44.40 3.51
2931 3012 4.584638 TTAGGACTTACCACAATGGCAT 57.415 40.909 0.00 0.00 42.67 4.40
2947 3028 7.618019 AGATCCAAACTATGTAGCATTAGGA 57.382 36.000 0.00 0.00 0.00 2.94
2997 3078 7.156876 TCATGTTCCACAAATTTCCTGATAC 57.843 36.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.