Multiple sequence alignment - TraesCS5D01G232800

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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 TraesCS5D01G232800 chr5D 100.000 3301 0 0 1 3301 340065072 340068372 0.000000e+00 6096
1 TraesCS5D01G232800 chr5D 82.817 1129 144 26 1239 2340 340099083 340100188 0.000000e+00 965
2 TraesCS5D01G232800 chr5D 86.179 123 17 0 1029 1151 340098840 340098962 2.070000e-27 134
3 TraesCS5D01G232800 chr5A 88.000 1525 108 38 337 1800 441181655 441183165 0.000000e+00 1733
4 TraesCS5D01G232800 chr5A 95.183 1038 40 8 1931 2961 441183162 441184196 0.000000e+00 1631
5 TraesCS5D01G232800 chr5A 93.830 389 24 0 1916 2304 441194808 441195196 1.320000e-163 586
6 TraesCS5D01G232800 chr5A 93.521 355 18 3 2950 3299 441184221 441184575 1.050000e-144 523
7 TraesCS5D01G232800 chr5A 79.795 584 89 15 1240 1801 441194150 441194726 6.640000e-107 398
8 TraesCS5D01G232800 chr5A 83.444 302 16 14 14 308 441181389 441181663 1.970000e-62 250
9 TraesCS5D01G232800 chr5A 86.992 123 16 0 1029 1151 441193899 441194021 4.440000e-29 139
10 TraesCS5D01G232800 chr5B 90.267 935 66 16 878 1800 399226126 399227047 0.000000e+00 1199
11 TraesCS5D01G232800 chr5B 82.251 1324 148 47 1031 2304 399274454 399275740 0.000000e+00 1062
12 TraesCS5D01G232800 chr5B 93.556 450 22 4 1931 2378 399227044 399227488 0.000000e+00 664
13 TraesCS5D01G232800 chr5B 91.912 408 20 6 434 836 399225646 399226045 2.880000e-155 558
14 TraesCS5D01G232800 chr5B 92.437 357 22 2 2950 3301 399228521 399228877 3.800000e-139 505
15 TraesCS5D01G232800 chr5B 87.286 409 21 14 2376 2781 399227769 399228149 3.910000e-119 438
16 TraesCS5D01G232800 chr5B 85.981 321 37 4 1894 2214 649866026 649866338 1.470000e-88 337
17 TraesCS5D01G232800 chr5B 80.251 319 21 21 1 317 399224935 399225213 5.590000e-48 202
18 TraesCS5D01G232800 chr4A 83.431 513 67 10 1681 2193 687393861 687394355 8.350000e-126 460
19 TraesCS5D01G232800 chr6D 87.578 322 32 5 1894 2214 66262690 66262376 1.870000e-97 366
20 TraesCS5D01G232800 chr6D 82.791 430 55 11 1786 2214 66627783 66627372 1.870000e-97 366
21 TraesCS5D01G232800 chr7D 85.950 121 17 0 1680 1800 603848573 603848693 2.670000e-26 130
22 TraesCS5D01G232800 chr7D 84.298 121 19 0 1680 1800 604476039 604476159 5.790000e-23 119
23 TraesCS5D01G232800 chr7A 85.950 121 17 0 1680 1800 696553344 696553464 2.670000e-26 130
24 TraesCS5D01G232800 chr7B 85.124 121 18 0 1680 1800 686850748 686850868 1.240000e-24 124


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 TraesCS5D01G232800 chr5D 340065072 340068372 3300 False 6096.000000 6096 100.000000 1 3301 1 chr5D.!!$F1 3300
1 TraesCS5D01G232800 chr5D 340098840 340100188 1348 False 549.500000 965 84.498000 1029 2340 2 chr5D.!!$F2 1311
2 TraesCS5D01G232800 chr5A 441181389 441184575 3186 False 1034.250000 1733 90.037000 14 3299 4 chr5A.!!$F1 3285
3 TraesCS5D01G232800 chr5A 441193899 441195196 1297 False 374.333333 586 86.872333 1029 2304 3 chr5A.!!$F2 1275
4 TraesCS5D01G232800 chr5B 399274454 399275740 1286 False 1062.000000 1062 82.251000 1031 2304 1 chr5B.!!$F1 1273
5 TraesCS5D01G232800 chr5B 399224935 399228877 3942 False 594.333333 1199 89.284833 1 3301 6 chr5B.!!$F3 3300

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
861 1290 0.099082 GACCAGACTACCGCTTCTCG 59.901 60.0 0.00 0.0 38.08 4.04 F
916 1371 0.100682 CGCTATATATCACCCGCGCT 59.899 55.0 5.56 0.0 34.05 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1913 2455 0.106369 CCTGCACCACCATGGATCAT 60.106 55.0 21.47 0.0 40.96 2.45 R
2800 3657 1.006086 TATGGCGTTTCGATGCACAG 58.994 50.0 0.00 0.0 0.00 3.66 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
50 57 1.757682 AAAGAAACAACAGGGACGCA 58.242 45.000 0.00 0.00 0.00 5.24
133 140 2.890371 GAGGGTCACGGCGTACAT 59.110 61.111 14.22 3.42 0.00 2.29
138 145 1.076533 GGTCACGGCGTACATGACAG 61.077 60.000 23.77 6.99 43.73 3.51
317 327 1.313129 CCAAAATAGGGGGTGGGGG 59.687 63.158 0.00 0.00 0.00 5.40
318 328 1.523818 CCAAAATAGGGGGTGGGGGT 61.524 60.000 0.00 0.00 0.00 4.95
319 329 1.310877 CAAAATAGGGGGTGGGGGTA 58.689 55.000 0.00 0.00 0.00 3.69
320 330 1.063492 CAAAATAGGGGGTGGGGGTAC 60.063 57.143 0.00 0.00 0.00 3.34
321 331 0.428520 AAATAGGGGGTGGGGGTACT 59.571 55.000 0.00 0.00 0.00 2.73
322 332 1.342589 AATAGGGGGTGGGGGTACTA 58.657 55.000 0.00 0.00 0.00 1.82
324 334 0.558419 TAGGGGGTGGGGGTACTAGT 60.558 60.000 0.00 0.00 0.00 2.57
325 335 1.083517 GGGGGTGGGGGTACTAGTT 59.916 63.158 0.00 0.00 0.00 2.24
326 336 0.343018 GGGGGTGGGGGTACTAGTTA 59.657 60.000 0.00 0.00 0.00 2.24
327 337 1.693726 GGGGGTGGGGGTACTAGTTAG 60.694 61.905 0.00 0.00 0.00 2.34
328 338 1.008815 GGGGTGGGGGTACTAGTTAGT 59.991 57.143 0.00 0.00 40.24 2.24
330 340 2.292455 GGGTGGGGGTACTAGTTAGTGA 60.292 54.545 0.00 0.00 37.10 3.41
331 341 3.631865 GGGTGGGGGTACTAGTTAGTGAT 60.632 52.174 0.00 0.00 37.10 3.06
332 342 3.640498 GGTGGGGGTACTAGTTAGTGATC 59.360 52.174 0.00 0.00 37.10 2.92
333 343 4.284178 GTGGGGGTACTAGTTAGTGATCA 58.716 47.826 0.00 0.00 37.10 2.92
334 344 4.099113 GTGGGGGTACTAGTTAGTGATCAC 59.901 50.000 18.47 18.47 37.10 3.06
335 345 3.317430 GGGGGTACTAGTTAGTGATCACG 59.683 52.174 19.85 7.36 37.10 4.35
336 346 3.243334 GGGGTACTAGTTAGTGATCACGC 60.243 52.174 19.85 13.83 37.10 5.34
337 347 3.379372 GGGTACTAGTTAGTGATCACGCA 59.621 47.826 19.85 9.50 37.10 5.24
338 348 4.142315 GGGTACTAGTTAGTGATCACGCAA 60.142 45.833 19.85 14.80 37.10 4.85
339 349 4.797349 GGTACTAGTTAGTGATCACGCAAC 59.203 45.833 26.27 26.27 37.10 4.17
340 350 4.514781 ACTAGTTAGTGATCACGCAACA 57.485 40.909 30.91 21.54 35.21 3.33
341 351 4.486090 ACTAGTTAGTGATCACGCAACAG 58.514 43.478 30.91 27.12 35.21 3.16
342 352 3.386768 AGTTAGTGATCACGCAACAGT 57.613 42.857 30.91 18.40 35.21 3.55
343 353 4.514781 AGTTAGTGATCACGCAACAGTA 57.485 40.909 30.91 14.00 35.21 2.74
344 354 4.486090 AGTTAGTGATCACGCAACAGTAG 58.514 43.478 30.91 0.00 35.21 2.57
345 355 4.022242 AGTTAGTGATCACGCAACAGTAGT 60.022 41.667 30.91 17.42 35.21 2.73
346 356 2.677199 AGTGATCACGCAACAGTAGTG 58.323 47.619 19.85 0.00 37.24 2.74
347 357 1.726791 GTGATCACGCAACAGTAGTGG 59.273 52.381 10.69 0.00 36.60 4.00
348 358 1.343142 TGATCACGCAACAGTAGTGGT 59.657 47.619 1.92 0.00 36.60 4.16
349 359 2.224185 TGATCACGCAACAGTAGTGGTT 60.224 45.455 1.92 0.00 36.60 3.67
375 385 3.067833 CAACTTTCTTCCTCCGTTCTCC 58.932 50.000 0.00 0.00 0.00 3.71
411 424 7.198390 ACAATCTGAACAAGTCATTCAAAGTG 58.802 34.615 0.00 0.00 35.70 3.16
508 875 7.772757 AGATAAGATGTTCTTTTTCTAGGGCTG 59.227 37.037 0.00 0.00 37.89 4.85
518 885 0.252696 TCTAGGGCTGGAGCTTTGGA 60.253 55.000 0.00 0.00 41.70 3.53
521 888 0.324091 AGGGCTGGAGCTTTGGAATG 60.324 55.000 0.00 0.00 41.70 2.67
522 889 1.325476 GGGCTGGAGCTTTGGAATGG 61.325 60.000 0.00 0.00 41.70 3.16
523 890 1.514553 GCTGGAGCTTTGGAATGGC 59.485 57.895 0.00 0.00 38.21 4.40
524 891 1.252904 GCTGGAGCTTTGGAATGGCA 61.253 55.000 0.00 0.00 38.21 4.92
525 892 0.529378 CTGGAGCTTTGGAATGGCAC 59.471 55.000 0.00 0.00 0.00 5.01
549 916 1.228003 TCGTGGAAAACATGCCGGT 60.228 52.632 1.90 0.00 36.01 5.28
567 934 2.289565 GGTCGGAGATGGAATTTGGAC 58.710 52.381 0.00 0.00 40.67 4.02
568 935 1.933853 GTCGGAGATGGAATTTGGACG 59.066 52.381 0.00 0.00 40.67 4.79
569 936 1.134521 TCGGAGATGGAATTTGGACGG 60.135 52.381 0.00 0.00 0.00 4.79
570 937 1.134521 CGGAGATGGAATTTGGACGGA 60.135 52.381 0.00 0.00 0.00 4.69
589 961 3.064271 CGGAGGAGTACTCTTTTCTCTCG 59.936 52.174 21.88 18.00 45.83 4.04
599 971 5.704888 ACTCTTTTCTCTCGTACACATCTG 58.295 41.667 0.00 0.00 0.00 2.90
600 972 5.060662 TCTTTTCTCTCGTACACATCTGG 57.939 43.478 0.00 0.00 0.00 3.86
654 1026 5.693961 TCCATGTGATTTGGTGCATAGTAT 58.306 37.500 0.00 0.00 35.64 2.12
655 1027 6.836242 TCCATGTGATTTGGTGCATAGTATA 58.164 36.000 0.00 0.00 35.64 1.47
656 1028 6.710295 TCCATGTGATTTGGTGCATAGTATAC 59.290 38.462 0.00 0.00 35.64 1.47
700 1076 2.802667 CGCGAGGCCGACTTCATTG 61.803 63.158 0.00 0.00 38.22 2.82
704 1080 2.821546 CGAGGCCGACTTCATTGATTA 58.178 47.619 0.00 0.00 38.22 1.75
709 1085 3.063997 GGCCGACTTCATTGATTACAGTG 59.936 47.826 0.00 0.00 35.52 3.66
777 1178 1.133792 CCTCGCCCCCTTCAATAATGT 60.134 52.381 0.00 0.00 0.00 2.71
833 1262 2.020131 CTGCAGATCCAATGGACGC 58.980 57.895 8.42 8.71 32.98 5.19
857 1286 1.889530 GCCAGACCAGACTACCGCTT 61.890 60.000 0.00 0.00 0.00 4.68
859 1288 1.178276 CAGACCAGACTACCGCTTCT 58.822 55.000 0.00 0.00 0.00 2.85
860 1289 1.133407 CAGACCAGACTACCGCTTCTC 59.867 57.143 0.00 0.00 0.00 2.87
861 1290 0.099082 GACCAGACTACCGCTTCTCG 59.901 60.000 0.00 0.00 38.08 4.04
888 1325 2.124860 CCGATTTCCCACGTCCCC 60.125 66.667 0.00 0.00 0.00 4.81
889 1326 2.124860 CGATTTCCCACGTCCCCC 60.125 66.667 0.00 0.00 0.00 5.40
890 1327 2.961893 CGATTTCCCACGTCCCCCA 61.962 63.158 0.00 0.00 0.00 4.96
891 1328 1.613061 GATTTCCCACGTCCCCCAT 59.387 57.895 0.00 0.00 0.00 4.00
892 1329 0.841289 GATTTCCCACGTCCCCCATA 59.159 55.000 0.00 0.00 0.00 2.74
893 1330 1.423921 GATTTCCCACGTCCCCCATAT 59.576 52.381 0.00 0.00 0.00 1.78
894 1331 0.841289 TTTCCCACGTCCCCCATATC 59.159 55.000 0.00 0.00 0.00 1.63
897 1334 2.526046 CCACGTCCCCCATATCCCC 61.526 68.421 0.00 0.00 0.00 4.81
899 1336 4.016706 CGTCCCCCATATCCCCGC 62.017 72.222 0.00 0.00 0.00 6.13
916 1371 0.100682 CGCTATATATCACCCGCGCT 59.899 55.000 5.56 0.00 34.05 5.92
918 1373 1.536284 GCTATATATCACCCGCGCTCC 60.536 57.143 5.56 0.00 0.00 4.70
1101 1557 2.434185 GCGAGATGCACCGGAACA 60.434 61.111 9.46 5.93 45.45 3.18
1114 1570 1.072505 GGAACAAGAACCGAGGCCA 59.927 57.895 5.01 0.00 0.00 5.36
1186 1662 1.069258 CTTACCCGCCCGATCCTTC 59.931 63.158 0.00 0.00 0.00 3.46
1208 1696 0.667487 CACTCCGTCTCGTGCATTGT 60.667 55.000 0.00 0.00 0.00 2.71
1214 1703 1.995484 CGTCTCGTGCATTGTCTCAAT 59.005 47.619 0.00 0.00 0.00 2.57
1311 1810 3.012518 CCGGAAGCTGACTGAAATGATT 58.987 45.455 0.00 0.00 0.00 2.57
1440 1945 1.078143 GGACAGCATGGACACCTCC 60.078 63.158 0.00 0.00 43.62 4.30
1515 2020 1.913262 TGTCGATGTGGACAGCCCT 60.913 57.895 0.00 0.00 41.76 5.19
1524 2029 1.203441 TGGACAGCCCTCTGAGCAAT 61.203 55.000 0.00 0.00 42.95 3.56
1609 2151 2.416547 CTCGTAAGTGCCAAATCACTGG 59.583 50.000 0.00 0.00 45.77 4.00
1620 2162 4.634199 CCAAATCACTGGTCAAAGCATTT 58.366 39.130 0.00 0.00 40.26 2.32
1621 2163 5.058490 CCAAATCACTGGTCAAAGCATTTT 58.942 37.500 0.00 0.00 35.03 1.82
1624 2166 4.998671 TCACTGGTCAAAGCATTTTTCA 57.001 36.364 0.00 0.00 35.03 2.69
1626 2168 5.108517 TCACTGGTCAAAGCATTTTTCAAC 58.891 37.500 0.00 0.00 35.03 3.18
1628 2170 3.452474 TGGTCAAAGCATTTTTCAACGG 58.548 40.909 0.00 0.00 35.03 4.44
1629 2171 3.131223 TGGTCAAAGCATTTTTCAACGGA 59.869 39.130 0.00 0.00 35.03 4.69
1630 2172 4.202202 TGGTCAAAGCATTTTTCAACGGAT 60.202 37.500 0.00 0.00 35.03 4.18
1631 2173 4.150451 GGTCAAAGCATTTTTCAACGGATG 59.850 41.667 0.00 0.00 35.03 3.51
1645 2187 0.865111 CGGATGAACGAACTGCAACA 59.135 50.000 0.00 0.00 35.47 3.33
1650 2192 2.894902 TGAACGAACTGCAACAGTACA 58.105 42.857 0.00 0.00 44.62 2.90
1651 2193 3.263261 TGAACGAACTGCAACAGTACAA 58.737 40.909 0.00 0.00 44.62 2.41
1652 2194 3.685272 TGAACGAACTGCAACAGTACAAA 59.315 39.130 0.00 0.00 44.62 2.83
1653 2195 4.334203 TGAACGAACTGCAACAGTACAAAT 59.666 37.500 0.00 0.00 44.62 2.32
1660 2202 6.254281 ACTGCAACAGTACAAATTGATACC 57.746 37.500 0.00 0.00 43.46 2.73
1661 2203 5.767665 ACTGCAACAGTACAAATTGATACCA 59.232 36.000 0.00 0.00 43.46 3.25
1665 2207 8.147058 TGCAACAGTACAAATTGATACCAAAAT 58.853 29.630 0.00 0.00 35.67 1.82
1695 2237 5.491070 CATCTGTAGGTTGTGAAAGATGGA 58.509 41.667 0.00 0.00 38.11 3.41
1801 2343 2.067013 GCCGTGTCAAGAAGAAGGTAC 58.933 52.381 0.00 0.00 0.00 3.34
1805 2347 3.057734 GTGTCAAGAAGAAGGTACCGTG 58.942 50.000 4.59 0.00 0.00 4.94
1807 2349 1.068474 CAAGAAGAAGGTACCGTGCG 58.932 55.000 4.59 0.00 0.00 5.34
1810 2352 1.549170 AGAAGAAGGTACCGTGCGAAT 59.451 47.619 4.59 0.00 0.00 3.34
1811 2353 1.925185 GAAGAAGGTACCGTGCGAATC 59.075 52.381 4.59 0.00 0.00 2.52
1815 2357 2.182537 GTACCGTGCGAATCCCGT 59.817 61.111 0.00 0.00 41.15 5.28
1824 2366 1.641677 CGAATCCCGTCCAATTCGC 59.358 57.895 4.77 0.00 45.13 4.70
1848 2390 0.319083 CATTGTGCAGCACCACCATT 59.681 50.000 23.06 0.00 34.85 3.16
1850 2392 1.697284 TTGTGCAGCACCACCATTTA 58.303 45.000 23.06 0.00 34.85 1.40
1851 2393 0.958091 TGTGCAGCACCACCATTTAC 59.042 50.000 23.06 0.00 34.85 2.01
1854 2396 1.247567 GCAGCACCACCATTTACAGT 58.752 50.000 0.00 0.00 0.00 3.55
1855 2397 1.200020 GCAGCACCACCATTTACAGTC 59.800 52.381 0.00 0.00 0.00 3.51
1856 2398 2.503331 CAGCACCACCATTTACAGTCA 58.497 47.619 0.00 0.00 0.00 3.41
1857 2399 2.226437 CAGCACCACCATTTACAGTCAC 59.774 50.000 0.00 0.00 0.00 3.67
1858 2400 2.158682 AGCACCACCATTTACAGTCACA 60.159 45.455 0.00 0.00 0.00 3.58
1859 2401 2.226437 GCACCACCATTTACAGTCACAG 59.774 50.000 0.00 0.00 0.00 3.66
1861 2403 2.158682 ACCACCATTTACAGTCACAGCA 60.159 45.455 0.00 0.00 0.00 4.41
1862 2404 2.884012 CCACCATTTACAGTCACAGCAA 59.116 45.455 0.00 0.00 0.00 3.91
1864 2406 4.379813 CCACCATTTACAGTCACAGCAATC 60.380 45.833 0.00 0.00 0.00 2.67
1865 2407 3.758554 ACCATTTACAGTCACAGCAATCC 59.241 43.478 0.00 0.00 0.00 3.01
1866 2408 3.758023 CCATTTACAGTCACAGCAATCCA 59.242 43.478 0.00 0.00 0.00 3.41
1867 2409 4.400251 CCATTTACAGTCACAGCAATCCAT 59.600 41.667 0.00 0.00 0.00 3.41
1868 2410 5.105635 CCATTTACAGTCACAGCAATCCATT 60.106 40.000 0.00 0.00 0.00 3.16
1869 2411 6.095300 CCATTTACAGTCACAGCAATCCATTA 59.905 38.462 0.00 0.00 0.00 1.90
1880 2422 5.105997 ACAGCAATCCATTACTGAAAAGCTC 60.106 40.000 6.54 0.00 35.29 4.09
1896 2438 1.226802 CTCATGCTCTGGTCCGTCG 60.227 63.158 0.00 0.00 0.00 5.12
1908 2450 1.062148 GGTCCGTCGCTAATTTCTTGC 59.938 52.381 0.00 0.00 0.00 4.01
1912 2454 1.802839 GTCGCTAATTTCTTGCTGCG 58.197 50.000 0.00 0.00 43.95 5.18
1914 2456 2.279741 TCGCTAATTTCTTGCTGCGAT 58.720 42.857 3.75 0.00 45.74 4.58
1934 2476 0.749454 GATCCATGGTGGTGCAGGTC 60.749 60.000 12.58 0.00 39.03 3.85
2084 2626 0.041238 TCTCCATCAACTCCTCCGGT 59.959 55.000 0.00 0.00 0.00 5.28
2141 2683 3.188786 GTGCAGGTCGTCGATGCC 61.189 66.667 16.10 6.12 39.22 4.40
2340 2885 4.117685 ACTACGCGAACTTCAGAAACTTT 58.882 39.130 15.93 0.00 0.00 2.66
2565 3400 6.202570 ACAAATTTTCTATGTGCGTGCAAAAT 59.797 30.769 0.00 0.00 0.00 1.82
2698 3533 6.015940 AGCTCTTGTGATGTCATATCGTCATA 60.016 38.462 0.00 0.00 36.07 2.15
2711 3546 1.996898 TCGTCATAAAGTTTCGCGCAT 59.003 42.857 8.75 0.00 0.00 4.73
2787 3627 8.430801 TTTTTCATTTTATTGTTCACCCACAG 57.569 30.769 0.00 0.00 0.00 3.66
2788 3628 6.968263 TTCATTTTATTGTTCACCCACAGA 57.032 33.333 0.00 0.00 0.00 3.41
2789 3629 6.968263 TCATTTTATTGTTCACCCACAGAA 57.032 33.333 0.00 0.00 0.00 3.02
2790 3630 6.980593 TCATTTTATTGTTCACCCACAGAAG 58.019 36.000 0.00 0.00 0.00 2.85
2791 3631 4.846779 TTTATTGTTCACCCACAGAAGC 57.153 40.909 0.00 0.00 0.00 3.86
2792 3632 2.363306 ATTGTTCACCCACAGAAGCA 57.637 45.000 0.00 0.00 0.00 3.91
2793 3633 1.679139 TTGTTCACCCACAGAAGCAG 58.321 50.000 0.00 0.00 0.00 4.24
2794 3634 0.836606 TGTTCACCCACAGAAGCAGA 59.163 50.000 0.00 0.00 0.00 4.26
2795 3635 1.421268 TGTTCACCCACAGAAGCAGAT 59.579 47.619 0.00 0.00 0.00 2.90
2796 3636 1.808945 GTTCACCCACAGAAGCAGATG 59.191 52.381 0.00 0.00 0.00 2.90
2797 3637 0.321919 TCACCCACAGAAGCAGATGC 60.322 55.000 0.00 0.00 42.49 3.91
2907 3944 1.684983 ACCCTCCGTACATAATGACCG 59.315 52.381 0.00 0.00 0.00 4.79
3039 4121 3.680937 CGTCCCTAAATTCAACGCTAACA 59.319 43.478 0.00 0.00 0.00 2.41
3132 4214 0.808125 TTCATTTTCCCACATCGCCG 59.192 50.000 0.00 0.00 0.00 6.46
3156 4238 1.537889 TCATCCTTGGGACCCACGT 60.538 57.895 14.59 0.00 32.98 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 67 2.670934 GTGGTGGCTGTCAGGCTG 60.671 66.667 25.17 8.58 41.96 4.85
83 90 5.451381 GCTAAAAGGAGGAGAAGAGAGCTAC 60.451 48.000 0.00 0.00 0.00 3.58
133 140 3.011566 TGGGTTTTCTTTGCTCTGTCA 57.988 42.857 0.00 0.00 0.00 3.58
138 145 4.918810 TCTCTTTGGGTTTTCTTTGCTC 57.081 40.909 0.00 0.00 0.00 4.26
174 181 9.607988 TGCAATTAGTTTTAATCTCGATCCTAA 57.392 29.630 0.00 0.00 0.00 2.69
175 182 9.607988 TTGCAATTAGTTTTAATCTCGATCCTA 57.392 29.630 0.00 0.00 0.00 2.94
176 183 8.506168 TTGCAATTAGTTTTAATCTCGATCCT 57.494 30.769 0.00 0.00 0.00 3.24
177 184 7.857885 CCTTGCAATTAGTTTTAATCTCGATCC 59.142 37.037 0.00 0.00 0.00 3.36
178 185 8.398665 ACCTTGCAATTAGTTTTAATCTCGATC 58.601 33.333 0.00 0.00 0.00 3.69
179 186 8.281212 ACCTTGCAATTAGTTTTAATCTCGAT 57.719 30.769 0.00 0.00 0.00 3.59
180 187 7.681939 ACCTTGCAATTAGTTTTAATCTCGA 57.318 32.000 0.00 0.00 0.00 4.04
181 188 8.665685 ACTACCTTGCAATTAGTTTTAATCTCG 58.334 33.333 12.86 0.00 0.00 4.04
186 193 9.005777 CCAGTACTACCTTGCAATTAGTTTTAA 57.994 33.333 20.28 5.68 0.00 1.52
187 194 8.158789 ACCAGTACTACCTTGCAATTAGTTTTA 58.841 33.333 20.28 5.95 0.00 1.52
188 195 7.002276 ACCAGTACTACCTTGCAATTAGTTTT 58.998 34.615 20.28 10.38 0.00 2.43
189 196 6.540083 ACCAGTACTACCTTGCAATTAGTTT 58.460 36.000 20.28 10.64 0.00 2.66
190 197 6.123045 ACCAGTACTACCTTGCAATTAGTT 57.877 37.500 20.28 6.50 0.00 2.24
191 198 5.757099 ACCAGTACTACCTTGCAATTAGT 57.243 39.130 19.43 19.43 0.00 2.24
192 199 6.636705 TGTACCAGTACTACCTTGCAATTAG 58.363 40.000 0.00 6.64 37.00 1.73
193 200 6.351541 CCTGTACCAGTACTACCTTGCAATTA 60.352 42.308 0.00 0.00 37.00 1.40
223 231 6.767456 AGATTCAGTTGATTCTCTTGTCACT 58.233 36.000 1.71 0.00 31.34 3.41
300 308 1.063492 GTACCCCCACCCCCTATTTTG 60.063 57.143 0.00 0.00 0.00 2.44
317 327 5.396484 TGTTGCGTGATCACTAACTAGTAC 58.604 41.667 28.00 15.42 34.13 2.73
318 328 5.182570 ACTGTTGCGTGATCACTAACTAGTA 59.817 40.000 28.00 15.97 34.13 1.82
319 329 4.022242 ACTGTTGCGTGATCACTAACTAGT 60.022 41.667 28.00 25.32 36.90 2.57
320 330 4.486090 ACTGTTGCGTGATCACTAACTAG 58.514 43.478 28.00 24.93 31.66 2.57
321 331 4.514781 ACTGTTGCGTGATCACTAACTA 57.485 40.909 28.00 19.22 31.66 2.24
322 332 3.386768 ACTGTTGCGTGATCACTAACT 57.613 42.857 28.00 15.81 31.66 2.24
324 334 4.234574 CACTACTGTTGCGTGATCACTAA 58.765 43.478 22.95 14.85 0.00 2.24
325 335 3.366985 CCACTACTGTTGCGTGATCACTA 60.367 47.826 22.95 9.69 0.00 2.74
326 336 2.610479 CCACTACTGTTGCGTGATCACT 60.610 50.000 22.95 5.56 0.00 3.41
327 337 1.726791 CCACTACTGTTGCGTGATCAC 59.273 52.381 16.21 16.21 0.00 3.06
328 338 1.343142 ACCACTACTGTTGCGTGATCA 59.657 47.619 0.00 0.00 0.00 2.92
330 340 2.413837 GAACCACTACTGTTGCGTGAT 58.586 47.619 6.26 0.00 0.00 3.06
331 341 1.860676 GAACCACTACTGTTGCGTGA 58.139 50.000 6.26 0.00 0.00 4.35
332 342 0.506932 CGAACCACTACTGTTGCGTG 59.493 55.000 0.00 0.00 0.00 5.34
333 343 0.103572 ACGAACCACTACTGTTGCGT 59.896 50.000 0.00 0.00 0.00 5.24
334 344 1.717645 GTACGAACCACTACTGTTGCG 59.282 52.381 0.00 0.00 0.00 4.85
335 345 2.746269 TGTACGAACCACTACTGTTGC 58.254 47.619 0.00 0.00 0.00 4.17
336 346 4.365723 AGTTGTACGAACCACTACTGTTG 58.634 43.478 0.00 0.00 32.04 3.33
337 347 4.660789 AGTTGTACGAACCACTACTGTT 57.339 40.909 0.00 0.00 32.04 3.16
338 348 4.660789 AAGTTGTACGAACCACTACTGT 57.339 40.909 0.00 0.00 33.28 3.55
339 349 5.287226 AGAAAGTTGTACGAACCACTACTG 58.713 41.667 0.00 0.00 33.28 2.74
340 350 5.526506 AGAAAGTTGTACGAACCACTACT 57.473 39.130 0.00 0.00 30.66 2.57
341 351 5.176406 GGAAGAAAGTTGTACGAACCACTAC 59.824 44.000 0.00 0.00 30.66 2.73
342 352 5.069516 AGGAAGAAAGTTGTACGAACCACTA 59.930 40.000 0.00 0.00 30.66 2.74
343 353 4.124970 GGAAGAAAGTTGTACGAACCACT 58.875 43.478 0.00 0.00 33.19 4.00
344 354 4.124970 AGGAAGAAAGTTGTACGAACCAC 58.875 43.478 0.00 0.00 0.00 4.16
345 355 4.374399 GAGGAAGAAAGTTGTACGAACCA 58.626 43.478 0.00 0.00 0.00 3.67
346 356 3.744942 GGAGGAAGAAAGTTGTACGAACC 59.255 47.826 0.00 0.00 0.00 3.62
347 357 3.427863 CGGAGGAAGAAAGTTGTACGAAC 59.572 47.826 0.00 0.00 0.00 3.95
348 358 3.068590 ACGGAGGAAGAAAGTTGTACGAA 59.931 43.478 0.00 0.00 0.00 3.85
349 359 2.624838 ACGGAGGAAGAAAGTTGTACGA 59.375 45.455 0.00 0.00 0.00 3.43
375 385 2.791383 TCAGATTGTTTTTGTGCCGG 57.209 45.000 0.00 0.00 0.00 6.13
411 424 3.760035 TCAGAGCGAACGGGCCTC 61.760 66.667 0.84 0.00 0.00 4.70
508 875 1.607801 GGGTGCCATTCCAAAGCTCC 61.608 60.000 0.00 0.00 39.01 4.70
518 885 1.077501 CCACGAGATGGGTGCCATT 60.078 57.895 0.00 0.00 45.26 3.16
549 916 1.134521 CCGTCCAAATTCCATCTCCGA 60.135 52.381 0.00 0.00 0.00 4.55
567 934 3.064271 CGAGAGAAAAGAGTACTCCTCCG 59.936 52.174 19.38 17.02 41.47 4.63
568 935 4.011698 ACGAGAGAAAAGAGTACTCCTCC 58.988 47.826 19.38 10.82 41.47 4.30
569 936 5.642919 TGTACGAGAGAAAAGAGTACTCCTC 59.357 44.000 19.38 16.99 38.63 3.71
570 937 5.412286 GTGTACGAGAGAAAAGAGTACTCCT 59.588 44.000 19.38 9.09 38.63 3.69
589 961 3.859961 CGATCACACTTCCAGATGTGTAC 59.140 47.826 16.25 11.06 44.55 2.90
599 971 3.043586 CGTACTATGCGATCACACTTCC 58.956 50.000 0.00 0.00 0.00 3.46
600 972 2.468040 GCGTACTATGCGATCACACTTC 59.532 50.000 0.00 0.00 0.00 3.01
654 1026 1.490490 GATGAATCTGGTGCAGGGGTA 59.510 52.381 0.00 0.00 31.51 3.69
655 1027 0.257039 GATGAATCTGGTGCAGGGGT 59.743 55.000 0.00 0.00 31.51 4.95
656 1028 0.466922 GGATGAATCTGGTGCAGGGG 60.467 60.000 0.00 0.00 31.51 4.79
700 1076 6.507900 TGCAGAATAGTCTAGCACTGTAATC 58.492 40.000 11.49 0.00 36.43 1.75
704 1080 3.430098 GCTGCAGAATAGTCTAGCACTGT 60.430 47.826 20.43 0.00 36.06 3.55
709 1085 3.791245 ACAAGCTGCAGAATAGTCTAGC 58.209 45.455 20.43 6.82 36.20 3.42
777 1178 0.747644 TCGCCTCCGGTTACGTCATA 60.748 55.000 0.00 0.00 38.78 2.15
861 1290 1.712018 GGGAAATCGGTTACGCAGCC 61.712 60.000 0.00 0.00 40.69 4.85
869 1306 1.002990 GGGACGTGGGAAATCGGTT 60.003 57.895 0.00 0.00 0.00 4.44
876 1313 1.057851 GGATATGGGGGACGTGGGAA 61.058 60.000 0.00 0.00 0.00 3.97
888 1325 4.223032 GGGTGATATATAGCGGGGATATGG 59.777 50.000 0.00 0.00 0.00 2.74
889 1326 4.082190 CGGGTGATATATAGCGGGGATATG 60.082 50.000 0.00 0.00 0.00 1.78
890 1327 4.087182 CGGGTGATATATAGCGGGGATAT 58.913 47.826 0.00 0.00 0.00 1.63
891 1328 3.493334 CGGGTGATATATAGCGGGGATA 58.507 50.000 0.00 0.00 0.00 2.59
892 1329 2.317040 CGGGTGATATATAGCGGGGAT 58.683 52.381 0.00 0.00 0.00 3.85
893 1330 1.771565 CGGGTGATATATAGCGGGGA 58.228 55.000 0.00 0.00 0.00 4.81
894 1331 0.104304 GCGGGTGATATATAGCGGGG 59.896 60.000 0.00 0.00 0.00 5.73
899 1336 2.025155 AGGAGCGCGGGTGATATATAG 58.975 52.381 8.83 0.00 0.00 1.31
916 1371 5.569355 TGAATGTTTGAGAATAGGCAAGGA 58.431 37.500 0.00 0.00 0.00 3.36
918 1373 5.803967 GCTTGAATGTTTGAGAATAGGCAAG 59.196 40.000 0.00 0.00 33.95 4.01
1082 1538 4.467084 TTCCGGTGCATCTCGCCC 62.467 66.667 0.00 0.00 42.41 6.13
1089 1545 1.234615 CGGTTCTTGTTCCGGTGCAT 61.235 55.000 0.00 0.00 42.61 3.96
1100 1556 1.164041 AACGTTGGCCTCGGTTCTTG 61.164 55.000 20.79 0.00 0.00 3.02
1101 1557 1.147600 AACGTTGGCCTCGGTTCTT 59.852 52.632 20.79 7.10 0.00 2.52
1114 1570 2.434359 GGCCGAGCTAGCAACGTT 60.434 61.111 24.56 0.00 0.00 3.99
1398 1903 2.510238 CTCTTCTTGCTCGCCGGG 60.510 66.667 2.18 0.00 0.00 5.73
1405 1910 2.664081 CCCGGCTCCTCTTCTTGCT 61.664 63.158 0.00 0.00 0.00 3.91
1494 1999 0.391661 GGCTGTCCACATCGACATGT 60.392 55.000 0.00 0.00 44.72 3.21
1609 2151 4.981674 TCATCCGTTGAAAAATGCTTTGAC 59.018 37.500 0.00 0.00 0.00 3.18
1620 2162 2.032377 GCAGTTCGTTCATCCGTTGAAA 60.032 45.455 0.14 0.00 45.71 2.69
1621 2163 1.529438 GCAGTTCGTTCATCCGTTGAA 59.471 47.619 0.00 0.00 42.09 2.69
1624 2166 1.263217 GTTGCAGTTCGTTCATCCGTT 59.737 47.619 0.00 0.00 0.00 4.44
1626 2168 0.865111 TGTTGCAGTTCGTTCATCCG 59.135 50.000 0.00 0.00 0.00 4.18
1628 2170 3.493129 TGTACTGTTGCAGTTCGTTCATC 59.507 43.478 7.11 0.00 42.59 2.92
1629 2171 3.462982 TGTACTGTTGCAGTTCGTTCAT 58.537 40.909 7.11 0.00 42.59 2.57
1630 2172 2.894902 TGTACTGTTGCAGTTCGTTCA 58.105 42.857 7.11 0.00 42.59 3.18
1631 2173 3.936902 TTGTACTGTTGCAGTTCGTTC 57.063 42.857 7.11 0.00 42.59 3.95
1635 2177 6.801862 GGTATCAATTTGTACTGTTGCAGTTC 59.198 38.462 7.11 3.25 42.59 3.01
1638 2180 6.252967 TGGTATCAATTTGTACTGTTGCAG 57.747 37.500 0.00 0.00 37.52 4.41
1645 2187 7.362574 CCACCGATTTTGGTATCAATTTGTACT 60.363 37.037 0.00 0.00 41.38 2.73
1650 2192 4.221703 TGCCACCGATTTTGGTATCAATTT 59.778 37.500 0.00 0.00 41.38 1.82
1651 2193 3.766591 TGCCACCGATTTTGGTATCAATT 59.233 39.130 0.00 0.00 41.38 2.32
1652 2194 3.360867 TGCCACCGATTTTGGTATCAAT 58.639 40.909 0.00 0.00 41.38 2.57
1653 2195 2.796557 TGCCACCGATTTTGGTATCAA 58.203 42.857 0.00 0.00 41.38 2.57
1660 2202 2.355756 CCTACAGATGCCACCGATTTTG 59.644 50.000 0.00 0.00 0.00 2.44
1661 2203 2.026262 ACCTACAGATGCCACCGATTTT 60.026 45.455 0.00 0.00 0.00 1.82
1665 2207 0.249120 CAACCTACAGATGCCACCGA 59.751 55.000 0.00 0.00 0.00 4.69
1695 2237 2.289444 CCCGTACTTCCGCCATTGATAT 60.289 50.000 0.00 0.00 0.00 1.63
1784 2326 3.057734 CACGGTACCTTCTTCTTGACAC 58.942 50.000 10.90 0.00 0.00 3.67
1805 2347 1.641677 CGAATTGGACGGGATTCGC 59.358 57.895 5.68 0.00 45.20 4.70
1807 2349 1.772063 CGGCGAATTGGACGGGATTC 61.772 60.000 7.97 0.00 33.92 2.52
1810 2352 3.365291 CTCGGCGAATTGGACGGGA 62.365 63.158 10.49 0.00 43.24 5.14
1811 2353 2.890474 CTCGGCGAATTGGACGGG 60.890 66.667 16.10 8.80 39.44 5.28
1815 2357 0.676466 ACAATGCTCGGCGAATTGGA 60.676 50.000 28.06 13.79 0.00 3.53
1824 2366 2.177531 GTGCTGCACAATGCTCGG 59.822 61.111 26.70 0.00 45.31 4.63
1848 2390 5.643348 CAGTAATGGATTGCTGTGACTGTAA 59.357 40.000 8.78 0.00 42.92 2.41
1850 2392 4.005650 CAGTAATGGATTGCTGTGACTGT 58.994 43.478 8.78 0.00 42.92 3.55
1851 2393 4.256110 TCAGTAATGGATTGCTGTGACTG 58.744 43.478 14.67 4.89 46.34 3.51
1854 2396 5.335897 GCTTTTCAGTAATGGATTGCTGTGA 60.336 40.000 14.67 5.28 46.34 3.58
1855 2397 4.860907 GCTTTTCAGTAATGGATTGCTGTG 59.139 41.667 14.67 7.36 46.34 3.66
1856 2398 4.768968 AGCTTTTCAGTAATGGATTGCTGT 59.231 37.500 14.67 0.00 46.34 4.40
1858 2400 5.012239 TGAGCTTTTCAGTAATGGATTGCT 58.988 37.500 0.00 0.00 32.81 3.91
1859 2401 5.314923 TGAGCTTTTCAGTAATGGATTGC 57.685 39.130 0.00 0.00 0.00 3.56
1861 2403 5.899299 GCATGAGCTTTTCAGTAATGGATT 58.101 37.500 0.00 0.00 39.68 3.01
1862 2404 5.511234 GCATGAGCTTTTCAGTAATGGAT 57.489 39.130 0.00 0.00 39.68 3.41
1880 2422 2.004808 TAGCGACGGACCAGAGCATG 62.005 60.000 0.00 0.00 0.00 4.06
1889 2431 2.000447 AGCAAGAAATTAGCGACGGAC 59.000 47.619 0.00 0.00 0.00 4.79
1890 2432 1.999735 CAGCAAGAAATTAGCGACGGA 59.000 47.619 0.00 0.00 0.00 4.69
1891 2433 1.529826 GCAGCAAGAAATTAGCGACGG 60.530 52.381 0.00 0.00 0.00 4.79
1892 2434 1.802839 GCAGCAAGAAATTAGCGACG 58.197 50.000 0.00 0.00 0.00 5.12
1896 2438 3.680642 TCATCGCAGCAAGAAATTAGC 57.319 42.857 0.00 0.00 0.00 3.09
1908 2450 0.179037 ACCACCATGGATCATCGCAG 60.179 55.000 21.47 0.00 40.96 5.18
1912 2454 1.315690 CTGCACCACCATGGATCATC 58.684 55.000 21.47 4.95 40.96 2.92
1913 2455 0.106369 CCTGCACCACCATGGATCAT 60.106 55.000 21.47 0.00 40.96 2.45
1914 2456 1.303948 CCTGCACCACCATGGATCA 59.696 57.895 21.47 7.31 40.96 2.92
1934 2476 3.452786 TCCTCCGCGCTTCTCTGG 61.453 66.667 5.56 0.00 0.00 3.86
2084 2626 2.678580 TCCAGCGTGATGGTCGGA 60.679 61.111 3.80 0.00 41.43 4.55
2340 2885 8.177119 AGTGTTCCAAATGCTACAAAATTAGA 57.823 30.769 0.00 0.00 0.00 2.10
2565 3400 6.193504 TCCCCAATGTCATATTGTCATTCAA 58.806 36.000 0.00 0.00 34.74 2.69
2662 3497 3.123804 TCACAAGAGCTCTCGACAAAAC 58.876 45.455 18.55 0.00 34.09 2.43
2698 3533 4.066710 GTTTCTAGATGCGCGAAACTTT 57.933 40.909 22.53 0.00 41.81 2.66
2711 3546 3.820467 CCAATGGTGCACAAGTTTCTAGA 59.180 43.478 20.43 0.00 0.00 2.43
2796 3636 1.421485 CGTTTCGATGCACAGGAGC 59.579 57.895 0.00 0.00 0.00 4.70
2797 3637 1.421485 GCGTTTCGATGCACAGGAG 59.579 57.895 0.00 0.00 0.00 3.69
2800 3657 1.006086 TATGGCGTTTCGATGCACAG 58.994 50.000 0.00 0.00 0.00 3.66
2807 3664 2.442212 TGTTGAGTATGGCGTTTCGA 57.558 45.000 0.00 0.00 0.00 3.71
2870 3907 3.693085 GAGGGTGTGTTATCGACTCTACA 59.307 47.826 0.00 0.00 0.00 2.74
2887 3924 1.684983 CGGTCATTATGTACGGAGGGT 59.315 52.381 0.00 0.00 0.00 4.34
2907 3944 1.863454 TCTAGTCTTCGTATCGGCGAC 59.137 52.381 13.76 0.00 40.85 5.19
3039 4121 0.751643 GCGTGGCAAGGATGGGTTAT 60.752 55.000 1.91 0.00 0.00 1.89
3132 4214 0.470341 GGTCCCAAGGATGAGGCTAC 59.530 60.000 0.00 0.00 32.73 3.58
3156 4238 2.284625 AGGACAGCCACCCATCGA 60.285 61.111 0.00 0.00 36.29 3.59
3238 4320 5.748630 GTCAAAGTCAACCTCAAAATCCAAC 59.251 40.000 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.