Multiple sequence alignment - TraesCS6D01G068400

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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 TraesCS6D01G068400 chr6D 100.000 4448 0 0 1 4448 34342354 34346801 0.000000e+00 8215
1 TraesCS6D01G068400 chr6A 91.960 2276 105 40 631 2892 38472021 38474232 0.000000e+00 3118
2 TraesCS6D01G068400 chr6A 96.429 1092 31 5 3157 4241 38474448 38475538 0.000000e+00 1794
3 TraesCS6D01G068400 chr6A 90.855 339 23 6 235 567 38471239 38471575 8.780000e-122 448
4 TraesCS6D01G068400 chr6A 97.608 209 5 0 4240 4448 38475622 38475830 4.230000e-95 359
5 TraesCS6D01G068400 chr6A 92.050 239 6 2 1 230 38470587 38470821 1.540000e-84 324
6 TraesCS6D01G068400 chr6A 92.366 131 8 2 2914 3043 38474224 38474353 7.600000e-43 185
7 TraesCS6D01G068400 chr6B 97.152 1229 22 5 1934 3161 71040853 71042069 0.000000e+00 2063
8 TraesCS6D01G068400 chr6B 94.946 1306 44 13 3157 4448 71042120 71043417 0.000000e+00 2026
9 TraesCS6D01G068400 chr6B 88.012 1318 80 35 631 1921 71039501 71040767 0.000000e+00 1487
10 TraesCS6D01G068400 chr6B 85.470 585 28 30 2 567 71038446 71038992 1.400000e-154 556


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 TraesCS6D01G068400 chr6D 34342354 34346801 4447 False 8215 8215 100.000000 1 4448 1 chr6D.!!$F1 4447
1 TraesCS6D01G068400 chr6A 38470587 38475830 5243 False 1038 3118 93.544667 1 4448 6 chr6A.!!$F1 4447
2 TraesCS6D01G068400 chr6B 71038446 71043417 4971 False 1533 2063 91.395000 2 4448 4 chr6B.!!$F1 4446

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
555 989 1.812571 ACTACTTTCGCTTGGCCAATG 59.187 47.619 20.85 15.01 0.00 2.82 F
1405 2315 0.036388 CGAGGAGGCTTGGCTTGTTA 60.036 55.000 0.00 0.00 0.00 2.41 F
1719 2629 0.319083 ACGCGGTTGGTATCAAGTCA 59.681 50.000 12.47 0.00 32.92 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 2720 0.678048 GGTAAGGGCAGCTGAACCAG 60.678 60.000 20.43 0.0 34.12 4.00 R
3234 4359 3.451178 AGTGAGTATACCACGCAGGAAAT 59.549 43.478 14.77 0.0 37.65 2.17 R
3515 4640 0.097674 GCGCATAGAACAGTTGGCAG 59.902 55.000 0.30 0.0 0.00 4.85 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
34 35 5.378230 TTGAGGATATGTGCTCCATCTTT 57.622 39.130 8.48 0.00 41.68 2.52
35 36 5.378230 TGAGGATATGTGCTCCATCTTTT 57.622 39.130 8.48 0.00 41.68 2.27
40 41 7.293073 AGGATATGTGCTCCATCTTTTTGTAT 58.707 34.615 0.00 0.00 35.08 2.29
189 201 8.613060 ACTGCCAATATTTGATGATGTACTAG 57.387 34.615 0.00 0.00 0.00 2.57
218 230 2.987413 TTCTACGCCATGTGCTTTTG 57.013 45.000 4.92 0.00 38.05 2.44
230 242 5.453198 CCATGTGCTTTTGTTCCTAAAACCT 60.453 40.000 0.00 0.00 0.00 3.50
232 244 6.139048 TGTGCTTTTGTTCCTAAAACCTAC 57.861 37.500 0.00 0.00 0.00 3.18
233 245 5.652891 TGTGCTTTTGTTCCTAAAACCTACA 59.347 36.000 0.00 0.00 0.00 2.74
352 780 3.263425 TGTGAACTGAAATACTCCCTCCC 59.737 47.826 0.00 0.00 0.00 4.30
357 785 3.705072 ACTGAAATACTCCCTCCCTTACG 59.295 47.826 0.00 0.00 0.00 3.18
392 823 6.913873 TTTGAACTAAGACCACACACTTAC 57.086 37.500 0.00 0.00 0.00 2.34
555 989 1.812571 ACTACTTTCGCTTGGCCAATG 59.187 47.619 20.85 15.01 0.00 2.82
567 1001 4.261909 GCTTGGCCAATGAAGATCCTATTG 60.262 45.833 20.85 2.71 0.00 1.90
569 1003 5.645056 TGGCCAATGAAGATCCTATTGTA 57.355 39.130 0.61 0.00 31.55 2.41
570 1004 6.012337 TGGCCAATGAAGATCCTATTGTAA 57.988 37.500 0.61 0.00 31.55 2.41
571 1005 6.430864 TGGCCAATGAAGATCCTATTGTAAA 58.569 36.000 0.61 0.00 31.55 2.01
572 1006 7.068702 TGGCCAATGAAGATCCTATTGTAAAT 58.931 34.615 0.61 0.00 31.55 1.40
573 1007 7.231317 TGGCCAATGAAGATCCTATTGTAAATC 59.769 37.037 0.61 0.00 31.55 2.17
607 1428 4.762289 AGGGGCAGTTAGATTCTACAAG 57.238 45.455 0.00 0.00 0.00 3.16
608 1429 3.118223 AGGGGCAGTTAGATTCTACAAGC 60.118 47.826 0.00 0.00 0.00 4.01
631 1453 3.290710 ACAAGATTCCGGGAATTCATGG 58.709 45.455 22.53 12.20 31.89 3.66
640 1462 3.397482 CGGGAATTCATGGTTTTTGCAA 58.603 40.909 7.93 0.00 0.00 4.08
641 1463 3.812053 CGGGAATTCATGGTTTTTGCAAA 59.188 39.130 8.05 8.05 0.00 3.68
642 1464 4.274459 CGGGAATTCATGGTTTTTGCAAAA 59.726 37.500 20.46 20.46 0.00 2.44
723 1606 9.777575 TTTTAAGCACACACTTTTAGTTCTTAC 57.222 29.630 0.00 0.00 0.00 2.34
726 1609 8.904099 AAGCACACACTTTTAGTTCTTACTAT 57.096 30.769 0.00 0.00 36.76 2.12
727 1610 8.904099 AGCACACACTTTTAGTTCTTACTATT 57.096 30.769 0.00 0.00 36.76 1.73
788 1689 5.979993 TCCTACAAGTAATTACCATTCGCA 58.020 37.500 12.05 0.00 0.00 5.10
789 1690 6.408035 TCCTACAAGTAATTACCATTCGCAA 58.592 36.000 12.05 0.00 0.00 4.85
792 1693 7.696453 CCTACAAGTAATTACCATTCGCAAAAG 59.304 37.037 12.05 0.00 0.00 2.27
827 1728 9.727859 ACATTTAATTACCCCAAAAATGTTACC 57.272 29.630 7.20 0.00 44.25 2.85
831 1732 6.614694 ATTACCCCAAAAATGTTACCCTTC 57.385 37.500 0.00 0.00 0.00 3.46
832 1733 4.207698 ACCCCAAAAATGTTACCCTTCT 57.792 40.909 0.00 0.00 0.00 2.85
843 1745 2.040679 GTTACCCTTCTAAACCTGGGCA 59.959 50.000 0.00 0.00 43.25 5.36
1223 2128 4.373116 TTCCGCCGACTCAGGTGC 62.373 66.667 0.00 0.00 40.31 5.01
1258 2163 0.383949 CTTCTCCTCGCCTCACTAGC 59.616 60.000 0.00 0.00 0.00 3.42
1260 2165 0.749818 TCTCCTCGCCTCACTAGCAG 60.750 60.000 0.00 0.00 0.00 4.24
1261 2166 1.000771 TCCTCGCCTCACTAGCAGT 60.001 57.895 0.00 0.00 0.00 4.40
1262 2167 1.032657 TCCTCGCCTCACTAGCAGTC 61.033 60.000 0.00 0.00 0.00 3.51
1275 2185 7.221067 CCTCACTAGCAGTCTTTTAAGTATTCG 59.779 40.741 0.00 0.00 0.00 3.34
1276 2186 7.600065 TCACTAGCAGTCTTTTAAGTATTCGT 58.400 34.615 0.00 0.00 0.00 3.85
1278 2188 9.350357 CACTAGCAGTCTTTTAAGTATTCGTTA 57.650 33.333 0.00 0.00 0.00 3.18
1292 2202 2.606717 TCGTTAGTGTACTGCTGTCG 57.393 50.000 0.00 0.00 0.00 4.35
1298 2208 1.080772 TGTACTGCTGTCGCCTTCG 60.081 57.895 0.00 0.00 34.43 3.79
1302 2212 4.680237 TGCTGTCGCCTTCGGTGG 62.680 66.667 0.00 0.00 33.43 4.61
1303 2213 4.681978 GCTGTCGCCTTCGGTGGT 62.682 66.667 0.00 0.00 33.43 4.16
1304 2214 2.738521 CTGTCGCCTTCGGTGGTG 60.739 66.667 2.46 2.46 38.85 4.17
1307 2217 2.915659 TCGCCTTCGGTGGTGTCT 60.916 61.111 7.75 0.00 38.63 3.41
1309 2219 2.047179 GCCTTCGGTGGTGTCTCC 60.047 66.667 0.00 0.00 0.00 3.71
1310 2220 2.879233 GCCTTCGGTGGTGTCTCCA 61.879 63.158 0.00 0.00 45.01 3.86
1325 2235 0.535780 CTCCAGGCAGAAGCACAACA 60.536 55.000 0.00 0.00 44.61 3.33
1328 2238 1.336517 CCAGGCAGAAGCACAACATTG 60.337 52.381 0.00 0.00 44.61 2.82
1329 2239 1.610038 CAGGCAGAAGCACAACATTGA 59.390 47.619 0.00 0.00 44.61 2.57
1330 2240 1.884579 AGGCAGAAGCACAACATTGAG 59.115 47.619 0.00 0.00 44.61 3.02
1331 2241 1.881973 GGCAGAAGCACAACATTGAGA 59.118 47.619 0.00 0.00 44.61 3.27
1332 2242 2.490903 GGCAGAAGCACAACATTGAGAT 59.509 45.455 0.00 0.00 44.61 2.75
1333 2243 3.691118 GGCAGAAGCACAACATTGAGATA 59.309 43.478 0.00 0.00 44.61 1.98
1334 2244 4.201891 GGCAGAAGCACAACATTGAGATAG 60.202 45.833 0.00 0.00 44.61 2.08
1335 2245 4.394300 GCAGAAGCACAACATTGAGATAGT 59.606 41.667 0.00 0.00 41.58 2.12
1336 2246 5.582269 GCAGAAGCACAACATTGAGATAGTA 59.418 40.000 0.00 0.00 41.58 1.82
1338 2248 7.201679 GCAGAAGCACAACATTGAGATAGTATT 60.202 37.037 0.00 0.00 41.58 1.89
1340 2250 8.887717 AGAAGCACAACATTGAGATAGTATTTC 58.112 33.333 0.00 0.00 0.00 2.17
1341 2251 7.559590 AGCACAACATTGAGATAGTATTTCC 57.440 36.000 0.00 0.00 0.00 3.13
1344 2254 8.125448 GCACAACATTGAGATAGTATTTCCTTC 58.875 37.037 0.00 0.00 0.00 3.46
1352 2262 9.658799 TTGAGATAGTATTTCCTTCTTCTTGTG 57.341 33.333 0.00 0.00 0.00 3.33
1353 2263 8.260818 TGAGATAGTATTTCCTTCTTCTTGTGG 58.739 37.037 0.00 0.00 0.00 4.17
1354 2264 7.051000 AGATAGTATTTCCTTCTTCTTGTGGC 58.949 38.462 0.00 0.00 0.00 5.01
1355 2265 4.003648 AGTATTTCCTTCTTCTTGTGGCG 58.996 43.478 0.00 0.00 0.00 5.69
1358 2268 3.478857 TTCCTTCTTCTTGTGGCGTTA 57.521 42.857 0.00 0.00 0.00 3.18
1359 2269 3.040147 TCCTTCTTCTTGTGGCGTTAG 57.960 47.619 0.00 0.00 0.00 2.34
1361 2271 3.139077 CCTTCTTCTTGTGGCGTTAGTT 58.861 45.455 0.00 0.00 0.00 2.24
1362 2272 4.039488 TCCTTCTTCTTGTGGCGTTAGTTA 59.961 41.667 0.00 0.00 0.00 2.24
1374 2284 3.742369 GGCGTTAGTTAAGTGTAGCAACA 59.258 43.478 0.00 0.00 0.00 3.33
1384 2294 9.672673 AGTTAAGTGTAGCAACAGATGAATTAT 57.327 29.630 0.00 0.00 35.91 1.28
1388 2298 5.753438 GTGTAGCAACAGATGAATTATCCGA 59.247 40.000 0.00 0.00 35.91 4.55
1389 2299 5.985530 TGTAGCAACAGATGAATTATCCGAG 59.014 40.000 0.00 0.00 36.40 4.63
1398 2308 2.104792 TGAATTATCCGAGGAGGCTTGG 59.895 50.000 0.00 0.00 40.77 3.61
1399 2309 0.398318 ATTATCCGAGGAGGCTTGGC 59.602 55.000 0.00 0.00 40.77 4.52
1400 2310 0.691078 TTATCCGAGGAGGCTTGGCT 60.691 55.000 0.00 0.00 40.77 4.75
1401 2311 0.691078 TATCCGAGGAGGCTTGGCTT 60.691 55.000 0.00 0.00 40.77 4.35
1402 2312 2.262774 ATCCGAGGAGGCTTGGCTTG 62.263 60.000 0.00 0.00 40.77 4.01
1404 2314 1.302832 CGAGGAGGCTTGGCTTGTT 60.303 57.895 0.00 0.00 0.00 2.83
1405 2315 0.036388 CGAGGAGGCTTGGCTTGTTA 60.036 55.000 0.00 0.00 0.00 2.41
1406 2316 1.743996 GAGGAGGCTTGGCTTGTTAG 58.256 55.000 0.00 0.00 0.00 2.34
1407 2317 1.003696 GAGGAGGCTTGGCTTGTTAGT 59.996 52.381 0.00 0.00 0.00 2.24
1408 2318 1.425448 AGGAGGCTTGGCTTGTTAGTT 59.575 47.619 0.00 0.00 0.00 2.24
1409 2319 1.541588 GGAGGCTTGGCTTGTTAGTTG 59.458 52.381 0.00 0.00 0.00 3.16
1410 2320 2.230660 GAGGCTTGGCTTGTTAGTTGT 58.769 47.619 0.00 0.00 0.00 3.32
1411 2321 2.623416 GAGGCTTGGCTTGTTAGTTGTT 59.377 45.455 0.00 0.00 0.00 2.83
1412 2322 3.818773 GAGGCTTGGCTTGTTAGTTGTTA 59.181 43.478 0.00 0.00 0.00 2.41
1413 2323 4.211920 AGGCTTGGCTTGTTAGTTGTTAA 58.788 39.130 0.00 0.00 0.00 2.01
1414 2324 4.647399 AGGCTTGGCTTGTTAGTTGTTAAA 59.353 37.500 0.00 0.00 0.00 1.52
1415 2325 5.128008 AGGCTTGGCTTGTTAGTTGTTAAAA 59.872 36.000 0.00 0.00 0.00 1.52
1416 2326 5.813157 GGCTTGGCTTGTTAGTTGTTAAAAA 59.187 36.000 0.00 0.00 0.00 1.94
1494 2404 6.697019 GTGTTATAATTGTGTTGATGGATGGC 59.303 38.462 0.00 0.00 0.00 4.40
1498 2408 5.999205 AATTGTGTTGATGGATGGCTTTA 57.001 34.783 0.00 0.00 0.00 1.85
1505 2415 4.032960 TGATGGATGGCTTTACTTGTGT 57.967 40.909 0.00 0.00 0.00 3.72
1584 2494 2.355818 GCAAATAAGGGAGGAAGTCGGT 60.356 50.000 0.00 0.00 0.00 4.69
1701 2611 1.222115 ACAAGAAGAAGGCGTGCGAC 61.222 55.000 0.00 0.00 0.00 5.19
1719 2629 0.319083 ACGCGGTTGGTATCAAGTCA 59.681 50.000 12.47 0.00 32.92 3.41
1791 2701 3.684788 ACATAGCAACCTTCAACGATGAC 59.315 43.478 0.00 0.00 34.61 3.06
1810 2720 3.576356 CGTCGGTGCATGGCATCC 61.576 66.667 0.00 0.00 41.91 3.51
1832 2742 0.324943 GTTCAGCTGCCCTTACCTCA 59.675 55.000 9.47 0.00 0.00 3.86
1867 2791 9.113838 CTCAATGGCTAGTATAATTGTTGAACT 57.886 33.333 0.00 0.00 32.92 3.01
2012 3009 4.623886 GCATCGATAATGGCAGATTCCCTA 60.624 45.833 0.00 0.00 35.77 3.53
2158 3155 9.746457 TTTATTTTATTTTGGGCTTTTGGCTAT 57.254 25.926 0.00 0.00 45.25 2.97
2199 3196 4.279671 TGGTTTTGTGTGTTTCTTGTCAGT 59.720 37.500 0.00 0.00 0.00 3.41
2205 3202 4.154015 TGTGTGTTTCTTGTCAGTGTTCTG 59.846 41.667 0.00 0.00 42.54 3.02
2321 3318 8.579850 TGAATGCTGTTAGTATTGAAAAGGAT 57.420 30.769 0.00 0.00 30.60 3.24
2885 3882 8.125978 TCTCAATGGAAAAGCTTGATAATGTT 57.874 30.769 0.00 0.00 0.00 2.71
2932 3929 7.281774 TGCACATTTTGTATCATGTTTTGGTTT 59.718 29.630 0.00 0.00 30.90 3.27
3043 4042 3.137360 GGGATCAAACTCTATGAAGCCCT 59.863 47.826 0.00 0.00 40.03 5.19
3056 4055 4.052518 GCCCTGTGCTCCCACCAT 62.053 66.667 0.00 0.00 41.35 3.55
3057 4056 2.765969 CCCTGTGCTCCCACCATT 59.234 61.111 0.00 0.00 41.35 3.16
3058 4057 1.679977 CCCTGTGCTCCCACCATTG 60.680 63.158 0.00 0.00 41.35 2.82
3059 4058 1.679977 CCTGTGCTCCCACCATTGG 60.680 63.158 0.00 0.00 41.35 3.16
3072 4071 5.395682 CCACCATTGGGCAGATATTTATG 57.604 43.478 7.78 0.00 39.57 1.90
3073 4072 4.221262 CCACCATTGGGCAGATATTTATGG 59.779 45.833 7.78 0.00 39.57 2.74
3074 4073 5.078949 CACCATTGGGCAGATATTTATGGA 58.921 41.667 7.78 0.00 37.90 3.41
3075 4074 5.539574 CACCATTGGGCAGATATTTATGGAA 59.460 40.000 7.78 0.00 37.90 3.53
3076 4075 5.776716 ACCATTGGGCAGATATTTATGGAAG 59.223 40.000 7.78 0.00 37.90 3.46
3077 4076 5.776716 CCATTGGGCAGATATTTATGGAAGT 59.223 40.000 0.00 0.00 34.39 3.01
3078 4077 6.268387 CCATTGGGCAGATATTTATGGAAGTT 59.732 38.462 0.00 0.00 34.39 2.66
3079 4078 6.713762 TTGGGCAGATATTTATGGAAGTTG 57.286 37.500 0.00 0.00 0.00 3.16
3080 4079 4.584325 TGGGCAGATATTTATGGAAGTTGC 59.416 41.667 0.00 0.00 0.00 4.17
3081 4080 4.584325 GGGCAGATATTTATGGAAGTTGCA 59.416 41.667 0.00 0.00 0.00 4.08
3082 4081 5.068987 GGGCAGATATTTATGGAAGTTGCAA 59.931 40.000 0.00 0.00 0.00 4.08
3083 4082 5.979517 GGCAGATATTTATGGAAGTTGCAAC 59.020 40.000 22.17 22.17 0.00 4.17
3084 4083 6.183360 GGCAGATATTTATGGAAGTTGCAACT 60.183 38.462 26.36 26.36 42.04 3.16
3085 4084 7.013274 GGCAGATATTTATGGAAGTTGCAACTA 59.987 37.037 31.31 17.32 38.57 2.24
3086 4085 8.072567 GCAGATATTTATGGAAGTTGCAACTAG 58.927 37.037 31.31 4.12 38.57 2.57
3087 4086 8.072567 CAGATATTTATGGAAGTTGCAACTAGC 58.927 37.037 31.31 24.25 45.96 3.42
3102 4101 6.670077 GCAACTAGCATAGCTTCTTAAGTT 57.330 37.500 1.63 0.00 44.39 2.66
3103 4102 7.078011 GCAACTAGCATAGCTTCTTAAGTTT 57.922 36.000 1.63 0.00 44.39 2.66
3104 4103 7.530863 GCAACTAGCATAGCTTCTTAAGTTTT 58.469 34.615 1.63 0.00 44.39 2.43
3105 4104 8.023706 GCAACTAGCATAGCTTCTTAAGTTTTT 58.976 33.333 1.63 0.00 44.39 1.94
3112 4111 9.840427 GCATAGCTTCTTAAGTTTTTATGAACA 57.160 29.630 16.53 0.00 32.60 3.18
3115 4114 8.232913 AGCTTCTTAAGTTTTTATGAACACCA 57.767 30.769 1.63 0.00 32.60 4.17
3116 4115 8.135529 AGCTTCTTAAGTTTTTATGAACACCAC 58.864 33.333 1.63 0.00 32.60 4.16
3117 4116 7.112984 GCTTCTTAAGTTTTTATGAACACCACG 59.887 37.037 1.63 0.00 32.60 4.94
3118 4117 7.556733 TCTTAAGTTTTTATGAACACCACGT 57.443 32.000 1.63 0.00 31.94 4.49
3180 4305 5.777732 AGGTTCTACTTGACTCATGTCTTCT 59.222 40.000 0.96 0.00 43.29 2.85
3232 4357 1.135527 CCCCTTGCAGCATGTGTATTG 59.864 52.381 0.00 0.00 39.31 1.90
3234 4359 1.202817 CCTTGCAGCATGTGTATTGCA 59.797 47.619 0.00 0.94 44.09 4.08
3330 4455 2.639347 TGGAGATGTCTGCTTTGAGGAA 59.361 45.455 3.22 0.00 35.18 3.36
3494 4619 1.197036 GGAGAGTGCTTAACGTTTGGC 59.803 52.381 5.91 12.01 0.00 4.52
3504 4629 4.687483 GCTTAACGTTTGGCTTAGTCTACA 59.313 41.667 5.91 0.00 0.00 2.74
3513 4638 2.236395 GGCTTAGTCTACAAGGCAAGGA 59.764 50.000 4.47 0.00 45.29 3.36
3514 4639 3.118223 GGCTTAGTCTACAAGGCAAGGAT 60.118 47.826 4.47 0.00 45.29 3.24
3515 4640 4.123506 GCTTAGTCTACAAGGCAAGGATC 58.876 47.826 0.00 0.00 0.00 3.36
3628 4754 4.251268 GGCTTCAAACTGTACCGTATTCT 58.749 43.478 0.00 0.00 0.00 2.40
3638 4764 7.642082 ACTGTACCGTATTCTCTAATGTTCT 57.358 36.000 0.00 0.00 0.00 3.01
3752 4878 2.292569 CTGATTGGGCATACATGAGTGC 59.707 50.000 15.49 15.49 40.55 4.40
3832 4958 7.513781 TCCAATGTCCAATCTAATCTATCCAGA 59.486 37.037 0.00 0.00 34.56 3.86
4013 5145 6.986231 TGCAGTTTCTAGACCACATACATATG 59.014 38.462 0.00 0.00 39.55 1.78
4201 5340 8.964533 ATCTATAACTATGACCTGGAACTGAT 57.035 34.615 0.00 0.00 0.00 2.90
4236 5375 8.708742 GTGCAAAAGGTTTCTGAAATAATAACC 58.291 33.333 6.06 2.46 38.78 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 7.283625 AGAAATAGGCAACACAACATACAAA 57.716 32.000 0.00 0.00 41.41 2.83
35 36 6.892658 AGAAATAGGCAACACAACATACAA 57.107 33.333 0.00 0.00 41.41 2.41
40 41 3.252215 CGGAAGAAATAGGCAACACAACA 59.748 43.478 0.00 0.00 41.41 3.33
132 142 6.199376 TCAACTTGTACTATGATACAGGGGA 58.801 40.000 0.00 1.45 36.67 4.81
133 143 6.479972 TCAACTTGTACTATGATACAGGGG 57.520 41.667 0.00 0.00 36.67 4.79
134 144 6.425114 GCATCAACTTGTACTATGATACAGGG 59.575 42.308 0.00 1.06 36.67 4.45
135 145 7.212976 AGCATCAACTTGTACTATGATACAGG 58.787 38.462 0.00 0.00 37.96 4.00
189 201 4.033358 CACATGGCGTAGAAAACATCTCTC 59.967 45.833 0.00 0.00 39.71 3.20
331 759 3.519913 AGGGAGGGAGTATTTCAGTTCAC 59.480 47.826 0.00 0.00 0.00 3.18
332 760 3.803340 AGGGAGGGAGTATTTCAGTTCA 58.197 45.455 0.00 0.00 0.00 3.18
427 859 8.969260 AGTTGCATCTTGAAGATTACATCATA 57.031 30.769 4.67 0.00 31.32 2.15
555 989 8.841300 GGTTCCTTGATTTACAATAGGATCTTC 58.159 37.037 0.00 0.00 37.88 2.87
590 1411 5.862924 TGTTGCTTGTAGAATCTAACTGC 57.137 39.130 0.00 0.00 0.00 4.40
593 1414 8.178313 GGAATCTTGTTGCTTGTAGAATCTAAC 58.822 37.037 0.00 0.00 0.00 2.34
607 1428 2.491693 TGAATTCCCGGAATCTTGTTGC 59.508 45.455 13.24 0.00 30.29 4.17
608 1429 4.440525 CCATGAATTCCCGGAATCTTGTTG 60.441 45.833 13.24 7.18 30.29 3.33
631 1453 5.526846 TGGACTGATGGAATTTTGCAAAAAC 59.473 36.000 27.10 21.82 30.51 2.43
640 1462 8.750515 AAACAAAATTTGGACTGATGGAATTT 57.249 26.923 10.71 0.00 32.89 1.82
641 1463 7.992033 TGAAACAAAATTTGGACTGATGGAATT 59.008 29.630 10.71 0.00 34.12 2.17
642 1464 7.507829 TGAAACAAAATTTGGACTGATGGAAT 58.492 30.769 10.71 0.00 34.12 3.01
760 1661 9.193133 CGAATGGTAATTACTTGTAGGAGTATG 57.807 37.037 15.05 0.00 32.51 2.39
761 1662 7.871463 GCGAATGGTAATTACTTGTAGGAGTAT 59.129 37.037 15.05 0.00 32.51 2.12
762 1663 7.147863 TGCGAATGGTAATTACTTGTAGGAGTA 60.148 37.037 15.05 0.00 0.00 2.59
763 1664 6.047231 GCGAATGGTAATTACTTGTAGGAGT 58.953 40.000 15.05 0.00 0.00 3.85
764 1665 6.046593 TGCGAATGGTAATTACTTGTAGGAG 58.953 40.000 15.05 2.11 0.00 3.69
827 1728 2.876581 ACTTTGCCCAGGTTTAGAAGG 58.123 47.619 0.00 0.00 0.00 3.46
831 1732 1.618343 CCCAACTTTGCCCAGGTTTAG 59.382 52.381 0.00 0.00 0.00 1.85
832 1733 1.710816 CCCAACTTTGCCCAGGTTTA 58.289 50.000 0.00 0.00 0.00 2.01
843 1745 1.144298 AGCGACCTAAACCCCAACTTT 59.856 47.619 0.00 0.00 0.00 2.66
979 1884 2.520536 CCGCTGGGATTCTAGGGGG 61.521 68.421 12.35 0.00 46.22 5.40
1009 1914 1.394618 GAGCAGTCGGAGAGTATGGT 58.605 55.000 0.00 0.00 38.70 3.55
1223 2128 3.609214 AAGACAAAATGGGCGCGCG 62.609 57.895 28.44 28.44 0.00 6.86
1228 2133 1.740025 CGAGGAGAAGACAAAATGGGC 59.260 52.381 0.00 0.00 0.00 5.36
1236 2141 0.251386 AGTGAGGCGAGGAGAAGACA 60.251 55.000 0.00 0.00 0.00 3.41
1261 2166 9.132521 GCAGTACACTAACGAATACTTAAAAGA 57.867 33.333 0.00 0.00 0.00 2.52
1262 2167 9.136952 AGCAGTACACTAACGAATACTTAAAAG 57.863 33.333 0.00 0.00 0.00 2.27
1292 2202 2.788191 CTGGAGACACCACCGAAGGC 62.788 65.000 0.00 0.00 46.17 4.35
1298 2208 1.768684 TTCTGCCTGGAGACACCACC 61.769 60.000 0.00 0.00 44.64 4.61
1302 2212 0.952984 GTGCTTCTGCCTGGAGACAC 60.953 60.000 0.00 0.24 38.71 3.67
1303 2213 1.372683 GTGCTTCTGCCTGGAGACA 59.627 57.895 0.00 0.00 38.71 3.41
1304 2214 0.250467 TTGTGCTTCTGCCTGGAGAC 60.250 55.000 0.00 0.00 38.71 3.36
1307 2217 0.111061 ATGTTGTGCTTCTGCCTGGA 59.889 50.000 0.00 0.00 38.71 3.86
1309 2219 1.610038 TCAATGTTGTGCTTCTGCCTG 59.390 47.619 0.00 0.00 38.71 4.85
1310 2220 1.884579 CTCAATGTTGTGCTTCTGCCT 59.115 47.619 0.00 0.00 38.71 4.75
1311 2221 1.881973 TCTCAATGTTGTGCTTCTGCC 59.118 47.619 0.00 0.00 38.71 4.85
1315 2225 8.125448 GGAAATACTATCTCAATGTTGTGCTTC 58.875 37.037 0.00 0.00 0.00 3.86
1328 2238 7.225734 GCCACAAGAAGAAGGAAATACTATCTC 59.774 40.741 0.00 0.00 0.00 2.75
1329 2239 7.051000 GCCACAAGAAGAAGGAAATACTATCT 58.949 38.462 0.00 0.00 0.00 1.98
1330 2240 6.018669 CGCCACAAGAAGAAGGAAATACTATC 60.019 42.308 0.00 0.00 0.00 2.08
1331 2241 5.817816 CGCCACAAGAAGAAGGAAATACTAT 59.182 40.000 0.00 0.00 0.00 2.12
1332 2242 5.175859 CGCCACAAGAAGAAGGAAATACTA 58.824 41.667 0.00 0.00 0.00 1.82
1333 2243 4.003648 CGCCACAAGAAGAAGGAAATACT 58.996 43.478 0.00 0.00 0.00 2.12
1334 2244 3.751698 ACGCCACAAGAAGAAGGAAATAC 59.248 43.478 0.00 0.00 0.00 1.89
1335 2245 4.015872 ACGCCACAAGAAGAAGGAAATA 57.984 40.909 0.00 0.00 0.00 1.40
1336 2246 2.863809 ACGCCACAAGAAGAAGGAAAT 58.136 42.857 0.00 0.00 0.00 2.17
1338 2248 2.341846 AACGCCACAAGAAGAAGGAA 57.658 45.000 0.00 0.00 0.00 3.36
1340 2250 2.767505 ACTAACGCCACAAGAAGAAGG 58.232 47.619 0.00 0.00 0.00 3.46
1341 2251 5.465724 ACTTAACTAACGCCACAAGAAGAAG 59.534 40.000 0.00 0.00 0.00 2.85
1344 2254 4.510340 ACACTTAACTAACGCCACAAGAAG 59.490 41.667 0.00 0.00 0.00 2.85
1347 2257 4.143179 GCTACACTTAACTAACGCCACAAG 60.143 45.833 0.00 0.00 0.00 3.16
1348 2258 3.742369 GCTACACTTAACTAACGCCACAA 59.258 43.478 0.00 0.00 0.00 3.33
1350 2260 3.319755 TGCTACACTTAACTAACGCCAC 58.680 45.455 0.00 0.00 0.00 5.01
1351 2261 3.663995 TGCTACACTTAACTAACGCCA 57.336 42.857 0.00 0.00 0.00 5.69
1352 2262 3.742369 TGTTGCTACACTTAACTAACGCC 59.258 43.478 0.00 0.00 0.00 5.68
1353 2263 4.682860 TCTGTTGCTACACTTAACTAACGC 59.317 41.667 0.00 0.00 0.00 4.84
1354 2264 6.584942 TCATCTGTTGCTACACTTAACTAACG 59.415 38.462 0.00 0.00 0.00 3.18
1355 2265 7.884816 TCATCTGTTGCTACACTTAACTAAC 57.115 36.000 0.00 0.00 0.00 2.34
1358 2268 7.986085 AATTCATCTGTTGCTACACTTAACT 57.014 32.000 0.00 0.00 0.00 2.24
1359 2269 9.922305 GATAATTCATCTGTTGCTACACTTAAC 57.078 33.333 0.00 0.00 0.00 2.01
1361 2271 7.438160 CGGATAATTCATCTGTTGCTACACTTA 59.562 37.037 0.00 0.00 35.57 2.24
1362 2272 6.258727 CGGATAATTCATCTGTTGCTACACTT 59.741 38.462 0.00 0.00 35.57 3.16
1374 2284 3.515562 AGCCTCCTCGGATAATTCATCT 58.484 45.455 0.00 0.00 33.78 2.90
1384 2294 2.607750 AAGCCAAGCCTCCTCGGA 60.608 61.111 0.00 0.00 33.16 4.55
1388 2298 1.068121 ACTAACAAGCCAAGCCTCCT 58.932 50.000 0.00 0.00 0.00 3.69
1389 2299 1.541588 CAACTAACAAGCCAAGCCTCC 59.458 52.381 0.00 0.00 0.00 4.30
1430 2340 7.390823 TGTAGAACAGGATTTACAGTTATGCA 58.609 34.615 0.00 0.00 0.00 3.96
1436 2346 7.624549 ACATGATGTAGAACAGGATTTACAGT 58.375 34.615 0.00 0.00 30.39 3.55
1542 2452 4.329545 GCCACCAGCTTCCCGTCA 62.330 66.667 0.00 0.00 38.99 4.35
1578 2488 1.215647 GGCGATCTCAACACCGACT 59.784 57.895 0.00 0.00 0.00 4.18
1584 2494 1.194218 TCATCCTGGCGATCTCAACA 58.806 50.000 0.00 0.00 0.00 3.33
1701 2611 1.651987 ATGACTTGATACCAACCGCG 58.348 50.000 0.00 0.00 0.00 6.46
1707 2617 6.806668 TTGACCTCATATGACTTGATACCA 57.193 37.500 0.00 0.00 0.00 3.25
1719 2629 3.327172 CCTCTGGCAGATTGACCTCATAT 59.673 47.826 19.11 0.00 0.00 1.78
1810 2720 0.678048 GGTAAGGGCAGCTGAACCAG 60.678 60.000 20.43 0.00 34.12 4.00
1832 2742 2.563179 ACTAGCCATTGAGAACTCACGT 59.437 45.455 3.88 0.00 39.66 4.49
1867 2791 1.003580 GACAGTCCCTTCAGGCAATGA 59.996 52.381 0.00 0.00 35.62 2.57
1911 2835 3.197983 AGGTCAGTAATCACTAGCCAACC 59.802 47.826 0.00 0.00 32.87 3.77
1978 2975 5.163814 GCCATTATCGATGCCTTAACAGATC 60.164 44.000 8.54 0.00 34.25 2.75
2012 3009 3.236047 GGGAATGTTTGGTGTAGGGTTT 58.764 45.455 0.00 0.00 0.00 3.27
2141 3138 2.708325 ACCAATAGCCAAAAGCCCAAAA 59.292 40.909 0.00 0.00 45.47 2.44
2142 3139 2.301583 GACCAATAGCCAAAAGCCCAAA 59.698 45.455 0.00 0.00 45.47 3.28
2143 3140 1.899142 GACCAATAGCCAAAAGCCCAA 59.101 47.619 0.00 0.00 45.47 4.12
2144 3141 1.203112 TGACCAATAGCCAAAAGCCCA 60.203 47.619 0.00 0.00 45.47 5.36
2145 3142 1.555967 TGACCAATAGCCAAAAGCCC 58.444 50.000 0.00 0.00 45.47 5.19
2146 3143 4.797275 GCATATGACCAATAGCCAAAAGCC 60.797 45.833 6.97 0.00 45.47 4.35
2147 3144 4.301628 GCATATGACCAATAGCCAAAAGC 58.698 43.478 6.97 0.00 44.25 3.51
2148 3145 4.341806 TGGCATATGACCAATAGCCAAAAG 59.658 41.667 5.99 0.00 39.78 2.27
2187 3184 8.736751 TTTTTAACAGAACACTGACAAGAAAC 57.263 30.769 0.00 0.00 35.80 2.78
2188 3185 9.352784 CATTTTTAACAGAACACTGACAAGAAA 57.647 29.630 0.00 0.00 35.80 2.52
2252 3249 7.816945 ATGCTGCAAATTAATTAGAACACAC 57.183 32.000 6.36 0.00 0.00 3.82
2885 3882 8.138074 TGTGCAGCATTATAACTGTTTTAACAA 58.862 29.630 0.00 0.00 38.66 2.83
3050 4049 4.221262 CCATAAATATCTGCCCAATGGTGG 59.779 45.833 0.00 0.00 45.53 4.61
3051 4050 5.078949 TCCATAAATATCTGCCCAATGGTG 58.921 41.667 0.00 0.00 35.12 4.17
3052 4051 5.337956 TCCATAAATATCTGCCCAATGGT 57.662 39.130 0.00 0.00 35.12 3.55
3053 4052 5.776716 ACTTCCATAAATATCTGCCCAATGG 59.223 40.000 0.00 0.00 34.91 3.16
3054 4053 6.906157 ACTTCCATAAATATCTGCCCAATG 57.094 37.500 0.00 0.00 0.00 2.82
3055 4054 6.239402 GCAACTTCCATAAATATCTGCCCAAT 60.239 38.462 0.00 0.00 0.00 3.16
3056 4055 5.068987 GCAACTTCCATAAATATCTGCCCAA 59.931 40.000 0.00 0.00 0.00 4.12
3057 4056 4.584325 GCAACTTCCATAAATATCTGCCCA 59.416 41.667 0.00 0.00 0.00 5.36
3058 4057 4.584325 TGCAACTTCCATAAATATCTGCCC 59.416 41.667 0.00 0.00 0.00 5.36
3059 4058 5.772825 TGCAACTTCCATAAATATCTGCC 57.227 39.130 0.00 0.00 0.00 4.85
3060 4059 6.799512 AGTTGCAACTTCCATAAATATCTGC 58.200 36.000 26.36 0.00 35.21 4.26
3061 4060 8.072567 GCTAGTTGCAACTTCCATAAATATCTG 58.927 37.037 35.20 6.30 40.37 2.90
3062 4061 8.159344 GCTAGTTGCAACTTCCATAAATATCT 57.841 34.615 35.20 10.19 40.37 1.98
3079 4078 6.670077 AACTTAAGAAGCTATGCTAGTTGC 57.330 37.500 10.09 0.00 38.25 4.17
3086 4085 9.840427 TGTTCATAAAAACTTAAGAAGCTATGC 57.160 29.630 10.09 1.35 0.00 3.14
3089 4088 9.344772 TGGTGTTCATAAAAACTTAAGAAGCTA 57.655 29.630 10.09 0.00 0.00 3.32
3090 4089 8.135529 GTGGTGTTCATAAAAACTTAAGAAGCT 58.864 33.333 10.09 0.00 0.00 3.74
3091 4090 7.112984 CGTGGTGTTCATAAAAACTTAAGAAGC 59.887 37.037 10.09 0.00 0.00 3.86
3092 4091 8.126700 ACGTGGTGTTCATAAAAACTTAAGAAG 58.873 33.333 10.09 0.00 0.00 2.85
3093 4092 7.987649 ACGTGGTGTTCATAAAAACTTAAGAA 58.012 30.769 10.09 0.00 0.00 2.52
3094 4093 7.556733 ACGTGGTGTTCATAAAAACTTAAGA 57.443 32.000 10.09 0.00 0.00 2.10
3095 4094 8.528295 CAAACGTGGTGTTCATAAAAACTTAAG 58.472 33.333 0.00 0.00 40.84 1.85
3096 4095 7.488471 CCAAACGTGGTGTTCATAAAAACTTAA 59.512 33.333 0.00 0.00 40.84 1.85
3097 4096 6.973474 CCAAACGTGGTGTTCATAAAAACTTA 59.027 34.615 0.00 0.00 40.84 2.24
3098 4097 5.808030 CCAAACGTGGTGTTCATAAAAACTT 59.192 36.000 0.00 0.00 40.84 2.66
3099 4098 5.125739 TCCAAACGTGGTGTTCATAAAAACT 59.874 36.000 0.00 0.00 46.11 2.66
3100 4099 5.341617 TCCAAACGTGGTGTTCATAAAAAC 58.658 37.500 0.00 0.00 46.11 2.43
3101 4100 5.578005 TCCAAACGTGGTGTTCATAAAAA 57.422 34.783 0.00 0.00 46.11 1.94
3102 4101 5.578005 TTCCAAACGTGGTGTTCATAAAA 57.422 34.783 0.00 0.00 46.11 1.52
3103 4102 5.776173 ATTCCAAACGTGGTGTTCATAAA 57.224 34.783 0.00 0.00 46.11 1.40
3104 4103 7.392113 AGAATATTCCAAACGTGGTGTTCATAA 59.608 33.333 11.92 0.00 46.11 1.90
3105 4104 6.882140 AGAATATTCCAAACGTGGTGTTCATA 59.118 34.615 11.92 0.00 46.11 2.15
3106 4105 5.710099 AGAATATTCCAAACGTGGTGTTCAT 59.290 36.000 11.92 0.00 46.11 2.57
3107 4106 5.049060 CAGAATATTCCAAACGTGGTGTTCA 60.049 40.000 11.92 0.00 46.11 3.18
3108 4107 5.390613 CAGAATATTCCAAACGTGGTGTTC 58.609 41.667 11.92 0.00 46.11 3.18
3109 4108 4.217550 CCAGAATATTCCAAACGTGGTGTT 59.782 41.667 11.92 0.00 46.11 3.32
3110 4109 3.756434 CCAGAATATTCCAAACGTGGTGT 59.244 43.478 11.92 0.00 46.11 4.16
3111 4110 3.756434 ACCAGAATATTCCAAACGTGGTG 59.244 43.478 18.87 6.37 46.11 4.17
3112 4111 3.756434 CACCAGAATATTCCAAACGTGGT 59.244 43.478 15.52 15.52 46.11 4.16
3113 4112 5.125417 ATTCACCAGAATATTCCAAACGTGG 59.875 40.000 11.92 13.43 43.45 4.94
3114 4113 5.621197 TTCACCAGAATATTCCAAACGTG 57.379 39.130 11.92 10.62 0.00 4.49
3115 4114 6.834168 AATTCACCAGAATATTCCAAACGT 57.166 33.333 11.92 0.00 43.52 3.99
3116 4115 7.090173 ACAAATTCACCAGAATATTCCAAACG 58.910 34.615 11.92 0.00 43.52 3.60
3117 4116 9.573133 CTACAAATTCACCAGAATATTCCAAAC 57.427 33.333 11.92 0.00 43.52 2.93
3118 4117 9.527157 TCTACAAATTCACCAGAATATTCCAAA 57.473 29.630 11.92 0.77 43.52 3.28
3180 4305 9.309516 CCGTAGCAAAAGAGAAAATATACACTA 57.690 33.333 0.00 0.00 0.00 2.74
3234 4359 3.451178 AGTGAGTATACCACGCAGGAAAT 59.549 43.478 14.77 0.00 37.65 2.17
3494 4619 5.355596 CAGATCCTTGCCTTGTAGACTAAG 58.644 45.833 0.00 0.00 0.00 2.18
3513 4638 2.283298 CGCATAGAACAGTTGGCAGAT 58.717 47.619 0.00 0.00 0.00 2.90
3514 4639 1.725641 CGCATAGAACAGTTGGCAGA 58.274 50.000 0.00 0.00 0.00 4.26
3515 4640 0.097674 GCGCATAGAACAGTTGGCAG 59.902 55.000 0.30 0.00 0.00 4.85
3628 4754 8.548025 TGAACTGGGATTTCATAGAACATTAGA 58.452 33.333 0.00 0.00 0.00 2.10
3638 4764 5.887598 CCACAGATTGAACTGGGATTTCATA 59.112 40.000 0.00 0.00 43.19 2.15
3692 4818 2.906354 ACATACGGTTCATCCAAGCTC 58.094 47.619 0.00 0.00 35.57 4.09
3832 4958 6.856757 ACAGCTAATAAAATCCAGGATCCAT 58.143 36.000 15.82 0.00 0.00 3.41
4013 5145 8.616076 ACTTAGAAGCAAAGCAATATGATACAC 58.384 33.333 0.00 0.00 0.00 2.90
4201 5340 2.435372 ACCTTTTGCACACCTCTGAA 57.565 45.000 0.00 0.00 0.00 3.02
4236 5375 3.835378 TTCAGTTGTGCATGCATACAG 57.165 42.857 25.64 20.16 0.00 2.74
4241 5380 1.689984 TCCTTTCAGTTGTGCATGCA 58.310 45.000 18.46 18.46 0.00 3.96
4242 5381 4.357142 CATATCCTTTCAGTTGTGCATGC 58.643 43.478 11.82 11.82 0.00 4.06
4291 5515 3.569701 GGCAAGACACCAAGATTCAGAAA 59.430 43.478 0.00 0.00 0.00 2.52
4400 5625 1.631388 CCCACACCACCATACCAACTA 59.369 52.381 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.