Multiple sequence alignment - TraesCS4D01G046200

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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 TraesCS4D01G046200 chr4D 100.000 3534 0 0 1 3534 21777785 21774252 0.000000e+00 6527
1 TraesCS4D01G046200 chr4A 92.707 3579 132 48 1 3534 580736965 580733471 0.000000e+00 5044
2 TraesCS4D01G046200 chr4B 92.484 3140 149 44 431 3534 32896060 32899148 0.000000e+00 4410
3 TraesCS4D01G046200 chr4B 90.268 298 22 5 138 433 32895561 32895853 1.990000e-102 383
4 TraesCS4D01G046200 chr6D 91.613 155 11 2 2204 2358 382588762 382588610 2.760000e-51 213
5 TraesCS4D01G046200 chr7D 94.853 136 5 2 2198 2332 167229395 167229529 9.940000e-51 211
6 TraesCS4D01G046200 chr7B 94.853 136 5 2 2198 2332 131377843 131377977 9.940000e-51 211
7 TraesCS4D01G046200 chr7A 94.853 136 5 2 2198 2332 168813528 168813662 9.940000e-51 211
8 TraesCS4D01G046200 chr6B 88.485 165 16 3 2204 2366 572392567 572392404 2.780000e-46 196


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 TraesCS4D01G046200 chr4D 21774252 21777785 3533 True 6527.0 6527 100.000 1 3534 1 chr4D.!!$R1 3533
1 TraesCS4D01G046200 chr4A 580733471 580736965 3494 True 5044.0 5044 92.707 1 3534 1 chr4A.!!$R1 3533
2 TraesCS4D01G046200 chr4B 32895561 32899148 3587 False 2396.5 4410 91.376 138 3534 2 chr4B.!!$F1 3396

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
469 682 0.108472 CGTGCATGCTCTCTCCTTCA 60.108 55.0 20.33 0.0 0.0 3.02 F
652 866 0.467844 ACCACCATCACAAGCTGCAA 60.468 50.0 1.02 0.0 0.0 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1535 1764 0.253044 GCATGGGGTTGTAGAGCTCA 59.747 55.0 17.77 0.0 41.23 4.26 R
2575 2823 0.251916 TGGTGAGGGCGTCCTATTTG 59.748 55.0 9.57 0.0 45.05 2.32 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 9.357652 CCACCATTATACATTTTGAAAGAACAG 57.642 33.333 0.00 0.00 0.00 3.16
37 38 9.093458 ACATTTTGAAAGAACAGGAGGATAAAT 57.907 29.630 0.00 0.00 0.00 1.40
53 54 4.759183 GGATAAATCCCTTGTCTCTGCATC 59.241 45.833 0.00 0.00 41.20 3.91
78 79 4.213513 TCATGCATGTGGCCATTAATACA 58.786 39.130 25.43 5.01 43.89 2.29
85 86 5.590530 TGTGGCCATTAATACAAACCATC 57.409 39.130 9.72 0.00 0.00 3.51
124 125 8.674263 ATGTGAAGGATGATTTTCTAGCTAAG 57.326 34.615 0.00 0.00 0.00 2.18
130 132 7.398024 AGGATGATTTTCTAGCTAAGTGTGTT 58.602 34.615 0.00 0.00 0.00 3.32
131 133 7.550906 AGGATGATTTTCTAGCTAAGTGTGTTC 59.449 37.037 0.00 0.00 0.00 3.18
133 135 8.621532 ATGATTTTCTAGCTAAGTGTGTTCAA 57.378 30.769 0.00 0.00 0.00 2.69
193 195 5.870978 CGAATGCCTGATTTTTCCAAGATTT 59.129 36.000 0.00 0.00 0.00 2.17
241 243 2.986479 GCGGTTTGTAGGATTTTTGCAG 59.014 45.455 0.00 0.00 0.00 4.41
263 265 7.106890 GCAGTATTCCTATAGGATTTCTTCCC 58.893 42.308 22.30 8.74 46.81 3.97
264 266 7.256691 GCAGTATTCCTATAGGATTTCTTCCCA 60.257 40.741 22.30 4.41 46.81 4.37
284 286 4.266714 CCACGGGATTTTTACCTATGTGT 58.733 43.478 0.00 0.00 0.00 3.72
324 327 7.001073 AGGATGGAGGCACTATATTTCTTTTC 58.999 38.462 0.00 0.00 41.55 2.29
328 331 8.650143 TGGAGGCACTATATTTCTTTTCTTTT 57.350 30.769 0.00 0.00 41.55 2.27
374 377 3.068732 TGACCTAGAGCATCATAGCACAC 59.931 47.826 0.00 0.00 37.82 3.82
397 400 7.653311 ACACTTTCAAATATGAAGTTGCTTTCC 59.347 33.333 0.00 0.00 45.82 3.13
441 654 1.933181 CTTCTGTGACTTGCGTGTGAA 59.067 47.619 0.00 0.00 0.00 3.18
447 660 3.623510 TGTGACTTGCGTGTGAATGTAAA 59.376 39.130 0.00 0.00 0.00 2.01
456 669 3.120683 CGTGTGAATGTAAACTCGTGCAT 60.121 43.478 0.00 0.00 0.00 3.96
457 670 4.151070 GTGTGAATGTAAACTCGTGCATG 58.849 43.478 0.00 0.00 0.00 4.06
458 671 3.163594 GTGAATGTAAACTCGTGCATGC 58.836 45.455 11.82 11.82 0.00 4.06
459 672 3.073678 TGAATGTAAACTCGTGCATGCT 58.926 40.909 20.33 0.00 0.00 3.79
469 682 0.108472 CGTGCATGCTCTCTCCTTCA 60.108 55.000 20.33 0.00 0.00 3.02
475 688 3.523547 CATGCTCTCTCCTTCACTTCAG 58.476 50.000 0.00 0.00 0.00 3.02
560 774 6.377327 TTGAACTTGCTCGAAAAAGATTCT 57.623 33.333 12.41 0.00 0.00 2.40
566 780 8.788409 ACTTGCTCGAAAAAGATTCTAAAAAG 57.212 30.769 12.41 0.00 0.00 2.27
652 866 0.467844 ACCACCATCACAAGCTGCAA 60.468 50.000 1.02 0.00 0.00 4.08
818 1034 1.606601 CTCCAGTCCACTCCCGTCA 60.607 63.158 0.00 0.00 0.00 4.35
1047 1263 4.537433 CGCCAGGGTGCCTAGCTC 62.537 72.222 0.00 0.00 36.16 4.09
1049 1265 3.854669 CCAGGGTGCCTAGCTCGG 61.855 72.222 0.00 0.00 29.64 4.63
1053 1269 4.874977 GGTGCCTAGCTCGGTCGC 62.875 72.222 6.11 5.11 0.00 5.19
1055 1271 3.068691 TGCCTAGCTCGGTCGCTT 61.069 61.111 6.11 0.00 41.30 4.68
1057 1273 3.064987 GCCTAGCTCGGTCGCTTGA 62.065 63.158 6.11 0.00 41.30 3.02
1451 1680 3.781770 CTCCGGCTCTGGCATCGTC 62.782 68.421 0.00 0.00 40.87 4.20
1457 1686 1.215382 CTCTGGCATCGTCGGTGAA 59.785 57.895 10.33 0.00 0.00 3.18
1487 1716 4.351938 CACGGCGTGGAGGTCGAA 62.352 66.667 31.19 0.00 38.63 3.71
1535 1764 3.390521 TTCGACCCCATGCTCGCT 61.391 61.111 0.00 0.00 0.00 4.93
1620 1849 3.843240 GCTTCTCGTCGCTTGCCG 61.843 66.667 0.00 0.00 38.61 5.69
1621 1850 3.181967 CTTCTCGTCGCTTGCCGG 61.182 66.667 0.00 0.00 37.59 6.13
1646 1875 0.660595 CGTCGTCGGAGTATGCATCC 60.661 60.000 0.19 0.00 0.00 3.51
1754 1983 1.039785 TGCTCATGGGAGGAGTCGAG 61.040 60.000 0.00 0.00 41.67 4.04
1757 1986 0.395862 TCATGGGAGGAGTCGAGGAC 60.396 60.000 0.00 0.00 0.00 3.85
1948 2180 0.338814 AGGGTTATCGACTCCTGGGT 59.661 55.000 0.00 0.00 30.58 4.51
2006 2238 0.460311 CCCACATCGACCCTAGTGAC 59.540 60.000 0.00 0.00 33.99 3.67
2051 2283 2.608988 ACCTGCCCTGACTCCTGG 60.609 66.667 0.00 0.00 0.00 4.45
2063 2302 2.697229 TGACTCCTGGCATGTGATCTAG 59.303 50.000 0.00 0.00 0.00 2.43
2065 2304 1.415289 CTCCTGGCATGTGATCTAGCA 59.585 52.381 0.00 0.00 0.00 3.49
2066 2305 1.415289 TCCTGGCATGTGATCTAGCAG 59.585 52.381 0.00 0.00 0.00 4.24
2070 2309 3.033909 TGGCATGTGATCTAGCAGTACT 58.966 45.455 0.00 0.00 0.00 2.73
2083 2322 9.810545 GATCTAGCAGTACTCTTATTTCACTTT 57.189 33.333 0.00 0.00 0.00 2.66
2133 2372 5.344066 GTCTAATCAAGCTCGATCTGTTGA 58.656 41.667 0.00 0.00 33.61 3.18
2451 2690 0.099968 GATCGTTCGTCCGTGGATGA 59.900 55.000 6.72 6.72 38.27 2.92
2626 2874 9.778993 GTACGACTGAATATACACTTGTAGAAA 57.221 33.333 0.00 0.00 33.52 2.52
2627 2875 8.912787 ACGACTGAATATACACTTGTAGAAAG 57.087 34.615 0.00 0.00 33.52 2.62
2629 2877 9.355215 CGACTGAATATACACTTGTAGAAAGTT 57.645 33.333 0.00 0.00 33.52 2.66
2669 2933 6.590234 AGCATCTGTATATACGTTCCATGA 57.410 37.500 8.33 0.00 0.00 3.07
2719 2989 4.726704 CGTCGTTTTTGTAAGGAAGTTGTG 59.273 41.667 0.00 0.00 0.00 3.33
2749 3019 8.967664 TTACAAAGGTTGTACTGTAGATGTTT 57.032 30.769 0.38 0.00 45.16 2.83
2784 3054 7.147794 ACGTAGGAGATACATTCATGGTACAAA 60.148 37.037 0.00 0.00 36.45 2.83
2834 3106 4.078922 ACTGAGAATGGTAGAGGGAGATCA 60.079 45.833 0.00 0.00 0.00 2.92
2845 3117 4.107820 AGAGGGAGATCAAAGCCTAGTTT 58.892 43.478 0.00 0.00 0.00 2.66
2888 3160 2.173356 CCAGCCTTCCATTCCTGATGTA 59.827 50.000 0.00 0.00 33.71 2.29
2929 3204 3.119708 GGGCACAATCTCTGAATCACAAC 60.120 47.826 0.00 0.00 0.00 3.32
3028 3307 4.331968 TCGATCAAAGCCTTGTACCATTT 58.668 39.130 0.00 0.00 33.94 2.32
3250 3532 4.827284 TCTTTTCCTTAGGCTTTGGTTCAG 59.173 41.667 0.00 0.00 0.00 3.02
3323 3605 5.584649 TCACATATTTGTCGGAAATCCTCAC 59.415 40.000 0.00 0.00 32.34 3.51
3336 3618 7.439056 TCGGAAATCCTCACCGTAATTTATAAC 59.561 37.037 0.00 0.00 45.71 1.89
3339 3621 8.672823 AAATCCTCACCGTAATTTATAACCTC 57.327 34.615 0.00 0.00 0.00 3.85
3371 3653 3.729862 TTTTGCTGTGACAATGCATCA 57.270 38.095 0.00 0.00 36.55 3.07
3375 3657 3.644823 TGCTGTGACAATGCATCAAAAG 58.355 40.909 0.00 0.00 0.00 2.27
3481 3763 9.750125 GTGTTACAATTCTTTCAAAATTCCTCT 57.250 29.630 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 8.753133 GGATTTATCCTCCTGTTCTTTCAAAAT 58.247 33.333 1.40 0.00 43.73 1.82
22 23 5.104318 AGACAAGGGATTTATCCTCCTGTTC 60.104 44.000 8.58 5.04 46.35 3.18
25 26 4.657969 AGAGACAAGGGATTTATCCTCCTG 59.342 45.833 8.58 6.32 46.35 3.86
27 28 4.745172 GCAGAGACAAGGGATTTATCCTCC 60.745 50.000 8.58 0.00 46.35 4.30
37 38 2.573009 TGATTGATGCAGAGACAAGGGA 59.427 45.455 0.00 0.00 0.00 4.20
53 54 2.613026 AATGGCCACATGCATGATTG 57.387 45.000 32.75 20.45 43.89 2.67
99 100 8.270744 ACTTAGCTAGAAAATCATCCTTCACAT 58.729 33.333 0.00 0.00 0.00 3.21
115 116 5.784578 TCACTTGAACACACTTAGCTAGA 57.215 39.130 0.00 0.00 0.00 2.43
124 125 6.215845 AGCCAAAATTATCACTTGAACACAC 58.784 36.000 0.00 0.00 0.00 3.82
130 132 6.183360 ACAACCAAGCCAAAATTATCACTTGA 60.183 34.615 10.93 0.00 37.32 3.02
131 133 5.990996 ACAACCAAGCCAAAATTATCACTTG 59.009 36.000 0.00 0.00 35.43 3.16
133 135 5.806654 ACAACCAAGCCAAAATTATCACT 57.193 34.783 0.00 0.00 0.00 3.41
193 195 4.588528 AGCCCTTTAATGCAAGAGAAACAA 59.411 37.500 0.00 0.00 0.00 2.83
263 265 4.095782 CCACACATAGGTAAAAATCCCGTG 59.904 45.833 0.00 0.00 0.00 4.94
264 266 4.266714 CCACACATAGGTAAAAATCCCGT 58.733 43.478 0.00 0.00 0.00 5.28
284 286 6.012113 CCTCCATCCTATAAAATGAATGCCA 58.988 40.000 0.00 0.00 0.00 4.92
337 340 8.870116 TGCTCTAGGTCAATAGATAAATAAGCA 58.130 33.333 0.00 0.00 31.50 3.91
338 341 9.883142 ATGCTCTAGGTCAATAGATAAATAAGC 57.117 33.333 0.00 0.00 31.50 3.09
374 377 9.565213 CTAGGAAAGCAACTTCATATTTGAAAG 57.435 33.333 0.20 0.00 41.22 2.62
441 654 2.932614 GAGAGCATGCACGAGTTTACAT 59.067 45.455 21.98 0.00 0.00 2.29
447 660 0.969917 AGGAGAGAGCATGCACGAGT 60.970 55.000 21.98 3.43 0.00 4.18
456 669 2.881734 TCTGAAGTGAAGGAGAGAGCA 58.118 47.619 0.00 0.00 0.00 4.26
457 670 3.951775 TTCTGAAGTGAAGGAGAGAGC 57.048 47.619 0.00 0.00 0.00 4.09
458 671 5.243730 ACTCTTTCTGAAGTGAAGGAGAGAG 59.756 44.000 18.57 11.97 46.47 3.20
459 672 5.144100 ACTCTTTCTGAAGTGAAGGAGAGA 58.856 41.667 18.57 2.42 46.47 3.10
469 682 8.831550 GTTGAAACATAAGACTCTTTCTGAAGT 58.168 33.333 0.00 0.00 33.46 3.01
475 688 7.794349 CGACAAGTTGAAACATAAGACTCTTTC 59.206 37.037 10.54 0.00 0.00 2.62
546 760 6.071896 AGCCCCTTTTTAGAATCTTTTTCGAG 60.072 38.462 0.00 0.00 0.00 4.04
584 798 5.147865 CGCGTAGAATCACGATATTTCTCT 58.852 41.667 0.00 0.00 44.69 3.10
595 809 1.593006 CATCAACCCGCGTAGAATCAC 59.407 52.381 4.92 0.00 0.00 3.06
796 1010 1.889530 CGGGAGTGGACTGGAGGAAC 61.890 65.000 0.00 0.00 0.00 3.62
797 1011 1.609501 CGGGAGTGGACTGGAGGAA 60.610 63.158 0.00 0.00 0.00 3.36
818 1034 1.663702 CTTTTCGACGACGTGGCCT 60.664 57.895 4.58 0.00 40.69 5.19
861 1077 2.372504 TGTGGGTGATTCGGGTAAAAGA 59.627 45.455 0.00 0.00 0.00 2.52
1033 1249 3.077556 ACCGAGCTAGGCACCCTG 61.078 66.667 13.48 0.00 34.61 4.45
1047 1263 2.504244 GTCGGACTCAAGCGACCG 60.504 66.667 0.00 0.00 45.61 4.79
1049 1265 1.512310 CTCGTCGGACTCAAGCGAC 60.512 63.158 6.57 0.00 0.00 5.19
1053 1269 0.526524 GCCATCTCGTCGGACTCAAG 60.527 60.000 6.57 1.57 0.00 3.02
1055 1271 2.761195 CGCCATCTCGTCGGACTCA 61.761 63.158 6.57 0.00 0.00 3.41
1057 1273 2.437895 TCGCCATCTCGTCGGACT 60.438 61.111 6.57 0.00 0.00 3.85
1442 1671 1.561717 CGTTTTCACCGACGATGCCA 61.562 55.000 0.00 0.00 41.53 4.92
1451 1680 2.841389 CCGTCGTCGTTTTCACCG 59.159 61.111 0.71 0.00 35.01 4.94
1487 1716 1.475392 CGGTACAGGAGATCCTCGTCT 60.475 57.143 0.00 0.00 46.65 4.18
1535 1764 0.253044 GCATGGGGTTGTAGAGCTCA 59.747 55.000 17.77 0.00 41.23 4.26
1751 1980 3.425713 TCGTCGAACCCGTCCTCG 61.426 66.667 0.00 0.00 37.05 4.63
1754 1983 3.368571 AGGTCGTCGAACCCGTCC 61.369 66.667 6.68 2.65 40.42 4.79
2000 2232 0.824109 CCAGCCAGGAATCGTCACTA 59.176 55.000 0.00 0.00 41.22 2.74
2051 2283 4.582701 AGAGTACTGCTAGATCACATGC 57.417 45.455 0.00 0.00 0.00 4.06
2097 2336 4.492791 TGATTAGACGACAACTCGACAA 57.507 40.909 0.00 0.00 43.06 3.18
2098 2337 4.473199 CTTGATTAGACGACAACTCGACA 58.527 43.478 0.00 0.00 43.06 4.35
2099 2338 3.301116 GCTTGATTAGACGACAACTCGAC 59.699 47.826 0.00 0.00 43.06 4.20
2100 2339 3.190744 AGCTTGATTAGACGACAACTCGA 59.809 43.478 0.00 0.00 43.06 4.04
2101 2340 3.502920 AGCTTGATTAGACGACAACTCG 58.497 45.455 0.00 0.00 46.06 4.18
2102 2341 3.544285 CGAGCTTGATTAGACGACAACTC 59.456 47.826 0.00 0.00 0.00 3.01
2103 2342 3.190744 TCGAGCTTGATTAGACGACAACT 59.809 43.478 0.00 0.00 32.41 3.16
2104 2343 3.499048 TCGAGCTTGATTAGACGACAAC 58.501 45.455 0.00 0.00 32.41 3.32
2133 2372 2.440796 CCGCCTGTCCATGCCAAT 60.441 61.111 0.00 0.00 0.00 3.16
2317 2556 4.719616 GTGCGCTTGACGAACCGC 62.720 66.667 9.73 0.00 45.32 5.68
2550 2798 5.300752 CAGAGGTTTCTGCTCAAAACTAGA 58.699 41.667 0.00 0.00 43.98 2.43
2575 2823 0.251916 TGGTGAGGGCGTCCTATTTG 59.748 55.000 9.57 0.00 45.05 2.32
2626 2874 4.184629 GCTTGCAGTACATAGCTACAACT 58.815 43.478 0.00 0.00 32.78 3.16
2627 2875 3.932710 TGCTTGCAGTACATAGCTACAAC 59.067 43.478 7.30 0.00 35.05 3.32
2629 2877 3.885724 TGCTTGCAGTACATAGCTACA 57.114 42.857 7.30 0.00 35.05 2.74
2719 2989 5.941948 ACAGTACAACCTTTGTAATCAGC 57.058 39.130 0.38 0.00 46.72 4.26
2749 3019 8.909923 TGAATGTATCTCCTACGTTTTGAGATA 58.090 33.333 19.26 19.26 42.50 1.98
2784 3054 3.179685 GTCCTTACCCACCCTAACTCTT 58.820 50.000 0.00 0.00 0.00 2.85
2834 3106 6.570378 GCATTGACATACACAAACTAGGCTTT 60.570 38.462 0.00 0.00 0.00 3.51
2845 3117 2.725637 AGGCATGCATTGACATACACA 58.274 42.857 21.36 0.00 34.87 3.72
2888 3160 0.541863 CTGGTTCGAGGCTACCCAAT 59.458 55.000 2.56 0.00 33.34 3.16
2929 3204 6.913170 AGACTTACAAATAAGCACATTGTGG 58.087 36.000 18.05 2.56 41.48 4.17
2970 3249 4.662278 ACATGCAACCTTTACACCAGTAT 58.338 39.130 0.00 0.00 0.00 2.12
3000 3279 3.077359 ACAAGGCTTTGATCGAGAAAGG 58.923 45.455 16.36 5.12 37.73 3.11
3001 3280 4.093556 GGTACAAGGCTTTGATCGAGAAAG 59.906 45.833 16.36 13.07 37.73 2.62
3002 3281 4.000988 GGTACAAGGCTTTGATCGAGAAA 58.999 43.478 16.36 0.00 37.73 2.52
3028 3307 8.463930 AAGTGTCAAGATGTTTAGATCCAAAA 57.536 30.769 0.00 0.00 0.00 2.44
3250 3532 6.242829 CGATTACGGTTGTGTTTACCATTAC 58.757 40.000 0.00 0.00 35.31 1.89
3323 3605 8.857694 AATATGTGGGAGGTTATAAATTACGG 57.142 34.615 0.00 0.00 0.00 4.02
3336 3618 6.096705 TCACAGCAAAATAAATATGTGGGAGG 59.903 38.462 3.57 0.00 38.78 4.30
3339 3621 6.629128 TGTCACAGCAAAATAAATATGTGGG 58.371 36.000 3.57 0.00 38.78 4.61
3371 3653 6.071051 TCCAAAGAGCTGGTTTTGTAACTTTT 60.071 34.615 0.00 0.00 37.74 2.27
3375 3657 4.911514 TCCAAAGAGCTGGTTTTGTAAC 57.088 40.909 0.00 0.00 37.74 2.50


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

AutoCloner maintained by Alex Coulton.