Multiple sequence alignment - TraesCS5D01G420600

Loading Multiple Alignment...

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 TraesCS5D01G420600 chr5D 100.000 3296 0 0 1 3296 481156978 481160273 0.000000e+00 6087
1 TraesCS5D01G420600 chr5A 92.695 3313 163 27 1 3275 600196266 600199537 0.000000e+00 4704
2 TraesCS5D01G420600 chr5B 89.467 2288 117 50 1098 3296 589568176 589570428 0.000000e+00 2776
3 TraesCS5D01G420600 chr5B 86.762 627 41 12 181 788 589567246 589567849 0.000000e+00 660
4 TraesCS5D01G420600 chr5B 88.235 187 14 4 909 1094 589567966 589568145 1.990000e-52 217
5 TraesCS5D01G420600 chr5B 96.000 100 4 0 827 926 589567851 589567950 2.630000e-36 163


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 TraesCS5D01G420600 chr5D 481156978 481160273 3295 False 6087 6087 100.000 1 3296 1 chr5D.!!$F1 3295
1 TraesCS5D01G420600 chr5A 600196266 600199537 3271 False 4704 4704 92.695 1 3275 1 chr5A.!!$F1 3274
2 TraesCS5D01G420600 chr5B 589567246 589570428 3182 False 954 2776 90.116 181 3296 4 chr5B.!!$F1 3115

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
952 1023 0.895530 CTCTCCTAAACCGTGCCTCA 59.104 55.0 0.0 0.0 0.0 3.86 F
1100 1205 0.251033 TCGAGACGGGAGGAGAACAA 60.251 55.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1919 2029 1.071605 GACTAGCAAGCACAACCGAG 58.928 55.0 0.0 0.0 0.00 4.63 R
2955 3142 0.393820 TTAGAGACGTTTTGGGCCGT 59.606 50.0 0.0 0.0 40.54 5.68 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
32 33 3.788766 CGCGGGCGTTCCTGAAAG 61.789 66.667 4.64 0.00 41.45 2.62
49 50 1.657804 AAGGTCTGGTGTCCCTTAGG 58.342 55.000 0.00 0.00 36.82 2.69
82 83 1.677966 TCCCCACGACGAGAAGGAG 60.678 63.158 0.00 0.00 0.00 3.69
104 105 2.550830 ATAATTCCGCCGCATCTTCT 57.449 45.000 0.00 0.00 0.00 2.85
151 152 2.676076 GCCGTTTCATTGTTGCAGAAT 58.324 42.857 0.00 0.00 0.00 2.40
154 155 3.244976 CGTTTCATTGTTGCAGAATCCC 58.755 45.455 0.00 0.00 0.00 3.85
258 259 1.880819 TTCCGCCCCTGTCGTTCTAC 61.881 60.000 0.00 0.00 0.00 2.59
549 550 2.044650 TACTCCACCTCCGACGGG 60.045 66.667 15.25 4.64 0.00 5.28
693 703 2.673893 CGTGGACAATGACGATGAGGAA 60.674 50.000 0.00 0.00 37.81 3.36
705 715 2.597455 GATGAGGAAGAGGAGGAGGAG 58.403 57.143 0.00 0.00 0.00 3.69
725 762 4.587262 GGAGGAGGAAGAGGAGAAGTAATC 59.413 50.000 0.00 0.00 0.00 1.75
821 858 4.442332 CGTTGCTCCAATACCCATGTACTA 60.442 45.833 0.00 0.00 0.00 1.82
822 859 4.682778 TGCTCCAATACCCATGTACTAC 57.317 45.455 0.00 0.00 0.00 2.73
825 862 5.900699 TGCTCCAATACCCATGTACTACTAA 59.099 40.000 0.00 0.00 0.00 2.24
871 908 5.346551 TGAACTGTCAAATAATCCGTGTACG 59.653 40.000 0.00 0.00 39.44 3.67
940 1010 1.103803 CGGTTGTAGCAGCTCTCCTA 58.896 55.000 0.00 0.00 0.00 2.94
952 1023 0.895530 CTCTCCTAAACCGTGCCTCA 59.104 55.000 0.00 0.00 0.00 3.86
1089 1167 3.900892 CCCGGTGGATCGAGACGG 61.901 72.222 12.15 12.15 43.89 4.79
1094 1172 1.453379 GTGGATCGAGACGGGAGGA 60.453 63.158 0.00 0.00 0.00 3.71
1095 1173 1.152943 TGGATCGAGACGGGAGGAG 60.153 63.158 0.00 0.00 0.00 3.69
1096 1174 1.148723 GGATCGAGACGGGAGGAGA 59.851 63.158 0.00 0.00 0.00 3.71
1100 1205 0.251033 TCGAGACGGGAGGAGAACAA 60.251 55.000 0.00 0.00 0.00 2.83
1104 1209 0.966920 GACGGGAGGAGAACAACTCA 59.033 55.000 0.00 0.00 46.54 3.41
1197 1302 1.662629 CTCGAAATCATTGCTCGCACT 59.337 47.619 0.00 0.00 32.66 4.40
1210 1315 0.935831 TCGCACTGACGTTACAACCG 60.936 55.000 0.00 0.00 0.00 4.44
1298 1403 4.386951 CATGGCCCACGACCACGA 62.387 66.667 0.00 0.00 40.82 4.35
1396 1501 1.531365 CCAGGGCCAACAAAGCTCA 60.531 57.895 6.18 0.00 31.12 4.26
1512 1622 2.591715 GTCAAGCTGCGGGTGTGT 60.592 61.111 0.00 0.00 0.00 3.72
1515 1625 1.968017 CAAGCTGCGGGTGTGTGAT 60.968 57.895 0.00 0.00 0.00 3.06
1533 1643 1.745087 GATGCATTCACCGGTCATGTT 59.255 47.619 19.91 11.07 0.00 2.71
1747 1857 1.600511 TTACTGCTCCGCCGTCATCA 61.601 55.000 0.00 0.00 0.00 3.07
2112 2243 1.739667 CGGTGCCGTCATCCTATCA 59.260 57.895 1.93 0.00 34.35 2.15
2151 2282 1.991121 ACAGTGGTGAGTTACTCCGA 58.009 50.000 10.10 0.00 35.17 4.55
2278 2409 7.974504 ACTCTCTTTACTGGATTTACTGGAAA 58.025 34.615 0.00 0.00 0.00 3.13
2502 2639 2.024414 GCTTTTACTCCGGCCATTCAT 58.976 47.619 2.24 0.00 0.00 2.57
2513 2650 3.317711 CCGGCCATTCATGCATAAGTAAA 59.682 43.478 2.24 0.00 0.00 2.01
2514 2651 4.290155 CGGCCATTCATGCATAAGTAAAC 58.710 43.478 2.24 0.00 0.00 2.01
2515 2652 4.620982 GGCCATTCATGCATAAGTAAACC 58.379 43.478 0.00 0.00 0.00 3.27
2516 2653 4.342092 GGCCATTCATGCATAAGTAAACCT 59.658 41.667 0.00 0.00 0.00 3.50
2580 2725 3.106054 AGGGTTTATTTCATGCATGGCA 58.894 40.909 25.97 13.48 44.86 4.92
2637 2798 8.065473 AGATGTGATATCTCTCGAAAGCATAT 57.935 34.615 3.98 0.00 0.00 1.78
2670 2831 3.055819 AGAGTCCATGCTTTCACACGTAT 60.056 43.478 0.00 0.00 0.00 3.06
2740 2903 4.579869 AGAAACTCTACAAATGATGGCGT 58.420 39.130 0.00 0.00 0.00 5.68
2755 2918 1.006571 GCGTTGTGTCCTCTTCCGA 60.007 57.895 0.00 0.00 0.00 4.55
2906 3093 3.402628 AGACAACACTCCACATGTACC 57.597 47.619 0.00 0.00 0.00 3.34
2914 3101 3.882888 CACTCCACATGTACCAGTGTTTT 59.117 43.478 17.20 0.00 33.99 2.43
2955 3142 8.792633 TCTATGACATGACGATATGACAACATA 58.207 33.333 0.00 0.00 42.18 2.29
2968 3155 0.594110 CAACATACGGCCCAAAACGT 59.406 50.000 0.00 0.00 46.17 3.99
2998 3190 6.494893 TGAATTACATGAGTAACCAAGTGC 57.505 37.500 0.00 0.00 42.60 4.40
3136 3339 4.508551 TGTAGGTCGGGTAGTAATCAGA 57.491 45.455 0.00 0.00 0.00 3.27
3138 3341 4.825634 TGTAGGTCGGGTAGTAATCAGATG 59.174 45.833 0.00 0.00 0.00 2.90
3159 3362 8.070171 CAGATGCAACCTTAATAAAAGGATACG 58.930 37.037 10.67 0.00 46.39 3.06
3160 3363 7.773690 AGATGCAACCTTAATAAAAGGATACGT 59.226 33.333 10.67 0.00 46.39 3.57
3161 3364 7.079182 TGCAACCTTAATAAAAGGATACGTG 57.921 36.000 10.67 2.50 46.39 4.49
3199 3402 6.311935 CCATATTGTTTGCAACTCATTTCCAG 59.688 38.462 0.00 0.00 37.44 3.86
3279 3484 3.578282 TCTGAGCTTGTCATAGGTGTGAA 59.422 43.478 0.00 0.00 33.51 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.955919 CCAGACCTTTCAGGAACGCC 60.956 60.000 0.00 0.00 37.67 5.68
27 28 1.518367 AAGGGACACCAGACCTTTCA 58.482 50.000 0.00 0.00 41.65 2.69
32 33 1.652947 TTCCTAAGGGACACCAGACC 58.347 55.000 0.00 0.00 42.05 3.85
55 56 0.250166 CGTCGTGGGGACTCCTTTTT 60.250 55.000 0.00 0.00 43.79 1.94
61 62 1.507174 CTTCTCGTCGTGGGGACTC 59.493 63.158 0.00 0.00 43.79 3.36
62 63 1.977544 CCTTCTCGTCGTGGGGACT 60.978 63.158 0.00 0.00 43.79 3.85
82 83 3.251004 AGAAGATGCGGCGGAATTATTTC 59.749 43.478 4.50 5.46 0.00 2.17
104 105 1.850755 GGAGGAGGGGGTGGACAAA 60.851 63.158 0.00 0.00 0.00 2.83
151 152 4.093952 GTCGACGAACTCGCGGGA 62.094 66.667 15.95 0.92 42.62 5.14
154 155 4.434938 TCCGTCGACGAACTCGCG 62.435 66.667 37.65 19.50 42.62 5.87
235 236 4.452733 CGACAGGGGCGGAAGGAC 62.453 72.222 0.00 0.00 0.00 3.85
693 703 0.933700 CTTCCTCCTCCTCCTCCTCT 59.066 60.000 0.00 0.00 0.00 3.69
705 715 3.319689 CGGATTACTTCTCCTCTTCCTCC 59.680 52.174 0.00 0.00 0.00 4.30
825 862 8.784043 GTTCAACTCTTCAAATACTACCATTGT 58.216 33.333 0.00 0.00 0.00 2.71
871 908 3.952967 ACCAACTACTAGAATCGGGAGTC 59.047 47.826 0.00 0.00 0.00 3.36
940 1010 0.823356 AGCAATGTGAGGCACGGTTT 60.823 50.000 0.00 0.00 37.14 3.27
1083 1161 1.202817 GAGTTGTTCTCCTCCCGTCTC 59.797 57.143 0.00 0.00 37.22 3.36
1089 1167 4.023707 CACATTGTTGAGTTGTTCTCCTCC 60.024 45.833 0.00 0.00 42.12 4.30
1094 1172 5.650543 GTTTCCACATTGTTGAGTTGTTCT 58.349 37.500 0.00 0.00 0.00 3.01
1095 1173 4.499040 CGTTTCCACATTGTTGAGTTGTTC 59.501 41.667 0.00 0.00 0.00 3.18
1096 1174 4.082463 ACGTTTCCACATTGTTGAGTTGTT 60.082 37.500 0.00 0.00 0.00 2.83
1100 1205 3.181491 CCAACGTTTCCACATTGTTGAGT 60.181 43.478 0.00 0.00 41.76 3.41
1104 1209 2.737039 GCACCAACGTTTCCACATTGTT 60.737 45.455 0.00 0.00 0.00 2.83
1512 1622 1.339920 ACATGACCGGTGAATGCATCA 60.340 47.619 14.63 0.00 35.05 3.07
1515 1625 2.080693 GTAACATGACCGGTGAATGCA 58.919 47.619 14.63 2.75 0.00 3.96
1533 1643 2.682494 GCGGGTGGGAGTGAGGTA 60.682 66.667 0.00 0.00 0.00 3.08
1551 1661 2.357760 TACACGCCGGGCAAACTC 60.358 61.111 20.71 0.00 0.00 3.01
1565 1675 1.859427 GAGCACGACGTGGAGGTACA 61.859 60.000 27.86 0.00 33.64 2.90
1747 1857 2.991076 GCCAGTAGACGGTGCGACT 61.991 63.158 0.00 0.00 35.90 4.18
1876 1986 2.350484 GGTGCTCGTTTTTCTTACTGGC 60.350 50.000 0.00 0.00 0.00 4.85
1919 2029 1.071605 GACTAGCAAGCACAACCGAG 58.928 55.000 0.00 0.00 0.00 4.63
2034 2165 3.323979 GGGCATATTCGTAGGGAGAGAAA 59.676 47.826 0.00 0.00 0.00 2.52
2151 2282 2.761208 CTCCATAGTTCCAAGGTCGAGT 59.239 50.000 0.00 0.00 0.00 4.18
2278 2409 4.441079 GCATGCTTAGAAATGCTTCATGGT 60.441 41.667 11.37 0.00 44.64 3.55
2435 2571 5.067283 CCGATAAACAATACCCCTTTCCTTG 59.933 44.000 0.00 0.00 0.00 3.61
2484 2621 1.748493 GCATGAATGGCCGGAGTAAAA 59.252 47.619 5.05 0.00 0.00 1.52
2502 2639 7.729124 ACTTCTAGGTAGGTTTACTTATGCA 57.271 36.000 0.00 0.00 0.00 3.96
2513 2650 8.661752 AAGTGTGTATTTACTTCTAGGTAGGT 57.338 34.615 0.00 0.00 31.88 3.08
2514 2651 9.367444 CAAAGTGTGTATTTACTTCTAGGTAGG 57.633 37.037 0.00 0.00 36.19 3.18
2515 2652 9.924650 ACAAAGTGTGTATTTACTTCTAGGTAG 57.075 33.333 0.00 0.00 39.29 3.18
2637 2798 3.264193 AGCATGGACTCTTCAACCATACA 59.736 43.478 0.00 0.00 41.68 2.29
2740 2903 3.578716 AGATCTTTCGGAAGAGGACACAA 59.421 43.478 12.62 0.00 44.65 3.33
2755 2918 5.844601 AGAACTAGGGGTGACTAGATCTTT 58.155 41.667 0.00 0.00 45.36 2.52
2839 3026 5.373222 CCTTTGATATTACCGTTGGATCCA 58.627 41.667 11.44 11.44 0.00 3.41
2840 3027 4.215613 GCCTTTGATATTACCGTTGGATCC 59.784 45.833 4.20 4.20 0.00 3.36
2853 3040 2.548920 GCTAGGTGCTCGCCTTTGATAT 60.549 50.000 7.35 0.00 39.94 1.63
2906 3093 2.230660 GGTGAAGGGAGGAAAACACTG 58.769 52.381 0.00 0.00 0.00 3.66
2914 3101 2.177016 TCATAGATCGGTGAAGGGAGGA 59.823 50.000 1.25 0.00 0.00 3.71
2955 3142 0.393820 TTAGAGACGTTTTGGGCCGT 59.606 50.000 0.00 0.00 40.54 5.68
2998 3190 1.743321 TTTTTCACCGCCTTGGCCAG 61.743 55.000 5.11 0.00 43.94 4.85
3136 3339 7.681065 GCACGTATCCTTTTATTAAGGTTGCAT 60.681 37.037 3.68 0.00 38.55 3.96
3138 3341 5.969435 GCACGTATCCTTTTATTAAGGTTGC 59.031 40.000 3.68 0.00 38.55 4.17
3159 3362 4.511082 ACAATATGGCAAACAAACAAGCAC 59.489 37.500 0.00 0.00 0.00 4.40
3160 3363 4.701765 ACAATATGGCAAACAAACAAGCA 58.298 34.783 0.00 0.00 0.00 3.91
3161 3364 5.671742 AACAATATGGCAAACAAACAAGC 57.328 34.783 0.00 0.00 0.00 4.01
3199 3402 1.134340 TGCGGTGATGGGGTATTGTAC 60.134 52.381 0.00 0.00 0.00 2.90
3228 3433 1.604593 CCAAGCAAGAGGGGTGGTG 60.605 63.158 0.00 0.00 0.00 4.17
3232 3437 4.351054 CGGCCAAGCAAGAGGGGT 62.351 66.667 2.24 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.