Multiple sequence alignment - TraesCS3A01G314200

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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 TraesCS3A01G314200 chr3A 100.000 7209 0 0 1 7209 554827431 554834639 0 13313
1 TraesCS3A01G314200 chr3A 96.526 7225 203 18 1 7209 662010418 662003226 0 11908
2 TraesCS3A01G314200 chr2A 96.955 7225 195 17 1 7209 685104332 685097117 0 12100
3 TraesCS3A01G314200 chr2A 96.664 7224 217 16 1 7209 284799900 284807114 0 11984
4 TraesCS3A01G314200 chr2A 96.514 7228 211 21 1 7209 572969929 572962724 0 11913
5 TraesCS3A01G314200 chr2A 96.235 7224 222 19 1 7209 80119622 80126810 0 11788
6 TraesCS3A01G314200 chr2A 96.096 7224 243 22 1 7209 716654171 716646972 0 11742
7 TraesCS3A01G314200 chr2A 96.841 4274 115 12 1 4262 384174900 384170635 0 7127
8 TraesCS3A01G314200 chr2A 86.773 1875 189 33 1 1855 377553047 377554882 0 2034
9 TraesCS3A01G314200 chr5A 96.636 7223 212 17 1 7209 465654112 465661317 0 11963
10 TraesCS3A01G314200 chr5A 96.474 7231 223 21 1 7209 34943383 34936163 0 11912
11 TraesCS3A01G314200 chr5A 96.373 7224 228 20 1 7209 541976892 541984096 0 11858
12 TraesCS3A01G314200 chr5A 96.503 5291 160 16 1 5276 141902086 141907366 0 8722
13 TraesCS3A01G314200 chr6A 96.538 7221 203 16 1 7209 158983455 158976270 0 11906
14 TraesCS3A01G314200 chr1A 96.898 6350 176 13 871 7209 70944907 70938568 0 10615
15 TraesCS3A01G314200 chr7A 96.183 3484 101 9 1 3473 245449805 245446343 0 5668
16 TraesCS3A01G314200 chr4A 85.409 1453 164 27 1 1441 52168604 52170020 0 1465


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 TraesCS3A01G314200 chr3A 554827431 554834639 7208 False 13313 13313 100.000 1 7209 1 chr3A.!!$F1 7208
1 TraesCS3A01G314200 chr3A 662003226 662010418 7192 True 11908 11908 96.526 1 7209 1 chr3A.!!$R1 7208
2 TraesCS3A01G314200 chr2A 685097117 685104332 7215 True 12100 12100 96.955 1 7209 1 chr2A.!!$R3 7208
3 TraesCS3A01G314200 chr2A 284799900 284807114 7214 False 11984 11984 96.664 1 7209 1 chr2A.!!$F2 7208
4 TraesCS3A01G314200 chr2A 572962724 572969929 7205 True 11913 11913 96.514 1 7209 1 chr2A.!!$R2 7208
5 TraesCS3A01G314200 chr2A 80119622 80126810 7188 False 11788 11788 96.235 1 7209 1 chr2A.!!$F1 7208
6 TraesCS3A01G314200 chr2A 716646972 716654171 7199 True 11742 11742 96.096 1 7209 1 chr2A.!!$R4 7208
7 TraesCS3A01G314200 chr2A 384170635 384174900 4265 True 7127 7127 96.841 1 4262 1 chr2A.!!$R1 4261
8 TraesCS3A01G314200 chr2A 377553047 377554882 1835 False 2034 2034 86.773 1 1855 1 chr2A.!!$F3 1854
9 TraesCS3A01G314200 chr5A 465654112 465661317 7205 False 11963 11963 96.636 1 7209 1 chr5A.!!$F2 7208
10 TraesCS3A01G314200 chr5A 34936163 34943383 7220 True 11912 11912 96.474 1 7209 1 chr5A.!!$R1 7208
11 TraesCS3A01G314200 chr5A 541976892 541984096 7204 False 11858 11858 96.373 1 7209 1 chr5A.!!$F3 7208
12 TraesCS3A01G314200 chr5A 141902086 141907366 5280 False 8722 8722 96.503 1 5276 1 chr5A.!!$F1 5275
13 TraesCS3A01G314200 chr6A 158976270 158983455 7185 True 11906 11906 96.538 1 7209 1 chr6A.!!$R1 7208
14 TraesCS3A01G314200 chr1A 70938568 70944907 6339 True 10615 10615 96.898 871 7209 1 chr1A.!!$R1 6338
15 TraesCS3A01G314200 chr7A 245446343 245449805 3462 True 5668 5668 96.183 1 3473 1 chr7A.!!$R1 3472
16 TraesCS3A01G314200 chr4A 52168604 52170020 1416 False 1465 1465 85.409 1 1441 1 chr4A.!!$F1 1440

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
938 971 0.397675 TCCACAAACCACCATTGCCA 60.398 50.000 0.00 0.0 0.00 4.92 F
2306 2359 2.101582 GCCAGACAACCTCATCGAGTAT 59.898 50.000 0.00 0.0 0.00 2.12 F
2474 2527 0.167470 GCCTTCGTTTTACTTCCGCC 59.833 55.000 0.00 0.0 0.00 6.13 F
3298 3363 0.834687 AGCGAGGTGGGACTAAACCA 60.835 55.000 0.00 0.0 39.05 3.67 F
3978 4049 1.811025 AATCTCAAACCCCCACCCCC 61.811 60.000 0.00 0.0 0.00 5.40 F
5000 5081 1.893808 CACATATGGCGGCAGTCCC 60.894 63.158 19.29 0.0 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2374 2427 0.375106 CTCCCGCTCTTTCGCAAATC 59.625 55.000 0.00 0.0 0.00 2.17 R
3925 3995 0.108281 TCGTTCGTTGTGGTGTGGAA 60.108 50.000 0.00 0.0 0.00 3.53 R
4444 4517 2.701951 TGGAAGAACTAACCGTCCAAGT 59.298 45.455 0.00 0.0 38.80 3.16 R
4735 4815 0.179137 GACGTCTCGGCATGATGACA 60.179 55.000 8.70 0.0 33.63 3.58 R
5784 5882 0.110010 GAAGTCTTTGAGGCGCTTGC 60.110 55.000 7.64 0.0 38.11 4.01 R
6461 6559 0.108662 CATGACTAGTGCTGCGTGGA 60.109 55.000 0.00 0.0 0.00 4.02 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
132 135 8.303876 TGATATATCTGATGCAAAACGCTACTA 58.696 33.333 13.79 0.00 43.06 1.82
531 550 7.425606 GTTCAATTACACTTCAATCACCAGTT 58.574 34.615 0.00 0.00 0.00 3.16
679 702 1.661509 CGCAGAGACGTGCAAGTGA 60.662 57.895 10.87 0.00 44.21 3.41
734 757 8.328864 CAAGACTAGTCAGTTCAACAGTAAAAC 58.671 37.037 24.44 0.00 34.21 2.43
919 952 2.498078 GTCTTCCATCTCTCCCTCGTTT 59.502 50.000 0.00 0.00 0.00 3.60
938 971 0.397675 TCCACAAACCACCATTGCCA 60.398 50.000 0.00 0.00 0.00 4.92
1215 1255 3.249189 TGGAGGAAGCTTGGCGGT 61.249 61.111 2.10 0.00 0.00 5.68
1371 1411 3.545703 AGCAATCCTACTCATTTTCCCG 58.454 45.455 0.00 0.00 0.00 5.14
1747 1794 2.744202 GCACTGGTTCTGTGTTATCCTG 59.256 50.000 6.76 0.00 36.06 3.86
1786 1833 5.416947 ACTAAACTAGTACCAATGCGGAAG 58.583 41.667 0.00 0.00 37.23 3.46
2248 2301 4.458295 AGGCATGAAGAACAAGATCAACAG 59.542 41.667 0.00 0.00 0.00 3.16
2306 2359 2.101582 GCCAGACAACCTCATCGAGTAT 59.898 50.000 0.00 0.00 0.00 2.12
2374 2427 2.168521 ACTACATCACAGATGGTTCGGG 59.831 50.000 11.29 0.00 0.00 5.14
2418 2471 1.144298 ACAACTTCTACAACCACCCCC 59.856 52.381 0.00 0.00 0.00 5.40
2433 2486 1.304952 CCCCATTGCCCCTTTACGA 59.695 57.895 0.00 0.00 0.00 3.43
2474 2527 0.167470 GCCTTCGTTTTACTTCCGCC 59.833 55.000 0.00 0.00 0.00 6.13
2476 2529 2.932187 GCCTTCGTTTTACTTCCGCCTA 60.932 50.000 0.00 0.00 0.00 3.93
2581 2635 9.729023 TCATGTTTGAACAAGTTTAGTTATGTG 57.271 29.630 0.10 0.00 43.03 3.21
2635 2689 9.742144 TTATATAAGTTTGGTTTGGTAGCTTCA 57.258 29.630 0.00 0.00 0.00 3.02
2764 2820 4.219944 TCCATGTCAGTACAACTCAGTACC 59.780 45.833 0.00 0.00 44.19 3.34
2771 2827 5.542635 TCAGTACAACTCAGTACCCTTGATT 59.457 40.000 0.00 0.00 44.19 2.57
3151 3210 2.482796 ATCCGCACAATGCAGGACCA 62.483 55.000 13.85 0.00 45.36 4.02
3184 3245 2.524306 CCACAGGTCAAGAGAGAGAGT 58.476 52.381 0.00 0.00 0.00 3.24
3298 3363 0.834687 AGCGAGGTGGGACTAAACCA 60.835 55.000 0.00 0.00 39.05 3.67
3528 3596 8.716646 ACAAAAACAATGAACCTCTAAAAAGG 57.283 30.769 0.00 0.00 42.55 3.11
3978 4049 1.811025 AATCTCAAACCCCCACCCCC 61.811 60.000 0.00 0.00 0.00 5.40
4046 4119 5.349817 CAGTACTAAAACAGCAGGATCAGTG 59.650 44.000 0.00 0.00 0.00 3.66
4223 4296 9.816354 AAATAAGTACAAGTTTTGAGCAACAAT 57.184 25.926 0.00 0.00 38.36 2.71
4466 4539 2.825861 TGGACGGTTAGTTCTTCCAC 57.174 50.000 0.00 0.00 0.00 4.02
4477 4550 4.263572 CTTCCACGCCACCACCCA 62.264 66.667 0.00 0.00 0.00 4.51
4803 4883 2.342648 GTCCCCGTCAAGAAGCGT 59.657 61.111 0.00 0.00 0.00 5.07
4888 4968 3.056328 GCGAACCAGACAAGGCCC 61.056 66.667 0.00 0.00 0.00 5.80
4903 4983 1.953138 GCCCACGAGATGATGAGCG 60.953 63.158 0.00 0.00 0.00 5.03
5000 5081 1.893808 CACATATGGCGGCAGTCCC 60.894 63.158 19.29 0.00 0.00 4.46
5009 5090 3.050275 GGCAGTCCCGCAGTTGTC 61.050 66.667 0.00 0.00 0.00 3.18
5109 5201 6.652481 TCTGTTGTACCAGTACTAGTCACTAC 59.348 42.308 0.00 3.71 37.00 2.73
5414 5509 6.822667 TGATGCACATGTTTCTCAAACTAT 57.177 33.333 0.00 0.00 41.90 2.12
5514 5609 5.772825 AACTAAACTTGAATCAAGCAGCA 57.227 34.783 21.69 5.18 44.43 4.41
5531 5626 3.497640 GCAGCACATCTATCATTGACTCC 59.502 47.826 0.00 0.00 0.00 3.85
5647 5743 7.828508 TCAGGACTTTGTGTACTAGTTTCTA 57.171 36.000 0.00 0.00 37.88 2.10
5718 5816 9.535878 TGGATTATCACTTGTAAAACAAAAACC 57.464 29.630 0.00 0.00 37.69 3.27
6042 6140 1.004277 GGCAGACCACAAACTATGGGA 59.996 52.381 0.00 0.00 41.97 4.37
6121 6219 5.305585 ACGTACAAGTCATGGAAGACAATT 58.694 37.500 0.00 0.00 40.98 2.32
6319 6417 2.309528 TGAACCAGCTACCTTATGCG 57.690 50.000 0.00 0.00 0.00 4.73
6372 6470 7.438459 GCCTATGTCTATCAAGTACATCGTTTT 59.562 37.037 0.00 0.00 35.54 2.43
6732 6841 7.602517 AGAAATTCACTAAGTACTGCATCAC 57.397 36.000 0.00 0.00 0.00 3.06
6876 6985 5.562890 GCTTCAGTTCGCATTCCTTAAAACT 60.563 40.000 0.00 0.00 0.00 2.66
6936 7045 9.562583 CTGAAATCTCAGTACAACTTAGTCTAC 57.437 37.037 0.00 0.00 43.64 2.59
6968 7077 7.346471 AGTGCTAGGATTATACCAAACATTGT 58.654 34.615 0.00 0.00 0.00 2.71
7057 7168 9.578439 AGACAAAAGAGAAAAATCACAAGAAAG 57.422 29.630 0.00 0.00 0.00 2.62
7175 7288 4.166523 CGGTAAGTGCTATGATGATACCG 58.833 47.826 7.02 7.02 45.39 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
531 550 2.495270 ACTCCTCTACTGTCGTACTCGA 59.505 50.000 0.00 0.00 44.12 4.04
563 582 3.712881 GTCAGCGTCGGTGTTGGC 61.713 66.667 22.58 9.20 32.43 4.52
679 702 4.980573 TGTACTTATGACCTGCAAAACCT 58.019 39.130 0.00 0.00 0.00 3.50
734 757 4.329392 ACTAACCGTCCAAGTTAAATGGG 58.671 43.478 8.32 0.00 38.54 4.00
919 952 0.397675 TGGCAATGGTGGTTTGTGGA 60.398 50.000 0.00 0.00 0.00 4.02
938 971 1.956477 GTGTGCAGTGGAAATGGAAGT 59.044 47.619 0.00 0.00 31.16 3.01
997 1037 1.983119 GATGGTTCCTCCGCCATGGA 61.983 60.000 18.40 0.00 44.73 3.41
1019 1059 0.806868 CTTGGCATGATGACGCTTGT 59.193 50.000 0.00 0.00 0.00 3.16
1215 1255 2.753452 GCCGATGATCCTACGAATCCTA 59.247 50.000 0.00 0.00 0.00 2.94
1299 1339 0.318699 CCAAGCAGAGTTCGTCGACA 60.319 55.000 17.16 0.00 0.00 4.35
1329 1369 2.339348 CATTTTGTGGCCGCTGCA 59.661 55.556 18.96 1.05 40.13 4.41
1876 1927 8.070171 GGATAAACAATGGATGAATGTACTTCG 58.930 37.037 0.00 0.00 36.60 3.79
2017 2069 2.046892 GCAGCATGTCGGTCAGGT 60.047 61.111 0.00 0.00 39.31 4.00
2248 2301 2.808543 CACAGTTTGTAGTCTTCCTGCC 59.191 50.000 0.00 0.00 0.00 4.85
2306 2359 0.380733 CGTACGCATCTACTCCTGCA 59.619 55.000 0.52 0.00 38.30 4.41
2374 2427 0.375106 CTCCCGCTCTTTCGCAAATC 59.625 55.000 0.00 0.00 0.00 2.17
2418 2471 2.917933 TCATCTCGTAAAGGGGCAATG 58.082 47.619 0.00 0.00 0.00 2.82
2433 2486 4.262549 GCAGGCTCTGATGTATCTTCATCT 60.263 45.833 6.40 0.00 43.03 2.90
2474 2527 6.624423 ACAACAAGATAAAAGGCAAGCATAG 58.376 36.000 0.00 0.00 0.00 2.23
2476 2529 5.473066 ACAACAAGATAAAAGGCAAGCAT 57.527 34.783 0.00 0.00 0.00 3.79
2581 2635 9.495754 GAGATAAGCAAAACATTGTACTTGATC 57.504 33.333 13.14 8.56 0.00 2.92
2764 2820 8.964476 AGTAAGTATGTAATGTCCAATCAAGG 57.036 34.615 0.00 0.00 0.00 3.61
3151 3210 4.954118 TGTGGGCCCTGGTCGACT 62.954 66.667 25.70 0.00 29.86 4.18
3184 3245 1.471287 AGTGCTTATACACGACGCTCA 59.529 47.619 0.00 0.00 45.45 4.26
3925 3995 0.108281 TCGTTCGTTGTGGTGTGGAA 60.108 50.000 0.00 0.00 0.00 3.53
3999 4072 9.719355 ACTGATGTTGTATGTATGTTTGAACTA 57.281 29.630 0.00 0.00 0.00 2.24
4046 4119 4.008933 AGTGGTGCGAGTGGCCTC 62.009 66.667 3.32 0.00 42.61 4.70
4223 4296 3.935371 TTTTTCAGTGCCCTGGGAA 57.065 47.368 19.27 1.51 39.31 3.97
4424 4497 8.750298 TCCAAGTTAAATGGTTTTTACTGTTGA 58.250 29.630 8.08 0.00 35.49 3.18
4427 4500 7.197703 CGTCCAAGTTAAATGGTTTTTACTGT 58.802 34.615 8.08 0.00 35.49 3.55
4437 4510 5.704053 AGAACTAACCGTCCAAGTTAAATGG 59.296 40.000 2.73 2.73 39.41 3.16
4443 4516 3.135167 TGGAAGAACTAACCGTCCAAGTT 59.865 43.478 0.00 0.00 38.80 2.66
4444 4517 2.701951 TGGAAGAACTAACCGTCCAAGT 59.298 45.455 0.00 0.00 38.80 3.16
4499 4572 1.200839 CCGTTTGCACTTCGTCGTC 59.799 57.895 0.00 0.00 0.00 4.20
4527 4600 1.068417 GGCGTGTGTGTAGTGGTCA 59.932 57.895 0.00 0.00 0.00 4.02
4552 4632 2.203294 GTGTGTGGGAGGCGGTTT 60.203 61.111 0.00 0.00 0.00 3.27
4735 4815 0.179137 GACGTCTCGGCATGATGACA 60.179 55.000 8.70 0.00 33.63 3.58
4793 4873 1.684450 TGGTGTACTCACGCTTCTTGA 59.316 47.619 0.00 0.00 44.68 3.02
4803 4883 1.324383 TGAGCGTTCTGGTGTACTCA 58.676 50.000 0.00 0.00 0.00 3.41
4888 4968 1.953138 GCCCGCTCATCATCTCGTG 60.953 63.158 0.00 0.00 0.00 4.35
4903 4983 2.194326 GCCCTTCATCCTGAGCCC 59.806 66.667 0.00 0.00 0.00 5.19
4923 5003 1.195115 TGAAGCTCGGATACAAGCCT 58.805 50.000 0.00 0.00 0.00 4.58
5000 5081 2.742710 TTCCTCGACGGACAACTGCG 62.743 60.000 3.44 0.00 42.97 5.18
5009 5090 0.734253 CAAGCAGAGTTCCTCGACGG 60.734 60.000 0.00 0.00 35.36 4.79
5038 5119 2.144833 TTTTGTGGCTGCTGCGATGG 62.145 55.000 9.65 0.00 40.82 3.51
5075 5156 7.624549 AGTACTGGTACAACAGATGAATGAAT 58.375 34.615 12.54 0.00 40.97 2.57
5289 5384 9.107177 CAGAATCTATGCTAGTTCATCAAGTTT 57.893 33.333 0.00 0.00 0.00 2.66
5514 5609 6.479972 TTTACCGGAGTCAATGATAGATGT 57.520 37.500 9.46 0.00 0.00 3.06
5531 5626 8.673711 TCACCAAATTAGAGAATCATTTTACCG 58.326 33.333 0.00 0.00 37.82 4.02
5647 5743 8.510243 TTATGAGTCATGCATGAATGTAGTTT 57.490 30.769 32.27 13.10 38.75 2.66
5686 5782 7.339212 TGTTTTACAAGTGATAATCCATGAGGG 59.661 37.037 0.00 0.00 34.83 4.30
5717 5815 5.818136 TTGAGGATTTAATTCTTCTGCGG 57.182 39.130 9.89 0.00 0.00 5.69
5784 5882 0.110010 GAAGTCTTTGAGGCGCTTGC 60.110 55.000 7.64 0.00 38.11 4.01
6042 6140 4.711949 CTGGCAGCGGGCTGTTCT 62.712 66.667 20.66 0.00 45.24 3.01
6121 6219 2.209273 CAACCTGTCACGATGTTGTCA 58.791 47.619 0.00 0.00 34.76 3.58
6319 6417 2.948979 TGTTCAAACCCTGACACACATC 59.051 45.455 0.00 0.00 32.21 3.06
6372 6470 4.024387 GCAAACTTGTTGGACGACATAAGA 60.024 41.667 0.00 0.00 31.70 2.10
6461 6559 0.108662 CATGACTAGTGCTGCGTGGA 60.109 55.000 0.00 0.00 0.00 4.02
6618 6726 9.585099 TTAGTGTTCGTCTGAAACTAAAAACTA 57.415 29.630 0.00 0.00 36.23 2.24
6732 6841 3.769536 ACTGGTGTTTCTTTGCTTTTCG 58.230 40.909 0.00 0.00 0.00 3.46
6828 6937 9.197306 AGCTTCCCGTTCCTTTTTATATATTTT 57.803 29.630 0.00 0.00 0.00 1.82
6876 6985 7.333423 GCCACTGTTAATTCTTAGTATGTCACA 59.667 37.037 0.00 0.00 0.00 3.58
6968 7077 0.687354 GGCTGTGGTTCTTCTCCAGA 59.313 55.000 0.00 0.00 35.49 3.86
7031 7142 9.578439 CTTTCTTGTGATTTTTCTCTTTTGTCT 57.422 29.630 0.00 0.00 0.00 3.41
7057 7168 6.333416 TGATGCTAGTATGTCTTCTGTTGTC 58.667 40.000 0.00 0.00 0.00 3.18
7113 7226 6.344500 ACTGAGATTCCAATTGTGCTAGTAG 58.656 40.000 4.43 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.