Multiple sequence alignment - TraesCS4A01G326500

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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 TraesCS4A01G326500 chr4A 100.000 4847 0 0 1 4847 613558481 613563327 0 8951
1 TraesCS4A01G326500 chr4A 93.500 4308 241 16 38 4311 673171627 673167325 0 6368
2 TraesCS4A01G326500 chr3A 97.718 4250 92 4 598 4847 5371965 5376209 0 7306
3 TraesCS4A01G326500 chr3A 97.671 4251 93 4 598 4847 2304375 2308620 0 7297
4 TraesCS4A01G326500 chr3A 97.578 4252 97 5 598 4847 4344786 4349033 0 7276
5 TraesCS4A01G326500 chr3A 97.435 4250 104 3 598 4847 4860323 4864567 0 7239
6 TraesCS4A01G326500 chr3A 97.412 4250 95 4 598 4847 3286162 3290396 0 7225
7 TraesCS4A01G326500 chr3A 92.169 4048 295 15 804 4841 730238683 730234648 0 5699
8 TraesCS4A01G326500 chr6A 97.428 4044 103 1 804 4847 219545305 219549347 0 6890
9 TraesCS4A01G326500 chr6A 92.928 806 57 0 1 806 219544473 219545278 0 1173
10 TraesCS4A01G326500 chr2A 96.094 4045 147 8 804 4842 773697245 773693206 0 6584
11 TraesCS4A01G326500 chr2A 91.174 2946 208 20 4 2901 720513300 720510359 0 3952
12 TraesCS4A01G326500 chr2A 93.424 806 52 1 1 806 773698076 773697272 0 1194
13 TraesCS4A01G326500 chr7B 92.811 4340 274 20 1 4311 750160651 750156321 0 6252
14 TraesCS4A01G326500 chr7B 92.068 769 58 3 38 806 629987256 629988021 0 1079
15 TraesCS4A01G326500 chr7A 91.152 4566 332 39 329 4841 62575232 62579778 0 6128
16 TraesCS4A01G326500 chr1B 93.498 769 47 2 38 806 676864744 676863979 0 1140
17 TraesCS4A01G326500 chr2B 93.368 769 50 1 38 806 785301110 785300343 0 1136
18 TraesCS4A01G326500 chr3B 92.328 769 58 1 38 806 667632844 667633611 0 1092
19 TraesCS4A01G326500 chr5B 94.231 572 31 1 235 806 18261669 18261100 0 872


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 TraesCS4A01G326500 chr4A 613558481 613563327 4846 False 8951.0 8951 100.000 1 4847 1 chr4A.!!$F1 4846
1 TraesCS4A01G326500 chr4A 673167325 673171627 4302 True 6368.0 6368 93.500 38 4311 1 chr4A.!!$R1 4273
2 TraesCS4A01G326500 chr3A 5371965 5376209 4244 False 7306.0 7306 97.718 598 4847 1 chr3A.!!$F5 4249
3 TraesCS4A01G326500 chr3A 2304375 2308620 4245 False 7297.0 7297 97.671 598 4847 1 chr3A.!!$F1 4249
4 TraesCS4A01G326500 chr3A 4344786 4349033 4247 False 7276.0 7276 97.578 598 4847 1 chr3A.!!$F3 4249
5 TraesCS4A01G326500 chr3A 4860323 4864567 4244 False 7239.0 7239 97.435 598 4847 1 chr3A.!!$F4 4249
6 TraesCS4A01G326500 chr3A 3286162 3290396 4234 False 7225.0 7225 97.412 598 4847 1 chr3A.!!$F2 4249
7 TraesCS4A01G326500 chr3A 730234648 730238683 4035 True 5699.0 5699 92.169 804 4841 1 chr3A.!!$R1 4037
8 TraesCS4A01G326500 chr6A 219544473 219549347 4874 False 4031.5 6890 95.178 1 4847 2 chr6A.!!$F1 4846
9 TraesCS4A01G326500 chr2A 720510359 720513300 2941 True 3952.0 3952 91.174 4 2901 1 chr2A.!!$R1 2897
10 TraesCS4A01G326500 chr2A 773693206 773698076 4870 True 3889.0 6584 94.759 1 4842 2 chr2A.!!$R2 4841
11 TraesCS4A01G326500 chr7B 750156321 750160651 4330 True 6252.0 6252 92.811 1 4311 1 chr7B.!!$R1 4310
12 TraesCS4A01G326500 chr7B 629987256 629988021 765 False 1079.0 1079 92.068 38 806 1 chr7B.!!$F1 768
13 TraesCS4A01G326500 chr7A 62575232 62579778 4546 False 6128.0 6128 91.152 329 4841 1 chr7A.!!$F1 4512
14 TraesCS4A01G326500 chr1B 676863979 676864744 765 True 1140.0 1140 93.498 38 806 1 chr1B.!!$R1 768
15 TraesCS4A01G326500 chr2B 785300343 785301110 767 True 1136.0 1136 93.368 38 806 1 chr2B.!!$R1 768
16 TraesCS4A01G326500 chr3B 667632844 667633611 767 False 1092.0 1092 92.328 38 806 1 chr3B.!!$F1 768
17 TraesCS4A01G326500 chr5B 18261100 18261669 569 True 872.0 872 94.231 235 806 1 chr5B.!!$R1 571

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
315 316 1.064825 AGTTTGGGATCCACCGACTT 58.935 50.000 15.23 0.0 40.11 3.01 F
885 983 1.282382 GCACCCTAAACCCTAGGACA 58.718 55.000 11.48 0.0 36.85 4.02 F
2138 2249 1.003696 GGCAGGAGTAGAAAGCCAAGT 59.996 52.381 0.00 0.0 44.59 3.16 F
3091 3207 1.301716 GTGGTCGATATGCCGCCAT 60.302 57.895 0.00 0.0 37.77 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1119 1217 2.158475 TCTGGCTGTGAATTTTCCCACT 60.158 45.455 0.00 0.0 34.57 4.00 R
2495 2608 3.632145 GGGCACGTAGGAATCATTGAAAT 59.368 43.478 0.00 0.0 0.00 2.17 R
3110 3227 0.178767 ATCGTGAAGCATAGCTGGCA 59.821 50.000 13.72 0.0 39.62 4.92 R
4787 4922 0.455410 CGGGTATGTAAACCGGTCGA 59.545 55.000 8.04 0.0 43.69 4.20 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
39 40 2.806745 CGGGGCTGACATCGTTCATATT 60.807 50.000 0.00 0.00 0.00 1.28
169 170 2.174969 GTCGGACACCAAACGCACA 61.175 57.895 2.62 0.00 0.00 4.57
233 234 7.282224 CGGAGAAAACCATAGGAAATTCATACA 59.718 37.037 0.00 0.00 0.00 2.29
254 255 6.036577 ACAGTGCCGGAAAATTATGAAAAT 57.963 33.333 5.05 0.00 0.00 1.82
264 265 6.519419 GGAAAATTATGAAAATTTGCACGCAC 59.481 34.615 0.00 0.00 29.13 5.34
312 313 2.625790 CAAAAAGTTTGGGATCCACCGA 59.374 45.455 15.23 0.00 40.11 4.69
315 316 1.064825 AGTTTGGGATCCACCGACTT 58.935 50.000 15.23 0.00 40.11 3.01
364 367 9.790389 AAAATGCATTAATAAATTCCGACGTTA 57.210 25.926 13.39 0.00 0.00 3.18
501 505 5.071788 AGAGTCCCACAAACTGAGATGTTTA 59.928 40.000 0.00 0.00 37.98 2.01
572 602 5.696724 GCTTAGCGATGTGGTATTGAACTAT 59.303 40.000 0.00 0.00 0.00 2.12
819 917 4.733371 TTCCGTCATCTGCGCGCA 62.733 61.111 34.12 34.12 0.00 6.09
885 983 1.282382 GCACCCTAAACCCTAGGACA 58.718 55.000 11.48 0.00 36.85 4.02
1119 1217 4.062293 CGGTTGAGAAGTGGTGTGAATTA 58.938 43.478 0.00 0.00 0.00 1.40
1497 1595 4.038271 TGATGATTTTGTGAGAAGGGCT 57.962 40.909 0.00 0.00 0.00 5.19
1503 1601 4.967084 TTTTGTGAGAAGGGCTGTACTA 57.033 40.909 0.00 0.00 0.00 1.82
1685 1783 6.662865 TGAAAAATTCAAGTGGCCTATTGA 57.337 33.333 16.36 16.36 36.59 2.57
1773 1873 9.403583 TGTGATATATGTGTCTGACTAGTTGTA 57.596 33.333 9.51 0.00 0.00 2.41
2138 2249 1.003696 GGCAGGAGTAGAAAGCCAAGT 59.996 52.381 0.00 0.00 44.59 3.16
2156 2267 2.537143 AGTACGTCAGGGGTTTCATCT 58.463 47.619 0.00 0.00 0.00 2.90
2396 2509 8.611757 CACCAATGACGAATTTGATAATGTAGA 58.388 33.333 0.00 0.00 0.00 2.59
2486 2599 2.615447 CCGACGTGGAGCTAGTAACATA 59.385 50.000 0.00 0.00 42.00 2.29
2495 2608 5.361571 TGGAGCTAGTAACATATTTCACGGA 59.638 40.000 0.00 0.00 0.00 4.69
2961 3075 6.587226 GCATTGTTTTAGATCTGTTTGCATCA 59.413 34.615 5.18 0.00 0.00 3.07
2964 3078 6.545508 TGTTTTAGATCTGTTTGCATCATCG 58.454 36.000 5.18 0.00 0.00 3.84
3003 3117 5.437060 GCAAGTTCCCTTAATATGACTCCA 58.563 41.667 0.00 0.00 0.00 3.86
3091 3207 1.301716 GTGGTCGATATGCCGCCAT 60.302 57.895 0.00 0.00 37.77 4.40
3285 3403 4.389374 ACAACACCGTGATTTCTCTGATT 58.611 39.130 5.28 0.00 0.00 2.57
3873 3997 9.410556 GTTAAATGAATACAAGAAAGTGCATGT 57.589 29.630 0.00 0.00 0.00 3.21
4147 4271 1.162698 GAAGGTTTCCCTACCGTTGC 58.837 55.000 0.00 0.00 41.56 4.17
4247 4371 8.892905 GCTTTCGTGAGACACTAAAAATTTAAG 58.107 33.333 0.00 0.00 41.84 1.85
4439 4563 1.676635 GATTCTGGTGGCAGCAGCA 60.677 57.895 35.28 28.38 43.02 4.41
4724 4859 1.154016 CGATCCTCTTCGTGTGCGT 60.154 57.895 0.00 0.00 39.49 5.24
4807 4942 0.173255 CGACCGGTTTACATACCCGT 59.827 55.000 9.42 0.00 40.10 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.375523 GAACGATGTCAGCCCCGTT 60.376 57.895 0.00 0.00 46.15 4.44
39 40 1.613317 ATCCAACCGGCACTGATCGA 61.613 55.000 0.00 0.00 0.00 3.59
185 186 0.099791 AAACGCACCGAAAACACTGG 59.900 50.000 0.00 0.00 0.00 4.00
233 234 6.128309 GCAAATTTTCATAATTTTCCGGCACT 60.128 34.615 0.00 0.00 0.00 4.40
254 255 2.612567 GGTCCATCGTGCGTGCAAA 61.613 57.895 0.00 0.00 0.00 3.68
264 265 2.280389 CCATCGCCAGGTCCATCG 60.280 66.667 0.00 0.00 0.00 3.84
456 460 6.962311 ACTCTATTTGGAGGATATGCAGGATA 59.038 38.462 0.00 0.00 37.63 2.59
819 917 1.617947 GGGCCTGAGATCCAAGTCGT 61.618 60.000 0.84 0.00 0.00 4.34
861 959 4.354162 GGGTTTAGGGTGCCGGCA 62.354 66.667 29.03 29.03 0.00 5.69
1119 1217 2.158475 TCTGGCTGTGAATTTTCCCACT 60.158 45.455 0.00 0.00 34.57 4.00
1497 1595 7.408543 AGACTGTACCCATAAGAACTAGTACA 58.591 38.462 0.00 0.00 38.12 2.90
1503 1601 5.720041 TGCTAAGACTGTACCCATAAGAACT 59.280 40.000 0.00 0.00 0.00 3.01
1683 1781 3.244353 CCTGAAGAAGAGCCAAGTTCTCA 60.244 47.826 0.00 0.00 31.61 3.27
1685 1783 2.708325 ACCTGAAGAAGAGCCAAGTTCT 59.292 45.455 0.00 0.00 34.37 3.01
1930 2030 7.928706 GGACTATACTCATTGACTTACATTGCT 59.071 37.037 0.00 0.00 32.12 3.91
2138 2249 3.833650 TGTTAGATGAAACCCCTGACGTA 59.166 43.478 0.00 0.00 0.00 3.57
2156 2267 4.142622 CGGTCCATACTGTTAGTCGTGTTA 60.143 45.833 0.00 0.00 0.00 2.41
2396 2509 4.934797 TTCTCCATCCCAACTTCTTCAT 57.065 40.909 0.00 0.00 0.00 2.57
2486 2599 6.780457 AGGAATCATTGAAATCCGTGAAAT 57.220 33.333 13.29 0.00 37.05 2.17
2495 2608 3.632145 GGGCACGTAGGAATCATTGAAAT 59.368 43.478 0.00 0.00 0.00 2.17
2668 2781 6.270000 CCACCCATAGACTCACCAGAAATATA 59.730 42.308 0.00 0.00 0.00 0.86
2961 3075 1.406539 GCCAGAATTGAATGTGGCGAT 59.593 47.619 14.02 0.00 45.73 4.58
3003 3117 1.693062 CTGGCTGCCTCTATGTGATCT 59.307 52.381 21.03 0.00 0.00 2.75
3091 3207 2.553685 GCATGCATATGTCCCCATCTGA 60.554 50.000 14.21 0.00 36.65 3.27
3110 3227 0.178767 ATCGTGAAGCATAGCTGGCA 59.821 50.000 13.72 0.00 39.62 4.92
3285 3403 5.278071 GGAACCACGTTGTTGATATGAAACA 60.278 40.000 10.08 0.00 35.78 2.83
3873 3997 7.360113 TGTGTGTGATCAGCTTAGGATATAA 57.640 36.000 0.00 0.00 0.00 0.98
4147 4271 6.128715 GCATTACAATCGATCACAGTATCCAG 60.129 42.308 0.00 0.00 0.00 3.86
4247 4371 1.444836 TATTACTTGCCCACACGCAC 58.555 50.000 0.00 0.00 38.83 5.34
4439 4563 1.162181 TATTCGTCGGACCGATCGCT 61.162 55.000 21.53 16.19 38.42 4.93
4698 4833 2.683933 AAGAGGATCGGCCCACGT 60.684 61.111 0.00 0.00 44.69 4.49
4787 4922 0.455410 CGGGTATGTAAACCGGTCGA 59.545 55.000 8.04 0.00 43.69 4.20
4807 4942 1.873903 GCTTGTGAGAAGGCGAAGACA 60.874 52.381 0.00 0.00 39.87 3.41


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

AutoCloner maintained by Alex Coulton.