Multiple sequence alignment - TraesCS4A01G378600

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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 TraesCS4A01G378600 chr4A 100.000 3268 0 0 1 3268 656148091 656151358 0.000000e+00 6035
1 TraesCS4A01G378600 chr4A 97.003 3270 96 1 1 3268 656355387 656358656 0.000000e+00 5494
2 TraesCS4A01G378600 chr4A 95.194 2892 134 3 378 3268 655846675 655849562 0.000000e+00 4566
3 TraesCS4A01G378600 chr4A 95.124 2892 136 3 378 3268 655893826 655896713 0.000000e+00 4554
4 TraesCS4A01G378600 chr6B 94.587 3270 169 2 1 3268 692863580 692866843 0.000000e+00 5051
5 TraesCS4A01G378600 chr6B 94.018 2892 169 4 377 3266 216895136 216898025 0.000000e+00 4379
6 TraesCS4A01G378600 chr6B 92.987 385 25 2 1 383 216894852 216895236 7.920000e-156 560
7 TraesCS4A01G378600 chr2B 94.553 3268 173 5 3 3268 177236729 177239993 0.000000e+00 5044
8 TraesCS4A01G378600 chr2B 94.792 2842 147 1 377 3217 791334312 791331471 0.000000e+00 4427
9 TraesCS4A01G378600 chr4B 94.404 3270 156 6 3 3268 16567563 16570809 0.000000e+00 5000
10 TraesCS4A01G378600 chr3B 95.227 2891 138 0 378 3268 729227105 729229995 0.000000e+00 4575
11 TraesCS4A01G378600 chr5B 93.109 1190 68 5 1 1190 230901281 230902456 0.000000e+00 1731
12 TraesCS4A01G378600 chr1B 92.708 384 25 3 3 383 48238670 48239053 4.770000e-153 551


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 TraesCS4A01G378600 chr4A 656148091 656151358 3267 False 6035.0 6035 100.0000 1 3268 1 chr4A.!!$F3 3267
1 TraesCS4A01G378600 chr4A 656355387 656358656 3269 False 5494.0 5494 97.0030 1 3268 1 chr4A.!!$F4 3267
2 TraesCS4A01G378600 chr4A 655846675 655849562 2887 False 4566.0 4566 95.1940 378 3268 1 chr4A.!!$F1 2890
3 TraesCS4A01G378600 chr4A 655893826 655896713 2887 False 4554.0 4554 95.1240 378 3268 1 chr4A.!!$F2 2890
4 TraesCS4A01G378600 chr6B 692863580 692866843 3263 False 5051.0 5051 94.5870 1 3268 1 chr6B.!!$F1 3267
5 TraesCS4A01G378600 chr6B 216894852 216898025 3173 False 2469.5 4379 93.5025 1 3266 2 chr6B.!!$F2 3265
6 TraesCS4A01G378600 chr2B 177236729 177239993 3264 False 5044.0 5044 94.5530 3 3268 1 chr2B.!!$F1 3265
7 TraesCS4A01G378600 chr2B 791331471 791334312 2841 True 4427.0 4427 94.7920 377 3217 1 chr2B.!!$R1 2840
8 TraesCS4A01G378600 chr4B 16567563 16570809 3246 False 5000.0 5000 94.4040 3 3268 1 chr4B.!!$F1 3265
9 TraesCS4A01G378600 chr3B 729227105 729229995 2890 False 4575.0 4575 95.2270 378 3268 1 chr3B.!!$F1 2890
10 TraesCS4A01G378600 chr5B 230901281 230902456 1175 False 1731.0 1731 93.1090 1 1190 1 chr5B.!!$F1 1189

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
909 1007 1.026718 GGCAACTGCGCTTCCATAGT 61.027 55.0 9.73 0.0 43.26 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2590 2692 1.198713 CCACTCCTGCCACTACTCAT 58.801 55.0 0.0 0.0 0.0 2.9 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
161 162 4.408921 AGAGATGGAAATGATGGAACCGTA 59.591 41.667 0.00 0.00 0.00 4.02
199 200 8.579006 ACTGTTTGATTTTAGCATCAAGATTCA 58.421 29.630 0.00 0.00 42.73 2.57
422 425 3.890756 TCAACTCTGTGGATGCACAAATT 59.109 39.130 21.10 12.16 34.35 1.82
465 561 6.686630 CATCTGAAGACTTACTCAGACAGTT 58.313 40.000 7.36 0.00 41.29 3.16
595 691 3.510360 AGCATTGGTCGTTCAGTAGTAGT 59.490 43.478 0.00 0.00 0.00 2.73
743 841 6.266168 ACGTGCTTAATTGGATGATTTGAA 57.734 33.333 0.00 0.00 0.00 2.69
909 1007 1.026718 GGCAACTGCGCTTCCATAGT 61.027 55.000 9.73 0.00 43.26 2.12
1093 1192 2.525629 TCCCCGGTCAGAAGCACA 60.526 61.111 0.00 0.00 0.00 4.57
1245 1344 1.464608 CAGTTCATCGGCGTTGATGTT 59.535 47.619 20.05 7.37 44.82 2.71
1268 1367 5.748402 TGAGTATACTAGGGAAGACGAACA 58.252 41.667 5.09 0.00 0.00 3.18
1646 1747 7.703621 AGTTCAGTTTCTTGAATTGATGTGTTG 59.296 33.333 0.00 0.00 39.13 3.33
1733 1834 0.646895 GCTTGTGCTTGTGTTTGTGC 59.353 50.000 0.00 0.00 36.03 4.57
1738 1839 0.455410 TGCTTGTGTTTGTGCACTCC 59.545 50.000 19.41 6.22 39.89 3.85
1834 1935 3.605634 TGGATCCACCTTAAATGTGTCG 58.394 45.455 11.44 0.00 39.86 4.35
2174 2276 1.612676 TAGATGCGTACGCCACCTAT 58.387 50.000 35.11 22.35 41.09 2.57
2179 2281 0.664761 GCGTACGCCACCTATGAGTA 59.335 55.000 29.51 0.00 34.56 2.59
2237 2339 3.080319 GAGTGCAAAAGAGGCAGAGAAT 58.920 45.455 0.00 0.00 42.85 2.40
2328 2430 3.378112 TGTGTTTCTGCTTGTCCTTTCTG 59.622 43.478 0.00 0.00 0.00 3.02
2362 2464 7.178097 AGGTTCGTAGTTTAGTTCTGTTAGGAT 59.822 37.037 0.00 0.00 0.00 3.24
2590 2692 2.881266 GCACACAAGCGCGACTTCA 61.881 57.895 12.10 0.00 36.04 3.02
2595 2697 0.319900 ACAAGCGCGACTTCATGAGT 60.320 50.000 12.10 3.92 42.70 3.41
2877 2979 2.028658 GCAAGTGTCATGTGAGAGAGGA 60.029 50.000 0.00 0.00 0.00 3.71
2878 2980 3.847542 CAAGTGTCATGTGAGAGAGGAG 58.152 50.000 0.00 0.00 0.00 3.69
2921 3023 2.432456 GGATGCGCTGTCGTGACA 60.432 61.111 9.73 2.28 39.32 3.58
3007 3109 0.940126 CGTGGATGCAGGCATAGAAC 59.060 55.000 6.76 5.25 36.70 3.01
3252 3354 0.676782 GCATGGTGGTGTGGTAGGAC 60.677 60.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.195741 ACATCTGTGCTTCATGTGCT 57.804 45.000 12.86 0.0 0.00 4.40
351 354 5.505819 CGTGACTGTCTGAGTAAGTCTTCAA 60.506 44.000 9.51 0.0 40.79 2.69
422 425 1.001020 CATGCCCCTGCCACTACAA 60.001 57.895 0.00 0.0 36.33 2.41
465 561 5.779529 ACTCTAAAGACTTCACAACCGTA 57.220 39.130 0.00 0.0 0.00 4.02
743 841 1.045911 TTGCCGGGAAAAAGCAACCT 61.046 50.000 5.67 0.0 41.35 3.50
909 1007 3.034721 AGTGTTTCCGTAATTGAGCGA 57.965 42.857 0.00 0.0 0.00 4.93
1245 1344 5.748402 TGTTCGTCTTCCCTAGTATACTCA 58.252 41.667 9.12 0.0 0.00 3.41
1317 1416 0.103390 CCGCGGTGATGTGGTATACA 59.897 55.000 19.50 0.0 44.87 2.29
1355 1454 3.314693 TGGAGAGGTTGAAGTTGTAGGT 58.685 45.455 0.00 0.0 0.00 3.08
1646 1747 3.317430 CCTATGTACTCCTTACCCACGTC 59.683 52.174 0.00 0.0 0.00 4.34
1733 1834 1.662629 CAGAAACTGCTATGCGGAGTG 59.337 52.381 5.31 0.0 44.21 3.51
1738 1839 6.695292 AAAAATTTCAGAAACTGCTATGCG 57.305 33.333 0.00 0.0 0.00 4.73
2037 2139 2.507944 GCGGATCATGCTCCCTGT 59.492 61.111 9.98 0.0 31.04 4.00
2174 2276 8.690203 TGTTTTCAATTCTCTTCCAATACTCA 57.310 30.769 0.00 0.0 0.00 3.41
2179 2281 8.413309 TCTGATGTTTTCAATTCTCTTCCAAT 57.587 30.769 0.00 0.0 32.78 3.16
2237 2339 8.362464 AGGCATAGTAAGGATCGTCATAATTA 57.638 34.615 0.00 0.0 0.00 1.40
2328 2430 6.594284 ACTAAACTACGAACCTGAAACAAC 57.406 37.500 0.00 0.0 0.00 3.32
2362 2464 4.973168 AGGTGACATTAGAAACTGCTTCA 58.027 39.130 0.00 0.0 36.40 3.02
2409 2511 9.347934 CACATAAACAAACTACAAACTTCACAA 57.652 29.630 0.00 0.0 0.00 3.33
2590 2692 1.198713 CCACTCCTGCCACTACTCAT 58.801 55.000 0.00 0.0 0.00 2.90
2595 2697 1.603842 CATGCCACTCCTGCCACTA 59.396 57.895 0.00 0.0 0.00 2.74
2842 2944 3.318017 ACACTTGCGATGACTCTTACAC 58.682 45.455 0.00 0.0 0.00 2.90
2921 3023 1.523758 GCCCGTGTCTCTTCACAAAT 58.476 50.000 0.00 0.0 38.12 2.32
2948 3050 1.078759 GCGACACTTACATGCTCGCT 61.079 55.000 4.21 0.0 41.58 4.93
3007 3109 3.594134 GTTGAGTCTTCACCTCCATGAG 58.406 50.000 0.00 0.0 31.71 2.90
3046 3148 5.747565 TGATAGCTGTTCGAAACAACAAAG 58.252 37.500 0.00 0.0 41.61 2.77
3113 3215 6.367983 ACCATGACTCCCTAACTACGTATTA 58.632 40.000 0.00 0.0 0.00 0.98


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

AutoCloner maintained by Alex Coulton.