Multiple sequence alignment - TraesCS2A01G432000

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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 TraesCS2A01G432000 chr2A 100.000 7209 0 0 1 7209 685104326 685097118 0.000000e+00 13313
1 TraesCS2A01G432000 chr2A 97.422 7216 171 13 1 7209 284799906 284807113 0.000000e+00 12281
2 TraesCS2A01G432000 chr2A 97.243 7218 171 12 1 7209 572969923 572962725 0.000000e+00 12201
3 TraesCS2A01G432000 chr2A 96.854 7216 197 17 1 7209 716654165 716646973 0.000000e+00 12041
4 TraesCS2A01G432000 chr2A 88.877 2769 253 34 1 2755 433263653 433266380 0.000000e+00 3356
5 TraesCS2A01G432000 chr2A 96.341 82 2 1 1 82 266689722 266689802 4.540000e-27 134
6 TraesCS2A01G432000 chr2A 96.341 82 2 1 1 82 270198861 270198781 4.540000e-27 134
7 TraesCS2A01G432000 chr2A 96.341 82 2 1 1 82 270226834 270226914 4.540000e-27 134
8 TraesCS2A01G432000 chr5A 97.464 7215 161 12 1 7209 465654118 465661316 0.000000e+00 12290
9 TraesCS2A01G432000 chr5A 97.273 7223 174 17 1 7209 34943377 34936164 0.000000e+00 12225
10 TraesCS2A01G432000 chr5A 97.103 7215 186 12 1 7209 541976898 541984095 0.000000e+00 12144
11 TraesCS2A01G432000 chr3A 97.077 7219 168 15 1 7209 662010412 662003227 0.000000e+00 12122
12 TraesCS2A01G432000 chr3A 96.952 7218 195 17 1 7209 554827437 554834638 0.000000e+00 12087
13 TraesCS2A01G432000 chr1A 97.841 6347 127 7 865 7209 70944907 70938569 0.000000e+00 10953


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 TraesCS2A01G432000 chr2A 685097118 685104326 7208 True 13313 13313 100.000 1 7209 1 chr2A.!!$R3 7208
1 TraesCS2A01G432000 chr2A 284799906 284807113 7207 False 12281 12281 97.422 1 7209 1 chr2A.!!$F3 7208
2 TraesCS2A01G432000 chr2A 572962725 572969923 7198 True 12201 12201 97.243 1 7209 1 chr2A.!!$R2 7208
3 TraesCS2A01G432000 chr2A 716646973 716654165 7192 True 12041 12041 96.854 1 7209 1 chr2A.!!$R4 7208
4 TraesCS2A01G432000 chr2A 433263653 433266380 2727 False 3356 3356 88.877 1 2755 1 chr2A.!!$F4 2754
5 TraesCS2A01G432000 chr5A 465654118 465661316 7198 False 12290 12290 97.464 1 7209 1 chr5A.!!$F1 7208
6 TraesCS2A01G432000 chr5A 34936164 34943377 7213 True 12225 12225 97.273 1 7209 1 chr5A.!!$R1 7208
7 TraesCS2A01G432000 chr5A 541976898 541984095 7197 False 12144 12144 97.103 1 7209 1 chr5A.!!$F2 7208
8 TraesCS2A01G432000 chr3A 662003227 662010412 7185 True 12122 12122 97.077 1 7209 1 chr3A.!!$R1 7208
9 TraesCS2A01G432000 chr3A 554827437 554834638 7201 False 12087 12087 96.952 1 7209 1 chr3A.!!$F1 7208
10 TraesCS2A01G432000 chr1A 70938569 70944907 6338 True 10953 10953 97.841 865 7209 1 chr1A.!!$R1 6344

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
558 565 0.528470 GAGGAGTTCAGACCTCCACG 59.472 60.0 16.07 0.0 44.70 4.94 F
1188 1207 0.968901 ACAAGGCCGACGAGGTGATA 60.969 55.0 0.00 0.0 43.70 2.15 F
1199 1218 2.108425 ACGAGGTGATATCCAGGCTCTA 59.892 50.0 0.00 0.0 0.00 2.43 F
3310 3349 0.107654 GGACTAAACCCAGAGCGCAT 60.108 55.0 11.47 0.0 0.00 4.73 F
4700 4748 0.179020 CTCCAAAGCCCACAGTCACA 60.179 55.0 0.00 0.0 0.00 3.58 F
4873 4921 0.900182 TGGAGATCGTCTGCACCAGT 60.900 55.0 5.39 0.0 39.98 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2513 2543 1.754226 TCAACCCAACAAGAGCAAACC 59.246 47.619 0.00 0.00 0.00 3.27 R
2848 2879 4.067192 TGCGTGTAGACTGAGTTGTACTA 58.933 43.478 7.35 0.00 0.00 1.82 R
4512 4558 4.941309 GTGGGGGTCGCCGTTTGT 62.941 66.667 0.00 0.00 0.00 2.83 R
4887 4935 1.000618 GCCTGCTCATCATCTCATCGA 59.999 52.381 0.00 0.00 0.00 3.59 R
6165 6220 1.272807 GCAGTGGTAGTAGGGGTCAA 58.727 55.000 0.00 0.00 0.00 3.18 R
6765 6827 2.292016 CAGTCCTAGGATGCTAGTGACG 59.708 54.545 23.87 18.53 34.89 4.35 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
147 148 3.876914 TGTCAACCAGTAACTCAGCAAAG 59.123 43.478 0.00 0.0 0.00 2.77
306 309 1.992557 TGCTCCTACCAGTCCCAATTT 59.007 47.619 0.00 0.0 0.00 1.82
323 326 7.775561 GTCCCAATTTAGAAAGACCATCAGTAT 59.224 37.037 0.00 0.0 0.00 2.12
418 424 7.876068 TGTAAAGTTACTCACAGGTTATCTTGG 59.124 37.037 3.07 0.0 34.77 3.61
558 565 0.528470 GAGGAGTTCAGACCTCCACG 59.472 60.000 16.07 0.0 44.70 4.94
908 927 3.201708 CCATTGTCTTCCATCTCTCCCTT 59.798 47.826 0.00 0.0 0.00 3.95
971 990 4.080299 ACACAAACCTCCAACTTCTCTCTT 60.080 41.667 0.00 0.0 0.00 2.85
1188 1207 0.968901 ACAAGGCCGACGAGGTGATA 60.969 55.000 0.00 0.0 43.70 2.15
1199 1218 2.108425 ACGAGGTGATATCCAGGCTCTA 59.892 50.000 0.00 0.0 0.00 2.43
1347 1366 2.650196 GCAGCGGCCACAAAATGA 59.350 55.556 2.24 0.0 0.00 2.57
1432 1451 9.533253 CTGAAAATTTAATCACACTTGTTTCCT 57.467 29.630 0.00 0.0 0.00 3.36
2071 2097 2.166459 TGTTCACATTTGCCGGTTTCAA 59.834 40.909 1.90 0.0 0.00 2.69
2106 2132 2.849294 AGAGAAGCTGAAGTTGTCCC 57.151 50.000 0.00 0.0 0.00 4.46
2776 2807 4.848562 ACAACTCAGTACACTTGATCGA 57.151 40.909 0.00 0.0 0.00 3.59
2848 2879 4.887748 AGCGCTACTATGAATGCACTATT 58.112 39.130 8.99 0.0 0.00 1.73
3046 3078 7.400339 TGGAGGAGTCAAGTACTAGATTCAAAT 59.600 37.037 0.00 0.0 39.07 2.32
3244 3283 0.318784 GAGTTCGACTGGTGAGCGTT 60.319 55.000 0.00 0.0 0.00 4.84
3310 3349 0.107654 GGACTAAACCCAGAGCGCAT 60.108 55.000 11.47 0.0 0.00 4.73
3312 3351 0.324943 ACTAAACCCAGAGCGCATGT 59.675 50.000 11.47 0.0 0.00 3.21
4512 4558 2.356553 GGTTGCCACGACGCACTA 60.357 61.111 0.00 0.0 38.83 2.74
4582 4628 4.901123 CACACACCACCGTCGGCA 62.901 66.667 12.28 0.0 0.00 5.69
4620 4668 3.201708 CCATTGTCTTCCATCTCTCCCTT 59.798 47.826 0.00 0.0 0.00 3.95
4698 4746 0.397941 CTCTCCAAAGCCCACAGTCA 59.602 55.000 0.00 0.0 0.00 3.41
4700 4748 0.179020 CTCCAAAGCCCACAGTCACA 60.179 55.000 0.00 0.0 0.00 3.58
4873 4921 0.900182 TGGAGATCGTCTGCACCAGT 60.900 55.000 5.39 0.0 39.98 4.00
4887 4935 1.134098 CACCAGTGAACCAGACAAGGT 60.134 52.381 0.00 0.0 45.91 3.50
4891 4939 1.971357 AGTGAACCAGACAAGGTCGAT 59.029 47.619 0.00 0.0 42.25 3.59
4909 4957 2.548280 CGATGAGATGATGAGCAGGCTT 60.548 50.000 0.00 0.0 0.00 4.35
6165 6220 5.196695 GGATATTTCAAAAGAGCAGGAGGT 58.803 41.667 0.00 0.0 0.00 3.85
6248 6303 4.224147 TGTTGAACCAGCTACCTTATGCTA 59.776 41.667 0.00 0.0 37.81 3.49
6593 6649 5.355596 GCTCAGTACAGCTTAGACATGAAT 58.644 41.667 0.00 0.0 36.38 2.57
6747 6809 5.217978 TGCATCAGGAAAAGCAAAGAAAT 57.782 34.783 0.00 0.0 33.48 2.17
6756 6818 6.775629 AGGAAAAGCAAAGAAATACCAGTACA 59.224 34.615 0.00 0.0 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 8.070034 TGACTGCATTCAAAAGGATTATCAAT 57.930 30.769 3.97 0.00 0.00 2.57
336 339 2.000429 ATTCGCATTTTGCTTGAGGC 58.000 45.000 0.00 0.00 42.25 4.70
398 402 9.880157 TTTATACCAAGATAACCTGTGAGTAAC 57.120 33.333 0.00 0.00 0.00 2.50
399 403 9.880157 GTTTATACCAAGATAACCTGTGAGTAA 57.120 33.333 0.00 0.00 0.00 2.24
558 565 2.645510 CGTGTCAGCGTCGGTGTTC 61.646 63.158 22.58 16.85 32.43 3.18
785 794 2.991190 GTTTGCACTTCATCATGGCAAG 59.009 45.455 0.00 0.00 44.24 4.01
876 895 5.993748 TGGAAGACAATGGGGTATTTTTC 57.006 39.130 0.00 0.00 0.00 2.29
908 927 1.759445 CAATGGTGGTTTGTGGGAACA 59.241 47.619 0.00 0.00 38.70 3.18
971 990 2.281484 GGCGACTGTGGGCTTTGA 60.281 61.111 9.08 0.00 0.00 2.69
1144 1163 2.163390 CGCTGGTGCAGACGATCTG 61.163 63.158 9.73 9.73 46.90 2.90
1188 1207 1.220236 AGCTTCCTCTAGAGCCTGGAT 59.780 52.381 14.73 0.00 0.00 3.41
1199 1218 3.618780 CTGCCGCCAAGCTTCCTCT 62.619 63.158 0.00 0.00 0.00 3.69
1528 1552 7.556275 TCCGCAAGATTTTCCAAATAGTAATCT 59.444 33.333 0.00 0.00 37.20 2.40
2071 2097 4.555511 GCTTCTCTTTGTCGCTTTCAATGT 60.556 41.667 0.00 0.00 0.00 2.71
2513 2543 1.754226 TCAACCCAACAAGAGCAAACC 59.246 47.619 0.00 0.00 0.00 3.27
2848 2879 4.067192 TGCGTGTAGACTGAGTTGTACTA 58.933 43.478 7.35 0.00 0.00 1.82
4512 4558 4.941309 GTGGGGGTCGCCGTTTGT 62.941 66.667 0.00 0.00 0.00 2.83
4620 4668 2.445427 CAATGGTGCTATGTGGGAACA 58.555 47.619 0.00 0.00 38.70 3.18
4698 4746 2.988839 GCCATGGCCTTCCTCCTGT 61.989 63.158 27.24 0.00 34.56 4.00
4700 4748 3.801997 CGCCATGGCCTTCCTCCT 61.802 66.667 30.79 0.00 37.98 3.69
4873 4921 1.967779 TCATCGACCTTGTCTGGTTCA 59.032 47.619 0.00 0.00 41.00 3.18
4887 4935 1.000618 GCCTGCTCATCATCTCATCGA 59.999 52.381 0.00 0.00 0.00 3.59
4891 4939 2.367894 CCTAAGCCTGCTCATCATCTCA 59.632 50.000 0.00 0.00 0.00 3.27
4909 4957 3.546543 CCGCCGCCCTTCATCCTA 61.547 66.667 0.00 0.00 0.00 2.94
5063 5114 7.187824 ACAGATGAATGAACAGTAGTATGGT 57.812 36.000 0.00 0.00 0.00 3.55
6165 6220 1.272807 GCAGTGGTAGTAGGGGTCAA 58.727 55.000 0.00 0.00 0.00 3.18
6248 6303 7.500892 TGAAACAACAATACTAAGGACACACAT 59.499 33.333 0.00 0.00 0.00 3.21
6747 6809 5.889853 AGTGACGAGGAAATATGTACTGGTA 59.110 40.000 0.00 0.00 0.00 3.25
6756 6818 4.835615 AGGATGCTAGTGACGAGGAAATAT 59.164 41.667 0.00 0.00 0.00 1.28
6765 6827 2.292016 CAGTCCTAGGATGCTAGTGACG 59.708 54.545 23.87 18.53 34.89 4.35
7032 7095 9.139174 GTTTCTTGTGATTTTTCTCTTTTGTCA 57.861 29.630 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.