Multiple sequence alignment - TraesCS2A01G537000

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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 TraesCS2A01G537000 chr2A 100.000 3574 0 0 1 3574 750956437 750952864 0.000000e+00 6601
1 TraesCS2A01G537000 chr2A 76.543 1053 191 39 117 1155 750563842 750564852 3.160000e-145 525
2 TraesCS2A01G537000 chr2A 75.981 1070 184 48 116 1155 750570133 750571159 5.360000e-133 484
3 TraesCS2A01G537000 chr2A 75.888 1070 185 50 116 1155 750593687 750594713 2.500000e-131 479
4 TraesCS2A01G537000 chr2A 75.655 1068 191 45 116 1155 750632146 750633172 5.400000e-128 468
5 TraesCS2A01G537000 chr2A 86.391 169 21 2 2014 2181 750564919 750565086 2.190000e-42 183
6 TraesCS2A01G537000 chr2D 95.197 3581 136 13 1 3574 619499690 619496139 0.000000e+00 5627
7 TraesCS2A01G537000 chr2D 76.644 1049 187 40 117 1150 619410020 619411025 8.790000e-146 527
8 TraesCS2A01G537000 chr2D 75.910 1071 183 47 116 1155 619414695 619415721 2.500000e-131 479
9 TraesCS2A01G537000 chr2D 78.044 501 89 14 2005 2501 619415772 619416255 2.700000e-76 296
10 TraesCS2A01G537000 chr2D 86.264 182 23 2 2001 2181 619411100 619411280 2.810000e-46 196
11 TraesCS2A01G537000 chr2D 82.703 185 29 3 2012 2196 585737236 585737055 1.030000e-35 161
12 TraesCS2A01G537000 chr2B 91.080 3038 184 39 1 3025 758557989 758555026 0.000000e+00 4028
13 TraesCS2A01G537000 chr2B 80.808 990 150 30 286 1248 757270081 757271057 0.000000e+00 739
14 TraesCS2A01G537000 chr2B 86.861 548 41 11 3030 3574 758543063 758542544 5.140000e-163 584
15 TraesCS2A01G537000 chr2B 77.294 1057 184 44 141 1174 758794772 758793749 4.000000e-159 571
16 TraesCS2A01G537000 chr2B 76.777 1055 193 41 117 1155 758117285 758118303 8.730000e-151 544
17 TraesCS2A01G537000 chr2B 78.831 770 136 19 1739 2501 757271489 757272238 8.910000e-136 494
18 TraesCS2A01G537000 chr2B 76.512 843 147 27 359 1155 758123671 758124508 2.570000e-111 412
19 TraesCS2A01G537000 chr2B 85.818 275 36 3 896 1168 758598560 758598287 4.510000e-74 289
20 TraesCS2A01G537000 chr2B 84.211 190 27 3 2000 2187 758793704 758793516 7.880000e-42 182
21 TraesCS2A01G537000 chr2B 85.799 169 22 2 2014 2181 758118370 758118537 1.020000e-40 178


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 TraesCS2A01G537000 chr2A 750952864 750956437 3573 True 6601.0 6601 100.0000 1 3574 1 chr2A.!!$R1 3573
1 TraesCS2A01G537000 chr2A 750570133 750571159 1026 False 484.0 484 75.9810 116 1155 1 chr2A.!!$F1 1039
2 TraesCS2A01G537000 chr2A 750593687 750594713 1026 False 479.0 479 75.8880 116 1155 1 chr2A.!!$F2 1039
3 TraesCS2A01G537000 chr2A 750632146 750633172 1026 False 468.0 468 75.6550 116 1155 1 chr2A.!!$F3 1039
4 TraesCS2A01G537000 chr2A 750563842 750565086 1244 False 354.0 525 81.4670 117 2181 2 chr2A.!!$F4 2064
5 TraesCS2A01G537000 chr2D 619496139 619499690 3551 True 5627.0 5627 95.1970 1 3574 1 chr2D.!!$R2 3573
6 TraesCS2A01G537000 chr2D 619410020 619416255 6235 False 374.5 527 79.2155 116 2501 4 chr2D.!!$F1 2385
7 TraesCS2A01G537000 chr2B 758555026 758557989 2963 True 4028.0 4028 91.0800 1 3025 1 chr2B.!!$R2 3024
8 TraesCS2A01G537000 chr2B 757270081 757272238 2157 False 616.5 739 79.8195 286 2501 2 chr2B.!!$F2 2215
9 TraesCS2A01G537000 chr2B 758542544 758543063 519 True 584.0 584 86.8610 3030 3574 1 chr2B.!!$R1 544
10 TraesCS2A01G537000 chr2B 758123671 758124508 837 False 412.0 412 76.5120 359 1155 1 chr2B.!!$F1 796
11 TraesCS2A01G537000 chr2B 758793516 758794772 1256 True 376.5 571 80.7525 141 2187 2 chr2B.!!$R4 2046
12 TraesCS2A01G537000 chr2B 758117285 758118537 1252 False 361.0 544 81.2880 117 2181 2 chr2B.!!$F3 2064

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
361 391 0.250467 GATCGGCCCTGCATGTACAT 60.25 55.0 1.41 1.41 0.0 2.29 F
1215 6007 0.250295 TCTTCAACTCGCCCCAACTG 60.25 55.0 0.00 0.00 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 6468 2.095692 CGAACGACATCCATGCAATCAA 59.904 45.455 0.0 0.0 0.0 2.57 R
3005 7859 2.414994 ATCGTAGTCTCCTCGGAACA 57.585 50.000 0.0 0.0 0.0 3.18 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
34 35 2.034104 ACGCCTAGTCGTGACTATCA 57.966 50.000 9.99 0.00 42.44 2.15
47 48 6.862090 GTCGTGACTATCAAAGAAACAGTAGT 59.138 38.462 0.00 0.00 0.00 2.73
67 68 3.161866 GTTTCATAAAGGCCTTGACCCA 58.838 45.455 21.33 0.16 0.00 4.51
93 94 8.643324 AGTACTCATTTCTGTACTTTCTTCACT 58.357 33.333 0.00 0.00 44.61 3.41
139 140 1.003580 ACAAGATCAGCGGTGTCCATT 59.996 47.619 15.22 3.13 0.00 3.16
200 201 3.244976 TGATACTCGCATGCATATGTCG 58.755 45.455 19.57 1.03 36.65 4.35
246 255 7.317722 AGGTAAATTAAGAGACAACACCTCT 57.682 36.000 0.00 0.00 42.37 3.69
323 335 9.276590 TGATATTTTCTGTAGGCATACATCAAG 57.723 33.333 12.22 0.22 41.05 3.02
337 349 2.846206 ACATCAAGACAATGGAGCCCTA 59.154 45.455 0.00 0.00 0.00 3.53
344 374 3.525199 AGACAATGGAGCCCTACAAAGAT 59.475 43.478 0.00 0.00 0.00 2.40
353 383 0.815615 CCTACAAAGATCGGCCCTGC 60.816 60.000 0.00 0.00 0.00 4.85
355 385 0.546122 TACAAAGATCGGCCCTGCAT 59.454 50.000 0.00 0.00 0.00 3.96
361 391 0.250467 GATCGGCCCTGCATGTACAT 60.250 55.000 1.41 1.41 0.00 2.29
595 5331 2.723322 TGATGAGAATCTTGCAGGGG 57.277 50.000 0.00 0.00 34.92 4.79
599 5335 1.704628 TGAGAATCTTGCAGGGGACAA 59.295 47.619 0.00 0.00 34.92 3.18
636 5372 8.470002 CAAGGAAGTTGCTATTAAAAGGCTTAT 58.530 33.333 0.00 0.00 0.00 1.73
637 5373 9.695155 AAGGAAGTTGCTATTAAAAGGCTTATA 57.305 29.630 0.00 0.00 0.00 0.98
699 5435 5.767665 TGAAGCTGTTCTTATTGCCAAACTA 59.232 36.000 0.00 0.00 34.56 2.24
784 5520 9.762933 TTATATACGAATACCTACCCAACAAAC 57.237 33.333 0.00 0.00 0.00 2.93
815 5551 6.869695 ACAAATTCCTTTTTGGTACGTTCTT 58.130 32.000 0.00 0.00 40.20 2.52
882 5631 1.667236 TACTTGCATGAATGGCTCCG 58.333 50.000 6.60 0.00 0.00 4.63
885 5634 2.224606 CTTGCATGAATGGCTCCGTAT 58.775 47.619 0.00 0.00 0.00 3.06
1016 5806 8.084684 AGATTCGAGAATGACGATAATTCATCA 58.915 33.333 2.72 0.00 39.45 3.07
1050 5840 2.680312 GCAACATCCTGCTAGACTCA 57.320 50.000 0.00 0.00 39.34 3.41
1215 6007 0.250295 TCTTCAACTCGCCCCAACTG 60.250 55.000 0.00 0.00 0.00 3.16
1249 6041 3.870633 ACCTCGAATCCTGAACTACAC 57.129 47.619 0.00 0.00 0.00 2.90
1826 6669 0.902531 GAGTCGGATGGGACCAAAGA 59.097 55.000 0.00 0.00 37.66 2.52
1980 6825 6.647212 TGCTTGAATCATACTCAAACTACG 57.353 37.500 0.00 0.00 32.57 3.51
1988 6833 8.462143 AATCATACTCAAACTACGTACACAAG 57.538 34.615 0.00 0.00 0.00 3.16
2042 6887 5.880332 GTGGTTACATGTCACCTGAATATGT 59.120 40.000 25.66 9.91 37.64 2.29
2095 6940 5.631119 ACACCTACAGCTTTGGTATTTTCT 58.369 37.500 2.19 0.00 32.13 2.52
2389 7239 2.957680 TGTCAAAGTGCATCCACATTGT 59.042 40.909 4.76 0.00 45.77 2.71
2502 7352 3.672241 GCCGAAGCAACCGATGTATTTTT 60.672 43.478 0.00 0.00 39.53 1.94
2513 7363 6.140110 ACCGATGTATTTTTCACAAAGAACG 58.860 36.000 0.00 0.00 35.56 3.95
2514 7364 6.140110 CCGATGTATTTTTCACAAAGAACGT 58.860 36.000 0.00 0.00 35.56 3.99
2940 7793 3.615224 TCATGCAGTCTGACTTGCATA 57.385 42.857 29.60 20.97 39.30 3.14
3005 7859 3.437931 GGAAATAGGGTAACATGGGGCAT 60.438 47.826 0.00 0.00 39.74 4.40
3059 7913 6.595716 CCTAGAACCAAACTCACATCCTTTAG 59.404 42.308 0.00 0.00 0.00 1.85
3111 7965 4.608951 GGATCACATCCTACAAGACGTAC 58.391 47.826 0.00 0.00 46.19 3.67
3205 8059 4.633565 GTCGAAAAGAGGAGCATTGAGAAT 59.366 41.667 0.00 0.00 0.00 2.40
3318 8172 4.890088 GCAAATGGATGCAATGGATGTAT 58.110 39.130 0.00 0.00 45.70 2.29
3331 8185 6.314896 GCAATGGATGTATAGAAGGATGTAGC 59.685 42.308 0.00 0.00 0.00 3.58
3359 8213 9.399797 GCTATGGATGAATTTGACATATATGGA 57.600 33.333 16.96 0.33 0.00 3.41
3365 8219 7.218228 TGAATTTGACATATATGGATGCCAC 57.782 36.000 16.96 4.63 35.80 5.01
3411 8265 4.079980 TGTGGTTTAGAGTAAGCTTGCA 57.920 40.909 17.21 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 3.181423 ACTGGGTCAAGGCCTTTATGAAA 60.181 43.478 17.61 0.00 0.00 2.69
93 94 3.096092 GGTTCTTGCATAATTGTCCCCA 58.904 45.455 0.00 0.00 0.00 4.96
139 140 7.924541 AGTGGGAGTACAATCTTAAATACCAA 58.075 34.615 0.00 0.00 0.00 3.67
187 188 3.680642 ACAGAAACGACATATGCATGC 57.319 42.857 11.82 11.82 35.39 4.06
200 201 5.066505 CCTCTGGGTTTGCATATACAGAAAC 59.933 44.000 12.31 1.37 34.90 2.78
323 335 3.350219 TCTTTGTAGGGCTCCATTGTC 57.650 47.619 0.00 0.00 0.00 3.18
337 349 1.033746 CATGCAGGGCCGATCTTTGT 61.034 55.000 0.00 0.00 0.00 2.83
344 374 0.034574 AAATGTACATGCAGGGCCGA 60.035 50.000 9.63 0.00 0.00 5.54
353 383 6.427853 TCTTGTGAAGGTCTCAAATGTACATG 59.572 38.462 9.63 0.00 35.22 3.21
355 385 5.924356 TCTTGTGAAGGTCTCAAATGTACA 58.076 37.500 0.00 0.00 35.22 2.90
443 5150 2.610232 GCATGTTGGTGTCATGGAAACC 60.610 50.000 0.00 0.00 40.23 3.27
595 5331 1.820519 TCCTTGCCATCTTGCATTGTC 59.179 47.619 0.00 0.00 41.70 3.18
599 5335 2.226962 ACTTCCTTGCCATCTTGCAT 57.773 45.000 0.00 0.00 41.70 3.96
636 5372 1.126488 CCTGCTCAGATCCCTTGCTA 58.874 55.000 0.00 0.00 0.00 3.49
637 5373 1.633915 CCCTGCTCAGATCCCTTGCT 61.634 60.000 0.00 0.00 0.00 3.91
699 5435 5.615289 AGTCTAACAAGATTCTTGTGCTGT 58.385 37.500 27.97 16.92 32.22 4.40
784 5520 6.313744 ACCAAAAAGGAATTTGTCTAGACG 57.686 37.500 17.85 1.20 41.22 4.18
911 5701 6.267471 TGGCCAATTGAGTGTAGATTTTCTTT 59.733 34.615 0.61 0.00 0.00 2.52
988 5778 9.914131 ATGAATTATCGTCATTCTCGAATCTTA 57.086 29.630 0.00 0.00 40.61 2.10
1016 5806 0.603975 GTTGCTCGGCTTGAGGTCTT 60.604 55.000 8.29 0.00 45.38 3.01
1050 5840 4.718774 TCTGCTATCTTTGGGTTCATCTCT 59.281 41.667 0.00 0.00 0.00 3.10
1189 5981 2.482142 GGGGCGAGTTGAAGATAGACTG 60.482 54.545 0.00 0.00 0.00 3.51
1215 6007 6.072119 AGGATTCGAGGTAAATCAACCAAAAC 60.072 38.462 0.00 0.00 42.40 2.43
1277 6069 6.095160 ACGTTAGGGTTCACACAAAACATTAA 59.905 34.615 0.00 0.00 0.00 1.40
1485 6312 6.657541 AGCAATAGGGTAAGAACAAAAATCGA 59.342 34.615 0.00 0.00 0.00 3.59
1486 6313 6.852664 AGCAATAGGGTAAGAACAAAAATCG 58.147 36.000 0.00 0.00 0.00 3.34
1631 6468 2.095692 CGAACGACATCCATGCAATCAA 59.904 45.455 0.00 0.00 0.00 2.57
1812 6655 3.245122 TGGTTAGTTCTTTGGTCCCATCC 60.245 47.826 0.00 0.00 0.00 3.51
1826 6669 6.764560 AGTGATTCACGTTTACTTGGTTAGTT 59.235 34.615 11.01 0.00 39.64 2.24
2042 6887 5.829986 TCAATGAAAAGATTCCCTCCATCA 58.170 37.500 0.00 0.00 34.49 3.07
2095 6940 4.574674 ATCCACTTACAATCTCCAGCAA 57.425 40.909 0.00 0.00 0.00 3.91
2357 7207 2.543848 GCACTTTGACACTTCATCACGA 59.456 45.455 0.00 0.00 0.00 4.35
2359 7209 3.969117 TGCACTTTGACACTTCATCAC 57.031 42.857 0.00 0.00 0.00 3.06
2389 7239 4.129380 GCTATCCTGCACACACATCAATA 58.871 43.478 0.00 0.00 0.00 1.90
2492 7342 9.015577 TCAAACGTTCTTTGTGAAAAATACATC 57.984 29.630 0.00 0.00 36.30 3.06
2502 7352 3.013921 AGCCTTCAAACGTTCTTTGTGA 58.986 40.909 0.00 0.00 0.00 3.58
2513 7363 4.590850 AGACATTTCCAAGCCTTCAAAC 57.409 40.909 0.00 0.00 0.00 2.93
2514 7364 4.522789 GGTAGACATTTCCAAGCCTTCAAA 59.477 41.667 0.00 0.00 0.00 2.69
2928 7781 7.558081 ACTCACTCTAGTAATATGCAAGTCAGA 59.442 37.037 0.00 0.00 0.00 3.27
2964 7817 4.488126 TCCAACGAAAGATGAAAAGCAG 57.512 40.909 0.00 0.00 35.71 4.24
3005 7859 2.414994 ATCGTAGTCTCCTCGGAACA 57.585 50.000 0.00 0.00 0.00 3.18
3090 7944 4.608951 GGTACGTCTTGTAGGATGTGATC 58.391 47.826 0.00 0.00 36.86 2.92
3111 7965 7.442364 ACAATTGATTCCATATCTCAACTACGG 59.558 37.037 13.59 0.00 32.16 4.02
3205 8059 4.707934 ACAATGTCCATCTTGATTGCATCA 59.292 37.500 0.00 0.00 37.55 3.07
3318 8172 2.826128 CCATAGCCGCTACATCCTTCTA 59.174 50.000 1.14 0.00 0.00 2.10
3331 8185 6.748333 ATATGTCAAATTCATCCATAGCCG 57.252 37.500 0.00 0.00 0.00 5.52
3359 8213 6.534475 AATTTTCATACATGTCAGTGGCAT 57.466 33.333 3.84 3.84 0.00 4.40
3411 8265 7.279750 TGTGACATGCAAGCATATATCAATT 57.720 32.000 7.29 0.00 34.91 2.32


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

AutoCloner maintained by Alex Coulton.