Multiple sequence alignment - TraesCS5A01G036400

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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 TraesCS5A01G036400 chr5A 100.000 3542 0 0 1 3542 33178954 33182495 0.000000e+00 6541.0
1 TraesCS5A01G036400 chr5D 95.506 2893 93 14 653 3542 43405447 43408305 0.000000e+00 4588.0
2 TraesCS5A01G036400 chr5D 82.132 2580 417 27 999 3538 43316285 43318860 0.000000e+00 2170.0
3 TraesCS5A01G036400 chr5D 81.261 2236 352 46 1161 3349 43748021 43750236 0.000000e+00 1746.0
4 TraesCS5A01G036400 chr5D 77.630 2548 480 62 1013 3523 537630740 537633234 0.000000e+00 1465.0
5 TraesCS5A01G036400 chr5D 90.555 667 34 9 1 659 43399423 43400068 0.000000e+00 856.0
6 TraesCS5A01G036400 chr5D 95.238 42 2 0 683 724 43405508 43405549 2.280000e-07 67.6
7 TraesCS5A01G036400 chr5B 91.841 1765 132 6 1786 3538 41272204 41273968 0.000000e+00 2451.0
8 TraesCS5A01G036400 chr5B 92.807 1696 78 14 70 1757 41270286 41271945 0.000000e+00 2416.0
9 TraesCS5A01G036400 chr5B 81.593 2499 412 29 1079 3538 41084431 41086920 0.000000e+00 2023.0
10 TraesCS5A01G036400 chr5B 76.007 546 111 14 2212 2740 678256062 678255520 7.540000e-67 265.0
11 TraesCS5A01G036400 chr5B 95.238 42 2 0 683 724 41270917 41270958 2.280000e-07 67.6
12 TraesCS5A01G036400 chr6D 73.832 1819 390 58 1025 2794 426490254 426488473 0.000000e+00 643.0
13 TraesCS5A01G036400 chr4A 78.246 901 173 15 2637 3523 631676839 631677730 1.110000e-154 556.0


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 TraesCS5A01G036400 chr5A 33178954 33182495 3541 False 6541.000000 6541 100.000000 1 3542 1 chr5A.!!$F1 3541
1 TraesCS5A01G036400 chr5D 43405447 43408305 2858 False 2327.800000 4588 95.372000 653 3542 2 chr5D.!!$F5 2889
2 TraesCS5A01G036400 chr5D 43316285 43318860 2575 False 2170.000000 2170 82.132000 999 3538 1 chr5D.!!$F1 2539
3 TraesCS5A01G036400 chr5D 43748021 43750236 2215 False 1746.000000 1746 81.261000 1161 3349 1 chr5D.!!$F3 2188
4 TraesCS5A01G036400 chr5D 537630740 537633234 2494 False 1465.000000 1465 77.630000 1013 3523 1 chr5D.!!$F4 2510
5 TraesCS5A01G036400 chr5D 43399423 43400068 645 False 856.000000 856 90.555000 1 659 1 chr5D.!!$F2 658
6 TraesCS5A01G036400 chr5B 41084431 41086920 2489 False 2023.000000 2023 81.593000 1079 3538 1 chr5B.!!$F1 2459
7 TraesCS5A01G036400 chr5B 41270286 41273968 3682 False 1644.866667 2451 93.295333 70 3538 3 chr5B.!!$F2 3468
8 TraesCS5A01G036400 chr5B 678255520 678256062 542 True 265.000000 265 76.007000 2212 2740 1 chr5B.!!$R1 528
9 TraesCS5A01G036400 chr6D 426488473 426490254 1781 True 643.000000 643 73.832000 1025 2794 1 chr6D.!!$R1 1769
10 TraesCS5A01G036400 chr4A 631676839 631677730 891 False 556.000000 556 78.246000 2637 3523 1 chr4A.!!$F1 886

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
198 206 0.107508 CAGGCACATGATCCTCCGTT 60.108 55.0 0.00 0.00 0.00 4.44 F
199 207 0.179000 AGGCACATGATCCTCCGTTC 59.821 55.0 0.00 0.00 0.00 3.95 F
500 515 0.238289 ATGTGCAACTGCTTGTACGC 59.762 50.0 2.95 1.67 43.82 4.42 F
869 885 0.752658 TGACTCATGGCTATGACCGG 59.247 55.0 8.93 0.00 38.37 5.28 F
2030 2295 0.946221 CTGAACACGACTGGGAGCAC 60.946 60.0 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1153 1169 1.694844 TCGAACACCGCCTGGATATA 58.305 50.000 0.0 0.0 39.21 0.86 R
2004 2269 2.036733 CCCAGTCGTGTTCAGTTCCTTA 59.963 50.000 0.0 0.0 0.00 2.69 R
2456 2733 1.269174 CAATCCACATTCGCACCAACA 59.731 47.619 0.0 0.0 0.00 3.33 R
2465 2742 4.706476 TCAATCCTGAACCAATCCACATTC 59.294 41.667 0.0 0.0 0.00 2.67 R
2964 3271 2.158957 TCTTGCGACCCCACATATCTTC 60.159 50.000 0.0 0.0 0.00 2.87 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
56 59 4.342665 GGCAGGGTATATAGCTGGATACTC 59.657 50.000 11.53 13.08 37.61 2.59
79 82 2.171448 AGTCTTGGAGGATATGGTGTGC 59.829 50.000 0.00 0.00 0.00 4.57
141 149 1.528076 ACGAGCACACAAATGGCCA 60.528 52.632 8.56 8.56 0.00 5.36
178 186 3.181474 CCTTACTACTACTTCAGGCAGGC 60.181 52.174 0.00 0.00 0.00 4.85
182 190 1.222936 CTACTTCAGGCAGGCCAGG 59.777 63.158 13.63 4.35 38.92 4.45
183 191 2.883267 CTACTTCAGGCAGGCCAGGC 62.883 65.000 14.43 14.43 38.92 4.85
184 192 4.355720 CTTCAGGCAGGCCAGGCA 62.356 66.667 23.91 0.47 38.92 4.75
185 193 4.666253 TTCAGGCAGGCCAGGCAC 62.666 66.667 23.91 11.32 38.92 5.01
187 195 4.753662 CAGGCAGGCCAGGCACAT 62.754 66.667 23.91 0.00 38.92 3.21
188 196 4.753662 AGGCAGGCCAGGCACATG 62.754 66.667 23.91 9.96 38.92 3.21
189 197 4.746309 GGCAGGCCAGGCACATGA 62.746 66.667 17.39 0.00 35.81 3.07
190 198 2.441532 GCAGGCCAGGCACATGAT 60.442 61.111 15.19 0.00 0.00 2.45
191 199 2.487532 GCAGGCCAGGCACATGATC 61.488 63.158 15.19 0.00 0.00 2.92
192 200 1.826921 CAGGCCAGGCACATGATCC 60.827 63.158 15.19 0.00 0.00 3.36
193 201 2.005266 AGGCCAGGCACATGATCCT 61.005 57.895 15.19 1.75 0.00 3.24
194 202 1.527844 GGCCAGGCACATGATCCTC 60.528 63.158 15.19 0.00 0.00 3.71
195 203 1.527844 GCCAGGCACATGATCCTCC 60.528 63.158 6.55 0.00 0.00 4.30
196 204 1.227764 CCAGGCACATGATCCTCCG 60.228 63.158 0.00 0.00 0.00 4.63
197 205 1.524002 CAGGCACATGATCCTCCGT 59.476 57.895 0.00 0.00 0.00 4.69
198 206 0.107508 CAGGCACATGATCCTCCGTT 60.108 55.000 0.00 0.00 0.00 4.44
199 207 0.179000 AGGCACATGATCCTCCGTTC 59.821 55.000 0.00 0.00 0.00 3.95
200 208 1.154205 GGCACATGATCCTCCGTTCG 61.154 60.000 0.00 0.00 0.00 3.95
201 209 1.154205 GCACATGATCCTCCGTTCGG 61.154 60.000 0.00 4.74 0.00 4.30
202 210 0.530650 CACATGATCCTCCGTTCGGG 60.531 60.000 11.37 2.52 37.02 5.14
203 211 0.686441 ACATGATCCTCCGTTCGGGA 60.686 55.000 11.37 2.27 44.68 5.14
204 212 0.249489 CATGATCCTCCGTTCGGGAC 60.249 60.000 11.37 0.54 40.94 4.46
205 213 0.397254 ATGATCCTCCGTTCGGGACT 60.397 55.000 11.37 0.00 40.94 3.85
206 214 1.035932 TGATCCTCCGTTCGGGACTC 61.036 60.000 11.37 4.69 40.94 3.36
251 259 3.702045 AGAGAAGGCTAGCTAATCGTGTT 59.298 43.478 15.72 0.00 0.00 3.32
268 276 2.724174 GTGTTACAATGGCGCAAGAAAC 59.276 45.455 10.83 6.19 43.02 2.78
272 280 0.717224 CAATGGCGCAAGAAACATGC 59.283 50.000 10.83 0.00 43.02 4.06
282 290 2.450609 AGAAACATGCGAACGGTACT 57.549 45.000 0.00 0.00 0.00 2.73
363 371 1.565305 CTAGACAATGAGGTGCGAGC 58.435 55.000 0.00 0.00 0.00 5.03
385 393 5.084722 GCAAATCTCTGAAGTTTCGATGTG 58.915 41.667 0.00 0.00 0.00 3.21
412 420 7.264373 AGTTCCATGTTATATTAGCAGTTGC 57.736 36.000 0.00 0.00 42.49 4.17
481 496 9.208022 GAATATAACGATGATGTGAATCTTCCA 57.792 33.333 0.00 0.00 0.00 3.53
500 515 0.238289 ATGTGCAACTGCTTGTACGC 59.762 50.000 2.95 1.67 43.82 4.42
580 596 3.964031 AGAGATGACCCATGGAGTAGTTC 59.036 47.826 15.22 4.26 0.00 3.01
626 642 2.582052 CCAGGGTTAACAGTTCAGCAA 58.418 47.619 8.10 0.00 0.00 3.91
642 658 1.349026 AGCAACACCAGATAGTGCAGT 59.651 47.619 0.00 0.00 41.67 4.40
666 682 4.679373 TGAGCTTCAGAACTTCAACTCT 57.321 40.909 0.00 0.00 0.00 3.24
677 693 7.438459 TCAGAACTTCAACTCTAGTTTTGCTAC 59.562 37.037 0.00 0.00 36.78 3.58
739 755 6.591448 GGTCATTTTCTGCCTTAAATTTGGAG 59.409 38.462 0.00 0.00 0.00 3.86
821 837 5.543405 TGGTGACCATGGAAATTTCTTTGAT 59.457 36.000 21.47 3.07 0.00 2.57
854 870 6.649141 TGATATTTGTTAGCAACGACTTGACT 59.351 34.615 0.00 0.00 33.82 3.41
867 883 3.462021 GACTTGACTCATGGCTATGACC 58.538 50.000 8.93 4.85 38.37 4.02
869 885 0.752658 TGACTCATGGCTATGACCGG 59.247 55.000 8.93 0.00 38.37 5.28
874 890 2.102420 CTCATGGCTATGACCGGTTGTA 59.898 50.000 9.42 3.94 38.37 2.41
918 934 1.550524 CGATTTCTCCCTCTCCACACA 59.449 52.381 0.00 0.00 0.00 3.72
920 936 2.930826 TTTCTCCCTCTCCACACAAC 57.069 50.000 0.00 0.00 0.00 3.32
979 995 1.553690 GCTGGCCCTCCTCTTACACA 61.554 60.000 0.00 0.00 0.00 3.72
1038 1054 2.296190 ACTCGTTTTTGCAGGGAAATCC 59.704 45.455 0.00 0.00 0.00 3.01
1140 1156 3.096852 TGAGTTGAAGAATCGGCTCCTA 58.903 45.455 0.00 0.00 31.76 2.94
2004 2269 4.289672 TGGGAGAAGTTATTTGCTCCTCTT 59.710 41.667 0.00 0.00 44.91 2.85
2030 2295 0.946221 CTGAACACGACTGGGAGCAC 60.946 60.000 0.00 0.00 0.00 4.40
2045 2310 3.256631 GGGAGCACAATTCTGTTGACAAT 59.743 43.478 0.00 0.00 31.64 2.71
2180 2448 2.593026 TGCCTTTTCCGGTTTGAATCT 58.407 42.857 0.00 0.00 0.00 2.40
2303 2574 7.931015 ATATAACACCTGAATACTGGAGGAA 57.069 36.000 0.00 0.00 38.29 3.36
2465 2742 3.143807 TGAAAAGAAAGTGTTGGTGCG 57.856 42.857 0.00 0.00 0.00 5.34
2539 2825 2.961062 ACTGCAGAACAATTCTTGGCTT 59.039 40.909 23.35 0.00 38.11 4.35
2873 3174 3.616821 TCAAAATCACTGCGACTATTCCG 59.383 43.478 0.00 0.00 0.00 4.30
2964 3271 3.172050 CGTGAGTTCGATACCACAAGAG 58.828 50.000 10.68 0.00 31.90 2.85
3046 3359 5.163612 GGGACCAAAATAGATGAAGCAAGAC 60.164 44.000 0.00 0.00 0.00 3.01
3238 3554 2.501723 GGTCTGCAGGGTCTTGAGAATA 59.498 50.000 15.13 0.00 0.00 1.75
3538 3854 3.207265 TGCTGGAGCTTTTAGTGTTGA 57.793 42.857 0.00 0.00 42.66 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 59 4.502259 GCACACCATATCCTCCAAGACTAG 60.502 50.000 0.00 0.00 0.00 2.57
141 149 3.869493 AAGGTCCACATTTGGCCTT 57.131 47.368 16.38 16.38 46.41 4.35
178 186 1.227764 CGGAGGATCATGTGCCTGG 60.228 63.158 12.71 0.00 36.25 4.45
182 190 1.154205 CCGAACGGAGGATCATGTGC 61.154 60.000 7.53 0.00 36.25 4.57
183 191 0.530650 CCCGAACGGAGGATCATGTG 60.531 60.000 15.07 0.00 36.25 3.21
184 192 0.686441 TCCCGAACGGAGGATCATGT 60.686 55.000 15.07 0.00 34.86 3.21
185 193 0.249489 GTCCCGAACGGAGGATCATG 60.249 60.000 15.07 0.00 43.19 3.07
186 194 0.397254 AGTCCCGAACGGAGGATCAT 60.397 55.000 15.07 0.00 43.19 2.45
187 195 1.000019 AGTCCCGAACGGAGGATCA 60.000 57.895 15.07 0.00 43.19 2.92
188 196 1.035932 TGAGTCCCGAACGGAGGATC 61.036 60.000 15.07 7.59 43.19 3.36
189 197 0.397254 ATGAGTCCCGAACGGAGGAT 60.397 55.000 15.07 0.00 43.19 3.24
190 198 1.000019 ATGAGTCCCGAACGGAGGA 60.000 57.895 15.07 1.52 43.19 3.71
191 199 1.141881 CATGAGTCCCGAACGGAGG 59.858 63.158 15.07 0.00 43.19 4.30
192 200 0.530744 TTCATGAGTCCCGAACGGAG 59.469 55.000 15.07 5.23 43.19 4.63
193 201 0.970640 TTTCATGAGTCCCGAACGGA 59.029 50.000 15.07 0.00 38.83 4.69
194 202 2.024176 ATTTCATGAGTCCCGAACGG 57.976 50.000 6.25 6.25 0.00 4.44
195 203 2.534349 CGTATTTCATGAGTCCCGAACG 59.466 50.000 0.00 0.00 0.00 3.95
196 204 3.777478 TCGTATTTCATGAGTCCCGAAC 58.223 45.455 0.00 0.00 0.00 3.95
197 205 3.697542 TCTCGTATTTCATGAGTCCCGAA 59.302 43.478 0.00 0.00 40.63 4.30
198 206 3.284617 TCTCGTATTTCATGAGTCCCGA 58.715 45.455 0.00 2.73 40.63 5.14
199 207 3.710326 TCTCGTATTTCATGAGTCCCG 57.290 47.619 0.00 0.00 40.63 5.14
200 208 3.804873 GCTTCTCGTATTTCATGAGTCCC 59.195 47.826 0.00 0.00 40.63 4.46
201 209 4.433615 TGCTTCTCGTATTTCATGAGTCC 58.566 43.478 0.00 0.00 40.63 3.85
202 210 5.578727 ACTTGCTTCTCGTATTTCATGAGTC 59.421 40.000 0.00 0.00 40.63 3.36
203 211 5.482908 ACTTGCTTCTCGTATTTCATGAGT 58.517 37.500 0.00 0.00 40.63 3.41
204 212 6.414408 AACTTGCTTCTCGTATTTCATGAG 57.586 37.500 0.00 0.00 41.08 2.90
205 213 6.801539 AAACTTGCTTCTCGTATTTCATGA 57.198 33.333 0.00 0.00 0.00 3.07
206 214 7.963981 TCTAAACTTGCTTCTCGTATTTCATG 58.036 34.615 0.00 0.00 0.00 3.07
251 259 2.670789 GCATGTTTCTTGCGCCATTGTA 60.671 45.455 4.18 0.00 0.00 2.41
268 276 0.999406 CCAAGAGTACCGTTCGCATG 59.001 55.000 0.00 0.00 0.00 4.06
272 280 2.427232 TGTTCCAAGAGTACCGTTCG 57.573 50.000 0.00 0.00 0.00 3.95
282 290 2.158957 ACTCACGCTCTTTGTTCCAAGA 60.159 45.455 0.00 0.00 0.00 3.02
298 306 2.030805 GGCAAGATTGTCACCAACTCAC 60.031 50.000 0.00 0.00 32.26 3.51
299 307 2.158623 AGGCAAGATTGTCACCAACTCA 60.159 45.455 0.00 0.00 34.61 3.41
314 322 3.186119 CTCTTCTCGCTTTCTAGGCAAG 58.814 50.000 0.00 0.00 0.00 4.01
317 325 2.926838 CAACTCTTCTCGCTTTCTAGGC 59.073 50.000 0.00 0.00 0.00 3.93
363 371 5.180117 ACCACATCGAAACTTCAGAGATTTG 59.820 40.000 0.00 0.00 0.00 2.32
385 393 8.774586 CAACTGCTAATATAACATGGAACTACC 58.225 37.037 0.00 0.00 39.54 3.18
404 412 4.785301 ACCATATCACTAATGCAACTGCT 58.215 39.130 2.95 0.00 42.66 4.24
412 420 7.859377 GCATCAACAAAGACCATATCACTAATG 59.141 37.037 0.00 0.00 0.00 1.90
448 463 7.272244 TCACATCATCGTTATATTCACAACCT 58.728 34.615 0.00 0.00 0.00 3.50
481 496 0.238289 GCGTACAAGCAGTTGCACAT 59.762 50.000 6.90 0.00 45.16 3.21
500 515 2.031420 CCCATGCACAAAGAGCGATATG 60.031 50.000 0.00 0.00 33.85 1.78
580 596 3.462021 GCTGATCTAGGTTGCCTAACAG 58.538 50.000 13.82 13.82 35.49 3.16
626 642 0.979665 AGCACTGCACTATCTGGTGT 59.020 50.000 3.30 0.00 39.21 4.16
642 658 2.874701 GTTGAAGTTCTGAAGCTCAGCA 59.125 45.455 0.00 0.00 43.95 4.41
666 682 3.697698 GACCCGGCGGTAGCAAAACTA 62.698 57.143 26.32 0.00 44.88 2.24
677 693 3.051392 GCAGAAAATGACCCGGCGG 62.051 63.158 21.46 21.46 0.00 6.13
739 755 0.246360 CCACGAAAATGGGCCTTTCC 59.754 55.000 4.53 0.00 35.95 3.13
821 837 7.041030 TCGTTGCTAACAAATATCAAGGAAACA 60.041 33.333 0.00 0.00 37.58 2.83
854 870 0.908910 ACAACCGGTCATAGCCATGA 59.091 50.000 8.04 0.00 38.90 3.07
867 883 1.815613 TGTTCAATGGCCATACAACCG 59.184 47.619 26.11 11.25 0.00 4.44
869 885 4.236935 CAACTGTTCAATGGCCATACAAC 58.763 43.478 21.15 22.95 0.00 3.32
874 890 1.636148 AGCAACTGTTCAATGGCCAT 58.364 45.000 14.09 14.09 0.00 4.40
979 995 3.426615 TGTTCTTTCTGGGTGTGTGTTT 58.573 40.909 0.00 0.00 0.00 2.83
1038 1054 2.971428 ATATGGCCGAAGTCGCCACG 62.971 60.000 15.70 0.00 43.94 4.94
1153 1169 1.694844 TCGAACACCGCCTGGATATA 58.305 50.000 0.00 0.00 39.21 0.86
1254 1270 4.193334 TCGATGGCGTCCTCAGCG 62.193 66.667 0.14 0.00 44.12 5.18
2004 2269 2.036733 CCCAGTCGTGTTCAGTTCCTTA 59.963 50.000 0.00 0.00 0.00 2.69
2019 2284 2.191128 ACAGAATTGTGCTCCCAGTC 57.809 50.000 1.83 0.00 35.83 3.51
2030 2295 4.560035 GCATTCGGATTGTCAACAGAATTG 59.440 41.667 8.44 6.79 31.09 2.32
2045 2310 2.168313 TCTGCTACAGATTGCATTCGGA 59.832 45.455 14.36 1.52 35.39 4.55
2244 2515 1.338973 TCAGCGACAACCTTCGTTACT 59.661 47.619 0.00 0.00 41.26 2.24
2303 2574 5.246656 TGTTCCAATCCTTGATGCAAGAATT 59.753 36.000 8.64 0.00 43.42 2.17
2456 2733 1.269174 CAATCCACATTCGCACCAACA 59.731 47.619 0.00 0.00 0.00 3.33
2465 2742 4.706476 TCAATCCTGAACCAATCCACATTC 59.294 41.667 0.00 0.00 0.00 2.67
2539 2825 7.879070 TCAAAGAACGACTTTCTAGTTAGCTA 58.121 34.615 8.74 0.00 44.41 3.32
2873 3174 3.489738 GGATGTGCTCCATAATTGTGCAC 60.490 47.826 10.75 10.75 44.26 4.57
2901 3202 7.221067 TGTTTTAAGTTACCAAAATTGACAGCG 59.779 33.333 0.00 0.00 0.00 5.18
2964 3271 2.158957 TCTTGCGACCCCACATATCTTC 60.159 50.000 0.00 0.00 0.00 2.87
3046 3359 5.219633 CAAACGTTCAAGGTTCCCTAAATG 58.780 41.667 0.00 0.00 31.13 2.32
3238 3554 9.706529 ATTCTTAGCTTCTTCCCAATTCTTAAT 57.293 29.630 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.