Multiple sequence alignment - TraesCS6D01G131800

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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 TraesCS6D01G131800 chr6D 100.000 3326 0 0 1 3326 98030169 98033494 0.000000e+00 6143
1 TraesCS6D01G131800 chr6A 95.133 3349 119 18 2 3326 117055845 117059173 0.000000e+00 5241
2 TraesCS6D01G131800 chr6B 97.294 3030 59 10 298 3326 183278865 183281872 0.000000e+00 5120
3 TraesCS6D01G131800 chr6B 95.102 245 12 0 1 245 183278466 183278710 1.450000e-103 387
4 TraesCS6D01G131800 chr7D 85.189 1823 207 29 978 2767 55074094 55072302 0.000000e+00 1812
5 TraesCS6D01G131800 chr7A 84.279 1832 213 38 959 2759 58842328 58844115 0.000000e+00 1718
6 TraesCS6D01G131800 chr4B 90.141 213 18 3 3117 3326 654700735 654700947 1.180000e-69 274
7 TraesCS6D01G131800 chr4A 90.338 207 16 4 3123 3326 658036077 658035872 5.470000e-68 268
8 TraesCS6D01G131800 chr1D 91.549 142 9 3 3187 3326 4677268 4677128 3.390000e-45 193
9 TraesCS6D01G131800 chr1D 89.437 142 12 3 3187 3326 10431448 10431308 3.410000e-40 176
10 TraesCS6D01G131800 chr3B 90.071 141 9 3 3187 3326 528693930 528693794 9.480000e-41 178
11 TraesCS6D01G131800 chr7B 89.437 142 12 3 3187 3326 511946906 511947046 3.410000e-40 176
12 TraesCS6D01G131800 chr5B 88.732 142 13 3 3187 3326 84735961 84735821 1.590000e-38 171


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 TraesCS6D01G131800 chr6D 98030169 98033494 3325 False 6143.0 6143 100.000 1 3326 1 chr6D.!!$F1 3325
1 TraesCS6D01G131800 chr6A 117055845 117059173 3328 False 5241.0 5241 95.133 2 3326 1 chr6A.!!$F1 3324
2 TraesCS6D01G131800 chr6B 183278466 183281872 3406 False 2753.5 5120 96.198 1 3326 2 chr6B.!!$F1 3325
3 TraesCS6D01G131800 chr7D 55072302 55074094 1792 True 1812.0 1812 85.189 978 2767 1 chr7D.!!$R1 1789
4 TraesCS6D01G131800 chr7A 58842328 58844115 1787 False 1718.0 1718 84.279 959 2759 1 chr7A.!!$F1 1800

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
247 249 0.898320 AGTAGTGACCAGCGAGCATT 59.102 50.000 0.0 0.0 0.00 3.56 F
290 293 0.982704 AAGCTCCACTCTGTCAGCAT 59.017 50.000 0.0 0.0 34.08 3.79 F
1143 1251 2.233676 TCTTGCCATTAGCTCGTCTGAA 59.766 45.455 0.0 0.0 44.23 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1197 1305 1.141254 TGCGGGACCTCAACAAACTTA 59.859 47.619 0.0 0.0 0.00 2.24 R
1926 2037 3.377346 CTGTCGGCTACTGCAAGATAT 57.623 47.619 0.0 0.0 41.91 1.63 R
2457 2574 0.871722 TTGTAAGTGCGACATGCCAC 59.128 50.000 0.0 0.0 45.60 5.01 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
42 43 2.103042 GTGCTTGCCGGCTACAGAG 61.103 63.158 29.70 17.39 0.00 3.35
130 131 1.963338 GGGACAGCAGTGCACAGTC 60.963 63.158 21.04 20.01 37.91 3.51
140 141 1.227645 TGCACAGTCGCAGAGCTTT 60.228 52.632 0.00 0.00 36.95 3.51
160 161 3.342377 TGGTGAACACAAGTGACTCAA 57.658 42.857 7.28 0.00 31.54 3.02
181 182 8.434392 ACTCAAAATACCAAGTAAGAAGGTGTA 58.566 33.333 0.00 0.00 36.87 2.90
182 183 8.611654 TCAAAATACCAAGTAAGAAGGTGTAC 57.388 34.615 0.00 0.00 36.87 2.90
247 249 0.898320 AGTAGTGACCAGCGAGCATT 59.102 50.000 0.00 0.00 0.00 3.56
290 293 0.982704 AAGCTCCACTCTGTCAGCAT 59.017 50.000 0.00 0.00 34.08 3.79
307 411 2.426024 AGCATGGCTAGCTTGTTTGATG 59.574 45.455 15.72 6.89 39.87 3.07
330 434 3.528905 TCCATGTGAGATGGGGAAATTCT 59.471 43.478 8.90 0.00 39.60 2.40
408 515 6.210784 TGAGTATTACTTTGCTGTAGACACCT 59.789 38.462 0.00 0.00 0.00 4.00
409 516 7.005709 AGTATTACTTTGCTGTAGACACCTT 57.994 36.000 0.00 0.00 0.00 3.50
450 557 3.958147 CCTTTATAAAATCCACGGGGCTT 59.042 43.478 0.00 0.00 0.00 4.35
499 606 2.655090 TCCTGACATTTGGTTCTGCA 57.345 45.000 0.00 0.00 0.00 4.41
522 629 3.007506 TCCGTAACTGATGTGAACCATGT 59.992 43.478 0.00 0.00 32.56 3.21
581 688 9.299963 TGCAAACTTAATGTGCATGTTATTATC 57.700 29.630 0.00 0.00 43.09 1.75
810 918 5.581085 GGTGGAGCATGTACTAAACTGTTAG 59.419 44.000 0.00 0.00 42.23 2.34
932 1040 6.997476 TGATTCCATTATATTGCAGCACAGTA 59.003 34.615 0.00 0.00 0.00 2.74
1143 1251 2.233676 TCTTGCCATTAGCTCGTCTGAA 59.766 45.455 0.00 0.00 44.23 3.02
1197 1305 2.643304 GTTCCCTGGAGTTAGGAAAGGT 59.357 50.000 0.00 0.00 41.21 3.50
1656 1764 4.111255 TGCTGTAGCTCCTGAGATAGAT 57.889 45.455 5.38 0.00 42.66 1.98
1926 2037 0.675208 TACGTCGCCCGGTTGTAGTA 60.675 55.000 0.00 0.00 42.24 1.82
2457 2574 3.999001 TGCTAGAATCTTGACAGTTGCAG 59.001 43.478 0.00 0.00 0.00 4.41
2689 2829 6.384178 TTGTATCAAGTGTATTCGTTCGTG 57.616 37.500 0.00 0.00 0.00 4.35
2766 2916 4.398319 TCTTCTTTGGATGTGTTCCTTCC 58.602 43.478 0.00 0.00 45.68 3.46
2779 2929 2.368548 GTTCCTTCCCAACAAAATGCCT 59.631 45.455 0.00 0.00 0.00 4.75
2850 3000 2.698274 GGTTTGATGTGGGGAAGTTTGT 59.302 45.455 0.00 0.00 0.00 2.83
2866 3016 2.203266 GTAGCTCATGGGGGCTGC 60.203 66.667 15.37 11.71 39.31 5.25
3022 3188 2.613977 GGATCTATCAAGGCATGGACCG 60.614 54.545 0.00 0.00 33.69 4.79
3190 3357 9.472361 CTGAAGATTGTGATTTTGTTCAGAAAT 57.528 29.630 3.60 0.00 41.16 2.17
3216 3383 3.362706 AGAGTAAACCACCTGCTATCGA 58.637 45.455 0.00 0.00 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 131 0.040958 GTGTTCACCAAAGCTCTGCG 60.041 55.000 0.00 0.00 0.00 5.18
140 141 3.342377 TTGAGTCACTTGTGTTCACCA 57.658 42.857 0.00 0.00 0.00 4.17
160 161 9.281371 GAAAGTACACCTTCTTACTTGGTATTT 57.719 33.333 0.00 0.00 38.32 1.40
256 259 5.948162 AGTGGAGCTTCATTAACATGAATGT 59.052 36.000 0.00 0.00 46.32 2.71
264 267 4.569943 TGACAGAGTGGAGCTTCATTAAC 58.430 43.478 0.00 0.00 0.00 2.01
268 271 1.066286 GCTGACAGAGTGGAGCTTCAT 60.066 52.381 6.65 0.00 0.00 2.57
278 281 0.177604 GCTAGCCATGCTGACAGAGT 59.822 55.000 6.65 0.00 40.10 3.24
279 282 0.464870 AGCTAGCCATGCTGACAGAG 59.535 55.000 12.13 0.00 40.10 3.35
281 284 1.015109 CAAGCTAGCCATGCTGACAG 58.985 55.000 12.13 0.00 40.10 3.51
290 293 2.224744 TGGACATCAAACAAGCTAGCCA 60.225 45.455 12.13 0.00 0.00 4.75
307 411 2.806945 TTTCCCCATCTCACATGGAC 57.193 50.000 1.96 0.00 41.64 4.02
372 476 9.031360 AGCAAAGTAATACTCATACATGTAACG 57.969 33.333 10.14 4.51 0.00 3.18
450 557 1.358152 ACGAATTCCAACAGGGGAGA 58.642 50.000 0.00 0.00 38.42 3.71
499 606 3.973206 TGGTTCACATCAGTTACGGAT 57.027 42.857 0.00 0.00 0.00 4.18
522 629 0.538746 TGTGGACACGCCTAGAGTCA 60.539 55.000 0.00 0.00 41.37 3.41
673 781 3.642705 GTGGCTCCACAAAGAACATTTC 58.357 45.455 13.81 0.00 45.53 2.17
810 918 1.318158 TACTCCTCGAACCCTTCCGC 61.318 60.000 0.00 0.00 0.00 5.54
932 1040 5.745312 TCCATCACTCAACAGAAGTACAT 57.255 39.130 0.00 0.00 0.00 2.29
946 1054 5.831103 ACCAGGTCATTTTTATCCATCACT 58.169 37.500 0.00 0.00 0.00 3.41
1143 1251 6.040504 GGGTTGGTGACTCATAAAAACTCTTT 59.959 38.462 0.00 0.00 0.00 2.52
1197 1305 1.141254 TGCGGGACCTCAACAAACTTA 59.859 47.619 0.00 0.00 0.00 2.24
1926 2037 3.377346 CTGTCGGCTACTGCAAGATAT 57.623 47.619 0.00 0.00 41.91 1.63
2457 2574 0.871722 TTGTAAGTGCGACATGCCAC 59.128 50.000 0.00 0.00 45.60 5.01
2689 2829 8.507249 ACAGAATCAAGAGTTTTAACAGCATAC 58.493 33.333 0.00 0.00 0.00 2.39
2766 2916 2.095263 CACCGACTAGGCATTTTGTTGG 60.095 50.000 0.00 0.00 46.52 3.77
2850 3000 1.648302 ATTGCAGCCCCCATGAGCTA 61.648 55.000 0.00 0.00 37.18 3.32
2982 3132 3.686016 TCCATAAAGAACTTGCCACCTC 58.314 45.455 0.00 0.00 0.00 3.85
3022 3188 3.885297 ACTATGCATCCTAAACATGCCAC 59.115 43.478 0.19 0.00 45.25 5.01
3121 3288 1.972872 AGGACAGTTGGAAGCAACAG 58.027 50.000 0.00 0.00 37.52 3.16
3190 3357 2.972713 AGCAGGTGGTTTACTCTCAGAA 59.027 45.455 0.00 0.00 0.00 3.02
3216 3383 2.332332 ACCTAACCCCTTCCGTACTT 57.668 50.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.