Multiple sequence alignment - TraesCS3B01G263700

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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 TraesCS3B01G263700 chr3B 100.000 3227 0 0 1 3227 422356001 422359227 0 5960
1 TraesCS3B01G263700 chr3B 90.554 3229 296 6 1 3227 252989552 252986331 0 4265
2 TraesCS3B01G263700 chr4B 92.194 3190 241 5 1 3188 240858784 240861967 0 4505
3 TraesCS3B01G263700 chr4B 90.715 3188 291 4 1 3188 293074321 293071139 0 4242
4 TraesCS3B01G263700 chr4B 90.153 3199 308 4 33 3227 293791016 293787821 0 4156
5 TraesCS3B01G263700 chr2B 91.362 3230 271 6 1 3227 654628910 654632134 0 4412
6 TraesCS3B01G263700 chr2B 91.492 3197 264 6 33 3227 318303481 318300291 0 4390
7 TraesCS3B01G263700 chr5B 90.211 3228 299 9 1 3227 138216467 138219678 0 4194
8 TraesCS3B01G263700 chr5B 89.836 3227 318 7 1 3224 300809631 300812850 0 4133
9 TraesCS3B01G263700 chr1B 90.155 3220 312 4 1 3218 160860506 160863722 0 4185


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 TraesCS3B01G263700 chr3B 422356001 422359227 3226 False 5960 5960 100.000 1 3227 1 chr3B.!!$F1 3226
1 TraesCS3B01G263700 chr3B 252986331 252989552 3221 True 4265 4265 90.554 1 3227 1 chr3B.!!$R1 3226
2 TraesCS3B01G263700 chr4B 240858784 240861967 3183 False 4505 4505 92.194 1 3188 1 chr4B.!!$F1 3187
3 TraesCS3B01G263700 chr4B 293071139 293074321 3182 True 4242 4242 90.715 1 3188 1 chr4B.!!$R1 3187
4 TraesCS3B01G263700 chr4B 293787821 293791016 3195 True 4156 4156 90.153 33 3227 1 chr4B.!!$R2 3194
5 TraesCS3B01G263700 chr2B 654628910 654632134 3224 False 4412 4412 91.362 1 3227 1 chr2B.!!$F1 3226
6 TraesCS3B01G263700 chr2B 318300291 318303481 3190 True 4390 4390 91.492 33 3227 1 chr2B.!!$R1 3194
7 TraesCS3B01G263700 chr5B 138216467 138219678 3211 False 4194 4194 90.211 1 3227 1 chr5B.!!$F1 3226
8 TraesCS3B01G263700 chr5B 300809631 300812850 3219 False 4133 4133 89.836 1 3224 1 chr5B.!!$F2 3223
9 TraesCS3B01G263700 chr1B 160860506 160863722 3216 False 4185 4185 90.155 1 3218 1 chr1B.!!$F1 3217

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
452 456 0.105142 GCCTATGACCCTACCCCAGA 60.105 60.0 0.0 0.0 0.00 3.86 F
1168 1182 0.035176 GGAGGATCTGGATGAGCTGC 59.965 60.0 0.0 0.0 33.73 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1688 1703 0.243907 GTTCTCAGCAGCGGTCACTA 59.756 55.0 0.00 0.0 0.00 2.74 R
2370 2396 0.609131 GAGCAACCTTGGGCTGCTTA 60.609 55.0 14.43 0.0 46.19 3.09 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
44 45 1.146263 GGAGGCGGTCGATTGGATT 59.854 57.895 0.00 0.0 0.00 3.01
45 46 0.391597 GGAGGCGGTCGATTGGATTA 59.608 55.000 0.00 0.0 0.00 1.75
110 111 4.109765 AGGAGGAGGGTGGCTTATATAGAA 59.890 45.833 0.00 0.0 0.00 2.10
247 248 0.320946 GCCTGCCCGTTGTAACACTA 60.321 55.000 0.00 0.0 0.00 2.74
452 456 0.105142 GCCTATGACCCTACCCCAGA 60.105 60.000 0.00 0.0 0.00 3.86
509 513 4.715713 AGGTTCAAGTGGAAAGTAGGTTC 58.284 43.478 0.00 0.0 37.23 3.62
514 518 3.662247 AGTGGAAAGTAGGTTCGAGTG 57.338 47.619 0.00 0.0 0.00 3.51
667 671 3.187700 CCGAGTGTTGTATTAGAGTGCC 58.812 50.000 0.00 0.0 0.00 5.01
785 795 2.618241 GCGGATAAACAATGATGCCTCA 59.382 45.455 0.00 0.0 35.41 3.86
811 821 3.972276 GCCGCCTTTTTCGCCACA 61.972 61.111 0.00 0.0 0.00 4.17
938 951 2.975536 CACGCCCGTTCCTCCTTA 59.024 61.111 0.00 0.0 0.00 2.69
1132 1146 4.399764 TCCAGGGCGATTGGATCT 57.600 55.556 0.00 0.0 39.74 2.75
1168 1182 0.035176 GGAGGATCTGGATGAGCTGC 59.965 60.000 0.00 0.0 33.73 5.25
1237 1251 1.459158 ATGGAGCCTCAGCCTCGAT 60.459 57.895 0.00 0.0 41.25 3.59
1340 1355 2.969300 TTTTTCGGCGCCCAACTCCT 62.969 55.000 23.46 0.0 0.00 3.69
1373 1388 3.383505 CCTAACACCATCACGTATCTGGA 59.616 47.826 14.98 0.0 34.08 3.86
1523 1538 1.602605 AGTTGTGCGGGGGTTTAGC 60.603 57.895 0.00 0.0 0.00 3.09
1559 1574 4.698575 CATAGGAGTTCTTTCCCTGCTAC 58.301 47.826 0.00 0.0 38.02 3.58
1578 1593 0.382515 CGACTCTCCCTGAATCGGTC 59.617 60.000 0.00 0.0 40.27 4.79
1688 1703 1.079490 TCAGACCCCTTCTCCACTCAT 59.921 52.381 0.00 0.0 28.96 2.90
1731 1746 0.976641 AGACGAAGATGCTGGTGGAA 59.023 50.000 0.00 0.0 0.00 3.53
1763 1778 4.020573 TCAACTTATCAACGAGGGTGTCAT 60.021 41.667 0.00 0.0 0.00 3.06
1944 1959 1.396653 GCAATCAGGACAATCCCAGG 58.603 55.000 0.00 0.0 37.19 4.45
2056 2072 1.989165 GCACTTGATGTCGACTGACTC 59.011 52.381 17.92 8.8 45.70 3.36
2079 2096 9.614792 ACTCTTACTTGACTTTTTGTCTTGTAT 57.385 29.630 0.00 0.0 45.54 2.29
2180 2197 1.179814 AGCGACGACTGGGAGTCTTT 61.180 55.000 0.00 0.0 42.92 2.52
2201 2224 1.062505 GGATGAAGAGGAGGAGGAGGT 60.063 57.143 0.00 0.0 0.00 3.85
2219 2245 2.041115 TGAGCGAGGAGTCAGACGG 61.041 63.158 0.00 0.0 0.00 4.79
2224 2250 2.034376 AGGAGTCAGACGGCGAGT 59.966 61.111 16.62 0.0 0.00 4.18
2278 2304 0.250467 ATCCAAGCAGCAACACGACT 60.250 50.000 0.00 0.0 0.00 4.18
2370 2396 3.111939 CCGACGGAGAAGATCGCT 58.888 61.111 8.64 0.0 34.52 4.93
2413 2439 2.224305 CCCAAGACTCGGAAGACTTTGT 60.224 50.000 0.00 0.0 35.71 2.83
2535 2561 1.779061 TTTCCAGTCCCACCTCTGCC 61.779 60.000 0.00 0.0 0.00 4.85
2712 2738 3.201487 TGTGCTCCCTGATGATGAAGAAT 59.799 43.478 0.00 0.0 0.00 2.40
2744 2770 4.093011 CTCTTCAGGAGAGGAGGAAGAAA 58.907 47.826 0.00 0.0 46.77 2.52
2769 2795 0.920438 AAGCTCGAGTAGGAGGAGGA 59.080 55.000 15.13 0.0 34.56 3.71
2792 2818 5.843019 TTGAAATCCAAGTCCCTTAGTCT 57.157 39.130 0.00 0.0 0.00 3.24
2817 2843 2.425592 CGCTTGAGGTGGTGGTCA 59.574 61.111 0.00 0.0 0.00 4.02
2833 2859 0.250338 GTCAAACGTTCCAGAGGGCT 60.250 55.000 0.00 0.0 0.00 5.19
2857 2883 2.234300 AGAACCAACGTCACATTCGT 57.766 45.000 0.00 0.0 43.45 3.85
2877 2903 2.510238 GCTCGCTGACGGCTGATT 60.510 61.111 0.00 0.0 40.63 2.57
2992 3018 0.530744 TTTGCCGCGTATCAGACTCT 59.469 50.000 4.92 0.0 0.00 3.24
2999 3025 2.154198 CGCGTATCAGACTCTAGACGAG 59.846 54.545 0.00 0.0 45.56 4.18
3137 3163 2.297701 GTTCAGGTCAGCAAAACTCCA 58.702 47.619 0.00 0.0 0.00 3.86
3194 3220 0.538746 ACCGGGGTGTTCCATTGTTC 60.539 55.000 6.32 0.0 37.22 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 6.790461 ACCCCCTGTAACATCACACATATATA 59.210 38.462 0.00 0.00 0.00 0.86
45 46 5.610982 ACCCCCTGTAACATCACACATATAT 59.389 40.000 0.00 0.00 0.00 0.86
110 111 1.038130 CGGAGAGGGTCCTGACGAAT 61.038 60.000 0.00 0.00 44.35 3.34
182 183 6.653740 GGTCATTAACAACACTTAAGGCTAGT 59.346 38.462 7.53 0.00 0.00 2.57
452 456 4.093011 GGGCTACTGATGAGGATACAGAT 58.907 47.826 0.00 0.00 41.41 2.90
509 513 3.053455 GACTCAGAACAAGTTCCACTCG 58.947 50.000 9.20 0.00 40.33 4.18
514 518 3.002759 GTGCAAGACTCAGAACAAGTTCC 59.997 47.826 9.20 0.00 40.33 3.62
667 671 2.588877 AATCGCGCCCAAGATCCG 60.589 61.111 0.00 0.00 0.00 4.18
716 720 1.270041 GCGCACTTCCCCAAAATTTCA 60.270 47.619 0.30 0.00 0.00 2.69
785 795 2.698803 GAAAAAGGCGGCATGGAAATT 58.301 42.857 13.08 0.00 0.00 1.82
811 821 2.095768 GCAACAGTCATGTGCAACGTAT 60.096 45.455 0.00 0.00 42.39 3.06
858 868 0.109272 TTCCGAGTGACTGATGCGTC 60.109 55.000 0.00 0.00 34.52 5.19
938 951 1.208293 GCGGAGAAGTGGAGGAAGAAT 59.792 52.381 0.00 0.00 0.00 2.40
1132 1146 0.690192 TCCTGCCGAATCAAAGACCA 59.310 50.000 0.00 0.00 0.00 4.02
1168 1182 1.440893 CGATCAGCCCAGACTCCAG 59.559 63.158 0.00 0.00 0.00 3.86
1237 1251 2.959372 CAGTACGCACTCACCCGA 59.041 61.111 0.00 0.00 30.46 5.14
1340 1355 5.710099 GTGATGGTGTTAGGAGAAAAATGGA 59.290 40.000 0.00 0.00 0.00 3.41
1578 1593 2.125753 GTCGACTGCCAGCCTCTG 60.126 66.667 8.70 0.00 0.00 3.35
1688 1703 0.243907 GTTCTCAGCAGCGGTCACTA 59.756 55.000 0.00 0.00 0.00 2.74
1731 1746 6.238648 CCTCGTTGATAAGTTGAACCACTTTT 60.239 38.462 0.00 0.00 38.07 2.27
1819 1834 2.170397 ACAACCACATAGGATGATCGCA 59.830 45.455 0.00 0.00 42.49 5.10
1944 1959 1.369321 GATGACTCGCCTGGATCCC 59.631 63.158 9.90 0.00 0.00 3.85
2079 2096 6.622679 GCATCGAATACATCTTGGTGAAAACA 60.623 38.462 0.00 0.00 0.00 2.83
2180 2197 1.062581 CCTCCTCCTCCTCTTCATCCA 60.063 57.143 0.00 0.00 0.00 3.41
2201 2224 2.041115 CCGTCTGACTCCTCGCTCA 61.041 63.158 6.21 0.00 0.00 4.26
2224 2250 1.136147 GCGGCGAGTCGACTTCTTA 59.864 57.895 21.08 0.00 29.68 2.10
2370 2396 0.609131 GAGCAACCTTGGGCTGCTTA 60.609 55.000 14.43 0.00 46.19 3.09
2413 2439 1.065764 CGTCCATCTTGATCCGCGA 59.934 57.895 8.23 0.00 0.00 5.87
2474 2500 7.039882 GGTCAGAATAGAAATTTCAGTCGGTA 58.960 38.462 19.99 3.26 0.00 4.02
2535 2561 2.892374 TCAACATCCATGTCAGTAGCG 58.108 47.619 0.00 0.00 40.80 4.26
2591 2617 1.259609 TGGTCGAACGGACTTACCAT 58.740 50.000 0.00 0.00 45.35 3.55
2744 2770 3.018149 CCTCCTACTCGAGCTTACACTT 58.982 50.000 13.61 0.00 0.00 3.16
2817 2843 4.800554 CAGCCCTCTGGAACGTTT 57.199 55.556 0.46 0.00 36.68 3.60
2871 2897 0.876342 GATCCCGACGGACAATCAGC 60.876 60.000 17.49 0.00 42.48 4.26
2992 3018 1.794864 GCACTCAGCGACTCGTCTA 59.205 57.895 0.00 0.00 0.00 2.59
3188 3214 8.341892 GGAAGATTTCCTAAACTCTGAACAAT 57.658 34.615 0.61 0.00 46.57 2.71


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

AutoCloner maintained by Alex Coulton.