Multiple sequence alignment - TraesCS6D01G188200

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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 TraesCS6D01G188200 chr6D 100.000 3485 0 0 1 3485 256020701 256024185 0 6436
1 TraesCS6D01G188200 chr3D 95.684 3499 116 12 1 3485 323154474 323157951 0 5592
2 TraesCS6D01G188200 chr3D 94.111 3498 152 18 1 3485 395861743 395865199 0 5269
3 TraesCS6D01G188200 chr1D 95.204 3503 121 17 2 3485 371719934 371723408 0 5494
4 TraesCS6D01G188200 chr5D 95.169 3498 135 12 1 3485 190781124 190777648 0 5493
5 TraesCS6D01G188200 chr2D 95.000 3500 132 15 1 3485 259243875 259240404 0 5454
6 TraesCS6D01G188200 chr2D 94.311 3498 140 16 1 3485 412331259 412334710 0 5302
7 TraesCS6D01G188200 chr7D 94.684 3499 152 10 1 3485 291611968 291615446 0 5400
8 TraesCS6D01G188200 chr7D 93.766 3513 156 28 6 3485 298312702 298316184 0 5216
9 TraesCS6D01G188200 chr7A 94.514 3500 154 15 1 3485 265358204 265361680 0 5365
10 TraesCS6D01G188200 chr7A 93.545 3501 180 26 4 3485 458658695 458655222 0 5171
11 TraesCS6D01G188200 chr4D 94.032 3502 134 26 1 3485 201252743 201256186 0 5240
12 TraesCS6D01G188200 chr4D 91.173 963 30 12 1 953 144579336 144578419 0 1256
13 TraesCS6D01G188200 chr2A 93.179 3504 179 25 1 3485 160670680 160667218 0 5092
14 TraesCS6D01G188200 chr5A 91.342 1513 91 23 1 1501 625199399 625200883 0 2032
15 TraesCS6D01G188200 chr5A 91.770 1373 75 21 1 1360 628643623 628642276 0 1875
16 TraesCS6D01G188200 chr3A 90.959 1283 66 21 1 1272 84712694 84713937 0 1681


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 TraesCS6D01G188200 chr6D 256020701 256024185 3484 False 6436 6436 100.000 1 3485 1 chr6D.!!$F1 3484
1 TraesCS6D01G188200 chr3D 323154474 323157951 3477 False 5592 5592 95.684 1 3485 1 chr3D.!!$F1 3484
2 TraesCS6D01G188200 chr3D 395861743 395865199 3456 False 5269 5269 94.111 1 3485 1 chr3D.!!$F2 3484
3 TraesCS6D01G188200 chr1D 371719934 371723408 3474 False 5494 5494 95.204 2 3485 1 chr1D.!!$F1 3483
4 TraesCS6D01G188200 chr5D 190777648 190781124 3476 True 5493 5493 95.169 1 3485 1 chr5D.!!$R1 3484
5 TraesCS6D01G188200 chr2D 259240404 259243875 3471 True 5454 5454 95.000 1 3485 1 chr2D.!!$R1 3484
6 TraesCS6D01G188200 chr2D 412331259 412334710 3451 False 5302 5302 94.311 1 3485 1 chr2D.!!$F1 3484
7 TraesCS6D01G188200 chr7D 291611968 291615446 3478 False 5400 5400 94.684 1 3485 1 chr7D.!!$F1 3484
8 TraesCS6D01G188200 chr7D 298312702 298316184 3482 False 5216 5216 93.766 6 3485 1 chr7D.!!$F2 3479
9 TraesCS6D01G188200 chr7A 265358204 265361680 3476 False 5365 5365 94.514 1 3485 1 chr7A.!!$F1 3484
10 TraesCS6D01G188200 chr7A 458655222 458658695 3473 True 5171 5171 93.545 4 3485 1 chr7A.!!$R1 3481
11 TraesCS6D01G188200 chr4D 201252743 201256186 3443 False 5240 5240 94.032 1 3485 1 chr4D.!!$F1 3484
12 TraesCS6D01G188200 chr4D 144578419 144579336 917 True 1256 1256 91.173 1 953 1 chr4D.!!$R1 952
13 TraesCS6D01G188200 chr2A 160667218 160670680 3462 True 5092 5092 93.179 1 3485 1 chr2A.!!$R1 3484
14 TraesCS6D01G188200 chr5A 625199399 625200883 1484 False 2032 2032 91.342 1 1501 1 chr5A.!!$F1 1500
15 TraesCS6D01G188200 chr5A 628642276 628643623 1347 True 1875 1875 91.770 1 1360 1 chr5A.!!$R1 1359
16 TraesCS6D01G188200 chr3A 84712694 84713937 1243 False 1681 1681 90.959 1 1272 1 chr3A.!!$F1 1271

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
832 921 2.839609 CCCCATGACCACCACACCA 61.840 63.158 0.00 0.0 0.00 4.17 F
1309 1403 1.291877 GCAGTTGTGCGTCGAGGAAT 61.292 55.000 9.75 0.0 40.71 3.01 F
2013 2139 8.154203 ACTTTCAAAACCAAAAAGGAGAAGAAA 58.846 29.630 0.00 0.0 41.22 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2337 2466 0.324614 TGATGATGTTGTCTGGCGGT 59.675 50.0 0.0 0.0 0.0 5.68 R
2339 2468 0.371301 CGTGATGATGTTGTCTGGCG 59.629 55.0 0.0 0.0 0.0 5.69 R
3228 3368 4.405358 TGGTTCTTCTCAAGGCAATGTTTT 59.595 37.5 0.0 0.0 0.0 2.43 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
436 508 9.243105 ACTAAACCATAAGTGCACTAAAATGAT 57.757 29.630 26.39 14.88 0.00 2.45
628 704 5.863397 CACGGAAAAACATCACAAAGCATAT 59.137 36.000 0.00 0.00 0.00 1.78
708 784 7.330700 GGATTTAGCAGATCATAAGTACAGCTC 59.669 40.741 0.00 0.00 32.70 4.09
832 921 2.839609 CCCCATGACCACCACACCA 61.840 63.158 0.00 0.00 0.00 4.17
1015 1109 2.892640 CGATGGCAGAGGAACCGA 59.107 61.111 0.00 0.00 0.00 4.69
1222 1316 4.856801 AGGGCGGCGGCTTGTATG 62.857 66.667 32.30 0.00 39.81 2.39
1309 1403 1.291877 GCAGTTGTGCGTCGAGGAAT 61.292 55.000 9.75 0.00 40.71 3.01
1588 1682 9.480053 CCAAATTAATTTCTGAACTTGATGTGT 57.520 29.630 10.53 0.00 0.00 3.72
2005 2114 8.773645 GGATTATCACTTTCAAAACCAAAAAGG 58.226 33.333 0.00 0.00 45.67 3.11
2013 2139 8.154203 ACTTTCAAAACCAAAAAGGAGAAGAAA 58.846 29.630 0.00 0.00 41.22 2.52
2055 2181 9.813080 GAAGACTAATCTTTAAATGTGTGTGTC 57.187 33.333 0.00 0.00 45.60 3.67
2350 2479 4.947147 GCCCACCGCCAGACAACA 62.947 66.667 0.00 0.00 0.00 3.33
2509 2638 3.333804 TGCATGAAAGTCTGCATTCGTA 58.666 40.909 0.00 0.00 43.11 3.43
2692 2821 5.277538 GCTAGCTTCCTATTTTGTTGATCCG 60.278 44.000 7.70 0.00 0.00 4.18
2702 2831 7.273381 CCTATTTTGTTGATCCGTCATTTGAAC 59.727 37.037 0.00 0.00 33.56 3.18
2739 2868 4.321042 AGTTGAAACTTGATGGCTGCCAT 61.321 43.478 33.02 33.02 41.00 4.40
2778 2907 6.127225 TGGAGAAACAAAAATCACACATGGAA 60.127 34.615 0.00 0.00 0.00 3.53
2779 2908 6.930722 GGAGAAACAAAAATCACACATGGAAT 59.069 34.615 0.00 0.00 0.00 3.01
2783 2912 9.437045 GAAACAAAAATCACACATGGAATTTTC 57.563 29.630 0.00 0.00 0.00 2.29
2784 2913 8.503458 AACAAAAATCACACATGGAATTTTCA 57.497 26.923 0.00 0.00 0.00 2.69
2785 2914 7.918643 ACAAAAATCACACATGGAATTTTCAC 58.081 30.769 0.00 0.00 0.00 3.18
2819 2955 3.901844 ACAGTGGCAGACTAACTAAGGAA 59.098 43.478 0.00 0.00 31.73 3.36
2843 2979 5.483685 ACAGCAAATAGTAGACTTGGACA 57.516 39.130 0.00 0.00 0.00 4.02
3001 3137 7.880195 AGTTAGAAATTGTCTGAGTACTGCAAT 59.120 33.333 0.00 3.09 37.12 3.56
3022 3158 6.183360 GCAATAGGAAAAGCAAAGAACAATCG 60.183 38.462 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
286 357 8.882736 TGATGTCATATGTATGTTTGAACTGAC 58.117 33.333 1.90 0.00 35.26 3.51
436 508 9.577222 AAGTTAGGCCTTTGTAGTTTTGTATTA 57.423 29.630 12.58 0.00 0.00 0.98
571 645 6.635030 AGTATTGTTTTTCCACTGAAGTCC 57.365 37.500 0.00 0.00 0.00 3.85
628 704 4.736168 GCATTTTGCACTGTTTAGGTGACA 60.736 41.667 0.00 0.00 44.26 3.58
708 784 2.590073 CTGCACTGACTAGTCTTGTCG 58.410 52.381 23.01 15.42 37.26 4.35
819 908 2.515057 GCGTTGGTGTGGTGGTCA 60.515 61.111 0.00 0.00 0.00 4.02
1095 1189 2.557056 CTCTGTGAGGGTTCTCGTGTAA 59.443 50.000 0.00 0.00 42.79 2.41
1222 1316 0.458543 TCAACTCCGATGAAGCTCGC 60.459 55.000 0.00 0.00 37.33 5.03
1409 1503 6.187727 AGTTCATCTAGTTGGGAAACAAGA 57.812 37.500 1.00 0.00 40.38 3.02
1588 1682 7.387122 GTGCATCAAGATCAGAATCTATGCTAA 59.613 37.037 17.51 3.52 45.79 3.09
1712 1820 9.570468 ACATCTTTGTGCATCAATTCTATATCT 57.430 29.630 0.00 0.00 35.84 1.98
1787 1895 7.939784 ATGATATATGTGCTGCTTGATTCAT 57.060 32.000 0.00 0.00 0.00 2.57
1834 1942 5.798125 TCACCAAATGCTTCACCAAATTA 57.202 34.783 0.00 0.00 0.00 1.40
2270 2399 1.526917 ATGCCGCTGTAGAATGGGC 60.527 57.895 0.00 0.00 44.00 5.36
2337 2466 0.324614 TGATGATGTTGTCTGGCGGT 59.675 50.000 0.00 0.00 0.00 5.68
2339 2468 0.371301 CGTGATGATGTTGTCTGGCG 59.629 55.000 0.00 0.00 0.00 5.69
2350 2479 2.890808 ATTCCTGCGTACGTGATGAT 57.109 45.000 17.90 3.61 0.00 2.45
2423 2552 6.015918 TCCTGCTCTTTTGAAATATCCCAAA 58.984 36.000 0.00 0.00 0.00 3.28
2692 2821 7.259290 TCAACCTACTTCAAGTTCAAATGAC 57.741 36.000 0.00 0.00 0.00 3.06
2702 2831 7.321745 AGTTTCAACTTCAACCTACTTCAAG 57.678 36.000 0.00 0.00 35.21 3.02
2739 2868 1.560505 TCTCCATGACTAGTGCTGCA 58.439 50.000 0.00 0.00 0.00 4.41
2819 2955 6.204882 GTGTCCAAGTCTACTATTTGCTGTTT 59.795 38.462 0.00 0.00 0.00 2.83
2843 2979 6.323266 CGTAAATGTCTAAGCTGTACTGAGT 58.677 40.000 3.61 0.00 0.00 3.41
2986 3122 5.064071 GCTTTTCCTATTGCAGTACTCAGAC 59.936 44.000 0.00 0.00 0.00 3.51
2987 3123 5.178797 GCTTTTCCTATTGCAGTACTCAGA 58.821 41.667 0.00 0.00 0.00 3.27
3001 3137 4.825085 ACCGATTGTTCTTTGCTTTTCCTA 59.175 37.500 0.00 0.00 0.00 2.94
3022 3158 5.297776 TGCTAGTGACTAGGAAATACGTACC 59.702 44.000 20.24 0.00 34.88 3.34
3228 3368 4.405358 TGGTTCTTCTCAAGGCAATGTTTT 59.595 37.500 0.00 0.00 0.00 2.43
3396 3537 7.820648 AGATTTCAATTGTGCTAGTACTTTGG 58.179 34.615 19.18 6.99 0.00 3.28


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

AutoCloner maintained by Alex Coulton.