Multiple sequence alignment - TraesCS6A01G126300

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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 TraesCS6A01G126300 chr6A 100.000 2258 0 0 1 2258 99784023 99786280 0.000000e+00 4170
1 TraesCS6A01G126300 chr6A 79.792 1346 260 11 867 2206 98313921 98315260 0.000000e+00 968
2 TraesCS6A01G126300 chr6A 77.166 1362 294 15 907 2258 98240453 98241807 0.000000e+00 776
3 TraesCS6A01G126300 chr6B 91.787 2277 148 18 1 2258 157776943 157779199 0.000000e+00 3133
4 TraesCS6A01G126300 chr6B 93.093 1332 75 6 443 1760 157932032 157930704 0.000000e+00 1934
5 TraesCS6A01G126300 chr6B 79.838 1354 263 9 867 2215 156652791 156654139 0.000000e+00 979
6 TraesCS6A01G126300 chr6B 79.509 1386 264 17 870 2245 157487263 157488638 0.000000e+00 968
7 TraesCS6A01G126300 chr6B 94.038 520 29 1 1741 2258 157912638 157912119 0.000000e+00 787
8 TraesCS6A01G126300 chr6B 75.126 1588 367 23 670 2243 159392631 159391058 0.000000e+00 719
9 TraesCS6A01G126300 chr6B 77.875 1026 207 18 1215 2231 157788721 157789735 8.860000e-174 619
10 TraesCS6A01G126300 chr6B 82.911 158 10 7 299 456 157932186 157932046 2.350000e-25 126
11 TraesCS6A01G126300 chr6D 92.371 2202 141 16 76 2258 82961800 82963993 0.000000e+00 3110
12 TraesCS6A01G126300 chr6D 80.074 1345 258 9 867 2206 81924136 81925475 0.000000e+00 990
13 TraesCS6A01G126300 chr6D 77.370 1361 291 15 908 2258 81748180 81749533 0.000000e+00 791
14 TraesCS6A01G126300 chr6D 83.250 603 97 3 1658 2258 81919528 81920128 3.280000e-153 551
15 TraesCS6A01G126300 chr6D 73.205 1198 286 23 898 2080 83044914 83046091 3.490000e-108 401
16 TraesCS6A01G126300 chr5D 89.918 1835 155 17 436 2257 372057869 372059686 0.000000e+00 2337


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 TraesCS6A01G126300 chr6A 99784023 99786280 2257 False 4170 4170 100.000 1 2258 1 chr6A.!!$F3 2257
1 TraesCS6A01G126300 chr6A 98313921 98315260 1339 False 968 968 79.792 867 2206 1 chr6A.!!$F2 1339
2 TraesCS6A01G126300 chr6A 98240453 98241807 1354 False 776 776 77.166 907 2258 1 chr6A.!!$F1 1351
3 TraesCS6A01G126300 chr6B 157776943 157779199 2256 False 3133 3133 91.787 1 2258 1 chr6B.!!$F3 2257
4 TraesCS6A01G126300 chr6B 157930704 157932186 1482 True 1030 1934 88.002 299 1760 2 chr6B.!!$R3 1461
5 TraesCS6A01G126300 chr6B 156652791 156654139 1348 False 979 979 79.838 867 2215 1 chr6B.!!$F1 1348
6 TraesCS6A01G126300 chr6B 157487263 157488638 1375 False 968 968 79.509 870 2245 1 chr6B.!!$F2 1375
7 TraesCS6A01G126300 chr6B 157912119 157912638 519 True 787 787 94.038 1741 2258 1 chr6B.!!$R1 517
8 TraesCS6A01G126300 chr6B 159391058 159392631 1573 True 719 719 75.126 670 2243 1 chr6B.!!$R2 1573
9 TraesCS6A01G126300 chr6B 157788721 157789735 1014 False 619 619 77.875 1215 2231 1 chr6B.!!$F4 1016
10 TraesCS6A01G126300 chr6D 82961800 82963993 2193 False 3110 3110 92.371 76 2258 1 chr6D.!!$F4 2182
11 TraesCS6A01G126300 chr6D 81924136 81925475 1339 False 990 990 80.074 867 2206 1 chr6D.!!$F3 1339
12 TraesCS6A01G126300 chr6D 81748180 81749533 1353 False 791 791 77.370 908 2258 1 chr6D.!!$F1 1350
13 TraesCS6A01G126300 chr6D 81919528 81920128 600 False 551 551 83.250 1658 2258 1 chr6D.!!$F2 600
14 TraesCS6A01G126300 chr6D 83044914 83046091 1177 False 401 401 73.205 898 2080 1 chr6D.!!$F5 1182
15 TraesCS6A01G126300 chr5D 372057869 372059686 1817 False 2337 2337 89.918 436 2257 1 chr5D.!!$F1 1821

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
229 247 1.065928 CCGTGCGGAGGTACATCTC 59.934 63.158 7.56 0.0 37.5 2.75 F
294 312 1.069227 GCTGCTTACCAAACCTGTTCG 60.069 52.381 0.00 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1039 1125 1.634973 TCTCATTGGTGCAATCCCAGA 59.365 47.619 0.0 0.0 31.05 3.86 R
2058 2159 2.015736 AGCTCAGCAATCTGGTTACG 57.984 50.000 0.0 0.0 40.69 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
18 19 3.443045 GGTCGACGGGCTCGGTAA 61.443 66.667 12.42 0.00 43.16 2.85
19 20 2.568090 GTCGACGGGCTCGGTAAA 59.432 61.111 12.42 0.00 43.16 2.01
67 71 2.509548 AGGCCAGGCATGTAGTAAATCA 59.490 45.455 15.19 0.00 0.00 2.57
119 123 3.997064 CTCTGGCTCCGCAGTTCCG 62.997 68.421 0.00 0.00 0.00 4.30
123 127 4.090057 GCTCCGCAGTTCCGCAAC 62.090 66.667 0.00 0.00 0.00 4.17
124 128 3.777925 CTCCGCAGTTCCGCAACG 61.778 66.667 0.00 0.00 37.61 4.10
195 213 2.764128 ATGCCGTCGGGAGGACAT 60.764 61.111 14.38 4.40 46.42 3.06
228 246 3.077519 GCCGTGCGGAGGTACATCT 62.078 63.158 15.45 0.00 37.50 2.90
229 247 1.065928 CCGTGCGGAGGTACATCTC 59.934 63.158 7.56 0.00 37.50 2.75
258 276 3.047877 CCTGCCACGGACGGTTTC 61.048 66.667 0.00 0.00 0.00 2.78
294 312 1.069227 GCTGCTTACCAAACCTGTTCG 60.069 52.381 0.00 0.00 0.00 3.95
336 354 8.292448 GCTTGTTCTAAGAAGATTTTGTGATGA 58.708 33.333 3.95 0.00 31.45 2.92
499 560 5.751243 TTCGTTTTCCTGAAAGAAGAAGG 57.249 39.130 0.00 0.00 34.07 3.46
514 575 6.394345 AGAAGAAGGAAATACAGGGAACAT 57.606 37.500 0.00 0.00 0.00 2.71
574 635 7.701539 TCAGCCAACAATCTTACATTGTTAT 57.298 32.000 11.39 0.85 46.73 1.89
622 683 5.232414 GGAATCACGCTTCACACTAGAATAC 59.768 44.000 0.00 0.00 0.00 1.89
664 739 1.691976 TCGAACCTTCTGGAAGCTTGA 59.308 47.619 2.10 0.00 37.11 3.02
720 799 9.600432 AGCCTAATCTCAAAGAAGTAGAGATAT 57.400 33.333 4.76 0.07 45.62 1.63
739 818 9.781425 AGAGATATACTGATATGGAAACTGGAT 57.219 33.333 0.00 0.00 0.00 3.41
740 820 9.814899 GAGATATACTGATATGGAAACTGGATG 57.185 37.037 0.00 0.00 0.00 3.51
857 942 3.059166 CAGTTTGTTTGGTTGCCATAGC 58.941 45.455 0.00 0.00 40.48 2.97
1039 1125 4.217118 GGAAGTTCAGTCTGTTCAATGCAT 59.783 41.667 5.01 0.00 0.00 3.96
1351 1444 4.304110 CAACATTTGCATATCCATCAGGC 58.696 43.478 0.00 0.00 33.74 4.85
1460 1553 4.122776 CCGGTGAGTTGATTTCCTGATAG 58.877 47.826 0.00 0.00 0.00 2.08
1570 1665 6.628185 AGATTCTCAAAACCATCAATGAAGC 58.372 36.000 0.00 0.00 0.00 3.86
1832 1931 7.230510 TCTGCCATTAAAGTTGTTGTACAGAAT 59.769 33.333 0.00 0.00 0.00 2.40
1995 2094 4.583871 AGTCCAAATGCAACTCTTCTAGG 58.416 43.478 0.00 0.00 0.00 3.02
2058 2159 6.828785 TGAAATTATTCCTTCCAAGGTCTAGC 59.171 38.462 5.24 0.00 46.54 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 2.509548 TGATTTACTACATGCCTGGCCT 59.490 45.455 17.53 2.69 0.00 5.19
50 51 3.492383 CGAGCTGATTTACTACATGCCTG 59.508 47.826 0.00 0.00 0.00 4.85
212 230 1.065928 GGAGATGTACCTCCGCACG 59.934 63.158 2.81 0.00 42.80 5.34
225 243 2.893489 GGCAGGTGTTTTTCTTGGAGAT 59.107 45.455 0.00 0.00 0.00 2.75
226 244 2.306847 GGCAGGTGTTTTTCTTGGAGA 58.693 47.619 0.00 0.00 0.00 3.71
228 246 1.754226 GTGGCAGGTGTTTTTCTTGGA 59.246 47.619 0.00 0.00 0.00 3.53
229 247 1.535860 CGTGGCAGGTGTTTTTCTTGG 60.536 52.381 0.00 0.00 0.00 3.61
233 251 0.030235 GTCCGTGGCAGGTGTTTTTC 59.970 55.000 6.43 0.00 0.00 2.29
265 283 1.226974 GGTAAGCAGCGCATCTCGA 60.227 57.895 11.47 0.00 41.67 4.04
266 284 1.083806 TTGGTAAGCAGCGCATCTCG 61.084 55.000 11.47 0.00 42.12 4.04
307 325 6.358030 CACAAAATCTTCTTAGAACAAGCACG 59.642 38.462 0.00 0.00 33.20 5.34
499 560 8.137437 CCATATTGTTGATGTTCCCTGTATTTC 58.863 37.037 0.00 0.00 0.00 2.17
514 575 5.725551 AGTAACCCATCCCATATTGTTGA 57.274 39.130 0.00 0.00 0.00 3.18
574 635 6.739112 CATCTCGTGGAGATTCACAAGTATA 58.261 40.000 5.42 0.00 45.86 1.47
595 656 2.350522 AGTGTGAAGCGTGATTCCATC 58.649 47.619 0.00 0.00 0.00 3.51
664 739 3.129287 GGTTCAGCAAAATGTCCATCGAT 59.871 43.478 0.00 0.00 0.00 3.59
720 799 5.071788 GGACCATCCAGTTTCCATATCAGTA 59.928 44.000 0.00 0.00 36.28 2.74
765 845 4.344102 GGGGTGTTGTATGATCAGCTAGTA 59.656 45.833 0.09 0.00 0.00 1.82
857 942 2.926901 TTCAACACGTCCACCCACCG 62.927 60.000 0.00 0.00 0.00 4.94
1039 1125 1.634973 TCTCATTGGTGCAATCCCAGA 59.365 47.619 0.00 0.00 31.05 3.86
1587 1682 3.196207 AAGCAGCTTCAGGGGCGAA 62.196 57.895 0.21 0.00 34.52 4.70
1832 1931 5.208890 TGCCTAGGCTGAAAACTCTAGATA 58.791 41.667 33.07 5.21 42.51 1.98
2058 2159 2.015736 AGCTCAGCAATCTGGTTACG 57.984 50.000 0.00 0.00 40.69 3.18


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

AutoCloner maintained by Alex Coulton.