Multiple sequence alignment - TraesCS3A01G349600

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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 TraesCS3A01G349600 chr3A 100.000 2240 0 0 1 2240 598548560 598550799 0.000000e+00 4137
1 TraesCS3A01G349600 chr3D 95.764 1983 54 11 260 2240 455863941 455865895 0.000000e+00 3169
2 TraesCS3A01G349600 chr3D 89.615 260 23 3 1 257 455863641 455863899 5.960000e-86 327
3 TraesCS3A01G349600 chr3B 95.664 1868 64 8 377 2240 602302406 602304260 0.000000e+00 2985
4 TraesCS3A01G349600 chr3B 92.053 302 21 2 1 299 602302019 602302320 2.660000e-114 422


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 TraesCS3A01G349600 chr3A 598548560 598550799 2239 False 4137.0 4137 100.0000 1 2240 1 chr3A.!!$F1 2239
1 TraesCS3A01G349600 chr3D 455863641 455865895 2254 False 1748.0 3169 92.6895 1 2240 2 chr3D.!!$F1 2239
2 TraesCS3A01G349600 chr3B 602302019 602304260 2241 False 1703.5 2985 93.8585 1 2240 2 chr3B.!!$F1 2239

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
91 92 0.031178 GCAAACAGCTGGTGAACTGG 59.969 55.0 19.93 0.0 41.15 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 2003 0.948623 CATGTCGCACTCCAACCGAA 60.949 55.0 0.0 0.0 32.31 4.3 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
38 39 2.486203 TGTTGTCAAGTGTTGTGTGGTC 59.514 45.455 0.00 0.00 0.00 4.02
68 69 1.072965 AGAAAAGCTCCAGTGTCAGGG 59.927 52.381 0.00 0.00 0.00 4.45
91 92 0.031178 GCAAACAGCTGGTGAACTGG 59.969 55.000 19.93 0.00 41.15 4.00
134 135 4.803452 TCATCAGGGTTCTTTGGTTTCTT 58.197 39.130 0.00 0.00 0.00 2.52
139 140 1.611977 GGTTCTTTGGTTTCTTCGGGG 59.388 52.381 0.00 0.00 0.00 5.73
143 144 2.953648 TCTTTGGTTTCTTCGGGGTTTC 59.046 45.455 0.00 0.00 0.00 2.78
144 145 1.694844 TTGGTTTCTTCGGGGTTTCC 58.305 50.000 0.00 0.00 0.00 3.13
149 150 3.243636 GGTTTCTTCGGGGTTTCCTTTTC 60.244 47.826 0.00 0.00 0.00 2.29
165 168 9.186323 GTTTCCTTTTCTTGAAAAAGCTATCTC 57.814 33.333 9.41 0.00 36.26 2.75
179 182 5.965033 AGCTATCTCTTTCTTGATTCCCA 57.035 39.130 0.00 0.00 0.00 4.37
196 199 1.203052 CCCACACCTCAAATGCACATC 59.797 52.381 0.00 0.00 0.00 3.06
198 201 2.494471 CCACACCTCAAATGCACATCAT 59.506 45.455 0.00 0.00 36.87 2.45
199 202 3.428452 CCACACCTCAAATGCACATCATC 60.428 47.826 0.00 0.00 33.40 2.92
239 242 4.944619 TCATCTGATCCACTATGGTCAC 57.055 45.455 0.00 0.00 39.03 3.67
257 260 2.299013 TCACGGTCACTCTGTTTGCTAT 59.701 45.455 0.00 0.00 32.67 2.97
285 327 5.469479 AGCTTTGTATTGTACATTTGCACC 58.531 37.500 0.00 0.00 38.68 5.01
300 342 4.968812 TTGCACCACATAGTTGATCATG 57.031 40.909 0.00 0.00 0.00 3.07
305 347 3.523157 ACCACATAGTTGATCATGGTGGA 59.477 43.478 25.57 0.00 38.99 4.02
313 355 2.170166 TGATCATGGTGGAAAACTGCC 58.830 47.619 0.00 0.00 0.00 4.85
320 362 0.387239 GTGGAAAACTGCCGACATGC 60.387 55.000 0.00 0.00 0.00 4.06
322 364 0.598065 GGAAAACTGCCGACATGCTT 59.402 50.000 0.00 0.00 0.00 3.91
403 491 4.083802 TGCTATCACTAGATCATGTCGTCG 60.084 45.833 0.00 0.00 35.67 5.12
404 492 4.083749 GCTATCACTAGATCATGTCGTCGT 60.084 45.833 0.00 0.00 35.67 4.34
405 493 5.120363 GCTATCACTAGATCATGTCGTCGTA 59.880 44.000 0.00 0.00 35.67 3.43
406 494 6.183360 GCTATCACTAGATCATGTCGTCGTAT 60.183 42.308 0.00 0.00 35.67 3.06
407 495 5.344207 TCACTAGATCATGTCGTCGTATG 57.656 43.478 0.00 0.00 0.00 2.39
408 496 4.814771 TCACTAGATCATGTCGTCGTATGT 59.185 41.667 0.00 1.81 0.00 2.29
409 497 5.050295 TCACTAGATCATGTCGTCGTATGTC 60.050 44.000 0.00 8.34 0.00 3.06
418 506 3.805971 TGTCGTCGTATGTCGTATCATCT 59.194 43.478 1.64 0.00 40.80 2.90
436 524 1.833630 TCTTGGCAGGATCTACAGGTG 59.166 52.381 0.00 0.00 0.00 4.00
448 536 2.158219 TCTACAGGTGAGGAAGGGTTGA 60.158 50.000 0.00 0.00 0.00 3.18
457 545 0.666577 GGAAGGGTTGAGTGTCGACG 60.667 60.000 11.62 0.00 31.46 5.12
468 556 2.337246 TGTCGACGGCCTTCATCGA 61.337 57.895 11.62 11.54 42.27 3.59
600 688 1.330655 GGATGGAGAAGAGCCCGTCA 61.331 60.000 0.00 0.00 39.61 4.35
767 855 1.878522 CGCTCGGGATGAAGTTCCG 60.879 63.158 0.00 0.00 44.59 4.30
768 856 2.174319 GCTCGGGATGAAGTTCCGC 61.174 63.158 0.00 0.00 43.10 5.54
1596 1684 4.555262 CGCCAAACACCTGAAATTACATT 58.445 39.130 0.00 0.00 0.00 2.71
1598 1686 5.799936 CGCCAAACACCTGAAATTACATTAG 59.200 40.000 0.00 0.00 0.00 1.73
1605 1693 4.876107 ACCTGAAATTACATTAGCAGTCGG 59.124 41.667 0.00 0.00 0.00 4.79
1608 1696 6.293081 CCTGAAATTACATTAGCAGTCGGATG 60.293 42.308 0.00 0.00 0.00 3.51
1637 1725 1.875813 GCATGTGCTCCTCGTCGAG 60.876 63.158 15.53 15.53 38.21 4.04
1663 1751 3.005050 TGTTGGTCGATCAGAAACTACGT 59.995 43.478 0.00 0.00 0.00 3.57
1894 1982 4.332819 ACACAACACAAGTAGCTTTCACTC 59.667 41.667 0.00 0.00 0.00 3.51
1908 1996 5.070714 AGCTTTCACTCATCATCTCTAGCAT 59.929 40.000 0.00 0.00 0.00 3.79
1915 2003 7.069208 TCACTCATCATCTCTAGCATGTAGTTT 59.931 37.037 0.00 0.00 0.00 2.66
1959 2048 8.088365 TGTAGAATGATGGATGGATAAGTTACG 58.912 37.037 0.00 0.00 0.00 3.18
1960 2049 7.067496 AGAATGATGGATGGATAAGTTACGT 57.933 36.000 0.00 0.00 0.00 3.57
1961 2050 8.190326 AGAATGATGGATGGATAAGTTACGTA 57.810 34.615 0.00 0.00 0.00 3.57
1962 2051 8.088981 AGAATGATGGATGGATAAGTTACGTAC 58.911 37.037 0.00 0.00 0.00 3.67
2101 2190 1.155042 CAGAGACACTTGCTTCCTGC 58.845 55.000 0.00 0.00 43.25 4.85
2143 2232 1.382522 ATGCATTACTCAACCCAGCG 58.617 50.000 0.00 0.00 0.00 5.18
2168 2257 7.010552 CGTTATCTTATCTTGTTGCTTGCTACT 59.989 37.037 8.43 0.00 0.00 2.57
2181 2276 0.610174 TGCTACTGGAGTTGAGCAGG 59.390 55.000 0.92 0.00 39.93 4.85
2196 2291 1.020437 GCAGGAGCTAGGTTTCATGC 58.980 55.000 4.80 4.80 42.72 4.06
2199 2294 2.617308 CAGGAGCTAGGTTTCATGCATG 59.383 50.000 21.07 21.07 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.095969 CACACAACACTTGACAACACGT 60.096 45.455 0.00 0.00 0.00 4.49
22 23 1.472552 CCTCGACCACACAACACTTGA 60.473 52.381 0.00 0.00 0.00 3.02
38 39 2.289072 TGGAGCTTTTCTTCAGACCTCG 60.289 50.000 0.00 0.00 0.00 4.63
91 92 2.490903 AGATGTGCAACTGATTTCTGCC 59.509 45.455 0.00 0.00 38.04 4.85
134 135 3.300239 TTCAAGAAAAGGAAACCCCGA 57.700 42.857 0.00 0.00 40.87 5.14
139 140 9.186323 GAGATAGCTTTTTCAAGAAAAGGAAAC 57.814 33.333 18.02 6.86 40.83 2.78
143 144 9.404348 GAAAGAGATAGCTTTTTCAAGAAAAGG 57.596 33.333 16.61 11.63 42.03 3.11
165 168 3.754965 TGAGGTGTGGGAATCAAGAAAG 58.245 45.455 0.00 0.00 0.00 2.62
179 182 2.756760 GGATGATGTGCATTTGAGGTGT 59.243 45.455 0.00 0.00 37.34 4.16
196 199 3.920231 TCAACAGATCAAGGAGGGATG 57.080 47.619 0.00 0.00 0.00 3.51
198 201 3.845992 TGAATCAACAGATCAAGGAGGGA 59.154 43.478 0.00 0.00 0.00 4.20
199 202 4.226427 TGAATCAACAGATCAAGGAGGG 57.774 45.455 0.00 0.00 0.00 4.30
239 242 3.067106 ACAATAGCAAACAGAGTGACCG 58.933 45.455 0.00 0.00 0.00 4.79
257 260 8.138074 TGCAAATGTACAATACAAAGCTAACAA 58.862 29.630 0.00 0.00 42.76 2.83
285 327 6.151648 AGTTTTCCACCATGATCAACTATGTG 59.848 38.462 0.00 3.19 0.00 3.21
300 342 0.240945 CATGTCGGCAGTTTTCCACC 59.759 55.000 0.00 0.00 0.00 4.61
305 347 1.317613 TCAAGCATGTCGGCAGTTTT 58.682 45.000 0.00 0.00 35.83 2.43
313 355 3.885484 ACAGACTTTTCAAGCATGTCG 57.115 42.857 0.00 0.00 33.40 4.35
320 362 7.012327 TGGTGTAGAATGAACAGACTTTTCAAG 59.988 37.037 8.07 0.00 36.57 3.02
322 364 6.353323 TGGTGTAGAATGAACAGACTTTTCA 58.647 36.000 6.51 6.51 37.38 2.69
344 386 2.126467 CTGCAATTGTTGGTCGTTTGG 58.874 47.619 7.40 0.00 0.00 3.28
403 491 3.990469 CCTGCCAAGATGATACGACATAC 59.010 47.826 0.00 0.00 0.00 2.39
404 492 3.895041 TCCTGCCAAGATGATACGACATA 59.105 43.478 0.00 0.00 0.00 2.29
405 493 2.700371 TCCTGCCAAGATGATACGACAT 59.300 45.455 0.00 0.00 0.00 3.06
406 494 2.107366 TCCTGCCAAGATGATACGACA 58.893 47.619 0.00 0.00 0.00 4.35
407 495 2.890808 TCCTGCCAAGATGATACGAC 57.109 50.000 0.00 0.00 0.00 4.34
408 496 3.234353 AGATCCTGCCAAGATGATACGA 58.766 45.455 0.00 0.00 0.00 3.43
409 497 3.674528 AGATCCTGCCAAGATGATACG 57.325 47.619 0.00 0.00 0.00 3.06
418 506 1.833630 CTCACCTGTAGATCCTGCCAA 59.166 52.381 0.00 0.00 0.00 4.52
436 524 0.966920 TCGACACTCAACCCTTCCTC 59.033 55.000 0.00 0.00 0.00 3.71
448 536 1.215647 GATGAAGGCCGTCGACACT 59.784 57.895 17.16 7.48 0.00 3.55
457 545 1.478510 TGAGAAGTCTCGATGAAGGCC 59.521 52.381 0.00 0.00 45.72 5.19
468 556 2.300437 GGCCACTGTACTTGAGAAGTCT 59.700 50.000 0.00 0.00 41.77 3.24
723 811 1.315257 GCATGGCCATGTCGTTCCTT 61.315 55.000 39.08 4.85 40.80 3.36
768 856 4.134187 CACTACAAGTGGCGCGCG 62.134 66.667 28.44 28.44 42.35 6.86
1596 1684 1.753078 ACGCTCCATCCGACTGCTA 60.753 57.895 0.00 0.00 0.00 3.49
1598 1686 2.887568 CACGCTCCATCCGACTGC 60.888 66.667 0.00 0.00 0.00 4.40
1605 1693 3.197790 ATGCACGCACGCTCCATC 61.198 61.111 0.00 0.00 0.00 3.51
1608 1696 4.450122 CACATGCACGCACGCTCC 62.450 66.667 0.00 0.00 0.00 4.70
1637 1725 4.499183 AGTTTCTGATCGACCAACAGATC 58.501 43.478 12.00 9.48 42.52 2.75
1663 1751 1.406341 GGCATCAACGGCTACAAGGTA 60.406 52.381 0.00 0.00 0.00 3.08
1834 1922 3.127030 GCTTCTACCTCAATTTGAACGGG 59.873 47.826 8.94 5.83 0.00 5.28
1894 1982 6.145209 CCGAAAACTACATGCTAGAGATGATG 59.855 42.308 8.71 0.00 0.00 3.07
1908 1996 2.215196 GCACTCCAACCGAAAACTACA 58.785 47.619 0.00 0.00 0.00 2.74
1915 2003 0.948623 CATGTCGCACTCCAACCGAA 60.949 55.000 0.00 0.00 32.31 4.30
1959 2048 2.522638 CGCCTTCAATCGCGGGTAC 61.523 63.158 6.13 0.00 44.57 3.34
1960 2049 2.202824 CGCCTTCAATCGCGGGTA 60.203 61.111 6.13 0.00 44.57 3.69
2031 2120 4.272489 TCATGTCCATCTTCCAATGGTTC 58.728 43.478 0.00 0.02 45.46 3.62
2054 2143 1.302511 TCGTGCCTGGGAAGCTTTC 60.303 57.895 0.00 0.00 0.00 2.62
2101 2190 2.673368 GGAGTGCCTCTGTTTCATAACG 59.327 50.000 2.79 0.00 37.06 3.18
2127 2216 4.442706 AGATAACGCTGGGTTGAGTAATG 58.557 43.478 18.95 0.00 39.75 1.90
2143 2232 8.119226 CAGTAGCAAGCAACAAGATAAGATAAC 58.881 37.037 0.00 0.00 0.00 1.89
2181 2276 3.273434 TCACATGCATGAAACCTAGCTC 58.727 45.455 32.75 0.00 0.00 4.09
2196 2291 4.675565 CGTACGGAGCTACTAAATCACATG 59.324 45.833 7.57 0.00 0.00 3.21
2199 2294 4.033684 CACGTACGGAGCTACTAAATCAC 58.966 47.826 21.06 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.