Multiple sequence alignment - TraesCS6A01G176000

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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 TraesCS6A01G176000 chr6A 100.000 4231 0 0 1 4231 192208662 192204432 0.000000e+00 7814.0
1 TraesCS6A01G176000 chr6B 95.359 4245 148 22 1 4231 276217555 276221764 0.000000e+00 6702.0
2 TraesCS6A01G176000 chr6B 74.033 181 33 11 2 174 619523511 619523685 1.270000e-05 62.1
3 TraesCS6A01G176000 chr6D 98.193 1992 32 1 2244 4231 151597448 151599439 0.000000e+00 3476.0
4 TraesCS6A01G176000 chr6D 93.342 2328 96 18 1 2292 151595144 151597448 0.000000e+00 3386.0
5 TraesCS6A01G176000 chrUn 94.340 53 0 2 1 51 135306545 135306494 1.260000e-10 78.7
6 TraesCS6A01G176000 chrUn 94.340 53 0 2 1 51 155972953 155973004 1.260000e-10 78.7


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 TraesCS6A01G176000 chr6A 192204432 192208662 4230 True 7814 7814 100.0000 1 4231 1 chr6A.!!$R1 4230
1 TraesCS6A01G176000 chr6B 276217555 276221764 4209 False 6702 6702 95.3590 1 4231 1 chr6B.!!$F1 4230
2 TraesCS6A01G176000 chr6D 151595144 151599439 4295 False 3431 3476 95.7675 1 4231 2 chr6D.!!$F1 4230

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
744 783 0.040425 GATTCGTGCTGCGGTTTTGT 60.040 50.0 0.00 0.00 41.72 2.83 F
904 943 0.461548 TGTTTGTGGAATTGCGGCAA 59.538 45.0 18.85 18.85 0.00 4.52 F
954 993 0.663153 AAAAGCTTCGTCTGTGTGGC 59.337 50.0 0.00 0.00 0.00 5.01 F
1054 1093 0.890542 GCTGGTGTCTGCAATGGTGA 60.891 55.0 0.00 0.00 37.71 4.02 F
2241 2281 0.928229 GCTTACTGTATCAACGCCCG 59.072 55.0 0.00 0.00 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2227 2267 0.390603 TTGACCGGGCGTTGATACAG 60.391 55.000 6.32 0.0 0.0 2.74 R
2238 2278 4.577834 AAGTATTTGTTGTTTGACCGGG 57.422 40.909 6.32 0.0 0.0 5.73 R
2934 3023 1.379576 GCTCAGCTGGCCCTTTCAT 60.380 57.895 15.13 0.0 0.0 2.57 R
3104 3193 5.312079 AGCTTGTGAACAGAAATTAGCTCT 58.688 37.500 0.00 0.0 29.5 4.09 R
3274 3367 1.761449 TGGCAAGAACAGCAGAAACA 58.239 45.000 0.00 0.0 0.0 2.83 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
52 53 8.400947 GGGCAATGTAGATATACTATGCAAATG 58.599 37.037 21.28 0.00 35.49 2.32
88 89 3.353029 CACATGCCGACCGTGCAA 61.353 61.111 8.97 0.00 42.92 4.08
100 101 1.604612 CCGTGCAAACGAAAATGCGG 61.605 55.000 0.00 0.00 45.47 5.69
130 131 1.383456 GCACAGACCAGCCAAACACA 61.383 55.000 0.00 0.00 0.00 3.72
136 137 1.686052 GACCAGCCAAACACAAATGGA 59.314 47.619 0.00 0.00 39.12 3.41
228 229 2.349886 GCGTTGGAGTTGCTCTAATCAG 59.650 50.000 0.00 0.00 33.81 2.90
256 257 1.222115 GACTCAGTTCGCGCTTGGTT 61.222 55.000 5.56 0.00 0.00 3.67
259 260 1.205064 CAGTTCGCGCTTGGTTCTG 59.795 57.895 5.56 1.81 0.00 3.02
364 370 7.744087 TTTACTTCTCTGCTTTTTATCTGCA 57.256 32.000 0.00 0.00 35.30 4.41
371 377 3.495331 TGCTTTTTATCTGCACCCTTCA 58.505 40.909 0.00 0.00 0.00 3.02
372 378 3.507233 TGCTTTTTATCTGCACCCTTCAG 59.493 43.478 0.00 0.00 0.00 3.02
374 380 4.218417 GCTTTTTATCTGCACCCTTCAGAA 59.782 41.667 0.00 0.00 43.01 3.02
375 381 5.278957 GCTTTTTATCTGCACCCTTCAGAAA 60.279 40.000 0.00 0.00 43.01 2.52
376 382 6.723298 TTTTTATCTGCACCCTTCAGAAAA 57.277 33.333 0.00 0.00 43.01 2.29
377 383 6.723298 TTTTATCTGCACCCTTCAGAAAAA 57.277 33.333 0.00 3.88 43.01 1.94
378 384 5.705609 TTATCTGCACCCTTCAGAAAAAC 57.294 39.130 0.00 0.00 43.01 2.43
379 385 3.297134 TCTGCACCCTTCAGAAAAACT 57.703 42.857 0.00 0.00 37.61 2.66
380 386 3.631250 TCTGCACCCTTCAGAAAAACTT 58.369 40.909 0.00 0.00 37.61 2.66
381 387 3.632145 TCTGCACCCTTCAGAAAAACTTC 59.368 43.478 0.00 0.00 37.61 3.01
382 388 3.360867 TGCACCCTTCAGAAAAACTTCA 58.639 40.909 0.00 0.00 0.00 3.02
383 389 3.381272 TGCACCCTTCAGAAAAACTTCAG 59.619 43.478 0.00 0.00 0.00 3.02
384 390 3.632145 GCACCCTTCAGAAAAACTTCAGA 59.368 43.478 0.00 0.00 0.00 3.27
649 682 2.582978 GGACCGCTCCCCACTTAC 59.417 66.667 0.00 0.00 0.00 2.34
650 683 1.988406 GGACCGCTCCCCACTTACT 60.988 63.158 0.00 0.00 0.00 2.24
652 685 1.229082 ACCGCTCCCCACTTACTGA 60.229 57.895 0.00 0.00 0.00 3.41
654 687 1.342674 ACCGCTCCCCACTTACTGATA 60.343 52.381 0.00 0.00 0.00 2.15
655 688 1.760613 CCGCTCCCCACTTACTGATAA 59.239 52.381 0.00 0.00 0.00 1.75
744 783 0.040425 GATTCGTGCTGCGGTTTTGT 60.040 50.000 0.00 0.00 41.72 2.83
769 808 2.442413 TCGGATTGATGTTTGGGGTTC 58.558 47.619 0.00 0.00 0.00 3.62
820 859 1.954382 CGGATGATCGGTAGGTCTGAA 59.046 52.381 0.00 0.00 34.86 3.02
851 890 4.280819 TGATAGAAAGGGGGATTTTGCTG 58.719 43.478 0.00 0.00 0.00 4.41
857 896 2.573340 GGGATTTTGCTGCCCGTG 59.427 61.111 0.00 0.00 31.06 4.94
901 940 2.479656 CCATTTGTTTGTGGAATTGCGG 59.520 45.455 0.00 0.00 37.72 5.69
904 943 0.461548 TGTTTGTGGAATTGCGGCAA 59.538 45.000 18.85 18.85 0.00 4.52
908 947 0.821301 TGTGGAATTGCGGCAACAGA 60.821 50.000 18.94 7.54 0.00 3.41
931 970 5.936054 AGAACTGATTCTTGAATTCTTGCG 58.064 37.500 7.05 0.00 42.91 4.85
938 977 7.424803 TGATTCTTGAATTCTTGCGAGAAAAA 58.575 30.769 20.22 13.37 44.61 1.94
947 986 1.865865 TGCGAGAAAAAGCTTCGTCT 58.134 45.000 10.76 10.76 0.00 4.18
954 993 0.663153 AAAAGCTTCGTCTGTGTGGC 59.337 50.000 0.00 0.00 0.00 5.01
981 1020 6.829229 TCGACTCTATCAGGAGTTGTTTTA 57.171 37.500 10.47 0.00 45.32 1.52
991 1030 5.367945 AGGAGTTGTTTTAGTGTCCTGAA 57.632 39.130 0.00 0.00 33.04 3.02
1054 1093 0.890542 GCTGGTGTCTGCAATGGTGA 60.891 55.000 0.00 0.00 37.71 4.02
1197 1236 2.672651 CACAAGATGCACGGCCCA 60.673 61.111 0.00 0.00 0.00 5.36
1332 1371 4.954118 TGGAGCTCGGTGGTGGGT 62.954 66.667 7.83 0.00 0.00 4.51
1632 1671 2.831526 GCCTGGTAATTTTGTGGATGGT 59.168 45.455 0.00 0.00 0.00 3.55
1646 1685 3.088532 TGGATGGTGCAATTGAGGTTAC 58.911 45.455 10.34 0.00 0.00 2.50
1767 1806 2.179427 TCCATGACTGTCAACGAGGAT 58.821 47.619 15.31 0.00 0.00 3.24
2009 2048 1.386533 ATCAGCAAGGGCATTCTTCG 58.613 50.000 0.00 0.00 44.61 3.79
2066 2105 7.066525 TCCGGTATGCTTTGTTATTTTCCTTAG 59.933 37.037 0.00 0.00 0.00 2.18
2114 2153 4.917385 TGCCATGCCTCTTAGTTTTCTAA 58.083 39.130 0.00 0.00 39.72 2.10
2227 2267 6.428159 TCTTCTGAGTTTCAAGATTGGCTTAC 59.572 38.462 0.00 0.00 34.31 2.34
2238 2278 3.871594 AGATTGGCTTACTGTATCAACGC 59.128 43.478 0.00 0.00 0.00 4.84
2241 2281 0.928229 GCTTACTGTATCAACGCCCG 59.072 55.000 0.00 0.00 0.00 6.13
2297 2385 7.432148 TCTACTTAGAGGGATTAATTGTGCA 57.568 36.000 0.00 0.00 0.00 4.57
2379 2468 2.304761 TGTGTTCCTGGATGGTTACCTC 59.695 50.000 2.07 0.00 37.07 3.85
2768 2857 5.927115 AGTTTCAAAACTAGTAGAAGGCTCG 59.073 40.000 3.59 0.00 46.75 5.03
2822 2911 4.816786 TCATATGCATGACATGGTTTCG 57.183 40.909 17.03 0.00 40.06 3.46
2837 2926 3.260884 TGGTTTCGCTCTACCTTGAGAAT 59.739 43.478 0.00 0.00 36.23 2.40
2934 3023 6.259829 GCTTTTTATTTTTGGCAAAGAGACCA 59.740 34.615 13.04 0.00 0.00 4.02
3104 3193 0.901827 TGCTTGGACCTCGAATAGCA 59.098 50.000 0.00 0.00 36.38 3.49
3195 3288 1.765314 AGACTATGCAAATCTCGCCCT 59.235 47.619 0.00 0.00 0.00 5.19
3274 3367 5.605908 TGAGGATTCTTCATCTCTAGCCAAT 59.394 40.000 0.00 0.00 33.82 3.16
3311 3404 2.158842 GCCAAGGTATCTGAGCATGTCT 60.159 50.000 0.00 0.00 0.00 3.41
3320 3413 1.199327 CTGAGCATGTCTGTGCCAAAG 59.801 52.381 0.00 0.00 46.19 2.77
3325 3418 0.538977 ATGTCTGTGCCAAAGCTGCT 60.539 50.000 0.00 0.00 40.80 4.24
3391 3484 4.982241 ACTGTCTCCAGAAAATGAGGAA 57.018 40.909 0.00 0.00 41.50 3.36
3421 3514 4.732285 AATTGTGTTCACAACTCTAGCG 57.268 40.909 18.52 0.00 31.89 4.26
3523 3616 1.272781 GTTGCGGTTCTGAGATCTCG 58.727 55.000 17.76 12.33 0.00 4.04
3739 3832 7.175347 TCTACAGACAGACAGCAAAGATATT 57.825 36.000 0.00 0.00 0.00 1.28
4057 4150 0.251916 TCGTGTATGCAAAGGGAGGG 59.748 55.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 1.273048 TGGCCAGATGTTTGCACAATC 59.727 47.619 0.00 0.00 36.16 2.67
83 84 1.486801 GCCGCATTTTCGTTTGCAC 59.513 52.632 0.00 0.00 38.80 4.57
87 88 2.799088 CGCGCCGCATTTTCGTTT 60.799 55.556 10.75 0.00 0.00 3.60
88 89 3.530398 AACGCGCCGCATTTTCGTT 62.530 52.632 10.75 0.23 38.36 3.85
130 131 4.388499 ACGGCGTCGGCTCCATTT 62.388 61.111 16.39 0.00 41.39 2.32
149 150 3.502595 TGTTCGTTTGGATCGGCATTTTA 59.497 39.130 0.00 0.00 0.00 1.52
186 187 1.667756 GCCGACGTAATCAGACACACA 60.668 52.381 0.00 0.00 0.00 3.72
190 191 1.515519 GCGCCGACGTAATCAGACA 60.516 57.895 0.00 0.00 42.83 3.41
191 192 2.565394 CGCGCCGACGTAATCAGAC 61.565 63.158 0.00 0.00 42.83 3.51
256 257 3.981416 GCGTCAAGATATATCAACGCAGA 59.019 43.478 32.59 15.04 45.77 4.26
259 260 2.470781 GCGCGTCAAGATATATCAACGC 60.471 50.000 30.32 30.32 44.45 4.84
352 355 5.964958 TTCTGAAGGGTGCAGATAAAAAG 57.035 39.130 0.00 0.00 41.60 2.27
354 360 6.323739 AGTTTTTCTGAAGGGTGCAGATAAAA 59.676 34.615 0.00 0.00 41.51 1.52
364 370 6.850752 TTTTCTGAAGTTTTTCTGAAGGGT 57.149 33.333 8.78 0.00 45.73 4.34
391 397 3.627577 TGCTGTGTGTTTTCCTCTTCTTC 59.372 43.478 0.00 0.00 0.00 2.87
398 404 1.750778 CAACCTGCTGTGTGTTTTCCT 59.249 47.619 0.00 0.00 0.00 3.36
520 534 2.033194 GGCGTTCTTCTTCCGGTGG 61.033 63.158 0.00 0.00 0.00 4.61
654 687 9.570488 GAACGAACTTACTTATCAGTGATACTT 57.430 33.333 12.50 5.28 34.06 2.24
655 688 8.189460 GGAACGAACTTACTTATCAGTGATACT 58.811 37.037 12.50 3.85 34.06 2.12
744 783 5.020132 ACCCCAAACATCAATCCGAATTTA 58.980 37.500 0.00 0.00 0.00 1.40
769 808 3.976701 AATCAGCCGTCCCAAGCCG 62.977 63.158 0.00 0.00 0.00 5.52
782 821 1.470098 CCGCTTCAACCCAGAAATCAG 59.530 52.381 0.00 0.00 0.00 2.90
820 859 3.205282 CCCCCTTTCTATCAATCTGGGTT 59.795 47.826 0.00 0.00 0.00 4.11
901 940 5.679734 TTCAAGAATCAGTTCTCTGTTGC 57.320 39.130 0.00 0.00 43.80 4.17
904 943 7.308469 GCAAGAATTCAAGAATCAGTTCTCTGT 60.308 37.037 8.44 0.00 43.80 3.41
908 947 5.936054 CGCAAGAATTCAAGAATCAGTTCT 58.064 37.500 8.44 0.00 43.58 3.01
931 970 3.303395 CCACACAGACGAAGCTTTTTCTC 60.303 47.826 0.00 0.00 0.00 2.87
938 977 2.159819 ATCGCCACACAGACGAAGCT 62.160 55.000 0.00 0.00 39.56 3.74
947 986 1.170442 TAGAGTCGAATCGCCACACA 58.830 50.000 7.29 0.00 0.00 3.72
954 993 4.035792 ACAACTCCTGATAGAGTCGAATCG 59.964 45.833 7.29 0.00 46.44 3.34
981 1020 1.004440 GGCTTCGCTTCAGGACACT 60.004 57.895 0.00 0.00 0.00 3.55
991 1030 2.125512 GACGTCCATGGCTTCGCT 60.126 61.111 6.96 3.25 0.00 4.93
1197 1236 0.601311 GAAACTGACGCTCCAGCTGT 60.601 55.000 13.81 0.00 37.68 4.40
1332 1371 2.335681 TGTACTTCATGAGGGGGTCA 57.664 50.000 9.90 0.37 40.38 4.02
1632 1671 3.244044 GGCCAAAAGTAACCTCAATTGCA 60.244 43.478 0.00 0.00 0.00 4.08
1646 1685 3.211564 CTGCACCACCGGCCAAAAG 62.212 63.158 0.00 0.00 0.00 2.27
1767 1806 5.724328 ACATCTTCAAGATCTTTGCTCGTA 58.276 37.500 4.86 0.00 31.32 3.43
1956 1995 8.964476 TGTCATCTTTGGATATTTCTACCTTC 57.036 34.615 0.00 0.00 0.00 3.46
2123 2162 9.559958 GGAAGTGATGAACATTGTGTAAATTAG 57.440 33.333 0.00 0.00 0.00 1.73
2133 2172 5.416639 TCATGAAGGGAAGTGATGAACATTG 59.583 40.000 0.00 0.00 0.00 2.82
2227 2267 0.390603 TTGACCGGGCGTTGATACAG 60.391 55.000 6.32 0.00 0.00 2.74
2238 2278 4.577834 AAGTATTTGTTGTTTGACCGGG 57.422 40.909 6.32 0.00 0.00 5.73
2379 2468 5.161358 TGCAACAGTCTGTAAAGTATCGAG 58.839 41.667 5.77 0.00 0.00 4.04
2768 2857 6.942532 TGGTATTCCAGTTTGATGATAAGC 57.057 37.500 0.00 0.00 39.03 3.09
2822 2911 6.743575 TTTGCTTTATTCTCAAGGTAGAGC 57.256 37.500 0.00 0.00 35.59 4.09
2934 3023 1.379576 GCTCAGCTGGCCCTTTCAT 60.380 57.895 15.13 0.00 0.00 2.57
3104 3193 5.312079 AGCTTGTGAACAGAAATTAGCTCT 58.688 37.500 0.00 0.00 29.50 4.09
3195 3288 6.711277 ACAGAACCTGCTGTTTCAATAGATA 58.289 36.000 3.81 0.00 46.42 1.98
3274 3367 1.761449 TGGCAAGAACAGCAGAAACA 58.239 45.000 0.00 0.00 0.00 2.83
3311 3404 2.545596 CGTCAGCAGCTTTGGCACA 61.546 57.895 0.00 0.00 41.70 4.57
3320 3413 2.998772 TGACAAAATTTCGTCAGCAGC 58.001 42.857 7.88 0.00 37.23 5.25
3325 3418 4.981674 GGAATGCTTGACAAAATTTCGTCA 59.018 37.500 7.88 7.88 40.30 4.35
3391 3484 4.603989 TGTGAACACAATTTCATGCCAT 57.396 36.364 5.11 0.00 37.80 4.40
3421 3514 9.974980 TTTAAATTTCCCACTTTTATCAGTGAC 57.025 29.630 0.00 0.00 46.29 3.67
3523 3616 3.367932 GCATGATAATTGCATGATGCTGC 59.632 43.478 19.19 13.02 45.31 5.25
3739 3832 9.569122 GGTAATAAACCTTGGATAGCTTCAATA 57.431 33.333 0.00 0.00 45.75 1.90
3862 3955 3.945285 GAGACCTCACTTGGTTGTTTTCA 59.055 43.478 0.00 0.00 41.00 2.69
4057 4150 5.948992 AAAACCTCTGCAAGACTAATGAC 57.051 39.130 0.00 0.00 38.67 3.06


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

AutoCloner maintained by Alex Coulton.