Multiple sequence alignment - TraesCS4B01G216100

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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 TraesCS4B01G216100 chr4B 100.000 1821 0 0 993 2813 455910354 455908534 0 3363
1 TraesCS4B01G216100 chr4B 100.000 747 0 0 1 747 455911346 455910600 0 1380
2 TraesCS4B01G216100 chr4D 94.638 1753 46 23 993 2727 370692414 370690692 0 2673
3 TraesCS4B01G216100 chr4D 91.979 748 25 20 9 747 370693126 370692405 0 1016
4 TraesCS4B01G216100 chr4A 93.211 1856 60 29 993 2810 93687011 93685184 0 2669
5 TraesCS4B01G216100 chr4A 91.021 568 16 15 188 747 93687542 93687002 0 734


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 TraesCS4B01G216100 chr4B 455908534 455911346 2812 True 2371.5 3363 100.0000 1 2813 2 chr4B.!!$R1 2812
1 TraesCS4B01G216100 chr4D 370690692 370693126 2434 True 1844.5 2673 93.3085 9 2727 2 chr4D.!!$R1 2718
2 TraesCS4B01G216100 chr4A 93685184 93687542 2358 True 1701.5 2669 92.1160 188 2810 2 chr4A.!!$R1 2622

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
169 172 0.391263 CTAGGGTTTGACCACTCGCC 60.391 60.0 0.0 0.0 41.02 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 2007 0.174845 GCTCAAAATTTACCCGGCCC 59.825 55.0 0.0 0.0 0.0 5.8 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
43 44 4.324991 GAACCCGCCTTCCGTGGT 62.325 66.667 0.00 0.00 40.93 4.16
84 86 4.758251 CCACCATCTGCCGCACGA 62.758 66.667 0.00 0.00 0.00 4.35
103 105 2.966309 GCTTTGCCCGACAACCTCG 61.966 63.158 0.00 0.00 38.23 4.63
116 118 1.614241 AACCTCGTCTAATGGCGGCT 61.614 55.000 11.43 0.00 0.00 5.52
117 119 1.592669 CCTCGTCTAATGGCGGCTG 60.593 63.158 11.43 0.00 0.00 4.85
138 141 2.046292 GAAGGGGAGAAGGATGGAGAG 58.954 57.143 0.00 0.00 0.00 3.20
160 163 4.770874 GCGGCGGCTAGGGTTTGA 62.771 66.667 9.78 0.00 35.83 2.69
169 172 0.391263 CTAGGGTTTGACCACTCGCC 60.391 60.000 0.00 0.00 41.02 5.54
174 177 0.814010 GTTTGACCACTCGCCTGTGT 60.814 55.000 3.55 0.00 36.30 3.72
193 196 5.178061 TGTGTCGCTCAAGTTTGATATGAT 58.822 37.500 0.00 0.00 36.46 2.45
198 201 8.892723 TGTCGCTCAAGTTTGATATGATAATTT 58.107 29.630 0.00 0.00 36.46 1.82
248 252 1.426751 TAGAAAACACGGGACACCCT 58.573 50.000 0.00 0.00 42.67 4.34
476 486 6.143278 ACGAGAGAACAAACAAACAAACAAAC 59.857 34.615 0.00 0.00 0.00 2.93
477 487 6.143118 CGAGAGAACAAACAAACAAACAAACA 59.857 34.615 0.00 0.00 0.00 2.83
478 488 7.306283 CGAGAGAACAAACAAACAAACAAACAA 60.306 33.333 0.00 0.00 0.00 2.83
479 489 8.202745 AGAGAACAAACAAACAAACAAACAAA 57.797 26.923 0.00 0.00 0.00 2.83
480 490 8.334632 AGAGAACAAACAAACAAACAAACAAAG 58.665 29.630 0.00 0.00 0.00 2.77
481 491 6.909895 AGAACAAACAAACAAACAAACAAAGC 59.090 30.769 0.00 0.00 0.00 3.51
482 492 6.370433 ACAAACAAACAAACAAACAAAGCT 57.630 29.167 0.00 0.00 0.00 3.74
483 493 6.426327 ACAAACAAACAAACAAACAAAGCTC 58.574 32.000 0.00 0.00 0.00 4.09
529 539 3.009805 ACCACCTATTTACACCCACTTCC 59.990 47.826 0.00 0.00 0.00 3.46
590 601 1.705745 ACTTTCCCCTCTTCCTTCCAC 59.294 52.381 0.00 0.00 0.00 4.02
591 602 0.690762 TTTCCCCTCTTCCTTCCACG 59.309 55.000 0.00 0.00 0.00 4.94
592 603 1.198759 TTCCCCTCTTCCTTCCACGG 61.199 60.000 0.00 0.00 0.00 4.94
1219 1234 2.943978 AAGCCCCAGTTCGACCTCG 61.944 63.158 0.00 0.00 41.45 4.63
1644 1665 3.603158 AAATTTTACCACCGCAATCCC 57.397 42.857 0.00 0.00 0.00 3.85
1755 1785 1.587350 CTGCGCGATCGACATCAGT 60.587 57.895 21.57 0.00 38.10 3.41
1963 1996 5.391312 AATCTCGGGTTTTGATTCCTTTG 57.609 39.130 0.00 0.00 0.00 2.77
2015 2049 1.153549 CACCTCACCTCGCCTTAGC 60.154 63.158 0.00 0.00 0.00 3.09
2197 2232 3.144193 CGCTCGCTCCTCCTCCTT 61.144 66.667 0.00 0.00 0.00 3.36
2198 2233 2.811799 GCTCGCTCCTCCTCCTTC 59.188 66.667 0.00 0.00 0.00 3.46
2199 2234 1.756561 GCTCGCTCCTCCTCCTTCT 60.757 63.158 0.00 0.00 0.00 2.85
2200 2235 1.734388 GCTCGCTCCTCCTCCTTCTC 61.734 65.000 0.00 0.00 0.00 2.87
2201 2236 1.076632 TCGCTCCTCCTCCTTCTCC 60.077 63.158 0.00 0.00 0.00 3.71
2202 2237 1.076339 CGCTCCTCCTCCTTCTCCT 60.076 63.158 0.00 0.00 0.00 3.69
2203 2238 0.686112 CGCTCCTCCTCCTTCTCCTT 60.686 60.000 0.00 0.00 0.00 3.36
2204 2239 0.829990 GCTCCTCCTCCTTCTCCTTG 59.170 60.000 0.00 0.00 0.00 3.61
2205 2240 1.899438 GCTCCTCCTCCTTCTCCTTGT 60.899 57.143 0.00 0.00 0.00 3.16
2323 2364 2.125106 GCTTCAGCCGGTAGTGGG 60.125 66.667 1.90 0.00 34.31 4.61
2434 2483 1.845809 GACCGTCAAAGGCAGCTGTG 61.846 60.000 16.64 5.59 33.69 3.66
2443 2495 3.339731 GCAGCTGTGCGGTTACAA 58.660 55.556 16.64 0.00 40.71 2.41
2498 2550 4.723754 GCGTGGAAAAAGTTTGTTTGAAGC 60.724 41.667 0.00 0.00 0.00 3.86
2500 2552 5.120053 CGTGGAAAAAGTTTGTTTGAAGCTT 59.880 36.000 0.00 0.00 0.00 3.74
2520 2572 5.476945 AGCTTAAATTTGACGTTCCATTCCT 59.523 36.000 0.00 0.00 0.00 3.36
2527 2579 0.953960 ACGTTCCATTCCTTGCGACC 60.954 55.000 0.00 0.00 0.00 4.79
2556 2616 4.260497 CGACAGACGACAGGAATATTACGA 60.260 45.833 0.00 0.00 45.77 3.43
2744 2808 2.166050 TGTGTTGATGCACAAGCTTGTT 59.834 40.909 29.23 15.72 45.17 2.83
2760 2824 0.957362 TGTTGTGCCATCGAATTGCA 59.043 45.000 3.12 3.12 0.00 4.08
2762 2826 2.029200 TGTTGTGCCATCGAATTGCATT 60.029 40.909 9.62 0.00 37.34 3.56
2763 2827 2.281140 TGTGCCATCGAATTGCATTG 57.719 45.000 9.62 0.00 37.34 2.82
2784 2848 7.524698 GCATTGTTTTTCCTCTATTGGTGGTTA 60.525 37.037 0.00 0.00 0.00 2.85
2798 2862 2.496070 GGTGGTTAGGGAAAAGGATTGC 59.504 50.000 0.00 0.00 0.00 3.56
2810 2874 2.332063 AGGATTGCCCTACATTCGTG 57.668 50.000 0.00 0.00 45.48 4.35
2811 2875 1.559682 AGGATTGCCCTACATTCGTGT 59.440 47.619 0.00 0.00 45.48 4.49
2812 2876 2.769663 AGGATTGCCCTACATTCGTGTA 59.230 45.455 0.00 0.00 45.48 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.151777 AACGTTGTGGTGCTCGTCAG 61.152 55.000 0.00 0.00 35.49 3.51
1 2 1.153529 AACGTTGTGGTGCTCGTCA 60.154 52.632 0.00 0.00 35.49 4.35
2 3 1.275657 CAACGTTGTGGTGCTCGTC 59.724 57.895 20.21 0.00 35.49 4.20
3 4 2.819552 GCAACGTTGTGGTGCTCGT 61.820 57.895 27.78 0.00 38.15 4.18
4 5 2.052237 GCAACGTTGTGGTGCTCG 60.052 61.111 27.78 1.06 0.00 5.03
5 6 1.298339 GTGCAACGTTGTGGTGCTC 60.298 57.895 27.78 12.24 0.00 4.26
6 7 2.798009 GTGCAACGTTGTGGTGCT 59.202 55.556 27.78 0.00 0.00 4.40
43 44 1.014044 GTGTCTTCGGCTCATCGCAA 61.014 55.000 0.00 0.00 41.67 4.85
84 86 1.600916 GAGGTTGTCGGGCAAAGCT 60.601 57.895 0.00 0.00 39.03 3.74
103 105 0.815615 CCTTCCAGCCGCCATTAGAC 60.816 60.000 0.00 0.00 0.00 2.59
116 118 0.421495 TCCATCCTTCTCCCCTTCCA 59.579 55.000 0.00 0.00 0.00 3.53
117 119 1.135960 CTCCATCCTTCTCCCCTTCC 58.864 60.000 0.00 0.00 0.00 3.46
159 162 2.430921 CGACACAGGCGAGTGGTC 60.431 66.667 15.64 10.23 43.72 4.02
160 163 4.664677 GCGACACAGGCGAGTGGT 62.665 66.667 15.64 3.79 43.72 4.16
169 172 4.627035 TCATATCAAACTTGAGCGACACAG 59.373 41.667 0.00 0.00 41.08 3.66
174 177 9.108284 TCAAATTATCATATCAAACTTGAGCGA 57.892 29.630 0.00 0.00 41.08 4.93
198 201 9.491675 TTGGTTATACGTTTTAAATCTCTGTCA 57.508 29.630 0.00 0.00 0.00 3.58
220 224 4.517832 GTCCCGTGTTTTCTAAATCTTGGT 59.482 41.667 0.00 0.00 0.00 3.67
512 522 2.914059 CCCGGAAGTGGGTGTAAATAG 58.086 52.381 0.73 0.00 44.76 1.73
592 603 2.668550 GTGCGAGTGGGGTGGAAC 60.669 66.667 0.00 0.00 0.00 3.62
1219 1234 4.436998 CTGGACGGCGACCTGGTC 62.437 72.222 27.09 16.99 0.00 4.02
1644 1665 4.636435 AGGTTGGTTCCGGGTGCG 62.636 66.667 0.00 0.00 0.00 5.34
1755 1785 2.203788 ACCGACTGCCTCTTGGGA 60.204 61.111 0.00 0.00 37.23 4.37
1850 1880 4.389576 CTTCTGCGGTGTTGCGGC 62.390 66.667 0.00 0.00 41.12 6.53
1851 1881 4.389576 GCTTCTGCGGTGTTGCGG 62.390 66.667 0.00 0.00 42.75 5.69
1974 2007 0.174845 GCTCAAAATTTACCCGGCCC 59.825 55.000 0.00 0.00 0.00 5.80
2015 2049 3.703001 ATCAGTGGTAACCTCAACCTG 57.297 47.619 0.00 0.00 37.91 4.00
2197 2232 1.006571 GACGCGGACAACAAGGAGA 60.007 57.895 12.47 0.00 0.00 3.71
2198 2233 2.027625 GGACGCGGACAACAAGGAG 61.028 63.158 12.47 0.00 0.00 3.69
2199 2234 2.029964 GGACGCGGACAACAAGGA 59.970 61.111 12.47 0.00 0.00 3.36
2200 2235 3.411351 CGGACGCGGACAACAAGG 61.411 66.667 12.47 0.00 0.00 3.61
2201 2236 2.660552 ACGGACGCGGACAACAAG 60.661 61.111 12.47 0.00 0.00 3.16
2202 2237 2.962786 CACGGACGCGGACAACAA 60.963 61.111 12.47 0.00 0.00 2.83
2203 2238 4.953868 CCACGGACGCGGACAACA 62.954 66.667 12.47 0.00 0.00 3.33
2204 2239 4.651008 TCCACGGACGCGGACAAC 62.651 66.667 12.47 0.00 0.00 3.32
2205 2240 3.229156 ATTCCACGGACGCGGACAA 62.229 57.895 12.47 0.00 0.00 3.18
2267 2307 3.036084 CGTCGGACAGCGCAGTTT 61.036 61.111 11.47 0.00 0.00 2.66
2371 2415 1.285950 GAAGCAGGAAACCAACCGC 59.714 57.895 0.00 0.00 0.00 5.68
2442 2494 0.995024 CCATCCCACTCTCCAAGGTT 59.005 55.000 0.00 0.00 0.00 3.50
2443 2495 0.916358 CCCATCCCACTCTCCAAGGT 60.916 60.000 0.00 0.00 0.00 3.50
2452 2504 2.357836 CAAGCTGCCCATCCCACT 59.642 61.111 0.00 0.00 0.00 4.00
2498 2550 6.089417 GCAAGGAATGGAACGTCAAATTTAAG 59.911 38.462 0.00 0.00 0.00 1.85
2500 2552 5.465935 GCAAGGAATGGAACGTCAAATTTA 58.534 37.500 0.00 0.00 0.00 1.40
2575 2639 3.421844 GCTGTAGACTCCCACCATTTTT 58.578 45.455 0.00 0.00 0.00 1.94
2588 2652 1.245732 ATATCCGGTCGGCTGTAGAC 58.754 55.000 0.00 0.00 37.86 2.59
2682 2746 4.370917 GCACAGATTCACAAAAACCATGT 58.629 39.130 0.00 0.00 0.00 3.21
2683 2747 3.426191 CGCACAGATTCACAAAAACCATG 59.574 43.478 0.00 0.00 0.00 3.66
2684 2748 3.317711 TCGCACAGATTCACAAAAACCAT 59.682 39.130 0.00 0.00 0.00 3.55
2685 2749 2.685388 TCGCACAGATTCACAAAAACCA 59.315 40.909 0.00 0.00 0.00 3.67
2686 2750 3.003275 TCTCGCACAGATTCACAAAAACC 59.997 43.478 0.00 0.00 0.00 3.27
2744 2808 1.545136 ACAATGCAATTCGATGGCACA 59.455 42.857 8.11 0.00 40.83 4.57
2760 2824 6.994421 AACCACCAATAGAGGAAAAACAAT 57.006 33.333 0.00 0.00 0.00 2.71
2762 2826 6.007703 CCTAACCACCAATAGAGGAAAAACA 58.992 40.000 0.00 0.00 0.00 2.83
2763 2827 5.417894 CCCTAACCACCAATAGAGGAAAAAC 59.582 44.000 0.00 0.00 0.00 2.43
2784 2848 2.000048 TGTAGGGCAATCCTTTTCCCT 59.000 47.619 3.96 3.96 45.47 4.20


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

AutoCloner maintained by Alex Coulton.