Multiple sequence alignment - TraesCS1A01G222300

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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 TraesCS1A01G222300 chr1A 100.000 2663 0 0 1 2663 391942582 391939920 0.000000e+00 4918.0
1 TraesCS1A01G222300 chr1D 94.291 2680 108 20 1 2663 311751426 311748775 0.000000e+00 4060.0
2 TraesCS1A01G222300 chr1B 93.750 2160 79 23 63 2203 422347890 422345768 0.000000e+00 3190.0
3 TraesCS1A01G222300 chr1B 100.000 28 0 0 2348 2375 62251344 62251371 5.000000e-03 52.8
4 TraesCS1A01G222300 chr5D 83.721 172 22 5 1245 1413 245198929 245198761 9.870000e-35 158.0
5 TraesCS1A01G222300 chr5D 76.786 112 22 4 2347 2457 399731228 399731120 2.860000e-05 60.2
6 TraesCS1A01G222300 chr5D 100.000 28 0 0 2348 2375 297970798 297970825 5.000000e-03 52.8
7 TraesCS1A01G222300 chr4B 83.432 169 28 0 1242 1410 11905169 11905337 9.870000e-35 158.0
8 TraesCS1A01G222300 chr5A 83.529 170 22 5 1247 1413 329240774 329240608 1.280000e-33 154.0
9 TraesCS1A01G222300 chr4D 81.657 169 31 0 1242 1410 6643363 6643531 9.940000e-30 141.0
10 TraesCS1A01G222300 chr7A 80.473 169 33 0 1242 1410 33148743 33148911 2.150000e-26 130.0
11 TraesCS1A01G222300 chr4A 80.723 166 32 0 1245 1410 596771009 596770844 2.150000e-26 130.0
12 TraesCS1A01G222300 chr3A 81.600 125 23 0 1245 1369 533131044 533130920 1.300000e-18 104.0
13 TraesCS1A01G222300 chr3A 92.308 39 3 0 2348 2386 691335587 691335625 3.700000e-04 56.5
14 TraesCS1A01G222300 chrUn 93.333 45 3 0 2347 2391 216378935 216378891 1.710000e-07 67.6


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 TraesCS1A01G222300 chr1A 391939920 391942582 2662 True 4918 4918 100.000 1 2663 1 chr1A.!!$R1 2662
1 TraesCS1A01G222300 chr1D 311748775 311751426 2651 True 4060 4060 94.291 1 2663 1 chr1D.!!$R1 2662
2 TraesCS1A01G222300 chr1B 422345768 422347890 2122 True 3190 3190 93.750 63 2203 1 chr1B.!!$R1 2140

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
93 94 0.252479 AGCCACAGCAGATGAAGGAG 59.748 55.0 6.17 0.0 43.56 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2083 2105 0.18135 GGGCCCATCATCGTCTCTTT 59.819 55.0 19.95 0.0 0.0 2.52 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
30 31 8.943002 ACAAAGTCGGGTAGTTAAATCTTATTG 58.057 33.333 0.00 0.00 0.00 1.90
31 32 7.549615 AAGTCGGGTAGTTAAATCTTATTGC 57.450 36.000 0.00 0.00 0.00 3.56
32 33 6.053650 AGTCGGGTAGTTAAATCTTATTGCC 58.946 40.000 0.00 0.00 0.00 4.52
33 34 5.818857 GTCGGGTAGTTAAATCTTATTGCCA 59.181 40.000 0.00 0.00 0.00 4.92
34 35 6.316890 GTCGGGTAGTTAAATCTTATTGCCAA 59.683 38.462 0.00 0.00 0.00 4.52
60 61 3.447944 AGAAGAAGAGGCGGGTAGTTAAG 59.552 47.826 0.00 0.00 0.00 1.85
93 94 0.252479 AGCCACAGCAGATGAAGGAG 59.748 55.000 6.17 0.00 43.56 3.69
99 100 3.188048 CACAGCAGATGAAGGAGAAACAC 59.812 47.826 0.00 0.00 0.00 3.32
107 108 0.317479 AAGGAGAAACACGACCTCGG 59.683 55.000 0.00 0.00 44.95 4.63
340 345 1.355210 CACTGCACCGTTGGTTCAC 59.645 57.895 0.00 0.00 31.02 3.18
363 368 6.201044 CACTTTAGGCCTTATCAATGTCGTAG 59.799 42.308 12.58 0.00 0.00 3.51
631 636 8.873215 TGTGCTGTCTAGATTAATTAAGCTAC 57.127 34.615 17.14 12.68 33.48 3.58
632 637 7.926555 TGTGCTGTCTAGATTAATTAAGCTACC 59.073 37.037 17.14 11.89 33.48 3.18
633 638 7.385478 GTGCTGTCTAGATTAATTAAGCTACCC 59.615 40.741 17.14 11.60 33.48 3.69
634 639 7.290248 TGCTGTCTAGATTAATTAAGCTACCCT 59.710 37.037 17.14 0.00 33.48 4.34
635 640 8.151596 GCTGTCTAGATTAATTAAGCTACCCTT 58.848 37.037 17.14 0.00 33.48 3.95
674 680 5.241662 ACTTTCTTCAAGTGATCCAGCTAC 58.758 41.667 0.00 0.00 44.70 3.58
675 681 5.012561 ACTTTCTTCAAGTGATCCAGCTACT 59.987 40.000 0.00 0.00 44.70 2.57
676 682 6.211584 ACTTTCTTCAAGTGATCCAGCTACTA 59.788 38.462 0.00 0.00 44.70 1.82
677 683 6.798427 TTCTTCAAGTGATCCAGCTACTAT 57.202 37.500 0.00 0.00 0.00 2.12
791 797 4.081030 ATGCGTCGTCGTCGTCGT 62.081 61.111 19.72 4.84 46.29 4.34
792 798 3.971780 ATGCGTCGTCGTCGTCGTC 62.972 63.158 19.72 13.60 46.29 4.20
840 846 3.518998 ACTCCGGTCGCCATCGAG 61.519 66.667 0.00 0.00 46.46 4.04
879 887 3.643159 GCTTCTCTAGCTCTAAGCCTC 57.357 52.381 9.81 0.00 46.77 4.70
880 888 3.222603 GCTTCTCTAGCTCTAAGCCTCT 58.777 50.000 9.81 0.00 46.77 3.69
883 891 5.621193 CTTCTCTAGCTCTAAGCCTCTAGT 58.379 45.833 0.00 0.00 43.77 2.57
1068 1076 1.251251 GCACCAAGGACTGCATCTTT 58.749 50.000 0.00 0.00 33.31 2.52
1125 1133 1.882352 GCCATCGTCCACAAGGTCTTT 60.882 52.381 0.00 0.00 35.89 2.52
1162 1170 1.645034 CAAGATGCTCCTGGTACGTG 58.355 55.000 0.00 0.00 0.00 4.49
1759 1772 6.451064 TGCGTTATGATGACTCTTCTCTTA 57.549 37.500 0.00 0.00 0.00 2.10
1904 1922 5.642063 TGTTCTTATCTAAAAAGGCTCACCG 59.358 40.000 0.00 0.00 42.76 4.94
1927 1945 6.183360 CCGCCTGTTTTATAGATAAAGCAACA 60.183 38.462 11.24 5.77 40.98 3.33
1991 2012 4.276678 CACATAGGCAGGATACAACAATGG 59.723 45.833 0.00 0.00 41.41 3.16
2001 2022 7.148086 GCAGGATACAACAATGGATAAGAACAA 60.148 37.037 0.00 0.00 41.41 2.83
2003 2024 7.888021 AGGATACAACAATGGATAAGAACAACA 59.112 33.333 0.00 0.00 41.41 3.33
2009 2030 4.921470 ATGGATAAGAACAACAACGACG 57.079 40.909 0.00 0.00 0.00 5.12
2040 2061 0.108329 CACTCCAAGCCCGTAACGAT 60.108 55.000 0.00 0.00 0.00 3.73
2073 2095 1.135746 CGGAGTTCTCTACCGTGACAC 60.136 57.143 0.00 0.00 41.47 3.67
2095 2117 2.628178 AGGTGTCACAAAGAGACGATGA 59.372 45.455 5.12 0.00 41.24 2.92
2098 2120 3.369147 GTGTCACAAAGAGACGATGATGG 59.631 47.826 0.00 0.00 38.83 3.51
2105 2127 1.821061 GAGACGATGATGGGCCCGAT 61.821 60.000 19.37 12.11 0.00 4.18
2140 2162 5.007034 TCCAAGACATCGCCTTCATAAAAA 58.993 37.500 0.00 0.00 0.00 1.94
2145 2167 4.969816 ACATCGCCTTCATAAAAAGAACG 58.030 39.130 0.00 0.00 0.00 3.95
2158 2180 0.753262 AAGAACGACACTGGAGCACT 59.247 50.000 0.00 0.00 0.00 4.40
2204 2226 6.780522 AGATTAAGGTTTTTACCCAGAGCAAA 59.219 34.615 0.00 0.00 0.00 3.68
2224 2246 3.505835 CGAAGGAGGAGAGTAGCCT 57.494 57.895 0.00 0.00 38.81 4.58
2253 2275 1.192534 CCTTCACAAAGAGAACGACGC 59.807 52.381 0.00 0.00 34.14 5.19
2258 2280 1.274167 ACAAAGAGAACGACGCCCATA 59.726 47.619 0.00 0.00 0.00 2.74
2260 2282 1.183549 AAGAGAACGACGCCCATAGT 58.816 50.000 0.00 0.00 0.00 2.12
2262 2284 0.454600 GAGAACGACGCCCATAGTCA 59.545 55.000 0.00 0.00 38.46 3.41
2265 2287 2.278596 CGACGCCCATAGTCACCG 60.279 66.667 0.00 0.00 38.46 4.94
2269 2291 4.157120 GCCCATAGTCACCGCCGT 62.157 66.667 0.00 0.00 0.00 5.68
2286 2317 3.978193 TCGTTGGGGCCAGGCAAT 61.978 61.111 15.19 0.00 0.00 3.56
2317 2348 2.110213 ACGCACTTTTCGCCTCCA 59.890 55.556 0.00 0.00 0.00 3.86
2324 2355 0.875059 CTTTTCGCCTCCAAGACCAC 59.125 55.000 0.00 0.00 0.00 4.16
2375 2406 3.422303 CACACGGTCATGGCCACG 61.422 66.667 18.31 10.31 0.00 4.94
2376 2407 4.697756 ACACGGTCATGGCCACGG 62.698 66.667 18.31 3.01 0.00 4.94
2414 2445 1.543802 GAGCCTCACTCATAGGGATCG 59.456 57.143 0.00 0.00 45.49 3.69
2430 2461 1.276989 GATCGTTACTCCCACCACCAA 59.723 52.381 0.00 0.00 0.00 3.67
2485 2516 2.573869 CCACCAGACGTCGCTGAT 59.426 61.111 10.46 0.00 38.14 2.90
2536 2567 1.138661 CTCAAAGCAAACCCTTGGCAA 59.861 47.619 0.00 0.00 32.76 4.52
2545 2576 1.068352 ACCCTTGGCAAGAAGGAGGT 61.068 55.000 28.18 21.61 44.87 3.85
2560 2592 4.070552 GGTCGAGCGGCCTGAACT 62.071 66.667 6.23 0.00 36.84 3.01
2604 2637 8.338259 CGACAAGCTATATTTTTATGTGCTCTT 58.662 33.333 0.00 0.00 0.00 2.85
2610 2643 8.405531 GCTATATTTTTATGTGCTCTTTGTGGA 58.594 33.333 0.00 0.00 0.00 4.02
2620 2653 2.678336 GCTCTTTGTGGAAGGGTTATCG 59.322 50.000 0.00 0.00 38.18 2.92
2649 2682 2.044352 TGCTCTCCGTGGGATCGA 60.044 61.111 0.00 0.00 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.991861 TGGCAATAAGATTTAACTACCCGA 58.008 37.500 0.00 0.00 0.00 5.14
34 35 2.658807 ACCCGCCTCTTCTTCTTTTT 57.341 45.000 0.00 0.00 0.00 1.94
39 40 3.195182 ACTTAACTACCCGCCTCTTCTTC 59.805 47.826 0.00 0.00 0.00 2.87
42 43 2.233186 ACACTTAACTACCCGCCTCTTC 59.767 50.000 0.00 0.00 0.00 2.87
43 44 2.233186 GACACTTAACTACCCGCCTCTT 59.767 50.000 0.00 0.00 0.00 2.85
44 45 1.823610 GACACTTAACTACCCGCCTCT 59.176 52.381 0.00 0.00 0.00 3.69
45 46 1.547372 TGACACTTAACTACCCGCCTC 59.453 52.381 0.00 0.00 0.00 4.70
48 49 2.093869 TCCATGACACTTAACTACCCGC 60.094 50.000 0.00 0.00 0.00 6.13
60 61 1.098050 GTGGCTCCAATCCATGACAC 58.902 55.000 0.00 0.00 35.81 3.67
93 94 0.249573 TTGTCCCGAGGTCGTGTTTC 60.250 55.000 0.00 0.00 37.74 2.78
99 100 1.614241 ATTCCCTTGTCCCGAGGTCG 61.614 60.000 0.00 0.00 33.27 4.79
107 108 1.280998 TCTTCCGGAATTCCCTTGTCC 59.719 52.381 19.21 0.00 0.00 4.02
246 247 0.535335 GTCGACCAGGGATACAAGCA 59.465 55.000 3.51 0.00 39.74 3.91
340 345 6.421202 GTCTACGACATTGATAAGGCCTAAAG 59.579 42.308 5.16 0.00 32.09 1.85
408 413 0.322322 TGTGACGGCCGGATTTACTT 59.678 50.000 31.76 4.91 0.00 2.24
631 636 4.368969 AGTAAAGGGTAAGGGACTAAGGG 58.631 47.826 0.00 0.00 38.49 3.95
632 637 6.215023 AGAAAGTAAAGGGTAAGGGACTAAGG 59.785 42.308 0.00 0.00 38.49 2.69
633 638 7.255199 AGAAAGTAAAGGGTAAGGGACTAAG 57.745 40.000 0.00 0.00 38.49 2.18
634 639 7.293062 TGAAGAAAGTAAAGGGTAAGGGACTAA 59.707 37.037 0.00 0.00 38.49 2.24
635 640 6.788957 TGAAGAAAGTAAAGGGTAAGGGACTA 59.211 38.462 0.00 0.00 38.49 2.59
637 642 5.872963 TGAAGAAAGTAAAGGGTAAGGGAC 58.127 41.667 0.00 0.00 0.00 4.46
638 643 6.518516 TTGAAGAAAGTAAAGGGTAAGGGA 57.481 37.500 0.00 0.00 0.00 4.20
674 680 0.763652 ATGCCCTGCCTCTGACATAG 59.236 55.000 0.00 0.00 0.00 2.23
675 681 0.761187 GATGCCCTGCCTCTGACATA 59.239 55.000 0.00 0.00 0.00 2.29
676 682 0.987081 AGATGCCCTGCCTCTGACAT 60.987 55.000 0.00 0.00 32.67 3.06
677 683 1.614525 AGATGCCCTGCCTCTGACA 60.615 57.895 0.00 0.00 32.67 3.58
791 797 5.388111 CGAGCAGTTATTTATATCGGTCGA 58.612 41.667 0.00 0.00 0.00 4.20
792 798 4.030306 GCGAGCAGTTATTTATATCGGTCG 59.970 45.833 0.00 0.00 0.00 4.79
793 799 5.162075 AGCGAGCAGTTATTTATATCGGTC 58.838 41.667 0.00 0.00 34.75 4.79
840 846 0.514691 CGAGTTCAGCAACAAGGAGC 59.485 55.000 0.00 0.00 34.60 4.70
1162 1170 4.936411 TCATCTAGCTACGTAGGAGTATGC 59.064 45.833 23.47 8.57 0.00 3.14
1759 1772 9.579932 AGAGAGAGGAGTTCAAAATGTAAAAAT 57.420 29.630 0.00 0.00 0.00 1.82
1778 1791 5.144100 AGAGGTAGAGAGAGAGAGAGAGAG 58.856 50.000 0.00 0.00 0.00 3.20
1779 1792 5.141182 GAGAGGTAGAGAGAGAGAGAGAGA 58.859 50.000 0.00 0.00 0.00 3.10
1780 1793 4.282195 GGAGAGGTAGAGAGAGAGAGAGAG 59.718 54.167 0.00 0.00 0.00 3.20
1781 1794 4.223953 GGAGAGGTAGAGAGAGAGAGAGA 58.776 52.174 0.00 0.00 0.00 3.10
1904 1922 9.237846 GATTGTTGCTTTATCTATAAAACAGGC 57.762 33.333 0.00 0.00 32.10 4.85
1927 1945 6.849085 TGTATGCTTTGGGTTGTAATGATT 57.151 33.333 0.00 0.00 0.00 2.57
1938 1956 3.189287 GTGTCAGAGTTGTATGCTTTGGG 59.811 47.826 0.00 0.00 0.00 4.12
1991 2012 4.375706 GGTGACGTCGTTGTTGTTCTTATC 60.376 45.833 11.62 0.00 0.00 1.75
2001 2022 1.522130 GTTGGGGTGACGTCGTTGT 60.522 57.895 11.62 0.00 0.00 3.32
2003 2024 2.109593 GGTTGGGGTGACGTCGTT 59.890 61.111 11.62 0.00 0.00 3.85
2009 2030 2.002018 TTGGAGTGGGTTGGGGTGAC 62.002 60.000 0.00 0.00 0.00 3.67
2040 2061 2.231478 AGAACTCCGAATCTTCAAGCGA 59.769 45.455 0.00 0.00 0.00 4.93
2073 2095 2.509052 TCGTCTCTTTGTGACACCTG 57.491 50.000 2.45 0.00 34.37 4.00
2083 2105 0.181350 GGGCCCATCATCGTCTCTTT 59.819 55.000 19.95 0.00 0.00 2.52
2095 2117 1.077501 CACAGTTCATCGGGCCCAT 60.078 57.895 24.92 11.92 0.00 4.00
2098 2120 1.745489 GTCCACAGTTCATCGGGCC 60.745 63.158 0.00 0.00 0.00 5.80
2105 2127 2.115427 TGTCTTGGAGTCCACAGTTCA 58.885 47.619 12.69 12.56 30.78 3.18
2140 2162 1.269998 GTAGTGCTCCAGTGTCGTTCT 59.730 52.381 0.00 0.00 0.00 3.01
2145 2167 2.350522 CAATGGTAGTGCTCCAGTGTC 58.649 52.381 4.56 0.00 43.29 3.67
2204 2226 0.396001 GGCTACTCTCCTCCTTCGGT 60.396 60.000 0.00 0.00 0.00 4.69
2223 2245 1.391485 CTTTGTGAAGGCATCGTCGAG 59.609 52.381 0.00 0.00 0.00 4.04
2224 2246 1.000394 TCTTTGTGAAGGCATCGTCGA 60.000 47.619 0.00 0.00 33.56 4.20
2253 2275 2.106332 GACGGCGGTGACTATGGG 59.894 66.667 13.24 0.00 0.00 4.00
2269 2291 3.978193 ATTGCCTGGCCCCAACGA 61.978 61.111 17.53 0.00 0.00 3.85
2276 2298 0.106015 AGGGTAATCATTGCCTGGCC 60.106 55.000 17.53 0.00 35.54 5.36
2281 2312 1.136891 GTGCCAAGGGTAATCATTGCC 59.863 52.381 0.00 0.00 34.30 4.52
2286 2317 0.958382 GTGCGTGCCAAGGGTAATCA 60.958 55.000 0.00 0.00 0.00 2.57
2317 2348 1.278985 TCTGCGATCAATGGTGGTCTT 59.721 47.619 0.00 0.00 32.15 3.01
2324 2355 1.202065 CCGTTGTTCTGCGATCAATGG 60.202 52.381 17.93 17.93 40.04 3.16
2398 2429 4.216687 GGAGTAACGATCCCTATGAGTGAG 59.783 50.000 0.00 0.00 0.00 3.51
2414 2445 3.644861 CCTTGGTGGTGGGAGTAAC 57.355 57.895 0.00 0.00 0.00 2.50
2435 2466 4.954970 CTTGTGTGCTGGGGCGGT 62.955 66.667 0.00 0.00 42.25 5.68
2485 2516 1.891150 GGGGCTTATATCCTTCGTCGA 59.109 52.381 0.00 0.00 0.00 4.20
2508 2539 1.341209 GGTTTGCTTTGAGGGTGGAAG 59.659 52.381 0.00 0.00 0.00 3.46
2536 2567 3.453679 GCCGCTCGACCTCCTTCT 61.454 66.667 0.00 0.00 0.00 2.85
2545 2576 4.069232 CCAGTTCAGGCCGCTCGA 62.069 66.667 0.00 0.00 0.00 4.04
2560 2592 1.229723 GACAACCCTCCCCTACCCA 60.230 63.158 0.00 0.00 0.00 4.51
2563 2595 0.901580 TGTCGACAACCCTCCCCTAC 60.902 60.000 17.62 0.00 0.00 3.18
2604 2637 5.687166 ATTAGTCGATAACCCTTCCACAA 57.313 39.130 0.00 0.00 0.00 3.33
2610 2643 5.527582 GCACATGAATTAGTCGATAACCCTT 59.472 40.000 0.00 0.00 0.00 3.95
2620 2653 3.553511 CACGGAGAGCACATGAATTAGTC 59.446 47.826 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.