Multiple sequence alignment - TraesCS1A01G286900

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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 TraesCS1A01G286900 chr1A 100.000 2565 0 0 1 2565 483680194 483677630 0.000000e+00 4737.0
1 TraesCS1A01G286900 chr1D 94.401 2054 76 20 528 2565 383760950 383758920 0.000000e+00 3120.0
2 TraesCS1A01G286900 chr1D 97.436 39 1 0 225 263 383761993 383761955 1.650000e-07 67.6
3 TraesCS1A01G286900 chr1B 91.154 1560 83 30 535 2078 514818660 514817140 0.000000e+00 2065.0
4 TraesCS1A01G286900 chr1B 83.621 696 75 26 1 690 514821434 514820772 3.630000e-173 617.0
5 TraesCS1A01G286900 chr1B 92.269 401 27 3 2165 2565 514816140 514815744 1.330000e-157 566.0
6 TraesCS1A01G286900 chr1B 85.658 509 45 17 1 488 514819758 514819257 6.330000e-141 510.0
7 TraesCS1A01G286900 chr6D 89.062 192 17 4 1024 1213 70634350 70634539 4.270000e-58 235.0
8 TraesCS1A01G286900 chr6D 90.058 171 16 1 1052 1222 29381258 29381089 1.190000e-53 220.0
9 TraesCS1A01G286900 chr6B 89.062 192 17 4 1024 1213 145043673 145043862 4.270000e-58 235.0
10 TraesCS1A01G286900 chr6B 88.265 196 19 4 1023 1216 144920698 144920505 5.520000e-57 231.0
11 TraesCS1A01G286900 chr6A 88.718 195 18 4 1024 1216 87653708 87653516 4.270000e-58 235.0
12 TraesCS1A01G286900 chr6A 88.021 192 19 4 1024 1213 87906912 87907101 9.240000e-55 224.0
13 TraesCS1A01G286900 chr5A 91.463 164 14 0 1052 1215 642919362 642919199 2.570000e-55 226.0
14 TraesCS1A01G286900 chr7A 76.611 419 85 12 1067 1482 690930210 690929802 4.300000e-53 219.0
15 TraesCS1A01G286900 chr7A 76.429 420 84 13 1067 1482 690918440 690918032 2.000000e-51 213.0
16 TraesCS1A01G286900 chr7A 87.302 189 21 3 1296 1483 711583414 711583228 2.000000e-51 213.0
17 TraesCS1A01G286900 chr7A 84.971 173 26 0 1303 1475 100064019 100064191 2.620000e-40 176.0
18 TraesCS1A01G286900 chr7D 84.579 214 30 3 1296 1508 617735497 617735286 2.590000e-50 209.0
19 TraesCS1A01G286900 chr7D 100.000 29 0 0 234 262 578724103 578724131 1.000000e-03 54.7
20 TraesCS1A01G286900 chr7B 83.410 217 33 3 1296 1511 711755859 711755645 5.600000e-47 198.0
21 TraesCS1A01G286900 chr7B 81.818 176 32 0 1307 1482 677538444 677538269 5.720000e-32 148.0


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 TraesCS1A01G286900 chr1A 483677630 483680194 2564 True 4737.0 4737 100.0000 1 2565 1 chr1A.!!$R1 2564
1 TraesCS1A01G286900 chr1D 383758920 383761993 3073 True 1593.8 3120 95.9185 225 2565 2 chr1D.!!$R1 2340
2 TraesCS1A01G286900 chr1B 514815744 514821434 5690 True 939.5 2065 88.1755 1 2565 4 chr1B.!!$R1 2564

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
752 3769 0.24912 TCTCACACGGATCGCCAAAT 59.751 50.0 0.0 0.0 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 5124 0.673985 CACTCGATGGCCTATTCCGA 59.326 55.0 3.32 4.87 0.0 4.55 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
75 76 5.462530 TGATGTGAATATGTACTACCCCG 57.537 43.478 0.00 0.00 0.00 5.73
81 82 4.470664 TGAATATGTACTACCCCGGTTTGT 59.529 41.667 0.00 0.00 0.00 2.83
82 83 2.773993 ATGTACTACCCCGGTTTGTG 57.226 50.000 0.00 0.00 0.00 3.33
83 84 1.714541 TGTACTACCCCGGTTTGTGA 58.285 50.000 0.00 0.00 0.00 3.58
84 85 2.045524 TGTACTACCCCGGTTTGTGAA 58.954 47.619 0.00 0.00 0.00 3.18
85 86 2.437281 TGTACTACCCCGGTTTGTGAAA 59.563 45.455 0.00 0.00 0.00 2.69
86 87 2.732844 ACTACCCCGGTTTGTGAAAA 57.267 45.000 0.00 0.00 0.00 2.29
93 94 1.681264 CCGGTTTGTGAAAAGAAGGCT 59.319 47.619 0.00 0.00 0.00 4.58
105 106 6.523546 GTGAAAAGAAGGCTTATAACTTTCGC 59.476 38.462 12.52 12.52 32.98 4.70
129 130 3.067320 TCATGGTGCAATGTTTGACGAAA 59.933 39.130 0.00 0.00 0.00 3.46
131 132 4.837896 TGGTGCAATGTTTGACGAAATA 57.162 36.364 0.00 0.00 0.00 1.40
141 142 9.787532 CAATGTTTGACGAAATATGTAGGAAAT 57.212 29.630 0.00 0.00 0.00 2.17
145 146 9.438291 GTTTGACGAAATATGTAGGAAATCATG 57.562 33.333 0.00 0.00 0.00 3.07
263 264 5.336744 ACAAACATGGTCAAAGTTTACACG 58.663 37.500 0.00 0.00 34.03 4.49
264 265 5.124138 ACAAACATGGTCAAAGTTTACACGA 59.876 36.000 0.00 0.00 34.03 4.35
292 322 6.828785 TGACTTGGAGAAAATTTATAGGCCTC 59.171 38.462 9.68 0.00 0.00 4.70
293 323 6.974795 ACTTGGAGAAAATTTATAGGCCTCT 58.025 36.000 9.68 0.46 0.00 3.69
300 330 8.435931 AGAAAATTTATAGGCCTCTTTTTGGT 57.564 30.769 9.68 0.00 0.00 3.67
301 331 8.314021 AGAAAATTTATAGGCCTCTTTTTGGTG 58.686 33.333 9.68 0.00 0.00 4.17
302 332 7.790782 AAATTTATAGGCCTCTTTTTGGTGA 57.209 32.000 9.68 0.00 0.00 4.02
303 333 6.775594 ATTTATAGGCCTCTTTTTGGTGAC 57.224 37.500 9.68 0.00 0.00 3.67
304 334 2.178912 TAGGCCTCTTTTTGGTGACG 57.821 50.000 9.68 0.00 0.00 4.35
390 434 1.353091 AGCCCTAGCATAGCTAACCC 58.647 55.000 0.00 0.00 40.82 4.11
403 452 3.686016 AGCTAACCCGACATGAAAACAT 58.314 40.909 0.00 0.00 0.00 2.71
420 469 8.726650 TGAAAACATTGTCATTTCTCATTACG 57.273 30.769 12.72 0.00 34.84 3.18
424 473 8.728088 AACATTGTCATTTCTCATTACGAAAC 57.272 30.769 0.00 0.00 33.64 2.78
653 3670 2.355837 GCTCGGTTCGTGCTGTCA 60.356 61.111 7.04 0.00 42.00 3.58
751 3768 0.389817 CTCTCACACGGATCGCCAAA 60.390 55.000 0.00 0.00 0.00 3.28
752 3769 0.249120 TCTCACACGGATCGCCAAAT 59.751 50.000 0.00 0.00 0.00 2.32
781 3798 1.918253 GGCTGACACCCATCATCCT 59.082 57.895 0.00 0.00 33.00 3.24
784 3801 1.474677 GCTGACACCCATCATCCTCTG 60.475 57.143 0.00 0.00 0.00 3.35
789 3807 2.446848 CCCATCATCCTCTGGCCGT 61.447 63.158 0.00 0.00 0.00 5.68
850 3868 1.527380 GTCCGGGGCAGAAACACAA 60.527 57.895 0.00 0.00 0.00 3.33
851 3869 1.527380 TCCGGGGCAGAAACACAAC 60.527 57.895 0.00 0.00 0.00 3.32
853 3871 1.358759 CGGGGCAGAAACACAACAC 59.641 57.895 0.00 0.00 0.00 3.32
854 3872 1.380403 CGGGGCAGAAACACAACACA 61.380 55.000 0.00 0.00 0.00 3.72
855 3873 0.385390 GGGGCAGAAACACAACACAG 59.615 55.000 0.00 0.00 0.00 3.66
856 3874 1.388547 GGGCAGAAACACAACACAGA 58.611 50.000 0.00 0.00 0.00 3.41
857 3875 1.748493 GGGCAGAAACACAACACAGAA 59.252 47.619 0.00 0.00 0.00 3.02
1324 4356 3.854669 CTCGAGCTGGCGGGGAAT 61.855 66.667 0.00 0.00 0.00 3.01
1459 4491 1.077265 CCTGCCCAACATCAACCCT 59.923 57.895 0.00 0.00 0.00 4.34
1468 4500 0.892358 ACATCAACCCTGTGCTGCTG 60.892 55.000 0.00 0.00 0.00 4.41
1629 4664 4.219115 TCCTCTCTGTTTGTCTCTGTCTT 58.781 43.478 0.00 0.00 0.00 3.01
1681 4718 3.400590 GTCGTGGTCGTCGTTGCC 61.401 66.667 0.00 0.00 38.33 4.52
1790 4827 0.324943 AGCCTGATTAACACCGCTGT 59.675 50.000 0.00 0.00 30.73 4.40
1791 4828 1.553248 AGCCTGATTAACACCGCTGTA 59.447 47.619 0.00 0.00 30.73 2.74
1792 4829 2.170607 AGCCTGATTAACACCGCTGTAT 59.829 45.455 0.00 0.00 30.73 2.29
1793 4830 2.287915 GCCTGATTAACACCGCTGTATG 59.712 50.000 0.00 0.00 0.00 2.39
1840 4877 0.253207 GAAAGGGAGGGAGGGGAAGA 60.253 60.000 0.00 0.00 0.00 2.87
1934 4976 2.217750 TCTTTTGCTGCACGCTAAGAA 58.782 42.857 0.00 0.00 37.19 2.52
2010 5053 1.410224 GGAGGAAAGCTATTGGGGTGG 60.410 57.143 0.00 0.00 0.00 4.61
2011 5054 0.631212 AGGAAAGCTATTGGGGTGGG 59.369 55.000 0.00 0.00 0.00 4.61
2012 5055 0.397114 GGAAAGCTATTGGGGTGGGG 60.397 60.000 0.00 0.00 0.00 4.96
2013 5056 0.335019 GAAAGCTATTGGGGTGGGGT 59.665 55.000 0.00 0.00 0.00 4.95
2014 5057 0.041090 AAAGCTATTGGGGTGGGGTG 59.959 55.000 0.00 0.00 0.00 4.61
2015 5058 1.146544 AAGCTATTGGGGTGGGGTGT 61.147 55.000 0.00 0.00 0.00 4.16
2078 5122 7.083875 TGAGTTTCTAAGTGAAAACCTTGTG 57.916 36.000 0.00 0.00 45.10 3.33
2079 5123 6.882140 TGAGTTTCTAAGTGAAAACCTTGTGA 59.118 34.615 0.00 0.00 45.10 3.58
2080 5124 7.556275 TGAGTTTCTAAGTGAAAACCTTGTGAT 59.444 33.333 0.00 0.00 45.10 3.06
2094 5145 2.839486 TGTGATCGGAATAGGCCATC 57.161 50.000 5.01 0.00 0.00 3.51
2126 5177 6.437928 TGTGCTGTTGAATTCTTGTTATGTC 58.562 36.000 7.05 0.00 0.00 3.06
2256 6240 9.703892 TTTCATTTCAATTGGTTAATCAACGAT 57.296 25.926 2.56 0.00 35.34 3.73
2325 6309 5.633830 ACTCATGAAATGCCAGTTTGTAG 57.366 39.130 0.00 0.00 46.21 2.74
2379 6363 7.264947 GGGGTATTTTGATTGTCTATTTGTGG 58.735 38.462 0.00 0.00 0.00 4.17
2394 6378 0.464870 TGTGGTTTTGCTGCATGCTT 59.535 45.000 20.33 0.00 43.37 3.91
2439 6423 3.704100 GCTTTGGGCATGTTTGGTT 57.296 47.368 0.00 0.00 41.35 3.67
2519 6503 8.795513 TGTCTCACATGATAATGTTCACATTTT 58.204 29.630 10.38 3.08 43.48 1.82
2520 6504 9.069078 GTCTCACATGATAATGTTCACATTTTG 57.931 33.333 10.38 6.73 43.48 2.44
2526 6510 9.414295 CATGATAATGTTCACATTTTGAAGTGT 57.586 29.630 10.38 0.00 45.23 3.55
2548 6532 8.591072 AGTGTAAACCTTATAGCTTGTAACTGA 58.409 33.333 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 4.470664 TCACAAACCGGGGTAGTACATATT 59.529 41.667 6.32 0.00 0.00 1.28
63 64 2.259012 TCACAAACCGGGGTAGTACAT 58.741 47.619 6.32 0.00 0.00 2.29
71 72 1.339929 CCTTCTTTTCACAAACCGGGG 59.660 52.381 6.32 0.00 0.00 5.73
75 76 7.658261 AGTTATAAGCCTTCTTTTCACAAACC 58.342 34.615 0.00 0.00 33.85 3.27
81 82 6.349033 GGCGAAAGTTATAAGCCTTCTTTTCA 60.349 38.462 5.63 0.00 44.06 2.69
82 83 6.028368 GGCGAAAGTTATAAGCCTTCTTTTC 58.972 40.000 5.63 0.00 44.06 2.29
83 84 5.950883 GGCGAAAGTTATAAGCCTTCTTTT 58.049 37.500 5.63 0.00 44.06 2.27
84 85 5.562506 GGCGAAAGTTATAAGCCTTCTTT 57.437 39.130 5.63 2.43 44.06 2.52
93 94 3.625764 GCACCATGAGGCGAAAGTTATAA 59.374 43.478 0.00 0.00 39.06 0.98
105 106 2.669113 CGTCAAACATTGCACCATGAGG 60.669 50.000 5.39 0.00 42.21 3.86
131 132 8.713971 TGTACCTATGAACATGATTTCCTACAT 58.286 33.333 0.00 0.00 0.00 2.29
255 256 4.365723 TCTCCAAGTCAAGTCGTGTAAAC 58.634 43.478 0.00 0.00 0.00 2.01
263 264 8.184848 GCCTATAAATTTTCTCCAAGTCAAGTC 58.815 37.037 0.00 0.00 0.00 3.01
264 265 7.122799 GGCCTATAAATTTTCTCCAAGTCAAGT 59.877 37.037 0.00 0.00 0.00 3.16
348 379 7.274447 GCTTGGGATTTTTAAATCATGATCCA 58.726 34.615 9.06 5.79 45.10 3.41
351 382 6.387807 AGGGCTTGGGATTTTTAAATCATGAT 59.612 34.615 15.04 1.18 45.10 2.45
352 383 5.725822 AGGGCTTGGGATTTTTAAATCATGA 59.274 36.000 15.04 0.00 45.10 3.07
353 384 5.993055 AGGGCTTGGGATTTTTAAATCATG 58.007 37.500 15.04 0.00 45.10 3.07
354 385 6.183361 GCTAGGGCTTGGGATTTTTAAATCAT 60.183 38.462 15.04 0.00 39.84 2.45
355 386 5.128663 GCTAGGGCTTGGGATTTTTAAATCA 59.871 40.000 15.04 0.00 39.84 2.57
356 387 5.128663 TGCTAGGGCTTGGGATTTTTAAATC 59.871 40.000 6.65 6.65 40.46 2.17
357 388 5.029474 TGCTAGGGCTTGGGATTTTTAAAT 58.971 37.500 0.00 0.00 39.59 1.40
360 391 3.748645 TGCTAGGGCTTGGGATTTTTA 57.251 42.857 0.00 0.00 39.59 1.52
390 434 6.857451 TGAGAAATGACAATGTTTTCATGTCG 59.143 34.615 11.64 0.00 40.24 4.35
403 452 6.533819 ACGTTTCGTAATGAGAAATGACAA 57.466 33.333 15.17 0.00 43.54 3.18
549 1299 4.026052 AGGCCCAAGATACCAAAAATCTG 58.974 43.478 0.00 0.00 33.95 2.90
653 3670 0.106167 TAGTATGAGCAGTCCGGCCT 60.106 55.000 0.00 0.00 0.00 5.19
660 3677 4.286032 TGGTTTTGGTCTAGTATGAGCAGT 59.714 41.667 0.00 0.00 43.85 4.40
705 3722 1.667724 CAACCAATCGGATGAGAGCAC 59.332 52.381 0.00 0.00 37.24 4.40
713 3730 0.749454 GGCAGAGCAACCAATCGGAT 60.749 55.000 0.00 0.00 35.59 4.18
751 3768 1.224592 GTCAGCCGTTGGATGGGAT 59.775 57.895 0.72 0.00 39.86 3.85
752 3769 2.220586 TGTCAGCCGTTGGATGGGA 61.221 57.895 0.72 0.00 39.86 4.37
781 3798 2.263540 GGAGCGTTAACGGCCAGA 59.736 61.111 27.82 0.00 40.23 3.86
784 3801 1.152383 GATCTGGAGCGTTAACGGCC 61.152 60.000 27.82 13.25 40.23 6.13
789 3807 1.203758 TGCTTCGATCTGGAGCGTTAA 59.796 47.619 8.06 0.00 41.48 2.01
850 3868 3.052455 TCTGTGTGTGTGTTTCTGTGT 57.948 42.857 0.00 0.00 0.00 3.72
851 3869 4.406069 CTTTCTGTGTGTGTGTTTCTGTG 58.594 43.478 0.00 0.00 0.00 3.66
853 3871 3.119884 TGCTTTCTGTGTGTGTGTTTCTG 60.120 43.478 0.00 0.00 0.00 3.02
854 3872 3.081061 TGCTTTCTGTGTGTGTGTTTCT 58.919 40.909 0.00 0.00 0.00 2.52
855 3873 3.171277 GTGCTTTCTGTGTGTGTGTTTC 58.829 45.455 0.00 0.00 0.00 2.78
856 3874 2.556189 TGTGCTTTCTGTGTGTGTGTTT 59.444 40.909 0.00 0.00 0.00 2.83
857 3875 2.158559 TGTGCTTTCTGTGTGTGTGTT 58.841 42.857 0.00 0.00 0.00 3.32
924 3947 2.380084 TTTCTCCCGGTCGATTTCTG 57.620 50.000 0.00 0.00 0.00 3.02
925 3948 2.354805 CCTTTTCTCCCGGTCGATTTCT 60.355 50.000 0.00 0.00 0.00 2.52
1417 4449 2.106332 CCGTAGGCGATGGTGACC 59.894 66.667 0.00 0.00 46.14 4.02
1629 4664 1.159098 GGTGCGTTACGGTTGAACCA 61.159 55.000 15.58 0.00 38.47 3.67
1681 4718 3.176661 TGACAACGATGGCATGCG 58.823 55.556 12.44 11.13 40.56 4.73
1790 4827 6.473131 CCTACGCACTTAAACGAACATACATA 59.527 38.462 0.00 0.00 0.00 2.29
1791 4828 5.290158 CCTACGCACTTAAACGAACATACAT 59.710 40.000 0.00 0.00 0.00 2.29
1792 4829 4.622313 CCTACGCACTTAAACGAACATACA 59.378 41.667 0.00 0.00 0.00 2.29
1793 4830 4.622740 ACCTACGCACTTAAACGAACATAC 59.377 41.667 0.00 0.00 0.00 2.39
1840 4877 7.624360 TTACAAACAGACATTCACAGTTTCT 57.376 32.000 0.00 0.00 30.68 2.52
1934 4976 6.668323 CAACCAGATAAACACAAGAAATCGT 58.332 36.000 0.00 0.00 0.00 3.73
2010 5053 1.076044 CCCCCAATGATCCACACCC 60.076 63.158 0.00 0.00 0.00 4.61
2011 5054 4.684623 CCCCCAATGATCCACACC 57.315 61.111 0.00 0.00 0.00 4.16
2078 5122 1.546476 ACTCGATGGCCTATTCCGATC 59.454 52.381 3.32 0.00 0.00 3.69
2079 5123 1.273606 CACTCGATGGCCTATTCCGAT 59.726 52.381 3.32 0.00 0.00 4.18
2080 5124 0.673985 CACTCGATGGCCTATTCCGA 59.326 55.000 3.32 4.87 0.00 4.55
2094 5145 1.159713 TTCAACAGCACAGCCACTCG 61.160 55.000 0.00 0.00 0.00 4.18
2126 5177 1.009829 GCAGCCTACCAGTTGAATCG 58.990 55.000 0.00 0.00 0.00 3.34
2394 6378 9.739276 AACCAAATGAACTCAAGAATCAGTATA 57.261 29.630 0.00 0.00 0.00 1.47
2439 6423 4.662468 TTCTGCTGCAAACAACCAAATA 57.338 36.364 3.02 0.00 0.00 1.40
2519 6503 9.211485 GTTACAAGCTATAAGGTTTACACTTCA 57.789 33.333 0.00 0.00 32.99 3.02
2520 6504 9.433153 AGTTACAAGCTATAAGGTTTACACTTC 57.567 33.333 0.00 0.00 32.99 3.01


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

AutoCloner maintained by Alex Coulton.