Multiple sequence alignment - TraesCS1D01G162700

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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 TraesCS1D01G162700 chr1D 100.000 3350 0 0 1 3350 233346610 233343261 0.000000e+00 6187.0
1 TraesCS1D01G162700 chr1B 96.252 2161 49 13 648 2804 367888929 367886797 0.000000e+00 3513.0
2 TraesCS1D01G162700 chr1B 93.066 548 21 7 2799 3340 367886744 367886208 0.000000e+00 785.0
3 TraesCS1D01G162700 chr1B 89.474 494 20 6 1 462 367890713 367890220 2.230000e-166 595.0
4 TraesCS1D01G162700 chr1B 98.598 214 2 1 454 666 367889160 367888947 8.770000e-101 377.0
5 TraesCS1D01G162700 chr1A 95.496 2176 67 19 530 2688 314511217 314513378 0.000000e+00 3446.0
6 TraesCS1D01G162700 chr1A 91.168 736 31 11 2611 3333 314513377 314514091 0.000000e+00 968.0
7 TraesCS1D01G162700 chr4A 100.000 38 0 0 2728 2765 574732008 574731971 1.670000e-08 71.3
8 TraesCS1D01G162700 chr4B 91.837 49 4 0 2717 2765 660420265 660420313 6.000000e-08 69.4
9 TraesCS1D01G162700 chr4B 91.837 49 4 0 2717 2765 660449573 660449621 6.000000e-08 69.4
10 TraesCS1D01G162700 chr3B 93.182 44 3 0 2717 2760 750141418 750141461 7.760000e-07 65.8
11 TraesCS1D01G162700 chr3D 100.000 30 0 0 2736 2765 79508396 79508425 4.670000e-04 56.5
12 TraesCS1D01G162700 chr5D 100.000 28 0 0 2718 2745 517757368 517757341 6.000000e-03 52.8


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 TraesCS1D01G162700 chr1D 233343261 233346610 3349 True 6187.0 6187 100.0000 1 3350 1 chr1D.!!$R1 3349
1 TraesCS1D01G162700 chr1B 367886208 367890713 4505 True 1317.5 3513 94.3475 1 3340 4 chr1B.!!$R1 3339
2 TraesCS1D01G162700 chr1A 314511217 314514091 2874 False 2207.0 3446 93.3320 530 3333 2 chr1A.!!$F1 2803

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
931 2082 0.456653 GCAAATCCGCAATTCGCACT 60.457 50.0 1.75 0.0 42.60 4.4 F
2115 3266 0.462581 TCATCACGATGGCAAGCTCC 60.463 55.0 7.17 0.0 39.24 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2313 3464 0.180171 CCCTGCATTGGATCACCGTA 59.820 55.0 0.00 0.0 39.42 4.02 R
3236 4537 2.835580 TTTGTATTGACCGTCCGGAA 57.164 45.0 5.23 0.0 38.96 4.30 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
46 47 1.410153 CAACAAGTTGCTCAAAGCCCT 59.590 47.619 1.81 0.00 41.51 5.19
77 78 3.258372 TCTGGACCTACAACTTGCACTAG 59.742 47.826 0.00 0.00 0.00 2.57
104 105 7.012704 CACCTAATAGGAATGTTGACATGGAAG 59.987 40.741 14.17 0.00 37.67 3.46
203 204 6.383436 TGATCAGGAATTGCATAATGGGAAAA 59.617 34.615 0.00 0.00 0.00 2.29
260 261 1.792006 CGGTACAAGTGGTTGAGGAC 58.208 55.000 0.00 0.00 37.10 3.85
270 271 5.767816 AGTGGTTGAGGACAATTTGTAAC 57.232 39.130 1.15 3.44 38.32 2.50
280 281 6.779860 AGGACAATTTGTAACAGGTAGATGT 58.220 36.000 1.15 0.00 33.96 3.06
304 305 6.785488 TGATAGCAATATCACCGATTCAAC 57.215 37.500 0.00 0.00 32.04 3.18
305 306 5.700832 TGATAGCAATATCACCGATTCAACC 59.299 40.000 0.00 0.00 32.04 3.77
322 323 3.975312 TCAACCGGGCCTCCTAATAATAA 59.025 43.478 6.32 0.00 0.00 1.40
325 326 3.279434 CCGGGCCTCCTAATAATAATGC 58.721 50.000 0.84 0.00 0.00 3.56
347 348 3.189287 CAGAAACGTCTGCCTTTGCTAAT 59.811 43.478 0.00 0.00 44.74 1.73
355 356 2.762327 CTGCCTTTGCTAATGGGTCATT 59.238 45.455 0.00 0.00 38.71 2.57
369 394 1.532868 GGTCATTAGCGCCAATAGCAG 59.467 52.381 2.29 0.00 44.04 4.24
442 467 7.121168 CCAAGAACAACTTCCAATAGCTATTGA 59.879 37.037 37.00 24.03 39.93 2.57
443 468 8.680903 CAAGAACAACTTCCAATAGCTATTGAT 58.319 33.333 37.00 21.34 39.93 2.57
447 472 8.388484 ACAACTTCCAATAGCTATTGATGATC 57.612 34.615 37.00 0.00 44.40 2.92
449 474 6.169094 ACTTCCAATAGCTATTGATGATCCG 58.831 40.000 37.00 22.80 44.40 4.18
450 475 4.507710 TCCAATAGCTATTGATGATCCGC 58.492 43.478 37.00 0.00 44.40 5.54
521 1622 9.665264 GCCCTATTTCGAGAAAATATGTTTAAG 57.335 33.333 2.17 0.00 38.75 1.85
626 1727 3.311322 TGGCAGTCAACGAGTTTTTACAG 59.689 43.478 0.00 0.00 0.00 2.74
931 2082 0.456653 GCAAATCCGCAATTCGCACT 60.457 50.000 1.75 0.00 42.60 4.40
1827 2978 0.937699 TGTTCGACGGCTTTGACTCG 60.938 55.000 0.00 0.00 0.00 4.18
2029 3180 0.615331 TCCAGGCATTGAGTCCTCAC 59.385 55.000 0.00 0.00 39.66 3.51
2115 3266 0.462581 TCATCACGATGGCAAGCTCC 60.463 55.000 7.17 0.00 39.24 4.70
2479 3630 5.471556 AAGATGATCAGTATGCCAGAGAG 57.528 43.478 0.09 0.00 34.76 3.20
2480 3631 4.738685 AGATGATCAGTATGCCAGAGAGA 58.261 43.478 0.09 0.00 34.76 3.10
2573 3727 2.691011 GTTGTGGCTTGTGTAAAAGGGA 59.309 45.455 0.00 0.00 0.00 4.20
2613 3768 3.402628 TGTACAAAGGTTCAGAGAGGC 57.597 47.619 0.00 0.00 0.00 4.70
2662 3887 7.742556 ACTAATACTACTACCGCTTTCCTAG 57.257 40.000 0.00 0.00 0.00 3.02
2744 3969 6.215636 ACACCCTCTGTTCCTAAATGTAAGAT 59.784 38.462 0.00 0.00 0.00 2.40
2745 3970 7.402071 ACACCCTCTGTTCCTAAATGTAAGATA 59.598 37.037 0.00 0.00 0.00 1.98
2860 4145 6.049149 GCTGGTAATACTGCATTCTGTCTTA 58.951 40.000 0.00 0.00 35.65 2.10
2862 4147 7.307632 GCTGGTAATACTGCATTCTGTCTTATG 60.308 40.741 0.00 0.00 35.65 1.90
2889 4174 8.548025 TGAAATGTTAGATCTCCATTAACTCCA 58.452 33.333 16.65 9.80 0.00 3.86
2905 4190 1.554160 CTCCAGCCAGTTGAGATGTCT 59.446 52.381 0.00 0.00 0.00 3.41
2962 4253 2.752354 TGCAACTGCTGTTTACTGTGTT 59.248 40.909 6.20 0.00 42.66 3.32
2963 4254 3.192422 TGCAACTGCTGTTTACTGTGTTT 59.808 39.130 6.20 0.00 42.66 2.83
2964 4255 3.791353 GCAACTGCTGTTTACTGTGTTTC 59.209 43.478 6.20 0.00 38.21 2.78
2965 4256 4.438744 GCAACTGCTGTTTACTGTGTTTCT 60.439 41.667 6.20 0.00 38.21 2.52
2966 4257 5.266242 CAACTGCTGTTTACTGTGTTTCTC 58.734 41.667 6.20 0.00 33.52 2.87
2967 4258 4.770795 ACTGCTGTTTACTGTGTTTCTCT 58.229 39.130 0.00 0.00 0.00 3.10
3160 4461 2.622942 CACTCATCAGGGCTCTCTAGAC 59.377 54.545 0.00 0.00 0.00 2.59
3163 4464 1.879380 CATCAGGGCTCTCTAGACGAG 59.121 57.143 12.34 12.34 41.30 4.18
3164 4465 1.205055 TCAGGGCTCTCTAGACGAGA 58.795 55.000 18.03 2.51 46.32 4.04
3236 4537 2.186826 GCGGCCGGCATTGATAACT 61.187 57.895 30.85 0.00 42.87 2.24
3304 4605 2.436292 GCTGGTGAGCAGAGCAGG 60.436 66.667 16.83 0.00 45.46 4.85
3337 4638 0.321671 TCCTTTCTGTTGCTCCTCCG 59.678 55.000 0.00 0.00 0.00 4.63
3340 4641 2.124507 TTTCTGTTGCTCCTCCGGGG 62.125 60.000 0.00 0.00 0.00 5.73
3341 4642 3.322466 CTGTTGCTCCTCCGGGGT 61.322 66.667 0.00 0.00 36.25 4.95
3342 4643 3.612247 CTGTTGCTCCTCCGGGGTG 62.612 68.421 0.00 3.52 36.25 4.61
3343 4644 4.410400 GTTGCTCCTCCGGGGTGG 62.410 72.222 0.00 1.12 40.09 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 3.184382 TGTAGGTCCAGATGAGGTTCA 57.816 47.619 0.00 0.00 0.00 3.18
77 78 5.009010 CCATGTCAACATTCCTATTAGGTGC 59.991 44.000 9.57 0.00 33.56 5.01
104 105 4.583871 ACTCCATCTTCCTCATTCACAAC 58.416 43.478 0.00 0.00 0.00 3.32
203 204 6.239232 GCCATCAGATCATTAAGAGCCAAAAT 60.239 38.462 0.00 0.00 31.44 1.82
270 271 7.332926 GGTGATATTGCTATCAACATCTACCTG 59.667 40.741 6.22 0.00 46.89 4.00
280 281 6.204688 GGTTGAATCGGTGATATTGCTATCAA 59.795 38.462 0.00 0.00 44.07 2.57
296 297 1.682451 TAGGAGGCCCGGTTGAATCG 61.682 60.000 0.00 0.00 37.58 3.34
304 305 3.279434 GCATTATTATTAGGAGGCCCGG 58.721 50.000 0.00 0.00 37.58 5.73
305 306 3.941483 CTGCATTATTATTAGGAGGCCCG 59.059 47.826 0.00 0.00 37.58 6.13
307 308 6.348540 CGTTTCTGCATTATTATTAGGAGGCC 60.349 42.308 0.00 0.00 0.00 5.19
310 311 8.491152 CAGACGTTTCTGCATTATTATTAGGAG 58.509 37.037 0.00 0.00 42.99 3.69
347 348 1.813862 GCTATTGGCGCTAATGACCCA 60.814 52.381 27.02 7.44 0.00 4.51
355 356 2.212652 CAACATCTGCTATTGGCGCTA 58.787 47.619 7.64 0.00 45.43 4.26
357 358 0.029834 CCAACATCTGCTATTGGCGC 59.970 55.000 0.00 0.00 45.43 6.53
369 394 6.205658 GGGAATAGCTTATTCAGTCCAACATC 59.794 42.308 14.07 0.00 44.92 3.06
450 475 6.258230 TCTAGTTGTGGAATTGCATTCTTG 57.742 37.500 1.94 4.00 39.24 3.02
626 1727 3.312697 GCTCCGGTACCTTGATGATTTTC 59.687 47.826 10.90 0.00 0.00 2.29
679 1817 7.619571 GCTCGTGATTTTGTACTACTTGTCTTC 60.620 40.741 0.00 0.00 0.00 2.87
830 1973 1.144936 GAGTGGAATGGAGCGGAGG 59.855 63.158 0.00 0.00 0.00 4.30
860 2003 4.779733 GAGGAGAGGGGGCGGTGA 62.780 72.222 0.00 0.00 0.00 4.02
1704 2855 4.731853 TCGGCCAGGTCCCATCCA 62.732 66.667 2.24 0.00 0.00 3.41
1854 3005 1.821332 GATTCCTTCCAGGGCTGCG 60.821 63.158 0.00 0.00 35.59 5.18
1857 3008 1.977293 GCTCGATTCCTTCCAGGGCT 61.977 60.000 0.00 0.00 35.59 5.19
1863 3014 1.012841 CTGCAAGCTCGATTCCTTCC 58.987 55.000 0.00 0.00 0.00 3.46
2029 3180 1.815003 GCAGTCTGGATTCCCAAACAG 59.185 52.381 1.14 0.00 42.98 3.16
2115 3266 4.036027 GCCAATCTGTGAAGTGTCCATATG 59.964 45.833 0.00 0.00 0.00 1.78
2313 3464 0.180171 CCCTGCATTGGATCACCGTA 59.820 55.000 0.00 0.00 39.42 4.02
2479 3630 5.220681 GCAACTTCGATTCTGAGGGTTTATC 60.221 44.000 0.00 0.00 0.00 1.75
2480 3631 4.636206 GCAACTTCGATTCTGAGGGTTTAT 59.364 41.667 0.00 0.00 0.00 1.40
2573 3727 4.127171 ACAACGCTACAATCAAGAACACT 58.873 39.130 0.00 0.00 0.00 3.55
2613 3768 6.287107 ACTCTTTGACAATGTTAGAACACG 57.713 37.500 0.00 0.00 42.51 4.49
2642 3797 7.263496 CAAAACTAGGAAAGCGGTAGTAGTAT 58.737 38.462 0.00 0.00 0.00 2.12
2714 3939 7.336396 ACATTTAGGAACAGAGGGTGTATAAC 58.664 38.462 0.00 0.00 39.03 1.89
2715 3940 7.504926 ACATTTAGGAACAGAGGGTGTATAA 57.495 36.000 0.00 0.00 39.03 0.98
2716 3941 8.612486 TTACATTTAGGAACAGAGGGTGTATA 57.388 34.615 0.00 0.00 39.03 1.47
2717 3942 7.402071 TCTTACATTTAGGAACAGAGGGTGTAT 59.598 37.037 0.00 0.00 39.03 2.29
2718 3943 6.727231 TCTTACATTTAGGAACAGAGGGTGTA 59.273 38.462 0.00 0.00 39.03 2.90
2719 3944 5.546499 TCTTACATTTAGGAACAGAGGGTGT 59.454 40.000 0.00 0.00 43.24 4.16
2720 3945 6.049955 TCTTACATTTAGGAACAGAGGGTG 57.950 41.667 0.00 0.00 0.00 4.61
2721 3946 6.893020 ATCTTACATTTAGGAACAGAGGGT 57.107 37.500 0.00 0.00 0.00 4.34
2860 4145 9.911788 AGTTAATGGAGATCTAACATTTCACAT 57.088 29.630 22.77 7.30 36.36 3.21
2862 4147 8.831550 GGAGTTAATGGAGATCTAACATTTCAC 58.168 37.037 22.77 19.50 36.36 3.18
2876 4161 3.012518 CAACTGGCTGGAGTTAATGGAG 58.987 50.000 0.00 0.00 34.29 3.86
2905 4190 1.377202 GCCCTCAATCAAGACGCCA 60.377 57.895 0.00 0.00 0.00 5.69
2962 4253 3.519510 CCATGTACCCAGGAGAAAGAGAA 59.480 47.826 0.00 0.00 0.00 2.87
2963 4254 3.107601 CCATGTACCCAGGAGAAAGAGA 58.892 50.000 0.00 0.00 0.00 3.10
2964 4255 2.840651 ACCATGTACCCAGGAGAAAGAG 59.159 50.000 2.73 0.00 0.00 2.85
2965 4256 2.915869 ACCATGTACCCAGGAGAAAGA 58.084 47.619 2.73 0.00 0.00 2.52
2966 4257 3.721087 AACCATGTACCCAGGAGAAAG 57.279 47.619 2.73 0.00 0.00 2.62
2967 4258 5.505780 CATTAACCATGTACCCAGGAGAAA 58.494 41.667 2.73 0.00 0.00 2.52
3163 4464 5.396324 GGAAAAGGGAGAAGAAGAGATCCTC 60.396 48.000 0.00 0.00 32.18 3.71
3164 4465 4.473196 GGAAAAGGGAGAAGAAGAGATCCT 59.527 45.833 0.00 0.00 32.18 3.24
3165 4466 4.226168 TGGAAAAGGGAGAAGAAGAGATCC 59.774 45.833 0.00 0.00 0.00 3.36
3166 4467 5.428184 TGGAAAAGGGAGAAGAAGAGATC 57.572 43.478 0.00 0.00 0.00 2.75
3236 4537 2.835580 TTTGTATTGACCGTCCGGAA 57.164 45.000 5.23 0.00 38.96 4.30


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

AutoCloner maintained by Alex Coulton.