Multiple sequence alignment - TraesCS6D01G199800

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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 TraesCS6D01G199800 chr6D 100.000 5001 0 0 1 5001 277669076 277674076 0.000000e+00 9236.0
1 TraesCS6D01G199800 chr6D 100.000 35 0 0 2439 2473 277671480 277671514 1.160000e-06 65.8
2 TraesCS6D01G199800 chr6A 96.689 2507 56 2 2495 5001 400122604 400125083 0.000000e+00 4145.0
3 TraesCS6D01G199800 chr6A 96.149 1714 52 2 730 2429 400120891 400122604 0.000000e+00 2787.0
4 TraesCS6D01G199800 chr6A 89.628 752 40 16 1 720 400119942 400120687 0.000000e+00 922.0
5 TraesCS6D01G199800 chr6B 96.867 2330 52 9 2677 5001 439401655 439403968 0.000000e+00 3879.0
6 TraesCS6D01G199800 chr6B 96.838 1929 45 8 132 2054 439397798 439399716 0.000000e+00 3210.0
7 TraesCS6D01G199800 chr6B 97.264 402 11 0 2038 2439 439399886 439400287 0.000000e+00 682.0
8 TraesCS6D01G199800 chr6B 98.319 238 4 0 2439 2676 439400253 439400490 7.740000e-113 418.0
9 TraesCS6D01G199800 chr6B 88.587 184 12 3 2214 2397 446847829 446848003 1.090000e-51 215.0
10 TraesCS6D01G199800 chr4D 90.726 248 21 2 2192 2439 233099226 233098981 3.730000e-86 329.0
11 TraesCS6D01G199800 chr3B 90.400 250 22 2 2191 2439 341226550 341226798 1.340000e-85 327.0
12 TraesCS6D01G199800 chr3B 80.100 201 21 2 2192 2392 417729945 417730126 1.130000e-26 132.0
13 TraesCS6D01G199800 chrUn 91.964 224 18 0 2192 2415 53802989 53802766 1.050000e-81 315.0
14 TraesCS6D01G199800 chr2A 87.739 261 24 4 2186 2439 216538054 216538313 1.050000e-76 298.0
15 TraesCS6D01G199800 chr1D 88.306 248 26 3 2192 2439 449669905 449670149 1.360000e-75 294.0
16 TraesCS6D01G199800 chr3D 88.000 250 24 3 2191 2439 239612381 239612625 1.760000e-74 291.0
17 TraesCS6D01G199800 chr5B 87.200 250 32 0 2193 2442 211143342 211143093 8.190000e-73 285.0
18 TraesCS6D01G199800 chr2B 90.000 50 5 0 2439 2488 435828742 435828693 1.160000e-06 65.8
19 TraesCS6D01G199800 chr2B 97.222 36 1 0 2453 2488 695598281 695598316 1.500000e-05 62.1


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 TraesCS6D01G199800 chr6D 277669076 277674076 5000 False 4650.90 9236 100.000000 1 5001 2 chr6D.!!$F1 5000
1 TraesCS6D01G199800 chr6A 400119942 400125083 5141 False 2618.00 4145 94.155333 1 5001 3 chr6A.!!$F1 5000
2 TraesCS6D01G199800 chr6B 439397798 439403968 6170 False 2047.25 3879 97.322000 132 5001 4 chr6B.!!$F2 4869

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
183 212 0.329596 GAGTCCCCAATTGCTCCAGT 59.670 55.0 0.00 0.0 0.00 4.00 F
244 277 0.827925 TCAGGTGGTCTCTTCAGCGT 60.828 55.0 0.00 0.0 37.66 5.07 F
2370 2814 0.597637 CGAGTGAGGACAAAGTGCGT 60.598 55.0 0.00 0.0 0.00 5.24 F
2456 2900 0.811616 GTAGATCCCAGGCGCAACAG 60.812 60.0 10.83 0.0 0.00 3.16 F
3644 5253 0.457337 CGCAAGCAGCCTCCAAATTC 60.457 55.0 0.00 0.0 41.38 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1630 1887 0.964358 AGCTTGAATGGGCAGACAGC 60.964 55.000 0.00 0.0 44.65 4.40 R
2372 2816 6.154021 TCCCATAGACCAACACTAGTCTTTAC 59.846 42.308 0.00 0.0 40.43 2.01 R
3499 5108 1.268999 GCACACAAAATGCTTCCGACA 60.269 47.619 0.00 0.0 40.08 4.35 R
3770 5379 2.407562 TGGAGGCTGCCAGTGATTATA 58.592 47.619 22.65 0.0 33.10 0.98 R
4733 6343 2.232941 TGTACCCTTCTGGACACGATTC 59.767 50.000 0.00 0.0 38.00 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
83 112 3.130516 TCCTATCGACAGATTGTCCACAC 59.869 47.826 0.00 0.00 44.20 3.82
103 132 0.746923 GGTCCAAATAGACGTGGCCC 60.747 60.000 0.00 0.00 37.66 5.80
128 157 2.365370 AGAGCCCAGAGCCCAGAG 60.365 66.667 0.00 0.00 45.47 3.35
181 210 1.299648 CGAGTCCCCAATTGCTCCA 59.700 57.895 0.00 0.00 0.00 3.86
183 212 0.329596 GAGTCCCCAATTGCTCCAGT 59.670 55.000 0.00 0.00 0.00 4.00
244 277 0.827925 TCAGGTGGTCTCTTCAGCGT 60.828 55.000 0.00 0.00 37.66 5.07
266 299 0.938637 CATCGGATCGCTGCAGTCTC 60.939 60.000 16.64 9.45 0.00 3.36
334 372 2.966309 GCGGCTCGTGGACTTTTGG 61.966 63.158 0.00 0.00 0.00 3.28
479 517 6.650807 TCGAATGCCTCATTATTTCATCTACC 59.349 38.462 0.00 0.00 33.90 3.18
490 528 3.746045 TTCATCTACCTTGCGGGATAC 57.254 47.619 2.42 0.00 38.76 2.24
581 620 7.243487 CGTAGTACTGTAGTTGGAATTTCGTA 58.757 38.462 5.39 0.00 0.00 3.43
721 770 9.912634 AAAACATTCTGTTGTTCCAATATACAG 57.087 29.630 0.00 0.00 40.14 2.74
818 1062 9.017509 TGCACTCTTCAAAGATAATTTGAATCT 57.982 29.630 14.22 0.77 44.41 2.40
866 1110 6.521527 AGGATCTTAGATTGCATTAGGGTT 57.478 37.500 0.00 0.00 0.00 4.11
1046 1303 6.777580 TCAGAGGACAAAGGCTTAAATTTTCT 59.222 34.615 0.00 0.00 0.00 2.52
1063 1320 5.784750 TTTTCTGTGCAATCTATCTGACG 57.215 39.130 0.00 0.00 0.00 4.35
1202 1459 3.637229 ACCGAACTATCAGGGTACATGAG 59.363 47.826 0.00 0.00 0.00 2.90
1228 1485 2.808543 AGATCTGAAACACTTGTTCGCC 59.191 45.455 0.00 0.00 37.25 5.54
1616 1873 6.917217 AGCTTCTTTCTGTGCTATTCATAC 57.083 37.500 0.00 0.00 33.64 2.39
1630 1887 4.536364 ATTCATACCGAAAAGCATGACG 57.464 40.909 0.00 0.00 37.12 4.35
2202 2646 1.675007 TTGGGGTATGTGACATCCCA 58.325 50.000 24.56 21.79 45.06 4.37
2370 2814 0.597637 CGAGTGAGGACAAAGTGCGT 60.598 55.000 0.00 0.00 0.00 5.24
2372 2816 2.329379 GAGTGAGGACAAAGTGCGTAG 58.671 52.381 0.00 0.00 0.00 3.51
2392 2836 6.128172 GCGTAGTAAAGACTAGTGTTGGTCTA 60.128 42.308 5.96 6.83 43.50 2.59
2397 2841 4.332683 AGACTAGTGTTGGTCTATGGGA 57.667 45.455 0.00 0.00 42.61 4.37
2421 2865 0.975556 TCTAGATCCCAGGCGCAACA 60.976 55.000 10.83 0.00 0.00 3.33
2453 2897 2.908015 GGTAGATCCCAGGCGCAA 59.092 61.111 10.83 0.00 0.00 4.85
2454 2898 1.523938 GGTAGATCCCAGGCGCAAC 60.524 63.158 10.83 0.00 0.00 4.17
2455 2899 1.220749 GTAGATCCCAGGCGCAACA 59.779 57.895 10.83 0.00 0.00 3.33
2456 2900 0.811616 GTAGATCCCAGGCGCAACAG 60.812 60.000 10.83 0.00 0.00 3.16
2457 2901 2.593468 TAGATCCCAGGCGCAACAGC 62.593 60.000 10.83 0.00 0.00 4.40
2465 2909 4.043200 GCGCAACAGCCAGGAACC 62.043 66.667 0.30 0.00 0.00 3.62
2466 2910 3.726517 CGCAACAGCCAGGAACCG 61.727 66.667 0.00 0.00 0.00 4.44
2467 2911 3.365265 GCAACAGCCAGGAACCGG 61.365 66.667 0.00 0.00 0.00 5.28
2468 2912 2.113139 CAACAGCCAGGAACCGGT 59.887 61.111 0.00 0.00 0.00 5.28
2469 2913 2.113139 AACAGCCAGGAACCGGTG 59.887 61.111 8.52 0.00 33.58 4.94
2470 2914 3.491598 AACAGCCAGGAACCGGTGG 62.492 63.158 8.52 6.07 36.85 4.61
2471 2915 4.722700 CAGCCAGGAACCGGTGGG 62.723 72.222 8.52 9.33 40.11 4.61
2557 3001 8.483758 AGTTTGGTTCAGTTTCTTAGAGAGTTA 58.516 33.333 0.00 0.00 0.00 2.24
2700 4308 4.760204 CCCTCGGTTTTGTCTTAAAGTGAT 59.240 41.667 0.00 0.00 0.00 3.06
2833 4441 9.990868 ACATTACAAAGAGGGTAATATTTCCTT 57.009 29.630 10.57 3.35 38.91 3.36
3125 4733 7.830099 AACAAGGATGAAGAAACTTGAGAAT 57.170 32.000 9.90 0.00 42.07 2.40
3299 4907 9.740710 AATATAGGTTGTAGAAAAGTCAGCTTT 57.259 29.630 0.00 0.00 46.01 3.51
3326 4934 9.577110 TTTTCAGATCAGTTGATAATTTGATGC 57.423 29.630 0.00 0.00 34.37 3.91
3499 5108 4.843728 TCCTTCTCAACAGTCAACACTTT 58.156 39.130 0.00 0.00 0.00 2.66
3520 5129 1.028130 TCGGAAGCATTTTGTGTGCA 58.972 45.000 0.69 0.00 44.87 4.57
3644 5253 0.457337 CGCAAGCAGCCTCCAAATTC 60.457 55.000 0.00 0.00 41.38 2.17
3698 5307 5.865552 CAGAAATATGCAGGTGGTTTTCTTG 59.134 40.000 0.00 0.00 32.65 3.02
3770 5379 2.325583 TTTGACTCAGCTTTGACGGT 57.674 45.000 0.00 0.00 0.00 4.83
4108 5717 8.442632 TGAAATAACTTCTGAATGCTGGATAG 57.557 34.615 0.00 0.00 34.86 2.08
4138 5747 4.398044 ACAGTTATTATTCAAAGTGGGCGG 59.602 41.667 0.00 0.00 31.60 6.13
4519 6128 1.661341 CATCAGCTACAGTTGGCCTC 58.339 55.000 3.32 0.00 0.00 4.70
4725 6335 4.956075 CACAATTAACTGAAAGGGGGCTAT 59.044 41.667 0.00 0.00 39.30 2.97
4733 6343 3.815401 CTGAAAGGGGGCTATCGTTATTG 59.185 47.826 0.00 0.00 0.00 1.90
4751 6361 1.348064 TGAATCGTGTCCAGAAGGGT 58.652 50.000 0.00 0.00 38.11 4.34
4948 6561 8.139989 AGATGCTTGCATTAAAGGATGAAATAC 58.860 33.333 9.59 0.00 38.22 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 112 1.087771 GGCCACGTCTATTTGGACCG 61.088 60.000 0.00 0.00 34.39 4.79
111 140 2.365370 CTCTGGGCTCTGGGCTCT 60.365 66.667 0.00 0.00 43.07 4.09
112 141 4.173924 GCTCTGGGCTCTGGGCTC 62.174 72.222 8.30 0.00 42.93 4.70
128 157 4.436998 CCCGTGACGACCCTCAGC 62.437 72.222 6.54 0.00 0.00 4.26
130 159 4.988716 AGCCCGTGACGACCCTCA 62.989 66.667 6.54 0.00 0.00 3.86
181 210 4.035102 GCCGGGGAGCAGGAAACT 62.035 66.667 2.18 0.00 46.44 2.66
244 277 1.227350 CTGCAGCGATCCGATGGAA 60.227 57.895 0.00 0.00 43.43 3.53
334 372 1.587547 GATCCACCGGAAATCAGAGC 58.412 55.000 9.46 0.00 34.34 4.09
374 412 2.220133 CGTGACAACAAACTAACCTCGG 59.780 50.000 0.00 0.00 0.00 4.63
386 424 0.249868 CAGAAGCCTCCGTGACAACA 60.250 55.000 0.00 0.00 0.00 3.33
479 517 3.802948 ACTGAGTTAGTATCCCGCAAG 57.197 47.619 0.00 0.00 38.04 4.01
490 528 5.233225 TCACTCAATCAGCAACTGAGTTAG 58.767 41.667 0.00 4.33 45.85 2.34
818 1062 1.552792 TCAACACGATCCACTATGGCA 59.447 47.619 0.00 0.00 37.47 4.92
1046 1303 4.036852 CCTCTACGTCAGATAGATTGCACA 59.963 45.833 0.00 0.00 31.13 4.57
1063 1320 4.275196 TGTCATGCTATGTACGACCTCTAC 59.725 45.833 0.00 0.00 0.00 2.59
1228 1485 2.354503 CCTCGCCTCCATCCATAGATTG 60.355 54.545 0.00 0.00 0.00 2.67
1630 1887 0.964358 AGCTTGAATGGGCAGACAGC 60.964 55.000 0.00 0.00 44.65 4.40
2370 2814 7.341256 CCCATAGACCAACACTAGTCTTTACTA 59.659 40.741 0.00 0.00 40.43 1.82
2372 2816 6.154021 TCCCATAGACCAACACTAGTCTTTAC 59.846 42.308 0.00 0.00 40.43 2.01
2397 2841 0.757188 CGCCTGGGATCTAGACTGGT 60.757 60.000 0.00 0.00 0.00 4.00
2421 2865 3.857521 TACCCACCGGTTCCTGGCT 62.858 63.158 2.97 0.00 40.58 4.75
2439 2883 2.270205 CTGTTGCGCCTGGGATCT 59.730 61.111 4.18 0.00 0.00 2.75
2440 2884 3.512516 GCTGTTGCGCCTGGGATC 61.513 66.667 4.18 0.00 0.00 3.36
2448 2892 4.043200 GGTTCCTGGCTGTTGCGC 62.043 66.667 0.00 0.00 40.82 6.09
2449 2893 3.726517 CGGTTCCTGGCTGTTGCG 61.727 66.667 0.00 0.00 40.82 4.85
2450 2894 3.365265 CCGGTTCCTGGCTGTTGC 61.365 66.667 0.00 0.00 38.76 4.17
2451 2895 2.113139 ACCGGTTCCTGGCTGTTG 59.887 61.111 0.00 0.00 0.00 3.33
2452 2896 2.113139 CACCGGTTCCTGGCTGTT 59.887 61.111 2.97 0.00 0.00 3.16
2453 2897 3.953775 CCACCGGTTCCTGGCTGT 61.954 66.667 2.97 0.00 0.00 4.40
2454 2898 4.722700 CCCACCGGTTCCTGGCTG 62.723 72.222 2.97 0.00 0.00 4.85
2471 2915 3.436924 CTAACGCCCCGGCCAAAC 61.437 66.667 2.24 0.00 37.98 2.93
2472 2916 3.615509 CTCTAACGCCCCGGCCAAA 62.616 63.158 2.24 0.00 37.98 3.28
2473 2917 4.090588 CTCTAACGCCCCGGCCAA 62.091 66.667 2.24 0.00 37.98 4.52
2480 2924 3.488216 CGTAGAAGTTACCTCTAACGCCC 60.488 52.174 0.00 0.00 37.85 6.13
2830 4438 6.142818 TCAACAATTACAACTTGGTGAAGG 57.857 37.500 1.51 0.00 44.91 3.46
2833 4441 6.549364 AGGATTCAACAATTACAACTTGGTGA 59.451 34.615 0.00 0.00 45.89 4.02
3125 4733 7.119709 TCATTATTTCCGTGACCTAAGATCA 57.880 36.000 0.00 0.00 0.00 2.92
3499 5108 1.268999 GCACACAAAATGCTTCCGACA 60.269 47.619 0.00 0.00 40.08 4.35
3644 5253 6.605849 GCATACATACAGGACATATTTGCAG 58.394 40.000 0.00 0.00 0.00 4.41
3698 5307 2.736721 TCTTCAGCATAACGAACTGCAC 59.263 45.455 9.70 0.00 40.88 4.57
3770 5379 2.407562 TGGAGGCTGCCAGTGATTATA 58.592 47.619 22.65 0.00 33.10 0.98
4021 5630 3.556999 TGAAAGAACAAAATGTCCGGGA 58.443 40.909 0.00 0.00 0.00 5.14
4138 5747 7.224297 TGGCATAGTTTAGGATTCTAACCATC 58.776 38.462 0.00 0.00 35.40 3.51
4425 6034 5.934043 TCTAGTTCAACATGTCAAGTGGATG 59.066 40.000 0.00 0.00 0.00 3.51
4519 6128 9.774413 AGTAGATACGTAAATATTTTTCCCTGG 57.226 33.333 5.91 0.00 0.00 4.45
4725 6335 4.443913 TCTGGACACGATTCAATAACGA 57.556 40.909 0.00 0.00 0.00 3.85
4733 6343 2.232941 TGTACCCTTCTGGACACGATTC 59.767 50.000 0.00 0.00 38.00 2.52
4796 6409 6.053650 ACATCCATGATTCTGACATGTAGTG 58.946 40.000 0.00 0.00 42.16 2.74


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

AutoCloner maintained by Alex Coulton.