Multiple sequence alignment - TraesCS2D01G578000

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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 TraesCS2D01G578000 chr2D 100.000 4314 0 0 1 4314 641063972 641068285 0.000000e+00 7967
1 TraesCS2D01G578000 chr2D 100.000 266 0 0 4729 4994 641068700 641068965 4.490000e-135 492
2 TraesCS2D01G578000 chr2A 96.818 4337 104 14 1 4314 766324516 766328841 0.000000e+00 7214
3 TraesCS2D01G578000 chr2A 96.992 266 8 0 4729 4994 766328896 766329161 9.860000e-122 448
4 TraesCS2D01G578000 chr2B 93.967 4343 203 23 1 4314 800191502 800187190 0.000000e+00 6514
5 TraesCS2D01G578000 chr2B 87.150 607 61 6 1 600 800232625 800232029 0.000000e+00 673
6 TraesCS2D01G578000 chr2B 87.218 266 22 2 4729 4994 800187139 800186886 4.890000e-75 292
7 TraesCS2D01G578000 chr2B 76.772 254 53 6 3 253 326295762 326295512 2.420000e-28 137
8 TraesCS2D01G578000 chr5D 79.459 1110 186 30 617 1712 368367706 368366625 0.000000e+00 749
9 TraesCS2D01G578000 chr5D 83.000 800 125 6 2206 3004 368366527 368365738 0.000000e+00 713
10 TraesCS2D01G578000 chr5D 88.270 503 59 0 3529 4031 368365098 368364596 1.990000e-168 603
11 TraesCS2D01G578000 chr1B 80.684 994 161 22 2004 2983 4522982 4522006 0.000000e+00 743
12 TraesCS2D01G578000 chr1B 79.942 1032 173 23 2004 3022 4813572 4812562 0.000000e+00 728
13 TraesCS2D01G578000 chr1B 82.218 568 79 15 3482 4031 3574561 3573998 2.100000e-128 470
14 TraesCS2D01G578000 chr5B 83.565 791 115 10 2205 2993 436283769 436282992 0.000000e+00 726
15 TraesCS2D01G578000 chr5B 86.453 561 69 6 3474 4031 436282397 436281841 4.270000e-170 608
16 TraesCS2D01G578000 chr5B 73.154 596 132 23 3 584 271179173 271179754 6.600000e-44 189
17 TraesCS2D01G578000 chr5A 84.459 740 108 7 2269 3004 470243372 470242636 0.000000e+00 723
18 TraesCS2D01G578000 chr5A 78.780 1131 185 35 617 1732 470244595 470243505 0.000000e+00 708
19 TraesCS2D01G578000 chr5A 86.275 561 71 5 3474 4031 470226884 470226327 5.530000e-169 604
20 TraesCS2D01G578000 chr5A 86.275 561 71 5 3474 4031 470242015 470241458 5.530000e-169 604
21 TraesCS2D01G578000 chr1A 79.737 987 172 20 2004 2978 2550269 2551239 0.000000e+00 689
22 TraesCS2D01G578000 chr1A 79.095 995 178 18 2004 2983 2848852 2849831 0.000000e+00 658
23 TraesCS2D01G578000 chr1A 82.343 572 94 7 3474 4041 3463075 3462507 1.620000e-134 490
24 TraesCS2D01G578000 chr1A 80.836 574 84 18 3479 4031 2850420 2850988 1.280000e-115 427
25 TraesCS2D01G578000 chr1D 82.042 568 81 14 3482 4031 798210 797646 9.790000e-127 464
26 TraesCS2D01G578000 chr6A 72.987 596 133 27 3 584 85760941 85760360 3.070000e-42 183
27 TraesCS2D01G578000 chr7A 72.819 596 134 27 3 584 171279637 171280218 1.430000e-40 178
28 TraesCS2D01G578000 chr6D 73.653 501 108 18 96 584 458351327 458350839 6.650000e-39 172
29 TraesCS2D01G578000 chr4B 73.653 501 108 22 96 584 629778586 629778098 6.650000e-39 172


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 TraesCS2D01G578000 chr2D 641063972 641068965 4993 False 4229.500000 7967 100.000000 1 4994 2 chr2D.!!$F1 4993
1 TraesCS2D01G578000 chr2A 766324516 766329161 4645 False 3831.000000 7214 96.905000 1 4994 2 chr2A.!!$F1 4993
2 TraesCS2D01G578000 chr2B 800186886 800191502 4616 True 3403.000000 6514 90.592500 1 4994 2 chr2B.!!$R3 4993
3 TraesCS2D01G578000 chr2B 800232029 800232625 596 True 673.000000 673 87.150000 1 600 1 chr2B.!!$R2 599
4 TraesCS2D01G578000 chr5D 368364596 368367706 3110 True 688.333333 749 83.576333 617 4031 3 chr5D.!!$R1 3414
5 TraesCS2D01G578000 chr1B 4522006 4522982 976 True 743.000000 743 80.684000 2004 2983 1 chr1B.!!$R2 979
6 TraesCS2D01G578000 chr1B 4812562 4813572 1010 True 728.000000 728 79.942000 2004 3022 1 chr1B.!!$R3 1018
7 TraesCS2D01G578000 chr1B 3573998 3574561 563 True 470.000000 470 82.218000 3482 4031 1 chr1B.!!$R1 549
8 TraesCS2D01G578000 chr5B 436281841 436283769 1928 True 667.000000 726 85.009000 2205 4031 2 chr5B.!!$R1 1826
9 TraesCS2D01G578000 chr5A 470241458 470244595 3137 True 678.333333 723 83.171333 617 4031 3 chr5A.!!$R2 3414
10 TraesCS2D01G578000 chr5A 470226327 470226884 557 True 604.000000 604 86.275000 3474 4031 1 chr5A.!!$R1 557
11 TraesCS2D01G578000 chr1A 2550269 2551239 970 False 689.000000 689 79.737000 2004 2978 1 chr1A.!!$F1 974
12 TraesCS2D01G578000 chr1A 2848852 2850988 2136 False 542.500000 658 79.965500 2004 4031 2 chr1A.!!$F2 2027
13 TraesCS2D01G578000 chr1A 3462507 3463075 568 True 490.000000 490 82.343000 3474 4041 1 chr1A.!!$R1 567
14 TraesCS2D01G578000 chr1D 797646 798210 564 True 464.000000 464 82.042000 3482 4031 1 chr1D.!!$R1 549

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
66 67 0.686224 CCTGCCATGAGATCCTCCTC 59.314 60.000 0.00 0.0 0.00 3.71 F
398 400 1.133792 CCAACCAGGGTCTTGAAGTGT 60.134 52.381 0.00 0.0 0.00 3.55 F
466 468 1.576577 ACAGATGGCATGACCTCTCA 58.423 50.000 3.81 0.0 40.22 3.27 F
1385 1398 1.608055 TCCAATGCAGAACACCACTG 58.392 50.000 0.00 0.0 38.27 3.66 F
2903 2946 0.537188 GTGGAGCTAAGCTAGTGCCA 59.463 55.000 0.00 0.0 39.88 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 1833 2.744494 GCTCATCACTTTCCTGCCCTAG 60.744 54.545 0.0 0.0 0.00 3.02 R
2259 2289 1.921748 AGGTTCTCCTACGGTCCTACT 59.078 52.381 0.0 0.0 43.12 2.57 R
2448 2480 9.578439 GATTCTTGAGAGTTTTCAATATTTGGG 57.422 33.333 0.0 0.0 36.55 4.12 R
3232 3337 1.041447 GCATCCCTGCCAAATCAGCT 61.041 55.000 0.0 0.0 42.88 4.24 R
4840 5256 2.124693 CCAAGCAACCAACCACGGT 61.125 57.895 0.0 0.0 42.71 4.83 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
66 67 0.686224 CCTGCCATGAGATCCTCCTC 59.314 60.000 0.00 0.00 0.00 3.71
70 71 1.190833 CCATGAGATCCTCCTCCCCG 61.191 65.000 0.00 0.00 32.32 5.73
190 192 2.038952 GGGCATGCATATCACCTCAGTA 59.961 50.000 21.36 0.00 0.00 2.74
279 281 2.613696 CCCCCTCCACACCCATCA 60.614 66.667 0.00 0.00 0.00 3.07
352 354 2.005451 GGTCATGAGCTACAAGTGCAG 58.995 52.381 17.59 0.00 0.00 4.41
384 386 2.902846 CCGTTTGCCGTCCAACCA 60.903 61.111 0.00 0.00 31.97 3.67
398 400 1.133792 CCAACCAGGGTCTTGAAGTGT 60.134 52.381 0.00 0.00 0.00 3.55
407 409 4.072131 GGGTCTTGAAGTGTTGCATCTTA 58.928 43.478 0.00 0.00 0.00 2.10
466 468 1.576577 ACAGATGGCATGACCTCTCA 58.423 50.000 3.81 0.00 40.22 3.27
574 576 4.352893 GAGAAAGGAATCCATTTGGGGAA 58.647 43.478 0.61 0.00 41.12 3.97
601 603 3.119388 CGTGGTTGAACGGTATAGGAAGA 60.119 47.826 0.00 0.00 39.89 2.87
602 604 4.441079 CGTGGTTGAACGGTATAGGAAGAT 60.441 45.833 0.00 0.00 39.89 2.40
851 859 6.531948 AGATGACTACTCGTTAAATGTTGAGC 59.468 38.462 0.00 0.00 31.64 4.26
1069 1080 1.678970 CCTTGCTACCCCACCTTGC 60.679 63.158 0.00 0.00 0.00 4.01
1257 1269 9.661187 AATCATTAGTAACGACTCTACATTACG 57.339 33.333 0.00 0.00 37.10 3.18
1385 1398 1.608055 TCCAATGCAGAACACCACTG 58.392 50.000 0.00 0.00 38.27 3.66
1772 1788 6.303839 ACAAGGTGGTACATAATTGACAACT 58.696 36.000 0.00 0.00 44.52 3.16
1808 1824 6.485171 ACACCTAAATGAACTAGGCTTGAAT 58.515 36.000 2.20 0.00 39.78 2.57
1817 1833 4.965200 ACTAGGCTTGAATCCCTACATC 57.035 45.455 2.20 0.00 32.65 3.06
1909 1925 6.174049 AGAAAGGAACAAAGCCATACTCTAC 58.826 40.000 0.00 0.00 0.00 2.59
1968 1984 4.672587 ATACGCTTCACACCTATCACAT 57.327 40.909 0.00 0.00 0.00 3.21
2017 2037 5.308825 GAGAGGGATAGAGAGAGAGTCAAG 58.691 50.000 0.00 0.00 0.00 3.02
2448 2480 4.457257 GCTGAAATGAGTATATGGGCTTCC 59.543 45.833 0.00 0.00 0.00 3.46
2590 2622 5.845391 ACCTCCAATTCTTTTGAACGAAA 57.155 34.783 0.00 0.00 41.77 3.46
2811 2848 3.884895 TCGACAATAATGCATGTTCCCT 58.115 40.909 0.00 0.00 0.00 4.20
2903 2946 0.537188 GTGGAGCTAAGCTAGTGCCA 59.463 55.000 0.00 0.00 39.88 4.92
3232 3337 4.226384 ACTATGAGGGACATGCATGACTA 58.774 43.478 32.75 13.18 39.77 2.59
3352 3471 6.183360 ACCTATACAATGAAAGTAGCGCAAAC 60.183 38.462 11.47 7.60 0.00 2.93
3576 3800 5.409826 ACTTGCTTATACTCTTCTTGTGCAC 59.590 40.000 10.75 10.75 0.00 4.57
3577 3801 4.253685 TGCTTATACTCTTCTTGTGCACC 58.746 43.478 15.69 0.00 0.00 5.01
3924 4309 9.455847 GATAGGAAAGATTGTTATGATGCAAAC 57.544 33.333 0.00 0.00 0.00 2.93
4210 4626 5.505181 AACACCATATGACTGAACCTCTT 57.495 39.130 3.65 0.00 0.00 2.85
4248 4664 6.183360 GCCATGGAACCTAAGTATAAAACCAC 60.183 42.308 18.40 0.00 0.00 4.16
4840 5256 6.043938 AGGGTGTGAGTTTATAGAACTTTGGA 59.956 38.462 0.00 0.00 0.00 3.53
4916 5332 3.130340 AGTCATGGTGTTGTTTTGGTCAC 59.870 43.478 0.00 0.00 0.00 3.67
4920 5336 1.202211 GGTGTTGTTTTGGTCACGTCC 60.202 52.381 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 0.402121 GGAGGCCCAACTATCCCATC 59.598 60.000 0.00 0.00 0.00 3.51
190 192 2.332312 TAACAAGTGCACCGTGGCCT 62.332 55.000 14.63 4.34 0.00 5.19
279 281 3.262660 TCAGTCTTGGTCATGCTCTTGAT 59.737 43.478 0.00 0.00 0.00 2.57
344 346 2.524306 TCCCAATTTACCCTGCACTTG 58.476 47.619 0.00 0.00 0.00 3.16
352 354 3.655486 CAAACGGTTTCCCAATTTACCC 58.345 45.455 2.51 0.00 0.00 3.69
384 386 2.107204 AGATGCAACACTTCAAGACCCT 59.893 45.455 0.00 0.00 0.00 4.34
398 400 6.349280 GCTCTACCAAATGTGTTAAGATGCAA 60.349 38.462 0.00 0.00 0.00 4.08
407 409 4.573900 CAGAGAGCTCTACCAAATGTGTT 58.426 43.478 18.25 0.00 37.98 3.32
466 468 2.158827 GCCTGAACCAACCCAAATGTTT 60.159 45.455 0.00 0.00 0.00 2.83
722 728 9.295825 CCAATTAATGATTGCTTGGTACCTATA 57.704 33.333 14.36 0.00 43.11 1.31
851 859 9.605955 TTTAAATGGCATCGTATTAATGATTCG 57.394 29.630 0.00 0.00 0.00 3.34
1069 1080 7.812690 TTCCATCCATGTCTATTGATTCAAG 57.187 36.000 5.21 0.00 0.00 3.02
1257 1269 9.850628 GTCCTAAAATTTTAGTTGGGAACATAC 57.149 33.333 27.93 10.38 36.30 2.39
1309 1321 5.849510 TGACATACAAAGTCTCCGAAAGAA 58.150 37.500 0.00 0.00 35.21 2.52
1385 1398 8.900511 AACTGAAAACGTTTAGGACTTAAAAC 57.099 30.769 15.03 0.00 33.22 2.43
1676 1691 7.654520 GGTGGATCATTAATGAATGTGGATTTG 59.345 37.037 21.50 0.00 42.71 2.32
1772 1788 9.084533 AGTTCATTTAGGTGTATGCCTTTTTAA 57.915 29.630 0.00 0.00 39.94 1.52
1817 1833 2.744494 GCTCATCACTTTCCTGCCCTAG 60.744 54.545 0.00 0.00 0.00 3.02
1825 1841 6.012658 TGTTTACAATGCTCATCACTTTCC 57.987 37.500 0.00 0.00 0.00 3.13
1909 1925 4.125703 GGCATGTGAGGATAAGTCTCAAG 58.874 47.826 0.00 0.00 42.13 3.02
1968 1984 9.442062 CCCTCTCTCTCTATCTACATATACCTA 57.558 40.741 0.00 0.00 0.00 3.08
1977 1993 4.225267 CCCTCTCCCTCTCTCTCTATCTAC 59.775 54.167 0.00 0.00 0.00 2.59
2017 2037 3.830178 ACATAGCAGGGGTAAAACCAAAC 59.170 43.478 0.00 0.00 41.02 2.93
2117 2142 6.245408 TCCTATGCAATTAGACCTTTTGTGT 58.755 36.000 0.00 0.00 0.00 3.72
2259 2289 1.921748 AGGTTCTCCTACGGTCCTACT 59.078 52.381 0.00 0.00 43.12 2.57
2448 2480 9.578439 GATTCTTGAGAGTTTTCAATATTTGGG 57.422 33.333 0.00 0.00 36.55 4.12
2874 2917 1.137872 CTTAGCTCCACTCGCAGGAAT 59.862 52.381 0.00 0.00 34.08 3.01
3143 3247 4.124851 GTGTTGGACACTCGGAGAATAT 57.875 45.455 12.86 0.00 45.27 1.28
3232 3337 1.041447 GCATCCCTGCCAAATCAGCT 61.041 55.000 0.00 0.00 42.88 4.24
3352 3471 9.436957 AGTCATGTATGGTAGTTCTAAGTTTTG 57.563 33.333 0.00 0.00 0.00 2.44
3523 3746 4.261578 AGCAAAAATCTTGGGTGACATG 57.738 40.909 0.00 0.00 0.00 3.21
3638 3862 0.035739 ATGACGGTACACCACCCAAC 59.964 55.000 0.00 0.00 45.52 3.77
3924 4309 9.651718 CCCTTCTTAAATTCGAGAAATAAATCG 57.348 33.333 5.34 0.00 40.26 3.34
4248 4664 9.896645 ATAGGGATAATATGCACATTTACTCTG 57.103 33.333 0.00 0.00 0.00 3.35
4840 5256 2.124693 CCAAGCAACCAACCACGGT 61.125 57.895 0.00 0.00 42.71 4.83
4920 5336 7.518370 CGAAACGACCATTCCATCCTTTATAAG 60.518 40.741 0.00 0.00 0.00 1.73
4933 5349 2.571206 GCAGAAACGAAACGACCATTC 58.429 47.619 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.