Multiple sequence alignment - TraesCS3D01G200500

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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 TraesCS3D01G200500 chr3D 100.000 2474 0 0 1 2474 231173936 231171463 0.000000e+00 4569.0
1 TraesCS3D01G200500 chr3D 96.437 421 14 1 213 633 231187570 231187151 0.000000e+00 693.0
2 TraesCS3D01G200500 chr3D 94.068 236 8 2 634 864 519327490 519327724 1.090000e-93 353.0
3 TraesCS3D01G200500 chr3D 98.246 57 1 0 1932 1988 231171958 231171902 1.570000e-17 100.0
4 TraesCS3D01G200500 chr3D 98.246 57 1 0 1979 2035 231172005 231171949 1.570000e-17 100.0
5 TraesCS3D01G200500 chr2A 93.157 643 33 7 1 633 511248695 511248054 0.000000e+00 933.0
6 TraesCS3D01G200500 chr2A 91.602 643 43 6 1 633 511265186 511264545 0.000000e+00 878.0
7 TraesCS3D01G200500 chr2A 97.436 39 1 0 2436 2474 511248043 511248005 1.590000e-07 67.6
8 TraesCS3D01G200500 chr2A 97.436 39 1 0 2436 2474 511264534 511264496 1.590000e-07 67.6
9 TraesCS3D01G200500 chr1D 94.205 604 8 1 1412 1988 302925782 302926385 0.000000e+00 896.0
10 TraesCS3D01G200500 chr1D 91.252 583 16 12 875 1428 302927105 302926529 0.000000e+00 761.0
11 TraesCS3D01G200500 chr1D 96.444 225 8 0 1979 2203 302926329 302926553 3.000000e-99 372.0
12 TraesCS3D01G200500 chr1D 96.244 213 6 1 2212 2422 359696761 359696549 5.060000e-92 348.0
13 TraesCS3D01G200500 chr1D 95.455 220 6 3 2212 2427 359714475 359714694 5.060000e-92 348.0
14 TraesCS3D01G200500 chr1B 93.805 565 21 5 875 1428 409838492 409837931 0.000000e+00 837.0
15 TraesCS3D01G200500 chr1B 91.914 606 20 2 1412 1988 409837182 409837787 0.000000e+00 821.0
16 TraesCS3D01G200500 chr1B 85.637 369 42 9 144 503 313275590 313275956 6.460000e-101 377.0
17 TraesCS3D01G200500 chr1B 93.421 228 15 0 1976 2203 409837728 409837955 3.050000e-89 339.0
18 TraesCS3D01G200500 chr1B 94.009 217 10 2 2211 2424 83627447 83627231 2.370000e-85 326.0
19 TraesCS3D01G200500 chr1B 96.825 63 2 0 1533 1595 626422427 626422365 3.360000e-19 106.0
20 TraesCS3D01G200500 chr1B 97.368 38 0 1 1601 1638 626422371 626422335 2.050000e-06 63.9
21 TraesCS3D01G200500 chr1A 91.626 609 18 4 1413 1988 380262886 380263494 0.000000e+00 811.0
22 TraesCS3D01G200500 chr1A 89.555 584 22 17 875 1428 380264212 380263638 0.000000e+00 704.0
23 TraesCS3D01G200500 chr1A 94.515 237 13 0 1967 2203 380263426 380263662 1.400000e-97 366.0
24 TraesCS3D01G200500 chr7B 92.216 501 33 6 136 633 355732990 355733487 0.000000e+00 704.0
25 TraesCS3D01G200500 chr7B 91.816 501 35 6 136 633 355723416 355723913 0.000000e+00 693.0
26 TraesCS3D01G200500 chr7B 94.118 102 5 1 1537 1638 643391671 643391571 1.180000e-33 154.0
27 TraesCS3D01G200500 chr7B 100.000 52 0 0 2423 2474 355733479 355733530 2.030000e-16 97.1
28 TraesCS3D01G200500 chr7B 98.077 52 1 0 2423 2474 355723905 355723956 9.420000e-15 91.6
29 TraesCS3D01G200500 chr6B 88.627 466 41 7 136 593 29217417 29216956 7.730000e-155 556.0
30 TraesCS3D01G200500 chr5A 89.679 436 31 8 202 633 580532886 580533311 6.020000e-151 544.0
31 TraesCS3D01G200500 chr5A 85.401 274 17 12 618 872 644861534 644861803 1.890000e-66 263.0
32 TraesCS3D01G200500 chr5A 93.478 46 1 2 2429 2474 580533317 580533360 1.590000e-07 67.6
33 TraesCS3D01G200500 chr7D 90.698 387 24 8 1039 1413 501383156 501383542 2.840000e-139 505.0
34 TraesCS3D01G200500 chr7D 85.433 508 45 10 134 633 309305171 309304685 3.670000e-138 501.0
35 TraesCS3D01G200500 chr7D 90.206 388 25 7 1039 1414 501384400 501384786 6.150000e-136 494.0
36 TraesCS3D01G200500 chr7D 84.554 505 53 14 134 633 309326737 309326253 6.190000e-131 477.0
37 TraesCS3D01G200500 chr7D 87.719 171 21 0 2033 2203 501383705 501383535 1.500000e-47 200.0
38 TraesCS3D01G200500 chr7D 100.000 39 0 0 2436 2474 309304674 309304636 3.410000e-09 73.1
39 TraesCS3D01G200500 chr6D 96.311 244 3 3 634 872 454293754 454293512 1.780000e-106 396.0
40 TraesCS3D01G200500 chr6D 93.220 236 10 2 634 864 454277073 454277307 2.360000e-90 342.0
41 TraesCS3D01G200500 chr5D 96.347 219 4 3 2212 2427 532658161 532658378 8.410000e-95 357.0
42 TraesCS3D01G200500 chr5D 96.262 214 6 2 2212 2423 387823712 387823925 1.410000e-92 350.0
43 TraesCS3D01G200500 chr5D 94.931 217 8 2 2212 2425 387815292 387815076 1.100000e-88 337.0
44 TraesCS3D01G200500 chr5D 93.450 229 9 2 633 856 532654432 532654659 3.940000e-88 335.0
45 TraesCS3D01G200500 chr5B 92.373 236 13 1 632 862 663517258 663517493 5.100000e-87 331.0
46 TraesCS3D01G200500 chr2D 94.860 214 8 2 2212 2422 60184026 60184239 5.100000e-87 331.0
47 TraesCS3D01G200500 chr2D 92.050 239 13 2 634 867 651700922 651701159 5.100000e-87 331.0
48 TraesCS3D01G200500 chr2D 93.981 216 10 2 2212 2424 60175205 60174990 8.530000e-85 324.0
49 TraesCS3D01G200500 chr2B 91.020 245 14 5 634 872 438613144 438612902 8.530000e-85 324.0
50 TraesCS3D01G200500 chr6A 91.561 237 15 4 2212 2444 66266821 66266586 3.070000e-84 322.0
51 TraesCS3D01G200500 chr4B 91.176 238 15 2 630 862 310957847 310958083 3.970000e-83 318.0
52 TraesCS3D01G200500 chr3A 90.283 247 15 4 634 872 619069950 619070195 5.140000e-82 315.0
53 TraesCS3D01G200500 chr3B 95.283 106 4 1 1533 1638 23381649 23381753 1.520000e-37 167.0


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 TraesCS3D01G200500 chr3D 231171463 231173936 2473 True 1589.666667 4569 98.830667 1 2474 3 chr3D.!!$R2 2473
1 TraesCS3D01G200500 chr2A 511248005 511248695 690 True 500.300000 933 95.296500 1 2474 2 chr2A.!!$R1 2473
2 TraesCS3D01G200500 chr2A 511264496 511265186 690 True 472.800000 878 94.519000 1 2474 2 chr2A.!!$R2 2473
3 TraesCS3D01G200500 chr1D 302926529 302927105 576 True 761.000000 761 91.252000 875 1428 1 chr1D.!!$R1 553
4 TraesCS3D01G200500 chr1D 302925782 302926553 771 False 634.000000 896 95.324500 1412 2203 2 chr1D.!!$F2 791
5 TraesCS3D01G200500 chr1B 409837931 409838492 561 True 837.000000 837 93.805000 875 1428 1 chr1B.!!$R2 553
6 TraesCS3D01G200500 chr1B 409837182 409837955 773 False 580.000000 821 92.667500 1412 2203 2 chr1B.!!$F2 791
7 TraesCS3D01G200500 chr1A 380263638 380264212 574 True 704.000000 704 89.555000 875 1428 1 chr1A.!!$R1 553
8 TraesCS3D01G200500 chr1A 380262886 380263662 776 False 588.500000 811 93.070500 1413 2203 2 chr1A.!!$F1 790
9 TraesCS3D01G200500 chr7B 355732990 355733530 540 False 400.550000 704 96.108000 136 2474 2 chr7B.!!$F2 2338
10 TraesCS3D01G200500 chr7B 355723416 355723956 540 False 392.300000 693 94.946500 136 2474 2 chr7B.!!$F1 2338
11 TraesCS3D01G200500 chr7D 501383156 501384786 1630 False 499.500000 505 90.452000 1039 1414 2 chr7D.!!$F1 375
12 TraesCS3D01G200500 chr7D 309304636 309305171 535 True 287.050000 501 92.716500 134 2474 2 chr7D.!!$R3 2340
13 TraesCS3D01G200500 chr5D 532654432 532658378 3946 False 346.000000 357 94.898500 633 2427 2 chr5D.!!$F2 1794

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
838 856 0.605319 TGAATCAACCCGCAGTCACC 60.605 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2207 5910 0.036164 TCCCTGAATCAACCCGTGTG 59.964 55.0 0.0 0.0 0.0 3.82 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
26 27 3.428870 CAGAACACACGTACATGTCTTCC 59.571 47.826 0.00 0.00 30.27 3.46
125 126 1.202651 CCGGACCTCTCTCTCTCTCTC 60.203 61.905 0.00 0.00 0.00 3.20
126 127 1.762957 CGGACCTCTCTCTCTCTCTCT 59.237 57.143 0.00 0.00 0.00 3.10
200 207 5.284079 GTTCTTGTTGTGCTGTGATTCATT 58.716 37.500 0.00 0.00 0.00 2.57
235 242 4.922026 GCCGGTGTTGGTGTCCGT 62.922 66.667 1.90 0.00 42.30 4.69
436 449 4.155826 TGCAAGATGTTGGTGTACTAATGC 59.844 41.667 4.57 0.00 33.87 3.56
508 521 6.364165 CCATGCTTTCTTGTACTGTTGATTTG 59.636 38.462 0.00 0.00 0.00 2.32
570 583 2.916640 TGTGTGCATCTGTGAAGAACA 58.083 42.857 0.00 0.00 37.22 3.18
590 603 5.772393 ACAAGTGAGGAATATTGTGGGTA 57.228 39.130 0.00 0.00 34.71 3.69
706 724 3.595173 AGTTGCAAAACTTGACCAAACC 58.405 40.909 0.00 0.00 0.00 3.27
724 742 1.640670 ACCATACCCCAACTTGCATCT 59.359 47.619 0.00 0.00 0.00 2.90
816 834 1.365999 CAAAACCCCCTGCCGTTTC 59.634 57.895 0.00 0.00 31.09 2.78
818 836 2.306715 AAAACCCCCTGCCGTTTCCT 62.307 55.000 0.00 0.00 31.09 3.36
835 853 0.804989 CCTTGAATCAACCCGCAGTC 59.195 55.000 0.00 0.00 0.00 3.51
836 854 1.522668 CTTGAATCAACCCGCAGTCA 58.477 50.000 0.00 0.00 0.00 3.41
837 855 1.197721 CTTGAATCAACCCGCAGTCAC 59.802 52.381 0.00 0.00 0.00 3.67
838 856 0.605319 TGAATCAACCCGCAGTCACC 60.605 55.000 0.00 0.00 0.00 4.02
840 858 2.764637 AATCAACCCGCAGTCACCCC 62.765 60.000 0.00 0.00 0.00 4.95
859 877 3.981212 CCCCCACCTGAATTAAATCTGT 58.019 45.455 0.00 0.00 0.00 3.41
860 878 3.954258 CCCCCACCTGAATTAAATCTGTC 59.046 47.826 0.00 0.00 0.00 3.51
862 880 3.627577 CCCACCTGAATTAAATCTGTCGG 59.372 47.826 0.00 0.00 0.00 4.79
863 881 4.513442 CCACCTGAATTAAATCTGTCGGA 58.487 43.478 0.00 0.00 0.00 4.55
864 882 4.941263 CCACCTGAATTAAATCTGTCGGAA 59.059 41.667 0.00 0.00 0.00 4.30
865 883 5.590259 CCACCTGAATTAAATCTGTCGGAAT 59.410 40.000 0.00 0.00 0.00 3.01
866 884 6.238484 CCACCTGAATTAAATCTGTCGGAATC 60.238 42.308 0.00 0.00 0.00 2.52
867 885 5.823045 ACCTGAATTAAATCTGTCGGAATCC 59.177 40.000 0.00 0.00 0.00 3.01
868 886 5.822519 CCTGAATTAAATCTGTCGGAATCCA 59.177 40.000 0.00 0.00 0.00 3.41
869 887 6.238484 CCTGAATTAAATCTGTCGGAATCCAC 60.238 42.308 0.00 0.00 0.00 4.02
871 889 6.884295 TGAATTAAATCTGTCGGAATCCACTT 59.116 34.615 0.00 0.00 0.00 3.16
872 890 8.044309 TGAATTAAATCTGTCGGAATCCACTTA 58.956 33.333 0.00 0.00 0.00 2.24
873 891 8.980481 AATTAAATCTGTCGGAATCCACTTAT 57.020 30.769 0.00 0.00 0.00 1.73
912 930 4.980805 GACAACACGCCGCCTCCA 62.981 66.667 0.00 0.00 0.00 3.86
931 949 4.254709 AGCAGCCTCGCCACAACA 62.255 61.111 0.00 0.00 0.00 3.33
1214 3864 2.419990 CCATCCACTACTTCATCCGCAA 60.420 50.000 0.00 0.00 0.00 4.85
1229 3879 3.126879 CAATCTCTGCCGCCGCAA 61.127 61.111 0.47 0.00 46.66 4.85
1956 5211 4.724602 GGCTGCTGACGCTGTCGA 62.725 66.667 0.00 0.00 39.41 4.20
1957 5212 3.177920 GCTGCTGACGCTGTCGAG 61.178 66.667 0.00 4.77 39.41 4.04
1958 5213 3.177920 CTGCTGACGCTGTCGAGC 61.178 66.667 17.26 17.26 42.37 5.03
1959 5214 3.623486 CTGCTGACGCTGTCGAGCT 62.623 63.158 20.89 0.00 43.77 4.09
1960 5215 2.878520 GCTGACGCTGTCGAGCTC 60.879 66.667 2.73 2.73 43.77 4.09
1961 5216 2.575525 CTGACGCTGTCGAGCTCG 60.576 66.667 30.03 30.03 43.77 5.03
1972 5227 4.244802 GAGCTCGACGCGGAGGAG 62.245 72.222 12.47 14.71 45.59 3.69
1975 5230 4.244802 CTCGACGCGGAGGAGCTC 62.245 72.222 12.47 4.71 34.40 4.09
2057 5675 2.125512 GGAGTGCGATGAAGGCGT 60.126 61.111 0.00 0.00 0.00 5.68
2207 5910 3.302347 CTGGACGACCTGGGACTGC 62.302 68.421 5.33 0.00 37.04 4.40
2209 5912 2.048127 GACGACCTGGGACTGCAC 60.048 66.667 0.00 0.00 0.00 4.57
2210 5913 2.842462 ACGACCTGGGACTGCACA 60.842 61.111 0.00 0.00 0.00 4.57
2404 6109 2.572209 TTGGGTGCAAGTTAGGGTAC 57.428 50.000 0.00 0.00 0.00 3.34
2422 6128 1.508256 ACCTGGGTGCTATTACCTCC 58.492 55.000 0.00 0.00 40.66 4.30
2423 6129 1.009675 ACCTGGGTGCTATTACCTCCT 59.990 52.381 0.00 0.00 40.66 3.69
2426 6132 3.714798 CCTGGGTGCTATTACCTCCTAAA 59.285 47.826 0.00 0.00 40.66 1.85
2427 6133 4.202367 CCTGGGTGCTATTACCTCCTAAAG 60.202 50.000 0.00 0.00 40.66 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.651770 AGGAGGGAGGGAAGACATGTA 59.348 52.381 0.00 0.00 0.00 2.29
26 27 1.132881 AGCAGAGGAATAGGAGGGAGG 60.133 57.143 0.00 0.00 0.00 4.30
125 126 7.310983 GGGATTAGAGATTAGGGATTTGGAGAG 60.311 44.444 0.00 0.00 0.00 3.20
126 127 6.502158 GGGATTAGAGATTAGGGATTTGGAGA 59.498 42.308 0.00 0.00 0.00 3.71
200 207 0.458543 GCGACTTCGATCTGGAGCAA 60.459 55.000 2.02 0.00 43.02 3.91
371 384 2.095919 CACACACATGCACATGAGACTG 60.096 50.000 17.19 7.41 41.20 3.51
570 583 5.772393 TGTACCCACAATATTCCTCACTT 57.228 39.130 0.00 0.00 0.00 3.16
590 603 0.779997 AAGAAGCCCAACCCAGATGT 59.220 50.000 0.00 0.00 0.00 3.06
706 724 3.003394 TGAGATGCAAGTTGGGGTATG 57.997 47.619 4.75 0.00 0.00 2.39
724 742 4.686944 GCCTGGGACTAAATCATCACATGA 60.687 45.833 0.00 0.00 44.55 3.07
816 834 0.804989 GACTGCGGGTTGATTCAAGG 59.195 55.000 0.00 0.00 0.00 3.61
818 836 1.234821 GTGACTGCGGGTTGATTCAA 58.765 50.000 0.00 0.00 0.00 2.69
838 856 3.954258 GACAGATTTAATTCAGGTGGGGG 59.046 47.826 0.56 0.00 0.00 5.40
840 858 3.627577 CCGACAGATTTAATTCAGGTGGG 59.372 47.826 0.56 5.01 0.00 4.61
841 859 4.513442 TCCGACAGATTTAATTCAGGTGG 58.487 43.478 0.56 0.00 0.00 4.61
856 874 4.058817 GGCTTATAAGTGGATTCCGACAG 58.941 47.826 13.91 0.00 0.00 3.51
857 875 3.452990 TGGCTTATAAGTGGATTCCGACA 59.547 43.478 13.91 0.00 0.00 4.35
859 877 3.452990 TGTGGCTTATAAGTGGATTCCGA 59.547 43.478 13.91 0.00 0.00 4.55
860 878 3.560068 GTGTGGCTTATAAGTGGATTCCG 59.440 47.826 13.91 0.00 0.00 4.30
871 889 5.294356 CGTGGCTTATAAGTGTGGCTTATA 58.706 41.667 13.91 3.41 45.70 0.98
873 891 3.527533 CGTGGCTTATAAGTGTGGCTTA 58.472 45.455 13.91 0.00 43.13 3.09
912 930 4.254709 TTGTGGCGAGGCTGCTGT 62.255 61.111 0.00 0.00 34.52 4.40
1429 4428 3.706373 GACAAGCTCCGGCCTCCA 61.706 66.667 0.00 0.00 39.73 3.86
1640 4868 4.719106 AGCAGCAGGTGGAGCAGC 62.719 66.667 0.86 0.00 43.76 5.25
1955 5210 4.244802 CTCCTCCGCGTCGAGCTC 62.245 72.222 4.92 2.73 45.59 4.09
1958 5213 4.244802 GAGCTCCTCCGCGTCGAG 62.245 72.222 4.92 5.26 34.40 4.04
2044 5662 4.695993 TGCCACGCCTTCATCGCA 62.696 61.111 0.00 0.00 0.00 5.10
2051 5669 3.710722 CCCTCTCTGCCACGCCTT 61.711 66.667 0.00 0.00 0.00 4.35
2057 5675 3.005539 GTCCTGCCCTCTCTGCCA 61.006 66.667 0.00 0.00 0.00 4.92
2105 5723 4.657824 CCACGCGTTCCACTCCGT 62.658 66.667 10.22 0.00 0.00 4.69
2203 5906 0.179032 TGAATCAACCCGTGTGCAGT 60.179 50.000 0.00 0.00 0.00 4.40
2204 5907 0.518636 CTGAATCAACCCGTGTGCAG 59.481 55.000 0.00 0.00 0.00 4.41
2205 5908 0.888736 CCTGAATCAACCCGTGTGCA 60.889 55.000 0.00 0.00 0.00 4.57
2207 5910 0.036164 TCCCTGAATCAACCCGTGTG 59.964 55.000 0.00 0.00 0.00 3.82
2209 5912 1.539827 GTTTCCCTGAATCAACCCGTG 59.460 52.381 0.00 0.00 0.00 4.94
2210 5913 1.880646 CGTTTCCCTGAATCAACCCGT 60.881 52.381 0.00 0.00 0.00 5.28
2368 6073 2.954318 CCCAATGTGATGATTCAGTCCC 59.046 50.000 0.00 0.00 30.85 4.46
2404 6109 1.807814 AGGAGGTAATAGCACCCAGG 58.192 55.000 2.39 0.00 39.62 4.45
2422 6128 6.370166 GGTGAGTTCTTCTGTCATTCCTTTAG 59.630 42.308 0.00 0.00 0.00 1.85
2423 6129 6.043243 AGGTGAGTTCTTCTGTCATTCCTTTA 59.957 38.462 0.00 0.00 0.00 1.85
2426 6132 3.906846 AGGTGAGTTCTTCTGTCATTCCT 59.093 43.478 0.00 0.00 0.00 3.36
2427 6133 4.278975 AGGTGAGTTCTTCTGTCATTCC 57.721 45.455 0.00 0.00 0.00 3.01
2428 6134 5.994668 AGAAAGGTGAGTTCTTCTGTCATTC 59.005 40.000 0.00 0.00 31.10 2.67
2429 6135 5.934781 AGAAAGGTGAGTTCTTCTGTCATT 58.065 37.500 0.00 0.00 31.10 2.57
2430 6136 5.559148 AGAAAGGTGAGTTCTTCTGTCAT 57.441 39.130 0.00 0.00 31.10 3.06
2431 6137 5.359194 AAGAAAGGTGAGTTCTTCTGTCA 57.641 39.130 0.00 0.00 40.50 3.58


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

AutoCloner maintained by Alex Coulton.