Multiple sequence alignment - TraesCS6D01G109300

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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 TraesCS6D01G109300 chr6D 100.000 2162 0 0 1 2162 74949306 74951467 0.000000e+00 3993
1 TraesCS6D01G109300 chr6D 85.693 664 63 17 1502 2155 144087678 144087037 0.000000e+00 671
2 TraesCS6D01G109300 chr6D 94.505 273 13 2 921 1191 168255334 168255606 9.230000e-114 420
3 TraesCS6D01G109300 chr6D 88.959 317 16 4 617 920 370025943 370026253 7.290000e-100 374
4 TraesCS6D01G109300 chr6D 86.010 193 24 3 1507 1697 144066988 144066797 1.010000e-48 204
5 TraesCS6D01G109300 chr6B 95.532 1992 76 4 1 1989 148681314 148683295 0.000000e+00 3173
6 TraesCS6D01G109300 chr6B 92.459 305 14 5 619 920 606999980 607000278 5.510000e-116 427
7 TraesCS6D01G109300 chr3A 85.978 649 68 9 1509 2155 11474913 11475540 0.000000e+00 673
8 TraesCS6D01G109300 chr3A 95.273 275 12 1 921 1194 672909599 672909325 3.300000e-118 435
9 TraesCS6D01G109300 chr3A 94.928 276 12 2 921 1194 594899216 594898941 4.260000e-117 431
10 TraesCS6D01G109300 chr3A 86.598 194 21 4 1507 1697 11479856 11480047 2.170000e-50 209
11 TraesCS6D01G109300 chr1D 85.474 654 72 12 1509 2160 208149110 208148478 0.000000e+00 660
12 TraesCS6D01G109300 chr1D 81.003 658 91 18 1522 2160 485362620 485361978 1.930000e-135 492
13 TraesCS6D01G109300 chr1D 89.905 317 17 2 617 920 269423324 269423010 5.590000e-106 394
14 TraesCS6D01G109300 chr1D 87.113 194 20 3 1507 1697 208125751 208125560 4.670000e-52 215
15 TraesCS6D01G109300 chr2B 85.038 655 71 12 1509 2160 150328853 150328223 1.810000e-180 641
16 TraesCS6D01G109300 chr4A 84.877 648 77 13 1509 2155 589897961 589897334 3.030000e-178 634
17 TraesCS6D01G109300 chr4A 93.506 308 13 4 617 920 199399785 199400089 3.270000e-123 451
18 TraesCS6D01G109300 chr1B 83.359 655 67 16 1509 2160 6135895 6135280 3.110000e-158 568
19 TraesCS6D01G109300 chr1B 86.010 193 24 3 1507 1697 6117690 6117499 1.010000e-48 204
20 TraesCS6D01G109300 chr5A 95.114 307 10 2 617 920 600263226 600263530 1.500000e-131 479
21 TraesCS6D01G109300 chr7A 94.463 307 11 3 617 920 211301076 211301379 3.250000e-128 468
22 TraesCS6D01G109300 chr7A 85.986 421 55 4 1744 2162 171869395 171869813 4.230000e-122 448
23 TraesCS6D01G109300 chrUn 85.748 421 56 4 1744 2162 247469115 247468697 1.970000e-120 442
24 TraesCS6D01G109300 chrUn 94.565 276 13 2 921 1194 93409223 93408948 1.980000e-115 425
25 TraesCS6D01G109300 chrUn 94.565 276 13 2 921 1194 372771245 372770970 1.980000e-115 425
26 TraesCS6D01G109300 chrUn 94.203 276 14 2 921 1194 346596086 346595811 9.230000e-114 420
27 TraesCS6D01G109300 chrUn 90.221 317 16 2 617 920 386740564 386740878 1.200000e-107 399
28 TraesCS6D01G109300 chrUn 90.221 317 16 2 617 920 400038820 400039134 1.200000e-107 399
29 TraesCS6D01G109300 chrUn 93.976 166 5 2 617 779 108363042 108363205 1.660000e-61 246
30 TraesCS6D01G109300 chr2D 94.565 276 13 2 921 1194 272793485 272793210 1.980000e-115 425
31 TraesCS6D01G109300 chr3D 94.203 276 14 2 921 1194 589279136 589278861 9.230000e-114 420
32 TraesCS6D01G109300 chr4D 89.905 317 17 2 617 920 123353557 123353871 5.590000e-106 394


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 TraesCS6D01G109300 chr6D 74949306 74951467 2161 False 3993 3993 100.000 1 2162 1 chr6D.!!$F1 2161
1 TraesCS6D01G109300 chr6D 144087037 144087678 641 True 671 671 85.693 1502 2155 1 chr6D.!!$R2 653
2 TraesCS6D01G109300 chr6B 148681314 148683295 1981 False 3173 3173 95.532 1 1989 1 chr6B.!!$F1 1988
3 TraesCS6D01G109300 chr3A 11474913 11475540 627 False 673 673 85.978 1509 2155 1 chr3A.!!$F1 646
4 TraesCS6D01G109300 chr1D 208148478 208149110 632 True 660 660 85.474 1509 2160 1 chr1D.!!$R2 651
5 TraesCS6D01G109300 chr1D 485361978 485362620 642 True 492 492 81.003 1522 2160 1 chr1D.!!$R4 638
6 TraesCS6D01G109300 chr2B 150328223 150328853 630 True 641 641 85.038 1509 2160 1 chr2B.!!$R1 651
7 TraesCS6D01G109300 chr4A 589897334 589897961 627 True 634 634 84.877 1509 2155 1 chr4A.!!$R1 646
8 TraesCS6D01G109300 chr1B 6135280 6135895 615 True 568 568 83.359 1509 2160 1 chr1B.!!$R2 651

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
981 984 0.977395 ATAGGCGCTTATGACCTCCC 59.023 55.0 11.7 0.0 34.92 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 2065 2.09877 GCAGAGATCATTTGGGTTCAGC 59.901 50.0 0.0 0.0 0.0 4.26 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
32 33 9.625747 TTCTGTGATTAGCAAATGTCCATATTA 57.374 29.630 0.00 0.00 0.00 0.98
49 50 6.825213 TCCATATTAAGACATGCATAGATGGC 59.175 38.462 11.92 0.00 32.00 4.40
50 51 6.827251 CCATATTAAGACATGCATAGATGGCT 59.173 38.462 0.00 0.00 44.12 4.75
51 52 7.012138 CCATATTAAGACATGCATAGATGGCTC 59.988 40.741 0.00 0.00 41.14 4.70
52 53 3.851458 AAGACATGCATAGATGGCTCA 57.149 42.857 0.00 0.00 41.14 4.26
53 54 3.851458 AGACATGCATAGATGGCTCAA 57.149 42.857 0.00 0.00 37.03 3.02
54 55 3.474600 AGACATGCATAGATGGCTCAAC 58.525 45.455 0.00 0.00 37.03 3.18
55 56 3.136077 AGACATGCATAGATGGCTCAACT 59.864 43.478 0.00 0.00 37.03 3.16
56 57 4.346127 AGACATGCATAGATGGCTCAACTA 59.654 41.667 0.00 0.00 37.03 2.24
57 58 5.039920 ACATGCATAGATGGCTCAACTAA 57.960 39.130 0.00 0.00 0.00 2.24
58 59 5.439721 ACATGCATAGATGGCTCAACTAAA 58.560 37.500 0.00 0.00 0.00 1.85
88 89 8.860128 CAAAACTAAGAAACAACTGAAAAGGAC 58.140 33.333 0.00 0.00 0.00 3.85
103 104 7.095187 ACTGAAAAGGACGAGATGACAATTTAC 60.095 37.037 0.00 0.00 0.00 2.01
120 121 9.875675 GACAATTTACTTTGCATGATCTATCTC 57.124 33.333 0.00 0.00 0.00 2.75
270 272 3.527533 TGAATATAGGACGTTGGTGCAC 58.472 45.455 8.80 8.80 36.89 4.57
277 279 2.812011 AGGACGTTGGTGCACTTTAATC 59.188 45.455 17.98 9.34 36.89 1.75
307 309 4.808414 TCATATATGCTCACCAGGTAGC 57.192 45.455 7.92 11.99 39.25 3.58
510 512 7.667575 ATATCGGATGTCTAATGAATAGGCT 57.332 36.000 0.00 0.00 37.14 4.58
564 566 1.242076 ATGCAACTTGACCTGAGTGC 58.758 50.000 0.00 0.00 0.00 4.40
604 606 7.238486 AGGTTTAAATGTTATCATGCACCAA 57.762 32.000 0.00 0.00 34.19 3.67
640 642 4.909880 CGAAAAAGCAAGCCTACTTACAAC 59.090 41.667 0.00 0.00 33.74 3.32
651 653 4.274214 GCCTACTTACAACGTGTTTTCCTT 59.726 41.667 0.00 0.00 0.00 3.36
658 660 9.887406 ACTTACAACGTGTTTTCCTTTATATTG 57.113 29.630 0.00 0.00 0.00 1.90
686 688 8.648097 CAAATACGCATATATTGACCTACTCAC 58.352 37.037 0.00 0.00 0.00 3.51
717 719 9.827198 ATATCTTGCATAAATAAATCCCCTCAA 57.173 29.630 0.00 0.00 0.00 3.02
779 781 4.876679 AGCCCTCGACTATTTAGAAAAAGC 59.123 41.667 0.00 0.00 0.00 3.51
848 850 7.066887 CACACACTATTTATGAGTTTATGCCCA 59.933 37.037 0.00 0.00 0.00 5.36
911 913 8.579850 AATATGAAAGTGCAAAATCTCCTACA 57.420 30.769 0.00 0.00 0.00 2.74
981 984 0.977395 ATAGGCGCTTATGACCTCCC 59.023 55.000 11.70 0.00 34.92 4.30
1028 1031 4.110482 CCTCTGGAATTACGACCTTTACG 58.890 47.826 0.00 0.00 0.00 3.18
1030 1033 4.737054 TCTGGAATTACGACCTTTACGAC 58.263 43.478 0.00 0.00 34.70 4.34
1040 1043 0.446222 CCTTTACGACAATGGTGCCG 59.554 55.000 0.00 0.00 0.00 5.69
1046 1049 1.802636 GACAATGGTGCCGTCCATG 59.197 57.895 6.05 0.00 46.14 3.66
1069 1072 7.637631 TGGATCAAATTATTTCGTGGATTGA 57.362 32.000 0.00 0.00 0.00 2.57
1400 1404 0.681175 AGGAAGGGTGTGCAATTTGC 59.319 50.000 14.49 14.49 45.29 3.68
1452 1456 3.303725 GCTCTACACAAAATTGTCGCACA 60.304 43.478 0.00 0.00 39.91 4.57
1468 1472 3.064207 CGCACAGGTTCACTTAAAGCTA 58.936 45.455 0.00 0.00 35.32 3.32
1485 1489 3.321950 AGCTATTGGATTAGCCTCTGGT 58.678 45.455 0.08 0.00 44.64 4.00
1576 1589 2.021457 GCGTGTTTATAATGCAGGGGT 58.979 47.619 0.00 0.00 0.00 4.95
1623 1636 8.301252 AGGGTTTGTTTAGATTACAACTTGTT 57.699 30.769 0.00 0.00 35.39 2.83
1961 1990 7.095017 GCATGAAAGATAGGGTTAGCAGATAAC 60.095 40.741 0.00 0.00 42.68 1.89
2008 2037 4.215349 GCATGGAGCCTGAGTGTC 57.785 61.111 0.00 0.00 37.23 3.67
2033 2063 4.469657 TCACACCAAGTTCCTTTAGCATT 58.530 39.130 0.00 0.00 0.00 3.56
2035 2065 3.573967 ACACCAAGTTCCTTTAGCATTGG 59.426 43.478 0.00 0.00 42.29 3.16
2086 2116 6.644592 GCATTACAAAAGTGCCTTGTATTCAA 59.355 34.615 0.00 0.00 38.65 2.69
2090 2120 7.341445 ACAAAAGTGCCTTGTATTCAACTTA 57.659 32.000 0.00 0.00 35.26 2.24
2097 2127 8.537016 AGTGCCTTGTATTCAACTTATGTACTA 58.463 33.333 0.00 0.00 0.00 1.82
2141 2171 7.890515 TGTTTCTTTGCACACCATGATATTAA 58.109 30.769 0.00 0.00 0.00 1.40
2155 2185 9.367160 ACCATGATATTAAATTAGGTCCAAAGG 57.633 33.333 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 9.836076 CTATGCATGTCTTAATATGGACATTTG 57.164 33.333 10.16 8.60 46.86 2.32
22 23 7.825761 CCATCTATGCATGTCTTAATATGGACA 59.174 37.037 10.16 8.28 44.84 4.02
32 33 3.851458 TGAGCCATCTATGCATGTCTT 57.149 42.857 10.16 0.00 0.00 3.01
69 70 5.183228 TCTCGTCCTTTTCAGTTGTTTCTT 58.817 37.500 0.00 0.00 0.00 2.52
78 79 5.869753 AATTGTCATCTCGTCCTTTTCAG 57.130 39.130 0.00 0.00 0.00 3.02
88 89 6.545508 TCATGCAAAGTAAATTGTCATCTCG 58.454 36.000 0.00 0.00 32.80 4.04
234 236 7.894364 GTCCTATATTCAGGAATGGAGGTAGTA 59.106 40.741 16.97 3.32 46.31 1.82
250 252 3.793559 AGTGCACCAACGTCCTATATTC 58.206 45.455 14.63 0.00 0.00 1.75
277 279 6.741109 TGGTGAGCATATATGATTTGCTTTG 58.259 36.000 17.10 0.00 45.47 2.77
347 349 9.669887 ATGTTGCATAATCAATTTGTAAATGGT 57.330 25.926 0.00 0.00 0.00 3.55
490 492 9.307121 CTTAATAGCCTATTCATTAGACATCCG 57.693 37.037 0.00 0.00 0.00 4.18
604 606 3.006323 TGCTTTTTCGTTGTTATGCCCAT 59.994 39.130 0.00 0.00 0.00 4.00
640 642 7.826260 ATTTGCCAATATAAAGGAAAACACG 57.174 32.000 2.87 0.00 35.30 4.49
658 660 5.880054 AGGTCAATATATGCGTATTTGCC 57.120 39.130 3.23 12.29 0.00 4.52
717 719 5.182570 GGAAGATACGGGCTAGTTTGTTTTT 59.817 40.000 0.00 0.00 0.00 1.94
733 735 4.443621 GGCAACAAGGACTAGGAAGATAC 58.556 47.826 0.00 0.00 0.00 2.24
848 850 2.099756 GTGCTCTTTTGCTCTGTTGGTT 59.900 45.455 0.00 0.00 0.00 3.67
943 946 7.117379 GCGCCTATACCGTAAAATAGATTTTCT 59.883 37.037 0.00 0.00 40.24 2.52
1028 1031 1.656818 CCATGGACGGCACCATTGTC 61.657 60.000 5.56 0.00 47.00 3.18
1030 1033 0.752743 ATCCATGGACGGCACCATTG 60.753 55.000 18.99 7.69 47.00 2.82
1040 1043 6.039270 TCCACGAAATAATTTGATCCATGGAC 59.961 38.462 18.99 11.83 0.00 4.02
1046 1049 9.533253 AATTCAATCCACGAAATAATTTGATCC 57.467 29.630 0.00 0.00 0.00 3.36
1069 1072 4.666512 ACCATAGACAGGCAAGTGAAATT 58.333 39.130 0.00 0.00 0.00 1.82
1420 1424 9.062524 ACAATTTTGTGTAGAGCTAATACAACA 57.937 29.630 11.73 6.26 40.49 3.33
1452 1456 7.283354 GCTAATCCAATAGCTTTAAGTGAACCT 59.717 37.037 0.00 0.00 43.94 3.50
1468 1472 4.079558 ACATCAACCAGAGGCTAATCCAAT 60.080 41.667 0.00 0.00 37.29 3.16
1485 1489 6.936335 ACATGAATAAGTCACAGTCACATCAA 59.064 34.615 0.00 0.00 39.72 2.57
1593 1606 9.582648 AGTTGTAATCTAAACAAACCCTTGTAT 57.417 29.630 0.00 0.00 45.25 2.29
1623 1636 4.211125 CCTCCTAGTCTATCTCTTGCACA 58.789 47.826 0.00 0.00 0.00 4.57
1731 1759 4.312443 AGGGTGTTAAATGTACGTGACAG 58.688 43.478 0.00 0.00 42.79 3.51
1961 1990 4.699735 TGTGATAACCTTGGTGCAACATAG 59.300 41.667 4.62 6.10 39.98 2.23
2033 2063 2.309755 AGAGATCATTTGGGTTCAGCCA 59.690 45.455 0.00 0.00 39.65 4.75
2035 2065 2.098770 GCAGAGATCATTTGGGTTCAGC 59.901 50.000 0.00 0.00 0.00 4.26
2086 2116 8.582657 ACTGTGTCAAGATCTAGTACATAAGT 57.417 34.615 0.00 6.58 0.00 2.24
2090 2120 6.831353 AGCTACTGTGTCAAGATCTAGTACAT 59.169 38.462 0.00 0.00 0.00 2.29
2097 2127 4.881019 ACAAGCTACTGTGTCAAGATCT 57.119 40.909 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.