Multiple sequence alignment - TraesCS3D01G304200

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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 TraesCS3D01G304200 chr3D 100.000 2471 0 0 1 2471 418705118 418707588 0.000000e+00 4564.0
1 TraesCS3D01G304200 chr3D 92.010 413 25 1 1 413 418482223 418482627 7.670000e-160 573.0
2 TraesCS3D01G304200 chr3D 90.130 385 29 3 71 447 418410376 418410759 2.210000e-135 492.0
3 TraesCS3D01G304200 chr3D 83.610 543 39 17 886 1421 416403936 416403437 4.810000e-127 464.0
4 TraesCS3D01G304200 chr3D 90.842 273 25 0 71 343 416404637 416404365 1.400000e-97 366.0
5 TraesCS3D01G304200 chr3D 77.662 385 42 17 921 1303 416481481 416481139 6.970000e-46 195.0
6 TraesCS3D01G304200 chr3D 81.509 265 21 18 527 774 416404292 416404039 2.510000e-45 193.0
7 TraesCS3D01G304200 chr3D 82.727 220 19 9 659 869 418410867 418411076 7.020000e-41 178.0
8 TraesCS3D01G304200 chr7D 97.018 1073 11 1 1420 2471 136695274 136696346 0.000000e+00 1784.0
9 TraesCS3D01G304200 chr7D 92.225 926 69 3 1548 2471 99610886 99609962 0.000000e+00 1308.0
10 TraesCS3D01G304200 chr7D 91.577 926 76 2 1548 2471 99611580 99612505 0.000000e+00 1277.0
11 TraesCS3D01G304200 chr7D 83.913 230 17 4 1420 1629 99611352 99611581 4.170000e-48 202.0
12 TraesCS3D01G304200 chr7D 72.250 400 83 23 1041 1420 611468060 611467669 5.620000e-17 99.0
13 TraesCS3D01G304200 chr7D 94.000 50 2 1 886 934 6443065 6443016 9.480000e-10 75.0
14 TraesCS3D01G304200 chr5A 95.433 1073 28 1 1420 2471 35274338 35275410 0.000000e+00 1690.0
15 TraesCS3D01G304200 chr2D 92.865 925 65 1 1548 2471 646276927 646277851 0.000000e+00 1341.0
16 TraesCS3D01G304200 chr2D 84.416 231 15 1 1420 1629 646276698 646276928 8.960000e-50 207.0
17 TraesCS3D01G304200 chr3A 91.577 926 76 2 1548 2471 667138945 667139870 0.000000e+00 1277.0
18 TraesCS3D01G304200 chr3A 93.318 853 45 3 16 867 532488732 532487891 0.000000e+00 1249.0
19 TraesCS3D01G304200 chr3A 94.545 550 18 1 872 1421 532487854 532487317 0.000000e+00 839.0
20 TraesCS3D01G304200 chr3A 88.685 327 27 4 177 503 532644776 532644460 8.290000e-105 390.0
21 TraesCS3D01G304200 chr3A 76.581 427 73 20 76 480 719360342 719360763 2.490000e-50 209.0
22 TraesCS3D01G304200 chr3A 75.116 430 77 23 76 480 719336858 719337282 9.080000e-40 174.0
23 TraesCS3D01G304200 chr3A 91.667 96 8 0 1534 1629 667138851 667138946 1.540000e-27 134.0
24 TraesCS3D01G304200 chr3B 93.072 765 45 1 1 765 545008449 545009205 0.000000e+00 1112.0
25 TraesCS3D01G304200 chr3B 85.842 897 83 17 1 874 544921804 544922679 0.000000e+00 913.0
26 TraesCS3D01G304200 chr3B 98.026 152 2 1 910 1060 545028171 545028322 1.880000e-66 263.0
27 TraesCS3D01G304200 chr3B 98.630 146 2 0 1276 1421 545044645 545044790 2.440000e-65 259.0
28 TraesCS3D01G304200 chr3B 80.000 320 34 4 71 390 544818893 544819182 2.490000e-50 209.0
29 TraesCS3D01G304200 chr3B 95.690 116 5 0 1161 1276 545043627 545043742 1.170000e-43 187.0
30 TraesCS3D01G304200 chr3B 82.569 218 19 11 659 868 544821327 544821533 9.080000e-40 174.0
31 TraesCS3D01G304200 chr3B 91.270 126 11 0 378 503 544821118 544821243 3.270000e-39 172.0
32 TraesCS3D01G304200 chr3B 98.462 65 1 0 1053 1117 545043314 545043378 5.580000e-22 115.0
33 TraesCS3D01G304200 chr3B 100.000 50 0 0 872 921 545013328 545013377 2.620000e-15 93.5
34 TraesCS3D01G304200 chr1A 92.479 718 51 3 1549 2263 33085180 33085897 0.000000e+00 1024.0
35 TraesCS3D01G304200 chr4B 84.582 934 126 13 1541 2468 168265236 168266157 0.000000e+00 911.0
36 TraesCS3D01G304200 chr4B 84.320 338 32 1 1420 1736 609429647 609429984 6.640000e-81 311.0
37 TraesCS3D01G304200 chr5B 84.154 934 129 14 1541 2468 668595376 668596296 0.000000e+00 887.0
38 TraesCS3D01G304200 chr7A 72.250 400 83 23 1041 1420 701459233 701458842 5.620000e-17 99.0


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 TraesCS3D01G304200 chr3D 418705118 418707588 2470 False 4564.0 4564 100.000000 1 2471 1 chr3D.!!$F2 2470
1 TraesCS3D01G304200 chr3D 416403437 416404637 1200 True 341.0 464 85.320333 71 1421 3 chr3D.!!$R2 1350
2 TraesCS3D01G304200 chr3D 418410376 418411076 700 False 335.0 492 86.428500 71 869 2 chr3D.!!$F3 798
3 TraesCS3D01G304200 chr7D 136695274 136696346 1072 False 1784.0 1784 97.018000 1420 2471 1 chr7D.!!$F1 1051
4 TraesCS3D01G304200 chr7D 99609962 99610886 924 True 1308.0 1308 92.225000 1548 2471 1 chr7D.!!$R2 923
5 TraesCS3D01G304200 chr7D 99611352 99612505 1153 False 739.5 1277 87.745000 1420 2471 2 chr7D.!!$F2 1051
6 TraesCS3D01G304200 chr5A 35274338 35275410 1072 False 1690.0 1690 95.433000 1420 2471 1 chr5A.!!$F1 1051
7 TraesCS3D01G304200 chr2D 646276698 646277851 1153 False 774.0 1341 88.640500 1420 2471 2 chr2D.!!$F1 1051
8 TraesCS3D01G304200 chr3A 532487317 532488732 1415 True 1044.0 1249 93.931500 16 1421 2 chr3A.!!$R2 1405
9 TraesCS3D01G304200 chr3A 667138851 667139870 1019 False 705.5 1277 91.622000 1534 2471 2 chr3A.!!$F3 937
10 TraesCS3D01G304200 chr3B 545008449 545009205 756 False 1112.0 1112 93.072000 1 765 1 chr3B.!!$F2 764
11 TraesCS3D01G304200 chr3B 544921804 544922679 875 False 913.0 913 85.842000 1 874 1 chr3B.!!$F1 873
12 TraesCS3D01G304200 chr1A 33085180 33085897 717 False 1024.0 1024 92.479000 1549 2263 1 chr1A.!!$F1 714
13 TraesCS3D01G304200 chr4B 168265236 168266157 921 False 911.0 911 84.582000 1541 2468 1 chr4B.!!$F1 927
14 TraesCS3D01G304200 chr5B 668595376 668596296 920 False 887.0 887 84.154000 1541 2468 1 chr5B.!!$F1 927

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
108 109 0.387929 AACTCGTCGAAGGTGAGCAA 59.612 50.0 0.0 0.0 32.98 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 2356 0.232303 GGTTCGTTTGAGCACTGACG 59.768 55.0 4.17 4.17 36.89 4.35 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
27 28 7.814264 ATTAAGGAATTACAATCAGCCAGAG 57.186 36.000 0.00 0.00 0.00 3.35
46 47 6.651225 GCCAGAGAAAGTATACAAAGTTCAGT 59.349 38.462 5.50 0.00 0.00 3.41
47 48 7.173390 GCCAGAGAAAGTATACAAAGTTCAGTT 59.827 37.037 5.50 0.00 0.00 3.16
48 49 9.057089 CCAGAGAAAGTATACAAAGTTCAGTTT 57.943 33.333 5.50 0.00 0.00 2.66
62 63 9.791838 CAAAGTTCAGTTTTTGACTTTTTGTAC 57.208 29.630 0.00 0.00 36.19 2.90
108 109 0.387929 AACTCGTCGAAGGTGAGCAA 59.612 50.000 0.00 0.00 32.98 3.91
127 128 4.351938 CCGTCGCCGTTGAGGTCA 62.352 66.667 0.00 0.00 43.70 4.02
155 164 2.315781 GATCATGGCCTGGCACTCGA 62.316 60.000 22.05 11.16 0.00 4.04
255 264 4.891727 CATCCCGAACGCCTCCCG 62.892 72.222 0.00 0.00 44.21 5.14
331 340 2.363018 TCCTCCTCGTCCAGCAGG 60.363 66.667 0.00 0.00 0.00 4.85
488 497 1.291877 GAACACGCGCCTGAACTCAT 61.292 55.000 13.48 0.00 0.00 2.90
503 512 1.228033 TCATCTGATGCGGCCATGG 60.228 57.895 7.63 7.63 0.00 3.66
522 549 1.160137 GTGAGTCGCCTGCAAAGATT 58.840 50.000 0.00 0.00 0.00 2.40
524 551 1.270785 TGAGTCGCCTGCAAAGATTGA 60.271 47.619 0.00 0.00 0.00 2.57
548 581 1.135859 GTCTTTCGGTGCTTGATGCTG 60.136 52.381 0.00 0.00 43.37 4.41
565 598 1.933500 GCTGAGTTCGTCGCTGGTTTA 60.934 52.381 0.00 0.00 0.00 2.01
589 625 2.284684 GCTGATTGAGATCGAGCTGTTG 59.715 50.000 8.50 0.00 35.44 3.33
615 655 7.567571 CGTGTTGGTATTTATAGCTGAGAATG 58.432 38.462 0.00 0.00 0.00 2.67
734 780 3.366985 GCGAGTTAAATTTTGGACCAGGG 60.367 47.826 0.00 0.00 0.00 4.45
823 875 1.024579 AGAACCGCCGTGCCATTTAG 61.025 55.000 0.00 0.00 0.00 1.85
837 889 6.348458 CGTGCCATTTAGAATTGAACTTCAGA 60.348 38.462 0.00 0.00 0.00 3.27
842 894 9.918630 CCATTTAGAATTGAACTTCAGATTTGT 57.081 29.630 0.00 0.00 0.00 2.83
1010 1097 4.455877 CAGTTAACTGACCATGGTTTCCTC 59.544 45.833 28.17 6.17 46.59 3.71
1011 1098 2.586648 AACTGACCATGGTTTCCTCC 57.413 50.000 20.85 5.36 0.00 4.30
1012 1099 0.324943 ACTGACCATGGTTTCCTCCG 59.675 55.000 20.85 4.59 0.00 4.63
1013 1100 0.392998 CTGACCATGGTTTCCTCCGG 60.393 60.000 20.85 6.12 0.00 5.14
1014 1101 1.749258 GACCATGGTTTCCTCCGGC 60.749 63.158 20.85 0.00 0.00 6.13
1015 1102 2.824041 CCATGGTTTCCTCCGGCG 60.824 66.667 2.57 0.00 0.00 6.46
1016 1103 2.267642 CATGGTTTCCTCCGGCGA 59.732 61.111 9.30 0.00 0.00 5.54
1131 1218 2.982130 GGCATATCGGCCGAGGAT 59.018 61.111 33.87 24.89 45.40 3.24
1214 1301 3.706373 GAAGCTGGTGGCCGAGGA 61.706 66.667 0.00 0.00 43.05 3.71
1239 1326 0.336737 GGGGAGAAGAGGACCAGAGA 59.663 60.000 0.00 0.00 0.00 3.10
1249 1336 2.526873 ACCAGAGACGCAGGGGTT 60.527 61.111 0.00 0.00 0.00 4.11
1257 1344 2.198304 GACGCAGGGGTTTGAGGGAT 62.198 60.000 0.00 0.00 0.00 3.85
1383 1477 2.605823 CGCTATGATCCAGAGGTTCGAC 60.606 54.545 0.00 0.00 0.00 4.20
1430 1524 4.154613 CGAGTTCGTCCACAGCTC 57.845 61.111 0.00 0.00 34.11 4.09
2008 2286 9.708092 GTATACTATTCCTCCCAAGTTAACATC 57.292 37.037 8.61 0.00 0.00 3.06
2078 2356 3.064207 TCGAGGACTTGCACATGTTAAC 58.936 45.455 0.00 0.00 0.00 2.01
2103 2381 2.549754 AGTGCTCAAACGAACCTGAATG 59.450 45.455 0.00 0.00 0.00 2.67
2207 2486 6.774656 ACATGATTTTTGAGAAGACCAAGTCT 59.225 34.615 0.00 0.00 45.64 3.24
2295 2574 1.065491 TCAGCGGTGGAAGCAACATAT 60.065 47.619 15.67 0.00 37.01 1.78
2454 2733 7.950512 TCATGGTACTGTGACAAATGATTTTT 58.049 30.769 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.441718 TCTCTGGCTGATTGTAATTCCTT 57.558 39.130 0.00 0.00 0.00 3.36
7 8 5.441718 TTCTCTGGCTGATTGTAATTCCT 57.558 39.130 0.00 0.00 0.00 3.36
8 9 5.649831 ACTTTCTCTGGCTGATTGTAATTCC 59.350 40.000 0.00 0.00 0.00 3.01
21 22 6.651225 ACTGAACTTTGTATACTTTCTCTGGC 59.349 38.462 4.17 0.00 0.00 4.85
51 52 3.889196 TGGCATGACGTACAAAAAGTC 57.111 42.857 0.00 0.00 37.14 3.01
52 53 3.818210 TGATGGCATGACGTACAAAAAGT 59.182 39.130 3.81 0.00 0.00 2.66
53 54 4.418013 TGATGGCATGACGTACAAAAAG 57.582 40.909 3.81 0.00 0.00 2.27
62 63 2.161609 CCATGATGATGATGGCATGACG 59.838 50.000 3.81 0.00 40.29 4.35
127 128 2.828549 GCCATGATCCGCCGGTTT 60.829 61.111 1.63 0.00 0.00 3.27
155 164 4.664677 GCTGCACCTGGACGTCGT 62.665 66.667 9.92 0.00 0.00 4.34
255 264 3.569200 GAACAGGGGGACAGGTGCC 62.569 68.421 0.73 0.73 40.73 5.01
270 279 4.699522 ACGCCGGCAAGGAGGAAC 62.700 66.667 28.98 0.00 44.78 3.62
488 497 2.124612 CACCATGGCCGCATCAGA 60.125 61.111 13.04 0.00 0.00 3.27
503 512 1.135859 CAATCTTTGCAGGCGACTCAC 60.136 52.381 0.00 0.00 40.21 3.51
522 549 3.210227 TCAAGCACCGAAAGACAAATCA 58.790 40.909 0.00 0.00 0.00 2.57
524 551 3.612479 GCATCAAGCACCGAAAGACAAAT 60.612 43.478 0.00 0.00 44.79 2.32
548 581 1.719780 CAGTAAACCAGCGACGAACTC 59.280 52.381 0.00 0.00 0.00 3.01
565 598 1.755959 AGCTCGATCTCAATCAGCAGT 59.244 47.619 0.00 0.00 37.95 4.40
589 625 5.047847 TCTCAGCTATAAATACCAACACGC 58.952 41.667 0.00 0.00 0.00 5.34
615 655 0.321830 ATTTGCTTGCCCATGCCAAC 60.322 50.000 4.05 0.00 36.33 3.77
823 875 7.805071 CACTGGTACAAATCTGAAGTTCAATTC 59.195 37.037 7.06 0.00 38.70 2.17
837 889 7.339466 AGTCAAAAGAAGTTCACTGGTACAAAT 59.661 33.333 5.50 0.00 38.70 2.32
842 894 5.741011 ACAGTCAAAAGAAGTTCACTGGTA 58.259 37.500 19.01 0.00 35.61 3.25
843 895 4.589908 ACAGTCAAAAGAAGTTCACTGGT 58.410 39.130 19.01 7.14 35.61 4.00
885 972 2.589014 GCACGGTATATGTAGGCGTAC 58.411 52.381 9.63 9.63 0.00 3.67
1239 1326 2.231380 ATCCCTCAAACCCCTGCGT 61.231 57.895 0.00 0.00 0.00 5.24
1249 1336 2.267642 CCCGAACGCATCCCTCAA 59.732 61.111 0.00 0.00 0.00 3.02
1257 1344 3.271706 CTCGTACACCCCGAACGCA 62.272 63.158 0.00 0.00 36.60 5.24
1383 1477 2.995574 ACCCCGTCTCCGTTGAGG 60.996 66.667 0.00 0.00 39.23 3.86
1817 2095 4.961438 AATTTGGCTTCTCACAAACCAT 57.039 36.364 0.00 0.00 39.15 3.55
2008 2286 1.688735 TGGTATTCTCGGATGCTGGAG 59.311 52.381 0.00 0.00 0.00 3.86
2078 2356 0.232303 GGTTCGTTTGAGCACTGACG 59.768 55.000 4.17 4.17 36.89 4.35
2103 2381 3.065371 CCAATATCAAACCGAGCTTGGAC 59.935 47.826 27.65 0.00 39.70 4.02
2207 2486 0.107643 TCACTTGCCATGTTGTCCGA 59.892 50.000 0.00 0.00 0.00 4.55
2295 2574 6.647334 TTGTGAGTGCCTTTCAATTATTGA 57.353 33.333 3.20 3.20 38.04 2.57


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

AutoCloner maintained by Alex Coulton.