Multiple sequence alignment - TraesCS3A01G509400

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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 TraesCS3A01G509400 chr3A 100.000 2401 0 0 1 2401 730084763 730087163 0.000000e+00 4434
1 TraesCS3A01G509400 chr3A 98.295 704 12 0 1 704 730075809 730076512 0.000000e+00 1234
2 TraesCS3A01G509400 chr3A 93.443 671 20 9 1306 1967 730006157 730006812 0.000000e+00 974
3 TraesCS3A01G509400 chr3A 93.443 671 20 9 1306 1967 730469272 730468617 0.000000e+00 974
4 TraesCS3A01G509400 chr3A 92.825 669 25 8 1306 1966 730448704 730448051 0.000000e+00 948
5 TraesCS3A01G509400 chr3A 92.793 666 25 8 1306 1963 730026199 730026849 0.000000e+00 942
6 TraesCS3A01G509400 chr3A 96.729 428 13 1 1539 1966 730097650 730097224 0.000000e+00 712
7 TraesCS3A01G509400 chr3A 80.462 1039 112 49 997 1973 730092023 730093032 0.000000e+00 710
8 TraesCS3A01G509400 chr3A 80.250 1038 114 51 998 1973 730463299 730464307 0.000000e+00 697
9 TraesCS3A01G509400 chr3A 79.942 1042 117 49 998 1976 730012189 730011177 0.000000e+00 682
10 TraesCS3A01G509400 chr3A 79.789 1044 118 49 998 1976 730032033 730031018 0.000000e+00 673
11 TraesCS3A01G509400 chr3A 79.827 1041 117 49 998 1973 730442874 730443886 0.000000e+00 673
12 TraesCS3A01G509400 chr3A 91.687 409 11 8 1306 1706 730524765 730524372 1.620000e-151 545
13 TraesCS3A01G509400 chr3A 79.327 208 25 11 2199 2401 730443894 730444088 1.940000e-26 130
14 TraesCS3A01G509400 chr3A 78.972 214 25 12 2195 2401 730031018 730030818 6.970000e-26 128
15 TraesCS3A01G509400 chr3A 78.972 214 25 12 2195 2401 730464310 730464510 6.970000e-26 128
16 TraesCS3A01G509400 chr3A 82.099 162 13 10 2243 2401 730093087 730093235 9.010000e-25 124
17 TraesCS3A01G509400 chr3A 78.641 206 25 11 2195 2394 730011177 730010985 4.190000e-23 119
18 TraesCS3A01G509400 chr3A 78.641 206 25 11 2195 2394 730592092 730592284 4.190000e-23 119
19 TraesCS3A01G509400 chr3A 83.099 142 6 8 760 901 730012416 730012293 1.950000e-21 113
20 TraesCS3A01G509400 chr3A 83.099 142 6 8 760 901 730032260 730032137 1.950000e-21 113
21 TraesCS3A01G509400 chr3A 83.099 142 6 8 760 901 730091792 730091915 1.950000e-21 113
22 TraesCS3A01G509400 chr3A 83.099 142 6 8 760 901 730463072 730463195 1.950000e-21 113
23 TraesCS3A01G509400 chr3A 98.246 57 0 1 845 901 730442715 730442770 5.460000e-17 99
24 TraesCS3A01G509400 chr3D 92.624 1437 60 25 997 2401 600655216 600656638 0.000000e+00 2025
25 TraesCS3A01G509400 chr3D 85.824 522 45 16 1012 1530 600665561 600666056 5.880000e-146 527
26 TraesCS3A01G509400 chr3D 83.871 155 8 9 751 901 600654957 600655098 5.390000e-27 132
27 TraesCS3A01G509400 chr2A 97.309 706 17 1 1 704 381317584 381318289 0.000000e+00 1197
28 TraesCS3A01G509400 chr2A 97.163 705 18 1 1 703 322743237 322742533 0.000000e+00 1190
29 TraesCS3A01G509400 chr2A 97.167 706 17 2 1 703 689114657 689115362 0.000000e+00 1190
30 TraesCS3A01G509400 chr6A 97.305 705 17 1 1 703 478071974 478071270 0.000000e+00 1195
31 TraesCS3A01G509400 chr5A 97.309 706 16 2 1 703 54601587 54602292 0.000000e+00 1195
32 TraesCS3A01G509400 chr5A 97.038 709 19 1 1 707 525495630 525494922 0.000000e+00 1192
33 TraesCS3A01G509400 chr5A 97.167 706 18 1 1 704 525504505 525503800 0.000000e+00 1192
34 TraesCS3A01G509400 chr5A 97.034 708 16 4 1 704 603046166 603046872 0.000000e+00 1186
35 TraesCS3A01G509400 chr3B 94.444 720 28 6 1501 2212 697706297 697707012 0.000000e+00 1098
36 TraesCS3A01G509400 chr3B 96.185 498 17 1 1012 1507 697683271 697683768 0.000000e+00 813
37 TraesCS3A01G509400 chr3B 84.198 848 69 39 707 1506 808019399 808020229 0.000000e+00 763
38 TraesCS3A01G509400 chr3B 95.960 198 6 2 706 901 697682947 697683144 1.070000e-83 320
39 TraesCS3A01G509400 chrUn 93.592 671 19 9 1306 1967 267997481 267996826 0.000000e+00 979
40 TraesCS3A01G509400 chrUn 92.793 666 25 8 1306 1963 317181848 317182498 0.000000e+00 942
41 TraesCS3A01G509400 chrUn 91.687 409 11 8 1306 1706 459755938 459755545 1.620000e-151 545
42 TraesCS3A01G509400 chrUn 84.676 509 46 21 998 1494 358203206 358203694 1.670000e-131 479
43 TraesCS3A01G509400 chrUn 98.246 57 0 1 845 901 358203047 358203102 5.460000e-17 99
44 TraesCS3A01G509400 chr5D 88.172 186 17 5 2016 2196 462454615 462454800 1.450000e-52 217
45 TraesCS3A01G509400 chr5D 85.484 186 22 4 2016 2198 456039585 456039768 3.150000e-44 189
46 TraesCS3A01G509400 chr7D 86.486 185 19 4 2016 2197 585665831 585666012 5.240000e-47 198
47 TraesCS3A01G509400 chr7D 87.356 174 16 5 2028 2198 575899160 575898990 6.770000e-46 195
48 TraesCS3A01G509400 chr6D 86.413 184 19 5 2019 2197 388209927 388209745 1.880000e-46 196
49 TraesCS3A01G509400 chr4B 86.264 182 18 5 2019 2197 27243823 27243646 8.760000e-45 191
50 TraesCS3A01G509400 chr2D 85.635 181 24 2 2019 2197 190023953 190024133 3.150000e-44 189


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 TraesCS3A01G509400 chr3A 730084763 730087163 2400 False 4434.000000 4434 100.000000 1 2401 1 chr3A.!!$F4 2400
1 TraesCS3A01G509400 chr3A 730075809 730076512 703 False 1234.000000 1234 98.295000 1 704 1 chr3A.!!$F3 703
2 TraesCS3A01G509400 chr3A 730006157 730006812 655 False 974.000000 974 93.443000 1306 1967 1 chr3A.!!$F1 661
3 TraesCS3A01G509400 chr3A 730468617 730469272 655 True 974.000000 974 93.443000 1306 1967 1 chr3A.!!$R3 661
4 TraesCS3A01G509400 chr3A 730448051 730448704 653 True 948.000000 948 92.825000 1306 1966 1 chr3A.!!$R2 660
5 TraesCS3A01G509400 chr3A 730026199 730026849 650 False 942.000000 942 92.793000 1306 1963 1 chr3A.!!$F2 657
6 TraesCS3A01G509400 chr3A 730091792 730093235 1443 False 315.666667 710 81.886667 760 2401 3 chr3A.!!$F6 1641
7 TraesCS3A01G509400 chr3A 730463072 730464510 1438 False 312.666667 697 80.773667 760 2401 3 chr3A.!!$F8 1641
8 TraesCS3A01G509400 chr3A 730010985 730012416 1431 True 304.666667 682 80.560667 760 2394 3 chr3A.!!$R5 1634
9 TraesCS3A01G509400 chr3A 730030818 730032260 1442 True 304.666667 673 80.620000 760 2401 3 chr3A.!!$R6 1641
10 TraesCS3A01G509400 chr3A 730442715 730444088 1373 False 300.666667 673 85.800000 845 2401 3 chr3A.!!$F7 1556
11 TraesCS3A01G509400 chr3D 600654957 600656638 1681 False 1078.500000 2025 88.247500 751 2401 2 chr3D.!!$F2 1650
12 TraesCS3A01G509400 chr2A 381317584 381318289 705 False 1197.000000 1197 97.309000 1 704 1 chr2A.!!$F1 703
13 TraesCS3A01G509400 chr2A 322742533 322743237 704 True 1190.000000 1190 97.163000 1 703 1 chr2A.!!$R1 702
14 TraesCS3A01G509400 chr2A 689114657 689115362 705 False 1190.000000 1190 97.167000 1 703 1 chr2A.!!$F2 702
15 TraesCS3A01G509400 chr6A 478071270 478071974 704 True 1195.000000 1195 97.305000 1 703 1 chr6A.!!$R1 702
16 TraesCS3A01G509400 chr5A 54601587 54602292 705 False 1195.000000 1195 97.309000 1 703 1 chr5A.!!$F1 702
17 TraesCS3A01G509400 chr5A 525494922 525495630 708 True 1192.000000 1192 97.038000 1 707 1 chr5A.!!$R1 706
18 TraesCS3A01G509400 chr5A 525503800 525504505 705 True 1192.000000 1192 97.167000 1 704 1 chr5A.!!$R2 703
19 TraesCS3A01G509400 chr5A 603046166 603046872 706 False 1186.000000 1186 97.034000 1 704 1 chr5A.!!$F2 703
20 TraesCS3A01G509400 chr3B 697706297 697707012 715 False 1098.000000 1098 94.444000 1501 2212 1 chr3B.!!$F1 711
21 TraesCS3A01G509400 chr3B 808019399 808020229 830 False 763.000000 763 84.198000 707 1506 1 chr3B.!!$F2 799
22 TraesCS3A01G509400 chr3B 697682947 697683768 821 False 566.500000 813 96.072500 706 1507 2 chr3B.!!$F3 801
23 TraesCS3A01G509400 chrUn 267996826 267997481 655 True 979.000000 979 93.592000 1306 1967 1 chrUn.!!$R1 661
24 TraesCS3A01G509400 chrUn 317181848 317182498 650 False 942.000000 942 92.793000 1306 1963 1 chrUn.!!$F1 657
25 TraesCS3A01G509400 chrUn 358203047 358203694 647 False 289.000000 479 91.461000 845 1494 2 chrUn.!!$F2 649

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
391 395 0.110104 GGGCTGCATCCAGATAGCTT 59.89 55.0 9.17 0.0 41.77 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1938 2105 1.263356 CGACTAGAGGTGGGGTCAAA 58.737 55.0 0.0 0.0 0.0 2.69 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
391 395 0.110104 GGGCTGCATCCAGATAGCTT 59.890 55.000 9.17 0.0 41.77 3.74
405 409 8.752005 TCCAGATAGCTTTAACTTTTGCATAT 57.248 30.769 0.00 0.0 0.00 1.78
476 480 6.274157 AGACGAAGACAATTCATGTAGAGT 57.726 37.500 0.00 0.0 44.12 3.24
609 617 5.413309 TGGTCCAAACATCAAAGTTGTTT 57.587 34.783 0.00 1.5 45.59 2.83
669 677 4.079844 TGTCATTTGAGGCCATCTCCATTA 60.080 41.667 5.01 0.0 41.76 1.90
720 728 3.609103 ACACGAACACAAAGCATCTTC 57.391 42.857 0.00 0.0 0.00 2.87
901 913 5.149273 GTCAAGCACATATCACAAACACAG 58.851 41.667 0.00 0.0 0.00 3.66
904 916 5.808042 AGCACATATCACAAACACAGATC 57.192 39.130 0.00 0.0 0.00 2.75
905 917 4.637534 AGCACATATCACAAACACAGATCC 59.362 41.667 0.00 0.0 0.00 3.36
906 918 4.637534 GCACATATCACAAACACAGATCCT 59.362 41.667 0.00 0.0 0.00 3.24
907 919 5.220739 GCACATATCACAAACACAGATCCTC 60.221 44.000 0.00 0.0 0.00 3.71
908 920 5.295292 CACATATCACAAACACAGATCCTCC 59.705 44.000 0.00 0.0 0.00 4.30
909 921 5.190528 ACATATCACAAACACAGATCCTCCT 59.809 40.000 0.00 0.0 0.00 3.69
910 922 3.685139 TCACAAACACAGATCCTCCTC 57.315 47.619 0.00 0.0 0.00 3.71
911 923 2.303022 TCACAAACACAGATCCTCCTCC 59.697 50.000 0.00 0.0 0.00 4.30
912 924 2.304180 CACAAACACAGATCCTCCTCCT 59.696 50.000 0.00 0.0 0.00 3.69
913 925 2.982488 ACAAACACAGATCCTCCTCCTT 59.018 45.455 0.00 0.0 0.00 3.36
914 926 3.008485 ACAAACACAGATCCTCCTCCTTC 59.992 47.826 0.00 0.0 0.00 3.46
915 927 2.630889 ACACAGATCCTCCTCCTTCA 57.369 50.000 0.00 0.0 0.00 3.02
916 928 2.907892 ACACAGATCCTCCTCCTTCAA 58.092 47.619 0.00 0.0 0.00 2.69
917 929 3.251484 ACACAGATCCTCCTCCTTCAAA 58.749 45.455 0.00 0.0 0.00 2.69
918 930 3.008485 ACACAGATCCTCCTCCTTCAAAC 59.992 47.826 0.00 0.0 0.00 2.93
926 938 4.536090 TCCTCCTCCTTCAAACACATACAT 59.464 41.667 0.00 0.0 0.00 2.29
942 954 5.957168 CACATACATAGATCCTCATCCTCCT 59.043 44.000 0.00 0.0 0.00 3.69
943 955 7.122048 CACATACATAGATCCTCATCCTCCTA 58.878 42.308 0.00 0.0 0.00 2.94
945 957 9.019542 ACATACATAGATCCTCATCCTCCTATA 57.980 37.037 0.00 0.0 0.00 1.31
950 962 6.288096 AGATCCTCATCCTCCTATATACCC 57.712 45.833 0.00 0.0 0.00 3.69
953 967 6.031964 TCCTCATCCTCCTATATACCCATC 57.968 45.833 0.00 0.0 0.00 3.51
956 981 6.281190 TCATCCTCCTATATACCCATCGAT 57.719 41.667 0.00 0.0 0.00 3.59
957 982 6.307776 TCATCCTCCTATATACCCATCGATC 58.692 44.000 0.00 0.0 0.00 3.69
960 985 5.044402 TCCTCCTATATACCCATCGATCACA 60.044 44.000 0.00 0.0 0.00 3.58
1087 1152 2.936919 TCACAAGCACATGGAGAAGT 57.063 45.000 0.00 0.0 0.00 3.01
1146 1213 2.434359 GTACGCCCCACAGCTCAC 60.434 66.667 0.00 0.0 0.00 3.51
1535 1634 5.793457 GCTGTTTGGTATGTGTATTTTCGTC 59.207 40.000 0.00 0.0 0.00 4.20
1596 1724 6.769512 TGGGCACATCTCCTCTAATAATAAC 58.230 40.000 0.00 0.0 0.00 1.89
1733 1900 3.880490 GGGCGTGAACCACATGATAAATA 59.120 43.478 0.00 0.0 37.69 1.40
2104 2274 5.000591 TCTTACATTGAGATCCGTGCAAAA 58.999 37.500 0.00 0.0 0.00 2.44
2109 2280 6.686630 ACATTGAGATCCGTGCAAAATTTTA 58.313 32.000 2.44 0.0 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 106 1.878953 CCGTGAACAGTAACCTTGCT 58.121 50.000 0.00 0.00 0.00 3.91
261 265 3.124636 CCTCGAATCGGAAAACGTTCAAT 59.875 43.478 0.00 0.00 44.69 2.57
391 395 7.624360 ATCCGAGTTCATATGCAAAAGTTAA 57.376 32.000 0.00 0.00 0.00 2.01
405 409 8.737168 ATAAAAATCATCTCAATCCGAGTTCA 57.263 30.769 0.00 0.00 42.88 3.18
476 480 4.901849 AGGACAATCTCGGATGAAGGAATA 59.098 41.667 0.00 0.00 0.00 1.75
609 617 3.820467 AGAAATTTCACATTGCCGAGTGA 59.180 39.130 19.99 0.00 42.55 3.41
704 712 7.558435 CACAAATAGAAGATGCTTTGTGTTC 57.442 36.000 15.32 0.19 46.70 3.18
713 721 5.583854 TCTTCTGCTCACAAATAGAAGATGC 59.416 40.000 10.51 0.00 45.97 3.91
720 728 5.659463 AGCTACTCTTCTGCTCACAAATAG 58.341 41.667 0.00 0.00 30.41 1.73
730 738 3.997021 TGTGCTTTTAGCTACTCTTCTGC 59.003 43.478 0.00 0.00 42.97 4.26
901 913 3.703001 TGTGTTTGAAGGAGGAGGATC 57.297 47.619 0.00 0.00 0.00 3.36
904 916 4.286297 TGTATGTGTTTGAAGGAGGAGG 57.714 45.455 0.00 0.00 0.00 4.30
905 917 6.878317 TCTATGTATGTGTTTGAAGGAGGAG 58.122 40.000 0.00 0.00 0.00 3.69
906 918 6.867519 TCTATGTATGTGTTTGAAGGAGGA 57.132 37.500 0.00 0.00 0.00 3.71
907 919 6.708054 GGATCTATGTATGTGTTTGAAGGAGG 59.292 42.308 0.00 0.00 0.00 4.30
908 920 7.504403 AGGATCTATGTATGTGTTTGAAGGAG 58.496 38.462 0.00 0.00 0.00 3.69
909 921 7.125659 TGAGGATCTATGTATGTGTTTGAAGGA 59.874 37.037 0.00 0.00 34.92 3.36
910 922 7.275183 TGAGGATCTATGTATGTGTTTGAAGG 58.725 38.462 0.00 0.00 34.92 3.46
911 923 8.899427 ATGAGGATCTATGTATGTGTTTGAAG 57.101 34.615 0.00 0.00 34.92 3.02
912 924 7.933577 GGATGAGGATCTATGTATGTGTTTGAA 59.066 37.037 0.00 0.00 34.92 2.69
913 925 7.290948 AGGATGAGGATCTATGTATGTGTTTGA 59.709 37.037 0.00 0.00 34.92 2.69
914 926 7.448420 AGGATGAGGATCTATGTATGTGTTTG 58.552 38.462 0.00 0.00 34.92 2.93
915 927 7.256475 GGAGGATGAGGATCTATGTATGTGTTT 60.256 40.741 0.00 0.00 34.92 2.83
916 928 6.212388 GGAGGATGAGGATCTATGTATGTGTT 59.788 42.308 0.00 0.00 34.92 3.32
917 929 5.719085 GGAGGATGAGGATCTATGTATGTGT 59.281 44.000 0.00 0.00 34.92 3.72
918 930 5.957168 AGGAGGATGAGGATCTATGTATGTG 59.043 44.000 0.00 0.00 34.92 3.21
926 938 6.920584 TGGGTATATAGGAGGATGAGGATCTA 59.079 42.308 0.00 0.00 34.92 1.98
942 954 5.337250 GCCTTGTGTGATCGATGGGTATATA 60.337 44.000 0.54 0.00 0.00 0.86
943 955 4.563580 GCCTTGTGTGATCGATGGGTATAT 60.564 45.833 0.54 0.00 0.00 0.86
945 957 2.485479 GCCTTGTGTGATCGATGGGTAT 60.485 50.000 0.54 0.00 0.00 2.73
946 958 1.134521 GCCTTGTGTGATCGATGGGTA 60.135 52.381 0.54 0.00 0.00 3.69
947 959 0.392998 GCCTTGTGTGATCGATGGGT 60.393 55.000 0.54 0.00 0.00 4.51
950 962 0.371301 CGTGCCTTGTGTGATCGATG 59.629 55.000 0.54 0.00 0.00 3.84
953 967 0.667487 ACTCGTGCCTTGTGTGATCG 60.667 55.000 0.00 0.00 0.00 3.69
956 981 4.436515 CACTCGTGCCTTGTGTGA 57.563 55.556 0.00 0.00 33.80 3.58
1146 1213 4.190304 TGCGCAAGTAATATGTAAAGCG 57.810 40.909 8.16 0.00 45.89 4.68
1209 1290 7.575365 TGCATATTGTCAAGTAATTATCAGCG 58.425 34.615 0.00 0.00 0.00 5.18
1382 1467 2.503846 ATCAGTGGTGGTGGCCATGG 62.504 60.000 9.72 7.63 41.08 3.66
1535 1634 7.119699 ACAAGAATGTACCAACATGACTATGTG 59.880 37.037 0.00 0.00 45.79 3.21
1596 1724 3.254892 GAGAGAAAAGAAGGCGTGTAGG 58.745 50.000 0.00 0.00 0.00 3.18
1933 2100 1.972588 AGAGGTGGGGTCAAATAGCT 58.027 50.000 0.00 0.00 0.00 3.32
1938 2105 1.263356 CGACTAGAGGTGGGGTCAAA 58.737 55.000 0.00 0.00 0.00 2.69
2038 2208 5.701855 AGTGAGACTTAACGAAGCTTAGTC 58.298 41.667 12.87 14.41 35.97 2.59
2294 2470 7.549147 AGTAATAACCTTGTCCTAGTTGTCA 57.451 36.000 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.