Multiple sequence alignment - TraesCS7D01G243200

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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 TraesCS7D01G243200 chr7D 100.000 2478 0 0 1 2478 209079996 209082473 0.000000e+00 4577.0
1 TraesCS7D01G243200 chr7D 96.119 1314 36 4 592 1902 370967554 370968855 0.000000e+00 2130.0
2 TraesCS7D01G243200 chr7D 97.361 758 20 0 1721 2478 370968730 370969487 0.000000e+00 1290.0
3 TraesCS7D01G243200 chr7D 80.272 882 127 33 599 1463 135502886 135503737 2.710000e-174 621.0
4 TraesCS7D01G243200 chr7D 91.781 146 12 0 1722 1867 370968760 370968905 1.160000e-48 204.0
5 TraesCS7D01G243200 chr7D 97.368 114 3 0 597 710 209094829 209094716 6.990000e-46 195.0
6 TraesCS7D01G243200 chr7D 97.368 114 3 0 597 710 370973278 370973165 6.990000e-46 195.0
7 TraesCS7D01G243200 chr7D 96.667 60 2 0 1837 1896 209081716 209081775 1.570000e-17 100.0
8 TraesCS7D01G243200 chr7B 89.963 1903 111 25 597 2475 407491168 407493014 0.000000e+00 2383.0
9 TraesCS7D01G243200 chr7B 86.121 562 67 8 1 554 726094170 726094728 1.640000e-166 595.0
10 TraesCS7D01G243200 chr7B 97.727 44 0 1 559 601 412559544 412559587 9.500000e-10 75.0
11 TraesCS7D01G243200 chr6D 96.333 1309 32 5 597 1902 433590744 433589449 0.000000e+00 2137.0
12 TraesCS7D01G243200 chr6D 93.799 758 23 4 1721 2478 433589603 433588870 0.000000e+00 1118.0
13 TraesCS7D01G243200 chr6D 95.238 147 7 0 1721 1867 433589574 433589428 1.480000e-57 233.0
14 TraesCS7D01G243200 chr4D 93.695 571 33 1 1 568 94778905 94778335 0.000000e+00 852.0
15 TraesCS7D01G243200 chr4D 92.845 573 36 3 1 568 210992257 210991685 0.000000e+00 826.0
16 TraesCS7D01G243200 chr4D 92.832 572 36 3 1 568 357604663 357605233 0.000000e+00 824.0
17 TraesCS7D01G243200 chr3D 93.838 568 32 1 4 568 333688450 333687883 0.000000e+00 852.0
18 TraesCS7D01G243200 chr3D 93.706 572 31 3 1 568 374567136 374567706 0.000000e+00 852.0
19 TraesCS7D01G243200 chr3D 93.345 571 35 1 1 568 281444465 281443895 0.000000e+00 841.0
20 TraesCS7D01G243200 chr3D 92.644 571 39 3 1 568 180034296 180034866 0.000000e+00 819.0
21 TraesCS7D01G243200 chr5D 93.486 568 34 1 4 568 268579200 268578633 0.000000e+00 841.0
22 TraesCS7D01G243200 chr5D 92.644 571 39 1 1 568 217984566 217985136 0.000000e+00 819.0
23 TraesCS7D01G243200 chr5D 86.624 157 18 3 596 751 306243933 306244087 1.180000e-38 171.0
24 TraesCS7D01G243200 chr5D 95.745 47 2 0 551 597 236621276 236621322 2.640000e-10 76.8
25 TraesCS7D01G243200 chr5A 79.339 1302 179 49 599 1852 638083212 638081953 0.000000e+00 832.0
26 TraesCS7D01G243200 chr3A 79.342 1307 177 56 599 1852 716987965 716986699 0.000000e+00 832.0
27 TraesCS7D01G243200 chr1D 78.344 1099 177 34 594 1668 267994874 267993813 0.000000e+00 654.0
28 TraesCS7D01G243200 chr1D 80.523 842 131 19 895 1716 18171933 18171105 1.260000e-172 616.0
29 TraesCS7D01G243200 chr7A 79.954 878 130 27 602 1463 80562765 80561918 2.730000e-169 604.0
30 TraesCS7D01G243200 chr6B 77.473 1092 179 39 596 1667 431404974 431406018 2.120000e-165 592.0
31 TraesCS7D01G243200 chr6B 85.370 540 73 6 9 544 197077191 197076654 2.780000e-154 555.0
32 TraesCS7D01G243200 chr6B 83.575 414 64 4 129 539 314737551 314737139 3.870000e-103 385.0
33 TraesCS7D01G243200 chr5B 85.740 561 72 6 1 554 648957601 648958160 9.870000e-164 586.0
34 TraesCS7D01G243200 chr3B 85.458 557 73 6 1 550 388359536 388358981 7.690000e-160 573.0
35 TraesCS7D01G243200 chr4B 85.607 535 66 9 1 530 311384619 311385147 3.600000e-153 551.0
36 TraesCS7D01G243200 chr4B 82.562 562 89 7 1 556 30238581 30239139 1.030000e-133 486.0
37 TraesCS7D01G243200 chr6A 83.562 584 81 11 893 1463 535279043 535279624 1.300000e-147 532.0


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 TraesCS7D01G243200 chr7D 209079996 209082473 2477 False 2338.500000 4577 98.333500 1 2478 2 chr7D.!!$F2 2477
1 TraesCS7D01G243200 chr7D 370967554 370969487 1933 False 1208.000000 2130 95.087000 592 2478 3 chr7D.!!$F3 1886
2 TraesCS7D01G243200 chr7D 135502886 135503737 851 False 621.000000 621 80.272000 599 1463 1 chr7D.!!$F1 864
3 TraesCS7D01G243200 chr7B 407491168 407493014 1846 False 2383.000000 2383 89.963000 597 2475 1 chr7B.!!$F1 1878
4 TraesCS7D01G243200 chr7B 726094170 726094728 558 False 595.000000 595 86.121000 1 554 1 chr7B.!!$F3 553
5 TraesCS7D01G243200 chr6D 433588870 433590744 1874 True 1162.666667 2137 95.123333 597 2478 3 chr6D.!!$R1 1881
6 TraesCS7D01G243200 chr4D 94778335 94778905 570 True 852.000000 852 93.695000 1 568 1 chr4D.!!$R1 567
7 TraesCS7D01G243200 chr4D 210991685 210992257 572 True 826.000000 826 92.845000 1 568 1 chr4D.!!$R2 567
8 TraesCS7D01G243200 chr4D 357604663 357605233 570 False 824.000000 824 92.832000 1 568 1 chr4D.!!$F1 567
9 TraesCS7D01G243200 chr3D 333687883 333688450 567 True 852.000000 852 93.838000 4 568 1 chr3D.!!$R2 564
10 TraesCS7D01G243200 chr3D 374567136 374567706 570 False 852.000000 852 93.706000 1 568 1 chr3D.!!$F2 567
11 TraesCS7D01G243200 chr3D 281443895 281444465 570 True 841.000000 841 93.345000 1 568 1 chr3D.!!$R1 567
12 TraesCS7D01G243200 chr3D 180034296 180034866 570 False 819.000000 819 92.644000 1 568 1 chr3D.!!$F1 567
13 TraesCS7D01G243200 chr5D 268578633 268579200 567 True 841.000000 841 93.486000 4 568 1 chr5D.!!$R1 564
14 TraesCS7D01G243200 chr5D 217984566 217985136 570 False 819.000000 819 92.644000 1 568 1 chr5D.!!$F1 567
15 TraesCS7D01G243200 chr5A 638081953 638083212 1259 True 832.000000 832 79.339000 599 1852 1 chr5A.!!$R1 1253
16 TraesCS7D01G243200 chr3A 716986699 716987965 1266 True 832.000000 832 79.342000 599 1852 1 chr3A.!!$R1 1253
17 TraesCS7D01G243200 chr1D 267993813 267994874 1061 True 654.000000 654 78.344000 594 1668 1 chr1D.!!$R2 1074
18 TraesCS7D01G243200 chr1D 18171105 18171933 828 True 616.000000 616 80.523000 895 1716 1 chr1D.!!$R1 821
19 TraesCS7D01G243200 chr7A 80561918 80562765 847 True 604.000000 604 79.954000 602 1463 1 chr7A.!!$R1 861
20 TraesCS7D01G243200 chr6B 431404974 431406018 1044 False 592.000000 592 77.473000 596 1667 1 chr6B.!!$F1 1071
21 TraesCS7D01G243200 chr6B 197076654 197077191 537 True 555.000000 555 85.370000 9 544 1 chr6B.!!$R1 535
22 TraesCS7D01G243200 chr5B 648957601 648958160 559 False 586.000000 586 85.740000 1 554 1 chr5B.!!$F1 553
23 TraesCS7D01G243200 chr3B 388358981 388359536 555 True 573.000000 573 85.458000 1 550 1 chr3B.!!$R1 549
24 TraesCS7D01G243200 chr4B 311384619 311385147 528 False 551.000000 551 85.607000 1 530 1 chr4B.!!$F2 529
25 TraesCS7D01G243200 chr4B 30238581 30239139 558 False 486.000000 486 82.562000 1 556 1 chr4B.!!$F1 555
26 TraesCS7D01G243200 chr6A 535279043 535279624 581 False 532.000000 532 83.562000 893 1463 1 chr6A.!!$F1 570

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
573 583 0.252881 TTCAGAGGATGAGGCCACCT 60.253 55.0 5.01 8.11 39.68 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2062 2323 1.176527 TCATGCTTACCTTTGGCTGC 58.823 50.0 0.0 0.0 0.0 5.25 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
25 27 8.840833 TTTGATTTGAAAATTTAGGGTTAGGC 57.159 30.769 0.00 0.00 0.00 3.93
28 30 7.896496 TGATTTGAAAATTTAGGGTTAGGCCTA 59.104 33.333 8.91 8.91 37.43 3.93
222 225 3.577415 ACCGAGTTCACTAGTTTAGGCTT 59.423 43.478 0.00 0.00 0.00 4.35
259 263 0.924090 CACCGAGTTTAGCAGATCGC 59.076 55.000 1.92 1.92 42.91 4.58
356 361 1.683385 TGATGCTCATCCACTCTACCG 59.317 52.381 7.34 0.00 37.02 4.02
504 511 3.118149 TGATGATGGCAGTAGAAGCACAT 60.118 43.478 0.00 0.00 0.00 3.21
523 530 1.064003 TCTAGCAACTTGCCCAAGGA 58.936 50.000 10.25 0.00 46.52 3.36
557 567 4.594920 ACAAGGAAGAGAACCTCAGATTCA 59.405 41.667 0.00 0.00 36.67 2.57
568 578 3.389925 CTCAGATTCAGAGGATGAGGC 57.610 52.381 0.00 0.00 39.68 4.70
569 579 2.037511 CTCAGATTCAGAGGATGAGGCC 59.962 54.545 0.00 0.00 39.68 5.19
570 580 1.767088 CAGATTCAGAGGATGAGGCCA 59.233 52.381 5.01 0.00 39.68 5.36
571 581 1.767681 AGATTCAGAGGATGAGGCCAC 59.232 52.381 5.01 0.00 39.68 5.01
572 582 0.842635 ATTCAGAGGATGAGGCCACC 59.157 55.000 5.01 2.48 39.68 4.61
573 583 0.252881 TTCAGAGGATGAGGCCACCT 60.253 55.000 5.01 8.11 39.68 4.00
585 595 2.868899 AGGCCACCTCAAAGAAGAAAG 58.131 47.619 5.01 0.00 0.00 2.62
586 596 2.175715 AGGCCACCTCAAAGAAGAAAGT 59.824 45.455 5.01 0.00 0.00 2.66
587 597 2.294512 GGCCACCTCAAAGAAGAAAGTG 59.705 50.000 0.00 0.00 0.00 3.16
588 598 2.287849 GCCACCTCAAAGAAGAAAGTGC 60.288 50.000 0.00 0.00 0.00 4.40
589 599 3.217626 CCACCTCAAAGAAGAAAGTGCT 58.782 45.455 0.00 0.00 0.00 4.40
590 600 4.389374 CCACCTCAAAGAAGAAAGTGCTA 58.611 43.478 0.00 0.00 0.00 3.49
665 675 0.550914 CCCCAATCTCCAAATCCCGA 59.449 55.000 0.00 0.00 0.00 5.14
704 714 4.469945 ACTCTCTAATCCCGGTCATTTTCA 59.530 41.667 0.00 0.00 0.00 2.69
828 849 9.604626 CAGCTCTCTGTTTTTGTTTTATAAGAG 57.395 33.333 0.00 0.00 35.61 2.85
849 871 2.520458 CAGGCTTGGTGGGGAACA 59.480 61.111 0.00 0.00 0.00 3.18
914 985 3.222603 GAACCACCATGTCTTTGTCCTT 58.777 45.455 0.00 0.00 0.00 3.36
1018 1092 0.813610 CATGGATTACGAGCCGGCAA 60.814 55.000 31.54 15.05 32.65 4.52
1081 1157 2.757099 GGAGTCCGGCGAACCCTA 60.757 66.667 9.30 0.00 0.00 3.53
1097 1173 7.093421 GGCGAACCCTAGTAGGAGATATTATTT 60.093 40.741 18.43 0.00 37.67 1.40
1967 2228 7.642978 GTGATTTCAGCAGTATAAATCAGCAAG 59.357 37.037 9.33 0.00 45.38 4.01
2062 2323 3.006110 AGCATCACATGGTTCAAAAGTGG 59.994 43.478 0.00 0.00 37.84 4.00
2219 2480 7.116805 GGAAAACATCTTTAGAAATTGCCACTG 59.883 37.037 0.00 0.00 0.00 3.66
2320 2581 1.309347 CTCTCCCTGAGCCTCTCCA 59.691 63.158 0.00 0.00 35.84 3.86
2407 2671 4.180057 GTGCCAACATGAAAACTTGTTGA 58.820 39.130 21.65 7.81 42.81 3.18
2422 2686 8.506168 AAACTTGTTGATGTAGTTCTTGAAGA 57.494 30.769 0.00 0.00 31.26 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 27 1.268794 CCGAGATGAGTTCAGCGTAGG 60.269 57.143 0.00 0.00 37.34 3.18
28 30 0.171455 GTCCGAGATGAGTTCAGCGT 59.829 55.000 0.00 0.00 37.34 5.07
92 94 1.200716 AGACCGAAAATGCATGTGCTG 59.799 47.619 0.00 0.00 42.66 4.41
199 202 3.577415 AGCCTAAACTAGTGAACTCGGTT 59.423 43.478 0.00 0.00 0.00 4.44
222 225 4.695217 GGTGATACCGAAGCAATTTTGA 57.305 40.909 0.00 0.00 0.00 2.69
251 255 0.249073 TTTCGGAGCTAGCGATCTGC 60.249 55.000 9.55 0.00 46.98 4.26
356 361 5.646577 ACCCTGTGAATAGATATAGACGC 57.353 43.478 0.00 0.00 0.00 5.19
504 511 1.064003 TCCTTGGGCAAGTTGCTAGA 58.936 50.000 26.16 13.27 44.28 2.43
523 530 3.904339 TCTCTTCCTTGTTCTAGTGGCTT 59.096 43.478 0.00 0.00 0.00 4.35
568 578 3.217626 AGCACTTTCTTCTTTGAGGTGG 58.782 45.455 0.00 0.00 0.00 4.61
569 579 6.260936 TCTTTAGCACTTTCTTCTTTGAGGTG 59.739 38.462 0.00 0.00 0.00 4.00
570 580 6.357367 TCTTTAGCACTTTCTTCTTTGAGGT 58.643 36.000 0.00 0.00 0.00 3.85
571 581 6.867662 TCTTTAGCACTTTCTTCTTTGAGG 57.132 37.500 0.00 0.00 0.00 3.86
572 582 8.147642 TCTTCTTTAGCACTTTCTTCTTTGAG 57.852 34.615 0.00 0.00 0.00 3.02
573 583 7.770897 ACTCTTCTTTAGCACTTTCTTCTTTGA 59.229 33.333 0.00 0.00 0.00 2.69
574 584 7.924940 ACTCTTCTTTAGCACTTTCTTCTTTG 58.075 34.615 0.00 0.00 0.00 2.77
575 585 9.614792 TTACTCTTCTTTAGCACTTTCTTCTTT 57.385 29.630 0.00 0.00 0.00 2.52
576 586 9.614792 TTTACTCTTCTTTAGCACTTTCTTCTT 57.385 29.630 0.00 0.00 0.00 2.52
577 587 9.267084 CTTTACTCTTCTTTAGCACTTTCTTCT 57.733 33.333 0.00 0.00 0.00 2.85
578 588 9.047371 ACTTTACTCTTCTTTAGCACTTTCTTC 57.953 33.333 0.00 0.00 0.00 2.87
579 589 8.966069 ACTTTACTCTTCTTTAGCACTTTCTT 57.034 30.769 0.00 0.00 0.00 2.52
580 590 8.425703 AGACTTTACTCTTCTTTAGCACTTTCT 58.574 33.333 0.00 0.00 0.00 2.52
581 591 8.491950 CAGACTTTACTCTTCTTTAGCACTTTC 58.508 37.037 0.00 0.00 0.00 2.62
582 592 7.988028 ACAGACTTTACTCTTCTTTAGCACTTT 59.012 33.333 0.00 0.00 0.00 2.66
583 593 7.501844 ACAGACTTTACTCTTCTTTAGCACTT 58.498 34.615 0.00 0.00 0.00 3.16
584 594 7.056844 ACAGACTTTACTCTTCTTTAGCACT 57.943 36.000 0.00 0.00 0.00 4.40
585 595 7.716768 AACAGACTTTACTCTTCTTTAGCAC 57.283 36.000 0.00 0.00 0.00 4.40
586 596 8.732746 AAAACAGACTTTACTCTTCTTTAGCA 57.267 30.769 0.00 0.00 0.00 3.49
665 675 7.554959 TTAGAGAGTTGAGGGTACAGATTTT 57.445 36.000 0.00 0.00 0.00 1.82
849 871 1.075896 CCCGAGGAACCCTAGCTCT 60.076 63.158 0.00 0.00 31.76 4.09
914 985 3.922850 GCGAGAATATGATGAATCAGCGA 59.077 43.478 0.00 0.00 40.64 4.93
1018 1092 1.016627 CCGCATCGACCACAAATCAT 58.983 50.000 0.00 0.00 0.00 2.45
1081 1157 7.952671 TCAACGCAGAAATAATATCTCCTACT 58.047 34.615 0.00 0.00 0.00 2.57
1531 1615 8.434733 TTCATTTTCATTTCAAACATCAGCAA 57.565 26.923 0.00 0.00 0.00 3.91
1967 2228 7.962917 ACGATGCCAAAATTTGTTATCAATTC 58.037 30.769 15.01 1.88 33.32 2.17
2062 2323 1.176527 TCATGCTTACCTTTGGCTGC 58.823 50.000 0.00 0.00 0.00 5.25
2219 2480 4.096532 GGGTTCTCAAGCTACTTTAATGCC 59.903 45.833 0.00 0.00 0.00 4.40
2320 2581 3.777522 AGTGGCAACTAGCTCTAATCCTT 59.222 43.478 0.00 0.00 44.79 3.36
2407 2671 5.736951 AGCTCAGTCTTCAAGAACTACAT 57.263 39.130 0.00 0.00 0.00 2.29
2422 2686 2.292267 CAACAACCAGTCAAGCTCAGT 58.708 47.619 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.