Multiple sequence alignment - TraesCS2D01G439800

Loading Multiple Alignment...

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 TraesCS2D01G439800 chr2D 100.000 2330 0 0 1 2330 549022599 549020270 0.000000e+00 4303.0
1 TraesCS2D01G439800 chr2D 82.143 588 76 19 1013 1579 548751156 548750577 5.820000e-131 477.0
2 TraesCS2D01G439800 chr2D 82.292 576 64 20 1748 2299 548750557 548749996 4.530000e-127 464.0
3 TraesCS2D01G439800 chr2D 82.983 476 39 13 1856 2296 550670416 550670884 2.170000e-105 392.0
4 TraesCS2D01G439800 chr2D 82.845 478 42 11 1856 2299 551143350 551142879 2.170000e-105 392.0
5 TraesCS2D01G439800 chr2D 82.672 479 41 13 1856 2299 549921337 549920866 1.010000e-103 387.0
6 TraesCS2D01G439800 chr2D 87.025 316 38 2 1016 1331 548744824 548744512 1.020000e-93 353.0
7 TraesCS2D01G439800 chr2D 90.000 70 5 2 601 669 24426354 24426422 3.190000e-14 89.8
8 TraesCS2D01G439800 chr2D 88.525 61 7 0 607 667 81947613 81947553 8.930000e-10 75.0
9 TraesCS2D01G439800 chr5A 98.288 1460 16 2 871 2330 504576657 504575207 0.000000e+00 2549.0
10 TraesCS2D01G439800 chr5A 93.453 611 29 6 2 610 504621476 504620875 0.000000e+00 896.0
11 TraesCS2D01G439800 chr5A 87.821 312 5 6 587 879 504577002 504576705 3.710000e-88 335.0
12 TraesCS2D01G439800 chr5A 95.455 44 2 0 630 673 456074829 456074786 1.160000e-08 71.3
13 TraesCS2D01G439800 chr5B 95.238 588 27 1 1 587 6670360 6670947 0.000000e+00 929.0
14 TraesCS2D01G439800 chrUn 95.060 587 26 3 1 586 42252773 42253357 0.000000e+00 920.0
15 TraesCS2D01G439800 chr7B 94.378 587 31 2 2 586 137448208 137448794 0.000000e+00 900.0
16 TraesCS2D01G439800 chr7B 91.652 587 45 4 2 586 488389023 488389607 0.000000e+00 809.0
17 TraesCS2D01G439800 chr7B 85.185 81 7 2 587 663 48342866 48342945 6.900000e-11 78.7
18 TraesCS2D01G439800 chr7B 95.556 45 2 0 629 673 54729570 54729526 3.210000e-09 73.1
19 TraesCS2D01G439800 chr6B 94.349 584 31 2 4 586 448139260 448139842 0.000000e+00 894.0
20 TraesCS2D01G439800 chr1B 94.208 587 32 2 2 586 554703339 554702753 0.000000e+00 894.0
21 TraesCS2D01G439800 chr1B 94.218 588 30 4 2 586 554714899 554714313 0.000000e+00 894.0
22 TraesCS2D01G439800 chr4B 95.741 540 22 1 48 586 622759021 622759560 0.000000e+00 869.0
23 TraesCS2D01G439800 chr4B 90.741 162 13 2 1589 1750 142521057 142520898 5.040000e-52 215.0
24 TraesCS2D01G439800 chr4A 92.203 590 38 6 2 586 699936911 699937497 0.000000e+00 828.0
25 TraesCS2D01G439800 chr4A 93.182 88 5 1 587 673 511238896 511238809 6.760000e-26 128.0
26 TraesCS2D01G439800 chr2A 83.951 567 70 14 1026 1576 691765305 691764744 7.380000e-145 523.0
27 TraesCS2D01G439800 chr2A 82.777 569 71 21 1748 2299 691764291 691763733 1.250000e-132 483.0
28 TraesCS2D01G439800 chr2A 88.291 316 34 2 1016 1331 691757961 691757649 2.190000e-100 375.0
29 TraesCS2D01G439800 chr2A 91.925 161 12 1 1589 1749 79315107 79315266 8.380000e-55 224.0
30 TraesCS2D01G439800 chr2B 82.594 586 74 16 1013 1579 655843114 655842538 2.080000e-135 492.0
31 TraesCS2D01G439800 chr2B 83.019 477 43 11 1856 2299 656230778 656230307 4.670000e-107 398.0
32 TraesCS2D01G439800 chr2B 82.989 435 54 10 1748 2167 655842518 655842089 2.190000e-100 375.0
33 TraesCS2D01G439800 chr2B 86.709 316 39 2 1016 1331 655839219 655838907 4.770000e-92 348.0
34 TraesCS2D01G439800 chr2B 79.710 483 54 15 1856 2303 656602827 656602354 2.250000e-80 309.0
35 TraesCS2D01G439800 chr6D 92.453 159 12 0 1589 1747 90135048 90134890 6.480000e-56 228.0
36 TraesCS2D01G439800 chr6D 88.158 76 4 3 587 658 13206040 13205966 4.130000e-13 86.1
37 TraesCS2D01G439800 chr1D 92.453 159 12 0 1589 1747 16899572 16899414 6.480000e-56 228.0
38 TraesCS2D01G439800 chr7A 92.453 159 11 1 1589 1747 719012596 719012439 2.330000e-55 226.0
39 TraesCS2D01G439800 chr7A 91.824 159 12 1 1589 1747 719286465 719286308 1.080000e-53 220.0
40 TraesCS2D01G439800 chr5D 90.909 165 15 0 1589 1753 59947685 59947849 3.010000e-54 222.0
41 TraesCS2D01G439800 chr3A 90.419 167 16 0 1589 1755 607058414 607058580 1.080000e-53 220.0
42 TraesCS2D01G439800 chr3D 91.566 83 4 2 587 667 333995418 333995337 6.810000e-21 111.0
43 TraesCS2D01G439800 chr4D 84.932 73 9 2 596 667 7179217 7179288 3.210000e-09 73.1


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 TraesCS2D01G439800 chr2D 549020270 549022599 2329 True 4303.0 4303 100.000000 1 2330 1 chr2D.!!$R3 2329
1 TraesCS2D01G439800 chr2D 548749996 548751156 1160 True 470.5 477 82.217500 1013 2299 2 chr2D.!!$R6 1286
2 TraesCS2D01G439800 chr5A 504575207 504577002 1795 True 1442.0 2549 93.054500 587 2330 2 chr5A.!!$R3 1743
3 TraesCS2D01G439800 chr5A 504620875 504621476 601 True 896.0 896 93.453000 2 610 1 chr5A.!!$R2 608
4 TraesCS2D01G439800 chr5B 6670360 6670947 587 False 929.0 929 95.238000 1 587 1 chr5B.!!$F1 586
5 TraesCS2D01G439800 chrUn 42252773 42253357 584 False 920.0 920 95.060000 1 586 1 chrUn.!!$F1 585
6 TraesCS2D01G439800 chr7B 137448208 137448794 586 False 900.0 900 94.378000 2 586 1 chr7B.!!$F2 584
7 TraesCS2D01G439800 chr7B 488389023 488389607 584 False 809.0 809 91.652000 2 586 1 chr7B.!!$F3 584
8 TraesCS2D01G439800 chr6B 448139260 448139842 582 False 894.0 894 94.349000 4 586 1 chr6B.!!$F1 582
9 TraesCS2D01G439800 chr1B 554702753 554703339 586 True 894.0 894 94.208000 2 586 1 chr1B.!!$R1 584
10 TraesCS2D01G439800 chr1B 554714313 554714899 586 True 894.0 894 94.218000 2 586 1 chr1B.!!$R2 584
11 TraesCS2D01G439800 chr4B 622759021 622759560 539 False 869.0 869 95.741000 48 586 1 chr4B.!!$F1 538
12 TraesCS2D01G439800 chr4A 699936911 699937497 586 False 828.0 828 92.203000 2 586 1 chr4A.!!$F1 584
13 TraesCS2D01G439800 chr2A 691763733 691765305 1572 True 503.0 523 83.364000 1026 2299 2 chr2A.!!$R2 1273
14 TraesCS2D01G439800 chr2B 655838907 655843114 4207 True 405.0 492 84.097333 1013 2167 3 chr2B.!!$R3 1154

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
644 654 2.38041 CGGTTTTCGAGAGGCACGG 61.38 63.158 0.0 0.0 42.43 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1484 1586 5.514204 GCACAATCAGCAGAAATAATCACAC 59.486 40.0 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
563 573 4.979943 TTTTCGGTAGGTTTTTCGGTTT 57.020 36.364 0.00 0.0 0.00 3.27
580 590 3.559242 CGGTTTGGTTTCAAAATGCACAT 59.441 39.130 0.00 0.0 43.56 3.21
608 618 4.502105 AAAAACCAAACCAGGAGCATTT 57.498 36.364 0.00 0.0 0.00 2.32
644 654 2.380410 CGGTTTTCGAGAGGCACGG 61.380 63.158 0.00 0.0 42.43 4.94
645 655 2.677979 GGTTTTCGAGAGGCACGGC 61.678 63.158 0.00 0.0 0.00 5.68
1484 1586 6.038603 CCACCATGGTTCAGTTATCTGTATTG 59.961 42.308 16.84 0.0 36.57 1.90
1787 2180 8.772705 CAATAATTCTGAGTAGGCAGATTTCTC 58.227 37.037 0.00 0.0 43.84 2.87
2237 2768 7.609097 TCATCTTCTTATAGCCTGTGAGAAT 57.391 36.000 0.00 0.0 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
307 310 3.423123 CCAAGCACGTACATTTTCTCGTC 60.423 47.826 0.00 0.00 34.30 4.20
372 379 2.969443 ATTTCTTGAGGCGAACAACG 57.031 45.000 0.00 0.00 45.66 4.10
563 573 5.781210 TCACTATGTGCATTTTGAAACCA 57.219 34.783 0.00 0.00 32.98 3.67
608 618 4.112716 ACCGCTTTCGAAAAAGGAAAAA 57.887 36.364 27.77 0.03 41.87 1.94
627 637 2.677979 GCCGTGCCTCTCGAAAACC 61.678 63.158 0.00 0.00 0.00 3.27
698 709 5.001232 GGCTATTTGGAGTTATTATCGCCA 58.999 41.667 0.00 0.00 33.31 5.69
995 1080 4.228097 CTTTCGCCGCCATCGCTG 62.228 66.667 0.00 0.00 0.00 5.18
996 1081 3.365291 TACTTTCGCCGCCATCGCT 62.365 57.895 0.00 0.00 0.00 4.93
1068 1153 2.609491 GCTGATATCCATCGCGGTGTAA 60.609 50.000 19.62 6.37 33.51 2.41
1484 1586 5.514204 GCACAATCAGCAGAAATAATCACAC 59.486 40.000 0.00 0.00 0.00 3.82
1642 1859 8.703743 AGAGTATAGATTCACTCATTTTGCTCT 58.296 33.333 4.70 0.00 42.99 4.09


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

AutoCloner maintained by Alex Coulton.