Multiple sequence alignment - TraesCS6A01G325800

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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 TraesCS6A01G325800 chr6A 100.000 3147 0 0 1 3147 559264924 559268070 0.000000e+00 5812.0
1 TraesCS6A01G325800 chr3B 99.111 3149 15 2 1 3147 53953740 53956877 0.000000e+00 5648.0
2 TraesCS6A01G325800 chr3B 92.285 337 21 4 1 337 187556288 187556619 1.020000e-129 473.0
3 TraesCS6A01G325800 chr1B 97.998 2847 43 3 1 2844 457534505 457537340 0.000000e+00 4929.0
4 TraesCS6A01G325800 chr1B 98.371 307 5 0 2841 3147 457537596 457537902 9.930000e-150 540.0
5 TraesCS6A01G325800 chr5D 89.683 1357 111 19 1 1330 505545757 505544403 0.000000e+00 1703.0
6 TraesCS6A01G325800 chr5D 90.061 815 55 6 1697 2511 505543702 505542914 0.000000e+00 1033.0
7 TraesCS6A01G325800 chr5D 92.901 324 17 4 1333 1650 505544021 505543698 1.710000e-127 466.0
8 TraesCS6A01G325800 chr5D 91.471 340 23 3 2809 3147 505542669 505542335 2.210000e-126 462.0
9 TraesCS6A01G325800 chr5D 85.000 160 22 2 2988 3146 505402621 505402463 9.030000e-36 161.0
10 TraesCS6A01G325800 chr5D 88.288 111 11 2 2574 2683 505542879 505542770 7.080000e-27 132.0
11 TraesCS6A01G325800 chr3D 86.612 1576 162 37 1000 2560 411871049 411872590 0.000000e+00 1696.0
12 TraesCS6A01G325800 chr3D 88.946 977 80 20 1595 2560 352943150 352944109 0.000000e+00 1181.0
13 TraesCS6A01G325800 chr3D 89.828 816 69 7 524 1330 208632701 208631891 0.000000e+00 1035.0
14 TraesCS6A01G325800 chr3D 90.485 536 29 9 1 536 352930187 352930700 0.000000e+00 688.0
15 TraesCS6A01G325800 chr3D 89.366 536 34 10 1 536 411870488 411871000 0.000000e+00 652.0
16 TraesCS6A01G325800 chr3D 86.352 403 49 3 6 408 208633199 208632803 4.820000e-118 435.0
17 TraesCS6A01G325800 chr2D 86.397 1507 155 38 1069 2560 128387352 128388823 0.000000e+00 1602.0
18 TraesCS6A01G325800 chr2D 83.901 851 97 31 1000 1835 128374192 128375017 0.000000e+00 776.0
19 TraesCS6A01G325800 chr2D 89.739 536 33 9 1 536 128373630 128374143 0.000000e+00 665.0
20 TraesCS6A01G325800 chr2D 87.714 350 22 1 1 350 128389145 128388817 3.810000e-104 388.0
21 TraesCS6A01G325800 chr5A 87.944 1352 110 33 1345 2683 633026623 633025312 0.000000e+00 1544.0
22 TraesCS6A01G325800 chr5A 90.621 821 63 8 524 1330 633027849 633027029 0.000000e+00 1077.0
23 TraesCS6A01G325800 chr5A 85.714 448 52 7 6 442 633028423 633027977 2.210000e-126 462.0
24 TraesCS6A01G325800 chr5B 85.755 1390 123 34 15 1330 635610800 635609412 0.000000e+00 1400.0
25 TraesCS6A01G325800 chr5B 87.919 1192 88 32 1345 2506 635609024 635607859 0.000000e+00 1352.0
26 TraesCS6A01G325800 chr5B 86.297 343 24 14 2600 2936 635607757 635607432 4.990000e-93 351.0
27 TraesCS6A01G325800 chr5B 94.186 172 7 1 2549 2717 635607856 635607685 3.110000e-65 259.0
28 TraesCS6A01G325800 chr5B 91.358 162 11 3 2987 3147 635607425 635607266 5.280000e-53 219.0
29 TraesCS6A01G325800 chr5B 82.822 163 19 6 2988 3146 635464222 635464065 1.520000e-28 137.0
30 TraesCS6A01G325800 chr2A 93.109 624 40 2 1937 2560 610064804 610064184 0.000000e+00 911.0
31 TraesCS6A01G325800 chr7A 93.559 590 35 2 1971 2560 606181494 606182080 0.000000e+00 876.0
32 TraesCS6A01G325800 chr7A 82.105 950 113 45 1000 1932 606180585 606181494 0.000000e+00 760.0
33 TraesCS6A01G325800 chr7A 88.000 350 21 1 1 350 606182402 606182074 8.180000e-106 394.0
34 TraesCS6A01G325800 chrUn 100.000 415 0 0 409 823 477304833 477304419 0.000000e+00 767.0
35 TraesCS6A01G325800 chrUn 81.897 116 18 1 524 636 41895987 41896102 9.290000e-16 95.3
36 TraesCS6A01G325800 chr6B 93.243 370 21 2 582 947 707241615 707241246 2.760000e-150 542.0
37 TraesCS6A01G325800 chr4A 81.897 116 18 1 524 636 16147123 16147238 9.290000e-16 95.3


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 TraesCS6A01G325800 chr6A 559264924 559268070 3146 False 5812.000000 5812 100.0000 1 3147 1 chr6A.!!$F1 3146
1 TraesCS6A01G325800 chr3B 53953740 53956877 3137 False 5648.000000 5648 99.1110 1 3147 1 chr3B.!!$F1 3146
2 TraesCS6A01G325800 chr1B 457534505 457537902 3397 False 2734.500000 4929 98.1845 1 3147 2 chr1B.!!$F1 3146
3 TraesCS6A01G325800 chr5D 505542335 505545757 3422 True 759.200000 1703 90.4808 1 3147 5 chr5D.!!$R2 3146
4 TraesCS6A01G325800 chr3D 352943150 352944109 959 False 1181.000000 1181 88.9460 1595 2560 1 chr3D.!!$F2 965
5 TraesCS6A01G325800 chr3D 411870488 411872590 2102 False 1174.000000 1696 87.9890 1 2560 2 chr3D.!!$F3 2559
6 TraesCS6A01G325800 chr3D 208631891 208633199 1308 True 735.000000 1035 88.0900 6 1330 2 chr3D.!!$R1 1324
7 TraesCS6A01G325800 chr3D 352930187 352930700 513 False 688.000000 688 90.4850 1 536 1 chr3D.!!$F1 535
8 TraesCS6A01G325800 chr2D 128387352 128388823 1471 False 1602.000000 1602 86.3970 1069 2560 1 chr2D.!!$F1 1491
9 TraesCS6A01G325800 chr2D 128373630 128375017 1387 False 720.500000 776 86.8200 1 1835 2 chr2D.!!$F2 1834
10 TraesCS6A01G325800 chr5A 633025312 633028423 3111 True 1027.666667 1544 88.0930 6 2683 3 chr5A.!!$R1 2677
11 TraesCS6A01G325800 chr5B 635607266 635610800 3534 True 716.200000 1400 89.1030 15 3147 5 chr5B.!!$R2 3132
12 TraesCS6A01G325800 chr2A 610064184 610064804 620 True 911.000000 911 93.1090 1937 2560 1 chr2A.!!$R1 623
13 TraesCS6A01G325800 chr7A 606180585 606182080 1495 False 818.000000 876 87.8320 1000 2560 2 chr7A.!!$F1 1560

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
1835 2395 5.479306 GCACTGAGAGTAAGTCATTACCAA 58.521 41.667 0.0 0.0 41.97 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3044 3954 2.950309 CAGCAATGGAAGCAGCTTCTAT 59.05 45.455 29.99 27.25 42.09 1.98 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
1835 2395 5.479306 GCACTGAGAGTAAGTCATTACCAA 58.521 41.667 0.00 0.00 41.97 3.67
1836 2396 5.578727 GCACTGAGAGTAAGTCATTACCAAG 59.421 44.000 0.00 0.00 41.97 3.61
1837 2397 6.692486 CACTGAGAGTAAGTCATTACCAAGT 58.308 40.000 0.00 0.00 41.97 3.16
1838 2398 6.809196 CACTGAGAGTAAGTCATTACCAAGTC 59.191 42.308 0.00 0.00 41.97 3.01
1839 2399 6.493802 ACTGAGAGTAAGTCATTACCAAGTCA 59.506 38.462 0.00 0.00 41.97 3.41
1840 2400 7.179338 ACTGAGAGTAAGTCATTACCAAGTCAT 59.821 37.037 0.00 0.00 41.97 3.06
1841 2401 7.907389 TGAGAGTAAGTCATTACCAAGTCATT 58.093 34.615 0.00 0.00 41.97 2.57
1842 2402 9.031537 TGAGAGTAAGTCATTACCAAGTCATTA 57.968 33.333 0.00 0.00 41.97 1.90
1843 2403 9.303537 GAGAGTAAGTCATTACCAAGTCATTAC 57.696 37.037 0.00 0.00 41.97 1.89
1844 2404 8.258708 AGAGTAAGTCATTACCAAGTCATTACC 58.741 37.037 0.00 0.00 41.97 2.85
1845 2405 7.913789 AGTAAGTCATTACCAAGTCATTACCA 58.086 34.615 0.00 0.00 41.97 3.25
1969 2537 0.745845 AAGACGTGAGCATGGGCATC 60.746 55.000 0.00 0.00 44.61 3.91
2047 2615 4.284550 TTCCAGGCCGGCTGCTTT 62.285 61.111 28.56 4.15 40.92 3.51
2382 2955 5.520751 ACCTAGGAACTATAACAGCTCTGT 58.479 41.667 17.98 0.00 43.02 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1499 2046 5.926542 GCATAATCATAGTTCGAGCTACCAA 59.073 40.000 11.46 0.70 0.00 3.67
1835 2395 0.331616 GGCAAGGGGTGGTAATGACT 59.668 55.000 0.00 0.00 0.00 3.41
1836 2396 0.039035 TGGCAAGGGGTGGTAATGAC 59.961 55.000 0.00 0.00 0.00 3.06
1837 2397 0.331278 CTGGCAAGGGGTGGTAATGA 59.669 55.000 0.00 0.00 0.00 2.57
1838 2398 0.039618 ACTGGCAAGGGGTGGTAATG 59.960 55.000 0.00 0.00 0.00 1.90
1839 2399 1.676248 TACTGGCAAGGGGTGGTAAT 58.324 50.000 0.00 0.00 0.00 1.89
1840 2400 1.074244 GTTACTGGCAAGGGGTGGTAA 59.926 52.381 0.00 0.00 0.00 2.85
1841 2401 0.694196 GTTACTGGCAAGGGGTGGTA 59.306 55.000 0.00 0.00 0.00 3.25
1842 2402 1.065997 AGTTACTGGCAAGGGGTGGT 61.066 55.000 0.00 0.00 0.00 4.16
1843 2403 0.988832 TAGTTACTGGCAAGGGGTGG 59.011 55.000 0.00 0.00 0.00 4.61
1844 2404 1.906574 TCTAGTTACTGGCAAGGGGTG 59.093 52.381 0.00 0.00 0.00 4.61
1845 2405 2.337359 TCTAGTTACTGGCAAGGGGT 57.663 50.000 0.00 0.00 0.00 4.95
1969 2537 4.035675 GTCTTGTTGAACTTCTGAACCCAG 59.964 45.833 0.00 0.00 41.74 4.45
2382 2955 3.704566 AGCCGGTATACAAGTGAGATCAA 59.295 43.478 1.90 0.00 0.00 2.57
2434 3007 6.363357 GCTCTGAACACACAAAATGATTTACC 59.637 38.462 0.00 0.00 0.00 2.85
3044 3954 2.950309 CAGCAATGGAAGCAGCTTCTAT 59.050 45.455 29.99 27.25 42.09 1.98


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

AutoCloner maintained by Alex Coulton.