Multiple sequence alignment - TraesCS6A01G364200

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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 TraesCS6A01G364200 chr6A 100.000 2375 0 0 1 2375 592939758 592937384 0.000000e+00 4386.0
1 TraesCS6A01G364200 chr6A 91.185 329 29 0 913 1241 199072675 199073003 4.660000e-122 448.0
2 TraesCS6A01G364200 chr6A 89.837 246 25 0 624 869 262375146 262374901 1.370000e-82 316.0
3 TraesCS6A01G364200 chr6A 89.806 206 19 2 750 954 158901311 158901515 1.810000e-66 263.0
4 TraesCS6A01G364200 chr6A 89.655 203 19 2 753 954 158891355 158891556 8.420000e-65 257.0
5 TraesCS6A01G364200 chr6A 89.320 206 20 2 750 954 200794914 200795118 8.420000e-65 257.0
6 TraesCS6A01G364200 chr6A 87.805 205 21 4 1267 1470 295626761 295626962 1.100000e-58 237.0
7 TraesCS6A01G364200 chr6A 87.970 133 13 3 824 954 138065993 138065862 1.140000e-33 154.0
8 TraesCS6A01G364200 chr6A 86.364 132 16 2 824 954 579550481 579550351 2.460000e-30 143.0
9 TraesCS6A01G364200 chr6A 93.333 90 4 1 1556 1643 107626803 107626892 5.330000e-27 132.0
10 TraesCS6A01G364200 chr6A 93.023 86 4 1 1556 1639 350634624 350634709 8.910000e-25 124.0
11 TraesCS6A01G364200 chr6A 93.902 82 3 1 1564 1643 347454021 347454102 3.210000e-24 122.0
12 TraesCS6A01G364200 chr1A 96.603 2355 62 5 1 2352 206951453 206953792 0.000000e+00 3890.0
13 TraesCS6A01G364200 chr1A 87.730 815 71 21 661 1456 222721664 222720860 0.000000e+00 924.0
14 TraesCS6A01G364200 chr1A 85.429 652 71 17 1 647 546003990 546004622 0.000000e+00 656.0
15 TraesCS6A01G364200 chr1A 92.562 121 8 1 750 870 207912474 207912355 3.140000e-39 172.0
16 TraesCS6A01G364200 chr1A 87.218 133 15 2 823 954 319372151 319372282 1.470000e-32 150.0
17 TraesCS6A01G364200 chr1A 89.286 112 11 1 755 866 438638284 438638174 3.180000e-29 139.0
18 TraesCS6A01G364200 chr4A 91.355 2383 142 35 1 2352 306488316 306485967 0.000000e+00 3201.0
19 TraesCS6A01G364200 chr4A 87.169 491 48 10 1 487 445174744 445175223 5.770000e-151 544.0
20 TraesCS6A01G364200 chr4A 85.577 520 59 11 1 515 347522944 347522436 4.490000e-147 531.0
21 TraesCS6A01G364200 chr4A 86.667 135 16 2 821 954 288842050 288842183 5.290000e-32 148.0
22 TraesCS6A01G364200 chr2A 94.507 710 22 15 1572 2276 216070096 216070793 0.000000e+00 1079.0
23 TraesCS6A01G364200 chr2A 92.090 708 21 14 1576 2276 216061942 216062621 0.000000e+00 965.0
24 TraesCS6A01G364200 chr2A 86.470 813 70 20 661 1456 500979126 500978337 0.000000e+00 856.0
25 TraesCS6A01G364200 chr2A 89.048 420 37 8 1828 2245 387676701 387677113 1.630000e-141 512.0
26 TraesCS6A01G364200 chr2A 80.570 597 82 23 1694 2276 306125181 306125757 1.690000e-116 429.0
27 TraesCS6A01G364200 chr2A 90.857 175 15 1 1297 1470 130281018 130280844 1.420000e-57 233.0
28 TraesCS6A01G364200 chr2A 90.588 85 6 1 1556 1640 719675326 719675408 6.940000e-21 111.0
29 TraesCS6A01G364200 chr7A 86.245 996 80 28 669 1615 163312626 163311639 0.000000e+00 1027.0
30 TraesCS6A01G364200 chr7A 85.168 654 72 19 1 647 415874710 415875345 0.000000e+00 647.0
31 TraesCS6A01G364200 chr7A 84.816 652 74 19 1 645 415441926 415442559 1.200000e-177 632.0
32 TraesCS6A01G364200 chr7A 83.626 513 70 13 1845 2352 717002893 717003396 9.940000e-129 470.0
33 TraesCS6A01G364200 chr7A 83.431 513 71 13 1845 2352 717011087 717011590 4.620000e-127 464.0
34 TraesCS6A01G364200 chr7A 81.407 597 78 23 1694 2276 159050322 159049745 7.740000e-125 457.0
35 TraesCS6A01G364200 chr5A 93.402 682 30 13 1586 2259 473367318 473367992 0.000000e+00 996.0
36 TraesCS6A01G364200 chr5A 87.097 806 64 24 668 1456 448123493 448122711 0.000000e+00 876.0
37 TraesCS6A01G364200 chr5A 87.110 737 55 24 668 1388 448137208 448136496 0.000000e+00 798.0
38 TraesCS6A01G364200 chr5A 85.015 654 70 21 1 647 562440517 562441149 7.160000e-180 640.0
39 TraesCS6A01G364200 chr5A 85.878 524 51 17 1 515 398146819 398147328 9.660000e-149 536.0
40 TraesCS6A01G364200 chr5A 93.313 329 22 0 913 1241 588129583 588129911 9.870000e-134 486.0
41 TraesCS6A01G364200 chr5A 83.463 514 69 15 1845 2352 33586575 33586072 4.620000e-127 464.0
42 TraesCS6A01G364200 chr5A 84.064 502 54 19 1775 2259 206295297 206295789 5.980000e-126 460.0
43 TraesCS6A01G364200 chr5A 91.071 336 29 1 913 1247 236857798 236857463 1.000000e-123 453.0
44 TraesCS6A01G364200 chr5A 88.253 332 36 3 624 954 397265490 397265161 6.150000e-106 394.0
45 TraesCS6A01G364200 chr5A 86.364 88 10 2 1387 1472 602296850 602296763 6.990000e-16 95.3
46 TraesCS6A01G364200 chr3A 95.210 334 16 0 475 808 177960000 177960333 1.620000e-146 529.0
47 TraesCS6A01G364200 chr3A 94.910 334 17 0 475 808 172045635 172045968 7.520000e-145 523.0
48 TraesCS6A01G364200 chr3A 94.910 334 17 0 475 808 177968410 177968743 7.520000e-145 523.0
49 TraesCS6A01G364200 chr3A 92.705 329 23 1 913 1241 323112513 323112840 7.680000e-130 473.0
50 TraesCS6A01G364200 chr3A 83.626 513 69 14 1845 2352 454844430 454844932 3.570000e-128 468.0
51 TraesCS6A01G364200 chr3A 91.185 329 29 0 913 1241 323120454 323120782 4.660000e-122 448.0
52 TraesCS6A01G364200 chr3B 81.047 554 73 22 1733 2270 183523861 183523324 1.700000e-111 412.0
53 TraesCS6A01G364200 chr3B 80.832 553 75 21 1733 2270 183532320 183532856 2.840000e-109 405.0
54 TraesCS6A01G364200 chr4D 91.667 48 3 1 820 866 228752889 228752936 5.480000e-07 65.8


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 TraesCS6A01G364200 chr6A 592937384 592939758 2374 True 4386 4386 100.000 1 2375 1 chr6A.!!$R4 2374
1 TraesCS6A01G364200 chr1A 206951453 206953792 2339 False 3890 3890 96.603 1 2352 1 chr1A.!!$F1 2351
2 TraesCS6A01G364200 chr1A 222720860 222721664 804 True 924 924 87.730 661 1456 1 chr1A.!!$R2 795
3 TraesCS6A01G364200 chr1A 546003990 546004622 632 False 656 656 85.429 1 647 1 chr1A.!!$F3 646
4 TraesCS6A01G364200 chr4A 306485967 306488316 2349 True 3201 3201 91.355 1 2352 1 chr4A.!!$R1 2351
5 TraesCS6A01G364200 chr4A 347522436 347522944 508 True 531 531 85.577 1 515 1 chr4A.!!$R2 514
6 TraesCS6A01G364200 chr2A 216070096 216070793 697 False 1079 1079 94.507 1572 2276 1 chr2A.!!$F2 704
7 TraesCS6A01G364200 chr2A 216061942 216062621 679 False 965 965 92.090 1576 2276 1 chr2A.!!$F1 700
8 TraesCS6A01G364200 chr2A 500978337 500979126 789 True 856 856 86.470 661 1456 1 chr2A.!!$R2 795
9 TraesCS6A01G364200 chr2A 306125181 306125757 576 False 429 429 80.570 1694 2276 1 chr2A.!!$F3 582
10 TraesCS6A01G364200 chr7A 163311639 163312626 987 True 1027 1027 86.245 669 1615 1 chr7A.!!$R2 946
11 TraesCS6A01G364200 chr7A 415874710 415875345 635 False 647 647 85.168 1 647 1 chr7A.!!$F2 646
12 TraesCS6A01G364200 chr7A 415441926 415442559 633 False 632 632 84.816 1 645 1 chr7A.!!$F1 644
13 TraesCS6A01G364200 chr7A 717002893 717003396 503 False 470 470 83.626 1845 2352 1 chr7A.!!$F3 507
14 TraesCS6A01G364200 chr7A 717011087 717011590 503 False 464 464 83.431 1845 2352 1 chr7A.!!$F4 507
15 TraesCS6A01G364200 chr7A 159049745 159050322 577 True 457 457 81.407 1694 2276 1 chr7A.!!$R1 582
16 TraesCS6A01G364200 chr5A 473367318 473367992 674 False 996 996 93.402 1586 2259 1 chr5A.!!$F3 673
17 TraesCS6A01G364200 chr5A 448122711 448123493 782 True 876 876 87.097 668 1456 1 chr5A.!!$R4 788
18 TraesCS6A01G364200 chr5A 448136496 448137208 712 True 798 798 87.110 668 1388 1 chr5A.!!$R5 720
19 TraesCS6A01G364200 chr5A 562440517 562441149 632 False 640 640 85.015 1 647 1 chr5A.!!$F4 646
20 TraesCS6A01G364200 chr5A 398146819 398147328 509 False 536 536 85.878 1 515 1 chr5A.!!$F2 514
21 TraesCS6A01G364200 chr5A 33586072 33586575 503 True 464 464 83.463 1845 2352 1 chr5A.!!$R1 507
22 TraesCS6A01G364200 chr3A 454844430 454844932 502 False 468 468 83.626 1845 2352 1 chr3A.!!$F6 507
23 TraesCS6A01G364200 chr3B 183523324 183523861 537 True 412 412 81.047 1733 2270 1 chr3B.!!$R1 537
24 TraesCS6A01G364200 chr3B 183532320 183532856 536 False 405 405 80.832 1733 2270 1 chr3B.!!$F1 537

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
665 680 0.388134 GCTTGTGACTCGCGGTTCTA 60.388 55.0 6.13 0.0 0.0 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2335 2446 0.251209 TAGTGTGACGCCCTGAGTCT 60.251 55.0 0.0 0.0 39.24 3.24 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
71 73 2.814336 GGATGACAGGTTCAAGTTGGAC 59.186 50.000 5.65 5.65 37.92 4.02
73 75 1.208535 TGACAGGTTCAAGTTGGACGT 59.791 47.619 8.22 5.93 0.00 4.34
127 130 7.592533 GCATTATATGAAGCATTTGTCATCGTT 59.407 33.333 0.00 0.00 36.00 3.85
502 517 1.065199 AGTAGGGGTACATGACGACGA 60.065 52.381 0.00 0.00 0.00 4.20
609 624 3.128938 CACGTTTCGAGGAGGAAGTAGAT 59.871 47.826 0.00 0.00 0.00 1.98
625 640 1.300481 AGATGTTCTCGCGATCTCGA 58.700 50.000 10.36 7.67 43.02 4.04
665 680 0.388134 GCTTGTGACTCGCGGTTCTA 60.388 55.000 6.13 0.00 0.00 2.10
850 868 1.956629 GACAAATCCGAGGGCTCCGA 61.957 60.000 0.00 0.00 0.00 4.55
1016 1045 3.498301 CCCAAAATGAAACAGCCCCAAAT 60.498 43.478 0.00 0.00 0.00 2.32
1031 1060 1.548582 CCAAATGGAGGCAACAGAGGT 60.549 52.381 0.00 0.00 37.39 3.85
1140 1169 0.416231 TGGCTACCCTCACCCTTAGT 59.584 55.000 0.00 0.00 0.00 2.24
1392 1436 2.760385 GGCGGGGTAGAGCAGAGT 60.760 66.667 0.00 0.00 34.54 3.24
1467 1512 2.501610 GAGAAGCTGTAGGGGCGG 59.498 66.667 0.00 0.00 34.52 6.13
1468 1513 2.038975 AGAAGCTGTAGGGGCGGA 59.961 61.111 0.00 0.00 34.52 5.54
2335 2446 1.375908 GAAGACACCTGGCGCATCA 60.376 57.895 10.83 0.00 0.00 3.07
2341 2452 2.285773 ACCTGGCGCATCAGACTCA 61.286 57.895 10.83 0.00 36.93 3.41
2352 2463 1.373497 CAGACTCAGGGCGTCACAC 60.373 63.158 0.00 0.00 33.89 3.82
2353 2464 1.531840 AGACTCAGGGCGTCACACT 60.532 57.895 0.00 0.00 33.89 3.55
2354 2465 0.251209 AGACTCAGGGCGTCACACTA 60.251 55.000 0.00 0.00 33.89 2.74
2355 2466 0.818296 GACTCAGGGCGTCACACTAT 59.182 55.000 0.00 0.00 0.00 2.12
2356 2467 2.022195 GACTCAGGGCGTCACACTATA 58.978 52.381 0.00 0.00 0.00 1.31
2357 2468 2.426024 GACTCAGGGCGTCACACTATAA 59.574 50.000 0.00 0.00 0.00 0.98
2358 2469 2.427453 ACTCAGGGCGTCACACTATAAG 59.573 50.000 0.00 0.00 0.00 1.73
2359 2470 2.688446 CTCAGGGCGTCACACTATAAGA 59.312 50.000 0.00 0.00 0.00 2.10
2360 2471 3.296854 TCAGGGCGTCACACTATAAGAT 58.703 45.455 0.00 0.00 0.00 2.40
2361 2472 3.068165 TCAGGGCGTCACACTATAAGATG 59.932 47.826 0.00 0.00 0.00 2.90
2362 2473 2.135933 GGGCGTCACACTATAAGATGC 58.864 52.381 0.00 0.00 42.14 3.91
2363 2474 2.483013 GGGCGTCACACTATAAGATGCA 60.483 50.000 7.96 0.00 44.07 3.96
2364 2475 3.194861 GGCGTCACACTATAAGATGCAA 58.805 45.455 7.96 0.00 44.07 4.08
2365 2476 3.621268 GGCGTCACACTATAAGATGCAAA 59.379 43.478 7.96 0.00 44.07 3.68
2366 2477 4.094294 GGCGTCACACTATAAGATGCAAAA 59.906 41.667 7.96 0.00 44.07 2.44
2367 2478 5.220854 GGCGTCACACTATAAGATGCAAAAT 60.221 40.000 7.96 0.00 44.07 1.82
2368 2479 5.678483 GCGTCACACTATAAGATGCAAAATG 59.322 40.000 0.00 0.00 42.36 2.32
2369 2480 6.675486 GCGTCACACTATAAGATGCAAAATGT 60.675 38.462 0.00 0.00 42.36 2.71
2370 2481 7.465379 GCGTCACACTATAAGATGCAAAATGTA 60.465 37.037 0.00 0.00 42.36 2.29
2371 2482 8.551205 CGTCACACTATAAGATGCAAAATGTAT 58.449 33.333 0.00 0.00 0.00 2.29
2372 2483 9.655769 GTCACACTATAAGATGCAAAATGTATG 57.344 33.333 0.00 0.00 0.00 2.39
2373 2484 9.612066 TCACACTATAAGATGCAAAATGTATGA 57.388 29.630 0.00 0.00 0.00 2.15
2374 2485 9.874215 CACACTATAAGATGCAAAATGTATGAG 57.126 33.333 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 130 1.152922 ACCCCTTTTCGTTTCCGCA 60.153 52.632 0.00 0.00 0.00 5.69
213 219 2.955660 TCCCGTCATTTTCTTTTGCACT 59.044 40.909 0.00 0.00 0.00 4.40
319 328 2.490509 TGCCTCGAGTTTGAACTATCGA 59.509 45.455 12.31 7.63 39.88 3.59
502 517 0.179062 ACCGTCGCGAGTACCTCTAT 60.179 55.000 10.24 0.00 0.00 1.98
625 640 1.938016 GCCGTGAACAACTACCATCGT 60.938 52.381 0.00 0.00 0.00 3.73
850 868 1.081641 CGACAAGTACCACGACGCT 60.082 57.895 0.00 0.00 0.00 5.07
932 960 1.307097 GTCGCGTCCAGTACCTCTAT 58.693 55.000 5.77 0.00 0.00 1.98
988 1016 3.809279 GGCTGTTTCATTTTGGGTTTCAG 59.191 43.478 0.00 0.00 0.00 3.02
1016 1045 1.461268 TCCACCTCTGTTGCCTCCA 60.461 57.895 0.00 0.00 0.00 3.86
1031 1060 1.725557 GCTATCCTCGTGCGTCTCCA 61.726 60.000 0.00 0.00 0.00 3.86
1092 1121 3.602513 CTGCTGCTCTTCCGGTGCT 62.603 63.158 0.00 0.00 35.67 4.40
1140 1169 4.020617 CGCCTCCCTTGCTCCACA 62.021 66.667 0.00 0.00 0.00 4.17
1368 1412 2.036098 TCTACCCCGCCTCAACGA 59.964 61.111 0.00 0.00 34.06 3.85
1467 1512 4.228567 GCTCCGCCCCTACAGCTC 62.229 72.222 0.00 0.00 0.00 4.09
1468 1513 4.787280 AGCTCCGCCCCTACAGCT 62.787 66.667 0.00 0.00 37.40 4.24
1470 1515 2.187946 CAAGCTCCGCCCCTACAG 59.812 66.667 0.00 0.00 0.00 2.74
1471 1516 3.399181 CCAAGCTCCGCCCCTACA 61.399 66.667 0.00 0.00 0.00 2.74
1713 1794 1.078955 CATCCATCCCCATAGCCCTT 58.921 55.000 0.00 0.00 0.00 3.95
1721 1802 2.156098 GCTAGGCCATCCATCCCCA 61.156 63.158 5.01 0.00 33.74 4.96
1982 2065 5.184892 AGCTCCACCAAGAATCTTAACAT 57.815 39.130 0.00 0.00 0.00 2.71
2035 2118 8.160765 TGTTATCTTAATTCTTGGTCTCCAACA 58.839 33.333 0.00 0.00 38.75 3.33
2335 2446 0.251209 TAGTGTGACGCCCTGAGTCT 60.251 55.000 0.00 0.00 39.24 3.24
2341 2452 2.224066 GCATCTTATAGTGTGACGCCCT 60.224 50.000 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.