Multiple sequence alignment - TraesCS4B01G373000

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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 TraesCS4B01G373000 chr4B 100.000 2591 0 0 1 2591 657805353 657802763 0.000000e+00 4785
1 TraesCS4B01G373000 chr3D 93.014 2634 93 30 2 2591 523400566 523403152 0.000000e+00 3760
2 TraesCS4B01G373000 chr3D 92.976 2634 95 34 2 2591 20288773 20291360 0.000000e+00 3757
3 TraesCS4B01G373000 chr3D 93.611 2301 122 12 151 2437 45062954 45060665 0.000000e+00 3411
4 TraesCS4B01G373000 chr3D 94.222 1471 48 15 1147 2591 160918206 160919665 0.000000e+00 2211
5 TraesCS4B01G373000 chr1D 92.214 2633 99 37 2 2591 30073736 30071167 0.000000e+00 3629
6 TraesCS4B01G373000 chr1D 93.304 2300 126 14 155 2437 414450967 414448679 0.000000e+00 3369
7 TraesCS4B01G373000 chr1D 86.003 1586 134 39 142 1711 829195 830708 0.000000e+00 1618
8 TraesCS4B01G373000 chr5A 92.408 2529 109 25 1 2510 650150633 650153097 0.000000e+00 3530
9 TraesCS4B01G373000 chr5A 91.390 813 45 7 1780 2591 647552996 647553784 0.000000e+00 1090
10 TraesCS4B01G373000 chr5A 90.361 83 7 1 1 82 650158046 650157964 9.800000e-20 108
11 TraesCS4B01G373000 chr2A 92.417 2532 103 27 1 2510 769227741 769230205 0.000000e+00 3530
12 TraesCS4B01G373000 chr2A 91.973 2529 116 26 1 2510 115130118 115132578 0.000000e+00 3465
13 TraesCS4B01G373000 chr4A 92.117 2537 109 29 1 2518 604389297 604386833 0.000000e+00 3493
14 TraesCS4B01G373000 chr6D 91.366 2606 125 52 1 2591 175423837 175426357 0.000000e+00 3474
15 TraesCS4B01G373000 chr6D 93.041 388 11 4 54 441 61166022 61165651 1.050000e-153 553
16 TraesCS4B01G373000 chr7D 93.634 2309 121 14 142 2437 92234272 92231977 0.000000e+00 3426
17 TraesCS4B01G373000 chr7D 90.996 2621 119 48 1 2591 540442287 540444820 0.000000e+00 3424
18 TraesCS4B01G373000 chr7D 93.596 2311 114 18 142 2437 631818319 631816028 0.000000e+00 3417
19 TraesCS4B01G373000 chr5D 93.553 2311 116 19 142 2437 408555065 408552773 0.000000e+00 3411
20 TraesCS4B01G373000 chr5D 93.475 1747 68 19 877 2591 494244468 494242736 0.000000e+00 2553
21 TraesCS4B01G373000 chr2D 90.746 2615 121 57 1 2591 513033986 513031469 0.000000e+00 3376
22 TraesCS4B01G373000 chr2D 94.544 1723 74 14 877 2591 568356763 568355053 0.000000e+00 2643
23 TraesCS4B01G373000 chr7A 90.613 2546 165 37 1 2513 147920308 147917804 0.000000e+00 3310
24 TraesCS4B01G373000 chr3B 93.898 803 33 6 1 803 470855941 470856727 0.000000e+00 1197
25 TraesCS4B01G373000 chr1B 89.071 915 41 18 1 897 460163933 460163060 0.000000e+00 1081
26 TraesCS4B01G373000 chr5B 87.869 915 62 17 1 894 69031305 69032191 0.000000e+00 1029
27 TraesCS4B01G373000 chr5B 80.410 439 45 20 142 569 498514257 498514665 1.950000e-76 296
28 TraesCS4B01G373000 chr6B 87.541 915 42 16 1 897 40798071 40797211 0.000000e+00 992
29 TraesCS4B01G373000 chr6B 81.765 680 60 34 235 902 61199437 61200064 6.400000e-141 510
30 TraesCS4B01G373000 chr4D 93.651 630 30 8 1965 2591 498703812 498703190 0.000000e+00 933
31 TraesCS4B01G373000 chr2B 89.157 83 8 1 1 82 69358727 69358645 4.560000e-18 102


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 TraesCS4B01G373000 chr4B 657802763 657805353 2590 True 4785 4785 100.000 1 2591 1 chr4B.!!$R1 2590
1 TraesCS4B01G373000 chr3D 523400566 523403152 2586 False 3760 3760 93.014 2 2591 1 chr3D.!!$F3 2589
2 TraesCS4B01G373000 chr3D 20288773 20291360 2587 False 3757 3757 92.976 2 2591 1 chr3D.!!$F1 2589
3 TraesCS4B01G373000 chr3D 45060665 45062954 2289 True 3411 3411 93.611 151 2437 1 chr3D.!!$R1 2286
4 TraesCS4B01G373000 chr3D 160918206 160919665 1459 False 2211 2211 94.222 1147 2591 1 chr3D.!!$F2 1444
5 TraesCS4B01G373000 chr1D 30071167 30073736 2569 True 3629 3629 92.214 2 2591 1 chr1D.!!$R1 2589
6 TraesCS4B01G373000 chr1D 414448679 414450967 2288 True 3369 3369 93.304 155 2437 1 chr1D.!!$R2 2282
7 TraesCS4B01G373000 chr1D 829195 830708 1513 False 1618 1618 86.003 142 1711 1 chr1D.!!$F1 1569
8 TraesCS4B01G373000 chr5A 650150633 650153097 2464 False 3530 3530 92.408 1 2510 1 chr5A.!!$F2 2509
9 TraesCS4B01G373000 chr5A 647552996 647553784 788 False 1090 1090 91.390 1780 2591 1 chr5A.!!$F1 811
10 TraesCS4B01G373000 chr2A 769227741 769230205 2464 False 3530 3530 92.417 1 2510 1 chr2A.!!$F2 2509
11 TraesCS4B01G373000 chr2A 115130118 115132578 2460 False 3465 3465 91.973 1 2510 1 chr2A.!!$F1 2509
12 TraesCS4B01G373000 chr4A 604386833 604389297 2464 True 3493 3493 92.117 1 2518 1 chr4A.!!$R1 2517
13 TraesCS4B01G373000 chr6D 175423837 175426357 2520 False 3474 3474 91.366 1 2591 1 chr6D.!!$F1 2590
14 TraesCS4B01G373000 chr7D 92231977 92234272 2295 True 3426 3426 93.634 142 2437 1 chr7D.!!$R1 2295
15 TraesCS4B01G373000 chr7D 540442287 540444820 2533 False 3424 3424 90.996 1 2591 1 chr7D.!!$F1 2590
16 TraesCS4B01G373000 chr7D 631816028 631818319 2291 True 3417 3417 93.596 142 2437 1 chr7D.!!$R2 2295
17 TraesCS4B01G373000 chr5D 408552773 408555065 2292 True 3411 3411 93.553 142 2437 1 chr5D.!!$R1 2295
18 TraesCS4B01G373000 chr5D 494242736 494244468 1732 True 2553 2553 93.475 877 2591 1 chr5D.!!$R2 1714
19 TraesCS4B01G373000 chr2D 513031469 513033986 2517 True 3376 3376 90.746 1 2591 1 chr2D.!!$R1 2590
20 TraesCS4B01G373000 chr2D 568355053 568356763 1710 True 2643 2643 94.544 877 2591 1 chr2D.!!$R2 1714
21 TraesCS4B01G373000 chr7A 147917804 147920308 2504 True 3310 3310 90.613 1 2513 1 chr7A.!!$R1 2512
22 TraesCS4B01G373000 chr3B 470855941 470856727 786 False 1197 1197 93.898 1 803 1 chr3B.!!$F1 802
23 TraesCS4B01G373000 chr1B 460163060 460163933 873 True 1081 1081 89.071 1 897 1 chr1B.!!$R1 896
24 TraesCS4B01G373000 chr5B 69031305 69032191 886 False 1029 1029 87.869 1 894 1 chr5B.!!$F1 893
25 TraesCS4B01G373000 chr6B 40797211 40798071 860 True 992 992 87.541 1 897 1 chr6B.!!$R1 896
26 TraesCS4B01G373000 chr6B 61199437 61200064 627 False 510 510 81.765 235 902 1 chr6B.!!$F1 667
27 TraesCS4B01G373000 chr4D 498703190 498703812 622 True 933 933 93.651 1965 2591 1 chr4D.!!$R1 626

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
280 303 1.137479 TGAAACGACGAGGAAACCAGT 59.863 47.619 0.0 0.0 0.0 4.00 F
428 472 2.621055 AGTGTTGTTGTTGTGTGTGTGT 59.379 40.909 0.0 0.0 0.0 3.72 F
1231 1318 2.162681 AGCTTTGCATTGAGTACACCC 58.837 47.619 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1145 1232 0.038166 CTTAAGCCTGGCCAACTCCA 59.962 55.000 16.57 0.0 34.42 3.86 R
1358 1448 1.067295 TTCCATCTGCACCTCCAACT 58.933 50.000 0.00 0.0 0.00 3.16 R
2147 2257 2.123683 CTGCGCCTCCTCCTCCTA 60.124 66.667 4.18 0.0 0.00 2.94 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
247 270 4.070552 GCCGTCGACCTCCTTGCT 62.071 66.667 10.58 0.00 0.00 3.91
280 303 1.137479 TGAAACGACGAGGAAACCAGT 59.863 47.619 0.00 0.00 0.00 4.00
427 471 3.281341 AGTGTTGTTGTTGTGTGTGTG 57.719 42.857 0.00 0.00 0.00 3.82
428 472 2.621055 AGTGTTGTTGTTGTGTGTGTGT 59.379 40.909 0.00 0.00 0.00 3.72
444 488 5.154932 GTGTGTGTGATACTGTCTCTGTAC 58.845 45.833 0.00 0.00 0.00 2.90
475 542 5.605488 GGATTGAGGTAACCTAGGGTTCATA 59.395 44.000 14.81 0.00 43.05 2.15
476 543 5.945144 TTGAGGTAACCTAGGGTTCATAC 57.055 43.478 14.81 0.59 43.05 2.39
477 544 5.216665 TGAGGTAACCTAGGGTTCATACT 57.783 43.478 14.81 0.81 43.05 2.12
478 545 5.206587 TGAGGTAACCTAGGGTTCATACTC 58.793 45.833 14.81 10.70 43.05 2.59
479 546 5.043582 TGAGGTAACCTAGGGTTCATACTCT 60.044 44.000 14.81 1.18 43.05 3.24
493 560 6.403855 GGTTCATACTCTCTCTGTACAGTGTC 60.404 46.154 21.99 8.38 0.00 3.67
578 648 5.181009 TCTGGTATTGAGTGCAGATTGAAG 58.819 41.667 0.00 0.00 0.00 3.02
1145 1232 4.349342 ACAGGACAAGGAGAAGTTTGAGAT 59.651 41.667 0.00 0.00 0.00 2.75
1176 1263 4.521146 CCAGGCTTAAGAGTGAACATGAT 58.479 43.478 6.67 0.00 0.00 2.45
1231 1318 2.162681 AGCTTTGCATTGAGTACACCC 58.837 47.619 0.00 0.00 0.00 4.61
1311 1398 3.201266 AGGTGTACCAGAAACAAGTGGAA 59.799 43.478 3.56 0.00 37.27 3.53
1358 1448 4.258457 AGGAGCTAGAGGAGAAAGCTAA 57.742 45.455 0.00 0.00 46.29 3.09
1530 1620 1.875514 CTTGTTGTTGCTGAGCTGCTA 59.124 47.619 5.83 0.00 0.00 3.49
1693 1786 1.719378 TGGGTGTACATTTTGGGGGAT 59.281 47.619 0.00 0.00 0.00 3.85
1768 1861 9.387397 TGTAATGGATCACCTATGGTATTAAGA 57.613 33.333 0.00 0.00 32.11 2.10
1805 1899 8.958060 TCTCCTATGCTATTAAGTAGTGGAAT 57.042 34.615 0.00 0.00 32.72 3.01
1830 1928 7.661536 TGGATCTCTTATGCTACTAAGTTGT 57.338 36.000 0.00 0.00 31.85 3.32
1831 1929 7.492524 TGGATCTCTTATGCTACTAAGTTGTG 58.507 38.462 0.00 0.00 31.85 3.33
1832 1930 6.926272 GGATCTCTTATGCTACTAAGTTGTGG 59.074 42.308 0.00 0.00 31.85 4.17
1833 1931 7.201920 GGATCTCTTATGCTACTAAGTTGTGGA 60.202 40.741 0.00 0.00 31.85 4.02
1834 1932 7.476540 TCTCTTATGCTACTAAGTTGTGGAA 57.523 36.000 0.00 0.00 31.85 3.53
1835 1933 7.903145 TCTCTTATGCTACTAAGTTGTGGAAA 58.097 34.615 0.00 0.00 31.85 3.13
1973 2077 2.301346 CAAATGCAACCCTAGGCCTAG 58.699 52.381 30.05 30.05 0.00 3.02
2006 2113 7.406620 ACCCCATCCATCTCTCAATATAAAA 57.593 36.000 0.00 0.00 0.00 1.52
2147 2257 1.147824 AGCAGCAGCAACACAGAGT 59.852 52.632 3.17 0.00 45.49 3.24
2383 2499 0.181587 TGGGTCCGTTTCTTTGAGCA 59.818 50.000 0.00 0.00 0.00 4.26
2393 2509 4.143030 CGTTTCTTTGAGCACTATGACTGG 60.143 45.833 0.00 0.00 0.00 4.00
2394 2510 4.623932 TTCTTTGAGCACTATGACTGGT 57.376 40.909 0.00 0.00 0.00 4.00
2395 2511 5.738619 TTCTTTGAGCACTATGACTGGTA 57.261 39.130 0.00 0.00 0.00 3.25
2396 2512 5.939764 TCTTTGAGCACTATGACTGGTAT 57.060 39.130 0.00 0.00 0.00 2.73
2397 2513 5.664457 TCTTTGAGCACTATGACTGGTATG 58.336 41.667 0.00 0.00 0.00 2.39
2398 2514 5.187772 TCTTTGAGCACTATGACTGGTATGT 59.812 40.000 0.00 0.00 0.00 2.29
2399 2515 4.655762 TGAGCACTATGACTGGTATGTC 57.344 45.455 0.00 0.00 37.47 3.06
2488 2651 9.046296 GGTAGTATTTGTGAGATTTGGATGTAG 57.954 37.037 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 76 4.101430 GGTATATTTACCCCAGTTCCGACA 59.899 45.833 1.06 0.00 41.91 4.35
120 127 1.226660 GAGAGAGTGAGCGAGCTGC 60.227 63.158 0.84 0.00 46.98 5.25
122 129 1.376683 ACGAGAGAGTGAGCGAGCT 60.377 57.895 0.00 0.00 0.00 4.09
129 136 1.160989 GAGTGAGCACGAGAGAGTGA 58.839 55.000 0.88 0.00 44.43 3.41
247 270 0.597568 CGTTTCAGGAAGGCATTGCA 59.402 50.000 11.39 0.00 0.00 4.08
280 303 2.035155 TCGCACTCCTCCTCCGAA 59.965 61.111 0.00 0.00 0.00 4.30
444 488 5.069251 CCTAGGTTACCTCAATCCTACACTG 59.931 48.000 7.39 0.00 34.61 3.66
475 542 3.417101 CCTGACACTGTACAGAGAGAGT 58.583 50.000 29.30 17.18 36.38 3.24
476 543 2.752354 CCCTGACACTGTACAGAGAGAG 59.248 54.545 29.30 19.29 36.38 3.20
477 544 2.108425 ACCCTGACACTGTACAGAGAGA 59.892 50.000 29.30 11.90 36.38 3.10
478 545 2.520069 ACCCTGACACTGTACAGAGAG 58.480 52.381 29.30 18.95 36.38 3.20
479 546 2.677542 ACCCTGACACTGTACAGAGA 57.322 50.000 29.30 5.74 36.38 3.10
578 648 5.167845 CCATAATAACCAACAAACACTGGC 58.832 41.667 0.00 0.00 36.03 4.85
940 1027 7.781324 ACCTTGTTTCAGTTCCATGATTAAT 57.219 32.000 0.00 0.00 0.00 1.40
1006 1093 5.096443 ACACCACAATTCACACCATTTTT 57.904 34.783 0.00 0.00 0.00 1.94
1145 1232 0.038166 CTTAAGCCTGGCCAACTCCA 59.962 55.000 16.57 0.00 34.42 3.86
1176 1263 1.559682 CTAAGCTTGGCCAACTCCCTA 59.440 52.381 16.05 6.03 0.00 3.53
1311 1398 6.553100 TCTTCTTCTTCTCAAGTTCTTCCTCT 59.447 38.462 0.00 0.00 0.00 3.69
1358 1448 1.067295 TTCCATCTGCACCTCCAACT 58.933 50.000 0.00 0.00 0.00 3.16
1530 1620 2.603075 TGCTGCCATACCCTTCTTTT 57.397 45.000 0.00 0.00 0.00 2.27
1693 1786 9.101655 GTTCTTACACTAGGTTAAACTTCACAA 57.898 33.333 0.00 0.00 0.00 3.33
1805 1899 7.981789 CACAACTTAGTAGCATAAGAGATCCAA 59.018 37.037 9.53 0.00 36.46 3.53
1830 1928 9.288576 CTTAATAGCATACAAGATCCATTTCCA 57.711 33.333 0.00 0.00 0.00 3.53
1831 1929 9.289782 ACTTAATAGCATACAAGATCCATTTCC 57.710 33.333 0.00 0.00 0.00 3.13
1833 1931 9.632638 ACACTTAATAGCATACAAGATCCATTT 57.367 29.630 0.00 0.00 0.00 2.32
1834 1932 9.632638 AACACTTAATAGCATACAAGATCCATT 57.367 29.630 0.00 0.00 0.00 3.16
1835 1933 9.277783 GAACACTTAATAGCATACAAGATCCAT 57.722 33.333 0.00 0.00 0.00 3.41
1973 2077 2.024369 AGATGGATGGGGTTGGGTTTAC 60.024 50.000 0.00 0.00 0.00 2.01
2147 2257 2.123683 CTGCGCCTCCTCCTCCTA 60.124 66.667 4.18 0.00 0.00 2.94
2383 2499 8.948401 AGATAGATTGACATACCAGTCATAGT 57.052 34.615 0.00 0.00 46.90 2.12
2437 2600 9.007901 CCAAAACTCTCTCTGAAATTGACTTAT 57.992 33.333 0.00 0.00 0.00 1.73
2449 2612 7.872993 TCACAAATACTACCAAAACTCTCTCTG 59.127 37.037 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.