Multiple sequence alignment - TraesCS4A01G490300

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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 TraesCS4A01G490300 chr4A 100.000 4313 0 0 1 4313 740542111 740537799 0.000000e+00 7928.0
1 TraesCS4A01G490300 chr4A 97.033 4348 61 18 1 4313 739631422 739627108 0.000000e+00 7215.0
2 TraesCS4A01G490300 chr4A 96.777 3382 54 12 974 4311 742036058 742032688 0.000000e+00 5590.0
3 TraesCS4A01G490300 chr4A 97.415 1625 28 6 1 1625 739845186 739843576 0.000000e+00 2760.0
4 TraesCS4A01G490300 chr4A 99.828 581 1 0 383 963 742037096 742036516 0.000000e+00 1068.0
5 TraesCS4A01G490300 chr4A 89.709 515 41 6 1 508 742124069 742123560 0.000000e+00 647.0
6 TraesCS4A01G490300 chr4A 90.244 492 38 4 1 487 739728832 739728346 6.080000e-178 634.0
7 TraesCS4A01G490300 chr4A 89.344 366 24 10 3953 4313 740161396 740161751 3.060000e-121 446.0
8 TraesCS4A01G490300 chr4A 95.122 41 2 0 3204 3244 742123535 742123495 1.000000e-06 65.8
9 TraesCS4A01G490300 chr7A 91.551 3385 219 20 980 4313 2827338 2830706 0.000000e+00 4604.0
10 TraesCS4A01G490300 chr7A 90.925 3383 243 19 981 4313 2093388 2096756 0.000000e+00 4488.0
11 TraesCS4A01G490300 chr7A 87.566 2453 237 25 1904 4302 3780565 3783003 0.000000e+00 2778.0
12 TraesCS4A01G490300 chr7A 91.756 837 55 9 1 834 2826211 2827036 0.000000e+00 1151.0
13 TraesCS4A01G490300 chr7A 86.985 461 29 6 467 900 2092705 2093161 1.390000e-134 490.0
14 TraesCS4A01G490300 chr7A 77.037 810 154 16 974 1773 3273210 3273997 1.840000e-118 436.0
15 TraesCS4A01G490300 chr7A 98.333 60 1 0 833 892 2827061 2827120 5.900000e-19 106.0
16 TraesCS4A01G490300 chr7D 85.463 3522 422 34 835 4313 3858863 3855389 0.000000e+00 3596.0
17 TraesCS4A01G490300 chr7D 85.288 3419 376 57 974 4313 2408350 2411720 0.000000e+00 3410.0
18 TraesCS4A01G490300 chr7D 85.896 2205 273 14 1899 4072 2651653 2653850 0.000000e+00 2314.0
19 TraesCS4A01G490300 chr7D 78.794 2537 408 73 1857 4313 3688296 3690782 0.000000e+00 1585.0
20 TraesCS4A01G490300 chr7D 78.894 796 135 20 987 1773 3685928 3686699 3.850000e-140 508.0
21 TraesCS4A01G490300 chr7D 77.376 747 139 16 975 1715 2650048 2650770 2.400000e-112 416.0
22 TraesCS4A01G490300 chr7D 88.211 246 18 6 4072 4313 2653883 2654121 2.540000e-72 283.0
23 TraesCS4A01G490300 chr7D 84.524 168 23 3 141 307 3859188 3859023 3.450000e-36 163.0
24 TraesCS4A01G490300 chr7D 76.129 310 64 5 10 316 2649427 2649729 2.080000e-33 154.0
25 TraesCS4A01G490300 chr7D 86.905 84 10 1 1 83 3859288 3859205 4.590000e-15 93.5
26 TraesCS4A01G490300 chrUn 97.819 963 2 1 1 963 444984475 444985418 0.000000e+00 1644.0
27 TraesCS4A01G490300 chr5D 74.525 526 86 31 2598 3102 422947517 422947019 7.370000e-43 185.0
28 TraesCS4A01G490300 chr4D 100.000 29 0 0 735 763 98936073 98936101 2.000000e-03 54.7
29 TraesCS4A01G490300 chr1B 96.875 32 1 0 1242 1273 658353068 658353099 2.000000e-03 54.7
30 TraesCS4A01G490300 chr1B 94.286 35 2 0 1242 1276 660532121 660532087 2.000000e-03 54.7
31 TraesCS4A01G490300 chr1A 94.286 35 2 0 1242 1276 570864726 570864692 2.000000e-03 54.7


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 TraesCS4A01G490300 chr4A 740537799 740542111 4312 True 7928.000000 7928 100.000000 1 4313 1 chr4A.!!$R4 4312
1 TraesCS4A01G490300 chr4A 739627108 739631422 4314 True 7215.000000 7215 97.033000 1 4313 1 chr4A.!!$R1 4312
2 TraesCS4A01G490300 chr4A 742032688 742037096 4408 True 3329.000000 5590 98.302500 383 4311 2 chr4A.!!$R5 3928
3 TraesCS4A01G490300 chr4A 739843576 739845186 1610 True 2760.000000 2760 97.415000 1 1625 1 chr4A.!!$R3 1624
4 TraesCS4A01G490300 chr4A 742123495 742124069 574 True 356.400000 647 92.415500 1 3244 2 chr4A.!!$R6 3243
5 TraesCS4A01G490300 chr7A 3780565 3783003 2438 False 2778.000000 2778 87.566000 1904 4302 1 chr7A.!!$F2 2398
6 TraesCS4A01G490300 chr7A 2092705 2096756 4051 False 2489.000000 4488 88.955000 467 4313 2 chr7A.!!$F3 3846
7 TraesCS4A01G490300 chr7A 2826211 2830706 4495 False 1953.666667 4604 93.880000 1 4313 3 chr7A.!!$F4 4312
8 TraesCS4A01G490300 chr7A 3273210 3273997 787 False 436.000000 436 77.037000 974 1773 1 chr7A.!!$F1 799
9 TraesCS4A01G490300 chr7D 2408350 2411720 3370 False 3410.000000 3410 85.288000 974 4313 1 chr7D.!!$F1 3339
10 TraesCS4A01G490300 chr7D 3855389 3859288 3899 True 1284.166667 3596 85.630667 1 4313 3 chr7D.!!$R1 4312
11 TraesCS4A01G490300 chr7D 3685928 3690782 4854 False 1046.500000 1585 78.844000 987 4313 2 chr7D.!!$F3 3326
12 TraesCS4A01G490300 chr7D 2649427 2654121 4694 False 791.750000 2314 81.903000 10 4313 4 chr7D.!!$F2 4303
13 TraesCS4A01G490300 chrUn 444984475 444985418 943 False 1644.000000 1644 97.819000 1 963 1 chrUn.!!$F1 962

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
2299 4508 4.821805 CAGGTAATCCAACACCCATGATAC 59.178 45.833 0.0 0.0 35.25 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3946 6200 1.15203 AACTGTGGAGAGGCAGGGA 60.152 57.895 0.0 0.0 37.07 4.2 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
2299 4508 4.821805 CAGGTAATCCAACACCCATGATAC 59.178 45.833 0.00 0.00 35.25 2.24
2436 4661 6.019479 GGACATTCTTGCTCTATTTGAGTACG 60.019 42.308 0.00 0.00 44.41 3.67
3212 5454 3.057104 CCAAGATTTTGCACAGCTCATGA 60.057 43.478 0.00 0.00 32.79 3.07
3260 5502 3.470645 AAATATGGTGCGAGTCTACCC 57.529 47.619 10.01 0.00 36.10 3.69
3365 5607 6.003326 TCACTATCACTCAATTTTGAAGGCA 58.997 36.000 0.00 0.00 36.64 4.75
3383 5625 1.956477 GCAAGTTGACCCAAGACATGT 59.044 47.619 7.16 0.00 0.00 3.21
3904 6158 4.108336 CTCTAGACACCATCAACACATCG 58.892 47.826 0.00 0.00 0.00 3.84
3917 6171 7.226523 CCATCAACACATCGAGGTAATGAATTA 59.773 37.037 17.37 0.31 0.00 1.40
3922 6176 6.767902 ACACATCGAGGTAATGAATTATGCTT 59.232 34.615 0.77 0.00 0.00 3.91
3938 6192 3.681593 TGCTTTACATGCCTTGCAATT 57.318 38.095 0.00 0.00 43.62 2.32
3945 6199 3.853475 ACATGCCTTGCAATTAGCTTTC 58.147 40.909 14.87 0.00 43.62 2.62
3946 6200 3.512724 ACATGCCTTGCAATTAGCTTTCT 59.487 39.130 14.87 0.00 43.62 2.52
3947 6201 3.855689 TGCCTTGCAATTAGCTTTCTC 57.144 42.857 14.87 0.00 45.94 2.87
3975 6238 1.625315 CTCCACAGTTCACATCCTGGA 59.375 52.381 0.00 0.00 32.90 3.86
3989 6252 5.693104 CACATCCTGGAAATGACACTTTTTG 59.307 40.000 0.00 0.00 0.00 2.44
4021 6284 3.217242 CAGTACAGGCTGCGACTTT 57.783 52.632 15.89 0.00 0.00 2.66
4165 6461 8.958119 TGTGTCACCACTAGGATTTATTTATC 57.042 34.615 0.00 0.00 42.34 1.75
4166 6462 8.768397 TGTGTCACCACTAGGATTTATTTATCT 58.232 33.333 0.00 0.00 42.34 1.98
4167 6463 9.614792 GTGTCACCACTAGGATTTATTTATCTT 57.385 33.333 0.00 0.00 38.61 2.40
4168 6464 9.613428 TGTCACCACTAGGATTTATTTATCTTG 57.387 33.333 0.00 0.00 38.69 3.02
4169 6465 9.614792 GTCACCACTAGGATTTATTTATCTTGT 57.385 33.333 0.00 0.00 38.69 3.16
4199 6499 4.269603 CAGATCGAAGTTAATGACCTGCTG 59.730 45.833 0.00 0.00 0.00 4.41
4200 6500 2.346803 TCGAAGTTAATGACCTGCTGC 58.653 47.619 0.00 0.00 0.00 5.25
4201 6501 2.076100 CGAAGTTAATGACCTGCTGCA 58.924 47.619 0.88 0.88 0.00 4.41
4202 6502 2.483877 CGAAGTTAATGACCTGCTGCAA 59.516 45.455 3.02 0.00 0.00 4.08
4203 6503 3.127548 CGAAGTTAATGACCTGCTGCAAT 59.872 43.478 3.02 0.00 0.00 3.56
4204 6504 4.332543 CGAAGTTAATGACCTGCTGCAATA 59.667 41.667 3.02 0.00 0.00 1.90
4205 6505 5.008019 CGAAGTTAATGACCTGCTGCAATAT 59.992 40.000 3.02 0.00 0.00 1.28
4206 6506 5.762825 AGTTAATGACCTGCTGCAATATG 57.237 39.130 3.02 0.00 0.00 1.78
4208 6508 2.742428 ATGACCTGCTGCAATATGGT 57.258 45.000 10.66 10.66 0.00 3.55
4209 6509 1.753930 TGACCTGCTGCAATATGGTG 58.246 50.000 15.06 0.00 0.00 4.17
4210 6510 1.027357 GACCTGCTGCAATATGGTGG 58.973 55.000 15.06 8.01 0.00 4.61
4242 6542 7.452880 TCTTTCCAAGAAATATGGTGACTTG 57.547 36.000 0.00 0.00 39.09 3.16
4301 6602 6.181190 TGGACATGTATTTGGTTATTTCGGA 58.819 36.000 0.00 0.00 0.00 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1859 4067 6.830873 AAAAGAGATGGGAAACTGAATGAG 57.169 37.500 0.00 0.00 0.00 2.90
2299 4508 2.102161 GGCGCATAGTTTTGCCCG 59.898 61.111 10.83 0.00 41.70 6.13
3212 5454 6.041979 ACCTTTGTCAAAGCCTTCATATTGTT 59.958 34.615 18.30 0.00 37.18 2.83
3260 5502 3.535629 TTGAGCTGCTGGTGTCGGG 62.536 63.158 7.01 0.00 0.00 5.14
3365 5607 3.897239 TCAACATGTCTTGGGTCAACTT 58.103 40.909 0.00 0.00 0.00 2.66
3455 5709 1.836604 GCAAGGCAACAAAGGGGGA 60.837 57.895 0.00 0.00 41.41 4.81
3904 6158 7.809806 GGCATGTAAAGCATAATTCATTACCTC 59.190 37.037 0.00 0.00 35.74 3.85
3917 6171 3.899052 ATTGCAAGGCATGTAAAGCAT 57.101 38.095 4.94 0.00 38.76 3.79
3922 6176 5.185635 AGAAAGCTAATTGCAAGGCATGTAA 59.814 36.000 19.10 0.00 45.94 2.41
3938 6192 1.490574 GAGAGGCAGGGAGAAAGCTA 58.509 55.000 0.00 0.00 0.00 3.32
3945 6199 1.197430 AACTGTGGAGAGGCAGGGAG 61.197 60.000 0.00 0.00 37.07 4.30
3946 6200 1.152030 AACTGTGGAGAGGCAGGGA 60.152 57.895 0.00 0.00 37.07 4.20
3947 6201 1.298014 GAACTGTGGAGAGGCAGGG 59.702 63.158 0.00 0.00 37.07 4.45
3975 6238 8.261492 TGCACAATAAACAAAAAGTGTCATTT 57.739 26.923 0.00 0.00 40.60 2.32
3989 6252 3.119849 CCTGTACTGCCTGCACAATAAAC 60.120 47.826 0.00 0.00 0.00 2.01
4021 6284 3.609853 ACGAGAATGCTTTGCCATTAGA 58.390 40.909 0.00 0.00 35.67 2.10
4165 6461 9.318041 CATTAACTTCGATCTGTTACAAACAAG 57.682 33.333 5.92 0.00 41.61 3.16
4166 6462 9.047371 TCATTAACTTCGATCTGTTACAAACAA 57.953 29.630 5.92 0.00 41.61 2.83
4167 6463 8.492748 GTCATTAACTTCGATCTGTTACAAACA 58.507 33.333 5.92 0.00 39.52 2.83
4168 6464 7.955864 GGTCATTAACTTCGATCTGTTACAAAC 59.044 37.037 5.92 5.12 0.00 2.93
4169 6465 7.876068 AGGTCATTAACTTCGATCTGTTACAAA 59.124 33.333 5.92 0.00 0.00 2.83
4199 6499 4.900635 AGAAAATCGTCCACCATATTGC 57.099 40.909 0.00 0.00 0.00 3.56
4200 6500 6.127758 TGGAAAGAAAATCGTCCACCATATTG 60.128 38.462 2.79 0.00 32.77 1.90
4201 6501 5.949354 TGGAAAGAAAATCGTCCACCATATT 59.051 36.000 2.79 0.00 32.77 1.28
4202 6502 5.505780 TGGAAAGAAAATCGTCCACCATAT 58.494 37.500 2.79 0.00 32.77 1.78
4203 6503 4.912586 TGGAAAGAAAATCGTCCACCATA 58.087 39.130 2.79 0.00 32.77 2.74
4204 6504 3.761897 TGGAAAGAAAATCGTCCACCAT 58.238 40.909 2.79 0.00 32.77 3.55
4205 6505 3.216187 TGGAAAGAAAATCGTCCACCA 57.784 42.857 2.79 0.00 32.77 4.17
4242 6542 9.922305 CAGAGTAAACTTATTTATTACAGCAGC 57.078 33.333 0.00 0.00 32.91 5.25


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

AutoCloner maintained by Alex Coulton.