Multiple sequence alignment - TraesCS4B01G395400

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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 TraesCS4B01G395400 chr4B 100.000 3917 0 0 1 3917 669574814 669578730 0.000000e+00 7234
1 TraesCS4B01G395400 chr4B 97.782 3922 76 10 1 3917 669478465 669482380 0.000000e+00 6750
2 TraesCS4B01G395400 chr4B 97.777 3374 65 7 550 3917 668519967 668523336 0.000000e+00 5806
3 TraesCS4B01G395400 chr4B 97.688 3373 71 6 550 3917 668368440 668371810 0.000000e+00 5790
4 TraesCS4B01G395400 chr4B 97.480 3373 76 8 550 3917 668460125 668463493 0.000000e+00 5749
5 TraesCS4B01G395400 chr4B 97.396 2919 66 7 1005 3917 669323937 669321023 0.000000e+00 4961
6 TraesCS4B01G395400 chr4B 97.287 2801 58 8 1011 3804 668980211 668983000 0.000000e+00 4735
7 TraesCS4B01G395400 chr4B 100.000 199 0 0 1 199 668607443 668607641 6.180000e-98 368
8 TraesCS4B01G395400 chr4B 99.497 199 1 0 1 199 668368249 668368447 2.880000e-96 363
9 TraesCS4B01G395400 chr4B 99.497 199 1 0 1 199 668459934 668460132 2.880000e-96 363
10 TraesCS4B01G395400 chr4B 99.497 199 1 0 1 199 668977747 668977945 2.880000e-96 363
11 TraesCS4B01G395400 chr4B 98.995 199 2 0 1 199 669157841 669157643 1.340000e-94 357
12 TraesCS4B01G395400 chr4B 98.995 199 2 0 1 199 669337672 669337474 1.340000e-94 357
13 TraesCS4B01G395400 chr4B 96.891 193 3 3 362 552 617916859 617917050 1.760000e-83 320
14 TraesCS4B01G395400 chr4B 95.812 191 3 5 365 552 123459790 123459602 1.770000e-78 303
15 TraesCS4B01G395400 chr4B 93.333 165 10 1 199 362 123460012 123459848 3.910000e-60 243
16 TraesCS4B01G395400 chr5A 97.956 3376 58 8 550 3917 707853271 707856643 0.000000e+00 5842
17 TraesCS4B01G395400 chr3B 97.333 3375 81 8 550 3917 34679953 34683325 0.000000e+00 5725
18 TraesCS4B01G395400 chr3B 97.269 3369 63 10 553 3917 9069061 9065718 0.000000e+00 5685
19 TraesCS4B01G395400 chr3B 99.500 200 0 1 1 199 9069256 9069057 2.880000e-96 363
20 TraesCS4B01G395400 chr3B 95.876 194 4 4 362 552 752667872 752667680 1.060000e-80 311
21 TraesCS4B01G395400 chr3B 94.512 164 8 1 200 362 743724882 743724719 6.500000e-63 252
22 TraesCS4B01G395400 chr5B 87.462 327 28 10 218 534 613321056 613321379 8.000000e-97 364
23 TraesCS4B01G395400 chr5B 96.891 193 4 2 362 552 589474455 589474647 4.880000e-84 322
24 TraesCS4B01G395400 chr5B 93.939 165 10 0 198 362 596915760 596915924 2.340000e-62 250
25 TraesCS4B01G395400 chr1B 99.497 199 1 0 1 199 175665666 175665864 2.880000e-96 363
26 TraesCS4B01G395400 chr1B 96.410 195 3 4 362 552 593616557 593616363 6.320000e-83 318
27 TraesCS4B01G395400 chr1B 93.902 164 9 1 200 362 593616775 593616612 3.020000e-61 246
28 TraesCS4B01G395400 chr4A 96.907 194 3 3 362 552 712656791 712656984 4.880000e-84 322
29 TraesCS4B01G395400 chr4A 95.876 194 5 3 362 552 712637898 712638091 1.060000e-80 311
30 TraesCS4B01G395400 chrUn 95.092 163 8 0 200 362 414559598 414559436 1.400000e-64 257
31 TraesCS4B01G395400 chr7B 94.611 167 5 2 200 362 499642864 499642698 5.020000e-64 255
32 TraesCS4B01G395400 chr7B 93.491 169 10 1 195 362 546015955 546015787 2.340000e-62 250


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 TraesCS4B01G395400 chr4B 669574814 669578730 3916 False 7234.0 7234 100.0000 1 3917 1 chr4B.!!$F5 3916
1 TraesCS4B01G395400 chr4B 669478465 669482380 3915 False 6750.0 6750 97.7820 1 3917 1 chr4B.!!$F4 3916
2 TraesCS4B01G395400 chr4B 668519967 668523336 3369 False 5806.0 5806 97.7770 550 3917 1 chr4B.!!$F2 3367
3 TraesCS4B01G395400 chr4B 669321023 669323937 2914 True 4961.0 4961 97.3960 1005 3917 1 chr4B.!!$R2 2912
4 TraesCS4B01G395400 chr4B 668368249 668371810 3561 False 3076.5 5790 98.5925 1 3917 2 chr4B.!!$F6 3916
5 TraesCS4B01G395400 chr4B 668459934 668463493 3559 False 3056.0 5749 98.4885 1 3917 2 chr4B.!!$F7 3916
6 TraesCS4B01G395400 chr4B 668977747 668983000 5253 False 2549.0 4735 98.3920 1 3804 2 chr4B.!!$F8 3803
7 TraesCS4B01G395400 chr5A 707853271 707856643 3372 False 5842.0 5842 97.9560 550 3917 1 chr5A.!!$F1 3367
8 TraesCS4B01G395400 chr3B 34679953 34683325 3372 False 5725.0 5725 97.3330 550 3917 1 chr3B.!!$F1 3367
9 TraesCS4B01G395400 chr3B 9065718 9069256 3538 True 3024.0 5685 98.3845 1 3917 2 chr3B.!!$R3 3916

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
332 336 2.676471 GTGAGGTGCGCCCCAAAT 60.676 61.111 12.68 0.0 34.57 2.32 F
1229 3046 1.630126 ATGCGGAGAAGGAGGTGCAT 61.630 55.000 0.00 0.0 38.16 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2103 3928 1.274650 ACCATGGGAGGAGGAACAGAT 60.275 52.381 18.09 0.0 0.0 2.90 R
3041 4868 0.392998 CTTACGCCAGCCTGAACCAT 60.393 55.000 0.00 0.0 0.0 3.55 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
332 336 2.676471 GTGAGGTGCGCCCCAAAT 60.676 61.111 12.68 0.00 34.57 2.32
453 457 3.000925 CACGCGTCAAATTATCTACCACC 59.999 47.826 9.86 0.00 0.00 4.61
550 554 2.677979 GGAGCCAAAACTCCGCGTC 61.678 63.158 4.92 0.00 46.52 5.19
824 830 5.271598 AGCCATCCAGGTTTTCAATTATGA 58.728 37.500 0.00 0.00 40.61 2.15
1037 2854 3.953612 TGCCTGGATATAGTTTGCTTTGG 59.046 43.478 0.00 0.00 0.00 3.28
1125 2942 3.164268 TGACAATTGGCCTGTAAATGCT 58.836 40.909 9.30 0.00 0.00 3.79
1127 2944 2.899256 ACAATTGGCCTGTAAATGCTGT 59.101 40.909 10.83 0.00 0.00 4.40
1229 3046 1.630126 ATGCGGAGAAGGAGGTGCAT 61.630 55.000 0.00 0.00 38.16 3.96
1591 3412 8.162085 AGATTATGAAATCCTGTAGTGCATCAT 58.838 33.333 0.00 0.00 42.20 2.45
1651 3472 1.814169 GGTTCCGACCTCATTCGCC 60.814 63.158 0.00 0.00 42.99 5.54
2103 3928 2.746279 TGACCTTTTTCTTCAGGGCA 57.254 45.000 0.00 0.00 46.87 5.36
2377 4203 6.927936 ACTCTTCTGAACGAGCGTATACTATA 59.072 38.462 13.31 0.00 0.00 1.31
2411 4237 8.803397 TGTATATCATATTACTGAGGTAGCGT 57.197 34.615 0.00 0.00 0.00 5.07
2523 4349 6.239217 TGATTGCTCCTGATATACAGTGTT 57.761 37.500 0.00 0.00 44.40 3.32
2959 4786 8.369424 GGAGTACTCTACTGTATCACTATCTGA 58.631 40.741 21.88 0.00 39.59 3.27
3103 4930 2.700722 AGGCTACAAGCTTAGCTTCC 57.299 50.000 17.37 14.68 46.77 3.46
3112 4939 1.019805 GCTTAGCTTCCGCCTTTCGT 61.020 55.000 0.00 0.00 36.60 3.85
3447 5274 7.967908 ACAGACTATATAGGGGTGATCAAAAG 58.032 38.462 14.25 0.00 0.00 2.27
3669 5496 3.793559 AGTGTTGTAGTGGTCTTGACAC 58.206 45.455 3.08 0.00 39.10 3.67
3674 5501 5.650266 TGTTGTAGTGGTCTTGACACAATTT 59.350 36.000 3.08 0.00 41.21 1.82
3774 5602 8.742777 TCTACAGAATGGTTAGTGTAAACGTAT 58.257 33.333 0.00 0.00 43.62 3.06
3870 5698 8.970020 TCAAATTATCCTGCAATGTATTGACTT 58.030 29.630 8.70 0.00 40.14 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
332 336 5.048504 GCTCAGATGTCCAAATGAGTTGAAA 60.049 40.000 0.00 0.00 41.00 2.69
522 526 2.837031 TTTTGGCTCCCGGGCTCATC 62.837 60.000 18.49 3.79 41.48 2.92
824 830 7.114754 TCTATGCTGAGTTTCCAAATCATCTT 58.885 34.615 0.00 0.00 0.00 2.40
1125 2942 5.391256 TCACACCTCTAGGAGAACTTTACA 58.609 41.667 2.23 0.00 38.94 2.41
1127 2944 6.017192 ACATCACACCTCTAGGAGAACTTTA 58.983 40.000 2.23 0.00 38.94 1.85
1211 3028 2.293318 ATGCACCTCCTTCTCCGCA 61.293 57.895 0.00 0.00 0.00 5.69
1235 3052 4.785453 CTCACCTCAAGCGCCCCC 62.785 72.222 2.29 0.00 0.00 5.40
1510 3331 9.892130 AGATTTTAGACGATGTTCTTCCTAATT 57.108 29.630 0.00 0.00 0.00 1.40
1591 3412 7.014711 TGTTCAAAAATTAGTGAAGGGTGCATA 59.985 33.333 4.41 0.00 34.52 3.14
1814 3635 4.753516 TCTTGTGTGAAGTGGAGAAGAA 57.246 40.909 0.00 0.00 0.00 2.52
2083 3908 3.025322 TGCCCTGAAGAAAAAGGTCAA 57.975 42.857 0.00 0.00 0.00 3.18
2103 3928 1.274650 ACCATGGGAGGAGGAACAGAT 60.275 52.381 18.09 0.00 0.00 2.90
2406 4232 2.438254 CAGCATGGCCCAACGCTA 60.438 61.111 10.39 0.00 37.74 4.26
2494 4320 6.963348 CTGTATATCAGGAGCAATCAGCAGTT 60.963 42.308 0.00 0.00 42.26 3.16
2523 4349 5.163269 ACAATCCTACTATCAGCTGCAATCA 60.163 40.000 9.47 0.00 0.00 2.57
2750 4576 8.723942 ACAACATTATAGAGTGAATCTTGTCC 57.276 34.615 0.00 0.00 39.64 4.02
3041 4868 0.392998 CTTACGCCAGCCTGAACCAT 60.393 55.000 0.00 0.00 0.00 3.55
3302 5129 8.239998 GCATAAACCATGAAATCTATAGGAAGC 58.760 37.037 0.00 0.00 36.69 3.86
3653 5480 5.680619 AGAAATTGTGTCAAGACCACTACA 58.319 37.500 0.00 0.00 0.00 2.74
3774 5602 9.701098 AGATACAGAATCGTGTACAACTTAAAA 57.299 29.630 0.00 0.00 39.79 1.52
3870 5698 3.066900 GCATAGTCAAGTTAGCTCCGAGA 59.933 47.826 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.