Multiple sequence alignment - TraesCS5B01G404400

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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 TraesCS5B01G404400 chr5B 100.000 3455 0 0 1 3455 580489759 580493213 0.000000e+00 6381
1 TraesCS5B01G404400 chr5B 98.548 551 8 0 1 551 415793277 415793827 0.000000e+00 974
2 TraesCS5B01G404400 chr5D 96.624 2251 45 6 550 2796 473096188 473098411 0.000000e+00 3707
3 TraesCS5B01G404400 chr5D 96.148 675 16 5 2786 3455 473099258 473099927 0.000000e+00 1094
4 TraesCS5B01G404400 chr5A 95.170 2298 49 15 550 2794 593077836 593080124 0.000000e+00 3572
5 TraesCS5B01G404400 chr5A 95.052 667 28 4 2786 3452 593080970 593081631 0.000000e+00 1044
6 TraesCS5B01G404400 chr2A 99.096 553 5 0 1 553 144864561 144865113 0.000000e+00 994
7 TraesCS5B01G404400 chr6B 99.089 549 5 0 1 549 715712192 715711644 0.000000e+00 987
8 TraesCS5B01G404400 chr6B 79.553 313 60 3 2488 2796 560700949 560700637 1.610000e-53 220
9 TraesCS5B01G404400 chr6B 79.553 313 60 3 2488 2796 560740396 560740084 1.610000e-53 220
10 TraesCS5B01G404400 chr6B 78.914 313 62 3 2488 2796 560793302 560792990 3.490000e-50 209
11 TraesCS5B01G404400 chr7A 98.907 549 6 0 1 549 256007621 256008169 0.000000e+00 981
12 TraesCS5B01G404400 chr7A 94.083 507 25 4 2786 3292 130439812 130439311 0.000000e+00 765
13 TraesCS5B01G404400 chr2B 98.561 556 7 1 1 556 512302508 512301954 0.000000e+00 981
14 TraesCS5B01G404400 chr2B 97.464 552 14 0 1 552 680579058 680578507 0.000000e+00 942
15 TraesCS5B01G404400 chr1B 98.907 549 5 1 1 549 543481402 543480855 0.000000e+00 979
16 TraesCS5B01G404400 chr4B 98.543 549 8 0 1 549 115079344 115079892 0.000000e+00 970
17 TraesCS5B01G404400 chr3B 98.185 551 10 0 1 551 814366764 814367314 0.000000e+00 963
18 TraesCS5B01G404400 chr6A 94.872 507 22 3 2786 3292 26756526 26757028 0.000000e+00 789
19 TraesCS5B01G404400 chrUn 79.553 313 60 3 2488 2796 413095334 413095022 1.610000e-53 220


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 TraesCS5B01G404400 chr5B 580489759 580493213 3454 False 6381.0 6381 100.000 1 3455 1 chr5B.!!$F2 3454
1 TraesCS5B01G404400 chr5B 415793277 415793827 550 False 974.0 974 98.548 1 551 1 chr5B.!!$F1 550
2 TraesCS5B01G404400 chr5D 473096188 473099927 3739 False 2400.5 3707 96.386 550 3455 2 chr5D.!!$F1 2905
3 TraesCS5B01G404400 chr5A 593077836 593081631 3795 False 2308.0 3572 95.111 550 3452 2 chr5A.!!$F1 2902
4 TraesCS5B01G404400 chr2A 144864561 144865113 552 False 994.0 994 99.096 1 553 1 chr2A.!!$F1 552
5 TraesCS5B01G404400 chr6B 715711644 715712192 548 True 987.0 987 99.089 1 549 1 chr6B.!!$R4 548
6 TraesCS5B01G404400 chr7A 256007621 256008169 548 False 981.0 981 98.907 1 549 1 chr7A.!!$F1 548
7 TraesCS5B01G404400 chr7A 130439311 130439812 501 True 765.0 765 94.083 2786 3292 1 chr7A.!!$R1 506
8 TraesCS5B01G404400 chr2B 512301954 512302508 554 True 981.0 981 98.561 1 556 1 chr2B.!!$R1 555
9 TraesCS5B01G404400 chr2B 680578507 680579058 551 True 942.0 942 97.464 1 552 1 chr2B.!!$R2 551
10 TraesCS5B01G404400 chr1B 543480855 543481402 547 True 979.0 979 98.907 1 549 1 chr1B.!!$R1 548
11 TraesCS5B01G404400 chr4B 115079344 115079892 548 False 970.0 970 98.543 1 549 1 chr4B.!!$F1 548
12 TraesCS5B01G404400 chr3B 814366764 814367314 550 False 963.0 963 98.185 1 551 1 chr3B.!!$F1 550
13 TraesCS5B01G404400 chr6A 26756526 26757028 502 False 789.0 789 94.872 2786 3292 1 chr6A.!!$F1 506

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
781 811 0.327000 CTTGAGGTGGAGGGAGGGAT 60.327 60.0 0.0 0.0 0.0 3.85 F
951 1005 0.834687 TGAAGTACGGGGGTTCTGCT 60.835 55.0 0.0 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2262 2316 2.382770 ACCCTTGTCACACAGCCCA 61.383 57.895 0.0 0.0 0.00 5.36 R
2755 2811 4.406456 TCCAGTTTGGTTGATAGCACAAT 58.594 39.130 0.0 0.0 39.03 2.71 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
435 436 2.957402 ATCCTGCTCAAAACCACTCA 57.043 45.000 0.00 0.00 0.00 3.41
668 695 0.612744 GCTTCTCTCTTCCACAGGCT 59.387 55.000 0.00 0.00 0.00 4.58
757 787 3.060866 GGTTGTGAGCGAGGAGGT 58.939 61.111 0.00 0.00 0.00 3.85
781 811 0.327000 CTTGAGGTGGAGGGAGGGAT 60.327 60.000 0.00 0.00 0.00 3.85
832 886 2.577700 CTACAGCTGGAGGTCGATACT 58.422 52.381 19.10 0.00 0.00 2.12
951 1005 0.834687 TGAAGTACGGGGGTTCTGCT 60.835 55.000 0.00 0.00 0.00 4.24
961 1015 1.519719 GGTTCTGCTCGAGCTCCAT 59.480 57.895 35.27 0.00 42.66 3.41
968 1022 1.588403 CTCGAGCTCCATCACAGCG 60.588 63.158 8.47 0.00 42.14 5.18
1110 1164 2.981350 GCTTTCGACCCCGCCAAA 60.981 61.111 0.00 0.00 35.37 3.28
1497 1551 0.892755 TCATGGAGAAGTACGGCGTT 59.107 50.000 21.24 0.00 0.00 4.84
1530 1584 1.208614 CGCTTTCAACAGCCTGCTC 59.791 57.895 0.00 0.00 36.31 4.26
1854 1908 0.874175 TGCTCGTGCATACATACGGC 60.874 55.000 8.30 0.00 45.31 5.68
2262 2316 2.998670 CACGTTCTCTGTGCTGATCAAT 59.001 45.455 0.00 0.00 0.00 2.57
2741 2797 8.301730 TGTAATTTCCAACTACAGTTACTTCG 57.698 34.615 0.00 0.00 36.32 3.79
2755 2811 6.016024 ACAGTTACTTCGTAAGTACCACATCA 60.016 38.462 6.88 0.00 43.30 3.07
2797 2853 6.935741 TGGATACAGTTTTATATGGTGCAC 57.064 37.500 8.80 8.80 46.17 4.57
3012 3952 5.448654 TCAGATGGCTATGGCTGTAAAAAT 58.551 37.500 0.00 0.00 38.73 1.82
3043 3983 0.035056 AGACCCTGGGCTGAATTTCG 60.035 55.000 14.08 0.00 0.00 3.46
3086 4026 0.106708 GGTAGCAGCGGAATCCATCA 59.893 55.000 0.00 0.00 0.00 3.07
3126 4066 1.348064 AATTCTGGTCTGACCGGTGA 58.652 50.000 29.70 21.31 45.01 4.02
3280 4220 4.419522 ACGGCACAAGTGAATTATTGAC 57.580 40.909 4.04 0.00 0.00 3.18
3344 4284 3.326006 TCAGAAAGTTCCTGATCAGCAGT 59.674 43.478 17.76 5.96 43.33 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
435 436 0.399949 TACCGGATCAATCAGGCCCT 60.400 55.000 9.46 0.0 44.62 5.19
668 695 4.643334 TCGTCGATTGAGGGAGAGAAAATA 59.357 41.667 2.86 0.0 0.00 1.40
751 781 0.618968 CACCTCAAGCCCTACCTCCT 60.619 60.000 0.00 0.0 0.00 3.69
757 787 1.306997 CCCTCCACCTCAAGCCCTA 60.307 63.158 0.00 0.0 0.00 3.53
781 811 3.059982 CCTCCACCGCTCTGTTCA 58.940 61.111 0.00 0.0 0.00 3.18
832 886 2.024868 CGCGATCACCACACCGAAA 61.025 57.895 0.00 0.0 0.00 3.46
901 955 2.276116 GGTCTCGCTCTGTGGTGGA 61.276 63.158 0.00 0.0 0.00 4.02
951 1005 2.491621 CGCTGTGATGGAGCTCGA 59.508 61.111 7.83 3.7 34.03 4.04
961 1015 3.911698 ACGCTGACACCGCTGTGA 61.912 61.111 15.72 0.0 45.76 3.58
968 1022 1.961277 CCTTCCACACGCTGACACC 60.961 63.158 0.00 0.0 0.00 4.16
1077 1131 4.783621 GCCTCCACAGCGGCATCA 62.784 66.667 1.45 0.0 45.59 3.07
1110 1164 1.449246 GATGAGCTTGCAGAGGCGT 60.449 57.895 0.00 0.0 45.35 5.68
1497 1551 4.752879 GCGGCGAGGTTAGGCACA 62.753 66.667 12.98 0.0 0.00 4.57
1848 1902 2.684001 TCCTCATTTCAACGCCGTAT 57.316 45.000 0.00 0.0 0.00 3.06
1854 1908 3.165058 TCCTCGATCCTCATTTCAACG 57.835 47.619 0.00 0.0 0.00 4.10
2262 2316 2.382770 ACCCTTGTCACACAGCCCA 61.383 57.895 0.00 0.0 0.00 5.36
2534 2588 5.303078 TCCCACAAGCAATAGCAAAAGTAAA 59.697 36.000 0.00 0.0 45.49 2.01
2755 2811 4.406456 TCCAGTTTGGTTGATAGCACAAT 58.594 39.130 0.00 0.0 39.03 2.71
2796 2852 6.098679 CAGTCTGAAGAAGAGATTTCATCGT 58.901 40.000 0.00 0.0 34.84 3.73
2797 2853 5.005586 GCAGTCTGAAGAAGAGATTTCATCG 59.994 44.000 3.32 0.0 34.84 3.84
3012 3952 0.907486 CAGGGTCTTGAGGCATCTGA 59.093 55.000 0.00 0.0 0.00 3.27
3086 4026 3.944250 CTTGCCTCCCGTTGCCCAT 62.944 63.158 0.00 0.0 0.00 4.00
3126 4066 2.895404 AGTGATTGTTCTGCCTTGCAAT 59.105 40.909 0.00 0.0 38.41 3.56
3280 4220 4.039730 ACCATGTCCCGAATCTGAAGATAG 59.960 45.833 0.00 0.0 33.73 2.08
3293 4233 3.141398 CCAGATTATCAACCATGTCCCG 58.859 50.000 0.00 0.0 0.00 5.14
3344 4284 2.280524 CCGAGTGAAACGCCACCA 60.281 61.111 0.00 0.0 45.86 4.17


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

AutoCloner maintained by Alex Coulton.