Multiple sequence alignment - TraesCS5A01G116300

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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 TraesCS5A01G116300 chr5A 100.000 3839 0 0 1 3839 237961362 237957524 0.000000e+00 7090
1 TraesCS5A01G116300 chr5A 97.864 2950 54 3 1 2941 416141969 416144918 0.000000e+00 5090
2 TraesCS5A01G116300 chr5A 80.196 2954 556 22 1 2938 275254306 275251366 0.000000e+00 2187
3 TraesCS5A01G116300 chr6A 98.309 2957 38 5 1 2946 123508575 123505620 0.000000e+00 5173
4 TraesCS5A01G116300 chr6A 98.368 2635 34 3 1 2626 283037281 283034647 0.000000e+00 4619
5 TraesCS5A01G116300 chr7B 97.253 2949 72 3 1 2940 241771317 241774265 0.000000e+00 4988
6 TraesCS5A01G116300 chr3A 97.918 2209 31 3 752 2945 63071350 63069142 0.000000e+00 3810
7 TraesCS5A01G116300 chr3A 92.375 1600 105 10 222 1813 740341046 740342636 0.000000e+00 2263
8 TraesCS5A01G116300 chr3A 80.027 2954 557 26 1 2938 556291607 556288671 0.000000e+00 2156
9 TraesCS5A01G116300 chr3A 95.696 697 25 2 2940 3631 123763324 123764020 0.000000e+00 1116
10 TraesCS5A01G116300 chr3A 88.601 386 30 6 2951 3326 387733693 387734074 1.260000e-124 457
11 TraesCS5A01G116300 chr3A 88.144 388 30 8 2951 3326 157601084 157601467 7.570000e-122 448
12 TraesCS5A01G116300 chr3A 98.122 213 4 0 3627 3839 123779531 123779743 4.680000e-99 372
13 TraesCS5A01G116300 chr7A 98.420 1835 26 2 1114 2945 702617951 702619785 0.000000e+00 3225
14 TraesCS5A01G116300 chr7A 98.317 1248 14 2 1 1241 702616702 702617949 0.000000e+00 2182
15 TraesCS5A01G116300 chr3D 91.983 1659 115 13 1294 2939 608063765 608065418 0.000000e+00 2311
16 TraesCS5A01G116300 chr3B 96.177 1177 39 5 1768 2940 370552626 370553800 0.000000e+00 1919
17 TraesCS5A01G116300 chr3B 91.504 1283 98 6 1660 2939 817819861 817821135 0.000000e+00 1755
18 TraesCS5A01G116300 chr3B 91.448 877 44 14 2972 3839 152122180 152121326 0.000000e+00 1175
19 TraesCS5A01G116300 chr7D 96.094 896 28 3 2951 3839 546694865 546693970 0.000000e+00 1454
20 TraesCS5A01G116300 chr5D 89.974 389 25 6 2951 3329 392054945 392054561 1.240000e-134 490
21 TraesCS5A01G116300 chr5B 88.205 390 30 8 2951 3329 473068021 473067637 5.850000e-123 451
22 TraesCS5A01G116300 chr4B 86.528 386 36 7 2951 3326 216834885 216835264 9.930000e-111 411
23 TraesCS5A01G116300 chr6B 86.234 385 35 7 2951 3326 418145531 418145906 5.970000e-108 401
24 TraesCS5A01G116300 chr2D 91.078 269 20 3 3572 3837 111349321 111349054 1.010000e-95 361
25 TraesCS5A01G116300 chr2B 88.593 263 14 9 3580 3839 161470466 161470217 4.820000e-79 305
26 TraesCS5A01G116300 chr2A 87.308 260 25 3 3580 3839 111439043 111438792 1.350000e-74 291


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 TraesCS5A01G116300 chr5A 237957524 237961362 3838 True 7090.0 7090 100.0000 1 3839 1 chr5A.!!$R1 3838
1 TraesCS5A01G116300 chr5A 416141969 416144918 2949 False 5090.0 5090 97.8640 1 2941 1 chr5A.!!$F1 2940
2 TraesCS5A01G116300 chr5A 275251366 275254306 2940 True 2187.0 2187 80.1960 1 2938 1 chr5A.!!$R2 2937
3 TraesCS5A01G116300 chr6A 123505620 123508575 2955 True 5173.0 5173 98.3090 1 2946 1 chr6A.!!$R1 2945
4 TraesCS5A01G116300 chr6A 283034647 283037281 2634 True 4619.0 4619 98.3680 1 2626 1 chr6A.!!$R2 2625
5 TraesCS5A01G116300 chr7B 241771317 241774265 2948 False 4988.0 4988 97.2530 1 2940 1 chr7B.!!$F1 2939
6 TraesCS5A01G116300 chr3A 63069142 63071350 2208 True 3810.0 3810 97.9180 752 2945 1 chr3A.!!$R1 2193
7 TraesCS5A01G116300 chr3A 740341046 740342636 1590 False 2263.0 2263 92.3750 222 1813 1 chr3A.!!$F5 1591
8 TraesCS5A01G116300 chr3A 556288671 556291607 2936 True 2156.0 2156 80.0270 1 2938 1 chr3A.!!$R2 2937
9 TraesCS5A01G116300 chr3A 123763324 123764020 696 False 1116.0 1116 95.6960 2940 3631 1 chr3A.!!$F1 691
10 TraesCS5A01G116300 chr7A 702616702 702619785 3083 False 2703.5 3225 98.3685 1 2945 2 chr7A.!!$F1 2944
11 TraesCS5A01G116300 chr3D 608063765 608065418 1653 False 2311.0 2311 91.9830 1294 2939 1 chr3D.!!$F1 1645
12 TraesCS5A01G116300 chr3B 370552626 370553800 1174 False 1919.0 1919 96.1770 1768 2940 1 chr3B.!!$F1 1172
13 TraesCS5A01G116300 chr3B 817819861 817821135 1274 False 1755.0 1755 91.5040 1660 2939 1 chr3B.!!$F2 1279
14 TraesCS5A01G116300 chr3B 152121326 152122180 854 True 1175.0 1175 91.4480 2972 3839 1 chr3B.!!$R1 867
15 TraesCS5A01G116300 chr7D 546693970 546694865 895 True 1454.0 1454 96.0940 2951 3839 1 chr7D.!!$R1 888

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
435 436 1.605232 CATTGTGTCTGCTCTTGCACA 59.395 47.619 0.0 0.0 45.31 4.57 F
1494 1634 0.961753 CCCTTTGGGCTTCTGTTCAC 59.038 55.000 0.0 0.0 35.35 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 2000 0.401738 CCTGTGGGAAGAGCTTTCCA 59.598 55.000 21.57 6.14 45.67 3.53 R
3115 3284 2.441410 TCAGACTCACTCATCTCGCTT 58.559 47.619 0.00 0.00 0.00 4.68 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
245 246 3.309296 AGGATTAAGCCTCATCTTCCGA 58.691 45.455 6.41 0.00 30.76 4.55
435 436 1.605232 CATTGTGTCTGCTCTTGCACA 59.395 47.619 0.00 0.00 45.31 4.57
688 691 7.448420 CAGATTGCCCTTCTATTCATTCTCTA 58.552 38.462 0.00 0.00 0.00 2.43
786 789 7.910162 CCATCACTTTTGTTATATTTCAGGTCG 59.090 37.037 0.00 0.00 0.00 4.79
1141 1280 2.859165 TTGGTGGACAGGAATCAGAC 57.141 50.000 0.00 0.00 0.00 3.51
1279 1418 2.991076 GCTGCTTGGAGGCTTGCTG 61.991 63.158 0.00 0.00 32.89 4.41
1494 1634 0.961753 CCCTTTGGGCTTCTGTTCAC 59.038 55.000 0.00 0.00 35.35 3.18
1570 1712 3.560453 CCTTTGGATACCGGGTCAGAAAA 60.560 47.826 6.32 0.46 0.00 2.29
1667 1809 3.941483 CACCAAGATTGCCCGGATATATC 59.059 47.826 0.73 3.96 0.00 1.63
1772 1914 6.267699 CCAAGAAATACTCCTTCCCAAGTTTT 59.732 38.462 0.00 0.00 0.00 2.43
1858 2000 2.104963 ACTTTCGCTTGGAGACTCCTTT 59.895 45.455 22.14 0.00 37.46 3.11
1881 2023 3.497942 GGAAAGCTCTTCCCACAGGTTTA 60.498 47.826 13.64 0.00 39.77 2.01
2602 2757 5.869579 ACTGTCTCTCTTTGGCTTCATTTA 58.130 37.500 0.00 0.00 0.00 1.40
2806 2961 1.172180 TTTTGCTTCGGCTCACAGGG 61.172 55.000 0.00 0.00 42.37 4.45
3115 3284 7.147966 CCTCCTGATGAATGAATGAATTGAACA 60.148 37.037 0.00 0.00 0.00 3.18
3286 3458 1.688772 CCTAGGAAGGTCGGATTCGA 58.311 55.000 1.05 0.00 38.19 3.71
3395 3567 6.317088 CACTCATGTGTAATGAACCAATGAC 58.683 40.000 0.00 0.00 39.24 3.06
3607 3779 8.542953 GCTAGCTTAATTGCAAATTTATCAACC 58.457 33.333 7.70 0.00 34.99 3.77
3671 3843 3.699671 GCAACGTTGTTTGCCACC 58.300 55.556 27.78 6.35 45.22 4.61
3685 3857 1.235281 GCCACCGAAAAGAGTGACCC 61.235 60.000 0.00 0.00 36.01 4.46
3737 3909 6.826668 TCCAACTCAGAACAAGAACAATCTA 58.173 36.000 0.00 0.00 33.77 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
245 246 4.776349 TGTTGTGCCGGATCAATATAGTT 58.224 39.130 5.05 0.00 0.00 2.24
278 279 7.120923 TGTTATCGCTAATTCTTCTACCCTT 57.879 36.000 0.00 0.00 0.00 3.95
435 436 5.263599 TGAAATGACCATGCAGACCTTTAT 58.736 37.500 0.00 0.00 0.00 1.40
786 789 2.629336 TTTGGCCCAATTTGGTGTTC 57.371 45.000 14.26 1.97 35.17 3.18
1141 1280 8.734386 ACAAAGGCTCTTGTTAGAATTATTCTG 58.266 33.333 16.86 0.76 35.91 3.02
1279 1418 0.547954 AGGTGGGAGGAAGGGTCTTC 60.548 60.000 0.00 0.00 0.00 2.87
1494 1634 7.307632 CCTGAAGGCTGAATAATAAGATTGTCG 60.308 40.741 0.00 0.00 0.00 4.35
1570 1712 6.725364 AGTTAATGAGGTCATTGTTCCAGAT 58.275 36.000 14.29 0.00 45.34 2.90
1667 1809 6.000219 CCATTAGGAGTTAGATCCCAACATG 59.000 44.000 9.71 0.00 40.53 3.21
1772 1914 8.199449 ACTTGAGAAGATTTTTCATCTGCAAAA 58.801 29.630 0.00 0.00 0.00 2.44
1858 2000 0.401738 CCTGTGGGAAGAGCTTTCCA 59.598 55.000 21.57 6.14 45.67 3.53
1881 2023 2.207229 GGAAAAGCGCCCAACCCTT 61.207 57.895 2.29 0.00 0.00 3.95
2602 2757 6.770746 TTCAGTAATCTTTCTACTAGCCGT 57.229 37.500 0.00 0.00 0.00 5.68
3115 3284 2.441410 TCAGACTCACTCATCTCGCTT 58.559 47.619 0.00 0.00 0.00 4.68
3286 3458 3.626924 GTGGACTGCAGGGACGGT 61.627 66.667 19.93 0.00 0.00 4.83
3395 3567 6.591448 TGTACTGTTGCTTCAGTGATAAGATG 59.409 38.462 19.21 0.00 46.36 2.90
3607 3779 3.873910 AGGAACCACATTTGAGTATCCG 58.126 45.455 0.00 0.00 0.00 4.18
3671 3843 4.568152 AAAATGTGGGTCACTCTTTTCG 57.432 40.909 0.00 0.00 35.11 3.46
3737 3909 0.388649 CGAGAACGGCTGTAGTGCTT 60.389 55.000 0.00 0.00 35.72 3.91


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

AutoCloner maintained by Alex Coulton.