Multiple sequence alignment - TraesCS6D01G181200

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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 TraesCS6D01G181200 chr6D 100.000 3437 0 0 1 3437 203750192 203746756 0.000000e+00 6348.0
1 TraesCS6D01G181200 chr6D 89.062 64 3 2 2897 2960 45479503 45479562 3.680000e-10 76.8
2 TraesCS6D01G181200 chr6D 85.507 69 5 2 2892 2960 447883207 447883270 2.210000e-07 67.6
3 TraesCS6D01G181200 chr6A 97.576 2682 38 9 769 3437 289027818 289025151 0.000000e+00 4567.0
4 TraesCS6D01G181200 chr6A 95.194 749 33 3 1 746 537033893 537034641 0.000000e+00 1181.0
5 TraesCS6D01G181200 chr6A 90.164 61 4 2 2930 2988 604890708 604890768 1.020000e-10 78.7
6 TraesCS6D01G181200 chr6A 89.062 64 3 2 2897 2960 59809632 59809691 3.680000e-10 76.8
7 TraesCS6D01G181200 chr6B 97.921 2164 29 7 746 2905 316460868 316458717 0.000000e+00 3733.0
8 TraesCS6D01G181200 chr6B 88.533 750 79 7 3 746 26400380 26399632 0.000000e+00 902.0
9 TraesCS6D01G181200 chr6B 95.538 493 20 1 2945 3437 316458717 316458227 0.000000e+00 787.0
10 TraesCS6D01G181200 chr5D 95.995 749 27 3 1 746 330401178 330401926 0.000000e+00 1214.0
11 TraesCS6D01G181200 chr5D 92.924 749 50 3 1 746 14105531 14106279 0.000000e+00 1086.0
12 TraesCS6D01G181200 chr5D 92.483 745 53 3 4 745 503129523 503128779 0.000000e+00 1062.0
13 TraesCS6D01G181200 chr5D 80.075 798 158 1 1510 2307 218260976 218260180 2.950000e-165 592.0
14 TraesCS6D01G181200 chr5D 87.195 164 11 6 2783 2940 173756405 173756246 9.800000e-41 178.0
15 TraesCS6D01G181200 chr5D 92.500 120 4 5 3319 3437 173753622 173753507 2.120000e-37 167.0
16 TraesCS6D01G181200 chr1D 93.423 745 42 5 4 746 103476044 103475305 0.000000e+00 1098.0
17 TraesCS6D01G181200 chr4A 92.800 750 47 4 4 746 103392262 103391513 0.000000e+00 1079.0
18 TraesCS6D01G181200 chr7D 91.425 723 60 2 3 723 186631220 186631942 0.000000e+00 990.0
19 TraesCS6D01G181200 chr7D 93.421 76 4 1 2897 2971 545221964 545222039 1.010000e-20 111.0
20 TraesCS6D01G181200 chr3D 87.682 755 86 5 4 751 612053503 612052749 0.000000e+00 872.0
21 TraesCS6D01G181200 chr5A 79.975 799 157 3 1510 2307 291271966 291271170 1.370000e-163 586.0
22 TraesCS6D01G181200 chr5A 93.056 144 10 0 3094 3237 195632459 195632316 9.660000e-51 211.0
23 TraesCS6D01G181200 chr5A 93.333 120 3 4 3319 3437 195632100 195631985 4.560000e-39 172.0
24 TraesCS6D01G181200 chr5B 79.315 817 162 7 1510 2323 234903947 234903135 1.790000e-157 566.0
25 TraesCS6D01G181200 chr5B 88.144 194 14 4 3086 3270 184769513 184769706 4.460000e-54 222.0
26 TraesCS6D01G181200 chr5B 90.756 119 7 4 3319 3437 184769877 184769991 4.590000e-34 156.0
27 TraesCS6D01G181200 chr5B 97.297 37 0 1 2783 2819 184766109 184766144 1.030000e-05 62.1
28 TraesCS6D01G181200 chr1B 88.235 68 5 1 2893 2960 9079219 9079283 1.020000e-10 78.7
29 TraesCS6D01G181200 chr1B 93.750 48 1 2 2897 2943 620494909 620494955 1.710000e-08 71.3
30 TraesCS6D01G181200 chr7A 85.000 80 6 4 2897 2970 474730880 474730801 3.680000e-10 76.8
31 TraesCS6D01G181200 chr7A 85.507 69 5 3 2908 2971 454049684 454049752 2.210000e-07 67.6


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 TraesCS6D01G181200 chr6D 203746756 203750192 3436 True 6348 6348 100.0000 1 3437 1 chr6D.!!$R1 3436
1 TraesCS6D01G181200 chr6A 289025151 289027818 2667 True 4567 4567 97.5760 769 3437 1 chr6A.!!$R1 2668
2 TraesCS6D01G181200 chr6A 537033893 537034641 748 False 1181 1181 95.1940 1 746 1 chr6A.!!$F2 745
3 TraesCS6D01G181200 chr6B 316458227 316460868 2641 True 2260 3733 96.7295 746 3437 2 chr6B.!!$R2 2691
4 TraesCS6D01G181200 chr6B 26399632 26400380 748 True 902 902 88.5330 3 746 1 chr6B.!!$R1 743
5 TraesCS6D01G181200 chr5D 330401178 330401926 748 False 1214 1214 95.9950 1 746 1 chr5D.!!$F2 745
6 TraesCS6D01G181200 chr5D 14105531 14106279 748 False 1086 1086 92.9240 1 746 1 chr5D.!!$F1 745
7 TraesCS6D01G181200 chr5D 503128779 503129523 744 True 1062 1062 92.4830 4 745 1 chr5D.!!$R2 741
8 TraesCS6D01G181200 chr5D 218260180 218260976 796 True 592 592 80.0750 1510 2307 1 chr5D.!!$R1 797
9 TraesCS6D01G181200 chr1D 103475305 103476044 739 True 1098 1098 93.4230 4 746 1 chr1D.!!$R1 742
10 TraesCS6D01G181200 chr4A 103391513 103392262 749 True 1079 1079 92.8000 4 746 1 chr4A.!!$R1 742
11 TraesCS6D01G181200 chr7D 186631220 186631942 722 False 990 990 91.4250 3 723 1 chr7D.!!$F1 720
12 TraesCS6D01G181200 chr3D 612052749 612053503 754 True 872 872 87.6820 4 751 1 chr3D.!!$R1 747
13 TraesCS6D01G181200 chr5A 291271170 291271966 796 True 586 586 79.9750 1510 2307 1 chr5A.!!$R1 797
14 TraesCS6D01G181200 chr5B 234903135 234903947 812 True 566 566 79.3150 1510 2323 1 chr5B.!!$R1 813

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
590 594 1.895020 ATCACTTGGGTTCGGCGCTA 61.895 55.0 7.64 0.0 0.00 4.26 F
1164 1199 0.033504 ACGTCAAGATCACCGTGCTT 59.966 50.0 0.00 0.0 31.43 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 1829 0.100682 GGTTGTCATAGCGCGAGAGA 59.899 55.000 12.10 0.0 0.00 3.1 R
3081 3156 3.250280 GCCACTTGTGATATGCTCAGATG 59.750 47.826 1.89 0.0 33.51 2.9 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
133 134 2.437281 GGAGAAGGATCCAAGATGCTCA 59.563 50.000 15.82 0.00 39.34 4.26
175 176 4.411869 TCACTGTTATATCCAGGAATGGCA 59.588 41.667 0.00 0.00 34.16 4.92
491 495 2.277591 TGGTGGCCATGCTTCAAGC 61.278 57.895 9.72 1.04 42.82 4.01
590 594 1.895020 ATCACTTGGGTTCGGCGCTA 61.895 55.000 7.64 0.00 0.00 4.26
739 751 8.700439 AGTTAAATAAAGTTGCAAGTTCCCTA 57.300 30.769 19.51 9.35 0.00 3.53
1164 1199 0.033504 ACGTCAAGATCACCGTGCTT 59.966 50.000 0.00 0.00 31.43 3.91
1794 1829 1.681327 CATGGCCTTTGAGCTGCCT 60.681 57.895 12.74 0.00 45.56 4.75
1860 1895 5.130643 TCATGATCTCCTCTTTGAGAAGCAT 59.869 40.000 0.00 0.00 44.16 3.79
2309 2344 1.078497 CCGATAACCAGGTGCTGCA 60.078 57.895 0.00 0.00 0.00 4.41
2388 2423 6.067217 AGTCAGACCACAAAGCCTATTAAT 57.933 37.500 0.00 0.00 0.00 1.40
2677 2712 6.942532 TTCATTTCAGTGCTACTTTCTTGT 57.057 33.333 0.00 0.00 0.00 3.16
2853 2888 3.450904 AGCCCTATAATAAGATCCCGCA 58.549 45.455 0.00 0.00 0.00 5.69
2905 2980 4.747009 GCTCCAAACTTTGTTACTCCCTCT 60.747 45.833 0.88 0.00 0.00 3.69
2906 2981 5.377478 CTCCAAACTTTGTTACTCCCTCTT 58.623 41.667 0.88 0.00 0.00 2.85
2907 2982 6.503560 TCCAAACTTTGTTACTCCCTCTTA 57.496 37.500 0.88 0.00 0.00 2.10
2908 2983 7.086685 TCCAAACTTTGTTACTCCCTCTTAT 57.913 36.000 0.88 0.00 0.00 1.73
2909 2984 7.166167 TCCAAACTTTGTTACTCCCTCTTATC 58.834 38.462 0.88 0.00 0.00 1.75
2910 2985 6.374613 CCAAACTTTGTTACTCCCTCTTATCC 59.625 42.308 0.88 0.00 0.00 2.59
2911 2986 6.697641 AACTTTGTTACTCCCTCTTATCCA 57.302 37.500 0.00 0.00 0.00 3.41
2912 2987 6.893020 ACTTTGTTACTCCCTCTTATCCAT 57.107 37.500 0.00 0.00 0.00 3.41
2913 2988 7.989947 ACTTTGTTACTCCCTCTTATCCATA 57.010 36.000 0.00 0.00 0.00 2.74
2914 2989 8.568617 ACTTTGTTACTCCCTCTTATCCATAT 57.431 34.615 0.00 0.00 0.00 1.78
2915 2990 9.004231 ACTTTGTTACTCCCTCTTATCCATATT 57.996 33.333 0.00 0.00 0.00 1.28
2923 2998 8.314751 ACTCCCTCTTATCCATATTAATTGTCG 58.685 37.037 0.00 0.00 0.00 4.35
2924 2999 8.202461 TCCCTCTTATCCATATTAATTGTCGT 57.798 34.615 0.00 0.00 0.00 4.34
2925 3000 8.656806 TCCCTCTTATCCATATTAATTGTCGTT 58.343 33.333 0.00 0.00 0.00 3.85
2926 3001 8.721478 CCCTCTTATCCATATTAATTGTCGTTG 58.279 37.037 0.00 0.00 0.00 4.10
2927 3002 9.489084 CCTCTTATCCATATTAATTGTCGTTGA 57.511 33.333 0.00 0.00 0.00 3.18
2994 3069 9.659830 GTAGTTCATTTCGTATTTGTCTTGTTT 57.340 29.630 0.00 0.00 0.00 2.83
3044 3119 9.416794 CATCTTTAGTGCCTAGATATGTTAGTG 57.583 37.037 0.00 0.00 0.00 2.74
3081 3156 5.976458 TGGAACCATTGAAGAAAATATGCC 58.024 37.500 0.00 0.00 0.00 4.40
3166 3241 3.070878 CCTAAACTTGGCATGGGTGTTTT 59.929 43.478 5.31 0.00 33.63 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 1.201429 AGCCTGGACCATCGTTTCCT 61.201 55.000 0.00 0.00 32.55 3.36
133 134 3.879892 GTGAACTTTCTCTGCCAACTCTT 59.120 43.478 0.00 0.00 0.00 2.85
175 176 2.769095 GGCTCCTTGGAGTGAACTAGAT 59.231 50.000 16.95 0.00 0.00 1.98
782 805 1.268066 GGACGGAGAAAGGAGAGGTT 58.732 55.000 0.00 0.00 0.00 3.50
1164 1199 3.950794 GATGGTGACGAGGCCGCAA 62.951 63.158 7.44 0.00 39.95 4.85
1557 1592 2.485795 GCCAAGCGGGTTGTCACAA 61.486 57.895 17.64 0.00 39.65 3.33
1794 1829 0.100682 GGTTGTCATAGCGCGAGAGA 59.899 55.000 12.10 0.00 0.00 3.10
1860 1895 0.320334 TGTTGAGCGCGATCCAAGAA 60.320 50.000 23.12 6.31 0.00 2.52
2677 2712 3.517901 CCACATTAGAGGTACTTGTCCCA 59.482 47.826 0.00 0.00 41.55 4.37
2690 2725 6.121776 ACAAGATACCAACACCACATTAGA 57.878 37.500 0.00 0.00 0.00 2.10
2926 3001 8.895932 AATTGTCGCTGATTTAGTACAAAATC 57.104 30.769 0.00 3.02 43.28 2.17
2933 3008 9.990360 TCCATATTAATTGTCGCTGATTTAGTA 57.010 29.630 0.00 0.00 0.00 1.82
2934 3009 8.774586 GTCCATATTAATTGTCGCTGATTTAGT 58.225 33.333 0.00 0.00 0.00 2.24
2935 3010 7.952101 CGTCCATATTAATTGTCGCTGATTTAG 59.048 37.037 0.00 0.00 0.00 1.85
2936 3011 7.095397 CCGTCCATATTAATTGTCGCTGATTTA 60.095 37.037 0.00 0.00 0.00 1.40
2937 3012 6.293407 CCGTCCATATTAATTGTCGCTGATTT 60.293 38.462 0.00 0.00 0.00 2.17
2938 3013 5.179368 CCGTCCATATTAATTGTCGCTGATT 59.821 40.000 0.00 0.00 0.00 2.57
2939 3014 4.690748 CCGTCCATATTAATTGTCGCTGAT 59.309 41.667 0.00 0.00 0.00 2.90
2940 3015 4.055360 CCGTCCATATTAATTGTCGCTGA 58.945 43.478 0.00 0.00 0.00 4.26
2941 3016 4.055360 TCCGTCCATATTAATTGTCGCTG 58.945 43.478 0.00 0.00 0.00 5.18
2942 3017 4.307432 CTCCGTCCATATTAATTGTCGCT 58.693 43.478 0.00 0.00 0.00 4.93
2943 3018 3.432252 CCTCCGTCCATATTAATTGTCGC 59.568 47.826 0.00 0.00 0.00 5.19
2944 3019 3.994392 CCCTCCGTCCATATTAATTGTCG 59.006 47.826 0.00 0.82 0.00 4.35
2994 3069 5.587043 GTCAATTCGGTAAATACCACCATCA 59.413 40.000 10.10 0.00 46.80 3.07
3017 3092 9.148879 ACTAACATATCTAGGCACTAAAGATGT 57.851 33.333 0.00 0.00 42.17 3.06
3044 3119 5.945466 ATGGTTCCATGAAACATTTTTGC 57.055 34.783 3.31 0.00 46.25 3.68
3081 3156 3.250280 GCCACTTGTGATATGCTCAGATG 59.750 47.826 1.89 0.00 33.51 2.90
3178 3253 5.945784 TCGTACTTAACAGGTACACCATACT 59.054 40.000 0.38 0.00 39.36 2.12


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

AutoCloner maintained by Alex Coulton.