Multiple sequence alignment - TraesCS4A01G436200

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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 TraesCS4A01G436200 chr4A 100.000 3188 0 0 1 3188 705954808 705951621 0.000000e+00 5888.0
1 TraesCS4A01G436200 chr4A 98.371 3192 23 12 1 3188 706090784 706087618 0.000000e+00 5579.0
2 TraesCS4A01G436200 chr4A 94.515 2042 92 8 665 2704 707487255 707489278 0.000000e+00 3133.0
3 TraesCS4A01G436200 chr4A 90.330 1634 137 15 967 2591 707674779 707676400 0.000000e+00 2122.0
4 TraesCS4A01G436200 chr4A 90.269 1634 138 15 967 2591 707702238 707703859 0.000000e+00 2117.0
5 TraesCS4A01G436200 chr4A 80.942 1317 218 21 996 2281 707305506 707304192 0.000000e+00 1011.0
6 TraesCS4A01G436200 chr4A 81.226 1044 176 11 1377 2420 707260630 707259607 0.000000e+00 824.0
7 TraesCS4A01G436200 chr4A 92.872 491 29 5 2701 3188 707494457 707494944 0.000000e+00 708.0
8 TraesCS4A01G436200 chr4A 83.495 206 26 5 720 922 707509724 707509924 5.430000e-43 185.0
9 TraesCS4A01G436200 chr4A 92.437 119 7 1 409 525 707486765 707486883 5.470000e-38 169.0
10 TraesCS4A01G436200 chr4A 85.799 169 11 10 512 673 707486911 707487073 1.970000e-37 167.0
11 TraesCS4A01G436200 chrUn 98.371 3192 22 13 1 3188 220050446 220047281 0.000000e+00 5579.0
12 TraesCS4A01G436200 chr7D 87.189 1889 192 30 711 2591 24119072 24117226 0.000000e+00 2102.0
13 TraesCS4A01G436200 chr7D 88.648 1709 169 16 890 2591 24021345 24019655 0.000000e+00 2058.0
14 TraesCS4A01G436200 chr7D 82.002 1239 203 12 967 2192 24326409 24327640 0.000000e+00 1035.0
15 TraesCS4A01G436200 chr7D 93.169 366 24 1 1 366 636717396 636717760 1.300000e-148 536.0
16 TraesCS4A01G436200 chr7D 95.918 98 3 1 711 807 24021494 24021397 1.180000e-34 158.0
17 TraesCS4A01G436200 chr7D 90.164 122 11 1 540 661 24141719 24141599 1.180000e-34 158.0
18 TraesCS4A01G436200 chr3D 92.935 368 24 2 1 368 489528012 489528377 4.680000e-148 534.0
19 TraesCS4A01G436200 chr3D 92.371 367 26 2 1 367 367334133 367333769 3.640000e-144 521.0
20 TraesCS4A01G436200 chr3D 77.778 126 17 3 3062 3185 97154434 97154550 2.050000e-07 67.6
21 TraesCS4A01G436200 chr3D 84.127 63 3 6 3096 3156 70709727 70709784 2.000000e-03 54.7
22 TraesCS4A01G436200 chr3B 92.935 368 24 2 1 368 24918772 24919137 4.680000e-148 534.0
23 TraesCS4A01G436200 chr3B 86.364 66 7 2 3060 3123 616949645 616949580 1.590000e-08 71.3
24 TraesCS4A01G436200 chr4B 92.453 371 26 2 1 370 574004102 574003733 2.180000e-146 529.0
25 TraesCS4A01G436200 chr1D 92.391 368 26 2 1 368 296632297 296631932 1.010000e-144 523.0
26 TraesCS4A01G436200 chr6D 91.957 373 29 1 1 373 448654613 448654242 3.640000e-144 521.0
27 TraesCS4A01G436200 chr5A 75.294 425 85 14 2622 3038 601649166 601648754 5.430000e-43 185.0
28 TraesCS4A01G436200 chr5B 74.099 444 98 13 2602 3037 511615559 511615993 1.970000e-37 167.0
29 TraesCS4A01G436200 chr6B 79.275 193 27 10 2851 3037 671391485 671391300 4.320000e-24 122.0
30 TraesCS4A01G436200 chr2B 81.410 156 20 7 2891 3040 657870336 657870184 5.590000e-23 119.0
31 TraesCS4A01G436200 chr2D 84.337 83 5 8 3065 3143 417213620 417213698 1.230000e-09 75.0
32 TraesCS4A01G436200 chr5D 83.133 83 9 5 3066 3145 450214321 450214241 1.590000e-08 71.3
33 TraesCS4A01G436200 chr5D 79.464 112 11 11 3078 3187 539863629 539863730 5.710000e-08 69.4
34 TraesCS4A01G436200 chr7B 82.051 78 6 7 3073 3145 40289031 40289105 3.430000e-05 60.2


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 TraesCS4A01G436200 chr4A 705951621 705954808 3187 True 5888.000000 5888 100.000 1 3188 1 chr4A.!!$R1 3187
1 TraesCS4A01G436200 chr4A 706087618 706090784 3166 True 5579.000000 5579 98.371 1 3188 1 chr4A.!!$R2 3187
2 TraesCS4A01G436200 chr4A 707674779 707676400 1621 False 2122.000000 2122 90.330 967 2591 1 chr4A.!!$F3 1624
3 TraesCS4A01G436200 chr4A 707702238 707703859 1621 False 2117.000000 2117 90.269 967 2591 1 chr4A.!!$F4 1624
4 TraesCS4A01G436200 chr4A 707486765 707489278 2513 False 1156.333333 3133 90.917 409 2704 3 chr4A.!!$F5 2295
5 TraesCS4A01G436200 chr4A 707304192 707305506 1314 True 1011.000000 1011 80.942 996 2281 1 chr4A.!!$R4 1285
6 TraesCS4A01G436200 chr4A 707259607 707260630 1023 True 824.000000 824 81.226 1377 2420 1 chr4A.!!$R3 1043
7 TraesCS4A01G436200 chrUn 220047281 220050446 3165 True 5579.000000 5579 98.371 1 3188 1 chrUn.!!$R1 3187
8 TraesCS4A01G436200 chr7D 24117226 24119072 1846 True 2102.000000 2102 87.189 711 2591 1 chr7D.!!$R1 1880
9 TraesCS4A01G436200 chr7D 24019655 24021494 1839 True 1108.000000 2058 92.283 711 2591 2 chr7D.!!$R3 1880
10 TraesCS4A01G436200 chr7D 24326409 24327640 1231 False 1035.000000 1035 82.002 967 2192 1 chr7D.!!$F1 1225

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
1626 1878 2.18203 GACGAGGCGGACTCCTTG 59.818 66.667 5.02 0.0 43.57 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2817 3115 0.103755 TCTGATGATGACTCCGCAGC 59.896 55.0 0.0 0.0 0.0 5.25 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
1626 1878 2.182030 GACGAGGCGGACTCCTTG 59.818 66.667 5.02 0.00 43.57 3.61
1896 2151 2.572095 TAGCCGGCATCGAAGGTGTG 62.572 60.000 31.54 0.00 39.00 3.82
2025 2280 2.850439 CGTGGTGAGAGAGTACGGA 58.150 57.895 0.00 0.00 0.00 4.69
2309 2599 7.719778 ATATACGTACGTGTAAGAGATGTGA 57.280 36.000 30.25 6.14 0.00 3.58
2310 2600 4.754372 ACGTACGTGTAAGAGATGTGAA 57.246 40.909 22.14 0.00 0.00 3.18
2523 2821 7.989947 TCTGGACAGTACCTATATTTTTCCT 57.010 36.000 0.00 0.00 0.00 3.36
2642 2940 2.033141 GCAGAGACAGCCAAGGCA 59.967 61.111 14.40 0.00 44.88 4.75
2781 3079 1.137282 TGTGGCGTCTGACTACAAACA 59.863 47.619 6.21 4.31 0.00 2.83
2782 3080 1.792949 GTGGCGTCTGACTACAAACAG 59.207 52.381 6.21 0.00 35.72 3.16
2783 3081 1.270094 TGGCGTCTGACTACAAACAGG 60.270 52.381 6.21 0.00 35.20 4.00
2784 3082 1.270147 GGCGTCTGACTACAAACAGGT 60.270 52.381 6.21 0.00 35.20 4.00
2785 3083 1.792949 GCGTCTGACTACAAACAGGTG 59.207 52.381 6.21 0.00 35.20 4.00
2786 3084 2.404215 CGTCTGACTACAAACAGGTGG 58.596 52.381 6.21 0.00 35.20 4.61
2787 3085 2.143925 GTCTGACTACAAACAGGTGGC 58.856 52.381 0.00 0.00 35.20 5.01
2788 3086 1.071699 TCTGACTACAAACAGGTGGCC 59.928 52.381 0.00 0.00 35.20 5.36
2789 3087 0.250124 TGACTACAAACAGGTGGCCG 60.250 55.000 0.00 0.00 0.00 6.13
2790 3088 0.034337 GACTACAAACAGGTGGCCGA 59.966 55.000 0.00 0.00 0.00 5.54
2791 3089 0.470766 ACTACAAACAGGTGGCCGAA 59.529 50.000 0.00 0.00 0.00 4.30
2792 3090 1.156736 CTACAAACAGGTGGCCGAAG 58.843 55.000 0.00 0.00 0.00 3.79
2793 3091 0.759959 TACAAACAGGTGGCCGAAGA 59.240 50.000 0.00 0.00 0.00 2.87
2794 3092 0.818040 ACAAACAGGTGGCCGAAGAC 60.818 55.000 0.00 0.00 0.00 3.01
2795 3093 0.817634 CAAACAGGTGGCCGAAGACA 60.818 55.000 0.00 0.00 0.00 3.41
2796 3094 0.110486 AAACAGGTGGCCGAAGACAT 59.890 50.000 0.00 0.00 0.00 3.06
2797 3095 0.110486 AACAGGTGGCCGAAGACATT 59.890 50.000 0.00 0.00 0.00 2.71
2798 3096 0.606401 ACAGGTGGCCGAAGACATTG 60.606 55.000 0.00 0.00 0.00 2.82
2799 3097 1.675641 AGGTGGCCGAAGACATTGC 60.676 57.895 0.00 0.00 0.00 3.56
2800 3098 1.675641 GGTGGCCGAAGACATTGCT 60.676 57.895 0.00 0.00 0.00 3.91
2801 3099 0.392461 GGTGGCCGAAGACATTGCTA 60.392 55.000 0.00 0.00 0.00 3.49
2802 3100 1.448985 GTGGCCGAAGACATTGCTAA 58.551 50.000 0.00 0.00 0.00 3.09
2817 3115 0.746923 GCTAAAGGTAACCAGGGGCG 60.747 60.000 0.00 0.00 37.17 6.13
2848 3146 7.541783 GGAGTCATCATCAGAGAGATAAAATCG 59.458 40.741 0.00 0.00 34.43 3.34
2878 3176 5.066764 GCCACCACTTACTTGTAACTTTTCA 59.933 40.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1626 1878 2.286121 TGGGGGATGAGGGTGTCC 60.286 66.667 0.00 0.00 0.00 4.02
1896 2151 0.250513 AGAGGCTGTTCCATTCGACC 59.749 55.000 0.00 0.00 37.29 4.79
2308 2598 3.002656 CACTGTCACACCACATGTTCTTC 59.997 47.826 0.00 0.00 40.64 2.87
2309 2599 2.945008 CACTGTCACACCACATGTTCTT 59.055 45.455 0.00 0.00 40.64 2.52
2310 2600 2.564771 CACTGTCACACCACATGTTCT 58.435 47.619 0.00 0.00 40.64 3.01
2395 2685 6.016777 GCTGAACCCAATATACAATTCAGGAG 60.017 42.308 15.82 0.00 42.05 3.69
2523 2821 1.410083 GGCCCTGATGCAAATGGACTA 60.410 52.381 0.00 0.00 0.00 2.59
2642 2940 3.711863 TGGCTGAGCTTCCCATAAAAAT 58.288 40.909 3.72 0.00 0.00 1.82
2781 3079 1.675641 GCAATGTCTTCGGCCACCT 60.676 57.895 2.24 0.00 0.00 4.00
2782 3080 0.392461 TAGCAATGTCTTCGGCCACC 60.392 55.000 2.24 0.00 0.00 4.61
2783 3081 1.448985 TTAGCAATGTCTTCGGCCAC 58.551 50.000 2.24 0.00 0.00 5.01
2784 3082 2.083774 CTTTAGCAATGTCTTCGGCCA 58.916 47.619 2.24 0.00 0.00 5.36
2785 3083 1.401905 CCTTTAGCAATGTCTTCGGCC 59.598 52.381 0.00 0.00 0.00 6.13
2786 3084 2.084546 ACCTTTAGCAATGTCTTCGGC 58.915 47.619 0.00 0.00 0.00 5.54
2787 3085 4.094442 GGTTACCTTTAGCAATGTCTTCGG 59.906 45.833 0.00 0.00 0.00 4.30
2788 3086 4.693566 TGGTTACCTTTAGCAATGTCTTCG 59.306 41.667 2.07 0.00 0.00 3.79
2789 3087 5.123979 CCTGGTTACCTTTAGCAATGTCTTC 59.876 44.000 2.07 0.00 0.00 2.87
2790 3088 5.010282 CCTGGTTACCTTTAGCAATGTCTT 58.990 41.667 2.07 0.00 0.00 3.01
2791 3089 4.567747 CCCTGGTTACCTTTAGCAATGTCT 60.568 45.833 2.07 0.00 0.00 3.41
2792 3090 3.694566 CCCTGGTTACCTTTAGCAATGTC 59.305 47.826 2.07 0.00 0.00 3.06
2793 3091 3.563479 CCCCTGGTTACCTTTAGCAATGT 60.563 47.826 2.07 0.00 0.00 2.71
2794 3092 3.023832 CCCCTGGTTACCTTTAGCAATG 58.976 50.000 2.07 0.00 0.00 2.82
2795 3093 2.623239 GCCCCTGGTTACCTTTAGCAAT 60.623 50.000 2.07 0.00 0.00 3.56
2796 3094 1.272258 GCCCCTGGTTACCTTTAGCAA 60.272 52.381 2.07 0.00 0.00 3.91
2797 3095 0.330267 GCCCCTGGTTACCTTTAGCA 59.670 55.000 2.07 0.00 0.00 3.49
2798 3096 0.746923 CGCCCCTGGTTACCTTTAGC 60.747 60.000 2.07 0.01 0.00 3.09
2799 3097 0.746923 GCGCCCCTGGTTACCTTTAG 60.747 60.000 2.07 0.00 0.00 1.85
2800 3098 1.202769 AGCGCCCCTGGTTACCTTTA 61.203 55.000 2.29 0.00 0.00 1.85
2801 3099 2.035155 GCGCCCCTGGTTACCTTT 59.965 61.111 2.07 0.00 0.00 3.11
2802 3100 2.933834 AGCGCCCCTGGTTACCTT 60.934 61.111 2.29 0.00 0.00 3.50
2817 3115 0.103755 TCTGATGATGACTCCGCAGC 59.896 55.000 0.00 0.00 0.00 5.25
2848 3146 0.252197 AAGTAAGTGGTGGCGATCCC 59.748 55.000 0.00 0.00 0.00 3.85
2878 3176 6.918569 CGATATTAACCTCACGTCTCTCAAAT 59.081 38.462 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.