Multiple sequence alignment - TraesCS3B01G349800

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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 TraesCS3B01G349800 chr3B 100.000 3725 0 0 1 3725 559889796 559893520 0.000000e+00 6879
1 TraesCS3B01G349800 chr3B 85.659 1813 254 4 911 2720 559882973 559884782 0.000000e+00 1903
2 TraesCS3B01G349800 chr3B 97.030 909 27 0 1 909 144256947 144257855 0.000000e+00 1530
3 TraesCS3B01G349800 chr3D 95.588 2040 79 3 911 2945 428253445 428255478 0.000000e+00 3258
4 TraesCS3B01G349800 chr3D 86.194 1818 240 10 911 2720 428247491 428249305 0.000000e+00 1956
5 TraesCS3B01G349800 chr3D 96.835 632 17 3 2943 3571 428255524 428256155 0.000000e+00 1053
6 TraesCS3B01G349800 chr3D 94.969 159 6 2 3567 3725 428256201 428256357 7.990000e-62 248
7 TraesCS3B01G349800 chr3A 95.381 2035 87 2 911 2945 557411325 557409298 0.000000e+00 3230
8 TraesCS3B01G349800 chr3A 84.701 1889 274 13 911 2794 557417050 557415172 0.000000e+00 1873
9 TraesCS3B01G349800 chr3A 95.070 284 12 2 3293 3574 557408949 557408666 2.640000e-121 446
10 TraesCS3B01G349800 chr3A 93.220 295 13 2 2954 3241 557409236 557408942 9.560000e-116 427
11 TraesCS3B01G349800 chr3A 92.453 159 12 0 3567 3725 557408623 557408465 1.040000e-55 228
12 TraesCS3B01G349800 chr6D 82.657 1874 303 15 911 2778 469802200 469804057 0.000000e+00 1640
13 TraesCS3B01G349800 chrUn 82.009 1901 309 23 913 2800 62077779 62075899 0.000000e+00 1585
14 TraesCS3B01G349800 chr1B 97.809 913 20 0 1 913 665854501 665855413 0.000000e+00 1576
15 TraesCS3B01G349800 chr1B 96.940 915 27 1 1 915 623691209 623690296 0.000000e+00 1533
16 TraesCS3B01G349800 chr6B 97.593 914 21 1 1 913 106516786 106515873 0.000000e+00 1565
17 TraesCS3B01G349800 chr4B 97.158 915 26 0 1 915 611400481 611399567 0.000000e+00 1546
18 TraesCS3B01G349800 chr4B 96.933 913 28 0 1 913 576470973 576470061 0.000000e+00 1531
19 TraesCS3B01G349800 chr5B 96.933 913 28 0 1 913 416324995 416324083 0.000000e+00 1531
20 TraesCS3B01G349800 chr5B 74.626 1135 270 15 959 2084 604164991 604166116 5.590000e-133 484
21 TraesCS3B01G349800 chr2B 96.933 913 28 0 1 913 195533234 195534146 0.000000e+00 1531
22 TraesCS3B01G349800 chr2B 96.612 915 31 0 1 915 704424600 704423686 0.000000e+00 1519
23 TraesCS3B01G349800 chr1D 77.361 1864 392 25 917 2771 459040198 459038356 0.000000e+00 1077
24 TraesCS3B01G349800 chr7A 75.069 1813 417 33 920 2713 7320274 7318478 0.000000e+00 811
25 TraesCS3B01G349800 chr7A 74.322 1807 428 28 911 2705 736342696 736344478 0.000000e+00 734
26 TraesCS3B01G349800 chr7D 74.588 1881 434 39 920 2777 5647320 5645461 0.000000e+00 785
27 TraesCS3B01G349800 chr7D 73.390 1879 440 51 920 2770 5786081 5784235 0.000000e+00 645
28 TraesCS3B01G349800 chr2D 73.896 1835 431 39 917 2723 633294023 633292209 0.000000e+00 691
29 TraesCS3B01G349800 chr4A 73.344 1887 445 49 911 2770 735735933 735737788 0.000000e+00 645
30 TraesCS3B01G349800 chr4A 72.940 1881 444 54 920 2770 736431780 736429935 8.910000e-166 593
31 TraesCS3B01G349800 chr4A 76.177 361 78 8 2271 2627 736712989 736713345 2.290000e-42 183


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 TraesCS3B01G349800 chr3B 559889796 559893520 3724 False 6879.000000 6879 100.000000 1 3725 1 chr3B.!!$F3 3724
1 TraesCS3B01G349800 chr3B 559882973 559884782 1809 False 1903.000000 1903 85.659000 911 2720 1 chr3B.!!$F2 1809
2 TraesCS3B01G349800 chr3B 144256947 144257855 908 False 1530.000000 1530 97.030000 1 909 1 chr3B.!!$F1 908
3 TraesCS3B01G349800 chr3D 428247491 428249305 1814 False 1956.000000 1956 86.194000 911 2720 1 chr3D.!!$F1 1809
4 TraesCS3B01G349800 chr3D 428253445 428256357 2912 False 1519.666667 3258 95.797333 911 3725 3 chr3D.!!$F2 2814
5 TraesCS3B01G349800 chr3A 557408465 557417050 8585 True 1240.800000 3230 92.165000 911 3725 5 chr3A.!!$R1 2814
6 TraesCS3B01G349800 chr6D 469802200 469804057 1857 False 1640.000000 1640 82.657000 911 2778 1 chr6D.!!$F1 1867
7 TraesCS3B01G349800 chrUn 62075899 62077779 1880 True 1585.000000 1585 82.009000 913 2800 1 chrUn.!!$R1 1887
8 TraesCS3B01G349800 chr1B 665854501 665855413 912 False 1576.000000 1576 97.809000 1 913 1 chr1B.!!$F1 912
9 TraesCS3B01G349800 chr1B 623690296 623691209 913 True 1533.000000 1533 96.940000 1 915 1 chr1B.!!$R1 914
10 TraesCS3B01G349800 chr6B 106515873 106516786 913 True 1565.000000 1565 97.593000 1 913 1 chr6B.!!$R1 912
11 TraesCS3B01G349800 chr4B 611399567 611400481 914 True 1546.000000 1546 97.158000 1 915 1 chr4B.!!$R2 914
12 TraesCS3B01G349800 chr4B 576470061 576470973 912 True 1531.000000 1531 96.933000 1 913 1 chr4B.!!$R1 912
13 TraesCS3B01G349800 chr5B 416324083 416324995 912 True 1531.000000 1531 96.933000 1 913 1 chr5B.!!$R1 912
14 TraesCS3B01G349800 chr5B 604164991 604166116 1125 False 484.000000 484 74.626000 959 2084 1 chr5B.!!$F1 1125
15 TraesCS3B01G349800 chr2B 195533234 195534146 912 False 1531.000000 1531 96.933000 1 913 1 chr2B.!!$F1 912
16 TraesCS3B01G349800 chr2B 704423686 704424600 914 True 1519.000000 1519 96.612000 1 915 1 chr2B.!!$R1 914
17 TraesCS3B01G349800 chr1D 459038356 459040198 1842 True 1077.000000 1077 77.361000 917 2771 1 chr1D.!!$R1 1854
18 TraesCS3B01G349800 chr7A 7318478 7320274 1796 True 811.000000 811 75.069000 920 2713 1 chr7A.!!$R1 1793
19 TraesCS3B01G349800 chr7A 736342696 736344478 1782 False 734.000000 734 74.322000 911 2705 1 chr7A.!!$F1 1794
20 TraesCS3B01G349800 chr7D 5645461 5647320 1859 True 785.000000 785 74.588000 920 2777 1 chr7D.!!$R1 1857
21 TraesCS3B01G349800 chr7D 5784235 5786081 1846 True 645.000000 645 73.390000 920 2770 1 chr7D.!!$R2 1850
22 TraesCS3B01G349800 chr2D 633292209 633294023 1814 True 691.000000 691 73.896000 917 2723 1 chr2D.!!$R1 1806
23 TraesCS3B01G349800 chr4A 735735933 735737788 1855 False 645.000000 645 73.344000 911 2770 1 chr4A.!!$F1 1859
24 TraesCS3B01G349800 chr4A 736429935 736431780 1845 True 593.000000 593 72.940000 920 2770 1 chr4A.!!$R1 1850

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
42 43 1.594293 CGTGCCGGCGAAATAGGAT 60.594 57.895 23.90 0.0 0.0 3.24 F
1313 7040 2.233676 TCGATTGCAGTGCCTTAGAAGA 59.766 45.455 13.72 0.2 0.0 2.87 F
2281 8029 1.001487 TGCCATTCTTGCAACTTCACG 60.001 47.619 0.00 0.0 35.4 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1367 7094 2.728922 ACGTTTTCAGAGTCGAGACAC 58.271 47.619 5.99 0.00 0.00 3.67 R
2312 8060 1.061799 CTGTGAAATGCAGTTCGCGC 61.062 55.000 28.72 18.39 46.97 6.86 R
3616 9488 0.321653 GTGGTGGAGCCGTTCAGAAT 60.322 55.000 0.00 0.00 41.21 2.40 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
42 43 1.594293 CGTGCCGGCGAAATAGGAT 60.594 57.895 23.90 0.00 0.00 3.24
259 260 2.835431 CGTCGCTCCAGGGGATCT 60.835 66.667 0.00 0.00 39.09 2.75
348 349 4.256180 GCGGGGGCGATGGAGAAT 62.256 66.667 0.00 0.00 0.00 2.40
817 818 2.610976 CGGACACAAAACGGACAGGATA 60.611 50.000 0.00 0.00 0.00 2.59
862 863 2.620627 CCGCCTCCTTTGTCCCTTTTAT 60.621 50.000 0.00 0.00 0.00 1.40
985 6712 2.269940 AGCAGAAGGGGTATGAGTTGT 58.730 47.619 0.00 0.00 0.00 3.32
1313 7040 2.233676 TCGATTGCAGTGCCTTAGAAGA 59.766 45.455 13.72 0.20 0.00 2.87
2150 7898 2.362077 GTGACTTGCCACACCTGAAAAT 59.638 45.455 0.00 0.00 37.04 1.82
2234 7982 3.543680 ATCCTTATCACTGGGACGTTG 57.456 47.619 0.00 0.00 31.48 4.10
2281 8029 1.001487 TGCCATTCTTGCAACTTCACG 60.001 47.619 0.00 0.00 35.40 4.35
2312 8060 0.534412 ACAGATGTCCCGAAGCTCAG 59.466 55.000 0.00 0.00 0.00 3.35
2382 8130 1.364626 GCCTCGTGATGCTCAACCAG 61.365 60.000 0.00 0.00 0.00 4.00
2404 8152 1.205655 TGCTCTCGGATGAAGGTTCTG 59.794 52.381 0.00 0.00 0.00 3.02
2804 8559 6.385033 CCTTTGCAAAGATAGTCCTTTTGAG 58.615 40.000 35.25 13.12 38.28 3.02
2922 8680 3.348119 TGTGTTTCAAACAGTAGGTGCA 58.652 40.909 2.26 0.00 43.10 4.57
2965 8778 2.613977 CCTTCAACTCTCTCGGCATTGT 60.614 50.000 0.00 0.00 0.00 2.71
3009 8822 4.119442 TCCCTTCTACGTTGATTACTGC 57.881 45.455 0.00 0.00 0.00 4.40
3017 8830 2.030823 ACGTTGATTACTGCATGCATCG 59.969 45.455 22.97 13.40 0.00 3.84
3037 8850 2.484770 CGTTCTTCCACTTTCTCCACCA 60.485 50.000 0.00 0.00 0.00 4.17
3052 8865 0.034059 CACCACCTGGACTGAGACAC 59.966 60.000 0.00 0.00 38.94 3.67
3053 8866 0.398522 ACCACCTGGACTGAGACACA 60.399 55.000 0.00 0.00 38.94 3.72
3054 8867 0.979665 CCACCTGGACTGAGACACAT 59.020 55.000 0.00 0.00 37.39 3.21
3055 8868 1.338484 CCACCTGGACTGAGACACATG 60.338 57.143 0.00 0.00 37.39 3.21
3057 8870 1.620819 ACCTGGACTGAGACACATGTC 59.379 52.381 0.00 3.72 45.08 3.06
3297 9118 5.488919 AGTCTTGGATGAAGGTAATTGGAGA 59.511 40.000 0.00 0.00 31.85 3.71
3340 9161 7.489160 AGCGAATAGTTGAATATACACTCACA 58.511 34.615 0.00 0.00 0.00 3.58
3371 9192 4.142026 TGAGAACCGTGAAGTCTGAAGAAA 60.142 41.667 0.00 0.00 0.00 2.52
3616 9488 1.078285 TGCATGCATCGCTCTTCCA 60.078 52.632 18.46 0.00 0.00 3.53
3653 9525 2.412870 CACCAGTGATGTAACGCTTGA 58.587 47.619 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
259 260 0.681887 TATTGGGAGACGAGGACGCA 60.682 55.000 0.00 0.00 43.96 5.24
985 6712 0.978907 TTCATGTCTCTGAGCTGCCA 59.021 50.000 0.00 0.00 0.00 4.92
1367 7094 2.728922 ACGTTTTCAGAGTCGAGACAC 58.271 47.619 5.99 0.00 0.00 3.67
2150 7898 3.118298 TCTGCAGCCATACATGCTAAGAA 60.118 43.478 9.47 0.00 42.98 2.52
2234 7982 1.377536 GAGAAAGCACAGATCAGGGC 58.622 55.000 3.76 3.76 0.00 5.19
2281 8029 3.617263 GGGACATCTGTCAAATGTACGTC 59.383 47.826 12.10 0.00 46.47 4.34
2312 8060 1.061799 CTGTGAAATGCAGTTCGCGC 61.062 55.000 28.72 18.39 46.97 6.86
2382 8130 2.102252 AGAACCTTCATCCGAGAGCATC 59.898 50.000 0.00 0.00 0.00 3.91
2404 8152 5.153950 AGAGACAGAAATGGTGGAACTAC 57.846 43.478 0.00 0.00 36.74 2.73
2819 8574 9.227777 ACTATTACGAAAGGCTGTCTTTATTTT 57.772 29.630 7.31 0.00 45.00 1.82
2820 8575 8.788325 ACTATTACGAAAGGCTGTCTTTATTT 57.212 30.769 7.31 0.00 45.00 1.40
2821 8576 8.788325 AACTATTACGAAAGGCTGTCTTTATT 57.212 30.769 7.31 0.23 45.00 1.40
2823 8578 9.880157 AATAACTATTACGAAAGGCTGTCTTTA 57.120 29.630 7.31 0.00 45.00 1.85
2902 8660 4.095782 TCTTGCACCTACTGTTTGAAACAC 59.904 41.667 6.66 0.00 36.25 3.32
2965 8778 1.681327 GAGGGGTCGGCAGTAGTGA 60.681 63.158 0.42 0.00 0.00 3.41
3009 8822 3.438087 AGAAAGTGGAAGAACGATGCATG 59.562 43.478 2.46 0.00 0.00 4.06
3017 8830 2.879026 GTGGTGGAGAAAGTGGAAGAAC 59.121 50.000 0.00 0.00 0.00 3.01
3037 8850 1.620819 GACATGTGTCTCAGTCCAGGT 59.379 52.381 1.15 0.00 41.65 4.00
3297 9118 2.546795 CGCTCAGTCTTGACAAAGAGGT 60.547 50.000 14.72 0.00 43.13 3.85
3340 9161 6.591834 CAGACTTCACGGTTCTCATCTAAAAT 59.408 38.462 0.00 0.00 0.00 1.82
3343 9164 4.765339 TCAGACTTCACGGTTCTCATCTAA 59.235 41.667 0.00 0.00 0.00 2.10
3344 9165 4.332828 TCAGACTTCACGGTTCTCATCTA 58.667 43.478 0.00 0.00 0.00 1.98
3616 9488 0.321653 GTGGTGGAGCCGTTCAGAAT 60.322 55.000 0.00 0.00 41.21 2.40


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

AutoCloner maintained by Alex Coulton.