Multiple sequence alignment - TraesCS6D01G217700

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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 TraesCS6D01G217700 chr6D 100.000 3578 0 0 1 3578 307416994 307413417 0.000000e+00 6608
1 TraesCS6D01G217700 chr6D 92.694 657 40 7 2926 3578 60446808 60446156 0.000000e+00 941
2 TraesCS6D01G217700 chr1B 91.272 2956 215 27 2 2926 406436719 406439662 0.000000e+00 3989
3 TraesCS6D01G217700 chr1B 92.024 2382 174 11 4 2374 593273430 593271054 0.000000e+00 3332
4 TraesCS6D01G217700 chr6B 90.731 2956 228 32 2 2926 335254645 335257585 0.000000e+00 3899
5 TraesCS6D01G217700 chr6B 83.103 290 34 6 1 287 471275975 471276252 2.130000e-62 250
6 TraesCS6D01G217700 chr6B 81.197 234 27 9 1 230 471280548 471280768 4.750000e-39 172
7 TraesCS6D01G217700 chr3A 90.483 2816 248 15 125 2926 392544735 392547544 0.000000e+00 3698
8 TraesCS6D01G217700 chr5A 89.965 2850 228 40 123 2926 229787717 229790554 0.000000e+00 3626
9 TraesCS6D01G217700 chr4B 92.830 2385 155 13 1 2373 567677981 567680361 0.000000e+00 3443
10 TraesCS6D01G217700 chr4B 92.221 2391 164 15 8 2384 78830776 78828394 0.000000e+00 3365
11 TraesCS6D01G217700 chr4B 84.483 986 137 11 1953 2926 376028866 376029847 0.000000e+00 959
12 TraesCS6D01G217700 chr7D 93.780 2283 130 9 112 2386 290732587 290730309 0.000000e+00 3419
13 TraesCS6D01G217700 chr7D 91.502 659 46 7 2923 3578 142594601 142595252 0.000000e+00 898
14 TraesCS6D01G217700 chr7D 91.489 658 46 8 2926 3578 142598077 142598729 0.000000e+00 896
15 TraesCS6D01G217700 chr7D 93.310 568 32 6 2925 3488 448718914 448718349 0.000000e+00 833
16 TraesCS6D01G217700 chr7B 92.446 2396 156 15 2 2384 242307489 242305106 0.000000e+00 3398
17 TraesCS6D01G217700 chr7B 91.429 140 9 2 3439 3578 293233246 293233382 4.720000e-44 189
18 TraesCS6D01G217700 chr3D 86.626 987 119 8 1948 2926 304094457 304095438 0.000000e+00 1079
19 TraesCS6D01G217700 chr2D 87.141 941 109 9 1995 2926 323247929 323246992 0.000000e+00 1057
20 TraesCS6D01G217700 chr2D 85.988 992 119 12 1948 2926 380725065 380724081 0.000000e+00 1044
21 TraesCS6D01G217700 chr2D 92.401 658 42 7 2925 3578 206643023 206643676 0.000000e+00 931
22 TraesCS6D01G217700 chr2D 89.774 665 47 19 2924 3578 198336576 198337229 0.000000e+00 832
23 TraesCS6D01G217700 chr2B 86.165 983 116 14 1958 2926 295833275 295834251 0.000000e+00 1044
24 TraesCS6D01G217700 chr2B 84.725 982 133 13 1953 2926 405162543 405163515 0.000000e+00 966
25 TraesCS6D01G217700 chr2A 91.945 658 42 8 2924 3577 690139655 690139005 0.000000e+00 911
26 TraesCS6D01G217700 chr2A 91.450 655 46 8 2926 3577 690125077 690124430 0.000000e+00 891
27 TraesCS6D01G217700 chr4D 93.298 567 30 8 2926 3488 406273498 406272936 0.000000e+00 830
28 TraesCS6D01G217700 chr5D 87.179 117 11 2 3462 3578 54954268 54954380 2.900000e-26 130


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 TraesCS6D01G217700 chr6D 307413417 307416994 3577 True 6608 6608 100.0000 1 3578 1 chr6D.!!$R2 3577
1 TraesCS6D01G217700 chr6D 60446156 60446808 652 True 941 941 92.6940 2926 3578 1 chr6D.!!$R1 652
2 TraesCS6D01G217700 chr1B 406436719 406439662 2943 False 3989 3989 91.2720 2 2926 1 chr1B.!!$F1 2924
3 TraesCS6D01G217700 chr1B 593271054 593273430 2376 True 3332 3332 92.0240 4 2374 1 chr1B.!!$R1 2370
4 TraesCS6D01G217700 chr6B 335254645 335257585 2940 False 3899 3899 90.7310 2 2926 1 chr6B.!!$F1 2924
5 TraesCS6D01G217700 chr3A 392544735 392547544 2809 False 3698 3698 90.4830 125 2926 1 chr3A.!!$F1 2801
6 TraesCS6D01G217700 chr5A 229787717 229790554 2837 False 3626 3626 89.9650 123 2926 1 chr5A.!!$F1 2803
7 TraesCS6D01G217700 chr4B 567677981 567680361 2380 False 3443 3443 92.8300 1 2373 1 chr4B.!!$F2 2372
8 TraesCS6D01G217700 chr4B 78828394 78830776 2382 True 3365 3365 92.2210 8 2384 1 chr4B.!!$R1 2376
9 TraesCS6D01G217700 chr4B 376028866 376029847 981 False 959 959 84.4830 1953 2926 1 chr4B.!!$F1 973
10 TraesCS6D01G217700 chr7D 290730309 290732587 2278 True 3419 3419 93.7800 112 2386 1 chr7D.!!$R1 2274
11 TraesCS6D01G217700 chr7D 142594601 142598729 4128 False 897 898 91.4955 2923 3578 2 chr7D.!!$F1 655
12 TraesCS6D01G217700 chr7D 448718349 448718914 565 True 833 833 93.3100 2925 3488 1 chr7D.!!$R2 563
13 TraesCS6D01G217700 chr7B 242305106 242307489 2383 True 3398 3398 92.4460 2 2384 1 chr7B.!!$R1 2382
14 TraesCS6D01G217700 chr3D 304094457 304095438 981 False 1079 1079 86.6260 1948 2926 1 chr3D.!!$F1 978
15 TraesCS6D01G217700 chr2D 323246992 323247929 937 True 1057 1057 87.1410 1995 2926 1 chr2D.!!$R1 931
16 TraesCS6D01G217700 chr2D 380724081 380725065 984 True 1044 1044 85.9880 1948 2926 1 chr2D.!!$R2 978
17 TraesCS6D01G217700 chr2D 206643023 206643676 653 False 931 931 92.4010 2925 3578 1 chr2D.!!$F2 653
18 TraesCS6D01G217700 chr2D 198336576 198337229 653 False 832 832 89.7740 2924 3578 1 chr2D.!!$F1 654
19 TraesCS6D01G217700 chr2B 295833275 295834251 976 False 1044 1044 86.1650 1958 2926 1 chr2B.!!$F1 968
20 TraesCS6D01G217700 chr2B 405162543 405163515 972 False 966 966 84.7250 1953 2926 1 chr2B.!!$F2 973
21 TraesCS6D01G217700 chr2A 690139005 690139655 650 True 911 911 91.9450 2924 3577 1 chr2A.!!$R2 653
22 TraesCS6D01G217700 chr2A 690124430 690125077 647 True 891 891 91.4500 2926 3577 1 chr2A.!!$R1 651
23 TraesCS6D01G217700 chr4D 406272936 406273498 562 True 830 830 93.2980 2926 3488 1 chr4D.!!$R1 562

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
872 883 1.270785 TGCGCAAGATGGAAGTGAGAA 60.271 47.619 8.16 0.0 43.02 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2642 2693 0.469494 TCACCAACTGCAGCTCTTCA 59.531 50.0 15.27 0.0 0.0 3.02 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
62 63 4.792068 TCATCTCCCTTTGTTTCTGTGTT 58.208 39.130 0.00 0.00 0.00 3.32
68 69 7.060421 TCTCCCTTTGTTTCTGTGTTATTTCT 58.940 34.615 0.00 0.00 0.00 2.52
93 95 9.612620 CTTTTGTTGATATCCTTGTTAGTGTTC 57.387 33.333 0.00 0.00 0.00 3.18
171 175 2.517875 GCCGTCGCCTAGTCCCTA 60.518 66.667 0.00 0.00 0.00 3.53
290 298 5.163509 TGTGTGAAGCTATAGACTAGGCTTG 60.164 44.000 22.16 0.00 43.74 4.01
419 428 2.542178 TGATGTTTGTGAGCGTGTGTAC 59.458 45.455 0.00 0.00 0.00 2.90
521 530 2.040544 GGACACAATGACAGGGCCG 61.041 63.158 0.00 0.00 0.00 6.13
593 603 2.159544 GCTCTTGTCTTGCAGAATCAGC 60.160 50.000 0.00 0.00 0.00 4.26
672 683 3.199946 CCAATACAGTCCAGTACCATGGT 59.800 47.826 23.55 23.55 41.43 3.55
685 696 4.538490 AGTACCATGGTGTTTCCCAAGATA 59.462 41.667 28.17 0.00 38.20 1.98
694 705 5.823045 GGTGTTTCCCAAGATACTATCAAGG 59.177 44.000 0.00 0.39 0.00 3.61
773 784 4.686944 GCCATCAAGATCATACACTTGGGA 60.687 45.833 0.00 0.00 42.27 4.37
824 835 8.514594 CAGATATTTTCCACTTTACAAGCAAGA 58.485 33.333 0.00 0.00 0.00 3.02
872 883 1.270785 TGCGCAAGATGGAAGTGAGAA 60.271 47.619 8.16 0.00 43.02 2.87
896 907 2.158856 TGTATGCAGCTTGGGAGAGATG 60.159 50.000 0.00 0.00 36.18 2.90
913 925 8.204836 GGGAGAGATGTAAGTATTTGCTTAGAA 58.795 37.037 0.00 0.00 32.30 2.10
1020 1032 2.363306 TGTCAGCTGGTGGAACAATT 57.637 45.000 15.13 0.00 44.16 2.32
1040 1052 4.610605 TTATGAACAAGACCGTTGAGGA 57.389 40.909 0.00 0.00 45.00 3.71
1067 1079 6.641314 GCAATTATTCTCATTGAGAGCATTGG 59.359 38.462 26.33 16.20 44.35 3.16
1380 1392 3.229293 TCATGGCAATGAAACTGTCCAA 58.771 40.909 0.00 0.00 39.92 3.53
1697 1715 4.230733 TCCAAGGAGAGAGATACAAGAGGA 59.769 45.833 0.00 0.00 0.00 3.71
1872 1890 0.116342 TCTCAGCACCCCTACCAGAA 59.884 55.000 0.00 0.00 0.00 3.02
1951 1969 6.210784 TGGTAGTAGCACCATAGAATATCCAC 59.789 42.308 0.00 0.00 43.76 4.02
2007 2025 4.705337 AGTAGACGAGGAACAAGATGAC 57.295 45.455 0.00 0.00 0.00 3.06
2008 2026 2.638556 AGACGAGGAACAAGATGACG 57.361 50.000 0.00 0.00 0.00 4.35
2045 2063 3.438087 CCAAGCGATGAAGTTGAAGACAT 59.562 43.478 0.00 0.00 0.00 3.06
2049 2067 6.595772 AGCGATGAAGTTGAAGACATAATC 57.404 37.500 0.00 0.00 0.00 1.75
2166 2184 5.010213 AGCAGGTTTATCTAATCCTCTCGAC 59.990 44.000 0.00 0.00 34.10 4.20
2181 2199 2.161012 TCTCGACGACATGTGTCCTTAC 59.839 50.000 1.15 0.00 41.86 2.34
2202 2220 5.864628 ACGATTTCTTTGCTTCTACCTTC 57.135 39.130 0.00 0.00 0.00 3.46
2242 2260 7.173863 TCACTTAAGCTAGACTTGAAAAACG 57.826 36.000 1.29 0.00 39.58 3.60
2520 2548 1.995484 CTTGTGCACGATCCACTACAG 59.005 52.381 13.13 0.00 34.38 2.74
2527 2555 0.817654 CGATCCACTACAGGCTGACA 59.182 55.000 23.66 7.47 0.00 3.58
2615 2644 3.487544 GGCACACACAAAGAAGAGTGAAC 60.488 47.826 0.00 0.00 39.03 3.18
2673 2725 2.106566 AGTTGGTGAGATGATCGAGCT 58.893 47.619 0.90 0.00 0.00 4.09
2700 2752 0.383231 CATCATTTGAAGAGCCCGGC 59.617 55.000 0.00 0.00 0.00 6.13
2763 2822 4.261363 GCTGAATTCTATTGCTAGTTGGGC 60.261 45.833 7.05 0.00 0.00 5.36
2771 2833 0.110295 TGCTAGTTGGGCTGCTTGAA 59.890 50.000 0.00 0.00 0.00 2.69
2841 2906 6.093082 TGCTTGATGTGAATATGTGAACTGAG 59.907 38.462 0.00 0.00 0.00 3.35
3006 3072 8.359642 TGTGTTTCTTTTGCTTGCTCTATTTAT 58.640 29.630 0.00 0.00 0.00 1.40
3108 3185 6.017109 CGATCCATTTAAATCGAGGGAAATGT 60.017 38.462 19.26 8.60 45.83 2.71
3523 7087 8.894768 TTTTCTTCTTTCTTTAGAGTGAGAGG 57.105 34.615 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 8.286800 CGAACACTAACAAGGATATCAACAAAA 58.713 33.333 4.83 0.00 0.00 2.44
118 120 9.701098 CGGCTAAATCTAGGTAACACAATATTA 57.299 33.333 0.00 0.00 41.41 0.98
171 175 1.292223 CGAGTGTCGTGTTCCCCAT 59.708 57.895 0.00 0.00 34.72 4.00
264 272 5.422331 AGCCTAGTCTATAGCTTCACACAAA 59.578 40.000 0.00 0.00 29.27 2.83
419 428 9.809096 AATCAGCCTACAAATAGTATGATATCG 57.191 33.333 0.00 0.00 33.63 2.92
509 518 2.886382 CCAAATCGGCCCTGTCATT 58.114 52.632 0.00 0.00 0.00 2.57
521 530 3.930634 GCCTCAATAGATGGCCAAATC 57.069 47.619 10.96 3.14 40.71 2.17
593 603 6.292150 GGTCTTCATTGGGTAATCCTCTAAG 58.708 44.000 0.00 0.00 36.20 2.18
672 683 5.491078 ACCCTTGATAGTATCTTGGGAAACA 59.509 40.000 30.48 3.92 41.61 2.83
685 696 6.121776 TGTGAACAACATACCCTTGATAGT 57.878 37.500 0.00 0.00 32.36 2.12
773 784 4.498682 GCAGGAAAGCTTGCGAAATATCAT 60.499 41.667 0.00 0.00 37.37 2.45
824 835 2.092753 AGGATCTGGTCACGAATTGCAT 60.093 45.455 0.00 0.00 0.00 3.96
872 883 1.630369 TCTCCCAAGCTGCATACAAGT 59.370 47.619 1.02 0.00 0.00 3.16
913 925 2.799126 TGCCCGTGATTAGGACATTT 57.201 45.000 0.00 0.00 0.00 2.32
1020 1032 4.503910 CATCCTCAACGGTCTTGTTCATA 58.496 43.478 0.00 0.00 0.00 2.15
1040 1052 6.954487 TGCTCTCAATGAGAATAATTGCAT 57.046 33.333 14.44 0.00 45.39 3.96
1067 1079 1.676615 CCCATTGCATTTGGTGGAAGC 60.677 52.381 13.50 0.00 41.68 3.86
1380 1392 6.152932 ACATCTTGCAACTTTGACTCATTT 57.847 33.333 0.00 0.00 0.00 2.32
1730 1748 1.134965 CACGTGGGATCTTCTCAGGAC 60.135 57.143 7.95 0.00 34.87 3.85
1872 1890 6.261603 CCATCTGTGAATATGCACTAACATGT 59.738 38.462 15.07 0.00 39.49 3.21
1945 1963 3.269643 TGAGGTCTCTCTTCCTGTGGATA 59.730 47.826 0.00 0.00 40.58 2.59
1951 1969 3.576118 TCAAGTTGAGGTCTCTCTTCCTG 59.424 47.826 0.08 0.00 40.58 3.86
1988 2006 3.340928 TCGTCATCTTGTTCCTCGTCTA 58.659 45.455 0.00 0.00 0.00 2.59
2007 2025 2.611518 CTTGGGTAGTCAAGCTCTTCG 58.388 52.381 0.00 0.00 37.84 3.79
2028 2046 9.689976 ATAGAGATTATGTCTTCAACTTCATCG 57.310 33.333 0.00 0.00 37.29 3.84
2049 2067 9.621629 TCTTGTACTTCTTTAGGAGAGATAGAG 57.378 37.037 0.00 0.00 35.37 2.43
2166 2184 4.174009 AGAAATCGTAAGGACACATGTCG 58.826 43.478 0.00 0.00 45.65 4.35
2181 2199 4.695455 TGGAAGGTAGAAGCAAAGAAATCG 59.305 41.667 0.00 0.00 0.00 3.34
2202 2220 7.663081 AGCTTAAGTGATGGTATCATGTAATGG 59.337 37.037 4.02 0.00 46.73 3.16
2242 2260 4.398988 TGTATGATCATGTCCAAGCAAACC 59.601 41.667 18.72 0.00 0.00 3.27
2520 2548 0.951040 CACCTCGAACCTTGTCAGCC 60.951 60.000 0.00 0.00 0.00 4.85
2527 2555 1.978580 AGGAATGTCACCTCGAACCTT 59.021 47.619 0.00 0.00 31.43 3.50
2642 2693 0.469494 TCACCAACTGCAGCTCTTCA 59.531 50.000 15.27 0.00 0.00 3.02
2673 2725 5.118990 GGCTCTTCAAATGATGTAGCACTA 58.881 41.667 15.51 0.00 31.10 2.74
2687 2739 4.760047 GCTCGCCGGGCTCTTCAA 62.760 66.667 18.34 0.00 0.00 2.69
2700 2752 1.742761 ATGGGTCATGAAACAGCTCG 58.257 50.000 0.00 0.00 0.00 5.03
2763 2822 6.857964 CAACAAGTAATAACTGGTTCAAGCAG 59.142 38.462 15.21 15.21 45.11 4.24
2841 2906 6.017440 TCACTAGTTTACAAGGCATTCAACAC 60.017 38.462 0.00 0.00 0.00 3.32
2919 2984 1.208535 TCTCGGGGCGTTACATTTGAT 59.791 47.619 0.00 0.00 0.00 2.57
3006 3072 3.433957 GCTGACATGATGCAATGCAAAAA 59.566 39.130 13.45 0.59 43.62 1.94
3108 3185 8.862325 ATGTTGTAAAGAGAAATCACCATGTA 57.138 30.769 0.00 0.00 0.00 2.29
3522 7086 1.685355 GCTGGGCTCTCTTCTCTCCC 61.685 65.000 0.00 0.00 37.49 4.30
3523 7087 0.975040 TGCTGGGCTCTCTTCTCTCC 60.975 60.000 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.