Multiple sequence alignment - TraesCS7D01G075800

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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 TraesCS7D01G075800 chr7D 100.000 2777 0 0 1 2777 45003211 45005987 0.000000e+00 5129.0
1 TraesCS7D01G075800 chr7D 89.041 73 8 0 1018 1090 45004072 45004144 1.060000e-14 91.6
2 TraesCS7D01G075800 chr7D 89.041 73 8 0 862 934 45004228 45004300 1.060000e-14 91.6
3 TraesCS7D01G075800 chr7D 97.297 37 1 0 1039 1075 45054209 45054245 2.310000e-06 63.9
4 TraesCS7D01G075800 chrUn 91.207 1956 105 29 129 2063 49007335 49009244 0.000000e+00 2597.0
5 TraesCS7D01G075800 chrUn 95.294 85 3 1 2 85 49005731 49005815 1.740000e-27 134.0
6 TraesCS7D01G075800 chrUn 87.179 78 10 0 1013 1090 49008060 49008137 3.810000e-14 89.8
7 TraesCS7D01G075800 chrUn 79.412 136 20 3 806 934 49008159 49008293 3.810000e-14 89.8
8 TraesCS7D01G075800 chr7A 90.265 2034 115 27 2 2007 47341361 47343339 0.000000e+00 2582.0
9 TraesCS7D01G075800 chr7A 90.507 769 49 5 811 1576 47344394 47345141 0.000000e+00 994.0
10 TraesCS7D01G075800 chr7A 95.174 373 18 0 2405 2777 7284929 7284557 8.570000e-165 590.0
11 TraesCS7D01G075800 chr7A 90.828 447 20 15 1635 2076 47345137 47345567 1.850000e-161 579.0
12 TraesCS7D01G075800 chr7A 93.902 328 18 2 2079 2406 7286170 7285845 6.910000e-136 494.0
13 TraesCS7D01G075800 chr7A 92.683 328 22 2 2079 2406 450400856 450401181 3.240000e-129 472.0
14 TraesCS7D01G075800 chr7A 95.971 273 8 3 2505 2777 450402136 450402405 9.130000e-120 440.0
15 TraesCS7D01G075800 chr7A 89.041 73 8 0 1018 1090 47342239 47342311 1.060000e-14 91.6
16 TraesCS7D01G075800 chr7A 89.041 73 8 0 862 934 47342395 47342467 1.060000e-14 91.6
17 TraesCS7D01G075800 chr7A 97.297 37 1 0 1039 1075 47426229 47426265 2.310000e-06 63.9
18 TraesCS7D01G075800 chr5A 96.515 373 13 0 2405 2777 632320724 632320352 3.930000e-173 617.0
19 TraesCS7D01G075800 chr3B 96.267 375 11 3 2405 2777 778162373 778162746 1.830000e-171 612.0
20 TraesCS7D01G075800 chr3B 94.428 341 18 1 2438 2777 89689113 89688773 8.810000e-145 523.0
21 TraesCS7D01G075800 chr3B 93.902 328 20 0 2079 2406 778161101 778161428 1.920000e-136 496.0
22 TraesCS7D01G075800 chr7B 95.989 374 14 1 2405 2777 34157154 34156781 8.510000e-170 606.0
23 TraesCS7D01G075800 chr7B 93.293 328 22 0 2079 2406 34158428 34158101 4.160000e-133 484.0
24 TraesCS7D01G075800 chr3D 95.455 374 14 2 2405 2777 10414539 10414910 6.620000e-166 593.0
25 TraesCS7D01G075800 chr3D 90.549 328 31 0 2079 2406 10412515 10412842 4.250000e-118 435.0
26 TraesCS7D01G075800 chr2A 94.667 375 17 3 2405 2777 762715886 762715513 1.850000e-161 579.0
27 TraesCS7D01G075800 chr2A 89.189 333 26 2 2072 2404 762717211 762716889 9.260000e-110 407.0
28 TraesCS7D01G075800 chr5D 93.850 374 21 2 2405 2777 30922985 30923357 1.870000e-156 562.0
29 TraesCS7D01G075800 chr5D 92.378 328 25 0 2079 2406 30920947 30921274 4.190000e-128 468.0
30 TraesCS7D01G075800 chr6A 94.817 328 16 1 2079 2406 614237811 614237485 6.860000e-141 510.0
31 TraesCS7D01G075800 chr2B 89.105 257 28 0 2146 2402 38886532 38886788 1.240000e-83 320.0
32 TraesCS7D01G075800 chr6B 84.821 112 14 3 2079 2188 19940804 19940914 2.920000e-20 110.0
33 TraesCS7D01G075800 chr4B 83.784 111 18 0 2079 2189 14163811 14163921 3.780000e-19 106.0


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 TraesCS7D01G075800 chr7D 45003211 45005987 2776 False 1770.733333 5129 92.6940 1 2777 3 chr7D.!!$F2 2776
1 TraesCS7D01G075800 chrUn 49005731 49009244 3513 False 727.650000 2597 88.2730 2 2063 4 chrUn.!!$F1 2061
2 TraesCS7D01G075800 chr7A 47341361 47345567 4206 False 867.640000 2582 89.9364 2 2076 5 chr7A.!!$F2 2074
3 TraesCS7D01G075800 chr7A 7284557 7286170 1613 True 542.000000 590 94.5380 2079 2777 2 chr7A.!!$R1 698
4 TraesCS7D01G075800 chr7A 450400856 450402405 1549 False 456.000000 472 94.3270 2079 2777 2 chr7A.!!$F3 698
5 TraesCS7D01G075800 chr3B 778161101 778162746 1645 False 554.000000 612 95.0845 2079 2777 2 chr3B.!!$F1 698
6 TraesCS7D01G075800 chr7B 34156781 34158428 1647 True 545.000000 606 94.6410 2079 2777 2 chr7B.!!$R1 698
7 TraesCS7D01G075800 chr3D 10412515 10414910 2395 False 514.000000 593 93.0020 2079 2777 2 chr3D.!!$F1 698
8 TraesCS7D01G075800 chr2A 762715513 762717211 1698 True 493.000000 579 91.9280 2072 2777 2 chr2A.!!$R1 705
9 TraesCS7D01G075800 chr5D 30920947 30923357 2410 False 515.000000 562 93.1140 2079 2777 2 chr5D.!!$F1 698

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
993 2486 0.182537 TGTGGAAGTGGAACCTGGTG 59.817 55.0 0.0 0.0 37.8 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 5711 0.387929 AGGCGCGATTCCGATCTTAA 59.612 50.0 12.1 0.0 38.22 1.85 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
78 79 4.215908 GTGGGAAAACCCTCTTTCTTTCT 58.784 43.478 6.85 0.00 39.07 2.52
90 91 7.727634 ACCCTCTTTCTTTCTTTTCATTCATCT 59.272 33.333 0.00 0.00 0.00 2.90
122 142 2.492773 CCCCAGATGGAAATGCGCC 61.493 63.158 4.18 0.00 37.39 6.53
183 1663 2.430248 ACCTTGGAGGACGTGTTTTT 57.570 45.000 0.00 0.00 37.67 1.94
297 1784 1.112113 TTCCTACTCAGATCCACGGC 58.888 55.000 0.00 0.00 0.00 5.68
600 2087 2.753043 CACCTCCTGCATGTGCCC 60.753 66.667 2.07 0.00 41.18 5.36
852 2345 3.644399 GAACCAGGCCGACGAGACC 62.644 68.421 0.00 0.00 0.00 3.85
901 2394 1.592400 GGTGACCATCGACACGGAGA 61.592 60.000 0.00 0.00 37.82 3.71
993 2486 0.182537 TGTGGAAGTGGAACCTGGTG 59.817 55.000 0.00 0.00 37.80 4.17
994 2487 0.472471 GTGGAAGTGGAACCTGGTGA 59.528 55.000 0.00 0.00 37.80 4.02
1269 2762 2.279851 CACGCGCCGGAATCCATA 60.280 61.111 5.05 0.00 0.00 2.74
1365 2858 4.408821 TTCATGCGCTCCGGCCTT 62.409 61.111 9.73 0.00 34.44 4.35
1419 2912 3.637273 GAGCCCCTCACGTGGGTT 61.637 66.667 15.66 6.59 45.70 4.11
1472 2965 1.678635 CCAGGATGCTTTTCCGCCA 60.679 57.895 0.00 0.00 40.94 5.69
1478 2971 1.880819 ATGCTTTTCCGCCAAGGCAG 61.881 55.000 12.19 0.00 42.06 4.85
1528 3021 2.048127 GAAGGCGCGTGGAGAAGT 60.048 61.111 8.43 0.00 0.00 3.01
1581 3074 3.512516 GCCAAGACCTGCCGCATC 61.513 66.667 0.00 0.00 0.00 3.91
1582 3075 3.197790 CCAAGACCTGCCGCATCG 61.198 66.667 0.00 0.00 0.00 3.84
1583 3076 2.125552 CAAGACCTGCCGCATCGA 60.126 61.111 0.00 0.00 0.00 3.59
1601 3094 2.683933 GGACGGAGGCCTGGAGAA 60.684 66.667 12.00 0.00 0.00 2.87
1612 3105 1.455849 CTGGAGAAGGTGGCCAACA 59.544 57.895 25.90 0.00 0.00 3.33
1713 5334 2.743928 GTGTTGCAGCTCGAGGGG 60.744 66.667 15.58 0.00 0.00 4.79
1792 5416 4.416505 GTGTAACTGCACGTACTAGACT 57.583 45.455 0.00 0.00 0.00 3.24
1799 5423 4.942483 ACTGCACGTACTAGACTTGTAGAT 59.058 41.667 16.84 5.70 40.94 1.98
1801 5425 6.258287 ACTGCACGTACTAGACTTGTAGATAG 59.742 42.308 16.84 0.00 40.94 2.08
1802 5426 6.343703 TGCACGTACTAGACTTGTAGATAGA 58.656 40.000 0.00 0.00 30.03 1.98
1803 5427 6.257411 TGCACGTACTAGACTTGTAGATAGAC 59.743 42.308 0.00 0.00 30.03 2.59
1804 5428 6.257411 GCACGTACTAGACTTGTAGATAGACA 59.743 42.308 0.00 0.00 30.03 3.41
1805 5429 7.041916 GCACGTACTAGACTTGTAGATAGACAT 60.042 40.741 0.00 0.00 30.03 3.06
1806 5430 9.473640 CACGTACTAGACTTGTAGATAGACATA 57.526 37.037 0.00 0.00 0.00 2.29
1813 5437 8.259049 AGACTTGTAGATAGACATATACTCGC 57.741 38.462 0.00 0.00 31.41 5.03
1892 5521 4.741676 GTGATTCAGTTTCCTTGCTTGTTG 59.258 41.667 0.00 0.00 0.00 3.33
1916 5545 4.377841 GCATTCTTCTACGCTTGGATATGC 60.378 45.833 0.00 0.00 0.00 3.14
1930 5564 7.547019 CGCTTGGATATGCTAATTCATCTCTAA 59.453 37.037 0.00 0.00 0.00 2.10
1935 5569 9.896645 GGATATGCTAATTCATCTCTAATTCCA 57.103 33.333 0.00 0.00 0.00 3.53
2041 5677 6.108015 ACACAAAAGAAGACGTAGGTTGTTA 58.892 36.000 0.00 0.00 0.00 2.41
2127 5763 1.890489 GCCGGTCCTAATGTTTTGGTT 59.110 47.619 1.90 0.00 0.00 3.67
2132 5768 4.670735 CGGTCCTAATGTTTTGGTTAAGCG 60.671 45.833 0.00 0.00 0.00 4.68
2144 5780 3.752665 TGGTTAAGCGGGTAATGTTGAA 58.247 40.909 0.00 0.00 0.00 2.69
2196 5833 7.027161 GCATTCATACAAAACAATTACCGAGT 58.973 34.615 0.00 0.00 0.00 4.18
2264 5901 6.000219 GCATCAGTCAATACATACCAGGAAT 59.000 40.000 0.00 0.00 0.00 3.01
2298 5935 7.558444 AGAACAATACACTTCCTACCAAAACAA 59.442 33.333 0.00 0.00 0.00 2.83
2307 5944 7.007723 ACTTCCTACCAAAACAAATGTATCCA 58.992 34.615 0.00 0.00 0.00 3.41
2364 6001 2.631160 TTGACGGACAACACTTGGAT 57.369 45.000 0.00 0.00 33.18 3.41
2463 8606 3.132111 TGGAACAAAGAAACTGGCCTTTC 59.868 43.478 3.32 6.85 31.92 2.62
2711 8856 6.156949 TGAAATGTCAGTAGGCTCTTAGGATT 59.843 38.462 0.00 0.00 0.00 3.01
2720 8865 1.606737 GCTCTTAGGATTAGGGCAGCG 60.607 57.143 0.00 0.00 38.99 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 7.831691 TTCAGGGTGTTTAGATGAATGAAAA 57.168 32.000 0.00 0.00 0.00 2.29
90 91 2.638325 TCTGGGGATTCAGGGTGTTTA 58.362 47.619 0.00 0.00 35.58 2.01
94 95 0.184451 CCATCTGGGGATTCAGGGTG 59.816 60.000 0.00 0.00 35.58 4.61
190 1670 5.794894 AGTCGGATTAGAAGAGCAAAAAGA 58.205 37.500 0.00 0.00 0.00 2.52
219 1699 4.477975 GGGCGTCAGTCGGACTCG 62.478 72.222 7.89 11.06 44.68 4.18
416 1903 4.096003 ATGGAACGGAGGTGGCGG 62.096 66.667 0.00 0.00 0.00 6.13
598 2085 3.238497 CATGGGCATGGGCATGGG 61.238 66.667 0.00 0.00 43.71 4.00
599 2086 3.936203 GCATGGGCATGGGCATGG 61.936 66.667 0.00 0.00 43.71 3.66
600 2087 3.936203 GGCATGGGCATGGGCATG 61.936 66.667 0.00 0.00 43.71 4.06
823 2316 0.967380 GCCTGGTTCCATTCCCACAG 60.967 60.000 0.00 0.00 0.00 3.66
993 2486 1.037030 TGATGGCCGCCATTTCCTTC 61.037 55.000 25.80 13.41 45.26 3.46
994 2487 1.000233 TGATGGCCGCCATTTCCTT 60.000 52.632 25.80 3.14 45.26 3.36
1107 2600 4.148825 AGCGCGTAGGCCTCCTTG 62.149 66.667 9.68 0.00 34.61 3.61
1339 2832 4.210304 GCGCATGAACTCGTCGGC 62.210 66.667 0.30 0.00 0.00 5.54
1528 3021 4.323477 CACCCACGGGCCGAAGAA 62.323 66.667 35.78 0.00 39.32 2.52
1582 3075 3.151022 CTCCAGGCCTCCGTCCTC 61.151 72.222 0.00 0.00 0.00 3.71
1583 3076 3.239627 TTCTCCAGGCCTCCGTCCT 62.240 63.158 0.00 0.00 0.00 3.85
1724 5345 1.002250 CTCGCGCACTTTGTAGTCGT 61.002 55.000 8.75 0.00 30.26 4.34
1773 5394 4.791974 ACAAGTCTAGTACGTGCAGTTAC 58.208 43.478 6.38 0.00 40.80 2.50
1792 5416 9.498176 TTGTAGCGAGTATATGTCTATCTACAA 57.502 33.333 18.47 18.47 37.41 2.41
1842 5470 9.947189 TTGGATTCCTTCCTTATAGAGTACTAA 57.053 33.333 3.95 0.00 45.68 2.24
1843 5471 9.589461 CTTGGATTCCTTCCTTATAGAGTACTA 57.411 37.037 3.95 0.00 45.68 1.82
1844 5472 8.068733 ACTTGGATTCCTTCCTTATAGAGTACT 58.931 37.037 3.95 0.00 45.68 2.73
1892 5521 2.024176 TCCAAGCGTAGAAGAATGCC 57.976 50.000 0.00 0.00 31.41 4.40
1916 5545 8.997323 GTGGTCATGGAATTAGAGATGAATTAG 58.003 37.037 0.00 0.00 0.00 1.73
1935 5569 4.305539 TCTTGATGGTTCATGTGGTCAT 57.694 40.909 0.00 0.00 34.21 3.06
1950 5584 7.038941 AGCCACTAGTGTAGTTAAGTTCTTGAT 60.039 37.037 21.18 0.00 36.76 2.57
2041 5677 2.027837 ACCGAAGCCGTTTGTATACCTT 60.028 45.455 0.00 0.00 0.00 3.50
2073 5709 2.230508 AGGCGCGATTCCGATCTTAATA 59.769 45.455 12.10 0.00 38.22 0.98
2074 5710 1.000955 AGGCGCGATTCCGATCTTAAT 59.999 47.619 12.10 0.00 38.22 1.40
2075 5711 0.387929 AGGCGCGATTCCGATCTTAA 59.612 50.000 12.10 0.00 38.22 1.85
2077 5713 1.144057 AAGGCGCGATTCCGATCTT 59.856 52.632 12.10 0.00 38.22 2.40
2115 5751 6.208994 ACATTACCCGCTTAACCAAAACATTA 59.791 34.615 0.00 0.00 0.00 1.90
2127 5763 6.987992 CCTACTAATTCAACATTACCCGCTTA 59.012 38.462 0.00 0.00 0.00 3.09
2132 5768 6.544931 GGGTTCCTACTAATTCAACATTACCC 59.455 42.308 0.00 0.00 32.97 3.69
2144 5780 4.721776 TGCTGAATCTGGGTTCCTACTAAT 59.278 41.667 0.00 0.00 0.00 1.73
2225 5862 5.764686 TGACTGATGCAGTAACTGATGTTTT 59.235 36.000 0.00 0.00 45.44 2.43
2307 5944 8.408043 TTGTCCATGTCAATTCTGATTTTAGT 57.592 30.769 0.00 0.00 33.05 2.24
2351 5988 3.988379 TTGCTTCATCCAAGTGTTGTC 57.012 42.857 0.00 0.00 34.13 3.18
2364 6001 6.179756 TGTAGGCTTAGAATGATTTGCTTCA 58.820 36.000 0.00 0.00 0.00 3.02
2463 8606 5.010112 CAGGTAGGACCATATAGACACAGTG 59.990 48.000 0.00 0.00 41.95 3.66
2711 8856 2.656069 GGTGAAGACCGCTGCCCTA 61.656 63.158 0.00 0.00 30.61 3.53
2720 8865 5.480205 AGAGAATTTTAGACGGTGAAGACC 58.520 41.667 0.00 0.00 39.14 3.85


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

AutoCloner maintained by Alex Coulton.