Multiple sequence alignment - TraesCS7A01G387300

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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 TraesCS7A01G387300 chr7A 100.000 2455 0 0 1 2455 563493388 563495842 0.000000e+00 4534
1 TraesCS7A01G387300 chr7A 95.612 2461 65 27 1 2455 435733612 435731189 0.000000e+00 3906
2 TraesCS7A01G387300 chr7A 93.878 1568 57 14 888 2455 87693048 87691520 0.000000e+00 2327
3 TraesCS7A01G387300 chr7A 95.374 908 30 6 1 898 87693977 87693072 0.000000e+00 1434
4 TraesCS7A01G387300 chr7A 88.558 839 67 14 76 898 139135876 139135051 0.000000e+00 990
5 TraesCS7A01G387300 chr7A 86.580 924 86 23 1541 2453 139134425 139133529 0.000000e+00 985
6 TraesCS7A01G387300 chr7A 89.011 546 47 7 888 1432 139135027 139134494 0.000000e+00 664
7 TraesCS7A01G387300 chr5A 94.677 2273 79 16 189 2455 690643132 690640896 0.000000e+00 3489
8 TraesCS7A01G387300 chr5A 96.330 545 16 2 189 729 698853177 698853721 0.000000e+00 893
9 TraesCS7A01G387300 chr2B 96.058 1725 49 10 94 1813 338729380 338727670 0.000000e+00 2791
10 TraesCS7A01G387300 chr1D 94.770 1568 43 14 888 2455 34022524 34020996 0.000000e+00 2405
11 TraesCS7A01G387300 chr1D 96.476 908 20 6 1 898 34023453 34022548 0.000000e+00 1489
12 TraesCS7A01G387300 chr3B 96.131 1370 44 7 94 1458 395707738 395706373 0.000000e+00 2228
13 TraesCS7A01G387300 chr3B 92.746 965 32 13 1493 2455 395706372 395705444 0.000000e+00 1360
14 TraesCS7A01G387300 chr1A 85.193 1479 144 45 1 1432 291625851 291624401 0.000000e+00 1448
15 TraesCS7A01G387300 chr5D 88.584 911 77 14 1 895 448013340 448014239 0.000000e+00 1081
16 TraesCS7A01G387300 chr5D 87.079 921 80 25 1541 2450 448014875 448015767 0.000000e+00 1005
17 TraesCS7A01G387300 chr5D 88.577 534 48 9 900 1432 448014285 448014806 9.580000e-179 636
18 TraesCS7A01G387300 chr2A 85.946 925 90 27 1541 2455 148842079 148842973 0.000000e+00 952
19 TraesCS7A01G387300 chr4D 89.901 505 38 6 1541 2044 170688985 170688493 2.660000e-179 638
20 TraesCS7A01G387300 chr4D 89.703 505 39 6 1541 2044 170623130 170622638 1.240000e-177 632
21 TraesCS7A01G387300 chr4D 93.056 360 12 6 2107 2455 294681915 294682272 4.680000e-142 514
22 TraesCS7A01G387300 chr4D 92.000 100 4 3 1415 1511 414999564 414999662 1.180000e-28 137
23 TraesCS7A01G387300 chr5B 93.611 360 10 5 2107 2455 102916815 102917172 2.160000e-145 525
24 TraesCS7A01G387300 chr5B 91.176 102 6 2 1415 1514 166379180 166379080 4.260000e-28 135
25 TraesCS7A01G387300 chr4B 91.919 99 5 2 1415 1511 511163711 511163808 4.260000e-28 135
26 TraesCS7A01G387300 chr3A 91.919 99 5 2 1415 1511 470095776 470095679 4.260000e-28 135


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 TraesCS7A01G387300 chr7A 563493388 563495842 2454 False 4534.000000 4534 100.000000 1 2455 1 chr7A.!!$F1 2454
1 TraesCS7A01G387300 chr7A 435731189 435733612 2423 True 3906.000000 3906 95.612000 1 2455 1 chr7A.!!$R1 2454
2 TraesCS7A01G387300 chr7A 87691520 87693977 2457 True 1880.500000 2327 94.626000 1 2455 2 chr7A.!!$R2 2454
3 TraesCS7A01G387300 chr7A 139133529 139135876 2347 True 879.666667 990 88.049667 76 2453 3 chr7A.!!$R3 2377
4 TraesCS7A01G387300 chr5A 690640896 690643132 2236 True 3489.000000 3489 94.677000 189 2455 1 chr5A.!!$R1 2266
5 TraesCS7A01G387300 chr5A 698853177 698853721 544 False 893.000000 893 96.330000 189 729 1 chr5A.!!$F1 540
6 TraesCS7A01G387300 chr2B 338727670 338729380 1710 True 2791.000000 2791 96.058000 94 1813 1 chr2B.!!$R1 1719
7 TraesCS7A01G387300 chr1D 34020996 34023453 2457 True 1947.000000 2405 95.623000 1 2455 2 chr1D.!!$R1 2454
8 TraesCS7A01G387300 chr3B 395705444 395707738 2294 True 1794.000000 2228 94.438500 94 2455 2 chr3B.!!$R1 2361
9 TraesCS7A01G387300 chr1A 291624401 291625851 1450 True 1448.000000 1448 85.193000 1 1432 1 chr1A.!!$R1 1431
10 TraesCS7A01G387300 chr5D 448013340 448015767 2427 False 907.333333 1081 88.080000 1 2450 3 chr5D.!!$F1 2449
11 TraesCS7A01G387300 chr2A 148842079 148842973 894 False 952.000000 952 85.946000 1541 2455 1 chr2A.!!$F1 914


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
583 604 2.104111 TCTGCCGGTCTCTTGAAAGAAA 59.896 45.455 1.9 0.0 34.03 2.52 F
1135 1202 3.117888 TCATCTCATTAGTTGGCTTCCCC 60.118 47.826 0.0 0.0 0.00 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1438 1506 1.197721 CACCTTAGTTCAAAGCTGCGG 59.802 52.381 0.0 0.00 0.00 5.69 R
2086 2169 1.420514 AGCCATCTGATCCATGACTGG 59.579 52.381 0.0 4.78 44.64 4.00 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
39 40 7.765695 TTTTTCCTCTCTTAACTGCATCATT 57.234 32.000 0.00 0.00 0.00 2.57
184 187 2.634600 TGTTCACCTTTGTTGTAGCGT 58.365 42.857 0.00 0.00 0.00 5.07
350 366 6.690957 ACAATCTGTTGACAAACACATTTACG 59.309 34.615 0.00 0.00 41.41 3.18
583 604 2.104111 TCTGCCGGTCTCTTGAAAGAAA 59.896 45.455 1.90 0.00 34.03 2.52
613 634 7.710896 AGAAATGCAGCCTTTATAACTGAATC 58.289 34.615 5.91 0.00 27.83 2.52
637 658 8.728337 TCTCTACATTCATTTTTGGAGATCAG 57.272 34.615 0.00 0.00 32.46 2.90
773 797 6.072064 GCAAGCTGCATAGGAGAAATTCATAT 60.072 38.462 1.02 0.00 44.26 1.78
1135 1202 3.117888 TCATCTCATTAGTTGGCTTCCCC 60.118 47.826 0.00 0.00 0.00 4.81
1438 1506 4.003648 CCCTCCGATCCAAATATAAGTGC 58.996 47.826 0.00 0.00 0.00 4.40
1517 1585 2.433239 TCGGAGGAAGTAGTAAATGCCC 59.567 50.000 0.00 0.00 0.00 5.36
1598 1679 8.940768 TCAATGAAAACTTTTAAAACCTGAGG 57.059 30.769 0.00 0.00 0.00 3.86
1623 1704 6.747280 GTGCAAGTATATTTTGTAGGCTTGTG 59.253 38.462 0.00 0.00 35.61 3.33
1624 1705 6.127758 TGCAAGTATATTTTGTAGGCTTGTGG 60.128 38.462 0.00 0.00 35.61 4.17
1625 1706 6.094881 GCAAGTATATTTTGTAGGCTTGTGGA 59.905 38.462 0.00 0.00 35.61 4.02
1626 1707 7.201821 GCAAGTATATTTTGTAGGCTTGTGGAT 60.202 37.037 0.00 0.00 35.61 3.41
1627 1708 8.686334 CAAGTATATTTTGTAGGCTTGTGGATT 58.314 33.333 0.00 0.00 0.00 3.01
1628 1709 8.225603 AGTATATTTTGTAGGCTTGTGGATTG 57.774 34.615 0.00 0.00 0.00 2.67
1629 1710 7.834181 AGTATATTTTGTAGGCTTGTGGATTGT 59.166 33.333 0.00 0.00 0.00 2.71
1630 1711 4.582701 TTTTGTAGGCTTGTGGATTGTG 57.417 40.909 0.00 0.00 0.00 3.33
1643 1724 1.612950 GGATTGTGGTGCATGTTCACA 59.387 47.619 11.78 11.78 39.31 3.58
1851 1934 2.165030 GAGGGATCGACCTTCAACGTTA 59.835 50.000 0.00 0.00 43.20 3.18
1906 1989 0.033208 TCCATTCCCCCATCTTGTGC 60.033 55.000 0.00 0.00 0.00 4.57
2044 2127 9.255304 GTGCTTCCAGTATTTGTAATTTTGAAA 57.745 29.630 0.00 0.00 0.00 2.69
2046 2129 9.476202 GCTTCCAGTATTTGTAATTTTGAAAGT 57.524 29.630 0.00 0.00 0.00 2.66
2048 2131 8.810652 TCCAGTATTTGTAATTTTGAAAGTGC 57.189 30.769 0.00 0.00 0.00 4.40
2049 2132 8.637986 TCCAGTATTTGTAATTTTGAAAGTGCT 58.362 29.630 0.00 0.00 0.00 4.40
2052 2135 9.476202 AGTATTTGTAATTTTGAAAGTGCTTCC 57.524 29.630 0.00 0.00 32.53 3.46
2054 2137 7.769272 TTTGTAATTTTGAAAGTGCTTCCAG 57.231 32.000 0.00 0.00 32.53 3.86
2058 2141 7.918562 TGTAATTTTGAAAGTGCTTCCAGTAAC 59.081 33.333 0.00 0.00 32.53 2.50
2059 2142 4.911514 TTTGAAAGTGCTTCCAGTAACC 57.088 40.909 0.00 0.00 32.53 2.85
2060 2143 3.569194 TGAAAGTGCTTCCAGTAACCA 57.431 42.857 0.00 0.00 32.53 3.67
2061 2144 4.098914 TGAAAGTGCTTCCAGTAACCAT 57.901 40.909 0.00 0.00 32.53 3.55
2062 2145 4.072131 TGAAAGTGCTTCCAGTAACCATC 58.928 43.478 0.00 0.00 32.53 3.51
2063 2146 4.202461 TGAAAGTGCTTCCAGTAACCATCT 60.202 41.667 0.00 0.00 32.53 2.90
2064 2147 3.618690 AGTGCTTCCAGTAACCATCTC 57.381 47.619 0.00 0.00 0.00 2.75
2065 2148 2.237392 AGTGCTTCCAGTAACCATCTCC 59.763 50.000 0.00 0.00 0.00 3.71
2066 2149 1.207089 TGCTTCCAGTAACCATCTCCG 59.793 52.381 0.00 0.00 0.00 4.63
2067 2150 1.941325 CTTCCAGTAACCATCTCCGC 58.059 55.000 0.00 0.00 0.00 5.54
2068 2151 1.482593 CTTCCAGTAACCATCTCCGCT 59.517 52.381 0.00 0.00 0.00 5.52
2069 2152 1.112113 TCCAGTAACCATCTCCGCTC 58.888 55.000 0.00 0.00 0.00 5.03
2070 2153 1.115467 CCAGTAACCATCTCCGCTCT 58.885 55.000 0.00 0.00 0.00 4.09
2071 2154 2.092049 TCCAGTAACCATCTCCGCTCTA 60.092 50.000 0.00 0.00 0.00 2.43
2072 2155 2.034812 CCAGTAACCATCTCCGCTCTAC 59.965 54.545 0.00 0.00 0.00 2.59
2073 2156 2.688446 CAGTAACCATCTCCGCTCTACA 59.312 50.000 0.00 0.00 0.00 2.74
2074 2157 3.130516 CAGTAACCATCTCCGCTCTACAA 59.869 47.826 0.00 0.00 0.00 2.41
2075 2158 3.961408 AGTAACCATCTCCGCTCTACAAT 59.039 43.478 0.00 0.00 0.00 2.71
2076 2159 5.009710 CAGTAACCATCTCCGCTCTACAATA 59.990 44.000 0.00 0.00 0.00 1.90
2077 2160 5.597182 AGTAACCATCTCCGCTCTACAATAA 59.403 40.000 0.00 0.00 0.00 1.40
2078 2161 5.552870 AACCATCTCCGCTCTACAATAAT 57.447 39.130 0.00 0.00 0.00 1.28
2079 2162 6.665992 AACCATCTCCGCTCTACAATAATA 57.334 37.500 0.00 0.00 0.00 0.98
2080 2163 6.274157 ACCATCTCCGCTCTACAATAATAG 57.726 41.667 0.00 0.00 0.00 1.73
2081 2164 5.775701 ACCATCTCCGCTCTACAATAATAGT 59.224 40.000 0.00 0.00 0.00 2.12
2082 2165 6.096036 CCATCTCCGCTCTACAATAATAGTG 58.904 44.000 0.00 0.00 0.00 2.74
2083 2166 5.122512 TCTCCGCTCTACAATAATAGTGC 57.877 43.478 0.00 0.00 37.99 4.40
2084 2167 4.827835 TCTCCGCTCTACAATAATAGTGCT 59.172 41.667 5.59 0.00 38.80 4.40
2085 2168 5.302059 TCTCCGCTCTACAATAATAGTGCTT 59.698 40.000 5.59 0.00 38.80 3.91
2086 2169 5.529791 TCCGCTCTACAATAATAGTGCTTC 58.470 41.667 5.59 0.00 38.80 3.86
2196 2304 8.450180 TGTACACAATGCAATGTAACTAGAATG 58.550 33.333 7.18 0.00 33.23 2.67
2222 2330 8.182227 GGTCTTTATCTTTTAATCAGTTTCCCG 58.818 37.037 0.00 0.00 0.00 5.14
2450 2562 4.766373 TCTTCCATTTCAACTGCAGCAATA 59.234 37.500 15.27 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 5.682234 TCAATGATGCAGTTAAGAGAGGA 57.318 39.130 0.00 0.00 0.00 3.71
35 36 2.119495 GGTCCTAGCCTCCTTCAATGA 58.881 52.381 0.00 0.00 0.00 2.57
39 40 0.395862 CTCGGTCCTAGCCTCCTTCA 60.396 60.000 0.00 0.00 0.00 3.02
184 187 9.177608 CATTTAAATATCTGGAACAAGTCTCCA 57.822 33.333 0.00 0.00 40.77 3.86
350 366 8.818057 CCTGAAGCATACTACACATACTTAAAC 58.182 37.037 0.00 0.00 0.00 2.01
583 604 9.807649 CAGTTATAAAGGCTGCATTTCTTTTAT 57.192 29.630 16.09 6.40 33.44 1.40
613 634 8.728337 TCTGATCTCCAAAAATGAATGTAGAG 57.272 34.615 0.00 0.00 0.00 2.43
886 912 4.917906 AGACTAAAGCAACCTCATCCTT 57.082 40.909 0.00 0.00 0.00 3.36
1065 1132 2.261671 CGGTGAGGGTTCGGTGAG 59.738 66.667 0.00 0.00 0.00 3.51
1438 1506 1.197721 CACCTTAGTTCAAAGCTGCGG 59.802 52.381 0.00 0.00 0.00 5.69
1598 1679 6.747280 CACAAGCCTACAAAATATACTTGCAC 59.253 38.462 0.00 0.00 37.20 4.57
1623 1704 1.612950 TGTGAACATGCACCACAATCC 59.387 47.619 11.45 0.00 37.80 3.01
1624 1705 3.247442 CATGTGAACATGCACCACAATC 58.753 45.455 16.01 0.00 45.92 2.67
1625 1706 3.306917 CATGTGAACATGCACCACAAT 57.693 42.857 16.01 5.97 45.92 2.71
1626 1707 2.797074 CATGTGAACATGCACCACAA 57.203 45.000 16.01 4.36 45.92 3.33
1643 1724 5.047235 ACAAAGGAAGTTCTAGCTCGTACAT 60.047 40.000 2.25 0.00 0.00 2.29
1906 1989 6.281405 ACATTAGTACTAAGAAGGCAATCGG 58.719 40.000 19.58 2.09 0.00 4.18
2047 2130 1.941325 CGGAGATGGTTACTGGAAGC 58.059 55.000 0.00 0.00 37.60 3.86
2048 2131 1.482593 AGCGGAGATGGTTACTGGAAG 59.517 52.381 0.00 0.00 42.29 3.46
2049 2132 1.480954 GAGCGGAGATGGTTACTGGAA 59.519 52.381 0.00 0.00 0.00 3.53
2052 2135 2.688446 TGTAGAGCGGAGATGGTTACTG 59.312 50.000 0.00 0.00 0.00 2.74
2054 2137 3.795623 TTGTAGAGCGGAGATGGTTAC 57.204 47.619 0.00 0.00 0.00 2.50
2058 2141 6.096036 CACTATTATTGTAGAGCGGAGATGG 58.904 44.000 0.00 0.00 0.00 3.51
2059 2142 5.574830 GCACTATTATTGTAGAGCGGAGATG 59.425 44.000 0.00 0.00 30.68 2.90
2060 2143 5.478679 AGCACTATTATTGTAGAGCGGAGAT 59.521 40.000 0.00 0.00 41.33 2.75
2061 2144 4.827835 AGCACTATTATTGTAGAGCGGAGA 59.172 41.667 0.00 0.00 41.33 3.71
2062 2145 5.127693 AGCACTATTATTGTAGAGCGGAG 57.872 43.478 0.00 0.00 41.33 4.63
2063 2146 5.509163 GGAAGCACTATTATTGTAGAGCGGA 60.509 44.000 0.00 0.00 41.33 5.54
2064 2147 4.686554 GGAAGCACTATTATTGTAGAGCGG 59.313 45.833 0.00 0.00 41.33 5.52
2065 2148 5.289595 TGGAAGCACTATTATTGTAGAGCG 58.710 41.667 0.00 0.00 41.33 5.03
2066 2149 6.284459 ACTGGAAGCACTATTATTGTAGAGC 58.716 40.000 0.00 0.00 37.60 4.09
2067 2150 7.492524 TGACTGGAAGCACTATTATTGTAGAG 58.507 38.462 0.00 0.00 37.60 2.43
2068 2151 7.418337 TGACTGGAAGCACTATTATTGTAGA 57.582 36.000 0.00 0.00 37.60 2.59
2069 2152 7.172190 CCATGACTGGAAGCACTATTATTGTAG 59.828 40.741 0.00 0.00 46.37 2.74
2070 2153 6.992123 CCATGACTGGAAGCACTATTATTGTA 59.008 38.462 0.00 0.00 46.37 2.41
2071 2154 5.824624 CCATGACTGGAAGCACTATTATTGT 59.175 40.000 0.00 0.00 46.37 2.71
2072 2155 6.309712 CCATGACTGGAAGCACTATTATTG 57.690 41.667 0.00 0.00 46.37 1.90
2086 2169 1.420514 AGCCATCTGATCCATGACTGG 59.579 52.381 0.00 4.78 44.64 4.00
2170 2278 7.971183 TTCTAGTTACATTGCATTGTGTACA 57.029 32.000 21.45 0.00 31.05 2.90
2196 2304 8.182227 CGGGAAACTGATTAAAAGATAAAGACC 58.818 37.037 0.00 0.00 39.98 3.85



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

AutoCloner maintained by Alex Coulton.