Multiple sequence alignment - TraesCS6A01G274800

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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 TraesCS6A01G274800 chr6A 100.000 3948 0 0 1 3948 501502641 501498694 0.000000e+00 7291.0
1 TraesCS6A01G274800 chr6D 94.263 4009 133 39 1 3948 360344667 360340695 0.000000e+00 6039.0
2 TraesCS6A01G274800 chr6D 79.404 403 68 9 1954 2342 218423387 218422986 1.810000e-68 270.0
3 TraesCS6A01G274800 chr6B 94.914 2379 101 11 1582 3948 542012653 542010283 0.000000e+00 3705.0
4 TraesCS6A01G274800 chr6B 94.839 1085 23 9 226 1297 542015919 542014855 0.000000e+00 1663.0
5 TraesCS6A01G274800 chr6B 90.265 226 21 1 1 226 542016442 542016218 1.070000e-75 294.0
6 TraesCS6A01G274800 chr6B 78.824 425 71 12 1933 2342 343006142 343006562 6.500000e-68 268.0
7 TraesCS6A01G274800 chr6B 93.671 79 3 2 1289 1365 542013002 542012924 2.490000e-22 117.0
8 TraesCS6A01G274800 chr6B 86.047 86 7 1 1365 1445 542012737 542012652 1.950000e-13 87.9
9 TraesCS6A01G274800 chr6B 82.609 69 11 1 4 72 154305877 154305810 4.260000e-05 60.2
10 TraesCS6A01G274800 chr7D 79.675 492 87 10 1933 2415 559042831 559042344 3.780000e-90 342.0
11 TraesCS6A01G274800 chr7D 80.137 146 22 7 88 227 98619600 98619744 6.980000e-18 102.0
12 TraesCS6A01G274800 chr7D 88.462 78 8 1 4 80 99187324 99187247 4.200000e-15 93.5
13 TraesCS6A01G274800 chr1B 77.391 460 69 22 1945 2401 642404309 642403882 1.420000e-59 241.0
14 TraesCS6A01G274800 chr1B 87.129 101 10 3 1931 2029 595508842 595508743 1.160000e-20 111.0
15 TraesCS6A01G274800 chr1A 80.894 246 35 10 1935 2170 399468753 399468996 2.420000e-42 183.0
16 TraesCS6A01G274800 chr1A 89.720 107 8 2 1941 2044 377424299 377424405 2.480000e-27 134.0
17 TraesCS6A01G274800 chr1A 82.353 153 23 3 1933 2082 574810308 574810459 3.200000e-26 130.0
18 TraesCS6A01G274800 chr1A 92.857 56 4 0 148 203 23335384 23335329 9.090000e-12 82.4
19 TraesCS6A01G274800 chr5B 73.874 444 87 21 1981 2406 10096657 10097089 2.460000e-32 150.0
20 TraesCS6A01G274800 chr5B 81.522 92 14 3 109 198 696483557 696483467 5.470000e-09 73.1
21 TraesCS6A01G274800 chr4A 75.455 330 67 9 2090 2406 540478072 540477744 8.840000e-32 148.0
22 TraesCS6A01G274800 chr7A 77.064 218 43 5 2096 2309 707624645 707624431 6.930000e-23 119.0
23 TraesCS6A01G274800 chr7A 78.212 179 34 3 2096 2270 707622378 707622201 4.170000e-20 110.0
24 TraesCS6A01G274800 chr7A 76.471 204 36 8 2141 2339 55436543 55436739 2.510000e-17 100.0
25 TraesCS6A01G274800 chr2B 89.744 78 6 2 4 80 451958728 451958804 9.030000e-17 99.0
26 TraesCS6A01G274800 chr2B 80.460 87 17 0 117 203 209243428 209243514 2.550000e-07 67.6
27 TraesCS6A01G274800 chr2D 84.211 95 15 0 109 203 493168757 493168663 4.200000e-15 93.5
28 TraesCS6A01G274800 chr5A 85.542 83 10 2 122 203 594336458 594336377 7.030000e-13 86.1
29 TraesCS6A01G274800 chr3B 85.526 76 9 2 6 80 77694810 77694884 1.180000e-10 78.7
30 TraesCS6A01G274800 chr2A 85.000 80 8 4 133 211 767169662 767169586 1.180000e-10 78.7


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 TraesCS6A01G274800 chr6A 501498694 501502641 3947 True 7291.00 7291 100.0000 1 3948 1 chr6A.!!$R1 3947
1 TraesCS6A01G274800 chr6D 360340695 360344667 3972 True 6039.00 6039 94.2630 1 3948 1 chr6D.!!$R2 3947
2 TraesCS6A01G274800 chr6B 542010283 542016442 6159 True 1173.38 3705 91.9472 1 3948 5 chr6B.!!$R2 3947

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
118 119 0.039978 ATCGGCGTATTCTGAGAGCG 60.040 55.000 6.85 0.16 0.0 5.03 F
263 563 1.007842 GGGAGGAAGAGGGAAGAGACT 59.992 57.143 0.00 0.00 0.0 3.24 F
1575 3963 0.584396 GTCATGTGCCGTTCGTTTCA 59.416 50.000 0.00 0.00 0.0 2.69 F
1577 3965 0.586319 CATGTGCCGTTCGTTTCAGT 59.414 50.000 0.00 0.00 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1548 3936 1.742880 CGGCACATGACTGGTCTGG 60.743 63.158 0.0 0.0 0.00 3.86 R
1626 4022 3.580458 CCGATTAGAAGGGATCATCACCT 59.420 47.826 0.0 0.0 39.21 4.00 R
2645 5041 0.035056 AATCCGTCCTTGCCCTGAAG 60.035 55.000 0.0 0.0 0.00 3.02 R
3237 5645 1.194547 CGACTGATGTTGGTTTGGTCG 59.805 52.381 0.0 0.0 38.86 4.79 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
36 37 2.892425 CGATTGCGGCTCCAGGAC 60.892 66.667 0.00 0.00 0.00 3.85
70 71 1.209128 CACGTGCACGAAGACTTTCT 58.791 50.000 42.94 16.79 43.02 2.52
114 115 1.399572 CGACATCGGCGTATTCTGAG 58.600 55.000 6.85 0.00 35.37 3.35
115 116 1.002792 CGACATCGGCGTATTCTGAGA 60.003 52.381 6.85 0.00 35.37 3.27
118 119 0.039978 ATCGGCGTATTCTGAGAGCG 60.040 55.000 6.85 0.16 0.00 5.03
122 123 1.066605 GGCGTATTCTGAGAGCGGTAA 59.933 52.381 0.00 0.00 0.00 2.85
123 124 2.288273 GGCGTATTCTGAGAGCGGTAAT 60.288 50.000 0.00 0.00 0.00 1.89
131 132 2.363680 CTGAGAGCGGTAATGGTCATCT 59.636 50.000 0.00 0.00 38.81 2.90
204 205 9.809096 TTGCACTGTTGATGAACTTTTATAAAA 57.191 25.926 10.16 10.16 32.79 1.52
263 563 1.007842 GGGAGGAAGAGGGAAGAGACT 59.992 57.143 0.00 0.00 0.00 3.24
285 592 1.141053 ACGAAAGCACTCTTGGAAGGT 59.859 47.619 0.00 0.00 31.78 3.50
383 690 2.681706 CAGCTCGTGCCCATATTCTAG 58.318 52.381 5.73 0.00 40.80 2.43
501 820 3.518590 ACCGAATCTATCACAAACCGTC 58.481 45.455 0.00 0.00 0.00 4.79
502 821 2.534349 CCGAATCTATCACAAACCGTCG 59.466 50.000 0.00 0.00 0.00 5.12
503 822 3.176708 CGAATCTATCACAAACCGTCGT 58.823 45.455 0.00 0.00 0.00 4.34
505 824 4.794762 CGAATCTATCACAAACCGTCGTAA 59.205 41.667 0.00 0.00 0.00 3.18
506 825 5.275602 CGAATCTATCACAAACCGTCGTAAC 60.276 44.000 0.00 0.00 0.00 2.50
507 826 4.502171 TCTATCACAAACCGTCGTAACA 57.498 40.909 0.00 0.00 0.00 2.41
508 827 4.229096 TCTATCACAAACCGTCGTAACAC 58.771 43.478 0.00 0.00 0.00 3.32
566 885 3.894547 TTTCCACGAAGAGGCGCCC 62.895 63.158 26.15 15.34 38.46 6.13
1035 1354 2.673523 GTGGTGGAGCTGCTGGAT 59.326 61.111 7.01 0.00 0.00 3.41
1246 1565 4.510038 AGGTTCTAGAACTTTTCGCGTA 57.490 40.909 29.66 0.00 40.94 4.42
1295 1626 3.619929 GTGACTGGTTTGTCGTACTGTTT 59.380 43.478 0.00 0.00 39.64 2.83
1296 1627 4.805192 GTGACTGGTTTGTCGTACTGTTTA 59.195 41.667 0.00 0.00 39.64 2.01
1370 3753 1.190833 ATTGCGGCCCAACCATTCAA 61.191 50.000 8.59 0.00 39.03 2.69
1425 3813 8.885494 ATTAACAAGAGCTGTGATCTAGAATC 57.115 34.615 0.00 0.00 38.67 2.52
1445 3833 2.811431 TCACTTCTGTAACCGCCAAATG 59.189 45.455 0.00 0.00 0.00 2.32
1492 3880 8.779354 AAATGTTATGGTCTACTTCTCACTTC 57.221 34.615 0.00 0.00 0.00 3.01
1501 3889 6.127842 GGTCTACTTCTCACTTCCTCAGTAAG 60.128 46.154 0.00 0.00 32.76 2.34
1548 3936 8.201554 TCATATGTCTGATACAAGAAACTTGC 57.798 34.615 10.78 0.00 42.70 4.01
1575 3963 0.584396 GTCATGTGCCGTTCGTTTCA 59.416 50.000 0.00 0.00 0.00 2.69
1577 3965 0.586319 CATGTGCCGTTCGTTTCAGT 59.414 50.000 0.00 0.00 0.00 3.41
1641 4037 4.762289 AAGTGTAGGTGATGATCCCTTC 57.238 45.455 7.60 4.34 32.08 3.46
1749 4145 6.619874 GCAATGATTTGGAATGCTCACTTTTG 60.620 38.462 0.00 0.00 34.29 2.44
1787 4183 5.847111 ATGAATCATGGTGGTTTGAGATG 57.153 39.130 0.00 0.00 0.00 2.90
1904 4300 3.716353 TCCATATTAGTGTCCTGGCACAT 59.284 43.478 18.81 10.05 41.52 3.21
2013 4409 5.543405 TGGATTTGGTTCATGATTTTGACCT 59.457 36.000 13.37 0.00 0.00 3.85
2243 4639 5.688814 ACTTACCCACCTAAGTATTGGTC 57.311 43.478 0.00 0.00 35.57 4.02
2250 4646 5.070047 CCCACCTAAGTATTGGTCGATTAGT 59.930 44.000 0.00 0.00 33.75 2.24
2251 4647 5.983720 CCACCTAAGTATTGGTCGATTAGTG 59.016 44.000 0.00 0.00 33.75 2.74
2362 4758 7.985476 ACCAACTTTTATCTTTGTGATATCCG 58.015 34.615 0.00 0.00 37.48 4.18
2371 4767 5.301555 TCTTTGTGATATCCGAACAACACA 58.698 37.500 6.60 0.00 33.73 3.72
2457 4853 4.215613 GTGTTTGGAGTTAAGGGTGATGAC 59.784 45.833 0.00 0.00 0.00 3.06
2472 4868 5.652014 GGGTGATGACAATCCAAGTTATCAA 59.348 40.000 0.00 0.00 41.62 2.57
2487 4883 7.502226 CCAAGTTATCAATTAGGCTGGATGTTA 59.498 37.037 0.00 0.00 0.00 2.41
2499 4895 5.183140 AGGCTGGATGTTACAAACAACATAC 59.817 40.000 4.56 4.56 46.53 2.39
2534 4930 5.784578 TTCATATGTTAGCGAGGCTTAGA 57.215 39.130 1.90 0.00 40.44 2.10
2645 5041 5.046950 TGAAGAGCTTCTAAGAGAGGTTTCC 60.047 44.000 11.16 0.00 40.14 3.13
2855 5251 1.963338 GGCAGACACACAGGCAGAC 60.963 63.158 0.00 0.00 0.00 3.51
2880 5276 4.866508 AAAACAGCCCCTAAAGTTTAGC 57.133 40.909 15.95 7.11 33.45 3.09
2932 5328 4.193865 TGCACATACAAGATCATCACTGG 58.806 43.478 0.00 0.00 0.00 4.00
2935 5331 5.220739 GCACATACAAGATCATCACTGGTTC 60.221 44.000 0.00 0.00 0.00 3.62
2989 5385 5.728637 TGTTGACACTGACATAGTCTGAT 57.271 39.130 10.39 0.00 37.60 2.90
2998 5394 7.286546 ACACTGACATAGTCTGATAAGCTGTAT 59.713 37.037 10.39 0.00 37.60 2.29
3053 5452 1.960417 GGCCTGTTTATCTGCCTCTC 58.040 55.000 0.00 0.00 40.77 3.20
3156 5557 9.890629 TGCTCTTAAATATGACTGATACAACTT 57.109 29.630 0.00 0.00 0.00 2.66
3237 5645 8.454106 ACATACGTATTACTACCGATGGAATAC 58.546 37.037 5.03 0.00 32.21 1.89
3542 5950 2.395619 ACCTACAACGGGATAGAAGGG 58.604 52.381 0.00 0.00 0.00 3.95
3694 6102 1.599518 CAGCGGTGGGTACTTTGCA 60.600 57.895 6.74 0.00 0.00 4.08
3703 6111 1.202891 GGGTACTTTGCAGTGTCCCTT 60.203 52.381 14.95 0.00 41.53 3.95
3713 6121 1.548719 CAGTGTCCCTTCACGTCCATA 59.451 52.381 0.00 0.00 42.40 2.74
3723 6131 6.055588 CCCTTCACGTCCATAGATAAATTGT 58.944 40.000 0.00 0.00 0.00 2.71
3782 6190 7.093727 TGAGGAAGAGATAGTAGGAACAAACTG 60.094 40.741 0.00 0.00 0.00 3.16
3810 6218 4.956075 TCACTGAGCAATGATCTGTACCTA 59.044 41.667 10.51 0.00 29.74 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.033504 ACGTGCCACTAAGGACAGTG 59.966 55.000 0.00 0.00 44.60 3.66
48 49 2.916502 AAGTCTTCGTGCACGTGCCA 62.917 55.000 35.72 21.60 41.18 4.92
70 71 0.817654 CTCCTACCGCATGACAGTCA 59.182 55.000 5.50 5.50 0.00 3.41
107 108 2.766263 TGACCATTACCGCTCTCAGAAT 59.234 45.455 0.00 0.00 0.00 2.40
114 115 2.890808 TCAGATGACCATTACCGCTC 57.109 50.000 0.00 0.00 0.00 5.03
115 116 2.224378 CCATCAGATGACCATTACCGCT 60.224 50.000 12.41 0.00 0.00 5.52
118 119 4.101585 TGAGACCATCAGATGACCATTACC 59.898 45.833 12.41 0.00 32.77 2.85
122 123 4.849813 TTTGAGACCATCAGATGACCAT 57.150 40.909 12.41 0.00 39.68 3.55
123 124 4.042062 AGTTTTGAGACCATCAGATGACCA 59.958 41.667 12.41 1.51 39.68 4.02
204 205 8.413229 TCCATCTTTTCTTTTTCGAAAGATGTT 58.587 29.630 24.65 2.17 41.60 2.71
263 563 2.483876 CTTCCAAGAGTGCTTTCGTGA 58.516 47.619 5.76 0.00 30.14 4.35
285 592 5.242838 GTCCCAAATTGTGAGACATGGTTTA 59.757 40.000 0.00 0.00 26.65 2.01
383 690 2.375766 CCTGCAAGACGAGCACGAC 61.376 63.158 11.40 3.84 43.06 4.34
422 729 6.388619 AAGGTTTGGGAGAATAAAGCTCTA 57.611 37.500 0.00 0.00 41.99 2.43
492 811 0.875474 CGGGTGTTACGACGGTTTGT 60.875 55.000 0.00 0.00 0.00 2.83
501 820 3.560278 GGCGCATCGGGTGTTACG 61.560 66.667 10.83 0.00 0.00 3.18
502 821 3.199891 GGGCGCATCGGGTGTTAC 61.200 66.667 10.83 0.00 0.00 2.50
503 822 2.862674 GAAGGGCGCATCGGGTGTTA 62.863 60.000 10.83 0.00 0.00 2.41
505 824 4.778143 GAAGGGCGCATCGGGTGT 62.778 66.667 10.83 0.00 0.00 4.16
1370 3753 5.888724 AGATATACTCGATTGATCCGTGGAT 59.111 40.000 0.00 0.00 37.59 3.41
1425 3813 2.811431 TCATTTGGCGGTTACAGAAGTG 59.189 45.455 0.00 0.00 0.00 3.16
1492 3880 7.112779 AGTGTTTCCCATAAATCTTACTGAGG 58.887 38.462 0.00 0.00 0.00 3.86
1522 3910 8.834465 GCAAGTTTCTTGTATCAGACATATGAT 58.166 33.333 10.38 0.00 42.52 2.45
1528 3916 4.713553 TGGCAAGTTTCTTGTATCAGACA 58.286 39.130 10.49 0.00 35.78 3.41
1548 3936 1.742880 CGGCACATGACTGGTCTGG 60.743 63.158 0.00 0.00 0.00 3.86
1575 3963 6.798427 TGAGAGCTCCACATAAATCTTACT 57.202 37.500 10.93 0.00 0.00 2.24
1577 3965 7.554118 CCTTTTGAGAGCTCCACATAAATCTTA 59.446 37.037 10.93 0.00 0.00 2.10
1612 4008 6.183361 GGATCATCACCTACACTTAACTCCAT 60.183 42.308 0.00 0.00 0.00 3.41
1626 4022 3.580458 CCGATTAGAAGGGATCATCACCT 59.420 47.826 0.00 0.00 39.21 4.00
1631 4027 3.973973 TCCAACCGATTAGAAGGGATCAT 59.026 43.478 0.00 0.00 0.00 2.45
1641 4037 6.489127 TGTTTGTAACATCCAACCGATTAG 57.511 37.500 0.00 0.00 36.25 1.73
1787 4183 4.454728 TTTGATCACCAATAAAGGCTGC 57.545 40.909 0.00 0.00 34.23 5.25
1904 4300 5.368523 ACTCCCTCCGTTCCATAATTATTGA 59.631 40.000 0.00 0.00 0.00 2.57
1961 4357 4.202556 TGAACACCTCAATTGAATGGGAGA 60.203 41.667 16.81 0.78 0.00 3.71
2013 4409 3.672511 GCTCGTCGAGAAATAGTTGACCA 60.673 47.826 26.11 0.00 0.00 4.02
2063 4459 8.723311 ACCGTCGAAAAATAGTGAATCAAATAA 58.277 29.630 0.00 0.00 0.00 1.40
2064 4460 8.259049 ACCGTCGAAAAATAGTGAATCAAATA 57.741 30.769 0.00 0.00 0.00 1.40
2164 4560 4.100529 GCTACAATGTCACATGTTGATGC 58.899 43.478 0.00 0.00 36.32 3.91
2167 4563 4.388485 AGTGCTACAATGTCACATGTTGA 58.612 39.130 0.00 0.00 33.44 3.18
2243 4639 6.756542 TGTGATTCTGTGTTATCCACTAATCG 59.243 38.462 12.25 0.00 43.10 3.34
2250 4646 4.323417 GTGGTGTGATTCTGTGTTATCCA 58.677 43.478 0.00 0.00 0.00 3.41
2251 4647 3.689649 GGTGGTGTGATTCTGTGTTATCC 59.310 47.826 0.00 0.00 0.00 2.59
2308 4704 4.261801 CGTGGGGAAGATGATTAAGTGTT 58.738 43.478 0.00 0.00 0.00 3.32
2361 4757 2.425124 CGCCGCTTGTGTTGTTCG 60.425 61.111 0.00 0.00 0.00 3.95
2362 4758 2.725815 GCGCCGCTTGTGTTGTTC 60.726 61.111 0.00 0.00 0.00 3.18
2457 4853 6.547141 TCCAGCCTAATTGATAACTTGGATTG 59.453 38.462 0.00 0.00 0.00 2.67
2472 4868 5.772672 TGTTGTTTGTAACATCCAGCCTAAT 59.227 36.000 0.00 0.00 41.79 1.73
2645 5041 0.035056 AATCCGTCCTTGCCCTGAAG 60.035 55.000 0.00 0.00 0.00 3.02
2803 5199 7.549842 GGTCTTTCTTATCCTTTTGACTCCTAC 59.450 40.741 0.00 0.00 0.00 3.18
2909 5305 4.820173 CCAGTGATGATCTTGTATGTGCAT 59.180 41.667 0.00 0.00 0.00 3.96
2932 5328 3.553511 CAGAAGATCATACCTGTGCGAAC 59.446 47.826 0.00 0.00 0.00 3.95
2935 5331 1.863454 GCAGAAGATCATACCTGTGCG 59.137 52.381 0.00 0.00 0.00 5.34
3227 5635 2.623535 TGGTTTGGTCGTATTCCATCG 58.376 47.619 0.00 0.00 34.75 3.84
3237 5645 1.194547 CGACTGATGTTGGTTTGGTCG 59.805 52.381 0.00 0.00 38.86 4.79
3542 5950 1.959282 CCTAATGCTCAAGGGATTGCC 59.041 52.381 0.00 0.00 36.64 4.52
3568 5976 2.278332 AACTCTCTGAACCCTTTGGC 57.722 50.000 0.00 0.00 33.59 4.52
3609 6017 5.636903 AGCATATCTTGGGTATGTCACTT 57.363 39.130 0.00 0.00 33.19 3.16
3694 6102 1.825474 CTATGGACGTGAAGGGACACT 59.175 52.381 0.00 0.00 38.47 3.55
3703 6111 7.915293 AACAACAATTTATCTATGGACGTGA 57.085 32.000 0.00 0.00 0.00 4.35
3746 6154 4.581309 ATCTCTTCCTCAATTGCCTCAA 57.419 40.909 0.00 0.00 0.00 3.02
3747 6155 4.718774 ACTATCTCTTCCTCAATTGCCTCA 59.281 41.667 0.00 0.00 0.00 3.86
3757 6165 7.093684 ACAGTTTGTTCCTACTATCTCTTCCTC 60.094 40.741 0.00 0.00 0.00 3.71
3810 6218 3.202818 TGGACTACCCAGCATTCATGATT 59.797 43.478 0.00 0.00 40.82 2.57


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

AutoCloner maintained by Alex Coulton.