Multiple sequence alignment - TraesCS6A01G025300

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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 TraesCS6A01G025300 chr6A 100.000 4011 0 0 1 4011 12471903 12475913 0.000000e+00 7408.0
1 TraesCS6A01G025300 chr6A 75.915 656 119 25 1027 1658 13734034 13734674 2.340000e-77 300.0
2 TraesCS6A01G025300 chr6D 97.254 3168 64 9 864 4011 11257976 11261140 0.000000e+00 5347.0
3 TraesCS6A01G025300 chr6D 76.061 660 114 24 1027 1658 12358140 12358783 1.810000e-78 303.0
4 TraesCS6A01G025300 chr6B 95.776 1823 44 7 2202 4011 21133510 21135312 0.000000e+00 2909.0
5 TraesCS6A01G025300 chr6B 93.602 1313 74 6 864 2173 21131935 21133240 0.000000e+00 1951.0
6 TraesCS6A01G025300 chr7A 81.902 978 151 21 1201 2173 31727449 31728405 0.000000e+00 802.0
7 TraesCS6A01G025300 chr7A 89.655 145 12 3 2174 2317 31712451 31712593 8.860000e-42 182.0
8 TraesCS6A01G025300 chr7A 88.966 145 12 4 2175 2317 31717814 31717956 4.120000e-40 176.0
9 TraesCS6A01G025300 chr7A 88.276 145 13 4 2175 2317 31729253 31729395 1.920000e-38 171.0
10 TraesCS6A01G025300 chr7A 88.276 145 13 4 2175 2317 31732113 31732255 1.920000e-38 171.0
11 TraesCS6A01G025300 chr7A 87.770 139 13 4 2181 2317 31720676 31720812 4.150000e-35 159.0
12 TraesCS6A01G025300 chr7D 83.130 901 128 19 1280 2173 31143787 31144670 0.000000e+00 800.0
13 TraesCS6A01G025300 chr7D 84.636 729 101 8 1448 2173 31147506 31148226 0.000000e+00 715.0
14 TraesCS6A01G025300 chr7D 89.404 151 11 4 2175 2323 31155306 31155453 6.850000e-43 185.0
15 TraesCS6A01G025300 chrUn 82.851 898 133 17 1280 2173 90556374 90555494 0.000000e+00 785.0
16 TraesCS6A01G025300 chrUn 82.686 901 132 19 1280 2173 90558791 90557908 0.000000e+00 778.0
17 TraesCS6A01G025300 chrUn 82.405 898 129 22 1284 2173 90539095 90538219 0.000000e+00 756.0
18 TraesCS6A01G025300 chrUn 84.499 729 102 8 1448 2173 90555072 90554352 0.000000e+00 710.0
19 TraesCS6A01G025300 chrUn 88.304 513 49 10 2 508 235931121 235931628 4.430000e-169 604.0
20 TraesCS6A01G025300 chrUn 85.030 501 47 15 2 495 135304478 135304957 6.030000e-133 484.0
21 TraesCS6A01G025300 chrUn 88.742 151 12 4 2175 2323 90529707 90529560 3.180000e-41 180.0
22 TraesCS6A01G025300 chr5D 91.440 514 37 6 2 508 104825453 104824940 0.000000e+00 699.0
23 TraesCS6A01G025300 chr5D 90.964 498 37 7 3 495 104560822 104561316 0.000000e+00 664.0
24 TraesCS6A01G025300 chr5D 88.330 497 38 14 375 857 104561290 104561780 2.690000e-161 579.0
25 TraesCS6A01G025300 chr7B 88.716 514 48 9 2 508 206623916 206623406 1.580000e-173 619.0
26 TraesCS6A01G025300 chr7B 79.183 514 79 22 262 761 485077651 485077152 8.310000e-87 331.0
27 TraesCS6A01G025300 chr2B 88.694 513 48 8 2 508 654506972 654507480 5.700000e-173 617.0
28 TraesCS6A01G025300 chr2B 88.304 513 49 10 2 508 654477717 654478224 4.430000e-169 604.0
29 TraesCS6A01G025300 chr2B 81.672 311 44 13 375 677 249219957 249219652 3.100000e-61 246.0
30 TraesCS6A01G025300 chr2B 100.000 28 0 0 573 600 587413393 587413366 7.000000e-03 52.8
31 TraesCS6A01G025300 chr1D 90.329 486 24 13 375 857 467367782 467368247 2.050000e-172 616.0
32 TraesCS6A01G025300 chr1D 79.691 517 68 20 246 734 74288556 74288049 4.970000e-89 339.0
33 TraesCS6A01G025300 chr3B 87.990 408 42 6 5 407 473254437 473254032 3.630000e-130 475.0
34 TraesCS6A01G025300 chr3B 87.685 406 42 7 5 404 810777880 810778283 2.180000e-127 466.0
35 TraesCS6A01G025300 chr2D 81.613 310 48 8 375 678 628185943 628185637 8.610000e-62 248.0
36 TraesCS6A01G025300 chr2A 82.222 270 48 0 1027 1296 348246400 348246131 2.410000e-57 233.0


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 TraesCS6A01G025300 chr6A 12471903 12475913 4010 False 7408.000000 7408 100.000000 1 4011 1 chr6A.!!$F1 4010
1 TraesCS6A01G025300 chr6A 13734034 13734674 640 False 300.000000 300 75.915000 1027 1658 1 chr6A.!!$F2 631
2 TraesCS6A01G025300 chr6D 11257976 11261140 3164 False 5347.000000 5347 97.254000 864 4011 1 chr6D.!!$F1 3147
3 TraesCS6A01G025300 chr6D 12358140 12358783 643 False 303.000000 303 76.061000 1027 1658 1 chr6D.!!$F2 631
4 TraesCS6A01G025300 chr6B 21131935 21135312 3377 False 2430.000000 2909 94.689000 864 4011 2 chr6B.!!$F1 3147
5 TraesCS6A01G025300 chr7A 31727449 31732255 4806 False 381.333333 802 86.151333 1201 2317 3 chr7A.!!$F3 1116
6 TraesCS6A01G025300 chr7D 31143787 31148226 4439 False 757.500000 800 83.883000 1280 2173 2 chr7D.!!$F2 893
7 TraesCS6A01G025300 chrUn 90554352 90558791 4439 True 757.666667 785 83.345333 1280 2173 3 chrUn.!!$R3 893
8 TraesCS6A01G025300 chrUn 90538219 90539095 876 True 756.000000 756 82.405000 1284 2173 1 chrUn.!!$R2 889
9 TraesCS6A01G025300 chrUn 235931121 235931628 507 False 604.000000 604 88.304000 2 508 1 chrUn.!!$F2 506
10 TraesCS6A01G025300 chr5D 104824940 104825453 513 True 699.000000 699 91.440000 2 508 1 chr5D.!!$R1 506
11 TraesCS6A01G025300 chr5D 104560822 104561780 958 False 621.500000 664 89.647000 3 857 2 chr5D.!!$F1 854
12 TraesCS6A01G025300 chr7B 206623406 206623916 510 True 619.000000 619 88.716000 2 508 1 chr7B.!!$R1 506
13 TraesCS6A01G025300 chr2B 654506972 654507480 508 False 617.000000 617 88.694000 2 508 1 chr2B.!!$F2 506
14 TraesCS6A01G025300 chr2B 654477717 654478224 507 False 604.000000 604 88.304000 2 508 1 chr2B.!!$F1 506
15 TraesCS6A01G025300 chr1D 74288049 74288556 507 True 339.000000 339 79.691000 246 734 1 chr1D.!!$R1 488

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
928 1077 1.856259 TGGAGCCCAGCCCATTTATTA 59.144 47.619 0.0 0.0 0.00 0.98 F
1016 1166 0.459237 CACATGACTCACGAGGGCTC 60.459 60.000 0.0 0.0 0.00 4.70 F
2022 4624 2.178106 AGTAGGGTACTCTGAGGATGGG 59.822 54.545 5.2 0.0 32.47 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2022 4624 2.349886 CACTGTTAGAAGAAGCGCATCC 59.650 50.000 11.47 0.0 0.00 3.51 R
2148 4753 6.724893 TTACCTGCAGTATAGAAGTATGCA 57.275 37.500 13.81 0.0 44.10 3.96 R
3173 10178 1.864711 GCTGACAAAGTGACAACGCTA 59.135 47.619 0.00 0.0 35.69 4.26 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
58 60 3.830178 TCGGAGTATTTTCTGAGACCACA 59.170 43.478 0.00 0.00 0.00 4.17
70 73 7.639113 TTCTGAGACCACAAACAGTTTTAAT 57.361 32.000 0.00 0.00 0.00 1.40
132 138 8.363029 GTTCAGAACAAAAACGTTTAAACAGAG 58.637 33.333 15.03 4.82 0.00 3.35
179 187 7.969536 TTTGAAACATGACCTTTGTTCAAAA 57.030 28.000 0.00 0.32 36.32 2.44
209 217 4.491234 AAATGTTGAAACCGCGAACATA 57.509 36.364 19.46 0.00 38.96 2.29
243 252 6.956202 TGAACAAATTTTGAATTGCCCAAT 57.044 29.167 15.81 0.00 0.00 3.16
333 345 4.228912 ACAGAGAACAAATTTGGAAGCG 57.771 40.909 21.74 8.34 0.00 4.68
335 347 2.622942 AGAGAACAAATTTGGAAGCGCA 59.377 40.909 21.74 0.00 0.00 6.09
390 422 2.955660 ACGGAGAACAAATTTGGAAGCA 59.044 40.909 21.74 0.00 0.00 3.91
542 675 4.433186 TCCGGTACATTTTCTGCATTTG 57.567 40.909 0.00 0.00 0.00 2.32
668 803 9.856488 AAAAGAGAAGAAACTAAAAGGACAAAC 57.144 29.630 0.00 0.00 0.00 2.93
708 843 8.980143 AGAAAGAAAACAAACAGAAAAATCGA 57.020 26.923 0.00 0.00 0.00 3.59
709 844 9.418045 AGAAAGAAAACAAACAGAAAAATCGAA 57.582 25.926 0.00 0.00 0.00 3.71
808 956 7.634671 ACTAGAAACGAAAGGAAAGGAAAAA 57.365 32.000 0.00 0.00 0.00 1.94
833 981 9.454859 AAGAGAAACAGAAAAAGAAGAAGAAGA 57.545 29.630 0.00 0.00 0.00 2.87
834 982 9.454859 AGAGAAACAGAAAAAGAAGAAGAAGAA 57.545 29.630 0.00 0.00 0.00 2.52
837 985 9.295214 GAAACAGAAAAAGAAGAAGAAGAAAGG 57.705 33.333 0.00 0.00 0.00 3.11
838 986 8.581253 AACAGAAAAAGAAGAAGAAGAAAGGA 57.419 30.769 0.00 0.00 0.00 3.36
849 997 9.509855 GAAGAAGAAGAAAGGAAAAAGAGAAAC 57.490 33.333 0.00 0.00 0.00 2.78
850 998 8.581253 AGAAGAAGAAAGGAAAAAGAGAAACA 57.419 30.769 0.00 0.00 0.00 2.83
857 1005 9.645059 AGAAAGGAAAAAGAGAAACAGAAAAAG 57.355 29.630 0.00 0.00 0.00 2.27
858 1006 9.639601 GAAAGGAAAAAGAGAAACAGAAAAAGA 57.360 29.630 0.00 0.00 0.00 2.52
859 1007 9.996554 AAAGGAAAAAGAGAAACAGAAAAAGAA 57.003 25.926 0.00 0.00 0.00 2.52
860 1008 9.996554 AAGGAAAAAGAGAAACAGAAAAAGAAA 57.003 25.926 0.00 0.00 0.00 2.52
861 1009 9.996554 AGGAAAAAGAGAAACAGAAAAAGAAAA 57.003 25.926 0.00 0.00 0.00 2.29
865 1013 9.981114 AAAAGAGAAACAGAAAAAGAAAACTCA 57.019 25.926 0.00 0.00 0.00 3.41
866 1014 8.972262 AAGAGAAACAGAAAAAGAAAACTCAC 57.028 30.769 0.00 0.00 0.00 3.51
867 1015 8.341892 AGAGAAACAGAAAAAGAAAACTCACT 57.658 30.769 0.00 0.00 0.00 3.41
868 1016 8.239998 AGAGAAACAGAAAAAGAAAACTCACTG 58.760 33.333 0.00 0.00 0.00 3.66
869 1017 6.808704 AGAAACAGAAAAAGAAAACTCACTGC 59.191 34.615 0.00 0.00 0.00 4.40
873 1021 3.443099 AAAAGAAAACTCACTGCTGGC 57.557 42.857 0.00 0.00 0.00 4.85
909 1057 3.136763 TGAGTGAGCTTGCTTTTCTCTG 58.863 45.455 16.52 0.00 0.00 3.35
928 1077 1.856259 TGGAGCCCAGCCCATTTATTA 59.144 47.619 0.00 0.00 0.00 0.98
1004 1154 2.030274 CCGTTTCTTTTCCCCACATGAC 60.030 50.000 0.00 0.00 0.00 3.06
1015 1165 1.593787 CACATGACTCACGAGGGCT 59.406 57.895 0.00 0.00 0.00 5.19
1016 1166 0.459237 CACATGACTCACGAGGGCTC 60.459 60.000 0.00 0.00 0.00 4.70
1173 1326 3.844090 GTCTCGAGGCTCTGGGGC 61.844 72.222 10.47 3.96 41.20 5.80
1635 1817 2.335092 TAGCCCGGGTCTACTCCTCG 62.335 65.000 24.63 0.00 0.00 4.63
2022 4624 2.178106 AGTAGGGTACTCTGAGGATGGG 59.822 54.545 5.20 0.00 32.47 4.00
2148 4753 4.035112 TGGAGTATTCCTACCATCCGTTT 58.965 43.478 5.79 0.00 44.36 3.60
2608 9613 3.062042 GCAGCTTCCAAAGGTTCAAATG 58.938 45.455 0.00 0.00 37.06 2.32
2699 9704 9.773328 CTGCGATCTTATTTGAAAAGAATGTTA 57.227 29.630 0.00 0.00 36.60 2.41
2809 9814 2.119495 ACCTAATCTTGGCGGAGTGAT 58.881 47.619 0.00 0.00 0.00 3.06
2998 10003 0.458889 CAATTCCAGCCATTGTGCCG 60.459 55.000 0.00 0.00 0.00 5.69
3000 10005 4.657408 TCCAGCCATTGTGCCGCA 62.657 61.111 0.00 0.00 0.00 5.69
3137 10142 4.401022 TGGTGCAATGAGATGAAAGACTT 58.599 39.130 0.00 0.00 0.00 3.01
3138 10143 5.559770 TGGTGCAATGAGATGAAAGACTTA 58.440 37.500 0.00 0.00 0.00 2.24
3173 10178 3.430651 CCCTGTGTTTTGCTGTGTGAAAT 60.431 43.478 0.00 0.00 0.00 2.17
3556 10575 6.436218 TCTTAGGTCAATAACTACTGTGCTGA 59.564 38.462 0.00 0.00 0.00 4.26
3950 11139 4.707105 TCATCGACTGTACCGGATTAGTA 58.293 43.478 9.46 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 43 6.619801 ACTGTTTGTGGTCTCAGAAAATAC 57.380 37.500 0.00 0.00 37.78 1.89
147 155 7.605691 ACAAAGGTCATGTTTCAAATTTGTTCA 59.394 29.630 17.47 14.33 36.51 3.18
179 187 5.389307 CGCGGTTTCAACATTTTATTTGCAT 60.389 36.000 0.00 0.00 0.00 3.96
257 268 9.995003 ATGTTCTTGCTTTATAAAATTGTCCAA 57.005 25.926 0.00 0.00 0.00 3.53
294 305 9.736023 GTTCTCTGTTTCAAAATTTGTACTCAT 57.264 29.630 5.56 0.00 0.00 2.90
780 923 8.735692 TTCCTTTCCTTTCGTTTCTAGTTTTA 57.264 30.769 0.00 0.00 0.00 1.52
792 935 6.560711 TGTTTCTCTTTTTCCTTTCCTTTCG 58.439 36.000 0.00 0.00 0.00 3.46
808 956 9.454859 TTCTTCTTCTTCTTTTTCTGTTTCTCT 57.545 29.630 0.00 0.00 0.00 3.10
832 980 9.639601 TCTTTTTCTGTTTCTCTTTTTCCTTTC 57.360 29.630 0.00 0.00 0.00 2.62
833 981 9.996554 TTCTTTTTCTGTTTCTCTTTTTCCTTT 57.003 25.926 0.00 0.00 0.00 3.11
834 982 9.996554 TTTCTTTTTCTGTTTCTCTTTTTCCTT 57.003 25.926 0.00 0.00 0.00 3.36
835 983 9.996554 TTTTCTTTTTCTGTTTCTCTTTTTCCT 57.003 25.926 0.00 0.00 0.00 3.36
843 991 7.008719 GCAGTGAGTTTTCTTTTTCTGTTTCTC 59.991 37.037 0.00 0.00 0.00 2.87
849 997 5.039333 CCAGCAGTGAGTTTTCTTTTTCTG 58.961 41.667 0.00 0.00 0.00 3.02
850 998 4.440663 GCCAGCAGTGAGTTTTCTTTTTCT 60.441 41.667 0.00 0.00 0.00 2.52
857 1005 1.856265 CGGGCCAGCAGTGAGTTTTC 61.856 60.000 4.39 0.00 0.00 2.29
858 1006 1.898574 CGGGCCAGCAGTGAGTTTT 60.899 57.895 4.39 0.00 0.00 2.43
859 1007 1.764571 TACGGGCCAGCAGTGAGTTT 61.765 55.000 4.39 0.00 0.00 2.66
860 1008 1.764571 TTACGGGCCAGCAGTGAGTT 61.765 55.000 4.39 0.00 0.00 3.01
861 1009 1.553690 ATTACGGGCCAGCAGTGAGT 61.554 55.000 4.39 0.00 0.00 3.41
862 1010 0.811616 GATTACGGGCCAGCAGTGAG 60.812 60.000 4.39 0.00 0.00 3.51
863 1011 1.220749 GATTACGGGCCAGCAGTGA 59.779 57.895 4.39 0.00 0.00 3.41
864 1012 1.819632 GGATTACGGGCCAGCAGTG 60.820 63.158 4.39 0.00 0.00 3.66
865 1013 1.847798 TTGGATTACGGGCCAGCAGT 61.848 55.000 4.39 0.79 35.23 4.40
866 1014 1.077787 TTGGATTACGGGCCAGCAG 60.078 57.895 4.39 0.00 35.23 4.24
867 1015 1.077787 CTTGGATTACGGGCCAGCA 60.078 57.895 4.39 0.00 35.23 4.41
868 1016 1.823899 CCTTGGATTACGGGCCAGC 60.824 63.158 4.39 0.00 35.23 4.85
869 1017 0.474184 ATCCTTGGATTACGGGCCAG 59.526 55.000 4.39 1.85 35.23 4.85
873 1021 2.434336 TCACTCATCCTTGGATTACGGG 59.566 50.000 0.00 0.00 0.00 5.28
909 1057 2.158460 AGTAATAAATGGGCTGGGCTCC 60.158 50.000 0.00 0.00 0.00 4.70
928 1077 2.168728 GGAGGATGCGTAAGAAGGAAGT 59.831 50.000 0.00 0.00 43.02 3.01
1397 1573 2.771762 GGAGCAGGGCCAGATCCT 60.772 66.667 24.31 0.00 38.50 3.24
1635 1817 4.016706 CCCCACTCACCGGTGTCC 62.017 72.222 32.74 0.00 35.63 4.02
2022 4624 2.349886 CACTGTTAGAAGAAGCGCATCC 59.650 50.000 11.47 0.00 0.00 3.51
2148 4753 6.724893 TTACCTGCAGTATAGAAGTATGCA 57.275 37.500 13.81 0.00 44.10 3.96
2291 8665 7.972301 AGGATAAGAACAGATGGGAAATCTAG 58.028 38.462 0.00 0.00 0.00 2.43
2635 9640 6.833416 CCAAAATCACCAGATTCCCAAGTATA 59.167 38.462 0.00 0.00 43.52 1.47
2676 9681 9.755064 ACGTAACATTCTTTTCAAATAAGATCG 57.245 29.630 0.00 0.00 32.09 3.69
3173 10178 1.864711 GCTGACAAAGTGACAACGCTA 59.135 47.619 0.00 0.00 35.69 4.26
3432 10451 2.530151 TTGCACCCTCAGCCCTCT 60.530 61.111 0.00 0.00 0.00 3.69
3950 11139 3.418684 AACCTAATTCTGTGCCTCGTT 57.581 42.857 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.