Multiple sequence alignment - TraesCS6D01G341600

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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 TraesCS6D01G341600 chr6D 100.000 3556 0 0 1 3556 440672614 440676169 0.000000e+00 6567.0
1 TraesCS6D01G341600 chr6D 93.599 1078 61 6 1651 2722 450189339 450188264 0.000000e+00 1602.0
2 TraesCS6D01G341600 chr6D 94.697 396 15 1 91 486 137153310 137152921 8.440000e-171 610.0
3 TraesCS6D01G341600 chr6D 89.247 465 24 4 810 1266 137148258 137147812 3.100000e-155 558.0
4 TraesCS6D01G341600 chr6D 95.000 40 2 0 3379 3418 13478547 13478586 2.960000e-06 63.9
5 TraesCS6D01G341600 chr2B 96.080 2245 63 12 488 2724 134341096 134343323 0.000000e+00 3635.0
6 TraesCS6D01G341600 chr2B 93.651 441 13 6 55 484 134340616 134341052 0.000000e+00 645.0
7 TraesCS6D01G341600 chr2B 95.181 249 12 0 2739 2987 134343472 134343720 9.250000e-106 394.0
8 TraesCS6D01G341600 chr4D 95.988 2243 75 10 488 2724 85853034 85850801 0.000000e+00 3629.0
9 TraesCS6D01G341600 chr4D 92.147 573 23 7 2993 3556 85850448 85849889 0.000000e+00 789.0
10 TraesCS6D01G341600 chr4D 95.277 487 19 2 1 486 85853559 85853076 0.000000e+00 769.0
11 TraesCS6D01G341600 chr4D 97.934 242 5 0 2746 2987 85850646 85850405 1.530000e-113 420.0
12 TraesCS6D01G341600 chr4D 94.898 98 3 2 1 96 85854235 85854138 6.150000e-33 152.0
13 TraesCS6D01G341600 chr2D 97.634 2029 44 2 1 2028 606092154 606090129 0.000000e+00 3478.0
14 TraesCS6D01G341600 chr2D 97.258 693 12 1 2871 3556 606090129 606089437 0.000000e+00 1168.0
15 TraesCS6D01G341600 chr2D 95.548 629 20 2 488 1115 29096983 29096362 0.000000e+00 1000.0
16 TraesCS6D01G341600 chr2D 94.921 571 21 2 2993 3556 29095006 29094437 0.000000e+00 887.0
17 TraesCS6D01G341600 chr2D 93.535 495 21 6 1 494 29097503 29097019 0.000000e+00 726.0
18 TraesCS6D01G341600 chr2D 96.787 249 8 0 2739 2987 29095211 29094963 1.970000e-112 416.0
19 TraesCS6D01G341600 chr5D 96.251 1814 49 9 488 2296 27280525 27282324 0.000000e+00 2955.0
20 TraesCS6D01G341600 chr5D 95.382 1386 55 6 1093 2473 431973345 431974726 0.000000e+00 2196.0
21 TraesCS6D01G341600 chr5D 93.468 1087 63 6 1642 2722 127940012 127938928 0.000000e+00 1607.0
22 TraesCS6D01G341600 chr5D 95.622 571 17 2 2993 3556 431988542 431989111 0.000000e+00 909.0
23 TraesCS6D01G341600 chr5D 95.447 571 19 1 2993 3556 27284837 27285407 0.000000e+00 904.0
24 TraesCS6D01G341600 chr5D 92.389 473 26 3 12 483 431972548 431973011 0.000000e+00 665.0
25 TraesCS6D01G341600 chr5D 90.631 491 14 7 1 486 27280023 27280486 1.080000e-174 623.0
26 TraesCS6D01G341600 chr5D 92.913 381 20 1 3008 3381 510554241 510554621 6.710000e-152 547.0
27 TraesCS6D01G341600 chr5D 95.349 301 5 2 488 788 431973056 431973347 1.490000e-128 470.0
28 TraesCS6D01G341600 chr5D 95.984 249 10 0 2739 2987 431988337 431988585 4.270000e-109 405.0
29 TraesCS6D01G341600 chr5D 95.582 249 11 0 2739 2987 27284632 27284880 1.990000e-107 399.0
30 TraesCS6D01G341600 chr4A 93.379 1450 57 11 488 1926 658381195 658382616 0.000000e+00 2109.0
31 TraesCS6D01G341600 chr6A 95.197 1166 52 2 722 1883 163168206 163167041 0.000000e+00 1840.0
32 TraesCS6D01G341600 chr6A 92.804 403 23 1 84 486 163168820 163168424 2.380000e-161 579.0
33 TraesCS6D01G341600 chr7D 93.738 1086 61 5 1642 2722 530740951 530739868 0.000000e+00 1622.0
34 TraesCS6D01G341600 chr7D 93.192 1087 66 6 1642 2722 340173622 340174706 0.000000e+00 1591.0
35 TraesCS6D01G341600 chr1D 92.916 1087 69 6 1642 2722 415596550 415597634 0.000000e+00 1574.0
36 TraesCS6D01G341600 chr7B 95.007 681 21 2 490 1164 228800394 228801067 0.000000e+00 1057.0
37 TraesCS6D01G341600 chr7B 94.320 581 16 3 2993 3556 228803084 228803664 0.000000e+00 874.0
38 TraesCS6D01G341600 chr7B 93.333 495 17 6 1 486 228799863 228800350 0.000000e+00 717.0
39 TraesCS6D01G341600 chr7B 94.862 253 9 1 2739 2987 228802875 228803127 3.330000e-105 392.0
40 TraesCS6D01G341600 chr7A 88.727 825 66 16 837 1650 617598489 617599297 0.000000e+00 983.0
41 TraesCS6D01G341600 chr7A 88.115 833 68 15 837 1653 41464795 41463978 0.000000e+00 961.0
42 TraesCS6D01G341600 chr7A 95.196 562 19 2 3002 3556 576791844 576791284 0.000000e+00 881.0
43 TraesCS6D01G341600 chr7A 94.746 571 21 3 2993 3556 658273181 658273749 0.000000e+00 880.0
44 TraesCS6D01G341600 chr7A 94.588 425 19 2 1 424 658271367 658271788 0.000000e+00 654.0
45 TraesCS6D01G341600 chr7A 95.565 248 10 1 2739 2986 658272976 658273222 2.570000e-106 396.0
46 TraesCS6D01G341600 chr7A 94.758 248 13 0 2739 2986 576792058 576791811 1.550000e-103 387.0
47 TraesCS6D01G341600 chr7A 92.857 210 5 3 523 732 658271801 658272000 2.680000e-76 296.0
48 TraesCS6D01G341600 chr7A 92.381 210 6 3 523 732 576793233 576793034 1.250000e-74 291.0
49 TraesCS6D01G341600 chr2A 88.485 825 68 15 837 1650 756524456 756525264 0.000000e+00 972.0
50 TraesCS6D01G341600 chr2A 94.746 571 22 2 2993 3556 764884020 764884589 0.000000e+00 881.0
51 TraesCS6D01G341600 chr2A 93.208 427 23 3 1 424 764882214 764882637 1.080000e-174 623.0
52 TraesCS6D01G341600 chr3B 95.582 249 11 0 2739 2987 60387606 60387854 1.990000e-107 399.0
53 TraesCS6D01G341600 chr3D 98.592 71 0 1 4 74 614101753 614101684 1.340000e-24 124.0


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 TraesCS6D01G341600 chr6D 440672614 440676169 3555 False 6567.000000 6567 100.000000 1 3556 1 chr6D.!!$F2 3555
1 TraesCS6D01G341600 chr6D 450188264 450189339 1075 True 1602.000000 1602 93.599000 1651 2722 1 chr6D.!!$R3 1071
2 TraesCS6D01G341600 chr2B 134340616 134343720 3104 False 1558.000000 3635 94.970667 55 2987 3 chr2B.!!$F1 2932
3 TraesCS6D01G341600 chr4D 85849889 85854235 4346 True 1151.800000 3629 95.248800 1 3556 5 chr4D.!!$R1 3555
4 TraesCS6D01G341600 chr2D 606089437 606092154 2717 True 2323.000000 3478 97.446000 1 3556 2 chr2D.!!$R2 3555
5 TraesCS6D01G341600 chr2D 29094437 29097503 3066 True 757.250000 1000 95.197750 1 3556 4 chr2D.!!$R1 3555
6 TraesCS6D01G341600 chr5D 127938928 127940012 1084 True 1607.000000 1607 93.468000 1642 2722 1 chr5D.!!$R1 1080
7 TraesCS6D01G341600 chr5D 27280023 27285407 5384 False 1220.250000 2955 94.477750 1 3556 4 chr5D.!!$F2 3555
8 TraesCS6D01G341600 chr5D 431972548 431974726 2178 False 1110.333333 2196 94.373333 12 2473 3 chr5D.!!$F3 2461
9 TraesCS6D01G341600 chr5D 431988337 431989111 774 False 657.000000 909 95.803000 2739 3556 2 chr5D.!!$F4 817
10 TraesCS6D01G341600 chr4A 658381195 658382616 1421 False 2109.000000 2109 93.379000 488 1926 1 chr4A.!!$F1 1438
11 TraesCS6D01G341600 chr6A 163167041 163168820 1779 True 1209.500000 1840 94.000500 84 1883 2 chr6A.!!$R1 1799
12 TraesCS6D01G341600 chr7D 530739868 530740951 1083 True 1622.000000 1622 93.738000 1642 2722 1 chr7D.!!$R1 1080
13 TraesCS6D01G341600 chr7D 340173622 340174706 1084 False 1591.000000 1591 93.192000 1642 2722 1 chr7D.!!$F1 1080
14 TraesCS6D01G341600 chr1D 415596550 415597634 1084 False 1574.000000 1574 92.916000 1642 2722 1 chr1D.!!$F1 1080
15 TraesCS6D01G341600 chr7B 228799863 228803664 3801 False 760.000000 1057 94.380500 1 3556 4 chr7B.!!$F1 3555
16 TraesCS6D01G341600 chr7A 617598489 617599297 808 False 983.000000 983 88.727000 837 1650 1 chr7A.!!$F1 813
17 TraesCS6D01G341600 chr7A 41463978 41464795 817 True 961.000000 961 88.115000 837 1653 1 chr7A.!!$R1 816
18 TraesCS6D01G341600 chr7A 658271367 658273749 2382 False 556.500000 880 94.439000 1 3556 4 chr7A.!!$F2 3555
19 TraesCS6D01G341600 chr7A 576791284 576793233 1949 True 519.666667 881 94.111667 523 3556 3 chr7A.!!$R2 3033
20 TraesCS6D01G341600 chr2A 756524456 756525264 808 False 972.000000 972 88.485000 837 1650 1 chr2A.!!$F1 813
21 TraesCS6D01G341600 chr2A 764882214 764884589 2375 False 752.000000 881 93.977000 1 3556 2 chr2A.!!$F2 3555

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
955 1715 1.152881 GGGCCGGAGCTTCAATGAT 60.153 57.895 5.05 0.0 39.73 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2593 5344 0.90961 TTGTCGGAGCCCTTGATCCT 60.91 55.0 0.0 0.0 45.19 3.24 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
113 800 2.973899 GCTCCTCCACTCTTCGCA 59.026 61.111 0.00 0.00 0.00 5.10
329 1021 4.227134 CGGAGCCGATGACCCTGG 62.227 72.222 2.00 0.00 42.83 4.45
547 1287 3.329889 TGGGCGTCCAAGAGGCAT 61.330 61.111 6.10 0.00 44.00 4.40
929 1689 4.935352 TTGCTTCCAATGCTTTGTTAGT 57.065 36.364 11.03 0.00 0.00 2.24
955 1715 1.152881 GGGCCGGAGCTTCAATGAT 60.153 57.895 5.05 0.00 39.73 2.45
1011 1779 1.611673 GCACTAGCCATGTCAACAGGT 60.612 52.381 0.00 0.00 33.58 4.00
1288 2117 3.071023 TGAAGATGAAACCGACCTCAACT 59.929 43.478 0.00 0.00 0.00 3.16
1315 2147 6.040166 GGTATGCAAGATTCTGATTTGGTCAT 59.960 38.462 0.00 0.00 35.97 3.06
1771 2614 6.485830 TTAGATGGAGGGAAGAACATACAG 57.514 41.667 0.00 0.00 0.00 2.74
1937 2783 3.244078 TGGTTGTTGTTCTGCGACTAGAT 60.244 43.478 0.00 0.00 32.64 1.98
2296 3310 6.542370 ACAATGAGCACCCACAAGTAATATAC 59.458 38.462 0.00 0.00 0.00 1.47
2343 5092 5.409826 GCCTACACAATGCTAGTAATCATCC 59.590 44.000 0.00 0.00 0.00 3.51
2410 5160 6.594788 ATGTTTCTTCACCTACATTTGCAT 57.405 33.333 0.00 0.00 0.00 3.96
2546 5297 1.478654 GGGGCTGTCAAGAACTCCAAA 60.479 52.381 0.00 0.00 0.00 3.28
2557 5308 2.489329 AGAACTCCAAATGGCATTGACG 59.511 45.455 14.47 5.57 34.44 4.35
2659 5410 1.153745 GCTCACGGAAGAGTGCGAT 60.154 57.895 0.00 0.00 41.88 4.58
2701 5452 5.964477 TCTGGGAGGAGTCATAAACAAGTAT 59.036 40.000 0.00 0.00 0.00 2.12
2724 5475 0.541998 TCTTCTTCCTCGTCCCAGCA 60.542 55.000 0.00 0.00 0.00 4.41
2725 5476 0.321671 CTTCTTCCTCGTCCCAGCAA 59.678 55.000 0.00 0.00 0.00 3.91
2727 5478 0.321671 TCTTCCTCGTCCCAGCAAAG 59.678 55.000 0.00 0.00 0.00 2.77
2728 5479 1.301677 CTTCCTCGTCCCAGCAAAGC 61.302 60.000 0.00 0.00 0.00 3.51
2729 5480 2.032528 CCTCGTCCCAGCAAAGCA 59.967 61.111 0.00 0.00 0.00 3.91
2730 5481 1.600636 CCTCGTCCCAGCAAAGCAA 60.601 57.895 0.00 0.00 0.00 3.91
2732 5483 0.239347 CTCGTCCCAGCAAAGCAAAG 59.761 55.000 0.00 0.00 0.00 2.77
2733 5484 0.465460 TCGTCCCAGCAAAGCAAAGT 60.465 50.000 0.00 0.00 0.00 2.66
2734 5485 1.202710 TCGTCCCAGCAAAGCAAAGTA 60.203 47.619 0.00 0.00 0.00 2.24
2735 5486 1.069227 CGTCCCAGCAAAGCAAAGTAC 60.069 52.381 0.00 0.00 0.00 2.73
2739 5490 2.557924 CCCAGCAAAGCAAAGTACATCA 59.442 45.455 0.00 0.00 0.00 3.07
2742 5493 4.093514 CAGCAAAGCAAAGTACATCATCG 58.906 43.478 0.00 0.00 0.00 3.84
2744 5495 4.093998 AGCAAAGCAAAGTACATCATCGAG 59.906 41.667 0.00 0.00 0.00 4.04
2929 5819 2.731571 GGGCGTGCTGATCCTACCA 61.732 63.158 0.00 0.00 0.00 3.25
2995 5885 1.456287 GGTGCAGAACCCCTCACTT 59.544 57.895 0.00 0.00 44.02 3.16
2999 5889 1.827399 GCAGAACCCCTCACTTCGGA 61.827 60.000 0.00 0.00 0.00 4.55
3078 5968 1.196012 GGAGAAGGTGAATCGGGAGT 58.804 55.000 0.00 0.00 0.00 3.85
3235 6127 6.183360 CCTGCTTTATATGAATTTCTTGCCCA 60.183 38.462 0.00 0.00 0.00 5.36
3382 6281 8.344831 GCATATGTTTGTACATTGCTGATCTAA 58.655 33.333 4.29 0.00 42.29 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 800 4.287766 AGGGCTCGAACAAGTTTTCTAT 57.712 40.909 0.00 0.00 0.00 1.98
547 1287 0.953471 CGTGATCCGGCAAGGTCAAA 60.953 55.000 0.00 0.00 41.99 2.69
587 1327 1.758514 GGCTCTCCACAGATCCGGA 60.759 63.158 6.61 6.61 0.00 5.14
874 1624 5.550290 TCAACAACTGCAGAATCAGTCATA 58.450 37.500 23.35 0.00 45.77 2.15
929 1689 0.623723 AAGCTCCGGCCCTTATCAAA 59.376 50.000 0.00 0.00 39.73 2.69
955 1715 4.442052 GCTGTGTGCTGGATAGTAGATTCA 60.442 45.833 0.00 0.00 38.95 2.57
1011 1779 3.094062 GCGAGCATGCCCCTGAGTA 62.094 63.158 15.66 0.00 0.00 2.59
1171 2000 3.295973 GCTTGATAGACTCCCTCTCTGT 58.704 50.000 0.00 0.00 0.00 3.41
1288 2117 5.716228 ACCAAATCAGAATCTTGCATACCAA 59.284 36.000 0.00 0.00 0.00 3.67
1400 2232 4.156922 ACAGTGAGGTTCAGATCTACTTCG 59.843 45.833 0.00 0.00 0.00 3.79
1771 2614 5.972107 ATGTGCAGAATAAAGGGATATGC 57.028 39.130 0.00 0.00 0.00 3.14
1937 2783 4.906747 AAATTTAAAGCTGGATGGCCAA 57.093 36.364 10.96 0.00 45.41 4.52
2296 3310 6.320171 GCATGCTTGTATATATTTGGCAGAG 58.680 40.000 11.37 0.00 0.00 3.35
2343 5092 1.382522 ATGGCGCCATTCTACACAAG 58.617 50.000 36.10 0.00 31.82 3.16
2410 5160 7.012704 GGCAAGAAGACAATAATTGCTCATCTA 59.987 37.037 7.98 0.00 44.33 1.98
2499 5250 2.151502 TCTCTGATGGAGACCACCTC 57.848 55.000 0.00 0.00 45.20 3.85
2593 5344 0.909610 TTGTCGGAGCCCTTGATCCT 60.910 55.000 0.00 0.00 45.19 3.24
2659 5410 4.783621 GCTGCCGGGATGAGCACA 62.784 66.667 2.18 0.00 34.68 4.57
2701 5452 2.563179 CTGGGACGAGGAAGAAGAAGAA 59.437 50.000 0.00 0.00 0.00 2.52
2724 5475 3.375299 GCCTCGATGATGTACTTTGCTTT 59.625 43.478 0.00 0.00 0.00 3.51
2725 5476 2.939103 GCCTCGATGATGTACTTTGCTT 59.061 45.455 0.00 0.00 0.00 3.91
2727 5478 2.279741 TGCCTCGATGATGTACTTTGC 58.720 47.619 0.00 0.00 0.00 3.68
2728 5479 4.393062 ACTTTGCCTCGATGATGTACTTTG 59.607 41.667 0.00 0.00 0.00 2.77
2729 5480 4.579869 ACTTTGCCTCGATGATGTACTTT 58.420 39.130 0.00 0.00 0.00 2.66
2730 5481 4.207891 ACTTTGCCTCGATGATGTACTT 57.792 40.909 0.00 0.00 0.00 2.24
2732 5483 4.430007 TGTACTTTGCCTCGATGATGTAC 58.570 43.478 0.00 0.00 0.00 2.90
2733 5484 4.729227 TGTACTTTGCCTCGATGATGTA 57.271 40.909 0.00 0.00 0.00 2.29
2734 5485 3.610040 TGTACTTTGCCTCGATGATGT 57.390 42.857 0.00 0.00 0.00 3.06
2735 5486 4.122046 TGATGTACTTTGCCTCGATGATG 58.878 43.478 0.00 0.00 0.00 3.07
2739 5490 3.068165 TCGATGATGTACTTTGCCTCGAT 59.932 43.478 0.00 0.00 0.00 3.59
2742 5493 3.126831 CCTCGATGATGTACTTTGCCTC 58.873 50.000 0.00 0.00 0.00 4.70
2744 5495 1.599542 GCCTCGATGATGTACTTTGCC 59.400 52.381 0.00 0.00 0.00 4.52
2929 5819 1.115467 CGGAGTTGGCTAGGATGTCT 58.885 55.000 0.00 0.00 0.00 3.41
2995 5885 1.323271 GCTCACCATCACTCCTCCGA 61.323 60.000 0.00 0.00 0.00 4.55
2999 5889 2.541233 AGTAGCTCACCATCACTCCT 57.459 50.000 0.00 0.00 0.00 3.69
3078 5968 1.670674 GCGGGTCATGTACGTCTTGAA 60.671 52.381 0.00 0.00 33.16 2.69


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

AutoCloner maintained by Alex Coulton.