Multiple sequence alignment - TraesCS5A01G065800

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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 TraesCS5A01G065800 chr5A 100.000 3660 0 0 1 3660 72230714 72227055 0.000000e+00 6759.0
1 TraesCS5A01G065800 chr5A 95.360 2823 102 6 788 3609 72331806 72329012 0.000000e+00 4460.0
2 TraesCS5A01G065800 chr5A 96.321 2066 65 6 1598 3660 72388939 72386882 0.000000e+00 3384.0
3 TraesCS5A01G065800 chr5A 95.732 1476 53 4 104 1570 72390410 72388936 0.000000e+00 2368.0
4 TraesCS5A01G065800 chr5A 92.496 693 37 7 3 681 72332500 72331809 0.000000e+00 977.0
5 TraesCS5A01G065800 chr5A 92.562 484 23 6 210 681 72260589 72260107 0.000000e+00 682.0
6 TraesCS5A01G065800 chr5A 92.920 339 16 2 797 1127 72260095 72259757 1.530000e-133 486.0
7 TraesCS5A01G065800 chr5A 92.000 175 13 1 1 174 72260768 72260594 1.020000e-60 244.0
8 TraesCS5A01G065800 chr5A 82.222 180 29 3 2 178 338255125 338255304 6.330000e-33 152.0
9 TraesCS5A01G065800 chr5D 92.811 3533 161 37 178 3660 76692058 76688569 0.000000e+00 5031.0
10 TraesCS5A01G065800 chr5D 92.893 3419 157 37 178 3556 76756283 76752911 0.000000e+00 4889.0
11 TraesCS5A01G065800 chr5D 77.660 282 32 17 763 1018 459581952 459582228 3.810000e-30 143.0
12 TraesCS5A01G065800 chr5B 92.359 3481 188 36 205 3643 85178693 85182137 0.000000e+00 4883.0
13 TraesCS5A01G065800 chr5B 92.026 3524 188 36 179 3660 85116574 85120046 0.000000e+00 4865.0
14 TraesCS5A01G065800 chr5B 80.899 178 28 3 2 178 690713014 690713186 6.380000e-28 135.0
15 TraesCS5A01G065800 chr5B 91.667 72 4 2 2939 3010 386655716 386655785 8.360000e-17 99.0
16 TraesCS5A01G065800 chr4D 83.146 178 25 3 2 178 14422679 14422852 1.360000e-34 158.0
17 TraesCS5A01G065800 chr4B 83.146 178 24 2 2 178 51007673 51007845 1.360000e-34 158.0
18 TraesCS5A01G065800 chr7A 81.667 180 27 5 2 178 540196654 540196478 1.060000e-30 145.0
19 TraesCS5A01G065800 chr6A 81.564 179 28 4 2 178 27303027 27302852 3.810000e-30 143.0
20 TraesCS5A01G065800 chr1A 83.660 153 21 3 2 152 68368249 68368099 1.370000e-29 141.0
21 TraesCS5A01G065800 chr7D 96.721 61 2 0 2946 3006 576283709 576283649 6.470000e-18 102.0
22 TraesCS5A01G065800 chr7D 91.429 70 6 0 2937 3006 463883623 463883554 3.010000e-16 97.1


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 TraesCS5A01G065800 chr5A 72227055 72230714 3659 True 6759.000000 6759 100.0000 1 3660 1 chr5A.!!$R1 3659
1 TraesCS5A01G065800 chr5A 72386882 72390410 3528 True 2876.000000 3384 96.0265 104 3660 2 chr5A.!!$R4 3556
2 TraesCS5A01G065800 chr5A 72329012 72332500 3488 True 2718.500000 4460 93.9280 3 3609 2 chr5A.!!$R3 3606
3 TraesCS5A01G065800 chr5A 72259757 72260768 1011 True 470.666667 682 92.4940 1 1127 3 chr5A.!!$R2 1126
4 TraesCS5A01G065800 chr5D 76688569 76692058 3489 True 5031.000000 5031 92.8110 178 3660 1 chr5D.!!$R1 3482
5 TraesCS5A01G065800 chr5D 76752911 76756283 3372 True 4889.000000 4889 92.8930 178 3556 1 chr5D.!!$R2 3378
6 TraesCS5A01G065800 chr5B 85178693 85182137 3444 False 4883.000000 4883 92.3590 205 3643 1 chr5B.!!$F2 3438
7 TraesCS5A01G065800 chr5B 85116574 85120046 3472 False 4865.000000 4865 92.0260 179 3660 1 chr5B.!!$F1 3481

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
582 609 0.252057 TCCCTCATTCCCGACTCACA 60.252 55.000 0.00 0.0 0.00 3.58 F
1572 1646 1.375396 CTGTGTCGCCCAATTCGGA 60.375 57.895 0.00 0.0 36.56 4.55 F
2398 2507 0.763223 AACACCGGGACCTTCTCAGT 60.763 55.000 6.32 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1579 1653 0.888619 ATGATGTCGTCCGTGAGTGT 59.111 50.000 0.00 0.0 0.00 3.55 R
2569 2678 2.106566 TCTGAAGCCTTGCTCTCTAGG 58.893 52.381 0.00 0.0 38.25 3.02 R
3515 3645 3.067180 CCTCATAGGCGCAATTCATGTTT 59.933 43.478 10.83 0.0 0.00 2.83 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
28 29 1.429463 GATTTCCCTCGCGCGAATAT 58.571 50.000 33.99 18.85 0.00 1.28
32 33 1.734477 CCCTCGCGCGAATATCCTG 60.734 63.158 33.99 19.39 0.00 3.86
49 51 1.757118 CCTGAATCTGAACTAGCGGGA 59.243 52.381 0.00 0.00 0.00 5.14
221 225 7.123247 GCGAGGTTATATTACCCCTGTCTTATA 59.877 40.741 7.28 0.00 39.08 0.98
438 459 0.627451 AGCCATGCCCTTCTCATGAA 59.373 50.000 0.00 0.00 42.84 2.57
474 495 1.334869 GCCACTGTCAAAACTGTCAGG 59.665 52.381 4.53 0.00 35.60 3.86
510 531 2.884894 ATCCCTCGATCGTTGTTACC 57.115 50.000 15.94 0.00 0.00 2.85
522 546 4.624015 TCGTTGTTACCGACTGAAGAAAT 58.376 39.130 0.00 0.00 0.00 2.17
582 609 0.252057 TCCCTCATTCCCGACTCACA 60.252 55.000 0.00 0.00 0.00 3.58
641 668 2.034685 GCTTTGACGCCCTTCTCTTTTT 59.965 45.455 0.00 0.00 0.00 1.94
786 836 3.077556 CGCTACTGACCTGGGGCT 61.078 66.667 0.00 0.00 0.00 5.19
969 1023 3.621558 CCAAACCTAATTCTCCTCACCC 58.378 50.000 0.00 0.00 0.00 4.61
1023 1077 1.825622 GGCCGGCGGTAGTAGTAGT 60.826 63.158 28.82 0.00 0.00 2.73
1254 1328 1.805945 GCAGATCCTCGCGAAACGT 60.806 57.895 11.33 0.00 44.19 3.99
1572 1646 1.375396 CTGTGTCGCCCAATTCGGA 60.375 57.895 0.00 0.00 36.56 4.55
1579 1653 1.889454 GCCCAATTCGGACATTGCA 59.111 52.632 0.00 0.00 36.56 4.08
1708 1813 1.551452 CCCTTCTCTCGAGGTCTTGT 58.449 55.000 13.56 0.00 32.15 3.16
1715 1820 6.752815 CCTTCTCTCGAGGTCTTGTTAATTAC 59.247 42.308 13.56 0.00 0.00 1.89
1717 1822 6.853720 TCTCTCGAGGTCTTGTTAATTACTG 58.146 40.000 13.56 0.00 0.00 2.74
1994 2099 9.525826 AACTGATCTTCTTCATTTTTACCATCT 57.474 29.630 0.00 0.00 0.00 2.90
2093 2202 7.814107 TGTCTAATGTTGGATTTCATGCTTTTC 59.186 33.333 0.00 0.00 0.00 2.29
2112 2221 2.435938 GAAGGGACCGCGCATTGA 60.436 61.111 8.75 0.00 0.00 2.57
2198 2307 8.642935 TCTATGTTTGGACATGGTTATTGAAA 57.357 30.769 0.00 0.00 45.80 2.69
2398 2507 0.763223 AACACCGGGACCTTCTCAGT 60.763 55.000 6.32 0.00 0.00 3.41
2569 2678 1.789506 AACAGCGTCAGAAGCTTCTC 58.210 50.000 26.18 14.90 44.06 2.87
2699 2808 6.663093 ACATATGGATGTGTGTTGTATTGGTT 59.337 34.615 7.80 0.00 44.90 3.67
2759 2868 1.679680 GATGGATGTGTGATTGGGCAG 59.320 52.381 0.00 0.00 0.00 4.85
2794 2907 8.474025 TGGGCAATTAGTATTTAGAATGGTTTG 58.526 33.333 0.00 0.00 0.00 2.93
2864 2982 5.709966 AGGCGAAATCAAACAAAAGATACC 58.290 37.500 0.00 0.00 0.00 2.73
3016 3136 4.211794 GTGAAATCCACAACAATGCCTTTG 59.788 41.667 0.00 0.00 45.03 2.77
3031 3151 3.317993 TGCCTTTGCACTTCTTTTCCTAC 59.682 43.478 0.00 0.00 44.23 3.18
3336 3466 6.613271 TCAAATTCCTAGCTAGATGAGGTCTT 59.387 38.462 22.70 3.31 38.42 3.01
3356 3486 7.878644 AGGTCTTTCAGTAACTTTCAAGGTATC 59.121 37.037 0.00 0.00 29.64 2.24
3478 3608 6.761117 TGAACGATTGTGAAATATTGACTCG 58.239 36.000 0.00 0.00 0.00 4.18
3601 3731 1.978617 CCACTGTGTGAATGGGGGC 60.979 63.158 7.08 0.00 35.23 5.80
3643 3775 2.240510 ACACTGTGTGAATGGGGGT 58.759 52.632 13.50 0.00 36.96 4.95
3644 3776 0.178992 ACACTGTGTGAATGGGGGTG 60.179 55.000 13.50 0.00 36.96 4.61
3645 3777 1.228552 ACTGTGTGAATGGGGGTGC 60.229 57.895 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.757118 CCCGCTAGTTCAGATTCAGGA 59.243 52.381 0.00 0.00 0.00 3.86
32 33 1.069358 CCCTCCCGCTAGTTCAGATTC 59.931 57.143 0.00 0.00 0.00 2.52
56 58 7.537596 CATAGTGTTATGGAGAGAGATTCCT 57.462 40.000 0.00 0.00 35.67 3.36
70 72 2.745152 GCGGACTTGGCCATAGTGTTAT 60.745 50.000 20.74 1.23 0.00 1.89
71 73 1.406341 GCGGACTTGGCCATAGTGTTA 60.406 52.381 20.74 0.00 0.00 2.41
452 473 0.317020 GACAGTTTTGACAGTGGCGC 60.317 55.000 0.00 0.00 0.00 6.53
474 495 7.431249 TCGAGGGATTAATACATTACACTGTC 58.569 38.462 0.00 0.00 0.00 3.51
510 531 4.868171 TGGAATTCCGTATTTCTTCAGTCG 59.132 41.667 19.57 0.00 39.43 4.18
522 546 7.608376 TGTTCTGACATTTTATGGAATTCCGTA 59.392 33.333 20.50 20.50 39.43 4.02
1023 1077 2.357257 CCTGCTGGTAGTCTCACTCCTA 60.357 54.545 0.51 0.00 0.00 2.94
1146 1220 3.209812 TGGAGATCTCGTCCGCCG 61.210 66.667 16.46 0.00 36.82 6.46
1152 1226 1.380403 CGCTGAGGTGGAGATCTCGT 61.380 60.000 16.46 1.07 31.04 4.18
1254 1328 4.033776 CGCCAGAGGGGAAGCCAA 62.034 66.667 0.00 0.00 40.01 4.52
1298 1372 3.804036 TGATTAGAACGGGCGATTTCAT 58.196 40.909 0.00 0.00 0.00 2.57
1572 1646 1.221466 CGTCCGTGAGTGTGCAATGT 61.221 55.000 0.00 0.00 0.00 2.71
1579 1653 0.888619 ATGATGTCGTCCGTGAGTGT 59.111 50.000 0.00 0.00 0.00 3.55
1715 1820 4.729918 GGGCTCCACTGCACCCAG 62.730 72.222 2.99 0.00 42.33 4.45
1994 2099 8.752005 AAATGCAAGTTATATAGAAGGCTGAA 57.248 30.769 0.00 0.00 0.00 3.02
2093 2202 2.436646 AATGCGCGGTCCCTTCAG 60.437 61.111 8.83 0.00 0.00 3.02
2112 2221 3.640967 TGCTGTTGAAAGGCTACCAATTT 59.359 39.130 5.05 0.00 0.00 1.82
2198 2307 3.346315 TGCACGGAAAACATCTCATCAT 58.654 40.909 0.00 0.00 0.00 2.45
2569 2678 2.106566 TCTGAAGCCTTGCTCTCTAGG 58.893 52.381 0.00 0.00 38.25 3.02
2699 2808 7.433680 TCGCTAATATGAAAAGCTCATGAGTA 58.566 34.615 23.38 6.97 44.84 2.59
2759 2868 9.410556 CTAAATACTAATTGCCCAAATATGCAC 57.589 33.333 0.00 0.00 37.18 4.57
2790 2903 3.195661 AGTGAGACTTCGGTTGACAAAC 58.804 45.455 0.00 0.00 35.40 2.93
2794 2907 3.454375 TGAAAGTGAGACTTCGGTTGAC 58.546 45.455 0.00 0.00 37.47 3.18
2864 2982 4.379394 CGAGTGTTTACATGGTGGATTTGG 60.379 45.833 0.00 0.00 0.00 3.28
3016 3136 6.560253 TTTCATCTGTAGGAAAAGAAGTGC 57.440 37.500 0.00 0.00 32.77 4.40
3336 3466 7.211573 TGTTCGATACCTTGAAAGTTACTGAA 58.788 34.615 0.00 0.00 0.00 3.02
3383 3513 9.221933 TCGCTTGAATTATCTTTTACCAGTTAA 57.778 29.630 0.00 0.00 0.00 2.01
3449 3579 7.325821 GTCAATATTTCACAATCGTTCAGCAAA 59.674 33.333 0.00 0.00 0.00 3.68
3478 3608 7.491696 GCTAATATTATTCCCACTACCATCGAC 59.508 40.741 0.00 0.00 0.00 4.20
3515 3645 3.067180 CCTCATAGGCGCAATTCATGTTT 59.933 43.478 10.83 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.