Multiple sequence alignment - TraesCS3D01G117500

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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 TraesCS3D01G117500 chr3D 100.000 2915 0 0 1 2915 71117057 71114143 0.000000e+00 5384.0
1 TraesCS3D01G117500 chr3D 83.768 345 50 6 715 1056 68072258 68071917 3.620000e-84 322.0
2 TraesCS3D01G117500 chr3D 74.062 320 60 17 713 1028 127903768 127904068 3.070000e-20 110.0
3 TraesCS3D01G117500 chr3B 94.477 2933 142 7 1 2915 116391274 116388344 0.000000e+00 4501.0
4 TraesCS3D01G117500 chr3B 93.690 2932 152 14 3 2915 116438737 116435820 0.000000e+00 4359.0
5 TraesCS3D01G117500 chr3B 84.348 345 49 5 709 1050 113930098 113930440 1.670000e-87 333.0
6 TraesCS3D01G117500 chr3B 80.645 217 27 9 175 384 638328225 638328017 1.400000e-33 154.0
7 TraesCS3D01G117500 chr3B 74.528 318 62 13 713 1028 182203230 182203530 1.420000e-23 121.0
8 TraesCS3D01G117500 chr3A 96.278 2176 80 1 1 2175 82745282 82743107 0.000000e+00 3568.0
9 TraesCS3D01G117500 chr3A 91.872 689 38 2 2245 2915 82743111 82742423 0.000000e+00 946.0
10 TraesCS3D01G117500 chr3A 83.761 351 51 6 709 1056 80102515 80102862 7.790000e-86 327.0
11 TraesCS3D01G117500 chr3A 74.843 318 59 16 714 1028 79875912 79875613 1.100000e-24 124.0
12 TraesCS3D01G117500 chr2D 81.818 517 81 12 175 683 617543428 617543939 3.470000e-114 422.0
13 TraesCS3D01G117500 chr2D 100.000 30 0 0 2662 2691 485591202 485591231 4.060000e-04 56.5
14 TraesCS3D01G117500 chr2D 100.000 30 0 0 2662 2691 485634405 485634434 4.060000e-04 56.5
15 TraesCS3D01G117500 chr1D 81.982 333 57 3 378 708 41587932 41588263 2.210000e-71 279.0
16 TraesCS3D01G117500 chr4D 80.240 334 46 10 378 708 375740454 375740138 1.750000e-57 233.0
17 TraesCS3D01G117500 chr7D 79.940 334 47 10 378 708 134104888 134104572 8.130000e-56 228.0
18 TraesCS3D01G117500 chr7D 87.500 64 8 0 2227 2290 271254125 271254188 1.120000e-09 75.0
19 TraesCS3D01G117500 chr5D 79.940 334 47 10 378 708 59885293 59885609 8.130000e-56 228.0
20 TraesCS3D01G117500 chr5D 79.701 335 46 13 378 708 464597341 464597657 3.780000e-54 222.0
21 TraesCS3D01G117500 chr5D 76.180 466 81 15 175 638 249528310 249528747 4.890000e-53 219.0
22 TraesCS3D01G117500 chr2A 77.073 410 79 6 175 583 769519569 769519174 3.780000e-54 222.0
23 TraesCS3D01G117500 chr2A 83.854 192 26 5 175 365 748291309 748291496 8.300000e-41 178.0
24 TraesCS3D01G117500 chr5B 81.731 104 15 1 207 310 267420291 267420390 1.860000e-12 84.2
25 TraesCS3D01G117500 chr7B 91.667 48 4 0 2227 2274 269846383 269846336 1.870000e-07 67.6


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 TraesCS3D01G117500 chr3D 71114143 71117057 2914 True 5384 5384 100.000 1 2915 1 chr3D.!!$R2 2914
1 TraesCS3D01G117500 chr3B 116388344 116391274 2930 True 4501 4501 94.477 1 2915 1 chr3B.!!$R1 2914
2 TraesCS3D01G117500 chr3B 116435820 116438737 2917 True 4359 4359 93.690 3 2915 1 chr3B.!!$R2 2912
3 TraesCS3D01G117500 chr3A 82742423 82745282 2859 True 2257 3568 94.075 1 2915 2 chr3A.!!$R2 2914
4 TraesCS3D01G117500 chr2D 617543428 617543939 511 False 422 422 81.818 175 683 1 chr2D.!!$F3 508

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
477 483 1.065031 CGAGCGTTTGCCGGAAATTG 61.065 55.0 5.05 0.0 44.31 2.32 F
1679 1686 0.102481 ACGCTAACCCGTGATGCTAG 59.898 55.0 0.00 0.0 40.40 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1703 1710 0.107703 TGAGGATGTGGCGAATGGAC 60.108 55.000 0.0 0.0 0.0 4.02 R
2654 2662 1.198867 CGTGATCTATCTCCCGAGCAG 59.801 57.143 0.0 0.0 0.0 4.24 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
124 125 9.903682 CTTTTATGTAGAAGATGGCATTATTGG 57.096 33.333 0.00 0.00 0.00 3.16
168 169 1.536907 TGACCCGAACCTGGCCTTA 60.537 57.895 3.32 0.00 0.00 2.69
202 203 1.272092 CCCAATTTGAGAGGCCACAGA 60.272 52.381 5.01 0.00 0.00 3.41
251 255 2.760092 CCTTGTTGTCCCAATGGGTATG 59.240 50.000 19.28 3.12 44.74 2.39
350 354 5.753921 GGAATCCGACTAGTGTAAGAATTGG 59.246 44.000 0.00 0.00 0.00 3.16
477 483 1.065031 CGAGCGTTTGCCGGAAATTG 61.065 55.000 5.05 0.00 44.31 2.32
507 513 1.218854 GCATCGCAAAATTGGGCCT 59.781 52.632 4.53 0.00 40.52 5.19
527 533 1.443802 TACGACAATGCCAATGCGAA 58.556 45.000 4.12 0.00 41.78 4.70
971 978 7.741554 ACATCTCTACTTTCCATACCTTTCT 57.258 36.000 0.00 0.00 0.00 2.52
1056 1063 4.287067 AGATCTAGTGAAAGTGAGGCCAAA 59.713 41.667 5.01 0.00 0.00 3.28
1077 1084 2.519771 TTTCTCCCTTGCATGATGCT 57.480 45.000 19.19 0.00 45.31 3.79
1355 1362 2.437413 GGAAATCTTTGAGAACCCGCT 58.563 47.619 0.00 0.00 0.00 5.52
1392 1399 3.230134 CCAAGATTTCCTGTCAAACCCA 58.770 45.455 0.00 0.00 0.00 4.51
1557 1564 0.620556 TTGAGATCCCAACCAGGAGC 59.379 55.000 0.00 0.00 42.90 4.70
1679 1686 0.102481 ACGCTAACCCGTGATGCTAG 59.898 55.000 0.00 0.00 40.40 3.42
1699 1706 2.647802 AGTTATGTTGTGCCTACCCCTT 59.352 45.455 0.00 0.00 0.00 3.95
1703 1710 0.966179 GTTGTGCCTACCCCTTTTGG 59.034 55.000 0.00 0.00 39.97 3.28
1727 1734 0.612744 TTCGCCACATCCTCACATGA 59.387 50.000 0.00 0.00 0.00 3.07
2057 2064 6.485313 TGTGTGGGTGTAAAAGATAGAACAAG 59.515 38.462 0.00 0.00 0.00 3.16
2174 2181 9.643693 AATTTATGAAGTAACCATGCTTTTGAG 57.356 29.630 0.00 0.00 31.06 3.02
2175 2182 7.759489 TTATGAAGTAACCATGCTTTTGAGT 57.241 32.000 0.00 0.00 31.06 3.41
2194 2201 6.798427 TGAGTGAAGAACCATTAGAGCTAT 57.202 37.500 0.00 0.00 0.00 2.97
2204 2211 8.709308 AGAACCATTAGAGCTATGTAAGTTGAT 58.291 33.333 0.00 0.00 0.00 2.57
2390 2397 3.822735 CCTTTCTCTGGCAATTCAAGACA 59.177 43.478 0.00 0.00 0.00 3.41
2413 2420 6.165577 CAGCTATGTTGGGTTATTTTTGCTT 58.834 36.000 0.00 0.00 0.00 3.91
2583 2591 3.848377 CCTCATGATATCCAAGATCCCCA 59.152 47.826 0.00 0.00 0.00 4.96
2654 2662 1.476891 TGCATAGAACACCCGAGAGAC 59.523 52.381 0.00 0.00 0.00 3.36
2752 2777 5.705397 TGTCCATTCAATTCATCTCCTCT 57.295 39.130 0.00 0.00 0.00 3.69
2756 2781 5.605908 TCCATTCAATTCATCTCCTCTAGCT 59.394 40.000 0.00 0.00 0.00 3.32
2766 2791 5.777732 TCATCTCCTCTAGCTAATTCCCTTC 59.222 44.000 0.00 0.00 0.00 3.46
2769 2794 6.146760 TCTCCTCTAGCTAATTCCCTTCAAT 58.853 40.000 0.00 0.00 0.00 2.57
2829 2854 1.448540 CAAGTGCACCGCCTCTAGG 60.449 63.158 14.63 0.00 38.53 3.02
2853 2878 2.561733 TCCTTGCGTGTAGATCGAAG 57.438 50.000 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
477 483 0.030773 TGCGATGCAGTCTATCGGAC 59.969 55.000 8.58 0.00 45.50 4.79
507 513 1.443802 TCGCATTGGCATTGTCGTAA 58.556 45.000 18.35 5.44 41.24 3.18
527 533 1.558294 TCACATCAGCTGCAATCTCCT 59.442 47.619 9.47 0.00 0.00 3.69
906 913 4.818546 TCGTTTCTTAGGAGGGATACTACG 59.181 45.833 0.00 0.00 34.15 3.51
911 918 5.021458 AGTGTTCGTTTCTTAGGAGGGATA 58.979 41.667 0.00 0.00 0.00 2.59
1056 1063 3.814005 GCATCATGCAAGGGAGAAATT 57.186 42.857 4.20 0.00 44.26 1.82
1077 1084 2.124109 ATCGCTCTGCCTCTCGGA 60.124 61.111 0.00 0.00 0.00 4.55
1315 1322 1.133976 CCTATGGTTGGGCAGAGAAGG 60.134 57.143 0.00 0.00 0.00 3.46
1322 1329 1.929494 AGATTTCCCTATGGTTGGGCA 59.071 47.619 0.00 0.00 44.23 5.36
1355 1362 7.226720 GGAAATCTTGGTGCGAGAATATTTCTA 59.773 37.037 0.00 0.00 40.87 2.10
1557 1564 6.913170 TGGTACTAAGTTTACCTTGTAGACG 58.087 40.000 5.55 0.00 39.94 4.18
1679 1686 2.801077 AGGGGTAGGCACAACATAAC 57.199 50.000 0.00 0.00 0.00 1.89
1699 1706 1.173043 GATGTGGCGAATGGACCAAA 58.827 50.000 0.00 0.00 37.79 3.28
1703 1710 0.107703 TGAGGATGTGGCGAATGGAC 60.108 55.000 0.00 0.00 0.00 4.02
1727 1734 2.252714 GAGTCTTGTCTTCTCTGGGGT 58.747 52.381 0.00 0.00 0.00 4.95
1793 1800 6.309009 TCTGTACTTACGTGAACTCGTAGTAG 59.691 42.308 0.00 7.52 44.90 2.57
1799 1806 3.542704 GCATCTGTACTTACGTGAACTCG 59.457 47.826 0.00 0.00 0.00 4.18
2174 2181 7.982354 ACTTACATAGCTCTAATGGTTCTTCAC 59.018 37.037 0.00 0.00 0.00 3.18
2175 2182 8.079211 ACTTACATAGCTCTAATGGTTCTTCA 57.921 34.615 0.00 0.00 0.00 3.02
2194 2201 7.395772 TCATTTGCCAATCCTTATCAACTTACA 59.604 33.333 0.00 0.00 0.00 2.41
2204 2211 4.621274 GCAAGCTTCATTTGCCAATCCTTA 60.621 41.667 0.00 0.00 43.88 2.69
2390 2397 6.211384 AGAAGCAAAAATAACCCAACATAGCT 59.789 34.615 0.00 0.00 0.00 3.32
2583 2591 2.548067 GCACGCTACATAGCCCAATAGT 60.548 50.000 5.33 0.00 46.34 2.12
2654 2662 1.198867 CGTGATCTATCTCCCGAGCAG 59.801 57.143 0.00 0.00 0.00 4.24
2752 2777 5.904984 TGGCTATTGAAGGGAATTAGCTA 57.095 39.130 0.00 0.00 0.00 3.32
2756 2781 6.494491 CCATGATTGGCTATTGAAGGGAATTA 59.506 38.462 0.00 0.00 35.85 1.40
2766 2791 4.413760 AGGGATTCCATGATTGGCTATTG 58.586 43.478 4.80 0.00 43.29 1.90
2769 2794 3.055328 TGAGGGATTCCATGATTGGCTA 58.945 45.455 4.80 0.00 43.29 3.93
2793 2818 3.630312 ACTTGCACCACACTAACGAATTT 59.370 39.130 0.00 0.00 0.00 1.82
2829 2854 3.190744 TCGATCTACACGCAAGGATATCC 59.809 47.826 14.41 14.41 46.39 2.59
2853 2878 3.680196 GCCTACCAGTCCATCTCTCAAAC 60.680 52.174 0.00 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.