Multiple sequence alignment - TraesCS6B01G143600

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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 TraesCS6B01G143600 chr6B 100.000 3257 0 0 1 3257 143206596 143203340 0.000000e+00 6015.0
1 TraesCS6B01G143600 chr6D 95.994 3195 97 17 76 3257 68105646 68102470 0.000000e+00 5162.0
2 TraesCS6B01G143600 chr6D 92.913 127 8 1 76 202 265510444 265510569 2.000000e-42 183.0
3 TraesCS6B01G143600 chr6D 92.308 78 5 1 1 78 68105763 68105687 3.440000e-20 110.0
4 TraesCS6B01G143600 chr6D 96.296 54 1 1 2949 3002 283795809 283795861 1.610000e-13 87.9
5 TraesCS6B01G143600 chr6D 83.333 78 11 2 1 78 101095100 101095175 1.620000e-08 71.3
6 TraesCS6B01G143600 chr6A 95.777 2889 97 10 388 3257 85592901 85590019 0.000000e+00 4636.0
7 TraesCS6B01G143600 chr6A 92.308 208 14 2 388 594 85697669 85697463 8.840000e-76 294.0
8 TraesCS6B01G143600 chr6A 86.765 68 8 1 11 78 75164717 75164651 1.250000e-09 75.0
9 TraesCS6B01G143600 chr3B 82.227 1311 149 41 963 2251 63392206 63393454 0.000000e+00 1053.0
10 TraesCS6B01G143600 chr3B 96.491 57 2 0 22 78 644934527 644934583 9.620000e-16 95.3
11 TraesCS6B01G143600 chr3A 88.583 508 46 4 980 1485 51404825 51404328 9.990000e-170 606.0
12 TraesCS6B01G143600 chr3A 82.982 617 83 8 1747 2351 51404129 51403523 3.700000e-149 538.0
13 TraesCS6B01G143600 chr3D 87.259 518 52 6 963 1475 39596653 39597161 2.180000e-161 579.0
14 TraesCS6B01G143600 chr3D 89.130 138 14 1 76 212 599436377 599436240 1.550000e-38 171.0
15 TraesCS6B01G143600 chr3D 89.474 133 14 0 76 208 287966961 287967093 5.590000e-38 169.0
16 TraesCS6B01G143600 chr1D 92.913 127 9 0 76 202 327306016 327306142 5.550000e-43 185.0
17 TraesCS6B01G143600 chr5A 91.339 127 11 0 76 202 347398599 347398473 1.200000e-39 174.0
18 TraesCS6B01G143600 chr5A 82.955 88 13 2 402 487 324500592 324500679 9.690000e-11 78.7
19 TraesCS6B01G143600 chrUn 89.209 139 14 1 76 213 45827807 45827669 4.320000e-39 172.0
20 TraesCS6B01G143600 chrUn 89.130 138 14 1 76 212 323578440 323578577 1.550000e-38 171.0
21 TraesCS6B01G143600 chrUn 79.866 149 25 5 368 513 476184742 476184888 1.600000e-18 104.0
22 TraesCS6B01G143600 chrUn 98.246 57 0 1 2947 3003 17053311 17053366 7.440000e-17 99.0
23 TraesCS6B01G143600 chrUn 100.000 49 0 0 2947 2995 346183970 346184018 1.240000e-14 91.6
24 TraesCS6B01G143600 chr5B 91.200 125 11 0 76 200 136666653 136666529 1.550000e-38 171.0
25 TraesCS6B01G143600 chr5B 89.474 76 7 1 3 78 291253224 291253150 9.620000e-16 95.3
26 TraesCS6B01G143600 chr2A 79.355 155 27 5 368 519 398445216 398445064 1.600000e-18 104.0
27 TraesCS6B01G143600 chr2A 79.866 149 25 5 368 513 398870767 398870913 1.600000e-18 104.0
28 TraesCS6B01G143600 chr2A 98.039 51 0 1 2949 2999 654910277 654910326 1.610000e-13 87.9
29 TraesCS6B01G143600 chr2A 81.053 95 16 2 402 494 622265633 622265539 1.250000e-09 75.0
30 TraesCS6B01G143600 chr1A 92.647 68 4 1 11 78 354827239 354827173 2.670000e-16 97.1
31 TraesCS6B01G143600 chr4B 94.828 58 2 1 2946 3003 673246034 673245978 4.480000e-14 89.8
32 TraesCS6B01G143600 chr4B 89.552 67 5 2 2954 3019 372825412 372825477 2.080000e-12 84.2
33 TraesCS6B01G143600 chr4D 89.706 68 6 1 11 78 105986188 105986122 5.790000e-13 86.1
34 TraesCS6B01G143600 chr1B 91.935 62 2 3 2949 3007 510225560 510225621 2.080000e-12 84.2
35 TraesCS6B01G143600 chr1B 86.667 75 9 1 5 78 475535550 475535624 7.490000e-12 82.4
36 TraesCS6B01G143600 chr2B 75.904 166 34 6 357 519 779172125 779171963 2.690000e-11 80.5
37 TraesCS6B01G143600 chr7D 87.879 66 7 1 11 76 313559843 313559779 3.480000e-10 76.8
38 TraesCS6B01G143600 chr7D 79.747 79 13 3 413 488 631092314 631092236 2.000000e-03 54.7


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 TraesCS6B01G143600 chr6B 143203340 143206596 3256 True 6015 6015 100.0000 1 3257 1 chr6B.!!$R1 3256
1 TraesCS6B01G143600 chr6D 68102470 68105763 3293 True 2636 5162 94.1510 1 3257 2 chr6D.!!$R1 3256
2 TraesCS6B01G143600 chr6A 85590019 85592901 2882 True 4636 4636 95.7770 388 3257 1 chr6A.!!$R2 2869
3 TraesCS6B01G143600 chr3B 63392206 63393454 1248 False 1053 1053 82.2270 963 2251 1 chr3B.!!$F1 1288
4 TraesCS6B01G143600 chr3A 51403523 51404825 1302 True 572 606 85.7825 980 2351 2 chr3A.!!$R1 1371
5 TraesCS6B01G143600 chr3D 39596653 39597161 508 False 579 579 87.2590 963 1475 1 chr3D.!!$F1 512

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
738 785 1.671469 CATGTCCGAGTCGTATACGC 58.329 55.000 20.42 14.81 39.6 4.42 F
850 897 2.222027 CAATCCCTAATCCACCGCTTC 58.778 52.381 0.00 0.00 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1548 1620 0.659957 CTTCTTCGCCATTAGCCTGC 59.340 55.0 0.0 0.0 38.78 4.85 R
2492 2582 1.545841 TCTAGCGACCAAGCAGAAGA 58.454 50.0 0.0 0.0 40.15 2.87 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
86 130 7.410174 GGAGAATATCTATCTCTCCCTCTTCA 58.590 42.308 8.65 0.00 46.53 3.02
203 247 9.585099 AACATAATGCAAAATTGACGTATCATT 57.415 25.926 0.00 0.00 33.85 2.57
206 250 7.975866 AATGCAAAATTGACGTATCATTCTC 57.024 32.000 0.00 0.00 33.85 2.87
208 252 4.963953 GCAAAATTGACGTATCATTCTCCG 59.036 41.667 0.00 0.00 33.85 4.63
317 361 2.996621 CCAACGACCTGACTTTCTCATC 59.003 50.000 0.00 0.00 0.00 2.92
330 374 2.988636 TCTCATCTCCGGATCCTCAT 57.011 50.000 3.57 0.00 0.00 2.90
358 402 5.234972 GTGGCATATTGCTTGAAATTTAGGC 59.765 40.000 0.00 0.00 44.28 3.93
360 404 4.445385 GCATATTGCTTGAAATTTAGGCCG 59.555 41.667 0.00 0.00 40.96 6.13
453 498 2.634940 AGGCGCTGTCATGACCTATATT 59.365 45.455 22.85 2.51 0.00 1.28
459 504 4.576053 GCTGTCATGACCTATATTTGTGCA 59.424 41.667 22.85 0.00 0.00 4.57
541 586 9.450807 CGCCATAATATCCTTTTCTTTTTACAG 57.549 33.333 0.00 0.00 0.00 2.74
575 620 3.479269 CTTGGCGGCGTTCTCGTC 61.479 66.667 9.37 0.00 39.49 4.20
607 652 3.306166 GGAGATGTTAATCGTCGTGTTGG 59.694 47.826 0.00 0.00 37.92 3.77
730 777 4.882671 AAATTGTATGCATGTCCGAGTC 57.117 40.909 10.16 0.00 0.00 3.36
738 785 1.671469 CATGTCCGAGTCGTATACGC 58.329 55.000 20.42 14.81 39.60 4.42
850 897 2.222027 CAATCCCTAATCCACCGCTTC 58.778 52.381 0.00 0.00 0.00 3.86
1644 1716 2.580962 TCAGACGAGGATGATCAGGAG 58.419 52.381 0.09 0.00 0.00 3.69
1787 1868 0.705253 TTCGAGGAGGAAGAGGAGGT 59.295 55.000 0.00 0.00 0.00 3.85
2193 2280 0.846693 AACTGCAGGTTGAGAAGGGT 59.153 50.000 19.93 0.00 36.70 4.34
2277 2367 6.041865 AGTGAGATAGGATGGAGTCTCATTTG 59.958 42.308 7.13 0.00 46.02 2.32
2299 2389 2.291209 TTCCAGAAGCAATTCCAGCA 57.709 45.000 0.00 0.00 0.00 4.41
2379 2469 2.028112 GTCTTCCTGGCAGTGTATGTGA 60.028 50.000 14.43 0.00 0.00 3.58
2492 2582 9.778993 CAAAAAGATCATCTGATATTTGTTCGT 57.221 29.630 12.16 0.00 42.90 3.85
2505 2595 1.865865 TGTTCGTCTTCTGCTTGGTC 58.134 50.000 0.00 0.00 0.00 4.02
2632 2722 6.590068 AGACATTCTGGACTGGAAATATCAG 58.410 40.000 0.00 0.00 38.16 2.90
2831 2926 4.568760 GCTCTGGCTTTGTCATCTTACTAC 59.431 45.833 0.00 0.00 35.22 2.73
2930 3026 3.496331 CCCCACCTGAATTGTTTGTACT 58.504 45.455 0.00 0.00 0.00 2.73
3076 3174 5.707764 AGCCTAAAGAAACTCATCCAAGTTC 59.292 40.000 0.00 0.00 38.52 3.01
3125 3223 8.743714 CCACCTTAATAAATCTTCTTCAGCTTT 58.256 33.333 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.308069 CCACGGCTCCAAATGACCTG 61.308 60.000 0.00 0.00 0.00 4.00
170 214 8.582930 CGTCAATTTTGCATTATGTTTTCGTAT 58.417 29.630 0.00 0.00 0.00 3.06
175 219 9.416794 TGATACGTCAATTTTGCATTATGTTTT 57.583 25.926 0.00 0.00 0.00 2.43
203 247 4.401925 TGAGCTATGAATCTGATCGGAGA 58.598 43.478 10.61 0.00 45.75 3.71
206 250 3.847542 CCTGAGCTATGAATCTGATCGG 58.152 50.000 0.00 0.00 0.00 4.18
208 252 4.268797 TGCCTGAGCTATGAATCTGATC 57.731 45.455 0.00 0.00 40.80 2.92
263 307 1.064946 CAGGAAGGAGAGCTACGCG 59.935 63.158 3.53 3.53 0.00 6.01
278 322 0.036671 GGTCGAAACTACCACCCAGG 60.037 60.000 0.00 0.00 45.67 4.45
279 323 0.682852 TGGTCGAAACTACCACCCAG 59.317 55.000 0.00 0.00 42.10 4.45
303 347 2.103373 TCCGGAGATGAGAAAGTCAGG 58.897 52.381 0.00 0.00 39.07 3.86
317 361 1.475751 CCACCAAATGAGGATCCGGAG 60.476 57.143 11.34 0.00 0.00 4.63
330 374 4.613925 TTTCAAGCAATATGCCACCAAA 57.386 36.364 0.00 0.00 46.52 3.28
453 498 2.228582 CGGATGATGGAAAAGTGCACAA 59.771 45.455 21.04 0.00 0.00 3.33
459 504 1.212935 CTCCCCGGATGATGGAAAAGT 59.787 52.381 0.73 0.00 0.00 2.66
520 565 9.747898 TGCCTCTGTAAAAAGAAAAGGATATTA 57.252 29.630 0.00 0.00 0.00 0.98
541 586 2.223572 CCAAGAAACAACACAGTGCCTC 60.224 50.000 0.00 0.00 0.00 4.70
575 620 7.088589 ACGATTAACATCTCCAAATTCAAGG 57.911 36.000 0.00 0.00 0.00 3.61
607 652 4.143179 CGATCCGTAAGAAACAACCTGAAC 60.143 45.833 0.00 0.00 43.02 3.18
672 717 4.590226 GCAAAGTTTGTGCATTTTTCCAG 58.410 39.130 16.70 0.00 41.80 3.86
675 720 4.257536 ACGCAAAGTTTGTGCATTTTTC 57.742 36.364 25.31 2.13 44.75 2.29
682 729 2.400408 CACGAATACGCAAAGTTTGTGC 59.600 45.455 25.31 9.10 44.75 4.57
711 758 2.159099 ACGACTCGGACATGCATACAAT 60.159 45.455 0.00 0.00 0.00 2.71
718 765 1.671469 CGTATACGACTCGGACATGC 58.329 55.000 20.58 0.00 43.02 4.06
730 777 1.264141 CGGTGGCTAACGCGTATACG 61.264 60.000 20.87 20.87 43.27 3.06
738 785 0.108804 ATCTGACACGGTGGCTAACG 60.109 55.000 16.16 5.75 0.00 3.18
942 989 4.678743 GGGGTTTGCGAGGGGCTT 62.679 66.667 0.00 0.00 44.05 4.35
1071 1134 1.153369 CATCTGGCAGTACCACCGG 60.153 63.158 15.27 0.00 46.36 5.28
1341 1404 1.315690 ACTTGACGAACTCGGTGAGA 58.684 50.000 3.88 0.00 44.95 3.27
1548 1620 0.659957 CTTCTTCGCCATTAGCCTGC 59.340 55.000 0.00 0.00 38.78 4.85
1956 2037 3.009143 CCTTCTGCTTGTAGTACCCCTTT 59.991 47.826 0.00 0.00 0.00 3.11
2193 2280 6.126940 CCTTGAGAACTTTCCCATCATAGAGA 60.127 42.308 0.00 0.00 0.00 3.10
2370 2460 5.088739 GCACAAGCATAGTTTCACATACAC 58.911 41.667 0.00 0.00 41.58 2.90
2379 2469 6.207417 ACAACATTCTAGCACAAGCATAGTTT 59.793 34.615 0.00 0.00 45.49 2.66
2420 2510 7.721399 AGAATGAACTAGAAACATCAACACCTT 59.279 33.333 0.00 0.00 0.00 3.50
2427 2517 6.348786 GCAGCAAGAATGAACTAGAAACATCA 60.349 38.462 0.00 0.00 0.00 3.07
2431 2521 5.180117 TCAGCAGCAAGAATGAACTAGAAAC 59.820 40.000 0.00 0.00 0.00 2.78
2492 2582 1.545841 TCTAGCGACCAAGCAGAAGA 58.454 50.000 0.00 0.00 40.15 2.87
2505 2595 9.449550 TTGCAAAATTGTCATATTATTCTAGCG 57.550 29.630 0.00 0.00 0.00 4.26
3076 3174 7.860872 GTGGACAGAATTAAGGTAACAAAGTTG 59.139 37.037 0.00 0.00 41.41 3.16
3226 3327 4.203226 TGTCATGTGGCAAGTTTGAACTA 58.797 39.130 0.00 0.00 38.57 2.24


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

AutoCloner maintained by Alex Coulton.