Multiple sequence alignment - TraesCS6B01G303200

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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 TraesCS6B01G303200 chr6B 100.000 3143 0 0 1 3143 543083572 543080430 0.000000e+00 5805.0
1 TraesCS6B01G303200 chr6B 86.603 418 38 9 2 402 546035427 546035011 2.220000e-121 446.0
2 TraesCS6B01G303200 chr5A 96.561 2326 57 9 834 3143 66824862 66827180 0.000000e+00 3831.0
3 TraesCS6B01G303200 chr5A 88.387 155 11 7 577 726 66818838 66818990 2.490000e-41 180.0
4 TraesCS6B01G303200 chr5A 96.364 110 2 2 721 830 66822450 66822557 2.490000e-41 180.0
5 TraesCS6B01G303200 chr6A 95.598 886 31 5 1504 2386 502544062 502543182 0.000000e+00 1413.0
6 TraesCS6B01G303200 chr6A 88.293 709 51 14 2453 3143 502509301 502509995 0.000000e+00 821.0
7 TraesCS6B01G303200 chr6A 97.561 451 10 1 1054 1503 502544636 502544186 0.000000e+00 771.0
8 TraesCS6B01G303200 chr6A 88.679 371 24 10 2791 3143 142076961 142076591 1.340000e-118 436.0
9 TraesCS6B01G303200 chr6A 88.571 350 17 14 613 955 502544982 502544649 1.360000e-108 403.0
10 TraesCS6B01G303200 chr6A 82.041 245 22 6 2597 2819 142077627 142077383 4.140000e-44 189.0
11 TraesCS6B01G303200 chr6D 96.633 802 7 5 721 1521 361416504 361415722 0.000000e+00 1314.0
12 TraesCS6B01G303200 chr6D 97.976 741 15 0 1511 2251 361414532 361413792 0.000000e+00 1286.0
13 TraesCS6B01G303200 chr6D 90.066 151 10 5 591 737 361416676 361416527 1.150000e-44 191.0
14 TraesCS6B01G303200 chr6D 100.000 46 0 0 1923 1968 361413734 361413689 5.590000e-13 86.1
15 TraesCS6B01G303200 chr3B 98.606 574 6 2 1 574 114559734 114559163 0.000000e+00 1014.0
16 TraesCS6B01G303200 chr7B 98.938 565 6 0 1 565 623980005 623979441 0.000000e+00 1011.0
17 TraesCS6B01G303200 chr7B 98.934 563 6 0 3 565 723777804 723778366 0.000000e+00 1007.0
18 TraesCS6B01G303200 chr7B 84.404 109 12 2 403 506 175185501 175185393 5.550000e-18 102.0
19 TraesCS6B01G303200 chr1A 98.761 565 7 0 1 565 352018234 352017670 0.000000e+00 1005.0
20 TraesCS6B01G303200 chr7A 98.421 570 8 1 1 570 712768413 712768981 0.000000e+00 1002.0
21 TraesCS6B01G303200 chr1B 96.814 565 13 1 1 565 540127771 540127212 0.000000e+00 939.0
22 TraesCS6B01G303200 chr1B 86.158 419 39 10 2 402 554654537 554654954 4.810000e-118 435.0
23 TraesCS6B01G303200 chr5B 88.148 405 31 9 2 390 461887874 461888277 1.710000e-127 466.0
24 TraesCS6B01G303200 chr2B 86.635 419 36 9 2 402 501796013 501796429 2.220000e-121 446.0
25 TraesCS6B01G303200 chr4D 86.702 376 33 9 2785 3143 258940768 258941143 4.880000e-108 401.0
26 TraesCS6B01G303200 chr4D 86.508 378 32 10 2781 3140 12320607 12320983 6.320000e-107 398.0
27 TraesCS6B01G303200 chr4D 82.883 222 16 9 2620 2819 12320391 12320612 2.490000e-41 180.0
28 TraesCS6B01G303200 chr2A 85.976 328 38 3 231 550 191895977 191896304 8.350000e-91 344.0
29 TraesCS6B01G303200 chr2A 85.366 328 40 3 231 550 279486524 279486197 1.810000e-87 333.0
30 TraesCS6B01G303200 chr7D 100.000 33 0 0 535 567 633935197 633935229 9.410000e-06 62.1


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 TraesCS6B01G303200 chr6B 543080430 543083572 3142 True 5805.000000 5805 100.000000 1 3143 1 chr6B.!!$R1 3142
1 TraesCS6B01G303200 chr5A 66818838 66827180 8342 False 1397.000000 3831 93.770667 577 3143 3 chr5A.!!$F1 2566
2 TraesCS6B01G303200 chr6A 502543182 502544982 1800 True 862.333333 1413 93.910000 613 2386 3 chr6A.!!$R2 1773
3 TraesCS6B01G303200 chr6A 502509301 502509995 694 False 821.000000 821 88.293000 2453 3143 1 chr6A.!!$F1 690
4 TraesCS6B01G303200 chr6A 142076591 142077627 1036 True 312.500000 436 85.360000 2597 3143 2 chr6A.!!$R1 546
5 TraesCS6B01G303200 chr6D 361413689 361416676 2987 True 719.275000 1314 96.168750 591 2251 4 chr6D.!!$R1 1660
6 TraesCS6B01G303200 chr3B 114559163 114559734 571 True 1014.000000 1014 98.606000 1 574 1 chr3B.!!$R1 573
7 TraesCS6B01G303200 chr7B 623979441 623980005 564 True 1011.000000 1011 98.938000 1 565 1 chr7B.!!$R2 564
8 TraesCS6B01G303200 chr7B 723777804 723778366 562 False 1007.000000 1007 98.934000 3 565 1 chr7B.!!$F1 562
9 TraesCS6B01G303200 chr1A 352017670 352018234 564 True 1005.000000 1005 98.761000 1 565 1 chr1A.!!$R1 564
10 TraesCS6B01G303200 chr7A 712768413 712768981 568 False 1002.000000 1002 98.421000 1 570 1 chr7A.!!$F1 569
11 TraesCS6B01G303200 chr1B 540127212 540127771 559 True 939.000000 939 96.814000 1 565 1 chr1B.!!$R1 564
12 TraesCS6B01G303200 chr4D 12320391 12320983 592 False 289.000000 398 84.695500 2620 3140 2 chr4D.!!$F2 520

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
753 4266 0.316841 CTTCGGCCTCCTGCTCTATC 59.683 60.0 0.0 0.0 40.92 2.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2409 9431 0.535335 TTCAGATACCCAGTCCACGC 59.465 55.0 0.0 0.0 0.0 5.34 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
296 297 2.231235 AGGGAAATGCATCGGTTCAAAC 59.769 45.455 0.00 0.00 0.00 2.93
537 538 1.475403 TTTGTCAAGTTTTCCGCCCA 58.525 45.000 0.00 0.00 0.00 5.36
550 551 4.036804 GCCCATTGCAACGCACGA 62.037 61.111 0.00 0.00 38.71 4.35
566 567 4.454847 ACGCACGAGCATATGTACTAGTAT 59.545 41.667 5.75 0.00 42.27 2.12
567 568 5.640783 ACGCACGAGCATATGTACTAGTATA 59.359 40.000 5.75 3.51 42.27 1.47
568 569 6.315642 ACGCACGAGCATATGTACTAGTATAT 59.684 38.462 15.47 15.47 42.27 0.86
753 4266 0.316841 CTTCGGCCTCCTGCTCTATC 59.683 60.000 0.00 0.00 40.92 2.08
772 4285 7.485418 TCTATCTAAGCTCGAACTTAGTCAG 57.515 40.000 26.69 23.41 46.13 3.51
773 4286 7.049133 TCTATCTAAGCTCGAACTTAGTCAGT 58.951 38.462 26.69 17.00 46.13 3.41
830 4343 5.529430 TGGTCGGTATTGGCATTGTAATTAG 59.471 40.000 0.00 0.00 0.00 1.73
831 4344 5.048991 GGTCGGTATTGGCATTGTAATTAGG 60.049 44.000 0.00 0.00 0.00 2.69
981 6799 3.146847 GGGACGAAAAGTTCAACTGGAT 58.853 45.455 0.00 0.00 0.00 3.41
982 6800 3.188667 GGGACGAAAAGTTCAACTGGATC 59.811 47.826 0.00 0.00 0.00 3.36
983 6801 3.120649 GGACGAAAAGTTCAACTGGATCG 60.121 47.826 14.83 14.83 35.71 3.69
984 6802 2.806244 ACGAAAAGTTCAACTGGATCGG 59.194 45.455 18.58 6.41 34.67 4.18
985 6803 3.064207 CGAAAAGTTCAACTGGATCGGA 58.936 45.455 10.52 0.00 30.09 4.55
1785 8804 2.125431 CGTGGGACGCCGGTAAAT 60.125 61.111 1.90 0.00 33.65 1.40
2014 9036 6.034591 GTGCCAAATTCAAGATTCTCAGATG 58.965 40.000 0.00 0.00 0.00 2.90
2109 9131 2.567985 TGGGAAACGGAGAAAGTGAAC 58.432 47.619 0.00 0.00 0.00 3.18
2400 9422 1.135603 CATCCAACACCGTGCATCAAG 60.136 52.381 0.00 0.00 0.00 3.02
2432 9454 4.261801 CGTGGACTGGGTATCTGAATTTT 58.738 43.478 0.00 0.00 0.00 1.82
2482 9514 0.546747 AGGGGAGTCCGAAACATCCA 60.547 55.000 2.26 0.00 41.52 3.41
2567 9599 2.359850 TGGCACATCTCGTTGCCC 60.360 61.111 10.03 0.00 46.14 5.36
2578 9610 1.867233 CTCGTTGCCCGGATTTGATAG 59.133 52.381 0.73 0.00 37.11 2.08
3057 10587 6.811170 CGGTTTCATGGTTTTGTATTGCTAAT 59.189 34.615 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
296 297 5.414454 TGTCGACCTAGATTTTCCAAAATGG 59.586 40.000 14.12 0.99 38.64 3.16
537 538 1.016627 ATATGCTCGTGCGTTGCAAT 58.983 45.000 9.76 0.00 41.47 3.56
628 634 9.678941 CAACGTAAGCAGTGATTCTCTTATATA 57.321 33.333 0.00 0.00 45.62 0.86
630 636 7.701078 GTCAACGTAAGCAGTGATTCTCTTATA 59.299 37.037 0.00 0.00 45.62 0.98
632 638 5.862323 GTCAACGTAAGCAGTGATTCTCTTA 59.138 40.000 0.00 0.00 45.62 2.10
830 4343 2.800544 CGACATGTCACCGGATTATTCC 59.199 50.000 24.93 0.00 38.81 3.01
831 4344 3.245284 CACGACATGTCACCGGATTATTC 59.755 47.826 24.93 0.00 0.00 1.75
981 6799 1.687563 TCAGTATGAGGCGATTCCGA 58.312 50.000 0.00 0.00 42.56 4.55
1298 7116 2.741985 CGGTGGCGCAACAGATCA 60.742 61.111 18.47 0.00 0.00 2.92
2014 9036 4.678309 GCCATAGTTATCCTCTATCGTGGC 60.678 50.000 0.00 0.00 35.44 5.01
2273 9295 5.215845 TCCCCACATCATGACTAGTGATAA 58.784 41.667 20.37 0.00 34.68 1.75
2391 9413 2.476051 CGTGGACGCTTGATGCAC 59.524 61.111 0.00 0.00 43.06 4.57
2409 9431 0.535335 TTCAGATACCCAGTCCACGC 59.465 55.000 0.00 0.00 0.00 5.34
2414 9436 7.829706 AGTTTAGGAAAATTCAGATACCCAGTC 59.170 37.037 0.00 0.00 0.00 3.51
2432 9454 4.349636 TCCAGGTTTGATGTCAGTTTAGGA 59.650 41.667 0.00 0.00 0.00 2.94
2482 9514 3.139397 TCCAAATAACAAGTGGTCCTGGT 59.861 43.478 0.00 0.00 33.88 4.00
2578 9610 8.979574 GCCACTAGTGTAGACATCAAATATAAC 58.020 37.037 21.18 0.00 0.00 1.89
3057 10587 6.952773 ATAAACACAACCTGCTTTGTTCTA 57.047 33.333 0.00 0.00 37.62 2.10


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

AutoCloner maintained by Alex Coulton.