Multiple sequence alignment - TraesCS4B01G244100

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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 TraesCS4B01G244100 chr4B 100.000 2363 0 0 1 2363 505497139 505499501 0.000000e+00 4364
1 TraesCS4B01G244100 chr4D 90.482 1702 113 16 1 1674 406200636 406202316 0.000000e+00 2200
2 TraesCS4B01G244100 chr4D 91.797 512 18 6 1736 2233 406202330 406202831 0.000000e+00 691
3 TraesCS4B01G244100 chr4D 81.884 138 6 11 2227 2363 406202857 406202976 5.370000e-17 99
4 TraesCS4B01G244100 chr4A 89.898 1762 79 36 687 2363 63813774 63815521 0.000000e+00 2176
5 TraesCS4B01G244100 chr4A 90.083 484 45 3 1 484 63799729 63800209 1.990000e-175 625
6 TraesCS4B01G244100 chr4A 88.889 144 14 2 520 661 63800192 63800335 2.410000e-40 176
7 TraesCS4B01G244100 chr3B 87.293 362 42 4 130 489 794589470 794589829 6.080000e-111 411
8 TraesCS4B01G244100 chr3A 87.052 363 43 4 129 489 742894210 742893850 7.860000e-110 407
9 TraesCS4B01G244100 chr3A 85.246 366 46 3 127 489 724015723 724016083 1.030000e-98 370
10 TraesCS4B01G244100 chr2D 83.784 370 56 4 130 497 598272364 598272731 4.830000e-92 348
11 TraesCS4B01G244100 chr1D 83.954 349 45 6 143 489 217603771 217603432 8.150000e-85 324
12 TraesCS4B01G244100 chr5D 82.432 370 56 8 130 495 9557611 9557247 4.900000e-82 315
13 TraesCS4B01G244100 chr2A 82.044 362 56 5 129 489 83229551 83229198 1.370000e-77 300


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 TraesCS4B01G244100 chr4B 505497139 505499501 2362 False 4364.000000 4364 100.000000 1 2363 1 chr4B.!!$F1 2362
1 TraesCS4B01G244100 chr4D 406200636 406202976 2340 False 996.666667 2200 88.054333 1 2363 3 chr4D.!!$F1 2362
2 TraesCS4B01G244100 chr4A 63813774 63815521 1747 False 2176.000000 2176 89.898000 687 2363 1 chr4A.!!$F1 1676
3 TraesCS4B01G244100 chr4A 63799729 63800335 606 False 400.500000 625 89.486000 1 661 2 chr4A.!!$F2 660

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
337 343 0.251916 CTAGACCGCCATCCAAACCA 59.748 55.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2296 2411 0.322816 GCATGTTCAAGGCTCTGGGA 60.323 55.0 0.0 0.0 31.2 4.37 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
24 25 3.484407 GCCTACTGATGAAGGATTGCAT 58.516 45.455 0.00 0.00 34.58 3.96
33 34 6.703319 TGATGAAGGATTGCATGTTGAAATT 58.297 32.000 0.00 0.00 0.00 1.82
36 37 5.927689 TGAAGGATTGCATGTTGAAATTGAC 59.072 36.000 0.00 0.00 0.00 3.18
38 39 3.613737 GGATTGCATGTTGAAATTGACGG 59.386 43.478 0.00 0.00 0.00 4.79
49 50 3.242518 GAAATTGACGGCCTTGCTAAAC 58.757 45.455 0.00 0.00 0.00 2.01
132 133 6.088016 TGACAACATCTTCAAAGGGATTTG 57.912 37.500 0.00 0.00 0.00 2.32
167 169 3.896272 GGATTACCCTCGACCTCTACATT 59.104 47.826 0.00 0.00 0.00 2.71
196 199 3.630168 TGCATGCAGCCCTTTATTAAGA 58.370 40.909 18.46 0.00 44.83 2.10
204 207 6.437162 TGCAGCCCTTTATTAAGAAAAGTGAT 59.563 34.615 10.54 0.00 33.05 3.06
205 208 7.039082 TGCAGCCCTTTATTAAGAAAAGTGATT 60.039 33.333 10.54 0.00 33.05 2.57
249 252 2.360553 CTCGCTCAGAGCTGAAGAAA 57.639 50.000 20.39 0.00 40.54 2.52
250 253 2.681706 CTCGCTCAGAGCTGAAGAAAA 58.318 47.619 20.39 0.00 40.54 2.29
251 254 3.062763 CTCGCTCAGAGCTGAAGAAAAA 58.937 45.455 20.39 0.00 40.54 1.94
252 255 3.668447 TCGCTCAGAGCTGAAGAAAAAT 58.332 40.909 20.39 0.00 39.60 1.82
287 293 2.179018 CCACAGCCGGCGAAAATG 59.821 61.111 23.20 16.34 0.00 2.32
337 343 0.251916 CTAGACCGCCATCCAAACCA 59.748 55.000 0.00 0.00 0.00 3.67
348 354 4.947388 GCCATCCAAACCAGTTGTAGATAA 59.053 41.667 0.00 0.00 35.23 1.75
391 397 2.370849 GGACAGACCCAGTAACCAAAGA 59.629 50.000 0.00 0.00 0.00 2.52
403 409 4.597940 AGTAACCAAAGACTCCCTAGCTTT 59.402 41.667 0.00 0.00 32.68 3.51
404 410 4.455070 AACCAAAGACTCCCTAGCTTTT 57.545 40.909 0.00 0.00 31.17 2.27
409 415 4.828072 AAGACTCCCTAGCTTTTACAGG 57.172 45.455 0.00 0.00 0.00 4.00
438 444 2.985896 ACAACCACATACGGATCCAAG 58.014 47.619 13.41 0.00 0.00 3.61
511 517 4.387026 ACATCCAACATCTTCAAAGGGA 57.613 40.909 0.00 0.00 0.00 4.20
537 543 0.802494 CAAGCCCATACCGTTGTCAC 59.198 55.000 0.00 0.00 0.00 3.67
543 549 3.078097 CCCATACCGTTGTCACAAATGA 58.922 45.455 0.00 0.00 0.00 2.57
552 558 4.911610 CGTTGTCACAAATGATTCAAGGAC 59.088 41.667 0.00 0.00 37.14 3.85
616 622 8.934023 ATACTCAACTTTTGAAGATTGGGTTA 57.066 30.769 11.12 3.23 39.58 2.85
618 624 8.250143 ACTCAACTTTTGAAGATTGGGTTAAT 57.750 30.769 0.00 0.00 39.58 1.40
670 677 7.360113 TCACTTGTATGAGATGCTTATACCA 57.640 36.000 6.83 0.00 33.72 3.25
671 678 7.966812 TCACTTGTATGAGATGCTTATACCAT 58.033 34.615 6.83 0.00 33.72 3.55
672 679 8.432013 TCACTTGTATGAGATGCTTATACCATT 58.568 33.333 6.83 0.00 33.72 3.16
673 680 8.501580 CACTTGTATGAGATGCTTATACCATTG 58.498 37.037 6.83 0.00 33.72 2.82
674 681 8.213679 ACTTGTATGAGATGCTTATACCATTGT 58.786 33.333 6.83 0.35 33.72 2.71
675 682 9.710900 CTTGTATGAGATGCTTATACCATTGTA 57.289 33.333 6.83 0.00 33.72 2.41
684 691 6.001460 TGCTTATACCATTGTAACCTATGGC 58.999 40.000 0.00 0.00 44.78 4.40
737 744 9.436957 TCATTGAACTCTCCTCTTTTGTATTAC 57.563 33.333 0.00 0.00 0.00 1.89
768 782 7.907214 TTAAAGCAGTAGAATCCTTCTGTTC 57.093 36.000 0.00 0.00 40.94 3.18
772 786 4.682050 GCAGTAGAATCCTTCTGTTCCCTC 60.682 50.000 0.00 0.00 40.94 4.30
875 894 0.521242 GCTTGCCGCTAAATGACACG 60.521 55.000 0.00 0.00 35.14 4.49
877 896 1.917782 TTGCCGCTAAATGACACGCC 61.918 55.000 0.00 0.00 0.00 5.68
879 898 0.808453 GCCGCTAAATGACACGCCTA 60.808 55.000 0.00 0.00 0.00 3.93
916 935 1.213430 CTTCTCCTCCTCCCGTAGTCT 59.787 57.143 0.00 0.00 0.00 3.24
917 936 1.296984 TCTCCTCCTCCCGTAGTCTT 58.703 55.000 0.00 0.00 0.00 3.01
1019 1058 0.627469 ATGGCCTCCCTTACCACCAT 60.627 55.000 3.32 0.00 35.99 3.55
1021 1060 1.279025 GGCCTCCCTTACCACCATCA 61.279 60.000 0.00 0.00 0.00 3.07
1035 1077 0.812811 CCATCACCGCTCCACATCTG 60.813 60.000 0.00 0.00 0.00 2.90
1040 1082 2.187946 CGCTCCACATCTGTCCCC 59.812 66.667 0.00 0.00 0.00 4.81
1049 1091 0.393537 CATCTGTCCCCAGCCTTGAC 60.394 60.000 0.00 0.00 38.66 3.18
1353 1398 1.227764 CGCCTGGGTCTCCATGATG 60.228 63.158 0.00 0.00 43.11 3.07
1494 1549 7.108194 TGATTCTGAGTTGAGAAGTTGCATAT 58.892 34.615 0.00 0.00 35.44 1.78
1497 1552 3.618594 TGAGTTGAGAAGTTGCATATCGC 59.381 43.478 0.00 0.00 42.89 4.58
1645 1701 2.663796 CAGCTGAGCTCAGTGGCT 59.336 61.111 37.25 28.81 45.45 4.75
1904 1977 3.120385 TGCTTCACGCGGCAGATG 61.120 61.111 12.47 8.88 43.27 2.90
2181 2254 5.047802 AGCATCTGGTGAAATGTTAACAAGG 60.048 40.000 13.23 0.00 0.00 3.61
2216 2297 9.710900 CAGATAACAACATCACTGGCTATAATA 57.289 33.333 0.00 0.00 0.00 0.98
2220 2301 8.613060 AACAACATCACTGGCTATAATATGAG 57.387 34.615 0.00 0.00 0.00 2.90
2306 2421 3.730269 ACTAGAGATTTTCCCAGAGCCT 58.270 45.455 0.00 0.00 0.00 4.58
2315 2430 0.322816 TCCCAGAGCCTTGAACATGC 60.323 55.000 0.00 0.00 0.00 4.06
2337 2452 5.170748 GCAGTCCATTCCAAATAAAACTGG 58.829 41.667 0.00 0.00 34.80 4.00
2356 2471 2.092968 TGGAAAGCAGTGTGTCTGAACT 60.093 45.455 0.00 0.00 46.27 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.225467 GCAATCCTTCATCAGTAGGCC 58.775 52.381 0.00 0.00 32.71 5.19
24 25 1.269517 GCAAGGCCGTCAATTTCAACA 60.270 47.619 0.00 0.00 0.00 3.33
33 34 0.533308 AACGTTTAGCAAGGCCGTCA 60.533 50.000 0.00 0.00 0.00 4.35
36 37 1.500396 GGAACGTTTAGCAAGGCCG 59.500 57.895 0.46 0.00 0.00 6.13
38 39 1.199327 GAAGGGAACGTTTAGCAAGGC 59.801 52.381 0.46 0.00 36.18 4.35
49 50 2.697431 TTTCAAATGCGAAGGGAACG 57.303 45.000 0.00 0.00 0.00 3.95
163 165 2.617308 GCTGCATGCATCACTCTAATGT 59.383 45.455 22.97 0.00 42.31 2.71
167 169 0.179037 GGGCTGCATGCATCACTCTA 60.179 55.000 22.97 0.00 45.15 2.43
196 199 7.068593 TGGATCACAGACTTTTCAATCACTTTT 59.931 33.333 0.00 0.00 0.00 2.27
275 281 2.202427 CGTTCCATTTTCGCCGGC 60.202 61.111 19.07 19.07 0.00 6.13
287 293 4.189639 AGGTGTTTAGTCATCTCGTTCC 57.810 45.455 0.00 0.00 0.00 3.62
318 324 0.251916 TGGTTTGGATGGCGGTCTAG 59.748 55.000 0.00 0.00 0.00 2.43
320 326 1.002134 CTGGTTTGGATGGCGGTCT 60.002 57.895 0.00 0.00 0.00 3.85
337 343 3.635836 GGTAGCTCGGGTTATCTACAACT 59.364 47.826 0.00 0.00 34.61 3.16
348 354 0.325296 TGGAAGATGGTAGCTCGGGT 60.325 55.000 0.00 0.00 0.00 5.28
391 397 3.792515 ACTCCTGTAAAAGCTAGGGAGT 58.207 45.455 12.96 12.96 45.69 3.85
403 409 4.406326 TGTGGTTGTTACTCACTCCTGTAA 59.594 41.667 0.00 0.00 33.04 2.41
404 410 3.962063 TGTGGTTGTTACTCACTCCTGTA 59.038 43.478 0.00 0.00 33.04 2.74
409 415 3.924686 CCGTATGTGGTTGTTACTCACTC 59.075 47.826 0.00 0.00 33.04 3.51
490 496 4.387026 TCCCTTTGAAGATGTTGGATGT 57.613 40.909 0.00 0.00 0.00 3.06
494 500 3.445096 GGTCATCCCTTTGAAGATGTTGG 59.555 47.826 0.00 0.00 40.63 3.77
511 517 1.930520 GGTATGGGCTTGGGGTCAT 59.069 57.895 0.00 0.00 0.00 3.06
524 530 5.937187 TGAATCATTTGTGACAACGGTATG 58.063 37.500 0.00 0.00 0.00 2.39
537 543 3.064545 GGAGCTCGTCCTTGAATCATTTG 59.935 47.826 7.83 0.00 42.99 2.32
552 558 4.188462 TGTATGTAAACCAATGGAGCTCG 58.812 43.478 6.16 0.00 0.00 5.03
661 668 6.238648 AGCCATAGGTTACAATGGTATAAGC 58.761 40.000 14.60 3.08 43.87 3.09
662 669 8.567948 CAAAGCCATAGGTTACAATGGTATAAG 58.432 37.037 14.60 2.48 43.87 1.73
663 670 8.056400 ACAAAGCCATAGGTTACAATGGTATAA 58.944 33.333 14.60 0.00 43.87 0.98
665 672 6.431722 ACAAAGCCATAGGTTACAATGGTAT 58.568 36.000 14.60 4.69 43.87 2.73
666 673 5.822204 ACAAAGCCATAGGTTACAATGGTA 58.178 37.500 14.60 0.00 43.87 3.25
667 674 4.672899 ACAAAGCCATAGGTTACAATGGT 58.327 39.130 14.60 3.02 43.87 3.55
668 675 5.659440 AACAAAGCCATAGGTTACAATGG 57.341 39.130 10.47 10.47 44.64 3.16
669 676 7.771183 ACATAACAAAGCCATAGGTTACAATG 58.229 34.615 0.00 0.00 32.14 2.82
670 677 7.954666 ACATAACAAAGCCATAGGTTACAAT 57.045 32.000 0.00 0.00 32.14 2.71
671 678 7.231722 ACAACATAACAAAGCCATAGGTTACAA 59.768 33.333 0.00 0.00 32.14 2.41
672 679 6.717540 ACAACATAACAAAGCCATAGGTTACA 59.282 34.615 0.00 0.00 32.14 2.41
673 680 7.153217 ACAACATAACAAAGCCATAGGTTAC 57.847 36.000 0.00 0.00 32.14 2.50
674 681 7.768807 AACAACATAACAAAGCCATAGGTTA 57.231 32.000 0.00 0.00 32.14 2.85
675 682 6.664428 AACAACATAACAAAGCCATAGGTT 57.336 33.333 0.00 0.00 34.43 3.50
676 683 6.664428 AAACAACATAACAAAGCCATAGGT 57.336 33.333 0.00 0.00 0.00 3.08
875 894 2.613223 GGGAAGACAGTGACAACTAGGC 60.613 54.545 0.00 0.00 33.79 3.93
877 896 4.282195 AGAAGGGAAGACAGTGACAACTAG 59.718 45.833 0.00 0.00 33.79 2.57
879 898 3.041946 AGAAGGGAAGACAGTGACAACT 58.958 45.455 0.00 0.00 36.98 3.16
916 935 4.270834 ACACGAGAGGATAAGTAGCTCAA 58.729 43.478 0.00 0.00 0.00 3.02
917 936 3.887352 ACACGAGAGGATAAGTAGCTCA 58.113 45.455 0.00 0.00 0.00 4.26
1019 1058 1.591703 GACAGATGTGGAGCGGTGA 59.408 57.895 0.00 0.00 0.00 4.02
1021 1060 2.660064 GGGACAGATGTGGAGCGGT 61.660 63.158 0.00 0.00 0.00 5.68
1035 1077 2.358737 CGTGTCAAGGCTGGGGAC 60.359 66.667 7.14 7.14 0.00 4.46
1040 1082 3.414700 GCCGTCGTGTCAAGGCTG 61.415 66.667 0.00 0.00 45.67 4.85
1494 1549 1.406069 GCTTCTTCCAAGATCTGGCGA 60.406 52.381 0.00 0.00 45.98 5.54
1554 1609 2.544267 GAGGTGTATGTAAGGCGAATGC 59.456 50.000 0.00 0.00 41.71 3.56
1645 1701 3.074094 AGTCAGGTCTGTAGTGGTGAGTA 59.926 47.826 0.00 0.00 0.00 2.59
2181 2254 9.552114 CAGTGATGTTGTTATCTGAAGAAAATC 57.448 33.333 0.00 0.00 0.00 2.17
2216 2297 3.446161 CACACCCATTTTCAGATGCTCAT 59.554 43.478 0.00 0.00 0.00 2.90
2220 2301 3.005684 TGAACACACCCATTTTCAGATGC 59.994 43.478 0.00 0.00 0.00 3.91
2278 2393 7.316393 TCTGGGAAAATCTCTAGTTTCAGAA 57.684 36.000 6.05 0.00 40.58 3.02
2296 2411 0.322816 GCATGTTCAAGGCTCTGGGA 60.323 55.000 0.00 0.00 31.20 4.37
2297 2412 0.609957 TGCATGTTCAAGGCTCTGGG 60.610 55.000 0.00 0.00 36.25 4.45
2306 2421 2.874014 TGGAATGGACTGCATGTTCAA 58.126 42.857 2.03 0.00 37.77 2.69
2315 2430 6.588719 TCCAGTTTTATTTGGAATGGACTG 57.411 37.500 0.00 0.00 40.41 3.51
2337 2452 3.790123 GCAAGTTCAGACACACTGCTTTC 60.790 47.826 0.00 0.00 45.38 2.62


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

AutoCloner maintained by Alex Coulton.