Multiple sequence alignment - TraesCS5B01G066200

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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 TraesCS5B01G066200 chr5B 100.000 2555 0 0 1 2555 74306817 74309371 0.000000e+00 4719.0
1 TraesCS5B01G066200 chr5D 92.051 2604 100 57 1 2555 68237557 68240102 0.000000e+00 3563.0
2 TraesCS5B01G066200 chr5A 89.590 1902 74 54 1 1815 59139930 59138066 0.000000e+00 2302.0
3 TraesCS5B01G066200 chr5A 91.304 46 4 0 1886 1931 519887082 519887127 2.120000e-06 63.9
4 TraesCS5B01G066200 chr2A 93.033 244 12 2 2140 2378 573237552 573237795 4.040000e-93 351.0
5 TraesCS5B01G066200 chr2A 82.524 103 11 6 1883 1980 635522347 635522447 1.630000e-12 84.2
6 TraesCS5B01G066200 chr2A 86.441 59 6 2 1876 1933 714628096 714628039 2.120000e-06 63.9
7 TraesCS5B01G066200 chr3D 92.095 253 13 4 2141 2386 269465508 269465760 1.450000e-92 350.0
8 TraesCS5B01G066200 chr2B 92.975 242 12 2 2141 2377 135101419 135101660 5.230000e-92 348.0
9 TraesCS5B01G066200 chr1D 92.975 242 12 2 2141 2377 448103378 448103137 5.230000e-92 348.0
10 TraesCS5B01G066200 chr1D 97.143 35 1 0 1890 1924 414138608 414138574 2.750000e-05 60.2
11 TraesCS5B01G066200 chr7A 92.917 240 12 2 2141 2375 424976368 424976607 6.770000e-91 344.0
12 TraesCS5B01G066200 chr2D 92.562 242 13 2 2141 2377 541547530 541547289 2.430000e-90 342.0
13 TraesCS5B01G066200 chr7D 90.000 270 16 6 2141 2401 25492995 25492728 3.150000e-89 339.0
14 TraesCS5B01G066200 chr3A 90.698 258 18 4 2141 2392 606609463 606609206 3.150000e-89 339.0
15 TraesCS5B01G066200 chr1A 78.676 136 13 9 1882 2004 428997337 428997205 2.730000e-10 76.8
16 TraesCS5B01G066200 chr1A 89.474 57 6 0 1869 1925 575401451 575401507 3.530000e-09 73.1
17 TraesCS5B01G066200 chr4A 88.710 62 6 1 1885 1945 606786795 606786734 9.800000e-10 75.0
18 TraesCS5B01G066200 chr4A 87.302 63 5 3 1882 1943 474121256 474121316 4.560000e-08 69.4


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 TraesCS5B01G066200 chr5B 74306817 74309371 2554 False 4719 4719 100.000 1 2555 1 chr5B.!!$F1 2554
1 TraesCS5B01G066200 chr5D 68237557 68240102 2545 False 3563 3563 92.051 1 2555 1 chr5D.!!$F1 2554
2 TraesCS5B01G066200 chr5A 59138066 59139930 1864 True 2302 2302 89.590 1 1815 1 chr5A.!!$R1 1814

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
463 476 0.109039 GTCACGTTCTCTCTGCCCTC 60.109 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2223 2336 0.038251 TGAGCGCTCGACATTGAAGT 60.038 50.0 30.75 0.0 0.0 3.01 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
262 266 1.371183 CTGGTCCAGCGGTGAAGAA 59.629 57.895 17.83 0.00 0.00 2.52
333 337 2.196925 CGCCGAGCATAGGAGAGGT 61.197 63.158 0.00 0.00 31.02 3.85
357 365 2.045045 CACGGCCATGATGGTGGT 60.045 61.111 13.84 8.45 40.46 4.16
386 394 1.902432 GTATCGTCCCTCCCCTCGG 60.902 68.421 0.00 0.00 0.00 4.63
400 413 1.421646 CCCTCGGCCCTCTTAAATGAT 59.578 52.381 0.00 0.00 0.00 2.45
401 414 2.498167 CCTCGGCCCTCTTAAATGATG 58.502 52.381 0.00 0.00 0.00 3.07
402 415 2.104792 CCTCGGCCCTCTTAAATGATGA 59.895 50.000 0.00 0.00 0.00 2.92
403 416 3.244700 CCTCGGCCCTCTTAAATGATGAT 60.245 47.826 0.00 0.00 0.00 2.45
404 417 4.020218 CCTCGGCCCTCTTAAATGATGATA 60.020 45.833 0.00 0.00 0.00 2.15
405 418 4.894784 TCGGCCCTCTTAAATGATGATAC 58.105 43.478 0.00 0.00 0.00 2.24
460 473 2.089349 GCGTCACGTTCTCTCTGCC 61.089 63.158 0.00 0.00 0.00 4.85
461 474 1.444553 CGTCACGTTCTCTCTGCCC 60.445 63.158 0.00 0.00 0.00 5.36
462 475 1.867919 CGTCACGTTCTCTCTGCCCT 61.868 60.000 0.00 0.00 0.00 5.19
463 476 0.109039 GTCACGTTCTCTCTGCCCTC 60.109 60.000 0.00 0.00 0.00 4.30
464 477 0.251386 TCACGTTCTCTCTGCCCTCT 60.251 55.000 0.00 0.00 0.00 3.69
465 478 0.605589 CACGTTCTCTCTGCCCTCTT 59.394 55.000 0.00 0.00 0.00 2.85
466 479 1.001406 CACGTTCTCTCTGCCCTCTTT 59.999 52.381 0.00 0.00 0.00 2.52
467 480 1.273886 ACGTTCTCTCTGCCCTCTTTC 59.726 52.381 0.00 0.00 0.00 2.62
468 481 1.404851 CGTTCTCTCTGCCCTCTTTCC 60.405 57.143 0.00 0.00 0.00 3.13
469 482 1.625818 GTTCTCTCTGCCCTCTTTCCA 59.374 52.381 0.00 0.00 0.00 3.53
529 559 1.697284 TGAGACGAGATGATCTGGGG 58.303 55.000 9.28 0.00 0.00 4.96
531 561 1.118356 AGACGAGATGATCTGGGGCC 61.118 60.000 9.28 0.00 0.00 5.80
532 562 1.074926 ACGAGATGATCTGGGGCCT 60.075 57.895 9.28 0.00 0.00 5.19
533 563 1.370437 CGAGATGATCTGGGGCCTG 59.630 63.158 0.00 0.00 0.00 4.85
534 564 1.759881 GAGATGATCTGGGGCCTGG 59.240 63.158 0.00 0.00 0.00 4.45
535 565 1.773391 AGATGATCTGGGGCCTGGG 60.773 63.158 0.84 0.00 0.00 4.45
579 609 5.120208 CACACACTAATTACTGCTGGTACAC 59.880 44.000 0.00 0.00 0.00 2.90
580 610 4.630069 CACACTAATTACTGCTGGTACACC 59.370 45.833 0.00 0.00 0.00 4.16
581 611 3.863424 CACTAATTACTGCTGGTACACCG 59.137 47.826 0.00 0.00 39.43 4.94
582 612 3.512724 ACTAATTACTGCTGGTACACCGT 59.487 43.478 0.00 0.00 39.43 4.83
583 613 4.706476 ACTAATTACTGCTGGTACACCGTA 59.294 41.667 0.00 0.00 39.43 4.02
584 614 3.515330 ATTACTGCTGGTACACCGTAC 57.485 47.619 0.00 0.00 39.43 3.67
585 615 1.908344 TACTGCTGGTACACCGTACA 58.092 50.000 6.62 0.00 39.43 2.90
605 637 4.316645 ACATGCACTGCTGATCATCTATC 58.683 43.478 1.98 0.00 34.93 2.08
647 691 3.270027 CATTGAATGCCACCTACGAAGA 58.730 45.455 0.00 0.00 0.00 2.87
677 722 0.463654 AATGGAGCGCGCCAGAATAA 60.464 50.000 35.47 13.62 42.15 1.40
806 851 4.096003 AGGCGGATCAACCACCGG 62.096 66.667 0.00 0.00 44.95 5.28
898 949 0.179000 CATCAGCTCACCTACCCACC 59.821 60.000 0.00 0.00 0.00 4.61
899 950 0.252696 ATCAGCTCACCTACCCACCA 60.253 55.000 0.00 0.00 0.00 4.17
900 951 1.192146 TCAGCTCACCTACCCACCAC 61.192 60.000 0.00 0.00 0.00 4.16
927 978 2.073816 ACCAGGAAACAAATACGAGCG 58.926 47.619 0.00 0.00 0.00 5.03
955 1006 2.665537 CGAGCTTGATCACACTTCAGTC 59.334 50.000 0.00 0.00 0.00 3.51
956 1007 3.613671 CGAGCTTGATCACACTTCAGTCT 60.614 47.826 0.00 0.00 0.00 3.24
957 1008 4.314121 GAGCTTGATCACACTTCAGTCTT 58.686 43.478 0.00 0.00 0.00 3.01
959 1010 4.060900 GCTTGATCACACTTCAGTCTTCA 58.939 43.478 0.00 0.00 0.00 3.02
960 1011 4.084118 GCTTGATCACACTTCAGTCTTCAC 60.084 45.833 0.00 0.00 0.00 3.18
962 1013 3.317993 TGATCACACTTCAGTCTTCACGA 59.682 43.478 0.00 0.00 0.00 4.35
967 1025 1.067212 ACTTCAGTCTTCACGAGCGTT 59.933 47.619 0.00 0.00 0.00 4.84
997 1055 2.379972 CCAACAACCACCACCAGTAAA 58.620 47.619 0.00 0.00 0.00 2.01
1013 1071 0.247185 TAAACCATGACGACCCGGAC 59.753 55.000 0.73 0.00 0.00 4.79
1027 1094 1.736586 CGGACCTCATTCCTCCTCG 59.263 63.158 0.00 0.00 32.88 4.63
1616 1719 7.758528 AGTCCTTGTGTTGATTATTACGTACTC 59.241 37.037 0.00 0.00 0.00 2.59
1656 1761 2.858344 ACTAGTAAGCGCGCATGTAAAG 59.142 45.455 35.10 23.24 0.00 1.85
1706 1811 5.978919 GCTCACAGTTTGAATTCACATGAAA 59.021 36.000 7.89 0.00 37.61 2.69
1827 1932 9.835389 AGAAGAGAAAGGATCAGATGATAAAAG 57.165 33.333 0.00 0.00 34.37 2.27
1828 1933 9.829507 GAAGAGAAAGGATCAGATGATAAAAGA 57.170 33.333 0.00 0.00 34.37 2.52
1837 1942 9.829507 GGATCAGATGATAAAAGAAGAAGAAGA 57.170 33.333 0.00 0.00 34.37 2.87
1918 2023 2.807967 CTCAAATGAGCTCGGTGAACAA 59.192 45.455 9.64 0.00 35.13 2.83
2008 2113 7.825270 ACATGTATGCAAATTTTTGTGATGGAT 59.175 29.630 0.00 0.00 40.24 3.41
2011 2116 5.842619 TGCAAATTTTTGTGATGGATTCG 57.157 34.783 5.05 0.00 40.24 3.34
2017 2122 4.780275 TTTTGTGATGGATTCGCATTCA 57.220 36.364 0.00 0.00 44.07 2.57
2019 2124 6.448207 TTTTGTGATGGATTCGCATTCATA 57.552 33.333 0.00 0.00 44.07 2.15
2026 2131 3.999001 TGGATTCGCATTCATAGAGATGC 59.001 43.478 0.00 0.00 36.74 3.91
2034 2139 4.972440 GCATTCATAGAGATGCGGAAAAAC 59.028 41.667 0.00 0.00 32.62 2.43
2059 2164 2.229543 AGCGATGCTCTGCAAAAATTGA 59.770 40.909 0.00 0.00 43.62 2.57
2195 2308 2.766313 TCCAATTAATCTCGGCCATCG 58.234 47.619 2.24 0.00 40.90 3.84
2252 2365 0.505231 CGAGCGCTCAACACGTTTAA 59.495 50.000 34.69 0.00 0.00 1.52
2354 2472 9.365311 CTTAATATACTTCCAAATTAACGTGCG 57.635 33.333 0.00 0.00 0.00 5.34
2355 2473 6.913873 ATATACTTCCAAATTAACGTGCGT 57.086 33.333 0.00 0.00 0.00 5.24
2356 2474 3.974871 ACTTCCAAATTAACGTGCGTT 57.025 38.095 14.41 14.41 41.65 4.84
2357 2475 3.623863 ACTTCCAAATTAACGTGCGTTG 58.376 40.909 18.63 3.62 38.92 4.10
2358 2476 2.039327 TCCAAATTAACGTGCGTTGC 57.961 45.000 18.63 0.00 38.92 4.17
2359 2477 1.333931 TCCAAATTAACGTGCGTTGCA 59.666 42.857 18.63 6.89 38.92 4.08
2360 2478 1.713404 CCAAATTAACGTGCGTTGCAG 59.287 47.619 18.63 5.54 40.08 4.41
2489 2608 6.432783 CGGCCCAAAACCATATATCTCAATAA 59.567 38.462 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
323 327 1.396185 TGGCCACCACCTCTCCTAT 59.604 57.895 0.00 0.00 0.00 2.57
353 357 1.202154 CGATACAGAGACGTCCACCAC 60.202 57.143 13.01 0.00 0.00 4.16
376 384 2.891307 TTAAGAGGGCCGAGGGGAGG 62.891 65.000 0.00 0.00 34.06 4.30
386 394 6.929606 ACGTTAGTATCATCATTTAAGAGGGC 59.070 38.462 0.00 0.00 0.00 5.19
400 413 4.430137 GTGGTCACTCACGTTAGTATCA 57.570 45.455 1.31 0.00 0.00 2.15
440 453 1.340657 GCAGAGAGAACGTGACGCTG 61.341 60.000 4.25 4.17 35.29 5.18
484 497 0.519077 GTTACTCAACTGGCAGCAGC 59.481 55.000 15.89 0.00 41.10 5.25
531 561 4.504916 CGAGCGACCTGAGCCCAG 62.505 72.222 0.00 0.00 40.09 4.45
533 563 2.579684 ATTTCGAGCGACCTGAGCCC 62.580 60.000 0.00 0.00 34.64 5.19
534 564 1.153549 ATTTCGAGCGACCTGAGCC 60.154 57.895 0.00 0.00 34.64 4.70
535 565 0.737715 ACATTTCGAGCGACCTGAGC 60.738 55.000 7.58 0.00 0.00 4.26
541 571 1.136611 GTGTGTGACATTTCGAGCGAC 60.137 52.381 0.00 0.00 0.00 5.19
579 609 0.933097 GATCAGCAGTGCATGTACGG 59.067 55.000 19.20 9.59 0.00 4.02
580 610 1.643880 TGATCAGCAGTGCATGTACG 58.356 50.000 19.20 5.01 0.00 3.67
581 611 3.464907 AGATGATCAGCAGTGCATGTAC 58.535 45.455 19.20 5.71 0.00 2.90
582 612 3.832615 AGATGATCAGCAGTGCATGTA 57.167 42.857 19.20 0.00 0.00 2.29
583 613 2.711978 AGATGATCAGCAGTGCATGT 57.288 45.000 19.20 1.40 0.00 3.21
584 614 3.685272 GGATAGATGATCAGCAGTGCATG 59.315 47.826 19.20 12.61 36.12 4.06
585 615 3.326880 TGGATAGATGATCAGCAGTGCAT 59.673 43.478 19.20 2.16 36.12 3.96
605 637 5.381174 TGGGACTTTATACGTATCGATGG 57.619 43.478 12.24 2.22 0.00 3.51
647 691 1.519455 GCTCCATTACTGCGCGTCT 60.519 57.895 8.43 0.00 0.00 4.18
677 722 2.186903 GCGACGGATGGGTCACAT 59.813 61.111 0.00 0.00 44.18 3.21
806 851 3.432252 TCGGATTTGCGTTTCTCTTCTTC 59.568 43.478 0.00 0.00 0.00 2.87
807 852 3.399330 TCGGATTTGCGTTTCTCTTCTT 58.601 40.909 0.00 0.00 0.00 2.52
808 853 3.040147 TCGGATTTGCGTTTCTCTTCT 57.960 42.857 0.00 0.00 0.00 2.85
898 949 1.468985 TGTTTCCTGGTGTGGTTGTG 58.531 50.000 0.00 0.00 0.00 3.33
899 950 2.223803 TTGTTTCCTGGTGTGGTTGT 57.776 45.000 0.00 0.00 0.00 3.32
900 951 3.817709 ATTTGTTTCCTGGTGTGGTTG 57.182 42.857 0.00 0.00 0.00 3.77
927 978 1.226802 TGATCAAGCTCGCTCGCTC 60.227 57.895 0.00 0.00 39.86 5.03
940 991 3.317993 TCGTGAAGACTGAAGTGTGATCA 59.682 43.478 0.00 0.00 0.00 2.92
955 1006 0.728129 TGACGCTAACGCTCGTGAAG 60.728 55.000 0.00 0.00 45.53 3.02
956 1007 0.728129 CTGACGCTAACGCTCGTGAA 60.728 55.000 0.00 0.00 45.53 3.18
957 1008 1.154282 CTGACGCTAACGCTCGTGA 60.154 57.895 0.00 0.00 45.53 4.35
959 1010 2.178521 CCTGACGCTAACGCTCGT 59.821 61.111 0.00 0.00 45.53 4.18
960 1011 3.248171 GCCTGACGCTAACGCTCG 61.248 66.667 0.00 0.00 45.53 5.03
962 1013 3.234630 TTGGCCTGACGCTAACGCT 62.235 57.895 3.32 0.00 45.53 5.07
967 1025 1.302192 GGTTGTTGGCCTGACGCTA 60.302 57.895 3.32 0.00 37.74 4.26
997 1055 3.387947 GGTCCGGGTCGTCATGGT 61.388 66.667 0.00 0.00 0.00 3.55
1013 1071 1.137872 CAAGGACGAGGAGGAATGAGG 59.862 57.143 0.00 0.00 0.00 3.86
1616 1719 6.879400 ACTAGTTTGATCAAGGCTAACTAGG 58.121 40.000 30.02 19.79 46.40 3.02
1623 1726 4.184629 CGCTTACTAGTTTGATCAAGGCT 58.815 43.478 8.41 12.89 0.00 4.58
1624 1727 3.242446 GCGCTTACTAGTTTGATCAAGGC 60.242 47.826 8.41 6.15 0.00 4.35
1656 1761 9.994432 CCTTGAGTGTTCATTCATAATCTAAAC 57.006 33.333 0.00 0.00 32.27 2.01
1706 1811 4.445452 TCACGCGATTAGAAAAGGTAGT 57.555 40.909 15.93 0.00 0.00 2.73
1846 1951 9.634021 TTTTGGGCCACTTTTCTTTATTAATTT 57.366 25.926 5.23 0.00 0.00 1.82
1999 2104 4.959723 TCTATGAATGCGAATCCATCACA 58.040 39.130 0.00 0.00 0.00 3.58
2011 2116 4.818534 TTTTCCGCATCTCTATGAATGC 57.181 40.909 0.00 0.00 34.84 3.56
2017 2122 5.402398 GCTTTTGTTTTTCCGCATCTCTAT 58.598 37.500 0.00 0.00 0.00 1.98
2019 2124 3.642705 GCTTTTGTTTTTCCGCATCTCT 58.357 40.909 0.00 0.00 0.00 3.10
2026 2131 2.393764 AGCATCGCTTTTGTTTTTCCG 58.606 42.857 0.00 0.00 33.89 4.30
2034 2139 2.054687 TTTGCAGAGCATCGCTTTTG 57.945 45.000 0.00 0.00 39.88 2.44
2099 2204 7.921214 GTGACGAAATCATATTCCTGAGAGTTA 59.079 37.037 0.00 0.00 40.28 2.24
2100 2205 6.758886 GTGACGAAATCATATTCCTGAGAGTT 59.241 38.462 0.00 0.00 40.28 3.01
2121 2228 5.971895 AGATGTGTGCAAAATTTTGTGAC 57.028 34.783 27.13 23.14 40.24 3.67
2169 2282 3.748568 GGCCGAGATTAATTGGATCTGTC 59.251 47.826 9.96 0.00 34.13 3.51
2170 2283 3.136443 TGGCCGAGATTAATTGGATCTGT 59.864 43.478 9.96 0.00 34.13 3.41
2216 2329 4.790123 GCGCTCGACATTGAAGTAGTCTAT 60.790 45.833 0.00 0.00 0.00 1.98
2223 2336 0.038251 TGAGCGCTCGACATTGAAGT 60.038 50.000 30.75 0.00 0.00 3.01
2252 2365 5.431420 TTGACATGAAATTAACTGCACGT 57.569 34.783 0.00 0.00 0.00 4.49
2300 2413 8.141909 GCATGCGGATATTAAGTAGGATATACA 58.858 37.037 0.00 0.00 0.00 2.29
2304 2417 6.154534 AGTGCATGCGGATATTAAGTAGGATA 59.845 38.462 14.09 0.00 0.00 2.59
2352 2470 0.871722 TCAATGTGTACCTGCAACGC 59.128 50.000 0.00 0.00 0.00 4.84
2353 2471 2.143122 AGTCAATGTGTACCTGCAACG 58.857 47.619 0.00 0.00 0.00 4.10
2354 2472 4.152402 CACTAGTCAATGTGTACCTGCAAC 59.848 45.833 0.00 0.00 0.00 4.17
2355 2473 4.202315 ACACTAGTCAATGTGTACCTGCAA 60.202 41.667 0.00 0.00 44.40 4.08
2356 2474 3.323691 ACACTAGTCAATGTGTACCTGCA 59.676 43.478 0.00 0.00 44.40 4.41
2357 2475 3.926616 ACACTAGTCAATGTGTACCTGC 58.073 45.455 0.00 0.00 44.40 4.85
2358 2476 7.956420 TTTTACACTAGTCAATGTGTACCTG 57.044 36.000 5.60 0.00 45.59 4.00
2387 2505 7.628235 CATTGTTTTTGCAACACACATTGATA 58.372 30.769 9.68 0.00 0.00 2.15
2388 2506 6.487960 CATTGTTTTTGCAACACACATTGAT 58.512 32.000 9.68 0.00 0.00 2.57
2424 2543 6.545504 TGAGCTCAAATGAACAGTAAAGTC 57.454 37.500 15.67 0.00 0.00 3.01
2489 2608 1.757306 CAGTCTCAGGGCAGGTGTT 59.243 57.895 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.