Multiple sequence alignment - TraesCS1B01G047200

Loading Multiple Alignment...

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 TraesCS1B01G047200 chr1B 100.000 6048 0 0 1 6048 26972712 26966665 0.000000e+00 11169
1 TraesCS1B01G047200 chr7A 97.447 3799 68 19 2266 6048 675268731 675264946 0.000000e+00 6451
2 TraesCS1B01G047200 chr7A 97.604 1920 38 7 1 1914 675270645 675268728 0.000000e+00 3284
3 TraesCS1B01G047200 chr2B 92.999 2914 129 39 3150 6048 725139558 725142411 0.000000e+00 4181
4 TraesCS1B01G047200 chr2B 93.718 2372 123 21 1 2359 725136284 725138642 0.000000e+00 3531
5 TraesCS1B01G047200 chr2B 94.823 734 34 4 2417 3147 725138642 725139374 0.000000e+00 1142
6 TraesCS1B01G047200 chr5D 88.346 3192 261 68 1 3147 431721030 431724155 0.000000e+00 3731
7 TraesCS1B01G047200 chr5D 90.162 1789 119 36 3569 5339 431724669 431726418 0.000000e+00 2276
8 TraesCS1B01G047200 chr5D 87.988 691 52 15 5379 6046 431726773 431727455 0.000000e+00 787
9 TraesCS1B01G047200 chr5D 89.937 318 25 7 3150 3466 431724308 431724619 2.630000e-108 403
10 TraesCS1B01G047200 chr6B 87.463 3047 267 67 1 3002 712390724 712387748 0.000000e+00 3404
11 TraesCS1B01G047200 chr6B 88.479 2031 144 44 3333 5339 712387744 712385780 0.000000e+00 2372
12 TraesCS1B01G047200 chr6B 86.579 380 31 9 5685 6048 712385540 712385165 9.440000e-108 401
13 TraesCS1B01G047200 chr3B 86.381 514 48 19 3150 3658 97078682 97079178 5.330000e-150 542
14 TraesCS1B01G047200 chr3D 85.659 516 47 21 3150 3658 61313909 61314404 8.990000e-143 518
15 TraesCS1B01G047200 chr5B 89.855 276 20 5 5341 5613 63615766 63615496 1.250000e-91 348


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 TraesCS1B01G047200 chr1B 26966665 26972712 6047 True 11169.000000 11169 100.000000 1 6048 1 chr1B.!!$R1 6047
1 TraesCS1B01G047200 chr7A 675264946 675270645 5699 True 4867.500000 6451 97.525500 1 6048 2 chr7A.!!$R1 6047
2 TraesCS1B01G047200 chr2B 725136284 725142411 6127 False 2951.333333 4181 93.846667 1 6048 3 chr2B.!!$F1 6047
3 TraesCS1B01G047200 chr5D 431721030 431727455 6425 False 1799.250000 3731 89.108250 1 6046 4 chr5D.!!$F1 6045
4 TraesCS1B01G047200 chr6B 712385165 712390724 5559 True 2059.000000 3404 87.507000 1 6048 3 chr6B.!!$R1 6047

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
349 356 0.899720 AGGCGTCCCACGAATTCTTA 59.100 50.000 3.52 0.00 46.05 2.10 F
850 876 2.037136 ATTGACAGCGCAGACTGCC 61.037 57.895 21.55 13.94 41.12 4.85 F
1294 1324 2.076100 CGTTAAGAGCAGCATCAACCA 58.924 47.619 0.00 0.00 0.00 3.67 F
2107 2151 0.111061 AGGACTGCAAGATTGGCACA 59.889 50.000 0.00 0.00 36.11 4.57 F
2925 2987 0.512518 TCAAACGAAGAGTGCATGCG 59.487 50.000 14.09 0.00 0.00 4.73 F
3660 3922 3.551846 CCCATAGAAAAGTATGGCCGTT 58.448 45.455 0.77 0.00 45.81 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1372 1402 1.999648 AGGTTGCAATGGAAGCTTGA 58.000 45.000 13.30 0.0 0.00 3.02 R
1876 1918 2.267961 GCCGGTTAGACTGGTGGG 59.732 66.667 1.90 0.0 46.46 4.61 R
2369 2421 2.352715 CGGTGAGCATGTAGAACACAGA 60.353 50.000 0.00 0.0 41.51 3.41 R
3600 3862 0.817634 CGGTGTTCTTGGTCTTGGCA 60.818 55.000 0.00 0.0 0.00 4.92 R
4743 5030 0.966875 GCAGATCCAATGGTGGTGCA 60.967 55.000 14.41 0.0 46.11 4.57 R
5487 6107 0.108472 CTGAGCATGGCGTCTCTCAA 60.108 55.000 8.86 0.0 35.44 3.02 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
60 61 4.890988 TCCTACTATCACAAGGGGATTCA 58.109 43.478 0.00 0.00 0.00 2.57
201 203 8.826710 TGTAAGTGTTCAGTATCTCTTTTGTTG 58.173 33.333 0.00 0.00 0.00 3.33
208 211 8.807581 GTTCAGTATCTCTTTTGTTGTTTTTGG 58.192 33.333 0.00 0.00 0.00 3.28
257 260 5.462068 CGATTGTTTTGTTCCTTTTCCTTCC 59.538 40.000 0.00 0.00 0.00 3.46
342 349 4.373116 GAGCAAGGCGTCCCACGA 62.373 66.667 0.00 0.00 46.05 4.35
349 356 0.899720 AGGCGTCCCACGAATTCTTA 59.100 50.000 3.52 0.00 46.05 2.10
471 479 6.960431 CGTTTTTCATTTTTGTGTTGAGCAAT 59.040 30.769 0.00 0.00 0.00 3.56
502 512 5.605488 TCTGTAGTTCAAAAGGGAGTTAGGT 59.395 40.000 0.00 0.00 0.00 3.08
518 532 6.299805 AGTTAGGTACATGCATCTCTTTCA 57.700 37.500 0.00 0.00 0.00 2.69
610 628 2.792674 CAGCATGTGTTTGCAACTGAAG 59.207 45.455 0.00 0.00 45.23 3.02
850 876 2.037136 ATTGACAGCGCAGACTGCC 61.037 57.895 21.55 13.94 41.12 4.85
866 892 3.821033 GACTGCCACAACATAAAGGAGTT 59.179 43.478 0.00 0.00 0.00 3.01
912 938 7.642071 AGCAATAACATCAAATGTGTTGAAC 57.358 32.000 16.35 0.00 44.07 3.18
989 1015 5.246429 CCTCTTCAAAACTAGGACCAGTAGT 59.754 44.000 0.00 0.00 31.80 2.73
990 1016 6.239629 CCTCTTCAAAACTAGGACCAGTAGTT 60.240 42.308 0.00 0.00 41.52 2.24
1069 1095 3.324993 GGTATGCATTTTTGGTGTGTGG 58.675 45.455 3.54 0.00 0.00 4.17
1294 1324 2.076100 CGTTAAGAGCAGCATCAACCA 58.924 47.619 0.00 0.00 0.00 3.67
1372 1402 3.452264 TCAGTCATCGGAATGAGGAACAT 59.548 43.478 0.00 0.00 42.67 2.71
1437 1467 3.704566 AGTTCATAAGGGCTCACACGATA 59.295 43.478 0.00 0.00 0.00 2.92
1455 1485 5.803461 CACGATACTTTAGGTTCATTCGTGA 59.197 40.000 14.81 0.00 46.49 4.35
1534 1573 8.968969 TCCTTGTTTTTAGTAGTGGCTTTTTAA 58.031 29.630 0.00 0.00 0.00 1.52
1876 1918 2.594592 AGGGCACTTTCACACGCC 60.595 61.111 0.00 0.00 44.10 5.68
1969 2011 7.465781 GCAATTACCAAATGATTAACCACATGC 60.466 37.037 0.00 0.00 0.00 4.06
1990 2032 3.746432 GCCACCAATAGGCCGTATAAAGT 60.746 47.826 0.00 0.00 46.50 2.66
1997 2039 6.094325 CCAATAGGCCGTATAAAGTTGTTCAA 59.906 38.462 0.00 0.00 0.00 2.69
2003 2045 5.353123 GCCGTATAAAGTTGTTCAATGAGGA 59.647 40.000 0.00 0.00 0.00 3.71
2014 2056 3.063510 TCAATGAGGAGGTCAGCTTTG 57.936 47.619 0.00 0.00 39.07 2.77
2107 2151 0.111061 AGGACTGCAAGATTGGCACA 59.889 50.000 0.00 0.00 36.11 4.57
2118 2162 4.024717 TGGCACAAGCAACAACCA 57.975 50.000 0.00 0.00 44.61 3.67
2153 2197 6.100404 TGGCATTAGCAGACAAGAATTTTT 57.900 33.333 0.00 0.00 44.61 1.94
2154 2198 6.158598 TGGCATTAGCAGACAAGAATTTTTC 58.841 36.000 0.00 0.00 44.61 2.29
2163 2207 7.390162 AGCAGACAAGAATTTTTCAAAAACCAA 59.610 29.630 0.00 0.00 0.00 3.67
2212 2256 0.909610 TCCCAGTGGCCGATCTTTCT 60.910 55.000 2.61 0.00 0.00 2.52
2234 2278 6.738635 TCTCCCTCTATGGTTAGTGTTTAGA 58.261 40.000 0.00 0.00 0.00 2.10
2637 2691 6.457934 GCAGACATTGTTGATATCAGTCCAAG 60.458 42.308 14.96 9.09 0.00 3.61
2665 2719 2.890311 TGGTGTCAGGCAAATCGAATTT 59.110 40.909 0.00 0.00 0.00 1.82
2718 2780 3.315765 TCGGACCAATTGCGAAACT 57.684 47.368 0.00 0.00 46.23 2.66
2772 2834 1.270785 TGTTGATGTGCCAGACGACAT 60.271 47.619 0.00 0.00 35.46 3.06
2805 2867 3.457234 TCATTATCGATGAACTTGCGCT 58.543 40.909 9.73 0.00 41.73 5.92
2816 2878 3.259064 GAACTTGCGCTAGACACCATTA 58.741 45.455 25.45 0.00 0.00 1.90
2820 2882 3.097877 TGCGCTAGACACCATTATCAG 57.902 47.619 9.73 0.00 0.00 2.90
2925 2987 0.512518 TCAAACGAAGAGTGCATGCG 59.487 50.000 14.09 0.00 0.00 4.73
2977 3039 6.541111 ACAAAAAGAATTCAGAGGTACGTC 57.459 37.500 8.44 7.49 0.00 4.34
3357 3618 9.232473 CTTAGTTCAAGTTTAGGGCTTTTAGAT 57.768 33.333 0.00 0.00 0.00 1.98
3521 3783 5.698545 GCTACTTGAATAGCTCATGGTAAGG 59.301 44.000 0.00 0.00 43.62 2.69
3660 3922 3.551846 CCCATAGAAAAGTATGGCCGTT 58.448 45.455 0.77 0.00 45.81 4.44
4125 4398 4.881850 TGTGTTCTTCTTTGTCCTTCTTCC 59.118 41.667 0.00 0.00 0.00 3.46
4274 4552 4.151883 ACCATTGGATAGTGTTTGCTGTT 58.848 39.130 10.37 0.00 0.00 3.16
4375 4653 9.125026 AGAGAAATTTGTAAGTTGTTCATCACT 57.875 29.630 0.00 0.00 0.00 3.41
4657 4940 8.673711 GCTCTTGTTTTTATTTTTGTTTTCCCT 58.326 29.630 0.00 0.00 0.00 4.20
4669 4952 7.841915 TTTTGTTTTCCCTCTTTTTAGCTTG 57.158 32.000 0.00 0.00 0.00 4.01
4743 5030 8.523915 TTGCAACAAAGATAATGGAGATATGT 57.476 30.769 0.00 0.00 0.00 2.29
4752 5039 1.284313 TGGAGATATGTGCACCACCA 58.716 50.000 15.69 10.03 32.73 4.17
4833 5120 6.593770 ACATGAACCAACTTTTCTTTTGGAAC 59.406 34.615 0.00 2.02 44.51 3.62
5165 5465 6.261381 TCAATTTTTGTGTAGTGTAGTGGTCC 59.739 38.462 0.00 0.00 0.00 4.46
5211 5511 4.318050 CGTTGGTTGTACGAGCATATCATG 60.318 45.833 15.56 3.06 41.33 3.07
5225 5525 7.305590 CGAGCATATCATGTTTGTTGTAAATGC 60.306 37.037 0.00 0.00 0.00 3.56
5235 5535 2.697751 TGTTGTAAATGCTGGCCACTTT 59.302 40.909 0.00 4.82 0.00 2.66
5312 5612 8.037758 CAGAGACAGACTATCATTTACCTTGTT 58.962 37.037 0.00 0.00 0.00 2.83
5339 5639 7.704899 AGTTTGTTTGTTCTCCCTTAATTTTCG 59.295 33.333 0.00 0.00 0.00 3.46
5392 6009 3.566742 TGCGTCTGTCAGTTTAGTGTCTA 59.433 43.478 0.00 0.00 0.00 2.59
5469 6089 7.857885 GTGTGATTTTTCTAAAACCTCACTCTG 59.142 37.037 20.03 0.00 39.33 3.35
5554 6175 6.365970 ACAAAGATGTCTACAATCAGTCCT 57.634 37.500 0.00 0.00 33.41 3.85
5754 6378 1.964223 CTATCCATGCAGGGTACGAGT 59.036 52.381 18.43 0.78 38.24 4.18
5888 6521 4.337145 TCGCCCTGTTAACAATACCATTT 58.663 39.130 10.03 0.00 0.00 2.32
6016 6655 2.612760 AGCTGATCTTGGCTGGCTA 58.387 52.632 2.00 0.00 37.41 3.93
6029 6668 2.700897 GGCTGGCTAGTCTTCCTTGATA 59.299 50.000 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 5.196341 TCGTAGACAAGAAGACACATGTT 57.804 39.130 0.00 0.00 0.00 2.71
342 349 8.893563 TCAAATTACCCTTCCATGTAAGAATT 57.106 30.769 0.00 0.00 31.05 2.17
349 356 8.429237 TGTTTAATCAAATTACCCTTCCATGT 57.571 30.769 0.00 0.00 0.00 3.21
471 479 7.614192 ACTCCCTTTTGAACTACAGAAGAAAAA 59.386 33.333 0.00 0.00 41.39 1.94
610 628 0.682209 ATGCCATGAGGAGCACCAAC 60.682 55.000 2.07 0.00 42.84 3.77
698 716 3.295973 AGGCAAGACTAAAACCTGCAAA 58.704 40.909 0.00 0.00 0.00 3.68
700 718 2.158682 TGAGGCAAGACTAAAACCTGCA 60.159 45.455 0.00 0.00 0.00 4.41
823 849 0.815213 GCGCTGTCAATGATGCCCTA 60.815 55.000 0.00 0.00 0.00 3.53
850 876 5.234116 GCAAACCAAACTCCTTTATGTTGTG 59.766 40.000 0.00 0.00 0.00 3.33
866 892 4.478206 TCCTGAACATTTTGCAAACCAA 57.522 36.364 12.39 0.00 0.00 3.67
989 1015 6.593382 GCTCATTATGCCCATGTTTTGTTTAA 59.407 34.615 0.00 0.00 0.00 1.52
990 1016 6.105333 GCTCATTATGCCCATGTTTTGTTTA 58.895 36.000 0.00 0.00 0.00 2.01
1069 1095 4.642429 TCTCAAGTAAAAAGGAGCCTCAC 58.358 43.478 0.00 0.00 0.00 3.51
1294 1324 6.698008 TTTCATTGATCTTGACAGTTGTGT 57.302 33.333 0.00 0.00 40.71 3.72
1372 1402 1.999648 AGGTTGCAATGGAAGCTTGA 58.000 45.000 13.30 0.00 0.00 3.02
1437 1467 6.937436 AAGTTTCACGAATGAACCTAAAGT 57.063 33.333 0.00 0.00 44.66 2.66
1833 1875 3.115554 GTTTTGCACACTAAACTGCAGG 58.884 45.455 19.93 1.96 44.05 4.85
1876 1918 2.267961 GCCGGTTAGACTGGTGGG 59.732 66.667 1.90 0.00 46.46 4.61
1941 1983 7.675062 TGTGGTTAATCATTTGGTAATTGCTT 58.325 30.769 0.00 0.00 0.00 3.91
1969 2011 4.081322 ACTTTATACGGCCTATTGGTGG 57.919 45.455 0.00 0.00 35.27 4.61
1985 2027 5.935945 TGACCTCCTCATTGAACAACTTTA 58.064 37.500 0.00 0.00 0.00 1.85
1990 2032 2.373169 AGCTGACCTCCTCATTGAACAA 59.627 45.455 0.00 0.00 0.00 2.83
1997 2039 2.683152 GCATCAAAGCTGACCTCCTCAT 60.683 50.000 0.00 0.00 33.30 2.90
2003 2045 2.803030 AGATGCATCAAAGCTGACCT 57.197 45.000 27.81 0.51 33.30 3.85
2107 2151 3.084786 GAGCTTAGGATGGTTGTTGCTT 58.915 45.455 0.00 0.00 0.00 3.91
2118 2162 3.073503 TGCTAATGCCATGAGCTTAGGAT 59.926 43.478 15.10 0.00 44.23 3.24
2212 2256 7.989947 AATCTAAACACTAACCATAGAGGGA 57.010 36.000 0.00 0.00 43.89 4.20
2367 2419 4.065088 GGTGAGCATGTAGAACACAGAAA 58.935 43.478 0.00 0.00 41.51 2.52
2368 2420 3.664107 GGTGAGCATGTAGAACACAGAA 58.336 45.455 0.00 0.00 41.51 3.02
2369 2421 2.352715 CGGTGAGCATGTAGAACACAGA 60.353 50.000 0.00 0.00 41.51 3.41
2507 2559 4.275689 CCAAAAATAGCTCCACATATGCGA 59.724 41.667 1.58 0.00 0.00 5.10
2637 2691 3.518634 TTTGCCTGACACCAAAACTTC 57.481 42.857 0.00 0.00 0.00 3.01
2665 2719 7.444299 TGTATACATGATCTGCATTCTTAGCA 58.556 34.615 0.08 0.00 40.19 3.49
2718 2780 3.369052 CCCTACTGTAGATTGGCGTTGAA 60.369 47.826 16.22 0.00 0.00 2.69
2805 2867 5.163550 CGACCTTGACTGATAATGGTGTCTA 60.164 44.000 0.00 0.00 0.00 2.59
2816 2878 3.448660 TCATCATGTCGACCTTGACTGAT 59.551 43.478 17.47 11.04 39.64 2.90
2820 2882 4.631377 TCAAATCATCATGTCGACCTTGAC 59.369 41.667 17.47 0.00 39.37 3.18
2925 2987 7.295201 TGCAAGTTCGATTATTGAGTTGTAAC 58.705 34.615 8.47 0.00 0.00 2.50
3259 3520 5.499139 AGCAAAATCAACAACGAGAAAGA 57.501 34.783 0.00 0.00 0.00 2.52
3357 3618 8.598202 TCAGACCTTAACTGGTGTATATACAA 57.402 34.615 17.07 2.24 41.00 2.41
3521 3783 4.595762 ATGGATTTTGTATGCTGCCATC 57.404 40.909 0.00 0.00 32.85 3.51
3547 3809 7.885297 TGATCATTGTTTAAGCTATATTGGCC 58.115 34.615 0.00 0.00 0.00 5.36
3600 3862 0.817634 CGGTGTTCTTGGTCTTGGCA 60.818 55.000 0.00 0.00 0.00 4.92
4274 4552 6.405538 AGCAAAAAGTTTCCACTTGAAATCA 58.594 32.000 2.61 0.00 42.89 2.57
4743 5030 0.966875 GCAGATCCAATGGTGGTGCA 60.967 55.000 14.41 0.00 46.11 4.57
4752 5039 3.698040 AGAAAATCTTGCGCAGATCCAAT 59.302 39.130 11.31 3.77 41.93 3.16
4833 5120 3.111098 GCTCTTGTCTGCAGTGTTTTTG 58.889 45.455 14.67 1.59 0.00 2.44
5165 5465 3.374058 ACAACTTCCTCAACAGTTCAACG 59.626 43.478 0.00 0.00 30.48 4.10
5211 5511 2.799978 GTGGCCAGCATTTACAACAAAC 59.200 45.455 5.11 0.00 0.00 2.93
5225 5525 4.326504 ACATGAAAAAGAAAGTGGCCAG 57.673 40.909 5.11 0.00 0.00 4.85
5392 6009 4.895668 TGAATTAGACACCTACGGGTTT 57.104 40.909 0.00 0.00 44.73 3.27
5487 6107 0.108472 CTGAGCATGGCGTCTCTCAA 60.108 55.000 8.86 0.00 35.44 3.02
5754 6378 3.366396 CCTGCAACTCTAACTCCCTCTA 58.634 50.000 0.00 0.00 0.00 2.43
5888 6521 7.037438 GGTATTGTTATCGACTAACTGTGGAA 58.963 38.462 14.56 5.36 40.40 3.53
5930 6568 5.129320 AGCACTCCATTGACACACTCATATA 59.871 40.000 0.00 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.