Multiple sequence alignment - TraesCS5D01G191300

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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 TraesCS5D01G191300 chr5D 100.000 3410 0 0 1 3410 293656030 293659439 0.000000e+00 6298
1 TraesCS5D01G191300 chr5B 96.473 2410 66 11 744 3142 335201359 335203760 0.000000e+00 3962
2 TraesCS5D01G191300 chr5B 95.956 272 8 2 3141 3410 335203798 335204068 4.040000e-119 438
3 TraesCS5D01G191300 chr5A 96.349 2191 61 11 738 2915 386697696 386699880 0.000000e+00 3585
4 TraesCS5D01G191300 chr5A 95.436 241 5 2 3176 3410 386700140 386700380 2.480000e-101 379
5 TraesCS5D01G191300 chr5A 95.477 199 7 1 2945 3141 386699874 386700072 1.970000e-82 316
6 TraesCS5D01G191300 chr3D 96.603 736 21 2 1 736 566012103 566012834 0.000000e+00 1218
7 TraesCS5D01G191300 chr6D 95.935 738 26 2 1 738 138312636 138313369 0.000000e+00 1194
8 TraesCS5D01G191300 chr4B 87.027 740 66 23 1 730 466993053 466993772 0.000000e+00 808
9 TraesCS5D01G191300 chr2A 89.791 431 32 7 1 427 757804067 757804489 2.990000e-150 542
10 TraesCS5D01G191300 chr2A 91.608 286 17 3 461 742 757804488 757804770 4.130000e-104 388
11 TraesCS5D01G191300 chr4A 89.559 431 33 9 1 427 120566464 120566886 1.390000e-148 536
12 TraesCS5D01G191300 chr4A 88.863 431 36 7 1 427 28569755 28570177 1.400000e-143 520
13 TraesCS5D01G191300 chr4A 91.727 278 15 4 461 733 28570176 28570450 2.480000e-101 379
14 TraesCS5D01G191300 chr4A 91.398 279 17 3 461 735 120566885 120567160 3.210000e-100 375
15 TraesCS5D01G191300 chr6B 93.407 182 8 2 554 734 636127599 636127421 2.020000e-67 267
16 TraesCS5D01G191300 chr6B 97.087 103 3 0 1 103 636129960 636129858 1.260000e-39 174


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 TraesCS5D01G191300 chr5D 293656030 293659439 3409 False 6298.000000 6298 100.0000 1 3410 1 chr5D.!!$F1 3409
1 TraesCS5D01G191300 chr5B 335201359 335204068 2709 False 2200.000000 3962 96.2145 744 3410 2 chr5B.!!$F1 2666
2 TraesCS5D01G191300 chr5A 386697696 386700380 2684 False 1426.666667 3585 95.7540 738 3410 3 chr5A.!!$F1 2672
3 TraesCS5D01G191300 chr3D 566012103 566012834 731 False 1218.000000 1218 96.6030 1 736 1 chr3D.!!$F1 735
4 TraesCS5D01G191300 chr6D 138312636 138313369 733 False 1194.000000 1194 95.9350 1 738 1 chr6D.!!$F1 737
5 TraesCS5D01G191300 chr4B 466993053 466993772 719 False 808.000000 808 87.0270 1 730 1 chr4B.!!$F1 729
6 TraesCS5D01G191300 chr2A 757804067 757804770 703 False 465.000000 542 90.6995 1 742 2 chr2A.!!$F1 741
7 TraesCS5D01G191300 chr4A 120566464 120567160 696 False 455.500000 536 90.4785 1 735 2 chr4A.!!$F2 734
8 TraesCS5D01G191300 chr4A 28569755 28570450 695 False 449.500000 520 90.2950 1 733 2 chr4A.!!$F1 732
9 TraesCS5D01G191300 chr6B 636127421 636129960 2539 True 220.500000 267 95.2470 1 734 2 chr6B.!!$R1 733

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
742 2655 0.171007 CAAACAAGGCCTACATGCGG 59.829 55.0 5.16 0.0 0.0 5.69 F
2034 3959 0.327924 TCACGGGGATTCAGCATGTT 59.672 50.0 0.00 0.0 37.4 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2064 3989 0.186143 TTGGTGGCCCAACATACACA 59.814 50.000 0.18 0.0 45.93 3.72 R
2937 4870 1.073763 TGTTTGTATGCCCTGTCAGCT 59.926 47.619 0.00 0.0 0.00 4.24 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
128 331 0.575390 CAACAACGACGTCGAGCTTT 59.425 50.000 41.52 23.72 43.02 3.51
232 436 3.841255 CCTCCTTCTCCTTGGACTTAGTT 59.159 47.826 0.00 0.00 0.00 2.24
458 665 3.181465 CGTGAGGCTCCCAACAATATACT 60.181 47.826 12.86 0.00 0.00 2.12
523 755 0.246635 GGGAGAAGCGCAGTCAGTAA 59.753 55.000 11.47 0.00 0.00 2.24
704 2617 5.687166 ACCCGTTTCCTATAATCTCACAA 57.313 39.130 0.00 0.00 0.00 3.33
705 2618 5.425630 ACCCGTTTCCTATAATCTCACAAC 58.574 41.667 0.00 0.00 0.00 3.32
706 2619 5.189145 ACCCGTTTCCTATAATCTCACAACT 59.811 40.000 0.00 0.00 0.00 3.16
742 2655 0.171007 CAAACAAGGCCTACATGCGG 59.829 55.000 5.16 0.00 0.00 5.69
783 2697 1.817099 GGGACATCGCTCAGCCAAG 60.817 63.158 0.00 0.00 0.00 3.61
854 2769 0.806102 CGTAACAGCACATCGAGGGG 60.806 60.000 0.69 0.00 0.00 4.79
855 2770 1.090052 GTAACAGCACATCGAGGGGC 61.090 60.000 18.18 18.18 0.00 5.80
856 2771 2.572095 TAACAGCACATCGAGGGGCG 62.572 60.000 19.75 15.93 42.69 6.13
904 2823 2.423577 CTCCCTAACAAACCTCCGTTG 58.576 52.381 0.00 0.00 30.72 4.10
949 2874 3.711782 CCCCTCCCCTCCCTTCCT 61.712 72.222 0.00 0.00 0.00 3.36
950 2875 2.040359 CCCTCCCCTCCCTTCCTC 60.040 72.222 0.00 0.00 0.00 3.71
951 2876 2.040359 CCTCCCCTCCCTTCCTCC 60.040 72.222 0.00 0.00 0.00 4.30
952 2877 2.652113 CCTCCCCTCCCTTCCTCCT 61.652 68.421 0.00 0.00 0.00 3.69
953 2878 1.383803 CTCCCCTCCCTTCCTCCTG 60.384 68.421 0.00 0.00 0.00 3.86
954 2879 1.866997 TCCCCTCCCTTCCTCCTGA 60.867 63.158 0.00 0.00 0.00 3.86
955 2880 1.383803 CCCCTCCCTTCCTCCTGAG 60.384 68.421 0.00 0.00 0.00 3.35
1170 3095 2.572647 GTCTACGACGTCACGCCG 60.573 66.667 17.16 3.69 38.88 6.46
1569 3494 1.984026 CCAAATCACCAGGCACCCC 60.984 63.158 0.00 0.00 0.00 4.95
1689 3614 3.461773 AGCCTCGACCATGACCCG 61.462 66.667 0.00 0.00 0.00 5.28
1749 3674 2.287009 GCTCTTCAACAACCTTTGGTCG 60.287 50.000 0.00 0.00 33.12 4.79
1929 3854 2.184322 GAGATCGCCGGAGTTGCA 59.816 61.111 5.05 0.00 0.00 4.08
2034 3959 0.327924 TCACGGGGATTCAGCATGTT 59.672 50.000 0.00 0.00 37.40 2.71
2064 3989 0.976641 TGAACCACTTCTCATCCGCT 59.023 50.000 0.00 0.00 0.00 5.52
2280 4205 0.106519 ATGGGCTGTCTTATGGTGCC 60.107 55.000 0.00 0.00 42.56 5.01
2912 4845 9.267084 TCAATTTCTTTGTATTTACTTTTGGGC 57.733 29.630 0.00 0.00 36.65 5.36
2913 4846 9.050601 CAATTTCTTTGTATTTACTTTTGGGCA 57.949 29.630 0.00 0.00 0.00 5.36
2914 4847 9.791801 AATTTCTTTGTATTTACTTTTGGGCAT 57.208 25.926 0.00 0.00 0.00 4.40
2915 4848 8.825667 TTTCTTTGTATTTACTTTTGGGCATC 57.174 30.769 0.00 0.00 0.00 3.91
2916 4849 7.775053 TCTTTGTATTTACTTTTGGGCATCT 57.225 32.000 0.00 0.00 0.00 2.90
2917 4850 7.601856 TCTTTGTATTTACTTTTGGGCATCTG 58.398 34.615 0.00 0.00 0.00 2.90
2918 4851 6.909550 TTGTATTTACTTTTGGGCATCTGT 57.090 33.333 0.00 0.00 0.00 3.41
2919 4852 8.410673 TTTGTATTTACTTTTGGGCATCTGTA 57.589 30.769 0.00 0.00 0.00 2.74
2920 4853 8.410673 TTGTATTTACTTTTGGGCATCTGTAA 57.589 30.769 0.00 0.00 0.00 2.41
2921 4854 8.410673 TGTATTTACTTTTGGGCATCTGTAAA 57.589 30.769 0.00 0.00 35.37 2.01
2922 4855 8.861086 TGTATTTACTTTTGGGCATCTGTAAAA 58.139 29.630 0.00 0.00 34.83 1.52
2923 4856 9.869757 GTATTTACTTTTGGGCATCTGTAAAAT 57.130 29.630 0.00 0.00 34.83 1.82
2924 4857 8.776376 ATTTACTTTTGGGCATCTGTAAAATG 57.224 30.769 0.00 0.00 34.83 2.32
2925 4858 5.151297 ACTTTTGGGCATCTGTAAAATGG 57.849 39.130 0.00 0.00 0.00 3.16
2926 4859 3.608316 TTTGGGCATCTGTAAAATGGC 57.392 42.857 1.40 1.40 46.00 4.40
2927 4860 2.530460 TGGGCATCTGTAAAATGGCT 57.470 45.000 9.15 0.00 45.99 4.75
2928 4861 2.101783 TGGGCATCTGTAAAATGGCTG 58.898 47.619 9.15 0.00 45.99 4.85
2929 4862 1.410153 GGGCATCTGTAAAATGGCTGG 59.590 52.381 9.15 0.00 45.99 4.85
2930 4863 2.378038 GGCATCTGTAAAATGGCTGGA 58.622 47.619 2.76 0.00 44.04 3.86
2931 4864 2.961062 GGCATCTGTAAAATGGCTGGAT 59.039 45.455 2.76 0.00 44.04 3.41
2932 4865 4.144297 GGCATCTGTAAAATGGCTGGATA 58.856 43.478 2.76 0.00 44.04 2.59
2933 4866 4.217118 GGCATCTGTAAAATGGCTGGATAG 59.783 45.833 2.76 0.00 44.04 2.08
2934 4867 5.065914 GCATCTGTAAAATGGCTGGATAGA 58.934 41.667 0.00 0.00 0.00 1.98
2935 4868 5.532406 GCATCTGTAAAATGGCTGGATAGAA 59.468 40.000 0.00 0.00 0.00 2.10
2936 4869 6.208204 GCATCTGTAAAATGGCTGGATAGAAT 59.792 38.462 0.00 0.00 0.00 2.40
2937 4870 7.391554 GCATCTGTAAAATGGCTGGATAGAATA 59.608 37.037 0.00 0.00 0.00 1.75
2938 4871 8.944029 CATCTGTAAAATGGCTGGATAGAATAG 58.056 37.037 0.00 0.00 0.00 1.73
2939 4872 6.936900 TCTGTAAAATGGCTGGATAGAATAGC 59.063 38.462 0.00 0.00 36.74 2.97
2940 4873 6.841601 TGTAAAATGGCTGGATAGAATAGCT 58.158 36.000 0.00 0.00 37.58 3.32
2941 4874 6.712095 TGTAAAATGGCTGGATAGAATAGCTG 59.288 38.462 0.00 0.00 37.58 4.24
2942 4875 5.573380 AAATGGCTGGATAGAATAGCTGA 57.427 39.130 0.00 0.00 37.58 4.26
2943 4876 4.550076 ATGGCTGGATAGAATAGCTGAC 57.450 45.455 0.00 0.00 37.58 3.51
3027 4995 7.010552 TCGCTAAGATCAAGCTTTCAGATTTAC 59.989 37.037 15.56 0.00 37.85 2.01
3094 5062 6.611381 TCGCCTAACAATTCAAGAAAAGATG 58.389 36.000 0.00 0.00 0.00 2.90
3101 5069 6.789262 ACAATTCAAGAAAAGATGCTATCCG 58.211 36.000 0.00 0.00 0.00 4.18
3145 5158 7.886446 TGCATATCATAGATTCACAATCCATGT 59.114 33.333 5.07 0.00 45.34 3.21
3167 5182 8.503196 CATGTTACTGTTCTTGCATAACTTGTA 58.497 33.333 12.19 11.61 31.39 2.41
3183 5198 9.826574 CATAACTTGTAGTATAAAACTAGGGCA 57.173 33.333 0.00 0.00 41.42 5.36
3190 5205 9.523168 TGTAGTATAAAACTAGGGCAAATTTGT 57.477 29.630 19.03 2.68 41.42 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 331 1.126948 TATCCCTCATCCATGCCGCA 61.127 55.000 0.00 0.00 0.00 5.69
458 665 3.159615 TGGGCACATGAGCACAGA 58.840 55.556 16.58 0.00 44.33 3.41
523 755 2.022129 CACTTCGCTCGTCGCCTTT 61.022 57.895 0.00 0.00 38.27 3.11
674 2587 8.728337 AGATTATAGGAAACGGGTTTTTAGAC 57.272 34.615 0.00 0.00 32.11 2.59
783 2697 5.234543 GCTCCACGGTAAAGATAATCTGAAC 59.765 44.000 0.00 0.00 0.00 3.18
904 2823 3.810386 GGGAGATCGGATCTTAAAACAGC 59.190 47.826 20.77 6.28 40.38 4.40
945 2870 0.487325 TGGTCAGGACTCAGGAGGAA 59.513 55.000 0.83 0.00 0.00 3.36
949 2874 1.229209 GGGTGGTCAGGACTCAGGA 60.229 63.158 0.00 0.00 0.00 3.86
950 2875 2.294078 GGGGTGGTCAGGACTCAGG 61.294 68.421 0.00 0.00 0.00 3.86
951 2876 1.229336 AGGGGTGGTCAGGACTCAG 60.229 63.158 0.00 0.00 0.00 3.35
952 2877 1.229209 GAGGGGTGGTCAGGACTCA 60.229 63.158 0.00 0.00 0.00 3.41
953 2878 1.990614 GGAGGGGTGGTCAGGACTC 60.991 68.421 0.00 0.00 0.00 3.36
954 2879 2.122954 GGAGGGGTGGTCAGGACT 59.877 66.667 0.00 0.00 0.00 3.85
955 2880 1.990614 GAGGAGGGGTGGTCAGGAC 60.991 68.421 0.00 0.00 0.00 3.85
1689 3614 2.360475 GGCAAGTGCTGGAGGTCC 60.360 66.667 2.85 0.00 41.70 4.46
1749 3674 2.881352 GTGCGCTCGTAGCAGACC 60.881 66.667 9.73 0.00 46.10 3.85
1929 3854 0.250597 GGTACCAAACCCAGAACGCT 60.251 55.000 7.15 0.00 43.16 5.07
1954 3879 2.435586 CGGCAGGCAAGAGACCAG 60.436 66.667 0.00 0.00 0.00 4.00
2064 3989 0.186143 TTGGTGGCCCAACATACACA 59.814 50.000 0.18 0.00 45.93 3.72
2112 4037 0.541392 TGATATCAAGTGTGCCCGCT 59.459 50.000 1.98 0.00 0.00 5.52
2280 4205 2.825836 GCCTCCCAGAATGTGGCG 60.826 66.667 0.00 0.00 46.45 5.69
2370 4295 2.646798 AGCTTCCCAGACCAGATTCTTT 59.353 45.455 0.00 0.00 0.00 2.52
2663 4589 6.808008 AGATAAGCCACGGATTTTATGATG 57.192 37.500 0.00 0.00 0.00 3.07
2669 4595 6.039382 GGATGTAAAGATAAGCCACGGATTTT 59.961 38.462 0.00 0.00 0.00 1.82
2909 4842 1.410153 CCAGCCATTTTACAGATGCCC 59.590 52.381 0.00 0.00 0.00 5.36
2910 4843 2.378038 TCCAGCCATTTTACAGATGCC 58.622 47.619 0.00 0.00 0.00 4.40
2911 4844 5.065914 TCTATCCAGCCATTTTACAGATGC 58.934 41.667 0.00 0.00 0.00 3.91
2912 4845 7.756395 ATTCTATCCAGCCATTTTACAGATG 57.244 36.000 0.00 0.00 0.00 2.90
2913 4846 7.609532 GCTATTCTATCCAGCCATTTTACAGAT 59.390 37.037 0.00 0.00 0.00 2.90
2914 4847 6.936900 GCTATTCTATCCAGCCATTTTACAGA 59.063 38.462 0.00 0.00 0.00 3.41
2915 4848 6.939163 AGCTATTCTATCCAGCCATTTTACAG 59.061 38.462 0.00 0.00 35.88 2.74
2916 4849 6.712095 CAGCTATTCTATCCAGCCATTTTACA 59.288 38.462 0.00 0.00 35.88 2.41
2917 4850 6.936900 TCAGCTATTCTATCCAGCCATTTTAC 59.063 38.462 0.00 0.00 35.88 2.01
2918 4851 6.936900 GTCAGCTATTCTATCCAGCCATTTTA 59.063 38.462 0.00 0.00 35.88 1.52
2919 4852 5.767168 GTCAGCTATTCTATCCAGCCATTTT 59.233 40.000 0.00 0.00 35.88 1.82
2920 4853 5.163163 TGTCAGCTATTCTATCCAGCCATTT 60.163 40.000 0.00 0.00 35.88 2.32
2921 4854 4.349048 TGTCAGCTATTCTATCCAGCCATT 59.651 41.667 0.00 0.00 35.88 3.16
2922 4855 3.906218 TGTCAGCTATTCTATCCAGCCAT 59.094 43.478 0.00 0.00 35.88 4.40
2923 4856 3.308401 TGTCAGCTATTCTATCCAGCCA 58.692 45.455 0.00 0.00 35.88 4.75
2924 4857 3.306641 CCTGTCAGCTATTCTATCCAGCC 60.307 52.174 0.00 0.00 35.88 4.85
2925 4858 3.306641 CCCTGTCAGCTATTCTATCCAGC 60.307 52.174 0.00 0.00 35.49 4.85
2926 4859 3.306641 GCCCTGTCAGCTATTCTATCCAG 60.307 52.174 0.00 0.00 0.00 3.86
2927 4860 2.634940 GCCCTGTCAGCTATTCTATCCA 59.365 50.000 0.00 0.00 0.00 3.41
2928 4861 2.634940 TGCCCTGTCAGCTATTCTATCC 59.365 50.000 0.00 0.00 0.00 2.59
2929 4862 4.550076 ATGCCCTGTCAGCTATTCTATC 57.450 45.455 0.00 0.00 0.00 2.08
2930 4863 4.840680 TGTATGCCCTGTCAGCTATTCTAT 59.159 41.667 0.00 0.00 0.00 1.98
2931 4864 4.223144 TGTATGCCCTGTCAGCTATTCTA 58.777 43.478 0.00 0.00 0.00 2.10
2932 4865 3.041211 TGTATGCCCTGTCAGCTATTCT 58.959 45.455 0.00 0.00 0.00 2.40
2933 4866 3.475566 TGTATGCCCTGTCAGCTATTC 57.524 47.619 0.00 0.00 0.00 1.75
2934 4867 3.931907 TTGTATGCCCTGTCAGCTATT 57.068 42.857 0.00 0.00 0.00 1.73
2935 4868 3.054434 TGTTTGTATGCCCTGTCAGCTAT 60.054 43.478 0.00 0.00 0.00 2.97
2936 4869 2.304470 TGTTTGTATGCCCTGTCAGCTA 59.696 45.455 0.00 0.00 0.00 3.32
2937 4870 1.073763 TGTTTGTATGCCCTGTCAGCT 59.926 47.619 0.00 0.00 0.00 4.24
2938 4871 1.200020 GTGTTTGTATGCCCTGTCAGC 59.800 52.381 0.00 0.00 0.00 4.26
2939 4872 2.783135 AGTGTTTGTATGCCCTGTCAG 58.217 47.619 0.00 0.00 0.00 3.51
2940 4873 2.949177 AGTGTTTGTATGCCCTGTCA 57.051 45.000 0.00 0.00 0.00 3.58
2941 4874 5.186198 AGAATAGTGTTTGTATGCCCTGTC 58.814 41.667 0.00 0.00 0.00 3.51
2942 4875 5.179452 AGAATAGTGTTTGTATGCCCTGT 57.821 39.130 0.00 0.00 0.00 4.00
2943 4876 5.647658 TCAAGAATAGTGTTTGTATGCCCTG 59.352 40.000 0.00 0.00 0.00 4.45
3027 4995 3.848846 CAGCATATAACACACTGCTCG 57.151 47.619 0.00 0.00 42.79 5.03
3094 5062 1.732259 CACACAAGACCAACGGATAGC 59.268 52.381 0.00 0.00 0.00 2.97
3101 5069 1.335324 GCAGATGCACACAAGACCAAC 60.335 52.381 0.00 0.00 41.59 3.77
3130 5100 7.383102 AGAACAGTAACATGGATTGTGAATC 57.617 36.000 0.00 0.00 38.99 2.52
3131 5101 7.596494 CAAGAACAGTAACATGGATTGTGAAT 58.404 34.615 0.00 0.00 38.99 2.57
3145 5158 9.938280 ATACTACAAGTTATGCAAGAACAGTAA 57.062 29.630 15.07 6.19 0.00 2.24
3167 5182 8.644374 TGACAAATTTGCCCTAGTTTTATACT 57.356 30.769 18.12 0.00 41.04 2.12
3190 5205 7.281549 CACATCCATGAATTGTCTATGACTTGA 59.718 37.037 0.00 0.00 33.15 3.02


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

AutoCloner maintained by Alex Coulton.