Multiple sequence alignment - TraesCS5A01G146200

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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 TraesCS5A01G146200 chr5A 100.000 2954 0 0 1 2954 322477806 322480759 0.000000e+00 5456.0
1 TraesCS5A01G146200 chr5B 91.243 2695 146 32 286 2954 272166289 272168919 0.000000e+00 3587.0
2 TraesCS5A01G146200 chr5B 93.548 62 4 0 2 63 272163964 272164025 3.130000e-15 93.5
3 TraesCS5A01G146200 chr5D 94.404 2037 83 6 7 2020 232850585 232848557 0.000000e+00 3101.0
4 TraesCS5A01G146200 chr5D 92.130 953 46 9 2017 2954 232848529 232847591 0.000000e+00 1317.0
5 TraesCS5A01G146200 chr4D 82.383 965 153 13 1016 1979 101506147 101505199 0.000000e+00 824.0
6 TraesCS5A01G146200 chr4A 81.855 981 153 19 1001 1976 473765656 473766616 0.000000e+00 802.0


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 TraesCS5A01G146200 chr5A 322477806 322480759 2953 False 5456.00 5456 100.0000 1 2954 1 chr5A.!!$F1 2953
1 TraesCS5A01G146200 chr5B 272163964 272168919 4955 False 1840.25 3587 92.3955 2 2954 2 chr5B.!!$F1 2952
2 TraesCS5A01G146200 chr5D 232847591 232850585 2994 True 2209.00 3101 93.2670 7 2954 2 chr5D.!!$R1 2947
3 TraesCS5A01G146200 chr4D 101505199 101506147 948 True 824.00 824 82.3830 1016 1979 1 chr4D.!!$R1 963
4 TraesCS5A01G146200 chr4A 473765656 473766616 960 False 802.00 802 81.8550 1001 1976 1 chr4A.!!$F1 975

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
970 3034 0.397941 CTCCTGGCTTTCTCACCACA 59.602 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2890 5007 0.25064 CCTGAAGCCAGCTCACAAGT 60.251 55.0 0.0 0.0 39.07 3.16 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
63 64 7.610580 AAAATTCCTGTATTTTGAACTCCCA 57.389 32.000 0.00 0.00 36.60 4.37
73 74 8.240682 TGTATTTTGAACTCCCAAATTCATACG 58.759 33.333 0.00 0.00 36.12 3.06
84 85 7.394016 TCCCAAATTCATACGACATATAGCAT 58.606 34.615 0.00 0.00 0.00 3.79
105 106 8.212259 AGCATCTAAATATCACTACCTCCAAT 57.788 34.615 0.00 0.00 0.00 3.16
119 120 9.099454 CACTACCTCCAATCTAAAATAAGTGTC 57.901 37.037 0.00 0.00 0.00 3.67
120 121 7.980099 ACTACCTCCAATCTAAAATAAGTGTCG 59.020 37.037 0.00 0.00 0.00 4.35
125 126 6.653320 TCCAATCTAAAATAAGTGTCGCAGTT 59.347 34.615 5.48 5.48 0.00 3.16
130 131 7.572759 TCTAAAATAAGTGTCGCAGTTTTGAG 58.427 34.615 5.46 0.02 0.00 3.02
160 161 6.663734 ACTATTTTGGATTGAAGGGAGTAGG 58.336 40.000 0.00 0.00 0.00 3.18
178 201 2.997897 AGGAGGTCGTGACTGGCC 60.998 66.667 0.00 0.00 0.00 5.36
228 251 0.997363 TGGAACCGAGACCTCTCCTA 59.003 55.000 0.00 0.00 39.79 2.94
247 271 2.490328 ACATGCAACAAACCGAACAG 57.510 45.000 0.00 0.00 0.00 3.16
256 280 2.450479 AAACCGAACAGAGCCCCTCG 62.450 60.000 0.00 0.00 35.36 4.63
279 303 4.495184 GGAATAATCCAAACGTTACGGCAG 60.495 45.833 10.20 0.00 45.79 4.85
280 304 2.172851 AATCCAAACGTTACGGCAGA 57.827 45.000 10.20 0.53 0.00 4.26
513 2575 2.266055 CTCCACTTCACTCCCCGC 59.734 66.667 0.00 0.00 0.00 6.13
584 2647 1.327764 GCAATCGTCTCAAATCCCGTC 59.672 52.381 0.00 0.00 0.00 4.79
637 2700 1.066573 ACTGATTCGCTCCAGAACCTG 60.067 52.381 0.00 0.00 34.65 4.00
656 2719 0.460722 GTTCTTACTCTCTCGGGGGC 59.539 60.000 0.00 0.00 0.00 5.80
728 2792 0.750546 TCCATCTCCATTGCTGCTGC 60.751 55.000 8.89 8.89 40.20 5.25
797 2861 0.796312 AGTAAATGCGCGTCCTTGTG 59.204 50.000 8.43 0.00 0.00 3.33
837 2901 0.736325 CGCCGAATCTCGTCCTTGTT 60.736 55.000 0.00 0.00 38.40 2.83
870 2934 3.532102 AGAGGTGGAGGTGGTAATTCTT 58.468 45.455 0.00 0.00 0.00 2.52
970 3034 0.397941 CTCCTGGCTTTCTCACCACA 59.602 55.000 0.00 0.00 0.00 4.17
1257 3324 4.079385 AGGAAAGGTTTGTCCCAGTACTTT 60.079 41.667 0.00 0.00 36.75 2.66
1395 3462 4.069232 CTCTCGCCGGTGCTTGGA 62.069 66.667 11.05 4.99 34.43 3.53
1401 3468 2.662596 CCGGTGCTTGGACTGCTA 59.337 61.111 0.00 0.00 0.00 3.49
1534 3601 4.602259 CAGCACCACGGTCACGGT 62.602 66.667 0.00 0.00 46.48 4.83
1839 3906 3.341823 CAAGAAGTTGGAGGTGATGGAG 58.658 50.000 0.00 0.00 0.00 3.86
1932 3999 1.600485 ACACGAACAAAACCGGTGATC 59.400 47.619 8.52 0.00 0.00 2.92
1979 4046 5.976458 TGTTTTGGATTTTCTGCAGAGTTT 58.024 33.333 17.43 5.28 0.00 2.66
2064 4177 0.767375 AGTCAGGGCTCAGCTTCAAA 59.233 50.000 0.00 0.00 0.00 2.69
2102 4215 9.263538 GTGGGTTTATTTCGAAGGTTAATTTTT 57.736 29.630 0.00 0.00 0.00 1.94
2130 4243 7.390162 TGCGATGGCTATAATTGATGTTCATAA 59.610 33.333 0.15 0.00 40.82 1.90
2169 4283 2.909006 AGGAGCTCTGTTCATCTCCAAA 59.091 45.455 14.64 0.00 45.69 3.28
2173 4287 2.419324 GCTCTGTTCATCTCCAAAGCAG 59.581 50.000 0.00 0.00 0.00 4.24
2217 4331 7.601705 AGTCAGATTTGGAATTCCTCAAAAA 57.398 32.000 24.73 16.48 36.60 1.94
2359 4474 2.427095 AGCACTGTTTGGTTTTCCTGTC 59.573 45.455 0.00 0.00 41.38 3.51
2366 4481 3.593442 TTGGTTTTCCTGTCCAGACAT 57.407 42.857 0.04 0.00 41.01 3.06
2480 4595 3.512329 TGTATGTGGTGTGAACTATCCGT 59.488 43.478 0.00 0.00 0.00 4.69
2491 4606 4.676018 GTGAACTATCCGTTATCTTCTCGC 59.324 45.833 0.00 0.00 35.56 5.03
2533 4648 7.025365 CAGTCTGTTGATGATTTGGTGTTATG 58.975 38.462 0.00 0.00 0.00 1.90
2537 4652 5.106357 TGTTGATGATTTGGTGTTATGGTCG 60.106 40.000 0.00 0.00 0.00 4.79
2550 4665 7.176865 TGGTGTTATGGTCGAATTCCAAATTAA 59.823 33.333 0.00 0.00 38.52 1.40
2595 4710 6.605119 AGGGTGTCATTATCATTTCCCTAAG 58.395 40.000 0.00 0.00 41.68 2.18
2611 4727 7.933215 TTCCCTAAGAAAAAGGTAGCATTAC 57.067 36.000 0.00 0.00 31.70 1.89
2676 4792 4.541973 TGCTGACTGAAGCTTTAGATGA 57.458 40.909 23.75 6.80 43.90 2.92
2698 4814 1.868498 TGACGGTTTAAACAAGAGGCG 59.132 47.619 19.57 14.18 0.00 5.52
2706 4822 6.567132 CGGTTTAAACAAGAGGCGTTCTATTT 60.567 38.462 19.57 0.00 34.14 1.40
2777 4893 5.680594 AACATTAACATGTACCCGGACTA 57.319 39.130 0.73 0.00 43.34 2.59
2843 4960 3.737559 TCAAAGTATGCATTCCCAGGT 57.262 42.857 3.54 0.00 0.00 4.00
2852 4969 1.272147 GCATTCCCAGGTCCTCTTGTT 60.272 52.381 0.00 0.00 0.00 2.83
2858 4975 2.242043 CCAGGTCCTCTTGTTGCAAAT 58.758 47.619 0.00 0.00 0.00 2.32
2890 5007 0.776810 TGGGCTTGAACATCCTCCAA 59.223 50.000 0.00 0.00 0.00 3.53
2917 5034 1.912043 AGCTGGCTTCAGGTCATACTT 59.088 47.619 0.00 0.00 45.01 2.24
2918 5035 2.307098 AGCTGGCTTCAGGTCATACTTT 59.693 45.455 0.00 0.00 45.01 2.66
2919 5036 2.680339 GCTGGCTTCAGGTCATACTTTC 59.320 50.000 0.00 0.00 38.87 2.62
2920 5037 3.620966 GCTGGCTTCAGGTCATACTTTCT 60.621 47.826 0.00 0.00 38.87 2.52
2921 5038 3.937706 CTGGCTTCAGGTCATACTTTCTG 59.062 47.826 0.00 0.00 34.96 3.02
2922 5039 3.582647 TGGCTTCAGGTCATACTTTCTGA 59.417 43.478 0.00 0.00 34.84 3.27
2923 5040 3.935828 GGCTTCAGGTCATACTTTCTGAC 59.064 47.826 0.00 0.00 41.83 3.51
2924 5041 4.323104 GGCTTCAGGTCATACTTTCTGACT 60.323 45.833 3.73 0.00 42.14 3.41
2925 5042 4.629200 GCTTCAGGTCATACTTTCTGACTG 59.371 45.833 3.73 0.00 42.14 3.51
2931 5048 4.932200 GGTCATACTTTCTGACTGTTCTGG 59.068 45.833 3.73 0.00 42.14 3.86
2942 5059 2.362077 GACTGTTCTGGGCATGTGTTTT 59.638 45.455 0.00 0.00 0.00 2.43
2943 5060 2.101249 ACTGTTCTGGGCATGTGTTTTG 59.899 45.455 0.00 0.00 0.00 2.44
2950 5067 7.559533 TGTTCTGGGCATGTGTTTTGTATATAT 59.440 33.333 0.00 0.00 0.00 0.86
2951 5068 9.062524 GTTCTGGGCATGTGTTTTGTATATATA 57.937 33.333 0.00 0.00 0.00 0.86
2952 5069 9.806448 TTCTGGGCATGTGTTTTGTATATATAT 57.194 29.630 0.00 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 9.099454 GACACTTATTTTAGATTGGAGGTAGTG 57.901 37.037 0.00 0.00 35.48 2.74
105 106 7.485418 TCAAAACTGCGACACTTATTTTAGA 57.515 32.000 0.00 0.00 0.00 2.10
119 120 5.786401 AATAGTTCTAGCTCAAAACTGCG 57.214 39.130 15.04 0.00 35.08 5.18
120 121 6.803807 CCAAAATAGTTCTAGCTCAAAACTGC 59.196 38.462 15.04 0.00 35.08 4.40
125 126 8.862325 TCAATCCAAAATAGTTCTAGCTCAAA 57.138 30.769 0.00 0.00 0.00 2.69
130 131 6.828785 TCCCTTCAATCCAAAATAGTTCTAGC 59.171 38.462 0.00 0.00 0.00 3.42
160 161 2.574399 GCCAGTCACGACCTCCTC 59.426 66.667 0.00 0.00 0.00 3.71
202 225 1.004745 AGGTCTCGGTTCCATTGCAAT 59.995 47.619 5.99 5.99 0.00 3.56
228 251 2.020720 TCTGTTCGGTTTGTTGCATGT 58.979 42.857 0.00 0.00 0.00 3.21
247 271 1.056660 TGGATTATTCCGAGGGGCTC 58.943 55.000 0.00 0.00 45.89 4.70
256 280 3.374678 TGCCGTAACGTTTGGATTATTCC 59.625 43.478 19.93 0.00 42.94 3.01
279 303 1.003233 GCTTGTCCAGGGTGTCCTC 60.003 63.158 0.00 0.00 42.67 3.71
280 304 1.770110 TGCTTGTCCAGGGTGTCCT 60.770 57.895 0.00 0.00 46.26 3.85
452 2514 5.188163 TGAGGGTCATAGTCGGAATTTACAA 59.812 40.000 0.00 0.00 0.00 2.41
463 2525 4.762289 ATTCTTGGTGAGGGTCATAGTC 57.238 45.455 0.00 0.00 0.00 2.59
513 2575 2.298729 GGGGATTGAGATCGAAGGAGAG 59.701 54.545 0.00 0.00 32.84 3.20
637 2700 0.460722 GCCCCCGAGAGAGTAAGAAC 59.539 60.000 0.00 0.00 0.00 3.01
741 2805 2.482333 CGGGACAGCTCTCTACGGG 61.482 68.421 0.00 0.00 0.00 5.28
837 2901 0.616679 CCACCTCTTAACTCGGGGGA 60.617 60.000 0.00 0.00 44.46 4.81
870 2934 3.975083 AAGATTGGCGCGCGTACGA 62.975 57.895 32.35 23.59 43.93 3.43
970 3034 2.285368 TCCGCCAGGAATCCAGGT 60.285 61.111 12.50 0.00 45.12 4.00
1089 3153 2.690881 ATTGCGTCCAGGGCCCTA 60.691 61.111 28.13 7.21 0.00 3.53
1155 3219 1.082117 GGACGGTGGCATTGTAGACG 61.082 60.000 0.00 0.00 0.00 4.18
1180 3247 4.052229 CGAGACGCCGGTGAGGTT 62.052 66.667 24.59 0.00 43.70 3.50
1257 3324 4.329545 GTGGGCAGGCCGAACTGA 62.330 66.667 8.81 0.00 40.97 3.41
1395 3462 1.270732 GCAGCATCATAGGCTAGCAGT 60.271 52.381 18.24 5.49 40.23 4.40
1401 3468 0.466922 GGTTGGCAGCATCATAGGCT 60.467 55.000 3.14 0.00 43.77 4.58
1530 3597 1.519898 GTCGAACCACACACACCGT 60.520 57.895 0.00 0.00 0.00 4.83
1531 3598 0.808453 AAGTCGAACCACACACACCG 60.808 55.000 0.00 0.00 0.00 4.94
1532 3599 0.655733 CAAGTCGAACCACACACACC 59.344 55.000 0.00 0.00 0.00 4.16
1533 3600 0.655733 CCAAGTCGAACCACACACAC 59.344 55.000 0.00 0.00 0.00 3.82
1534 3601 0.537653 TCCAAGTCGAACCACACACA 59.462 50.000 0.00 0.00 0.00 3.72
1545 3612 2.390599 CGGCACACCATCCAAGTCG 61.391 63.158 0.00 0.00 34.57 4.18
1839 3906 1.032114 CCCCAACCTCTGAATTCCGC 61.032 60.000 2.27 0.00 0.00 5.54
1932 3999 0.318529 ATGCAGCATACTCGCTCTCG 60.319 55.000 5.94 0.00 41.38 4.04
1979 4046 3.275143 CGGGCATTGTTAGTGATGGTTA 58.725 45.455 0.00 0.00 0.00 2.85
2064 4177 2.159179 AAACCCACCAAAAGAGTGCT 57.841 45.000 0.00 0.00 33.75 4.40
2102 4215 6.878389 TGAACATCAATTATAGCCATCGCATA 59.122 34.615 0.00 0.00 37.52 3.14
2169 4283 4.223700 TGATACATTCACTTCTCCACTGCT 59.776 41.667 0.00 0.00 0.00 4.24
2173 4287 6.166279 TGACTTGATACATTCACTTCTCCAC 58.834 40.000 0.00 0.00 32.84 4.02
2217 4331 8.091449 TGAAATACAGCGTCCCAATTTTATTTT 58.909 29.630 0.00 0.00 0.00 1.82
2218 4332 7.607250 TGAAATACAGCGTCCCAATTTTATTT 58.393 30.769 0.00 0.00 0.00 1.40
2221 4335 5.941058 TCTGAAATACAGCGTCCCAATTTTA 59.059 36.000 0.00 0.00 45.38 1.52
2366 4481 8.208903 ACATCATCATGTAATCATCTCAACAGA 58.791 33.333 0.00 0.00 41.81 3.41
2480 4595 6.268825 ACAAGAACTGTAGCGAGAAGATAA 57.731 37.500 0.00 0.00 36.10 1.75
2491 4606 2.731976 GACTGCGGAACAAGAACTGTAG 59.268 50.000 0.00 0.00 37.23 2.74
2550 4665 7.121463 CACCCTAGTAAGCTTCGAGTATCATAT 59.879 40.741 0.00 0.00 33.17 1.78
2676 4792 2.876550 GCCTCTTGTTTAAACCGTCAGT 59.123 45.455 15.59 0.00 0.00 3.41
2755 4871 4.563140 AGTCCGGGTACATGTTAATGTT 57.437 40.909 2.30 0.00 44.94 2.71
2757 4873 7.562454 AAATTAGTCCGGGTACATGTTAATG 57.438 36.000 2.30 0.00 39.89 1.90
2758 4874 9.280174 CATAAATTAGTCCGGGTACATGTTAAT 57.720 33.333 2.30 0.00 0.00 1.40
2759 4875 8.484575 TCATAAATTAGTCCGGGTACATGTTAA 58.515 33.333 2.30 0.00 0.00 2.01
2760 4876 8.020777 TCATAAATTAGTCCGGGTACATGTTA 57.979 34.615 2.30 0.00 0.00 2.41
2843 4960 5.280945 CGAAGAAAATTTGCAACAAGAGGA 58.719 37.500 0.00 0.00 0.00 3.71
2852 4969 3.243704 CCCACTTCCGAAGAAAATTTGCA 60.244 43.478 15.23 0.00 0.00 4.08
2858 4975 1.953686 CAAGCCCACTTCCGAAGAAAA 59.046 47.619 15.23 0.00 32.29 2.29
2890 5007 0.250640 CCTGAAGCCAGCTCACAAGT 60.251 55.000 0.00 0.00 39.07 3.16
2915 5032 2.260844 TGCCCAGAACAGTCAGAAAG 57.739 50.000 0.00 0.00 0.00 2.62
2917 5034 1.421268 ACATGCCCAGAACAGTCAGAA 59.579 47.619 0.00 0.00 0.00 3.02
2918 5035 1.059098 ACATGCCCAGAACAGTCAGA 58.941 50.000 0.00 0.00 0.00 3.27
2919 5036 1.162698 CACATGCCCAGAACAGTCAG 58.837 55.000 0.00 0.00 0.00 3.51
2920 5037 0.473755 ACACATGCCCAGAACAGTCA 59.526 50.000 0.00 0.00 0.00 3.41
2921 5038 1.609208 AACACATGCCCAGAACAGTC 58.391 50.000 0.00 0.00 0.00 3.51
2922 5039 2.071778 AAACACATGCCCAGAACAGT 57.928 45.000 0.00 0.00 0.00 3.55
2923 5040 2.101249 ACAAAACACATGCCCAGAACAG 59.899 45.455 0.00 0.00 0.00 3.16
2924 5041 2.106566 ACAAAACACATGCCCAGAACA 58.893 42.857 0.00 0.00 0.00 3.18
2925 5042 2.888834 ACAAAACACATGCCCAGAAC 57.111 45.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.