Multiple sequence alignment - TraesCS4B01G306700

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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 TraesCS4B01G306700 chr4B 100.000 3296 0 0 1 3296 596281280 596284575 0 6087
1 TraesCS4B01G306700 chr4B 93.691 3297 204 3 1 3296 500138101 500141394 0 4933
2 TraesCS4B01G306700 chr6B 94.845 3298 168 2 1 3296 216853248 216856545 0 5147
3 TraesCS4B01G306700 chr6B 93.907 3299 192 5 1 3296 186269881 186266589 0 4970
4 TraesCS4B01G306700 chr1B 94.359 3297 183 2 1 3296 577771878 577768584 0 5055
5 TraesCS4B01G306700 chr2B 94.177 3297 190 2 1 3296 573738504 573741799 0 5024
6 TraesCS4B01G306700 chr2B 93.718 3295 201 5 1 3294 479064799 479068088 0 4933
7 TraesCS4B01G306700 chr7B 93.966 3298 193 6 1 3295 326575479 326578773 0 4983
8 TraesCS4B01G306700 chr7B 93.909 3300 194 6 1 3296 451264412 451261116 0 4974
9 TraesCS4B01G306700 chr7B 93.695 3299 200 7 1 3296 353138764 353142057 0 4933


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 TraesCS4B01G306700 chr4B 596281280 596284575 3295 False 6087 6087 100.000 1 3296 1 chr4B.!!$F2 3295
1 TraesCS4B01G306700 chr4B 500138101 500141394 3293 False 4933 4933 93.691 1 3296 1 chr4B.!!$F1 3295
2 TraesCS4B01G306700 chr6B 216853248 216856545 3297 False 5147 5147 94.845 1 3296 1 chr6B.!!$F1 3295
3 TraesCS4B01G306700 chr6B 186266589 186269881 3292 True 4970 4970 93.907 1 3296 1 chr6B.!!$R1 3295
4 TraesCS4B01G306700 chr1B 577768584 577771878 3294 True 5055 5055 94.359 1 3296 1 chr1B.!!$R1 3295
5 TraesCS4B01G306700 chr2B 573738504 573741799 3295 False 5024 5024 94.177 1 3296 1 chr2B.!!$F2 3295
6 TraesCS4B01G306700 chr2B 479064799 479068088 3289 False 4933 4933 93.718 1 3294 1 chr2B.!!$F1 3293
7 TraesCS4B01G306700 chr7B 326575479 326578773 3294 False 4983 4983 93.966 1 3295 1 chr7B.!!$F1 3294
8 TraesCS4B01G306700 chr7B 451261116 451264412 3296 True 4974 4974 93.909 1 3296 1 chr7B.!!$R1 3295
9 TraesCS4B01G306700 chr7B 353138764 353142057 3293 False 4933 4933 93.695 1 3296 1 chr7B.!!$F2 3295

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
940 943 0.104304 GGCATAGTTCGATGTCCGGT 59.896 55.0 0.0 0.0 39.14 5.28 F
1696 1701 0.179004 AGAGATGCGGACCGAGATCT 60.179 55.0 20.5 21.6 32.83 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2231 2237 0.464554 GGCACCTTCTATGACCTGCC 60.465 60.000 0.0 0.0 37.62 4.85 R
3198 3215 1.067776 CGATACCCTTCCAGGATACGC 60.068 57.143 0.0 0.0 46.39 4.42 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
28 29 3.196394 TTGCCGTGCAAACGTCGT 61.196 55.556 8.58 0.00 45.96 4.34
298 299 0.250513 GGCGGAGAGAATCAGGTGTT 59.749 55.000 0.00 0.00 37.82 3.32
303 304 1.205893 GAGAGAATCAGGTGTTCGGCT 59.794 52.381 0.00 0.00 37.82 5.52
351 352 1.526575 CCGTTGCCAAGATGCTTGGT 61.527 55.000 22.95 0.00 41.53 3.67
495 496 3.741325 GCTAAAGCCTCCTCCCCA 58.259 61.111 0.00 0.00 34.31 4.96
673 674 2.233271 TCGAAGGTACGGTGTTTCTCT 58.767 47.619 0.00 0.00 0.00 3.10
679 680 3.833070 AGGTACGGTGTTTCTCTGAGATT 59.167 43.478 8.42 0.00 0.00 2.40
687 688 6.173339 GGTGTTTCTCTGAGATTCATAACCA 58.827 40.000 8.42 0.00 0.00 3.67
756 757 0.637195 TCTTCGGGGGATCTTCCTCT 59.363 55.000 0.00 0.00 37.15 3.69
776 777 2.629137 CTGGAGATGATGGAGAGTGAGG 59.371 54.545 0.00 0.00 0.00 3.86
799 800 3.775654 CCCACCTCTCCGCCTCAC 61.776 72.222 0.00 0.00 0.00 3.51
940 943 0.104304 GGCATAGTTCGATGTCCGGT 59.896 55.000 0.00 0.00 39.14 5.28
944 947 0.677731 TAGTTCGATGTCCGGTCGGT 60.678 55.000 12.42 1.89 39.45 4.69
972 975 3.780173 GGCCTTCTGGAGCGAGCT 61.780 66.667 0.00 0.00 34.57 4.09
1026 1029 2.549754 CACGGTGCTCACAAAGATTTCT 59.450 45.455 0.00 0.00 0.00 2.52
1165 1169 3.331294 GGATAGTAGCCCCTGAGACTCTA 59.669 52.174 3.68 0.00 0.00 2.43
1204 1208 2.944094 GCAAACGGGGGATCACATAGTT 60.944 50.000 0.00 0.00 0.00 2.24
1250 1254 1.896465 GTATCTAAGGATCCGGCAGCT 59.104 52.381 5.98 0.00 33.71 4.24
1266 1270 2.564771 CAGCTGACCAGTCTGTTGAAA 58.435 47.619 8.42 0.00 40.37 2.69
1514 1519 0.331616 AATGCGGCTTCCCTAAAGGT 59.668 50.000 0.00 0.00 35.37 3.50
1696 1701 0.179004 AGAGATGCGGACCGAGATCT 60.179 55.000 20.50 21.60 32.83 2.75
1756 1761 0.768609 GGCTGGGGGCTCCTACTTAT 60.769 60.000 4.32 0.00 41.46 1.73
1764 1769 1.138266 GGCTCCTACTTATTGCGGACA 59.862 52.381 0.00 0.00 0.00 4.02
1916 1922 2.227388 AGCTTTTCTGGTCGCAATTCAG 59.773 45.455 0.00 0.00 0.00 3.02
1918 1924 3.550842 GCTTTTCTGGTCGCAATTCAGTT 60.551 43.478 0.00 0.00 0.00 3.16
1921 1927 3.126001 TCTGGTCGCAATTCAGTTCTT 57.874 42.857 0.00 0.00 0.00 2.52
1944 1950 2.892425 CGCCCGCTGCCTCTAAAG 60.892 66.667 0.00 0.00 36.24 1.85
2085 2091 3.691342 CTTGGGGCCGTGTCTCGA 61.691 66.667 0.00 0.00 42.86 4.04
2105 2111 0.620556 ATTGACGCCATGAGGAGGTT 59.379 50.000 0.00 0.00 39.30 3.50
2570 2584 7.000472 ACCGGACTATATAGCTGTAACACTTA 59.000 38.462 9.46 0.00 0.00 2.24
2712 2727 6.095580 GGAATCCTAAAGATTTTGGTGAGTCC 59.904 42.308 5.83 3.06 45.52 3.85
2827 2843 0.321298 GTAGTTCTCCTTTGGCCGCA 60.321 55.000 0.00 0.00 0.00 5.69
2870 2887 4.351054 CCGGCAAACCCAGGAGCT 62.351 66.667 0.00 0.00 31.45 4.09
2940 2957 2.970324 GCCAAACTCGTGACGCCA 60.970 61.111 0.00 0.00 0.00 5.69
2954 2971 1.597027 CGCCAAACACTCCCGAAGT 60.597 57.895 0.00 0.00 39.44 3.01
2959 2976 3.254903 GCCAAACACTCCCGAAGTTATTT 59.745 43.478 0.00 0.00 35.45 1.40
3170 3187 2.931105 TTGAACGGGGCCCTGCTA 60.931 61.111 31.77 14.35 0.00 3.49
3198 3215 1.841663 CGCCTTTGTCTCCGTTGTGG 61.842 60.000 0.00 0.00 40.09 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
246 247 1.377229 CTGGCCACGGAGGGTTTTA 59.623 57.895 0.00 0.00 38.09 1.52
298 299 1.544825 CCTTCAGGAAGTGGAGCCGA 61.545 60.000 8.14 0.00 36.72 5.54
303 304 1.975327 CGAGCCTTCAGGAAGTGGA 59.025 57.895 8.14 0.00 36.72 4.02
351 352 0.960364 GGATTTTGCTGAGCACCCGA 60.960 55.000 6.64 0.00 38.71 5.14
382 383 1.302832 CACTGCCCTTTCCTTCGCT 60.303 57.895 0.00 0.00 0.00 4.93
411 412 1.871039 GTTTGGATGCGTAGTGTGTGT 59.129 47.619 0.00 0.00 0.00 3.72
517 518 2.815647 CGCCTCCAAGTCTTCGGC 60.816 66.667 6.90 6.90 37.40 5.54
629 630 8.577939 CGAATTAACGATTAACTTACAACTCGA 58.422 33.333 0.00 0.00 35.09 4.04
673 674 4.466370 ACGAAGTCCTGGTTATGAATCTCA 59.534 41.667 0.00 0.00 29.74 3.27
756 757 2.675583 CCTCACTCTCCATCATCTCCA 58.324 52.381 0.00 0.00 0.00 3.86
799 800 4.717629 TCAGTGTCGCCCGCTTCG 62.718 66.667 0.00 0.00 0.00 3.79
900 903 2.366972 CCCTTCCCATCGTCCCCT 60.367 66.667 0.00 0.00 0.00 4.79
905 908 3.081409 CCGGACCCTTCCCATCGT 61.081 66.667 0.00 0.00 38.99 3.73
940 943 2.338015 GGCCTGTCAGTACGACCGA 61.338 63.158 12.97 0.00 44.71 4.69
944 947 0.888619 CAGAAGGCCTGTCAGTACGA 59.111 55.000 5.69 0.00 38.10 3.43
1137 1141 3.001086 TCAGGGGCTACTATCCATAGGA 58.999 50.000 0.00 0.00 34.69 2.94
1165 1169 2.272146 CACCTATGGCGGGCAACT 59.728 61.111 8.78 0.00 0.00 3.16
1204 1208 2.409012 CACATATACGGCGCAACCATA 58.591 47.619 10.83 0.90 39.03 2.74
1250 1254 2.622942 GGCAATTTCAACAGACTGGTCA 59.377 45.455 7.51 0.00 0.00 4.02
1266 1270 3.478540 GCCTCCTTAGTTCGGCAAT 57.521 52.632 0.00 0.00 42.06 3.56
1312 1316 1.453015 AGCCGTTTGTTCACCAGCA 60.453 52.632 0.00 0.00 0.00 4.41
1514 1519 0.392998 GGCTCTCAATTCTTCGGCCA 60.393 55.000 2.24 0.00 38.16 5.36
1696 1701 2.445845 CTCCTCCCGCATACCCCA 60.446 66.667 0.00 0.00 0.00 4.96
1723 1728 0.523072 CCAGCCACGATTTTGTCAGG 59.477 55.000 0.00 0.00 0.00 3.86
1756 1761 3.491792 GGATCCAAAAACTTTGTCCGCAA 60.492 43.478 6.95 0.00 0.00 4.85
1764 1769 5.476945 AGCATACTTCGGATCCAAAAACTTT 59.523 36.000 13.41 0.00 0.00 2.66
1916 1922 3.119096 GCGGGCGAGTGGAAGAAC 61.119 66.667 0.00 0.00 0.00 3.01
1918 1924 4.069232 CAGCGGGCGAGTGGAAGA 62.069 66.667 0.00 0.00 0.00 2.87
1944 1950 1.673665 CACAGCAGCCACCTTCTCC 60.674 63.158 0.00 0.00 0.00 3.71
2034 2040 2.946990 CAAACCAAAGTAACTGTCCGGT 59.053 45.455 0.00 0.00 0.00 5.28
2085 2091 0.620556 ACCTCCTCATGGCGTCAATT 59.379 50.000 0.00 0.00 0.00 2.32
2105 2111 2.584064 CACCCTCTATGCACGCCA 59.416 61.111 0.00 0.00 0.00 5.69
2231 2237 0.464554 GGCACCTTCTATGACCTGCC 60.465 60.000 0.00 0.00 37.62 4.85
2570 2584 3.015145 ACCCCCATGGCTAAGCGT 61.015 61.111 6.09 0.00 37.83 5.07
2712 2727 2.294791 AGAGACTGTTCAACCACTCGAG 59.705 50.000 11.84 11.84 0.00 4.04
2827 2843 3.811083 TGTTCCGTTATTATCGGCCAAT 58.189 40.909 2.24 0.00 46.49 3.16
2853 2870 4.351054 AGCTCCTGGGTTTGCCGG 62.351 66.667 0.00 0.00 34.97 6.13
2940 2957 4.466827 ACCAAATAACTTCGGGAGTGTTT 58.533 39.130 0.00 0.00 39.00 2.83
2959 2976 7.504238 TCAGCCTATTTTCTTTTACAAAGACCA 59.496 33.333 0.00 0.00 0.00 4.02
3098 3115 5.562298 ACCTTTTCTACTGCCTCTTGTTA 57.438 39.130 0.00 0.00 0.00 2.41
3198 3215 1.067776 CGATACCCTTCCAGGATACGC 60.068 57.143 0.00 0.00 46.39 4.42


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

AutoCloner maintained by Alex Coulton.