Multiple sequence alignment - TraesCS5A01G128600

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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 TraesCS5A01G128600 chr5A 100.000 3003 0 0 1 3003 287609229 287612231 0.000000e+00 5546
1 TraesCS5A01G128600 chr5D 96.598 2616 41 20 56 2658 216997616 217000196 0.000000e+00 4294
2 TraesCS5A01G128600 chr5D 98.013 302 4 1 2704 3003 217014094 217014395 9.540000e-145 523
3 TraesCS5A01G128600 chr5D 98.462 65 1 0 1 65 216997224 216997288 6.800000e-22 115
4 TraesCS5A01G128600 chr5B 95.612 2712 57 33 1 2697 232787107 232784443 0.000000e+00 4292
5 TraesCS5A01G128600 chr5B 98.333 300 4 1 2704 3003 232784361 232784063 2.650000e-145 525


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 TraesCS5A01G128600 chr5A 287609229 287612231 3002 False 5546.0 5546 100.0000 1 3003 1 chr5A.!!$F1 3002
1 TraesCS5A01G128600 chr5D 216997224 217000196 2972 False 2204.5 4294 97.5300 1 2658 2 chr5D.!!$F2 2657
2 TraesCS5A01G128600 chr5B 232784063 232787107 3044 True 2408.5 4292 96.9725 1 3003 2 chr5B.!!$R1 3002

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
392 737 3.435105 TGCAAAACTAAGCACCACTTG 57.565 42.857 0.0 0.0 39.58 3.16 F
1092 1449 2.358195 CCAAAATACCTCCCTCCCCTTG 60.358 54.545 0.0 0.0 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 2139 0.998928 TGTGGATGCCTATGTTGGGT 59.001 50.000 0.0 0.0 0.00 4.51 R
2736 3186 2.583143 GGCCGTTAAAATGCCTCCTAT 58.417 47.619 0.0 0.0 42.01 2.57 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
23 24 4.643387 AGGCTTCCACGTGGGCAC 62.643 66.667 33.40 21.50 36.21 5.01
103 441 9.866655 ATATCAGAAAGCCAGACCATAAATTTA 57.133 29.630 0.00 0.00 0.00 1.40
392 737 3.435105 TGCAAAACTAAGCACCACTTG 57.565 42.857 0.00 0.00 39.58 3.16
407 752 6.226988 CACCACTTGCAAAACCAAATATTC 57.773 37.500 0.00 0.00 0.00 1.75
408 753 5.990996 CACCACTTGCAAAACCAAATATTCT 59.009 36.000 0.00 0.00 0.00 2.40
409 754 5.990996 ACCACTTGCAAAACCAAATATTCTG 59.009 36.000 0.00 0.00 0.00 3.02
410 755 5.106987 CCACTTGCAAAACCAAATATTCTGC 60.107 40.000 0.00 0.00 0.00 4.26
411 756 5.697633 CACTTGCAAAACCAAATATTCTGCT 59.302 36.000 0.00 0.00 0.00 4.24
412 757 5.697633 ACTTGCAAAACCAAATATTCTGCTG 59.302 36.000 0.00 0.00 0.00 4.41
702 1057 5.689383 ACGAAGATAAAACAAGTGTGCAT 57.311 34.783 0.00 0.00 0.00 3.96
979 1336 5.522460 GCGTTCTTGCCACTATAAATAGACA 59.478 40.000 4.02 0.00 34.50 3.41
1092 1449 2.358195 CCAAAATACCTCCCTCCCCTTG 60.358 54.545 0.00 0.00 0.00 3.61
1388 1745 6.430864 TCTTCCTAATGGCCACAATTATTCA 58.569 36.000 8.16 0.00 0.00 2.57
1389 1746 7.068702 TCTTCCTAATGGCCACAATTATTCAT 58.931 34.615 8.16 0.00 0.00 2.57
1614 1972 4.352009 TGGGAGCCATTTTGTCATATGTT 58.648 39.130 1.90 0.00 0.00 2.71
1941 2301 4.804108 CTGTCTACTTCAACTGTCAGAGG 58.196 47.826 6.91 0.00 0.00 3.69
2231 2591 0.736053 TTTGTGGTTCCAAGTCGTGC 59.264 50.000 0.00 0.00 0.00 5.34
2506 2866 7.630082 TCACCCACTAGAAATGCTAAAAGTAT 58.370 34.615 0.00 0.00 0.00 2.12
2508 2868 6.318900 ACCCACTAGAAATGCTAAAAGTATGC 59.681 38.462 0.00 0.00 0.00 3.14
2509 2869 6.318648 CCCACTAGAAATGCTAAAAGTATGCA 59.681 38.462 0.00 0.00 41.13 3.96
2510 2870 7.412853 CCACTAGAAATGCTAAAAGTATGCAG 58.587 38.462 0.00 0.00 40.18 4.41
2511 2871 7.066284 CCACTAGAAATGCTAAAAGTATGCAGT 59.934 37.037 0.00 0.00 40.18 4.40
2512 2872 7.907045 CACTAGAAATGCTAAAAGTATGCAGTG 59.093 37.037 0.00 0.00 40.18 3.66
2513 2873 6.199937 AGAAATGCTAAAAGTATGCAGTGG 57.800 37.500 0.00 0.00 40.18 4.00
2514 2874 4.989279 AATGCTAAAAGTATGCAGTGGG 57.011 40.909 0.00 0.00 40.18 4.61
2515 2875 3.712016 TGCTAAAAGTATGCAGTGGGA 57.288 42.857 0.00 0.00 32.55 4.37
2516 2876 4.027674 TGCTAAAAGTATGCAGTGGGAA 57.972 40.909 0.00 0.00 32.55 3.97
2517 2877 3.756434 TGCTAAAAGTATGCAGTGGGAAC 59.244 43.478 0.00 0.00 32.55 3.62
2518 2878 5.346101 TGCTAAAAGTATGCAGTGGGAACC 61.346 45.833 0.00 0.00 39.74 3.62
2547 2922 2.358898 CCACCCTATTTTGCCTTCATCG 59.641 50.000 0.00 0.00 0.00 3.84
2639 3014 4.439253 AGCTGTAAACTGACCCTCTTTT 57.561 40.909 0.00 0.00 0.00 2.27
2691 3066 9.515226 ACCTTGTACACATTCATTATTTGTAGT 57.485 29.630 0.00 0.00 31.75 2.73
2698 3073 9.515226 ACACATTCATTATTTGTAGTACCTTGT 57.485 29.630 0.00 0.00 0.00 3.16
2736 3186 2.355108 GCTGAGTCCAAGCCATACAAGA 60.355 50.000 0.00 0.00 0.00 3.02
2762 3212 0.037790 GCATTTTAACGGCCTGGCAA 60.038 50.000 22.05 5.08 0.00 4.52
2862 3312 2.094026 GCCAATTCATCCTGAACCCAAC 60.094 50.000 0.00 0.00 39.45 3.77
2977 3427 3.127548 TCACGATGGTAAACTCGACCTAC 59.872 47.826 0.00 0.00 37.88 3.18
2996 3446 7.762615 CGACCTACTTTGGACAATTAATGTAGA 59.237 37.037 10.89 0.00 44.12 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.236616 TGGAGACAAACATGCGGCAG 61.237 55.000 9.25 3.35 37.44 4.85
103 441 9.926158 TTTGCATACTTGATTTGATGTTTACAT 57.074 25.926 0.00 0.00 39.70 2.29
386 731 5.106987 GCAGAATATTTGGTTTTGCAAGTGG 60.107 40.000 0.00 0.00 36.86 4.00
391 736 5.212532 ACAGCAGAATATTTGGTTTTGCA 57.787 34.783 4.57 0.00 38.66 4.08
392 737 6.389906 AGTACAGCAGAATATTTGGTTTTGC 58.610 36.000 0.00 0.00 37.06 3.68
394 739 8.299570 CAAGAGTACAGCAGAATATTTGGTTTT 58.700 33.333 0.00 0.00 0.00 2.43
395 740 7.575720 GCAAGAGTACAGCAGAATATTTGGTTT 60.576 37.037 0.00 0.00 0.00 3.27
396 741 6.127897 GCAAGAGTACAGCAGAATATTTGGTT 60.128 38.462 0.00 0.00 0.00 3.67
397 742 5.355350 GCAAGAGTACAGCAGAATATTTGGT 59.645 40.000 0.00 0.00 0.00 3.67
398 743 5.355071 TGCAAGAGTACAGCAGAATATTTGG 59.645 40.000 0.00 0.00 33.75 3.28
399 744 6.426980 TGCAAGAGTACAGCAGAATATTTG 57.573 37.500 0.00 0.00 33.75 2.32
400 745 7.452880 TTTGCAAGAGTACAGCAGAATATTT 57.547 32.000 0.00 0.00 39.72 1.40
401 746 7.452880 TTTTGCAAGAGTACAGCAGAATATT 57.547 32.000 0.00 0.00 39.72 1.28
402 747 7.452880 TTTTTGCAAGAGTACAGCAGAATAT 57.547 32.000 0.00 0.00 39.72 1.28
403 748 6.875948 TTTTTGCAAGAGTACAGCAGAATA 57.124 33.333 0.00 0.00 39.72 1.75
404 749 5.772825 TTTTTGCAAGAGTACAGCAGAAT 57.227 34.783 0.00 0.00 39.72 2.40
436 781 8.744011 CGCTGACTATCTTATGTTGTACTTAAC 58.256 37.037 0.00 0.00 0.00 2.01
437 782 8.680001 TCGCTGACTATCTTATGTTGTACTTAA 58.320 33.333 0.00 0.00 0.00 1.85
438 783 8.127327 GTCGCTGACTATCTTATGTTGTACTTA 58.873 37.037 0.00 0.00 0.00 2.24
754 1109 9.096823 TGTGTCTTCTTTTAAGTTCTAGGGATA 57.903 33.333 0.00 0.00 0.00 2.59
755 1110 7.974504 TGTGTCTTCTTTTAAGTTCTAGGGAT 58.025 34.615 0.00 0.00 0.00 3.85
756 1111 7.369551 TGTGTCTTCTTTTAAGTTCTAGGGA 57.630 36.000 0.00 0.00 0.00 4.20
757 1112 7.878127 TCATGTGTCTTCTTTTAAGTTCTAGGG 59.122 37.037 0.00 0.00 0.00 3.53
758 1113 8.833231 TCATGTGTCTTCTTTTAAGTTCTAGG 57.167 34.615 0.00 0.00 0.00 3.02
979 1336 3.041211 TGGGCAATGCTAGAGTATGAGT 58.959 45.455 4.82 0.00 0.00 3.41
994 1351 1.820519 CTTGAGCTGCTTATTGGGCAA 59.179 47.619 2.53 0.36 39.30 4.52
1092 1449 2.350522 CACAGACCTAGACATGGTTGC 58.649 52.381 0.00 0.00 38.03 4.17
1388 1745 8.511748 AGGGTCTGTCATAACCTGAAATATAT 57.488 34.615 0.00 0.00 35.07 0.86
1389 1746 7.931015 AGGGTCTGTCATAACCTGAAATATA 57.069 36.000 0.00 0.00 35.07 0.86
1612 1970 5.865552 TCAGTAACAATCCTGTAAGCGTAAC 59.134 40.000 0.00 0.00 33.45 2.50
1614 1972 5.648178 TCAGTAACAATCCTGTAAGCGTA 57.352 39.130 0.00 0.00 33.45 4.42
1779 2139 0.998928 TGTGGATGCCTATGTTGGGT 59.001 50.000 0.00 0.00 0.00 4.51
1941 2301 2.583520 CTCCTGGCAGCAGTCTCC 59.416 66.667 9.56 0.00 0.00 3.71
1982 2342 5.067805 GGCCTTTATTTGTCATAACTGGGAG 59.932 44.000 0.00 0.00 0.00 4.30
2231 2591 5.527214 TGGATTTCGTGATAACTGGCTAATG 59.473 40.000 0.00 0.00 0.00 1.90
2563 2938 9.853555 GTGTATCAAATGGATATTGTTTTGTCA 57.146 29.630 0.00 0.00 40.49 3.58
2639 3014 5.106631 ACCATATTTCTAGAGGATGGGGA 57.893 43.478 23.31 0.00 41.21 4.81
2691 3066 6.920758 GCAAAATGTCAAATGTGTACAAGGTA 59.079 34.615 0.00 0.00 0.00 3.08
2694 3069 6.696583 TCAGCAAAATGTCAAATGTGTACAAG 59.303 34.615 0.00 0.00 0.00 3.16
2697 3072 6.208644 ACTCAGCAAAATGTCAAATGTGTAC 58.791 36.000 0.00 0.00 0.00 2.90
2698 3073 6.389830 ACTCAGCAAAATGTCAAATGTGTA 57.610 33.333 0.00 0.00 0.00 2.90
2699 3074 5.266733 ACTCAGCAAAATGTCAAATGTGT 57.733 34.783 0.00 0.00 0.00 3.72
2702 3077 4.873817 TGGACTCAGCAAAATGTCAAATG 58.126 39.130 0.00 0.00 0.00 2.32
2736 3186 2.583143 GGCCGTTAAAATGCCTCCTAT 58.417 47.619 0.00 0.00 42.01 2.57


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

AutoCloner maintained by Alex Coulton.