Multiple sequence alignment - TraesCS2B01G201800

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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 TraesCS2B01G201800 chr2B 100.000 3008 0 0 442 3449 180824192 180821185 0.000000e+00 5555
1 TraesCS2B01G201800 chr2B 100.000 181 0 0 1 181 180824633 180824453 5.520000e-88 335
2 TraesCS2B01G201800 chr2D 97.206 3042 50 5 442 3449 127089348 127086308 0.000000e+00 5114
3 TraesCS2B01G201800 chr2D 96.133 181 6 1 1 181 127089890 127089711 9.360000e-76 294
4 TraesCS2B01G201800 chr2A 96.627 2698 65 7 762 3449 133963135 133960454 0.000000e+00 4455


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 TraesCS2B01G201800 chr2B 180821185 180824633 3448 True 2945 5555 100.0000 1 3449 2 chr2B.!!$R1 3448
1 TraesCS2B01G201800 chr2D 127086308 127089890 3582 True 2704 5114 96.6695 1 3449 2 chr2D.!!$R1 3448
2 TraesCS2B01G201800 chr2A 133960454 133963135 2681 True 4455 4455 96.6270 762 3449 1 chr2A.!!$R1 2687

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
39 40 1.081641 CCAGCAAAGCAACTCGCAG 60.082 57.895 0.00 0.00 46.13 5.18 F
950 1086 1.601759 CTGGCACCCAGTGGAAGTG 60.602 63.158 11.95 12.46 45.82 3.16 F
1047 1189 2.808206 CCTACCATCTCCGGCCACC 61.808 68.421 2.24 0.00 0.00 4.61 F
1926 2068 2.943690 CAGGACTGAGGATGCAATGAAG 59.056 50.000 0.00 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1100 1242 0.974010 GGTGGTATCGGTGGTGGAGA 60.974 60.000 0.0 0.0 0.00 3.71 R
1926 2068 1.212751 GCCCATTTGTCGGAACAGC 59.787 57.895 0.0 0.0 36.57 4.40 R
2212 2354 2.441750 CCCCTAAGTTATGCCTAGCCAA 59.558 50.000 0.0 0.0 0.00 4.52 R
3333 3484 3.132289 CCAGGATTCTTCGCTGTACCTAA 59.868 47.826 0.0 0.0 0.00 2.69 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
39 40 1.081641 CCAGCAAAGCAACTCGCAG 60.082 57.895 0.00 0.00 46.13 5.18
105 106 9.489084 CCAAATCCTATATCAAATAACACGAGA 57.511 33.333 0.00 0.00 0.00 4.04
172 173 1.956170 GCGGCGTCATCCTACATGG 60.956 63.158 9.37 0.00 37.10 3.66
542 650 5.354513 CACTAACTCACTTCGAGATACTCCA 59.645 44.000 0.00 0.00 45.45 3.86
543 651 4.974368 AACTCACTTCGAGATACTCCAG 57.026 45.455 0.00 0.00 45.45 3.86
544 652 2.685897 ACTCACTTCGAGATACTCCAGC 59.314 50.000 0.00 0.00 45.45 4.85
571 679 5.726980 TGGCTATTTCAAATGTTCAAGCT 57.273 34.783 2.59 0.00 0.00 3.74
583 691 2.095110 TGTTCAAGCTTGCCATCATTCG 60.095 45.455 21.99 0.00 0.00 3.34
629 737 7.878644 GGCTAAGGTTAGATGTAGAAATAAGGG 59.121 40.741 0.71 0.00 32.47 3.95
638 746 4.250464 TGTAGAAATAAGGGCACACTTCG 58.750 43.478 0.00 0.00 32.02 3.79
647 755 3.975992 GCACACTTCGCCATACTTG 57.024 52.632 0.00 0.00 0.00 3.16
658 766 5.290493 TCGCCATACTTGGATAATCTTGT 57.710 39.130 0.00 0.00 46.92 3.16
732 840 3.181495 CCTTTTACAAGTGTGGCGACAAA 60.181 43.478 2.03 0.00 46.06 2.83
949 1085 2.839098 CTGGCACCCAGTGGAAGT 59.161 61.111 11.95 0.00 45.82 3.01
950 1086 1.601759 CTGGCACCCAGTGGAAGTG 60.602 63.158 11.95 12.46 45.82 3.16
1047 1189 2.808206 CCTACCATCTCCGGCCACC 61.808 68.421 2.24 0.00 0.00 4.61
1089 1231 4.436998 CGCCACCTCTCCACGACC 62.437 72.222 0.00 0.00 0.00 4.79
1767 1909 5.266733 ACAATGCTGTTCTTGATTGTGTT 57.733 34.783 0.00 0.00 37.58 3.32
1926 2068 2.943690 CAGGACTGAGGATGCAATGAAG 59.056 50.000 0.00 0.00 0.00 3.02
2085 2227 5.428457 TGGAGATAAACTTGATAGGAAGGCA 59.572 40.000 0.00 0.00 0.00 4.75
2212 2354 5.306419 TCATATAGCCTGCTGATTGAGAAGT 59.694 40.000 0.97 0.00 0.00 3.01
2220 2362 2.941720 GCTGATTGAGAAGTTGGCTAGG 59.058 50.000 0.00 0.00 0.00 3.02
2226 2368 3.873910 TGAGAAGTTGGCTAGGCATAAC 58.126 45.455 20.94 15.97 0.00 1.89
2539 2684 4.762251 AGAATTTGCTTAGGTGGACTGTTC 59.238 41.667 0.00 0.00 0.00 3.18
2647 2796 7.066766 CACTCTGCTTTTAAAGGAGCTGATATT 59.933 37.037 19.20 6.79 45.49 1.28
2709 2858 5.682943 TCCACTTAAAGATGGTCAAAACG 57.317 39.130 0.00 0.00 37.27 3.60
2712 2861 4.911610 CACTTAAAGATGGTCAAAACGCAG 59.088 41.667 0.00 0.00 0.00 5.18
2799 2948 9.612620 GGATAGGCTGTTAAATCGATAAATTTG 57.387 33.333 0.00 0.00 31.50 2.32
3108 3259 3.696051 GCACTTCTATGGCCTGATTTTCA 59.304 43.478 3.32 0.00 0.00 2.69
3122 3273 5.278463 CCTGATTTTCAACAACCCACTACAG 60.278 44.000 0.00 0.00 0.00 2.74
3333 3484 6.067217 ACTTTTGCTAGGACTGGATAATGT 57.933 37.500 0.00 0.00 0.00 2.71
3352 3503 4.119442 TGTTAGGTACAGCGAAGAATCC 57.881 45.455 0.00 0.00 31.68 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 4.010349 GGATTTGGTCTTGTTGTCTAGGG 58.990 47.826 0.00 0.00 0.00 3.53
121 122 5.765576 TGTCCCAACATTAAGGTTAGCTA 57.234 39.130 5.01 0.00 0.00 3.32
144 145 1.686325 ATGACGCCGCACTAGGGATT 61.686 55.000 0.00 0.00 0.00 3.01
542 650 3.696051 ACATTTGAAATAGCCATCGTGCT 59.304 39.130 0.00 2.75 45.38 4.40
543 651 4.032703 ACATTTGAAATAGCCATCGTGC 57.967 40.909 0.00 0.00 0.00 5.34
544 652 5.639757 TGAACATTTGAAATAGCCATCGTG 58.360 37.500 0.00 0.00 0.00 4.35
571 679 2.401583 AGTGTAGCGAATGATGGCAA 57.598 45.000 0.00 0.00 31.86 4.52
629 737 0.447801 CCAAGTATGGCGAAGTGTGC 59.552 55.000 0.00 0.00 40.58 4.57
732 840 2.104281 ACGAGTTAGCCTTCTGTTTGGT 59.896 45.455 0.00 0.00 0.00 3.67
949 1085 0.197661 AGGGTTAGGGGAGGTTTCCA 59.802 55.000 0.00 0.00 45.98 3.53
950 1086 0.917533 GAGGGTTAGGGGAGGTTTCC 59.082 60.000 0.00 0.00 43.23 3.13
951 1087 1.665137 TGAGGGTTAGGGGAGGTTTC 58.335 55.000 0.00 0.00 0.00 2.78
952 1088 2.206223 GATGAGGGTTAGGGGAGGTTT 58.794 52.381 0.00 0.00 0.00 3.27
1089 1231 3.339093 GTGGAGAAGGGGGTGGGG 61.339 72.222 0.00 0.00 0.00 4.96
1100 1242 0.974010 GGTGGTATCGGTGGTGGAGA 60.974 60.000 0.00 0.00 0.00 3.71
1143 1285 2.435059 GAGAGCTTGGTGACCGCC 60.435 66.667 0.00 0.00 0.00 6.13
1623 1765 3.884895 AGTGCAAATATTGTCATCCGGA 58.115 40.909 6.61 6.61 0.00 5.14
1926 2068 1.212751 GCCCATTTGTCGGAACAGC 59.787 57.895 0.00 0.00 36.57 4.40
2212 2354 2.441750 CCCCTAAGTTATGCCTAGCCAA 59.558 50.000 0.00 0.00 0.00 4.52
2220 2362 4.067972 TGAACGATCCCCTAAGTTATGC 57.932 45.455 0.00 0.00 0.00 3.14
2226 2368 3.065371 GTGCATTTGAACGATCCCCTAAG 59.935 47.826 0.00 0.00 0.00 2.18
2647 2796 3.712016 TCCATGAAGTTCCAAATCGGA 57.288 42.857 0.00 0.00 44.40 4.55
2799 2948 5.651530 TCGTTTCTCACATAGATGAAGGTC 58.348 41.667 0.00 0.00 33.05 3.85
3108 3259 4.103469 TGGTCATTACTGTAGTGGGTTGTT 59.897 41.667 9.98 0.00 0.00 2.83
3122 3273 4.511826 GCACTAAGGCACTATGGTCATTAC 59.488 45.833 0.00 0.00 38.49 1.89
3213 3364 3.735746 GCAACTGTTTGGATGCACTAAAC 59.264 43.478 15.95 15.95 45.74 2.01
3333 3484 3.132289 CCAGGATTCTTCGCTGTACCTAA 59.868 47.826 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.