Multiple sequence alignment - TraesCS6B01G237300

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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 TraesCS6B01G237300 chr6B 100.000 2935 0 0 1 2935 410679140 410682074 0.000000e+00 5421
1 TraesCS6B01G237300 chr6B 98.406 2949 26 3 1 2935 410229771 410232712 0.000000e+00 5166
2 TraesCS6B01G237300 chr5B 91.781 146 12 0 1 146 396137601 396137456 1.380000e-48 204
3 TraesCS6B01G237300 chr3B 92.308 143 11 0 1 143 636430689 636430547 1.380000e-48 204
4 TraesCS6B01G237300 chr3B 91.034 145 11 2 1 144 48082235 48082378 8.300000e-46 195
5 TraesCS6B01G237300 chr3B 90.345 145 12 2 1 144 47812406 47812549 3.860000e-44 189
6 TraesCS6B01G237300 chr3B 90.345 145 12 2 1 144 47866300 47866443 3.860000e-44 189
7 TraesCS6B01G237300 chr3B 89.262 149 15 1 1 149 663484430 663484577 5.000000e-43 185
8 TraesCS6B01G237300 chr2B 90.210 143 14 0 2 144 598487969 598488111 1.390000e-43 187
9 TraesCS6B01G237300 chr2B 88.667 150 17 0 1 150 772677910 772678059 1.800000e-42 183


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 TraesCS6B01G237300 chr6B 410679140 410682074 2934 False 5421 5421 100.000 1 2935 1 chr6B.!!$F2 2934
1 TraesCS6B01G237300 chr6B 410229771 410232712 2941 False 5166 5166 98.406 1 2935 1 chr6B.!!$F1 2934

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
69 71 3.125316 GGACGCTACACAAAAAGATCAGG 59.875 47.826 0.0 0.0 0.0 3.86 F
226 228 4.619227 CTGGACGGTGGGCGTTGT 62.619 66.667 0.0 0.0 0.0 3.32 F
792 794 4.963276 TTGCTGCTGTTATGGTAATGTC 57.037 40.909 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1440 1442 5.728471 TGCATATTAGGATAAGCTCAGAGC 58.272 41.667 15.25 15.25 42.84 4.09 R
1538 1540 6.546428 AGCTAGTAAAAGGAGATGCAGTAA 57.454 37.500 0.00 0.00 0.00 2.24 R
2783 2798 3.434641 GGCATCTCATGTGGACATTATCG 59.565 47.826 0.00 0.00 33.61 2.92 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
40 42 3.706373 AGTAGGGTGTGGCGCCTG 61.706 66.667 29.70 0.00 33.98 4.85
69 71 3.125316 GGACGCTACACAAAAAGATCAGG 59.875 47.826 0.00 0.00 0.00 3.86
122 124 6.540189 ACTCTATGAATTGATTTTGTCCCGAG 59.460 38.462 0.00 0.00 0.00 4.63
123 125 6.649155 TCTATGAATTGATTTTGTCCCGAGA 58.351 36.000 0.00 0.00 0.00 4.04
226 228 4.619227 CTGGACGGTGGGCGTTGT 62.619 66.667 0.00 0.00 0.00 3.32
757 759 7.255491 ACTGCTGTTTGTATGATCATGTATG 57.745 36.000 18.72 3.49 0.00 2.39
758 760 7.049754 ACTGCTGTTTGTATGATCATGTATGA 58.950 34.615 18.72 0.00 41.70 2.15
760 762 7.867752 TGCTGTTTGTATGATCATGTATGATG 58.132 34.615 18.72 5.26 46.84 3.07
761 763 7.499895 TGCTGTTTGTATGATCATGTATGATGT 59.500 33.333 18.72 3.92 46.84 3.06
762 764 8.992073 GCTGTTTGTATGATCATGTATGATGTA 58.008 33.333 18.72 2.22 46.84 2.29
792 794 4.963276 TTGCTGCTGTTATGGTAATGTC 57.037 40.909 0.00 0.00 0.00 3.06
1440 1442 5.771469 TGCATTTGGTGATGTTGTTAGAAG 58.229 37.500 0.00 0.00 0.00 2.85
1538 1540 5.160641 GTTTTCTTGAACATGTGTGTGTGT 58.839 37.500 0.00 0.00 38.92 3.72
2350 2352 8.556194 GTTTGTCTATTGTGACATGTCAAGTAA 58.444 33.333 29.42 22.74 45.03 2.24
2783 2798 6.987403 TTTATAATAACTTGGGGGCATTCC 57.013 37.500 0.00 0.00 0.00 3.01
2805 2820 3.434641 CGATAATGTCCACATGAGATGCC 59.565 47.826 0.00 0.00 36.56 4.40
2814 2829 1.680735 ACATGAGATGCCGAGTCTCTC 59.319 52.381 0.00 1.14 42.04 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 47 2.228138 TCTTTTTGTGTAGCGTCCGT 57.772 45.000 0.00 0.00 0.00 4.69
49 51 3.074412 CCCTGATCTTTTTGTGTAGCGT 58.926 45.455 0.00 0.00 0.00 5.07
96 98 7.561251 TCGGGACAAAATCAATTCATAGAGTA 58.439 34.615 0.00 0.00 0.00 2.59
102 104 5.887598 TGATCTCGGGACAAAATCAATTCAT 59.112 36.000 0.00 0.00 0.00 2.57
114 116 4.014569 TGACAATTTTGATCTCGGGACA 57.985 40.909 0.00 0.00 0.00 4.02
117 119 6.401367 GCAAATTTGACAATTTTGATCTCGGG 60.401 38.462 27.56 9.09 40.09 5.14
122 124 6.146021 ACTCGGCAAATTTGACAATTTTGATC 59.854 34.615 27.56 19.91 40.09 2.92
123 125 5.990996 ACTCGGCAAATTTGACAATTTTGAT 59.009 32.000 27.56 11.98 40.09 2.57
756 758 5.047872 ACAGCAGCAAAAATGTGATACATCA 60.048 36.000 0.00 0.00 37.97 3.07
757 759 5.404946 ACAGCAGCAAAAATGTGATACATC 58.595 37.500 0.00 0.00 37.97 3.06
758 760 5.395682 ACAGCAGCAAAAATGTGATACAT 57.604 34.783 0.00 0.00 41.31 2.29
759 761 4.852134 ACAGCAGCAAAAATGTGATACA 57.148 36.364 0.00 0.00 0.00 2.29
760 762 6.254157 CCATAACAGCAGCAAAAATGTGATAC 59.746 38.462 0.00 0.00 0.00 2.24
761 763 6.071447 ACCATAACAGCAGCAAAAATGTGATA 60.071 34.615 0.00 0.00 0.00 2.15
762 764 5.172934 CCATAACAGCAGCAAAAATGTGAT 58.827 37.500 0.00 0.00 0.00 3.06
792 794 0.598158 ACAGCAAAAATGTGGCAGCG 60.598 50.000 0.00 0.00 0.00 5.18
1440 1442 5.728471 TGCATATTAGGATAAGCTCAGAGC 58.272 41.667 15.25 15.25 42.84 4.09
1538 1540 6.546428 AGCTAGTAAAAGGAGATGCAGTAA 57.454 37.500 0.00 0.00 0.00 2.24
2350 2352 3.447229 GCACCCCAAATAACAACTAGCAT 59.553 43.478 0.00 0.00 0.00 3.79
2513 2515 6.070194 AGCTTTGTGCCTAGGAATTAAGACTA 60.070 38.462 14.75 0.00 44.23 2.59
2783 2798 3.434641 GGCATCTCATGTGGACATTATCG 59.565 47.826 0.00 0.00 33.61 2.92
2805 2820 2.620585 TCACATGCCATAGAGAGACTCG 59.379 50.000 0.00 0.00 35.36 4.18


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

AutoCloner maintained by Alex Coulton.