Multiple sequence alignment - TraesCS7D01G273400

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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 TraesCS7D01G273400 chr7D 100.000 2435 0 0 1 2435 263957094 263954660 0.000000e+00 4497.0
1 TraesCS7D01G273400 chr7A 95.989 2468 65 16 1 2435 287213629 287211163 0.000000e+00 3978.0
2 TraesCS7D01G273400 chr7A 81.591 880 123 29 775 1632 287215506 287214644 0.000000e+00 691.0
3 TraesCS7D01G273400 chr7B 92.777 1952 93 22 1 1917 244248252 244246314 0.000000e+00 2780.0
4 TraesCS7D01G273400 chr7B 92.884 534 22 6 1914 2435 244243724 244243195 0.000000e+00 761.0
5 TraesCS7D01G273400 chr7B 80.993 947 130 36 718 1632 244270178 244269250 0.000000e+00 706.0
6 TraesCS7D01G273400 chr7B 87.500 80 4 3 550 623 244247608 244247687 1.200000e-13 87.9
7 TraesCS7D01G273400 chr7B 100.000 41 0 0 1730 1770 244248032 244247992 2.600000e-10 76.8


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 TraesCS7D01G273400 chr7D 263954660 263957094 2434 True 4497.000000 4497 100.000000 1 2435 1 chr7D.!!$R1 2434
1 TraesCS7D01G273400 chr7A 287211163 287215506 4343 True 2334.500000 3978 88.790000 1 2435 2 chr7A.!!$R1 2434
2 TraesCS7D01G273400 chr7B 244243195 244248252 5057 True 1205.933333 2780 95.220333 1 2435 3 chr7B.!!$R2 2434
3 TraesCS7D01G273400 chr7B 244269250 244270178 928 True 706.000000 706 80.993000 718 1632 1 chr7B.!!$R1 914

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
812 2728 1.545428 GCAACATCACACCAAGGGAGA 60.545 52.381 0.0 0.0 29.38 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1718 3667 0.95228 GCATCTCACATGCCATCCAG 59.048 55.0 0.0 0.0 39.01 3.86 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
245 2147 2.964209 TCCTGACTCCAAGCCTATAGG 58.036 52.381 15.01 15.01 38.53 2.57
285 2187 7.667043 ATACGAGTTTTTGTATCAGCTGAAA 57.333 32.000 22.50 7.97 29.50 2.69
298 2200 8.514594 TGTATCAGCTGAAACCTGAATTAAAAG 58.485 33.333 22.50 0.00 42.12 2.27
370 2272 7.865706 ACATTTACATGATCCACCTTTCTAC 57.134 36.000 0.00 0.00 34.11 2.59
466 2368 6.697395 TCAGTAAATGCAGCAGAGTAACTTA 58.303 36.000 0.00 0.00 0.00 2.24
573 2475 5.440234 TTAATCAGGCACGCAAAAACTAA 57.560 34.783 0.00 0.00 0.00 2.24
667 2574 2.061509 ACCCAAAACTTTGTACCGCT 57.938 45.000 1.76 0.00 36.45 5.52
812 2728 1.545428 GCAACATCACACCAAGGGAGA 60.545 52.381 0.00 0.00 29.38 3.71
1186 3117 1.758440 GATCCCCATAGCGTGCCTCA 61.758 60.000 0.00 0.00 0.00 3.86
1187 3118 1.344953 ATCCCCATAGCGTGCCTCAA 61.345 55.000 0.00 0.00 0.00 3.02
1202 3133 2.196749 CCTCAACACGATGATCTTCGG 58.803 52.381 28.17 20.58 43.33 4.30
1266 3197 2.300967 GGGGAGGATCACACTGCCA 61.301 63.158 9.60 0.00 43.69 4.92
1346 3277 3.791640 TGAGAGGGCGCTTCTCAA 58.208 55.556 29.72 19.02 45.87 3.02
1353 3284 0.678048 GGGCGCTTCTCAACTCCATT 60.678 55.000 7.64 0.00 0.00 3.16
1461 3392 7.390162 AGAGTGAACATCTCCAGATTTTTCTTC 59.610 37.037 8.30 6.81 31.21 2.87
1659 3591 5.646577 ACTACTGCTAGTGTAGTTTCTGG 57.353 43.478 18.49 2.64 45.60 3.86
1709 3658 5.104193 AGCCAACTAGGAATCACATGAAGAT 60.104 40.000 0.00 0.00 41.22 2.40
1779 3728 2.259204 CACAAGGTGCAATGGCCG 59.741 61.111 0.00 0.00 40.13 6.13
1930 6476 3.054802 GGTAGGCCTCATATGAATCTGGG 60.055 52.174 9.68 5.27 0.00 4.45
2071 6617 1.417890 GCCTATCAGCTAAGGAAGGCA 59.582 52.381 15.86 0.00 46.95 4.75
2148 6694 3.181450 ACTTATTCACAGCTATGGCCTCC 60.181 47.826 3.32 0.00 39.73 4.30
2180 6726 3.119990 ACAAATGTATGTAGCAACCGCAC 60.120 43.478 0.00 0.00 42.27 5.34
2186 6732 2.753055 TGTAGCAACCGCACTAATCA 57.247 45.000 0.00 0.00 42.27 2.57
2187 6733 3.260475 TGTAGCAACCGCACTAATCAT 57.740 42.857 0.00 0.00 42.27 2.45
2205 6762 7.995488 ACTAATCATATTGCCTCCATTATAGCC 59.005 37.037 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
219 2098 1.528129 GCTTGGAGTCAGGAACCTTG 58.472 55.000 0.00 0.00 0.00 3.61
245 2147 5.521544 ACTCGTATTTCCGCTTAGATTCTC 58.478 41.667 0.00 0.00 0.00 2.87
298 2200 6.890268 AGAGGTTCCATGTTCCTATTTAAACC 59.110 38.462 0.00 0.00 35.08 3.27
370 2272 7.984050 AGATGACTTAACTATCACCACATCTTG 59.016 37.037 0.00 0.00 38.75 3.02
667 2574 0.950836 AGCTTTAACATGCGCACACA 59.049 45.000 14.90 0.00 0.00 3.72
812 2728 0.904649 TCCAGAGACAACGCCATGAT 59.095 50.000 0.00 0.00 0.00 2.45
919 2840 2.555547 GGTCAGCTTGTGTGTGGCC 61.556 63.158 0.00 0.00 0.00 5.36
1186 3117 1.137086 CTCCCCGAAGATCATCGTGTT 59.863 52.381 18.05 0.00 41.16 3.32
1187 3118 0.747255 CTCCCCGAAGATCATCGTGT 59.253 55.000 18.05 0.00 41.16 4.49
1202 3133 1.743321 CGACATCCTCAGGAGCTCCC 61.743 65.000 29.54 11.59 34.05 4.30
1266 3197 5.282055 ACTCCATCATTGTCGTATCACAT 57.718 39.130 0.00 0.00 0.00 3.21
1346 3277 4.189231 GTGGCAAGTCGTTATAATGGAGT 58.811 43.478 4.86 0.00 0.00 3.85
1353 3284 2.502130 TGGATGGTGGCAAGTCGTTATA 59.498 45.455 0.00 0.00 0.00 0.98
1659 3591 3.031736 TGGTGGCCTCTCTAATACAGTC 58.968 50.000 3.32 0.00 0.00 3.51
1709 3658 4.469586 TCACATGCCATCCAGTTCTTAGTA 59.530 41.667 0.00 0.00 0.00 1.82
1718 3667 0.952280 GCATCTCACATGCCATCCAG 59.048 55.000 0.00 0.00 39.01 3.86
1779 3728 5.119125 GGCAACTTGCTCAACAATTTCATAC 59.881 40.000 13.43 0.00 44.28 2.39
2005 6551 3.840831 CTCACTTCATGGGCTTCGA 57.159 52.632 0.00 0.00 0.00 3.71
2071 6617 6.828785 GTGGGTAACTTAGGATGTTTCATGAT 59.171 38.462 0.00 0.00 0.00 2.45
2148 6694 1.401552 CATACATTTGTGGTCCTGGCG 59.598 52.381 0.00 0.00 0.00 5.69
2180 6726 7.994911 TGGCTATAATGGAGGCAATATGATTAG 59.005 37.037 0.00 0.00 45.56 1.73
2221 6778 2.619074 GCAGGTAAGAAGGCCATGAGTT 60.619 50.000 5.01 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.