Multiple sequence alignment - TraesCS7B01G140800

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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 TraesCS7B01G140800 chr7B 100.000 2985 0 0 1 2985 178586378 178583394 0 5513
1 TraesCS7B01G140800 chr7A 97.253 2985 82 0 1 2985 418781926 418784910 0 5059
2 TraesCS7B01G140800 chr7A 96.828 2963 90 3 1 2963 457889646 457892604 0 4948
3 TraesCS7B01G140800 chr7A 96.693 2963 95 2 1 2963 452689783 452686824 0 4926
4 TraesCS7B01G140800 chr7A 95.950 2988 115 4 1 2985 659443814 659440830 0 4843
5 TraesCS7B01G140800 chr2A 96.719 2987 94 2 1 2985 450903036 450900052 0 4970
6 TraesCS7B01G140800 chr4B 96.683 2985 94 4 1 2985 479380658 479383637 0 4959
7 TraesCS7B01G140800 chr4B 96.254 2963 111 0 1 2963 494769235 494766273 0 4857
8 TraesCS7B01G140800 chr1A 96.013 2985 118 1 1 2985 515881260 515884243 0 4852
9 TraesCS7B01G140800 chr3A 95.946 2985 116 5 1 2985 434853621 434856600 0 4837


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 TraesCS7B01G140800 chr7B 178583394 178586378 2984 True 5513 5513 100.000 1 2985 1 chr7B.!!$R1 2984
1 TraesCS7B01G140800 chr7A 418781926 418784910 2984 False 5059 5059 97.253 1 2985 1 chr7A.!!$F1 2984
2 TraesCS7B01G140800 chr7A 457889646 457892604 2958 False 4948 4948 96.828 1 2963 1 chr7A.!!$F2 2962
3 TraesCS7B01G140800 chr7A 452686824 452689783 2959 True 4926 4926 96.693 1 2963 1 chr7A.!!$R1 2962
4 TraesCS7B01G140800 chr7A 659440830 659443814 2984 True 4843 4843 95.950 1 2985 1 chr7A.!!$R2 2984
5 TraesCS7B01G140800 chr2A 450900052 450903036 2984 True 4970 4970 96.719 1 2985 1 chr2A.!!$R1 2984
6 TraesCS7B01G140800 chr4B 479380658 479383637 2979 False 4959 4959 96.683 1 2985 1 chr4B.!!$F1 2984
7 TraesCS7B01G140800 chr4B 494766273 494769235 2962 True 4857 4857 96.254 1 2963 1 chr4B.!!$R1 2962
8 TraesCS7B01G140800 chr1A 515881260 515884243 2983 False 4852 4852 96.013 1 2985 1 chr1A.!!$F1 2984
9 TraesCS7B01G140800 chr3A 434853621 434856600 2979 False 4837 4837 95.946 1 2985 1 chr3A.!!$F1 2984

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
197 198 0.808755 GATGCGAAATTTGGGGACGT 59.191 50.0 0.0 0.0 0.0 4.34 F
1346 1351 0.107831 TGGTTGTACTGTGGGACTGC 59.892 55.0 0.0 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1744 1749 1.289530 TCCTCCTCCTCTTCTTCCTCC 59.710 57.143 0.00 0.00 0.0 4.30 R
2707 2715 0.459237 CAGCAGTCGACCTTAGCCTG 60.459 60.000 13.01 2.92 0.0 4.85 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
50 51 4.393990 TCTTCGTCGATAGTGAGCAACTTA 59.606 41.667 0.00 0.00 40.56 2.24
82 83 5.105716 TCGACTCGATCCATTCTCTTCTTTT 60.106 40.000 0.00 0.00 0.00 2.27
197 198 0.808755 GATGCGAAATTTGGGGACGT 59.191 50.000 0.00 0.00 0.00 4.34
271 272 3.423154 CTCCGCGCCGCTTTCTTT 61.423 61.111 7.78 0.00 0.00 2.52
459 462 1.961277 CTCGCCTCCGCACAACTTT 60.961 57.895 0.00 0.00 34.03 2.66
589 592 1.038130 CGGGTCTTCGTCCAGATCCT 61.038 60.000 8.90 0.00 41.50 3.24
648 651 3.057174 AGTCGACCATCACAGAGAAAGAC 60.057 47.826 13.01 0.00 0.00 3.01
696 699 2.364186 TCCCATGGAGCTGCGAGA 60.364 61.111 15.22 0.00 0.00 4.04
699 702 1.227205 CCATGGAGCTGCGAGACTC 60.227 63.158 5.56 0.00 0.00 3.36
717 720 3.646715 CCGGGGAAGGAGTGGCAA 61.647 66.667 0.00 0.00 0.00 4.52
725 728 3.971702 GGAGTGGCAACCCCAGCT 61.972 66.667 0.00 0.00 46.54 4.24
783 786 3.153130 TGATCGTGGATTTTCTTTGCCA 58.847 40.909 0.00 0.00 0.00 4.92
971 976 3.181967 CGTGAAGAAGGCGAGCCG 61.182 66.667 8.63 0.00 41.95 5.52
988 993 1.080705 CGAGGCGACGAAAGAACCT 60.081 57.895 0.00 0.00 34.78 3.50
1098 1103 0.824759 GGCAGTCGACCTGGTTCTAT 59.175 55.000 13.01 0.00 41.81 1.98
1270 1275 0.689080 AGTGACGGGCATGGATCTCT 60.689 55.000 0.00 0.00 0.00 3.10
1346 1351 0.107831 TGGTTGTACTGTGGGACTGC 59.892 55.000 0.00 0.00 0.00 4.40
1569 1574 2.939103 GGTCGATTGATCCTTGTCTTGG 59.061 50.000 0.00 0.00 0.00 3.61
1744 1749 3.862267 GTGATGAAGATGACGGTGAAGAG 59.138 47.826 0.00 0.00 0.00 2.85
1767 1775 1.119684 GAAGAAGAGGAGGAGGAGGC 58.880 60.000 0.00 0.00 0.00 4.70
1865 1873 2.049156 CTCAGTCGACCAAGCGCA 60.049 61.111 13.01 0.00 0.00 6.09
1931 1939 2.747855 GGGCAGCTCCGTCAAAGG 60.748 66.667 0.00 0.00 34.94 3.11
1988 1996 3.244911 CCCCACCATATCAGGGTAATCAC 60.245 52.174 0.00 0.00 41.16 3.06
2492 2500 2.092049 AGCAGGAATCATGATGGAGCAA 60.092 45.455 9.46 0.00 0.00 3.91
2534 2542 2.125912 CAGGCAGCTTACGACGCT 60.126 61.111 0.00 0.00 38.49 5.07
2707 2715 3.782443 CGCTGGGTGTAGTCCCCC 61.782 72.222 0.00 0.00 46.48 5.40
2888 2896 1.226717 GAGGCTAAGGTCGACTGCG 60.227 63.158 16.46 3.08 39.35 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 2.644676 TGGATCGAGTCGACTGAAGAT 58.355 47.619 25.58 22.56 39.18 2.40
82 83 0.108804 GCCCGAAAGATCACTCGACA 60.109 55.000 15.69 0.00 37.23 4.35
271 272 4.155733 CAGGCGGGATACGTGGCA 62.156 66.667 0.00 0.00 46.52 4.92
648 651 1.450312 GTTGGCCATGTCGAGGAGG 60.450 63.158 6.09 0.00 0.00 4.30
717 720 1.791230 ACCCTCTTCTAGCTGGGGT 59.209 57.895 9.24 7.75 44.66 4.95
725 728 0.888619 CACGCACTCACCCTCTTCTA 59.111 55.000 0.00 0.00 0.00 2.10
783 786 2.301009 ACCACGGAAGAAAATACTCGGT 59.699 45.455 0.00 0.00 0.00 4.69
971 976 0.038526 TCAGGTTCTTTCGTCGCCTC 60.039 55.000 0.00 0.00 0.00 4.70
988 993 1.542328 CCCACACATTTGGACGACTCA 60.542 52.381 0.00 0.00 39.24 3.41
1098 1103 1.296392 CATCGACTGGTCCTGGCAA 59.704 57.895 2.09 0.00 0.00 4.52
1127 1132 2.103153 AAACTGAGGGAGTCCACTCA 57.897 50.000 21.93 21.93 44.60 3.41
1200 1205 1.795768 TCAACATCTTCACGTCAGCC 58.204 50.000 0.00 0.00 0.00 4.85
1346 1351 1.329292 GATGGACTCGAGTCTCGTCTG 59.671 57.143 36.98 14.56 44.20 3.51
1569 1574 1.597461 GTGAGGGCCTGGTAGACAC 59.403 63.158 12.95 8.08 0.00 3.67
1744 1749 1.289530 TCCTCCTCCTCTTCTTCCTCC 59.710 57.143 0.00 0.00 0.00 4.30
1988 1996 4.842139 AAATAAGAAGACTTACGCAGCG 57.158 40.909 14.82 14.82 40.71 5.18
2492 2500 1.477558 GCATCCCGGATGGTCTTCAAT 60.478 52.381 25.73 0.00 40.10 2.57
2534 2542 2.975536 CGTTGGAGGGCGGAACTA 59.024 61.111 0.00 0.00 0.00 2.24
2707 2715 0.459237 CAGCAGTCGACCTTAGCCTG 60.459 60.000 13.01 2.92 0.00 4.85


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

AutoCloner maintained by Alex Coulton.