Multiple sequence alignment - TraesCS7A01G332400

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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 TraesCS7A01G332400 chr7A 100.000 1489 0 0 776 2264 485698119 485696631 0.000000e+00 2750.0
1 TraesCS7A01G332400 chr7A 96.203 1185 44 1 776 1960 485690001 485688818 0.000000e+00 1938.0
2 TraesCS7A01G332400 chr7A 100.000 508 0 0 1 508 485698894 485698387 0.000000e+00 939.0
3 TraesCS7A01G332400 chr2A 97.045 1489 44 0 776 2264 485967445 485968933 0.000000e+00 2507.0
4 TraesCS7A01G332400 chr5A 96.373 1489 53 1 776 2264 334649836 334648349 0.000000e+00 2449.0
5 TraesCS7A01G332400 chr5A 96.437 449 15 1 1 449 334642254 334641807 0.000000e+00 739.0
6 TraesCS7A01G332400 chr5A 95.796 452 15 2 1 449 334650585 334650135 0.000000e+00 726.0
7 TraesCS7A01G332400 chr3A 94.840 1279 61 3 776 2054 174791229 174789956 0.000000e+00 1991.0
8 TraesCS7A01G332400 chr3A 96.000 450 13 3 5 449 595748792 595749241 0.000000e+00 726.0
9 TraesCS7A01G332400 chr3A 95.768 449 17 2 1 449 174792040 174791594 0.000000e+00 723.0
10 TraesCS7A01G332400 chr3A 95.323 449 19 2 1 449 174769120 174768674 0.000000e+00 712.0
11 TraesCS7A01G332400 chr3A 87.500 56 0 1 453 508 595749269 595749317 8.730000e-05 58.4
12 TraesCS7A01G332400 chr3B 95.521 1228 50 4 776 2000 234961596 234960371 0.000000e+00 1958.0
13 TraesCS7A01G332400 chr3B 93.193 1190 74 6 776 1962 116637920 116636735 0.000000e+00 1742.0
14 TraesCS7A01G332400 chr3B 94.808 1117 53 4 847 1960 234953080 234951966 0.000000e+00 1736.0
15 TraesCS7A01G332400 chr3B 94.954 1090 50 4 776 1863 116649404 116648318 0.000000e+00 1703.0
16 TraesCS7A01G332400 chr3B 89.177 462 36 11 1 449 116638534 116638074 4.220000e-157 564.0
17 TraesCS7A01G332400 chr7B 93.378 1193 67 7 776 1960 388612822 388614010 0.000000e+00 1755.0
18 TraesCS7A01G332400 chr7B 93.126 451 26 4 1 447 120184609 120185058 0.000000e+00 656.0
19 TraesCS7A01G332400 chr2B 85.773 731 88 14 1540 2264 93602432 93603152 0.000000e+00 760.0
20 TraesCS7A01G332400 chr1A 93.541 449 22 2 4 446 39063691 39063244 0.000000e+00 662.0
21 TraesCS7A01G332400 chr1B 91.353 451 26 7 1 449 217618062 217618501 2.490000e-169 604.0
22 TraesCS7A01G332400 chr1B 88.119 505 33 13 1 491 217610951 217611442 1.950000e-160 575.0


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 TraesCS7A01G332400 chr7A 485696631 485698894 2263 True 1844.5 2750 100.0000 1 2264 2 chr7A.!!$R2 2263
1 TraesCS7A01G332400 chr7A 485688818 485690001 1183 True 1938.0 1938 96.2030 776 1960 1 chr7A.!!$R1 1184
2 TraesCS7A01G332400 chr2A 485967445 485968933 1488 False 2507.0 2507 97.0450 776 2264 1 chr2A.!!$F1 1488
3 TraesCS7A01G332400 chr5A 334648349 334650585 2236 True 1587.5 2449 96.0845 1 2264 2 chr5A.!!$R2 2263
4 TraesCS7A01G332400 chr3A 174789956 174792040 2084 True 1357.0 1991 95.3040 1 2054 2 chr3A.!!$R2 2053
5 TraesCS7A01G332400 chr3A 595748792 595749317 525 False 392.2 726 91.7500 5 508 2 chr3A.!!$F1 503
6 TraesCS7A01G332400 chr3B 234960371 234961596 1225 True 1958.0 1958 95.5210 776 2000 1 chr3B.!!$R3 1224
7 TraesCS7A01G332400 chr3B 234951966 234953080 1114 True 1736.0 1736 94.8080 847 1960 1 chr3B.!!$R2 1113
8 TraesCS7A01G332400 chr3B 116648318 116649404 1086 True 1703.0 1703 94.9540 776 1863 1 chr3B.!!$R1 1087
9 TraesCS7A01G332400 chr3B 116636735 116638534 1799 True 1153.0 1742 91.1850 1 1962 2 chr3B.!!$R4 1961
10 TraesCS7A01G332400 chr7B 388612822 388614010 1188 False 1755.0 1755 93.3780 776 1960 1 chr7B.!!$F2 1184
11 TraesCS7A01G332400 chr2B 93602432 93603152 720 False 760.0 760 85.7730 1540 2264 1 chr2B.!!$F1 724

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
109 124 0.471617 GGCTAGCCACAGTGGATGAT 59.528 55.0 29.33 7.95 40.96 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1586 1651 0.248296 GCCACGTTTCGCTCAAAACA 60.248 50.0 0.0 0.0 38.73 2.83 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
109 124 0.471617 GGCTAGCCACAGTGGATGAT 59.528 55.000 29.33 7.95 40.96 2.45
221 239 9.669353 CCTAATGACTTATGAAATGATTTTCCG 57.331 33.333 0.00 0.00 40.49 4.30
300 318 7.093945 GGGATTTGGTGAGCTGTTTTATCTAAA 60.094 37.037 0.00 0.00 0.00 1.85
434 457 3.535629 CTCGGCCACAACCAGCAGA 62.536 63.158 2.24 0.00 0.00 4.26
988 1051 1.392534 GAGGAGGAAGAGGGGGTCA 59.607 63.158 0.00 0.00 0.00 4.02
1008 1071 2.105128 GAGGACCGGATGCTCACG 59.895 66.667 9.46 0.00 44.95 4.35
1021 1084 0.736325 GCTCACGTTGGTGCTCGTAT 60.736 55.000 0.00 0.00 44.03 3.06
1054 1117 2.583441 CCAGGGAAGCACGAGGTCA 61.583 63.158 0.00 0.00 0.00 4.02
1143 1206 1.407979 CCGCGGTACAACTCCTTCTAT 59.592 52.381 19.50 0.00 0.00 1.98
1276 1339 5.303333 GGACGAAATTAAGAGGGAGAGAGAT 59.697 44.000 0.00 0.00 0.00 2.75
1291 1354 2.103941 GAGAGATGAGCGAGGGGAAAAT 59.896 50.000 0.00 0.00 0.00 1.82
1676 1748 7.595130 GGTCAAAATGAGTTGTCTAACCATTTC 59.405 37.037 14.21 7.31 41.46 2.17
1727 1800 7.338800 AGATGCTGGACCACTAAATAATTTG 57.661 36.000 0.00 0.00 0.00 2.32
1730 1803 5.244851 TGCTGGACCACTAAATAATTTGCAA 59.755 36.000 0.00 0.00 0.00 4.08
2033 2108 1.423921 GGGAAAGACTTGGGAAGGACA 59.576 52.381 0.00 0.00 0.00 4.02
2071 2146 0.469518 GTACCTGGGGGCTATCTCGT 60.470 60.000 0.00 0.00 35.63 4.18
2097 2172 2.092598 TGGCATAGAGGCATCTCTCA 57.907 50.000 3.06 0.00 46.79 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 124 1.074471 GGCCCTCTGGACCCATCTA 60.074 63.158 0.00 0.00 30.93 1.98
178 196 4.546829 TTAGGACACTTACATGTGGGAC 57.453 45.455 9.11 0.00 41.84 4.46
221 239 6.548622 GTGGGTCCCCCTTATTTTAGATTAAC 59.451 42.308 5.13 0.00 45.70 2.01
247 265 6.787225 TGTTAAAGTGTACAACCAATGACAC 58.213 36.000 0.00 0.00 38.89 3.67
300 318 3.416414 ACATACTAACTAGTGGGCCCT 57.584 47.619 25.70 5.93 37.10 5.19
413 436 4.335647 CTGGTTGTGGCCGAGGCT 62.336 66.667 14.33 0.00 41.60 4.58
490 537 3.184683 CACTCGCCGCTGCTTCTC 61.185 66.667 0.00 0.00 34.43 2.87
805 866 2.792599 CTCGCCTCGCTCGTTACT 59.207 61.111 0.00 0.00 0.00 2.24
988 1051 2.444895 GAGCATCCGGTCCTCCCT 60.445 66.667 0.00 0.00 33.34 4.20
1008 1071 2.000447 GAGACCAATACGAGCACCAAC 59.000 52.381 0.00 0.00 0.00 3.77
1021 1084 2.528127 TGGCTTCCCCGAGACCAA 60.528 61.111 0.00 0.00 35.87 3.67
1143 1206 1.901948 AGCGTCCTCGACACCTGAA 60.902 57.895 0.00 0.00 39.71 3.02
1276 1339 0.322456 CACCATTTTCCCCTCGCTCA 60.322 55.000 0.00 0.00 0.00 4.26
1291 1354 3.074281 CGAAACCCTAGCCCACCA 58.926 61.111 0.00 0.00 0.00 4.17
1586 1651 0.248296 GCCACGTTTCGCTCAAAACA 60.248 50.000 0.00 0.00 38.73 2.83
1587 1652 0.248296 TGCCACGTTTCGCTCAAAAC 60.248 50.000 0.00 0.00 36.09 2.43
2000 2075 1.636519 TCTTTCCCCCTTATTCCGCAA 59.363 47.619 0.00 0.00 0.00 4.85
2033 2108 5.780793 AGGTACCTATCTTGTGTTGAACTCT 59.219 40.000 14.41 0.00 0.00 3.24
2071 2146 0.323302 TGCCTCTATGCCACGTTCAA 59.677 50.000 0.00 0.00 0.00 2.69
2097 2172 5.916883 CGATGACTTGCTTGAATTTCAACTT 59.083 36.000 7.74 0.00 32.21 2.66
2174 2249 1.071071 CACCCTCCGTTTCAGGTAACA 59.929 52.381 0.00 0.00 41.41 2.41


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

AutoCloner maintained by Alex Coulton.