Multiple sequence alignment - TraesCS7A01G274400

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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 TraesCS7A01G274400 chr7A 100.000 2714 0 0 1 2714 287525434 287528147 0.000000e+00 5012.0
1 TraesCS7A01G274400 chr7A 92.949 2028 106 9 3 2016 287491148 287493152 0.000000e+00 2918.0
2 TraesCS7A01G274400 chr7A 92.263 1383 82 16 401 1775 287499150 287500515 0.000000e+00 1938.0
3 TraesCS7A01G274400 chr7A 86.295 861 117 1 937 1797 287484941 287485800 0.000000e+00 935.0
4 TraesCS7A01G274400 chr7A 88.038 209 11 4 2118 2320 287484030 287484230 4.520000e-58 235.0
5 TraesCS7A01G274400 chr7A 85.586 222 24 5 2381 2596 287493717 287493936 2.720000e-55 226.0
6 TraesCS7A01G274400 chr7A 95.000 120 6 0 2595 2714 287493964 287494083 3.570000e-44 189.0
7 TraesCS7A01G274400 chr7A 100.000 34 0 0 1973 2006 287527309 287527342 2.260000e-06 63.9
8 TraesCS7A01G274400 chr7A 100.000 34 0 0 1876 1909 287527406 287527439 2.260000e-06 63.9
9 TraesCS7A01G274400 chr7B 95.030 2193 69 15 548 2713 244409617 244411796 0.000000e+00 3410.0
10 TraesCS7A01G274400 chr7B 91.473 1466 91 10 572 2019 244404675 244406124 0.000000e+00 1984.0
11 TraesCS7A01G274400 chr7B 84.545 990 138 11 818 1797 244406805 244407789 0.000000e+00 966.0
12 TraesCS7A01G274400 chr7B 88.571 245 14 2 2483 2714 244406505 244406748 4.420000e-73 285.0
13 TraesCS7A01G274400 chr7B 85.159 283 26 7 2123 2400 244406189 244406460 2.660000e-70 276.0
14 TraesCS7A01G274400 chr7B 81.329 316 44 11 2 304 694228382 694228069 2.700000e-60 243.0
15 TraesCS7A01G274400 chr7B 91.667 84 7 0 2106 2189 244395286 244395369 1.710000e-22 117.0
16 TraesCS7A01G274400 chr7B 82.418 91 10 5 159 246 666581863 666581776 1.040000e-09 75.0
17 TraesCS7A01G274400 chr7B 100.000 34 0 0 1973 2006 244410943 244410976 2.260000e-06 63.9
18 TraesCS7A01G274400 chr7B 100.000 34 0 0 1876 1909 244411043 244411076 2.260000e-06 63.9
19 TraesCS7A01G274400 chr7D 93.354 1926 83 17 818 2714 264054301 264056210 0.000000e+00 2806.0
20 TraesCS7A01G274400 chr7D 93.509 1710 79 12 321 2019 264034149 264035837 0.000000e+00 2514.0
21 TraesCS7A01G274400 chr7D 93.564 637 37 2 330 962 264044558 264045194 0.000000e+00 946.0
22 TraesCS7A01G274400 chr7D 86.179 861 118 1 937 1797 264028916 264029775 0.000000e+00 929.0
23 TraesCS7A01G274400 chr7D 82.545 613 41 25 2123 2714 264035902 264036469 1.890000e-131 479.0
24 TraesCS7A01G274400 chr7D 90.583 223 13 3 2106 2320 264028025 264028247 3.420000e-74 289.0
25 TraesCS7A01G274400 chr7D 85.772 246 20 8 2106 2336 264053513 264053758 2.090000e-61 246.0
26 TraesCS7A01G274400 chr7D 97.059 34 1 0 1876 1909 264055455 264055488 1.050000e-04 58.4
27 TraesCS7A01G274400 chrUn 81.329 316 42 12 2 302 339584702 339584389 9.710000e-60 241.0
28 TraesCS7A01G274400 chr6B 80.696 316 45 11 2 302 707716702 707717016 5.840000e-57 231.0
29 TraesCS7A01G274400 chr1A 79.870 308 37 13 1 305 249149228 249148943 4.580000e-48 202.0


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 TraesCS7A01G274400 chr7A 287525434 287528147 2713 False 1713.266667 5012 100.000000 1 2714 3 chr7A.!!$F4 2713
1 TraesCS7A01G274400 chr7A 287499150 287500515 1365 False 1938.000000 1938 92.263000 401 1775 1 chr7A.!!$F1 1374
2 TraesCS7A01G274400 chr7A 287491148 287494083 2935 False 1111.000000 2918 91.178333 3 2714 3 chr7A.!!$F3 2711
3 TraesCS7A01G274400 chr7A 287484030 287485800 1770 False 585.000000 935 87.166500 937 2320 2 chr7A.!!$F2 1383
4 TraesCS7A01G274400 chr7B 244404675 244411796 7121 False 1006.971429 3410 92.111143 548 2714 7 chr7B.!!$F2 2166
5 TraesCS7A01G274400 chr7D 264034149 264036469 2320 False 1496.500000 2514 88.027000 321 2714 2 chr7D.!!$F3 2393
6 TraesCS7A01G274400 chr7D 264053513 264056210 2697 False 1036.800000 2806 92.061667 818 2714 3 chr7D.!!$F4 1896
7 TraesCS7A01G274400 chr7D 264044558 264045194 636 False 946.000000 946 93.564000 330 962 1 chr7D.!!$F1 632
8 TraesCS7A01G274400 chr7D 264028025 264029775 1750 False 609.000000 929 88.381000 937 2320 2 chr7D.!!$F2 1383

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
272 275 0.033405 CTAGGGTTCCCTCTCGGTCA 60.033 60.0 14.24 0.00 37.64 4.02 F
1191 5605 0.694771 AGATGATGTGCACACCCAGT 59.305 50.0 24.37 5.44 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1430 5844 0.242825 ATCGTTCTTGTCGGAAGCGA 59.757 50.0 0.0 0.0 35.31 4.93 R
2220 6707 1.050204 ATTGGTTGCATGTGTTGGCT 58.950 45.0 0.0 0.0 0.00 4.75 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
165 166 1.004918 AGACGAAAGAACCCTGCCG 60.005 57.895 0.00 0.00 0.00 5.69
167 168 2.358737 CGAAAGAACCCTGCCGCT 60.359 61.111 0.00 0.00 0.00 5.52
169 170 2.282462 AAAGAACCCTGCCGCTGG 60.282 61.111 9.30 9.30 0.00 4.85
272 275 0.033405 CTAGGGTTCCCTCTCGGTCA 60.033 60.000 14.24 0.00 37.64 4.02
739 5143 1.522668 TTCACACTTGCTGCGCTAAT 58.477 45.000 9.73 0.00 0.00 1.73
740 5144 2.378445 TCACACTTGCTGCGCTAATA 57.622 45.000 9.73 0.00 0.00 0.98
781 5185 2.380064 TTGTCTGATTGGGCTTTGGT 57.620 45.000 0.00 0.00 0.00 3.67
900 5314 7.342769 TCCGTTATAAATACAGAGAGAAGCA 57.657 36.000 0.00 0.00 0.00 3.91
988 5402 2.100584 AGAAAGTAGCATCAGAGCCTCG 59.899 50.000 0.00 0.00 34.23 4.63
1191 5605 0.694771 AGATGATGTGCACACCCAGT 59.305 50.000 24.37 5.44 0.00 4.00
1279 5693 1.300931 GTGCTCGACCTCTGCAACA 60.301 57.895 0.00 0.00 38.50 3.33
1430 5844 7.811713 GCAGTTCAAGAAGATAAGCAAGAAAAT 59.188 33.333 0.00 0.00 0.00 1.82
1431 5845 9.339492 CAGTTCAAGAAGATAAGCAAGAAAATC 57.661 33.333 0.00 0.00 0.00 2.17
1609 6023 1.160137 GTGCGAAGAGGAGCAATTGT 58.840 50.000 7.40 0.00 45.61 2.71
2085 6543 3.019564 AGTTGACCGTAATAGCCTACGT 58.980 45.455 0.00 0.00 42.47 3.57
2220 6707 9.734984 ATGATGCTGATGACTATCAATAATCAA 57.265 29.630 0.00 0.00 42.48 2.57
2295 6786 3.149005 TCATGTTGTTGTACCTTCCCC 57.851 47.619 0.00 0.00 0.00 4.81
2359 6850 9.757227 TCGTTGGATTAGTTTCAAAAATGAAAT 57.243 25.926 7.21 1.05 39.58 2.17
2429 7173 8.025243 TCGTAGGTAATTTTCTTTCACATGAC 57.975 34.615 0.00 0.00 0.00 3.06
2451 7198 2.395336 TCTCAGCTAGCCAGATGGAT 57.605 50.000 12.13 0.00 38.75 3.41
2457 7204 4.282957 TCAGCTAGCCAGATGGATCTTAAG 59.717 45.833 12.13 0.00 38.75 1.85
2474 7221 6.653273 TCTTAAGATCGAAAGCATCAGTTG 57.347 37.500 0.00 0.00 0.00 3.16
2519 7268 3.120442 GCGTACACTTACATGGTTGTTCC 60.120 47.826 0.00 0.00 37.28 3.62
2580 7329 6.797540 ACAGGAATAAGACCCCCATCATAATA 59.202 38.462 0.00 0.00 0.00 0.98
2701 7479 4.575885 TCTGTTACCAATAGCCAAGACAC 58.424 43.478 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 170 4.814294 AAGCCCGGTCATCGTCGC 62.814 66.667 0.00 0.00 37.11 5.19
532 537 0.039437 GTTCTCTGCGTTCTCCGACA 60.039 55.000 0.00 0.00 39.56 4.35
574 4970 1.001745 GCAATGCGGGTTTCGTGTTC 61.002 55.000 0.00 0.00 41.72 3.18
781 5185 3.703556 TCTGTTGAAAGAAACATGGCCAA 59.296 39.130 10.96 0.00 39.25 4.52
900 5314 3.706086 AGTTTGTTGGTGCTCAATCCTTT 59.294 39.130 0.00 0.00 37.73 3.11
1191 5605 1.002430 CTGCAGAGGCTGACTTGGTTA 59.998 52.381 8.42 0.00 41.06 2.85
1279 5693 1.064906 CATCAAGGTCTCCTGCATGGT 60.065 52.381 0.00 0.00 32.13 3.55
1430 5844 0.242825 ATCGTTCTTGTCGGAAGCGA 59.757 50.000 0.00 0.00 35.31 4.93
1431 5845 1.059264 GAATCGTTCTTGTCGGAAGCG 59.941 52.381 0.00 0.00 0.00 4.68
1609 6023 0.625316 ATACTGCACTCCAATGCCCA 59.375 50.000 0.00 0.00 45.50 5.36
2085 6543 8.677300 GCTTGAGTAAAATAATTCCATGAGACA 58.323 33.333 0.00 0.00 0.00 3.41
2220 6707 1.050204 ATTGGTTGCATGTGTTGGCT 58.950 45.000 0.00 0.00 0.00 4.75
2295 6786 5.674525 TCATTGTACCATTAGGAAGCAGAG 58.325 41.667 0.00 0.00 38.69 3.35
2359 6850 6.716628 AGAAGTGTAATCCATTTGCTTCTGAA 59.283 34.615 0.00 0.00 39.45 3.02
2429 7173 3.429492 TCCATCTGGCTAGCTGAGATAG 58.571 50.000 21.89 17.36 34.44 2.08
2451 7198 6.166279 ACAACTGATGCTTTCGATCTTAAGA 58.834 36.000 7.82 7.82 0.00 2.10
2457 7204 5.554636 CAAGTACAACTGATGCTTTCGATC 58.445 41.667 0.00 0.00 0.00 3.69
2471 7218 3.120792 TCTCGACACAAGCAAGTACAAC 58.879 45.455 0.00 0.00 0.00 3.32
2474 7221 4.090642 CAGATTCTCGACACAAGCAAGTAC 59.909 45.833 0.00 0.00 0.00 2.73
2519 7268 2.417933 GTGTTTCAGCTATCCACAGCAG 59.582 50.000 0.00 0.00 44.35 4.24
2580 7329 5.600696 ACAGGTTTTCGCTGATTTTTCAAT 58.399 33.333 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.