Multiple sequence alignment - TraesCS7A01G275700

Loading Multiple Alignment...

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 TraesCS7A01G275700 chr7A 100.000 2330 0 0 1 2330 287891784 287889455 0.000000e+00 4303
1 TraesCS7A01G275700 chr7A 94.620 855 42 3 651 1504 287863500 287862649 0.000000e+00 1321
2 TraesCS7A01G275700 chr7B 96.468 2010 66 4 1 2008 244653649 244651643 0.000000e+00 3314
3 TraesCS7A01G275700 chr7B 89.608 2117 160 39 199 2306 244694840 244692775 0.000000e+00 2636
4 TraesCS7A01G275700 chr7B 91.647 1664 105 29 651 2306 244646610 244644973 0.000000e+00 2272
5 TraesCS7A01G275700 chr7B 92.077 1502 91 25 810 2306 244717727 244716249 0.000000e+00 2089
6 TraesCS7A01G275700 chr7B 83.077 455 50 13 199 652 244647078 244646650 2.810000e-104 388
7 TraesCS7A01G275700 chr7B 96.364 220 7 1 2087 2306 244651644 244651426 6.120000e-96 361
8 TraesCS7A01G275700 chr7D 95.316 2071 85 8 1 2067 264340990 264338928 0.000000e+00 3277
9 TraesCS7A01G275700 chr7D 95.290 1656 58 7 651 2305 264327566 264325930 0.000000e+00 2608
10 TraesCS7A01G275700 chr7D 91.717 1666 103 28 651 2306 264362405 264360765 0.000000e+00 2279
11 TraesCS7A01G275700 chr7D 91.744 1502 97 24 810 2306 264372117 264370638 0.000000e+00 2061
12 TraesCS7A01G275700 chr7D 87.692 455 45 6 199 652 264362889 264362445 9.540000e-144 520


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 TraesCS7A01G275700 chr7A 287889455 287891784 2329 True 4303.0 4303 100.0000 1 2330 1 chr7A.!!$R2 2329
1 TraesCS7A01G275700 chr7A 287862649 287863500 851 True 1321.0 1321 94.6200 651 1504 1 chr7A.!!$R1 853
2 TraesCS7A01G275700 chr7B 244692775 244694840 2065 True 2636.0 2636 89.6080 199 2306 1 chr7B.!!$R1 2107
3 TraesCS7A01G275700 chr7B 244716249 244717727 1478 True 2089.0 2089 92.0770 810 2306 1 chr7B.!!$R2 1496
4 TraesCS7A01G275700 chr7B 244651426 244653649 2223 True 1837.5 3314 96.4160 1 2306 2 chr7B.!!$R4 2305
5 TraesCS7A01G275700 chr7B 244644973 244647078 2105 True 1330.0 2272 87.3620 199 2306 2 chr7B.!!$R3 2107
6 TraesCS7A01G275700 chr7D 264338928 264340990 2062 True 3277.0 3277 95.3160 1 2067 1 chr7D.!!$R2 2066
7 TraesCS7A01G275700 chr7D 264325930 264327566 1636 True 2608.0 2608 95.2900 651 2305 1 chr7D.!!$R1 1654
8 TraesCS7A01G275700 chr7D 264370638 264372117 1479 True 2061.0 2061 91.7440 810 2306 1 chr7D.!!$R3 1496
9 TraesCS7A01G275700 chr7D 264360765 264362889 2124 True 1399.5 2279 89.7045 199 2306 2 chr7D.!!$R4 2107

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
582 590 1.381056 ACCACAGCCTTGCCAACAA 60.381 52.632 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2259 2321 1.003928 AGATGCCATGTGTTGCTCAGA 59.996 47.619 0.0 0.0 0.0 3.27 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
23 24 4.532834 ACCTACCTTCACAAAAAGAAGCA 58.467 39.130 0.00 0.00 40.83 3.91
170 173 3.689832 CCCCCACCAAGCTTATGTT 57.310 52.632 0.00 0.00 0.00 2.71
182 185 2.700897 AGCTTATGTTAGGATGCCTCGT 59.299 45.455 0.00 0.00 34.61 4.18
233 236 7.411486 TGCATCTAGTTAGCTCTTAGTTCTT 57.589 36.000 0.00 0.00 0.00 2.52
305 308 7.277319 CCTGTGATGACGAATGATTATATGAGG 59.723 40.741 0.00 0.00 0.00 3.86
411 414 5.369685 TTTGCATGTAATTTCTCGCTCAA 57.630 34.783 0.00 0.00 0.00 3.02
425 428 6.119144 TCTCGCTCAATTAACTTATTTGGC 57.881 37.500 4.39 5.71 0.00 4.52
488 491 4.595198 CACTATCATGTGTGTGCTCAAG 57.405 45.455 0.00 0.00 33.61 3.02
582 590 1.381056 ACCACAGCCTTGCCAACAA 60.381 52.632 0.00 0.00 0.00 2.83
648 657 1.396648 GCTGGGTGCAAACAAAACAAC 59.603 47.619 0.00 0.00 42.31 3.32
847 898 6.072508 GCAAAGGTTGAATTCACAGTATGAGA 60.073 38.462 7.89 0.00 39.69 3.27
972 1025 1.751351 TCGCATAGTGCAAGAGTAGCT 59.249 47.619 2.63 0.00 45.36 3.32
1137 1191 3.594134 CGAGTTCTTCTTCTGGAATGCT 58.406 45.455 0.00 0.00 33.01 3.79
1351 1405 3.648067 AGACTGGATCTTGACCTGAACAA 59.352 43.478 0.00 0.00 31.62 2.83
1382 1436 1.695242 TCCTTTTCTGGTCGCCACTTA 59.305 47.619 0.00 0.00 0.00 2.24
1575 1629 1.089920 CAAGCCTCCTCAAACCATCG 58.910 55.000 0.00 0.00 0.00 3.84
1999 2054 9.060347 AGATATCACATTGTCATGTTCCATTAC 57.940 33.333 5.32 0.00 41.16 1.89
2022 2077 1.153353 GCGACAAGAATCAACCGGAA 58.847 50.000 9.46 0.00 0.00 4.30
2050 2105 5.762179 ACTCTATTGGTGGATCTTGACAA 57.238 39.130 0.00 0.00 0.00 3.18
2060 2115 5.451798 GGTGGATCTTGACAAAATTGTGTGT 60.452 40.000 5.84 0.00 42.43 3.72
2062 2118 6.198966 GTGGATCTTGACAAAATTGTGTGTTC 59.801 38.462 5.84 0.00 42.43 3.18
2306 2369 3.110705 ACATGGCCATCTTGTAGAGACT 58.889 45.455 17.61 0.00 37.17 3.24
2307 2370 3.521126 ACATGGCCATCTTGTAGAGACTT 59.479 43.478 17.61 0.00 37.17 3.01
2308 2371 3.616956 TGGCCATCTTGTAGAGACTTG 57.383 47.619 0.00 0.00 37.17 3.16
2309 2372 2.906389 TGGCCATCTTGTAGAGACTTGT 59.094 45.455 0.00 0.00 37.17 3.16
2310 2373 3.327757 TGGCCATCTTGTAGAGACTTGTT 59.672 43.478 0.00 0.00 37.17 2.83
2311 2374 3.686726 GGCCATCTTGTAGAGACTTGTTG 59.313 47.826 0.00 0.00 37.17 3.33
2312 2375 4.563580 GGCCATCTTGTAGAGACTTGTTGA 60.564 45.833 0.00 0.00 37.17 3.18
2313 2376 5.181748 GCCATCTTGTAGAGACTTGTTGAT 58.818 41.667 0.00 0.00 37.17 2.57
2314 2377 5.064452 GCCATCTTGTAGAGACTTGTTGATG 59.936 44.000 0.00 0.00 37.17 3.07
2315 2378 6.401394 CCATCTTGTAGAGACTTGTTGATGA 58.599 40.000 0.00 0.00 37.17 2.92
2316 2379 6.534436 CCATCTTGTAGAGACTTGTTGATGAG 59.466 42.308 0.00 0.00 37.17 2.90
2317 2380 5.473931 TCTTGTAGAGACTTGTTGATGAGC 58.526 41.667 0.00 0.00 0.00 4.26
2318 2381 4.871933 TGTAGAGACTTGTTGATGAGCA 57.128 40.909 0.00 0.00 0.00 4.26
2319 2382 5.411831 TGTAGAGACTTGTTGATGAGCAT 57.588 39.130 0.00 0.00 0.00 3.79
2320 2383 5.798132 TGTAGAGACTTGTTGATGAGCATT 58.202 37.500 0.00 0.00 0.00 3.56
2321 2384 6.233434 TGTAGAGACTTGTTGATGAGCATTT 58.767 36.000 0.00 0.00 0.00 2.32
2322 2385 5.876612 AGAGACTTGTTGATGAGCATTTC 57.123 39.130 0.00 0.00 0.00 2.17
2323 2386 5.558818 AGAGACTTGTTGATGAGCATTTCT 58.441 37.500 0.00 0.00 0.00 2.52
2324 2387 5.411977 AGAGACTTGTTGATGAGCATTTCTG 59.588 40.000 0.00 0.00 0.00 3.02
2325 2388 5.311265 AGACTTGTTGATGAGCATTTCTGA 58.689 37.500 0.00 0.00 0.00 3.27
2326 2389 5.411977 AGACTTGTTGATGAGCATTTCTGAG 59.588 40.000 0.00 0.00 0.00 3.35
2327 2390 5.068636 ACTTGTTGATGAGCATTTCTGAGT 58.931 37.500 0.00 0.00 0.00 3.41
2328 2391 6.233434 ACTTGTTGATGAGCATTTCTGAGTA 58.767 36.000 0.00 0.00 0.00 2.59
2329 2392 6.712095 ACTTGTTGATGAGCATTTCTGAGTAA 59.288 34.615 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 135 4.572571 GCCGGTGGTGGTTGGTGA 62.573 66.667 1.90 0.00 0.00 4.02
170 173 3.224324 GGCGGACGAGGCATCCTA 61.224 66.667 0.00 0.00 31.76 2.94
189 192 4.087892 CCACGGTGGGAGCTCTGG 62.088 72.222 19.63 8.40 32.67 3.86
233 236 1.812235 CATGGCAGCAGACACTACAA 58.188 50.000 0.00 0.00 33.89 2.41
305 308 6.500910 TGATGACTCAATAATTCTGCATTGC 58.499 36.000 0.46 0.46 33.14 3.56
335 338 8.579006 GGATTTGGAATAACATGATAAGATGCA 58.421 33.333 0.00 0.00 0.00 3.96
411 414 6.010219 ACTGACACCAGCCAAATAAGTTAAT 58.990 36.000 0.00 0.00 44.16 1.40
425 428 5.171476 CACTACCTTCATTACTGACACCAG 58.829 45.833 0.00 0.00 45.76 4.00
488 491 4.039730 ACTCAGTACTGGCATCCATATCAC 59.960 45.833 22.48 0.00 30.82 3.06
582 590 8.087750 TGATAGCGATTCCAACTTCAAATTTTT 58.912 29.630 0.00 0.00 0.00 1.94
598 606 9.638239 AAAAACACAATTACAATGATAGCGATT 57.362 25.926 0.00 0.00 0.00 3.34
763 814 8.104566 ACCTGCTTGTTTGTACCTTGTATATTA 58.895 33.333 0.00 0.00 0.00 0.98
764 815 6.946009 ACCTGCTTGTTTGTACCTTGTATATT 59.054 34.615 0.00 0.00 0.00 1.28
847 898 8.197439 AGAAAGGAAACAAAAGTTTTGATCGAT 58.803 29.630 30.20 17.19 0.00 3.59
905 958 2.810274 CTGATCTTTCCCAGTGTGTGTG 59.190 50.000 0.00 0.00 0.00 3.82
972 1025 6.721704 AGCTCATAGATACACTCAACATCA 57.278 37.500 0.00 0.00 0.00 3.07
1137 1191 4.065088 CAAAATGGTCTCTCGTCTCCAAA 58.935 43.478 0.00 0.00 33.55 3.28
1351 1405 2.289694 CCAGAAAAGGAGATGACACCGT 60.290 50.000 0.00 0.00 32.13 4.83
1382 1436 4.166725 TGAAGGCCATTATCCAAGATCTGT 59.833 41.667 5.01 0.00 0.00 3.41
1575 1629 3.192422 CCATGACCATCGAGACTATCTCC 59.808 52.174 0.00 0.00 40.34 3.71
2022 2077 6.443849 TCAAGATCCACCAATAGAGTAAACCT 59.556 38.462 0.00 0.00 0.00 3.50
2028 2083 5.762179 TTGTCAAGATCCACCAATAGAGT 57.238 39.130 0.00 0.00 0.00 3.24
2068 2124 6.704310 ACTCGGTTAGTACACCATACAAAAT 58.296 36.000 3.50 0.00 36.36 1.82
2072 2128 5.300034 CCATACTCGGTTAGTACACCATACA 59.700 44.000 3.50 0.00 43.47 2.29
2073 2129 5.278660 CCCATACTCGGTTAGTACACCATAC 60.279 48.000 3.50 0.00 43.47 2.39
2082 2138 2.235402 CACCAACCCATACTCGGTTAGT 59.765 50.000 0.00 0.00 41.78 2.24
2138 2194 3.255642 GCAACACACCACACCTATTCAAT 59.744 43.478 0.00 0.00 0.00 2.57
2237 2299 2.949447 ACAAGCAAAGGATCCTTGTGT 58.051 42.857 27.71 22.96 45.22 3.72
2259 2321 1.003928 AGATGCCATGTGTTGCTCAGA 59.996 47.619 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.