Multiple sequence alignment - TraesCS3A01G302900

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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 TraesCS3A01G302900 chr3A 100.000 2837 0 0 1 2837 536895430 536898266 0.000000e+00 5240.0
1 TraesCS3A01G302900 chr3D 94.735 2868 81 29 1 2834 413678269 413675438 0.000000e+00 4396.0
2 TraesCS3A01G302900 chr3B 93.175 2828 85 39 1 2773 539944508 539941734 0.000000e+00 4054.0
3 TraesCS3A01G302900 chr3B 92.188 64 3 1 2773 2834 539941569 539941506 3.890000e-14 89.8
4 TraesCS3A01G302900 chr1A 86.780 295 36 2 1072 1366 520939480 520939771 2.730000e-85 326.0
5 TraesCS3A01G302900 chr1B 86.441 295 37 2 1072 1366 575441280 575441571 1.270000e-83 320.0


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 TraesCS3A01G302900 chr3A 536895430 536898266 2836 False 5240.0 5240 100.0000 1 2837 1 chr3A.!!$F1 2836
1 TraesCS3A01G302900 chr3D 413675438 413678269 2831 True 4396.0 4396 94.7350 1 2834 1 chr3D.!!$R1 2833
2 TraesCS3A01G302900 chr3B 539941506 539944508 3002 True 2071.9 4054 92.6815 1 2834 2 chr3B.!!$R1 2833

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
842 885 0.036732 TTGGTGGCTTGCTCCTGTAG 59.963 55.0 8.22 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2480 2549 1.133976 AGTCACTATGGCAGAATGGGC 60.134 52.381 0.0 0.0 35.86 5.36 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
28 30 8.289618 GGATTTCTTAATTTTTGGTGCCTTTTC 58.710 33.333 0.00 0.00 0.00 2.29
57 59 4.202040 CCTTGATTAGAATTTCATGCGGCA 60.202 41.667 4.58 4.58 0.00 5.69
64 66 1.315690 ATTTCATGCGGCAGATCTGG 58.684 50.000 23.89 9.58 0.00 3.86
96 100 6.097839 TGTTAATCCCTCTCGCTTTGTATACT 59.902 38.462 4.17 0.00 0.00 2.12
162 167 2.666508 CCACCGAAGTGTTCTTGTATCG 59.333 50.000 0.00 0.00 42.88 2.92
272 280 6.373216 TGAACCGAATAGTTTGAATTACCCAG 59.627 38.462 0.00 0.00 0.00 4.45
349 358 3.880490 CCCAATCGAATCCACGGAATTAA 59.120 43.478 0.00 0.00 0.00 1.40
389 398 1.030488 CAGACAGGCCTGCAGGATTG 61.030 60.000 37.21 30.78 37.39 2.67
476 493 1.276421 CCCAGTGGTGAGACTTGTAGG 59.724 57.143 8.74 0.00 0.00 3.18
496 513 2.159000 GGACGACCCCGATTCATAACTT 60.159 50.000 0.00 0.00 39.50 2.66
519 536 3.152341 ACTGCAGAACAATCAAAGAGGG 58.848 45.455 23.35 0.00 0.00 4.30
561 593 3.907221 ACCATGGAATCATTCTCTTGGG 58.093 45.455 21.47 8.27 33.49 4.12
842 885 0.036732 TTGGTGGCTTGCTCCTGTAG 59.963 55.000 8.22 0.00 0.00 2.74
861 904 7.037586 TCCTGTAGAAACACCATTAAATCTCCT 60.038 37.037 0.00 0.00 0.00 3.69
999 1042 0.313043 GTCGTCGGAGGTCACTTGAA 59.687 55.000 0.00 0.00 0.00 2.69
1016 1059 1.199789 TGAAATGATGAGCGGCAACAC 59.800 47.619 1.45 0.00 31.69 3.32
1032 1075 4.694233 ACCCAGCAGCAGCAGTCG 62.694 66.667 3.17 0.00 45.49 4.18
1060 1115 2.043450 CGGAGGAGGAGCAGGAGT 60.043 66.667 0.00 0.00 0.00 3.85
1545 1600 1.076777 CCGGTTCATGGGGCTCAAT 60.077 57.895 0.00 0.00 0.00 2.57
1611 1666 1.416401 ACCGGCGAGTCATGGAATAAT 59.584 47.619 9.30 0.00 0.00 1.28
1659 1714 1.513158 CTCGCCACAGGTCTCGATT 59.487 57.895 0.00 0.00 0.00 3.34
1830 1885 1.952367 GCTTTCCATGACCAGACAGGG 60.952 57.143 0.00 0.00 43.89 4.45
1996 2051 5.123502 GCTAGCTAGTAGAAGTGTGTGTGTA 59.876 44.000 21.62 0.00 0.00 2.90
1997 2052 6.183360 GCTAGCTAGTAGAAGTGTGTGTGTAT 60.183 42.308 21.62 0.00 0.00 2.29
2113 2174 4.381292 GCTTTGGAAGTTGAGCAATGCTAT 60.381 41.667 8.12 0.00 39.88 2.97
2259 2325 6.942532 TTAATCTCTCTCTCTCTCTCTTGC 57.057 41.667 0.00 0.00 0.00 4.01
2295 2361 9.747898 ATGTCCAGGTATGTTATTTGAGTTTTA 57.252 29.630 0.00 0.00 0.00 1.52
2366 2435 4.380444 CCCCGTTCCATTGATTGTACTTTG 60.380 45.833 0.00 0.00 0.00 2.77
2434 2503 4.870021 AGCAACTAGAGAAAATCCCCAT 57.130 40.909 0.00 0.00 0.00 4.00
2471 2540 7.670605 AATAACAGGTTCACTAGCTACCATA 57.329 36.000 5.43 0.00 34.32 2.74
2477 2546 6.929606 CAGGTTCACTAGCTACCATATAAACC 59.070 42.308 5.43 5.63 34.32 3.27
2480 2549 6.665992 TCACTAGCTACCATATAAACCAGG 57.334 41.667 0.00 0.00 0.00 4.45
2530 2599 2.684881 CAAACTCAAGACACACCAAGCT 59.315 45.455 0.00 0.00 0.00 3.74
2548 2617 6.126361 ACCAAGCTCCCACTCAATAAATCTAT 60.126 38.462 0.00 0.00 0.00 1.98
2549 2618 7.072454 ACCAAGCTCCCACTCAATAAATCTATA 59.928 37.037 0.00 0.00 0.00 1.31
2550 2619 7.389053 CCAAGCTCCCACTCAATAAATCTATAC 59.611 40.741 0.00 0.00 0.00 1.47
2621 2690 8.451908 AGTTACAGGCAATGTTAAAGGATATC 57.548 34.615 0.00 0.00 39.96 1.63
2622 2691 8.275040 AGTTACAGGCAATGTTAAAGGATATCT 58.725 33.333 2.05 0.00 39.96 1.98
2834 3074 2.305927 CTCCTGCAGGTTCTCCCTTAAA 59.694 50.000 31.58 7.42 42.73 1.52
2835 3075 2.305927 TCCTGCAGGTTCTCCCTTAAAG 59.694 50.000 31.58 1.40 42.73 1.85
2836 3076 2.087646 CTGCAGGTTCTCCCTTAAAGC 58.912 52.381 5.57 0.00 42.73 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.550976 ACCACGAAAAGGCACCAAAAA 59.449 42.857 0.00 0.00 0.00 1.94
28 30 6.489675 CATGAAATTCTAATCAAGGACCACG 58.510 40.000 0.00 0.00 0.00 4.94
57 59 5.946486 GGGATTAACAAATCTCCCAGATCT 58.054 41.667 4.91 0.00 45.66 2.75
64 66 3.810386 GCGAGAGGGATTAACAAATCTCC 59.190 47.826 0.00 0.00 29.85 3.71
80 84 7.254252 CCAAAGAATCAGTATACAAAGCGAGAG 60.254 40.741 5.50 0.00 0.00 3.20
162 167 3.552890 GGATCCAGTGCAGTTTTGGTTTC 60.553 47.826 6.95 0.00 33.65 2.78
272 280 6.633634 GTGATTAGTACTACAAGCGATGAGAC 59.366 42.308 0.91 0.00 0.00 3.36
349 358 8.924303 TGTCTGTCATACAGCCTAAATTACTAT 58.076 33.333 2.12 0.00 45.54 2.12
389 398 3.486285 GCAGCTGCTTCCTTTTCAC 57.514 52.632 31.33 0.00 38.21 3.18
476 493 2.864343 CAAGTTATGAATCGGGGTCGTC 59.136 50.000 0.00 0.00 37.69 4.20
496 513 3.817084 CCTCTTTGATTGTTCTGCAGTCA 59.183 43.478 14.67 11.60 41.22 3.41
519 536 2.279741 TGAACATATGAACGGCTCAGC 58.720 47.619 10.38 0.00 37.52 4.26
842 885 6.272822 AGCAAGGAGATTTAATGGTGTTTC 57.727 37.500 0.00 0.00 0.00 2.78
943 986 1.423395 GGCTTTCGATCATCCGCTAG 58.577 55.000 0.00 0.00 0.00 3.42
944 987 0.318699 CGGCTTTCGATCATCCGCTA 60.319 55.000 0.00 0.00 42.43 4.26
945 988 1.592669 CGGCTTTCGATCATCCGCT 60.593 57.895 0.00 0.00 42.43 5.52
946 989 1.591594 TCGGCTTTCGATCATCCGC 60.592 57.895 9.96 0.00 43.74 5.54
947 990 4.730081 TCGGCTTTCGATCATCCG 57.270 55.556 8.89 8.89 43.74 4.18
977 1020 1.168407 AAGTGACCTCCGACGACGAA 61.168 55.000 9.28 0.00 42.66 3.85
999 1042 1.315257 GGGTGTTGCCGCTCATCATT 61.315 55.000 0.00 0.00 38.44 2.57
1110 1165 0.663688 CTATCCGTGACTCCGTCTGG 59.336 60.000 0.00 0.00 33.15 3.86
1490 1545 1.615116 CCATGTTGTGGTGAGCTCCAT 60.615 52.381 12.15 2.25 43.44 3.41
1545 1600 1.358152 CCAGTCCCAGGGAGTTGTTA 58.642 55.000 14.01 0.00 32.26 2.41
1611 1666 1.004560 GCTCTGGTGCACACTGCTA 60.005 57.895 20.43 0.00 45.31 3.49
1852 1907 3.547413 CGATCGATCCAGCGTTGTACTAA 60.547 47.826 19.51 0.00 0.00 2.24
2011 2071 9.535170 CTTGACCCATAGGAAGAAGTATATCTA 57.465 37.037 0.00 0.00 36.73 1.98
2033 2093 2.791501 GAACCCGCGGTTAGGCTTGA 62.792 60.000 26.12 0.00 46.95 3.02
2113 2174 2.113774 CACAGCAAGCCCACCAGA 59.886 61.111 0.00 0.00 0.00 3.86
2178 2239 8.360390 TGTTATTGCACAATAAACCATTACACA 58.640 29.630 15.46 6.16 42.75 3.72
2249 2315 5.426504 ACATGGTTTCATAGCAAGAGAGAG 58.573 41.667 0.00 0.00 37.87 3.20
2250 2316 5.423015 GACATGGTTTCATAGCAAGAGAGA 58.577 41.667 0.00 0.00 37.87 3.10
2251 2317 4.574013 GGACATGGTTTCATAGCAAGAGAG 59.426 45.833 0.00 0.00 37.87 3.20
2252 2318 4.019411 TGGACATGGTTTCATAGCAAGAGA 60.019 41.667 0.00 0.00 37.87 3.10
2253 2319 4.264253 TGGACATGGTTTCATAGCAAGAG 58.736 43.478 0.00 0.00 37.87 2.85
2254 2320 4.264253 CTGGACATGGTTTCATAGCAAGA 58.736 43.478 0.00 0.00 37.87 3.02
2255 2321 3.379372 CCTGGACATGGTTTCATAGCAAG 59.621 47.826 0.00 0.00 37.87 4.01
2259 2325 5.684704 ACATACCTGGACATGGTTTCATAG 58.315 41.667 0.00 0.00 38.88 2.23
2295 2361 3.899734 TGTAGCACGTACGTGTAACAAT 58.100 40.909 39.56 24.14 46.90 2.71
2303 2369 2.860062 CTAAAGCTGTAGCACGTACGT 58.140 47.619 16.72 16.72 45.16 3.57
2304 2370 1.582502 GCTAAAGCTGTAGCACGTACG 59.417 52.381 27.82 15.01 44.94 3.67
2434 2503 9.575783 GTGAACCTGTTATTTTTGTAGTTTTCA 57.424 29.630 0.00 0.00 0.00 2.69
2471 2540 1.780503 GCAGAATGGGCCTGGTTTAT 58.219 50.000 4.53 0.00 35.86 1.40
2480 2549 1.133976 AGTCACTATGGCAGAATGGGC 60.134 52.381 0.00 0.00 35.86 5.36
2556 2625 6.375945 TGCGTGCATATATGATTTCTTGTT 57.624 33.333 17.10 0.00 0.00 2.83
2571 2640 1.978080 TGCTTTGGGATGCGTGCAT 60.978 52.632 7.12 7.12 39.69 3.96
2709 2779 6.484308 TCAACTAATCATGTGTGATGCTATGG 59.516 38.462 0.00 0.00 44.20 2.74


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

AutoCloner maintained by Alex Coulton.