Multiple sequence alignment - TraesCS3A01G293200

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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 TraesCS3A01G293200 chr3A 100.000 2495 0 0 1 2495 523747499 523745005 0.000000e+00 4608.0
1 TraesCS3A01G293200 chr3D 92.582 2022 96 25 422 2415 402797031 402795036 0.000000e+00 2854.0
2 TraesCS3A01G293200 chr3D 91.048 458 12 9 1 435 402797504 402797053 2.140000e-165 592.0
3 TraesCS3A01G293200 chr3D 96.154 52 2 0 2442 2493 402795035 402794984 4.420000e-13 86.1
4 TraesCS3A01G293200 chr3B 90.222 2117 129 32 422 2493 528632080 528629997 0.000000e+00 2691.0
5 TraesCS3A01G293200 chr3B 85.327 443 33 14 1 435 528632520 528632102 1.770000e-116 429.0


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 TraesCS3A01G293200 chr3A 523745005 523747499 2494 True 4608.000000 4608 100.000000 1 2495 1 chr3A.!!$R1 2494
1 TraesCS3A01G293200 chr3D 402794984 402797504 2520 True 1177.366667 2854 93.261333 1 2493 3 chr3D.!!$R1 2492
2 TraesCS3A01G293200 chr3B 528629997 528632520 2523 True 1560.000000 2691 87.774500 1 2493 2 chr3B.!!$R1 2492

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
777 842 0.108945 GTACTATCGCCGGGCATACC 60.109 60.0 20.71 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2168 2279 0.368227 CGAAGCTGTGTCGATCAAGC 59.632 55.0 0.0 7.81 41.02 4.01 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
69 70 9.692749 CCTCTCTATTTACTATACGATTTTGCA 57.307 33.333 0.00 0.00 0.00 4.08
132 133 2.290367 TGAAAGCAATTGTGACGGTCTG 59.710 45.455 9.88 0.00 0.00 3.51
133 134 1.967319 AAGCAATTGTGACGGTCTGT 58.033 45.000 9.88 0.00 0.00 3.41
167 168 1.409790 GGGTGGTTTAACGCCAAAAGT 59.590 47.619 0.00 0.00 42.82 2.66
297 327 2.271800 GAGTGTGGAAGGTTATCGCTG 58.728 52.381 0.00 0.00 0.00 5.18
453 518 1.872773 AGCCTACCTTTCTCCTCCAG 58.127 55.000 0.00 0.00 0.00 3.86
460 525 1.271597 CCTTTCTCCTCCAGTGTTGGG 60.272 57.143 0.00 0.00 45.10 4.12
480 545 2.557452 GGCTCCCCTTTTCTTCCATTCA 60.557 50.000 0.00 0.00 0.00 2.57
585 650 8.215050 TCTACTCAAAAGTTGGGAGTAATTTGA 58.785 33.333 14.40 8.18 41.94 2.69
602 667 4.345271 TTTGATGAGTTCGATCGTCGTA 57.655 40.909 15.94 5.16 41.35 3.43
603 668 4.547406 TTGATGAGTTCGATCGTCGTAT 57.453 40.909 15.94 9.23 41.35 3.06
670 735 1.219664 CCGATAACCGTCCAAGCCA 59.780 57.895 0.00 0.00 36.31 4.75
777 842 0.108945 GTACTATCGCCGGGCATACC 60.109 60.000 20.71 0.00 0.00 2.73
778 843 0.251474 TACTATCGCCGGGCATACCT 60.251 55.000 20.71 0.08 36.97 3.08
812 877 3.626977 CCTCTGATTGATCGAGAAGACG 58.373 50.000 11.65 0.00 32.84 4.18
991 1060 6.732896 AATCTCTTACGTGGAGTCCATAAT 57.267 37.500 16.67 6.58 35.28 1.28
993 1062 4.051922 CTCTTACGTGGAGTCCATAATGC 58.948 47.826 16.67 0.31 35.28 3.56
1084 1161 4.453093 TGCAGTGTCGTTGCATCA 57.547 50.000 0.00 0.00 45.89 3.07
1136 1226 1.375853 GGGCATACATTGTCGCTGCA 61.376 55.000 16.15 0.00 34.56 4.41
1145 1235 3.117171 GTCGCTGCAGCTCACCAG 61.117 66.667 34.22 18.83 39.32 4.00
1172 1271 1.441729 CCGCCTCTCCGAAGCAATA 59.558 57.895 0.00 0.00 0.00 1.90
1269 1368 0.891373 CTCGGGTCTTGAGAGAAGCA 59.109 55.000 0.00 0.00 35.43 3.91
1322 1421 0.468226 GTATCCATGAAGGTGCCCGA 59.532 55.000 0.00 0.00 39.02 5.14
1346 1445 4.704833 GCAGAGGCAGGTCGGCAA 62.705 66.667 0.00 0.00 44.47 4.52
1544 1646 4.160635 GCCCATTCGTTCGGTGCG 62.161 66.667 0.00 0.00 0.00 5.34
1570 1680 7.255139 GGTTACTGTATGCTTTCACTTTGTCTT 60.255 37.037 0.00 0.00 0.00 3.01
1601 1711 4.463186 AGGGCGCTTTCCTACTATATACTG 59.537 45.833 7.64 0.00 31.86 2.74
1786 1896 4.262506 GGAGTGTCTGGTACTTTAGTTGCT 60.263 45.833 0.00 0.00 0.00 3.91
1787 1897 5.047519 GGAGTGTCTGGTACTTTAGTTGCTA 60.048 44.000 0.00 0.00 0.00 3.49
1825 1935 2.171725 GTAACGACTCATGCCCGCC 61.172 63.158 0.00 0.00 0.00 6.13
1845 1955 2.485479 CCGTTTGGCATGATAGGCTAGT 60.485 50.000 0.00 0.00 34.73 2.57
1852 1962 2.229062 GCATGATAGGCTAGTGCTACGA 59.771 50.000 17.13 0.00 39.59 3.43
1881 1991 3.040147 ACACAAAGTCATCCACTACGG 57.960 47.619 0.00 0.00 32.30 4.02
1904 2014 5.046231 GGACCAACCTCTGTTCTCTAATTCT 60.046 44.000 0.00 0.00 35.41 2.40
2004 2114 7.436080 CACCAACTTACGAGTGTAAACTCTAAA 59.564 37.037 11.33 4.48 39.95 1.85
2042 2152 5.541953 AGAGTTGAGCTATCACATGCATA 57.458 39.130 0.00 0.00 34.35 3.14
2052 2162 7.226441 AGCTATCACATGCATAGAAATACCAA 58.774 34.615 13.98 0.00 0.00 3.67
2213 2324 1.071471 CGGTGAGTGAAGCAAGGGT 59.929 57.895 0.00 0.00 0.00 4.34
2269 2380 5.267587 AGATCGTGATATCTGATGGATGGA 58.732 41.667 13.54 0.00 34.87 3.41
2325 2437 0.942252 CGATACGTCGTGGAGATGGA 59.058 55.000 8.47 0.00 42.78 3.41
2352 2464 2.489938 TGTGTAAGAAGGGGATGCAC 57.510 50.000 0.00 0.00 0.00 4.57
2375 2487 2.338015 CGGCTCAAATGCAGCTGGT 61.338 57.895 17.12 0.00 39.29 4.00
2390 2502 2.646798 AGCTGGTGGGAGAAAGAGAAAT 59.353 45.455 0.00 0.00 0.00 2.17
2425 2537 5.378292 TTCTCATCACGCTGGATATCTAC 57.622 43.478 2.05 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.925285 ATCAAAGATCGCTGGGGCCA 61.925 55.000 4.39 0.00 34.44 5.36
58 59 5.216566 GCACTAGTTCATGCAAAATCGTA 57.783 39.130 0.00 0.00 41.65 3.43
69 70 6.238566 GCATATTGTGATGTGCACTAGTTCAT 60.239 38.462 19.41 1.05 46.19 2.57
154 155 3.067461 AGCACATTGACTTTTGGCGTTAA 59.933 39.130 0.00 0.00 0.00 2.01
324 354 2.365582 ACCAACGTTGATATGGCCTTC 58.634 47.619 29.35 0.00 37.77 3.46
332 362 6.148150 GGACTCACAATAAACCAACGTTGATA 59.852 38.462 29.35 18.07 30.72 2.15
334 364 4.273969 GGACTCACAATAAACCAACGTTGA 59.726 41.667 29.35 9.95 30.72 3.18
460 525 2.807676 TGAATGGAAGAAAAGGGGAGC 58.192 47.619 0.00 0.00 0.00 4.70
480 545 2.738743 ACCTTTTGCGGATGATCCAAT 58.261 42.857 12.67 0.00 35.91 3.16
585 650 4.143368 CGAGTATACGACGATCGAACTCAT 60.143 45.833 24.34 10.22 43.74 2.90
727 792 4.555709 AGGCGCAACCACAACCGA 62.556 61.111 10.83 0.00 43.14 4.69
753 818 2.724721 CCGGCGATAGTACGTGCG 60.725 66.667 9.30 0.00 36.99 5.34
777 842 1.204704 TCAGAGGCGACCAATGTGTAG 59.795 52.381 0.00 0.00 0.00 2.74
778 843 1.262417 TCAGAGGCGACCAATGTGTA 58.738 50.000 0.00 0.00 0.00 2.90
812 877 0.166814 GCTTCAACCACTCGCACATC 59.833 55.000 0.00 0.00 0.00 3.06
931 996 1.324740 TGGGATGGACCGGTTAGACG 61.325 60.000 9.42 0.00 40.11 4.18
958 1023 6.053005 TCCACGTAAGAGATTTTGAAACACT 58.947 36.000 0.00 0.00 43.62 3.55
959 1024 6.018180 ACTCCACGTAAGAGATTTTGAAACAC 60.018 38.462 18.76 0.00 43.62 3.32
960 1025 6.053005 ACTCCACGTAAGAGATTTTGAAACA 58.947 36.000 18.76 0.00 43.62 2.83
961 1026 6.347483 GGACTCCACGTAAGAGATTTTGAAAC 60.347 42.308 18.76 2.51 43.62 2.78
962 1027 5.699458 GGACTCCACGTAAGAGATTTTGAAA 59.301 40.000 18.76 0.00 43.62 2.69
963 1028 5.221561 TGGACTCCACGTAAGAGATTTTGAA 60.222 40.000 18.76 0.00 43.62 2.69
991 1060 1.614903 CGACTTATATACACGGGGGCA 59.385 52.381 0.00 0.00 0.00 5.36
993 1062 2.229784 GACCGACTTATATACACGGGGG 59.770 54.545 18.87 4.96 46.45 5.40
1084 1161 2.636830 CAAAGATGAGGCAGGATCGTT 58.363 47.619 0.00 0.00 0.00 3.85
1089 1166 0.674581 CGTGCAAAGATGAGGCAGGA 60.675 55.000 0.00 0.00 43.84 3.86
1136 1226 2.358003 GCGCTTGACTGGTGAGCT 60.358 61.111 0.00 0.00 34.33 4.09
1288 1387 1.183549 GATACCTCGGTGACACCAGT 58.816 55.000 24.18 18.70 38.47 4.00
1293 1392 2.153034 TCATGGATACCTCGGTGACA 57.847 50.000 0.00 0.00 0.00 3.58
1353 1452 2.125350 CTCAGGCGCTTGGACTCC 60.125 66.667 20.24 0.00 0.00 3.85
1487 1586 6.110707 TCCTCGTCAACCTTAATTATTGTCC 58.889 40.000 0.00 0.00 0.00 4.02
1519 1621 1.801395 CGAACGAATGGGCAGTACGAT 60.801 52.381 0.00 0.00 0.00 3.73
1544 1646 6.204882 AGACAAAGTGAAAGCATACAGTAACC 59.795 38.462 0.00 0.00 0.00 2.85
1570 1680 0.322187 GGAAAGCGCCCTCACCTAAA 60.322 55.000 2.29 0.00 0.00 1.85
1825 1935 2.545526 CACTAGCCTATCATGCCAAACG 59.454 50.000 0.00 0.00 0.00 3.60
1845 1955 8.626526 TGACTTTGTGTATTAGATATCGTAGCA 58.373 33.333 0.00 0.00 0.00 3.49
1881 1991 6.043854 AGAATTAGAGAACAGAGGTTGGTC 57.956 41.667 0.00 0.00 44.24 4.02
1904 2014 4.213270 GCCTTACAGCAAATACATCGCATA 59.787 41.667 0.00 0.00 0.00 3.14
1936 2046 1.821332 GCTGGATGCACTACAGGCC 60.821 63.158 13.87 0.00 42.31 5.19
2042 2152 5.878406 ATCTCATCTCGGTTGGTATTTCT 57.122 39.130 0.00 0.00 0.00 2.52
2052 2162 3.494048 GCCTTGATCAATCTCATCTCGGT 60.494 47.826 8.96 0.00 0.00 4.69
2168 2279 0.368227 CGAAGCTGTGTCGATCAAGC 59.632 55.000 0.00 7.81 41.02 4.01
2205 2316 3.363787 GGGATTCAACACCCTTGCT 57.636 52.632 0.00 0.00 42.56 3.91
2213 2324 1.407299 CGAGGCATGAGGGATTCAACA 60.407 52.381 0.00 0.00 39.77 3.33
2269 2380 0.977395 CCACCTCGGTCTTCTCCTTT 59.023 55.000 0.00 0.00 0.00 3.11
2313 2425 4.279420 CACAAGATATCTCCATCTCCACGA 59.721 45.833 5.51 0.00 34.08 4.35
2325 2437 6.465035 GCATCCCCTTCTTACACAAGATATCT 60.465 42.308 0.00 0.00 40.47 1.98
2352 2464 1.712081 CTGCATTTGAGCCGTCTCG 59.288 57.895 0.00 0.00 42.26 4.04
2375 2487 3.010472 TGCATCCATTTCTCTTTCTCCCA 59.990 43.478 0.00 0.00 0.00 4.37
2390 2502 3.881089 GTGATGAGAATGTGATGCATCCA 59.119 43.478 23.67 19.81 36.67 3.41
2425 2537 3.375299 GTCCTGTTCAAATGAGATTCCGG 59.625 47.826 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.