Multiple sequence alignment - TraesCS4A01G430000

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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 TraesCS4A01G430000 chr4A 100.000 2598 0 0 1 2598 701313189 701310592 0.000000e+00 4798
1 TraesCS4A01G430000 chr4A 85.450 2165 274 28 333 2480 702398791 702400931 0.000000e+00 2215
2 TraesCS4A01G430000 chr4A 83.454 1378 159 37 839 2192 702381010 702382342 0.000000e+00 1218
3 TraesCS4A01G430000 chr4A 85.320 1124 141 14 880 1994 702339890 702340998 0.000000e+00 1140
4 TraesCS4A01G430000 chr4A 85.159 849 116 8 880 1724 702505158 702506000 0.000000e+00 861
5 TraesCS4A01G430000 chr4A 86.867 731 84 5 116 845 702380237 702380956 0.000000e+00 808
6 TraesCS4A01G430000 chr4A 81.915 752 99 16 1714 2450 702508020 702508749 3.700000e-168 601
7 TraesCS4A01G430000 chr4A 82.483 588 89 14 116 697 702504475 702505054 1.070000e-138 503
8 TraesCS4A01G430000 chr4A 84.086 421 58 9 116 533 702339259 702339673 5.210000e-107 398
9 TraesCS4A01G430000 chr4A 86.473 207 22 3 566 767 702339673 702339878 3.370000e-54 222
10 TraesCS4A01G430000 chr4A 94.828 116 6 0 1 116 702380052 702380167 5.710000e-42 182
11 TraesCS4A01G430000 chr7D 94.342 2492 104 15 116 2598 28696065 28698528 0.000000e+00 3786
12 TraesCS4A01G430000 chr7D 86.174 2394 263 39 116 2480 28674089 28676443 0.000000e+00 2525
13 TraesCS4A01G430000 chr7D 96.552 116 4 0 1 116 28673905 28674020 2.640000e-45 193
14 TraesCS4A01G430000 chr7D 96.552 116 4 0 1 116 28695882 28695997 2.640000e-45 193
15 TraesCS4A01G430000 chr7A 93.753 2417 96 19 116 2522 29109808 29112179 0.000000e+00 3576
16 TraesCS4A01G430000 chr7A 86.654 1551 193 10 116 1661 29032496 29034037 0.000000e+00 1705
17 TraesCS4A01G430000 chr7A 97.414 116 3 0 1 116 29109625 29109740 5.670000e-47 198


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 TraesCS4A01G430000 chr4A 701310592 701313189 2597 True 4798.000000 4798 100.000000 1 2598 1 chr4A.!!$R1 2597
1 TraesCS4A01G430000 chr4A 702398791 702400931 2140 False 2215.000000 2215 85.450000 333 2480 1 chr4A.!!$F1 2147
2 TraesCS4A01G430000 chr4A 702380052 702382342 2290 False 736.000000 1218 88.383000 1 2192 3 chr4A.!!$F3 2191
3 TraesCS4A01G430000 chr4A 702504475 702508749 4274 False 655.000000 861 83.185667 116 2450 3 chr4A.!!$F4 2334
4 TraesCS4A01G430000 chr4A 702339259 702340998 1739 False 586.666667 1140 85.293000 116 1994 3 chr4A.!!$F2 1878
5 TraesCS4A01G430000 chr7D 28695882 28698528 2646 False 1989.500000 3786 95.447000 1 2598 2 chr7D.!!$F2 2597
6 TraesCS4A01G430000 chr7D 28673905 28676443 2538 False 1359.000000 2525 91.363000 1 2480 2 chr7D.!!$F1 2479
7 TraesCS4A01G430000 chr7A 29109625 29112179 2554 False 1887.000000 3576 95.583500 1 2522 2 chr7A.!!$F2 2521
8 TraesCS4A01G430000 chr7A 29032496 29034037 1541 False 1705.000000 1705 86.654000 116 1661 1 chr7A.!!$F1 1545

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
935 1100 0.179062 CCTGCTCCTCCTGCACATAC 60.179 60.0 0.0 0.0 36.37 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2108 4346 1.136147 GCAAGATGGCTGAAGTGCG 59.864 57.895 0.0 0.0 0.0 5.34 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
400 479 4.976987 ACGTGGTAATTCTAAAATTGCGG 58.023 39.130 0.00 0.00 38.08 5.69
402 481 4.109766 GTGGTAATTCTAAAATTGCGGGC 58.890 43.478 0.00 0.00 38.08 6.13
544 626 6.808008 ACACCAAATCATGTCTACAAGAAG 57.192 37.500 0.00 0.00 0.00 2.85
568 650 7.302184 AGTCTAGAAAATGGCTCTATAGTCCT 58.698 38.462 0.00 0.00 0.00 3.85
693 775 5.775195 TCATAATGTGTATGGAGGAGACGAT 59.225 40.000 0.00 0.00 0.00 3.73
775 883 6.345096 TCTAGAAAAGCAAAATCCTTTGGG 57.655 37.500 0.00 0.00 41.96 4.12
824 932 4.451900 CAGCACTATACTAACCCCTTTGG 58.548 47.826 0.00 0.00 41.37 3.28
827 935 2.436911 ACTATACTAACCCCTTTGGCCG 59.563 50.000 0.00 0.00 37.83 6.13
923 1088 2.445654 CCCTCCTCCTCCTGCTCC 60.446 72.222 0.00 0.00 0.00 4.70
924 1089 2.695597 CCTCCTCCTCCTGCTCCT 59.304 66.667 0.00 0.00 0.00 3.69
925 1090 1.457455 CCTCCTCCTCCTGCTCCTC 60.457 68.421 0.00 0.00 0.00 3.71
926 1091 1.457455 CTCCTCCTCCTGCTCCTCC 60.457 68.421 0.00 0.00 0.00 4.30
927 1092 1.938596 TCCTCCTCCTGCTCCTCCT 60.939 63.158 0.00 0.00 0.00 3.69
935 1100 0.179062 CCTGCTCCTCCTGCACATAC 60.179 60.000 0.00 0.00 36.37 2.39
1067 1234 2.301577 ACCTCACTGCTAAAGCGATC 57.698 50.000 0.00 0.00 45.83 3.69
1069 1236 1.137872 CCTCACTGCTAAAGCGATCCT 59.862 52.381 0.00 0.00 45.83 3.24
1213 1380 1.269166 CAACGCACGTGAGATCCTAC 58.731 55.000 26.44 0.56 0.00 3.18
1573 1744 2.097825 GGCAATCAGAGCTCCATGTTT 58.902 47.619 10.93 1.77 0.00 2.83
1582 1753 2.887152 GAGCTCCATGTTTTTCACCTGT 59.113 45.455 0.87 0.00 0.00 4.00
1590 1761 1.134848 GTTTTTCACCTGTGCTGGCAA 60.135 47.619 0.00 0.00 0.00 4.52
1591 1762 1.189752 TTTTCACCTGTGCTGGCAAA 58.810 45.000 0.00 0.00 0.00 3.68
1683 1867 6.313744 ACTGTATAACTTGGTGCTTTTGTC 57.686 37.500 0.00 0.00 0.00 3.18
1686 1870 2.584492 AACTTGGTGCTTTTGTCAGC 57.416 45.000 0.00 0.00 40.55 4.26
1703 1893 2.079158 CAGCACACCTGATGGTTAGTG 58.921 52.381 0.00 0.00 46.05 2.74
1815 4036 5.582269 ACACATTACATGCTAGCTGTACAAG 59.418 40.000 17.23 14.18 0.00 3.16
1824 4045 4.020218 TGCTAGCTGTACAAGACTTCCAAT 60.020 41.667 17.23 0.00 0.00 3.16
1832 4055 7.320443 TGTACAAGACTTCCAATCATATTGC 57.680 36.000 0.00 0.00 0.00 3.56
1860 4083 1.202582 AGCTCGACGTGAAAGCTACAT 59.797 47.619 12.76 0.00 44.28 2.29
2037 4267 7.472381 CGTTAGGCTAAGATTTACCCCTCATTA 60.472 40.741 7.33 0.00 0.00 1.90
2085 4323 1.207811 GTATGCCTTGGCCAAAAGCAT 59.792 47.619 37.88 37.88 46.50 3.79
2121 4359 0.750546 ATCATGCGCACTTCAGCCAT 60.751 50.000 14.90 0.00 0.00 4.40
2284 4524 3.649073 AGCATAAGCATATACGTCGCAA 58.351 40.909 0.00 0.00 45.49 4.85
2286 4526 4.690748 AGCATAAGCATATACGTCGCAAAT 59.309 37.500 0.00 0.00 45.49 2.32
2364 4608 2.878406 GTTGTCTTGCATGTGTGTACCT 59.122 45.455 0.00 0.00 0.00 3.08
2415 4659 7.041848 TCACAATACATCAGTCTGACAAAAGTG 60.042 37.037 10.88 10.08 0.00 3.16
2420 4664 2.092968 TCAGTCTGACAAAAGTGTGCCT 60.093 45.455 10.88 0.00 38.41 4.75
2425 4669 4.275936 GTCTGACAAAAGTGTGCCTACAAT 59.724 41.667 2.24 0.00 38.41 2.71
2481 4739 1.869767 GATGGGAGCAATTCTACAGCG 59.130 52.381 0.00 0.00 0.00 5.18
2495 4753 2.108157 AGCGTGCAAACACCGAGA 59.892 55.556 0.00 0.00 44.40 4.04
2550 4808 3.055094 AGGAACATATTCAGGCGAGTGTT 60.055 43.478 0.00 0.00 36.46 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 9.762933 GCCAACAAAATATATTCACACCATAAT 57.237 29.630 0.00 0.0 0.00 1.28
255 328 7.230108 CGAACTAATATGTAGTTCTCCCTACCA 59.770 40.741 21.94 0.0 46.72 3.25
512 594 6.507023 AGACATGATTTGGTGTTTTGAAGAC 58.493 36.000 0.00 0.0 0.00 3.01
544 626 7.533289 AGGACTATAGAGCCATTTTCTAGAC 57.467 40.000 6.78 0.0 31.17 2.59
568 650 9.915629 AATTACAATATTGAAAGGTTTTGCGTA 57.084 25.926 22.16 0.0 0.00 4.42
693 775 5.959743 GGTTAACACCAATACGTTGCAAACA 60.960 40.000 8.10 0.0 45.03 2.83
775 883 4.618489 GCACATGTTGTAATTGCAGAACTC 59.382 41.667 0.00 0.0 33.24 3.01
827 935 3.064324 GTGTGTGCATGGGGAGGC 61.064 66.667 0.00 0.0 0.00 4.70
923 1088 3.792401 TCAAATACCGTATGTGCAGGAG 58.208 45.455 4.03 0.0 0.00 3.69
924 1089 3.897141 TCAAATACCGTATGTGCAGGA 57.103 42.857 4.03 0.0 0.00 3.86
925 1090 4.024048 GGATTCAAATACCGTATGTGCAGG 60.024 45.833 4.03 0.0 0.00 4.85
926 1091 4.816385 AGGATTCAAATACCGTATGTGCAG 59.184 41.667 4.03 0.0 0.00 4.41
927 1092 4.776349 AGGATTCAAATACCGTATGTGCA 58.224 39.130 4.03 0.0 0.00 4.57
935 1100 5.874810 TGTCTTTGAGAGGATTCAAATACCG 59.125 40.000 11.79 0.0 43.80 4.02
1069 1236 1.741401 GCGACTGTGCTATGCCACA 60.741 57.895 0.00 0.0 42.99 4.17
1292 1459 1.614241 GGTGCCACTACCGATCCAGT 61.614 60.000 0.00 0.0 0.00 4.00
1573 1744 0.459489 GTTTGCCAGCACAGGTGAAA 59.541 50.000 3.10 0.0 32.22 2.69
1582 1753 1.473677 GTGCATCATAGTTTGCCAGCA 59.526 47.619 0.00 0.0 38.08 4.41
1591 1762 9.440773 CAAACATATATGTAGGTGCATCATAGT 57.559 33.333 18.56 0.0 40.80 2.12
1703 1893 7.538575 ACCATGTCAAAAGTGTATTGCTATTC 58.461 34.615 0.00 0.0 0.00 1.75
1815 4036 7.516198 AGTTATGGCAATATGATTGGAAGTC 57.484 36.000 0.00 0.0 0.00 3.01
1824 4045 5.470368 GTCGAGCTAGTTATGGCAATATGA 58.530 41.667 0.00 0.0 34.85 2.15
1832 4055 3.416119 TTCACGTCGAGCTAGTTATGG 57.584 47.619 0.00 0.0 0.00 2.74
1989 4212 8.589335 AACGTATGGATTACACTCAATCATAC 57.411 34.615 0.00 0.0 36.77 2.39
2108 4346 1.136147 GCAAGATGGCTGAAGTGCG 59.864 57.895 0.00 0.0 0.00 5.34
2303 4547 3.677121 CGGCACACTATCATGCTATCTTC 59.323 47.826 0.00 0.0 41.74 2.87
2364 4608 2.291153 CCTTTGGGATTGGAGCTTCTGA 60.291 50.000 0.00 0.0 33.58 3.27
2415 4659 5.565592 TTGTGATGATTGATTGTAGGCAC 57.434 39.130 0.00 0.0 0.00 5.01


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

AutoCloner maintained by Alex Coulton.