Multiple sequence alignment - TraesCS5A01G062200

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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 TraesCS5A01G062200 chr5A 100.000 3002 0 0 1 3002 66824168 66827169 0.000000e+00 5544.0
1 TraesCS5A01G062200 chr5A 95.559 698 30 1 1 697 601069743 601070440 0.000000e+00 1116.0
2 TraesCS5A01G062200 chr6B 96.544 2315 57 9 695 3002 543082739 543080441 0.000000e+00 3810.0
3 TraesCS5A01G062200 chr6A 93.792 886 47 4 1363 2245 502544062 502543182 0.000000e+00 1325.0
4 TraesCS5A01G062200 chr6A 97.131 697 19 1 1 696 472970178 472970874 0.000000e+00 1175.0
5 TraesCS5A01G062200 chr6A 96.557 697 23 1 1 696 595510831 595510135 0.000000e+00 1153.0
6 TraesCS5A01G062200 chr6A 88.539 698 49 11 2322 3002 502509301 502509984 0.000000e+00 817.0
7 TraesCS5A01G062200 chr6A 96.009 451 16 2 914 1362 502544636 502544186 0.000000e+00 732.0
8 TraesCS5A01G062200 chr6A 87.812 361 26 12 2659 3002 142076961 142076602 1.000000e-109 407.0
9 TraesCS5A01G062200 chr6A 82.449 245 21 7 2465 2687 142077627 142077383 8.490000e-46 195.0
10 TraesCS5A01G062200 chr6A 93.651 126 2 3 697 820 502544770 502544649 1.840000e-42 183.0
11 TraesCS5A01G062200 chr1A 98.852 697 7 1 1 696 432524110 432524806 0.000000e+00 1242.0
12 TraesCS5A01G062200 chr6D 95.816 741 31 0 1370 2110 361414532 361413792 0.000000e+00 1197.0
13 TraesCS5A01G062200 chr6D 97.089 687 12 3 695 1380 361416401 361415722 0.000000e+00 1151.0
14 TraesCS5A01G062200 chr6D 100.000 46 0 0 1782 1827 361413734 361413689 5.330000e-13 86.1
15 TraesCS5A01G062200 chr3A 95.994 699 27 1 1 698 27583305 27584003 0.000000e+00 1134.0
16 TraesCS5A01G062200 chr3A 95.136 699 33 1 1 698 27582560 27583258 0.000000e+00 1101.0
17 TraesCS5A01G062200 chr5B 95.702 698 28 2 1 696 492816093 492815396 0.000000e+00 1122.0
18 TraesCS5A01G062200 chr7A 95.429 700 28 4 1 697 677975237 677975935 0.000000e+00 1112.0
19 TraesCS5A01G062200 chr4B 95.265 697 32 1 1 696 604143826 604144522 0.000000e+00 1103.0
20 TraesCS5A01G062200 chr4D 85.559 367 34 11 2653 3002 258940768 258941132 1.700000e-97 366.0
21 TraesCS5A01G062200 chr4D 85.359 362 34 11 2649 2993 12320607 12320966 1.020000e-94 357.0
22 TraesCS5A01G062200 chr4D 83.673 245 18 6 2465 2687 258940110 258940354 8.430000e-51 211.0


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 TraesCS5A01G062200 chr5A 66824168 66827169 3001 False 5544.000000 5544 100.0000 1 3002 1 chr5A.!!$F1 3001
1 TraesCS5A01G062200 chr5A 601069743 601070440 697 False 1116.000000 1116 95.5590 1 697 1 chr5A.!!$F2 696
2 TraesCS5A01G062200 chr6B 543080441 543082739 2298 True 3810.000000 3810 96.5440 695 3002 1 chr6B.!!$R1 2307
3 TraesCS5A01G062200 chr6A 472970178 472970874 696 False 1175.000000 1175 97.1310 1 696 1 chr6A.!!$F1 695
4 TraesCS5A01G062200 chr6A 595510135 595510831 696 True 1153.000000 1153 96.5570 1 696 1 chr6A.!!$R1 695
5 TraesCS5A01G062200 chr6A 502509301 502509984 683 False 817.000000 817 88.5390 2322 3002 1 chr6A.!!$F2 680
6 TraesCS5A01G062200 chr6A 502543182 502544770 1588 True 746.666667 1325 94.4840 697 2245 3 chr6A.!!$R3 1548
7 TraesCS5A01G062200 chr6A 142076602 142077627 1025 True 301.000000 407 85.1305 2465 3002 2 chr6A.!!$R2 537
8 TraesCS5A01G062200 chr1A 432524110 432524806 696 False 1242.000000 1242 98.8520 1 696 1 chr1A.!!$F1 695
9 TraesCS5A01G062200 chr6D 361413689 361416401 2712 True 811.366667 1197 97.6350 695 2110 3 chr6D.!!$R1 1415
10 TraesCS5A01G062200 chr3A 27582560 27584003 1443 False 1117.500000 1134 95.5650 1 698 2 chr3A.!!$F1 697
11 TraesCS5A01G062200 chr5B 492815396 492816093 697 True 1122.000000 1122 95.7020 1 696 1 chr5B.!!$R1 695
12 TraesCS5A01G062200 chr7A 677975237 677975935 698 False 1112.000000 1112 95.4290 1 697 1 chr7A.!!$F1 696
13 TraesCS5A01G062200 chr4B 604143826 604144522 696 False 1103.000000 1103 95.2650 1 696 1 chr4B.!!$F1 695
14 TraesCS5A01G062200 chr4D 258940110 258941132 1022 False 288.500000 366 84.6160 2465 3002 2 chr4D.!!$F2 537

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
768 1518 0.596083 CCCGCACGAGAGCTCATAAG 60.596 60.0 17.77 6.36 0.0 1.73 F
1376 3456 0.623723 AACAATATGGGCGAGTGGGT 59.376 50.0 0.00 0.00 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1610 3690 0.402504 ACGGTGCCCAATAAGGACAA 59.597 50.0 0.0 0.0 41.22 3.18 R
2739 5301 0.884704 ACATGGACACGAGCAACCAC 60.885 55.0 0.0 0.0 35.19 4.16 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
86 87 6.151144 AGCCCCACGATTCTTATTTAATATGC 59.849 38.462 0.00 0.00 0.00 3.14
618 1365 2.702592 TTTAGTGGGCCTAATCGTGG 57.297 50.000 4.53 0.00 35.59 4.94
766 1516 3.120105 CCCGCACGAGAGCTCATA 58.880 61.111 17.77 0.00 0.00 2.15
767 1517 1.437573 CCCGCACGAGAGCTCATAA 59.562 57.895 17.77 0.00 0.00 1.90
768 1518 0.596083 CCCGCACGAGAGCTCATAAG 60.596 60.000 17.77 6.36 0.00 1.73
1050 1805 4.873129 CCCGGCGTGGATCACTCG 62.873 72.222 6.01 0.00 42.00 4.18
1190 1945 0.808453 CACCGGACAACACTTGACGT 60.808 55.000 9.46 0.00 34.57 4.34
1217 1973 0.680061 GAAGAACCTGGTCTCACGGT 59.320 55.000 0.00 0.00 0.00 4.83
1270 2026 0.750850 ACCGATCATACGTGGAAGGG 59.249 55.000 0.00 4.43 0.00 3.95
1317 2073 2.296752 TCGTAGGATGTTTGGTGTCGAA 59.703 45.455 0.00 0.00 0.00 3.71
1376 3456 0.623723 AACAATATGGGCGAGTGGGT 59.376 50.000 0.00 0.00 0.00 4.51
1414 3494 1.065418 GGTTTGATCCAGACGGTCCAT 60.065 52.381 4.14 0.00 0.00 3.41
1423 3503 0.768622 AGACGGTCCATTGTTTCCCA 59.231 50.000 4.14 0.00 0.00 4.37
1473 3553 5.113383 CACAACGGCTTGATGTACCTATTA 58.887 41.667 4.13 0.00 31.58 0.98
1482 3562 7.375053 GCTTGATGTACCTATTAGGAGAAGAG 58.625 42.308 16.80 6.39 37.67 2.85
1485 3565 5.745988 TGTACCTATTAGGAGAAGAGGGT 57.254 43.478 16.80 0.00 37.67 4.34
1494 3574 2.022240 GAGAAGAGGGTGGGCTAGCG 62.022 65.000 9.00 0.00 0.00 4.26
1605 3685 2.022129 GTCGGACCAACACGAGCTG 61.022 63.158 0.00 0.00 40.09 4.24
1610 3690 4.701663 CCAACACGAGCTGATGGT 57.298 55.556 0.00 0.00 37.91 3.55
1618 3698 1.899814 ACGAGCTGATGGTTGTCCTTA 59.100 47.619 0.00 0.00 33.38 2.69
1645 3725 2.030862 GTGGGACGCCGGTAAACA 59.969 61.111 1.90 0.00 0.00 2.83
1699 3779 6.608002 GTGGGAGAAGATAGAAAACCTAGAGA 59.392 42.308 0.00 0.00 0.00 3.10
1878 3961 6.611613 AACTCAAGATTCTCAGATACCACA 57.388 37.500 0.68 0.00 0.00 4.17
1886 3969 6.496565 AGATTCTCAGATACCACAATAGAGGG 59.503 42.308 0.00 0.00 0.00 4.30
2070 4153 8.317891 TGAAATTGTACATGAAACACTATCGT 57.682 30.769 0.00 0.00 0.00 3.73
2071 4154 8.779303 TGAAATTGTACATGAAACACTATCGTT 58.221 29.630 0.00 0.00 0.00 3.85
2110 4193 8.869897 CGTAGCATCTTCTTCTTTTTGTATGTA 58.130 33.333 0.00 0.00 0.00 2.29
2259 4342 2.898612 ACATCCAACACCATGCATCAAA 59.101 40.909 0.00 0.00 0.00 2.69
2268 4351 0.794229 CATGCATCAAACGTCCACGC 60.794 55.000 0.00 0.00 44.43 5.34
2273 4356 2.981977 ATCAAACGTCCACGCCGTGT 62.982 55.000 16.99 0.00 44.43 4.49
2291 4374 4.809426 CCGTGTACTGGGTATCTGAATTTC 59.191 45.833 0.00 0.00 0.00 2.17
2292 4375 4.809426 CGTGTACTGGGTATCTGAATTTCC 59.191 45.833 0.00 0.00 0.00 3.13
2293 4376 5.123936 GTGTACTGGGTATCTGAATTTCCC 58.876 45.833 0.00 0.00 38.68 3.97
2294 4377 5.036916 TGTACTGGGTATCTGAATTTCCCT 58.963 41.667 0.00 0.00 38.95 4.20
2295 4378 6.099269 GTGTACTGGGTATCTGAATTTCCCTA 59.901 42.308 0.00 0.00 38.95 3.53
2296 4379 6.674861 TGTACTGGGTATCTGAATTTCCCTAA 59.325 38.462 0.00 0.00 38.95 2.69
2297 4380 6.652205 ACTGGGTATCTGAATTTCCCTAAA 57.348 37.500 0.00 0.00 38.95 1.85
2298 4381 7.226059 ACTGGGTATCTGAATTTCCCTAAAT 57.774 36.000 0.00 0.00 38.95 1.40
2299 4382 7.652554 ACTGGGTATCTGAATTTCCCTAAATT 58.347 34.615 0.00 0.00 45.78 1.82
2300 4383 8.122481 ACTGGGTATCTGAATTTCCCTAAATTT 58.878 33.333 0.00 0.00 43.69 1.82
2301 4384 8.533569 TGGGTATCTGAATTTCCCTAAATTTC 57.466 34.615 0.00 0.00 43.69 2.17
2330 4413 3.173151 TGACATCAAACCTGGAGAGCTA 58.827 45.455 0.00 0.00 0.00 3.32
2535 4619 4.979815 GCGTTGCTAATTAGGTTGTTGTTT 59.020 37.500 14.28 0.00 0.00 2.83
2739 5301 1.733912 CATCATCAGGACAACCACACG 59.266 52.381 0.00 0.00 38.94 4.49
2797 5367 6.765036 TCAATCATAAAGACAAGGAGAGATGC 59.235 38.462 0.00 0.00 0.00 3.91
2883 5460 5.998981 TCGTTTATGGTTACAGGTCAATTGT 59.001 36.000 5.13 0.00 0.00 2.71
2907 5484 0.460722 GCTCTCCTCCCTTACGGTTC 59.539 60.000 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
618 1365 4.282703 ACGTATACAGATCCAATACCACCC 59.717 45.833 3.32 0.00 0.00 4.61
766 1516 2.161012 TCGATCTCGTGCGTAACTTCTT 59.839 45.455 0.00 0.00 40.80 2.52
767 1517 1.736126 TCGATCTCGTGCGTAACTTCT 59.264 47.619 0.00 0.00 40.80 2.85
768 1518 2.102633 CTCGATCTCGTGCGTAACTTC 58.897 52.381 0.00 0.00 40.80 3.01
1050 1805 0.179097 GGCGACATTGAGGAGGAGAC 60.179 60.000 0.00 0.00 0.00 3.36
1095 1850 1.271707 TGTGGTAAAAGGGGCTGTAGC 60.272 52.381 0.00 0.00 41.14 3.58
1190 1945 4.019411 TGAGACCAGGTTCTTCATGCATAA 60.019 41.667 0.00 0.00 0.00 1.90
1217 1973 0.601558 GTCGCCTGTCAGGAGTTGTA 59.398 55.000 23.77 0.00 37.67 2.41
1294 2050 2.858344 CGACACCAAACATCCTACGATC 59.142 50.000 0.00 0.00 0.00 3.69
1317 2073 1.772063 GCAGCACACCGAACGACTTT 61.772 55.000 0.00 0.00 0.00 2.66
1376 3456 2.283834 ACCACCTGTATTCCCATTCCA 58.716 47.619 0.00 0.00 0.00 3.53
1414 3494 1.890041 CTGGCGACGTGGGAAACAA 60.890 57.895 0.00 0.00 0.00 2.83
1423 3503 0.390735 GGGTTACAATCTGGCGACGT 60.391 55.000 0.00 0.00 0.00 4.34
1473 3553 0.031616 CTAGCCCACCCTCTTCTCCT 60.032 60.000 0.00 0.00 0.00 3.69
1482 3562 1.837499 ATAGACCGCTAGCCCACCC 60.837 63.158 9.66 0.00 0.00 4.61
1485 3565 0.969149 CATCATAGACCGCTAGCCCA 59.031 55.000 9.66 0.00 0.00 5.36
1494 3574 4.281941 TCATGCCTACTCACATCATAGACC 59.718 45.833 0.00 0.00 0.00 3.85
1605 3685 2.427095 GTGCCCAATAAGGACAACCATC 59.573 50.000 0.00 0.00 41.22 3.51
1610 3690 0.402504 ACGGTGCCCAATAAGGACAA 59.597 50.000 0.00 0.00 41.22 3.18
1618 3698 4.715523 CGTCCCACGGTGCCCAAT 62.716 66.667 1.68 0.00 38.08 3.16
1728 3808 5.970317 TGTTAGTCTCCTTCATTGTCGTA 57.030 39.130 0.00 0.00 0.00 3.43
1764 3844 8.164057 AGAACCTAGGGAGAAATATCTTGTTT 57.836 34.615 14.81 0.00 35.54 2.83
1833 3916 1.523154 GCACGAAGGCCAATTCACCA 61.523 55.000 5.01 0.00 0.00 4.17
1857 3940 8.637099 TCTATTGTGGTATCTGAGAATCTTGAG 58.363 37.037 0.00 0.00 34.92 3.02
1878 3961 5.070580 GTCTGTGCCATAGTTACCCTCTATT 59.929 44.000 0.00 0.00 0.00 1.73
1886 3969 5.696724 GTCCATATGTCTGTGCCATAGTTAC 59.303 44.000 1.24 0.00 0.00 2.50
2070 4153 8.467598 AGAAGATGCTACGACAAAGTTATCTAA 58.532 33.333 0.00 0.00 0.00 2.10
2071 4154 7.997482 AGAAGATGCTACGACAAAGTTATCTA 58.003 34.615 0.00 0.00 0.00 1.98
2138 4221 5.103982 ACATCATTCCCCACATCATGACTAA 60.104 40.000 0.00 0.00 0.00 2.24
2250 4333 1.501741 GCGTGGACGTTTGATGCAT 59.498 52.632 0.00 0.00 42.22 3.96
2268 4351 4.402056 AATTCAGATACCCAGTACACGG 57.598 45.455 0.00 0.00 0.00 4.94
2273 4356 7.758820 TTTAGGGAAATTCAGATACCCAGTA 57.241 36.000 0.00 0.00 42.62 2.74
2291 4374 6.889722 TGATGTCAGTTTAGGGAAATTTAGGG 59.110 38.462 0.00 0.00 0.00 3.53
2292 4375 7.938140 TGATGTCAGTTTAGGGAAATTTAGG 57.062 36.000 0.00 0.00 0.00 2.69
2293 4376 9.626045 GTTTGATGTCAGTTTAGGGAAATTTAG 57.374 33.333 0.00 0.00 0.00 1.85
2294 4377 8.581578 GGTTTGATGTCAGTTTAGGGAAATTTA 58.418 33.333 0.00 0.00 0.00 1.40
2295 4378 7.290014 AGGTTTGATGTCAGTTTAGGGAAATTT 59.710 33.333 0.00 0.00 0.00 1.82
2296 4379 6.782494 AGGTTTGATGTCAGTTTAGGGAAATT 59.218 34.615 0.00 0.00 0.00 1.82
2297 4380 6.209391 CAGGTTTGATGTCAGTTTAGGGAAAT 59.791 38.462 0.00 0.00 0.00 2.17
2298 4381 5.534654 CAGGTTTGATGTCAGTTTAGGGAAA 59.465 40.000 0.00 0.00 0.00 3.13
2299 4382 5.070001 CAGGTTTGATGTCAGTTTAGGGAA 58.930 41.667 0.00 0.00 0.00 3.97
2300 4383 4.506625 CCAGGTTTGATGTCAGTTTAGGGA 60.507 45.833 0.00 0.00 0.00 4.20
2301 4384 3.758554 CCAGGTTTGATGTCAGTTTAGGG 59.241 47.826 0.00 0.00 0.00 3.53
2330 4413 2.047830 GGATGTTTCGGACTCCCCTAT 58.952 52.381 0.00 0.00 0.00 2.57
2535 4619 2.618241 GTGGTGCTGATGAGTGAACAAA 59.382 45.455 0.00 0.00 0.00 2.83
2739 5301 0.884704 ACATGGACACGAGCAACCAC 60.885 55.000 0.00 0.00 35.19 4.16
2766 5336 6.299141 TCCTTGTCTTTATGATTGATAGGGC 58.701 40.000 0.00 0.00 0.00 5.19
2797 5367 1.604593 CCCTTTGGTCACCTGCTGG 60.605 63.158 8.29 8.29 39.83 4.85
2883 5460 1.757118 CGTAAGGGAGGAGAGCAATGA 59.243 52.381 0.00 0.00 0.00 2.57
2907 5484 6.266168 TCTGTTAGCAATACAAAACCATGG 57.734 37.500 11.19 11.19 0.00 3.66


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

AutoCloner maintained by Alex Coulton.