Multiple sequence alignment - TraesCS2A01G327800

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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 TraesCS2A01G327800 chr2A 100.000 2432 0 0 1 2432 559608315 559610746 0.000000e+00 4492.0
1 TraesCS2A01G327800 chr2A 86.765 68 9 0 414 481 753732759 753732692 2.590000e-10 76.8
2 TraesCS2A01G327800 chr2B 92.641 2052 100 29 4 2006 505007635 505005586 0.000000e+00 2905.0
3 TraesCS2A01G327800 chr2B 96.966 758 21 1 757 1512 512305954 512306711 0.000000e+00 1271.0
4 TraesCS2A01G327800 chr2B 91.886 875 37 13 1517 2376 512306775 512307630 0.000000e+00 1192.0
5 TraesCS2A01G327800 chr2B 94.221 571 30 3 1 570 512305389 512305957 0.000000e+00 869.0
6 TraesCS2A01G327800 chr2B 85.042 361 22 8 2025 2376 505005599 505005262 3.000000e-89 339.0
7 TraesCS2A01G327800 chr2D 94.486 1886 80 16 1 1867 427971060 427969180 0.000000e+00 2885.0
8 TraesCS2A01G327800 chr2D 90.305 361 26 2 2025 2376 427969005 427968645 4.740000e-127 464.0
9 TraesCS2A01G327800 chr2D 91.275 149 9 2 1860 2005 427969140 427968993 1.470000e-47 200.0
10 TraesCS2A01G327800 chr7D 80.128 312 57 4 1112 1419 41800439 41800749 6.760000e-56 228.0
11 TraesCS2A01G327800 chr7A 79.868 303 61 0 1112 1414 41449777 41450079 3.150000e-54 222.0
12 TraesCS2A01G327800 chr7A 92.453 53 4 0 418 470 96392796 96392848 2.590000e-10 76.8
13 TraesCS2A01G327800 chr4B 84.211 95 11 4 38 129 566977080 566977173 3.330000e-14 89.8
14 TraesCS2A01G327800 chr4B 92.727 55 3 1 196 249 35522828 35522774 7.210000e-11 78.7
15 TraesCS2A01G327800 chr4B 86.765 68 9 0 418 485 75348064 75347997 2.590000e-10 76.8
16 TraesCS2A01G327800 chr5B 93.103 58 3 1 194 250 300394509 300394452 1.550000e-12 84.2
17 TraesCS2A01G327800 chr5B 92.157 51 3 1 200 249 347698722 347698672 1.210000e-08 71.3
18 TraesCS2A01G327800 chr4D 92.982 57 3 1 194 249 23422741 23422685 5.570000e-12 82.4
19 TraesCS2A01G327800 chr4A 92.727 55 3 1 196 249 578537010 578537064 7.210000e-11 78.7
20 TraesCS2A01G327800 chr4A 80.220 91 14 4 384 472 522458223 522458135 5.610000e-07 65.8
21 TraesCS2A01G327800 chr3A 84.286 70 11 0 414 483 340409981 340409912 4.340000e-08 69.4
22 TraesCS2A01G327800 chr3A 80.645 93 10 6 384 472 200913203 200913291 5.610000e-07 65.8
23 TraesCS2A01G327800 chr1A 82.716 81 9 2 73 148 238683290 238683210 1.560000e-07 67.6


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 TraesCS2A01G327800 chr2A 559608315 559610746 2431 False 4492.000000 4492 100.000000 1 2432 1 chr2A.!!$F1 2431
1 TraesCS2A01G327800 chr2B 505005262 505007635 2373 True 1622.000000 2905 88.841500 4 2376 2 chr2B.!!$R1 2372
2 TraesCS2A01G327800 chr2B 512305389 512307630 2241 False 1110.666667 1271 94.357667 1 2376 3 chr2B.!!$F1 2375
3 TraesCS2A01G327800 chr2D 427968645 427971060 2415 True 1183.000000 2885 92.022000 1 2376 3 chr2D.!!$R1 2375


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
86 87 0.906756 CTGGTCTGCTCCTCCCTTGA 60.907 60.0 0.00 0.00 0.0 3.02 F
618 626 1.045350 TCCTGGGCTCGAGAATCCTG 61.045 60.0 18.75 16.27 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1161 1176 1.002468 CCACACTGAAAAAGCAGGACG 60.002 52.381 0.0 0.0 40.20 4.79 R
2391 2555 0.167908 CGGCTAATTCTTGCGTTGCA 59.832 50.000 0.0 0.0 36.47 4.08 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
83 84 2.686835 GCTGGTCTGCTCCTCCCT 60.687 66.667 0.00 0.00 0.00 4.20
86 87 0.906756 CTGGTCTGCTCCTCCCTTGA 60.907 60.000 0.00 0.00 0.00 3.02
90 91 1.280421 GTCTGCTCCTCCCTTGATTGT 59.720 52.381 0.00 0.00 0.00 2.71
101 105 1.402456 CCTTGATTGTTGCTGCTGCTC 60.402 52.381 17.00 10.19 40.48 4.26
286 294 6.547402 AGTAGAGTAGGAGATCATGTATGCA 58.453 40.000 0.00 0.00 0.00 3.96
295 303 1.939974 TCATGTATGCAGGCGACTTC 58.060 50.000 0.00 0.00 40.21 3.01
332 340 2.477357 CGAATCGACTTGCTTCCGTCTA 60.477 50.000 0.00 0.00 0.00 2.59
336 344 2.555325 TCGACTTGCTTCCGTCTAAAGA 59.445 45.455 0.00 0.00 0.00 2.52
410 418 1.710809 AGGTGTACTTCAGCCCCAATT 59.289 47.619 0.00 0.00 44.62 2.32
495 503 2.738846 GTGAGTATAAGATGGCATGCCG 59.261 50.000 30.87 0.00 39.42 5.69
500 508 1.667236 TAAGATGGCATGCCGTTCTG 58.333 50.000 31.52 0.00 39.42 3.02
519 527 7.094975 CCGTTCTGTTCATGTGTTTTTCCTATA 60.095 37.037 0.00 0.00 0.00 1.31
531 539 9.632807 TGTGTTTTTCCTATACATGCATTTTAC 57.367 29.630 0.00 0.00 0.00 2.01
550 558 9.962759 CATTTTACAATTCTTGCAAATAGAAGC 57.037 29.630 0.00 0.00 35.28 3.86
618 626 1.045350 TCCTGGGCTCGAGAATCCTG 61.045 60.000 18.75 16.27 0.00 3.86
714 723 2.100252 AGCCTATGCATGCAACAACATC 59.900 45.455 26.68 10.14 41.13 3.06
718 727 5.696822 CCTATGCATGCAACAACATCTATC 58.303 41.667 26.68 0.00 0.00 2.08
895 907 1.521681 GCGGCGCTTGAGGACTATT 60.522 57.895 26.86 0.00 0.00 1.73
1015 1027 4.771577 TCCACACAATGCCAACAAGATATT 59.228 37.500 0.00 0.00 0.00 1.28
1016 1028 5.245751 TCCACACAATGCCAACAAGATATTT 59.754 36.000 0.00 0.00 0.00 1.40
1161 1176 1.984297 GAGTTCTACGGCGACTTCAAC 59.016 52.381 16.62 8.76 0.00 3.18
1519 1593 7.108194 TGGATCAGCTGGATTTATGTCATATC 58.892 38.462 15.13 4.32 36.00 1.63
1537 1611 2.244486 TCTCTCTCTGAATGGCTGGT 57.756 50.000 0.00 0.00 0.00 4.00
1693 1767 0.309922 TTCTGAGACGTGTCGTGTCC 59.690 55.000 14.71 1.12 46.99 4.02
1696 1770 0.240145 TGAGACGTGTCGTGTCCATC 59.760 55.000 14.71 0.95 46.99 3.51
1706 1780 1.520342 GTGTCCATCGCTGCCTCTC 60.520 63.158 0.00 0.00 0.00 3.20
1723 1797 3.555168 CCTCTCCTCACGTTTATATGCCC 60.555 52.174 0.00 0.00 0.00 5.36
1745 1819 1.474330 ATTTGGCCACCGAAGATTCC 58.526 50.000 3.88 0.00 29.47 3.01
1796 1870 4.802051 GCAGGGGCGGCAGATCAA 62.802 66.667 12.47 0.00 0.00 2.57
1798 1872 4.496336 AGGGGCGGCAGATCAAGC 62.496 66.667 12.47 0.00 0.00 4.01
1814 1901 2.025037 TCAAGCCTGGATGCCTTTACAT 60.025 45.455 0.00 0.00 0.00 2.29
1816 1903 2.381911 AGCCTGGATGCCTTTACATTG 58.618 47.619 0.00 0.00 0.00 2.82
1881 2031 8.532977 AAGTTACCATGTCATTTTTATTGTGC 57.467 30.769 0.00 0.00 0.00 4.57
1882 2032 7.665690 AGTTACCATGTCATTTTTATTGTGCA 58.334 30.769 0.00 0.00 0.00 4.57
1883 2033 8.313292 AGTTACCATGTCATTTTTATTGTGCAT 58.687 29.630 0.00 0.00 0.00 3.96
1884 2034 9.579768 GTTACCATGTCATTTTTATTGTGCATA 57.420 29.630 0.00 0.00 0.00 3.14
1886 2036 8.876275 ACCATGTCATTTTTATTGTGCATATC 57.124 30.769 0.00 0.00 0.00 1.63
1887 2037 8.476447 ACCATGTCATTTTTATTGTGCATATCA 58.524 29.630 0.00 0.00 0.00 2.15
1888 2038 9.483916 CCATGTCATTTTTATTGTGCATATCAT 57.516 29.630 0.00 0.00 0.00 2.45
1909 2059 7.475771 TCATTGCCAAATTCTTTTTGTACAC 57.524 32.000 0.00 0.00 0.00 2.90
1929 2082 3.122948 CACAGCGTACGTTAAAATCTGCT 59.877 43.478 17.90 0.00 0.00 4.24
1981 2135 3.388308 TCCAATTTGTTTTGCCGTGATG 58.612 40.909 0.00 0.00 0.00 3.07
2010 2164 7.553881 AGTGAACATATTATTTCTTCCACCG 57.446 36.000 0.00 0.00 0.00 4.94
2268 2431 6.284459 TGTGTCCATTACAAATTCCCAAAAC 58.716 36.000 0.00 0.00 40.63 2.43
2294 2457 6.738114 TGACATGTGCTTTTAGAGGAAAAAG 58.262 36.000 1.15 5.01 45.29 2.27
2409 2573 2.346099 TTGCAACGCAAGAATTAGCC 57.654 45.000 0.00 0.00 43.99 3.93
2410 2574 0.167908 TGCAACGCAAGAATTAGCCG 59.832 50.000 0.00 0.00 43.62 5.52
2411 2575 0.446222 GCAACGCAAGAATTAGCCGA 59.554 50.000 0.00 0.00 43.62 5.54
2412 2576 1.529826 GCAACGCAAGAATTAGCCGAG 60.530 52.381 0.00 0.00 43.62 4.63
2413 2577 1.732259 CAACGCAAGAATTAGCCGAGT 59.268 47.619 0.00 0.00 43.62 4.18
2414 2578 1.359848 ACGCAAGAATTAGCCGAGTG 58.640 50.000 0.00 0.00 43.62 3.51
2415 2579 1.067142 ACGCAAGAATTAGCCGAGTGA 60.067 47.619 0.00 0.00 43.62 3.41
2416 2580 1.999735 CGCAAGAATTAGCCGAGTGAA 59.000 47.619 0.00 0.00 43.02 3.18
2417 2581 2.222819 CGCAAGAATTAGCCGAGTGAAC 60.223 50.000 0.00 0.00 43.02 3.18
2418 2582 2.742053 GCAAGAATTAGCCGAGTGAACA 59.258 45.455 0.00 0.00 0.00 3.18
2419 2583 3.424962 GCAAGAATTAGCCGAGTGAACAC 60.425 47.826 0.00 0.00 0.00 3.32
2420 2584 3.963428 AGAATTAGCCGAGTGAACACT 57.037 42.857 7.20 7.20 45.84 3.55
2421 2585 5.168569 CAAGAATTAGCCGAGTGAACACTA 58.831 41.667 7.46 0.00 42.66 2.74
2422 2586 5.599999 AGAATTAGCCGAGTGAACACTAT 57.400 39.130 7.46 0.00 42.66 2.12
2423 2587 5.352284 AGAATTAGCCGAGTGAACACTATG 58.648 41.667 7.46 3.97 42.66 2.23
2424 2588 5.127194 AGAATTAGCCGAGTGAACACTATGA 59.873 40.000 7.46 0.00 42.66 2.15
2425 2589 4.794278 TTAGCCGAGTGAACACTATGAA 57.206 40.909 7.46 0.00 42.66 2.57
2426 2590 3.895232 AGCCGAGTGAACACTATGAAT 57.105 42.857 7.46 0.00 42.66 2.57
2427 2591 4.207891 AGCCGAGTGAACACTATGAATT 57.792 40.909 7.46 0.00 42.66 2.17
2428 2592 4.579869 AGCCGAGTGAACACTATGAATTT 58.420 39.130 7.46 0.00 42.66 1.82
2429 2593 5.003804 AGCCGAGTGAACACTATGAATTTT 58.996 37.500 7.46 0.00 42.66 1.82
2430 2594 5.473504 AGCCGAGTGAACACTATGAATTTTT 59.526 36.000 7.46 0.00 42.66 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 0.239082 CGAGCAGCAGCAACAATCAA 59.761 50.000 3.17 0.00 45.49 2.57
86 87 0.604780 AGACGAGCAGCAGCAACAAT 60.605 50.000 3.17 0.00 45.49 2.71
90 91 3.046087 GCAGACGAGCAGCAGCAA 61.046 61.111 3.17 0.00 45.49 3.91
101 105 3.465403 CCAGGGGAGGAGCAGACG 61.465 72.222 0.00 0.00 0.00 4.18
332 340 3.515602 ACACAAGCTGGAATCCTCTTT 57.484 42.857 0.00 0.00 0.00 2.52
336 344 2.519013 GGAAACACAAGCTGGAATCCT 58.481 47.619 0.00 0.00 0.00 3.24
410 418 6.070251 TGACCAAGAGACATAATTAAGGAGCA 60.070 38.462 0.00 0.00 0.00 4.26
495 503 8.564574 TGTATAGGAAAAACACATGAACAGAAC 58.435 33.333 0.00 0.00 0.00 3.01
500 508 7.312154 TGCATGTATAGGAAAAACACATGAAC 58.688 34.615 15.18 1.70 45.95 3.18
550 558 1.406477 GGGTTACAGAACTAAGGGCCG 60.406 57.143 0.00 0.00 35.74 6.13
660 669 9.013490 GTCTCTATTTTATAAGACGCGTTGTAA 57.987 33.333 15.53 4.44 0.00 2.41
714 723 3.328931 ACTCATAGGGCCATTGGTGATAG 59.671 47.826 6.18 0.00 0.00 2.08
718 727 2.026641 CAACTCATAGGGCCATTGGTG 58.973 52.381 6.18 0.00 0.00 4.17
772 782 7.823745 AAAGATATACCGCCTTCATTTCAAT 57.176 32.000 0.00 0.00 0.00 2.57
895 907 4.524714 TGGGATTTCAACTTTAATGCGGAA 59.475 37.500 0.00 0.00 0.00 4.30
1015 1027 5.286797 CGAAAAACACGTCTATATCACGGAA 59.713 40.000 10.86 0.00 41.73 4.30
1016 1028 4.794762 CGAAAAACACGTCTATATCACGGA 59.205 41.667 10.86 0.00 41.73 4.69
1161 1176 1.002468 CCACACTGAAAAAGCAGGACG 60.002 52.381 0.00 0.00 40.20 4.79
1519 1593 1.202394 CGACCAGCCATTCAGAGAGAG 60.202 57.143 0.00 0.00 0.00 3.20
1559 1633 3.687212 CGGCAACATAATGTACCAGAACA 59.313 43.478 0.00 0.00 29.80 3.18
1693 1767 1.227205 GTGAGGAGAGGCAGCGATG 60.227 63.158 0.00 0.00 0.00 3.84
1696 1770 2.771763 AAACGTGAGGAGAGGCAGCG 62.772 60.000 0.00 0.00 0.00 5.18
1706 1780 2.631160 TGGGGCATATAAACGTGAGG 57.369 50.000 0.00 0.00 0.00 3.86
1723 1797 1.185315 ATCTTCGGTGGCCAAATTGG 58.815 50.000 7.24 7.84 41.55 3.16
1789 1863 2.716814 GGCATCCAGGCTTGATCTG 58.283 57.895 0.00 0.00 40.24 2.90
1798 1872 2.428171 CCACAATGTAAAGGCATCCAGG 59.572 50.000 0.00 0.00 0.00 4.45
1800 1874 1.824230 GCCACAATGTAAAGGCATCCA 59.176 47.619 8.16 0.00 46.26 3.41
1814 1901 5.931146 GGTGAATACAATGAATTTGCCACAA 59.069 36.000 0.00 0.00 39.03 3.33
1816 1903 5.477510 TGGTGAATACAATGAATTTGCCAC 58.522 37.500 0.00 0.00 39.03 5.01
1876 2026 7.390996 AAAAGAATTTGGCAATGATATGCACAA 59.609 29.630 0.00 1.18 42.73 3.33
1877 2027 6.879993 AAAAGAATTTGGCAATGATATGCACA 59.120 30.769 0.00 0.00 42.73 4.57
1878 2028 7.311364 AAAAGAATTTGGCAATGATATGCAC 57.689 32.000 0.00 0.00 42.73 4.57
1879 2029 7.390996 ACAAAAAGAATTTGGCAATGATATGCA 59.609 29.630 0.00 0.00 42.73 3.96
1880 2030 7.754625 ACAAAAAGAATTTGGCAATGATATGC 58.245 30.769 0.00 0.00 41.07 3.14
1882 2032 9.941325 TGTACAAAAAGAATTTGGCAATGATAT 57.059 25.926 0.00 0.00 39.02 1.63
1883 2033 9.202273 GTGTACAAAAAGAATTTGGCAATGATA 57.798 29.630 0.00 0.00 39.02 2.15
1884 2034 7.714377 TGTGTACAAAAAGAATTTGGCAATGAT 59.286 29.630 0.00 0.00 39.02 2.45
1885 2035 7.044181 TGTGTACAAAAAGAATTTGGCAATGA 58.956 30.769 0.00 0.00 39.02 2.57
1886 2036 7.244166 TGTGTACAAAAAGAATTTGGCAATG 57.756 32.000 0.00 0.00 39.02 2.82
1887 2037 6.018016 GCTGTGTACAAAAAGAATTTGGCAAT 60.018 34.615 0.00 0.00 39.02 3.56
1888 2038 5.293079 GCTGTGTACAAAAAGAATTTGGCAA 59.707 36.000 0.00 0.00 39.02 4.52
1909 2059 3.991605 AGCAGATTTTAACGTACGCTG 57.008 42.857 16.72 13.29 0.00 5.18
2199 2361 5.647658 TCTTCGAACAGATGGCAAATGTAAT 59.352 36.000 8.19 0.00 0.00 1.89
2268 2431 3.942829 TCCTCTAAAAGCACATGTCAGG 58.057 45.455 0.00 0.00 0.00 3.86
2390 2554 1.400888 CGGCTAATTCTTGCGTTGCAA 60.401 47.619 0.00 0.00 46.80 4.08
2391 2555 0.167908 CGGCTAATTCTTGCGTTGCA 59.832 50.000 0.00 0.00 36.47 4.08
2392 2556 0.446222 TCGGCTAATTCTTGCGTTGC 59.554 50.000 0.00 0.00 0.00 4.17
2393 2557 1.732259 ACTCGGCTAATTCTTGCGTTG 59.268 47.619 0.00 0.00 0.00 4.10
2394 2558 1.732259 CACTCGGCTAATTCTTGCGTT 59.268 47.619 0.00 0.00 0.00 4.84
2395 2559 1.067142 TCACTCGGCTAATTCTTGCGT 60.067 47.619 0.00 0.00 0.00 5.24
2396 2560 1.640428 TCACTCGGCTAATTCTTGCG 58.360 50.000 0.00 0.00 0.00 4.85
2397 2561 2.742053 TGTTCACTCGGCTAATTCTTGC 59.258 45.455 0.00 0.00 0.00 4.01
2398 2562 3.997021 AGTGTTCACTCGGCTAATTCTTG 59.003 43.478 0.00 0.00 0.00 3.02
2399 2563 4.273148 AGTGTTCACTCGGCTAATTCTT 57.727 40.909 0.00 0.00 0.00 2.52
2400 2564 3.963428 AGTGTTCACTCGGCTAATTCT 57.037 42.857 0.00 0.00 0.00 2.40
2401 2565 5.348986 TCATAGTGTTCACTCGGCTAATTC 58.651 41.667 8.80 0.00 0.00 2.17
2402 2566 5.339008 TCATAGTGTTCACTCGGCTAATT 57.661 39.130 8.80 0.00 0.00 1.40
2403 2567 5.339008 TTCATAGTGTTCACTCGGCTAAT 57.661 39.130 8.80 0.00 0.00 1.73
2404 2568 4.794278 TTCATAGTGTTCACTCGGCTAA 57.206 40.909 8.80 0.00 0.00 3.09
2405 2569 5.339008 AATTCATAGTGTTCACTCGGCTA 57.661 39.130 8.80 0.00 0.00 3.93
2406 2570 3.895232 ATTCATAGTGTTCACTCGGCT 57.105 42.857 8.80 0.00 0.00 5.52
2407 2571 4.946784 AAATTCATAGTGTTCACTCGGC 57.053 40.909 8.80 0.00 0.00 5.54



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

AutoCloner maintained by Alex Coulton.