Multiple sequence alignment - TraesCS2D01G300700

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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 TraesCS2D01G300700 chr2D 100.000 2786 0 0 1 2786 383095080 383092295 0 5145
1 TraesCS2D01G300700 chr2B 91.579 2838 157 34 1 2786 453639198 453636391 0 3842
2 TraesCS2D01G300700 chr2A 92.819 1880 97 20 1 1850 517401030 517399159 0 2689
3 TraesCS2D01G300700 chr2A 90.645 791 42 8 2014 2786 517399057 517398281 0 1022


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 TraesCS2D01G300700 chr2D 383092295 383095080 2785 True 5145.0 5145 100.000 1 2786 1 chr2D.!!$R1 2785
1 TraesCS2D01G300700 chr2B 453636391 453639198 2807 True 3842.0 3842 91.579 1 2786 1 chr2B.!!$R1 2785
2 TraesCS2D01G300700 chr2A 517398281 517401030 2749 True 1855.5 2689 91.732 1 2786 2 chr2A.!!$R1 2785

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
884 912 1.070471 CGCTGCACCGTTTTAATGGC 61.07 55.0 0.0 0.0 38.7 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 1985 0.441533 CTTGCTGCTCACGATGTGAC 59.558 55.0 0.0 0.0 37.67 3.67 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
48 49 3.715628 ATGGCAAACTCTGTTGTCAAC 57.284 42.857 8.86 8.86 45.60 3.18
117 119 6.376299 GGACCCGGTTGTAATTTCTTTATTCT 59.624 38.462 0.00 0.00 0.00 2.40
134 136 6.636454 TTATTCTGTGGGGTTCTCTGTATT 57.364 37.500 0.00 0.00 0.00 1.89
148 150 8.897752 GGTTCTCTGTATTATTGCTCATCTTTT 58.102 33.333 0.00 0.00 0.00 2.27
260 278 8.863872 ATAGTGTTGGCTTTCAGTTAAATAGT 57.136 30.769 0.00 0.00 0.00 2.12
409 430 7.201929 GGTTATAAATAATCTTCCCCCGCAAAA 60.202 37.037 0.00 0.00 0.00 2.44
468 492 1.226888 CTACTCGCGGTAAGTGGGC 60.227 63.158 6.13 0.00 33.06 5.36
474 498 3.076278 CGGTAAGTGGGCCCGGTA 61.076 66.667 19.37 5.99 38.09 4.02
501 526 5.612725 AGAAGGTGCCAAAAATGAAAAGA 57.387 34.783 0.00 0.00 0.00 2.52
506 531 6.851609 AGGTGCCAAAAATGAAAAGAAAAAC 58.148 32.000 0.00 0.00 0.00 2.43
511 536 7.275123 TGCCAAAAATGAAAAGAAAAACATTGC 59.725 29.630 0.00 0.00 34.02 3.56
538 566 2.281762 GCTTGCTGACGTATTTCTACCG 59.718 50.000 0.00 0.00 0.00 4.02
542 570 2.529090 GCTGACGTATTTCTACCGTTCG 59.471 50.000 0.00 0.00 0.00 3.95
550 578 1.167851 TTCTACCGTTCGTCCGTCAT 58.832 50.000 0.00 0.00 0.00 3.06
617 645 3.307199 GGGGGTCAAACTCGAGTCATAAA 60.307 47.826 20.33 0.10 0.00 1.40
843 871 7.123830 CGCTCCCTTTATTTATTACACTTTCG 58.876 38.462 0.00 0.00 0.00 3.46
884 912 1.070471 CGCTGCACCGTTTTAATGGC 61.070 55.000 0.00 0.00 38.70 4.40
976 1015 1.125566 CGCGTCGAGGTTTTAAGGAAC 59.874 52.381 7.01 0.00 0.00 3.62
1248 1305 2.595463 ACGTCGTCCCGAGGAACA 60.595 61.111 12.56 0.00 43.12 3.18
1323 1383 2.359169 GGCTGAGATCCGTGACCCA 61.359 63.158 0.00 0.00 0.00 4.51
1446 1506 2.603776 AACTTCCCCGAGGACGCT 60.604 61.111 0.00 0.00 43.90 5.07
1608 1668 3.950794 GAGCAACGTGATGGGCCGA 62.951 63.158 0.00 0.00 0.00 5.54
1611 1671 2.047274 AACGTGATGGGCCGACTG 60.047 61.111 0.00 0.00 0.00 3.51
1612 1672 2.879233 AACGTGATGGGCCGACTGT 61.879 57.895 0.00 0.00 0.00 3.55
1859 1919 1.071605 CGAGCAAAAGAGAAGACCGG 58.928 55.000 0.00 0.00 0.00 5.28
1925 1985 5.704053 TCATCCTATGCATGCATAAGTTCTG 59.296 40.000 33.71 25.17 38.30 3.02
1953 2013 0.035725 TGAGCAGCAAGTCAGATGGG 60.036 55.000 0.00 0.00 0.00 4.00
1996 2056 2.746362 CACTTTCTTGGACTGATGAGCC 59.254 50.000 0.00 0.00 0.00 4.70
2003 2063 1.227205 GACTGATGAGCCAGAGCCG 60.227 63.158 0.00 0.00 41.25 5.52
2016 2076 1.411977 CAGAGCCGAGAGATGTGGAAT 59.588 52.381 0.00 0.00 0.00 3.01
2065 2125 7.119846 AGCAAGCAACTAAAGACGAAGATTTAT 59.880 33.333 0.00 0.00 0.00 1.40
2098 2172 4.207891 AGTAGTGCCATGTAGGTTCTTG 57.792 45.455 0.00 0.00 40.61 3.02
2107 2181 5.622233 GCCATGTAGGTTCTTGGTTTTCATC 60.622 44.000 0.00 0.00 40.61 2.92
2115 2189 3.664107 TCTTGGTTTTCATCGAGGTCAG 58.336 45.455 0.00 0.00 0.00 3.51
2143 2217 3.866883 ACTGAAGCTCTCTAACTCAGC 57.133 47.619 8.84 0.00 0.00 4.26
2349 2427 3.119708 GGCTCGCTTGTGATTTCAAATCT 60.120 43.478 11.46 0.00 0.00 2.40
2358 2436 7.014038 GCTTGTGATTTCAAATCTCATAGGGAT 59.986 37.037 14.15 0.00 0.00 3.85
2372 2450 4.961730 TCATAGGGATTGTTTGGGATTTGG 59.038 41.667 0.00 0.00 0.00 3.28
2373 2451 3.558608 AGGGATTGTTTGGGATTTGGA 57.441 42.857 0.00 0.00 0.00 3.53
2419 2497 7.413644 GCAGATTGAGAAAATTAAGGCTAGAC 58.586 38.462 0.00 0.00 0.00 2.59
2451 2529 3.892588 GAGGGAGATAGGAACACTACCTG 59.107 52.174 0.00 0.00 44.08 4.00
2461 2539 3.504906 GGAACACTACCTGTTTTTAGGCC 59.495 47.826 0.00 0.00 43.60 5.19
2534 2612 5.435686 TGAGGCACCTGTTACAGATAATT 57.564 39.130 14.66 0.00 32.44 1.40
2547 2625 9.109393 TGTTACAGATAATTAAAGGATGAGCAC 57.891 33.333 0.00 0.00 0.00 4.40
2562 2640 6.765036 AGGATGAGCACAATTACAGTAGATTG 59.235 38.462 11.14 11.14 38.79 2.67
2657 2735 4.749048 AAGGTTTCTGGAGAGGGAAATT 57.251 40.909 0.00 0.00 34.60 1.82
2678 2757 7.512117 AATTCTAGGTTAGAGGCTAGGTTTT 57.488 36.000 0.00 0.00 35.96 2.43
2679 2758 6.541934 TTCTAGGTTAGAGGCTAGGTTTTC 57.458 41.667 0.00 0.00 35.96 2.29
2687 2766 2.169561 GAGGCTAGGTTTTCTGAGGAGG 59.830 54.545 0.00 0.00 0.00 4.30
2688 2767 2.188817 GGCTAGGTTTTCTGAGGAGGA 58.811 52.381 0.00 0.00 0.00 3.71
2689 2768 2.169561 GGCTAGGTTTTCTGAGGAGGAG 59.830 54.545 0.00 0.00 0.00 3.69
2691 2770 3.709141 GCTAGGTTTTCTGAGGAGGAGAT 59.291 47.826 0.00 0.00 0.00 2.75
2725 2804 3.350219 TTGGTTCTTACTCAGATGGGC 57.650 47.619 0.00 0.00 0.00 5.36
2729 2808 0.343372 TCTTACTCAGATGGGCCCCT 59.657 55.000 22.27 10.21 0.00 4.79
2730 2809 0.471617 CTTACTCAGATGGGCCCCTG 59.528 60.000 22.27 20.50 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 9.520204 CCACCATCATAAGCTTAAAACTAATTG 57.480 33.333 10.85 1.67 0.00 2.32
117 119 4.227300 AGCAATAATACAGAGAACCCCACA 59.773 41.667 0.00 0.00 0.00 4.17
361 381 6.165577 ACCATCACTTCAAATTTTGGTATGC 58.834 36.000 9.18 0.00 34.37 3.14
409 430 7.797038 AGCATTCAAAGCAAAGATTTTTCTT 57.203 28.000 0.00 0.00 0.00 2.52
468 492 0.175073 GCACCTTCTAGTGTACCGGG 59.825 60.000 6.32 0.00 40.04 5.73
474 498 4.469657 TCATTTTTGGCACCTTCTAGTGT 58.530 39.130 0.00 0.00 40.04 3.55
501 526 2.867975 GCAAGCTCACAGCAATGTTTTT 59.132 40.909 0.00 0.00 45.56 1.94
506 531 0.879090 TCAGCAAGCTCACAGCAATG 59.121 50.000 0.00 0.00 45.56 2.82
511 536 2.001812 ATACGTCAGCAAGCTCACAG 57.998 50.000 0.00 0.00 0.00 3.66
538 566 4.727235 AAAGAAAAGATGACGGACGAAC 57.273 40.909 0.00 0.00 0.00 3.95
542 570 6.251549 GCAGATAAAAGAAAAGATGACGGAC 58.748 40.000 0.00 0.00 0.00 4.79
550 578 4.261801 CGGAGGGCAGATAAAAGAAAAGA 58.738 43.478 0.00 0.00 0.00 2.52
617 645 0.404040 TTGGAGAAGGCCAACGGATT 59.596 50.000 5.01 0.00 42.75 3.01
843 871 0.388520 GGCAAATCGGGCTTCAACAC 60.389 55.000 0.00 0.00 0.00 3.32
846 874 0.965363 GGAGGCAAATCGGGCTTCAA 60.965 55.000 0.00 0.00 44.62 2.69
904 935 3.004752 ACTCGGATTAAGCCAGCAATT 57.995 42.857 10.94 0.00 0.00 2.32
976 1015 2.227194 GGGTGCAATTTATACTCCCCG 58.773 52.381 0.00 0.00 32.12 5.73
1122 1179 3.203442 GTGAGGGCGGACACGATA 58.797 61.111 0.00 0.00 44.60 2.92
1263 1323 2.230940 CCTCACGCCGCGATACTTG 61.231 63.158 21.79 6.90 0.00 3.16
1296 1356 1.450531 GGATCTCAGCCGCCCATTTG 61.451 60.000 0.00 0.00 0.00 2.32
1830 1890 5.702622 TCTCTTTTGCTCGTTTATCATCG 57.297 39.130 0.00 0.00 0.00 3.84
1859 1919 0.796870 CGAAAGGCGGGAAATTTCGC 60.797 55.000 21.85 21.85 45.76 4.70
1925 1985 0.441533 CTTGCTGCTCACGATGTGAC 59.558 55.000 0.00 0.00 37.67 3.67
1966 2026 1.416401 TCCAAGAAAGTGACCTTCGCT 59.584 47.619 0.00 0.00 39.20 4.93
1996 2056 0.820226 TTCCACATCTCTCGGCTCTG 59.180 55.000 0.00 0.00 0.00 3.35
2003 2063 4.766891 TGAACCCAAAATTCCACATCTCTC 59.233 41.667 0.00 0.00 0.00 3.20
2016 2076 5.618236 TGATGAATGCAATTGAACCCAAAA 58.382 33.333 10.34 0.00 36.07 2.44
2065 2125 7.759489 ACATGGCACTACTAAAAGAAAATCA 57.241 32.000 0.00 0.00 0.00 2.57
2098 2172 4.065789 AGAAACTGACCTCGATGAAAACC 58.934 43.478 0.00 0.00 0.00 3.27
2115 2189 7.868415 TGAGTTAGAGAGCTTCAGTTTAGAAAC 59.132 37.037 0.00 0.00 39.17 2.78
2143 2217 6.385649 AGCTCTAGTAACTTTGCTAGCTAG 57.614 41.667 16.84 16.84 41.46 3.42
2154 2231 9.635404 AATGAACACTATCTAGCTCTAGTAACT 57.365 33.333 0.00 0.00 34.84 2.24
2257 2335 9.386010 TCCATACAACACCTTTATATACAACAC 57.614 33.333 0.00 0.00 0.00 3.32
2301 2379 2.491693 CGGGGAATGAAAAGCAAAGCTA 59.508 45.455 0.00 0.00 38.25 3.32
2349 2427 4.961730 CCAAATCCCAAACAATCCCTATGA 59.038 41.667 0.00 0.00 0.00 2.15
2372 2450 7.721399 TCTGCCTTATTCTTCAGGGAAATATTC 59.279 37.037 0.00 0.00 28.68 1.75
2373 2451 7.586349 TCTGCCTTATTCTTCAGGGAAATATT 58.414 34.615 0.00 0.00 28.68 1.28
2419 2497 5.068215 TCCTATCTCCCTCTAAACCTCTG 57.932 47.826 0.00 0.00 0.00 3.35
2451 2529 3.861276 AATTAGCCACGGCCTAAAAAC 57.139 42.857 3.95 0.00 43.17 2.43
2461 2539 3.223435 TCTCCTCCTCTAATTAGCCACG 58.777 50.000 7.67 0.00 0.00 4.94
2534 2612 7.847096 TCTACTGTAATTGTGCTCATCCTTTA 58.153 34.615 0.00 0.00 0.00 1.85
2552 2630 9.384764 GAAAAGGTTCTTATAGCAATCTACTGT 57.615 33.333 0.00 0.00 0.00 3.55
2562 2640 7.404671 TCCCATTTGAAAAGGTTCTTATAGC 57.595 36.000 0.00 0.00 34.60 2.97
2644 2722 5.850278 TCTAACCTAGAATTTCCCTCTCCA 58.150 41.667 0.00 0.00 0.00 3.86
2657 2735 5.657302 CAGAAAACCTAGCCTCTAACCTAGA 59.343 44.000 0.00 0.00 34.36 2.43
2678 2757 5.190528 ACTGCATTTTTATCTCCTCCTCAGA 59.809 40.000 0.00 0.00 0.00 3.27
2679 2758 5.296283 CACTGCATTTTTATCTCCTCCTCAG 59.704 44.000 0.00 0.00 0.00 3.35
2687 2766 7.147976 AGAACCAAACACTGCATTTTTATCTC 58.852 34.615 0.00 0.00 0.00 2.75
2688 2767 7.054491 AGAACCAAACACTGCATTTTTATCT 57.946 32.000 0.00 0.00 0.00 1.98
2689 2768 7.713764 AAGAACCAAACACTGCATTTTTATC 57.286 32.000 0.00 0.00 0.00 1.75
2691 2770 7.777095 AGTAAGAACCAAACACTGCATTTTTA 58.223 30.769 0.00 0.00 0.00 1.52
2725 2804 3.384555 AAGCCATCATGCCCAGGGG 62.385 63.158 7.91 3.48 38.57 4.79
2734 2814 3.036452 ACATAAAGGGCAAGCCATCAT 57.964 42.857 13.87 1.40 37.98 2.45


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

AutoCloner maintained by Alex Coulton.