Multiple sequence alignment - TraesCS2D01G462200

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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 TraesCS2D01G462200 chr2D 100.000 3455 0 0 1 3455 568233162 568229708 0.000000e+00 6381
1 TraesCS2D01G462200 chr2A 93.730 2791 124 25 445 3204 707751476 707748706 0.000000e+00 4137
2 TraesCS2D01G462200 chr2A 90.909 209 15 4 3234 3438 707748710 707748502 9.440000e-71 278
3 TraesCS2D01G462200 chr2B 95.612 2484 76 14 1000 3454 680769699 680767220 0.000000e+00 3952
4 TraesCS2D01G462200 chr2B 96.603 942 26 3 1 938 680771121 680770182 0.000000e+00 1557
5 TraesCS2D01G462200 chr6D 85.460 337 29 17 947 1276 67518566 67518243 1.990000e-87 333
6 TraesCS2D01G462200 chr6B 84.431 334 31 13 947 1271 142503406 142503085 3.350000e-80 309
7 TraesCS2D01G462200 chr6A 85.185 297 26 8 987 1276 85023391 85023106 4.360000e-74 289


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 TraesCS2D01G462200 chr2D 568229708 568233162 3454 True 6381.0 6381 100.0000 1 3455 1 chr2D.!!$R1 3454
1 TraesCS2D01G462200 chr2A 707748502 707751476 2974 True 2207.5 4137 92.3195 445 3438 2 chr2A.!!$R1 2993
2 TraesCS2D01G462200 chr2B 680767220 680771121 3901 True 2754.5 3952 96.1075 1 3454 2 chr2B.!!$R1 3453

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
398 402 2.516227 AGCTCCTTTAGGCTTTTCCC 57.484 50.0 0.0 0.0 34.96 3.97 F
1506 1945 0.314935 AGGAAAATGCCACTGTTGCG 59.685 50.0 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1853 2292 0.535797 GGTCCAACCTTCTCCCGTAG 59.464 60.0 0.0 0.0 34.73 3.51 R
3261 3716 1.576577 TCAGGACATCAGCCATGAGT 58.423 50.0 0.0 0.0 39.29 3.41 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
46 47 5.480642 TTGTTGGGATATGTGCATTTTGT 57.519 34.783 0.00 0.00 0.00 2.83
208 212 4.796830 CGTGTAGTGTTGTTATGTCGCTAT 59.203 41.667 0.00 0.00 0.00 2.97
231 235 5.178797 TCTAGTGACTTCTATTGGCTTTGC 58.821 41.667 0.00 0.00 0.00 3.68
235 239 4.333926 GTGACTTCTATTGGCTTTGCTAGG 59.666 45.833 0.00 0.00 0.00 3.02
280 284 8.073768 ACAAAACACACATTTTTACTAGATCCG 58.926 33.333 0.00 0.00 29.17 4.18
398 402 2.516227 AGCTCCTTTAGGCTTTTCCC 57.484 50.000 0.00 0.00 34.96 3.97
787 792 2.625790 CGGACCCAAACATTCCAGAAAA 59.374 45.455 0.00 0.00 0.00 2.29
876 885 2.731875 CCGCAATAAACGGCAAACC 58.268 52.632 0.00 0.00 44.90 3.27
1086 1525 2.360475 GTCTGCACCAAGCCCCTC 60.360 66.667 0.00 0.00 44.83 4.30
1323 1762 1.996191 GCAGACGGAGAAACTGATGTC 59.004 52.381 0.00 0.00 34.07 3.06
1350 1789 0.740737 CCCTTGCCGGAAATCATGAC 59.259 55.000 5.05 0.00 33.16 3.06
1378 1817 2.530151 TTCCTGGGCAGACTGGCT 60.530 61.111 26.27 0.00 43.20 4.75
1394 1833 3.264193 ACTGGCTTACAAGATGGTGATGA 59.736 43.478 0.00 0.00 0.00 2.92
1403 1842 2.477825 AGATGGTGATGATTTCGAGCG 58.522 47.619 0.00 0.00 0.00 5.03
1501 1940 0.890683 GGGTGAGGAAAATGCCACTG 59.109 55.000 0.00 0.00 0.00 3.66
1506 1945 0.314935 AGGAAAATGCCACTGTTGCG 59.685 50.000 0.00 0.00 0.00 4.85
1535 1974 1.457346 CAAGCTGGTGGTGAAGGATC 58.543 55.000 0.00 0.00 0.00 3.36
1558 1997 8.731591 ATCAGATAATGGGGAAATAAGCAATT 57.268 30.769 0.00 0.00 0.00 2.32
1565 2004 5.934781 TGGGGAAATAAGCAATTGTGTTTT 58.065 33.333 7.40 2.82 30.03 2.43
1619 2058 5.449588 GCATTGAATGTGACTCTAATGGTGG 60.450 44.000 7.05 0.00 0.00 4.61
1638 2077 3.184581 GTGGTGAGTGTTTCAGATTCGAC 59.815 47.826 0.00 0.00 36.21 4.20
1701 2140 0.321346 TCTCAGCCGCAAATCAGTCA 59.679 50.000 0.00 0.00 0.00 3.41
1713 2152 5.330295 GCAAATCAGTCAGAAAGCTATGTG 58.670 41.667 0.00 0.00 0.00 3.21
1743 2182 1.133790 GCTAATGCTGAAGGCCAACAG 59.866 52.381 20.18 20.18 40.92 3.16
1768 2207 5.237996 AGAAGTGAGACATGTGTGACAAATG 59.762 40.000 14.00 14.00 35.38 2.32
1778 2217 4.967036 TGTGTGACAAATGAGGTACATGA 58.033 39.130 0.00 0.00 39.39 3.07
1853 2292 2.514205 AATGTTGAAGTTGGTGCTGC 57.486 45.000 0.00 0.00 0.00 5.25
1857 2296 1.069906 GTTGAAGTTGGTGCTGCTACG 60.070 52.381 0.00 0.00 0.00 3.51
1887 2326 3.943671 TGGACCGTGGAAAATATGGAT 57.056 42.857 0.00 0.00 0.00 3.41
2025 2464 5.527951 TGGCTTTACTGTCACGAAAATACAA 59.472 36.000 0.00 0.00 0.00 2.41
2529 2968 4.946160 TTTATTGGGGACTTCTGGATGT 57.054 40.909 0.00 0.00 0.00 3.06
2657 3097 4.288626 GGATGGAGCATATTACCAACCCTA 59.711 45.833 0.00 0.00 39.61 3.53
2661 3101 5.222048 TGGAGCATATTACCAACCCTATTCC 60.222 44.000 0.00 0.00 0.00 3.01
2810 3259 4.202430 TGGGGTTAAAAGGAGAGTCAGTTC 60.202 45.833 0.00 0.00 0.00 3.01
2854 3303 7.364522 TCTTGATTGGATTTACAAACTCTCG 57.635 36.000 0.00 0.00 33.48 4.04
2860 3309 4.988540 TGGATTTACAAACTCTCGTGTCAG 59.011 41.667 0.00 0.00 0.00 3.51
2912 3362 7.122650 TCCACTCCATATCTTCAAATTTTGGTC 59.877 37.037 9.18 0.00 0.00 4.02
2953 3405 5.765677 TGGTGCATACTCTACTATCACTCTC 59.234 44.000 0.00 0.00 0.00 3.20
2954 3406 6.001460 GGTGCATACTCTACTATCACTCTCT 58.999 44.000 0.00 0.00 0.00 3.10
3012 3464 7.624764 GCAATTTCATTTGGCTTCATACCTTTG 60.625 37.037 0.00 0.00 0.00 2.77
3049 3502 2.656947 AGTGTGGCCTCTGCTAAAAA 57.343 45.000 3.32 0.00 37.74 1.94
3118 3571 9.371136 TCACAGTATGATTTACATGTTCTCTTC 57.629 33.333 2.30 0.00 39.69 2.87
3131 3584 6.538742 ACATGTTCTCTTCATTAACCCATACG 59.461 38.462 0.00 0.00 0.00 3.06
3218 3673 2.094854 GCATGACAAGGCCTTTTCAGAG 60.095 50.000 31.86 27.03 33.44 3.35
3261 3716 4.935205 CGTGGACATCAGTATTTTCCTGAA 59.065 41.667 0.00 0.00 41.93 3.02
3276 3739 2.093288 TCCTGAACTCATGGCTGATGTC 60.093 50.000 0.00 0.00 33.29 3.06
3279 3742 2.286872 GAACTCATGGCTGATGTCCTG 58.713 52.381 0.00 0.00 33.29 3.86
3280 3743 1.576577 ACTCATGGCTGATGTCCTGA 58.423 50.000 0.00 0.00 33.29 3.86
3281 3744 2.125233 ACTCATGGCTGATGTCCTGAT 58.875 47.619 0.00 0.00 33.29 2.90
3327 3792 7.415765 CCAGAGTCTCGTTCTATACATTGTCTT 60.416 40.741 0.00 0.00 0.00 3.01
3332 3798 8.709646 GTCTCGTTCTATACATTGTCTTGTTTT 58.290 33.333 0.00 0.00 0.00 2.43
3393 3863 6.933514 ATCCTGGAACAATTTTAACCACAT 57.066 33.333 0.00 0.00 38.70 3.21
3429 3899 2.793288 TACCTCCGTCCCAAAATTCC 57.207 50.000 0.00 0.00 0.00 3.01
3438 3908 4.705023 CCGTCCCAAAATTCCTGTCTTATT 59.295 41.667 0.00 0.00 0.00 1.40
3439 3909 5.163652 CCGTCCCAAAATTCCTGTCTTATTC 60.164 44.000 0.00 0.00 0.00 1.75
3441 3911 6.403636 CGTCCCAAAATTCCTGTCTTATTCAG 60.404 42.308 0.00 0.00 0.00 3.02
3442 3912 6.434340 GTCCCAAAATTCCTGTCTTATTCAGT 59.566 38.462 0.00 0.00 0.00 3.41
3443 3913 7.610305 GTCCCAAAATTCCTGTCTTATTCAGTA 59.390 37.037 0.00 0.00 0.00 2.74
3444 3914 7.829211 TCCCAAAATTCCTGTCTTATTCAGTAG 59.171 37.037 0.00 0.00 0.00 2.57
3445 3915 7.415653 CCCAAAATTCCTGTCTTATTCAGTAGC 60.416 40.741 0.00 0.00 0.00 3.58
3446 3916 7.121168 CCAAAATTCCTGTCTTATTCAGTAGCA 59.879 37.037 0.00 0.00 0.00 3.49
3448 3918 8.814038 AAATTCCTGTCTTATTCAGTAGCATT 57.186 30.769 0.00 0.00 0.00 3.56
3449 3919 8.814038 AATTCCTGTCTTATTCAGTAGCATTT 57.186 30.769 0.00 0.00 0.00 2.32
3450 3920 7.615582 TTCCTGTCTTATTCAGTAGCATTTG 57.384 36.000 0.00 0.00 0.00 2.32
3452 3922 6.818644 TCCTGTCTTATTCAGTAGCATTTGTC 59.181 38.462 0.00 0.00 0.00 3.18
3454 3924 7.981789 CCTGTCTTATTCAGTAGCATTTGTCTA 59.018 37.037 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 6.090129 CACATATCCCAACAAAAACCTAACG 58.910 40.000 0.00 0.00 0.00 3.18
208 212 5.046304 AGCAAAGCCAATAGAAGTCACTAGA 60.046 40.000 0.00 0.00 0.00 2.43
344 348 4.695455 CACTAAATCGGTTGGTTCATCAGT 59.305 41.667 0.00 0.00 0.00 3.41
765 770 0.768622 TCTGGAATGTTTGGGTCCGT 59.231 50.000 0.00 0.00 33.87 4.69
787 792 4.162888 CCCAATTAGGTTAGGTTAGTCCGT 59.837 45.833 0.00 0.00 37.14 4.69
876 885 1.137404 CGCTTTGGAGGCAAATCCG 59.863 57.895 0.00 0.00 42.77 4.18
986 1005 4.802051 CCATGGGTGGCGAGGTGG 62.802 72.222 2.85 0.00 39.01 4.61
1350 1789 1.964373 CCCAGGAACAACCGAACCG 60.964 63.158 0.00 0.00 44.74 4.44
1378 1817 5.294306 GCTCGAAATCATCACCATCTTGTAA 59.706 40.000 0.00 0.00 0.00 2.41
1394 1833 1.648467 GCCTTGGCTTCGCTCGAAAT 61.648 55.000 4.11 0.00 33.34 2.17
1403 1842 1.895131 TCAATCCTTTGCCTTGGCTTC 59.105 47.619 13.18 0.00 32.61 3.86
1501 1940 0.933796 GCTTGCCTAGAGATCGCAAC 59.066 55.000 0.00 0.00 37.58 4.17
1506 1945 1.202627 CCACCAGCTTGCCTAGAGATC 60.203 57.143 0.00 0.00 0.00 2.75
1535 1974 7.654520 CACAATTGCTTATTTCCCCATTATCTG 59.345 37.037 5.05 0.00 0.00 2.90
1558 1997 4.220602 TCGATCCAGATCAGAGAAAACACA 59.779 41.667 8.31 0.00 37.69 3.72
1565 2004 4.163441 ACTTCTCGATCCAGATCAGAGA 57.837 45.455 19.22 19.22 41.24 3.10
1619 2058 4.084328 CCTTGTCGAATCTGAAACACTCAC 60.084 45.833 0.00 0.00 0.00 3.51
1638 2077 2.741612 TGTTCATTGCTTTTCGCCTTG 58.258 42.857 0.00 0.00 38.05 3.61
1701 2140 1.753073 GCATTGGCCACATAGCTTTCT 59.247 47.619 3.88 0.00 0.00 2.52
1724 2163 2.681848 CTCTGTTGGCCTTCAGCATTAG 59.318 50.000 18.39 9.91 46.50 1.73
1743 2182 3.982475 TGTCACACATGTCTCACTTCTC 58.018 45.455 0.00 0.00 0.00 2.87
1768 2207 3.323115 TGAGGCAGATCATCATGTACCTC 59.677 47.826 0.00 0.00 42.26 3.85
1778 2217 3.118531 ACTAAAGGGTGAGGCAGATCAT 58.881 45.455 0.00 0.00 0.00 2.45
1853 2292 0.535797 GGTCCAACCTTCTCCCGTAG 59.464 60.000 0.00 0.00 34.73 3.51
1857 2296 1.003718 CACGGTCCAACCTTCTCCC 60.004 63.158 0.00 0.00 35.66 4.30
1887 2326 6.280855 TCTGTATAAGCAACAGAGCACTTA 57.719 37.500 1.92 0.00 46.38 2.24
2025 2464 4.369182 CTGTACGTCTGGACTTGTTCTTT 58.631 43.478 0.00 0.00 0.00 2.52
2205 2644 4.164796 AGTTGTAGCCATGGATTCTCATGA 59.835 41.667 18.40 0.00 45.30 3.07
2646 3086 4.264038 GGAAACTGGGAATAGGGTTGGTAA 60.264 45.833 0.00 0.00 0.00 2.85
2657 3097 2.657459 TGGTTATGGGGAAACTGGGAAT 59.343 45.455 0.00 0.00 0.00 3.01
2661 3101 2.041081 TCAGTGGTTATGGGGAAACTGG 59.959 50.000 0.00 0.00 36.53 4.00
2689 3137 8.620116 TCATGTTCAGAGTCATCAAAATACAA 57.380 30.769 0.00 0.00 0.00 2.41
2810 3259 5.143376 AGAAAAACTGATTCATTGCAGGG 57.857 39.130 0.00 0.00 36.47 4.45
2854 3303 6.430451 CAATGTACTCTTGGTTTTCTGACAC 58.570 40.000 0.00 0.00 0.00 3.67
2860 3309 5.689383 TGAGCAATGTACTCTTGGTTTTC 57.311 39.130 12.53 4.17 34.68 2.29
2912 3362 9.541724 GTATGCACCATAATATTACATGTTTCG 57.458 33.333 2.30 0.00 0.00 3.46
2953 3405 4.025015 GCATAAAGCAAGATGTGGACAG 57.975 45.455 0.00 0.00 44.79 3.51
3012 3464 6.801862 GCCACACTTCATATGACAAAACTTAC 59.198 38.462 4.48 0.00 0.00 2.34
3049 3502 9.857957 ATGCTTGTGAAAATTGAAATTGTTTTT 57.142 22.222 0.00 0.00 0.00 1.94
3058 3511 7.534282 TCGCTAATATGCTTGTGAAAATTGAA 58.466 30.769 0.00 0.00 0.00 2.69
3118 3571 5.743026 TGTATGTTGCGTATGGGTTAATG 57.257 39.130 0.00 0.00 0.00 1.90
3131 3584 2.393764 ACGCTTTTTGCTGTATGTTGC 58.606 42.857 0.00 0.00 40.11 4.17
3218 3673 6.533723 TCCACGATCATACAGTTCAATAACAC 59.466 38.462 0.00 0.00 38.12 3.32
3261 3716 1.576577 TCAGGACATCAGCCATGAGT 58.423 50.000 0.00 0.00 39.29 3.41
3276 3739 6.773976 TTTGGGCACTATTTTAGAATCAGG 57.226 37.500 0.00 0.00 0.00 3.86
3279 3742 6.930731 TGGTTTTGGGCACTATTTTAGAATC 58.069 36.000 0.00 0.00 0.00 2.52
3280 3743 6.723977 TCTGGTTTTGGGCACTATTTTAGAAT 59.276 34.615 0.00 0.00 0.00 2.40
3281 3744 6.071984 TCTGGTTTTGGGCACTATTTTAGAA 58.928 36.000 0.00 0.00 0.00 2.10
3332 3798 8.311836 TGTGGTTAAAAGTGTGTCCAAAAATTA 58.688 29.630 0.00 0.00 0.00 1.40
3416 3886 5.414454 TGAATAAGACAGGAATTTTGGGACG 59.586 40.000 0.00 0.00 0.00 4.79
3429 3899 7.840342 AGACAAATGCTACTGAATAAGACAG 57.160 36.000 0.00 0.00 40.68 3.51


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

AutoCloner maintained by Alex Coulton.