Multiple sequence alignment - TraesCS2D01G134200

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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 TraesCS2D01G134200 chr2D 100.000 3886 0 0 1 3886 79069117 79065232 0.000000e+00 7177.0
1 TraesCS2D01G134200 chr2A 92.976 3175 134 34 481 3593 79333907 79330760 0.000000e+00 4545.0
2 TraesCS2D01G134200 chr2A 94.704 321 5 4 1 317 79334510 79334198 4.510000e-134 488.0
3 TraesCS2D01G134200 chr2A 89.535 258 16 5 3627 3884 79330566 79330320 2.250000e-82 316.0
4 TraesCS2D01G134200 chr2A 95.804 143 5 1 351 492 79334087 79333945 3.020000e-56 230.0
5 TraesCS2D01G134200 chr2A 86.667 75 4 4 319 387 79334169 79334095 1.160000e-10 78.7
6 TraesCS2D01G134200 chr2B 94.917 1869 58 14 1 1836 122757907 122756043 0.000000e+00 2891.0
7 TraesCS2D01G134200 chr2B 92.418 1253 48 16 2358 3591 122755517 122754293 0.000000e+00 1744.0
8 TraesCS2D01G134200 chr2B 88.403 526 17 10 1825 2327 122756022 122755518 9.300000e-166 593.0
9 TraesCS2D01G134200 chr2B 84.545 110 9 2 3652 3754 122754114 122754006 6.870000e-18 102.0
10 TraesCS2D01G134200 chr7B 82.375 1061 135 27 598 1646 500233685 500234705 0.000000e+00 876.0
11 TraesCS2D01G134200 chr7B 82.778 180 24 5 78 253 500233188 500233364 1.870000e-33 154.0
12 TraesCS2D01G134200 chr7A 84.697 758 98 15 899 1649 519674058 519673312 0.000000e+00 741.0
13 TraesCS2D01G134200 chr7A 79.379 708 107 20 2518 3212 519672333 519671652 2.740000e-126 462.0
14 TraesCS2D01G134200 chr7D 82.588 827 98 15 598 1403 476031375 476032176 0.000000e+00 688.0
15 TraesCS2D01G134200 chr7D 85.321 109 12 3 147 253 476030949 476031055 4.100000e-20 110.0


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 TraesCS2D01G134200 chr2D 79065232 79069117 3885 True 7177.00 7177 100.00000 1 3886 1 chr2D.!!$R1 3885
1 TraesCS2D01G134200 chr2A 79330320 79334510 4190 True 1131.54 4545 91.93720 1 3884 5 chr2A.!!$R1 3883
2 TraesCS2D01G134200 chr2B 122754006 122757907 3901 True 1332.50 2891 90.07075 1 3754 4 chr2B.!!$R1 3753
3 TraesCS2D01G134200 chr7B 500233188 500234705 1517 False 515.00 876 82.57650 78 1646 2 chr7B.!!$F1 1568
4 TraesCS2D01G134200 chr7A 519671652 519674058 2406 True 601.50 741 82.03800 899 3212 2 chr7A.!!$R1 2313
5 TraesCS2D01G134200 chr7D 476030949 476032176 1227 False 399.00 688 83.95450 147 1403 2 chr7D.!!$F1 1256

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
650 856 2.315176 AGAGATCTCCCTCGTGGAATG 58.685 52.381 19.3 0.0 44.57 2.67 F
1611 1847 0.104855 GCGCAGGATGGTGACTGATA 59.895 55.000 0.3 0.0 36.86 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 2657 2.503331 TGGCAAAGTCACATGGTACTG 58.497 47.619 0.0 0.00 0.0 2.74 R
3571 4256 2.186076 GCCAAACTACATCTCGAGACG 58.814 52.381 19.3 13.08 0.0 4.18 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
30 33 2.749621 AGCCATTCGTTGCTTTTAGAGG 59.250 45.455 0.00 0.00 32.94 3.69
279 291 8.250143 TCTTCATAGCTGTATGTTAGATCCAA 57.750 34.615 0.00 0.00 37.81 3.53
407 497 7.623630 AGCAACAAATTGAAAGGCCTAAATAT 58.376 30.769 5.16 0.00 38.15 1.28
596 802 5.163642 CCGAGCTAGCCAAGTAATATATCGT 60.164 44.000 12.13 0.00 0.00 3.73
650 856 2.315176 AGAGATCTCCCTCGTGGAATG 58.685 52.381 19.30 0.00 44.57 2.67
724 930 5.003804 AGGATATATGCGATTCCCAAACAC 58.996 41.667 0.00 0.00 0.00 3.32
806 1012 7.697691 ACGAAGGAATAATGTCTAAAATGCTG 58.302 34.615 0.00 0.00 0.00 4.41
828 1038 3.944087 ACAAGTAGAAGGGCATCTTGTC 58.056 45.455 0.00 0.00 42.98 3.18
1125 1357 1.091771 ATGGCATGGAGTTTCGCTCG 61.092 55.000 0.00 0.00 45.03 5.03
1148 1380 2.050144 AGCAGTCTCTCTGAAACCCAA 58.950 47.619 0.00 0.00 46.27 4.12
1155 1387 2.544267 CTCTCTGAAACCCAACGTTGAC 59.456 50.000 29.35 14.28 33.93 3.18
1275 1508 5.069781 GGCCATAGTATGAACTTGAGAGAGT 59.930 44.000 11.91 0.00 37.15 3.24
1368 1603 7.615757 GCCCAATCCAAATTATAGCTAGGTTAT 59.384 37.037 0.00 0.00 0.00 1.89
1611 1847 0.104855 GCGCAGGATGGTGACTGATA 59.895 55.000 0.30 0.00 36.86 2.15
1730 2050 9.179909 CATATTAGGTACTAGTATCTCAGGTGG 57.820 40.741 19.05 3.11 41.02 4.61
1742 2062 2.567169 TCTCAGGTGGTGTTCCATAGTG 59.433 50.000 0.00 0.00 46.20 2.74
1744 2064 3.181329 TCAGGTGGTGTTCCATAGTGAT 58.819 45.455 0.00 0.00 46.20 3.06
1859 2211 9.635520 TTAGTTAACAAAGCAGTAGATCTGTAC 57.364 33.333 5.18 0.00 45.23 2.90
1869 2221 6.038825 AGCAGTAGATCTGTACAGTGTGTATC 59.961 42.308 21.99 16.20 45.23 2.24
1873 2225 7.996066 AGTAGATCTGTACAGTGTGTATCAGAT 59.004 37.037 21.99 22.52 44.48 2.90
2097 2543 3.906720 ATGGTTGCATAAGGTACTCGT 57.093 42.857 0.00 0.00 38.49 4.18
2239 2685 4.322198 CCATGTGACTTTGCCAAATTAGCT 60.322 41.667 0.00 0.00 0.00 3.32
2270 2716 5.006261 GGTTTTTCTACATGGCAAAACACAC 59.994 40.000 18.08 7.82 39.74 3.82
2518 3180 5.765576 TCCCACCTTACTGCAAAATAGTA 57.234 39.130 0.00 0.00 0.00 1.82
2519 3181 5.493809 TCCCACCTTACTGCAAAATAGTAC 58.506 41.667 0.00 0.00 30.81 2.73
2520 3182 5.249852 TCCCACCTTACTGCAAAATAGTACT 59.750 40.000 0.00 0.00 30.81 2.73
2562 3224 9.233232 CAAGAAAGGACACAAATACAGTAAAAC 57.767 33.333 0.00 0.00 0.00 2.43
2667 3333 2.276732 TGAACTGGCAGGAAAAGAGG 57.723 50.000 20.34 0.00 0.00 3.69
2991 3666 7.727181 TCTAGAGAAGCTGGAATAAATGTACC 58.273 38.462 0.00 0.00 30.36 3.34
3307 3985 7.541162 TGATCTTCAGGTTGAGCAAAATTATG 58.459 34.615 0.00 0.00 0.00 1.90
3345 4023 7.446931 TGAGTTAAATTAGAACAACCATGAGCA 59.553 33.333 0.00 0.00 0.00 4.26
3381 4059 7.754475 CCGATATAGAGATCAAAGTGATGACAG 59.246 40.741 0.00 0.00 37.20 3.51
3389 4067 4.329392 TCAAAGTGATGACAGATGCACAT 58.671 39.130 0.00 0.00 33.85 3.21
3440 4118 8.436046 TTGAAATCAAATTTTGGTCCAAAGAG 57.564 30.769 16.47 8.62 32.19 2.85
3443 4128 5.930837 TCAAATTTTGGTCCAAAGAGTGT 57.069 34.783 16.47 0.96 34.72 3.55
3491 4176 4.960938 TGGTACGTACGATCTACCAGTAT 58.039 43.478 24.48 2.62 35.93 2.12
3547 4232 7.465353 TTGAATTTATTTCTGGACTCATGCA 57.535 32.000 0.00 0.00 35.23 3.96
3548 4233 7.649533 TGAATTTATTTCTGGACTCATGCAT 57.350 32.000 0.00 0.00 35.23 3.96
3549 4234 7.485810 TGAATTTATTTCTGGACTCATGCATG 58.514 34.615 21.07 21.07 35.23 4.06
3567 4252 3.119708 GCATGGCAAAACTTCTCGAAGAT 60.120 43.478 13.22 0.00 40.79 2.40
3610 4433 1.405463 GCGCTTAAATTCCTTGGGAGG 59.595 52.381 0.00 0.00 45.02 4.30
3612 4435 1.405463 GCTTAAATTCCTTGGGAGGCG 59.595 52.381 0.00 0.00 43.21 5.52
3616 4439 1.852157 AATTCCTTGGGAGGCGCTGA 61.852 55.000 7.64 0.00 43.21 4.26
3619 4442 3.207669 CTTGGGAGGCGCTGATGC 61.208 66.667 7.64 0.00 0.00 3.91
3638 4489 6.321717 TGATGCGATGTTCTAACAAAAATCC 58.678 36.000 0.00 0.00 43.03 3.01
3664 4515 4.399303 GGTCGAAATGTTCTTTGATGGGAT 59.601 41.667 0.00 0.00 0.00 3.85
3697 4548 4.796290 GCTTCATGCATCATTCCCTTCATG 60.796 45.833 0.00 0.00 42.31 3.07
3721 4579 3.260884 GGGACATTATCTTGGAGCCGATA 59.739 47.826 0.00 0.00 0.00 2.92
3725 4583 6.227298 ACATTATCTTGGAGCCGATATAGG 57.773 41.667 0.00 0.00 0.00 2.57
3727 4585 5.661056 TTATCTTGGAGCCGATATAGGTG 57.339 43.478 3.62 0.00 0.00 4.00
3731 4589 2.239400 TGGAGCCGATATAGGTGTGAG 58.761 52.381 3.62 0.00 0.00 3.51
3766 4624 2.107204 GGCTTGACCATATGGAGGACAT 59.893 50.000 28.77 4.15 40.15 3.06
3785 4643 7.887381 AGGACATATTAGTTTCTGTAGATCCG 58.113 38.462 0.00 0.00 0.00 4.18
3833 4691 4.475016 AGAAACTGATGTTAGTGGGGCTAT 59.525 41.667 0.00 0.00 34.96 2.97
3846 4704 3.194542 GTGGGGCTATGTTGCATTACAAA 59.805 43.478 0.00 0.00 40.82 2.83
3855 4713 5.994887 TGTTGCATTACAAACTTCTACGT 57.005 34.783 0.00 0.00 40.82 3.57
3884 4742 3.926616 TCGACTTCATTTGGTTCTCTCC 58.073 45.455 0.00 0.00 0.00 3.71
3885 4743 2.668457 CGACTTCATTTGGTTCTCTCCG 59.332 50.000 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
349 388 5.207768 GCATGTTTAATATTGCTCTCGGTG 58.792 41.667 0.00 0.00 32.41 4.94
407 497 8.171164 TGTACAAATGGACAAAACATATGTGA 57.829 30.769 9.63 0.00 0.00 3.58
425 515 4.836175 TGACAGGGAGTAGACATGTACAAA 59.164 41.667 0.00 0.00 0.00 2.83
537 677 4.525487 CCCCGGTGCTTGATATAGTACTTA 59.475 45.833 0.00 0.00 32.20 2.24
556 697 4.530857 GGTGTCGATCAGGCCCCG 62.531 72.222 0.00 0.00 0.00 5.73
596 802 7.123997 ACTTTACATGGTATCATTGGCAATTGA 59.876 33.333 10.65 11.81 0.00 2.57
724 930 5.629435 TCGCGATAAGAGCATATGTAACAAG 59.371 40.000 3.71 0.00 34.19 3.16
806 1012 3.944087 ACAAGATGCCCTTCTACTTGTC 58.056 45.455 0.00 0.00 44.75 3.18
932 1164 5.665916 AAAGCTTGAGAAATTACATGGGG 57.334 39.130 0.00 0.00 0.00 4.96
1125 1357 1.437625 GTTTCAGAGAGACTGCTGGC 58.562 55.000 0.00 0.00 45.38 4.85
1148 1380 0.535335 ATCACCGCCTATGTCAACGT 59.465 50.000 0.00 0.00 0.00 3.99
1155 1387 2.872245 ACGAAAATCATCACCGCCTATG 59.128 45.455 0.00 0.00 0.00 2.23
1257 1490 5.544176 TCCCAAACTCTCTCAAGTTCATACT 59.456 40.000 0.00 0.00 38.52 2.12
1260 1493 4.594920 TCTCCCAAACTCTCTCAAGTTCAT 59.405 41.667 0.00 0.00 38.52 2.57
1275 1508 3.561313 GGTGAAGCCATTAGTCTCCCAAA 60.561 47.826 0.00 0.00 37.17 3.28
1593 1829 2.611473 GGATATCAGTCACCATCCTGCG 60.611 54.545 4.83 0.00 35.15 5.18
1611 1847 4.516698 GCTATCGTTTGTTGATGATGGGAT 59.483 41.667 0.00 0.00 0.00 3.85
1730 2050 3.119291 CTCGAGCATCACTATGGAACAC 58.881 50.000 0.00 0.00 36.24 3.32
1742 2062 4.619336 GCACTAAGTATAAGCTCGAGCATC 59.381 45.833 36.87 21.05 45.16 3.91
1744 2064 3.632604 AGCACTAAGTATAAGCTCGAGCA 59.367 43.478 36.87 19.86 45.16 4.26
1859 2211 9.101655 TGATTTAACATCATCTGATACACACTG 57.898 33.333 0.00 0.00 32.63 3.66
1893 2245 7.535139 TCACTTTTAGTTAAGCCACATATTGC 58.465 34.615 0.00 0.00 0.00 3.56
1896 2248 8.863872 AACTCACTTTTAGTTAAGCCACATAT 57.136 30.769 0.00 0.00 35.44 1.78
1904 2256 7.407337 AGCGTTTGAACTCACTTTTAGTTAAG 58.593 34.615 0.00 0.00 37.31 1.85
2097 2543 9.740239 GAGAATATATTTTTCAGCAGCATTTCA 57.260 29.630 0.00 0.00 0.00 2.69
2211 2657 2.503331 TGGCAAAGTCACATGGTACTG 58.497 47.619 0.00 0.00 0.00 2.74
2239 2685 6.656632 TGCCATGTAGAAAAACCAATGTAA 57.343 33.333 0.00 0.00 0.00 2.41
2279 2725 7.729116 AGCATTAAAATGGCAGTTGCTATATT 58.271 30.769 9.82 0.76 41.54 1.28
2416 3051 4.880120 CACTGATTGAAGTACATGCCAGAT 59.120 41.667 0.00 0.00 0.00 2.90
2518 3180 8.253113 CCTTTCTTGGCATCATTAATTTGTAGT 58.747 33.333 0.00 0.00 0.00 2.73
2519 3181 8.469200 TCCTTTCTTGGCATCATTAATTTGTAG 58.531 33.333 0.00 0.00 0.00 2.74
2520 3182 8.250332 GTCCTTTCTTGGCATCATTAATTTGTA 58.750 33.333 0.00 0.00 0.00 2.41
2534 3196 4.278419 ACTGTATTTGTGTCCTTTCTTGGC 59.722 41.667 0.00 0.00 0.00 4.52
2614 3280 9.668497 GTAAGGGAATTCAGATAAGTTAACTGT 57.332 33.333 16.96 0.78 33.93 3.55
2615 3281 9.892130 AGTAAGGGAATTCAGATAAGTTAACTG 57.108 33.333 9.34 12.68 0.00 3.16
2991 3666 3.533606 AGATCAGACATGAACCTTCCG 57.466 47.619 0.00 0.00 39.39 4.30
3326 4004 8.297470 ACATTATGCTCATGGTTGTTCTAATT 57.703 30.769 0.00 0.00 0.00 1.40
3345 4023 7.423844 TGATCTCTATATCGGCCAACATTAT 57.576 36.000 2.24 0.00 0.00 1.28
3381 4059 6.877556 CACGATAGAGGTATAATGTGCATC 57.122 41.667 0.00 0.00 41.38 3.91
3389 4067 5.601583 TTTGTGGCACGATAGAGGTATAA 57.398 39.130 13.77 0.00 41.38 0.98
3462 4147 4.978083 AGATCGTACGTACCAAGTTCAT 57.022 40.909 19.67 0.00 0.00 2.57
3547 4232 5.302357 GAATCTTCGAGAAGTTTTGCCAT 57.698 39.130 12.01 0.00 39.38 4.40
3548 4233 4.749245 GAATCTTCGAGAAGTTTTGCCA 57.251 40.909 12.01 0.00 39.38 4.92
3571 4256 2.186076 GCCAAACTACATCTCGAGACG 58.814 52.381 19.30 13.08 0.00 4.18
3612 4435 4.340894 TTTGTTAGAACATCGCATCAGC 57.659 40.909 0.00 0.00 38.95 4.26
3616 4439 6.515272 AGGATTTTTGTTAGAACATCGCAT 57.485 33.333 0.00 0.00 38.95 4.73
3619 4442 6.677913 ACCAAGGATTTTTGTTAGAACATCG 58.322 36.000 0.00 0.00 38.95 3.84
3632 4483 6.405278 AAGAACATTTCGACCAAGGATTTT 57.595 33.333 0.00 0.00 34.02 1.82
3638 4489 5.156355 CCATCAAAGAACATTTCGACCAAG 58.844 41.667 0.00 0.00 34.02 3.61
3664 4515 2.570365 GCATGAAGCACCACCATCA 58.430 52.632 0.00 0.00 44.79 3.07
3697 4548 1.202940 GGCTCCAAGATAATGTCCCCC 60.203 57.143 0.00 0.00 0.00 5.40
3707 4558 3.259374 CACACCTATATCGGCTCCAAGAT 59.741 47.826 0.00 0.00 0.00 2.40
3721 4579 1.614241 GCCACCGGTCTCACACCTAT 61.614 60.000 2.59 0.00 44.21 2.57
3725 4583 2.357517 CAGCCACCGGTCTCACAC 60.358 66.667 2.59 0.00 0.00 3.82
3766 4624 6.127281 TGCCAACGGATCTACAGAAACTAATA 60.127 38.462 0.00 0.00 0.00 0.98
3776 4634 1.339535 TGCAATGCCAACGGATCTACA 60.340 47.619 1.53 0.00 0.00 2.74
3777 4635 1.378531 TGCAATGCCAACGGATCTAC 58.621 50.000 1.53 0.00 0.00 2.59
3785 4643 1.080569 CCCGAGTTGCAATGCCAAC 60.081 57.895 0.59 7.55 44.12 3.77
3833 4691 5.332732 CGACGTAGAAGTTTGTAATGCAACA 60.333 40.000 0.00 0.00 36.72 3.33


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

AutoCloner maintained by Alex Coulton.