Multiple sequence alignment - TraesCS2D01G215000

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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 TraesCS2D01G215000 chr2D 100.000 3624 0 0 1 3624 177092539 177096162 0.000000e+00 6693
1 TraesCS2D01G215000 chr2A 94.523 3104 94 30 547 3617 189600712 189603772 0.000000e+00 4721
2 TraesCS2D01G215000 chr2A 91.395 430 37 0 1 430 189599968 189600397 1.120000e-164 590
3 TraesCS2D01G215000 chr2B 93.607 2456 67 32 497 2897 234084579 234086999 0.000000e+00 3583
4 TraesCS2D01G215000 chr2B 90.377 717 27 15 2917 3624 234086985 234087668 0.000000e+00 904
5 TraesCS2D01G215000 chr2B 92.641 462 33 1 1 462 234084133 234084593 0.000000e+00 664


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 TraesCS2D01G215000 chr2D 177092539 177096162 3623 False 6693.0 6693 100.000000 1 3624 1 chr2D.!!$F1 3623
1 TraesCS2D01G215000 chr2A 189599968 189603772 3804 False 2655.5 4721 92.959000 1 3617 2 chr2A.!!$F1 3616
2 TraesCS2D01G215000 chr2B 234084133 234087668 3535 False 1717.0 3583 92.208333 1 3624 3 chr2B.!!$F1 3623


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
472 473 0.106419 AAGGACCTCACCCGCAAAAA 60.106 50.000 0.0 0.0 0.00 1.94 F
654 853 1.513586 GCCACGGAGTAACTCGTCG 60.514 63.158 0.0 0.0 41.61 5.12 F
2246 2470 0.491823 TCCTTTGGGAGAGGAGACCA 59.508 55.000 0.0 0.0 38.37 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 2173 0.250234 CCATCTTCACCTCTGCGGAA 59.750 55.0 0.0 0.0 36.31 4.30 R
2334 2568 0.941542 TCCGGCGAGAAAACAACAAG 59.058 50.0 9.3 0.0 0.00 3.16 R
3208 3477 0.887387 GCGTTGACCACCCTTGCTTA 60.887 55.0 0.0 0.0 0.00 3.09 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
90 91 1.669115 ACTCGCGCATTGCAGACTT 60.669 52.632 8.75 0.00 46.97 3.01
112 113 2.125269 AGATGGGTACGTTGGCGC 60.125 61.111 0.00 0.00 42.83 6.53
136 137 3.947196 TGCTGGAAAATTGCTATGACGAT 59.053 39.130 0.00 0.00 0.00 3.73
189 190 3.320673 CCCGTTATGGCTCCTAGATTC 57.679 52.381 0.00 0.00 35.87 2.52
192 193 2.352814 CGTTATGGCTCCTAGATTCCGG 60.353 54.545 0.00 0.00 0.00 5.14
219 220 4.101585 GTGGATGGATGGATCTTGACTACA 59.898 45.833 0.00 0.00 0.00 2.74
331 332 1.604378 CTCCCTCTGAAACCGCCAT 59.396 57.895 0.00 0.00 0.00 4.40
451 452 3.944871 GGGAAATGCGCCATAGTTG 57.055 52.632 4.18 0.00 0.00 3.16
452 453 0.249031 GGGAAATGCGCCATAGTTGC 60.249 55.000 4.18 0.00 0.00 4.17
453 454 0.455410 GGAAATGCGCCATAGTTGCA 59.545 50.000 4.18 0.00 43.67 4.08
454 455 1.135141 GGAAATGCGCCATAGTTGCAA 60.135 47.619 4.18 0.00 42.65 4.08
455 456 2.187707 GAAATGCGCCATAGTTGCAAG 58.812 47.619 4.18 0.00 42.65 4.01
456 457 0.457035 AATGCGCCATAGTTGCAAGG 59.543 50.000 4.18 0.00 42.65 3.61
457 458 0.394216 ATGCGCCATAGTTGCAAGGA 60.394 50.000 4.18 0.00 42.65 3.36
458 459 1.305219 TGCGCCATAGTTGCAAGGAC 61.305 55.000 4.18 0.00 35.33 3.85
459 460 1.993369 GCGCCATAGTTGCAAGGACC 61.993 60.000 0.00 0.00 0.00 4.46
460 461 0.392998 CGCCATAGTTGCAAGGACCT 60.393 55.000 0.00 0.00 0.00 3.85
461 462 1.383523 GCCATAGTTGCAAGGACCTC 58.616 55.000 0.00 0.00 0.00 3.85
462 463 1.340017 GCCATAGTTGCAAGGACCTCA 60.340 52.381 0.00 0.00 0.00 3.86
463 464 2.359900 CCATAGTTGCAAGGACCTCAC 58.640 52.381 0.00 0.00 0.00 3.51
464 465 2.359900 CATAGTTGCAAGGACCTCACC 58.640 52.381 0.00 0.00 0.00 4.02
465 466 0.690762 TAGTTGCAAGGACCTCACCC 59.309 55.000 0.00 0.00 0.00 4.61
466 467 1.966451 GTTGCAAGGACCTCACCCG 60.966 63.158 0.00 0.00 0.00 5.28
467 468 3.842925 TTGCAAGGACCTCACCCGC 62.843 63.158 0.00 0.00 0.00 6.13
468 469 4.329545 GCAAGGACCTCACCCGCA 62.330 66.667 0.00 0.00 0.00 5.69
469 470 2.429930 CAAGGACCTCACCCGCAA 59.570 61.111 0.00 0.00 0.00 4.85
470 471 1.228124 CAAGGACCTCACCCGCAAA 60.228 57.895 0.00 0.00 0.00 3.68
471 472 0.821711 CAAGGACCTCACCCGCAAAA 60.822 55.000 0.00 0.00 0.00 2.44
472 473 0.106419 AAGGACCTCACCCGCAAAAA 60.106 50.000 0.00 0.00 0.00 1.94
521 522 8.240267 AGTTACAAGGATCTCTACTTATGTCC 57.760 38.462 0.00 0.00 0.00 4.02
529 530 7.037586 AGGATCTCTACTTATGTCCACCAAAAA 60.038 37.037 0.00 0.00 0.00 1.94
554 753 5.049060 TGTGGTGATTAGTGTTGTACAATGC 60.049 40.000 12.26 7.83 0.00 3.56
570 769 4.555262 ACAATGCCGTCAACATTTTTAGG 58.445 39.130 0.00 0.00 35.58 2.69
654 853 1.513586 GCCACGGAGTAACTCGTCG 60.514 63.158 0.00 0.00 41.61 5.12
679 878 2.591429 CAGGGTCACGCACAAGCA 60.591 61.111 0.00 0.00 42.27 3.91
681 880 4.012895 GGGTCACGCACAAGCACG 62.013 66.667 0.00 0.00 42.27 5.34
762 962 4.851252 CCTCCATGCCCTCCCCCT 62.851 72.222 0.00 0.00 0.00 4.79
828 1028 2.009681 ACCCCAAATCCACACCTTTC 57.990 50.000 0.00 0.00 0.00 2.62
1015 1215 3.807839 CCATGGACATGCCGGGGA 61.808 66.667 5.56 0.00 40.66 4.81
1398 1619 6.432472 AGATGGTGTCTTTCTTTCAAGAATCC 59.568 38.462 2.83 3.13 43.92 3.01
1574 1795 6.256321 CGATGATTATTGCCCTTTTCCTTTTG 59.744 38.462 0.00 0.00 0.00 2.44
1623 1844 5.123979 GGGGATTAGTTGTCAATCAAGTGTC 59.876 44.000 0.00 0.00 39.67 3.67
1687 1908 4.429212 CGACGCGGTGACCATCCA 62.429 66.667 12.47 0.00 0.00 3.41
1952 2173 1.536662 AACCGCTGACCTCTTCCCT 60.537 57.895 0.00 0.00 0.00 4.20
2136 2358 3.030291 ACATTTTTGTTCTCCACTGCCA 58.970 40.909 0.00 0.00 0.00 4.92
2168 2392 6.570654 CCCCCTTAATTCTCCACTACTAAA 57.429 41.667 0.00 0.00 0.00 1.85
2176 2400 7.932120 AATTCTCCACTACTAAATCGAATCG 57.068 36.000 0.00 0.00 0.00 3.34
2191 2415 0.675522 AATCGCCCAAGTAACCACCG 60.676 55.000 0.00 0.00 0.00 4.94
2208 2432 2.816360 CGCCTGTCATGTCATGCCG 61.816 63.158 8.03 6.27 0.00 5.69
2246 2470 0.491823 TCCTTTGGGAGAGGAGACCA 59.508 55.000 0.00 0.00 38.37 4.02
2326 2560 3.499737 CGATTGACCCGCACTGCC 61.500 66.667 0.00 0.00 0.00 4.85
2334 2568 3.272334 CCGCACTGCCGATAAGCC 61.272 66.667 0.00 0.00 0.00 4.35
2337 2571 1.723870 GCACTGCCGATAAGCCTTG 59.276 57.895 0.00 0.00 0.00 3.61
2700 2947 3.857157 TTACTCTTGCCCTGTTGTTCT 57.143 42.857 0.00 0.00 0.00 3.01
2774 3027 1.262683 GTAAGCAGCGATGCAGATTCC 59.737 52.381 29.24 0.08 37.25 3.01
2841 3094 3.817709 TGTTTCCCTTGGCTTTTCTTG 57.182 42.857 0.00 0.00 0.00 3.02
2911 3170 4.409187 AGGCTGGTATTTTCCCGTAAAAA 58.591 39.130 0.00 0.00 40.37 1.94
3022 3281 5.503927 ACCATGTGCTCATTACTGATCTTT 58.496 37.500 0.00 0.00 31.15 2.52
3030 3290 8.510505 GTGCTCATTACTGATCTTTTCTTTCTT 58.489 33.333 0.00 0.00 0.00 2.52
3035 3295 5.854431 ACTGATCTTTTCTTTCTTCTCGC 57.146 39.130 0.00 0.00 0.00 5.03
3059 3319 6.292008 GCTTCTGTTTTGAAAAGTCTTCATGC 60.292 38.462 0.00 0.00 0.00 4.06
3060 3320 5.273170 TCTGTTTTGAAAAGTCTTCATGCG 58.727 37.500 0.00 0.00 0.00 4.73
3194 3463 7.201574 GGCTCTGTAGATACGTATGAGTAGATG 60.202 44.444 13.97 7.03 0.00 2.90
3207 3476 9.151471 CGTATGAGTAGATGGAAAGAAAGAAAA 57.849 33.333 0.00 0.00 0.00 2.29
3227 3501 0.887387 TAAGCAAGGGTGGTCAACGC 60.887 55.000 0.00 0.00 41.96 4.84
3416 3692 5.409520 CCATGCGTACGTACTATTACTCCTA 59.590 44.000 22.55 0.00 0.00 2.94
3421 3697 6.089685 GCGTACGTACTATTACTCCTACTACC 59.910 46.154 22.55 0.00 0.00 3.18
3438 3714 2.370281 ACCACTACGAAGAGTGCATG 57.630 50.000 10.18 0.00 44.65 4.06
3617 3902 1.754234 GGCTTACATGTGGGCCCAG 60.754 63.158 29.55 17.45 38.77 4.45
3618 3903 1.754234 GCTTACATGTGGGCCCAGG 60.754 63.158 29.55 20.71 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 5.045215 TCCCACTATTTACGCGACTAAATG 58.955 41.667 15.93 10.69 30.53 2.32
17 18 4.924305 AATCCCACTATTTACGCGACTA 57.076 40.909 15.93 0.00 0.00 2.59
90 91 1.609580 GCCAACGTACCCATCTGTCAA 60.610 52.381 0.00 0.00 0.00 3.18
112 113 3.429085 GTCATAGCAATTTTCCAGCACG 58.571 45.455 0.00 0.00 0.00 5.34
136 137 2.125310 CACGCGATAACCCAGGCA 60.125 61.111 15.93 0.00 0.00 4.75
176 177 1.382557 TGCCGGAATCTAGGAGCCA 60.383 57.895 5.05 0.00 0.00 4.75
189 190 2.896854 CATCCATCCACGTGCCGG 60.897 66.667 10.91 9.89 0.00 6.13
192 193 0.107456 AGATCCATCCATCCACGTGC 59.893 55.000 10.91 0.00 0.00 5.34
196 197 3.853355 AGTCAAGATCCATCCATCCAC 57.147 47.619 0.00 0.00 0.00 4.02
277 278 2.764010 GGGAAGAGTCCTTTCTCTCTCC 59.236 54.545 12.18 12.18 43.03 3.71
350 351 2.743636 AAAAGAAGGAGATCACGCGA 57.256 45.000 15.93 0.00 0.00 5.87
439 440 1.002746 TCCTTGCAACTATGGCGCA 60.003 52.632 10.83 0.00 0.00 6.09
444 445 2.359900 GGTGAGGTCCTTGCAACTATG 58.640 52.381 0.00 0.00 0.00 2.23
447 448 1.456287 GGGTGAGGTCCTTGCAACT 59.544 57.895 0.00 0.00 0.00 3.16
448 449 1.966451 CGGGTGAGGTCCTTGCAAC 60.966 63.158 0.00 0.00 0.00 4.17
449 450 2.429930 CGGGTGAGGTCCTTGCAA 59.570 61.111 0.00 0.00 0.00 4.08
450 451 4.329545 GCGGGTGAGGTCCTTGCA 62.330 66.667 0.00 0.00 0.00 4.08
451 452 3.842925 TTGCGGGTGAGGTCCTTGC 62.843 63.158 0.00 0.00 0.00 4.01
452 453 0.821711 TTTTGCGGGTGAGGTCCTTG 60.822 55.000 0.00 0.00 0.00 3.61
453 454 0.106419 TTTTTGCGGGTGAGGTCCTT 60.106 50.000 0.00 0.00 0.00 3.36
454 455 1.534697 TTTTTGCGGGTGAGGTCCT 59.465 52.632 0.00 0.00 0.00 3.85
455 456 4.167597 TTTTTGCGGGTGAGGTCC 57.832 55.556 0.00 0.00 0.00 4.46
495 496 8.697292 GGACATAAGTAGAGATCCTTGTAACTT 58.303 37.037 0.00 0.00 0.00 2.66
529 530 6.349280 GCATTGTACAACACTAATCACCACAT 60.349 38.462 11.22 0.00 0.00 3.21
538 539 3.729966 TGACGGCATTGTACAACACTAA 58.270 40.909 11.22 0.00 0.00 2.24
554 753 8.512138 AGTAATTCTTCCTAAAAATGTTGACGG 58.488 33.333 0.00 0.00 0.00 4.79
570 769 9.362539 TGAAGAAACGTGGTATAGTAATTCTTC 57.637 33.333 18.36 18.36 45.78 2.87
648 847 2.701780 CCCTGTGAGACCCGACGAG 61.702 68.421 0.00 0.00 0.00 4.18
654 853 2.657237 CGTGACCCTGTGAGACCC 59.343 66.667 0.00 0.00 0.00 4.46
762 962 2.683933 GGCCCGAGACAGGAGGAA 60.684 66.667 0.00 0.00 0.00 3.36
828 1028 4.402528 TCCGGGGACAATGGCACG 62.403 66.667 0.00 0.00 0.00 5.34
1398 1619 5.812127 TGTCAGATCAGACCGAAATATTGTG 59.188 40.000 14.91 0.00 37.73 3.33
1574 1795 2.811317 CTCGCGACAGAGCAACCC 60.811 66.667 3.71 0.00 36.85 4.11
1884 2105 2.028733 CGGGTTTGCTTGGCATTGC 61.029 57.895 0.00 0.00 38.76 3.56
1943 2164 1.519719 CTCTGCGGAAGGGAAGAGG 59.480 63.158 0.00 0.00 33.91 3.69
1952 2173 0.250234 CCATCTTCACCTCTGCGGAA 59.750 55.000 0.00 0.00 36.31 4.30
2168 2392 1.208535 TGGTTACTTGGGCGATTCGAT 59.791 47.619 10.88 0.00 0.00 3.59
2176 2400 3.060000 GGCGGTGGTTACTTGGGC 61.060 66.667 0.00 0.00 0.00 5.36
2191 2415 3.104766 CGGCATGACATGACAGGC 58.895 61.111 23.22 23.22 45.01 4.85
2208 2432 1.237285 ATCTGGAGTGTGTTTGGCGC 61.237 55.000 0.00 0.00 0.00 6.53
2246 2470 1.228862 GAACAGTTGGGGTGGCCAT 60.229 57.895 9.72 0.00 0.00 4.40
2326 2560 4.394795 CGAGAAAACAACAAGGCTTATCG 58.605 43.478 0.00 0.00 0.00 2.92
2334 2568 0.941542 TCCGGCGAGAAAACAACAAG 59.058 50.000 9.30 0.00 0.00 3.16
2337 2571 0.942252 AACTCCGGCGAGAAAACAAC 59.058 50.000 9.30 0.00 38.52 3.32
2774 3027 0.246635 CTACCACCACCGGTTCTCTG 59.753 60.000 2.97 0.00 40.67 3.35
2841 3094 3.552890 GCAAAAATCACTCCAGGGAACAC 60.553 47.826 0.00 0.00 0.00 3.32
2926 3185 6.720748 CACATCCCAATATATTCATCCACCAA 59.279 38.462 0.00 0.00 0.00 3.67
3022 3281 5.584649 TCAAAACAGAAGCGAGAAGAAAGAA 59.415 36.000 0.00 0.00 0.00 2.52
3030 3290 4.876107 AGACTTTTCAAAACAGAAGCGAGA 59.124 37.500 0.00 0.00 0.00 4.04
3035 3295 6.075205 CGCATGAAGACTTTTCAAAACAGAAG 60.075 38.462 0.00 0.00 31.55 2.85
3059 3319 5.346551 TCAACATACAAAATCTCACGTACCG 59.653 40.000 0.00 0.00 0.00 4.02
3060 3320 6.715344 TCAACATACAAAATCTCACGTACC 57.285 37.500 0.00 0.00 0.00 3.34
3068 3331 6.040842 ACTGGCAACTTCAACATACAAAATCT 59.959 34.615 0.00 0.00 37.61 2.40
3079 3342 2.223572 CCAGAACACTGGCAACTTCAAC 60.224 50.000 3.31 0.00 43.51 3.18
3158 3426 2.211532 TCTACAGAGCCCAGTACCCTA 58.788 52.381 0.00 0.00 0.00 3.53
3194 3463 6.646653 CACCCTTGCTTATTTTCTTTCTTTCC 59.353 38.462 0.00 0.00 0.00 3.13
3207 3476 1.821216 CGTTGACCACCCTTGCTTAT 58.179 50.000 0.00 0.00 0.00 1.73
3208 3477 0.887387 GCGTTGACCACCCTTGCTTA 60.887 55.000 0.00 0.00 0.00 3.09
3211 3480 2.904866 TGCGTTGACCACCCTTGC 60.905 61.111 0.00 0.00 0.00 4.01
3279 3553 1.736126 GTCTGCCCGTAAAGGTAAAGC 59.264 52.381 0.00 0.00 38.74 3.51
3416 3692 2.511659 TGCACTCTTCGTAGTGGTAGT 58.488 47.619 14.14 0.00 45.75 2.73
3438 3714 1.009389 GCAGTGTCACGAGTAGCACC 61.009 60.000 0.00 0.00 32.75 5.01
3557 3840 1.032114 GTTCCTACAGGCATGGTGGC 61.032 60.000 2.31 0.00 44.10 5.01
3591 3874 1.474077 CCACATGTAAGCCTGCTTTCC 59.526 52.381 10.01 2.33 37.47 3.13



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

AutoCloner maintained by Alex Coulton.