Multiple sequence alignment - TraesCS5A01G227900

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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 TraesCS5A01G227900 chr5A 100.000 4424 0 0 1 4424 444526329 444530752 0.000000e+00 8170
1 TraesCS5A01G227900 chr5B 94.872 4232 151 31 241 4424 403701992 403706205 0.000000e+00 6553
2 TraesCS5A01G227900 chr5B 88.889 567 48 9 1 562 403701439 403701995 0.000000e+00 684
3 TraesCS5A01G227900 chr5D 96.801 3564 77 6 873 4424 347449854 347446316 0.000000e+00 5915
4 TraesCS5A01G227900 chr5D 85.795 352 24 5 1 350 347478378 347478051 2.530000e-92 350
5 TraesCS5A01G227900 chr5D 91.892 222 10 5 514 733 347450165 347449950 2.000000e-78 303
6 TraesCS5A01G227900 chr5D 91.333 150 10 2 367 516 347475327 347475181 7.500000e-48 202
7 TraesCS5A01G227900 chr3A 89.777 851 61 16 2813 3645 431818533 431819375 0.000000e+00 1066
8 TraesCS5A01G227900 chr3A 92.105 342 18 2 2355 2696 431818071 431818403 1.440000e-129 473
9 TraesCS5A01G227900 chr3A 95.376 173 8 0 3640 3812 431819511 431819683 4.360000e-70 276
10 TraesCS5A01G227900 chr3D 91.678 769 47 11 2816 3574 302934439 302933678 0.000000e+00 1050
11 TraesCS5A01G227900 chr3D 91.291 333 19 4 2358 2689 302935070 302934747 3.140000e-121 446
12 TraesCS5A01G227900 chr3D 91.632 239 14 4 3576 3812 302933510 302933276 4.270000e-85 326
13 TraesCS5A01G227900 chr3D 93.458 107 4 2 571 674 26467757 26467863 5.920000e-34 156
14 TraesCS5A01G227900 chr3B 94.545 110 2 4 563 671 44789065 44789171 2.740000e-37 167
15 TraesCS5A01G227900 chr3B 95.050 101 4 1 571 671 44755849 44755750 1.650000e-34 158
16 TraesCS5A01G227900 chr1B 95.283 106 3 2 572 676 509565970 509566074 2.740000e-37 167
17 TraesCS5A01G227900 chr2D 97.849 93 2 0 590 682 107696213 107696121 1.270000e-35 161
18 TraesCS5A01G227900 chr7D 93.578 109 4 3 569 674 507304301 507304409 4.580000e-35 159
19 TraesCS5A01G227900 chr7A 97.849 93 0 1 582 674 572874544 572874634 4.580000e-35 159


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 TraesCS5A01G227900 chr5A 444526329 444530752 4423 False 8170.000000 8170 100.000000 1 4424 1 chr5A.!!$F1 4423
1 TraesCS5A01G227900 chr5B 403701439 403706205 4766 False 3618.500000 6553 91.880500 1 4424 2 chr5B.!!$F1 4423
2 TraesCS5A01G227900 chr5D 347446316 347450165 3849 True 3109.000000 5915 94.346500 514 4424 2 chr5D.!!$R1 3910
3 TraesCS5A01G227900 chr5D 347475181 347478378 3197 True 276.000000 350 88.564000 1 516 2 chr5D.!!$R2 515
4 TraesCS5A01G227900 chr3A 431818071 431819683 1612 False 605.000000 1066 92.419333 2355 3812 3 chr3A.!!$F1 1457
5 TraesCS5A01G227900 chr3D 302933276 302935070 1794 True 607.333333 1050 91.533667 2358 3812 3 chr3D.!!$R1 1454

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
913 3985 0.040958 CAAGTGCAGAAGTTCACCGC 60.041 55.0 5.5 5.39 33.9 5.68 F
1701 4785 1.195442 TGCCGGTCTGGAATGTGGTA 61.195 55.0 1.9 0.00 42.0 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1783 4867 0.249699 TTGTTGATCGACACGCCACT 60.25 50.0 15.65 0.0 0.00 4.00 R
3499 6858 0.749649 CTCAGAACTCCCCGAGATGG 59.25 60.0 0.00 0.0 33.32 3.51 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
32 35 5.540337 TCATGGTAATGTTTGGCCAAGTTTA 59.460 36.000 19.48 14.25 35.15 2.01
35 38 7.540474 TGGTAATGTTTGGCCAAGTTTATAA 57.460 32.000 19.48 0.00 0.00 0.98
73 76 9.396022 ACCACAATACCAAATTAATCTCTACTG 57.604 33.333 0.00 0.00 0.00 2.74
109 112 9.039870 TCAACAACAATCAAATAAATCACCAAC 57.960 29.630 0.00 0.00 0.00 3.77
114 117 6.869913 ACAATCAAATAAATCACCAACAGCAG 59.130 34.615 0.00 0.00 0.00 4.24
131 134 1.973138 CAGGAAATCACTTGCAAGCG 58.027 50.000 26.27 17.45 0.00 4.68
137 140 3.648339 AATCACTTGCAAGCGAACAAT 57.352 38.095 26.27 4.40 0.00 2.71
178 183 7.833786 AGTTGCATGTACAAAATCTCAATCAT 58.166 30.769 0.00 0.00 0.00 2.45
230 235 7.866898 CCTCACAACATATCTCTATCTCAACTG 59.133 40.741 0.00 0.00 0.00 3.16
258 263 4.841443 AAATTTCCTACGTTGAACCACC 57.159 40.909 0.00 0.00 0.00 4.61
280 286 4.866486 CCAGAATAAAGTTGCTTCCATTGC 59.134 41.667 0.00 0.00 0.00 3.56
357 1537 5.416083 TGCAACACACGAGTATTTAGCTAT 58.584 37.500 0.00 0.00 0.00 2.97
358 1538 5.518847 TGCAACACACGAGTATTTAGCTATC 59.481 40.000 0.00 0.00 0.00 2.08
381 3094 5.890419 TCAGTAGCTCTCATTGAGATGAAGA 59.110 40.000 16.48 7.88 45.39 2.87
399 3112 4.455533 TGAAGATGTACATGTGGAAGTTGC 59.544 41.667 14.43 0.00 0.00 4.17
557 3577 9.061435 GGATGAGAAAGGGCATATATAATTAGC 57.939 37.037 0.00 0.00 0.00 3.09
677 3709 0.379669 CGGCCATCTTGACTTGATGC 59.620 55.000 2.24 0.00 39.76 3.91
706 3738 5.921976 TGTCTGCAATCAAGCTAAACATTTG 59.078 36.000 0.00 0.00 34.99 2.32
707 3739 4.925054 TCTGCAATCAAGCTAAACATTTGC 59.075 37.500 0.00 0.00 38.68 3.68
708 3740 4.629092 TGCAATCAAGCTAAACATTTGCA 58.371 34.783 12.48 12.48 43.84 4.08
745 3778 5.049129 GGCTACCATTCTTATTAGCAGCAAG 60.049 44.000 0.00 0.00 39.00 4.01
758 3791 2.860062 GCAGCAAGCACTAACATCTTG 58.140 47.619 0.00 0.00 44.79 3.02
760 3793 3.076621 CAGCAAGCACTAACATCTTGGA 58.923 45.455 0.00 0.00 38.05 3.53
761 3794 3.693085 CAGCAAGCACTAACATCTTGGAT 59.307 43.478 0.00 0.00 38.05 3.41
762 3795 3.944015 AGCAAGCACTAACATCTTGGATC 59.056 43.478 0.00 0.00 38.05 3.36
763 3796 3.944015 GCAAGCACTAACATCTTGGATCT 59.056 43.478 0.00 0.00 38.05 2.75
764 3797 5.104776 AGCAAGCACTAACATCTTGGATCTA 60.105 40.000 0.00 0.00 38.05 1.98
765 3798 5.236047 GCAAGCACTAACATCTTGGATCTAG 59.764 44.000 0.00 0.00 38.05 2.43
766 3799 6.577103 CAAGCACTAACATCTTGGATCTAGA 58.423 40.000 0.00 0.00 34.98 2.43
767 3800 6.403866 AGCACTAACATCTTGGATCTAGAG 57.596 41.667 0.00 0.00 0.00 2.43
825 3896 4.911390 AGTAGGCTAGACTTGCATGTTTT 58.089 39.130 1.68 1.81 0.00 2.43
857 3929 1.825474 ACATAGACACTAGCAAGCCGT 59.175 47.619 0.00 0.00 0.00 5.68
858 3930 3.021695 ACATAGACACTAGCAAGCCGTA 58.978 45.455 0.00 0.00 0.00 4.02
859 3931 3.066900 ACATAGACACTAGCAAGCCGTAG 59.933 47.826 0.00 0.00 0.00 3.51
860 3932 1.546961 AGACACTAGCAAGCCGTAGT 58.453 50.000 0.00 0.00 0.00 2.73
884 3956 1.608717 GACAGACACTCCCATCGCCT 61.609 60.000 0.00 0.00 0.00 5.52
913 3985 0.040958 CAAGTGCAGAAGTTCACCGC 60.041 55.000 5.50 5.39 33.90 5.68
951 4023 4.680237 CTCAACCACGCGCCCTCA 62.680 66.667 5.73 0.00 0.00 3.86
1191 4275 2.678934 AGCCAGTTCGCCTACGGA 60.679 61.111 0.00 0.00 40.63 4.69
1500 4584 3.672295 CTCCTGCGAGCCCAACTCC 62.672 68.421 0.00 0.00 43.01 3.85
1515 4599 2.299297 CAACTCCTTCACTTACTCCGGT 59.701 50.000 0.00 0.00 0.00 5.28
1569 4653 2.045926 GTCGGGAAGGCAGTGCAT 60.046 61.111 18.61 7.05 0.00 3.96
1635 4719 1.487482 CGGCGATCGTCAACATGTAT 58.513 50.000 21.12 0.00 0.00 2.29
1690 4774 1.306141 TTCTGGAGGATGCCGGTCT 60.306 57.895 1.90 0.00 35.72 3.85
1701 4785 1.195442 TGCCGGTCTGGAATGTGGTA 61.195 55.000 1.90 0.00 42.00 3.25
1728 4812 2.358247 ACCGCGATCGCTGGTTTT 60.358 55.556 34.84 21.55 42.17 2.43
1747 4831 3.714001 TGCAGCAGGAGGAGCCAG 61.714 66.667 0.00 0.00 40.02 4.85
1783 4867 1.133482 TGCTCAGAGATATGGTCCGGA 60.133 52.381 0.00 0.00 0.00 5.14
1785 4869 2.870175 CTCAGAGATATGGTCCGGAGT 58.130 52.381 3.06 0.00 0.00 3.85
1938 5022 3.137913 AGGAGGCTTTGATCTGCACATAT 59.862 43.478 0.00 0.00 0.00 1.78
1977 5061 2.169769 TGAGTTGTCCGAGAAGGTGTTT 59.830 45.455 0.00 0.00 41.99 2.83
2040 5124 7.724506 TCGACTTTCATATCTGGGATTAGTAGT 59.275 37.037 0.00 0.00 0.00 2.73
2271 5355 3.009473 TGGAAGATAGCTGCAAGGTCTTT 59.991 43.478 1.02 0.00 44.61 2.52
2442 5526 3.334583 TCAGCTTGTAATGGACCAGAC 57.665 47.619 0.00 1.04 0.00 3.51
2445 5529 4.716784 TCAGCTTGTAATGGACCAGACTAT 59.283 41.667 0.00 0.00 0.00 2.12
2475 5559 2.040412 AGGGAAGGAAGTTCATGGACAC 59.960 50.000 6.96 0.00 36.82 3.67
2534 5618 5.177327 GCACTTGTTTGGTTTCCATGTATTG 59.823 40.000 0.00 0.00 31.53 1.90
2659 5743 1.741732 GCACTGACGAGGCAATCTCAT 60.742 52.381 0.00 0.00 42.55 2.90
2780 6036 7.563188 TGGAAAACTATTACATGGGTATGCAAT 59.437 33.333 0.00 0.00 37.85 3.56
3011 6360 6.093633 GGAGTGAAACCAGATAATGTTGTACC 59.906 42.308 0.00 0.00 37.80 3.34
3205 6554 2.370189 AGTATGCCTATGAAGCCTGACC 59.630 50.000 0.00 0.00 0.00 4.02
3281 6630 9.146984 TGTACTTGGACGATTTGTAGAAAATAG 57.853 33.333 0.00 0.00 0.00 1.73
3392 6741 6.721208 AGAGTCAGAAAATCATTAAAGGGCAA 59.279 34.615 0.00 0.00 0.00 4.52
3393 6742 7.233348 AGAGTCAGAAAATCATTAAAGGGCAAA 59.767 33.333 0.00 0.00 0.00 3.68
3499 6858 8.671921 ACATTGACTGAGATGAAATAATGACAC 58.328 33.333 0.00 0.00 0.00 3.67
3939 7607 3.598019 AATGTACAAGGGCAATTGCTG 57.402 42.857 28.42 21.07 41.70 4.41
4033 7701 3.036819 AGCAGCTATTGGACATCTCTCA 58.963 45.455 0.00 0.00 0.00 3.27
4100 7768 9.730705 GGATATCCAATCATCTGAAGAATGTAA 57.269 33.333 17.34 0.00 35.64 2.41
4242 7910 4.034048 GTGTCTATAACCCAATCAACTGCG 59.966 45.833 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.540474 TTATAAACTTGGCCAAACATTACCA 57.460 32.000 20.91 7.83 0.00 3.25
109 112 2.925306 GCTTGCAAGTGATTTCCTGCTG 60.925 50.000 26.55 0.00 0.00 4.41
114 117 2.287547 TGTTCGCTTGCAAGTGATTTCC 60.288 45.455 35.96 24.85 44.24 3.13
178 183 7.963532 AGGCGAAGGTAAAGAAAGATATGATA 58.036 34.615 0.00 0.00 0.00 2.15
191 196 1.344065 TGTGAGGAGGCGAAGGTAAA 58.656 50.000 0.00 0.00 0.00 2.01
199 204 2.363680 AGAGATATGTTGTGAGGAGGCG 59.636 50.000 0.00 0.00 0.00 5.52
230 235 6.199531 GGTTCAACGTAGGAAATTTTTGGTTC 59.800 38.462 4.36 0.00 0.00 3.62
258 263 5.472148 TGCAATGGAAGCAACTTTATTCTG 58.528 37.500 0.00 0.00 39.39 3.02
357 1537 5.890419 TCTTCATCTCAATGAGAGCTACTGA 59.110 40.000 18.49 13.26 42.26 3.41
358 1538 6.146601 TCTTCATCTCAATGAGAGCTACTG 57.853 41.667 18.49 11.20 42.26 2.74
370 3083 6.298441 TCCACATGTACATCTTCATCTCAA 57.702 37.500 5.07 0.00 0.00 3.02
381 3094 6.434028 AGTTAATGCAACTTCCACATGTACAT 59.566 34.615 1.41 1.41 45.54 2.29
487 3201 5.928976 TCAGAGTTCTCTTTTCACAATCCA 58.071 37.500 0.00 0.00 0.00 3.41
524 3238 4.657814 TGCCCTTTCTCATCCTAGTTTT 57.342 40.909 0.00 0.00 0.00 2.43
577 3597 6.878923 CCCACTCTTGACATACAGTTTTCATA 59.121 38.462 0.00 0.00 0.00 2.15
579 3599 5.063204 CCCACTCTTGACATACAGTTTTCA 58.937 41.667 0.00 0.00 0.00 2.69
677 3709 2.434428 AGCTTGATTGCAGACAAGAGG 58.566 47.619 27.24 11.40 43.98 3.69
706 3738 1.033746 TAGCCCTCATTGCTGCTTGC 61.034 55.000 0.00 0.00 39.91 4.01
707 3739 0.737219 GTAGCCCTCATTGCTGCTTG 59.263 55.000 0.00 0.00 39.91 4.01
708 3740 0.394899 GGTAGCCCTCATTGCTGCTT 60.395 55.000 0.00 0.00 40.71 3.91
745 3778 6.155475 ACTCTAGATCCAAGATGTTAGTGC 57.845 41.667 0.00 0.00 0.00 4.40
752 3785 9.695526 CAAGAAATCTACTCTAGATCCAAGATG 57.304 37.037 0.00 0.00 44.44 2.90
753 3786 9.653516 TCAAGAAATCTACTCTAGATCCAAGAT 57.346 33.333 0.00 0.00 44.44 2.40
754 3787 9.130661 CTCAAGAAATCTACTCTAGATCCAAGA 57.869 37.037 0.00 0.00 44.44 3.02
755 3788 9.130661 TCTCAAGAAATCTACTCTAGATCCAAG 57.869 37.037 0.00 0.00 44.44 3.61
857 3929 1.340405 GGGAGTGTCTGTCCCGTACTA 60.340 57.143 0.00 0.00 44.54 1.82
858 3930 0.611340 GGGAGTGTCTGTCCCGTACT 60.611 60.000 0.00 0.00 44.54 2.73
859 3931 1.888736 GGGAGTGTCTGTCCCGTAC 59.111 63.158 0.00 0.00 44.54 3.67
860 3932 4.428845 GGGAGTGTCTGTCCCGTA 57.571 61.111 0.00 0.00 44.54 4.02
871 3943 1.533625 TTTTCAAGGCGATGGGAGTG 58.466 50.000 0.00 0.00 0.00 3.51
884 3956 7.063308 GTGAACTTCTGCACTTGAATTTTTCAA 59.937 33.333 2.96 2.96 46.68 2.69
902 3974 3.119096 GCCTCGGCGGTGAACTTC 61.119 66.667 7.21 0.00 34.25 3.01
946 4018 1.450312 GATGCAACCGGAGTGAGGG 60.450 63.158 9.46 0.00 0.00 4.30
951 4023 2.933287 TGGGGATGCAACCGGAGT 60.933 61.111 9.46 0.00 0.00 3.85
957 4029 2.679996 GTGGGGTGGGGATGCAAC 60.680 66.667 0.00 0.00 0.00 4.17
991 4063 3.838271 TGGAGGCATCGAGACGGC 61.838 66.667 0.00 0.00 0.00 5.68
1500 4584 1.893801 AGGACACCGGAGTAAGTGAAG 59.106 52.381 9.46 0.00 37.43 3.02
1635 4719 0.104120 CCATATCACCCGACTTCGCA 59.896 55.000 0.00 0.00 38.18 5.10
1690 4774 1.843851 GGTCCAGGATACCACATTCCA 59.156 52.381 0.00 0.00 36.96 3.53
1701 4785 2.764128 ATCGCGGTGGTCCAGGAT 60.764 61.111 6.13 0.00 0.00 3.24
1728 4812 4.025858 GGCTCCTCCTGCTGCACA 62.026 66.667 0.00 0.00 0.00 4.57
1747 4831 3.188786 CAGCCGAACAGCGCCTAC 61.189 66.667 2.29 0.00 39.11 3.18
1752 4836 3.485431 CTGAGCAGCCGAACAGCG 61.485 66.667 0.00 0.00 35.59 5.18
1783 4867 0.249699 TTGTTGATCGACACGCCACT 60.250 50.000 15.65 0.00 0.00 4.00
1785 4869 1.518325 ATTTGTTGATCGACACGCCA 58.482 45.000 15.65 0.00 0.00 5.69
1938 5022 5.582950 ACTCAATAGCCCCAATATTAGCA 57.417 39.130 6.96 0.00 0.00 3.49
1977 5061 3.181455 TGCTTACTCTGCCAACTTCTTCA 60.181 43.478 0.00 0.00 0.00 3.02
2040 5124 6.724893 TGAATTGATCTCGGTAGGTTATGA 57.275 37.500 0.00 0.00 0.00 2.15
2271 5355 1.073125 TCCCGTTCCTGCATTTCTTCA 59.927 47.619 0.00 0.00 0.00 3.02
2385 5469 2.359900 GACACATGGTCAGGCTTAAGG 58.640 52.381 4.29 0.00 46.19 2.69
2442 5526 5.012893 ACTTCCTTCCCTTTGAGCAAATAG 58.987 41.667 0.00 0.00 0.00 1.73
2445 5529 3.312736 ACTTCCTTCCCTTTGAGCAAA 57.687 42.857 0.00 0.00 0.00 3.68
2475 5559 6.102663 AGTTTCTCCATAGACACGAAGAATG 58.897 40.000 0.00 0.00 37.48 2.67
2534 5618 5.090652 TGTTTGTACTTCTCGACATTTGC 57.909 39.130 0.00 0.00 0.00 3.68
2659 5743 5.135383 AGCTGCCATCATAAGCTGAAATAA 58.865 37.500 0.00 0.00 45.36 1.40
2780 6036 5.663106 AGATCAGACAGTATTCCTGCCTTAA 59.337 40.000 0.00 0.00 45.68 1.85
2814 6155 4.122776 AGTACAGCTTCACAAGTGAACTG 58.877 43.478 25.96 25.96 43.90 3.16
3011 6360 6.426980 TGCAAGCAGATAAAATACTCACTG 57.573 37.500 0.00 0.00 0.00 3.66
3205 6554 2.558378 CAGTGTGCTCCATACCATCAG 58.442 52.381 0.00 0.00 0.00 2.90
3281 6630 7.383687 TGGGTCATAATTATCTTCACGTATCC 58.616 38.462 0.00 0.00 0.00 2.59
3392 6741 4.734266 ACTCAATCCAGGCTCTTTCTTTT 58.266 39.130 0.00 0.00 0.00 2.27
3393 6742 4.379302 ACTCAATCCAGGCTCTTTCTTT 57.621 40.909 0.00 0.00 0.00 2.52
3457 6816 2.488937 CAATGTACTGTGCTGCATTCCA 59.511 45.455 5.27 0.00 30.17 3.53
3499 6858 0.749649 CTCAGAACTCCCCGAGATGG 59.250 60.000 0.00 0.00 33.32 3.51
3579 7104 5.433526 ACAGTGTAAAAAGGCTCAACAGTA 58.566 37.500 0.00 0.00 0.00 2.74
3939 7607 5.105997 ACCTTCATTTGCTAGCATTTCTGTC 60.106 40.000 20.13 0.00 0.00 3.51
4004 7672 1.831106 TCCAATAGCTGCTCGAAGGAA 59.169 47.619 4.91 0.00 0.00 3.36
4005 7673 1.137086 GTCCAATAGCTGCTCGAAGGA 59.863 52.381 4.91 7.19 0.00 3.36
4033 7701 0.551131 AATTGTCCCCCTGCCTCTCT 60.551 55.000 0.00 0.00 0.00 3.10
4242 7910 0.865769 CTGAACAGTGCAACGGGTAC 59.134 55.000 0.00 0.00 45.86 3.34


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

AutoCloner maintained by Alex Coulton.