Multiple sequence alignment - TraesCS1A01G388400

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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 TraesCS1A01G388400 chr1A 100.000 6092 0 0 1 6092 556943747 556937656 0.000000e+00 11250.0
1 TraesCS1A01G388400 chr1A 89.730 185 13 3 4507 4691 556830464 556830286 1.320000e-56 231.0
2 TraesCS1A01G388400 chr1A 82.178 101 16 2 5958 6058 182151424 182151522 1.090000e-12 86.1
3 TraesCS1A01G388400 chr1B 92.935 6129 226 82 1 6040 640850700 640844690 0.000000e+00 8728.0
4 TraesCS1A01G388400 chr1B 93.238 281 16 1 5807 6087 599175857 599175580 1.580000e-110 411.0
5 TraesCS1A01G388400 chr1B 89.811 265 14 5 416 669 640850348 640850086 1.640000e-85 327.0
6 TraesCS1A01G388400 chr1B 87.719 57 3 2 377 429 640850279 640850223 5.100000e-06 63.9
7 TraesCS1A01G388400 chr1D 96.795 3494 70 7 1 3479 464598703 464595237 0.000000e+00 5794.0
8 TraesCS1A01G388400 chr1D 95.496 2065 67 14 3472 5527 464595204 464593157 0.000000e+00 3275.0
9 TraesCS1A01G388400 chr1D 94.000 450 22 2 5643 6092 464593083 464592639 0.000000e+00 676.0
10 TraesCS1A01G388400 chr1D 90.909 143 13 0 4549 4691 464404888 464404746 6.230000e-45 193.0
11 TraesCS1A01G388400 chr1D 84.524 168 24 2 5662 5829 464631070 464631235 1.360000e-36 165.0
12 TraesCS1A01G388400 chr1D 81.319 91 13 3 5956 6044 178833133 178833221 3.050000e-08 71.3
13 TraesCS1A01G388400 chr2D 84.337 498 47 15 1 483 627820506 627820987 5.560000e-125 459.0
14 TraesCS1A01G388400 chr2D 84.800 250 33 4 418 664 627820866 627821113 4.720000e-61 246.0
15 TraesCS1A01G388400 chr5A 90.270 185 15 1 4507 4691 412229902 412230083 7.890000e-59 239.0
16 TraesCS1A01G388400 chr4A 87.363 182 14 4 4507 4685 538724706 538724881 3.720000e-47 200.0
17 TraesCS1A01G388400 chr2B 88.710 62 5 2 370 429 770068988 770069049 2.350000e-09 75.0


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 TraesCS1A01G388400 chr1A 556937656 556943747 6091 True 11250.000000 11250 100.000000 1 6092 1 chr1A.!!$R2 6091
1 TraesCS1A01G388400 chr1B 640844690 640850700 6010 True 3039.633333 8728 90.155000 1 6040 3 chr1B.!!$R2 6039
2 TraesCS1A01G388400 chr1D 464592639 464598703 6064 True 3248.333333 5794 95.430333 1 6092 3 chr1D.!!$R2 6091
3 TraesCS1A01G388400 chr2D 627820506 627821113 607 False 352.500000 459 84.568500 1 664 2 chr2D.!!$F1 663

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
511 531 0.319040 TCAGACAGCGACTGTTCTGC 60.319 55.000 20.64 9.53 45.44 4.26 F
701 760 1.839354 TGCTATCTTGGCACATCTCCA 59.161 47.619 0.00 0.00 39.30 3.86 F
1626 1704 3.264193 TGCATGTGAACTGGATAACCTCT 59.736 43.478 0.00 0.00 37.04 3.69 F
1944 2022 0.842635 TTTGGCCAGGGCAATTTGTT 59.157 45.000 28.16 0.00 46.84 2.83 F
3508 3637 1.561076 TCCACAGGACAGCATAGCATT 59.439 47.619 0.00 0.00 0.00 3.56 F
3925 4060 0.326264 ATCACTTGTCTGCAGGGACC 59.674 55.000 15.13 0.18 35.54 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 1704 0.467384 CACCCCAAACATTTGCCACA 59.533 50.000 0.00 0.00 36.86 4.17 R
1743 1821 1.202663 CCATCATGACCAGCAGAGAGG 60.203 57.143 0.00 0.00 0.00 3.69 R
3486 3615 0.539051 GCTATGCTGTCCTGTGGAGT 59.461 55.000 0.00 0.00 29.39 3.85 R
3614 3745 4.218635 AGCTTGATCAACTTCTCGTACTCA 59.781 41.667 3.38 0.00 0.00 3.41 R
4355 4492 0.393537 CAGTCCCTGCCCATGTCTTC 60.394 60.000 0.00 0.00 0.00 2.87 R
5715 5916 0.108089 TACTACCACGGCCGTACGTA 60.108 55.000 33.70 29.33 46.75 3.57 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
233 234 1.940613 GAACAGTCGTTGGTTGCTCTT 59.059 47.619 0.00 0.00 34.75 2.85
247 248 3.627395 TGCTCTTGGGACGAATATTGT 57.373 42.857 0.00 0.00 0.00 2.71
275 276 3.327757 GGGTGGTGGCATATTCTCTGATA 59.672 47.826 0.00 0.00 0.00 2.15
342 362 5.125100 GAAATCATTTCCTGTGACAAGCA 57.875 39.130 0.00 0.00 33.56 3.91
343 363 5.531634 GAAATCATTTCCTGTGACAAGCAA 58.468 37.500 0.00 0.00 33.56 3.91
344 364 5.733620 AATCATTTCCTGTGACAAGCAAT 57.266 34.783 0.00 0.00 0.00 3.56
345 365 5.733620 ATCATTTCCTGTGACAAGCAATT 57.266 34.783 0.00 0.00 0.00 2.32
346 366 5.125100 TCATTTCCTGTGACAAGCAATTC 57.875 39.130 0.00 0.00 0.00 2.17
511 531 0.319040 TCAGACAGCGACTGTTCTGC 60.319 55.000 20.64 9.53 45.44 4.26
701 760 1.839354 TGCTATCTTGGCACATCTCCA 59.161 47.619 0.00 0.00 39.30 3.86
914 989 3.383505 AGCTTGTTACAAAAAGGTGGGAC 59.616 43.478 0.00 0.00 33.10 4.46
1158 1236 6.981722 TGATTTCCTTACTTTTGAAAGAGGC 58.018 36.000 10.26 0.00 39.31 4.70
1626 1704 3.264193 TGCATGTGAACTGGATAACCTCT 59.736 43.478 0.00 0.00 37.04 3.69
1944 2022 0.842635 TTTGGCCAGGGCAATTTGTT 59.157 45.000 28.16 0.00 46.84 2.83
2420 2500 7.789831 ACCCATCTTTTCTAGATACATGGTCTA 59.210 37.037 14.47 3.88 41.78 2.59
2468 2548 4.018506 TCTCCCTTGTATCAATTTCAGGCA 60.019 41.667 0.00 0.00 0.00 4.75
2572 2652 1.609208 GAGGCTGAGCAGGAAACAAA 58.391 50.000 6.82 0.00 0.00 2.83
2751 2831 6.619801 TTCTACTTCTCCAAAACAGCTTTC 57.380 37.500 0.00 0.00 0.00 2.62
2891 2971 8.375506 AGATCAAGTTGTGGTTTCAGATTACTA 58.624 33.333 2.11 0.00 0.00 1.82
3251 3331 8.877864 ATCTTACAAAATGATTTACCAGGTCA 57.122 30.769 0.00 0.00 0.00 4.02
3254 3334 9.226606 CTTACAAAATGATTTACCAGGTCAGTA 57.773 33.333 0.00 0.00 0.00 2.74
3486 3615 7.406031 TGGTTTGTGGTTAAAATGTTCTACA 57.594 32.000 0.00 0.00 0.00 2.74
3508 3637 1.561076 TCCACAGGACAGCATAGCATT 59.439 47.619 0.00 0.00 0.00 3.56
3694 3825 2.688507 ACAGAACATGCGTACTCTTGG 58.311 47.619 4.06 0.00 0.00 3.61
3712 3843 4.407621 TCTTGGGAGTTGTCAGTGTTCTTA 59.592 41.667 0.00 0.00 0.00 2.10
3782 3913 9.855021 ATTATGCAAACATTAGTAAGTGGAAAC 57.145 29.630 0.00 0.00 37.74 2.78
3783 3914 6.952773 TGCAAACATTAGTAAGTGGAAACT 57.047 33.333 0.00 0.00 0.00 2.66
3784 3915 6.966021 TGCAAACATTAGTAAGTGGAAACTC 58.034 36.000 0.00 0.00 0.00 3.01
3785 3916 6.544197 TGCAAACATTAGTAAGTGGAAACTCA 59.456 34.615 0.00 0.00 0.00 3.41
3786 3917 7.078228 GCAAACATTAGTAAGTGGAAACTCAG 58.922 38.462 0.00 0.00 0.00 3.35
3787 3918 7.255139 GCAAACATTAGTAAGTGGAAACTCAGT 60.255 37.037 0.00 0.00 0.00 3.41
3788 3919 9.268268 CAAACATTAGTAAGTGGAAACTCAGTA 57.732 33.333 0.00 0.00 0.00 2.74
3799 3930 5.527582 GTGGAAACTCAGTAACTCACACAAT 59.472 40.000 0.00 0.00 0.00 2.71
3925 4060 0.326264 ATCACTTGTCTGCAGGGACC 59.674 55.000 15.13 0.18 35.54 4.46
4047 4184 4.261572 GCTTACATGGTGTTCTTTGCTTCA 60.262 41.667 0.00 0.00 0.00 3.02
4355 4492 4.333926 GGCAAAGTATGTCTAAGCCTTCTG 59.666 45.833 0.00 0.00 40.65 3.02
4427 4564 4.252073 CTGTTCTTCAACTGCTGCTATCT 58.748 43.478 0.00 0.00 33.17 1.98
4613 4750 5.531287 GGTAAGTCACCAACTCTGTGAATTT 59.469 40.000 10.71 4.62 45.53 1.82
4650 4787 5.928976 TGACCTGAATATCCCATACACTTG 58.071 41.667 0.00 0.00 0.00 3.16
4722 4859 8.340443 GTTTTGAGTAGAACGTAAACCAAGATT 58.660 33.333 0.00 0.00 0.00 2.40
4723 4860 7.647907 TTGAGTAGAACGTAAACCAAGATTC 57.352 36.000 0.00 0.00 0.00 2.52
4724 4861 6.161381 TGAGTAGAACGTAAACCAAGATTCC 58.839 40.000 0.00 0.00 0.00 3.01
4725 4862 5.485620 AGTAGAACGTAAACCAAGATTCCC 58.514 41.667 0.00 0.00 0.00 3.97
4726 4863 3.682696 AGAACGTAAACCAAGATTCCCC 58.317 45.455 0.00 0.00 0.00 4.81
4727 4864 2.502142 ACGTAAACCAAGATTCCCCC 57.498 50.000 0.00 0.00 0.00 5.40
4756 4900 2.763039 TCTCAGATGCATCCCCTAACA 58.237 47.619 23.06 0.00 0.00 2.41
4773 4917 7.070322 TCCCCTAACAAACCTACATACAGTATC 59.930 40.741 0.00 0.00 30.93 2.24
4796 4940 4.773323 AAATAACTTCTGCTGCACCTTC 57.227 40.909 0.00 0.00 0.00 3.46
4963 5107 0.248661 CGATCTCGTCGGTCATGCTT 60.249 55.000 0.00 0.00 46.47 3.91
5028 5172 3.209410 GACCGGATTCAAGATCATGCTT 58.791 45.455 9.46 0.00 0.00 3.91
5199 5346 0.681887 TGCCTGGCACATGATCCTTG 60.682 55.000 19.30 0.00 38.20 3.61
5431 5585 3.631686 TGATGTGCCTGCAATAATACCAC 59.368 43.478 0.00 0.00 0.00 4.16
5432 5586 3.078891 TGTGCCTGCAATAATACCACA 57.921 42.857 0.00 0.00 0.00 4.17
5436 5590 3.016736 GCCTGCAATAATACCACAGTGT 58.983 45.455 0.00 0.00 0.00 3.55
5437 5591 3.181497 GCCTGCAATAATACCACAGTGTG 60.181 47.826 16.70 16.70 0.00 3.82
5439 5593 4.699735 CCTGCAATAATACCACAGTGTGAA 59.300 41.667 24.99 12.43 35.23 3.18
5589 5746 5.812642 GTCACACTAGTCATGTTCTAATGGG 59.187 44.000 0.00 8.58 0.00 4.00
5598 5755 5.009631 TCATGTTCTAATGGGTTGTTGGAG 58.990 41.667 0.00 0.00 0.00 3.86
5599 5756 3.761897 TGTTCTAATGGGTTGTTGGAGG 58.238 45.455 0.00 0.00 0.00 4.30
5600 5757 2.492088 GTTCTAATGGGTTGTTGGAGGC 59.508 50.000 0.00 0.00 0.00 4.70
5675 5876 2.923121 TCATGCTCAGCTAATCCAACC 58.077 47.619 0.00 0.00 0.00 3.77
5684 5885 5.116180 TCAGCTAATCCAACCGTATTTCTG 58.884 41.667 0.00 0.00 0.00 3.02
5689 5890 6.073222 GCTAATCCAACCGTATTTCTGTATGG 60.073 42.308 0.00 0.00 36.89 2.74
5715 5916 3.222354 GAGTCGCCCGAACACCAGT 62.222 63.158 0.00 0.00 0.00 4.00
5786 5987 7.921786 TGATGAATATGGAGTTTCTTTCGTT 57.078 32.000 0.00 0.00 0.00 3.85
5885 6089 5.229887 GCAAATTAAGCAACATATGGACGTG 59.770 40.000 7.80 0.98 0.00 4.49
5904 6108 3.059868 CGTGTTGCTTGTCGTGTTTCTAT 60.060 43.478 0.00 0.00 0.00 1.98
5928 6132 3.886505 ACTTTGTAGAAAAATGCGGGTCA 59.113 39.130 0.00 0.00 0.00 4.02
5933 6137 4.764823 TGTAGAAAAATGCGGGTCAAGAAT 59.235 37.500 0.00 0.00 0.00 2.40
5991 6195 6.877322 CGAAAAGGAAGATTACCCTTGACTTA 59.123 38.462 0.00 0.00 41.61 2.24
6058 6262 5.741388 ATCAAAGTGCGAATAACATCTCC 57.259 39.130 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
233 234 3.951037 CCCAATGAACAATATTCGTCCCA 59.049 43.478 0.00 0.00 0.00 4.37
247 248 2.844654 ATATGCCACCACCCAATGAA 57.155 45.000 0.00 0.00 0.00 2.57
275 276 4.897509 TGATCACCAGACATGAGAAGTT 57.102 40.909 0.00 0.00 0.00 2.66
342 362 6.607600 GGAGATTTGCCCTAAAACTAGGAATT 59.392 38.462 0.00 0.00 39.60 2.17
343 363 6.068794 AGGAGATTTGCCCTAAAACTAGGAAT 60.069 38.462 0.00 0.00 39.60 3.01
344 364 5.253096 AGGAGATTTGCCCTAAAACTAGGAA 59.747 40.000 0.00 0.00 39.60 3.36
345 365 4.788617 AGGAGATTTGCCCTAAAACTAGGA 59.211 41.667 0.00 0.00 39.60 2.94
346 366 5.117406 AGGAGATTTGCCCTAAAACTAGG 57.883 43.478 0.00 0.00 32.28 3.02
511 531 2.026449 AGGAGATTTGCCCAGAGAACTG 60.026 50.000 0.00 0.00 43.12 3.16
701 760 3.717294 CCCAGCCTAGTTGCCGGT 61.717 66.667 1.90 0.00 0.00 5.28
1158 1236 5.121811 CAGACTATGTCCCCATGAAGAAAG 58.878 45.833 0.00 0.00 32.18 2.62
1626 1704 0.467384 CACCCCAAACATTTGCCACA 59.533 50.000 0.00 0.00 36.86 4.17
1743 1821 1.202663 CCATCATGACCAGCAGAGAGG 60.203 57.143 0.00 0.00 0.00 3.69
1944 2022 2.828520 CTCTACTGCCAGTTTCTCCAGA 59.171 50.000 1.02 0.00 0.00 3.86
2572 2652 6.041069 GCTAACCTTAGTACTCTCATGGTGAT 59.959 42.308 0.00 0.00 33.32 3.06
2663 2743 1.273327 GGGCATTCTGGGTGAAAACAG 59.727 52.381 0.00 0.00 38.29 3.16
2751 2831 4.164822 AGCCACATTTGTCAGAAAATCG 57.835 40.909 0.00 0.00 0.00 3.34
3254 3334 8.149647 TGCAATGGACAATAAAGAACAAGAAAT 58.850 29.630 0.00 0.00 0.00 2.17
3424 3504 5.446073 GCATCATGACAGATTCGCATCTATG 60.446 44.000 0.00 0.00 37.71 2.23
3486 3615 0.539051 GCTATGCTGTCCTGTGGAGT 59.461 55.000 0.00 0.00 29.39 3.85
3550 3680 8.924511 AGACCTTTTTAACTTCAATCATCTCA 57.075 30.769 0.00 0.00 0.00 3.27
3614 3745 4.218635 AGCTTGATCAACTTCTCGTACTCA 59.781 41.667 3.38 0.00 0.00 3.41
3620 3751 7.329717 AGTTTAACTAGCTTGATCAACTTCTCG 59.670 37.037 3.38 1.50 0.00 4.04
3694 3825 4.338379 AGGTAAGAACACTGACAACTCC 57.662 45.455 0.00 0.00 0.00 3.85
3712 3843 6.071278 AGCTCGTTAGTTTTATCAGAGAAGGT 60.071 38.462 0.00 0.00 0.00 3.50
3767 3898 8.867097 TGAGTTACTGAGTTTCCACTTACTAAT 58.133 33.333 0.00 0.00 31.22 1.73
3781 3912 8.539770 CTCAAATATTGTGTGAGTTACTGAGT 57.460 34.615 7.27 0.00 35.17 3.41
4023 4158 2.226437 AGCAAAGAACACCATGTAAGCG 59.774 45.455 0.00 0.00 0.00 4.68
4047 4184 7.687388 ACTCTAACATGGATATCATCTGCATT 58.313 34.615 4.83 0.00 32.92 3.56
4355 4492 0.393537 CAGTCCCTGCCCATGTCTTC 60.394 60.000 0.00 0.00 0.00 2.87
4427 4564 3.733337 GTTGAGAACAAGAGCCTGAAGA 58.267 45.455 0.00 0.00 36.64 2.87
4608 4745 6.088085 CAGGTCATTCGTTAAGTGCAAAATTC 59.912 38.462 0.00 0.00 0.00 2.17
4613 4750 3.734463 TCAGGTCATTCGTTAAGTGCAA 58.266 40.909 0.00 0.00 0.00 4.08
4650 4787 2.680339 GCCCTATCAGTTTTGTCAGAGC 59.320 50.000 0.00 0.00 0.00 4.09
4725 4862 1.071385 GCATCTGAGATACAGTGGGGG 59.929 57.143 0.00 0.00 45.86 5.40
4726 4863 1.764723 TGCATCTGAGATACAGTGGGG 59.235 52.381 0.00 0.00 45.86 4.96
4727 4864 3.556633 GGATGCATCTGAGATACAGTGGG 60.557 52.174 25.28 0.00 45.86 4.61
4728 4865 3.556633 GGGATGCATCTGAGATACAGTGG 60.557 52.174 25.28 0.00 45.86 4.00
4773 4917 5.163713 GGAAGGTGCAGCAGAAGTTATTTAG 60.164 44.000 19.63 0.00 0.00 1.85
4816 4960 8.275187 AGACCCATCAGTAATATTCATTACCA 57.725 34.615 0.00 0.00 45.19 3.25
4817 4961 8.598041 AGAGACCCATCAGTAATATTCATTACC 58.402 37.037 0.00 0.00 45.19 2.85
4963 5107 1.133407 TGATATGTACGTGCTGTCGCA 59.867 47.619 4.97 0.00 45.60 5.10
5199 5346 4.503741 ACAAGATGCCATTACACAACAC 57.496 40.909 0.00 0.00 0.00 3.32
5436 5590 6.640499 GCAGTAATTTAGCAATGTGTGTTTCA 59.360 34.615 0.00 0.00 0.00 2.69
5437 5591 6.863126 AGCAGTAATTTAGCAATGTGTGTTTC 59.137 34.615 0.00 0.00 0.00 2.78
5439 5593 6.331369 AGCAGTAATTTAGCAATGTGTGTT 57.669 33.333 0.00 0.00 0.00 3.32
5460 5614 7.277319 GGTGATACCAAGTAAAGTACAAGTAGC 59.723 40.741 0.00 0.00 38.42 3.58
5598 5755 2.143876 TTAAGAGAATGCTTGGGGCC 57.856 50.000 0.00 0.00 40.92 5.80
5599 5756 3.258123 TGTTTTAAGAGAATGCTTGGGGC 59.742 43.478 0.00 0.00 42.22 5.80
5600 5757 5.665916 ATGTTTTAAGAGAATGCTTGGGG 57.334 39.130 0.00 0.00 0.00 4.96
5675 5876 2.612212 GGCCACACCATACAGAAATACG 59.388 50.000 0.00 0.00 38.86 3.06
5684 5885 1.518572 CGACTCGGCCACACCATAC 60.519 63.158 2.24 0.00 39.03 2.39
5715 5916 0.108089 TACTACCACGGCCGTACGTA 60.108 55.000 33.70 29.33 46.75 3.57
5857 6061 7.463119 CGTCCATATGTTGCTTAATTTGCTTTG 60.463 37.037 1.24 0.00 0.00 2.77
5885 6089 4.211374 AGTCATAGAAACACGACAAGCAAC 59.789 41.667 0.00 0.00 0.00 4.17
5904 6108 3.886505 ACCCGCATTTTTCTACAAAGTCA 59.113 39.130 0.00 0.00 0.00 3.41
5928 6132 6.239829 CCTCCATCACTAGCCATCTTATTCTT 60.240 42.308 0.00 0.00 0.00 2.52
5933 6137 4.155709 CTCCTCCATCACTAGCCATCTTA 58.844 47.826 0.00 0.00 0.00 2.10
5965 6169 5.012768 AGTCAAGGGTAATCTTCCTTTTCGA 59.987 40.000 0.00 0.00 41.06 3.71
5975 6179 6.620877 TGACACATAAGTCAAGGGTAATCT 57.379 37.500 0.00 0.00 44.92 2.40
5991 6195 0.518636 GTGTGCATCGCTTGACACAT 59.481 50.000 13.74 0.00 41.26 3.21


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

AutoCloner maintained by Alex Coulton.