Multiple sequence alignment - TraesCS4D01G187700

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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 TraesCS4D01G187700 chr4D 100.000 2351 0 0 1 2351 326388058 326385708 0.000000e+00 4342
1 TraesCS4D01G187700 chr4B 94.923 1615 42 18 713 2316 406396149 406394564 0.000000e+00 2492
2 TraesCS4D01G187700 chr4A 93.128 1659 39 23 713 2351 144623164 144624767 0.000000e+00 2362
3 TraesCS4D01G187700 chr4A 74.255 738 153 29 3 716 158480267 158479543 2.300000e-70 276
4 TraesCS4D01G187700 chr2D 94.952 733 22 6 1 718 534495954 534495222 0.000000e+00 1134
5 TraesCS4D01G187700 chr1B 93.004 729 35 6 1 714 611700638 611701365 0.000000e+00 1050
6 TraesCS4D01G187700 chr1B 93.564 404 21 5 320 718 553977103 553977506 4.320000e-167 597
7 TraesCS4D01G187700 chr1B 93.353 331 14 1 1 323 553976502 553976832 1.260000e-132 483
8 TraesCS4D01G187700 chr3B 88.696 575 52 5 1 563 777810435 777811008 0.000000e+00 689
9 TraesCS4D01G187700 chr3B 87.755 588 52 7 1 576 777762640 777763219 0.000000e+00 669
10 TraesCS4D01G187700 chr2A 93.017 401 19 3 320 716 725887065 725886670 5.630000e-161 577
11 TraesCS4D01G187700 chr2A 93.051 331 14 2 1 323 725889238 725888909 2.110000e-130 475
12 TraesCS4D01G187700 chr7B 90.931 408 32 4 312 715 516786894 516786488 5.710000e-151 544
13 TraesCS4D01G187700 chr7B 90.000 320 25 5 1 313 516787307 516786988 7.820000e-110 407
14 TraesCS4D01G187700 chr5D 79.354 712 124 12 4 697 492294087 492293381 1.630000e-131 479


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 TraesCS4D01G187700 chr4D 326385708 326388058 2350 True 4342.0 4342 100.0000 1 2351 1 chr4D.!!$R1 2350
1 TraesCS4D01G187700 chr4B 406394564 406396149 1585 True 2492.0 2492 94.9230 713 2316 1 chr4B.!!$R1 1603
2 TraesCS4D01G187700 chr4A 144623164 144624767 1603 False 2362.0 2362 93.1280 713 2351 1 chr4A.!!$F1 1638
3 TraesCS4D01G187700 chr4A 158479543 158480267 724 True 276.0 276 74.2550 3 716 1 chr4A.!!$R1 713
4 TraesCS4D01G187700 chr2D 534495222 534495954 732 True 1134.0 1134 94.9520 1 718 1 chr2D.!!$R1 717
5 TraesCS4D01G187700 chr1B 611700638 611701365 727 False 1050.0 1050 93.0040 1 714 1 chr1B.!!$F1 713
6 TraesCS4D01G187700 chr1B 553976502 553977506 1004 False 540.0 597 93.4585 1 718 2 chr1B.!!$F2 717
7 TraesCS4D01G187700 chr3B 777810435 777811008 573 False 689.0 689 88.6960 1 563 1 chr3B.!!$F2 562
8 TraesCS4D01G187700 chr3B 777762640 777763219 579 False 669.0 669 87.7550 1 576 1 chr3B.!!$F1 575
9 TraesCS4D01G187700 chr2A 725886670 725889238 2568 True 526.0 577 93.0340 1 716 2 chr2A.!!$R1 715
10 TraesCS4D01G187700 chr7B 516786488 516787307 819 True 475.5 544 90.4655 1 715 2 chr7B.!!$R1 714
11 TraesCS4D01G187700 chr5D 492293381 492294087 706 True 479.0 479 79.3540 4 697 1 chr5D.!!$R1 693

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
929 2812 0.257905 AGAACCGGGGGAATAAAGGC 59.742 55.0 6.32 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2207 4096 0.320771 GATGCCTCCGTCACACTGTT 60.321 55.0 0.0 0.0 0.0 3.16 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
55 56 0.749818 TTCACGCAAAACCAGCTCCA 60.750 50.000 0.00 0.00 0.00 3.86
208 219 1.308069 ACTGCAATTGCTAGCACCCG 61.308 55.000 29.37 9.51 42.66 5.28
330 2193 5.687285 GGAAATATCATTTTTAGTGCCTGCG 59.313 40.000 0.00 0.00 0.00 5.18
399 2262 4.142447 CGATTCGAGAGGGAGTTAGTTTGA 60.142 45.833 0.00 0.00 0.00 2.69
435 2301 8.734386 GTCTTCTACCATTTGATGTTGAATCTT 58.266 33.333 0.00 0.00 0.00 2.40
449 2315 5.592282 TGTTGAATCTTACTGTTTGGAAGCA 59.408 36.000 0.00 0.00 0.00 3.91
636 2503 0.469144 ATGGTTTGGCTTGGTTCGGT 60.469 50.000 0.00 0.00 0.00 4.69
829 2709 5.643379 TTCTTTCTTTGTGCTGTCAAACT 57.357 34.783 0.00 0.00 34.30 2.66
850 2730 2.029838 AAAAGGCGTCAGCTCATAGG 57.970 50.000 0.00 0.00 44.37 2.57
929 2812 0.257905 AGAACCGGGGGAATAAAGGC 59.742 55.000 6.32 0.00 0.00 4.35
1368 3252 2.887151 AAGGTCACCTCCATTCCTTG 57.113 50.000 0.00 0.00 37.17 3.61
1427 3311 2.158608 CCCCGCTCCCTTCTAATTTCAT 60.159 50.000 0.00 0.00 0.00 2.57
1430 3314 3.561725 CCGCTCCCTTCTAATTTCATCAC 59.438 47.826 0.00 0.00 0.00 3.06
1631 3515 4.079844 TCCTGTTTCATCCTCCATTATGCA 60.080 41.667 0.00 0.00 0.00 3.96
1798 3682 7.995488 CCTGATATTTCAACCTCACCTCTAATT 59.005 37.037 0.00 0.00 0.00 1.40
1852 3736 4.003648 GTGGTCTTGGGTGAGTTCTATTG 58.996 47.826 0.00 0.00 0.00 1.90
1853 3737 3.009033 TGGTCTTGGGTGAGTTCTATTGG 59.991 47.826 0.00 0.00 0.00 3.16
1911 3795 1.545582 GGATGCTGTTGCCTTTGCTAA 59.454 47.619 0.00 0.00 38.71 3.09
1912 3796 2.167075 GGATGCTGTTGCCTTTGCTAAT 59.833 45.455 0.00 0.00 38.71 1.73
1913 3797 3.368739 GGATGCTGTTGCCTTTGCTAATT 60.369 43.478 0.00 0.00 38.71 1.40
1914 3798 3.749665 TGCTGTTGCCTTTGCTAATTT 57.250 38.095 0.00 0.00 38.71 1.82
1915 3799 3.391965 TGCTGTTGCCTTTGCTAATTTG 58.608 40.909 0.00 0.00 38.71 2.32
1916 3800 2.158254 GCTGTTGCCTTTGCTAATTTGC 59.842 45.455 4.83 4.83 38.71 3.68
1917 3801 3.656559 CTGTTGCCTTTGCTAATTTGCT 58.343 40.909 12.99 0.00 38.71 3.91
1918 3802 3.652274 TGTTGCCTTTGCTAATTTGCTC 58.348 40.909 12.99 0.00 38.71 4.26
1919 3803 2.995939 GTTGCCTTTGCTAATTTGCTCC 59.004 45.455 12.99 0.00 38.71 4.70
1920 3804 1.550072 TGCCTTTGCTAATTTGCTCCC 59.450 47.619 12.99 0.00 38.71 4.30
1921 3805 1.550072 GCCTTTGCTAATTTGCTCCCA 59.450 47.619 12.99 0.00 33.53 4.37
1922 3806 2.028203 GCCTTTGCTAATTTGCTCCCAA 60.028 45.455 12.99 0.00 33.53 4.12
1923 3807 3.556843 GCCTTTGCTAATTTGCTCCCAAA 60.557 43.478 12.99 4.56 38.72 3.28
1924 3808 4.640364 CCTTTGCTAATTTGCTCCCAAAA 58.360 39.130 12.99 4.23 43.58 2.44
1925 3809 4.452114 CCTTTGCTAATTTGCTCCCAAAAC 59.548 41.667 12.99 0.00 43.58 2.43
1926 3810 4.679373 TTGCTAATTTGCTCCCAAAACA 57.321 36.364 12.99 0.00 43.58 2.83
1927 3811 4.888326 TGCTAATTTGCTCCCAAAACAT 57.112 36.364 12.99 0.00 43.58 2.71
1928 3812 4.567971 TGCTAATTTGCTCCCAAAACATG 58.432 39.130 12.99 0.00 43.58 3.21
1955 3839 4.082571 GGATTTTGTCCATGAGGTTGTGAG 60.083 45.833 0.00 0.00 46.96 3.51
1981 3865 7.170277 GGTAACTTTTGGGTCAGGTTTATAGA 58.830 38.462 0.00 0.00 0.00 1.98
2010 3897 7.039223 ACAAAAATTGAAGAGCTTCCTCATGAT 60.039 33.333 7.69 0.00 40.68 2.45
2124 4011 8.840321 AGGAACTGGTTAATTTTCATGATATCG 58.160 33.333 0.00 0.00 37.18 2.92
2164 4053 3.125829 CCACGCCATTCTGCATATGTATC 59.874 47.826 4.29 0.00 0.00 2.24
2226 4115 0.320771 AACAGTGTGACGGAGGCATC 60.321 55.000 0.00 0.00 0.00 3.91
2335 4234 5.985530 GCCAATTTGCTAAGACAAGACTTTT 59.014 36.000 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 0.677288 TCGTTGAGACGTCAATGGGT 59.323 50.000 19.50 0.00 46.06 4.51
208 219 0.539438 TTGACATGGAGGTTGCCACC 60.539 55.000 0.00 0.00 41.56 4.61
330 2193 7.665690 ACATCTGTACAGACATCAAGATATCC 58.334 38.462 27.41 0.00 40.75 2.59
360 2223 4.635765 TCGAATCGCAAGGATTTCTGATTT 59.364 37.500 0.00 0.00 45.33 2.17
399 2262 5.505181 AATGGTAGAAGACTCCATTGTGT 57.495 39.130 7.69 0.00 46.15 3.72
449 2315 3.956199 CCAATGCTTTCACCATGGATACT 59.044 43.478 21.47 0.00 37.61 2.12
636 2503 7.147105 AGACAATATCTAAGACCTCACTAGGGA 60.147 40.741 0.00 0.00 41.08 4.20
744 2622 7.128234 TGTACCCTAGTGAACAGTAAAGTTT 57.872 36.000 0.00 0.00 0.00 2.66
749 2627 7.305813 TCAAATGTACCCTAGTGAACAGTAA 57.694 36.000 0.00 0.00 0.00 2.24
829 2709 3.055385 ACCTATGAGCTGACGCCTTTTTA 60.055 43.478 0.00 0.00 36.60 1.52
929 2812 0.671781 CTGGTGCCTTCTCTTGTCCG 60.672 60.000 0.00 0.00 0.00 4.79
1164 3047 2.125912 CCTCCGCTCTTGGTGACG 60.126 66.667 0.00 0.00 0.00 4.35
1368 3252 2.360475 GGTGGGAGCAGCCAAGTC 60.360 66.667 0.00 0.00 38.95 3.01
1427 3311 3.000819 ACGGCCGATTCAGGGTGA 61.001 61.111 35.90 0.00 0.00 4.02
1852 3736 1.227292 GCGTCTTCTTCGATCCCCC 60.227 63.158 0.00 0.00 0.00 5.40
1853 3737 0.528684 CAGCGTCTTCTTCGATCCCC 60.529 60.000 0.00 0.00 0.00 4.81
1911 3795 4.276058 CTTCCATGTTTTGGGAGCAAAT 57.724 40.909 0.00 0.00 44.44 2.32
1912 3796 3.749665 CTTCCATGTTTTGGGAGCAAA 57.250 42.857 0.00 0.00 44.44 3.68
1917 3801 4.657969 ACAAAATCCTTCCATGTTTTGGGA 59.342 37.500 16.63 7.07 46.45 4.37
1918 3802 4.971939 ACAAAATCCTTCCATGTTTTGGG 58.028 39.130 16.63 2.73 46.45 4.12
1919 3803 4.996758 GGACAAAATCCTTCCATGTTTTGG 59.003 41.667 16.63 4.16 45.22 3.28
1920 3804 6.232692 ATGGACAAAATCCTTCCATGTTTTG 58.767 36.000 12.75 12.75 46.41 2.44
1921 3805 6.438186 ATGGACAAAATCCTTCCATGTTTT 57.562 33.333 1.50 0.00 46.41 2.43
1933 3817 4.082571 CCTCACAACCTCATGGACAAAATC 60.083 45.833 0.00 0.00 37.04 2.17
1955 3839 2.670019 ACCTGACCCAAAAGTTACCC 57.330 50.000 0.00 0.00 0.00 3.69
1981 3865 7.330262 TGAGGAAGCTCTTCAATTTTTGTTTT 58.670 30.769 11.27 0.00 41.20 2.43
1993 3880 5.307204 AGCAATATCATGAGGAAGCTCTTC 58.693 41.667 0.09 1.12 38.80 2.87
2010 3897 4.158949 ACAGCATCTGCAATCAAAGCAATA 59.841 37.500 4.79 0.00 45.16 1.90
2124 4011 3.723260 GTGGCTTAAGGAGAGACATAGC 58.277 50.000 4.29 0.00 34.05 2.97
2205 4094 1.961277 GCCTCCGTCACACTGTTGG 60.961 63.158 0.00 0.00 0.00 3.77
2206 4095 0.603707 ATGCCTCCGTCACACTGTTG 60.604 55.000 0.00 0.00 0.00 3.33
2207 4096 0.320771 GATGCCTCCGTCACACTGTT 60.321 55.000 0.00 0.00 0.00 3.16
2208 4097 1.293498 GATGCCTCCGTCACACTGT 59.707 57.895 0.00 0.00 0.00 3.55
2226 4115 6.968131 TTTCCTCTCATGATTCAGTTAACG 57.032 37.500 0.00 0.00 0.00 3.18
2289 4178 1.130955 CAACGGCACAGCAAATTGAC 58.869 50.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.