Multiple sequence alignment - TraesCS1D01G224100

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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 TraesCS1D01G224100 chr1D 100.000 2855 0 0 1 2855 311989926 311987072 0.000000e+00 5273
1 TraesCS1D01G224100 chr1D 87.850 428 46 6 1179 1603 393750501 393750077 5.490000e-137 497
2 TraesCS1D01G224100 chr1A 96.060 2716 68 14 146 2846 392085996 392083305 0.000000e+00 4386
3 TraesCS1D01G224100 chr1A 88.308 402 43 4 1204 1603 492046063 492046462 1.990000e-131 479
4 TraesCS1D01G224100 chr1A 91.200 125 6 3 1 120 392086106 392085982 6.330000e-37 165
5 TraesCS1D01G224100 chr1B 95.608 2732 64 28 146 2855 422564264 422561567 0.000000e+00 4329
6 TraesCS1D01G224100 chr1B 86.168 441 55 6 1166 1603 529288172 529288609 3.330000e-129 472
7 TraesCS1D01G224100 chr3B 88.702 416 43 4 1204 1617 598468515 598468102 3.280000e-139 505
8 TraesCS1D01G224100 chr3D 87.981 416 46 4 1204 1617 455106860 455106447 3.310000e-134 488
9 TraesCS1D01G224100 chr3A 87.740 416 47 4 1204 1617 597547647 597547234 1.540000e-132 483
10 TraesCS1D01G224100 chr6B 85.057 435 55 9 1204 1630 687525401 687524969 4.370000e-118 435


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 TraesCS1D01G224100 chr1D 311987072 311989926 2854 True 5273.0 5273 100.000 1 2855 1 chr1D.!!$R1 2854
1 TraesCS1D01G224100 chr1A 392083305 392086106 2801 True 2275.5 4386 93.630 1 2846 2 chr1A.!!$R1 2845
2 TraesCS1D01G224100 chr1B 422561567 422564264 2697 True 4329.0 4329 95.608 146 2855 1 chr1B.!!$R1 2709

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
34 35 1.210967 AGAATCCGTAAAATCCGCCCA 59.789 47.619 0.0 0.0 0.00 5.36 F
402 416 1.268539 CGCAAGAACAACAAGGACACC 60.269 52.381 0.0 0.0 43.02 4.16 F
980 1008 1.613630 GGGTGGGAGAGAAGCAGGA 60.614 63.158 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1575 1606 1.473278 CGCTTCTTCTTCTCGTAGGGT 59.527 52.381 0.00 0.0 0.00 4.34 R
1797 1828 2.000323 CGTTGTCGTCGTCGTCGTT 61.000 57.895 11.41 0.0 38.33 3.85 R
2834 2866 1.678627 GCGAGCTCCATGAACTCTCTA 59.321 52.381 8.47 0.0 0.00 2.43 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
22 23 4.755266 AGCTACAAACCATAGAATCCGT 57.245 40.909 0.00 0.00 0.00 4.69
31 32 4.062991 ACCATAGAATCCGTAAAATCCGC 58.937 43.478 0.00 0.00 0.00 5.54
34 35 1.210967 AGAATCCGTAAAATCCGCCCA 59.789 47.619 0.00 0.00 0.00 5.36
40 41 2.014128 CGTAAAATCCGCCCATGAGTT 58.986 47.619 0.00 0.00 0.00 3.01
82 88 2.229543 TCATCACAAGACAAAGCATGCC 59.770 45.455 15.66 0.00 0.00 4.40
105 111 6.302269 CCCACCTATGCTATTTTGAATCTCT 58.698 40.000 0.00 0.00 0.00 3.10
106 112 6.206243 CCCACCTATGCTATTTTGAATCTCTG 59.794 42.308 0.00 0.00 0.00 3.35
107 113 6.994496 CCACCTATGCTATTTTGAATCTCTGA 59.006 38.462 0.00 0.00 0.00 3.27
108 114 7.664731 CCACCTATGCTATTTTGAATCTCTGAT 59.335 37.037 0.00 0.00 0.00 2.90
109 115 9.716531 CACCTATGCTATTTTGAATCTCTGATA 57.283 33.333 0.00 0.00 0.00 2.15
191 198 1.961394 TCTATAAGCTAGCGGGTGGTG 59.039 52.381 9.55 0.00 0.00 4.17
402 416 1.268539 CGCAAGAACAACAAGGACACC 60.269 52.381 0.00 0.00 43.02 4.16
412 427 4.099419 ACAACAAGGACACCATCTTTTTCC 59.901 41.667 0.00 0.00 0.00 3.13
474 489 2.817258 CAACCCCAAGAAAAGCGTCATA 59.183 45.455 0.00 0.00 0.00 2.15
485 500 6.163476 AGAAAAGCGTCATATGTGTACAGAA 58.837 36.000 0.00 0.00 0.00 3.02
845 868 3.891366 CCATTCCCTTCTCTCTCTCTCTC 59.109 52.174 0.00 0.00 0.00 3.20
846 869 4.386761 CCATTCCCTTCTCTCTCTCTCTCT 60.387 50.000 0.00 0.00 0.00 3.10
847 870 4.503714 TTCCCTTCTCTCTCTCTCTCTC 57.496 50.000 0.00 0.00 0.00 3.20
848 871 3.736094 TCCCTTCTCTCTCTCTCTCTCT 58.264 50.000 0.00 0.00 0.00 3.10
849 872 3.711704 TCCCTTCTCTCTCTCTCTCTCTC 59.288 52.174 0.00 0.00 0.00 3.20
919 946 3.580794 AAACAAGAAACGACGTAGCAC 57.419 42.857 0.00 0.00 0.00 4.40
929 956 2.180769 CGTAGCACGGTAGCAGCA 59.819 61.111 8.76 0.00 38.08 4.41
936 964 1.795768 CACGGTAGCAGCAAAGAGAA 58.204 50.000 0.00 0.00 0.00 2.87
980 1008 1.613630 GGGTGGGAGAGAAGCAGGA 60.614 63.158 0.00 0.00 0.00 3.86
1389 1420 4.858680 GCCTACTTCGGCCAGCCC 62.859 72.222 2.24 0.00 44.41 5.19
1895 1926 9.248291 CAAATTACCCTTTTGATTATTCCATCG 57.752 33.333 0.00 0.00 36.40 3.84
1912 1943 5.624159 TCCATCGCATCCAAATTCTAATCT 58.376 37.500 0.00 0.00 0.00 2.40
2042 2073 3.192633 TCATGATATGACGGGGTACATCG 59.807 47.826 0.00 0.00 33.59 3.84
2136 2167 8.352942 AGATAACTTTCCTTGCTTAGTTTGTTG 58.647 33.333 0.00 0.00 33.28 3.33
2139 2170 5.417580 ACTTTCCTTGCTTAGTTTGTTGTGA 59.582 36.000 0.00 0.00 0.00 3.58
2356 2388 1.962807 TCTTCGGAAAGGGACGTACAA 59.037 47.619 0.00 0.00 33.03 2.41
2476 2508 3.664107 TCTTTGACTTCGGAGACAATGG 58.336 45.455 17.40 10.78 37.39 3.16
2496 2528 5.748670 TGGGCAGTACTCTTAACAATACA 57.251 39.130 0.00 0.00 0.00 2.29
2577 2609 5.315982 CACATACACGAAAAGTAGCACATG 58.684 41.667 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 6.597562 AGTAATAACTCATGGGCGGATTTTA 58.402 36.000 0.00 0.00 0.00 1.52
77 83 3.890756 TCAAAATAGCATAGGTGGGCATG 59.109 43.478 0.00 0.00 0.00 4.06
82 88 6.994496 TCAGAGATTCAAAATAGCATAGGTGG 59.006 38.462 0.00 0.00 0.00 4.61
130 136 9.725019 TCTGATATATCACCTGCGAAAATAAAT 57.275 29.630 11.49 0.00 32.50 1.40
131 137 9.725019 ATCTGATATATCACCTGCGAAAATAAA 57.275 29.630 11.49 0.00 32.50 1.40
134 140 9.539825 GATATCTGATATATCACCTGCGAAAAT 57.460 33.333 11.49 5.81 32.68 1.82
135 141 7.702348 CGATATCTGATATATCACCTGCGAAAA 59.298 37.037 11.49 1.66 32.09 2.29
136 142 7.196331 CGATATCTGATATATCACCTGCGAAA 58.804 38.462 11.49 0.00 32.09 3.46
137 143 6.729187 CGATATCTGATATATCACCTGCGAA 58.271 40.000 11.49 0.42 32.09 4.70
138 144 5.278022 GCGATATCTGATATATCACCTGCGA 60.278 44.000 11.49 7.59 32.09 5.10
139 145 4.914504 GCGATATCTGATATATCACCTGCG 59.085 45.833 11.49 12.01 32.09 5.18
140 146 4.914504 CGCGATATCTGATATATCACCTGC 59.085 45.833 11.49 8.83 32.09 4.85
141 147 4.914504 GCGCGATATCTGATATATCACCTG 59.085 45.833 12.10 2.92 32.09 4.00
142 148 4.022762 GGCGCGATATCTGATATATCACCT 60.023 45.833 12.10 4.67 32.09 4.00
143 149 4.230657 GGCGCGATATCTGATATATCACC 58.769 47.826 12.10 4.61 32.09 4.02
144 150 3.908978 CGGCGCGATATCTGATATATCAC 59.091 47.826 12.10 1.11 32.09 3.06
155 161 5.733572 GCTTATAGATATACGGCGCGATATC 59.266 44.000 24.21 24.21 35.93 1.63
191 198 1.607628 AGCAGGGTACGATCGTGTATC 59.392 52.381 30.23 11.95 0.00 2.24
412 427 7.717436 ACCCTCTAGTCTCTTCTTTTCTTTTTG 59.283 37.037 0.00 0.00 0.00 2.44
474 489 2.305927 CCCCTGAACCTTCTGTACACAT 59.694 50.000 0.00 0.00 0.00 3.21
485 500 0.106519 GCATGCATACCCCTGAACCT 60.107 55.000 14.21 0.00 0.00 3.50
617 637 0.033781 TACCCGTCCTTGTTGTTCCG 59.966 55.000 0.00 0.00 0.00 4.30
845 868 4.834453 CTGGCCAGGCAGCGAGAG 62.834 72.222 26.14 0.00 40.70 3.20
919 946 2.670414 CTCTTTCTCTTTGCTGCTACCG 59.330 50.000 0.00 0.00 0.00 4.02
922 949 4.769488 TCTCTCTCTTTCTCTTTGCTGCTA 59.231 41.667 0.00 0.00 0.00 3.49
923 950 3.577848 TCTCTCTCTTTCTCTTTGCTGCT 59.422 43.478 0.00 0.00 0.00 4.24
924 951 3.924144 TCTCTCTCTTTCTCTTTGCTGC 58.076 45.455 0.00 0.00 0.00 5.25
925 952 5.163513 GTCTCTCTCTCTTTCTCTTTGCTG 58.836 45.833 0.00 0.00 0.00 4.41
928 955 5.243730 AGTGGTCTCTCTCTCTTTCTCTTTG 59.756 44.000 0.00 0.00 0.00 2.77
929 956 5.243730 CAGTGGTCTCTCTCTCTTTCTCTTT 59.756 44.000 0.00 0.00 0.00 2.52
936 964 2.990740 ACCAGTGGTCTCTCTCTCTT 57.009 50.000 9.70 0.00 0.00 2.85
1575 1606 1.473278 CGCTTCTTCTTCTCGTAGGGT 59.527 52.381 0.00 0.00 0.00 4.34
1797 1828 2.000323 CGTTGTCGTCGTCGTCGTT 61.000 57.895 11.41 0.00 38.33 3.85
1798 1829 2.424157 CGTTGTCGTCGTCGTCGT 60.424 61.111 11.41 0.00 38.33 4.34
1799 1830 2.128017 TCGTTGTCGTCGTCGTCG 60.128 61.111 5.50 5.50 38.33 5.12
1895 1926 5.506982 GGTGCAGAGATTAGAATTTGGATGC 60.507 44.000 0.00 0.00 0.00 3.91
1912 1943 7.701539 ACAACTAAAATTATGATGGTGCAGA 57.298 32.000 0.00 0.00 0.00 4.26
1986 2017 9.715121 CGAACTACTTAGACCTCTCTCTTATAT 57.285 37.037 0.00 0.00 0.00 0.86
1987 2018 8.703743 ACGAACTACTTAGACCTCTCTCTTATA 58.296 37.037 0.00 0.00 0.00 0.98
1988 2019 7.567458 ACGAACTACTTAGACCTCTCTCTTAT 58.433 38.462 0.00 0.00 0.00 1.73
1989 2020 6.945218 ACGAACTACTTAGACCTCTCTCTTA 58.055 40.000 0.00 0.00 0.00 2.10
1990 2021 5.807909 ACGAACTACTTAGACCTCTCTCTT 58.192 41.667 0.00 0.00 0.00 2.85
2042 2073 5.879237 TGCACGGATTTTCTTTGATGATAC 58.121 37.500 0.00 0.00 0.00 2.24
2094 2125 8.581253 AAAGTTATCTCTTTCACCTATTTGGG 57.419 34.615 0.00 0.00 35.02 4.12
2121 2152 7.140705 TGATTGATCACAACAAACTAAGCAAG 58.859 34.615 0.00 0.00 38.90 4.01
2139 2170 2.479566 AACAGTGGAGCGTGATTGAT 57.520 45.000 0.00 0.00 0.00 2.57
2230 2261 5.920840 GGAAGGCACTAAGACAAATTTGTTC 59.079 40.000 24.02 16.47 39.06 3.18
2356 2388 4.401022 TCATCAGCCACTGTTCAGAAATT 58.599 39.130 6.83 0.00 32.61 1.82
2476 2508 6.594159 ACACATGTATTGTTAAGAGTACTGCC 59.406 38.462 0.00 0.00 36.00 4.85
2496 2528 8.991026 CCACATGAAAATTGTTAAATCACACAT 58.009 29.630 0.00 0.00 0.00 3.21
2834 2866 1.678627 GCGAGCTCCATGAACTCTCTA 59.321 52.381 8.47 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.