Multiple sequence alignment - TraesCS1A01G117200

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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 TraesCS1A01G117200 chr1A 100.000 2841 0 0 1 2841 124204739 124201899 0 5247
1 TraesCS1A01G117200 chr1A 89.818 1866 159 23 4 1851 252751400 252753252 0 2364
2 TraesCS1A01G117200 chr1A 96.263 990 37 0 1852 2841 109480441 109479452 0 1624
3 TraesCS1A01G117200 chr1A 95.565 992 43 1 1851 2841 449227334 449228325 0 1587
4 TraesCS1A01G117200 chr4A 93.258 1854 116 6 4 1851 276809391 276811241 0 2723
5 TraesCS1A01G117200 chr4A 92.353 1857 127 10 4 1851 163285067 163283217 0 2628
6 TraesCS1A01G117200 chr4A 91.314 1865 144 13 4 1851 348502902 348504765 0 2531
7 TraesCS1A01G117200 chr4A 95.964 991 40 0 1851 2841 259711628 259710638 0 1609
8 TraesCS1A01G117200 chr4A 95.960 990 39 1 1852 2841 376861656 376860668 0 1605
9 TraesCS1A01G117200 chr4A 95.661 991 43 0 1851 2841 434684711 434685701 0 1592
10 TraesCS1A01G117200 chr7D 91.237 1860 132 19 4 1851 195568792 195566952 0 2503
11 TraesCS1A01G117200 chr5D 91.070 1859 135 20 4 1851 438200130 438198292 0 2484
12 TraesCS1A01G117200 chr6A 90.612 1864 149 17 4 1851 178096005 178094152 0 2449
13 TraesCS1A01G117200 chr2D 90.474 1858 147 24 4 1851 275220465 275222302 0 2423
14 TraesCS1A01G117200 chr2D 90.354 1866 149 22 4 1851 554138642 554136790 0 2420
15 TraesCS1A01G117200 chr3A 95.670 993 43 0 1849 2841 429633463 429634455 0 1596
16 TraesCS1A01G117200 chr2A 95.758 990 40 1 1852 2841 593214364 593213377 0 1594
17 TraesCS1A01G117200 chr5A 95.556 990 44 0 1852 2841 387686666 387687655 0 1585
18 TraesCS1A01G117200 chr5A 95.473 994 44 1 1849 2841 408788099 408789092 0 1585


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 TraesCS1A01G117200 chr1A 124201899 124204739 2840 True 5247 5247 100.000 1 2841 1 chr1A.!!$R2 2840
1 TraesCS1A01G117200 chr1A 252751400 252753252 1852 False 2364 2364 89.818 4 1851 1 chr1A.!!$F1 1847
2 TraesCS1A01G117200 chr1A 109479452 109480441 989 True 1624 1624 96.263 1852 2841 1 chr1A.!!$R1 989
3 TraesCS1A01G117200 chr1A 449227334 449228325 991 False 1587 1587 95.565 1851 2841 1 chr1A.!!$F2 990
4 TraesCS1A01G117200 chr4A 276809391 276811241 1850 False 2723 2723 93.258 4 1851 1 chr4A.!!$F1 1847
5 TraesCS1A01G117200 chr4A 163283217 163285067 1850 True 2628 2628 92.353 4 1851 1 chr4A.!!$R1 1847
6 TraesCS1A01G117200 chr4A 348502902 348504765 1863 False 2531 2531 91.314 4 1851 1 chr4A.!!$F2 1847
7 TraesCS1A01G117200 chr4A 259710638 259711628 990 True 1609 1609 95.964 1851 2841 1 chr4A.!!$R2 990
8 TraesCS1A01G117200 chr4A 376860668 376861656 988 True 1605 1605 95.960 1852 2841 1 chr4A.!!$R3 989
9 TraesCS1A01G117200 chr4A 434684711 434685701 990 False 1592 1592 95.661 1851 2841 1 chr4A.!!$F3 990
10 TraesCS1A01G117200 chr7D 195566952 195568792 1840 True 2503 2503 91.237 4 1851 1 chr7D.!!$R1 1847
11 TraesCS1A01G117200 chr5D 438198292 438200130 1838 True 2484 2484 91.070 4 1851 1 chr5D.!!$R1 1847
12 TraesCS1A01G117200 chr6A 178094152 178096005 1853 True 2449 2449 90.612 4 1851 1 chr6A.!!$R1 1847
13 TraesCS1A01G117200 chr2D 275220465 275222302 1837 False 2423 2423 90.474 4 1851 1 chr2D.!!$F1 1847
14 TraesCS1A01G117200 chr2D 554136790 554138642 1852 True 2420 2420 90.354 4 1851 1 chr2D.!!$R1 1847
15 TraesCS1A01G117200 chr3A 429633463 429634455 992 False 1596 1596 95.670 1849 2841 1 chr3A.!!$F1 992
16 TraesCS1A01G117200 chr2A 593213377 593214364 987 True 1594 1594 95.758 1852 2841 1 chr2A.!!$R1 989
17 TraesCS1A01G117200 chr5A 387686666 387687655 989 False 1585 1585 95.556 1852 2841 1 chr5A.!!$F1 989
18 TraesCS1A01G117200 chr5A 408788099 408789092 993 False 1585 1585 95.473 1849 2841 1 chr5A.!!$F2 992

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
576 584 0.527113 TGCGCATGGTGAATTCAAGG 59.473 50.0 5.66 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2444 2492 0.035343 ACGACTCTCAGTCATCCGGA 60.035 55.0 6.61 6.61 45.3 5.14 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
40 41 1.565390 CCCCTGGATCTGTGAGGCAA 61.565 60.000 0.00 0.00 0.00 4.52
41 42 0.549950 CCCTGGATCTGTGAGGCAAT 59.450 55.000 0.00 0.00 0.00 3.56
56 57 4.966168 TGAGGCAATATAGGGTAGTTCACA 59.034 41.667 0.00 0.00 0.00 3.58
67 68 1.687297 TAGTTCACACACCACCCGCA 61.687 55.000 0.00 0.00 0.00 5.69
68 69 1.896660 GTTCACACACCACCCGCAT 60.897 57.895 0.00 0.00 0.00 4.73
92 93 2.427453 GACTATGAGCCCGAAGTCAAGA 59.573 50.000 0.00 0.00 38.56 3.02
113 114 1.477558 CCACAAAGGAGCAGAACCACT 60.478 52.381 0.00 0.00 41.22 4.00
125 126 6.543831 GGAGCAGAACCACTTGTATGATATTT 59.456 38.462 0.00 0.00 0.00 1.40
164 165 4.025401 GGTCCAACGGCAAGCACG 62.025 66.667 0.00 0.00 37.36 5.34
174 175 2.253758 GCAAGCACGTGAAGGAGCA 61.254 57.895 22.23 0.00 0.00 4.26
255 261 4.220533 GCTATTCTAGCCATGCTTTGTG 57.779 45.455 0.00 0.00 45.95 3.33
352 359 8.642935 TTGGACAGAACCAAAATCATACAATA 57.357 30.769 0.00 0.00 45.36 1.90
466 473 6.000219 ACTTCATCAACAGGCATATGGATAC 59.000 40.000 4.56 0.00 0.00 2.24
520 527 3.953612 GTGACCTGCAAAATATGGGATGA 59.046 43.478 0.00 0.00 0.00 2.92
521 528 4.402155 GTGACCTGCAAAATATGGGATGAA 59.598 41.667 0.00 0.00 0.00 2.57
529 536 5.595952 GCAAAATATGGGATGAAGACTTCCT 59.404 40.000 12.66 2.51 39.41 3.36
576 584 0.527113 TGCGCATGGTGAATTCAAGG 59.473 50.000 5.66 0.00 0.00 3.61
786 803 9.824534 CAATTTCAATTAAAATAGTTGGCAACC 57.175 29.630 25.81 9.05 0.00 3.77
866 884 1.742831 GGCGCATTTATGGACACTTGA 59.257 47.619 10.83 0.00 0.00 3.02
879 898 4.341806 TGGACACTTGATGCTTTGTCATTT 59.658 37.500 3.23 0.00 40.18 2.32
1099 1127 4.240096 CCAACATTTTGAGGTGCTTGATC 58.760 43.478 0.00 0.00 34.24 2.92
1117 1145 2.760634 TCCAATGCGTTCAGAAGCTA 57.239 45.000 0.00 0.00 0.00 3.32
1176 1204 4.990526 ACAACCTCAAAGAGACATGGAAT 58.009 39.130 0.00 0.00 0.00 3.01
1185 1213 5.860941 AAGAGACATGGAATCGTCACTAT 57.139 39.130 0.00 0.00 32.81 2.12
1217 1245 2.092914 GGGTCCAGATCGGTCATTTTCT 60.093 50.000 0.00 0.00 35.57 2.52
1253 1281 2.762745 GACTACGAAGCAAGGAAACCA 58.237 47.619 0.00 0.00 0.00 3.67
1438 1470 3.246880 AAGGCCGACGGTTCCCTT 61.247 61.111 16.73 16.33 33.02 3.95
1507 1539 7.104043 TGGAATTGGTTGATGAATGAAGATC 57.896 36.000 0.00 0.00 0.00 2.75
1543 1575 5.171476 CCAACACACGAGATTTCATAGAGT 58.829 41.667 0.00 0.00 0.00 3.24
1616 1648 2.297701 CCGCATGCCTACCTTACATTT 58.702 47.619 13.15 0.00 0.00 2.32
1715 1749 5.104360 CCCCGTAGCCTAGTATATAGTGGTA 60.104 48.000 0.00 0.00 0.00 3.25
1733 1776 3.930229 TGGTAGCGTGTGACATTGAATAC 59.070 43.478 0.00 0.00 0.00 1.89
1814 1861 8.462811 TGTTTGAGTATTGTTATGTGTTTGTGT 58.537 29.630 0.00 0.00 0.00 3.72
1823 1870 2.834574 TGTGTTTGTGTTTGGTAGCG 57.165 45.000 0.00 0.00 0.00 4.26
1932 1979 9.392259 GTCAGTAGTTAATTATGTTAAAGCCCT 57.608 33.333 0.00 0.00 0.00 5.19
2155 2203 4.608951 ACAGACAACAACTCGAGACTTAC 58.391 43.478 21.68 4.24 0.00 2.34
2177 2225 2.884639 GTGAAGCTTGTTTGCTCCCTAA 59.115 45.455 2.10 0.00 43.24 2.69
2342 2390 2.248248 TCCTTTCACGAGGACATCTGT 58.752 47.619 0.00 0.00 40.87 3.41
2412 2460 2.243736 TGGTTTCAAGTTCTTGGAGGGT 59.756 45.455 11.82 0.00 0.00 4.34
2433 2481 0.321996 GCTTTGAAGGACTCGAGGGT 59.678 55.000 18.41 0.00 0.00 4.34
2444 2492 1.874345 CTCGAGGGTTACGCTGTGGT 61.874 60.000 6.68 0.00 0.00 4.16
2455 2503 1.448540 GCTGTGGTCCGGATGACTG 60.449 63.158 7.81 12.47 43.89 3.51
2629 2677 0.800683 CGTCGAAATGGCTCAGCGTA 60.801 55.000 0.00 0.00 0.00 4.42
2795 2843 5.086621 TCTATATCAGCTACAAGATGGCCA 58.913 41.667 8.56 8.56 34.70 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.765339 GGGTGGCACTTCTAACAGTATTTT 59.235 41.667 18.45 0.00 0.00 1.82
2 3 3.308188 GGGGTGGCACTTCTAACAGTATT 60.308 47.826 18.45 0.00 0.00 1.89
7 8 0.400213 CAGGGGTGGCACTTCTAACA 59.600 55.000 18.45 0.00 0.00 2.41
40 41 4.407945 GGTGGTGTGTGAACTACCCTATAT 59.592 45.833 0.00 0.00 43.86 0.86
41 42 3.770933 GGTGGTGTGTGAACTACCCTATA 59.229 47.826 0.00 0.00 43.86 1.31
56 57 1.491668 TAGTCATATGCGGGTGGTGT 58.508 50.000 0.00 0.00 0.00 4.16
67 68 4.152647 TGACTTCGGGCTCATAGTCATAT 58.847 43.478 12.45 0.00 41.34 1.78
68 69 3.562182 TGACTTCGGGCTCATAGTCATA 58.438 45.455 12.45 0.00 41.34 2.15
92 93 0.550914 TGGTTCTGCTCCTTTGTGGT 59.449 50.000 0.00 0.00 37.07 4.16
125 126 2.363680 TCGCCTTTCCAAAATGCTTGAA 59.636 40.909 0.00 0.00 0.00 2.69
164 165 3.181516 CGTTATGCTTTCTGCTCCTTCAC 60.182 47.826 0.00 0.00 43.37 3.18
174 175 2.224426 TGGTGTGGACGTTATGCTTTCT 60.224 45.455 0.00 0.00 0.00 2.52
181 182 2.215196 GTTGTGTGGTGTGGACGTTAT 58.785 47.619 0.00 0.00 0.00 1.89
319 326 3.855255 TGGTTCTGTCCAAACATGAGA 57.145 42.857 0.00 0.00 34.13 3.27
481 488 3.588955 GTCACACTGTACTGCATGATCA 58.411 45.455 0.00 0.00 0.00 2.92
520 527 3.767711 GGGATTTTGTGGAGGAAGTCTT 58.232 45.455 0.00 0.00 0.00 3.01
521 528 2.290323 CGGGATTTTGTGGAGGAAGTCT 60.290 50.000 0.00 0.00 0.00 3.24
529 536 1.613255 GCTTCCTCGGGATTTTGTGGA 60.613 52.381 0.00 0.00 0.00 4.02
743 757 5.638657 TGAAATTGCCACATAAGTTGCATTC 59.361 36.000 0.00 1.51 44.66 2.67
786 803 3.949754 AGTTGCCATCCATGTATGAACAG 59.050 43.478 0.00 0.00 39.49 3.16
866 884 7.944729 AAGAGGTACATAAATGACAAAGCAT 57.055 32.000 0.00 0.00 0.00 3.79
879 898 3.572682 CCGGATGCAGTAAGAGGTACATA 59.427 47.826 0.00 0.00 34.88 2.29
1055 1083 4.037923 GGTTCTTCAAGTCAAGGCAAATCA 59.962 41.667 0.00 0.00 0.00 2.57
1099 1127 3.688272 CATTAGCTTCTGAACGCATTGG 58.312 45.455 0.00 0.00 0.00 3.16
1117 1145 6.154534 TCAGTATGTGTAGTAAGGTCTGCATT 59.845 38.462 0.00 0.00 37.40 3.56
1176 1204 4.039973 ACCCTTGAAGTTTCATAGTGACGA 59.960 41.667 0.00 0.00 37.00 4.20
1185 1213 3.557054 CGATCTGGACCCTTGAAGTTTCA 60.557 47.826 0.00 0.00 34.92 2.69
1217 1245 3.121227 CGTAGTCGCGACATACTCGATTA 60.121 47.826 37.85 17.27 46.14 1.75
1277 1305 2.587060 TAGGGATTGGTGTGGAGGAT 57.413 50.000 0.00 0.00 0.00 3.24
1385 1417 4.160252 GGTATTCCAACATGTGAAAGCCAT 59.840 41.667 0.00 0.00 0.00 4.40
1432 1464 0.884704 GCAGCTGTGACGAAAGGGAA 60.885 55.000 16.64 0.00 0.00 3.97
1438 1470 0.534877 ACCATTGCAGCTGTGACGAA 60.535 50.000 16.64 1.35 0.00 3.85
1507 1539 4.025401 GTTGGCCCGCGTGTTGAG 62.025 66.667 4.92 0.00 0.00 3.02
1572 1604 2.894765 TGGAGAACCACGTGATCACTTA 59.105 45.455 22.95 4.97 41.77 2.24
1616 1648 2.375174 ACCTTACATTCCTCAGCCACAA 59.625 45.455 0.00 0.00 0.00 3.33
1715 1749 4.065088 ACAAGTATTCAATGTCACACGCT 58.935 39.130 0.00 0.00 0.00 5.07
1733 1776 8.559536 GGTTCACATCCACACATATATTACAAG 58.440 37.037 0.00 0.00 0.00 3.16
1823 1870 0.958822 ATTCAAAACACCCGACTGGC 59.041 50.000 0.00 0.00 37.83 4.85
1932 1979 1.343377 TGAGCCCTCATCTGCCTTCTA 60.343 52.381 0.00 0.00 34.14 2.10
2131 2178 3.707793 AGTCTCGAGTTGTTGTCTGTTC 58.292 45.455 13.13 0.00 0.00 3.18
2155 2203 0.040067 GGGAGCAAACAAGCTTCACG 60.040 55.000 0.00 0.00 46.75 4.35
2177 2225 3.891366 GGAATTGATGGGGTTTCGATGAT 59.109 43.478 0.00 0.00 0.00 2.45
2389 2437 3.897505 CCCTCCAAGAACTTGAAACCATT 59.102 43.478 14.99 0.00 42.93 3.16
2412 2460 0.243907 CCTCGAGTCCTTCAAAGCGA 59.756 55.000 12.31 0.00 0.00 4.93
2433 2481 1.216977 CATCCGGACCACAGCGTAA 59.783 57.895 6.12 0.00 0.00 3.18
2444 2492 0.035343 ACGACTCTCAGTCATCCGGA 60.035 55.000 6.61 6.61 45.30 5.14
2455 2503 2.876645 CTTGCCGCGACGACTCTC 60.877 66.667 8.23 0.00 0.00 3.20
2644 2692 1.641123 CGCTTCACGGCCGGTTTAAT 61.641 55.000 31.76 3.35 38.44 1.40
2694 2742 3.085533 AGATTCCGATCCATCCTCGTAG 58.914 50.000 0.00 0.00 34.36 3.51
2730 2778 0.244450 ACTCGTCGCCGGAATAAACA 59.756 50.000 5.05 0.00 33.95 2.83
2795 2843 1.923395 TCGGAACAGCCCCCAATCT 60.923 57.895 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.