Multiple sequence alignment - TraesCS4A01G227100

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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 TraesCS4A01G227100 chr4A 100.000 2975 0 0 1 2975 535424668 535427642 0.000000e+00 5494.0
1 TraesCS4A01G227100 chr4A 80.266 527 74 15 227 726 464770623 464770100 1.300000e-98 370.0
2 TraesCS4A01G227100 chr4B 93.455 3025 125 22 1 2975 90507705 90504704 0.000000e+00 4421.0
3 TraesCS4A01G227100 chr4D 93.272 3032 122 30 1 2975 62095207 62098213 0.000000e+00 4394.0
4 TraesCS4A01G227100 chr3D 77.046 501 81 24 237 716 25138751 25139238 1.060000e-64 257.0
5 TraesCS4A01G227100 chr5A 78.882 161 29 4 609 764 44606174 44606014 1.460000e-18 104.0
6 TraesCS4A01G227100 chr1D 81.000 100 17 2 626 723 347253198 347253297 8.840000e-11 78.7


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 TraesCS4A01G227100 chr4A 535424668 535427642 2974 False 5494 5494 100.000 1 2975 1 chr4A.!!$F1 2974
1 TraesCS4A01G227100 chr4A 464770100 464770623 523 True 370 370 80.266 227 726 1 chr4A.!!$R1 499
2 TraesCS4A01G227100 chr4B 90504704 90507705 3001 True 4421 4421 93.455 1 2975 1 chr4B.!!$R1 2974
3 TraesCS4A01G227100 chr4D 62095207 62098213 3006 False 4394 4394 93.272 1 2975 1 chr4D.!!$F1 2974

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
946 982 0.040781 CACCACGCTAAACCAAACCG 60.041 55.0 0.0 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2168 2214 0.60864 GTGTTCATCCTGGAGTCCGT 59.391 55.0 4.3 0.0 0.0 4.69 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
121 122 1.153745 GCGAGATTGTCTCACCGCT 60.154 57.895 7.64 0.00 43.55 5.52
141 142 4.669197 CGCTGCGATGCTTAAAGTTAGTTT 60.669 41.667 18.66 0.00 0.00 2.66
362 376 6.430616 TGCATGTATGTGATCTCAACTCAAAA 59.569 34.615 0.90 0.00 0.00 2.44
363 377 7.040548 TGCATGTATGTGATCTCAACTCAAAAA 60.041 33.333 0.90 0.00 0.00 1.94
432 446 2.990195 TGTCATAGTAGATGGGGGCAT 58.010 47.619 0.00 0.00 0.00 4.40
459 473 7.013464 ACAAATTGCAATTTCAACATGGTGATT 59.987 29.630 29.92 3.75 36.52 2.57
473 488 3.678289 TGGTGATTGATGTTGTCTCCTG 58.322 45.455 0.00 0.00 0.00 3.86
517 532 7.066163 TGCATTCAACTTACTCATACCATTCAG 59.934 37.037 0.00 0.00 0.00 3.02
534 549 6.209391 ACCATTCAGAAAAAGGTTACTCATGG 59.791 38.462 0.00 0.00 33.82 3.66
583 610 8.100791 TCGCTATAAATATTGCAAAGGACCTAT 58.899 33.333 1.71 0.00 34.78 2.57
601 628 8.549731 AGGACCTATTATGATCACTCGATACTA 58.450 37.037 0.00 0.00 29.66 1.82
667 699 0.667993 CTTGTGAACCATGCAACGGT 59.332 50.000 5.36 5.36 38.85 4.83
672 704 0.881118 GAACCATGCAACGGTCACAT 59.119 50.000 11.31 0.00 34.99 3.21
816 852 6.889198 TCAAATCCATTAAACACCCACAAAA 58.111 32.000 0.00 0.00 0.00 2.44
946 982 0.040781 CACCACGCTAAACCAAACCG 60.041 55.000 0.00 0.00 0.00 4.44
956 992 1.828979 AACCAAACCGCCGTGATATT 58.171 45.000 0.00 0.00 0.00 1.28
978 1014 2.270297 ATCGCATTGCCGAAAGTGCC 62.270 55.000 2.41 0.00 41.01 5.01
1179 1215 4.794439 TCGCACGCCAGATCACCG 62.794 66.667 0.00 0.00 0.00 4.94
1239 1275 4.610890 CGCAACACGCAGCAGCAA 62.611 61.111 0.82 0.00 42.60 3.91
1240 1276 3.026311 GCAACACGCAGCAGCAAC 61.026 61.111 0.82 0.00 42.27 4.17
1241 1277 2.408428 CAACACGCAGCAGCAACA 59.592 55.556 0.82 0.00 42.27 3.33
1398 1443 4.003788 CTCCTGGTGTTCGGCGGT 62.004 66.667 7.21 0.00 0.00 5.68
1401 1446 2.030562 CTGGTGTTCGGCGGTCTT 59.969 61.111 7.21 0.00 0.00 3.01
1782 1827 1.809619 CGCGATATACATGGCCGGG 60.810 63.158 0.00 0.00 32.63 5.73
1824 1869 3.827898 GGGAGTGGCGAGACGGAG 61.828 72.222 0.00 0.00 0.00 4.63
1833 1878 1.080705 CGAGACGGAGGTGTTGGTC 60.081 63.158 0.00 0.00 0.00 4.02
1896 1941 2.046892 CTGTGCGCAGGCTACCTT 60.047 61.111 19.78 0.00 40.82 3.50
1956 2001 0.112412 GCCACAGGGAAAAGGAAGGA 59.888 55.000 0.00 0.00 35.59 3.36
1991 2036 4.479619 CCTTGAGAGCAAAACATAAGCAC 58.520 43.478 0.00 0.00 32.73 4.40
2057 2102 2.564062 ACCAAAAGGATCTGCAACATGG 59.436 45.455 0.00 0.00 0.00 3.66
2099 2144 0.395862 TTTTTGTTGCCCTGGGACGA 60.396 50.000 19.27 3.32 0.00 4.20
2166 2212 3.459828 TGGGAAGATGGGATCTGTTGTA 58.540 45.455 0.00 0.00 40.13 2.41
2168 2214 5.223655 TGGGAAGATGGGATCTGTTGTATA 58.776 41.667 0.00 0.00 40.13 1.47
2171 2217 4.873746 AGATGGGATCTGTTGTATACGG 57.126 45.455 0.00 0.00 38.44 4.02
2246 2292 8.868522 TGAATTTCAGTGATCTATCTTTTGGT 57.131 30.769 0.00 0.00 0.00 3.67
2269 2317 7.116948 TGGTGTACATTTTAAATTTTCCATGCG 59.883 33.333 0.00 0.00 0.00 4.73
2384 2457 4.314961 CAACAACTTAAAAGGAATGGCCC 58.685 43.478 0.00 0.00 37.37 5.80
2428 2501 5.416952 CACCTTTTGTTAGCAGGATCAGATT 59.583 40.000 0.00 0.00 0.00 2.40
2446 2519 6.801575 TCAGATTTACAACCACCTTTTGTTC 58.198 36.000 0.00 0.00 38.21 3.18
2458 2531 4.994852 CACCTTTTGTTCTCAAGATACGGA 59.005 41.667 0.00 0.00 34.88 4.69
2487 2566 8.733092 ATGGGGTATATGTCATAGGAGATATG 57.267 38.462 15.17 0.00 39.54 1.78
2497 2576 7.933223 TGTCATAGGAGATATGGTCTGATCTA 58.067 38.462 0.00 0.00 41.51 1.98
2581 2660 1.609072 CTGATTCCCAGCAGCATCATG 59.391 52.381 0.00 0.00 35.89 3.07
2697 2776 2.844654 AATGCATCCACCATGGGTTA 57.155 45.000 18.09 0.00 38.32 2.85
2840 2924 5.818678 TTGTACTGTACATCCTTCCTTGT 57.181 39.130 20.31 0.00 38.68 3.16
2887 2971 5.817296 TCATCACGAAGACAAAATATGAGGG 59.183 40.000 0.00 0.00 0.00 4.30
2892 2976 5.063204 CGAAGACAAAATATGAGGGCCATA 58.937 41.667 6.18 0.00 41.58 2.74
2940 3029 5.586643 CCTTGGCTTGTATTTCTTAGACCTC 59.413 44.000 0.00 0.00 0.00 3.85
2941 3030 5.099042 TGGCTTGTATTTCTTAGACCTCC 57.901 43.478 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 5.008217 ACACAAACTAACTTTAAGCATCGCA 59.992 36.000 0.00 0.00 0.00 5.10
141 142 8.874744 TGCGTATTAATTGCTAGTATAACACA 57.125 30.769 12.02 0.00 0.00 3.72
195 196 3.922375 TGTCCTTGGAAATCCTTTTGGT 58.078 40.909 0.44 0.00 41.38 3.67
362 376 7.227156 AGAGAAACTACAATCAAGACCATGTT 58.773 34.615 0.00 0.00 0.00 2.71
363 377 6.773638 AGAGAAACTACAATCAAGACCATGT 58.226 36.000 0.00 0.00 0.00 3.21
432 446 6.988580 TCACCATGTTGAAATTGCAATTTGTA 59.011 30.769 35.57 23.11 38.64 2.41
459 473 3.776969 AGATTAGGCAGGAGACAACATCA 59.223 43.478 0.00 0.00 0.00 3.07
473 488 3.808728 TGCACAAGATGGTAGATTAGGC 58.191 45.455 0.00 0.00 0.00 3.93
517 532 5.405935 AATGGCCATGAGTAACCTTTTTC 57.594 39.130 21.63 0.00 0.00 2.29
601 628 9.725019 TGAAAGATCATGTTGTAGTAACTGAAT 57.275 29.630 0.00 0.00 0.00 2.57
650 682 0.464554 TGACCGTTGCATGGTTCACA 60.465 50.000 12.01 3.98 37.69 3.58
672 704 6.820335 AGATCGTCAAAAGATGATGGTATCA 58.180 36.000 5.02 0.00 43.93 2.15
737 769 0.372334 CAATGCCCGTGCGTTACTAC 59.628 55.000 0.00 0.00 44.83 2.73
816 852 2.486592 CGTTTGTTAGATTTTCCCCGCT 59.513 45.455 0.00 0.00 0.00 5.52
946 982 3.228749 CAATGCGATGAAATATCACGGC 58.771 45.455 0.00 0.00 38.69 5.68
956 992 1.135717 CACTTTCGGCAATGCGATGAA 60.136 47.619 0.00 0.43 0.00 2.57
978 1014 1.327460 GTGTATGCGGTATGCTGTGTG 59.673 52.381 0.00 0.00 46.63 3.82
1069 1105 4.008933 GAGGGTGACGTGCTGCCT 62.009 66.667 0.00 0.00 0.00 4.75
1811 1856 3.222354 AACACCTCCGTCTCGCCAC 62.222 63.158 0.00 0.00 0.00 5.01
1824 1869 2.107546 ACGTCGTGGACCAACACC 59.892 61.111 0.00 0.00 38.11 4.16
1896 1941 2.363018 CTGCCGACCTCCTCCTCA 60.363 66.667 0.00 0.00 0.00 3.86
2057 2102 8.543862 AAAGAAATCAAGAATCTTGGAATTGC 57.456 30.769 21.35 13.52 33.86 3.56
2111 2156 9.835389 AACTGAAAATGGATCAAAAGAAATCAA 57.165 25.926 0.00 0.00 0.00 2.57
2123 2168 8.912988 TCCCATGTTTATAACTGAAAATGGATC 58.087 33.333 6.82 0.00 0.00 3.36
2124 2169 8.837099 TCCCATGTTTATAACTGAAAATGGAT 57.163 30.769 6.82 0.00 0.00 3.41
2125 2170 8.657387 TTCCCATGTTTATAACTGAAAATGGA 57.343 30.769 6.82 0.00 0.00 3.41
2126 2171 8.748412 TCTTCCCATGTTTATAACTGAAAATGG 58.252 33.333 0.00 0.00 0.00 3.16
2166 2212 2.431057 GTGTTCATCCTGGAGTCCGTAT 59.569 50.000 4.30 0.00 0.00 3.06
2168 2214 0.608640 GTGTTCATCCTGGAGTCCGT 59.391 55.000 4.30 0.00 0.00 4.69
2171 2217 1.208293 GGGAGTGTTCATCCTGGAGTC 59.792 57.143 1.52 0.00 37.01 3.36
2246 2292 7.061210 CGTCGCATGGAAAATTTAAAATGTACA 59.939 33.333 0.00 0.00 0.00 2.90
2263 2311 1.580893 CGATTGCAACGTCGCATGG 60.581 57.895 0.04 0.00 42.62 3.66
2269 2317 1.128507 TGCTTGATCGATTGCAACGTC 59.871 47.619 15.77 14.35 32.12 4.34
2280 2328 2.009051 TGGCACTACATTGCTTGATCG 58.991 47.619 0.00 0.00 42.56 3.69
2384 2457 3.921021 GTGGTTAGTTCATGAGTCGACTG 59.079 47.826 25.58 10.12 0.00 3.51
2428 2501 5.946972 TCTTGAGAACAAAAGGTGGTTGTAA 59.053 36.000 0.00 0.00 38.24 2.41
2446 2519 2.487934 CCCATTGCTCCGTATCTTGAG 58.512 52.381 0.00 0.00 0.00 3.02
2458 2531 5.100811 TCCTATGACATATACCCCATTGCT 58.899 41.667 0.00 0.00 0.00 3.91
2487 2566 6.690194 AAAATGCAATGACTAGATCAGACC 57.310 37.500 0.00 0.00 41.91 3.85
2497 2576 9.558396 TGAAAAATTAGGAAAAATGCAATGACT 57.442 25.926 0.00 0.00 0.00 3.41
2581 2660 2.297033 TGAAAATGCAGAAGCTGAACCC 59.703 45.455 0.00 0.00 42.74 4.11
2626 2705 3.965539 CTTGGGCCTGCCTCAGTCG 62.966 68.421 4.53 0.00 36.10 4.18
2697 2776 3.066208 AGTCCAGTATCCCACCATGAT 57.934 47.619 0.00 0.00 0.00 2.45
2887 2971 3.175929 CGGATTTTTGACGGTTTATGGC 58.824 45.455 0.00 0.00 0.00 4.40
2892 2976 2.879646 TGTAGCGGATTTTTGACGGTTT 59.120 40.909 0.00 0.00 39.24 3.27
2940 3029 2.308722 TGAAGCTTAGGGGCTGGGG 61.309 63.158 0.00 0.00 42.24 4.96
2941 3030 1.077429 GTGAAGCTTAGGGGCTGGG 60.077 63.158 0.00 0.00 42.24 4.45


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

AutoCloner maintained by Alex Coulton.