Multiple sequence alignment - TraesCS5A01G320800

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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 TraesCS5A01G320800 chr5A 100.000 2407 0 0 1 2407 533960360 533962766 0.000000e+00 4446.0
1 TraesCS5A01G320800 chr5B 93.424 1764 83 14 664 2407 506691962 506693712 0.000000e+00 2584.0
2 TraesCS5A01G320800 chr5B 93.371 1765 83 15 664 2407 506724974 506726725 0.000000e+00 2580.0
3 TraesCS5A01G320800 chr2A 93.631 628 33 2 2 628 199717550 199716929 0.000000e+00 931.0
4 TraesCS5A01G320800 chr6A 93.182 396 27 0 141 536 571708000 571708395 1.240000e-162 582.0
5 TraesCS5A01G320800 chr6A 89.655 116 9 2 2 117 571707902 571708014 6.940000e-31 145.0
6 TraesCS5A01G320800 chr7B 93.350 391 25 1 141 531 691147665 691148054 5.770000e-161 577.0
7 TraesCS5A01G320800 chr3D 94.558 294 15 1 141 434 554965561 554965853 1.010000e-123 453.0
8 TraesCS5A01G320800 chr3D 93.534 232 15 0 434 665 554965984 554966215 1.770000e-91 346.0
9 TraesCS5A01G320800 chr3D 94.737 114 5 1 2 115 554965461 554965573 2.460000e-40 176.0
10 TraesCS5A01G320800 chr1D 88.329 377 41 3 141 516 398463085 398463459 1.310000e-122 449.0
11 TraesCS5A01G320800 chr1D 90.000 60 6 0 558 617 398463469 398463528 7.130000e-11 78.7
12 TraesCS5A01G320800 chr3B 93.537 294 18 1 141 434 737704499 737704207 1.020000e-118 436.0
13 TraesCS5A01G320800 chr3B 94.397 232 13 0 434 665 737704075 737703844 8.180000e-95 357.0
14 TraesCS5A01G320800 chr2D 87.234 376 39 3 141 516 14356268 14356634 1.030000e-113 420.0
15 TraesCS5A01G320800 chr2D 88.333 60 7 0 558 617 14356644 14356703 3.320000e-09 73.1
16 TraesCS5A01G320800 chr1B 74.893 466 78 25 127 558 678403690 678404150 2.460000e-40 176.0
17 TraesCS5A01G320800 chr2B 90.588 85 8 0 533 617 644610188 644610104 1.960000e-21 113.0


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 TraesCS5A01G320800 chr5A 533960360 533962766 2406 False 4446.0 4446 100.000000 1 2407 1 chr5A.!!$F1 2406
1 TraesCS5A01G320800 chr5B 506691962 506693712 1750 False 2584.0 2584 93.424000 664 2407 1 chr5B.!!$F1 1743
2 TraesCS5A01G320800 chr5B 506724974 506726725 1751 False 2580.0 2580 93.371000 664 2407 1 chr5B.!!$F2 1743
3 TraesCS5A01G320800 chr2A 199716929 199717550 621 True 931.0 931 93.631000 2 628 1 chr2A.!!$R1 626
4 TraesCS5A01G320800 chr3D 554965461 554966215 754 False 325.0 453 94.276333 2 665 3 chr3D.!!$F1 663
5 TraesCS5A01G320800 chr3B 737703844 737704499 655 True 396.5 436 93.967000 141 665 2 chr3B.!!$R1 524

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
599 734 1.95662 GCGTACGTTTCAGCCTGCTC 61.957 60.0 17.9 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2212 2368 0.036306 AACACCGACCTGTCCCATTC 59.964 55.0 0.0 0.0 0.0 2.67 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 5.239359 TGCATCAATAGACAATTGCTCAC 57.761 39.130 5.05 0.00 44.03 3.51
134 135 3.735237 TTGCTCACCCGCAAAAATAAA 57.265 38.095 0.00 0.00 46.00 1.40
135 136 3.735237 TGCTCACCCGCAAAAATAAAA 57.265 38.095 0.00 0.00 36.89 1.52
136 137 4.060038 TGCTCACCCGCAAAAATAAAAA 57.940 36.364 0.00 0.00 36.89 1.94
196 197 4.930405 CGGCTATTCATCTACGAGACTAGA 59.070 45.833 0.00 0.00 0.00 2.43
296 297 3.317603 CGCAGGGAATTGAAATTTGGT 57.682 42.857 0.00 0.00 0.00 3.67
349 350 7.787424 TGAATTTAGGAGAAAAGGGAAAAGGAA 59.213 33.333 0.00 0.00 0.00 3.36
365 366 4.341502 AACGGCAAGCGCGCAATT 62.342 55.556 35.10 17.64 39.92 2.32
409 410 3.012518 CTGCTGGGAAATTGAGAATCGT 58.987 45.455 0.00 0.00 38.61 3.73
456 590 6.183361 GGATTAGGAAGGGATCAATCAGTTCT 60.183 42.308 0.00 0.00 0.00 3.01
486 620 3.531538 GGCATGCACTTACTAGCTAACA 58.468 45.455 21.36 0.00 0.00 2.41
599 734 1.956620 GCGTACGTTTCAGCCTGCTC 61.957 60.000 17.90 0.00 0.00 4.26
644 779 6.489127 TTGATGACCGAAAATATGTTTCGT 57.511 33.333 20.83 13.90 46.85 3.85
654 789 7.117812 CCGAAAATATGTTTCGTCATAGCCTAT 59.882 37.037 20.83 0.00 46.85 2.57
731 866 4.219944 TCATAGAGAAACCGCGGCTATATT 59.780 41.667 28.58 12.85 0.00 1.28
736 871 5.465724 AGAGAAACCGCGGCTATATTAAAAG 59.534 40.000 28.58 0.00 0.00 2.27
742 877 6.047231 ACCGCGGCTATATTAAAAGGATATC 58.953 40.000 28.58 0.00 0.00 1.63
804 939 5.939764 AGGTGCTATTGACACAGAAGATA 57.060 39.130 0.00 0.00 39.87 1.98
808 943 6.540189 GGTGCTATTGACACAGAAGATATTGT 59.460 38.462 0.00 0.00 39.87 2.71
837 972 7.273381 CCGACAATCAAGGATTTAATTGACAAC 59.727 37.037 0.00 0.00 38.19 3.32
899 1034 6.959639 TTGTATGCCATAAAAAGATCCTCC 57.040 37.500 0.00 0.00 0.00 4.30
916 1051 8.948401 AGATCCTCCGTATGCATCTATATAAT 57.052 34.615 0.19 0.00 0.00 1.28
919 1054 7.952671 TCCTCCGTATGCATCTATATAATTCC 58.047 38.462 0.19 0.00 0.00 3.01
941 1076 3.420799 CGTGAAAGAAACATTGCAATGCG 60.421 43.478 33.94 22.75 40.04 4.73
988 1123 6.023357 TGAGCATAAAACAAAGCATTAGCA 57.977 33.333 0.00 0.00 45.49 3.49
1015 1150 3.691118 TCTCGAAATGGCAATCTCAAAGG 59.309 43.478 0.00 0.00 0.00 3.11
1050 1185 2.364324 CCTGATTTTGATGGCCCTCATG 59.636 50.000 11.85 0.00 35.97 3.07
1120 1255 5.253330 TGTTACATCCATCCCTTTTCTCAC 58.747 41.667 0.00 0.00 0.00 3.51
1168 1303 7.277981 CGCATTATATAATAGTGAACTCCCCAC 59.722 40.741 7.65 0.00 34.89 4.61
1237 1372 1.353022 ACCTTCCACAAAATCGGCCTA 59.647 47.619 0.00 0.00 0.00 3.93
1248 1383 1.094785 ATCGGCCTAACAATGTGTGC 58.905 50.000 0.00 0.00 0.00 4.57
1261 1396 2.445565 TGTGTGCTTTTGTGTTTGCA 57.554 40.000 0.00 0.00 0.00 4.08
1264 1399 2.992543 GTGTGCTTTTGTGTTTGCAGAA 59.007 40.909 0.00 0.00 36.03 3.02
1338 1473 4.389576 GCACAAAGGAGGCGTGCG 62.390 66.667 0.00 0.00 45.69 5.34
1412 1547 1.713647 TGCCCTGTTTCCTAAATGGGA 59.286 47.619 13.92 0.00 38.49 4.37
1610 1745 9.528489 AACCTACCTAAATACAACATGTGAAAT 57.472 29.630 0.00 0.00 0.00 2.17
1696 1831 3.241067 TGTGGTCGCTATAAACACCTC 57.759 47.619 0.00 0.00 0.00 3.85
1767 1902 5.879223 AGCTTCCTCTTTTATCATGACAGTG 59.121 40.000 0.00 0.00 0.00 3.66
1845 1997 6.278172 TGTGGCAATGTAAATTAGCATTCA 57.722 33.333 0.00 0.61 33.55 2.57
1928 2081 6.553100 TCAATTGAAACAAATCCAAGGGTAGT 59.447 34.615 5.45 0.00 0.00 2.73
1929 2082 5.782893 TTGAAACAAATCCAAGGGTAGTG 57.217 39.130 0.00 0.00 0.00 2.74
1932 2085 3.154827 ACAAATCCAAGGGTAGTGGTG 57.845 47.619 0.00 0.00 37.43 4.17
1980 2133 1.319614 CCTATGTTTTGGTGGCCCCG 61.320 60.000 0.00 0.00 35.15 5.73
1991 2144 0.730840 GTGGCCCCGTTTAAAGATCG 59.269 55.000 0.00 0.00 0.00 3.69
2002 2155 7.420800 CCCGTTTAAAGATCGTATACACTACT 58.579 38.462 3.32 0.00 0.00 2.57
2091 2247 7.695618 TGTTTCAATTAAATTTTGTGCAAGTGC 59.304 29.630 0.00 0.00 42.50 4.40
2136 2292 3.890756 TGGAATTTGTGCTCAGAACATGT 59.109 39.130 0.00 0.00 0.00 3.21
2153 2309 9.590088 CAGAACATGTGATCAATTTATGTATCG 57.410 33.333 0.00 5.08 32.18 2.92
2198 2354 1.139853 GCAGTGACTATCTTGGGGGAG 59.860 57.143 0.00 0.00 0.00 4.30
2233 2389 1.448497 TGGGACAGGTCGGTGTTTC 59.552 57.895 0.00 0.00 0.00 2.78
2235 2391 0.320508 GGGACAGGTCGGTGTTTCTC 60.321 60.000 0.00 0.00 0.00 2.87
2244 2400 3.760684 GGTCGGTGTTTCTCTCCTACTTA 59.239 47.826 0.00 0.00 0.00 2.24
2272 2428 6.651755 AAAGAGAAAAAGTTACGTCGTTCA 57.348 33.333 1.78 0.00 0.00 3.18
2302 2458 4.640771 TGGTCCAATCTTATCTATGGGC 57.359 45.455 0.00 0.00 36.82 5.36
2326 2482 4.356436 CCCTTCCTCCCATCTTTGATTTT 58.644 43.478 0.00 0.00 0.00 1.82
2327 2483 4.779489 CCCTTCCTCCCATCTTTGATTTTT 59.221 41.667 0.00 0.00 0.00 1.94
2368 2524 3.564225 CAGAAAACCGCTTCAACTAACCT 59.436 43.478 0.00 0.00 0.00 3.50
2376 2532 4.083484 CCGCTTCAACTAACCTACCTTTTG 60.083 45.833 0.00 0.00 0.00 2.44
2388 2544 5.948842 ACCTACCTTTTGTTCTGTTACCAT 58.051 37.500 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 9.950496 ATTGTGTCTTATTCTGTTGTCTAGAAT 57.050 29.630 0.00 0.00 44.61 2.40
56 57 7.118245 CAGCATTGTGTCTTATTCTGTTGTCTA 59.882 37.037 0.00 0.00 0.00 2.59
136 137 9.199982 CTGCTCAACAATTGTCTATTGATTTTT 57.800 29.630 12.39 0.00 45.35 1.94
296 297 2.965831 CCTCCCTAATTCAGATCGTCCA 59.034 50.000 0.00 0.00 0.00 4.02
349 350 3.427425 TAATTGCGCGCTTGCCGT 61.427 55.556 33.29 13.52 39.71 5.68
365 366 0.167470 CCGACGCTTGTCTCTTCGTA 59.833 55.000 0.00 0.00 40.61 3.43
409 410 1.962100 TCACACATGCATTTCAGGCAA 59.038 42.857 0.00 0.00 45.60 4.52
486 620 4.884164 GGAACTGATTGATCCTTCCGATTT 59.116 41.667 0.00 0.00 35.07 2.17
612 747 2.892373 TCGGTCATCAATTTTGACGC 57.108 45.000 10.62 5.17 43.53 5.19
718 853 3.756933 TCCTTTTAATATAGCCGCGGT 57.243 42.857 28.70 16.08 0.00 5.68
808 943 8.026607 GTCAATTAAATCCTTGATTGTCGGAAA 58.973 33.333 3.29 0.00 38.82 3.13
867 1002 9.814899 TCTTTTTATGGCATACAATTAATGGTG 57.185 29.630 6.72 0.00 0.00 4.17
878 1013 5.063880 ACGGAGGATCTTTTTATGGCATAC 58.936 41.667 6.72 0.00 33.73 2.39
897 1032 7.067737 TCACGGAATTATATAGATGCATACGGA 59.932 37.037 0.00 0.00 0.00 4.69
899 1034 8.628882 TTCACGGAATTATATAGATGCATACG 57.371 34.615 0.00 0.00 0.00 3.06
916 1051 4.377839 TTGCAATGTTTCTTTCACGGAA 57.622 36.364 0.00 0.00 0.00 4.30
919 1054 3.420799 CGCATTGCAATGTTTCTTTCACG 60.421 43.478 33.67 22.98 38.65 4.35
952 1087 5.556355 TTTATGCTCAGTTGATCTGCTTG 57.444 39.130 0.00 0.00 43.32 4.01
956 1091 6.307318 GCTTTGTTTTATGCTCAGTTGATCTG 59.693 38.462 0.00 0.00 44.85 2.90
967 1102 5.413499 CCTGCTAATGCTTTGTTTTATGCT 58.587 37.500 0.00 0.00 40.48 3.79
988 1123 0.257039 ATTGCCATTTCGAGAGCCCT 59.743 50.000 0.00 0.00 0.00 5.19
1015 1150 0.674895 ATCAGGGCGCTTGTGTTCTC 60.675 55.000 7.64 0.00 0.00 2.87
1050 1185 1.078143 GAGGACAGTGGCCATGACC 60.078 63.158 19.84 17.31 33.40 4.02
1148 1283 9.936329 AATTTTGTGGGGAGTTCACTATTATAT 57.064 29.630 0.00 0.00 36.21 0.86
1184 1319 8.386264 CCATCTTATGTTTCCCCAATACTAGAT 58.614 37.037 0.00 0.00 0.00 1.98
1185 1320 7.349859 ACCATCTTATGTTTCCCCAATACTAGA 59.650 37.037 0.00 0.00 0.00 2.43
1231 1366 0.881118 AAGCACACATTGTTAGGCCG 59.119 50.000 0.00 0.00 0.00 6.13
1237 1372 4.378253 GCAAACACAAAAGCACACATTGTT 60.378 37.500 0.00 0.00 35.22 2.83
1248 1383 7.195646 TCTATCTGTTTCTGCAAACACAAAAG 58.804 34.615 0.00 0.00 45.73 2.27
1306 1441 1.429930 TGTGCAGTTAGGGAGTTCCA 58.570 50.000 0.00 0.00 38.24 3.53
1338 1473 1.408702 TGGGCTGTTGCAAAGTTTCTC 59.591 47.619 0.00 0.00 41.91 2.87
1412 1547 6.604396 TCATGGCATCTTTGTATCATTTCAGT 59.396 34.615 0.00 0.00 0.00 3.41
1646 1781 7.838079 TTTTTCCTTCTGAAATTCATCTCCA 57.162 32.000 0.00 0.00 42.38 3.86
1680 1815 5.235831 GGGTTATTGAGGTGTTTATAGCGAC 59.764 44.000 0.00 0.00 0.00 5.19
1696 1831 7.871973 TCATGTGAGAAAATTGTTGGGTTATTG 59.128 33.333 0.00 0.00 0.00 1.90
1845 1997 6.084326 AGGTTTGCAACTTCGATTGTTTAT 57.916 33.333 0.00 0.00 31.83 1.40
1855 2007 9.833182 TTTTAATTTTCAAAGGTTTGCAACTTC 57.167 25.926 0.00 0.00 38.05 3.01
1912 2065 2.445525 ACACCACTACCCTTGGATTTGT 59.554 45.455 0.00 0.00 37.58 2.83
1951 2104 1.133790 CAAAACATAGGCCAGCAGAGC 59.866 52.381 5.01 0.00 0.00 4.09
1991 2144 6.748198 GCTGAGTCTCAACAAGTAGTGTATAC 59.252 42.308 3.67 0.00 40.60 1.47
2002 2155 3.133691 GTCACATGCTGAGTCTCAACAA 58.866 45.455 9.90 0.00 0.00 2.83
2104 2260 9.023962 TCTGAGCACAAATTCCATAGTTTTTAT 57.976 29.630 0.00 0.00 0.00 1.40
2105 2261 8.402798 TCTGAGCACAAATTCCATAGTTTTTA 57.597 30.769 0.00 0.00 0.00 1.52
2106 2262 7.288810 TCTGAGCACAAATTCCATAGTTTTT 57.711 32.000 0.00 0.00 0.00 1.94
2112 2268 5.711506 ACATGTTCTGAGCACAAATTCCATA 59.288 36.000 0.00 0.00 0.00 2.74
2136 2292 4.450757 CGGGCACGATACATAAATTGATCA 59.549 41.667 0.00 0.00 44.60 2.92
2177 2333 0.181350 CCCCCAAGATAGTCACTGCC 59.819 60.000 0.00 0.00 0.00 4.85
2198 2354 1.261619 CCCATTCGTCTAAGCAATCGC 59.738 52.381 0.00 0.00 38.99 4.58
2212 2368 0.036306 AACACCGACCTGTCCCATTC 59.964 55.000 0.00 0.00 0.00 2.67
2221 2377 2.169330 GTAGGAGAGAAACACCGACCT 58.831 52.381 0.00 0.00 34.46 3.85
2250 2406 6.839820 ATGAACGACGTAACTTTTTCTCTT 57.160 33.333 0.00 0.00 0.00 2.85
2253 2409 5.332808 CCGAATGAACGACGTAACTTTTTCT 60.333 40.000 0.00 0.00 35.09 2.52
2264 2420 1.419922 CAAGGCCGAATGAACGACG 59.580 57.895 0.00 0.00 35.09 5.12
2272 2428 0.625849 AGATTGGACCAAGGCCGAAT 59.374 50.000 13.43 0.00 0.00 3.34
2302 2458 0.259938 CAAAGATGGGAGGAAGGGGG 59.740 60.000 0.00 0.00 0.00 5.40
2344 2500 1.318576 AGTTGAAGCGGTTTTCTGGG 58.681 50.000 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.