Multiple sequence alignment - TraesCS2B01G294300

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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 TraesCS2B01G294300 chr2B 100.000 1316 0 0 877 2192 410942881 410944196 0.000000e+00 2431.0
1 TraesCS2B01G294300 chr2B 100.000 581 0 0 1 581 410942005 410942585 0.000000e+00 1074.0
2 TraesCS2B01G294300 chr2A 93.042 618 29 8 877 1488 457221523 457222132 0.000000e+00 891.0
3 TraesCS2B01G294300 chr2A 93.728 287 9 3 1 287 457220550 457220827 2.600000e-114 422.0
4 TraesCS2B01G294300 chr2A 85.511 421 17 19 1618 2013 457222583 457222984 1.220000e-107 399.0
5 TraesCS2B01G294300 chr2A 86.486 259 20 8 321 566 457221136 457221392 9.970000e-69 270.0
6 TraesCS2B01G294300 chr2D 92.348 575 28 9 885 1454 345247973 345248536 0.000000e+00 804.0
7 TraesCS2B01G294300 chr2D 86.767 733 36 15 1505 2191 345249439 345250156 0.000000e+00 760.0
8 TraesCS2B01G294300 chr2D 90.878 581 11 7 2 581 345247296 345247835 0.000000e+00 741.0
9 TraesCS2B01G294300 chr1B 79.667 541 55 30 887 1397 655858538 655859053 2.700000e-89 339.0
10 TraesCS2B01G294300 chr1B 85.135 74 7 1 1 74 655858040 655858109 3.020000e-09 73.1
11 TraesCS2B01G294300 chr1A 78.155 206 22 9 378 581 566123573 566123757 2.300000e-20 110.0


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 TraesCS2B01G294300 chr2B 410942005 410944196 2191 False 1752.500000 2431 100.000000 1 2192 2 chr2B.!!$F1 2191
1 TraesCS2B01G294300 chr2A 457220550 457222984 2434 False 495.500000 891 89.691750 1 2013 4 chr2A.!!$F1 2012
2 TraesCS2B01G294300 chr2D 345247296 345250156 2860 False 768.333333 804 89.997667 2 2191 3 chr2D.!!$F1 2189
3 TraesCS2B01G294300 chr1B 655858040 655859053 1013 False 206.050000 339 82.401000 1 1397 2 chr1B.!!$F1 1396

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
470 751 0.534203 AATCAACGGTGCTGAACGGT 60.534 50.0 0.0 0.0 43.62 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 3676 0.179 AATCGCATGAGACCCCTGAC 59.821 55.0 0.0 0.0 0.0 3.51 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
38 39 2.153366 AAAGGAATGCGTGCTTTTGG 57.847 45.000 0.00 0.00 44.79 3.28
62 63 3.468770 TCTGAATTCGTTCGGGTCAAAA 58.531 40.909 0.04 0.00 0.00 2.44
139 145 3.268103 ATGGGTTGGTCCTGGTCGC 62.268 63.158 0.00 0.00 36.25 5.19
292 298 1.057851 TCCGGTGGACCAAAAGGAGT 61.058 55.000 0.00 0.00 35.14 3.85
293 299 0.688487 CCGGTGGACCAAAAGGAGTA 59.312 55.000 0.00 0.00 35.14 2.59
319 339 6.783708 ATAGAGTTCGAGTCAGAAAGGATT 57.216 37.500 0.00 0.00 0.00 3.01
466 747 3.134574 AGGTAAATCAACGGTGCTGAA 57.865 42.857 0.00 0.00 0.00 3.02
469 750 0.591170 AAATCAACGGTGCTGAACGG 59.409 50.000 0.00 0.00 35.32 4.44
470 751 0.534203 AATCAACGGTGCTGAACGGT 60.534 50.000 0.00 0.00 43.62 4.83
519 812 2.481185 TCCAACACGAAAAATACGAGGC 59.519 45.455 0.00 0.00 34.70 4.70
987 1303 2.936912 GCTGTCTCCCGTCTGCACT 61.937 63.158 0.00 0.00 0.00 4.40
1075 1394 1.338011 TGCAGATGCTCAACGTCATGA 60.338 47.619 6.35 0.00 42.66 3.07
1217 1562 2.808543 ACCGATCAAGCAGACAGTTTTC 59.191 45.455 0.00 0.00 0.00 2.29
1248 1593 1.858091 AGATGTAAAGATGCGAGGCG 58.142 50.000 0.00 0.00 0.00 5.52
1259 1604 4.285851 CGAGGCGCTCTTTTCCTT 57.714 55.556 7.64 0.00 0.00 3.36
1320 1665 8.138712 AGATAGGATCATTCTTTCGTTGTAGAC 58.861 37.037 0.00 0.00 0.00 2.59
1389 1738 8.746922 TTGAGCACAAAATATGTTCATTCTTC 57.253 30.769 0.00 0.00 41.46 2.87
1397 1746 8.991026 CAAAATATGTTCATTCTTCCAAGCAAA 58.009 29.630 0.00 0.00 0.00 3.68
1454 2673 6.736853 GTCTTAAATGTTTCGACCGATTTCAG 59.263 38.462 0.00 0.00 0.00 3.02
1459 2678 3.987868 TGTTTCGACCGATTTCAGAGAAG 59.012 43.478 0.00 0.00 0.00 2.85
1460 2679 4.235360 GTTTCGACCGATTTCAGAGAAGA 58.765 43.478 0.00 0.00 0.00 2.87
1528 2747 5.486526 AGCTCTTGTGAGTTATTCCTCTTG 58.513 41.667 0.00 0.00 42.13 3.02
1529 2748 5.012561 AGCTCTTGTGAGTTATTCCTCTTGT 59.987 40.000 0.00 0.00 42.13 3.16
1530 2749 5.121454 GCTCTTGTGAGTTATTCCTCTTGTG 59.879 44.000 0.00 0.00 42.13 3.33
1532 2751 3.674997 TGTGAGTTATTCCTCTTGTGCC 58.325 45.455 0.00 0.00 32.50 5.01
1537 3122 6.430000 GTGAGTTATTCCTCTTGTGCCTTTTA 59.570 38.462 0.00 0.00 32.50 1.52
1548 3133 6.919721 TCTTGTGCCTTTTATTTATGTCCAC 58.080 36.000 0.00 0.00 0.00 4.02
1549 3134 6.719370 TCTTGTGCCTTTTATTTATGTCCACT 59.281 34.615 0.00 0.00 0.00 4.00
1550 3135 6.909550 TGTGCCTTTTATTTATGTCCACTT 57.090 33.333 0.00 0.00 0.00 3.16
1581 3166 9.947897 CTTTCAGAAAATATTGCTTTTCGAATG 57.052 29.630 0.00 0.00 45.51 2.67
1591 3176 2.589841 GCTTTTCGAATGCAATGTCGAC 59.410 45.455 17.04 9.11 45.35 4.20
1593 3178 3.887339 TTTCGAATGCAATGTCGACAA 57.113 38.095 24.13 6.18 45.35 3.18
1602 3187 1.391485 CAATGTCGACAAGCCTTCGAG 59.609 52.381 24.13 0.00 45.76 4.04
1610 3195 3.362693 CGACAAGCCTTCGAGTTTTACAC 60.363 47.826 0.00 0.00 38.85 2.90
1613 3198 4.201881 ACAAGCCTTCGAGTTTTACACAAC 60.202 41.667 0.00 0.00 0.00 3.32
1667 3254 6.993878 ACGAACAAATAGACTCAAATGATCG 58.006 36.000 0.00 0.00 38.50 3.69
1693 3281 9.495754 GTACACGAAATACTTTACGAGTCTAAT 57.504 33.333 0.00 0.00 39.86 1.73
1694 3282 8.976986 ACACGAAATACTTTACGAGTCTAATT 57.023 30.769 0.00 0.00 39.86 1.40
1786 3387 3.420893 TGCTGACCAATTAAACTGGAGG 58.579 45.455 12.66 4.83 37.40 4.30
1842 3443 3.562779 GAACACGTCCGCGGGAGAA 62.563 63.158 27.83 1.61 45.97 2.87
1908 3533 0.175073 ACGGGAGATTTCTACACGGC 59.825 55.000 0.00 0.00 0.00 5.68
2015 3650 1.808945 CACGCCTTTCTTCTGCTTGAT 59.191 47.619 0.00 0.00 0.00 2.57
2034 3669 1.598130 GGCGGCTCTTCACACTTGT 60.598 57.895 0.00 0.00 0.00 3.16
2041 3676 2.665537 GCTCTTCACACTTGTCATCGAG 59.334 50.000 0.00 0.00 0.00 4.04
2056 3691 1.142748 CGAGTCAGGGGTCTCATGC 59.857 63.158 0.00 0.00 0.00 4.06
2065 3700 1.154205 GGGTCTCATGCGATTCACCG 61.154 60.000 0.00 0.00 0.00 4.94
2066 3701 1.154205 GGTCTCATGCGATTCACCGG 61.154 60.000 0.00 0.00 0.00 5.28
2163 3806 1.855513 CCGTACATTTTCGGCCGATA 58.144 50.000 31.56 22.87 40.28 2.92
2174 3817 1.695242 TCGGCCGATACCAATGGTAAT 59.305 47.619 27.28 5.22 41.85 1.89
2187 3830 6.988522 ACCAATGGTAATTTTGTAGGTTGAC 58.011 36.000 1.52 0.00 32.11 3.18
2191 3834 4.828387 TGGTAATTTTGTAGGTTGACCCAC 59.172 41.667 0.00 0.00 36.42 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 3.259064 TGACCCGAACGAATTCAGAATC 58.741 45.455 6.22 0.00 34.14 2.52
62 63 8.511321 TGAACAAATAATATTCGTGTTCTTGCT 58.489 29.630 24.56 4.19 45.29 3.91
159 165 1.798223 TGCGTGTCTGTATGCAAGTTC 59.202 47.619 0.00 0.00 39.47 3.01
292 298 8.975663 TCCTTTCTGACTCGAACTCTATAATA 57.024 34.615 0.00 0.00 0.00 0.98
293 299 7.883391 TCCTTTCTGACTCGAACTCTATAAT 57.117 36.000 0.00 0.00 0.00 1.28
319 339 3.263170 TGGCAAGAGCTACCAACAGATAA 59.737 43.478 0.00 0.00 41.70 1.75
466 747 1.675552 CTTTGACCTTTGGACACCGT 58.324 50.000 0.00 0.00 0.00 4.83
469 750 0.673985 GCCCTTTGACCTTTGGACAC 59.326 55.000 0.00 0.00 0.00 3.67
470 751 0.469144 GGCCCTTTGACCTTTGGACA 60.469 55.000 0.00 0.00 0.00 4.02
519 812 2.311688 CTTCCGATCTCCCAACCCCG 62.312 65.000 0.00 0.00 0.00 5.73
987 1303 2.644418 GCCATCGCTGTTGTTGCA 59.356 55.556 0.00 0.00 0.00 4.08
1248 1593 4.697514 AGGCAAAAGAAAAGGAAAAGAGC 58.302 39.130 0.00 0.00 0.00 4.09
1256 1601 3.805971 CAGCAAAGAGGCAAAAGAAAAGG 59.194 43.478 0.00 0.00 35.83 3.11
1257 1602 4.436332 ACAGCAAAGAGGCAAAAGAAAAG 58.564 39.130 0.00 0.00 35.83 2.27
1258 1603 4.470334 ACAGCAAAGAGGCAAAAGAAAA 57.530 36.364 0.00 0.00 35.83 2.29
1259 1604 4.887071 TCTACAGCAAAGAGGCAAAAGAAA 59.113 37.500 0.00 0.00 35.83 2.52
1320 1665 3.663995 TTGTTGAATGGCCAGTTGATG 57.336 42.857 13.05 0.00 0.00 3.07
1369 1718 7.599621 TGCTTGGAAGAATGAACATATTTTGTG 59.400 33.333 0.00 0.00 38.99 3.33
1377 1726 5.404946 CGATTTGCTTGGAAGAATGAACAT 58.595 37.500 0.00 0.00 0.00 2.71
1389 1738 1.213537 CTGCCACCGATTTGCTTGG 59.786 57.895 0.00 0.00 0.00 3.61
1397 1746 0.613260 ATACACACACTGCCACCGAT 59.387 50.000 0.00 0.00 0.00 4.18
1454 2673 1.747924 GGGGATGCAAAAGCTCTTCTC 59.252 52.381 0.00 0.00 0.00 2.87
1459 2678 0.975887 TTTGGGGGATGCAAAAGCTC 59.024 50.000 0.00 0.00 0.00 4.09
1460 2679 1.433121 TTTTGGGGGATGCAAAAGCT 58.567 45.000 0.00 0.00 0.00 3.74
1509 2728 4.154918 GGCACAAGAGGAATAACTCACAAG 59.845 45.833 0.00 0.00 39.97 3.16
1513 2732 4.640771 AAGGCACAAGAGGAATAACTCA 57.359 40.909 0.00 0.00 39.97 3.41
1528 2747 7.158099 AGAAGTGGACATAAATAAAAGGCAC 57.842 36.000 0.00 0.00 0.00 5.01
1529 2748 7.775053 AAGAAGTGGACATAAATAAAAGGCA 57.225 32.000 0.00 0.00 0.00 4.75
1530 2749 8.523658 AGAAAGAAGTGGACATAAATAAAAGGC 58.476 33.333 0.00 0.00 0.00 4.35
1537 3122 8.924511 TCTGAAAGAAAGAAGTGGACATAAAT 57.075 30.769 0.00 0.00 42.31 1.40
1569 3154 2.225255 TCGACATTGCATTCGAAAAGCA 59.775 40.909 20.49 20.49 41.16 3.91
1581 3166 0.179215 CGAAGGCTTGTCGACATTGC 60.179 55.000 26.05 26.05 41.02 3.56
1587 3172 2.234300 AAAACTCGAAGGCTTGTCGA 57.766 45.000 3.46 7.92 44.82 4.20
1591 3176 4.035208 AGTTGTGTAAAACTCGAAGGCTTG 59.965 41.667 3.46 0.00 35.44 4.01
1593 3178 3.805207 AGTTGTGTAAAACTCGAAGGCT 58.195 40.909 0.00 0.00 35.44 4.58
1644 3229 6.993878 ACGATCATTTGAGTCTATTTGTTCG 58.006 36.000 12.49 12.49 34.33 3.95
1667 3254 8.880768 TTAGACTCGTAAAGTATTTCGTGTAC 57.119 34.615 0.00 0.00 40.09 2.90
1693 3281 5.805994 GTCAAATTTTGTGGTCGGTTTGTAA 59.194 36.000 8.89 0.00 0.00 2.41
1694 3282 5.341617 GTCAAATTTTGTGGTCGGTTTGTA 58.658 37.500 8.89 0.00 0.00 2.41
1695 3283 4.177783 GTCAAATTTTGTGGTCGGTTTGT 58.822 39.130 8.89 0.00 0.00 2.83
1696 3284 3.553917 GGTCAAATTTTGTGGTCGGTTTG 59.446 43.478 8.89 0.00 0.00 2.93
1786 3387 1.782028 GACCACACCAGTTTCGGCAC 61.782 60.000 0.00 0.00 0.00 5.01
1842 3443 1.617018 TACCATGCAGCGGCTTCTCT 61.617 55.000 10.92 0.00 41.91 3.10
1949 3584 3.793144 GCGCGCTGTTTCCTCTGG 61.793 66.667 26.67 0.00 0.00 3.86
2015 3650 1.597854 CAAGTGTGAAGAGCCGCCA 60.598 57.895 0.00 0.00 0.00 5.69
2034 3669 0.331616 TGAGACCCCTGACTCGATGA 59.668 55.000 0.00 0.00 36.27 2.92
2041 3676 0.179000 AATCGCATGAGACCCCTGAC 59.821 55.000 0.00 0.00 0.00 3.51
2056 3691 2.125673 AAGGACGCCGGTGAATCG 60.126 61.111 24.59 9.75 0.00 3.34
2065 3700 0.949105 AACATCACACGAAGGACGCC 60.949 55.000 0.00 0.00 46.94 5.68
2066 3701 0.438830 GAACATCACACGAAGGACGC 59.561 55.000 0.00 0.00 46.94 5.19
2163 3806 6.014925 GGTCAACCTACAAAATTACCATTGGT 60.015 38.462 13.94 13.94 40.16 3.67


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

AutoCloner maintained by Alex Coulton.