Multiple sequence alignment - TraesCS2B01G110600

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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 TraesCS2B01G110600 chr2B 100.000 2588 0 0 1 2588 72582057 72579470 0.000000e+00 4780
1 TraesCS2B01G110600 chr2A 91.520 2052 88 36 565 2586 48866646 48864651 0.000000e+00 2747
2 TraesCS2B01G110600 chr2D 94.669 1782 51 20 351 2100 45540098 45538329 0.000000e+00 2724
3 TraesCS2B01G110600 chr2D 91.685 457 25 9 2143 2588 45538323 45537869 2.830000e-174 621
4 TraesCS2B01G110600 chr2D 95.798 357 10 1 1 357 45540610 45540259 2.890000e-159 571


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 TraesCS2B01G110600 chr2B 72579470 72582057 2587 True 4780.000000 4780 100.000000 1 2588 1 chr2B.!!$R1 2587
1 TraesCS2B01G110600 chr2A 48864651 48866646 1995 True 2747.000000 2747 91.520000 565 2586 1 chr2A.!!$R1 2021
2 TraesCS2B01G110600 chr2D 45537869 45540610 2741 True 1305.333333 2724 94.050667 1 2588 3 chr2D.!!$R1 2587

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
367 535 0.392863 CACCAACATCCATCGCCAGA 60.393 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2117 2330 0.036022 GTTGCTCTGAGCCCTTGACT 59.964 55.0 25.61 0.0 41.51 3.41 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
31 32 7.650504 TGAAAATCAGATTCAGCTTGAACTTTG 59.349 33.333 0.00 2.10 39.45 2.77
56 57 4.275508 AGCCACCACCCTGCACAG 62.276 66.667 0.00 0.00 0.00 3.66
160 161 9.476202 TCATTAGGTAATTTGTCTGTATCATCG 57.524 33.333 0.00 0.00 0.00 3.84
173 174 7.915923 TGTCTGTATCATCGTCAAAACTATCTC 59.084 37.037 0.00 0.00 0.00 2.75
229 230 0.951558 CCTGTTCAAAACCCTCCACG 59.048 55.000 0.00 0.00 0.00 4.94
305 306 2.416431 GGGTGTCTCTGCATGCAATTTC 60.416 50.000 22.88 12.88 0.00 2.17
331 332 7.602517 ATCCATCGCTTAAAGATAATGTAGC 57.397 36.000 0.00 0.00 0.00 3.58
367 535 0.392863 CACCAACATCCATCGCCAGA 60.393 55.000 0.00 0.00 0.00 3.86
384 552 1.370051 GAAACCGCGGTGCTTGTTC 60.370 57.895 34.95 26.38 0.00 3.18
393 561 1.653151 GGTGCTTGTTCCCGATAGTC 58.347 55.000 0.00 0.00 0.00 2.59
468 644 2.721603 GTGCGACGTCTTATGCTAGATG 59.278 50.000 14.70 0.00 37.23 2.90
523 699 6.385649 TTGCGGGAAATAGTGATTTTATCC 57.614 37.500 0.00 0.00 35.33 2.59
605 786 1.526986 GCATGAACGAAACACGATCCG 60.527 52.381 0.00 0.00 45.77 4.18
636 817 3.572584 AGTCGTGTGGATCGTAAAGAAC 58.427 45.455 0.00 0.00 0.00 3.01
657 838 2.672478 CGCAAGTGACCGAAGATCTCTT 60.672 50.000 0.00 0.00 39.23 2.85
997 1192 1.671742 GTCGCCTTCCACTCTTCCA 59.328 57.895 0.00 0.00 0.00 3.53
1035 1231 2.345244 CCACACTTCGCAGGAGCT 59.655 61.111 0.00 0.00 39.10 4.09
1506 1708 4.785453 CTGCCGAGGAAGGTGCCC 62.785 72.222 0.00 0.00 0.00 5.36
1563 1765 4.754618 ACTGCAAACGAATGTGATCTTGTA 59.245 37.500 0.00 0.00 0.00 2.41
1566 1768 7.119116 ACTGCAAACGAATGTGATCTTGTATAA 59.881 33.333 0.00 0.00 0.00 0.98
1599 1802 3.603532 TGGCATGTGATGAGAGACTTTC 58.396 45.455 0.00 0.00 0.00 2.62
1601 1804 3.622163 GGCATGTGATGAGAGACTTTCTG 59.378 47.826 0.00 0.00 35.87 3.02
1602 1805 4.502016 GCATGTGATGAGAGACTTTCTGA 58.498 43.478 0.00 0.00 35.87 3.27
1603 1806 4.934001 GCATGTGATGAGAGACTTTCTGAA 59.066 41.667 0.00 0.00 35.87 3.02
1604 1807 5.163874 GCATGTGATGAGAGACTTTCTGAAC 60.164 44.000 0.00 0.00 35.87 3.18
1605 1808 4.887748 TGTGATGAGAGACTTTCTGAACC 58.112 43.478 0.00 0.00 35.87 3.62
1703 1914 2.798499 CGGCCCGTGATACTGTTCTAAG 60.798 54.545 0.00 0.00 0.00 2.18
1704 1915 2.167900 GGCCCGTGATACTGTTCTAAGT 59.832 50.000 0.00 0.00 0.00 2.24
1705 1916 3.369157 GGCCCGTGATACTGTTCTAAGTT 60.369 47.826 0.00 0.00 0.00 2.66
1706 1917 4.142093 GGCCCGTGATACTGTTCTAAGTTA 60.142 45.833 0.00 0.00 0.00 2.24
1707 1918 4.802563 GCCCGTGATACTGTTCTAAGTTAC 59.197 45.833 0.00 0.00 0.00 2.50
1708 1919 5.622914 GCCCGTGATACTGTTCTAAGTTACA 60.623 44.000 0.00 0.00 0.00 2.41
1710 1921 6.869913 CCCGTGATACTGTTCTAAGTTACAAA 59.130 38.462 0.00 0.00 0.00 2.83
1711 1922 7.548075 CCCGTGATACTGTTCTAAGTTACAAAT 59.452 37.037 0.00 0.00 0.00 2.32
1712 1923 8.932791 CCGTGATACTGTTCTAAGTTACAAATT 58.067 33.333 0.00 0.00 0.00 1.82
1713 1924 9.953825 CGTGATACTGTTCTAAGTTACAAATTC 57.046 33.333 0.00 0.00 0.00 2.17
1830 2043 1.758783 GTCAAGCTTGGTTCGCTTTG 58.241 50.000 25.73 0.00 44.76 2.77
2075 2288 2.368439 GGCCTGCACATGAATAAGTCA 58.632 47.619 0.00 0.00 41.67 3.41
2100 2313 4.278170 GGGATGAGAGTGTCTGATGAGTAG 59.722 50.000 0.00 0.00 0.00 2.57
2101 2314 4.278170 GGATGAGAGTGTCTGATGAGTAGG 59.722 50.000 0.00 0.00 0.00 3.18
2102 2315 3.625853 TGAGAGTGTCTGATGAGTAGGG 58.374 50.000 0.00 0.00 0.00 3.53
2104 2317 1.410882 GAGTGTCTGATGAGTAGGGCC 59.589 57.143 0.00 0.00 0.00 5.80
2105 2318 1.007721 AGTGTCTGATGAGTAGGGCCT 59.992 52.381 12.58 12.58 0.00 5.19
2106 2319 1.137872 GTGTCTGATGAGTAGGGCCTG 59.862 57.143 18.53 0.00 0.00 4.85
2107 2320 0.105778 GTCTGATGAGTAGGGCCTGC 59.894 60.000 18.53 16.41 0.00 4.85
2108 2321 1.068753 CTGATGAGTAGGGCCTGCG 59.931 63.158 18.53 0.00 0.00 5.18
2109 2322 2.280457 GATGAGTAGGGCCTGCGC 60.280 66.667 18.53 18.22 0.00 6.09
2110 2323 3.083349 ATGAGTAGGGCCTGCGCA 61.083 61.111 27.85 27.85 36.38 6.09
2111 2324 2.388890 GATGAGTAGGGCCTGCGCAT 62.389 60.000 33.69 33.69 38.91 4.73
2112 2325 2.590007 GAGTAGGGCCTGCGCATG 60.590 66.667 19.69 10.09 36.38 4.06
2113 2326 3.083349 AGTAGGGCCTGCGCATGA 61.083 61.111 18.53 0.00 36.38 3.07
2114 2327 2.124736 GTAGGGCCTGCGCATGAA 60.125 61.111 18.53 0.00 36.38 2.57
2115 2328 1.526917 GTAGGGCCTGCGCATGAAT 60.527 57.895 18.53 3.61 36.38 2.57
2116 2329 0.250295 GTAGGGCCTGCGCATGAATA 60.250 55.000 18.53 2.65 36.38 1.75
2117 2330 0.472044 TAGGGCCTGCGCATGAATAA 59.528 50.000 18.53 0.00 36.38 1.40
2118 2331 0.820891 AGGGCCTGCGCATGAATAAG 60.821 55.000 17.36 0.00 36.38 1.73
2119 2332 1.103398 GGGCCTGCGCATGAATAAGT 61.103 55.000 17.36 0.00 36.38 2.24
2120 2333 0.308993 GGCCTGCGCATGAATAAGTC 59.691 55.000 17.36 0.00 36.38 3.01
2121 2334 1.016627 GCCTGCGCATGAATAAGTCA 58.983 50.000 17.36 0.00 41.67 3.41
2122 2335 1.401552 GCCTGCGCATGAATAAGTCAA 59.598 47.619 17.36 0.00 40.50 3.18
2123 2336 2.540361 GCCTGCGCATGAATAAGTCAAG 60.540 50.000 17.36 0.00 40.50 3.02
2124 2337 2.032550 CCTGCGCATGAATAAGTCAAGG 59.967 50.000 12.24 0.00 40.50 3.61
2125 2338 2.016318 TGCGCATGAATAAGTCAAGGG 58.984 47.619 5.66 0.00 40.50 3.95
2126 2339 2.763249 CGCATGAATAAGTCAAGGGC 57.237 50.000 0.00 0.00 40.50 5.19
2127 2340 2.292267 CGCATGAATAAGTCAAGGGCT 58.708 47.619 0.00 0.00 40.50 5.19
2128 2341 2.289002 CGCATGAATAAGTCAAGGGCTC 59.711 50.000 0.00 0.00 40.50 4.70
2129 2342 3.282021 GCATGAATAAGTCAAGGGCTCA 58.718 45.455 0.00 0.00 40.50 4.26
2130 2343 3.314635 GCATGAATAAGTCAAGGGCTCAG 59.685 47.826 0.00 0.00 40.50 3.35
2131 2344 4.774124 CATGAATAAGTCAAGGGCTCAGA 58.226 43.478 0.00 0.00 40.50 3.27
2132 2345 4.478206 TGAATAAGTCAAGGGCTCAGAG 57.522 45.455 0.00 0.00 31.51 3.35
2133 2346 2.998316 ATAAGTCAAGGGCTCAGAGC 57.002 50.000 14.69 14.69 41.46 4.09
2137 2350 0.957888 GTCAAGGGCTCAGAGCAACC 60.958 60.000 24.09 16.27 44.75 3.77
2362 2582 5.418676 TGAGATGACAATAATTGACTGCGA 58.581 37.500 0.00 0.00 0.00 5.10
2422 2644 1.846439 CCTCCATGGAGCCCTTCTTTA 59.154 52.381 32.97 0.00 40.69 1.85
2523 2746 4.827692 TCATCGGTTTTATGTAGTGCAGT 58.172 39.130 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 1.871418 AGATGAGCTGGACAAGGCTA 58.129 50.000 0.00 0.00 39.05 3.93
160 161 7.615582 TGACAATGATGGAGATAGTTTTGAC 57.384 36.000 0.00 0.00 0.00 3.18
173 174 5.128171 ACCCTTTTGATGATGACAATGATGG 59.872 40.000 0.00 0.00 0.00 3.51
229 230 2.239400 CTTTTCCTCCTGGGTTTCACC 58.761 52.381 0.00 0.00 37.60 4.02
243 244 8.654230 AAAAGAGATGAAAAAGAAGCTTTTCC 57.346 30.769 0.00 0.00 42.27 3.13
271 272 4.524714 CAGAGACACCCACTAAGAAGAAGA 59.475 45.833 0.00 0.00 0.00 2.87
272 273 4.815269 CAGAGACACCCACTAAGAAGAAG 58.185 47.826 0.00 0.00 0.00 2.85
273 274 3.006967 GCAGAGACACCCACTAAGAAGAA 59.993 47.826 0.00 0.00 0.00 2.52
274 275 2.563179 GCAGAGACACCCACTAAGAAGA 59.437 50.000 0.00 0.00 0.00 2.87
275 276 2.300152 TGCAGAGACACCCACTAAGAAG 59.700 50.000 0.00 0.00 0.00 2.85
305 306 7.959651 GCTACATTATCTTTAAGCGATGGATTG 59.040 37.037 0.00 0.00 0.00 2.67
367 535 2.719354 GAACAAGCACCGCGGTTT 59.281 55.556 32.11 20.98 32.94 3.27
393 561 3.699779 TCGTCTTCTTGATCTCATCCG 57.300 47.619 0.00 0.00 0.00 4.18
547 723 7.687837 GCCACAGAACAGATCCAGAAGATATTA 60.688 40.741 0.00 0.00 34.42 0.98
548 724 6.590068 CCACAGAACAGATCCAGAAGATATT 58.410 40.000 0.00 0.00 34.42 1.28
549 725 5.454471 GCCACAGAACAGATCCAGAAGATAT 60.454 44.000 0.00 0.00 34.42 1.63
605 786 1.340248 TCCACACGACTCACTTTCTCC 59.660 52.381 0.00 0.00 0.00 3.71
636 817 1.135257 AGAGATCTTCGGTCACTTGCG 60.135 52.381 0.00 0.00 0.00 4.85
657 838 2.243602 AAAACGCGTGGAGTAGGAAA 57.756 45.000 14.98 0.00 0.00 3.13
685 866 4.974275 GTGCTGACGCGATATTACTTTAGA 59.026 41.667 15.93 0.00 39.65 2.10
686 867 4.738252 TGTGCTGACGCGATATTACTTTAG 59.262 41.667 15.93 0.00 39.65 1.85
687 868 4.501559 GTGTGCTGACGCGATATTACTTTA 59.498 41.667 15.93 0.00 39.65 1.85
688 869 3.306166 GTGTGCTGACGCGATATTACTTT 59.694 43.478 15.93 0.00 39.65 2.66
691 886 2.460918 AGTGTGCTGACGCGATATTAC 58.539 47.619 15.93 6.87 39.65 1.89
716 911 2.733227 CGTTATACTCGCCGTTTGGTCT 60.733 50.000 0.00 0.00 37.67 3.85
997 1192 1.299976 GATGTCTTTGGCCGAGGGT 59.700 57.895 1.56 0.00 0.00 4.34
1506 1708 1.739562 GCGTCAGAAGAGCCAGTGG 60.740 63.158 4.20 4.20 0.00 4.00
1589 1792 5.619625 CCAAATGGTTCAGAAAGTCTCTC 57.380 43.478 0.00 0.00 29.07 3.20
1604 1807 4.859304 ACATATATGCAGCACCAAATGG 57.141 40.909 12.79 0.00 42.17 3.16
1703 1914 9.696917 ATCCATTCTGTTTTGAGAATTTGTAAC 57.303 29.630 0.00 0.00 40.11 2.50
1705 1916 9.695526 CAATCCATTCTGTTTTGAGAATTTGTA 57.304 29.630 0.00 0.00 40.11 2.41
1706 1917 7.172019 GCAATCCATTCTGTTTTGAGAATTTGT 59.828 33.333 0.00 0.00 40.11 2.83
1707 1918 7.171848 TGCAATCCATTCTGTTTTGAGAATTTG 59.828 33.333 0.00 0.00 40.11 2.32
1708 1919 7.218614 TGCAATCCATTCTGTTTTGAGAATTT 58.781 30.769 0.00 0.00 40.11 1.82
1710 1921 6.209986 TCTGCAATCCATTCTGTTTTGAGAAT 59.790 34.615 0.00 0.00 42.34 2.40
1711 1922 5.535783 TCTGCAATCCATTCTGTTTTGAGAA 59.464 36.000 0.00 0.00 36.41 2.87
1712 1923 5.072055 TCTGCAATCCATTCTGTTTTGAGA 58.928 37.500 0.00 0.00 0.00 3.27
1713 1924 5.381174 TCTGCAATCCATTCTGTTTTGAG 57.619 39.130 0.00 0.00 0.00 3.02
1716 1927 6.527423 ACAATTCTGCAATCCATTCTGTTTT 58.473 32.000 0.00 0.00 0.00 2.43
1747 1960 2.047679 ACGTAGCAGTCGTTCAGTTC 57.952 50.000 0.00 0.00 38.38 3.01
2075 2288 3.705579 CTCATCAGACACTCTCATCCCTT 59.294 47.826 0.00 0.00 0.00 3.95
2100 2313 1.103398 ACTTATTCATGCGCAGGCCC 61.103 55.000 18.83 0.00 38.85 5.80
2101 2314 0.308993 GACTTATTCATGCGCAGGCC 59.691 55.000 18.83 0.00 38.85 5.19
2102 2315 1.016627 TGACTTATTCATGCGCAGGC 58.983 50.000 18.83 2.79 40.52 4.85
2104 2317 2.032550 CCCTTGACTTATTCATGCGCAG 59.967 50.000 18.32 8.46 32.84 5.18
2105 2318 2.016318 CCCTTGACTTATTCATGCGCA 58.984 47.619 14.96 14.96 32.84 6.09
2106 2319 1.268743 GCCCTTGACTTATTCATGCGC 60.269 52.381 0.00 0.00 32.84 6.09
2107 2320 2.289002 GAGCCCTTGACTTATTCATGCG 59.711 50.000 0.00 0.00 32.84 4.73
2108 2321 3.282021 TGAGCCCTTGACTTATTCATGC 58.718 45.455 0.00 0.00 32.84 4.06
2109 2322 4.774124 TCTGAGCCCTTGACTTATTCATG 58.226 43.478 0.00 0.00 32.84 3.07
2110 2323 4.685575 GCTCTGAGCCCTTGACTTATTCAT 60.686 45.833 18.80 0.00 34.48 2.57
2111 2324 3.369892 GCTCTGAGCCCTTGACTTATTCA 60.370 47.826 18.80 0.00 34.48 2.57
2112 2325 3.202097 GCTCTGAGCCCTTGACTTATTC 58.798 50.000 18.80 0.00 34.48 1.75
2113 2326 2.573462 TGCTCTGAGCCCTTGACTTATT 59.427 45.455 25.61 0.00 41.51 1.40
2114 2327 2.191400 TGCTCTGAGCCCTTGACTTAT 58.809 47.619 25.61 0.00 41.51 1.73
2115 2328 1.644509 TGCTCTGAGCCCTTGACTTA 58.355 50.000 25.61 1.79 41.51 2.24
2116 2329 0.767375 TTGCTCTGAGCCCTTGACTT 59.233 50.000 25.61 0.00 41.51 3.01
2117 2330 0.036022 GTTGCTCTGAGCCCTTGACT 59.964 55.000 25.61 0.00 41.51 3.41
2118 2331 0.957888 GGTTGCTCTGAGCCCTTGAC 60.958 60.000 25.61 15.37 41.51 3.18
2119 2332 1.376466 GGTTGCTCTGAGCCCTTGA 59.624 57.895 25.61 4.83 41.51 3.02
2120 2333 2.037136 CGGTTGCTCTGAGCCCTTG 61.037 63.158 25.61 10.42 41.51 3.61
2121 2334 2.056906 AACGGTTGCTCTGAGCCCTT 62.057 55.000 25.61 12.00 41.51 3.95
2122 2335 2.520536 AACGGTTGCTCTGAGCCCT 61.521 57.895 25.61 8.65 41.51 5.19
2123 2336 2.032681 AACGGTTGCTCTGAGCCC 59.967 61.111 25.61 18.90 41.51 5.19
2124 2337 0.884704 TTCAACGGTTGCTCTGAGCC 60.885 55.000 25.61 11.85 41.51 4.70
2125 2338 0.514691 CTTCAACGGTTGCTCTGAGC 59.485 55.000 22.38 22.38 42.82 4.26
2126 2339 2.154854 TCTTCAACGGTTGCTCTGAG 57.845 50.000 15.89 0.00 0.00 3.35
2127 2340 2.613026 TTCTTCAACGGTTGCTCTGA 57.387 45.000 15.89 8.09 0.00 3.27
2128 2341 3.904136 ATTTCTTCAACGGTTGCTCTG 57.096 42.857 15.89 6.06 0.00 3.35
2129 2342 5.763204 TCTTAATTTCTTCAACGGTTGCTCT 59.237 36.000 15.89 0.00 0.00 4.09
2130 2343 5.997385 TCTTAATTTCTTCAACGGTTGCTC 58.003 37.500 15.89 0.00 0.00 4.26
2131 2344 6.385649 TTCTTAATTTCTTCAACGGTTGCT 57.614 33.333 15.89 0.00 0.00 3.91
2132 2345 6.032460 CGATTCTTAATTTCTTCAACGGTTGC 59.968 38.462 15.89 0.00 0.00 4.17
2133 2346 6.523201 CCGATTCTTAATTTCTTCAACGGTTG 59.477 38.462 14.62 14.62 0.00 3.77
2137 2350 5.627172 TGCCGATTCTTAATTTCTTCAACG 58.373 37.500 0.00 0.00 0.00 4.10
2286 2503 4.505922 GCTTCATTCCATCGAGTTCTACTG 59.494 45.833 0.00 0.00 0.00 2.74
2362 2582 6.726299 TCACTCAGCTACTAATGGGCTATAAT 59.274 38.462 0.00 0.00 34.71 1.28
2503 2725 4.391830 CACACTGCACTACATAAAACCGAT 59.608 41.667 0.00 0.00 0.00 4.18
2508 2730 4.260990 GCACACACACTGCACTACATAAAA 60.261 41.667 0.00 0.00 34.56 1.52
2512 2734 1.229428 GCACACACACTGCACTACAT 58.771 50.000 0.00 0.00 34.56 2.29
2514 2737 0.583438 CTGCACACACACTGCACTAC 59.417 55.000 0.00 0.00 39.76 2.73
2542 2766 8.674263 ACAAATTGGTGATTTTGAAAATAGCA 57.326 26.923 2.71 5.72 35.79 3.49
2543 2767 8.992073 AGACAAATTGGTGATTTTGAAAATAGC 58.008 29.630 2.71 3.43 35.79 2.97


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

AutoCloner maintained by Alex Coulton.