Multiple sequence alignment - TraesCS5B01G076200

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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 TraesCS5B01G076200 chr5B 100.000 2318 0 0 1 2318 91111112 91113429 0.000000e+00 4281.0
1 TraesCS5B01G076200 chr5D 90.987 2330 153 32 2 2318 84184680 84186965 0.000000e+00 3086.0
2 TraesCS5B01G076200 chr5A 90.085 1755 125 26 586 2318 78480210 78481937 0.000000e+00 2231.0
3 TraesCS5B01G076200 chr5A 90.413 605 37 10 2 599 78477926 78478516 0.000000e+00 776.0
4 TraesCS5B01G076200 chr2B 79.479 921 136 38 658 1552 654546527 654545634 2.550000e-169 604.0
5 TraesCS5B01G076200 chr2B 79.391 854 127 36 658 1485 654528278 654527448 7.240000e-155 556.0
6 TraesCS5B01G076200 chr2B 79.459 740 116 28 801 1516 654588688 654587961 2.070000e-135 492.0
7 TraesCS5B01G076200 chr2B 88.636 44 4 1 252 295 654549695 654549653 4.000000e-03 52.8
8 TraesCS5B01G076200 chr2A 79.162 883 133 39 694 1549 691115798 691116656 4.320000e-157 564.0
9 TraesCS5B01G076200 chr2A 79.904 622 91 26 911 1516 691159528 691160131 2.130000e-115 425.0
10 TraesCS5B01G076200 chr2A 80.576 278 33 14 658 924 691158251 691158518 6.540000e-46 195.0
11 TraesCS5B01G076200 chr2A 87.692 65 4 2 235 295 691168183 691168247 3.190000e-09 73.1


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 TraesCS5B01G076200 chr5B 91111112 91113429 2317 False 4281.0 4281 100.0000 1 2318 1 chr5B.!!$F1 2317
1 TraesCS5B01G076200 chr5D 84184680 84186965 2285 False 3086.0 3086 90.9870 2 2318 1 chr5D.!!$F1 2316
2 TraesCS5B01G076200 chr5A 78477926 78481937 4011 False 1503.5 2231 90.2490 2 2318 2 chr5A.!!$F1 2316
3 TraesCS5B01G076200 chr2B 654527448 654528278 830 True 556.0 556 79.3910 658 1485 1 chr2B.!!$R1 827
4 TraesCS5B01G076200 chr2B 654587961 654588688 727 True 492.0 492 79.4590 801 1516 1 chr2B.!!$R2 715
5 TraesCS5B01G076200 chr2B 654545634 654549695 4061 True 328.4 604 84.0575 252 1552 2 chr2B.!!$R3 1300
6 TraesCS5B01G076200 chr2A 691115798 691116656 858 False 564.0 564 79.1620 694 1549 1 chr2A.!!$F1 855
7 TraesCS5B01G076200 chr2A 691158251 691160131 1880 False 310.0 425 80.2400 658 1516 2 chr2A.!!$F3 858

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
847 5008 1.680338 AGTGTTGTTCCTGCTTGACC 58.32 50.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2179 7404 0.109827 TGTTGCATTGCCGTTCGATG 60.11 50.0 6.12 0.0 39.19 3.84 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
523 543 5.788450 ACATAGAACACTTGAGAGTTCAGG 58.212 41.667 18.85 11.89 44.43 3.86
547 567 4.096984 GGATGTCTGAATGGATTTGGTCAC 59.903 45.833 0.00 0.00 0.00 3.67
582 602 7.944061 TCAATCTTCAAAATGTTGTCATGAGT 58.056 30.769 0.00 0.00 36.07 3.41
593 613 6.791887 TGTTGTCATGAGTCATCTTTCTTC 57.208 37.500 1.56 0.00 0.00 2.87
731 4883 7.667043 TGCTTCGTTGTATATCTTTTTGTCT 57.333 32.000 0.00 0.00 0.00 3.41
846 5007 3.877508 ACTTAGTGTTGTTCCTGCTTGAC 59.122 43.478 0.00 0.00 0.00 3.18
847 5008 1.680338 AGTGTTGTTCCTGCTTGACC 58.320 50.000 0.00 0.00 0.00 4.02
966 6151 3.600388 AGACCGAAAACTCCAATAGCAG 58.400 45.455 0.00 0.00 0.00 4.24
1007 6193 0.681887 TCACCAGCATCAATGGCCAG 60.682 55.000 13.05 0.00 41.87 4.85
1177 6363 2.967076 CTGAGTGTTGTGCCGCGT 60.967 61.111 4.92 0.00 0.00 6.01
1355 6543 2.874701 CCATAAGCATCTAGGTGTGTGC 59.125 50.000 4.60 1.37 37.84 4.57
1364 6552 0.679505 TAGGTGTGTGCCAGAGTGTC 59.320 55.000 0.00 0.00 0.00 3.67
1653 6870 9.048446 GTGTGTTTCCTAGTGAACAAGTAAATA 57.952 33.333 9.06 0.00 31.05 1.40
1663 6880 8.942338 AGTGAACAAGTAAATATAGATCGCAA 57.058 30.769 0.00 0.00 0.00 4.85
1665 6882 9.982291 GTGAACAAGTAAATATAGATCGCAAAA 57.018 29.630 0.00 0.00 0.00 2.44
1738 6962 2.190578 CCCATGTCCGAAGCCTCC 59.809 66.667 0.00 0.00 0.00 4.30
1739 6963 2.202932 CCATGTCCGAAGCCTCCG 60.203 66.667 0.00 0.00 0.00 4.63
1777 7001 0.761702 ACCGCATATAACCCGGACCT 60.762 55.000 0.73 0.00 44.55 3.85
1779 7003 0.320421 CGCATATAACCCGGACCTGG 60.320 60.000 0.73 0.00 0.00 4.45
1810 7034 4.518970 AGCACTACATTGGGTAACAGTTTG 59.481 41.667 0.00 0.00 39.74 2.93
1812 7036 5.067273 CACTACATTGGGTAACAGTTTGGA 58.933 41.667 0.00 0.00 39.74 3.53
1815 7039 5.529581 ACATTGGGTAACAGTTTGGAAAG 57.470 39.130 0.00 0.00 39.74 2.62
1940 7165 2.869101 TCCAACACGAAATCCCATCA 57.131 45.000 0.00 0.00 0.00 3.07
1955 7180 1.077716 ATCACTAGCCCCCGCAAAC 60.078 57.895 0.00 0.00 37.52 2.93
1960 7185 1.001887 TAGCCCCCGCAAACGAAAT 60.002 52.632 0.00 0.00 43.93 2.17
1969 7194 2.093783 CCGCAAACGAAATCTAGGTCAC 59.906 50.000 0.00 0.00 43.93 3.67
1999 7224 0.984230 TCACCAACTCATGTCCCCTC 59.016 55.000 0.00 0.00 0.00 4.30
2007 7232 1.077212 CATGTCCCCTCCCAAGCAG 60.077 63.158 0.00 0.00 0.00 4.24
2010 7235 3.333219 TCCCCTCCCAAGCAGCAG 61.333 66.667 0.00 0.00 0.00 4.24
2012 7237 2.759114 CCCTCCCAAGCAGCAGAA 59.241 61.111 0.00 0.00 0.00 3.02
2015 7240 1.302033 CTCCCAAGCAGCAGAACGT 60.302 57.895 0.00 0.00 0.00 3.99
2073 7298 4.424711 GGGCATTGGGCTCCGTCA 62.425 66.667 0.00 0.00 44.01 4.35
2080 7305 3.148279 GGGCTCCGTCACCGATCT 61.148 66.667 0.00 0.00 35.63 2.75
2095 7320 1.153289 ATCTGCATCCGCACTGTCC 60.153 57.895 0.00 0.00 45.36 4.02
2101 7326 1.977009 ATCCGCACTGTCCTGACGA 60.977 57.895 0.00 0.00 0.00 4.20
2109 7334 0.315251 CTGTCCTGACGAGCAAGACA 59.685 55.000 11.78 11.78 43.75 3.41
2117 7342 1.079543 CGAGCAAGACAGAGGTGGG 60.080 63.158 0.00 0.00 0.00 4.61
2130 7355 2.281484 GTGGGAGCTGCGTTTGGA 60.281 61.111 0.00 0.00 0.00 3.53
2135 7360 4.269523 AGCTGCGTTTGGAGGGCA 62.270 61.111 0.00 0.00 33.49 5.36
2166 7391 3.515286 TCGTCCATCGACTCGGCC 61.515 66.667 0.00 0.00 44.01 6.13
2167 7392 3.518998 CGTCCATCGACTCGGCCT 61.519 66.667 0.00 0.00 42.86 5.19
2168 7393 2.105128 GTCCATCGACTCGGCCTG 59.895 66.667 0.00 0.00 35.99 4.85
2169 7394 3.147595 TCCATCGACTCGGCCTGG 61.148 66.667 0.00 0.00 0.00 4.45
2170 7395 4.227134 CCATCGACTCGGCCTGGG 62.227 72.222 0.00 0.00 0.00 4.45
2171 7396 4.899239 CATCGACTCGGCCTGGGC 62.899 72.222 10.75 10.75 41.06 5.36
2184 7409 3.304251 TGGGCGAACCATCATCGA 58.696 55.556 0.00 0.00 46.80 3.59
2185 7410 1.599576 TGGGCGAACCATCATCGAA 59.400 52.632 0.00 0.00 46.80 3.71
2186 7411 0.742990 TGGGCGAACCATCATCGAAC 60.743 55.000 0.00 0.00 46.80 3.95
2187 7412 1.636340 GGCGAACCATCATCGAACG 59.364 57.895 0.00 0.00 42.76 3.95
2188 7413 1.636340 GCGAACCATCATCGAACGG 59.364 57.895 0.00 0.00 42.76 4.44
2189 7414 1.636340 CGAACCATCATCGAACGGC 59.364 57.895 0.00 0.00 42.76 5.68
2190 7415 1.081556 CGAACCATCATCGAACGGCA 61.082 55.000 0.00 0.00 42.76 5.69
2196 7421 1.093972 ATCATCGAACGGCAATGCAA 58.906 45.000 7.79 0.00 0.00 4.08
2200 7425 0.595588 TCGAACGGCAATGCAACATT 59.404 45.000 7.79 0.00 0.00 2.71
2202 7427 2.421775 TCGAACGGCAATGCAACATTAT 59.578 40.909 7.79 0.00 0.00 1.28
2209 7434 4.319405 CGGCAATGCAACATTATATCGACA 60.319 41.667 7.79 0.00 0.00 4.35
2230 7455 4.956075 ACAATTCAAAGGACACAAGAAGGT 59.044 37.500 0.00 0.00 0.00 3.50
2232 7457 6.605594 ACAATTCAAAGGACACAAGAAGGTTA 59.394 34.615 0.00 0.00 0.00 2.85
2253 7478 1.407299 CCACCATGATTCTCGAAGCCA 60.407 52.381 0.00 0.00 0.00 4.75
2277 7502 4.054671 GACCGATCAAGAGACATGGATTC 58.945 47.826 0.00 0.00 0.00 2.52
2286 7511 0.740149 GACATGGATTCGGCATGCAA 59.260 50.000 21.36 6.46 36.69 4.08
2308 7533 4.329638 TTTTTGGGATGCCTGGATCTTA 57.670 40.909 4.35 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 0.252148 TCAGGGCATGGAAATTGGCA 60.252 50.000 0.00 0.00 41.14 4.92
303 310 1.722011 AAATCACTACAGTTCGGCCG 58.278 50.000 22.12 22.12 0.00 6.13
476 496 5.611796 TCACTGCCGAATTATATGAATGC 57.388 39.130 0.00 0.00 0.00 3.56
523 543 3.633986 GACCAAATCCATTCAGACATCCC 59.366 47.826 0.00 0.00 0.00 3.85
582 602 8.246180 GCCATTTACATTGAAGAAGAAAGATGA 58.754 33.333 0.00 0.00 0.00 2.92
593 613 6.705381 TCAACCTTTTGCCATTTACATTGAAG 59.295 34.615 0.00 0.00 32.17 3.02
731 4883 6.093909 TGAACGATAACGACTACCATAGTTGA 59.906 38.462 9.73 0.00 41.76 3.18
846 5007 4.634004 TGTTCATTAAGCGTGTATTCTGGG 59.366 41.667 0.00 0.00 0.00 4.45
847 5008 5.121611 TGTGTTCATTAAGCGTGTATTCTGG 59.878 40.000 0.00 0.00 0.00 3.86
966 6151 7.244192 GTGATGTATTTAGTTTTCTGCTGGAC 58.756 38.462 0.00 0.00 0.00 4.02
1007 6193 3.281240 CAGCCAATGCCTGTGACC 58.719 61.111 0.00 0.00 38.69 4.02
1177 6363 4.644685 GCATGATAGGTTTGCCTTTCCTAA 59.355 41.667 0.00 0.00 44.18 2.69
1355 6543 3.706698 CATATGTACACCGACACTCTGG 58.293 50.000 0.00 0.00 30.52 3.86
1573 6783 6.676950 TGCAAAAGACACATACAAGGTATTG 58.323 36.000 0.00 0.00 42.46 1.90
1574 6784 6.892658 TGCAAAAGACACATACAAGGTATT 57.107 33.333 0.00 0.00 0.00 1.89
1653 6870 6.319658 AGTGACCAATGAATTTTGCGATCTAT 59.680 34.615 0.00 0.00 0.00 1.98
1655 6872 4.460382 AGTGACCAATGAATTTTGCGATCT 59.540 37.500 0.00 0.00 0.00 2.75
1656 6873 4.560035 CAGTGACCAATGAATTTTGCGATC 59.440 41.667 0.00 0.00 0.00 3.69
1663 6880 7.701539 TTACATAGCAGTGACCAATGAATTT 57.298 32.000 1.32 0.00 0.00 1.82
1665 6882 7.886629 AATTACATAGCAGTGACCAATGAAT 57.113 32.000 1.32 0.00 0.00 2.57
1702 6925 1.379527 GGTTTTAGCCCGATGTGAGG 58.620 55.000 0.00 0.00 0.00 3.86
1761 6985 1.053424 TCCAGGTCCGGGTTATATGC 58.947 55.000 8.03 0.00 0.00 3.14
1763 6987 3.117776 GGTTTTCCAGGTCCGGGTTATAT 60.118 47.826 8.03 0.00 40.31 0.86
1779 7003 3.320826 ACCCAATGTAGTGCTTGGTTTTC 59.679 43.478 8.04 0.00 40.28 2.29
1907 7132 3.934579 CGTGTTGGATCATCTCAATGTGA 59.065 43.478 0.00 0.00 34.32 3.58
1909 7134 4.206477 TCGTGTTGGATCATCTCAATGT 57.794 40.909 0.00 0.00 34.32 2.71
1913 7138 4.191544 GGATTTCGTGTTGGATCATCTCA 58.808 43.478 0.00 0.00 0.00 3.27
1921 7146 2.039746 AGTGATGGGATTTCGTGTTGGA 59.960 45.455 0.00 0.00 0.00 3.53
1940 7165 2.400269 TTTCGTTTGCGGGGGCTAGT 62.400 55.000 0.00 0.00 38.89 2.57
1955 7180 3.427243 GAGTCACGTGACCTAGATTTCG 58.573 50.000 38.00 0.00 45.85 3.46
1960 7185 2.168947 GCGAGTCACGTGACCTAGA 58.831 57.895 38.00 6.68 45.85 2.43
1999 7224 1.302033 AGACGTTCTGCTGCTTGGG 60.302 57.895 0.00 0.00 0.00 4.12
2056 7281 4.424711 TGACGGAGCCCAATGCCC 62.425 66.667 0.00 0.00 42.71 5.36
2095 7320 0.600557 ACCTCTGTCTTGCTCGTCAG 59.399 55.000 0.00 0.00 0.00 3.51
2101 7326 1.835927 GCTCCCACCTCTGTCTTGCT 61.836 60.000 0.00 0.00 0.00 3.91
2109 7334 2.520536 AAACGCAGCTCCCACCTCT 61.521 57.895 0.00 0.00 0.00 3.69
2117 7342 3.435186 GCCCTCCAAACGCAGCTC 61.435 66.667 0.00 0.00 0.00 4.09
2168 7393 1.762222 CGTTCGATGATGGTTCGCCC 61.762 60.000 0.00 0.00 36.56 6.13
2169 7394 1.636340 CGTTCGATGATGGTTCGCC 59.364 57.895 0.00 0.00 36.56 5.54
2170 7395 1.636340 CCGTTCGATGATGGTTCGC 59.364 57.895 0.00 0.00 36.56 4.70
2171 7396 1.081556 TGCCGTTCGATGATGGTTCG 61.082 55.000 0.00 0.00 37.94 3.95
2172 7397 1.083489 TTGCCGTTCGATGATGGTTC 58.917 50.000 0.00 0.00 0.00 3.62
2173 7398 1.401552 CATTGCCGTTCGATGATGGTT 59.598 47.619 0.00 0.00 38.60 3.67
2174 7399 1.016627 CATTGCCGTTCGATGATGGT 58.983 50.000 0.00 0.00 38.60 3.55
2175 7400 0.317269 GCATTGCCGTTCGATGATGG 60.317 55.000 0.00 0.00 38.60 3.51
2176 7401 0.377905 TGCATTGCCGTTCGATGATG 59.622 50.000 6.12 0.00 38.60 3.07
2177 7402 1.093972 TTGCATTGCCGTTCGATGAT 58.906 45.000 6.12 0.00 38.60 2.45
2178 7403 0.167908 GTTGCATTGCCGTTCGATGA 59.832 50.000 6.12 0.00 38.60 2.92
2179 7404 0.109827 TGTTGCATTGCCGTTCGATG 60.110 50.000 6.12 0.00 39.19 3.84
2180 7405 0.810648 ATGTTGCATTGCCGTTCGAT 59.189 45.000 6.12 0.00 0.00 3.59
2181 7406 0.595588 AATGTTGCATTGCCGTTCGA 59.404 45.000 6.12 0.00 0.00 3.71
2182 7407 2.254918 TAATGTTGCATTGCCGTTCG 57.745 45.000 6.12 0.00 0.00 3.95
2183 7408 4.612614 CGATATAATGTTGCATTGCCGTTC 59.387 41.667 6.12 0.00 0.00 3.95
2184 7409 4.274705 TCGATATAATGTTGCATTGCCGTT 59.725 37.500 6.12 2.13 0.00 4.44
2185 7410 3.812609 TCGATATAATGTTGCATTGCCGT 59.187 39.130 6.12 0.00 0.00 5.68
2186 7411 4.151070 GTCGATATAATGTTGCATTGCCG 58.849 43.478 6.12 0.00 0.00 5.69
2187 7412 5.107109 TGTCGATATAATGTTGCATTGCC 57.893 39.130 6.12 0.00 0.00 4.52
2188 7413 7.379262 TGAATTGTCGATATAATGTTGCATTGC 59.621 33.333 0.46 0.46 0.00 3.56
2189 7414 8.785468 TGAATTGTCGATATAATGTTGCATTG 57.215 30.769 4.78 0.00 0.00 2.82
2190 7415 9.800433 TTTGAATTGTCGATATAATGTTGCATT 57.200 25.926 0.00 0.00 0.00 3.56
2196 7421 8.612619 GTGTCCTTTGAATTGTCGATATAATGT 58.387 33.333 0.00 0.00 0.00 2.71
2200 7425 8.038351 TCTTGTGTCCTTTGAATTGTCGATATA 58.962 33.333 0.00 0.00 0.00 0.86
2202 7427 6.227522 TCTTGTGTCCTTTGAATTGTCGATA 58.772 36.000 0.00 0.00 0.00 2.92
2209 7434 6.040504 GGTAACCTTCTTGTGTCCTTTGAATT 59.959 38.462 0.00 0.00 0.00 2.17
2230 7455 3.531538 GCTTCGAGAATCATGGTGGTAA 58.468 45.455 0.00 0.00 33.17 2.85
2232 7457 1.407437 GGCTTCGAGAATCATGGTGGT 60.407 52.381 0.00 0.00 33.17 4.16
2240 7465 1.140407 CGGTCGTGGCTTCGAGAATC 61.140 60.000 5.72 0.00 40.52 2.52
2253 7478 1.135139 CCATGTCTCTTGATCGGTCGT 59.865 52.381 0.00 0.00 0.00 4.34
2277 7502 1.666700 CATCCCAAAAATTGCATGCCG 59.333 47.619 16.68 0.00 0.00 5.69
2286 7511 3.409804 AGATCCAGGCATCCCAAAAAT 57.590 42.857 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.