Multiple sequence alignment - TraesCS5B01G342400

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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 TraesCS5B01G342400 chr5B 100.000 2389 0 0 1 2389 526664782 526667170 0.000000e+00 4412.0
1 TraesCS5B01G342400 chr5D 94.495 1199 47 7 1177 2362 433190263 433191455 0.000000e+00 1831.0
2 TraesCS5B01G342400 chr5D 95.751 659 28 0 136 794 433184096 433184754 0.000000e+00 1062.0
3 TraesCS5B01G342400 chr5D 98.294 469 7 1 789 1257 433189827 433190294 0.000000e+00 821.0
4 TraesCS5B01G342400 chr5D 97.222 144 4 0 1 144 433183796 433183939 6.600000e-61 244.0
5 TraesCS5B01G342400 chr4A 77.083 144 31 1 237 378 637194715 637194572 5.470000e-12 82.4


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 TraesCS5B01G342400 chr5B 526664782 526667170 2388 False 4412 4412 100.0000 1 2389 1 chr5B.!!$F1 2388
1 TraesCS5B01G342400 chr5D 433189827 433191455 1628 False 1326 1831 96.3945 789 2362 2 chr5D.!!$F2 1573
2 TraesCS5B01G342400 chr5D 433183796 433184754 958 False 653 1062 96.4865 1 794 2 chr5D.!!$F1 793

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
450 616 0.89327 CCCACATCTGGTTTGCGGAA 60.893 55.0 0.0 0.0 35.46 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2182 2410 0.17899 AGGCCACAACCCTTTCTGAC 60.179 55.0 5.01 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
62 63 9.857656 ACATCTCAGTTCACCAATATATTGATT 57.142 29.630 24.17 9.80 40.14 2.57
187 353 8.884323 ACTCAAATAGCAAATATCAGGAGGATA 58.116 33.333 0.00 0.00 42.50 2.59
198 364 4.007581 TCAGGAGGATAGGAACCATGAA 57.992 45.455 0.00 0.00 0.00 2.57
215 381 6.005823 ACCATGAAAGTGACAAAGATGATGA 58.994 36.000 0.00 0.00 0.00 2.92
216 382 6.072286 ACCATGAAAGTGACAAAGATGATGAC 60.072 38.462 0.00 0.00 0.00 3.06
232 398 5.955961 TGATGACATGGTAGGAGATGAAA 57.044 39.130 0.00 0.00 0.00 2.69
264 430 4.475051 TTTGGATCTGGCATGGAAAATG 57.525 40.909 0.00 0.00 0.00 2.32
274 440 3.454375 GCATGGAAAATGCTGGAGAATG 58.546 45.455 3.10 0.00 41.52 2.67
303 469 4.379918 GCAATAGTTGAGAAGAGCCCAAAC 60.380 45.833 0.00 0.00 0.00 2.93
305 471 1.777272 AGTTGAGAAGAGCCCAAACCT 59.223 47.619 0.00 0.00 0.00 3.50
313 479 2.551270 AGAGCCCAAACCTCACTATGA 58.449 47.619 0.00 0.00 0.00 2.15
325 491 6.301169 ACCTCACTATGAAGAAGGTTAAGG 57.699 41.667 0.00 0.00 38.46 2.69
360 526 1.339438 GCTGCAGTCCATGGAAAGAGA 60.339 52.381 18.20 0.00 0.00 3.10
374 540 7.226325 CCATGGAAAGAGACAGTCTCAATTATC 59.774 40.741 28.76 18.33 45.73 1.75
378 544 9.308318 GGAAAGAGACAGTCTCAATTATCTTAC 57.692 37.037 28.76 11.95 45.73 2.34
450 616 0.893270 CCCACATCTGGTTTGCGGAA 60.893 55.000 0.00 0.00 35.46 4.30
467 633 3.367498 GCGGAAGACATAGACAACTCACT 60.367 47.826 0.00 0.00 0.00 3.41
486 652 5.724328 TCACTCGATGACTATTTCAAAGCT 58.276 37.500 0.00 0.00 37.92 3.74
527 693 2.169769 TGGTTGACCCAGATAATCGTCC 59.830 50.000 0.00 0.00 38.72 4.79
692 858 9.936759 TTAAACTGAATTTTATGGCTAAAAGGG 57.063 29.630 7.56 0.00 39.52 3.95
716 882 6.745116 GGTGCTTTTAATATTGTACCCATCC 58.255 40.000 0.00 0.00 30.67 3.51
760 926 4.098960 TGATTCGTATCTTGGACAGGTACC 59.901 45.833 2.73 2.73 35.84 3.34
764 930 3.446161 CGTATCTTGGACAGGTACCTTCA 59.554 47.826 13.15 8.47 35.84 3.02
774 940 8.555896 TGGACAGGTACCTTCATTTATGTATA 57.444 34.615 13.15 0.00 0.00 1.47
912 1078 6.893554 TGATTCAATCATGGAAACTGAAGGAT 59.106 34.615 0.00 0.00 33.59 3.24
971 1137 3.443329 TGCGATTCCATATTGTGCAAAGT 59.557 39.130 0.00 0.00 0.00 2.66
983 1149 9.128107 CATATTGTGCAAAGTCTTTTTCGTTAT 57.872 29.630 0.00 0.00 0.00 1.89
985 1151 5.885881 TGTGCAAAGTCTTTTTCGTTATGT 58.114 33.333 0.00 0.00 0.00 2.29
1174 1340 6.072948 TGTTCATGTTATTGTTACCGACTTGG 60.073 38.462 0.00 0.00 46.41 3.61
1267 1482 4.293415 CAAGAAATGACAACACCAAGCTC 58.707 43.478 0.00 0.00 0.00 4.09
1365 1580 6.823689 TGCATCTTCTCCAACTAAATCTTACC 59.176 38.462 0.00 0.00 0.00 2.85
1405 1620 4.910458 ACTAGGTGGCTGAAAGTAATGT 57.090 40.909 0.00 0.00 35.30 2.71
1427 1642 4.650972 AACTGACCTTGGGTTATAAGCA 57.349 40.909 16.07 0.51 35.25 3.91
1449 1664 8.524870 AGCAGAAGCATAAAACTATGTTTTTG 57.475 30.769 12.63 5.49 45.49 2.44
1472 1687 7.048629 TGTTGAATTTAAACCTGATGCTTGA 57.951 32.000 0.00 0.00 0.00 3.02
1505 1720 7.882179 TGCTAGTTTTCTGTTAAAAGGGAATC 58.118 34.615 0.00 0.00 0.00 2.52
1583 1798 2.967397 CGTCACCGTTGAGCCCTA 59.033 61.111 0.00 0.00 30.10 3.53
1616 1831 6.983307 CGTATTTTGGAGATCTCTGATCTTGT 59.017 38.462 21.81 4.57 0.00 3.16
1671 1886 1.622811 CTTTGGTCAGAGAGTGAGGCT 59.377 52.381 0.00 0.00 35.13 4.58
1672 1887 2.604912 TTGGTCAGAGAGTGAGGCTA 57.395 50.000 0.00 0.00 35.13 3.93
1681 1896 3.205507 AGAGAGTGAGGCTATACTTGGGA 59.794 47.826 5.49 0.00 0.00 4.37
1791 2006 7.549488 GCTATTAGTTTGTTGGTGTGAGTAGAT 59.451 37.037 0.00 0.00 0.00 1.98
1823 2038 2.375509 CTGTGTTCCTTAAAGGAGGGGT 59.624 50.000 0.00 0.00 46.73 4.95
1827 2042 2.643304 GTTCCTTAAAGGAGGGGTGACT 59.357 50.000 0.00 0.00 46.73 3.41
1844 2059 5.279056 GGGTGACTGTAATATCTGGACTAGC 60.279 48.000 0.00 0.00 0.00 3.42
1869 2084 6.994421 ATTTAAGGAGCAAGGAAGGAAAAA 57.006 33.333 0.00 0.00 0.00 1.94
1897 2112 5.126067 AGGAACACCATACATATTCAGTGC 58.874 41.667 0.00 0.00 0.00 4.40
1917 2132 2.863704 GCTGAACTGTTGATTTGTGCCC 60.864 50.000 0.00 0.00 0.00 5.36
1952 2167 6.183360 CCAATGATGGGCATTTATACGGATAC 60.183 42.308 0.00 0.00 44.68 2.24
1953 2168 5.491323 TGATGGGCATTTATACGGATACA 57.509 39.130 0.00 0.00 0.00 2.29
1960 2175 7.720074 TGGGCATTTATACGGATACATGTAAAA 59.280 33.333 10.14 4.47 31.10 1.52
1970 2185 6.106673 CGGATACATGTAAAAGGTCTTCTGT 58.893 40.000 10.14 0.00 0.00 3.41
1974 2189 6.435292 ACATGTAAAAGGTCTTCTGTAGGT 57.565 37.500 0.00 0.00 0.00 3.08
2038 2253 5.913137 AGTTCCAACATGACTTGTTTTCA 57.087 34.783 0.00 0.00 46.51 2.69
2041 2256 6.757947 AGTTCCAACATGACTTGTTTTCATTG 59.242 34.615 0.00 0.00 46.51 2.82
2053 2268 7.651808 ACTTGTTTTCATTGTTCCTGTATCTG 58.348 34.615 0.00 0.00 0.00 2.90
2054 2269 7.502226 ACTTGTTTTCATTGTTCCTGTATCTGA 59.498 33.333 0.00 0.00 0.00 3.27
2089 2317 5.514204 GTGATGCTTGTATCTTTGTTGATGC 59.486 40.000 0.90 0.00 0.00 3.91
2106 2334 6.375174 TGTTGATGCTGTGCTAATAACATTCT 59.625 34.615 0.00 0.00 0.00 2.40
2117 2345 7.497249 GTGCTAATAACATTCTGGATGACTTCT 59.503 37.037 2.19 0.00 39.15 2.85
2153 2381 1.397672 TCGAGAGAAGCCCATGAGAG 58.602 55.000 0.00 0.00 37.03 3.20
2175 2403 2.921754 CAAGTTTCGTCTACCCTTAGCG 59.078 50.000 0.00 0.00 0.00 4.26
2182 2410 5.679734 TCGTCTACCCTTAGCGTAATAAG 57.320 43.478 0.00 0.00 33.37 1.73
2194 2422 5.161943 AGCGTAATAAGTCAGAAAGGGTT 57.838 39.130 0.00 0.00 0.00 4.11
2195 2423 4.935808 AGCGTAATAAGTCAGAAAGGGTTG 59.064 41.667 0.00 0.00 0.00 3.77
2231 2459 3.031013 TCAACGGGATCTTCAGATGCTA 58.969 45.455 8.09 0.00 41.79 3.49
2291 2519 3.118038 GGGCATGTACTTCTGTTGGGATA 60.118 47.826 0.00 0.00 0.00 2.59
2324 2552 6.918626 TGATTTCACTGAACTGTTTGTTTCA 58.081 32.000 0.00 0.00 39.30 2.69
2345 2573 6.275494 TCATAGTTTCAAGTATGGACGTGA 57.725 37.500 12.49 0.00 41.55 4.35
2346 2574 6.330278 TCATAGTTTCAAGTATGGACGTGAG 58.670 40.000 12.49 0.00 43.58 3.51
2347 2575 4.866508 AGTTTCAAGTATGGACGTGAGA 57.133 40.909 0.00 0.00 43.58 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 8.811994 TCAACCGATATAAGGTGATCATCATTA 58.188 33.333 9.06 6.78 41.95 1.90
100 101 1.816835 GCCATGGCTGGATGACATATG 59.183 52.381 29.98 0.00 43.93 1.78
187 353 4.792068 TCTTTGTCACTTTCATGGTTCCT 58.208 39.130 0.00 0.00 0.00 3.36
198 364 5.319453 ACCATGTCATCATCTTTGTCACTT 58.681 37.500 0.00 0.00 31.15 3.16
215 381 9.347240 CAGAATAATTTTCATCTCCTACCATGT 57.653 33.333 0.00 0.00 0.00 3.21
216 382 9.565090 TCAGAATAATTTTCATCTCCTACCATG 57.435 33.333 0.00 0.00 0.00 3.66
232 398 7.256190 CCATGCCAGATCCAAATCAGAATAATT 60.256 37.037 0.00 0.00 34.07 1.40
264 430 1.679977 TGCCCTTGCATTCTCCAGC 60.680 57.895 0.00 0.00 44.23 4.85
274 440 3.347216 TCTTCTCAACTATTGCCCTTGC 58.653 45.455 0.00 0.00 38.26 4.01
303 469 6.155393 AGACCTTAACCTTCTTCATAGTGAGG 59.845 42.308 0.00 0.00 34.27 3.86
305 471 7.455008 AGAAGACCTTAACCTTCTTCATAGTGA 59.545 37.037 11.94 0.00 44.69 3.41
313 479 4.595350 AGCAGAGAAGACCTTAACCTTCTT 59.405 41.667 0.00 1.42 46.35 2.52
325 491 0.740516 GCAGCCAGAGCAGAGAAGAC 60.741 60.000 0.00 0.00 43.56 3.01
450 616 4.944317 TCATCGAGTGAGTTGTCTATGTCT 59.056 41.667 0.00 0.00 31.80 3.41
467 633 6.037172 GGCTAAAGCTTTGAAATAGTCATCGA 59.963 38.462 22.02 0.00 41.70 3.59
486 652 7.398618 TCAACCAAATTATCCAAGATGGCTAAA 59.601 33.333 0.00 0.00 37.47 1.85
527 693 5.043903 CAGGAGGATACAGTGTAACAATCG 58.956 45.833 7.16 0.00 41.43 3.34
640 806 9.933723 ACAGACTAAAATATACACGTAAAACCT 57.066 29.630 0.00 0.00 0.00 3.50
692 858 6.514376 CGGATGGGTACAATATTAAAAGCACC 60.514 42.308 0.00 0.00 0.00 5.01
715 881 5.411361 TCAACTCAAATTACCTGAATCACGG 59.589 40.000 0.00 0.00 0.00 4.94
716 882 6.480524 TCAACTCAAATTACCTGAATCACG 57.519 37.500 0.00 0.00 0.00 4.35
862 1028 9.353999 CAAGGAAATTAAAAGGAAGAATAACCG 57.646 33.333 0.00 0.00 0.00 4.44
912 1078 2.483714 GCCAGTTCAGAGACAGAACACA 60.484 50.000 8.54 0.00 45.93 3.72
983 1149 9.104965 GGTTTAGCATACTGTATGTGATTTACA 57.895 33.333 24.32 5.43 44.87 2.41
985 1151 9.325198 CAGGTTTAGCATACTGTATGTGATTTA 57.675 33.333 24.32 10.26 38.43 1.40
1267 1482 6.200854 GGCAATCAAAACCTCACTTGTAAAAG 59.799 38.462 0.00 0.00 0.00 2.27
1314 1529 0.242017 GACTTGAAATTGCCAGCGCT 59.758 50.000 2.64 2.64 35.36 5.92
1405 1620 5.486063 TCTGCTTATAACCCAAGGTCAGTTA 59.514 40.000 0.00 0.00 33.12 2.24
1449 1664 8.538409 AATCAAGCATCAGGTTTAAATTCAAC 57.462 30.769 0.00 0.00 32.07 3.18
1467 1682 5.356470 AGAAAACTAGCATCCTGAATCAAGC 59.644 40.000 0.00 0.00 0.00 4.01
1472 1687 8.635765 TTTAACAGAAAACTAGCATCCTGAAT 57.364 30.769 9.01 2.43 0.00 2.57
1505 1720 1.276421 CTGAACTACACCTGGGACCAG 59.724 57.143 11.44 11.44 43.26 4.00
1575 1790 0.396556 TACGCACCAGATAGGGCTCA 60.397 55.000 0.00 0.00 43.89 4.26
1583 1798 3.627395 TCTCCAAAATACGCACCAGAT 57.373 42.857 0.00 0.00 0.00 2.90
1642 1857 1.004044 CTCTGACCAAAGCACCATCCT 59.996 52.381 0.00 0.00 0.00 3.24
1672 1887 5.902613 CATGTCAACATGTTCCCAAGTAT 57.097 39.130 8.48 0.00 46.40 2.12
1791 2006 3.593442 AGGAACACAGTCCCAAATTCA 57.407 42.857 0.00 0.00 38.59 2.57
1823 2038 8.941995 AATAGCTAGTCCAGATATTACAGTCA 57.058 34.615 0.00 0.00 42.63 3.41
1844 2059 7.703058 TTTTCCTTCCTTGCTCCTTAAATAG 57.297 36.000 0.00 0.00 0.00 1.73
1869 2084 6.969043 TGAATATGTATGGTGTTCCTCCTTT 58.031 36.000 0.00 0.00 34.23 3.11
1873 2088 5.237344 GCACTGAATATGTATGGTGTTCCTC 59.763 44.000 0.00 0.00 34.23 3.71
1897 2112 2.605338 CGGGCACAAATCAACAGTTCAG 60.605 50.000 0.00 0.00 0.00 3.02
1917 2132 0.816825 CCATCATTGGACAGCCCTCG 60.817 60.000 0.00 0.00 46.92 4.63
1926 2141 4.078537 CCGTATAAATGCCCATCATTGGA 58.921 43.478 0.00 0.00 46.92 3.53
1937 2152 8.780249 ACCTTTTACATGTATCCGTATAAATGC 58.220 33.333 6.36 0.00 36.95 3.56
1946 2161 6.106673 ACAGAAGACCTTTTACATGTATCCG 58.893 40.000 6.36 0.00 0.00 4.18
1952 2167 6.702329 AGACCTACAGAAGACCTTTTACATG 58.298 40.000 0.00 0.00 0.00 3.21
1953 2168 6.497259 TGAGACCTACAGAAGACCTTTTACAT 59.503 38.462 0.00 0.00 0.00 2.29
1960 2175 3.196685 GCAATGAGACCTACAGAAGACCT 59.803 47.826 0.00 0.00 0.00 3.85
1970 2185 6.299141 ACTTTGAAAGAAGCAATGAGACCTA 58.701 36.000 12.53 0.00 0.00 3.08
1974 2189 8.345565 GTTTCTACTTTGAAAGAAGCAATGAGA 58.654 33.333 12.53 0.00 36.72 3.27
2070 2298 4.855388 CACAGCATCAACAAAGATACAAGC 59.145 41.667 0.00 0.00 0.00 4.01
2089 2317 6.765036 AGTCATCCAGAATGTTATTAGCACAG 59.235 38.462 0.00 0.00 36.68 3.66
2106 2334 4.890158 TTCTGCAGTAAGAAGTCATCCA 57.110 40.909 14.67 0.00 32.42 3.41
2117 2345 5.084818 TCTCGATCCATTTTCTGCAGTAA 57.915 39.130 14.67 7.78 0.00 2.24
2153 2381 2.671888 GCTAAGGGTAGACGAAACTTGC 59.328 50.000 0.00 0.00 0.00 4.01
2175 2403 5.106277 GCCACAACCCTTTCTGACTTATTAC 60.106 44.000 0.00 0.00 0.00 1.89
2182 2410 0.178990 AGGCCACAACCCTTTCTGAC 60.179 55.000 5.01 0.00 0.00 3.51
2194 2422 0.257328 TTGACAACCTTCAGGCCACA 59.743 50.000 5.01 0.00 39.32 4.17
2195 2423 0.668535 GTTGACAACCTTCAGGCCAC 59.331 55.000 5.01 0.00 39.32 5.01
2231 2459 4.167319 ACCAGGGCAAAAAGGATAAACAT 58.833 39.130 0.00 0.00 0.00 2.71
2291 2519 3.708403 TCAGTGAAATCAGCATCCACT 57.292 42.857 0.00 0.00 38.48 4.00
2324 2552 6.525578 TCTCACGTCCATACTTGAAACTAT 57.474 37.500 0.00 0.00 33.89 2.12


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

AutoCloner maintained by Alex Coulton.