Multiple sequence alignment - TraesCS5D01G452900

Loading Multiple Alignment...

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 TraesCS5D01G452900 chr5D 100.000 4148 0 0 1 4148 500675515 500679662 0.000000e+00 7661.0
1 TraesCS5D01G452900 chr5D 79.812 213 41 2 2486 2697 555192293 555192504 2.000000e-33 154.0
2 TraesCS5D01G452900 chr5B 97.128 4179 74 13 1 4140 622067883 622072054 0.000000e+00 7011.0
3 TraesCS5D01G452900 chr2D 76.735 735 150 18 2084 2803 186996657 186995929 1.400000e-104 390.0
4 TraesCS5D01G452900 chr2D 76.023 684 149 13 2085 2763 32365093 32365766 1.430000e-89 340.0
5 TraesCS5D01G452900 chr7B 100.000 31 0 0 4064 4094 721532301 721532271 1.610000e-04 58.4
6 TraesCS5D01G452900 chr7B 100.000 31 0 0 4064 4094 721612369 721612339 1.610000e-04 58.4


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 TraesCS5D01G452900 chr5D 500675515 500679662 4147 False 7661 7661 100.000 1 4148 1 chr5D.!!$F1 4147
1 TraesCS5D01G452900 chr5B 622067883 622072054 4171 False 7011 7011 97.128 1 4140 1 chr5B.!!$F1 4139
2 TraesCS5D01G452900 chr2D 186995929 186996657 728 True 390 390 76.735 2084 2803 1 chr2D.!!$R1 719
3 TraesCS5D01G452900 chr2D 32365093 32365766 673 False 340 340 76.023 2085 2763 1 chr2D.!!$F1 678

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
72 73 0.821301 TTGCCATGCCGTTGTTCTGA 60.821 50.000 0.0 0.0 0.00 3.27 F
962 971 1.000506 TGTGACCCGCTACTTCAGAAC 59.999 52.381 0.0 0.0 0.00 3.01 F
2053 2076 0.324943 GGTGCTTGCTCTGGGAACTA 59.675 55.000 0.0 0.0 0.00 2.24 F
2059 2082 1.204146 TGCTCTGGGAACTACCATCC 58.796 55.000 0.0 0.0 40.36 3.51 F
2790 2820 1.217244 GCAAAGGCCCATCAAGCAG 59.783 57.895 0.0 0.0 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1418 1441 0.309922 TCCGTCAACACTCGTCTCAC 59.690 55.000 0.00 0.00 0.00 3.51 R
2279 2302 0.034670 GAACTCCTTCATGCCCTGCT 60.035 55.000 0.00 0.00 0.00 4.24 R
2929 2959 0.321671 TGCAAGCACAGGAGACCTAC 59.678 55.000 0.00 0.00 29.64 3.18 R
2940 2970 0.529378 CAGGGAAAGGATGCAAGCAC 59.471 55.000 0.00 0.00 0.00 4.40 R
3762 3808 1.068588 TGGTCTCACAAGTCCTTGACG 59.931 52.381 13.69 4.78 42.93 4.35 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
72 73 0.821301 TTGCCATGCCGTTGTTCTGA 60.821 50.000 0.00 0.00 0.00 3.27
97 98 1.207488 AAGGAGGCCCATGTACTGCA 61.207 55.000 0.00 0.00 33.88 4.41
392 396 3.455177 TGGTCACCAGTACCAGTAACAAA 59.545 43.478 0.00 0.00 42.10 2.83
425 429 1.377856 GGCCAAGGAAGAGGAGCAC 60.378 63.158 0.00 0.00 0.00 4.40
430 434 1.134965 CAAGGAAGAGGAGCACTACGG 60.135 57.143 0.00 0.00 0.00 4.02
575 579 1.701847 AGTCATGCCAGTCCTGTCTTT 59.298 47.619 0.00 0.00 0.00 2.52
598 607 3.119291 CACAAGCATCTTAGTCTAGGCG 58.881 50.000 0.00 0.00 0.00 5.52
615 624 1.497278 CGTGAGTGCCATTCAACGG 59.503 57.895 0.00 0.00 0.00 4.44
639 648 6.201425 GGTAGTGACAACAGAAACGACATTTA 59.799 38.462 0.00 0.00 0.00 1.40
669 678 3.371097 CTACATGACGGGCACGCCT 62.371 63.158 9.12 0.00 46.04 5.52
764 773 2.867472 CAACAATGCCCGGACGTC 59.133 61.111 7.13 7.13 0.00 4.34
850 859 9.961265 TTGGTATTATGAAGATACTTGTCTACG 57.039 33.333 0.00 0.00 32.02 3.51
962 971 1.000506 TGTGACCCGCTACTTCAGAAC 59.999 52.381 0.00 0.00 0.00 3.01
993 1013 1.942657 CAGGCATATCCACAAACCTCG 59.057 52.381 0.00 0.00 37.29 4.63
1151 1174 4.287067 AGGTGTGTCATTCCTTCTACATGT 59.713 41.667 2.69 2.69 0.00 3.21
1244 1267 2.222027 CTTCACTGGGACAAACCTCAC 58.778 52.381 0.00 0.00 38.70 3.51
1322 1345 1.296727 GTTAACCTCTACGGCCATGC 58.703 55.000 2.24 0.00 35.61 4.06
1357 1380 1.439365 CTGCGTTTCTGCAAGTCGC 60.439 57.895 14.94 14.94 45.74 5.19
1368 1391 1.376609 GCAAGTCGCCCAATGGTAGG 61.377 60.000 0.00 0.00 32.94 3.18
1374 1397 2.124320 CCCAATGGTAGGGTGCGG 60.124 66.667 0.00 0.00 41.61 5.69
1385 1408 2.584391 GGGTGCGGTCCTTCTCTGT 61.584 63.158 0.00 0.00 0.00 3.41
1418 1441 1.665448 CGGCATCAGCTCTGTCTATCG 60.665 57.143 0.00 0.00 41.70 2.92
1456 1479 2.174424 GGAATGGCCTTCTTCATCTCCT 59.826 50.000 3.32 0.00 34.08 3.69
1602 1625 3.745975 TGAAGGACATCAACGACAATCAC 59.254 43.478 0.00 0.00 0.00 3.06
1728 1751 1.200519 TGCAGGTATGGGTGGACTAC 58.799 55.000 0.00 0.00 0.00 2.73
1949 1972 4.073052 GGTCATTGACACCGCCAA 57.927 55.556 18.09 0.00 33.68 4.52
1986 2009 6.831976 ACCTCAACTTGTTCTGAAGAATACT 58.168 36.000 0.08 0.00 36.33 2.12
2053 2076 0.324943 GGTGCTTGCTCTGGGAACTA 59.675 55.000 0.00 0.00 0.00 2.24
2059 2082 1.204146 TGCTCTGGGAACTACCATCC 58.796 55.000 0.00 0.00 40.36 3.51
2089 2112 1.354506 CGGAGGCGACTAAGGTACG 59.645 63.158 0.00 0.00 44.43 3.67
2279 2302 4.437682 AGAAGTTGTCCCATGAACTGAA 57.562 40.909 0.00 0.00 32.66 3.02
2723 2752 1.221021 CAGGTAAAGCGTCCCCTCC 59.779 63.158 0.00 0.00 0.00 4.30
2790 2820 1.217244 GCAAAGGCCCATCAAGCAG 59.783 57.895 0.00 0.00 0.00 4.24
2929 2959 6.708054 AGATGAGGTCTGTCTTGTGTTAAAAG 59.292 38.462 0.00 0.00 35.31 2.27
2940 2970 6.424207 GTCTTGTGTTAAAAGTAGGTCTCCTG 59.576 42.308 0.00 0.00 34.61 3.86
2980 3010 3.818787 CAAGGCCCAGCATGCGAC 61.819 66.667 13.01 0.00 31.97 5.19
3092 3122 0.403271 GCAGGATCCATGCCATACCT 59.597 55.000 15.82 0.00 37.73 3.08
3229 3266 3.678289 TGCATGTAAACTCTGCAGATGT 58.322 40.909 18.63 14.38 40.75 3.06
3258 3295 8.375506 TGCTTTATTATATGAATCTCGAAGGGT 58.624 33.333 0.00 0.00 0.00 4.34
3379 3416 9.669353 CTTTGTAATAATCTTATGGCATCACAC 57.331 33.333 1.65 0.00 0.00 3.82
3494 3531 4.714308 TGAGGGACAAGAAAAACATTTGGT 59.286 37.500 0.00 0.00 0.00 3.67
3762 3808 2.262423 AGGCAACAAGAGTGGACTTC 57.738 50.000 0.00 0.00 30.70 3.01
3891 3937 5.241728 GGGGATCAGTAAAACATCATTAGCC 59.758 44.000 0.00 0.00 0.00 3.93
3937 3983 7.148120 GCAAATATCTGATGGCAGTAGCATTAT 60.148 37.037 0.00 0.00 44.61 1.28
3941 3987 5.303165 TCTGATGGCAGTAGCATTATCTTG 58.697 41.667 0.00 0.00 44.61 3.02
3972 4018 6.734502 TTTGCATGGTCATATCCAAATGAT 57.265 33.333 0.00 0.00 41.09 2.45
3973 4019 5.715434 TGCATGGTCATATCCAAATGATG 57.285 39.130 0.00 0.00 41.09 3.07
3974 4020 5.141910 TGCATGGTCATATCCAAATGATGT 58.858 37.500 0.00 0.00 41.09 3.06
4098 4145 0.460987 GTCCGCCTTGACAGATCCTG 60.461 60.000 0.00 0.00 37.52 3.86
4144 4191 2.399916 GAGCATCCTCATATCTGCCC 57.600 55.000 0.00 0.00 38.03 5.36
4145 4192 1.907936 GAGCATCCTCATATCTGCCCT 59.092 52.381 0.00 0.00 38.03 5.19
4146 4193 1.629353 AGCATCCTCATATCTGCCCTG 59.371 52.381 0.00 0.00 35.21 4.45
4147 4194 1.339824 GCATCCTCATATCTGCCCTGG 60.340 57.143 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 1.056700 ACATGGGCCTCCTTAGCGAT 61.057 55.000 4.53 0.00 0.00 4.58
97 98 2.835431 CTCAGACGCCCTCCCGAT 60.835 66.667 0.00 0.00 0.00 4.18
109 110 3.134623 TCACCAAGCAAGAACTTCTCAGA 59.865 43.478 0.00 0.00 0.00 3.27
274 278 1.383523 GACCTAACCAATGGCTCTGC 58.616 55.000 0.00 0.00 0.00 4.26
324 328 1.084370 CCAATCTGGTTCTCGACGGC 61.084 60.000 0.00 0.00 31.35 5.68
350 354 3.443037 CAGTTCATCTACTCTGGCTTCG 58.557 50.000 0.00 0.00 0.00 3.79
392 396 5.337788 TCCTTGGCCTTAACCAACAAATAT 58.662 37.500 3.32 0.00 44.80 1.28
425 429 3.854669 CTCTGCCCTGGCCCGTAG 61.855 72.222 5.57 0.00 41.09 3.51
570 574 5.241662 AGACTAAGATGCTTGTGGAAAGAC 58.758 41.667 0.00 0.00 0.00 3.01
575 579 3.133003 GCCTAGACTAAGATGCTTGTGGA 59.867 47.826 0.00 0.00 0.00 4.02
598 607 1.732259 CTACCGTTGAATGGCACTCAC 59.268 52.381 0.00 0.00 0.00 3.51
615 624 5.652744 AATGTCGTTTCTGTTGTCACTAC 57.347 39.130 0.00 0.00 0.00 2.73
639 648 0.473755 TCATGTAGGCGCCCATCAAT 59.526 50.000 26.15 5.68 0.00 2.57
669 678 4.686191 AATTGGGTGCACAATTGAAGAA 57.314 36.364 20.43 0.00 46.23 2.52
810 819 6.719370 TCATAATACCAAGGGCCACATAATTC 59.281 38.462 6.18 0.00 0.00 2.17
850 859 2.587522 GGCATAAATCTTCTGGTCCCC 58.412 52.381 0.00 0.00 0.00 4.81
949 958 3.362237 CGAAGACTTGTTCTGAAGTAGCG 59.638 47.826 0.00 0.00 36.27 4.26
962 971 1.869767 GATATGCCTGCCGAAGACTTG 59.130 52.381 0.00 0.00 0.00 3.16
1151 1174 2.472029 CCAAGCTAAGGAAGAGGAGGA 58.528 52.381 0.00 0.00 0.00 3.71
1261 1284 2.994995 TCCGTCCGCTGTGACCAT 60.995 61.111 0.00 0.00 31.35 3.55
1368 1391 1.374758 CACAGAGAAGGACCGCACC 60.375 63.158 0.00 0.00 0.00 5.01
1374 1397 3.053455 CACGAAAGACACAGAGAAGGAC 58.947 50.000 0.00 0.00 0.00 3.85
1385 1408 1.144969 GATGCCGAACACGAAAGACA 58.855 50.000 0.00 0.00 0.00 3.41
1418 1441 0.309922 TCCGTCAACACTCGTCTCAC 59.690 55.000 0.00 0.00 0.00 3.51
1425 1448 0.321653 AGGCCATTCCGTCAACACTC 60.322 55.000 5.01 0.00 40.77 3.51
1456 1479 3.609853 CATTGGAGAAATGGTTCCTCGA 58.390 45.455 0.00 0.00 41.80 4.04
1728 1751 1.746615 CTGTGTGGCCCCTTCATCG 60.747 63.158 0.00 0.00 0.00 3.84
1949 1972 3.500343 AGTTGAGGTAGCTTTGGCAATT 58.500 40.909 0.00 0.00 41.70 2.32
1986 2009 3.441922 CGATCTTCAAGACTCTGGACTGA 59.558 47.826 0.00 0.00 0.00 3.41
2044 2067 3.107601 TCAGAAGGATGGTAGTTCCCAG 58.892 50.000 0.00 0.00 38.07 4.45
2053 2076 3.576118 CTCCGTATGATCAGAAGGATGGT 59.424 47.826 22.62 0.00 36.00 3.55
2059 2082 1.609072 TCGCCTCCGTATGATCAGAAG 59.391 52.381 0.09 0.00 35.54 2.85
2149 2172 1.548582 CCCCTCTGTTGCAAGGAACAT 60.549 52.381 7.59 0.00 35.32 2.71
2279 2302 0.034670 GAACTCCTTCATGCCCTGCT 60.035 55.000 0.00 0.00 0.00 4.24
2723 2752 1.986378 CGAAGGCAAAGACGTCTGTAG 59.014 52.381 20.85 12.97 0.00 2.74
2929 2959 0.321671 TGCAAGCACAGGAGACCTAC 59.678 55.000 0.00 0.00 29.64 3.18
2940 2970 0.529378 CAGGGAAAGGATGCAAGCAC 59.471 55.000 0.00 0.00 0.00 4.40
2980 3010 1.079127 CAAGGTACTGGAGCACCCG 60.079 63.158 0.00 0.00 40.86 5.28
2981 3011 0.912486 ATCAAGGTACTGGAGCACCC 59.088 55.000 0.00 0.00 44.46 4.61
3172 3202 3.727726 TCATTGCATATACACCAGACCG 58.272 45.455 0.00 0.00 0.00 4.79
3238 3275 5.249393 AGCCACCCTTCGAGATTCATATAAT 59.751 40.000 0.00 0.00 0.00 1.28
3255 3292 5.652994 TGTTTCATATAACAAAGCCACCC 57.347 39.130 0.00 0.00 35.22 4.61
3258 3295 6.194235 AGGGATGTTTCATATAACAAAGCCA 58.806 36.000 0.00 0.00 41.02 4.75
3468 3505 6.406849 CCAAATGTTTTTCTTGTCCCTCAGAA 60.407 38.462 0.00 0.00 0.00 3.02
3472 3509 5.276461 ACCAAATGTTTTTCTTGTCCCTC 57.724 39.130 0.00 0.00 0.00 4.30
3494 3531 8.356657 CGGATGCTTGTATTTTTAATGGGATTA 58.643 33.333 0.00 0.00 0.00 1.75
3510 3547 3.366052 AATAAAGGGTCGGATGCTTGT 57.634 42.857 0.00 0.00 0.00 3.16
3762 3808 1.068588 TGGTCTCACAAGTCCTTGACG 59.931 52.381 13.69 4.78 42.93 4.35
3921 3967 7.173907 ACAATACAAGATAATGCTACTGCCATC 59.826 37.037 0.00 0.00 38.71 3.51
3937 3983 6.154203 TGACCATGCAAAAACAATACAAGA 57.846 33.333 0.00 0.00 0.00 3.02
3941 3987 7.264221 TGGATATGACCATGCAAAAACAATAC 58.736 34.615 0.00 0.00 34.77 1.89


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

AutoCloner maintained by Alex Coulton.