Multiple sequence alignment - TraesCS6D01G032500

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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 TraesCS6D01G032500 chr6D 100.000 1988 0 0 649 2636 13618888 13620875 0.000000e+00 3672
1 TraesCS6D01G032500 chr6D 100.000 67 0 0 1 67 13618240 13618306 9.910000e-25 124
2 TraesCS6D01G032500 chr6B 97.289 1955 48 4 685 2636 9876006 9874054 0.000000e+00 3312
3 TraesCS6D01G032500 chr6B 94.030 67 4 0 1 67 9876652 9876586 4.640000e-18 102


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 TraesCS6D01G032500 chr6D 13618240 13620875 2635 False 1898 3672 100.0000 1 2636 2 chr6D.!!$F1 2635
1 TraesCS6D01G032500 chr6B 9874054 9876652 2598 True 1707 3312 95.6595 1 2636 2 chr6B.!!$R1 2635

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
26 27 0.707024 TTCTCAGCCTCCTCCTCTCA 59.293 55.0 0.00 0.0 0.0 3.27 F
1358 1883 0.035725 TGCCATGTTCAGGAGCTCAG 60.036 55.0 17.19 7.6 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1481 2006 1.252904 TTCTTCCAATGCAGGGCAGC 61.253 55.0 2.33 0.0 43.65 5.25 R
2489 3016 4.500716 GCTCCTCTAGAATAGGTGAGTTGC 60.501 50.0 0.00 0.0 39.78 4.17 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
26 27 0.707024 TTCTCAGCCTCCTCCTCTCA 59.293 55.000 0.00 0.0 0.00 3.27
31 32 1.413445 CAGCCTCCTCCTCTCATTCAG 59.587 57.143 0.00 0.0 0.00 3.02
703 1227 1.067582 CCCTTCTACCGCCACGATC 59.932 63.158 0.00 0.0 0.00 3.69
736 1261 2.770048 CCCTCGCCCCTCCAATCT 60.770 66.667 0.00 0.0 0.00 2.40
757 1282 6.578313 TCTACTCCACCTAGATCTACACTT 57.422 41.667 0.00 0.0 0.00 3.16
765 1290 6.434596 CACCTAGATCTACACTTCAATCGAG 58.565 44.000 0.00 0.0 0.00 4.04
785 1310 3.892588 GAGATCTTCTAGTGGGTGGTAGG 59.107 52.174 0.00 0.0 0.00 3.18
791 1316 3.438183 TCTAGTGGGTGGTAGGTCTTTC 58.562 50.000 0.00 0.0 0.00 2.62
810 1335 3.314307 TCCGTCATCTGACCTCCTAAT 57.686 47.619 4.81 0.0 41.86 1.73
860 1385 2.485657 GGAGCAGCACTTACCCTAATCC 60.486 54.545 0.00 0.0 0.00 3.01
912 1437 9.358872 GTTATTTTTCTCCACAATTTCATCCTC 57.641 33.333 0.00 0.0 0.00 3.71
1014 1539 7.439056 CCAATTTGCAGAATGGGTGATATAAAC 59.561 37.037 3.33 0.0 35.86 2.01
1099 1624 4.061596 GCTTGAGCACATAGTATCCTTCC 58.938 47.826 0.00 0.0 41.59 3.46
1178 1703 2.681344 GGAAATTTGTGCCTACCCTACG 59.319 50.000 0.00 0.0 0.00 3.51
1192 1717 6.239120 GCCTACCCTACGTATTTCTGATACAA 60.239 42.308 0.00 0.0 0.00 2.41
1194 1719 8.027771 CCTACCCTACGTATTTCTGATACAATC 58.972 40.741 0.00 0.0 0.00 2.67
1239 1764 2.829003 TTTTTGCGTGGCCGTGGA 60.829 55.556 0.00 0.0 36.15 4.02
1358 1883 0.035725 TGCCATGTTCAGGAGCTCAG 60.036 55.000 17.19 7.6 0.00 3.35
1376 1901 6.303054 AGCTCAGAGTCATTAGCTGTATAGA 58.697 40.000 11.71 0.0 43.46 1.98
1427 1952 3.867600 GCTCTCATCTCCAAGCACTTGAA 60.868 47.826 11.94 0.0 42.93 2.69
1450 1975 6.628644 AGAGGTTAGAGCTTGATAAGGTTT 57.371 37.500 0.00 0.0 39.77 3.27
1456 1981 7.120726 GGTTAGAGCTTGATAAGGTTTGCTTAA 59.879 37.037 0.00 0.0 39.77 1.85
1481 2006 7.551035 AAGCTAGCACTATTGATTTCTCAAG 57.449 36.000 18.83 0.0 44.32 3.02
1738 2265 9.654663 GAGGACTGTTTAGACTATTGTAACAAT 57.345 33.333 0.00 0.0 0.00 2.71
1834 2361 5.418840 TCTTCTGGAAGGTTTATCAAATGCC 59.581 40.000 10.01 0.0 38.88 4.40
1894 2421 2.200337 GCACTTTTTGGGCGTCCCT 61.200 57.895 2.12 0.0 45.70 4.20
1899 2426 0.892063 TTTTTGGGCGTCCCTATTGC 59.108 50.000 2.12 0.0 45.70 3.56
1901 2428 0.393808 TTTGGGCGTCCCTATTGCTC 60.394 55.000 2.12 0.0 45.70 4.26
1907 2434 3.412386 GGCGTCCCTATTGCTCATATTT 58.588 45.455 0.00 0.0 0.00 1.40
2085 2612 5.151297 AGTGGGCTGTTATTTTGGATTTG 57.849 39.130 0.00 0.0 0.00 2.32
2130 2657 7.863901 ATTAATCTATAGAGCCCTGAACACT 57.136 36.000 8.70 0.0 0.00 3.55
2328 2855 1.274167 CATGGCTTTCCACACTTGCAT 59.726 47.619 0.00 0.0 46.92 3.96
2332 2859 3.694072 TGGCTTTCCACACTTGCATATAC 59.306 43.478 0.00 0.0 37.47 1.47
2442 2969 6.365970 AACTTGAGGACACTGATACTCAAT 57.634 37.500 10.39 0.0 45.60 2.57
2489 3016 1.154836 GACTTGCACGCGTTCTTCG 60.155 57.895 10.22 0.0 43.12 3.79
2513 3040 3.839778 ACTCACCTATTCTAGAGGAGCC 58.160 50.000 3.61 0.0 37.53 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.341877 TGAGAGGAGGAGGCTGAGAAG 60.342 57.143 0.00 0.00 0.00 2.85
13 14 1.412343 GACTGAATGAGAGGAGGAGGC 59.588 57.143 0.00 0.00 0.00 4.70
26 27 1.123928 GATGGTCGAGGGGACTGAAT 58.876 55.000 0.00 0.00 45.35 2.57
31 32 2.901042 GTGGATGGTCGAGGGGAC 59.099 66.667 0.00 0.00 45.31 4.46
648 649 5.798518 AGATATAGTAGATCTGGGTGGAGGA 59.201 44.000 5.18 0.00 32.30 3.71
652 653 4.884744 CGGAGATATAGTAGATCTGGGTGG 59.115 50.000 11.98 0.00 33.71 4.61
656 657 7.735917 AGATCTCGGAGATATAGTAGATCTGG 58.264 42.308 19.95 4.42 44.84 3.86
657 658 7.595130 CGAGATCTCGGAGATATAGTAGATCTG 59.405 44.444 32.81 2.20 45.91 2.90
703 1227 2.124693 GGGAGAGGAGACAGAGCGG 61.125 68.421 0.00 0.00 0.00 5.52
736 1261 6.323210 TGAAGTGTAGATCTAGGTGGAGTA 57.677 41.667 1.64 0.00 0.00 2.59
757 1282 4.339530 CACCCACTAGAAGATCTCGATTGA 59.660 45.833 0.00 0.00 0.00 2.57
765 1290 3.637694 GACCTACCACCCACTAGAAGATC 59.362 52.174 0.00 0.00 0.00 2.75
785 1310 2.417515 GGAGGTCAGATGACGGAAAGAC 60.418 54.545 6.87 0.00 45.65 3.01
791 1316 2.030717 CGATTAGGAGGTCAGATGACGG 60.031 54.545 6.87 0.00 45.65 4.79
810 1335 2.419574 GGTAGCTCCAAAAGTATGCCGA 60.420 50.000 0.00 0.00 35.97 5.54
912 1437 2.366916 GGGGAGGTGTGATAGTGATGAG 59.633 54.545 0.00 0.00 0.00 2.90
1014 1539 4.393062 TCTTGCGCTAATTTCTTCCTCTTG 59.607 41.667 9.73 0.00 0.00 3.02
1099 1624 3.732212 TCACGGCCTCATTCAATGATAG 58.268 45.455 0.00 0.00 38.85 2.08
1235 1760 2.288152 ACAATGATTGCGGTGTTTCCAC 60.288 45.455 4.84 0.00 41.06 4.02
1239 1764 3.555139 CACAAACAATGATTGCGGTGTTT 59.445 39.130 4.84 0.00 43.18 2.83
1358 1883 7.695480 TCATCCTCTATACAGCTAATGACTC 57.305 40.000 0.00 0.00 0.00 3.36
1390 1915 2.235650 TGAGAGCTTGATCCCTGAACTG 59.764 50.000 0.00 0.00 0.00 3.16
1427 1952 6.410540 CAAACCTTATCAAGCTCTAACCTCT 58.589 40.000 0.00 0.00 0.00 3.69
1456 1981 7.414984 GCTTGAGAAATCAATAGTGCTAGCTTT 60.415 37.037 17.23 5.13 0.00 3.51
1466 1991 4.036498 CAGGGCAGCTTGAGAAATCAATAG 59.964 45.833 0.00 0.00 0.00 1.73
1468 1993 2.758979 CAGGGCAGCTTGAGAAATCAAT 59.241 45.455 0.00 0.00 0.00 2.57
1481 2006 1.252904 TTCTTCCAATGCAGGGCAGC 61.253 55.000 2.33 0.00 43.65 5.25
1834 2361 5.297547 TCACTTAGCAACTCCAAGTAACTG 58.702 41.667 0.00 0.00 31.46 3.16
1889 2416 5.048434 GCAAGGAAATATGAGCAATAGGGAC 60.048 44.000 0.00 0.00 0.00 4.46
1894 2421 6.238842 GCAAGAGCAAGGAAATATGAGCAATA 60.239 38.462 0.00 0.00 41.58 1.90
2489 3016 4.500716 GCTCCTCTAGAATAGGTGAGTTGC 60.501 50.000 0.00 0.00 39.78 4.17
2513 3040 7.371936 CCATACCTCTAAAAGTAGGAGATTCG 58.628 42.308 0.00 0.00 36.66 3.34


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

AutoCloner maintained by Alex Coulton.