Multiple sequence alignment - TraesCS4D01G040100

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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 TraesCS4D01G040100 chr4D 100.000 1628 0 0 556 2183 18463810 18465437 0.000000e+00 3007
1 TraesCS4D01G040100 chr4D 100.000 567 0 0 2493 3059 18465747 18466313 0.000000e+00 1048
2 TraesCS4D01G040100 chr4D 100.000 402 0 0 1 402 18463255 18463656 0.000000e+00 743
3 TraesCS4D01G040100 chr4B 95.863 1571 51 4 574 2130 30361842 30363412 0.000000e+00 2529
4 TraesCS4D01G040100 chr4B 95.018 542 18 5 2497 3036 30363439 30363973 0.000000e+00 843
5 TraesCS4D01G040100 chr4B 95.899 317 13 0 86 402 30361449 30361765 5.850000e-142 514
6 TraesCS4D01G040100 chr4A 96.774 1457 46 1 674 2129 582841317 582839861 0.000000e+00 2429
7 TraesCS4D01G040100 chr4A 94.200 569 30 2 2493 3059 582839837 582839270 0.000000e+00 865
8 TraesCS4D01G040100 chr4A 96.585 410 5 4 1 402 582841938 582841530 0.000000e+00 671
9 TraesCS4D01G040100 chr4A 98.305 118 1 1 574 690 582841442 582841325 4.000000e-49 206
10 TraesCS4D01G040100 chr4A 92.806 139 9 1 72 209 582842015 582841877 1.860000e-47 200
11 TraesCS4D01G040100 chr5A 89.634 164 17 0 1313 1476 1347288 1347125 3.090000e-50 209
12 TraesCS4D01G040100 chr5B 90.196 153 15 0 1318 1470 3475045 3475197 1.860000e-47 200
13 TraesCS4D01G040100 chr5D 87.574 169 21 0 1322 1490 2511786 2511618 2.410000e-46 196
14 TraesCS4D01G040100 chr5D 82.550 149 24 2 1321 1468 322577525 322577672 2.480000e-26 130
15 TraesCS4D01G040100 chr2A 86.713 143 15 3 1328 1468 8543566 8543706 4.080000e-34 156
16 TraesCS4D01G040100 chr2D 86.014 143 16 3 1328 1468 9079999 9080139 1.900000e-32 150
17 TraesCS4D01G040100 chr2B 85.315 143 17 3 1328 1468 11837364 11837224 8.840000e-31 145


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 TraesCS4D01G040100 chr4D 18463255 18466313 3058 False 1599.333333 3007 100.000000 1 3059 3 chr4D.!!$F1 3058
1 TraesCS4D01G040100 chr4B 30361449 30363973 2524 False 1295.333333 2529 95.593333 86 3036 3 chr4B.!!$F1 2950
2 TraesCS4D01G040100 chr4A 582839270 582842015 2745 True 874.200000 2429 95.734000 1 3059 5 chr4A.!!$R1 3058

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
263 343 0.593128 CAAGGAACAAAGGCGTCCAG 59.407 55.000 0.00 0.0 0.0 3.86 F
891 1002 1.203523 GATCATAGCTCCTAGGCCACG 59.796 57.143 5.01 0.0 0.0 4.94 F
966 1077 2.279408 GAGGGCCTAGAGACGGGT 59.721 66.667 5.73 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1110 1222 0.181114 CGAATGCAGGGGAGGAATGA 59.819 55.0 0.0 0.0 0.00 2.57 R
1835 1953 1.683790 CGGATTCGTGACCAACTCGC 61.684 60.0 0.0 0.0 35.79 5.03 R
2761 2879 1.691196 TCCAACAGGCAACAGGAAAG 58.309 50.0 0.0 0.0 41.41 2.62 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
111 191 1.379977 CTCGGTCCCCAGAGTAGCA 60.380 63.158 0.00 0.00 0.00 3.49
263 343 0.593128 CAAGGAACAAAGGCGTCCAG 59.407 55.000 0.00 0.00 0.00 3.86
368 454 1.603455 CACACATGCCCTTTCCCGT 60.603 57.895 0.00 0.00 0.00 5.28
578 664 6.656632 CTGTCAATATCAAGTAGCTAGGGA 57.343 41.667 0.00 0.00 0.00 4.20
579 665 6.656632 TGTCAATATCAAGTAGCTAGGGAG 57.343 41.667 0.00 0.00 0.00 4.30
580 666 5.540337 TGTCAATATCAAGTAGCTAGGGAGG 59.460 44.000 0.00 0.00 0.00 4.30
690 777 2.006169 TGATGTGTGTGTGTGTGTGTC 58.994 47.619 0.00 0.00 0.00 3.67
807 918 8.347035 CCTAGACCTCTTTAACTATCTCTTTCG 58.653 40.741 0.00 0.00 0.00 3.46
891 1002 1.203523 GATCATAGCTCCTAGGCCACG 59.796 57.143 5.01 0.00 0.00 4.94
966 1077 2.279408 GAGGGCCTAGAGACGGGT 59.721 66.667 5.73 0.00 0.00 5.28
1020 1132 6.369059 AGCATGTTTCCTTTCTATGATTCG 57.631 37.500 0.00 0.00 0.00 3.34
1110 1222 6.107901 GATCACCAATCCTTGCTCTACTAT 57.892 41.667 0.00 0.00 0.00 2.12
1623 1741 3.717294 GGCGAGGGGAAGAAGCCA 61.717 66.667 0.00 0.00 46.48 4.75
1662 1780 3.055580 GCACCCGCCAATCCAAAA 58.944 55.556 0.00 0.00 0.00 2.44
1850 1968 2.029964 GGGCGAGTTGGTCACGAA 59.970 61.111 0.00 0.00 32.20 3.85
1851 1969 1.375523 GGGCGAGTTGGTCACGAAT 60.376 57.895 0.00 0.00 32.20 3.34
1891 2009 1.406069 GCTCCTCGTCCATGAACACAT 60.406 52.381 0.00 0.00 0.00 3.21
2038 2156 0.034337 GCTCGGTGGAGTGGTGTTTA 59.966 55.000 0.00 0.00 42.53 2.01
2575 2693 5.575218 TGATGCAGTACGTATTGTAGTTGTG 59.425 40.000 17.98 0.00 34.39 3.33
2585 2703 6.071728 ACGTATTGTAGTTGTGGCTACTACTT 60.072 38.462 20.90 7.20 45.20 2.24
2674 2792 9.699410 ATTCTATAATTGTCAAACTGGAATCCA 57.301 29.630 0.48 0.48 0.00 3.41
3008 3128 7.255173 GCTAAATTCTCATGACATCTGCTGAAT 60.255 37.037 0.00 0.00 0.00 2.57
3027 3147 8.494433 TGCTGAATAAGGAGTAGGTTGATTTAT 58.506 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.373540 TAGATTGAACGTCGTTGGGG 57.626 50.000 16.75 0.00 0.00 4.96
3 4 3.484649 CGGTATAGATTGAACGTCGTTGG 59.515 47.826 16.75 0.00 0.00 3.77
557 643 5.046950 CCCTCCCTAGCTACTTGATATTGAC 60.047 48.000 0.00 0.00 0.00 3.18
563 649 4.108124 TGATACCCTCCCTAGCTACTTGAT 59.892 45.833 0.00 0.00 0.00 2.57
572 658 3.260269 TGGATGTGATACCCTCCCTAG 57.740 52.381 0.00 0.00 0.00 3.02
573 659 3.717507 TTGGATGTGATACCCTCCCTA 57.282 47.619 0.00 0.00 0.00 3.53
576 662 5.449553 AGAATTTTGGATGTGATACCCTCC 58.550 41.667 0.00 0.00 0.00 4.30
577 663 6.712547 CCTAGAATTTTGGATGTGATACCCTC 59.287 42.308 0.00 0.00 0.00 4.30
578 664 6.605119 CCTAGAATTTTGGATGTGATACCCT 58.395 40.000 0.00 0.00 0.00 4.34
579 665 5.241728 GCCTAGAATTTTGGATGTGATACCC 59.758 44.000 0.00 0.00 0.00 3.69
580 666 5.827797 TGCCTAGAATTTTGGATGTGATACC 59.172 40.000 0.00 0.00 0.00 2.73
690 777 3.324117 CTCATCCTGAGTTCACACACAG 58.676 50.000 0.00 0.00 39.58 3.66
773 884 7.042106 AGTTAAAGAGGTCTAGGACTAGGAA 57.958 40.000 6.52 0.00 34.06 3.36
807 918 0.390472 CTGCGGGTGGAAGAGAGAAC 60.390 60.000 0.00 0.00 0.00 3.01
891 1002 2.607750 TGAGAGAGGGGTGTGGCC 60.608 66.667 0.00 0.00 0.00 5.36
966 1077 0.191064 ACTCCAAGACCCTGAGACCA 59.809 55.000 0.00 0.00 0.00 4.02
1020 1132 1.152881 CAAGTCCATGGGGCTAGGC 60.153 63.158 13.02 8.00 0.00 3.93
1110 1222 0.181114 CGAATGCAGGGGAGGAATGA 59.819 55.000 0.00 0.00 0.00 2.57
1468 1586 0.814010 ATGGCGCCCTTTGACGTATC 60.814 55.000 26.77 0.00 0.00 2.24
1662 1780 1.118356 TGGCCAATTTCCTTTGCGGT 61.118 50.000 0.61 0.00 0.00 5.68
1835 1953 1.683790 CGGATTCGTGACCAACTCGC 61.684 60.000 0.00 0.00 35.79 5.03
1850 1968 4.336433 AGCGATTGATCAAATTGTTCGGAT 59.664 37.500 22.83 6.64 32.79 4.18
1851 1969 3.689161 AGCGATTGATCAAATTGTTCGGA 59.311 39.130 22.83 0.00 32.79 4.55
1891 2009 2.238144 CCTCCTCCAATTCAGCTCTTGA 59.762 50.000 2.52 0.00 0.00 3.02
2038 2156 1.913762 AGTAGGGCTGCGAGTTGGT 60.914 57.895 0.00 0.00 0.00 3.67
2575 2693 2.832733 AGGTTCTGGACAAGTAGTAGCC 59.167 50.000 0.00 0.00 0.00 3.93
2585 2703 3.576078 AATCAACACAGGTTCTGGACA 57.424 42.857 0.00 0.00 35.51 4.02
2674 2792 5.883685 TCACCAGAATAGCAGATCTGATT 57.116 39.130 27.04 17.13 44.64 2.57
2761 2879 1.691196 TCCAACAGGCAACAGGAAAG 58.309 50.000 0.00 0.00 41.41 2.62
2944 3064 8.313944 ACTTGTGAGTATATGTACCACCATAA 57.686 34.615 14.24 7.19 34.15 1.90
2945 3065 7.562088 TGACTTGTGAGTATATGTACCACCATA 59.438 37.037 14.24 0.00 35.88 2.74
2983 3103 7.549615 TTCAGCAGATGTCATGAGAATTTAG 57.450 36.000 0.00 0.00 0.00 1.85
3027 3147 6.216801 AGCACGTTGACATTCTACCTAATA 57.783 37.500 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.