Multiple sequence alignment - TraesCS3D01G044500

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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 TraesCS3D01G044500 chr3D 100.000 2955 0 0 1 2955 17289085 17286131 0.000000e+00 5457.0
1 TraesCS3D01G044500 chr3D 97.014 2780 77 5 3 2778 17324222 17321445 0.000000e+00 4669.0
2 TraesCS3D01G044500 chr3D 97.627 927 22 0 2029 2955 17238611 17237685 0.000000e+00 1591.0
3 TraesCS3D01G044500 chr3D 95.402 522 21 3 1 520 17239564 17239044 0.000000e+00 828.0
4 TraesCS3D01G044500 chr3D 96.774 155 5 0 2801 2955 17321333 17321179 2.920000e-65 259.0
5 TraesCS3D01G044500 chr3D 92.357 157 9 1 590 743 87926000 87926156 1.380000e-53 220.0
6 TraesCS3D01G044500 chr3B 94.628 2960 148 10 1 2955 24834845 24831892 0.000000e+00 4575.0
7 TraesCS3D01G044500 chr5D 91.143 2755 203 16 211 2955 35479353 35476630 0.000000e+00 3698.0
8 TraesCS3D01G044500 chr5D 88.462 208 23 1 1 207 207769219 207769012 1.760000e-62 250.0
9 TraesCS3D01G044500 chr5D 90.625 160 12 1 587 743 204324444 204324603 2.980000e-50 209.0
10 TraesCS3D01G044500 chrUn 92.192 2062 153 5 209 2264 334202214 334200155 0.000000e+00 2909.0
11 TraesCS3D01G044500 chrUn 91.383 1938 160 4 1025 2955 324174626 324176563 0.000000e+00 2647.0
12 TraesCS3D01G044500 chrUn 91.667 816 66 2 209 1023 373420161 373419347 0.000000e+00 1129.0
13 TraesCS3D01G044500 chr2B 88.462 208 23 1 1 207 450525155 450524948 1.760000e-62 250.0
14 TraesCS3D01G044500 chr6D 88.406 207 22 2 1 205 187086335 187086129 6.320000e-62 248.0
15 TraesCS3D01G044500 chr1D 88.038 209 22 3 1 207 127323082 127322875 8.180000e-61 244.0
16 TraesCS3D01G044500 chr1D 91.358 162 11 1 590 748 449595569 449595408 4.960000e-53 219.0
17 TraesCS3D01G044500 chr5B 87.864 206 24 1 1 205 72637373 72637168 1.060000e-59 241.0
18 TraesCS3D01G044500 chr4D 87.923 207 22 3 1 205 293821049 293820844 1.060000e-59 241.0
19 TraesCS3D01G044500 chr4D 90.683 161 11 2 580 736 3590463 3590623 8.300000e-51 211.0
20 TraesCS3D01G044500 chr2A 89.552 67 7 0 218 284 695776648 695776582 5.250000e-13 86.1
21 TraesCS3D01G044500 chr2A 89.552 67 7 0 218 284 695952364 695952298 5.250000e-13 86.1
22 TraesCS3D01G044500 chr4B 85.915 71 10 0 214 284 474399748 474399818 3.160000e-10 76.8


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 TraesCS3D01G044500 chr3D 17286131 17289085 2954 True 5457.0 5457 100.0000 1 2955 1 chr3D.!!$R1 2954
1 TraesCS3D01G044500 chr3D 17321179 17324222 3043 True 2464.0 4669 96.8940 3 2955 2 chr3D.!!$R3 2952
2 TraesCS3D01G044500 chr3D 17237685 17239564 1879 True 1209.5 1591 96.5145 1 2955 2 chr3D.!!$R2 2954
3 TraesCS3D01G044500 chr3B 24831892 24834845 2953 True 4575.0 4575 94.6280 1 2955 1 chr3B.!!$R1 2954
4 TraesCS3D01G044500 chr5D 35476630 35479353 2723 True 3698.0 3698 91.1430 211 2955 1 chr5D.!!$R1 2744
5 TraesCS3D01G044500 chrUn 334200155 334202214 2059 True 2909.0 2909 92.1920 209 2264 1 chrUn.!!$R1 2055
6 TraesCS3D01G044500 chrUn 324174626 324176563 1937 False 2647.0 2647 91.3830 1025 2955 1 chrUn.!!$F1 1930
7 TraesCS3D01G044500 chrUn 373419347 373420161 814 True 1129.0 1129 91.6670 209 1023 1 chrUn.!!$R2 814

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
36 38 3.334272 AACTTTTGCGCTCAGTAACAC 57.666 42.857 9.73 0.0 0.00 3.32 F
1206 1220 1.221021 GACCGGAAGTGATGGGGTC 59.779 63.158 9.46 0.0 40.24 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1314 1328 1.644786 GGTGTGTTGTGATAGGGCGC 61.645 60.0 0.00 0.0 0.0 6.53 R
2414 2434 0.390124 AAAGTTCCCACGCGTACTCA 59.610 50.0 13.44 0.0 0.0 3.41 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
36 38 3.334272 AACTTTTGCGCTCAGTAACAC 57.666 42.857 9.73 0.00 0.00 3.32
172 178 9.900710 GTATGTAGTTGTCTAGATCATTACAGG 57.099 37.037 12.23 0.00 33.25 4.00
190 196 3.701040 ACAGGCTGTTCTGTTTTTGACAT 59.299 39.130 15.88 0.00 44.74 3.06
196 202 7.665559 AGGCTGTTCTGTTTTTGACATATTCTA 59.334 33.333 0.00 0.00 37.69 2.10
275 281 7.818930 GGATATTTCAACATGGACAACAAACAT 59.181 33.333 0.00 0.00 0.00 2.71
893 905 8.155821 TCTTTCGTTATTTGTATGTGGTGAAA 57.844 30.769 0.00 0.00 0.00 2.69
987 1001 5.546621 TTCCCTTATATATATGAGGCCGC 57.453 43.478 22.55 0.00 37.94 6.53
1158 1172 3.074094 TCCTCTTTAGCCTCCTAGCGATA 59.926 47.826 0.00 0.00 38.01 2.92
1206 1220 1.221021 GACCGGAAGTGATGGGGTC 59.779 63.158 9.46 0.00 40.24 4.46
1314 1328 1.351017 TGTAGGCCCTTGTTCCTTCAG 59.649 52.381 0.00 0.00 34.02 3.02
1365 1379 1.105167 CCATGCGGGCATCTGTTCAT 61.105 55.000 2.58 0.00 33.90 2.57
1370 1384 1.307647 GGGCATCTGTTCATGGGGT 59.692 57.895 0.00 0.00 0.00 4.95
1478 1492 6.738086 TCCTCTCTCTATGGGTCTATCATAGT 59.262 42.308 9.88 0.00 42.63 2.12
1508 1522 1.302511 ACGTGCAAGGCCTGGTTAG 60.303 57.895 5.69 0.49 0.00 2.34
1754 1773 5.859205 AGGCTTCAATGAATTCCAATACC 57.141 39.130 14.07 0.00 0.00 2.73
1786 1805 2.905075 TGTGTTCCTGTCTGACAACAG 58.095 47.619 12.16 4.08 45.10 3.16
1858 1877 6.881602 GGTGAGAAGAAACAAGATAACATCCT 59.118 38.462 0.00 0.00 0.00 3.24
1908 1927 6.318648 TGCACTATGTTACCATTTGGAGAATC 59.681 38.462 3.01 0.00 38.94 2.52
2162 2182 6.808321 AGTATTCTTATCACCTGGCACTAA 57.192 37.500 0.00 0.00 0.00 2.24
2414 2434 8.009622 TCCAATTACAATTCATACATGTGCAT 57.990 30.769 9.11 0.00 0.00 3.96
2555 2575 4.893608 AGTGCTTCCACAAAACAAAGTTT 58.106 34.783 0.00 0.00 44.53 2.66
2738 2759 3.994931 AAGGTGTTAAATAGGAGGCGT 57.005 42.857 0.00 0.00 0.00 5.68
2874 2984 3.503748 AGCAAGACAGTGCCAAATTACTC 59.496 43.478 0.00 0.00 46.14 2.59
2895 3005 6.530120 ACTCGGTGTATGGAATTGCATATAA 58.470 36.000 20.77 11.06 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 38 6.740002 CACGTTCTAGAAAAGCAGATCAATTG 59.260 38.462 6.78 0.00 0.00 2.32
172 178 9.846248 AATAGAATATGTCAAAAACAGAACAGC 57.154 29.630 0.00 0.00 42.37 4.40
196 202 7.435068 AGTACAAACAGCTCGTATTGAAAAT 57.565 32.000 0.00 0.00 0.00 1.82
874 886 9.997482 ATACGATTTTCACCACATACAAATAAC 57.003 29.630 0.00 0.00 0.00 1.89
987 1001 2.862541 TGAATGATAATTGGGAGCCCG 58.137 47.619 0.29 0.00 39.42 6.13
1068 1082 3.515630 CTTCTTGTCGATGAGCAGCTTA 58.484 45.455 0.00 0.00 0.00 3.09
1314 1328 1.644786 GGTGTGTTGTGATAGGGCGC 61.645 60.000 0.00 0.00 0.00 6.53
1370 1384 5.163447 GCATACTGTAGTGGGTAAGATGTCA 60.163 44.000 0.00 0.00 0.00 3.58
1508 1522 5.986135 GTGAGGTCATCCATGATAGTGTAAC 59.014 44.000 0.00 0.00 39.30 2.50
1786 1805 5.141182 TCTTGGATAGGGAGACATCAGTAC 58.859 45.833 0.00 0.00 0.00 2.73
2055 2074 9.814899 CTAGAGATCTCAAAGAAACATGTATGT 57.185 33.333 24.39 0.24 44.20 2.29
2162 2182 6.246919 ACTACTGGTAGTCTGACAGTTGTAT 58.753 40.000 17.53 2.74 44.86 2.29
2414 2434 0.390124 AAAGTTCCCACGCGTACTCA 59.610 50.000 13.44 0.00 0.00 3.41
2732 2753 3.751698 ACTTTCTTGTAATTCCACGCCTC 59.248 43.478 0.00 0.00 0.00 4.70
2738 2759 6.775142 TGATCCAACACTTTCTTGTAATTCCA 59.225 34.615 0.00 0.00 0.00 3.53
2874 2984 6.855914 GTGTTTATATGCAATTCCATACACCG 59.144 38.462 2.83 0.00 30.38 4.94
2895 3005 6.455360 AGTCAAACTTTGATGATGTGTGTT 57.545 33.333 7.47 0.00 42.47 3.32


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

AutoCloner maintained by Alex Coulton.