Multiple sequence alignment - TraesCS3A01G478000

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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 TraesCS3A01G478000 chr3A 100.000 2348 0 0 1 2348 710263190 710265537 0.000000e+00 4337.0
1 TraesCS3A01G478000 chr3D 95.290 1911 75 8 452 2348 575137074 575135165 0.000000e+00 3016.0
2 TraesCS3A01G478000 chr3D 87.931 870 96 5 825 1690 575218682 575219546 0.000000e+00 1016.0
3 TraesCS3A01G478000 chr3D 95.089 448 19 3 1 446 575137728 575137282 0.000000e+00 702.0
4 TraesCS3A01G478000 chr3D 85.714 448 59 3 1383 1830 575137416 575136974 3.530000e-128 468.0
5 TraesCS3A01G478000 chr3D 93.478 230 13 2 1 229 228158078 228157850 8.040000e-90 340.0
6 TraesCS3A01G478000 chr3D 88.820 161 11 4 1866 2025 575219553 575219707 8.560000e-45 191.0
7 TraesCS3A01G478000 chr3D 88.119 101 12 0 452 552 575135786 575135686 1.140000e-23 121.0
8 TraesCS3A01G478000 chr3D 91.860 86 7 0 312 397 612763847 612763932 1.140000e-23 121.0
9 TraesCS3A01G478000 chr3B 91.495 1117 83 8 1085 2193 764685608 764686720 0.000000e+00 1526.0
10 TraesCS3A01G478000 chr3B 85.834 833 109 7 768 1595 764053334 764052506 0.000000e+00 876.0
11 TraesCS3A01G478000 chr3B 85.254 590 78 8 891 1474 764049551 764048965 1.200000e-167 599.0
12 TraesCS3A01G478000 chr3B 84.783 414 33 12 550 933 764684714 764685127 2.830000e-104 388.0
13 TraesCS3A01G478000 chr3B 80.544 478 80 9 1000 1470 813373377 813372906 2.870000e-94 355.0
14 TraesCS3A01G478000 chr3B 91.429 245 20 1 932 1176 764685372 764685615 3.740000e-88 335.0
15 TraesCS3A01G478000 chr3B 88.406 138 13 1 312 446 764685906 764686043 1.870000e-36 163.0
16 TraesCS3A01G478000 chr2D 94.323 229 11 2 2 229 330463690 330463917 1.340000e-92 350.0
17 TraesCS3A01G478000 chr2D 94.323 229 11 2 1 228 376827978 376827751 1.340000e-92 350.0
18 TraesCS3A01G478000 chr2D 93.913 230 12 2 1 229 154116183 154116411 1.730000e-91 346.0
19 TraesCS3A01G478000 chr5D 93.562 233 12 3 1 231 366106229 366106460 6.210000e-91 344.0
20 TraesCS3A01G478000 chr5D 86.667 75 6 4 222 295 35479976 35479905 1.930000e-11 80.5
21 TraesCS3A01G478000 chr5B 93.478 230 13 2 1 229 209095787 209095559 8.040000e-90 340.0
22 TraesCS3A01G478000 chr4D 93.478 230 13 2 1 229 57887010 57886782 8.040000e-90 340.0
23 TraesCS3A01G478000 chr4B 93.478 230 13 2 1 229 260574143 260574371 8.040000e-90 340.0
24 TraesCS3A01G478000 chr1A 94.565 92 3 1 228 317 10149591 10149682 8.750000e-30 141.0
25 TraesCS3A01G478000 chr1A 93.651 63 4 0 227 289 10149565 10149627 6.910000e-16 95.3
26 TraesCS3A01G478000 chr4A 89.130 92 6 3 229 317 723043811 723043721 6.860000e-21 111.0
27 TraesCS3A01G478000 chr7A 89.011 91 6 3 228 315 102052072 102052161 2.470000e-20 110.0
28 TraesCS3A01G478000 chr1B 84.000 100 13 2 228 324 482946208 482946109 2.480000e-15 93.5
29 TraesCS3A01G478000 chr1D 90.141 71 5 1 221 289 417622353 417622423 8.940000e-15 91.6
30 TraesCS3A01G478000 chr6D 92.157 51 4 0 227 277 288435111 288435161 3.240000e-09 73.1


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 TraesCS3A01G478000 chr3A 710263190 710265537 2347 False 4337.00 4337 100.00000 1 2348 1 chr3A.!!$F1 2347
1 TraesCS3A01G478000 chr3D 575135165 575137728 2563 True 1076.75 3016 91.05300 1 2348 4 chr3D.!!$R2 2347
2 TraesCS3A01G478000 chr3D 575218682 575219707 1025 False 603.50 1016 88.37550 825 2025 2 chr3D.!!$F2 1200
3 TraesCS3A01G478000 chr3B 764048965 764053334 4369 True 737.50 876 85.54400 768 1595 2 chr3B.!!$R2 827
4 TraesCS3A01G478000 chr3B 764684714 764686720 2006 False 603.00 1526 89.02825 312 2193 4 chr3B.!!$F1 1881

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
807 1045 0.038166 ACTGCCCACCCAACTATGTG 59.962 55.0 0.0 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 5602 0.59868 GAGTAGCAAGATGGCGCGAT 60.599 55.0 12.1 3.93 39.27 4.58 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 9.294030 CTTTGATCTTTAATACAATGTTCTGCC 57.706 33.333 0.00 0.00 0.00 4.85
48 50 0.804989 GTTCTGCCCGATGTTCTTGG 59.195 55.000 0.00 0.00 0.00 3.61
58 60 5.615289 CCCGATGTTCTTGGAGATCTATTT 58.385 41.667 0.00 0.00 0.00 1.40
60 62 5.049818 CCGATGTTCTTGGAGATCTATTTGC 60.050 44.000 0.00 0.00 0.00 3.68
80 83 2.408368 GCTGTAATTTCTTTTGCGGTGC 59.592 45.455 0.00 0.00 0.00 5.01
105 108 5.550232 TTGTTGAGATCCGATGAATTGTG 57.450 39.130 0.00 0.00 0.00 3.33
106 109 4.831107 TGTTGAGATCCGATGAATTGTGA 58.169 39.130 0.00 0.00 0.00 3.58
213 216 5.499139 TCGATCTATTGATTTGGTTTGGC 57.501 39.130 0.00 0.00 32.19 4.52
235 238 9.944376 TTGGCCAACTAGATTAGATTATATGAC 57.056 33.333 16.05 0.00 0.00 3.06
477 682 2.217750 TGCTGTCGTGTTGTATTGCTT 58.782 42.857 0.00 0.00 0.00 3.91
489 694 5.468746 TGTTGTATTGCTTGTCAACCTACTC 59.531 40.000 0.00 0.00 39.22 2.59
517 722 0.999406 CGGTATGACGCAACCTTCTG 59.001 55.000 0.00 0.00 33.34 3.02
531 736 3.046374 ACCTTCTGTAACCAAGACCAGT 58.954 45.455 0.00 0.00 0.00 4.00
676 886 7.047460 TGGATACCGTCTTAAAGATAGAACC 57.953 40.000 0.00 0.00 0.00 3.62
807 1045 0.038166 ACTGCCCACCCAACTATGTG 59.962 55.000 0.00 0.00 0.00 3.21
904 1142 9.921637 GATTTTTGGTATATTTGAGTGAACCAA 57.078 29.630 0.76 0.76 43.34 3.67
1041 1525 4.935352 TCTTTGCTTTATGGTGCTTGTT 57.065 36.364 0.00 0.00 0.00 2.83
1201 1770 1.140852 CAGGGAATTGCCATACCGAGA 59.859 52.381 19.16 0.00 38.95 4.04
1218 1787 2.792890 CGAGAGTGCTTACTCACATCCG 60.793 54.545 9.79 2.37 39.35 4.18
1320 1889 5.588648 AGTTCGAGGATTTTTCAAAGTGTCA 59.411 36.000 0.00 0.00 0.00 3.58
1562 2136 1.000060 CGGTTAGTCCTTGTCGTGGAA 60.000 52.381 0.00 0.00 35.10 3.53
1657 5442 4.034048 CCTTAAGGCATGTATGACACGTTC 59.966 45.833 9.00 0.00 38.64 3.95
1658 5443 2.760634 AGGCATGTATGACACGTTCA 57.239 45.000 0.00 3.49 38.64 3.18
1659 5444 2.621338 AGGCATGTATGACACGTTCAG 58.379 47.619 0.00 0.00 38.64 3.02
1774 5559 1.454111 ATCGACCTACTCGCTGCCT 60.454 57.895 0.00 0.00 42.62 4.75
1785 5570 1.153647 CGCTGCCTTCGGTATGACA 60.154 57.895 0.00 0.00 0.00 3.58
1817 5602 1.595311 ACCAGGACCAGCCATCAATA 58.405 50.000 0.00 0.00 40.02 1.90
1879 5664 1.779061 ATCCGTCAGGTTGTTGCCCT 61.779 55.000 0.00 0.00 39.05 5.19
1900 5685 2.842496 TGGCCATCTCTGAAGTCTGAAT 59.158 45.455 0.00 0.00 0.00 2.57
1901 5686 3.204526 GGCCATCTCTGAAGTCTGAATG 58.795 50.000 0.00 0.00 0.00 2.67
1955 5741 8.803397 AATTACCTTCAAGTGTAAGGGATAAC 57.197 34.615 6.80 0.00 46.56 1.89
2060 5846 8.813643 AGTTAAGTATGTCACTTACAGAACAC 57.186 34.615 14.88 2.71 46.96 3.32
2085 5871 7.125204 ACTCTATGCACTTGTACTATAACCCAA 59.875 37.037 0.00 0.00 0.00 4.12
2129 5915 8.049117 AGCAGAAATATCATCCACTAAGTTTGA 58.951 33.333 0.00 0.00 0.00 2.69
2130 5916 8.125448 GCAGAAATATCATCCACTAAGTTTGAC 58.875 37.037 0.00 0.00 0.00 3.18
2202 5988 5.640732 AGTTTGTGAGTGTTGTCATCAAAC 58.359 37.500 16.08 16.08 41.94 2.93
2215 6001 2.647299 TCATCAAACCAAGAAGCCCCTA 59.353 45.455 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 11 9.846248 GCAGAACATTGTATTAAAGATCAAAGT 57.154 29.630 0.00 0.00 0.00 2.66
20 22 4.776349 ACATCGGGCAGAACATTGTATTA 58.224 39.130 0.00 0.00 0.00 0.98
34 36 1.139853 AGATCTCCAAGAACATCGGGC 59.860 52.381 0.00 0.00 0.00 6.13
36 38 5.049818 GCAAATAGATCTCCAAGAACATCGG 60.050 44.000 0.00 0.00 0.00 4.18
58 60 3.637432 CACCGCAAAAGAAATTACAGCA 58.363 40.909 0.00 0.00 0.00 4.41
60 62 2.656422 CGCACCGCAAAAGAAATTACAG 59.344 45.455 0.00 0.00 0.00 2.74
74 77 0.452784 GATCTCAACAAACGCACCGC 60.453 55.000 0.00 0.00 0.00 5.68
80 83 4.864916 ATTCATCGGATCTCAACAAACG 57.135 40.909 0.00 0.00 0.00 3.60
235 238 9.645059 AATGATATAACAACTCATCATCCGTAG 57.355 33.333 0.00 0.00 37.18 3.51
331 334 7.784037 ACATGCATGTCACCATAATGTTTTAT 58.216 30.769 26.61 0.00 35.55 1.40
415 418 4.546674 GGTTATGAACCCCCATTTCATCT 58.453 43.478 0.94 0.00 46.12 2.90
416 419 4.937201 GGTTATGAACCCCCATTTCATC 57.063 45.455 0.94 0.00 46.12 2.92
477 682 3.609853 GATGGCAATGAGTAGGTTGACA 58.390 45.455 0.00 0.00 46.48 3.58
489 694 0.235665 GCGTCATACCGATGGCAATG 59.764 55.000 0.00 0.00 37.55 2.82
517 722 2.806608 TGACGACTGGTCTTGGTTAC 57.193 50.000 0.00 0.00 46.24 2.50
531 736 2.125713 ATGGCGCGACATTGACGA 60.126 55.556 24.82 0.00 0.00 4.20
744 980 0.806868 TCTACGACGATGGTGTCCAC 59.193 55.000 0.00 0.00 35.80 4.02
749 985 2.617308 ACCTGTATCTACGACGATGGTG 59.383 50.000 0.00 0.00 0.00 4.17
936 1420 5.665943 GCGTGCAAATGTACATGATGTTTTG 60.666 40.000 9.63 13.93 32.00 2.44
953 1437 0.179124 GTTTCTGTTTGGGCGTGCAA 60.179 50.000 0.00 0.00 0.00 4.08
956 1440 0.041312 CTCGTTTCTGTTTGGGCGTG 60.041 55.000 0.00 0.00 0.00 5.34
1041 1525 4.763073 CATGAGTTGAATGTCCTAGCAGA 58.237 43.478 0.00 0.00 0.00 4.26
1201 1770 2.299013 TCAACGGATGTGAGTAAGCACT 59.701 45.455 0.00 0.00 39.49 4.40
1218 1787 6.313164 GGCAAGTAGTACCTAGACAAATCAAC 59.687 42.308 0.00 0.00 0.00 3.18
1320 1889 2.493035 TCGCAGACAACACATTCACAT 58.507 42.857 0.00 0.00 0.00 3.21
1484 2056 3.104519 TCAACCTCCATTCCATGCAAT 57.895 42.857 0.00 0.00 0.00 3.56
1545 2119 1.000060 CCGTTCCACGACAAGGACTAA 60.000 52.381 0.00 0.00 46.05 2.24
1659 5444 0.972883 AGGAGCTTGAGTCCTGTGAC 59.027 55.000 0.00 0.00 43.24 3.67
1774 5559 3.070446 ACAGAAGGTTGTGTCATACCGAA 59.930 43.478 0.00 0.00 39.46 4.30
1817 5602 0.598680 GAGTAGCAAGATGGCGCGAT 60.599 55.000 12.10 3.93 39.27 4.58
1879 5664 1.942776 TCAGACTTCAGAGATGGCCA 58.057 50.000 8.56 8.56 0.00 5.36
1900 5685 2.019951 GCGCGGAGAGAACGAAACA 61.020 57.895 8.83 0.00 0.00 2.83
1901 5686 2.727684 GGCGCGGAGAGAACGAAAC 61.728 63.158 8.83 0.00 0.00 2.78
2060 5846 7.050970 TGGGTTATAGTACAAGTGCATAGAG 57.949 40.000 0.00 0.00 0.00 2.43
2085 5871 2.500098 TGCTCTCACCGCTTACCTTTAT 59.500 45.455 0.00 0.00 0.00 1.40
2129 5915 9.787435 TCAACTAGGAATTACATTTTGTACTGT 57.213 29.630 0.00 0.00 31.69 3.55
2150 5936 6.487668 TGTGATGTGTGAGATGAATTTCAACT 59.512 34.615 8.74 8.74 31.87 3.16
2202 5988 2.190578 CCGCTAGGGGCTTCTTGG 59.809 66.667 13.61 0.00 39.13 3.61
2295 6084 1.402968 GCGAGGAGGATACAACGTACA 59.597 52.381 0.00 0.00 41.41 2.90
2299 6088 1.927174 CTTTGCGAGGAGGATACAACG 59.073 52.381 0.00 0.00 41.41 4.10


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

AutoCloner maintained by Alex Coulton.