Multiple sequence alignment - TraesCS3D01G433200

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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 TraesCS3D01G433200 chr3D 100.000 3591 0 0 1 3591 546468136 546471726 0.000000e+00 6632.0
1 TraesCS3D01G433200 chr3D 77.446 368 42 20 3212 3553 30241111 30240759 7.920000e-42 182.0
2 TraesCS3D01G433200 chr3B 94.810 2813 83 15 1 2792 723498800 723501570 0.000000e+00 4327.0
3 TraesCS3D01G433200 chr3B 97.810 548 9 3 2790 3334 723501693 723502240 0.000000e+00 942.0
4 TraesCS3D01G433200 chr3B 96.465 198 4 1 3348 3545 723502865 723503059 1.240000e-84 324.0
5 TraesCS3D01G433200 chr3B 83.815 346 38 16 3207 3545 51819692 51819358 2.690000e-81 313.0
6 TraesCS3D01G433200 chr3B 91.837 98 4 2 3456 3553 52769425 52769518 2.250000e-27 134.0
7 TraesCS3D01G433200 chr3A 95.588 2017 55 6 1 1989 683238378 683240388 0.000000e+00 3201.0
8 TraesCS3D01G433200 chr3A 95.411 1264 26 11 2357 3591 683241301 683242561 0.000000e+00 1984.0
9 TraesCS3D01G433200 chr3A 95.143 350 11 1 1987 2336 683240490 683240833 6.780000e-152 547.0
10 TraesCS3D01G433200 chr3A 89.655 145 11 4 3207 3348 42000163 42000020 7.920000e-42 182.0
11 TraesCS3D01G433200 chr3A 91.057 123 8 1 3423 3545 41999987 41999868 2.870000e-36 163.0
12 TraesCS3D01G433200 chr6A 91.716 169 11 2 2088 2253 478925120 478924952 7.750000e-57 231.0
13 TraesCS3D01G433200 chr7A 91.716 169 9 2 2087 2254 451519973 451519809 2.790000e-56 230.0
14 TraesCS3D01G433200 chr5A 91.279 172 9 3 2087 2256 558675659 558675492 2.790000e-56 230.0
15 TraesCS3D01G433200 chr5A 91.228 171 10 2 2085 2254 320214241 320214407 1.000000e-55 228.0
16 TraesCS3D01G433200 chr5A 89.503 181 12 4 2078 2256 688327038 688327213 4.670000e-54 222.0
17 TraesCS3D01G433200 chr5D 90.805 174 11 2 2083 2255 204324442 204324611 1.000000e-55 228.0
18 TraesCS3D01G433200 chr5D 97.561 41 1 0 3551 3591 174002372 174002332 1.790000e-08 71.3
19 TraesCS3D01G433200 chr4D 90.000 180 11 4 2075 2252 334164378 334164552 3.610000e-55 226.0
20 TraesCS3D01G433200 chr1B 91.667 84 6 1 1860 1942 588448625 588448708 8.150000e-22 115.0
21 TraesCS3D01G433200 chr1A 92.500 80 5 1 1864 1942 532673065 532673144 2.930000e-21 113.0
22 TraesCS3D01G433200 chr1A 90.476 84 7 1 1860 1942 532714388 532714471 3.790000e-20 110.0


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 TraesCS3D01G433200 chr3D 546468136 546471726 3590 False 6632.000000 6632 100.000000 1 3591 1 chr3D.!!$F1 3590
1 TraesCS3D01G433200 chr3B 723498800 723503059 4259 False 1864.333333 4327 96.361667 1 3545 3 chr3B.!!$F2 3544
2 TraesCS3D01G433200 chr3A 683238378 683242561 4183 False 1910.666667 3201 95.380667 1 3591 3 chr3A.!!$F1 3590

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
991 1017 3.700038 AGAAGGTTCCGATCGACATTAGT 59.300 43.478 18.66 0.08 0.0 2.24 F
2071 2205 0.248289 GTGCCACACTACCACCGTAT 59.752 55.000 0.00 0.00 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2488 3069 1.270826 TCAGAGCTCAAGACCTGTTCG 59.729 52.381 17.77 0.0 0.0 3.95 R
3039 3745 2.145397 AGACCGATAAGCAGGACTCA 57.855 50.000 0.00 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
28 29 5.801350 TTTCTGAATCTAGTTGCCAATCG 57.199 39.130 0.00 0.00 0.00 3.34
61 62 8.848474 TCTTAATTAATACCAGCTAGAATGCC 57.152 34.615 0.00 0.00 0.00 4.40
103 111 7.678829 CGCGTTTATCATACTTGATACGAATTC 59.321 37.037 12.83 0.00 42.74 2.17
372 380 8.877864 TCCCTTACATATTGAATCAACTGTTT 57.122 30.769 15.27 0.00 0.00 2.83
412 421 8.749499 CACAAAGAGAAATAAGAAGTTGCAAAG 58.251 33.333 0.00 0.00 0.00 2.77
567 592 7.954788 TGTGGAATTTTGCAACTTTATAACC 57.045 32.000 0.00 0.00 0.00 2.85
754 779 6.336842 AGTTTTTGATGTTGAAGATCCTGG 57.663 37.500 0.00 0.00 0.00 4.45
991 1017 3.700038 AGAAGGTTCCGATCGACATTAGT 59.300 43.478 18.66 0.08 0.00 2.24
1120 1146 1.006922 GCTGCTGTCAACCTTTGCC 60.007 57.895 0.00 0.00 0.00 4.52
1224 1250 1.107114 TTGTCACAACGCCAATGGTT 58.893 45.000 0.00 0.00 0.00 3.67
1335 1361 1.906574 ACTAGCAAGAAATCCCGGACA 59.093 47.619 0.73 0.00 0.00 4.02
1360 1386 2.422832 CCCTCGGTAAGGCTACGATATC 59.577 54.545 8.89 0.00 44.71 1.63
1524 1550 1.291588 CTCTTCGTCCTGCTGCAGT 59.708 57.895 26.41 0.00 0.00 4.40
1558 1584 0.659957 GATTGGCGCATCTGAGGAAC 59.340 55.000 10.83 0.00 0.00 3.62
1765 1791 3.257393 AGAAATTGAGAGTACTGCAGCG 58.743 45.455 15.27 0.00 0.00 5.18
1775 1801 2.906182 TACTGCAGCGCCTGATTCCG 62.906 60.000 15.27 0.00 32.44 4.30
1965 1995 5.048991 ACTTGTTTATGTTCCAGTTAAGCCG 60.049 40.000 0.00 0.00 0.00 5.52
1979 2009 3.508840 GCCGTTCGCCATTCCTGG 61.509 66.667 0.00 0.00 46.17 4.45
1993 2127 5.478407 CCATTCCTGGAAAAATGTAACACC 58.522 41.667 14.03 0.00 46.37 4.16
2003 2137 7.087639 GGAAAAATGTAACACCGAATTCATCA 58.912 34.615 6.22 0.00 0.00 3.07
2071 2205 0.248289 GTGCCACACTACCACCGTAT 59.752 55.000 0.00 0.00 0.00 3.06
2096 2230 6.139679 TCCAAAATTCAACATACTCCCTCT 57.860 37.500 0.00 0.00 0.00 3.69
2105 2239 5.422331 TCAACATACTCCCTCTGTTCCTAAG 59.578 44.000 0.00 0.00 30.99 2.18
2250 2384 9.495382 AGACTTATATTTAGAAACAGAGGGAGT 57.505 33.333 0.00 0.00 0.00 3.85
2488 3069 8.214364 AGTATTATTCTGATCTTCCCTTGTTCC 58.786 37.037 0.00 0.00 0.00 3.62
2580 3161 3.089284 TGAGTCTGAGAATTACCGCAGA 58.911 45.455 0.00 0.00 35.22 4.26
2630 3211 3.438360 CCTTGTTGCTGTCAAGTCAAAC 58.562 45.455 12.35 0.00 40.15 2.93
2936 3642 8.868522 TTTTGGCATATAAGAATAGATCCTGG 57.131 34.615 0.00 0.00 0.00 4.45
3039 3745 3.725634 AGCTCTGGTAGGGATGTAAACT 58.274 45.455 0.00 0.00 0.00 2.66
3348 4644 4.022849 TGAGTACGTGATCCATATGCTCAG 60.023 45.833 0.00 0.71 0.00 3.35
3354 4674 4.449068 CGTGATCCATATGCTCAGTTAACC 59.551 45.833 0.88 0.00 0.00 2.85
3479 4799 3.267031 ACTTGGTGCCCTAAGCTTTATCT 59.733 43.478 3.20 0.00 44.23 1.98
3480 4800 4.473559 ACTTGGTGCCCTAAGCTTTATCTA 59.526 41.667 3.20 0.00 44.23 1.98
3481 4801 5.045140 ACTTGGTGCCCTAAGCTTTATCTAA 60.045 40.000 3.20 0.00 44.23 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 8.159344 AGCTGGTATTAATTAAGATGCAGAAC 57.841 34.615 3.94 0.00 0.00 3.01
61 62 1.657181 GCGTTTTGTGCAAGGGTCG 60.657 57.895 0.00 0.00 0.00 4.79
438 447 6.093219 GTGCTCGCAGATCATAAATGGAATAT 59.907 38.462 0.00 0.00 34.28 1.28
567 592 4.083643 GCCACCAAGTGATTCATATGATCG 60.084 45.833 6.17 0.00 35.23 3.69
754 779 0.535102 CGAGCAATGACCCATACCCC 60.535 60.000 0.00 0.00 0.00 4.95
991 1017 0.690192 TTCGCCTCCATTCTGTTGGA 59.310 50.000 0.00 0.00 43.56 3.53
1032 1058 2.833582 TCGCTCCTCCCATCGACC 60.834 66.667 0.00 0.00 0.00 4.79
1120 1146 0.754957 TTGGCACTGGTGTTTGGAGG 60.755 55.000 2.64 0.00 0.00 4.30
1167 1193 6.486657 TGTCAAGAGGAAGGAACAAATTACTG 59.513 38.462 0.00 0.00 0.00 2.74
1206 1232 1.968704 TAACCATTGGCGTTGTGACA 58.031 45.000 1.54 0.00 0.00 3.58
1207 1233 2.033550 TGTTAACCATTGGCGTTGTGAC 59.966 45.455 1.54 0.00 0.00 3.67
1224 1250 2.421388 GCATAGGTCCATGCCAGTGTTA 60.421 50.000 12.68 0.00 44.55 2.41
1246 1272 1.293924 GTCTGATGCCGGTGATCAAG 58.706 55.000 16.26 11.62 29.44 3.02
1335 1361 1.482954 GTAGCCTTACCGAGGGAACT 58.517 55.000 0.00 0.00 46.40 3.01
1371 1397 5.998454 ATTTCAAGAGAGGATGCATAACG 57.002 39.130 0.00 0.00 0.00 3.18
1448 1474 2.416893 GCTAGGCTTAAACACAGAGCAC 59.583 50.000 0.00 0.00 38.14 4.40
1524 1550 3.126858 CGCCAATCAAATCTTCTTCCGAA 59.873 43.478 0.00 0.00 0.00 4.30
1544 1570 0.678048 AAAGGGTTCCTCAGATGCGC 60.678 55.000 0.00 0.00 30.89 6.09
1558 1584 0.893727 CCCTGGTTCGGAACAAAGGG 60.894 60.000 30.69 30.69 0.00 3.95
1775 1801 5.003804 TGAGAGCTTACTTTGGTTCCATTC 58.996 41.667 0.00 0.00 0.00 2.67
1831 1857 2.271800 GCCGTGTTAGATGGACTCTTG 58.728 52.381 0.00 0.00 35.28 3.02
1832 1858 1.899814 TGCCGTGTTAGATGGACTCTT 59.100 47.619 0.00 0.00 35.28 2.85
1965 1995 3.253230 CATTTTTCCAGGAATGGCGAAC 58.747 45.455 1.58 0.00 31.28 3.95
1979 2009 8.514136 TTGATGAATTCGGTGTTACATTTTTC 57.486 30.769 0.04 0.00 0.00 2.29
1993 2127 5.444983 TGTTGTAACGGTTTGATGAATTCG 58.555 37.500 0.00 0.00 0.00 3.34
2003 2137 4.989168 TGCAAACTTTTGTTGTAACGGTTT 59.011 33.333 0.00 0.00 42.67 3.27
2071 2205 7.010160 AGAGGGAGTATGTTGAATTTTGGAAA 58.990 34.615 0.00 0.00 0.00 3.13
2252 2386 9.092338 ACAACCTCCCAACGTGTTATATATATA 57.908 33.333 0.00 0.00 0.00 0.86
2253 2387 7.970102 ACAACCTCCCAACGTGTTATATATAT 58.030 34.615 0.00 0.00 0.00 0.86
2254 2388 7.364149 ACAACCTCCCAACGTGTTATATATA 57.636 36.000 0.00 0.00 0.00 0.86
2255 2389 6.243216 ACAACCTCCCAACGTGTTATATAT 57.757 37.500 0.00 0.00 0.00 0.86
2419 3000 7.443302 TCTTGTATCCTCCTTCTCAAATCAT 57.557 36.000 0.00 0.00 0.00 2.45
2488 3069 1.270826 TCAGAGCTCAAGACCTGTTCG 59.729 52.381 17.77 0.00 0.00 3.95
2580 3161 5.888161 GGATTATGACCAGTTCATTCTTGGT 59.112 40.000 0.00 0.00 42.87 3.67
2630 3211 4.216042 TGAACAAATGCACCATGTACTGAG 59.784 41.667 0.00 0.00 0.00 3.35
2746 3327 4.467082 TGGCATGCTCCAACTTATTTGATT 59.533 37.500 18.92 0.00 37.39 2.57
3039 3745 2.145397 AGACCGATAAGCAGGACTCA 57.855 50.000 0.00 0.00 0.00 3.41
3348 4644 9.480053 TCATTAACGCCTATATTACTGGTTAAC 57.520 33.333 0.00 0.00 33.02 2.01
3479 4799 7.888021 AGTTGGACACCTCAATCACAATTATTA 59.112 33.333 0.00 0.00 0.00 0.98
3480 4800 6.721208 AGTTGGACACCTCAATCACAATTATT 59.279 34.615 0.00 0.00 0.00 1.40
3481 4801 6.248433 AGTTGGACACCTCAATCACAATTAT 58.752 36.000 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.