Multiple sequence alignment - TraesCS3D01G119500

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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 TraesCS3D01G119500 chr3D 100.000 2687 0 0 718 3404 74761080 74758394 0.000000e+00 4963.0
1 TraesCS3D01G119500 chr3D 100.000 57 0 0 1 57 74761797 74761741 4.650000e-19 106.0
2 TraesCS3D01G119500 chr3B 92.985 1454 51 15 718 2154 120405320 120403901 0.000000e+00 2073.0
3 TraesCS3D01G119500 chr3B 89.462 930 31 31 2508 3404 120403321 120402426 0.000000e+00 1112.0
4 TraesCS3D01G119500 chr3B 94.477 344 16 1 2163 2506 120403854 120403514 8.370000e-146 527.0
5 TraesCS3D01G119500 chr3B 87.387 111 11 2 2226 2336 543184939 543185046 1.280000e-24 124.0
6 TraesCS3D01G119500 chr3A 90.852 1443 63 24 718 2111 88189389 88190811 0.000000e+00 1869.0
7 TraesCS3D01G119500 chr3A 91.405 605 17 12 2508 3089 88191355 88191947 0.000000e+00 797.0
8 TraesCS3D01G119500 chr3A 94.477 344 16 1 2163 2506 88190819 88191159 8.370000e-146 527.0
9 TraesCS3D01G119500 chr3A 89.623 318 32 1 3087 3404 88194679 88194995 1.470000e-108 403.0
10 TraesCS3D01G119500 chr3A 94.828 58 2 1 1 57 88189277 88189334 4.680000e-14 89.8
11 TraesCS3D01G119500 chr2B 83.019 159 19 8 2203 2356 674065860 674065705 1.650000e-28 137.0
12 TraesCS3D01G119500 chr1D 75.517 290 55 13 1454 1738 119405042 119404764 9.910000e-26 128.0
13 TraesCS3D01G119500 chr1D 97.143 70 1 1 1109 1177 7591370 7591301 2.150000e-22 117.0
14 TraesCS3D01G119500 chr4B 83.453 139 18 5 2202 2337 563996851 563996715 1.280000e-24 124.0
15 TraesCS3D01G119500 chr4A 82.432 148 19 7 2203 2346 532222542 532222398 4.610000e-24 122.0
16 TraesCS3D01G119500 chr7D 97.143 70 1 1 1109 1177 151316082 151316013 2.150000e-22 117.0
17 TraesCS3D01G119500 chr7A 91.111 45 1 3 1187 1230 664052277 664052235 1.320000e-04 58.4


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 TraesCS3D01G119500 chr3D 74758394 74761797 3403 True 2534.500000 4963 100.000 1 3404 2 chr3D.!!$R1 3403
1 TraesCS3D01G119500 chr3B 120402426 120405320 2894 True 1237.333333 2073 92.308 718 3404 3 chr3B.!!$R1 2686
2 TraesCS3D01G119500 chr3A 88189277 88194995 5718 False 737.160000 1869 92.237 1 3404 5 chr3A.!!$F1 3403

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
800 808 1.023502 GGTAGAGAGAGTACGTGCCC 58.976 60.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2506 2613 0.105039 CCCAGATCCCTGCGAGTAAC 59.895 60.0 0.0 0.0 39.07 2.5 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
784 792 2.891580 GACGGAGATATTCCTGCTGGTA 59.108 50.000 9.73 0.00 44.41 3.25
800 808 1.023502 GGTAGAGAGAGTACGTGCCC 58.976 60.000 0.00 0.00 0.00 5.36
957 999 4.797471 TGCGGATTTGTGATCTTCTTTTG 58.203 39.130 0.00 0.00 0.00 2.44
969 1023 2.287915 TCTTCTTTTGCGTGCTCTTGAC 59.712 45.455 0.00 0.00 0.00 3.18
989 1043 3.053896 CCCGGTTTCAGGCGGTTC 61.054 66.667 0.00 0.00 0.00 3.62
1823 1880 4.680237 CCTGGTGGTCAAGCGCGA 62.680 66.667 12.10 0.00 0.00 5.87
2007 2071 3.520569 ACCAATAATTGCGGCATTGTTC 58.479 40.909 2.28 0.00 0.00 3.18
2008 2072 2.535166 CCAATAATTGCGGCATTGTTCG 59.465 45.455 2.28 0.00 0.00 3.95
2009 2073 3.178267 CAATAATTGCGGCATTGTTCGT 58.822 40.909 2.28 0.00 0.00 3.85
2010 2074 2.999507 TAATTGCGGCATTGTTCGTT 57.000 40.000 2.28 0.00 0.00 3.85
2012 2076 0.454285 ATTGCGGCATTGTTCGTTCG 60.454 50.000 2.28 0.00 0.00 3.95
2013 2077 1.777030 TTGCGGCATTGTTCGTTCGT 61.777 50.000 2.28 0.00 0.00 3.85
2014 2078 1.509162 GCGGCATTGTTCGTTCGTC 60.509 57.895 0.00 0.00 0.00 4.20
2015 2079 1.897398 GCGGCATTGTTCGTTCGTCT 61.897 55.000 0.00 0.00 0.00 4.18
2016 2080 0.511221 CGGCATTGTTCGTTCGTCTT 59.489 50.000 0.00 0.00 0.00 3.01
2017 2081 1.721489 CGGCATTGTTCGTTCGTCTTG 60.721 52.381 0.00 0.00 0.00 3.02
2020 2084 2.032377 GCATTGTTCGTTCGTCTTGGAA 60.032 45.455 0.00 0.00 0.00 3.53
2038 2102 5.596836 TGGAACATCCCATATTCTTTTGC 57.403 39.130 0.00 0.00 35.03 3.68
2054 2118 2.791383 TTGCGGAACAAATCTTGTGG 57.209 45.000 0.00 0.00 44.59 4.17
2100 2168 6.202570 GCAATCCAAACAAAATGAAGCACTAA 59.797 34.615 0.00 0.00 0.00 2.24
2140 2209 6.840527 TGCTGAATTACCATCAGATTCCATA 58.159 36.000 7.67 0.00 45.74 2.74
2185 2292 5.683302 GCAGCAACTGTTCTTTCTTTCTAAC 59.317 40.000 0.00 0.00 33.43 2.34
2250 2357 1.730547 GTGTCAACATTGCAGCGGC 60.731 57.895 0.31 0.31 41.68 6.53
2382 2489 0.179100 ACGAGGACATCTTCATGGCG 60.179 55.000 0.00 0.00 39.27 5.69
2407 2514 3.680620 ATGGTGGCGACATGACCCG 62.681 63.158 0.00 0.81 46.14 5.28
2497 2604 1.279271 CCTTGCTAGCTACAACCAGGT 59.721 52.381 17.23 0.00 0.00 4.00
2647 2949 1.225704 CCAGAGCCACCCATCCTTC 59.774 63.158 0.00 0.00 0.00 3.46
2785 3103 2.268796 TTGGGTCATCTCCATCTCCA 57.731 50.000 0.00 0.00 33.82 3.86
3048 3376 1.699083 TCCAGCCAAGTGATCAACTCA 59.301 47.619 0.00 0.00 38.56 3.41
3049 3377 2.082231 CCAGCCAAGTGATCAACTCAG 58.918 52.381 0.00 0.00 38.56 3.35
3114 6176 0.396974 AACCAACATGGCCTGTGTGT 60.397 50.000 13.91 6.49 42.67 3.72
3135 6213 1.270907 AGATGAGACACACACTCCCC 58.729 55.000 0.00 0.00 33.95 4.81
3137 6215 0.687354 ATGAGACACACACTCCCCAC 59.313 55.000 0.00 0.00 33.95 4.61
3138 6216 0.689412 TGAGACACACACTCCCCACA 60.689 55.000 0.00 0.00 33.95 4.17
3147 6225 2.697751 CACACTCCCCACAATTTTCCAA 59.302 45.455 0.00 0.00 0.00 3.53
3171 6259 6.409524 TTTTCTTCAAGGCATTTGACTGAT 57.590 33.333 2.70 0.00 45.22 2.90
3226 6314 0.387565 GGGTGAAAATGGCGTTGTGT 59.612 50.000 0.00 0.00 0.00 3.72
3239 6327 1.999735 CGTTGTGTGTTGTGACTGACT 59.000 47.619 0.00 0.00 0.00 3.41
3400 6488 0.254178 TCCAGAAATGGGCTCTGCTC 59.746 55.000 0.00 0.00 39.23 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.332514 CAGCCAAACCGCACTGTG 59.667 61.111 2.76 2.76 0.00 3.66
33 34 4.057943 AGCTAGGGGACGGACGGT 62.058 66.667 0.00 0.00 0.00 4.83
784 792 1.316706 GCTGGGCACGTACTCTCTCT 61.317 60.000 0.00 0.00 0.00 3.10
1614 1671 4.368543 GACCCGAAGAACCGCCGT 62.369 66.667 0.00 0.00 0.00 5.68
1845 1902 2.492090 CTCAGGAAGTCCTCGCCG 59.508 66.667 0.00 0.00 46.65 6.46
1975 2039 6.926272 GCCGCAATTATTGGTTGGATAAATTA 59.074 34.615 7.08 0.00 0.00 1.40
1976 2040 5.757808 GCCGCAATTATTGGTTGGATAAATT 59.242 36.000 7.08 0.00 0.00 1.82
1977 2041 5.163364 TGCCGCAATTATTGGTTGGATAAAT 60.163 36.000 7.08 0.00 0.00 1.40
2007 2071 1.076332 GGGATGTTCCAAGACGAACG 58.924 55.000 0.00 0.00 44.22 3.95
2008 2072 2.178912 TGGGATGTTCCAAGACGAAC 57.821 50.000 0.00 0.00 42.10 3.95
2009 2073 4.771114 ATATGGGATGTTCCAAGACGAA 57.229 40.909 0.00 0.00 40.62 3.85
2010 2074 4.408921 AGAATATGGGATGTTCCAAGACGA 59.591 41.667 0.00 0.00 40.62 4.20
2012 2076 7.260603 CAAAAGAATATGGGATGTTCCAAGAC 58.739 38.462 0.00 0.00 40.62 3.01
2013 2077 6.127366 GCAAAAGAATATGGGATGTTCCAAGA 60.127 38.462 0.00 0.00 40.62 3.02
2014 2078 6.044682 GCAAAAGAATATGGGATGTTCCAAG 58.955 40.000 0.00 0.00 40.62 3.61
2015 2079 5.394005 CGCAAAAGAATATGGGATGTTCCAA 60.394 40.000 0.00 0.00 40.62 3.53
2016 2080 4.097741 CGCAAAAGAATATGGGATGTTCCA 59.902 41.667 0.00 0.00 38.64 3.53
2017 2081 4.499696 CCGCAAAAGAATATGGGATGTTCC 60.500 45.833 0.00 0.00 35.23 3.62
2020 2084 3.897239 TCCGCAAAAGAATATGGGATGT 58.103 40.909 0.00 0.00 0.00 3.06
2038 2102 4.537015 GAGTTTCCACAAGATTTGTTCCG 58.463 43.478 0.00 0.00 43.23 4.30
2054 2118 5.040635 TGCCAAAGAAATGTTTCGAGTTTC 58.959 37.500 0.24 6.57 41.92 2.78
2100 2168 1.200716 CAGCATGCCGTTCAGTTCAAT 59.799 47.619 15.66 0.00 0.00 2.57
2147 2216 1.117994 TGCTGCCATTTTGTCCAACA 58.882 45.000 0.00 0.00 0.00 3.33
2149 2218 1.761784 AGTTGCTGCCATTTTGTCCAA 59.238 42.857 0.00 0.00 0.00 3.53
2154 2223 3.102052 AGAACAGTTGCTGCCATTTTG 57.898 42.857 0.00 0.00 34.37 2.44
2156 2225 3.385755 AGAAAGAACAGTTGCTGCCATTT 59.614 39.130 0.00 0.00 34.37 2.32
2158 2227 2.590821 AGAAAGAACAGTTGCTGCCAT 58.409 42.857 0.00 0.00 34.37 4.40
2159 2228 2.057137 AGAAAGAACAGTTGCTGCCA 57.943 45.000 0.00 0.00 34.37 4.92
2160 2229 3.067320 AGAAAGAAAGAACAGTTGCTGCC 59.933 43.478 0.00 0.00 34.37 4.85
2161 2230 4.298744 AGAAAGAAAGAACAGTTGCTGC 57.701 40.909 0.00 0.00 34.37 5.25
2206 2313 8.556194 CACAACAAATCAGTTTGCTTACTAGTA 58.444 33.333 0.00 0.00 46.84 1.82
2207 2314 7.067008 ACACAACAAATCAGTTTGCTTACTAGT 59.933 33.333 0.00 0.00 46.84 2.57
2208 2315 7.376866 CACACAACAAATCAGTTTGCTTACTAG 59.623 37.037 1.12 0.00 46.84 2.57
2211 2318 5.804979 ACACACAACAAATCAGTTTGCTTAC 59.195 36.000 1.12 0.00 46.84 2.34
2286 2393 4.022068 GCTTCCTCTTCGATCATGATCTCT 60.022 45.833 28.48 0.00 35.72 3.10
2382 2489 3.211963 GTCGCCACCATCATGCCC 61.212 66.667 0.00 0.00 0.00 5.36
2506 2613 0.105039 CCCAGATCCCTGCGAGTAAC 59.895 60.000 0.00 0.00 39.07 2.50
2577 2879 1.145571 ACTACAGGACCAAAGGCCAA 58.854 50.000 5.01 0.00 0.00 4.52
2785 3103 8.237811 TGCTCAAAGTAAAAGAAAAGAGGAAT 57.762 30.769 0.00 0.00 0.00 3.01
3114 6176 2.832129 GGGGAGTGTGTGTCTCATCTTA 59.168 50.000 0.00 0.00 34.04 2.10
3135 6213 7.134163 GCCTTGAAGAAAATTGGAAAATTGTG 58.866 34.615 0.00 0.00 0.00 3.33
3137 6215 7.261829 TGCCTTGAAGAAAATTGGAAAATTG 57.738 32.000 0.00 0.00 0.00 2.32
3138 6216 8.467963 AATGCCTTGAAGAAAATTGGAAAATT 57.532 26.923 0.00 0.00 0.00 1.82
3147 6225 6.409524 TCAGTCAAATGCCTTGAAGAAAAT 57.590 33.333 0.00 0.00 45.67 1.82
3226 6314 0.829990 TCTGCCAGTCAGTCACAACA 59.170 50.000 0.00 0.00 43.32 3.33


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

AutoCloner maintained by Alex Coulton.