Multiple sequence alignment - TraesCS3D01G379500

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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 TraesCS3D01G379500 chr3D 100.000 3287 0 0 1 3287 496407893 496404607 0.000000e+00 6071
1 TraesCS3D01G379500 chr3B 93.603 3314 125 36 12 3283 655423826 655420558 0.000000e+00 4865
2 TraesCS3D01G379500 chr3A 93.245 3079 101 35 274 3283 635732406 635729366 0.000000e+00 4434
3 TraesCS3D01G379500 chr3A 90.833 240 20 2 14 252 635732629 635732391 1.470000e-83 320
4 TraesCS3D01G379500 chrUn 79.377 257 45 8 1271 1525 124906482 124906732 1.210000e-39 174
5 TraesCS3D01G379500 chr2D 79.457 258 43 10 1271 1525 635650954 635650704 1.210000e-39 174
6 TraesCS3D01G379500 chr2D 88.710 124 8 3 2861 2984 526253316 526253433 2.640000e-31 147
7 TraesCS3D01G379500 chr7D 78.707 263 47 7 1264 1523 404062840 404063096 2.030000e-37 167
8 TraesCS3D01G379500 chr7A 78.707 263 47 7 1264 1523 462984866 462985122 2.030000e-37 167


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 TraesCS3D01G379500 chr3D 496404607 496407893 3286 True 6071 6071 100.000 1 3287 1 chr3D.!!$R1 3286
1 TraesCS3D01G379500 chr3B 655420558 655423826 3268 True 4865 4865 93.603 12 3283 1 chr3B.!!$R1 3271
2 TraesCS3D01G379500 chr3A 635729366 635732629 3263 True 2377 4434 92.039 14 3283 2 chr3A.!!$R1 3269

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
958 992 0.110056 CGCGTAGTGGAGTTGTACGT 60.110 55.0 0.0 0.0 41.25 3.57 F
1203 1240 0.615331 CCACCACCACTGTCTATGCT 59.385 55.0 0.0 0.0 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2145 2195 1.156322 TCCTCCACCTCCTCCTCCTT 61.156 60.000 0.00 0.00 0.0 3.36 R
3037 3115 1.271652 TGCTTGGCCGAGGAATTTACA 60.272 47.619 22.06 6.13 0.0 2.41 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
43 44 1.409802 CCTTGAGGCCATCATCTTGCT 60.410 52.381 5.01 0.00 37.89 3.91
143 144 4.403752 AGTCTATTTACCCTAACCCACGAC 59.596 45.833 0.00 0.00 0.00 4.34
149 150 1.447314 CCTAACCCACGACGCCTTC 60.447 63.158 0.00 0.00 0.00 3.46
153 154 0.539986 AACCCACGACGCCTTCATAT 59.460 50.000 0.00 0.00 0.00 1.78
184 185 4.039245 CCAGATTACACATATCCGACACCT 59.961 45.833 0.00 0.00 0.00 4.00
222 223 3.420943 GCGAATATGCCCGTTGCT 58.579 55.556 0.00 0.00 42.00 3.91
232 233 1.271652 TGCCCGTTGCTATCCTTGAAA 60.272 47.619 0.00 0.00 42.00 2.69
236 237 3.438360 CCGTTGCTATCCTTGAAATTGC 58.562 45.455 0.00 0.00 0.00 3.56
274 276 3.181540 GCGCTAGTACATGCAATCATACG 60.182 47.826 0.00 0.00 0.00 3.06
279 281 5.023533 AGTACATGCAATCATACGTCCTT 57.976 39.130 0.00 0.00 0.00 3.36
922 947 1.504900 CCGTCGTTCATGTCGAGGA 59.495 57.895 24.57 9.67 42.95 3.71
924 949 0.523546 CGTCGTTCATGTCGAGGAGG 60.524 60.000 21.14 10.25 42.95 4.30
958 992 0.110056 CGCGTAGTGGAGTTGTACGT 60.110 55.000 0.00 0.00 41.25 3.57
982 1016 3.276091 CTTGTTGCGTGGCGTGGA 61.276 61.111 0.00 0.00 0.00 4.02
1041 1075 3.000727 CGACTTGAGGGTTATGTTCACC 58.999 50.000 0.00 0.00 0.00 4.02
1203 1240 0.615331 CCACCACCACTGTCTATGCT 59.385 55.000 0.00 0.00 0.00 3.79
1335 1372 2.090524 CGCCGAGTACCCGTTCAAC 61.091 63.158 0.00 0.00 0.00 3.18
2145 2195 4.314440 GCGGCGATCCAGGGCATA 62.314 66.667 12.98 0.00 0.00 3.14
2376 2429 0.694771 TTCAGCAGCCTCTTGACCAT 59.305 50.000 0.00 0.00 0.00 3.55
2404 2457 1.129811 CCCGTGAACATAAAACGCCTC 59.870 52.381 0.00 0.00 36.02 4.70
2612 2670 0.248621 GCACACACACAAGTTGCTCC 60.249 55.000 1.81 0.00 0.00 4.70
2613 2671 0.027979 CACACACACAAGTTGCTCCG 59.972 55.000 1.81 0.00 0.00 4.63
2619 2677 0.040958 CACAAGTTGCTCCGTTCTGC 60.041 55.000 1.81 0.00 0.00 4.26
2660 2718 1.039068 CAATTGGCACTGAACCACCA 58.961 50.000 0.00 0.00 36.76 4.17
2782 2840 4.179599 CCTCCTCCCCTCCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
2784 2842 4.761304 TCCTCCCCTCCCCTCCCT 62.761 72.222 0.00 0.00 0.00 4.20
2785 2843 3.711782 CCTCCCCTCCCCTCCCTT 61.712 72.222 0.00 0.00 0.00 3.95
2786 2844 2.040359 CTCCCCTCCCCTCCCTTC 60.040 72.222 0.00 0.00 0.00 3.46
2787 2845 3.707189 TCCCCTCCCCTCCCTTCC 61.707 72.222 0.00 0.00 0.00 3.46
2788 2846 4.845307 CCCCTCCCCTCCCTTCCC 62.845 77.778 0.00 0.00 0.00 3.97
2789 2847 4.038804 CCCTCCCCTCCCTTCCCA 62.039 72.222 0.00 0.00 0.00 4.37
2817 2875 7.704899 CAGCTAGATCATTTCATTCAATTTGCA 59.295 33.333 0.00 0.00 0.00 4.08
2862 2920 1.405526 CCATGGTCCAGTTTCGTCGAT 60.406 52.381 2.57 0.00 0.00 3.59
2984 3045 3.071874 TGAGATTTAAGCACCACCAGG 57.928 47.619 0.00 0.00 42.21 4.45
3066 3144 0.550914 TCGGCCAAGCAAGGGATTAT 59.449 50.000 2.24 0.00 0.00 1.28
3126 3204 1.135689 CGAGCACCAATTAACTGCACC 60.136 52.381 4.51 0.00 33.06 5.01
3127 3205 2.162681 GAGCACCAATTAACTGCACCT 58.837 47.619 4.51 0.00 33.06 4.00
3129 3207 2.558359 AGCACCAATTAACTGCACCTTC 59.442 45.455 4.51 0.00 33.06 3.46
3267 3357 4.511454 GCTTGCCTCACGTTTCATCATATA 59.489 41.667 0.00 0.00 0.00 0.86
3268 3358 5.180117 GCTTGCCTCACGTTTCATCATATAT 59.820 40.000 0.00 0.00 0.00 0.86
3269 3359 6.619446 GCTTGCCTCACGTTTCATCATATATC 60.619 42.308 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.678336 GCTTTTGTGATACGGGGAGAAG 59.322 50.000 0.00 0.00 0.00 2.85
2 3 1.065709 GGCTTTTGTGATACGGGGAGA 60.066 52.381 0.00 0.00 0.00 3.71
3 4 1.379527 GGCTTTTGTGATACGGGGAG 58.620 55.000 0.00 0.00 0.00 4.30
4 5 0.034863 GGGCTTTTGTGATACGGGGA 60.035 55.000 0.00 0.00 0.00 4.81
5 6 1.035385 GGGGCTTTTGTGATACGGGG 61.035 60.000 0.00 0.00 0.00 5.73
6 7 0.034477 AGGGGCTTTTGTGATACGGG 60.034 55.000 0.00 0.00 0.00 5.28
7 8 1.472480 CAAGGGGCTTTTGTGATACGG 59.528 52.381 0.00 0.00 0.00 4.02
8 9 2.420022 CTCAAGGGGCTTTTGTGATACG 59.580 50.000 2.43 0.00 0.00 3.06
9 10 2.755103 CCTCAAGGGGCTTTTGTGATAC 59.245 50.000 5.56 0.00 0.00 2.24
10 11 3.085952 CCTCAAGGGGCTTTTGTGATA 57.914 47.619 5.56 0.00 0.00 2.15
11 12 1.928868 CCTCAAGGGGCTTTTGTGAT 58.071 50.000 5.56 0.00 0.00 3.06
12 13 3.437642 CCTCAAGGGGCTTTTGTGA 57.562 52.632 5.56 0.00 0.00 3.58
43 44 0.957395 GTGGTGGTCGGTCGACTCTA 60.957 60.000 20.55 10.90 44.04 2.43
130 131 2.847435 GAAGGCGTCGTGGGTTAGGG 62.847 65.000 0.00 0.00 0.00 3.53
143 144 1.535028 TGGCGCAAATATATGAAGGCG 59.465 47.619 10.83 13.13 46.47 5.52
149 150 6.239908 TGTGTAATCTGGCGCAAATATATG 57.760 37.500 10.83 0.00 0.00 1.78
153 154 5.411361 GGATATGTGTAATCTGGCGCAAATA 59.589 40.000 10.83 0.00 0.00 1.40
184 185 4.585879 GCCAAGGTGAAGTTTGGTAGATA 58.414 43.478 5.28 0.00 44.52 1.98
217 218 3.119495 ACGGCAATTTCAAGGATAGCAAC 60.119 43.478 0.00 0.00 0.00 4.17
218 219 3.088532 ACGGCAATTTCAAGGATAGCAA 58.911 40.909 0.00 0.00 0.00 3.91
222 223 3.621268 CGAAGACGGCAATTTCAAGGATA 59.379 43.478 0.00 0.00 35.72 2.59
232 233 0.928229 GAATACGCGAAGACGGCAAT 59.072 50.000 15.93 0.00 40.15 3.56
256 257 5.784578 AGGACGTATGATTGCATGTACTA 57.215 39.130 0.00 0.00 35.94 1.82
258 259 4.808895 TGAAGGACGTATGATTGCATGTAC 59.191 41.667 0.00 0.00 35.94 2.90
262 263 4.454678 ACATGAAGGACGTATGATTGCAT 58.545 39.130 0.00 0.00 38.54 3.96
274 276 6.161381 TCGGTTTTAGAAGTACATGAAGGAC 58.839 40.000 0.00 0.00 0.00 3.85
582 589 3.641906 GAGATAGGGATCGAGGGAACAAA 59.358 47.826 0.00 0.00 37.15 2.83
922 947 1.826709 CGGCAAAACCAAAACCCCT 59.173 52.632 0.00 0.00 39.03 4.79
924 949 2.241190 CGCGGCAAAACCAAAACCC 61.241 57.895 0.00 0.00 39.03 4.11
958 992 1.063327 CCACGCAACAAGACGCAAA 59.937 52.632 0.00 0.00 0.00 3.68
982 1016 3.394836 GGCCGAGCTCCCTTGTCT 61.395 66.667 8.47 0.00 0.00 3.41
1461 1498 0.677288 TGGAGACGTTGACGGTCATT 59.323 50.000 12.26 0.00 44.95 2.57
1467 1504 1.728426 GTCGGTGGAGACGTTGACG 60.728 63.158 1.41 1.41 46.33 4.35
1470 1507 1.442184 CGAGTCGGTGGAGACGTTG 60.442 63.158 4.10 0.00 45.26 4.10
1532 1569 1.736645 GTGCCGTGTCGTGTAGCAT 60.737 57.895 0.00 0.00 35.62 3.79
1647 1697 1.607713 CGTCCATCAGCGATATCGAC 58.392 55.000 28.63 18.50 43.02 4.20
1930 1980 4.773117 GGTGTCGGCGAGGACGTC 62.773 72.222 11.20 7.13 39.83 4.34
2145 2195 1.156322 TCCTCCACCTCCTCCTCCTT 61.156 60.000 0.00 0.00 0.00 3.36
2325 2376 8.934023 TCCTAAGTTACAAACATGGAAGAATT 57.066 30.769 0.00 0.00 0.00 2.17
2376 2429 1.634960 TATGTTCACGGGTCACAGGA 58.365 50.000 0.00 0.00 0.00 3.86
2404 2457 1.508088 GTGCCGGCAAATGAAGAGG 59.492 57.895 34.66 0.00 0.00 3.69
2493 2551 5.064962 GGAGATATGCTGCTGAATGCTTATC 59.935 44.000 0.00 10.74 42.03 1.75
2612 2670 3.429141 CCCAGCAGCAGCAGAACG 61.429 66.667 3.17 0.00 45.49 3.95
2613 2671 2.809861 TAGCCCAGCAGCAGCAGAAC 62.810 60.000 3.17 0.00 45.49 3.01
2619 2677 1.303561 TTTGGTAGCCCAGCAGCAG 60.304 57.895 0.00 0.00 43.15 4.24
2782 2840 4.637387 AATGATCTAGCTGATGGGAAGG 57.363 45.455 0.00 0.00 35.14 3.46
2784 2842 5.635278 TGAAATGATCTAGCTGATGGGAA 57.365 39.130 0.00 0.00 35.14 3.97
2785 2843 5.837770 ATGAAATGATCTAGCTGATGGGA 57.162 39.130 0.00 0.00 35.14 4.37
2786 2844 6.002082 TGAATGAAATGATCTAGCTGATGGG 58.998 40.000 0.00 0.00 35.14 4.00
2787 2845 7.506328 TTGAATGAAATGATCTAGCTGATGG 57.494 36.000 0.00 0.00 35.14 3.51
2788 2846 9.967346 AAATTGAATGAAATGATCTAGCTGATG 57.033 29.630 0.00 0.00 35.14 3.07
2789 2847 9.967346 CAAATTGAATGAAATGATCTAGCTGAT 57.033 29.630 0.00 0.00 38.27 2.90
3034 3112 3.630312 GCTTGGCCGAGGAATTTACATTA 59.370 43.478 22.06 0.00 0.00 1.90
3035 3113 2.427095 GCTTGGCCGAGGAATTTACATT 59.573 45.455 22.06 0.00 0.00 2.71
3036 3114 2.024414 GCTTGGCCGAGGAATTTACAT 58.976 47.619 22.06 0.00 0.00 2.29
3037 3115 1.271652 TGCTTGGCCGAGGAATTTACA 60.272 47.619 22.06 6.13 0.00 2.41
3038 3116 1.459450 TGCTTGGCCGAGGAATTTAC 58.541 50.000 22.06 3.38 0.00 2.01


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

AutoCloner maintained by Alex Coulton.