Multiple sequence alignment - TraesCS2B01G283100

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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 TraesCS2B01G283100 chr2B 100.000 3215 0 0 1 3215 391112759 391109545 0 5938
1 TraesCS2B01G283100 chr4D 98.445 3215 47 3 2 3215 123299973 123303185 0 5657
2 TraesCS2B01G283100 chr7B 98.196 3215 54 3 2 3215 644467527 644470738 0 5613
3 TraesCS2B01G283100 chr7D 98.165 3216 56 3 2 3215 203515559 203518773 0 5609
4 TraesCS2B01G283100 chr6B 97.917 3216 64 2 2 3215 306995907 306992693 0 5565
5 TraesCS2B01G283100 chr3A 97.822 3214 65 4 2 3215 633111337 633114545 0 5542
6 TraesCS2B01G283100 chr1B 97.605 3215 70 5 5 3215 638700580 638697369 0 5504
7 TraesCS2B01G283100 chr1B 97.231 3214 86 2 2 3215 672479244 672482454 0 5439
8 TraesCS2B01G283100 chr2A 97.201 3215 84 5 2 3215 332944214 332941005 0 5433
9 TraesCS2B01G283100 chr4B 97.138 3215 88 3 2 3215 209077435 209074224 0 5424


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 TraesCS2B01G283100 chr2B 391109545 391112759 3214 True 5938 5938 100.000 1 3215 1 chr2B.!!$R1 3214
1 TraesCS2B01G283100 chr4D 123299973 123303185 3212 False 5657 5657 98.445 2 3215 1 chr4D.!!$F1 3213
2 TraesCS2B01G283100 chr7B 644467527 644470738 3211 False 5613 5613 98.196 2 3215 1 chr7B.!!$F1 3213
3 TraesCS2B01G283100 chr7D 203515559 203518773 3214 False 5609 5609 98.165 2 3215 1 chr7D.!!$F1 3213
4 TraesCS2B01G283100 chr6B 306992693 306995907 3214 True 5565 5565 97.917 2 3215 1 chr6B.!!$R1 3213
5 TraesCS2B01G283100 chr3A 633111337 633114545 3208 False 5542 5542 97.822 2 3215 1 chr3A.!!$F1 3213
6 TraesCS2B01G283100 chr1B 638697369 638700580 3211 True 5504 5504 97.605 5 3215 1 chr1B.!!$R1 3210
7 TraesCS2B01G283100 chr1B 672479244 672482454 3210 False 5439 5439 97.231 2 3215 1 chr1B.!!$F1 3213
8 TraesCS2B01G283100 chr2A 332941005 332944214 3209 True 5433 5433 97.201 2 3215 1 chr2A.!!$R1 3213
9 TraesCS2B01G283100 chr4B 209074224 209077435 3211 True 5424 5424 97.138 2 3215 1 chr4B.!!$R1 3213

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
37 38 1.492176 GAATGATTGGAGAGAGCCCCA 59.508 52.381 0.0 0.0 0.0 4.96 F
1175 1188 0.807496 GCCGACGACTTACTACTGGT 59.193 55.000 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 1653 0.035725 TGATGGCACCTTGCTCTGAG 60.036 55.0 0.0 0.0 44.28 3.35 R
2726 2743 0.178068 ATGTGCATAGACCGGGTGAC 59.822 55.0 3.3 0.0 0.00 3.67 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
37 38 1.492176 GAATGATTGGAGAGAGCCCCA 59.508 52.381 0.00 0.00 0.00 4.96
61 62 4.974721 CTTGGTTGGTGCCGGGCT 62.975 66.667 21.46 0.00 0.00 5.19
164 166 2.023760 AAACAGGCTTTGCTCCCCCT 62.024 55.000 0.00 0.00 0.00 4.79
247 249 7.059156 CCCATAGAAAAGATCATGAAAGAGGT 58.941 38.462 0.00 0.00 0.00 3.85
402 404 6.148811 GGAATTCGACATCAGGAAGTGTTTTA 59.851 38.462 0.00 0.00 0.00 1.52
510 512 3.885521 CCGGACGACTCGTAGGGC 61.886 72.222 14.60 0.00 41.37 5.19
587 589 5.131142 AGGCAATATCTACCTACACAAGCTT 59.869 40.000 0.00 0.00 29.98 3.74
761 763 3.013648 TCATAGTGGGGAGGGTAAAGAGT 59.986 47.826 0.00 0.00 0.00 3.24
859 871 1.673920 GTGACCAGAAAACGCCTTTCA 59.326 47.619 11.81 0.00 45.15 2.69
922 935 2.032528 CGAGCCTCCTTTGCACCA 59.967 61.111 0.00 0.00 0.00 4.17
986 999 7.254590 CGAATTCAATGGTAGAGAAGGCTTTAG 60.255 40.741 0.00 0.00 0.00 1.85
1175 1188 0.807496 GCCGACGACTTACTACTGGT 59.193 55.000 0.00 0.00 0.00 4.00
1481 1494 9.775539 TTATAGTATCCCTATCAAAGAGCTGAT 57.224 33.333 0.00 0.00 37.54 2.90
1515 1528 2.657143 GGAAGAGGTCGTCTACTGGAT 58.343 52.381 0.00 0.00 32.65 3.41
1573 1586 5.056553 ACTAAAAAGTCCCCAAGTTAGCA 57.943 39.130 0.00 0.00 0.00 3.49
1640 1653 1.061711 CTCGTTGTTGCATAGCTCAGC 59.938 52.381 0.00 0.00 0.00 4.26
1692 1705 0.596083 CAGTCTCACGATCGGGCATC 60.596 60.000 20.98 8.59 0.00 3.91
1764 1778 3.256960 GGAAGGGGACACTGGGCA 61.257 66.667 0.00 0.00 0.00 5.36
1793 1807 0.839946 AGCAGCGAATTCCCCATACT 59.160 50.000 0.00 0.00 0.00 2.12
1927 1941 3.131577 AGACATAGTAAATTGGTCCGCGA 59.868 43.478 8.23 0.00 0.00 5.87
2165 2179 0.891373 CTTGGGAAGCTCAGACTCGA 59.109 55.000 0.00 0.00 0.00 4.04
2500 2516 0.741326 AGATCGCTGCTTCGCTTCTA 59.259 50.000 0.00 0.00 0.00 2.10
2726 2743 1.068753 CACGGAGCTGCATCCCTAG 59.931 63.158 5.91 0.00 35.82 3.02
2910 2927 4.870636 TGATCAATTAATGGGACTTGGCT 58.129 39.130 0.00 0.00 0.00 4.75
3013 3030 4.469657 TGTATGTGCCAGGAAGTTTCTTT 58.530 39.130 0.00 0.00 0.00 2.52
3130 3147 5.746065 GCCTAATTTCTAGAATAGGGCTGCA 60.746 44.000 24.27 2.98 39.78 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.198635 TCATTCCAAAGAGCCGAGATCTT 59.801 43.478 0.00 0.00 40.14 2.40
15 16 1.492176 GGGCTCTCTCCAATCATTCCA 59.508 52.381 0.00 0.00 0.00 3.53
37 38 1.456287 GCACCAACCAAGAGGAGGT 59.544 57.895 0.00 0.00 43.98 3.85
61 62 3.280295 GAAGTAGTCCCATCACTCTCGA 58.720 50.000 0.00 0.00 0.00 4.04
402 404 1.544246 TCGATGTCAGTCGATGGTGTT 59.456 47.619 0.00 0.00 44.87 3.32
414 416 6.576185 TCAAGATTGAGATGAATCGATGTCA 58.424 36.000 0.00 5.72 37.41 3.58
510 512 2.232298 GAGTCAGGGCCCTTCTCACG 62.232 65.000 32.64 19.77 0.00 4.35
587 589 3.012274 GGATCCTCCCTATCTCCTGATCA 59.988 52.174 3.84 0.00 34.32 2.92
716 718 0.397941 CTCTGTTGTCTTGGGGAGCA 59.602 55.000 0.00 0.00 0.00 4.26
840 852 2.045561 TGAAAGGCGTTTTCTGGTCA 57.954 45.000 5.76 0.00 44.49 4.02
922 935 0.466124 GCGGCTTCTATGAGGAAGGT 59.534 55.000 6.40 0.00 41.93 3.50
986 999 4.336713 GGTCTCTCATGGCCAAATTCTTAC 59.663 45.833 10.96 2.99 0.00 2.34
1096 1109 1.077276 TTAAAGGGGGCCAGCTTACA 58.923 50.000 4.39 0.00 0.00 2.41
1175 1188 2.168936 AGAAATACGGCACCCACGATTA 59.831 45.455 0.00 0.00 34.93 1.75
1481 1494 0.617535 TCTTCCGCTCATCCCCTTCA 60.618 55.000 0.00 0.00 0.00 3.02
1515 1528 1.080093 CTCCGCTAGTTGAACCGCA 60.080 57.895 7.75 0.00 0.00 5.69
1573 1586 2.039879 GCTTGACGGTCCCCCATAATAT 59.960 50.000 5.55 0.00 0.00 1.28
1640 1653 0.035725 TGATGGCACCTTGCTCTGAG 60.036 55.000 0.00 0.00 44.28 3.35
1670 1683 2.105128 CCGATCGTGAGACTGCCC 59.895 66.667 15.09 0.00 46.97 5.36
1692 1705 7.678947 ATACAATTTCTTCTTCAGGACACTG 57.321 36.000 0.00 0.00 46.30 3.66
1764 1778 2.706339 ATTCGCTGCTGAAAGATCCT 57.294 45.000 10.06 0.00 34.07 3.24
1927 1941 1.000827 CAGAGGACTTATCGCGATGCT 60.001 52.381 31.05 16.66 0.00 3.79
2158 2172 3.017442 TGTTCGGATCTTGATCGAGTCT 58.983 45.455 9.87 0.00 34.33 3.24
2165 2179 2.259618 CGTCGTTGTTCGGATCTTGAT 58.740 47.619 0.00 0.00 40.32 2.57
2240 2254 2.695359 TCTCATGTAAACGCCTGTTCC 58.305 47.619 0.00 0.00 37.31 3.62
2726 2743 0.178068 ATGTGCATAGACCGGGTGAC 59.822 55.000 3.30 0.00 0.00 3.67
2844 2861 7.126268 TGCTGCACAGACCCATATATATAGAAT 59.874 37.037 0.00 0.00 0.00 2.40
2862 2879 2.106477 TATCGTGGAAATGCTGCACA 57.894 45.000 3.57 0.00 46.25 4.57
2910 2927 4.041567 TGATAGAGGCAAGAACACTTTCCA 59.958 41.667 0.00 0.00 31.24 3.53
3031 3048 3.537961 AAGGGGCGGGGCATTTTCA 62.538 57.895 0.00 0.00 0.00 2.69
3130 3147 0.829182 CAAACAAAGCCCTCCTGCCT 60.829 55.000 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.