Multiple sequence alignment - TraesCS6B01G119400

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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 TraesCS6B01G119400 chr6B 100.000 2640 0 0 1 2640 114144834 114142195 0.000000e+00 4876
1 TraesCS6B01G119400 chr6B 94.964 2244 74 17 1 2233 661051604 661053819 0.000000e+00 3482
2 TraesCS6B01G119400 chr6B 94.470 1989 58 21 1 1950 687514440 687512465 0.000000e+00 3016
3 TraesCS6B01G119400 chr6B 93.785 901 44 4 1748 2640 650644914 650644018 0.000000e+00 1343
4 TraesCS6B01G119400 chr4B 93.073 2584 119 28 1 2540 49105642 49108209 0.000000e+00 3725
5 TraesCS6B01G119400 chr7B 91.733 2625 155 35 1 2569 27326573 27329191 0.000000e+00 3589
6 TraesCS6B01G119400 chr7B 95.062 2106 80 8 548 2638 235457544 235455448 0.000000e+00 3291
7 TraesCS6B01G119400 chr7B 95.720 1986 68 5 669 2640 130334623 130336605 0.000000e+00 3181
8 TraesCS6B01G119400 chr7B 94.904 471 14 2 2178 2640 335929294 335929762 0.000000e+00 728
9 TraesCS6B01G119400 chr2B 94.162 2244 101 11 1 2233 154585546 154583322 0.000000e+00 3391
10 TraesCS6B01G119400 chr2B 96.221 2064 58 5 591 2640 717652642 717654699 0.000000e+00 3362
11 TraesCS6B01G119400 chr2B 93.127 291 11 2 2358 2640 153867423 153867712 4.060000e-113 418
12 TraesCS6B01G119400 chr1B 95.591 2064 68 6 591 2640 550439508 550437454 0.000000e+00 3286
13 TraesCS6B01G119400 chr1B 94.110 730 30 4 1920 2640 357900183 357899458 0.000000e+00 1098
14 TraesCS6B01G119400 chr5B 94.070 2108 96 11 548 2640 530940281 530938188 0.000000e+00 3173
15 TraesCS6B01G119400 chr5B 96.331 1826 56 4 1 1815 454660895 454662720 0.000000e+00 2990
16 TraesCS6B01G119400 chr5B 94.118 612 24 5 2038 2640 658086055 658086663 0.000000e+00 920
17 TraesCS6B01G119400 chr3B 92.009 901 45 5 1748 2640 393330850 393331731 0.000000e+00 1240
18 TraesCS6B01G119400 chr3B 89.369 856 70 12 1738 2582 28618692 28619537 0.000000e+00 1057


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 TraesCS6B01G119400 chr6B 114142195 114144834 2639 True 4876 4876 100.000 1 2640 1 chr6B.!!$R1 2639
1 TraesCS6B01G119400 chr6B 661051604 661053819 2215 False 3482 3482 94.964 1 2233 1 chr6B.!!$F1 2232
2 TraesCS6B01G119400 chr6B 687512465 687514440 1975 True 3016 3016 94.470 1 1950 1 chr6B.!!$R3 1949
3 TraesCS6B01G119400 chr6B 650644018 650644914 896 True 1343 1343 93.785 1748 2640 1 chr6B.!!$R2 892
4 TraesCS6B01G119400 chr4B 49105642 49108209 2567 False 3725 3725 93.073 1 2540 1 chr4B.!!$F1 2539
5 TraesCS6B01G119400 chr7B 27326573 27329191 2618 False 3589 3589 91.733 1 2569 1 chr7B.!!$F1 2568
6 TraesCS6B01G119400 chr7B 235455448 235457544 2096 True 3291 3291 95.062 548 2638 1 chr7B.!!$R1 2090
7 TraesCS6B01G119400 chr7B 130334623 130336605 1982 False 3181 3181 95.720 669 2640 1 chr7B.!!$F2 1971
8 TraesCS6B01G119400 chr2B 154583322 154585546 2224 True 3391 3391 94.162 1 2233 1 chr2B.!!$R1 2232
9 TraesCS6B01G119400 chr2B 717652642 717654699 2057 False 3362 3362 96.221 591 2640 1 chr2B.!!$F2 2049
10 TraesCS6B01G119400 chr1B 550437454 550439508 2054 True 3286 3286 95.591 591 2640 1 chr1B.!!$R2 2049
11 TraesCS6B01G119400 chr1B 357899458 357900183 725 True 1098 1098 94.110 1920 2640 1 chr1B.!!$R1 720
12 TraesCS6B01G119400 chr5B 530938188 530940281 2093 True 3173 3173 94.070 548 2640 1 chr5B.!!$R1 2092
13 TraesCS6B01G119400 chr5B 454660895 454662720 1825 False 2990 2990 96.331 1 1815 1 chr5B.!!$F1 1814
14 TraesCS6B01G119400 chr5B 658086055 658086663 608 False 920 920 94.118 2038 2640 1 chr5B.!!$F2 602
15 TraesCS6B01G119400 chr3B 393330850 393331731 881 False 1240 1240 92.009 1748 2640 1 chr3B.!!$F2 892
16 TraesCS6B01G119400 chr3B 28618692 28619537 845 False 1057 1057 89.369 1738 2582 1 chr3B.!!$F1 844

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
768 930 0.681564 CTAGAGGTGGTGGTCGAGCT 60.682 60.0 16.64 0.0 33.17 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2411 2762 1.448013 GACGTTGGCAGGGCTAGAC 60.448 63.158 0.0 0.0 0.0 2.59 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
348 350 4.271661 ACGAAGGGTAGAAGGAGAACTAG 58.728 47.826 0.00 0.00 0.00 2.57
472 474 1.599797 CGGTGAAGGGGGACACAAC 60.600 63.158 0.00 0.00 38.57 3.32
634 640 2.175878 CACAAGTGCTAGAGGTGCTT 57.824 50.000 0.00 0.00 0.00 3.91
768 930 0.681564 CTAGAGGTGGTGGTCGAGCT 60.682 60.000 16.64 0.00 33.17 4.09
793 955 0.977395 AAGTGCTAGAGGTGGTGGTC 59.023 55.000 0.00 0.00 0.00 4.02
797 965 1.810532 CTAGAGGTGGTGGTCGAGC 59.189 63.158 7.89 7.89 0.00 5.03
799 967 0.965866 TAGAGGTGGTGGTCGAGCAG 60.966 60.000 19.24 0.00 30.97 4.24
849 1017 5.365605 TCGTAGAGGAATGGTTGATAATGGT 59.634 40.000 0.00 0.00 0.00 3.55
1188 1356 4.678256 AGTCATGGACAGAAGGTAGAAGA 58.322 43.478 0.00 0.00 34.60 2.87
1426 1595 1.404986 CGAGATTGGTTACGGAGGCAA 60.405 52.381 0.00 0.00 0.00 4.52
1657 1827 2.380064 AGACAAATGGAAAGGCACCA 57.620 45.000 0.00 0.00 41.83 4.17
1760 1990 9.684448 TTATGTCATTCGAGACTATTTGAGATC 57.316 33.333 6.40 0.00 39.27 2.75
1777 2007 6.822667 TGAGATCATGTGCAAACTATGTTT 57.177 33.333 0.00 0.00 0.00 2.83
1950 2181 1.987855 CCAAGGACCCTGGCGTCTA 60.988 63.158 12.89 0.00 33.07 2.59
1965 2196 0.456995 GTCTAGCTCGCTTTGCTCGT 60.457 55.000 0.00 0.00 41.46 4.18
2069 2419 4.101448 AGGGACCATGGCGTCTGC 62.101 66.667 13.04 0.00 41.71 4.26
2356 2707 1.045911 CCCACCTCTAGCCCTCTCAC 61.046 65.000 0.00 0.00 0.00 3.51
2373 2724 3.041211 CTCACCCATTCATCTCCACCTA 58.959 50.000 0.00 0.00 0.00 3.08
2410 2761 3.645212 CACTCATATCCACCCACTCTCAT 59.355 47.826 0.00 0.00 0.00 2.90
2411 2762 3.645212 ACTCATATCCACCCACTCTCATG 59.355 47.826 0.00 0.00 0.00 3.07
2449 2800 3.083349 TCCCTCATCCAGCACCCG 61.083 66.667 0.00 0.00 0.00 5.28
2451 2802 2.187946 CCTCATCCAGCACCCGAC 59.812 66.667 0.00 0.00 0.00 4.79
2452 2803 2.187946 CTCATCCAGCACCCGACC 59.812 66.667 0.00 0.00 0.00 4.79
2453 2804 3.391665 CTCATCCAGCACCCGACCC 62.392 68.421 0.00 0.00 0.00 4.46
2454 2805 4.489771 CATCCAGCACCCGACCCC 62.490 72.222 0.00 0.00 0.00 4.95
2512 2879 2.422832 ACCGTTGGATCTTCGAGACTAC 59.577 50.000 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
348 350 1.421646 CCATATCACCCCTGAACCTCC 59.578 57.143 0.00 0.00 0.00 4.30
472 474 1.570813 TATTCTTGCATGTCCGCTCG 58.429 50.000 0.00 0.00 0.00 5.03
634 640 3.144657 TGTACTCCCTCTACGAACACA 57.855 47.619 0.00 0.00 0.00 3.72
727 853 0.038251 CTTGTGCTAGCTCGACCACA 60.038 55.000 17.23 7.77 36.51 4.17
768 930 1.550524 CCACCTCTAGCACTTGTGCTA 59.449 52.381 27.11 27.11 44.28 3.49
793 955 1.357258 CTAGCACTTGTGCCTGCTCG 61.357 60.000 20.39 1.66 42.86 5.03
797 965 0.322975 ACCTCTAGCACTTGTGCCTG 59.677 55.000 20.39 13.89 34.90 4.85
799 967 0.674895 CCACCTCTAGCACTTGTGCC 60.675 60.000 20.39 4.86 34.90 5.01
1188 1356 4.320935 GCATAGTTGGGACACACGAAAAAT 60.321 41.667 0.00 0.00 39.29 1.82
1426 1595 0.106619 AGGACTCCTCGAATAGGCGT 60.107 55.000 0.00 0.00 46.29 5.68
1657 1827 1.474478 AGACAGTTCATCATCGACGCT 59.526 47.619 0.00 0.00 0.00 5.07
1760 1990 6.183359 CGAATGACAAACATAGTTTGCACATG 60.183 38.462 23.02 14.66 38.38 3.21
1777 2007 6.542735 AGCATACTAACTAGTCTCGAATGACA 59.457 38.462 7.47 0.00 39.27 3.58
1950 2181 3.418068 GCACGAGCAAAGCGAGCT 61.418 61.111 0.00 0.16 46.82 4.09
1965 2196 1.598962 GCTTGTCTGGTCAGCTGCA 60.599 57.895 9.47 0.70 0.00 4.41
2154 2505 3.625897 CTGGCGTCTGGGTGTGGA 61.626 66.667 0.00 0.00 0.00 4.02
2356 2707 3.264450 GGGTATAGGTGGAGATGAATGGG 59.736 52.174 0.00 0.00 0.00 4.00
2373 2724 6.214412 GGATATGAGTGAAATGAGAGGGGTAT 59.786 42.308 0.00 0.00 0.00 2.73
2410 2761 2.167398 GACGTTGGCAGGGCTAGACA 62.167 60.000 0.00 0.00 0.00 3.41
2411 2762 1.448013 GACGTTGGCAGGGCTAGAC 60.448 63.158 0.00 0.00 0.00 2.59
2512 2879 3.089284 GGGGTGGAGTTGATTTACCTTG 58.911 50.000 0.00 0.00 0.00 3.61
2576 2943 4.773013 AGACCACGAGGAAAACAAACTAA 58.227 39.130 5.68 0.00 38.69 2.24


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

AutoCloner maintained by Alex Coulton.