Multiple sequence alignment - TraesCS3A01G202400

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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 TraesCS3A01G202400 chr3A 100.000 2435 0 0 1 2435 342256289 342253855 0 4497
1 TraesCS3A01G202400 chr3A 95.597 1817 76 4 622 2435 275869251 275871066 0 2909
2 TraesCS3A01G202400 chr3A 94.989 1816 86 5 622 2434 331240709 331238896 0 2844
3 TraesCS3A01G202400 chr3A 93.422 1809 114 5 629 2434 324217174 324215368 0 2676
4 TraesCS3A01G202400 chr3A 93.007 1816 117 10 622 2434 623207005 623208813 0 2641
5 TraesCS3A01G202400 chr3A 94.612 631 30 4 1 628 275868580 275869209 0 974
6 TraesCS3A01G202400 chr3A 94.304 632 32 4 1 628 331241381 331240750 0 965
7 TraesCS3A01G202400 chr3A 93.153 628 40 3 4 628 227378702 227379329 0 918
8 TraesCS3A01G202400 chr5A 94.001 1817 103 6 622 2435 86546020 86547833 0 2747
9 TraesCS3A01G202400 chr5A 93.286 1817 112 7 622 2434 47161184 47162994 0 2671
10 TraesCS3A01G202400 chr5A 92.675 628 43 3 4 628 320333363 320332736 0 902
11 TraesCS3A01G202400 chr5A 92.393 631 44 4 1 628 111357617 111358246 0 896
12 TraesCS3A01G202400 chr5A 92.417 633 41 6 1 628 551132202 551132832 0 896
13 TraesCS3A01G202400 chr1A 93.502 1816 114 4 622 2435 222295262 222297075 0 2697
14 TraesCS3A01G202400 chr1A 93.532 1809 107 6 629 2434 18193966 18192165 0 2684
15 TraesCS3A01G202400 chr1A 93.455 1803 107 8 635 2434 540098212 540096418 0 2665
16 TraesCS3A01G202400 chr7A 93.027 631 41 3 1 628 483243989 483243359 0 918
17 TraesCS3A01G202400 chr4A 92.800 625 43 2 4 626 69935322 69935946 0 904
18 TraesCS3A01G202400 chr2A 92.915 621 42 2 4 622 420087315 420087935 0 902


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 TraesCS3A01G202400 chr3A 342253855 342256289 2434 True 4497.0 4497 100.0000 1 2435 1 chr3A.!!$R2 2434
1 TraesCS3A01G202400 chr3A 324215368 324217174 1806 True 2676.0 2676 93.4220 629 2434 1 chr3A.!!$R1 1805
2 TraesCS3A01G202400 chr3A 623207005 623208813 1808 False 2641.0 2641 93.0070 622 2434 1 chr3A.!!$F2 1812
3 TraesCS3A01G202400 chr3A 275868580 275871066 2486 False 1941.5 2909 95.1045 1 2435 2 chr3A.!!$F3 2434
4 TraesCS3A01G202400 chr3A 331238896 331241381 2485 True 1904.5 2844 94.6465 1 2434 2 chr3A.!!$R3 2433
5 TraesCS3A01G202400 chr3A 227378702 227379329 627 False 918.0 918 93.1530 4 628 1 chr3A.!!$F1 624
6 TraesCS3A01G202400 chr5A 86546020 86547833 1813 False 2747.0 2747 94.0010 622 2435 1 chr5A.!!$F2 1813
7 TraesCS3A01G202400 chr5A 47161184 47162994 1810 False 2671.0 2671 93.2860 622 2434 1 chr5A.!!$F1 1812
8 TraesCS3A01G202400 chr5A 320332736 320333363 627 True 902.0 902 92.6750 4 628 1 chr5A.!!$R1 624
9 TraesCS3A01G202400 chr5A 111357617 111358246 629 False 896.0 896 92.3930 1 628 1 chr5A.!!$F3 627
10 TraesCS3A01G202400 chr5A 551132202 551132832 630 False 896.0 896 92.4170 1 628 1 chr5A.!!$F4 627
11 TraesCS3A01G202400 chr1A 222295262 222297075 1813 False 2697.0 2697 93.5020 622 2435 1 chr1A.!!$F1 1813
12 TraesCS3A01G202400 chr1A 18192165 18193966 1801 True 2684.0 2684 93.5320 629 2434 1 chr1A.!!$R1 1805
13 TraesCS3A01G202400 chr1A 540096418 540098212 1794 True 2665.0 2665 93.4550 635 2434 1 chr1A.!!$R2 1799
14 TraesCS3A01G202400 chr7A 483243359 483243989 630 True 918.0 918 93.0270 1 628 1 chr7A.!!$R1 627
15 TraesCS3A01G202400 chr4A 69935322 69935946 624 False 904.0 904 92.8000 4 626 1 chr4A.!!$F1 622
16 TraesCS3A01G202400 chr2A 420087315 420087935 620 False 902.0 902 92.9150 4 622 1 chr2A.!!$F1 618


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
314 318 1.894093 CGCCGGTAATCCCCCTATAGT 60.894 57.143 1.9 0.0 0.0 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2083 2139 0.32748 ACTCATCATACCTGGGGGCA 60.327 55.0 0.0 0.0 35.63 5.36 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
182 183 3.546020 CGAAATGTAATGACGCCCATGTC 60.546 47.826 0.00 0.00 39.37 3.06
218 221 2.472695 TGCTCGCCATAATATGTCCC 57.527 50.000 0.00 0.00 0.00 4.46
243 246 1.969208 TGTTGCCAATCATGCTTCCAA 59.031 42.857 0.00 0.00 0.00 3.53
244 247 2.568062 TGTTGCCAATCATGCTTCCAAT 59.432 40.909 0.00 0.00 0.00 3.16
314 318 1.894093 CGCCGGTAATCCCCCTATAGT 60.894 57.143 1.90 0.00 0.00 2.12
333 337 6.761099 ATAGTGGACGCGAATAGATTATCT 57.239 37.500 15.93 0.00 0.00 1.98
376 380 2.938354 GCCATGAATCATAGGCGCT 58.062 52.632 16.63 0.00 37.41 5.92
605 610 8.757982 ATCATCTTTATTGTGCAGGTTCTTAT 57.242 30.769 0.00 0.00 0.00 1.73
627 681 4.664150 AGAGAAGAATACTAGGCTGCAC 57.336 45.455 0.50 0.00 0.00 4.57
708 762 2.541547 ATAGTGTGCGGCATGGCTGT 62.542 55.000 18.09 0.44 37.24 4.40
720 775 4.036734 CGGCATGGCTGTAGATTAACAATT 59.963 41.667 18.09 0.00 0.00 2.32
763 818 4.698575 AGAAAATCCGGAGAACTAGCATC 58.301 43.478 11.34 0.00 0.00 3.91
769 824 2.294791 CCGGAGAACTAGCATCTAGTGG 59.705 54.545 0.00 1.20 0.00 4.00
1033 1088 4.794648 CCGCGGAGGAAATGCCCA 62.795 66.667 24.07 0.00 45.00 5.36
1347 1402 6.699575 ATTAGCTTAGTTTATGGGCAAGTG 57.300 37.500 0.00 0.00 0.00 3.16
1496 1551 5.528690 CGGATTGTAGATCATTTGTCATGGT 59.471 40.000 0.00 0.00 0.00 3.55
1550 1605 4.794334 AGTCCGGAGTGTATCTGAATACT 58.206 43.478 12.08 0.00 38.87 2.12
1592 1647 1.614241 GGTATGCGTGGAGACCAGGT 61.614 60.000 11.21 0.00 40.97 4.00
2411 2475 5.120208 CGAGCTTGTTCTTTTTCTTATCCGA 59.880 40.000 0.00 0.00 0.00 4.55
2413 2477 5.998363 AGCTTGTTCTTTTTCTTATCCGACT 59.002 36.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.250305 AGTTGCTGCGGGTTCGGT 62.250 61.111 0.00 0.00 36.79 4.69
208 211 3.118223 TGGCAACATCACGGGACATATTA 60.118 43.478 0.00 0.00 46.17 0.98
243 246 3.537874 GTCCTGGCGCCCGACTAT 61.538 66.667 27.81 0.00 0.00 2.12
314 318 3.255888 AGCAGATAATCTATTCGCGTCCA 59.744 43.478 5.77 0.00 0.00 4.02
333 337 4.415881 TTCCACTTCTGAGTTTGTAGCA 57.584 40.909 0.00 0.00 32.54 3.49
577 582 4.210331 ACCTGCACAATAAAGATGATCCC 58.790 43.478 0.00 0.00 0.00 3.85
605 610 5.300539 CAGTGCAGCCTAGTATTCTTCTCTA 59.699 44.000 0.00 0.00 0.00 2.43
627 681 3.186613 GGAGACTTTTTCGGTTACTGCAG 59.813 47.826 13.48 13.48 0.00 4.41
633 687 1.345415 AGCGGGAGACTTTTTCGGTTA 59.655 47.619 0.00 0.00 0.00 2.85
708 762 9.176460 TCATCTGCAACATCAATTGTTAATCTA 57.824 29.630 5.13 0.00 46.90 1.98
720 775 2.093021 TCCGGATTCATCTGCAACATCA 60.093 45.455 0.00 0.00 31.76 3.07
757 812 0.399091 AGCTGCCCCACTAGATGCTA 60.399 55.000 0.00 0.00 0.00 3.49
763 818 1.753368 GCCTCTAGCTGCCCCACTAG 61.753 65.000 0.00 0.00 38.99 2.57
964 1019 3.050619 CGCTGTTAGTCGACTTCTTTGT 58.949 45.455 25.44 0.00 0.00 2.83
966 1021 3.366440 ACGCTGTTAGTCGACTTCTTT 57.634 42.857 25.44 0.61 0.00 2.52
1033 1088 0.616111 AGAAGATCACCCGCAGACCT 60.616 55.000 0.00 0.00 0.00 3.85
1190 1245 3.557054 GCAGGCCGATATCTTCCATAACA 60.557 47.826 0.00 0.00 0.00 2.41
1237 1292 1.537814 TACCGCGTCTTCACCATGGT 61.538 55.000 13.00 13.00 0.00 3.55
1347 1402 3.004419 GGGAATACTTTGCGGCTAATTCC 59.996 47.826 15.21 15.21 40.97 3.01
1496 1551 1.133915 AGGTTGAAGCGAAAAGGTCCA 60.134 47.619 0.00 0.00 0.00 4.02
1550 1605 6.585695 CCTAGTTCTTATATAACTGGGCGA 57.414 41.667 14.18 0.00 45.08 5.54
1592 1647 3.178046 TCAAGCACTAATGACCCCTACA 58.822 45.455 0.00 0.00 0.00 2.74
1659 1714 8.986929 AAACTATTCTCCCTGGAAGATATTTG 57.013 34.615 0.00 0.00 34.07 2.32
1663 1718 5.897824 ACGAAACTATTCTCCCTGGAAGATA 59.102 40.000 0.00 0.00 31.50 1.98
2083 2139 0.327480 ACTCATCATACCTGGGGGCA 60.327 55.000 0.00 0.00 35.63 5.36
2226 2290 2.235402 GACCTTATGTTCGTCCCCTTCA 59.765 50.000 0.00 0.00 0.00 3.02
2331 2395 0.968901 TTCTGACCGGTGGAGCGTAT 60.969 55.000 14.63 0.00 0.00 3.06
2411 2475 1.817447 GGTGAACTAGTCTACGCCAGT 59.183 52.381 16.84 0.00 33.73 4.00
2413 2477 1.913778 TGGTGAACTAGTCTACGCCA 58.086 50.000 19.09 19.09 39.98 5.69



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

AutoCloner maintained by Alex Coulton.