Multiple sequence alignment - TraesCS6D01G373500

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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 TraesCS6D01G373500 chr6D 100.000 2847 0 0 1 2847 458382225 458379379 0.000000e+00 5258.0
1 TraesCS6D01G373500 chr6D 97.382 573 14 1 2276 2847 439909513 439908941 0.000000e+00 974.0
2 TraesCS6D01G373500 chr6D 97.028 572 17 0 2276 2847 232753467 232754038 0.000000e+00 963.0
3 TraesCS6D01G373500 chr6B 95.270 1945 83 7 1 1938 696746795 696744853 0.000000e+00 3073.0
4 TraesCS6D01G373500 chr6B 86.270 823 105 4 1 822 696854604 696855419 0.000000e+00 887.0
5 TraesCS6D01G373500 chr6B 81.320 1076 179 16 877 1938 696852834 696851767 0.000000e+00 854.0
6 TraesCS6D01G373500 chr6A 91.977 1907 148 4 1 1905 605222344 605224247 0.000000e+00 2669.0
7 TraesCS6D01G373500 chr6A 81.939 825 122 19 66 869 605145533 605146351 0.000000e+00 673.0
8 TraesCS6D01G373500 chr5D 99.476 572 2 1 2276 2847 70413469 70412899 0.000000e+00 1038.0
9 TraesCS6D01G373500 chr5D 97.674 344 7 1 1929 2271 70413845 70413502 8.780000e-165 590.0
10 TraesCS6D01G373500 chr4D 99.126 572 5 0 2276 2847 440265499 440266070 0.000000e+00 1029.0
11 TraesCS6D01G373500 chr4D 98.427 572 8 1 2276 2847 484249640 484249070 0.000000e+00 1005.0
12 TraesCS6D01G373500 chr4D 99.399 333 1 1 1939 2271 484250004 484249673 1.130000e-168 603.0
13 TraesCS6D01G373500 chr4D 97.941 340 1 3 1932 2271 440265133 440265466 4.090000e-163 584.0
14 TraesCS6D01G373500 chr7D 98.252 572 9 1 2276 2847 66442086 66442656 0.000000e+00 1000.0
15 TraesCS6D01G373500 chr7D 97.028 572 17 0 2276 2847 105879402 105878831 0.000000e+00 963.0
16 TraesCS6D01G373500 chr7D 95.882 340 2 5 1939 2272 66441721 66442054 8.970000e-150 540.0
17 TraesCS6D01G373500 chr7B 97.203 572 16 0 2276 2847 71588767 71588196 0.000000e+00 968.0
18 TraesCS6D01G373500 chr3A 97.028 572 17 0 2276 2847 14798744 14799315 0.000000e+00 963.0
19 TraesCS6D01G373500 chr3A 97.297 333 7 1 1939 2271 24719452 24719122 5.320000e-157 564.0
20 TraesCS6D01G373500 chr3A 97.232 289 7 1 1939 2227 648599454 648599741 3.300000e-134 488.0
21 TraesCS6D01G373500 chr3A 91.304 46 2 2 1931 1975 730427186 730427142 8.520000e-06 62.1
22 TraesCS6D01G373500 chr3D 86.421 869 72 26 1970 2815 101290793 101291638 0.000000e+00 909.0
23 TraesCS6D01G373500 chr7A 93.798 258 14 2 1970 2227 724074437 724074182 1.240000e-103 387.0
24 TraesCS6D01G373500 chr7A 93.023 258 16 2 1970 2227 724046018 724045763 2.680000e-100 375.0
25 TraesCS6D01G373500 chr7A 95.122 41 2 0 1931 1971 629017752 629017792 6.580000e-07 65.8
26 TraesCS6D01G373500 chr2B 100.000 34 0 0 1936 1969 534667936 534667969 2.370000e-06 63.9


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 TraesCS6D01G373500 chr6D 458379379 458382225 2846 True 5258.0 5258 100.0000 1 2847 1 chr6D.!!$R2 2846
1 TraesCS6D01G373500 chr6D 439908941 439909513 572 True 974.0 974 97.3820 2276 2847 1 chr6D.!!$R1 571
2 TraesCS6D01G373500 chr6D 232753467 232754038 571 False 963.0 963 97.0280 2276 2847 1 chr6D.!!$F1 571
3 TraesCS6D01G373500 chr6B 696744853 696746795 1942 True 3073.0 3073 95.2700 1 1938 1 chr6B.!!$R1 1937
4 TraesCS6D01G373500 chr6B 696854604 696855419 815 False 887.0 887 86.2700 1 822 1 chr6B.!!$F1 821
5 TraesCS6D01G373500 chr6B 696851767 696852834 1067 True 854.0 854 81.3200 877 1938 1 chr6B.!!$R2 1061
6 TraesCS6D01G373500 chr6A 605222344 605224247 1903 False 2669.0 2669 91.9770 1 1905 1 chr6A.!!$F2 1904
7 TraesCS6D01G373500 chr6A 605145533 605146351 818 False 673.0 673 81.9390 66 869 1 chr6A.!!$F1 803
8 TraesCS6D01G373500 chr5D 70412899 70413845 946 True 814.0 1038 98.5750 1929 2847 2 chr5D.!!$R1 918
9 TraesCS6D01G373500 chr4D 440265133 440266070 937 False 806.5 1029 98.5335 1932 2847 2 chr4D.!!$F1 915
10 TraesCS6D01G373500 chr4D 484249070 484250004 934 True 804.0 1005 98.9130 1939 2847 2 chr4D.!!$R1 908
11 TraesCS6D01G373500 chr7D 105878831 105879402 571 True 963.0 963 97.0280 2276 2847 1 chr7D.!!$R1 571
12 TraesCS6D01G373500 chr7D 66441721 66442656 935 False 770.0 1000 97.0670 1939 2847 2 chr7D.!!$F1 908
13 TraesCS6D01G373500 chr7B 71588196 71588767 571 True 968.0 968 97.2030 2276 2847 1 chr7B.!!$R1 571
14 TraesCS6D01G373500 chr3A 14798744 14799315 571 False 963.0 963 97.0280 2276 2847 1 chr3A.!!$F1 571
15 TraesCS6D01G373500 chr3D 101290793 101291638 845 False 909.0 909 86.4210 1970 2815 1 chr3D.!!$F1 845

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
685 707 0.537371 AGTTGCCTTGACCTTTCCCG 60.537 55.0 0.00 0.00 0.00 5.14 F
1489 1517 1.604604 TGCCAACAGCTGTTTACCTC 58.395 50.0 29.23 15.77 44.23 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 1712 1.018226 CGAGTTGCAAGCTCTCCAGG 61.018 60.000 19.77 6.85 0.00 4.45 R
2621 2702 3.830178 AGTTGCCCCAAAACTGGTAATAC 59.170 43.478 0.00 0.00 36.52 1.89 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
29 30 3.227614 GGTTTACTCAGAAAAAGGGGCA 58.772 45.455 0.00 0.00 0.00 5.36
85 86 9.549509 TCGTAAATGTTGTTTACAATTATCTGC 57.450 29.630 10.26 0.00 40.89 4.26
100 101 7.120579 ACAATTATCTGCAAGTTCGAACCATAA 59.879 33.333 24.22 15.61 33.76 1.90
107 108 5.182190 TGCAAGTTCGAACCATAAATTAGCA 59.818 36.000 24.22 17.39 0.00 3.49
347 357 1.016627 TAAGCGATGCTGCAATGACC 58.983 50.000 6.36 0.00 39.62 4.02
360 370 2.872038 GCAATGACCGACTGTCTTTCCT 60.872 50.000 6.21 0.00 44.75 3.36
444 454 3.049708 TGCCAGAGTCAGAAATCTGTG 57.950 47.619 10.06 1.74 44.12 3.66
535 545 4.581077 TGCGCAATCATTATGGCAATAA 57.419 36.364 8.16 0.00 30.64 1.40
653 663 2.941720 GCTCTGCCTTGACCTTTATGAG 59.058 50.000 0.00 0.00 0.00 2.90
685 707 0.537371 AGTTGCCTTGACCTTTCCCG 60.537 55.000 0.00 0.00 0.00 5.14
837 859 2.028876 TCCTTGAACTCAGTCGTGTGA 58.971 47.619 0.00 0.00 0.00 3.58
934 956 4.505191 CCATCAATTGATTCATTTGACGGC 59.495 41.667 18.41 0.00 36.84 5.68
965 987 4.022935 TCACAATTGCTGAAGTTGGATGTC 60.023 41.667 5.05 0.00 0.00 3.06
968 990 1.795768 TGCTGAAGTTGGATGTCGAC 58.204 50.000 9.11 9.11 0.00 4.20
1010 1032 6.389830 AGTGTTTGTATTCATGCTGACAAA 57.610 33.333 12.17 12.17 38.97 2.83
1323 1349 5.175673 GCACACTTTCAGGTTTGCTAATTTC 59.824 40.000 0.00 0.00 39.10 2.17
1401 1427 3.181475 CGTATCTCCTTAAAGCAGCTCCA 60.181 47.826 0.00 0.00 0.00 3.86
1454 1480 3.247411 TGTGCACTTGTGATTTCTACACG 59.753 43.478 19.41 0.00 40.61 4.49
1489 1517 1.604604 TGCCAACAGCTGTTTACCTC 58.395 50.000 29.23 15.77 44.23 3.85
1568 1596 2.440539 ACAACCTAGTGAGCTCAACG 57.559 50.000 20.19 9.51 0.00 4.10
1727 1764 1.762419 GCGTGCATATGAGCCATTTG 58.238 50.000 6.97 0.00 0.00 2.32
1783 1820 0.671472 AAAGGTGCCGTTACGCTACC 60.671 55.000 16.85 16.85 33.03 3.18
1819 1856 1.265454 ACCTGGCTCCTAAGGTTCCG 61.265 60.000 0.00 0.00 44.63 4.30
1869 1906 0.586319 TTCCGTGCTCGCTGAAAAAG 59.414 50.000 1.89 0.00 35.54 2.27
1927 1968 2.440539 ACTACCTTGAGCTTGTCACG 57.559 50.000 0.00 0.00 33.71 4.35
2303 2380 4.097135 TGTGTGGCAATATAAAATGTCCGG 59.903 41.667 0.00 0.00 0.00 5.14
2528 2609 6.959639 TTGAGTTGAAAGGCTCAAACTAAT 57.040 33.333 8.79 0.00 45.67 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 6.747280 CCTTGCTAATTTATGGTTCGAACTTG 59.253 38.462 26.32 8.16 0.00 3.16
347 357 3.948473 TCCATCTAGAGGAAAGACAGTCG 59.052 47.826 5.84 0.00 30.71 4.18
360 370 2.853077 TCCAGAGGTGTCTCCATCTAGA 59.147 50.000 0.00 0.00 40.83 2.43
444 454 5.807011 GCAGACATGGTTTTTGATGGTAATC 59.193 40.000 0.00 0.00 0.00 1.75
535 545 7.094032 GGAATCTGACAGTGAATTCCTTGATTT 60.094 37.037 19.91 1.04 35.81 2.17
653 663 2.534231 GGCAACTTGAGCGATTCTTC 57.466 50.000 0.00 0.00 0.00 2.87
934 956 6.064846 ACTTCAGCAATTGTGAACAAGTAG 57.935 37.500 15.17 9.70 39.47 2.57
965 987 1.640428 TTAAGCCATCGCAGAAGTCG 58.360 50.000 0.00 0.00 43.58 4.18
968 990 4.572389 ACACTAATTAAGCCATCGCAGAAG 59.428 41.667 0.00 0.00 43.58 2.85
1010 1032 2.151202 CCTTGTACATGAACGCCAAGT 58.849 47.619 10.20 0.00 32.56 3.16
1146 1170 3.188460 GCAAGATCAACGTTTCCAGCTTA 59.812 43.478 0.00 0.00 0.00 3.09
1323 1349 5.063186 CACCAGAAAGAAGACGATCATCTTG 59.937 44.000 9.10 0.00 39.08 3.02
1489 1517 6.317140 TGGCTAACATGAGAAAAAGCATAGAG 59.683 38.462 0.00 0.00 0.00 2.43
1568 1596 1.227674 GATCCTCGGGCCATGTCAC 60.228 63.158 4.39 0.00 0.00 3.67
1684 1712 1.018226 CGAGTTGCAAGCTCTCCAGG 61.018 60.000 19.77 6.85 0.00 4.45
1727 1764 2.037772 TGTGCTTCTCCTTCCTGAAGAC 59.962 50.000 8.46 0.00 41.38 3.01
1819 1856 3.041940 CTGAACGCCACGGTGGAC 61.042 66.667 30.65 19.34 40.96 4.02
1922 1963 6.906143 GTCTACTAGTCATCATAACACGTGAC 59.094 42.308 25.01 7.13 40.87 3.67
1927 1968 6.210078 GGCAGTCTACTAGTCATCATAACAC 58.790 44.000 0.00 0.00 0.00 3.32
2528 2609 5.736951 ACCTTGCAAATATTTGTTGGCTA 57.263 34.783 25.15 10.15 40.24 3.93
2621 2702 3.830178 AGTTGCCCCAAAACTGGTAATAC 59.170 43.478 0.00 0.00 36.52 1.89


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

AutoCloner maintained by Alex Coulton.