Multiple sequence alignment - TraesCS4D01G100900

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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 TraesCS4D01G100900 chr4D 100.000 2552 0 0 1 2552 78733368 78730817 0.000000e+00 4713
1 TraesCS4D01G100900 chr5D 94.807 1964 87 13 598 2552 44511941 44513898 0.000000e+00 3048
2 TraesCS4D01G100900 chr5D 95.470 596 21 5 6 599 281154379 281154970 0.000000e+00 946
3 TraesCS4D01G100900 chrUn 95.255 1918 78 11 643 2552 43407879 43409791 0.000000e+00 3025
4 TraesCS4D01G100900 chrUn 93.801 1968 101 12 600 2552 20573301 20575262 0.000000e+00 2939
5 TraesCS4D01G100900 chr3B 93.890 1964 104 11 597 2552 370213878 370215833 0.000000e+00 2948
6 TraesCS4D01G100900 chr3B 93.616 1958 114 10 600 2552 763485553 763483602 0.000000e+00 2913
7 TraesCS4D01G100900 chr3B 86.038 265 24 6 2294 2551 738131296 738131554 3.240000e-69 272
8 TraesCS4D01G100900 chr6D 93.435 1965 103 16 602 2552 12108135 12106183 0.000000e+00 2891
9 TraesCS4D01G100900 chr6D 92.734 1968 103 12 599 2552 312544303 312542362 0.000000e+00 2806
10 TraesCS4D01G100900 chr6D 95.134 596 26 3 6 599 124977578 124976984 0.000000e+00 937
11 TraesCS4D01G100900 chr6D 95.126 595 28 1 6 599 426946739 426947333 0.000000e+00 937
12 TraesCS4D01G100900 chr5A 93.137 1967 114 14 596 2552 650703526 650701571 0.000000e+00 2865
13 TraesCS4D01G100900 chr5A 92.608 1948 122 13 598 2536 702815062 702813128 0.000000e+00 2780
14 TraesCS4D01G100900 chr5A 95.126 595 27 2 6 599 21551772 21552365 0.000000e+00 937
15 TraesCS4D01G100900 chr5A 90.688 247 10 3 2319 2552 555203534 555203288 1.470000e-82 316
16 TraesCS4D01G100900 chr7B 93.731 1675 84 9 893 2551 702337578 702339247 0.000000e+00 2492
17 TraesCS4D01G100900 chr3D 96.233 584 20 2 18 599 318597299 318597882 0.000000e+00 955
18 TraesCS4D01G100900 chr2D 95.302 596 26 2 6 599 379981638 379981043 0.000000e+00 944
19 TraesCS4D01G100900 chr2D 95.142 597 27 2 5 599 37602525 37603121 0.000000e+00 941
20 TraesCS4D01G100900 chr2D 95.134 596 27 2 6 599 341931765 341932360 0.000000e+00 939
21 TraesCS4D01G100900 chr2D 95.712 583 23 2 18 599 599308145 599307564 0.000000e+00 937


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 TraesCS4D01G100900 chr4D 78730817 78733368 2551 True 4713 4713 100.000 1 2552 1 chr4D.!!$R1 2551
1 TraesCS4D01G100900 chr5D 44511941 44513898 1957 False 3048 3048 94.807 598 2552 1 chr5D.!!$F1 1954
2 TraesCS4D01G100900 chr5D 281154379 281154970 591 False 946 946 95.470 6 599 1 chr5D.!!$F2 593
3 TraesCS4D01G100900 chrUn 43407879 43409791 1912 False 3025 3025 95.255 643 2552 1 chrUn.!!$F2 1909
4 TraesCS4D01G100900 chrUn 20573301 20575262 1961 False 2939 2939 93.801 600 2552 1 chrUn.!!$F1 1952
5 TraesCS4D01G100900 chr3B 370213878 370215833 1955 False 2948 2948 93.890 597 2552 1 chr3B.!!$F1 1955
6 TraesCS4D01G100900 chr3B 763483602 763485553 1951 True 2913 2913 93.616 600 2552 1 chr3B.!!$R1 1952
7 TraesCS4D01G100900 chr6D 12106183 12108135 1952 True 2891 2891 93.435 602 2552 1 chr6D.!!$R1 1950
8 TraesCS4D01G100900 chr6D 312542362 312544303 1941 True 2806 2806 92.734 599 2552 1 chr6D.!!$R3 1953
9 TraesCS4D01G100900 chr6D 124976984 124977578 594 True 937 937 95.134 6 599 1 chr6D.!!$R2 593
10 TraesCS4D01G100900 chr6D 426946739 426947333 594 False 937 937 95.126 6 599 1 chr6D.!!$F1 593
11 TraesCS4D01G100900 chr5A 650701571 650703526 1955 True 2865 2865 93.137 596 2552 1 chr5A.!!$R2 1956
12 TraesCS4D01G100900 chr5A 702813128 702815062 1934 True 2780 2780 92.608 598 2536 1 chr5A.!!$R3 1938
13 TraesCS4D01G100900 chr5A 21551772 21552365 593 False 937 937 95.126 6 599 1 chr5A.!!$F1 593
14 TraesCS4D01G100900 chr7B 702337578 702339247 1669 False 2492 2492 93.731 893 2551 1 chr7B.!!$F1 1658
15 TraesCS4D01G100900 chr3D 318597299 318597882 583 False 955 955 96.233 18 599 1 chr3D.!!$F1 581
16 TraesCS4D01G100900 chr2D 379981043 379981638 595 True 944 944 95.302 6 599 1 chr2D.!!$R1 593
17 TraesCS4D01G100900 chr2D 37602525 37603121 596 False 941 941 95.142 5 599 1 chr2D.!!$F1 594
18 TraesCS4D01G100900 chr2D 341931765 341932360 595 False 939 939 95.134 6 599 1 chr2D.!!$F2 593
19 TraesCS4D01G100900 chr2D 599307564 599308145 581 True 937 937 95.712 18 599 1 chr2D.!!$R2 581

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
777 786 0.392461 GTACCAGGCGGCAAAGATGA 60.392 55.0 13.08 0.0 34.57 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2402 2486 0.178944 AACCTAAACCAAGGGCCACC 60.179 55.0 6.18 0.0 41.32 4.61 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
163 164 7.182026 TGAGTCTCCTTGAATATTTACTTGGGA 59.818 37.037 0.00 0.00 0.00 4.37
166 167 7.993183 GTCTCCTTGAATATTTACTTGGGATGA 59.007 37.037 0.00 0.00 0.00 2.92
220 221 1.407258 CCTCCTTCTCCTCACATCGAC 59.593 57.143 0.00 0.00 0.00 4.20
277 278 6.937436 AAACTCAACAGAAAGTTCGGTAAT 57.063 33.333 0.00 0.00 38.74 1.89
722 731 1.007271 CGTGAACTCTGCCGTGTCT 60.007 57.895 0.00 0.00 0.00 3.41
750 759 1.873591 CAACCTTTTGACTCGTCCCTG 59.126 52.381 0.00 0.00 34.24 4.45
759 768 1.908793 CTCGTCCCTGACAGGTGGT 60.909 63.158 20.24 0.00 31.93 4.16
771 780 4.338710 GGTGGTACCAGGCGGCAA 62.339 66.667 16.93 0.00 38.42 4.52
777 786 0.392461 GTACCAGGCGGCAAAGATGA 60.392 55.000 13.08 0.00 34.57 2.92
921 945 4.388499 GGCGGTGACCACGGTGAT 62.388 66.667 10.28 0.00 34.59 3.06
1021 1049 1.913262 TCTTCCTCAAGCTCCCGCA 60.913 57.895 0.00 0.00 39.10 5.69
1075 1103 3.786635 GACATGCCTGTCTTCGTCTATT 58.213 45.455 14.17 0.00 46.84 1.73
1088 1116 2.055633 TCTATTCGCGGTGCCAGGA 61.056 57.895 6.13 0.00 0.00 3.86
1136 1164 0.818296 CCGAGGAACCAGAATCGTCT 59.182 55.000 0.00 0.00 33.43 4.18
1215 1243 4.043310 TGGTCAGGATCTTTGAGAAATGGT 59.957 41.667 0.00 0.00 0.00 3.55
1321 1349 4.914983 AGAAGAGCATGAAGAATGGTTGA 58.085 39.130 0.00 0.00 46.95 3.18
1480 1508 3.442273 ACAAGTACCAATACCCATTTGCG 59.558 43.478 0.00 0.00 30.88 4.85
1493 1521 3.194542 CCCATTTGCGATTACTTTTGGGA 59.805 43.478 0.00 0.00 44.36 4.37
1516 1544 6.430000 GGAATTTGTAGGTATGGTAATCGCAT 59.570 38.462 0.00 0.00 0.00 4.73
1569 1597 5.987347 GGCATGAATTATGGAGGAATTTGTG 59.013 40.000 0.00 0.00 37.26 3.33
1616 1644 7.266922 TCACCTAGTTTAAATGTTGGTCAAC 57.733 36.000 6.87 6.87 41.50 3.18
1780 1820 2.241941 TCTATGGGCCAAATTCAGAGCA 59.758 45.455 11.89 0.00 0.00 4.26
2227 2280 0.537828 GGGTTTGTGGCGTTTAGGGA 60.538 55.000 0.00 0.00 0.00 4.20
2301 2354 6.282568 AGGAAGGTATACATAGTGAGACCT 57.717 41.667 5.01 0.00 38.98 3.85
2302 2355 7.403837 AGGAAGGTATACATAGTGAGACCTA 57.596 40.000 5.01 0.00 36.27 3.08
2402 2486 3.511146 ACTGCCACATGATTTTGGTTAGG 59.489 43.478 0.00 0.00 35.09 2.69
2408 2492 1.931635 TGATTTTGGTTAGGGTGGCC 58.068 50.000 0.00 0.00 0.00 5.36
2481 2591 5.375417 TTGCATGTTAGTTCATGACTTGG 57.625 39.130 10.28 0.00 45.41 3.61
2482 2592 4.397420 TGCATGTTAGTTCATGACTTGGT 58.603 39.130 10.28 0.00 45.41 3.67
2525 2639 1.368374 TCTCACCCCCTCCGATTTTT 58.632 50.000 0.00 0.00 0.00 1.94
2530 2644 5.043737 TCACCCCCTCCGATTTTTATTAG 57.956 43.478 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.413048 CGTGTGCTTTTTATTTCCCTTTTAATA 57.587 29.630 0.00 0.00 0.00 0.98
3 4 7.435784 GTCGTGTGCTTTTTATTTCCCTTTTAA 59.564 33.333 0.00 0.00 0.00 1.52
4 5 6.919115 GTCGTGTGCTTTTTATTTCCCTTTTA 59.081 34.615 0.00 0.00 0.00 1.52
5 6 5.751509 GTCGTGTGCTTTTTATTTCCCTTTT 59.248 36.000 0.00 0.00 0.00 2.27
6 7 5.286438 GTCGTGTGCTTTTTATTTCCCTTT 58.714 37.500 0.00 0.00 0.00 3.11
7 8 4.555906 CGTCGTGTGCTTTTTATTTCCCTT 60.556 41.667 0.00 0.00 0.00 3.95
9 10 3.231160 CGTCGTGTGCTTTTTATTTCCC 58.769 45.455 0.00 0.00 0.00 3.97
10 11 2.655001 GCGTCGTGTGCTTTTTATTTCC 59.345 45.455 0.00 0.00 0.00 3.13
11 12 3.551551 AGCGTCGTGTGCTTTTTATTTC 58.448 40.909 0.00 0.00 40.48 2.17
15 16 0.863144 GGAGCGTCGTGTGCTTTTTA 59.137 50.000 0.00 0.00 44.18 1.52
16 17 1.092921 TGGAGCGTCGTGTGCTTTTT 61.093 50.000 0.00 0.00 44.18 1.94
24 25 0.179215 GCAAATCTTGGAGCGTCGTG 60.179 55.000 0.00 0.00 0.00 4.35
26 27 0.179215 GTGCAAATCTTGGAGCGTCG 60.179 55.000 0.00 0.00 0.00 5.12
337 340 5.530915 ACAGTAGCTACAATGCAAAAACAGA 59.469 36.000 25.28 0.00 34.99 3.41
338 341 5.762045 ACAGTAGCTACAATGCAAAAACAG 58.238 37.500 25.28 0.00 34.99 3.16
612 621 0.251341 GGACACCACTGAGGGCAAAT 60.251 55.000 0.00 0.00 43.89 2.32
745 754 0.544357 CTGGTACCACCTGTCAGGGA 60.544 60.000 23.06 2.54 40.58 4.20
750 759 2.264794 CGCCTGGTACCACCTGTC 59.735 66.667 11.60 0.00 39.58 3.51
759 768 0.392461 GTCATCTTTGCCGCCTGGTA 60.392 55.000 0.00 0.00 37.67 3.25
771 780 6.051717 CGGTCTGAATAGAATTGGTCATCTT 58.948 40.000 0.00 0.00 34.01 2.40
777 786 3.689649 GCAACGGTCTGAATAGAATTGGT 59.310 43.478 0.00 0.00 34.01 3.67
918 936 2.844946 CCGTGCTCTCTCTCTCTATCA 58.155 52.381 0.00 0.00 0.00 2.15
921 945 0.812014 CGCCGTGCTCTCTCTCTCTA 60.812 60.000 0.00 0.00 0.00 2.43
1088 1116 2.032071 CCCTCCGAACAACGCCTT 59.968 61.111 0.00 0.00 41.07 4.35
1136 1164 0.663269 CTCGCTGCACACGTAGAACA 60.663 55.000 0.00 0.00 0.00 3.18
1215 1243 4.099113 TGCATGAACACCAAACAGATCAAA 59.901 37.500 0.00 0.00 0.00 2.69
1321 1349 1.447838 CCGTTCGTGGTAGCATGCT 60.448 57.895 25.99 25.99 0.00 3.79
1355 1383 1.484240 CCATCTCTTCTTCCGGAGCTT 59.516 52.381 3.34 0.00 0.00 3.74
1462 1490 4.911514 AATCGCAAATGGGTATTGGTAC 57.088 40.909 0.00 0.00 0.00 3.34
1493 1521 7.255451 CCAATGCGATTACCATACCTACAAATT 60.255 37.037 0.00 0.00 0.00 1.82
1516 1544 8.642432 TCCATACATTTTCAACATTACAACCAA 58.358 29.630 0.00 0.00 0.00 3.67
1569 1597 9.070149 GTGAATTTCTCATACAATTTCAAGCTC 57.930 33.333 0.00 0.00 36.14 4.09
1691 1729 9.973450 TTTCATTGATCAAAAGTTTCGGAATTA 57.027 25.926 13.09 0.00 0.00 1.40
1697 1735 7.107834 TGCATTTCATTGATCAAAAGTTTCG 57.892 32.000 13.09 0.30 0.00 3.46
1754 1794 3.631250 TGAATTTGGCCCATAGAGGAAC 58.369 45.455 0.00 0.00 41.22 3.62
1780 1820 4.972875 GCCTGCACTTGGCTCTAT 57.027 55.556 8.16 0.00 46.38 1.98
1881 1923 6.381481 TTCAGCATTATGATTTACTGCCTG 57.619 37.500 0.00 0.00 33.34 4.85
2301 2354 1.070242 CACGCGTGTGCAAACATTCTA 60.070 47.619 30.50 0.00 42.97 2.10
2302 2355 0.316937 CACGCGTGTGCAAACATTCT 60.317 50.000 30.50 0.00 42.97 2.40
2370 2431 3.090790 TCATGTGGCAGTGCAAACATAT 58.909 40.909 26.21 13.59 35.98 1.78
2402 2486 0.178944 AACCTAAACCAAGGGCCACC 60.179 55.000 6.18 0.00 41.32 4.61
2408 2492 3.244770 TGCCACTCTAACCTAAACCAAGG 60.245 47.826 0.00 0.00 42.82 3.61
2525 2639 7.211573 TCGAGAACTTGTGGTTTTCACTAATA 58.788 34.615 0.00 0.00 46.20 0.98
2530 2644 4.609691 TTCGAGAACTTGTGGTTTTCAC 57.390 40.909 0.00 0.00 46.23 3.18


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

AutoCloner maintained by Alex Coulton.