Multiple sequence alignment - TraesCS4A01G426500

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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 TraesCS4A01G426500 chr4A 100.000 2855 0 0 1 2855 698015267 698018121 0.000000e+00 5273
1 TraesCS4A01G426500 chr6A 95.822 1867 39 8 1 1831 387222897 387221034 0.000000e+00 2979
2 TraesCS4A01G426500 chr6A 95.298 1680 46 8 180 1831 74985211 74986885 0.000000e+00 2634
3 TraesCS4A01G426500 chr7A 95.771 1868 40 7 1 1831 509521764 509519899 0.000000e+00 2976
4 TraesCS4A01G426500 chr7A 92.733 1032 42 7 1854 2855 696574161 696575189 0.000000e+00 1459
5 TraesCS4A01G426500 chr5A 95.394 1867 47 7 1 1831 334531211 334529348 0.000000e+00 2935
6 TraesCS4A01G426500 chr5A 97.183 994 16 3 1 982 591480630 591479637 0.000000e+00 1670
7 TraesCS4A01G426500 chr2A 95.238 1869 49 7 1 1831 601808202 601810068 0.000000e+00 2922
8 TraesCS4A01G426500 chr7B 97.586 994 12 3 1 982 577218291 577217298 0.000000e+00 1692
9 TraesCS4A01G426500 chr7B 98.115 849 16 0 983 1831 516816214 516817062 0.000000e+00 1480
10 TraesCS4A01G426500 chr7B 97.762 849 19 0 983 1831 577217269 577216421 0.000000e+00 1463
11 TraesCS4A01G426500 chr7B 97.527 849 21 0 983 1831 720229300 720230148 0.000000e+00 1452
12 TraesCS4A01G426500 chr3B 97.581 992 13 3 1 982 179355962 179356952 0.000000e+00 1688
13 TraesCS4A01G426500 chr3B 97.527 849 21 0 983 1831 179356981 179357829 0.000000e+00 1452
14 TraesCS4A01G426500 chr3B 81.473 869 88 25 2004 2813 166532232 166531378 0.000000e+00 645
15 TraesCS4A01G426500 chr3B 95.266 338 11 2 1 333 803578717 803579054 5.420000e-147 531
16 TraesCS4A01G426500 chr3A 97.576 990 15 2 1 982 44767585 44768573 0.000000e+00 1687
17 TraesCS4A01G426500 chr3A 90.132 1064 54 20 1830 2855 12155263 12156313 0.000000e+00 1336
18 TraesCS4A01G426500 chr3A 85.714 546 44 11 2340 2851 709896353 709895808 1.930000e-151 545
19 TraesCS4A01G426500 chr3A 85.531 546 45 11 2340 2851 709924349 709923804 9.000000e-150 540
20 TraesCS4A01G426500 chr2D 93.251 1052 41 6 1831 2852 579972864 579973915 0.000000e+00 1522
21 TraesCS4A01G426500 chr2D 92.655 1062 41 7 1831 2855 298933165 298934226 0.000000e+00 1495
22 TraesCS4A01G426500 chr1B 98.704 849 11 0 983 1831 14538302 14539150 0.000000e+00 1507
23 TraesCS4A01G426500 chr1B 92.653 1048 44 8 1837 2852 50134650 50135696 0.000000e+00 1478
24 TraesCS4A01G426500 chr5B 98.587 849 12 0 983 1831 454666844 454665996 0.000000e+00 1502
25 TraesCS4A01G426500 chr5B 97.644 849 20 0 983 1831 351463698 351464546 0.000000e+00 1458
26 TraesCS4A01G426500 chr6B 98.233 849 15 0 983 1831 661057829 661056981 0.000000e+00 1485
27 TraesCS4A01G426500 chr2B 98.115 849 16 0 983 1831 154579485 154580333 0.000000e+00 1480
28 TraesCS4A01G426500 chr2B 90.048 1045 56 14 1837 2836 586771180 586772221 0.000000e+00 1310
29 TraesCS4A01G426500 chr6D 83.281 963 71 34 1948 2842 415964048 415964988 0.000000e+00 804
30 TraesCS4A01G426500 chr6D 89.727 623 32 6 1835 2426 443401087 443400466 0.000000e+00 767
31 TraesCS4A01G426500 chr6D 82.573 964 75 31 1948 2842 416942918 416943857 0.000000e+00 763
32 TraesCS4A01G426500 chr6D 81.744 986 75 47 1948 2851 278934351 278933389 0.000000e+00 726
33 TraesCS4A01G426500 chr6D 91.200 125 9 1 1832 1954 278934496 278934372 4.890000e-38 169
34 TraesCS4A01G426500 chr6D 91.667 120 8 1 1831 1948 415963902 415964021 6.330000e-37 165


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 TraesCS4A01G426500 chr4A 698015267 698018121 2854 False 5273.0 5273 100.000 1 2855 1 chr4A.!!$F1 2854
1 TraesCS4A01G426500 chr6A 387221034 387222897 1863 True 2979.0 2979 95.822 1 1831 1 chr6A.!!$R1 1830
2 TraesCS4A01G426500 chr6A 74985211 74986885 1674 False 2634.0 2634 95.298 180 1831 1 chr6A.!!$F1 1651
3 TraesCS4A01G426500 chr7A 509519899 509521764 1865 True 2976.0 2976 95.771 1 1831 1 chr7A.!!$R1 1830
4 TraesCS4A01G426500 chr7A 696574161 696575189 1028 False 1459.0 1459 92.733 1854 2855 1 chr7A.!!$F1 1001
5 TraesCS4A01G426500 chr5A 334529348 334531211 1863 True 2935.0 2935 95.394 1 1831 1 chr5A.!!$R1 1830
6 TraesCS4A01G426500 chr5A 591479637 591480630 993 True 1670.0 1670 97.183 1 982 1 chr5A.!!$R2 981
7 TraesCS4A01G426500 chr2A 601808202 601810068 1866 False 2922.0 2922 95.238 1 1831 1 chr2A.!!$F1 1830
8 TraesCS4A01G426500 chr7B 577216421 577218291 1870 True 1577.5 1692 97.674 1 1831 2 chr7B.!!$R1 1830
9 TraesCS4A01G426500 chr7B 516816214 516817062 848 False 1480.0 1480 98.115 983 1831 1 chr7B.!!$F1 848
10 TraesCS4A01G426500 chr7B 720229300 720230148 848 False 1452.0 1452 97.527 983 1831 1 chr7B.!!$F2 848
11 TraesCS4A01G426500 chr3B 179355962 179357829 1867 False 1570.0 1688 97.554 1 1831 2 chr3B.!!$F2 1830
12 TraesCS4A01G426500 chr3B 166531378 166532232 854 True 645.0 645 81.473 2004 2813 1 chr3B.!!$R1 809
13 TraesCS4A01G426500 chr3A 44767585 44768573 988 False 1687.0 1687 97.576 1 982 1 chr3A.!!$F2 981
14 TraesCS4A01G426500 chr3A 12155263 12156313 1050 False 1336.0 1336 90.132 1830 2855 1 chr3A.!!$F1 1025
15 TraesCS4A01G426500 chr3A 709895808 709896353 545 True 545.0 545 85.714 2340 2851 1 chr3A.!!$R1 511
16 TraesCS4A01G426500 chr3A 709923804 709924349 545 True 540.0 540 85.531 2340 2851 1 chr3A.!!$R2 511
17 TraesCS4A01G426500 chr2D 579972864 579973915 1051 False 1522.0 1522 93.251 1831 2852 1 chr2D.!!$F2 1021
18 TraesCS4A01G426500 chr2D 298933165 298934226 1061 False 1495.0 1495 92.655 1831 2855 1 chr2D.!!$F1 1024
19 TraesCS4A01G426500 chr1B 14538302 14539150 848 False 1507.0 1507 98.704 983 1831 1 chr1B.!!$F1 848
20 TraesCS4A01G426500 chr1B 50134650 50135696 1046 False 1478.0 1478 92.653 1837 2852 1 chr1B.!!$F2 1015
21 TraesCS4A01G426500 chr5B 454665996 454666844 848 True 1502.0 1502 98.587 983 1831 1 chr5B.!!$R1 848
22 TraesCS4A01G426500 chr5B 351463698 351464546 848 False 1458.0 1458 97.644 983 1831 1 chr5B.!!$F1 848
23 TraesCS4A01G426500 chr6B 661056981 661057829 848 True 1485.0 1485 98.233 983 1831 1 chr6B.!!$R1 848
24 TraesCS4A01G426500 chr2B 154579485 154580333 848 False 1480.0 1480 98.115 983 1831 1 chr2B.!!$F1 848
25 TraesCS4A01G426500 chr2B 586771180 586772221 1041 False 1310.0 1310 90.048 1837 2836 1 chr2B.!!$F2 999
26 TraesCS4A01G426500 chr6D 443400466 443401087 621 True 767.0 767 89.727 1835 2426 1 chr6D.!!$R1 591
27 TraesCS4A01G426500 chr6D 416942918 416943857 939 False 763.0 763 82.573 1948 2842 1 chr6D.!!$F1 894
28 TraesCS4A01G426500 chr6D 415963902 415964988 1086 False 484.5 804 87.474 1831 2842 2 chr6D.!!$F2 1011
29 TraesCS4A01G426500 chr6D 278933389 278934496 1107 True 447.5 726 86.472 1832 2851 2 chr6D.!!$R2 1019

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
920 935 0.041663 GTTGCAGTTTAAGCGACGCA 60.042 50.0 23.7 0.0 36.72 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1933 1978 1.737793 CCTATCTTGCGTGGGTGTTTC 59.262 52.381 0.0 0.0 0.0 2.78 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
161 172 7.775397 TTGATAGATGATGTGTGTATGTGTG 57.225 36.000 0.00 0.00 0.00 3.82
859 874 1.347221 CTTTGATTACGACCCGCGC 59.653 57.895 0.00 0.00 46.04 6.86
920 935 0.041663 GTTGCAGTTTAAGCGACGCA 60.042 50.000 23.70 0.00 36.72 5.24
994 1037 2.959707 GGAGACTCAACGATGACCCTAT 59.040 50.000 4.53 0.00 0.00 2.57
1213 1256 0.606944 GGGTGCCAATGACGTGGTTA 60.607 55.000 0.00 0.00 41.12 2.85
1457 1500 5.512753 TTGTTTGATTGCAGCTTGACTTA 57.487 34.783 0.00 0.00 0.00 2.24
1458 1501 5.710513 TGTTTGATTGCAGCTTGACTTAT 57.289 34.783 0.00 0.00 0.00 1.73
1872 1915 4.799564 TTAGCCATTGGGTTCATTTGTC 57.200 40.909 13.49 0.00 34.28 3.18
1933 1978 2.859165 ACAGGTGTATCCAGTGTTGG 57.141 50.000 0.00 0.00 46.49 3.77
2002 2110 1.239968 GCTGGTTGGAACTCAGGCTG 61.240 60.000 8.58 8.58 31.84 4.85
2193 2313 8.659925 ATGACTTCATAGCTTCAGATAAAGTG 57.340 34.615 0.00 0.00 34.26 3.16
2276 2424 8.336235 TCATTCTTGTCCTTATTGTTATCCCTT 58.664 33.333 0.00 0.00 0.00 3.95
2560 2749 5.489792 ACTGGACTTGATGTGTCTGTATT 57.510 39.130 0.00 0.00 35.04 1.89
2657 2848 7.182060 AGAATAAGCAATTAGAAAACCTGGGA 58.818 34.615 0.00 0.00 0.00 4.37
2845 3058 2.027285 TGGGAAGTCATTGAGCGATCAA 60.027 45.455 19.60 19.60 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
859 874 4.855715 TCTCCGAATGTAAGGCTCATAG 57.144 45.455 0.00 0.00 0.00 2.23
920 935 4.309950 GTGGTTCACCGGCGGAGT 62.310 66.667 35.78 8.46 39.43 3.85
994 1037 3.195610 CCGCTTATCATAGCCATGTCCTA 59.804 47.826 0.00 0.00 37.90 2.94
1457 1500 1.000019 TCCCTTCCTCCGACACGAT 60.000 57.895 0.00 0.00 0.00 3.73
1458 1501 1.677966 CTCCCTTCCTCCGACACGA 60.678 63.158 0.00 0.00 0.00 4.35
1659 1702 1.186200 TGCGAGCTTCCTGTGTAGAT 58.814 50.000 0.00 0.00 0.00 1.98
1872 1915 4.472691 TCAAATCTTCACAGCAAAGTCG 57.527 40.909 0.00 0.00 0.00 4.18
1933 1978 1.737793 CCTATCTTGCGTGGGTGTTTC 59.262 52.381 0.00 0.00 0.00 2.78
2193 2313 5.423015 TCAATGCTTACAGGAAGATGAGAC 58.577 41.667 0.00 0.00 37.33 3.36
2281 2429 7.786178 ACGATCTTTTGTTATTGCTGCTATA 57.214 32.000 0.00 0.00 0.00 1.31
2301 2449 7.220741 AGTATAGTGACAAGATGCATACGAT 57.779 36.000 0.00 0.00 0.00 3.73
2465 2628 6.036083 CGGCTGATCGAAAAATTCTAAGAAGA 59.964 38.462 0.00 0.00 0.00 2.87
2632 2823 7.182060 TCCCAGGTTTTCTAATTGCTTATTCT 58.818 34.615 0.00 0.00 0.00 2.40
2634 2825 7.790782 TTCCCAGGTTTTCTAATTGCTTATT 57.209 32.000 0.00 0.00 0.00 1.40
2667 2858 9.999660 TCTCTAGTCTCGTATGTCACTATAATT 57.000 33.333 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.