Multiple sequence alignment - TraesCS2B01G592300

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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 TraesCS2B01G592300 chr2B 100.000 2637 0 0 1 2637 777365704 777368340 0.000000e+00 4870.0
1 TraesCS2B01G592300 chr2B 91.142 1953 118 25 1 1940 456032068 456033978 0.000000e+00 2597.0
2 TraesCS2B01G592300 chr2B 87.817 1970 204 24 1 1947 479890337 479888381 0.000000e+00 2276.0
3 TraesCS2B01G592300 chr2B 97.568 699 16 1 1940 2637 381488865 381488167 0.000000e+00 1195.0
4 TraesCS2B01G592300 chr2B 84.188 917 103 14 1051 1947 783932662 783931768 0.000000e+00 852.0
5 TraesCS2B01G592300 chr2B 87.561 410 37 10 1540 1942 612692317 612691915 1.850000e-126 462.0
6 TraesCS2B01G592300 chr4A 90.951 1956 139 12 1 1940 743366078 743364145 0.000000e+00 2597.0
7 TraesCS2B01G592300 chr4A 96.270 697 14 2 1941 2637 706855188 706855872 0.000000e+00 1133.0
8 TraesCS2B01G592300 chr4A 85.043 575 74 10 2072 2637 548877676 548877105 2.280000e-160 575.0
9 TraesCS2B01G592300 chr4A 81.194 670 112 12 1977 2637 575059247 575059911 6.460000e-146 527.0
10 TraesCS2B01G592300 chr6B 90.321 1963 154 18 1 1938 313315423 313313472 0.000000e+00 2540.0
11 TraesCS2B01G592300 chr6B 85.536 1203 117 25 1 1168 577462180 577463360 0.000000e+00 1205.0
12 TraesCS2B01G592300 chr3D 89.532 1987 135 30 1 1939 81833008 81834969 0.000000e+00 2449.0
13 TraesCS2B01G592300 chr3D 88.373 2004 134 42 1 1947 41618894 41616933 0.000000e+00 2318.0
14 TraesCS2B01G592300 chr3D 92.294 1142 59 6 820 1942 6288084 6289215 0.000000e+00 1594.0
15 TraesCS2B01G592300 chr3D 89.599 1096 79 10 881 1947 45633424 45632335 0.000000e+00 1360.0
16 TraesCS2B01G592300 chr5B 92.234 1674 119 7 269 1940 616369692 616371356 0.000000e+00 2361.0
17 TraesCS2B01G592300 chr5B 87.965 1961 188 25 1 1942 507200435 507202366 0.000000e+00 2270.0
18 TraesCS2B01G592300 chr5B 86.191 1977 199 28 1 1942 477756063 477758000 0.000000e+00 2071.0
19 TraesCS2B01G592300 chr5B 86.617 665 76 11 1983 2637 56847985 56847324 0.000000e+00 723.0
20 TraesCS2B01G592300 chr5B 86.486 666 75 12 1983 2637 56835149 56834488 0.000000e+00 717.0
21 TraesCS2B01G592300 chr5B 95.652 46 2 0 1941 1986 56837232 56837187 1.010000e-09 75.0
22 TraesCS2B01G592300 chr6D 87.905 1976 174 23 1 1942 305745007 305746951 0.000000e+00 2265.0
23 TraesCS2B01G592300 chr6D 90.031 1635 126 14 313 1940 446604659 446603055 0.000000e+00 2082.0
24 TraesCS2B01G592300 chr3B 88.964 1785 145 24 179 1942 804610169 804611922 0.000000e+00 2158.0
25 TraesCS2B01G592300 chr3B 94.118 51 3 0 1941 1991 588699243 588699193 7.830000e-11 78.7
26 TraesCS2B01G592300 chr1D 87.658 1823 154 29 147 1940 369900349 369902129 0.000000e+00 2054.0
27 TraesCS2B01G592300 chr2D 86.114 1966 195 39 1 1942 647091509 647089598 0.000000e+00 2047.0
28 TraesCS2B01G592300 chr2D 92.879 1306 77 5 644 1942 469162165 469163461 0.000000e+00 1882.0
29 TraesCS2B01G592300 chr4B 91.674 1069 62 9 874 1940 541446474 541447517 0.000000e+00 1456.0
30 TraesCS2B01G592300 chr4B 88.876 836 78 6 1 824 541445642 541446474 0.000000e+00 1014.0
31 TraesCS2B01G592300 chr4B 85.206 703 91 9 1941 2637 68421837 68422532 0.000000e+00 710.0
32 TraesCS2B01G592300 chr4B 81.413 651 109 10 1977 2617 671691986 671692634 3.010000e-144 521.0
33 TraesCS2B01G592300 chr7B 90.751 1038 71 9 1 1016 602018513 602017479 0.000000e+00 1362.0
34 TraesCS2B01G592300 chr7B 92.908 282 18 1 1661 1940 729609599 729609318 2.440000e-110 409.0
35 TraesCS2B01G592300 chr4D 85.258 1221 114 27 3 1186 442390242 442391433 0.000000e+00 1197.0
36 TraesCS2B01G592300 chr4D 83.234 668 67 23 1942 2596 122282326 122282961 2.940000e-159 571.0
37 TraesCS2B01G592300 chr6A 92.857 700 47 2 1941 2637 2044035 2043336 0.000000e+00 1013.0
38 TraesCS2B01G592300 chr6A 86.036 666 78 13 1983 2637 10461560 10460899 0.000000e+00 701.0
39 TraesCS2B01G592300 chr3A 92.319 703 47 5 1940 2637 641334046 641333346 0.000000e+00 992.0
40 TraesCS2B01G592300 chr3A 91.737 714 51 6 1929 2637 641794694 641795404 0.000000e+00 985.0
41 TraesCS2B01G592300 chr7A 91.441 701 53 5 1942 2637 602025419 602026117 0.000000e+00 955.0
42 TraesCS2B01G592300 chr7A 93.671 632 37 2 2009 2637 679854642 679855273 0.000000e+00 942.0
43 TraesCS2B01G592300 chr5A 93.987 632 35 2 2009 2637 325836876 325837507 0.000000e+00 953.0
44 TraesCS2B01G592300 chr5D 86.043 695 83 9 1941 2629 436796058 436795372 0.000000e+00 734.0
45 TraesCS2B01G592300 chr5D 81.818 671 109 11 1977 2637 531480084 531480751 3.840000e-153 551.0
46 TraesCS2B01G592300 chr5D 81.231 666 110 13 1983 2637 354481159 354480498 8.360000e-145 523.0
47 TraesCS2B01G592300 chr5D 83.733 375 50 8 2266 2637 433504815 433505181 6.990000e-91 344.0
48 TraesCS2B01G592300 chr1A 81.504 665 110 11 1983 2637 590753382 590752721 3.860000e-148 534.0
49 TraesCS2B01G592300 chr1A 86.567 201 25 2 2435 2634 33084248 33084447 1.230000e-53 220.0
50 TraesCS2B01G592300 chr1A 94.444 36 2 0 1951 1986 33074387 33074422 3.670000e-04 56.5
51 TraesCS2B01G592300 chr1B 92.880 309 21 1 1634 1942 684578734 684579041 5.180000e-122 448.0
52 TraesCS2B01G592300 chr7D 94.118 51 2 1 1941 1991 626623621 626623670 2.810000e-10 76.8


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 TraesCS2B01G592300 chr2B 777365704 777368340 2636 False 4870 4870 100.000 1 2637 1 chr2B.!!$F2 2636
1 TraesCS2B01G592300 chr2B 456032068 456033978 1910 False 2597 2597 91.142 1 1940 1 chr2B.!!$F1 1939
2 TraesCS2B01G592300 chr2B 479888381 479890337 1956 True 2276 2276 87.817 1 1947 1 chr2B.!!$R2 1946
3 TraesCS2B01G592300 chr2B 381488167 381488865 698 True 1195 1195 97.568 1940 2637 1 chr2B.!!$R1 697
4 TraesCS2B01G592300 chr2B 783931768 783932662 894 True 852 852 84.188 1051 1947 1 chr2B.!!$R4 896
5 TraesCS2B01G592300 chr4A 743364145 743366078 1933 True 2597 2597 90.951 1 1940 1 chr4A.!!$R2 1939
6 TraesCS2B01G592300 chr4A 706855188 706855872 684 False 1133 1133 96.270 1941 2637 1 chr4A.!!$F2 696
7 TraesCS2B01G592300 chr4A 548877105 548877676 571 True 575 575 85.043 2072 2637 1 chr4A.!!$R1 565
8 TraesCS2B01G592300 chr4A 575059247 575059911 664 False 527 527 81.194 1977 2637 1 chr4A.!!$F1 660
9 TraesCS2B01G592300 chr6B 313313472 313315423 1951 True 2540 2540 90.321 1 1938 1 chr6B.!!$R1 1937
10 TraesCS2B01G592300 chr6B 577462180 577463360 1180 False 1205 1205 85.536 1 1168 1 chr6B.!!$F1 1167
11 TraesCS2B01G592300 chr3D 81833008 81834969 1961 False 2449 2449 89.532 1 1939 1 chr3D.!!$F2 1938
12 TraesCS2B01G592300 chr3D 41616933 41618894 1961 True 2318 2318 88.373 1 1947 1 chr3D.!!$R1 1946
13 TraesCS2B01G592300 chr3D 6288084 6289215 1131 False 1594 1594 92.294 820 1942 1 chr3D.!!$F1 1122
14 TraesCS2B01G592300 chr3D 45632335 45633424 1089 True 1360 1360 89.599 881 1947 1 chr3D.!!$R2 1066
15 TraesCS2B01G592300 chr5B 616369692 616371356 1664 False 2361 2361 92.234 269 1940 1 chr5B.!!$F3 1671
16 TraesCS2B01G592300 chr5B 507200435 507202366 1931 False 2270 2270 87.965 1 1942 1 chr5B.!!$F2 1941
17 TraesCS2B01G592300 chr5B 477756063 477758000 1937 False 2071 2071 86.191 1 1942 1 chr5B.!!$F1 1941
18 TraesCS2B01G592300 chr5B 56847324 56847985 661 True 723 723 86.617 1983 2637 1 chr5B.!!$R1 654
19 TraesCS2B01G592300 chr5B 56834488 56837232 2744 True 396 717 91.069 1941 2637 2 chr5B.!!$R2 696
20 TraesCS2B01G592300 chr6D 305745007 305746951 1944 False 2265 2265 87.905 1 1942 1 chr6D.!!$F1 1941
21 TraesCS2B01G592300 chr6D 446603055 446604659 1604 True 2082 2082 90.031 313 1940 1 chr6D.!!$R1 1627
22 TraesCS2B01G592300 chr3B 804610169 804611922 1753 False 2158 2158 88.964 179 1942 1 chr3B.!!$F1 1763
23 TraesCS2B01G592300 chr1D 369900349 369902129 1780 False 2054 2054 87.658 147 1940 1 chr1D.!!$F1 1793
24 TraesCS2B01G592300 chr2D 647089598 647091509 1911 True 2047 2047 86.114 1 1942 1 chr2D.!!$R1 1941
25 TraesCS2B01G592300 chr2D 469162165 469163461 1296 False 1882 1882 92.879 644 1942 1 chr2D.!!$F1 1298
26 TraesCS2B01G592300 chr4B 541445642 541447517 1875 False 1235 1456 90.275 1 1940 2 chr4B.!!$F3 1939
27 TraesCS2B01G592300 chr4B 68421837 68422532 695 False 710 710 85.206 1941 2637 1 chr4B.!!$F1 696
28 TraesCS2B01G592300 chr4B 671691986 671692634 648 False 521 521 81.413 1977 2617 1 chr4B.!!$F2 640
29 TraesCS2B01G592300 chr7B 602017479 602018513 1034 True 1362 1362 90.751 1 1016 1 chr7B.!!$R1 1015
30 TraesCS2B01G592300 chr4D 442390242 442391433 1191 False 1197 1197 85.258 3 1186 1 chr4D.!!$F2 1183
31 TraesCS2B01G592300 chr4D 122282326 122282961 635 False 571 571 83.234 1942 2596 1 chr4D.!!$F1 654
32 TraesCS2B01G592300 chr6A 2043336 2044035 699 True 1013 1013 92.857 1941 2637 1 chr6A.!!$R1 696
33 TraesCS2B01G592300 chr6A 10460899 10461560 661 True 701 701 86.036 1983 2637 1 chr6A.!!$R2 654
34 TraesCS2B01G592300 chr3A 641333346 641334046 700 True 992 992 92.319 1940 2637 1 chr3A.!!$R1 697
35 TraesCS2B01G592300 chr3A 641794694 641795404 710 False 985 985 91.737 1929 2637 1 chr3A.!!$F1 708
36 TraesCS2B01G592300 chr7A 602025419 602026117 698 False 955 955 91.441 1942 2637 1 chr7A.!!$F1 695
37 TraesCS2B01G592300 chr7A 679854642 679855273 631 False 942 942 93.671 2009 2637 1 chr7A.!!$F2 628
38 TraesCS2B01G592300 chr5A 325836876 325837507 631 False 953 953 93.987 2009 2637 1 chr5A.!!$F1 628
39 TraesCS2B01G592300 chr5D 436795372 436796058 686 True 734 734 86.043 1941 2629 1 chr5D.!!$R2 688
40 TraesCS2B01G592300 chr5D 531480084 531480751 667 False 551 551 81.818 1977 2637 1 chr5D.!!$F2 660
41 TraesCS2B01G592300 chr5D 354480498 354481159 661 True 523 523 81.231 1983 2637 1 chr5D.!!$R1 654
42 TraesCS2B01G592300 chr1A 590752721 590753382 661 True 534 534 81.504 1983 2637 1 chr1A.!!$R1 654

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
164 209 0.030369 GTAGATTCGATCCACGGCGT 59.970 55.0 6.77 6.77 42.82 5.68 F
517 694 0.104725 CTCCTCCTTAGGCTCCCCAT 60.105 60.0 0.00 0.00 43.31 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1290 1520 0.034059 CCTTGCAGAAGTGAGTCGGT 59.966 55.0 0.0 0.0 0.0 4.69 R
1793 2053 0.466543 TACCAACACACTTCGGCACT 59.533 50.0 0.0 0.0 0.0 4.40 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
110 151 3.983044 ATGGCGGTAAGAACTTCTCTT 57.017 42.857 0.00 0.00 46.52 2.85
123 168 6.210078 AGAACTTCTCTTTTCGTCACACTAG 58.790 40.000 0.00 0.00 0.00 2.57
142 187 0.435769 GTTTTTCGCGTTCGATCCGA 59.564 50.000 5.77 6.17 45.04 4.55
164 209 0.030369 GTAGATTCGATCCACGGCGT 59.970 55.000 6.77 6.77 42.82 5.68
199 244 5.721960 GGGGAATAGAGGTAGATAAGCATGA 59.278 44.000 0.00 0.00 0.00 3.07
205 250 8.941995 ATAGAGGTAGATAAGCATGACAGTTA 57.058 34.615 0.00 0.00 0.00 2.24
306 420 0.426022 AGTAGAAGGGGGATTGGGGT 59.574 55.000 0.00 0.00 0.00 4.95
307 421 0.551396 GTAGAAGGGGGATTGGGGTG 59.449 60.000 0.00 0.00 0.00 4.61
370 515 2.613977 CGACTGGCTGTCCTTCATCTTT 60.614 50.000 17.42 0.00 42.49 2.52
445 601 0.454600 GTCGATCTGCCAGGTACGAA 59.545 55.000 9.41 0.00 0.00 3.85
489 660 0.687354 ACATCTGCACCGGTTCTTCT 59.313 50.000 2.97 0.00 0.00 2.85
490 661 1.072331 ACATCTGCACCGGTTCTTCTT 59.928 47.619 2.97 0.00 0.00 2.52
491 662 1.734465 CATCTGCACCGGTTCTTCTTC 59.266 52.381 2.97 0.00 0.00 2.87
517 694 0.104725 CTCCTCCTTAGGCTCCCCAT 60.105 60.000 0.00 0.00 43.31 4.00
566 752 1.051556 TCCCAGTACACTGTGGCACA 61.052 55.000 20.76 20.76 42.27 4.57
609 795 5.031066 AGTTCTTGTACTTGCACCACTTA 57.969 39.130 0.00 0.00 0.00 2.24
627 813 5.869888 CCACTTATTTCTCTGTTTAGCGTCT 59.130 40.000 0.00 0.00 0.00 4.18
708 894 3.771577 AGGTCAGGAATCAACGTCTTT 57.228 42.857 0.00 0.00 0.00 2.52
729 917 1.981495 AGCTCTTCTGTAGTGGCCTTT 59.019 47.619 3.32 0.00 0.00 3.11
851 1040 1.403687 CCTAGGAAGAAGGCCCTCCG 61.404 65.000 1.05 0.00 37.47 4.63
1089 1287 2.816087 ACTCCATGAATTGTGTGCAGAC 59.184 45.455 7.12 7.12 0.00 3.51
1357 1588 2.124570 CCATGCCCCTGGACTTCG 60.125 66.667 0.00 0.00 38.69 3.79
1381 1612 4.657824 ACTTCGTCGTGGTGCCGG 62.658 66.667 0.00 0.00 0.00 6.13
1441 1680 1.134580 AGGTGACGATGAAGCTGATGG 60.135 52.381 0.00 0.00 0.00 3.51
1520 1759 0.102481 ATCGGCTACATGGTGACGTC 59.898 55.000 9.11 9.11 0.00 4.34
1850 2112 2.770164 AGAGGTTACCACACATCAGC 57.230 50.000 3.51 0.00 29.53 4.26
1860 2122 1.672363 CACACATCAGCCGTTGCATAT 59.328 47.619 0.00 0.00 41.13 1.78
1880 2142 1.786937 AACCAAACACCATGCCTTGA 58.213 45.000 0.00 0.00 0.00 3.02
1881 2143 1.786937 ACCAAACACCATGCCTTGAA 58.213 45.000 0.00 0.00 0.00 2.69
2322 4643 6.151985 ACCGTTCCAGTCATTAATTGCAAATA 59.848 34.615 1.71 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 151 3.301963 CGCGAAAAACTAGTGTGACGAAA 60.302 43.478 0.00 0.00 0.00 3.46
142 187 1.067212 GCCGTGGATCGAATCTACTGT 59.933 52.381 0.00 0.00 42.86 3.55
164 209 3.181395 CCTCTATTCCCCATTCCCCTCTA 60.181 52.174 0.00 0.00 0.00 2.43
359 504 4.093408 CGCGATGAAGAAAAAGATGAAGGA 59.907 41.667 0.00 0.00 0.00 3.36
370 515 2.387445 CCCGCACGCGATGAAGAAA 61.387 57.895 15.93 0.00 42.83 2.52
566 752 0.541863 CTGGGCTCCTAATGACCGTT 59.458 55.000 0.00 0.00 0.00 4.44
609 795 3.927142 CCGAAGACGCTAAACAGAGAAAT 59.073 43.478 0.00 0.00 38.29 2.17
627 813 2.920912 AACCAGGCCGTCTCCGAA 60.921 61.111 0.00 0.00 35.63 4.30
642 828 1.173043 TCATTCGTTGGGCCATGAAC 58.827 50.000 20.09 9.93 0.00 3.18
708 894 2.534042 AGGCCACTACAGAAGAGCTA 57.466 50.000 5.01 0.00 0.00 3.32
729 917 5.557576 AGGAATCTAATGCAGTGCTCATA 57.442 39.130 17.60 5.85 0.00 2.15
851 1040 0.397114 CTTCCCTTGGGGTATTGGCC 60.397 60.000 5.78 0.00 44.74 5.36
905 1101 1.081174 TCAACCTTCCTCCTCCCATCT 59.919 52.381 0.00 0.00 0.00 2.90
1089 1287 0.179089 CACCTCATTGCTCTCCTCGG 60.179 60.000 0.00 0.00 0.00 4.63
1290 1520 0.034059 CCTTGCAGAAGTGAGTCGGT 59.966 55.000 0.00 0.00 0.00 4.69
1381 1612 2.147150 GTTCCTGAGCTTGAACTCCAC 58.853 52.381 14.11 0.00 38.24 4.02
1520 1759 1.984570 TCGGGAGTGAGGAGCTTGG 60.985 63.158 0.00 0.00 0.00 3.61
1655 1894 4.883083 ACAGTTCAAAGCAGACTCGATAA 58.117 39.130 0.00 0.00 0.00 1.75
1793 2053 0.466543 TACCAACACACTTCGGCACT 59.533 50.000 0.00 0.00 0.00 4.40
1850 2112 3.191581 TGGTGTTTGGTTATATGCAACGG 59.808 43.478 0.00 0.00 0.00 4.44
1860 2122 2.950781 TCAAGGCATGGTGTTTGGTTA 58.049 42.857 0.00 0.00 0.00 2.85
1880 2142 4.826733 TGTCTGCATGTTAGTGGACAAATT 59.173 37.500 0.00 0.00 32.47 1.82
1881 2143 4.397420 TGTCTGCATGTTAGTGGACAAAT 58.603 39.130 0.00 0.00 32.47 2.32
2046 4349 8.378172 TGACGAGTCAAAAGAGTCAAAAATAT 57.622 30.769 3.11 0.00 38.66 1.28


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

AutoCloner maintained by Alex Coulton.