Multiple sequence alignment - TraesCS7B01G178900

Loading Multiple Alignment...

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 TraesCS7B01G178900 chr7B 100.000 2582 0 0 1 2582 261996165 261998746 0.000000e+00 4769.0
1 TraesCS7B01G178900 chr7B 94.990 978 34 4 938 1901 577140299 577141275 0.000000e+00 1520.0
2 TraesCS7B01G178900 chr7B 93.813 986 44 7 929 1899 153644977 153643994 0.000000e+00 1467.0
3 TraesCS7B01G178900 chr7B 88.880 1187 79 22 761 1910 706233620 706234790 0.000000e+00 1411.0
4 TraesCS7B01G178900 chr7B 91.218 706 57 4 2 705 685891423 685892125 0.000000e+00 955.0
5 TraesCS7B01G178900 chr7B 95.434 438 19 1 1899 2335 262045953 262046390 0.000000e+00 697.0
6 TraesCS7B01G178900 chr7B 96.226 106 3 1 2477 2582 262046381 262046485 3.420000e-39 172.0
7 TraesCS7B01G178900 chr5B 94.836 1007 36 5 911 1904 440290701 440289698 0.000000e+00 1557.0
8 TraesCS7B01G178900 chr5B 90.341 1025 55 13 888 1899 513988695 513989688 0.000000e+00 1304.0
9 TraesCS7B01G178900 chr5B 91.527 956 60 9 965 1905 509466682 509465733 0.000000e+00 1297.0
10 TraesCS7B01G178900 chr5B 90.583 977 56 12 911 1863 609842945 609843909 0.000000e+00 1262.0
11 TraesCS7B01G178900 chr5B 80.711 928 128 35 992 1899 436102204 436103100 0.000000e+00 675.0
12 TraesCS7B01G178900 chr5B 84.897 629 87 8 964 1588 623099370 623098746 1.690000e-176 628.0
13 TraesCS7B01G178900 chr1B 93.288 1028 48 8 889 1899 466286687 466285664 0.000000e+00 1496.0
14 TraesCS7B01G178900 chr1B 93.353 1008 52 10 903 1902 259489404 259488404 0.000000e+00 1476.0
15 TraesCS7B01G178900 chr1B 90.294 1020 65 13 911 1904 39908034 39907023 0.000000e+00 1304.0
16 TraesCS7B01G178900 chr2B 93.461 994 43 8 923 1901 29143778 29144764 0.000000e+00 1456.0
17 TraesCS7B01G178900 chr2B 93.591 983 37 9 937 1903 202908624 202909596 0.000000e+00 1443.0
18 TraesCS7B01G178900 chr2B 93.661 915 40 7 888 1786 418650931 418650019 0.000000e+00 1352.0
19 TraesCS7B01G178900 chr2B 89.550 756 68 10 2 748 275318740 275317987 0.000000e+00 948.0
20 TraesCS7B01G178900 chr4B 92.958 994 51 10 923 1899 428464176 428465167 0.000000e+00 1430.0
21 TraesCS7B01G178900 chr4B 80.796 1005 141 40 915 1903 455008296 455007328 0.000000e+00 739.0
22 TraesCS7B01G178900 chr4B 91.767 498 27 10 1408 1899 168782957 168782468 0.000000e+00 680.0
23 TraesCS7B01G178900 chr3B 92.167 983 58 6 937 1901 593141350 593142331 0.000000e+00 1371.0
24 TraesCS7B01G178900 chr3B 95.122 533 19 4 1378 1906 367716263 367715734 0.000000e+00 833.0
25 TraesCS7B01G178900 chr3B 84.524 84 7 5 671 748 762805913 762805830 7.660000e-11 78.7
26 TraesCS7B01G178900 chr5D 86.503 1178 80 45 756 1899 25466358 25467490 0.000000e+00 1221.0
27 TraesCS7B01G178900 chr5D 89.139 755 73 8 2 748 332819469 332820222 0.000000e+00 931.0
28 TraesCS7B01G178900 chr2A 93.717 764 38 3 2 756 41753864 41754626 0.000000e+00 1136.0
29 TraesCS7B01G178900 chr7D 93.521 710 38 4 2 705 85556207 85556914 0.000000e+00 1050.0
30 TraesCS7B01G178900 chr7D 94.606 686 22 7 1908 2582 274859979 274859298 0.000000e+00 1048.0
31 TraesCS7B01G178900 chr7D 80.503 954 113 28 983 1899 487869289 487870206 0.000000e+00 664.0
32 TraesCS7B01G178900 chr1A 87.291 897 89 8 970 1850 39823718 39822831 0.000000e+00 1002.0
33 TraesCS7B01G178900 chr1A 78.903 948 134 37 994 1901 578332381 578333302 1.330000e-162 582.0
34 TraesCS7B01G178900 chr6A 90.765 758 52 11 2 748 411090567 411091317 0.000000e+00 996.0
35 TraesCS7B01G178900 chr6A 80.822 949 132 33 992 1902 106477688 106476752 0.000000e+00 699.0
36 TraesCS7B01G178900 chr6A 80.693 953 133 30 992 1901 566598098 566597154 0.000000e+00 693.0
37 TraesCS7B01G178900 chr6A 78.908 934 128 41 1007 1904 572160830 572159930 1.040000e-158 569.0
38 TraesCS7B01G178900 chr4D 89.934 755 67 7 2 748 346465267 346466020 0.000000e+00 965.0
39 TraesCS7B01G178900 chr4D 80.579 726 105 24 983 1681 365313819 365314535 6.330000e-146 527.0
40 TraesCS7B01G178900 chr3D 89.536 755 69 9 2 748 323292952 323293704 0.000000e+00 948.0
41 TraesCS7B01G178900 chrUn 89.272 755 72 7 2 748 110777699 110778452 0.000000e+00 937.0
42 TraesCS7B01G178900 chr6D 80.761 972 122 30 954 1901 409482848 409481918 0.000000e+00 699.0
43 TraesCS7B01G178900 chr6D 80.880 727 99 14 992 1684 148078217 148077497 1.050000e-148 536.0
44 TraesCS7B01G178900 chr6D 80.597 737 102 20 980 1681 30067749 30068479 4.890000e-147 531.0
45 TraesCS7B01G178900 chr6D 80.743 727 101 17 992 1684 354544943 354544222 4.890000e-147 531.0
46 TraesCS7B01G178900 chr6D 80.605 727 102 19 992 1684 60170201 60169480 2.280000e-145 525.0
47 TraesCS7B01G178900 chr6D 85.185 108 3 3 1585 1680 407209472 407209366 5.880000e-17 99.0
48 TraesCS7B01G178900 chr1D 81.194 888 110 29 983 1832 362919512 362920380 0.000000e+00 662.0
49 TraesCS7B01G178900 chr1D 80.488 738 94 23 983 1685 335078342 335079064 1.060000e-143 520.0
50 TraesCS7B01G178900 chr6B 84.977 639 81 12 970 1597 701468340 701467706 3.620000e-178 634.0
51 TraesCS7B01G178900 chr6B 88.957 163 17 1 1742 1903 52133893 52133731 1.570000e-47 200.0
52 TraesCS7B01G178900 chr2D 96.032 126 5 0 1778 1903 86520721 86520846 3.370000e-49 206.0


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 TraesCS7B01G178900 chr7B 261996165 261998746 2581 False 4769.0 4769 100.000 1 2582 1 chr7B.!!$F1 2581
1 TraesCS7B01G178900 chr7B 577140299 577141275 976 False 1520.0 1520 94.990 938 1901 1 chr7B.!!$F2 963
2 TraesCS7B01G178900 chr7B 153643994 153644977 983 True 1467.0 1467 93.813 929 1899 1 chr7B.!!$R1 970
3 TraesCS7B01G178900 chr7B 706233620 706234790 1170 False 1411.0 1411 88.880 761 1910 1 chr7B.!!$F4 1149
4 TraesCS7B01G178900 chr7B 685891423 685892125 702 False 955.0 955 91.218 2 705 1 chr7B.!!$F3 703
5 TraesCS7B01G178900 chr7B 262045953 262046485 532 False 434.5 697 95.830 1899 2582 2 chr7B.!!$F5 683
6 TraesCS7B01G178900 chr5B 440289698 440290701 1003 True 1557.0 1557 94.836 911 1904 1 chr5B.!!$R1 993
7 TraesCS7B01G178900 chr5B 513988695 513989688 993 False 1304.0 1304 90.341 888 1899 1 chr5B.!!$F2 1011
8 TraesCS7B01G178900 chr5B 509465733 509466682 949 True 1297.0 1297 91.527 965 1905 1 chr5B.!!$R2 940
9 TraesCS7B01G178900 chr5B 609842945 609843909 964 False 1262.0 1262 90.583 911 1863 1 chr5B.!!$F3 952
10 TraesCS7B01G178900 chr5B 436102204 436103100 896 False 675.0 675 80.711 992 1899 1 chr5B.!!$F1 907
11 TraesCS7B01G178900 chr5B 623098746 623099370 624 True 628.0 628 84.897 964 1588 1 chr5B.!!$R3 624
12 TraesCS7B01G178900 chr1B 466285664 466286687 1023 True 1496.0 1496 93.288 889 1899 1 chr1B.!!$R3 1010
13 TraesCS7B01G178900 chr1B 259488404 259489404 1000 True 1476.0 1476 93.353 903 1902 1 chr1B.!!$R2 999
14 TraesCS7B01G178900 chr1B 39907023 39908034 1011 True 1304.0 1304 90.294 911 1904 1 chr1B.!!$R1 993
15 TraesCS7B01G178900 chr2B 29143778 29144764 986 False 1456.0 1456 93.461 923 1901 1 chr2B.!!$F1 978
16 TraesCS7B01G178900 chr2B 202908624 202909596 972 False 1443.0 1443 93.591 937 1903 1 chr2B.!!$F2 966
17 TraesCS7B01G178900 chr2B 418650019 418650931 912 True 1352.0 1352 93.661 888 1786 1 chr2B.!!$R2 898
18 TraesCS7B01G178900 chr2B 275317987 275318740 753 True 948.0 948 89.550 2 748 1 chr2B.!!$R1 746
19 TraesCS7B01G178900 chr4B 428464176 428465167 991 False 1430.0 1430 92.958 923 1899 1 chr4B.!!$F1 976
20 TraesCS7B01G178900 chr4B 455007328 455008296 968 True 739.0 739 80.796 915 1903 1 chr4B.!!$R2 988
21 TraesCS7B01G178900 chr3B 593141350 593142331 981 False 1371.0 1371 92.167 937 1901 1 chr3B.!!$F1 964
22 TraesCS7B01G178900 chr3B 367715734 367716263 529 True 833.0 833 95.122 1378 1906 1 chr3B.!!$R1 528
23 TraesCS7B01G178900 chr5D 25466358 25467490 1132 False 1221.0 1221 86.503 756 1899 1 chr5D.!!$F1 1143
24 TraesCS7B01G178900 chr5D 332819469 332820222 753 False 931.0 931 89.139 2 748 1 chr5D.!!$F2 746
25 TraesCS7B01G178900 chr2A 41753864 41754626 762 False 1136.0 1136 93.717 2 756 1 chr2A.!!$F1 754
26 TraesCS7B01G178900 chr7D 85556207 85556914 707 False 1050.0 1050 93.521 2 705 1 chr7D.!!$F1 703
27 TraesCS7B01G178900 chr7D 274859298 274859979 681 True 1048.0 1048 94.606 1908 2582 1 chr7D.!!$R1 674
28 TraesCS7B01G178900 chr7D 487869289 487870206 917 False 664.0 664 80.503 983 1899 1 chr7D.!!$F2 916
29 TraesCS7B01G178900 chr1A 39822831 39823718 887 True 1002.0 1002 87.291 970 1850 1 chr1A.!!$R1 880
30 TraesCS7B01G178900 chr1A 578332381 578333302 921 False 582.0 582 78.903 994 1901 1 chr1A.!!$F1 907
31 TraesCS7B01G178900 chr6A 411090567 411091317 750 False 996.0 996 90.765 2 748 1 chr6A.!!$F1 746
32 TraesCS7B01G178900 chr6A 106476752 106477688 936 True 699.0 699 80.822 992 1902 1 chr6A.!!$R1 910
33 TraesCS7B01G178900 chr6A 566597154 566598098 944 True 693.0 693 80.693 992 1901 1 chr6A.!!$R2 909
34 TraesCS7B01G178900 chr6A 572159930 572160830 900 True 569.0 569 78.908 1007 1904 1 chr6A.!!$R3 897
35 TraesCS7B01G178900 chr4D 346465267 346466020 753 False 965.0 965 89.934 2 748 1 chr4D.!!$F1 746
36 TraesCS7B01G178900 chr4D 365313819 365314535 716 False 527.0 527 80.579 983 1681 1 chr4D.!!$F2 698
37 TraesCS7B01G178900 chr3D 323292952 323293704 752 False 948.0 948 89.536 2 748 1 chr3D.!!$F1 746
38 TraesCS7B01G178900 chrUn 110777699 110778452 753 False 937.0 937 89.272 2 748 1 chrUn.!!$F1 746
39 TraesCS7B01G178900 chr6D 409481918 409482848 930 True 699.0 699 80.761 954 1901 1 chr6D.!!$R5 947
40 TraesCS7B01G178900 chr6D 148077497 148078217 720 True 536.0 536 80.880 992 1684 1 chr6D.!!$R2 692
41 TraesCS7B01G178900 chr6D 30067749 30068479 730 False 531.0 531 80.597 980 1681 1 chr6D.!!$F1 701
42 TraesCS7B01G178900 chr6D 354544222 354544943 721 True 531.0 531 80.743 992 1684 1 chr6D.!!$R3 692
43 TraesCS7B01G178900 chr6D 60169480 60170201 721 True 525.0 525 80.605 992 1684 1 chr6D.!!$R1 692
44 TraesCS7B01G178900 chr1D 362919512 362920380 868 False 662.0 662 81.194 983 1832 1 chr1D.!!$F2 849
45 TraesCS7B01G178900 chr1D 335078342 335079064 722 False 520.0 520 80.488 983 1685 1 chr1D.!!$F1 702
46 TraesCS7B01G178900 chr6B 701467706 701468340 634 True 634.0 634 84.977 970 1597 1 chr6B.!!$R2 627

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
644 651 0.405585 CCACCATGAGTTTGAGGGGT 59.594 55.0 0.0 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 2451 0.466124 GAGTTTCCTCTCCCATCCCG 59.534 60.0 0.0 0.0 34.69 5.14 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
33 34 1.983691 TCGTCCGGATATCTCCTACCT 59.016 52.381 7.81 0.00 39.65 3.08
60 61 7.502226 TGTCCATATTCTGAGTCAGTTTGTTTT 59.498 33.333 19.53 1.71 32.61 2.43
157 158 1.125093 TCTTTCCCCGTTCCAGCTCA 61.125 55.000 0.00 0.00 0.00 4.26
225 226 3.883489 TCGGATCGTCATTCACTATCTGT 59.117 43.478 0.00 0.00 35.77 3.41
259 260 2.106338 TCTTGGTGGTTCTCTCATTGCA 59.894 45.455 0.00 0.00 0.00 4.08
307 308 2.811317 CGTTCGAGTGCAGAGGCC 60.811 66.667 0.00 0.00 40.13 5.19
338 339 2.806745 GCTATGGCTCTATTGACGGCAA 60.807 50.000 5.94 5.94 36.78 4.52
394 396 3.804036 TGGTGTTTCTGTTACTCACCTG 58.196 45.455 12.66 0.00 45.82 4.00
490 493 4.541973 ATTGGGGTTGATGCTTTCTTTC 57.458 40.909 0.00 0.00 0.00 2.62
507 510 0.746204 TTCTGCACGCTGGTGTTCAA 60.746 50.000 0.00 0.00 46.13 2.69
526 529 8.025445 GTGTTCAAGATCATGTTATTGCTCTTT 58.975 33.333 6.31 0.00 31.53 2.52
644 651 0.405585 CCACCATGAGTTTGAGGGGT 59.594 55.000 0.00 0.00 0.00 4.95
918 957 1.415659 CGATTCCTCTTCCTCTGCCAT 59.584 52.381 0.00 0.00 0.00 4.40
1375 1484 4.101448 CCTACTGGGCAAGGCGCT 62.101 66.667 7.64 0.00 42.10 5.92
1573 1689 2.422276 TGGTGATGATGATAGCGACG 57.578 50.000 0.00 0.00 0.00 5.12
1906 2211 4.935885 GTTGGAGATGCTCTAACAACTG 57.064 45.455 15.79 0.00 46.43 3.16
1913 2218 3.124578 TGCTCTAACAACTGTGATGCA 57.875 42.857 0.00 0.00 0.00 3.96
2035 2340 1.880027 GGTTGGATGAACTCGCTTGTT 59.120 47.619 0.00 0.00 34.66 2.83
2141 2451 4.143301 GGGATGGTTGGAGGGGGC 62.143 72.222 0.00 0.00 0.00 5.80
2423 2737 8.255905 TGAGCACACATCTAATGATCTATATGG 58.744 37.037 0.00 0.00 30.14 2.74
2444 2758 5.514169 TGGTTTATACTGCATTCCATTCCA 58.486 37.500 0.00 0.00 0.00 3.53
2488 2803 6.036408 TGACTCTTTTCGTATGATCATGCTTG 59.964 38.462 18.72 5.47 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 6.533730 ACAAACTGACTCAGAATATGGACAA 58.466 36.000 13.25 0.00 35.18 3.18
60 61 2.204461 TGAACCGAAGTGGGAGCGA 61.204 57.895 0.00 0.00 44.64 4.93
119 120 0.736053 AAGAGACGGTGAGAGATCGC 59.264 55.000 0.00 0.00 0.00 4.58
157 158 2.043227 GAATAGGCCTGGAGCTGTAGT 58.957 52.381 17.99 0.00 43.05 2.73
225 226 5.986501 ACCACCAAGAAAAACACAGTAAA 57.013 34.783 0.00 0.00 0.00 2.01
259 260 5.105392 TGCAGTTTGTTTCTTTGTCTTCCAT 60.105 36.000 0.00 0.00 0.00 3.41
307 308 3.313750 GCCATAGCTCGCAACTCG 58.686 61.111 0.00 0.00 40.15 4.18
338 339 2.365293 GCCATCAAAACCAAGTCACCTT 59.635 45.455 0.00 0.00 0.00 3.50
352 353 2.519771 AATCCTCAAGCAGCCATCAA 57.480 45.000 0.00 0.00 0.00 2.57
394 396 1.896465 ACTGTCTGACAAGAGGGTAGC 59.104 52.381 12.16 0.00 31.37 3.58
490 493 1.159713 TCTTGAACACCAGCGTGCAG 61.160 55.000 0.00 0.00 44.40 4.41
526 529 4.018490 TGTAACTCGGAAGGCACATACTA 58.982 43.478 0.00 0.00 0.00 1.82
765 784 0.958382 ATCTTTTGGCGCGCCTGTTA 60.958 50.000 45.79 28.92 36.94 2.41
769 788 4.120331 GCATCTTTTGGCGCGCCT 62.120 61.111 45.79 26.18 36.94 5.52
801 820 3.788766 CGCGCGCTAAAAGCTGGT 61.789 61.111 30.48 0.00 39.60 4.00
824 843 3.659092 CTGGAGCGCGGCAAAACA 61.659 61.111 8.83 0.00 0.00 2.83
918 957 1.959226 GAGTCGTGGAAAAGGCGCA 60.959 57.895 10.83 0.00 0.00 6.09
1573 1689 5.972382 CGCAACTAGATAGAAACTACTCCAC 59.028 44.000 0.00 0.00 0.00 4.02
1906 2211 1.423056 GCGAGCTTCAGTGCATCAC 59.577 57.895 0.00 0.00 34.99 3.06
1986 2291 2.402557 ATACTCCTCCCCCATCCCCG 62.403 65.000 0.00 0.00 0.00 5.73
2035 2340 2.282110 CAACCCATGCACGACCCA 60.282 61.111 0.00 0.00 0.00 4.51
2141 2451 0.466124 GAGTTTCCTCTCCCATCCCG 59.534 60.000 0.00 0.00 34.69 5.14
2201 2512 6.313519 AGAAGATTGTAATTAGGTGCCAGA 57.686 37.500 0.00 0.00 0.00 3.86
2388 2702 2.040813 AGATGTGTGCTCATGGAACCTT 59.959 45.455 0.00 0.00 0.00 3.50
2423 2737 7.333528 TCTTGGAATGGAATGCAGTATAAAC 57.666 36.000 0.00 0.00 0.00 2.01
2442 2756 8.899427 AGTCATGTGTATCATCTAAATCTTGG 57.101 34.615 0.00 0.00 34.09 3.61
2488 2803 9.196552 CAGGGAGATGAACAAAGAAATAAAAAC 57.803 33.333 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.