Multiple sequence alignment - TraesCS7B01G012100

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 TraesCS7B01G012100 chr7B 100.000 2333 0 0 1 2333 7726905 7729237 0.000000e+00 4309.0
1 TraesCS7B01G012100 chr7B 86.203 964 82 36 764 1714 10241767 10240842 0.000000e+00 996.0
2 TraesCS7B01G012100 chr7B 94.207 656 29 4 1 647 479235309 479234654 0.000000e+00 992.0
3 TraesCS7B01G012100 chr7B 93.210 648 33 5 1 645 728090921 728091560 0.000000e+00 942.0
4 TraesCS7B01G012100 chr7B 91.150 113 7 2 1530 1641 9814883 9814773 1.440000e-32 150.0
5 TraesCS7B01G012100 chr7B 100.000 45 0 0 1368 1412 10241201 10241157 1.490000e-12 84.2
6 TraesCS7B01G012100 chr3B 94.793 653 28 2 1 647 41333610 41334262 0.000000e+00 1013.0
7 TraesCS7B01G012100 chr3B 84.032 501 70 8 1754 2247 665477904 665477407 7.540000e-130 473.0
8 TraesCS7B01G012100 chr7D 92.693 698 38 7 1409 2096 66485243 66485937 0.000000e+00 994.0
9 TraesCS7B01G012100 chr7D 88.828 734 40 15 686 1412 68935428 68934730 0.000000e+00 863.0
10 TraesCS7B01G012100 chr7D 90.881 658 32 4 759 1412 66484564 66485197 0.000000e+00 857.0
11 TraesCS7B01G012100 chr7D 89.726 438 38 6 976 1412 68806005 68805574 9.420000e-154 553.0
12 TraesCS7B01G012100 chr7D 96.375 331 10 1 2003 2333 68932306 68931978 5.670000e-151 544.0
13 TraesCS7B01G012100 chr7D 83.800 500 65 12 1758 2245 186394569 186395064 5.870000e-126 460.0
14 TraesCS7B01G012100 chr7D 85.045 448 45 16 977 1412 66513486 66513923 9.900000e-119 436.0
15 TraesCS7B01G012100 chr7D 91.146 192 13 4 1412 1602 68934681 68934493 8.270000e-65 257.0
16 TraesCS7B01G012100 chr7D 96.262 107 4 0 1594 1700 68932410 68932304 2.380000e-40 176.0
17 TraesCS7B01G012100 chr7D 90.476 105 10 0 1614 1718 69014539 69014435 3.130000e-29 139.0
18 TraesCS7B01G012100 chr7D 97.826 46 1 0 684 729 66484520 66484565 1.920000e-11 80.5
19 TraesCS7B01G012100 chr5B 94.127 647 36 1 1 645 597328017 597327371 0.000000e+00 983.0
20 TraesCS7B01G012100 chr6A 92.988 656 35 6 1 645 21310935 21310280 0.000000e+00 946.0
21 TraesCS7B01G012100 chr6A 92.977 655 35 6 2 648 24203930 24204581 0.000000e+00 944.0
22 TraesCS7B01G012100 chr6A 92.824 655 38 4 1 647 616962642 616963295 0.000000e+00 941.0
23 TraesCS7B01G012100 chr7A 92.956 653 38 3 1 645 668039027 668039679 0.000000e+00 944.0
24 TraesCS7B01G012100 chr7A 88.771 757 41 10 677 1412 74611084 74610351 0.000000e+00 887.0
25 TraesCS7B01G012100 chr7A 92.411 448 26 3 1409 1852 71110686 71111129 1.180000e-177 632.0
26 TraesCS7B01G012100 chr7A 90.578 467 40 3 1867 2330 71111115 71111580 1.180000e-172 616.0
27 TraesCS7B01G012100 chr7A 91.685 445 26 5 975 1412 70894167 70894607 7.130000e-170 606.0
28 TraesCS7B01G012100 chr7A 81.940 670 29 19 759 1412 71110047 71110640 1.250000e-132 483.0
29 TraesCS7B01G012100 chr7A 91.714 350 25 3 975 1321 74596502 74596154 1.250000e-132 483.0
30 TraesCS7B01G012100 chr7A 83.730 504 69 13 1754 2248 103105832 103106331 4.540000e-127 464.0
31 TraesCS7B01G012100 chr7A 92.784 291 17 3 973 1260 71118688 71118977 3.590000e-113 418.0
32 TraesCS7B01G012100 chr7A 90.152 132 7 3 1499 1624 70894672 70894803 1.430000e-37 167.0
33 TraesCS7B01G012100 chr7A 91.892 111 8 1 1532 1641 74608944 74608834 1.120000e-33 154.0
34 TraesCS7B01G012100 chr7A 90.476 105 10 0 1614 1718 70780678 70780782 3.130000e-29 139.0
35 TraesCS7B01G012100 chr7A 92.473 93 7 0 1626 1718 74608670 74608578 1.450000e-27 134.0
36 TraesCS7B01G012100 chr7A 92.958 71 5 0 746 816 70893977 70894047 1.140000e-18 104.0
37 TraesCS7B01G012100 chr7A 96.610 59 2 0 758 816 71118523 71118581 5.310000e-17 99.0
38 TraesCS7B01G012100 chr2A 92.824 655 39 4 1 647 753032167 753032821 0.000000e+00 942.0
39 TraesCS7B01G012100 chr1D 94.262 366 20 1 976 1341 486922451 486922815 2.020000e-155 558.0
40 TraesCS7B01G012100 chr1D 82.803 314 29 12 1415 1718 486922912 486923210 8.270000e-65 257.0
41 TraesCS7B01G012100 chr4D 85.177 479 63 8 1777 2248 502028989 502028512 3.490000e-133 484.0
42 TraesCS7B01G012100 chr6D 83.433 501 75 8 1754 2248 10433398 10432900 2.110000e-125 459.0
43 TraesCS7B01G012100 chr5D 82.863 496 80 5 1758 2248 480971694 480971199 7.650000e-120 440.0
44 TraesCS7B01G012100 chr4A 80.747 509 89 7 1747 2248 246717103 246716597 2.810000e-104 388.0
45 TraesCS7B01G012100 chr3A 76.040 601 107 13 1748 2332 19308941 19308362 6.350000e-71 278.0
46 TraesCS7B01G012100 chr1B 91.346 104 7 2 1616 1718 678113126 678113228 8.690000e-30 141.0


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 TraesCS7B01G012100 chr7B 7726905 7729237 2332 False 4309.000000 4309 100.000000 1 2333 1 chr7B.!!$F1 2332
1 TraesCS7B01G012100 chr7B 479234654 479235309 655 True 992.000000 992 94.207000 1 647 1 chr7B.!!$R2 646
2 TraesCS7B01G012100 chr7B 728090921 728091560 639 False 942.000000 942 93.210000 1 645 1 chr7B.!!$F2 644
3 TraesCS7B01G012100 chr7B 10240842 10241767 925 True 540.100000 996 93.101500 764 1714 2 chr7B.!!$R3 950
4 TraesCS7B01G012100 chr3B 41333610 41334262 652 False 1013.000000 1013 94.793000 1 647 1 chr3B.!!$F1 646
5 TraesCS7B01G012100 chr7D 66484520 66485937 1417 False 643.833333 994 93.800000 684 2096 3 chr7D.!!$F3 1412
6 TraesCS7B01G012100 chr7D 68931978 68935428 3450 True 460.000000 863 93.152750 686 2333 4 chr7D.!!$R3 1647
7 TraesCS7B01G012100 chr5B 597327371 597328017 646 True 983.000000 983 94.127000 1 645 1 chr5B.!!$R1 644
8 TraesCS7B01G012100 chr6A 21310280 21310935 655 True 946.000000 946 92.988000 1 645 1 chr6A.!!$R1 644
9 TraesCS7B01G012100 chr6A 24203930 24204581 651 False 944.000000 944 92.977000 2 648 1 chr6A.!!$F1 646
10 TraesCS7B01G012100 chr6A 616962642 616963295 653 False 941.000000 941 92.824000 1 647 1 chr6A.!!$F2 646
11 TraesCS7B01G012100 chr7A 668039027 668039679 652 False 944.000000 944 92.956000 1 645 1 chr7A.!!$F3 644
12 TraesCS7B01G012100 chr7A 71110047 71111580 1533 False 577.000000 632 88.309667 759 2330 3 chr7A.!!$F5 1571
13 TraesCS7B01G012100 chr7A 74608578 74611084 2506 True 391.666667 887 91.045333 677 1718 3 chr7A.!!$R2 1041
14 TraesCS7B01G012100 chr7A 70893977 70894803 826 False 292.333333 606 91.598333 746 1624 3 chr7A.!!$F4 878
15 TraesCS7B01G012100 chr2A 753032167 753032821 654 False 942.000000 942 92.824000 1 647 1 chr2A.!!$F1 646
16 TraesCS7B01G012100 chr1D 486922451 486923210 759 False 407.500000 558 88.532500 976 1718 2 chr1D.!!$F1 742
17 TraesCS7B01G012100 chr4A 246716597 246717103 506 True 388.000000 388 80.747000 1747 2248 1 chr4A.!!$R1 501
18 TraesCS7B01G012100 chr3A 19308362 19308941 579 True 278.000000 278 76.040000 1748 2332 1 chr3A.!!$R1 584

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
538 556 0.891904 GGCACTAGTTTTGGCCCGAA 60.892 55.0 10.21 0.0 40.55 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2236 5888 1.005867 GGTTGTGCCTCGTCGGTAA 60.006 57.895 0.0 0.0 34.25 2.85 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
50 56 3.610619 CTGGGCATGGCTGACGACA 62.611 63.158 19.78 6.35 0.00 4.35
77 83 2.284625 ATCCCTGCCTGGTCGACA 60.285 61.111 18.91 2.63 0.00 4.35
78 84 1.918293 ATCCCTGCCTGGTCGACAA 60.918 57.895 18.91 4.84 0.00 3.18
165 171 4.717629 CGGCGGTGACTGCTTCGA 62.718 66.667 16.87 0.00 0.00 3.71
397 407 1.215647 GAGCGGGAAAGAAGCGAGA 59.784 57.895 0.00 0.00 35.78 4.04
538 556 0.891904 GGCACTAGTTTTGGCCCGAA 60.892 55.000 10.21 0.00 40.55 4.30
649 672 2.777832 GGCTGGAGATGCCCTAATAG 57.222 55.000 0.00 0.00 44.32 1.73
650 673 1.280421 GGCTGGAGATGCCCTAATAGG 59.720 57.143 0.00 0.00 44.32 2.57
722 745 3.130227 CCCAGGCGGACTAGCTAC 58.870 66.667 0.00 0.00 37.29 3.58
861 892 2.060383 TCGGAGTGGGCAGATCCTG 61.060 63.158 0.00 0.00 34.39 3.86
870 902 4.965532 AGTGGGCAGATCCTGTATATATCC 59.034 45.833 0.00 0.00 33.43 2.59
871 903 4.101741 GTGGGCAGATCCTGTATATATCCC 59.898 50.000 0.00 0.00 33.43 3.85
872 904 4.265261 TGGGCAGATCCTGTATATATCCCA 60.265 45.833 0.00 0.00 33.62 4.37
874 906 5.163258 GGGCAGATCCTGTATATATCCCAAG 60.163 48.000 0.00 0.00 33.43 3.61
875 907 5.426833 GGCAGATCCTGTATATATCCCAAGT 59.573 44.000 0.00 0.00 33.43 3.16
896 929 2.442502 TCCCAACCCTTTCCTTACGAAA 59.557 45.455 0.00 0.00 38.16 3.46
1236 1282 2.885861 GACTGGATCGACGCCTGT 59.114 61.111 15.57 15.57 39.84 4.00
1295 1341 4.025401 CCACAAACGACAGCGGCC 62.025 66.667 0.00 0.00 43.17 6.13
1334 1380 1.667177 CGACGATAGCGATGCCTGATT 60.667 52.381 7.69 0.00 41.64 2.57
1346 1400 2.358957 TGCCTGATTGATCGAGTTTGG 58.641 47.619 0.00 0.00 0.00 3.28
1367 1421 4.280929 TGGTTTCATGGATCGATCGATACT 59.719 41.667 34.05 20.33 36.45 2.12
1451 1572 4.695396 AGCTCATGAGTTCTGATCATCAC 58.305 43.478 23.38 2.56 35.20 3.06
1492 1621 0.586802 GAACCTGTGACTGGTTTCGC 59.413 55.000 24.62 11.12 43.82 4.70
1535 1748 4.015764 ACGAGAGTACCTAGTCCTTTTCC 58.984 47.826 0.00 0.00 46.88 3.13
1644 5281 1.131638 ACAAGGGTGAAGCAGACAGA 58.868 50.000 0.00 0.00 0.00 3.41
1706 5343 0.036732 CACAAGAGCTGCTGGGGTTA 59.963 55.000 7.01 0.00 0.00 2.85
1756 5397 8.129211 GCTTATATACACAACCCAACATCTTTC 58.871 37.037 0.00 0.00 0.00 2.62
1840 5483 1.402259 CACCCTAACACACGCACAAAA 59.598 47.619 0.00 0.00 0.00 2.44
1961 5606 4.942761 ACACAAGAATTTGCAACCAGAT 57.057 36.364 0.00 0.00 37.85 2.90
1984 5629 5.668471 TCTAAGCAGGTCATCATCTTCAAG 58.332 41.667 0.00 0.00 0.00 3.02
2063 5713 2.797074 CACACATGTGCATCCAACAA 57.203 45.000 25.68 0.00 39.39 2.83
2068 5718 2.093890 CATGTGCATCCAACAAGCCTA 58.906 47.619 0.00 0.00 0.00 3.93
2236 5888 3.691609 GGAAGAACATCAGCGGAAAATCT 59.308 43.478 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 83 1.745489 GGCGGCGTCTTCCTCATTT 60.745 57.895 9.37 0.00 0.00 2.32
78 84 2.125106 GGCGGCGTCTTCCTCATT 60.125 61.111 9.37 0.00 0.00 2.57
165 171 2.032681 GGTGGAAGTTCAGCGGCT 59.967 61.111 5.01 0.00 0.00 5.52
397 407 1.557443 CGCCGTTTCTTGACGCTTCT 61.557 55.000 0.00 0.00 41.50 2.85
524 542 1.302671 CCGGTTCGGGCCAAAACTA 60.303 57.895 16.39 0.00 44.15 2.24
538 556 4.941309 AGGCCGTTTTTCGCCGGT 62.941 61.111 1.90 0.00 45.91 5.28
558 576 4.910585 GCCCCAGTCGCATACCCG 62.911 72.222 0.00 0.00 0.00 5.28
562 580 0.039035 AAAAAGGCCCCAGTCGCATA 59.961 50.000 0.00 0.00 0.00 3.14
564 582 2.197324 AAAAAGGCCCCAGTCGCA 59.803 55.556 0.00 0.00 0.00 5.10
597 618 1.919771 CCCTCCCCAGGCGATTTTA 59.080 57.895 0.00 0.00 38.72 1.52
672 695 0.752658 GCTGGGTTGGTGCTCTTTTT 59.247 50.000 0.00 0.00 0.00 1.94
673 696 1.115326 GGCTGGGTTGGTGCTCTTTT 61.115 55.000 0.00 0.00 0.00 2.27
674 697 1.531602 GGCTGGGTTGGTGCTCTTT 60.532 57.895 0.00 0.00 0.00 2.52
675 698 2.116125 GGCTGGGTTGGTGCTCTT 59.884 61.111 0.00 0.00 0.00 2.85
722 745 1.739338 CGGGAGAAGATGACGGGAGG 61.739 65.000 0.00 0.00 0.00 4.30
792 817 2.132762 CAACGAAGCCACTAACGAGTT 58.867 47.619 0.00 0.00 31.73 3.01
861 892 4.850386 AGGGTTGGGACTTGGGATATATAC 59.150 45.833 0.00 0.00 0.00 1.47
870 902 0.482887 AGGAAAGGGTTGGGACTTGG 59.517 55.000 0.00 0.00 0.00 3.61
871 903 2.381752 AAGGAAAGGGTTGGGACTTG 57.618 50.000 0.00 0.00 0.00 3.16
872 904 2.224695 CGTAAGGAAAGGGTTGGGACTT 60.225 50.000 0.00 0.00 0.00 3.01
874 906 1.348696 TCGTAAGGAAAGGGTTGGGAC 59.651 52.381 0.00 0.00 38.47 4.46
875 907 1.732117 TCGTAAGGAAAGGGTTGGGA 58.268 50.000 0.00 0.00 38.47 4.37
1236 1282 1.228552 GCCTTGGTTGGCCTTCTCA 60.229 57.895 3.32 0.00 46.82 3.27
1320 1366 1.613437 TCGATCAATCAGGCATCGCTA 59.387 47.619 0.00 0.00 39.42 4.26
1334 1380 4.014569 TCCATGAAACCAAACTCGATCA 57.985 40.909 0.00 0.00 0.00 2.92
1346 1400 5.800941 GGTAGTATCGATCGATCCATGAAAC 59.199 44.000 32.50 22.28 36.17 2.78
1367 1421 5.138276 ACTACGCAGGATTAGATTGAGGTA 58.862 41.667 0.00 0.00 0.00 3.08
1512 1649 4.142425 GGAAAAGGACTAGGTACTCTCGTG 60.142 50.000 0.00 0.00 41.75 4.35
1706 5343 6.979238 GCTGTCTTGTACGTTAGATTTAGGAT 59.021 38.462 0.00 0.00 0.00 3.24
1810 5453 2.436542 TGTGTTAGGGTGTGCTTGTACT 59.563 45.455 0.00 0.00 0.00 2.73
1840 5483 4.767409 GGGCACTCTCTATTTTTCTGGTTT 59.233 41.667 0.00 0.00 0.00 3.27
1859 5502 4.710375 TGTTTTACTGGTTGTTTTAGGGCA 59.290 37.500 0.00 0.00 0.00 5.36
1961 5606 5.668471 CTTGAAGATGATGACCTGCTTAGA 58.332 41.667 0.00 0.00 0.00 2.10
1984 5629 2.908817 CGGGGTGATTATACCGTGC 58.091 57.895 0.00 0.00 41.79 5.34
2170 5822 1.675641 GATGTCCTGCTTTGCCCGT 60.676 57.895 0.00 0.00 0.00 5.28
2236 5888 1.005867 GGTTGTGCCTCGTCGGTAA 60.006 57.895 0.00 0.00 34.25 2.85


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

AutoCloner maintained by Alex Coulton.