Multiple sequence alignment - TraesCS7B01G429800

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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 TraesCS7B01G429800 chr7B 100.000 4674 0 0 1 4674 698656623 698651950 0.000000e+00 8632
1 TraesCS7B01G429800 chr7B 95.382 4482 100 32 1 4466 694365907 694361517 0.000000e+00 7031
2 TraesCS7B01G429800 chr7B 99.828 3493 5 1 710 4201 699146225 699142733 0.000000e+00 6416
3 TraesCS7B01G429800 chr7B 91.432 2953 176 27 1754 4674 699141480 699138573 0.000000e+00 3980
4 TraesCS7B01G429800 chr7B 90.627 2902 199 30 959 3844 696145894 696143050 0.000000e+00 3784
5 TraesCS7B01G429800 chr7B 91.048 2625 156 33 1557 4149 699182593 699180016 0.000000e+00 3472
6 TraesCS7B01G429800 chr7B 93.149 1985 90 20 2710 4674 693621424 693619466 0.000000e+00 2870
7 TraesCS7B01G429800 chr7B 87.579 1272 111 28 1342 2590 693314804 693316051 0.000000e+00 1430
8 TraesCS7B01G429800 chr7B 84.686 1084 119 31 1252 2326 697024502 697025547 0.000000e+00 1038
9 TraesCS7B01G429800 chr7B 89.689 708 65 6 1 706 435821778 435822479 0.000000e+00 896
10 TraesCS7B01G429800 chr7B 80.903 864 76 33 870 1707 694189171 694189971 2.410000e-167 599
11 TraesCS7B01G429800 chr7B 84.764 571 74 9 1983 2546 685283350 685282786 1.140000e-155 560
12 TraesCS7B01G429800 chr7B 84.007 594 58 13 3840 4426 696142881 696142318 1.910000e-148 536
13 TraesCS7B01G429800 chr7B 91.096 292 21 1 4383 4674 699179743 699179457 1.580000e-104 390
14 TraesCS7B01G429800 chr7B 82.326 430 46 15 998 1410 699142638 699142222 3.460000e-91 346
15 TraesCS7B01G429800 chr7B 97.674 172 4 0 4503 4674 694361523 694361352 3.540000e-76 296
16 TraesCS7B01G429800 chr7B 90.500 200 19 0 4475 4674 696142310 696142111 9.970000e-67 265
17 TraesCS7B01G429800 chr7B 90.104 192 14 4 973 1162 697024262 697024450 1.300000e-60 244
18 TraesCS7B01G429800 chr7D 88.623 3463 243 58 714 4136 608200098 608196747 0.000000e+00 4072
19 TraesCS7B01G429800 chr7D 86.266 3131 270 86 703 3762 514750563 514747522 0.000000e+00 3253
20 TraesCS7B01G429800 chr7D 82.896 1906 206 81 991 2823 600232204 600234062 0.000000e+00 1604
21 TraesCS7B01G429800 chr7D 91.621 1086 77 9 1652 2728 610532295 610533375 0.000000e+00 1489
22 TraesCS7B01G429800 chr7D 83.117 1078 120 28 1263 2326 609861944 609862973 0.000000e+00 926
23 TraesCS7B01G429800 chr7D 86.842 608 29 18 3840 4426 610534742 610535319 2.370000e-177 632
24 TraesCS7B01G429800 chr7D 88.372 516 38 7 3760 4253 514747037 514746522 6.690000e-168 601
25 TraesCS7B01G429800 chr7D 84.946 558 47 19 998 1538 610531534 610532071 8.910000e-147 531
26 TraesCS7B01G429800 chr7D 91.498 247 16 3 4184 4426 600235585 600235830 7.490000e-88 335
27 TraesCS7B01G429800 chr7D 81.675 382 37 20 785 1162 609348825 609348473 2.130000e-73 287
28 TraesCS7B01G429800 chr7D 91.878 197 16 0 4472 4668 610535324 610535520 4.610000e-70 276
29 TraesCS7B01G429800 chr7D 90.306 196 15 1 4475 4670 514746379 514746188 2.160000e-63 254
30 TraesCS7B01G429800 chr7D 87.736 212 13 10 707 917 610531335 610531534 7.820000e-58 235
31 TraesCS7B01G429800 chr7D 82.564 195 16 5 1266 1448 609348211 609348023 6.260000e-34 156
32 TraesCS7B01G429800 chr7A 84.954 3456 320 97 703 4073 700503358 700506698 0.000000e+00 3317
33 TraesCS7B01G429800 chr7A 89.293 1896 144 26 2822 4674 700208119 700206240 0.000000e+00 2322
34 TraesCS7B01G429800 chr7A 89.385 358 31 5 4073 4426 700506725 700507079 1.190000e-120 444
35 TraesCS7B01G429800 chr4A 91.885 1109 73 10 2514 3621 661823500 661822408 0.000000e+00 1533
36 TraesCS7B01G429800 chr4A 93.863 831 45 4 1691 2516 661826027 661825198 0.000000e+00 1247
37 TraesCS7B01G429800 chr4A 86.901 1023 70 19 3673 4674 661822411 661821432 0.000000e+00 1088
38 TraesCS7B01G429800 chrUn 83.163 1075 119 28 1266 2326 209380911 209379885 0.000000e+00 926
39 TraesCS7B01G429800 chr5B 89.773 704 69 3 3 706 691261179 691261879 0.000000e+00 898
40 TraesCS7B01G429800 chr5B 89.853 680 66 3 1 680 616679543 616680219 0.000000e+00 870
41 TraesCS7B01G429800 chr3A 89.400 717 65 7 1 708 20437030 20437744 0.000000e+00 893
42 TraesCS7B01G429800 chr3A 89.083 687 65 9 1 684 9619509 9618830 0.000000e+00 845
43 TraesCS7B01G429800 chr4D 89.577 710 63 7 1 709 416623706 416624405 0.000000e+00 891
44 TraesCS7B01G429800 chr4D 89.155 710 67 8 1 709 416687701 416688401 0.000000e+00 876
45 TraesCS7B01G429800 chr6D 89.504 705 69 3 1 705 430368411 430367712 0.000000e+00 887
46 TraesCS7B01G429800 chr6B 88.604 702 70 8 8 706 88253928 88253234 0.000000e+00 845
47 TraesCS7B01G429800 chr4B 82.586 379 32 12 1333 1697 55721793 55721435 2.110000e-78 303


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 TraesCS7B01G429800 chr7B 698651950 698656623 4673 True 8632.000000 8632 100.000000 1 4674 1 chr7B.!!$R3 4673
1 TraesCS7B01G429800 chr7B 694361352 694365907 4555 True 3663.500000 7031 96.528000 1 4674 2 chr7B.!!$R4 4673
2 TraesCS7B01G429800 chr7B 699138573 699146225 7652 True 3580.666667 6416 91.195333 710 4674 3 chr7B.!!$R6 3964
3 TraesCS7B01G429800 chr7B 693619466 693621424 1958 True 2870.000000 2870 93.149000 2710 4674 1 chr7B.!!$R2 1964
4 TraesCS7B01G429800 chr7B 699179457 699182593 3136 True 1931.000000 3472 91.072000 1557 4674 2 chr7B.!!$R7 3117
5 TraesCS7B01G429800 chr7B 696142111 696145894 3783 True 1528.333333 3784 88.378000 959 4674 3 chr7B.!!$R5 3715
6 TraesCS7B01G429800 chr7B 693314804 693316051 1247 False 1430.000000 1430 87.579000 1342 2590 1 chr7B.!!$F2 1248
7 TraesCS7B01G429800 chr7B 435821778 435822479 701 False 896.000000 896 89.689000 1 706 1 chr7B.!!$F1 705
8 TraesCS7B01G429800 chr7B 697024262 697025547 1285 False 641.000000 1038 87.395000 973 2326 2 chr7B.!!$F4 1353
9 TraesCS7B01G429800 chr7B 694189171 694189971 800 False 599.000000 599 80.903000 870 1707 1 chr7B.!!$F3 837
10 TraesCS7B01G429800 chr7B 685282786 685283350 564 True 560.000000 560 84.764000 1983 2546 1 chr7B.!!$R1 563
11 TraesCS7B01G429800 chr7D 608196747 608200098 3351 True 4072.000000 4072 88.623000 714 4136 1 chr7D.!!$R1 3422
12 TraesCS7B01G429800 chr7D 514746188 514750563 4375 True 1369.333333 3253 88.314667 703 4670 3 chr7D.!!$R2 3967
13 TraesCS7B01G429800 chr7D 600232204 600235830 3626 False 969.500000 1604 87.197000 991 4426 2 chr7D.!!$F2 3435
14 TraesCS7B01G429800 chr7D 609861944 609862973 1029 False 926.000000 926 83.117000 1263 2326 1 chr7D.!!$F1 1063
15 TraesCS7B01G429800 chr7D 610531335 610535520 4185 False 632.600000 1489 88.604600 707 4668 5 chr7D.!!$F3 3961
16 TraesCS7B01G429800 chr7D 609348023 609348825 802 True 221.500000 287 82.119500 785 1448 2 chr7D.!!$R3 663
17 TraesCS7B01G429800 chr7A 700206240 700208119 1879 True 2322.000000 2322 89.293000 2822 4674 1 chr7A.!!$R1 1852
18 TraesCS7B01G429800 chr7A 700503358 700507079 3721 False 1880.500000 3317 87.169500 703 4426 2 chr7A.!!$F1 3723
19 TraesCS7B01G429800 chr4A 661821432 661826027 4595 True 1289.333333 1533 90.883000 1691 4674 3 chr4A.!!$R1 2983
20 TraesCS7B01G429800 chrUn 209379885 209380911 1026 True 926.000000 926 83.163000 1266 2326 1 chrUn.!!$R1 1060
21 TraesCS7B01G429800 chr5B 691261179 691261879 700 False 898.000000 898 89.773000 3 706 1 chr5B.!!$F2 703
22 TraesCS7B01G429800 chr5B 616679543 616680219 676 False 870.000000 870 89.853000 1 680 1 chr5B.!!$F1 679
23 TraesCS7B01G429800 chr3A 20437030 20437744 714 False 893.000000 893 89.400000 1 708 1 chr3A.!!$F1 707
24 TraesCS7B01G429800 chr3A 9618830 9619509 679 True 845.000000 845 89.083000 1 684 1 chr3A.!!$R1 683
25 TraesCS7B01G429800 chr4D 416623706 416624405 699 False 891.000000 891 89.577000 1 709 1 chr4D.!!$F1 708
26 TraesCS7B01G429800 chr4D 416687701 416688401 700 False 876.000000 876 89.155000 1 709 1 chr4D.!!$F2 708
27 TraesCS7B01G429800 chr6D 430367712 430368411 699 True 887.000000 887 89.504000 1 705 1 chr6D.!!$R1 704
28 TraesCS7B01G429800 chr6B 88253234 88253928 694 True 845.000000 845 88.604000 8 706 1 chr6B.!!$R1 698

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
652 666 0.038159 GATTATACCGCTGGCTCGCT 60.038 55.0 0.0 0.0 0.0 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4208 11166 2.025155 TGCAGGCTGAGTAGTAGCTAC 58.975 52.381 20.86 16.43 40.92 3.58 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
104 105 1.612442 TGGTACCCTGCTCAGACCC 60.612 63.158 10.07 0.00 0.00 4.46
228 229 0.178903 TACAGGCAGGGTCCTCTTGT 60.179 55.000 8.39 8.39 33.25 3.16
243 244 2.738846 CTCTTGTCCAAGTTGATCACCG 59.261 50.000 3.87 0.00 39.38 4.94
340 341 1.129917 AGGATCTGATGGAGCACCTG 58.870 55.000 0.71 0.00 37.04 4.00
351 352 0.835941 GAGCACCTGTGGAGGATCAT 59.164 55.000 0.00 0.00 42.93 2.45
478 479 8.032952 TGATTTTCTGTGATGAACTATGTGAC 57.967 34.615 0.00 0.00 0.00 3.67
535 540 0.465460 GCCGAATATGGGCCAACTCA 60.465 55.000 11.89 0.00 44.97 3.41
543 548 3.499737 GGCCAACTCACGCCGATG 61.500 66.667 0.00 0.00 34.94 3.84
559 564 0.808755 GATGTCGGGCCATTTTTCGT 59.191 50.000 4.39 0.00 0.00 3.85
589 595 1.135402 GCCGAAAAATGAGCCGACATT 60.135 47.619 0.00 0.00 41.43 2.71
590 596 2.518949 CCGAAAAATGAGCCGACATTG 58.481 47.619 0.00 0.00 39.88 2.82
644 658 0.603569 CCAGAGCCGATTATACCGCT 59.396 55.000 0.00 0.00 0.00 5.52
652 666 0.038159 GATTATACCGCTGGCTCGCT 60.038 55.000 0.00 0.00 0.00 4.93
654 668 2.083835 TTATACCGCTGGCTCGCTCC 62.084 60.000 0.00 0.00 0.00 4.70
676 690 0.948678 GGCGGCGATTTTTATGCCTA 59.051 50.000 12.98 0.00 46.67 3.93
679 693 2.602217 GCGGCGATTTTTATGCCTACTG 60.602 50.000 12.98 0.00 46.67 2.74
680 694 2.869801 CGGCGATTTTTATGCCTACTGA 59.130 45.455 0.00 0.00 46.67 3.41
723 738 3.118519 GCTCTAATTACCCGAACCAAGGA 60.119 47.826 0.00 0.00 0.00 3.36
1322 1679 0.108615 CAGGCTCTGTAGTTGGTCGG 60.109 60.000 0.00 0.00 0.00 4.79
4208 11166 4.153117 ACAGCAGCAAGAAAGAAACTATCG 59.847 41.667 0.00 0.00 0.00 2.92
4598 11705 1.222113 GGGCAGTTAGGCAGGAGAC 59.778 63.158 0.00 0.00 46.44 3.36
4608 11715 1.744741 GCAGGAGACAGAAGCTGCC 60.745 63.158 0.00 0.00 34.37 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 5.278610 CCAGACAACAGCAAATCAAGATTGA 60.279 40.000 0.00 0.00 42.14 2.57
104 105 3.000041 TCCACATTTGATCTTTCGACCG 59.000 45.455 0.00 0.00 0.00 4.79
228 229 1.066430 GTAGCCGGTGATCAACTTGGA 60.066 52.381 9.52 0.00 0.00 3.53
253 254 0.614979 TGAGGTAGGCAGTCCAGGTC 60.615 60.000 0.00 0.00 33.74 3.85
340 341 1.233019 CATCGCCAATGATCCTCCAC 58.767 55.000 0.00 0.00 37.59 4.02
507 512 0.238289 CCATATTCGGCATGGTTCGC 59.762 55.000 0.00 0.00 38.53 4.70
543 548 1.133869 CGACGAAAAATGGCCCGAC 59.866 57.895 0.00 0.00 0.00 4.79
559 564 1.268352 CATTTTTCGGCCCACTTTCGA 59.732 47.619 0.00 0.00 0.00 3.71
622 636 1.349067 GGTATAATCGGCTCTGGGGT 58.651 55.000 0.00 0.00 0.00 4.95
654 668 0.657368 GCATAAAAATCGCCGCCTCG 60.657 55.000 0.00 0.00 0.00 4.63
656 670 1.733526 GGCATAAAAATCGCCGCCT 59.266 52.632 0.00 0.00 35.79 5.52
1322 1679 9.737427 TCTATCTCGACTCAATTGATTACTTTC 57.263 33.333 8.96 0.00 0.00 2.62
4208 11166 2.025155 TGCAGGCTGAGTAGTAGCTAC 58.975 52.381 20.86 16.43 40.92 3.58
4598 11705 1.222936 CTAGGTGGGGCAGCTTCTG 59.777 63.158 0.00 0.00 42.44 3.02


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

AutoCloner maintained by Alex Coulton.