Multiple sequence alignment - TraesCS1A01G324700

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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 TraesCS1A01G324700 chr1A 100.000 3331 0 0 1 3331 515238218 515234888 0.000000e+00 6152.0
1 TraesCS1A01G324700 chr1A 99.311 2032 9 2 714 2744 514963540 514961513 0.000000e+00 3670.0
2 TraesCS1A01G324700 chr1A 99.385 1951 7 2 714 2663 514702399 514700453 0.000000e+00 3531.0
3 TraesCS1A01G324700 chr1A 93.741 719 34 3 1 709 514714895 514714178 0.000000e+00 1068.0
4 TraesCS1A01G324700 chr1A 93.086 593 32 2 2739 3331 504104182 504104765 0.000000e+00 859.0
5 TraesCS1A01G324700 chr1A 87.500 384 33 9 2303 2684 514698785 514698415 2.370000e-116 429.0
6 TraesCS1A01G324700 chr1A 80.000 305 38 11 1801 2094 514947175 514946883 1.570000e-48 204.0
7 TraesCS1A01G324700 chr1A 80.000 305 38 11 1801 2094 515203826 515203534 1.570000e-48 204.0
8 TraesCS1A01G324700 chr1D 94.792 960 41 6 844 1803 418102224 418101274 0.000000e+00 1487.0
9 TraesCS1A01G324700 chr1D 88.303 949 51 32 1801 2707 418101398 418100468 0.000000e+00 1083.0
10 TraesCS1A01G324700 chr1D 92.985 613 34 2 2718 3330 435760965 435761568 0.000000e+00 885.0
11 TraesCS1A01G324700 chr1D 90.260 616 45 7 2718 3331 20656417 20657019 0.000000e+00 791.0
12 TraesCS1A01G324700 chr1D 87.195 328 29 7 2360 2684 418098662 418098345 8.790000e-96 361.0
13 TraesCS1A01G324700 chr1B 91.158 950 48 6 855 1803 565567993 565567079 0.000000e+00 1256.0
14 TraesCS1A01G324700 chr1B 92.839 796 39 5 1872 2660 565567144 565566360 0.000000e+00 1138.0
15 TraesCS1A01G324700 chr1B 92.754 621 31 5 2712 3329 502644592 502645201 0.000000e+00 885.0
16 TraesCS1A01G324700 chr1B 93.548 465 13 3 1989 2445 564919615 564919160 0.000000e+00 676.0
17 TraesCS1A01G324700 chr1B 94.624 186 6 2 2523 2706 564918769 564918586 5.440000e-73 285.0
18 TraesCS1A01G324700 chr7A 93.851 683 29 4 3 673 118437571 118438252 0.000000e+00 1016.0
19 TraesCS1A01G324700 chr7A 93.421 684 33 7 1 673 58371520 58372202 0.000000e+00 1003.0
20 TraesCS1A01G324700 chr5A 93.443 671 36 5 1 664 459426515 459425846 0.000000e+00 989.0
21 TraesCS1A01G324700 chr5A 92.971 626 28 4 3 614 573803745 573804368 0.000000e+00 898.0
22 TraesCS1A01G324700 chr3A 92.962 682 35 4 1 670 702477661 702476981 0.000000e+00 981.0
23 TraesCS1A01G324700 chr5D 92.899 676 33 11 3 664 419286798 419287472 0.000000e+00 968.0
24 TraesCS1A01G324700 chr5D 94.346 619 23 6 2714 3331 450524955 450524348 0.000000e+00 939.0
25 TraesCS1A01G324700 chr4A 92.251 684 42 3 1 673 555999113 555998430 0.000000e+00 959.0
26 TraesCS1A01G324700 chr4D 93.750 608 26 5 2724 3331 1615235 1615830 0.000000e+00 902.0
27 TraesCS1A01G324700 chr4D 89.333 75 3 5 2714 2784 86767727 86767654 4.580000e-14 89.8
28 TraesCS1A01G324700 chr7D 93.160 614 32 2 2718 3331 543095645 543096248 0.000000e+00 893.0
29 TraesCS1A01G324700 chr7D 93.160 614 29 2 2718 3331 634756411 634755811 0.000000e+00 889.0
30 TraesCS1A01G324700 chr7D 94.086 558 32 1 2775 3331 63814560 63815117 0.000000e+00 846.0
31 TraesCS1A01G324700 chr7D 91.143 621 38 9 2714 3331 561542045 561541439 0.000000e+00 826.0
32 TraesCS1A01G324700 chr4B 92.076 631 42 5 1 625 488619469 488618841 0.000000e+00 881.0
33 TraesCS1A01G324700 chr6D 92.569 619 34 5 2714 3331 471618846 471619453 0.000000e+00 878.0
34 TraesCS1A01G324700 chr6D 92.962 611 27 5 2721 3331 262277378 262276784 0.000000e+00 876.0
35 TraesCS1A01G324700 chr5B 91.205 614 39 8 2717 3329 506530401 506529802 0.000000e+00 821.0
36 TraesCS1A01G324700 chrUn 93.548 62 1 3 2714 2773 352829906 352829966 4.580000e-14 89.8


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 TraesCS1A01G324700 chr1A 515234888 515238218 3330 True 6152.0 6152 100.000000 1 3331 1 chr1A.!!$R5 3330
1 TraesCS1A01G324700 chr1A 514961513 514963540 2027 True 3670.0 3670 99.311000 714 2744 1 chr1A.!!$R3 2030
2 TraesCS1A01G324700 chr1A 514698415 514702399 3984 True 1980.0 3531 93.442500 714 2684 2 chr1A.!!$R6 1970
3 TraesCS1A01G324700 chr1A 514714178 514714895 717 True 1068.0 1068 93.741000 1 709 1 chr1A.!!$R1 708
4 TraesCS1A01G324700 chr1A 504104182 504104765 583 False 859.0 859 93.086000 2739 3331 1 chr1A.!!$F1 592
5 TraesCS1A01G324700 chr1D 418098345 418102224 3879 True 977.0 1487 90.096667 844 2707 3 chr1D.!!$R1 1863
6 TraesCS1A01G324700 chr1D 435760965 435761568 603 False 885.0 885 92.985000 2718 3330 1 chr1D.!!$F2 612
7 TraesCS1A01G324700 chr1D 20656417 20657019 602 False 791.0 791 90.260000 2718 3331 1 chr1D.!!$F1 613
8 TraesCS1A01G324700 chr1B 565566360 565567993 1633 True 1197.0 1256 91.998500 855 2660 2 chr1B.!!$R2 1805
9 TraesCS1A01G324700 chr1B 502644592 502645201 609 False 885.0 885 92.754000 2712 3329 1 chr1B.!!$F1 617
10 TraesCS1A01G324700 chr1B 564918586 564919615 1029 True 480.5 676 94.086000 1989 2706 2 chr1B.!!$R1 717
11 TraesCS1A01G324700 chr7A 118437571 118438252 681 False 1016.0 1016 93.851000 3 673 1 chr7A.!!$F2 670
12 TraesCS1A01G324700 chr7A 58371520 58372202 682 False 1003.0 1003 93.421000 1 673 1 chr7A.!!$F1 672
13 TraesCS1A01G324700 chr5A 459425846 459426515 669 True 989.0 989 93.443000 1 664 1 chr5A.!!$R1 663
14 TraesCS1A01G324700 chr5A 573803745 573804368 623 False 898.0 898 92.971000 3 614 1 chr5A.!!$F1 611
15 TraesCS1A01G324700 chr3A 702476981 702477661 680 True 981.0 981 92.962000 1 670 1 chr3A.!!$R1 669
16 TraesCS1A01G324700 chr5D 419286798 419287472 674 False 968.0 968 92.899000 3 664 1 chr5D.!!$F1 661
17 TraesCS1A01G324700 chr5D 450524348 450524955 607 True 939.0 939 94.346000 2714 3331 1 chr5D.!!$R1 617
18 TraesCS1A01G324700 chr4A 555998430 555999113 683 True 959.0 959 92.251000 1 673 1 chr4A.!!$R1 672
19 TraesCS1A01G324700 chr4D 1615235 1615830 595 False 902.0 902 93.750000 2724 3331 1 chr4D.!!$F1 607
20 TraesCS1A01G324700 chr7D 543095645 543096248 603 False 893.0 893 93.160000 2718 3331 1 chr7D.!!$F2 613
21 TraesCS1A01G324700 chr7D 634755811 634756411 600 True 889.0 889 93.160000 2718 3331 1 chr7D.!!$R2 613
22 TraesCS1A01G324700 chr7D 63814560 63815117 557 False 846.0 846 94.086000 2775 3331 1 chr7D.!!$F1 556
23 TraesCS1A01G324700 chr7D 561541439 561542045 606 True 826.0 826 91.143000 2714 3331 1 chr7D.!!$R1 617
24 TraesCS1A01G324700 chr4B 488618841 488619469 628 True 881.0 881 92.076000 1 625 1 chr4B.!!$R1 624
25 TraesCS1A01G324700 chr6D 471618846 471619453 607 False 878.0 878 92.569000 2714 3331 1 chr6D.!!$F1 617
26 TraesCS1A01G324700 chr6D 262276784 262277378 594 True 876.0 876 92.962000 2721 3331 1 chr6D.!!$R1 610
27 TraesCS1A01G324700 chr5B 506529802 506530401 599 True 821.0 821 91.205000 2717 3329 1 chr5B.!!$R1 612

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
800 822 0.830648 CCTCTTTACAGGATCCCGCA 59.169 55.0 8.55 0.0 35.2 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3032 4630 2.687566 GGGGATCCCTCCACACGT 60.688 66.667 30.08 0.0 45.19 4.49 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
97 98 5.423886 TGTTATTGTCATCGTGGATGCTTA 58.576 37.500 0.76 0.00 39.63 3.09
153 154 4.655963 ACATTGCCACTGTAAGACTCATT 58.344 39.130 0.00 0.00 37.43 2.57
202 203 4.213270 TGTTCGTCTTCATCCAATGACAAC 59.787 41.667 0.00 0.00 39.39 3.32
365 366 4.424566 TCGCGTACCTCGTTGCCC 62.425 66.667 5.77 0.00 42.13 5.36
575 595 2.095847 GTCATTCGGGCGTACGCAA 61.096 57.895 37.99 25.51 44.11 4.85
688 709 2.815503 CCCTACCCTTTGTACGTTTTGG 59.184 50.000 0.00 0.00 0.00 3.28
692 713 1.694844 CCTTTGTACGTTTTGGGGGT 58.305 50.000 0.00 0.00 0.00 4.95
697 718 2.843046 TACGTTTTGGGGGTGGGGG 61.843 63.158 0.00 0.00 0.00 5.40
742 763 2.561419 CGAAGACCACCTCTTTACAGGA 59.439 50.000 0.00 0.00 39.53 3.86
750 771 1.417890 CCTCTTTACAGGATCCCGCAT 59.582 52.381 8.55 0.00 35.20 4.73
763 785 4.022849 GGATCCCGCATTGAAAATTAGAGG 60.023 45.833 0.00 0.00 0.00 3.69
791 813 3.473625 ACCGAAAACCACCTCTTTACAG 58.526 45.455 0.00 0.00 0.00 2.74
800 822 0.830648 CCTCTTTACAGGATCCCGCA 59.169 55.000 8.55 0.00 35.20 5.69
801 823 1.473434 CCTCTTTACAGGATCCCGCAC 60.473 57.143 8.55 0.00 35.20 5.34
802 824 1.482593 CTCTTTACAGGATCCCGCACT 59.517 52.381 8.55 0.00 0.00 4.40
803 825 1.207089 TCTTTACAGGATCCCGCACTG 59.793 52.381 8.55 1.77 38.19 3.66
814 836 1.631388 TCCCGCACTGAAAATTAGGGA 59.369 47.619 0.00 0.00 43.48 4.20
928 950 1.612739 GAACCTCCTCCCCCTTCGT 60.613 63.158 0.00 0.00 0.00 3.85
2803 3803 2.257207 CGCCTCCTCCCCTTATTGATA 58.743 52.381 0.00 0.00 0.00 2.15
2804 3804 2.028020 CGCCTCCTCCCCTTATTGATAC 60.028 54.545 0.00 0.00 0.00 2.24
2805 3805 2.979678 GCCTCCTCCCCTTATTGATACA 59.020 50.000 0.00 0.00 0.00 2.29
2819 3819 3.165160 ATACATGTCCTCGCCGCCC 62.165 63.158 0.00 0.00 0.00 6.13
3118 4755 2.752238 CTCCTCGTCAGTCCGCCT 60.752 66.667 0.00 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
173 174 2.230266 TGGATGAAGACGAACATGACGA 59.770 45.455 19.43 2.24 34.70 4.20
277 278 9.221775 GTTACGTGATGTTTGAATGGATATTTC 57.778 33.333 0.00 0.00 0.00 2.17
365 366 1.226802 CCGCCTCATGTCTGACGAG 60.227 63.158 2.98 4.70 0.00 4.18
508 513 1.604023 AAGACGCCTCCTCTCGTGT 60.604 57.895 0.00 0.00 39.22 4.49
557 577 2.095847 TTGCGTACGCCCGAATGAC 61.096 57.895 35.11 7.28 41.09 3.06
710 731 1.297689 GGTCTTCGGTACAACCCCC 59.702 63.158 0.00 0.00 33.75 5.40
711 732 0.321034 GTGGTCTTCGGTACAACCCC 60.321 60.000 0.00 0.00 33.75 4.95
712 733 0.321034 GGTGGTCTTCGGTACAACCC 60.321 60.000 0.00 0.00 33.75 4.11
742 763 3.891366 CCCTCTAATTTTCAATGCGGGAT 59.109 43.478 0.00 0.00 0.00 3.85
750 771 5.005094 CGGTACAACCCCTCTAATTTTCAA 58.995 41.667 0.00 0.00 33.75 2.69
763 785 0.953727 GGTGGTTTTCGGTACAACCC 59.046 55.000 9.64 2.86 33.75 4.11
791 813 2.618709 CCTAATTTTCAGTGCGGGATCC 59.381 50.000 1.92 1.92 0.00 3.36
800 822 6.555463 TCTATCCGTTCCCTAATTTTCAGT 57.445 37.500 0.00 0.00 0.00 3.41
801 823 8.148351 TGTATCTATCCGTTCCCTAATTTTCAG 58.852 37.037 0.00 0.00 0.00 3.02
802 824 8.025270 TGTATCTATCCGTTCCCTAATTTTCA 57.975 34.615 0.00 0.00 0.00 2.69
803 825 7.603024 CCTGTATCTATCCGTTCCCTAATTTTC 59.397 40.741 0.00 0.00 0.00 2.29
814 836 4.411927 AGCAGATCCTGTATCTATCCGTT 58.588 43.478 0.00 0.00 43.42 4.44
928 950 2.706952 CTTGGTTTGGGCTTCGGGGA 62.707 60.000 0.00 0.00 0.00 4.81
3032 4630 2.687566 GGGGATCCCTCCACACGT 60.688 66.667 30.08 0.00 45.19 4.49
3215 4852 2.831685 TCAAGAAGGAAACAGCGCTA 57.168 45.000 10.99 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.