Multiple sequence alignment - TraesCS6B01G087100

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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 TraesCS6B01G087100 chr6B 100.000 3764 0 0 1 3764 63152030 63148267 0.000000e+00 6951.0
1 TraesCS6B01G087100 chr6B 98.828 2475 13 1 1306 3764 63169016 63166542 0.000000e+00 4396.0
2 TraesCS6B01G087100 chr6B 80.733 1718 316 14 1037 2748 565393604 565395312 0.000000e+00 1325.0
3 TraesCS6B01G087100 chr6B 93.481 675 23 13 637 1310 63188148 63187494 0.000000e+00 983.0
4 TraesCS6B01G087100 chr6B 93.481 675 23 13 637 1310 63199238 63198584 0.000000e+00 983.0
5 TraesCS6B01G087100 chr6B 90.826 654 40 6 1 637 286751360 286752010 0.000000e+00 857.0
6 TraesCS6B01G087100 chr6B 90.701 656 40 11 1 638 526739986 526740638 0.000000e+00 854.0
7 TraesCS6B01G087100 chr6B 90.701 656 39 8 1 637 691347221 691347873 0.000000e+00 854.0
8 TraesCS6B01G087100 chr6B 90.244 656 44 6 1 639 131887168 131886516 0.000000e+00 839.0
9 TraesCS6B01G087100 chr6B 90.199 653 44 6 1 636 704376622 704377271 0.000000e+00 833.0
10 TraesCS6B01G087100 chr6B 87.903 620 50 16 3153 3764 26074511 26073909 0.000000e+00 706.0
11 TraesCS6B01G087100 chr6A 80.664 1717 319 12 1037 2748 520441097 520442805 0.000000e+00 1319.0
12 TraesCS6B01G087100 chr6D 80.617 1718 318 14 1037 2748 379048808 379050516 0.000000e+00 1314.0
13 TraesCS6B01G087100 chr7D 90.813 664 39 8 1 646 509902708 509902049 0.000000e+00 869.0
14 TraesCS6B01G087100 chr7D 87.967 615 50 16 3153 3764 36967133 36967726 0.000000e+00 704.0
15 TraesCS6B01G087100 chr7D 88.167 600 49 14 3169 3764 141649355 141649936 0.000000e+00 695.0
16 TraesCS6B01G087100 chr7D 86.201 587 58 9 1 567 461896091 461895508 6.910000e-172 614.0
17 TraesCS6B01G087100 chr7D 85.650 223 14 12 3155 3375 36983613 36983819 6.330000e-53 219.0
18 TraesCS6B01G087100 chrUn 91.393 639 36 9 1 621 30343888 30344525 0.000000e+00 857.0
19 TraesCS6B01G087100 chrUn 98.391 373 6 0 938 1310 320453231 320452859 0.000000e+00 656.0
20 TraesCS6B01G087100 chr7B 90.701 656 42 10 1 639 374712620 374711967 0.000000e+00 856.0
21 TraesCS6B01G087100 chr7B 90.196 663 45 6 1 644 716137548 716136887 0.000000e+00 846.0
22 TraesCS6B01G087100 chr7B 90.431 627 40 5 1 607 244205614 244204988 0.000000e+00 808.0
23 TraesCS6B01G087100 chr7B 82.068 619 84 19 3155 3763 675065376 675065977 1.560000e-138 503.0
24 TraesCS6B01G087100 chr3B 89.774 665 46 8 2 646 165783723 165784385 0.000000e+00 832.0
25 TraesCS6B01G087100 chr3B 90.407 615 54 2 3155 3764 492650213 492649599 0.000000e+00 804.0
26 TraesCS6B01G087100 chr3B 87.832 641 53 14 1 620 788074763 788074127 0.000000e+00 728.0
27 TraesCS6B01G087100 chr3B 82.258 620 83 19 3155 3764 625715254 625714652 9.330000e-141 510.0
28 TraesCS6B01G087100 chr5B 91.028 613 51 4 3155 3764 656710584 656709973 0.000000e+00 824.0
29 TraesCS6B01G087100 chr5B 83.951 81 6 3 3073 3152 654916839 654916765 1.880000e-08 71.3
30 TraesCS6B01G087100 chr2B 90.877 559 33 3 1 541 486767250 486766692 0.000000e+00 734.0
31 TraesCS6B01G087100 chr7A 87.213 610 57 15 3158 3764 733389861 733389270 0.000000e+00 675.0
32 TraesCS6B01G087100 chr7A 84.983 606 70 16 3169 3764 585312316 585312910 2.500000e-166 595.0
33 TraesCS6B01G087100 chr2A 87.076 619 53 16 3154 3764 642660467 642659868 0.000000e+00 675.0
34 TraesCS6B01G087100 chr2A 80.000 220 22 13 3158 3374 16908451 16908251 3.920000e-30 143.0
35 TraesCS6B01G087100 chr4D 84.165 581 48 17 1 563 403142964 403143518 1.200000e-144 523.0
36 TraesCS6B01G087100 chr3A 84.413 571 47 10 3 558 93081178 93081721 1.200000e-144 523.0
37 TraesCS6B01G087100 chr5D 88.136 59 4 1 2994 3049 557889517 557889575 2.430000e-07 67.6


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 TraesCS6B01G087100 chr6B 63148267 63152030 3763 True 6951 6951 100.000 1 3764 1 chr6B.!!$R2 3763
1 TraesCS6B01G087100 chr6B 63166542 63169016 2474 True 4396 4396 98.828 1306 3764 1 chr6B.!!$R3 2458
2 TraesCS6B01G087100 chr6B 565393604 565395312 1708 False 1325 1325 80.733 1037 2748 1 chr6B.!!$F3 1711
3 TraesCS6B01G087100 chr6B 63187494 63188148 654 True 983 983 93.481 637 1310 1 chr6B.!!$R4 673
4 TraesCS6B01G087100 chr6B 63198584 63199238 654 True 983 983 93.481 637 1310 1 chr6B.!!$R5 673
5 TraesCS6B01G087100 chr6B 286751360 286752010 650 False 857 857 90.826 1 637 1 chr6B.!!$F1 636
6 TraesCS6B01G087100 chr6B 526739986 526740638 652 False 854 854 90.701 1 638 1 chr6B.!!$F2 637
7 TraesCS6B01G087100 chr6B 691347221 691347873 652 False 854 854 90.701 1 637 1 chr6B.!!$F4 636
8 TraesCS6B01G087100 chr6B 131886516 131887168 652 True 839 839 90.244 1 639 1 chr6B.!!$R6 638
9 TraesCS6B01G087100 chr6B 704376622 704377271 649 False 833 833 90.199 1 636 1 chr6B.!!$F5 635
10 TraesCS6B01G087100 chr6B 26073909 26074511 602 True 706 706 87.903 3153 3764 1 chr6B.!!$R1 611
11 TraesCS6B01G087100 chr6A 520441097 520442805 1708 False 1319 1319 80.664 1037 2748 1 chr6A.!!$F1 1711
12 TraesCS6B01G087100 chr6D 379048808 379050516 1708 False 1314 1314 80.617 1037 2748 1 chr6D.!!$F1 1711
13 TraesCS6B01G087100 chr7D 509902049 509902708 659 True 869 869 90.813 1 646 1 chr7D.!!$R2 645
14 TraesCS6B01G087100 chr7D 36967133 36967726 593 False 704 704 87.967 3153 3764 1 chr7D.!!$F1 611
15 TraesCS6B01G087100 chr7D 141649355 141649936 581 False 695 695 88.167 3169 3764 1 chr7D.!!$F3 595
16 TraesCS6B01G087100 chr7D 461895508 461896091 583 True 614 614 86.201 1 567 1 chr7D.!!$R1 566
17 TraesCS6B01G087100 chrUn 30343888 30344525 637 False 857 857 91.393 1 621 1 chrUn.!!$F1 620
18 TraesCS6B01G087100 chr7B 374711967 374712620 653 True 856 856 90.701 1 639 1 chr7B.!!$R2 638
19 TraesCS6B01G087100 chr7B 716136887 716137548 661 True 846 846 90.196 1 644 1 chr7B.!!$R3 643
20 TraesCS6B01G087100 chr7B 244204988 244205614 626 True 808 808 90.431 1 607 1 chr7B.!!$R1 606
21 TraesCS6B01G087100 chr7B 675065376 675065977 601 False 503 503 82.068 3155 3763 1 chr7B.!!$F1 608
22 TraesCS6B01G087100 chr3B 165783723 165784385 662 False 832 832 89.774 2 646 1 chr3B.!!$F1 644
23 TraesCS6B01G087100 chr3B 492649599 492650213 614 True 804 804 90.407 3155 3764 1 chr3B.!!$R1 609
24 TraesCS6B01G087100 chr3B 788074127 788074763 636 True 728 728 87.832 1 620 1 chr3B.!!$R3 619
25 TraesCS6B01G087100 chr3B 625714652 625715254 602 True 510 510 82.258 3155 3764 1 chr3B.!!$R2 609
26 TraesCS6B01G087100 chr5B 656709973 656710584 611 True 824 824 91.028 3155 3764 1 chr5B.!!$R2 609
27 TraesCS6B01G087100 chr2B 486766692 486767250 558 True 734 734 90.877 1 541 1 chr2B.!!$R1 540
28 TraesCS6B01G087100 chr7A 733389270 733389861 591 True 675 675 87.213 3158 3764 1 chr7A.!!$R1 606
29 TraesCS6B01G087100 chr7A 585312316 585312910 594 False 595 595 84.983 3169 3764 1 chr7A.!!$F1 595
30 TraesCS6B01G087100 chr2A 642659868 642660467 599 True 675 675 87.076 3154 3764 1 chr2A.!!$R2 610
31 TraesCS6B01G087100 chr4D 403142964 403143518 554 False 523 523 84.165 1 563 1 chr4D.!!$F1 562
32 TraesCS6B01G087100 chr3A 93081178 93081721 543 False 523 523 84.413 3 558 1 chr3A.!!$F1 555

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
607 663 1.072505 TGGGTGCGTCTTCTTTCCC 59.927 57.895 0.00 0.00 35.85 3.97 F
753 809 2.132762 CGTATACGTGGAGCCCATTTC 58.867 52.381 17.16 0.00 35.28 2.17 F
964 1020 3.075283 TGTTTTCCTAAGGATTCTGGCCA 59.925 43.478 4.71 4.71 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2025 2081 1.009552 TCCCCAATGCTCCCTTCTAGA 59.990 52.381 0.0 0.0 0.00 2.43 R
2750 2806 4.712337 AGATCACCGACTAATGGAGAGTTT 59.288 41.667 0.0 0.0 29.47 2.66 R
2998 3054 7.850935 AGGTCGTATATTTAGAAATGGAGGA 57.149 36.000 0.0 0.0 0.00 3.71 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
55 62 8.187480 CCATGTTGATATGTTTTGACGGATTTA 58.813 33.333 0.00 0.00 0.00 1.40
260 287 1.473258 TTATGGTGCATGGCAAGTCC 58.527 50.000 0.00 0.00 41.47 3.85
399 450 9.398170 CAATAGACATGACAACTTTTAACCAAG 57.602 33.333 0.00 0.00 0.00 3.61
458 512 3.961480 TTGAAGATCTCAAAGCGAGGA 57.039 42.857 0.00 0.00 41.21 3.71
607 663 1.072505 TGGGTGCGTCTTCTTTCCC 59.927 57.895 0.00 0.00 35.85 3.97
654 710 4.261447 CGTCCTTTTCTTTTGACCCGAAAT 60.261 41.667 0.00 0.00 0.00 2.17
662 718 6.642707 TCTTTTGACCCGAAATTAACACAT 57.357 33.333 0.00 0.00 0.00 3.21
663 719 6.442952 TCTTTTGACCCGAAATTAACACATG 58.557 36.000 0.00 0.00 0.00 3.21
664 720 3.840890 TGACCCGAAATTAACACATGC 57.159 42.857 0.00 0.00 0.00 4.06
665 721 3.149981 TGACCCGAAATTAACACATGCA 58.850 40.909 0.00 0.00 0.00 3.96
753 809 2.132762 CGTATACGTGGAGCCCATTTC 58.867 52.381 17.16 0.00 35.28 2.17
764 820 3.282885 GAGCCCATTTCTCCCTTTACAG 58.717 50.000 0.00 0.00 0.00 2.74
770 826 5.484715 CCATTTCTCCCTTTACAGAACGTA 58.515 41.667 0.00 0.00 0.00 3.57
789 845 6.861065 ACGTAACCCATATCTAGCAATTTG 57.139 37.500 0.00 0.00 0.00 2.32
791 847 7.224297 ACGTAACCCATATCTAGCAATTTGAT 58.776 34.615 0.00 0.00 0.00 2.57
793 849 8.873830 CGTAACCCATATCTAGCAATTTGATAG 58.126 37.037 14.15 14.15 37.68 2.08
794 850 9.726438 GTAACCCATATCTAGCAATTTGATAGT 57.274 33.333 18.39 10.37 37.59 2.12
796 852 9.646522 AACCCATATCTAGCAATTTGATAGTTT 57.353 29.630 18.39 11.45 37.59 2.66
797 853 9.289782 ACCCATATCTAGCAATTTGATAGTTTC 57.710 33.333 18.39 0.00 37.59 2.78
804 860 8.830580 TCTAGCAATTTGATAGTTTCTACATGC 58.169 33.333 18.39 0.00 37.59 4.06
805 861 7.395190 AGCAATTTGATAGTTTCTACATGCA 57.605 32.000 0.00 0.00 0.00 3.96
807 863 7.919091 AGCAATTTGATAGTTTCTACATGCATG 59.081 33.333 25.09 25.09 0.00 4.06
818 874 8.239314 AGTTTCTACATGCATGTAAAATGAGTG 58.761 33.333 33.05 21.47 42.20 3.51
819 875 7.920160 TTCTACATGCATGTAAAATGAGTGA 57.080 32.000 33.05 23.04 42.20 3.41
823 879 7.400599 ACATGCATGTAAAATGAGTGAATCT 57.599 32.000 30.50 0.00 39.68 2.40
824 880 8.510243 ACATGCATGTAAAATGAGTGAATCTA 57.490 30.769 30.50 0.00 39.68 1.98
825 881 8.400947 ACATGCATGTAAAATGAGTGAATCTAC 58.599 33.333 30.50 0.00 39.68 2.59
826 882 7.003939 TGCATGTAAAATGAGTGAATCTACG 57.996 36.000 0.00 0.00 0.00 3.51
827 883 5.904080 GCATGTAAAATGAGTGAATCTACGC 59.096 40.000 0.00 0.00 0.00 4.42
828 884 6.456853 GCATGTAAAATGAGTGAATCTACGCA 60.457 38.462 0.00 0.00 34.92 5.24
829 885 6.647212 TGTAAAATGAGTGAATCTACGCAG 57.353 37.500 0.00 0.00 33.95 5.18
831 887 7.317390 TGTAAAATGAGTGAATCTACGCAGTA 58.683 34.615 0.00 0.00 45.11 2.74
832 888 7.815549 TGTAAAATGAGTGAATCTACGCAGTAA 59.184 33.333 0.00 0.00 45.13 2.24
833 889 7.667043 AAAATGAGTGAATCTACGCAGTAAA 57.333 32.000 0.00 0.00 45.13 2.01
834 890 7.667043 AAATGAGTGAATCTACGCAGTAAAA 57.333 32.000 0.00 0.00 45.13 1.52
835 891 7.849804 AATGAGTGAATCTACGCAGTAAAAT 57.150 32.000 0.00 0.00 45.13 1.82
836 892 8.942338 AATGAGTGAATCTACGCAGTAAAATA 57.058 30.769 0.00 0.00 45.13 1.40
837 893 9.547753 AATGAGTGAATCTACGCAGTAAAATAT 57.452 29.630 0.00 0.00 45.13 1.28
838 894 8.352752 TGAGTGAATCTACGCAGTAAAATATG 57.647 34.615 0.00 0.00 45.13 1.78
839 895 7.979537 TGAGTGAATCTACGCAGTAAAATATGT 59.020 33.333 0.00 0.00 45.13 2.29
840 896 8.354011 AGTGAATCTACGCAGTAAAATATGTC 57.646 34.615 0.00 0.00 45.13 3.06
964 1020 3.075283 TGTTTTCCTAAGGATTCTGGCCA 59.925 43.478 4.71 4.71 0.00 5.36
2025 2081 3.370840 TTGCAGGGTATGAATGCTCTT 57.629 42.857 0.00 0.00 40.62 2.85
2998 3054 9.700831 AATAAAGGCTTGACCAGAATAATACTT 57.299 29.630 0.00 0.00 43.14 2.24
3064 3120 7.333423 ACAAACTACATGCAGATGTACGTAAAT 59.667 33.333 0.00 0.00 41.27 1.40
3563 3674 8.650490 AGTGGGAATCAACTTTGATATGTTTTT 58.350 29.630 4.89 0.00 46.60 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 5.892348 ACATGGGGTCTAGTTTTGAAGATT 58.108 37.500 0.00 0.00 0.00 2.40
200 227 4.020396 ACATGCACTTAAAATTGCCATGGA 60.020 37.500 18.40 0.00 38.00 3.41
399 450 8.655378 ATCGATATATTTCGGCGAAATTTTTC 57.345 30.769 41.55 33.90 41.64 2.29
450 504 5.975693 TTTCACCATTAAATTCCTCGCTT 57.024 34.783 0.00 0.00 0.00 4.68
451 505 5.619086 CGTTTTCACCATTAAATTCCTCGCT 60.619 40.000 0.00 0.00 0.00 4.93
458 512 7.891561 TGAAGATCCGTTTTCACCATTAAATT 58.108 30.769 0.00 0.00 0.00 1.82
628 684 2.292569 GGGTCAAAAGAAAAGGACGTCC 59.707 50.000 27.67 27.67 0.00 4.79
654 710 3.489398 GGAAACCAACGTGCATGTGTTAA 60.489 43.478 13.39 0.00 0.00 2.01
662 718 2.485795 GCCAGGAAACCAACGTGCA 61.486 57.895 0.00 0.00 0.00 4.57
663 719 2.335011 GCCAGGAAACCAACGTGC 59.665 61.111 0.00 0.00 0.00 5.34
664 720 1.720694 AACGCCAGGAAACCAACGTG 61.721 55.000 0.00 0.00 31.24 4.49
665 721 1.033202 AAACGCCAGGAAACCAACGT 61.033 50.000 0.00 0.00 31.88 3.99
753 809 3.007182 TGGGTTACGTTCTGTAAAGGGAG 59.993 47.826 0.00 0.00 44.36 4.30
764 820 7.225931 TCAAATTGCTAGATATGGGTTACGTTC 59.774 37.037 0.00 0.00 0.00 3.95
770 826 9.646522 AAACTATCAAATTGCTAGATATGGGTT 57.353 29.630 10.41 0.00 0.00 4.11
791 847 9.448438 ACTCATTTTACATGCATGTAGAAACTA 57.552 29.630 33.63 23.76 43.44 2.24
793 849 8.236586 TCACTCATTTTACATGCATGTAGAAAC 58.763 33.333 33.63 0.00 43.44 2.78
794 850 8.334263 TCACTCATTTTACATGCATGTAGAAA 57.666 30.769 33.63 30.93 43.44 2.52
795 851 7.920160 TCACTCATTTTACATGCATGTAGAA 57.080 32.000 32.70 32.70 43.44 2.10
796 852 7.920160 TTCACTCATTTTACATGCATGTAGA 57.080 32.000 32.09 27.40 43.44 2.59
797 853 8.618677 AGATTCACTCATTTTACATGCATGTAG 58.381 33.333 32.09 25.36 43.44 2.74
799 855 7.400599 AGATTCACTCATTTTACATGCATGT 57.599 32.000 33.20 33.20 44.48 3.21
800 856 7.585210 CGTAGATTCACTCATTTTACATGCATG 59.415 37.037 25.09 25.09 0.00 4.06
803 859 5.904080 GCGTAGATTCACTCATTTTACATGC 59.096 40.000 0.00 0.00 0.00 4.06
804 860 7.003939 TGCGTAGATTCACTCATTTTACATG 57.996 36.000 0.00 0.00 0.00 3.21
805 861 6.818644 ACTGCGTAGATTCACTCATTTTACAT 59.181 34.615 7.78 0.00 0.00 2.29
807 863 6.648725 ACTGCGTAGATTCACTCATTTTAC 57.351 37.500 7.78 0.00 0.00 2.01
809 865 7.667043 TTTACTGCGTAGATTCACTCATTTT 57.333 32.000 7.78 0.00 0.00 1.82
810 866 7.667043 TTTTACTGCGTAGATTCACTCATTT 57.333 32.000 7.78 0.00 0.00 2.32
812 868 8.982685 CATATTTTACTGCGTAGATTCACTCAT 58.017 33.333 7.78 0.00 0.00 2.90
813 869 7.979537 ACATATTTTACTGCGTAGATTCACTCA 59.020 33.333 7.78 0.00 0.00 3.41
814 870 8.354011 ACATATTTTACTGCGTAGATTCACTC 57.646 34.615 7.78 0.00 0.00 3.51
816 872 8.354011 AGACATATTTTACTGCGTAGATTCAC 57.646 34.615 7.78 0.00 0.00 3.18
900 956 1.123077 ACAGCTCTCACTGGAACACA 58.877 50.000 0.00 0.00 42.21 3.72
964 1020 6.204882 GCGTACCCTTATTTAGATGCAAAGAT 59.795 38.462 0.00 0.00 0.00 2.40
2025 2081 1.009552 TCCCCAATGCTCCCTTCTAGA 59.990 52.381 0.00 0.00 0.00 2.43
2750 2806 4.712337 AGATCACCGACTAATGGAGAGTTT 59.288 41.667 0.00 0.00 29.47 2.66
2998 3054 7.850935 AGGTCGTATATTTAGAAATGGAGGA 57.149 36.000 0.00 0.00 0.00 3.71
3563 3674 4.717233 ATCCTATTTTTCATGCACGCAA 57.283 36.364 0.00 0.00 0.00 4.85
3712 3827 6.155475 AGATCCAGTACAGAAGCTGAATAC 57.845 41.667 0.82 0.00 35.18 1.89


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

AutoCloner maintained by Alex Coulton.