Multiple sequence alignment - TraesCS3A01G165700

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 TraesCS3A01G165700 chr3A 100.000 2717 0 0 1 2717 170743171 170740455 0.000000e+00 5018.0
1 TraesCS3A01G165700 chr3A 75.879 597 102 20 43 627 419338646 419338080 1.600000e-67 267.0
2 TraesCS3A01G165700 chr3D 95.592 1157 43 3 734 1889 157474653 157475802 0.000000e+00 1847.0
3 TraesCS3A01G165700 chr3B 93.863 1108 47 12 783 1889 228736068 228737155 0.000000e+00 1650.0
4 TraesCS3A01G165700 chr7A 97.710 786 14 3 1929 2714 690059572 690058791 0.000000e+00 1349.0
5 TraesCS3A01G165700 chr7A 77.641 729 123 18 7 732 558086032 558085341 9.060000e-110 407.0
6 TraesCS3A01G165700 chr7A 78.409 440 90 5 18 456 202530203 202529768 5.730000e-72 281.0
7 TraesCS3A01G165700 chr4A 94.686 828 29 9 1893 2714 722504555 722503737 0.000000e+00 1271.0
8 TraesCS3A01G165700 chr4A 92.788 832 48 8 1889 2714 42836830 42836005 0.000000e+00 1194.0
9 TraesCS3A01G165700 chr2B 94.451 829 34 9 1891 2714 51941802 51940981 0.000000e+00 1266.0
10 TraesCS3A01G165700 chr2B 81.469 572 92 8 109 679 596895136 596895694 8.870000e-125 457.0
11 TraesCS3A01G165700 chr6D 94.231 832 40 7 1889 2714 14980718 14979889 0.000000e+00 1264.0
12 TraesCS3A01G165700 chr6D 80.655 672 112 11 18 677 144100775 144100110 3.120000e-139 505.0
13 TraesCS3A01G165700 chr5D 93.735 830 39 7 1891 2714 525387620 525386798 0.000000e+00 1232.0
14 TraesCS3A01G165700 chr5D 77.893 484 98 9 198 677 29646520 29646998 2.650000e-75 292.0
15 TraesCS3A01G165700 chr2A 93.873 816 42 6 1904 2714 633240174 633239362 0.000000e+00 1223.0
16 TraesCS3A01G165700 chr2A 92.995 828 45 7 1893 2714 721656436 721657256 0.000000e+00 1195.0
17 TraesCS3A01G165700 chr2A 81.915 564 80 14 3 555 608942645 608942093 8.870000e-125 457.0
18 TraesCS3A01G165700 chr5B 94.074 810 35 7 1910 2714 670711737 670712538 0.000000e+00 1218.0
19 TraesCS3A01G165700 chr7B 81.058 718 115 16 1 715 337157130 337157829 1.100000e-153 553.0
20 TraesCS3A01G165700 chr7D 81.153 711 100 18 1 687 454069018 454069718 8.560000e-150 540.0
21 TraesCS3A01G165700 chr7D 81.185 675 112 10 59 731 619045525 619044864 1.850000e-146 529.0
22 TraesCS3A01G165700 chr7D 80.342 702 121 11 1 690 543085833 543085137 1.440000e-142 516.0
23 TraesCS3A01G165700 chr7D 79.515 742 120 17 7 731 575754716 575755442 1.450000e-137 499.0
24 TraesCS3A01G165700 chr6A 79.972 704 109 23 4 694 585085929 585085245 8.740000e-135 490.0
25 TraesCS3A01G165700 chr1A 81.614 533 92 6 150 680 451359281 451358753 1.160000e-118 436.0
26 TraesCS3A01G165700 chr5A 80.119 503 87 6 58 549 340412954 340413454 1.990000e-96 363.0
27 TraesCS3A01G165700 chr5A 84.644 267 41 0 1 267 451250499 451250765 1.600000e-67 267.0
28 TraesCS3A01G165700 chr5A 77.465 142 32 0 590 731 275969781 275969922 4.820000e-13 86.1


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 TraesCS3A01G165700 chr3A 170740455 170743171 2716 True 5018 5018 100.000 1 2717 1 chr3A.!!$R1 2716
1 TraesCS3A01G165700 chr3A 419338080 419338646 566 True 267 267 75.879 43 627 1 chr3A.!!$R2 584
2 TraesCS3A01G165700 chr3D 157474653 157475802 1149 False 1847 1847 95.592 734 1889 1 chr3D.!!$F1 1155
3 TraesCS3A01G165700 chr3B 228736068 228737155 1087 False 1650 1650 93.863 783 1889 1 chr3B.!!$F1 1106
4 TraesCS3A01G165700 chr7A 690058791 690059572 781 True 1349 1349 97.710 1929 2714 1 chr7A.!!$R3 785
5 TraesCS3A01G165700 chr7A 558085341 558086032 691 True 407 407 77.641 7 732 1 chr7A.!!$R2 725
6 TraesCS3A01G165700 chr4A 722503737 722504555 818 True 1271 1271 94.686 1893 2714 1 chr4A.!!$R2 821
7 TraesCS3A01G165700 chr4A 42836005 42836830 825 True 1194 1194 92.788 1889 2714 1 chr4A.!!$R1 825
8 TraesCS3A01G165700 chr2B 51940981 51941802 821 True 1266 1266 94.451 1891 2714 1 chr2B.!!$R1 823
9 TraesCS3A01G165700 chr2B 596895136 596895694 558 False 457 457 81.469 109 679 1 chr2B.!!$F1 570
10 TraesCS3A01G165700 chr6D 14979889 14980718 829 True 1264 1264 94.231 1889 2714 1 chr6D.!!$R1 825
11 TraesCS3A01G165700 chr6D 144100110 144100775 665 True 505 505 80.655 18 677 1 chr6D.!!$R2 659
12 TraesCS3A01G165700 chr5D 525386798 525387620 822 True 1232 1232 93.735 1891 2714 1 chr5D.!!$R1 823
13 TraesCS3A01G165700 chr2A 633239362 633240174 812 True 1223 1223 93.873 1904 2714 1 chr2A.!!$R2 810
14 TraesCS3A01G165700 chr2A 721656436 721657256 820 False 1195 1195 92.995 1893 2714 1 chr2A.!!$F1 821
15 TraesCS3A01G165700 chr2A 608942093 608942645 552 True 457 457 81.915 3 555 1 chr2A.!!$R1 552
16 TraesCS3A01G165700 chr5B 670711737 670712538 801 False 1218 1218 94.074 1910 2714 1 chr5B.!!$F1 804
17 TraesCS3A01G165700 chr7B 337157130 337157829 699 False 553 553 81.058 1 715 1 chr7B.!!$F1 714
18 TraesCS3A01G165700 chr7D 454069018 454069718 700 False 540 540 81.153 1 687 1 chr7D.!!$F1 686
19 TraesCS3A01G165700 chr7D 619044864 619045525 661 True 529 529 81.185 59 731 1 chr7D.!!$R2 672
20 TraesCS3A01G165700 chr7D 543085137 543085833 696 True 516 516 80.342 1 690 1 chr7D.!!$R1 689
21 TraesCS3A01G165700 chr7D 575754716 575755442 726 False 499 499 79.515 7 731 1 chr7D.!!$F2 724
22 TraesCS3A01G165700 chr6A 585085245 585085929 684 True 490 490 79.972 4 694 1 chr6A.!!$R1 690
23 TraesCS3A01G165700 chr1A 451358753 451359281 528 True 436 436 81.614 150 680 1 chr1A.!!$R1 530
24 TraesCS3A01G165700 chr5A 340412954 340413454 500 False 363 363 80.119 58 549 1 chr5A.!!$F2 491

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
284 313 0.032540 CCTTTGCAGCCTTCGCTTTT 59.967 50.0 0.0 0.0 45.55 2.27 F
514 569 0.732571 AAACAATGCGGGATGCTACG 59.267 50.0 0.0 0.0 46.63 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1660 1734 1.155042 GGCTCTGCTTTCTGACACAG 58.845 55.0 0.0 0.0 0.0 3.66 R
1878 1952 3.114065 CGTAGCCGTTATCCAGAACTTC 58.886 50.0 0.0 0.0 0.0 3.01 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
24 25 3.350492 CGAGCGACGTCGAAGAAC 58.650 61.111 39.74 21.95 42.85 3.01
52 53 1.796459 GAAGTGTGGTGTCGCGTTAAT 59.204 47.619 5.77 0.00 0.00 1.40
101 106 1.360192 GTTTGCGAGTTGCTTGGCT 59.640 52.632 3.50 0.00 46.63 4.75
153 158 1.435925 CATGGCGCCGTCAGTACTA 59.564 57.895 20.90 0.00 0.00 1.82
260 289 1.649664 CCAGACGCTTCCTCATCTTG 58.350 55.000 0.00 0.00 0.00 3.02
284 313 0.032540 CCTTTGCAGCCTTCGCTTTT 59.967 50.000 0.00 0.00 45.55 2.27
370 403 0.987294 CACCTCCACACCTCCATCTT 59.013 55.000 0.00 0.00 0.00 2.40
389 422 2.126031 GACAGGTTCTCCGACGGC 60.126 66.667 9.66 0.00 39.05 5.68
394 427 2.126031 GTTCTCCGACGGCTCCAC 60.126 66.667 9.66 0.00 0.00 4.02
421 455 1.990614 GGCGGAGGGAAGAAGAGGT 60.991 63.158 0.00 0.00 0.00 3.85
453 497 1.485066 GAGTAGGAATTGGGCGGAGAA 59.515 52.381 0.00 0.00 0.00 2.87
454 498 1.209747 AGTAGGAATTGGGCGGAGAAC 59.790 52.381 0.00 0.00 0.00 3.01
456 500 2.112815 GGAATTGGGCGGAGAACGG 61.113 63.158 0.00 0.00 44.51 4.44
457 501 1.078708 GAATTGGGCGGAGAACGGA 60.079 57.895 0.00 0.00 44.51 4.69
458 502 1.078426 AATTGGGCGGAGAACGGAG 60.078 57.895 0.00 0.00 44.51 4.63
459 503 2.536997 AATTGGGCGGAGAACGGAGG 62.537 60.000 0.00 0.00 44.51 4.30
474 518 1.623811 CGGAGGGGAGTGAAAGAAGAA 59.376 52.381 0.00 0.00 0.00 2.52
481 525 4.202367 GGGGAGTGAAAGAAGAAAGTGAGA 60.202 45.833 0.00 0.00 0.00 3.27
514 569 0.732571 AAACAATGCGGGATGCTACG 59.267 50.000 0.00 0.00 46.63 3.51
551 614 2.201210 CCTTTTGGGTGGGCCAGT 59.799 61.111 6.40 0.00 36.17 4.00
559 623 2.597510 GTGGGCCAGTGGGTGAAC 60.598 66.667 6.40 0.00 36.17 3.18
563 627 1.454847 GGCCAGTGGGTGAACAACA 60.455 57.895 12.15 0.00 36.17 3.33
571 635 2.162809 GTGGGTGAACAACAACGTTTCT 59.837 45.455 0.00 0.00 37.02 2.52
582 646 3.399330 ACAACGTTTCTCATGTTCGGAT 58.601 40.909 0.00 0.00 31.67 4.18
599 663 3.585732 TCGGATTCCTGTAAACCTTTCCT 59.414 43.478 0.30 0.00 0.00 3.36
657 722 1.892862 CTCTCCGCGGACCGATACT 60.893 63.158 27.28 0.00 40.02 2.12
697 767 1.137459 CGTGATCCGAACGATTGCGA 61.137 55.000 0.00 0.00 43.68 5.10
717 787 1.134560 AGAGGTTTACGAGTCGGCATC 59.865 52.381 18.30 10.70 0.00 3.91
732 802 0.871057 GCATCGAAGATGCCCTAAGC 59.129 55.000 20.69 0.00 45.12 3.09
738 808 6.066514 ATCGAAGATGCCCTAAGCGTACAT 62.067 45.833 0.00 0.00 45.12 2.29
757 827 6.256539 CGTACATAGCTCAACAACATCTGATT 59.743 38.462 0.00 0.00 0.00 2.57
764 834 5.514204 GCTCAACAACATCTGATTAATGTGC 59.486 40.000 0.00 0.00 37.42 4.57
767 837 5.314923 ACAACATCTGATTAATGTGCACC 57.685 39.130 15.69 0.00 37.42 5.01
829 902 1.202463 CCATCTCAATCGCGAGTCCTT 60.202 52.381 16.66 0.00 34.46 3.36
830 903 2.123342 CATCTCAATCGCGAGTCCTTC 58.877 52.381 16.66 0.00 34.46 3.46
831 904 1.464734 TCTCAATCGCGAGTCCTTCT 58.535 50.000 16.66 0.00 34.46 2.85
916 989 4.772886 ATAATACCTTCGCCTTCCAAGT 57.227 40.909 0.00 0.00 0.00 3.16
924 997 0.875059 CGCCTTCCAAGTTCCAAGTC 59.125 55.000 0.00 0.00 0.00 3.01
925 998 1.813862 CGCCTTCCAAGTTCCAAGTCA 60.814 52.381 0.00 0.00 0.00 3.41
926 999 1.882623 GCCTTCCAAGTTCCAAGTCAG 59.117 52.381 0.00 0.00 0.00 3.51
927 1000 2.749800 GCCTTCCAAGTTCCAAGTCAGT 60.750 50.000 0.00 0.00 0.00 3.41
1047 1121 4.077184 TCCGCCGAAGCCGTGAAT 62.077 61.111 0.00 0.00 34.57 2.57
1157 1231 2.752238 AGGCGTCCTCGAGGTCAG 60.752 66.667 30.17 21.86 39.71 3.51
1440 1514 3.050275 GACGTGGGCAACTGCTCC 61.050 66.667 0.00 0.93 41.95 4.70
1736 1810 7.551035 AGTGAAGAACTATCTGATGAAATGC 57.449 36.000 0.00 0.00 37.36 3.56
1871 1945 2.282555 CGATCTGTATGTTTCCGCTGTG 59.717 50.000 0.00 0.00 0.00 3.66
1878 1952 1.236616 TGTTTCCGCTGTGCTCCATG 61.237 55.000 0.00 0.00 0.00 3.66
2019 2094 1.118356 GGCCGGTGGAGATGAGAGAT 61.118 60.000 1.90 0.00 0.00 2.75
2087 2163 2.100749 CCCAAGTTTCCCAAGTGTGTTC 59.899 50.000 0.00 0.00 0.00 3.18
2092 2168 5.072040 AGTTTCCCAAGTGTGTTCTTTTG 57.928 39.130 0.00 0.00 0.00 2.44
2203 2279 2.951642 CACAGTGGCTTCTCTTTTTCCA 59.048 45.455 0.00 0.00 0.00 3.53
2596 2685 3.916172 TCGATTGAGTTTAACCGAAGTCG 59.084 43.478 0.00 0.00 39.44 4.18
2599 2688 2.129607 TGAGTTTAACCGAAGTCGCAC 58.870 47.619 0.00 0.00 38.18 5.34
2714 2803 9.590451 TTCTTCTTTCTTTACTTTTCTCGTGTA 57.410 29.630 0.00 0.00 0.00 2.90
2715 2804 9.245962 TCTTCTTTCTTTACTTTTCTCGTGTAG 57.754 33.333 0.00 0.00 0.00 2.74
2716 2805 9.245962 CTTCTTTCTTTACTTTTCTCGTGTAGA 57.754 33.333 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.717707 CACTTCTTGGAGTGTTCTTCGA 58.282 45.455 1.02 0.00 41.62 3.71
52 53 4.724074 ACGGTTCCTTACATCGTTGATA 57.276 40.909 0.00 0.00 0.00 2.15
101 106 1.742761 AGCCTTCGTACTACTACGCA 58.257 50.000 0.00 0.00 44.64 5.24
260 289 1.301677 CGAAGGCTGCAAAGGAGGAC 61.302 60.000 0.50 0.00 0.00 3.85
284 313 1.573932 CAGCAAAATCACCGCGTCA 59.426 52.632 4.92 0.00 0.00 4.35
370 403 1.663739 CCGTCGGAGAACCTGTCAA 59.336 57.895 4.91 0.00 39.69 3.18
415 448 3.049344 ACTCTTTTCTCCCACACCTCTT 58.951 45.455 0.00 0.00 0.00 2.85
416 449 2.695585 ACTCTTTTCTCCCACACCTCT 58.304 47.619 0.00 0.00 0.00 3.69
421 455 5.514834 CCAATTCCTACTCTTTTCTCCCACA 60.515 44.000 0.00 0.00 0.00 4.17
453 497 0.977395 CTTCTTTCACTCCCCTCCGT 59.023 55.000 0.00 0.00 0.00 4.69
454 498 1.267121 TCTTCTTTCACTCCCCTCCG 58.733 55.000 0.00 0.00 0.00 4.63
455 499 3.073209 ACTTTCTTCTTTCACTCCCCTCC 59.927 47.826 0.00 0.00 0.00 4.30
456 500 4.068599 CACTTTCTTCTTTCACTCCCCTC 58.931 47.826 0.00 0.00 0.00 4.30
457 501 3.716872 TCACTTTCTTCTTTCACTCCCCT 59.283 43.478 0.00 0.00 0.00 4.79
458 502 4.068599 CTCACTTTCTTCTTTCACTCCCC 58.931 47.826 0.00 0.00 0.00 4.81
459 503 4.962155 TCTCACTTTCTTCTTTCACTCCC 58.038 43.478 0.00 0.00 0.00 4.30
460 504 5.848406 TCTCTCACTTTCTTCTTTCACTCC 58.152 41.667 0.00 0.00 0.00 3.85
461 505 7.961325 AATCTCTCACTTTCTTCTTTCACTC 57.039 36.000 0.00 0.00 0.00 3.51
462 506 8.744568 AAAATCTCTCACTTTCTTCTTTCACT 57.255 30.769 0.00 0.00 0.00 3.41
474 518 2.094182 TCCGCGCTAAAATCTCTCACTT 60.094 45.455 5.56 0.00 0.00 3.16
481 525 3.758300 CATTGTTTCCGCGCTAAAATCT 58.242 40.909 5.56 0.00 0.00 2.40
551 614 2.420722 GAGAAACGTTGTTGTTCACCCA 59.579 45.455 0.00 0.00 0.00 4.51
557 621 4.339429 CGAACATGAGAAACGTTGTTGTT 58.661 39.130 0.00 7.82 0.00 2.83
559 623 3.001838 TCCGAACATGAGAAACGTTGTTG 59.998 43.478 0.00 0.00 0.00 3.33
563 627 3.435671 GGAATCCGAACATGAGAAACGTT 59.564 43.478 0.00 0.00 0.00 3.99
571 635 4.019681 AGGTTTACAGGAATCCGAACATGA 60.020 41.667 0.00 0.00 32.79 3.07
582 646 4.961438 ACGTAGGAAAGGTTTACAGGAA 57.039 40.909 0.00 0.00 0.00 3.36
599 663 2.285756 CCGCAAACTGAAGACAAACGTA 59.714 45.455 0.00 0.00 0.00 3.57
657 722 3.865164 CGAAAGTCATCCAATGTCGATCA 59.135 43.478 0.00 0.00 29.73 2.92
691 761 2.731341 CGACTCGTAAACCTCTCGCAAT 60.731 50.000 0.00 0.00 0.00 3.56
697 767 1.134560 GATGCCGACTCGTAAACCTCT 59.865 52.381 0.00 0.00 0.00 3.69
717 787 1.202371 TGTACGCTTAGGGCATCTTCG 60.202 52.381 0.00 0.00 41.91 3.79
732 802 5.102313 TCAGATGTTGTTGAGCTATGTACG 58.898 41.667 0.00 0.00 0.00 3.67
738 808 7.414429 GCACATTAATCAGATGTTGTTGAGCTA 60.414 37.037 0.00 0.00 35.64 3.32
757 827 2.328856 CGCCCAACGGTGCACATTA 61.329 57.895 20.43 0.00 38.44 1.90
829 902 0.321346 TGGCTCGCTGTCAAATGAGA 59.679 50.000 0.00 0.00 0.00 3.27
830 903 1.376543 ATGGCTCGCTGTCAAATGAG 58.623 50.000 0.00 0.00 32.16 2.90
831 904 1.469703 CAATGGCTCGCTGTCAAATGA 59.530 47.619 0.00 0.00 32.16 2.57
916 989 2.965831 ACTGCTGAGTACTGACTTGGAA 59.034 45.455 0.00 0.00 35.45 3.53
924 997 3.584406 ACTGCTTACTGCTGAGTACTG 57.416 47.619 0.00 0.00 42.27 2.74
925 998 4.608948 AAACTGCTTACTGCTGAGTACT 57.391 40.909 0.00 0.00 42.27 2.73
926 999 5.674933 AAAAACTGCTTACTGCTGAGTAC 57.325 39.130 0.00 0.00 42.27 2.73
1036 1110 1.464997 GAACTGGTGATTCACGGCTTC 59.535 52.381 10.56 6.89 34.83 3.86
1047 1121 1.331399 TGACCACGGTGAACTGGTGA 61.331 55.000 10.28 0.00 41.09 4.02
1254 1328 3.414700 GCGTCGCACCTGTGGAAG 61.415 66.667 13.44 0.00 0.00 3.46
1660 1734 1.155042 GGCTCTGCTTTCTGACACAG 58.845 55.000 0.00 0.00 0.00 3.66
1758 1832 9.662947 AAAAGGAAATATAGTAGTACCACACAC 57.337 33.333 0.00 0.00 0.00 3.82
1878 1952 3.114065 CGTAGCCGTTATCCAGAACTTC 58.886 50.000 0.00 0.00 0.00 3.01
1927 2001 6.706270 ACACGATTGTTATTGACTGAGACTTT 59.294 34.615 0.00 0.00 28.43 2.66
2019 2094 7.441836 GCCCAGAAGAAAAATAAAAGAAAGGA 58.558 34.615 0.00 0.00 0.00 3.36
2087 2163 7.206687 TGTAGGCTGACAAAAATAACCAAAAG 58.793 34.615 0.00 0.00 0.00 2.27
2092 2168 6.569179 TCTTGTAGGCTGACAAAAATAACC 57.431 37.500 0.00 0.00 38.80 2.85
2414 2501 8.534778 GCTCGAAATTTGGAAAATATGCTAAAG 58.465 33.333 4.38 0.00 0.00 1.85
2596 2685 3.040147 ACGGCCATATATGTGTAGTGC 57.960 47.619 11.73 6.43 0.00 4.40
2599 2688 6.752351 GTGATCTAACGGCCATATATGTGTAG 59.248 42.308 11.73 5.76 0.00 2.74


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

AutoCloner maintained by Alex Coulton.