Multiple sequence alignment - TraesCS7B01G261400

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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 TraesCS7B01G261400 chr7B 100.000 3755 0 0 1 3755 482078345 482074591 0.000000e+00 6935
1 TraesCS7B01G261400 chr7B 90.604 3725 329 13 48 3755 481856891 481853171 0.000000e+00 4920
2 TraesCS7B01G261400 chr7B 83.513 2881 457 14 49 2917 482684530 482687404 0.000000e+00 2673
3 TraesCS7B01G261400 chr7B 80.876 434 77 5 2963 3392 482489616 482490047 1.670000e-88 337
4 TraesCS7B01G261400 chr7D 95.767 3685 118 16 44 3709 459790071 459786406 0.000000e+00 5906
5 TraesCS7B01G261400 chr7D 90.323 3617 314 16 56 3649 459752630 459749027 0.000000e+00 4708
6 TraesCS7B01G261400 chr7D 83.438 2880 455 18 52 2917 460279887 460282758 0.000000e+00 2656
7 TraesCS7B01G261400 chr7D 81.422 436 75 5 2963 3393 460110166 460110600 5.970000e-93 351
8 TraesCS7B01G261400 chr7A 91.369 2943 230 14 826 3754 539928022 539930954 0.000000e+00 4006
9 TraesCS7B01G261400 chr7A 83.050 2885 463 22 52 2920 539325806 539322932 0.000000e+00 2595
10 TraesCS7B01G261400 chr7A 94.337 777 39 4 2803 3574 539849420 539850196 0.000000e+00 1186
11 TraesCS7B01G261400 chr7A 81.892 740 132 2 45 783 539927121 539927859 1.150000e-174 623
12 TraesCS7B01G261400 chr7A 80.631 444 78 6 2957 3393 539322828 539322386 1.670000e-88 337
13 TraesCS7B01G261400 chr7A 80.000 450 83 6 2958 3403 539446518 539446072 3.620000e-85 326
14 TraesCS7B01G261400 chr2B 79.413 2895 540 45 73 2929 784188803 784191679 0.000000e+00 1993
15 TraesCS7B01G261400 chr2B 78.556 2840 567 26 119 2922 798128491 798131324 0.000000e+00 1832
16 TraesCS7B01G261400 chr2D 78.210 2827 574 29 119 2909 638724388 638727208 0.000000e+00 1770
17 TraesCS7B01G261400 chr2A 87.755 98 12 0 49 146 208167086 208167183 8.520000e-22 115


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 TraesCS7B01G261400 chr7B 482074591 482078345 3754 True 6935.0 6935 100.0000 1 3755 1 chr7B.!!$R2 3754
1 TraesCS7B01G261400 chr7B 481853171 481856891 3720 True 4920.0 4920 90.6040 48 3755 1 chr7B.!!$R1 3707
2 TraesCS7B01G261400 chr7B 482684530 482687404 2874 False 2673.0 2673 83.5130 49 2917 1 chr7B.!!$F2 2868
3 TraesCS7B01G261400 chr7D 459786406 459790071 3665 True 5906.0 5906 95.7670 44 3709 1 chr7D.!!$R2 3665
4 TraesCS7B01G261400 chr7D 459749027 459752630 3603 True 4708.0 4708 90.3230 56 3649 1 chr7D.!!$R1 3593
5 TraesCS7B01G261400 chr7D 460279887 460282758 2871 False 2656.0 2656 83.4380 52 2917 1 chr7D.!!$F2 2865
6 TraesCS7B01G261400 chr7A 539927121 539930954 3833 False 2314.5 4006 86.6305 45 3754 2 chr7A.!!$F2 3709
7 TraesCS7B01G261400 chr7A 539322386 539325806 3420 True 1466.0 2595 81.8405 52 3393 2 chr7A.!!$R2 3341
8 TraesCS7B01G261400 chr7A 539849420 539850196 776 False 1186.0 1186 94.3370 2803 3574 1 chr7A.!!$F1 771
9 TraesCS7B01G261400 chr2B 784188803 784191679 2876 False 1993.0 1993 79.4130 73 2929 1 chr2B.!!$F1 2856
10 TraesCS7B01G261400 chr2B 798128491 798131324 2833 False 1832.0 1832 78.5560 119 2922 1 chr2B.!!$F2 2803
11 TraesCS7B01G261400 chr2D 638724388 638727208 2820 False 1770.0 1770 78.2100 119 2909 1 chr2D.!!$F1 2790

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
46 47 0.630673 CCTCACCATCCCAATTCCCA 59.369 55.0 0.00 0.0 0.00 4.37 F
458 459 0.757188 AGCTGAGTGGAGGTATCCCG 60.757 60.0 0.00 0.0 46.04 5.14 F
1635 1792 0.547712 TCCCAGGAGCTTTAGCAGGT 60.548 55.0 4.33 0.0 45.16 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1259 1416 3.220940 TGTGTGCAATTGGTCAATGAGA 58.779 40.909 7.72 0.0 0.00 3.27 R
2126 2283 1.102978 AAATGGCACCCGTAGCAATC 58.897 50.000 0.00 0.0 0.00 2.67 R
2859 3041 0.038166 CTTGGCCCCACTAAGCTTGA 59.962 55.000 9.86 0.0 29.31 3.02 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
20 21 3.921969 CATCACAGATTCAAGCGTCTC 57.078 47.619 0.00 0.00 0.00 3.36
21 22 3.256558 CATCACAGATTCAAGCGTCTCA 58.743 45.455 0.00 0.00 0.00 3.27
22 23 3.385193 TCACAGATTCAAGCGTCTCAA 57.615 42.857 0.00 0.00 0.00 3.02
23 24 3.930336 TCACAGATTCAAGCGTCTCAAT 58.070 40.909 0.00 0.00 0.00 2.57
24 25 3.928992 TCACAGATTCAAGCGTCTCAATC 59.071 43.478 0.00 0.00 0.00 2.67
25 26 3.681417 CACAGATTCAAGCGTCTCAATCA 59.319 43.478 10.95 0.00 0.00 2.57
26 27 4.152938 CACAGATTCAAGCGTCTCAATCAA 59.847 41.667 10.95 0.00 0.00 2.57
27 28 4.153117 ACAGATTCAAGCGTCTCAATCAAC 59.847 41.667 10.95 0.00 0.00 3.18
28 29 3.686726 AGATTCAAGCGTCTCAATCAACC 59.313 43.478 10.95 0.00 0.00 3.77
29 30 2.839486 TCAAGCGTCTCAATCAACCT 57.161 45.000 0.00 0.00 0.00 3.50
30 31 2.688507 TCAAGCGTCTCAATCAACCTC 58.311 47.619 0.00 0.00 0.00 3.85
31 32 2.037121 TCAAGCGTCTCAATCAACCTCA 59.963 45.455 0.00 0.00 0.00 3.86
32 33 2.086054 AGCGTCTCAATCAACCTCAC 57.914 50.000 0.00 0.00 0.00 3.51
33 34 1.079503 GCGTCTCAATCAACCTCACC 58.920 55.000 0.00 0.00 0.00 4.02
34 35 1.608025 GCGTCTCAATCAACCTCACCA 60.608 52.381 0.00 0.00 0.00 4.17
35 36 2.936993 GCGTCTCAATCAACCTCACCAT 60.937 50.000 0.00 0.00 0.00 3.55
36 37 2.932614 CGTCTCAATCAACCTCACCATC 59.067 50.000 0.00 0.00 0.00 3.51
37 38 3.274288 GTCTCAATCAACCTCACCATCC 58.726 50.000 0.00 0.00 0.00 3.51
38 39 2.239654 TCTCAATCAACCTCACCATCCC 59.760 50.000 0.00 0.00 0.00 3.85
39 40 1.991813 TCAATCAACCTCACCATCCCA 59.008 47.619 0.00 0.00 0.00 4.37
40 41 2.378208 TCAATCAACCTCACCATCCCAA 59.622 45.455 0.00 0.00 0.00 4.12
41 42 3.011595 TCAATCAACCTCACCATCCCAAT 59.988 43.478 0.00 0.00 0.00 3.16
42 43 3.763557 ATCAACCTCACCATCCCAATT 57.236 42.857 0.00 0.00 0.00 2.32
43 44 3.085952 TCAACCTCACCATCCCAATTC 57.914 47.619 0.00 0.00 0.00 2.17
44 45 2.102578 CAACCTCACCATCCCAATTCC 58.897 52.381 0.00 0.00 0.00 3.01
45 46 0.631212 ACCTCACCATCCCAATTCCC 59.369 55.000 0.00 0.00 0.00 3.97
46 47 0.630673 CCTCACCATCCCAATTCCCA 59.369 55.000 0.00 0.00 0.00 4.37
53 54 2.459644 CATCCCAATTCCCAAGCTTCA 58.540 47.619 0.00 0.00 0.00 3.02
117 118 4.436448 GCAGCAAGAGACACGCGC 62.436 66.667 5.73 0.00 0.00 6.86
210 211 2.549754 ACTTTCCTCACAAGAATGCACG 59.450 45.455 0.00 0.00 0.00 5.34
306 307 6.214191 TCAGCTCAAACTATCTTAGTGGAG 57.786 41.667 10.16 10.16 40.84 3.86
423 424 2.169978 TGTTCAGATATGCAGCAGCTCT 59.830 45.455 0.00 2.23 42.74 4.09
443 444 1.283793 CTTGGGTCGCAACAAGCTG 59.716 57.895 0.00 0.00 42.61 4.24
458 459 0.757188 AGCTGAGTGGAGGTATCCCG 60.757 60.000 0.00 0.00 46.04 5.14
489 490 2.811317 CGCTCCGCAACCTCTCAC 60.811 66.667 0.00 0.00 0.00 3.51
492 493 1.016653 GCTCCGCAACCTCTCACTTC 61.017 60.000 0.00 0.00 0.00 3.01
499 500 3.526534 GCAACCTCTCACTTCTACATCC 58.473 50.000 0.00 0.00 0.00 3.51
542 543 1.746615 CATCCCGACTGCACTTGGG 60.747 63.158 11.57 11.57 43.36 4.12
661 662 6.734137 TGGACTTAACAAACAATCACATGAC 58.266 36.000 0.00 0.00 0.00 3.06
665 666 2.582052 ACAAACAATCACATGACCGGT 58.418 42.857 6.92 6.92 0.00 5.28
720 728 7.552687 TGTCGCTTCAAAAATTATCACTAGGAT 59.447 33.333 0.00 0.00 40.14 3.24
1020 1177 4.036734 GGCATGGGTATGAACATACTTGTG 59.963 45.833 19.71 16.23 42.42 3.33
1065 1222 5.070685 GGATATACCCTTCCAAACATCCAC 58.929 45.833 0.00 0.00 32.65 4.02
1095 1252 3.733443 ATGCAAGGAAACAACTTCACC 57.267 42.857 0.00 0.00 35.55 4.02
1114 1271 2.175202 CCGGACAAATCCCCATTTCAA 58.825 47.619 0.00 0.00 42.83 2.69
1259 1416 6.072199 AGCAGGAGATTGGTCTTTCTTATT 57.928 37.500 0.00 0.00 33.97 1.40
1635 1792 0.547712 TCCCAGGAGCTTTAGCAGGT 60.548 55.000 4.33 0.00 45.16 4.00
1652 1809 4.290969 GCAGGTTGCAAGAAGTTAGAAAC 58.709 43.478 0.00 0.00 44.26 2.78
2126 2283 1.323534 GAAGTTATGTACCAGCACGCG 59.676 52.381 3.53 3.53 0.00 6.01
2460 2623 5.357032 AGTTTTCAAACTCAATCAACTCGGT 59.643 36.000 0.00 0.00 45.65 4.69
2859 3041 7.607991 ACAATTCTTCGGACATTCATACTTCTT 59.392 33.333 0.00 0.00 0.00 2.52
3176 3429 5.576563 TGAGGAGATTCTAGACCCTAGAG 57.423 47.826 0.00 0.00 0.00 2.43
3246 3499 0.740737 CGGGAAACTCATCCAATGGC 59.259 55.000 0.00 0.00 41.55 4.40
3335 3594 2.290641 CGGCCAACTATGCAGGAAATAC 59.709 50.000 2.24 0.00 0.00 1.89
3562 3827 3.882888 CACGGCATCAATGTAAACCCTAT 59.117 43.478 0.00 0.00 0.00 2.57
3687 3964 3.326836 AGCTTTCCTGTCTTACTCTGC 57.673 47.619 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.599730 TGAGACGCTTGAATCTGTGAT 57.400 42.857 0.00 0.00 0.00 3.06
3 4 3.681417 TGATTGAGACGCTTGAATCTGTG 59.319 43.478 0.00 0.00 0.00 3.66
4 5 3.930336 TGATTGAGACGCTTGAATCTGT 58.070 40.909 0.00 0.00 0.00 3.41
6 7 3.686726 GGTTGATTGAGACGCTTGAATCT 59.313 43.478 0.00 0.00 0.00 2.40
7 8 3.686726 AGGTTGATTGAGACGCTTGAATC 59.313 43.478 0.00 0.00 0.00 2.52
8 9 3.679389 AGGTTGATTGAGACGCTTGAAT 58.321 40.909 0.00 0.00 0.00 2.57
9 10 3.067106 GAGGTTGATTGAGACGCTTGAA 58.933 45.455 0.00 0.00 0.00 2.69
11 12 2.158449 GTGAGGTTGATTGAGACGCTTG 59.842 50.000 0.00 0.00 0.00 4.01
12 13 2.417719 GTGAGGTTGATTGAGACGCTT 58.582 47.619 0.00 0.00 0.00 4.68
14 15 1.079503 GGTGAGGTTGATTGAGACGC 58.920 55.000 0.00 0.00 0.00 5.19
15 16 2.455674 TGGTGAGGTTGATTGAGACG 57.544 50.000 0.00 0.00 0.00 4.18
16 17 3.274288 GGATGGTGAGGTTGATTGAGAC 58.726 50.000 0.00 0.00 0.00 3.36
17 18 2.239654 GGGATGGTGAGGTTGATTGAGA 59.760 50.000 0.00 0.00 0.00 3.27
18 19 2.025981 TGGGATGGTGAGGTTGATTGAG 60.026 50.000 0.00 0.00 0.00 3.02
19 20 1.991813 TGGGATGGTGAGGTTGATTGA 59.008 47.619 0.00 0.00 0.00 2.57
20 21 2.512692 TGGGATGGTGAGGTTGATTG 57.487 50.000 0.00 0.00 0.00 2.67
21 22 3.763557 ATTGGGATGGTGAGGTTGATT 57.236 42.857 0.00 0.00 0.00 2.57
22 23 3.628257 GGAATTGGGATGGTGAGGTTGAT 60.628 47.826 0.00 0.00 0.00 2.57
23 24 2.291540 GGAATTGGGATGGTGAGGTTGA 60.292 50.000 0.00 0.00 0.00 3.18
24 25 2.102578 GGAATTGGGATGGTGAGGTTG 58.897 52.381 0.00 0.00 0.00 3.77
25 26 1.007118 GGGAATTGGGATGGTGAGGTT 59.993 52.381 0.00 0.00 0.00 3.50
26 27 0.631212 GGGAATTGGGATGGTGAGGT 59.369 55.000 0.00 0.00 0.00 3.85
27 28 0.630673 TGGGAATTGGGATGGTGAGG 59.369 55.000 0.00 0.00 0.00 3.86
28 29 2.381911 CTTGGGAATTGGGATGGTGAG 58.618 52.381 0.00 0.00 0.00 3.51
29 30 1.619432 GCTTGGGAATTGGGATGGTGA 60.619 52.381 0.00 0.00 0.00 4.02
30 31 0.826062 GCTTGGGAATTGGGATGGTG 59.174 55.000 0.00 0.00 0.00 4.17
31 32 0.712380 AGCTTGGGAATTGGGATGGT 59.288 50.000 0.00 0.00 0.00 3.55
32 33 1.758862 GAAGCTTGGGAATTGGGATGG 59.241 52.381 2.10 0.00 0.00 3.51
33 34 2.459644 TGAAGCTTGGGAATTGGGATG 58.540 47.619 2.10 0.00 0.00 3.51
34 35 2.925966 TGAAGCTTGGGAATTGGGAT 57.074 45.000 2.10 0.00 0.00 3.85
35 36 2.459644 CATGAAGCTTGGGAATTGGGA 58.540 47.619 2.10 0.00 0.00 4.37
36 37 1.483415 CCATGAAGCTTGGGAATTGGG 59.517 52.381 2.10 0.00 0.00 4.12
37 38 2.459644 TCCATGAAGCTTGGGAATTGG 58.540 47.619 2.10 1.68 34.85 3.16
38 39 3.765511 TCTTCCATGAAGCTTGGGAATTG 59.234 43.478 18.87 11.64 39.29 2.32
39 40 4.051661 TCTTCCATGAAGCTTGGGAATT 57.948 40.909 18.87 0.00 39.29 2.17
40 41 3.744940 TCTTCCATGAAGCTTGGGAAT 57.255 42.857 18.87 0.77 39.29 3.01
41 42 3.157087 GTTCTTCCATGAAGCTTGGGAA 58.843 45.455 17.99 17.99 39.29 3.97
42 43 2.795329 GTTCTTCCATGAAGCTTGGGA 58.205 47.619 2.10 5.24 39.29 4.37
43 44 1.470098 CGTTCTTCCATGAAGCTTGGG 59.530 52.381 2.10 2.46 39.29 4.12
44 45 2.160417 GTCGTTCTTCCATGAAGCTTGG 59.840 50.000 2.10 0.00 39.29 3.61
45 46 3.070018 AGTCGTTCTTCCATGAAGCTTG 58.930 45.455 2.10 0.00 39.29 4.01
46 47 3.244215 TGAGTCGTTCTTCCATGAAGCTT 60.244 43.478 0.00 0.00 39.29 3.74
53 54 1.344438 TGCAGTGAGTCGTTCTTCCAT 59.656 47.619 0.00 0.00 0.00 3.41
117 118 3.767230 CAGCGCAACGACACGAGG 61.767 66.667 11.47 0.00 0.00 4.63
210 211 1.165270 CCGAGTTGATTGTTGGGGAC 58.835 55.000 0.00 0.00 0.00 4.46
306 307 1.277557 AGACAGAGTGCTTGGGATCAC 59.722 52.381 0.00 0.00 0.00 3.06
423 424 2.624169 GCTTGTTGCGACCCAAGTA 58.376 52.632 0.45 0.00 40.13 2.24
458 459 2.044946 AGCGTCCCCAATCCTTGC 60.045 61.111 0.00 0.00 0.00 4.01
489 490 5.403766 CGCTATTTGTAGCAGGATGTAGAAG 59.596 44.000 8.04 0.00 42.95 2.85
492 493 4.445718 CACGCTATTTGTAGCAGGATGTAG 59.554 45.833 8.04 0.00 42.95 2.74
499 500 1.588404 CCGTCACGCTATTTGTAGCAG 59.412 52.381 8.04 3.77 42.95 4.24
534 535 1.303155 AAGAGCTGCTCCCAAGTGC 60.303 57.895 25.09 0.00 0.00 4.40
542 543 0.173255 AGCGAAGAGAAGAGCTGCTC 59.827 55.000 21.72 21.72 38.67 4.26
661 662 0.807667 CGCAGAAGGAATCTCACCGG 60.808 60.000 0.00 0.00 35.73 5.28
665 666 1.002430 AGCAACGCAGAAGGAATCTCA 59.998 47.619 0.00 0.00 35.73 3.27
720 728 2.018515 GGACCCGACAAAGTTGTTCAA 58.981 47.619 0.00 0.00 42.43 2.69
1020 1177 4.705023 CCGATGTTATATGGAATTTCCCCC 59.295 45.833 12.90 0.00 35.03 5.40
1065 1222 6.925165 AGTTGTTTCCTTGCATAATCAAAGTG 59.075 34.615 0.00 0.00 0.00 3.16
1095 1252 4.499696 GCTATTGAAATGGGGATTTGTCCG 60.500 45.833 0.00 0.00 0.00 4.79
1114 1271 4.406456 TGAAGATTGGTTGTGTTGGCTAT 58.594 39.130 0.00 0.00 0.00 2.97
1259 1416 3.220940 TGTGTGCAATTGGTCAATGAGA 58.779 40.909 7.72 0.00 0.00 3.27
1635 1792 7.338449 AGGTTTAGTGTTTCTAACTTCTTGCAA 59.662 33.333 0.00 0.00 38.22 4.08
1652 1809 6.619801 AGCTGTTACAAGAAAGGTTTAGTG 57.380 37.500 0.00 0.00 0.00 2.74
1913 2070 3.282885 CCTCCCAAACTTATGAAGGAGC 58.717 50.000 0.00 0.00 39.68 4.70
2126 2283 1.102978 AAATGGCACCCGTAGCAATC 58.897 50.000 0.00 0.00 0.00 2.67
2460 2623 2.158928 AGCAATGAAGCTTTTTGGTGCA 60.159 40.909 20.34 5.77 43.70 4.57
2859 3041 0.038166 CTTGGCCCCACTAAGCTTGA 59.962 55.000 9.86 0.00 29.31 3.02
3176 3429 7.288158 ACCTTCATCTCTATAACCTGGAACTAC 59.712 40.741 0.00 0.00 0.00 2.73
3347 3606 6.453396 GCTGAAAATGATTCTTTGATTGCGAC 60.453 38.462 0.00 0.00 0.00 5.19
3469 3732 4.336713 GGCTAGGAAAAGCTTCACAATAGG 59.663 45.833 0.00 0.00 42.37 2.57
3562 3827 8.825774 TGGGCTGCTTCATTATATTTAGATAGA 58.174 33.333 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.