Multiple sequence alignment - TraesCS4B01G112200

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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 TraesCS4B01G112200 chr4B 100.000 4305 0 0 1 4305 126318900 126323204 0.000000e+00 7950
1 TraesCS4B01G112200 chr4B 78.837 860 125 38 25 868 26318232 26317414 1.060000e-145 527
2 TraesCS4B01G112200 chr4B 85.648 216 27 3 654 868 26014682 26014470 1.560000e-54 224
3 TraesCS4B01G112200 chr4B 85.648 216 27 3 654 868 26056358 26056146 1.560000e-54 224
4 TraesCS4B01G112200 chr4D 94.108 3513 110 38 883 4305 89419406 89422911 0.000000e+00 5251
5 TraesCS4B01G112200 chr4A 93.150 3416 125 27 882 4211 501958950 501962342 0.000000e+00 4911
6 TraesCS4B01G112200 chr4A 94.118 102 3 3 4204 4305 501962377 501962475 7.460000e-33 152
7 TraesCS4B01G112200 chr1A 98.299 882 13 1 1 882 396290920 396290041 0.000000e+00 1544
8 TraesCS4B01G112200 chr3D 89.551 890 66 18 1 877 153226879 153227754 0.000000e+00 1103
9 TraesCS4B01G112200 chr3D 80.586 649 87 19 25 643 572151612 572152251 8.430000e-127 464
10 TraesCS4B01G112200 chr3D 79.792 673 92 23 15 644 611890623 611889952 2.360000e-122 449
11 TraesCS4B01G112200 chr5A 81.209 910 123 26 5 877 125210651 125209753 0.000000e+00 689
12 TraesCS4B01G112200 chr5A 81.099 910 123 26 5 877 111608833 111609730 0.000000e+00 682
13 TraesCS4B01G112200 chr6A 81.271 881 118 22 25 868 12219617 12218747 0.000000e+00 669
14 TraesCS4B01G112200 chr5B 79.909 881 151 24 5 877 266002930 266003792 1.310000e-174 623
15 TraesCS4B01G112200 chr3A 80.309 777 123 23 116 877 191839505 191840266 1.050000e-155 560
16 TraesCS4B01G112200 chr7A 79.923 777 126 23 116 877 448091578 448092339 1.050000e-150 544
17 TraesCS4B01G112200 chr3B 79.871 775 130 19 116 877 790409524 790410285 1.050000e-150 544
18 TraesCS4B01G112200 chr6B 79.794 777 127 23 116 877 551949023 551948262 4.900000e-149 538
19 TraesCS4B01G112200 chr2B 79.794 777 126 24 116 877 131078728 131079488 1.760000e-148 536


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 TraesCS4B01G112200 chr4B 126318900 126323204 4304 False 7950.0 7950 100.000 1 4305 1 chr4B.!!$F1 4304
1 TraesCS4B01G112200 chr4B 26317414 26318232 818 True 527.0 527 78.837 25 868 1 chr4B.!!$R3 843
2 TraesCS4B01G112200 chr4D 89419406 89422911 3505 False 5251.0 5251 94.108 883 4305 1 chr4D.!!$F1 3422
3 TraesCS4B01G112200 chr4A 501958950 501962475 3525 False 2531.5 4911 93.634 882 4305 2 chr4A.!!$F1 3423
4 TraesCS4B01G112200 chr1A 396290041 396290920 879 True 1544.0 1544 98.299 1 882 1 chr1A.!!$R1 881
5 TraesCS4B01G112200 chr3D 153226879 153227754 875 False 1103.0 1103 89.551 1 877 1 chr3D.!!$F1 876
6 TraesCS4B01G112200 chr3D 572151612 572152251 639 False 464.0 464 80.586 25 643 1 chr3D.!!$F2 618
7 TraesCS4B01G112200 chr3D 611889952 611890623 671 True 449.0 449 79.792 15 644 1 chr3D.!!$R1 629
8 TraesCS4B01G112200 chr5A 125209753 125210651 898 True 689.0 689 81.209 5 877 1 chr5A.!!$R1 872
9 TraesCS4B01G112200 chr5A 111608833 111609730 897 False 682.0 682 81.099 5 877 1 chr5A.!!$F1 872
10 TraesCS4B01G112200 chr6A 12218747 12219617 870 True 669.0 669 81.271 25 868 1 chr6A.!!$R1 843
11 TraesCS4B01G112200 chr5B 266002930 266003792 862 False 623.0 623 79.909 5 877 1 chr5B.!!$F1 872
12 TraesCS4B01G112200 chr3A 191839505 191840266 761 False 560.0 560 80.309 116 877 1 chr3A.!!$F1 761
13 TraesCS4B01G112200 chr7A 448091578 448092339 761 False 544.0 544 79.923 116 877 1 chr7A.!!$F1 761
14 TraesCS4B01G112200 chr3B 790409524 790410285 761 False 544.0 544 79.871 116 877 1 chr3B.!!$F1 761
15 TraesCS4B01G112200 chr6B 551948262 551949023 761 True 538.0 538 79.794 116 877 1 chr6B.!!$R1 761
16 TraesCS4B01G112200 chr2B 131078728 131079488 760 False 536.0 536 79.794 116 877 1 chr2B.!!$F1 761

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
214 235 2.358247 GGCGAGAAACAAGGCCGA 60.358 61.111 0.00 0.00 35.59 5.54 F
798 916 7.896383 TTGATCTGGTTTTAGATATTTGGGG 57.104 36.000 0.00 0.00 37.53 4.96 F
1671 1798 0.032017 ACTAGCAAGGATCCCCGAGT 60.032 55.000 8.55 6.38 37.58 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1236 1356 0.116541 AAAAGGGGAGGACGAGGAGA 59.883 55.0 0.0 0.0 0.00 3.71 R
1698 1825 0.389817 TTTGAGGTGTCGATGCGGAG 60.390 55.0 0.0 0.0 0.00 4.63 R
3505 3686 0.251077 CTGCTTCTTCACCAGCCCTT 60.251 55.0 0.0 0.0 34.91 3.95 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
30 31 4.514577 CTCCGCCGACGCATCCTT 62.515 66.667 0.00 0.00 38.22 3.36
214 235 2.358247 GGCGAGAAACAAGGCCGA 60.358 61.111 0.00 0.00 35.59 5.54
796 914 9.956720 GTGATTGATCTGGTTTTAGATATTTGG 57.043 33.333 0.00 0.00 37.53 3.28
797 915 9.135189 TGATTGATCTGGTTTTAGATATTTGGG 57.865 33.333 0.00 0.00 37.53 4.12
798 916 7.896383 TTGATCTGGTTTTAGATATTTGGGG 57.104 36.000 0.00 0.00 37.53 4.96
1300 1420 0.315251 CTCTCACTTGCGTCTCACCA 59.685 55.000 0.00 0.00 0.00 4.17
1315 1435 0.734889 CACCATTCCCTCATTGCGTC 59.265 55.000 0.00 0.00 0.00 5.19
1321 1441 2.436646 CCTCATTGCGTCGGCCTT 60.437 61.111 0.00 0.00 38.85 4.35
1500 1621 3.056536 AGTCGCAGAAATCTCAGCAAGTA 60.057 43.478 0.00 0.00 39.69 2.24
1553 1680 8.458573 TCTTGACTACAAATTTAAAGGAGCAA 57.541 30.769 0.00 0.00 35.49 3.91
1622 1749 3.255969 ACCATTTCCAAATGATGCAGC 57.744 42.857 12.72 0.00 46.72 5.25
1655 1782 0.036164 ATCACCGGCAAAGCACACTA 59.964 50.000 0.00 0.00 0.00 2.74
1667 1794 0.464554 GCACACTAGCAAGGATCCCC 60.465 60.000 8.55 0.00 0.00 4.81
1668 1795 0.179073 CACACTAGCAAGGATCCCCG 60.179 60.000 8.55 0.03 37.58 5.73
1671 1798 0.032017 ACTAGCAAGGATCCCCGAGT 60.032 55.000 8.55 6.38 37.58 4.18
1698 1825 0.252197 ATGCCCGACTAACCTTGACC 59.748 55.000 0.00 0.00 0.00 4.02
1718 1845 0.389817 TCCGCATCGACACCTCAAAG 60.390 55.000 0.00 0.00 0.00 2.77
1774 1901 6.943718 TCCAATAAGTTTACATCGGAAAACCT 59.056 34.615 1.27 0.00 36.46 3.50
1795 1922 1.267932 CGATTCCGTGAGTAGGACGAC 60.268 57.143 0.00 0.00 39.21 4.34
1824 1977 5.487433 TCATGTTCCTGTTCATTGTATCGT 58.513 37.500 0.00 0.00 0.00 3.73
1825 1978 5.580691 TCATGTTCCTGTTCATTGTATCGTC 59.419 40.000 0.00 0.00 0.00 4.20
1877 2031 2.433604 TCTTCTCATCCAGGAGACATGC 59.566 50.000 0.00 0.00 43.31 4.06
1923 2077 3.078837 GAGGAGCGGGTTTCAAATGTTA 58.921 45.455 0.00 0.00 0.00 2.41
2355 2512 3.304251 TGGTAGCCGCATAGCACA 58.696 55.556 0.00 0.00 34.23 4.57
2443 2600 6.554982 AGGAGTGCTCTCACATTAATGGTATA 59.445 38.462 19.37 2.11 45.49 1.47
2812 2969 5.689819 ACATCTGAAACTTATTGTGTTCGC 58.310 37.500 0.00 0.00 0.00 4.70
3108 3287 5.925509 ACTACAGACAATACAACCAACACT 58.074 37.500 0.00 0.00 0.00 3.55
3127 3306 1.078848 GCAGAGATCGCCAAGGTGT 60.079 57.895 0.00 0.00 0.00 4.16
3133 3312 0.517316 GATCGCCAAGGTGTGTGTTC 59.483 55.000 0.00 0.00 0.00 3.18
3198 3377 9.715121 TTAGTAGTTTAGTTGTTCATACCTTGG 57.285 33.333 0.00 0.00 0.00 3.61
3274 3453 1.179152 TCGCACTAAGGATGGACGAA 58.821 50.000 0.00 0.00 0.00 3.85
3340 3519 3.559069 CTGGATGGCAATCTGGTGTATT 58.441 45.455 0.00 0.00 32.95 1.89
3345 3524 6.885918 TGGATGGCAATCTGGTGTATTATATG 59.114 38.462 0.00 0.00 32.95 1.78
3482 3663 4.006319 GCCTGAAGCTGTTTAAGATCAGT 58.994 43.478 6.95 0.00 38.65 3.41
3504 3685 0.909610 TTGATGCGGAAGAGTCCCCT 60.910 55.000 0.00 0.00 41.44 4.79
3505 3686 0.032515 TGATGCGGAAGAGTCCCCTA 60.033 55.000 0.00 0.00 41.44 3.53
3507 3688 1.069358 GATGCGGAAGAGTCCCCTAAG 59.931 57.143 0.00 0.00 41.44 2.18
3508 3689 0.976073 TGCGGAAGAGTCCCCTAAGG 60.976 60.000 0.00 0.00 41.44 2.69
3532 3721 2.300152 TGGTGAAGAAGCAGAGACGATT 59.700 45.455 0.00 0.00 0.00 3.34
3534 3723 2.670414 GTGAAGAAGCAGAGACGATTGG 59.330 50.000 0.00 0.00 0.00 3.16
3621 3810 9.768662 ATTATTGAGGTTTGCCATGAAAATATC 57.231 29.630 0.00 0.00 37.19 1.63
3627 3816 5.928264 GGTTTGCCATGAAAATATCCTATGC 59.072 40.000 0.00 0.00 34.09 3.14
3662 3866 3.586174 AGCCATCATCTAGTGCATACCAT 59.414 43.478 0.00 0.00 0.00 3.55
3790 4007 5.134202 TGACTTGATATCACGAGTGTTGT 57.866 39.130 15.55 1.03 35.00 3.32
3791 4008 5.538118 TGACTTGATATCACGAGTGTTGTT 58.462 37.500 15.55 0.00 35.00 2.83
3792 4009 5.405269 TGACTTGATATCACGAGTGTTGTTG 59.595 40.000 15.55 0.00 35.00 3.33
3793 4010 4.152402 ACTTGATATCACGAGTGTTGTTGC 59.848 41.667 15.55 0.00 33.77 4.17
3794 4011 3.925379 TGATATCACGAGTGTTGTTGCT 58.075 40.909 0.00 0.00 0.00 3.91
3795 4012 3.679502 TGATATCACGAGTGTTGTTGCTG 59.320 43.478 0.00 0.00 0.00 4.41
3796 4013 0.588252 ATCACGAGTGTTGTTGCTGC 59.412 50.000 2.97 0.00 0.00 5.25
3797 4014 1.009675 CACGAGTGTTGTTGCTGCC 60.010 57.895 0.00 0.00 0.00 4.85
3798 4015 2.249309 CGAGTGTTGTTGCTGCCG 59.751 61.111 0.00 0.00 0.00 5.69
3859 4076 4.031314 TGTTTATTCGTTCGAGAGCATTCG 59.969 41.667 3.75 3.75 41.79 3.34
3874 4091 3.119352 AGCATTCGGCCTTGAAATTTCTC 60.119 43.478 18.64 5.91 46.50 2.87
3908 4131 0.482446 ATCCTTGCCTGTTTCCCACA 59.518 50.000 0.00 0.00 0.00 4.17
3981 4204 5.664294 TGGCTTGCTGTATGATTTTCATT 57.336 34.783 0.00 0.00 38.26 2.57
4083 4306 0.691078 GAGGTGGGAGGGTGATAGCA 60.691 60.000 0.00 0.00 0.00 3.49
4169 4392 3.181510 GGCAAAGTCATCGACATTACCAC 60.182 47.826 0.00 0.00 34.60 4.16
4173 4396 3.018856 AGTCATCGACATTACCACGGTA 58.981 45.455 0.00 0.00 34.60 4.02
4223 4485 5.122396 CCGTTTCCATTTGTAAGAGGAGAAG 59.878 44.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.194781 GCTGGAGGTGAAGGAGGACA 61.195 60.000 0.00 0.00 0.00 4.02
861 979 3.379057 GGGAAAGAAGTGTCGTTTTTCCA 59.621 43.478 14.18 0.00 45.38 3.53
1236 1356 0.116541 AAAAGGGGAGGACGAGGAGA 59.883 55.000 0.00 0.00 0.00 3.71
1300 1420 1.819632 GCCGACGCAATGAGGGAAT 60.820 57.895 0.00 0.00 34.03 3.01
1315 1435 3.996150 AGCATAATCAATTGAAGGCCG 57.004 42.857 13.09 1.80 0.00 6.13
1321 1441 7.022979 CGAAACAGACAAGCATAATCAATTGA 58.977 34.615 11.26 11.26 0.00 2.57
1364 1484 3.196469 CACCCTTGAAGTCATCAGCTCTA 59.804 47.826 0.00 0.00 39.77 2.43
1370 1490 0.321564 CGGCACCCTTGAAGTCATCA 60.322 55.000 0.00 0.00 35.85 3.07
1373 1493 2.429930 CCGGCACCCTTGAAGTCA 59.570 61.111 0.00 0.00 0.00 3.41
1500 1621 8.953368 AAAAGAAGAAGAAAATTCAGTTGCAT 57.047 26.923 0.00 0.00 0.00 3.96
1553 1680 3.130351 GTGCATACACTCCACTGCAAGT 61.130 50.000 0.00 0.00 46.92 3.16
1588 1715 3.621715 GGAAATGGTATGTCACGAGGTTC 59.378 47.826 0.00 0.00 0.00 3.62
1622 1749 3.700577 GTGATCAAATGCCACCACG 57.299 52.632 0.00 0.00 0.00 4.94
1655 1782 1.604378 CAACTCGGGGATCCTTGCT 59.396 57.895 12.58 0.00 0.00 3.91
1698 1825 0.389817 TTTGAGGTGTCGATGCGGAG 60.390 55.000 0.00 0.00 0.00 4.63
1718 1845 1.033574 ATACAGCTCGGGCACTACTC 58.966 55.000 11.40 0.00 41.70 2.59
1758 1885 4.632688 GGAATCGAGGTTTTCCGATGTAAA 59.367 41.667 0.00 0.00 43.72 2.01
1774 1901 1.012086 CGTCCTACTCACGGAATCGA 58.988 55.000 0.00 0.00 40.11 3.59
1824 1977 6.016024 CCTCATGTTCTTGTTTCCAAATGAGA 60.016 38.462 10.15 0.00 40.98 3.27
1825 1978 6.154445 CCTCATGTTCTTGTTTCCAAATGAG 58.846 40.000 0.00 0.00 39.61 2.90
1857 2011 2.802415 CGCATGTCTCCTGGATGAGAAG 60.802 54.545 0.00 0.00 42.75 2.85
1877 2031 1.089920 CTTGGCCCAACAGATTCTCG 58.910 55.000 0.00 0.00 0.00 4.04
1923 2077 8.041919 CAGATCAGCATCCTCTACATATTTGAT 58.958 37.037 0.00 0.00 0.00 2.57
2368 2525 5.407407 AAGAAATCTAAGGACGCTTCAGA 57.593 39.130 0.00 0.00 0.00 3.27
2443 2600 7.331791 CCTTTGAACTAGACTTAATGTAGCCT 58.668 38.462 0.00 0.00 0.00 4.58
2880 3037 0.323725 GGCTCAGCTTTGAATCCCCA 60.324 55.000 0.00 0.00 0.00 4.96
3108 3287 1.078918 CACCTTGGCGATCTCTGCA 60.079 57.895 0.00 0.00 0.00 4.41
3127 3306 5.808366 ACAGAGACAATAAGAGGAACACA 57.192 39.130 0.00 0.00 0.00 3.72
3133 3312 5.582665 GCAGGTTTACAGAGACAATAAGAGG 59.417 44.000 0.00 0.00 0.00 3.69
3184 3363 1.824230 GGCATGCCAAGGTATGAACAA 59.176 47.619 32.08 0.00 39.96 2.83
3198 3377 2.595386 CCTAAGTTTCAAACGGCATGC 58.405 47.619 9.90 9.90 36.23 4.06
3274 3453 1.843851 TCCCTAATCCAGGCGTTGAAT 59.156 47.619 0.00 0.00 43.98 2.57
3340 3519 4.932799 GGCATACACGCATGTTACCATATA 59.067 41.667 0.00 0.00 40.48 0.86
3345 3524 1.663695 AGGCATACACGCATGTTACC 58.336 50.000 0.00 0.00 40.48 2.85
3358 3537 2.384828 TCTTCCTCGCAACTAGGCATA 58.615 47.619 0.00 0.00 33.84 3.14
3482 3663 1.610624 GGGACTCTTCCGCATCAACAA 60.611 52.381 0.00 0.00 43.94 2.83
3504 3685 1.003580 CTGCTTCTTCACCAGCCCTTA 59.996 52.381 0.00 0.00 34.91 2.69
3505 3686 0.251077 CTGCTTCTTCACCAGCCCTT 60.251 55.000 0.00 0.00 34.91 3.95
3507 3688 0.676151 CTCTGCTTCTTCACCAGCCC 60.676 60.000 0.00 0.00 34.91 5.19
3508 3689 0.322975 TCTCTGCTTCTTCACCAGCC 59.677 55.000 0.00 0.00 34.91 4.85
3509 3690 1.437625 GTCTCTGCTTCTTCACCAGC 58.562 55.000 0.00 0.00 36.49 4.85
3510 3691 1.270826 TCGTCTCTGCTTCTTCACCAG 59.729 52.381 0.00 0.00 0.00 4.00
3511 3692 1.328279 TCGTCTCTGCTTCTTCACCA 58.672 50.000 0.00 0.00 0.00 4.17
3524 3713 2.002127 CGCTGCTTCCAATCGTCTC 58.998 57.895 0.00 0.00 0.00 3.36
3532 3721 1.865788 GACCAATTGCGCTGCTTCCA 61.866 55.000 9.73 0.00 0.00 3.53
3534 3723 0.455633 CAGACCAATTGCGCTGCTTC 60.456 55.000 9.73 0.00 0.00 3.86
3600 3789 5.271598 AGGATATTTTCATGGCAAACCTCA 58.728 37.500 0.00 0.00 36.63 3.86
3604 3793 6.752168 AGCATAGGATATTTTCATGGCAAAC 58.248 36.000 0.00 0.00 0.00 2.93
3621 3810 7.549134 TGATGGCTAATCGTATAAAAGCATAGG 59.451 37.037 0.00 0.00 38.22 2.57
3627 3816 9.862371 ACTAGATGATGGCTAATCGTATAAAAG 57.138 33.333 0.00 0.00 38.22 2.27
3637 3826 5.249163 TGGTATGCACTAGATGATGGCTAAT 59.751 40.000 0.00 0.00 0.00 1.73
3798 4015 2.684843 CCTTCGACCAAGCAGCAGC 61.685 63.158 0.00 0.00 42.56 5.25
3859 4076 0.179163 CGCCGAGAAATTTCAAGGCC 60.179 55.000 32.56 22.19 44.00 5.19
3874 4091 2.180204 GGATGATGGTTCACCGCCG 61.180 63.158 0.00 0.00 39.43 6.46
3908 4131 2.030457 CGCTCGTCGAAATTATTGCCTT 59.970 45.455 0.00 0.00 41.67 4.35
4083 4306 3.551846 CCAGAAACTGGTAAAGTGGTGT 58.448 45.455 9.36 0.00 45.82 4.16
4169 4392 3.944871 GCAAGGGCAATGAATACCG 57.055 52.632 0.00 0.00 40.72 4.02


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

AutoCloner maintained by Alex Coulton.