Multiple sequence alignment - TraesCS3B01G456700

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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 TraesCS3B01G456700 chr3B 100.000 2459 0 0 1 2459 698121257 698123715 0.000000e+00 4542.0
1 TraesCS3B01G456700 chr3B 88.312 2079 148 57 431 2459 697982679 697984712 0.000000e+00 2405.0
2 TraesCS3B01G456700 chr3B 85.531 1168 83 37 431 1569 697999631 698000741 0.000000e+00 1142.0
3 TraesCS3B01G456700 chr3B 90.769 845 47 5 1640 2459 698001165 698002003 0.000000e+00 1099.0
4 TraesCS3B01G456700 chr3B 86.484 947 59 32 779 1688 698194659 698195573 0.000000e+00 976.0
5 TraesCS3B01G456700 chr3B 86.070 804 44 28 12 750 698192990 698193790 0.000000e+00 802.0
6 TraesCS3B01G456700 chr3B 81.071 280 30 14 1815 2072 390086734 390087012 4.150000e-48 202.0
7 TraesCS3B01G456700 chr3B 79.928 279 33 20 1815 2072 193212386 193212662 1.500000e-42 183.0
8 TraesCS3B01G456700 chr3B 83.648 159 22 4 2072 2228 386226709 386226865 1.970000e-31 147.0
9 TraesCS3B01G456700 chr3D 88.393 1413 86 29 431 1802 527735125 527736500 0.000000e+00 1629.0
10 TraesCS3B01G456700 chr3D 88.793 1276 77 28 260 1483 528094080 528095341 0.000000e+00 1504.0
11 TraesCS3B01G456700 chr3D 87.722 790 43 20 431 1179 528083191 528083967 0.000000e+00 872.0
12 TraesCS3B01G456700 chr3D 92.081 543 31 4 1175 1717 528084506 528085036 0.000000e+00 754.0
13 TraesCS3B01G456700 chr3D 89.567 393 34 6 1684 2073 528012060 528012448 2.200000e-135 492.0
14 TraesCS3B01G456700 chr3D 88.921 343 31 6 1736 2073 527738924 527739264 1.360000e-112 416.0
15 TraesCS3B01G456700 chr3D 90.909 121 7 3 431 550 528011862 528011979 2.530000e-35 159.0
16 TraesCS3B01G456700 chr3A 84.162 1187 110 38 515 1660 662519712 662520861 0.000000e+00 1079.0
17 TraesCS3B01G456700 chr3A 90.385 52 2 2 463 513 662513419 662513468 5.680000e-07 65.8
18 TraesCS3B01G456700 chr5D 86.500 400 40 5 2072 2459 457566396 457566793 6.280000e-116 427.0
19 TraesCS3B01G456700 chr5D 82.338 402 56 6 2072 2459 358769212 358768812 3.920000e-88 335.0
20 TraesCS3B01G456700 chr5B 86.035 401 40 9 2072 2459 559630295 559630692 1.360000e-112 416.0
21 TraesCS3B01G456700 chr5B 83.289 377 53 7 2072 2445 336415060 336415429 3.030000e-89 339.0
22 TraesCS3B01G456700 chr5B 75.000 668 110 34 1815 2437 514297581 514298236 3.140000e-64 255.0
23 TraesCS3B01G456700 chr4D 82.500 400 53 8 2072 2459 163714083 163714477 3.920000e-88 335.0
24 TraesCS3B01G456700 chr4D 81.495 281 26 20 1815 2072 209047689 209047412 8.910000e-50 207.0
25 TraesCS3B01G456700 chr4D 78.853 279 37 14 1815 2072 75312304 75312027 4.210000e-38 169.0
26 TraesCS3B01G456700 chr7A 82.687 387 53 7 2072 2445 26951843 26952228 5.070000e-87 331.0
27 TraesCS3B01G456700 chr1D 82.564 390 53 12 2072 2459 205034373 205033997 1.820000e-86 329.0
28 TraesCS3B01G456700 chr6A 88.696 115 13 0 62 176 91978803 91978689 9.170000e-30 141.0


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 TraesCS3B01G456700 chr3B 698121257 698123715 2458 False 4542.0 4542 100.0000 1 2459 1 chr3B.!!$F5 2458
1 TraesCS3B01G456700 chr3B 697982679 697984712 2033 False 2405.0 2405 88.3120 431 2459 1 chr3B.!!$F4 2028
2 TraesCS3B01G456700 chr3B 697999631 698002003 2372 False 1120.5 1142 88.1500 431 2459 2 chr3B.!!$F6 2028
3 TraesCS3B01G456700 chr3B 698192990 698195573 2583 False 889.0 976 86.2770 12 1688 2 chr3B.!!$F7 1676
4 TraesCS3B01G456700 chr3D 528094080 528095341 1261 False 1504.0 1504 88.7930 260 1483 1 chr3D.!!$F1 1223
5 TraesCS3B01G456700 chr3D 527735125 527739264 4139 False 1022.5 1629 88.6570 431 2073 2 chr3D.!!$F2 1642
6 TraesCS3B01G456700 chr3D 528083191 528085036 1845 False 813.0 872 89.9015 431 1717 2 chr3D.!!$F4 1286
7 TraesCS3B01G456700 chr3D 528011862 528012448 586 False 325.5 492 90.2380 431 2073 2 chr3D.!!$F3 1642
8 TraesCS3B01G456700 chr3A 662519712 662520861 1149 False 1079.0 1079 84.1620 515 1660 1 chr3A.!!$F2 1145
9 TraesCS3B01G456700 chr5B 514297581 514298236 655 False 255.0 255 75.0000 1815 2437 1 chr5B.!!$F2 622

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
215 221 0.034089 AGACATTGCCCTTACCTGCC 60.034 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1509 3124 1.59626 TCGCTATTCGAGTGTACTCCG 59.404 52.381 6.46 3.66 43.16 4.63 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
46 49 5.819825 AAGTGAGTTTTCTTCCTTCACAC 57.180 39.130 5.81 0.00 40.35 3.82
61 64 8.519799 TTCCTTCACACAAATTAACTCTCTTT 57.480 30.769 0.00 0.00 0.00 2.52
73 78 7.946381 ATTAACTCTCTTTCCCCTGATTTTC 57.054 36.000 0.00 0.00 0.00 2.29
96 101 3.897122 TGTGGGCCCCTTCACACC 61.897 66.667 22.27 0.00 38.75 4.16
105 110 0.551396 CCCTTCACACCCCCTAATCC 59.449 60.000 0.00 0.00 0.00 3.01
106 111 1.295020 CCTTCACACCCCCTAATCCA 58.705 55.000 0.00 0.00 0.00 3.41
115 120 4.731929 ACACCCCCTAATCCAATCAGTAAT 59.268 41.667 0.00 0.00 0.00 1.89
116 121 5.072741 CACCCCCTAATCCAATCAGTAATG 58.927 45.833 0.00 0.00 0.00 1.90
117 122 4.106341 ACCCCCTAATCCAATCAGTAATGG 59.894 45.833 0.00 0.00 38.09 3.16
146 151 7.612677 ACTAAGATCAATCCGTAAACTCTGTT 58.387 34.615 0.00 0.00 0.00 3.16
163 169 3.632604 TCTGTTAAATTTTGCCCGTGACA 59.367 39.130 0.00 0.00 0.00 3.58
197 203 0.882042 CCCAATTCCCATCGAGCGAG 60.882 60.000 0.00 0.00 0.00 5.03
215 221 0.034089 AGACATTGCCCTTACCTGCC 60.034 55.000 0.00 0.00 0.00 4.85
234 240 1.930908 CAGCAAAGCTAGGCAGTGCC 61.931 60.000 27.50 27.50 43.27 5.01
286 319 3.834732 GCTTTAGCGACCTCTGGAA 57.165 52.632 0.00 0.00 0.00 3.53
385 421 0.537188 GAGGCAATGGACGGAGAGAA 59.463 55.000 0.00 0.00 0.00 2.87
410 463 2.703798 CGCTGCCATCCAGGTTTGG 61.704 63.158 6.79 6.79 46.49 3.28
421 474 0.109597 CAGGTTTGGACGAAGCATGC 60.110 55.000 10.51 10.51 0.00 4.06
493 569 1.405526 CCAAGAATCGACCGATGGTGT 60.406 52.381 5.62 0.00 35.25 4.16
494 570 1.660607 CAAGAATCGACCGATGGTGTG 59.339 52.381 5.62 0.00 35.25 3.82
510 586 4.747529 TGCGACGCAGCTCAGCAT 62.748 61.111 20.50 0.00 38.13 3.79
513 589 1.059994 CGACGCAGCTCAGCATTTC 59.940 57.895 0.00 0.00 0.00 2.17
577 664 2.353704 CCTATGAACCACGACAGAAGCA 60.354 50.000 0.00 0.00 0.00 3.91
615 719 4.589675 GGAACCCAACCCCACGCA 62.590 66.667 0.00 0.00 0.00 5.24
642 746 0.812549 TACATCTGTCTACGCGGCAA 59.187 50.000 12.47 0.00 0.00 4.52
683 796 1.303074 TACGTGTCTCCTCTGCGGT 60.303 57.895 0.00 0.00 0.00 5.68
711 831 0.759436 GCCTCGTCCCTATCCTTCCA 60.759 60.000 0.00 0.00 0.00 3.53
764 1703 2.409055 TATGCGTACCGGAGCACGT 61.409 57.895 21.70 12.40 46.83 4.49
830 1807 1.968540 GCTCCAGCAACGCCTTTCT 60.969 57.895 0.00 0.00 41.59 2.52
837 1820 1.172812 GCAACGCCTTTCTGTTCCCT 61.173 55.000 0.00 0.00 0.00 4.20
880 1865 0.447801 GCATCTATAAATGCCGGCCG 59.552 55.000 26.77 21.04 45.07 6.13
976 1985 4.730487 ACCAGCAGTGATCTTGCC 57.270 55.556 16.00 2.95 0.00 4.52
1509 3124 1.261619 GCGCCAGAGTATGCAATGTAC 59.738 52.381 0.00 0.00 0.00 2.90
1511 3126 1.867233 GCCAGAGTATGCAATGTACGG 59.133 52.381 0.00 0.00 0.00 4.02
1512 3127 2.483013 GCCAGAGTATGCAATGTACGGA 60.483 50.000 0.00 0.00 0.00 4.69
1513 3128 3.384668 CCAGAGTATGCAATGTACGGAG 58.615 50.000 0.00 0.00 0.00 4.63
1587 3238 4.788521 GCGGTCAAAGTTTTGTAAGGTCTG 60.789 45.833 4.67 0.00 39.18 3.51
1594 3245 3.262405 AGTTTTGTAAGGTCTGCCGGATA 59.738 43.478 5.05 0.00 40.50 2.59
1618 3270 6.726258 AAAAAGTTTTGCAAGAAGAGTTGG 57.274 33.333 0.61 0.00 0.00 3.77
1619 3271 4.391405 AAGTTTTGCAAGAAGAGTTGGG 57.609 40.909 0.00 0.00 0.00 4.12
1620 3272 2.695147 AGTTTTGCAAGAAGAGTTGGGG 59.305 45.455 0.00 0.00 0.00 4.96
1791 3800 6.258727 GCTCGATCATTTTGTGGATCTTCTAA 59.741 38.462 0.00 0.00 38.18 2.10
2048 6570 9.694137 ATCTCTTGAAGTTTACACACTAACTAC 57.306 33.333 0.00 0.00 33.66 2.73
2051 6573 7.707893 TCTTGAAGTTTACACACTAACTACCAC 59.292 37.037 0.00 0.00 33.66 4.16
2079 6646 8.010733 TCTGGATTGACAAAATTATGGGAATC 57.989 34.615 0.00 0.00 0.00 2.52
2083 6650 7.928167 GGATTGACAAAATTATGGGAATCCTTC 59.072 37.037 0.00 0.00 38.22 3.46
2231 6808 6.346838 GCAACAACCAAGCTTCATAAAACATC 60.347 38.462 0.00 0.00 0.00 3.06
2382 6960 2.933287 AGTCCGGGCCCATCAACA 60.933 61.111 24.92 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 40 7.228706 GGAAAGAGAGTTAATTTGTGTGAAGGA 59.771 37.037 0.00 0.00 0.00 3.36
46 49 7.709149 AATCAGGGGAAAGAGAGTTAATTTG 57.291 36.000 0.00 0.00 0.00 2.32
77 82 4.263572 TGTGAAGGGGCCCACACG 62.264 66.667 32.05 0.00 38.26 4.49
79 84 3.897122 GGTGTGAAGGGGCCCACA 61.897 66.667 27.72 21.33 40.56 4.17
90 95 2.509548 CTGATTGGATTAGGGGGTGTGA 59.490 50.000 0.00 0.00 0.00 3.58
96 101 4.082125 GCCATTACTGATTGGATTAGGGG 58.918 47.826 0.00 0.00 34.81 4.79
105 110 6.543465 TGATCTTAGTTGGCCATTACTGATTG 59.457 38.462 18.61 7.27 0.00 2.67
106 111 6.662755 TGATCTTAGTTGGCCATTACTGATT 58.337 36.000 18.61 3.15 0.00 2.57
115 120 2.238646 ACGGATTGATCTTAGTTGGCCA 59.761 45.455 0.00 0.00 0.00 5.36
116 121 2.919228 ACGGATTGATCTTAGTTGGCC 58.081 47.619 0.00 0.00 0.00 5.36
117 122 5.585047 AGTTTACGGATTGATCTTAGTTGGC 59.415 40.000 0.00 0.00 0.00 4.52
146 151 3.189702 GCTAGTGTCACGGGCAAAATTTA 59.810 43.478 15.04 0.00 0.00 1.40
163 169 4.103311 GGAATTGGGAGGAGTAATGCTAGT 59.897 45.833 0.00 0.00 0.00 2.57
197 203 0.323360 TGGCAGGTAAGGGCAATGTC 60.323 55.000 0.00 0.00 37.93 3.06
215 221 1.505353 GCACTGCCTAGCTTTGCTG 59.495 57.895 10.99 10.99 40.10 4.41
234 240 0.671796 TATACGATCGTGTGGCCCTG 59.328 55.000 30.23 0.00 0.00 4.45
286 319 1.414061 ATTCGGCCTGCCTAGCTCAT 61.414 55.000 6.60 0.00 0.00 2.90
385 421 3.127533 GGATGGCAGCGCGTTCTT 61.128 61.111 8.43 0.00 0.00 2.52
410 463 1.059264 GAAGTACGTGCATGCTTCGTC 59.941 52.381 31.76 24.61 38.69 4.20
421 474 1.270550 ACGGTGTTAGGGAAGTACGTG 59.729 52.381 0.00 0.00 31.60 4.49
493 569 4.747529 ATGCTGAGCTGCGTCGCA 62.748 61.111 20.44 20.44 36.92 5.10
494 570 2.893114 GAAATGCTGAGCTGCGTCGC 62.893 60.000 11.10 11.10 35.36 5.19
510 586 1.144708 TCACTTGTGCAGGGGATGAAA 59.855 47.619 0.00 0.00 0.00 2.69
513 589 0.250858 TGTCACTTGTGCAGGGGATG 60.251 55.000 0.00 0.00 0.00 3.51
577 664 2.128853 CTGGTCCGCACGCAAATTGT 62.129 55.000 0.00 0.00 0.00 2.71
592 685 2.160853 GGGGTTGGGTTCCTCTGGT 61.161 63.158 0.00 0.00 0.00 4.00
615 719 2.012673 GTAGACAGATGTACGGGTCGT 58.987 52.381 0.00 0.00 44.35 4.34
683 796 3.845259 GGACGAGGCGGTGGCATA 61.845 66.667 0.00 0.00 42.47 3.14
764 1703 1.227497 TGCATCGCATGACGGCATA 60.227 52.632 1.73 0.00 43.89 3.14
830 1807 4.263572 CGGGTGGTGCAGGGAACA 62.264 66.667 0.00 0.00 0.00 3.18
863 1848 1.019278 CGCGGCCGGCATTTATAGAT 61.019 55.000 30.85 0.00 43.84 1.98
960 1957 0.524862 GTTGGCAAGATCACTGCTGG 59.475 55.000 16.60 0.00 0.00 4.85
973 1982 2.178856 CACTGTGTGTGTGTTGGCA 58.821 52.632 0.00 0.00 41.53 4.92
1026 2045 2.203907 AGGAGGAGTGTGCAGGCT 60.204 61.111 0.00 0.00 0.00 4.58
1304 2878 2.494870 ACGCGGAGGTAGTACTTGATTT 59.505 45.455 12.47 0.00 0.00 2.17
1474 3066 4.117372 CGCGCAAGTTCGTCCGAC 62.117 66.667 8.75 0.00 41.68 4.79
1509 3124 1.596260 TCGCTATTCGAGTGTACTCCG 59.404 52.381 6.46 3.66 43.16 4.63
1615 3267 3.791953 TTTATTTCGACACTCCCCCAA 57.208 42.857 0.00 0.00 0.00 4.12
1618 3270 6.937436 ATTGTATTTATTTCGACACTCCCC 57.063 37.500 0.00 0.00 0.00 4.81
1791 3800 4.058817 GTCATGTCCACGTTTTCTTCTCT 58.941 43.478 0.00 0.00 0.00 3.10
2051 6573 5.069516 CCCATAATTTTGTCAATCCAGAGGG 59.930 44.000 0.00 0.00 0.00 4.30
2169 6746 7.550551 TGACAAGATCAAGGAATTGACTATGAC 59.449 37.037 0.00 0.00 33.02 3.06


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

AutoCloner maintained by Alex Coulton.