Multiple sequence alignment - TraesCS1B01G362300

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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 TraesCS1B01G362300 chr1B 100.000 3379 0 0 1 3379 591203344 591206722 0.000000e+00 6240.0
1 TraesCS1B01G362300 chr1B 97.727 3387 66 4 1 3379 591152132 591155515 0.000000e+00 5818.0
2 TraesCS1B01G362300 chr1B 94.523 1844 82 7 1549 3378 637633989 637632151 0.000000e+00 2828.0
3 TraesCS1B01G362300 chr1B 93.557 1583 72 10 1810 3378 141731527 141729961 0.000000e+00 2331.0
4 TraesCS1B01G362300 chr7D 91.813 2846 174 25 583 3378 596123081 596120245 0.000000e+00 3910.0
5 TraesCS1B01G362300 chr7D 91.687 2863 151 25 583 3378 530867456 530864614 0.000000e+00 3888.0
6 TraesCS1B01G362300 chr7D 93.279 2068 95 16 1350 3378 70680311 70678249 0.000000e+00 3009.0
7 TraesCS1B01G362300 chr7D 91.618 1706 107 17 583 2261 592400973 592402669 0.000000e+00 2326.0
8 TraesCS1B01G362300 chr4D 91.298 2873 171 29 577 3378 440465460 440462596 0.000000e+00 3847.0
9 TraesCS1B01G362300 chr6A 90.196 2856 199 30 580 3378 508298178 508301009 0.000000e+00 3648.0
10 TraesCS1B01G362300 chr2B 90.007 2842 179 48 583 3378 62334853 62337635 0.000000e+00 3578.0
11 TraesCS1B01G362300 chr3B 89.838 2834 208 39 585 3378 3763429 3760636 0.000000e+00 3565.0
12 TraesCS1B01G362300 chr3B 89.566 2837 214 45 583 3378 4663904 4661109 0.000000e+00 3524.0
13 TraesCS1B01G362300 chr3B 79.861 432 61 16 2954 3378 85163946 85163534 3.300000e-75 292.0
14 TraesCS1B01G362300 chr5B 89.702 2855 204 47 584 3378 455290989 455288165 0.000000e+00 3561.0
15 TraesCS1B01G362300 chr5B 93.001 1586 77 11 1810 3378 14354567 14356135 0.000000e+00 2283.0
16 TraesCS1B01G362300 chr5B 89.878 899 66 10 2490 3378 670105979 670105096 0.000000e+00 1133.0
17 TraesCS1B01G362300 chr5B 90.645 791 60 8 583 1366 14353437 14354220 0.000000e+00 1038.0
18 TraesCS1B01G362300 chr5A 89.327 2839 230 36 583 3378 562130734 562133542 0.000000e+00 3496.0
19 TraesCS1B01G362300 chr5A 89.929 1976 146 19 583 2523 633045665 633043708 0.000000e+00 2497.0
20 TraesCS1B01G362300 chr5A 90.691 1665 88 27 1769 3378 513858011 513859663 0.000000e+00 2154.0
21 TraesCS1B01G362300 chr2A 88.734 2512 175 30 582 3042 14783665 14786119 0.000000e+00 2972.0
22 TraesCS1B01G362300 chr2A 90.822 2081 143 22 583 2625 458970802 458968732 0.000000e+00 2741.0
23 TraesCS1B01G362300 chr2A 85.694 720 52 18 2705 3378 38526824 38526110 0.000000e+00 712.0
24 TraesCS1B01G362300 chr2A 77.123 424 76 17 2967 3378 202213792 202214206 3.390000e-55 226.0
25 TraesCS1B01G362300 chr2A 78.363 342 48 19 59 379 319049354 319049690 7.400000e-47 198.0
26 TraesCS1B01G362300 chr5D 93.279 1949 84 15 1470 3378 351321021 351322962 0.000000e+00 2830.0
27 TraesCS1B01G362300 chr5D 90.487 1293 86 11 581 1845 443521252 443522535 0.000000e+00 1672.0
28 TraesCS1B01G362300 chr6B 95.392 1172 52 2 581 1751 164440881 164439711 0.000000e+00 1864.0
29 TraesCS1B01G362300 chr6B 94.504 1128 37 5 2275 3379 164399429 164398304 0.000000e+00 1716.0
30 TraesCS1B01G362300 chr1A 88.431 873 82 13 582 1441 572013710 572012844 0.000000e+00 1035.0
31 TraesCS1B01G362300 chr3A 78.673 211 42 3 172 380 496725060 496725269 1.640000e-28 137.0
32 TraesCS1B01G362300 chr3A 90.698 43 4 0 1 43 246040142 246040184 1.310000e-04 58.4
33 TraesCS1B01G362300 chr2D 74.848 330 40 24 70 379 273000663 273000357 3.560000e-20 110.0
34 TraesCS1B01G362300 chr7B 90.698 43 4 0 1 43 25335774 25335732 1.310000e-04 58.4
35 TraesCS1B01G362300 chr3D 90.698 43 4 0 1 43 185797357 185797399 1.310000e-04 58.4


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 TraesCS1B01G362300 chr1B 591203344 591206722 3378 False 6240.0 6240 100.000 1 3379 1 chr1B.!!$F2 3378
1 TraesCS1B01G362300 chr1B 591152132 591155515 3383 False 5818.0 5818 97.727 1 3379 1 chr1B.!!$F1 3378
2 TraesCS1B01G362300 chr1B 637632151 637633989 1838 True 2828.0 2828 94.523 1549 3378 1 chr1B.!!$R2 1829
3 TraesCS1B01G362300 chr1B 141729961 141731527 1566 True 2331.0 2331 93.557 1810 3378 1 chr1B.!!$R1 1568
4 TraesCS1B01G362300 chr7D 596120245 596123081 2836 True 3910.0 3910 91.813 583 3378 1 chr7D.!!$R3 2795
5 TraesCS1B01G362300 chr7D 530864614 530867456 2842 True 3888.0 3888 91.687 583 3378 1 chr7D.!!$R2 2795
6 TraesCS1B01G362300 chr7D 70678249 70680311 2062 True 3009.0 3009 93.279 1350 3378 1 chr7D.!!$R1 2028
7 TraesCS1B01G362300 chr7D 592400973 592402669 1696 False 2326.0 2326 91.618 583 2261 1 chr7D.!!$F1 1678
8 TraesCS1B01G362300 chr4D 440462596 440465460 2864 True 3847.0 3847 91.298 577 3378 1 chr4D.!!$R1 2801
9 TraesCS1B01G362300 chr6A 508298178 508301009 2831 False 3648.0 3648 90.196 580 3378 1 chr6A.!!$F1 2798
10 TraesCS1B01G362300 chr2B 62334853 62337635 2782 False 3578.0 3578 90.007 583 3378 1 chr2B.!!$F1 2795
11 TraesCS1B01G362300 chr3B 3760636 3763429 2793 True 3565.0 3565 89.838 585 3378 1 chr3B.!!$R1 2793
12 TraesCS1B01G362300 chr3B 4661109 4663904 2795 True 3524.0 3524 89.566 583 3378 1 chr3B.!!$R2 2795
13 TraesCS1B01G362300 chr5B 455288165 455290989 2824 True 3561.0 3561 89.702 584 3378 1 chr5B.!!$R1 2794
14 TraesCS1B01G362300 chr5B 14353437 14356135 2698 False 1660.5 2283 91.823 583 3378 2 chr5B.!!$F1 2795
15 TraesCS1B01G362300 chr5B 670105096 670105979 883 True 1133.0 1133 89.878 2490 3378 1 chr5B.!!$R2 888
16 TraesCS1B01G362300 chr5A 562130734 562133542 2808 False 3496.0 3496 89.327 583 3378 1 chr5A.!!$F2 2795
17 TraesCS1B01G362300 chr5A 633043708 633045665 1957 True 2497.0 2497 89.929 583 2523 1 chr5A.!!$R1 1940
18 TraesCS1B01G362300 chr5A 513858011 513859663 1652 False 2154.0 2154 90.691 1769 3378 1 chr5A.!!$F1 1609
19 TraesCS1B01G362300 chr2A 14783665 14786119 2454 False 2972.0 2972 88.734 582 3042 1 chr2A.!!$F1 2460
20 TraesCS1B01G362300 chr2A 458968732 458970802 2070 True 2741.0 2741 90.822 583 2625 1 chr2A.!!$R2 2042
21 TraesCS1B01G362300 chr2A 38526110 38526824 714 True 712.0 712 85.694 2705 3378 1 chr2A.!!$R1 673
22 TraesCS1B01G362300 chr5D 351321021 351322962 1941 False 2830.0 2830 93.279 1470 3378 1 chr5D.!!$F1 1908
23 TraesCS1B01G362300 chr5D 443521252 443522535 1283 False 1672.0 1672 90.487 581 1845 1 chr5D.!!$F2 1264
24 TraesCS1B01G362300 chr6B 164439711 164440881 1170 True 1864.0 1864 95.392 581 1751 1 chr6B.!!$R2 1170
25 TraesCS1B01G362300 chr6B 164398304 164399429 1125 True 1716.0 1716 94.504 2275 3379 1 chr6B.!!$R1 1104
26 TraesCS1B01G362300 chr1A 572012844 572013710 866 True 1035.0 1035 88.431 582 1441 1 chr1A.!!$R1 859

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
203 204 0.031994 ATGTTGTTTGTGAAGGCGGC 59.968 50.0 0.00 0.0 0.0 6.53 F
574 575 0.807667 GCAGCTGACGACCACCATAG 60.808 60.0 20.43 0.0 0.0 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1276 1315 2.291741 GCCTCACAGTCAAAGAACCTTG 59.708 50.000 0.00 0.00 0.00 3.61 R
2437 2639 2.011947 ACCTGACATGCATGACATTCG 58.988 47.619 32.75 21.83 36.64 3.34 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
37 38 0.759060 ACAAAAGGAGGGGTTGCACC 60.759 55.000 0.00 0.00 37.60 5.01
104 105 4.658901 TGAGGTGAAGTAGGAAAAGAAGGT 59.341 41.667 0.00 0.00 0.00 3.50
137 138 2.744202 ACGTGTTCATGGAGATTCAAGC 59.256 45.455 0.00 0.00 0.00 4.01
203 204 0.031994 ATGTTGTTTGTGAAGGCGGC 59.968 50.000 0.00 0.00 0.00 6.53
320 321 0.951040 GAGGTCTTTGGCACGGACAG 60.951 60.000 17.07 0.00 0.00 3.51
360 361 7.946655 TTGGAATCGATGATGTATACAACTC 57.053 36.000 10.14 4.58 0.00 3.01
389 390 4.336433 ACATTTGATGATTTCGCGGATCTT 59.664 37.500 19.21 14.75 0.00 2.40
537 538 9.193133 CATACTTATTCCAGTTGGACTTATACG 57.807 37.037 0.00 0.00 45.39 3.06
556 557 1.971962 CGCATTGAGAAACGAAACTGC 59.028 47.619 0.00 0.00 0.00 4.40
572 573 2.046892 GCAGCTGACGACCACCAT 60.047 61.111 20.43 0.00 0.00 3.55
574 575 0.807667 GCAGCTGACGACCACCATAG 60.808 60.000 20.43 0.00 0.00 2.23
731 732 2.181021 CTTCGACCGCGCTAACCT 59.819 61.111 5.56 0.00 37.46 3.50
788 789 3.598715 TGGCGAACTGACGACCGT 61.599 61.111 0.00 0.00 40.96 4.83
1276 1315 2.162408 CCGAAGAAGATGGTGGCTTTTC 59.838 50.000 0.00 0.00 0.00 2.29
1527 1600 3.572642 TGAACCTGAGAACACCTACAGA 58.427 45.455 0.00 0.00 32.90 3.41
2437 2639 5.782845 AGGCCTATATATATAGCTGGCCTTC 59.217 44.000 30.26 16.32 43.10 3.46
2851 3107 6.839454 AGCAACTAGTAGTAGATAGTGCCTA 58.161 40.000 15.51 0.00 32.62 3.93
2893 3149 6.710597 AGTAGATATTGCCTGACGAAACTA 57.289 37.500 0.00 0.00 0.00 2.24
2906 3162 6.165700 TGACGAAACTAAACCTAGGAACTT 57.834 37.500 17.98 8.20 41.75 2.66
2907 3163 7.288810 TGACGAAACTAAACCTAGGAACTTA 57.711 36.000 17.98 8.93 41.75 2.24
3180 3483 1.475169 CGAGGATGGGAGCCAGCATA 61.475 60.000 0.00 0.00 42.36 3.14
3215 3518 0.675837 TCGTTGGAGAGGACGACGAT 60.676 55.000 0.00 0.00 46.48 3.73
3232 3535 1.135139 CGATCTCATCCACCTTGTCGT 59.865 52.381 0.00 0.00 0.00 4.34
3233 3536 2.417379 CGATCTCATCCACCTTGTCGTT 60.417 50.000 0.00 0.00 0.00 3.85
3234 3537 3.181490 CGATCTCATCCACCTTGTCGTTA 60.181 47.826 0.00 0.00 0.00 3.18
3235 3538 3.868757 TCTCATCCACCTTGTCGTTAG 57.131 47.619 0.00 0.00 0.00 2.34
3236 3539 3.427573 TCTCATCCACCTTGTCGTTAGA 58.572 45.455 0.00 0.00 0.00 2.10
3237 3540 3.444034 TCTCATCCACCTTGTCGTTAGAG 59.556 47.826 0.00 0.00 0.00 2.43
3238 3541 3.162666 TCATCCACCTTGTCGTTAGAGT 58.837 45.455 0.00 0.00 0.00 3.24
3239 3542 3.192844 TCATCCACCTTGTCGTTAGAGTC 59.807 47.826 0.00 0.00 0.00 3.36
3240 3543 2.589720 TCCACCTTGTCGTTAGAGTCA 58.410 47.619 0.00 0.00 0.00 3.41
3296 3656 2.338984 GTCAGTGGACTCGCCGTT 59.661 61.111 0.00 0.00 40.99 4.44
3300 3660 0.456221 CAGTGGACTCGCCGTTAGAT 59.544 55.000 0.00 0.00 40.66 1.98
3303 3663 1.135199 GTGGACTCGCCGTTAGATTCA 60.135 52.381 0.00 0.00 40.66 2.57
3342 3702 1.925285 ATGGATTGCGCCTCTCCCAA 61.925 55.000 4.18 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 1.483004 TGAACACGTCAAACCTCTCCA 59.517 47.619 0.00 0.00 31.51 3.86
137 138 2.730550 AGCAATCTTTTTCCGCCAAG 57.269 45.000 0.00 0.00 0.00 3.61
203 204 0.877649 CGCATCTGGATCCAAGTCCG 60.878 60.000 17.00 12.38 41.35 4.79
320 321 2.034221 AAAAGCCTCCAGTCCGGC 59.966 61.111 0.00 0.00 46.65 6.13
360 361 6.471841 TCCGCGAAATCATCAAATGTTTATTG 59.528 34.615 8.23 0.00 0.00 1.90
389 390 0.608130 ACACATAGCAAGCCAGACGA 59.392 50.000 0.00 0.00 0.00 4.20
503 504 8.553153 TCCAACTGGAATAAGTATGTAAATGGA 58.447 33.333 0.00 0.00 42.18 3.41
522 523 5.109210 TCTCAATGCGTATAAGTCCAACTG 58.891 41.667 0.00 0.00 0.00 3.16
537 538 2.975851 CTGCAGTTTCGTTTCTCAATGC 59.024 45.455 5.25 0.00 0.00 3.56
556 557 0.179100 CCTATGGTGGTCGTCAGCTG 60.179 60.000 7.63 7.63 43.76 4.24
572 573 4.105577 TGGTTAAATACTCCAGCCACCTA 58.894 43.478 0.00 0.00 0.00 3.08
574 575 3.359695 TGGTTAAATACTCCAGCCACC 57.640 47.619 0.00 0.00 0.00 4.61
731 732 1.900351 CCAGGCCAGTCAGATTCGA 59.100 57.895 5.01 0.00 0.00 3.71
788 789 2.696409 TTAACGGCCGTCAACAGCGA 62.696 55.000 34.29 8.46 0.00 4.93
973 1007 0.181114 TTCTATCAGCGGCAATGGCT 59.819 50.000 5.02 0.00 42.61 4.75
985 1019 4.202398 GGATGGCATCCTCAACTTCTATCA 60.202 45.833 34.15 0.00 46.19 2.15
1276 1315 2.291741 GCCTCACAGTCAAAGAACCTTG 59.708 50.000 0.00 0.00 0.00 3.61
2437 2639 2.011947 ACCTGACATGCATGACATTCG 58.988 47.619 32.75 21.83 36.64 3.34
3180 3483 1.446792 CGACGAGCCTGAACTGCAT 60.447 57.895 0.00 0.00 0.00 3.96
3215 3518 3.427573 TCTAACGACAAGGTGGATGAGA 58.572 45.455 0.00 0.00 0.00 3.27
3232 3535 2.302260 CGAGCCCTCTGATGACTCTAA 58.698 52.381 0.00 0.00 0.00 2.10
3233 3536 1.213182 ACGAGCCCTCTGATGACTCTA 59.787 52.381 0.00 0.00 0.00 2.43
3234 3537 0.033601 ACGAGCCCTCTGATGACTCT 60.034 55.000 0.00 0.00 0.00 3.24
3235 3538 0.383949 GACGAGCCCTCTGATGACTC 59.616 60.000 0.00 0.00 0.00 3.36
3236 3539 1.040339 GGACGAGCCCTCTGATGACT 61.040 60.000 0.00 0.00 0.00 3.41
3237 3540 1.040339 AGGACGAGCCCTCTGATGAC 61.040 60.000 0.00 0.00 37.37 3.06
3238 3541 1.307986 AGGACGAGCCCTCTGATGA 59.692 57.895 0.00 0.00 37.37 2.92
3239 3542 3.947173 AGGACGAGCCCTCTGATG 58.053 61.111 0.00 0.00 37.37 3.07
3296 3656 2.494888 TGGGCCCTCTGATGAATCTA 57.505 50.000 25.70 0.00 0.00 1.98
3300 3660 0.549902 TCCTTGGGCCCTCTGATGAA 60.550 55.000 25.70 5.72 0.00 2.57
3303 3663 2.003548 GGTCCTTGGGCCCTCTGAT 61.004 63.158 25.70 0.00 0.00 2.90
3342 3702 1.762708 CCCCAATCAACAACGCCTAT 58.237 50.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.