Multiple sequence alignment - TraesCS1D01G234200

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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 TraesCS1D01G234200 chr1D 100.000 4217 0 0 1 4217 322380000 322384216 0.000000e+00 7788.0
1 TraesCS1D01G234200 chr1D 89.222 2134 198 15 986 3116 323636487 323638591 0.000000e+00 2638.0
2 TraesCS1D01G234200 chr1D 86.898 2366 265 30 902 3242 328446087 328443742 0.000000e+00 2610.0
3 TraesCS1D01G234200 chr1D 91.117 349 11 12 1 343 328453315 328452981 4.970000e-124 455.0
4 TraesCS1D01G234200 chr1D 87.037 216 20 5 600 813 328446361 328446152 1.960000e-58 237.0
5 TraesCS1D01G234200 chr1D 90.805 87 7 1 509 595 323635646 323635731 9.580000e-22 115.0
6 TraesCS1D01G234200 chr1A 95.449 3977 161 11 246 4217 421637240 421641201 0.000000e+00 6324.0
7 TraesCS1D01G234200 chr1A 96.186 3304 119 6 920 4217 425258001 425254699 0.000000e+00 5397.0
8 TraesCS1D01G234200 chr1A 96.040 3232 111 7 990 4217 407518165 407514947 0.000000e+00 5243.0
9 TraesCS1D01G234200 chr1A 96.286 2504 81 4 990 3483 406582576 406585077 0.000000e+00 4098.0
10 TraesCS1D01G234200 chr1A 84.876 1858 244 24 1402 3242 417389158 417387321 0.000000e+00 1840.0
11 TraesCS1D01G234200 chr1A 96.313 895 20 4 1 891 407519156 407518271 0.000000e+00 1458.0
12 TraesCS1D01G234200 chr1A 96.076 892 22 4 1 888 406581582 406582464 0.000000e+00 1441.0
13 TraesCS1D01G234200 chr1A 96.042 758 25 4 3463 4217 406597386 406598141 0.000000e+00 1229.0
14 TraesCS1D01G234200 chr1A 94.461 343 12 5 1 343 425258830 425258495 4.830000e-144 521.0
15 TraesCS1D01G234200 chr1A 93.314 344 17 5 1 343 417396599 417396261 1.750000e-138 503.0
16 TraesCS1D01G234200 chr1A 98.425 254 2 1 1 254 421635863 421636114 2.990000e-121 446.0
17 TraesCS1D01G234200 chr1A 86.574 216 20 8 600 813 425258281 425258073 3.280000e-56 230.0
18 TraesCS1D01G234200 chr1A 91.045 134 9 1 774 907 406582415 406582545 1.200000e-40 178.0
19 TraesCS1D01G234200 chr1A 90.076 131 7 1 777 907 407518320 407518196 9.380000e-37 165.0
20 TraesCS1D01G234200 chr1B 95.608 3233 136 5 990 4217 435360632 435363863 0.000000e+00 5179.0
21 TraesCS1D01G234200 chr1B 87.121 2275 252 27 987 3242 442621036 442618784 0.000000e+00 2540.0
22 TraesCS1D01G234200 chr1B 87.175 2230 250 23 990 3201 326927499 326925288 0.000000e+00 2501.0
23 TraesCS1D01G234200 chr1B 90.082 1593 141 10 986 2576 435927024 435928601 0.000000e+00 2050.0
24 TraesCS1D01G234200 chr1B 86.378 1248 147 14 2005 3242 442551746 442550512 0.000000e+00 1341.0
25 TraesCS1D01G234200 chr1B 93.645 535 21 3 354 888 435360002 435360523 0.000000e+00 787.0
26 TraesCS1D01G234200 chr1B 89.580 547 23 11 345 891 326928119 326927607 0.000000e+00 664.0
27 TraesCS1D01G234200 chr1B 95.942 345 8 4 1 345 435359583 435359921 4.760000e-154 555.0
28 TraesCS1D01G234200 chr1B 95.690 348 9 3 1 343 442621803 442621457 4.760000e-154 555.0
29 TraesCS1D01G234200 chr1B 94.328 335 11 6 1 334 326928489 326928162 1.350000e-139 507.0
30 TraesCS1D01G234200 chr1B 92.174 345 23 2 733 1077 435808496 435808836 6.340000e-133 484.0
31 TraesCS1D01G234200 chr1B 86.391 169 15 5 600 766 442621240 442621078 1.200000e-40 178.0
32 TraesCS1D01G234200 chr1B 87.786 131 11 3 777 907 326927656 326927531 9.450000e-32 148.0
33 TraesCS1D01G234200 chr3B 93.370 362 20 1 3859 4216 169901543 169901904 2.230000e-147 532.0
34 TraesCS1D01G234200 chr7B 91.071 56 5 0 3872 3927 276178124 276178069 4.520000e-10 76.8
35 TraesCS1D01G234200 chr6B 91.071 56 5 0 3872 3927 35811971 35811916 4.520000e-10 76.8
36 TraesCS1D01G234200 chr6A 91.071 56 5 0 3872 3927 50238891 50238946 4.520000e-10 76.8


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 TraesCS1D01G234200 chr1D 322380000 322384216 4216 False 7788.000000 7788 100.00000 1 4217 1 chr1D.!!$F1 4216
1 TraesCS1D01G234200 chr1D 328443742 328446361 2619 True 1423.500000 2610 86.96750 600 3242 2 chr1D.!!$R2 2642
2 TraesCS1D01G234200 chr1D 323635646 323638591 2945 False 1376.500000 2638 90.01350 509 3116 2 chr1D.!!$F2 2607
3 TraesCS1D01G234200 chr1A 421635863 421641201 5338 False 3385.000000 6324 96.93700 1 4217 2 chr1A.!!$F3 4216
4 TraesCS1D01G234200 chr1A 407514947 407519156 4209 True 2288.666667 5243 94.14300 1 4217 3 chr1A.!!$R3 4216
5 TraesCS1D01G234200 chr1A 425254699 425258830 4131 True 2049.333333 5397 92.40700 1 4217 3 chr1A.!!$R4 4216
6 TraesCS1D01G234200 chr1A 406581582 406585077 3495 False 1905.666667 4098 94.46900 1 3483 3 chr1A.!!$F2 3482
7 TraesCS1D01G234200 chr1A 417387321 417389158 1837 True 1840.000000 1840 84.87600 1402 3242 1 chr1A.!!$R1 1840
8 TraesCS1D01G234200 chr1A 406597386 406598141 755 False 1229.000000 1229 96.04200 3463 4217 1 chr1A.!!$F1 754
9 TraesCS1D01G234200 chr1B 435359583 435363863 4280 False 2173.666667 5179 95.06500 1 4217 3 chr1B.!!$F3 4216
10 TraesCS1D01G234200 chr1B 435927024 435928601 1577 False 2050.000000 2050 90.08200 986 2576 1 chr1B.!!$F2 1590
11 TraesCS1D01G234200 chr1B 442550512 442551746 1234 True 1341.000000 1341 86.37800 2005 3242 1 chr1B.!!$R1 1237
12 TraesCS1D01G234200 chr1B 442618784 442621803 3019 True 1091.000000 2540 89.73400 1 3242 3 chr1B.!!$R3 3241
13 TraesCS1D01G234200 chr1B 326925288 326928489 3201 True 955.000000 2501 89.71725 1 3201 4 chr1B.!!$R2 3200

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
930 2585 0.609131 CCTTTCATCACCGCCACCTT 60.609 55.0 0.00 0.0 0.00 3.50 F
1311 3052 0.035056 CCATGGTGTCCCAGAGGAAC 60.035 60.0 2.57 0.0 46.38 3.62 F
2011 3758 0.790814 CCGAAGCTTCAAGACCGTTC 59.209 55.0 25.47 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2002 3749 0.886490 CCAAGCTGCAGAACGGTCTT 60.886 55.000 20.43 7.07 28.78 3.01 R
2188 3941 1.198637 GTCAGACTGGTTGATGCTTGC 59.801 52.381 1.81 0.00 0.00 4.01 R
3501 5254 0.033306 TGGAGGCAGCAATGGCATAA 60.033 50.000 0.00 0.00 44.61 1.90 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
783 2086 1.203237 AGGCAGAGTGAGGGAAAGAGA 60.203 52.381 0.00 0.00 0.00 3.10
915 2528 1.304217 TCGTCCTCTCGGCTCCTTT 60.304 57.895 0.00 0.00 0.00 3.11
923 2536 0.807667 CTCGGCTCCTTTCATCACCG 60.808 60.000 0.00 0.00 41.92 4.94
930 2585 0.609131 CCTTTCATCACCGCCACCTT 60.609 55.000 0.00 0.00 0.00 3.50
1238 2979 0.320247 GAGCCACGCCTCATCCATAG 60.320 60.000 0.00 0.00 0.00 2.23
1311 3052 0.035056 CCATGGTGTCCCAGAGGAAC 60.035 60.000 2.57 0.00 46.38 3.62
1785 3532 5.047660 GGACATAGTAGCTGGGTTAGATGAG 60.048 48.000 0.00 0.00 0.00 2.90
1794 3541 2.642311 TGGGTTAGATGAGGCTGTCAAA 59.358 45.455 0.00 0.00 39.19 2.69
2011 3758 0.790814 CCGAAGCTTCAAGACCGTTC 59.209 55.000 25.47 0.00 0.00 3.95
2067 3814 2.961062 AGCTTTCAACCAGACTGCAAAT 59.039 40.909 0.00 0.00 0.00 2.32
2192 3945 4.092771 CAATGAATGACACTGGAGCAAG 57.907 45.455 0.00 0.00 0.00 4.01
2193 3946 1.527034 TGAATGACACTGGAGCAAGC 58.473 50.000 0.00 0.00 0.00 4.01
2375 4128 0.877213 GCAACAAGCAAAGCCAGTGG 60.877 55.000 4.20 4.20 44.79 4.00
2396 4149 6.714810 AGTGGCAAAGTCATATACAAGAACAA 59.285 34.615 0.00 0.00 0.00 2.83
2428 4181 1.257750 CCGTCCATCTCCCACTGTCA 61.258 60.000 0.00 0.00 0.00 3.58
2532 4285 3.434319 GCATGGCCACCACTCACG 61.434 66.667 8.16 0.00 35.80 4.35
2664 4417 3.308401 TGCTATCAAGTCAGCCATCCTA 58.692 45.455 0.00 0.00 36.95 2.94
2682 4435 2.289631 CCTAACCACAGCTGACATCACA 60.290 50.000 23.35 0.00 0.00 3.58
3174 4927 1.691196 TGAGCTGGGTGTCCAAAAAG 58.309 50.000 0.00 0.00 43.51 2.27
3244 4997 5.106197 GGAAAAGCATGTGTGACATATGACA 60.106 40.000 23.73 6.76 36.53 3.58
3294 5047 8.792633 TGTAATTAGGGAAATGACTGTCTTTTG 58.207 33.333 21.75 0.00 30.91 2.44
3471 5224 3.968265 AGGTGTAAAATCCATCCAGGTG 58.032 45.455 0.00 0.00 39.02 4.00
3501 5254 2.584773 ACCCTTTCCCTCATATGGGTT 58.415 47.619 1.00 0.00 44.68 4.11
3514 5267 4.281435 TCATATGGGTTTATGCCATTGCTG 59.719 41.667 2.13 0.00 38.71 4.41
3588 5341 7.049754 TGAGCTATTGATGATAAACTTGCTCA 58.950 34.615 0.00 0.00 46.84 4.26
3679 5432 6.089417 CGGGTGCTTTGAAATTAGATTTTGAC 59.911 38.462 0.00 0.00 31.47 3.18
3699 5452 8.593492 TTTGACGATATTAAGGTCATCATCAG 57.407 34.615 0.00 0.00 40.10 2.90
3756 5509 7.506328 ACTCGTAGCTAAATTGGTTTTTCTT 57.494 32.000 0.00 0.00 0.00 2.52
3966 5721 2.265367 TGTTAGCTCATTCCCCTGTCA 58.735 47.619 0.00 0.00 0.00 3.58
4005 5762 3.412386 GAGTTAGACCTTGCCAACACAT 58.588 45.455 0.00 0.00 0.00 3.21
4039 5796 1.696336 TCAACTCCTCTGCTTTCTGCT 59.304 47.619 0.00 0.00 43.37 4.24
4135 5892 5.531659 CCTTCATCTTTGCTGATGCTATTCT 59.468 40.000 9.11 0.00 42.44 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
232 238 0.941542 CAAAGAAAGGTTCGACCGCA 59.058 50.000 0.00 0.00 44.90 5.69
316 1456 0.249531 CTGCAAAGCACACAATGGCA 60.250 50.000 0.00 0.00 33.79 4.92
320 1460 0.675633 GTCCCTGCAAAGCACACAAT 59.324 50.000 0.00 0.00 33.79 2.71
641 1942 4.219115 GCCTAGATGCTCCTATGCCTATA 58.781 47.826 0.00 0.00 0.00 1.31
643 1944 2.461695 GCCTAGATGCTCCTATGCCTA 58.538 52.381 0.00 0.00 0.00 3.93
644 1945 1.274712 GCCTAGATGCTCCTATGCCT 58.725 55.000 0.00 0.00 0.00 4.75
645 1946 0.108424 CGCCTAGATGCTCCTATGCC 60.108 60.000 0.00 0.00 29.93 4.40
649 1950 1.796190 CGCACGCCTAGATGCTCCTA 61.796 60.000 10.59 0.00 39.79 2.94
713 2016 0.514691 GCAGAGCACAAGCACAGTAC 59.485 55.000 0.00 0.00 45.49 2.73
715 2018 1.895707 GGCAGAGCACAAGCACAGT 60.896 57.895 1.60 0.00 45.49 3.55
915 2528 2.668632 GGAAGGTGGCGGTGATGA 59.331 61.111 0.00 0.00 0.00 2.92
923 2536 1.600916 GTGTGTGAGGGAAGGTGGC 60.601 63.158 0.00 0.00 0.00 5.01
930 2585 0.692756 TGAGGTTGGTGTGTGAGGGA 60.693 55.000 0.00 0.00 0.00 4.20
1238 2979 1.402984 CCGTGAAGACCTCAGTGTAGC 60.403 57.143 0.00 0.00 33.60 3.58
1311 3052 3.175976 AAACGCCCGCACAAACTCG 62.176 57.895 0.00 0.00 0.00 4.18
1558 3305 6.872920 TGAAATTATGGAATTTGGCACCTAC 58.127 36.000 0.56 0.00 43.76 3.18
1785 3532 2.229792 TCAACACCATCTTTGACAGCC 58.770 47.619 0.00 0.00 0.00 4.85
1794 3541 2.303890 TGAGAGCACATCAACACCATCT 59.696 45.455 0.00 0.00 0.00 2.90
1873 3620 3.771978 TGCTACCGCACTGAGTGA 58.228 55.556 18.18 0.00 42.25 3.41
1917 3664 3.361977 CTTGGCCCGTTGTTCCCG 61.362 66.667 0.00 0.00 0.00 5.14
2002 3749 0.886490 CCAAGCTGCAGAACGGTCTT 60.886 55.000 20.43 7.07 28.78 3.01
2011 3758 4.712425 GCCGTTGCCAAGCTGCAG 62.712 66.667 10.11 10.11 43.21 4.41
2067 3814 1.542547 GGAACGGACTTGGAGCTTGAA 60.543 52.381 0.00 0.00 0.00 2.69
2188 3941 1.198637 GTCAGACTGGTTGATGCTTGC 59.801 52.381 1.81 0.00 0.00 4.01
2191 3944 2.303890 TGATGTCAGACTGGTTGATGCT 59.696 45.455 1.81 0.00 0.00 3.79
2192 3945 2.676839 CTGATGTCAGACTGGTTGATGC 59.323 50.000 3.96 0.00 46.59 3.91
2193 3946 3.683340 CACTGATGTCAGACTGGTTGATG 59.317 47.826 16.41 0.00 46.59 3.07
2375 4128 7.008628 GCACATTGTTCTTGTATATGACTTTGC 59.991 37.037 0.00 0.00 0.00 3.68
2396 4149 1.302511 GGACGGACACCAAGCACAT 60.303 57.895 0.00 0.00 0.00 3.21
2532 4285 2.671896 ATGGCCCAGATCCAAGAATC 57.328 50.000 0.00 0.00 37.13 2.52
2664 4417 1.417517 TCTGTGATGTCAGCTGTGGTT 59.582 47.619 14.67 0.00 35.63 3.67
3092 4845 3.728864 GCTCACCGTAATGCTGAATGTTG 60.729 47.826 0.00 0.00 0.00 3.33
3244 4997 7.229306 ACAATATTACATGTGCGATTCTCCAAT 59.771 33.333 9.11 0.00 0.00 3.16
3471 5224 1.921049 AGGGAAAGGGTAGGTTTAGGC 59.079 52.381 0.00 0.00 0.00 3.93
3501 5254 0.033306 TGGAGGCAGCAATGGCATAA 60.033 50.000 0.00 0.00 44.61 1.90
3588 5341 8.727910 GGAACTAATGTAGAGGAAACGAAAAAT 58.272 33.333 0.00 0.00 0.00 1.82
3679 5432 8.515414 TGTAGACTGATGATGACCTTAATATCG 58.485 37.037 0.00 0.00 0.00 2.92
3699 5452 5.153950 ACCTCTCCTTTGTTCATGTAGAC 57.846 43.478 0.00 0.00 0.00 2.59
3756 5509 3.202151 AGGACCAGAAAAGAAACACAGGA 59.798 43.478 0.00 0.00 0.00 3.86
3851 5606 5.591643 AACTGTACAATTACTGCAACGAG 57.408 39.130 0.00 0.00 31.85 4.18
3956 5711 4.257810 TCCGGGGTGACAGGGGAA 62.258 66.667 0.00 0.00 0.00 3.97
4005 5762 4.682563 AGGAGTTGAGGAAGAAGAGATCA 58.317 43.478 0.00 0.00 0.00 2.92
4039 5796 2.203788 AGCGACCTGGACCTGGAA 60.204 61.111 23.36 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.