Multiple sequence alignment - TraesCS1A01G238600

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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 TraesCS1A01G238600 chr1A 100.000 4217 0 0 1 4217 425258917 425254701 0.000000e+00 7788.0
1 TraesCS1A01G238600 chr1A 97.428 3305 80 3 913 4217 421637900 421641199 0.000000e+00 5627.0
2 TraesCS1A01G238600 chr1A 97.832 3229 57 4 990 4217 407518165 407514949 0.000000e+00 5563.0
3 TraesCS1A01G238600 chr1A 97.962 2503 41 5 990 3483 406582576 406585077 0.000000e+00 4331.0
4 TraesCS1A01G238600 chr1A 90.833 1440 58 27 1 1406 417396693 417395294 0.000000e+00 1860.0
5 TraesCS1A01G238600 chr1A 98.789 743 8 1 3475 4217 406597398 406598139 0.000000e+00 1321.0
6 TraesCS1A01G238600 chr1A 91.284 436 19 9 7 423 406581492 406581927 1.020000e-160 577.0
7 TraesCS1A01G238600 chr1A 91.284 436 19 9 7 423 407519246 407518811 1.020000e-160 577.0
8 TraesCS1A01G238600 chr1A 91.445 339 15 6 7 332 421635773 421636110 1.790000e-123 453.0
9 TraesCS1A01G238600 chr1A 87.097 217 13 9 635 844 407518555 407518347 9.120000e-57 231.0
10 TraesCS1A01G238600 chr1A 86.175 217 15 9 635 844 406582183 406582391 1.970000e-53 220.0
11 TraesCS1A01G238600 chr1A 85.780 218 16 10 635 845 421637591 421637800 2.550000e-52 217.0
12 TraesCS1A01G238600 chr1A 92.553 94 7 0 327 420 421637240 421637333 7.350000e-28 135.0
13 TraesCS1A01G238600 chr1D 96.157 3305 120 6 914 4217 322380916 322384214 0.000000e+00 5393.0
14 TraesCS1A01G238600 chr1D 87.312 2790 273 30 446 3198 328446528 328443783 0.000000e+00 3116.0
15 TraesCS1A01G238600 chr1D 88.277 2124 220 13 995 3116 323636495 323638591 0.000000e+00 2516.0
16 TraesCS1A01G238600 chr1D 91.935 434 18 10 7 423 322379909 322380342 3.630000e-165 592.0
17 TraesCS1A01G238600 chr1D 92.289 415 13 6 24 429 328453379 328452975 4.730000e-159 571.0
18 TraesCS1A01G238600 chr1D 86.574 216 20 8 637 845 322380599 322380812 3.280000e-56 230.0
19 TraesCS1A01G238600 chr1D 85.345 232 12 13 12 233 323635328 323635547 1.970000e-53 220.0
20 TraesCS1A01G238600 chr1B 96.811 3230 101 2 990 4217 435360632 435363861 0.000000e+00 5393.0
21 TraesCS1A01G238600 chr1B 86.933 2227 261 17 987 3198 442621036 442618825 0.000000e+00 2473.0
22 TraesCS1A01G238600 chr1B 86.810 2229 260 21 990 3201 326927499 326925288 0.000000e+00 2457.0
23 TraesCS1A01G238600 chr1B 88.692 1583 165 7 995 2576 435927032 435928601 0.000000e+00 1919.0
24 TraesCS1A01G238600 chr1B 86.689 1202 144 8 2005 3198 442551746 442550553 0.000000e+00 1319.0
25 TraesCS1A01G238600 chr1B 92.393 815 40 10 1 798 442621887 442621078 0.000000e+00 1142.0
26 TraesCS1A01G238600 chr1B 93.706 429 15 7 7 423 435359491 435359919 2.140000e-177 632.0
27 TraesCS1A01G238600 chr1B 94.057 387 11 7 38 414 326928546 326928162 1.020000e-160 577.0
28 TraesCS1A01G238600 chr1B 86.977 215 14 10 637 844 435360243 435360450 3.280000e-56 230.0
29 TraesCS1A01G238600 chr1B 84.049 163 11 9 637 792 326927877 326927723 4.400000e-30 143.0
30 TraesCS1A01G238600 chr1B 92.000 75 5 1 771 844 435808500 435808574 2.070000e-18 104.0
31 TraesCS1A01G238600 chr3B 92.521 361 25 1 3859 4217 169901543 169901903 2.250000e-142 516.0
32 TraesCS1A01G238600 chr3B 91.228 228 17 3 3630 3856 169901205 169901430 1.470000e-79 307.0
33 TraesCS1A01G238600 chr7B 85.000 80 7 4 3872 3946 276178124 276178045 4.520000e-10 76.8
34 TraesCS1A01G238600 chr6B 85.000 80 7 4 3872 3946 35811971 35811892 4.520000e-10 76.8
35 TraesCS1A01G238600 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 TraesCS1A01G238600 chr1A 425254701 425258917 4216 True 7788.000000 7788 100.000000 1 4217 1 chr1A.!!$R2 4216
1 TraesCS1A01G238600 chr1A 407514949 407519246 4297 True 2123.666667 5563 92.071000 7 4217 3 chr1A.!!$R3 4210
2 TraesCS1A01G238600 chr1A 417395294 417396693 1399 True 1860.000000 1860 90.833000 1 1406 1 chr1A.!!$R1 1405
3 TraesCS1A01G238600 chr1A 406581492 406585077 3585 False 1709.333333 4331 91.807000 7 3483 3 chr1A.!!$F2 3476
4 TraesCS1A01G238600 chr1A 421635773 421641199 5426 False 1608.000000 5627 91.801500 7 4217 4 chr1A.!!$F3 4210
5 TraesCS1A01G238600 chr1A 406597398 406598139 741 False 1321.000000 1321 98.789000 3475 4217 1 chr1A.!!$F1 742
6 TraesCS1A01G238600 chr1D 328443783 328446528 2745 True 3116.000000 3116 87.312000 446 3198 1 chr1D.!!$R1 2752
7 TraesCS1A01G238600 chr1D 322379909 322384214 4305 False 2071.666667 5393 91.555333 7 4217 3 chr1D.!!$F1 4210
8 TraesCS1A01G238600 chr1D 323635328 323638591 3263 False 1368.000000 2516 86.811000 12 3116 2 chr1D.!!$F2 3104
9 TraesCS1A01G238600 chr1B 435359491 435363861 4370 False 2085.000000 5393 92.498000 7 4217 3 chr1B.!!$F3 4210
10 TraesCS1A01G238600 chr1B 435927032 435928601 1569 False 1919.000000 1919 88.692000 995 2576 1 chr1B.!!$F2 1581
11 TraesCS1A01G238600 chr1B 442618825 442621887 3062 True 1807.500000 2473 89.663000 1 3198 2 chr1B.!!$R3 3197
12 TraesCS1A01G238600 chr1B 442550553 442551746 1193 True 1319.000000 1319 86.689000 2005 3198 1 chr1B.!!$R1 1193
13 TraesCS1A01G238600 chr1B 326925288 326928546 3258 True 1059.000000 2457 88.305333 38 3201 3 chr1B.!!$R2 3163
14 TraesCS1A01G238600 chr3B 169901205 169901903 698 False 411.500000 516 91.874500 3630 4217 2 chr3B.!!$F1 587

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
334 1514 0.234884 CGGTCGAACCTTTGCTTGTC 59.765 55.0 0.0 0.0 35.66 3.18 F
1048 3148 0.038159 ACTTTTCTCGCTCACCCTCG 60.038 55.0 0.0 0.0 0.00 4.63 F
1092 3192 0.041488 CGGTATGCGACGACCTAGTC 60.041 60.0 0.0 0.0 37.76 2.59 F
1463 3563 0.387929 CTGGACACCGGCATATACGT 59.612 55.0 0.0 0.0 0.00 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1599 3705 1.846712 TTCCATGCCCCGTGTCATCA 61.847 55.000 0.00 0.00 0.00 3.07 R
2829 4944 0.248825 CTTGATCACCGAGGAGAGCG 60.249 60.000 0.00 0.00 0.00 5.03 R
3036 5151 0.456995 GGTAGACTCGCACTGTGAGC 60.457 60.000 17.86 11.39 43.14 4.26 R
4008 6235 6.407979 GCAGAGGAGTTGAGGAATAAGAGATT 60.408 42.308 0.00 0.00 0.00 2.40 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
108 121 2.120355 TAGCGCAACACTCGACACGA 62.120 55.000 11.47 0.00 0.00 4.35
135 148 1.738099 CCTCTCGGCCACTTTCACG 60.738 63.158 2.24 0.00 0.00 4.35
277 319 1.971357 GTCACTTCTCTGTTCCCTCCA 59.029 52.381 0.00 0.00 0.00 3.86
292 338 2.559478 CCCTCCACCATTTTCCCATCAA 60.559 50.000 0.00 0.00 0.00 2.57
334 1514 0.234884 CGGTCGAACCTTTGCTTGTC 59.765 55.000 0.00 0.00 35.66 3.18
453 1799 6.395629 TGTTGATCGAAACTCTTACCTTAGG 58.604 40.000 0.00 0.00 0.00 2.69
588 1937 5.980715 GCCTTTTCGTTTGGAATCTTTTACA 59.019 36.000 0.00 0.00 33.85 2.41
764 2149 1.129998 CGAAGCCATTTCTGTGCTCTG 59.870 52.381 0.00 0.00 33.36 3.35
768 2160 0.609957 CCATTTCTGTGCTCTGCCCA 60.610 55.000 0.00 0.00 0.00 5.36
770 2162 1.404391 CATTTCTGTGCTCTGCCCATC 59.596 52.381 0.00 0.00 0.00 3.51
773 2165 0.694771 TCTGTGCTCTGCCCATCTTT 59.305 50.000 0.00 0.00 0.00 2.52
940 2964 1.599606 CCACCTCTCCTCCTCACACG 61.600 65.000 0.00 0.00 0.00 4.49
1048 3148 0.038159 ACTTTTCTCGCTCACCCTCG 60.038 55.000 0.00 0.00 0.00 4.63
1091 3191 2.020131 CGGTATGCGACGACCTAGT 58.980 57.895 0.00 0.00 33.21 2.57
1092 3192 0.041488 CGGTATGCGACGACCTAGTC 60.041 60.000 0.00 0.00 37.76 2.59
1284 3384 1.513158 CGTGAGGCTCACCGAAGAT 59.487 57.895 35.01 0.00 44.20 2.40
1333 3433 1.602323 TTTCTGCGGGCGTTTCCAT 60.602 52.632 0.00 0.00 36.21 3.41
1463 3563 0.387929 CTGGACACCGGCATATACGT 59.612 55.000 0.00 0.00 0.00 3.57
1599 3705 1.349026 CCCAGAGCATATGATTCCGGT 59.651 52.381 6.97 0.00 0.00 5.28
1730 3836 0.958091 GCACACTTGGCCATGTACAA 59.042 50.000 22.76 0.00 0.00 2.41
2072 4178 3.727726 TCAATCAGACTGCGAACTCAAA 58.272 40.909 0.00 0.00 0.00 2.69
2398 4513 7.333423 GTGCCAAAGTCATATACAAGAACACTA 59.667 37.037 0.00 0.00 0.00 2.74
2730 4845 1.378250 GCAGCATCAGAGGGCAACT 60.378 57.895 0.14 0.00 0.00 3.16
2778 4893 7.510549 TGCCAATCCTATAAAAGCTATTGAC 57.489 36.000 3.66 0.00 32.67 3.18
2829 4944 4.940046 ACTGAATATGCTGGCTACATATGC 59.060 41.667 1.58 10.83 39.28 3.14
3036 5151 0.905357 AGATGGAGGTTCCCAAGTCG 59.095 55.000 0.00 0.00 40.04 4.18
3221 5336 4.323104 GGCTTCTCCTCTGTTGTAATCAGT 60.323 45.833 0.00 0.00 34.86 3.41
4008 6235 2.092646 AGTTAGACCTTGCCAACACACA 60.093 45.455 0.00 0.00 0.00 3.72
4016 6243 3.820467 CCTTGCCAACACACAATCTCTTA 59.180 43.478 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.017026 GGGAGCTAAGCCATATTTAGTGTTTC 60.017 42.308 0.00 0.00 32.09 2.78
85 97 1.009389 GTCGAGTGTTGCGCTAGCTT 61.009 55.000 13.93 0.00 45.42 3.74
135 148 2.196997 TATGCTGCTGGTGGGTGGTC 62.197 60.000 0.00 0.00 0.00 4.02
277 319 2.827921 GCAGAGTTGATGGGAAAATGGT 59.172 45.455 0.00 0.00 0.00 3.55
292 338 3.352222 GCACGCAGCTTGCAGAGT 61.352 61.111 18.59 0.00 45.36 3.24
453 1799 4.399934 CAGGGGAGTAGTAGAGACAGAAAC 59.600 50.000 0.00 0.00 0.00 2.78
588 1937 3.941188 CGTCTGTGGGGTGGCTGT 61.941 66.667 0.00 0.00 0.00 4.40
613 1962 0.320050 GCTACATGGCTAGGGAGAGC 59.680 60.000 0.00 0.00 42.05 4.09
773 2165 4.456535 TCGGTTGGATTTGTGAGAGAAAA 58.543 39.130 0.00 0.00 0.00 2.29
1091 3191 2.283894 TTGGAGAGAGGCCTGCGA 60.284 61.111 12.00 0.00 0.00 5.10
1092 3192 2.186384 CTTGGAGAGAGGCCTGCG 59.814 66.667 12.00 0.00 0.00 5.18
1284 3384 2.662596 GACACCATGGCGAGGTCA 59.337 61.111 13.04 0.00 37.23 4.02
1333 3433 3.161450 GGGGCGCCAGAGATGGTA 61.161 66.667 30.85 0.00 0.00 3.25
1463 3563 4.471025 TGTCATCAAAGGAAGGATGCTCTA 59.529 41.667 0.00 0.00 40.50 2.43
1599 3705 1.846712 TTCCATGCCCCGTGTCATCA 61.847 55.000 0.00 0.00 0.00 3.07
1730 3836 3.091545 CACCCAAGAATTATGCACACCT 58.908 45.455 0.00 0.00 0.00 4.00
1883 3989 2.028130 CAACAACACCCTTTGCTACCA 58.972 47.619 0.00 0.00 0.00 3.25
2072 4178 2.683768 ACAGAGGAACAGAGTTGGAGT 58.316 47.619 0.00 0.00 0.00 3.85
2398 4513 0.392998 GATGGACGGACACCAAGCAT 60.393 55.000 0.00 0.00 40.93 3.79
2730 4845 2.828095 GCACCCATGGCATACGCA 60.828 61.111 6.09 0.00 41.24 5.24
2778 4893 1.451387 GTCATACACAAGGCCCGGG 60.451 63.158 19.09 19.09 0.00 5.73
2829 4944 0.248825 CTTGATCACCGAGGAGAGCG 60.249 60.000 0.00 0.00 0.00 5.03
3036 5151 0.456995 GGTAGACTCGCACTGTGAGC 60.457 60.000 17.86 11.39 43.14 4.26
4008 6235 6.407979 GCAGAGGAGTTGAGGAATAAGAGATT 60.408 42.308 0.00 0.00 0.00 2.40
4016 6243 3.586618 AGAAAGCAGAGGAGTTGAGGAAT 59.413 43.478 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.