Multiple sequence alignment - TraesCS7A01G133900

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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 TraesCS7A01G133900 chr7A 100.000 2237 0 0 1 2237 85879434 85877198 0.000000e+00 4132.0
1 TraesCS7A01G133900 chr7A 97.900 2190 42 2 48 2237 2869685 2871870 0.000000e+00 3786.0
2 TraesCS7A01G133900 chr7A 89.163 406 32 5 218 619 607605737 607606134 1.540000e-136 496.0
3 TraesCS7A01G133900 chr4A 99.772 2190 5 0 48 2237 684407850 684410039 0.000000e+00 4017.0
4 TraesCS7A01G133900 chr2A 99.680 2190 6 1 48 2237 756945934 756943746 0.000000e+00 4004.0
5 TraesCS7A01G133900 chr2A 93.727 1626 89 7 617 2235 305826240 305824621 0.000000e+00 2425.0
6 TraesCS7A01G133900 chr2A 90.421 261 20 4 46 303 374482844 374483102 2.750000e-89 339.0
7 TraesCS7A01G133900 chr2A 93.651 63 2 2 1 62 138518703 138518642 2.370000e-15 93.5
8 TraesCS7A01G133900 chr6A 99.178 2190 16 1 48 2237 604391214 604393401 0.000000e+00 3943.0
9 TraesCS7A01G133900 chr6A 90.038 261 21 4 46 303 610962418 610962676 1.280000e-87 333.0
10 TraesCS7A01G133900 chr6A 90.038 261 21 4 46 303 610986899 610987157 1.280000e-87 333.0
11 TraesCS7A01G133900 chr3A 97.900 2190 42 1 48 2237 26422445 26420260 0.000000e+00 3786.0
12 TraesCS7A01G133900 chr3A 97.484 1113 24 2 1125 2237 716469591 716468483 0.000000e+00 1897.0
13 TraesCS7A01G133900 chr5B 94.280 1626 80 7 617 2235 411795409 411797028 0.000000e+00 2475.0
14 TraesCS7A01G133900 chr5B 95.253 316 13 1 306 619 629257733 629257418 1.190000e-137 499.0
15 TraesCS7A01G133900 chr4B 92.185 1625 116 8 617 2237 256157989 256156372 0.000000e+00 2287.0
16 TraesCS7A01G133900 chr2D 91.939 980 62 4 617 1596 276943146 276944108 0.000000e+00 1356.0
17 TraesCS7A01G133900 chr2D 89.851 404 35 4 218 617 276940511 276940912 4.260000e-142 514.0
18 TraesCS7A01G133900 chr2B 95.253 316 13 1 306 619 244700936 244701251 1.190000e-137 499.0
19 TraesCS7A01G133900 chr3D 90.038 261 22 3 46 303 531301770 531302029 3.560000e-88 335.0
20 TraesCS7A01G133900 chr6B 98.246 57 1 0 1 57 564520868 564520924 1.410000e-17 100.0
21 TraesCS7A01G133900 chr6B 95.082 61 1 2 1 60 455424053 455424112 6.580000e-16 95.3
22 TraesCS7A01G133900 chr3B 95.238 63 3 0 1 63 302245098 302245036 1.410000e-17 100.0
23 TraesCS7A01G133900 chr3B 96.552 58 0 2 1 58 540519339 540519394 6.580000e-16 95.3
24 TraesCS7A01G133900 chr1B 95.082 61 3 0 1 61 151842998 151842938 1.830000e-16 97.1
25 TraesCS7A01G133900 chr1B 95.161 62 1 2 1 62 540278885 540278826 1.830000e-16 97.1
26 TraesCS7A01G133900 chr1A 96.610 59 0 2 1 59 67827863 67827807 1.830000e-16 97.1
27 TraesCS7A01G133900 chr7B 98.148 54 0 1 1 54 443307334 443307386 2.370000e-15 93.5


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 TraesCS7A01G133900 chr7A 85877198 85879434 2236 True 4132 4132 100.000 1 2237 1 chr7A.!!$R1 2236
1 TraesCS7A01G133900 chr7A 2869685 2871870 2185 False 3786 3786 97.900 48 2237 1 chr7A.!!$F1 2189
2 TraesCS7A01G133900 chr4A 684407850 684410039 2189 False 4017 4017 99.772 48 2237 1 chr4A.!!$F1 2189
3 TraesCS7A01G133900 chr2A 756943746 756945934 2188 True 4004 4004 99.680 48 2237 1 chr2A.!!$R3 2189
4 TraesCS7A01G133900 chr2A 305824621 305826240 1619 True 2425 2425 93.727 617 2235 1 chr2A.!!$R2 1618
5 TraesCS7A01G133900 chr6A 604391214 604393401 2187 False 3943 3943 99.178 48 2237 1 chr6A.!!$F1 2189
6 TraesCS7A01G133900 chr3A 26420260 26422445 2185 True 3786 3786 97.900 48 2237 1 chr3A.!!$R1 2189
7 TraesCS7A01G133900 chr3A 716468483 716469591 1108 True 1897 1897 97.484 1125 2237 1 chr3A.!!$R2 1112
8 TraesCS7A01G133900 chr5B 411795409 411797028 1619 False 2475 2475 94.280 617 2235 1 chr5B.!!$F1 1618
9 TraesCS7A01G133900 chr4B 256156372 256157989 1617 True 2287 2287 92.185 617 2237 1 chr4B.!!$R1 1620
10 TraesCS7A01G133900 chr2D 276940511 276944108 3597 False 935 1356 90.895 218 1596 2 chr2D.!!$F1 1378

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
29 30 1.425448 ACTTGCTTGGGACTAAAGGCT 59.575 47.619 0.0 0.0 0.0 4.58 F
30 31 2.158460 ACTTGCTTGGGACTAAAGGCTT 60.158 45.455 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1141 3381 3.055747 GGGATCTTGAAGACTCGGAAAGT 60.056 47.826 0.00 0.00 42.42 2.66 R
1662 3905 6.830912 AGATATATGTTGACCAGCTAGCAAA 58.169 36.000 18.83 0.08 0.00 3.68 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
26 27 3.923017 CCAACTTGCTTGGGACTAAAG 57.077 47.619 0.00 0.00 45.46 1.85
27 28 2.558359 CCAACTTGCTTGGGACTAAAGG 59.442 50.000 0.00 0.00 45.46 3.11
28 29 1.911057 ACTTGCTTGGGACTAAAGGC 58.089 50.000 0.00 0.00 0.00 4.35
29 30 1.425448 ACTTGCTTGGGACTAAAGGCT 59.575 47.619 0.00 0.00 0.00 4.58
30 31 2.158460 ACTTGCTTGGGACTAAAGGCTT 60.158 45.455 0.00 0.00 0.00 4.35
31 32 2.675658 TGCTTGGGACTAAAGGCTTT 57.324 45.000 17.76 17.76 0.00 3.51
32 33 2.238521 TGCTTGGGACTAAAGGCTTTG 58.761 47.619 22.32 13.97 0.00 2.77
33 34 2.239400 GCTTGGGACTAAAGGCTTTGT 58.761 47.619 22.32 16.86 0.00 2.83
34 35 2.628178 GCTTGGGACTAAAGGCTTTGTT 59.372 45.455 22.32 8.73 0.00 2.83
35 36 3.552890 GCTTGGGACTAAAGGCTTTGTTG 60.553 47.826 22.32 13.85 0.00 3.33
36 37 3.306472 TGGGACTAAAGGCTTTGTTGT 57.694 42.857 22.32 16.69 0.00 3.32
37 38 3.637769 TGGGACTAAAGGCTTTGTTGTT 58.362 40.909 22.32 1.84 0.00 2.83
38 39 3.383185 TGGGACTAAAGGCTTTGTTGTTG 59.617 43.478 22.32 7.79 0.00 3.33
39 40 3.383505 GGGACTAAAGGCTTTGTTGTTGT 59.616 43.478 22.32 10.58 0.00 3.32
40 41 4.142026 GGGACTAAAGGCTTTGTTGTTGTT 60.142 41.667 22.32 0.00 0.00 2.83
41 42 4.803613 GGACTAAAGGCTTTGTTGTTGTTG 59.196 41.667 22.32 0.00 0.00 3.33
42 43 5.400066 ACTAAAGGCTTTGTTGTTGTTGT 57.600 34.783 22.32 0.00 0.00 3.32
43 44 5.789521 ACTAAAGGCTTTGTTGTTGTTGTT 58.210 33.333 22.32 0.00 0.00 2.83
44 45 5.637387 ACTAAAGGCTTTGTTGTTGTTGTTG 59.363 36.000 22.32 0.00 0.00 3.33
45 46 3.676291 AGGCTTTGTTGTTGTTGTTGT 57.324 38.095 0.00 0.00 0.00 3.32
46 47 4.001618 AGGCTTTGTTGTTGTTGTTGTT 57.998 36.364 0.00 0.00 0.00 2.83
1141 3381 2.251818 CACCTGAGGAAGAGGTCAAGA 58.748 52.381 4.99 0.00 42.25 3.02
1714 3957 8.078596 GTCAGTATTTCTTTGCTCACTTGATTT 58.921 33.333 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.029918 GCCTTTAGTCCCAAGCAAGTTG 60.030 50.000 0.00 0.00 35.71 3.16
8 9 2.158460 AGCCTTTAGTCCCAAGCAAGTT 60.158 45.455 0.00 0.00 0.00 2.66
9 10 1.425448 AGCCTTTAGTCCCAAGCAAGT 59.575 47.619 0.00 0.00 0.00 3.16
10 11 2.206576 AGCCTTTAGTCCCAAGCAAG 57.793 50.000 0.00 0.00 0.00 4.01
11 12 2.627699 CAAAGCCTTTAGTCCCAAGCAA 59.372 45.455 0.00 0.00 0.00 3.91
12 13 2.238521 CAAAGCCTTTAGTCCCAAGCA 58.761 47.619 0.00 0.00 0.00 3.91
13 14 2.239400 ACAAAGCCTTTAGTCCCAAGC 58.761 47.619 0.00 0.00 0.00 4.01
14 15 3.636764 ACAACAAAGCCTTTAGTCCCAAG 59.363 43.478 0.00 0.00 0.00 3.61
15 16 3.637769 ACAACAAAGCCTTTAGTCCCAA 58.362 40.909 0.00 0.00 0.00 4.12
16 17 3.306472 ACAACAAAGCCTTTAGTCCCA 57.694 42.857 0.00 0.00 0.00 4.37
17 18 3.383505 ACAACAACAAAGCCTTTAGTCCC 59.616 43.478 0.00 0.00 0.00 4.46
18 19 4.649088 ACAACAACAAAGCCTTTAGTCC 57.351 40.909 0.00 0.00 0.00 3.85
19 20 5.407502 ACAACAACAACAAAGCCTTTAGTC 58.592 37.500 0.00 0.00 0.00 2.59
20 21 5.400066 ACAACAACAACAAAGCCTTTAGT 57.600 34.783 0.00 0.00 0.00 2.24
21 22 5.637387 ACAACAACAACAACAAAGCCTTTAG 59.363 36.000 0.00 0.00 0.00 1.85
22 23 5.542779 ACAACAACAACAACAAAGCCTTTA 58.457 33.333 0.00 0.00 0.00 1.85
23 24 4.384940 ACAACAACAACAACAAAGCCTTT 58.615 34.783 0.00 0.00 0.00 3.11
24 25 4.001618 ACAACAACAACAACAAAGCCTT 57.998 36.364 0.00 0.00 0.00 4.35
25 26 3.676291 ACAACAACAACAACAAAGCCT 57.324 38.095 0.00 0.00 0.00 4.58
26 27 3.496507 ACAACAACAACAACAACAAAGCC 59.503 39.130 0.00 0.00 0.00 4.35
27 28 4.723879 ACAACAACAACAACAACAAAGC 57.276 36.364 0.00 0.00 0.00 3.51
28 29 7.381139 AGACTAACAACAACAACAACAACAAAG 59.619 33.333 0.00 0.00 0.00 2.77
29 30 7.203910 AGACTAACAACAACAACAACAACAAA 58.796 30.769 0.00 0.00 0.00 2.83
30 31 6.740110 AGACTAACAACAACAACAACAACAA 58.260 32.000 0.00 0.00 0.00 2.83
31 32 6.320494 AGACTAACAACAACAACAACAACA 57.680 33.333 0.00 0.00 0.00 3.33
32 33 8.905103 AATAGACTAACAACAACAACAACAAC 57.095 30.769 0.00 0.00 0.00 3.32
33 34 9.562583 GAAATAGACTAACAACAACAACAACAA 57.437 29.630 0.00 0.00 0.00 2.83
34 35 8.952278 AGAAATAGACTAACAACAACAACAACA 58.048 29.630 0.00 0.00 0.00 3.33
35 36 9.783256 AAGAAATAGACTAACAACAACAACAAC 57.217 29.630 0.00 0.00 0.00 3.32
36 37 9.781834 CAAGAAATAGACTAACAACAACAACAA 57.218 29.630 0.00 0.00 0.00 2.83
37 38 8.402472 CCAAGAAATAGACTAACAACAACAACA 58.598 33.333 0.00 0.00 0.00 3.33
38 39 8.403236 ACCAAGAAATAGACTAACAACAACAAC 58.597 33.333 0.00 0.00 0.00 3.32
39 40 8.514330 ACCAAGAAATAGACTAACAACAACAA 57.486 30.769 0.00 0.00 0.00 2.83
40 41 9.787435 ATACCAAGAAATAGACTAACAACAACA 57.213 29.630 0.00 0.00 0.00 3.33
512 517 5.422012 TGTAGCACAGATCTATTGACCAAGA 59.578 40.000 7.54 0.00 0.00 3.02
1141 3381 3.055747 GGGATCTTGAAGACTCGGAAAGT 60.056 47.826 0.00 0.00 42.42 2.66
1662 3905 6.830912 AGATATATGTTGACCAGCTAGCAAA 58.169 36.000 18.83 0.08 0.00 3.68
1714 3957 7.014134 TGAGATGTCTTACTTTTGGCAATCAAA 59.986 33.333 0.00 0.00 42.98 2.69


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

AutoCloner maintained by Alex Coulton.