Multiple sequence alignment - TraesCS6A01G110700

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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 TraesCS6A01G110700 chr6A 100.000 2309 0 0 1 2309 79832113 79829805 0.000000e+00 4265.0
1 TraesCS6A01G110700 chr6A 93.459 2018 86 11 1 1992 516298172 516296175 0.000000e+00 2953.0
2 TraesCS6A01G110700 chr6A 96.448 366 13 0 1944 2309 516295824 516295459 2.540000e-169 604.0
3 TraesCS6A01G110700 chr6A 94.595 37 2 0 1867 1903 516296381 516296345 8.910000e-05 58.4
4 TraesCS6A01G110700 chr1A 93.527 1931 76 22 1 1883 480958091 480960020 0.000000e+00 2828.0
5 TraesCS6A01G110700 chr1A 96.655 837 27 1 1 837 559589326 559590161 0.000000e+00 1389.0
6 TraesCS6A01G110700 chr1A 96.970 363 11 0 1944 2306 559591831 559592193 5.450000e-171 610.0
7 TraesCS6A01G110700 chr7A 96.075 1554 61 0 1 1554 719952612 719951059 0.000000e+00 2532.0
8 TraesCS6A01G110700 chr7A 95.143 1256 43 7 660 1897 643609844 643611099 0.000000e+00 1965.0
9 TraesCS6A01G110700 chr7A 96.511 1175 35 2 734 1902 130557908 130559082 0.000000e+00 1938.0
10 TraesCS6A01G110700 chr7A 97.013 837 25 0 1 837 643609125 643609961 0.000000e+00 1408.0
11 TraesCS6A01G110700 chr7A 96.655 837 28 0 1 837 134595825 134596661 0.000000e+00 1391.0
12 TraesCS6A01G110700 chr7A 96.655 837 28 0 1 837 192624557 192625393 0.000000e+00 1391.0
13 TraesCS6A01G110700 chr7A 97.814 366 8 0 1944 2309 699320620 699320255 1.160000e-177 632.0
14 TraesCS6A01G110700 chr7A 96.143 363 14 0 1944 2306 130559311 130559673 5.490000e-166 593.0
15 TraesCS6A01G110700 chr7A 95.902 366 15 0 1944 2309 719950341 719949976 5.490000e-166 593.0
16 TraesCS6A01G110700 chr2A 95.008 1262 45 7 660 1903 677898801 677897540 0.000000e+00 1965.0
17 TraesCS6A01G110700 chr7D 95.169 1242 44 7 643 1877 16799047 16797815 0.000000e+00 1947.0
18 TraesCS6A01G110700 chr7D 96.259 401 14 1 1910 2309 16797383 16796983 0.000000e+00 656.0
19 TraesCS6A01G110700 chr4A 95.387 1214 47 5 671 1877 514406953 514405742 0.000000e+00 1923.0
20 TraesCS6A01G110700 chr4A 97.133 837 24 0 1 837 637837348 637836512 0.000000e+00 1413.0
21 TraesCS6A01G110700 chr4A 81.481 189 17 4 1807 1988 637835561 637835384 3.090000e-29 139.0
22 TraesCS6A01G110700 chr7B 93.886 1243 62 8 648 1877 34281666 34280425 0.000000e+00 1862.0
23 TraesCS6A01G110700 chr5A 96.535 837 28 1 1 837 288269224 288268389 0.000000e+00 1384.0
24 TraesCS6A01G110700 chr3A 96.416 837 30 0 1 837 635312020 635312856 0.000000e+00 1380.0
25 TraesCS6A01G110700 chr3A 95.902 366 15 0 1944 2309 22601915 22601550 5.490000e-166 593.0
26 TraesCS6A01G110700 chr1D 92.250 400 25 6 1910 2306 490890814 490891210 1.550000e-156 562.0
27 TraesCS6A01G110700 chr2B 90.323 403 33 6 1910 2309 47385756 47385357 7.310000e-145 523.0


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 TraesCS6A01G110700 chr6A 79829805 79832113 2308 True 4265.000000 4265 100.0000 1 2309 1 chr6A.!!$R1 2308
1 TraesCS6A01G110700 chr6A 516295459 516298172 2713 True 1205.133333 2953 94.8340 1 2309 3 chr6A.!!$R2 2308
2 TraesCS6A01G110700 chr1A 480958091 480960020 1929 False 2828.000000 2828 93.5270 1 1883 1 chr1A.!!$F1 1882
3 TraesCS6A01G110700 chr1A 559589326 559592193 2867 False 999.500000 1389 96.8125 1 2306 2 chr1A.!!$F2 2305
4 TraesCS6A01G110700 chr7A 643609125 643611099 1974 False 1686.500000 1965 96.0780 1 1897 2 chr7A.!!$F4 1896
5 TraesCS6A01G110700 chr7A 719949976 719952612 2636 True 1562.500000 2532 95.9885 1 2309 2 chr7A.!!$R2 2308
6 TraesCS6A01G110700 chr7A 134595825 134596661 836 False 1391.000000 1391 96.6550 1 837 1 chr7A.!!$F1 836
7 TraesCS6A01G110700 chr7A 192624557 192625393 836 False 1391.000000 1391 96.6550 1 837 1 chr7A.!!$F2 836
8 TraesCS6A01G110700 chr7A 130557908 130559673 1765 False 1265.500000 1938 96.3270 734 2306 2 chr7A.!!$F3 1572
9 TraesCS6A01G110700 chr2A 677897540 677898801 1261 True 1965.000000 1965 95.0080 660 1903 1 chr2A.!!$R1 1243
10 TraesCS6A01G110700 chr7D 16796983 16799047 2064 True 1301.500000 1947 95.7140 643 2309 2 chr7D.!!$R1 1666
11 TraesCS6A01G110700 chr4A 514405742 514406953 1211 True 1923.000000 1923 95.3870 671 1877 1 chr4A.!!$R1 1206
12 TraesCS6A01G110700 chr4A 637835384 637837348 1964 True 776.000000 1413 89.3070 1 1988 2 chr4A.!!$R2 1987
13 TraesCS6A01G110700 chr7B 34280425 34281666 1241 True 1862.000000 1862 93.8860 648 1877 1 chr7B.!!$R1 1229
14 TraesCS6A01G110700 chr5A 288268389 288269224 835 True 1384.000000 1384 96.5350 1 837 1 chr5A.!!$R1 836
15 TraesCS6A01G110700 chr3A 635312020 635312856 836 False 1380.000000 1380 96.4160 1 837 1 chr3A.!!$F1 836

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
249 250 0.741574 TCGCATTTGATAACGGCGGT 60.742 50.0 13.24 7.51 46.95 5.68 F
1114 1428 0.323725 GAAGGATGTGCCCACACCAT 60.324 55.0 16.64 8.97 46.86 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1219 1533 0.947180 GCGTTAGTTGGCCTTCGACA 60.947 55.0 3.32 0.0 32.09 4.35 R
1964 2872 1.580059 GATAGGGACCCAGACACCAA 58.420 55.0 14.60 0.0 0.00 3.67 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
181 182 1.470098 GCATTTGAGGTGCGTCTGAAT 59.530 47.619 0.00 0.00 32.29 2.57
194 195 1.204941 GTCTGAATACTCGGTGGTGCT 59.795 52.381 0.00 0.00 0.00 4.40
249 250 0.741574 TCGCATTTGATAACGGCGGT 60.742 50.000 13.24 7.51 46.95 5.68
270 271 2.677836 TGAAGGCGAGAAACATACATGC 59.322 45.455 0.00 0.00 0.00 4.06
296 297 0.820074 TGGAAAAACCGTGCGGATGT 60.820 50.000 18.16 0.00 42.61 3.06
405 406 1.276421 CCCTCATATTAGGCCAGACCG 59.724 57.143 5.01 0.00 46.52 4.79
412 413 2.519771 TTAGGCCAGACCGTCTTCTA 57.480 50.000 5.01 0.00 46.52 2.10
453 454 6.210984 GGTAGAAGGAGAACTAAGAGGTTCAA 59.789 42.308 9.50 0.00 45.52 2.69
563 564 2.933287 TGTGCGGTGAAGGGGGAT 60.933 61.111 0.00 0.00 0.00 3.85
574 575 1.141053 GAAGGGGGATACAATGAGCGT 59.859 52.381 0.00 0.00 39.74 5.07
852 1164 6.310149 GGAGAGGAATGGTTGATAATGGATT 58.690 40.000 0.00 0.00 0.00 3.01
1017 1331 0.749454 GCATGGCTTCATCCGGTTCT 60.749 55.000 0.00 0.00 0.00 3.01
1053 1367 1.079127 CGCGGACCAAGAGGACATT 60.079 57.895 0.00 0.00 38.69 2.71
1114 1428 0.323725 GAAGGATGTGCCCACACCAT 60.324 55.000 16.64 8.97 46.86 3.55
1199 1513 5.296035 CAGAAGGTAGAAGGTTTTTCGTGTT 59.704 40.000 0.00 0.00 0.00 3.32
1219 1533 4.771577 TGTTTCCCAACTATGCACATGATT 59.228 37.500 0.00 0.00 33.58 2.57
1361 1675 4.127171 TCCACTTTGCAAGTACTTCACTC 58.873 43.478 4.77 0.00 40.46 3.51
1502 1817 3.385577 GAGAAGAACGAGCACAAGAAGT 58.614 45.455 0.00 0.00 0.00 3.01
1632 1983 1.567175 GGGAAAGTGGCCCCATACTAA 59.433 52.381 0.00 0.00 42.24 2.24
1929 2837 2.158696 ACTATCCAGAGAGCATTTGCCC 60.159 50.000 0.00 0.00 43.38 5.36
1964 2872 3.322466 CCCAGACGCCAAGGTCCT 61.322 66.667 0.00 0.00 37.66 3.85
2044 2952 1.987855 CCAAGGTCCCTGGCGTCTA 60.988 63.158 0.00 0.00 0.00 2.59
2181 3089 1.856259 TCACCTCTAGCCCTCTCATCT 59.144 52.381 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
181 182 1.888018 GCACTAGCACCACCGAGTA 59.112 57.895 0.00 0.00 41.58 2.59
194 195 3.709587 ACTTACTAGGCCTCTTGCACTA 58.290 45.455 9.68 0.00 43.89 2.74
200 201 5.221742 GCCAATGATACTTACTAGGCCTCTT 60.222 44.000 9.68 0.00 34.94 2.85
249 250 2.677836 GCATGTATGTTTCTCGCCTTCA 59.322 45.455 0.00 0.00 0.00 3.02
270 271 2.393764 GCACGGTTTTTCCATCACAAG 58.606 47.619 0.00 0.00 35.57 3.16
371 372 0.042581 TGAGGGCCATGGTACTCAGA 59.957 55.000 26.58 12.64 35.24 3.27
405 406 4.563786 CCTTGGTCTCCACCTTTAGAAGAC 60.564 50.000 0.00 0.00 44.17 3.01
412 413 1.985895 CTACCCTTGGTCTCCACCTTT 59.014 52.381 0.00 0.00 44.17 3.11
453 454 2.342659 CCAGGTCATCCATATCACCCT 58.657 52.381 0.00 0.00 35.89 4.34
563 564 3.855858 TCTTGCATGTACGCTCATTGTA 58.144 40.909 0.00 0.00 0.00 2.41
574 575 7.531857 TTTGGTTTTCCTATTCTTGCATGTA 57.468 32.000 0.00 0.00 41.38 2.29
1053 1367 1.320344 CCTCCATCCACGTCTTCGGA 61.320 60.000 0.00 0.00 41.85 4.55
1114 1428 2.655090 ACATCACCACACCAACATGA 57.345 45.000 0.00 0.00 0.00 3.07
1199 1513 4.343231 ACAATCATGTGCATAGTTGGGAA 58.657 39.130 0.00 0.00 38.69 3.97
1219 1533 0.947180 GCGTTAGTTGGCCTTCGACA 60.947 55.000 3.32 0.00 32.09 4.35
1361 1675 2.501261 TGGTACCTCGTGATCTATCCG 58.499 52.381 14.36 0.00 0.00 4.18
1502 1817 1.372683 GTGCCCTCTCTTGCTCACA 59.627 57.895 0.00 0.00 0.00 3.58
1632 1983 4.702131 GTGCCTTTCCATTTGTCTACTGAT 59.298 41.667 0.00 0.00 0.00 2.90
1853 2204 5.254842 GTTGCACACACTTTTAAACATTGC 58.745 37.500 0.00 0.00 0.00 3.56
1964 2872 1.580059 GATAGGGACCCAGACACCAA 58.420 55.000 14.60 0.00 0.00 3.67
2181 3089 3.528078 AGGGTACTGGATGAGAGTGAGTA 59.472 47.826 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.