Multiple sequence alignment - TraesCS1A01G318800

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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 TraesCS1A01G318800 chr1A 100.000 2679 0 0 1 2679 510110589 510113267 0.000000e+00 4948
1 TraesCS1A01G318800 chr1A 96.567 2680 80 3 1 2679 509542918 509540250 0.000000e+00 4429
2 TraesCS1A01G318800 chr1B 93.083 1171 78 3 945 2114 556834856 556836024 0.000000e+00 1711
3 TraesCS1A01G318800 chr1B 93.083 1171 78 3 945 2114 556863277 556864445 0.000000e+00 1711
4 TraesCS1A01G318800 chr1B 92.308 1196 83 8 945 2139 556252183 556253370 0.000000e+00 1690
5 TraesCS1A01G318800 chr1B 92.900 831 57 2 945 1775 556663900 556664728 0.000000e+00 1206
6 TraesCS1A01G318800 chr1B 93.976 332 16 4 1788 2118 556666532 556666860 1.430000e-137 499
7 TraesCS1A01G318800 chr1B 94.558 147 8 0 2126 2272 556666917 556667063 7.460000e-56 228
8 TraesCS1A01G318800 chr1B 91.195 159 12 2 2115 2272 556253411 556253568 5.810000e-52 215
9 TraesCS1A01G318800 chr1B 89.873 158 14 2 2114 2271 556836082 556836237 4.520000e-48 202
10 TraesCS1A01G318800 chr1B 89.873 158 14 2 2114 2271 556864503 556864658 4.520000e-48 202
11 TraesCS1A01G318800 chr1D 91.709 1182 72 8 945 2125 412684831 412685987 0.000000e+00 1616
12 TraesCS1A01G318800 chr1D 85.897 936 114 13 945 1871 412642991 412643917 0.000000e+00 981
13 TraesCS1A01G318800 chr1D 85.095 946 112 15 945 1871 412746969 412747904 0.000000e+00 941
14 TraesCS1A01G318800 chr1D 87.826 805 82 11 945 1742 412764132 412764927 0.000000e+00 929
15 TraesCS1A01G318800 chr1D 89.796 147 12 2 2126 2272 412686049 412686192 4.550000e-43 185
16 TraesCS1A01G318800 chr5D 93.284 953 58 4 1 948 247544504 247545455 0.000000e+00 1400
17 TraesCS1A01G318800 chr5D 90.663 407 35 2 2275 2679 371488214 371487809 3.030000e-149 538
18 TraesCS1A01G318800 chr2B 93.277 952 60 2 1 948 113311157 113312108 0.000000e+00 1400
19 TraesCS1A01G318800 chr2B 93.053 950 61 3 3 948 640117638 640118586 0.000000e+00 1384
20 TraesCS1A01G318800 chr2B 84.553 246 36 2 1870 2114 800495480 800495236 2.660000e-60 243
21 TraesCS1A01G318800 chr4D 93.172 952 61 2 1 948 93109107 93110058 0.000000e+00 1395
22 TraesCS1A01G318800 chr4D 91.111 405 36 0 2275 2679 191750870 191751274 1.400000e-152 549
23 TraesCS1A01G318800 chr4D 91.133 406 32 4 2276 2679 495440742 495440339 5.040000e-152 547
24 TraesCS1A01G318800 chr4B 93.418 942 58 2 11 948 374037653 374038594 0.000000e+00 1393
25 TraesCS1A01G318800 chr4B 93.182 132 9 0 1740 1871 633468427 633468558 7.570000e-46 195
26 TraesCS1A01G318800 chr4B 92.424 132 10 0 1740 1871 633401300 633401431 3.520000e-44 189
27 TraesCS1A01G318800 chr7D 93.067 952 61 3 1 948 312530007 312529057 0.000000e+00 1387
28 TraesCS1A01G318800 chr7D 91.605 405 32 2 2276 2679 605492140 605492543 2.330000e-155 558
29 TraesCS1A01G318800 chr7D 90.887 406 33 4 2271 2676 335879096 335878695 2.350000e-150 542
30 TraesCS1A01G318800 chr7D 85.214 257 34 4 1870 2124 21096411 21096665 7.360000e-66 261
31 TraesCS1A01G318800 chr6B 93.067 952 61 3 1 948 274183974 274183024 0.000000e+00 1387
32 TraesCS1A01G318800 chr5B 92.962 952 62 4 1 948 103552002 103551052 0.000000e+00 1382
33 TraesCS1A01G318800 chr6D 93.612 407 25 1 2273 2679 93891363 93890958 8.200000e-170 606
34 TraesCS1A01G318800 chr7A 92.079 404 32 0 2276 2679 635867568 635867971 1.080000e-158 569
35 TraesCS1A01G318800 chr2D 90.842 404 35 1 2276 2679 55667341 55666940 8.440000e-150 540
36 TraesCS1A01G318800 chr6A 85.657 251 34 2 1869 2118 216006979 216006730 2.050000e-66 263


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 TraesCS1A01G318800 chr1A 510110589 510113267 2678 False 4948.000000 4948 100.000000 1 2679 1 chr1A.!!$F1 2678
1 TraesCS1A01G318800 chr1A 509540250 509542918 2668 True 4429.000000 4429 96.567000 1 2679 1 chr1A.!!$R1 2678
2 TraesCS1A01G318800 chr1B 556834856 556836237 1381 False 956.500000 1711 91.478000 945 2271 2 chr1B.!!$F3 1326
3 TraesCS1A01G318800 chr1B 556863277 556864658 1381 False 956.500000 1711 91.478000 945 2271 2 chr1B.!!$F4 1326
4 TraesCS1A01G318800 chr1B 556252183 556253568 1385 False 952.500000 1690 91.751500 945 2272 2 chr1B.!!$F1 1327
5 TraesCS1A01G318800 chr1B 556663900 556667063 3163 False 644.333333 1206 93.811333 945 2272 3 chr1B.!!$F2 1327
6 TraesCS1A01G318800 chr1D 412642991 412643917 926 False 981.000000 981 85.897000 945 1871 1 chr1D.!!$F1 926
7 TraesCS1A01G318800 chr1D 412746969 412747904 935 False 941.000000 941 85.095000 945 1871 1 chr1D.!!$F2 926
8 TraesCS1A01G318800 chr1D 412764132 412764927 795 False 929.000000 929 87.826000 945 1742 1 chr1D.!!$F3 797
9 TraesCS1A01G318800 chr1D 412684831 412686192 1361 False 900.500000 1616 90.752500 945 2272 2 chr1D.!!$F4 1327
10 TraesCS1A01G318800 chr5D 247544504 247545455 951 False 1400.000000 1400 93.284000 1 948 1 chr5D.!!$F1 947
11 TraesCS1A01G318800 chr2B 113311157 113312108 951 False 1400.000000 1400 93.277000 1 948 1 chr2B.!!$F1 947
12 TraesCS1A01G318800 chr2B 640117638 640118586 948 False 1384.000000 1384 93.053000 3 948 1 chr2B.!!$F2 945
13 TraesCS1A01G318800 chr4D 93109107 93110058 951 False 1395.000000 1395 93.172000 1 948 1 chr4D.!!$F1 947
14 TraesCS1A01G318800 chr4B 374037653 374038594 941 False 1393.000000 1393 93.418000 11 948 1 chr4B.!!$F1 937
15 TraesCS1A01G318800 chr7D 312529057 312530007 950 True 1387.000000 1387 93.067000 1 948 1 chr7D.!!$R1 947
16 TraesCS1A01G318800 chr6B 274183024 274183974 950 True 1387.000000 1387 93.067000 1 948 1 chr6B.!!$R1 947
17 TraesCS1A01G318800 chr5B 103551052 103552002 950 True 1382.000000 1382 92.962000 1 948 1 chr5B.!!$R1 947

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
433 436 1.212616 GCTTATAGCGAGGCACACAG 58.787 55.0 0.0 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2378 4269 0.541863 GTAGCACTGCCCATACCAGT 59.458 55.0 0.0 0.0 43.92 4.0 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
279 281 2.942376 AGTGTCAAAACTTGCATCGACA 59.058 40.909 0.00 0.00 0.00 4.35
299 301 6.040247 CGACATAACTGTTTATGGTGAGCTA 58.960 40.000 0.00 0.00 46.27 3.32
314 316 5.240713 GTGAGCTATTTTTCACCTCCATG 57.759 43.478 0.00 0.00 38.16 3.66
423 426 3.006967 ACCTCCCTGTTATGCTTATAGCG 59.993 47.826 0.00 0.00 46.26 4.26
433 436 1.212616 GCTTATAGCGAGGCACACAG 58.787 55.000 0.00 0.00 0.00 3.66
495 501 4.400567 GCTGAAGCATAGGGAATGACTTTT 59.599 41.667 0.00 0.00 41.59 2.27
629 635 9.906660 CAAAACTTTATCAAGGTATGTGCTTTA 57.093 29.630 0.00 0.00 33.82 1.85
972 978 3.506455 CCTTCTCTGACCGACTCTACAAA 59.494 47.826 0.00 0.00 0.00 2.83
980 986 4.202274 TGACCGACTCTACAAATTCACCAA 60.202 41.667 0.00 0.00 0.00 3.67
1010 1016 2.501128 CAGCGACATCGACCCCAT 59.499 61.111 5.26 0.00 43.02 4.00
1019 1025 3.790437 CGACCCCATGCTGGAGCT 61.790 66.667 6.51 0.00 40.96 4.09
1021 1027 2.937689 ACCCCATGCTGGAGCTGT 60.938 61.111 6.51 0.00 40.96 4.40
1092 1098 1.500783 CCCTTGTGGACATGGACCCT 61.501 60.000 12.21 0.00 42.04 4.34
1141 1147 6.406692 ACTACTTCAAGTTAGTGAGCAAGA 57.593 37.500 0.00 0.00 0.00 3.02
1168 1174 1.672854 CCTATTCCACTCCGACGGCA 61.673 60.000 9.66 0.00 0.00 5.69
1242 1248 2.495084 GCCTTCAAGGACGAGTTCTTT 58.505 47.619 7.98 0.00 37.67 2.52
1323 1329 3.515562 AGGTGAGATCAGGAAGAAGTGT 58.484 45.455 0.00 0.00 0.00 3.55
1794 3600 5.277779 CGTGCATTTGGTCTCTTCTTGTTAA 60.278 40.000 0.00 0.00 0.00 2.01
1892 3707 3.072768 ACTCCCTCCGTCTAGGTGTATAG 59.927 52.174 0.00 0.00 41.99 1.31
2248 4139 8.521176 GGCGTTTATAGACCTAAGAATATGAGA 58.479 37.037 0.00 0.00 0.00 3.27
2272 4163 5.256389 ACCTCCTTAATTTTTCCTCCTCCAT 59.744 40.000 0.00 0.00 0.00 3.41
2292 4183 5.786457 TCCATAACACTACTAGGGAAAACCA 59.214 40.000 0.00 0.00 43.89 3.67
2337 4228 2.185350 CAGTAGCGCTGGGTCCAG 59.815 66.667 22.90 12.42 46.15 3.86
2371 4262 2.731341 CGCGCTACAGCTAAGTTGTAGT 60.731 50.000 18.59 0.00 44.98 2.73
2378 4269 6.183360 GCTACAGCTAAGTTGTAGTAGTAGCA 60.183 42.308 20.94 0.00 44.98 3.49
2479 4370 3.664107 TCTTGTTTATCTGAAGCGCTGT 58.336 40.909 12.58 0.03 0.00 4.40
2533 4424 1.267732 GCGCTACTGCTAATGTTGCTG 60.268 52.381 0.00 0.00 34.87 4.41
2542 4433 2.855180 CTAATGTTGCTGCTTTCACCG 58.145 47.619 0.00 0.00 0.00 4.94
2658 4549 9.157104 CATATCATAGACATACAGTAGTCTCGT 57.843 37.037 13.07 4.96 43.59 4.18
2659 4550 6.846325 TCATAGACATACAGTAGTCTCGTG 57.154 41.667 13.07 12.98 43.59 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 7.928908 TGAAAATCTTTTGTGACAATACTGC 57.071 32.000 0.00 0.00 0.00 4.40
57 58 2.102588 GTCATACCTAGTGCATCGGGTT 59.897 50.000 11.57 0.43 33.74 4.11
108 110 4.464951 TCGGAAGCAGTAAATGAAGGAGTA 59.535 41.667 0.00 0.00 0.00 2.59
238 240 7.343057 TGACACTGATCCATATGACTCTAAGTT 59.657 37.037 3.65 0.00 0.00 2.66
299 301 4.651778 TCTCGTTCATGGAGGTGAAAAAT 58.348 39.130 0.00 0.00 39.61 1.82
314 316 7.222000 AGGACTAAGGATATGATTCTCGTTC 57.778 40.000 0.00 0.00 0.00 3.95
423 426 3.822607 CACTAGACCTGTGTGCCTC 57.177 57.895 0.00 0.00 0.00 4.70
433 436 2.778299 TGGAATGTTGTGCACTAGACC 58.222 47.619 19.41 13.59 0.00 3.85
495 501 7.124901 ACCACTGCAGAAGATAGAGAGAAAATA 59.875 37.037 23.35 0.00 0.00 1.40
814 820 3.924114 TCACAAGAAAGTGAGTGGGAA 57.076 42.857 0.00 0.00 43.18 3.97
957 963 3.322541 TGGTGAATTTGTAGAGTCGGTCA 59.677 43.478 0.00 0.00 0.00 4.02
972 978 2.450476 GGCTTCTCCATGTTGGTGAAT 58.550 47.619 10.49 0.00 45.51 2.57
980 986 2.270205 CGCTGGGCTTCTCCATGT 59.730 61.111 0.00 0.00 36.05 3.21
1010 1016 2.456577 TCATGTACTACAGCTCCAGCA 58.543 47.619 0.48 0.00 45.16 4.41
1019 1025 1.754226 TGAGCCGCATCATGTACTACA 59.246 47.619 0.00 0.00 0.00 2.74
1021 1027 2.693074 TCTTGAGCCGCATCATGTACTA 59.307 45.455 0.00 0.00 0.00 1.82
1057 1063 1.385528 AGGGTGGTGTTTTCGTTGAC 58.614 50.000 0.00 0.00 0.00 3.18
1092 1098 1.346395 TCGAAGGTCTTAAAGCTGCCA 59.654 47.619 0.00 0.00 35.40 4.92
1168 1174 4.716977 GGGGTCGGTGAGGAGGGT 62.717 72.222 0.00 0.00 0.00 4.34
1458 1465 8.650143 AGGAACTAACATGGTTGTAATGAAAT 57.350 30.769 0.00 0.00 36.02 2.17
1892 3707 2.609459 CGATGCACAACCTTAGATGACC 59.391 50.000 0.00 0.00 0.00 4.02
2176 4067 0.806868 ACATGAGCTCAAATGCACCG 59.193 50.000 22.50 4.55 34.99 4.94
2248 4139 4.606255 TGGAGGAGGAAAAATTAAGGAGGT 59.394 41.667 0.00 0.00 0.00 3.85
2292 4183 6.455647 TGCATATTTCAAGCGCTACTACTAT 58.544 36.000 12.05 3.00 0.00 2.12
2371 4262 2.039418 CTGCCCATACCAGTGCTACTA 58.961 52.381 0.00 0.00 0.00 1.82
2378 4269 0.541863 GTAGCACTGCCCATACCAGT 59.458 55.000 0.00 0.00 43.92 4.00
2458 4349 3.664107 ACAGCGCTTCAGATAAACAAGA 58.336 40.909 7.50 0.00 0.00 3.02
2493 4384 4.045104 CGCTGTAAATCACCTAGCAGTAG 58.955 47.826 0.00 0.00 34.16 2.57
2498 4389 1.941325 AGCGCTGTAAATCACCTAGC 58.059 50.000 10.39 0.00 0.00 3.42
2533 4424 1.749258 GGTGGGGATCGGTGAAAGC 60.749 63.158 0.00 0.00 0.00 3.51
2542 4433 2.715763 TACATAGAGGGGTGGGGATC 57.284 55.000 0.00 0.00 0.00 3.36
2626 4517 9.949174 CTACTGTATGTCTATGATATGATGAGC 57.051 37.037 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.