Multiple sequence alignment - TraesCS1B01G151100

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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 TraesCS1B01G151100 chr1B 100.000 1518 0 0 777 2294 235897778 235899295 0.000000e+00 2804.0
1 TraesCS1B01G151100 chr1B 96.593 1174 38 2 807 1979 658504122 658502950 0.000000e+00 1945.0
2 TraesCS1B01G151100 chr1B 100.000 382 0 0 1 382 235897002 235897383 0.000000e+00 706.0
3 TraesCS1B01G151100 chr1B 96.501 343 11 1 1 343 658504828 658504487 1.190000e-157 566.0
4 TraesCS1B01G151100 chr1B 98.423 317 4 1 1974 2289 658502597 658502281 7.160000e-155 556.0
5 TraesCS1B01G151100 chr2B 97.297 1480 37 3 817 2294 811341 809863 0.000000e+00 2508.0
6 TraesCS1B01G151100 chr7A 95.012 1203 58 2 778 1979 650260763 650259562 0.000000e+00 1888.0
7 TraesCS1B01G151100 chr7A 95.278 1186 54 2 796 1979 707844389 707845574 0.000000e+00 1879.0
8 TraesCS1B01G151100 chr7A 94.574 1198 63 2 784 1979 650324573 650323376 0.000000e+00 1851.0
9 TraesCS1B01G151100 chr7A 97.205 322 8 1 1974 2294 512542103 512542424 5.570000e-151 544.0
10 TraesCS1B01G151100 chr1A 94.435 1204 65 2 778 1979 380400793 380401996 0.000000e+00 1851.0
11 TraesCS1B01G151100 chr1A 94.181 1203 68 2 778 1979 531840070 531838869 0.000000e+00 1832.0
12 TraesCS1B01G151100 chr1A 95.198 354 16 1 30 382 11026862 11026509 1.990000e-155 558.0
13 TraesCS1B01G151100 chr1A 96.584 322 10 1 1974 2294 31699452 31699773 1.210000e-147 532.0
14 TraesCS1B01G151100 chr1A 96.285 323 10 2 1974 2294 531838516 531838194 1.560000e-146 529.0
15 TraesCS1B01G151100 chr1A 95.238 63 2 1 321 382 380400719 380400781 5.220000e-17 99.0
16 TraesCS1B01G151100 chr2A 94.574 1198 62 3 784 1979 600113447 600112251 0.000000e+00 1849.0
17 TraesCS1B01G151100 chr2A 95.177 1161 55 1 820 1979 23796207 23797367 0.000000e+00 1832.0
18 TraesCS1B01G151100 chr2A 94.366 355 18 2 30 382 23795588 23795942 5.570000e-151 544.0
19 TraesCS1B01G151100 chr2A 96.894 322 8 2 1974 2294 23797719 23798039 2.590000e-149 538.0
20 TraesCS1B01G151100 chr2A 96.584 322 9 2 1974 2294 107527695 107528015 1.210000e-147 532.0
21 TraesCS1B01G151100 chr7B 94.723 379 19 1 2 379 544972316 544972694 2.540000e-164 588.0
22 TraesCS1B01G151100 chr7B 94.910 334 17 0 1 334 656625303 656624970 7.260000e-145 523.0
23 TraesCS1B01G151100 chr7B 92.453 53 4 0 778 830 544972709 544972761 2.440000e-10 76.8
24 TraesCS1B01G151100 chr3B 98.142 323 4 2 1974 2294 59101569 59101891 1.540000e-156 562.0
25 TraesCS1B01G151100 chr5A 95.198 354 15 2 30 382 603018657 603019009 1.990000e-155 558.0
26 TraesCS1B01G151100 chr5A 93.503 354 21 2 30 382 507566262 507565910 2.020000e-145 525.0
27 TraesCS1B01G151100 chrUn 95.224 335 15 1 1 334 24704736 24705070 1.560000e-146 529.0
28 TraesCS1B01G151100 chr3A 96.562 320 9 2 1977 2294 688930816 688930497 1.560000e-146 529.0
29 TraesCS1B01G151100 chr6B 93.503 354 22 1 30 382 363202951 363203304 2.020000e-145 525.0
30 TraesCS1B01G151100 chr5B 95.833 48 1 1 336 382 61755074 61755121 2.440000e-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 TraesCS1B01G151100 chr1B 235897002 235899295 2293 False 1755.000000 2804 100.000000 1 2294 2 chr1B.!!$F1 2293
1 TraesCS1B01G151100 chr1B 658502281 658504828 2547 True 1022.333333 1945 97.172333 1 2289 3 chr1B.!!$R1 2288
2 TraesCS1B01G151100 chr2B 809863 811341 1478 True 2508.000000 2508 97.297000 817 2294 1 chr2B.!!$R1 1477
3 TraesCS1B01G151100 chr7A 650259562 650260763 1201 True 1888.000000 1888 95.012000 778 1979 1 chr7A.!!$R1 1201
4 TraesCS1B01G151100 chr7A 707844389 707845574 1185 False 1879.000000 1879 95.278000 796 1979 1 chr7A.!!$F2 1183
5 TraesCS1B01G151100 chr7A 650323376 650324573 1197 True 1851.000000 1851 94.574000 784 1979 1 chr7A.!!$R2 1195
6 TraesCS1B01G151100 chr1A 531838194 531840070 1876 True 1180.500000 1832 95.233000 778 2294 2 chr1A.!!$R2 1516
7 TraesCS1B01G151100 chr1A 380400719 380401996 1277 False 975.000000 1851 94.836500 321 1979 2 chr1A.!!$F2 1658
8 TraesCS1B01G151100 chr2A 600112251 600113447 1196 True 1849.000000 1849 94.574000 784 1979 1 chr2A.!!$R1 1195
9 TraesCS1B01G151100 chr2A 23795588 23798039 2451 False 971.333333 1832 95.479000 30 2294 3 chr2A.!!$F2 2264

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
846 1060 1.061812 ACATCCTCCCACCATAGCTCT 60.062 52.381 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 2171 2.233922 AGGCGACACTGCTACATAAAGT 59.766 45.455 0.0 0.0 34.52 2.66 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
106 108 1.402896 CCCTAAGCCGATCTGAGCCA 61.403 60.000 0.00 0.00 0.00 4.75
127 129 4.525996 CATCCACACCATACAGATCCAAA 58.474 43.478 0.00 0.00 0.00 3.28
143 145 2.103432 TCCAAAGTCTCCTAAACGCACA 59.897 45.455 0.00 0.00 0.00 4.57
247 249 1.231751 TGACCCAGATCTCCCTCCCT 61.232 60.000 0.00 0.00 0.00 4.20
258 260 2.122729 CCTCCCTGACCCAGACCA 59.877 66.667 0.00 0.00 32.44 4.02
291 293 3.072468 CAACTCCTACCCCGCCGA 61.072 66.667 0.00 0.00 0.00 5.54
793 796 3.700970 TCATTCTCGCCACCGCCA 61.701 61.111 0.00 0.00 0.00 5.69
822 1036 1.298953 CCCCCTTCTCCCTGATTCAA 58.701 55.000 0.00 0.00 0.00 2.69
846 1060 1.061812 ACATCCTCCCACCATAGCTCT 60.062 52.381 0.00 0.00 0.00 4.09
1007 1222 2.203070 GGTAGCAGCCATGGACGG 60.203 66.667 18.40 8.93 0.00 4.79
1052 1267 4.354155 CGAGTTCGCCAAGGACAA 57.646 55.556 0.00 0.00 0.00 3.18
1286 1501 3.402110 TCAACAACATCATCGTCAGCTT 58.598 40.909 0.00 0.00 0.00 3.74
1495 1710 5.826643 TGCCAATTTCTACCTTGTTAGGAT 58.173 37.500 0.00 0.00 45.05 3.24
1521 1736 3.772572 TCGGATGAGTCAAGGGTAATCAA 59.227 43.478 0.00 0.00 0.00 2.57
1547 1763 2.358195 GGGGAACTGGGTCATGCTTAAT 60.358 50.000 0.00 0.00 0.00 1.40
1570 1786 4.452733 GCCGCTAGTTGCCTCCGT 62.453 66.667 0.00 0.00 38.78 4.69
1626 1842 4.501400 CCACACAATTTGGGAAAAGAGGAC 60.501 45.833 5.47 0.00 0.00 3.85
1912 2128 3.388345 TGTAGGACACGTGTTATGCAA 57.612 42.857 24.26 4.75 0.00 4.08
1955 2171 2.093181 ACCTATGTTCACGCATGGCTAA 60.093 45.455 0.00 0.00 0.00 3.09
2135 2711 5.295950 TGTTGCATTTTGTTGGTTCCTATG 58.704 37.500 0.00 0.00 0.00 2.23
2185 2761 0.609662 GGTGGCCATTTGTGCTTCAT 59.390 50.000 9.72 0.00 0.00 2.57
2290 2866 3.009473 TGGTATTCTGCTTTCTCCTTGCT 59.991 43.478 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 108 4.228210 ACTTTGGATCTGTATGGTGTGGAT 59.772 41.667 0.00 0.00 0.00 3.41
127 129 1.000955 CCAGTGTGCGTTTAGGAGACT 59.999 52.381 0.00 0.00 45.34 3.24
143 145 0.112412 CTAGGGTTTGGTTGGCCAGT 59.888 55.000 5.11 0.00 46.91 4.00
247 249 1.229209 GAGAGGGTGGTCTGGGTCA 60.229 63.158 0.00 0.00 0.00 4.02
311 313 0.882042 CGTTGCAGGTCAAGAGCAGT 60.882 55.000 1.84 0.00 39.72 4.40
350 353 3.483869 GAAGGAGGGGGCAGCGAT 61.484 66.667 0.00 0.00 0.00 4.58
776 779 2.535485 AATGGCGGTGGCGAGAATGA 62.535 55.000 0.00 0.00 41.24 2.57
822 1036 1.846439 CTATGGTGGGAGGATGTGGTT 59.154 52.381 0.00 0.00 0.00 3.67
864 1078 0.909610 TTTGGATCTGCGAGGAGGGT 60.910 55.000 0.00 0.00 0.00 4.34
1007 1222 2.509336 CCACCATGGAGTCGACGC 60.509 66.667 21.47 11.19 40.96 5.19
1052 1267 4.719369 GCTTGACGAGGCGGACGT 62.719 66.667 7.07 7.07 46.58 4.34
1210 1425 1.760479 AACCCCATGACGACGAACCA 61.760 55.000 0.00 0.00 0.00 3.67
1286 1501 2.586079 GCATTCGCAGCTAGCCGA 60.586 61.111 12.13 11.70 41.38 5.54
1294 1509 1.140589 AGAGGAGACGCATTCGCAG 59.859 57.895 0.00 0.00 39.84 5.18
1405 1620 4.630644 AATATTGGTCAGATCGCAGGAT 57.369 40.909 0.00 0.00 34.96 3.24
1495 1710 5.943349 TTACCCTTGACTCATCCGAATTA 57.057 39.130 0.00 0.00 0.00 1.40
1521 1736 0.772124 ATGACCCAGTTCCCCACAGT 60.772 55.000 0.00 0.00 0.00 3.55
1570 1786 1.697432 CTATGCCCCCAATTCGTCCTA 59.303 52.381 0.00 0.00 0.00 2.94
1626 1842 2.472816 ACAGCGAAACATTGCAAAAGG 58.527 42.857 1.71 0.00 0.00 3.11
1955 2171 2.233922 AGGCGACACTGCTACATAAAGT 59.766 45.455 0.00 0.00 34.52 2.66
2011 2586 6.763355 AGTAGATATTGACACCCATGACATC 58.237 40.000 0.00 0.00 30.49 3.06


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

AutoCloner maintained by Alex Coulton.