Multiple sequence alignment - TraesCS7B01G473100

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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 TraesCS7B01G473100 chr7B 100.000 2338 0 0 1 2338 729023348 729025685 0 4318
1 TraesCS7B01G473100 chr5B 97.224 1369 32 2 1 1363 59780964 59779596 0 2313
2 TraesCS7B01G473100 chr5B 96.569 1370 41 2 1 1364 547493218 547491849 0 2265
3 TraesCS7B01G473100 chr2B 97.087 1373 31 5 1 1366 390803532 390802162 0 2305
4 TraesCS7B01G473100 chr1B 96.857 1368 36 3 1 1362 92336392 92337758 0 2281
5 TraesCS7B01G473100 chr1B 96.423 1370 41 4 1 1364 482480369 482481736 0 2252
6 TraesCS7B01G473100 chr3B 96.786 1369 38 2 1 1363 161678850 161677482 0 2279
7 TraesCS7B01G473100 chr3B 96.501 1372 41 3 1 1365 772414836 772413465 0 2261
8 TraesCS7B01G473100 chr3B 96.499 1371 41 3 1 1365 571263367 571261998 0 2259
9 TraesCS7B01G473100 chr1A 96.416 1367 42 3 1 1361 213935669 213937034 0 2246
10 TraesCS7B01G473100 chr5D 93.955 976 50 6 1364 2338 471523176 471522209 0 1467
11 TraesCS7B01G473100 chr7A 93.231 975 61 3 1364 2338 43740013 43739044 0 1430
12 TraesCS7B01G473100 chr3A 91.812 977 70 8 1364 2338 477675767 477674799 0 1352
13 TraesCS7B01G473100 chr2A 90.780 987 74 15 1361 2338 56640644 56641622 0 1303
14 TraesCS7B01G473100 chr2A 90.428 982 83 10 1361 2338 39824429 39825403 0 1282
15 TraesCS7B01G473100 chr2A 90.214 981 89 7 1361 2337 198315309 198316286 0 1273
16 TraesCS7B01G473100 chr1D 90.826 981 79 7 1361 2338 247761504 247762476 0 1303
17 TraesCS7B01G473100 chr6D 90.276 977 81 10 1364 2338 424997537 424996573 0 1266
18 TraesCS7B01G473100 chr6B 90.092 979 89 5 1361 2337 32257908 32258880 0 1264


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 TraesCS7B01G473100 chr7B 729023348 729025685 2337 False 4318 4318 100.000 1 2338 1 chr7B.!!$F1 2337
1 TraesCS7B01G473100 chr5B 59779596 59780964 1368 True 2313 2313 97.224 1 1363 1 chr5B.!!$R1 1362
2 TraesCS7B01G473100 chr5B 547491849 547493218 1369 True 2265 2265 96.569 1 1364 1 chr5B.!!$R2 1363
3 TraesCS7B01G473100 chr2B 390802162 390803532 1370 True 2305 2305 97.087 1 1366 1 chr2B.!!$R1 1365
4 TraesCS7B01G473100 chr1B 92336392 92337758 1366 False 2281 2281 96.857 1 1362 1 chr1B.!!$F1 1361
5 TraesCS7B01G473100 chr1B 482480369 482481736 1367 False 2252 2252 96.423 1 1364 1 chr1B.!!$F2 1363
6 TraesCS7B01G473100 chr3B 161677482 161678850 1368 True 2279 2279 96.786 1 1363 1 chr3B.!!$R1 1362
7 TraesCS7B01G473100 chr3B 772413465 772414836 1371 True 2261 2261 96.501 1 1365 1 chr3B.!!$R3 1364
8 TraesCS7B01G473100 chr3B 571261998 571263367 1369 True 2259 2259 96.499 1 1365 1 chr3B.!!$R2 1364
9 TraesCS7B01G473100 chr1A 213935669 213937034 1365 False 2246 2246 96.416 1 1361 1 chr1A.!!$F1 1360
10 TraesCS7B01G473100 chr5D 471522209 471523176 967 True 1467 1467 93.955 1364 2338 1 chr5D.!!$R1 974
11 TraesCS7B01G473100 chr7A 43739044 43740013 969 True 1430 1430 93.231 1364 2338 1 chr7A.!!$R1 974
12 TraesCS7B01G473100 chr3A 477674799 477675767 968 True 1352 1352 91.812 1364 2338 1 chr3A.!!$R1 974
13 TraesCS7B01G473100 chr2A 56640644 56641622 978 False 1303 1303 90.780 1361 2338 1 chr2A.!!$F2 977
14 TraesCS7B01G473100 chr2A 39824429 39825403 974 False 1282 1282 90.428 1361 2338 1 chr2A.!!$F1 977
15 TraesCS7B01G473100 chr2A 198315309 198316286 977 False 1273 1273 90.214 1361 2337 1 chr2A.!!$F3 976
16 TraesCS7B01G473100 chr1D 247761504 247762476 972 False 1303 1303 90.826 1361 2338 1 chr1D.!!$F1 977
17 TraesCS7B01G473100 chr6D 424996573 424997537 964 True 1266 1266 90.276 1364 2338 1 chr6D.!!$R1 974
18 TraesCS7B01G473100 chr6B 32257908 32258880 972 False 1264 1264 90.092 1361 2337 1 chr6B.!!$F1 976

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
925 932 0.042131 TCTCAGGGGTACGATTGGGT 59.958 55.0 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 1948 0.104304 CTATGCCTAACGCCGGACTT 59.896 55.0 5.05 0.0 36.24 3.01 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
253 254 9.558396 TTTCATAGCTTGGAATTTCACAAAAAT 57.442 25.926 0.00 0.00 0.00 1.82
430 431 3.632700 GCGTACACTTCACGGCAA 58.367 55.556 0.00 0.00 39.75 4.52
458 464 5.593095 TCCGTGTCATGTTAGCTAATAGACT 59.407 40.000 24.01 4.04 0.00 3.24
714 720 3.134623 CCATATCAGCCTGGTACTTGTGA 59.865 47.826 0.00 0.00 0.00 3.58
857 863 1.876473 AGGAGGATGGTCTAATCCCCT 59.124 52.381 0.00 4.06 46.40 4.79
921 927 2.108970 GACCTTCTCAGGGGTACGATT 58.891 52.381 0.00 0.00 46.01 3.34
925 932 0.042131 TCTCAGGGGTACGATTGGGT 59.958 55.000 0.00 0.00 0.00 4.51
963 970 3.139397 ACAAAGGTAGGTTCATTGGTGGA 59.861 43.478 0.00 0.00 0.00 4.02
1050 1057 0.672091 TATCGCTTGCGCAAAGGACA 60.672 50.000 25.01 10.57 36.30 4.02
1119 1126 1.084370 CCATGAACGAAGGAGGACGC 61.084 60.000 0.00 0.00 0.00 5.19
1449 1458 3.568007 AGAAACGCAGGCAAAAACATCTA 59.432 39.130 0.00 0.00 0.00 1.98
1461 1470 0.625849 AACATCTAGGGGCAAGTGGG 59.374 55.000 0.00 0.00 0.00 4.61
1462 1471 0.253160 ACATCTAGGGGCAAGTGGGA 60.253 55.000 0.00 0.00 0.00 4.37
1463 1472 0.918983 CATCTAGGGGCAAGTGGGAA 59.081 55.000 0.00 0.00 0.00 3.97
1544 1556 1.376553 GCTTCACCCAGTCTGAGGC 60.377 63.158 0.00 0.00 34.09 4.70
1584 1596 2.744202 GCAGTAACAATCACAGAGGTGG 59.256 50.000 0.00 0.00 45.32 4.61
1784 1797 4.561752 AGAAGCCTCCAGGTATAATGAGT 58.438 43.478 0.00 0.00 37.57 3.41
1845 1863 3.577389 CCCTTCAAGGCCTCGAAAT 57.423 52.632 5.23 0.00 32.73 2.17
1891 1914 9.469807 GATAAAAGAGACAGATGACGAATATGT 57.530 33.333 3.41 3.41 43.41 2.29
1925 1948 1.808945 GAGGTAAGGAGACGAACACGA 59.191 52.381 0.00 0.00 0.00 4.35
1934 1957 3.467119 CGAACACGAAGTCCGGCG 61.467 66.667 0.00 0.00 41.61 6.46
1935 1958 2.355481 GAACACGAAGTCCGGCGT 60.355 61.111 6.01 0.00 41.61 5.68
1951 1974 3.131396 CGGCGTTAGGCATAGAATCTTT 58.869 45.455 0.00 0.00 46.16 2.52
1988 2011 0.465097 CATGGATTTGGCTCGAGGCT 60.465 55.000 35.12 18.98 41.69 4.58
2227 2251 1.961180 CTCCTCGAGGGCGTCCAAAT 61.961 60.000 30.80 0.00 38.98 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 137 5.427806 TGTCTGAGAAGATCTTCATCCCAAT 59.572 40.000 31.79 13.53 41.84 3.16
402 403 6.402334 CCGTGAAGTGTACGCCAAATAAATAA 60.402 38.462 1.98 0.00 40.04 1.40
430 431 8.803235 TCTATTAGCTAACATGACACGGAATAT 58.197 33.333 8.70 0.00 0.00 1.28
458 464 3.181469 ACACTTAGGCGAGACTTTCACAA 60.181 43.478 0.00 0.00 0.00 3.33
714 720 0.249955 CCAATTTGCGCCTTTCCCAT 59.750 50.000 4.18 0.00 0.00 4.00
748 754 4.024218 GGATATCTGTTGTGCATTCTGAGC 60.024 45.833 2.05 0.00 0.00 4.26
857 863 5.526846 ACGTTAAGTTTAACAAATCCCGTCA 59.473 36.000 13.44 0.00 42.34 4.35
921 927 4.416516 TGTCATCTCTTAAGACAGACCCA 58.583 43.478 17.75 5.70 38.33 4.51
925 932 6.672266 ACCTTTGTCATCTCTTAAGACAGA 57.328 37.500 0.00 0.00 42.54 3.41
963 970 5.222130 ACACCAGTCAATCTTACCATTTCCT 60.222 40.000 0.00 0.00 0.00 3.36
1133 1140 4.553323 ACAGTCATCAAAAATTGCAGCTC 58.447 39.130 0.00 0.00 0.00 4.09
1544 1556 2.436646 GGGTCAGCCGGATGTGTG 60.437 66.667 20.97 0.53 34.97 3.82
1584 1596 1.761822 GGCTAGGGCATAAGGGGAC 59.238 63.158 0.00 0.00 40.87 4.46
1655 1667 6.486248 TGCATCGATATGACTTAAGTTTTGC 58.514 36.000 10.02 10.29 34.84 3.68
1769 1782 1.070134 GCCGCACTCATTATACCTGGA 59.930 52.381 0.00 0.00 0.00 3.86
1901 1924 3.444388 GTGTTCGTCTCCTTACCTCTGAT 59.556 47.826 0.00 0.00 0.00 2.90
1902 1925 2.818432 GTGTTCGTCTCCTTACCTCTGA 59.182 50.000 0.00 0.00 0.00 3.27
1925 1948 0.104304 CTATGCCTAACGCCGGACTT 59.896 55.000 5.05 0.00 36.24 3.01
1934 1957 6.481644 CAGACTCCAAAGATTCTATGCCTAAC 59.518 42.308 0.00 0.00 31.25 2.34
1935 1958 6.408548 CCAGACTCCAAAGATTCTATGCCTAA 60.409 42.308 0.00 0.00 31.25 2.69
1951 1974 2.343758 GAACGCAGCCAGACTCCA 59.656 61.111 0.00 0.00 0.00 3.86
1988 2011 1.449423 CGGGATGCATCGGACAACA 60.449 57.895 20.15 0.00 0.00 3.33
2133 2156 6.710597 AGATACCAAAGCATAGAAGTACGA 57.289 37.500 0.00 0.00 0.00 3.43
2143 2166 4.164988 ACAGGCTAGAAGATACCAAAGCAT 59.835 41.667 0.00 0.00 0.00 3.79
2189 2212 0.163146 GGAGCGTGACGTAGCAAAAC 59.837 55.000 6.91 0.00 35.48 2.43
2196 2219 2.104859 CGAGGAGGAGCGTGACGTA 61.105 63.158 6.91 0.00 0.00 3.57
2227 2251 2.184322 GCTCGATCGGCAGGACAA 59.816 61.111 16.41 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.