Multiple sequence alignment - TraesCS5A01G220100

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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 TraesCS5A01G220100 chr5A 100.000 1368 0 0 1 1368 436879985 436881352 0.000000e+00 2527
1 TraesCS5A01G220100 chr5A 100.000 648 0 0 1590 2237 436881574 436882221 0.000000e+00 1197
2 TraesCS5A01G220100 chr5B 87.907 1414 54 39 1 1365 393576593 393577938 0.000000e+00 1555
3 TraesCS5A01G220100 chr5B 93.475 659 27 8 1590 2237 393577952 393578605 0.000000e+00 965
4 TraesCS5A01G220100 chr5D 91.639 909 28 16 489 1364 335750898 335751791 0.000000e+00 1214
5 TraesCS5A01G220100 chr5D 91.843 662 33 12 1590 2237 335751805 335752459 0.000000e+00 904
6 TraesCS5A01G220100 chr5D 95.385 260 7 2 1 259 335750433 335750688 2.070000e-110 409
7 TraesCS5A01G220100 chr5D 95.477 199 6 2 309 506 335750687 335750883 4.640000e-82 315


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 TraesCS5A01G220100 chr5A 436879985 436882221 2236 False 1862.0 2527 100.000 1 2237 2 chr5A.!!$F1 2236
1 TraesCS5A01G220100 chr5B 393576593 393578605 2012 False 1260.0 1555 90.691 1 2237 2 chr5B.!!$F1 2236
2 TraesCS5A01G220100 chr5D 335750433 335752459 2026 False 710.5 1214 93.586 1 2237 4 chr5D.!!$F1 2236

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
592 648 0.54341 ATGTACACCGGACCAGACCA 60.543 55.0 9.46 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 1729 0.451783 GTAACAATGGCCGGCTTCTG 59.548 55.0 28.56 21.68 0.0 3.02 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
191 195 5.164620 TGATTGTGATTAGGACAAGAGCA 57.835 39.130 0.00 0.00 36.77 4.26
205 209 3.141398 CAAGAGCACTTGTTTGGAGCTA 58.859 45.455 14.94 0.00 45.73 3.32
206 210 3.051081 AGAGCACTTGTTTGGAGCTAG 57.949 47.619 0.00 0.00 35.36 3.42
207 211 1.466558 GAGCACTTGTTTGGAGCTAGC 59.533 52.381 6.62 6.62 35.36 3.42
208 212 1.202806 AGCACTTGTTTGGAGCTAGCA 60.203 47.619 18.83 0.00 33.06 3.49
209 213 1.198637 GCACTTGTTTGGAGCTAGCAG 59.801 52.381 18.83 5.15 0.00 4.24
210 214 1.198637 CACTTGTTTGGAGCTAGCAGC 59.801 52.381 18.83 8.33 42.84 5.25
211 215 1.202806 ACTTGTTTGGAGCTAGCAGCA 60.203 47.619 18.83 0.88 45.56 4.41
212 216 1.881973 CTTGTTTGGAGCTAGCAGCAA 59.118 47.619 18.83 9.49 45.56 3.91
213 217 1.979855 TGTTTGGAGCTAGCAGCAAA 58.020 45.000 18.83 5.37 45.56 3.68
283 287 7.777910 AGTGCCTTGCTGGTTTGTTTATATATA 59.222 33.333 0.00 0.00 38.35 0.86
286 290 7.593825 CCTTGCTGGTTTGTTTATATATAGCC 58.406 38.462 0.00 0.00 0.00 3.93
287 291 7.448469 CCTTGCTGGTTTGTTTATATATAGCCT 59.552 37.037 0.00 0.00 0.00 4.58
288 292 8.760980 TTGCTGGTTTGTTTATATATAGCCTT 57.239 30.769 0.00 0.00 0.00 4.35
289 293 8.165239 TGCTGGTTTGTTTATATATAGCCTTG 57.835 34.615 0.00 0.00 0.00 3.61
310 322 0.882474 GGCTCATAGCGATCGGTAGT 59.118 55.000 28.39 15.78 43.62 2.73
414 430 6.749923 AAAGAACAAGATAATCCTGTCAGC 57.250 37.500 0.00 0.00 0.00 4.26
428 444 2.799412 CTGTCAGCTCACTCTCACAAAC 59.201 50.000 0.00 0.00 0.00 2.93
439 455 5.105106 TCACTCTCACAAACTGGTGTCTAAA 60.105 40.000 0.00 0.00 39.76 1.85
440 456 5.760253 CACTCTCACAAACTGGTGTCTAAAT 59.240 40.000 0.00 0.00 39.76 1.40
453 469 8.833493 ACTGGTGTCTAAATAATAATAAACCGC 58.167 33.333 0.00 0.00 0.00 5.68
552 601 8.409358 AAGGCCAAAGCTAATTATATTAGGTG 57.591 34.615 5.01 2.45 39.73 4.00
590 646 2.691526 TGATATGTACACCGGACCAGAC 59.308 50.000 9.46 0.00 0.00 3.51
591 647 1.477553 TATGTACACCGGACCAGACC 58.522 55.000 9.46 0.00 0.00 3.85
592 648 0.543410 ATGTACACCGGACCAGACCA 60.543 55.000 9.46 0.00 0.00 4.02
593 649 1.183030 TGTACACCGGACCAGACCAG 61.183 60.000 9.46 0.00 0.00 4.00
673 729 5.055144 GCAGCTGAGACAATCATTAGATGA 58.945 41.667 20.43 0.00 44.55 2.92
729 785 3.905678 CCGGTCGAGCAGCCTAGG 61.906 72.222 15.89 3.67 0.00 3.02
828 884 0.972883 CCTGTGGGAGCTAGCTATCC 59.027 60.000 19.38 21.58 34.64 2.59
912 968 1.266175 CCTCGCCCCTATATATACGCG 59.734 57.143 3.53 3.53 40.88 6.01
961 1021 0.829990 TCCACACAGCACAAGTCAGA 59.170 50.000 0.00 0.00 0.00 3.27
1029 1107 3.061848 GCCATGTTCACGGTGGGG 61.062 66.667 8.50 4.14 33.58 4.96
1122 1200 3.304829 GGAGCTCAAGAAGATAGTCCCT 58.695 50.000 17.19 0.00 0.00 4.20
1125 1203 3.704061 AGCTCAAGAAGATAGTCCCTGAC 59.296 47.826 0.00 0.00 0.00 3.51
1261 1339 0.805322 GCCGCATCTCTGTCTCAGTG 60.805 60.000 0.00 0.00 32.61 3.66
1627 1716 2.034879 GTGCGGTCACACATGGGAG 61.035 63.158 0.00 0.00 42.66 4.30
1650 1739 2.040544 TTTAGCAGCAGAAGCCGGC 61.041 57.895 21.89 21.89 43.56 6.13
1723 1812 0.251077 GCCCCTCCCTGCATCTTATG 60.251 60.000 0.00 0.00 0.00 1.90
1797 1886 5.820423 TGACTACAACTAATGCACAACAAGT 59.180 36.000 0.00 0.00 0.00 3.16
1801 1890 8.289618 ACTACAACTAATGCACAACAAGTAATG 58.710 33.333 0.00 0.00 0.00 1.90
1815 1904 8.721478 ACAACAAGTAATGCACTGTTTAGATAG 58.279 33.333 0.00 0.00 37.63 2.08
1994 2090 3.047877 GGGGCTCCGACACAAACG 61.048 66.667 0.00 0.00 0.00 3.60
2008 2104 0.457509 CAAACGCACAGTGTTGGCAA 60.458 50.000 1.61 0.00 36.34 4.52
2022 2118 6.364165 CAGTGTTGGCAAATTCTTCAACATAG 59.636 38.462 17.39 12.01 46.96 2.23
2067 2163 2.257286 ATAACAGCTGCCGCGCAAAG 62.257 55.000 15.27 1.89 38.41 2.77
2142 2245 6.940867 ACAGAACTTATTTTAGTCAAGGTCCC 59.059 38.462 0.00 0.00 36.80 4.46
2229 2333 7.722728 ACATCAACATATGCTCCAGTGATTATT 59.277 33.333 1.58 0.00 0.00 1.40
2230 2334 7.500720 TCAACATATGCTCCAGTGATTATTG 57.499 36.000 1.58 0.00 0.00 1.90
2231 2335 7.281841 TCAACATATGCTCCAGTGATTATTGA 58.718 34.615 1.58 0.00 0.00 2.57
2232 2336 7.227314 TCAACATATGCTCCAGTGATTATTGAC 59.773 37.037 1.58 0.00 0.00 3.18
2233 2337 6.594744 ACATATGCTCCAGTGATTATTGACA 58.405 36.000 1.58 0.00 0.00 3.58
2234 2338 6.709397 ACATATGCTCCAGTGATTATTGACAG 59.291 38.462 1.58 0.00 0.00 3.51
2236 2340 5.164620 TGCTCCAGTGATTATTGACAGAA 57.835 39.130 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
191 195 1.202806 TGCTGCTAGCTCCAAACAAGT 60.203 47.619 17.23 0.00 42.97 3.16
206 210 4.748679 CTCGCCTGCGTTTGCTGC 62.749 66.667 11.68 0.00 43.34 5.25
207 211 4.748679 GCTCGCCTGCGTTTGCTG 62.749 66.667 11.68 0.00 43.34 4.41
209 213 4.326766 TTGCTCGCCTGCGTTTGC 62.327 61.111 11.68 13.98 40.74 3.68
210 214 2.116736 TTCTTGCTCGCCTGCGTTTG 62.117 55.000 11.68 4.74 40.74 2.93
211 215 1.891919 TTCTTGCTCGCCTGCGTTT 60.892 52.632 11.68 0.00 40.74 3.60
212 216 2.280797 TTCTTGCTCGCCTGCGTT 60.281 55.556 11.68 0.00 40.74 4.84
213 217 3.044305 GTTCTTGCTCGCCTGCGT 61.044 61.111 11.68 0.00 40.74 5.24
262 266 8.396272 AGGCTATATATAAACAAACCAGCAAG 57.604 34.615 0.00 0.00 0.00 4.01
286 290 0.668706 CGATCGCTATGAGCCCCAAG 60.669 60.000 0.26 0.00 38.18 3.61
287 291 1.367471 CGATCGCTATGAGCCCCAA 59.633 57.895 0.26 0.00 38.18 4.12
288 292 2.574018 CCGATCGCTATGAGCCCCA 61.574 63.158 10.32 0.00 38.18 4.96
289 293 1.248785 TACCGATCGCTATGAGCCCC 61.249 60.000 10.32 0.00 38.18 5.80
293 305 2.809119 ACAGACTACCGATCGCTATGAG 59.191 50.000 10.32 4.15 0.00 2.90
298 310 1.267261 GCATACAGACTACCGATCGCT 59.733 52.381 10.32 0.00 0.00 4.93
414 430 3.126831 GACACCAGTTTGTGAGAGTGAG 58.873 50.000 0.00 0.00 39.57 3.51
428 444 9.052759 AGCGGTTTATTATTATTTAGACACCAG 57.947 33.333 0.00 0.00 0.00 4.00
440 456 9.356433 GTTTGCCTTTTTAGCGGTTTATTATTA 57.644 29.630 0.00 0.00 0.00 0.98
453 469 6.803807 GTGCATTCTCTAGTTTGCCTTTTTAG 59.196 38.462 0.00 0.00 34.20 1.85
590 646 1.139853 GGAACTATCTGGTCTGGCTGG 59.860 57.143 0.00 0.00 31.77 4.85
591 647 2.102252 GAGGAACTATCTGGTCTGGCTG 59.898 54.545 0.00 0.00 41.55 4.85
592 648 2.393646 GAGGAACTATCTGGTCTGGCT 58.606 52.381 0.00 0.00 41.55 4.75
593 649 1.414550 GGAGGAACTATCTGGTCTGGC 59.585 57.143 0.00 0.00 41.55 4.85
637 693 7.448748 TGTCTCAGCTGCTCGTATATTATTA 57.551 36.000 9.47 0.00 0.00 0.98
638 694 6.332735 TGTCTCAGCTGCTCGTATATTATT 57.667 37.500 9.47 0.00 0.00 1.40
649 705 4.750021 TCTAATGATTGTCTCAGCTGCT 57.250 40.909 9.47 0.00 37.28 4.24
673 729 0.829333 ACTTCCGCTCAGCTGATGAT 59.171 50.000 18.63 0.00 37.28 2.45
675 731 0.725686 CAACTTCCGCTCAGCTGATG 59.274 55.000 18.63 12.84 0.00 3.07
729 785 3.258228 CTTGTGGTGGTTTGGTTGAAAC 58.742 45.455 0.00 0.00 42.97 2.78
745 801 1.060409 GTTTGGCGTTTGCAACTTGTG 59.940 47.619 0.00 0.00 45.35 3.33
746 802 1.337260 TGTTTGGCGTTTGCAACTTGT 60.337 42.857 0.00 0.00 45.35 3.16
772 828 3.067106 CGGTCATTGTATAGGATGGTGC 58.933 50.000 0.00 0.00 0.00 5.01
828 884 4.792521 AACCTGTAGACTGAGCTGTAAG 57.207 45.455 0.00 0.00 0.00 2.34
961 1021 1.004745 CCCCAGGTTGCTATGTCACTT 59.995 52.381 0.00 0.00 0.00 3.16
969 1029 1.306997 CTCCCTCCCCAGGTTGCTA 60.307 63.158 0.00 0.00 38.30 3.49
1029 1107 1.303643 CACCACCCCCTTGCTCTTC 60.304 63.158 0.00 0.00 0.00 2.87
1248 1326 1.463553 TTGCGGCACTGAGACAGAGA 61.464 55.000 0.05 0.00 35.18 3.10
1252 1330 2.327343 GCATTGCGGCACTGAGACA 61.327 57.895 22.50 0.00 0.00 3.41
1261 1339 2.354074 CTAACCATGGGCATTGCGGC 62.354 60.000 18.09 0.00 40.20 6.53
1595 1684 2.176273 CGCACATAGGAGCCACAGC 61.176 63.158 0.00 0.00 40.32 4.40
1596 1685 1.522355 CCGCACATAGGAGCCACAG 60.522 63.158 0.00 0.00 0.00 3.66
1597 1686 2.238847 GACCGCACATAGGAGCCACA 62.239 60.000 0.00 0.00 0.00 4.17
1598 1687 1.521681 GACCGCACATAGGAGCCAC 60.522 63.158 0.00 0.00 0.00 5.01
1627 1716 1.402062 GGCTTCTGCTGCTAAACAAGC 60.402 52.381 0.00 7.06 43.20 4.01
1639 1728 1.312371 TAACAATGGCCGGCTTCTGC 61.312 55.000 28.56 9.87 38.76 4.26
1640 1729 0.451783 GTAACAATGGCCGGCTTCTG 59.548 55.000 28.56 21.68 0.00 3.02
1642 1731 0.451783 CAGTAACAATGGCCGGCTTC 59.548 55.000 28.56 11.61 0.00 3.86
1650 1739 4.218200 TCATTGCCTTGTCAGTAACAATGG 59.782 41.667 12.14 0.00 46.53 3.16
1856 1945 5.957132 AGATCCTGTACCATTGCCAAATAT 58.043 37.500 0.00 0.00 0.00 1.28
1878 1971 9.959749 GTTCTTCACTCTGAGGATAATAACTAG 57.040 37.037 9.85 0.00 32.38 2.57
1994 2090 2.514205 AGAATTTGCCAACACTGTGC 57.486 45.000 7.90 0.00 0.00 4.57
2022 2118 9.764363 TGTGTTATCCAAGATAGATCAACATAC 57.236 33.333 0.00 0.00 0.00 2.39
2085 2181 5.407407 ACGGACTGACAGATCTTTATGTT 57.593 39.130 10.08 0.00 0.00 2.71
2142 2245 3.003689 CCCACAGTTGTACTTGAAGCAAG 59.996 47.826 5.67 5.67 45.85 4.01


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

AutoCloner maintained by Alex Coulton.