Multiple sequence alignment - TraesCS3A01G174700

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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 TraesCS3A01G174700 chr3A 100.000 2276 0 0 1 2276 193916854 193914579 0.000000e+00 4204
1 TraesCS3A01G174700 chr3A 96.968 2276 66 2 1 2276 194072245 194069973 0.000000e+00 3818
2 TraesCS3A01G174700 chr3A 84.416 1309 193 9 2 1301 606270448 606269142 0.000000e+00 1277
3 TraesCS3A01G174700 chr4A 96.772 1301 41 1 1 1301 48931088 48932387 0.000000e+00 2169
4 TraesCS3A01G174700 chr4A 91.925 322 22 4 1517 1836 124889177 124889496 4.460000e-122 448
5 TraesCS3A01G174700 chr7B 95.395 1303 55 4 1 1301 686802820 686804119 0.000000e+00 2069
6 TraesCS3A01G174700 chr7B 94.656 262 12 2 2016 2276 164593235 164593495 2.720000e-109 405
7 TraesCS3A01G174700 chr7B 94.595 259 12 2 2019 2276 255033434 255033177 1.270000e-107 399
8 TraesCS3A01G174700 chr7B 94.595 259 12 2 2019 2276 603479326 603479583 1.270000e-107 399
9 TraesCS3A01G174700 chr2B 95.245 1304 61 1 1 1304 382727893 382729195 0.000000e+00 2063
10 TraesCS3A01G174700 chr2B 94.275 262 12 3 2016 2276 679893711 679893970 4.560000e-107 398
11 TraesCS3A01G174700 chr5B 94.943 1305 66 0 1 1305 402575377 402576681 0.000000e+00 2045
12 TraesCS3A01G174700 chr1B 95.004 1301 63 2 1 1300 343998119 343999418 0.000000e+00 2041
13 TraesCS3A01G174700 chr1B 84.327 1174 182 2 63 1235 28311083 28312255 0.000000e+00 1147
14 TraesCS3A01G174700 chr3B 93.462 1300 80 2 2 1301 811417270 811415976 0.000000e+00 1925
15 TraesCS3A01G174700 chr3B 92.754 276 14 5 2002 2276 565362703 565362973 5.890000e-106 394
16 TraesCS3A01G174700 chr1D 93.590 312 19 1 1516 1827 313817340 313817030 4.430000e-127 464
17 TraesCS3A01G174700 chr3D 93.831 308 18 1 1520 1827 20893209 20892903 1.590000e-126 462
18 TraesCS3A01G174700 chr2D 93.811 307 18 1 1520 1826 76640742 76640437 5.730000e-126 460
19 TraesCS3A01G174700 chr2D 92.138 318 23 2 1520 1837 402238849 402238534 4.460000e-122 448
20 TraesCS3A01G174700 chrUn 92.971 313 20 2 1515 1827 119910255 119909945 2.670000e-124 455
21 TraesCS3A01G174700 chrUn 94.636 261 12 2 2017 2276 31476976 31477235 9.790000e-109 403
22 TraesCS3A01G174700 chr6A 92.675 314 22 1 1520 1833 408053209 408052897 3.450000e-123 451
23 TraesCS3A01G174700 chr2A 92.405 316 22 2 1513 1827 554453622 554453936 1.240000e-122 449
24 TraesCS3A01G174700 chr7A 93.382 272 15 3 2007 2276 6649222 6649492 1.270000e-107 399
25 TraesCS3A01G174700 chr7A 93.333 270 14 4 2010 2276 729525156 729525424 1.640000e-106 396


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 TraesCS3A01G174700 chr3A 193914579 193916854 2275 True 4204 4204 100.000 1 2276 1 chr3A.!!$R1 2275
1 TraesCS3A01G174700 chr3A 194069973 194072245 2272 True 3818 3818 96.968 1 2276 1 chr3A.!!$R2 2275
2 TraesCS3A01G174700 chr3A 606269142 606270448 1306 True 1277 1277 84.416 2 1301 1 chr3A.!!$R3 1299
3 TraesCS3A01G174700 chr4A 48931088 48932387 1299 False 2169 2169 96.772 1 1301 1 chr4A.!!$F1 1300
4 TraesCS3A01G174700 chr7B 686802820 686804119 1299 False 2069 2069 95.395 1 1301 1 chr7B.!!$F3 1300
5 TraesCS3A01G174700 chr2B 382727893 382729195 1302 False 2063 2063 95.245 1 1304 1 chr2B.!!$F1 1303
6 TraesCS3A01G174700 chr5B 402575377 402576681 1304 False 2045 2045 94.943 1 1305 1 chr5B.!!$F1 1304
7 TraesCS3A01G174700 chr1B 343998119 343999418 1299 False 2041 2041 95.004 1 1300 1 chr1B.!!$F2 1299
8 TraesCS3A01G174700 chr1B 28311083 28312255 1172 False 1147 1147 84.327 63 1235 1 chr1B.!!$F1 1172
9 TraesCS3A01G174700 chr3B 811415976 811417270 1294 True 1925 1925 93.462 2 1301 1 chr3B.!!$R1 1299

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
546 548 1.458639 GCTGGCTGCACCTCAAGTTT 61.459 55.0 11.8 0.0 42.31 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1615 1624 0.454957 CGGTTCAGATTTTGGCAGCG 60.455 55.0 0.0 0.0 0.0 5.18 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
28 29 4.142138 GGAGATTGTCACTTCGACCTACAT 60.142 45.833 0.00 0.00 44.71 2.29
320 322 4.018960 AGAGAACAATAAGCAGGTGTGGAT 60.019 41.667 0.00 0.00 0.00 3.41
546 548 1.458639 GCTGGCTGCACCTCAAGTTT 61.459 55.000 11.80 0.00 42.31 2.66
866 869 5.189934 ACAAGAGTGGAATAGGAGGTTTAGG 59.810 44.000 0.00 0.00 0.00 2.69
1152 1160 6.125719 TGTAATAAGAAGTGCCAATATGCCA 58.874 36.000 0.00 0.00 0.00 4.92
1213 1221 0.898320 CGACTGTTGGATGGACTCCT 59.102 55.000 0.00 0.00 45.21 3.69
1450 1459 2.808543 GTTGGCGCTAGATTATCCCTTG 59.191 50.000 7.64 0.00 0.00 3.61
1452 1461 1.270839 GGCGCTAGATTATCCCTTGCA 60.271 52.381 7.64 0.00 33.17 4.08
1470 1479 5.180868 CCTTGCATGCTTCCTCATTAGTATC 59.819 44.000 20.33 0.00 0.00 2.24
1522 1531 4.004196 AGTTGTTAGCTAGTTTTCGGCT 57.996 40.909 0.00 0.00 37.47 5.52
1546 1555 5.705441 TCTGTTTGGTTCAGCTTTTATCGAT 59.295 36.000 2.16 2.16 33.48 3.59
1547 1556 5.698832 TGTTTGGTTCAGCTTTTATCGATG 58.301 37.500 8.54 0.00 0.00 3.84
1553 1562 6.152661 TGGTTCAGCTTTTATCGATGGATTTT 59.847 34.615 8.54 0.00 34.00 1.82
1554 1563 6.473455 GGTTCAGCTTTTATCGATGGATTTTG 59.527 38.462 8.54 0.52 34.00 2.44
1558 1567 4.207841 GCTTTTATCGATGGATTTTGCTGC 59.792 41.667 8.54 0.00 34.00 5.25
1562 1571 1.512230 GATGGATTTTGCTGCCGCA 59.488 52.632 0.00 0.00 46.24 5.69
1574 1583 1.596408 TGCCGCACAGCAGAATCTA 59.404 52.632 0.00 0.00 38.00 1.98
1615 1624 4.578105 AGCAGAATCCGATTTCAGAAATCC 59.422 41.667 24.39 13.34 43.39 3.01
1640 1649 2.584791 CCAAAATCTGAACCGAAAGCG 58.415 47.619 0.00 0.00 37.24 4.68
1676 1685 5.809051 GGATGTGCTTTCCAAAATCTGATTC 59.191 40.000 2.92 0.00 33.21 2.52
1696 1705 1.243342 CGCTGTGGGCCAAAATCTGA 61.243 55.000 8.40 0.00 37.74 3.27
1702 1711 2.807967 GTGGGCCAAAATCTGAAAAAGC 59.192 45.455 8.40 0.00 0.00 3.51
1705 1714 3.494924 GGGCCAAAATCTGAAAAAGCTGT 60.495 43.478 4.39 0.00 0.00 4.40
1768 1777 6.924111 TCAGATTTTCCACAGCTATTTTTCC 58.076 36.000 0.00 0.00 0.00 3.13
1784 1793 6.849588 ATTTTTCCACAGCAGATTTTTCAC 57.150 33.333 0.00 0.00 0.00 3.18
1810 1819 3.894427 TGCTTTTAGAAAATCCACAGCCA 59.106 39.130 0.00 0.00 0.00 4.75
1836 1845 4.019174 CAAACAGGGCCTTCAACTGATAT 58.981 43.478 1.32 0.00 36.17 1.63
1844 1853 6.331307 AGGGCCTTCAACTGATATCTCTTATT 59.669 38.462 0.00 0.00 0.00 1.40
1886 1895 1.403780 GGTAGGTCGTGTCGCATCTTT 60.404 52.381 0.00 0.00 0.00 2.52
2013 2022 7.381323 CAGGGAAGAAAAACTAGCAAAATCAT 58.619 34.615 0.00 0.00 0.00 2.45
2163 2172 8.901793 TCATAATAAATGTCATGCTGCTTTGTA 58.098 29.630 0.00 0.00 0.00 2.41
2184 2193 9.478768 TTTGTATCATGCATGGCAATAAAATAG 57.521 29.630 25.97 0.00 43.62 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
320 322 6.650807 CAGCACTTTTAGTTTCCATAGTCTCA 59.349 38.462 0.00 0.00 0.00 3.27
546 548 0.040058 TACAAGGGTGTAGCTCCGGA 59.960 55.000 2.93 2.93 39.30 5.14
866 869 5.163943 GCAACAAACGAAGAAGGAGATCTAC 60.164 44.000 0.00 0.00 0.00 2.59
1213 1221 0.036388 GTCATGAGGAAACTGGGCGA 60.036 55.000 0.00 0.00 44.43 5.54
1450 1459 6.874288 AAAGATACTAATGAGGAAGCATGC 57.126 37.500 10.51 10.51 0.00 4.06
1452 1461 7.972301 AGCTAAAGATACTAATGAGGAAGCAT 58.028 34.615 0.00 0.00 0.00 3.79
1470 1479 0.529555 GGAGCAGGCTCGAGCTAAAG 60.530 60.000 34.46 22.10 43.59 1.85
1522 1531 5.060506 TCGATAAAAGCTGAACCAAACAGA 58.939 37.500 0.00 0.00 37.54 3.41
1558 1567 1.398390 GGTTTAGATTCTGCTGTGCGG 59.602 52.381 0.00 0.00 36.06 5.69
1562 1571 5.869579 TCTCTTTGGTTTAGATTCTGCTGT 58.130 37.500 0.00 0.00 0.00 4.40
1574 1583 2.091885 TGCTGGGTTCTCTCTTTGGTTT 60.092 45.455 0.00 0.00 0.00 3.27
1615 1624 0.454957 CGGTTCAGATTTTGGCAGCG 60.455 55.000 0.00 0.00 0.00 5.18
1640 1649 0.817229 GCACATCCTAGCCTGCTTCC 60.817 60.000 0.00 0.00 0.00 3.46
1650 1659 5.569355 TCAGATTTTGGAAAGCACATCCTA 58.431 37.500 4.39 0.00 37.85 2.94
1676 1685 1.978617 AGATTTTGGCCCACAGCGG 60.979 57.895 0.00 0.00 45.17 5.52
1702 1711 1.825090 TGGCAAACCAGCTGATACAG 58.175 50.000 17.39 0.00 42.67 2.74
1768 1777 3.305964 CAGCTGTGAAAAATCTGCTGTG 58.694 45.455 5.25 0.00 45.07 3.66
1784 1793 5.125100 TGTGGATTTTCTAAAAGCAGCTG 57.875 39.130 10.11 10.11 36.09 4.24
1810 1819 1.484653 GTTGAAGGCCCTGTTTGGTTT 59.515 47.619 0.00 0.00 0.00 3.27
1836 1845 6.324254 GGCCAACTAGGAGTAGAAATAAGAGA 59.676 42.308 0.00 0.00 41.22 3.10
1844 1853 3.185880 ACTGGCCAACTAGGAGTAGAA 57.814 47.619 7.01 0.00 41.22 2.10
1886 1895 2.375173 GGGTGGGGGAGGGATACA 59.625 66.667 0.00 0.00 39.74 2.29
2002 2011 4.141711 ACGAGCCTTAGGATGATTTTGCTA 60.142 41.667 0.69 0.00 0.00 3.49
2013 2022 1.679680 CCATTACGACGAGCCTTAGGA 59.320 52.381 0.69 0.00 0.00 2.94
2098 2107 6.227298 TGATACTCCACCATCTCTTTCTTC 57.773 41.667 0.00 0.00 0.00 2.87
2148 2157 3.181494 TGCATGATACAAAGCAGCATGAC 60.181 43.478 0.00 0.00 39.69 3.06
2149 2158 3.018149 TGCATGATACAAAGCAGCATGA 58.982 40.909 0.00 0.00 39.69 3.07
2163 2172 7.534723 ACTCTATTTTATTGCCATGCATGAT 57.465 32.000 28.31 15.63 38.76 2.45


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

AutoCloner maintained by Alex Coulton.