Multiple sequence alignment - TraesCS3B01G328000

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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 TraesCS3B01G328000 chr3B 100.000 2228 0 0 1 2228 528632309 528630082 0.000000e+00 4115
1 TraesCS3B01G328000 chr3D 92.206 2117 119 24 130 2228 402797131 402795043 0.000000e+00 2953
2 TraesCS3B01G328000 chr3D 96.850 127 4 0 1 127 402797298 402797172 1.730000e-51 213
3 TraesCS3B01G328000 chr3A 90.059 2032 124 32 230 2228 523747078 523745092 0.000000e+00 2562
4 TraesCS3B01G328000 chr3A 83.929 224 19 8 1 208 523747287 523747065 4.850000e-47 198


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 TraesCS3B01G328000 chr3B 528630082 528632309 2227 True 4115 4115 100.000 1 2228 1 chr3B.!!$R1 2227
1 TraesCS3B01G328000 chr3D 402795043 402797298 2255 True 1583 2953 94.528 1 2228 2 chr3D.!!$R1 2227
2 TraesCS3B01G328000 chr3A 523745092 523747287 2195 True 1380 2562 86.994 1 2228 2 chr3A.!!$R1 2227

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
868 922 0.112995 AGAACCCATTGCCTTGCAGA 59.887 50.0 0.0 0.0 40.61 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 1831 0.936764 CAGCCGCTAGATGCACTACG 60.937 60.0 0.0 0.7 43.06 3.51 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
48 49 4.269523 TGGTGCTGGTGTGGAGGC 62.270 66.667 0.00 0.00 0.00 4.70
69 70 2.571653 CTGTGGAGGAACCCATTGAGTA 59.428 50.000 0.00 0.00 38.66 2.59
179 218 4.128643 CAATGGCTTTTCACATGGTTTGT 58.871 39.130 0.00 0.00 39.91 2.83
210 249 1.472728 GGCTCAACCATACACCTACGG 60.473 57.143 0.00 0.00 38.86 4.02
338 377 5.223382 GTGTATCGAATCATGGACGAGATT 58.777 41.667 13.01 0.00 39.31 2.40
339 378 5.692204 GTGTATCGAATCATGGACGAGATTT 59.308 40.000 13.01 2.77 39.31 2.17
340 379 6.201044 GTGTATCGAATCATGGACGAGATTTT 59.799 38.462 13.01 2.50 39.31 1.82
571 623 0.599558 GTACTATCGCCGGGCATACA 59.400 55.000 20.71 0.00 0.00 2.29
737 789 2.416296 CGATGCAACTGTCTAACCGGTA 60.416 50.000 8.00 0.00 0.00 4.02
759 812 1.354101 TCCCACCGGTGTAGTGATTT 58.646 50.000 31.80 0.00 37.42 2.17
852 906 3.390175 ACTTCCTAGCTAGCTCCAGAA 57.610 47.619 23.26 19.85 0.00 3.02
862 916 1.000396 GCTCCAGAACCCATTGCCT 60.000 57.895 0.00 0.00 0.00 4.75
863 917 0.613012 GCTCCAGAACCCATTGCCTT 60.613 55.000 0.00 0.00 0.00 4.35
864 918 1.180029 CTCCAGAACCCATTGCCTTG 58.820 55.000 0.00 0.00 0.00 3.61
865 919 0.899717 TCCAGAACCCATTGCCTTGC 60.900 55.000 0.00 0.00 0.00 4.01
866 920 1.186917 CCAGAACCCATTGCCTTGCA 61.187 55.000 0.00 0.00 36.47 4.08
867 921 0.245539 CAGAACCCATTGCCTTGCAG 59.754 55.000 0.00 0.00 40.61 4.41
868 922 0.112995 AGAACCCATTGCCTTGCAGA 59.887 50.000 0.00 0.00 40.61 4.26
869 923 0.529378 GAACCCATTGCCTTGCAGAG 59.471 55.000 0.00 0.00 40.61 3.35
954 1008 1.705337 GGCATACATTGTCGCTGCGT 61.705 55.000 22.48 3.71 33.69 5.24
960 1014 1.006220 ATTGTCGCTGCGTCTCACA 60.006 52.632 22.48 15.63 0.00 3.58
961 1015 1.010935 ATTGTCGCTGCGTCTCACAG 61.011 55.000 22.48 0.00 38.22 3.66
969 1023 3.753434 CGTCTCACAGCGGCCTCT 61.753 66.667 0.00 0.00 0.00 3.69
981 1035 2.124983 GCCTCTGATCAAGCGCCA 60.125 61.111 2.29 0.00 0.00 5.69
987 1041 2.899339 GATCAAGCGCCAGCCTCC 60.899 66.667 2.29 0.00 46.67 4.30
1078 1132 2.284331 TGCCCTTGGAGTCGGCTA 60.284 61.111 8.07 0.00 43.42 3.93
1283 1338 0.729116 TCGAACGCCGTAGTAGGAAG 59.271 55.000 0.00 0.00 39.75 3.46
1289 1344 2.094854 ACGCCGTAGTAGGAAGAAACAG 60.095 50.000 0.00 0.00 0.00 3.16
1293 1348 4.015084 CCGTAGTAGGAAGAAACAGAGGA 58.985 47.826 0.00 0.00 0.00 3.71
1296 1351 5.357314 CGTAGTAGGAAGAAACAGAGGATGA 59.643 44.000 0.00 0.00 0.00 2.92
1302 1357 2.530701 AGAAACAGAGGATGACGAGGT 58.469 47.619 0.00 0.00 0.00 3.85
1305 1360 0.247736 ACAGAGGATGACGAGGTTGC 59.752 55.000 0.00 0.00 0.00 4.17
1307 1362 0.820871 AGAGGATGACGAGGTTGCTC 59.179 55.000 0.00 0.00 0.00 4.26
1310 1365 1.066573 AGGATGACGAGGTTGCTCTTG 60.067 52.381 0.00 0.00 0.00 3.02
1315 1370 1.448540 CGAGGTTGCTCTTGGCGAT 60.449 57.895 0.00 0.00 45.43 4.58
1316 1371 0.179111 CGAGGTTGCTCTTGGCGATA 60.179 55.000 0.00 0.00 45.43 2.92
1317 1372 1.291132 GAGGTTGCTCTTGGCGATAC 58.709 55.000 0.00 0.00 45.43 2.24
1318 1373 0.460284 AGGTTGCTCTTGGCGATACG 60.460 55.000 0.00 0.00 45.43 3.06
1350 1405 5.805728 AGGTTGACGAGGATAATGTTTTCT 58.194 37.500 0.00 0.00 0.00 2.52
1367 1422 3.410631 TTCTTACTGCCCATTCGTTCA 57.589 42.857 0.00 0.00 0.00 3.18
1381 1436 2.469826 TCGTTCAGTGCTGTTACTGTG 58.530 47.619 11.88 6.09 46.32 3.66
1395 1450 2.566952 ACTGTGTGCTTTCACTTTGC 57.433 45.000 8.22 0.00 43.49 3.68
1396 1451 1.134946 ACTGTGTGCTTTCACTTTGCC 59.865 47.619 8.22 0.00 43.49 4.52
1397 1452 1.406539 CTGTGTGCTTTCACTTTGCCT 59.593 47.619 8.22 0.00 43.49 4.75
1398 1453 1.405105 TGTGTGCTTTCACTTTGCCTC 59.595 47.619 8.22 0.00 43.49 4.70
1399 1454 1.678101 GTGTGCTTTCACTTTGCCTCT 59.322 47.619 0.00 0.00 43.49 3.69
1400 1455 2.099756 GTGTGCTTTCACTTTGCCTCTT 59.900 45.455 0.00 0.00 43.49 2.85
1401 1456 3.315191 GTGTGCTTTCACTTTGCCTCTTA 59.685 43.478 0.00 0.00 43.49 2.10
1402 1457 3.565482 TGTGCTTTCACTTTGCCTCTTAG 59.435 43.478 0.00 0.00 43.49 2.18
1403 1458 2.554032 TGCTTTCACTTTGCCTCTTAGC 59.446 45.455 0.00 0.00 0.00 3.09
1431 1486 2.093606 GGTGAGGGTGCTTTCCTACTAC 60.094 54.545 0.00 0.00 34.21 2.73
1432 1487 2.832733 GTGAGGGTGCTTTCCTACTACT 59.167 50.000 0.00 0.00 34.21 2.57
1433 1488 4.021916 GTGAGGGTGCTTTCCTACTACTA 58.978 47.826 0.00 0.00 34.21 1.82
1434 1489 4.650131 GTGAGGGTGCTTTCCTACTACTAT 59.350 45.833 0.00 0.00 34.21 2.12
1435 1490 5.832060 GTGAGGGTGCTTTCCTACTACTATA 59.168 44.000 0.00 0.00 34.21 1.31
1525 1592 1.066430 GTGTGCACCCTTTCCGATCTA 60.066 52.381 15.69 0.00 0.00 1.98
1558 1625 1.474077 CTAACCTCTGCATTGCCAACC 59.526 52.381 6.12 0.00 0.00 3.77
1641 1710 5.105756 GCATGGGCTTAAGTAACAACTCATT 60.106 40.000 4.02 0.00 36.96 2.57
1642 1711 6.572314 GCATGGGCTTAAGTAACAACTCATTT 60.572 38.462 4.02 0.00 36.96 2.32
1727 1797 5.701224 ACCAACCTCTGTTCTTAATTCCAA 58.299 37.500 0.00 0.00 30.42 3.53
1743 1813 1.401552 TCCAAGCGATGTATTTGCTGC 59.598 47.619 0.00 0.00 44.81 5.25
1750 1820 2.223641 CGATGTATTTGCTGCAAGGCAT 60.224 45.455 15.39 18.36 42.09 4.40
1751 1821 3.735820 CGATGTATTTGCTGCAAGGCATT 60.736 43.478 15.39 2.30 42.09 3.56
1772 1842 3.497332 TCTTATAGCCCGTAGTGCATCT 58.503 45.455 0.00 0.00 0.00 2.90
1801 1871 2.868839 GCTCTGCATGCACCAAAAACAT 60.869 45.455 18.46 0.00 0.00 2.71
1810 1880 4.688021 TGCACCAAAAACATCAACTTACC 58.312 39.130 0.00 0.00 0.00 2.85
1822 1892 5.995897 ACATCAACTTACCAGTGTAAACTCC 59.004 40.000 0.00 0.00 36.54 3.85
1823 1893 4.964593 TCAACTTACCAGTGTAAACTCCC 58.035 43.478 0.00 0.00 36.54 4.30
1849 1920 2.540265 CTCTGCTCCAAGAGTTGTGT 57.460 50.000 0.00 0.00 39.14 3.72
1953 2025 4.632974 GGCCATGCCTAGCTCCGG 62.633 72.222 0.00 0.00 46.69 5.14
1983 2055 1.678970 GCCAAGGAGGAAACGGCAT 60.679 57.895 0.00 0.00 42.50 4.40
2062 2134 3.382832 CGTGCCTCGAGGGGAAGT 61.383 66.667 32.06 0.00 42.86 3.01
2156 2228 3.062763 CGTGGAGATGGTGATATCTTGC 58.937 50.000 3.98 0.00 37.53 4.01
2178 2251 3.181471 CGTAAGAAGGGATGCATGAGACT 60.181 47.826 2.46 0.00 43.02 3.24
2209 2282 0.742635 GCTGGCGGGAGAAAGAGAAG 60.743 60.000 0.00 0.00 0.00 2.85
2213 2286 1.153549 CGGGAGAAAGAGAAGCGGG 60.154 63.158 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 1.352352 ACTCAATGGGTTCCTCCACAG 59.648 52.381 0.00 0.00 39.97 3.66
69 70 7.732222 TTTAATTCCAGCAATAACCTTCCAT 57.268 32.000 0.00 0.00 0.00 3.41
80 81 6.404293 GCGATAACCTCTTTTAATTCCAGCAA 60.404 38.462 0.00 0.00 0.00 3.91
127 128 0.540923 TTGCTTTGGCTTTTGTGGCT 59.459 45.000 0.00 0.00 39.59 4.75
128 129 1.532437 GATTGCTTTGGCTTTTGTGGC 59.468 47.619 0.00 0.00 39.59 5.01
179 218 2.265367 TGGTTGAGCCAATAGGACTGA 58.735 47.619 0.00 0.00 45.94 3.41
210 249 1.959226 TCACAACGAAGCGAAGGGC 60.959 57.895 0.00 0.00 44.05 5.19
342 381 9.297037 TGAGTAGATATATCAATCTCCGTCAAA 57.703 33.333 15.08 1.08 37.41 2.69
343 382 8.863872 TGAGTAGATATATCAATCTCCGTCAA 57.136 34.615 15.08 1.65 37.41 3.18
344 383 8.863872 TTGAGTAGATATATCAATCTCCGTCA 57.136 34.615 15.08 3.69 37.41 4.35
571 623 0.603707 CAGAGGCGACCAATGTGTGT 60.604 55.000 0.00 0.00 0.00 3.72
737 789 2.464796 TCACTACACCGGTGGGATAT 57.535 50.000 36.47 19.00 36.97 1.63
759 812 6.153851 TGGACTCCACGTAAGAGATTTTGATA 59.846 38.462 18.76 0.00 43.62 2.15
852 906 0.178953 AACTCTGCAAGGCAATGGGT 60.179 50.000 0.00 0.00 38.41 4.51
865 919 0.041839 GCAACGACACTGCAACTCTG 60.042 55.000 0.00 0.00 39.69 3.35
866 920 0.461870 TGCAACGACACTGCAACTCT 60.462 50.000 0.00 0.00 46.47 3.24
867 921 2.013807 TGCAACGACACTGCAACTC 58.986 52.632 0.00 0.00 46.47 3.01
868 922 4.217035 TGCAACGACACTGCAACT 57.783 50.000 0.00 0.00 46.47 3.16
904 958 2.094894 CGTGCAAAGATGAGCTAACTGG 59.905 50.000 0.00 0.00 0.00 4.00
906 960 3.319137 TCGTGCAAAGATGAGCTAACT 57.681 42.857 0.00 0.00 0.00 2.24
954 1008 1.670949 GATCAGAGGCCGCTGTGAGA 61.671 60.000 32.08 16.37 37.20 3.27
960 1014 2.188994 GCTTGATCAGAGGCCGCT 59.811 61.111 1.77 1.77 0.00 5.52
961 1015 3.267860 CGCTTGATCAGAGGCCGC 61.268 66.667 0.00 0.00 0.00 6.53
963 1017 2.899339 GGCGCTTGATCAGAGGCC 60.899 66.667 7.64 14.62 41.49 5.19
969 1023 2.124983 GAGGCTGGCGCTTGATCA 60.125 61.111 7.64 0.00 36.09 2.92
981 1035 2.592308 GATTGCTTCGGGGAGGCT 59.408 61.111 1.47 0.00 35.64 4.58
1018 1072 1.078214 CGCAGATGAAGAGCCCCAA 60.078 57.895 0.00 0.00 0.00 4.12
1078 1132 1.594310 GCGCTTCTCTCAAGACCCT 59.406 57.895 0.00 0.00 0.00 4.34
1125 1179 1.490490 GGCACCTTCATGGATACCTCA 59.510 52.381 0.00 0.00 39.71 3.86
1262 1316 1.297158 CCTACTACGGCGTTCGACG 60.297 63.158 21.24 18.75 45.88 5.12
1269 1323 2.163010 TCTGTTTCTTCCTACTACGGCG 59.837 50.000 4.80 4.80 0.00 6.46
1272 1326 5.357314 TCATCCTCTGTTTCTTCCTACTACG 59.643 44.000 0.00 0.00 0.00 3.51
1277 1331 4.341487 TCGTCATCCTCTGTTTCTTCCTA 58.659 43.478 0.00 0.00 0.00 2.94
1283 1338 2.996621 CAACCTCGTCATCCTCTGTTTC 59.003 50.000 0.00 0.00 0.00 2.78
1289 1344 0.820871 AGAGCAACCTCGTCATCCTC 59.179 55.000 0.00 0.00 43.05 3.71
1293 1348 0.674895 GCCAAGAGCAACCTCGTCAT 60.675 55.000 0.00 0.00 43.05 3.06
1296 1351 2.172483 ATCGCCAAGAGCAACCTCGT 62.172 55.000 0.00 0.00 44.04 4.18
1302 1357 2.309528 ATTCGTATCGCCAAGAGCAA 57.690 45.000 0.00 0.00 44.04 3.91
1305 1360 6.645415 ACCTTAATTATTCGTATCGCCAAGAG 59.355 38.462 0.00 0.00 0.00 2.85
1307 1362 6.780706 ACCTTAATTATTCGTATCGCCAAG 57.219 37.500 0.00 0.00 0.00 3.61
1310 1365 6.587651 GTCAACCTTAATTATTCGTATCGCC 58.412 40.000 0.00 0.00 0.00 5.54
1315 1370 7.099266 TCCTCGTCAACCTTAATTATTCGTA 57.901 36.000 0.00 0.00 0.00 3.43
1316 1371 5.969423 TCCTCGTCAACCTTAATTATTCGT 58.031 37.500 0.00 0.00 0.00 3.85
1317 1372 8.583810 TTATCCTCGTCAACCTTAATTATTCG 57.416 34.615 0.00 0.00 0.00 3.34
1350 1405 2.422597 CACTGAACGAATGGGCAGTAA 58.577 47.619 0.00 0.00 39.40 2.24
1367 1422 2.332063 AAGCACACAGTAACAGCACT 57.668 45.000 0.00 0.00 0.00 4.40
1381 1436 3.610349 GCTAAGAGGCAAAGTGAAAGCAC 60.610 47.826 0.00 0.00 45.49 4.40
1450 1517 8.458052 TGGACATGATGACATTATAAAACACAC 58.542 33.333 0.00 0.00 34.15 3.82
1512 1579 5.793030 ATTAGACAGTAGATCGGAAAGGG 57.207 43.478 0.00 0.00 0.00 3.95
1525 1592 7.241042 TGCAGAGGTTAGTTAATTAGACAGT 57.759 36.000 0.00 0.00 0.00 3.55
1576 1643 4.699522 ACACTCCCTTTCCGCGGC 62.700 66.667 23.51 0.00 0.00 6.53
1634 1703 1.000274 GCCAAACAGCGGAAATGAGTT 60.000 47.619 0.00 0.00 0.00 3.01
1641 1710 2.016318 CTATCATGCCAAACAGCGGAA 58.984 47.619 0.00 0.00 34.65 4.30
1642 1711 1.667236 CTATCATGCCAAACAGCGGA 58.333 50.000 0.00 0.00 34.65 5.54
1674 1743 7.268586 AGTGGATGACTTTGTGTATTAGCTAG 58.731 38.462 0.00 0.00 0.00 3.42
1677 1746 6.019801 CGTAGTGGATGACTTTGTGTATTAGC 60.020 42.308 0.00 0.00 35.96 3.09
1727 1797 1.402968 CCTTGCAGCAAATACATCGCT 59.597 47.619 9.65 0.00 36.10 4.93
1743 1813 2.851195 ACGGGCTATAAGAATGCCTTG 58.149 47.619 0.00 0.00 45.45 3.61
1750 1820 3.895656 AGATGCACTACGGGCTATAAGAA 59.104 43.478 0.00 0.00 0.00 2.52
1751 1821 3.497332 AGATGCACTACGGGCTATAAGA 58.503 45.455 0.00 0.00 0.00 2.10
1761 1831 0.936764 CAGCCGCTAGATGCACTACG 60.937 60.000 0.00 0.70 43.06 3.51
1791 1861 5.420739 ACACTGGTAAGTTGATGTTTTTGGT 59.579 36.000 0.00 0.00 32.98 3.67
1801 1871 4.409574 TGGGAGTTTACACTGGTAAGTTGA 59.590 41.667 0.00 0.00 40.40 3.18
1810 1880 1.873591 GTGTGCTGGGAGTTTACACTG 59.126 52.381 0.00 0.00 38.76 3.66
1847 1918 5.890419 TGGTATTTCCATGCATGTGATAACA 59.110 36.000 24.58 21.59 41.93 2.41
1849 1920 5.009911 GCTGGTATTTCCATGCATGTGATAA 59.990 40.000 24.58 16.21 46.12 1.75
1876 1947 3.200483 CACGCCTTGATCAATCTCATCA 58.800 45.455 8.96 0.00 0.00 3.07
1953 2025 2.512515 CTTGGCCGGTGCTAGCTC 60.513 66.667 17.23 12.62 37.74 4.09
1983 2055 2.232208 AGCTGTGTCGATCAAGTCATCA 59.768 45.455 0.00 0.00 0.00 3.07
2014 2086 2.743928 CCTTGCCTCACTCACCGC 60.744 66.667 0.00 0.00 0.00 5.68
2046 2118 1.376037 CAACTTCCCCTCGAGGCAC 60.376 63.158 26.87 0.00 0.00 5.01
2062 2134 5.079643 TCCATCAGATATCACGATCTCCAA 58.920 41.667 5.32 0.00 33.75 3.53
2127 2199 1.404035 CACCATCTCCACGTCGTATCA 59.596 52.381 0.00 0.00 0.00 2.15
2156 2228 3.126831 GTCTCATGCATCCCTTCTTACG 58.873 50.000 0.00 0.00 0.00 3.18
2178 2251 2.967397 GCCAGCTGCATTTGAGCA 59.033 55.556 8.66 0.00 43.35 4.26
2209 2282 1.723870 GAGAATGTGATGCACCCGC 59.276 57.895 0.00 0.00 39.24 6.13


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

AutoCloner maintained by Alex Coulton.