Multiple sequence alignment - TraesCS2D01G547600

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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 TraesCS2D01G547600 chr2D 100.000 3107 0 0 1 3107 623947037 623950143 0.000000e+00 5738
1 TraesCS2D01G547600 chr2D 94.105 1408 81 2 714 2120 624054153 624052747 0.000000e+00 2139
2 TraesCS2D01G547600 chr2D 96.904 872 23 3 2240 3107 70390878 70391749 0.000000e+00 1458
3 TraesCS2D01G547600 chr2A 94.444 1440 76 2 716 2152 755118535 755119973 0.000000e+00 2213
4 TraesCS2D01G547600 chr2A 92.552 1544 105 5 714 2252 755340903 755339365 0.000000e+00 2206
5 TraesCS2D01G547600 chr2A 90.074 403 21 8 350 740 755118128 755118523 3.580000e-139 505
6 TraesCS2D01G547600 chr2A 84.940 332 31 7 2 323 755116537 755116859 5.000000e-83 318
7 TraesCS2D01G547600 chr2B 94.337 1395 76 1 716 2107 765586468 765587862 0.000000e+00 2135
8 TraesCS2D01G547600 chr2B 93.295 1387 91 2 735 2120 765792901 765791516 0.000000e+00 2045
9 TraesCS2D01G547600 chr2B 88.914 451 18 9 306 740 765586022 765586456 7.630000e-146 527
10 TraesCS2D01G547600 chr7D 96.667 870 23 4 2243 3107 114467274 114468142 0.000000e+00 1441
11 TraesCS2D01G547600 chr7D 96.313 868 23 5 2247 3107 603599337 603598472 0.000000e+00 1417
12 TraesCS2D01G547600 chr7D 96.083 868 30 4 2243 3107 151540072 151540938 0.000000e+00 1411
13 TraesCS2D01G547600 chr7D 85.192 1040 94 31 2 1022 534358458 534357460 0.000000e+00 1013
14 TraesCS2D01G547600 chr7D 83.310 725 98 12 1295 2005 246388410 246389125 0.000000e+00 647
15 TraesCS2D01G547600 chr7D 94.220 346 6 4 1 346 534455814 534455483 1.650000e-142 516
16 TraesCS2D01G547600 chr7D 84.978 446 60 7 835 1278 246373954 246374394 2.200000e-121 446
17 TraesCS2D01G547600 chr7D 89.313 262 18 5 337 597 534449707 534449455 1.390000e-83 320
18 TraesCS2D01G547600 chr3D 96.211 871 26 5 2242 3107 214958664 214959532 0.000000e+00 1419
19 TraesCS2D01G547600 chr3D 95.553 877 34 5 2235 3107 460502841 460501966 0.000000e+00 1399
20 TraesCS2D01G547600 chr1D 95.977 870 29 3 2244 3107 426586359 426585490 0.000000e+00 1408
21 TraesCS2D01G547600 chr1D 95.944 863 33 2 2247 3107 487866330 487865468 0.000000e+00 1399
22 TraesCS2D01G547600 chr6D 95.853 868 32 4 2244 3107 460305770 460306637 0.000000e+00 1400
23 TraesCS2D01G547600 chr4A 87.553 948 100 11 716 1649 677272550 677273493 0.000000e+00 1081
24 TraesCS2D01G547600 chr7A 83.389 1192 159 25 835 2005 262852448 262853621 0.000000e+00 1068
25 TraesCS2D01G547600 chr5D 83.390 1186 161 24 835 2005 238670460 238669296 0.000000e+00 1066
26 TraesCS2D01G547600 chr7B 83.137 1186 161 24 835 1999 222553197 222554364 0.000000e+00 1046


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 TraesCS2D01G547600 chr2D 623947037 623950143 3106 False 5738 5738 100.000000 1 3107 1 chr2D.!!$F2 3106
1 TraesCS2D01G547600 chr2D 624052747 624054153 1406 True 2139 2139 94.105000 714 2120 1 chr2D.!!$R1 1406
2 TraesCS2D01G547600 chr2D 70390878 70391749 871 False 1458 1458 96.904000 2240 3107 1 chr2D.!!$F1 867
3 TraesCS2D01G547600 chr2A 755339365 755340903 1538 True 2206 2206 92.552000 714 2252 1 chr2A.!!$R1 1538
4 TraesCS2D01G547600 chr2A 755116537 755119973 3436 False 1012 2213 89.819333 2 2152 3 chr2A.!!$F1 2150
5 TraesCS2D01G547600 chr2B 765791516 765792901 1385 True 2045 2045 93.295000 735 2120 1 chr2B.!!$R1 1385
6 TraesCS2D01G547600 chr2B 765586022 765587862 1840 False 1331 2135 91.625500 306 2107 2 chr2B.!!$F1 1801
7 TraesCS2D01G547600 chr7D 114467274 114468142 868 False 1441 1441 96.667000 2243 3107 1 chr7D.!!$F1 864
8 TraesCS2D01G547600 chr7D 603598472 603599337 865 True 1417 1417 96.313000 2247 3107 1 chr7D.!!$R4 860
9 TraesCS2D01G547600 chr7D 151540072 151540938 866 False 1411 1411 96.083000 2243 3107 1 chr7D.!!$F2 864
10 TraesCS2D01G547600 chr7D 534357460 534358458 998 True 1013 1013 85.192000 2 1022 1 chr7D.!!$R1 1020
11 TraesCS2D01G547600 chr7D 246388410 246389125 715 False 647 647 83.310000 1295 2005 1 chr7D.!!$F4 710
12 TraesCS2D01G547600 chr3D 214958664 214959532 868 False 1419 1419 96.211000 2242 3107 1 chr3D.!!$F1 865
13 TraesCS2D01G547600 chr3D 460501966 460502841 875 True 1399 1399 95.553000 2235 3107 1 chr3D.!!$R1 872
14 TraesCS2D01G547600 chr1D 426585490 426586359 869 True 1408 1408 95.977000 2244 3107 1 chr1D.!!$R1 863
15 TraesCS2D01G547600 chr1D 487865468 487866330 862 True 1399 1399 95.944000 2247 3107 1 chr1D.!!$R2 860
16 TraesCS2D01G547600 chr6D 460305770 460306637 867 False 1400 1400 95.853000 2244 3107 1 chr6D.!!$F1 863
17 TraesCS2D01G547600 chr4A 677272550 677273493 943 False 1081 1081 87.553000 716 1649 1 chr4A.!!$F1 933
18 TraesCS2D01G547600 chr7A 262852448 262853621 1173 False 1068 1068 83.389000 835 2005 1 chr7A.!!$F1 1170
19 TraesCS2D01G547600 chr5D 238669296 238670460 1164 True 1066 1066 83.390000 835 2005 1 chr5D.!!$R1 1170
20 TraesCS2D01G547600 chr7B 222553197 222554364 1167 False 1046 1046 83.137000 835 1999 1 chr7B.!!$F1 1164

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
334 345 0.186873 CCCCAATTAGCCAGCATCCT 59.813 55.0 0.0 0.0 0.0 3.24 F
506 1766 0.319211 TCGAACCGACTTGCACGAAT 60.319 50.0 0.0 0.0 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 3328 1.003839 GCAGGTGTGATTCCGGACA 60.004 57.895 1.83 0.00 0.0 4.02 R
2158 3506 1.179152 TTACAATGACTCTCGGCGGA 58.821 50.000 7.21 2.06 0.0 5.54 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
29 30 2.079925 GATCACACTTCTTCCCTGTGC 58.920 52.381 0.00 0.00 36.12 4.57
42 49 3.426615 TCCCTGTGCGTAATCCAAAAAT 58.573 40.909 0.00 0.00 0.00 1.82
49 56 6.982852 TGTGCGTAATCCAAAAATAGGAAAA 58.017 32.000 0.00 0.00 38.93 2.29
51 58 7.088272 GTGCGTAATCCAAAAATAGGAAAACT 58.912 34.615 0.00 0.00 38.93 2.66
66 73 6.215495 AGGAAAACTTTTGACGATTTTGGA 57.785 33.333 0.00 0.00 0.00 3.53
165 172 8.868522 AGTTTGAAATGTCAAGATAATCCTGA 57.131 30.769 0.00 0.00 44.49 3.86
205 212 8.865090 TGAAAATTAGGCCTAGAATTTGTGAAA 58.135 29.630 21.60 3.18 35.84 2.69
213 220 6.430000 GGCCTAGAATTTGTGAAAGTCAGTAA 59.570 38.462 0.00 0.00 37.90 2.24
215 222 9.162764 GCCTAGAATTTGTGAAAGTCAGTAATA 57.837 33.333 0.00 0.00 37.90 0.98
334 345 0.186873 CCCCAATTAGCCAGCATCCT 59.813 55.000 0.00 0.00 0.00 3.24
401 1654 1.642037 CTCCAGCCGCAGTTGTCATG 61.642 60.000 0.00 0.00 0.00 3.07
414 1667 1.517257 GTCATGGTGCTCGTCTCGG 60.517 63.158 0.00 0.00 0.00 4.63
447 1700 5.869344 TCTGAATCGAATACACCTCAAAGTG 59.131 40.000 0.00 0.00 43.65 3.16
504 1764 2.723116 TCGAACCGACTTGCACGA 59.277 55.556 0.00 0.00 0.00 4.35
505 1765 1.066093 TCGAACCGACTTGCACGAA 59.934 52.632 0.00 0.00 0.00 3.85
506 1766 0.319211 TCGAACCGACTTGCACGAAT 60.319 50.000 0.00 0.00 0.00 3.34
507 1767 0.511221 CGAACCGACTTGCACGAATT 59.489 50.000 0.00 0.00 0.00 2.17
635 1907 3.644966 AAATAAGATCACCGGCCTTCA 57.355 42.857 0.00 0.00 0.00 3.02
656 1928 1.026718 CCCAGAACCACAAGCGATCC 61.027 60.000 0.00 0.00 0.00 3.36
717 2034 0.685785 AGCCGATCCAGAGAAGAGCA 60.686 55.000 0.00 0.00 0.00 4.26
964 2287 3.141522 TTCGTCGACGCCCACAACT 62.142 57.895 32.19 0.00 39.60 3.16
1455 2778 3.776656 GTCGTTTCCATCGACGGG 58.223 61.111 0.00 0.00 45.64 5.28
1533 2864 3.982372 GGTGAGCGTCGCCATCGAA 62.982 63.158 14.86 0.00 46.03 3.71
1974 3322 1.890894 CCCGTCAGAGTACCCTGTG 59.109 63.158 4.14 0.00 35.71 3.66
1980 3328 1.977854 TCAGAGTACCCTGTGTGCAAT 59.022 47.619 4.14 0.00 33.78 3.56
1982 3330 1.699634 AGAGTACCCTGTGTGCAATGT 59.300 47.619 0.00 0.00 31.00 2.71
1984 3332 1.165270 GTACCCTGTGTGCAATGTCC 58.835 55.000 0.00 0.00 0.00 4.02
1991 3339 1.164411 GTGTGCAATGTCCGGAATCA 58.836 50.000 5.23 0.00 0.00 2.57
2016 3364 2.694760 CGCCAAGAGCAAGGGAAGC 61.695 63.158 0.00 0.00 44.04 3.86
2124 3472 1.435577 AGGCGTTTTAGGTTACAGCG 58.564 50.000 0.00 0.00 0.00 5.18
2131 3479 5.736338 CGTTTTAGGTTACAGCGTTTTGTA 58.264 37.500 0.00 0.00 32.56 2.41
2132 3480 5.616785 CGTTTTAGGTTACAGCGTTTTGTAC 59.383 40.000 0.00 0.00 33.50 2.90
2181 3529 4.038763 TCCGCCGAGAGTCATTGTAAATAT 59.961 41.667 0.00 0.00 0.00 1.28
2183 3531 5.107453 CCGCCGAGAGTCATTGTAAATATTC 60.107 44.000 0.00 0.00 0.00 1.75
2187 3535 7.328737 GCCGAGAGTCATTGTAAATATTCGTAT 59.671 37.037 0.00 0.00 0.00 3.06
2188 3536 8.639428 CCGAGAGTCATTGTAAATATTCGTATG 58.361 37.037 0.00 0.00 0.00 2.39
2189 3537 9.181805 CGAGAGTCATTGTAAATATTCGTATGT 57.818 33.333 0.00 0.00 0.00 2.29
2220 3572 6.521151 AGGAGTCATCATTTTTCAATGGTC 57.479 37.500 0.00 0.00 40.41 4.02
2262 3614 1.886886 ACGAAAAGTGTAACGCCCAT 58.113 45.000 0.00 0.00 45.86 4.00
2331 3683 4.211164 CAGTAACTTCTGCACGAATGTTGA 59.789 41.667 15.36 0.00 30.79 3.18
2332 3684 4.997395 AGTAACTTCTGCACGAATGTTGAT 59.003 37.500 15.36 7.85 30.79 2.57
2348 3700 7.528516 CGAATGTTGATACGAATTAGCTGATTG 59.471 37.037 8.68 4.09 0.00 2.67
2455 3808 2.776072 CGTTTAGCAGTTCGCCCG 59.224 61.111 0.00 0.00 44.04 6.13
2460 3813 2.796483 TTAGCAGTTCGCCCGCACAT 62.796 55.000 0.00 0.00 44.04 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.210120 GGAAGAAGTGTGATCGACATATGC 59.790 45.833 1.58 0.00 36.78 3.14
1 2 4.747108 GGGAAGAAGTGTGATCGACATATG 59.253 45.833 0.00 0.00 36.78 1.78
2 3 4.651503 AGGGAAGAAGTGTGATCGACATAT 59.348 41.667 0.00 0.00 36.78 1.78
6 7 2.028930 ACAGGGAAGAAGTGTGATCGAC 60.029 50.000 0.00 0.00 0.00 4.20
7 8 2.029020 CACAGGGAAGAAGTGTGATCGA 60.029 50.000 0.00 0.00 43.58 3.59
15 16 2.354805 GGATTACGCACAGGGAAGAAGT 60.355 50.000 0.00 0.00 0.00 3.01
16 17 2.280628 GGATTACGCACAGGGAAGAAG 58.719 52.381 0.00 0.00 0.00 2.85
21 22 2.570415 TTTTGGATTACGCACAGGGA 57.430 45.000 0.00 0.00 0.00 4.20
42 49 7.336161 TCCAAAATCGTCAAAAGTTTTCCTA 57.664 32.000 0.00 0.00 0.00 2.94
49 56 6.626302 TCAAACTTCCAAAATCGTCAAAAGT 58.374 32.000 0.00 0.00 0.00 2.66
51 58 8.485976 AAATCAAACTTCCAAAATCGTCAAAA 57.514 26.923 0.00 0.00 0.00 2.44
97 104 9.717942 TTTCAGAAAATCAAGTTTCTTTTTGGA 57.282 25.926 2.90 0.00 43.74 3.53
185 192 6.539173 TGACTTTCACAAATTCTAGGCCTAA 58.461 36.000 14.85 1.39 0.00 2.69
193 200 9.793259 TTCCTATTACTGACTTTCACAAATTCT 57.207 29.630 0.00 0.00 0.00 2.40
250 261 3.638160 TGCCTGATCAGCTTTCTGTTTTT 59.362 39.130 17.76 0.00 41.10 1.94
251 262 3.225104 TGCCTGATCAGCTTTCTGTTTT 58.775 40.909 17.76 0.00 41.10 2.43
252 263 2.867624 TGCCTGATCAGCTTTCTGTTT 58.132 42.857 17.76 0.00 41.10 2.83
253 264 2.555757 GTTGCCTGATCAGCTTTCTGTT 59.444 45.455 17.76 0.00 41.10 3.16
254 265 2.157738 GTTGCCTGATCAGCTTTCTGT 58.842 47.619 17.76 0.00 41.10 3.41
255 266 1.129998 CGTTGCCTGATCAGCTTTCTG 59.870 52.381 17.76 3.64 41.67 3.02
447 1700 2.807045 CTGAGACGCACGCTGACC 60.807 66.667 0.00 0.00 0.00 4.02
475 1735 1.095600 CGGTTCGACCTCTCTGATCA 58.904 55.000 0.00 0.00 35.66 2.92
503 1763 6.984474 TGATTGACGTGGAGGTAGATTAATTC 59.016 38.462 0.00 0.00 0.00 2.17
504 1764 6.884832 TGATTGACGTGGAGGTAGATTAATT 58.115 36.000 0.00 0.00 0.00 1.40
505 1765 6.323996 TCTGATTGACGTGGAGGTAGATTAAT 59.676 38.462 0.00 0.00 0.00 1.40
506 1766 5.655090 TCTGATTGACGTGGAGGTAGATTAA 59.345 40.000 0.00 0.00 0.00 1.40
507 1767 5.198207 TCTGATTGACGTGGAGGTAGATTA 58.802 41.667 0.00 0.00 0.00 1.75
604 1866 7.174253 GCCGGTGATCTTATTTTATATTGGTCA 59.826 37.037 1.90 0.00 0.00 4.02
635 1907 0.110486 ATCGCTTGTGGTTCTGGGTT 59.890 50.000 0.00 0.00 0.00 4.11
656 1928 4.809426 GTCGTACTAGGGATCATTGGTTTG 59.191 45.833 0.00 0.00 0.00 2.93
730 2047 1.672356 CGAGGAACACCAAGGCCAG 60.672 63.158 5.01 0.00 0.00 4.85
1962 3310 1.699634 ACATTGCACACAGGGTACTCT 59.300 47.619 0.00 0.00 0.00 3.24
1974 3322 1.135689 GTGTGATTCCGGACATTGCAC 60.136 52.381 1.83 8.95 0.00 4.57
1980 3328 1.003839 GCAGGTGTGATTCCGGACA 60.004 57.895 1.83 0.00 0.00 4.02
1982 3330 2.264480 CGCAGGTGTGATTCCGGA 59.736 61.111 0.00 0.00 0.00 5.14
1984 3332 3.499737 GGCGCAGGTGTGATTCCG 61.500 66.667 10.83 0.00 0.00 4.30
1991 3339 3.772853 TTGCTCTTGGCGCAGGTGT 62.773 57.895 10.83 0.00 45.43 4.16
2016 3364 1.809619 CGCATCCACAGTGTACGGG 60.810 63.158 0.00 0.00 0.00 5.28
2103 3451 3.192466 CGCTGTAACCTAAAACGCCTAT 58.808 45.455 0.00 0.00 0.00 2.57
2124 3472 6.364165 TGACTGCTACGTTATGAGTACAAAAC 59.636 38.462 0.00 0.00 0.00 2.43
2158 3506 1.179152 TTACAATGACTCTCGGCGGA 58.821 50.000 7.21 2.06 0.00 5.54
2159 3507 2.004583 TTTACAATGACTCTCGGCGG 57.995 50.000 7.21 0.00 0.00 6.13
2160 3508 5.387444 CGAATATTTACAATGACTCTCGGCG 60.387 44.000 0.00 0.00 0.00 6.46
2161 3509 5.462398 ACGAATATTTACAATGACTCTCGGC 59.538 40.000 0.00 0.00 0.00 5.54
2331 3683 6.147821 GGCATACACAATCAGCTAATTCGTAT 59.852 38.462 0.00 0.00 0.00 3.06
2332 3684 5.465390 GGCATACACAATCAGCTAATTCGTA 59.535 40.000 0.00 0.00 0.00 3.43
2348 3700 1.997606 GTTGTCCTACGTGGCATACAC 59.002 52.381 0.00 0.00 46.78 2.90
2455 3808 2.908634 CGTGACTGAAAACTGATGTGC 58.091 47.619 0.00 0.00 0.00 4.57
2460 3813 2.017138 TGTGCGTGACTGAAAACTGA 57.983 45.000 0.00 0.00 0.00 3.41
2745 4103 5.172205 GTTCGGATAAAAGAGAGAGTTGCT 58.828 41.667 0.00 0.00 0.00 3.91
2922 4284 1.815003 GTTGCCATCTCAGGTCAAAGG 59.185 52.381 0.00 0.00 0.00 3.11
3060 4423 0.876777 CCACGTGACACTTTACCGCA 60.877 55.000 19.30 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.