Multiple sequence alignment - TraesCS2D01G370500

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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 TraesCS2D01G370500 chr2D 100.000 2408 0 0 1 2408 474887958 474885551 0.000000e+00 4447
1 TraesCS2D01G370500 chr2A 89.992 2468 119 52 9 2402 617434969 617432556 0.000000e+00 3072
2 TraesCS2D01G370500 chr2B 90.817 1971 94 32 481 2408 555841899 555839973 0.000000e+00 2556
3 TraesCS2D01G370500 chr2B 93.135 437 18 6 12 443 555842329 555841900 4.370000e-177 630


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 TraesCS2D01G370500 chr2D 474885551 474887958 2407 True 4447 4447 100.000 1 2408 1 chr2D.!!$R1 2407
1 TraesCS2D01G370500 chr2A 617432556 617434969 2413 True 3072 3072 89.992 9 2402 1 chr2A.!!$R1 2393
2 TraesCS2D01G370500 chr2B 555839973 555842329 2356 True 1593 2556 91.976 12 2408 2 chr2B.!!$R1 2396

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
610 646 0.880278 CCTGACCATTATCGTGCCCG 60.88 60.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1652 1737 0.467804 GCCAGGGGAGAAGATGAGAC 59.532 60.0 0.0 0.0 0.0 3.36 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
35 36 8.126871 TGAAGTGTTGCGAATATGAGTATTAC 57.873 34.615 0.00 0.00 30.75 1.89
39 43 3.239254 TGCGAATATGAGTATTACGCCG 58.761 45.455 0.00 0.00 41.15 6.46
78 82 2.624316 AGCGCACACATCATTTTCAG 57.376 45.000 11.47 0.00 0.00 3.02
180 184 6.814076 GAGTTGGACTCTTTATCATGTACG 57.186 41.667 0.97 0.00 41.88 3.67
191 195 8.470040 TCTTTATCATGTACGTACCAACTTTC 57.530 34.615 22.43 0.00 0.00 2.62
229 233 4.871871 TGCAATTATACTTCTTCCCCCA 57.128 40.909 0.00 0.00 0.00 4.96
239 243 1.218316 CTTCCCCCAGTGCTCGTAC 59.782 63.158 0.00 0.00 0.00 3.67
450 465 4.500035 CCCTCGAGCTTAAGAGACCATAAC 60.500 50.000 6.99 0.00 36.65 1.89
479 496 1.209504 CCTGGCTCGGGATAGAAACAA 59.790 52.381 0.00 0.00 29.82 2.83
512 529 3.493129 TCAAACTACGCAGACACAATCAC 59.507 43.478 0.00 0.00 0.00 3.06
519 536 2.029288 AGACACAATCACAGCGGCG 61.029 57.895 0.51 0.51 0.00 6.46
552 569 3.572682 CCACTGTCAGTACACCTGTCTTA 59.427 47.826 4.85 0.00 42.19 2.10
610 646 0.880278 CCTGACCATTATCGTGCCCG 60.880 60.000 0.00 0.00 0.00 6.13
817 860 2.599032 CCATGCAGATGGCTCCCA 59.401 61.111 0.00 0.00 43.00 4.37
829 872 0.977108 GGCTCCCATTTCCATGCCAA 60.977 55.000 0.00 0.00 40.04 4.52
830 873 0.903942 GCTCCCATTTCCATGCCAAA 59.096 50.000 0.00 0.00 0.00 3.28
831 874 1.134610 GCTCCCATTTCCATGCCAAAG 60.135 52.381 0.00 0.00 0.00 2.77
832 875 2.181975 CTCCCATTTCCATGCCAAAGT 58.818 47.619 0.00 0.00 0.00 2.66
833 876 2.167075 CTCCCATTTCCATGCCAAAGTC 59.833 50.000 0.00 0.00 0.00 3.01
834 877 1.901159 CCCATTTCCATGCCAAAGTCA 59.099 47.619 0.00 0.00 0.00 3.41
835 878 2.354003 CCCATTTCCATGCCAAAGTCAC 60.354 50.000 0.00 0.00 0.00 3.67
836 879 2.564062 CCATTTCCATGCCAAAGTCACT 59.436 45.455 0.00 0.00 0.00 3.41
837 880 3.007182 CCATTTCCATGCCAAAGTCACTT 59.993 43.478 0.00 0.00 0.00 3.16
838 881 4.240096 CATTTCCATGCCAAAGTCACTTC 58.760 43.478 0.00 0.00 0.00 3.01
839 882 1.909700 TCCATGCCAAAGTCACTTCC 58.090 50.000 0.00 0.00 0.00 3.46
840 883 1.144708 TCCATGCCAAAGTCACTTCCA 59.855 47.619 0.00 0.00 0.00 3.53
841 884 2.173519 CCATGCCAAAGTCACTTCCAT 58.826 47.619 0.00 0.00 0.00 3.41
842 885 2.094390 CCATGCCAAAGTCACTTCCATG 60.094 50.000 14.41 14.41 31.02 3.66
871 915 4.498894 TCCTTGCTGATGATGACTTGAT 57.501 40.909 0.00 0.00 0.00 2.57
920 964 1.375523 CCTCACCTGCACCGGTAAC 60.376 63.158 6.87 2.61 34.94 2.50
1013 1071 1.522092 CCAGCATGAAGGCGTCCTA 59.478 57.895 0.00 0.00 39.69 2.94
1364 1440 3.760035 CGACCACGTCCCCTCCAG 61.760 72.222 0.00 0.00 34.56 3.86
1436 1512 1.065410 TGGTTGCTCCTTCCCTTCCA 61.065 55.000 0.80 0.00 37.07 3.53
1444 1520 3.110705 CTCCTTCCCTTCCATCTTCTGA 58.889 50.000 0.00 0.00 0.00 3.27
1490 1566 1.802880 GCTCGATCCGTGCATGTTAGT 60.803 52.381 4.96 0.00 44.15 2.24
1506 1587 6.090763 GCATGTTAGTTACATTTGCTTTTCCC 59.909 38.462 0.00 0.00 45.19 3.97
1543 1624 6.320418 TCATTCATGCATCAGTTGAATAAGCT 59.680 34.615 11.17 0.00 37.86 3.74
1572 1657 2.354656 CGCCATCATGCATGCAGC 60.355 61.111 26.69 21.09 45.96 5.25
1585 1670 2.487934 CATGCAGCATAGGTAGTGGAC 58.512 52.381 7.82 0.00 0.00 4.02
1586 1671 1.567357 TGCAGCATAGGTAGTGGACA 58.433 50.000 0.00 0.00 0.00 4.02
1587 1672 2.118679 TGCAGCATAGGTAGTGGACAT 58.881 47.619 0.00 0.00 0.00 3.06
1588 1673 3.304829 TGCAGCATAGGTAGTGGACATA 58.695 45.455 0.00 0.00 0.00 2.29
1589 1674 3.069586 TGCAGCATAGGTAGTGGACATAC 59.930 47.826 0.00 0.00 0.00 2.39
1590 1675 3.857383 GCAGCATAGGTAGTGGACATACG 60.857 52.174 0.00 0.00 0.00 3.06
1591 1676 2.891580 AGCATAGGTAGTGGACATACGG 59.108 50.000 0.00 0.00 0.00 4.02
1592 1677 2.029290 GCATAGGTAGTGGACATACGGG 60.029 54.545 0.00 0.00 0.00 5.28
1593 1678 3.228453 CATAGGTAGTGGACATACGGGT 58.772 50.000 0.00 0.00 0.00 5.28
1594 1679 2.242882 AGGTAGTGGACATACGGGTT 57.757 50.000 0.00 0.00 0.00 4.11
1595 1680 2.105766 AGGTAGTGGACATACGGGTTC 58.894 52.381 0.00 0.00 0.00 3.62
1609 1694 7.545489 ACATACGGGTTCTACTCTAAAAGAAG 58.455 38.462 0.00 0.00 32.56 2.85
1687 1772 3.071023 CCCTGGCGATGAATAGTTTCCTA 59.929 47.826 0.00 0.00 0.00 2.94
1696 1781 5.456548 TGAATAGTTTCCTACACGTGACA 57.543 39.130 25.01 8.55 0.00 3.58
1762 1852 1.532868 GATCGTTGTGTGCAGCTTTCT 59.467 47.619 0.00 0.00 0.00 2.52
1954 2050 1.589803 CTTTCCAGTTCGACCCGTTT 58.410 50.000 0.00 0.00 0.00 3.60
1955 2051 1.944709 CTTTCCAGTTCGACCCGTTTT 59.055 47.619 0.00 0.00 0.00 2.43
2053 2155 3.499338 TGCACATGAGATGAAAACCCTT 58.501 40.909 0.00 0.00 0.00 3.95
2069 2171 0.671781 CCTTCGTGGCTCCAAGACAG 60.672 60.000 4.05 5.81 30.96 3.51
2120 2222 6.324561 TGTACCACAATAACTGTACGTACA 57.675 37.500 25.88 25.88 43.68 2.90
2138 2241 3.708563 ACATGTGTTTCCCGTCAAAAG 57.291 42.857 0.00 0.00 0.00 2.27
2143 2246 4.069304 TGTGTTTCCCGTCAAAAGATAGG 58.931 43.478 0.00 0.00 0.00 2.57
2145 2248 4.153655 GTGTTTCCCGTCAAAAGATAGGAC 59.846 45.833 0.00 0.00 0.00 3.85
2298 2408 1.260033 GCTGCTCGATCAAATCCTTCG 59.740 52.381 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.576447 TCGCAACACTTCAGTCTATATGA 57.424 39.130 0.00 0.00 0.00 2.15
1 2 6.834959 ATTCGCAACACTTCAGTCTATATG 57.165 37.500 0.00 0.00 0.00 1.78
2 3 8.360390 TCATATTCGCAACACTTCAGTCTATAT 58.640 33.333 0.00 0.00 0.00 0.86
3 4 7.712797 TCATATTCGCAACACTTCAGTCTATA 58.287 34.615 0.00 0.00 0.00 1.31
4 5 6.573434 TCATATTCGCAACACTTCAGTCTAT 58.427 36.000 0.00 0.00 0.00 1.98
5 6 5.961272 TCATATTCGCAACACTTCAGTCTA 58.039 37.500 0.00 0.00 0.00 2.59
6 7 4.820897 TCATATTCGCAACACTTCAGTCT 58.179 39.130 0.00 0.00 0.00 3.24
7 8 4.627467 ACTCATATTCGCAACACTTCAGTC 59.373 41.667 0.00 0.00 0.00 3.51
35 36 2.585845 CTCTATGCTACATGTACGGCG 58.414 52.381 4.80 4.80 0.00 6.46
39 43 4.795795 CGCTATGCTCTATGCTACATGTAC 59.204 45.833 0.08 0.16 43.37 2.90
62 66 3.004629 TGACCACTGAAAATGATGTGTGC 59.995 43.478 0.00 0.00 0.00 4.57
78 82 0.387565 ACCAAATTTGCGGTGACCAC 59.612 50.000 12.92 0.00 33.05 4.16
116 120 3.071457 CAGGGAGGGAAAACTTTGCAAAT 59.929 43.478 13.23 0.00 0.00 2.32
202 206 8.700973 GGGGGAAGAAGTATAATTGCAATTTAA 58.299 33.333 28.45 13.24 0.00 1.52
203 207 7.841729 TGGGGGAAGAAGTATAATTGCAATTTA 59.158 33.333 28.45 17.10 0.00 1.40
204 208 6.671779 TGGGGGAAGAAGTATAATTGCAATTT 59.328 34.615 28.45 18.01 0.00 1.82
229 233 0.939577 CAAGCACACGTACGAGCACT 60.940 55.000 24.41 12.11 0.00 4.40
239 243 1.193203 CTGTAGCAAGTCAAGCACACG 59.807 52.381 0.00 0.00 0.00 4.49
299 305 2.656069 ATGACCCCGGTGTCGAAGG 61.656 63.158 12.62 0.51 38.11 3.46
479 496 2.484264 GCGTAGTTTGATTGCAAGGACT 59.516 45.455 4.94 8.44 35.04 3.85
512 529 2.507992 CTTCTCAGGACGCCGCTG 60.508 66.667 0.00 0.00 0.00 5.18
519 536 0.681733 TGACAGTGGCTTCTCAGGAC 59.318 55.000 0.00 0.00 0.00 3.85
552 569 0.617413 CTCTCCTTCCACAGCACCAT 59.383 55.000 0.00 0.00 0.00 3.55
610 646 0.321919 TGCCTGATGGTGCTTCAGTC 60.322 55.000 0.00 0.00 39.16 3.51
817 860 3.259123 GGAAGTGACTTTGGCATGGAAAT 59.741 43.478 0.00 0.00 0.00 2.17
829 872 1.180029 GCATGGCATGGAAGTGACTT 58.820 50.000 27.48 0.00 0.00 3.01
830 873 0.038599 TGCATGGCATGGAAGTGACT 59.961 50.000 27.48 0.00 31.71 3.41
831 874 2.570365 TGCATGGCATGGAAGTGAC 58.430 52.632 27.48 10.42 31.71 3.67
871 915 6.710597 AACACTGTTCTCTTATATAGGCGA 57.289 37.500 0.00 0.00 0.00 5.54
920 964 4.243270 GTTACAGTACCACTTGCCACTAG 58.757 47.826 0.00 0.00 0.00 2.57
1013 1071 0.034059 CAGAAGCACGACCAGGAAGT 59.966 55.000 0.00 0.00 0.00 3.01
1106 1176 2.969238 CGGCCTTGGCTATGAGCG 60.969 66.667 11.71 1.65 43.62 5.03
1436 1512 1.887198 ACGACACGGAACTCAGAAGAT 59.113 47.619 0.00 0.00 0.00 2.40
1444 1520 1.298863 CACGACACGACACGGAACT 60.299 57.895 0.00 0.00 0.00 3.01
1490 1566 5.656416 CCTATGGAGGGAAAAGCAAATGTAA 59.344 40.000 0.00 0.00 39.48 2.41
1506 1587 4.209538 TGCATGAATGAAACCCTATGGAG 58.790 43.478 0.00 0.00 34.81 3.86
1518 1599 6.320418 AGCTTATTCAACTGATGCATGAATGA 59.680 34.615 18.42 11.70 42.20 2.57
1519 1600 6.417930 CAGCTTATTCAACTGATGCATGAATG 59.582 38.462 18.42 7.34 42.20 2.67
1520 1601 6.461092 CCAGCTTATTCAACTGATGCATGAAT 60.461 38.462 2.46 10.86 43.91 2.57
1521 1602 5.163591 CCAGCTTATTCAACTGATGCATGAA 60.164 40.000 2.46 2.40 37.47 2.57
1522 1603 4.337274 CCAGCTTATTCAACTGATGCATGA 59.663 41.667 2.46 0.00 33.10 3.07
1572 1657 3.228453 ACCCGTATGTCCACTACCTATG 58.772 50.000 0.00 0.00 0.00 2.23
1585 1670 7.488471 CACTTCTTTTAGAGTAGAACCCGTATG 59.512 40.741 0.00 0.00 0.00 2.39
1586 1671 7.178097 ACACTTCTTTTAGAGTAGAACCCGTAT 59.822 37.037 0.00 0.00 0.00 3.06
1587 1672 6.491403 ACACTTCTTTTAGAGTAGAACCCGTA 59.509 38.462 0.00 0.00 0.00 4.02
1588 1673 5.303845 ACACTTCTTTTAGAGTAGAACCCGT 59.696 40.000 0.00 0.00 0.00 5.28
1589 1674 5.780984 ACACTTCTTTTAGAGTAGAACCCG 58.219 41.667 0.00 0.00 0.00 5.28
1590 1675 7.095910 GGTACACTTCTTTTAGAGTAGAACCC 58.904 42.308 0.00 0.00 0.00 4.11
1591 1676 7.664758 TGGTACACTTCTTTTAGAGTAGAACC 58.335 38.462 0.00 0.00 31.27 3.62
1652 1737 0.467804 GCCAGGGGAGAAGATGAGAC 59.532 60.000 0.00 0.00 0.00 3.36
1687 1772 0.531974 AGTCGGCATTTGTCACGTGT 60.532 50.000 16.51 0.00 0.00 4.49
1696 1781 2.159282 CCACTACGTAGAGTCGGCATTT 60.159 50.000 28.74 0.00 34.94 2.32
1762 1852 1.872952 CCACATGACTTTTGCGTCTCA 59.127 47.619 0.00 0.00 35.00 3.27
1954 2050 1.904287 AAACGGTGCCAGAATAGCAA 58.096 45.000 0.00 0.00 43.02 3.91
1955 2051 1.810151 GAAAACGGTGCCAGAATAGCA 59.190 47.619 0.00 0.00 38.08 3.49
2053 2155 1.967535 CTCTGTCTTGGAGCCACGA 59.032 57.895 0.00 0.00 0.00 4.35
2069 2171 1.911057 AGTAACAGCAAAAGGGGCTC 58.089 50.000 0.00 0.00 40.23 4.70
2120 2222 4.700213 CCTATCTTTTGACGGGAAACACAT 59.300 41.667 0.00 0.00 0.00 3.21
2138 2241 7.528307 CAACCAGATACGTATACAGTCCTATC 58.472 42.308 8.34 0.00 0.00 2.08
2143 2246 4.928601 TGCAACCAGATACGTATACAGTC 58.071 43.478 8.34 0.00 0.00 3.51
2145 2248 4.933330 ACTGCAACCAGATACGTATACAG 58.067 43.478 8.34 9.67 41.77 2.74
2298 2408 1.733399 GGGCGAGAGACGTTCACAC 60.733 63.158 0.00 0.00 43.44 3.82
2380 2490 7.234885 ACGATAGCTAGCTAGTACAGTGGTAC 61.235 46.154 27.42 1.39 45.24 3.34
2381 2491 5.221601 ACGATAGCTAGCTAGTACAGTGGTA 60.222 44.000 27.42 4.26 42.67 3.25
2384 2494 4.611807 GCACGATAGCTAGCTAGTACAGTG 60.612 50.000 27.42 26.64 42.67 3.66
2385 2495 3.499157 GCACGATAGCTAGCTAGTACAGT 59.501 47.826 27.42 18.59 42.67 3.55
2386 2496 4.073169 GCACGATAGCTAGCTAGTACAG 57.927 50.000 27.42 18.05 42.67 2.74


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

AutoCloner maintained by Alex Coulton.