Multiple sequence alignment - TraesCS7D01G249600

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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 TraesCS7D01G249600 chr7D 100.000 2628 0 0 1 2628 220980475 220977848 0.000000e+00 4854
1 TraesCS7D01G249600 chr7A 94.191 2651 87 15 1 2628 235470194 235467588 0.000000e+00 3980
2 TraesCS7D01G249600 chr7B 95.988 1695 41 8 939 2628 175998719 176000391 0.000000e+00 2728
3 TraesCS7D01G249600 chr7B 96.130 956 31 1 1 956 175996254 175997203 0.000000e+00 1555
4 TraesCS7D01G249600 chr2A 89.381 113 12 0 125 237 750963572 750963460 2.730000e-30 143


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 TraesCS7D01G249600 chr7D 220977848 220980475 2627 True 4854.0 4854 100.000 1 2628 1 chr7D.!!$R1 2627
1 TraesCS7D01G249600 chr7A 235467588 235470194 2606 True 3980.0 3980 94.191 1 2628 1 chr7A.!!$R1 2627
2 TraesCS7D01G249600 chr7B 175996254 176000391 4137 False 2141.5 2728 96.059 1 2628 2 chr7B.!!$F1 2627

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
749 750 0.111446 TAATGGTGGTGGTGGTGGTG 59.889 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2104 3650 0.754217 CAGGCAAGCCAGCACCATAT 60.754 55.0 14.4 0.0 38.92 1.78 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
354 355 4.334118 TCGGGGAGGACGTCGTCA 62.334 66.667 32.23 14.66 33.68 4.35
713 714 0.586802 GTGACGGCAACAAGGAAGAC 59.413 55.000 0.00 0.00 0.00 3.01
718 719 0.250338 GGCAACAAGGAAGACGAGGT 60.250 55.000 0.00 0.00 0.00 3.85
730 731 1.152312 ACGAGGTGGAGGACAAGGT 60.152 57.895 0.00 0.00 0.00 3.50
747 748 0.610785 GGTAATGGTGGTGGTGGTGG 60.611 60.000 0.00 0.00 0.00 4.61
748 749 0.111639 GTAATGGTGGTGGTGGTGGT 59.888 55.000 0.00 0.00 0.00 4.16
749 750 0.111446 TAATGGTGGTGGTGGTGGTG 59.889 55.000 0.00 0.00 0.00 4.17
750 751 2.655077 AATGGTGGTGGTGGTGGTGG 62.655 60.000 0.00 0.00 0.00 4.61
751 752 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
752 753 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
774 775 2.126228 GACGACGGCATGGACGAA 60.126 61.111 0.00 0.00 35.20 3.85
883 894 2.665185 GCGGTTTGACTCGTGGCT 60.665 61.111 0.00 0.00 0.00 4.75
930 941 3.948719 GGGGCCGTGGTGTCAGAA 61.949 66.667 0.00 0.00 0.00 3.02
1283 2828 1.202627 GCACCTGATCCTCCAAGCTAG 60.203 57.143 0.00 0.00 0.00 3.42
1421 2966 4.704103 AGTCCGAGAGCAGCCCCA 62.704 66.667 0.00 0.00 0.00 4.96
1429 2974 0.193069 AGAGCAGCCCCAGGATCTAT 59.807 55.000 0.00 0.00 0.00 1.98
1483 3029 8.935741 AGTTCTCTTTCTTTCTCCTACCTTAAA 58.064 33.333 0.00 0.00 0.00 1.52
1541 3087 1.074889 ACCGGCTTCCCTTGTTATTGT 59.925 47.619 0.00 0.00 0.00 2.71
1542 3088 2.167662 CCGGCTTCCCTTGTTATTGTT 58.832 47.619 0.00 0.00 0.00 2.83
1543 3089 2.094752 CCGGCTTCCCTTGTTATTGTTG 60.095 50.000 0.00 0.00 0.00 3.33
1544 3090 2.556622 CGGCTTCCCTTGTTATTGTTGT 59.443 45.455 0.00 0.00 0.00 3.32
1545 3091 3.005367 CGGCTTCCCTTGTTATTGTTGTT 59.995 43.478 0.00 0.00 0.00 2.83
1546 3092 4.306600 GGCTTCCCTTGTTATTGTTGTTG 58.693 43.478 0.00 0.00 0.00 3.33
1644 3190 0.741927 TGATCGACACAGGCATGCAG 60.742 55.000 21.36 13.91 0.00 4.41
1669 3215 0.038343 GCAGATCGAGCTGGAGATCC 60.038 60.000 30.05 10.17 43.03 3.36
1674 3220 0.467106 TCGAGCTGGAGATCCTCTGG 60.467 60.000 0.00 0.00 36.82 3.86
1686 3232 0.250295 TCCTCTGGTCGTTTTGCTGG 60.250 55.000 0.00 0.00 0.00 4.85
1812 3358 7.706159 TGCTCCATTGTCAATGAATGTTATAC 58.294 34.615 24.31 6.14 41.46 1.47
2104 3650 0.536687 AGTCGTCGGTGAGGAAGTCA 60.537 55.000 0.00 0.00 0.00 3.41
2536 4086 2.029918 GGGTGTGAAATTGACCTTGCTC 60.030 50.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
658 659 1.671901 GCACTCGGAGGAGGAGAAGG 61.672 65.000 10.23 0.0 44.93 3.46
713 714 1.263356 TTACCTTGTCCTCCACCTCG 58.737 55.000 0.00 0.0 0.00 4.63
718 719 1.633432 CCACCATTACCTTGTCCTCCA 59.367 52.381 0.00 0.0 0.00 3.86
730 731 0.111446 CACCACCACCACCACCATTA 59.889 55.000 0.00 0.0 0.00 1.90
883 894 1.136891 CACATCGGCCAGATCACTACA 59.863 52.381 2.24 0.0 37.52 2.74
920 931 1.596934 GATCCCGCTTCTGACACCA 59.403 57.895 0.00 0.0 0.00 4.17
985 2529 1.914798 AGCCATTCTCTTCCTTGCTCT 59.085 47.619 0.00 0.0 0.00 4.09
1185 2730 4.129737 ATGTCCACGTCCGCCTCG 62.130 66.667 0.00 0.0 0.00 4.63
1195 2740 2.171448 AGATGCTAACCTCCATGTCCAC 59.829 50.000 0.00 0.0 0.00 4.02
1283 2828 0.674895 AGACGGCAGGTGAGAATTGC 60.675 55.000 0.00 0.0 37.11 3.56
1421 2966 2.653702 GCAGCGGCGATAGATCCT 59.346 61.111 12.98 0.0 39.76 3.24
1456 3001 7.381789 AAGGTAGGAGAAAGAAAGAGAACTT 57.618 36.000 0.00 0.0 38.05 2.66
1483 3029 5.686124 CGGAGCTTAAGAAGAGGATGGAAAT 60.686 44.000 6.67 0.0 0.00 2.17
1527 3073 6.287589 ACAACAACAACAATAACAAGGGAA 57.712 33.333 0.00 0.0 0.00 3.97
1541 3087 1.140589 CGGCCTGCAACAACAACAA 59.859 52.632 0.00 0.0 0.00 2.83
1542 3088 2.780094 CCGGCCTGCAACAACAACA 61.780 57.895 0.00 0.0 0.00 3.33
1543 3089 2.027460 CCGGCCTGCAACAACAAC 59.973 61.111 0.00 0.0 0.00 3.32
1544 3090 2.626255 TACCCGGCCTGCAACAACAA 62.626 55.000 0.00 0.0 0.00 2.83
1545 3091 3.121406 TACCCGGCCTGCAACAACA 62.121 57.895 0.00 0.0 0.00 3.33
1546 3092 2.281900 TACCCGGCCTGCAACAAC 60.282 61.111 0.00 0.0 0.00 3.32
1644 3190 1.152989 CCAGCTCGATCTGCTTGCTC 61.153 60.000 10.79 0.0 38.92 4.26
1669 3215 1.264288 GAACCAGCAAAACGACCAGAG 59.736 52.381 0.00 0.0 0.00 3.35
1674 3220 3.059120 GGTAGAAGAACCAGCAAAACGAC 60.059 47.826 0.00 0.0 39.50 4.34
1686 3232 4.572795 GCAGCATAAGGAAGGTAGAAGAAC 59.427 45.833 0.00 0.0 0.00 3.01
1812 3358 5.006386 AGTTTTTCCTGATGACCAAGCTAG 58.994 41.667 0.00 0.0 0.00 3.42
1969 3515 1.338105 CGCCCTGATGTTTGAGAGACA 60.338 52.381 0.00 0.0 0.00 3.41
2104 3650 0.754217 CAGGCAAGCCAGCACCATAT 60.754 55.000 14.40 0.0 38.92 1.78


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

AutoCloner maintained by Alex Coulton.