Multiple sequence alignment - TraesCS5D01G135700

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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 TraesCS5D01G135700 chr5D 100.000 2558 0 0 1 2558 216153127 216155684 0.000000e+00 4724.0
1 TraesCS5D01G135700 chr5B 96.444 1631 33 3 953 2558 232293778 232295408 0.000000e+00 2667.0
2 TraesCS5D01G135700 chr5B 95.906 171 6 1 752 921 232293621 232293791 2.510000e-70 276.0
3 TraesCS5D01G135700 chr5A 94.465 1644 41 10 951 2558 285395666 285397295 0.000000e+00 2486.0
4 TraesCS5D01G135700 chr5A 92.903 155 10 1 767 921 285395528 285395681 9.210000e-55 224.0
5 TraesCS5D01G135700 chr3D 92.162 740 51 5 1 737 170548741 170549476 0.000000e+00 1038.0
6 TraesCS5D01G135700 chr3D 90.934 739 65 2 1 737 520675786 520675048 0.000000e+00 992.0
7 TraesCS5D01G135700 chr3D 90.798 739 64 4 1 736 601219747 601220484 0.000000e+00 985.0
8 TraesCS5D01G135700 chr7B 90.353 736 66 5 1 733 244746228 244746961 0.000000e+00 961.0
9 TraesCS5D01G135700 chr2B 89.851 739 71 4 1 737 662915449 662916185 0.000000e+00 946.0
10 TraesCS5D01G135700 chr2B 90.698 43 3 1 2083 2125 131182289 131182248 3.560000e-04 56.5
11 TraesCS5D01G135700 chr6A 89.160 738 76 4 3 737 587747169 587746433 0.000000e+00 917.0
12 TraesCS5D01G135700 chr6A 81.976 921 67 34 956 1815 22684469 22685351 0.000000e+00 689.0
13 TraesCS5D01G135700 chr7A 88.649 740 81 3 1 737 736282482 736283221 0.000000e+00 898.0
14 TraesCS5D01G135700 chr6D 88.331 737 82 4 1 735 437408854 437408120 0.000000e+00 881.0
15 TraesCS5D01G135700 chr6D 82.568 958 86 32 951 1852 24219545 24220477 0.000000e+00 769.0
16 TraesCS5D01G135700 chr4A 88.243 740 84 3 1 737 541034631 541035370 0.000000e+00 881.0
17 TraesCS5D01G135700 chr1B 91.379 58 5 0 2057 2114 523233977 523233920 2.110000e-11 80.5


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 TraesCS5D01G135700 chr5D 216153127 216155684 2557 False 4724.0 4724 100.000 1 2558 1 chr5D.!!$F1 2557
1 TraesCS5D01G135700 chr5B 232293621 232295408 1787 False 1471.5 2667 96.175 752 2558 2 chr5B.!!$F1 1806
2 TraesCS5D01G135700 chr5A 285395528 285397295 1767 False 1355.0 2486 93.684 767 2558 2 chr5A.!!$F1 1791
3 TraesCS5D01G135700 chr3D 170548741 170549476 735 False 1038.0 1038 92.162 1 737 1 chr3D.!!$F1 736
4 TraesCS5D01G135700 chr3D 520675048 520675786 738 True 992.0 992 90.934 1 737 1 chr3D.!!$R1 736
5 TraesCS5D01G135700 chr3D 601219747 601220484 737 False 985.0 985 90.798 1 736 1 chr3D.!!$F2 735
6 TraesCS5D01G135700 chr7B 244746228 244746961 733 False 961.0 961 90.353 1 733 1 chr7B.!!$F1 732
7 TraesCS5D01G135700 chr2B 662915449 662916185 736 False 946.0 946 89.851 1 737 1 chr2B.!!$F1 736
8 TraesCS5D01G135700 chr6A 587746433 587747169 736 True 917.0 917 89.160 3 737 1 chr6A.!!$R1 734
9 TraesCS5D01G135700 chr6A 22684469 22685351 882 False 689.0 689 81.976 956 1815 1 chr6A.!!$F1 859
10 TraesCS5D01G135700 chr7A 736282482 736283221 739 False 898.0 898 88.649 1 737 1 chr7A.!!$F1 736
11 TraesCS5D01G135700 chr6D 437408120 437408854 734 True 881.0 881 88.331 1 735 1 chr6D.!!$R1 734
12 TraesCS5D01G135700 chr6D 24219545 24220477 932 False 769.0 769 82.568 951 1852 1 chr6D.!!$F1 901
13 TraesCS5D01G135700 chr4A 541034631 541035370 739 False 881.0 881 88.243 1 737 1 chr4A.!!$F1 736

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
738 746 0.462937 CCTTGGGTGTGTGTGTCGAA 60.463 55.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 2301 2.192608 CTGCGAGGCCTTTTGCTCAC 62.193 60.0 21.51 0.93 40.92 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
37 38 2.451294 GGGCTGGAGGGATGGGAT 60.451 66.667 0.00 0.0 0.00 3.85
110 111 3.382832 CGTCTGCTCCCCGTCCTT 61.383 66.667 0.00 0.0 0.00 3.36
113 114 4.148825 CTGCTCCCCGTCCTTCCG 62.149 72.222 0.00 0.0 0.00 4.30
145 147 4.982701 GTGTGGGCTGGCAGGCTT 62.983 66.667 35.56 0.0 41.09 4.35
181 183 1.878522 GGACGTATGCTGCGGTCTG 60.879 63.158 11.01 0.0 0.00 3.51
284 286 4.351938 CGGGAGGCACGACGTTCA 62.352 66.667 0.00 0.0 0.00 3.18
347 353 2.527123 TTGGGTGGGTGGTCGCTA 60.527 61.111 0.00 0.0 0.00 4.26
456 464 0.464452 CGTGGACACCCTATCCTTCC 59.536 60.000 0.00 0.0 37.13 3.46
563 571 1.356738 TGGTCGTTCCCTTCTAGGAGA 59.643 52.381 0.00 0.0 37.67 3.71
610 618 2.833631 TTTTTCGTCTCACCTCTCCC 57.166 50.000 0.00 0.0 0.00 4.30
629 637 3.215671 CGGAGGATTGGAGGTCTCT 57.784 57.895 0.00 0.0 0.00 3.10
655 663 1.411977 CTCCAAGCAGATCATCCTCGT 59.588 52.381 0.00 0.0 0.00 4.18
688 696 0.682852 CTTGGTAGTCGTTGGGGTGA 59.317 55.000 0.00 0.0 0.00 4.02
694 702 1.072505 GTCGTTGGGGTGATGTGGT 59.927 57.895 0.00 0.0 0.00 4.16
696 704 1.072332 CGTTGGGGTGATGTGGTGA 59.928 57.895 0.00 0.0 0.00 4.02
737 745 1.145156 CCTTGGGTGTGTGTGTCGA 59.855 57.895 0.00 0.0 0.00 4.20
738 746 0.462937 CCTTGGGTGTGTGTGTCGAA 60.463 55.000 0.00 0.0 0.00 3.71
739 747 1.374560 CTTGGGTGTGTGTGTCGAAA 58.625 50.000 0.00 0.0 0.00 3.46
740 748 1.330521 CTTGGGTGTGTGTGTCGAAAG 59.669 52.381 0.00 0.0 0.00 2.62
741 749 1.092921 TGGGTGTGTGTGTCGAAAGC 61.093 55.000 0.00 0.0 0.00 3.51
742 750 1.647084 GGTGTGTGTGTCGAAAGCC 59.353 57.895 0.00 0.0 0.00 4.35
743 751 0.814010 GGTGTGTGTGTCGAAAGCCT 60.814 55.000 0.00 0.0 0.00 4.58
744 752 1.014352 GTGTGTGTGTCGAAAGCCTT 58.986 50.000 0.00 0.0 0.00 4.35
745 753 1.400494 GTGTGTGTGTCGAAAGCCTTT 59.600 47.619 0.00 0.0 0.00 3.11
746 754 2.088423 TGTGTGTGTCGAAAGCCTTTT 58.912 42.857 0.00 0.0 0.00 2.27
747 755 2.490115 TGTGTGTGTCGAAAGCCTTTTT 59.510 40.909 0.00 0.0 0.00 1.94
795 804 4.593634 ACTTCACTTCACTTAAGGTAGGCT 59.406 41.667 7.53 0.0 39.73 4.58
921 930 6.881602 GGACATTCTCTACCATCACTTCTTTT 59.118 38.462 0.00 0.0 0.00 2.27
922 931 7.065204 GGACATTCTCTACCATCACTTCTTTTC 59.935 40.741 0.00 0.0 0.00 2.29
923 932 7.684529 ACATTCTCTACCATCACTTCTTTTCT 58.315 34.615 0.00 0.0 0.00 2.52
924 933 8.160106 ACATTCTCTACCATCACTTCTTTTCTT 58.840 33.333 0.00 0.0 0.00 2.52
925 934 9.007901 CATTCTCTACCATCACTTCTTTTCTTT 57.992 33.333 0.00 0.0 0.00 2.52
926 935 8.980481 TTCTCTACCATCACTTCTTTTCTTTT 57.020 30.769 0.00 0.0 0.00 2.27
927 936 8.980481 TCTCTACCATCACTTCTTTTCTTTTT 57.020 30.769 0.00 0.0 0.00 1.94
959 968 2.830186 TTTGCGGGGGCTACCATCAC 62.830 60.000 0.60 0.0 42.91 3.06
1275 1321 1.268539 CGCAGAAACAACACCTCAACC 60.269 52.381 0.00 0.0 0.00 3.77
1379 1431 0.036010 CCGTCATGAGGGTGAAGCTT 60.036 55.000 23.58 0.0 0.00 3.74
1891 1981 1.009829 GTCAGTAATGCCAAGCCTCG 58.990 55.000 0.00 0.0 0.00 4.63
2160 2250 6.060136 CCACCTCATCATTTATCTCACATGT 58.940 40.000 0.00 0.0 0.00 3.21
2170 2260 8.708378 TCATTTATCTCACATGTCACTTCCTAT 58.292 33.333 0.00 0.0 0.00 2.57
2211 2301 5.163581 CCCTTTGGCTCTCAGTTGATTTATG 60.164 44.000 0.00 0.0 0.00 1.90
2224 2314 4.454728 TGATTTATGTGAGCAAAAGGCC 57.545 40.909 0.00 0.0 46.50 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.414956 TCCAGCCCGTCTCCCCAT 62.415 66.667 0.00 0.00 0.00 4.00
20 21 2.451294 ATCCCATCCCTCCAGCCC 60.451 66.667 0.00 0.00 0.00 5.19
37 38 4.680237 CCCGAGCTCGTTGGTGCA 62.680 66.667 32.41 0.00 37.74 4.57
87 88 3.785859 GGGGAGCAGACGCATCCA 61.786 66.667 0.00 0.00 42.27 3.41
125 126 4.584518 CCTGCCAGCCCACACACA 62.585 66.667 0.00 0.00 0.00 3.72
138 139 3.595108 GAACAACGCCGAAGCCTGC 62.595 63.158 0.00 0.00 34.57 4.85
330 333 2.527123 TAGCGACCACCCACCCAA 60.527 61.111 0.00 0.00 0.00 4.12
347 353 1.192146 TCCTAGCTTCGCCAACCACT 61.192 55.000 0.00 0.00 0.00 4.00
358 364 1.736586 CTCCGACGCATCCTAGCTT 59.263 57.895 0.00 0.00 0.00 3.74
456 464 3.121030 CCGCAACCGAGCCTTCAG 61.121 66.667 0.00 0.00 36.29 3.02
479 487 2.099263 TCGGAGCAATTCGAAGGAGTAG 59.901 50.000 3.35 0.00 32.11 2.57
563 571 2.057922 ACAAGGACTCCAAGATGGTGT 58.942 47.619 3.91 3.91 45.87 4.16
610 618 0.397816 AGAGACCTCCAATCCTCCGG 60.398 60.000 0.00 0.00 0.00 5.14
629 637 0.401356 TGATCTGCTTGGAGCCAACA 59.599 50.000 0.00 1.77 41.51 3.33
655 663 0.110295 ACCAAGCCACTACACATGCA 59.890 50.000 0.00 0.00 0.00 3.96
688 696 1.746615 GTGCCGAGCATCACCACAT 60.747 57.895 1.90 0.00 41.91 3.21
694 702 1.549243 TACAAGGGTGCCGAGCATCA 61.549 55.000 10.63 0.00 42.13 3.07
696 704 0.179045 GATACAAGGGTGCCGAGCAT 60.179 55.000 1.90 0.00 41.91 3.79
744 752 4.882427 TCCTCCGTACAACAACATCAAAAA 59.118 37.500 0.00 0.00 0.00 1.94
745 753 4.452825 TCCTCCGTACAACAACATCAAAA 58.547 39.130 0.00 0.00 0.00 2.44
746 754 4.062293 CTCCTCCGTACAACAACATCAAA 58.938 43.478 0.00 0.00 0.00 2.69
747 755 3.556213 CCTCCTCCGTACAACAACATCAA 60.556 47.826 0.00 0.00 0.00 2.57
748 756 2.028476 CCTCCTCCGTACAACAACATCA 60.028 50.000 0.00 0.00 0.00 3.07
749 757 2.618053 CCTCCTCCGTACAACAACATC 58.382 52.381 0.00 0.00 0.00 3.06
750 758 1.338769 GCCTCCTCCGTACAACAACAT 60.339 52.381 0.00 0.00 0.00 2.71
762 770 1.072331 TGAAGTGAAGTTGCCTCCTCC 59.928 52.381 0.00 0.00 0.00 4.30
795 804 0.985760 TAAAGCGGCCTTGGACCTTA 59.014 50.000 0.00 0.00 0.00 2.69
837 846 8.018677 TCTCTACTTACTTTCATTTTTGCGAG 57.981 34.615 0.00 0.00 0.00 5.03
938 947 0.968393 GATGGTAGCCCCCGCAAAAA 60.968 55.000 0.00 0.00 37.52 1.94
939 948 1.379309 GATGGTAGCCCCCGCAAAA 60.379 57.895 0.00 0.00 37.52 2.44
940 949 2.274104 GATGGTAGCCCCCGCAAA 59.726 61.111 0.00 0.00 37.52 3.68
941 950 3.012119 TGATGGTAGCCCCCGCAA 61.012 61.111 0.00 0.00 37.52 4.85
942 951 3.792736 GTGATGGTAGCCCCCGCA 61.793 66.667 0.00 0.00 37.52 5.69
943 952 2.942648 GAAGTGATGGTAGCCCCCGC 62.943 65.000 0.00 0.00 0.00 6.13
944 953 1.146263 GAAGTGATGGTAGCCCCCG 59.854 63.158 0.00 0.00 0.00 5.73
945 954 0.919710 AAGAAGTGATGGTAGCCCCC 59.080 55.000 0.00 0.00 0.00 5.40
946 955 2.808906 AAAGAAGTGATGGTAGCCCC 57.191 50.000 0.00 0.00 0.00 5.80
947 956 7.280356 TCTATTTAAAGAAGTGATGGTAGCCC 58.720 38.462 0.00 0.00 0.00 5.19
948 957 7.041712 GCTCTATTTAAAGAAGTGATGGTAGCC 60.042 40.741 0.00 0.00 0.00 3.93
949 958 7.495934 TGCTCTATTTAAAGAAGTGATGGTAGC 59.504 37.037 0.00 0.00 0.00 3.58
959 968 6.314896 CCAGTGGAGTGCTCTATTTAAAGAAG 59.685 42.308 1.68 0.00 0.00 2.85
1262 1308 0.463116 GGACGTGGTTGAGGTGTTGT 60.463 55.000 0.00 0.00 0.00 3.32
1379 1431 0.675837 GCTCCTGCTTGCTGATGACA 60.676 55.000 1.05 0.00 36.03 3.58
2076 2166 6.560003 TTAAGGGATGATCTCTTAGCAACA 57.440 37.500 13.94 0.00 40.26 3.33
2160 2250 4.283337 TCCCGTGTTATCATAGGAAGTGA 58.717 43.478 0.00 0.00 0.00 3.41
2211 2301 2.192608 CTGCGAGGCCTTTTGCTCAC 62.193 60.000 21.51 0.93 40.92 3.51
2224 2314 5.847715 CAGTATGTTTGAAACTACTGCGAG 58.152 41.667 22.33 9.50 36.87 5.03


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

AutoCloner maintained by Alex Coulton.