Multiple sequence alignment - TraesCS1D01G235400

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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 TraesCS1D01G235400 chr1D 100.000 2357 0 0 1 2357 324623965 324621609 0.000000e+00 4353.0
1 TraesCS1D01G235400 chr1D 93.814 97 5 1 2123 2219 412087681 412087586 6.790000e-31 145.0
2 TraesCS1D01G235400 chr1D 91.525 59 5 0 649 707 324623261 324623203 5.400000e-12 82.4
3 TraesCS1D01G235400 chr1D 91.525 59 5 0 705 763 324623317 324623259 5.400000e-12 82.4
4 TraesCS1D01G235400 chr1A 96.425 1790 43 6 253 2039 420381401 420383172 0.000000e+00 2931.0
5 TraesCS1D01G235400 chr1A 96.935 261 4 2 1 257 420380837 420381097 3.600000e-118 435.0
6 TraesCS1D01G235400 chr1A 93.382 136 9 0 2212 2347 420383248 420383383 3.970000e-48 202.0
7 TraesCS1D01G235400 chr1A 87.755 147 12 6 2186 2331 420383397 420383538 1.450000e-37 167.0
8 TraesCS1D01G235400 chr1A 92.661 109 6 2 2108 2216 508639830 508639724 3.140000e-34 156.0
9 TraesCS1D01G235400 chr1A 92.857 56 4 0 649 704 420381849 420381904 5.400000e-12 82.4
10 TraesCS1D01G235400 chr1A 96.000 50 1 1 705 754 420381793 420381841 1.940000e-11 80.5
11 TraesCS1D01G235400 chr1B 95.875 1818 53 11 1 1810 436931356 436929553 0.000000e+00 2922.0
12 TraesCS1D01G235400 chr1B 86.235 247 21 7 2068 2311 436929134 436928898 3.010000e-64 255.0
13 TraesCS1D01G235400 chr1B 87.336 229 11 2 1808 2036 436929345 436929135 1.810000e-61 246.0
14 TraesCS1D01G235400 chr1B 94.949 99 3 2 2123 2219 555636690 555636592 1.130000e-33 154.0
15 TraesCS1D01G235400 chr1B 95.161 62 3 0 2250 2311 436928616 436928555 5.360000e-17 99.0
16 TraesCS1D01G235400 chr1B 95.082 61 3 0 2251 2311 436928740 436928680 1.930000e-16 97.1
17 TraesCS1D01G235400 chr1B 96.000 50 1 1 705 754 436930701 436930653 1.940000e-11 80.5
18 TraesCS1D01G235400 chr1B 87.324 71 5 1 641 707 436930657 436930587 6.980000e-11 78.7
19 TraesCS1D01G235400 chr5D 81.818 858 115 24 936 1784 233488887 233489712 0.000000e+00 682.0
20 TraesCS1D01G235400 chr5B 81.437 835 116 21 939 1763 271576685 271575880 0.000000e+00 647.0
21 TraesCS1D01G235400 chr5A 84.102 629 85 11 943 1565 321713135 321713754 5.610000e-166 593.0
22 TraesCS1D01G235400 chr3D 80.734 218 32 4 481 690 600167332 600167547 6.740000e-36 161.0
23 TraesCS1D01G235400 chr3D 77.778 108 20 3 1200 1306 323246319 323246423 1.960000e-06 63.9
24 TraesCS1D01G235400 chr3B 93.458 107 4 3 2123 2229 800696273 800696170 3.140000e-34 156.0
25 TraesCS1D01G235400 chr2B 93.878 98 4 2 2123 2218 183651617 183651714 1.890000e-31 147.0
26 TraesCS1D01G235400 chr2B 88.696 115 8 5 2118 2229 766524111 766524223 4.090000e-28 135.0
27 TraesCS1D01G235400 chr4B 91.589 107 6 3 2123 2229 664319819 664319922 6.790000e-31 145.0
28 TraesCS1D01G235400 chr2D 89.815 108 9 2 2118 2225 624319511 624319406 1.140000e-28 137.0


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 TraesCS1D01G235400 chr1D 324621609 324623965 2356 True 1505.933333 4353 94.350000 1 2357 3 chr1D.!!$R2 2356
1 TraesCS1D01G235400 chr1A 420380837 420383538 2701 False 649.650000 2931 93.892333 1 2347 6 chr1A.!!$F1 2346
2 TraesCS1D01G235400 chr1B 436928555 436931356 2801 True 539.757143 2922 91.859000 1 2311 7 chr1B.!!$R2 2310
3 TraesCS1D01G235400 chr5D 233488887 233489712 825 False 682.000000 682 81.818000 936 1784 1 chr5D.!!$F1 848
4 TraesCS1D01G235400 chr5B 271575880 271576685 805 True 647.000000 647 81.437000 939 1763 1 chr5B.!!$R1 824
5 TraesCS1D01G235400 chr5A 321713135 321713754 619 False 593.000000 593 84.102000 943 1565 1 chr5A.!!$F1 622

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
753 1071 1.661509 GCTGCTCGTTTTGTTGCCC 60.662 57.895 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2061 2614 0.60478 ATAGACAGGATGCATGCCGC 60.605 55.0 16.68 6.8 42.53 6.53 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
233 242 8.470040 TTTTTCATTGCAGCTCTAATTTGATC 57.530 30.769 0.00 0.00 0.00 2.92
290 607 2.238646 CCATCTGGTAACTGGCACCTAA 59.761 50.000 0.00 0.00 36.96 2.69
291 608 3.308117 CCATCTGGTAACTGGCACCTAAA 60.308 47.826 0.00 0.00 36.96 1.85
328 646 5.605564 TGTGTCTAACATGTTACATGTGC 57.394 39.130 28.49 19.04 32.36 4.57
423 741 3.561725 CCATTCCAGCTATTTTCCGAGTC 59.438 47.826 0.00 0.00 0.00 3.36
699 1017 2.158608 AGCTGCTAGTTTTGTTCCCAGT 60.159 45.455 0.00 0.00 0.00 4.00
753 1071 1.661509 GCTGCTCGTTTTGTTGCCC 60.662 57.895 0.00 0.00 0.00 5.36
905 1224 7.176340 AGTGGACAGATAATTAGGGTACGATAC 59.824 40.741 0.00 0.00 0.00 2.24
988 1308 4.219288 AGGAAACAATCTGAATCAAGGCAC 59.781 41.667 0.00 0.00 0.00 5.01
1284 1608 2.548920 GCAAGTCACTGTAAGGAGTGCT 60.549 50.000 0.00 0.00 42.74 4.40
1381 1706 3.865446 TCTATGTCATGACTTGGTGCAG 58.135 45.455 25.55 13.30 0.00 4.41
1382 1707 1.171308 ATGTCATGACTTGGTGCAGC 58.829 50.000 25.55 9.47 0.00 5.25
1528 1870 2.494059 GGCAAAAGTACACTCTGCTCA 58.506 47.619 13.19 0.00 33.49 4.26
1792 2137 3.132646 TGCTGTTTTGCCACAAGAGAATT 59.867 39.130 0.00 0.00 0.00 2.17
1793 2138 4.122046 GCTGTTTTGCCACAAGAGAATTT 58.878 39.130 0.00 0.00 0.00 1.82
1822 2375 7.502120 AAATGCGATGTAGAGAATAAAGCAT 57.498 32.000 0.00 0.00 43.49 3.79
2013 2566 7.878477 TTTAGTTCGACGTTTCTGTATCAAT 57.122 32.000 0.00 0.00 0.00 2.57
2025 2578 7.426456 CGTTTCTGTATCAATATGAACTGTTGC 59.574 37.037 0.00 0.00 0.00 4.17
2049 2602 7.858052 CGAAGCAACTTCATTTGTCTAAATT 57.142 32.000 7.99 0.00 40.17 1.82
2050 2603 8.285776 CGAAGCAACTTCATTTGTCTAAATTT 57.714 30.769 7.99 0.00 40.17 1.82
2051 2604 9.393249 CGAAGCAACTTCATTTGTCTAAATTTA 57.607 29.630 7.99 0.00 40.17 1.40
2062 2615 9.282247 CATTTGTCTAAATTTATCTGTCAGTGC 57.718 33.333 0.00 0.00 34.34 4.40
2063 2616 6.647212 TGTCTAAATTTATCTGTCAGTGCG 57.353 37.500 0.00 0.00 0.00 5.34
2064 2617 5.580691 TGTCTAAATTTATCTGTCAGTGCGG 59.419 40.000 0.00 0.00 0.00 5.69
2065 2618 3.764885 AAATTTATCTGTCAGTGCGGC 57.235 42.857 0.00 0.00 0.00 6.53
2066 2619 2.401583 ATTTATCTGTCAGTGCGGCA 57.598 45.000 0.00 0.00 0.00 5.69
2083 2636 2.031420 CGGCATGCATCCTGTCTATTTG 60.031 50.000 21.36 0.00 0.00 2.32
2096 2649 8.877864 TCCTGTCTATTTGTTTGGTATTCATT 57.122 30.769 0.00 0.00 0.00 2.57
2111 2664 7.192913 TGGTATTCATTATTTGCACGATGTTC 58.807 34.615 0.00 0.00 0.00 3.18
2198 2751 2.851071 CGAGCCCTCCTTCTAGCGG 61.851 68.421 0.00 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
233 242 7.270047 TCCCTTAATCTGGACTATAACAAACG 58.730 38.462 0.00 0.00 0.00 3.60
328 646 7.107542 ACTTCTAGAGTTCTAGTACAGGACTG 58.892 42.308 14.15 0.00 43.78 3.51
423 741 1.072965 ACTCCTGGAGCCAACAAAGAG 59.927 52.381 23.43 0.00 32.04 2.85
471 789 4.946784 ATGTTCAACGAGGATACAAAGC 57.053 40.909 0.00 0.00 41.41 3.51
474 792 6.045072 ACCTTATGTTCAACGAGGATACAA 57.955 37.500 10.47 0.00 41.41 2.41
522 840 3.003378 GCACTAAACCAAGGTCACAAGTC 59.997 47.826 0.00 0.00 0.00 3.01
699 1017 5.728471 TCAGGATTCTTGCAAACAAACAAA 58.272 33.333 0.00 0.00 34.74 2.83
753 1071 3.545703 AGAAGTCCTCACCACACAAAAG 58.454 45.455 0.00 0.00 0.00 2.27
988 1308 0.806102 AAAGACATCACGCCGATCCG 60.806 55.000 0.00 0.00 29.21 4.18
1284 1608 2.552315 GTTCCTTCGCCATTTCTCAACA 59.448 45.455 0.00 0.00 0.00 3.33
1381 1706 5.861787 ACTTTTATTTTCAGTATTGGTGCGC 59.138 36.000 0.00 0.00 0.00 6.09
1382 1707 6.861055 ACACTTTTATTTTCAGTATTGGTGCG 59.139 34.615 0.00 0.00 0.00 5.34
1800 2145 7.502120 AAATGCTTTATTCTCTACATCGCAT 57.498 32.000 0.00 0.00 37.19 4.73
1822 2375 1.142060 TGAGGGGAAAGCTCGTGAAAA 59.858 47.619 0.00 0.00 0.00 2.29
1997 2550 8.186178 ACAGTTCATATTGATACAGAAACGTC 57.814 34.615 0.00 0.00 0.00 4.34
2025 2578 7.858052 AATTTAGACAAATGAAGTTGCTTCG 57.142 32.000 4.69 0.00 42.78 3.79
2039 2592 6.092122 CCGCACTGACAGATAAATTTAGACAA 59.908 38.462 10.08 0.00 0.00 3.18
2041 2594 5.502544 GCCGCACTGACAGATAAATTTAGAC 60.503 44.000 10.08 1.17 0.00 2.59
2042 2595 4.570772 GCCGCACTGACAGATAAATTTAGA 59.429 41.667 10.08 0.00 0.00 2.10
2043 2596 4.332543 TGCCGCACTGACAGATAAATTTAG 59.667 41.667 10.08 0.00 0.00 1.85
2044 2597 4.257731 TGCCGCACTGACAGATAAATTTA 58.742 39.130 10.08 0.00 0.00 1.40
2045 2598 3.081061 TGCCGCACTGACAGATAAATTT 58.919 40.909 10.08 0.00 0.00 1.82
2046 2599 2.710377 TGCCGCACTGACAGATAAATT 58.290 42.857 10.08 0.00 0.00 1.82
2047 2600 2.401583 TGCCGCACTGACAGATAAAT 57.598 45.000 10.08 0.00 0.00 1.40
2048 2601 2.009051 CATGCCGCACTGACAGATAAA 58.991 47.619 10.08 0.00 0.00 1.40
2049 2602 1.655484 CATGCCGCACTGACAGATAA 58.345 50.000 10.08 0.00 0.00 1.75
2050 2603 0.811219 GCATGCCGCACTGACAGATA 60.811 55.000 10.08 0.00 41.79 1.98
2051 2604 2.110967 GCATGCCGCACTGACAGAT 61.111 57.895 10.08 0.00 41.79 2.90
2052 2605 2.743538 GCATGCCGCACTGACAGA 60.744 61.111 10.08 0.00 41.79 3.41
2061 2614 0.604780 ATAGACAGGATGCATGCCGC 60.605 55.000 16.68 6.80 42.53 6.53
2062 2615 1.888215 AATAGACAGGATGCATGCCG 58.112 50.000 16.68 7.30 42.53 5.69
2063 2616 2.954318 ACAAATAGACAGGATGCATGCC 59.046 45.455 16.68 10.55 42.53 4.40
2064 2617 4.644103 AACAAATAGACAGGATGCATGC 57.356 40.909 11.82 11.82 42.53 4.06
2065 2618 5.105635 ACCAAACAAATAGACAGGATGCATG 60.106 40.000 2.46 0.00 42.53 4.06
2066 2619 5.018809 ACCAAACAAATAGACAGGATGCAT 58.981 37.500 0.00 0.00 42.53 3.96
2083 2636 7.487829 ACATCGTGCAAATAATGAATACCAAAC 59.512 33.333 0.00 0.00 0.00 2.93
2096 2649 5.412904 TGTGGTAATGAACATCGTGCAAATA 59.587 36.000 0.00 0.00 0.00 1.40
2111 2664 5.998454 CTATTCCAGCTTCTGTGGTAATG 57.002 43.478 0.00 0.00 36.37 1.90
2247 2800 4.148891 GCAGAAACGAAAACGTAATGAGG 58.851 43.478 0.00 0.00 0.00 3.86
2263 2816 3.573538 AGTGGCAATGTGTAATGCAGAAA 59.426 39.130 0.00 0.00 44.32 2.52
2266 2819 2.871133 CAGTGGCAATGTGTAATGCAG 58.129 47.619 6.80 0.00 44.32 4.41
2333 3027 4.377738 GTGTAATGGAAAAGCGAAAACGTC 59.622 41.667 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.