Multiple sequence alignment - TraesCS7D01G298600

Loading Multiple Alignment...

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 TraesCS7D01G298600 chr7D 100.000 8462 0 0 1 8462 378176772 378168311 0.000000e+00 15627.0
1 TraesCS7D01G298600 chr7D 99.419 688 3 1 7776 8462 394360760 394360073 0.000000e+00 1247.0
2 TraesCS7D01G298600 chr7D 85.572 201 29 0 3529 3729 378160019 378159819 2.390000e-50 211.0
3 TraesCS7D01G298600 chr7D 84.314 102 9 4 1801 1896 25322312 25322412 9.040000e-15 93.5
4 TraesCS7D01G298600 chr7B 98.025 5924 93 13 1861 7776 372833704 372827797 0.000000e+00 10270.0
5 TraesCS7D01G298600 chr7B 96.700 1212 26 5 642 1841 372834982 372833773 0.000000e+00 2004.0
6 TraesCS7D01G298600 chr7B 93.906 640 25 3 1 640 372835738 372835113 0.000000e+00 953.0
7 TraesCS7D01G298600 chr7B 85.572 201 29 0 3529 3729 372823892 372823692 2.390000e-50 211.0
8 TraesCS7D01G298600 chr7B 96.226 53 2 0 7724 7776 607618021 607617969 4.210000e-13 87.9
9 TraesCS7D01G298600 chr7B 96.078 51 1 1 7726 7776 162834745 162834696 1.960000e-11 82.4
10 TraesCS7D01G298600 chr7A 95.523 4177 110 28 1 4156 425793800 425789680 0.000000e+00 6606.0
11 TraesCS7D01G298600 chr7A 98.212 3299 45 9 4485 7776 425786540 425783249 0.000000e+00 5753.0
12 TraesCS7D01G298600 chr7A 97.523 323 7 1 4155 4477 425789495 425789174 1.240000e-152 551.0
13 TraesCS7D01G298600 chr7A 83.550 231 36 2 3500 3729 425777748 425777519 1.850000e-51 215.0
14 TraesCS7D01G298600 chr7A 84.536 97 13 2 1802 1897 513221043 513221138 2.510000e-15 95.3
15 TraesCS7D01G298600 chr7A 95.000 40 2 0 4040 4079 116122595 116122556 7.090000e-06 63.9
16 TraesCS7D01G298600 chr4D 99.854 686 1 0 7777 8462 208388684 208389369 0.000000e+00 1262.0
17 TraesCS7D01G298600 chr4D 99.127 687 6 0 7776 8462 339054790 339055476 0.000000e+00 1236.0
18 TraesCS7D01G298600 chr4D 99.125 686 6 0 7777 8462 179855826 179855141 0.000000e+00 1234.0
19 TraesCS7D01G298600 chr4D 87.879 99 8 2 1802 1896 358476838 358476936 6.940000e-21 113.0
20 TraesCS7D01G298600 chr4D 87.629 97 10 2 1801 1895 500440032 500440128 2.500000e-20 111.0
21 TraesCS7D01G298600 chr4D 94.444 36 2 0 4089 4124 261053113 261053148 1.000000e-03 56.5
22 TraesCS7D01G298600 chr4D 94.444 36 2 0 4089 4124 261075540 261075575 1.000000e-03 56.5
23 TraesCS7D01G298600 chr3D 99.708 686 2 0 7777 8462 231145067 231145752 0.000000e+00 1256.0
24 TraesCS7D01G298600 chr3D 99.417 686 4 0 7777 8462 239605529 239606214 0.000000e+00 1245.0
25 TraesCS7D01G298600 chr1D 99.271 686 5 0 7777 8462 479727575 479726890 0.000000e+00 1240.0
26 TraesCS7D01G298600 chr1D 84.211 95 13 2 1802 1895 337898603 337898696 3.250000e-14 91.6
27 TraesCS7D01G298600 chr1D 98.039 51 1 0 7726 7776 419720470 419720520 1.170000e-13 89.8
28 TraesCS7D01G298600 chr1D 94.444 36 2 0 4089 4124 319565753 319565718 1.000000e-03 56.5
29 TraesCS7D01G298600 chr5D 99.127 687 6 0 7776 8462 397830381 397831067 0.000000e+00 1236.0
30 TraesCS7D01G298600 chr5D 99.125 686 6 0 7777 8462 95875149 95874464 0.000000e+00 1234.0
31 TraesCS7D01G298600 chr5D 100.000 28 0 0 4088 4115 41760720 41760747 1.500000e-02 52.8
32 TraesCS7D01G298600 chrUn 100.000 387 0 0 6268 6654 480515477 480515863 0.000000e+00 715.0
33 TraesCS7D01G298600 chrUn 98.148 54 0 1 7724 7776 10263770 10263823 9.040000e-15 93.5
34 TraesCS7D01G298600 chr1B 85.263 95 12 2 1802 1895 452754369 452754462 6.990000e-16 97.1
35 TraesCS7D01G298600 chr1B 95.000 40 1 1 4037 4076 583952436 583952474 2.550000e-05 62.1
36 TraesCS7D01G298600 chr1B 94.595 37 0 1 4035 4069 188263437 188263473 1.000000e-03 56.5
37 TraesCS7D01G298600 chr6D 84.536 97 12 2 1802 1895 327364451 327364355 9.040000e-15 93.5
38 TraesCS7D01G298600 chr2B 83.168 101 14 3 1801 1899 146666637 146666538 1.170000e-13 89.8
39 TraesCS7D01G298600 chr2B 94.340 53 3 0 7724 7776 416184071 416184019 1.960000e-11 82.4
40 TraesCS7D01G298600 chr4A 94.643 56 2 1 7723 7777 627968547 627968602 1.510000e-12 86.1
41 TraesCS7D01G298600 chr4A 82.051 78 4 4 4040 4117 621122373 621122306 3.300000e-04 58.4
42 TraesCS7D01G298600 chr4B 94.444 54 2 1 7724 7776 645330103 645330156 1.960000e-11 82.4
43 TraesCS7D01G298600 chr4B 90.698 43 3 1 4037 4078 666667009 666666967 1.000000e-03 56.5
44 TraesCS7D01G298600 chr4B 90.698 43 3 1 4037 4078 666703624 666703582 1.000000e-03 56.5
45 TraesCS7D01G298600 chr3A 94.444 36 2 0 4089 4124 6681294 6681329 1.000000e-03 56.5
46 TraesCS7D01G298600 chr2A 94.444 36 2 0 4089 4124 683927999 683927964 1.000000e-03 56.5
47 TraesCS7D01G298600 chr5A 100.000 29 0 0 4087 4115 86874794 86874822 4.000000e-03 54.7


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 TraesCS7D01G298600 chr7D 378168311 378176772 8461 True 15627.000000 15627 100.00000 1 8462 1 chr7D.!!$R2 8461
1 TraesCS7D01G298600 chr7D 394360073 394360760 687 True 1247.000000 1247 99.41900 7776 8462 1 chr7D.!!$R3 686
2 TraesCS7D01G298600 chr7B 372823692 372835738 12046 True 3359.500000 10270 93.55075 1 7776 4 chr7B.!!$R3 7775
3 TraesCS7D01G298600 chr7A 425783249 425793800 10551 True 4303.333333 6606 97.08600 1 7776 3 chr7A.!!$R3 7775
4 TraesCS7D01G298600 chr4D 208388684 208389369 685 False 1262.000000 1262 99.85400 7777 8462 1 chr4D.!!$F1 685
5 TraesCS7D01G298600 chr4D 339054790 339055476 686 False 1236.000000 1236 99.12700 7776 8462 1 chr4D.!!$F4 686
6 TraesCS7D01G298600 chr4D 179855141 179855826 685 True 1234.000000 1234 99.12500 7777 8462 1 chr4D.!!$R1 685
7 TraesCS7D01G298600 chr3D 231145067 231145752 685 False 1256.000000 1256 99.70800 7777 8462 1 chr3D.!!$F1 685
8 TraesCS7D01G298600 chr3D 239605529 239606214 685 False 1245.000000 1245 99.41700 7777 8462 1 chr3D.!!$F2 685
9 TraesCS7D01G298600 chr1D 479726890 479727575 685 True 1240.000000 1240 99.27100 7777 8462 1 chr1D.!!$R2 685
10 TraesCS7D01G298600 chr5D 397830381 397831067 686 False 1236.000000 1236 99.12700 7776 8462 1 chr5D.!!$F2 686
11 TraesCS7D01G298600 chr5D 95874464 95875149 685 True 1234.000000 1234 99.12500 7777 8462 1 chr5D.!!$R1 685

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
246 247 0.034059 ACGCTCCTTCTTGGACACAG 59.966 55.000 0.00 0.00 40.56 3.66 F
386 387 2.041081 CCCCAGTTATTCCAAGACACCA 59.959 50.000 0.00 0.00 0.00 4.17 F
2094 2291 1.208165 AAGAGGTTGGGGCCTTCGAT 61.208 55.000 0.84 0.00 39.34 3.59 F
2104 2301 1.207329 GGGCCTTCGATACAGACTTGT 59.793 52.381 0.84 0.00 41.39 3.16 F
2391 2589 2.917933 GCTATTGGAGCCACATACACA 58.082 47.619 0.00 0.00 46.41 3.72 F
3794 3993 2.941453 TTGACTGAAGGCTAGCTACG 57.059 50.000 15.72 1.82 0.00 3.51 F
4898 7911 2.079925 GGACACATCAAGAGTTGCTCC 58.920 52.381 0.00 0.00 0.00 4.70 F
5259 8276 0.108138 CTCCGGAGTTGTGCCCTTAG 60.108 60.000 24.04 0.00 0.00 2.18 F
5621 8638 1.263217 CGAATTTGGTATGGGCTACGC 59.737 52.381 0.00 0.00 0.00 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2070 2267 1.681229 AGGCCCCAACCTCTTGATTA 58.319 50.000 0.00 0.0 33.62 1.75 R
2104 2301 2.161855 GGTGATGATGTTTGCAGTGGA 58.838 47.619 0.00 0.0 0.00 4.02 R
3242 3440 1.002430 CTGCTTCCTACCAGAGCAACA 59.998 52.381 0.00 0.0 44.89 3.33 R
3268 3466 4.154918 GTGAAATAACTGTGCTCTTCCCAG 59.845 45.833 0.00 0.0 0.00 4.45 R
4351 4736 4.998979 GCATTCATTGCGCTTAGTTTAC 57.001 40.909 9.73 0.0 42.54 2.01 R
5061 8075 1.798223 TGCACTACTTAGCAAAGCACG 59.202 47.619 0.00 0.0 37.90 5.34 R
5967 8984 4.278170 AGCACAGCTGCAGTGTATTAAAAA 59.722 37.500 23.27 0.0 46.97 1.94 R
6900 9917 5.839063 CCATCTGAGGTTGTAGTCCCTTATA 59.161 44.000 0.00 0.0 0.00 0.98 R
7557 10574 8.338259 GCTATGTTATTACAATCTGTCAACTGG 58.662 37.037 0.00 0.0 37.91 4.00 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
39 40 4.201891 CCTTCTGGATTGCATCTCGAAAAG 60.202 45.833 0.00 0.00 34.57 2.27
50 51 2.341257 TCTCGAAAAGCTAGCTGCAAG 58.659 47.619 20.16 11.69 45.94 4.01
144 145 1.084370 ACGGCGCAGATGTTAGCTTC 61.084 55.000 16.26 0.00 0.00 3.86
196 197 9.896645 ACATGAGTTCTGATAACACATAGAATT 57.103 29.630 0.00 0.00 31.83 2.17
246 247 0.034059 ACGCTCCTTCTTGGACACAG 59.966 55.000 0.00 0.00 40.56 3.66
386 387 2.041081 CCCCAGTTATTCCAAGACACCA 59.959 50.000 0.00 0.00 0.00 4.17
387 388 3.499563 CCCCAGTTATTCCAAGACACCAA 60.500 47.826 0.00 0.00 0.00 3.67
519 520 6.238759 CCAGAAATATTAGTTAACTGGCAGCC 60.239 42.308 18.56 3.66 37.27 4.85
595 600 6.601332 ACATCTAAGTCAAGGTGAAGGAAAA 58.399 36.000 0.00 0.00 31.70 2.29
802 939 8.848474 AATATGCTAATGTATACCTTGACCAC 57.152 34.615 0.00 0.00 0.00 4.16
1825 1974 4.042187 ACTCCCTCCATTCCATATAAGTGC 59.958 45.833 0.00 0.00 0.00 4.40
1847 1996 5.044558 GCCGTGGTTTTAGTTCAAATTTGA 58.955 37.500 16.91 16.91 34.92 2.69
1848 1997 5.520649 GCCGTGGTTTTAGTTCAAATTTGAA 59.479 36.000 26.01 26.01 44.31 2.69
2067 2264 4.617995 CGGCTGGAATATCTGAGATCAGTC 60.618 50.000 9.56 0.62 44.12 3.51
2070 2267 5.011943 GCTGGAATATCTGAGATCAGTCCTT 59.988 44.000 15.70 6.19 44.12 3.36
2094 2291 1.208165 AAGAGGTTGGGGCCTTCGAT 61.208 55.000 0.84 0.00 39.34 3.59
2104 2301 1.207329 GGGCCTTCGATACAGACTTGT 59.793 52.381 0.84 0.00 41.39 3.16
2391 2589 2.917933 GCTATTGGAGCCACATACACA 58.082 47.619 0.00 0.00 46.41 3.72
2623 2821 3.733337 TCAAGACTGTCTTCTCCTTTGC 58.267 45.455 19.65 0.00 33.78 3.68
2679 2877 6.384224 CAGTGCACAGACAATCAATACAAAT 58.616 36.000 21.04 0.00 0.00 2.32
2892 3090 4.355543 GATTGCTTCAATCGCCTAAACA 57.644 40.909 4.09 0.00 40.33 2.83
2995 3193 5.869344 TCAATAGACTTGACTGATTTCACCG 59.131 40.000 0.00 0.00 0.00 4.94
3431 3630 7.118723 AGGTTAGAATTTGGCTGTCATCAATA 58.881 34.615 0.00 0.00 0.00 1.90
3730 3929 7.181305 TCCCAATGAATACTTAACAGAGGTACA 59.819 37.037 0.00 0.00 0.00 2.90
3794 3993 2.941453 TTGACTGAAGGCTAGCTACG 57.059 50.000 15.72 1.82 0.00 3.51
4362 4747 7.864307 AGTTGTACAGTTAGTAAACTAAGCG 57.136 36.000 2.83 0.90 44.28 4.68
4898 7911 2.079925 GGACACATCAAGAGTTGCTCC 58.920 52.381 0.00 0.00 0.00 4.70
4930 7943 4.870426 ACATTCTACTCAAACGTATGCAGG 59.130 41.667 0.00 0.00 0.00 4.85
5200 8217 1.461127 GCAGTTGATTCACGTGTCTCC 59.539 52.381 16.51 4.39 0.00 3.71
5207 8224 3.509967 TGATTCACGTGTCTCCACTGTAT 59.490 43.478 16.51 0.00 39.55 2.29
5259 8276 0.108138 CTCCGGAGTTGTGCCCTTAG 60.108 60.000 24.04 0.00 0.00 2.18
5268 8285 5.242795 AGTTGTGCCCTTAGTGATTACTT 57.757 39.130 0.00 0.00 38.36 2.24
5621 8638 1.263217 CGAATTTGGTATGGGCTACGC 59.737 52.381 0.00 0.00 0.00 4.42
6685 9702 2.038387 ACCAAAAGCGACAAGTGACT 57.962 45.000 0.00 0.00 0.00 3.41
6900 9917 5.126067 ACAGTGCTAGTTGACAACAAAGAT 58.874 37.500 20.08 1.85 37.77 2.40
7672 10689 9.165035 CATCCAACTTAATATTTGCCACATTTT 57.835 29.630 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.311871 CAGCTAGCTTTTCGAGATGCAAT 59.688 43.478 16.46 0.00 27.77 3.56
25 26 2.674852 CAGCTAGCTTTTCGAGATGCAA 59.325 45.455 16.46 0.00 27.77 4.08
39 40 0.579156 GCGTATGTCTTGCAGCTAGC 59.421 55.000 6.62 6.62 45.96 3.42
70 71 2.315901 GCGGTTTGTTCTCGGATTTTG 58.684 47.619 0.00 0.00 0.00 2.44
134 135 4.021544 TCAAATTTTGGCCGAAGCTAACAT 60.022 37.500 5.34 0.00 39.45 2.71
144 145 5.170021 TCATTTCTCATCAAATTTTGGCCG 58.830 37.500 9.18 0.00 0.00 6.13
519 520 3.102972 TCTCACTTGAGAGATCCCCAAG 58.897 50.000 4.76 14.21 45.48 3.61
1017 1154 3.599343 TGATGAAATGGAGTGGTCTTCG 58.401 45.455 0.00 0.00 0.00 3.79
1724 1872 8.871629 TTTTAGGATGTGCTTTTATGTCCTTA 57.128 30.769 0.00 0.00 37.31 2.69
1847 1996 8.361889 AGTGTTGTGGTTTTAGTTGTTTTAGTT 58.638 29.630 0.00 0.00 0.00 2.24
1848 1997 7.888424 AGTGTTGTGGTTTTAGTTGTTTTAGT 58.112 30.769 0.00 0.00 0.00 2.24
1849 1998 8.751302 AAGTGTTGTGGTTTTAGTTGTTTTAG 57.249 30.769 0.00 0.00 0.00 1.85
1851 2000 9.713713 AATAAGTGTTGTGGTTTTAGTTGTTTT 57.286 25.926 0.00 0.00 0.00 2.43
1854 2003 9.959749 CATAATAAGTGTTGTGGTTTTAGTTGT 57.040 29.630 0.00 0.00 0.00 3.32
2067 2264 2.379005 GCCCCAACCTCTTGATTAAGG 58.621 52.381 0.00 0.00 38.70 2.69
2070 2267 1.681229 AGGCCCCAACCTCTTGATTA 58.319 50.000 0.00 0.00 33.62 1.75
2094 2291 3.202906 GTTTGCAGTGGACAAGTCTGTA 58.797 45.455 0.00 0.00 35.30 2.74
2104 2301 2.161855 GGTGATGATGTTTGCAGTGGA 58.838 47.619 0.00 0.00 0.00 4.02
2553 2751 8.752005 ATGCACACAAGGATTACATAGTTAAT 57.248 30.769 0.00 0.00 0.00 1.40
2560 2758 5.472148 CACAAATGCACACAAGGATTACAT 58.528 37.500 0.00 0.00 0.00 2.29
2623 2821 2.370445 ATGGCCCAGTTCTCTCCGG 61.370 63.158 0.00 0.00 0.00 5.14
2679 2877 2.236146 TCATCGCCTCCTTCTTGCTTAA 59.764 45.455 0.00 0.00 0.00 1.85
3111 3309 5.353394 TCTAATATCGCTCCACCTTTTGT 57.647 39.130 0.00 0.00 0.00 2.83
3112 3310 6.677781 TTTCTAATATCGCTCCACCTTTTG 57.322 37.500 0.00 0.00 0.00 2.44
3242 3440 1.002430 CTGCTTCCTACCAGAGCAACA 59.998 52.381 0.00 0.00 44.89 3.33
3268 3466 4.154918 GTGAAATAACTGTGCTCTTCCCAG 59.845 45.833 0.00 0.00 0.00 4.45
3431 3630 5.047092 AGCTTGCAAGTACATAGGCATTTTT 60.047 36.000 26.55 0.00 35.98 1.94
3794 3993 7.141363 AGACAATTCATGTTTAAGTGCAGAAC 58.859 34.615 0.00 0.00 44.12 3.01
4351 4736 4.998979 GCATTCATTGCGCTTAGTTTAC 57.001 40.909 9.73 0.00 42.54 2.01
4594 7607 5.875224 TGATGAACCAAGATGTTGTAAGGA 58.125 37.500 1.49 0.00 30.95 3.36
4898 7911 5.848036 CGTTTGAGTAGAATGTGCTTTTCTG 59.152 40.000 6.62 0.00 35.19 3.02
4930 7943 7.866393 CCAGATTCCTTCTCAATATTTTGCATC 59.134 37.037 0.00 0.00 29.93 3.91
5061 8075 1.798223 TGCACTACTTAGCAAAGCACG 59.202 47.619 0.00 0.00 37.90 5.34
5259 8276 7.391148 TGGGAAATCTTTAGCAAGTAATCAC 57.609 36.000 0.00 0.00 0.00 3.06
5268 8285 8.087750 CAGTTACATTTTGGGAAATCTTTAGCA 58.912 33.333 0.00 0.00 33.25 3.49
5280 8297 6.391227 AAGTGAGTTCAGTTACATTTTGGG 57.609 37.500 0.44 0.00 37.71 4.12
5621 8638 5.455392 AGAATTTTTGCAATGTCGTCTCTG 58.545 37.500 0.00 0.00 0.00 3.35
5967 8984 4.278170 AGCACAGCTGCAGTGTATTAAAAA 59.722 37.500 23.27 0.00 46.97 1.94
5993 9010 4.751767 TCAAACCAACCAAGCTCATTTT 57.248 36.364 0.00 0.00 0.00 1.82
6900 9917 5.839063 CCATCTGAGGTTGTAGTCCCTTATA 59.161 44.000 0.00 0.00 0.00 0.98
7557 10574 8.338259 GCTATGTTATTACAATCTGTCAACTGG 58.662 37.037 0.00 0.00 37.91 4.00


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

AutoCloner maintained by Alex Coulton.