Multiple sequence alignment - TraesCS5D01G525600

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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 TraesCS5D01G525600 chr5D 100.000 2861 0 0 1 2861 543816184 543819044 0.000000e+00 5284.0
1 TraesCS5D01G525600 chr5D 88.652 1269 133 4 731 1998 543771681 543772939 0.000000e+00 1535.0
2 TraesCS5D01G525600 chr5D 82.302 1147 158 27 742 1868 543830351 543831472 0.000000e+00 952.0
3 TraesCS5D01G525600 chr5D 89.889 722 61 4 731 1451 543803359 543804069 0.000000e+00 918.0
4 TraesCS5D01G525600 chr5D 88.732 213 19 5 1855 2065 543777982 543778191 3.660000e-64 255.0
5 TraesCS5D01G525600 chr5D 90.164 122 11 1 525 645 543801021 543801142 1.060000e-34 158.0
6 TraesCS5D01G525600 chr4A 97.416 2864 58 6 1 2861 625283120 625280270 0.000000e+00 4865.0
7 TraesCS5D01G525600 chr4A 87.579 1272 142 11 731 1998 625372987 625371728 0.000000e+00 1459.0
8 TraesCS5D01G525600 chr4A 84.267 1017 148 8 855 1863 625368253 625367241 0.000000e+00 981.0
9 TraesCS5D01G525600 chr4A 89.474 722 71 4 731 1451 625322518 625321801 0.000000e+00 907.0
10 TraesCS5D01G525600 chr4A 87.093 767 72 12 1485 2229 625321803 625321042 0.000000e+00 843.0
11 TraesCS5D01G525600 chr4A 84.088 861 130 7 990 1848 625265214 625264359 0.000000e+00 824.0
12 TraesCS5D01G525600 chr4A 85.714 210 20 7 742 951 625265421 625265222 2.230000e-51 213.0
13 TraesCS5D01G525600 chr4A 83.938 193 26 3 1876 2063 625264286 625264094 2.260000e-41 180.0
14 TraesCS5D01G525600 chr5B 92.841 1718 76 12 398 2075 685692429 685690719 0.000000e+00 2447.0
15 TraesCS5D01G525600 chr5B 82.753 1148 154 27 742 1868 685658028 685656904 0.000000e+00 983.0
16 TraesCS5D01G525600 chr5B 92.090 177 13 1 861 1036 685608009 685608185 6.120000e-62 248.0
17 TraesCS5D01G525600 chr5B 86.310 168 14 6 233 397 384587699 384587538 1.050000e-39 174.0
18 TraesCS5D01G525600 chr5B 84.884 172 21 3 229 398 294096437 294096605 4.900000e-38 169.0
19 TraesCS5D01G525600 chr3D 86.905 168 16 4 233 398 498263640 498263803 1.750000e-42 183.0
20 TraesCS5D01G525600 chr2D 86.826 167 17 3 233 397 73402885 73403048 6.300000e-42 182.0
21 TraesCS5D01G525600 chr2D 84.571 175 25 2 224 397 367502174 367502001 3.790000e-39 172.0
22 TraesCS5D01G525600 chr2D 85.714 168 13 8 233 397 532176554 532176713 1.760000e-37 167.0
23 TraesCS5D01G525600 chr2B 85.380 171 20 4 233 401 540729104 540729271 3.790000e-39 172.0
24 TraesCS5D01G525600 chr4D 85.629 167 19 3 233 397 498049953 498050116 1.360000e-38 171.0
25 TraesCS5D01G525600 chr1B 82.927 123 19 2 63 184 369544982 369545103 3.010000e-20 110.0
26 TraesCS5D01G525600 chr1A 94.118 51 1 2 96 145 333501653 333501702 3.060000e-10 76.8


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 TraesCS5D01G525600 chr5D 543816184 543819044 2860 False 5284.000000 5284 100.0000 1 2861 1 chr5D.!!$F3 2860
1 TraesCS5D01G525600 chr5D 543771681 543772939 1258 False 1535.000000 1535 88.6520 731 1998 1 chr5D.!!$F1 1267
2 TraesCS5D01G525600 chr5D 543830351 543831472 1121 False 952.000000 952 82.3020 742 1868 1 chr5D.!!$F4 1126
3 TraesCS5D01G525600 chr5D 543801021 543804069 3048 False 538.000000 918 90.0265 525 1451 2 chr5D.!!$F5 926
4 TraesCS5D01G525600 chr4A 625280270 625283120 2850 True 4865.000000 4865 97.4160 1 2861 1 chr4A.!!$R1 2860
5 TraesCS5D01G525600 chr4A 625367241 625372987 5746 True 1220.000000 1459 85.9230 731 1998 2 chr4A.!!$R4 1267
6 TraesCS5D01G525600 chr4A 625321042 625322518 1476 True 875.000000 907 88.2835 731 2229 2 chr4A.!!$R3 1498
7 TraesCS5D01G525600 chr4A 625264094 625265421 1327 True 405.666667 824 84.5800 742 2063 3 chr4A.!!$R2 1321
8 TraesCS5D01G525600 chr5B 685690719 685692429 1710 True 2447.000000 2447 92.8410 398 2075 1 chr5B.!!$R3 1677
9 TraesCS5D01G525600 chr5B 685656904 685658028 1124 True 983.000000 983 82.7530 742 1868 1 chr5B.!!$R2 1126

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
25 26 1.324435 CGATGGCATGTCGTGTTGTAG 59.676 52.381 3.81 0.0 34.56 2.74 F
141 142 2.010145 ATTTGAGATGTGACCGGTCG 57.990 50.000 28.70 0.0 0.00 4.79 F
1083 3263 1.227556 GTGCCACACTGACGACCTT 60.228 57.895 0.00 0.0 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1074 3254 1.737735 CAGCGCATGAAGGTCGTCA 60.738 57.895 11.47 0.0 0.00 4.35 R
1431 3611 3.118555 CCATACCCAATGAACGACCAGTA 60.119 47.826 0.00 0.0 37.86 2.74 R
2610 6944 0.336737 AGATCCCTTCGACTCACCCT 59.663 55.000 0.00 0.0 0.00 4.34 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
25 26 1.324435 CGATGGCATGTCGTGTTGTAG 59.676 52.381 3.81 0.0 34.56 2.74
40 41 6.600427 TCGTGTTGTAGTAACAGGATGATCTA 59.400 38.462 10.12 0.0 39.29 1.98
141 142 2.010145 ATTTGAGATGTGACCGGTCG 57.990 50.000 28.70 0.0 0.00 4.79
148 149 4.057428 GTGACCGGTCGCTGCTCT 62.057 66.667 35.30 0.0 37.16 4.09
182 183 2.355363 TGTCCGCCGACGTTTGAG 60.355 61.111 0.00 0.0 42.37 3.02
246 247 5.106277 GCTTGCTAATTACTTCCTCCGTTTT 60.106 40.000 0.00 0.0 0.00 2.43
300 301 9.464714 ACTATAGACTACATACGAAGCAAAATG 57.535 33.333 6.78 0.0 0.00 2.32
313 314 7.519002 ACGAAGCAAAATGACTGAAACTATAC 58.481 34.615 0.00 0.0 0.00 1.47
324 325 8.407457 TGACTGAAACTATACTCTAAAATGCG 57.593 34.615 0.00 0.0 0.00 4.73
388 389 6.812879 AAAAGGACTTGTATTTAGGAACGG 57.187 37.500 0.00 0.0 0.00 4.44
390 391 5.340439 AGGACTTGTATTTAGGAACGGAG 57.660 43.478 0.00 0.0 0.00 4.63
657 2740 2.154139 TGGCATGGGTGACAAGAGT 58.846 52.632 0.00 0.0 41.45 3.24
883 3048 7.062255 CACACACACACACACACTATAAGATAG 59.938 40.741 0.00 0.0 0.00 2.08
1074 3254 2.049433 GCTACGTCGTGCCACACT 60.049 61.111 8.47 0.0 31.34 3.55
1083 3263 1.227556 GTGCCACACTGACGACCTT 60.228 57.895 0.00 0.0 0.00 3.50
1396 3576 4.953579 ACAATTTATTGGTTGGCGAGGTAT 59.046 37.500 7.33 0.0 41.96 2.73
1698 3879 5.600484 TGTTGTTTCTGGGACCAAACATATT 59.400 36.000 8.88 0.0 39.03 1.28
2505 6839 1.950973 GAAGGGAGCCGACTCAGACC 61.951 65.000 0.00 0.0 45.42 3.85
2610 6944 2.642427 ACACACACAGCTTGATGTCAA 58.358 42.857 3.37 0.0 0.00 3.18
2670 7004 7.936847 CAGGGCTTTGTGTACATCCTAATAATA 59.063 37.037 0.00 0.0 0.00 0.98
2673 7007 8.774586 GGCTTTGTGTACATCCTAATAATACAG 58.225 37.037 0.00 0.0 0.00 2.74
2691 7025 2.573915 ACAGAGATCAGGGTTTTCCTCC 59.426 50.000 0.00 0.0 46.12 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 8.198109 ACATAGATCATCCTGTTACTACAACAC 58.802 37.037 0.00 0.00 32.92 3.32
25 26 6.128715 CGATGCAACATAGATCATCCTGTTAC 60.129 42.308 0.00 0.04 33.62 2.50
40 41 1.999735 CCTACGTGAACGATGCAACAT 59.000 47.619 10.26 0.00 43.02 2.71
182 183 3.624861 CCGCATATAGCAAATCTGGATCC 59.375 47.826 4.20 4.20 46.13 3.36
278 279 7.488150 CAGTCATTTTGCTTCGTATGTAGTCTA 59.512 37.037 0.00 0.00 0.00 2.59
300 301 8.408743 ACGCATTTTAGAGTATAGTTTCAGTC 57.591 34.615 0.00 0.00 0.00 3.51
313 314 9.556030 TCGAATGTATATAGACGCATTTTAGAG 57.444 33.333 0.00 0.00 32.47 2.43
369 370 4.439968 CCTCCGTTCCTAAATACAAGTCC 58.560 47.826 0.00 0.00 0.00 3.85
388 389 4.202233 GCCAATGTAAGGTAGTACTCCCTC 60.202 50.000 7.57 0.00 0.00 4.30
390 391 3.181457 GGCCAATGTAAGGTAGTACTCCC 60.181 52.174 0.00 0.00 0.00 4.30
657 2740 2.367894 CCATATGCAAGCAGAGAGAGGA 59.632 50.000 0.00 0.00 0.00 3.71
883 3048 3.807538 CTGCTCGGTGGTGCATGC 61.808 66.667 11.82 11.82 41.37 4.06
1074 3254 1.737735 CAGCGCATGAAGGTCGTCA 60.738 57.895 11.47 0.00 0.00 4.35
1083 3263 4.728110 AAGCCCTGCAGCGCATGA 62.728 61.111 24.46 0.00 38.13 3.07
1396 3576 4.890158 TGAGCTGTATCAAACTCTTGGA 57.110 40.909 0.00 0.00 33.01 3.53
1431 3611 3.118555 CCATACCCAATGAACGACCAGTA 60.119 47.826 0.00 0.00 37.86 2.74
1587 3768 5.003804 GTGTTGTCATTCCCAGATACAACT 58.996 41.667 15.24 0.00 46.29 3.16
2531 6865 1.758440 AAGGCTCTTGCACGGACAGA 61.758 55.000 0.00 0.00 41.91 3.41
2589 6923 2.642427 TGACATCAAGCTGTGTGTGTT 58.358 42.857 4.58 0.00 30.75 3.32
2610 6944 0.336737 AGATCCCTTCGACTCACCCT 59.663 55.000 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.