Multiple sequence alignment - TraesCS5B01G078900

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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 TraesCS5B01G078900 chr5B 100.000 2714 0 0 1 2714 96020522 96017809 0.000000e+00 5012.0
1 TraesCS5B01G078900 chr5D 93.938 2722 79 31 48 2714 90688327 90685637 0.000000e+00 4034.0
2 TraesCS5B01G078900 chr5A 92.069 2383 78 47 48 2370 84152261 84149930 0.000000e+00 3251.0
3 TraesCS5B01G078900 chr4A 90.000 80 7 1 1008 1087 546485392 546485314 4.780000e-18 102.0
4 TraesCS5B01G078900 chr4D 90.769 65 6 0 1019 1083 50327262 50327326 1.340000e-13 87.9


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 TraesCS5B01G078900 chr5B 96017809 96020522 2713 True 5012 5012 100.000 1 2714 1 chr5B.!!$R1 2713
1 TraesCS5B01G078900 chr5D 90685637 90688327 2690 True 4034 4034 93.938 48 2714 1 chr5D.!!$R1 2666
2 TraesCS5B01G078900 chr5A 84149930 84152261 2331 True 3251 3251 92.069 48 2370 1 chr5A.!!$R1 2322

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
28 29 0.032912 AATGTGCATCATCCAGGCCA 60.033 50.0 5.01 0.0 35.48 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 1962 0.335019 TCAGAACTCGATCCTCCCCA 59.665 55.0 0.0 0.0 0.0 4.96 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
23 24 5.683681 AGTACATACAATGTGCATCATCCA 58.316 37.500 10.14 0.00 46.52 3.41
24 25 5.761726 AGTACATACAATGTGCATCATCCAG 59.238 40.000 10.14 0.00 46.52 3.86
25 26 3.887110 ACATACAATGTGCATCATCCAGG 59.113 43.478 0.00 0.00 43.01 4.45
26 27 1.108776 ACAATGTGCATCATCCAGGC 58.891 50.000 0.00 0.00 35.48 4.85
27 28 0.387929 CAATGTGCATCATCCAGGCC 59.612 55.000 0.00 0.00 35.48 5.19
28 29 0.032912 AATGTGCATCATCCAGGCCA 60.033 50.000 5.01 0.00 35.48 5.36
29 30 0.032912 ATGTGCATCATCCAGGCCAA 60.033 50.000 5.01 0.00 29.76 4.52
30 31 0.681887 TGTGCATCATCCAGGCCAAG 60.682 55.000 5.01 0.00 0.00 3.61
31 32 0.682209 GTGCATCATCCAGGCCAAGT 60.682 55.000 5.01 0.00 0.00 3.16
32 33 0.681887 TGCATCATCCAGGCCAAGTG 60.682 55.000 5.01 0.00 0.00 3.16
33 34 1.389609 GCATCATCCAGGCCAAGTGG 61.390 60.000 5.01 3.84 36.28 4.00
41 42 3.597182 TCCAGGCCAAGTGGATATATGA 58.403 45.455 8.12 0.00 39.28 2.15
42 43 3.980022 TCCAGGCCAAGTGGATATATGAA 59.020 43.478 8.12 0.00 39.28 2.57
43 44 4.074970 CCAGGCCAAGTGGATATATGAAC 58.925 47.826 5.01 0.00 37.23 3.18
44 45 4.202503 CCAGGCCAAGTGGATATATGAACT 60.203 45.833 5.01 0.00 37.23 3.01
45 46 4.999950 CAGGCCAAGTGGATATATGAACTC 59.000 45.833 5.01 0.00 37.39 3.01
46 47 4.660303 AGGCCAAGTGGATATATGAACTCA 59.340 41.667 5.01 0.00 37.39 3.41
68 69 9.730705 ACTCAATTATGAATCATACCATGTAGG 57.269 33.333 1.88 0.00 38.17 3.18
69 70 9.948964 CTCAATTATGAATCATACCATGTAGGA 57.051 33.333 1.88 0.00 36.48 2.94
167 168 6.582295 CACATACATACACAAAGTTCCAAAGC 59.418 38.462 0.00 0.00 0.00 3.51
362 373 2.060050 TCCTGAGCTAGTAGGAGCAC 57.940 55.000 9.21 0.00 45.43 4.40
364 375 1.680735 CCTGAGCTAGTAGGAGCACTG 59.319 57.143 5.43 0.00 45.43 3.66
654 675 2.364970 TGCAACTTCCATTCCCAGTTTG 59.635 45.455 0.00 0.00 0.00 2.93
726 747 2.849880 TGCAAGTTTGAGTGCAGAAC 57.150 45.000 0.00 0.00 45.52 3.01
805 834 3.574826 AGGTCAGTTACTTCTCTGTGGTC 59.425 47.826 0.00 0.00 33.89 4.02
806 835 3.321111 GGTCAGTTACTTCTCTGTGGTCA 59.679 47.826 0.00 0.00 33.89 4.02
846 879 0.109412 GCTGTTTGCATCTCTGGCAC 60.109 55.000 0.00 0.00 41.75 5.01
912 945 4.689062 ACCAGAGTTCCTTCCTTCAGATA 58.311 43.478 0.00 0.00 0.00 1.98
913 946 4.714308 ACCAGAGTTCCTTCCTTCAGATAG 59.286 45.833 0.00 0.00 0.00 2.08
914 947 4.959210 CCAGAGTTCCTTCCTTCAGATAGA 59.041 45.833 0.00 0.00 0.00 1.98
915 948 5.602145 CCAGAGTTCCTTCCTTCAGATAGAT 59.398 44.000 0.00 0.00 0.00 1.98
916 949 6.780031 CCAGAGTTCCTTCCTTCAGATAGATA 59.220 42.308 0.00 0.00 0.00 1.98
924 957 7.039152 TCCTTCCTTCAGATAGATAGATGCTTG 60.039 40.741 0.00 0.00 0.00 4.01
971 1004 5.625150 AGTTTCTTCTACATTTCAGCAGGT 58.375 37.500 0.00 0.00 0.00 4.00
982 1015 3.492102 TTCAGCAGGTTTAGAGCAAGT 57.508 42.857 0.00 0.00 0.00 3.16
1101 1137 8.514594 CAACAGGTTAGCAATTAATCTTCTTCA 58.485 33.333 0.00 0.00 30.07 3.02
1102 1138 8.045176 ACAGGTTAGCAATTAATCTTCTTCAC 57.955 34.615 0.00 0.00 30.07 3.18
1148 1195 3.270027 TGCGTGCTATGAACTGCTAATT 58.730 40.909 0.00 0.00 0.00 1.40
1149 1196 3.689161 TGCGTGCTATGAACTGCTAATTT 59.311 39.130 0.00 0.00 0.00 1.82
1150 1197 4.873259 TGCGTGCTATGAACTGCTAATTTA 59.127 37.500 0.00 0.00 0.00 1.40
1182 1234 2.126071 GCGCAGGTTCACGAGCTA 60.126 61.111 0.30 0.00 33.99 3.32
1311 1363 2.188829 CCCCGCCGACGAGTACATA 61.189 63.158 0.00 0.00 43.93 2.29
1314 1366 0.041488 CCGCCGACGAGTACATAGTC 60.041 60.000 0.00 0.45 43.93 2.59
1440 1492 3.006967 ACAACGTTAGCAAGAGAGGACAT 59.993 43.478 0.00 0.00 0.00 3.06
1804 1865 5.407691 TGATCGCATCGTACTACTTAGTAGG 59.592 44.000 21.63 10.01 42.78 3.18
1910 1974 1.762460 GGAGCTTGGGGAGGATCGA 60.762 63.158 0.00 0.00 34.37 3.59
2095 2162 0.037975 GCATGCAAAGGTTCACAGGG 60.038 55.000 14.21 0.00 0.00 4.45
2096 2163 0.604578 CATGCAAAGGTTCACAGGGG 59.395 55.000 0.00 0.00 0.00 4.79
2184 2254 6.491403 AGAAAGCATGAAAAGTGAATAGTGGT 59.509 34.615 0.00 0.00 0.00 4.16
2261 2344 4.012374 ACAATGGATGTGGTCATGAAGAC 58.988 43.478 0.00 0.00 41.93 3.01
2445 2528 2.557056 GCCAAAAAGTTACAGGGAGGAC 59.443 50.000 0.00 0.00 0.00 3.85
2472 2555 5.336150 TCAAGTTCCAGCACAAAATTTCA 57.664 34.783 0.00 0.00 0.00 2.69
2644 2732 5.356470 AGCATTCCTAATTGAACAGAGAAGC 59.644 40.000 0.00 0.00 0.00 3.86
2663 2751 0.829333 CATGTGAGAGCTAGGCACCT 59.171 55.000 9.70 0.00 0.00 4.00
2686 2774 3.446516 GCCCAAAGCTGAAGAAATCTCAT 59.553 43.478 0.00 0.00 38.99 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.683681 TGGATGATGCACATTGTATGTACT 58.316 37.500 0.00 0.00 42.70 2.73
1 2 5.049198 CCTGGATGATGCACATTGTATGTAC 60.049 44.000 0.00 0.00 42.70 2.90
2 3 5.065235 CCTGGATGATGCACATTGTATGTA 58.935 41.667 0.00 0.00 42.70 2.29
3 4 3.887110 CCTGGATGATGCACATTGTATGT 59.113 43.478 0.00 0.00 46.22 2.29
4 5 3.305131 GCCTGGATGATGCACATTGTATG 60.305 47.826 0.00 0.00 39.56 2.39
5 6 2.889045 GCCTGGATGATGCACATTGTAT 59.111 45.455 0.00 0.00 39.56 2.29
6 7 2.300433 GCCTGGATGATGCACATTGTA 58.700 47.619 0.00 0.00 39.56 2.41
7 8 1.108776 GCCTGGATGATGCACATTGT 58.891 50.000 0.00 0.00 39.56 2.71
8 9 0.387929 GGCCTGGATGATGCACATTG 59.612 55.000 0.00 0.00 39.56 2.82
9 10 0.032912 TGGCCTGGATGATGCACATT 60.033 50.000 3.32 0.00 39.56 2.71
10 11 0.032912 TTGGCCTGGATGATGCACAT 60.033 50.000 3.32 0.00 42.47 3.21
11 12 0.681887 CTTGGCCTGGATGATGCACA 60.682 55.000 3.32 0.00 0.00 4.57
12 13 0.682209 ACTTGGCCTGGATGATGCAC 60.682 55.000 3.32 0.00 0.00 4.57
13 14 0.681887 CACTTGGCCTGGATGATGCA 60.682 55.000 3.32 0.00 0.00 3.96
14 15 1.389609 CCACTTGGCCTGGATGATGC 61.390 60.000 3.32 0.00 0.00 3.91
15 16 0.256752 TCCACTTGGCCTGGATGATG 59.743 55.000 8.12 0.00 32.52 3.07
16 17 1.229131 ATCCACTTGGCCTGGATGAT 58.771 50.000 21.20 7.82 45.30 2.45
17 18 1.891933 TATCCACTTGGCCTGGATGA 58.108 50.000 27.44 13.50 46.27 2.92
18 19 2.965671 ATATCCACTTGGCCTGGATG 57.034 50.000 27.44 11.47 46.27 3.51
20 21 3.597182 TCATATATCCACTTGGCCTGGA 58.403 45.455 14.20 14.20 42.17 3.86
21 22 4.074970 GTTCATATATCCACTTGGCCTGG 58.925 47.826 3.32 3.14 34.44 4.45
22 23 4.978099 AGTTCATATATCCACTTGGCCTG 58.022 43.478 3.32 0.00 34.44 4.85
23 24 4.660303 TGAGTTCATATATCCACTTGGCCT 59.340 41.667 3.32 0.00 34.44 5.19
24 25 4.973168 TGAGTTCATATATCCACTTGGCC 58.027 43.478 0.00 0.00 34.44 5.36
25 26 7.516198 AATTGAGTTCATATATCCACTTGGC 57.484 36.000 0.00 0.00 34.44 4.52
39 40 9.631257 ACATGGTATGATTCATAATTGAGTTCA 57.369 29.630 7.93 0.00 33.21 3.18
42 43 9.730705 CCTACATGGTATGATTCATAATTGAGT 57.269 33.333 7.93 6.61 32.27 3.41
43 44 9.948964 TCCTACATGGTATGATTCATAATTGAG 57.051 33.333 7.93 2.43 37.07 3.02
44 45 9.725019 GTCCTACATGGTATGATTCATAATTGA 57.275 33.333 7.93 0.00 37.07 2.57
45 46 8.950210 GGTCCTACATGGTATGATTCATAATTG 58.050 37.037 7.93 8.51 37.07 2.32
46 47 8.894592 AGGTCCTACATGGTATGATTCATAATT 58.105 33.333 7.93 0.00 37.07 1.40
67 68 3.130340 TCACTGAAAACAAGCAAAGGTCC 59.870 43.478 0.00 0.00 0.00 4.46
68 69 4.105486 GTCACTGAAAACAAGCAAAGGTC 58.895 43.478 0.00 0.00 0.00 3.85
69 70 3.509575 TGTCACTGAAAACAAGCAAAGGT 59.490 39.130 0.00 0.00 0.00 3.50
167 168 8.865420 TCCAGCTCCATTTAGTACTAGTATAG 57.135 38.462 5.75 0.74 46.50 1.31
286 290 6.625873 TTGTGTGTGATGCAAAACTATACA 57.374 33.333 0.00 0.00 0.00 2.29
408 428 5.006386 CCCTGCAAGAGTCTTGTTTAATCT 58.994 41.667 28.95 0.00 34.07 2.40
567 587 2.123428 GCCTCCAATGGCGAATGCT 61.123 57.895 0.00 0.00 43.74 3.79
600 620 4.941263 AGGTGCTCATTTATAAACGCAGAA 59.059 37.500 15.08 0.00 0.00 3.02
654 675 5.181748 ACTAAAGATCAGGTGTTGATGCTC 58.818 41.667 0.00 0.00 46.51 4.26
805 834 8.115491 CAGCATGTTTGACAAATATTGATCTG 57.885 34.615 7.37 8.66 0.00 2.90
868 901 3.004629 TCATGCTTGACAACATGGTTCAC 59.995 43.478 20.72 0.00 43.12 3.18
899 932 6.855763 AGCATCTATCTATCTGAAGGAAGG 57.144 41.667 0.00 0.00 0.00 3.46
912 945 6.579666 TCAAAAACTTGCAAGCATCTATCT 57.420 33.333 26.27 0.83 0.00 1.98
913 946 7.642071 TTTCAAAAACTTGCAAGCATCTATC 57.358 32.000 26.27 0.00 0.00 2.08
914 947 8.611654 AATTTCAAAAACTTGCAAGCATCTAT 57.388 26.923 26.27 2.45 0.00 1.98
915 948 8.436046 AAATTTCAAAAACTTGCAAGCATCTA 57.564 26.923 26.27 5.18 0.00 1.98
916 949 6.930667 AATTTCAAAAACTTGCAAGCATCT 57.069 29.167 26.27 3.68 0.00 2.90
947 980 6.064717 ACCTGCTGAAATGTAGAAGAAACTT 58.935 36.000 0.00 0.00 0.00 2.66
950 983 6.959639 AAACCTGCTGAAATGTAGAAGAAA 57.040 33.333 0.00 0.00 0.00 2.52
957 990 4.905429 TGCTCTAAACCTGCTGAAATGTA 58.095 39.130 0.00 0.00 0.00 2.29
971 1004 6.601613 TCCTCAAACTCAAAACTTGCTCTAAA 59.398 34.615 0.00 0.00 0.00 1.85
982 1015 4.655963 CCCATCTCTCCTCAAACTCAAAA 58.344 43.478 0.00 0.00 0.00 2.44
1062 1095 0.689623 CCTGTTGCCTGAAGGTCTCT 59.310 55.000 0.00 0.00 37.57 3.10
1101 1137 5.471456 CAGTTTGCTATGGTGAAGAAGAAGT 59.529 40.000 0.00 0.00 0.00 3.01
1102 1138 5.471456 ACAGTTTGCTATGGTGAAGAAGAAG 59.529 40.000 0.00 0.00 0.00 2.85
1148 1195 4.275689 CCTGCGCAAGGTGATTATCAATAA 59.724 41.667 13.05 0.00 41.74 1.40
1149 1196 3.814842 CCTGCGCAAGGTGATTATCAATA 59.185 43.478 13.05 0.00 41.74 1.90
1150 1197 2.620115 CCTGCGCAAGGTGATTATCAAT 59.380 45.455 13.05 0.00 41.74 2.57
1182 1234 3.659089 GATGCGGTACAGGCGGTGT 62.659 63.158 0.00 0.00 43.86 4.16
1804 1865 3.963665 TGCTTCTACAATGCAACACAAC 58.036 40.909 0.00 0.00 33.48 3.32
1898 1962 0.335019 TCAGAACTCGATCCTCCCCA 59.665 55.000 0.00 0.00 0.00 4.96
1910 1974 4.202305 GGATCAGGATCGGAATTCAGAACT 60.202 45.833 12.38 10.61 38.69 3.01
2184 2254 3.498121 CGTAGCCTCCTTCTCCCTATGTA 60.498 52.174 0.00 0.00 0.00 2.29
2261 2344 8.600625 CATCTGAATTCCATGTTAATTTGCAAG 58.399 33.333 2.27 0.00 0.00 4.01
2308 2391 1.482182 TCCATGACTTCATCTCCACCG 59.518 52.381 0.00 0.00 33.61 4.94
2445 2528 5.947228 TTTTGTGCTGGAACTTGATCTAG 57.053 39.130 2.37 2.37 0.00 2.43
2472 2555 8.947055 ATTGCACAAAATCTGTAACTTCTTTT 57.053 26.923 0.00 0.00 36.10 2.27
2524 2607 7.573968 ACATAATCTCTTGGGCTTTGAATAC 57.426 36.000 0.00 0.00 0.00 1.89
2633 2721 2.672381 GCTCTCACATGCTTCTCTGTTC 59.328 50.000 0.00 0.00 0.00 3.18
2636 2724 2.676632 AGCTCTCACATGCTTCTCTG 57.323 50.000 0.00 0.00 35.86 3.35
2644 2732 0.829333 AGGTGCCTAGCTCTCACATG 59.171 55.000 12.86 0.00 32.69 3.21
2663 2751 2.821969 GAGATTTCTTCAGCTTTGGGCA 59.178 45.455 0.00 0.00 44.79 5.36


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

AutoCloner maintained by Alex Coulton.