Multiple sequence alignment - TraesCS3D01G248200

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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 TraesCS3D01G248200 chr3D 100.000 3527 0 0 1 3527 346980096 346976570 0.000000e+00 6514.0
1 TraesCS3D01G248200 chr3B 96.880 3462 70 11 76 3527 447010077 447006644 0.000000e+00 5760.0
2 TraesCS3D01G248200 chr3B 93.827 81 5 0 1 81 447010180 447010100 4.780000e-24 122.0
3 TraesCS3D01G248200 chr3A 95.851 3543 112 16 2 3527 466113616 466110092 0.000000e+00 5696.0
4 TraesCS3D01G248200 chr4D 89.700 233 13 5 2835 3064 7831711 7831487 1.600000e-73 287.0
5 TraesCS3D01G248200 chr4A 86.250 240 20 6 2828 3064 595566777 595567006 7.560000e-62 248.0
6 TraesCS3D01G248200 chr4B 86.730 211 15 6 2828 3035 14120969 14121169 4.580000e-54 222.0
7 TraesCS3D01G248200 chr5A 86.239 109 12 3 2959 3064 43689729 43689837 8.000000e-22 115.0
8 TraesCS3D01G248200 chr5A 85.321 109 13 3 2959 3064 43737652 43737760 3.720000e-20 110.0
9 TraesCS3D01G248200 chr5B 82.812 128 18 4 2959 3082 57871848 57871975 1.030000e-20 111.0
10 TraesCS3D01G248200 chr2D 86.364 88 11 1 2931 3017 522750928 522750841 1.040000e-15 95.3
11 TraesCS3D01G248200 chr1D 94.444 36 2 0 2844 2879 176382692 176382727 4.920000e-04 56.5
12 TraesCS3D01G248200 chr1D 100.000 28 0 0 2800 2827 176386072 176386099 6.000000e-03 52.8
13 TraesCS3D01G248200 chr1B 94.444 36 2 0 2844 2879 242736246 242736281 4.920000e-04 56.5
14 TraesCS3D01G248200 chr1B 100.000 28 0 0 2800 2827 242737823 242737850 6.000000e-03 52.8


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 TraesCS3D01G248200 chr3D 346976570 346980096 3526 True 6514 6514 100.0000 1 3527 1 chr3D.!!$R1 3526
1 TraesCS3D01G248200 chr3B 447006644 447010180 3536 True 2941 5760 95.3535 1 3527 2 chr3B.!!$R1 3526
2 TraesCS3D01G248200 chr3A 466110092 466113616 3524 True 5696 5696 95.8510 2 3527 1 chr3A.!!$R1 3525

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
31 32 0.454600 ACGTCGAGCATATGTTCGGT 59.545 50.0 32.6 23.57 46.43 4.69 F
247 277 1.072266 AGGATGCCACCAAACCAGTA 58.928 50.0 0.0 0.00 0.00 2.74 F
1310 1358 1.130054 AAGTTGCAGGAGGAGCTGGA 61.130 55.0 0.0 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1214 1262 0.320771 CCCACTGGAAGACGACTTGG 60.321 60.0 4.51 0.02 37.43 3.61 R
1586 1634 0.536006 AGAGGACAGTGCAACCAAGC 60.536 55.0 0.00 0.00 37.80 4.01 R
2730 2787 1.129058 CCCCTAGAAACTATGCCGGT 58.871 55.0 1.90 0.00 0.00 5.28 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
31 32 0.454600 ACGTCGAGCATATGTTCGGT 59.545 50.000 32.60 23.57 46.43 4.69
81 82 2.474735 CGCAATTCGTTTCCCAAAAAGG 59.525 45.455 0.00 0.00 37.03 3.11
83 84 3.493129 GCAATTCGTTTCCCAAAAAGGAC 59.507 43.478 0.00 0.00 41.22 3.85
84 85 4.688021 CAATTCGTTTCCCAAAAAGGACA 58.312 39.130 0.00 0.00 41.22 4.02
85 86 5.296748 CAATTCGTTTCCCAAAAAGGACAT 58.703 37.500 0.00 0.00 41.22 3.06
93 122 6.755542 TTCCCAAAAAGGACATTTAATGGT 57.244 33.333 9.88 0.00 41.22 3.55
139 169 7.862512 AATTCTCCAACATTTTTGCAAAGAA 57.137 28.000 12.41 9.20 0.00 2.52
151 181 5.467035 TTTGCAAAGAATTAACTGGAGGG 57.533 39.130 8.05 0.00 0.00 4.30
160 190 1.802553 TAACTGGAGGGGCAGGATAC 58.197 55.000 0.00 0.00 0.00 2.24
176 206 2.290641 GGATACCCAAAATGCTGTAGCG 59.709 50.000 0.00 0.00 45.83 4.26
183 213 2.282701 AAATGCTGTAGCGCCAATTG 57.717 45.000 2.29 0.00 45.83 2.32
247 277 1.072266 AGGATGCCACCAAACCAGTA 58.928 50.000 0.00 0.00 0.00 2.74
363 393 3.681417 AGGCCAAGTCGTCGTTTATAAAC 59.319 43.478 16.87 16.87 35.59 2.01
393 423 2.023318 CCTGGTAGTAGCCTCGTCG 58.977 63.158 0.00 0.00 0.00 5.12
521 551 1.282875 GAAGCACGGTTCAACTGGC 59.717 57.895 0.32 1.58 0.00 4.85
541 571 7.642669 ACTGGCACATTTTATATCGAGAAATG 58.357 34.615 17.49 17.49 43.13 2.32
557 587 6.968904 TCGAGAAATGATAAAGAAATGCAAGC 59.031 34.615 0.00 0.00 0.00 4.01
964 996 2.832201 GCTTGATCCTGGGCTGCC 60.832 66.667 11.05 11.05 0.00 4.85
965 997 2.679092 CTTGATCCTGGGCTGCCA 59.321 61.111 22.05 5.83 0.00 4.92
966 998 1.453379 CTTGATCCTGGGCTGCCAG 60.453 63.158 22.05 15.10 37.54 4.85
967 999 3.650298 TTGATCCTGGGCTGCCAGC 62.650 63.158 22.05 8.55 41.46 4.85
968 1000 4.119363 GATCCTGGGCTGCCAGCA 62.119 66.667 22.05 9.28 44.75 4.41
1039 1077 8.751242 AGTCCAGGTAGAGTATTTAGTTTCTTC 58.249 37.037 0.00 0.00 0.00 2.87
1066 1112 6.422223 CGAGTTTTCTTATCCAAATCATCGG 58.578 40.000 0.00 0.00 0.00 4.18
1074 1120 8.327941 TCTTATCCAAATCATCGGATCATTTC 57.672 34.615 0.00 0.00 41.23 2.17
1105 1151 2.234414 GGCCAACATGAATCATGGTTGT 59.766 45.455 24.99 4.83 38.83 3.32
1214 1262 3.121362 GCTTTGTTTTATGTTCACAGCGC 60.121 43.478 0.00 0.00 0.00 5.92
1310 1358 1.130054 AAGTTGCAGGAGGAGCTGGA 61.130 55.000 0.00 0.00 0.00 3.86
1357 1405 3.230134 GCACTGGATCAGATAGAGGAGT 58.770 50.000 1.59 0.00 35.18 3.85
1473 1521 1.821332 GGAGGCAGCAAGGGATTCG 60.821 63.158 0.00 0.00 0.00 3.34
1537 1585 5.010012 CAGCTTGAACAAACCAAGGTATCTT 59.990 40.000 7.17 0.00 46.66 2.40
1586 1634 3.309682 TCGCTTCAAGACAACAACAAGAG 59.690 43.478 0.00 0.00 0.00 2.85
1613 1661 3.616956 TGCACTGTCCTCTAATCCAAG 57.383 47.619 0.00 0.00 0.00 3.61
1833 1881 0.538584 TCTCGATGGTGCAAGCTCAT 59.461 50.000 0.00 0.00 33.76 2.90
1836 1884 2.938451 CTCGATGGTGCAAGCTCATTTA 59.062 45.455 0.00 0.00 33.76 1.40
2103 2151 1.076024 AGGCTGAGGGAAATGCTGAAA 59.924 47.619 0.00 0.00 0.00 2.69
2307 2355 5.723492 TGATTGATGCTATGTTCAGTTCG 57.277 39.130 0.00 0.00 0.00 3.95
2734 2791 5.646360 ACAGGTAGTGAAAATATGAAACCGG 59.354 40.000 0.00 0.00 0.00 5.28
3053 3110 3.583086 TGCTAAGGATAACTAGGGATGCC 59.417 47.826 0.00 0.00 0.00 4.40
3449 3507 5.080337 ACCCAATCATAAGCTCTCGAGATA 58.920 41.667 17.03 6.12 0.00 1.98
3450 3508 5.540337 ACCCAATCATAAGCTCTCGAGATAA 59.460 40.000 17.03 2.06 0.00 1.75
3451 3509 6.042093 ACCCAATCATAAGCTCTCGAGATAAA 59.958 38.462 17.03 2.44 0.00 1.40
3452 3510 6.931281 CCCAATCATAAGCTCTCGAGATAAAA 59.069 38.462 17.03 2.82 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.536928 GCAAACCGAACATATGCTCGAC 60.537 50.000 25.93 9.11 35.85 4.20
81 82 5.242838 TGGAGGAACAACACCATTAAATGTC 59.757 40.000 0.00 0.00 0.00 3.06
83 84 5.010516 TGTGGAGGAACAACACCATTAAATG 59.989 40.000 0.00 0.00 36.61 2.32
84 85 5.144100 TGTGGAGGAACAACACCATTAAAT 58.856 37.500 0.00 0.00 36.61 1.40
85 86 4.537751 TGTGGAGGAACAACACCATTAAA 58.462 39.130 0.00 0.00 36.61 1.52
139 169 1.912862 ATCCTGCCCCTCCAGTTAAT 58.087 50.000 0.00 0.00 0.00 1.40
151 181 1.410153 CAGCATTTTGGGTATCCTGCC 59.590 52.381 0.51 0.00 32.72 4.85
160 190 1.139520 GGCGCTACAGCATTTTGGG 59.860 57.895 7.64 0.00 42.21 4.12
176 206 5.062558 GCATTTCATACTTGACACAATTGGC 59.937 40.000 10.83 0.00 0.00 4.52
183 213 8.915871 ATTAATGTGCATTTCATACTTGACAC 57.084 30.769 2.56 0.00 32.50 3.67
247 277 7.497579 TGCACGTATTGACCATTAGAATATTGT 59.502 33.333 0.00 0.00 0.00 2.71
393 423 4.262036 GGTTGAATTGTTGAGGGGAAGAAC 60.262 45.833 0.00 0.00 0.00 3.01
446 476 2.805353 CCGTCAGACGAAGGCACG 60.805 66.667 24.88 1.45 46.05 5.34
482 512 2.383245 CTGACCTGAGCGTTGGTGGT 62.383 60.000 2.45 0.00 36.59 4.16
541 571 7.656707 TTCTTTTGGCTTGCATTTCTTTATC 57.343 32.000 0.00 0.00 0.00 1.75
711 743 5.104569 AGGGGAAAAGATGAATCAGAGACTC 60.105 44.000 0.00 0.00 0.00 3.36
964 996 3.667282 GTGCTGGTGCTGGTGCTG 61.667 66.667 0.00 0.00 40.48 4.41
965 997 4.962836 GGTGCTGGTGCTGGTGCT 62.963 66.667 0.00 0.00 40.48 4.40
967 999 4.935495 ACGGTGCTGGTGCTGGTG 62.935 66.667 0.00 0.00 40.48 4.17
968 1000 4.189580 AACGGTGCTGGTGCTGGT 62.190 61.111 0.00 0.00 40.48 4.00
969 1001 3.357079 GAACGGTGCTGGTGCTGG 61.357 66.667 0.00 0.00 40.48 4.85
970 1002 3.357079 GGAACGGTGCTGGTGCTG 61.357 66.667 0.00 0.00 40.48 4.41
971 1003 3.560251 AGGAACGGTGCTGGTGCT 61.560 61.111 0.00 0.00 40.48 4.40
972 1004 3.357079 CAGGAACGGTGCTGGTGC 61.357 66.667 15.11 0.00 39.43 5.01
973 1005 1.961277 GTCAGGAACGGTGCTGGTG 60.961 63.158 22.59 0.00 43.13 4.17
974 1006 2.426023 GTCAGGAACGGTGCTGGT 59.574 61.111 22.59 0.00 43.13 4.00
975 1007 2.358737 GGTCAGGAACGGTGCTGG 60.359 66.667 22.59 3.54 43.13 4.85
1039 1077 4.947388 TGATTTGGATAAGAAAACTCGGGG 59.053 41.667 0.00 0.00 0.00 5.73
1066 1112 6.127647 TGTTGGCCAACAGATAAGAAATGATC 60.128 38.462 40.89 14.59 45.42 2.92
1105 1151 6.553100 ACAGAAACCTAAATTTCATGGAACCA 59.447 34.615 10.53 0.00 40.43 3.67
1214 1262 0.320771 CCCACTGGAAGACGACTTGG 60.321 60.000 4.51 0.02 37.43 3.61
1310 1358 3.603697 ACCTTCTCCTCTTTCTCCCTTT 58.396 45.455 0.00 0.00 0.00 3.11
1357 1405 8.506168 TTCTTCTTACTGCTTTTCTTCTTGAA 57.494 30.769 0.00 0.00 0.00 2.69
1416 1464 1.550524 TCTAATCTGCGTGCAAGGTCT 59.449 47.619 0.79 0.00 0.00 3.85
1473 1521 3.182967 CGACACTAGCATGTTCTTCTCC 58.817 50.000 0.00 0.00 31.24 3.71
1537 1585 1.075482 CAAGCTTGGCCTCCTCCAA 59.925 57.895 19.14 0.00 43.36 3.53
1586 1634 0.536006 AGAGGACAGTGCAACCAAGC 60.536 55.000 0.00 0.00 37.80 4.01
1613 1661 0.543749 ATTCCTGGCTGGCTGTCTAC 59.456 55.000 5.39 0.00 35.26 2.59
2103 2151 1.832883 TGGCTTCATTAACCGCATGT 58.167 45.000 0.00 0.00 0.00 3.21
2307 2355 2.033194 CGAGGTTTTGGCCGACTCC 61.033 63.158 0.00 0.90 0.00 3.85
2730 2787 1.129058 CCCCTAGAAACTATGCCGGT 58.871 55.000 1.90 0.00 0.00 5.28
2734 2791 2.945668 CAAGCACCCCTAGAAACTATGC 59.054 50.000 0.00 0.00 0.00 3.14
3167 3225 4.507710 TGCTAGGTTTCTGCATTAGTCTG 58.492 43.478 0.00 0.00 0.00 3.51
3340 3398 6.045106 ACAAGGAGGTTTAGAACTGGGAAATA 59.955 38.462 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.