Multiple sequence alignment - TraesCS4D01G274600

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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 TraesCS4D01G274600 chr4D 100.000 2459 0 0 1 2459 444884456 444886914 0.000000e+00 4542.0
1 TraesCS4D01G274600 chr4D 94.118 204 10 2 1 203 444877683 444877885 2.370000e-80 309.0
2 TraesCS4D01G274600 chr4D 89.320 103 9 1 2221 2323 444886322 444886422 7.140000e-26 128.0
3 TraesCS4D01G274600 chr4D 89.320 103 9 1 1867 1967 444886676 444886778 7.140000e-26 128.0
4 TraesCS4D01G274600 chr4B 94.192 2066 95 12 409 2459 555215171 555213116 0.000000e+00 3127.0
5 TraesCS4D01G274600 chr4B 92.329 1108 72 8 409 1505 555539690 555538585 0.000000e+00 1563.0
6 TraesCS4D01G274600 chr4B 92.865 897 59 4 1508 2402 555515806 555514913 0.000000e+00 1297.0
7 TraesCS4D01G274600 chr4B 92.019 426 31 3 1 425 555540903 555540480 1.630000e-166 595.0
8 TraesCS4D01G274600 chr4B 91.080 426 34 4 1 425 555216447 555216025 7.630000e-160 573.0
9 TraesCS4D01G274600 chr4B 93.772 289 18 0 2151 2439 555514981 555514693 3.760000e-118 435.0
10 TraesCS4D01G274600 chr4B 90.291 103 10 0 2221 2323 555213702 555213600 4.270000e-28 135.0
11 TraesCS4D01G274600 chr4B 89.320 103 9 1 1867 1967 555514911 555514809 7.140000e-26 128.0
12 TraesCS4D01G274600 chr4B 89.320 103 9 1 1867 1967 555515094 555514992 7.140000e-26 128.0
13 TraesCS4D01G274600 chr4B 87.500 104 9 2 1867 1968 555213351 555213250 1.540000e-22 117.0
14 TraesCS4D01G274600 chr4A 95.766 1110 41 4 503 1608 22082535 22083642 0.000000e+00 1784.0
15 TraesCS4D01G274600 chr4A 89.793 676 52 5 1800 2459 22085463 22086137 0.000000e+00 850.0
16 TraesCS4D01G274600 chr4A 95.322 171 7 1 1642 1812 22083639 22083808 1.120000e-68 270.0
17 TraesCS4D01G274600 chr4A 90.576 191 17 1 219 409 22080430 22080619 4.060000e-63 252.0
18 TraesCS4D01G274600 chr4A 85.034 147 22 0 1988 2134 713615192 713615338 1.520000e-32 150.0
19 TraesCS4D01G274600 chr4A 90.110 91 8 1 432 521 22081939 22082029 1.540000e-22 117.0
20 TraesCS4D01G274600 chr4A 88.889 63 7 0 2065 2127 650409491 650409553 7.290000e-11 78.7
21 TraesCS4D01G274600 chr1A 86.014 143 20 0 1988 2130 360461048 360461190 1.180000e-33 154.0
22 TraesCS4D01G274600 chr7D 88.889 63 7 0 2065 2127 42900840 42900902 7.290000e-11 78.7


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 TraesCS4D01G274600 chr4D 444884456 444886914 2458 False 1599.333333 4542 92.88000 1 2459 3 chr4D.!!$F2 2458
1 TraesCS4D01G274600 chr4B 555538585 555540903 2318 True 1079.000000 1563 92.17400 1 1505 2 chr4B.!!$R3 1504
2 TraesCS4D01G274600 chr4B 555213116 555216447 3331 True 988.000000 3127 90.76575 1 2459 4 chr4B.!!$R1 2458
3 TraesCS4D01G274600 chr4B 555514693 555515806 1113 True 497.000000 1297 91.31925 1508 2439 4 chr4B.!!$R2 931
4 TraesCS4D01G274600 chr4A 22080430 22086137 5707 False 654.600000 1784 92.31340 219 2459 5 chr4A.!!$F3 2240

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
905 3276 0.178068 GGCAAGGAAGGCATACTCGA 59.822 55.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2145 6192 0.499147 TGGGGTTCCTTCCCTCCTTA 59.501 55.0 1.72 0.0 46.27 2.69 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
24 25 7.741554 AGGAGGTAGAGTTGTGAATTAAGAT 57.258 36.000 0.00 0.00 0.00 2.40
79 80 8.234546 GCGAAGAAGAAACAAGGACAATAATTA 58.765 33.333 0.00 0.00 0.00 1.40
239 241 4.051922 GGAATACCTAGAGTTGCATCACG 58.948 47.826 0.00 0.00 0.00 4.35
344 346 7.672983 TGTACCAATCTGAAGAAAGATGAAC 57.327 36.000 0.00 0.00 36.99 3.18
345 347 7.453393 TGTACCAATCTGAAGAAAGATGAACT 58.547 34.615 0.00 0.00 36.99 3.01
404 406 5.078949 TGTGAAAATTCCTCCATGACACAT 58.921 37.500 0.00 0.00 32.23 3.21
425 427 3.609853 TCTCTGGATTTTGGGATTCACG 58.390 45.455 0.00 0.00 0.00 4.35
489 2326 7.043300 ACCCATAATATGATGCCAATCCTTA 57.957 36.000 1.10 0.00 31.15 2.69
608 2970 1.033574 ACCGGCCTTATCTTCGAGAG 58.966 55.000 0.00 0.00 0.00 3.20
615 2977 2.035632 CTTATCTTCGAGAGGCCACCT 58.964 52.381 5.01 0.11 36.03 4.00
663 3025 2.176314 TAGCAGCACACCAGGCAGAG 62.176 60.000 0.00 0.00 0.00 3.35
713 3075 2.974698 GCGCACCAACACTGCTCT 60.975 61.111 0.30 0.00 32.03 4.09
784 3155 2.919856 CTCATCGATCCCCGGGCT 60.920 66.667 17.73 3.63 39.14 5.19
905 3276 0.178068 GGCAAGGAAGGCATACTCGA 59.822 55.000 0.00 0.00 0.00 4.04
907 3278 1.405526 GCAAGGAAGGCATACTCGACA 60.406 52.381 0.00 0.00 0.00 4.35
945 3317 0.333312 AGGGACAGAGGTGAGATCGT 59.667 55.000 0.00 0.00 0.00 3.73
1158 3530 2.433318 GCGCTCCACTTCTTCGCT 60.433 61.111 0.00 0.00 42.19 4.93
1462 3834 1.423845 GTGGCCGTGCAATAGAACG 59.576 57.895 0.00 0.00 46.65 3.95
1527 3902 5.995282 CACCTAGTCTGAGTCTATCTGGTAG 59.005 48.000 0.00 0.00 0.00 3.18
1805 4182 1.266718 TGTTTGCCAGATTTCGTCAGC 59.733 47.619 0.00 0.00 0.00 4.26
2002 6049 4.141205 GCCTCTTACCTCTTACCTCCTCTA 60.141 50.000 0.00 0.00 0.00 2.43
2058 6105 6.998074 TCCAAGCCGTTGATCTCATTAATTAT 59.002 34.615 0.00 0.00 35.46 1.28
2061 6108 7.206981 AGCCGTTGATCTCATTAATTATTGG 57.793 36.000 7.35 0.45 0.00 3.16
2187 6234 6.316390 CCACGGCTTTGTAATTAAGAGAGAAT 59.684 38.462 0.00 0.00 0.00 2.40
2213 6260 2.357952 GAGACCCAAGTTCAAACACACC 59.642 50.000 0.00 0.00 0.00 4.16
2402 6632 6.989659 ACTCAAGTTCAAACCTACGAGATTA 58.010 36.000 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.868782 CATGAGATCCATCGATGCCATAGCA 62.869 48.000 20.25 12.58 43.44 3.49
33 34 0.972134 ACCGCATGAGATCCATCGAT 59.028 50.000 0.00 0.00 31.94 3.59
36 37 1.563435 CGCACCGCATGAGATCCATC 61.563 60.000 0.00 0.00 31.94 3.51
79 80 7.175104 TGGAAGATAGGTTTTTGCTCTTACAT 58.825 34.615 0.00 0.00 33.06 2.29
87 88 7.611770 AGGTTAAATGGAAGATAGGTTTTTGC 58.388 34.615 0.00 0.00 0.00 3.68
160 162 2.015090 GCCTAACGTATCGAGGCGC 61.015 63.158 13.06 0.00 45.94 6.53
183 185 2.582202 AAAATGTCATGCCGCTCGCG 62.582 55.000 0.00 0.00 42.08 5.87
270 272 6.652245 CCATTTTTGCAAAGTCATGTCTTTC 58.348 36.000 13.97 10.14 35.77 2.62
345 347 9.905713 GTATATGGATAATTCCCTCTTGCATTA 57.094 33.333 0.00 0.00 41.83 1.90
384 386 5.884792 AGAGATGTGTCATGGAGGAATTTTC 59.115 40.000 0.00 0.00 0.00 2.29
404 406 3.609853 CGTGAATCCCAAAATCCAGAGA 58.390 45.455 0.00 0.00 0.00 3.10
425 427 1.336240 GCAACACAGAAATCAGGCACC 60.336 52.381 0.00 0.00 0.00 5.01
489 2326 7.438564 AGGAATTTTATTACGTGCCTTTGTTT 58.561 30.769 0.00 0.00 0.00 2.83
495 2332 7.990886 TGATTCTAGGAATTTTATTACGTGCCT 59.009 33.333 0.00 0.00 0.00 4.75
511 2872 5.178096 TGTGGCATTCTTTGATTCTAGGA 57.822 39.130 0.00 0.00 0.00 2.94
586 2948 2.818432 TCTCGAAGATAAGGCCGGTATC 59.182 50.000 17.39 17.39 33.89 2.24
663 3025 2.551270 CGACGGCAGTGAGTTTGC 59.449 61.111 0.00 0.00 40.80 3.68
713 3075 1.340248 GGACGGCGATAGGATGAAGAA 59.660 52.381 16.62 0.00 0.00 2.52
784 3155 2.640826 AGTGACGTGGGGGAAAGATAAA 59.359 45.455 0.00 0.00 0.00 1.40
905 3276 1.344763 CTCTTCCGGTTCCTCTGTTGT 59.655 52.381 0.00 0.00 0.00 3.32
907 3278 1.896465 CTCTCTTCCGGTTCCTCTGTT 59.104 52.381 0.00 0.00 0.00 3.16
945 3317 1.164662 CCGACGAGCTCCGAATCCTA 61.165 60.000 13.15 0.00 41.76 2.94
1206 3578 2.203182 ACCTTGACGACCCCAGGA 59.797 61.111 0.00 0.00 0.00 3.86
1209 3581 2.446994 ACCACCTTGACGACCCCA 60.447 61.111 0.00 0.00 0.00 4.96
1396 3768 1.376424 CATTGCAGCACCTCCGAGT 60.376 57.895 0.00 0.00 0.00 4.18
1462 3834 1.673808 CGCTCACTAGTACCCCACCC 61.674 65.000 0.00 0.00 0.00 4.61
1494 3866 5.126384 AGACTCAGACTAGGTGAGCAATTAC 59.874 44.000 19.32 8.27 44.60 1.89
1505 3877 6.042781 AGACTACCAGATAGACTCAGACTAGG 59.957 46.154 0.00 0.00 31.19 3.02
1527 3902 2.789409 ATGGCAAGGAGTAACCAGAC 57.211 50.000 0.00 0.00 42.04 3.51
1676 4052 6.036735 GCATTCACATTTGATTCCATGGAAAG 59.963 38.462 30.28 17.20 37.69 2.62
1818 5862 7.495279 TGCATAATTCCTATTTGCAATTGAACC 59.505 33.333 10.34 0.00 36.14 3.62
1909 5953 0.770557 AGGTGGGGAGTAAAGGCACA 60.771 55.000 0.00 0.00 0.00 4.57
2035 6082 7.592533 CCAATAATTAATGAGATCAACGGCTTG 59.407 37.037 1.92 0.00 0.00 4.01
2036 6083 7.651808 CCAATAATTAATGAGATCAACGGCTT 58.348 34.615 1.92 0.00 0.00 4.35
2081 6128 8.335532 CCTCATCTTTTTACATGTGAGGTAAA 57.664 34.615 9.11 0.00 44.75 2.01
2145 6192 0.499147 TGGGGTTCCTTCCCTCCTTA 59.501 55.000 1.72 0.00 46.27 2.69
2146 6193 1.140772 GTGGGGTTCCTTCCCTCCTT 61.141 60.000 1.72 0.00 46.27 3.36
2163 6210 6.721571 TTCTCTCTTAATTACAAAGCCGTG 57.278 37.500 0.00 0.00 0.00 4.94
2187 6234 4.819630 GTGTTTGAACTTGGGTCTCACATA 59.180 41.667 0.00 0.00 0.00 2.29
2213 6260 9.282247 CGAATGAAAGAGGTTAGATTCAATTTG 57.718 33.333 0.00 0.00 35.62 2.32
2402 6632 4.223144 GGGGTCATTTGGCTATATTGGTT 58.777 43.478 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.