Multiple sequence alignment - TraesCS4D01G043300

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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 TraesCS4D01G043300 chr4D 100.000 2222 0 0 1 2222 19916788 19919009 0.000000e+00 4104
1 TraesCS4D01G043300 chr5D 97.258 2225 57 4 1 2221 560872761 560874985 0.000000e+00 3768
2 TraesCS4D01G043300 chr5D 95.506 2225 73 9 1 2221 6200988 6198787 0.000000e+00 3530
3 TraesCS4D01G043300 chr5D 96.368 2065 67 8 1 2061 329162470 329164530 0.000000e+00 3391
4 TraesCS4D01G043300 chr1D 96.897 2224 66 3 1 2221 254498291 254500514 0.000000e+00 3722
5 TraesCS4D01G043300 chr1D 90.889 1822 115 29 1 1813 244483756 244481977 0.000000e+00 2398
6 TraesCS4D01G043300 chr1A 95.638 2224 88 8 1 2222 168450274 168448058 0.000000e+00 3561
7 TraesCS4D01G043300 chr7A 93.795 2224 128 10 3 2221 352193729 352191511 0.000000e+00 3334
8 TraesCS4D01G043300 chr3B 96.663 1618 47 7 608 2221 201515580 201517194 0.000000e+00 2682
9 TraesCS4D01G043300 chr3B 93.300 1000 51 7 1223 2221 524777564 524776580 0.000000e+00 1461
10 TraesCS4D01G043300 chr6B 95.286 1188 52 4 1 1185 22426237 22427423 0.000000e+00 1881
11 TraesCS4D01G043300 chrUn 96.967 1055 28 4 233 1284 445812538 445811485 0.000000e+00 1768
12 TraesCS4D01G043300 chrUn 97.422 737 17 2 1486 2221 439559440 439558705 0.000000e+00 1254
13 TraesCS4D01G043300 chr2B 88.725 204 17 4 1223 1421 799021656 799021454 6.130000e-61 244
14 TraesCS4D01G043300 chr2B 94.505 91 5 0 1379 1469 756060882 756060972 8.270000e-30 141


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 TraesCS4D01G043300 chr4D 19916788 19919009 2221 False 4104 4104 100.000 1 2222 1 chr4D.!!$F1 2221
1 TraesCS4D01G043300 chr5D 560872761 560874985 2224 False 3768 3768 97.258 1 2221 1 chr5D.!!$F2 2220
2 TraesCS4D01G043300 chr5D 6198787 6200988 2201 True 3530 3530 95.506 1 2221 1 chr5D.!!$R1 2220
3 TraesCS4D01G043300 chr5D 329162470 329164530 2060 False 3391 3391 96.368 1 2061 1 chr5D.!!$F1 2060
4 TraesCS4D01G043300 chr1D 254498291 254500514 2223 False 3722 3722 96.897 1 2221 1 chr1D.!!$F1 2220
5 TraesCS4D01G043300 chr1D 244481977 244483756 1779 True 2398 2398 90.889 1 1813 1 chr1D.!!$R1 1812
6 TraesCS4D01G043300 chr1A 168448058 168450274 2216 True 3561 3561 95.638 1 2222 1 chr1A.!!$R1 2221
7 TraesCS4D01G043300 chr7A 352191511 352193729 2218 True 3334 3334 93.795 3 2221 1 chr7A.!!$R1 2218
8 TraesCS4D01G043300 chr3B 201515580 201517194 1614 False 2682 2682 96.663 608 2221 1 chr3B.!!$F1 1613
9 TraesCS4D01G043300 chr3B 524776580 524777564 984 True 1461 1461 93.300 1223 2221 1 chr3B.!!$R1 998
10 TraesCS4D01G043300 chr6B 22426237 22427423 1186 False 1881 1881 95.286 1 1185 1 chr6B.!!$F1 1184
11 TraesCS4D01G043300 chrUn 445811485 445812538 1053 True 1768 1768 96.967 233 1284 1 chrUn.!!$R2 1051
12 TraesCS4D01G043300 chrUn 439558705 439559440 735 True 1254 1254 97.422 1486 2221 1 chrUn.!!$R1 735

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
193 194 0.831307 GAGGCGGTCTCAATTAGGGT 59.169 55.000 4.4 0.0 42.02 4.34 F
230 231 1.267806 CCGTGCTGCTTTGAAATCTGT 59.732 47.619 0.0 0.0 0.00 3.41 F
231 232 2.313234 CGTGCTGCTTTGAAATCTGTG 58.687 47.619 0.0 0.0 0.00 3.66 F
1103 1107 1.217942 GGAATATGGGAAAGTGGCCCT 59.782 52.381 0.0 0.0 46.19 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1038 1042 0.030638 CTGCACCAGTTCGTTTTGGG 59.969 55.000 6.75 0.0 38.82 4.12 R
1103 1107 1.850755 GGAGAAGTCCCCCAACCCA 60.851 63.158 0.00 0.0 36.76 4.51 R
1117 1121 2.123589 TGCGATCCCCATAAAAGGAGA 58.876 47.619 0.00 0.0 35.08 3.71 R
2103 2113 7.910162 CGTTCCTCAAACCAATCATATACTTTG 59.090 37.037 0.00 0.0 34.11 2.77 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
193 194 0.831307 GAGGCGGTCTCAATTAGGGT 59.169 55.000 4.40 0.00 42.02 4.34
213 214 7.770366 AGGGTAAATTTTTGAATTAGACCGT 57.230 32.000 0.00 0.00 32.87 4.83
217 218 7.061789 GGTAAATTTTTGAATTAGACCGTGCTG 59.938 37.037 0.00 0.00 0.00 4.41
230 231 1.267806 CCGTGCTGCTTTGAAATCTGT 59.732 47.619 0.00 0.00 0.00 3.41
231 232 2.313234 CGTGCTGCTTTGAAATCTGTG 58.687 47.619 0.00 0.00 0.00 3.66
241 242 6.045955 GCTTTGAAATCTGTGGGTGTTTTTA 58.954 36.000 0.00 0.00 0.00 1.52
300 301 4.455877 GCTACCTTTGCTTTGCTCTTCTTA 59.544 41.667 0.00 0.00 0.00 2.10
342 343 3.250744 CGCTAGAACATTGTTCCGAGAA 58.749 45.455 22.70 6.09 0.00 2.87
393 394 5.279156 GGATGCTCAAGTTGAATTTGGAACT 60.279 40.000 7.06 0.00 33.75 3.01
862 866 6.433093 CCCAGTAAAGCTTACAAGTAAACCAT 59.567 38.462 0.00 0.00 0.00 3.55
886 890 3.247006 TGGAGATGGCGACTAAAGTTC 57.753 47.619 0.00 0.00 0.00 3.01
935 939 9.613428 TCAAGATTACAATGGATCTACGAAAAT 57.387 29.630 0.00 0.00 32.52 1.82
1038 1042 6.476053 CCGTTGAAGATAGTTCTAAACCTAGC 59.524 42.308 0.00 0.00 30.38 3.42
1098 1102 6.449635 TTGAATTCGGAATATGGGAAAGTG 57.550 37.500 3.22 0.00 0.00 3.16
1103 1107 1.217942 GGAATATGGGAAAGTGGCCCT 59.782 52.381 0.00 0.00 46.19 5.19
1117 1121 2.863988 CCCTGGGTTGGGGGACTT 60.864 66.667 3.97 0.00 45.18 3.01
1141 1145 2.288395 CCTTTTATGGGGATCGCAATGC 60.288 50.000 12.32 0.00 0.00 3.56
1320 1324 7.164122 TCTAGATATTATGGTAGTTCGACCGT 58.836 38.462 0.00 2.73 42.99 4.83
1326 1331 2.445427 TGGTAGTTCGACCGTGGAATA 58.555 47.619 0.00 0.00 42.99 1.75
1557 1563 9.657121 CAGACTGAAAAATTCAAGTAGTTCTTC 57.343 33.333 0.00 0.00 39.58 2.87
1607 1614 7.112779 TCCTTCTAATTTTGTTTGCCCAAAAA 58.887 30.769 9.24 0.00 44.76 1.94
1710 1718 4.442753 CCCTTGCCTTTTGTTTAGCTTGAA 60.443 41.667 0.00 0.00 0.00 2.69
1727 1735 4.662145 CTTGAAACTAAATCATCGTGGCC 58.338 43.478 0.00 0.00 0.00 5.36
2082 2091 1.110518 CGGCTCTTAGAGGGGGACTC 61.111 65.000 11.54 0.00 46.98 3.36
2192 2202 1.202879 TGTTCCTCCCCATGTCAACAC 60.203 52.381 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 6.444704 TCTAACAATTCCCTCCTCATCTACT 58.555 40.000 0.00 0.00 0.00 2.57
193 194 6.584563 GCAGCACGGTCTAATTCAAAAATTTA 59.415 34.615 0.00 0.00 36.49 1.40
213 214 1.614903 CCCACAGATTTCAAAGCAGCA 59.385 47.619 0.00 0.00 0.00 4.41
217 218 3.733443 AACACCCACAGATTTCAAAGC 57.267 42.857 0.00 0.00 0.00 3.51
230 231 1.953686 GACTGCTGCTAAAAACACCCA 59.046 47.619 0.00 0.00 0.00 4.51
231 232 1.269723 GGACTGCTGCTAAAAACACCC 59.730 52.381 0.00 0.00 0.00 4.61
241 242 2.464403 AACCCCTTGGACTGCTGCT 61.464 57.895 0.00 0.00 34.81 4.24
300 301 1.477700 CCATGCCAAATGTGTCCGAAT 59.522 47.619 0.00 0.00 0.00 3.34
342 343 5.649782 CTGGATCAATACCAGCAAAAACT 57.350 39.130 0.00 0.00 46.30 2.66
475 476 5.665916 GGAGATGTTTCCCATGTCAAATT 57.334 39.130 2.49 0.00 43.82 1.82
588 590 4.527509 TGCTTCCATAGATTCGATCCTC 57.472 45.455 0.00 0.00 0.00 3.71
862 866 6.295123 GGAACTTTAGTCGCCATCTCCATATA 60.295 42.308 0.00 0.00 0.00 0.86
935 939 6.096141 TCCGTTGTAGTTGTAAATACCCGATA 59.904 38.462 10.71 0.95 0.00 2.92
940 944 8.707938 ACTATTCCGTTGTAGTTGTAAATACC 57.292 34.615 0.49 0.00 0.00 2.73
1038 1042 0.030638 CTGCACCAGTTCGTTTTGGG 59.969 55.000 6.75 0.00 38.82 4.12
1103 1107 1.850755 GGAGAAGTCCCCCAACCCA 60.851 63.158 0.00 0.00 36.76 4.51
1117 1121 2.123589 TGCGATCCCCATAAAAGGAGA 58.876 47.619 0.00 0.00 35.08 3.71
1320 1324 8.673711 CAGAGATACCGAAACAAAAATATTCCA 58.326 33.333 0.00 0.00 0.00 3.53
1326 1331 7.703058 ATTCCAGAGATACCGAAACAAAAAT 57.297 32.000 0.00 0.00 0.00 1.82
1411 1416 9.689976 CTGACGAATTAGAATCATCTTGATAGT 57.310 33.333 0.00 0.00 35.76 2.12
1710 1718 3.454812 ACTAGGGCCACGATGATTTAGTT 59.545 43.478 6.18 0.00 0.00 2.24
2103 2113 7.910162 CGTTCCTCAAACCAATCATATACTTTG 59.090 37.037 0.00 0.00 34.11 2.77
2192 2202 9.594478 GTGTAATTCCCCCTAAACAATAAAATG 57.406 33.333 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.