Multiple sequence alignment - TraesCS3D01G193000

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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 TraesCS3D01G193000 chr3D 100.000 2416 0 0 1 2416 183136779 183134364 0.000000e+00 4462.0
1 TraesCS3D01G193000 chr3D 86.047 86 8 1 1574 1655 585175007 585174922 3.310000e-14 89.8
2 TraesCS3D01G193000 chr3A 93.917 2433 112 26 1 2416 233024159 233021746 0.000000e+00 3640.0
3 TraesCS3D01G193000 chr3A 83.951 81 9 2 1575 1655 430527808 430527884 9.260000e-10 75.0
4 TraesCS3D01G193000 chr3B 93.883 1602 82 10 561 2149 262079442 262077844 0.000000e+00 2401.0
5 TraesCS3D01G193000 chr3B 95.028 362 13 2 167 526 262080392 262080034 4.510000e-157 564.0
6 TraesCS3D01G193000 chr3B 90.945 254 20 3 2166 2416 262077857 262077604 2.980000e-89 339.0
7 TraesCS3D01G193000 chr3B 89.937 159 2 4 1 155 262081315 262081167 2.450000e-45 193.0
8 TraesCS3D01G193000 chr5B 86.047 86 9 2 1570 1655 315165269 315165351 3.310000e-14 89.8
9 TraesCS3D01G193000 chr2D 83.908 87 9 4 1574 1655 378756779 378756865 7.160000e-11 78.7
10 TraesCS3D01G193000 chr6D 85.526 76 7 2 1580 1655 32062234 32062163 2.580000e-10 76.8
11 TraesCS3D01G193000 chr6D 84.416 77 8 2 1580 1656 32062163 32062235 3.330000e-09 73.1
12 TraesCS3D01G193000 chr6D 82.558 86 10 3 1575 1655 28336608 28336693 1.200000e-08 71.3
13 TraesCS3D01G193000 chr1B 97.143 35 1 0 1360 1394 645519335 645519301 2.590000e-05 60.2


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 TraesCS3D01G193000 chr3D 183134364 183136779 2415 True 4462.00 4462 100.00000 1 2416 1 chr3D.!!$R1 2415
1 TraesCS3D01G193000 chr3A 233021746 233024159 2413 True 3640.00 3640 93.91700 1 2416 1 chr3A.!!$R1 2415
2 TraesCS3D01G193000 chr3B 262077604 262081315 3711 True 874.25 2401 92.44825 1 2416 4 chr3B.!!$R1 2415

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
526 1517 1.607148 CACACGCCTATCGGATCTGTA 59.393 52.381 0.42 0.0 43.86 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 3195 1.464734 AAGGAGAAGAGATGCGACGA 58.535 50.0 0.0 0.0 0.0 4.2 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
146 151 4.021456 TCGACCGCCACATATGATCTTAAT 60.021 41.667 10.38 0.00 0.00 1.40
149 154 6.367695 CGACCGCCACATATGATCTTAATTAA 59.632 38.462 10.38 0.00 0.00 1.40
150 155 7.435068 ACCGCCACATATGATCTTAATTAAC 57.565 36.000 10.38 0.00 0.00 2.01
151 156 7.224297 ACCGCCACATATGATCTTAATTAACT 58.776 34.615 10.38 0.00 0.00 2.24
152 157 7.719633 ACCGCCACATATGATCTTAATTAACTT 59.280 33.333 10.38 0.00 0.00 2.66
153 158 8.017373 CCGCCACATATGATCTTAATTAACTTG 58.983 37.037 10.38 0.00 0.00 3.16
215 986 3.060003 GTCATCGCCATTGAAGAATCTCG 60.060 47.826 0.00 0.00 0.00 4.04
447 1220 4.739716 GCCAATATTAACGAACATGCTTGG 59.260 41.667 4.44 0.00 34.99 3.61
526 1517 1.607148 CACACGCCTATCGGATCTGTA 59.393 52.381 0.42 0.00 43.86 2.74
557 1548 2.805671 TCACACGCCACAAAACTAGATG 59.194 45.455 0.00 0.00 0.00 2.90
828 2169 2.061773 CTAGTGTGCTCGTTTGACCTG 58.938 52.381 0.00 0.00 0.00 4.00
977 2324 6.483640 GTGATAAGCTTCTCGGTCCATTAATT 59.516 38.462 0.00 0.00 0.00 1.40
986 2333 2.419574 CGGTCCATTAATTGGTCGACCT 60.420 50.000 33.39 17.54 46.52 3.85
1061 2408 1.970352 CTGGCCTTCCTCTCCTGCTC 61.970 65.000 3.32 0.00 0.00 4.26
1091 2438 2.144730 CCACGGTTTGTACGGATTGAA 58.855 47.619 0.00 0.00 35.23 2.69
1101 2448 3.430895 TGTACGGATTGAACGAGCTTTTC 59.569 43.478 0.00 0.00 34.93 2.29
1307 2655 2.509569 GTCGGAGGAGAGATGCATCTA 58.490 52.381 28.78 8.33 37.25 1.98
1522 2874 4.391216 GCATATCAGCACCATGTAGCTAAG 59.609 45.833 8.59 0.00 39.50 2.18
1538 2890 8.543862 TGTAGCTAAGCATCATGATCTTAATG 57.456 34.615 19.34 13.71 0.00 1.90
1686 3040 5.670361 TCCCTGTAGCTTGGGATTAAGTATT 59.330 40.000 15.24 0.00 46.69 1.89
1687 3041 5.765182 CCCTGTAGCTTGGGATTAAGTATTG 59.235 44.000 12.24 0.00 46.15 1.90
1690 3044 7.012421 CCTGTAGCTTGGGATTAAGTATTGTTC 59.988 40.741 0.00 0.00 0.00 3.18
1704 3058 5.595885 AGTATTGTTCCATCTCTGTCATCG 58.404 41.667 0.00 0.00 0.00 3.84
1840 3195 3.706373 ACGAGCGCTCATTGGGGT 61.706 61.111 34.69 21.09 42.09 4.95
1843 3198 3.665675 GAGCGCTCATTGGGGTCGT 62.666 63.158 31.91 0.00 44.04 4.34
1863 3218 4.098044 TCGTCGCATCTCTTCTCCTTTTAT 59.902 41.667 0.00 0.00 0.00 1.40
1896 3251 8.408601 CCACTAATCTCATCCACCTTTATTTTG 58.591 37.037 0.00 0.00 0.00 2.44
1911 3266 7.232534 ACCTTTATTTTGACTAGTTGAATGCCA 59.767 33.333 0.00 0.00 0.00 4.92
1931 3286 3.119029 CCAGTGGTTGCCATGGAATAAAG 60.119 47.826 18.40 0.00 35.61 1.85
2000 3355 3.896888 ACATGACACATGTGGTTTCCATT 59.103 39.130 28.64 5.90 35.28 3.16
2009 3364 7.395772 ACACATGTGGTTTCCATTCATATAACA 59.604 33.333 28.64 0.00 35.28 2.41
2059 3414 5.607477 TCGTGTCTCTTTAACCAACATCTT 58.393 37.500 0.00 0.00 0.00 2.40
2079 3434 9.136323 ACATCTTTCCTTGTAAGAAGACAAAAT 57.864 29.630 0.00 0.00 38.80 1.82
2132 3487 3.802948 TCCTTCTACCTTCATTCTCGC 57.197 47.619 0.00 0.00 0.00 5.03
2215 3570 8.438676 ACTTCCATCCTATCAAAATCTTTACG 57.561 34.615 0.00 0.00 0.00 3.18
2300 3657 6.707440 TTGTTGTGAATTGCCTAGAAAAGA 57.293 33.333 0.00 0.00 0.00 2.52
2335 3692 6.311055 AGTGTGATCTTTCTCTTGCTTTTC 57.689 37.500 0.00 0.00 0.00 2.29
2396 3753 4.639171 CAAACGCGGTGCCCAACC 62.639 66.667 12.47 0.00 46.60 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.058817 CTCTTTAGTCCTCGTGTGCTTTT 58.941 43.478 0.00 0.00 0.00 2.27
146 151 2.334977 TGCTGAGTCCTCCCAAGTTAA 58.665 47.619 0.00 0.00 0.00 2.01
149 154 1.004044 CATTGCTGAGTCCTCCCAAGT 59.996 52.381 0.00 0.00 0.00 3.16
150 155 1.280133 TCATTGCTGAGTCCTCCCAAG 59.720 52.381 0.00 0.00 0.00 3.61
151 156 1.361204 TCATTGCTGAGTCCTCCCAA 58.639 50.000 0.00 0.00 0.00 4.12
152 157 1.211212 CATCATTGCTGAGTCCTCCCA 59.789 52.381 0.00 0.00 34.12 4.37
153 158 1.964552 CATCATTGCTGAGTCCTCCC 58.035 55.000 0.00 0.00 34.12 4.30
196 967 2.868583 CACGAGATTCTTCAATGGCGAT 59.131 45.455 0.00 0.00 0.00 4.58
215 986 3.390135 TGTGTCCTTGTCTCGATTTCAC 58.610 45.455 0.00 0.00 0.00 3.18
526 1517 1.815421 GGCGTGTGAGATTCGGCAT 60.815 57.895 5.57 0.00 46.44 4.40
557 1548 1.419374 ACACGTTTCATCGAGCTGAC 58.581 50.000 0.00 0.00 34.70 3.51
768 2104 1.580845 GCACTGAGCGCCAGAAATGT 61.581 55.000 26.07 7.23 45.78 2.71
828 2169 4.530857 CGAGGGTCACATCGGCCC 62.531 72.222 0.00 0.00 42.64 5.80
906 2253 4.771684 GCAAGCACTGGTATTGCG 57.228 55.556 6.95 0.00 45.15 4.85
986 2333 1.296392 CCCATCTTCACCAGACGCA 59.704 57.895 0.00 0.00 32.83 5.24
1061 2408 3.546714 AAACCGTGGGCGAGGAAGG 62.547 63.158 0.00 0.00 41.33 3.46
1307 2655 2.282251 TCGTCGTCCCTCAGCAGT 60.282 61.111 0.00 0.00 0.00 4.40
1316 2664 0.179134 CCAACATCTCCTCGTCGTCC 60.179 60.000 0.00 0.00 0.00 4.79
1538 2890 9.023967 CCAAAGATGCATAAACTAGCAAATTAC 57.976 33.333 0.00 0.00 44.88 1.89
1667 3021 6.826741 TGGAACAATACTTAATCCCAAGCTAC 59.173 38.462 0.00 0.00 31.92 3.58
1687 3041 4.047822 GTGATCGATGACAGAGATGGAAC 58.952 47.826 10.32 0.00 0.00 3.62
1690 3044 2.627221 AGGTGATCGATGACAGAGATGG 59.373 50.000 16.93 0.00 0.00 3.51
1840 3195 1.464734 AAGGAGAAGAGATGCGACGA 58.535 50.000 0.00 0.00 0.00 4.20
1843 3198 7.726216 TGAATATAAAAGGAGAAGAGATGCGA 58.274 34.615 0.00 0.00 0.00 5.10
1863 3218 6.789457 AGGTGGATGAGATTAGTGGATGAATA 59.211 38.462 0.00 0.00 0.00 1.75
1881 3236 8.934023 TTCAACTAGTCAAAATAAAGGTGGAT 57.066 30.769 0.00 0.00 0.00 3.41
1896 3251 3.059352 ACCACTGGCATTCAACTAGTC 57.941 47.619 0.00 0.00 0.00 2.59
1911 3266 4.046286 TCTTTATTCCATGGCAACCACT 57.954 40.909 6.96 0.00 35.80 4.00
1967 3322 6.292328 CCACATGTGTCATGTTCGACATATAC 60.292 42.308 23.79 0.00 46.98 1.47
2009 3364 9.767228 TGATTGTCAAGAATGAATCAATTTGTT 57.233 25.926 0.00 0.00 37.30 2.83
2037 3392 5.924475 AAGATGTTGGTTAAAGAGACACG 57.076 39.130 0.00 0.00 0.00 4.49
2079 3434 8.151596 GGATGGTTTGGGTTTGAAAAGTTATTA 58.848 33.333 0.00 0.00 0.00 0.98
2086 3441 3.388913 AGGGATGGTTTGGGTTTGAAAA 58.611 40.909 0.00 0.00 0.00 2.29
2096 3451 4.411013 AGAAGGAAAAGAGGGATGGTTTG 58.589 43.478 0.00 0.00 0.00 2.93
2103 3458 4.499472 TGAAGGTAGAAGGAAAAGAGGGA 58.501 43.478 0.00 0.00 0.00 4.20
2132 3487 5.902613 TTTGAAAAGATGGCTCATAGTGG 57.097 39.130 0.00 0.00 0.00 4.00
2178 3533 9.488762 TGATAGGATGGAAGTAAAGTCTTCTAA 57.511 33.333 6.44 0.00 42.19 2.10
2179 3534 9.488762 TTGATAGGATGGAAGTAAAGTCTTCTA 57.511 33.333 6.44 1.49 42.19 2.10
2240 3597 8.477419 TTCCATTTTTATGGTGGAGATAATCC 57.523 34.615 4.24 0.00 42.54 3.01


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

AutoCloner maintained by Alex Coulton.