Multiple sequence alignment - TraesCS5D01G321000

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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 TraesCS5D01G321000 chr5D 100.000 3324 0 0 1 3324 413060074 413056751 0.000000e+00 6139.0
1 TraesCS5D01G321000 chr5D 82.456 228 37 2 1086 1310 352219226 352219453 2.620000e-46 196.0
2 TraesCS5D01G321000 chr5D 77.828 221 42 7 1094 1312 558247775 558247560 2.690000e-26 130.0
3 TraesCS5D01G321000 chr5D 83.200 125 11 5 89 204 529218187 529218310 4.540000e-19 106.0
4 TraesCS5D01G321000 chr5D 81.967 122 14 4 90 204 361672105 361671985 2.730000e-16 97.1
5 TraesCS5D01G321000 chr5A 92.620 3198 115 42 203 3323 525080162 525077009 0.000000e+00 4486.0
6 TraesCS5D01G321000 chr5A 82.805 221 35 2 1086 1303 453877134 453876914 9.410000e-46 195.0
7 TraesCS5D01G321000 chr5A 93.258 89 4 2 24 112 525081431 525081345 2.690000e-26 130.0
8 TraesCS5D01G321000 chr5A 92.000 50 4 0 18 67 566793513 566793464 1.650000e-08 71.3
9 TraesCS5D01G321000 chr5B 93.039 2988 116 47 208 3126 497758866 497755902 0.000000e+00 4281.0
10 TraesCS5D01G321000 chr5B 82.805 221 35 2 1086 1303 416851154 416850934 9.410000e-46 195.0
11 TraesCS5D01G321000 chr5B 91.241 137 7 4 1 132 497759219 497759083 7.330000e-42 182.0
12 TraesCS5D01G321000 chr2B 83.077 195 31 2 1113 1306 146442441 146442248 3.410000e-40 176.0
13 TraesCS5D01G321000 chr2A 83.077 195 31 2 1113 1306 92318255 92318062 3.410000e-40 176.0
14 TraesCS5D01G321000 chr1B 82.292 192 28 6 1114 1302 595176892 595177080 9.540000e-36 161.0
15 TraesCS5D01G321000 chr1A 82.292 192 28 6 1114 1302 535312154 535312342 9.540000e-36 161.0
16 TraesCS5D01G321000 chr1D 80.628 191 33 4 1114 1302 439022280 439022468 9.610000e-31 145.0
17 TraesCS5D01G321000 chr1D 79.487 117 12 6 98 204 449819561 449819447 4.600000e-09 73.1
18 TraesCS5D01G321000 chr7D 89.109 101 11 0 1429 1529 256444267 256444167 3.480000e-25 126.0
19 TraesCS5D01G321000 chr7B 89.109 101 11 0 1429 1529 235449833 235449733 3.480000e-25 126.0
20 TraesCS5D01G321000 chr7B 81.967 122 12 5 92 204 410844344 410844464 9.820000e-16 95.3
21 TraesCS5D01G321000 chr7A 89.109 101 11 0 1429 1529 276185855 276185755 3.480000e-25 126.0
22 TraesCS5D01G321000 chr7A 80.645 124 14 6 90 204 254846608 254846730 1.640000e-13 87.9
23 TraesCS5D01G321000 chr7A 89.286 56 5 1 19 74 671822431 671822377 5.950000e-08 69.4
24 TraesCS5D01G321000 chr6A 92.453 53 4 0 10 62 96982026 96981974 3.560000e-10 76.8
25 TraesCS5D01G321000 chr6D 92.308 52 4 0 10 61 451327916 451327967 1.280000e-09 75.0
26 TraesCS5D01G321000 chr6D 77.869 122 17 4 90 204 211672739 211672621 2.140000e-07 67.6
27 TraesCS5D01G321000 chr4A 92.000 50 4 0 18 67 577058507 577058458 1.650000e-08 71.3
28 TraesCS5D01G321000 chr4A 92.000 50 4 0 18 67 609917706 609917755 1.650000e-08 71.3
29 TraesCS5D01G321000 chr3A 90.741 54 4 1 15 67 491454147 491454200 1.650000e-08 71.3
30 TraesCS5D01G321000 chr4B 77.966 118 17 4 96 204 19758616 19758733 7.700000e-07 65.8
31 TraesCS5D01G321000 chr2D 100.000 35 0 0 170 204 107131981 107132015 7.700000e-07 65.8
32 TraesCS5D01G321000 chr3D 97.143 35 1 0 170 204 583616484 583616450 3.580000e-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 TraesCS5D01G321000 chr5D 413056751 413060074 3323 True 6139.0 6139 100.000 1 3324 1 chr5D.!!$R2 3323
1 TraesCS5D01G321000 chr5A 525077009 525081431 4422 True 2308.0 4486 92.939 24 3323 2 chr5A.!!$R3 3299
2 TraesCS5D01G321000 chr5B 497755902 497759219 3317 True 2231.5 4281 92.140 1 3126 2 chr5B.!!$R2 3125

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
531 1755 0.037326 AGCCATCGAAGTTTCTCGCA 60.037 50.0 0.0 0.0 38.73 5.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2519 3761 0.098376 GGTACGCTCTACCACGACAG 59.902 60.0 0.0 0.0 37.53 3.51 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
83 85 3.055021 GGTCTCTCTTAACCTCCCCTTTG 60.055 52.174 0.00 0.00 32.54 2.77
94 96 1.675641 CCCCTTTGGCTCCAAGTCG 60.676 63.158 1.26 0.00 37.24 4.18
187 1375 7.792374 TTTACATAGTCTGCATTGGAATCTC 57.208 36.000 0.00 0.00 0.00 2.75
205 1395 9.151471 TGGAATCTCTAAAAAGACTTGTATTCG 57.849 33.333 0.00 0.00 0.00 3.34
274 1489 5.347364 CAGAAGATCAGAGAACGTTCTTTCC 59.653 44.000 30.22 18.27 37.73 3.13
426 1650 7.032580 CGCAAAACAAAATCTTATCCATACCA 58.967 34.615 0.00 0.00 0.00 3.25
466 1690 4.478371 CTCGCATCCAGCCTGGCA 62.478 66.667 22.65 0.00 41.38 4.92
531 1755 0.037326 AGCCATCGAAGTTTCTCGCA 60.037 50.000 0.00 0.00 38.73 5.10
538 1762 1.194772 CGAAGTTTCTCGCACTTTCCC 59.805 52.381 0.00 0.00 34.49 3.97
648 1872 1.995066 ACCAGATGCCCATCCGACA 60.995 57.895 4.72 0.00 38.58 4.35
857 2082 2.102588 CCTCCCGTTGGGTATAAGTCTG 59.897 54.545 1.04 0.00 44.74 3.51
1540 2773 3.607370 GAAGGTGGTCCAGTCGGCC 62.607 68.421 0.00 0.00 35.89 6.13
2008 3241 1.153309 CCTGATGCCATCGTGCTCA 60.153 57.895 0.00 0.00 0.00 4.26
2354 3596 0.246635 TGTAGAAGCTTCGAGCACCC 59.753 55.000 20.43 4.18 45.56 4.61
2364 3606 3.495001 GCTTCGAGCACCCACTAATTATC 59.505 47.826 2.53 0.00 41.89 1.75
2538 3780 0.098376 CTGTCGTGGTAGAGCGTACC 59.902 60.000 10.55 10.55 38.07 3.34
2569 3811 2.516225 GGTGCATTCCCGGTAGGC 60.516 66.667 0.00 1.53 35.76 3.93
2604 3846 9.778993 CATTTCATATGCTGTATGTAAATAGCC 57.221 33.333 0.00 0.00 35.36 3.93
2626 3889 2.289945 CCTTCCTGCTTGTGCTAGAAGT 60.290 50.000 14.46 0.00 42.24 3.01
2755 4018 2.026636 GGGTTTGGCGGCCAGATATATA 60.027 50.000 22.59 2.00 33.81 0.86
2756 4019 3.371595 GGGTTTGGCGGCCAGATATATAT 60.372 47.826 22.59 0.00 33.81 0.86
2757 4020 3.627577 GGTTTGGCGGCCAGATATATATG 59.372 47.826 22.59 0.08 33.81 1.78
2761 4024 2.170607 GGCGGCCAGATATATATGGTGT 59.829 50.000 23.89 0.00 41.15 4.16
2839 4105 0.930726 AGGGGTTTGGTTCCAACTCA 59.069 50.000 3.56 0.00 0.00 3.41
2843 4109 3.431626 GGGGTTTGGTTCCAACTCAAAAG 60.432 47.826 3.56 0.00 33.82 2.27
2893 4166 0.108019 GGTCGGTTTGGTCTGGTCTT 59.892 55.000 0.00 0.00 0.00 3.01
2896 4169 1.515521 CGGTTTGGTCTGGTCTTGCC 61.516 60.000 0.00 0.00 37.90 4.52
2949 4272 4.496927 GCGGAATGCGCCCCTTTG 62.497 66.667 8.22 0.00 0.00 2.77
3019 4342 4.680237 CGCTGCGGGTCAGGTGAA 62.680 66.667 15.40 0.00 43.06 3.18
3154 4477 1.840650 AGAGGGACAGCTGCTGTGT 60.841 57.895 37.29 21.95 45.44 3.72
3169 4492 4.111016 TGTCGCTACTCGCCGGTG 62.111 66.667 9.28 9.28 38.27 4.94
3173 4496 3.450115 GCTACTCGCCGGTGGAGT 61.450 66.667 26.27 26.27 46.05 3.85
3174 4497 2.799371 CTACTCGCCGGTGGAGTC 59.201 66.667 26.66 0.00 43.39 3.36
3175 4498 2.753043 TACTCGCCGGTGGAGTCC 60.753 66.667 26.66 0.73 43.39 3.85
3185 4508 3.367743 TGGAGTCCGTTCCGTCCG 61.368 66.667 4.30 0.00 40.27 4.79
3222 4555 3.072468 CGCCGGGGTTCTGGTAGA 61.072 66.667 11.01 0.00 41.53 2.59
3223 4556 2.901042 GCCGGGGTTCTGGTAGAG 59.099 66.667 2.18 0.00 41.53 2.43
3224 4557 1.988406 GCCGGGGTTCTGGTAGAGT 60.988 63.158 2.18 0.00 41.53 3.24
3225 4558 1.898154 CCGGGGTTCTGGTAGAGTG 59.102 63.158 0.00 0.00 34.69 3.51
3226 4559 1.614241 CCGGGGTTCTGGTAGAGTGG 61.614 65.000 0.00 0.00 34.69 4.00
3231 4564 1.275573 GGTTCTGGTAGAGTGGACCAC 59.724 57.143 17.43 17.43 42.15 4.16
3267 4600 4.431416 TGGGTTCTTGCTAGAAACTTCA 57.569 40.909 22.37 12.10 45.59 3.02
3270 4604 3.189495 GGTTCTTGCTAGAAACTTCAGGC 59.811 47.826 17.29 1.28 43.43 4.85
3274 4608 1.003108 GCTAGAAACTTCAGGCGCTC 58.997 55.000 7.64 0.00 0.00 5.03
3301 4635 1.299926 GCGTGACGGAACAGACACT 60.300 57.895 7.25 0.00 35.31 3.55
3302 4636 0.039798 GCGTGACGGAACAGACACTA 60.040 55.000 7.25 0.00 35.31 2.74
3304 4638 1.266175 CGTGACGGAACAGACACTACT 59.734 52.381 0.00 0.00 35.31 2.57
3305 4639 2.287427 CGTGACGGAACAGACACTACTT 60.287 50.000 0.00 0.00 35.31 2.24
3306 4640 3.714391 GTGACGGAACAGACACTACTTT 58.286 45.455 0.00 0.00 34.79 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 85 3.660865 TCTCTAAAAACGACTTGGAGCC 58.339 45.455 0.00 0.00 32.91 4.70
174 1362 7.231317 ACAAGTCTTTTTAGAGATTCCAATGCA 59.769 33.333 0.00 0.00 0.00 3.96
187 1375 8.818057 CCACTATCCGAATACAAGTCTTTTTAG 58.182 37.037 0.00 0.00 0.00 1.85
205 1395 5.880332 TGCTATTTTTGTCAGTCCACTATCC 59.120 40.000 0.00 0.00 0.00 2.59
531 1755 3.167414 CCGAGGGGTTGGGAAAGT 58.833 61.111 0.00 0.00 0.00 2.66
580 1804 2.287915 CGGGCGAGATTTGGTTCTATTG 59.712 50.000 0.00 0.00 0.00 1.90
581 1805 2.169769 TCGGGCGAGATTTGGTTCTATT 59.830 45.455 0.00 0.00 0.00 1.73
828 2053 1.901085 CCAACGGGAGGAGGAGAAG 59.099 63.158 0.00 0.00 35.59 2.85
1394 2627 3.855689 AGCAAAATCCAAGGATCAACG 57.144 42.857 1.37 0.00 33.08 4.10
2154 3393 4.821589 CCTCCTCCGGCTTCACGC 62.822 72.222 0.00 0.00 38.13 5.34
2383 3625 6.479331 CGACTCTAGTGATGCTTACAGTAGTA 59.521 42.308 14.66 0.00 40.26 1.82
2384 3626 5.294799 CGACTCTAGTGATGCTTACAGTAGT 59.705 44.000 14.66 0.00 40.26 2.73
2385 3627 5.294799 ACGACTCTAGTGATGCTTACAGTAG 59.705 44.000 0.00 0.00 40.53 2.57
2519 3761 0.098376 GGTACGCTCTACCACGACAG 59.902 60.000 0.00 0.00 37.53 3.51
2538 3780 2.420628 TGCACCTTTTCATTTCTGCG 57.579 45.000 0.00 0.00 0.00 5.18
2569 3811 3.079578 AGCATATGAAATGGCCGATCAG 58.920 45.455 6.97 0.00 0.00 2.90
2604 3846 0.615331 TCTAGCACAAGCAGGAAGGG 59.385 55.000 0.00 0.00 45.49 3.95
2755 4018 3.107601 ACATGACTAGCACCTACACCAT 58.892 45.455 0.00 0.00 0.00 3.55
2756 4019 2.536066 ACATGACTAGCACCTACACCA 58.464 47.619 0.00 0.00 0.00 4.17
2757 4020 3.056107 TGAACATGACTAGCACCTACACC 60.056 47.826 0.00 0.00 0.00 4.16
2761 4024 3.128764 CGTCTGAACATGACTAGCACCTA 59.871 47.826 0.00 0.00 32.70 3.08
2853 4126 0.326143 AAACCAAACCAAGCCCCTGT 60.326 50.000 0.00 0.00 0.00 4.00
3098 4421 6.932356 TTATAGTACTACCACACCTTCTCG 57.068 41.667 4.31 0.00 0.00 4.04
3176 4499 1.610554 TTGGAGATCCCGGACGGAAC 61.611 60.000 13.13 3.22 46.47 3.62
3177 4500 0.905809 TTTGGAGATCCCGGACGGAA 60.906 55.000 13.13 0.00 46.47 4.30
3204 4527 4.832608 CTACCAGAACCCCGGCGC 62.833 72.222 0.00 0.00 0.00 6.53
3209 4542 0.903236 GTCCACTCTACCAGAACCCC 59.097 60.000 0.00 0.00 0.00 4.95
3222 4555 4.760047 GATGCGCCGTGGTCCACT 62.760 66.667 19.82 0.00 31.34 4.00
3240 4573 1.138266 TCTAGCAAGAACCCATACGCC 59.862 52.381 0.00 0.00 0.00 5.68
3288 4622 3.454375 CACAAAGTAGTGTCTGTTCCGT 58.546 45.455 0.00 0.00 34.83 4.69
3291 4625 2.864343 ACGCACAAAGTAGTGTCTGTTC 59.136 45.455 0.00 0.00 41.52 3.18
3301 4635 2.546368 CACAAAGGCTACGCACAAAGTA 59.454 45.455 0.00 0.00 0.00 2.24
3302 4636 1.333619 CACAAAGGCTACGCACAAAGT 59.666 47.619 0.00 0.00 0.00 2.66
3304 4638 1.384525 ACACAAAGGCTACGCACAAA 58.615 45.000 0.00 0.00 0.00 2.83
3305 4639 3.088259 ACACAAAGGCTACGCACAA 57.912 47.368 0.00 0.00 0.00 3.33
3306 4640 4.868026 ACACAAAGGCTACGCACA 57.132 50.000 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.