Multiple sequence alignment - TraesCS2D01G438400

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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 TraesCS2D01G438400 chr2D 100.000 2318 0 0 1 2318 547807431 547805114 0.000000e+00 4281
1 TraesCS2D01G438400 chr2D 95.054 2325 100 9 1 2318 547952869 547950553 0.000000e+00 3642
2 TraesCS2D01G438400 chr2D 83.733 1795 217 46 334 2080 547791942 547790175 0.000000e+00 1628
3 TraesCS2D01G438400 chr2A 89.979 2355 171 33 1 2318 691115090 691117416 0.000000e+00 2981
4 TraesCS2D01G438400 chr2A 88.418 967 76 18 1367 2318 691134199 691135144 0.000000e+00 1133
5 TraesCS2D01G438400 chr2A 87.149 249 31 1 81 328 69311213 69310965 4.880000e-72 281
6 TraesCS2D01G438400 chr2B 94.142 1673 86 9 647 2318 654653562 654651901 0.000000e+00 2536
7 TraesCS2D01G438400 chr2B 94.023 1673 88 9 647 2318 654703665 654702004 0.000000e+00 2525
8 TraesCS2D01G438400 chr2B 93.787 1674 91 10 647 2318 654681833 654680171 0.000000e+00 2503
9 TraesCS2D01G438400 chr2B 93.639 1179 64 8 1141 2318 654730650 654729482 0.000000e+00 1751
10 TraesCS2D01G438400 chr2B 83.333 1416 157 41 334 1695 654649920 654648530 0.000000e+00 1234
11 TraesCS2D01G438400 chr2B 88.600 500 36 11 1 483 654656742 654656247 2.570000e-164 588
12 TraesCS2D01G438400 chr2B 88.400 500 36 12 1 483 654735773 654735279 1.190000e-162 582
13 TraesCS2D01G438400 chr2B 88.200 500 38 11 1 483 654685014 654684519 5.550000e-161 577
14 TraesCS2D01G438400 chr2B 88.200 500 38 11 1 483 654706848 654706353 5.550000e-161 577
15 TraesCS2D01G438400 chr2B 87.215 219 21 2 2100 2318 654421059 654420848 2.300000e-60 243
16 TraesCS2D01G438400 chr2B 93.082 159 7 4 471 628 654705119 654704964 1.790000e-56 230
17 TraesCS2D01G438400 chr2B 92.453 159 8 4 471 628 654683287 654683132 8.330000e-55 224
18 TraesCS2D01G438400 chr2B 91.824 159 9 4 471 628 654655016 654654861 3.880000e-53 219
19 TraesCS2D01G438400 chrUn 93.843 1673 91 9 647 2318 248126996 248125335 0.000000e+00 2508
20 TraesCS2D01G438400 chrUn 83.475 1416 155 41 334 1695 248123355 248121965 0.000000e+00 1245
21 TraesCS2D01G438400 chrUn 88.600 500 36 11 1 483 248130177 248129682 2.570000e-164 588
22 TraesCS2D01G438400 chrUn 92.453 159 8 4 471 628 248128450 248128295 8.330000e-55 224
23 TraesCS2D01G438400 chr5B 86.111 252 32 3 77 326 527760360 527760610 3.800000e-68 268


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 TraesCS2D01G438400 chr2D 547805114 547807431 2317 True 4281.000000 4281 100.000000 1 2318 1 chr2D.!!$R2 2317
1 TraesCS2D01G438400 chr2D 547950553 547952869 2316 True 3642.000000 3642 95.054000 1 2318 1 chr2D.!!$R3 2317
2 TraesCS2D01G438400 chr2D 547790175 547791942 1767 True 1628.000000 1628 83.733000 334 2080 1 chr2D.!!$R1 1746
3 TraesCS2D01G438400 chr2A 691115090 691117416 2326 False 2981.000000 2981 89.979000 1 2318 1 chr2A.!!$F1 2317
4 TraesCS2D01G438400 chr2A 691134199 691135144 945 False 1133.000000 1133 88.418000 1367 2318 1 chr2A.!!$F2 951
5 TraesCS2D01G438400 chr2B 654729482 654730650 1168 True 1751.000000 1751 93.639000 1141 2318 1 chr2B.!!$R2 1177
6 TraesCS2D01G438400 chr2B 654648530 654656742 8212 True 1144.250000 2536 89.474750 1 2318 4 chr2B.!!$R4 2317
7 TraesCS2D01G438400 chr2B 654702004 654706848 4844 True 1110.666667 2525 91.768333 1 2318 3 chr2B.!!$R6 2317
8 TraesCS2D01G438400 chr2B 654680171 654685014 4843 True 1101.333333 2503 91.480000 1 2318 3 chr2B.!!$R5 2317
9 TraesCS2D01G438400 chrUn 248121965 248130177 8212 True 1141.250000 2508 89.592750 1 2318 4 chrUn.!!$R1 2317

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
607 1897 5.692654 TGTAAAATTCTTTTAAAGGCACGCC 59.307 36.0 4.77 0.0 36.91 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1518 4143 0.173255 AATAACATGCAAGGCACGCC 59.827 50.0 0.0 0.0 43.04 5.68 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
123 128 9.817365 CTTCACATATTAACTTTGTCTCAAGTG 57.183 33.333 0.00 0.0 0.00 3.16
483 514 6.752351 GCTAATGAAGTCACTCGTCTAATTCA 59.248 38.462 0.00 0.0 0.00 2.57
544 1826 6.581166 GCCTTAATCGTTGGTCAGTTAAAAAG 59.419 38.462 0.00 0.0 0.00 2.27
607 1897 5.692654 TGTAAAATTCTTTTAAAGGCACGCC 59.307 36.000 4.77 0.0 36.91 5.68
687 3258 6.261118 GTCTTAATTTGCAGCATACTCTTGG 58.739 40.000 0.00 0.0 0.00 3.61
699 3297 5.769662 AGCATACTCTTGGTGTTGAAATCAA 59.230 36.000 0.00 0.0 0.00 2.57
706 3304 8.137437 ACTCTTGGTGTTGAAATCAATAGTTTG 58.863 33.333 0.00 0.0 38.24 2.93
930 3531 7.235935 ACATTCATCTCACACATTTCCAAAT 57.764 32.000 0.00 0.0 0.00 2.32
1323 3926 2.738314 CAACAACTGCTCGTGATGATCA 59.262 45.455 0.00 0.0 0.00 2.92
1341 3946 7.730332 TGATGATCAGATGTACTACCCATAAGT 59.270 37.037 0.09 0.0 0.00 2.24
1360 3965 3.633418 AGTATCTAGGAGTCGGTTGCTT 58.367 45.455 0.00 0.0 0.00 3.91
1364 3969 2.163010 TCTAGGAGTCGGTTGCTTTACG 59.837 50.000 0.00 0.0 0.00 3.18
1370 3975 1.129809 CGGTTGCTTTACGTCTGCG 59.870 57.895 0.00 0.0 44.93 5.18
1518 4143 2.636830 CTGGAAGTGTAAGGATGGCAG 58.363 52.381 0.00 0.0 0.00 4.85
1588 4213 2.275253 CGTTCGTGTCAAAAAGTTGCAC 59.725 45.455 0.00 0.0 37.90 4.57
1604 4229 4.574828 AGTTGCACGTTTTCTAGTGAACAT 59.425 37.500 0.00 0.0 40.56 2.71
1689 4316 2.948979 AGAAGATTGTCCGTTTGTGCAA 59.051 40.909 0.00 0.0 0.00 4.08
1822 4450 1.137872 CAACAGCTCTCCGGCTTCTAT 59.862 52.381 0.00 0.0 41.00 1.98
1829 4457 5.184096 CAGCTCTCCGGCTTCTATAGAAATA 59.816 44.000 15.85 0.0 41.00 1.40
1892 4520 4.264614 GCATCGCAGTTCATTCAGAATTTG 59.735 41.667 0.00 0.0 38.76 2.32
2015 4645 0.109735 TCTACGCGAGCACAACTCAG 60.110 55.000 15.93 0.0 46.63 3.35
2018 4648 0.387367 ACGCGAGCACAACTCAGTAG 60.387 55.000 15.93 0.0 46.63 2.57
2033 4663 3.997021 CTCAGTAGTTGCTAGGTGGTTTG 59.003 47.826 0.00 0.0 0.00 2.93
2202 4856 4.161189 TGGTTGTTGGATCACACAATGTTT 59.839 37.500 11.05 0.0 0.00 2.83
2206 4860 7.370383 GTTGTTGGATCACACAATGTTTCTAT 58.630 34.615 11.05 0.0 0.00 1.98
2207 4861 7.523293 TGTTGGATCACACAATGTTTCTATT 57.477 32.000 0.00 0.0 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 128 6.632171 CTTGGTCAAAGTTCACAAAGTTTC 57.368 37.500 0.00 0.00 36.16 2.78
154 159 7.819644 GGTATTGTGGACGTTAATACCTTTTT 58.180 34.615 23.36 1.97 46.52 1.94
326 331 7.230849 ACAACAATCTTGGCTTATCATTTCA 57.769 32.000 0.00 0.00 0.00 2.69
328 333 8.370182 AGAAACAACAATCTTGGCTTATCATTT 58.630 29.630 0.00 0.00 0.00 2.32
336 357 5.343307 ACAAAGAAACAACAATCTTGGCT 57.657 34.783 0.00 0.00 36.09 4.75
483 514 0.979665 ATGGTATATGCTCCGCTGCT 59.020 50.000 0.00 0.00 0.00 4.24
607 1897 1.069596 GCCCACCCACAAGCTTTTG 59.930 57.895 5.59 5.59 0.00 2.44
930 3531 7.231467 AGATTTTGGTCTTAGCTAGGTTTTGA 58.769 34.615 0.00 0.00 0.00 2.69
1037 3640 0.389948 GAGGGACACCGACATGACAC 60.390 60.000 0.00 0.00 43.47 3.67
1323 3926 9.125255 TCCTAGATACTTATGGGTAGTACATCT 57.875 37.037 2.06 2.20 31.37 2.90
1341 3946 4.036027 CGTAAAGCAACCGACTCCTAGATA 59.964 45.833 0.00 0.00 0.00 1.98
1364 3969 5.342525 CCATATATAAAGTGTCGACGCAGAC 59.657 44.000 29.21 13.37 41.30 3.51
1490 4115 6.761714 CCATCCTTACACTTCCAGTATAACAC 59.238 42.308 0.00 0.00 0.00 3.32
1518 4143 0.173255 AATAACATGCAAGGCACGCC 59.827 50.000 0.00 0.00 43.04 5.68
1588 4213 7.474332 CGTCATTTACATGTTCACTAGAAAACG 59.526 37.037 2.30 1.08 35.08 3.60
1604 4229 7.040062 AGGGAAAAATTGTGATCGTCATTTACA 60.040 33.333 0.00 0.00 0.00 2.41
1722 4350 9.403110 GCTGCATTTTCTTTTATCATACATAGG 57.597 33.333 0.00 0.00 0.00 2.57
1892 4520 0.539986 TGCTTCCCGGTATCACCTTC 59.460 55.000 0.00 0.00 35.66 3.46
1923 4553 3.187700 GAGCACATGTCCGTTTACTAGG 58.812 50.000 0.00 0.00 0.00 3.02
2015 4645 4.004196 ACTCAAACCACCTAGCAACTAC 57.996 45.455 0.00 0.00 0.00 2.73
2018 4648 3.630312 TCAAACTCAAACCACCTAGCAAC 59.370 43.478 0.00 0.00 0.00 4.17
2033 4663 6.317391 CCAAGGATTATCAGACCTTCAAACTC 59.683 42.308 0.00 0.00 41.33 3.01
2147 4794 7.068470 TGGATGCTTTCATGCAATTCAATACTA 59.932 33.333 0.00 0.00 45.99 1.82
2202 4856 8.202461 TCTCTCTTCCCACACTTAAAAATAGA 57.798 34.615 0.00 0.00 0.00 1.98
2206 4860 6.003950 CCATCTCTCTTCCCACACTTAAAAA 58.996 40.000 0.00 0.00 0.00 1.94
2207 4861 5.309543 TCCATCTCTCTTCCCACACTTAAAA 59.690 40.000 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.