Multiple sequence alignment - TraesCS3D01G462300

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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 TraesCS3D01G462300 chr3D 100.000 2597 0 0 1 2597 566889445 566892041 0.000000e+00 4796
1 TraesCS3D01G462300 chr3D 83.415 1019 129 27 925 1926 567046176 567047171 0.000000e+00 909
2 TraesCS3D01G462300 chrUn 93.198 2617 115 32 1 2588 268821931 268819349 0.000000e+00 3788
3 TraesCS3D01G462300 chrUn 93.198 2617 115 32 1 2588 268829760 268832342 0.000000e+00 3788
4 TraesCS3D01G462300 chrUn 87.743 1901 148 42 725 2597 312095580 312097423 0.000000e+00 2141
5 TraesCS3D01G462300 chrUn 82.651 415 43 15 2146 2550 479182136 479181741 8.900000e-90 340
6 TraesCS3D01G462300 chr3A 95.108 2167 72 23 450 2595 702150146 702147993 0.000000e+00 3384
7 TraesCS3D01G462300 chr3A 88.455 1897 148 38 728 2597 702380841 702378989 0.000000e+00 2224
8 TraesCS3D01G462300 chr3A 87.363 1915 155 39 728 2597 702329538 702327666 0.000000e+00 2115
9 TraesCS3D01G462300 chr3A 93.080 1344 65 16 1268 2595 702115597 702114266 0.000000e+00 1941
10 TraesCS3D01G462300 chr3A 94.021 853 41 7 728 1576 702383508 702382662 0.000000e+00 1284
11 TraesCS3D01G462300 chr3A 94.021 853 41 7 728 1576 702401136 702400290 0.000000e+00 1284
12 TraesCS3D01G462300 chr3A 95.924 785 30 2 450 1233 702116373 702115590 0.000000e+00 1271
13 TraesCS3D01G462300 chr3A 96.283 269 9 1 1 268 702150633 702150365 8.530000e-120 440
14 TraesCS3D01G462300 chr3A 90.435 115 6 2 241 355 702329692 702329583 2.080000e-31 147
15 TraesCS3D01G462300 chr3A 89.216 102 4 4 511 605 702322766 702322665 1.260000e-23 121


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 TraesCS3D01G462300 chr3D 566889445 566892041 2596 False 4796 4796 100.0000 1 2597 1 chr3D.!!$F1 2596
1 TraesCS3D01G462300 chr3D 567046176 567047171 995 False 909 909 83.4150 925 1926 1 chr3D.!!$F2 1001
2 TraesCS3D01G462300 chrUn 268819349 268821931 2582 True 3788 3788 93.1980 1 2588 1 chrUn.!!$R1 2587
3 TraesCS3D01G462300 chrUn 268829760 268832342 2582 False 3788 3788 93.1980 1 2588 1 chrUn.!!$F1 2587
4 TraesCS3D01G462300 chrUn 312095580 312097423 1843 False 2141 2141 87.7430 725 2597 1 chrUn.!!$F2 1872
5 TraesCS3D01G462300 chr3A 702147993 702150633 2640 True 1912 3384 95.6955 1 2595 2 chr3A.!!$R4 2594
6 TraesCS3D01G462300 chr3A 702378989 702383508 4519 True 1754 2224 91.2380 728 2597 2 chr3A.!!$R6 1869
7 TraesCS3D01G462300 chr3A 702114266 702116373 2107 True 1606 1941 94.5020 450 2595 2 chr3A.!!$R3 2145
8 TraesCS3D01G462300 chr3A 702400290 702401136 846 True 1284 1284 94.0210 728 1576 1 chr3A.!!$R2 848
9 TraesCS3D01G462300 chr3A 702327666 702329692 2026 True 1131 2115 88.8990 241 2597 2 chr3A.!!$R5 2356

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
332 340 1.317613 TGATTGATTACATGGGCGGC 58.682 50.0 0.0 0.0 0.0 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2005 4766 1.213296 TCATAGCCTTGGAACTCCCC 58.787 55.0 0.0 0.0 34.29 4.81 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
132 133 6.927936 AGTACATGAAGAAGCAGCTATGTATG 59.072 38.462 15.10 10.21 34.65 2.39
268 276 2.679837 CCATCCCACTTGAACTTGATCG 59.320 50.000 0.00 0.00 0.00 3.69
280 288 4.864806 TGAACTTGATCGTCTGCTAATCAC 59.135 41.667 0.00 0.00 0.00 3.06
292 300 5.296283 GTCTGCTAATCACTTCTTCATGCAT 59.704 40.000 0.00 0.00 0.00 3.96
317 325 3.208747 ACTTGACCCAACGACTTGATT 57.791 42.857 0.00 0.00 0.00 2.57
332 340 1.317613 TGATTGATTACATGGGCGGC 58.682 50.000 0.00 0.00 0.00 6.53
448 456 7.352739 CACGGTTAATCATCCAGCTAATTAAC 58.647 38.462 13.76 13.76 40.97 2.01
538 588 6.776116 ACGGATACAGATGTAATTAGTCCAGA 59.224 38.462 9.22 0.00 33.76 3.86
583 633 7.519008 GCTTAATTACCTTGACAAGATGATCCG 60.519 40.741 16.99 0.50 0.00 4.18
612 662 2.595386 GCATGAACGTGGTTTGGATTC 58.405 47.619 0.00 0.00 0.00 2.52
1106 3845 2.919839 TGGAAGTGCCACGGGAAA 59.080 55.556 0.00 0.00 43.33 3.13
1112 3851 2.528127 TGCCACGGGAAAGGGAGA 60.528 61.111 0.00 0.00 0.00 3.71
1230 3975 2.529389 GGTGGAGGTGGAGGTGGT 60.529 66.667 0.00 0.00 0.00 4.16
1296 4041 4.821589 GGCTCTGGCTCCGGTTCG 62.822 72.222 0.00 0.00 38.73 3.95
1660 4406 8.251026 CCTACTGTACTGTGTCAAATTGATAGA 58.749 37.037 15.01 0.00 0.00 1.98
1822 4580 3.575965 ATCGTTTTGGCCAATTGACTC 57.424 42.857 21.26 5.60 0.00 3.36
1829 4587 0.527565 GGCCAATTGACTCGCAATGT 59.472 50.000 7.12 0.00 46.25 2.71
1853 4613 2.009774 CTCTTTGCCCGTCTTATGGTG 58.990 52.381 0.00 0.00 0.00 4.17
1893 4654 8.564574 TGCTCACTTATGTTTAAGTACCAAAAG 58.435 33.333 0.00 0.00 44.94 2.27
2005 4766 0.459237 CTCGCTGGGTAGTGCTTCTG 60.459 60.000 0.00 0.00 34.41 3.02
2072 4834 0.898320 CCTTCACATCCTCGGTCACT 59.102 55.000 0.00 0.00 0.00 3.41
2503 5292 7.094420 TGCGAAATTTGATTTCCACTCAAGATA 60.094 33.333 0.00 0.00 44.40 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
228 235 1.064060 GGCAAGATCGATCCAAAACCG 59.936 52.381 21.66 4.18 0.00 4.44
268 276 4.633126 TGCATGAAGAAGTGATTAGCAGAC 59.367 41.667 0.00 0.00 0.00 3.51
280 288 3.943381 TCAAGTAGCCATGCATGAAGAAG 59.057 43.478 28.31 11.71 0.00 2.85
317 325 1.522806 GACGCCGCCCATGTAATCA 60.523 57.895 0.00 0.00 0.00 2.57
380 388 2.590575 CGACGTGGGCAAGTGGTT 60.591 61.111 0.00 0.00 0.00 3.67
412 420 3.576982 TGATTAACCGTGGGCTAGGATAG 59.423 47.826 0.00 0.00 43.09 2.08
518 568 8.977412 TGAATGTCTGGACTAATTACATCTGTA 58.023 33.333 2.38 0.00 30.71 2.74
538 588 1.271379 GCCTACACCACCACTGAATGT 60.271 52.381 0.00 0.00 0.00 2.71
583 633 4.101790 CGTTCATGCCGGCACCAC 62.102 66.667 35.50 25.95 0.00 4.16
751 801 4.701171 ACGTTGGGTCAACAGTTCTAAAAA 59.299 37.500 10.75 0.00 43.70 1.94
952 3691 4.936411 ACTCTTGCAAGATGAGATGAGTTG 59.064 41.667 28.57 14.72 33.93 3.16
1106 3845 0.998945 CTCTCCTCCTCCCTCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
1112 3851 2.641746 CCACCCTCTCCTCCTCCCT 61.642 68.421 0.00 0.00 0.00 4.20
1758 4506 5.627499 ACATTGCGATGTAACATTCTTGT 57.373 34.783 18.34 0.00 44.51 3.16
1801 4559 3.611530 CGAGTCAATTGGCCAAAACGATT 60.612 43.478 24.71 15.32 0.00 3.34
1822 4580 1.468054 GGGCAAAGAGCTTACATTGCG 60.468 52.381 15.69 0.00 46.88 4.85
1829 4587 3.531538 CATAAGACGGGCAAAGAGCTTA 58.468 45.455 0.00 0.00 44.79 3.09
1935 4696 7.280876 GTGGATGTGAGTTATGTGTTACATGAT 59.719 37.037 0.00 0.00 39.53 2.45
2005 4766 1.213296 TCATAGCCTTGGAACTCCCC 58.787 55.000 0.00 0.00 34.29 4.81
2072 4834 3.811497 CACTCTCTCAAAGCAATGTGTCA 59.189 43.478 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.