Multiple sequence alignment - TraesCS3A01G409900

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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 TraesCS3A01G409900 chr3A 100.000 3665 0 0 1 3665 654319340 654315676 0.000000e+00 6769.0
1 TraesCS3A01G409900 chr3D 96.700 3697 87 12 1 3665 519250709 519247016 0.000000e+00 6119.0
2 TraesCS3A01G409900 chr3D 94.203 138 7 1 978 1115 519315933 519315797 3.710000e-50 209.0
3 TraesCS3A01G409900 chr3D 94.203 138 7 1 978 1115 519316369 519316233 3.710000e-50 209.0
4 TraesCS3A01G409900 chr3B 94.910 1670 69 10 1200 2861 683429456 683427795 0.000000e+00 2599.0
5 TraesCS3A01G409900 chr3B 96.157 1197 38 4 1 1193 683430728 683429536 0.000000e+00 1949.0
6 TraesCS3A01G409900 chr3B 92.978 769 47 5 1200 1966 683513565 683512802 0.000000e+00 1114.0
7 TraesCS3A01G409900 chr3B 92.338 770 52 6 1200 1966 683828683 683827918 0.000000e+00 1088.0
8 TraesCS3A01G409900 chr3B 87.836 707 72 3 1311 2017 683827618 683826926 0.000000e+00 817.0
9 TraesCS3A01G409900 chr3B 87.588 709 70 6 1311 2017 683365988 683365296 0.000000e+00 806.0
10 TraesCS3A01G409900 chr3B 87.482 711 67 8 1311 2017 683512505 683511813 0.000000e+00 800.0
11 TraesCS3A01G409900 chr3B 93.263 475 21 2 3202 3665 683425249 683424775 0.000000e+00 689.0
12 TraesCS3A01G409900 chr3B 94.279 402 22 1 1565 1966 683366687 683366287 6.730000e-172 614.0
13 TraesCS3A01G409900 chr3B 91.667 372 29 2 1200 1570 683367248 683366878 7.020000e-142 514.0
14 TraesCS3A01G409900 chr3B 89.714 175 10 2 978 1144 683514095 683513921 2.220000e-52 217.0
15 TraesCS3A01G409900 chr3B 89.714 175 10 2 978 1144 683829283 683829109 2.220000e-52 217.0
16 TraesCS3A01G409900 chr3B 93.458 107 7 0 1038 1144 683367780 683367674 3.790000e-35 159.0
17 TraesCS3A01G409900 chr3B 95.122 41 2 0 1153 1193 683828803 683828763 8.500000e-07 65.8
18 TraesCS3A01G409900 chr7D 92.837 712 44 4 2002 2708 45680383 45679674 0.000000e+00 1026.0
19 TraesCS3A01G409900 chr7D 90.037 542 46 6 1467 2006 45696057 45695522 0.000000e+00 695.0
20 TraesCS3A01G409900 chr7A 93.642 519 23 6 2002 2518 47876315 47875805 0.000000e+00 767.0
21 TraesCS3A01G409900 chr7A 91.312 541 45 2 1467 2006 47897880 47897341 0.000000e+00 737.0
22 TraesCS3A01G409900 chr4A 88.582 543 55 7 1467 2006 658894982 658894444 0.000000e+00 652.0
23 TraesCS3A01G409900 chr4A 92.099 443 31 3 2012 2451 658881730 658881289 4.020000e-174 621.0
24 TraesCS3A01G409900 chr4A 93.137 204 14 0 2002 2205 658882118 658881915 2.140000e-77 300.0
25 TraesCS3A01G409900 chr4A 92.784 194 14 0 2012 2205 658881919 658881726 7.750000e-72 281.0
26 TraesCS3A01G409900 chr5D 88.806 134 13 2 539 671 563593871 563594003 2.930000e-36 163.0


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 TraesCS3A01G409900 chr3A 654315676 654319340 3664 True 6769.000000 6769 100.000000 1 3665 1 chr3A.!!$R1 3664
1 TraesCS3A01G409900 chr3D 519247016 519250709 3693 True 6119.000000 6119 96.700000 1 3665 1 chr3D.!!$R1 3664
2 TraesCS3A01G409900 chr3D 519315797 519316369 572 True 209.000000 209 94.203000 978 1115 2 chr3D.!!$R2 137
3 TraesCS3A01G409900 chr3B 683424775 683430728 5953 True 1745.666667 2599 94.776667 1 3665 3 chr3B.!!$R2 3664
4 TraesCS3A01G409900 chr3B 683511813 683514095 2282 True 710.333333 1114 90.058000 978 2017 3 chr3B.!!$R3 1039
5 TraesCS3A01G409900 chr3B 683826926 683829283 2357 True 546.950000 1088 91.252500 978 2017 4 chr3B.!!$R4 1039
6 TraesCS3A01G409900 chr3B 683365296 683367780 2484 True 523.250000 806 91.748000 1038 2017 4 chr3B.!!$R1 979
7 TraesCS3A01G409900 chr7D 45679674 45680383 709 True 1026.000000 1026 92.837000 2002 2708 1 chr7D.!!$R1 706
8 TraesCS3A01G409900 chr7D 45695522 45696057 535 True 695.000000 695 90.037000 1467 2006 1 chr7D.!!$R2 539
9 TraesCS3A01G409900 chr7A 47875805 47876315 510 True 767.000000 767 93.642000 2002 2518 1 chr7A.!!$R1 516
10 TraesCS3A01G409900 chr7A 47897341 47897880 539 True 737.000000 737 91.312000 1467 2006 1 chr7A.!!$R2 539
11 TraesCS3A01G409900 chr4A 658894444 658894982 538 True 652.000000 652 88.582000 1467 2006 1 chr4A.!!$R1 539
12 TraesCS3A01G409900 chr4A 658881289 658882118 829 True 400.666667 621 92.673333 2002 2451 3 chr4A.!!$R2 449

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
926 932 1.821753 ACCTTGATCCTCTGTCTGACG 59.178 52.381 2.98 0.0 0.00 4.35 F
1517 1905 0.035056 GACCCTGCTAATGCTGTGGT 60.035 55.000 0.00 0.0 40.96 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1771 4237 0.870393 CACAGTCCATGTCACTGCAC 59.130 55.0 17.85 0.00 44.5 4.57 R
2835 6044 1.144969 CGACGGCACTGTTTACATGT 58.855 50.0 2.69 2.69 0.0 3.21 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
647 649 4.459337 GGTTTGCTAGAGCTATGGTTTGTT 59.541 41.667 2.72 0.00 42.66 2.83
656 658 6.016555 AGAGCTATGGTTTGTTTTGGGTTAT 58.983 36.000 0.00 0.00 0.00 1.89
740 742 6.497259 TCTCCCTGGTTATTGATATGAGGTAC 59.503 42.308 0.00 0.00 0.00 3.34
926 932 1.821753 ACCTTGATCCTCTGTCTGACG 59.178 52.381 2.98 0.00 0.00 4.35
968 974 4.142988 CGAGCCACGAAAGCATTTTTACTA 60.143 41.667 0.00 0.00 45.77 1.82
1228 1612 7.876936 AATGCTGACATGATGTAATTTCTCT 57.123 32.000 0.00 0.00 36.36 3.10
1273 1658 0.036164 TCAGCAGTACCGCCACATTT 59.964 50.000 0.00 0.00 0.00 2.32
1296 1681 3.470888 CCGGGATGGAAGCTCGGT 61.471 66.667 0.00 0.00 42.00 4.69
1318 1706 1.420138 GGGTGTGGTCAAAGAAGGAGA 59.580 52.381 0.00 0.00 0.00 3.71
1342 1730 1.915489 TCTGGTATGTGCAAGGTGGAT 59.085 47.619 0.00 0.00 0.00 3.41
1378 1766 3.196254 AGGCGATTGCTCCAAATTCAAAT 59.804 39.130 4.59 0.00 42.25 2.32
1380 1768 5.069516 AGGCGATTGCTCCAAATTCAAATAT 59.930 36.000 4.59 0.00 42.25 1.28
1381 1769 5.176223 GGCGATTGCTCCAAATTCAAATATG 59.824 40.000 4.59 0.00 42.25 1.78
1382 1770 5.978919 GCGATTGCTCCAAATTCAAATATGA 59.021 36.000 0.00 0.00 38.39 2.15
1418 1806 0.831307 AAGGTGAACCCGGAGATAGC 59.169 55.000 0.73 0.00 38.74 2.97
1517 1905 0.035056 GACCCTGCTAATGCTGTGGT 60.035 55.000 0.00 0.00 40.96 4.16
1518 1906 0.322816 ACCCTGCTAATGCTGTGGTG 60.323 55.000 0.00 0.00 38.84 4.17
1520 1908 0.806868 CCTGCTAATGCTGTGGTGTG 59.193 55.000 0.00 0.00 40.48 3.82
1530 1918 1.534595 GCTGTGGTGTGCTTTGAAGTG 60.535 52.381 0.00 0.00 0.00 3.16
1563 1951 1.462238 AGGGACCACAGCCAAGACT 60.462 57.895 0.00 0.00 0.00 3.24
1706 2291 3.270877 CCCACAGTAAGCCATTGTCTAC 58.729 50.000 0.00 0.00 0.00 2.59
1868 4334 0.302288 GCGTGTTTTACAGCGACACA 59.698 50.000 6.65 0.00 42.81 3.72
2244 5446 3.006323 CCTAGTAGCTCAGCACCCTAATG 59.994 52.174 0.00 0.00 0.00 1.90
2646 5855 2.568509 CCCATTGGTTCTTTGGATGCTT 59.431 45.455 1.20 0.00 31.94 3.91
2835 6044 3.008923 TGCAAGTCATTGACACCCTGATA 59.991 43.478 18.57 1.99 38.83 2.15
2868 6077 0.813184 CCGTCGTAGGCCTGAAGTTA 59.187 55.000 17.99 0.00 0.00 2.24
3008 6217 3.181487 GGTCATGTTGTTGCAGAACAGTT 60.181 43.478 15.94 0.00 43.03 3.16
3086 6295 4.370364 TGGTGAAAACACTCTTTTCTGC 57.630 40.909 7.00 1.56 38.75 4.26
3105 6314 3.286353 TGCGAAGATTTATGGATTGGCA 58.714 40.909 0.00 0.00 34.62 4.92
3121 6330 3.644966 TGGCAATAACTCACTTAGGGG 57.355 47.619 0.00 0.00 0.00 4.79
3195 6404 5.891551 AGCTAAGGTTTTTGAAGAAGGTTGA 59.108 36.000 0.00 0.00 0.00 3.18
3317 8756 7.719633 AGTTGTAGATGGCTTTTGACTAAGAAA 59.280 33.333 0.00 0.00 0.00 2.52
3318 8757 8.515414 GTTGTAGATGGCTTTTGACTAAGAAAT 58.485 33.333 0.00 0.00 0.00 2.17
3383 8822 6.867816 TGCAGCAGGTTCAATGTAAATTTAAG 59.132 34.615 0.00 0.00 0.00 1.85
3609 9057 3.559069 AGATTGTAATGTGATGCCTGGG 58.441 45.455 0.00 0.00 0.00 4.45
3656 9104 5.699001 GGATTTTGCCGTTTAAAGGAAATGT 59.301 36.000 9.43 0.00 32.87 2.71
3660 9108 4.142790 TGCCGTTTAAAGGAAATGTGGTA 58.857 39.130 9.43 0.00 32.87 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 168 9.685828 TTTGTCAGCCTTATTTGTAATTTACAC 57.314 29.630 8.75 0.00 38.63 2.90
647 649 7.455058 TGAAAGACTAGCAGTTATAACCCAAA 58.545 34.615 12.05 0.00 0.00 3.28
740 742 1.888215 TGCAGGAACAGCTGAAGAAG 58.112 50.000 23.35 8.25 43.00 2.85
871 877 4.169508 CAATCTCTGGTCTTACACAGTCG 58.830 47.826 0.00 0.00 36.17 4.18
926 932 6.072893 TGGCTCGGAGTAAAAATGTTAACTTC 60.073 38.462 7.22 0.00 0.00 3.01
945 951 2.050477 AAAAATGCTTTCGTGGCTCG 57.950 45.000 1.94 1.94 41.41 5.03
968 974 7.001073 AGAGAACAGCAGAGGAAAAAGTAAAT 58.999 34.615 0.00 0.00 0.00 1.40
1228 1612 5.248477 AGTTGAATAGTGAAACCTCAGCCTA 59.752 40.000 0.00 0.00 37.80 3.93
1273 1658 2.742116 GCTTCCATCCCGGTGGCTA 61.742 63.158 6.22 0.00 39.19 3.93
1296 1681 1.566703 TCCTTCTTTGACCACACCCAA 59.433 47.619 0.00 0.00 0.00 4.12
1318 1706 4.165950 TCCACCTTGCACATACCAGATTAT 59.834 41.667 0.00 0.00 0.00 1.28
1378 1766 3.242011 TGCAGCTGTGAGGGATATCATA 58.758 45.455 16.64 0.00 0.00 2.15
1380 1768 1.499368 TGCAGCTGTGAGGGATATCA 58.501 50.000 16.64 0.00 0.00 2.15
1381 1769 2.492012 CTTGCAGCTGTGAGGGATATC 58.508 52.381 16.64 0.00 0.00 1.63
1382 1770 1.142465 CCTTGCAGCTGTGAGGGATAT 59.858 52.381 22.57 0.00 0.00 1.63
1517 1905 2.423185 CCAACTGACACTTCAAAGCACA 59.577 45.455 0.00 0.00 0.00 4.57
1518 1906 2.423538 ACCAACTGACACTTCAAAGCAC 59.576 45.455 0.00 0.00 0.00 4.40
1520 1908 2.286418 CGACCAACTGACACTTCAAAGC 60.286 50.000 0.00 0.00 0.00 3.51
1530 1918 0.895530 TCCCTGATCGACCAACTGAC 59.104 55.000 0.00 0.00 0.00 3.51
1555 1943 0.813821 GGCAATTCCAGAGTCTTGGC 59.186 55.000 0.00 0.00 38.16 4.52
1563 1951 6.189859 AGTGAAATTCATAGGCAATTCCAGA 58.810 36.000 0.00 0.00 37.29 3.86
1706 2291 9.193133 GATATTCTTTCCATGCATCAAGAAATG 57.807 33.333 20.97 13.27 38.44 2.32
1771 4237 0.870393 CACAGTCCATGTCACTGCAC 59.130 55.000 17.85 0.00 44.50 4.57
1868 4334 2.247358 CATTTGGGGCAGGTAACAAGT 58.753 47.619 0.00 0.00 41.41 3.16
1913 4380 5.063204 TCTACACAGATTCCTGGTTTTGTG 58.937 41.667 15.91 15.91 44.60 3.33
2364 5570 5.525378 GTCATCTGCGATAAGAGGATTTGTT 59.475 40.000 1.78 0.00 39.04 2.83
2646 5855 5.519808 TCTTCTCAGAAGTAGGGATTAGCA 58.480 41.667 14.32 0.00 0.00 3.49
2835 6044 1.144969 CGACGGCACTGTTTACATGT 58.855 50.000 2.69 2.69 0.00 3.21
2868 6077 7.667043 TTGTTATCTCAAGCGTCATAGTTTT 57.333 32.000 0.00 0.00 0.00 2.43
3086 6295 7.651808 AGTTATTGCCAATCCATAAATCTTCG 58.348 34.615 0.00 0.00 0.00 3.79
3105 6314 9.990868 ATTAAAACATCCCCTAAGTGAGTTATT 57.009 29.630 0.00 0.00 0.00 1.40
3195 6404 7.560626 AGGACTCTACGAAATCTAATACAACCT 59.439 37.037 0.00 0.00 0.00 3.50
3285 8724 6.019479 GTCAAAAGCCATCTACAACTATCTCG 60.019 42.308 0.00 0.00 0.00 4.04
3383 8822 9.929180 AGAGGTATTTTAATTTTCCAAAAGCTC 57.071 29.630 0.00 0.00 0.00 4.09
3425 8864 9.778741 TTAGAATACTGTCCATAAAAGCCATAG 57.221 33.333 0.00 0.00 0.00 2.23
3426 8865 9.555727 GTTAGAATACTGTCCATAAAAGCCATA 57.444 33.333 0.00 0.00 0.00 2.74
3427 8866 8.275040 AGTTAGAATACTGTCCATAAAAGCCAT 58.725 33.333 0.00 0.00 0.00 4.40
3428 8867 7.630082 AGTTAGAATACTGTCCATAAAAGCCA 58.370 34.615 0.00 0.00 0.00 4.75
3429 8868 9.609346 TTAGTTAGAATACTGTCCATAAAAGCC 57.391 33.333 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.