Multiple sequence alignment - TraesCS6D01G137900

Loading Multiple Alignment...

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 TraesCS6D01G137900 chr6D 100.000 2522 0 0 1 2522 106665309 106667830 0.000000e+00 4658.0
1 TraesCS6D01G137900 chr6D 93.659 962 59 2 1562 2522 91107813 91106853 0.000000e+00 1437.0
2 TraesCS6D01G137900 chr2A 96.865 1563 47 1 1 1561 733427292 733425730 0.000000e+00 2614.0
3 TraesCS6D01G137900 chr5D 96.235 1567 56 2 1 1565 377295155 377296720 0.000000e+00 2564.0
4 TraesCS6D01G137900 chr1B 95.144 1565 72 3 1 1563 569706355 569704793 0.000000e+00 2466.0
5 TraesCS6D01G137900 chr1B 96.429 336 11 1 1233 1567 13964486 13964151 1.020000e-153 553.0
6 TraesCS6D01G137900 chr6B 95.144 1565 71 2 1 1563 27116467 27118028 0.000000e+00 2464.0
7 TraesCS6D01G137900 chr3B 91.635 1566 127 3 1 1563 647233120 647231556 0.000000e+00 2163.0
8 TraesCS6D01G137900 chr3A 87.580 1554 177 7 13 1563 50967692 50966152 0.000000e+00 1786.0
9 TraesCS6D01G137900 chr4D 93.035 962 66 1 1562 2522 443885209 443886170 0.000000e+00 1404.0
10 TraesCS6D01G137900 chr4D 92.604 960 68 3 1564 2522 110288270 110289227 0.000000e+00 1376.0
11 TraesCS6D01G137900 chr4D 92.083 960 75 1 1564 2522 367058008 367057049 0.000000e+00 1351.0
12 TraesCS6D01G137900 chr3D 92.812 960 67 2 1564 2522 71073883 71072925 0.000000e+00 1389.0
13 TraesCS6D01G137900 chr3D 79.697 1586 286 26 1 1563 19311140 19312712 0.000000e+00 1112.0
14 TraesCS6D01G137900 chr3D 81.593 728 127 7 839 1563 571867881 571867158 1.670000e-166 595.0
15 TraesCS6D01G137900 chr1D 92.620 962 70 1 1562 2522 300548847 300549808 0.000000e+00 1382.0
16 TraesCS6D01G137900 chr2D 92.516 962 70 2 1562 2522 288490112 288489152 0.000000e+00 1376.0
17 TraesCS6D01G137900 chr2D 92.292 960 73 1 1564 2522 134734627 134733668 0.000000e+00 1362.0
18 TraesCS6D01G137900 chr2D 92.196 961 71 4 1564 2522 300908490 300909448 0.000000e+00 1356.0
19 TraesCS6D01G137900 chr5B 92.264 530 40 1 1034 1563 56593285 56592757 0.000000e+00 750.0
20 TraesCS6D01G137900 chr4B 94.161 411 22 1 1153 1563 424062932 424063340 2.130000e-175 625.0
21 TraesCS6D01G137900 chr4B 92.553 94 7 0 294 387 424062761 424062854 4.380000e-28 135.0
22 TraesCS6D01G137900 chr4B 96.154 52 2 0 440 491 424062881 424062932 4.470000e-13 86.1


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 TraesCS6D01G137900 chr6D 106665309 106667830 2521 False 4658.000000 4658 100.000000 1 2522 1 chr6D.!!$F1 2521
1 TraesCS6D01G137900 chr6D 91106853 91107813 960 True 1437.000000 1437 93.659000 1562 2522 1 chr6D.!!$R1 960
2 TraesCS6D01G137900 chr2A 733425730 733427292 1562 True 2614.000000 2614 96.865000 1 1561 1 chr2A.!!$R1 1560
3 TraesCS6D01G137900 chr5D 377295155 377296720 1565 False 2564.000000 2564 96.235000 1 1565 1 chr5D.!!$F1 1564
4 TraesCS6D01G137900 chr1B 569704793 569706355 1562 True 2466.000000 2466 95.144000 1 1563 1 chr1B.!!$R2 1562
5 TraesCS6D01G137900 chr6B 27116467 27118028 1561 False 2464.000000 2464 95.144000 1 1563 1 chr6B.!!$F1 1562
6 TraesCS6D01G137900 chr3B 647231556 647233120 1564 True 2163.000000 2163 91.635000 1 1563 1 chr3B.!!$R1 1562
7 TraesCS6D01G137900 chr3A 50966152 50967692 1540 True 1786.000000 1786 87.580000 13 1563 1 chr3A.!!$R1 1550
8 TraesCS6D01G137900 chr4D 443885209 443886170 961 False 1404.000000 1404 93.035000 1562 2522 1 chr4D.!!$F2 960
9 TraesCS6D01G137900 chr4D 110288270 110289227 957 False 1376.000000 1376 92.604000 1564 2522 1 chr4D.!!$F1 958
10 TraesCS6D01G137900 chr4D 367057049 367058008 959 True 1351.000000 1351 92.083000 1564 2522 1 chr4D.!!$R1 958
11 TraesCS6D01G137900 chr3D 71072925 71073883 958 True 1389.000000 1389 92.812000 1564 2522 1 chr3D.!!$R1 958
12 TraesCS6D01G137900 chr3D 19311140 19312712 1572 False 1112.000000 1112 79.697000 1 1563 1 chr3D.!!$F1 1562
13 TraesCS6D01G137900 chr3D 571867158 571867881 723 True 595.000000 595 81.593000 839 1563 1 chr3D.!!$R2 724
14 TraesCS6D01G137900 chr1D 300548847 300549808 961 False 1382.000000 1382 92.620000 1562 2522 1 chr1D.!!$F1 960
15 TraesCS6D01G137900 chr2D 288489152 288490112 960 True 1376.000000 1376 92.516000 1562 2522 1 chr2D.!!$R2 960
16 TraesCS6D01G137900 chr2D 134733668 134734627 959 True 1362.000000 1362 92.292000 1564 2522 1 chr2D.!!$R1 958
17 TraesCS6D01G137900 chr2D 300908490 300909448 958 False 1356.000000 1356 92.196000 1564 2522 1 chr2D.!!$F1 958
18 TraesCS6D01G137900 chr5B 56592757 56593285 528 True 750.000000 750 92.264000 1034 1563 1 chr5B.!!$R1 529
19 TraesCS6D01G137900 chr4B 424062761 424063340 579 False 282.033333 625 94.289333 294 1563 3 chr4B.!!$F1 1269

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
666 672 2.831333 CACATAGGCCACATCTCTCAC 58.169 52.381 5.01 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2249 2280 0.178861 AACACTCTCCCCTGGGTGAT 60.179 55.0 12.71 0.0 37.2 3.06 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
73 74 4.565652 CCTGTGTGCAAGGGTATTAAGAGT 60.566 45.833 0.00 0.00 0.00 3.24
92 93 4.417183 AGAGTGAGATACTATCCCACTGGA 59.583 45.833 15.84 0.00 46.54 3.86
110 111 6.544931 CCACTGGAGACATATTGAATTGTGAT 59.455 38.462 0.00 0.00 41.51 3.06
217 218 7.013750 TGGCGATGGTGCAAAAATTAATATCTA 59.986 33.333 0.00 0.00 36.28 1.98
475 476 7.418408 TCAGTCAGATCAGCTTACTATAAACG 58.582 38.462 0.00 0.00 30.08 3.60
633 639 3.206964 TGCAATTCCGTGTTTCAGTGTA 58.793 40.909 0.00 0.00 0.00 2.90
666 672 2.831333 CACATAGGCCACATCTCTCAC 58.169 52.381 5.01 0.00 0.00 3.51
826 832 7.549134 CAGCAGTACTGGAATTTCTATTGTGTA 59.451 37.037 23.95 0.00 43.19 2.90
871 877 7.176165 CGTATATGGATCAGTTTGACCTACCTA 59.824 40.741 0.00 0.00 0.00 3.08
1333 1358 4.700448 CAATGGTGGCTGGCCCCA 62.700 66.667 18.92 18.92 39.53 4.96
1486 1512 3.153919 GAGGCACCACCAAGTTTCATTA 58.846 45.455 0.00 0.00 43.14 1.90
1588 1617 4.771590 TGATCATCTTGAAGTTGTTGCC 57.228 40.909 3.45 0.00 0.00 4.52
1788 1817 2.022195 CCGTTATCTCGTTCCTCCTGA 58.978 52.381 0.00 0.00 0.00 3.86
1791 1820 3.315470 CGTTATCTCGTTCCTCCTGATCA 59.685 47.826 0.00 0.00 0.00 2.92
1830 1859 1.334599 GCTTCATTGTTTTCGGCGTCA 60.335 47.619 6.85 0.00 0.00 4.35
1834 1863 1.468520 CATTGTTTTCGGCGTCATCCT 59.531 47.619 6.85 0.00 0.00 3.24
1889 1918 0.167470 TTCGAGCGACGTGACTTAGG 59.833 55.000 0.00 0.00 43.13 2.69
2000 2030 5.815581 AGGTGTATCAACCATGTACACATT 58.184 37.500 19.39 8.84 43.20 2.71
2077 2107 1.021968 ATCGTCATCGTCGTCCATGA 58.978 50.000 0.00 0.00 38.33 3.07
2210 2241 1.202417 CGGACATAGTTCGGCTGTGAT 60.202 52.381 10.44 0.00 38.42 3.06
2225 2256 2.006415 TGATTCCCCCGCCAAGGAT 61.006 57.895 0.00 0.00 45.00 3.24
2252 2283 4.797693 TTTTAACGAGTTTCGCACATCA 57.202 36.364 0.00 0.00 45.12 3.07
2417 2448 1.006922 CGAGTCTGTGTGCAGCTCA 60.007 57.895 14.39 0.00 41.53 4.26
2418 2449 1.280886 CGAGTCTGTGTGCAGCTCAC 61.281 60.000 18.83 18.83 45.82 3.51
2433 2464 1.923227 CTCACACGCCGCAGACTCTA 61.923 60.000 0.00 0.00 0.00 2.43
2440 2471 1.826024 CCGCAGACTCTATGGCCTT 59.174 57.895 3.32 0.00 0.00 4.35
2478 2509 0.523966 CGGATTTAAGGCCGTTGCAA 59.476 50.000 0.00 0.00 42.49 4.08
2490 2521 0.591236 CGTTGCAACAACAGGAACCG 60.591 55.000 28.01 7.35 34.33 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.228367 CCTCCAACACTGCTTGGCT 60.228 57.895 0.00 0.00 40.66 4.75
73 74 4.168088 TGTCTCCAGTGGGATAGTATCTCA 59.832 45.833 8.74 8.74 43.91 3.27
92 93 9.676861 TTCTTCAGATCACAATTCAATATGTCT 57.323 29.630 0.00 0.00 0.00 3.41
110 111 7.996758 AATATAAGAGGAACCCTTCTTCAGA 57.003 36.000 0.00 0.00 38.16 3.27
217 218 1.280457 GGGGATCCAACAGTCACTCT 58.720 55.000 15.23 0.00 0.00 3.24
475 476 3.747708 GCCTACATATGAAACCTCCCACC 60.748 52.174 10.38 0.00 0.00 4.61
633 639 2.941415 GCCTATGTGCCTGTTTGCTAGT 60.941 50.000 0.00 0.00 0.00 2.57
666 672 1.202290 GCCAAACGACATATTGGGCAG 60.202 52.381 6.67 0.00 45.03 4.85
826 832 1.760192 GCCTTCTGATGCACCTGATT 58.240 50.000 0.00 0.00 0.00 2.57
871 877 1.664151 GCTTGCCGTAGCGATAAGTTT 59.336 47.619 0.00 0.00 44.31 2.66
1290 1315 4.040339 TGTCCTTCATTCAGTTGTAGAGCA 59.960 41.667 0.00 0.00 0.00 4.26
1333 1358 8.358582 AGTAAATCTCTGCATTCTTCCAAAAT 57.641 30.769 0.00 0.00 0.00 1.82
1486 1512 0.400213 TCGTCTGCCAAGGAATTGGT 59.600 50.000 8.69 0.00 43.90 3.67
1573 1602 1.333619 GAAGCGGCAACAACTTCAAGA 59.666 47.619 1.45 0.00 44.67 3.02
1581 1610 1.603802 CTGAAGAAGAAGCGGCAACAA 59.396 47.619 1.45 0.00 0.00 2.83
1588 1617 2.091852 AGAAGCCTGAAGAAGAAGCG 57.908 50.000 0.00 0.00 0.00 4.68
1773 1802 3.304911 TCTGATCAGGAGGAACGAGAT 57.695 47.619 22.42 0.00 0.00 2.75
1810 1839 1.327507 GACGCCGAAAACAATGAAGC 58.672 50.000 0.00 0.00 0.00 3.86
1830 1859 6.407525 GCACCAGAGAAAATAGTACTCAGGAT 60.408 42.308 0.00 0.00 38.85 3.24
1834 1863 4.530553 TGGCACCAGAGAAAATAGTACTCA 59.469 41.667 0.00 0.00 33.69 3.41
2000 2030 0.535335 GACGGCCACTTCCTCATACA 59.465 55.000 2.24 0.00 0.00 2.29
2028 2058 1.614413 GGTCAAAACCCGCCATTTACA 59.386 47.619 0.00 0.00 39.93 2.41
2051 2081 1.738350 ACGACGATGACGATGAGAAGT 59.262 47.619 0.00 0.00 42.66 3.01
2054 2084 0.656259 GGACGACGATGACGATGAGA 59.344 55.000 0.00 0.00 42.66 3.27
2210 2241 2.076184 CCTATCCTTGGCGGGGGAA 61.076 63.158 0.00 0.00 35.08 3.97
2244 2275 3.687321 CTCCCCTGGGTGATGTGCG 62.687 68.421 12.71 0.00 36.47 5.34
2249 2280 0.178861 AACACTCTCCCCTGGGTGAT 60.179 55.000 12.71 0.00 37.20 3.06
2252 2283 1.847968 CCAACACTCTCCCCTGGGT 60.848 63.158 12.71 0.00 36.47 4.51
2279 2310 0.661780 TTTTCAAATTCGGCACCGCG 60.662 50.000 3.66 0.00 39.59 6.46
2417 2448 1.139734 CATAGAGTCTGCGGCGTGT 59.860 57.895 9.37 0.00 0.00 4.49
2418 2449 1.589993 CCATAGAGTCTGCGGCGTG 60.590 63.158 9.37 1.75 0.00 5.34
2478 2509 2.836020 AGGAGACGGTTCCTGTTGT 58.164 52.632 8.96 0.00 45.84 3.32


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

AutoCloner maintained by Alex Coulton.