Multiple sequence alignment - TraesCS3B01G419100

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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 TraesCS3B01G419100 chr3B 100.000 2723 0 0 1 2723 655637430 655640152 0.000000e+00 5029.0
1 TraesCS3B01G419100 chr3D 89.240 2119 163 38 7 2090 496681619 496683707 0.000000e+00 2590.0
2 TraesCS3B01G419100 chr3D 88.832 394 12 7 2334 2723 496686022 496686387 3.200000e-124 455.0
3 TraesCS3B01G419100 chr3D 84.906 212 22 5 8 217 496681160 496681363 3.550000e-49 206.0
4 TraesCS3B01G419100 chr3D 89.600 125 13 0 2119 2243 496684730 496684854 2.810000e-35 159.0
5 TraesCS3B01G419100 chr3D 100.000 37 0 0 2087 2123 496684418 496684454 4.870000e-08 69.4
6 TraesCS3B01G419100 chr3A 91.887 1516 82 18 453 1948 638201609 638200115 0.000000e+00 2080.0
7 TraesCS3B01G419100 chr3A 84.924 524 48 12 1937 2457 638200096 638199601 4.050000e-138 501.0
8 TraesCS3B01G419100 chr3A 97.531 243 5 1 159 400 638201851 638201609 5.420000e-112 414.0
9 TraesCS3B01G419100 chr3A 91.007 278 14 8 2449 2723 638199374 638199105 5.540000e-97 364.0
10 TraesCS3B01G419100 chr3A 96.203 158 5 1 4 160 638202090 638201933 9.670000e-65 257.0
11 TraesCS3B01G419100 chr5A 78.037 601 82 25 1197 1749 322836770 322837368 1.560000e-87 333.0
12 TraesCS3B01G419100 chr4A 77.704 601 84 24 1197 1749 507597711 507598309 3.380000e-84 322.0


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 TraesCS3B01G419100 chr3B 655637430 655640152 2722 False 5029.00 5029 100.0000 1 2723 1 chr3B.!!$F1 2722
1 TraesCS3B01G419100 chr3D 496681160 496686387 5227 False 695.88 2590 90.5156 7 2723 5 chr3D.!!$F1 2716
2 TraesCS3B01G419100 chr3A 638199105 638202090 2985 True 723.20 2080 92.3104 4 2723 5 chr3A.!!$R1 2719
3 TraesCS3B01G419100 chr5A 322836770 322837368 598 False 333.00 333 78.0370 1197 1749 1 chr5A.!!$F1 552
4 TraesCS3B01G419100 chr4A 507597711 507598309 598 False 322.00 322 77.7040 1197 1749 1 chr4A.!!$F1 552

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
790 1359 0.319297 GCCTTTTCTTGTGCAGCTGG 60.319 55.0 17.12 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 3848 0.17668 GAAGCTGCCTCCATCTCGAA 59.823 55.0 0.0 0.0 0.0 3.71 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
206 753 6.449635 TGTTTTGTGATTTCTGTGCTAAGT 57.550 33.333 0.00 0.00 0.00 2.24
292 845 1.531058 GCGTGGTGTGTTGACAAGTTC 60.531 52.381 0.00 0.00 32.49 3.01
377 931 2.754472 TGTTCAGATTGTCACTGTCCG 58.246 47.619 0.00 0.00 36.81 4.79
400 954 2.076863 CCACCTAAAAACGAGCCTCTG 58.923 52.381 0.00 0.00 0.00 3.35
405 959 1.620822 AAAAACGAGCCTCTGCCAAT 58.379 45.000 0.00 0.00 38.69 3.16
407 961 1.620822 AAACGAGCCTCTGCCAATTT 58.379 45.000 0.00 0.00 38.69 1.82
408 962 0.883833 AACGAGCCTCTGCCAATTTG 59.116 50.000 0.00 0.00 38.69 2.32
420 974 4.883585 TCTGCCAATTTGTGATACTCATCC 59.116 41.667 0.00 0.00 0.00 3.51
488 1044 1.512926 AGCACGAAATTTGAGTCGCT 58.487 45.000 0.00 5.23 40.95 4.93
489 1045 1.873591 AGCACGAAATTTGAGTCGCTT 59.126 42.857 0.00 0.00 40.95 4.68
595 1160 0.326927 CGGACCCCTTAAAGCCTTCA 59.673 55.000 0.00 0.00 0.00 3.02
636 1201 2.623535 TGAAGGCATGCATCATTTTGC 58.376 42.857 21.36 0.00 43.07 3.68
789 1358 0.386476 TGCCTTTTCTTGTGCAGCTG 59.614 50.000 10.11 10.11 0.00 4.24
790 1359 0.319297 GCCTTTTCTTGTGCAGCTGG 60.319 55.000 17.12 0.00 0.00 4.85
869 1438 2.664851 TGCGCCGTTTGTCTCCAG 60.665 61.111 4.18 0.00 0.00 3.86
970 1545 4.430007 CAGCCATACACGTACATGTAGTT 58.570 43.478 5.62 0.00 38.43 2.24
971 1546 4.503007 CAGCCATACACGTACATGTAGTTC 59.497 45.833 5.62 0.00 38.43 3.01
973 1548 4.678574 GCCATACACGTACATGTAGTTCCA 60.679 45.833 5.62 0.00 38.43 3.53
979 1554 3.259064 CGTACATGTAGTTCCACCTTGG 58.741 50.000 5.62 0.00 39.43 3.61
1004 1581 4.437930 GGAAATCTTCCGAGTTTGCATGAG 60.438 45.833 0.00 0.00 40.59 2.90
1115 1692 1.273886 GGAGTCCAGCGTCTTCTTCTT 59.726 52.381 3.60 0.00 0.00 2.52
1116 1693 2.289133 GGAGTCCAGCGTCTTCTTCTTT 60.289 50.000 3.60 0.00 0.00 2.52
1139 1716 4.308458 CGTGACGTCCAGGGCCAA 62.308 66.667 14.12 0.00 0.00 4.52
1140 1717 2.358737 GTGACGTCCAGGGCCAAG 60.359 66.667 14.12 0.00 0.00 3.61
1164 1744 1.001597 GACAGGCTATCGTACTTCCGG 60.002 57.143 0.00 0.00 0.00 5.14
1302 1883 1.153086 GGTCCTTGCAGCCGATGAT 60.153 57.895 0.00 0.00 0.00 2.45
1388 1982 2.957489 CGTCCGTGACACGTGCAA 60.957 61.111 25.18 0.00 40.58 4.08
1389 1983 2.624264 GTCCGTGACACGTGCAAC 59.376 61.111 25.18 13.19 40.58 4.17
1500 2094 0.739462 CGGCTGCAAACTCGATGGTA 60.739 55.000 0.50 0.00 0.00 3.25
1501 2095 1.668419 GGCTGCAAACTCGATGGTAT 58.332 50.000 0.50 0.00 0.00 2.73
1556 2158 4.069232 CAAGGACGAGGAGGCGCA 62.069 66.667 10.83 0.00 33.86 6.09
1668 2288 2.980233 GTGGTGCTGTGCCTGGTC 60.980 66.667 0.00 0.00 0.00 4.02
1805 2441 4.919168 CGTCGTCTTATTGTACTTCACCAA 59.081 41.667 0.00 0.00 0.00 3.67
1815 2451 3.830178 TGTACTTCACCAACTAGCTAGCA 59.170 43.478 20.91 3.08 0.00 3.49
1816 2452 3.601443 ACTTCACCAACTAGCTAGCAG 57.399 47.619 20.91 14.32 0.00 4.24
1817 2453 2.275318 CTTCACCAACTAGCTAGCAGC 58.725 52.381 20.91 0.00 42.84 5.25
1862 2498 2.673862 GGAAAGAAACTAAGCTCCGAGC 59.326 50.000 12.80 12.80 42.84 5.03
1871 2507 4.921834 GCTCCGAGCTTAGCTTGT 57.078 55.556 18.99 0.00 39.88 3.16
1872 2508 3.145228 GCTCCGAGCTTAGCTTGTT 57.855 52.632 18.99 0.00 39.88 2.83
1873 2509 0.723981 GCTCCGAGCTTAGCTTGTTG 59.276 55.000 18.99 12.25 39.88 3.33
1874 2510 0.723981 CTCCGAGCTTAGCTTGTTGC 59.276 55.000 18.99 0.41 39.88 4.17
1897 2533 6.133392 GCTGCTGCGACGATTAATTTATTTA 58.867 36.000 0.00 0.00 0.00 1.40
1920 2573 4.084013 ACGTAGTTGCATGCTAAGAAACAC 60.084 41.667 20.33 12.84 37.78 3.32
1935 2626 4.649692 AGAAACACATCTCATGCTTCTGT 58.350 39.130 0.00 0.00 30.49 3.41
1959 2650 7.094420 TGTTCATCGTCATGTCCAAATAACAAT 60.094 33.333 0.00 0.00 0.00 2.71
1998 2689 4.081406 TGAATTGTCAGTTCATCCTTGGG 58.919 43.478 6.67 0.00 31.07 4.12
2002 2693 0.613260 TCAGTTCATCCTTGGGACGG 59.387 55.000 0.00 0.00 32.98 4.79
2070 2761 1.440938 TTTTGACAACCGGCCTGTCG 61.441 55.000 24.58 1.36 45.10 4.35
2129 3814 1.881973 TGAGGTGCATCAGAAAACAGC 59.118 47.619 0.00 0.00 0.00 4.40
2245 3930 5.606505 GGAACCCTATGAAATCTCTCTGTC 58.393 45.833 0.00 0.00 0.00 3.51
2248 3933 3.553922 CCCTATGAAATCTCTCTGTCGCC 60.554 52.174 0.00 0.00 0.00 5.54
2255 3941 1.256812 TCTCTCTGTCGCCACAATGA 58.743 50.000 0.00 0.00 29.82 2.57
2280 4768 3.181479 CGCTGCTAGTGATAACCCAGTAA 60.181 47.826 0.00 0.00 0.00 2.24
2299 4787 6.272318 CAGTAAAGAACACCTTGAATTGCAA 58.728 36.000 0.00 0.00 34.79 4.08
2300 4788 6.756074 CAGTAAAGAACACCTTGAATTGCAAA 59.244 34.615 1.71 0.00 35.74 3.68
2301 4789 7.277539 CAGTAAAGAACACCTTGAATTGCAAAA 59.722 33.333 1.71 0.00 35.74 2.44
2302 4790 7.821846 AGTAAAGAACACCTTGAATTGCAAAAA 59.178 29.630 1.71 0.00 35.74 1.94
2400 5162 3.425404 GCAAAGTATACACCGCAATGTG 58.575 45.455 5.50 0.00 42.05 3.21
2487 5485 5.439721 CTGGGGTAGTTGATGAATGATTCA 58.560 41.667 10.65 10.65 45.01 2.57
2490 5488 6.896860 TGGGGTAGTTGATGAATGATTCAAAT 59.103 34.615 12.36 0.00 43.95 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.942829 CAGAGCTGTGAAATCTGGGTAA 58.057 45.455 4.50 0.00 37.41 2.85
1 2 3.616956 CAGAGCTGTGAAATCTGGGTA 57.383 47.619 4.50 0.00 37.41 3.69
2 3 2.486472 CAGAGCTGTGAAATCTGGGT 57.514 50.000 4.50 0.00 37.41 4.51
13 14 8.011795 CATAATTATATGTGGCTCCAGAGCTGT 61.012 40.741 18.54 5.89 42.39 4.40
206 753 4.734398 AGACAAAAACCAGCAATGACAA 57.266 36.364 0.00 0.00 0.00 3.18
292 845 7.148623 GGAACATCACTAGTAGGAAAAAGAACG 60.149 40.741 1.45 0.00 0.00 3.95
346 899 4.130118 ACAATCTGAACAAGTCACCTGTC 58.870 43.478 0.00 0.00 31.13 3.51
377 931 1.162698 GGCTCGTTTTTAGGTGGTCC 58.837 55.000 0.00 0.00 0.00 4.46
420 974 1.264288 GCAGAACCGAAACAAGTGGAG 59.736 52.381 0.00 0.00 0.00 3.86
483 1039 1.070776 GTGAGTCAAAACGGAAGCGAC 60.071 52.381 0.00 0.00 0.00 5.19
488 1044 3.469739 GGTTAGGTGAGTCAAAACGGAA 58.530 45.455 0.00 0.00 0.00 4.30
489 1045 2.224354 GGGTTAGGTGAGTCAAAACGGA 60.224 50.000 0.00 0.00 0.00 4.69
569 1134 2.878526 GCTTTAAGGGGTCCGATGTTGT 60.879 50.000 0.00 0.00 0.00 3.32
595 1160 1.076632 TGTGGTTTTCGGCCTTGGT 60.077 52.632 0.00 0.00 0.00 3.67
636 1201 0.029035 GAAGCGCCATCTTGATGCAG 59.971 55.000 2.29 2.94 0.00 4.41
789 1358 9.965824 ATGATTTCGGTTTTCATATAATGTTCC 57.034 29.630 0.00 0.00 0.00 3.62
971 1546 0.811281 GAAGATTTCCGCCAAGGTGG 59.189 55.000 12.54 12.54 46.45 4.61
973 1548 3.266240 GGAAGATTTCCGCCAAGGT 57.734 52.632 0.00 0.00 40.59 3.50
1076 1653 4.373116 GGCCGTCACCTTCGCTGA 62.373 66.667 0.00 0.00 0.00 4.26
1136 1713 1.482593 ACGATAGCCTGTCCTTCTTGG 59.517 52.381 0.00 0.00 42.67 3.61
1138 1715 3.633418 AGTACGATAGCCTGTCCTTCTT 58.367 45.455 0.00 0.00 42.67 2.52
1139 1716 3.300239 AGTACGATAGCCTGTCCTTCT 57.700 47.619 0.00 0.00 42.67 2.85
1140 1717 3.243468 GGAAGTACGATAGCCTGTCCTTC 60.243 52.174 0.00 0.00 42.67 3.46
1164 1744 4.373116 TCGCCAACCTCGCTGGAC 62.373 66.667 1.32 0.00 39.71 4.02
1345 1939 3.437795 GAAGCGGACGACCTCGGA 61.438 66.667 1.72 0.00 44.95 4.55
1389 1983 4.559063 CTCCTCCTGGGCATGGCG 62.559 72.222 13.76 0.00 34.39 5.69
1495 2089 2.826702 GTCGCCGGGGAATACCAT 59.173 61.111 24.36 0.00 42.91 3.55
1533 2131 1.248785 CCTCCTCGTCCTTGTCGGAA 61.249 60.000 0.00 0.00 45.32 4.30
1668 2288 2.047274 ATCCACACGCCGAACAGG 60.047 61.111 0.00 0.00 44.97 4.00
1765 2398 2.269241 GGAGAAGGCCTTCGTGGG 59.731 66.667 34.27 0.00 43.97 4.61
1786 2419 7.097834 AGCTAGTTGGTGAAGTACAATAAGAC 58.902 38.462 0.00 0.00 0.00 3.01
1866 2502 2.428071 GTCGCAGCAGCAACAAGC 60.428 61.111 0.82 0.00 42.27 4.01
1867 2503 1.904852 ATCGTCGCAGCAGCAACAAG 61.905 55.000 0.82 0.00 42.27 3.16
1868 2504 1.506309 AATCGTCGCAGCAGCAACAA 61.506 50.000 0.82 0.00 42.27 2.83
1869 2505 0.669012 TAATCGTCGCAGCAGCAACA 60.669 50.000 0.82 0.00 42.27 3.33
1870 2506 0.442310 TTAATCGTCGCAGCAGCAAC 59.558 50.000 0.82 0.00 42.27 4.17
1871 2507 1.368641 ATTAATCGTCGCAGCAGCAA 58.631 45.000 0.82 0.00 42.27 3.91
1872 2508 1.368641 AATTAATCGTCGCAGCAGCA 58.631 45.000 0.82 0.00 42.27 4.41
1873 2509 2.458592 AAATTAATCGTCGCAGCAGC 57.541 45.000 0.00 0.00 37.42 5.25
1874 2510 6.297641 CGTAAATAAATTAATCGTCGCAGCAG 59.702 38.462 0.00 0.00 0.00 4.24
1875 2511 6.124099 CGTAAATAAATTAATCGTCGCAGCA 58.876 36.000 0.00 0.00 0.00 4.41
1876 2512 6.124759 ACGTAAATAAATTAATCGTCGCAGC 58.875 36.000 0.00 0.00 0.00 5.25
1877 2513 8.474577 ACTACGTAAATAAATTAATCGTCGCAG 58.525 33.333 0.00 0.00 0.00 5.18
1878 2514 8.338985 ACTACGTAAATAAATTAATCGTCGCA 57.661 30.769 0.00 0.00 0.00 5.10
1879 2515 9.074316 CAACTACGTAAATAAATTAATCGTCGC 57.926 33.333 0.00 0.00 0.00 5.19
1880 2516 9.074316 GCAACTACGTAAATAAATTAATCGTCG 57.926 33.333 0.00 0.00 0.00 5.12
1881 2517 9.904647 TGCAACTACGTAAATAAATTAATCGTC 57.095 29.630 0.00 0.00 0.00 4.20
1897 2533 4.062293 TGTTTCTTAGCATGCAACTACGT 58.938 39.130 21.98 0.00 0.00 3.57
1912 2565 5.068636 ACAGAAGCATGAGATGTGTTTCTT 58.931 37.500 0.00 0.00 42.15 2.52
1920 2573 3.869832 ACGATGAACAGAAGCATGAGATG 59.130 43.478 0.00 0.00 0.00 2.90
1935 2626 6.809630 TTGTTATTTGGACATGACGATGAA 57.190 33.333 0.00 0.00 33.36 2.57
1959 2650 2.136298 TCACAACAACCTTCTGCCAA 57.864 45.000 0.00 0.00 0.00 4.52
1998 2689 0.716108 CTGAAAGACATCGCACCGTC 59.284 55.000 0.00 0.00 34.07 4.79
2002 2693 1.421485 CCGCTGAAAGACATCGCAC 59.579 57.895 0.00 0.00 36.90 5.34
2140 3825 6.097915 AGACTTTAACAGCTACAGCAGTAA 57.902 37.500 3.70 0.00 45.16 2.24
2149 3834 5.417894 TCCATCTCGAAGACTTTAACAGCTA 59.582 40.000 0.00 0.00 0.00 3.32
2157 3842 1.902508 TGCCTCCATCTCGAAGACTTT 59.097 47.619 0.00 0.00 0.00 2.66
2163 3848 0.176680 GAAGCTGCCTCCATCTCGAA 59.823 55.000 0.00 0.00 0.00 3.71
2220 3905 4.657969 CAGAGAGATTTCATAGGGTTCCCT 59.342 45.833 15.19 15.19 40.06 4.20
2223 3908 5.285651 CGACAGAGAGATTTCATAGGGTTC 58.714 45.833 0.00 0.00 0.00 3.62
2227 3912 3.068732 TGGCGACAGAGAGATTTCATAGG 59.931 47.826 0.00 0.00 35.01 2.57
2229 3914 3.447229 TGTGGCGACAGAGAGATTTCATA 59.553 43.478 0.00 0.00 44.46 2.15
2248 3933 1.346197 CTAGCAGCGCGTCATTGTG 59.654 57.895 8.43 0.00 0.00 3.33
2255 3941 0.527817 GGTTATCACTAGCAGCGCGT 60.528 55.000 8.43 0.00 0.00 6.01
2400 5162 1.293179 GGTCTGCAAATGGCCCAAC 59.707 57.895 0.00 0.00 43.89 3.77
2507 5508 1.600957 AGCTCGATTGATTGCCATTCG 59.399 47.619 0.00 0.00 45.08 3.34
2586 5588 6.248569 AGTCATAGGTTGGTAGGGTTATTG 57.751 41.667 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.