Multiple sequence alignment - TraesCS6A01G115600

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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 TraesCS6A01G115600 chr6A 100.000 2378 0 0 1 2378 85572013 85574390 0.000000e+00 4392
1 TraesCS6A01G115600 chr6D 93.422 2250 98 20 1 2219 68080631 68082861 0.000000e+00 3290
2 TraesCS6A01G115600 chr6B 93.304 1374 57 7 155 1505 142990903 142992264 0.000000e+00 1995
3 TraesCS6A01G115600 chr6B 91.964 784 36 10 1606 2376 142992321 142993090 0.000000e+00 1074
4 TraesCS6A01G115600 chr6B 92.275 233 16 2 2146 2378 142993116 142993346 1.760000e-86 329
5 TraesCS6A01G115600 chr6B 89.571 163 3 4 1 156 142990718 142990873 6.710000e-46 195
6 TraesCS6A01G115600 chr2D 78.859 298 52 8 2068 2360 14827213 14826922 8.680000e-45 191
7 TraesCS6A01G115600 chr2B 78.523 298 53 9 2068 2360 26709845 26709554 4.040000e-43 185
8 TraesCS6A01G115600 chr2B 78.523 298 53 9 2068 2360 26730488 26730197 4.040000e-43 185
9 TraesCS6A01G115600 chr7A 84.783 184 26 2 1099 1280 609410808 609410991 1.450000e-42 183
10 TraesCS6A01G115600 chr7A 81.383 188 30 4 2173 2358 19078042 19077858 5.300000e-32 148
11 TraesCS6A01G115600 chr7A 79.245 212 36 7 2148 2356 188573718 188573924 8.860000e-30 141
12 TraesCS6A01G115600 chr2A 82.011 189 28 6 2173 2359 27627284 27627468 3.160000e-34 156
13 TraesCS6A01G115600 chr7B 75.347 288 58 12 2078 2360 606211337 606211616 2.480000e-25 126


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 TraesCS6A01G115600 chr6A 85572013 85574390 2377 False 4392.00 4392 100.0000 1 2378 1 chr6A.!!$F1 2377
1 TraesCS6A01G115600 chr6D 68080631 68082861 2230 False 3290.00 3290 93.4220 1 2219 1 chr6D.!!$F1 2218
2 TraesCS6A01G115600 chr6B 142990718 142993346 2628 False 898.25 1995 91.7785 1 2378 4 chr6B.!!$F1 2377

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
962 1031 0.108585 GACCAACCAGCCACTCTTCA 59.891 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2168 2253 3.565902 CAGAGTGAGGTGAACTTTTTCCC 59.434 47.826 0.0 0.0 0.0 3.97 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
50 51 7.178712 AGTGAACTTTATGATACAATAGCGC 57.821 36.000 0.00 0.00 0.00 5.92
212 251 6.803154 AGACTGAAATTAACCAGCTAACAC 57.197 37.500 0.00 0.00 33.90 3.32
231 270 8.284693 GCTAACACTAGTCGGTGAATTTAAAAA 58.715 33.333 0.00 0.00 40.13 1.94
254 294 5.776358 ACAGATGCATATTTTCCCCCTTTA 58.224 37.500 0.00 0.00 0.00 1.85
398 439 9.661563 AATAAATGAAGATAAGACGTGTAACCA 57.338 29.630 0.00 0.00 0.00 3.67
445 490 4.463050 AGTCCCTAACCAAAACCATTGA 57.537 40.909 0.00 0.00 0.00 2.57
452 497 6.705825 CCCTAACCAAAACCATTGAAGAAAAG 59.294 38.462 0.00 0.00 0.00 2.27
483 528 0.965363 ACACGCCATTCCATTGACCC 60.965 55.000 0.00 0.00 0.00 4.46
510 557 4.334443 CACATACGCTTTCATTACACTGC 58.666 43.478 0.00 0.00 0.00 4.40
535 582 1.881973 GACAGCCAGCTGAACATTTGA 59.118 47.619 25.66 0.00 46.30 2.69
536 583 1.884579 ACAGCCAGCTGAACATTTGAG 59.115 47.619 25.66 0.00 46.30 3.02
559 606 5.009010 AGCAATAATCAAGAAAGCATACCCG 59.991 40.000 0.00 0.00 0.00 5.28
766 814 2.358737 AAGAACAAGAGCCGCCCG 60.359 61.111 0.00 0.00 0.00 6.13
771 819 2.978010 CAAGAGCCGCCCGTTGTT 60.978 61.111 0.00 0.00 0.00 2.83
797 845 4.614036 CAACCACCCCACCCCACC 62.614 72.222 0.00 0.00 0.00 4.61
813 861 1.406341 CCACCCCGCCCATAATATACG 60.406 57.143 0.00 0.00 0.00 3.06
859 907 2.356432 CCTCACATGCTTTGATCCCTCA 60.356 50.000 0.00 0.00 0.00 3.86
940 1003 1.958205 GGAGCCGATCATCGCAAGG 60.958 63.158 0.00 0.00 38.82 3.61
943 1006 2.589492 GCCGATCATCGCAAGGTCG 61.589 63.158 0.00 0.00 38.82 4.79
962 1031 0.108585 GACCAACCAGCCACTCTTCA 59.891 55.000 0.00 0.00 0.00 3.02
976 1045 0.941542 TCTTCACCGTTTCTTTGGCG 59.058 50.000 0.00 0.00 0.00 5.69
1171 1240 2.047655 GGTTCGTGGTGCCGATGA 60.048 61.111 0.00 0.00 36.62 2.92
1436 1505 0.695924 TTTGTCCCGGTCATGTGGAT 59.304 50.000 0.00 0.00 0.00 3.41
1498 1567 0.818938 TGATCCGTCCGATTTCCGAA 59.181 50.000 0.00 0.00 41.76 4.30
1506 1583 2.943033 GTCCGATTTCCGAATCACCATT 59.057 45.455 0.00 0.00 41.43 3.16
1514 1591 1.545582 CCGAATCACCATTGGTTTGCT 59.454 47.619 5.34 0.00 31.02 3.91
1527 1604 8.934697 ACCATTGGTTTGCTAGTAGATAGATAA 58.065 33.333 1.37 0.00 28.76 1.75
1537 1614 9.884636 TGCTAGTAGATAGATAATCTCTCACTC 57.115 37.037 0.00 0.00 44.17 3.51
1540 1617 8.771920 AGTAGATAGATAATCTCTCACTCGTG 57.228 38.462 0.00 0.00 44.17 4.35
1543 1620 7.450074 AGATAGATAATCTCTCACTCGTGTCT 58.550 38.462 0.00 0.00 41.32 3.41
1544 1621 5.749596 AGATAATCTCTCACTCGTGTCTG 57.250 43.478 0.00 0.00 0.00 3.51
1546 1623 2.498644 ATCTCTCACTCGTGTCTGGA 57.501 50.000 0.00 0.00 0.00 3.86
1549 1626 1.466950 CTCTCACTCGTGTCTGGACTC 59.533 57.143 2.38 0.00 0.00 3.36
1550 1627 1.072489 TCTCACTCGTGTCTGGACTCT 59.928 52.381 2.38 0.00 0.00 3.24
1551 1628 1.198867 CTCACTCGTGTCTGGACTCTG 59.801 57.143 2.38 0.00 0.00 3.35
1554 1633 1.248486 CTCGTGTCTGGACTCTGGAA 58.752 55.000 2.38 0.00 0.00 3.53
1558 1637 3.192844 TCGTGTCTGGACTCTGGAATAAC 59.807 47.826 2.38 0.00 0.00 1.89
1572 1651 8.258007 ACTCTGGAATAACGATGATCTTGTAAA 58.742 33.333 0.00 0.00 0.00 2.01
1578 1657 2.222027 CGATGATCTTGTAAAGGGGCC 58.778 52.381 0.00 0.00 46.24 5.80
1583 1662 1.755200 TCTTGTAAAGGGGCCCTTCT 58.245 50.000 37.04 26.77 43.92 2.85
1729 1808 6.320672 AGCCAGATATTGTTCTCCAGAAATTG 59.679 38.462 0.00 0.00 35.58 2.32
1994 2077 3.591789 CCATAATTCCTGGGAGAGAGGA 58.408 50.000 0.00 0.00 37.87 3.71
2058 2141 7.616313 AGGAGAAACACTACCTTCTAATCTTG 58.384 38.462 0.00 0.00 32.01 3.02
2096 2180 5.306114 AGCCCCACACTAACCTATTTATC 57.694 43.478 0.00 0.00 0.00 1.75
2130 2214 2.110967 GCCACATCAGCATGCGACT 61.111 57.895 13.01 0.00 34.76 4.18
2168 2253 2.019249 ACCTCAACATCCAATCATGCG 58.981 47.619 0.00 0.00 0.00 4.73
2170 2255 1.335810 CTCAACATCCAATCATGCGGG 59.664 52.381 0.00 0.00 0.00 6.13
2188 2530 2.548480 CGGGAAAAAGTTCACCTCACTC 59.452 50.000 0.00 0.00 33.14 3.51
2340 2682 8.165239 TCAAAATATCCATGTACCATACAAGC 57.835 34.615 0.00 0.00 42.76 4.01
2348 2690 7.286313 TCCATGTACCATACAAGCAAATATCA 58.714 34.615 0.00 0.00 42.76 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 6.572182 ACTAGTAGTACACACCCTCTCATA 57.428 41.667 0.00 0.00 0.00 2.15
212 251 7.481798 GCATCTGTTTTTAAATTCACCGACTAG 59.518 37.037 0.00 0.00 0.00 2.57
231 270 3.979501 AGGGGGAAAATATGCATCTGT 57.020 42.857 0.19 0.00 0.00 3.41
398 439 2.158219 TCCATGTAGGGGACGGTGATAT 60.158 50.000 0.00 0.00 38.24 1.63
445 490 5.451908 CGTGTGTTCATATGTGCTTTTCTT 58.548 37.500 1.90 0.00 0.00 2.52
452 497 0.801872 TGGCGTGTGTTCATATGTGC 59.198 50.000 1.90 0.00 0.00 4.57
483 528 4.629634 TGTAATGAAAGCGTATGTGGAGTG 59.370 41.667 0.00 0.00 0.00 3.51
510 557 0.524862 GTTCAGCTGGCTGTCATTGG 59.475 55.000 20.00 0.00 43.96 3.16
535 582 5.009010 CGGGTATGCTTTCTTGATTATTGCT 59.991 40.000 0.00 0.00 0.00 3.91
536 583 5.215160 CGGGTATGCTTTCTTGATTATTGC 58.785 41.667 0.00 0.00 0.00 3.56
559 606 8.950208 AAGCTACTGTATTATTTCTCTTGGAC 57.050 34.615 0.00 0.00 0.00 4.02
771 819 2.609920 GGGTGGTTGGGGTTGGAA 59.390 61.111 0.00 0.00 0.00 3.53
795 843 0.251073 GCGTATATTATGGGCGGGGT 59.749 55.000 0.00 0.00 0.00 4.95
797 845 0.463116 GGGCGTATATTATGGGCGGG 60.463 60.000 0.00 0.00 0.00 6.13
831 879 0.773644 AAAGCATGTGAGGTCTGGGT 59.226 50.000 0.00 0.00 0.00 4.51
832 880 1.171308 CAAAGCATGTGAGGTCTGGG 58.829 55.000 0.00 0.00 0.00 4.45
859 907 1.707200 GAGGAGGAGGAGGAAGGGT 59.293 63.158 0.00 0.00 0.00 4.34
940 1003 1.668151 GAGTGGCTGGTTGGTCGAC 60.668 63.158 7.13 7.13 0.00 4.20
943 1006 0.108585 TGAAGAGTGGCTGGTTGGTC 59.891 55.000 0.00 0.00 0.00 4.02
962 1031 2.517402 TGGCGCCAAAGAAACGGT 60.517 55.556 30.74 0.00 0.00 4.83
991 1060 0.668706 CCCATCATCATCTCGGCGAC 60.669 60.000 4.99 0.00 0.00 5.19
1044 1113 1.001503 CAGGCTCTGGTCCCTCTCT 59.998 63.158 0.00 0.00 0.00 3.10
1171 1240 3.077556 CGGCTGGTGGAGGTAGCT 61.078 66.667 0.00 0.00 37.58 3.32
1436 1505 2.970324 GCAAAGACACGGCGTCCA 60.970 61.111 10.85 0.00 46.69 4.02
1498 1567 5.435686 TCTACTAGCAAACCAATGGTGAT 57.564 39.130 5.34 0.00 35.34 3.06
1506 1583 9.815306 AGAGATTATCTATCTACTAGCAAACCA 57.185 33.333 0.00 0.00 43.75 3.67
1514 1591 9.863845 CACGAGTGAGAGATTATCTATCTACTA 57.136 37.037 16.40 0.00 43.75 1.82
1527 1604 2.088423 GTCCAGACACGAGTGAGAGAT 58.912 52.381 10.50 0.00 0.00 2.75
1536 1613 1.924731 ATTCCAGAGTCCAGACACGA 58.075 50.000 0.00 0.00 0.00 4.35
1537 1614 3.512680 GTTATTCCAGAGTCCAGACACG 58.487 50.000 0.00 0.00 0.00 4.49
1540 1617 4.098044 TCATCGTTATTCCAGAGTCCAGAC 59.902 45.833 0.00 0.00 0.00 3.51
1543 1620 4.895889 AGATCATCGTTATTCCAGAGTCCA 59.104 41.667 0.00 0.00 0.00 4.02
1544 1621 5.461032 AGATCATCGTTATTCCAGAGTCC 57.539 43.478 0.00 0.00 0.00 3.85
1546 1623 6.227298 ACAAGATCATCGTTATTCCAGAGT 57.773 37.500 0.00 0.00 0.00 3.24
1549 1626 7.041780 CCCTTTACAAGATCATCGTTATTCCAG 60.042 40.741 0.00 0.00 0.00 3.86
1550 1627 6.765989 CCCTTTACAAGATCATCGTTATTCCA 59.234 38.462 0.00 0.00 0.00 3.53
1551 1628 6.204882 CCCCTTTACAAGATCATCGTTATTCC 59.795 42.308 0.00 0.00 0.00 3.01
1554 1633 5.063880 GCCCCTTTACAAGATCATCGTTAT 58.936 41.667 0.00 0.00 0.00 1.89
1558 1637 2.222027 GGCCCCTTTACAAGATCATCG 58.778 52.381 0.00 0.00 0.00 3.84
1917 2000 7.545265 CCAGCTGCAAGTATCTTCTTAGATATC 59.455 40.741 8.66 0.00 43.42 1.63
1994 2077 7.956328 AAAAACAGTAAAAGGAGGAGAAGTT 57.044 32.000 0.00 0.00 0.00 2.66
2032 2115 8.750298 CAAGATTAGAAGGTAGTGTTTCTCCTA 58.250 37.037 0.00 0.00 35.42 2.94
2058 2141 5.046591 TGTGGGGCTAGCTATTCATATACAC 60.047 44.000 15.72 9.09 0.00 2.90
2107 2191 4.347865 ATGCTGATGTGGCATGCA 57.652 50.000 21.36 2.54 46.85 3.96
2168 2253 3.565902 CAGAGTGAGGTGAACTTTTTCCC 59.434 47.826 0.00 0.00 0.00 3.97
2170 2255 3.627577 TGCAGAGTGAGGTGAACTTTTTC 59.372 43.478 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.