Multiple sequence alignment - TraesCS6B01G208000

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 TraesCS6B01G208000 chr6B 100.000 2486 0 0 1 2486 264980152 264977667 0.000000e+00 4591.0
1 TraesCS6B01G208000 chr6B 95.619 2488 105 4 1 2486 388136402 388138887 0.000000e+00 3988.0
2 TraesCS6B01G208000 chr6B 97.251 1746 46 2 1 1744 128897084 128895339 0.000000e+00 2957.0
3 TraesCS6B01G208000 chr6B 82.190 758 112 15 1736 2484 606986215 606986958 4.510000e-177 630.0
4 TraesCS6B01G208000 chr6B 93.443 61 3 1 1952 2012 72337414 72337355 3.410000e-14 89.8
5 TraesCS6B01G208000 chr3B 95.701 2489 102 5 1 2486 669904715 669907201 0.000000e+00 3999.0
6 TraesCS6B01G208000 chr2B 95.498 2488 104 8 1 2486 526494335 526491854 0.000000e+00 3967.0
7 TraesCS6B01G208000 chr2B 95.221 2490 113 6 1 2486 357333382 357335869 0.000000e+00 3934.0
8 TraesCS6B01G208000 chr2B 94.868 721 29 2 1767 2486 391176537 391177250 0.000000e+00 1120.0
9 TraesCS6B01G208000 chr7A 97.194 1746 47 2 1 1744 200014075 200012330 0.000000e+00 2952.0
10 TraesCS6B01G208000 chr7B 97.136 1746 48 2 1 1744 742930384 742932129 0.000000e+00 2946.0
11 TraesCS6B01G208000 chr7B 97.079 1746 48 3 1 1744 698133711 698131967 0.000000e+00 2939.0
12 TraesCS6B01G208000 chrUn 96.966 1747 50 2 1 1744 246704097 246702351 0.000000e+00 2929.0
13 TraesCS6B01G208000 chr6A 93.710 779 42 1 1708 2486 597223374 597224145 0.000000e+00 1160.0
14 TraesCS6B01G208000 chr3D 83.201 756 100 17 1735 2484 308557205 308556471 0.000000e+00 667.0
15 TraesCS6B01G208000 chr3D 82.322 758 108 17 1735 2484 399731330 399732069 3.490000e-178 634.0
16 TraesCS6B01G208000 chr4D 82.804 756 105 20 1735 2484 450896753 450896017 0.000000e+00 652.0
17 TraesCS6B01G208000 chr6D 83.688 141 21 2 1735 1875 370023945 370024083 5.580000e-27 132.0


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 TraesCS6B01G208000 chr6B 264977667 264980152 2485 True 4591 4591 100.000 1 2486 1 chr6B.!!$R3 2485
1 TraesCS6B01G208000 chr6B 388136402 388138887 2485 False 3988 3988 95.619 1 2486 1 chr6B.!!$F1 2485
2 TraesCS6B01G208000 chr6B 128895339 128897084 1745 True 2957 2957 97.251 1 1744 1 chr6B.!!$R2 1743
3 TraesCS6B01G208000 chr6B 606986215 606986958 743 False 630 630 82.190 1736 2484 1 chr6B.!!$F2 748
4 TraesCS6B01G208000 chr3B 669904715 669907201 2486 False 3999 3999 95.701 1 2486 1 chr3B.!!$F1 2485
5 TraesCS6B01G208000 chr2B 526491854 526494335 2481 True 3967 3967 95.498 1 2486 1 chr2B.!!$R1 2485
6 TraesCS6B01G208000 chr2B 357333382 357335869 2487 False 3934 3934 95.221 1 2486 1 chr2B.!!$F1 2485
7 TraesCS6B01G208000 chr2B 391176537 391177250 713 False 1120 1120 94.868 1767 2486 1 chr2B.!!$F2 719
8 TraesCS6B01G208000 chr7A 200012330 200014075 1745 True 2952 2952 97.194 1 1744 1 chr7A.!!$R1 1743
9 TraesCS6B01G208000 chr7B 742930384 742932129 1745 False 2946 2946 97.136 1 1744 1 chr7B.!!$F1 1743
10 TraesCS6B01G208000 chr7B 698131967 698133711 1744 True 2939 2939 97.079 1 1744 1 chr7B.!!$R1 1743
11 TraesCS6B01G208000 chrUn 246702351 246704097 1746 True 2929 2929 96.966 1 1744 1 chrUn.!!$R1 1743
12 TraesCS6B01G208000 chr6A 597223374 597224145 771 False 1160 1160 93.710 1708 2486 1 chr6A.!!$F1 778
13 TraesCS6B01G208000 chr3D 308556471 308557205 734 True 667 667 83.201 1735 2484 1 chr3D.!!$R1 749
14 TraesCS6B01G208000 chr3D 399731330 399732069 739 False 634 634 82.322 1735 2484 1 chr3D.!!$F1 749
15 TraesCS6B01G208000 chr4D 450896017 450896753 736 True 652 652 82.804 1735 2484 1 chr4D.!!$R1 749

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
231 232 0.323629 TCGACCGGGAGAAGCAAAAT 59.676 50.0 6.32 0.0 0.00 1.82 F
493 494 0.843343 AAAAAGGACCCTCCCCGCTA 60.843 55.0 0.00 0.0 37.19 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1284 1293 0.390860 CACCCCCTAATCGAGCAGAG 59.609 60.0 0.0 0.0 0.00 3.35 R
1988 2001 0.610174 CCAGCAGCTCTGTTCCTACA 59.390 55.0 0.0 0.0 41.25 2.74 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
87 88 5.733620 AGAAATCAAGACCCGTACTACAA 57.266 39.130 0.00 0.00 0.00 2.41
90 91 4.985538 ATCAAGACCCGTACTACAAGAG 57.014 45.455 0.00 0.00 0.00 2.85
231 232 0.323629 TCGACCGGGAGAAGCAAAAT 59.676 50.000 6.32 0.00 0.00 1.82
238 239 3.445096 CCGGGAGAAGCAAAATGAAATCT 59.555 43.478 0.00 0.00 0.00 2.40
340 341 1.671742 GTGAGCGGGACCTTCAAGA 59.328 57.895 0.00 0.00 0.00 3.02
493 494 0.843343 AAAAAGGACCCTCCCCGCTA 60.843 55.000 0.00 0.00 37.19 4.26
790 793 5.221541 GGGAACAACAAAAACCACCATATCA 60.222 40.000 0.00 0.00 0.00 2.15
807 810 6.151817 ACCATATCACTCTTTCCTTTCTTTGC 59.848 38.462 0.00 0.00 0.00 3.68
842 848 1.077298 TCAAAGGGATGGGGTTGGGT 61.077 55.000 0.00 0.00 0.00 4.51
853 859 6.137559 GGATGGGGTTGGGTTGTATAATAAA 58.862 40.000 0.00 0.00 0.00 1.40
859 866 7.038160 GGGGTTGGGTTGTATAATAAACCTTTT 60.038 37.037 11.18 0.00 44.43 2.27
980 988 7.949006 TCATAGACCTAGGTAGGATAGGAAAAC 59.051 40.741 16.29 0.00 46.63 2.43
1003 1012 7.072263 ACTGATAAAGGGAATAGAGTGATGG 57.928 40.000 0.00 0.00 0.00 3.51
1016 1025 8.588290 AATAGAGTGATGGTAGAGATCATACC 57.412 38.462 16.49 16.49 42.62 2.73
1060 1069 5.613329 ACGGGTACAACTCTTATTTGAACA 58.387 37.500 0.00 0.00 0.00 3.18
1212 1221 6.349280 GGAACAATCCAATCTCATTTCGTTCA 60.349 38.462 0.00 0.00 45.79 3.18
1284 1293 5.052481 GTGGAGGGGATACGTATTTGTTAC 58.948 45.833 9.92 0.91 37.60 2.50
1289 1298 4.748600 GGGGATACGTATTTGTTACTCTGC 59.251 45.833 9.92 0.00 37.60 4.26
1305 1314 1.971505 CTGCTCGATTAGGGGGTGCA 61.972 60.000 0.00 0.00 0.00 4.57
1476 1485 6.041296 AGGGACTTGTTATATCCGAAACGTAT 59.959 38.462 0.00 0.00 27.25 3.06
1566 1575 4.799564 TTGGAAGATATGGCACCAAAAC 57.200 40.909 2.80 0.00 37.62 2.43
1588 1597 1.199327 TGTAGAGCTGGTCGTCTTTCG 59.801 52.381 0.00 0.00 41.41 3.46
1602 1611 2.540101 GTCTTTCGTATCGAGCCATTGG 59.460 50.000 0.00 0.00 37.14 3.16
1667 1676 4.168760 GAGCGGACAATTCCAAAGAAATG 58.831 43.478 0.00 0.00 43.00 2.32
1799 1811 8.512966 TTATTCTTTTTGTTTCTTTTTGGGGG 57.487 30.769 0.00 0.00 0.00 5.40
1842 1854 4.006989 TGTGATTGCGGCTGTAGTTTTAT 58.993 39.130 0.00 0.00 0.00 1.40
1931 1943 7.827236 ACCCAATCTTTTTATCACATTCTACGA 59.173 33.333 0.00 0.00 0.00 3.43
1980 1992 2.017559 GAGTGGACGGGAGCGCTATT 62.018 60.000 11.50 0.00 0.00 1.73
2112 2128 1.951602 GAGCGTTAACCAACAAAGGGT 59.048 47.619 0.00 0.00 41.41 4.34
2154 2170 6.145048 CGTTTAACTATTGACTTGAACCGACT 59.855 38.462 0.00 0.00 0.00 4.18
2294 2310 0.945099 CGCCTACGTCAGAGATGCTA 59.055 55.000 0.00 0.00 33.53 3.49
2419 2435 5.469421 GCAAAGAAGAGTCATATGGGATCTG 59.531 44.000 2.13 0.00 0.00 2.90
2471 2487 4.993705 AAGATCCCACCTGAACTACAAA 57.006 40.909 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 123 1.330655 ATGAAGACACCCGATCGGCT 61.331 55.000 29.12 17.06 33.26 5.52
231 232 2.505650 TCGGCCAAATCCAGATTTCA 57.494 45.000 2.24 0.00 38.84 2.69
238 239 2.353605 GCATCTTTTTCGGCCAAATCCA 60.354 45.455 2.24 0.00 0.00 3.41
430 431 1.550976 AGAGCGGGACTTCTTTGGTAG 59.449 52.381 0.00 0.00 0.00 3.18
493 494 0.550914 TAATTCAAGGAGGGGCGCAT 59.449 50.000 10.83 0.00 0.00 4.73
759 762 1.096416 TTTTGTTGTTCCCGCGAAGT 58.904 45.000 8.23 0.00 0.00 3.01
790 793 3.560105 AGCAGCAAAGAAAGGAAAGAGT 58.440 40.909 0.00 0.00 0.00 3.24
825 831 0.178906 CAACCCAACCCCATCCCTTT 60.179 55.000 0.00 0.00 0.00 3.11
859 866 5.127491 AGTTGTTTCCGGACATACTCAAAA 58.873 37.500 1.83 0.00 0.00 2.44
870 878 1.549170 GAGCTAGGAGTTGTTTCCGGA 59.451 52.381 0.00 0.00 42.29 5.14
980 988 7.072263 ACCATCACTCTATTCCCTTTATCAG 57.928 40.000 0.00 0.00 0.00 2.90
1003 1012 5.998981 TCCTCTTTCTCGGTATGATCTCTAC 59.001 44.000 0.00 0.00 0.00 2.59
1016 1025 4.910456 CGTACGGAATTATCCTCTTTCTCG 59.090 45.833 7.57 0.00 44.17 4.04
1284 1293 0.390860 CACCCCCTAATCGAGCAGAG 59.609 60.000 0.00 0.00 0.00 3.35
1289 1298 0.830648 TTCTGCACCCCCTAATCGAG 59.169 55.000 0.00 0.00 0.00 4.04
1305 1314 5.053145 CCGCATTCAGTTCTAGCTATTTCT 58.947 41.667 0.00 0.00 0.00 2.52
1365 1374 4.214980 CGCAGGAGCATAATCGATTTTT 57.785 40.909 17.19 1.51 42.27 1.94
1538 1547 4.020662 GGTGCCATATCTTCCAAAACCAAA 60.021 41.667 0.00 0.00 0.00 3.28
1566 1575 3.246619 GAAAGACGACCAGCTCTACAAG 58.753 50.000 0.00 0.00 0.00 3.16
1588 1597 1.506493 CTGCTCCAATGGCTCGATAC 58.494 55.000 0.00 0.00 0.00 2.24
1667 1676 6.679843 CGAGAACTCTTACCCATATCTTACC 58.320 44.000 0.41 0.00 0.00 2.85
1718 1727 3.307059 CCTCTTCCCATTCGAACTTCTGT 60.307 47.826 0.00 0.00 0.00 3.41
1799 1811 7.500992 TCACAATGAGAACTATTATCAGTCCC 58.499 38.462 0.00 0.00 0.00 4.46
1842 1854 4.278310 TCTGTCACGATCAAAGAGGGATA 58.722 43.478 0.00 0.00 0.00 2.59
1931 1943 2.289010 CCGCATTTCTTCAAAAAGGGCT 60.289 45.455 0.00 0.00 33.03 5.19
1988 2001 0.610174 CCAGCAGCTCTGTTCCTACA 59.390 55.000 0.00 0.00 41.25 2.74
2112 2128 2.268920 GAGGCACATCGCTCCCAA 59.731 61.111 0.00 0.00 41.91 4.12
2130 2146 7.288672 CAGTCGGTTCAAGTCAATAGTTAAAC 58.711 38.462 0.00 0.00 0.00 2.01
2154 2170 2.187239 ATCTTCCTGATCCTGAGCCA 57.813 50.000 0.00 0.00 0.00 4.75
2294 2310 7.013464 TCGGATACACTGGTTTTTAACAACATT 59.987 33.333 6.81 0.00 0.00 2.71
2374 2390 1.404717 CCTTCACTGTCATCCGTCTGG 60.405 57.143 0.00 0.00 0.00 3.86
2419 2435 4.885907 TCATCCTGGAAATGAAGCTTGATC 59.114 41.667 2.10 0.00 30.37 2.92


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

AutoCloner maintained by Alex Coulton.