Multiple sequence alignment - TraesCS6A01G224500

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 TraesCS6A01G224500 chr6A 100.000 3201 0 0 1 3201 421532853 421529653 0.000000e+00 5912.0
1 TraesCS6A01G224500 chr6A 80.652 491 64 18 45 511 426809712 426809229 5.080000e-93 351.0
2 TraesCS6A01G224500 chr6A 77.256 277 55 8 2272 2546 270729757 270729487 4.280000e-34 156.0
3 TraesCS6A01G224500 chr6A 95.181 83 4 0 621 703 207828016 207827934 7.210000e-27 132.0
4 TraesCS6A01G224500 chr2A 98.408 3204 47 4 1 3201 193457709 193454507 0.000000e+00 5631.0
5 TraesCS6A01G224500 chr2A 98.606 2582 34 2 621 3201 193453998 193451418 0.000000e+00 4567.0
6 TraesCS6A01G224500 chr5B 85.343 1576 181 22 1446 2989 319876531 319878088 0.000000e+00 1585.0
7 TraesCS6A01G224500 chr5B 90.411 73 6 1 621 692 297128021 297127949 9.450000e-16 95.3
8 TraesCS6A01G224500 chr3A 98.074 623 9 3 1 620 705112678 705113300 0.000000e+00 1081.0
9 TraesCS6A01G224500 chr3A 83.230 322 32 9 1 303 713795483 713795165 3.150000e-70 276.0
10 TraesCS6A01G224500 chr3A 95.402 87 3 1 619 704 701882626 701882540 1.550000e-28 137.0
11 TraesCS6A01G224500 chr3A 88.636 88 8 2 781 868 723146756 723146671 4.370000e-19 106.0
12 TraesCS6A01G224500 chr2B 87.224 634 63 11 1 618 42138485 42137854 0.000000e+00 706.0
13 TraesCS6A01G224500 chr2B 94.505 91 5 0 621 711 381908863 381908953 1.200000e-29 141.0
14 TraesCS6A01G224500 chr2B 93.478 92 6 0 620 711 381909922 381910013 1.550000e-28 137.0
15 TraesCS6A01G224500 chr7B 85.618 591 74 10 37 618 159581052 159580464 7.590000e-171 610.0
16 TraesCS6A01G224500 chr3D 79.438 783 128 25 2212 2985 557964532 557965290 1.020000e-144 523.0
17 TraesCS6A01G224500 chr3D 78.880 786 132 26 2212 2988 524214128 524213368 4.770000e-138 501.0
18 TraesCS6A01G224500 chr1D 79.363 785 126 27 2212 2985 226842817 226843576 1.320000e-143 520.0
19 TraesCS6A01G224500 chr1D 80.533 488 67 22 45 511 408541979 408541499 1.830000e-92 350.0
20 TraesCS6A01G224500 chr1D 75.000 412 80 14 2402 2800 471620149 471619748 5.490000e-38 169.0
21 TraesCS6A01G224500 chr4D 78.807 788 131 24 2212 2989 137022796 137023557 6.170000e-137 497.0
22 TraesCS6A01G224500 chr1B 78.680 788 133 25 2212 2988 681064682 681063919 2.870000e-135 492.0
23 TraesCS6A01G224500 chr1B 75.064 389 77 16 2402 2776 655782680 655782298 2.560000e-36 163.0
24 TraesCS6A01G224500 chr2D 88.936 235 22 3 388 618 256679289 256679055 1.450000e-73 287.0
25 TraesCS6A01G224500 chr1A 79.365 441 55 26 45 462 427365029 427364602 8.750000e-71 278.0
26 TraesCS6A01G224500 chr1A 76.295 502 85 23 2402 2888 566011097 566010615 1.480000e-58 237.0
27 TraesCS6A01G224500 chr1A 87.500 88 6 5 620 704 548996117 548996032 2.630000e-16 97.1
28 TraesCS6A01G224500 chr6D 81.287 342 42 17 45 370 320065163 320064828 1.140000e-64 257.0
29 TraesCS6A01G224500 chrUn 80.892 157 13 12 700 851 96447710 96447566 1.210000e-19 108.0
30 TraesCS6A01G224500 chr3B 82.540 126 12 6 722 847 460321977 460322092 5.650000e-18 102.0
31 TraesCS6A01G224500 chr3B 94.030 67 4 0 781 847 460340711 460340777 5.650000e-18 102.0
32 TraesCS6A01G224500 chr3B 81.746 126 13 6 722 847 460327965 460328080 2.630000e-16 97.1
33 TraesCS6A01G224500 chr3B 96.000 50 2 0 781 830 460334744 460334793 7.360000e-12 82.4
34 TraesCS6A01G224500 chr3B 96.000 50 2 0 781 830 550725449 550725498 7.360000e-12 82.4
35 TraesCS6A01G224500 chr7D 91.667 72 0 4 616 684 157399939 157399871 9.450000e-16 95.3


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 TraesCS6A01G224500 chr6A 421529653 421532853 3200 True 5912 5912 100.000 1 3201 1 chr6A.!!$R3 3200
1 TraesCS6A01G224500 chr2A 193451418 193457709 6291 True 5099 5631 98.507 1 3201 2 chr2A.!!$R1 3200
2 TraesCS6A01G224500 chr5B 319876531 319878088 1557 False 1585 1585 85.343 1446 2989 1 chr5B.!!$F1 1543
3 TraesCS6A01G224500 chr3A 705112678 705113300 622 False 1081 1081 98.074 1 620 1 chr3A.!!$F1 619
4 TraesCS6A01G224500 chr2B 42137854 42138485 631 True 706 706 87.224 1 618 1 chr2B.!!$R1 617
5 TraesCS6A01G224500 chr7B 159580464 159581052 588 True 610 610 85.618 37 618 1 chr7B.!!$R1 581
6 TraesCS6A01G224500 chr3D 557964532 557965290 758 False 523 523 79.438 2212 2985 1 chr3D.!!$F1 773
7 TraesCS6A01G224500 chr3D 524213368 524214128 760 True 501 501 78.880 2212 2988 1 chr3D.!!$R1 776
8 TraesCS6A01G224500 chr1D 226842817 226843576 759 False 520 520 79.363 2212 2985 1 chr1D.!!$F1 773
9 TraesCS6A01G224500 chr4D 137022796 137023557 761 False 497 497 78.807 2212 2989 1 chr4D.!!$F1 777
10 TraesCS6A01G224500 chr1B 681063919 681064682 763 True 492 492 78.680 2212 2988 1 chr1B.!!$R2 776

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
921 944 1.445716 CCCGCTATCGTCGGTTCTCT 61.446 60.0 0.66 0.0 45.09 3.10 F
1059 1082 0.707616 CAACCCAATCCCCAACCCTA 59.292 55.0 0.00 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2033 2079 1.697432 GTCCACCCATCCCGATATTCA 59.303 52.381 0.0 0.0 0.0 2.57 R
2656 2719 6.822667 AATTGTCAACATCACTTCATAGCA 57.177 33.333 0.0 0.0 0.0 3.49 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
358 374 8.644318 AGAAATGTGACCGTATTCACTTATAC 57.356 34.615 9.63 0.00 45.34 1.47
487 508 9.287373 ACCGGACATCTTTTTAGTGTTAATTAA 57.713 29.630 9.46 0.00 0.00 1.40
522 543 2.945008 CCACACTACATGGGCATTACAG 59.055 50.000 0.00 0.00 33.18 2.74
856 879 2.046292 CCTCATCTCTCCCTCTTTCCC 58.954 57.143 0.00 0.00 0.00 3.97
881 904 3.507143 AACCCTGCACCCTCCCTCT 62.507 63.158 0.00 0.00 0.00 3.69
895 918 3.386402 CCTCCCTCTGATCAAACTCCTAC 59.614 52.174 0.00 0.00 0.00 3.18
921 944 1.445716 CCCGCTATCGTCGGTTCTCT 61.446 60.000 0.66 0.00 45.09 3.10
1007 1030 3.797353 CACCCTACCCATGGCGCT 61.797 66.667 6.09 0.00 0.00 5.92
1013 1036 3.365291 TACCCATGGCGCTGTCGAC 62.365 63.158 9.11 9.11 45.94 4.20
1045 1068 0.953960 CTACAAGTGCGGTCCAACCC 60.954 60.000 0.00 0.00 33.75 4.11
1059 1082 0.707616 CAACCCAATCCCCAACCCTA 59.292 55.000 0.00 0.00 0.00 3.53
1099 1122 2.722201 GCCCTACCACCAGAGACGG 61.722 68.421 0.00 0.00 0.00 4.79
1141 1164 4.154347 GAGGGTGAGGAGGCGCAG 62.154 72.222 10.83 0.00 0.00 5.18
1238 1261 4.541779 CTTCGTCCTCTGATAATTCTCCG 58.458 47.826 0.00 0.00 0.00 4.63
1730 1770 7.069208 AGAGTGAGATAGATGTTGATACTGCAA 59.931 37.037 0.00 0.00 0.00 4.08
2124 2170 2.696759 GGTGGTGGCATTGTACCGC 61.697 63.158 13.85 13.85 44.66 5.68
2143 2189 3.465122 GCGACACGACCATATTTTTGT 57.535 42.857 0.00 0.00 0.00 2.83
2161 2209 1.299850 TCGTTCTGCGTGGTGACTG 60.300 57.895 0.00 0.00 42.13 3.51
2325 2375 1.554617 TGATCCCTCGAGTTTGCATCA 59.445 47.619 12.31 8.07 0.00 3.07
2593 2656 6.862209 TCTGTGACATGCTTGTAAACTTTTT 58.138 32.000 5.05 0.00 35.79 1.94
3118 6276 3.500289 CCCAAGTTCCTCAAAGGATTCCA 60.500 47.826 5.29 0.00 45.34 3.53
3147 6305 6.968904 GGTGTTTATTAGCATTCTGTCACATG 59.031 38.462 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
237 251 5.238650 GCTCCCTATATTTTGTTGCGTGTAT 59.761 40.000 0.00 0.0 0.00 2.29
358 374 7.772292 TCCTCTTGATTTCTGACATTGAATAGG 59.228 37.037 0.00 0.0 0.00 2.57
639 662 1.990563 GAACCATCACGACGTTCGATT 59.009 47.619 13.06 0.0 43.74 3.34
881 904 2.163010 GGACGACGTAGGAGTTTGATCA 59.837 50.000 0.00 0.0 0.00 2.92
921 944 2.225624 TGGGAACAATCAGGGAGAGAGA 60.226 50.000 0.00 0.0 37.44 3.10
951 974 1.450312 GGGAATCGTGGTGGCTCAG 60.450 63.158 0.00 0.0 0.00 3.35
1023 1046 2.334838 GTTGGACCGCACTTGTAGTAG 58.665 52.381 0.00 0.0 0.00 2.57
1045 1068 2.547218 CGTACGATAGGGTTGGGGATTG 60.547 54.545 10.44 0.0 43.77 2.67
1059 1082 2.125673 GTGGCAGGTGCGTACGAT 60.126 61.111 21.65 0.0 43.26 3.73
1099 1122 1.155424 TCGCAACGAACTTGGGTGTC 61.155 55.000 0.00 0.0 42.25 3.67
1141 1164 4.388499 TCCTTCCCGCCTTCGTGC 62.388 66.667 0.00 0.0 0.00 5.34
1638 1678 5.753721 AAGCAAGAGAATACTCCAGTTCT 57.246 39.130 0.00 0.0 43.53 3.01
1730 1770 5.357878 TGATTGAAACTTGAGCTGTTTGAGT 59.642 36.000 5.46 0.0 37.70 3.41
2033 2079 1.697432 GTCCACCCATCCCGATATTCA 59.303 52.381 0.00 0.0 0.00 2.57
2656 2719 6.822667 AATTGTCAACATCACTTCATAGCA 57.177 33.333 0.00 0.0 0.00 3.49
3118 6276 6.714810 TGACAGAATGCTAATAAACACCTGTT 59.285 34.615 0.00 0.0 42.53 3.16
3147 6305 4.953579 TGGGAAAAATAATACCAGGTCAGC 59.046 41.667 0.00 0.0 0.00 4.26


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

AutoCloner maintained by Alex Coulton.