Multiple sequence alignment - TraesCS6A01G113400

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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 TraesCS6A01G113400 chr6A 100.000 3305 0 0 1 3305 83361169 83364473 0.000000e+00 6104.0
1 TraesCS6A01G113400 chr6A 84.890 867 101 7 983 1846 520872462 520871623 0.000000e+00 848.0
2 TraesCS6A01G113400 chr6A 91.071 56 3 2 2701 2756 83647301 83647354 1.270000e-09 75.0
3 TraesCS6A01G113400 chr6D 94.764 2139 86 9 692 2813 65390347 65388218 0.000000e+00 3306.0
4 TraesCS6A01G113400 chr6D 84.544 867 104 7 983 1846 379721447 379722286 0.000000e+00 832.0
5 TraesCS6A01G113400 chr6D 93.346 511 25 3 2794 3304 65386510 65386009 0.000000e+00 747.0
6 TraesCS6A01G113400 chr6B 92.563 2017 123 13 691 2696 140451726 140449726 0.000000e+00 2868.0
7 TraesCS6A01G113400 chr6B 92.259 1253 73 13 1453 2696 140434372 140433135 0.000000e+00 1755.0
8 TraesCS6A01G113400 chr6B 92.019 1253 76 14 1453 2696 140423851 140422614 0.000000e+00 1738.0
9 TraesCS6A01G113400 chr6B 92.019 1253 75 14 1453 2696 140413214 140411978 0.000000e+00 1736.0
10 TraesCS6A01G113400 chr6B 85.480 854 101 12 997 1846 147961480 147962314 0.000000e+00 869.0
11 TraesCS6A01G113400 chr6B 84.660 867 97 7 983 1846 566537923 566537090 0.000000e+00 832.0
12 TraesCS6A01G113400 chr6B 92.652 313 15 4 2864 3173 140420340 140420033 8.420000e-121 444.0
13 TraesCS6A01G113400 chr6B 92.652 313 15 4 2864 3173 140430859 140430552 8.420000e-121 444.0
14 TraesCS6A01G113400 chr6B 92.652 313 15 4 2864 3173 140447460 140447153 8.420000e-121 444.0
15 TraesCS6A01G113400 chr6B 92.114 317 17 4 2860 3173 140409708 140409397 1.090000e-119 440.0
16 TraesCS6A01G113400 chr6B 91.071 56 3 2 2701 2756 140093615 140093562 1.270000e-09 75.0
17 TraesCS6A01G113400 chr1A 98.661 672 8 1 1 672 75740114 75739444 0.000000e+00 1190.0
18 TraesCS6A01G113400 chr1A 95.946 148 5 1 525 672 20881144 20880998 4.260000e-59 239.0
19 TraesCS6A01G113400 chr1A 84.397 141 18 4 535 673 446143997 446144135 5.750000e-28 135.0
20 TraesCS6A01G113400 chr5A 98.512 672 6 3 1 672 547534118 547534785 0.000000e+00 1182.0
21 TraesCS6A01G113400 chr5A 97.321 672 6 4 1 672 671874749 671874090 0.000000e+00 1131.0
22 TraesCS6A01G113400 chr5A 83.688 141 19 4 535 673 316506806 316506668 2.680000e-26 130.0
23 TraesCS6A01G113400 chr3A 86.478 636 66 14 1 627 671626111 671626735 0.000000e+00 680.0
24 TraesCS6A01G113400 chr4B 83.652 679 89 16 3 672 295123369 295122704 1.300000e-173 619.0
25 TraesCS6A01G113400 chr2B 84.966 592 68 16 92 672 47064050 47063469 6.150000e-162 580.0
26 TraesCS6A01G113400 chr2B 90.187 214 16 4 1 210 283189923 283189711 1.170000e-69 274.0
27 TraesCS6A01G113400 chr2B 92.157 102 7 1 2867 2967 734490503 734490402 3.440000e-30 143.0
28 TraesCS6A01G113400 chr2B 87.379 103 11 1 2866 2968 504639671 504639571 2.080000e-22 117.0
29 TraesCS6A01G113400 chr2B 89.535 86 5 4 2775 2857 150613554 150613470 4.510000e-19 106.0
30 TraesCS6A01G113400 chrUn 93.243 222 14 1 2475 2696 398950424 398950204 3.180000e-85 326.0
31 TraesCS6A01G113400 chr5B 90.952 210 15 3 1 207 191977438 191977646 2.510000e-71 279.0
32 TraesCS6A01G113400 chr5D 90.000 210 15 4 1 207 177306373 177306579 1.960000e-67 267.0
33 TraesCS6A01G113400 chr5D 90.000 80 5 1 2773 2849 111788634 111788713 2.100000e-17 100.0
34 TraesCS6A01G113400 chr7B 87.963 108 13 0 2861 2968 525703022 525703129 9.630000e-26 128.0
35 TraesCS6A01G113400 chr7B 87.037 108 13 1 2861 2968 525625706 525625812 1.610000e-23 121.0
36 TraesCS6A01G113400 chr2D 94.286 70 1 1 2783 2849 32304070 32304139 1.620000e-18 104.0
37 TraesCS6A01G113400 chr1D 88.372 86 8 2 2773 2857 199427873 199427789 5.830000e-18 102.0
38 TraesCS6A01G113400 chr7A 89.873 79 4 2 2783 2857 636899791 636899713 7.550000e-17 99.0
39 TraesCS6A01G113400 chr7D 89.744 78 5 3 2783 2857 493547895 493547818 2.710000e-16 97.1
40 TraesCS6A01G113400 chr4A 89.610 77 6 2 2783 2857 577318731 577318655 2.710000e-16 97.1
41 TraesCS6A01G113400 chr3D 87.209 86 7 3 2778 2859 562507861 562507946 9.760000e-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 TraesCS6A01G113400 chr6A 83361169 83364473 3304 False 6104.0 6104 100.0000 1 3305 1 chr6A.!!$F1 3304
1 TraesCS6A01G113400 chr6A 520871623 520872462 839 True 848.0 848 84.8900 983 1846 1 chr6A.!!$R1 863
2 TraesCS6A01G113400 chr6D 65386009 65390347 4338 True 2026.5 3306 94.0550 692 3304 2 chr6D.!!$R1 2612
3 TraesCS6A01G113400 chr6D 379721447 379722286 839 False 832.0 832 84.5440 983 1846 1 chr6D.!!$F1 863
4 TraesCS6A01G113400 chr6B 140447153 140451726 4573 True 1656.0 2868 92.6075 691 3173 2 chr6B.!!$R6 2482
5 TraesCS6A01G113400 chr6B 140430552 140434372 3820 True 1099.5 1755 92.4555 1453 3173 2 chr6B.!!$R5 1720
6 TraesCS6A01G113400 chr6B 140420033 140423851 3818 True 1091.0 1738 92.3355 1453 3173 2 chr6B.!!$R4 1720
7 TraesCS6A01G113400 chr6B 140409397 140413214 3817 True 1088.0 1736 92.0665 1453 3173 2 chr6B.!!$R3 1720
8 TraesCS6A01G113400 chr6B 147961480 147962314 834 False 869.0 869 85.4800 997 1846 1 chr6B.!!$F1 849
9 TraesCS6A01G113400 chr6B 566537090 566537923 833 True 832.0 832 84.6600 983 1846 1 chr6B.!!$R2 863
10 TraesCS6A01G113400 chr1A 75739444 75740114 670 True 1190.0 1190 98.6610 1 672 1 chr1A.!!$R2 671
11 TraesCS6A01G113400 chr5A 547534118 547534785 667 False 1182.0 1182 98.5120 1 672 1 chr5A.!!$F1 671
12 TraesCS6A01G113400 chr5A 671874090 671874749 659 True 1131.0 1131 97.3210 1 672 1 chr5A.!!$R2 671
13 TraesCS6A01G113400 chr3A 671626111 671626735 624 False 680.0 680 86.4780 1 627 1 chr3A.!!$F1 626
14 TraesCS6A01G113400 chr4B 295122704 295123369 665 True 619.0 619 83.6520 3 672 1 chr4B.!!$R1 669
15 TraesCS6A01G113400 chr2B 47063469 47064050 581 True 580.0 580 84.9660 92 672 1 chr2B.!!$R1 580

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
966 986 2.094338 GGCTCTTGCTTCTGAATTTGGG 60.094 50.0 0.00 0.0 39.59 4.12 F
1166 1186 0.995024 AGGCCTGCTTCCTACACAAT 59.005 50.0 3.11 0.0 30.79 2.71 F
1926 1964 0.392595 CTGCAGCTCAGATCAAGGCA 60.393 55.0 0.00 0.0 45.72 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1909 1947 0.392729 ACTGCCTTGATCTGAGCTGC 60.393 55.0 0.00 0.00 0.00 5.25 R
2171 2209 0.538977 TTCTTCCTCCAGGACGTCGT 60.539 55.0 9.92 7.31 45.39 4.34 R
2731 4309 0.657840 GACAGCACCACACAACACTC 59.342 55.0 0.00 0.00 0.00 3.51 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
244 258 7.201609 CGTACTGATTTGTACATTGCCTATTGT 60.202 37.037 0.00 0.00 41.92 2.71
262 277 7.541437 GCCTATTGTTATAATCCAGTACGTCTC 59.459 40.741 0.00 0.00 0.00 3.36
682 702 4.981389 CTTCAGGAAGCACGCTATATTC 57.019 45.455 0.00 0.00 0.00 1.75
683 703 4.371786 CTTCAGGAAGCACGCTATATTCA 58.628 43.478 0.00 0.00 0.00 2.57
684 704 3.982475 TCAGGAAGCACGCTATATTCAG 58.018 45.455 0.00 0.00 0.00 3.02
685 705 3.384789 TCAGGAAGCACGCTATATTCAGT 59.615 43.478 0.00 0.00 0.00 3.41
686 706 4.122776 CAGGAAGCACGCTATATTCAGTT 58.877 43.478 0.00 0.00 0.00 3.16
687 707 5.068591 TCAGGAAGCACGCTATATTCAGTTA 59.931 40.000 0.00 0.00 0.00 2.24
688 708 5.928839 CAGGAAGCACGCTATATTCAGTTAT 59.071 40.000 0.00 0.00 0.00 1.89
689 709 6.425114 CAGGAAGCACGCTATATTCAGTTATT 59.575 38.462 0.00 0.00 0.00 1.40
690 710 6.992715 AGGAAGCACGCTATATTCAGTTATTT 59.007 34.615 0.00 0.00 0.00 1.40
691 711 7.499232 AGGAAGCACGCTATATTCAGTTATTTT 59.501 33.333 0.00 0.00 0.00 1.82
692 712 8.129211 GGAAGCACGCTATATTCAGTTATTTTT 58.871 33.333 0.00 0.00 0.00 1.94
719 739 7.994425 TCTTTCAATCTTACCTTGTATGCAA 57.006 32.000 0.00 0.00 0.00 4.08
750 770 4.339872 TGCATGATCTTTGGCTTGTTTT 57.660 36.364 0.00 0.00 0.00 2.43
836 856 4.780815 TCTTTCATGTCTGGACAACACTT 58.219 39.130 7.53 0.00 45.41 3.16
847 867 3.133901 TGGACAACACTTGCTCTACTTCA 59.866 43.478 0.00 0.00 0.00 3.02
853 873 5.474578 ACACTTGCTCTACTTCAGATCAA 57.525 39.130 0.00 0.00 37.12 2.57
911 931 5.520748 AAAAGGGATAAGCTTCTCTTCCA 57.479 39.130 0.00 0.00 35.34 3.53
966 986 2.094338 GGCTCTTGCTTCTGAATTTGGG 60.094 50.000 0.00 0.00 39.59 4.12
1047 1067 3.738281 CGAACAAGGATGACGCCTTCTAT 60.738 47.826 0.00 0.00 44.89 1.98
1110 1130 5.337410 CCATGGTAATGGCATCAAGACAAAA 60.337 40.000 2.57 0.00 46.89 2.44
1166 1186 0.995024 AGGCCTGCTTCCTACACAAT 59.005 50.000 3.11 0.00 30.79 2.71
1167 1187 1.098050 GGCCTGCTTCCTACACAATG 58.902 55.000 0.00 0.00 0.00 2.82
1263 1283 1.530013 ATGACACTGCAAAGCTGGCC 61.530 55.000 8.04 0.00 0.00 5.36
1408 1431 1.739466 CGGATGTTGACATGGACAAGG 59.261 52.381 0.57 0.00 36.57 3.61
1423 1446 3.521560 GACAAGGTCGCTACATTCATCA 58.478 45.455 0.00 0.00 0.00 3.07
1474 1497 3.009473 AGGCAAGGACAAGAAAGCTATGA 59.991 43.478 0.00 0.00 0.00 2.15
1538 1561 5.975282 TGATGAGGAGATGAAGAAACTCAG 58.025 41.667 0.00 0.00 38.23 3.35
1926 1964 0.392595 CTGCAGCTCAGATCAAGGCA 60.393 55.000 0.00 0.00 45.72 4.75
1952 1990 3.787001 CTCCTCAACCCTCCCCGC 61.787 72.222 0.00 0.00 0.00 6.13
1994 2032 1.079819 TCTTTGAGGCGCTCTTCCG 60.080 57.895 7.64 0.00 0.00 4.30
2148 2186 1.987855 CCTGAAGGAGGTGCCGGTA 60.988 63.158 1.90 0.00 43.43 4.02
2171 2209 4.164796 AGTCCTGAAATGCCTGTATGATGA 59.835 41.667 0.00 0.00 0.00 2.92
2181 2219 2.541794 CCTGTATGATGACGACGTCCTG 60.542 54.545 24.33 11.49 0.00 3.86
2270 2308 2.992817 AATGCCAGGCCGTTTGTGGA 62.993 55.000 9.64 0.00 32.60 4.02
2271 2309 3.365265 GCCAGGCCGTTTGTGGAG 61.365 66.667 12.05 0.00 32.60 3.86
2463 2502 6.951062 TGTTATGGTTGATTCTGTGTTGAA 57.049 33.333 0.00 0.00 0.00 2.69
2480 2519 9.840427 CTGTGTTGAATCGGTTAAAATATTTCT 57.160 29.630 0.10 0.00 0.00 2.52
2557 2598 2.654749 TGAAGTGTCAGAGGTATGCG 57.345 50.000 0.00 0.00 0.00 4.73
2731 4309 3.249799 TGAACATTTGTAAGCAGACCACG 59.750 43.478 0.00 0.00 0.00 4.94
3044 6919 1.851653 AGTGATACTCCTAGTCCCCGT 59.148 52.381 0.00 0.00 0.00 5.28
3071 6946 0.250727 TGCTGGTGGTTAAGCTGTCC 60.251 55.000 6.19 6.68 40.21 4.02
3090 6965 2.029020 TCCCTCATGTTCAGTCAAGACG 60.029 50.000 0.00 0.00 36.20 4.18
3168 7043 3.259064 GCTCACATTTGTTCGCCTACTA 58.741 45.455 0.00 0.00 0.00 1.82
3191 7066 3.808726 ACTATATCGTGTCACCGTCTCTC 59.191 47.826 0.00 0.00 0.00 3.20
3199 7074 3.750130 GTGTCACCGTCTCTCTTGTACTA 59.250 47.826 0.00 0.00 0.00 1.82
3292 7167 4.264460 CAGATAGACTGTAAGGGATGCC 57.736 50.000 0.00 0.00 41.30 4.40
3294 7169 6.355064 CAGATAGACTGTAAGGGATGCCCG 62.355 54.167 0.00 0.00 44.03 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
244 258 6.203530 CCTACACGAGACGTACTGGATTATAA 59.796 42.308 0.00 0.00 38.32 0.98
262 277 6.592994 TGTCCGAGTATCTATTATCCTACACG 59.407 42.308 0.00 0.00 0.00 4.49
313 329 5.066893 CCTACAACCACGTACTCTGCTATAA 59.933 44.000 0.00 0.00 0.00 0.98
691 711 9.691362 GCATACAAGGTAAGATTGAAAGAAAAA 57.309 29.630 0.00 0.00 0.00 1.94
692 712 8.855110 TGCATACAAGGTAAGATTGAAAGAAAA 58.145 29.630 0.00 0.00 0.00 2.29
693 713 8.402798 TGCATACAAGGTAAGATTGAAAGAAA 57.597 30.769 0.00 0.00 0.00 2.52
694 714 7.994425 TGCATACAAGGTAAGATTGAAAGAA 57.006 32.000 0.00 0.00 0.00 2.52
695 715 7.994425 TTGCATACAAGGTAAGATTGAAAGA 57.006 32.000 0.00 0.00 0.00 2.52
696 716 9.643693 ATTTTGCATACAAGGTAAGATTGAAAG 57.356 29.630 0.00 0.00 37.04 2.62
707 727 5.581605 CATTAGCGATTTTGCATACAAGGT 58.418 37.500 0.00 0.00 37.04 3.50
719 739 5.526115 CCAAAGATCATGCATTAGCGATTT 58.474 37.500 0.00 0.00 46.23 2.17
766 786 6.767902 ACTTTGTCAGATTGTAGCAAAGAGAA 59.232 34.615 18.29 0.00 44.97 2.87
809 829 5.296780 TGTTGTCCAGACATGAAAGAAACTC 59.703 40.000 0.00 0.00 41.52 3.01
847 867 1.215173 TCCCGGCAATCCAATTGATCT 59.785 47.619 7.12 0.00 42.83 2.75
853 873 0.107017 CACTCTCCCGGCAATCCAAT 60.107 55.000 0.00 0.00 0.00 3.16
878 898 6.415573 AGCTTATCCCTTTTTCTCGTTGTAT 58.584 36.000 0.00 0.00 0.00 2.29
911 931 1.531423 CTTGAGCAGTGGCAAGTGAT 58.469 50.000 0.00 0.00 44.61 3.06
1047 1067 4.929479 ACATTTTGGGCATCTTGTACCTA 58.071 39.130 0.00 0.00 0.00 3.08
1110 1130 1.614996 TGCCAACCATGTTCACGATT 58.385 45.000 0.00 0.00 0.00 3.34
1166 1186 2.104792 AGCTCACAGCCAAAGTACTTCA 59.895 45.455 8.95 0.00 43.77 3.02
1167 1187 2.772287 AGCTCACAGCCAAAGTACTTC 58.228 47.619 8.95 0.00 43.77 3.01
1263 1283 4.560128 TGATGAAGTTCTCAAGAAGACCG 58.440 43.478 4.17 0.00 37.67 4.79
1408 1431 5.258622 GTTGTTCATGATGAATGTAGCGAC 58.741 41.667 11.46 4.49 38.79 5.19
1423 1446 0.110486 AGTTCTGGCGGGTTGTTCAT 59.890 50.000 0.00 0.00 0.00 2.57
1474 1497 0.817013 CGCTCCTTCTCAGCTCTTCT 59.183 55.000 0.00 0.00 34.45 2.85
1538 1561 3.010696 ACCTTTCTTCTTCCCATCCTTCC 59.989 47.826 0.00 0.00 0.00 3.46
1909 1947 0.392729 ACTGCCTTGATCTGAGCTGC 60.393 55.000 0.00 0.00 0.00 5.25
1926 1964 1.484444 GGGTTGAGGAGGACAGCACT 61.484 60.000 0.00 0.00 0.00 4.40
2064 2102 1.523258 CAGCATCTGGGCTCCTTCG 60.523 63.158 0.00 0.00 43.68 3.79
2148 2186 4.164796 TCATCATACAGGCATTTCAGGACT 59.835 41.667 0.00 0.00 0.00 3.85
2171 2209 0.538977 TTCTTCCTCCAGGACGTCGT 60.539 55.000 9.92 7.31 45.39 4.34
2181 2219 1.004745 TGGACAATGGCTTCTTCCTCC 59.995 52.381 0.00 0.00 0.00 4.30
2557 2598 2.126346 GCGGATGCAGCAAACCAC 60.126 61.111 18.18 8.10 42.15 4.16
2629 2670 5.221880 CAAGCATGATTTTGGAAAACGAGA 58.778 37.500 0.00 0.00 0.00 4.04
2632 2673 3.493877 TGCAAGCATGATTTTGGAAAACG 59.506 39.130 0.00 0.00 0.00 3.60
2731 4309 0.657840 GACAGCACCACACAACACTC 59.342 55.000 0.00 0.00 0.00 3.51
2849 6281 1.523758 AGCATCGCTTCTTCCGTTTT 58.476 45.000 0.00 0.00 33.89 2.43
2850 6282 1.523758 AAGCATCGCTTCTTCCGTTT 58.476 45.000 0.00 0.00 46.77 3.60
2935 6807 7.653311 GGAATCGCATAAGGCAAAATCTAAAAT 59.347 33.333 0.00 0.00 45.17 1.82
2948 6820 5.749596 TGTTAACATGGAATCGCATAAGG 57.250 39.130 3.59 0.00 0.00 2.69
3013 6888 4.789807 AGGAGTATCACTCGTAGCCTTAA 58.210 43.478 0.00 0.00 45.96 1.85
3024 6899 1.851653 ACGGGGACTAGGAGTATCACT 59.148 52.381 0.00 0.00 36.25 3.41
3044 6919 3.420893 CTTAACCACCAGCAGAATCCAA 58.579 45.455 0.00 0.00 0.00 3.53
3071 6946 2.029020 TCCGTCTTGACTGAACATGAGG 60.029 50.000 0.00 0.00 33.10 3.86
3090 6965 4.797349 CGTCCGTTAACTGAATCTAAGTCC 59.203 45.833 3.71 0.00 0.00 3.85
3158 7033 5.759763 TGACACGATATAGTTAGTAGGCGAA 59.240 40.000 0.00 0.00 0.00 4.70
3168 7043 4.197750 AGAGACGGTGACACGATATAGTT 58.802 43.478 0.00 0.00 37.61 2.24
3213 7088 5.235516 CCGACTTTTATATAGCCCGACAAT 58.764 41.667 0.00 0.00 0.00 2.71
3270 7145 6.606456 GGGCATCCCTTACAGTCTATCTGC 62.606 54.167 0.00 0.00 43.20 4.26


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

AutoCloner maintained by Alex Coulton.