Multiple sequence alignment - TraesCS5D01G396700

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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 TraesCS5D01G396700 chr5D 100.000 3409 0 0 1 3409 464074092 464070684 0.000000e+00 6296.0
1 TraesCS5D01G396700 chr5D 94.231 52 3 0 3068 3119 433387199 433387148 2.820000e-11 80.5
2 TraesCS5D01G396700 chr5A 92.212 2722 127 31 740 3409 584456411 584453723 0.000000e+00 3773.0
3 TraesCS5D01G396700 chr5A 89.196 759 31 16 1 743 584457239 584456516 0.000000e+00 900.0
4 TraesCS5D01G396700 chr5B 93.859 2410 85 24 999 3359 570930792 570928397 0.000000e+00 3572.0
5 TraesCS5D01G396700 chr5B 89.815 648 39 19 1 632 570931500 570930864 0.000000e+00 806.0
6 TraesCS5D01G396700 chr2B 88.798 366 39 2 2 366 752834540 752834904 6.710000e-122 448.0
7 TraesCS5D01G396700 chr2D 87.978 366 42 2 2 366 617077532 617077896 6.760000e-117 431.0
8 TraesCS5D01G396700 chr2D 94.231 52 3 0 3068 3119 643859108 643859159 2.820000e-11 80.5
9 TraesCS5D01G396700 chr2A 85.203 419 51 9 2 413 746981938 746982352 1.460000e-113 420.0
10 TraesCS5D01G396700 chr2A 84.524 420 46 9 2 413 747153577 747153985 6.850000e-107 398.0
11 TraesCS5D01G396700 chr3A 83.824 340 50 5 3 339 11414608 11414945 5.490000e-83 318.0
12 TraesCS5D01G396700 chr3A 81.471 340 61 2 1 339 11383343 11383681 9.320000e-71 278.0
13 TraesCS5D01G396700 chr3A 90.698 86 8 0 3144 3229 491189511 491189426 7.730000e-22 115.0
14 TraesCS5D01G396700 chrUn 83.030 330 54 2 11 339 35311217 35310889 7.150000e-77 298.0
15 TraesCS5D01G396700 chr7B 94.118 85 5 0 3145 3229 490685098 490685182 2.760000e-26 130.0
16 TraesCS5D01G396700 chr6B 91.954 87 5 1 3144 3230 191534717 191534633 1.660000e-23 121.0
17 TraesCS5D01G396700 chr3D 91.860 86 7 0 3144 3229 370115713 370115798 1.660000e-23 121.0
18 TraesCS5D01G396700 chr4A 90.805 87 8 0 3150 3236 695134925 695135011 2.150000e-22 117.0
19 TraesCS5D01G396700 chr6A 90.805 87 6 1 3144 3230 127186199 127186115 7.730000e-22 115.0
20 TraesCS5D01G396700 chr4B 90.000 90 8 1 3142 3230 486282279 486282368 7.730000e-22 115.0


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 TraesCS5D01G396700 chr5D 464070684 464074092 3408 True 6296.0 6296 100.000 1 3409 1 chr5D.!!$R2 3408
1 TraesCS5D01G396700 chr5A 584453723 584457239 3516 True 2336.5 3773 90.704 1 3409 2 chr5A.!!$R1 3408
2 TraesCS5D01G396700 chr5B 570928397 570931500 3103 True 2189.0 3572 91.837 1 3359 2 chr5B.!!$R1 3358

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
852 999 0.854218 TAGGGGGTGGCAGTTTTCAA 59.146 50.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2830 3048 0.300789 GGCGATTACTTACAGCGTGC 59.699 55.0 0.0 0.0 0.0 5.34 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
27 28 7.310485 GGGATATCCTACAAGTCGGATGTTTAT 60.310 40.741 21.18 2.48 40.17 1.40
40 41 4.537015 GGATGTTTATAGTTTCGGCATGC 58.463 43.478 9.90 9.90 0.00 4.06
42 43 5.468746 GGATGTTTATAGTTTCGGCATGCTA 59.531 40.000 18.92 3.12 0.00 3.49
163 164 2.093921 GGAGAGGAACTGGTGCTTACTC 60.094 54.545 0.00 0.00 41.55 2.59
193 194 4.080015 TGACACCAGAAGGGAAAGAAAAGA 60.080 41.667 0.00 0.00 41.15 2.52
204 205 3.810386 GGAAAGAAAAGACGAGACAGCTT 59.190 43.478 0.00 0.00 0.00 3.74
303 304 4.005650 CTGGAAGCTTACAGAATCTGCAA 58.994 43.478 31.64 2.64 41.85 4.08
413 421 6.375455 ACATTTGAGGGACATAGTTGATTCAC 59.625 38.462 0.00 0.00 0.00 3.18
432 440 4.623002 TCACGTGTGTATTGCTCTTTACA 58.377 39.130 16.51 0.00 0.00 2.41
453 465 1.933853 GTAGCACGGTTTCTAGCATGG 59.066 52.381 0.00 0.00 0.00 3.66
457 469 2.802816 GCACGGTTTCTAGCATGGATAG 59.197 50.000 0.00 0.00 0.00 2.08
482 504 7.986889 AGAAAAATTATTGCCAAGTCAACTGTT 59.013 29.630 0.00 0.00 0.00 3.16
505 527 3.118775 TGTGTGTTAGCTAGCATACCTGG 60.119 47.826 26.63 0.00 29.84 4.45
507 529 4.098960 GTGTGTTAGCTAGCATACCTGGTA 59.901 45.833 21.66 9.36 34.31 3.25
538 560 9.664332 GATCTAGTTCATGAGCCATTATATTGT 57.336 33.333 5.87 0.00 0.00 2.71
600 622 4.247258 GCCATTGCTGTGATTTTGATGAA 58.753 39.130 0.00 0.00 33.53 2.57
603 625 5.929992 CCATTGCTGTGATTTTGATGAAGTT 59.070 36.000 0.00 0.00 0.00 2.66
604 626 7.092079 CCATTGCTGTGATTTTGATGAAGTTA 58.908 34.615 0.00 0.00 0.00 2.24
605 627 7.762615 CCATTGCTGTGATTTTGATGAAGTTAT 59.237 33.333 0.00 0.00 0.00 1.89
606 628 9.146984 CATTGCTGTGATTTTGATGAAGTTATT 57.853 29.630 0.00 0.00 0.00 1.40
634 662 5.578005 TCAGTTGTGTAGTATCCACTAGC 57.422 43.478 0.00 0.00 37.94 3.42
717 745 7.654520 CACAATCACAAGAGGATTTTCAATTGT 59.345 33.333 5.13 0.00 34.83 2.71
718 746 7.869429 ACAATCACAAGAGGATTTTCAATTGTC 59.131 33.333 5.13 0.00 32.86 3.18
720 748 7.206981 TCACAAGAGGATTTTCAATTGTCTC 57.793 36.000 5.13 4.86 0.00 3.36
722 750 7.040892 TCACAAGAGGATTTTCAATTGTCTCTG 60.041 37.037 5.13 3.80 31.47 3.35
750 886 9.817809 ATCTAGTGAACGATTAAAAGATGCTTA 57.182 29.630 0.00 0.00 0.00 3.09
770 906 5.863935 GCTTACCTCCTGCTATTTTGTTTTG 59.136 40.000 0.00 0.00 0.00 2.44
774 910 4.321974 CCTCCTGCTATTTTGTTTTGGGAC 60.322 45.833 0.00 0.00 0.00 4.46
776 912 2.986479 CTGCTATTTTGTTTTGGGACGC 59.014 45.455 0.00 0.00 0.00 5.19
799 935 1.597027 CCCCAGCGAACGTTCACTT 60.597 57.895 26.71 9.47 0.00 3.16
815 951 5.232463 GTTCACTTCCATGCATGACATTTT 58.768 37.500 28.31 4.07 36.64 1.82
829 976 6.621164 GCATGACATTTTGGTGGCAATTTTAG 60.621 38.462 0.00 0.00 41.24 1.85
842 989 3.194755 GCAATTTTAGTGTTAGGGGGTGG 59.805 47.826 0.00 0.00 0.00 4.61
845 992 0.988832 TTAGTGTTAGGGGGTGGCAG 59.011 55.000 0.00 0.00 0.00 4.85
852 999 0.854218 TAGGGGGTGGCAGTTTTCAA 59.146 50.000 0.00 0.00 0.00 2.69
855 1002 1.474320 GGGGGTGGCAGTTTTCAAAAC 60.474 52.381 4.72 4.72 0.00 2.43
859 1006 3.753797 GGGTGGCAGTTTTCAAAACAAAA 59.246 39.130 15.41 0.00 0.00 2.44
904 1055 7.304735 CAATTTTCGTCAATTACTGTCATCCA 58.695 34.615 0.00 0.00 0.00 3.41
906 1057 6.662414 TTTCGTCAATTACTGTCATCCATC 57.338 37.500 0.00 0.00 0.00 3.51
914 1065 2.670939 ACTGTCATCCATCGGATCTGA 58.329 47.619 6.72 6.72 40.98 3.27
921 1072 2.031870 TCCATCGGATCTGAATCGTGT 58.968 47.619 8.65 0.00 32.24 4.49
939 1090 4.821589 GGCTCTGGAGGCGTTCGG 62.822 72.222 8.34 0.00 44.15 4.30
977 1128 2.090195 GCGAACGTCAGCTAGTTAACAC 59.910 50.000 8.61 0.00 0.00 3.32
979 1130 4.715896 CGAACGTCAGCTAGTTAACACTA 58.284 43.478 8.61 0.00 34.06 2.74
990 1141 8.995220 CAGCTAGTTAACACTACCATTGTTTTA 58.005 33.333 8.61 0.00 38.21 1.52
991 1142 9.734984 AGCTAGTTAACACTACCATTGTTTTAT 57.265 29.630 8.61 0.00 38.21 1.40
1044 1206 1.593196 TCGAAGAGGCCACACAAAAG 58.407 50.000 5.01 0.00 0.00 2.27
1097 1260 1.067416 TGCAGATAAGGCTACCGCG 59.933 57.895 0.00 0.00 36.88 6.46
1221 1384 0.907486 CCATCACCTTCCTCAGCTCA 59.093 55.000 0.00 0.00 0.00 4.26
1233 1396 2.352617 CCTCAGCTCATCGAGGCTAATC 60.353 54.545 4.98 0.00 42.30 1.75
1234 1397 2.295629 CTCAGCTCATCGAGGCTAATCA 59.704 50.000 9.43 0.00 37.00 2.57
1235 1398 2.295629 TCAGCTCATCGAGGCTAATCAG 59.704 50.000 9.43 0.00 37.00 2.90
1329 1495 3.372554 CTTCCCTCCTCCGAACGCC 62.373 68.421 0.00 0.00 0.00 5.68
1659 1849 3.480133 CCCACGGGGTCCATCTCC 61.480 72.222 1.28 0.00 38.25 3.71
2151 2341 3.047093 GGTACGTGACAAATGCAAAACC 58.953 45.455 0.00 0.00 0.00 3.27
2153 2343 0.502275 CGTGACAAATGCAAAACCGC 59.498 50.000 0.00 0.00 0.00 5.68
2282 2495 3.072468 TACGTCTTCAGCCCGGGG 61.072 66.667 25.28 9.31 0.00 5.73
2461 2678 7.680442 TTTGTAGATATACTGCAGCAACAAA 57.320 32.000 15.27 11.35 41.74 2.83
2462 2679 6.662414 TGTAGATATACTGCAGCAACAAAC 57.338 37.500 15.27 5.18 36.38 2.93
2463 2680 5.584649 TGTAGATATACTGCAGCAACAAACC 59.415 40.000 15.27 0.00 36.38 3.27
2514 2732 3.650647 TGTGAAACAGGGGATCAGC 57.349 52.632 0.00 0.00 45.67 4.26
2523 2741 1.000396 GGGGATCAGCAGGCTTTGT 60.000 57.895 0.00 0.00 0.00 2.83
2560 2778 9.364989 ACACAATAATTTAATACAATGTGTGCC 57.635 29.630 13.76 0.00 45.82 5.01
2595 2813 3.123620 GCCGCACCTTCAGCTCAG 61.124 66.667 0.00 0.00 0.00 3.35
2598 2816 2.389020 CGCACCTTCAGCTCAGCAG 61.389 63.158 0.00 0.00 0.00 4.24
2599 2817 1.004080 GCACCTTCAGCTCAGCAGA 60.004 57.895 0.00 0.00 0.00 4.26
2600 2818 1.020333 GCACCTTCAGCTCAGCAGAG 61.020 60.000 0.00 0.94 44.96 3.35
2845 3063 7.414098 CCAAAATAAGAGCACGCTGTAAGTAAT 60.414 37.037 0.00 0.00 35.30 1.89
2915 3133 2.636893 AGAAAAGCTTCTGAGAGCCTCA 59.363 45.455 0.00 5.03 43.74 3.86
2983 3201 0.987294 CTCCCCTCATCAACACTGGT 59.013 55.000 0.00 0.00 0.00 4.00
2993 3211 1.013596 CAACACTGGTGAGCAAACGA 58.986 50.000 7.78 0.00 0.00 3.85
3313 3531 7.094377 TGGGTGTTTTTCTCAATAGCTTATGTC 60.094 37.037 0.00 0.00 0.00 3.06
3359 3578 2.100584 TGTGAAATTGCAGTGGGTGTTC 59.899 45.455 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.328382 AACACTAGCATGCCGAAACTA 57.672 42.857 15.66 0.00 0.00 2.24
40 41 5.869888 GTCCACTCACCATTTCTAACACTAG 59.130 44.000 0.00 0.00 0.00 2.57
42 43 4.642429 GTCCACTCACCATTTCTAACACT 58.358 43.478 0.00 0.00 0.00 3.55
86 87 1.434188 TTCTTGGTTCTGGCTCTCCA 58.566 50.000 0.00 0.00 40.85 3.86
193 194 0.811915 ACGATAGCAAGCTGTCTCGT 59.188 50.000 15.27 16.48 42.67 4.18
204 205 0.036164 ACCAAAGTGCCACGATAGCA 59.964 50.000 0.00 0.00 42.67 3.49
413 421 5.220228 GCTACTGTAAAGAGCAATACACACG 60.220 44.000 0.00 0.00 36.20 4.49
432 440 2.418746 CCATGCTAGAAACCGTGCTACT 60.419 50.000 0.00 0.00 0.00 2.57
453 465 9.860898 AGTTGACTTGGCAATAATTTTTCTATC 57.139 29.630 0.00 0.00 0.00 2.08
457 469 7.713764 ACAGTTGACTTGGCAATAATTTTTC 57.286 32.000 0.00 0.00 0.00 2.29
482 504 4.503910 CAGGTATGCTAGCTAACACACAA 58.496 43.478 17.23 0.00 34.67 3.33
505 527 5.244851 TGGCTCATGAACTAGATCAGGATAC 59.755 44.000 16.33 12.72 39.18 2.24
507 529 4.229639 TGGCTCATGAACTAGATCAGGAT 58.770 43.478 16.33 0.00 39.18 3.24
538 560 9.571816 TCAATGCACATCAAATCCAGTATTATA 57.428 29.630 0.00 0.00 0.00 0.98
539 561 8.467963 TCAATGCACATCAAATCCAGTATTAT 57.532 30.769 0.00 0.00 0.00 1.28
605 627 9.787435 AGTGGATACTACACAACTGAAAATTAA 57.213 29.630 0.00 0.00 41.21 1.40
608 630 7.549488 GCTAGTGGATACTACACAACTGAAAAT 59.451 37.037 0.00 0.00 41.21 1.82
632 660 4.579869 ACATTACTCGAGTTCATTTGGCT 58.420 39.130 25.44 0.00 0.00 4.75
634 662 5.347635 TCGAACATTACTCGAGTTCATTTGG 59.652 40.000 25.44 13.14 40.25 3.28
722 750 9.250624 AGCATCTTTTAATCGTTCACTAGATAC 57.749 33.333 0.00 0.00 0.00 2.24
746 882 5.644977 AAACAAAATAGCAGGAGGTAAGC 57.355 39.130 0.00 0.00 0.00 3.09
750 886 3.578282 CCCAAAACAAAATAGCAGGAGGT 59.422 43.478 0.00 0.00 0.00 3.85
776 912 1.287425 GAACGTTCGCTGGGGATTAG 58.713 55.000 13.36 0.00 0.00 1.73
799 935 2.234168 CCACCAAAATGTCATGCATGGA 59.766 45.455 25.97 13.72 37.96 3.41
815 951 3.829601 CCCTAACACTAAAATTGCCACCA 59.170 43.478 0.00 0.00 0.00 4.17
829 976 0.178973 AAACTGCCACCCCCTAACAC 60.179 55.000 0.00 0.00 0.00 3.32
862 1009 9.260002 ACGAAAATTGCATTGAAACTAAAGATT 57.740 25.926 0.00 0.00 0.00 2.40
863 1010 8.816640 ACGAAAATTGCATTGAAACTAAAGAT 57.183 26.923 0.00 0.00 0.00 2.40
870 1021 8.487176 AGTAATTGACGAAAATTGCATTGAAAC 58.513 29.630 14.21 3.29 35.37 2.78
874 1025 7.114670 TGACAGTAATTGACGAAAATTGCATTG 59.885 33.333 14.21 9.24 35.37 2.82
904 1055 1.539065 GCCACACGATTCAGATCCGAT 60.539 52.381 0.00 0.00 0.00 4.18
906 1057 0.179100 AGCCACACGATTCAGATCCG 60.179 55.000 0.00 0.00 0.00 4.18
914 1065 1.599047 CCTCCAGAGCCACACGATT 59.401 57.895 0.00 0.00 0.00 3.34
921 1072 4.069232 CGAACGCCTCCAGAGCCA 62.069 66.667 0.00 0.00 0.00 4.75
934 1085 4.934989 GGTGAGATCCCACCGAAC 57.065 61.111 11.00 0.00 46.00 3.95
954 1105 2.257974 TAACTAGCTGACGTTCGCTG 57.742 50.000 19.01 12.60 37.05 5.18
990 1141 8.792830 TCGTCTTTCCTTTCATTTCTTGATAT 57.207 30.769 0.00 0.00 33.34 1.63
991 1142 8.792830 ATCGTCTTTCCTTTCATTTCTTGATA 57.207 30.769 0.00 0.00 33.34 2.15
992 1143 7.148171 GGATCGTCTTTCCTTTCATTTCTTGAT 60.148 37.037 0.00 0.00 33.34 2.57
993 1144 6.149474 GGATCGTCTTTCCTTTCATTTCTTGA 59.851 38.462 0.00 0.00 0.00 3.02
994 1145 6.072508 TGGATCGTCTTTCCTTTCATTTCTTG 60.073 38.462 0.00 0.00 34.17 3.02
995 1146 6.003950 TGGATCGTCTTTCCTTTCATTTCTT 58.996 36.000 0.00 0.00 34.17 2.52
996 1147 5.560724 TGGATCGTCTTTCCTTTCATTTCT 58.439 37.500 0.00 0.00 34.17 2.52
997 1148 5.880054 TGGATCGTCTTTCCTTTCATTTC 57.120 39.130 0.00 0.00 34.17 2.17
1011 1166 4.150804 GCCTCTTCGATATTTTGGATCGTC 59.849 45.833 5.08 0.00 45.09 4.20
1044 1206 4.766404 TTTCCTTCGGCTTGAGATTTTC 57.234 40.909 0.00 0.00 0.00 2.29
1285 1451 1.730902 CCGCAGTCGCCGATGATAG 60.731 63.158 0.00 0.00 33.11 2.08
1659 1849 3.991051 ACGGACACCAGCTCCACG 61.991 66.667 0.00 0.00 0.00 4.94
1974 2164 1.739049 GGAGAGGAGCATGTCGAGG 59.261 63.158 0.00 0.00 0.00 4.63
2151 2341 2.807967 TCAGTTTTGTGATCCTTCTGCG 59.192 45.455 0.00 0.00 0.00 5.18
2153 2343 7.221452 CAGTTTTTCAGTTTTGTGATCCTTCTG 59.779 37.037 0.00 0.00 0.00 3.02
2282 2495 1.135575 CCGTACCACTCGTACTTGGAC 60.136 57.143 10.98 5.35 44.52 4.02
2491 2708 1.474077 GATCCCCTGTTTCACATGTGC 59.526 52.381 21.38 7.96 0.00 4.57
2514 2732 5.756347 TGTGTAACTACAACTACAAAGCCTG 59.244 40.000 0.00 0.00 38.04 4.85
2580 2798 2.357881 TGCTGAGCTGAAGGTGCG 60.358 61.111 5.83 0.00 35.28 5.34
2595 2813 0.810823 GTCTGCTGCATCTCCTCTGC 60.811 60.000 1.31 0.00 40.10 4.26
2598 2816 1.941294 CATTGTCTGCTGCATCTCCTC 59.059 52.381 1.31 0.00 0.00 3.71
2599 2817 1.408405 CCATTGTCTGCTGCATCTCCT 60.408 52.381 1.31 0.00 0.00 3.69
2600 2818 1.022735 CCATTGTCTGCTGCATCTCC 58.977 55.000 1.31 0.00 0.00 3.71
2830 3048 0.300789 GGCGATTACTTACAGCGTGC 59.699 55.000 0.00 0.00 0.00 5.34
2834 3052 2.892784 AGGAGGCGATTACTTACAGC 57.107 50.000 0.00 0.00 0.00 4.40
2845 3063 4.138290 TGTTTCAATTTGTAAGGAGGCGA 58.862 39.130 0.00 0.00 0.00 5.54
2915 3133 3.430042 ACATGCAGGACTCTTCAACAT 57.570 42.857 4.84 0.00 0.00 2.71
2967 3185 1.947678 GCTCACCAGTGTTGATGAGGG 60.948 57.143 1.39 0.00 39.20 4.30
3031 3249 3.714280 TCATCGGGATAATTCTTGGGTCA 59.286 43.478 0.00 0.00 0.00 4.02
3313 3531 8.899771 CATAAAGGCCCTATAATTAATTACCGG 58.100 37.037 10.07 12.34 0.00 5.28


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

AutoCloner maintained by Alex Coulton.