Multiple sequence alignment - TraesCS5B01G117000

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 TraesCS5B01G117000 chr5B 100.000 5429 0 0 1 5429 204617113 204611685 0.000000e+00 10026
1 TraesCS5B01G117000 chr5B 96.618 5440 168 13 1 5429 176795013 176789579 0.000000e+00 9012
2 TraesCS5B01G117000 chr5B 95.556 90 4 0 6 95 342899261 342899172 1.580000e-30 145
3 TraesCS5B01G117000 chr1B 95.550 5438 205 20 1 5426 177157363 177162775 0.000000e+00 8667
4 TraesCS5B01G117000 chr1B 95.465 5447 212 20 1 5429 192672642 192678071 0.000000e+00 8658
5 TraesCS5B01G117000 chr1B 95.035 705 34 1 775 1478 411019001 411018297 0.000000e+00 1107
6 TraesCS5B01G117000 chr1B 90.802 511 39 6 4926 5429 180009123 180009632 0.000000e+00 676
7 TraesCS5B01G117000 chr1B 94.286 105 5 1 6 109 468212206 468212310 5.630000e-35 159
8 TraesCS5B01G117000 chr1B 96.667 90 3 0 6 95 521340841 521340930 3.390000e-32 150
9 TraesCS5B01G117000 chr6B 95.310 4670 193 19 776 5429 361272421 361267762 0.000000e+00 7387
10 TraesCS5B01G117000 chr6B 95.182 4670 185 17 775 5429 570079120 570083764 0.000000e+00 7341
11 TraesCS5B01G117000 chr6B 95.355 3854 165 6 775 4618 308976668 308980517 0.000000e+00 6113
12 TraesCS5B01G117000 chr6B 96.667 90 3 0 6 95 142541594 142541505 3.390000e-32 150
13 TraesCS5B01G117000 chr6D 90.675 3721 255 44 1311 5006 77327964 77331617 0.000000e+00 4865
14 TraesCS5B01G117000 chr6D 92.258 465 35 1 2237 2700 387786119 387786583 0.000000e+00 658
15 TraesCS5B01G117000 chr6D 83.124 557 70 12 2697 3233 10401596 10402148 2.270000e-133 486
16 TraesCS5B01G117000 chr2D 92.997 2813 166 16 1311 4107 244754335 244757132 0.000000e+00 4074
17 TraesCS5B01G117000 chr2D 87.194 859 77 12 4053 4880 300875309 300876165 0.000000e+00 946
18 TraesCS5B01G117000 chr7B 95.495 1665 60 12 3356 5011 131515161 131513503 0.000000e+00 2645
19 TraesCS5B01G117000 chr7B 93.881 670 41 0 97 766 40674038 40673369 0.000000e+00 1011
20 TraesCS5B01G117000 chr7B 92.697 671 46 3 97 766 459347914 459348582 0.000000e+00 965
21 TraesCS5B01G117000 chr7B 91.585 511 34 7 4926 5429 120492979 120493487 0.000000e+00 697
22 TraesCS5B01G117000 chr7B 95.556 90 4 0 6 95 576353551 576353640 1.580000e-30 145
23 TraesCS5B01G117000 chr2B 92.825 1770 68 15 3242 5000 407887555 407889276 0.000000e+00 2510
24 TraesCS5B01G117000 chr2B 94.875 1522 68 8 3915 5429 51455682 51454164 0.000000e+00 2370
25 TraesCS5B01G117000 chr2B 95.859 1449 58 2 775 2222 407886103 407887550 0.000000e+00 2342
26 TraesCS5B01G117000 chr2B 95.467 706 29 3 775 1478 371366908 371366204 0.000000e+00 1123
27 TraesCS5B01G117000 chr4D 94.486 671 36 1 97 766 37437578 37438248 0.000000e+00 1033
28 TraesCS5B01G117000 chr1D 93.145 671 45 1 97 766 361478320 361477650 0.000000e+00 983
29 TraesCS5B01G117000 chr1D 92.708 672 46 2 97 766 396367436 396366766 0.000000e+00 966
30 TraesCS5B01G117000 chr5A 92.250 671 51 1 97 766 492057379 492058049 0.000000e+00 950
31 TraesCS5B01G117000 chrUn 90.643 513 38 8 4926 5429 14055035 14055546 0.000000e+00 673
32 TraesCS5B01G117000 chr3B 95.294 85 4 0 6 90 451157736 451157652 9.490000e-28 135


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 TraesCS5B01G117000 chr5B 204611685 204617113 5428 True 10026 10026 100.000 1 5429 1 chr5B.!!$R2 5428
1 TraesCS5B01G117000 chr5B 176789579 176795013 5434 True 9012 9012 96.618 1 5429 1 chr5B.!!$R1 5428
2 TraesCS5B01G117000 chr1B 177157363 177162775 5412 False 8667 8667 95.550 1 5426 1 chr1B.!!$F1 5425
3 TraesCS5B01G117000 chr1B 192672642 192678071 5429 False 8658 8658 95.465 1 5429 1 chr1B.!!$F3 5428
4 TraesCS5B01G117000 chr1B 411018297 411019001 704 True 1107 1107 95.035 775 1478 1 chr1B.!!$R1 703
5 TraesCS5B01G117000 chr1B 180009123 180009632 509 False 676 676 90.802 4926 5429 1 chr1B.!!$F2 503
6 TraesCS5B01G117000 chr6B 361267762 361272421 4659 True 7387 7387 95.310 776 5429 1 chr6B.!!$R2 4653
7 TraesCS5B01G117000 chr6B 570079120 570083764 4644 False 7341 7341 95.182 775 5429 1 chr6B.!!$F2 4654
8 TraesCS5B01G117000 chr6B 308976668 308980517 3849 False 6113 6113 95.355 775 4618 1 chr6B.!!$F1 3843
9 TraesCS5B01G117000 chr6D 77327964 77331617 3653 False 4865 4865 90.675 1311 5006 1 chr6D.!!$F2 3695
10 TraesCS5B01G117000 chr6D 10401596 10402148 552 False 486 486 83.124 2697 3233 1 chr6D.!!$F1 536
11 TraesCS5B01G117000 chr2D 244754335 244757132 2797 False 4074 4074 92.997 1311 4107 1 chr2D.!!$F1 2796
12 TraesCS5B01G117000 chr2D 300875309 300876165 856 False 946 946 87.194 4053 4880 1 chr2D.!!$F2 827
13 TraesCS5B01G117000 chr7B 131513503 131515161 1658 True 2645 2645 95.495 3356 5011 1 chr7B.!!$R2 1655
14 TraesCS5B01G117000 chr7B 40673369 40674038 669 True 1011 1011 93.881 97 766 1 chr7B.!!$R1 669
15 TraesCS5B01G117000 chr7B 459347914 459348582 668 False 965 965 92.697 97 766 1 chr7B.!!$F2 669
16 TraesCS5B01G117000 chr7B 120492979 120493487 508 False 697 697 91.585 4926 5429 1 chr7B.!!$F1 503
17 TraesCS5B01G117000 chr2B 407886103 407889276 3173 False 2426 2510 94.342 775 5000 2 chr2B.!!$F1 4225
18 TraesCS5B01G117000 chr2B 51454164 51455682 1518 True 2370 2370 94.875 3915 5429 1 chr2B.!!$R1 1514
19 TraesCS5B01G117000 chr2B 371366204 371366908 704 True 1123 1123 95.467 775 1478 1 chr2B.!!$R2 703
20 TraesCS5B01G117000 chr4D 37437578 37438248 670 False 1033 1033 94.486 97 766 1 chr4D.!!$F1 669
21 TraesCS5B01G117000 chr1D 361477650 361478320 670 True 983 983 93.145 97 766 1 chr1D.!!$R1 669
22 TraesCS5B01G117000 chr1D 396366766 396367436 670 True 966 966 92.708 97 766 1 chr1D.!!$R2 669
23 TraesCS5B01G117000 chr5A 492057379 492058049 670 False 950 950 92.250 97 766 1 chr5A.!!$F1 669
24 TraesCS5B01G117000 chrUn 14055035 14055546 511 False 673 673 90.643 4926 5429 1 chrUn.!!$F1 503

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
76 77 1.077357 TCCCTCGTGAGCTCTCTCC 60.077 63.158 16.19 0.0 38.58 3.71 F
746 756 2.045926 GCACAGGTAGCAGTGGGG 60.046 66.667 17.66 0.0 36.29 4.96 F
2119 2141 0.329261 CTTCTTCCCCAGACCATGCA 59.671 55.000 0.00 0.0 0.00 3.96 F
2381 2404 0.108281 TCGTTGAACGACACAACCCA 60.108 50.000 17.28 0.0 46.73 4.51 F
3677 3726 0.110295 TAAAGCCAGCTGCACCTTCA 59.890 50.000 8.66 0.0 44.83 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 1689 1.442769 CCACAGAATAGCAACAGCGT 58.557 50.000 0.00 0.0 0.00 5.07 R
2367 2390 0.736053 TGCTTTGGGTTGTGTCGTTC 59.264 50.000 0.00 0.0 0.00 3.95 R
3966 4019 1.744741 TTGGCAGCATCGCGAATGA 60.745 52.632 15.24 0.0 37.59 2.57 R
4175 4340 2.235016 TGTAGCATGTGAACCCCAAAC 58.765 47.619 0.00 0.0 0.00 2.93 R
5375 5579 2.030540 GGTTCCGAAAAAGGGTACTTGC 60.031 50.000 0.00 0.0 36.93 4.01 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
76 77 1.077357 TCCCTCGTGAGCTCTCTCC 60.077 63.158 16.19 0.00 38.58 3.71
93 100 3.309296 TCTCCCTCTCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
398 405 3.407967 CCCCAGGCCGTACACCAT 61.408 66.667 0.00 0.00 0.00 3.55
517 527 3.503363 CAGAATAGTTGGTGTGTGTGCAT 59.497 43.478 0.00 0.00 0.00 3.96
746 756 2.045926 GCACAGGTAGCAGTGGGG 60.046 66.667 17.66 0.00 36.29 4.96
786 796 5.221461 CCCTATATAACTCAGGAAGCACGTT 60.221 44.000 0.00 0.00 0.00 3.99
833 843 9.322773 GTAACCTATATAACTCCTGTTTGTTCC 57.677 37.037 0.00 0.00 37.59 3.62
852 862 5.068723 TGTTCCGACTTCTTGTTTCTCTACT 59.931 40.000 0.00 0.00 0.00 2.57
853 863 5.373981 TCCGACTTCTTGTTTCTCTACTC 57.626 43.478 0.00 0.00 0.00 2.59
854 864 4.825634 TCCGACTTCTTGTTTCTCTACTCA 59.174 41.667 0.00 0.00 0.00 3.41
858 868 3.577649 TCTTGTTTCTCTACTCAGGCG 57.422 47.619 0.00 0.00 0.00 5.52
940 950 4.678256 TCTATAAGCTCCTCGGGAATGAT 58.322 43.478 0.00 0.00 0.00 2.45
1284 1296 3.253188 GTGCCAAAACTAGATGCAAGTCA 59.747 43.478 0.00 0.00 33.11 3.41
1364 1376 7.572523 TGTTGATAAAATCTAGCCCATTCAG 57.427 36.000 0.00 0.00 0.00 3.02
1458 1470 7.653713 GTGGAGTACATCATTATCTTACAGTGG 59.346 40.741 0.00 0.00 0.00 4.00
1628 1649 5.437289 CAACTTACTTGCTTCCAACATGA 57.563 39.130 0.00 0.00 0.00 3.07
1668 1689 4.418392 GTTCGTAATCGGCTACTTCAGAA 58.582 43.478 0.00 0.00 37.69 3.02
1742 1763 6.123651 TCTTACAAAGAAAAGGTAACCTGCA 58.876 36.000 0.00 0.00 33.83 4.41
1787 1808 7.775561 ACTTTGCCCTTCAAATATAGAAGTAGG 59.224 37.037 13.68 10.65 43.14 3.18
1841 1862 0.737715 ATTGTCGGTCGCTCAGAAGC 60.738 55.000 0.00 0.00 45.56 3.86
1842 1863 2.507324 GTCGGTCGCTCAGAAGCC 60.507 66.667 0.00 0.00 46.34 4.35
1848 1869 4.785512 CGCTCAGAAGCCGCTCGT 62.786 66.667 0.00 0.00 46.34 4.18
1963 1984 4.082125 GGTCTGAACATTGGGATCAAACT 58.918 43.478 0.00 0.00 36.36 2.66
2119 2141 0.329261 CTTCTTCCCCAGACCATGCA 59.671 55.000 0.00 0.00 0.00 3.96
2127 2149 1.210931 CAGACCATGCACGGCTTTG 59.789 57.895 0.00 0.00 0.00 2.77
2180 2202 3.530535 GCACAACCACAACATCCTTTTT 58.469 40.909 0.00 0.00 0.00 1.94
2367 2390 2.032634 CCACCACACCGGATCGTTG 61.033 63.158 9.46 0.00 38.63 4.10
2381 2404 0.108281 TCGTTGAACGACACAACCCA 60.108 50.000 17.28 0.00 46.73 4.51
2541 2565 3.626924 GCACCGTCCCAGTCCAGT 61.627 66.667 0.00 0.00 0.00 4.00
2757 2781 0.877743 GCAGCCTCCTTCAGTTCAAC 59.122 55.000 0.00 0.00 0.00 3.18
2971 3012 8.603304 ACCAGAACTAGTGTACTTTGGATTATT 58.397 33.333 8.46 0.00 0.00 1.40
3223 3266 6.001460 TGTAAAGGGTCATCGATTGAAAAGT 58.999 36.000 0.00 0.00 35.70 2.66
3267 3310 8.379161 CGTCTCAGATAAGTTCATGAAAAAGAG 58.621 37.037 10.35 10.46 0.00 2.85
3268 3311 9.213799 GTCTCAGATAAGTTCATGAAAAAGAGT 57.786 33.333 10.35 0.00 0.00 3.24
3570 3619 4.082523 GTGCCCTGGTCGCTGCTA 62.083 66.667 0.00 0.00 0.00 3.49
3616 3665 7.401493 AGAAAGAGATTACTGAGAGGGATTTGA 59.599 37.037 0.00 0.00 0.00 2.69
3632 3681 1.689984 TTGATGCTGCTGTTGTTCCA 58.310 45.000 0.00 0.00 0.00 3.53
3677 3726 0.110295 TAAAGCCAGCTGCACCTTCA 59.890 50.000 8.66 0.00 44.83 3.02
3854 3907 9.535878 AAGAAACTAAATATTTTGGTGCGAAAA 57.464 25.926 5.91 0.00 0.00 2.29
3966 4019 4.518211 CACTTGTTTCAAATGCTCTCCTCT 59.482 41.667 0.00 0.00 0.00 3.69
4108 4253 7.221450 AGTAGGTGTTTGTTGCATAAGTTCTA 58.779 34.615 0.00 0.00 0.00 2.10
4175 4340 5.106475 CGGAGAAGCTACTACTATTGCTAGG 60.106 48.000 0.00 0.00 35.09 3.02
4369 4543 4.711846 ACATCAGCACAGTGAGTAAGGATA 59.288 41.667 4.15 0.00 0.00 2.59
4406 4583 1.315257 ATGCCTACAAAGCAAGCCCG 61.315 55.000 0.00 0.00 44.83 6.13
4668 4850 4.184629 ACAATTATCAGTTCGAGTGCTCC 58.815 43.478 0.00 0.00 0.00 4.70
4797 4982 3.408634 TGGAATTTGAGGAAGTTCGTCC 58.591 45.455 19.95 7.30 38.03 4.79
4860 5046 9.941325 AAAAAGCACATCACATTTATTATGGAA 57.059 25.926 0.00 0.00 0.00 3.53
5375 5579 0.892755 AACCCATGCAAGCATCAGTG 59.107 50.000 4.24 0.00 33.90 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 5.878406 ACTTAGAGAGAGAGAGAGAGAGG 57.122 47.826 0.00 0.00 0.00 3.69
93 100 5.817816 ACTGGTTGAAGTGAACTGAACTTAG 59.182 40.000 5.89 6.98 37.98 2.18
361 368 3.766691 GCGGAGGTGAACGGCCTA 61.767 66.667 0.00 0.00 36.29 3.93
398 405 0.392706 TGAACAGGCTCTCTTCGCAA 59.607 50.000 0.00 0.00 0.00 4.85
493 500 3.315191 GCACACACACCAACTATTCTGTT 59.685 43.478 0.00 0.00 0.00 3.16
517 527 7.428282 TTGAAACTTGCACTGACGATATTTA 57.572 32.000 0.00 0.00 0.00 1.40
639 649 5.111293 ACAGAATTTTCAAACTTGCACTGG 58.889 37.500 0.00 0.00 0.00 4.00
833 843 5.157781 CCTGAGTAGAGAAACAAGAAGTCG 58.842 45.833 0.00 0.00 0.00 4.18
854 864 1.675641 GTGTGCCAGGATTTCGCCT 60.676 57.895 0.00 0.00 39.37 5.52
858 868 2.134789 ATCAGGTGTGCCAGGATTTC 57.865 50.000 0.00 0.00 37.19 2.17
940 950 2.124411 GGGATCCCAGCTACTACCAAA 58.876 52.381 26.95 0.00 35.81 3.28
1284 1296 8.630054 TGTATACATTTGCTGAAGTTACCTTT 57.370 30.769 0.08 0.00 0.00 3.11
1364 1376 6.686630 CATCCTAGTCCAATCATGACTACTC 58.313 44.000 0.00 0.00 42.78 2.59
1411 1423 5.983118 CCACTTAGATAACGATGTATGCACA 59.017 40.000 0.00 0.00 39.52 4.57
1524 1545 4.821260 TGCAGCAGTTTCTGTAGAAATTCA 59.179 37.500 9.98 0.00 44.69 2.57
1626 1647 7.833786 ACGAACCTTAGAATGTGTTACTATCA 58.166 34.615 0.00 0.00 0.00 2.15
1627 1648 9.793252 TTACGAACCTTAGAATGTGTTACTATC 57.207 33.333 0.00 0.00 0.00 2.08
1668 1689 1.442769 CCACAGAATAGCAACAGCGT 58.557 50.000 0.00 0.00 0.00 5.07
1787 1808 8.692110 TGTGAAAATGCTTATTGACATTGATC 57.308 30.769 0.00 0.00 36.64 2.92
1841 1862 4.457810 CATTGCTTGAATTATACGAGCGG 58.542 43.478 0.00 0.00 44.84 5.52
1842 1863 4.457810 CCATTGCTTGAATTATACGAGCG 58.542 43.478 0.00 0.00 44.84 5.03
1848 1869 9.881649 TTAACATTTGCCATTGCTTGAATTATA 57.118 25.926 0.00 0.00 38.71 0.98
2180 2202 2.301870 AGTCAGCGGTCAATTTGGACTA 59.698 45.455 0.26 0.00 37.91 2.59
2367 2390 0.736053 TGCTTTGGGTTGTGTCGTTC 59.264 50.000 0.00 0.00 0.00 3.95
2381 2404 2.331451 GCGGCGTTGAACTGCTTT 59.669 55.556 9.37 0.00 36.45 3.51
2541 2565 3.860605 CATCGGGATGCCACGGGA 61.861 66.667 3.39 0.00 31.39 5.14
2736 2760 1.644509 TGAACTGAAGGAGGCTGCTA 58.355 50.000 9.60 0.00 0.00 3.49
2757 2781 8.777865 TTCTCTGATTACTTTAGTTCATGTGG 57.222 34.615 0.00 0.00 0.00 4.17
2971 3012 4.551702 TTGAGGCTACATTTGCACTAGA 57.448 40.909 0.00 0.00 0.00 2.43
3146 3189 4.035091 CCTCTCGAGTCAGAACTGATACAG 59.965 50.000 13.13 0.00 42.18 2.74
3196 3239 3.262151 TCAATCGATGACCCTTTACACCA 59.738 43.478 0.00 0.00 31.50 4.17
3198 3241 5.873179 TTTCAATCGATGACCCTTTACAC 57.127 39.130 0.00 0.00 37.92 2.90
3223 3266 5.125100 AGACGTCGTGGTGAACTTATAAA 57.875 39.130 10.46 0.00 0.00 1.40
3496 3539 2.049433 GGCGGCGCACTATATCGT 60.049 61.111 34.36 0.00 0.00 3.73
3497 3540 2.809601 GGGCGGCGCACTATATCG 60.810 66.667 34.36 2.00 0.00 2.92
3570 3619 5.728937 TCTCACTCACCTTACCCTATAGT 57.271 43.478 0.00 0.00 0.00 2.12
3632 3681 8.811017 AGATTCGACAATCCTCTATCAATACAT 58.189 33.333 0.00 0.00 39.58 2.29
3677 3726 3.920231 ATGTGACAGTGCATAGGATGT 57.080 42.857 0.00 0.00 0.00 3.06
3854 3907 2.099756 GCACCAGAGAAAAGCAACAACT 59.900 45.455 0.00 0.00 0.00 3.16
3966 4019 1.744741 TTGGCAGCATCGCGAATGA 60.745 52.632 15.24 0.00 37.59 2.57
4108 4253 4.490743 GTGCAACAAACACCTACAAGTTT 58.509 39.130 0.00 0.00 38.40 2.66
4175 4340 2.235016 TGTAGCATGTGAACCCCAAAC 58.765 47.619 0.00 0.00 0.00 2.93
4222 4387 9.334947 ACACAACCAAATTATCTCTCTCATATG 57.665 33.333 0.00 0.00 0.00 1.78
4369 4543 2.681422 CATTATTCCCCAAGGTGCCAT 58.319 47.619 0.00 0.00 0.00 4.40
4406 4583 1.069823 AGTGATCAGCATCGTCATCCC 59.930 52.381 0.00 0.00 0.00 3.85
4668 4850 5.264395 ACATCAACCAAAATAGGAAGGAGG 58.736 41.667 0.00 0.00 0.00 4.30
4761 4946 5.642063 TCAAATTCCATAGAAGAACCGACAC 59.358 40.000 0.00 0.00 34.86 3.67
4797 4982 6.470278 TGAGCATATATTCCTCAGGTTCATG 58.530 40.000 8.19 0.00 32.30 3.07
4901 5090 4.318332 TGAGCAGTCGAACTTTCATCATT 58.682 39.130 0.00 0.00 0.00 2.57
5062 5252 4.619336 CGAACGGACCACCATTTTTAATTG 59.381 41.667 0.00 0.00 35.59 2.32
5064 5254 3.191791 CCGAACGGACCACCATTTTTAAT 59.808 43.478 7.53 0.00 37.50 1.40
5375 5579 2.030540 GGTTCCGAAAAAGGGTACTTGC 60.031 50.000 0.00 0.00 36.93 4.01


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

AutoCloner maintained by Alex Coulton.