Multiple sequence alignment - TraesCS5D01G154600

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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 TraesCS5D01G154600 chr5D 100.000 3533 0 0 1 3533 242846548 242850080 0.000000e+00 6525.0
1 TraesCS5D01G154600 chr5D 84.066 1525 212 14 1037 2541 5632330 5630817 0.000000e+00 1441.0
2 TraesCS5D01G154600 chr5D 95.833 264 5 4 1 258 374502658 374502921 4.220000e-114 422.0
3 TraesCS5D01G154600 chr5A 95.573 1965 56 7 916 2856 309313041 309311084 0.000000e+00 3118.0
4 TraesCS5D01G154600 chr5A 84.275 1469 192 14 1088 2541 3432834 3431390 0.000000e+00 1397.0
5 TraesCS5D01G154600 chr5A 91.069 683 33 4 2853 3533 283578673 283578017 0.000000e+00 898.0
6 TraesCS5D01G154600 chr5A 80.374 107 6 6 257 353 309313136 309313035 2.280000e-07 67.6
7 TraesCS5D01G154600 chr5B 95.771 1608 50 7 916 2511 255682893 255681292 0.000000e+00 2577.0
8 TraesCS5D01G154600 chr5B 96.629 445 14 1 2857 3301 569217415 569217858 0.000000e+00 737.0
9 TraesCS5D01G154600 chr5B 81.310 626 85 16 1031 1641 6535963 6536571 2.470000e-131 479.0
10 TraesCS5D01G154600 chr5B 85.670 321 44 2 1818 2137 6536606 6536925 1.570000e-88 337.0
11 TraesCS5D01G154600 chr5B 85.938 320 26 10 2547 2852 637396909 637397223 1.220000e-84 324.0
12 TraesCS5D01G154600 chr5B 88.889 243 19 6 2511 2748 255672084 255671845 3.450000e-75 292.0
13 TraesCS5D01G154600 chr5B 96.939 98 3 0 2759 2856 255670573 255670476 7.850000e-37 165.0
14 TraesCS5D01G154600 chr5B 81.818 99 14 3 257 353 255682983 255682887 2.920000e-11 80.5
15 TraesCS5D01G154600 chr3D 98.525 678 10 0 2856 3533 330070964 330070287 0.000000e+00 1197.0
16 TraesCS5D01G154600 chr3D 89.855 621 31 10 2921 3533 306737130 306736534 0.000000e+00 769.0
17 TraesCS5D01G154600 chr3D 88.909 559 60 2 356 914 303776094 303775538 0.000000e+00 688.0
18 TraesCS5D01G154600 chr1D 97.801 682 9 3 2857 3533 62720176 62720856 0.000000e+00 1171.0
19 TraesCS5D01G154600 chr1D 93.393 560 36 1 356 914 362792019 362791460 0.000000e+00 828.0
20 TraesCS5D01G154600 chr1D 97.308 260 3 2 1 256 250404728 250404987 4.190000e-119 438.0
21 TraesCS5D01G154600 chr2A 95.520 692 22 6 2848 3533 139903771 139904459 0.000000e+00 1098.0
22 TraesCS5D01G154600 chr2A 94.858 564 27 2 356 918 33313583 33314145 0.000000e+00 880.0
23 TraesCS5D01G154600 chr2A 74.660 588 116 23 1833 2393 771539487 771540068 2.740000e-56 230.0
24 TraesCS5D01G154600 chr6D 95.710 676 10 1 2858 3533 472156957 472156301 0.000000e+00 1070.0
25 TraesCS5D01G154600 chr6D 94.444 270 8 5 1 264 99595911 99596179 3.280000e-110 409.0
26 TraesCS5D01G154600 chr3A 95.266 676 28 3 2861 3532 707112565 707111890 0.000000e+00 1068.0
27 TraesCS5D01G154600 chr3A 96.538 260 5 2 1 256 167545436 167545177 9.060000e-116 427.0
28 TraesCS5D01G154600 chr7D 95.126 677 10 2 2857 3533 235472332 235472985 0.000000e+00 1046.0
29 TraesCS5D01G154600 chr7D 93.381 559 36 1 356 914 418639278 418638721 0.000000e+00 826.0
30 TraesCS5D01G154600 chr7D 88.929 560 60 2 356 915 367585922 367585365 0.000000e+00 689.0
31 TraesCS5D01G154600 chr2B 95.000 560 26 2 356 914 410102294 410101736 0.000000e+00 878.0
32 TraesCS5D01G154600 chr2B 96.197 447 14 3 2857 3301 164866033 164866478 0.000000e+00 728.0
33 TraesCS5D01G154600 chr4A 96.413 446 14 1 2856 3301 743670679 743670236 0.000000e+00 734.0
34 TraesCS5D01G154600 chr4A 99.153 236 2 0 3298 3533 743670134 743669899 3.260000e-115 425.0
35 TraesCS5D01G154600 chr4B 95.526 447 16 3 2857 3301 434714861 434715305 0.000000e+00 712.0
36 TraesCS5D01G154600 chr4B 85.981 321 25 11 2547 2852 117036924 117036609 3.400000e-85 326.0
37 TraesCS5D01G154600 chr4B 73.071 609 131 30 1833 2417 500053699 500054298 6.020000e-43 185.0
38 TraesCS5D01G154600 chr4D 89.127 561 57 4 356 915 351068466 351067909 0.000000e+00 695.0
39 TraesCS5D01G154600 chr4D 95.420 262 6 4 1 256 479509817 479509556 2.540000e-111 412.0
40 TraesCS5D01G154600 chr4D 73.978 538 111 24 1899 2417 403183120 403183647 1.290000e-44 191.0
41 TraesCS5D01G154600 chr2D 88.909 559 60 2 356 914 602338819 602339375 0.000000e+00 688.0
42 TraesCS5D01G154600 chr2D 88.556 568 59 4 355 921 277825419 277824857 0.000000e+00 684.0
43 TraesCS5D01G154600 chr2D 75.145 519 99 18 1899 2393 645839085 645839597 2.140000e-52 217.0
44 TraesCS5D01G154600 chr7A 96.154 260 6 2 1 256 332399115 332399374 4.220000e-114 422.0
45 TraesCS5D01G154600 chr7A 95.785 261 7 2 1 257 332415268 332415528 5.450000e-113 418.0
46 TraesCS5D01G154600 chr7A 95.769 260 7 2 1 256 639788682 639788423 1.960000e-112 416.0
47 TraesCS5D01G154600 chr7A 95.385 260 8 2 1 256 639787160 639786901 9.130000e-111 411.0
48 TraesCS5D01G154600 chr6B 86.250 320 24 11 2547 2852 463260775 463261088 2.630000e-86 329.0


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 TraesCS5D01G154600 chr5D 242846548 242850080 3532 False 6525.00 6525 100.0000 1 3533 1 chr5D.!!$F1 3532
1 TraesCS5D01G154600 chr5D 5630817 5632330 1513 True 1441.00 1441 84.0660 1037 2541 1 chr5D.!!$R1 1504
2 TraesCS5D01G154600 chr5A 309311084 309313136 2052 True 1592.80 3118 87.9735 257 2856 2 chr5A.!!$R3 2599
3 TraesCS5D01G154600 chr5A 3431390 3432834 1444 True 1397.00 1397 84.2750 1088 2541 1 chr5A.!!$R1 1453
4 TraesCS5D01G154600 chr5A 283578017 283578673 656 True 898.00 898 91.0690 2853 3533 1 chr5A.!!$R2 680
5 TraesCS5D01G154600 chr5B 255681292 255682983 1691 True 1328.75 2577 88.7945 257 2511 2 chr5B.!!$R2 2254
6 TraesCS5D01G154600 chr5B 6535963 6536925 962 False 408.00 479 83.4900 1031 2137 2 chr5B.!!$F3 1106
7 TraesCS5D01G154600 chr5B 255670476 255672084 1608 True 228.50 292 92.9140 2511 2856 2 chr5B.!!$R1 345
8 TraesCS5D01G154600 chr3D 330070287 330070964 677 True 1197.00 1197 98.5250 2856 3533 1 chr3D.!!$R3 677
9 TraesCS5D01G154600 chr3D 306736534 306737130 596 True 769.00 769 89.8550 2921 3533 1 chr3D.!!$R2 612
10 TraesCS5D01G154600 chr3D 303775538 303776094 556 True 688.00 688 88.9090 356 914 1 chr3D.!!$R1 558
11 TraesCS5D01G154600 chr1D 62720176 62720856 680 False 1171.00 1171 97.8010 2857 3533 1 chr1D.!!$F1 676
12 TraesCS5D01G154600 chr1D 362791460 362792019 559 True 828.00 828 93.3930 356 914 1 chr1D.!!$R1 558
13 TraesCS5D01G154600 chr2A 139903771 139904459 688 False 1098.00 1098 95.5200 2848 3533 1 chr2A.!!$F2 685
14 TraesCS5D01G154600 chr2A 33313583 33314145 562 False 880.00 880 94.8580 356 918 1 chr2A.!!$F1 562
15 TraesCS5D01G154600 chr2A 771539487 771540068 581 False 230.00 230 74.6600 1833 2393 1 chr2A.!!$F3 560
16 TraesCS5D01G154600 chr6D 472156301 472156957 656 True 1070.00 1070 95.7100 2858 3533 1 chr6D.!!$R1 675
17 TraesCS5D01G154600 chr3A 707111890 707112565 675 True 1068.00 1068 95.2660 2861 3532 1 chr3A.!!$R2 671
18 TraesCS5D01G154600 chr7D 235472332 235472985 653 False 1046.00 1046 95.1260 2857 3533 1 chr7D.!!$F1 676
19 TraesCS5D01G154600 chr7D 418638721 418639278 557 True 826.00 826 93.3810 356 914 1 chr7D.!!$R2 558
20 TraesCS5D01G154600 chr7D 367585365 367585922 557 True 689.00 689 88.9290 356 915 1 chr7D.!!$R1 559
21 TraesCS5D01G154600 chr2B 410101736 410102294 558 True 878.00 878 95.0000 356 914 1 chr2B.!!$R1 558
22 TraesCS5D01G154600 chr4A 743669899 743670679 780 True 579.50 734 97.7830 2856 3533 2 chr4A.!!$R1 677
23 TraesCS5D01G154600 chr4D 351067909 351068466 557 True 695.00 695 89.1270 356 915 1 chr4D.!!$R1 559
24 TraesCS5D01G154600 chr2D 602338819 602339375 556 False 688.00 688 88.9090 356 914 1 chr2D.!!$F1 558
25 TraesCS5D01G154600 chr2D 277824857 277825419 562 True 684.00 684 88.5560 355 921 1 chr2D.!!$R1 566
26 TraesCS5D01G154600 chr2D 645839085 645839597 512 False 217.00 217 75.1450 1899 2393 1 chr2D.!!$F2 494
27 TraesCS5D01G154600 chr7A 639786901 639788682 1781 True 413.50 416 95.5770 1 256 2 chr7A.!!$R1 255

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
349 396 0.029035 CTTGAATCTGCATGCGAGGC 59.971 55.000 14.09 9.64 0.0 4.70 F
384 431 1.233949 GGGTAGGGTATGGGACGGA 59.766 63.158 0.00 0.00 0.0 4.69 F
832 2024 2.424812 GGGTAAGGGTACTATCCGTGGA 60.425 54.545 0.00 0.00 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 3035 0.737715 CGTCTCTGCTTTCTTCCCCG 60.738 60.0 0.00 0.0 0.00 5.73 R
2364 3611 0.541392 TCATCTGCACGTAGGCCATT 59.459 50.0 5.01 0.0 0.00 3.16 R
2545 3795 0.978907 TGCTCTGAAGATCCAGCACA 59.021 50.0 0.00 0.0 36.96 4.57 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
163 164 1.130777 GGGTGCCAATTTATGCCCAT 58.869 50.000 0.00 0.00 36.25 4.00
178 179 2.292785 TGCCCATGGGTATTGAAATGGT 60.293 45.455 31.58 0.00 38.32 3.55
183 184 3.551635 TGGGTATTGAAATGGTTGGGT 57.448 42.857 0.00 0.00 0.00 4.51
265 270 2.770447 TGCCATCCCTACCATACTCAA 58.230 47.619 0.00 0.00 0.00 3.02
345 392 1.265568 GCAACTTGAATCTGCATGCG 58.734 50.000 14.09 8.20 36.09 4.73
347 394 2.782163 CAACTTGAATCTGCATGCGAG 58.218 47.619 14.09 11.65 0.00 5.03
348 395 1.376543 ACTTGAATCTGCATGCGAGG 58.623 50.000 14.09 6.00 0.00 4.63
349 396 0.029035 CTTGAATCTGCATGCGAGGC 59.971 55.000 14.09 9.64 0.00 4.70
384 431 1.233949 GGGTAGGGTATGGGACGGA 59.766 63.158 0.00 0.00 0.00 4.69
678 1858 8.051901 ACAACTTTAACATAGGTTCATAAGCC 57.948 34.615 0.00 0.00 38.45 4.35
719 1899 8.306313 ACATAGGTACACTTATGAATCACAGA 57.694 34.615 15.89 0.00 37.92 3.41
816 2008 3.451902 CCATGACTTAACGGGTAGGGTAA 59.548 47.826 0.00 0.00 0.00 2.85
825 2017 2.791774 ACGGGTAGGGTAAGGGTACTAT 59.208 50.000 0.00 0.00 0.00 2.12
832 2024 2.424812 GGGTAAGGGTACTATCCGTGGA 60.425 54.545 0.00 0.00 0.00 4.02
889 2082 4.730949 CGGTATCCGTGAATACCCATAT 57.269 45.455 11.26 0.00 45.70 1.78
895 2088 3.907474 TCCGTGAATACCCATATCCATGT 59.093 43.478 0.00 0.00 0.00 3.21
910 2103 4.368874 TCCATGTGTAAAATTGCCATCG 57.631 40.909 0.00 0.00 0.00 3.84
971 2164 8.298854 CCATCAAAATATTCACAGTTCAACAGA 58.701 33.333 0.00 0.00 0.00 3.41
972 2165 9.338291 CATCAAAATATTCACAGTTCAACAGAG 57.662 33.333 0.00 0.00 0.00 3.35
978 2171 3.872696 TCACAGTTCAACAGAGCAAAGA 58.127 40.909 0.00 0.00 0.00 2.52
1397 2602 3.649986 GTGGCAGCGCAAGAACGT 61.650 61.111 11.47 0.00 43.02 3.99
1695 2915 3.282374 ATTCCTTGACCCCGTGGCC 62.282 63.158 0.00 0.00 33.59 5.36
1826 3046 2.813908 CGCGTCCGGGGAAGAAAG 60.814 66.667 0.00 0.00 0.00 2.62
2364 3611 1.005394 GACGTGCTTCGGGAAGGAA 60.005 57.895 10.22 0.00 40.42 3.36
2545 3795 0.317479 AGCGTAGGACGAGCAAGTTT 59.683 50.000 2.65 0.00 46.05 2.66
2565 3821 1.066358 TGTGCTGGATCTTCAGAGCAG 60.066 52.381 3.41 0.00 41.96 4.24
2598 3854 8.774586 GTGGGCTATTAACAATAATGTCTGTAG 58.225 37.037 0.00 0.00 39.40 2.74
2946 5468 0.844503 GCGTAGTTATTCGTGCGAGG 59.155 55.000 0.00 0.00 0.00 4.63
3129 5657 3.386768 TCCCTCTGTTTCTTGTCTTCG 57.613 47.619 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 5.828328 TCAAGTGATCATGGACGAGTAGTAT 59.172 40.000 0.00 0.00 0.00 2.12
163 164 3.551635 ACCCAACCATTTCAATACCCA 57.448 42.857 0.00 0.00 0.00 4.51
178 179 6.557568 ACCCACAGAAAATTTCTATACCCAA 58.442 36.000 8.03 0.00 38.11 4.12
183 184 7.878495 ACCCATACCCACAGAAAATTTCTATA 58.122 34.615 8.03 0.00 38.11 1.31
229 233 0.991893 GGCAAGGGTAGGGTATGGGT 60.992 60.000 0.00 0.00 0.00 4.51
300 305 3.199946 GTCCAACCCATACCTGAAGATGA 59.800 47.826 0.00 0.00 0.00 2.92
349 396 4.303603 CATTGCCATCCTCGCGCG 62.304 66.667 26.76 26.76 0.00 6.86
351 398 2.658679 TACCCATTGCCATCCTCGCG 62.659 60.000 0.00 0.00 0.00 5.87
352 399 0.886490 CTACCCATTGCCATCCTCGC 60.886 60.000 0.00 0.00 0.00 5.03
353 400 0.250467 CCTACCCATTGCCATCCTCG 60.250 60.000 0.00 0.00 0.00 4.63
384 431 5.428783 GGGTATGGGTATGGTATTGCTCTAT 59.571 44.000 0.00 0.00 0.00 1.98
719 1899 8.836413 CCGTTTATATTGACATGTGAACCTTAT 58.164 33.333 1.15 0.00 0.00 1.73
816 2008 3.889859 TGTATCCACGGATAGTACCCT 57.110 47.619 6.02 0.00 37.72 4.34
825 2017 2.490115 GGCACAATTTTGTATCCACGGA 59.510 45.455 0.00 0.00 39.91 4.69
832 2024 7.397192 GGATAGGATATGGGCACAATTTTGTAT 59.603 37.037 0.00 0.00 39.91 2.29
851 2043 1.183030 CCGTACCCGCATGGATAGGA 61.183 60.000 0.00 0.00 37.49 2.94
889 2082 3.761218 ACGATGGCAATTTTACACATGGA 59.239 39.130 0.00 0.00 0.00 3.41
895 2088 4.095782 GCCTCTAACGATGGCAATTTTACA 59.904 41.667 0.00 0.00 45.46 2.41
910 2103 6.324819 TGGTTTATATATACGCGCCTCTAAC 58.675 40.000 5.73 0.62 0.00 2.34
971 2164 7.807977 TCTGACTTTTTATCTTGTCTTTGCT 57.192 32.000 0.00 0.00 0.00 3.91
972 2165 9.122613 GATTCTGACTTTTTATCTTGTCTTTGC 57.877 33.333 0.00 0.00 0.00 3.68
978 2171 9.300681 TCCATTGATTCTGACTTTTTATCTTGT 57.699 29.630 0.00 0.00 0.00 3.16
1014 2207 0.532573 TGAGTAGCAGGGAAGAAGCG 59.467 55.000 0.00 0.00 0.00 4.68
1015 2208 2.484594 GGATGAGTAGCAGGGAAGAAGC 60.485 54.545 0.00 0.00 0.00 3.86
1397 2602 1.666011 GTGGTGAACTCGAGGCTGA 59.334 57.895 18.41 0.00 0.00 4.26
1677 2897 2.355115 GCCACGGGGTCAAGGAAT 59.645 61.111 5.12 0.00 36.17 3.01
1695 2915 1.078848 CTTGACCTTCCAGGAGGCG 60.079 63.158 0.00 0.00 40.65 5.52
1815 3035 0.737715 CGTCTCTGCTTTCTTCCCCG 60.738 60.000 0.00 0.00 0.00 5.73
1826 3046 1.154188 GACAGGACGTCGTCTCTGC 60.154 63.158 28.64 21.56 35.68 4.26
1895 3121 1.227497 GCGATCAGGAAGCTGAGGG 60.227 63.158 0.00 0.00 36.73 4.30
1920 3146 3.371063 GCCGAGGACGTGGTCTCA 61.371 66.667 0.00 0.00 37.88 3.27
2353 3600 1.064979 GTAGGCCATTTCCTTCCCGAA 60.065 52.381 5.01 0.00 37.66 4.30
2364 3611 0.541392 TCATCTGCACGTAGGCCATT 59.459 50.000 5.01 0.00 0.00 3.16
2545 3795 0.978907 TGCTCTGAAGATCCAGCACA 59.021 50.000 0.00 0.00 36.96 4.57
2744 4005 7.360113 TGTGCATATAGGAGTACTGATTTGA 57.640 36.000 0.00 0.00 0.00 2.69
2839 5361 6.475207 CAATCCCGAAAAACTAATGTAGACG 58.525 40.000 0.00 0.00 0.00 4.18
2946 5468 2.665185 AACAGCCGGTTCGCTCAC 60.665 61.111 1.90 0.00 36.82 3.51
3129 5657 1.858458 GAAAAAGAAACAACCGCTGCC 59.142 47.619 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.