Multiple sequence alignment - TraesCS3D01G535800

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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 TraesCS3D01G535800 chr3D 100.000 2853 0 0 1 2853 609811587 609814439 0.000000e+00 5269
1 TraesCS3D01G535800 chr3D 100.000 641 0 0 3108 3748 609814694 609815334 0.000000e+00 1184
2 TraesCS3D01G535800 chr3D 97.512 402 10 0 3347 3748 21804909 21805310 0.000000e+00 688
3 TraesCS3D01G535800 chr7D 98.248 2854 47 3 1 2853 43550727 43547876 0.000000e+00 4990
4 TraesCS3D01G535800 chr7D 98.109 2855 50 3 1 2853 70693859 70691007 0.000000e+00 4970
5 TraesCS3D01G535800 chr7D 98.507 402 6 0 3347 3748 161278619 161279020 0.000000e+00 710
6 TraesCS3D01G535800 chr7D 85.446 426 39 13 3165 3584 70690011 70689603 4.480000e-114 422
7 TraesCS3D01G535800 chr7D 90.811 185 15 2 3110 3293 136197050 136197233 2.890000e-61 246
8 TraesCS3D01G535800 chr7D 90.476 168 16 0 3130 3297 500984024 500983857 4.870000e-54 222
9 TraesCS3D01G535800 chr6D 97.828 2854 52 4 1 2853 59072816 59075660 0.000000e+00 4918
10 TraesCS3D01G535800 chr6D 97.828 2854 44 7 1 2853 460234953 460232117 0.000000e+00 4911
11 TraesCS3D01G535800 chr6D 96.577 409 12 2 3341 3748 33258756 33258349 0.000000e+00 676
12 TraesCS3D01G535800 chr6D 94.565 184 10 0 3110 3293 33259899 33259716 6.130000e-73 285
13 TraesCS3D01G535800 chr6D 93.514 185 9 2 3110 3293 59075779 59075961 4.770000e-69 272
14 TraesCS3D01G535800 chr6D 90.217 184 16 2 3110 3292 85195521 85195703 4.840000e-59 239
15 TraesCS3D01G535800 chr6D 88.172 186 17 5 3110 3293 79732 79550 2.270000e-52 217
16 TraesCS3D01G535800 chr2D 97.828 2854 53 5 1 2853 13298821 13301666 0.000000e+00 4918
17 TraesCS3D01G535800 chr2D 98.010 402 8 0 3347 3748 558100313 558099912 0.000000e+00 699
18 TraesCS3D01G535800 chr2D 93.125 160 10 1 3128 3287 138169394 138169236 2.250000e-57 233
19 TraesCS3D01G535800 chr5D 97.654 2856 62 4 1 2853 12322088 12319235 0.000000e+00 4898
20 TraesCS3D01G535800 chr5D 97.454 2867 56 8 1 2853 431148666 431145803 0.000000e+00 4874
21 TraesCS3D01G535800 chr5D 98.507 402 6 0 3347 3748 565890431 565890832 0.000000e+00 710
22 TraesCS3D01G535800 chr5D 98.259 402 6 1 3347 3748 431144694 431144294 0.000000e+00 702
23 TraesCS3D01G535800 chr5D 97.761 402 9 0 3347 3748 12318031 12317630 0.000000e+00 693
24 TraesCS3D01G535800 chr4D 97.617 2854 59 4 1 2853 51851026 51853871 0.000000e+00 4885
25 TraesCS3D01G535800 chr4D 97.547 2854 62 3 1 2853 359858877 359856031 0.000000e+00 4876
26 TraesCS3D01G535800 chr4D 98.010 402 8 0 3347 3748 311956210 311955809 0.000000e+00 699
27 TraesCS3D01G535800 chr4D 93.865 163 10 0 3108 3270 51853987 51854149 2.890000e-61 246
28 TraesCS3D01G535800 chr1D 97.500 400 8 1 3349 3748 400130542 400130145 0.000000e+00 682
29 TraesCS3D01G535800 chr1D 91.379 174 15 0 3120 3293 420773174 420773347 4.840000e-59 239
30 TraesCS3D01G535800 chr1D 89.130 184 19 1 3110 3293 76922328 76922146 1.050000e-55 228


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 TraesCS3D01G535800 chr3D 609811587 609815334 3747 False 3226.5 5269 100.0000 1 3748 2 chr3D.!!$F2 3747
1 TraesCS3D01G535800 chr7D 43547876 43550727 2851 True 4990.0 4990 98.2480 1 2853 1 chr7D.!!$R1 2852
2 TraesCS3D01G535800 chr7D 70689603 70693859 4256 True 2696.0 4970 91.7775 1 3584 2 chr7D.!!$R3 3583
3 TraesCS3D01G535800 chr6D 460232117 460234953 2836 True 4911.0 4911 97.8280 1 2853 1 chr6D.!!$R2 2852
4 TraesCS3D01G535800 chr6D 59072816 59075961 3145 False 2595.0 4918 95.6710 1 3293 2 chr6D.!!$F2 3292
5 TraesCS3D01G535800 chr6D 33258349 33259899 1550 True 480.5 676 95.5710 3110 3748 2 chr6D.!!$R3 638
6 TraesCS3D01G535800 chr2D 13298821 13301666 2845 False 4918.0 4918 97.8280 1 2853 1 chr2D.!!$F1 2852
7 TraesCS3D01G535800 chr5D 12317630 12322088 4458 True 2795.5 4898 97.7075 1 3748 2 chr5D.!!$R1 3747
8 TraesCS3D01G535800 chr5D 431144294 431148666 4372 True 2788.0 4874 97.8565 1 3748 2 chr5D.!!$R2 3747
9 TraesCS3D01G535800 chr4D 359856031 359858877 2846 True 4876.0 4876 97.5470 1 2853 1 chr4D.!!$R2 2852
10 TraesCS3D01G535800 chr4D 51851026 51854149 3123 False 2565.5 4885 95.7410 1 3270 2 chr4D.!!$F1 3269

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
335 343 0.535335 CTTTCCATCTTCGGACCGGA 59.465 55.0 15.25 3.72 33.75 5.14 F
1183 1191 0.468226 GTGGAATGGGAGCCGTATGA 59.532 55.0 0.00 0.00 0.00 2.15 F
1237 1245 0.745845 AGGCTGAATCCGATGTGCAC 60.746 55.0 10.75 10.75 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1926 1934 0.038166 GAAGTGCACCTTCCCCATCA 59.962 55.000 14.63 0.0 43.25 3.07 R
2120 2128 0.835941 AGCTGGATCTGATGGTGTCC 59.164 55.000 0.00 0.0 0.00 4.02 R
3147 3183 3.389002 TGCACATGTCTGTAGCTATCCAT 59.611 43.478 0.00 0.0 33.14 3.41 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
26 27 0.590732 GTCGTACGCTATGTCGGTGG 60.591 60.000 11.24 0.00 0.00 4.61
153 157 0.605589 ACCTCTGAAGCTTCGGTCTG 59.394 55.000 29.82 21.71 35.11 3.51
335 343 0.535335 CTTTCCATCTTCGGACCGGA 59.465 55.000 15.25 3.72 33.75 5.14
431 439 1.153369 CGATTCTGATGGGTGGCGT 60.153 57.895 0.00 0.00 0.00 5.68
442 450 3.726517 GTGGCGTGCGCAGATGTT 61.727 61.111 12.22 0.00 44.11 2.71
443 451 2.977456 TGGCGTGCGCAGATGTTT 60.977 55.556 12.22 0.00 44.11 2.83
566 574 2.486472 ACTTCTGTCATTGCCCTGAG 57.514 50.000 0.00 0.00 0.00 3.35
632 640 2.957006 GTGGTACGTGATATCCAGGACT 59.043 50.000 0.00 0.00 34.88 3.85
822 830 5.156355 CGGAAAATTTGACCATGTTCTCTG 58.844 41.667 12.90 0.00 0.00 3.35
853 861 1.334160 TGGACGAAGCCTGTTGTAGA 58.666 50.000 0.00 0.00 0.00 2.59
958 966 1.101331 AGTACGAGGATTGGGACGAC 58.899 55.000 0.00 0.00 0.00 4.34
1183 1191 0.468226 GTGGAATGGGAGCCGTATGA 59.532 55.000 0.00 0.00 0.00 2.15
1211 1219 5.189934 AGGAGAGAGTTTTGGTAACCCTATG 59.810 44.000 0.00 0.00 0.00 2.23
1237 1245 0.745845 AGGCTGAATCCGATGTGCAC 60.746 55.000 10.75 10.75 0.00 4.57
1447 1455 7.576750 GACGGTTTCGATGATGCTAATATTA 57.423 36.000 0.00 0.00 40.11 0.98
1850 1858 5.870978 GCCTAACACTTTGATACCGTTTCTA 59.129 40.000 0.00 0.00 0.00 2.10
1926 1934 3.749284 AACCCCGGCTGGCAAAAGT 62.749 57.895 5.85 0.00 0.00 2.66
2120 2128 0.818296 CCAGAACGGTCTAGGTCAGG 59.182 60.000 0.64 0.00 30.85 3.86
2136 2144 1.206878 CAGGGACACCATCAGATCCA 58.793 55.000 0.00 0.00 40.13 3.41
2537 2570 4.564769 GTGAAGAAGATAAGCGTCAAGAGG 59.435 45.833 0.00 0.00 0.00 3.69
3147 3183 2.837591 TGCCATACCTTCTGTTGCTCTA 59.162 45.455 0.00 0.00 0.00 2.43
3163 3199 4.729868 TGCTCTATGGATAGCTACAGACA 58.270 43.478 0.00 0.00 39.53 3.41
3311 5954 0.394216 ATGTAGATTGCAGCGCCCAA 60.394 50.000 12.66 12.66 0.00 4.12
3335 5978 3.631686 TGTGAAGTAGCAAGCAAACACAT 59.368 39.130 0.00 0.00 33.22 3.21
3336 5979 4.819088 TGTGAAGTAGCAAGCAAACACATA 59.181 37.500 0.00 0.00 33.22 2.29
3337 5980 5.049474 TGTGAAGTAGCAAGCAAACACATAG 60.049 40.000 0.00 0.00 33.22 2.23
3338 5981 4.083324 TGAAGTAGCAAGCAAACACATAGC 60.083 41.667 0.00 0.00 0.00 2.97
3339 5982 3.411446 AGTAGCAAGCAAACACATAGCA 58.589 40.909 0.00 0.00 0.00 3.49
3340 5983 3.820467 AGTAGCAAGCAAACACATAGCAA 59.180 39.130 0.00 0.00 0.00 3.91
3341 5984 3.293311 AGCAAGCAAACACATAGCAAG 57.707 42.857 0.00 0.00 0.00 4.01
3342 5985 1.723003 GCAAGCAAACACATAGCAAGC 59.277 47.619 0.00 0.00 0.00 4.01
3343 5986 2.863312 GCAAGCAAACACATAGCAAGCA 60.863 45.455 0.00 0.00 32.83 3.91
3344 5987 3.382855 CAAGCAAACACATAGCAAGCAA 58.617 40.909 0.00 0.00 0.00 3.91
3345 5988 3.731652 AGCAAACACATAGCAAGCAAA 57.268 38.095 0.00 0.00 0.00 3.68
3433 6076 9.944376 AGTTGTTCATAACACATAGTACTTCAT 57.056 29.630 0.00 0.00 41.97 2.57
3495 6153 3.505464 AGTAGTTCACCGCACATAGTC 57.495 47.619 0.00 0.00 0.00 2.59
3550 6208 3.585862 AGTTCACGGCACATAGTAGTTG 58.414 45.455 0.00 0.00 0.00 3.16
3726 6386 3.558746 CCACCCTCTCCATGAATATCTGC 60.559 52.174 0.00 0.00 0.00 4.26
3729 6389 4.041444 ACCCTCTCCATGAATATCTGCTTC 59.959 45.833 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.596904 TTCAGTATTACCCGCTGCTC 57.403 50.000 0.00 0.00 0.00 4.26
153 157 1.144936 CTCCAAGGCTGATCCCGTC 59.855 63.158 0.00 0.00 34.51 4.79
335 343 1.508545 CAGCGTCACGGTCATCTCT 59.491 57.895 0.00 0.00 34.62 3.10
441 449 3.547746 GAACCATACCGATAAGGGCAAA 58.452 45.455 0.00 0.00 46.96 3.68
442 450 2.158726 GGAACCATACCGATAAGGGCAA 60.159 50.000 0.00 0.00 46.96 4.52
443 451 1.418637 GGAACCATACCGATAAGGGCA 59.581 52.381 0.00 0.00 46.96 5.36
566 574 3.144506 CACCATGTCCTCATTAGCATCC 58.855 50.000 0.00 0.00 31.15 3.51
802 810 8.641541 ACATAACAGAGAACATGGTCAAATTTT 58.358 29.630 14.46 1.92 0.00 1.82
822 830 2.412847 GCTTCGTCCAACTGCACATAAC 60.413 50.000 0.00 0.00 0.00 1.89
853 861 1.351017 CCACCAATACCTCCAGTGTGT 59.649 52.381 0.00 0.00 0.00 3.72
958 966 1.012486 GCCGTAGTGGGTCGTCTTTG 61.012 60.000 0.00 0.00 38.63 2.77
1183 1191 5.597182 GGGTTACCAAAACTCTCTCCTTTTT 59.403 40.000 2.98 0.00 36.50 1.94
1211 1219 0.537188 TCGGATTCAGCCTGAACTCC 59.463 55.000 9.77 15.46 39.45 3.85
1237 1245 2.043664 TGCCAGAGATCCCTATCCCTAG 59.956 54.545 0.00 0.00 31.98 3.02
1447 1455 8.047310 CCTATCCAACCTACAAGTTAGAAACAT 58.953 37.037 0.00 0.00 0.00 2.71
1850 1858 1.417517 TGATCTGGGCACGCTATGAAT 59.582 47.619 0.00 0.00 0.00 2.57
1926 1934 0.038166 GAAGTGCACCTTCCCCATCA 59.962 55.000 14.63 0.00 43.25 3.07
2120 2128 0.835941 AGCTGGATCTGATGGTGTCC 59.164 55.000 0.00 0.00 0.00 4.02
2227 2235 7.605309 TGAGGATATAGTTAGCAATGCATCAAG 59.395 37.037 8.35 0.00 0.00 3.02
3147 3183 3.389002 TGCACATGTCTGTAGCTATCCAT 59.611 43.478 0.00 0.00 33.14 3.41
3163 3199 3.790437 AGGCTAGGCGCTGCACAT 61.790 61.111 7.64 0.00 39.13 3.21
3250 4253 4.087892 ACCTGTGCAGCGCCTAGG 62.088 66.667 2.29 3.67 36.92 3.02
3311 5954 4.097741 TGTGTTTGCTTGCTACTTCACATT 59.902 37.500 0.00 0.00 31.22 2.71
3335 5978 4.438148 TGCTACGTATCATTTGCTTGCTA 58.562 39.130 0.00 0.00 0.00 3.49
3336 5979 3.270027 TGCTACGTATCATTTGCTTGCT 58.730 40.909 0.00 0.00 0.00 3.91
3337 5980 3.673746 TGCTACGTATCATTTGCTTGC 57.326 42.857 0.00 0.00 0.00 4.01
3338 5981 4.031028 GCTTGCTACGTATCATTTGCTTG 58.969 43.478 0.00 0.00 0.00 4.01
3339 5982 3.689161 TGCTTGCTACGTATCATTTGCTT 59.311 39.130 15.34 0.00 0.00 3.91
3340 5983 3.270027 TGCTTGCTACGTATCATTTGCT 58.730 40.909 15.34 0.00 0.00 3.91
3341 5984 3.673746 TGCTTGCTACGTATCATTTGC 57.326 42.857 0.00 6.34 0.00 3.68
3342 5985 5.389778 TGTTTGCTTGCTACGTATCATTTG 58.610 37.500 0.00 0.00 0.00 2.32
3343 5986 5.621197 TGTTTGCTTGCTACGTATCATTT 57.379 34.783 0.00 0.00 0.00 2.32
3344 5987 5.181245 AGTTGTTTGCTTGCTACGTATCATT 59.819 36.000 0.00 0.00 0.00 2.57
3345 5988 4.695455 AGTTGTTTGCTTGCTACGTATCAT 59.305 37.500 0.00 0.00 0.00 2.45
3433 6076 7.292713 TGGTTGTAAGAACTACTATGTGTCA 57.707 36.000 0.00 0.00 32.70 3.58
3495 6153 3.991773 TCCTCGATTTGGTTGTAAGAACG 59.008 43.478 0.00 0.00 0.00 3.95
3550 6208 3.680458 GTCTCCTCTTCGATTTGGTTGTC 59.320 47.826 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.