Multiple sequence alignment - TraesCS3B01G414500

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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 TraesCS3B01G414500 chr3B 100.000 3563 0 0 1 3563 651369614 651373176 0.000000e+00 6580
1 TraesCS3B01G414500 chr3D 94.744 2854 118 17 1 2829 488382521 488385367 0.000000e+00 4410
2 TraesCS3B01G414500 chr3D 86.404 684 47 22 2885 3563 488385542 488386184 0.000000e+00 706
3 TraesCS3B01G414500 chr3A 94.549 2825 115 20 65 2873 632025356 632028157 0.000000e+00 4327
4 TraesCS3B01G414500 chr3A 91.502 506 30 9 2872 3371 632028212 632028710 0.000000e+00 684
5 TraesCS3B01G414500 chr3A 98.340 241 4 0 3323 3563 632028876 632029116 1.180000e-114 424


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 TraesCS3B01G414500 chr3B 651369614 651373176 3562 False 6580.000000 6580 100.000 1 3563 1 chr3B.!!$F1 3562
1 TraesCS3B01G414500 chr3D 488382521 488386184 3663 False 2558.000000 4410 90.574 1 3563 2 chr3D.!!$F1 3562
2 TraesCS3B01G414500 chr3A 632025356 632029116 3760 False 1811.666667 4327 94.797 65 3563 3 chr3A.!!$F1 3498

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
188 200 0.817654 CTATGTGGAGTGACGAGGCA 59.182 55.0 0.0 0.0 0.00 4.75 F
1260 1286 0.035630 AGAGCAATCCTGTGGCAGAC 60.036 55.0 0.0 0.0 32.44 3.51 F
1752 1778 0.689080 AGGAGAGCGATGATGGTGGT 60.689 55.0 0.0 0.0 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1509 1535 0.249911 GAGAACCAGGCGTGTTGAGT 60.250 55.000 5.57 0.0 0.00 3.41 R
2471 2497 0.394565 GGAGATGTCGAATCCAGGGG 59.605 60.000 0.00 0.0 33.08 4.79 R
3129 3287 3.250744 CCATGAGAAATGCAGCTGTTTG 58.749 45.455 16.64 0.0 0.00 2.93 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
62 66 2.967362 ACAAAATGGTAGCGATCGTCA 58.033 42.857 17.81 10.55 0.00 4.35
75 79 1.302383 ATCGTCAAAAATCGCCGCCA 61.302 50.000 0.00 0.00 0.00 5.69
97 102 3.168292 CCCCAAAGAAAGAGGAAAGCAT 58.832 45.455 0.00 0.00 0.00 3.79
115 120 7.114953 GGAAAGCATAAAAAGGAAAGAACTTCG 59.885 37.037 0.00 0.00 34.56 3.79
118 123 5.449304 CATAAAAAGGAAAGAACTTCGCGT 58.551 37.500 5.77 0.00 34.56 6.01
123 128 1.798813 GGAAAGAACTTCGCGTCATGT 59.201 47.619 5.77 0.00 34.56 3.21
125 130 3.181533 GGAAAGAACTTCGCGTCATGTAC 60.182 47.826 5.77 0.00 34.56 2.90
146 151 1.822990 TGGGTGTAGTTAGGCTCGAAG 59.177 52.381 0.00 0.00 0.00 3.79
188 200 0.817654 CTATGTGGAGTGACGAGGCA 59.182 55.000 0.00 0.00 0.00 4.75
207 219 1.135024 CAGCCATATGTTGTTGCCACC 60.135 52.381 1.24 0.00 0.00 4.61
239 251 4.819630 TGACCGTAGCAATTCACTCTTTTT 59.180 37.500 0.00 0.00 0.00 1.94
242 254 5.298276 ACCGTAGCAATTCACTCTTTTTCAA 59.702 36.000 0.00 0.00 0.00 2.69
244 256 6.430451 CGTAGCAATTCACTCTTTTTCAAGT 58.570 36.000 0.00 0.00 0.00 3.16
246 258 5.594926 AGCAATTCACTCTTTTTCAAGTGG 58.405 37.500 2.96 0.00 42.52 4.00
264 276 3.009473 AGTGGGTACATCACAAGCTTGAT 59.991 43.478 32.50 14.33 36.62 2.57
266 278 3.758023 TGGGTACATCACAAGCTTGATTG 59.242 43.478 32.50 24.53 33.74 2.67
406 422 7.994425 TTGCAGACTCTGTATATTTCCAAAA 57.006 32.000 7.89 0.00 33.43 2.44
485 506 6.150140 CCTAAAATTCCAGAGTCAAACTCCAG 59.850 42.308 3.54 0.00 46.18 3.86
661 686 1.827399 GCCGTCCCTGTTCTTCCTCA 61.827 60.000 0.00 0.00 0.00 3.86
719 744 4.787135 TTGGCCATTGAGGTATGTATGA 57.213 40.909 6.09 0.00 40.61 2.15
726 751 5.824624 CCATTGAGGTATGTATGAGCTTTGT 59.175 40.000 0.00 0.00 0.00 2.83
771 796 1.895798 CGGCAGGCCATCTAGATCTTA 59.104 52.381 5.01 0.00 35.37 2.10
776 801 3.513515 CAGGCCATCTAGATCTTAGTCCC 59.486 52.174 5.01 0.00 0.00 4.46
907 933 7.420800 GGTTTGATGCTATTCCTGTCTTATTG 58.579 38.462 0.00 0.00 0.00 1.90
1244 1270 1.550524 TGAACCGAATCCTCCACAGAG 59.449 52.381 0.00 0.00 40.09 3.35
1260 1286 0.035630 AGAGCAATCCTGTGGCAGAC 60.036 55.000 0.00 0.00 32.44 3.51
1509 1535 1.675310 CAATCCAGCGGTCAGGCAA 60.675 57.895 0.00 0.00 34.64 4.52
1611 1637 4.141756 CCTGACATTAGCAAGACCTCTGAT 60.142 45.833 0.00 0.00 0.00 2.90
1644 1670 4.188462 TGATGAATACCCTTAACACAGCG 58.812 43.478 0.00 0.00 0.00 5.18
1671 1697 7.563888 TGATGAAAAGGATGATCTGATCAAC 57.436 36.000 22.91 19.69 43.50 3.18
1752 1778 0.689080 AGGAGAGCGATGATGGTGGT 60.689 55.000 0.00 0.00 0.00 4.16
1794 1820 3.411446 TGGTTCTTATGTGGTCTTGCAG 58.589 45.455 0.00 0.00 0.00 4.41
1824 1850 4.677182 AGGAGGAAATTTTAGCACCACAT 58.323 39.130 0.00 0.00 0.00 3.21
1848 1874 5.188434 ACTCATTTCTGTGTGATATGTGGG 58.812 41.667 0.00 0.00 36.15 4.61
2259 2285 1.536418 AGGGCACACACCTGCTCTA 60.536 57.895 0.00 0.00 46.73 2.43
2260 2286 1.078848 GGGCACACACCTGCTCTAG 60.079 63.158 0.00 0.00 34.49 2.43
2517 2543 0.107945 CCTTCTCCTTCCTGCCTTCG 60.108 60.000 0.00 0.00 0.00 3.79
2529 2555 4.091939 CCTTCGGGACCGGGTTCC 62.092 72.222 15.13 15.13 40.25 3.62
2568 2594 1.189752 GTGGAGACAGCTGATGGAGA 58.810 55.000 23.35 0.00 44.46 3.71
2782 2816 1.961793 TCTTTAACTGTGTTGGCGCT 58.038 45.000 7.64 0.00 0.00 5.92
2853 2909 2.835764 ACATTGAATGCAATCCCAGCTT 59.164 40.909 4.84 0.00 42.66 3.74
2869 2925 3.056322 CCAGCTTAGCAAAAGCCAAGATT 60.056 43.478 17.34 0.00 44.01 2.40
2873 2929 4.321527 GCTTAGCAAAAGCCAAGATTGAGT 60.322 41.667 11.63 0.00 37.30 3.41
2874 2930 5.106157 GCTTAGCAAAAGCCAAGATTGAGTA 60.106 40.000 11.63 0.00 37.30 2.59
2910 3066 6.928348 TGATCTTACTGGAAACTTCACCTA 57.072 37.500 0.00 0.00 0.00 3.08
2914 3070 6.708285 TCTTACTGGAAACTTCACCTATTCC 58.292 40.000 0.00 0.00 41.37 3.01
2966 3122 7.994425 TCAGTTGGAGCAATCTGTTAAAATA 57.006 32.000 0.00 0.00 30.55 1.40
3096 3254 5.719173 GCTCATACAGCCAACCAAATAAAA 58.281 37.500 0.00 0.00 43.17 1.52
3097 3255 6.340522 GCTCATACAGCCAACCAAATAAAAT 58.659 36.000 0.00 0.00 43.17 1.82
3098 3256 7.488322 GCTCATACAGCCAACCAAATAAAATA 58.512 34.615 0.00 0.00 43.17 1.40
3099 3257 7.978975 GCTCATACAGCCAACCAAATAAAATAA 59.021 33.333 0.00 0.00 43.17 1.40
3139 3297 1.921243 AAACGAAACCAAACAGCTGC 58.079 45.000 15.27 0.00 0.00 5.25
3158 3316 2.037144 GCATTTCTCATGGCCCTCATT 58.963 47.619 0.00 0.00 32.92 2.57
3173 3331 3.371273 CCCTCATTGATGGACACTCACAT 60.371 47.826 1.98 0.00 0.00 3.21
3174 3332 3.875727 CCTCATTGATGGACACTCACATC 59.124 47.826 0.00 0.00 42.86 3.06
3222 3380 5.738619 TCCATAGCCTGCGAAAATATCTA 57.261 39.130 0.00 0.00 0.00 1.98
3233 3391 7.543868 CCTGCGAAAATATCTAGACTTGATAGG 59.456 40.741 11.44 4.01 31.03 2.57
3234 3392 8.178313 TGCGAAAATATCTAGACTTGATAGGA 57.822 34.615 11.44 0.00 31.03 2.94
3250 3410 4.403752 TGATAGGACCAGTTGACATCTCAG 59.596 45.833 0.00 0.00 0.00 3.35
3251 3411 1.905215 AGGACCAGTTGACATCTCAGG 59.095 52.381 0.00 0.00 0.00 3.86
3252 3412 1.902508 GGACCAGTTGACATCTCAGGA 59.097 52.381 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 8.707839 CGCTACCATTTTGTTTGTGATTTTATT 58.292 29.630 0.00 0.00 0.00 1.40
31 32 7.426410 TCGCTACCATTTTGTTTGTGATTTTA 58.574 30.769 0.00 0.00 0.00 1.52
34 35 5.446143 TCGCTACCATTTTGTTTGTGATT 57.554 34.783 0.00 0.00 0.00 2.57
45 49 5.560966 ATTTTTGACGATCGCTACCATTT 57.439 34.783 16.60 0.00 0.00 2.32
62 66 3.378602 GGGGTGGCGGCGATTTTT 61.379 61.111 12.98 0.00 0.00 1.94
75 79 2.091333 TGCTTTCCTCTTTCTTTGGGGT 60.091 45.455 0.00 0.00 0.00 4.95
97 102 4.571580 TGACGCGAAGTTCTTTCCTTTTTA 59.428 37.500 15.93 0.00 31.82 1.52
115 120 1.203994 ACTACACCCAGTACATGACGC 59.796 52.381 0.00 0.00 0.00 5.19
118 123 3.449737 GCCTAACTACACCCAGTACATGA 59.550 47.826 0.00 0.00 0.00 3.07
123 128 2.025981 TCGAGCCTAACTACACCCAGTA 60.026 50.000 0.00 0.00 0.00 2.74
125 130 1.471119 TCGAGCCTAACTACACCCAG 58.529 55.000 0.00 0.00 0.00 4.45
207 219 5.983118 TGAATTGCTACGGTCATGTATACTG 59.017 40.000 4.17 0.58 0.00 2.74
239 251 2.371841 AGCTTGTGATGTACCCACTTGA 59.628 45.455 14.13 3.35 35.66 3.02
242 254 2.371841 TCAAGCTTGTGATGTACCCACT 59.628 45.455 25.19 0.00 35.66 4.00
244 256 3.719268 ATCAAGCTTGTGATGTACCCA 57.281 42.857 25.19 2.96 36.86 4.51
246 258 5.376854 AACAATCAAGCTTGTGATGTACC 57.623 39.130 25.19 0.00 39.25 3.34
264 276 7.113658 TGCAACAATTTAGGAGGTAAAACAA 57.886 32.000 0.00 0.00 34.21 2.83
266 278 8.301002 TGTATGCAACAATTTAGGAGGTAAAAC 58.699 33.333 0.00 0.00 34.29 2.43
485 506 0.315568 CTATAGCGTGGTGGAGGAGC 59.684 60.000 0.00 0.00 0.00 4.70
719 744 2.582052 TCACCGGATGAAAACAAAGCT 58.418 42.857 9.46 0.00 33.02 3.74
726 751 5.355910 GGTTTAGCTAATCACCGGATGAAAA 59.644 40.000 9.46 2.12 41.93 2.29
771 796 2.114616 CAGATCTGTAAGCAGGGGACT 58.885 52.381 14.95 0.00 42.78 3.85
776 801 4.305769 GCATAGACAGATCTGTAAGCAGG 58.694 47.826 27.95 15.13 45.05 4.85
893 919 8.868522 TGAGAAATTGACAATAAGACAGGAAT 57.131 30.769 0.00 0.00 0.00 3.01
907 933 5.982890 TCTTCCCCAAATGAGAAATTGAC 57.017 39.130 0.00 0.00 0.00 3.18
1086 1112 2.096417 GTCCATGGAACTGAAACGAACG 60.096 50.000 18.20 0.00 0.00 3.95
1244 1270 1.310933 CCAGTCTGCCACAGGATTGC 61.311 60.000 0.00 0.00 33.25 3.56
1260 1286 1.454976 CATGGCCTGAGGATCCCAG 59.545 63.158 18.45 18.45 0.00 4.45
1509 1535 0.249911 GAGAACCAGGCGTGTTGAGT 60.250 55.000 5.57 0.00 0.00 3.41
1611 1637 5.158141 AGGGTATTCATCAGCTCCTCATAA 58.842 41.667 0.00 0.00 0.00 1.90
1644 1670 6.206829 TGATCAGATCATCCTTTTCATCATGC 59.793 38.462 9.21 0.00 33.59 4.06
1671 1697 0.523072 CGACACAAGGATTTGGGCAG 59.477 55.000 0.00 0.00 41.59 4.85
1794 1820 5.476945 TGCTAAAATTTCCTCCTTCTCCAAC 59.523 40.000 0.00 0.00 0.00 3.77
1824 1850 6.156083 TCCCACATATCACACAGAAATGAGTA 59.844 38.462 0.00 0.00 0.00 2.59
1848 1874 2.095461 GCATCCCTCTTGAAACCCTTC 58.905 52.381 0.00 0.00 0.00 3.46
2109 2135 4.997395 GCAATGACTGAGAACTTCTTGGTA 59.003 41.667 0.00 0.00 0.00 3.25
2259 2285 7.350744 TGTTGCTTTAATATCATCCATTGCT 57.649 32.000 0.00 0.00 0.00 3.91
2260 2286 6.643770 CCTGTTGCTTTAATATCATCCATTGC 59.356 38.462 0.00 0.00 0.00 3.56
2471 2497 0.394565 GGAGATGTCGAATCCAGGGG 59.605 60.000 0.00 0.00 33.08 4.79
2517 2543 4.410400 CTGCAGGAACCCGGTCCC 62.410 72.222 5.57 1.80 38.59 4.46
2628 2654 6.323482 CCTGAATAGAGGAAGAACTGAGATGA 59.677 42.308 0.00 0.00 34.69 2.92
2630 2656 5.602145 CCCTGAATAGAGGAAGAACTGAGAT 59.398 44.000 0.00 0.00 34.69 2.75
2782 2816 8.606040 TGATATGACAAGATATTGATTGCGAA 57.394 30.769 7.16 0.00 0.00 4.70
2853 2909 6.625740 GCAATACTCAATCTTGGCTTTTGCTA 60.626 38.462 0.00 0.00 46.54 3.49
2874 2930 9.466497 TTCCAGTAAGATCAAAAGATAAGCAAT 57.534 29.630 0.00 0.00 0.00 3.56
2899 3055 9.462606 AGATAAATTTCGGAATAGGTGAAGTTT 57.537 29.630 0.00 0.00 36.16 2.66
2910 3066 6.001449 TGTCCAGGAGATAAATTTCGGAAT 57.999 37.500 0.00 0.00 0.00 3.01
2980 3136 3.638160 TGCAATCCTGATGCTATTTTCCC 59.362 43.478 0.00 0.00 44.14 3.97
3009 3165 8.853077 AAATATTCTGCGAGGATCAATTGATA 57.147 30.769 20.75 3.66 34.37 2.15
3129 3287 3.250744 CCATGAGAAATGCAGCTGTTTG 58.749 45.455 16.64 0.00 0.00 2.93
3139 3297 3.293337 TCAATGAGGGCCATGAGAAATG 58.707 45.455 6.18 0.00 35.24 2.32
3158 3316 5.419239 TGTATTGATGTGAGTGTCCATCA 57.581 39.130 0.00 0.00 44.17 3.07
3173 3331 6.389091 GTGGTGCATTCTTTTGATGTATTGA 58.611 36.000 0.00 0.00 0.00 2.57
3174 3332 5.577945 GGTGGTGCATTCTTTTGATGTATTG 59.422 40.000 0.00 0.00 0.00 1.90
3222 3380 4.160329 TGTCAACTGGTCCTATCAAGTCT 58.840 43.478 0.00 0.00 0.00 3.24
3233 3391 3.685139 TTCCTGAGATGTCAACTGGTC 57.315 47.619 0.00 0.00 30.14 4.02
3234 3392 4.437682 TTTTCCTGAGATGTCAACTGGT 57.562 40.909 0.00 0.00 30.14 4.00
3348 3509 7.934855 TTCAAGAGTACTGGTTACTACCTAG 57.065 40.000 0.00 0.00 45.27 3.02


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

AutoCloner maintained by Alex Coulton.