Multiple sequence alignment - TraesCS5B01G099600

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 TraesCS5B01G099600 chr5B 100.000 3298 0 0 1 3298 132587155 132590452 0.000000e+00 6091.0
1 TraesCS5B01G099600 chr5B 79.299 314 41 14 2840 3135 244641336 244641029 7.220000e-47 198.0
2 TraesCS5B01G099600 chr5B 78.997 319 39 22 2839 3134 194126958 194126645 3.360000e-45 193.0
3 TraesCS5B01G099600 chr5B 82.979 94 11 4 2839 2928 38227434 38227342 2.730000e-11 80.5
4 TraesCS5B01G099600 chr5B 97.619 42 1 0 1931 1972 132589016 132589057 4.570000e-09 73.1
5 TraesCS5B01G099600 chr5B 97.619 42 1 0 1862 1903 132589085 132589126 4.570000e-09 73.1
6 TraesCS5B01G099600 chr5A 92.375 3331 202 29 1 3298 129748453 129751764 0.000000e+00 4697.0
7 TraesCS5B01G099600 chr5A 94.318 352 15 5 2840 3188 129757647 129757996 4.840000e-148 534.0
8 TraesCS5B01G099600 chr5A 94.872 117 5 1 3182 3298 129800902 129801017 7.270000e-42 182.0
9 TraesCS5B01G099600 chr5A 95.238 42 2 0 1862 1903 129750398 129750439 2.120000e-07 67.6
10 TraesCS5B01G099600 chr5D 93.557 2778 131 15 1 2731 119658139 119660915 0.000000e+00 4095.0
11 TraesCS5B01G099600 chr6D 86.499 2111 239 26 690 2779 1540241 1538156 0.000000e+00 2278.0
12 TraesCS5B01G099600 chr6D 84.978 1804 196 44 625 2398 8140100 8141858 0.000000e+00 1760.0
13 TraesCS5B01G099600 chr6D 88.929 280 28 2 2235 2513 3618463 3618186 3.150000e-90 342.0
14 TraesCS5B01G099600 chr6D 79.286 420 59 13 564 957 438384 438801 5.420000e-68 268.0
15 TraesCS5B01G099600 chr6D 80.345 290 34 15 2840 3109 89261555 89261269 7.220000e-47 198.0
16 TraesCS5B01G099600 chr6D 100.000 33 0 0 1871 1903 8141408 8141440 9.880000e-06 62.1
17 TraesCS5B01G099600 chr6B 84.860 2107 266 31 690 2779 5715672 5713602 0.000000e+00 2074.0
18 TraesCS5B01G099600 chr6B 84.598 1805 208 38 625 2403 15105596 15107356 0.000000e+00 1729.0
19 TraesCS5B01G099600 chr6B 75.779 1284 218 56 324 1575 2126088 2127310 2.220000e-156 562.0
20 TraesCS5B01G099600 chr6B 79.934 304 41 18 2840 3135 171471679 171471388 4.310000e-49 206.0
21 TraesCS5B01G099600 chr6A 84.539 1811 206 42 625 2403 8608597 8610365 0.000000e+00 1725.0
22 TraesCS5B01G099600 chr6A 83.896 1838 203 53 625 2403 8387490 8389293 0.000000e+00 1668.0
23 TraesCS5B01G099600 chr6A 77.288 295 53 13 2840 3127 107561973 107561686 9.470000e-36 161.0
24 TraesCS5B01G099600 chr6A 74.763 317 53 22 2839 3135 317354876 317355185 2.080000e-22 117.0
25 TraesCS5B01G099600 chr6A 97.368 38 1 0 1866 1903 8388823 8388860 7.640000e-07 65.8
26 TraesCS5B01G099600 chr6A 100.000 33 0 0 1871 1903 8609907 8609939 9.880000e-06 62.1
27 TraesCS5B01G099600 chr7D 84.989 1379 155 30 658 2012 558888744 558887394 0.000000e+00 1352.0
28 TraesCS5B01G099600 chr7D 89.291 719 76 1 2058 2776 558848876 558848159 0.000000e+00 900.0
29 TraesCS5B01G099600 chr7B 87.041 463 49 11 2840 3298 390615815 390616270 2.270000e-141 512.0
30 TraesCS5B01G099600 chr2B 82.083 480 60 15 2840 3298 579596014 579595540 1.440000e-103 387.0
31 TraesCS5B01G099600 chr2B 89.888 89 8 1 2840 2927 367116413 367116501 2.690000e-21 113.0
32 TraesCS5B01G099600 chr7A 78.557 499 72 22 972 1461 8381133 8381605 2.490000e-76 296.0
33 TraesCS5B01G099600 chr1B 77.116 319 43 17 2840 3135 685080089 685080400 1.230000e-34 158.0
34 TraesCS5B01G099600 chr1A 76.875 320 43 17 2840 3135 590751076 590751388 5.700000e-33 152.0
35 TraesCS5B01G099600 chr1D 75.472 318 51 21 2840 3135 130847898 130847586 2.670000e-26 130.0


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 TraesCS5B01G099600 chr5B 132587155 132590452 3297 False 2079.066667 6091 98.412667 1 3298 3 chr5B.!!$F1 3297
1 TraesCS5B01G099600 chr5A 129748453 129751764 3311 False 2382.300000 4697 93.806500 1 3298 2 chr5A.!!$F3 3297
2 TraesCS5B01G099600 chr5D 119658139 119660915 2776 False 4095.000000 4095 93.557000 1 2731 1 chr5D.!!$F1 2730
3 TraesCS5B01G099600 chr6D 1538156 1540241 2085 True 2278.000000 2278 86.499000 690 2779 1 chr6D.!!$R1 2089
4 TraesCS5B01G099600 chr6D 8140100 8141858 1758 False 911.050000 1760 92.489000 625 2398 2 chr6D.!!$F2 1773
5 TraesCS5B01G099600 chr6B 5713602 5715672 2070 True 2074.000000 2074 84.860000 690 2779 1 chr6B.!!$R1 2089
6 TraesCS5B01G099600 chr6B 15105596 15107356 1760 False 1729.000000 1729 84.598000 625 2403 1 chr6B.!!$F2 1778
7 TraesCS5B01G099600 chr6B 2126088 2127310 1222 False 562.000000 562 75.779000 324 1575 1 chr6B.!!$F1 1251
8 TraesCS5B01G099600 chr6A 8608597 8610365 1768 False 893.550000 1725 92.269500 625 2403 2 chr6A.!!$F3 1778
9 TraesCS5B01G099600 chr6A 8387490 8389293 1803 False 866.900000 1668 90.632000 625 2403 2 chr6A.!!$F2 1778
10 TraesCS5B01G099600 chr7D 558887394 558888744 1350 True 1352.000000 1352 84.989000 658 2012 1 chr7D.!!$R2 1354
11 TraesCS5B01G099600 chr7D 558848159 558848876 717 True 900.000000 900 89.291000 2058 2776 1 chr7D.!!$R1 718

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
494 495 0.179076 AGGACATTCGCGATGCATCA 60.179 50.0 25.7 7.21 39.47 3.07 F
502 503 0.302890 CGCGATGCATCAAGGAACTC 59.697 55.0 25.7 0.00 38.49 3.01 F
1066 1111 0.324368 GGGTTTCCCTGATCCCCAAC 60.324 60.0 0.0 0.00 41.34 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1422 1506 0.110678 AGAGAGTGTCAGGGTCGACA 59.889 55.000 18.91 0.0 43.54 4.35 R
1921 2031 3.942748 GACCTATCGTGTGAGAGAGAAGT 59.057 47.826 0.00 0.0 35.40 3.01 R
2664 2797 1.059098 AGGAGATGAGCCACACACAA 58.941 50.000 0.00 0.0 0.00 3.33 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
133 134 4.150897 TGACAAACTTTAGTGCTCAGGT 57.849 40.909 0.00 0.00 0.00 4.00
134 135 4.523083 TGACAAACTTTAGTGCTCAGGTT 58.477 39.130 0.00 0.00 0.00 3.50
173 174 4.671831 ACCACAATACAATGATGTCCCAA 58.328 39.130 0.00 0.00 41.05 4.12
238 239 1.371558 GGGTCGCTTCCTTGTGAGT 59.628 57.895 0.00 0.00 0.00 3.41
242 243 2.547218 GGTCGCTTCCTTGTGAGTTACA 60.547 50.000 0.00 0.00 37.56 2.41
296 297 4.066071 TCCCCCATTAAATATCCCAACCT 58.934 43.478 0.00 0.00 0.00 3.50
305 306 3.674358 ATATCCCAACCTGGACCCTAT 57.326 47.619 0.00 0.00 40.96 2.57
462 463 3.901005 ATGGTGGGTGGTGGGGCTA 62.901 63.158 0.00 0.00 0.00 3.93
494 495 0.179076 AGGACATTCGCGATGCATCA 60.179 50.000 25.70 7.21 39.47 3.07
502 503 0.302890 CGCGATGCATCAAGGAACTC 59.697 55.000 25.70 0.00 38.49 3.01
546 547 2.599281 TCGGCGTTGGAGGAGACA 60.599 61.111 6.85 0.00 0.00 3.41
604 606 4.684134 GTGGTGGTGGGCAGCCAT 62.684 66.667 15.19 0.00 38.40 4.40
618 620 1.004044 CAGCCATGACAAAGAGGAGGT 59.996 52.381 0.00 0.00 0.00 3.85
682 684 0.402887 TAGATCGGGATCCACGGCTA 59.597 55.000 15.23 15.21 38.58 3.93
688 690 2.435693 GGATCCACGGCTAGCTGGT 61.436 63.158 26.90 16.25 0.00 4.00
694 696 3.854669 CGGCTAGCTGGTGGAGGG 61.855 72.222 16.30 0.00 0.00 4.30
695 697 2.365635 GGCTAGCTGGTGGAGGGA 60.366 66.667 15.72 0.00 0.00 4.20
696 698 1.768077 GGCTAGCTGGTGGAGGGAT 60.768 63.158 15.72 0.00 0.00 3.85
769 787 5.523438 TGGCGGAAGTCTTTTTGTAAAAT 57.477 34.783 0.00 0.00 36.07 1.82
884 915 5.374921 TGGTTCGATTTGGTTTGGTAGTAA 58.625 37.500 0.00 0.00 0.00 2.24
918 949 7.808381 CGTTTCCTTGTGATGTACGATAGATAT 59.192 37.037 0.00 0.00 41.38 1.63
936 969 5.972935 AGATATGTGTCCATTCACGTGTTA 58.027 37.500 16.51 5.48 40.74 2.41
1022 1057 4.016105 TCCCATCTTTTCCTCTCCTCTACT 60.016 45.833 0.00 0.00 0.00 2.57
1024 1059 4.714308 CCATCTTTTCCTCTCCTCTACTGT 59.286 45.833 0.00 0.00 0.00 3.55
1025 1060 5.163457 CCATCTTTTCCTCTCCTCTACTGTC 60.163 48.000 0.00 0.00 0.00 3.51
1026 1061 4.011023 TCTTTTCCTCTCCTCTACTGTCG 58.989 47.826 0.00 0.00 0.00 4.35
1027 1062 3.436577 TTTCCTCTCCTCTACTGTCGT 57.563 47.619 0.00 0.00 0.00 4.34
1066 1111 0.324368 GGGTTTCCCTGATCCCCAAC 60.324 60.000 0.00 0.00 41.34 3.77
1199 1274 1.807165 CAGTCACCATGGAGTCGCG 60.807 63.158 21.47 0.00 0.00 5.87
1422 1506 2.947652 CTGGGACGCAGAATTCATCAAT 59.052 45.455 14.07 0.00 0.00 2.57
1528 1612 0.779997 ATGTTCCCCTTCTGGCACTT 59.220 50.000 0.00 0.00 0.00 3.16
1545 1629 4.444876 GGCACTTGAATCTAGATTGGGCTA 60.445 45.833 22.61 4.88 0.00 3.93
1546 1630 4.513318 GCACTTGAATCTAGATTGGGCTAC 59.487 45.833 22.61 7.58 0.00 3.58
1641 1725 9.930693 GATTCGATTGGACTAGATTAGGTTTAT 57.069 33.333 0.00 0.00 0.00 1.40
1745 1830 8.549548 CATCTTGTGATCTGATATGTTTCACTC 58.450 37.037 7.95 0.00 38.00 3.51
1762 1847 9.883142 TGTTTCACTCATATGTGTATGTCATTA 57.117 29.630 9.95 0.00 39.01 1.90
1781 1866 7.654520 TGTCATTATTATGCGTAACCTAGGAAC 59.345 37.037 17.98 12.16 0.00 3.62
1804 1889 7.865706 ACCTTTATTATGATCAGTGTGAACC 57.134 36.000 0.09 0.00 0.00 3.62
1807 1892 9.784531 CCTTTATTATGATCAGTGTGAACCTAT 57.215 33.333 0.09 0.00 0.00 2.57
1901 2010 9.213799 ACTTCATGTGTTGTTTTGTGTTTTATT 57.786 25.926 0.00 0.00 0.00 1.40
2503 2636 7.547019 TCATCTAAAGCACTCATGTCAAGTAAG 59.453 37.037 0.00 0.00 0.00 2.34
2745 2878 3.308688 CCCAAGGGACATGATATGATCCC 60.309 52.174 8.46 8.46 44.26 3.85
2751 2884 3.776969 GGACATGATATGATCCCAGGCTA 59.223 47.826 0.00 0.00 0.00 3.93
2757 2890 5.103687 TGATATGATCCCAGGCTAAGGAAT 58.896 41.667 9.31 3.07 35.30 3.01
2789 2922 5.068987 TCCAAAAGAATCTCCACCAACTTTG 59.931 40.000 0.00 0.00 0.00 2.77
2790 2923 4.590850 AAAGAATCTCCACCAACTTTGC 57.409 40.909 0.00 0.00 0.00 3.68
2803 2936 3.568538 CAACTTTGCGATCAAGAAAGGG 58.431 45.455 11.00 2.39 33.12 3.95
2814 2947 4.021102 TCAAGAAAGGGTCACCAATCTC 57.979 45.455 0.00 0.00 40.13 2.75
2815 2948 3.394274 TCAAGAAAGGGTCACCAATCTCA 59.606 43.478 0.00 0.00 40.13 3.27
2842 2975 3.220110 CTCTTAGCGGTGACCCTATGTA 58.780 50.000 0.00 0.00 0.00 2.29
2855 2988 5.018374 ACCCTATGTAACACCCCAAAAAT 57.982 39.130 0.00 0.00 0.00 1.82
2869 3003 8.053355 ACACCCCAAAAATTTAACCATGTTTTA 58.947 29.630 0.00 0.00 0.00 1.52
3292 3435 3.329520 GGGCCCTTTTAGACCCAAATTTT 59.670 43.478 17.04 0.00 42.33 1.82
3293 3436 4.532916 GGGCCCTTTTAGACCCAAATTTTA 59.467 41.667 17.04 0.00 42.33 1.52
3296 3439 7.172342 GGCCCTTTTAGACCCAAATTTTATTT 58.828 34.615 0.00 0.00 0.00 1.40
3297 3440 7.335924 GGCCCTTTTAGACCCAAATTTTATTTC 59.664 37.037 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 134 4.651503 TGTGGTTTCCTAATTTGGCTTCAA 59.348 37.500 0.45 0.00 0.00 2.69
134 135 4.219115 TGTGGTTTCCTAATTTGGCTTCA 58.781 39.130 0.45 0.00 0.00 3.02
238 239 4.404715 GCCTGGTAGGATAGAGTGTTGTAA 59.595 45.833 0.00 0.00 37.67 2.41
242 243 2.032620 CGCCTGGTAGGATAGAGTGTT 58.967 52.381 0.00 0.00 37.67 3.32
272 273 4.107311 GGTTGGGATATTTAATGGGGGAGA 59.893 45.833 0.00 0.00 0.00 3.71
296 297 1.218844 GGTTGGGCTTATAGGGTCCA 58.781 55.000 0.00 0.00 36.60 4.02
305 306 1.447099 TGTAAGGTGGGTTGGGCTTA 58.553 50.000 0.00 0.00 0.00 3.09
462 463 2.334006 ATGTCCTCCTCTGTTCCAGT 57.666 50.000 0.00 0.00 32.61 4.00
546 547 0.944999 TCTCCTCTATGCCCTTCCCT 59.055 55.000 0.00 0.00 0.00 4.20
599 601 1.366319 ACCTCCTCTTTGTCATGGCT 58.634 50.000 0.00 0.00 0.00 4.75
604 606 3.007940 CCACACATACCTCCTCTTTGTCA 59.992 47.826 0.00 0.00 0.00 3.58
618 620 2.353189 CCCCCAACGCCACACATA 59.647 61.111 0.00 0.00 0.00 2.29
682 684 2.693864 CCCATCCCTCCACCAGCT 60.694 66.667 0.00 0.00 0.00 4.24
688 690 2.763215 GTGCAACCCATCCCTCCA 59.237 61.111 0.00 0.00 0.00 3.86
694 696 3.995506 CTCCCCCGTGCAACCCATC 62.996 68.421 0.00 0.00 0.00 3.51
695 697 4.047125 CTCCCCCGTGCAACCCAT 62.047 66.667 0.00 0.00 0.00 4.00
743 761 3.222603 ACAAAAAGACTTCCGCCAATCT 58.777 40.909 0.00 0.00 0.00 2.40
746 764 4.985538 TTTACAAAAAGACTTCCGCCAA 57.014 36.364 0.00 0.00 0.00 4.52
769 787 5.144832 TCTATATGTAGCTAGTGGTGGCAA 58.855 41.667 0.00 0.00 30.99 4.52
884 915 2.582052 TCACAAGGAAACGAAGCCAAT 58.418 42.857 0.00 0.00 0.00 3.16
918 949 2.485903 GGTAACACGTGAATGGACACA 58.514 47.619 25.01 0.00 40.34 3.72
936 969 4.587262 GGAATTTATTTATTGAGGCGGGGT 59.413 41.667 0.00 0.00 0.00 4.95
992 1027 5.339530 GGAGAGGAAAAGATGGGAGATTTGA 60.340 44.000 0.00 0.00 0.00 2.69
1056 1101 0.548031 GGCAGATGAGTTGGGGATCA 59.452 55.000 0.00 0.00 0.00 2.92
1066 1111 1.980784 CTGAGGTGGGGGCAGATGAG 61.981 65.000 0.00 0.00 0.00 2.90
1199 1274 0.886490 GATCATGTGGCGGATGGTCC 60.886 60.000 0.00 0.00 0.00 4.46
1383 1467 0.324738 AGATCTTGAGGTCCTCGGCA 60.325 55.000 14.34 0.26 32.35 5.69
1422 1506 0.110678 AGAGAGTGTCAGGGTCGACA 59.889 55.000 18.91 0.00 43.54 4.35
1545 1629 6.930068 ATATAAATAGTAGCAAGACGGGGT 57.070 37.500 0.00 0.00 0.00 4.95
1546 1630 8.746530 TCTAATATAAATAGTAGCAAGACGGGG 58.253 37.037 0.64 0.00 32.59 5.73
1762 1847 5.625568 AAGGTTCCTAGGTTACGCATAAT 57.374 39.130 9.08 0.00 0.00 1.28
1781 1866 9.784531 ATAGGTTCACACTGATCATAATAAAGG 57.215 33.333 0.00 0.00 0.00 3.11
1921 2031 3.942748 GACCTATCGTGTGAGAGAGAAGT 59.057 47.826 0.00 0.00 35.40 3.01
2503 2636 4.521146 TCAGATTGGCTGGAGAGAAAATC 58.479 43.478 0.00 0.00 44.98 2.17
2586 2719 6.107343 TCAAATGGTTTATGCAACATCATGG 58.893 36.000 0.00 0.00 37.07 3.66
2648 2781 5.122239 CACACACAATACCTTGTACCATCAG 59.878 44.000 0.00 0.00 43.76 2.90
2664 2797 1.059098 AGGAGATGAGCCACACACAA 58.941 50.000 0.00 0.00 0.00 3.33
2745 2878 3.556004 GGAAGATCGGATTCCTTAGCCTG 60.556 52.174 0.30 0.00 42.52 4.85
2751 2884 5.179452 TCTTTTGGAAGATCGGATTCCTT 57.821 39.130 12.13 2.45 45.45 3.36
2757 2890 4.225042 TGGAGATTCTTTTGGAAGATCGGA 59.775 41.667 0.00 0.00 41.35 4.55
2789 2922 1.087501 GGTGACCCTTTCTTGATCGC 58.912 55.000 0.00 0.00 0.00 4.58
2790 2923 2.472695 TGGTGACCCTTTCTTGATCG 57.527 50.000 0.00 0.00 0.00 3.69
2803 2936 2.503356 AGAGGGTGATGAGATTGGTGAC 59.497 50.000 0.00 0.00 0.00 3.67
2842 2975 6.007485 ACATGGTTAAATTTTTGGGGTGTT 57.993 33.333 0.00 0.00 0.00 3.32
3084 3220 6.543831 AGTGCAACAGAAACATTCTAGAGTTT 59.456 34.615 9.25 9.25 41.43 2.66
3087 3223 7.658179 TTAGTGCAACAGAAACATTCTAGAG 57.342 36.000 0.00 0.00 41.43 2.43
3088 3224 8.342634 GTTTTAGTGCAACAGAAACATTCTAGA 58.657 33.333 0.00 0.00 40.92 2.43
3089 3225 8.345565 AGTTTTAGTGCAACAGAAACATTCTAG 58.654 33.333 14.61 0.00 42.51 2.43
3129 3266 9.619316 ACAAGAAAATTTTAAACACCAAAAAGC 57.381 25.926 2.75 0.00 0.00 3.51
3247 3384 8.286800 GCCCCAGTTTAATAAAACAAAATGAAC 58.713 33.333 4.04 0.00 46.18 3.18
3250 3387 6.150307 GGGCCCCAGTTTAATAAAACAAAATG 59.850 38.462 12.23 0.00 46.18 2.32
3251 3388 6.044989 AGGGCCCCAGTTTAATAAAACAAAAT 59.955 34.615 21.43 0.00 46.18 1.82
3256 3393 5.492855 AAAGGGCCCCAGTTTAATAAAAC 57.507 39.130 21.43 0.00 44.47 2.43
3261 3398 4.350245 GTCTAAAAGGGCCCCAGTTTAAT 58.650 43.478 21.43 1.04 0.00 1.40
3263 3400 2.042026 GGTCTAAAAGGGCCCCAGTTTA 59.958 50.000 21.43 18.94 0.00 2.01
3264 3401 1.203137 GGTCTAAAAGGGCCCCAGTTT 60.203 52.381 21.43 18.82 0.00 2.66
3265 3402 0.408309 GGTCTAAAAGGGCCCCAGTT 59.592 55.000 21.43 13.03 0.00 3.16
3266 3403 1.506907 GGGTCTAAAAGGGCCCCAGT 61.507 60.000 21.43 5.96 35.32 4.00


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

AutoCloner maintained by Alex Coulton.