Multiple sequence alignment - TraesCS7B01G353400

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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 TraesCS7B01G353400 chr7B 100.000 3248 0 0 1 3248 611050940 611047693 0.000000e+00 5999
1 TraesCS7B01G353400 chr7B 95.549 3258 128 12 1 3248 610758000 610754750 0.000000e+00 5197
2 TraesCS7B01G353400 chr7B 95.038 2922 132 9 1 2912 122467162 122470080 0.000000e+00 4580
3 TraesCS7B01G353400 chr7B 97.289 332 8 1 2918 3248 452428844 452429175 2.190000e-156 562
4 TraesCS7B01G353400 chr5B 95.467 2934 107 19 1 2912 209178611 209175682 0.000000e+00 4658
5 TraesCS7B01G353400 chr5B 95.092 2934 116 21 1 2912 265539965 265537038 0.000000e+00 4595
6 TraesCS7B01G353400 chr3B 95.262 2934 114 18 1 2912 228483501 228480571 0.000000e+00 4625
7 TraesCS7B01G353400 chr3B 93.981 648 38 1 2263 2910 787153292 787153938 0.000000e+00 979
8 TraesCS7B01G353400 chr3B 97.576 330 8 0 2918 3247 228480465 228480136 1.690000e-157 566
9 TraesCS7B01G353400 chr3B 97.281 331 8 1 2918 3248 142227829 142228158 7.870000e-156 560
10 TraesCS7B01G353400 chr2B 95.354 2906 104 21 1 2884 731067875 731070771 0.000000e+00 4590
11 TraesCS7B01G353400 chr2B 95.002 2921 131 11 1 2912 103760826 103757912 0.000000e+00 4571
12 TraesCS7B01G353400 chr2B 94.938 2924 114 12 1 2912 780648056 780650957 0.000000e+00 4549
13 TraesCS7B01G353400 chr2B 97.281 331 9 0 2918 3248 739862935 739862605 2.190000e-156 562
14 TraesCS7B01G353400 chr4B 94.365 2928 146 14 1 2912 15090842 15087918 0.000000e+00 4475
15 TraesCS7B01G353400 chr4B 97.281 331 9 0 2918 3248 647870911 647870581 2.190000e-156 562
16 TraesCS7B01G353400 chr5D 93.420 2614 112 16 557 3115 384513909 384511301 0.000000e+00 3819
17 TraesCS7B01G353400 chr6B 90.558 932 42 13 2288 3196 152340196 152341104 0.000000e+00 1192
18 TraesCS7B01G353400 chr6B 97.885 331 7 0 2918 3248 674460531 674460861 1.010000e-159 573
19 TraesCS7B01G353400 chr6B 97.281 331 9 0 2918 3248 208209601 208209931 2.190000e-156 562
20 TraesCS7B01G353400 chr4A 93.255 593 37 3 2256 2848 723937888 723937299 0.000000e+00 870
21 TraesCS7B01G353400 chr1B 97.583 331 8 0 2918 3248 600337230 600336900 4.700000e-158 568


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 TraesCS7B01G353400 chr7B 611047693 611050940 3247 True 5999.0 5999 100.000 1 3248 1 chr7B.!!$R2 3247
1 TraesCS7B01G353400 chr7B 610754750 610758000 3250 True 5197.0 5197 95.549 1 3248 1 chr7B.!!$R1 3247
2 TraesCS7B01G353400 chr7B 122467162 122470080 2918 False 4580.0 4580 95.038 1 2912 1 chr7B.!!$F1 2911
3 TraesCS7B01G353400 chr5B 209175682 209178611 2929 True 4658.0 4658 95.467 1 2912 1 chr5B.!!$R1 2911
4 TraesCS7B01G353400 chr5B 265537038 265539965 2927 True 4595.0 4595 95.092 1 2912 1 chr5B.!!$R2 2911
5 TraesCS7B01G353400 chr3B 228480136 228483501 3365 True 2595.5 4625 96.419 1 3247 2 chr3B.!!$R1 3246
6 TraesCS7B01G353400 chr3B 787153292 787153938 646 False 979.0 979 93.981 2263 2910 1 chr3B.!!$F2 647
7 TraesCS7B01G353400 chr2B 731067875 731070771 2896 False 4590.0 4590 95.354 1 2884 1 chr2B.!!$F1 2883
8 TraesCS7B01G353400 chr2B 103757912 103760826 2914 True 4571.0 4571 95.002 1 2912 1 chr2B.!!$R1 2911
9 TraesCS7B01G353400 chr2B 780648056 780650957 2901 False 4549.0 4549 94.938 1 2912 1 chr2B.!!$F2 2911
10 TraesCS7B01G353400 chr4B 15087918 15090842 2924 True 4475.0 4475 94.365 1 2912 1 chr4B.!!$R1 2911
11 TraesCS7B01G353400 chr5D 384511301 384513909 2608 True 3819.0 3819 93.420 557 3115 1 chr5D.!!$R1 2558
12 TraesCS7B01G353400 chr6B 152340196 152341104 908 False 1192.0 1192 90.558 2288 3196 1 chr6B.!!$F1 908
13 TraesCS7B01G353400 chr4A 723937299 723937888 589 True 870.0 870 93.255 2256 2848 1 chr4A.!!$R1 592

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
729 779 2.264005 ACCGTTGGTATGCAACTTGA 57.736 45.0 0.0 0.0 32.11 3.02 F
1037 1089 1.198094 TTCCAGTCCCTTGGCATCGA 61.198 55.0 0.0 0.0 38.16 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1550 1609 0.105760 ACCCATTTGCACCAAGGTCA 60.106 50.0 0.00 0.00 0.00 4.02 R
2565 2644 0.846693 AGTGCCTGGAACCAGTTCTT 59.153 50.0 17.92 0.84 42.15 2.52 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
38 40 2.294449 TATCAGCATAGAGGCCGTCT 57.706 50.000 0.00 3.31 39.59 4.18
101 113 5.082251 ACCGGGAACTTTATTGAGTAGTC 57.918 43.478 6.32 0.00 0.00 2.59
107 119 7.095270 GGGAACTTTATTGAGTAGTCGAGAAA 58.905 38.462 7.27 7.27 0.00 2.52
286 299 5.163513 GTTGCTTGCTTGCTAACATACATT 58.836 37.500 3.47 0.00 0.00 2.71
388 420 6.858478 GCTACTTGCTTGCTTATTAATTAGGC 59.142 38.462 3.80 2.62 38.95 3.93
533 565 6.475402 GCTTGTTTAGTGCACTTACATGTTTT 59.525 34.615 27.06 0.00 0.00 2.43
729 779 2.264005 ACCGTTGGTATGCAACTTGA 57.736 45.000 0.00 0.00 32.11 3.02
746 796 6.183360 GCAACTTGATCCTTGTGGTTATACTC 60.183 42.308 0.00 0.00 34.23 2.59
810 860 7.812690 ATGTATTGCTGCAATCTGAATAAGA 57.187 32.000 29.29 10.77 39.94 2.10
1037 1089 1.198094 TTCCAGTCCCTTGGCATCGA 61.198 55.000 0.00 0.00 38.16 3.59
1058 1110 6.086871 TCGATGCAATAGAGTCGATGATTAC 58.913 40.000 3.82 0.00 38.09 1.89
1115 1167 2.907042 AGGTTCAAGAAGGTAGTGGAGG 59.093 50.000 0.00 0.00 0.00 4.30
1394 1452 4.888326 AGAAGAGCTCAGAAACATCTGT 57.112 40.909 17.77 0.00 38.75 3.41
1477 1536 1.329906 CTGATGAACCTGCGCTTGATC 59.670 52.381 9.73 4.58 0.00 2.92
1550 1609 2.435586 GCTGCGCATGGACTCTGT 60.436 61.111 12.24 0.00 0.00 3.41
1556 1615 0.036952 CGCATGGACTCTGTGACCTT 60.037 55.000 0.00 0.00 0.00 3.50
1906 1965 6.839124 TTTTCAGATGCAATGACTACCAAT 57.161 33.333 4.57 0.00 0.00 3.16
2311 2371 8.897872 ATTCTGCAGAAAAATTCAAAGAACAT 57.102 26.923 31.55 7.69 37.61 2.71
2378 2442 7.362056 GCAAATAAAGTCAGCATTAAGTCTCCA 60.362 37.037 0.00 0.00 0.00 3.86
2494 2573 3.876341 TGTTCTGCACATGATCATGCTA 58.124 40.909 31.17 18.16 42.39 3.49
2504 2583 5.469084 CACATGATCATGCTAACAGTATGCT 59.531 40.000 31.17 8.03 40.60 3.79
2531 2610 4.713824 TGTAGGAAACCTATGTGTCGAG 57.286 45.455 0.00 0.00 38.48 4.04
2565 2644 5.749588 TCGAGAAAAAGTCGTGTACAATCAA 59.250 36.000 0.00 0.00 38.60 2.57
2586 2665 2.054799 AGAACTGGTTCCAGGCACTAA 58.945 47.619 20.88 0.00 40.33 2.24
2603 2683 5.177327 GGCACTAAACATCACACATTTTTGG 59.823 40.000 0.00 0.00 0.00 3.28
2620 2700 5.906113 TTTTGGCACTGTGAGAACTTTTA 57.094 34.783 12.86 0.00 0.00 1.52
2789 2874 2.869233 GCAAGAAGCACAGGTTTTCA 57.131 45.000 0.00 0.00 44.79 2.69
2790 2875 3.163630 GCAAGAAGCACAGGTTTTCAA 57.836 42.857 0.00 0.00 44.79 2.69
2955 3140 5.808540 CCATGCTTTGATGTTGTTTGATAGG 59.191 40.000 0.00 0.00 0.00 2.57
2968 3153 8.564574 TGTTGTTTGATAGGTCAACAAAGATAC 58.435 33.333 7.04 0.00 43.72 2.24
3222 3424 6.718454 ACTAATGCCTATCATTTTCCTCCATG 59.282 38.462 0.00 0.00 42.48 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.040617 CCTCTATGCTGATAAGAAATGTGCATT 60.041 37.037 0.00 0.00 39.79 3.56
10 11 5.180868 GGCCTCTATGCTGATAAGAAATGTG 59.819 44.000 0.00 0.00 0.00 3.21
11 12 5.312079 GGCCTCTATGCTGATAAGAAATGT 58.688 41.667 0.00 0.00 0.00 2.71
70 82 1.995376 AAGTTCCCGGTCTTTGCAAT 58.005 45.000 0.00 0.00 0.00 3.56
110 122 6.865205 GCAGAAGTACAAAAGCAGATGAATTT 59.135 34.615 0.00 0.00 0.00 1.82
111 123 6.016024 TGCAGAAGTACAAAAGCAGATGAATT 60.016 34.615 0.00 0.00 0.00 2.17
112 124 5.474532 TGCAGAAGTACAAAAGCAGATGAAT 59.525 36.000 0.00 0.00 0.00 2.57
388 420 9.793252 AAGCAAGCAAATACTATTGATACAAAG 57.207 29.630 0.00 0.00 31.84 2.77
729 779 6.875972 AACTGAGAGTATAACCACAAGGAT 57.124 37.500 0.00 0.00 38.69 3.24
1037 1089 6.013842 TCGTAATCATCGACTCTATTGCAT 57.986 37.500 0.00 0.00 32.30 3.96
1046 1098 6.148811 ACCATTTGTTTTCGTAATCATCGACT 59.851 34.615 0.00 0.00 37.05 4.18
1058 1110 5.685511 CCTTCTTGTACACCATTTGTTTTCG 59.314 40.000 0.00 0.00 39.91 3.46
1115 1167 6.161855 TGTACTCTGGGTCATCATTGATAC 57.838 41.667 0.00 0.00 33.56 2.24
1394 1452 0.612732 CCTTCCTGGAGGCATTGCAA 60.613 55.000 11.39 0.00 38.35 4.08
1477 1536 0.514691 GCTTTCTGCCTTGTGACTCG 59.485 55.000 0.00 0.00 35.15 4.18
1550 1609 0.105760 ACCCATTTGCACCAAGGTCA 60.106 50.000 0.00 0.00 0.00 4.02
1556 1615 1.203038 ACTCATCACCCATTTGCACCA 60.203 47.619 0.00 0.00 0.00 4.17
1637 1696 1.280133 TGCAGATGGTTCCTCCTTCAG 59.720 52.381 0.00 0.00 41.23 3.02
1684 1743 2.925706 TGCAACGGGGCTGAGGTA 60.926 61.111 2.27 0.00 34.04 3.08
1811 1870 6.539826 TCGACAAAAGCATACATGATCATTCT 59.460 34.615 5.16 0.00 0.00 2.40
1906 1965 5.189145 CCCTTTGCCCTTTCTAAGTCTAGTA 59.811 44.000 0.00 0.00 0.00 1.82
1994 2053 2.650116 GCAGAGGCTTCTCGGGACA 61.650 63.158 0.00 0.00 42.18 4.02
2109 2169 4.755123 ACAACTTTCCCAATGTAGTTCTCG 59.245 41.667 0.00 0.00 0.00 4.04
2157 2217 8.726988 GGTGTAACAGAAAAATAGATAGCACAA 58.273 33.333 0.00 0.00 39.98 3.33
2169 2229 7.392953 TGATCATGCATAGGTGTAACAGAAAAA 59.607 33.333 0.00 0.00 39.98 1.94
2311 2371 4.160439 ACTTCTTCTTGATCTGATGGCGTA 59.840 41.667 0.00 0.00 0.00 4.42
2391 2455 1.434696 CTTGCCATTCACCATCCGC 59.565 57.895 0.00 0.00 0.00 5.54
2531 2610 5.018240 CGACTTTTTCTCGATTCATCTTGC 58.982 41.667 0.00 0.00 32.65 4.01
2565 2644 0.846693 AGTGCCTGGAACCAGTTCTT 59.153 50.000 17.92 0.84 42.15 2.52
2586 2665 4.121317 CAGTGCCAAAAATGTGTGATGTT 58.879 39.130 0.00 0.00 0.00 2.71
2603 2683 7.274686 GTCTCTAGATAAAAGTTCTCACAGTGC 59.725 40.741 0.00 0.00 0.00 4.40
2620 2700 5.302313 GGATCAAACGGTAAGGTCTCTAGAT 59.698 44.000 0.00 0.00 0.00 1.98
2789 2874 3.710209 ATAGCAGTCTTGACTGGCTTT 57.290 42.857 25.99 17.09 38.14 3.51
2790 2875 3.772025 ACTATAGCAGTCTTGACTGGCTT 59.228 43.478 25.99 16.79 38.14 4.35
2955 3140 6.619801 ACAAGTTCTGGTATCTTTGTTGAC 57.380 37.500 0.00 0.00 0.00 3.18
2968 3153 6.560253 ACAAATAGCTACAACAAGTTCTGG 57.440 37.500 0.00 0.00 0.00 3.86
3089 3291 3.028850 CCTGGAGACATGCAATTGGAAT 58.971 45.455 2.94 0.00 41.51 3.01


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

AutoCloner maintained by Alex Coulton.