Multiple sequence alignment - TraesCS7D01G246000

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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 TraesCS7D01G246000 chr7D 100.000 3119 0 0 1 3119 215054574 215057692 0.000000e+00 5760
1 TraesCS7D01G246000 chr7B 94.007 3020 131 30 123 3119 185013278 185016270 0.000000e+00 4529
2 TraesCS7D01G246000 chr7B 84.524 168 17 8 319 479 468211513 468211348 1.160000e-34 158
3 TraesCS7D01G246000 chr7A 93.102 2421 113 29 160 2547 228169758 228172157 0.000000e+00 3496
4 TraesCS7D01G246000 chr7A 89.214 547 33 6 2575 3119 228172157 228172679 0.000000e+00 660
5 TraesCS7D01G246000 chr1A 86.127 173 20 4 300 468 442477832 442478004 1.910000e-42 183
6 TraesCS7D01G246000 chr6D 85.897 156 18 4 319 470 93633415 93633260 2.490000e-36 163
7 TraesCS7D01G246000 chr6A 86.667 150 17 3 321 467 115034624 115034773 2.490000e-36 163
8 TraesCS7D01G246000 chr6A 84.967 153 19 4 319 468 196171600 196171449 5.390000e-33 152
9 TraesCS7D01G246000 chr2A 85.443 158 18 4 316 468 14504517 14504360 3.220000e-35 159
10 TraesCS7D01G246000 chr5A 84.049 163 21 5 300 457 538756935 538757097 5.390000e-33 152
11 TraesCS7D01G246000 chr3D 84.713 157 18 6 319 470 415688540 415688695 5.390000e-33 152


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 TraesCS7D01G246000 chr7D 215054574 215057692 3118 False 5760 5760 100.000 1 3119 1 chr7D.!!$F1 3118
1 TraesCS7D01G246000 chr7B 185013278 185016270 2992 False 4529 4529 94.007 123 3119 1 chr7B.!!$F1 2996
2 TraesCS7D01G246000 chr7A 228169758 228172679 2921 False 2078 3496 91.158 160 3119 2 chr7A.!!$F1 2959

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
28 29 0.458370 AATTCGCCCAAATTCGCTGC 60.458 50.0 0.0 0.0 0.0 5.25 F
1312 1334 0.459899 TCGTCATGGAAGGTCGGATG 59.540 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1569 1591 1.400846 CTGCTGATCATGCTTGTCCAC 59.599 52.381 15.2 0.0 0.0 4.02 R
2918 2954 1.053835 TCACCAGCTCACACCCTGAA 61.054 55.000 0.0 0.0 0.0 3.02 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
19 20 4.396271 TCGGCCGAATTCGCCCAA 62.396 61.111 28.99 6.52 36.56 4.12
20 21 3.436055 CGGCCGAATTCGCCCAAA 61.436 61.111 25.63 0.00 36.56 3.28
21 22 2.770589 CGGCCGAATTCGCCCAAAT 61.771 57.895 25.63 0.00 36.56 2.32
22 23 1.515487 GGCCGAATTCGCCCAAATT 59.485 52.632 22.07 0.00 36.79 1.82
23 24 0.527600 GGCCGAATTCGCCCAAATTC 60.528 55.000 22.07 3.66 40.63 2.17
27 28 1.548986 GAATTCGCCCAAATTCGCTG 58.451 50.000 0.00 0.00 36.29 5.18
28 29 0.458370 AATTCGCCCAAATTCGCTGC 60.458 50.000 0.00 0.00 0.00 5.25
29 30 1.315257 ATTCGCCCAAATTCGCTGCT 61.315 50.000 0.00 0.00 0.00 4.24
30 31 2.198906 TTCGCCCAAATTCGCTGCTG 62.199 55.000 0.00 0.00 0.00 4.41
31 32 2.507769 GCCCAAATTCGCTGCTGC 60.508 61.111 5.34 5.34 0.00 5.25
32 33 2.182537 CCCAAATTCGCTGCTGCC 59.817 61.111 10.24 0.00 35.36 4.85
33 34 2.638354 CCCAAATTCGCTGCTGCCA 61.638 57.895 10.24 0.00 35.36 4.92
34 35 1.444895 CCAAATTCGCTGCTGCCAC 60.445 57.895 10.24 0.00 35.36 5.01
35 36 1.444895 CAAATTCGCTGCTGCCACC 60.445 57.895 10.24 0.00 35.36 4.61
36 37 2.981560 AAATTCGCTGCTGCCACCG 61.982 57.895 10.24 0.00 35.36 4.94
37 38 4.704833 ATTCGCTGCTGCCACCGT 62.705 61.111 10.24 0.00 35.36 4.83
38 39 2.796483 AATTCGCTGCTGCCACCGTA 62.796 55.000 10.24 0.00 35.36 4.02
39 40 3.932580 TTCGCTGCTGCCACCGTAG 62.933 63.158 10.24 0.00 35.36 3.51
91 92 2.943653 GGTTTCAACCGTCAGCCG 59.056 61.111 0.00 0.00 39.66 5.52
92 93 2.251371 GTTTCAACCGTCAGCCGC 59.749 61.111 0.00 0.00 34.38 6.53
93 94 2.975799 TTTCAACCGTCAGCCGCC 60.976 61.111 0.00 0.00 34.38 6.13
112 113 4.459331 CCACACGCCGCGAATTGG 62.459 66.667 21.79 17.34 0.00 3.16
113 114 4.459331 CACACGCCGCGAATTGGG 62.459 66.667 21.79 4.53 0.00 4.12
115 116 4.459331 CACGCCGCGAATTGGGTG 62.459 66.667 21.79 11.96 38.75 4.61
117 118 3.732892 CGCCGCGAATTGGGTGTT 61.733 61.111 8.23 0.00 0.00 3.32
118 119 2.648454 GCCGCGAATTGGGTGTTT 59.352 55.556 8.23 0.00 0.00 2.83
119 120 1.006688 GCCGCGAATTGGGTGTTTT 60.007 52.632 8.23 0.00 0.00 2.43
120 121 0.598942 GCCGCGAATTGGGTGTTTTT 60.599 50.000 8.23 0.00 0.00 1.94
121 122 1.414378 CCGCGAATTGGGTGTTTTTC 58.586 50.000 8.23 0.00 0.00 2.29
122 123 1.414378 CGCGAATTGGGTGTTTTTCC 58.586 50.000 0.00 0.00 0.00 3.13
123 124 1.414378 GCGAATTGGGTGTTTTTCCG 58.586 50.000 0.00 0.00 0.00 4.30
124 125 1.414378 CGAATTGGGTGTTTTTCCGC 58.586 50.000 0.00 0.00 0.00 5.54
125 126 1.790755 GAATTGGGTGTTTTTCCGCC 58.209 50.000 0.00 0.00 0.00 6.13
390 406 6.882140 TCAATATACATGTTCCGTTGGAGTTT 59.118 34.615 2.30 0.00 31.21 2.66
394 410 2.721425 TGTTCCGTTGGAGTTTCCTT 57.279 45.000 0.00 0.00 37.46 3.36
398 414 4.142337 TGTTCCGTTGGAGTTTCCTTTTTC 60.142 41.667 0.00 0.00 37.46 2.29
400 416 5.038651 TCCGTTGGAGTTTCCTTTTTCTA 57.961 39.130 0.00 0.00 37.46 2.10
401 417 5.438833 TCCGTTGGAGTTTCCTTTTTCTAA 58.561 37.500 0.00 0.00 37.46 2.10
472 491 9.656040 TTTACATCTTTAAATTTGCATCATGCT 57.344 25.926 11.84 0.00 45.31 3.79
530 550 6.849085 TTTGAGCTGGGATAAAATTTAGCA 57.151 33.333 10.21 0.00 33.81 3.49
697 717 3.003173 CCTGCTGACCTTCCGGGA 61.003 66.667 0.00 0.00 38.76 5.14
816 836 3.636231 CCCTTCGGTGCCTCCACA 61.636 66.667 0.00 0.00 43.88 4.17
836 856 1.900498 GCAGCTTGCCAAGTCTGGT 60.900 57.895 21.89 0.00 45.53 4.00
1024 1046 4.767255 CGCGCTTCAGGGAGGCTT 62.767 66.667 5.56 0.00 32.35 4.35
1312 1334 0.459899 TCGTCATGGAAGGTCGGATG 59.540 55.000 0.00 0.00 0.00 3.51
1384 1406 1.773052 AGGTGACATGGCTGAGCATAT 59.227 47.619 6.82 0.00 0.00 1.78
1569 1591 3.193267 TCAAAGGAAAGGATTTGATGGCG 59.807 43.478 0.00 0.00 39.27 5.69
1678 1700 3.243805 TGTTCCAGACCATGTTGCATTTG 60.244 43.478 0.00 0.00 0.00 2.32
1691 1713 1.737236 TGCATTTGTAGGCGTGCTTAG 59.263 47.619 0.00 0.00 38.37 2.18
1736 1758 4.279420 GGTGGATGAAGGCAGGAAATATTC 59.721 45.833 0.00 0.00 0.00 1.75
2157 2180 5.728741 AGAGGGGAGAATATTGTGAAAGACT 59.271 40.000 0.00 0.00 0.00 3.24
2182 2205 4.241590 TGTGGAAATGTGACATCAAAGC 57.758 40.909 0.00 0.00 0.00 3.51
2213 2236 2.976185 TCCTGTCTGGACCATGTGTTTA 59.024 45.455 0.00 0.00 40.56 2.01
2227 2250 6.769822 ACCATGTGTTTAAATTGAATTGCCAA 59.230 30.769 0.00 0.00 0.00 4.52
2253 2276 3.520290 TGTGCGGACATAGAGGTAAAG 57.480 47.619 5.33 0.00 0.00 1.85
2279 2307 9.649167 GATCTAACTTAAAGTGCTTACCAGTTA 57.351 33.333 0.00 8.77 36.07 2.24
2318 2346 4.827835 ACCTTTCCCTTTTTGAAGCTAGAC 59.172 41.667 0.00 0.00 0.00 2.59
2370 2403 9.185680 GATGGTAAGGTCAAAATAGGTAAATGT 57.814 33.333 0.00 0.00 0.00 2.71
2371 2404 8.943594 TGGTAAGGTCAAAATAGGTAAATGTT 57.056 30.769 0.00 0.00 0.00 2.71
2421 2454 4.810191 ATGTCTGTCTACTTGGAGGTTC 57.190 45.455 0.00 0.00 0.00 3.62
2570 2603 9.620660 ACGCTTTTGTTATATAGTTTTTCCTTG 57.379 29.630 0.00 0.00 0.00 3.61
2639 2673 5.950758 ACTTTGTTTATCATGCACCGTTA 57.049 34.783 0.00 0.00 0.00 3.18
2640 2674 5.695818 ACTTTGTTTATCATGCACCGTTAC 58.304 37.500 0.00 0.00 0.00 2.50
2650 2684 1.535028 TGCACCGTTACTTCAATGCAG 59.465 47.619 0.00 0.00 38.11 4.41
2674 2708 9.322776 CAGAAAGAAAAGAAGTGTCATATTTCG 57.677 33.333 0.00 0.00 32.63 3.46
2701 2735 9.636879 TGTGTAACATGACAATTTGGAATATTG 57.363 29.630 0.00 0.00 45.67 1.90
2705 2739 8.991243 AACATGACAATTTGGAATATTGACAG 57.009 30.769 0.00 0.00 39.61 3.51
2749 2783 3.596101 AGAGGGGCATCTGAACAGATAT 58.404 45.455 15.52 2.35 45.78 1.63
2757 2791 6.462500 GGCATCTGAACAGATATACACTGAT 58.538 40.000 15.52 4.15 45.78 2.90
2895 2930 9.755804 CTCAAGCTAAGATTGATGTCATACTAA 57.244 33.333 0.00 0.00 36.16 2.24
3000 3036 6.677913 AGGGAAAATGTTTTTACACGATCAG 58.322 36.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.548986 CAGCGAATTTGGGCGAATTC 58.451 50.000 12.36 12.36 40.80 2.17
9 10 0.458370 GCAGCGAATTTGGGCGAATT 60.458 50.000 0.00 0.00 32.16 2.17
10 11 1.139520 GCAGCGAATTTGGGCGAAT 59.860 52.632 0.00 0.00 0.00 3.34
11 12 1.971167 AGCAGCGAATTTGGGCGAA 60.971 52.632 0.00 0.00 0.00 4.70
12 13 2.359850 AGCAGCGAATTTGGGCGA 60.360 55.556 0.00 0.00 0.00 5.54
13 14 2.202518 CAGCAGCGAATTTGGGCG 60.203 61.111 0.00 0.00 0.00 6.13
14 15 2.507769 GCAGCAGCGAATTTGGGC 60.508 61.111 0.00 0.00 0.00 5.36
15 16 2.182537 GGCAGCAGCGAATTTGGG 59.817 61.111 0.00 0.00 43.41 4.12
16 17 1.444895 GTGGCAGCAGCGAATTTGG 60.445 57.895 0.00 0.00 43.41 3.28
17 18 1.444895 GGTGGCAGCAGCGAATTTG 60.445 57.895 12.58 0.00 43.41 2.32
18 19 2.964978 GGTGGCAGCAGCGAATTT 59.035 55.556 12.58 0.00 43.41 1.82
74 75 2.943653 CGGCTGACGGTTGAAACC 59.056 61.111 0.00 1.88 45.76 3.27
75 76 2.251371 GCGGCTGACGGTTGAAAC 59.749 61.111 4.52 0.00 44.51 2.78
76 77 2.975799 GGCGGCTGACGGTTGAAA 60.976 61.111 4.52 0.00 44.51 2.69
95 96 4.459331 CCAATTCGCGGCGTGTGG 62.459 66.667 22.90 21.58 0.00 4.17
96 97 4.459331 CCCAATTCGCGGCGTGTG 62.459 66.667 22.90 17.09 0.00 3.82
98 99 4.459331 CACCCAATTCGCGGCGTG 62.459 66.667 22.90 15.42 0.00 5.34
100 101 2.741116 AAAACACCCAATTCGCGGCG 62.741 55.000 17.70 17.70 0.00 6.46
101 102 0.598942 AAAAACACCCAATTCGCGGC 60.599 50.000 6.13 0.00 0.00 6.53
102 103 1.414378 GAAAAACACCCAATTCGCGG 58.586 50.000 6.13 0.00 0.00 6.46
103 104 1.414378 GGAAAAACACCCAATTCGCG 58.586 50.000 0.00 0.00 0.00 5.87
104 105 1.414378 CGGAAAAACACCCAATTCGC 58.586 50.000 0.00 0.00 0.00 4.70
105 106 1.414378 GCGGAAAAACACCCAATTCG 58.586 50.000 0.00 0.00 0.00 3.34
106 107 1.790755 GGCGGAAAAACACCCAATTC 58.209 50.000 0.00 0.00 0.00 2.17
107 108 0.032815 CGGCGGAAAAACACCCAATT 59.967 50.000 0.00 0.00 0.00 2.32
108 109 1.663173 CGGCGGAAAAACACCCAAT 59.337 52.632 0.00 0.00 0.00 3.16
109 110 3.121019 CGGCGGAAAAACACCCAA 58.879 55.556 0.00 0.00 0.00 4.12
110 111 3.597728 GCGGCGGAAAAACACCCA 61.598 61.111 9.78 0.00 0.00 4.51
111 112 4.351938 GGCGGCGGAAAAACACCC 62.352 66.667 9.78 0.00 0.00 4.61
112 113 4.693525 CGGCGGCGGAAAAACACC 62.694 66.667 25.36 0.00 0.00 4.16
291 306 0.815734 TCAACTAGTACTCAGGCGGC 59.184 55.000 0.00 0.00 0.00 6.53
327 343 6.604396 ACAACTCCAATAGATGATGCAAATGA 59.396 34.615 0.00 0.00 32.52 2.57
376 392 4.097437 AGAAAAAGGAAACTCCAACGGAAC 59.903 41.667 0.00 0.00 42.68 3.62
468 487 8.930846 AGCATATCATAACTCCTTAAAAGCAT 57.069 30.769 0.00 0.00 0.00 3.79
470 489 7.385205 TCGAGCATATCATAACTCCTTAAAAGC 59.615 37.037 0.00 0.00 0.00 3.51
471 490 8.818141 TCGAGCATATCATAACTCCTTAAAAG 57.182 34.615 0.00 0.00 0.00 2.27
472 491 9.261180 CTTCGAGCATATCATAACTCCTTAAAA 57.739 33.333 0.00 0.00 0.00 1.52
477 497 6.849085 ATCTTCGAGCATATCATAACTCCT 57.151 37.500 0.00 0.00 0.00 3.69
530 550 1.024579 CGCACGGCTGGATTTACCTT 61.025 55.000 0.00 0.00 39.86 3.50
563 583 5.725042 GCTTGCATGAACGAATACTGTACTG 60.725 44.000 3.33 0.00 0.00 2.74
816 836 2.111878 AGACTTGGCAAGCTGCGT 59.888 55.556 26.45 8.01 46.21 5.24
852 872 1.132073 GACGAGGGAGGAAGTAACGTC 59.868 57.143 0.00 0.00 40.77 4.34
938 958 2.354188 CAGGTGACGACGTTGCGA 60.354 61.111 0.13 0.00 34.83 5.10
1312 1334 4.517075 AGCAGCAAAAGTTTCTAGAACCTC 59.483 41.667 4.18 0.00 0.00 3.85
1384 1406 1.459209 CTTCGATGTACAAGCACGCAA 59.541 47.619 0.00 1.16 0.00 4.85
1424 1446 1.681780 CCATGTATGCGTGAACCCCTT 60.682 52.381 4.37 0.00 33.58 3.95
1569 1591 1.400846 CTGCTGATCATGCTTGTCCAC 59.599 52.381 15.20 0.00 0.00 4.02
1736 1758 4.269603 CGTAAAGATTCAGCATGGAGTCAG 59.730 45.833 0.00 0.00 36.16 3.51
1865 1887 3.394606 ACTTCCCCACATTCTAACACTGT 59.605 43.478 0.00 0.00 0.00 3.55
2041 2063 0.257039 ATCTGCCACATCAACCTCCC 59.743 55.000 0.00 0.00 0.00 4.30
2122 2144 2.379972 TCTCCCCTCTCACTTCGATTC 58.620 52.381 0.00 0.00 0.00 2.52
2157 2180 5.588958 TTGATGTCACATTTCCACAACAA 57.411 34.783 0.00 0.00 32.33 2.83
2182 2205 3.912496 TCCAGACAGGAATGTACATGG 57.088 47.619 9.63 5.30 45.65 3.66
2227 2250 5.036117 ACCTCTATGTCCGCACATAAAAT 57.964 39.130 0.02 0.00 43.57 1.82
2253 2276 8.549338 AACTGGTAAGCACTTTAAGTTAGATC 57.451 34.615 0.00 0.00 0.00 2.75
2370 2403 6.702716 AACACCGACCTCTCAAAAATAAAA 57.297 33.333 0.00 0.00 0.00 1.52
2371 2404 6.702716 AAACACCGACCTCTCAAAAATAAA 57.297 33.333 0.00 0.00 0.00 1.40
2421 2454 3.559069 AGGTGATTCCAGGCAACATATG 58.441 45.455 0.00 0.00 39.02 1.78
2570 2603 6.205464 TCACAACATCTTCAGTTTTCTCCATC 59.795 38.462 0.00 0.00 0.00 3.51
2622 2656 5.539582 TGAAGTAACGGTGCATGATAAAC 57.460 39.130 0.00 0.00 0.00 2.01
2639 2673 6.976925 CACTTCTTTTCTTTCTGCATTGAAGT 59.023 34.615 0.00 0.00 41.15 3.01
2640 2674 6.976925 ACACTTCTTTTCTTTCTGCATTGAAG 59.023 34.615 0.00 0.00 35.78 3.02
2650 2684 9.107367 CACGAAATATGACACTTCTTTTCTTTC 57.893 33.333 0.00 0.00 0.00 2.62
2674 2708 9.638239 AATATTCCAAATTGTCATGTTACACAC 57.362 29.630 0.00 0.00 0.00 3.82
2693 2727 5.644636 TGTCCCGTTTAACTGTCAATATTCC 59.355 40.000 0.00 0.00 0.00 3.01
2695 2729 7.610305 AGATTGTCCCGTTTAACTGTCAATATT 59.390 33.333 0.00 0.00 0.00 1.28
2701 2735 5.684550 AAAGATTGTCCCGTTTAACTGTC 57.315 39.130 0.00 0.00 0.00 3.51
2705 2739 7.197703 TCTTTGAAAAGATTGTCCCGTTTAAC 58.802 34.615 1.31 0.00 39.95 2.01
2749 2783 1.977854 ACACCTTGCAGGATCAGTGTA 59.022 47.619 6.77 0.00 37.67 2.90
2895 2930 3.990318 GCTCAAGTAAGCAAAAGGTGT 57.010 42.857 0.00 0.00 42.05 4.16
2918 2954 1.053835 TCACCAGCTCACACCCTGAA 61.054 55.000 0.00 0.00 0.00 3.02
2954 2990 9.060137 TCCCTAATAACTAACTTGTTTGGGATA 57.940 33.333 7.39 0.00 44.52 2.59
3000 3036 3.653835 ATTAAAGGGAGACAAGAGCCC 57.346 47.619 0.00 0.00 42.37 5.19


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

AutoCloner maintained by Alex Coulton.