Multiple sequence alignment - TraesCS5B01G094400

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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 TraesCS5B01G094400 chr5B 100.000 2264 0 0 1 2264 123786974 123789237 0.000000e+00 4181
1 TraesCS5B01G094400 chr5B 94.356 2126 62 22 3 2123 353930733 353928661 0.000000e+00 3208
2 TraesCS5B01G094400 chr5B 94.129 2129 62 25 1 2123 18184112 18186183 0.000000e+00 3181
3 TraesCS5B01G094400 chr5B 86.268 619 54 22 1674 2264 514052370 514052985 0.000000e+00 643
4 TraesCS5B01G094400 chr5B 87.500 192 22 2 1912 2102 514052738 514052928 1.050000e-53 220
5 TraesCS5B01G094400 chr5B 89.706 136 13 1 2130 2264 353928690 353928555 2.990000e-39 172
6 TraesCS5B01G094400 chr5B 88.571 105 9 2 1718 1821 514052344 514052446 8.490000e-25 124
7 TraesCS5B01G094400 chr5B 90.426 94 7 1 1718 1811 123788656 123788747 3.050000e-24 122
8 TraesCS5B01G094400 chr5B 91.765 85 7 0 2123 2207 514052633 514052717 3.950000e-23 119
9 TraesCS5B01G094400 chr7B 96.526 2130 47 10 1 2123 666615842 666617951 0.000000e+00 3498
10 TraesCS5B01G094400 chr7B 98.169 1912 32 2 1 1911 535437150 535435241 0.000000e+00 3334
11 TraesCS5B01G094400 chr7B 97.544 1588 32 6 1 1584 664951469 664949885 0.000000e+00 2710
12 TraesCS5B01G094400 chr7B 89.928 139 13 1 2127 2264 666617919 666618057 6.430000e-41 178
13 TraesCS5B01G094400 chr3B 94.408 2128 59 24 1 2123 734227365 734225293 0.000000e+00 3216
14 TraesCS5B01G094400 chr3B 91.221 1868 131 21 1 1861 21644987 21646828 0.000000e+00 2510
15 TraesCS5B01G094400 chr3D 94.492 1870 74 21 1 1861 581472629 581474478 0.000000e+00 2856
16 TraesCS5B01G094400 chr4B 96.144 1608 36 8 680 2264 522404483 522406087 0.000000e+00 2603
17 TraesCS5B01G094400 chr4B 86.631 187 23 2 2023 2207 522405738 522405924 2.950000e-49 206
18 TraesCS5B01G094400 chr4B 91.489 94 6 1 1718 1811 522405485 522405576 6.560000e-26 128
19 TraesCS5B01G094400 chr6B 91.079 1872 132 21 1 1861 715471836 715469989 0.000000e+00 2499
20 TraesCS5B01G094400 chr6B 89.881 168 17 0 2097 2264 77326183 77326016 1.360000e-52 217
21 TraesCS5B01G094400 chr4A 90.358 363 31 2 1905 2264 692375205 692374844 7.320000e-130 473
22 TraesCS5B01G094400 chr4A 88.482 191 21 1 1912 2102 692375090 692374901 1.750000e-56 230
23 TraesCS5B01G094400 chr4A 93.750 144 7 1 1718 1861 692375412 692375271 4.900000e-52 215
24 TraesCS5B01G094400 chr2D 89.024 82 9 0 2183 2264 89189482 89189563 3.980000e-18 102
25 TraesCS5B01G094400 chr2D 89.024 82 9 0 2183 2264 104927505 104927424 3.980000e-18 102


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 TraesCS5B01G094400 chr5B 123786974 123789237 2263 False 2151.5 4181 95.213000 1 2264 2 chr5B.!!$F2 2263
1 TraesCS5B01G094400 chr5B 18184112 18186183 2071 False 3181.0 3181 94.129000 1 2123 1 chr5B.!!$F1 2122
2 TraesCS5B01G094400 chr5B 353928555 353930733 2178 True 1690.0 3208 92.031000 3 2264 2 chr5B.!!$R1 2261
3 TraesCS5B01G094400 chr5B 514052344 514052985 641 False 276.5 643 88.526000 1674 2264 4 chr5B.!!$F3 590
4 TraesCS5B01G094400 chr7B 535435241 535437150 1909 True 3334.0 3334 98.169000 1 1911 1 chr7B.!!$R1 1910
5 TraesCS5B01G094400 chr7B 664949885 664951469 1584 True 2710.0 2710 97.544000 1 1584 1 chr7B.!!$R2 1583
6 TraesCS5B01G094400 chr7B 666615842 666618057 2215 False 1838.0 3498 93.227000 1 2264 2 chr7B.!!$F1 2263
7 TraesCS5B01G094400 chr3B 734225293 734227365 2072 True 3216.0 3216 94.408000 1 2123 1 chr3B.!!$R1 2122
8 TraesCS5B01G094400 chr3B 21644987 21646828 1841 False 2510.0 2510 91.221000 1 1861 1 chr3B.!!$F1 1860
9 TraesCS5B01G094400 chr3D 581472629 581474478 1849 False 2856.0 2856 94.492000 1 1861 1 chr3D.!!$F1 1860
10 TraesCS5B01G094400 chr4B 522404483 522406087 1604 False 979.0 2603 91.421333 680 2264 3 chr4B.!!$F1 1584
11 TraesCS5B01G094400 chr6B 715469989 715471836 1847 True 2499.0 2499 91.079000 1 1861 1 chr6B.!!$R2 1860
12 TraesCS5B01G094400 chr4A 692374844 692375412 568 True 306.0 473 90.863333 1718 2264 3 chr4A.!!$R1 546

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
84 86 1.884579 CAAAGCAAGTCCTCAGCACAT 59.115 47.619 0.0 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1534 1556 0.324738 TGCCCTCTCCTCTTGACGAT 60.325 55.0 0.0 0.0 0.0 3.73 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
84 86 1.884579 CAAAGCAAGTCCTCAGCACAT 59.115 47.619 0.00 0.00 0.00 3.21
613 620 6.739112 ACATGCTCTAAGAAAAGGAAAACAC 58.261 36.000 0.00 0.00 0.00 3.32
724 740 3.465403 CCCGTGCTGCTAGAGGCT 61.465 66.667 0.00 0.00 42.39 4.58
1186 1207 0.109226 GTCGTGGACGGAAGGAAGAG 60.109 60.000 0.00 0.00 40.29 2.85
1187 1208 0.251033 TCGTGGACGGAAGGAAGAGA 60.251 55.000 0.00 0.00 40.29 3.10
1534 1556 2.029288 CGCGCAAAGAGAAGGCAGA 61.029 57.895 8.75 0.00 0.00 4.26
1716 1779 5.056480 TGGACCTATTGTGCTATTTGATCG 58.944 41.667 0.00 0.00 36.06 3.69
1726 1789 6.811954 TGTGCTATTTGATCGGAACTATGTA 58.188 36.000 0.00 0.00 0.00 2.29
1730 1793 8.147704 TGCTATTTGATCGGAACTATGTAATGA 58.852 33.333 0.00 0.00 0.00 2.57
1736 1799 8.014070 TGATCGGAACTATGTAATGAACCTAA 57.986 34.615 0.00 0.00 0.00 2.69
1737 1800 8.141909 TGATCGGAACTATGTAATGAACCTAAG 58.858 37.037 0.00 0.00 0.00 2.18
1738 1801 7.414222 TCGGAACTATGTAATGAACCTAAGT 57.586 36.000 0.00 0.00 0.00 2.24
1739 1802 7.844009 TCGGAACTATGTAATGAACCTAAGTT 58.156 34.615 0.00 0.00 39.54 2.66
1978 2316 3.153919 GGAAAATGTGTGGTTGCTCCTA 58.846 45.455 0.80 0.00 37.07 2.94
2009 2347 2.805546 GCCAGAGATCACGGCGTA 59.194 61.111 14.22 1.37 35.79 4.42
2025 2363 1.302949 GTATGCACCTCTGCCCCAA 59.697 57.895 0.00 0.00 43.51 4.12
2041 2379 1.300620 CAAACGCCAGAGACCACGA 60.301 57.895 0.00 0.00 0.00 4.35
2043 2381 2.023414 AAACGCCAGAGACCACGACA 62.023 55.000 0.00 0.00 0.00 4.35
2115 2453 4.002797 GCCAGGAATCAAGGCGTT 57.997 55.556 0.00 0.00 38.86 4.84
2116 2454 2.267045 GCCAGGAATCAAGGCGTTT 58.733 52.632 0.00 0.00 38.86 3.60
2117 2455 0.109132 GCCAGGAATCAAGGCGTTTG 60.109 55.000 0.00 0.00 38.86 2.93
2118 2456 0.527565 CCAGGAATCAAGGCGTTTGG 59.472 55.000 0.00 0.00 37.39 3.28
2119 2457 1.533625 CAGGAATCAAGGCGTTTGGA 58.466 50.000 0.00 0.00 37.39 3.53
2120 2458 1.200020 CAGGAATCAAGGCGTTTGGAC 59.800 52.381 0.00 0.00 37.39 4.02
2121 2459 0.526211 GGAATCAAGGCGTTTGGACC 59.474 55.000 0.00 0.00 37.39 4.46
2122 2460 1.534729 GAATCAAGGCGTTTGGACCT 58.465 50.000 0.00 0.00 37.39 3.85
2123 2461 1.468914 GAATCAAGGCGTTTGGACCTC 59.531 52.381 0.00 0.00 37.39 3.85
2124 2462 0.693049 ATCAAGGCGTTTGGACCTCT 59.307 50.000 0.00 0.00 37.39 3.69
2125 2463 0.250295 TCAAGGCGTTTGGACCTCTG 60.250 55.000 0.00 0.00 37.39 3.35
2126 2464 1.600916 AAGGCGTTTGGACCTCTGC 60.601 57.895 0.00 0.00 34.31 4.26
2127 2465 3.056328 GGCGTTTGGACCTCTGCC 61.056 66.667 0.00 0.00 35.04 4.85
2128 2466 3.056328 GCGTTTGGACCTCTGCCC 61.056 66.667 0.00 0.00 0.00 5.36
2129 2467 2.429930 CGTTTGGACCTCTGCCCA 59.570 61.111 0.00 0.00 0.00 5.36
2130 2468 1.672356 CGTTTGGACCTCTGCCCAG 60.672 63.158 0.00 0.00 33.43 4.45
2131 2469 1.761174 GTTTGGACCTCTGCCCAGA 59.239 57.895 0.00 0.00 33.43 3.86
2132 2470 0.606673 GTTTGGACCTCTGCCCAGAC 60.607 60.000 0.00 0.00 33.43 3.51
2133 2471 2.111999 TTTGGACCTCTGCCCAGACG 62.112 60.000 0.00 0.00 33.43 4.18
2134 2472 4.459089 GGACCTCTGCCCAGACGC 62.459 72.222 0.00 0.00 33.22 5.19
2135 2473 4.459089 GACCTCTGCCCAGACGCC 62.459 72.222 0.00 0.00 33.22 5.68
2137 2475 4.463879 CCTCTGCCCAGACGCCAG 62.464 72.222 0.00 0.00 33.22 4.85
2138 2476 3.385384 CTCTGCCCAGACGCCAGA 61.385 66.667 0.00 0.00 33.22 3.86
2139 2477 3.368190 CTCTGCCCAGACGCCAGAG 62.368 68.421 2.89 2.89 34.32 3.35
2140 2478 3.385384 CTGCCCAGACGCCAGAGA 61.385 66.667 0.00 0.00 0.00 3.10
2141 2479 3.655810 CTGCCCAGACGCCAGAGAC 62.656 68.421 0.00 0.00 0.00 3.36
2142 2480 4.459089 GCCCAGACGCCAGAGACC 62.459 72.222 0.00 0.00 0.00 3.85
2143 2481 2.997315 CCCAGACGCCAGAGACCA 60.997 66.667 0.00 0.00 0.00 4.02
2144 2482 2.262915 CCAGACGCCAGAGACCAC 59.737 66.667 0.00 0.00 0.00 4.16
2145 2483 2.126307 CAGACGCCAGAGACCACG 60.126 66.667 0.00 0.00 0.00 4.94
2146 2484 3.374402 AGACGCCAGAGACCACGG 61.374 66.667 0.00 0.00 0.00 4.94
2244 2618 5.708736 TGGTCCTTTGCAGATTATAAGGA 57.291 39.130 10.59 10.59 42.81 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 86 7.037438 CGTAGGTGTTGAATAGCCTAAGTTTA 58.963 38.462 0.00 0.00 35.62 2.01
316 318 6.533367 GTCAACCTAGTAGCTTCAAGATCAAG 59.467 42.308 0.00 0.00 0.00 3.02
613 620 1.276138 GGTTGGATTGCCCTTCTTTGG 59.724 52.381 0.00 0.00 35.38 3.28
724 740 2.173782 CACTCCTAGCACCTCCTCTAGA 59.826 54.545 0.00 0.00 35.48 2.43
1186 1207 6.751888 GCATAGTTGGGACACACAAAATATTC 59.248 38.462 0.00 0.00 39.29 1.75
1187 1208 6.210385 TGCATAGTTGGGACACACAAAATATT 59.790 34.615 0.00 0.00 39.29 1.28
1534 1556 0.324738 TGCCCTCTCCTCTTGACGAT 60.325 55.000 0.00 0.00 0.00 3.73
1730 1793 9.474313 TTCCAATCAAATAGCATAACTTAGGTT 57.526 29.630 0.00 0.00 39.26 3.50
1736 1799 9.632638 ACATAGTTCCAATCAAATAGCATAACT 57.367 29.630 0.00 0.00 0.00 2.24
1978 2316 1.219124 CTGGCGTCTAGGTGTGCAT 59.781 57.895 0.00 0.00 0.00 3.96
2025 2363 1.816863 ATGTCGTGGTCTCTGGCGTT 61.817 55.000 0.00 0.00 0.00 4.84
2041 2379 3.456277 CTCTCTGGTTAGGGCCTAAATGT 59.544 47.826 26.95 0.00 0.00 2.71
2043 2381 3.049344 CCTCTCTGGTTAGGGCCTAAAT 58.951 50.000 26.95 0.00 0.00 1.40
2117 2455 4.459089 GCGTCTGGGCAGAGGTCC 62.459 72.222 0.00 0.00 43.21 4.46
2118 2456 4.459089 GGCGTCTGGGCAGAGGTC 62.459 72.222 0.00 0.00 43.21 3.85
2125 2463 4.459089 GGTCTCTGGCGTCTGGGC 62.459 72.222 0.00 0.00 42.69 5.36
2126 2464 2.997315 TGGTCTCTGGCGTCTGGG 60.997 66.667 0.00 0.00 0.00 4.45
2127 2465 2.262915 GTGGTCTCTGGCGTCTGG 59.737 66.667 0.00 0.00 0.00 3.86
2128 2466 2.126307 CGTGGTCTCTGGCGTCTG 60.126 66.667 0.00 0.00 0.00 3.51
2129 2467 3.374402 CCGTGGTCTCTGGCGTCT 61.374 66.667 0.00 0.00 0.00 4.18
2133 2471 2.775032 TAAACGCCGTGGTCTCTGGC 62.775 60.000 0.00 0.00 45.39 4.85
2134 2472 0.736325 CTAAACGCCGTGGTCTCTGG 60.736 60.000 0.00 0.00 0.00 3.86
2135 2473 0.736325 CCTAAACGCCGTGGTCTCTG 60.736 60.000 0.00 0.00 0.00 3.35
2136 2474 1.590147 CCTAAACGCCGTGGTCTCT 59.410 57.895 0.00 0.00 0.00 3.10
2137 2475 2.098831 GCCTAAACGCCGTGGTCTC 61.099 63.158 0.00 0.00 0.00 3.36
2138 2476 2.047560 GCCTAAACGCCGTGGTCT 60.048 61.111 0.00 0.00 0.00 3.85
2139 2477 3.122971 GGCCTAAACGCCGTGGTC 61.123 66.667 0.00 0.00 39.64 4.02
2146 2484 3.531934 TTCTAGTTAGGGCCTAAACGC 57.468 47.619 26.95 15.09 0.00 4.84
2147 2485 4.081254 ACCTTTCTAGTTAGGGCCTAAACG 60.081 45.833 26.95 17.23 35.79 3.60
2148 2486 5.432680 ACCTTTCTAGTTAGGGCCTAAAC 57.567 43.478 26.95 19.61 35.79 2.01
2162 2535 3.687698 GCAACCGCAGATTTACCTTTCTA 59.312 43.478 0.00 0.00 38.36 2.10


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

AutoCloner maintained by Alex Coulton.