Multiple sequence alignment - TraesCS5D01G259700

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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 TraesCS5D01G259700 chr5D 100.000 3177 0 0 1 3177 365991363 365994539 0.000000e+00 5867.0
1 TraesCS5D01G259700 chr5B 93.513 2790 95 34 409 3177 432322618 432325342 0.000000e+00 4071.0
2 TraesCS5D01G259700 chr5B 91.837 392 27 3 3 390 432322145 432322535 2.790000e-150 542.0
3 TraesCS5D01G259700 chr5B 83.333 168 20 3 1601 1767 432323755 432323915 7.100000e-32 148.0
4 TraesCS5D01G259700 chr5B 91.228 57 4 1 1583 1639 432323896 432323951 3.400000e-10 76.8
5 TraesCS5D01G259700 chr5B 97.500 40 0 1 2477 2515 432324693 432324732 2.050000e-07 67.6
6 TraesCS5D01G259700 chr5A 86.766 2826 158 104 480 3177 467585028 467587765 0.000000e+00 2948.0
7 TraesCS5D01G259700 chr5A 88.940 434 29 8 1 429 467584490 467584909 4.700000e-143 518.0
8 TraesCS5D01G259700 chr5A 82.500 160 18 7 1610 1767 467586172 467586323 7.150000e-27 132.0
9 TraesCS5D01G259700 chr5A 92.000 50 4 0 1583 1632 467586304 467586353 1.580000e-08 71.3
10 TraesCS5D01G259700 chr6D 89.404 151 16 0 1220 1370 358326157 358326007 1.160000e-44 191.0
11 TraesCS5D01G259700 chr6D 88.667 150 17 0 1220 1369 378379440 378379291 1.950000e-42 183.0
12 TraesCS5D01G259700 chr6A 89.404 151 16 0 1220 1370 500083776 500083626 1.160000e-44 191.0
13 TraesCS5D01G259700 chr6B 88.742 151 17 0 1220 1370 539727701 539727551 5.410000e-43 185.0
14 TraesCS5D01G259700 chr7D 82.775 209 29 6 1163 1369 174992560 174992763 2.520000e-41 180.0
15 TraesCS5D01G259700 chr3D 87.421 159 17 3 1212 1369 61703556 61703400 2.520000e-41 180.0
16 TraesCS5D01G259700 chr7A 82.629 213 25 11 1163 1369 177136107 177136313 9.060000e-41 178.0


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 TraesCS5D01G259700 chr5D 365991363 365994539 3176 False 5867.000 5867 100.0000 1 3177 1 chr5D.!!$F1 3176
1 TraesCS5D01G259700 chr5B 432322145 432325342 3197 False 981.080 4071 91.4822 3 3177 5 chr5B.!!$F1 3174
2 TraesCS5D01G259700 chr5A 467584490 467587765 3275 False 917.325 2948 87.5515 1 3177 4 chr5A.!!$F1 3176

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
187 193 1.286880 GCCACCAATCACACTGTGC 59.713 57.895 7.9 0.0 32.98 4.57 F
1083 1258 1.080434 GCTCGCTCTCTCGTTGGTT 60.080 57.895 0.0 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1533 1720 0.939577 CTGTTGTCACGTCCTCGGTG 60.940 60.0 0.00 0.00 41.85 4.94 R
2472 2691 0.038618 TGCCTGTGCTGTACTGTACG 60.039 55.0 12.87 8.93 38.71 3.67 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
82 88 2.489971 CACCTGGTGCGTTTTCTCTTA 58.510 47.619 14.87 0.00 0.00 2.10
110 116 2.163010 TGTTCCGTTATCTCCGACACTC 59.837 50.000 0.00 0.00 0.00 3.51
164 170 1.964223 ACGTCAGTCTGTCCATCAGTT 59.036 47.619 0.00 0.00 43.97 3.16
170 176 2.234908 AGTCTGTCCATCAGTTACTGGC 59.765 50.000 12.79 0.00 43.97 4.85
187 193 1.286880 GCCACCAATCACACTGTGC 59.713 57.895 7.90 0.00 32.98 4.57
265 271 3.950794 ATTCGTGGCACCATCGCGT 62.951 57.895 12.86 0.00 38.95 6.01
473 577 2.359230 GGGTGCCACTGCTGAGAC 60.359 66.667 0.00 0.00 38.71 3.36
755 899 4.382320 GGTGGCGGCTGGTTCGTA 62.382 66.667 11.43 0.00 0.00 3.43
893 1059 2.636462 CGCACACCGTCAAATGCA 59.364 55.556 0.00 0.00 37.97 3.96
1002 1176 2.501222 ACGCACGTTCGAGCTACG 60.501 61.111 15.92 5.98 44.20 3.51
1071 1246 3.859414 GATCAGGGCCAGCTCGCT 61.859 66.667 6.18 0.00 0.00 4.93
1083 1258 1.080434 GCTCGCTCTCTCGTTGGTT 60.080 57.895 0.00 0.00 0.00 3.67
1392 1579 2.048784 TCCTCGTCGTCGTCGTCT 60.049 61.111 11.41 0.00 38.33 4.18
1651 1838 2.572290 CGGAAGGGTGTTTCACTTTCT 58.428 47.619 12.90 3.24 40.25 2.52
1652 1839 2.949644 CGGAAGGGTGTTTCACTTTCTT 59.050 45.455 12.90 8.96 40.25 2.52
1657 1844 1.754226 GGTGTTTCACTTTCTTGGCCA 59.246 47.619 0.00 0.00 34.40 5.36
1664 1851 1.673665 CTTTCTTGGCCAGCGAGCT 60.674 57.895 5.11 0.00 0.00 4.09
1665 1852 1.642952 CTTTCTTGGCCAGCGAGCTC 61.643 60.000 5.11 2.73 0.00 4.09
1701 1888 1.685820 GGAGGGAGACAGGGGTTTG 59.314 63.158 0.00 0.00 0.00 2.93
2035 2227 5.073428 TCTTACTATCATCATCGTCTGGCT 58.927 41.667 0.00 0.00 0.00 4.75
2060 2252 2.404559 TCCGGCCAGTAGTATTTGGAT 58.595 47.619 2.24 0.00 36.55 3.41
2061 2253 2.104111 TCCGGCCAGTAGTATTTGGATG 59.896 50.000 2.24 0.35 36.55 3.51
2062 2254 2.494059 CGGCCAGTAGTATTTGGATGG 58.506 52.381 2.24 0.00 36.55 3.51
2171 2367 4.719773 AGGTGCCTGTATAAATCAGTACCA 59.280 41.667 14.27 0.00 39.00 3.25
2362 2575 4.781087 ACCTGGAAATGTACCTGTAGCTAA 59.219 41.667 0.00 0.00 0.00 3.09
2370 2589 3.691118 TGTACCTGTAGCTAACCAGTACG 59.309 47.826 9.74 0.00 37.94 3.67
2384 2603 0.029567 AGTACGTCGCTGCTAGCATC 59.970 55.000 19.72 13.77 42.58 3.91
2390 2609 1.300775 CGCTGCTAGCATCCCTGAG 60.301 63.158 19.72 5.64 42.58 3.35
2391 2610 1.597578 GCTGCTAGCATCCCTGAGC 60.598 63.158 19.72 12.54 41.89 4.26
2392 2611 1.300775 CTGCTAGCATCCCTGAGCG 60.301 63.158 19.72 0.00 37.77 5.03
2398 2617 0.392193 AGCATCCCTGAGCGTTCTTG 60.392 55.000 0.00 0.00 35.48 3.02
2399 2618 1.372087 GCATCCCTGAGCGTTCTTGG 61.372 60.000 0.00 3.03 0.00 3.61
2400 2619 1.078143 ATCCCTGAGCGTTCTTGGC 60.078 57.895 0.00 0.00 0.00 4.52
2401 2620 1.841302 ATCCCTGAGCGTTCTTGGCA 61.841 55.000 0.00 0.00 0.00 4.92
2402 2621 1.600636 CCCTGAGCGTTCTTGGCAA 60.601 57.895 0.00 0.00 0.00 4.52
2403 2622 1.172180 CCCTGAGCGTTCTTGGCAAA 61.172 55.000 0.00 0.00 0.00 3.68
2404 2623 0.883833 CCTGAGCGTTCTTGGCAAAT 59.116 50.000 0.00 0.00 0.00 2.32
2405 2624 2.083774 CCTGAGCGTTCTTGGCAAATA 58.916 47.619 0.00 0.00 0.00 1.40
2406 2625 2.159517 CCTGAGCGTTCTTGGCAAATAC 60.160 50.000 0.00 1.30 0.00 1.89
2407 2626 1.463056 TGAGCGTTCTTGGCAAATACG 59.537 47.619 22.13 22.13 35.48 3.06
2408 2627 0.802494 AGCGTTCTTGGCAAATACGG 59.198 50.000 25.35 13.47 33.17 4.02
2409 2628 0.519961 GCGTTCTTGGCAAATACGGT 59.480 50.000 25.35 0.00 33.17 4.83
2410 2629 1.727857 GCGTTCTTGGCAAATACGGTG 60.728 52.381 25.35 5.26 33.17 4.94
2411 2630 1.727857 CGTTCTTGGCAAATACGGTGC 60.728 52.381 19.95 0.00 41.45 5.01
2431 2650 3.132481 CTCCGGCGAAGAGAGGAGC 62.132 68.421 9.30 0.00 42.99 4.70
2453 2672 4.736896 GCCGACCTCGCTCCGTTT 62.737 66.667 0.00 0.00 38.18 3.60
2454 2673 2.879907 CCGACCTCGCTCCGTTTA 59.120 61.111 0.00 0.00 38.18 2.01
2455 2674 1.226603 CCGACCTCGCTCCGTTTAG 60.227 63.158 0.00 0.00 38.18 1.85
2456 2675 1.226603 CGACCTCGCTCCGTTTAGG 60.227 63.158 0.00 0.00 42.97 2.69
2457 2676 1.888736 GACCTCGCTCCGTTTAGGT 59.111 57.895 0.00 0.00 45.02 3.08
2458 2677 0.458025 GACCTCGCTCCGTTTAGGTG 60.458 60.000 0.00 0.00 42.40 4.00
2459 2678 1.153628 CCTCGCTCCGTTTAGGTGG 60.154 63.158 0.00 0.00 41.99 4.61
2460 2679 1.601419 CCTCGCTCCGTTTAGGTGGA 61.601 60.000 0.00 0.00 41.99 4.02
2461 2680 0.245539 CTCGCTCCGTTTAGGTGGAA 59.754 55.000 0.00 0.00 41.99 3.53
2462 2681 0.245539 TCGCTCCGTTTAGGTGGAAG 59.754 55.000 0.00 0.00 41.99 3.46
2463 2682 1.359459 CGCTCCGTTTAGGTGGAAGC 61.359 60.000 0.00 0.00 41.99 3.86
2549 2774 0.390340 AGTACAGCACAGGCATGTCG 60.390 55.000 0.00 0.00 44.61 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 74 7.692705 GGAACAAAGATATAAGAGAAAACGCAC 59.307 37.037 0.00 0.00 0.00 5.34
82 88 6.183360 TGTCGGAGATAACGGAACAAAGATAT 60.183 38.462 0.00 0.00 40.67 1.63
131 137 3.937079 AGACTGACGTTTCTTTTCGGTTT 59.063 39.130 0.00 0.00 0.00 3.27
136 142 3.869246 TGGACAGACTGACGTTTCTTTTC 59.131 43.478 10.08 0.00 0.00 2.29
164 170 1.064003 AGTGTGATTGGTGGCCAGTA 58.936 50.000 5.11 0.00 33.81 2.74
170 176 1.200716 GATGCACAGTGTGATTGGTGG 59.799 52.381 27.37 0.00 35.23 4.61
187 193 2.436646 GGTGCCCGGTGACTGATG 60.437 66.667 0.00 0.00 0.00 3.07
670 796 4.451150 TGTCGTGCGCATCCCCTC 62.451 66.667 15.91 0.00 0.00 4.30
671 797 4.760047 GTGTCGTGCGCATCCCCT 62.760 66.667 15.91 0.00 0.00 4.79
755 899 1.672881 GGGCATACGACGTACAGTACT 59.327 52.381 10.41 0.00 0.00 2.73
873 1026 1.725625 CATTTGACGGTGTGCGTGC 60.726 57.895 0.00 0.00 0.00 5.34
893 1059 1.674322 AGCATTTTACGGTGCGGCT 60.674 52.632 0.00 0.00 45.69 5.52
1002 1176 1.370051 GACGAGGCGTTTGGTTTGC 60.370 57.895 0.00 0.00 41.37 3.68
1070 1245 0.951040 GCCACCAACCAACGAGAGAG 60.951 60.000 0.00 0.00 0.00 3.20
1071 1246 1.070786 GCCACCAACCAACGAGAGA 59.929 57.895 0.00 0.00 0.00 3.10
1392 1579 4.697756 CGCTTGGGGCTGGACGAA 62.698 66.667 0.00 0.00 39.13 3.85
1533 1720 0.939577 CTGTTGTCACGTCCTCGGTG 60.940 60.000 0.00 0.00 41.85 4.94
1534 1721 1.362717 CTGTTGTCACGTCCTCGGT 59.637 57.895 0.00 0.00 41.85 4.69
1535 1722 2.022129 GCTGTTGTCACGTCCTCGG 61.022 63.158 0.00 0.00 41.85 4.63
1545 1732 1.078759 CGGGATCGTCAGCTGTTGTC 61.079 60.000 14.67 7.96 0.00 3.18
1626 1813 4.572571 AAACACCCTTCCGCCGCA 62.573 61.111 0.00 0.00 0.00 5.69
1651 1838 4.742201 GTCGAGCTCGCTGGCCAA 62.742 66.667 30.97 9.43 39.60 4.52
1686 1873 2.035783 GCCAAACCCCTGTCTCCC 59.964 66.667 0.00 0.00 0.00 4.30
1693 1880 1.530655 CCGTGAAAGCCAAACCCCT 60.531 57.895 0.00 0.00 0.00 4.79
1963 2150 4.687215 TGCCGTGCTCAGCTCACC 62.687 66.667 0.00 0.00 0.00 4.02
2035 2227 2.097110 ATACTACTGGCCGGAATCCA 57.903 50.000 21.41 1.33 0.00 3.41
2060 2252 6.775142 TGGTGAGTAGTGAAATGAAAATTCCA 59.225 34.615 0.00 0.00 0.00 3.53
2061 2253 7.174946 TCTGGTGAGTAGTGAAATGAAAATTCC 59.825 37.037 0.00 0.00 0.00 3.01
2062 2254 8.099364 TCTGGTGAGTAGTGAAATGAAAATTC 57.901 34.615 0.00 0.00 0.00 2.17
2072 2264 1.938585 CCCCTCTGGTGAGTAGTGAA 58.061 55.000 0.00 0.00 38.61 3.18
2171 2367 1.816863 AACACGCCGTGATCAGACCT 61.817 55.000 25.94 0.00 36.96 3.85
2362 2575 1.801332 CTAGCAGCGACGTACTGGT 59.199 57.895 21.84 21.84 46.82 4.00
2370 2589 1.593750 CAGGGATGCTAGCAGCGAC 60.594 63.158 25.41 20.23 46.26 5.19
2384 2603 1.172180 TTTGCCAAGAACGCTCAGGG 61.172 55.000 0.00 0.00 0.00 4.45
2390 2609 0.519961 ACCGTATTTGCCAAGAACGC 59.480 50.000 7.80 0.00 32.43 4.84
2391 2610 1.727857 GCACCGTATTTGCCAAGAACG 60.728 52.381 6.65 6.65 33.58 3.95
2392 2611 1.727857 CGCACCGTATTTGCCAAGAAC 60.728 52.381 0.00 0.00 36.57 3.01
2398 2617 2.403586 GAGCGCACCGTATTTGCC 59.596 61.111 11.47 0.00 36.57 4.52
2399 2618 2.403586 GGAGCGCACCGTATTTGC 59.596 61.111 11.47 0.00 36.57 3.68
2400 2619 2.701006 CGGAGCGCACCGTATTTG 59.299 61.111 33.92 8.88 46.70 2.32
2418 2637 4.484258 ACGCGCTCCTCTCTTCGC 62.484 66.667 5.73 0.00 43.62 4.70
2419 2638 2.578178 CACGCGCTCCTCTCTTCG 60.578 66.667 5.73 0.00 0.00 3.79
2443 2662 0.245539 CTTCCACCTAAACGGAGCGA 59.754 55.000 0.00 0.00 36.31 4.93
2446 2665 1.726853 CAGCTTCCACCTAAACGGAG 58.273 55.000 0.00 0.00 36.31 4.63
2447 2666 0.321298 GCAGCTTCCACCTAAACGGA 60.321 55.000 0.00 0.00 36.31 4.69
2448 2667 1.305930 GGCAGCTTCCACCTAAACGG 61.306 60.000 0.00 0.00 39.35 4.44
2449 2668 0.605319 TGGCAGCTTCCACCTAAACG 60.605 55.000 0.00 0.00 0.00 3.60
2450 2669 3.339547 TGGCAGCTTCCACCTAAAC 57.660 52.632 0.00 0.00 0.00 2.01
2457 2676 2.512355 TACGTGGTGGCAGCTTCCA 61.512 57.895 18.53 0.00 0.00 3.53
2458 2677 2.033194 GTACGTGGTGGCAGCTTCC 61.033 63.158 18.53 0.00 0.00 3.46
2459 2678 1.291877 CTGTACGTGGTGGCAGCTTC 61.292 60.000 18.53 9.93 0.00 3.86
2460 2679 1.301716 CTGTACGTGGTGGCAGCTT 60.302 57.895 18.53 4.84 0.00 3.74
2461 2680 1.183030 TACTGTACGTGGTGGCAGCT 61.183 55.000 18.53 0.00 32.65 4.24
2462 2681 1.012486 GTACTGTACGTGGTGGCAGC 61.012 60.000 10.30 10.30 32.65 5.25
2463 2682 0.315886 TGTACTGTACGTGGTGGCAG 59.684 55.000 12.87 1.43 35.31 4.85
2464 2683 0.315886 CTGTACTGTACGTGGTGGCA 59.684 55.000 12.87 0.00 0.00 4.92
2465 2684 1.012486 GCTGTACTGTACGTGGTGGC 61.012 60.000 12.87 6.74 0.00 5.01
2466 2685 0.315886 TGCTGTACTGTACGTGGTGG 59.684 55.000 12.87 1.34 0.00 4.61
2467 2686 1.269361 TGTGCTGTACTGTACGTGGTG 60.269 52.381 12.87 2.83 0.00 4.17
2468 2687 1.000607 CTGTGCTGTACTGTACGTGGT 60.001 52.381 12.87 0.00 0.00 4.16
2469 2688 1.668919 CCTGTGCTGTACTGTACGTGG 60.669 57.143 12.87 14.32 0.00 4.94
2472 2691 0.038618 TGCCTGTGCTGTACTGTACG 60.039 55.000 12.87 8.93 38.71 3.67
2524 2749 1.376424 CCTGTGCTGTACTGCCCTG 60.376 63.158 20.46 13.37 0.00 4.45


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

AutoCloner maintained by Alex Coulton.