Multiple sequence alignment - TraesCS1D01G330900

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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 TraesCS1D01G330900 chr1D 100.000 2474 0 0 1 2474 421086956 421084483 0.000000e+00 4569
1 TraesCS1D01G330900 chr4D 96.883 1893 56 2 1 1890 504270137 504272029 0.000000e+00 3166
2 TraesCS1D01G330900 chr4D 95.540 1906 61 11 1 1890 466289167 466291064 0.000000e+00 3027
3 TraesCS1D01G330900 chr4D 91.200 1909 128 19 3 1893 380246014 380247900 0.000000e+00 2558
4 TraesCS1D01G330900 chr7D 96.324 1904 57 5 1 1892 98406502 98404600 0.000000e+00 3116
5 TraesCS1D01G330900 chr7D 94.324 370 11 1 1 370 235569521 235569162 2.150000e-155 558
6 TraesCS1D01G330900 chr1A 95.735 1899 70 3 1 1896 493296373 493294483 0.000000e+00 3048
7 TraesCS1D01G330900 chr1A 89.077 531 25 9 1888 2415 517507390 517506890 1.610000e-176 628
8 TraesCS1D01G330900 chr3D 95.581 1901 61 7 1 1889 479622525 479624414 0.000000e+00 3024
9 TraesCS1D01G330900 chr2D 94.844 1920 67 9 1 1889 644388603 644390521 0.000000e+00 2968
10 TraesCS1D01G330900 chr2A 94.947 1900 76 6 1 1889 165347764 165345874 0.000000e+00 2959
11 TraesCS1D01G330900 chr2A 94.704 1907 83 6 1 1892 68890557 68888654 0.000000e+00 2946
12 TraesCS1D01G330900 chr5D 94.372 1919 62 11 1 1892 424049259 424047360 0.000000e+00 2904
13 TraesCS1D01G330900 chr6A 94.429 1849 91 5 55 1892 479912809 479910962 0.000000e+00 2833
14 TraesCS1D01G330900 chr7B 91.359 1921 117 25 1 1892 389093151 389095051 0.000000e+00 2582
15 TraesCS1D01G330900 chr7A 92.040 402 23 3 1 393 527988336 527988737 7.730000e-155 556
16 TraesCS1D01G330900 chr5A 95.820 311 13 0 1 311 651645118 651644808 1.020000e-138 503
17 TraesCS1D01G330900 chr1B 92.537 335 14 6 2103 2436 570487163 570486839 1.040000e-128 470
18 TraesCS1D01G330900 chr1B 92.143 280 10 6 1888 2157 570487425 570487148 3.860000e-103 385


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 TraesCS1D01G330900 chr1D 421084483 421086956 2473 True 4569.0 4569 100.000 1 2474 1 chr1D.!!$R1 2473
1 TraesCS1D01G330900 chr4D 504270137 504272029 1892 False 3166.0 3166 96.883 1 1890 1 chr4D.!!$F3 1889
2 TraesCS1D01G330900 chr4D 466289167 466291064 1897 False 3027.0 3027 95.540 1 1890 1 chr4D.!!$F2 1889
3 TraesCS1D01G330900 chr4D 380246014 380247900 1886 False 2558.0 2558 91.200 3 1893 1 chr4D.!!$F1 1890
4 TraesCS1D01G330900 chr7D 98404600 98406502 1902 True 3116.0 3116 96.324 1 1892 1 chr7D.!!$R1 1891
5 TraesCS1D01G330900 chr1A 493294483 493296373 1890 True 3048.0 3048 95.735 1 1896 1 chr1A.!!$R1 1895
6 TraesCS1D01G330900 chr1A 517506890 517507390 500 True 628.0 628 89.077 1888 2415 1 chr1A.!!$R2 527
7 TraesCS1D01G330900 chr3D 479622525 479624414 1889 False 3024.0 3024 95.581 1 1889 1 chr3D.!!$F1 1888
8 TraesCS1D01G330900 chr2D 644388603 644390521 1918 False 2968.0 2968 94.844 1 1889 1 chr2D.!!$F1 1888
9 TraesCS1D01G330900 chr2A 165345874 165347764 1890 True 2959.0 2959 94.947 1 1889 1 chr2A.!!$R2 1888
10 TraesCS1D01G330900 chr2A 68888654 68890557 1903 True 2946.0 2946 94.704 1 1892 1 chr2A.!!$R1 1891
11 TraesCS1D01G330900 chr5D 424047360 424049259 1899 True 2904.0 2904 94.372 1 1892 1 chr5D.!!$R1 1891
12 TraesCS1D01G330900 chr6A 479910962 479912809 1847 True 2833.0 2833 94.429 55 1892 1 chr6A.!!$R1 1837
13 TraesCS1D01G330900 chr7B 389093151 389095051 1900 False 2582.0 2582 91.359 1 1892 1 chr7B.!!$F1 1891
14 TraesCS1D01G330900 chr1B 570486839 570487425 586 True 427.5 470 92.340 1888 2436 2 chr1B.!!$R1 548

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
413 438 0.330604 AGCCGTCTCCCAGTACACTA 59.669 55.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 2164 0.107459 GAGAGGGATTGGACCTGTGC 60.107 60.0 0.0 0.0 38.79 4.57 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
76 77 7.147776 GGGGTAGTTCATACTAGTTCTTAGCAA 60.148 40.741 0.00 0.00 37.53 3.91
127 131 5.305585 GGAATGCATAAGGTAGATTTCGGA 58.694 41.667 0.00 0.00 0.00 4.55
312 336 2.893398 CCAGGTAGGACGGACTGC 59.107 66.667 0.00 0.00 41.22 4.40
413 438 0.330604 AGCCGTCTCCCAGTACACTA 59.669 55.000 0.00 0.00 0.00 2.74
597 624 1.031571 GCCTTCATGACCGGCATTCA 61.032 55.000 23.68 0.00 43.25 2.57
639 666 2.430921 AGCCGAAGTTCGAGCACG 60.431 61.111 28.36 14.89 43.74 5.34
1128 1174 0.907704 ACGGCCACTACCATCAGGAA 60.908 55.000 2.24 0.00 38.69 3.36
1325 1375 3.643554 GGGTTGGGCCACCTACGT 61.644 66.667 19.97 0.00 42.49 3.57
1458 1510 2.279918 AAGCACGACGACGCCTTT 60.280 55.556 7.30 0.00 43.96 3.11
1461 1513 3.036084 CACGACGACGCCTTTGCT 61.036 61.111 7.30 0.00 43.96 3.91
1618 1682 2.228582 TGTTGTGCTTATGATGTGTGCC 59.771 45.455 0.00 0.00 0.00 5.01
1714 1778 1.205417 CATGCCTTGGATTTGTGGACC 59.795 52.381 0.00 0.00 0.00 4.46
1723 1787 2.234414 GGATTTGTGGACCAACATGCAT 59.766 45.455 0.00 0.00 31.20 3.96
1793 1859 2.034878 TGCAGGCAACCAAACAACATA 58.965 42.857 0.00 0.00 37.17 2.29
1949 2015 3.474570 CGCCCTTCCCTCCTGGAG 61.475 72.222 17.02 17.02 46.24 3.86
2222 2340 5.105997 GGATATTTGATGGGCTATTGCTGAC 60.106 44.000 0.00 0.00 39.59 3.51
2239 2357 3.065095 GCTGACACTTACCGGAGTACTAG 59.935 52.174 9.46 2.18 0.00 2.57
2372 2490 1.798813 CAGCCAACTCCGAACAAGTAC 59.201 52.381 0.00 0.00 0.00 2.73
2385 2503 2.695359 ACAAGTACGCATGGTTACCAG 58.305 47.619 10.74 3.44 36.75 4.00
2428 2547 6.746745 TTTATTACCTCGCGGAATTTTCTT 57.253 33.333 6.13 0.00 0.00 2.52
2429 2548 4.616181 ATTACCTCGCGGAATTTTCTTG 57.384 40.909 6.13 0.00 0.00 3.02
2430 2549 2.178912 ACCTCGCGGAATTTTCTTGA 57.821 45.000 6.13 0.00 0.00 3.02
2431 2550 1.804748 ACCTCGCGGAATTTTCTTGAC 59.195 47.619 6.13 0.00 0.00 3.18
2433 2552 2.159653 CCTCGCGGAATTTTCTTGACTG 60.160 50.000 6.13 0.00 0.00 3.51
2434 2553 2.480419 CTCGCGGAATTTTCTTGACTGT 59.520 45.455 6.13 0.00 0.00 3.55
2435 2554 3.655486 TCGCGGAATTTTCTTGACTGTA 58.345 40.909 6.13 0.00 0.00 2.74
2436 2555 4.250464 TCGCGGAATTTTCTTGACTGTAT 58.750 39.130 6.13 0.00 0.00 2.29
2437 2556 4.092821 TCGCGGAATTTTCTTGACTGTATG 59.907 41.667 6.13 0.00 0.00 2.39
2438 2557 4.142902 CGCGGAATTTTCTTGACTGTATGT 60.143 41.667 0.00 0.00 0.00 2.29
2439 2558 5.088739 GCGGAATTTTCTTGACTGTATGTG 58.911 41.667 0.00 0.00 0.00 3.21
2440 2559 5.088739 CGGAATTTTCTTGACTGTATGTGC 58.911 41.667 0.00 0.00 0.00 4.57
2441 2560 5.088739 GGAATTTTCTTGACTGTATGTGCG 58.911 41.667 0.00 0.00 0.00 5.34
2442 2561 5.334879 GGAATTTTCTTGACTGTATGTGCGT 60.335 40.000 0.00 0.00 0.00 5.24
2443 2562 4.466567 TTTTCTTGACTGTATGTGCGTG 57.533 40.909 0.00 0.00 0.00 5.34
2444 2563 2.812358 TCTTGACTGTATGTGCGTGT 57.188 45.000 0.00 0.00 0.00 4.49
2445 2564 3.926821 TCTTGACTGTATGTGCGTGTA 57.073 42.857 0.00 0.00 0.00 2.90
2446 2565 4.450082 TCTTGACTGTATGTGCGTGTAT 57.550 40.909 0.00 0.00 0.00 2.29
2447 2566 4.421058 TCTTGACTGTATGTGCGTGTATC 58.579 43.478 0.00 0.00 0.00 2.24
2448 2567 4.157840 TCTTGACTGTATGTGCGTGTATCT 59.842 41.667 0.00 0.00 0.00 1.98
2449 2568 5.355910 TCTTGACTGTATGTGCGTGTATCTA 59.644 40.000 0.00 0.00 0.00 1.98
2450 2569 5.570234 TGACTGTATGTGCGTGTATCTAA 57.430 39.130 0.00 0.00 0.00 2.10
2451 2570 5.337554 TGACTGTATGTGCGTGTATCTAAC 58.662 41.667 0.00 0.00 0.00 2.34
2452 2571 4.679662 ACTGTATGTGCGTGTATCTAACC 58.320 43.478 0.00 0.00 0.00 2.85
2453 2572 4.158949 ACTGTATGTGCGTGTATCTAACCA 59.841 41.667 0.00 0.00 0.00 3.67
2454 2573 4.426416 TGTATGTGCGTGTATCTAACCAC 58.574 43.478 0.00 0.00 0.00 4.16
2455 2574 3.603158 ATGTGCGTGTATCTAACCACA 57.397 42.857 0.00 0.00 35.03 4.17
2456 2575 2.954316 TGTGCGTGTATCTAACCACAG 58.046 47.619 0.00 0.00 30.42 3.66
2457 2576 2.559231 TGTGCGTGTATCTAACCACAGA 59.441 45.455 0.00 0.00 30.42 3.41
2458 2577 3.194755 TGTGCGTGTATCTAACCACAGAT 59.805 43.478 0.00 0.00 38.76 2.90
2459 2578 3.551890 GTGCGTGTATCTAACCACAGATG 59.448 47.826 0.00 0.00 35.99 2.90
2460 2579 3.194755 TGCGTGTATCTAACCACAGATGT 59.805 43.478 0.00 0.00 35.99 3.06
2461 2580 3.551890 GCGTGTATCTAACCACAGATGTG 59.448 47.826 5.97 5.97 45.23 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 6.986231 TCTTGCATGTATGAACTCGTATGAAT 59.014 34.615 0.00 0.00 0.00 2.57
127 131 3.277971 CCTATTCCCCTATCCCCCAATT 58.722 50.000 0.00 0.00 0.00 2.32
265 289 3.437795 GACTCCGCCGAGGACGAA 61.438 66.667 7.01 0.00 45.98 3.85
312 336 4.899239 CAGCTAGGGCGCCGAAGG 62.899 72.222 22.54 11.55 44.28 3.46
413 438 1.153901 CTAATGACCGTCGTGCCGT 60.154 57.895 0.00 0.00 0.00 5.68
421 446 0.617820 ACTGGGCTCCTAATGACCGT 60.618 55.000 0.00 0.00 0.00 4.83
639 666 1.541588 GTTTGAGAACACCATGGAGGC 59.458 52.381 21.47 7.49 43.14 4.70
1045 1089 2.187163 GCCACCCTTAGGCGTCTC 59.813 66.667 0.00 0.00 43.15 3.36
1054 1098 4.052229 CTCGTCGTCGCCACCCTT 62.052 66.667 0.00 0.00 36.96 3.95
1128 1174 1.004044 CAGAAGTGAGTTGGGCCATCT 59.996 52.381 16.89 16.89 0.00 2.90
1325 1375 4.557496 CGATCTTGATCTGATGAACGGCTA 60.557 45.833 8.70 0.00 0.00 3.93
1458 1510 2.971598 GCCCTACTCCTTGGCAGCA 61.972 63.158 0.00 0.00 44.70 4.41
1618 1682 1.301087 TTACCACCACACTTCGGCG 60.301 57.895 0.00 0.00 0.00 6.46
1704 1768 2.613474 GCATGCATGTTGGTCCACAAAT 60.613 45.455 26.79 0.00 41.58 2.32
1714 1778 2.032722 GTGTTTGGTTGCATGCATGTTG 60.033 45.455 26.79 4.87 0.00 3.33
1723 1787 1.674764 CTGCCTGGTGTTTGGTTGCA 61.675 55.000 0.00 0.00 0.00 4.08
1793 1859 3.005472 GCAGCCTCAAATGCATCATATGT 59.995 43.478 0.00 0.00 42.11 2.29
2049 2122 3.213402 GAGGGGACGAGCGGAGAG 61.213 72.222 0.00 0.00 0.00 3.20
2089 2164 0.107459 GAGAGGGATTGGACCTGTGC 60.107 60.000 0.00 0.00 38.79 4.57
2190 2308 2.325082 ATCAAATATCCGCCGCCGC 61.325 57.895 0.00 0.00 0.00 6.53
2191 2309 1.497278 CATCAAATATCCGCCGCCG 59.503 57.895 0.00 0.00 0.00 6.46
2354 2472 0.788391 CGTACTTGTTCGGAGTTGGC 59.212 55.000 0.00 0.00 0.00 4.52
2359 2477 0.999406 CCATGCGTACTTGTTCGGAG 59.001 55.000 2.37 0.00 0.00 4.63
2372 2490 5.054390 ACAAATTTACTGGTAACCATGCG 57.946 39.130 0.00 0.00 30.82 4.73
2426 2545 4.424626 AGATACACGCACATACAGTCAAG 58.575 43.478 0.00 0.00 0.00 3.02
2428 2547 5.337554 GTTAGATACACGCACATACAGTCA 58.662 41.667 0.00 0.00 0.00 3.41
2429 2548 4.738740 GGTTAGATACACGCACATACAGTC 59.261 45.833 0.00 0.00 0.00 3.51
2430 2549 4.158949 TGGTTAGATACACGCACATACAGT 59.841 41.667 0.00 0.00 0.00 3.55
2431 2550 4.503007 GTGGTTAGATACACGCACATACAG 59.497 45.833 0.00 0.00 0.00 2.74
2433 2552 4.426416 TGTGGTTAGATACACGCACATAC 58.574 43.478 0.00 0.00 40.39 2.39
2434 2553 4.399934 TCTGTGGTTAGATACACGCACATA 59.600 41.667 0.00 0.00 40.39 2.29
2435 2554 3.194755 TCTGTGGTTAGATACACGCACAT 59.805 43.478 0.00 0.00 40.39 3.21
2436 2555 2.559231 TCTGTGGTTAGATACACGCACA 59.441 45.455 0.00 0.00 40.39 4.57
2437 2556 3.226346 TCTGTGGTTAGATACACGCAC 57.774 47.619 0.00 0.00 40.39 5.34
2438 2557 3.194755 ACATCTGTGGTTAGATACACGCA 59.805 43.478 0.00 0.00 40.39 5.24
2439 2558 3.551890 CACATCTGTGGTTAGATACACGC 59.448 47.826 2.29 0.00 42.10 5.34
2440 2559 4.993905 TCACATCTGTGGTTAGATACACG 58.006 43.478 10.26 0.00 45.65 4.49
2441 2560 7.201644 CCATTTCACATCTGTGGTTAGATACAC 60.202 40.741 10.26 0.00 45.65 2.90
2442 2561 6.823182 CCATTTCACATCTGTGGTTAGATACA 59.177 38.462 10.26 0.00 45.65 2.29
2443 2562 7.011482 GTCCATTTCACATCTGTGGTTAGATAC 59.989 40.741 10.26 0.00 45.65 2.24
2444 2563 7.047891 GTCCATTTCACATCTGTGGTTAGATA 58.952 38.462 10.26 0.00 45.65 1.98
2445 2564 5.882557 GTCCATTTCACATCTGTGGTTAGAT 59.117 40.000 10.26 0.00 45.65 1.98
2446 2565 5.013079 AGTCCATTTCACATCTGTGGTTAGA 59.987 40.000 10.26 0.02 45.65 2.10
2447 2566 5.248640 AGTCCATTTCACATCTGTGGTTAG 58.751 41.667 10.26 0.00 45.65 2.34
2448 2567 5.241403 AGTCCATTTCACATCTGTGGTTA 57.759 39.130 10.26 0.00 45.65 2.85
2449 2568 4.104383 AGTCCATTTCACATCTGTGGTT 57.896 40.909 10.26 0.00 45.65 3.67
2450 2569 3.795688 AGTCCATTTCACATCTGTGGT 57.204 42.857 10.26 0.00 45.65 4.16
2451 2570 4.801891 CAAAGTCCATTTCACATCTGTGG 58.198 43.478 10.26 0.00 45.65 4.17


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

AutoCloner maintained by Alex Coulton.