Multiple sequence alignment - TraesCS6D01G335600

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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 TraesCS6D01G335600 chr6D 100.000 2654 0 0 664 3317 436832065 436834718 0.000000e+00 4902
1 TraesCS6D01G335600 chr6D 100.000 351 0 0 1 351 436831402 436831752 0.000000e+00 649
2 TraesCS6D01G335600 chr6A 91.826 2716 95 64 664 3317 585108239 585110889 0.000000e+00 3668
3 TraesCS6D01G335600 chr6A 87.535 361 9 12 8 351 585107869 585108210 5.190000e-103 385
4 TraesCS6D01G335600 chr6B 90.774 2699 98 51 670 3317 660564723 660562125 0.000000e+00 3465
5 TraesCS6D01G335600 chr6B 89.503 362 13 8 1 351 660565359 660565012 5.080000e-118 435
6 TraesCS6D01G335600 chr7D 87.209 1290 162 2 1012 2301 101783170 101781884 0.000000e+00 1465
7 TraesCS6D01G335600 chr7A 87.142 1291 161 4 1012 2301 105641655 105640369 0.000000e+00 1459
8 TraesCS6D01G335600 chr7B 86.522 1291 171 2 1012 2302 59100888 59099601 0.000000e+00 1417
9 TraesCS6D01G335600 chr7B 78.085 1013 200 20 1289 2287 204686952 204685948 3.630000e-174 621
10 TraesCS6D01G335600 chr5B 81.180 983 143 31 1289 2253 466333657 466332699 0.000000e+00 752
11 TraesCS6D01G335600 chr5D 80.957 982 147 29 1289 2253 387728912 387727954 0.000000e+00 741
12 TraesCS6D01G335600 chr5A 80.635 976 149 32 1295 2253 490816292 490815340 0.000000e+00 719


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 TraesCS6D01G335600 chr6D 436831402 436834718 3316 False 2775.5 4902 100.0000 1 3317 2 chr6D.!!$F1 3316
1 TraesCS6D01G335600 chr6A 585107869 585110889 3020 False 2026.5 3668 89.6805 8 3317 2 chr6A.!!$F1 3309
2 TraesCS6D01G335600 chr6B 660562125 660565359 3234 True 1950.0 3465 90.1385 1 3317 2 chr6B.!!$R1 3316
3 TraesCS6D01G335600 chr7D 101781884 101783170 1286 True 1465.0 1465 87.2090 1012 2301 1 chr7D.!!$R1 1289
4 TraesCS6D01G335600 chr7A 105640369 105641655 1286 True 1459.0 1459 87.1420 1012 2301 1 chr7A.!!$R1 1289
5 TraesCS6D01G335600 chr7B 59099601 59100888 1287 True 1417.0 1417 86.5220 1012 2302 1 chr7B.!!$R1 1290
6 TraesCS6D01G335600 chr7B 204685948 204686952 1004 True 621.0 621 78.0850 1289 2287 1 chr7B.!!$R2 998
7 TraesCS6D01G335600 chr5B 466332699 466333657 958 True 752.0 752 81.1800 1289 2253 1 chr5B.!!$R1 964
8 TraesCS6D01G335600 chr5D 387727954 387728912 958 True 741.0 741 80.9570 1289 2253 1 chr5D.!!$R1 964
9 TraesCS6D01G335600 chr5A 490815340 490816292 952 True 719.0 719 80.6350 1295 2253 1 chr5A.!!$R1 958


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
854 898 1.198408 CTTGCTTGCTTGCTTGATCGA 59.802 47.619 0.0 0.0 0.0 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2425 2526 0.387367 CGACGACGATCCATCCATCC 60.387 60.0 0.0 0.0 42.66 3.51 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
42 44 3.356639 GACGGACAGAGCGGCATCA 62.357 63.158 1.45 0.00 0.00 3.07
56 61 1.802636 CATCACATTCACACCCCGC 59.197 57.895 0.00 0.00 0.00 6.13
69 74 1.741032 CCCCGCCGCGTAAAAAGTA 60.741 57.895 12.58 0.00 0.00 2.24
238 266 3.411517 CCCCAACATCCTCCGCCT 61.412 66.667 0.00 0.00 0.00 5.52
239 267 2.190578 CCCAACATCCTCCGCCTC 59.809 66.667 0.00 0.00 0.00 4.70
240 268 2.202932 CCAACATCCTCCGCCTCG 60.203 66.667 0.00 0.00 0.00 4.63
241 269 2.892425 CAACATCCTCCGCCTCGC 60.892 66.667 0.00 0.00 0.00 5.03
242 270 4.162690 AACATCCTCCGCCTCGCC 62.163 66.667 0.00 0.00 0.00 5.54
288 316 1.986695 AATCCTCCCCTCCCCTACCC 61.987 65.000 0.00 0.00 0.00 3.69
852 896 1.336517 TGCTTGCTTGCTTGCTTGATC 60.337 47.619 10.35 0.00 0.00 2.92
853 897 1.614385 CTTGCTTGCTTGCTTGATCG 58.386 50.000 3.47 0.00 0.00 3.69
854 898 1.198408 CTTGCTTGCTTGCTTGATCGA 59.802 47.619 0.00 0.00 0.00 3.59
855 899 1.456296 TGCTTGCTTGCTTGATCGAT 58.544 45.000 0.00 0.00 0.00 3.59
1152 1211 4.498520 CTCGTCGCCATGACCGCT 62.499 66.667 0.00 0.00 45.23 5.52
1512 1571 1.066114 CCAAGCTCTTCGACGTCGTC 61.066 60.000 34.40 15.51 40.80 4.20
2354 2432 1.596496 GGAATTCTTCTCCTCCCCCA 58.404 55.000 5.23 0.00 0.00 4.96
2355 2433 1.923148 GGAATTCTTCTCCTCCCCCAA 59.077 52.381 5.23 0.00 0.00 4.12
2405 2503 3.119495 CCACTCCCGGATCAAACATTTTC 60.119 47.826 0.73 0.00 0.00 2.29
2442 2543 1.273606 GATGGATGGATGGATCGTCGT 59.726 52.381 0.00 0.00 0.00 4.34
2540 2648 4.836125 AAATCAATCCCGGATCGAATTG 57.164 40.909 0.73 5.14 0.00 2.32
2549 2657 3.006940 CCGGATCGAATTGTTTCCTTCA 58.993 45.455 0.00 0.00 0.00 3.02
2609 2717 7.382218 AGCGAAACCTTTTCTCATTGTTTATTG 59.618 33.333 0.00 0.00 29.89 1.90
2616 2724 7.201376 CCTTTTCTCATTGTTTATTGTCGCATG 60.201 37.037 0.00 0.00 0.00 4.06
2625 2734 8.667987 TTGTTTATTGTCGCATGTTTTATCTC 57.332 30.769 0.00 0.00 0.00 2.75
2688 2801 6.710744 TGGCTCTCGATTAGTTTCTTCTTTTT 59.289 34.615 0.00 0.00 0.00 1.94
2690 2803 7.118535 GGCTCTCGATTAGTTTCTTCTTTTTCT 59.881 37.037 0.00 0.00 0.00 2.52
2696 2809 7.387948 CGATTAGTTTCTTCTTTTTCTCTCCCA 59.612 37.037 0.00 0.00 0.00 4.37
2751 2866 9.988350 AATTAAAAGTATGTAATCTTGCTGACG 57.012 29.630 0.00 0.00 0.00 4.35
2757 2872 1.075542 TAATCTTGCTGACGCGGTTG 58.924 50.000 12.47 0.00 39.65 3.77
2764 2879 0.163146 GCTGACGCGGTTGTTCTAAC 59.837 55.000 12.47 0.00 0.00 2.34
2765 2880 1.779569 CTGACGCGGTTGTTCTAACT 58.220 50.000 12.47 0.00 0.00 2.24
2767 2882 2.542595 CTGACGCGGTTGTTCTAACTTT 59.457 45.455 12.47 0.00 0.00 2.66
2768 2883 2.540931 TGACGCGGTTGTTCTAACTTTC 59.459 45.455 12.47 0.00 0.00 2.62
2770 2885 3.981211 ACGCGGTTGTTCTAACTTTCTA 58.019 40.909 12.47 0.00 0.00 2.10
2771 2886 4.370917 ACGCGGTTGTTCTAACTTTCTAA 58.629 39.130 12.47 0.00 0.00 2.10
2772 2887 4.209911 ACGCGGTTGTTCTAACTTTCTAAC 59.790 41.667 12.47 0.00 0.00 2.34
2773 2888 4.446719 CGCGGTTGTTCTAACTTTCTAACT 59.553 41.667 0.00 0.00 0.00 2.24
2774 2889 5.630680 CGCGGTTGTTCTAACTTTCTAACTA 59.369 40.000 0.00 0.00 0.00 2.24
2775 2890 6.144402 CGCGGTTGTTCTAACTTTCTAACTAA 59.856 38.462 0.00 0.00 0.00 2.24
2777 2892 8.501580 GCGGTTGTTCTAACTTTCTAACTAAAT 58.498 33.333 0.00 0.00 0.00 1.40
2944 3064 2.403586 GGAAAATTCGCGGCGGAG 59.596 61.111 23.46 0.00 0.00 4.63
2945 3065 2.403586 GAAAATTCGCGGCGGAGG 59.596 61.111 23.46 0.00 0.00 4.30
2946 3066 2.359478 AAAATTCGCGGCGGAGGT 60.359 55.556 23.46 2.79 0.00 3.85
2947 3067 1.918868 GAAAATTCGCGGCGGAGGTT 61.919 55.000 23.46 11.92 0.00 3.50
2948 3068 1.918868 AAAATTCGCGGCGGAGGTTC 61.919 55.000 23.46 0.00 0.00 3.62
2960 3087 1.574702 GGAGGTTCCGCTTCCGTTTG 61.575 60.000 0.00 0.00 33.51 2.93
3145 3273 4.740822 ATTGGTCGGTGGCTGGGC 62.741 66.667 0.00 0.00 0.00 5.36
3195 3323 4.402528 CAACGCGGATGGGGTGGA 62.403 66.667 12.47 0.00 41.75 4.02
3201 3329 4.176752 GGATGGGGTGGAGCCGAC 62.177 72.222 0.00 0.00 38.44 4.79
3202 3330 3.399181 GATGGGGTGGAGCCGACA 61.399 66.667 0.00 0.00 38.44 4.35
3252 3390 5.880054 ACTGCATTTCTTTATTGCTACGT 57.120 34.783 0.00 0.00 37.28 3.57
3253 3391 6.978343 ACTGCATTTCTTTATTGCTACGTA 57.022 33.333 0.00 0.00 37.28 3.57
3254 3392 6.772078 ACTGCATTTCTTTATTGCTACGTAC 58.228 36.000 0.00 0.00 37.28 3.67
3273 3412 4.034510 CGTACTACGTACCAAGTTCTAGGG 59.965 50.000 0.09 0.00 35.81 3.53
3274 3413 3.359950 ACTACGTACCAAGTTCTAGGGG 58.640 50.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.096976 GTCCGTCGCATTCATTGGTG 59.903 55.000 0.00 0.00 0.00 4.17
12 13 0.321210 TGTCCGTCGCATTCATTGGT 60.321 50.000 0.00 0.00 0.00 3.67
56 61 4.206814 GGGTTGTTTTTACTTTTTACGCGG 59.793 41.667 12.47 0.00 0.00 6.46
69 74 0.531200 TTTCCGCGTGGGTTGTTTTT 59.469 45.000 16.49 0.00 37.00 1.94
788 832 4.953868 TCGGACGGGTGCACAACG 62.954 66.667 25.32 25.32 0.00 4.10
790 834 4.953868 CGTCGGACGGGTGCACAA 62.954 66.667 22.18 0.00 38.08 3.33
852 896 2.194212 ACGGACGGATGGAGGATCG 61.194 63.158 0.00 0.00 34.37 3.69
853 897 1.364171 CACGGACGGATGGAGGATC 59.636 63.158 0.00 0.00 0.00 3.36
854 898 2.134287 CCACGGACGGATGGAGGAT 61.134 63.158 0.00 0.00 38.34 3.24
855 899 2.758327 CCACGGACGGATGGAGGA 60.758 66.667 0.00 0.00 38.34 3.71
1152 1211 2.180276 GACTGGAAGCTGAGGTAGGAA 58.820 52.381 0.00 0.00 37.60 3.36
2423 2524 1.273606 GACGACGATCCATCCATCCAT 59.726 52.381 0.00 0.00 0.00 3.41
2424 2525 0.673985 GACGACGATCCATCCATCCA 59.326 55.000 0.00 0.00 0.00 3.41
2425 2526 0.387367 CGACGACGATCCATCCATCC 60.387 60.000 0.00 0.00 42.66 3.51
2426 2527 0.591659 TCGACGACGATCCATCCATC 59.408 55.000 5.75 0.00 43.81 3.51
2427 2528 2.715536 TCGACGACGATCCATCCAT 58.284 52.632 5.75 0.00 43.81 3.41
2428 2529 4.228899 TCGACGACGATCCATCCA 57.771 55.556 5.75 0.00 43.81 3.41
2442 2543 5.700832 AGACAAGAATGCTGTTAATGTTCGA 59.299 36.000 0.00 0.00 0.00 3.71
2540 2648 1.285950 GGCGCCAAGTGAAGGAAAC 59.714 57.895 24.80 0.00 0.00 2.78
2609 2717 6.654793 AAGAGAAGAGATAAAACATGCGAC 57.345 37.500 0.00 0.00 0.00 5.19
2616 2724 7.049133 GGGAGGGTAAAGAGAAGAGATAAAAC 58.951 42.308 0.00 0.00 0.00 2.43
2625 2734 4.041691 TGAACAAGGGAGGGTAAAGAGAAG 59.958 45.833 0.00 0.00 0.00 2.85
2670 2783 7.387948 TGGGAGAGAAAAAGAAGAAACTAATCG 59.612 37.037 0.00 0.00 0.00 3.34
2688 2801 6.627087 AAGTTTTAGATCATGTGGGAGAGA 57.373 37.500 0.00 0.00 0.00 3.10
2731 2846 3.551890 CGCGTCAGCAAGATTACATACTT 59.448 43.478 0.00 0.00 45.49 2.24
2732 2847 3.116300 CGCGTCAGCAAGATTACATACT 58.884 45.455 0.00 0.00 45.49 2.12
2751 2866 5.919272 AGTTAGAAAGTTAGAACAACCGC 57.081 39.130 0.00 0.00 0.00 5.68
2764 2879 9.141400 AGTTCGTAGCTTCATTTAGTTAGAAAG 57.859 33.333 0.00 0.00 0.00 2.62
2765 2880 8.922676 CAGTTCGTAGCTTCATTTAGTTAGAAA 58.077 33.333 0.00 0.00 0.00 2.52
2767 2882 7.033791 CCAGTTCGTAGCTTCATTTAGTTAGA 58.966 38.462 0.00 0.00 0.00 2.10
2768 2883 6.237861 GCCAGTTCGTAGCTTCATTTAGTTAG 60.238 42.308 0.00 0.00 0.00 2.34
2770 2885 4.392138 GCCAGTTCGTAGCTTCATTTAGTT 59.608 41.667 0.00 0.00 0.00 2.24
2771 2886 3.933332 GCCAGTTCGTAGCTTCATTTAGT 59.067 43.478 0.00 0.00 0.00 2.24
2772 2887 4.184629 AGCCAGTTCGTAGCTTCATTTAG 58.815 43.478 0.00 0.00 31.27 1.85
2773 2888 4.202245 AGCCAGTTCGTAGCTTCATTTA 57.798 40.909 0.00 0.00 31.27 1.40
2774 2889 3.059352 AGCCAGTTCGTAGCTTCATTT 57.941 42.857 0.00 0.00 31.27 2.32
2775 2890 2.770164 AGCCAGTTCGTAGCTTCATT 57.230 45.000 0.00 0.00 31.27 2.57
2777 2892 3.430374 GGATAAGCCAGTTCGTAGCTTCA 60.430 47.826 0.00 0.00 43.12 3.02
2876 2996 4.778143 CGCTTTCTCCGGGGGTGG 62.778 72.222 0.00 0.00 0.00 4.61
2918 3038 2.339556 CGAATTTTCCGGGCTGCCA 61.340 57.895 22.05 0.00 0.00 4.92
2922 3042 3.131478 CCGCGAATTTTCCGGGCT 61.131 61.111 8.23 0.00 37.37 5.19
2944 3064 2.254350 GCAAACGGAAGCGGAACC 59.746 61.111 0.00 0.00 0.00 3.62
2982 3109 1.287739 CCCTCCAAAGCTTATCCCCAA 59.712 52.381 0.00 0.00 0.00 4.12
3195 3323 2.967473 CTCGAGTGTCGTGTCGGCT 61.967 63.158 3.62 0.00 41.35 5.52
3197 3325 1.645704 ATCCTCGAGTGTCGTGTCGG 61.646 60.000 12.31 0.00 41.35 4.79
3200 3328 0.805614 CTCATCCTCGAGTGTCGTGT 59.194 55.000 12.31 0.00 41.35 4.49
3201 3329 0.524392 GCTCATCCTCGAGTGTCGTG 60.524 60.000 12.31 2.84 41.35 4.35
3202 3330 0.678366 AGCTCATCCTCGAGTGTCGT 60.678 55.000 12.31 0.00 41.35 4.34
3252 3390 4.227300 TCCCCTAGAACTTGGTACGTAGTA 59.773 45.833 0.00 0.00 45.11 1.82
3253 3391 5.986878 TTTCCCCTAGAACTTGGTACGTAGT 60.987 44.000 0.00 0.00 38.46 2.73
3254 3392 3.624777 TCCCCTAGAACTTGGTACGTAG 58.375 50.000 0.00 0.00 0.00 3.51



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

AutoCloner maintained by Alex Coulton.