AutoCloner

Multiple sequence alignment - TraesCS7D01G427100

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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	TraesCS7D01G427100	chr7D	100.000	2966	0	0	1	2966	548206207	548209172	0.000000e+00	5478.0
1	TraesCS7D01G427100	chr7D	88.346	1064	64	11	1924	2961	463877211	463876182	0.000000e+00	1223.0
2	TraesCS7D01G427100	chr7D	83.102	361	35	14	1	350	3761784	3762129	3.710000e-79	305.0
3	TraesCS7D01G427100	chr3D	95.251	1074	13	7	1916	2966	28478496	28479554	0.000000e+00	1666.0
4	TraesCS7D01G427100	chr3D	99.264	815	6	0	2152	2966	40718834	40718020	0.000000e+00	1472.0
5	TraesCS7D01G427100	chr3D	88.341	669	50	22	336	999	560881821	560882466	0.000000e+00	778.0
6	TraesCS7D01G427100	chr3D	93.043	115	7	1	1936	2050	40718976	40718863	1.830000e-37	167.0
7	TraesCS7D01G427100	chr3D	89.216	102	9	2	1	101	520706564	520706664	3.100000e-25	126.0
8	TraesCS7D01G427100	chr6D	94.577	1051	14	12	1935	2966	24030315	24031341	0.000000e+00	1585.0
9	TraesCS7D01G427100	chr6D	98.345	423	7	0	336	758	437169924	437170346	0.000000e+00	743.0
10	TraesCS7D01G427100	chr6D	99.612	258	1	0	2709	2966	246208417	246208160	3.460000e-129	472.0
11	TraesCS7D01G427100	chr6D	83.292	407	43	11	595	999	303524669	303524286	4.700000e-93	351.0
12	TraesCS7D01G427100	chr7A	95.657	921	40	0	999	1919	631978713	631979633	0.000000e+00	1480.0
13	TraesCS7D01G427100	chr7A	91.776	839	49	11	176	999	10532245	10531412	0.000000e+00	1149.0
14	TraesCS7D01G427100	chr7B	95.440	921	38	4	1000	1919	591452717	591453634	0.000000e+00	1465.0
15	TraesCS7D01G427100	chr7B	88.350	103	11	1	1	102	605365220	605365322	4.010000e-24	122.0
16	TraesCS7D01G427100	chr4B	92.991	1013	41	4	1	999	14623146	14624142	0.000000e+00	1450.0
17	TraesCS7D01G427100	chr4B	81.887	795	116	11	1084	1864	636987832	636987052	0.000000e+00	645.0
18	TraesCS7D01G427100	chr4B	92.632	190	13	1	811	999	14623192	14623003	3.770000e-69	272.0
19	TraesCS7D01G427100	chr4B	93.478	46	3	0	1874	1919	636987024	636986979	5.300000e-08	69.4
20	TraesCS7D01G427100	chr3B	90.200	1051	68	6	1943	2966	782651446	782650404	0.000000e+00	1338.0
21	TraesCS7D01G427100	chr3B	82.548	361	49	4	1	350	106659274	106658917	3.710000e-79	305.0
22	TraesCS7D01G427100	chr5B	91.344	982	45	9	42	999	481956556	481955591	0.000000e+00	1306.0
23	TraesCS7D01G427100	chr5B	88.839	224	24	1	777	999	481956505	481956728	1.050000e-69	274.0
24	TraesCS7D01G427100	chr4A	89.649	1053	68	14	1941	2966	343932908	343933946	0.000000e+00	1303.0
25	TraesCS7D01G427100	chr4D	88.761	1041	60	31	1942	2966	450714181	450715180	0.000000e+00	1221.0
26	TraesCS7D01G427100	chr4D	88.241	1046	62	11	1942	2961	134536826	134537836	0.000000e+00	1194.0
27	TraesCS7D01G427100	chr2D	87.011	1047	73	15	1942	2961	93808369	93809379	0.000000e+00	1122.0
28	TraesCS7D01G427100	chr2D	93.548	93	6	0	1	93	50040749	50040657	3.990000e-29	139.0
29	TraesCS7D01G427100	chrUn	87.680	901	82	20	122	998	331457368	331456473	0.000000e+00	1022.0
30	TraesCS7D01G427100	chrUn	87.295	913	87	17	110	998	71415030	71415937	0.000000e+00	1016.0
31	TraesCS7D01G427100	chrUn	87.140	902	94	9	110	998	71474092	71474984	0.000000e+00	1003.0
32	TraesCS7D01G427100	chrUn	87.961	407	34	6	595	999	103514763	103515156	1.610000e-127	466.0
33	TraesCS7D01G427100	chrUn	88.433	268	24	6	202	465	103514346	103514610	1.720000e-82	316.0
34	TraesCS7D01G427100	chrUn	81.163	361	55	6	1	350	103514066	103514424	8.100000e-71	278.0
35	TraesCS7D01G427100	chr1A	84.106	1057	102	21	1943	2966	55131564	55132587	0.000000e+00	961.0
36	TraesCS7D01G427100	chr5D	97.552	531	13	0	171	701	217296047	217295517	0.000000e+00	909.0
37	TraesCS7D01G427100	chr1D	83.047	407	43	12	595	999	355173277	355173659	2.190000e-91	346.0
38	TraesCS7D01G427100	chr2B	84.979	233	29	6	770	999	776689024	776689253	6.390000e-57	231.0
39	TraesCS7D01G427100	chr6B	91.398	93	8	0	1	93	2795353	2795445	8.630000e-26	128.0
40	TraesCS7D01G427100	chr6A	88.350	103	11	1	1	102	192837275	192837377	4.010000e-24	122.0
41	TraesCS7D01G427100	chr3A	84.615	91	10	4	2182	2271	1738303	1738216	1.460000e-13	87.9

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	TraesCS7D01G427100	chr7D	548206207	548209172	2965	False	5478.000000	5478	100.000000	1	2966	1	chr7D.!!$F2	2965
1	TraesCS7D01G427100	chr7D	463876182	463877211	1029	True	1223.000000	1223	88.346000	1924	2961	1	chr7D.!!$R1	1037
2	TraesCS7D01G427100	chr3D	28478496	28479554	1058	False	1666.000000	1666	95.251000	1916	2966	1	chr3D.!!$F1	1050
3	TraesCS7D01G427100	chr3D	40718020	40718976	956	True	819.500000	1472	96.153500	1936	2966	2	chr3D.!!$R1	1030
4	TraesCS7D01G427100	chr3D	560881821	560882466	645	False	778.000000	778	88.341000	336	999	1	chr3D.!!$F3	663
5	TraesCS7D01G427100	chr6D	24030315	24031341	1026	False	1585.000000	1585	94.577000	1935	2966	1	chr6D.!!$F1	1031
6	TraesCS7D01G427100	chr7A	631978713	631979633	920	False	1480.000000	1480	95.657000	999	1919	1	chr7A.!!$F1	920
7	TraesCS7D01G427100	chr7A	10531412	10532245	833	True	1149.000000	1149	91.776000	176	999	1	chr7A.!!$R1	823
8	TraesCS7D01G427100	chr7B	591452717	591453634	917	False	1465.000000	1465	95.440000	1000	1919	1	chr7B.!!$F1	919
9	TraesCS7D01G427100	chr4B	14623146	14624142	996	False	1450.000000	1450	92.991000	1	999	1	chr4B.!!$F1	998
10	TraesCS7D01G427100	chr4B	636986979	636987832	853	True	357.200000	645	87.682500	1084	1919	2	chr4B.!!$R2	835
11	TraesCS7D01G427100	chr3B	782650404	782651446	1042	True	1338.000000	1338	90.200000	1943	2966	1	chr3B.!!$R2	1023
12	TraesCS7D01G427100	chr5B	481955591	481956556	965	True	1306.000000	1306	91.344000	42	999	1	chr5B.!!$R1	957
13	TraesCS7D01G427100	chr4A	343932908	343933946	1038	False	1303.000000	1303	89.649000	1941	2966	1	chr4A.!!$F1	1025
14	TraesCS7D01G427100	chr4D	450714181	450715180	999	False	1221.000000	1221	88.761000	1942	2966	1	chr4D.!!$F2	1024
15	TraesCS7D01G427100	chr4D	134536826	134537836	1010	False	1194.000000	1194	88.241000	1942	2961	1	chr4D.!!$F1	1019
16	TraesCS7D01G427100	chr2D	93808369	93809379	1010	False	1122.000000	1122	87.011000	1942	2961	1	chr2D.!!$F1	1019
17	TraesCS7D01G427100	chrUn	331456473	331457368	895	True	1022.000000	1022	87.680000	122	998	1	chrUn.!!$R1	876
18	TraesCS7D01G427100	chrUn	71415030	71415937	907	False	1016.000000	1016	87.295000	110	998	1	chrUn.!!$F1	888
19	TraesCS7D01G427100	chrUn	71474092	71474984	892	False	1003.000000	1003	87.140000	110	998	1	chrUn.!!$F2	888
20	TraesCS7D01G427100	chrUn	103514066	103515156	1090	False	353.333333	466	85.852333	1	999	3	chrUn.!!$F3	998
21	TraesCS7D01G427100	chr1A	55131564	55132587	1023	False	961.000000	961	84.106000	1943	2966	1	chr1A.!!$F1	1023
22	TraesCS7D01G427100	chr5D	217295517	217296047	530	True	909.000000	909	97.552000	171	701	1	chr5D.!!$R1	530

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
74	75	1.448985	CGTTAACTGACATGTGGGGG	58.551	55.0	1.15	0.0	0.0	5.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1976	2321	0.037326	TCGCTGTGTGGCTTTAGAGG	60.037	55.0	0.0	0.0	0.0	3.69	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
26	27	3.404438	TCGGGCCCGCACCTAAAT	61.404	61.111	39.89	0.00	39.59	1.40
74	75	1.448985	CGTTAACTGACATGTGGGGG	58.551	55.000	1.15	0.00	0.00	5.40
102	103	3.244561	TGTGAGTGTCTCTCCCCATTTTC	60.245	47.826	0.00	0.00	42.12	2.29
138	160	4.402155	GCAATCTTCTTCTCCTCTCTCTCA	59.598	45.833	0.00	0.00	0.00	3.27
321	425	3.958860	GCTGCCACCACCTCCAGT	61.959	66.667	0.00	0.00	0.00	4.00
473	588	4.722700	TGGCCGGCAAGGAGCTTC	62.723	66.667	30.85	7.78	45.00	3.86
477	592	4.767255	CGGCAAGGAGCTTCGCCT	62.767	66.667	9.04	0.00	42.59	5.52
478	593	3.130160	GGCAAGGAGCTTCGCCTG	61.130	66.667	3.75	0.00	44.79	4.85
479	594	3.130160	GCAAGGAGCTTCGCCTGG	61.130	66.667	0.00	0.00	41.15	4.45
480	595	2.665000	CAAGGAGCTTCGCCTGGA	59.335	61.111	0.00	0.00	33.05	3.86
481	596	1.743252	CAAGGAGCTTCGCCTGGAC	60.743	63.158	0.00	0.00	33.05	4.02
482	597	2.960688	AAGGAGCTTCGCCTGGACC	61.961	63.158	0.00	0.00	33.05	4.46
483	598	4.475135	GGAGCTTCGCCTGGACCC	62.475	72.222	0.00	0.00	0.00	4.46
484	599	3.394836	GAGCTTCGCCTGGACCCT	61.395	66.667	0.00	0.00	0.00	4.34
485	600	3.378399	GAGCTTCGCCTGGACCCTC	62.378	68.421	0.00	0.00	0.00	4.30
486	601	4.821589	GCTTCGCCTGGACCCTCG	62.822	72.222	0.00	0.00	0.00	4.63
487	602	4.821589	CTTCGCCTGGACCCTCGC	62.822	72.222	0.00	0.00	0.00	5.03
548	827	4.457496	CGACCTGGCATGCGACCT	62.457	66.667	12.44	0.00	0.00	3.85
549	828	2.045926	GACCTGGCATGCGACCTT	60.046	61.111	12.44	0.00	0.00	3.50
550	829	2.360350	ACCTGGCATGCGACCTTG	60.360	61.111	12.44	0.00	0.00	3.61
551	830	3.818787	CCTGGCATGCGACCTTGC	61.819	66.667	12.44	0.00	40.36	4.01
555	834	3.869272	GCATGCGACCTTGCCGAG	61.869	66.667	0.00	0.00	36.44	4.63
556	835	3.869272	CATGCGACCTTGCCGAGC	61.869	66.667	0.00	0.00	0.00	5.03
561	840	4.070552	GACCTTGCCGAGCCGTCT	62.071	66.667	0.00	0.00	0.00	4.18
562	841	3.991536	GACCTTGCCGAGCCGTCTC	62.992	68.421	0.00	0.00	35.99	3.36
563	842	4.821589	CCTTGCCGAGCCGTCTCC	62.822	72.222	0.00	0.00	35.94	3.71
564	843	3.764466	CTTGCCGAGCCGTCTCCT	61.764	66.667	0.00	0.00	35.94	3.69
565	844	3.302347	CTTGCCGAGCCGTCTCCTT	62.302	63.158	0.00	0.00	35.94	3.36
566	845	3.296709	TTGCCGAGCCGTCTCCTTC	62.297	63.158	0.00	0.00	35.94	3.46
567	846	4.516195	GCCGAGCCGTCTCCTTCC	62.516	72.222	0.00	0.00	35.94	3.46
568	847	3.839432	CCGAGCCGTCTCCTTCCC	61.839	72.222	0.00	0.00	35.94	3.97
569	848	2.756283	CGAGCCGTCTCCTTCCCT	60.756	66.667	0.00	0.00	35.94	4.20
570	849	2.896443	GAGCCGTCTCCTTCCCTG	59.104	66.667	0.00	0.00	33.19	4.45
571	850	1.682684	GAGCCGTCTCCTTCCCTGA	60.683	63.158	0.00	0.00	33.19	3.86
572	851	1.950973	GAGCCGTCTCCTTCCCTGAC	61.951	65.000	0.00	0.00	33.19	3.51
573	852	3.020237	GCCGTCTCCTTCCCTGACC	62.020	68.421	0.00	0.00	0.00	4.02
574	853	2.359967	CCGTCTCCTTCCCTGACCC	61.360	68.421	0.00	0.00	0.00	4.46
575	854	2.711922	CGTCTCCTTCCCTGACCCG	61.712	68.421	0.00	0.00	0.00	5.28
576	855	2.683933	TCTCCTTCCCTGACCCGC	60.684	66.667	0.00	0.00	0.00	6.13
577	856	4.148825	CTCCTTCCCTGACCCGCG	62.149	72.222	0.00	0.00	0.00	6.46
741	1022	9.561069	TGCTTTTTAAAAATATTTACAAGGGCA	57.439	25.926	13.55	11.53	33.78	5.36
1012	1322	8.985315	TGCTATTTACTCAATGGAATCAGATT	57.015	30.769	0.00	0.00	0.00	2.40
1032	1342	2.001812	CTGTCAACAGAGATGACCCG	57.998	55.000	4.05	0.00	46.59	5.28
1155	1466	3.044305	AGCGCGCTGTTTCCAGAC	61.044	61.111	36.13	0.00	41.50	3.51
1329	1640	1.369448	CTACGCTGATCCTCGTCGC	60.369	63.158	11.78	0.00	39.79	5.19
1338	1649	4.796231	CCTCGTCGCGGAAGTGGG	62.796	72.222	6.13	0.00	43.13	4.61
1448	1759	2.793946	GCATACCTGCCAACTGCG	59.206	61.111	0.00	0.00	45.60	5.18
1573	1888	4.872124	TGATCTTCGACATCACAGAAATGG	59.128	41.667	2.65	0.00	0.00	3.16
1689	2013	2.032054	TGCGAGTGCTTTCAAGTTCTTG	59.968	45.455	6.24	6.24	43.34	3.02
1844	2168	3.251571	CAAGAGGACGTGGTAACTTAGC	58.748	50.000	0.00	0.00	37.61	3.09
2394	2781	0.957362	TCGAGATGCATCTGAGCGAT	59.043	50.000	33.33	8.09	37.25	4.58
2616	3003	7.040409	ACTCTCTTTTGCTTAAATTACTGTGGG	60.040	37.037	0.00	0.00	0.00	4.61

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
74	75	0.037790	GAGAGACACTCACAGGTGGC	60.038	60.000	0.00	0.00	44.95	5.01
83	84	3.990959	AGAAAATGGGGAGAGACACTC	57.009	47.619	0.00	0.00	44.24	3.51
102	103	6.322201	AGAAGAAGATTGCTAGAGAGGAGAAG	59.678	42.308	0.00	0.00	0.00	2.85
138	160	2.048503	GTGTGCTTCGGCGTAGGT	60.049	61.111	15.34	0.00	45.37	3.08
483	598	4.521062	CTTCTCCAGGCGGGCGAG	62.521	72.222	0.00	0.00	36.21	5.03
534	813	3.818787	GCAAGGTCGCATGCCAGG	61.819	66.667	13.15	0.00	36.56	4.45
538	817	3.869272	CTCGGCAAGGTCGCATGC	61.869	66.667	7.91	7.91	41.82	4.06
539	818	3.869272	GCTCGGCAAGGTCGCATG	61.869	66.667	0.00	0.00	0.00	4.06
544	823	3.991536	GAGACGGCTCGGCAAGGTC	62.992	68.421	0.41	3.05	37.34	3.85
545	824	4.070552	GAGACGGCTCGGCAAGGT	62.071	66.667	0.41	0.00	37.34	3.50
546	825	4.821589	GGAGACGGCTCGGCAAGG	62.822	72.222	13.25	0.00	42.25	3.61
547	826	3.302347	AAGGAGACGGCTCGGCAAG	62.302	63.158	13.25	0.00	42.25	4.01
548	827	3.296709	GAAGGAGACGGCTCGGCAA	62.297	63.158	13.25	0.00	42.25	4.52
549	828	3.760035	GAAGGAGACGGCTCGGCA	61.760	66.667	13.25	0.00	42.25	5.69
550	829	4.516195	GGAAGGAGACGGCTCGGC	62.516	72.222	13.25	3.48	42.25	5.54
551	830	3.839432	GGGAAGGAGACGGCTCGG	61.839	72.222	13.25	0.00	42.25	4.63
552	831	2.756283	AGGGAAGGAGACGGCTCG	60.756	66.667	13.25	0.00	42.25	5.03
553	832	1.682684	TCAGGGAAGGAGACGGCTC	60.683	63.158	10.76	10.76	40.54	4.70
554	833	1.985116	GTCAGGGAAGGAGACGGCT	60.985	63.158	0.00	0.00	0.00	5.52
555	834	2.579738	GTCAGGGAAGGAGACGGC	59.420	66.667	0.00	0.00	0.00	5.68
556	835	2.359967	GGGTCAGGGAAGGAGACGG	61.360	68.421	0.00	0.00	33.18	4.79
557	836	2.711922	CGGGTCAGGGAAGGAGACG	61.712	68.421	0.00	0.00	33.18	4.18
558	837	3.020237	GCGGGTCAGGGAAGGAGAC	62.020	68.421	0.00	0.00	0.00	3.36
559	838	2.683933	GCGGGTCAGGGAAGGAGA	60.684	66.667	0.00	0.00	0.00	3.71
560	839	4.148825	CGCGGGTCAGGGAAGGAG	62.149	72.222	0.00	0.00	0.00	3.69
561	840	4.689549	TCGCGGGTCAGGGAAGGA	62.690	66.667	6.13	0.00	0.00	3.36
562	841	4.452733	GTCGCGGGTCAGGGAAGG	62.453	72.222	6.13	0.00	34.84	3.46
563	842	4.452733	GGTCGCGGGTCAGGGAAG	62.453	72.222	6.13	0.00	34.84	3.46
590	869	1.018148	CTATCGTGTGGAGCTCTCGT	58.982	55.000	14.64	7.33	0.00	4.18
1026	1336	2.636412	CGCCTCTTCAGACGGGTCA	61.636	63.158	1.17	0.00	0.00	4.02
1030	1340	2.492090	CCTCGCCTCTTCAGACGG	59.508	66.667	0.00	0.00	0.00	4.79
1032	1342	1.216710	CACCCTCGCCTCTTCAGAC	59.783	63.158	0.00	0.00	0.00	3.51
1062	1372	2.064434	TGTGTTCCATGGCAAACAGA	57.936	45.000	17.04	13.96	36.14	3.41
1155	1466	1.321743	CTCTCGAATTCGACAAAGGCG	59.678	52.381	25.96	14.57	44.22	5.52
1338	1649	2.991540	GCAACAACCAGGGGAGCC	60.992	66.667	0.00	0.00	0.00	4.70
1448	1759	1.503542	CACATTGCTTCCGACAGGC	59.496	57.895	0.00	0.00	37.47	4.85
1469	1780	5.139727	TGATCAAAGTGTTGTGGAAGGATT	58.860	37.500	0.00	0.00	36.07	3.01
1689	2013	2.758089	CGCTTCCATGTCCAGCTGC	61.758	63.158	8.66	0.00	0.00	5.25
1844	2168	1.098129	TCCATCCGAGCTCTCTGTCG	61.098	60.000	12.85	0.00	35.91	4.35
1976	2321	0.037326	TCGCTGTGTGGCTTTAGAGG	60.037	55.000	0.00	0.00	0.00	3.69
2006	2351	4.012374	TGATCTAACGTCTCCGGTACTTT	58.988	43.478	0.00	4.05	38.78	2.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.