AutoCloner

Multiple sequence alignment - TraesCS3D01G304100

Loading Multiple Alignment...

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	TraesCS3D01G304100	chr3D	100.000	2438	0	0	1	2438	418706619	418704182	0.000000e+00	4503.0
1	TraesCS3D01G304100	chr3D	97.112	658	18	1	1781	2438	418481530	418480874	0.000000e+00	1109.0
2	TraesCS3D01G304100	chr3D	93.643	645	29	3	1090	1733	418482627	418481994	0.000000e+00	953.0
3	TraesCS3D01G304100	chr3D	90.130	385	29	3	1056	1432	418410759	418410376	2.180000e-135	492.0
4	TraesCS3D01G304100	chr3D	83.610	543	39	17	82	617	416403437	416403936	4.750000e-127	464.0
5	TraesCS3D01G304100	chr3D	90.842	273	25	0	1160	1432	416404365	416404637	1.380000e-97	366.0
6	TraesCS3D01G304100	chr3D	89.683	252	9	5	1482	1733	418410253	418410019	3.050000e-79	305.0
7	TraesCS3D01G304100	chr3D	77.662	385	42	17	200	582	416481139	416481481	6.880000e-46	195.0
8	TraesCS3D01G304100	chr3D	81.509	265	21	18	729	976	416404039	416404292	2.470000e-45	193.0
9	TraesCS3D01G304100	chr3D	82.727	220	19	9	634	844	418411076	418410867	6.930000e-41	178.0
10	TraesCS3D01G304100	chr3B	93.103	899	50	3	738	1636	545009205	545008319	0.000000e+00	1306.0
11	TraesCS3D01G304100	chr3B	95.590	703	30	1	1736	2438	544898823	544898122	0.000000e+00	1125.0
12	TraesCS3D01G304100	chr3B	86.712	1031	89	19	629	1636	544922679	544921674	0.000000e+00	1101.0
13	TraesCS3D01G304100	chr3B	94.805	462	22	2	1820	2281	545001303	545000844	0.000000e+00	719.0
14	TraesCS3D01G304100	chr3B	93.617	282	14	2	1452	1733	544818780	544818503	3.750000e-113	418.0
15	TraesCS3D01G304100	chr3B	98.026	152	2	1	443	593	545028322	545028171	1.860000e-66	263.0
16	TraesCS3D01G304100	chr3B	98.630	146	2	0	82	227	545044790	545044645	2.400000e-65	259.0
17	TraesCS3D01G304100	chr3B	92.683	164	12	0	2275	2438	544999274	544999111	1.130000e-58	237.0
18	TraesCS3D01G304100	chr3B	80.000	320	34	4	1113	1432	544819182	544818893	2.460000e-50	209.0
19	TraesCS3D01G304100	chr3B	95.690	116	5	0	227	342	545043742	545043627	1.150000e-43	187.0
20	TraesCS3D01G304100	chr3B	82.569	218	19	11	635	844	544821533	544821327	8.960000e-40	174.0
21	TraesCS3D01G304100	chr3B	91.270	126	11	0	1000	1125	544821243	544821118	3.220000e-39	172.0
22	TraesCS3D01G304100	chr3B	98.462	65	1	0	386	450	545043378	545043314	5.510000e-22	115.0
23	TraesCS3D01G304100	chr3B	100.000	50	0	0	582	631	545013377	545013328	2.580000e-15	93.5
24	TraesCS3D01G304100	chr3A	92.650	898	49	5	636	1528	532487891	532488776	0.000000e+00	1277.0
25	TraesCS3D01G304100	chr3A	94.545	550	18	1	82	631	532487317	532487854	0.000000e+00	839.0
26	TraesCS3D01G304100	chr3A	88.685	327	27	4	1000	1326	532644460	532644776	8.170000e-105	390.0
27	TraesCS3D01G304100	chr3A	88.612	281	13	7	1451	1730	532644944	532645206	8.410000e-85	324.0
28	TraesCS3D01G304100	chr3A	76.581	427	73	20	1023	1427	719360763	719360342	2.460000e-50	209.0
29	TraesCS3D01G304100	chr3A	75.116	430	77	23	1023	1427	719337282	719336858	8.960000e-40	174.0
30	TraesCS3D01G304100	chr3A	91.818	110	9	0	2320	2429	532490784	532490893	1.170000e-33	154.0
31	TraesCS3D01G304100	chrUn	95.590	703	30	1	1736	2438	351404234	351404935	0.000000e+00	1125.0
32	TraesCS3D01G304100	chr4A	82.682	537	77	13	1757	2281	666951709	666952241	1.710000e-126	462.0
33	TraesCS3D01G304100	chr5B	82.123	537	79	12	1757	2281	19743919	19744450	6.190000e-121	444.0
34	TraesCS3D01G304100	chr7D	81.495	535	85	13	1757	2281	52354367	52354897	6.230000e-116	427.0
35	TraesCS3D01G304100	chr7D	80.568	458	73	11	1757	2203	52473963	52474415	3.000000e-89	339.0
36	TraesCS3D01G304100	chr7D	98.795	83	1	0	1	83	136695356	136695274	5.430000e-32	148.0
37	TraesCS3D01G304100	chr7D	96.296	81	3	0	3	83	99611432	99611352	1.520000e-27	134.0
38	TraesCS3D01G304100	chr7D	72.250	400	83	23	83	462	611467669	611468060	5.550000e-17	99.0
39	TraesCS3D01G304100	chr7D	94.000	50	2	1	569	617	6443016	6443065	9.350000e-10	75.0
40	TraesCS3D01G304100	chr5D	80.597	536	89	12	1757	2281	27354447	27354978	1.360000e-107	399.0
41	TraesCS3D01G304100	chr7A	81.786	280	40	9	1757	2029	54851715	54851990	8.770000e-55	224.0
42	TraesCS3D01G304100	chr7A	72.250	400	83	23	83	462	701458842	701459233	5.550000e-17	99.0
43	TraesCS3D01G304100	chr5A	96.386	83	3	0	1	83	35274420	35274338	1.180000e-28	137.0
44	TraesCS3D01G304100	chr2D	95.062	81	4	0	3	83	646276778	646276698	7.080000e-26	128.0
45	TraesCS3D01G304100	chr4B	92.593	81	6	0	3	83	609429727	609429647	1.530000e-22	117.0
46	TraesCS3D01G304100	chr4D	91.228	57	2	3	2272	2327	95285970	95286024	9.350000e-10	75.0

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	TraesCS3D01G304100	chr3D	418704182	418706619	2437	True	4503.000000	4503	100.000000	1	2438	1	chr3D.!!$R1	2437
1	TraesCS3D01G304100	chr3D	418480874	418482627	1753	True	1031.000000	1109	95.377500	1090	2438	2	chr3D.!!$R3	1348
2	TraesCS3D01G304100	chr3D	416403437	416404637	1200	False	341.000000	464	85.320333	82	1432	3	chr3D.!!$F2	1350
3	TraesCS3D01G304100	chr3D	418410019	418411076	1057	True	325.000000	492	87.513333	634	1733	3	chr3D.!!$R2	1099
4	TraesCS3D01G304100	chr3B	545008319	545009205	886	True	1306.000000	1306	93.103000	738	1636	1	chr3B.!!$R3	898
5	TraesCS3D01G304100	chr3B	544898122	544898823	701	True	1125.000000	1125	95.590000	1736	2438	1	chr3B.!!$R1	702
6	TraesCS3D01G304100	chr3B	544921674	544922679	1005	True	1101.000000	1101	86.712000	629	1636	1	chr3B.!!$R2	1007
7	TraesCS3D01G304100	chr3B	544999111	545001303	2192	True	478.000000	719	93.744000	1820	2438	2	chr3B.!!$R7	618
8	TraesCS3D01G304100	chr3B	544818503	544821533	3030	True	243.250000	418	86.864000	635	1733	4	chr3B.!!$R6	1098
9	TraesCS3D01G304100	chr3A	532487317	532490893	3576	False	756.666667	1277	93.004333	82	2429	3	chr3A.!!$F1	2347
10	TraesCS3D01G304100	chr3A	532644460	532645206	746	False	357.000000	390	88.648500	1000	1730	2	chr3A.!!$F2	730
11	TraesCS3D01G304100	chrUn	351404234	351404935	701	False	1125.000000	1125	95.590000	1736	2438	1	chrUn.!!$F1	702
12	TraesCS3D01G304100	chr4A	666951709	666952241	532	False	462.000000	462	82.682000	1757	2281	1	chr4A.!!$F1	524
13	TraesCS3D01G304100	chr5B	19743919	19744450	531	False	444.000000	444	82.123000	1757	2281	1	chr5B.!!$F1	524
14	TraesCS3D01G304100	chr7D	52354367	52354897	530	False	427.000000	427	81.495000	1757	2281	1	chr7D.!!$F2	524
15	TraesCS3D01G304100	chr5D	27354447	27354978	531	False	399.000000	399	80.597000	1757	2281	1	chr5D.!!$F1	524

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
886	960	0.32183	ATTTGCTTGCCCATGCCAAC	60.322	50.0	4.05	0.0	36.33	3.77	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2377	8417	3.121025	GCATTAACCTTGCACTTTTTCGC	60.121	43.478	0.0	0.0	39.9	4.7	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
20	21	3.999229	GTTAGGCGAATCACTTGACTG	57.001	47.619	0.00	0.00	0.00	3.51
21	22	2.672961	TAGGCGAATCACTTGACTGG	57.327	50.000	0.00	0.00	0.00	4.00
22	23	0.976641	AGGCGAATCACTTGACTGGA	59.023	50.000	0.00	0.00	0.00	3.86
23	24	1.079503	GGCGAATCACTTGACTGGAC	58.920	55.000	0.00	0.00	0.00	4.02
24	25	0.716108	GCGAATCACTTGACTGGACG	59.284	55.000	0.00	0.00	0.00	4.79
25	26	0.716108	CGAATCACTTGACTGGACGC	59.284	55.000	0.00	0.00	0.00	5.19
26	27	1.795768	GAATCACTTGACTGGACGCA	58.204	50.000	0.00	0.00	0.00	5.24
27	28	1.728971	GAATCACTTGACTGGACGCAG	59.271	52.381	0.00	0.00	0.00	5.18
43	44	3.074504	CGCAGTTACTAATAGCGTCCA	57.925	47.619	6.64	0.00	43.08	4.02
44	45	3.043586	CGCAGTTACTAATAGCGTCCAG	58.956	50.000	6.64	0.00	43.08	3.86
45	46	3.242969	CGCAGTTACTAATAGCGTCCAGA	60.243	47.826	6.64	0.00	43.08	3.86
46	47	4.043073	GCAGTTACTAATAGCGTCCAGAC	58.957	47.826	0.00	0.00	0.00	3.51
47	48	4.608951	CAGTTACTAATAGCGTCCAGACC	58.391	47.826	0.00	0.00	0.00	3.85
48	49	4.338682	CAGTTACTAATAGCGTCCAGACCT	59.661	45.833	0.00	0.00	0.00	3.85
49	50	4.338682	AGTTACTAATAGCGTCCAGACCTG	59.661	45.833	0.00	0.00	0.00	4.00
118	119	2.995574	ACCCCGTCTCCGTTGAGG	60.996	66.667	0.00	0.00	39.23	3.86
244	266	3.271706	CTCGTACACCCCGAACGCA	62.272	63.158	0.00	0.00	36.60	5.24
252	274	2.267642	CCCGAACGCATCCCTCAA	59.732	61.111	0.00	0.00	0.00	3.02
262	284	2.231380	ATCCCTCAAACCCCTGCGT	61.231	57.895	0.00	0.00	0.00	5.24
616	638	2.589014	GCACGGTATATGTAGGCGTAC	58.411	52.381	9.63	9.63	0.00	3.67
658	715	4.589908	ACAGTCAAAAGAAGTTCACTGGT	58.410	39.130	19.01	7.14	35.61	4.00
659	716	5.741011	ACAGTCAAAAGAAGTTCACTGGTA	58.259	37.500	19.01	0.00	35.61	3.25
664	721	7.339466	AGTCAAAAGAAGTTCACTGGTACAAAT	59.661	33.333	5.50	0.00	38.70	2.32
678	735	7.805071	CACTGGTACAAATCTGAAGTTCAATTC	59.195	37.037	7.06	0.00	38.70	2.17
886	960	0.321830	ATTTGCTTGCCCATGCCAAC	60.322	50.000	4.05	0.00	36.33	3.77
912	990	5.047847	TCTCAGCTATAAATACCAACACGC	58.952	41.667	0.00	0.00	0.00	5.34
936	1017	1.755959	AGCTCGATCTCAATCAGCAGT	59.244	47.619	0.00	0.00	37.95	4.40
953	1034	1.719780	CAGTAAACCAGCGACGAACTC	59.280	52.381	0.00	0.00	0.00	3.01
977	1064	3.612479	GCATCAAGCACCGAAAGACAAAT	60.612	43.478	0.00	0.00	44.79	2.32
979	1066	3.210227	TCAAGCACCGAAAGACAAATCA	58.790	40.909	0.00	0.00	0.00	2.57
998	1103	1.135859	CAATCTTTGCAGGCGACTCAC	60.136	52.381	0.00	0.00	40.21	3.51
1013	1118	2.124612	CACCATGGCCGCATCAGA	60.125	61.111	13.04	0.00	0.00	3.27
1231	3290	4.699522	ACGCCGGCAAGGAGGAAC	62.700	66.667	28.98	0.00	44.78	3.62
1246	3305	3.569200	GAACAGGGGGACAGGTGCC	62.569	68.421	0.73	0.73	40.73	5.01
1346	3405	4.664677	GCTGCACCTGGACGTCGT	62.665	66.667	9.92	0.00	0.00	4.34
1374	3441	2.828549	GCCATGATCCGCCGGTTT	60.829	61.111	1.63	0.00	0.00	3.27
1439	3529	2.161609	CCATGATGATGATGGCATGACG	59.838	50.000	3.81	0.00	40.29	4.35
1448	3538	4.418013	TGATGGCATGACGTACAAAAAG	57.582	40.909	3.81	0.00	0.00	2.27
1480	3641	6.651225	ACTGAACTTTGTATACTTTCTCTGGC	59.349	38.462	4.17	0.00	0.00	4.85
1542	3707	9.203421	CGGCAGATACAATTGTATTGTTCTATA	57.797	33.333	27.48	2.89	40.99	1.31
1584	3763	6.524192	GCTTAATATCCCAACACCCATATCCT	60.524	42.308	0.00	0.00	0.00	3.24
1921	4643	7.653713	GCCATAGAATTCAGGTACCATATATCG	59.346	40.741	15.94	0.00	0.00	2.92
2006	4744	8.787852	ACATAACAAAAGAGAGTTTCCAAGATC	58.212	33.333	0.00	0.00	0.00	2.75
2110	4849	3.006940	TCACCAACTTTCGGCATCATAC	58.993	45.455	0.00	0.00	0.00	2.39
2168	4907	1.408422	GTGAACGATGTGCTTTTGGC	58.592	50.000	0.00	0.00	42.22	4.52
2354	8394	4.098349	ACCACAAGTTACGAACAGAGTACA	59.902	41.667	0.00	0.00	0.00	2.90
2377	8417	3.436700	AGAAAACAGAAAAACAGCGGG	57.563	42.857	0.00	0.00	0.00	6.13

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.673368	CCAGTCAAGTGATTCGCCTAAC	59.327	50.000	0.00	0.00	0.00	2.34
1	2	2.565391	TCCAGTCAAGTGATTCGCCTAA	59.435	45.455	0.00	0.00	0.00	2.69
2	3	2.094182	GTCCAGTCAAGTGATTCGCCTA	60.094	50.000	0.00	0.00	0.00	3.93
4	5	1.079503	GTCCAGTCAAGTGATTCGCC	58.920	55.000	0.00	0.00	0.00	5.54
5	6	0.716108	CGTCCAGTCAAGTGATTCGC	59.284	55.000	0.00	0.00	0.00	4.70
7	8	1.728971	CTGCGTCCAGTCAAGTGATTC	59.271	52.381	0.00	0.00	34.31	2.52
8	9	1.800805	CTGCGTCCAGTCAAGTGATT	58.199	50.000	0.00	0.00	34.31	2.57
18	19	3.043586	CGCTATTAGTAACTGCGTCCAG	58.956	50.000	17.81	0.00	44.80	3.86
19	20	3.074504	CGCTATTAGTAACTGCGTCCA	57.925	47.619	17.81	0.00	41.45	4.02
24	25	4.043073	GTCTGGACGCTATTAGTAACTGC	58.957	47.826	0.00	0.00	0.00	4.40
25	26	4.338682	AGGTCTGGACGCTATTAGTAACTG	59.661	45.833	0.00	0.00	0.00	3.16
26	27	4.338682	CAGGTCTGGACGCTATTAGTAACT	59.661	45.833	0.00	0.00	0.00	2.24
27	28	4.608951	CAGGTCTGGACGCTATTAGTAAC	58.391	47.826	0.00	0.00	0.00	2.50
28	29	4.913335	CAGGTCTGGACGCTATTAGTAA	57.087	45.455	0.00	0.00	0.00	2.24
66	67	1.446099	TTCGTCCACAGCTCGATGC	60.446	57.895	0.00	0.00	43.29	3.91
67	68	0.109086	AGTTCGTCCACAGCTCGATG	60.109	55.000	0.00	0.00	33.72	3.84
68	69	0.171455	GAGTTCGTCCACAGCTCGAT	59.829	55.000	0.00	0.00	33.72	3.59
69	70	1.579932	GAGTTCGTCCACAGCTCGA	59.420	57.895	0.00	0.00	0.00	4.04
70	71	1.797933	CGAGTTCGTCCACAGCTCG	60.798	63.158	0.00	0.00	42.01	5.03
71	72	4.154613	CGAGTTCGTCCACAGCTC	57.845	61.111	0.00	0.00	34.11	4.09
118	119	2.605823	CGCTATGATCCAGAGGTTCGAC	60.606	54.545	0.00	0.00	0.00	4.20
244	266	2.198304	GACGCAGGGGTTTGAGGGAT	62.198	60.000	0.00	0.00	0.00	3.85
252	274	2.526873	ACCAGAGACGCAGGGGTT	60.527	61.111	0.00	0.00	0.00	4.11
262	284	0.336737	GGGGAGAAGAGGACCAGAGA	59.663	60.000	0.00	0.00	0.00	3.10
287	309	3.706373	GAAGCTGGTGGCCGAGGA	61.706	66.667	0.00	0.00	43.05	3.71
370	392	2.982130	GGCATATCGGCCGAGGAT	59.018	61.111	33.87	24.89	45.40	3.24
485	507	2.267642	CATGGTTTCCTCCGGCGA	59.732	61.111	9.30	0.00	0.00	5.54
486	508	2.824041	CCATGGTTTCCTCCGGCG	60.824	66.667	2.57	0.00	0.00	6.46
487	509	1.749258	GACCATGGTTTCCTCCGGC	60.749	63.158	20.85	0.00	0.00	6.13
488	510	0.392998	CTGACCATGGTTTCCTCCGG	60.393	60.000	20.85	6.12	0.00	5.14
489	511	0.324943	ACTGACCATGGTTTCCTCCG	59.675	55.000	20.85	4.59	0.00	4.63
490	512	2.586648	AACTGACCATGGTTTCCTCC	57.413	50.000	20.85	5.36	0.00	4.30
491	513	4.455877	CAGTTAACTGACCATGGTTTCCTC	59.544	45.833	28.17	6.17	46.59	3.71
659	716	9.918630	CCATTTAGAATTGAACTTCAGATTTGT	57.081	29.630	0.00	0.00	0.00	2.83
664	721	6.348458	CGTGCCATTTAGAATTGAACTTCAGA	60.348	38.462	0.00	0.00	0.00	3.27
678	735	1.024579	AGAACCGCCGTGCCATTTAG	61.025	55.000	0.00	0.00	0.00	1.85
767	835	3.366985	GCGAGTTAAATTTTGGACCAGGG	60.367	47.826	0.00	0.00	0.00	4.45
886	960	7.567571	CGTGTTGGTATTTATAGCTGAGAATG	58.432	38.462	0.00	0.00	0.00	2.67
912	990	2.284684	GCTGATTGAGATCGAGCTGTTG	59.715	50.000	8.50	0.00	35.44	3.33
936	1017	1.933500	GCTGAGTTCGTCGCTGGTTTA	60.934	52.381	0.00	0.00	0.00	2.01
953	1034	1.135859	GTCTTTCGGTGCTTGATGCTG	60.136	52.381	0.00	0.00	43.37	4.41
977	1064	1.270785	TGAGTCGCCTGCAAAGATTGA	60.271	47.619	0.00	0.00	0.00	2.57
979	1066	1.160137	GTGAGTCGCCTGCAAAGATT	58.840	50.000	0.00	0.00	0.00	2.40
998	1103	1.228033	TCATCTGATGCGGCCATGG	60.228	57.895	7.63	7.63	0.00	3.66
1013	1118	1.291877	GAACACGCGCCTGAACTCAT	61.292	55.000	13.48	0.00	0.00	2.90
1170	3229	2.363018	TCCTCCTCGTCCAGCAGG	60.363	66.667	0.00	0.00	0.00	4.85
1246	3305	4.891727	CATCCCGAACGCCTCCCG	62.892	72.222	0.00	0.00	44.21	5.14
1346	3405	2.315781	GATCATGGCCTGGCACTCGA	62.316	60.000	22.05	11.16	0.00	4.04
1374	3441	4.351938	CCGTCGCCGTTGAGGTCA	62.352	66.667	0.00	0.00	43.70	4.02
1393	3460	0.387929	AACTCGTCGAAGGTGAGCAA	59.612	50.000	0.00	0.00	32.98	3.91
1439	3529	9.791838	CAAAGTTCAGTTTTTGACTTTTTGTAC	57.208	29.630	0.00	0.00	36.19	2.90
1584	3763	5.994668	AGTTTGGCACTTTGTTTTTCTCAAA	59.005	32.000	0.00	0.00	34.34	2.69
2006	4744	4.383052	CGGAACTATGTAAGCTTGCTATCG	59.617	45.833	15.83	6.54	0.00	2.92
2168	4907	8.814235	AGTTTGTGACGGTTTATATTATCTTCG	58.186	33.333	0.00	0.00	0.00	3.79
2354	8394	4.629634	CCCGCTGTTTTTCTGTTTTCTTTT	59.370	37.500	0.00	0.00	0.00	2.27
2377	8417	3.121025	GCATTAACCTTGCACTTTTTCGC	60.121	43.478	0.00	0.00	39.90	4.70
2410	8450	4.431416	TTCTCTTTAGGGCTTGTTGACA	57.569	40.909	0.00	0.00	0.00	3.58
2411	8451	5.531287	TCTTTTCTCTTTAGGGCTTGTTGAC	59.469	40.000	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.