AutoCloner

Multiple sequence alignment - TraesCS6D01G225800

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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	TraesCS6D01G225800	chr6D	100.000	3158	0	0	1	3158	317480617	317477460	0.000000e+00	5832.0
1	TraesCS6D01G225800	chr6D	92.704	699	48	3	103	799	11898438	11899135	0.000000e+00	1005.0
2	TraesCS6D01G225800	chr6A	95.000	2300	94	11	880	3158	454945868	454943569	0.000000e+00	3591.0
3	TraesCS6D01G225800	chr6A	92.105	532	38	3	104	634	585089276	585088748	0.000000e+00	747.0
4	TraesCS6D01G225800	chr6B	94.517	1295	51	8	807	2089	506720176	506721462	0.000000e+00	1980.0
5	TraesCS6D01G225800	chr6B	81.786	571	70	14	2602	3158	506721887	506722437	6.210000e-122	448.0
6	TraesCS6D01G225800	chr6B	90.385	104	9	1	1	104	506720084	506720186	5.490000e-28	135.0
7	TraesCS6D01G225800	chr6B	94.118	85	5	0	2336	2420	506721459	506721543	2.560000e-26	130.0
8	TraesCS6D01G225800	chr3A	94.564	699	35	3	104	799	670666947	670666249	0.000000e+00	1077.0
9	TraesCS6D01G225800	chr3A	90.566	53	3	2	827	879	690963352	690963402	5.650000e-08	69.4
10	TraesCS6D01G225800	chr3A	95.349	43	1	1	834	875	141970205	141970247	2.030000e-07	67.6
11	TraesCS6D01G225800	chr3A	91.667	48	3	1	826	873	586870531	586870577	7.310000e-07	65.8
12	TraesCS6D01G225800	chr5B	92.275	699	50	4	103	799	456975823	456976519	0.000000e+00	989.0
13	TraesCS6D01G225800	chr5B	91.559	699	57	2	103	799	529119552	529118854	0.000000e+00	963.0
14	TraesCS6D01G225800	chr4A	92.264	698	52	2	104	799	554641810	554641113	0.000000e+00	989.0
15	TraesCS6D01G225800	chr4A	92.253	697	50	4	104	797	85901080	85900385	0.000000e+00	985.0
16	TraesCS6D01G225800	chr4A	82.569	109	16	3	3020	3126	683964022	683963915	3.350000e-15	93.5
17	TraesCS6D01G225800	chr3D	91.702	699	56	2	103	799	441430717	441431415	0.000000e+00	968.0
18	TraesCS6D01G225800	chr5A	91.342	693	57	3	109	799	106686673	106687364	0.000000e+00	944.0
19	TraesCS6D01G225800	chr5A	90.000	50	4	1	829	877	635404820	635404771	2.630000e-06	63.9
20	TraesCS6D01G225800	chr2A	95.745	47	1	1	830	876	739845385	739845340	1.210000e-09	75.0
21	TraesCS6D01G225800	chr7D	89.655	58	4	2	820	876	223819431	223819487	4.370000e-09	73.1
22	TraesCS6D01G225800	chr5D	93.478	46	2	1	830	875	29159962	29160006	2.030000e-07	67.6
23	TraesCS6D01G225800	chr4B	90.196	51	4	1	825	875	636767787	636767836	7.310000e-07	65.8

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	TraesCS6D01G225800	chr6D	317477460	317480617	3157	True	5832.00	5832	100.0000	1	3158	1	chr6D.!!$R1	3157
1	TraesCS6D01G225800	chr6D	11898438	11899135	697	False	1005.00	1005	92.7040	103	799	1	chr6D.!!$F1	696
2	TraesCS6D01G225800	chr6A	454943569	454945868	2299	True	3591.00	3591	95.0000	880	3158	1	chr6A.!!$R1	2278
3	TraesCS6D01G225800	chr6A	585088748	585089276	528	True	747.00	747	92.1050	104	634	1	chr6A.!!$R2	530
4	TraesCS6D01G225800	chr6B	506720084	506722437	2353	False	673.25	1980	90.2015	1	3158	4	chr6B.!!$F1	3157
5	TraesCS6D01G225800	chr3A	670666249	670666947	698	True	1077.00	1077	94.5640	104	799	1	chr3A.!!$R1	695
6	TraesCS6D01G225800	chr5B	456975823	456976519	696	False	989.00	989	92.2750	103	799	1	chr5B.!!$F1	696
7	TraesCS6D01G225800	chr5B	529118854	529119552	698	True	963.00	963	91.5590	103	799	1	chr5B.!!$R1	696
8	TraesCS6D01G225800	chr4A	554641113	554641810	697	True	989.00	989	92.2640	104	799	1	chr4A.!!$R2	695
9	TraesCS6D01G225800	chr4A	85900385	85901080	695	True	985.00	985	92.2530	104	797	1	chr4A.!!$R1	693
10	TraesCS6D01G225800	chr3D	441430717	441431415	698	False	968.00	968	91.7020	103	799	1	chr3D.!!$F1	696
11	TraesCS6D01G225800	chr5A	106686673	106687364	691	False	944.00	944	91.3420	109	799	1	chr5A.!!$F1	690

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
623	625	0.251634	AAGCTAGAAGCAGCCCACTC	59.748	55.000	1.22	0.0	45.56	3.51	F
884	887	1.279271	GTCACATGGTGAGGCCTAACT	59.721	52.381	20.30	0.0	43.57	2.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1928	1946	0.516877	TTCAAGCAGATTTGGACGCG	59.483	50.000	3.53	3.53	0.00	6.01	R
2755	3017	1.433879	GACATGAGAGGGACGTCCG	59.566	63.158	27.68	14.58	41.52	4.79	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
27	28	2.740714	GGAGCGTCCAACATGCGAC	61.741	63.158	0.00	0.00	42.55	5.19
33	34	1.155889	GTCCAACATGCGACATGTGA	58.844	50.000	20.86	14.10	31.80	3.58
34	35	1.135972	GTCCAACATGCGACATGTGAC	60.136	52.381	20.86	19.41	31.80	3.67
38	39	0.319469	ACATGCGACATGTGACGTCA	60.319	50.000	15.76	15.76	35.76	4.35
42	43	0.456142	GCGACATGTGACGTCAGCTA	60.456	55.000	20.73	9.07	35.76	3.32
72	73	2.202810	GGCGTGCTCTCAGCCTAC	60.203	66.667	0.00	0.00	46.83	3.18
107	108	1.271926	TGGTTCCTGCTAGGGCTTTTC	60.272	52.381	0.00	0.00	39.59	2.29
320	321	7.323052	AGGGACAAAAGATATCTAATCTCCC	57.677	40.000	21.02	21.02	31.10	4.30
438	439	7.870445	GTCGCTTCTCTGGATAGAAAAAGATAT	59.130	37.037	0.00	0.00	35.14	1.63
459	460	2.026641	ACCTTCCATGCATGCACATAC	58.973	47.619	25.37	0.00	0.00	2.39
566	568	2.041922	ACCAGCCGAGCCATCCTA	60.042	61.111	0.00	0.00	0.00	2.94
578	580	2.158505	AGCCATCCTATGCAAATGAGCT	60.159	45.455	0.00	0.00	34.99	4.09
623	625	0.251634	AAGCTAGAAGCAGCCCACTC	59.748	55.000	1.22	0.00	45.56	3.51
773	776	1.604604	CGTGAAACTTCCATGGTGGT	58.395	50.000	12.58	9.01	34.55	4.16
802	805	5.553290	TTGTTGTGAACAATCTCGTCAAA	57.447	34.783	0.00	0.00	45.79	2.69
803	806	5.553290	TGTTGTGAACAATCTCGTCAAAA	57.447	34.783	0.00	0.00	38.72	2.44
804	807	5.944013	TGTTGTGAACAATCTCGTCAAAAA	58.056	33.333	0.00	0.00	38.72	1.94
805	808	6.559810	TGTTGTGAACAATCTCGTCAAAAAT	58.440	32.000	0.00	0.00	38.72	1.82
806	809	6.690957	TGTTGTGAACAATCTCGTCAAAAATC	59.309	34.615	0.00	0.00	38.72	2.17
807	810	6.618287	TGTGAACAATCTCGTCAAAAATCT	57.382	33.333	0.00	0.00	0.00	2.40
808	811	6.429624	TGTGAACAATCTCGTCAAAAATCTG	58.570	36.000	0.00	0.00	0.00	2.90
809	812	5.340667	GTGAACAATCTCGTCAAAAATCTGC	59.659	40.000	0.00	0.00	0.00	4.26
810	813	5.239306	TGAACAATCTCGTCAAAAATCTGCT	59.761	36.000	0.00	0.00	0.00	4.24
811	814	6.426633	TGAACAATCTCGTCAAAAATCTGCTA	59.573	34.615	0.00	0.00	0.00	3.49
812	815	6.414408	ACAATCTCGTCAAAAATCTGCTAG	57.586	37.500	0.00	0.00	0.00	3.42
813	816	5.352569	ACAATCTCGTCAAAAATCTGCTAGG	59.647	40.000	0.00	0.00	0.00	3.02
814	817	3.861840	TCTCGTCAAAAATCTGCTAGGG	58.138	45.455	0.00	0.00	0.00	3.53
815	818	2.352960	CTCGTCAAAAATCTGCTAGGGC	59.647	50.000	0.00	0.00	39.26	5.19
816	819	2.027192	TCGTCAAAAATCTGCTAGGGCT	60.027	45.455	0.00	0.00	39.59	5.19
878	881	3.254629	ATGTGTCACATGGTGAGGC	57.745	52.632	17.74	0.00	43.57	4.70
884	887	1.279271	GTCACATGGTGAGGCCTAACT	59.721	52.381	20.30	0.00	43.57	2.24
885	888	1.555075	TCACATGGTGAGGCCTAACTC	59.445	52.381	20.30	10.66	37.67	3.01
943	948	9.724839	TTTTGTACTGTATACTTGCTTGTTTTC	57.275	29.630	4.17	0.00	0.00	2.29
1015	1022	2.403252	AAGAACTAGCCCAACATCCG	57.597	50.000	0.00	0.00	0.00	4.18
1041	1051	3.197983	AGTCCTATAGCCCAGAACACAAC	59.802	47.826	0.00	0.00	0.00	3.32
1125	1135	1.306141	ATCCCGGAAGAGGCAGACA	60.306	57.895	0.73	0.00	0.00	3.41
1171	1186	2.338500	CTAGTTCGTTTCAGTGCCTCC	58.662	52.381	0.00	0.00	0.00	4.30
1565	1583	3.325201	GATTCCGTTCGTGGCCCCT	62.325	63.158	0.00	0.00	0.00	4.79
1757	1775	3.753434	CTGGAGCTCGCGGACAGT	61.753	66.667	6.13	0.00	0.00	3.55
1838	1856	3.262151	TCTTGATTAACCACACATCCGGA	59.738	43.478	6.61	6.61	0.00	5.14
1922	1940	1.808133	GCTTATGCTCGGAAGACTGGG	60.808	57.143	0.00	0.00	35.39	4.45
1928	1946	1.270041	GCTCGGAAGACTGGGATGATC	60.270	57.143	0.00	0.00	35.39	2.92
1943	1961	0.108186	TGATCGCGTCCAAATCTGCT	60.108	50.000	5.77	0.00	0.00	4.24
1970	1988	9.832445	TGAACAAAAAGTGAGTATTCTTCTACT	57.168	29.630	0.00	0.00	34.65	2.57
1987	2005	8.293699	TCTTCTACTGCATATTAAGTCACAGA	57.706	34.615	0.00	0.00	0.00	3.41
2047	2066	1.268625	TGTGTGACTATGACGCGAACT	59.731	47.619	15.93	0.00	0.00	3.01
2089	2108	1.741706	CGAGCATCAGTTTTCTGCCAT	59.258	47.619	0.00	0.00	46.59	4.40
2091	2110	3.730061	CGAGCATCAGTTTTCTGCCATTC	60.730	47.826	0.00	0.00	46.59	2.67
2097	2116	3.191162	TCAGTTTTCTGCCATTCCGATTG	59.809	43.478	0.00	0.00	46.59	2.67
2100	2119	1.037030	TTCTGCCATTCCGATTGGGC	61.037	55.000	10.61	5.26	46.58	5.36
2101	2120	1.454479	CTGCCATTCCGATTGGGCT	60.454	57.895	10.61	0.00	46.53	5.19
2118	2137	7.362574	CGATTGGGCTAACCTTTATCTTGAAAA	60.363	37.037	0.00	0.00	41.11	2.29
2323	2350	7.069950	TCTGATACCAGCTATACACAAGAACAT	59.930	37.037	0.00	0.00	40.20	2.71
2564	2593	6.258160	CACTCCTTATTTTGATTGCGTTAGG	58.742	40.000	0.00	0.00	0.00	2.69
2577	2606	5.811399	TTGCGTTAGGATGGAATAACTTG	57.189	39.130	0.00	0.00	31.15	3.16
2583	2612	4.162040	AGGATGGAATAACTTGCCTGAG	57.838	45.455	0.00	0.00	0.00	3.35
2616	2878	8.438676	ACTTAGAAGGTATTATGTGAATGTGC	57.561	34.615	0.00	0.00	0.00	4.57
2663	2925	4.897670	CCAAAAATCCTGGGATTAGCATCT	59.102	41.667	14.34	0.00	43.26	2.90
2724	2986	7.093771	GGAATTCAACTAGGAATGGACACAAAT	60.094	37.037	7.93	0.00	37.55	2.32
2792	3054	1.369091	CGCCTCCCACCATTTTCTCG	61.369	60.000	0.00	0.00	0.00	4.04
2900	3169	4.342092	TCGCTCATATGTTCATCTTCCTCA	59.658	41.667	1.90	0.00	0.00	3.86
2921	3190	1.179152	TCAACATGGCTGCTGGAATG	58.821	50.000	0.00	1.94	0.00	2.67
3045	3315	1.207791	TTGTGGTGGCCAAATTGGTT	58.792	45.000	7.24	0.00	40.46	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	2.109126	GCATGTTGGACGCTCCCTC	61.109	63.158	0.00	0.00	35.03	4.30
9	10	2.434185	TCGCATGTTGGACGCTCC	60.434	61.111	0.00	0.00	36.96	4.70
27	28	1.857217	GCATCTAGCTGACGTCACATG	59.143	52.381	15.76	12.19	41.15	3.21
33	34	1.753649	AGTGATGCATCTAGCTGACGT	59.246	47.619	26.32	0.00	45.94	4.34
34	35	2.505628	AGTGATGCATCTAGCTGACG	57.494	50.000	26.32	0.00	45.94	4.35
38	39	1.809271	CGCCAAGTGATGCATCTAGCT	60.809	52.381	26.32	18.00	45.94	3.32
107	108	8.241367	AGTAATACAAATTTCTACCCGCAAAAG	58.759	33.333	0.00	0.00	0.00	2.27
142	143	4.800914	GCTGCGATGGATTGTAAGGACTAT	60.801	45.833	0.00	0.00	0.00	2.12
143	144	3.492656	GCTGCGATGGATTGTAAGGACTA	60.493	47.826	0.00	0.00	0.00	2.59
261	262	9.811995	TTTGTATTACTCATGTAAATCGTAGCT	57.188	29.630	0.00	0.00	41.36	3.32
320	321	3.116300	CGGTTTACTCGTCCATCATCAG	58.884	50.000	0.00	0.00	0.00	2.90
438	439	2.440517	ATGTGCATGCATGGAAGGTA	57.559	45.000	25.64	12.57	0.00	3.08
459	460	4.785512	ACGCGCTCGAAGCTGAGG	62.786	66.667	5.73	0.00	39.60	3.86
566	568	5.909621	AAATACTGACAGCTCATTTGCAT	57.090	34.783	1.25	0.00	34.99	3.96
578	580	6.544197	TGGCTTTGTCAAGTTAAATACTGACA	59.456	34.615	6.38	6.38	40.20	3.58
623	625	1.374758	GACAAGAGTGCAGACCCCG	60.375	63.158	0.00	0.00	0.00	5.73
699	701	8.009622	TCATTGGCATAAAATCTAATCTTGCA	57.990	30.769	0.00	0.00	0.00	4.08
773	776	3.289797	TGTTCACAACAAAGCCCCA	57.710	47.368	0.00	0.00	38.72	4.96
799	802	4.273318	AGGTTAGCCCTAGCAGATTTTTG	58.727	43.478	0.00	0.00	43.87	2.44
800	803	4.592997	AGGTTAGCCCTAGCAGATTTTT	57.407	40.909	0.00	0.00	43.87	1.94
801	804	4.592997	AAGGTTAGCCCTAGCAGATTTT	57.407	40.909	0.00	0.00	45.47	1.82
802	805	4.592997	AAAGGTTAGCCCTAGCAGATTT	57.407	40.909	0.00	0.00	45.47	2.17
803	806	4.722279	ACTAAAGGTTAGCCCTAGCAGATT	59.278	41.667	0.00	0.00	45.47	2.40
804	807	4.101741	CACTAAAGGTTAGCCCTAGCAGAT	59.898	45.833	0.00	0.00	45.47	2.90
805	808	3.451178	CACTAAAGGTTAGCCCTAGCAGA	59.549	47.826	0.00	0.00	45.47	4.26
806	809	3.197983	ACACTAAAGGTTAGCCCTAGCAG	59.802	47.826	0.00	0.00	45.47	4.24
807	810	3.178865	ACACTAAAGGTTAGCCCTAGCA	58.821	45.455	0.00	0.00	45.47	3.49
808	811	3.908643	ACACTAAAGGTTAGCCCTAGC	57.091	47.619	0.00	0.00	45.47	3.42
809	812	6.002082	ACAAAACACTAAAGGTTAGCCCTAG	58.998	40.000	0.00	0.00	45.47	3.02
810	813	5.944135	ACAAAACACTAAAGGTTAGCCCTA	58.056	37.500	0.00	0.00	45.47	3.53
812	815	5.524971	AACAAAACACTAAAGGTTAGCCC	57.475	39.130	0.00	0.00	34.57	5.19
813	816	7.837202	AAAAACAAAACACTAAAGGTTAGCC	57.163	32.000	0.00	0.00	0.00	3.93
943	948	1.062587	CAGGCTTCATTTCGGCTTACG	59.937	52.381	0.00	0.00	46.11	3.18
992	999	4.379499	CGGATGTTGGGCTAGTTCTTTTTC	60.379	45.833	0.00	0.00	0.00	2.29
1015	1022	5.304614	TGTGTTCTGGGCTATAGGACTATTC	59.695	44.000	1.04	0.00	0.00	1.75
1112	1122	1.268079	GTTTTGCTGTCTGCCTCTTCC	59.732	52.381	0.00	0.00	42.00	3.46
1125	1135	1.652563	GGCGTCCTTTCGTTTTGCT	59.347	52.632	0.00	0.00	0.00	3.91
1171	1186	2.734723	CGTGTGGTGGAGACTGCG	60.735	66.667	0.00	0.00	0.00	5.18
1757	1775	2.113774	CACTCCTTGCTGGCACCA	59.886	61.111	0.00	0.00	35.26	4.17
1781	1799	1.492133	CCACTGTGACCACATCCCCT	61.492	60.000	9.86	0.00	41.01	4.79
1838	1856	1.882623	GGCTTCAGCTTGTACTGCTTT	59.117	47.619	10.44	0.00	38.92	3.51
1922	1940	1.070309	GCAGATTTGGACGCGATCATC	60.070	52.381	15.93	6.76	0.00	2.92
1928	1946	0.516877	TTCAAGCAGATTTGGACGCG	59.483	50.000	3.53	3.53	0.00	6.01
1970	1988	7.977789	TGAAACTTCTGTGACTTAATATGCA	57.022	32.000	0.00	0.00	0.00	3.96
1981	1999	6.507958	TCAACAATGTTGAAACTTCTGTGA	57.492	33.333	24.63	0.00	0.00	3.58
1987	2005	8.542132	CAATTCGAATCAACAATGTTGAAACTT	58.458	29.630	29.28	20.14	31.55	2.66
2072	2091	2.733227	CGGAATGGCAGAAAACTGATGC	60.733	50.000	0.00	0.00	39.25	3.91
2089	2108	2.891191	AAAGGTTAGCCCAATCGGAA	57.109	45.000	0.00	0.00	34.66	4.30
2091	2110	4.086706	AGATAAAGGTTAGCCCAATCGG	57.913	45.455	0.00	0.00	34.66	4.18
2118	2137	4.196193	TGATCAACTGAACGGAACACTTT	58.804	39.130	0.00	0.00	0.00	2.66
2126	2145	3.684305	TGCTTACATGATCAACTGAACGG	59.316	43.478	0.00	0.00	0.00	4.44
2323	2350	5.482526	TCCTAGTTTTGGCTACTGTGACATA	59.517	40.000	0.00	0.00	0.00	2.29
2564	2593	5.189180	ACTTCTCAGGCAAGTTATTCCATC	58.811	41.667	0.00	0.00	29.29	3.51
2577	2606	6.231951	ACCTTCTAAGTTTTACTTCTCAGGC	58.768	40.000	0.00	0.00	39.51	4.85
2616	2878	1.878953	AGGAGCGTGTAAACAGTTGG	58.121	50.000	0.00	0.00	0.00	3.77
2663	2925	4.824479	TGAAGGTGCAGATTCACTATGA	57.176	40.909	8.99	0.00	37.16	2.15
2724	2986	4.019231	TCAGTGAGACTGTAGGCTTCTAGA	60.019	45.833	0.00	0.00	46.03	2.43
2755	3017	1.433879	GACATGAGAGGGACGTCCG	59.566	63.158	27.68	14.58	41.52	4.79
2792	3054	1.822371	GTCTGACTGGGAGGAGAACTC	59.178	57.143	0.00	0.00	45.84	3.01
2900	3169	1.927487	TTCCAGCAGCCATGTTGATT	58.073	45.000	0.00	0.00	39.83	2.57
2921	3190	0.180171	ACCAAGGGGCAAGCAAAAAC	59.820	50.000	0.00	0.00	37.90	2.43
3073	3343	4.504864	CCTCACTTGTCATGGACTTGGTTA	60.505	45.833	0.00	0.00	33.15	2.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.