AutoCloner

Multiple sequence alignment - TraesCS2D01G155600

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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	TraesCS2D01G155600	chr2D	100.000	3228	0	0	606	3833	99132257	99135484	0.000000e+00	5962.0
1	TraesCS2D01G155600	chr2D	100.000	216	0	0	1	216	99131652	99131867	2.150000e-107	399.0
2	TraesCS2D01G155600	chr2B	95.481	2390	80	17	606	2982	150710326	150712700	0.000000e+00	3790.0
3	TraesCS2D01G155600	chr2B	95.076	792	17	5	3062	3833	150712697	150713486	0.000000e+00	1227.0
4	TraesCS2D01G155600	chr2B	94.366	213	12	0	1	213	150710062	150710274	1.030000e-85	327.0
5	TraesCS2D01G155600	chr2A	94.865	2376	86	14	606	2978	98136714	98139056	0.000000e+00	3679.0
6	TraesCS2D01G155600	chr2A	95.128	780	17	9	3070	3831	98139058	98139834	0.000000e+00	1210.0
7	TraesCS2D01G155600	chr2A	91.244	217	17	2	1	216	98136442	98136657	1.040000e-75	294.0
8	TraesCS2D01G155600	chr2A	91.818	110	5	4	2962	3070	712843520	712843626	2.390000e-32	150.0
9	TraesCS2D01G155600	chr3D	92.729	894	28	18	1029	1922	284204420	284205276	0.000000e+00	1256.0
10	TraesCS2D01G155600	chr7B	91.163	894	42	17	1029	1922	29705080	29704224	0.000000e+00	1179.0
11	TraesCS2D01G155600	chr3B	93.139	583	24	10	1029	1610	245914013	245914580	0.000000e+00	841.0
12	TraesCS2D01G155600	chr3B	95.816	239	10	0	1684	1922	245921643	245921881	1.670000e-103	387.0
13	TraesCS2D01G155600	chr6A	92.442	172	12	1	622	793	24832593	24832423	1.060000e-60	244.0
14	TraesCS2D01G155600	chr6A	92.537	67	5	0	1	67	24832656	24832590	3.150000e-16	97.1
15	TraesCS2D01G155600	chr7D	98.864	88	1	0	2978	3065	548669050	548668963	1.430000e-34	158.0
16	TraesCS2D01G155600	chr5D	94.175	103	4	2	2970	3071	57225951	57226052	5.130000e-34	156.0
17	TraesCS2D01G155600	chr1D	94.175	103	3	3	2967	3066	85191614	85191512	1.840000e-33	154.0
18	TraesCS2D01G155600	chr1D	94.845	97	5	0	2978	3074	494560366	494560270	6.630000e-33	152.0
19	TraesCS2D01G155600	chr6D	92.381	105	8	0	2976	3080	34809012	34808908	2.390000e-32	150.0
20	TraesCS2D01G155600	chr1B	93.204	103	6	1	2977	3078	250420351	250420249	2.390000e-32	150.0
21	TraesCS2D01G155600	chr7A	91.071	112	6	4	2958	3066	13666786	13666896	8.580000e-32	148.0
22	TraesCS2D01G155600	chr3A	89.076	119	6	7	2968	3080	711064929	711064812	1.440000e-29	141.0

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	TraesCS2D01G155600	chr2D	99131652	99135484	3832	False	3180.500000	5962	100.000000	1	3833	2	chr2D.!!$F1	3832
1	TraesCS2D01G155600	chr2B	150710062	150713486	3424	False	1781.333333	3790	94.974333	1	3833	3	chr2B.!!$F1	3832
2	TraesCS2D01G155600	chr2A	98136442	98139834	3392	False	1727.666667	3679	93.745667	1	3831	3	chr2A.!!$F2	3830
3	TraesCS2D01G155600	chr3D	284204420	284205276	856	False	1256.000000	1256	92.729000	1029	1922	1	chr3D.!!$F1	893
4	TraesCS2D01G155600	chr7B	29704224	29705080	856	True	1179.000000	1179	91.163000	1029	1922	1	chr7B.!!$R1	893
5	TraesCS2D01G155600	chr3B	245914013	245914580	567	False	841.000000	841	93.139000	1029	1610	1	chr3B.!!$F1	581

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
812	834	0.664466	TGCTCGAACGAAGCACTCAG	60.664	55.000	13.73	0.0	33.24	3.35	F
2319	2350	1.066573	AGAGTGTTGGATCCTCTTGCG	60.067	52.381	14.23	0.0	31.64	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2598	2629	0.179000	CCAGTGCCCGCTTCTTAGAT	59.821	55.000	0.0	0.0	0.0	1.98	R
3651	3699	1.743252	CTTCCCTTGCTGAGTCCGC	60.743	63.158	0.0	0.0	0.0	5.54	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
85	86	3.072184	ACCTGCAACAGAAGATTCAGAGT	59.928	43.478	0.00	0.00	32.44	3.24
149	150	4.400567	ACCAAAATCCAGCAGAAATAGCTC	59.599	41.667	0.00	0.00	41.14	4.09
151	152	5.450137	CCAAAATCCAGCAGAAATAGCTCAG	60.450	44.000	0.00	0.00	41.14	3.35
692	696	1.363443	CTCGCTGCTCCTCATCTCC	59.637	63.158	0.00	0.00	0.00	3.71
699	710	0.831711	GCTCCTCATCTCCCTCCCTC	60.832	65.000	0.00	0.00	0.00	4.30
709	720	2.131067	CCCTCCCTCTCTTCCTCGC	61.131	68.421	0.00	0.00	0.00	5.03
727	738	3.554692	GCGATCGCACCGGACAAG	61.555	66.667	33.89	0.00	41.49	3.16
729	740	2.125512	GATCGCACCGGACAAGCT	60.126	61.111	9.46	0.00	0.00	3.74
810	832	4.245054	TGCTCGAACGAAGCACTC	57.755	55.556	13.73	0.00	33.24	3.51
811	833	1.362355	TGCTCGAACGAAGCACTCA	59.638	52.632	13.73	0.00	33.24	3.41
812	834	0.664466	TGCTCGAACGAAGCACTCAG	60.664	55.000	13.73	0.00	33.24	3.35
813	835	1.950098	GCTCGAACGAAGCACTCAGC	61.950	60.000	11.40	0.00	46.19	4.26
828	850	2.925170	AGCAGGAGAAGCCACGGT	60.925	61.111	0.00	0.00	40.02	4.83
983	1011	3.879912	GAAGGACTCGAACGGTTCA	57.120	52.632	19.91	7.16	0.00	3.18
1504	1535	1.735198	GTGTTCGACGGAATGCGGA	60.735	57.895	0.00	0.00	34.05	5.54
1560	1591	2.125961	GTACGCCGTGAGAGGGGAT	61.126	63.158	0.00	0.00	45.92	3.85
1566	1597	2.786495	CGTGAGAGGGGATGTCGGG	61.786	68.421	0.00	0.00	0.00	5.14
1668	1699	4.821589	CGGTCCAAGGAGGCGCTC	62.822	72.222	7.64	2.45	37.29	5.03
1737	1768	1.079612	CATGGTGAGCGTGCTCTCA	60.080	57.895	21.36	18.50	43.12	3.27
1889	1920	4.347876	TGAGAATTCTCTGAAGGTGTTCCA	59.652	41.667	30.45	8.48	43.25	3.53
1983	2014	5.220548	CCATGATGCTCTAAGTTTGTTCTCG	60.221	44.000	0.00	0.00	0.00	4.04
2214	2245	1.252904	GGAGCATGCCTTTTGAGCCA	61.253	55.000	15.66	0.00	0.00	4.75
2319	2350	1.066573	AGAGTGTTGGATCCTCTTGCG	60.067	52.381	14.23	0.00	31.64	4.85
2325	2356	1.072159	GGATCCTCTTGCGGATGGG	59.928	63.158	3.84	0.00	43.71	4.00
2337	2368	1.474320	GCGGATGGGCACTATGTGTTA	60.474	52.381	0.00	0.00	35.75	2.41
2514	2545	4.022416	CCGAGGATTGAGGAGATCTACAAG	60.022	50.000	7.93	0.00	0.00	3.16
2518	2549	5.011943	AGGATTGAGGAGATCTACAAGATGC	59.988	44.000	7.93	3.02	34.53	3.91
2583	2614	4.171005	CAATGACAAGCTTGGTATTGCAG	58.829	43.478	28.93	16.13	32.78	4.41
2598	2629	5.474532	GGTATTGCAGGATATTGATGAGCAA	59.525	40.000	0.00	0.00	43.50	3.91
2881	2912	4.272261	GGTTTTGGTGTAGCAATTGTTTGG	59.728	41.667	7.40	0.00	33.22	3.28
2988	3019	8.700439	AGAACAATCTTCTATAGTACTCCCTC	57.300	38.462	0.00	0.00	29.15	4.30
2989	3020	8.507761	AGAACAATCTTCTATAGTACTCCCTCT	58.492	37.037	0.00	0.00	29.15	3.69
2990	3021	8.472007	AACAATCTTCTATAGTACTCCCTCTG	57.528	38.462	0.00	0.00	0.00	3.35
2991	3022	7.588169	ACAATCTTCTATAGTACTCCCTCTGT	58.412	38.462	0.00	0.00	0.00	3.41
2992	3023	8.725256	ACAATCTTCTATAGTACTCCCTCTGTA	58.275	37.037	0.00	0.00	0.00	2.74
2993	3024	9.575868	CAATCTTCTATAGTACTCCCTCTGTAA	57.424	37.037	0.00	0.00	0.00	2.41
2995	3026	8.977267	TCTTCTATAGTACTCCCTCTGTAAAC	57.023	38.462	0.00	0.00	0.00	2.01
2996	3027	8.780003	TCTTCTATAGTACTCCCTCTGTAAACT	58.220	37.037	0.00	0.00	0.00	2.66
3038	3069	9.351570	AGATTACTAAAGTAGTGTTCTAAACGC	57.648	33.333	0.00	0.00	39.81	4.84
3056	3087	9.669353	TCTAAACGCTCTTATATTAGTTTACGG	57.331	33.333	0.00	0.00	34.29	4.02
3057	3088	9.669353	CTAAACGCTCTTATATTAGTTTACGGA	57.331	33.333	0.00	0.00	34.29	4.69
3058	3089	8.571461	AAACGCTCTTATATTAGTTTACGGAG	57.429	34.615	0.00	0.00	31.14	4.63
3059	3090	6.675987	ACGCTCTTATATTAGTTTACGGAGG	58.324	40.000	0.00	0.00	0.00	4.30
3060	3091	6.091437	CGCTCTTATATTAGTTTACGGAGGG	58.909	44.000	0.00	0.00	0.00	4.30
3287	3319	7.405292	ACTATCATGAACCATCCAAGAGAAAA	58.595	34.615	0.00	0.00	0.00	2.29
3634	3682	6.183360	GCTGTGACCGAAATGATCAAGAAATA	60.183	38.462	0.00	0.00	0.00	1.40
3638	3686	9.405587	GTGACCGAAATGATCAAGAAATAAAAA	57.594	29.630	0.00	0.00	0.00	1.94
3800	3852	2.566833	TGCAGCAATGTCTAACAGGT	57.433	45.000	0.00	0.00	0.00	4.00

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
149	150	2.679355	CTCCGACGAGCTAATCTCTG	57.321	55.000	0.00	0.00	39.70	3.35
605	606	2.639839	CGAGGTATCCATCTTCCCCAAT	59.360	50.000	0.00	0.00	0.00	3.16
606	607	2.047061	CGAGGTATCCATCTTCCCCAA	58.953	52.381	0.00	0.00	0.00	4.12
607	608	1.717032	CGAGGTATCCATCTTCCCCA	58.283	55.000	0.00	0.00	0.00	4.96
608	609	0.977395	CCGAGGTATCCATCTTCCCC	59.023	60.000	0.00	0.00	0.00	4.81
609	610	2.011122	TCCGAGGTATCCATCTTCCC	57.989	55.000	0.00	0.00	0.00	3.97
610	611	2.300437	CCTTCCGAGGTATCCATCTTCC	59.700	54.545	0.00	0.00	38.32	3.46
611	612	2.300437	CCCTTCCGAGGTATCCATCTTC	59.700	54.545	0.00	0.00	41.85	2.87
612	613	2.330216	CCCTTCCGAGGTATCCATCTT	58.670	52.381	0.00	0.00	41.85	2.40
659	663	1.834378	CGAGGCCATGGAGCTCCTA	60.834	63.158	32.28	19.38	36.82	2.94
692	696	2.485795	CGCGAGGAAGAGAGGGAGG	61.486	68.421	0.00	0.00	0.00	4.30
699	710	2.723995	CGATCGCGCGAGGAAGAG	60.724	66.667	36.99	19.41	0.00	2.85
808	830	1.447489	CGTGGCTTCTCCTGCTGAG	60.447	63.158	0.00	0.00	42.90	3.35
809	831	2.659016	CGTGGCTTCTCCTGCTGA	59.341	61.111	0.00	0.00	35.26	4.26
810	832	2.435586	CCGTGGCTTCTCCTGCTG	60.436	66.667	0.00	0.00	35.26	4.41
811	833	2.925170	ACCGTGGCTTCTCCTGCT	60.925	61.111	0.00	0.00	35.26	4.24
812	834	2.435059	GACCGTGGCTTCTCCTGC	60.435	66.667	0.00	0.00	35.26	4.85
813	835	2.125912	CGACCGTGGCTTCTCCTG	60.126	66.667	0.00	0.00	35.26	3.86
814	836	4.070552	GCGACCGTGGCTTCTCCT	62.071	66.667	0.00	0.00	35.26	3.69
819	841	4.681978	GTGGAGCGACCGTGGCTT	62.682	66.667	9.60	0.00	41.72	4.35
965	987	2.144482	TTGAACCGTTCGAGTCCTTC	57.856	50.000	6.78	0.00	0.00	3.46
966	988	2.480845	CTTTGAACCGTTCGAGTCCTT	58.519	47.619	6.78	0.00	0.00	3.36
967	989	1.872653	GCTTTGAACCGTTCGAGTCCT	60.873	52.381	6.78	0.00	0.00	3.85
968	990	0.511653	GCTTTGAACCGTTCGAGTCC	59.488	55.000	6.78	0.00	0.00	3.85
969	991	1.214367	TGCTTTGAACCGTTCGAGTC	58.786	50.000	6.78	1.92	0.00	3.36
979	1007	0.110010	GCCGAGAGCTTGCTTTGAAC	60.110	55.000	0.00	0.00	38.99	3.18
983	1011	1.078848	ATCGCCGAGAGCTTGCTTT	60.079	52.632	0.00	0.00	40.39	3.51
1087	1115	3.764049	GGTGCTGACGACGAACGC	61.764	66.667	0.00	0.70	46.94	4.84
1483	1514	1.787847	GCATTCCGTCGAACACCTG	59.212	57.895	0.00	0.00	0.00	4.00
1484	1515	1.736645	CGCATTCCGTCGAACACCT	60.737	57.895	0.00	0.00	0.00	4.00
1560	1591	4.770362	TCCCTCGCCATCCCGACA	62.770	66.667	0.00	0.00	33.12	4.35
1566	1597	1.819288	TCGAATATCTCCCTCGCCATC	59.181	52.381	0.00	0.00	32.66	3.51
1668	1699	1.364626	GCATCACCTTCCACAGCTCG	61.365	60.000	0.00	0.00	0.00	5.03
1699	1730	0.179089	GTGATGCAGTCTGGAGCGAT	60.179	55.000	5.09	0.00	0.00	4.58
1889	1920	0.179073	GTCCATCACAGGCATAGCGT	60.179	55.000	0.00	0.00	0.00	5.07
1983	2014	4.202295	TGCAGTCCTTGTGATATCATCTCC	60.202	45.833	9.02	0.00	0.00	3.71
2214	2245	7.395489	AGAAGTGTTCTCCAAATAATTGCATCT	59.605	33.333	0.00	0.00	34.07	2.90
2292	2323	5.087323	AGAGGATCCAACACTCTCAGTTTA	58.913	41.667	15.82	0.00	36.96	2.01
2296	2327	3.859443	CAAGAGGATCCAACACTCTCAG	58.141	50.000	15.82	0.71	40.49	3.35
2300	2331	1.363744	CGCAAGAGGATCCAACACTC	58.636	55.000	15.82	1.71	43.02	3.51
2319	2350	3.206150	CAGTAACACATAGTGCCCATCC	58.794	50.000	0.00	0.00	36.98	3.51
2325	2356	5.666969	TGTTTGACAGTAACACATAGTGC	57.333	39.130	0.00	0.00	38.32	4.40
2337	2368	5.415389	TGCTTGTGCATATATGTTTGACAGT	59.585	36.000	14.14	0.00	45.31	3.55
2433	2464	0.955178	TCTCCCATTCGATCGAGCTC	59.045	55.000	18.54	2.73	0.00	4.09
2514	2545	2.553172	GCCAATCATCTCTTCCAGCATC	59.447	50.000	0.00	0.00	0.00	3.91
2518	2549	1.590932	CGGCCAATCATCTCTTCCAG	58.409	55.000	2.24	0.00	0.00	3.86
2583	2614	7.412781	CGCTTCTTAGATTGCTCATCAATATCC	60.413	40.741	6.27	0.00	44.95	2.59
2598	2629	0.179000	CCAGTGCCCGCTTCTTAGAT	59.821	55.000	0.00	0.00	0.00	1.98
2798	2829	0.330604	ACATGAGCACTGCCCTTCAT	59.669	50.000	0.00	0.00	0.00	2.57
2847	2878	5.243060	GCTACACCAAAACCTTTTCTGGTAT	59.757	40.000	0.00	0.00	39.83	2.73
2858	2889	4.272261	CCAAACAATTGCTACACCAAAACC	59.728	41.667	5.05	0.00	35.10	3.27
2881	2912	0.880718	GAATGCTAGCAGGGTACGGC	60.881	60.000	23.89	2.25	38.13	5.68
3012	3043	9.351570	GCGTTTAGAACACTACTTTAGTAATCT	57.648	33.333	5.76	5.76	37.23	2.40
3013	3044	9.351570	AGCGTTTAGAACACTACTTTAGTAATC	57.648	33.333	0.00	0.00	37.23	1.75
3014	3045	9.351570	GAGCGTTTAGAACACTACTTTAGTAAT	57.648	33.333	0.00	0.00	37.23	1.89
3015	3046	8.571336	AGAGCGTTTAGAACACTACTTTAGTAA	58.429	33.333	0.00	0.00	37.23	2.24
3016	3047	8.103948	AGAGCGTTTAGAACACTACTTTAGTA	57.896	34.615	0.00	0.00	37.23	1.82
3017	3048	6.979465	AGAGCGTTTAGAACACTACTTTAGT	58.021	36.000	0.00	0.00	40.28	2.24
3018	3049	7.870588	AAGAGCGTTTAGAACACTACTTTAG	57.129	36.000	0.00	0.00	0.00	1.85
3030	3061	9.669353	CCGTAAACTAATATAAGAGCGTTTAGA	57.331	33.333	0.00	0.00	30.36	2.10
3031	3062	9.669353	TCCGTAAACTAATATAAGAGCGTTTAG	57.331	33.333	0.00	0.00	30.36	1.85
3032	3063	9.669353	CTCCGTAAACTAATATAAGAGCGTTTA	57.331	33.333	0.00	0.00	0.00	2.01
3033	3064	7.650903	CCTCCGTAAACTAATATAAGAGCGTTT	59.349	37.037	0.00	0.00	0.00	3.60
3034	3065	7.144000	CCTCCGTAAACTAATATAAGAGCGTT	58.856	38.462	0.00	0.00	0.00	4.84
3035	3066	6.294397	CCCTCCGTAAACTAATATAAGAGCGT	60.294	42.308	0.00	0.00	0.00	5.07
3036	3067	6.072286	TCCCTCCGTAAACTAATATAAGAGCG	60.072	42.308	0.00	0.00	0.00	5.03
3037	3068	7.039853	ACTCCCTCCGTAAACTAATATAAGAGC	60.040	40.741	0.00	0.00	0.00	4.09
3038	3069	8.406730	ACTCCCTCCGTAAACTAATATAAGAG	57.593	38.462	0.00	0.00	0.00	2.85
3041	3072	9.812347	TGATACTCCCTCCGTAAACTAATATAA	57.188	33.333	0.00	0.00	0.00	0.98
3042	3073	9.986157	ATGATACTCCCTCCGTAAACTAATATA	57.014	33.333	0.00	0.00	0.00	0.86
3043	3074	8.896722	ATGATACTCCCTCCGTAAACTAATAT	57.103	34.615	0.00	0.00	0.00	1.28
3044	3075	9.986157	ATATGATACTCCCTCCGTAAACTAATA	57.014	33.333	0.00	0.00	0.00	0.98
3045	3076	8.896722	ATATGATACTCCCTCCGTAAACTAAT	57.103	34.615	0.00	0.00	0.00	1.73
3046	3077	9.986157	ATATATGATACTCCCTCCGTAAACTAA	57.014	33.333	0.00	0.00	0.00	2.24
3047	3078	9.986157	AATATATGATACTCCCTCCGTAAACTA	57.014	33.333	0.00	0.00	0.00	2.24
3048	3079	8.896722	AATATATGATACTCCCTCCGTAAACT	57.103	34.615	0.00	0.00	0.00	2.66
3513	3545	4.996122	CAGCAACTTCTGAAGAATGACTCT	59.004	41.667	23.36	11.00	36.19	3.24
3638	3686	6.919721	TGCTGAGTCCGCTTTAAATAATTTT	58.080	32.000	8.09	0.00	0.00	1.82
3651	3699	1.743252	CTTCCCTTGCTGAGTCCGC	60.743	63.158	0.00	0.00	0.00	5.54
3800	3852	4.453177	CCATTTCATGGTGCAATGTGTA	57.547	40.909	0.00	0.00	45.54	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.