AutoCloner

Multiple sequence alignment - TraesCS2D01G292700

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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	TraesCS2D01G292700	chr2D	100.000	3297	0	0	1	3297	375253761	375257057	0.000000e+00	6089.0
1	TraesCS2D01G292700	chr2D	87.596	653	63	8	3	646	470759803	470759160	0.000000e+00	741.0
2	TraesCS2D01G292700	chr2D	85.672	670	62	24	1	649	591574417	591575073	0.000000e+00	675.0
3	TraesCS2D01G292700	chr2A	92.575	1872	71	26	647	2477	507601442	507603286	0.000000e+00	2625.0
4	TraesCS2D01G292700	chr2A	93.901	787	20	2	2515	3297	507603286	507604048	0.000000e+00	1162.0
5	TraesCS2D01G292700	chr2A	84.352	671	75	23	1	653	669555076	669555734	6.000000e-177	630.0
6	TraesCS2D01G292700	chr2B	91.620	1253	57	14	646	1882	445489618	445490838	0.000000e+00	1688.0
7	TraesCS2D01G292700	chr2B	90.711	1012	44	15	2312	3297	445496316	445497303	0.000000e+00	1303.0
8	TraesCS2D01G292700	chr2B	84.896	192	23	4	1886	2075	445491327	445491514	4.340000e-44	189.0
9	TraesCS2D01G292700	chr2B	91.525	118	5	2	2205	2322	445496186	445496298	1.220000e-34	158.0
10	TraesCS2D01G292700	chr6D	89.939	656	54	6	1	646	58438932	58439585	0.000000e+00	835.0
11	TraesCS2D01G292700	chr7A	90.285	597	40	5	1	588	612409543	612410130	0.000000e+00	765.0
12	TraesCS2D01G292700	chr5A	87.746	661	60	10	1	648	307706870	307706218	0.000000e+00	752.0
13	TraesCS2D01G292700	chr5D	86.950	659	62	16	1	646	127884291	127884938	0.000000e+00	719.0
14	TraesCS2D01G292700	chr4B	85.994	664	74	10	1	650	43761232	43760574	0.000000e+00	693.0
15	TraesCS2D01G292700	chr3B	87.415	588	55	11	1	580	128811138	128810562	0.000000e+00	658.0
16	TraesCS2D01G292700	chr3B	94.828	58	2	1	589	646	71129032	71128976	4.530000e-14	89.8

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	TraesCS2D01G292700	chr2D	375253761	375257057	3296	False	6089.0	6089	100.000	1	3297	1	chr2D.!!$F1	3296
1	TraesCS2D01G292700	chr2D	470759160	470759803	643	True	741.0	741	87.596	3	646	1	chr2D.!!$R1	643
2	TraesCS2D01G292700	chr2D	591574417	591575073	656	False	675.0	675	85.672	1	649	1	chr2D.!!$F2	648
3	TraesCS2D01G292700	chr2A	507601442	507604048	2606	False	1893.5	2625	93.238	647	3297	2	chr2A.!!$F2	2650
4	TraesCS2D01G292700	chr2A	669555076	669555734	658	False	630.0	630	84.352	1	653	1	chr2A.!!$F1	652
5	TraesCS2D01G292700	chr2B	445489618	445491514	1896	False	938.5	1688	88.258	646	2075	2	chr2B.!!$F1	1429
6	TraesCS2D01G292700	chr2B	445496186	445497303	1117	False	730.5	1303	91.118	2205	3297	2	chr2B.!!$F2	1092
7	TraesCS2D01G292700	chr6D	58438932	58439585	653	False	835.0	835	89.939	1	646	1	chr6D.!!$F1	645
8	TraesCS2D01G292700	chr7A	612409543	612410130	587	False	765.0	765	90.285	1	588	1	chr7A.!!$F1	587
9	TraesCS2D01G292700	chr5A	307706218	307706870	652	True	752.0	752	87.746	1	648	1	chr5A.!!$R1	647
10	TraesCS2D01G292700	chr5D	127884291	127884938	647	False	719.0	719	86.950	1	646	1	chr5D.!!$F1	645
11	TraesCS2D01G292700	chr4B	43760574	43761232	658	True	693.0	693	85.994	1	650	1	chr4B.!!$R1	649
12	TraesCS2D01G292700	chr3B	128810562	128811138	576	True	658.0	658	87.415	1	580	1	chr3B.!!$R2	579

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
622	677	1.077645	CCGAAATCGCCGTCCGTTTA	61.078	55.0	0.0	0.0	38.18	2.01	F
1719	1809	0.036388	TGAATCTGGGGCGAGTGAAC	60.036	55.0	0.0	0.0	0.00	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1911	2487	0.040958	CCAAAGCACGCAAGACTCAC	60.041	55.0	0.0	0.0	43.62	3.51	R
2807	3501	0.391661	GGAGCTTGGACGAGATGCAA	60.392	55.0	0.0	0.0	36.08	4.08	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
99	100	1.664321	GGCGTACCTCGAGATGTGGT	61.664	60.000	15.71	6.23	46.03	4.16
372	402	3.616721	CCTAGGGTAGCGCGCCAT	61.617	66.667	30.33	13.66	0.00	4.40
460	496	3.507786	CTGGCCGGCTTTAATGTTTAAC	58.492	45.455	28.56	4.81	0.00	2.01
622	677	1.077645	CCGAAATCGCCGTCCGTTTA	61.078	55.000	0.00	0.00	38.18	2.01
653	708	3.127548	CGTTGGAGTTGCTCTTAATGCAT	59.872	43.478	0.00	0.00	40.34	3.96
734	789	2.176798	AGATGTGACCCAAGAAACCCAA	59.823	45.455	0.00	0.00	0.00	4.12
923	985	4.760047	CCTCCCAACGGCACTCGG	62.760	72.222	0.00	0.00	44.45	4.63
979	1042	2.547855	GCCAAGCCAACCTTTCGAAATT	60.548	45.455	11.70	0.53	0.00	1.82
1001	1064	4.394712	CGCCTTTGTCGCCTCCCT	62.395	66.667	0.00	0.00	0.00	4.20
1102	1165	1.303074	CAGCAGGCAAGAAGAGGCA	60.303	57.895	0.00	0.00	0.00	4.75
1719	1809	0.036388	TGAATCTGGGGCGAGTGAAC	60.036	55.000	0.00	0.00	0.00	3.18
1799	1889	0.978146	CGGTTCTGGGTCTGGGAGAT	60.978	60.000	0.00	0.00	0.00	2.75
1860	1951	0.729140	GCGGTGCTTGGTTTGAATCG	60.729	55.000	0.00	0.00	0.00	3.34
1872	1963	0.110238	TTGAATCGCTTGCGTGCTTC	60.110	50.000	14.70	14.92	0.00	3.86
1882	1973	2.328099	GCGTGCTTCAGGAACAGGG	61.328	63.158	0.00	0.00	0.00	4.45
1883	1974	1.672356	CGTGCTTCAGGAACAGGGG	60.672	63.158	0.00	0.00	0.00	4.79
1903	2479	2.226437	GGGCAGTTGTGTACACATCTTG	59.774	50.000	28.83	24.75	41.52	3.02
1911	2487	6.701841	AGTTGTGTACACATCTTGAGTTGTAG	59.298	38.462	28.35	0.00	41.52	2.74
1912	2488	6.156748	TGTGTACACATCTTGAGTTGTAGT	57.843	37.500	24.62	0.62	36.21	2.73
2014	2595	0.309612	CGCCCGTGCTAAACAAAACT	59.690	50.000	0.00	0.00	34.43	2.66
2092	2680	6.547880	ACAGCTAGTAGTAGTATCATTGTGCT	59.452	38.462	6.47	0.00	0.00	4.40
2114	2702	5.746721	GCTAAATCGGTGTTTGACTTTTGTT	59.253	36.000	0.00	0.00	0.00	2.83
2115	2703	6.913673	GCTAAATCGGTGTTTGACTTTTGTTA	59.086	34.615	0.00	0.00	0.00	2.41
2116	2704	7.593644	GCTAAATCGGTGTTTGACTTTTGTTAT	59.406	33.333	0.00	0.00	0.00	1.89
2118	2706	8.791355	AAATCGGTGTTTGACTTTTGTTATAC	57.209	30.769	0.00	0.00	0.00	1.47
2119	2707	7.739498	ATCGGTGTTTGACTTTTGTTATACT	57.261	32.000	0.00	0.00	0.00	2.12
2143	2741	3.575687	CTCTTTCTTTGGGGCACAATCTT	59.424	43.478	1.47	0.00	39.21	2.40
2152	2750	1.599542	GGGCACAATCTTATCACTCGC	59.400	52.381	0.00	0.00	0.00	5.03
2202	2800	6.014499	GGCAATGTGTACTACTCCTATATGGT	60.014	42.308	0.00	0.00	37.07	3.55
2251	2849	2.051692	TCTCACCGGGAAGAAAAAGGA	58.948	47.619	6.32	0.00	0.00	3.36
2257	2855	3.136992	ACCGGGAAGAAAAAGGAACTACA	59.863	43.478	6.32	0.00	38.49	2.74
2258	2856	3.751698	CCGGGAAGAAAAAGGAACTACAG	59.248	47.826	0.00	0.00	38.49	2.74
2264	2862	5.541953	AGAAAAAGGAACTACAGTACGGT	57.458	39.130	3.62	3.62	38.49	4.83
2395	3022	3.146828	AACCCAACCCAGTGAGGCC	62.147	63.158	0.00	0.00	35.39	5.19
2412	3039	3.801997	CGGAGAGGCCAGCCCAAT	61.802	66.667	5.01	0.00	35.94	3.16
2419	3046	0.186873	AGGCCAGCCCAATCCAATAG	59.813	55.000	5.01	0.00	36.58	1.73
2485	3121	1.734748	TTTTTCGGTTTGCGGACCC	59.265	52.632	3.01	0.00	36.28	4.46
2486	3122	0.752376	TTTTTCGGTTTGCGGACCCT	60.752	50.000	3.01	0.00	36.28	4.34
2487	3123	1.167781	TTTTCGGTTTGCGGACCCTC	61.168	55.000	3.01	0.00	36.28	4.30
2488	3124	3.540367	TTCGGTTTGCGGACCCTCC	62.540	63.158	3.01	0.00	36.28	4.30
2489	3125	4.016706	CGGTTTGCGGACCCTCCT	62.017	66.667	3.01	0.00	36.28	3.69
2490	3126	2.046217	GGTTTGCGGACCCTCCTC	60.046	66.667	0.00	0.00	33.30	3.71
2491	3127	2.593956	GGTTTGCGGACCCTCCTCT	61.594	63.158	0.00	0.00	33.30	3.69
2492	3128	1.375326	GTTTGCGGACCCTCCTCTT	59.625	57.895	0.00	0.00	33.30	2.85
2493	3129	0.673956	GTTTGCGGACCCTCCTCTTC	60.674	60.000	0.00	0.00	33.30	2.87
2494	3130	0.836400	TTTGCGGACCCTCCTCTTCT	60.836	55.000	0.00	0.00	33.30	2.85
2495	3131	1.258445	TTGCGGACCCTCCTCTTCTC	61.258	60.000	0.00	0.00	33.30	2.87
2496	3132	1.380650	GCGGACCCTCCTCTTCTCT	60.381	63.158	0.00	0.00	33.30	3.10
2497	3133	1.671901	GCGGACCCTCCTCTTCTCTG	61.672	65.000	0.00	0.00	33.30	3.35
2498	3134	1.040339	CGGACCCTCCTCTTCTCTGG	61.040	65.000	0.00	0.00	33.30	3.86
2499	3135	1.334384	GGACCCTCCTCTTCTCTGGC	61.334	65.000	0.00	0.00	32.53	4.85
2500	3136	1.671901	GACCCTCCTCTTCTCTGGCG	61.672	65.000	0.00	0.00	0.00	5.69
2501	3137	2.498726	CCTCCTCTTCTCTGGCGC	59.501	66.667	0.00	0.00	0.00	6.53
2502	3138	2.103934	CTCCTCTTCTCTGGCGCG	59.896	66.667	0.00	0.00	0.00	6.86
2503	3139	3.423162	CTCCTCTTCTCTGGCGCGG	62.423	68.421	8.83	0.00	0.00	6.46
2504	3140	4.521062	CCTCTTCTCTGGCGCGGG	62.521	72.222	8.83	0.00	0.00	6.13
2523	3207	2.204151	ACCAACCCTCTCCCCCAG	60.204	66.667	0.00	0.00	0.00	4.45
2769	3463	4.421479	AGTGCTTCTCCGTCGCCG	62.421	66.667	0.00	0.00	0.00	6.46
2771	3465	3.057548	TGCTTCTCCGTCGCCGTA	61.058	61.111	0.00	0.00	0.00	4.02
2774	3468	2.749044	TTCTCCGTCGCCGTAGCT	60.749	61.111	0.00	0.00	36.60	3.32
2784	3478	4.849329	CCGTAGCTGTCGCCGTCC	62.849	72.222	0.00	0.00	36.60	4.79
2786	3480	4.509737	GTAGCTGTCGCCGTCCCC	62.510	72.222	0.00	0.00	36.60	4.81
3074	3768	2.031465	GTCCCGGACGCCAAGAAA	59.969	61.111	0.73	0.00	0.00	2.52
3119	3813	0.179009	CCGGCATGGAGGTGATCAAT	60.179	55.000	0.00	0.00	42.00	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
410	446	3.948086	GAGAGTCCACGCGTCCACG	62.948	68.421	9.86	0.00	43.27	4.94
505	546	1.209127	GACCCATTTTGACGGTGCG	59.791	57.895	0.00	0.00	0.00	5.34
603	658	1.077645	TAAACGGACGGCGATTTCGG	61.078	55.000	16.62	8.01	40.23	4.30
669	724	7.584123	CAGTTTCTCGACTGTTACTTGAAATTG	59.416	37.037	0.00	0.00	41.62	2.32
674	729	5.067413	ACTCAGTTTCTCGACTGTTACTTGA	59.933	40.000	5.09	0.00	45.64	3.02
684	739	5.155643	GGTCTTTCTACTCAGTTTCTCGAC	58.844	45.833	0.00	0.00	0.00	4.20
734	789	2.048503	GTGACGTACTGCCGGCTT	60.049	61.111	29.70	17.30	36.61	4.35
979	1042	2.975799	GGCGACAAAGGCGTGGAA	60.976	61.111	0.00	0.00	0.00	3.53
1001	1064	5.247862	GGAGTCGGAGGTTTGGTATAAAAA	58.752	41.667	0.00	0.00	0.00	1.94
1102	1165	0.254178	ATCGAGCTGTGGCATCCTTT	59.746	50.000	0.00	0.00	41.70	3.11
1361	1433	1.628846	GCCTCCAACTCCAACCTCTTA	59.371	52.381	0.00	0.00	0.00	2.10
1363	1435	0.768221	TGCCTCCAACTCCAACCTCT	60.768	55.000	0.00	0.00	0.00	3.69
1514	1586	2.863346	CGACACCTTCGGGGACACA	61.863	63.158	2.52	0.00	44.60	3.72
1830	1920	2.898920	AAGCACCGCCCATCTCCATG	62.899	60.000	0.00	0.00	0.00	3.66
1860	1951	1.081840	GTTCCTGAAGCACGCAAGC	60.082	57.895	0.00	0.00	45.62	4.01
1872	1963	1.604593	CAACTGCCCCCTGTTCCTG	60.605	63.158	0.00	0.00	31.71	3.86
1882	1973	2.185004	AGATGTGTACACAACTGCCC	57.815	50.000	30.98	16.85	45.41	5.36
1883	1974	3.138304	TCAAGATGTGTACACAACTGCC	58.862	45.455	31.83	18.77	42.50	4.85
1903	2479	2.726760	CACGCAAGACTCACTACAACTC	59.273	50.000	0.00	0.00	43.62	3.01
1911	2487	0.040958	CCAAAGCACGCAAGACTCAC	60.041	55.000	0.00	0.00	43.62	3.51
1912	2488	0.463654	ACCAAAGCACGCAAGACTCA	60.464	50.000	0.00	0.00	43.62	3.41
2014	2595	3.066064	GCACGAGAGAAGATCAGAGCTTA	59.934	47.826	0.00	0.00	0.00	3.09
2092	2680	9.881529	GTATAACAAAAGTCAAACACCGATTTA	57.118	29.630	0.00	0.00	0.00	1.40
2114	2702	5.486063	TGTGCCCCAAAGAAAGAGTAGTATA	59.514	40.000	0.00	0.00	0.00	1.47
2115	2703	4.288626	TGTGCCCCAAAGAAAGAGTAGTAT	59.711	41.667	0.00	0.00	0.00	2.12
2116	2704	3.649023	TGTGCCCCAAAGAAAGAGTAGTA	59.351	43.478	0.00	0.00	0.00	1.82
2117	2705	2.441750	TGTGCCCCAAAGAAAGAGTAGT	59.558	45.455	0.00	0.00	0.00	2.73
2118	2706	3.140325	TGTGCCCCAAAGAAAGAGTAG	57.860	47.619	0.00	0.00	0.00	2.57
2119	2707	3.586470	TTGTGCCCCAAAGAAAGAGTA	57.414	42.857	0.00	0.00	0.00	2.59
2143	2741	0.733150	CGACCAGTGAGCGAGTGATA	59.267	55.000	0.00	0.00	0.00	2.15
2251	2849	4.099881	TCTTTGACCAACCGTACTGTAGTT	59.900	41.667	0.00	0.00	0.00	2.24
2257	2855	1.682854	TCGTCTTTGACCAACCGTACT	59.317	47.619	0.00	0.00	0.00	2.73
2258	2856	2.138596	TCGTCTTTGACCAACCGTAC	57.861	50.000	0.00	0.00	0.00	3.67
2264	2862	1.492319	CCGCGTTCGTCTTTGACCAA	61.492	55.000	4.92	0.00	0.00	3.67
2395	3022	3.764160	GATTGGGCTGGCCTCTCCG	62.764	68.421	21.72	0.00	37.80	4.63
2412	3039	0.245266	TTGAGTCGCGCACTATTGGA	59.755	50.000	8.75	0.00	34.41	3.53
2419	3046	1.472276	CTATCCGTTGAGTCGCGCAC	61.472	60.000	8.75	4.91	0.00	5.34
2476	3112	1.229209	AGAAGAGGAGGGTCCGCAA	60.229	57.895	0.00	0.00	42.75	4.85
2477	3113	1.682684	GAGAAGAGGAGGGTCCGCA	60.683	63.158	0.00	0.00	42.75	5.69
2478	3114	1.380650	AGAGAAGAGGAGGGTCCGC	60.381	63.158	0.00	0.00	42.75	5.54
2479	3115	1.040339	CCAGAGAAGAGGAGGGTCCG	61.040	65.000	0.00	0.00	42.75	4.79
2480	3116	1.334384	GCCAGAGAAGAGGAGGGTCC	61.334	65.000	0.00	0.00	36.58	4.46
2481	3117	1.671901	CGCCAGAGAAGAGGAGGGTC	61.672	65.000	0.00	0.00	0.00	4.46
2482	3118	1.684049	CGCCAGAGAAGAGGAGGGT	60.684	63.158	0.00	0.00	0.00	4.34
2483	3119	3.087666	GCGCCAGAGAAGAGGAGGG	62.088	68.421	0.00	0.00	0.00	4.30
2484	3120	2.498726	GCGCCAGAGAAGAGGAGG	59.501	66.667	0.00	0.00	0.00	4.30
2485	3121	2.103934	CGCGCCAGAGAAGAGGAG	59.896	66.667	0.00	0.00	0.00	3.69
2486	3122	3.452786	CCGCGCCAGAGAAGAGGA	61.453	66.667	0.00	0.00	0.00	3.71
2487	3123	4.521062	CCCGCGCCAGAGAAGAGG	62.521	72.222	0.00	0.00	0.00	3.69
2503	3139	4.048470	GGGGAGAGGGTTGGTGCC	62.048	72.222	0.00	0.00	0.00	5.01
2504	3140	4.048470	GGGGGAGAGGGTTGGTGC	62.048	72.222	0.00	0.00	0.00	5.01
2505	3141	2.531685	TGGGGGAGAGGGTTGGTG	60.532	66.667	0.00	0.00	0.00	4.17
2506	3142	2.204151	CTGGGGGAGAGGGTTGGT	60.204	66.667	0.00	0.00	0.00	3.67
2507	3143	2.204151	ACTGGGGGAGAGGGTTGG	60.204	66.667	0.00	0.00	0.00	3.77
2508	3144	2.660064	CGACTGGGGGAGAGGGTTG	61.660	68.421	0.00	0.00	0.00	3.77
2509	3145	2.182858	ATCGACTGGGGGAGAGGGTT	62.183	60.000	0.00	0.00	0.00	4.11
2510	3146	2.182858	AATCGACTGGGGGAGAGGGT	62.183	60.000	0.00	0.00	0.00	4.34
2511	3147	1.383248	AATCGACTGGGGGAGAGGG	60.383	63.158	0.00	0.00	0.00	4.30
2512	3148	1.739338	CGAATCGACTGGGGGAGAGG	61.739	65.000	0.00	0.00	0.00	3.69
2513	3149	0.752009	TCGAATCGACTGGGGGAGAG	60.752	60.000	0.00	0.00	0.00	3.20
2769	3463	4.509737	GGGGACGGCGACAGCTAC	62.510	72.222	16.62	0.00	44.37	3.58
2807	3501	0.391661	GGAGCTTGGACGAGATGCAA	60.392	55.000	0.00	0.00	36.08	4.08
2897	3591	1.616628	GGTGGTGGAGGTGAGGGAT	60.617	63.158	0.00	0.00	0.00	3.85
2963	3657	4.432741	GGCAGGTCCTTGGCTCCC	62.433	72.222	1.50	0.00	40.23	4.30
3099	3793	1.561769	TTGATCACCTCCATGCCGGT	61.562	55.000	1.90	0.00	35.57	5.28
3119	3813	2.190313	GCCATGATCTCCCACGCA	59.810	61.111	0.00	0.00	0.00	5.24
3263	3957	2.592993	CGGGCTGTTCTCCTTCCCA	61.593	63.158	0.00	0.00	36.79	4.37

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.