AutoCloner

Multiple sequence alignment - TraesCS2A01G333600

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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	TraesCS2A01G333600	chr2A	100.000	2498	0	0	1	2498	566987979	566985482	0.000000e+00	4614.0
1	TraesCS2A01G333600	chr2A	96.526	1900	42	3	1	1876	547775194	547777093	0.000000e+00	3121.0
2	TraesCS2A01G333600	chr2A	95.404	544	21	3	1864	2405	547783791	547784332	0.000000e+00	863.0
3	TraesCS2A01G333600	chr2A	84.948	485	37	17	653	1113	547271185	547271657	2.260000e-125	459.0
4	TraesCS2A01G333600	chr2A	88.889	135	9	5	2043	2175	547271676	547271806	7.150000e-36	161.0
5	TraesCS2A01G333600	chr2D	83.816	2280	161	73	1	2169	420992081	420989899	0.000000e+00	1975.0
6	TraesCS2A01G333600	chr2B	83.677	2230	157	69	1	2148	493651798	493649694	0.000000e+00	1910.0
7	TraesCS2A01G333600	chr2B	96.875	32	0	1	295	325	798373925	798373956	4.000000e-03	52.8
8	TraesCS2A01G333600	chr7D	90.184	326	31	1	2170	2494	484338450	484338125	8.260000e-115	424.0
9	TraesCS2A01G333600	chr7D	89.164	323	32	3	2173	2494	8872490	8872810	1.390000e-107	399.0
10	TraesCS2A01G333600	chr7D	89.130	322	34	1	2173	2494	574912527	574912847	1.390000e-107	399.0
11	TraesCS2A01G333600	chr7D	88.854	323	35	1	2173	2494	599692053	599692375	1.800000e-106	396.0
12	TraesCS2A01G333600	chr6D	90.415	313	28	2	2183	2494	283772065	283772376	6.430000e-111	411.0
13	TraesCS2A01G333600	chr6D	90.064	312	31	0	2183	2494	396006476	396006165	2.990000e-109	405.0
14	TraesCS2A01G333600	chr6D	83.851	161	23	3	42	202	337026977	337026820	1.550000e-32	150.0
15	TraesCS2A01G333600	chr1D	89.744	312	32	0	2183	2494	387055756	387056067	1.390000e-107	399.0
16	TraesCS2A01G333600	chr7B	88.820	322	36	0	2173	2494	621350515	621350194	1.800000e-106	396.0
17	TraesCS2A01G333600	chr4A	80.162	247	43	6	2	246	631374769	631375011	1.970000e-41	180.0
18	TraesCS2A01G333600	chr3B	74.400	250	46	14	2	245	714500709	714500946	9.510000e-15	91.6
19	TraesCS2A01G333600	chr3A	81.053	95	14	4	153	246	681326632	681326541	3.450000e-09	73.1
20	TraesCS2A01G333600	chr5D	93.023	43	3	0	281	323	562727213	562727171	2.070000e-06	63.9
21	TraesCS2A01G333600	chr1B	100.000	34	0	0	288	321	484286528	484286561	2.070000e-06	63.9
22	TraesCS2A01G333600	chr1A	85.246	61	9	0	154	214	362208395	362208455	2.070000e-06	63.9
23	TraesCS2A01G333600	chr7A	97.059	34	1	0	289	322	222415136	222415169	9.650000e-05	58.4

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	TraesCS2A01G333600	chr2A	566985482	566987979	2497	True	4614	4614	100.0000	1	2498	1	chr2A.!!$R1	2497
1	TraesCS2A01G333600	chr2A	547775194	547777093	1899	False	3121	3121	96.5260	1	1876	1	chr2A.!!$F1	1875
2	TraesCS2A01G333600	chr2A	547783791	547784332	541	False	863	863	95.4040	1864	2405	1	chr2A.!!$F2	541
3	TraesCS2A01G333600	chr2A	547271185	547271806	621	False	310	459	86.9185	653	2175	2	chr2A.!!$F3	1522
4	TraesCS2A01G333600	chr2D	420989899	420992081	2182	True	1975	1975	83.8160	1	2169	1	chr2D.!!$R1	2168
5	TraesCS2A01G333600	chr2B	493649694	493651798	2104	True	1910	1910	83.6770	1	2148	1	chr2B.!!$R1	2147

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
467	493	1.003718	CCCCTCGGTGAAAGTGGAC	60.004	63.158	0.0	0.0	0.0	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2459	2639	0.178953	ATTTTGGAGGCTGGCTGTGT	60.179	50.0	9.06	0.0	0.0	3.72	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
100	101	3.863543	CGACATGAATGCGGCGCA	61.864	61.111	38.09	38.09	44.86	6.09
249	251	1.339610	CGGTTTGTGGAAGAAATGGCA	59.660	47.619	0.00	0.00	29.33	4.92
276	278	2.701107	TCGCGTTGGGTGATTTTCATA	58.299	42.857	5.77	0.00	0.00	2.15
337	339	5.467063	GGAGATGCCTAAAAAGATCTTACGG	59.533	44.000	8.75	7.97	0.00	4.02
467	493	1.003718	CCCCTCGGTGAAAGTGGAC	60.004	63.158	0.00	0.00	0.00	4.02
619	655	2.817258	GGACCAAATTTCCACACGATCA	59.183	45.455	0.00	0.00	32.82	2.92
687	726	4.443881	GGGTAGCCCGTGTGTTTATCTATT	60.444	45.833	0.00	0.00	32.13	1.73
699	738	9.503427	GTGTGTTTATCTATTTGTAATCAAGGC	57.497	33.333	0.00	0.00	34.88	4.35
805	878	1.588082	CCATTGGGCAAGTGCAGTC	59.412	57.895	5.52	0.00	44.36	3.51
944	1041	2.465860	TTAACCATCACACAGACCCG	57.534	50.000	0.00	0.00	0.00	5.28
1469	1622	0.902984	TGCTACACCGACTGGACCAT	60.903	55.000	0.00	0.00	39.21	3.55
1482	1635	1.371635	GACCATGCACGGCAACAAC	60.372	57.895	0.00	0.00	43.62	3.32
1686	1860	5.526506	AAAGAGTAAGTACGTGTTGTCCT	57.473	39.130	0.00	0.00	0.00	3.85
1725	1899	2.431419	TCGTGTAATAAAGCCCATCCGA	59.569	45.455	0.00	0.00	0.00	4.55
1769	1943	3.067742	GGTTCTCTTGCTAGCCGTATACA	59.932	47.826	13.29	0.00	0.00	2.29
1826	2000	4.416601	CCCCCTCCCTCGTCCCTT	62.417	72.222	0.00	0.00	0.00	3.95
2176	2356	3.581755	AGATTGCGCGTACTTTGTTAGA	58.418	40.909	8.43	0.00	0.00	2.10
2181	2361	3.119388	TGCGCGTACTTTGTTAGACCTAT	60.119	43.478	8.43	0.00	0.00	2.57
2194	2374	2.029073	CCTATTCCACCGCGCGAT	59.971	61.111	34.63	13.37	0.00	4.58
2205	2385	3.861263	GCGCGATCCCAAACGGAC	61.861	66.667	12.10	0.00	46.09	4.79
2219	2399	3.555917	AACGGACGTTTGTTTTGTTCA	57.444	38.095	3.99	0.00	34.22	3.18
2229	2409	6.128007	ACGTTTGTTTTGTTCAGATTCTGTCT	60.128	34.615	13.23	0.00	37.80	3.41
2249	2429	5.480073	TGTCTGTTTGGAATGGAATTTAGGG	59.520	40.000	0.00	0.00	36.07	3.53
2258	2438	1.066716	TGGAATTTAGGGTCGTGTCGG	60.067	52.381	0.00	0.00	0.00	4.79
2295	2475	3.872603	TGGCCGTGCACTCAAGGT	61.873	61.111	16.19	0.00	42.76	3.50
2322	2502	2.543031	CGCATCCATTTGCTTCATCCTG	60.543	50.000	0.00	0.00	40.54	3.86
2324	2504	3.118884	GCATCCATTTGCTTCATCCTGTT	60.119	43.478	0.00	0.00	39.57	3.16
2408	2588	4.073052	GGTTCATCACACCGGCAA	57.927	55.556	0.00	0.00	0.00	4.52
2409	2589	1.579429	GGTTCATCACACCGGCAAC	59.421	57.895	0.00	0.00	0.00	4.17
2410	2590	1.169661	GGTTCATCACACCGGCAACA	61.170	55.000	0.00	0.00	0.00	3.33
2411	2591	0.238289	GTTCATCACACCGGCAACAG	59.762	55.000	0.00	0.00	0.00	3.16
2412	2592	0.107643	TTCATCACACCGGCAACAGA	59.892	50.000	0.00	0.00	0.00	3.41
2413	2593	0.320683	TCATCACACCGGCAACAGAG	60.321	55.000	0.00	0.00	0.00	3.35
2414	2594	1.672356	ATCACACCGGCAACAGAGC	60.672	57.895	0.00	0.00	0.00	4.09
2431	2611	4.814294	CCAGCGGCCTACACGTCC	62.814	72.222	0.00	0.00	0.00	4.79
2432	2612	4.063967	CAGCGGCCTACACGTCCA	62.064	66.667	0.00	0.00	0.00	4.02
2433	2613	3.075005	AGCGGCCTACACGTCCAT	61.075	61.111	0.00	0.00	0.00	3.41
2434	2614	2.585247	GCGGCCTACACGTCCATC	60.585	66.667	0.00	0.00	0.00	3.51
2435	2615	2.278596	CGGCCTACACGTCCATCG	60.279	66.667	0.00	0.00	46.00	3.84
2436	2616	2.585247	GGCCTACACGTCCATCGC	60.585	66.667	0.00	0.00	44.19	4.58
2437	2617	2.585247	GCCTACACGTCCATCGCC	60.585	66.667	0.00	0.00	44.19	5.54
2438	2618	2.278596	CCTACACGTCCATCGCCG	60.279	66.667	0.00	0.00	44.19	6.46
2439	2619	2.278596	CTACACGTCCATCGCCGG	60.279	66.667	0.00	0.00	44.19	6.13
2440	2620	3.060020	CTACACGTCCATCGCCGGT	62.060	63.158	1.90	0.00	44.19	5.28
2441	2621	1.717791	CTACACGTCCATCGCCGGTA	61.718	60.000	1.90	0.00	44.19	4.02
2442	2622	1.102809	TACACGTCCATCGCCGGTAT	61.103	55.000	1.90	0.00	44.19	2.73
2443	2623	1.660575	CACGTCCATCGCCGGTATC	60.661	63.158	1.90	0.00	44.19	2.24
2444	2624	2.122797	ACGTCCATCGCCGGTATCA	61.123	57.895	1.90	0.00	44.19	2.15
2445	2625	1.371758	CGTCCATCGCCGGTATCAG	60.372	63.158	1.90	0.00	0.00	2.90
2446	2626	1.664965	GTCCATCGCCGGTATCAGC	60.665	63.158	1.90	0.00	0.00	4.26
2447	2627	2.357517	CCATCGCCGGTATCAGCC	60.358	66.667	1.90	0.00	0.00	4.85
2448	2628	2.421314	CATCGCCGGTATCAGCCA	59.579	61.111	1.90	0.00	0.00	4.75
2449	2629	1.665916	CATCGCCGGTATCAGCCAG	60.666	63.158	1.90	0.00	0.00	4.85
2450	2630	3.521529	ATCGCCGGTATCAGCCAGC	62.522	63.158	1.90	0.00	0.00	4.85
2473	2653	3.368571	GCAACACAGCCAGCCTCC	61.369	66.667	0.00	0.00	0.00	4.30
2474	2654	2.113774	CAACACAGCCAGCCTCCA	59.886	61.111	0.00	0.00	0.00	3.86
2475	2655	1.529010	CAACACAGCCAGCCTCCAA	60.529	57.895	0.00	0.00	0.00	3.53
2476	2656	1.108727	CAACACAGCCAGCCTCCAAA	61.109	55.000	0.00	0.00	0.00	3.28
2477	2657	0.396974	AACACAGCCAGCCTCCAAAA	60.397	50.000	0.00	0.00	0.00	2.44
2478	2658	0.178953	ACACAGCCAGCCTCCAAAAT	60.179	50.000	0.00	0.00	0.00	1.82
2479	2659	1.075374	ACACAGCCAGCCTCCAAAATA	59.925	47.619	0.00	0.00	0.00	1.40
2480	2660	2.170166	CACAGCCAGCCTCCAAAATAA	58.830	47.619	0.00	0.00	0.00	1.40
2481	2661	2.562298	CACAGCCAGCCTCCAAAATAAA	59.438	45.455	0.00	0.00	0.00	1.40
2482	2662	3.196254	CACAGCCAGCCTCCAAAATAAAT	59.804	43.478	0.00	0.00	0.00	1.40
2483	2663	4.402155	CACAGCCAGCCTCCAAAATAAATA	59.598	41.667	0.00	0.00	0.00	1.40
2484	2664	4.646492	ACAGCCAGCCTCCAAAATAAATAG	59.354	41.667	0.00	0.00	0.00	1.73
2485	2665	4.646492	CAGCCAGCCTCCAAAATAAATAGT	59.354	41.667	0.00	0.00	0.00	2.12
2486	2666	5.127682	CAGCCAGCCTCCAAAATAAATAGTT	59.872	40.000	0.00	0.00	0.00	2.24
2487	2667	5.127682	AGCCAGCCTCCAAAATAAATAGTTG	59.872	40.000	0.00	0.00	0.00	3.16
2488	2668	5.105351	GCCAGCCTCCAAAATAAATAGTTGT	60.105	40.000	0.00	0.00	0.00	3.32
2489	2669	6.564328	CCAGCCTCCAAAATAAATAGTTGTC	58.436	40.000	0.00	0.00	0.00	3.18
2490	2670	6.405842	CCAGCCTCCAAAATAAATAGTTGTCC	60.406	42.308	0.00	0.00	0.00	4.02
2491	2671	6.378280	CAGCCTCCAAAATAAATAGTTGTCCT	59.622	38.462	0.00	0.00	0.00	3.85
2492	2672	6.603599	AGCCTCCAAAATAAATAGTTGTCCTC	59.396	38.462	0.00	0.00	0.00	3.71
2493	2673	6.458342	GCCTCCAAAATAAATAGTTGTCCTCG	60.458	42.308	0.00	0.00	0.00	4.63
2494	2674	6.598064	CCTCCAAAATAAATAGTTGTCCTCGT	59.402	38.462	0.00	0.00	0.00	4.18
2495	2675	7.201617	CCTCCAAAATAAATAGTTGTCCTCGTC	60.202	40.741	0.00	0.00	0.00	4.20
2496	2676	7.162761	TCCAAAATAAATAGTTGTCCTCGTCA	58.837	34.615	0.00	0.00	0.00	4.35
2497	2677	7.333423	TCCAAAATAAATAGTTGTCCTCGTCAG	59.667	37.037	0.00	0.00	0.00	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
276	278	1.472480	CCTTCCGCAACCATTCGAATT	59.528	47.619	8.21	0.00	0.00	2.17
337	339	5.819901	CCTAGGATTTGTCTGATCAAGTTCC	59.180	44.000	1.05	0.00	34.53	3.62
459	481	1.312815	GTTGAGCTGCAGTCCACTTT	58.687	50.000	16.64	0.00	0.00	2.66
646	682	1.538634	CCCCGATTGCGTTCCGTATAA	60.539	52.381	0.00	0.00	35.23	0.98
687	726	0.407528	TGCCCTGGCCTTGATTACAA	59.592	50.000	3.32	0.00	41.09	2.41
817	890	2.403586	GCGTAAATGGTCTGCGGC	59.596	61.111	0.00	0.00	0.00	6.53
944	1041	1.884235	CTGTGTGGTCTCTTTGGGTC	58.116	55.000	0.00	0.00	0.00	4.46
1377	1530	2.341101	GCTGCAGCACTTGAGGCAT	61.341	57.895	33.36	0.00	41.59	4.40
1469	1622	2.276863	CTTGGTGTTGTTGCCGTGCA	62.277	55.000	0.00	0.00	36.47	4.57
1482	1635	2.092212	AGATATTCAGGGGCACTTGGTG	60.092	50.000	0.00	0.00	36.51	4.17
1686	1860	1.135527	CGAGAAATACGCCCACCTACA	59.864	52.381	0.00	0.00	0.00	2.74
1725	1899	4.081531	CCATGCATTCACCACATAAACCTT	60.082	41.667	0.00	0.00	0.00	3.50
1769	1943	7.352079	ACTTTTCATCTCAAACAAAGGTGAT	57.648	32.000	0.00	0.00	34.00	3.06
1826	2000	9.057089	GGATAAGAACTCTCTTTTCTTTGAACA	57.943	33.333	2.86	0.00	39.77	3.18
2080	2256	1.075542	TACTGTCACGTACGGTACCG	58.924	55.000	32.22	32.22	46.23	4.02
2176	2356	2.694829	GATCGCGCGGTGGAATAGGT	62.695	60.000	31.69	3.03	0.00	3.08
2203	2383	6.027749	ACAGAATCTGAACAAAACAAACGTC	58.972	36.000	18.20	0.00	35.18	4.34
2205	2385	6.258160	AGACAGAATCTGAACAAAACAAACG	58.742	36.000	18.20	0.00	35.81	3.60
2219	2399	5.246981	TCCATTCCAAACAGACAGAATCT	57.753	39.130	0.00	0.00	38.66	2.40
2229	2409	4.461081	CGACCCTAAATTCCATTCCAAACA	59.539	41.667	0.00	0.00	0.00	2.83
2237	2417	2.419574	CCGACACGACCCTAAATTCCAT	60.420	50.000	0.00	0.00	0.00	3.41
2238	2418	1.066716	CCGACACGACCCTAAATTCCA	60.067	52.381	0.00	0.00	0.00	3.53
2249	2429	4.955774	AACACGCCCCGACACGAC	62.956	66.667	0.00	0.00	0.00	4.34
2258	2438	2.456119	CGCATCTCAGAACACGCCC	61.456	63.158	0.00	0.00	0.00	6.13
2322	2502	7.917720	TTTGGCTTTTTAAATAGACACGAAC	57.082	32.000	13.10	0.00	0.00	3.95
2324	2504	6.639279	GCTTTTGGCTTTTTAAATAGACACGA	59.361	34.615	13.10	3.72	38.06	4.35
2414	2594	4.814294	GGACGTGTAGGCCGCTGG	62.814	72.222	0.00	0.00	38.99	4.85
2420	2600	2.585247	GGCGATGGACGTGTAGGC	60.585	66.667	0.00	0.00	44.60	3.93
2421	2601	2.278596	CGGCGATGGACGTGTAGG	60.279	66.667	0.00	0.00	40.74	3.18
2422	2602	1.717791	TACCGGCGATGGACGTGTAG	61.718	60.000	9.30	0.00	45.55	2.74
2423	2603	1.102809	ATACCGGCGATGGACGTGTA	61.103	55.000	9.30	4.57	45.55	2.90
2424	2604	2.345880	GATACCGGCGATGGACGTGT	62.346	60.000	9.30	2.27	45.55	4.49
2425	2605	1.660575	GATACCGGCGATGGACGTG	60.661	63.158	9.30	0.00	45.55	4.49
2426	2606	2.071844	CTGATACCGGCGATGGACGT	62.072	60.000	9.30	0.00	45.55	4.34
2427	2607	1.371758	CTGATACCGGCGATGGACG	60.372	63.158	9.30	0.00	46.94	4.79
2428	2608	1.664965	GCTGATACCGGCGATGGAC	60.665	63.158	9.30	0.00	34.60	4.02
2429	2609	2.734591	GCTGATACCGGCGATGGA	59.265	61.111	9.30	0.00	34.60	3.41
2430	2610	2.357517	GGCTGATACCGGCGATGG	60.358	66.667	9.30	0.00	45.55	3.51
2431	2611	1.665916	CTGGCTGATACCGGCGATG	60.666	63.158	9.30	0.00	45.55	3.84
2432	2612	2.737180	CTGGCTGATACCGGCGAT	59.263	61.111	9.30	0.00	45.55	4.58
2456	2636	3.368571	GGAGGCTGGCTGTGTTGC	61.369	66.667	9.06	0.00	0.00	4.17
2457	2637	1.108727	TTTGGAGGCTGGCTGTGTTG	61.109	55.000	9.06	0.00	0.00	3.33
2458	2638	0.396974	TTTTGGAGGCTGGCTGTGTT	60.397	50.000	9.06	0.00	0.00	3.32
2459	2639	0.178953	ATTTTGGAGGCTGGCTGTGT	60.179	50.000	9.06	0.00	0.00	3.72
2460	2640	1.838112	TATTTTGGAGGCTGGCTGTG	58.162	50.000	9.06	0.00	0.00	3.66
2461	2641	2.603075	TTATTTTGGAGGCTGGCTGT	57.397	45.000	9.06	0.00	0.00	4.40
2462	2642	4.646492	ACTATTTATTTTGGAGGCTGGCTG	59.354	41.667	9.06	0.00	0.00	4.85
2463	2643	4.871822	ACTATTTATTTTGGAGGCTGGCT	58.128	39.130	2.24	2.24	0.00	4.75
2464	2644	5.105351	ACAACTATTTATTTTGGAGGCTGGC	60.105	40.000	0.00	0.00	0.00	4.85
2465	2645	6.405842	GGACAACTATTTATTTTGGAGGCTGG	60.406	42.308	0.00	0.00	0.00	4.85
2466	2646	6.378280	AGGACAACTATTTATTTTGGAGGCTG	59.622	38.462	0.00	0.00	0.00	4.85
2467	2647	6.494059	AGGACAACTATTTATTTTGGAGGCT	58.506	36.000	0.00	0.00	0.00	4.58
2468	2648	6.458342	CGAGGACAACTATTTATTTTGGAGGC	60.458	42.308	0.00	0.00	0.00	4.70
2469	2649	6.598064	ACGAGGACAACTATTTATTTTGGAGG	59.402	38.462	0.00	0.00	0.00	4.30
2470	2650	7.333423	TGACGAGGACAACTATTTATTTTGGAG	59.667	37.037	0.00	0.00	0.00	3.86
2471	2651	7.162761	TGACGAGGACAACTATTTATTTTGGA	58.837	34.615	0.00	0.00	0.00	3.53
2472	2652	7.372451	TGACGAGGACAACTATTTATTTTGG	57.628	36.000	0.00	0.00	0.00	3.28

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.