AutoCloner

Multiple sequence alignment - TraesCS2B01G541200

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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	TraesCS2B01G541200	chr2B	100.000	2726	0	0	1	2726	737489368	737492093	0.000000e+00	5035
1	TraesCS2B01G541200	chr2B	93.222	1800	117	3	738	2536	737310801	737312596	0.000000e+00	2643
2	TraesCS2B01G541200	chr2B	82.242	2382	398	14	1	2378	409216407	409214047	0.000000e+00	2032
3	TraesCS2B01G541200	chr2B	81.314	2344	400	23	42	2375	121230739	121228424	0.000000e+00	1868
4	TraesCS2B01G541200	chr2B	92.782	665	47	1	1	664	737309905	737310569	0.000000e+00	961
5	TraesCS2B01G541200	chr2B	90.374	187	15	3	2541	2726	737313478	737313662	2.710000e-60	243
6	TraesCS2B01G541200	chr2B	86.559	186	24	1	2541	2726	589132858	589133042	1.280000e-48	204
7	TraesCS2B01G541200	chr2B	83.810	210	21	9	2337	2540	121228419	121228217	1.290000e-43	187
8	TraesCS2B01G541200	chr2B	81.667	180	33	0	2547	2726	409205738	409205559	1.690000e-32	150
9	TraesCS2B01G541200	chr3B	88.140	2538	269	20	1	2529	475834883	475837397	0.000000e+00	2990
10	TraesCS2B01G541200	chr3B	87.393	349	42	2	2188	2535	571200550	571200203	1.520000e-107	399
11	TraesCS2B01G541200	chr3B	88.816	304	32	2	2234	2536	506203394	506203696	3.320000e-99	372
12	TraesCS2B01G541200	chr3B	89.247	186	20	0	2541	2726	566651370	566651555	1.630000e-57	233
13	TraesCS2B01G541200	chr3B	88.202	178	17	4	2541	2716	506140493	506140318	2.750000e-50	209
14	TraesCS2B01G541200	chr3B	86.022	186	26	0	2541	2726	285341325	285341140	1.660000e-47	200
15	TraesCS2B01G541200	chr1B	87.483	2253	250	16	292	2536	202125476	202123248	0.000000e+00	2569
16	TraesCS2B01G541200	chr1B	85.020	2243	302	20	4	2236	543388004	543385786	0.000000e+00	2250
17	TraesCS2B01G541200	chr1B	82.043	2467	390	35	83	2532	541850932	541853362	0.000000e+00	2052
18	TraesCS2B01G541200	chr1B	85.472	826	104	7	1	823	228201867	228202679	0.000000e+00	846
19	TraesCS2B01G541200	chr1B	91.935	186	15	0	2541	2726	202122374	202122189	7.490000e-66	261
20	TraesCS2B01G541200	chr1B	90.909	176	16	0	2541	2716	228206893	228207068	1.260000e-58	237
21	TraesCS2B01G541200	chr6B	84.434	2454	336	26	100	2536	162821267	162818843	0.000000e+00	2374
22	TraesCS2B01G541200	chr6B	81.792	2477	394	34	82	2536	378039179	378041620	0.000000e+00	2023
23	TraesCS2B01G541200	chr6B	74.581	1967	416	53	97	2021	469306797	469308721	0.000000e+00	785
24	TraesCS2B01G541200	chr6B	84.962	133	20	0	1	133	365343058	365342926	4.730000e-28	135
25	TraesCS2B01G541200	chr7B	83.700	2454	353	21	99	2536	299381711	299384133	0.000000e+00	2272
26	TraesCS2B01G541200	chr7B	83.047	2383	354	19	1	2375	274645374	274647714	0.000000e+00	2117
27	TraesCS2B01G541200	chr7B	84.292	643	95	5	1	640	532282615	532283254	8.290000e-175	623
28	TraesCS2B01G541200	chr7B	83.974	156	25	0	2541	2696	45876177	45876332	1.690000e-32	150
29	TraesCS2B01G541200	chr4B	86.720	1860	227	18	685	2536	222157295	222159142	0.000000e+00	2049
30	TraesCS2B01G541200	chr4B	81.352	2381	399	26	1	2375	87020970	87023311	0.000000e+00	1895
31	TraesCS2B01G541200	chr4B	73.632	1718	386	47	92	1782	582733262	582731585	3.880000e-168	601
32	TraesCS2B01G541200	chr5B	84.933	1115	144	13	1	1109	70239711	70238615	0.000000e+00	1107
33	TraesCS2B01G541200	chr3D	75.968	1885	388	41	23	1880	290206430	290204584	0.000000e+00	911
34	TraesCS2B01G541200	chr4A	75.587	1831	387	39	96	1898	457671855	457670057	0.000000e+00	850
35	TraesCS2B01G541200	chr2D	75.355	1830	378	54	92	1890	473443295	473445082	0.000000e+00	813

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	TraesCS2B01G541200	chr2B	737489368	737492093	2725	False	5035.000000	5035	100.000	1	2726	1	chr2B.!!$F2	2725
1	TraesCS2B01G541200	chr2B	409214047	409216407	2360	True	2032.000000	2032	82.242	1	2378	1	chr2B.!!$R2	2377
2	TraesCS2B01G541200	chr2B	737309905	737313662	3757	False	1282.333333	2643	92.126	1	2726	3	chr2B.!!$F3	2725
3	TraesCS2B01G541200	chr2B	121228217	121230739	2522	True	1027.500000	1868	82.562	42	2540	2	chr2B.!!$R3	2498
4	TraesCS2B01G541200	chr3B	475834883	475837397	2514	False	2990.000000	2990	88.140	1	2529	1	chr3B.!!$F1	2528
5	TraesCS2B01G541200	chr1B	543385786	543388004	2218	True	2250.000000	2250	85.020	4	2236	1	chr1B.!!$R1	2232
6	TraesCS2B01G541200	chr1B	541850932	541853362	2430	False	2052.000000	2052	82.043	83	2532	1	chr1B.!!$F3	2449
7	TraesCS2B01G541200	chr1B	202122189	202125476	3287	True	1415.000000	2569	89.709	292	2726	2	chr1B.!!$R2	2434
8	TraesCS2B01G541200	chr1B	228201867	228202679	812	False	846.000000	846	85.472	1	823	1	chr1B.!!$F1	822
9	TraesCS2B01G541200	chr6B	162818843	162821267	2424	True	2374.000000	2374	84.434	100	2536	1	chr6B.!!$R1	2436
10	TraesCS2B01G541200	chr6B	378039179	378041620	2441	False	2023.000000	2023	81.792	82	2536	1	chr6B.!!$F1	2454
11	TraesCS2B01G541200	chr6B	469306797	469308721	1924	False	785.000000	785	74.581	97	2021	1	chr6B.!!$F2	1924
12	TraesCS2B01G541200	chr7B	299381711	299384133	2422	False	2272.000000	2272	83.700	99	2536	1	chr7B.!!$F3	2437
13	TraesCS2B01G541200	chr7B	274645374	274647714	2340	False	2117.000000	2117	83.047	1	2375	1	chr7B.!!$F2	2374
14	TraesCS2B01G541200	chr7B	532282615	532283254	639	False	623.000000	623	84.292	1	640	1	chr7B.!!$F4	639
15	TraesCS2B01G541200	chr4B	222157295	222159142	1847	False	2049.000000	2049	86.720	685	2536	1	chr4B.!!$F2	1851
16	TraesCS2B01G541200	chr4B	87020970	87023311	2341	False	1895.000000	1895	81.352	1	2375	1	chr4B.!!$F1	2374
17	TraesCS2B01G541200	chr4B	582731585	582733262	1677	True	601.000000	601	73.632	92	1782	1	chr4B.!!$R1	1690
18	TraesCS2B01G541200	chr5B	70238615	70239711	1096	True	1107.000000	1107	84.933	1	1109	1	chr5B.!!$R1	1108
19	TraesCS2B01G541200	chr3D	290204584	290206430	1846	True	911.000000	911	75.968	23	1880	1	chr3D.!!$R1	1857
20	TraesCS2B01G541200	chr4A	457670057	457671855	1798	True	850.000000	850	75.587	96	1898	1	chr4A.!!$R1	1802
21	TraesCS2B01G541200	chr2D	473443295	473445082	1787	False	813.000000	813	75.355	92	1890	1	chr2D.!!$F1	1798

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
501	521	0.107017	CTTCGGTGCCCAGATCCATT	60.107	55.0	0.0	0.0	0.0	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1965	2193	0.5966	TGTGACGTCCGTCTTGAAGC	60.597	55.0	19.3	5.22	44.8	3.86	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
57	58	2.605837	TATCCATTTAAGGCGACGCA	57.394	45.000	23.09	0.00	0.00	5.24
143	146	4.715130	AGCACCACGCCCCCTAGA	62.715	66.667	0.00	0.00	44.04	2.43
250	262	1.079127	CAAAGGGGTCGACATCGCT	60.079	57.895	18.91	11.53	39.60	4.93
251	263	0.174845	CAAAGGGGTCGACATCGCTA	59.825	55.000	18.91	0.00	39.60	4.26
253	265	1.120530	AAGGGGTCGACATCGCTATT	58.879	50.000	18.91	0.00	39.60	1.73
315	328	0.905357	CACCGTCTCAGGGGAAGATT	59.095	55.000	0.00	0.00	36.61	2.40
369	382	1.384191	GGGTCTTGGAGGTTGCCAT	59.616	57.895	0.00	0.00	37.86	4.40
415	429	3.479269	CGGTGAGCGCGTTCTTCC	61.479	66.667	23.51	21.75	0.00	3.46
501	521	0.107017	CTTCGGTGCCCAGATCCATT	60.107	55.000	0.00	0.00	0.00	3.16
640	671	3.425758	CGGTAAAGAAAGCAAATCCGACC	60.426	47.826	0.00	0.00	39.17	4.79
664	695	0.949105	AAAGGACGCACGTGATCCAC	60.949	55.000	30.10	13.64	34.73	4.02
673	720	2.463620	CGTGATCCACATGTGCGGG	61.464	63.158	20.81	7.37	33.40	6.13
674	721	2.114670	GTGATCCACATGTGCGGGG	61.115	63.158	20.81	6.98	34.08	5.73
675	722	2.297129	TGATCCACATGTGCGGGGA	61.297	57.895	20.81	12.61	0.00	4.81
676	723	1.524621	GATCCACATGTGCGGGGAG	60.525	63.158	20.81	5.76	31.96	4.30
677	724	2.947938	GATCCACATGTGCGGGGAGG	62.948	65.000	20.81	5.01	31.96	4.30
678	725	4.802051	CCACATGTGCGGGGAGGG	62.802	72.222	20.81	0.00	0.00	4.30
679	726	4.033776	CACATGTGCGGGGAGGGT	62.034	66.667	13.94	0.00	0.00	4.34
680	727	4.033776	ACATGTGCGGGGAGGGTG	62.034	66.667	0.00	0.00	0.00	4.61
681	728	4.802051	CATGTGCGGGGAGGGTGG	62.802	72.222	0.00	0.00	0.00	4.61
699	746	1.012049	TGGGAGGGGTTAGGAATCCAT	59.988	52.381	0.61	0.00	0.00	3.41
728	775	2.278332	AGGAGTTCTTTTCCTGCCAC	57.722	50.000	0.00	0.00	43.38	5.01
748	937	4.537015	CACGGTTTTTCCTGAATCTGTTC	58.463	43.478	0.00	0.00	34.85	3.18
793	982	7.769044	GGTTCTATTGCAAAGACATCCTAACTA	59.231	37.037	1.71	0.00	0.00	2.24
804	993	4.936802	ACATCCTAACTACTGGTCAGTCT	58.063	43.478	6.91	0.00	42.54	3.24
1035	1227	0.674534	GACCAGAAGACACCACTCGT	59.325	55.000	0.00	0.00	0.00	4.18
1110	1304	2.747446	CACTGGGAATAAAGACAACCCG	59.253	50.000	0.00	0.00	43.04	5.28
1440	1655	1.998315	CGATCCAAGCAGACACAAGAG	59.002	52.381	0.00	0.00	0.00	2.85
1469	1685	1.303888	ACCATGGCAAGGCTGTGAG	60.304	57.895	13.04	0.00	0.00	3.51
1489	1705	2.125912	CGAGTGCGAAGACCCAGG	60.126	66.667	0.00	0.00	40.82	4.45
1541	1757	1.064017	TGAGAAGGTTGCCAAACAGGT	60.064	47.619	0.00	0.00	40.61	4.00
1592	1810	1.888512	TCTGCCCAGAATCAAAGTTGC	59.111	47.619	0.00	0.00	33.91	4.17
1767	1994	1.973281	CTGCGGACATGGCCACTTT	60.973	57.895	20.22	0.00	0.00	2.66
1768	1995	2.203972	CTGCGGACATGGCCACTTTG	62.204	60.000	20.22	5.14	0.00	2.77
1839	2067	2.874701	GGTGGTCGATTGGAATCTCATG	59.125	50.000	0.00	0.00	33.24	3.07
1926	2154	1.066573	AGAACACATGAGGAAGAGGCG	60.067	52.381	0.00	0.00	0.00	5.52
1965	2193	3.259633	AACCCTGCCAAGAGAGCGG	62.260	63.158	0.00	0.00	36.32	5.52
2034	2262	0.320374	TGGTGGTTCATCGTGGACTC	59.680	55.000	0.00	0.00	0.00	3.36
2049	2277	2.971330	TGGACTCCCGTAACCTTTGTTA	59.029	45.455	0.00	0.00	33.68	2.41
2185	2414	8.432805	GGATCAAATAGGATCTGTTAAGGAAGA	58.567	37.037	0.00	0.00	42.63	2.87
2197	2445	7.689299	TCTGTTAAGGAAGAAATGATCCAAGA	58.311	34.615	0.00	0.00	0.00	3.02
2232	2480	1.694844	TCGACTGAAGGTGGTGTACA	58.305	50.000	0.00	0.00	0.00	2.90
2264	2512	1.421410	CTGCATACGACGCCAGTTCC	61.421	60.000	0.00	0.00	0.00	3.62
2340	2588	0.034896	GTCTTCGCCTTGGACCTTGA	59.965	55.000	0.00	0.00	0.00	3.02
2354	2602	8.830741	CCTTGGACCTTGATCTATTAGGATATT	58.169	37.037	9.67	0.00	33.21	1.28
2536	2834	2.093394	TGTCGAGTGGAGTTTTTGGTCA	60.093	45.455	0.00	0.00	0.00	4.02
2537	2835	3.139077	GTCGAGTGGAGTTTTTGGTCAT	58.861	45.455	0.00	0.00	0.00	3.06
2538	2836	3.564225	GTCGAGTGGAGTTTTTGGTCATT	59.436	43.478	0.00	0.00	0.00	2.57
2539	2837	3.813166	TCGAGTGGAGTTTTTGGTCATTC	59.187	43.478	0.00	0.00	0.00	2.67
2545	3731	1.956477	AGTTTTTGGTCATTCGCTGCT	59.044	42.857	0.00	0.00	0.00	4.24
2594	3780	3.368531	CCAACTAAAGGAGGAGAAGGTCG	60.369	52.174	0.00	0.00	0.00	4.79
2621	3807	0.390472	GGAGAAAGTGGACCAGCTCG	60.390	60.000	0.00	0.00	0.00	5.03
2624	3810	0.603975	GAAAGTGGACCAGCTCGCTT	60.604	55.000	0.00	0.00	35.52	4.68
2625	3811	0.886490	AAAGTGGACCAGCTCGCTTG	60.886	55.000	0.00	0.00	34.44	4.01
2690	3876	7.254117	CGAAGAAACTGTACATTATGCTCGAAT	60.254	37.037	0.00	0.00	0.00	3.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
28	29	3.320541	CCTTAAATGGATATGCCGCCAAA	59.679	43.478	0.00	0.00	40.66	3.28
34	35	2.159627	CGTCGCCTTAAATGGATATGCC	59.840	50.000	0.00	0.00	37.10	4.40
57	58	2.033757	CTGTTCAGGGCAGCAGCT	59.966	61.111	0.00	0.00	41.70	4.24
143	146	0.746563	CGGAGCTCGAGAGGAAGAGT	60.747	60.000	18.75	0.00	42.43	3.24
250	262	3.420893	CAACCAGGTGGAAGAGCAAATA	58.579	45.455	2.10	0.00	38.94	1.40
251	263	2.242043	CAACCAGGTGGAAGAGCAAAT	58.758	47.619	2.10	0.00	38.94	2.32
253	265	0.178992	CCAACCAGGTGGAAGAGCAA	60.179	55.000	2.10	0.00	41.65	3.91
315	328	3.394274	TCATCAGAGGTGAGGTTTTCCAA	59.606	43.478	0.00	0.00	43.73	3.53
369	382	2.597805	GGGCTCGATCTCCGCCTA	60.598	66.667	11.89	0.00	43.29	3.93
398	412	3.479269	GGAAGAACGCGCTCACCG	61.479	66.667	12.67	0.00	40.75	4.94
415	429	2.582265	CGGTCGACGTGTGTTGTGG	61.582	63.158	9.92	0.00	37.93	4.17
501	521	4.325030	GGAGATGGTGTTGGGAGGAAAATA	60.325	45.833	0.00	0.00	0.00	1.40
640	671	2.728383	ACGTGCGTCCTTTCGTCG	60.728	61.111	0.00	0.00	36.82	5.12
664	695	4.802051	CCACCCTCCCCGCACATG	62.802	72.222	0.00	0.00	0.00	3.21
673	720	1.693103	CTAACCCCTCCCACCCTCC	60.693	68.421	0.00	0.00	0.00	4.30
674	721	1.693103	CCTAACCCCTCCCACCCTC	60.693	68.421	0.00	0.00	0.00	4.30
675	722	1.768231	TTCCTAACCCCTCCCACCCT	61.768	60.000	0.00	0.00	0.00	4.34
676	723	0.626574	ATTCCTAACCCCTCCCACCC	60.627	60.000	0.00	0.00	0.00	4.61
677	724	0.844660	GATTCCTAACCCCTCCCACC	59.155	60.000	0.00	0.00	0.00	4.61
678	725	0.844660	GGATTCCTAACCCCTCCCAC	59.155	60.000	0.00	0.00	0.00	4.61
679	726	0.423956	TGGATTCCTAACCCCTCCCA	59.576	55.000	3.95	0.00	0.00	4.37
680	727	1.834540	ATGGATTCCTAACCCCTCCC	58.165	55.000	3.95	0.00	0.00	4.30
681	728	4.175962	TCATATGGATTCCTAACCCCTCC	58.824	47.826	2.13	0.00	0.00	4.30
682	729	4.226168	CCTCATATGGATTCCTAACCCCTC	59.774	50.000	2.13	0.00	0.00	4.30
683	730	4.179133	CCTCATATGGATTCCTAACCCCT	58.821	47.826	2.13	0.00	0.00	4.79
699	746	4.720273	GGAAAAGAACTCCTACCCCTCATA	59.280	45.833	0.00	0.00	0.00	2.15
728	775	3.496884	TCGAACAGATTCAGGAAAAACCG	59.503	43.478	0.00	0.00	44.74	4.44
748	937	4.436998	GGTCGACTGCCACCCTCG	62.437	72.222	16.46	0.00	0.00	4.63
793	982	2.982339	AGACCAGTAGACTGACCAGT	57.018	50.000	11.31	1.78	46.59	4.00
804	993	5.906772	AAGAAAAAGGAGGAAGACCAGTA	57.093	39.130	0.00	0.00	38.94	2.74
994	1185	1.837439	TGAGTACATCCACATGGGGTC	59.163	52.381	15.27	3.20	37.22	4.46
1469	1685	2.126031	GGGTCTTCGCACTCGACC	60.126	66.667	0.00	0.00	45.43	4.79
1489	1705	2.280186	GGTCGTCCGGGCATGATC	60.280	66.667	6.96	0.00	0.00	2.92
1839	2067	2.807045	CGCTGCAGTCACTCGACC	60.807	66.667	16.64	0.00	43.73	4.79
1965	2193	0.596600	TGTGACGTCCGTCTTGAAGC	60.597	55.000	19.30	5.22	44.80	3.86
2034	2262	3.353370	TGGGATAACAAAGGTTACGGG	57.647	47.619	0.00	0.00	41.99	5.28
2049	2277	2.719739	CTGAGCACTTGACAATGGGAT	58.280	47.619	0.00	0.00	0.00	3.85
2185	2414	3.675348	TCAGGCCATCTTGGATCATTT	57.325	42.857	5.01	0.00	40.96	2.32
2197	2445	1.002888	GTCGATCCATCATCAGGCCAT	59.997	52.381	5.01	0.00	0.00	4.40
2264	2512	4.409218	ACATTGGCTTGCAGCGCG	62.409	61.111	0.00	0.00	43.62	6.86
2354	2602	7.928307	AATGAAGCAGCAGTTTTTAGATAGA	57.072	32.000	0.00	0.00	0.00	1.98
2536	2834	0.392193	CCTCCTCAACAGCAGCGAAT	60.392	55.000	0.00	0.00	0.00	3.34
2537	2835	1.004560	CCTCCTCAACAGCAGCGAA	60.005	57.895	0.00	0.00	0.00	4.70
2538	2836	2.659016	CCTCCTCAACAGCAGCGA	59.341	61.111	0.00	0.00	0.00	4.93
2539	2837	3.123620	GCCTCCTCAACAGCAGCG	61.124	66.667	0.00	0.00	0.00	5.18
2545	3731	3.973206	TCTATTTTCGCCTCCTCAACA	57.027	42.857	0.00	0.00	0.00	3.33
2594	3780	2.353505	GGTCCACTTTCTCCGTTAGGAC	60.354	54.545	0.00	0.00	42.75	3.85
2599	3785	0.250338	GCTGGTCCACTTTCTCCGTT	60.250	55.000	0.00	0.00	0.00	4.44
2621	3807	2.419851	CCAGGTCATCTCTCTTCCAAGC	60.420	54.545	0.00	0.00	0.00	4.01
2624	3810	2.625352	CCTCCAGGTCATCTCTCTTCCA	60.625	54.545	0.00	0.00	0.00	3.53
2625	3811	2.038659	CCTCCAGGTCATCTCTCTTCC	58.961	57.143	0.00	0.00	0.00	3.46
2690	3876	2.036733	CACTCGAGTGGGAAAGGTTACA	59.963	50.000	33.36	0.00	42.10	2.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.