AutoCloner

Multiple sequence alignment - TraesCS4A01G027300

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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	TraesCS4A01G027300	chr4A	100.000	3398	0	0	1	3398	19116502	19119899	0.000000e+00	6276.0
1	TraesCS4A01G027300	chr4A	76.293	464	88	18	2538	2987	540951947	540952402	9.490000e-56	228.0
2	TraesCS4A01G027300	chr7B	95.068	2433	112	7	3	2433	117154293	117151867	0.000000e+00	3821.0
3	TraesCS4A01G027300	chr7B	83.045	578	67	20	2434	2986	631057489	631056918	2.360000e-136	496.0
4	TraesCS4A01G027300	chr7B	82.230	574	80	11	2434	2985	683996478	683997051	3.070000e-130	475.0
5	TraesCS4A01G027300	chr7B	77.283	427	64	28	2571	2987	158591731	158592134	1.590000e-53	220.0
6	TraesCS4A01G027300	chr7B	94.340	53	3	0	2991	3043	271290403	271290351	7.820000e-12	82.4
7	TraesCS4A01G027300	chr1A	85.881	2146	289	13	3	2144	179512283	179510148	0.000000e+00	2272.0
8	TraesCS4A01G027300	chr4D	94.262	976	46	2	2433	3398	390735550	390736525	0.000000e+00	1483.0
9	TraesCS4A01G027300	chr4D	94.057	976	48	2	2433	3398	448618692	448617717	0.000000e+00	1472.0
10	TraesCS4A01G027300	chr4D	93.654	977	51	3	2432	3398	390672393	390673368	0.000000e+00	1450.0
11	TraesCS4A01G027300	chr4D	91.148	418	27	4	2990	3398	448187719	448187303	2.960000e-155	558.0
12	TraesCS4A01G027300	chr4D	80.551	581	82	17	2436	2986	344947380	344946801	5.240000e-113	418.0
13	TraesCS4A01G027300	chr2A	91.707	820	68	0	1510	2329	644061442	644062261	0.000000e+00	1138.0
14	TraesCS4A01G027300	chr2A	82.641	409	55	10	2028	2435	307707920	307708313	6.980000e-92	348.0
15	TraesCS4A01G027300	chr2A	93.103	116	7	1	2319	2434	644063241	644063355	5.830000e-38	169.0
16	TraesCS4A01G027300	chr7D	84.599	948	123	14	951	1886	99937066	99938002	0.000000e+00	920.0
17	TraesCS4A01G027300	chr3A	82.394	568	85	11	2434	2986	550553108	550552541	6.590000e-132	481.0
18	TraesCS4A01G027300	chr6A	80.796	578	88	19	2436	3002	169206121	169206686	6.740000e-117	431.0
19	TraesCS4A01G027300	chr4B	78.866	582	81	25	2437	2986	95678171	95677600	4.170000e-94	355.0
20	TraesCS4A01G027300	chr1D	86.817	311	30	5	3086	3386	62923613	62923922	1.510000e-88	337.0
21	TraesCS4A01G027300	chr1D	80.000	245	32	13	2986	3226	62923644	62923875	7.540000e-37	165.0
22	TraesCS4A01G027300	chrUn	86.174	311	32	3	3086	3386	62655171	62655480	3.270000e-85	326.0
23	TraesCS4A01G027300	chrUn	92.453	159	11	1	3085	3243	36424924	36425081	3.410000e-55	226.0
24	TraesCS4A01G027300	chrUn	91.195	159	13	1	3085	3243	35473162	35473005	7.380000e-52	215.0
25	TraesCS4A01G027300	chrUn	80.567	247	28	15	2986	3226	62655202	62655434	4.510000e-39	172.0
26	TraesCS4A01G027300	chrUn	81.119	143	10	14	2986	3117	62655134	62655270	7.760000e-17	99.0
27	TraesCS4A01G027300	chr6B	87.560	209	19	5	3038	3243	151160271	151160067	5.670000e-58	235.0
28	TraesCS4A01G027300	chr3B	73.721	567	102	35	2442	2986	749310603	749311144	9.690000e-41	178.0
29	TraesCS4A01G027300	chr2D	78.512	242	44	6	2751	2988	444379620	444379857	5.870000e-33	152.0
30	TraesCS4A01G027300	chr7A	87.879	66	6	2	2993	3056	734054268	734054203	3.640000e-10	76.8

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	TraesCS4A01G027300	chr4A	19116502	19119899	3397	False	6276.0	6276	100.000	1	3398	1	chr4A.!!$F1	3397
1	TraesCS4A01G027300	chr7B	117151867	117154293	2426	True	3821.0	3821	95.068	3	2433	1	chr7B.!!$R1	2430
2	TraesCS4A01G027300	chr7B	631056918	631057489	571	True	496.0	496	83.045	2434	2986	1	chr7B.!!$R3	552
3	TraesCS4A01G027300	chr7B	683996478	683997051	573	False	475.0	475	82.230	2434	2985	1	chr7B.!!$F2	551
4	TraesCS4A01G027300	chr1A	179510148	179512283	2135	True	2272.0	2272	85.881	3	2144	1	chr1A.!!$R1	2141
5	TraesCS4A01G027300	chr4D	390735550	390736525	975	False	1483.0	1483	94.262	2433	3398	1	chr4D.!!$F2	965
6	TraesCS4A01G027300	chr4D	448617717	448618692	975	True	1472.0	1472	94.057	2433	3398	1	chr4D.!!$R3	965
7	TraesCS4A01G027300	chr4D	390672393	390673368	975	False	1450.0	1450	93.654	2432	3398	1	chr4D.!!$F1	966
8	TraesCS4A01G027300	chr4D	344946801	344947380	579	True	418.0	418	80.551	2436	2986	1	chr4D.!!$R1	550
9	TraesCS4A01G027300	chr2A	644061442	644063355	1913	False	653.5	1138	92.405	1510	2434	2	chr2A.!!$F2	924
10	TraesCS4A01G027300	chr7D	99937066	99938002	936	False	920.0	920	84.599	951	1886	1	chr7D.!!$F1	935
11	TraesCS4A01G027300	chr3A	550552541	550553108	567	True	481.0	481	82.394	2434	2986	1	chr3A.!!$R1	552
12	TraesCS4A01G027300	chr6A	169206121	169206686	565	False	431.0	431	80.796	2436	3002	1	chr6A.!!$F1	566
13	TraesCS4A01G027300	chr4B	95677600	95678171	571	True	355.0	355	78.866	2437	2986	1	chr4B.!!$R1	549

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
435	436	1.071542	TGCTCGGGTCAAGTGATCAAA	59.928	47.619	0.0	0.0	0.00	2.69	F
1916	1931	1.143684	CAGATGGATACCCCCACTTGG	59.856	57.143	0.0	0.0	39.34	3.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1961	1976	0.679960	GCCCCAACCACCTGTATGAC	60.680	60.000	0.0	0.0	0.0	3.06	R
2794	3807	1.471287	CAGGTGACGACGTAGATGGAA	59.529	52.381	0.0	0.0	0.0	3.53	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
33	34	4.455606	AGTTGGATATGAGCAAAGCCTAC	58.544	43.478	0.00	0.00	0.00	3.18
76	77	3.066342	CCTCCATGACATGTTGATGAAGC	59.934	47.826	14.26	0.00	33.36	3.86
125	126	2.884012	TGGTGATGAAATGTGTGACCAC	59.116	45.455	0.00	0.00	42.19	4.16
245	246	7.466746	TCTTAATATGTGCAGAAGGCTTTTT	57.533	32.000	0.00	0.00	45.15	1.94
309	310	4.571176	GGAATTAAAGTCTCTGTTAGGGCG	59.429	45.833	0.00	0.00	0.00	6.13
400	401	4.749099	CGCAGGAGATAGAGAGAATTTTGG	59.251	45.833	0.00	0.00	0.00	3.28
435	436	1.071542	TGCTCGGGTCAAGTGATCAAA	59.928	47.619	0.00	0.00	0.00	2.69
471	472	5.221204	TGCAATCATGTTTAGCAAGAACACA	60.221	36.000	9.65	0.00	39.57	3.72
518	519	4.150897	TGGGGATCCTTCAATTAAGACG	57.849	45.455	12.58	0.00	37.38	4.18
578	580	5.927689	TGTTCATTGGCAAATCTAAAAGCAG	59.072	36.000	3.01	0.00	0.00	4.24
588	590	2.151202	TCTAAAAGCAGGGCGTTTGAG	58.849	47.619	11.42	6.23	40.08	3.02
674	676	6.461648	GCAGGGAAAGAAATCCTAATTAAGGC	60.462	42.308	0.00	0.00	46.10	4.35
803	805	6.647334	TGACAAAGAGCACAAAATCCATTA	57.353	33.333	0.00	0.00	0.00	1.90
868	870	1.447838	GGCTTCCGCGATCTTCACA	60.448	57.895	8.23	0.00	36.88	3.58
891	893	1.836802	TCAACATGGCTATGCTTGCA	58.163	45.000	10.37	0.00	37.85	4.08
1022	1026	2.488937	TGTCGTACTCATGGCGAAGTAA	59.511	45.455	0.00	0.00	36.37	2.24
1172	1176	8.907885	AGGGCAAAATATAATTCAGAAAGTCTC	58.092	33.333	0.00	0.00	0.00	3.36
1200	1204	5.144159	TGATAGATCCAGTAACAGGAGGT	57.856	43.478	0.00	0.00	38.83	3.85
1348	1354	8.911918	TTTGGTAAAGTCAGCTTATAAAGTCA	57.088	30.769	0.00	0.00	33.95	3.41
1382	1388	5.394224	GGGAGGCCAAGAAAACTAATAAAGC	60.394	44.000	5.01	0.00	0.00	3.51
1408	1414	9.784531	CCATTCAATTAACTACTGGTATCTCAT	57.215	33.333	0.00	0.00	0.00	2.90
1633	1639	1.559682	CTAAGCAGGTTTGGAGGGCTA	59.440	52.381	0.00	0.00	33.80	3.93
1762	1776	3.649023	ACTCCTATGGTTGTTGTGGTACA	59.351	43.478	0.00	0.00	0.00	2.90
1783	1797	7.387948	GGTACAAGAGAAACAGAGAAAATGCTA	59.612	37.037	0.00	0.00	0.00	3.49
1867	1881	5.725551	TTTGGAATATAGCAAGAAGGGGA	57.274	39.130	0.00	0.00	0.00	4.81
1879	1894	4.273318	CAAGAAGGGGAAACAGAATAGGG	58.727	47.826	0.00	0.00	0.00	3.53
1888	1903	2.263895	ACAGAATAGGGGTGTGGCTA	57.736	50.000	0.00	0.00	0.00	3.93
1916	1931	1.143684	CAGATGGATACCCCCACTTGG	59.856	57.143	0.00	0.00	39.34	3.61
2007	2022	0.410663	TCAGGAACTCGGAGGGGTTA	59.589	55.000	10.23	0.00	34.60	2.85
2067	2082	2.072298	GACGCTCTTCATGCAGAAACT	58.928	47.619	0.00	0.00	35.40	2.66
2113	2128	3.043419	CCGGAGAGATAGGGTGCG	58.957	66.667	0.00	0.00	0.00	5.34
2144	2159	7.008357	GGTTATTTTCGAAACTGATGCTTTAGC	59.992	37.037	10.79	0.00	42.50	3.09
2227	2242	6.614694	TGGAAGCCAAGTATTTACTGAGTA	57.385	37.500	0.00	0.00	36.50	2.59
2232	2247	9.765795	GAAGCCAAGTATTTACTGAGTATGTAT	57.234	33.333	0.00	0.00	36.50	2.29
2379	3384	1.332997	GTATCATCTGCAGTTGCTGGC	59.667	52.381	18.21	6.37	42.66	4.85
2412	3417	4.946157	AGCCTGTGAAAGTAATGGAATCTG	59.054	41.667	0.00	0.00	0.00	2.90
2425	3430	4.543590	TGGAATCTGAGTGTTCCTTCTC	57.456	45.455	16.17	0.00	43.41	2.87
2535	3540	1.290955	CCTTACCACTCGCGGTTCA	59.709	57.895	6.13	0.00	40.67	3.18
2607	3612	4.201920	GGTTCCGAATAAGCTTGTGATTCC	60.202	45.833	9.86	0.00	0.00	3.01
2609	3614	4.780815	TCCGAATAAGCTTGTGATTCCAT	58.219	39.130	9.86	0.00	0.00	3.41
2794	3807	1.410882	GCAGAGCCGGACTAGATCTTT	59.589	52.381	5.05	0.00	0.00	2.52
2961	4019	4.628333	TGTGCTCGGTAGTTTGCTTTATAC	59.372	41.667	0.00	0.00	0.00	1.47
3080	4138	2.422479	CTGAAGCTCATGTGTTGGATGG	59.578	50.000	0.00	0.00	0.00	3.51
3129	4187	2.867109	AGCTCATTGGTACTTGTGCT	57.133	45.000	11.87	11.87	37.25	4.40
3207	4265	8.578448	TCATGTGTTGGATGAATTTTAGATGA	57.422	30.769	0.00	0.00	0.00	2.92
3221	4279	9.606631	GAATTTTAGATGACCTTGTATCTCTGT	57.393	33.333	0.00	0.00	35.42	3.41
3269	4327	3.552132	TGTGCCGATATTTTGCTAGGA	57.448	42.857	0.00	0.00	0.00	2.94
3272	4330	3.495001	GTGCCGATATTTTGCTAGGAGAC	59.505	47.826	0.00	0.00	0.00	3.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.107950	TATCCAACTTCAAGGCCGTG	57.892	50.000	13.08	13.08	0.00	4.94
33	34	0.744414	AAGCCCATTCCACACGATCG	60.744	55.000	14.88	14.88	0.00	3.69
76	77	4.428294	TCCATCTTCTATCAAAGCCCAG	57.572	45.455	0.00	0.00	0.00	4.45
245	246	0.874390	CGCTTCTTGCAGTAAAGCCA	59.126	50.000	18.41	0.00	41.83	4.75
309	310	3.375299	ACAGAAGATGATTAACGCTTGGC	59.625	43.478	0.00	0.00	0.00	4.52
471	472	4.510340	ACTTCTTGTTTATCTTTGTCGCGT	59.490	37.500	5.77	0.00	0.00	6.01
518	519	8.233190	CCAAGTATTTCTCTGATCTTGTTTCAC	58.767	37.037	0.00	0.00	33.00	3.18
578	580	3.078837	TCCTTCAAATACTCAAACGCCC	58.921	45.455	0.00	0.00	0.00	6.13
588	590	9.103861	CTCTTCCATACTTTCTCCTTCAAATAC	57.896	37.037	0.00	0.00	0.00	1.89
674	676	1.098050	GGGGATTGCTTGTGCTACAG	58.902	55.000	0.00	0.00	40.48	2.74
803	805	9.178758	GTTGTGATAATCTTTCCCAACTAATCT	57.821	33.333	0.00	0.00	0.00	2.40
868	870	2.756760	CAAGCATAGCCATGTTGAAGGT	59.243	45.455	0.00	0.00	34.40	3.50
891	893	2.334023	AGGAGTCTCCAAGCTTGTCTT	58.666	47.619	24.35	9.05	39.61	3.01
1172	1176	5.508153	CCTGTTACTGGATCTATCAACTCCG	60.508	48.000	1.81	0.00	31.36	4.63
1200	1204	0.703488	TGACCATGGCTTCATCCCAA	59.297	50.000	13.04	0.00	35.67	4.12
1348	1354	2.323999	TTGGCCTCCCAATCAACAAT	57.676	45.000	3.32	0.00	46.01	2.71
1382	1388	9.784531	ATGAGATACCAGTAGTTAATTGAATGG	57.215	33.333	0.00	0.00	0.00	3.16
1633	1639	3.435601	GCCCTCATATCCTCCAATTGTGT	60.436	47.826	4.43	0.00	0.00	3.72
1762	1776	7.675062	TCTCTAGCATTTTCTCTGTTTCTCTT	58.325	34.615	0.00	0.00	0.00	2.85
1783	1797	8.571461	TCTATGCAATTTCTTGAACATTCTCT	57.429	30.769	0.00	0.00	34.04	3.10
1812	1826	4.836125	ATGTTGTTCAACTGATGACACC	57.164	40.909	15.18	0.00	37.92	4.16
1867	1881	1.710809	AGCCACACCCCTATTCTGTTT	59.289	47.619	0.00	0.00	0.00	2.83
1879	1894	1.160137	CTGCTCTGTTTAGCCACACC	58.840	55.000	0.00	0.00	42.05	4.16
1888	1903	2.173569	GGGGTATCCATCTGCTCTGTTT	59.826	50.000	0.00	0.00	35.00	2.83
1916	1931	8.936864	CATCAATATTTATCTTCGGGTAAGGAC	58.063	37.037	0.00	0.00	35.75	3.85
1961	1976	0.679960	GCCCCAACCACCTGTATGAC	60.680	60.000	0.00	0.00	0.00	3.06
2007	2022	4.393693	GCTCCAGCAGCTTCAACT	57.606	55.556	0.00	0.00	45.83	3.16
2067	2082	3.282885	TGCCGCCATGATAAATGTTGTA	58.717	40.909	0.00	0.00	0.00	2.41
2113	2128	5.934935	TCAGTTTCGAAAATAACCTGACC	57.065	39.130	18.80	2.76	0.00	4.02
2144	2159	2.287788	CCCAACACAGCTTGCTTTAGTG	60.288	50.000	9.16	9.16	36.34	2.74
2232	2247	7.171167	CACCAATTTACAGTTGCATCATCAAAA	59.829	33.333	0.00	0.00	0.00	2.44
2253	2268	6.094464	CAGAATTACATGATCTTGAGCACCAA	59.906	38.462	15.03	0.00	0.00	3.67
2379	3384	1.737838	TTCACAGGCTGGCTAAATCG	58.262	50.000	20.34	0.00	0.00	3.34
2454	3459	3.424703	CAACTTCCACCCATCACTTCAT	58.575	45.455	0.00	0.00	0.00	2.57
2794	3807	1.471287	CAGGTGACGACGTAGATGGAA	59.529	52.381	0.00	0.00	0.00	3.53
2988	4046	7.620880	TCCTAGCAAAATAGTGACACAAGTAT	58.379	34.615	8.59	0.00	0.00	2.12
3108	4166	3.077359	AGCACAAGTACCAATGAGCTTC	58.923	45.455	9.11	0.00	39.90	3.86
3129	4187	8.435187	AGATGATAATCTCCTAGCAAAATGTCA	58.565	33.333	0.00	0.00	0.00	3.58
3172	4230	4.280436	TCCAACACATGAACTTCGGTAT	57.720	40.909	0.00	0.00	0.00	2.73
3181	4239	9.022884	TCATCTAAAATTCATCCAACACATGAA	57.977	29.630	0.00	0.00	42.93	2.57
3221	4279	6.043127	TGCCCATGAGCTTCAGTAGAAATATA	59.957	38.462	0.00	0.00	32.35	0.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.