AutoCloner

Multiple sequence alignment - TraesCS5D01G107400

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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	TraesCS5D01G107400	chr5D	100.000	1392	0	0	1	1392	120896003	120897394	0.000000e+00	2571.0
1	TraesCS5D01G107400	chr5D	100.000	794	0	0	1588	2381	120897590	120898383	0.000000e+00	1467.0
2	TraesCS5D01G107400	chr5A	96.520	862	30	0	506	1367	131802462	131803323	0.000000e+00	1426.0
3	TraesCS5D01G107400	chr5A	94.848	330	9	5	1	327	131801374	131801698	2.110000e-140	508.0
4	TraesCS5D01G107400	chr5A	90.580	138	13	0	352	489	131801691	131801828	1.450000e-42	183.0
5	TraesCS5D01G107400	chr5A	81.690	213	33	4	1783	1994	546358898	546358691	3.150000e-39	172.0
6	TraesCS5D01G107400	chr5A	97.222	72	2	0	1672	1743	131803809	131803880	3.210000e-24	122.0
7	TraesCS5D01G107400	chr5B	96.612	856	24	2	535	1389	134049825	134050676	0.000000e+00	1415.0
8	TraesCS5D01G107400	chr5B	95.479	376	13	3	1	373	134048459	134048833	4.380000e-167	597.0
9	TraesCS5D01G107400	chr5B	92.771	166	10	2	1588	1753	134050750	134050913	3.060000e-59	239.0
10	TraesCS5D01G107400	chr5B	97.727	132	3	0	371	502	134049098	134049229	6.620000e-56	228.0
11	TraesCS5D01G107400	chr2B	84.337	581	76	6	1756	2336	667245514	667246079	2.670000e-154	555.0
12	TraesCS5D01G107400	chr2B	82.979	376	57	6	1751	2125	59644179	59644548	1.360000e-87	333.0
13	TraesCS5D01G107400	chr2B	72.269	595	119	26	1789	2368	727086969	727087532	2.470000e-30	143.0
14	TraesCS5D01G107400	chr2B	100.000	43	0	0	641	683	133948257	133948215	1.960000e-11	80.5
15	TraesCS5D01G107400	chr2B	100.000	33	0	0	2340	2372	667246071	667246103	7.110000e-06	62.1
16	TraesCS5D01G107400	chr4D	87.204	422	34	11	1750	2171	320194219	320194620	1.670000e-126	462.0
17	TraesCS5D01G107400	chr4D	79.262	569	92	14	1814	2372	19326756	19326204	8.040000e-100	374.0
18	TraesCS5D01G107400	chr4A	83.264	484	66	6	1900	2381	251274801	251275271	4.700000e-117	431.0
19	TraesCS5D01G107400	chr3D	81.664	529	86	6	1753	2276	153508602	153509124	1.690000e-116	429.0
20	TraesCS5D01G107400	chrUn	77.413	487	78	19	1829	2308	24397164	24397625	6.530000e-66	261.0
21	TraesCS5D01G107400	chrUn	96.154	52	2	0	2330	2381	42480450	42480501	4.220000e-13	86.1
22	TraesCS5D01G107400	chr3A	75.826	575	95	26	1763	2305	382151718	382151156	3.930000e-63	252.0
23	TraesCS5D01G107400	chr7B	74.379	644	127	25	1752	2372	75788767	75789395	8.500000e-60	241.0
24	TraesCS5D01G107400	chr2A	72.549	561	116	20	1778	2331	41228576	41229105	5.300000e-32	148.0

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	TraesCS5D01G107400	chr5D	120896003	120898383	2380	False	2019.00	2571	100.00000	1	2381	2	chr5D.!!$F1	2380
1	TraesCS5D01G107400	chr5A	131801374	131803880	2506	False	559.75	1426	94.79250	1	1743	4	chr5A.!!$F1	1742
2	TraesCS5D01G107400	chr5B	134048459	134050913	2454	False	619.75	1415	95.64725	1	1753	4	chr5B.!!$F1	1752
3	TraesCS5D01G107400	chr2B	667245514	667246103	589	False	308.55	555	92.16850	1756	2372	2	chr2B.!!$F3	616
4	TraesCS5D01G107400	chr4D	19326204	19326756	552	True	374.00	374	79.26200	1814	2372	1	chr4D.!!$R1	558
5	TraesCS5D01G107400	chr3D	153508602	153509124	522	False	429.00	429	81.66400	1753	2276	1	chr3D.!!$F1	523
6	TraesCS5D01G107400	chr3A	382151156	382151718	562	True	252.00	252	75.82600	1763	2305	1	chr3A.!!$R1	542
7	TraesCS5D01G107400	chr7B	75788767	75789395	628	False	241.00	241	74.37900	1752	2372	1	chr7B.!!$F1	620

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
479	751	0.868406	GACTGTGTAAGCTGGTGTGC	59.132	55.0	0.0	0.0	0.00	4.57	F
633	1684	1.305201	GCGACACTCAGGAAAAACCA	58.695	50.0	0.0	0.0	42.04	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1370	2422	0.107508	AGCATCGATTCACACCCCTG	60.108	55.0	0.00	0.0	0.0	4.45	R
1804	3069	0.108615	CTTCTGATCCGACGGCTTGT	60.109	55.0	9.66	0.0	0.0	3.16	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
353	358	6.547141	TGGCACAATCAATTCCTAATAGAAGG	59.453	38.462	0.00	0.00	34.26	3.46
438	710	3.008375	TGTCTCCTTATTTGCTGAGTGCT	59.992	43.478	0.00	0.00	43.37	4.40
479	751	0.868406	GACTGTGTAAGCTGGTGTGC	59.132	55.000	0.00	0.00	0.00	4.57
523	1574	3.159984	CGCTCTCGTCAAAGGCAC	58.840	61.111	0.00	0.00	0.00	5.01
556	1607	4.558095	GCGTTTCTACCTTCACTGAGTGTA	60.558	45.833	12.93	1.61	34.79	2.90
623	1674	1.954146	GCAAAGACGGCGACACTCA	60.954	57.895	16.62	0.00	0.00	3.41
633	1684	1.305201	GCGACACTCAGGAAAAACCA	58.695	50.000	0.00	0.00	42.04	3.67
686	1737	2.616842	ACAACTGTTGGAAATGGACGTC	59.383	45.455	23.15	7.13	34.12	4.34
706	1757	7.489113	GGACGTCATAAATTGCATTTCTCATTT	59.511	33.333	18.91	0.00	33.82	2.32
747	1798	6.035005	CGTTATTCCATAGACTCACACTGTTG	59.965	42.308	0.00	0.00	0.00	3.33
874	1926	4.339872	TTTCCCTACTTGTGTTAAGCGA	57.660	40.909	0.00	0.00	0.00	4.93
890	1942	1.560860	GCGAGGCGGATACATGCTTC	61.561	60.000	0.00	0.00	34.23	3.86
943	1995	1.317613	TGAACTGATGTTGCACCCAC	58.682	50.000	0.00	0.00	36.39	4.61
1014	2066	1.669779	GCTGAGATGCAAGGACATGAC	59.330	52.381	0.00	0.00	0.00	3.06
1243	2295	1.784525	CTTTCTCGGACGACAGCTTT	58.215	50.000	0.00	0.00	0.00	3.51
1299	2351	1.996292	TGTCTTCTTTCGGATCGCTG	58.004	50.000	0.00	0.00	0.00	5.18
1370	2422	2.545742	GGTCCTGTGATTTGTGGTTTGC	60.546	50.000	0.00	0.00	0.00	3.68
1381	2433	1.040339	GTGGTTTGCAGGGGTGTGAA	61.040	55.000	0.00	0.00	0.00	3.18
1389	2441	0.107508	CAGGGGTGTGAATCGATGCT	60.108	55.000	4.68	0.00	0.00	3.79
1606	2658	2.496899	ATCTGGGACGTCTGCATTTT	57.503	45.000	16.46	0.00	0.00	1.82
1607	2659	1.808411	TCTGGGACGTCTGCATTTTC	58.192	50.000	16.46	0.00	0.00	2.29
1608	2660	1.347707	TCTGGGACGTCTGCATTTTCT	59.652	47.619	16.46	0.00	0.00	2.52
1609	2661	1.734465	CTGGGACGTCTGCATTTTCTC	59.266	52.381	16.46	0.00	0.00	2.87
1627	2679	5.468540	TTCTCAAAGTGAGCAGCTTAGTA	57.531	39.130	0.00	0.00	43.95	1.82
1628	2680	5.667539	TCTCAAAGTGAGCAGCTTAGTAT	57.332	39.130	0.00	0.00	43.95	2.12
1629	2681	5.655488	TCTCAAAGTGAGCAGCTTAGTATC	58.345	41.667	0.00	0.00	43.95	2.24
1640	2901	4.884164	GCAGCTTAGTATCAATTGAGGGTT	59.116	41.667	14.54	0.00	0.00	4.11
1670	2931	2.417586	GGTTGTACACAGGCGTATTTCC	59.582	50.000	0.00	0.00	0.00	3.13
1729	2990	5.485708	ACAGCTACAAAGAAGAGTAAGGGAT	59.514	40.000	0.00	0.00	0.00	3.85
1748	3009	6.433441	AGGGATAGGGAGATTACCTTATACG	58.567	44.000	0.00	0.00	39.54	3.06
1760	3021	2.366266	ACCTTATACGAAATGGGCGCTA	59.634	45.455	7.64	0.00	0.00	4.26
1776	3041	2.890109	CTACTACGCGTCGGCCGAT	61.890	63.158	33.58	18.35	39.56	4.18
1804	3069	0.321741	TTAAAACATCCGCCGCCTCA	60.322	50.000	0.00	0.00	0.00	3.86
1822	3087	0.389817	CACAAGCCGTCGGATCAGAA	60.390	55.000	17.49	0.00	0.00	3.02
1860	3126	0.394488	TCACCTTCAACCACCGCAAA	60.394	50.000	0.00	0.00	0.00	3.68
1865	3131	2.393764	CTTCAACCACCGCAAAACATC	58.606	47.619	0.00	0.00	0.00	3.06
1923	3190	4.511617	TGCGGAAAATTTGCAACATAGA	57.488	36.364	0.00	0.00	35.33	1.98
2097	3395	7.990917	TGCAACATAGAACTTGTTACAGAAAA	58.009	30.769	0.00	0.00	35.61	2.29
2106	3404	9.601217	AGAACTTGTTACAGAAAATCGCTATAT	57.399	29.630	0.00	0.00	0.00	0.86
2134	3439	4.702081	GCAGCGACCACGACGACT	62.702	66.667	0.00	0.00	42.66	4.18
2141	3446	1.401148	CGACCACGACGACTGAAAGAT	60.401	52.381	0.00	0.00	42.66	2.40
2142	3447	1.986378	GACCACGACGACTGAAAGATG	59.014	52.381	0.00	0.00	37.43	2.90
2166	3471	0.469331	AATGCTCCCTCGGGATCGTA	60.469	55.000	4.90	0.00	44.24	3.43
2179	3488	2.473664	GATCGTAGGGGATGGACGCG	62.474	65.000	3.53	3.53	36.54	6.01
2243	3554	2.270923	CGAATGCATCTTGAGTTCGGA	58.729	47.619	0.00	0.00	38.30	4.55
2276	3587	0.541392	CCGATGTTCATGGTGGAGGA	59.459	55.000	0.00	0.00	0.00	3.71
2280	3591	1.741028	TGTTCATGGTGGAGGAGGAA	58.259	50.000	0.00	0.00	0.00	3.36
2286	3597	0.191064	TGGTGGAGGAGGAAGACAGT	59.809	55.000	0.00	0.00	0.00	3.55
2378	3689	4.200283	GAGGAGGCGTCGCAGGAG	62.200	72.222	20.50	0.00	0.00	3.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
184	187	8.428063	TCATAAACCTAATAATTTTGGCCATGG	58.572	33.333	6.09	7.63	31.68	3.66
438	710	2.831685	TGCCGAGTTTCTTTCTAGCA	57.168	45.000	0.00	0.00	0.00	3.49
507	1558	0.793250	GAAGTGCCTTTGACGAGAGC	59.207	55.000	0.00	0.00	0.00	4.09
523	1574	3.064931	AGGTAGAAACGCGGAAAAGAAG	58.935	45.455	12.47	0.00	0.00	2.85
556	1607	4.388577	AAGATGGCCTTTTAGGAGTGTT	57.611	40.909	3.32	0.00	37.67	3.32
623	1674	6.883744	TGCTACTCAAAATTTGGTTTTTCCT	58.116	32.000	5.83	0.00	37.93	3.36
633	1684	7.226523	GGGTTTCACAAATGCTACTCAAAATTT	59.773	33.333	0.00	0.00	0.00	1.82
706	1757	6.874664	TGGAATAACGCATACAAGTGTCTTTA	59.125	34.615	0.00	0.00	0.00	1.85
874	1926	0.767375	ATGGAAGCATGTATCCGCCT	59.233	50.000	12.43	0.57	38.63	5.52
890	1942	1.656818	ATTTTCGCACCTCGCCATGG	61.657	55.000	7.63	7.63	37.30	3.66
1174	2226	1.591703	GATGAGCCACTCGGTGACA	59.408	57.895	5.71	4.17	35.23	3.58
1243	2295	2.359169	GGCGATGGAGAGGGTGACA	61.359	63.158	0.00	0.00	0.00	3.58
1275	2327	3.061429	GCGATCCGAAAGAAGACAAGAAG	59.939	47.826	0.00	0.00	0.00	2.85
1299	2351	3.951663	AGCTAACACCAAGTCCATTACC	58.048	45.455	0.00	0.00	0.00	2.85
1370	2422	0.107508	AGCATCGATTCACACCCCTG	60.108	55.000	0.00	0.00	0.00	4.45
1607	2659	5.414360	TGATACTAAGCTGCTCACTTTGAG	58.586	41.667	1.00	0.00	46.90	3.02
1608	2660	5.405935	TGATACTAAGCTGCTCACTTTGA	57.594	39.130	1.00	0.00	0.00	2.69
1609	2661	6.674694	ATTGATACTAAGCTGCTCACTTTG	57.325	37.500	1.00	0.00	0.00	2.77
1627	2679	5.190677	CCGTTAACCTAACCCTCAATTGAT	58.809	41.667	8.96	0.00	35.27	2.57
1628	2680	4.041938	ACCGTTAACCTAACCCTCAATTGA	59.958	41.667	8.12	8.12	35.27	2.57
1629	2681	4.329392	ACCGTTAACCTAACCCTCAATTG	58.671	43.478	0.00	0.00	35.27	2.32
1640	2901	3.554752	GCCTGTGTACAACCGTTAACCTA	60.555	47.826	0.00	0.00	0.00	3.08
1676	2937	5.178096	TGCCCTCTCAATTTTCTCACATA	57.822	39.130	0.00	0.00	0.00	2.29
1729	2990	7.179694	CCCATTTCGTATAAGGTAATCTCCCTA	59.820	40.741	0.00	0.00	0.00	3.53
1760	3021	4.547905	CATCGGCCGACGCGTAGT	62.548	66.667	33.75	10.25	43.86	2.73
1776	3041	5.583495	CGGCGGATGTTTTAAAAATATCCA	58.417	37.500	27.87	14.62	35.37	3.41
1804	3069	0.108615	CTTCTGATCCGACGGCTTGT	60.109	55.000	9.66	0.00	0.00	3.16
1822	3087	2.427245	CCCTCGACCGCTCAATCCT	61.427	63.158	0.00	0.00	0.00	3.24
1849	3115	0.591170	CGAGATGTTTTGCGGTGGTT	59.409	50.000	0.00	0.00	0.00	3.67
1973	3240	0.464036	ACACGACCTCTGTTGCAAGA	59.536	50.000	0.00	0.00	0.00	3.02
1974	3241	1.003545	CAACACGACCTCTGTTGCAAG	60.004	52.381	0.00	0.00	41.45	4.01
1975	3242	1.013596	CAACACGACCTCTGTTGCAA	58.986	50.000	0.00	0.00	41.45	4.08
1976	3243	2.689083	CAACACGACCTCTGTTGCA	58.311	52.632	3.30	0.00	41.45	4.08
2004	3275	0.896226	AACTAGACCTCCGTTGCCTC	59.104	55.000	0.00	0.00	0.00	4.70
2005	3276	0.608640	CAACTAGACCTCCGTTGCCT	59.391	55.000	0.00	0.00	32.68	4.75
2079	3377	8.997621	ATAGCGATTTTCTGTAACAAGTTCTA	57.002	30.769	0.00	0.00	0.00	2.10
2083	3381	7.919091	TCGATATAGCGATTTTCTGTAACAAGT	59.081	33.333	9.38	0.00	35.01	3.16
2097	3395	2.873609	CTTGCTGCTCGATATAGCGAT	58.126	47.619	14.22	0.00	45.85	4.58
2106	3404	4.362476	TCGCTGCTTGCTGCTCGA	62.362	61.111	19.16	9.57	43.37	4.04
2129	3434	0.400213	TTGCCCCATCTTTCAGTCGT	59.600	50.000	0.00	0.00	0.00	4.34
2134	3439	1.477553	GAGCATTGCCCCATCTTTCA	58.522	50.000	4.70	0.00	0.00	2.69
2196	3505	4.778143	GGAAGCACCGGCATCCGT	62.778	66.667	0.00	0.00	46.70	4.69
2225	3536	2.002586	CGTCCGAACTCAAGATGCATT	58.997	47.619	0.00	0.00	0.00	3.56
2243	3554	2.927580	ATCGGTTCTCACGGTGCGT	61.928	57.895	2.51	0.00	42.36	5.24
2276	3587	2.651361	CGCGACCACTGTCTTCCT	59.349	61.111	0.00	0.00	39.47	3.36
2335	3646	3.545124	TTTGACTGCCGCCACCGAT	62.545	57.895	0.00	0.00	36.29	4.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.