AutoCloner

Multiple sequence alignment - TraesCS5D01G288200

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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	TraesCS5D01G288200	chr5D	100.000	2690	0	0	1	2690	387631829	387629140	0.000000e+00	4968.0
1	TraesCS5D01G288200	chr5D	83.834	699	87	17	998	1685	387712278	387711595	2.260000e-180	641.0
2	TraesCS5D01G288200	chr5D	80.422	853	125	28	998	1842	387705732	387704914	1.770000e-171	612.0
3	TraesCS5D01G288200	chr2D	95.382	996	36	2	1	996	542514896	542515881	0.000000e+00	1576.0
4	TraesCS5D01G288200	chr5B	93.071	1068	47	12	998	2049	466003853	466002797	0.000000e+00	1537.0
5	TraesCS5D01G288200	chr5B	81.936	692	110	13	998	1685	466172351	466171671	3.000000e-159	571.0
6	TraesCS5D01G288200	chr5B	90.884	362	26	6	2331	2690	466002432	466002076	1.870000e-131	479.0
7	TraesCS5D01G288200	chr5B	86.946	429	46	9	999	1426	466221247	466220828	8.720000e-130	473.0
8	TraesCS5D01G288200	chr5B	90.303	165	11	4	1013	1176	466026469	466026309	7.550000e-51	211.0
9	TraesCS5D01G288200	chr5B	81.553	103	16	3	1581	1682	466005376	466005276	6.170000e-12	82.4
10	TraesCS5D01G288200	chr5A	94.111	934	48	5	1761	2690	490319527	490318597	0.000000e+00	1413.0
11	TraesCS5D01G288200	chr5A	91.436	759	43	10	998	1756	490320472	490319736	0.000000e+00	1022.0
12	TraesCS5D01G288200	chr5A	83.792	691	95	13	998	1685	490651554	490650878	8.120000e-180	640.0
13	TraesCS5D01G288200	chr5A	81.700	694	108	14	998	1685	490593824	490593144	6.500000e-156	560.0
14	TraesCS5D01G288200	chr1B	91.733	1004	76	2	1	999	10796771	10795770	0.000000e+00	1387.0
15	TraesCS5D01G288200	chr2A	89.240	1013	94	7	1	999	111893784	111892773	0.000000e+00	1253.0
16	TraesCS5D01G288200	chr2A	88.944	1013	97	5	1	999	49737508	49738519	0.000000e+00	1236.0
17	TraesCS5D01G288200	chr7A	89.286	1008	93	5	1	999	721725302	721724301	0.000000e+00	1249.0
18	TraesCS5D01G288200	chr6B	89.184	1017	88	8	1	999	657310280	657309268	0.000000e+00	1249.0
19	TraesCS5D01G288200	chr3A	89.197	1009	98	5	1	1000	99293878	99294884	0.000000e+00	1249.0
20	TraesCS5D01G288200	chr3A	89.411	1001	91	7	3	999	30403837	30404826	0.000000e+00	1247.0
21	TraesCS5D01G288200	chr6D	89.173	1016	89	10	1	1000	434792155	434791145	0.000000e+00	1247.0

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	TraesCS5D01G288200	chr5D	387629140	387631829	2689	True	4968.000000	4968	100.000000	1	2690	1	chr5D.!!$R1	2689
1	TraesCS5D01G288200	chr5D	387711595	387712278	683	True	641.000000	641	83.834000	998	1685	1	chr5D.!!$R3	687
2	TraesCS5D01G288200	chr5D	387704914	387705732	818	True	612.000000	612	80.422000	998	1842	1	chr5D.!!$R2	844
3	TraesCS5D01G288200	chr2D	542514896	542515881	985	False	1576.000000	1576	95.382000	1	996	1	chr2D.!!$F1	995
4	TraesCS5D01G288200	chr5B	466002076	466005376	3300	True	699.466667	1537	88.502667	998	2690	3	chr5B.!!$R4	1692
5	TraesCS5D01G288200	chr5B	466171671	466172351	680	True	571.000000	571	81.936000	998	1685	1	chr5B.!!$R2	687
6	TraesCS5D01G288200	chr5A	490318597	490320472	1875	True	1217.500000	1413	92.773500	998	2690	2	chr5A.!!$R3	1692
7	TraesCS5D01G288200	chr5A	490650878	490651554	676	True	640.000000	640	83.792000	998	1685	1	chr5A.!!$R2	687
8	TraesCS5D01G288200	chr5A	490593144	490593824	680	True	560.000000	560	81.700000	998	1685	1	chr5A.!!$R1	687
9	TraesCS5D01G288200	chr1B	10795770	10796771	1001	True	1387.000000	1387	91.733000	1	999	1	chr1B.!!$R1	998
10	TraesCS5D01G288200	chr2A	111892773	111893784	1011	True	1253.000000	1253	89.240000	1	999	1	chr2A.!!$R1	998
11	TraesCS5D01G288200	chr2A	49737508	49738519	1011	False	1236.000000	1236	88.944000	1	999	1	chr2A.!!$F1	998
12	TraesCS5D01G288200	chr7A	721724301	721725302	1001	True	1249.000000	1249	89.286000	1	999	1	chr7A.!!$R1	998
13	TraesCS5D01G288200	chr6B	657309268	657310280	1012	True	1249.000000	1249	89.184000	1	999	1	chr6B.!!$R1	998
14	TraesCS5D01G288200	chr3A	99293878	99294884	1006	False	1249.000000	1249	89.197000	1	1000	1	chr3A.!!$F2	999
15	TraesCS5D01G288200	chr3A	30403837	30404826	989	False	1247.000000	1247	89.411000	3	999	1	chr3A.!!$F1	996
16	TraesCS5D01G288200	chr6D	434791145	434792155	1010	True	1247.000000	1247	89.173000	1	1000	1	chr6D.!!$R1	999

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
443	482	0.108424	CCTCTTCCTCTCGCCACAAG	60.108	60.0	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
2200	3097	0.032615	TGTGAACAAAGCTTGGGGGT	60.033	50.0	5.66	0.0	34.12	4.95	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
314	351	2.734673	CTCTTCGCGTTCTGCCTGC	61.735	63.158	5.77	0.00	42.08	4.85
443	482	0.108424	CCTCTTCCTCTCGCCACAAG	60.108	60.000	0.00	0.00	0.00	3.16
550	590	2.615493	CCGCACCTTTTGAGTCCTGTAT	60.615	50.000	0.00	0.00	0.00	2.29
674	718	1.227734	CCCCAACGTCGACAACCTT	60.228	57.895	17.16	0.00	0.00	3.50
701	745	0.251922	ACATGGCTGGCAAGGATGTT	60.252	50.000	8.35	0.00	0.00	2.71
777	824	3.069079	TCGAGGTTCTGCTACAGTACT	57.931	47.619	4.67	0.00	33.36	2.73
901	948	4.640771	TGCCATTTACCTTCTCTCTGTT	57.359	40.909	0.00	0.00	0.00	3.16
1042	1569	3.277133	GCAAATTCTGCCGCCTCA	58.723	55.556	2.35	0.00	46.13	3.86
1153	1680	3.340814	TGCCTGGAGACTTTCATCTTC	57.659	47.619	0.00	0.00	0.00	2.87
1278	1816	2.808543	GCATGATTCAGTTATCGGGGAC	59.191	50.000	0.00	0.00	0.00	4.46
1279	1817	3.744214	GCATGATTCAGTTATCGGGGACA	60.744	47.826	0.00	0.00	0.00	4.02
1498	2038	5.221601	CGGAGAGTGTACTATACAGGGAGTA	60.222	48.000	0.00	0.00	39.77	2.59
1564	2104	3.187942	AGGGATATCCTCATGGTCATGG	58.812	50.000	21.18	2.67	44.06	3.66
1577	2117	2.693864	CATGGAGGCTCCCAGGGT	60.694	66.667	30.03	8.71	39.97	4.34
1763	2516	9.335891	CAAAGTGTATTGTTTATGATGCGTTAA	57.664	29.630	0.00	0.00	0.00	2.01
1857	2610	1.065401	CACAACACAAGTGCCGAATGT	59.935	47.619	0.00	0.00	0.00	2.71
1916	2669	6.552008	AGACAGATAAAGTGGGGAAAATGAA	58.448	36.000	0.00	0.00	0.00	2.57
1919	2672	6.725834	ACAGATAAAGTGGGGAAAATGAACAT	59.274	34.615	0.00	0.00	0.00	2.71
1952	2705	7.388290	TGTTACGCAAGATTTTGTTCATTTC	57.612	32.000	0.00	0.00	43.62	2.17
1958	2719	6.347110	GCAAGATTTTGTTCATTTCACGTTC	58.653	36.000	0.00	0.00	36.65	3.95
1967	2728	6.258899	TGTTCATTTCACGTTCGAAAATGAA	58.741	32.000	26.97	26.97	38.33	2.57
2046	2807	7.748847	ACCAATTGTTCTCGTATAATTGTGTC	58.251	34.615	4.43	0.00	38.30	3.67
2086	2980	6.548321	TCCTCCAGGCTAAACTAAATCAAAA	58.452	36.000	0.00	0.00	34.44	2.44
2105	2999	5.721000	TCAAAATTTAGCCAATCACCATCCT	59.279	36.000	0.00	0.00	0.00	3.24
2137	3034	6.150140	ACTCATCATCTTGAAGTAACCAAAGC	59.850	38.462	0.00	0.00	0.00	3.51
2148	3045	3.560068	AGTAACCAAAGCTGTTGAACTCG	59.440	43.478	9.37	0.00	0.00	4.18
2151	3048	1.264288	CCAAAGCTGTTGAACTCGGTC	59.736	52.381	9.37	0.00	0.00	4.79
2158	3055	1.613925	TGTTGAACTCGGTCCTCAGAG	59.386	52.381	0.00	0.00	40.69	3.35
2204	3101	1.541588	CTAAGCAGCACAAAGAACCCC	59.458	52.381	0.00	0.00	0.00	4.95
2205	3102	1.115326	AAGCAGCACAAAGAACCCCC	61.115	55.000	0.00	0.00	0.00	5.40
2206	3103	1.832167	GCAGCACAAAGAACCCCCA	60.832	57.895	0.00	0.00	0.00	4.96
2232	3129	5.669848	GCTTTGTTCACATCGATCTCTCAAC	60.670	44.000	0.00	0.00	0.00	3.18
2255	3153	2.287788	ACAGCAAGGATTTCAAGCAACG	60.288	45.455	0.00	0.00	0.00	4.10
2270	3168	4.216411	AGCAACGATACCAATACCAGTT	57.784	40.909	0.00	0.00	0.00	3.16
2273	3171	4.574828	GCAACGATACCAATACCAGTTGAT	59.425	41.667	9.24	0.00	39.60	2.57
2366	3264	1.136891	GCCCAACCATTAACTGATGCC	59.863	52.381	0.00	0.00	0.00	4.40
2385	3283	4.954875	TGCCAAAACAGAAACTAATTGGG	58.045	39.130	4.69	0.00	38.17	4.12
2528	3426	8.262715	TCATTAACTAAAATCTGACGATGCAA	57.737	30.769	0.00	0.00	0.00	4.08

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
306	343	3.633094	GACGAAGCGAGCAGGCAGA	62.633	63.158	0.00	0.00	34.64	4.26
314	351	1.388065	ATGGAGGGAGACGAAGCGAG	61.388	60.000	0.00	0.00	0.00	5.03
443	482	3.426568	GCGCAGTGCTCAGGAACC	61.427	66.667	14.33	0.00	41.73	3.62
503	542	1.455217	GGCCTACTGTCCCGAGCTA	60.455	63.158	0.00	0.00	0.00	3.32
506	545	2.128507	GGAGGCCTACTGTCCCGAG	61.129	68.421	8.12	0.00	0.00	4.63
550	590	2.661176	ACCTTATCACCCTTCTCCCA	57.339	50.000	0.00	0.00	0.00	4.37
619	663	1.446907	GAAGTAGTCGTCGGAGTCCA	58.553	55.000	10.49	0.00	0.00	4.02
674	718	2.885113	CCAGCCATGTCGTCGAGA	59.115	61.111	0.00	0.00	0.00	4.04
701	745	1.348064	CAGTACTGGACTTGGGGTCA	58.652	55.000	15.49	0.00	46.16	4.02
777	824	1.859302	AGGGCAAACACCAGAACAAA	58.141	45.000	0.00	0.00	0.00	2.83
1033	1560	1.234615	GCAAGTACTTTGAGGCGGCA	61.235	55.000	13.08	0.00	39.21	5.69
1153	1680	6.007677	GCAAGATGAAACGTAACTTACTTCG	58.992	40.000	0.00	0.00	0.00	3.79
1278	1816	1.734477	CCGCTTCAGACACGAGGTG	60.734	63.158	0.00	0.00	39.75	4.00
1279	1817	2.651361	CCGCTTCAGACACGAGGT	59.349	61.111	0.00	0.00	0.00	3.85
1306	1844	1.349688	CCTTAGGCTGTTGTGGTGGTA	59.650	52.381	0.00	0.00	0.00	3.25
1498	2038	2.590092	GGCCCAAGTGCGGATACT	59.410	61.111	0.00	0.00	0.00	2.12
1559	2099	2.367377	CCCTGGGAGCCTCCATGA	60.367	66.667	13.90	0.00	38.64	3.07
1560	2100	2.693864	ACCCTGGGAGCCTCCATG	60.694	66.667	22.23	4.14	38.64	3.66
1561	2101	2.693864	CACCCTGGGAGCCTCCAT	60.694	66.667	22.23	0.00	38.64	3.41
1564	2104	2.432174	AAAAGCACCCTGGGAGCCTC	62.432	60.000	28.34	4.94	40.09	4.70
1617	2157	3.119792	CGACTTTTAGCACGACTCTTGAC	59.880	47.826	0.00	0.00	0.00	3.18
1712	2255	3.327626	TGATTCAACATTGCACATTGCC	58.672	40.909	0.00	0.00	44.23	4.52
1763	2516	4.218312	GGCCCATTCTGATAGTTTGGAAT	58.782	43.478	0.00	0.00	0.00	3.01
1916	2669	1.577328	GCGTAACAGCCAGCACATGT	61.577	55.000	0.00	0.00	0.00	3.21
1919	2672	1.506309	CTTGCGTAACAGCCAGCACA	61.506	55.000	0.00	0.00	39.51	4.57
1952	2705	3.870723	TCCTGTTCATTTTCGAACGTG	57.129	42.857	0.00	0.00	46.77	4.49
1958	2719	5.448438	TCGTTCATTTCCTGTTCATTTTCG	58.552	37.500	0.00	0.00	0.00	3.46
1967	2728	7.928706	CCTCTTCTAATATCGTTCATTTCCTGT	59.071	37.037	0.00	0.00	0.00	4.00
2046	2807	4.029520	TGGAGGAGGAAGATGAAGAGAAG	58.970	47.826	0.00	0.00	0.00	2.85
2105	2999	4.828939	ACTTCAAGATGATGAGTTTTGCCA	59.171	37.500	0.00	0.00	0.00	4.92
2137	3034	1.613925	TCTGAGGACCGAGTTCAACAG	59.386	52.381	0.00	0.00	0.00	3.16
2148	3045	1.536943	AACGTGAGCCTCTGAGGACC	61.537	60.000	27.53	16.76	37.67	4.46
2151	3048	0.668706	CACAACGTGAGCCTCTGAGG	60.669	60.000	19.55	19.55	35.30	3.86
2158	3055	1.658409	GCTTTGCACAACGTGAGCC	60.658	57.895	0.00	0.00	35.23	4.70
2184	3081	1.541588	GGGGTTCTTTGTGCTGCTTAG	59.458	52.381	0.00	0.00	0.00	2.18
2197	3094	1.063266	TGAACAAAGCTTGGGGGTTCT	60.063	47.619	22.83	0.00	38.82	3.01
2198	3095	1.068588	GTGAACAAAGCTTGGGGGTTC	59.931	52.381	18.87	18.87	38.59	3.62
2200	3097	0.032615	TGTGAACAAAGCTTGGGGGT	60.033	50.000	5.66	0.00	34.12	4.95
2202	3099	1.068333	CGATGTGAACAAAGCTTGGGG	60.068	52.381	5.66	0.00	34.12	4.96
2204	3101	3.438087	AGATCGATGTGAACAAAGCTTGG	59.562	43.478	0.54	0.00	34.12	3.61
2205	3102	4.391216	AGAGATCGATGTGAACAAAGCTTG	59.609	41.667	0.54	0.00	0.00	4.01
2206	3103	4.573900	AGAGATCGATGTGAACAAAGCTT	58.426	39.130	0.54	0.00	0.00	3.74
2232	3129	4.479619	GTTGCTTGAAATCCTTGCTGTAG	58.520	43.478	0.00	0.00	0.00	2.74
2255	3153	7.055667	TGAGAGATCAACTGGTATTGGTATC	57.944	40.000	0.00	0.00	32.21	2.24
2270	3168	6.350629	TCAGAACATGTCTTTGAGAGATCA	57.649	37.500	0.00	0.00	36.61	2.92
2273	3171	6.348498	TGTTTCAGAACATGTCTTTGAGAGA	58.652	36.000	0.00	0.00	40.71	3.10
2366	3264	8.485976	TTTGAACCCAATTAGTTTCTGTTTTG	57.514	30.769	0.00	0.00	31.46	2.44
2521	3419	3.531538	TCCTTAGCCTTAAGTTGCATCG	58.468	45.455	0.97	0.00	35.51	3.84
2528	3426	9.608718	AGATATACATTCTCCTTAGCCTTAAGT	57.391	33.333	0.97	0.00	35.51	2.24
2570	3468	2.644798	AGAACCAAGACAAGTAGGGCAT	59.355	45.455	0.00	0.00	0.00	4.40
2602	3500	2.353607	CGCCGATACGAGCAGGAC	60.354	66.667	0.00	0.00	34.06	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.