AutoCloner

Multiple sequence alignment - TraesCS1D01G215100

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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	TraesCS1D01G215100	chr1D	100.000	3029	0	0	1	3029	300327816	300324788	0.000000e+00	5594.0
1	TraesCS1D01G215100	chr1D	79.762	336	59	4	1703	2029	300859829	300860164	5.050000e-58	235.0
2	TraesCS1D01G215100	chr1D	86.598	194	25	1	1513	1705	300718827	300718634	2.370000e-51	213.0
3	TraesCS1D01G215100	chr1B	91.709	2581	115	50	47	2573	405527030	405524495	0.000000e+00	3489.0
4	TraesCS1D01G215100	chr1B	91.503	459	32	7	2571	3025	405524430	405523975	2.560000e-175	625.0
5	TraesCS1D01G215100	chr1B	80.952	336	55	4	1703	2029	406037241	406037576	1.080000e-64	257.0
6	TraesCS1D01G215100	chr1B	86.458	192	26	0	1514	1705	405905985	405905794	8.510000e-51	211.0
7	TraesCS1D01G215100	chr1B	88.608	79	9	0	1121	1199	405673634	405673556	2.490000e-16	97.1
8	TraesCS1D01G215100	chr1A	90.847	1606	92	26	1459	3029	374690236	374688651	0.000000e+00	2100.0
9	TraesCS1D01G215100	chr1A	92.774	1453	52	24	1	1410	374691682	374690240	0.000000e+00	2052.0
10	TraesCS1D01G215100	chr1A	80.952	336	55	4	1703	2029	375468980	375469315	1.080000e-64	257.0
11	TraesCS1D01G215100	chr1A	86.979	192	25	0	1514	1705	375113130	375112939	1.830000e-52	217.0
12	TraesCS1D01G215100	chr6D	79.802	505	84	13	1541	2030	15551133	15550632	4.800000e-93	351.0
13	TraesCS1D01G215100	chr6D	78.543	508	95	10	1540	2034	15640543	15641049	3.770000e-84	322.0
14	TraesCS1D01G215100	chr6D	83.756	197	30	2	78	274	37441138	37441332	5.160000e-43	185.0
15	TraesCS1D01G215100	chr6D	80.905	199	31	5	80	274	227789865	227789670	1.880000e-32	150.0
16	TraesCS1D01G215100	chr6D	86.777	121	16	0	1286	1406	15640251	15640371	5.270000e-28	135.0
17	TraesCS1D01G215100	chrUn	79.365	504	79	17	1541	2023	319197530	319197031	6.260000e-87	331.0
18	TraesCS1D01G215100	chr6B	78.082	511	92	16	1540	2034	27669232	27669738	3.790000e-79	305.0
19	TraesCS1D01G215100	chr6B	86.822	129	12	4	1286	1411	27668940	27669066	4.070000e-29	139.0
20	TraesCS1D01G215100	chr6B	90.000	50	5	0	2	51	567214618	567214667	7.010000e-07	65.8
21	TraesCS1D01G215100	chr5A	88.652	141	16	0	1559	1699	694759690	694759830	4.010000e-39	172.0
22	TraesCS1D01G215100	chr4B	88.652	141	16	0	1559	1699	659330243	659330103	4.010000e-39	172.0
23	TraesCS1D01G215100	chr3D	91.525	118	6	3	1290	1405	391736	391621	3.130000e-35	159.0
24	TraesCS1D01G215100	chr3A	90.517	116	11	0	1290	1405	9110405	9110520	1.450000e-33	154.0
25	TraesCS1D01G215100	chr3B	89.831	118	8	3	1290	1405	5802830	5802715	6.770000e-32	148.0
26	TraesCS1D01G215100	chr3B	89.831	118	8	3	1290	1405	6117725	6117840	6.770000e-32	148.0
27	TraesCS1D01G215100	chr6A	86.400	125	16	1	1286	1409	16337905	16338029	5.270000e-28	135.0

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	TraesCS1D01G215100	chr1D	300324788	300327816	3028	True	5594.0	5594	100.0000	1	3029	1	chr1D.!!$R1	3028
1	TraesCS1D01G215100	chr1B	405523975	405527030	3055	True	2057.0	3489	91.6060	47	3025	2	chr1B.!!$R3	2978
2	TraesCS1D01G215100	chr1A	374688651	374691682	3031	True	2076.0	2100	91.8105	1	3029	2	chr1A.!!$R2	3028
3	TraesCS1D01G215100	chr6D	15550632	15551133	501	True	351.0	351	79.8020	1541	2030	1	chr6D.!!$R1	489
4	TraesCS1D01G215100	chr6D	15640251	15641049	798	False	228.5	322	82.6600	1286	2034	2	chr6D.!!$F2	748
5	TraesCS1D01G215100	chr6B	27668940	27669738	798	False	222.0	305	82.4520	1286	2034	2	chr6B.!!$F2	748

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
194	196	0.761702	GGGGTTGCCTCCTATCCGTA	60.762	60.0	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
2118	2249	1.591594	GATTTCGATCGGCCGAGCA	60.592	57.895	38.97	24.81	39.9	4.26	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
25	26	3.060602	GAGCTCAGTGTGGTAGTTGTTC	58.939	50.000	9.40	0.00	0.00	3.18
33	34	1.944709	GTGGTAGTTGTTCCGCTTGTT	59.055	47.619	0.00	0.00	0.00	2.83
136	138	1.757118	GGTGAGACGGGATGAAGATGA	59.243	52.381	0.00	0.00	0.00	2.92
137	139	2.366916	GGTGAGACGGGATGAAGATGAT	59.633	50.000	0.00	0.00	0.00	2.45
138	140	3.574396	GGTGAGACGGGATGAAGATGATA	59.426	47.826	0.00	0.00	0.00	2.15
139	141	4.551388	GTGAGACGGGATGAAGATGATAC	58.449	47.826	0.00	0.00	0.00	2.24
181	183	1.411977	TGCAAATGTGAAGTGGGGTTG	59.588	47.619	0.00	0.00	0.00	3.77
183	185	1.047801	AAATGTGAAGTGGGGTTGCC	58.952	50.000	0.00	0.00	0.00	4.52
194	196	0.761702	GGGGTTGCCTCCTATCCGTA	60.762	60.000	0.00	0.00	0.00	4.02
250	252	4.517285	ACAGGTACATCATCATCACCAAC	58.483	43.478	0.00	0.00	0.00	3.77
322	325	1.351707	GTATCGTTGCGTGCCCATG	59.648	57.895	0.00	0.00	0.00	3.66
323	326	1.078778	TATCGTTGCGTGCCCATGT	60.079	52.632	0.00	0.00	0.00	3.21
337	340	3.181462	TGCCCATGTATTTTGTTGTTGCA	60.181	39.130	0.00	0.00	0.00	4.08
429	437	4.156455	ACGATGATTGCCTCCATAGTTT	57.844	40.909	0.00	0.00	0.00	2.66
958	1007	2.173519	GCACCACTACTACTACCACCA	58.826	52.381	0.00	0.00	0.00	4.17
1027	1076	1.190643	GCTACTCTCTGTCAAGGCCT	58.809	55.000	0.00	0.00	0.00	5.19
1272	1328	3.057596	TCGTTGCTCAATTTGGTTCATCC	60.058	43.478	0.00	0.00	0.00	3.51
1412	1468	4.639334	CTGCTACCAGGTACGTCTATAGA	58.361	47.826	0.00	0.00	35.38	1.98
1415	1471	5.163269	TGCTACCAGGTACGTCTATAGAAGA	60.163	44.000	20.65	3.72	0.00	2.87
1451	1523	3.390175	TTCCTGGACCTTGGTGAAAAA	57.610	42.857	0.00	0.00	0.00	1.94
1490	1562	3.997021	GCACTACACACAGTTATCAGCTT	59.003	43.478	0.00	0.00	0.00	3.74
2035	2154	3.288484	AGTTCAGCTGATCGGCGA	58.712	55.556	19.04	13.87	37.29	5.54
2036	2155	1.153745	AGTTCAGCTGATCGGCGAC	60.154	57.895	19.04	18.83	37.29	5.19
2118	2249	3.495100	CCCTCTGCTGGCTACGATTAATT	60.495	47.826	0.00	0.00	0.00	1.40
2459	2603	5.764192	AGCAAAAGCTTTGCCATTTCATTAA	59.236	32.000	21.98	0.00	45.98	1.40
2461	2605	6.293571	GCAAAAGCTTTGCCATTTCATTAAGT	60.294	34.615	13.54	0.00	39.38	2.24
2469	2613	9.912634	CTTTGCCATTTCATTAAGTAGAAGAAA	57.087	29.630	0.00	0.00	33.33	2.52
2470	2614	9.912634	TTTGCCATTTCATTAAGTAGAAGAAAG	57.087	29.630	0.00	0.00	32.45	2.62
2478	2622	8.818141	TCATTAAGTAGAAGAAAGAGTGTGTG	57.182	34.615	0.00	0.00	0.00	3.82
2490	2634	8.934507	AGAAAGAGTGTGTGTATATAAAGAGC	57.065	34.615	0.00	0.00	0.00	4.09
2492	2636	6.163135	AGAGTGTGTGTATATAAAGAGCCC	57.837	41.667	0.00	0.00	0.00	5.19
2494	2638	3.493503	GTGTGTGTATATAAAGAGCCCGC	59.506	47.826	0.00	0.00	0.00	6.13
2552	2696	6.650239	TTACAATTCTAACGCGATTTGCTA	57.350	33.333	15.93	0.00	43.27	3.49
2553	2697	5.539582	ACAATTCTAACGCGATTTGCTAA	57.460	34.783	15.93	0.00	43.27	3.09
2616	2826	7.068716	GGGAGAAGATAATTGTAGGCATTTGTT	59.931	37.037	0.00	0.00	0.00	2.83
2619	2829	9.193806	AGAAGATAATTGTAGGCATTTGTTGAT	57.806	29.630	0.00	0.00	0.00	2.57
2633	2843	6.360681	GCATTTGTTGATATATGCCGAAAGAC	59.639	38.462	0.00	0.00	37.90	3.01
2638	2848	6.183361	TGTTGATATATGCCGAAAGACCCTAA	60.183	38.462	0.00	0.00	0.00	2.69
2668	2879	4.610945	CTCGTTTCAAAATTGCAAGAGGT	58.389	39.130	4.94	0.00	0.00	3.85
2674	2885	3.054878	CAAAATTGCAAGAGGTGAGCAC	58.945	45.455	4.94	0.00	38.11	4.40
2700	2911	2.093890	TGGACGCGGTAGATTTAGACA	58.906	47.619	12.47	0.00	0.00	3.41
2705	2916	4.194640	ACGCGGTAGATTTAGACACTCTA	58.805	43.478	12.47	0.00	0.00	2.43
2712	2923	7.701809	GTAGATTTAGACACTCTACCATTGC	57.298	40.000	0.00	0.00	36.80	3.56
2737	2948	1.306654	AGACCGCCTCCCACCATTA	60.307	57.895	0.00	0.00	0.00	1.90
2792	3005	2.942376	GTCGACATTATGCCATCCAACA	59.058	45.455	11.55	0.00	0.00	3.33
2826	3039	1.376609	ATTCCAAATCCGCACCGAGC	61.377	55.000	0.00	0.00	40.87	5.03
2853	3067	1.806461	TTGAAGAGCGAGTGAGCCGT	61.806	55.000	0.00	0.00	38.01	5.68
2861	3075	1.666011	GAGTGAGCCGTTGTCTCCA	59.334	57.895	0.00	0.00	0.00	3.86
2911	3125	7.997482	TGACACATCCAAGTTATACTACTCTC	58.003	38.462	0.00	0.00	0.00	3.20
2976	3190	3.369385	AGTACGTTCTATCAAATCCGCG	58.631	45.455	0.00	0.00	0.00	6.46

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
25	26	0.588252	CTGTCACCTTCAACAAGCGG	59.412	55.000	0.00	0.00	0.00	5.52
33	34	2.583441	CGCCTCCCTGTCACCTTCA	61.583	63.158	0.00	0.00	0.00	3.02
136	138	5.321927	ACAAACCCCTCATTCTTTTCGTAT	58.678	37.500	0.00	0.00	0.00	3.06
137	139	4.721132	ACAAACCCCTCATTCTTTTCGTA	58.279	39.130	0.00	0.00	0.00	3.43
138	140	3.562182	ACAAACCCCTCATTCTTTTCGT	58.438	40.909	0.00	0.00	0.00	3.85
139	141	4.584327	AACAAACCCCTCATTCTTTTCG	57.416	40.909	0.00	0.00	0.00	3.46
194	196	3.314307	TGACCGTCTAATCTGGATCCT	57.686	47.619	14.23	0.00	0.00	3.24
201	203	4.624015	TGTCGTTTTTGACCGTCTAATCT	58.376	39.130	0.00	0.00	38.11	2.40
205	207	5.574055	GTCATATGTCGTTTTTGACCGTCTA	59.426	40.000	1.90	0.00	38.11	2.59
267	269	9.019764	GTCTCGAAATCATTTTCTCTTCTCTAG	57.980	37.037	0.00	0.00	39.30	2.43
288	290	0.379669	ATACAGTTACCGCCGTCTCG	59.620	55.000	0.00	0.00	0.00	4.04
429	437	5.133941	ACTAGCTAGTCTCGGAATCAATGA	58.866	41.667	20.95	0.00	0.00	2.57
809	845	2.592993	CGTCACCCTCACCCACCAT	61.593	63.158	0.00	0.00	0.00	3.55
958	1007	1.932156	TTGTCAGGGTTGCCACTGGT	61.932	55.000	0.00	0.00	35.47	4.00
1272	1328	1.911293	GCCTGCATGTACACCACACG	61.911	60.000	0.00	0.00	40.86	4.49
1427	1483	2.944129	TCACCAAGGTCCAGGAAAAAG	58.056	47.619	7.34	0.00	0.00	2.27
1429	1485	3.390175	TTTCACCAAGGTCCAGGAAAA	57.610	42.857	7.34	5.00	0.00	2.29
1430	1486	3.390175	TTTTCACCAAGGTCCAGGAAA	57.610	42.857	7.34	0.00	0.00	3.13
1431	1487	3.390175	TTTTTCACCAAGGTCCAGGAA	57.610	42.857	7.34	0.00	0.00	3.36
1432	1488	3.611025	ATTTTTCACCAAGGTCCAGGA	57.389	42.857	7.34	0.00	0.00	3.86
1433	1489	3.640967	TCAATTTTTCACCAAGGTCCAGG	59.359	43.478	0.00	0.00	0.00	4.45
1435	1491	4.467795	TGTTCAATTTTTCACCAAGGTCCA	59.532	37.500	0.00	0.00	0.00	4.02
1451	1523	6.590292	GTGTAGTGCAGTGTACTATGTTCAAT	59.410	38.462	21.79	0.00	33.60	2.57
2118	2249	1.591594	GATTTCGATCGGCCGAGCA	60.592	57.895	38.97	24.81	39.90	4.26
2153	2284	4.804108	TGATCCCACGCAAAATACAAAAG	58.196	39.130	0.00	0.00	0.00	2.27
2304	2436	5.292765	GGTAGTGTCATCTCATGTATGGTG	58.707	45.833	9.80	1.82	0.00	4.17
2388	2523	6.322712	GGGAGCTGATAAGAAGAGACTTAGAA	59.677	42.308	0.00	0.00	36.11	2.10
2391	2526	4.580995	CGGGAGCTGATAAGAAGAGACTTA	59.419	45.833	0.00	0.00	36.89	2.24
2392	2527	3.383185	CGGGAGCTGATAAGAAGAGACTT	59.617	47.826	0.00	0.00	0.00	3.01
2469	2613	5.221263	CGGGCTCTTTATATACACACACTCT	60.221	44.000	0.00	0.00	0.00	3.24
2470	2614	4.982916	CGGGCTCTTTATATACACACACTC	59.017	45.833	0.00	0.00	0.00	3.51
2478	2622	1.274447	ACGGGCGGGCTCTTTATATAC	59.726	52.381	0.26	0.00	0.00	1.47
2492	2636	4.745751	TCGTTTGGGCTACGGGCG	62.746	66.667	0.00	0.00	42.94	6.13
2494	2638	0.391927	TCATTCGTTTGGGCTACGGG	60.392	55.000	0.00	0.00	39.38	5.28
2543	2687	2.749621	AGGTCAAAGCCTTAGCAAATCG	59.250	45.455	0.00	0.00	43.56	3.34
2552	2696	1.429299	AGCCCTTTAGGTCAAAGCCTT	59.571	47.619	0.00	0.00	42.07	4.35
2553	2697	1.076438	AGCCCTTTAGGTCAAAGCCT	58.924	50.000	0.00	0.00	42.07	4.58
2592	2802	8.677300	TCAACAAATGCCTACAATTATCTTCTC	58.323	33.333	0.00	0.00	0.00	2.87
2616	2826	5.305902	TGTTAGGGTCTTTCGGCATATATCA	59.694	40.000	0.00	0.00	0.00	2.15
2619	2829	5.818678	ATGTTAGGGTCTTTCGGCATATA	57.181	39.130	0.00	0.00	0.00	0.86
2625	2835	1.396996	CGCAATGTTAGGGTCTTTCGG	59.603	52.381	0.00	0.00	0.00	4.30
2633	2843	0.802494	AAACGAGCGCAATGTTAGGG	59.198	50.000	11.47	0.00	0.00	3.53
2638	2848	2.483583	TTTTGAAACGAGCGCAATGT	57.516	40.000	11.47	0.80	0.00	2.71
2668	2879	1.375908	GCGTCCATTCTGGTGCTCA	60.376	57.895	6.09	0.00	39.03	4.26
2674	2885	0.389391	ATCTACCGCGTCCATTCTGG	59.611	55.000	4.92	0.00	39.43	3.86
2675	2886	2.225068	AATCTACCGCGTCCATTCTG	57.775	50.000	4.92	0.00	0.00	3.02
2737	2948	3.119495	GCGCAACCATAACTCCATTCTTT	60.119	43.478	0.30	0.00	0.00	2.52
2761	2973	3.886123	CATAATGTCGACCCCCTTTCTT	58.114	45.455	14.12	0.00	0.00	2.52
2792	3005	7.470424	CGGATTTGGAATATGGTGAATGATTGT	60.470	37.037	0.00	0.00	0.00	2.71
2826	3039	2.280971	CACTCGCTCTTCAATGTCGATG	59.719	50.000	0.00	0.00	0.00	3.84
2853	3067	1.181741	AGCACGAGAGCTGGAGACAA	61.182	55.000	0.00	0.00	44.66	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.