AutoCloner

Multiple sequence alignment - TraesCS1D01G017300

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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	TraesCS1D01G017300	chr1D	100.000	3530	0	0	1	3530	7767698	7771227	0.000000e+00	6519.0
1	TraesCS1D01G017300	chr1D	85.851	1675	164	32	458	2103	7342588	7340958	0.000000e+00	1712.0
2	TraesCS1D01G017300	chr1D	83.188	1606	191	48	458	2026	7715192	7716755	0.000000e+00	1397.0
3	TraesCS1D01G017300	chr1D	80.050	802	132	18	2068	2861	7716761	7717542	1.420000e-158	569.0
4	TraesCS1D01G017300	chr1D	90.226	399	25	8	7	393	7343091	7342695	3.140000e-140	508.0
5	TraesCS1D01G017300	chr1D	86.260	393	49	4	2324	2712	7340962	7340571	4.210000e-114	422.0
6	TraesCS1D01G017300	chr1D	95.397	239	8	2	2855	3093	446708317	446708552	9.250000e-101	377.0
7	TraesCS1D01G017300	chr1D	90.688	247	16	4	153	393	7714839	7715084	4.400000e-84	322.0
8	TraesCS1D01G017300	chr1D	89.583	240	20	5	2854	3093	82333097	82332863	2.060000e-77	300.0
9	TraesCS1D01G017300	chr1D	88.947	190	16	2	2	187	7714652	7714840	2.740000e-56	230.0
10	TraesCS1D01G017300	chr1A	95.287	2737	103	18	802	3530	9203332	9206050	0.000000e+00	4316.0
11	TraesCS1D01G017300	chr1A	82.306	746	99	20	2113	2845	9222613	9223338	1.800000e-172	616.0
12	TraesCS1D01G017300	chr1A	79.245	901	127	30	863	1722	9221799	9220918	1.100000e-159	573.0
13	TraesCS1D01G017300	chr1A	89.590	317	30	1	460	773	9203018	9203334	1.970000e-107	399.0
14	TraesCS1D01G017300	chr1A	77.778	639	110	20	2093	2704	9220466	9219833	7.200000e-97	364.0
15	TraesCS1D01G017300	chr1A	82.821	390	33	16	458	832	9222239	9221869	5.690000e-83	318.0
16	TraesCS1D01G017300	chr1A	88.889	243	26	1	2853	3095	22251501	22251260	7.410000e-77	298.0
17	TraesCS1D01G017300	chr1A	84.360	211	24	5	2401	2610	9223371	9223573	7.730000e-47	198.0
18	TraesCS1D01G017300	chr1A	92.045	88	6	1	1	88	9175259	9175345	4.790000e-24	122.0
19	TraesCS1D01G017300	chr1A	92.771	83	5	1	1	83	9202653	9202734	6.190000e-23	119.0
20	TraesCS1D01G017300	chr1A	91.837	49	2	2	272	318	9231783	9231831	2.270000e-07	67.6
21	TraesCS1D01G017300	chr1B	91.835	1433	81	5	1274	2706	9915363	9916759	0.000000e+00	1965.0
22	TraesCS1D01G017300	chr1B	91.423	513	31	8	458	962	9934621	9935128	0.000000e+00	691.0
23	TraesCS1D01G017300	chr1B	79.348	1012	145	36	989	1968	9935122	9936101	0.000000e+00	652.0
24	TraesCS1D01G017300	chr1B	95.291	361	14	1	918	1278	9909980	9910337	1.420000e-158	569.0
25	TraesCS1D01G017300	chr1B	83.074	579	89	3	2071	2640	9936177	9936755	5.220000e-143	518.0
26	TraesCS1D01G017300	chr1B	94.606	241	13	0	2853	3093	611523209	611522969	1.200000e-99	374.0
27	TraesCS1D01G017300	chr1B	92.135	89	6	1	1	89	9934259	9934346	1.330000e-24	124.0
28	TraesCS1D01G017300	chr1B	80.220	91	14	1	531	621	9933083	9933169	8.180000e-07	65.8
29	TraesCS1D01G017300	chr7D	92.083	240	18	1	2854	3093	471219167	471219405	1.570000e-88	337.0
30	TraesCS1D01G017300	chr7D	89.474	247	18	2	2854	3093	294422044	294421799	4.430000e-79	305.0
31	TraesCS1D01G017300	chr2D	90.083	242	23	1	2853	3094	518006896	518007136	2.650000e-81	313.0
32	TraesCS1D01G017300	chr5D	89.076	238	24	2	2854	3091	214614545	214614310	9.580000e-76	294.0
33	TraesCS1D01G017300	chr3B	75.709	247	33	20	2850	3089	149012649	149012875	8.060000e-17	99.0
34	TraesCS1D01G017300	chrUn	93.443	61	4	0	28	88	318884216	318884156	1.350000e-14	91.6
35	TraesCS1D01G017300	chrUn	93.443	61	4	0	28	88	349769797	349769737	1.350000e-14	91.6

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	TraesCS1D01G017300	chr1D	7767698	7771227	3529	False	6519.000000	6519	100.000000	1	3530	1	chr1D.!!$F1	3529
1	TraesCS1D01G017300	chr1D	7340571	7343091	2520	True	880.666667	1712	87.445667	7	2712	3	chr1D.!!$R2	2705
2	TraesCS1D01G017300	chr1D	7714652	7717542	2890	False	629.500000	1397	85.718250	2	2861	4	chr1D.!!$F3	2859
3	TraesCS1D01G017300	chr1A	9202653	9206050	3397	False	1611.333333	4316	92.549333	1	3530	3	chr1A.!!$F3	3529
4	TraesCS1D01G017300	chr1A	9219833	9222239	2406	True	418.333333	573	79.948000	458	2704	3	chr1A.!!$R2	2246
5	TraesCS1D01G017300	chr1A	9222613	9223573	960	False	407.000000	616	83.333000	2113	2845	2	chr1A.!!$F4	732
6	TraesCS1D01G017300	chr1B	9915363	9916759	1396	False	1965.000000	1965	91.835000	1274	2706	1	chr1B.!!$F2	1432
7	TraesCS1D01G017300	chr1B	9933083	9936755	3672	False	410.160000	691	85.240000	1	2640	5	chr1B.!!$F3	2639

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
887	2213	0.466124	ATAAGAGGAGCGACAAGGCC	59.534	55.0	0.00	0.0	0.0	5.19	F
1703	3091	0.397816	CCCTGGGTGGTGGTTCAAAA	60.398	55.0	3.97	0.0	0.0	2.44	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1993	3507	1.271379	GGTCATGTGCACTAACCCTGT	60.271	52.381	19.41	0.0	0.0	4.00	R
3115	4670	0.806868	AATGCATGCAGGTTCAGTCG	59.193	50.000	26.69	0.0	0.0	4.18	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
83	1260	3.573538	ACAAATGCTTGCAATACTGTCCA	59.426	39.130	0.00	0.00	35.84	4.02
93	1274	7.120285	GCTTGCAATACTGTCCATGTATATCAT	59.880	37.037	0.00	0.00	37.22	2.45
167	1350	8.668510	AGCAACTTATATCTATGTTGGTTCTG	57.331	34.615	12.77	0.00	44.59	3.02
270	1486	2.154462	CCAACTCATTCCACCAGTCAC	58.846	52.381	0.00	0.00	0.00	3.67
329	1549	2.863740	TGTCGACGGCAACATGATTATC	59.136	45.455	11.62	0.00	0.00	1.75
333	1553	0.943673	CGGCAACATGATTATCGGCA	59.056	50.000	0.00	0.00	0.00	5.69
336	1556	2.098934	GGCAACATGATTATCGGCAACA	59.901	45.455	0.00	0.00	0.00	3.33
484	1748	5.708230	ACGCAATATTTAGTGGTTTCTTCCA	59.292	36.000	0.00	0.00	34.85	3.53
488	1752	7.542130	GCAATATTTAGTGGTTTCTTCCAAGTG	59.458	37.037	0.00	0.00	39.34	3.16
527	1792	5.728471	TCTTGAAAAGGCAACACAATTTGA	58.272	33.333	2.79	0.00	46.24	2.69
564	1829	2.361119	ACATGCATGCCAGATCAATCAC	59.639	45.455	26.53	0.00	0.00	3.06
657	1931	6.412362	ACTAGAGTTGAACATGTGAAGACT	57.588	37.500	0.00	1.40	0.00	3.24
661	1935	3.804325	AGTTGAACATGTGAAGACTGACG	59.196	43.478	0.00	0.00	0.00	4.35
688	1962	4.817517	CAACGTAGGACAGAGGTACATTT	58.182	43.478	0.00	0.00	0.00	2.32
718	1996	9.796120	AATAAATAATACCATCAAACAACACCG	57.204	29.630	0.00	0.00	0.00	4.94
790	2075	1.399440	GAGCCATGTGTGTACTGCATG	59.601	52.381	13.89	13.89	39.54	4.06
795	2080	4.801147	CATGTGTGTACTGCATGGATAC	57.199	45.455	13.35	0.00	37.08	2.24
855	2144	4.830765	GCATGGGCGACGTGGCTA	62.831	66.667	22.08	12.00	44.11	3.93
887	2213	0.466124	ATAAGAGGAGCGACAAGGCC	59.534	55.000	0.00	0.00	0.00	5.19
908	2234	2.290367	CGTGTGCTTCTTTGTTCCATCA	59.710	45.455	0.00	0.00	0.00	3.07
911	2237	4.515191	GTGTGCTTCTTTGTTCCATCAGTA	59.485	41.667	0.00	0.00	0.00	2.74
912	2238	4.515191	TGTGCTTCTTTGTTCCATCAGTAC	59.485	41.667	0.00	0.00	0.00	2.73
921	2247	4.801891	TGTTCCATCAGTACGTAGTTCAC	58.198	43.478	0.00	0.00	37.78	3.18
936	2265	2.028294	AGTTCACTCATCTCTGCCACTG	60.028	50.000	0.00	0.00	0.00	3.66
973	2304	4.079096	AGGTAGGTAGCTAGTCCACTCATT	60.079	45.833	0.86	0.00	31.28	2.57
1066	2403	1.377536	GTCCATGGAAGAAGCAGCTC	58.622	55.000	18.20	0.00	0.00	4.09
1067	2404	1.065564	GTCCATGGAAGAAGCAGCTCT	60.066	52.381	18.20	0.00	0.00	4.09
1073	2413	1.271054	GGAAGAAGCAGCTCTGTGGAA	60.271	52.381	0.00	0.00	0.00	3.53
1369	2730	2.683933	ATGGTCTTCGTCCCGGCT	60.684	61.111	0.00	0.00	0.00	5.52
1428	2801	1.899437	AATGCATCACGGACTCGGGT	61.899	55.000	0.00	0.00	41.28	5.28
1449	2822	1.428869	GCCCAGTCCAGGAGATGTAT	58.571	55.000	0.00	0.00	0.00	2.29
1703	3091	0.397816	CCCTGGGTGGTGGTTCAAAA	60.398	55.000	3.97	0.00	0.00	2.44
1806	3215	5.536497	ATTCTAAGAAAGTCCCACCCATT	57.464	39.130	0.00	0.00	0.00	3.16
1993	3507	2.507484	TCGTACCCGAGACAGAAAAGA	58.493	47.619	0.00	0.00	38.40	2.52
2041	3555	2.230660	AGAAAAGGTTAGTGCACAGGC	58.769	47.619	21.04	7.80	41.68	4.85
2247	3776	1.748122	CATGCTGCTGGACCAGGAC	60.748	63.158	23.09	14.60	35.97	3.85
2280	3809	1.407618	GACCTGCGGAAAACAAAGGTT	59.592	47.619	0.00	0.00	41.33	3.50
2577	4110	6.363577	GCATTAGCTTGCATGTTCTACTTA	57.636	37.500	5.50	0.00	42.31	2.24
2799	4352	8.944029	GGTACATAGTGCTATAATCTAACGAGA	58.056	37.037	0.00	0.00	35.71	4.04
2878	4433	3.447950	ACCTCCGTCCTGGTTTATTAGT	58.552	45.455	0.00	0.00	39.52	2.24
2891	4446	5.429435	TGGTTTATTAGTCCCCCTCGTATTT	59.571	40.000	0.00	0.00	0.00	1.40
3013	4568	7.862372	ACGATATAATTTTTGGTGACATGCATC	59.138	33.333	0.00	0.00	42.32	3.91
3015	4570	9.188588	GATATAATTTTTGGTGACATGCATCAG	57.811	33.333	0.00	0.00	39.18	2.90
3067	4622	3.773418	TGACACAAAATACGAAGGGGA	57.227	42.857	0.00	0.00	0.00	4.81
3094	4649	0.998145	ACCAGGACGGAGGTAGTAGT	59.002	55.000	0.00	0.00	36.07	2.73
3097	4652	2.444421	CAGGACGGAGGTAGTAGTTGT	58.556	52.381	0.00	0.00	0.00	3.32
3177	4732	6.218746	ACGACGAAGGTGATAAACTTAGTTT	58.781	36.000	14.99	14.99	39.24	2.66
3258	4813	6.773638	AGTATAGGAATCACTATTTGGGCAG	58.226	40.000	0.00	0.00	35.41	4.85
3271	4826	0.913205	TGGGCAGGTTTAATCCGCTA	59.087	50.000	14.65	6.28	0.00	4.26
3352	4907	8.680903	CACAAGCAGATATCCACTCTTAATTTT	58.319	33.333	0.00	0.00	0.00	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	1208	7.618502	TGCCTAATAACAACATTCACGTTAT	57.381	32.000	0.00	0.00	37.41	1.89
142	1325	8.486210	TCAGAACCAACATAGATATAAGTTGCT	58.514	33.333	9.40	0.59	39.86	3.91
167	1350	6.760770	TGTGACATTTCCAAATTGTCCTTTTC	59.239	34.615	10.51	0.00	31.45	2.29
329	1549	2.979813	GTGCTTTTATCACTTGTTGCCG	59.020	45.455	0.00	0.00	0.00	5.69
484	1748	8.125978	TCAAGAGATAAAATTTGGATGCACTT	57.874	30.769	0.00	0.00	0.00	3.16
488	1752	8.876790	CCTTTTCAAGAGATAAAATTTGGATGC	58.123	33.333	0.00	0.00	0.00	3.91
527	1792	4.525996	TGCATGTGACAACCAGCTATATT	58.474	39.130	0.00	0.00	0.00	1.28
657	1931	2.201708	TCCTACGTTGCCACCGTCA	61.202	57.895	0.00	0.00	39.60	4.35
661	1935	0.389948	CTCTGTCCTACGTTGCCACC	60.390	60.000	0.00	0.00	0.00	4.61
710	1988	2.440539	TTGTTTGCAAACGGTGTTGT	57.559	40.000	31.20	0.00	41.74	3.32
718	1996	7.328846	GCAAATTGCTAATTTTGTTTGCAAAC	58.671	30.769	30.95	30.95	46.27	2.93
725	2003	5.610235	ATGCGCAAATTGCTAATTTTGTT	57.390	30.435	17.11	0.00	42.25	2.83
790	2075	3.520290	TGTGTGTCTCGGAATGTATCC	57.480	47.619	0.00	0.00	45.57	2.59
795	2080	1.441738	TGCATGTGTGTCTCGGAATG	58.558	50.000	0.00	0.00	0.00	2.67
855	2144	3.964031	CTCCTCTTATAGACCAACCAGCT	59.036	47.826	0.00	0.00	0.00	4.24
908	2234	4.095185	GCAGAGATGAGTGAACTACGTACT	59.905	45.833	0.00	0.00	0.00	2.73
911	2237	2.164624	GGCAGAGATGAGTGAACTACGT	59.835	50.000	0.00	0.00	0.00	3.57
912	2238	2.164422	TGGCAGAGATGAGTGAACTACG	59.836	50.000	0.00	0.00	0.00	3.51
921	2247	1.001746	ACACACAGTGGCAGAGATGAG	59.998	52.381	5.31	0.00	37.94	2.90
936	2265	7.101700	AGCTACCTACCTAAATACAAACACAC	58.898	38.462	0.00	0.00	0.00	3.82
973	2304	1.276421	GCTGCCCAAGAGTACTCAAGA	59.724	52.381	24.44	1.83	0.00	3.02
1066	2403	7.816995	GCTAATCCTATCTTCACTATTCCACAG	59.183	40.741	0.00	0.00	0.00	3.66
1067	2404	7.510685	AGCTAATCCTATCTTCACTATTCCACA	59.489	37.037	0.00	0.00	0.00	4.17
1073	2413	8.497910	TTGGAAGCTAATCCTATCTTCACTAT	57.502	34.615	6.03	0.00	40.35	2.12
1369	2730	3.393970	CCTCTCCGCCTCCAGCAA	61.394	66.667	0.00	0.00	44.04	3.91
1428	2801	2.060383	CATCTCCTGGACTGGGCGA	61.060	63.158	0.00	0.00	0.00	5.54
1481	2854	0.395448	GTCCGGGTAGTAGAGGCTGT	60.395	60.000	0.00	0.00	0.00	4.40
1703	3091	4.820716	GCTCTGGCATGAACTTCAAGATAT	59.179	41.667	0.00	0.00	38.54	1.63
1993	3507	1.271379	GGTCATGTGCACTAACCCTGT	60.271	52.381	19.41	0.00	0.00	4.00
2247	3776	1.492873	CAGGTCATGCACGTGTTCG	59.507	57.895	18.38	5.66	43.34	3.95
2280	3809	2.423088	GGTGAGTCCTCCTCCTTCGATA	60.423	54.545	0.00	0.00	39.65	2.92
2476	4005	1.331756	GATGCCGATAACTGCACCAAG	59.668	52.381	0.00	0.00	38.88	3.61
2577	4110	5.046304	ACAATGCGGATAGTAAGAGGCATAT	60.046	40.000	0.00	0.00	39.94	1.78
2868	4423	5.557576	AATACGAGGGGGACTAATAAACC	57.442	43.478	0.00	0.00	0.00	3.27
3067	4622	1.280998	CCTCCGTCCTGGTTTATTGGT	59.719	52.381	0.00	0.00	39.52	3.67
3094	4649	8.239314	CAGTCGTTTGTACTATCTAGGTAACAA	58.761	37.037	0.00	0.00	41.41	2.83
3097	4652	8.454106	GTTCAGTCGTTTGTACTATCTAGGTAA	58.546	37.037	0.00	0.00	0.00	2.85
3111	4666	1.664016	GCATGCAGGTTCAGTCGTTTG	60.664	52.381	14.21	0.00	0.00	2.93
3115	4670	0.806868	AATGCATGCAGGTTCAGTCG	59.193	50.000	26.69	0.00	0.00	4.18
3200	4755	5.407407	ACTGGAGGATATAAGCAATACGG	57.593	43.478	0.00	0.00	0.00	4.02
3258	4813	7.328737	ACATATGGAGTATAGCGGATTAAACC	58.671	38.462	7.80	0.00	0.00	3.27
3352	4907	9.492973	GGTAACTAACAACATACTGTAGGAAAA	57.507	33.333	6.47	0.00	0.00	2.29
3367	4922	8.687242	TGATGTTGATTTTGTGGTAACTAACAA	58.313	29.630	0.00	0.00	34.57	2.83
3435	4990	8.087982	ACCAACAATTATATCTTGATGCTACG	57.912	34.615	5.25	0.00	0.00	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.