AutoCloner

Multiple sequence alignment - TraesCS7D01G026800

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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	TraesCS7D01G026800	chr7D	100.000	3380	0	0	1	3380	13030511	13027132	0.000000e+00	6242.0
1	TraesCS7D01G026800	chr7D	83.292	2442	217	102	669	3063	13098457	13096160	0.000000e+00	2073.0
2	TraesCS7D01G026800	chr7D	85.683	1376	125	37	1326	2683	13066917	13065596	0.000000e+00	1384.0
3	TraesCS7D01G026800	chr7D	92.204	667	25	10	668	1332	13067830	13067189	0.000000e+00	918.0
4	TraesCS7D01G026800	chr7D	87.871	371	29	6	8	378	13068588	13068234	4.030000e-114	422.0
5	TraesCS7D01G026800	chr7D	82.094	363	25	10	399	746	13068160	13067823	1.190000e-69	274.0
6	TraesCS7D01G026800	chr7D	94.872	156	7	1	2727	2882	13065584	13065430	3.370000e-60	243.0
7	TraesCS7D01G026800	chr7D	83.422	187	16	10	3198	3380	13096013	13095838	3.490000e-35	159.0
8	TraesCS7D01G026800	chr7A	93.411	2914	127	34	493	3380	12430147	12427273	0.000000e+00	4257.0
9	TraesCS7D01G026800	chr7A	84.984	2504	191	79	618	3063	12455705	12453329	0.000000e+00	2370.0
10	TraesCS7D01G026800	chr7A	85.387	1047	92	37	669	1703	12653025	12652028	0.000000e+00	1029.0
11	TraesCS7D01G026800	chr7A	85.339	723	63	24	1741	2452	12652023	12651333	0.000000e+00	708.0
12	TraesCS7D01G026800	chr7A	79.412	714	76	44	2705	3380	12650780	12650100	4.000000e-119	438.0
13	TraesCS7D01G026800	chr7A	84.365	307	32	9	73	378	12430572	12430281	1.530000e-73	287.0
14	TraesCS7D01G026800	chr7A	91.818	110	6	1	506	612	12457557	12457448	2.100000e-32	150.0
15	TraesCS7D01G026800	chr4A	91.788	3020	130	45	395	3380	724782057	724784992	0.000000e+00	4095.0
16	TraesCS7D01G026800	chr4A	81.238	1583	160	54	1394	2947	724399909	724398435	0.000000e+00	1151.0
17	TraesCS7D01G026800	chr4A	84.459	1229	107	29	998	2211	724580124	724578965	0.000000e+00	1134.0
18	TraesCS7D01G026800	chr4A	77.938	902	100	60	2531	3380	724578761	724577907	3.950000e-129	472.0
19	TraesCS7D01G026800	chr4A	95.620	274	12	0	998	1271	724400263	724399990	1.110000e-119	440.0
20	TraesCS7D01G026800	chr4A	93.103	87	4	1	3296	3380	724398398	724398312	3.540000e-25	126.0
21	TraesCS7D01G026800	chr4A	93.333	45	3	0	493	537	724400689	724400645	2.180000e-07	67.6
22	TraesCS7D01G026800	chr4D	92.461	2560	126	37	669	3200	506607452	506604932	0.000000e+00	3596.0
23	TraesCS7D01G026800	chr4D	97.110	173	5	0	3208	3380	506604852	506604680	3.300000e-75	292.0
24	TraesCS7D01G026800	chr2B	90.789	76	5	2	1342	1416	545366058	545365984	2.150000e-17	100.0

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	TraesCS7D01G026800	chr7D	13027132	13030511	3379	True	6242.00	6242	100.000000	1	3380	1	chr7D.!!$R1	3379
1	TraesCS7D01G026800	chr7D	13095838	13098457	2619	True	1116.00	2073	83.357000	669	3380	2	chr7D.!!$R3	2711
2	TraesCS7D01G026800	chr7D	13065430	13068588	3158	True	648.20	1384	88.544800	8	2882	5	chr7D.!!$R2	2874
3	TraesCS7D01G026800	chr7A	12427273	12430572	3299	True	2272.00	4257	88.888000	73	3380	2	chr7A.!!$R1	3307
4	TraesCS7D01G026800	chr7A	12453329	12457557	4228	True	1260.00	2370	88.401000	506	3063	2	chr7A.!!$R2	2557
5	TraesCS7D01G026800	chr7A	12650100	12653025	2925	True	725.00	1029	83.379333	669	3380	3	chr7A.!!$R3	2711
6	TraesCS7D01G026800	chr4A	724782057	724784992	2935	False	4095.00	4095	91.788000	395	3380	1	chr4A.!!$F1	2985
7	TraesCS7D01G026800	chr4A	724577907	724580124	2217	True	803.00	1134	81.198500	998	3380	2	chr4A.!!$R2	2382
8	TraesCS7D01G026800	chr4A	724398312	724400689	2377	True	446.15	1151	90.823500	493	3380	4	chr4A.!!$R1	2887
9	TraesCS7D01G026800	chr4D	506604680	506607452	2772	True	1944.00	3596	94.785500	669	3380	2	chr4D.!!$R1	2711

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	End Stability	Orientation
273	275	0.108520	GTATTCGTCCCGCCACTCAA	60.109	55.0	0.00	3.02	F
411	466	0.534877	TCCACCCACGCATGCATATC	60.535	55.0	19.57	1.63	F
947	2876	1.040339	CCTCTCTCCGCCAAGCTACT	61.040	60.0	0.00	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1652	3893	1.604593	GTTGTCCATGCCAGGTGCT	60.605	57.895	42.00	4.40	R
2118	4382	9.965824	TTCTTTTTGATAGAAAGTTGATGGAAC	57.034	29.630	35.95	3.62	R
2456	4759	1.529438	GATCAACCGAAAAGTGCGTCA	59.471	47.619	0.00	4.35	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
30	31	3.516615	GCTCTATAGATCCGTGAATGCC	58.483	50.000	2.11	0.00	0.00	4.40
31	32	3.056536	GCTCTATAGATCCGTGAATGCCA	60.057	47.826	2.11	0.00	0.00	4.92
39	40	3.297830	TCCGTGAATGCCACTATATCG	57.702	47.619	0.00	0.00	43.53	2.92
43	44	0.366871	GAATGCCACTATATCGCGCG	59.633	55.000	26.76	26.76	0.00	6.86
44	45	1.626654	AATGCCACTATATCGCGCGC	61.627	55.000	27.95	23.91	0.00	6.86
45	46	3.827784	GCCACTATATCGCGCGCG	61.828	66.667	44.84	44.84	41.35	6.86
46	47	2.428569	CCACTATATCGCGCGCGT	60.429	61.111	46.54	35.56	40.74	6.01
61	62	2.798689	CGTCGGCTAGCTGCACTA	59.201	61.111	19.27	0.00	45.15	2.74
71	72	0.399091	AGCTGCACTATGGGCCTAGA	60.399	55.000	4.53	0.00	0.00	2.43
99	100	3.868077	GGTCATCGTCAATCTTCTTCCTG	59.132	47.826	0.00	0.00	0.00	3.86
103	104	2.300152	TCGTCAATCTTCTTCCTGCACT	59.700	45.455	0.00	0.00	0.00	4.40
105	106	4.021456	TCGTCAATCTTCTTCCTGCACTTA	60.021	41.667	0.00	0.00	0.00	2.24
106	107	4.872691	CGTCAATCTTCTTCCTGCACTTAT	59.127	41.667	0.00	0.00	0.00	1.73
126	127	1.603455	CCTGCCCCATTGTTGTCGT	60.603	57.895	0.00	0.00	0.00	4.34
144	146	0.109132	GTCAATGCCCTTTTGCCTCG	60.109	55.000	0.00	0.00	0.00	4.63
268	270	1.448893	GCTTGTATTCGTCCCGCCA	60.449	57.895	0.00	0.00	0.00	5.69
273	275	0.108520	GTATTCGTCCCGCCACTCAA	60.109	55.000	0.00	0.00	0.00	3.02
279	281	1.841556	TCCCGCCACTCAACTCCTT	60.842	57.895	0.00	0.00	0.00	3.36
329	331	6.017605	CGGATGTAGCTTGCTTAGATTTGATT	60.018	38.462	0.00	0.00	0.00	2.57
379	381	9.944376	ATATTCATTTGGAGCATAACGTATAGT	57.056	29.630	0.00	0.00	0.00	2.12
380	382	7.477144	TTCATTTGGAGCATAACGTATAGTG	57.523	36.000	0.00	0.00	0.00	2.74
382	384	6.700081	TCATTTGGAGCATAACGTATAGTGTC	59.300	38.462	0.00	0.00	0.00	3.67
383	385	5.847111	TTGGAGCATAACGTATAGTGTCT	57.153	39.130	0.00	0.00	0.00	3.41
384	386	5.434352	TGGAGCATAACGTATAGTGTCTC	57.566	43.478	0.00	0.00	0.00	3.36
385	387	5.131067	TGGAGCATAACGTATAGTGTCTCT	58.869	41.667	0.00	0.00	0.00	3.10
389	391	7.096884	AGCATAACGTATAGTGTCTCTTGAA	57.903	36.000	0.00	0.00	0.00	2.69
391	393	8.198109	AGCATAACGTATAGTGTCTCTTGAATT	58.802	33.333	0.00	0.00	0.00	2.17
411	466	0.534877	TCCACCCACGCATGCATATC	60.535	55.000	19.57	0.00	0.00	1.63
416	471	1.642753	CACGCATGCATATCACGCA	59.357	52.632	19.57	0.00	44.94	5.24
499	558	3.445096	AGTATACGCACGTAGGGAAAACT	59.555	43.478	8.99	3.10	33.77	2.66
501	560	2.358939	ACGCACGTAGGGAAAACTAG	57.641	50.000	0.00	0.00	0.00	2.57
504	563	3.243839	ACGCACGTAGGGAAAACTAGAAA	60.244	43.478	0.00	0.00	0.00	2.52
538	603	1.736645	ACACACGTACGCCAGCATC	60.737	57.895	16.72	0.00	0.00	3.91
634	2450	3.384789	CGGAGAGAGAGAGAGAGAGAGAA	59.615	52.174	0.00	0.00	0.00	2.87
656	2472	9.353999	GAGAAAGAGATTTAGAGAGAGAAACAC	57.646	37.037	0.00	0.00	0.00	3.32
679	2507	3.011257	AGAGGTGCCTAGAGAGAGAAACT	59.989	47.826	0.00	0.00	0.00	2.66
701	2529	2.870411	GAGAGGTCGCTAGAGAGAGAAC	59.130	54.545	0.00	0.00	39.36	3.01
808	2728	2.333938	GCCATGCACGCATCATCC	59.666	61.111	0.44	0.00	33.90	3.51
822	2742	2.136878	CATCCTCCACCTCCCTCCG	61.137	68.421	0.00	0.00	0.00	4.63
905	2831	2.082140	ACCTCAAAAACCCAACTCCC	57.918	50.000	0.00	0.00	0.00	4.30
946	2875	1.324005	ACCTCTCTCCGCCAAGCTAC	61.324	60.000	0.00	0.00	0.00	3.58
947	2876	1.040339	CCTCTCTCCGCCAAGCTACT	61.040	60.000	0.00	0.00	0.00	2.57
954	2886	1.676678	CCGCCAAGCTACTAGCCTCA	61.677	60.000	4.32	0.00	43.77	3.86
958	2890	1.827969	CCAAGCTACTAGCCTCACAGT	59.172	52.381	4.32	0.00	43.77	3.55
1107	3053	3.003173	CAGGAGAAGGGGCACGGA	61.003	66.667	0.00	0.00	0.00	4.69
2118	4382	0.681564	AGAGTGAGTACCTGCTCCCG	60.682	60.000	0.00	0.00	34.74	5.14
2195	4478	7.124147	TCTCTTTTCCATCCACCCAAATAATTC	59.876	37.037	0.00	0.00	0.00	2.17
2198	4481	5.464588	TCCATCCACCCAAATAATTCTGA	57.535	39.130	0.00	0.00	0.00	3.27
2205	4488	7.054124	TCCACCCAAATAATTCTGACTCATAC	58.946	38.462	0.00	0.00	0.00	2.39
2429	4727	9.874205	CAAGAATGCCAAAAATAATAAGGAAGA	57.126	29.630	0.00	0.00	0.00	2.87
2491	4799	5.659048	GGTTGATCAATACCGAAGATGTC	57.341	43.478	12.12	0.00	0.00	3.06
2700	5350	5.569059	GTGACATAAATTGAAAGCACCTTCG	59.431	40.000	0.00	0.00	0.00	3.79
2794	5456	4.035208	GCATAATGACGGAGGGTTTAGTTG	59.965	45.833	0.00	0.00	0.00	3.16
3246	6070	1.048601	TGTGGGGTCTTCTCAGTCAC	58.951	55.000	0.00	0.00	0.00	3.67
3367	6210	7.596749	AGCATGCAAACGGTATAATAGTATC	57.403	36.000	21.98	0.00	0.00	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.235200	GGATCTATAGAGCCCTGTGTGT	58.765	50.000	24.02	0.00	44.46	3.72
1	2	3.951775	GGATCTATAGAGCCCTGTGTG	57.048	52.381	24.02	0.00	44.46	3.82
43	44	2.685387	ATAGTGCAGCTAGCCGACGC	62.685	60.000	12.13	10.01	44.83	5.19
44	45	0.936764	CATAGTGCAGCTAGCCGACG	60.937	60.000	12.13	0.00	44.83	5.12
45	46	0.598680	CCATAGTGCAGCTAGCCGAC	60.599	60.000	12.13	5.66	44.83	4.79
46	47	1.742146	CCATAGTGCAGCTAGCCGA	59.258	57.895	12.13	0.00	44.83	5.54
87	88	6.352516	CAGGTATAAGTGCAGGAAGAAGATT	58.647	40.000	0.00	0.00	0.00	2.40
99	100	1.956477	CAATGGGGCAGGTATAAGTGC	59.044	52.381	0.00	0.00	39.08	4.40
103	104	3.626930	GACAACAATGGGGCAGGTATAA	58.373	45.455	0.00	0.00	0.00	0.98
105	106	1.681780	CGACAACAATGGGGCAGGTAT	60.682	52.381	0.00	0.00	0.00	2.73
106	107	0.322098	CGACAACAATGGGGCAGGTA	60.322	55.000	0.00	0.00	0.00	3.08
126	127	0.251121	TCGAGGCAAAAGGGCATTGA	60.251	50.000	0.00	0.00	46.44	2.57
144	146	2.325166	CGCGAGAGGTAGAGCGTC	59.675	66.667	0.00	0.00	46.48	5.19
189	191	1.541620	GGAGGAACAAGGAGGGGGT	60.542	63.158	0.00	0.00	0.00	4.95
190	192	0.921256	ATGGAGGAACAAGGAGGGGG	60.921	60.000	0.00	0.00	0.00	5.40
191	193	1.893315	TATGGAGGAACAAGGAGGGG	58.107	55.000	0.00	0.00	0.00	4.79
192	194	2.780010	ACATATGGAGGAACAAGGAGGG	59.220	50.000	7.80	0.00	0.00	4.30
268	270	1.421268	TCACATGCCAAGGAGTTGAGT	59.579	47.619	0.00	0.00	35.46	3.41
273	275	2.165167	CATGTTCACATGCCAAGGAGT	58.835	47.619	6.99	0.00	45.92	3.85
298	300	6.167685	TCTAAGCAAGCTACATCCGTTTTTA	58.832	36.000	0.00	0.00	0.00	1.52
301	303	4.202245	TCTAAGCAAGCTACATCCGTTT	57.798	40.909	0.00	0.00	0.00	3.60
302	304	3.887621	TCTAAGCAAGCTACATCCGTT	57.112	42.857	0.00	0.00	0.00	4.44
303	305	4.408182	AATCTAAGCAAGCTACATCCGT	57.592	40.909	0.00	0.00	0.00	4.69
304	306	4.811024	TCAAATCTAAGCAAGCTACATCCG	59.189	41.667	0.00	0.00	0.00	4.18
305	307	6.874288	ATCAAATCTAAGCAAGCTACATCC	57.126	37.500	0.00	0.00	0.00	3.51
306	308	7.923888	TCAATCAAATCTAAGCAAGCTACATC	58.076	34.615	0.00	0.00	0.00	3.06
329	331	6.977213	TCTTGATGTCGAATATTCCGTATCA	58.023	36.000	9.87	12.64	33.61	2.15
363	365	5.692613	AGAGACACTATACGTTATGCTCC	57.307	43.478	0.00	0.00	0.00	4.70
378	380	3.253432	GTGGGTGGAAATTCAAGAGACAC	59.747	47.826	0.00	0.00	0.00	3.67
379	381	3.486383	GTGGGTGGAAATTCAAGAGACA	58.514	45.455	0.00	0.00	0.00	3.41
380	382	2.484264	CGTGGGTGGAAATTCAAGAGAC	59.516	50.000	0.00	0.00	0.00	3.36
382	384	1.200020	GCGTGGGTGGAAATTCAAGAG	59.800	52.381	0.00	0.00	0.00	2.85
383	385	1.243902	GCGTGGGTGGAAATTCAAGA	58.756	50.000	0.00	0.00	0.00	3.02
384	386	0.958091	TGCGTGGGTGGAAATTCAAG	59.042	50.000	0.00	0.00	0.00	3.02
385	387	1.271934	CATGCGTGGGTGGAAATTCAA	59.728	47.619	0.00	0.00	0.00	2.69
389	391	0.971959	ATGCATGCGTGGGTGGAAAT	60.972	50.000	12.68	0.00	0.00	2.17
391	393	0.106769	ATATGCATGCGTGGGTGGAA	60.107	50.000	22.77	0.20	0.00	3.53
471	529	6.241207	TCCCTACGTGCGTATACTTATTAC	57.759	41.667	0.00	0.00	0.00	1.89
472	530	6.875948	TTCCCTACGTGCGTATACTTATTA	57.124	37.500	0.00	0.00	0.00	0.98
473	531	5.772825	TTCCCTACGTGCGTATACTTATT	57.227	39.130	0.00	0.00	0.00	1.40
474	532	5.772825	TTTCCCTACGTGCGTATACTTAT	57.227	39.130	0.00	0.00	0.00	1.73
475	533	5.125417	AGTTTTCCCTACGTGCGTATACTTA	59.875	40.000	0.00	0.00	0.00	2.24
476	534	4.082026	AGTTTTCCCTACGTGCGTATACTT	60.082	41.667	0.00	0.00	0.00	2.24
499	558	3.315191	GTGCTGTCTTGTTGCCTTTTCTA	59.685	43.478	0.00	0.00	0.00	2.10
501	560	2.159254	TGTGCTGTCTTGTTGCCTTTTC	60.159	45.455	0.00	0.00	0.00	2.29
504	563	0.740737	GTGTGCTGTCTTGTTGCCTT	59.259	50.000	0.00	0.00	0.00	4.35
538	603	7.256286	AGCAGGTACGTTGTTTAGTTAGATAG	58.744	38.462	0.00	0.00	0.00	2.08
605	676	1.208535	TCTCTCTCTCTCCGTCTGTCC	59.791	57.143	0.00	0.00	0.00	4.02
634	2450	8.415950	TCTGTGTTTCTCTCTCTAAATCTCTT	57.584	34.615	0.00	0.00	0.00	2.85
656	2472	2.727123	TCTCTCTCTAGGCACCTCTG	57.273	55.000	0.00	0.00	0.00	3.35
663	2479	3.632145	CCTCTCAGTTTCTCTCTCTAGGC	59.368	52.174	0.00	0.00	0.00	3.93
664	2480	4.855340	ACCTCTCAGTTTCTCTCTCTAGG	58.145	47.826	0.00	0.00	0.00	3.02
679	2507	2.112190	TCTCTCTCTAGCGACCTCTCA	58.888	52.381	0.00	0.00	0.00	3.27
701	2529	1.337260	CCTCTGTGTTTCCCACTCTCG	60.337	57.143	0.00	0.00	44.81	4.04
709	2605	3.432378	TCTCTCTACCCTCTGTGTTTCC	58.568	50.000	0.00	0.00	0.00	3.13
716	2612	2.507886	TCTCACCTCTCTCTACCCTCTG	59.492	54.545	0.00	0.00	0.00	3.35
822	2742	4.890306	GGAGAGGGAGAGGGGCCC	62.890	77.778	17.12	17.12	46.40	5.80
946	2875	4.887748	TCTTTCTTTGACTGTGAGGCTAG	58.112	43.478	0.00	0.00	0.00	3.42
947	2876	4.588951	TCTCTTTCTTTGACTGTGAGGCTA	59.411	41.667	0.00	0.00	0.00	3.93
954	2886	5.679601	AGCTTCTTCTCTTTCTTTGACTGT	58.320	37.500	0.00	0.00	0.00	3.55
958	2890	6.107901	AGCTAGCTTCTTCTCTTTCTTTGA	57.892	37.500	12.68	0.00	0.00	2.69
1547	3788	4.776322	TTCATGTCCCAGGCGCCG	62.776	66.667	23.20	16.10	0.00	6.46
1652	3893	1.604593	GTTGTCCATGCCAGGTGCT	60.605	57.895	0.00	0.00	42.00	4.40
2118	4382	9.965824	TTCTTTTTGATAGAAAGTTGATGGAAC	57.034	29.630	0.00	0.00	35.95	3.62
2456	4759	1.529438	GATCAACCGAAAAGTGCGTCA	59.471	47.619	0.00	0.00	0.00	4.35
2491	4799	5.782893	TCCCCTATCAACAAACAAACTTG	57.217	39.130	0.00	0.00	0.00	3.16
2700	5350	5.687285	CACATACTTTGCTGTCTGGAAAAAC	59.313	40.000	0.00	0.00	35.61	2.43
2794	5456	5.743872	ACGCAAGAGAAAGTTCAAACAAATC	59.256	36.000	0.00	0.00	43.62	2.17
3121	5808	7.572759	TGCAATTGTCTTTCTTAGTTAGAACG	58.427	34.615	7.40	0.00	42.50	3.95
3196	5940	9.672673	GAGGAATTAATCAAAGGCAGCTATATA	57.327	33.333	0.00	0.00	0.00	0.86
3205	6029	5.183904	ACACACAGAGGAATTAATCAAAGGC	59.816	40.000	0.00	0.00	0.00	4.35
3206	6030	6.349611	CCACACACAGAGGAATTAATCAAAGG	60.350	42.308	0.00	0.00	0.00	3.11
3246	6070	2.806244	CCTCCAACAAGTAACCTCGTTG	59.194	50.000	0.00	0.00	38.73	4.10

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.