AutoCloner

Multiple sequence alignment - TraesCS4A01G363000

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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	TraesCS4A01G363000	chr4A	100.000	2621	0	0	1	2621	636375422	636378042	0.000000e+00	4841.0
1	TraesCS4A01G363000	chr5D	93.347	1518	87	8	701	2217	535591511	535590007	0.000000e+00	2231.0
2	TraesCS4A01G363000	chr5D	92.613	731	35	7	1	716	535593716	535592990	0.000000e+00	1033.0
3	TraesCS4A01G363000	chr5D	91.262	309	20	5	2315	2621	535579713	535579410	5.220000e-112	414.0
4	TraesCS4A01G363000	chr5D	83.395	271	21	6	1016	1264	535525724	535525456	2.030000e-56	230.0
5	TraesCS4A01G363000	chr5B	93.605	1470	68	7	257	1703	676174138	676172672	0.000000e+00	2170.0
6	TraesCS4A01G363000	chr5B	88.453	892	92	6	1700	2585	676172298	676171412	0.000000e+00	1066.0
7	TraesCS4A01G363000	chr2D	82.705	769	99	24	1709	2453	102865286	102864528	0.000000e+00	652.0
8	TraesCS4A01G363000	chr2D	80.624	769	112	18	1709	2450	589507582	589508340	6.330000e-156	560.0
9	TraesCS4A01G363000	chr6D	82.068	764	99	26	1710	2453	418458433	418459178	3.710000e-173	617.0
10	TraesCS4A01G363000	chr6D	100.000	28	0	0	2541	2568	3025291	3025264	5.000000e-03	52.8
11	TraesCS4A01G363000	chr3A	81.617	767	102	24	1715	2453	328930970	328930215	1.340000e-167	599.0
12	TraesCS4A01G363000	chr3A	81.392	704	83	24	1781	2446	653329780	653329087	4.970000e-147	531.0
13	TraesCS4A01G363000	chr1A	80.774	775	103	31	1707	2453	561623117	561622361	4.900000e-157	564.0
14	TraesCS4A01G363000	chrUn	81.560	705	86	31	1779	2452	103931800	103932491	2.290000e-150	542.0
15	TraesCS4A01G363000	chr6A	80.000	780	116	23	1704	2453	2937852	2938621	8.250000e-150	540.0
16	TraesCS4A01G363000	chr6A	100.000	28	0	0	2541	2568	219581370	219581343	5.000000e-03	52.8
17	TraesCS4A01G363000	chr7A	80.102	784	101	29	1701	2451	608995104	608995865	1.380000e-147	532.0
18	TraesCS4A01G363000	chr7A	100.000	30	0	0	2542	2571	516798759	516798730	3.640000e-04	56.5
19	TraesCS4A01G363000	chr1D	79.922	767	108	30	1712	2453	119296236	119296981	2.990000e-144	521.0
20	TraesCS4A01G363000	chr7B	79.587	774	115	25	1708	2453	453015945	453016703	5.000000e-142	514.0
21	TraesCS4A01G363000	chr1B	79.578	759	121	28	1707	2454	520375209	520375944	1.800000e-141	512.0
22	TraesCS4A01G363000	chr6B	82.850	379	52	12	1701	2075	648811356	648811725	6.990000e-86	327.0
23	TraesCS4A01G363000	chr3B	75.871	373	53	18	1708	2077	730316760	730317098	3.490000e-34	156.0
24	TraesCS4A01G363000	chr5A	94.444	36	2	0	2535	2570	32667763	32667798	3.640000e-04	56.5
25	TraesCS4A01G363000	chr5A	100.000	29	0	0	2542	2570	469056942	469056970	1.000000e-03	54.7
26	TraesCS4A01G363000	chr7D	96.875	32	0	1	2543	2574	468000555	468000525	5.000000e-03	52.8
27	TraesCS4A01G363000	chr4D	100.000	28	0	0	2543	2570	471964240	471964213	5.000000e-03	52.8

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	TraesCS4A01G363000	chr4A	636375422	636378042	2620	False	4841	4841	100.000	1	2621	1	chr4A.!!$F1	2620
1	TraesCS4A01G363000	chr5D	535590007	535593716	3709	True	1632	2231	92.980	1	2217	2	chr5D.!!$R3	2216
2	TraesCS4A01G363000	chr5B	676171412	676174138	2726	True	1618	2170	91.029	257	2585	2	chr5B.!!$R1	2328
3	TraesCS4A01G363000	chr2D	102864528	102865286	758	True	652	652	82.705	1709	2453	1	chr2D.!!$R1	744
4	TraesCS4A01G363000	chr2D	589507582	589508340	758	False	560	560	80.624	1709	2450	1	chr2D.!!$F1	741
5	TraesCS4A01G363000	chr6D	418458433	418459178	745	False	617	617	82.068	1710	2453	1	chr6D.!!$F1	743
6	TraesCS4A01G363000	chr3A	328930215	328930970	755	True	599	599	81.617	1715	2453	1	chr3A.!!$R1	738
7	TraesCS4A01G363000	chr3A	653329087	653329780	693	True	531	531	81.392	1781	2446	1	chr3A.!!$R2	665
8	TraesCS4A01G363000	chr1A	561622361	561623117	756	True	564	564	80.774	1707	2453	1	chr1A.!!$R1	746
9	TraesCS4A01G363000	chrUn	103931800	103932491	691	False	542	542	81.560	1779	2452	1	chrUn.!!$F1	673
10	TraesCS4A01G363000	chr6A	2937852	2938621	769	False	540	540	80.000	1704	2453	1	chr6A.!!$F1	749
11	TraesCS4A01G363000	chr7A	608995104	608995865	761	False	532	532	80.102	1701	2451	1	chr7A.!!$F1	750
12	TraesCS4A01G363000	chr1D	119296236	119296981	745	False	521	521	79.922	1712	2453	1	chr1D.!!$F1	741
13	TraesCS4A01G363000	chr7B	453015945	453016703	758	False	514	514	79.587	1708	2453	1	chr7B.!!$F1	745
14	TraesCS4A01G363000	chr1B	520375209	520375944	735	False	512	512	79.578	1707	2454	1	chr1B.!!$F1	747

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
360	363	0.673437	AACAAACCATGCAAGGACCG	59.327	50.0	16.33	4.41	0.0	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1680	3204	0.30684	GTCTCACATGGCATGATGCG	59.693	55.0	32.74	20.26	46.21	4.73	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
60	63	1.522668	CGGAAGGCATTGAGAACACA	58.477	50.000	0.00	0.00	0.00	3.72
67	70	1.171308	CATTGAGAACACAGGCCAGG	58.829	55.000	5.01	0.00	0.00	4.45
133	136	3.615709	GGCCCACAACAGCAACCC	61.616	66.667	0.00	0.00	0.00	4.11
136	139	2.518349	CCACAACAGCAACCCGGT	60.518	61.111	0.00	0.00	0.00	5.28
193	196	2.028484	GACGCCGACAACCTCACA	59.972	61.111	0.00	0.00	0.00	3.58
203	206	3.243434	CGACAACCTCACAAGACAGTAGT	60.243	47.826	0.00	0.00	0.00	2.73
241	244	6.635641	GGTAGGTAAGTTCTTTTCTTTTTGCG	59.364	38.462	0.00	0.00	0.00	4.85
246	249	4.928601	AGTTCTTTTCTTTTTGCGGGTAC	58.071	39.130	0.00	0.00	0.00	3.34
255	258	2.661840	TTTGCGGGTACGACAGGCAA	62.662	55.000	0.00	0.38	44.60	4.52
325	328	6.388100	TCATCAGGAGATATTTGAGGGAACTT	59.612	38.462	0.00	0.00	34.62	2.66
333	336	3.842007	TTTGAGGGAACTTTACGACCA	57.158	42.857	0.00	0.00	44.43	4.02
360	363	0.673437	AACAAACCATGCAAGGACCG	59.327	50.000	16.33	4.41	0.00	4.79
369	372	3.119029	CCATGCAAGGACCGATTGATTTT	60.119	43.478	0.35	0.00	0.00	1.82
370	373	4.097741	CCATGCAAGGACCGATTGATTTTA	59.902	41.667	0.35	0.00	0.00	1.52
388	391	7.397221	TGATTTTACCATGCTGATATAGGGAG	58.603	38.462	0.00	0.00	0.00	4.30
398	401	7.855784	TGCTGATATAGGGAGACAAGATTAA	57.144	36.000	0.00	0.00	0.00	1.40
560	563	8.729805	TTCACATTAAAGAAGCAAAAACCAAT	57.270	26.923	0.00	0.00	0.00	3.16
600	604	3.490439	TCATCAACACAGAAAGGCTCA	57.510	42.857	0.00	0.00	0.00	4.26
658	675	4.774124	TGAATGCAGTAATCTTCCTCCAG	58.226	43.478	0.00	0.00	0.00	3.86
794	2305	8.577939	GTGAACAAAAGTTAACTAAAAACGGAC	58.422	33.333	8.92	0.00	32.00	4.79
902	2415	8.279970	TCATATCCTTTGGACTTTATGTGTTG	57.720	34.615	0.00	0.00	32.98	3.33
934	2447	2.051334	TCAATTGGGACCGCCTATTG	57.949	50.000	5.42	7.90	37.44	1.90
1008	2531	4.134563	AGTTCTGAGTTGCCACGTAATTT	58.865	39.130	0.00	0.00	0.00	1.82
1049	2572	0.034670	ATTGTCCCTCTGGCTCTTGC	60.035	55.000	0.00	0.00	38.76	4.01
1316	2840	2.496899	ACAGATTGTGTGGATGTCCC	57.503	50.000	0.00	0.00	38.28	4.46
1322	2846	1.200760	TGTGTGGATGTCCCTGAGGG	61.201	60.000	12.53	12.53	46.11	4.30
1518	3042	4.285260	TGGAAGGGTAAGAAGGTCTACAAC	59.715	45.833	0.00	0.00	0.00	3.32
1677	3201	1.269936	GCATGGGATTGTATGCTTGGC	60.270	52.381	0.00	0.00	44.70	4.52
1680	3204	0.386838	GGGATTGTATGCTTGGCAGC	59.613	55.000	0.00	2.53	43.65	5.25
1713	3614	9.088987	TGCCATGTGAGACATAATCTATACTAA	57.911	33.333	0.00	0.00	36.53	2.24
1744	3646	2.720758	CGCTATATGCTGCGCCGTC	61.721	63.158	4.18	0.00	45.50	4.79
1756	3658	2.898343	GCCGTCGGTGTTGTTGGT	60.898	61.111	13.94	0.00	0.00	3.67
1759	3661	0.028374	CCGTCGGTGTTGTTGGTTTC	59.972	55.000	2.08	0.00	0.00	2.78
1761	3663	1.096416	GTCGGTGTTGTTGGTTTCCA	58.904	50.000	0.00	0.00	0.00	3.53
1763	3665	2.094649	GTCGGTGTTGTTGGTTTCCAAA	60.095	45.455	2.65	0.00	45.73	3.28
1764	3666	2.561419	TCGGTGTTGTTGGTTTCCAAAA	59.439	40.909	2.65	0.00	45.73	2.44
1765	3667	3.006537	TCGGTGTTGTTGGTTTCCAAAAA	59.993	39.130	2.65	1.53	45.73	1.94
2321	4310	7.614494	ACCAAATCCAAAATTGAATACCTCAG	58.386	34.615	0.00	0.00	34.81	3.35
2385	4376	5.359194	AAAGAATCGAATGGGAGAGCTTA	57.641	39.130	0.00	0.00	0.00	3.09
2395	4386	6.931281	CGAATGGGAGAGCTTATTGAGAAATA	59.069	38.462	0.00	0.00	0.00	1.40
2475	4468	4.491676	CTCAATTGAATGTGGGCTCTTTG	58.508	43.478	9.88	0.00	0.00	2.77
2483	4476	4.640771	ATGTGGGCTCTTTGAAACTAGA	57.359	40.909	0.00	0.00	0.00	2.43
2486	4479	3.008049	GTGGGCTCTTTGAAACTAGAGGA	59.992	47.826	0.00	0.00	38.63	3.71
2520	4513	5.511386	AGAGGATTGTCTCATGGAAAAGT	57.489	39.130	0.00	0.00	36.30	2.66
2526	4519	6.421801	GGATTGTCTCATGGAAAAGTTGTTTG	59.578	38.462	0.00	0.00	0.00	2.93
2548	4541	6.413783	TGAAGGCAAATATCGTATACTCCA	57.586	37.500	0.56	0.00	0.00	3.86
2550	4543	7.097192	TGAAGGCAAATATCGTATACTCCATC	58.903	38.462	0.56	0.00	0.00	3.51
2551	4544	5.978814	AGGCAAATATCGTATACTCCATCC	58.021	41.667	0.56	0.00	0.00	3.51
2552	4545	4.804139	GGCAAATATCGTATACTCCATCCG	59.196	45.833	0.56	0.00	0.00	4.18
2555	4548	6.625300	GCAAATATCGTATACTCCATCCGTCT	60.625	42.308	0.56	0.00	0.00	4.18
2560	4553	5.554070	TCGTATACTCCATCCGTCTCATAA	58.446	41.667	0.56	0.00	0.00	1.90
2573	4566	7.147143	TCCGTCTCATAATATAAGAGCACTC	57.853	40.000	0.00	0.00	0.00	3.51
2574	4567	6.024664	CCGTCTCATAATATAAGAGCACTCG	58.975	44.000	0.00	0.00	34.09	4.18
2610	4603	9.778741	ATGCTCTTATATTATGAAACGAAAGGA	57.221	29.630	0.00	0.00	0.00	3.36
2611	4604	9.261180	TGCTCTTATATTATGAAACGAAAGGAG	57.739	33.333	0.00	0.00	0.00	3.69
2612	4605	9.262358	GCTCTTATATTATGAAACGAAAGGAGT	57.738	33.333	0.00	0.00	0.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	1.908299	CTTGGGGGTTCTTGTGGGC	60.908	63.158	0.00	0.00	0.00	5.36
43	46	1.200948	GCCTGTGTTCTCAATGCCTTC	59.799	52.381	0.00	0.00	0.00	3.46
46	49	0.895100	TGGCCTGTGTTCTCAATGCC	60.895	55.000	3.32	0.00	36.49	4.40
94	97	1.758440	AACTCTGCCTCGCTTCCACA	61.758	55.000	0.00	0.00	0.00	4.17
183	186	4.894114	ACTACTACTGTCTTGTGAGGTTGT	59.106	41.667	0.00	0.00	0.00	3.32
193	196	5.589452	CCCGTCAGATTACTACTACTGTCTT	59.411	44.000	0.00	0.00	0.00	3.01
203	206	6.006275	ACTTACCTACCCGTCAGATTACTA	57.994	41.667	0.00	0.00	0.00	1.82
241	244	0.389948	CTCACTTGCCTGTCGTACCC	60.390	60.000	0.00	0.00	0.00	3.69
246	249	2.755650	ACTAAACTCACTTGCCTGTCG	58.244	47.619	0.00	0.00	0.00	4.35
325	328	1.982660	TGTTGGGCAAATGGTCGTAA	58.017	45.000	0.00	0.00	0.00	3.18
360	363	8.680903	CCCTATATCAGCATGGTAAAATCAATC	58.319	37.037	0.00	0.00	33.90	2.67
369	372	5.010708	TGTCTCCCTATATCAGCATGGTA	57.989	43.478	0.00	0.00	35.27	3.25
370	373	3.861846	TGTCTCCCTATATCAGCATGGT	58.138	45.455	0.00	0.00	36.16	3.55
530	533	9.730420	GTTTTTGCTTCTTTAATGTGAAGTCTA	57.270	29.630	12.06	3.59	41.05	2.59
560	563	6.208402	TGATGATGCTTTGTAACCAGCTAAAA	59.792	34.615	0.00	0.00	36.92	1.52
600	604	8.859090	TGTCATTGTTTGATAATTTGAAGAGGT	58.141	29.630	0.00	0.00	36.54	3.85
633	637	5.591472	TGGAGGAAGATTACTGCATTCATTG	59.409	40.000	0.00	0.00	34.26	2.82
658	675	7.101054	TGTAATACACATAGGTCAGTGAAACC	58.899	38.462	0.00	0.00	39.03	3.27
794	2305	4.710324	TGACCAAGTACTAAAAGGTGGTG	58.290	43.478	17.38	0.00	39.44	4.17
902	2415	2.229784	CCCAATTGAAAGCCAGAGTGAC	59.770	50.000	7.12	0.00	0.00	3.67
934	2447	7.562135	TCCACAAGATAAGATTACCAAGTACC	58.438	38.462	0.00	0.00	0.00	3.34
1049	2572	7.770433	TGTCCATTCTTTCAGTATACATTCCAG	59.230	37.037	5.50	0.00	0.00	3.86
1257	2781	8.114331	TGAGAAAACTCTTGGTAATACGACTA	57.886	34.615	0.00	0.00	0.00	2.59
1288	2812	7.337938	ACATCCACACAATCTGTATCAACATA	58.662	34.615	0.00	0.00	34.37	2.29
1316	2840	1.659098	GTACGATGCGAAAACCCTCAG	59.341	52.381	0.00	0.00	0.00	3.35
1518	3042	2.403252	AGAACTTATCGCACCAAGGG	57.597	50.000	0.00	0.00	0.00	3.95
1643	3167	6.015688	ACAATCCCATGCATAAATCAGTGATC	60.016	38.462	5.98	0.00	0.00	2.92
1677	3201	1.299089	CACATGGCATGATGCGCTG	60.299	57.895	32.74	15.89	46.21	5.18
1680	3204	0.306840	GTCTCACATGGCATGATGCG	59.693	55.000	32.74	20.26	46.21	4.73
1683	3207	5.877491	AGATTATGTCTCACATGGCATGAT	58.123	37.500	32.74	16.92	39.53	2.45
1713	3614	0.621609	TATAGCGTGCCCAACCCTTT	59.378	50.000	0.00	0.00	0.00	3.11
1744	3646	2.656560	TTTGGAAACCAACAACACCG	57.343	45.000	2.53	0.00	43.82	4.94
1814	3735	4.316205	ACTTAAAAGGTTGGGCTTTTCG	57.684	40.909	0.00	0.00	34.94	3.46
1920	3843	9.787532	ATCGACATCCATAATACAAAACAAAAG	57.212	29.630	0.00	0.00	0.00	2.27
2014	3947	4.781934	ACTAAATATTCCACCAGCTCCAC	58.218	43.478	0.00	0.00	0.00	4.02
2079	4048	1.818060	TGAAAGGCCCATCAAATCACG	59.182	47.619	0.00	0.00	0.00	4.35
2204	4191	3.184628	TCCACATATCCTCCCATCATCC	58.815	50.000	0.00	0.00	0.00	3.51
2209	4196	5.075483	ACATCAATTCCACATATCCTCCCAT	59.925	40.000	0.00	0.00	0.00	4.00
2334	4323	8.547967	TTCTCTATGTTCGCTAATTTTGAAGT	57.452	30.769	0.00	0.00	0.00	3.01
2385	4376	8.506168	TTTAATCGGCTCAACTATTTCTCAAT	57.494	30.769	0.00	0.00	0.00	2.57
2483	4476	8.007742	AGACAATCCTCTATAACACTATGTCCT	58.992	37.037	0.00	0.00	35.30	3.85
2486	4479	8.768501	TGAGACAATCCTCTATAACACTATGT	57.231	34.615	0.00	0.00	34.38	2.29
2520	4513	8.500753	AGTATACGATATTTGCCTTCAAACAA	57.499	30.769	0.00	0.00	44.11	2.83
2526	4519	6.535508	GGATGGAGTATACGATATTTGCCTTC	59.464	42.308	0.00	0.00	0.00	3.46
2548	4541	7.414651	CGAGTGCTCTTATATTATGAGACGGAT	60.415	40.741	0.00	0.00	33.20	4.18
2550	4543	6.024664	CGAGTGCTCTTATATTATGAGACGG	58.975	44.000	0.00	0.00	33.20	4.79
2551	4544	6.521477	CACGAGTGCTCTTATATTATGAGACG	59.479	42.308	0.00	0.00	33.20	4.18
2552	4545	7.364200	ACACGAGTGCTCTTATATTATGAGAC	58.636	38.462	2.76	0.00	33.20	3.36
2585	4578	9.261180	CTCCTTTCGTTTCATAATATAAGAGCA	57.739	33.333	0.00	0.00	0.00	4.26
2586	4579	9.262358	ACTCCTTTCGTTTCATAATATAAGAGC	57.738	33.333	0.00	0.00	0.00	4.09

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.