AutoCloner

Multiple sequence alignment - TraesCS3D01G428800

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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	TraesCS3D01G428800	chr3D	100.000	2552	0	0	1	2552	543087521	543084970	0.000000e+00	4713
1	TraesCS3D01G428800	chr1B	93.973	2555	116	18	1	2547	640802642	640805166	0.000000e+00	3831
2	TraesCS3D01G428800	chr1B	93.794	2562	116	22	1	2547	599166278	599168811	0.000000e+00	3810
3	TraesCS3D01G428800	chr1B	93.440	2561	122	21	1	2547	641276081	641273553	0.000000e+00	3757
4	TraesCS3D01G428800	chr1D	93.214	2579	134	23	1	2552	464583880	464586444	0.000000e+00	3755
5	TraesCS3D01G428800	chr1D	81.535	482	77	10	2	479	464740794	464740321	1.110000e-103	387
6	TraesCS3D01G428800	chr1D	80.082	487	77	12	2	481	464745267	464744794	6.760000e-91	344
7	TraesCS3D01G428800	chr1A	92.218	2583	159	22	1	2552	556879478	556882049	0.000000e+00	3618
8	TraesCS3D01G428800	chr1A	87.573	861	75	18	1594	2438	557050999	557050155	0.000000e+00	968
9	TraesCS3D01G428800	chr5A	93.548	1643	92	9	919	2552	412189374	412187737	0.000000e+00	2435
10	TraesCS3D01G428800	chr6D	93.517	1635	87	11	926	2552	103932858	103934481	0.000000e+00	2414
11	TraesCS3D01G428800	chr6D	89.006	664	39	10	1	637	103931041	103931697	0.000000e+00	791
12	TraesCS3D01G428800	chr6D	95.019	261	11	2	628	887	103932598	103932857	2.360000e-110	409
13	TraesCS3D01G428800	chr6A	92.953	1632	105	8	926	2552	125300226	125301852	0.000000e+00	2368
14	TraesCS3D01G428800	chr6A	90.670	911	48	15	5	887	125299178	125300079	0.000000e+00	1177
15	TraesCS3D01G428800	chr7B	89.428	577	44	10	971	1539	28312315	28311748	0.000000e+00	712
16	TraesCS3D01G428800	chr7B	83.903	497	21	11	483	932	28313388	28312904	1.090000e-113	420
17	TraesCS3D01G428800	chr7D	83.702	497	22	9	483	932	80789264	80788780	5.080000e-112	414
18	TraesCS3D01G428800	chr3B	88.021	192	18	4	2361	2549	43731539	43731728	3.300000e-54	222

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	TraesCS3D01G428800	chr3D	543084970	543087521	2551	True	4713.000000	4713	100.0000	1	2552	1	chr3D.!!$R1	2551
1	TraesCS3D01G428800	chr1B	640802642	640805166	2524	False	3831.000000	3831	93.9730	1	2547	1	chr1B.!!$F2	2546
2	TraesCS3D01G428800	chr1B	599166278	599168811	2533	False	3810.000000	3810	93.7940	1	2547	1	chr1B.!!$F1	2546
3	TraesCS3D01G428800	chr1B	641273553	641276081	2528	True	3757.000000	3757	93.4400	1	2547	1	chr1B.!!$R1	2546
4	TraesCS3D01G428800	chr1D	464583880	464586444	2564	False	3755.000000	3755	93.2140	1	2552	1	chr1D.!!$F1	2551
5	TraesCS3D01G428800	chr1A	556879478	556882049	2571	False	3618.000000	3618	92.2180	1	2552	1	chr1A.!!$F1	2551
6	TraesCS3D01G428800	chr1A	557050155	557050999	844	True	968.000000	968	87.5730	1594	2438	1	chr1A.!!$R1	844
7	TraesCS3D01G428800	chr5A	412187737	412189374	1637	True	2435.000000	2435	93.5480	919	2552	1	chr5A.!!$R1	1633
8	TraesCS3D01G428800	chr6D	103931041	103934481	3440	False	1204.666667	2414	92.5140	1	2552	3	chr6D.!!$F1	2551
9	TraesCS3D01G428800	chr6A	125299178	125301852	2674	False	1772.500000	2368	91.8115	5	2552	2	chr6A.!!$F1	2547
10	TraesCS3D01G428800	chr7B	28311748	28313388	1640	True	566.000000	712	86.6655	483	1539	2	chr7B.!!$R1	1056

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
845	1847	1.26402	TGACAAATGCACAGCGTTCTC	59.736	47.619	0.0	0.0	36.71	2.87	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2023	3782	0.389426	CGACACTGAAACTACCCGGG	60.389	60.0	22.25	22.25	0.0	5.73	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
77	78	6.737254	TCGGTGGATAAAAAGATCTTGAAC	57.263	37.500	9.17	0.50	0.00	3.18
304	306	9.822185	ATTAATCTTGGACAATTTGGATTTAGC	57.178	29.630	0.78	0.00	0.00	3.09
310	312	6.964464	TGGACAATTTGGATTTAGCTAGGTA	58.036	36.000	0.00	0.00	0.00	3.08
361	363	6.931840	GGTAGATTATGAGATTTCAGGTGGAC	59.068	42.308	0.00	0.00	36.61	4.02
406	408	4.174762	GAGGTAGTCAAAGATGTTCGGTC	58.825	47.826	0.00	0.00	0.00	4.79
425	427	6.444633	TCGGTCGATTATGAGATTTTAGGTC	58.555	40.000	0.00	0.00	0.00	3.85
436	438	8.840200	ATGAGATTTTAGGTCTAGTAGGTGAA	57.160	34.615	0.00	0.00	0.00	3.18
525	568	1.400494	CCACAATAGGCGCTTAACACC	59.600	52.381	7.64	0.00	0.00	4.16
543	597	5.715439	ACACCAAGATTCATGGGATAGAA	57.285	39.130	12.29	0.00	42.48	2.10
598	678	2.496899	CCACACTTTGGCCTATGACT	57.503	50.000	3.32	0.00	39.07	3.41
613	693	6.203723	GGCCTATGACTTTTAAGCAGTATGAG	59.796	42.308	0.00	0.00	39.69	2.90
845	1847	1.264020	TGACAAATGCACAGCGTTCTC	59.736	47.619	0.00	0.00	36.71	2.87
846	1848	1.264020	GACAAATGCACAGCGTTCTCA	59.736	47.619	0.00	0.00	36.71	3.27
967	2142	5.998363	CAGCTAGAATATTAACTGGTTCCCC	59.002	44.000	0.00	0.00	0.00	4.81
1040	2773	9.982651	GAAGGTAATAATCATGCTAACTGTAGA	57.017	33.333	0.00	0.00	0.00	2.59
1079	2812	8.492673	TGGCAATATCTCTGTTGTAGTAAAAG	57.507	34.615	0.00	0.00	0.00	2.27
1163	2900	3.386078	TGTATGTGCTGAGGGAGAGAATC	59.614	47.826	0.00	0.00	0.00	2.52
1175	2912	4.016105	AGGGAGAGAATCAGAAAGGGTCTA	60.016	45.833	0.00	0.00	37.82	2.59
1176	2913	4.717280	GGGAGAGAATCAGAAAGGGTCTAA	59.283	45.833	0.00	0.00	37.82	2.10
1180	2917	6.941857	AGAGAATCAGAAAGGGTCTAAAGTC	58.058	40.000	0.00	0.00	37.82	3.01
1241	2978	6.038825	CACAGAACTACGGAGAGATATTCAGT	59.961	42.308	0.00	0.00	0.00	3.41
1469	3210	2.227388	GCATCACAACTTGGAAGACTGG	59.773	50.000	0.00	0.00	0.00	4.00
1471	3212	0.954452	CACAACTTGGAAGACTGGCC	59.046	55.000	0.00	0.00	0.00	5.36
1522	3263	1.064003	TCCACACAAGTGTATGGGCT	58.936	50.000	8.84	0.00	44.39	5.19
1559	3300	5.011090	AGTTTCTCAGCATAGTAATCGCA	57.989	39.130	0.00	0.00	0.00	5.10
1686	3438	2.373169	TGAGTTCCTTGCTGACTTGGAT	59.627	45.455	0.00	0.00	0.00	3.41
1762	3514	9.436957	TCTCACTACCATTTTCTATCTTCAAAC	57.563	33.333	0.00	0.00	0.00	2.93
1832	3584	6.917477	TGAATTTCAGTGCACAATTCTGTAAC	59.083	34.615	27.67	12.25	37.66	2.50
1877	3629	1.480789	TCCATGAGCGGCTAACTGTA	58.519	50.000	0.60	0.00	0.00	2.74
2015	3772	8.932945	TTGTTAATTGCACATTTTACAAGTGA	57.067	26.923	0.00	0.00	35.33	3.41
2040	3804	1.426751	TTCCCGGGTAGTTTCAGTGT	58.573	50.000	22.86	0.00	0.00	3.55
2068	3832	6.923928	ATTGTTGATTCTGTTGTTTTTGGG	57.076	33.333	0.00	0.00	0.00	4.12
2111	3878	0.111061	TTGCCTGTGAGCCATTGTCT	59.889	50.000	0.00	0.00	0.00	3.41
2120	3896	4.118410	GTGAGCCATTGTCTCTACTGATG	58.882	47.826	0.00	0.00	0.00	3.07
2121	3897	3.771479	TGAGCCATTGTCTCTACTGATGT	59.229	43.478	0.00	0.00	0.00	3.06
2122	3898	4.223700	TGAGCCATTGTCTCTACTGATGTT	59.776	41.667	0.00	0.00	0.00	2.71
2323	4108	4.015872	TCTTGGGTCAGTGGTTATGTTC	57.984	45.455	0.00	0.00	0.00	3.18
2489	4281	5.893897	ATTTCATCTGGTTGCTCTTCTTC	57.106	39.130	0.00	0.00	0.00	2.87
2490	4282	4.630644	TTCATCTGGTTGCTCTTCTTCT	57.369	40.909	0.00	0.00	0.00	2.85
2491	4283	4.630644	TCATCTGGTTGCTCTTCTTCTT	57.369	40.909	0.00	0.00	0.00	2.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
96	97	9.903682	CAAGATCACAATCTCACAAACTAAATT	57.096	29.630	0.00	0.00	41.54	1.82
230	231	4.744795	ATAATCATCATCCTCGCCTACC	57.255	45.455	0.00	0.00	0.00	3.18
304	306	7.461182	TTGGGTCAAAATCACAATTACCTAG	57.539	36.000	0.00	0.00	0.00	3.02
310	312	7.254727	CGTGAAATTTGGGTCAAAATCACAATT	60.255	33.333	24.85	5.83	44.68	2.32
361	363	8.887717	CCTCCTCAAAAGTCATATCAACTAAAG	58.112	37.037	0.00	0.00	0.00	1.85
425	427	8.715998	GCAATAATCATCATGTTCACCTACTAG	58.284	37.037	0.00	0.00	0.00	2.57
505	548	1.400494	GGTGTTAAGCGCCTATTGTGG	59.600	52.381	2.29	0.00	44.20	4.17
525	568	7.175641	GGGTATGTTTCTATCCCATGAATCTTG	59.824	40.741	0.00	0.00	38.15	3.02
543	597	5.881923	ATAGTGTTGATACGGGGTATGTT	57.118	39.130	0.00	0.00	0.00	2.71
598	678	4.905429	TCAGCACCTCATACTGCTTAAAA	58.095	39.130	0.00	0.00	41.97	1.52
613	693	1.620822	ATGGGTTCTGTTTCAGCACC	58.379	50.000	9.42	9.42	44.77	5.01
845	1847	5.404466	TTGTTGGGGATTTGATTAAGCTG	57.596	39.130	0.00	0.00	0.00	4.24
846	1848	6.269769	TCTTTTGTTGGGGATTTGATTAAGCT	59.730	34.615	0.00	0.00	0.00	3.74
924	1926	3.381590	GCTGAACCTGAAAAGTGGAAACT	59.618	43.478	0.00	0.00	0.00	2.66
1025	2758	7.555965	TGCTAGATTTTCTACAGTTAGCATGA	58.444	34.615	0.00	0.00	37.64	3.07
1040	2773	9.750783	AGAGATATTGCCATAATGCTAGATTTT	57.249	29.630	0.00	0.00	0.00	1.82
1163	2900	6.395629	TGAATACGACTTTAGACCCTTTCTG	58.604	40.000	0.00	0.00	35.55	3.02
1175	2912	4.935808	GTGGGTTCAGATGAATACGACTTT	59.064	41.667	0.00	0.00	36.33	2.66
1176	2913	4.504858	GTGGGTTCAGATGAATACGACTT	58.495	43.478	0.00	0.00	36.33	3.01
1180	2917	2.159156	TCGGTGGGTTCAGATGAATACG	60.159	50.000	0.00	0.93	36.33	3.06
1241	2978	7.554476	TCATCCACAAACCGTATGATTTGATTA	59.446	33.333	8.84	0.00	38.82	1.75
1522	3263	4.056050	GAGAAACTAGACGCTTTTGTCCA	58.944	43.478	0.00	0.00	39.77	4.02
1559	3300	9.807921	TTAAATCTAAGAATGAGGAAAACTGGT	57.192	29.630	0.00	0.00	0.00	4.00
1600	3349	2.103538	CATGCTGTGGCGGAATGC	59.896	61.111	0.00	0.00	42.25	3.56
1686	3438	2.241281	TTCGACTAGGTCCCAATGGA	57.759	50.000	0.00	0.00	38.75	3.41
1698	3450	2.099921	GCTGAGGAGCTTCATTCGACTA	59.900	50.000	0.00	0.00	42.52	2.59
1762	3514	4.599041	TGGATAAGAATCACAAGGTTGGG	58.401	43.478	0.00	0.00	33.41	4.12
1832	3584	3.562973	ACATAAATCTGCTTGATCAGGCG	59.437	43.478	23.01	17.51	36.05	5.52
1877	3629	5.044624	TCAGAATTCAAATGTCCCAGGAGAT	60.045	40.000	8.44	0.00	0.00	2.75
2023	3782	0.389426	CGACACTGAAACTACCCGGG	60.389	60.000	22.25	22.25	0.00	5.73
2024	3783	0.599558	TCGACACTGAAACTACCCGG	59.400	55.000	0.00	0.00	0.00	5.73
2025	3784	2.427232	TTCGACACTGAAACTACCCG	57.573	50.000	0.00	0.00	0.00	5.28
2028	3792	6.711579	TCAACAATTTCGACACTGAAACTAC	58.288	36.000	0.00	0.00	40.40	2.73
2040	3804	8.379161	CAAAAACAACAGAATCAACAATTTCGA	58.621	29.630	0.00	0.00	0.00	3.71
2111	3878	6.017109	GGCAAGAAAGAAACAACATCAGTAGA	60.017	38.462	0.00	0.00	0.00	2.59
2120	3896	5.232838	CAGAATGTGGCAAGAAAGAAACAAC	59.767	40.000	0.00	0.00	0.00	3.32
2121	3897	5.350633	CAGAATGTGGCAAGAAAGAAACAA	58.649	37.500	0.00	0.00	0.00	2.83
2122	3898	4.935702	CAGAATGTGGCAAGAAAGAAACA	58.064	39.130	0.00	0.00	0.00	2.83
2323	4108	3.187700	CACGATAGGTTTTCTTCTCCCG	58.812	50.000	0.00	0.00	43.77	5.14
2489	4281	9.727627	GAAATCTGCAAGTAATCCAATCTTAAG	57.272	33.333	0.00	0.00	33.76	1.85
2490	4282	9.466497	AGAAATCTGCAAGTAATCCAATCTTAA	57.534	29.630	0.00	0.00	33.76	1.85
2491	4283	9.466497	AAGAAATCTGCAAGTAATCCAATCTTA	57.534	29.630	0.00	0.00	33.76	2.10

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.