AutoCloner

Multiple sequence alignment - TraesCS3B01G374400

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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	TraesCS3B01G374400	chr3B	100.000	3717	0	0	690	4406	587565687	587569403	0.000000e+00	6865.0
1	TraesCS3B01G374400	chr3B	100.000	346	0	0	1	346	587564998	587565343	1.340000e-179	640.0
2	TraesCS3B01G374400	chr3A	96.729	1804	54	4	690	2491	589392796	589394596	0.000000e+00	3000.0
3	TraesCS3B01G374400	chr3A	87.005	1716	106	54	2716	4374	589394933	589396588	0.000000e+00	1825.0
4	TraesCS3B01G374400	chr3A	93.966	348	13	4	1	346	589392434	589392775	1.820000e-143	520.0
5	TraesCS3B01G374400	chr3A	92.488	213	11	2	2511	2718	589394668	589394880	2.580000e-77	300.0
6	TraesCS3B01G374400	chr3D	97.588	1617	38	1	693	2308	447989258	447990874	0.000000e+00	2769.0
7	TraesCS3B01G374400	chr3D	88.139	1703	86	49	2717	4374	447991531	447993162	0.000000e+00	1919.0
8	TraesCS3B01G374400	chr3D	93.476	935	56	2	930	1859	206467204	206466270	0.000000e+00	1384.0
9	TraesCS3B01G374400	chr3D	93.678	348	11	4	1	346	447988895	447989233	1.090000e-140	510.0
10	TraesCS3B01G374400	chr3D	93.458	214	8	3	2511	2718	447991264	447991477	3.310000e-81	313.0
11	TraesCS3B01G374400	chr1A	89.173	859	80	5	930	1787	193040815	193041661	0.000000e+00	1059.0
12	TraesCS3B01G374400	chr1A	77.283	1325	265	27	993	2299	496046317	496045011	0.000000e+00	747.0
13	TraesCS3B01G374400	chr1A	81.726	591	100	7	2790	3376	496044270	496043684	1.840000e-133	486.0
14	TraesCS3B01G374400	chr1D	78.145	1240	239	22	1076	2299	399190925	399189702	0.000000e+00	760.0
15	TraesCS3B01G374400	chr1D	82.712	590	96	5	2790	3376	399188907	399188321	1.820000e-143	520.0
16	TraesCS3B01G374400	chr1D	79.891	184	32	5	1511	1692	399044424	399044244	3.580000e-26	130.0
17	TraesCS3B01G374400	chr1B	81.895	591	99	7	2790	3376	535384850	535384264	3.960000e-135	492.0
18	TraesCS3B01G374400	chr1B	79.196	572	111	8	2790	3357	535143911	535143344	1.490000e-104	390.0
19	TraesCS3B01G374400	chr2D	77.713	341	71	3	3018	3357	56106718	56107054	2.080000e-48	204.0
20	TraesCS3B01G374400	chr2A	77.551	343	68	5	3018	3357	57549151	57549487	9.670000e-47	198.0
21	TraesCS3B01G374400	chr2B	78.716	296	60	1	3062	3357	88841215	88841507	1.250000e-45	195.0
22	TraesCS3B01G374400	chr5D	90.000	50	3	2	3066	3114	432041665	432041617	3.680000e-06	63.9
23	TraesCS3B01G374400	chr5B	97.297	37	1	0	3066	3102	523908273	523908309	3.680000e-06	63.9

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	TraesCS3B01G374400	chr3B	587564998	587569403	4405	False	3752.50	6865	100.00000	1	4406	2	chr3B.!!$F1	4405
1	TraesCS3B01G374400	chr3A	589392434	589396588	4154	False	1411.25	3000	92.54700	1	4374	4	chr3A.!!$F1	4373
2	TraesCS3B01G374400	chr3D	206466270	206467204	934	True	1384.00	1384	93.47600	930	1859	1	chr3D.!!$R1	929
3	TraesCS3B01G374400	chr3D	447988895	447993162	4267	False	1377.75	2769	93.21575	1	4374	4	chr3D.!!$F1	4373
4	TraesCS3B01G374400	chr1A	193040815	193041661	846	False	1059.00	1059	89.17300	930	1787	1	chr1A.!!$F1	857
5	TraesCS3B01G374400	chr1A	496043684	496046317	2633	True	616.50	747	79.50450	993	3376	2	chr1A.!!$R1	2383
6	TraesCS3B01G374400	chr1D	399188321	399190925	2604	True	640.00	760	80.42850	1076	3376	2	chr1D.!!$R2	2300
7	TraesCS3B01G374400	chr1B	535384264	535384850	586	True	492.00	492	81.89500	2790	3376	1	chr1B.!!$R2	586
8	TraesCS3B01G374400	chr1B	535143344	535143911	567	True	390.00	390	79.19600	2790	3357	1	chr1B.!!$R1	567

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	Hairpin	End Stability	Orientation
45	46	4.642429	ACGGAAGAGTTCTTAAATGCTGT	58.358	39.13	36.11	4.40	F
1569	1589	1.177401	GTCTCCCCAAATTGAGGCAC	58.823	55.00	33.44	5.01	F
1714	1735	0.250513	GCCTTCTCCTTCACCGACAT	59.749	55.00	0.00	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1714	1735	2.128290	CTGGGCACTGATGGTGGTGA	62.128	60.0	0.00	45.44	4.02	R
3057	3743	0.826672	AGACGTCCGACTTCTGGGTT	60.827	55.0	13.01	0.00	4.11	R
3666	4373	0.248458	CAGGACAACACAAACACCGC	60.248	55.0	0.00	0.00	5.68	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
27	28	6.774170	TGATAGCTAAGATAGGTACAAACGGA	59.226	38.462	0.00	41.07	4.69
45	46	4.642429	ACGGAAGAGTTCTTAAATGCTGT	58.358	39.130	0.00	36.11	4.40
70	71	6.213397	TCCCAGAACTCTCAAGAACATTATCA	59.787	38.462	0.00	0.00	2.15
264	265	5.581126	ATGCAACCCATACACTGTTAATG	57.419	39.130	0.00	30.69	1.90
267	268	5.182950	TGCAACCCATACACTGTTAATGAAG	59.817	40.000	0.00	0.00	3.02
268	269	5.414454	GCAACCCATACACTGTTAATGAAGA	59.586	40.000	1.66	0.00	2.87
269	270	6.403636	GCAACCCATACACTGTTAATGAAGAG	60.404	42.308	1.66	32.20	2.85
270	271	6.620877	ACCCATACACTGTTAATGAAGAGA	57.379	37.500	0.00	30.50	3.10
272	273	6.879458	ACCCATACACTGTTAATGAAGAGAAC	59.121	38.462	0.00	30.50	3.01
273	274	6.878923	CCCATACACTGTTAATGAAGAGAACA	59.121	38.462	0.00	30.50	3.18
714	717	6.234177	GGAATCCACTATTAGTCCTTCCATG	58.766	44.000	16.52	31.98	3.66
727	730	5.105063	GTCCTTCCATGCTTCTATTTTTGC	58.895	41.667	0.00	0.00	3.68
739	742	8.959548	TGCTTCTATTTTTGCATATCTCTTGAA	58.040	29.630	0.00	0.00	2.69
862	866	5.174037	TGGGACCTTCCTTTTACATGTAG	57.826	43.478	5.56	36.57	2.74
1569	1589	1.177401	GTCTCCCCAAATTGAGGCAC	58.823	55.000	0.00	33.44	5.01
1714	1735	0.250513	GCCTTCTCCTTCACCGACAT	59.749	55.000	0.00	0.00	3.06
1773	1794	1.004745	TGGAAAAGGATCAGGACAGGC	59.995	52.381	0.00	0.00	4.85
1818	1839	2.025887	AGGAGGGGTATTGTTGCTTCTG	60.026	50.000	0.00	0.00	3.02
1971	1995	4.041444	AGTGTTCAGGAAGCAGAGAGAAAT	59.959	41.667	0.00	0.00	2.17
1998	2022	2.479275	GGTTTTCTTCGAGGGTTCTTCG	59.521	50.000	0.00	0.00	3.79
2133	2157	3.848975	AGAGATTGAAGGAGATGGTGGTT	59.151	43.478	0.00	0.00	3.67
2260	2284	4.298626	ACTGGTGTATGACTATGTCCCAT	58.701	43.478	0.00	0.00	4.00
2304	2328	6.403866	TTGCATGGTATGTTCTTTGTTTCT	57.596	33.333	0.00	0.00	2.52
2311	2335	7.284074	TGGTATGTTCTTTGTTTCTCCTGTTA	58.716	34.615	0.00	0.00	2.41
2353	2396	7.117092	GCCTATTAGTGCTTATGAACTTCTAGC	59.883	40.741	0.00	33.29	3.42

Showing 1 to 25 of 133 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
25	26	4.396478	GGGACAGCATTTAAGAACTCTTCC	59.604	45.833	0.00	0.00	37.40	3.46
27	28	4.985538	TGGGACAGCATTTAAGAACTCTT	58.014	39.130	0.00	0.00	39.85	2.85
45	46	4.982241	AATGTTCTTGAGAGTTCTGGGA	57.018	40.909	0.00	0.00	0.00	4.37
70	71	5.304614	AGCAATAGTATACCTCGTCCAACAT	59.695	40.000	0.00	0.00	0.00	2.71
254	255	8.562892	ACTGAAATGTTCTCTTCATTAACAGTG	58.437	33.333	19.25	0.00	42.88	3.66
264	265	8.770438	AAGTGAGATACTGAAATGTTCTCTTC	57.230	34.615	0.00	0.00	40.26	2.87
691	694	5.703130	GCATGGAAGGACTAATAGTGGATTC	59.297	44.000	0.00	0.00	0.00	2.52
714	717	9.230932	GTTCAAGAGATATGCAAAAATAGAAGC	57.769	33.333	0.00	0.00	0.00	3.86
739	742	8.814038	AACTGCCTGAGAATTAGAAAATATGT	57.186	30.769	0.00	0.00	0.00	2.29
862	866	8.774586	ACAAAACATCGAGGCAATAATAGATAC	58.225	33.333	0.00	0.00	0.00	2.24
1569	1589	6.017400	AGGTTGTTGTTGCTCATATTCAAG	57.983	37.500	0.00	0.00	0.00	3.02
1714	1735	2.128290	CTGGGCACTGATGGTGGTGA	62.128	60.000	0.00	0.00	45.44	4.02
1971	1995	4.426736	ACCCTCGAAGAAAACCAGTTTA	57.573	40.909	0.00	0.00	34.09	2.01
1998	2022	6.183360	GCAAATCCTCCAGGTCAAAGTTATAC	60.183	42.308	0.00	0.00	36.34	1.47
2133	2157	3.728845	CTGTTCGAAGTCTTTCTTCCCA	58.271	45.455	0.00	0.00	46.97	4.37
2236	2260	5.274015	TGGGACATAGTCATACACCAGTAA	58.726	41.667	0.00	0.00	33.68	2.24
2260	2284	1.297689	CAGCAGCAAGGCTACCAGA	59.702	57.895	0.00	0.00	43.68	3.86
2304	2328	7.771183	GGCAACTGATTTCAAATATAACAGGA	58.229	34.615	0.00	0.00	0.00	3.86
2353	2396	6.316390	AGAAACATTTTGAATAGGCTAGACCG	59.684	38.462	0.00	0.00	46.52	4.79
2400	2443	5.867174	GTGCCAACAGTTGAGTTTTAAGTTT	59.133	36.000	15.36	0.00	0.00	2.66
2407	2450	3.886123	ACTAGTGCCAACAGTTGAGTTT	58.114	40.909	15.36	0.75	0.00	2.66
2412	2455	2.076863	GCCTACTAGTGCCAACAGTTG	58.923	52.381	5.39	6.28	0.00	3.16
2429	2472	2.148446	TTTGGATATGCTTGCAGCCT	57.852	45.000	0.87	0.00	41.51	4.58
2434	2477	5.750067	CCAACTATGTTTTGGATATGCTTGC	59.250	40.000	0.00	0.00	45.69	4.01
2442	2485	9.936329	AGTATTAATCCCAACTATGTTTTGGAT	57.064	29.630	2.58	2.63	45.69	3.41

Showing 1 to 25 of 117 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.