AutoCloner

Multiple sequence alignment - TraesCS3A01G100200

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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	TraesCS3A01G100200	chr3A	100.000	8193	0	0	1	8193	64795388	64787196	0.000000e+00	15130.0
1	TraesCS3A01G100200	chr3A	98.578	211	3	0	1	211	87682406	87682196	2.790000e-99	374.0
2	TraesCS3A01G100200	chr3A	95.270	148	4	3	4566	4713	64790690	64790546	1.780000e-56	231.0
3	TraesCS3A01G100200	chr3A	95.270	148	4	3	4699	4843	64790823	64790676	1.780000e-56	231.0
4	TraesCS3A01G100200	chr3A	95.614	114	5	0	1271	1384	64794082	64793969	5.050000e-42	183.0
5	TraesCS3A01G100200	chr3A	95.614	114	5	0	1307	1420	64794118	64794005	5.050000e-42	183.0
6	TraesCS3A01G100200	chr3A	93.590	78	5	0	1271	1348	64794046	64793969	5.200000e-22	117.0
7	TraesCS3A01G100200	chr3A	93.590	78	5	0	1343	1420	64794118	64794041	5.200000e-22	117.0
8	TraesCS3A01G100200	chr3D	96.898	7866	169	36	375	8193	53492840	53485003	0.000000e+00	13104.0
9	TraesCS3A01G100200	chr3D	91.500	200	5	1	1185	1384	53491945	53491758	1.750000e-66	265.0
10	TraesCS3A01G100200	chr3D	95.946	148	3	3	4566	4713	53488480	53488336	3.820000e-58	237.0
11	TraesCS3A01G100200	chr3D	93.919	148	6	3	4699	4843	53488613	53488466	3.850000e-53	220.0
12	TraesCS3A01G100200	chr3D	89.820	167	16	1	211	377	7928280	7928445	6.440000e-51	213.0
13	TraesCS3A01G100200	chr3B	94.843	2133	70	18	1307	3423	83911480	83909372	0.000000e+00	3293.0
14	TraesCS3A01G100200	chr3B	93.000	2100	107	23	6118	8193	83906840	83904757	0.000000e+00	3027.0
15	TraesCS3A01G100200	chr3B	95.783	1660	52	5	4699	6352	83908307	83906660	0.000000e+00	2662.0
16	TraesCS3A01G100200	chr3B	95.967	1215	34	5	3498	4711	83909362	83908162	0.000000e+00	1958.0
17	TraesCS3A01G100200	chr3B	88.196	1042	27	25	376	1350	83912416	83911404	0.000000e+00	1155.0
18	TraesCS3A01G100200	chr3B	86.310	168	19	4	211	376	9108932	9108767	6.530000e-41	180.0
19	TraesCS3A01G100200	chrUn	100.000	415	0	0	1652	2066	477248799	477249213	0.000000e+00	767.0
20	TraesCS3A01G100200	chrUn	85.799	169	20	4	211	377	477604368	477604202	8.450000e-40	176.0
21	TraesCS3A01G100200	chr6A	98.598	214	3	0	1	214	206736376	206736163	6.000000e-101	379.0
22	TraesCS3A01G100200	chr6A	91.304	46	4	0	2553	2598	156195737	156195692	6.860000e-06	63.9
23	TraesCS3A01G100200	chr2A	98.578	211	3	0	1	211	537033818	537034028	2.790000e-99	374.0
24	TraesCS3A01G100200	chr2A	98.104	211	4	0	1	211	448463960	448464170	1.300000e-97	368.0
25	TraesCS3A01G100200	chr2A	98.104	211	4	0	1	211	490503845	490504055	1.300000e-97	368.0
26	TraesCS3A01G100200	chr2A	82.286	175	27	4	211	383	12619652	12619480	1.840000e-31	148.0
27	TraesCS3A01G100200	chr7A	98.104	211	4	0	1	211	604227715	604227925	1.300000e-97	368.0
28	TraesCS3A01G100200	chr7A	82.036	167	30	0	211	377	42661380	42661546	8.570000e-30	143.0
29	TraesCS3A01G100200	chr5A	97.664	214	5	0	1	214	8953984	8953771	1.300000e-97	368.0
30	TraesCS3A01G100200	chr5A	98.104	211	4	0	1	211	635172398	635172608	1.300000e-97	368.0
31	TraesCS3A01G100200	chr1A	98.104	211	4	0	1	211	312959274	312959484	1.300000e-97	368.0
32	TraesCS3A01G100200	chr6B	85.799	169	20	4	211	377	11369973	11370139	8.450000e-40	176.0
33	TraesCS3A01G100200	chr6B	85.799	169	20	4	211	377	11393242	11393408	8.450000e-40	176.0
34	TraesCS3A01G100200	chr4A	84.524	168	24	2	211	377	166145871	166146037	1.830000e-36	165.0
35	TraesCS3A01G100200	chr1B	83.432	169	24	4	211	377	74120094	74119928	3.960000e-33	154.0
36	TraesCS3A01G100200	chr6D	93.478	46	3	0	2553	2598	124944804	124944849	1.480000e-07	69.4

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	TraesCS3A01G100200	chr3A	64787196	64795388	8192	True	15130.000000	15130	100.000000	1	8193	1	chr3A.!!$R1	8192
1	TraesCS3A01G100200	chr3D	53485003	53492840	7837	True	13104.000000	13104	96.898000	375	8193	1	chr3D.!!$R1	7818
2	TraesCS3A01G100200	chr3D	53488336	53491945	3609	True	240.666667	265	93.788333	1185	4843	3	chr3D.!!$R2	3658
3	TraesCS3A01G100200	chr3B	83904757	83912416	7659	True	2419.000000	3293	93.557800	376	8193	5	chr3B.!!$R2	7817

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	Hairpin	End Stability	Orientation
247	248	0.034863	GGCCGAGGTTGATTGGGTAA	60.035	55.000	0.00	0.00	2.85	F
361	362	0.112412	AGGCTCCATTTTGGTTCGGT	59.888	50.000	0.00	39.03	4.69	F
362	363	0.526211	GGCTCCATTTTGGTTCGGTC	59.474	55.000	0.00	39.03	4.79	F
1386	1511	0.752743	AAGGTCAGCAAGCACAGCAA	60.753	50.000	0.00	0.00	3.91	F
1387	1512	1.008079	GGTCAGCAAGCACAGCAAC	60.008	57.895	0.00	0.00	4.17	F
1388	1513	1.008079	GTCAGCAAGCACAGCAACC	60.008	57.895	0.00	0.00	3.77	F
1450	1575	1.799258	GCAAGGGTCACAACAGCCAG	61.799	60.000	0.00	36.28	4.85	F
2288	2413	2.954318	GCGGAGTGGATACTAACTACCA	59.046	50.000	0.00	37.25	3.25	F
3454	3594	3.872511	TCTGCAGTTGGCCATAAATTG	57.127	42.857	14.67	43.89	2.32	F
5321	5592	2.681848	CCATGCTTTTGTTTGTTTGCCA	59.318	40.909	0.00	0.00	4.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1404	1529	0.879765	GCATCTGTTCTTGCTGCTGT	59.120	50.000	0.00	35.95	4.40	R
2288	2413	2.100605	GCTACTAGCCAGTTGTTGCT	57.899	50.000	0.00	41.57	3.91	R
2789	2917	8.458573	AGTTAGTGGTGTCAATTTCATAAACA	57.541	30.769	0.00	0.00	2.83	R
3177	3305	1.877443	AGTTGCGTTTGGAATAGCGTT	59.123	42.857	0.00	0.00	4.84	R
3720	3860	5.221722	ACAACTCAAGAGAAAGCATACCTCA	60.222	40.000	3.73	0.00	3.86	R
3924	4064	0.615331	ATGTCACTACACTGCCCAGG	59.385	55.000	0.00	38.78	4.45	R
3963	4103	5.520288	ACATCAATTCTTCCGATAGTTGTCG	59.480	40.000	0.00	41.13	4.35	R
4286	4426	0.543749	CCAGTGTCTTCCCTGATCCC	59.456	60.000	0.00	0.00	3.85	R
5434	5708	0.737715	GAATCTGCTCCAAGCGACGT	60.738	55.000	0.00	46.26	4.34	R
7440	7768	0.255890	AACTACCGCCCATGCTTCAT	59.744	50.000	0.00	34.43	2.57	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
17	18	4.506039	GTTTTAGGTGGCCCCGTT	57.494	55.556	0.00	38.74	4.44
18	19	2.736197	GTTTTAGGTGGCCCCGTTT	58.264	52.632	0.00	38.74	3.60
19	20	1.908344	GTTTTAGGTGGCCCCGTTTA	58.092	50.000	0.00	38.74	2.01
20	21	2.237643	GTTTTAGGTGGCCCCGTTTAA	58.762	47.619	0.00	38.74	1.52
21	22	2.203470	TTTAGGTGGCCCCGTTTAAG	57.797	50.000	0.00	38.74	1.85
22	23	1.360185	TTAGGTGGCCCCGTTTAAGA	58.640	50.000	0.00	38.74	2.10
23	24	0.906775	TAGGTGGCCCCGTTTAAGAG	59.093	55.000	0.00	38.74	2.85
24	25	2.044555	GGTGGCCCCGTTTAAGAGC	61.045	63.158	0.00	0.00	4.09
25	26	2.046700	TGGCCCCGTTTAAGAGCG	60.047	61.111	0.00	0.00	5.03
46	47	4.159857	CGGATATCACGCTTTACTAGAGC	58.840	47.826	4.83	36.79	4.09
71	72	5.273523	GAAGCATTCACAATTTTCCAAGC	57.726	39.130	0.00	46.62	4.01
72	73	4.339872	AGCATTCACAATTTTCCAAGCA	57.660	36.364	0.00	0.00	3.91
73	74	4.706035	AGCATTCACAATTTTCCAAGCAA	58.294	34.783	0.00	0.00	3.91
74	75	5.310451	AGCATTCACAATTTTCCAAGCAAT	58.690	33.333	0.00	0.00	3.56
75	76	6.465948	AGCATTCACAATTTTCCAAGCAATA	58.534	32.000	0.00	0.00	1.90
76	77	6.369615	AGCATTCACAATTTTCCAAGCAATAC	59.630	34.615	0.00	0.00	1.89
77	78	6.402442	GCATTCACAATTTTCCAAGCAATACC	60.402	38.462	0.00	0.00	2.73
78	79	5.146010	TCACAATTTTCCAAGCAATACCC	57.854	39.130	0.00	0.00	3.69
79	80	4.020662	TCACAATTTTCCAAGCAATACCCC	60.021	41.667	0.00	0.00	4.95
80	81	3.906846	ACAATTTTCCAAGCAATACCCCA	59.093	39.130	0.00	0.00	4.96
81	82	4.535692	ACAATTTTCCAAGCAATACCCCAT	59.464	37.500	0.00	0.00	4.00
82	83	5.014018	ACAATTTTCCAAGCAATACCCCATT	59.986	36.000	0.00	0.00	3.16
83	84	6.214412	ACAATTTTCCAAGCAATACCCCATTA	59.786	34.615	0.00	0.00	1.90
84	85	5.669164	TTTTCCAAGCAATACCCCATTAC	57.331	39.130	0.00	0.00	1.89
85	86	2.925724	TCCAAGCAATACCCCATTACG	58.074	47.619	0.00	0.00	3.18

Showing 1 to 25 of 339 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	2.107901	TCTTAAACGGGGCCACCTAAAA	59.892	45.455	4.39	0.00	36.97	1.52
4	5	0.906775	CTCTTAAACGGGGCCACCTA	59.093	55.000	4.39	0.00	36.97	3.08
5	6	1.683441	CTCTTAAACGGGGCCACCT	59.317	57.895	4.39	0.00	36.97	4.00
6	7	2.044555	GCTCTTAAACGGGGCCACC	61.045	63.158	4.39	1.95	0.00	4.61
7	8	2.396157	CGCTCTTAAACGGGGCCAC	61.396	63.158	4.39	0.00	0.00	5.01
8	9	2.046700	CGCTCTTAAACGGGGCCA	60.047	61.111	4.39	0.00	0.00	5.36
9	10	2.822701	CCGCTCTTAAACGGGGCC	60.823	66.667	0.00	0.00	45.74	5.80
24	25	4.159857	GCTCTAGTAAAGCGTGATATCCG	58.840	47.826	0.00	4.84	0.00	4.18
34	35	1.134788	TGCTTCCCGCTCTAGTAAAGC	60.135	52.381	0.00	0.00	39.55	3.51
35	36	2.961526	TGCTTCCCGCTCTAGTAAAG	57.038	50.000	0.00	0.00	40.11	1.85
36	37	3.196901	TGAATGCTTCCCGCTCTAGTAAA	59.803	43.478	0.00	0.00	40.11	2.01
37	38	2.764010	TGAATGCTTCCCGCTCTAGTAA	59.236	45.455	0.00	0.00	40.11	2.24
38	39	2.100916	GTGAATGCTTCCCGCTCTAGTA	59.899	50.000	0.00	0.00	40.11	1.82
39	40	1.134670	GTGAATGCTTCCCGCTCTAGT	60.135	52.381	0.00	0.00	40.11	2.57
40	41	1.134699	TGTGAATGCTTCCCGCTCTAG	60.135	52.381	0.00	0.00	40.11	2.43
41	42	0.901827	TGTGAATGCTTCCCGCTCTA	59.098	50.000	0.00	0.00	40.11	2.43
42	43	0.036732	TTGTGAATGCTTCCCGCTCT	59.963	50.000	0.00	0.00	40.11	4.09
43	44	1.098050	ATTGTGAATGCTTCCCGCTC	58.902	50.000	0.00	0.00	40.11	5.03
44	45	1.549203	AATTGTGAATGCTTCCCGCT	58.451	45.000	0.00	0.00	40.11	5.52
45	46	2.368655	AAATTGTGAATGCTTCCCGC	57.631	45.000	0.00	0.00	39.77	6.13
46	47	3.253230	GGAAAATTGTGAATGCTTCCCG	58.747	45.455	0.00	0.00	31.87	5.14
47	48	4.270245	TGGAAAATTGTGAATGCTTCCC	57.730	40.909	0.00	0.00	34.82	3.97
48	49	4.152938	GCTTGGAAAATTGTGAATGCTTCC	59.847	41.667	0.00	0.00	35.64	3.46
49	50	4.751098	TGCTTGGAAAATTGTGAATGCTTC	59.249	37.500	0.00	0.00	0.00	3.86
50	51	4.706035	TGCTTGGAAAATTGTGAATGCTT	58.294	34.783	0.00	0.00	0.00	3.91

Showing 1 to 25 of 377 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.