AutoCloner

Multiple sequence alignment - TraesCS3B01G395300

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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	TraesCS3B01G395300	chr3B	100.000	9418	0	0	1	9418	622778781	622769364	0.000000e+00	17392.0
1	TraesCS3B01G395300	chr3B	94.680	2237	98	13	5722	7953	279642643	279644863	0.000000e+00	3452.0
2	TraesCS3B01G395300	chr3B	93.489	1459	73	11	4210	5658	279641196	279642642	0.000000e+00	2148.0
3	TraesCS3B01G395300	chr3B	83.025	972	133	20	4254	5202	672736145	672737107	0.000000e+00	852.0
4	TraesCS3B01G395300	chr3B	99.686	318	1	0	4209	4526	622771145	622770828	4.900000e-162	582.0
5	TraesCS3B01G395300	chr3B	99.686	318	1	0	7637	7954	622774573	622774256	4.900000e-162	582.0
6	TraesCS3B01G395300	chr3B	83.534	249	31	3	5171	5411	525629103	525629349	3.420000e-54	224.0
7	TraesCS3B01G395300	chr3B	77.419	155	33	2	4498	4651	525628637	525628790	3.620000e-14	91.6
8	TraesCS3B01G395300	chr5B	98.960	3749	32	2	4210	7952	403745673	403749420	0.000000e+00	6700.0
9	TraesCS3B01G395300	chr5B	98.738	317	4	0	7638	7954	403745673	403745989	1.780000e-156	564.0
10	TraesCS3B01G395300	chr5B	87.640	178	20	2	5227	5403	7050727	7050903	1.240000e-48	206.0
11	TraesCS3B01G395300	chr5B	95.349	129	5	1	459	586	684770831	684770703	4.460000e-48	204.0
12	TraesCS3B01G395300	chr6B	94.989	2235	93	11	5722	7952	625291646	625289427	0.000000e+00	3489.0
13	TraesCS3B01G395300	chr6B	93.283	1459	70	11	4210	5658	625293087	625291647	0.000000e+00	2126.0
14	TraesCS3B01G395300	chr6B	85.120	1539	199	28	6427	7952	143470530	143472051	0.000000e+00	1546.0
15	TraesCS3B01G395300	chr6B	82.449	1527	250	14	6110	7627	214886032	214887549	0.000000e+00	1319.0
16	TraesCS3B01G395300	chr3A	94.425	2009	56	17	741	2696	611205159	611203154	0.000000e+00	3038.0
17	TraesCS3B01G395300	chr3A	97.175	1522	41	1	2690	4209	611203083	611201562	0.000000e+00	2571.0
18	TraesCS3B01G395300	chr3A	95.291	1444	47	12	7984	9418	611200724	611199293	0.000000e+00	2270.0
19	TraesCS3B01G395300	chr3A	76.446	484	102	9	4418	4893	20306390	20306869	1.570000e-62	252.0
20	TraesCS3B01G395300	chr3A	92.073	164	10	3	456	617	719597950	719598112	2.650000e-55	228.0
21	TraesCS3B01G395300	chr3A	97.619	42	0	1	7953	7994	611201566	611201526	4.720000e-08	71.3
22	TraesCS3B01G395300	chr1B	94.202	1949	93	12	6009	7953	421536442	421534510	0.000000e+00	2955.0
23	TraesCS3B01G395300	chr1B	93.694	1459	71	10	4210	5658	421537895	421536448	0.000000e+00	2165.0
24	TraesCS3B01G395300	chr1B	86.008	243	32	2	5417	5659	449257090	449257330	9.380000e-65	259.0
25	TraesCS3B01G395300	chr3D	93.648	2015	56	13	722	2696	468979905	468977923	0.000000e+00	2946.0
26	TraesCS3B01G395300	chr3D	95.225	1445	59	8	7953	9389	468976220	468974778	0.000000e+00	2278.0
27	TraesCS3B01G395300	chr3D	96.746	799	23	1	2690	3488	468977855	468977060	0.000000e+00	1328.0
28	TraesCS3B01G395300	chr3D	94.467	723	20	2	3487	4209	468976918	468976216	0.000000e+00	1096.0
29	TraesCS3B01G395300	chr3D	82.828	297	40	6	4877	5170	335658220	335657932	1.210000e-63	255.0
30	TraesCS3B01G395300	chr3D	85.366	246	34	2	5417	5662	299095405	299095162	4.370000e-63	254.0
31	TraesCS3B01G395300	chr3D	81.818	297	42	6	4877	5170	335661877	335661590	1.220000e-58	239.0
32	TraesCS3B01G395300	chr3D	88.649	185	21	0	5227	5411	555442461	555442277	9.520000e-55	226.0
33	TraesCS3B01G395300	chr3D	87.978	183	22	0	5229	5411	555430183	555430001	5.730000e-52	217.0
34	TraesCS3B01G395300	chr7B	97.408	1582	12	3	4210	5785	3854035	3855593	0.000000e+00	2667.0
35	TraesCS3B01G395300	chr7B	98.423	951	14	1	7003	7953	3855694	3856643	0.000000e+00	1672.0
36	TraesCS3B01G395300	chr7B	99.054	317	3	0	4209	4525	3856327	3856643	3.820000e-158	569.0
37	TraesCS3B01G395300	chr7B	98.738	317	4	0	7638	7954	3854035	3854351	1.780000e-156	564.0
38	TraesCS3B01G395300	chr7B	94.304	158	8	1	460	616	80518111	80517954	3.400000e-59	241.0
39	TraesCS3B01G395300	chrUn	99.449	1270	7	0	5732	7001	417864695	417863426	0.000000e+00	2307.0
40	TraesCS3B01G395300	chr2A	79.835	1696	320	22	5940	7626	182301848	182300166	0.000000e+00	1218.0
41	TraesCS3B01G395300	chr4B	81.081	1332	237	14	6301	7626	14542605	14541283	0.000000e+00	1050.0
42	TraesCS3B01G395300	chr4D	85.199	831	111	10	4210	5034	44621934	44622758	0.000000e+00	843.0
43	TraesCS3B01G395300	chr4D	87.616	323	32	6	7638	7954	44621934	44622254	1.490000e-97	368.0
44	TraesCS3B01G395300	chr2B	96.933	163	4	1	455	616	46809617	46809779	1.210000e-68	272.0
45	TraesCS3B01G395300	chr2B	96.875	160	4	1	459	617	272676858	272677017	5.610000e-67	267.0
46	TraesCS3B01G395300	chr2B	96.732	153	4	1	463	614	798954282	798954130	4.370000e-63	254.0
47	TraesCS3B01G395300	chr2B	94.969	159	7	1	459	616	28263978	28264136	2.030000e-61	248.0
48	TraesCS3B01G395300	chr2D	96.273	161	5	1	459	618	58202360	58202200	7.250000e-66	263.0
49	TraesCS3B01G395300	chr6D	85.425	247	34	2	5417	5663	143480198	143480442	1.210000e-63	255.0

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	TraesCS3B01G395300	chr3B	622769364	622778781	9417	True	17392.000	17392	100.00000	1	9418	1	chr3B.!!$R1	9417
1	TraesCS3B01G395300	chr3B	279641196	279644863	3667	False	2800.000	3452	94.08450	4210	7953	2	chr3B.!!$F2	3743
2	TraesCS3B01G395300	chr3B	672736145	672737107	962	False	852.000	852	83.02500	4254	5202	1	chr3B.!!$F1	948
3	TraesCS3B01G395300	chr3B	622770828	622774573	3745	True	582.000	582	99.68600	4209	7954	2	chr3B.!!$R2	3745
4	TraesCS3B01G395300	chr5B	403745673	403749420	3747	False	3632.000	6700	98.84900	4210	7954	2	chr5B.!!$F2	3744
5	TraesCS3B01G395300	chr6B	625289427	625293087	3660	True	2807.500	3489	94.13600	4210	7952	2	chr6B.!!$R1	3742
6	TraesCS3B01G395300	chr6B	143470530	143472051	1521	False	1546.000	1546	85.12000	6427	7952	1	chr6B.!!$F1	1525
7	TraesCS3B01G395300	chr6B	214886032	214887549	1517	False	1319.000	1319	82.44900	6110	7627	1	chr6B.!!$F2	1517
8	TraesCS3B01G395300	chr3A	611199293	611205159	5866	True	1987.575	3038	96.12750	741	9418	4	chr3A.!!$R1	8677
9	TraesCS3B01G395300	chr1B	421534510	421537895	3385	True	2560.000	2955	93.94800	4210	7953	2	chr1B.!!$R1	3743
10	TraesCS3B01G395300	chr3D	468974778	468979905	5127	True	1912.000	2946	95.02150	722	9389	4	chr3D.!!$R5	8667
11	TraesCS3B01G395300	chr3D	335657932	335661877	3945	True	247.000	255	82.32300	4877	5170	2	chr3D.!!$R4	293
12	TraesCS3B01G395300	chr7B	3854035	3856643	2608	False	1368.000	2667	98.40575	4209	7954	4	chr7B.!!$F1	3745
13	TraesCS3B01G395300	chrUn	417863426	417864695	1269	True	2307.000	2307	99.44900	5732	7001	1	chrUn.!!$R1	1269
14	TraesCS3B01G395300	chr2A	182300166	182301848	1682	True	1218.000	1218	79.83500	5940	7626	1	chr2A.!!$R1	1686
15	TraesCS3B01G395300	chr4B	14541283	14542605	1322	True	1050.000	1050	81.08100	6301	7626	1	chr4B.!!$R1	1325
16	TraesCS3B01G395300	chr4D	44621934	44622758	824	False	605.500	843	86.40750	4210	7954	2	chr4D.!!$F1	3744

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
206	207	0.035439	ACTGTTGTCGCCCCCAATAG	60.035	55.000	0.00	0.0	37.16	1.73	F
1976	1994	0.032130	TCAGTGTCCAGAACGACAGC	59.968	55.000	0.00	0.0	43.26	4.40	F
2066	2107	0.542467	TTGTTGCTCCCATGGCATGT	60.542	50.000	24.80	0.0	39.54	3.21	F
2543	2630	0.613260	AACAAGCCGCACTATCTCCA	59.387	50.000	0.00	0.0	0.00	3.86	F
3868	4180	0.956633	AGGATGTGTTGCTGCACTTG	59.043	50.000	0.00	0.0	39.89	3.16	F
4205	4519	2.008242	TTTGCTGTATGTTTGGGGCT	57.992	45.000	0.00	0.0	0.00	5.19	F
7988	9156	1.692519	AGTTGACAAGCCGGTAGTCTT	59.307	47.619	19.01	5.6	33.56	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1981	1999	0.043637	TTTACCCCATCCGGTCCTCT	59.956	55.000	0.00	37.34	3.69	R
3805	4117	0.112218	TGTGCTTTGCCAGGGTACAT	59.888	50.000	0.00	0.00	2.29	R
3868	4180	2.480419	GAGAGAGAGAGAGAGCATACGC	59.520	54.545	0.00	38.99	4.42	R
4207	4521	1.116308	TGAGTCTGGGTCGTGACAAA	58.884	50.000	2.00	35.81	2.83	R
7988	9156	6.216801	ACTAACTGTTTGTACTGTGTGAGA	57.783	37.500	5.84	36.67	3.27	R
8282	9452	0.390340	CGCTTCTAACTCCAGCAGCA	60.390	55.000	0.00	34.88	4.41	R
9390	10570	0.179116	CTCTCGCAGCTACAGTGCAT	60.179	55.000	0.00	41.26	3.96	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	Self end TH	Hairpin	End Stability
19	20	2.175811	GGCGATGTTGTTGACGGC	59.824	61.111	0.00	0.00	42.98	5.68
20	21	2.202171	GCGATGTTGTTGACGGCG	60.202	61.111	4.80	4.80	0.00	6.46
22	23	1.129809	CGATGTTGTTGACGGCGAC	59.870	57.895	16.62	8.59	31.58	5.19
23	24	1.495951	GATGTTGTTGACGGCGACC	59.504	57.895	16.62	5.38	0.00	4.79
24	25	1.225376	GATGTTGTTGACGGCGACCA	61.225	55.000	16.62	8.43	0.00	4.02
25	26	1.227999	ATGTTGTTGACGGCGACCAG	61.228	55.000	16.62	0.00	0.00	4.00
26	27	1.593209	GTTGTTGACGGCGACCAGA	60.593	57.895	16.62	0.00	0.00	3.86
27	28	1.300620	TTGTTGACGGCGACCAGAG	60.301	57.895	16.62	0.00	0.00	3.35
28	29	2.023414	TTGTTGACGGCGACCAGAGT	62.023	55.000	16.62	0.00	0.00	3.24
29	30	1.174078	TGTTGACGGCGACCAGAGTA	61.174	55.000	16.62	0.00	0.00	2.59
32	33	0.963856	TGACGGCGACCAGAGTACAT	60.964	55.000	16.62	0.00	0.00	2.29
34	35	1.248785	ACGGCGACCAGAGTACATGT	61.249	55.000	16.62	2.69	0.00	3.21
35	36	0.802222	CGGCGACCAGAGTACATGTG	60.802	60.000	9.11	0.00	0.00	3.21
36	37	1.084370	GGCGACCAGAGTACATGTGC	61.084	60.000	9.11	7.34	0.00	4.57
37	38	1.413767	GCGACCAGAGTACATGTGCG	61.414	60.000	9.11	0.00	0.00	5.34
39	40	1.202302	CGACCAGAGTACATGTGCGAT	60.202	52.381	9.11	0.00	0.00	4.58
41	42	1.824852	ACCAGAGTACATGTGCGATGA	59.175	47.619	18.25	0.00	0.00	2.92
42	43	2.159184	ACCAGAGTACATGTGCGATGAG	60.159	50.000	18.25	12.46	0.00	2.90
44	45	2.099756	CAGAGTACATGTGCGATGAGGA	59.900	50.000	9.11	0.00	0.00	3.71
45	46	2.760650	AGAGTACATGTGCGATGAGGAA	59.239	45.455	9.11	0.00	0.00	3.36
46	47	2.860735	GAGTACATGTGCGATGAGGAAC	59.139	50.000	9.11	0.00	0.00	3.62
48	49	0.740868	ACATGTGCGATGAGGAACGG	60.741	55.000	0.00	0.00	0.00	4.44
49	50	1.153369	ATGTGCGATGAGGAACGGG	60.153	57.895	0.00	0.00	0.00	5.28
50	51	3.195698	GTGCGATGAGGAACGGGC	61.196	66.667	0.00	0.00	0.00	6.13
54	55	4.508128	GATGAGGAACGGGCGCGA	62.508	66.667	30.98	6.28	0.00	5.87

Showing 1 to 25 of 378 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self end TH	Hairpin	End Stability
1	2	2.325082	GCCGTCAACAACATCGCCT	61.325	57.895	0.00	0.00	5.52
2	3	2.175811	GCCGTCAACAACATCGCC	59.824	61.111	0.00	0.00	5.54
3	4	2.202171	CGCCGTCAACAACATCGC	60.202	61.111	0.00	0.00	4.58
4	5	1.129809	GTCGCCGTCAACAACATCG	59.870	57.895	0.00	0.00	3.84
5	6	1.225376	TGGTCGCCGTCAACAACATC	61.225	55.000	0.00	0.00	3.06
8	9	1.557443	CTCTGGTCGCCGTCAACAAC	61.557	60.000	0.00	0.00	3.32
11	12	0.731855	GTACTCTGGTCGCCGTCAAC	60.732	60.000	0.00	0.00	3.18
13	14	0.963856	ATGTACTCTGGTCGCCGTCA	60.964	55.000	0.00	0.00	4.35
14	15	0.525668	CATGTACTCTGGTCGCCGTC	60.526	60.000	0.00	0.00	4.79
16	17	0.802222	CACATGTACTCTGGTCGCCG	60.802	60.000	0.00	0.00	6.46
17	18	1.084370	GCACATGTACTCTGGTCGCC	61.084	60.000	0.00	0.00	5.54
19	20	0.170339	TCGCACATGTACTCTGGTCG	59.830	55.000	1.01	0.00	4.79
20	21	2.159240	TCATCGCACATGTACTCTGGTC	60.159	50.000	0.00	0.00	4.02
22	23	2.467838	CTCATCGCACATGTACTCTGG	58.532	52.381	0.00	0.00	3.86
23	24	2.099756	TCCTCATCGCACATGTACTCTG	59.900	50.000	0.00	0.00	3.35
24	25	2.379005	TCCTCATCGCACATGTACTCT	58.621	47.619	0.00	0.00	3.24
25	26	2.860735	GTTCCTCATCGCACATGTACTC	59.139	50.000	0.00	0.00	2.59
26	27	2.735444	CGTTCCTCATCGCACATGTACT	60.735	50.000	0.00	0.00	2.73
27	28	1.588404	CGTTCCTCATCGCACATGTAC	59.412	52.381	0.00	0.00	2.90
28	29	1.470805	CCGTTCCTCATCGCACATGTA	60.471	52.381	0.00	0.00	2.29
29	30	0.740868	CCGTTCCTCATCGCACATGT	60.741	55.000	0.00	0.00	3.21
32	33	2.264480	CCCGTTCCTCATCGCACA	59.736	61.111	0.00	0.00	4.57
34	35	4.812476	CGCCCGTTCCTCATCGCA	62.812	66.667	0.00	0.00	5.10
37	38	4.508128	TCGCGCCCGTTCCTCATC	62.508	66.667	0.00	35.54	2.92
56	57	1.291132	GACTATGGTGAGCCTTTCGC	58.709	55.000	0.00	35.27	4.70

Showing 1 to 25 of 383 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.