AutoCloner

Multiple sequence alignment - TraesCS2D01G261100

Loading Multiple Alignment...

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	TraesCS2D01G261100	chr2D	100.000	3665	0	0	1	3665	317939748	317943412	0.000000e+00	6769.0
1	TraesCS2D01G261100	chr2D	86.441	531	44	9	1108	1631	610709438	610708929	1.150000e-154	556.0
2	TraesCS2D01G261100	chr2D	92.593	216	16	0	2158	2373	610707533	610707318	9.880000e-81	311.0
3	TraesCS2D01G261100	chr2D	92.810	153	9	1	2009	2161	610708860	610708710	1.710000e-53	220.0
4	TraesCS2D01G261100	chr2D	84.571	175	14	4	657	830	317886160	317886322	1.050000e-35	161.0
5	TraesCS2D01G261100	chr2D	94.595	37	2	0	2383	2419	12523826	12523790	1.420000e-04	58.4
6	TraesCS2D01G261100	chr2B	95.438	2784	81	16	895	3652	385560623	385563386	0.000000e+00	4396.0
7	TraesCS2D01G261100	chr2B	96.296	54	2	0	660	713	385560546	385560599	5.040000e-14	89.8
8	TraesCS2D01G261100	chr2B	97.778	45	1	0	572	616	385560490	385560534	1.090000e-10	78.7
9	TraesCS2D01G261100	chr2A	95.050	1919	62	13	895	2792	415063994	415062088	0.000000e+00	2987.0
10	TraesCS2D01G261100	chr2A	89.753	1698	122	22	1012	2665	750148206	750149895	0.000000e+00	2124.0
11	TraesCS2D01G261100	chr2A	93.252	904	40	6	2778	3665	414995404	414994506	0.000000e+00	1312.0
12	TraesCS2D01G261100	chr2A	93.651	63	4	0	655	717	415064494	415064432	1.080000e-15	95.3
13	TraesCS2D01G261100	chr7D	89.363	1711	108	26	1008	2677	498273474	498275151	0.000000e+00	2084.0
14	TraesCS2D01G261100	chr3B	90.761	368	28	5	5	369	727898311	727897947	1.530000e-133	486.0
15	TraesCS2D01G261100	chr3B	81.126	302	40	13	5	302	447228295	447228583	3.680000e-55	226.0
16	TraesCS2D01G261100	chr6D	88.040	301	30	4	5	302	8675955	8676252	5.820000e-93	351.0
17	TraesCS2D01G261100	chr6D	75.130	193	38	9	2225	2412	97520438	97520251	8.440000e-12	82.4
18	TraesCS2D01G261100	chr5D	76.480	625	110	28	1143	1741	472626965	472627578	4.600000e-79	305.0
19	TraesCS2D01G261100	chr5B	76.129	620	115	25	1143	1741	580073374	580073981	9.950000e-76	294.0
20	TraesCS2D01G261100	chr5B	75.446	505	105	15	2040	2539	579809563	579810053	1.020000e-55	228.0
21	TraesCS2D01G261100	chr1B	80.464	302	42	12	5	302	109427189	109427477	7.970000e-52	215.0
22	TraesCS2D01G261100	chrUn	93.421	76	3	1	5	80	321454679	321454752	1.080000e-20	111.0
23	TraesCS2D01G261100	chrUn	93.421	76	3	1	5	80	357695306	357695379	1.080000e-20	111.0
24	TraesCS2D01G261100	chrUn	77.368	190	37	6	2226	2412	293161351	293161165	1.390000e-19	108.0
25	TraesCS2D01G261100	chrUn	77.368	190	37	6	2226	2412	409868781	409868967	1.390000e-19	108.0
26	TraesCS2D01G261100	chr4A	93.421	76	3	1	5	80	698101976	698101903	1.080000e-20	111.0

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	TraesCS2D01G261100	chr2D	317939748	317943412	3664	False	6769.000000	6769	100.000000	1	3665	1	chr2D.!!$F2	3664
1	TraesCS2D01G261100	chr2D	610707318	610709438	2120	True	362.333333	556	90.614667	1108	2373	3	chr2D.!!$R2	1265
2	TraesCS2D01G261100	chr2B	385560490	385563386	2896	False	1521.500000	4396	96.504000	572	3652	3	chr2B.!!$F1	3080
3	TraesCS2D01G261100	chr2A	750148206	750149895	1689	False	2124.000000	2124	89.753000	1012	2665	1	chr2A.!!$F1	1653
4	TraesCS2D01G261100	chr2A	415062088	415064494	2406	True	1541.150000	2987	94.350500	655	2792	2	chr2A.!!$R2	2137
5	TraesCS2D01G261100	chr2A	414994506	414995404	898	True	1312.000000	1312	93.252000	2778	3665	1	chr2A.!!$R1	887
6	TraesCS2D01G261100	chr7D	498273474	498275151	1677	False	2084.000000	2084	89.363000	1008	2677	1	chr7D.!!$F1	1669
7	TraesCS2D01G261100	chr5D	472626965	472627578	613	False	305.000000	305	76.480000	1143	1741	1	chr5D.!!$F1	598
8	TraesCS2D01G261100	chr5B	580073374	580073981	607	False	294.000000	294	76.129000	1143	1741	1	chr5B.!!$F2	598

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
186	187	0.027979	ATGCATGTATGTTGCGTCGC	59.972	50.0	11.10	11.10	43.10	5.19	F
883	1201	0.034283	ACTACCTGAGAGGGACGACC	60.034	60.0	0.00	0.00	40.58	4.79	F
884	1202	0.034380	CTACCTGAGAGGGACGACCA	60.034	60.0	6.20	0.00	40.58	4.02	F
1962	2348	0.099613	CCGTGAGTCTCTGTCATCGG	59.900	60.0	0.65	2.85	34.56	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1959	2345	0.391130	CGGAGCTTGAATGGAACCGA	60.391	55.000	0.00	41.09	4.69	R
1960	2346	0.673644	ACGGAGCTTGAATGGAACCG	60.674	55.000	0.00	43.61	4.44	R
2228	3821	1.520120	CACAGCCGCATCGTCTCAT	60.520	57.895	0.00	0.00	2.90	R
3307	4923	1.803922	CGTGCAGATGTTCGCGGTA	60.804	57.895	6.13	33.14	4.02	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	End Stability
25	26	7.825681	TCACCTAAACCATATTGTGATTTGTG	58.174	34.615	0.00	0.00	3.33
26	27	7.667635	TCACCTAAACCATATTGTGATTTGTGA	59.332	33.333	0.00	0.00	3.58
27	28	8.303156	CACCTAAACCATATTGTGATTTGTGAA	58.697	33.333	0.00	0.00	3.18
28	29	9.034800	ACCTAAACCATATTGTGATTTGTGAAT	57.965	29.630	0.00	0.00	2.57
32	33	9.859427	AAACCATATTGTGATTTGTGAATAGTG	57.141	29.630	0.00	0.00	2.74
33	34	7.999679	ACCATATTGTGATTTGTGAATAGTGG	58.000	34.615	0.00	0.00	4.00
34	35	6.919662	CCATATTGTGATTTGTGAATAGTGGC	59.080	38.462	0.00	0.00	5.01
35	36	7.201848	CCATATTGTGATTTGTGAATAGTGGCT	60.202	37.037	0.00	0.00	4.75
36	37	5.375417	TTGTGATTTGTGAATAGTGGCTG	57.625	39.130	0.00	0.00	4.85
37	38	3.191162	TGTGATTTGTGAATAGTGGCTGC	59.809	43.478	0.00	0.00	5.25
38	39	2.754552	TGATTTGTGAATAGTGGCTGCC	59.245	45.455	12.87	12.87	4.85
39	40	2.584835	TTTGTGAATAGTGGCTGCCT	57.415	45.000	21.03	2.51	4.75
40	41	3.712016	TTTGTGAATAGTGGCTGCCTA	57.288	42.857	21.03	5.07	3.93
41	42	2.691409	TGTGAATAGTGGCTGCCTAC	57.309	50.000	21.03	15.64	3.18
42	43	1.209504	TGTGAATAGTGGCTGCCTACC	59.790	52.381	21.03	7.82	3.18
43	44	0.837272	TGAATAGTGGCTGCCTACCC	59.163	55.000	21.03	5.23	3.69
44	45	0.108774	GAATAGTGGCTGCCTACCCC	59.891	60.000	21.03	2.69	4.95
45	46	0.327576	AATAGTGGCTGCCTACCCCT	60.328	55.000	21.03	9.92	4.79
46	47	1.056700	ATAGTGGCTGCCTACCCCTG	61.057	60.000	21.03	0.00	4.45
47	48	2.176202	TAGTGGCTGCCTACCCCTGA	62.176	60.000	21.03	0.00	3.86
48	49	3.009115	TGGCTGCCTACCCCTGAC	61.009	66.667	21.03	0.00	3.51
49	50	2.689034	GGCTGCCTACCCCTGACT	60.689	66.667	12.43	0.00	3.41
50	51	1.382695	GGCTGCCTACCCCTGACTA	60.383	63.158	12.43	0.00	2.59
51	52	1.403687	GGCTGCCTACCCCTGACTAG	61.404	65.000	12.43	0.00	2.57
52	53	2.034048	GCTGCCTACCCCTGACTAGC	62.034	65.000	0.00	0.00	3.42

Showing 1 to 25 of 454 entries

Previous1 2 3 4 5…19Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
0	1	7.667635	TCACAAATCACAATATGGTTTAGGTGA	59.332	33.333	0.00	39.77	4.02
1	2	7.825681	TCACAAATCACAATATGGTTTAGGTG	58.174	34.615	0.00	39.77	4.00
2	3	8.415950	TTCACAAATCACAATATGGTTTAGGT	57.584	30.769	0.00	39.77	3.08
6	7	9.859427	CACTATTCACAAATCACAATATGGTTT	57.141	29.630	0.00	42.70	3.27
7	8	8.469200	CCACTATTCACAAATCACAATATGGTT	58.531	33.333	0.00	30.67	3.67
8	9	7.416664	GCCACTATTCACAAATCACAATATGGT	60.417	37.037	0.00	0.00	3.55
9	10	6.919662	GCCACTATTCACAAATCACAATATGG	59.080	38.462	0.00	0.00	2.74
10	11	7.646526	CAGCCACTATTCACAAATCACAATATG	59.353	37.037	0.00	0.00	1.78
11	12	7.682741	GCAGCCACTATTCACAAATCACAATAT	60.683	37.037	0.00	0.00	1.28
12	13	6.404623	GCAGCCACTATTCACAAATCACAATA	60.405	38.462	0.00	0.00	1.90
13	14	5.622914	GCAGCCACTATTCACAAATCACAAT	60.623	40.000	0.00	0.00	2.71
14	15	4.321156	GCAGCCACTATTCACAAATCACAA	60.321	41.667	0.00	0.00	3.33
15	16	3.191162	GCAGCCACTATTCACAAATCACA	59.809	43.478	0.00	0.00	3.58
16	17	3.428045	GGCAGCCACTATTCACAAATCAC	60.428	47.826	6.55	0.00	3.06
17	18	2.754552	GGCAGCCACTATTCACAAATCA	59.245	45.455	6.55	0.00	2.57
18	19	3.019564	AGGCAGCCACTATTCACAAATC	58.980	45.455	15.80	0.00	2.17
19	20	3.091633	AGGCAGCCACTATTCACAAAT	57.908	42.857	15.80	0.00	2.32
20	21	2.584835	AGGCAGCCACTATTCACAAA	57.415	45.000	15.80	0.00	2.83
21	22	2.355716	GGTAGGCAGCCACTATTCACAA	60.356	50.000	15.80	0.00	3.33
22	23	1.209504	GGTAGGCAGCCACTATTCACA	59.790	52.381	15.80	0.00	3.58
23	24	1.475213	GGGTAGGCAGCCACTATTCAC	60.475	57.143	15.80	42.27	3.18
24	25	0.837272	GGGTAGGCAGCCACTATTCA	59.163	55.000	15.80	42.27	2.57
25	26	0.108774	GGGGTAGGCAGCCACTATTC	59.891	60.000	15.80	44.67	1.75
26	27	0.327576	AGGGGTAGGCAGCCACTATT	60.328	55.000	15.80	44.67	1.73
27	28	1.056700	CAGGGGTAGGCAGCCACTAT	61.057	60.000	15.80	44.67	2.12

Showing 1 to 25 of 526 entries

Previous1 2 3 4 5…22Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.