AutoCloner

Multiple sequence alignment - TraesCS3A01G061300

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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	TraesCS3A01G061300	chr3A	100.000	3329	0	0	1	3329	36653822	36650494	0.000000e+00	6148.0
1	TraesCS3A01G061300	chr3A	97.317	410	9	1	1	408	680297355	680297764	0.000000e+00	695.0
2	TraesCS3A01G061300	chr3A	96.970	33	1	0	1619	1651	36652153	36652121	4.640000e-04	56.5
3	TraesCS3A01G061300	chr3A	96.970	33	1	0	1670	1702	36652204	36652172	4.640000e-04	56.5
4	TraesCS3A01G061300	chr3B	92.328	1877	88	22	474	2320	44775035	44773185	0.000000e+00	2617.0
5	TraesCS3A01G061300	chr3B	96.970	33	1	0	1619	1651	44773832	44773800	4.640000e-04	56.5
6	TraesCS3A01G061300	chr3B	96.970	33	1	0	1670	1702	44773883	44773851	4.640000e-04	56.5
7	TraesCS3A01G061300	chr3D	91.096	1943	96	40	573	2476	26577677	26579581	0.000000e+00	2558.0
8	TraesCS3A01G061300	chr3D	92.715	151	7	4	2537	2686	26579589	26579736	7.230000e-52	215.0
9	TraesCS3A01G061300	chr3D	94.444	36	2	0	1667	1702	26578730	26578765	4.640000e-04	56.5
10	TraesCS3A01G061300	chr7A	97.317	410	9	1	1	408	140042616	140043025	0.000000e+00	695.0
11	TraesCS3A01G061300	chr7A	97.317	410	9	1	1	408	140062519	140062928	0.000000e+00	695.0
12	TraesCS3A01G061300	chr6A	97.317	410	9	1	1	408	498237173	498237582	0.000000e+00	695.0
13	TraesCS3A01G061300	chr6A	97.073	410	10	1	1	408	121990347	121989938	0.000000e+00	689.0
14	TraesCS3A01G061300	chr5A	97.317	410	9	1	1	408	577628645	577628236	0.000000e+00	695.0
15	TraesCS3A01G061300	chr4A	97.317	410	9	1	1	408	587296380	587296789	0.000000e+00	695.0
16	TraesCS3A01G061300	chr1A	97.073	410	10	1	1	408	430168880	430168471	0.000000e+00	689.0
17	TraesCS3A01G061300	chr1A	97.073	410	10	1	1	408	474956038	474955629	0.000000e+00	689.0
18	TraesCS3A01G061300	chr1A	80.539	334	56	3	1082	1406	24246754	24247087	7.130000e-62	248.0
19	TraesCS3A01G061300	chr1A	77.440	461	61	21	1847	2300	24247596	24248020	5.550000e-58	235.0
20	TraesCS3A01G061300	chr1D	80.236	339	56	6	1078	1406	22974516	22974853	9.230000e-61	244.0
21	TraesCS3A01G061300	chr1D	92.254	142	11	0	2158	2299	22975605	22975746	5.630000e-48	202.0
22	TraesCS3A01G061300	chr1B	77.751	418	49	25	1889	2299	39541587	39541967	2.010000e-52	217.0
23	TraesCS3A01G061300	chr1B	92.361	144	11	0	2158	2301	39543988	39544131	4.350000e-49	206.0

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	TraesCS3A01G061300	chr3A	36650494	36653822	3328	True	2087.000000	6148	97.980000	1	3329	3	chr3A.!!$R1	3328
1	TraesCS3A01G061300	chr3B	44773185	44775035	1850	True	910.000000	2617	95.422667	474	2320	3	chr3B.!!$R1	1846
2	TraesCS3A01G061300	chr3D	26577677	26579736	2059	False	943.166667	2558	92.751667	573	2686	3	chr3D.!!$F1	2113
3	TraesCS3A01G061300	chr1A	24246754	24248020	1266	False	241.500000	248	78.989500	1082	2300	2	chr1A.!!$F1	1218
4	TraesCS3A01G061300	chr1D	22974516	22975746	1230	False	223.000000	244	86.245000	1078	2299	2	chr1D.!!$F1	1221
5	TraesCS3A01G061300	chr1B	39541587	39544131	2544	False	211.500000	217	85.056000	1889	2301	2	chr1B.!!$F1	412

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
842	854	0.098376	CGGTTCCTACTTCCGAGTCG	59.902	60.0	5.29	5.29	46.05	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2766	4513	0.039256	CCAAATGGAGTTGTGCCACG	60.039	55.0	0.0	0.0	38.44	4.94	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
27	28	3.723348	GTGAAACTCGGTGGCGCC	61.723	66.667	22.73	22.73	0.00	6.53
37	38	4.038080	GTGGCGCCGGGTTGAAAG	62.038	66.667	23.90	0.00	0.00	2.62
38	39	4.257654	TGGCGCCGGGTTGAAAGA	62.258	61.111	23.90	0.00	0.00	2.52
39	40	2.981350	GGCGCCGGGTTGAAAGAA	60.981	61.111	12.58	0.00	0.00	2.52
40	41	2.340328	GGCGCCGGGTTGAAAGAAT	61.340	57.895	12.58	0.00	0.00	2.40
41	42	1.136774	GCGCCGGGTTGAAAGAATC	59.863	57.895	2.18	0.00	0.00	2.52
42	43	1.423845	CGCCGGGTTGAAAGAATCG	59.576	57.895	2.18	0.00	0.00	3.34
43	44	1.800681	GCCGGGTTGAAAGAATCGG	59.199	57.895	2.18	0.00	40.33	4.18
44	45	0.958876	GCCGGGTTGAAAGAATCGGT	60.959	55.000	2.18	0.00	39.64	4.69
45	46	1.676615	GCCGGGTTGAAAGAATCGGTA	60.677	52.381	2.18	0.00	39.64	4.02
46	47	2.277084	CCGGGTTGAAAGAATCGGTAG	58.723	52.381	0.00	0.00	33.63	3.18
47	48	2.277084	CGGGTTGAAAGAATCGGTAGG	58.723	52.381	0.00	0.00	0.00	3.18
48	49	2.640184	GGGTTGAAAGAATCGGTAGGG	58.360	52.381	0.00	0.00	0.00	3.53
49	50	2.014857	GGTTGAAAGAATCGGTAGGGC	58.985	52.381	0.00	0.00	0.00	5.19
50	51	2.014857	GTTGAAAGAATCGGTAGGGCC	58.985	52.381	0.00	0.00	0.00	5.80
66	67	4.174305	CCGAGTTTGGCTTTGGGT	57.826	55.556	0.00	0.00	0.00	4.51
67	68	2.425562	CCGAGTTTGGCTTTGGGTT	58.574	52.632	0.00	0.00	0.00	4.11
68	69	0.750249	CCGAGTTTGGCTTTGGGTTT	59.250	50.000	0.00	0.00	0.00	3.27
69	70	1.957877	CCGAGTTTGGCTTTGGGTTTA	59.042	47.619	0.00	0.00	0.00	2.01
70	71	2.030274	CCGAGTTTGGCTTTGGGTTTAG	60.030	50.000	0.00	0.00	0.00	1.85
71	72	2.030274	CGAGTTTGGCTTTGGGTTTAGG	60.030	50.000	0.00	0.00	0.00	2.69
72	73	2.963101	GAGTTTGGCTTTGGGTTTAGGT	59.037	45.455	0.00	0.00	0.00	3.08
73	74	2.963101	AGTTTGGCTTTGGGTTTAGGTC	59.037	45.455	0.00	0.00	0.00	3.85
74	75	2.696187	GTTTGGCTTTGGGTTTAGGTCA	59.304	45.455	0.00	0.00	0.00	4.02
75	76	2.757894	TGGCTTTGGGTTTAGGTCAA	57.242	45.000	0.00	0.00	0.00	3.18

Showing 1 to 25 of 698 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.123621	CACCGAGTTTCACTTGTCATAGC	59.876	47.826	0.00	0.00	0.00	2.97
1	2	3.679980	CCACCGAGTTTCACTTGTCATAG	59.320	47.826	0.00	0.00	0.00	2.23
2	3	3.659786	CCACCGAGTTTCACTTGTCATA	58.340	45.455	0.00	0.00	0.00	2.15
3	4	2.494059	CCACCGAGTTTCACTTGTCAT	58.506	47.619	0.00	0.00	0.00	3.06
4	5	1.948104	CCACCGAGTTTCACTTGTCA	58.052	50.000	0.00	0.00	0.00	3.58
5	6	0.586802	GCCACCGAGTTTCACTTGTC	59.413	55.000	0.00	0.00	0.00	3.18
6	7	1.157870	CGCCACCGAGTTTCACTTGT	61.158	55.000	0.00	0.00	36.29	3.16
7	8	1.569493	CGCCACCGAGTTTCACTTG	59.431	57.895	0.00	0.00	36.29	3.16
8	9	2.251642	GCGCCACCGAGTTTCACTT	61.252	57.895	0.00	0.00	36.29	3.16
9	10	2.665185	GCGCCACCGAGTTTCACT	60.665	61.111	0.00	0.00	36.29	3.41
10	11	3.723348	GGCGCCACCGAGTTTCAC	61.723	66.667	24.80	0.00	36.29	3.18
20	21	4.038080	CTTTCAACCCGGCGCCAC	62.038	66.667	28.98	0.00	0.00	5.01
21	22	3.776347	TTCTTTCAACCCGGCGCCA	62.776	57.895	28.98	1.46	0.00	5.69
22	23	2.266376	GATTCTTTCAACCCGGCGCC	62.266	60.000	19.07	19.07	0.00	6.53
23	24	1.136774	GATTCTTTCAACCCGGCGC	59.863	57.895	0.00	0.00	0.00	6.53
24	25	1.423845	CGATTCTTTCAACCCGGCG	59.576	57.895	0.00	0.00	0.00	6.46
25	26	0.958876	ACCGATTCTTTCAACCCGGC	60.959	55.000	0.00	0.00	40.48	6.13
26	27	2.277084	CTACCGATTCTTTCAACCCGG	58.723	52.381	0.00	0.00	42.30	5.73
27	28	2.277084	CCTACCGATTCTTTCAACCCG	58.723	52.381	0.00	0.00	0.00	5.28
28	29	2.640184	CCCTACCGATTCTTTCAACCC	58.360	52.381	0.00	0.00	0.00	4.11
29	30	2.014857	GCCCTACCGATTCTTTCAACC	58.985	52.381	0.00	0.00	0.00	3.77
30	31	2.014857	GGCCCTACCGATTCTTTCAAC	58.985	52.381	0.00	0.00	0.00	3.18
31	32	2.413310	GGCCCTACCGATTCTTTCAA	57.587	50.000	0.00	0.00	0.00	2.69
49	50	0.750249	AAACCCAAAGCCAAACTCGG	59.250	50.000	0.00	0.00	0.00	4.63
50	51	2.030274	CCTAAACCCAAAGCCAAACTCG	60.030	50.000	0.00	0.00	0.00	4.18

Showing 1 to 25 of 701 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.