AutoCloner

Multiple sequence alignment - TraesCS4A01G023600

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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	TraesCS4A01G023600	chr4A	100.000	3011	0	0	1	3011	16960085	16957075	0.000000e+00	5561.0
1	TraesCS4A01G023600	chr4A	93.627	659	36	4	131	787	733340225	733340879	0.000000e+00	979.0
2	TraesCS4A01G023600	chr4A	93.151	657	40	3	133	787	661815876	661815223	0.000000e+00	959.0
3	TraesCS4A01G023600	chr4D	95.814	1314	40	6	867	2170	450016076	450017384	0.000000e+00	2108.0
4	TraesCS4A01G023600	chr4D	98.333	60	1	0	49	108	450013599	450013658	4.110000e-19	106.0
5	TraesCS4A01G023600	chr4D	97.674	43	1	0	824	866	450015877	450015919	1.160000e-09	75.0
6	TraesCS4A01G023600	chr2B	93.902	656	36	2	133	787	95792990	95792338	0.000000e+00	987.0
7	TraesCS4A01G023600	chr2B	89.711	311	32	0	2701	3011	110030746	110030436	6.050000e-107	398.0
8	TraesCS4A01G023600	chr1B	93.303	657	39	3	133	787	57805676	57805023	0.000000e+00	965.0
9	TraesCS4A01G023600	chr2D	93.041	661	42	2	128	787	62068112	62067455	0.000000e+00	963.0
10	TraesCS4A01G023600	chr2D	87.333	300	34	3	2712	3011	143480643	143480348	1.030000e-89	340.0
11	TraesCS4A01G023600	chr2D	86.230	305	39	2	2701	3005	484970556	484970857	8.050000e-86	327.0
12	TraesCS4A01G023600	chr5D	93.041	661	41	3	130	788	472425795	472426452	0.000000e+00	961.0
13	TraesCS4A01G023600	chr5A	93.051	662	39	5	129	787	580517822	580517165	0.000000e+00	961.0
14	TraesCS4A01G023600	chrUn	92.793	666	43	3	124	787	68800599	68801261	0.000000e+00	959.0
15	TraesCS4A01G023600	chr6B	93.140	656	41	2	133	787	151215845	151215193	0.000000e+00	959.0
16	TraesCS4A01G023600	chr7A	78.281	861	152	23	1134	1981	612976362	612975524	3.440000e-144	521.0
17	TraesCS4A01G023600	chr7A	85.804	317	39	3	2700	3010	671710491	671710807	6.220000e-87	331.0
18	TraesCS4A01G023600	chr7A	75.610	369	72	16	1019	1380	659429224	659428867	1.860000e-37	167.0
19	TraesCS4A01G023600	chr7A	94.444	54	3	0	1	54	731038755	731038702	1.920000e-12	84.2
20	TraesCS4A01G023600	chr7A	94.118	51	3	0	1	51	700267846	700267896	8.950000e-11	78.7
21	TraesCS4A01G023600	chr7A	94.118	51	3	0	1	51	731043516	731043466	8.950000e-11	78.7
22	TraesCS4A01G023600	chr3D	92.283	311	20	3	2699	3005	33197348	33197658	3.560000e-119	438.0
23	TraesCS4A01G023600	chr3D	77.493	351	55	18	1131	1478	600179358	600179029	3.960000e-44	189.0
24	TraesCS4A01G023600	chr7D	89.655	319	31	2	2690	3008	597502299	597502615	3.610000e-109	405.0
25	TraesCS4A01G023600	chr7D	74.775	888	159	40	1131	1981	570653393	570652534	3.720000e-89	339.0
26	TraesCS4A01G023600	chr7B	74.126	1001	192	50	1022	1981	626183780	626182806	4.780000e-93	351.0
27	TraesCS4A01G023600	chr7B	76.888	662	121	22	1336	1981	573133448	573132803	2.220000e-91	346.0
28	TraesCS4A01G023600	chr7B	80.132	302	56	4	2694	2994	443330786	443330488	3.910000e-54	222.0
29	TraesCS4A01G023600	chr7B	92.958	71	5	0	1134	1204	573140414	573140344	1.480000e-18	104.0
30	TraesCS4A01G023600	chr5B	89.224	232	23	2	2700	2930	478319405	478319175	3.800000e-74	289.0
31	TraesCS4A01G023600	chr6D	82.315	311	55	0	2701	3011	1617154	1616844	1.380000e-68	270.0
32	TraesCS4A01G023600	chr3B	76.570	414	70	20	1071	1478	807358016	807357624	5.090000e-48	202.0
33	TraesCS4A01G023600	chr3A	98.000	50	1	0	1	50	698714616	698714567	1.490000e-13	87.9
34	TraesCS4A01G023600	chr3A	96.078	51	2	0	1	51	37996865	37996915	1.920000e-12	84.2
35	TraesCS4A01G023600	chr3A	96.078	51	2	0	1	51	698719448	698719398	1.920000e-12	84.2
36	TraesCS4A01G023600	chr3A	96.000	50	2	0	1	50	38012060	38012109	6.920000e-12	82.4
37	TraesCS4A01G023600	chr1A	96.078	51	2	0	1	51	24798856	24798906	1.920000e-12	84.2
38	TraesCS4A01G023600	chr1A	96.078	51	2	0	1	51	77061626	77061676	1.920000e-12	84.2

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	TraesCS4A01G023600	chr4A	16957075	16960085	3010	True	5561	5561	100.000000	1	3011	1	chr4A.!!$R1	3010
1	TraesCS4A01G023600	chr4A	733340225	733340879	654	False	979	979	93.627000	131	787	1	chr4A.!!$F1	656
2	TraesCS4A01G023600	chr4A	661815223	661815876	653	True	959	959	93.151000	133	787	1	chr4A.!!$R2	654
3	TraesCS4A01G023600	chr4D	450013599	450017384	3785	False	763	2108	97.273667	49	2170	3	chr4D.!!$F1	2121
4	TraesCS4A01G023600	chr2B	95792338	95792990	652	True	987	987	93.902000	133	787	1	chr2B.!!$R1	654
5	TraesCS4A01G023600	chr1B	57805023	57805676	653	True	965	965	93.303000	133	787	1	chr1B.!!$R1	654
6	TraesCS4A01G023600	chr2D	62067455	62068112	657	True	963	963	93.041000	128	787	1	chr2D.!!$R1	659
7	TraesCS4A01G023600	chr5D	472425795	472426452	657	False	961	961	93.041000	130	788	1	chr5D.!!$F1	658
8	TraesCS4A01G023600	chr5A	580517165	580517822	657	True	961	961	93.051000	129	787	1	chr5A.!!$R1	658
9	TraesCS4A01G023600	chrUn	68800599	68801261	662	False	959	959	92.793000	124	787	1	chrUn.!!$F1	663
10	TraesCS4A01G023600	chr6B	151215193	151215845	652	True	959	959	93.140000	133	787	1	chr6B.!!$R1	654
11	TraesCS4A01G023600	chr7A	612975524	612976362	838	True	521	521	78.281000	1134	1981	1	chr7A.!!$R1	847
12	TraesCS4A01G023600	chr7D	570652534	570653393	859	True	339	339	74.775000	1131	1981	1	chr7D.!!$R1	850
13	TraesCS4A01G023600	chr7B	626182806	626183780	974	True	351	351	74.126000	1022	1981	1	chr7B.!!$R4	959
14	TraesCS4A01G023600	chr7B	573132803	573133448	645	True	346	346	76.888000	1336	1981	1	chr7B.!!$R2	645

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
973	2778	0.10576	TGCACCAGGAAACCCACAAT	60.106	50.0	0.0	0.0	0.0	2.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2237	4106	0.032952	CCCAAACCGAAGTCAGACGA	59.967	55.0	0.0	0.0	0.0	4.2	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	Hairpin	End Stability
33	34	8.450578	TCAGGTTAATTGAATATAGTTGCAGG	57.549	34.615	0.00	4.85
34	35	8.271458	TCAGGTTAATTGAATATAGTTGCAGGA	58.729	33.333	0.00	3.86
35	36	8.345565	CAGGTTAATTGAATATAGTTGCAGGAC	58.654	37.037	0.00	3.85
36	37	8.052748	AGGTTAATTGAATATAGTTGCAGGACA	58.947	33.333	0.00	4.02
37	38	8.129211	GGTTAATTGAATATAGTTGCAGGACAC	58.871	37.037	0.00	3.67
38	39	8.673711	GTTAATTGAATATAGTTGCAGGACACA	58.326	33.333	0.00	3.72
39	40	7.886629	AATTGAATATAGTTGCAGGACACAT	57.113	32.000	0.00	3.21
40	41	8.978874	AATTGAATATAGTTGCAGGACACATA	57.021	30.769	0.00	2.29
41	42	8.978874	ATTGAATATAGTTGCAGGACACATAA	57.021	30.769	0.00	1.90
42	43	8.978874	TTGAATATAGTTGCAGGACACATAAT	57.021	30.769	0.00	1.28
43	44	8.978874	TGAATATAGTTGCAGGACACATAATT	57.021	30.769	0.00	1.40
44	45	9.056005	TGAATATAGTTGCAGGACACATAATTC	57.944	33.333	0.00	2.17
45	46	9.277783	GAATATAGTTGCAGGACACATAATTCT	57.722	33.333	0.00	2.40
115	116	8.707938	AAAAGCATATTCTCATAAAAGTTGGC	57.292	30.769	0.00	4.52
284	1400	1.609841	GGGAGGGTTCCGTTGTTAGTG	60.610	57.143	45.04	2.74
337	1453	0.169230	CTCAGGAAGACGAGACGGTG	59.831	60.000	0.00	4.94
338	1454	1.213013	CAGGAAGACGAGACGGTGG	59.787	63.158	0.00	4.61
393	1527	1.076777	CCTAGTCCCCGTTCCGGTA	60.077	63.158	46.80	4.02
404	1538	0.807496	GTTCCGGTAGTGCGTCTAGT	59.193	55.000	0.00	2.57
494	2142	5.321516	GTTGTGGTTCGTCTATATTTGTGC	58.678	41.667	0.00	4.57
566	2214	0.107410	TTGTTCTGGTGCGTTGGTCT	60.107	50.000	0.00	3.85
649	2298	2.692368	GGGAGGGGTGATGAGGCA	60.692	66.667	0.00	4.75
660	2309	0.390340	GATGAGGCAGCACGTCTTCA	60.390	55.000	37.32	3.02
661	2310	0.671781	ATGAGGCAGCACGTCTTCAC	60.672	55.000	34.19	3.18
687	2336	3.909776	TTCAGTGATTGTAGTCGTCGT	57.090	42.857	0.00	4.34

Showing 1 to 25 of 581 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	8.902806	CCTGCAACTATATTCAATTAACCTGAA	58.097	33.333	4.71	4.71	37.22	3.02
8	9	8.271458	TCCTGCAACTATATTCAATTAACCTGA	58.729	33.333	0.00	0.00	0.00	3.86
9	10	8.345565	GTCCTGCAACTATATTCAATTAACCTG	58.654	37.037	0.00	0.00	0.00	4.00
10	11	8.052748	TGTCCTGCAACTATATTCAATTAACCT	58.947	33.333	0.00	0.00	0.00	3.50
11	12	8.129211	GTGTCCTGCAACTATATTCAATTAACC	58.871	37.037	0.00	0.00	0.00	2.85
12	13	8.673711	TGTGTCCTGCAACTATATTCAATTAAC	58.326	33.333	0.00	0.00	0.00	2.01
13	14	8.800370	TGTGTCCTGCAACTATATTCAATTAA	57.200	30.769	0.00	0.00	0.00	1.40
14	15	8.978874	ATGTGTCCTGCAACTATATTCAATTA	57.021	30.769	0.00	0.00	0.00	1.40
15	16	7.886629	ATGTGTCCTGCAACTATATTCAATT	57.113	32.000	0.00	0.00	0.00	2.32
16	17	8.978874	TTATGTGTCCTGCAACTATATTCAAT	57.021	30.769	0.00	0.00	0.00	2.57
17	18	8.978874	ATTATGTGTCCTGCAACTATATTCAA	57.021	30.769	0.00	0.00	0.00	2.69
18	19	8.978874	AATTATGTGTCCTGCAACTATATTCA	57.021	30.769	0.00	0.00	0.00	2.57
19	20	9.277783	AGAATTATGTGTCCTGCAACTATATTC	57.722	33.333	0.00	0.00	0.00	1.75
22	23	9.542462	GTTAGAATTATGTGTCCTGCAACTATA	57.458	33.333	0.00	0.00	0.00	1.31
23	24	8.046708	TGTTAGAATTATGTGTCCTGCAACTAT	58.953	33.333	0.00	0.00	0.00	2.12
24	25	7.390823	TGTTAGAATTATGTGTCCTGCAACTA	58.609	34.615	0.00	0.00	0.00	2.24
25	26	6.237901	TGTTAGAATTATGTGTCCTGCAACT	58.762	36.000	0.00	0.00	0.00	3.16
26	27	6.494893	TGTTAGAATTATGTGTCCTGCAAC	57.505	37.500	0.00	0.00	0.00	4.17
27	28	8.800370	TTATGTTAGAATTATGTGTCCTGCAA	57.200	30.769	0.00	0.00	0.00	4.08
28	29	8.673711	GTTTATGTTAGAATTATGTGTCCTGCA	58.326	33.333	0.00	0.00	0.00	4.41
29	30	8.893727	AGTTTATGTTAGAATTATGTGTCCTGC	58.106	33.333	0.00	0.00	0.00	4.85
46	47	8.723311	CCATCAAATTTGCATGAAGTTTATGTT	58.277	29.630	21.91	0.00	0.00	2.71
47	48	7.148373	GCCATCAAATTTGCATGAAGTTTATGT	60.148	33.333	21.91	0.00	0.00	2.29
59	60	3.985019	ATTCAGGCCATCAAATTTGCA	57.015	38.095	13.54	3.26	0.00	4.08
108	109	4.013728	TCCTGCGTTTATTATGCCAACTT	58.986	39.130	0.00	0.00	38.02	2.66

Showing 1 to 25 of 579 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.