AutoCloner

Multiple sequence alignment - TraesCS2D01G475500

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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	TraesCS2D01G475500	chr2D	100.000	5096	0	0	1	5096	577830672	577825577	0.000000e+00	9411.0
1	TraesCS2D01G475500	chr2D	82.279	1676	245	34	1038	2687	578307430	578309079	0.000000e+00	1402.0
2	TraesCS2D01G475500	chr2D	81.143	1575	221	39	1038	2578	578040819	578042351	0.000000e+00	1194.0
3	TraesCS2D01G475500	chr2D	80.404	1434	216	30	1032	2451	577581919	577580537	0.000000e+00	1031.0
4	TraesCS2D01G475500	chr2D	78.322	1716	267	74	1026	2680	577802859	577801188	0.000000e+00	1011.0
5	TraesCS2D01G475500	chr2D	78.981	1237	209	26	1227	2451	577440842	577442039	0.000000e+00	797.0
6	TraesCS2D01G475500	chr2D	81.734	646	96	13	1038	1672	578312714	578313348	2.100000e-143	520.0
7	TraesCS2D01G475500	chr2D	96.629	89	2	1	4751	4839	577825835	577825748	4.110000e-31	147.0
8	TraesCS2D01G475500	chr2D	96.629	89	2	1	4838	4925	577825922	577825834	4.110000e-31	147.0
9	TraesCS2D01G475500	chr2D	88.136	118	11	3	2717	2832	268894351	268894467	2.470000e-28	137.0
10	TraesCS2D01G475500	chr2A	92.552	1893	98	27	692	2580	715967527	715965674	0.000000e+00	2675.0
11	TraesCS2D01G475500	chr2A	94.508	965	40	5	3007	3967	715964233	715963278	0.000000e+00	1476.0
12	TraesCS2D01G475500	chr2A	82.635	1670	229	36	1020	2658	716163628	716165267	0.000000e+00	1421.0
13	TraesCS2D01G475500	chr2A	79.779	1449	222	41	1026	2451	715951234	715949834	0.000000e+00	987.0
14	TraesCS2D01G475500	chr2A	92.217	424	21	1	2589	3000	715965583	715965160	1.580000e-164	590.0
15	TraesCS2D01G475500	chr2A	89.003	291	25	5	4549	4839	715962778	715962495	2.260000e-93	353.0
16	TraesCS2D01G475500	chr2A	86.395	294	24	7	3996	4284	715963210	715962928	1.780000e-79	307.0
17	TraesCS2D01G475500	chr2A	88.136	118	12	2	2717	2833	161944741	161944625	6.880000e-29	139.0
18	TraesCS2D01G475500	chr2A	77.559	254	27	15	4449	4678	715947894	715947647	5.360000e-25	126.0
19	TraesCS2D01G475500	chr2B	93.165	1785	79	18	806	2580	695440131	695438380	0.000000e+00	2580.0
20	TraesCS2D01G475500	chr2B	95.987	897	30	1	1005	1901	695414361	695413471	0.000000e+00	1452.0
21	TraesCS2D01G475500	chr2B	84.846	1399	174	20	1038	2414	695508138	695509520	0.000000e+00	1375.0
22	TraesCS2D01G475500	chr2B	93.985	665	32	6	3007	3668	296067386	296066727	0.000000e+00	1000.0
23	TraesCS2D01G475500	chr2B	79.736	1441	221	36	1032	2451	695106851	695108241	0.000000e+00	977.0
24	TraesCS2D01G475500	chr2B	94.028	653	26	5	1928	2580	695412333	695411694	0.000000e+00	977.0
25	TraesCS2D01G475500	chr2B	92.180	601	38	6	3369	3967	695436639	695436046	0.000000e+00	841.0
26	TraesCS2D01G475500	chr2B	95.405	457	21	0	3024	3480	695410264	695409808	0.000000e+00	728.0
27	TraesCS2D01G475500	chr2B	84.429	700	79	19	3694	4381	695409802	695409121	0.000000e+00	662.0
28	TraesCS2D01G475500	chr2B	90.762	433	25	7	2581	3000	695411638	695411208	9.580000e-157	564.0
29	TraesCS2D01G475500	chr2B	90.762	433	25	7	2581	3000	695438324	695437894	9.580000e-157	564.0
30	TraesCS2D01G475500	chr2B	94.493	345	19	0	3024	3368	695436951	695436607	2.700000e-147	532.0
31	TraesCS2D01G475500	chr2B	84.638	345	47	4	3025	3365	695515278	695515620	6.320000e-89	339.0
32	TraesCS2D01G475500	chr2B	87.037	270	26	5	4549	4818	695408867	695408607	3.860000e-76	296.0
33	TraesCS2D01G475500	chr2B	87.597	258	26	5	4129	4381	695435802	695435546	1.390000e-75	294.0
34	TraesCS2D01G475500	chr2B	88.953	172	18	1	4838	5008	695435013	695434842	1.440000e-50	211.0
35	TraesCS2D01G475500	chr2B	87.778	180	11	2	3665	3834	296066648	296066470	3.110000e-47	200.0
36	TraesCS2D01G475500	chr2B	79.801	302	33	16	4396	4678	695376899	695376607	1.450000e-45	195.0
37	TraesCS2D01G475500	chr2B	83.981	206	27	6	4645	4849	695435115	695434915	5.210000e-45	193.0
38	TraesCS2D01G475500	chr2B	76.263	396	54	23	97	487	695440665	695440305	1.890000e-39	174.0
39	TraesCS2D01G475500	chr2B	90.226	133	9	3	3996	4128	695435981	695435853	2.440000e-38	171.0
40	TraesCS2D01G475500	chr2B	93.878	98	6	0	4549	4646	695435373	695435276	1.140000e-31	148.0
41	TraesCS2D01G475500	chr2B	81.875	160	16	6	152	308	695416584	695416435	6.930000e-24	122.0
42	TraesCS2D01G475500	chr2B	90.909	66	5	1	4838	4902	695408674	695408609	2.530000e-13	87.9
43	TraesCS2D01G475500	chr7B	92.840	838	49	2	3007	3834	511462113	511461277	0.000000e+00	1205.0
44	TraesCS2D01G475500	chr7A	92.363	838	43	7	3007	3834	299568522	299567696	0.000000e+00	1173.0
45	TraesCS2D01G475500	chr7A	92.243	838	43	8	3007	3834	296604328	296605153	0.000000e+00	1168.0
46	TraesCS2D01G475500	chr7A	91.647	838	49	10	3007	3834	305708842	305708016	0.000000e+00	1140.0
47	TraesCS2D01G475500	chr3A	90.766	444	31	1	3401	3834	71265643	71266086	7.350000e-163	584.0
48	TraesCS2D01G475500	chrUn	93.897	213	13	0	2581	2793	476501723	476501935	6.360000e-84	322.0
49	TraesCS2D01G475500	chrUn	91.566	166	6	2	2415	2580	476501510	476501667	6.640000e-54	222.0
50	TraesCS2D01G475500	chr3B	91.346	104	8	1	2724	2826	440886205	440886308	1.910000e-29	141.0
51	TraesCS2D01G475500	chr4D	88.785	107	11	1	2725	2830	12445259	12445153	4.140000e-26	130.0
52	TraesCS2D01G475500	chr3D	84.874	119	16	2	2717	2833	168853024	168852906	8.960000e-23	119.0

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	TraesCS2D01G475500	chr2D	577825577	577830672	5095	True	9411.0000	9411	100.0000	1	5096	1	chr2D.!!$R3	5095
1	TraesCS2D01G475500	chr2D	578040819	578042351	1532	False	1194.0000	1194	81.1430	1038	2578	1	chr2D.!!$F3	1540
2	TraesCS2D01G475500	chr2D	577580537	577581919	1382	True	1031.0000	1031	80.4040	1032	2451	1	chr2D.!!$R1	1419
3	TraesCS2D01G475500	chr2D	577801188	577802859	1671	True	1011.0000	1011	78.3220	1026	2680	1	chr2D.!!$R2	1654
4	TraesCS2D01G475500	chr2D	578307430	578313348	5918	False	961.0000	1402	82.0065	1038	2687	2	chr2D.!!$F4	1649
5	TraesCS2D01G475500	chr2D	577440842	577442039	1197	False	797.0000	797	78.9810	1227	2451	1	chr2D.!!$F2	1224
6	TraesCS2D01G475500	chr2A	716163628	716165267	1639	False	1421.0000	1421	82.6350	1020	2658	1	chr2A.!!$F1	1638
7	TraesCS2D01G475500	chr2A	715962495	715967527	5032	True	1080.2000	2675	90.9350	692	4839	5	chr2A.!!$R3	4147
8	TraesCS2D01G475500	chr2A	715947647	715951234	3587	True	556.5000	987	78.6690	1026	4678	2	chr2A.!!$R2	3652
9	TraesCS2D01G475500	chr2B	695508138	695509520	1382	False	1375.0000	1375	84.8460	1038	2414	1	chr2B.!!$F2	1376
10	TraesCS2D01G475500	chr2B	695106851	695108241	1390	False	977.0000	977	79.7360	1032	2451	1	chr2B.!!$F1	1419
11	TraesCS2D01G475500	chr2B	695408607	695416584	7977	True	611.1125	1452	90.0540	152	4902	8	chr2B.!!$R3	4750
12	TraesCS2D01G475500	chr2B	296066470	296067386	916	True	600.0000	1000	90.8815	3007	3834	2	chr2B.!!$R2	827
13	TraesCS2D01G475500	chr2B	695434842	695440665	5823	True	570.8000	2580	89.1498	97	5008	10	chr2B.!!$R4	4911
14	TraesCS2D01G475500	chr7B	511461277	511462113	836	True	1205.0000	1205	92.8400	3007	3834	1	chr7B.!!$R1	827
15	TraesCS2D01G475500	chr7A	299567696	299568522	826	True	1173.0000	1173	92.3630	3007	3834	1	chr7A.!!$R1	827
16	TraesCS2D01G475500	chr7A	296604328	296605153	825	False	1168.0000	1168	92.2430	3007	3834	1	chr7A.!!$F1	827
17	TraesCS2D01G475500	chr7A	305708016	305708842	826	True	1140.0000	1140	91.6470	3007	3834	1	chr7A.!!$R2	827

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
36	37	0.096628	GTCGAGATGCTGCAGCTTTG	59.903	55.000	36.61	24.59	42.66	2.77	F
83	84	0.543749	CCATGGTCAACTCCTCCTCC	59.456	60.000	2.57	0.00	0.00	4.30	F
84	85	0.543749	CATGGTCAACTCCTCCTCCC	59.456	60.000	0.00	0.00	0.00	4.30	F
1097	2631	0.759436	ATACCCTAGACCACCCGCTG	60.759	60.000	0.00	0.00	0.00	5.18	F
2198	4887	0.524862	CAGAAAGCGAATTGGCTGCT	59.475	50.000	16.19	13.08	43.93	4.24	F
2769	5708	2.076863	GCAAGGAAAGACTGCGTACAT	58.923	47.619	0.00	0.00	0.00	2.29	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1587	3156	0.725686	CGAGTAGTCGTGACGGACAT	59.274	55.000	11.92	0.0	41.57	3.06	R
2030	4710	3.244814	GTCATAAGCTGCACTGAGAATCG	59.755	47.826	1.02	0.0	38.61	3.34	R
2031	4711	3.244814	CGTCATAAGCTGCACTGAGAATC	59.755	47.826	1.02	0.0	0.00	2.52	R
3000	7287	0.246635	CTCCGTCCCGAATTCAGTGT	59.753	55.000	6.22	0.0	0.00	3.55	R
3001	7288	0.460284	CCTCCGTCCCGAATTCAGTG	60.460	60.000	6.22	0.0	0.00	3.66	R
4523	10285	0.179062	CTGTCTACTGCTCCCCATGC	60.179	60.000	0.00	0.0	0.00	4.06	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
18	19	3.317449	GCCTTTCAGTACCCGTTGT	57.683	52.632	0.00	0.00	0.00	3.32
19	20	1.154197	GCCTTTCAGTACCCGTTGTC	58.846	55.000	0.00	0.00	0.00	3.18
20	21	1.425412	CCTTTCAGTACCCGTTGTCG	58.575	55.000	0.00	0.00	0.00	4.35
21	22	1.000060	CCTTTCAGTACCCGTTGTCGA	60.000	52.381	0.00	0.00	39.71	4.20
22	23	2.325761	CTTTCAGTACCCGTTGTCGAG	58.674	52.381	0.00	0.00	39.71	4.04
23	24	1.608055	TTCAGTACCCGTTGTCGAGA	58.392	50.000	0.00	0.00	39.71	4.04
24	25	1.830279	TCAGTACCCGTTGTCGAGAT	58.170	50.000	0.00	0.00	39.71	2.75
25	26	1.471287	TCAGTACCCGTTGTCGAGATG	59.529	52.381	0.00	0.00	39.71	2.90
26	27	0.172803	AGTACCCGTTGTCGAGATGC	59.827	55.000	0.00	0.00	39.71	3.91
27	28	0.172803	GTACCCGTTGTCGAGATGCT	59.827	55.000	0.00	0.00	39.71	3.79
28	29	0.172578	TACCCGTTGTCGAGATGCTG	59.827	55.000	0.00	0.00	39.71	4.41
29	30	2.456119	CCCGTTGTCGAGATGCTGC	61.456	63.158	0.00	0.00	39.71	5.25
30	31	1.737735	CCGTTGTCGAGATGCTGCA	60.738	57.895	4.13	4.13	39.71	4.41
31	32	1.690283	CCGTTGTCGAGATGCTGCAG	61.690	60.000	10.11	10.11	39.71	4.41
32	33	1.423056	GTTGTCGAGATGCTGCAGC	59.577	57.895	31.89	31.89	42.50	5.25
33	34	1.018226	GTTGTCGAGATGCTGCAGCT	61.018	55.000	36.61	21.67	42.66	4.24
34	35	0.321034	TTGTCGAGATGCTGCAGCTT	60.321	50.000	36.61	31.25	42.66	3.74
35	36	0.321034	TGTCGAGATGCTGCAGCTTT	60.321	50.000	36.61	25.01	42.66	3.51
36	37	0.096628	GTCGAGATGCTGCAGCTTTG	59.903	55.000	36.61	24.59	42.66	2.77
37	38	1.226323	CGAGATGCTGCAGCTTTGC	60.226	57.895	36.61	23.68	42.66	3.68
38	39	1.226323	GAGATGCTGCAGCTTTGCG	60.226	57.895	36.61	0.70	42.66	4.85
39	40	2.202570	GATGCTGCAGCTTTGCGG	60.203	61.111	36.61	2.45	43.64	5.69
40	41	3.695022	GATGCTGCAGCTTTGCGGG	62.695	63.158	36.61	0.00	41.25	6.13
47	48	3.958860	AGCTTTGCGGGCTGACCT	61.959	61.111	0.00	0.00	38.73	3.85
48	49	2.985847	GCTTTGCGGGCTGACCTT	60.986	61.111	0.00	0.00	36.97	3.50

Showing 1 to 25 of 300 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	1.608055	TCTCGACAACGGGTACTGAA	58.392	50.000	0.00	0.00	41.23	3.02
5	6	1.471287	CATCTCGACAACGGGTACTGA	59.529	52.381	0.00	0.00	41.23	3.41
6	7	1.909376	CATCTCGACAACGGGTACTG	58.091	55.000	0.00	0.00	41.23	2.74
7	8	0.172803	GCATCTCGACAACGGGTACT	59.827	55.000	0.00	0.00	41.23	2.73
8	9	0.172803	AGCATCTCGACAACGGGTAC	59.827	55.000	0.00	0.00	41.23	3.34
9	10	0.172578	CAGCATCTCGACAACGGGTA	59.827	55.000	0.00	0.00	41.23	3.69
10	11	1.079819	CAGCATCTCGACAACGGGT	60.080	57.895	0.00	0.00	41.23	5.28
11	12	2.456119	GCAGCATCTCGACAACGGG	61.456	63.158	0.00	0.00	41.91	5.28
12	13	1.690283	CTGCAGCATCTCGACAACGG	61.690	60.000	0.00	0.00	40.21	4.44
13	14	1.706301	CTGCAGCATCTCGACAACG	59.294	57.895	0.00	0.00	41.26	4.10
14	15	1.018226	AGCTGCAGCATCTCGACAAC	61.018	55.000	38.24	6.46	45.16	3.32
15	16	0.321034	AAGCTGCAGCATCTCGACAA	60.321	50.000	38.24	0.00	45.16	3.18
16	17	0.321034	AAAGCTGCAGCATCTCGACA	60.321	50.000	38.24	0.00	45.16	4.35
17	18	0.096628	CAAAGCTGCAGCATCTCGAC	59.903	55.000	38.24	8.57	45.16	4.20
18	19	2.463592	CAAAGCTGCAGCATCTCGA	58.536	52.632	38.24	0.00	45.16	4.04
30	31	3.497884	AAGGTCAGCCCGCAAAGCT	62.498	57.895	0.00	0.00	42.70	3.74
31	32	2.982744	GAAGGTCAGCCCGCAAAGC	61.983	63.158	0.00	0.00	38.74	3.51
32	33	1.301677	GAGAAGGTCAGCCCGCAAAG	61.302	60.000	0.00	0.00	38.74	2.77
33	34	1.302511	GAGAAGGTCAGCCCGCAAA	60.303	57.895	0.00	0.00	38.74	3.68
34	35	1.768684	AAGAGAAGGTCAGCCCGCAA	61.769	55.000	0.00	0.00	38.74	4.85
35	36	2.172483	GAAGAGAAGGTCAGCCCGCA	62.172	60.000	0.00	0.00	38.74	5.69
36	37	1.448717	GAAGAGAAGGTCAGCCCGC	60.449	63.158	0.00	0.00	38.74	6.13
37	38	1.475403	TAGAAGAGAAGGTCAGCCCG	58.525	55.000	0.00	0.00	38.74	6.13
38	39	3.181459	GGATTAGAAGAGAAGGTCAGCCC	60.181	52.174	0.00	0.00	34.57	5.19
39	40	3.709141	AGGATTAGAAGAGAAGGTCAGCC	59.291	47.826	0.00	0.00	0.00	4.85

Showing 1 to 25 of 293 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.