AutoCloner

Multiple sequence alignment - TraesCS2D01G192400

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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	TraesCS2D01G192400	chr2D	100.000	3155	0	0	1	3155	136516622	136513468	0.000000e+00	5827.0
1	TraesCS2D01G192400	chr2D	80.076	1320	160	59	893	2166	136523575	136522313	0.000000e+00	885.0
2	TraesCS2D01G192400	chr2D	96.721	427	14	0	2729	3155	607090817	607090391	0.000000e+00	712.0
3	TraesCS2D01G192400	chr2D	96.253	427	16	0	2729	3155	45120145	45119719	0.000000e+00	701.0
4	TraesCS2D01G192400	chr2D	96.253	427	16	0	2729	3155	138692473	138692047	0.000000e+00	701.0
5	TraesCS2D01G192400	chr2D	96.253	427	16	0	2729	3155	571775367	571774941	0.000000e+00	701.0
6	TraesCS2D01G192400	chr2D	83.768	690	63	28	890	1569	136634645	136633995	2.690000e-170	608.0
7	TraesCS2D01G192400	chr2D	79.534	772	75	45	1734	2484	136612184	136611475	1.020000e-129	473.0
8	TraesCS2D01G192400	chr2D	80.655	641	69	31	953	1569	136613001	136612392	2.230000e-121	446.0
9	TraesCS2D01G192400	chr2D	90.823	316	28	1	1	315	484044627	484044942	3.760000e-114	422.0
10	TraesCS2D01G192400	chr2D	81.261	571	55	24	890	1454	136651667	136651143	6.300000e-112	414.0
11	TraesCS2D01G192400	chr2D	83.447	441	43	19	944	1374	136608394	136607974	1.780000e-102	383.0
12	TraesCS2D01G192400	chr2D	73.907	732	128	39	1517	2232	136651058	136650374	5.260000e-58	235.0
13	TraesCS2D01G192400	chr2D	93.103	58	4	0	2189	2246	136525323	136525266	5.610000e-13	86.1
14	TraesCS2D01G192400	chr2B	89.386	1856	107	39	890	2703	194955075	194953268	0.000000e+00	2254.0
15	TraesCS2D01G192400	chr2B	87.633	469	37	14	314	764	194996618	194996153	2.790000e-145	525.0
16	TraesCS2D01G192400	chr2B	82.683	589	74	13	1706	2291	194997368	194996805	6.080000e-137	497.0
17	TraesCS2D01G192400	chr2B	80.153	655	81	27	951	1596	195060045	195059431	8.030000e-121	444.0
18	TraesCS2D01G192400	chr2B	81.570	586	56	20	1010	1569	195167856	195167297	1.340000e-118	436.0
19	TraesCS2D01G192400	chr2B	91.167	317	26	2	1	315	12022581	12022265	2.250000e-116	429.0
20	TraesCS2D01G192400	chr2B	74.518	726	136	33	1516	2231	195368004	195367318	1.440000e-68	270.0
21	TraesCS2D01G192400	chr2B	83.019	265	30	10	1423	1683	194997696	194997443	3.170000e-55	226.0
22	TraesCS2D01G192400	chr2B	83.436	163	16	7	577	731	194953225	194953066	1.180000e-29	141.0
23	TraesCS2D01G192400	chr1B	90.082	1593	91	31	893	2459	512051623	512053174	0.000000e+00	2004.0
24	TraesCS2D01G192400	chr1B	86.425	221	16	5	2497	2703	512053172	512053392	2.450000e-56	230.0
25	TraesCS2D01G192400	chr1B	84.375	160	17	6	577	731	512053439	512053595	1.960000e-32	150.0
26	TraesCS2D01G192400	chr2A	89.831	1593	94	32	893	2459	165104286	165105836	0.000000e+00	1982.0
27	TraesCS2D01G192400	chr2A	75.703	1387	211	74	890	2232	164866960	164868264	2.110000e-161	579.0
28	TraesCS2D01G192400	chr2A	79.210	962	97	51	1511	2449	165007071	165007952	9.820000e-160	573.0
29	TraesCS2D01G192400	chr2A	81.395	688	87	29	890	1566	164981210	164981867	1.000000e-144	523.0
30	TraesCS2D01G192400	chr2A	92.571	350	17	4	416	764	165008575	165008916	7.860000e-136	494.0
31	TraesCS2D01G192400	chr2A	83.755	474	44	21	1057	1515	164878033	164878488	4.870000e-113	418.0
32	TraesCS2D01G192400	chr2A	90.159	315	30	1	1	315	8366501	8366188	2.930000e-110	409.0
33	TraesCS2D01G192400	chr2A	82.628	449	59	15	1160	1595	164997836	164998278	2.300000e-101	379.0
34	TraesCS2D01G192400	chr2A	81.951	410	45	15	1734	2129	164982031	164982425	1.410000e-83	320.0
35	TraesCS2D01G192400	chr2A	77.719	570	73	35	1734	2282	164878668	164879204	1.840000e-77	300.0
36	TraesCS2D01G192400	chr2A	86.425	221	16	5	2497	2703	165105834	165106054	2.450000e-56	230.0
37	TraesCS2D01G192400	chr2A	90.909	110	8	1	314	421	165008305	165008414	2.540000e-31	147.0
38	TraesCS2D01G192400	chr2A	83.750	160	18	6	577	731	165106101	165106257	9.120000e-31	145.0
39	TraesCS2D01G192400	chr2A	83.766	154	11	5	890	1043	164999178	164999317	1.970000e-27	134.0
40	TraesCS2D01G192400	chr2A	92.188	64	1	2	890	952	164877463	164877523	1.560000e-13	87.9
41	TraesCS2D01G192400	chr1D	96.487	427	15	0	2729	3155	232434930	232434504	0.000000e+00	706.0
42	TraesCS2D01G192400	chr1D	96.487	427	15	0	2729	3155	421526955	421527381	0.000000e+00	706.0
43	TraesCS2D01G192400	chr1D	96.253	427	16	0	2729	3155	424929363	424928937	0.000000e+00	701.0
44	TraesCS2D01G192400	chr5D	96.253	427	16	0	2729	3155	286163363	286162937	0.000000e+00	701.0
45	TraesCS2D01G192400	chr3D	96.253	427	16	0	2729	3155	286226042	286226468	0.000000e+00	701.0
46	TraesCS2D01G192400	chr3D	92.381	315	24	0	1	315	457067227	457067541	1.730000e-122	449.0
47	TraesCS2D01G192400	chr3D	90.476	315	30	0	1	315	170706215	170705901	1.750000e-112	416.0
48	TraesCS2D01G192400	chr3A	92.405	316	21	2	1	315	267070381	267070068	6.210000e-122	448.0
49	TraesCS2D01G192400	chr7D	91.290	310	24	3	1	310	559399196	559398890	1.350000e-113	420.0
50	TraesCS2D01G192400	chr7D	100.000	31	0	0	2702	2732	88987855	88987825	1.220000e-04	58.4
51	TraesCS2D01G192400	chr4D	90.221	317	27	3	1	315	374302833	374302519	8.140000e-111	411.0
52	TraesCS2D01G192400	chr5A	89.937	318	29	3	1	315	44932413	44932730	1.050000e-109	407.0
53	TraesCS2D01G192400	chrUn	86.425	221	16	5	2497	2703	477031114	477030894	2.450000e-56	230.0
54	TraesCS2D01G192400	chrUn	84.932	219	11	9	893	1104	480490361	480490158	5.340000e-48	202.0
55	TraesCS2D01G192400	chrUn	90.476	84	3	4	577	657	477030847	477030766	4.300000e-19	106.0
56	TraesCS2D01G192400	chr3B	86.857	175	18	4	1511	1683	462061436	462061265	1.160000e-44	191.0
57	TraesCS2D01G192400	chr4A	100.000	31	0	0	2702	2732	696601592	696601562	1.220000e-04	58.4

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	TraesCS2D01G192400	chr2D	136513468	136516622	3154	True	5827.000000	5827	100.000000	1	3155	1	chr2D.!!$R2	3154
1	TraesCS2D01G192400	chr2D	136633995	136634645	650	True	608.000000	608	83.768000	890	1569	1	chr2D.!!$R3	679
2	TraesCS2D01G192400	chr2D	136522313	136525323	3010	True	485.550000	885	86.589500	893	2246	2	chr2D.!!$R7	1353
3	TraesCS2D01G192400	chr2D	136607974	136613001	5027	True	434.000000	473	81.212000	944	2484	3	chr2D.!!$R8	1540
4	TraesCS2D01G192400	chr2D	136650374	136651667	1293	True	324.500000	414	77.584000	890	2232	2	chr2D.!!$R9	1342
5	TraesCS2D01G192400	chr2B	194953066	194955075	2009	True	1197.500000	2254	86.411000	577	2703	2	chr2B.!!$R5	2126
6	TraesCS2D01G192400	chr2B	195059431	195060045	614	True	444.000000	444	80.153000	951	1596	1	chr2B.!!$R2	645
7	TraesCS2D01G192400	chr2B	195167297	195167856	559	True	436.000000	436	81.570000	1010	1569	1	chr2B.!!$R3	559
8	TraesCS2D01G192400	chr2B	194996153	194997696	1543	True	416.000000	525	84.445000	314	2291	3	chr2B.!!$R6	1977
9	TraesCS2D01G192400	chr2B	195367318	195368004	686	True	270.000000	270	74.518000	1516	2231	1	chr2B.!!$R4	715
10	TraesCS2D01G192400	chr1B	512051623	512053595	1972	False	794.666667	2004	86.960667	577	2703	3	chr1B.!!$F1	2126
11	TraesCS2D01G192400	chr2A	165104286	165106257	1971	False	785.666667	1982	86.668667	577	2703	3	chr2A.!!$F6	2126
12	TraesCS2D01G192400	chr2A	164866960	164868264	1304	False	579.000000	579	75.703000	890	2232	1	chr2A.!!$F1	1342
13	TraesCS2D01G192400	chr2A	164981210	164982425	1215	False	421.500000	523	81.673000	890	2129	2	chr2A.!!$F3	1239
14	TraesCS2D01G192400	chr2A	165007071	165008916	1845	False	404.666667	573	87.563333	314	2449	3	chr2A.!!$F5	2135
15	TraesCS2D01G192400	chr2A	164877463	164879204	1741	False	268.633333	418	84.554000	890	2282	3	chr2A.!!$F2	1392
16	TraesCS2D01G192400	chr2A	164997836	164999317	1481	False	256.500000	379	83.197000	890	1595	2	chr2A.!!$F4	705

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
245	246	0.032952	GGCCTCGGGGTTTGTTTTTC	59.967	55.0	1.62	0.0	34.45	2.29	F
683	684	0.036388	GCATCTTCCCGACTTGACCA	60.036	55.0	0.00	0.0	0.00	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1119	2479	0.166814	GCACTGGATGAAACAGCGAC	59.833	55.0	0.0	0.0	39.55	5.19	R
2356	4393	0.179029	ACCCCAACGGAACAAGACAG	60.179	55.0	0.0	0.0	34.64	3.51	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	4.994201	TCGTCGTGCACCTGCGTC	62.994	66.667	12.15	0.00	45.83	5.19
23	24	3.702555	GTGCACCTGCGTCGTGTC	61.703	66.667	5.22	0.00	45.83	3.67
24	25	3.911698	TGCACCTGCGTCGTGTCT	61.912	61.111	0.00	0.00	45.83	3.41
26	27	2.244651	GCACCTGCGTCGTGTCTTT	61.245	57.895	0.00	0.00	33.61	2.52
27	28	1.564622	CACCTGCGTCGTGTCTTTG	59.435	57.895	0.00	0.00	0.00	2.77
28	29	1.143183	ACCTGCGTCGTGTCTTTGT	59.857	52.632	0.00	0.00	0.00	2.83
29	30	0.461339	ACCTGCGTCGTGTCTTTGTT	60.461	50.000	0.00	0.00	0.00	2.83
30	31	0.042188	CCTGCGTCGTGTCTTTGTTG	60.042	55.000	0.00	0.00	0.00	3.33
31	32	0.927537	CTGCGTCGTGTCTTTGTTGA	59.072	50.000	0.00	0.00	0.00	3.18
33	34	1.326245	TGCGTCGTGTCTTTGTTGAAG	59.674	47.619	0.00	0.00	36.67	3.02
35	36	1.931172	CGTCGTGTCTTTGTTGAAGGT	59.069	47.619	0.00	0.00	35.98	3.50
37	38	2.933906	GTCGTGTCTTTGTTGAAGGTGA	59.066	45.455	0.00	0.00	35.98	4.02
38	39	3.560068	GTCGTGTCTTTGTTGAAGGTGAT	59.440	43.478	0.00	0.00	35.98	3.06
40	41	3.303990	CGTGTCTTTGTTGAAGGTGATGG	60.304	47.826	0.00	0.00	35.98	3.51
41	42	3.882888	GTGTCTTTGTTGAAGGTGATGGA	59.117	43.478	0.00	0.00	35.98	3.41
45	46	5.241506	GTCTTTGTTGAAGGTGATGGATTGA	59.758	40.000	0.00	0.00	35.98	2.57
46	47	5.832595	TCTTTGTTGAAGGTGATGGATTGAA	59.167	36.000	0.00	0.00	35.98	2.69
47	48	5.710513	TTGTTGAAGGTGATGGATTGAAG	57.289	39.130	0.00	0.00	0.00	3.02
48	49	3.507233	TGTTGAAGGTGATGGATTGAAGC	59.493	43.478	0.00	0.00	0.00	3.86
49	50	3.726557	TGAAGGTGATGGATTGAAGCT	57.273	42.857	0.00	0.00	0.00	3.74
52	53	4.219070	TGAAGGTGATGGATTGAAGCTTTG	59.781	41.667	0.00	0.00	30.95	2.77
54	55	2.494870	GGTGATGGATTGAAGCTTTGCT	59.505	45.455	0.00	0.00	42.56	3.91
64	65	3.772096	AGCTTTGCTTTGGGGATGA	57.228	47.368	0.00	0.00	33.89	2.92
65	66	1.553706	AGCTTTGCTTTGGGGATGAG	58.446	50.000	0.00	0.00	33.89	2.90
66	67	1.076024	AGCTTTGCTTTGGGGATGAGA	59.924	47.619	0.00	0.00	33.89	3.27

Showing 1 to 25 of 810 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	4.994201	GACGCAGGTGCACGACGA	62.994	66.667	25.19	0.00	42.21	4.20
6	7	3.702555	GACACGACGCAGGTGCAC	61.703	66.667	8.80	8.80	42.21	4.57
7	8	2.916502	AAAGACACGACGCAGGTGCA	62.917	55.000	2.33	0.00	42.21	4.57
9	10	1.151777	ACAAAGACACGACGCAGGTG	61.152	55.000	0.00	0.17	41.15	4.00
10	11	0.461339	AACAAAGACACGACGCAGGT	60.461	50.000	0.00	0.00	0.00	4.00
11	12	0.042188	CAACAAAGACACGACGCAGG	60.042	55.000	0.00	0.00	0.00	4.85
12	13	0.927537	TCAACAAAGACACGACGCAG	59.072	50.000	0.00	0.00	0.00	5.18
13	14	1.326245	CTTCAACAAAGACACGACGCA	59.674	47.619	0.00	0.00	37.12	5.24
14	15	1.332904	CCTTCAACAAAGACACGACGC	60.333	52.381	0.00	0.00	37.12	5.19
15	16	1.931172	ACCTTCAACAAAGACACGACG	59.069	47.619	0.00	0.00	37.12	5.12
16	17	2.933906	TCACCTTCAACAAAGACACGAC	59.066	45.455	0.00	0.00	37.12	4.34
18	19	3.303990	CCATCACCTTCAACAAAGACACG	60.304	47.826	0.00	0.00	37.12	4.49
19	20	3.882888	TCCATCACCTTCAACAAAGACAC	59.117	43.478	0.00	0.00	37.12	3.67
22	23	5.384336	TCAATCCATCACCTTCAACAAAGA	58.616	37.500	0.00	0.00	37.12	2.52
23	24	5.710513	TCAATCCATCACCTTCAACAAAG	57.289	39.130	0.00	0.00	34.52	2.77
24	25	5.509501	GCTTCAATCCATCACCTTCAACAAA	60.510	40.000	0.00	0.00	0.00	2.83
26	27	3.507233	GCTTCAATCCATCACCTTCAACA	59.493	43.478	0.00	0.00	0.00	3.33
27	28	3.760684	AGCTTCAATCCATCACCTTCAAC	59.239	43.478	0.00	0.00	0.00	3.18
28	29	4.038271	AGCTTCAATCCATCACCTTCAA	57.962	40.909	0.00	0.00	0.00	2.69
29	30	3.726557	AGCTTCAATCCATCACCTTCA	57.273	42.857	0.00	0.00	0.00	3.02
30	31	4.741342	CAAAGCTTCAATCCATCACCTTC	58.259	43.478	0.00	0.00	0.00	3.46
31	32	3.056322	GCAAAGCTTCAATCCATCACCTT	60.056	43.478	0.00	0.00	0.00	3.50
33	34	2.494870	AGCAAAGCTTCAATCCATCACC	59.505	45.455	0.00	0.00	33.89	4.02
46	47	1.076024	TCTCATCCCCAAAGCAAAGCT	59.924	47.619	0.00	0.00	42.56	3.74
47	48	1.549203	TCTCATCCCCAAAGCAAAGC	58.451	50.000	0.00	0.00	0.00	3.51

Showing 1 to 25 of 762 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.