AutoCloner

Multiple sequence alignment - TraesCS2A01G318900

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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	TraesCS2A01G318900	chr2A	100.000	2794	0	0	1	2794	544285260	544288053	0.000000e+00	5160.0
1	TraesCS2A01G318900	chr2A	88.889	108	11	1	2592	2698	202777919	202777812	6.280000e-27	132.0
2	TraesCS2A01G318900	chr2D	91.500	1353	88	17	926	2266	406140637	406141974	0.000000e+00	1836.0
3	TraesCS2A01G318900	chr2D	84.046	865	93	22	3	840	406139590	406140436	0.000000e+00	791.0
4	TraesCS2A01G318900	chr2D	88.983	118	7	4	2367	2478	406142077	406142194	1.040000e-29	141.0
5	TraesCS2A01G318900	chr2B	93.655	1182	47	15	926	2093	481628483	481629650	0.000000e+00	1742.0
6	TraesCS2A01G318900	chr2B	92.382	932	55	7	3	921	481627392	481628320	0.000000e+00	1314.0
7	TraesCS2A01G318900	chr2B	89.982	559	31	10	1544	2093	702206438	702206980	0.000000e+00	699.0
8	TraesCS2A01G318900	chr2B	92.955	440	22	6	1660	2096	128053630	128053197	1.410000e-177	632.0
9	TraesCS2A01G318900	chr3A	93.139	787	38	8	926	1703	611010337	611011116	0.000000e+00	1140.0
10	TraesCS2A01G318900	chr3A	92.476	319	13	4	611	921	611009857	611010172	1.970000e-121	446.0
11	TraesCS2A01G318900	chr3A	92.163	319	13	4	611	921	714222879	714223193	9.190000e-120	440.0
12	TraesCS2A01G318900	chr3A	89.796	98	10	0	2697	2794	57085308	57085211	2.920000e-25	126.0
13	TraesCS2A01G318900	chr3A	86.458	96	12	1	2695	2789	27543469	27543374	1.370000e-18	104.0
14	TraesCS2A01G318900	chr7A	93.011	787	39	8	926	1703	21043216	21042437	0.000000e+00	1134.0
15	TraesCS2A01G318900	chr7A	92.884	787	40	8	926	1703	688929556	688930335	0.000000e+00	1129.0
16	TraesCS2A01G318900	chr7A	89.655	377	14	13	553	921	688929052	688929411	9.120000e-125	457.0
17	TraesCS2A01G318900	chr7A	92.790	319	13	4	611	921	21043697	21043381	1.180000e-123	453.0
18	TraesCS2A01G318900	chr7A	89.815	108	10	1	2592	2698	36996007	36995900	1.350000e-28	137.0
19	TraesCS2A01G318900	chr7A	86.777	121	14	2	2583	2701	289141626	289141746	1.750000e-27	134.0
20	TraesCS2A01G318900	chr5A	93.011	787	39	8	926	1703	663200992	663201771	0.000000e+00	1134.0
21	TraesCS2A01G318900	chr5A	93.417	319	11	4	611	921	542385091	542385407	5.450000e-127	464.0
22	TraesCS2A01G318900	chr5A	92.790	319	12	4	611	921	4425176	4425491	4.240000e-123	451.0
23	TraesCS2A01G318900	chr5A	89.390	377	15	13	553	921	663200471	663200830	4.240000e-123	451.0
24	TraesCS2A01G318900	chr5A	88.976	381	17	13	553	925	100350019	100349656	5.490000e-122	448.0
25	TraesCS2A01G318900	chr5A	88.136	118	13	1	2583	2699	598668188	598668305	3.750000e-29	139.0
26	TraesCS2A01G318900	chr5A	88.991	109	9	3	2592	2698	396184860	396184753	6.280000e-27	132.0
27	TraesCS2A01G318900	chr5A	88.889	108	11	1	2592	2698	553144337	553144230	6.280000e-27	132.0
28	TraesCS2A01G318900	chr5A	86.869	99	12	1	2696	2794	410200380	410200477	2.940000e-20	110.0
29	TraesCS2A01G318900	chr5A	85.417	96	12	2	2696	2789	6718147	6718242	6.370000e-17	99.0
30	TraesCS2A01G318900	chr5A	84.000	100	13	3	2697	2794	438781205	438781107	2.960000e-15	93.5
31	TraesCS2A01G318900	chr6A	92.884	787	40	8	926	1703	562225389	562224610	0.000000e+00	1129.0
32	TraesCS2A01G318900	chr3B	92.748	786	41	8	926	1702	778355526	778354748	0.000000e+00	1122.0
33	TraesCS2A01G318900	chr3B	92.532	549	26	7	1557	2096	738051719	738051177	0.000000e+00	773.0
34	TraesCS2A01G318900	chrUn	92.630	787	42	8	926	1703	308011760	308010981	0.000000e+00	1118.0
35	TraesCS2A01G318900	chrUn	96.098	205	7	1	721	925	308012124	308011921	1.600000e-87	333.0
36	TraesCS2A01G318900	chrUn	96.098	205	7	1	721	925	308106821	308107024	1.600000e-87	333.0
37	TraesCS2A01G318900	chrUn	96.098	205	7	1	721	925	323644452	323644655	1.600000e-87	333.0
38	TraesCS2A01G318900	chrUn	87.719	114	13	1	2583	2695	32095259	32095372	6.280000e-27	132.0
39	TraesCS2A01G318900	chr7B	91.637	562	32	6	1544	2096	63964205	63963650	0.000000e+00	763.0
40	TraesCS2A01G318900	chr7B	83.810	105	13	4	2692	2793	715656423	715656526	2.290000e-16	97.1
41	TraesCS2A01G318900	chr1B	91.637	562	32	6	1544	2096	152576517	152575962	0.000000e+00	763.0
42	TraesCS2A01G318900	chr1B	93.000	500	25	7	1601	2096	569796601	569796108	0.000000e+00	721.0
43	TraesCS2A01G318900	chr1B	90.536	560	29	10	1544	2096	639385099	639384557	0.000000e+00	719.0
44	TraesCS2A01G318900	chr1B	88.776	98	10	1	2697	2794	306237353	306237449	4.890000e-23	119.0
45	TraesCS2A01G318900	chr1B	83.333	90	14	1	2178	2266	152575951	152575862	6.410000e-12	82.4
46	TraesCS2A01G318900	chr4A	93.417	319	11	4	611	921	644677445	644677761	5.450000e-127	464.0
47	TraesCS2A01G318900	chr4A	92.790	319	13	4	611	921	644725898	644726214	1.180000e-123	453.0
48	TraesCS2A01G318900	chr4A	87.719	114	13	1	2583	2695	429978680	429978793	6.280000e-27	132.0
49	TraesCS2A01G318900	chr4A	84.848	99	14	1	2697	2794	606528984	606529082	6.370000e-17	99.0
50	TraesCS2A01G318900	chr1A	88.596	114	12	1	2583	2695	28615987	28616100	1.350000e-28	137.0
51	TraesCS2A01G318900	chr1A	89.109	101	10	1	2695	2794	139632328	139632428	1.050000e-24	124.0

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	TraesCS2A01G318900	chr2A	544285260	544288053	2793	False	5160.000000	5160	100.000000	1	2794	1	chr2A.!!$F1	2793
1	TraesCS2A01G318900	chr2D	406139590	406142194	2604	False	922.666667	1836	88.176333	3	2478	3	chr2D.!!$F1	2475
2	TraesCS2A01G318900	chr2B	481627392	481629650	2258	False	1528.000000	1742	93.018500	3	2093	2	chr2B.!!$F2	2090
3	TraesCS2A01G318900	chr2B	702206438	702206980	542	False	699.000000	699	89.982000	1544	2093	1	chr2B.!!$F1	549
4	TraesCS2A01G318900	chr3A	611009857	611011116	1259	False	793.000000	1140	92.807500	611	1703	2	chr3A.!!$F2	1092
5	TraesCS2A01G318900	chr7A	21042437	21043697	1260	True	793.500000	1134	92.900500	611	1703	2	chr7A.!!$R2	1092
6	TraesCS2A01G318900	chr7A	688929052	688930335	1283	False	793.000000	1129	91.269500	553	1703	2	chr7A.!!$F2	1150
7	TraesCS2A01G318900	chr5A	663200471	663201771	1300	False	792.500000	1134	91.200500	553	1703	2	chr5A.!!$F6	1150
8	TraesCS2A01G318900	chr6A	562224610	562225389	779	True	1129.000000	1129	92.884000	926	1703	1	chr6A.!!$R1	777
9	TraesCS2A01G318900	chr3B	778354748	778355526	778	True	1122.000000	1122	92.748000	926	1702	1	chr3B.!!$R2	776
10	TraesCS2A01G318900	chr3B	738051177	738051719	542	True	773.000000	773	92.532000	1557	2096	1	chr3B.!!$R1	539
11	TraesCS2A01G318900	chrUn	308010981	308012124	1143	True	725.500000	1118	94.364000	721	1703	2	chrUn.!!$R1	982
12	TraesCS2A01G318900	chr7B	63963650	63964205	555	True	763.000000	763	91.637000	1544	2096	1	chr7B.!!$R1	552
13	TraesCS2A01G318900	chr1B	639384557	639385099	542	True	719.000000	719	90.536000	1544	2096	1	chr1B.!!$R2	552
14	TraesCS2A01G318900	chr1B	152575862	152576517	655	True	422.700000	763	87.485000	1544	2266	2	chr1B.!!$R3	722

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
138	142	1.210204	TCTGCTGGCCCCTCAAATCT	61.21	55.0	0.0	0.0	0.0	2.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1910	2150	0.526211	TGGCACAGAGTACGCTACTG	59.474	55.0	0.0	5.01	39.59	2.74	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	1.583054	ATGATTTCGCGTCTTAGCCC	58.417	50.000	5.77	0.00	0.00	5.19
39	40	4.437524	GCGTCTTAGCCCTCAAAAGAATTC	60.438	45.833	0.00	0.00	31.41	2.17
59	60	1.413382	CCGCAGATCTGTAGATTCGC	58.587	55.000	23.38	5.99	34.37	4.70
65	66	4.788690	CAGATCTGTAGATTCGCGTACAT	58.211	43.478	14.95	0.00	34.37	2.29
113	114	3.443329	TGTGCCATATTTGATTTGCGTCT	59.557	39.130	0.00	0.00	0.00	4.18
117	121	4.500477	GCCATATTTGATTTGCGTCTGTTC	59.500	41.667	0.00	0.00	0.00	3.18
138	142	1.210204	TCTGCTGGCCCCTCAAATCT	61.210	55.000	0.00	0.00	0.00	2.40
149	153	5.437060	GCCCCTCAAATCTGTAGTTTCATA	58.563	41.667	0.00	0.00	0.00	2.15
157	162	9.990360	TCAAATCTGTAGTTTCATAGTGTTACA	57.010	29.630	0.00	0.00	0.00	2.41
176	181	7.691050	GTGTTACAGTGGTATAAATTTCGCTTC	59.309	37.037	0.00	0.00	0.00	3.86
179	184	5.063060	ACAGTGGTATAAATTTCGCTTCGAC	59.937	40.000	0.00	0.00	34.89	4.20
186	191	8.545420	GGTATAAATTTCGCTTCGACTTATTGA	58.455	33.333	0.00	0.00	34.89	2.57
197	202	3.058085	TCGACTTATTGACGTGTGTGCTA	60.058	43.478	0.00	0.00	35.51	3.49
208	213	6.106003	TGACGTGTGTGCTATATCTTTTGAT	58.894	36.000	0.00	0.00	42.66	2.57
271	276	7.172190	GGTTGGTAGTTTCTTTTAGGACTGTAC	59.828	40.741	0.00	0.00	0.00	2.90
298	303	3.383825	GGAAAGAATTGGCATGAGCTCAT	59.616	43.478	23.75	23.75	41.70	2.90
300	305	5.278364	GGAAAGAATTGGCATGAGCTCATAG	60.278	44.000	28.27	21.64	41.70	2.23
387	400	7.538303	AATTTTGTTACTGTTTTGAGCTTGG	57.462	32.000	0.00	0.00	0.00	3.61
431	444	8.679725	AGTCTAGGTATCTGGGAATGATAGTAA	58.320	37.037	0.00	0.00	0.00	2.24
473	486	6.376018	ACTTGTCTACTCTGATAGTGGAAGTC	59.624	42.308	0.00	0.00	46.10	3.01
491	504	5.069516	GGAAGTCAATTGGGTGCATTGATAT	59.930	40.000	5.42	0.00	41.55	1.63
626	660	9.546909	CTTGTGATAAACTAAAAGCATACACAG	57.453	33.333	0.00	0.00	36.27	3.66
648	682	8.709386	ACAGATAACTATGTGAAGTTGATGTC	57.291	34.615	1.19	0.00	39.95	3.06
650	684	6.980978	AGATAACTATGTGAAGTTGATGTCCG	59.019	38.462	0.00	0.00	39.95	4.79
719	753	6.017400	TGCTATTTCTTTTCTTGCTTCTGG	57.983	37.500	0.00	0.00	0.00	3.86

Showing 1 to 25 of 283 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	5.994235	AAGACGCGAAATCATATATCGTC	57.006	39.130	15.93	11.03	43.30	4.20
1	2	5.512082	GCTAAGACGCGAAATCATATATCGT	59.488	40.000	15.93	0.00	38.75	3.73
15	16	0.721718	CTTTTGAGGGCTAAGACGCG	59.278	55.000	3.53	3.53	0.00	6.01
27	28	3.944015	AGATCTGCGGGAATTCTTTTGAG	59.056	43.478	5.23	0.00	0.00	3.02
39	40	1.932604	GCGAATCTACAGATCTGCGGG	60.933	57.143	22.83	12.46	32.75	6.13
65	66	4.877378	ACGAACTTGGGTACAACTATGA	57.123	40.909	0.00	0.00	32.14	2.15
113	114	2.202236	GAGGGGCCAGCAGATGAACA	62.202	60.000	4.39	0.00	0.00	3.18
117	121	0.396695	ATTTGAGGGGCCAGCAGATG	60.397	55.000	4.39	0.00	0.00	2.90
138	142	7.058023	ACCACTGTAACACTATGAAACTACA	57.942	36.000	0.00	0.00	0.00	2.74
149	153	6.877322	AGCGAAATTTATACCACTGTAACACT	59.123	34.615	0.00	0.00	0.00	3.55
157	162	5.416947	AGTCGAAGCGAAATTTATACCACT	58.583	37.500	0.00	0.00	37.72	4.00
176	181	2.058798	AGCACACACGTCAATAAGTCG	58.941	47.619	0.00	0.00	34.89	4.18
179	184	7.700322	AAGATATAGCACACACGTCAATAAG	57.300	36.000	0.00	0.00	0.00	1.73
186	191	6.106003	TCATCAAAAGATATAGCACACACGT	58.894	36.000	0.00	0.00	0.00	4.49
197	202	9.436957	ACGTTAGTTCAACTCATCAAAAGATAT	57.563	29.630	0.00	0.00	34.77	1.63
208	213	5.013568	TCTCCAAACGTTAGTTCAACTCA	57.986	39.130	0.00	0.00	40.18	3.41
219	224	4.630069	CAGATACCGAATTCTCCAAACGTT	59.370	41.667	3.52	0.00	0.00	3.99
220	225	4.181578	CAGATACCGAATTCTCCAAACGT	58.818	43.478	3.52	0.00	0.00	3.99
221	226	3.001330	GCAGATACCGAATTCTCCAAACG	59.999	47.826	3.52	0.00	0.00	3.60
271	276	2.230992	TCATGCCAATTCTTTCCAACCG	59.769	45.455	0.00	0.00	0.00	4.44
387	400	2.675348	GACTGCAGGTTGCTCTCAATAC	59.325	50.000	19.93	0.00	45.31	1.89
453	466	7.147828	CCAATTGACTTCCACTATCAGAGTAGA	60.148	40.741	7.12	0.00	35.64	2.59
473	486	6.593268	TCCATATATCAATGCACCCAATTG	57.407	37.500	0.00	0.00	0.00	2.32
491	504	2.092484	TGGCTATGCAACTGCTTCCATA	60.092	45.455	2.95	0.00	42.66	2.74
622	656	8.484641	ACATCAACTTCACATAGTTATCTGTG	57.515	34.615	0.00	0.00	43.24	3.66

Showing 1 to 25 of 276 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.