AutoCloner

Multiple sequence alignment - TraesCS2D01G440900

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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	TraesCS2D01G440900	chr2D	100.000	3512	0	0	1	3512	551210322	551213833	0.000000e+00	6486.0
1	TraesCS2D01G440900	chr2D	81.643	572	93	10	190	753	559121681	559121114	6.870000e-127	464.0
2	TraesCS2D01G440900	chr2D	83.636	275	35	6	2826	3094	645666083	645666353	2.090000e-62	250.0
3	TraesCS2D01G440900	chr2D	82.909	275	37	6	2826	3094	543288427	543288157	4.530000e-59	239.0
4	TraesCS2D01G440900	chr2D	90.604	149	14	0	3364	3512	580234459	580234311	7.690000e-47	198.0
5	TraesCS2D01G440900	chr2A	92.821	2535	157	20	829	3344	692229689	692232217	0.000000e+00	3650.0
6	TraesCS2D01G440900	chr2A	90.156	833	61	6	1	813	692210546	692211377	0.000000e+00	1064.0
7	TraesCS2D01G440900	chr2A	82.909	275	37	6	2826	3094	26932898	26933168	4.530000e-59	239.0
8	TraesCS2D01G440900	chr2A	84.772	197	15	10	976	1168	692207298	692207483	2.150000e-42	183.0
9	TraesCS2D01G440900	chr2A	84.659	176	26	1	3337	3511	777533580	777533405	1.300000e-39	174.0
10	TraesCS2D01G440900	chr2B	93.689	1933	99	16	857	2781	656511307	656513224	0.000000e+00	2872.0
11	TraesCS2D01G440900	chr2B	92.810	153	8	2	1	150	656510944	656511096	5.900000e-53	219.0
12	TraesCS2D01G440900	chr2B	83.237	173	29	0	3340	3512	693065871	693066043	3.630000e-35	159.0
13	TraesCS2D01G440900	chr2B	82.857	140	13	10	968	1102	656377815	656377948	7.970000e-22	115.0
14	TraesCS2D01G440900	chr2B	88.571	70	4	3	788	855	183313709	183313776	8.080000e-12	82.4
15	TraesCS2D01G440900	chr2B	100.000	32	0	0	3289	3320	744198126	744198095	3.790000e-05	60.2
16	TraesCS2D01G440900	chr7B	83.160	576	82	13	183	754	665287631	665287067	2.420000e-141	512.0
17	TraesCS2D01G440900	chr7A	80.717	586	101	9	175	751	518646068	518646650	2.490000e-121	446.0
18	TraesCS2D01G440900	chr7A	82.545	275	40	4	2827	3094	510900972	510901245	5.860000e-58	235.0
19	TraesCS2D01G440900	chr3D	81.559	526	90	4	213	735	142634328	142633807	9.010000e-116	427.0
20	TraesCS2D01G440900	chr3D	82.609	276	36	8	2826	3094	56362308	56362578	2.110000e-57	233.0
21	TraesCS2D01G440900	chr3D	94.737	38	2	0	3284	3321	475554026	475553989	3.790000e-05	60.2
22	TraesCS2D01G440900	chr3D	100.000	28	0	0	3294	3321	393648332	393648305	6.000000e-03	52.8
23	TraesCS2D01G440900	chr1B	80.783	562	91	7	193	753	341935431	341934886	1.170000e-114	424.0
24	TraesCS2D01G440900	chr1B	82.386	176	30	1	3337	3511	465362242	465362417	6.070000e-33	152.0
25	TraesCS2D01G440900	chr3B	82.222	495	83	5	187	678	204378169	204377677	4.190000e-114	422.0
26	TraesCS2D01G440900	chr3B	82.909	275	37	6	2826	3094	792853608	792853338	4.530000e-59	239.0
27	TraesCS2D01G440900	chr3B	83.051	177	29	1	3337	3512	732945478	732945654	3.630000e-35	159.0
28	TraesCS2D01G440900	chr3B	100.000	28	0	0	3292	3319	818938442	818938469	6.000000e-03	52.8
29	TraesCS2D01G440900	chr5D	81.928	498	75	12	200	691	472371895	472371407	1.170000e-109	407.0
30	TraesCS2D01G440900	chr5B	82.303	469	75	6	263	729	705828554	705829016	1.960000e-107	399.0
31	TraesCS2D01G440900	chr5B	81.757	148	17	3	751	896	478519924	478519785	7.970000e-22	115.0
32	TraesCS2D01G440900	chr6A	78.853	558	89	16	196	752	552582725	552583254	2.010000e-92	350.0
33	TraesCS2D01G440900	chr6A	83.051	177	27	3	3337	3511	232331237	232331062	1.310000e-34	158.0
34	TraesCS2D01G440900	chr4A	72.218	1285	275	67	1197	2440	572302359	572303602	1.570000e-83	320.0
35	TraesCS2D01G440900	chr4A	77.419	465	94	6	211	666	661590972	661590510	2.080000e-67	267.0
36	TraesCS2D01G440900	chr4A	82.909	275	37	6	2826	3094	69305824	69306094	4.530000e-59	239.0
37	TraesCS2D01G440900	chr4A	82.877	146	15	5	753	896	454761433	454761296	4.760000e-24	122.0
38	TraesCS2D01G440900	chr6B	81.390	403	61	8	350	751	610011313	610011702	2.030000e-82	316.0
39	TraesCS2D01G440900	chr4D	75.513	682	116	38	1163	1820	464234941	464235595	1.600000e-73	287.0
40	TraesCS2D01G440900	chr4D	81.944	144	16	5	753	894	63144414	63144279	2.870000e-21	113.0
41	TraesCS2D01G440900	chr4D	91.667	48	4	0	3284	3331	421524605	421524558	2.260000e-07	67.6
42	TraesCS2D01G440900	chr4B	75.403	683	117	41	1162	1820	580385065	580385720	2.060000e-72	283.0
43	TraesCS2D01G440900	chr4B	82.418	91	10	3	2357	2441	608262012	608261922	1.350000e-09	75.0
44	TraesCS2D01G440900	chr7D	83.273	275	36	6	2826	3094	162984968	162984698	9.740000e-61	244.0
45	TraesCS2D01G440900	chr7D	87.273	55	7	0	3284	3338	204115895	204115949	2.930000e-06	63.9
46	TraesCS2D01G440900	chr7D	89.583	48	5	0	3284	3331	192054791	192054838	1.050000e-05	62.1
47	TraesCS2D01G440900	chr1A	71.221	1237	234	86	1317	2488	10151110	10152289	2.140000e-47	200.0
48	TraesCS2D01G440900	chr3A	85.057	174	25	1	3337	3509	476399249	476399422	3.600000e-40	176.0
49	TraesCS2D01G440900	chr3A	82.584	178	28	3	3337	3512	495591214	495591390	1.690000e-33	154.0
50	TraesCS2D01G440900	chr1D	88.028	142	17	0	3369	3510	431920179	431920320	6.030000e-38	169.0
51	TraesCS2D01G440900	chr1D	78.534	191	29	6	2303	2481	8857595	8857785	7.970000e-22	115.0
52	TraesCS2D01G440900	chr1D	78.534	191	29	6	2303	2481	8883308	8883498	7.970000e-22	115.0
53	TraesCS2D01G440900	chr1D	78.010	191	30	6	2303	2481	8870450	8870640	3.710000e-20	110.0
54	TraesCS2D01G440900	chr5A	81.333	150	18	5	753	900	510549580	510549439	2.870000e-21	113.0

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	TraesCS2D01G440900	chr2D	551210322	551213833	3511	False	6486.0	6486	100.0000	1	3512	1	chr2D.!!$F1	3511
1	TraesCS2D01G440900	chr2D	559121114	559121681	567	True	464.0	464	81.6430	190	753	1	chr2D.!!$R2	563
2	TraesCS2D01G440900	chr2A	692229689	692232217	2528	False	3650.0	3650	92.8210	829	3344	1	chr2A.!!$F2	2515
3	TraesCS2D01G440900	chr2A	692207298	692211377	4079	False	623.5	1064	87.4640	1	1168	2	chr2A.!!$F3	1167
4	TraesCS2D01G440900	chr2B	656510944	656513224	2280	False	1545.5	2872	93.2495	1	2781	2	chr2B.!!$F4	2780
5	TraesCS2D01G440900	chr7B	665287067	665287631	564	True	512.0	512	83.1600	183	754	1	chr7B.!!$R1	571
6	TraesCS2D01G440900	chr7A	518646068	518646650	582	False	446.0	446	80.7170	175	751	1	chr7A.!!$F2	576
7	TraesCS2D01G440900	chr3D	142633807	142634328	521	True	427.0	427	81.5590	213	735	1	chr3D.!!$R1	522
8	TraesCS2D01G440900	chr1B	341934886	341935431	545	True	424.0	424	80.7830	193	753	1	chr1B.!!$R1	560
9	TraesCS2D01G440900	chr6A	552582725	552583254	529	False	350.0	350	78.8530	196	752	1	chr6A.!!$F1	556
10	TraesCS2D01G440900	chr4A	572302359	572303602	1243	False	320.0	320	72.2180	1197	2440	1	chr4A.!!$F2	1243
11	TraesCS2D01G440900	chr4D	464234941	464235595	654	False	287.0	287	75.5130	1163	1820	1	chr4D.!!$F1	657
12	TraesCS2D01G440900	chr4B	580385065	580385720	655	False	283.0	283	75.4030	1162	1820	1	chr4B.!!$F1	658

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
207	3477	0.114168	CGGAGGAGGAGGAGGATGAT	59.886	60.0	0.0	0.0	0.0	2.45	F
820	4105	0.625849	GTGGGTGACATGAGGGGATT	59.374	55.0	0.0	0.0	0.0	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1118	4409	0.259647	CATTGCTGGGGAGGGATTGA	59.740	55.0	0.0	0.0	0.0	2.57	R
2659	5996	0.906775	AAATCCCCATACGACACGGT	59.093	50.0	0.0	0.0	0.0	4.83	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
29	3278	0.452987	GCCATGAGCGATTGCAAGAA	59.547	50.000	7.90	0.00	46.23	2.52
58	3310	2.824489	TTGGCGTCGTTGTGGCAA	60.824	55.556	0.00	0.00	46.71	4.52
90	3342	7.883311	AGCAAGTGTGTAGGTAAATAATTCAGT	59.117	33.333	0.00	0.00	0.00	3.41
116	3368	4.416620	GACTCTTTCGTTGATCAGTCGAT	58.583	43.478	20.02	9.39	33.72	3.59
155	3419	1.643832	CTAAATTCAGCCTCGCCGC	59.356	57.895	0.00	0.00	0.00	6.53
173	3437	2.128507	CCGGGCTACCTCCTGACTC	61.129	68.421	0.00	0.00	34.34	3.36
207	3477	0.114168	CGGAGGAGGAGGAGGATGAT	59.886	60.000	0.00	0.00	0.00	2.45
292	3562	2.669133	CCGGGGTTCAGCATGGAGA	61.669	63.158	0.00	0.00	36.16	3.71
357	3627	1.377202	GCAACAGAGCATCCCGGAA	60.377	57.895	0.73	0.00	33.66	4.30
500	3774	2.743636	CGAAGGAGCCAGAACTACAA	57.256	50.000	0.00	0.00	0.00	2.41
525	3799	1.758440	GCCCATGTATCAGGAGCCGA	61.758	60.000	0.00	0.00	0.00	5.54
680	3956	3.005539	AGTGCCCGATCACTGCCT	61.006	61.111	8.41	0.00	44.88	4.75
730	4014	4.006989	TGTTTGAGGGGTCATATTTGTCG	58.993	43.478	0.00	0.00	0.00	4.35
740	4024	3.057019	TCATATTTGTCGTATGCGGCTC	58.943	45.455	9.69	0.00	44.07	4.70
742	4026	2.024176	ATTTGTCGTATGCGGCTCTT	57.976	45.000	9.69	0.00	44.07	2.85
814	4099	2.268920	CGGGGTGGGTGACATGAG	59.731	66.667	0.00	0.00	0.00	2.90
815	4100	2.677228	GGGGTGGGTGACATGAGG	59.323	66.667	0.00	0.00	0.00	3.86
816	4101	2.677228	GGGTGGGTGACATGAGGG	59.323	66.667	0.00	0.00	0.00	4.30
817	4102	2.677228	GGTGGGTGACATGAGGGG	59.323	66.667	0.00	0.00	0.00	4.79
818	4103	1.923395	GGTGGGTGACATGAGGGGA	60.923	63.158	0.00	0.00	0.00	4.81
819	4104	1.281925	GGTGGGTGACATGAGGGGAT	61.282	60.000	0.00	0.00	0.00	3.85
820	4105	0.625849	GTGGGTGACATGAGGGGATT	59.374	55.000	0.00	0.00	0.00	3.01
821	4106	0.918983	TGGGTGACATGAGGGGATTC	59.081	55.000	0.00	0.00	0.00	2.52
822	4107	0.918983	GGGTGACATGAGGGGATTCA	59.081	55.000	0.00	0.00	0.00	2.57
823	4108	1.408822	GGGTGACATGAGGGGATTCAC	60.409	57.143	0.00	0.24	36.63	3.18

Showing 1 to 25 of 229 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
58	3310	1.971357	ACCTACACACTTGCTAGCAGT	59.029	47.619	18.45	14.16	0.00	4.40
116	3368	3.588842	AGGGTTCATCAATCAGACCAGAA	59.411	43.478	0.00	0.00	0.00	3.02
155	3419	2.042843	AGTCAGGAGGTAGCCCGG	60.043	66.667	0.00	0.00	35.12	5.73
162	3426	4.361971	TCCGGCGAGTCAGGAGGT	62.362	66.667	9.30	0.00	33.99	3.85
187	3451	1.532794	CATCCTCCTCCTCCTCCGG	60.533	68.421	0.00	0.00	0.00	5.14
204	3474	1.078918	CGGCAACTGCTCTCCATCA	60.079	57.895	1.06	0.00	41.70	3.07
207	3477	2.922503	TCCGGCAACTGCTCTCCA	60.923	61.111	0.00	0.00	41.70	3.86
292	3562	2.125106	GAACTCCGCATCCGCCTT	60.125	61.111	0.00	0.00	33.11	4.35
342	3612	0.982852	TGGATTCCGGGATGCTCTGT	60.983	55.000	16.14	0.00	0.00	3.41
347	3617	4.404691	GGATGGATTCCGGGATGC	57.595	61.111	7.42	7.42	33.93	3.91
357	3627	6.185511	CACATAAGCCTCATTATGGATGGAT	58.814	40.000	10.31	0.00	44.13	3.41
500	3774	1.146930	CTGATACATGGGCGGCAGT	59.853	57.895	12.47	8.78	0.00	4.40
525	3799	5.000012	GAGATGTTGACTATCTCCGTGTT	58.000	43.478	0.00	0.00	42.94	3.32
593	3868	8.613060	TTAAATCCATACAAAAGCATGCAAAA	57.387	26.923	21.98	0.00	0.00	2.44
680	3956	4.680237	CGTCAGGGCGCCTTCACA	62.680	66.667	28.56	1.10	0.00	3.58
730	4014	0.864455	GAGCATCAAGAGCCGCATAC	59.136	55.000	0.00	0.00	33.17	2.39
740	4024	3.849911	TCTGTTCGGTTAGAGCATCAAG	58.150	45.455	0.00	0.00	39.36	3.02
742	4026	3.953712	TTCTGTTCGGTTAGAGCATCA	57.046	42.857	0.00	0.00	39.36	3.07
816	4101	2.092914	CCTACAGGAGTTGGGTGAATCC	60.093	54.545	0.00	0.00	37.05	3.01
817	4102	3.268023	CCTACAGGAGTTGGGTGAATC	57.732	52.381	0.00	0.00	37.05	2.52
827	4112	1.697982	GAACCAACACCCTACAGGAGT	59.302	52.381	0.00	0.00	41.89	3.85
839	4124	2.112297	GCCACGGAGGAACCAACA	59.888	61.111	0.00	0.00	41.22	3.33
901	4187	7.511028	ACACCTCAAATTTTCCCCACTTAATTA	59.489	33.333	0.00	0.00	0.00	1.40
919	4205	1.388547	GTTGCAACCTCACACCTCAA	58.611	50.000	19.15	0.00	0.00	3.02
920	4206	0.813610	CGTTGCAACCTCACACCTCA	60.814	55.000	23.42	0.00	0.00	3.86

Showing 1 to 25 of 227 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.