AutoCloner

Multiple sequence alignment - TraesCS4B01G071900

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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	TraesCS4B01G071900	chr4B	100.000	3394	0	0	1	3394	66474047	66470654	0.000000e+00	6268
1	TraesCS4B01G071900	chr4B	95.000	180	8	1	2526	2705	352122364	352122542	7.170000e-72	281
2	TraesCS4B01G071900	chr4B	76.140	570	100	29	1304	1853	662421246	662420693	2.010000e-67	267
3	TraesCS4B01G071900	chr4B	89.595	173	12	5	673	842	95865757	95865588	7.380000e-52	215
4	TraesCS4B01G071900	chr4D	91.822	1614	93	26	836	2448	45711128	45712703	0.000000e+00	2213
5	TraesCS4B01G071900	chr4D	97.110	173	4	1	2528	2700	75782221	75782050	1.190000e-74	291
6	TraesCS4B01G071900	chr4D	94.118	187	10	1	2533	2718	46028701	46028515	1.990000e-72	283
7	TraesCS4B01G071900	chr4D	85.130	269	25	14	2736	3001	55235575	55235319	9.340000e-66	261
8	TraesCS4B01G071900	chr4D	80.495	323	50	10	1533	1853	506286973	506286662	5.660000e-58	235
9	TraesCS4B01G071900	chr4D	85.859	99	14	0	1	99	45710162	45710260	4.630000e-19	106
10	TraesCS4B01G071900	chr4A	91.342	1282	87	19	1079	2350	553317589	553316322	0.000000e+00	1731
11	TraesCS4B01G071900	chr4A	94.898	98	4	1	944	1040	553317677	553317580	5.870000e-33	152
12	TraesCS4B01G071900	chr5D	77.046	1063	187	43	1303	2348	117243707	117242685	2.960000e-155	558
13	TraesCS4B01G071900	chr5D	86.891	267	28	7	2732	2997	531657650	531657390	3.310000e-75	292
14	TraesCS4B01G071900	chr5D	87.755	147	18	0	525	671	524576761	524576615	4.500000e-39	172
15	TraesCS4B01G071900	chr5A	76.938	1058	197	39	1302	2348	126100970	126099949	2.960000e-155	558
16	TraesCS4B01G071900	chr5B	76.124	1068	204	44	1303	2348	129859550	129860588	2.340000e-141	512
17	TraesCS4B01G071900	chr5B	85.556	180	21	4	673	849	6370990	6370813	2.080000e-42	183
18	TraesCS4B01G071900	chr1A	82.114	369	51	12	2735	3096	571292299	571292659	5.500000e-78	302
19	TraesCS4B01G071900	chr2D	79.610	461	49	24	2731	3154	109728035	109728487	4.290000e-74	289
20	TraesCS4B01G071900	chr2D	89.262	149	16	0	525	673	221497331	221497479	1.610000e-43	187
21	TraesCS4B01G071900	chr2D	89.262	149	16	0	523	671	221497543	221497395	1.610000e-43	187
22	TraesCS4B01G071900	chr7A	86.567	268	26	10	2736	3001	146754122	146754381	1.540000e-73	287
23	TraesCS4B01G071900	chr7A	79.258	458	58	20	2736	3165	577828666	577829114	5.540000e-73	285
24	TraesCS4B01G071900	chr7A	90.964	166	12	2	673	835	206036154	206036319	1.590000e-53	220
25	TraesCS4B01G071900	chr3B	95.531	179	8	0	2520	2698	571752512	571752690	1.540000e-73	287
26	TraesCS4B01G071900	chr3B	90.604	149	14	0	523	671	807484267	807484119	7.430000e-47	198
27	TraesCS4B01G071900	chr3B	85.326	184	21	5	673	850	364538201	364538384	5.780000e-43	185
28	TraesCS4B01G071900	chr1D	96.552	174	5	1	2527	2700	178466475	178466303	1.540000e-73	287
29	TraesCS4B01G071900	chr1D	95.556	180	6	2	2529	2707	323833257	323833079	1.540000e-73	287
30	TraesCS4B01G071900	chr1D	90.588	170	13	2	673	839	378803645	378803814	4.410000e-54	222
31	TraesCS4B01G071900	chr6D	96.023	176	6	1	2530	2704	270689343	270689518	5.540000e-73	285
32	TraesCS4B01G071900	chr6D	88.398	181	15	5	673	849	13575057	13574879	2.650000e-51	213
33	TraesCS4B01G071900	chr2B	94.086	186	8	3	2533	2716	719520669	719520485	2.580000e-71	279
34	TraesCS4B01G071900	chr2B	96.407	167	4	2	2534	2700	127147882	127148046	1.200000e-69	274
35	TraesCS4B01G071900	chr2B	84.644	267	33	8	2736	3001	762242196	762241937	3.360000e-65	259
36	TraesCS4B01G071900	chr2B	89.143	175	14	4	673	844	672040529	672040701	2.650000e-51	213
37	TraesCS4B01G071900	chr2B	90.789	152	14	0	520	671	719970789	719970940	1.600000e-48	204
38	TraesCS4B01G071900	chr2B	77.953	254	40	16	2736	2981	786239910	786239665	9.820000e-31	145
39	TraesCS4B01G071900	chr2B	76.800	250	43	14	2736	2981	786257380	786257142	3.560000e-25	126
40	TraesCS4B01G071900	chr1B	85.714	266	32	6	2738	3001	112353052	112353313	3.340000e-70	276
41	TraesCS4B01G071900	chr1B	90.588	170	13	2	673	839	621352405	621352236	4.410000e-54	222
42	TraesCS4B01G071900	chr1B	89.157	166	15	2	673	835	403974115	403974280	1.600000e-48	204
43	TraesCS4B01G071900	chr1B	89.542	153	15	1	520	671	404815163	404815315	3.460000e-45	193
44	TraesCS4B01G071900	chr3A	84.926	272	33	8	2731	3001	644195648	644195912	5.580000e-68	268
45	TraesCS4B01G071900	chr6B	90.964	166	11	3	673	835	12076919	12077083	1.590000e-53	220
46	TraesCS4B01G071900	chr6B	88.827	179	17	2	673	848	8131796	8131974	2.050000e-52	217
47	TraesCS4B01G071900	chr6B	88.268	179	16	4	673	848	8131910	8131734	3.430000e-50	209
48	TraesCS4B01G071900	chr6B	88.591	149	17	0	523	671	23595510	23595658	7.480000e-42	182
49	TraesCS4B01G071900	chr7D	89.080	174	15	3	670	840	160296317	160296489	2.650000e-51	213
50	TraesCS4B01G071900	chr7B	88.591	149	17	0	523	671	661456554	661456702	7.480000e-42	182
51	TraesCS4B01G071900	chr3D	88.591	149	17	0	523	671	305979678	305979826	7.480000e-42	182
52	TraesCS4B01G071900	chr6A	79.703	202	31	10	2795	2992	35257315	35257510	1.640000e-28	137

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	TraesCS4B01G071900	chr4B	66470654	66474047	3393	True	6268.0	6268	100.0000	1	3394	1	chr4B.!!$R1	3393
1	TraesCS4B01G071900	chr4B	662420693	662421246	553	True	267.0	267	76.1400	1304	1853	1	chr4B.!!$R3	549
2	TraesCS4B01G071900	chr4D	45710162	45712703	2541	False	1159.5	2213	88.8405	1	2448	2	chr4D.!!$F1	2447
3	TraesCS4B01G071900	chr4A	553316322	553317677	1355	True	941.5	1731	93.1200	944	2350	2	chr4A.!!$R1	1406
4	TraesCS4B01G071900	chr5D	117242685	117243707	1022	True	558.0	558	77.0460	1303	2348	1	chr5D.!!$R1	1045
5	TraesCS4B01G071900	chr5A	126099949	126100970	1021	True	558.0	558	76.9380	1302	2348	1	chr5A.!!$R1	1046
6	TraesCS4B01G071900	chr5B	129859550	129860588	1038	False	512.0	512	76.1240	1303	2348	1	chr5B.!!$F1	1045

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
570	1042	0.042731	TCTTCCAGAATCCGACCCCT	59.957	55.0	0.0	0.0	0.0	4.79	F
1493	2011	0.037605	GAACTCACCCACCACCTACG	60.038	60.0	0.0	0.0	0.0	3.51	F
1922	2472	0.036765	TAATCCTTCGCACCGCAAGT	60.037	50.0	0.0	0.0	0.0	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1903	2453	0.036765	ACTTGCGGTGCGAAGGATTA	60.037	50.0	0.00	0.00	0.00	1.75	R
2356	2906	0.095245	GCGTGGTTGATGTCGTGATG	59.905	55.0	0.00	0.00	0.00	3.07	R
3347	3897	0.107263	TCATTGCAAGCGCTATCCCA	60.107	50.0	12.05	2.31	39.64	4.37	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
30	31	6.788684	TGATACGAGTAGAAGCTAAGCTAG	57.211	41.667	0.00	0.00	38.25	3.42
33	34	2.619177	CGAGTAGAAGCTAAGCTAGGCA	59.381	50.000	12.34	0.00	38.25	4.75
39	40	3.966665	AGAAGCTAAGCTAGGCAGAGAAT	59.033	43.478	12.34	0.00	38.25	2.40
42	43	4.735369	AGCTAAGCTAGGCAGAGAATCTA	58.265	43.478	12.34	0.00	40.14	1.98
59	60	7.701809	AGAATCTAGCTTGCGAATTAAGTAC	57.298	36.000	0.00	0.00	0.00	2.73
62	63	5.107133	TCTAGCTTGCGAATTAAGTACCAC	58.893	41.667	0.00	0.00	0.00	4.16
72	73	5.163540	CGAATTAAGTACCACTCCTACTGCT	60.164	44.000	0.00	0.00	0.00	4.24
73	74	6.039047	CGAATTAAGTACCACTCCTACTGCTA	59.961	42.308	0.00	0.00	0.00	3.49
82	83	5.595133	ACCACTCCTACTGCTAACTCTAATC	59.405	44.000	0.00	0.00	0.00	1.75
84	85	6.460399	CCACTCCTACTGCTAACTCTAATCAC	60.460	46.154	0.00	0.00	0.00	3.06
86	87	6.095720	ACTCCTACTGCTAACTCTAATCACAC	59.904	42.308	0.00	0.00	0.00	3.82
95	150	6.813649	GCTAACTCTAATCACACATTCACTCA	59.186	38.462	0.00	0.00	0.00	3.41
104	159	6.698008	TCACACATTCACTCAGTTTCAATT	57.302	33.333	0.00	0.00	0.00	2.32
111	166	8.070171	ACATTCACTCAGTTTCAATTTACTTCG	58.930	33.333	0.00	0.00	0.00	3.79
133	189	5.127194	TCGCATATTAGGTGTCTTGAGTCTT	59.873	40.000	0.00	0.00	0.00	3.01
136	192	6.037610	GCATATTAGGTGTCTTGAGTCTTTGG	59.962	42.308	0.00	0.00	0.00	3.28
144	200	4.876107	TGTCTTGAGTCTTTGGTCAAGTTC	59.124	41.667	10.91	7.25	46.57	3.01
268	325	6.061441	TCTAATGGCATCGATTTGGTATTGT	58.939	36.000	0.00	0.00	0.00	2.71
273	330	5.469760	TGGCATCGATTTGGTATTGTAGATG	59.530	40.000	0.00	0.00	37.76	2.90
276	333	6.596703	CATCGATTTGGTATTGTAGATGCTG	58.403	40.000	0.00	0.00	0.00	4.41
281	338	8.939929	CGATTTGGTATTGTAGATGCTGATAAT	58.060	33.333	0.00	0.00	0.00	1.28
323	380	8.702163	CTTTGTTAAAGTTCACAAGGTTTGAT	57.298	30.769	0.00	0.00	34.43	2.57
331	388	7.881775	AGTTCACAAGGTTTGATTTAAGACT	57.118	32.000	0.00	0.00	0.00	3.24
332	389	7.707104	AGTTCACAAGGTTTGATTTAAGACTG	58.293	34.615	0.00	0.00	0.00	3.51
333	390	6.633500	TCACAAGGTTTGATTTAAGACTGG	57.367	37.500	0.00	0.00	0.00	4.00

Showing 1 to 25 of 900 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
30	31	1.202463	TCGCAAGCTAGATTCTCTGCC	60.202	52.381	0.00	0.00	37.18	4.85
33	34	6.578023	ACTTAATTCGCAAGCTAGATTCTCT	58.422	36.000	0.00	0.00	37.18	3.10
39	40	5.105473	AGTGGTACTTAATTCGCAAGCTAGA	60.105	40.000	0.00	0.00	37.18	2.43
42	43	3.933332	GAGTGGTACTTAATTCGCAAGCT	59.067	43.478	0.00	0.00	37.18	3.74
49	50	6.223351	AGCAGTAGGAGTGGTACTTAATTC	57.777	41.667	0.00	0.00	0.00	2.17
59	60	5.594725	TGATTAGAGTTAGCAGTAGGAGTGG	59.405	44.000	0.00	0.00	0.00	4.00
62	63	6.095580	TGTGTGATTAGAGTTAGCAGTAGGAG	59.904	42.308	0.00	0.00	0.00	3.69
72	73	7.896811	ACTGAGTGAATGTGTGATTAGAGTTA	58.103	34.615	0.00	0.00	0.00	2.24
73	74	6.763355	ACTGAGTGAATGTGTGATTAGAGTT	58.237	36.000	0.00	0.00	0.00	3.01
82	83	8.131100	AGTAAATTGAAACTGAGTGAATGTGTG	58.869	33.333	0.00	0.00	0.00	3.82
84	85	9.173939	GAAGTAAATTGAAACTGAGTGAATGTG	57.826	33.333	0.00	0.00	0.00	3.21
86	87	7.059945	GCGAAGTAAATTGAAACTGAGTGAATG	59.940	37.037	0.00	0.00	0.00	2.67
95	150	9.174166	ACCTAATATGCGAAGTAAATTGAAACT	57.826	29.630	0.00	0.00	0.00	2.66
104	159	6.869695	TCAAGACACCTAATATGCGAAGTAA	58.130	36.000	0.00	0.00	0.00	2.24
111	166	6.037610	CCAAAGACTCAAGACACCTAATATGC	59.962	42.308	0.00	0.00	0.00	3.14
235	292	7.514784	AATCGATGCCATTAGATTCATTGAA	57.485	32.000	0.00	0.75	34.23	2.69
252	309	6.424812	TCAGCATCTACAATACCAAATCGATG	59.575	38.462	0.00	0.00	0.00	3.84
255	312	6.791887	ATCAGCATCTACAATACCAAATCG	57.208	37.500	0.00	0.00	0.00	3.34
298	355	8.702163	ATCAAACCTTGTGAACTTTAACAAAG	57.298	30.769	0.00	0.00	44.10	2.77
299	356	9.495572	AAATCAAACCTTGTGAACTTTAACAAA	57.504	25.926	0.00	0.00	35.95	2.83
305	362	8.749354	AGTCTTAAATCAAACCTTGTGAACTTT	58.251	29.630	0.00	0.00	0.00	2.66
306	363	8.190784	CAGTCTTAAATCAAACCTTGTGAACTT	58.809	33.333	0.00	0.00	0.00	2.66
307	364	7.201821	CCAGTCTTAAATCAAACCTTGTGAACT	60.202	37.037	0.00	0.00	0.00	3.01
308	365	6.918022	CCAGTCTTAAATCAAACCTTGTGAAC	59.082	38.462	0.00	0.00	0.00	3.18
309	366	6.040391	CCCAGTCTTAAATCAAACCTTGTGAA	59.960	38.462	0.00	0.00	0.00	3.18

Showing 1 to 25 of 874 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.