AutoCloner

Multiple sequence alignment - TraesCS6D01G274900

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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	TraesCS6D01G274900	chr6D	100.000	2996	0	0	1	2996	383746561	383743566	0.000000e+00	5533.0
1	TraesCS6D01G274900	chr6B	91.308	2278	124	35	23	2272	574022457	574020226	0.000000e+00	3042.0
2	TraesCS6D01G274900	chr6B	93.455	550	28	6	2443	2988	574020235	574019690	0.000000e+00	809.0
3	TraesCS6D01G274900	chr6A	90.303	2310	119	40	9	2272	525993613	525991363	0.000000e+00	2928.0
4	TraesCS6D01G274900	chr6A	92.730	564	28	8	2443	2996	525991372	525990812	0.000000e+00	802.0
5	TraesCS6D01G274900	chr7D	79.445	613	86	32	993	1581	165634705	165635301	6.020000e-107	398.0
6	TraesCS6D01G274900	chr7D	87.586	145	11	6	2272	2416	480049496	480049359	8.590000e-36	161.0
7	TraesCS6D01G274900	chr7D	82.707	133	19	4	1240	1370	262698821	262698691	6.790000e-22	115.0
8	TraesCS6D01G274900	chr7B	79.368	601	90	27	999	1581	128822081	128822665	2.800000e-105	392.0
9	TraesCS6D01G274900	chr7B	81.159	138	24	2	1234	1370	241107810	241107946	3.160000e-20	110.0
10	TraesCS6D01G274900	chr7A	78.734	616	90	30	992	1581	167179673	167180273	1.010000e-99	374.0
11	TraesCS6D01G274900	chr7A	82.443	131	23	0	1240	1370	285576473	285576343	6.790000e-22	115.0
12	TraesCS6D01G274900	chr3D	86.585	164	14	6	2272	2435	565410032	565410187	1.100000e-39	174.0
13	TraesCS6D01G274900	chr3D	84.906	159	19	5	2272	2426	17671031	17671188	4.000000e-34	156.0
14	TraesCS6D01G274900	chr3D	90.411	73	7	0	1235	1307	357141493	357141565	2.460000e-16	97.1
15	TraesCS6D01G274900	chr5D	89.706	136	12	2	1001	1135	319254271	319254405	3.970000e-39	172.0
16	TraesCS6D01G274900	chr5D	88.652	141	12	4	2273	2412	234820704	234820841	5.140000e-38	169.0
17	TraesCS6D01G274900	chr5B	89.706	136	12	2	1001	1135	369485439	369485573	3.970000e-39	172.0
18	TraesCS6D01G274900	chr5B	87.097	124	16	0	1458	1581	369485857	369485980	1.120000e-29	141.0
19	TraesCS6D01G274900	chr5A	89.706	136	12	2	1001	1135	414934854	414934720	3.970000e-39	172.0
20	TraesCS6D01G274900	chr5A	84.028	144	21	2	1463	1605	414934422	414934280	1.450000e-28	137.0
21	TraesCS6D01G274900	chr2A	88.112	143	13	3	2272	2410	615747590	615747448	1.850000e-37	167.0
22	TraesCS6D01G274900	chr2A	86.486	111	13	2	1471	1580	696316052	696316161	1.460000e-23	121.0
23	TraesCS6D01G274900	chr1B	85.276	163	18	5	2271	2431	87969626	87969468	2.390000e-36	163.0
24	TraesCS6D01G274900	chr1B	73.585	318	59	20	1230	1535	487951356	487951052	6.830000e-17	99.0
25	TraesCS6D01G274900	chr4A	83.425	181	18	5	2271	2445	473937360	473937534	1.110000e-34	158.0
26	TraesCS6D01G274900	chr2D	84.756	164	16	7	2273	2435	106123306	106123461	4.000000e-34	156.0
27	TraesCS6D01G274900	chr4B	82.609	184	23	6	2259	2435	406463688	406463869	1.440000e-33	154.0

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	TraesCS6D01G274900	chr6D	383743566	383746561	2995	True	5533.0	5533	100.0000	1	2996	1	chr6D.!!$R1	2995
1	TraesCS6D01G274900	chr6B	574019690	574022457	2767	True	1925.5	3042	92.3815	23	2988	2	chr6B.!!$R1	2965
2	TraesCS6D01G274900	chr6A	525990812	525993613	2801	True	1865.0	2928	91.5165	9	2996	2	chr6A.!!$R1	2987
3	TraesCS6D01G274900	chr7D	165634705	165635301	596	False	398.0	398	79.4450	993	1581	1	chr7D.!!$F1	588
4	TraesCS6D01G274900	chr7B	128822081	128822665	584	False	392.0	392	79.3680	999	1581	1	chr7B.!!$F1	582
5	TraesCS6D01G274900	chr7A	167179673	167180273	600	False	374.0	374	78.7340	992	1581	1	chr7A.!!$F1	589

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
414	424	0.174389	AGTGTCAGCTATGCCTCGTG	59.826	55.0	0.00	0.0	0.00	4.35	F
1155	1199	0.096628	AGCGACGCTTACACTCGTAG	59.903	55.0	18.46	0.0	39.22	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1457	1543	0.179100	CGCGATCTTGGACCATCTGT	60.179	55.0	0.0	0.0	0.0	3.41	R
2664	2783	0.034059	AAGCACTCCTCACACTTCCG	59.966	55.0	0.0	0.0	0.0	4.30	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
77	81	2.355481	ACGGCTCGTTTGGTCGAC	60.355	61.111	7.13	7.13	36.35	4.20
84	88	2.305127	CGTTTGGTCGACGGTCACC	61.305	63.158	9.92	17.46	36.90	4.02
141	145	0.518636	GCAAGAAAGAGTGCATCGCA	59.481	50.000	0.00	0.00	40.58	5.10
287	296	2.099431	GTGCGAGGCAGCTTCTCTG	61.099	63.158	2.62	6.74	45.62	3.35
314	323	1.529152	GGTGGCCCGGAAAATTTCGT	61.529	55.000	0.73	0.00	0.00	3.85
316	325	1.540707	GTGGCCCGGAAAATTTCGTTA	59.459	47.619	0.73	0.00	0.00	3.18
361	370	2.434336	ACTCCTGTGCAAACTACAGTCA	59.566	45.455	0.00	0.00	43.05	3.41
362	371	2.802816	CTCCTGTGCAAACTACAGTCAC	59.197	50.000	0.00	0.00	43.05	3.67
365	374	1.137282	TGTGCAAACTACAGTCACCGA	59.863	47.619	0.00	0.00	0.00	4.69
414	424	0.174389	AGTGTCAGCTATGCCTCGTG	59.826	55.000	0.00	0.00	0.00	4.35
427	437	1.878102	GCCTCGTGAACATCAGTGGTT	60.878	52.381	0.00	0.00	0.00	3.67
437	447	6.586844	GTGAACATCAGTGGTTACTTCTCTAC	59.413	42.308	0.00	0.00	34.07	2.59
439	449	6.274157	ACATCAGTGGTTACTTCTCTACAG	57.726	41.667	0.00	0.00	34.07	2.74
443	453	7.120923	TCAGTGGTTACTTCTCTACAGTTTT	57.879	36.000	0.00	0.00	34.07	2.43
444	454	7.208080	TCAGTGGTTACTTCTCTACAGTTTTC	58.792	38.462	0.00	0.00	34.07	2.29
445	455	6.984474	CAGTGGTTACTTCTCTACAGTTTTCA	59.016	38.462	0.00	0.00	34.07	2.69
446	456	7.657761	CAGTGGTTACTTCTCTACAGTTTTCAT	59.342	37.037	0.00	0.00	34.07	2.57
447	457	8.211629	AGTGGTTACTTCTCTACAGTTTTCATT	58.788	33.333	0.00	0.00	31.66	2.57
448	458	8.837389	GTGGTTACTTCTCTACAGTTTTCATTT	58.163	33.333	0.00	0.00	0.00	2.32
449	459	9.403583	TGGTTACTTCTCTACAGTTTTCATTTT	57.596	29.630	0.00	0.00	0.00	1.82
469	479	1.488390	TCAACAGTATACCCCGGGTC	58.512	55.000	21.85	0.00	37.09	4.46
790	834	3.760035	ACGTACTGGGGCTCTGCG	61.760	66.667	0.00	0.00	0.00	5.18
982	1026	3.680786	CACTGGTGCTCGTCCGGA	61.681	66.667	0.00	0.00	35.49	5.14
1032	1076	3.241530	TGCTGCGAGAAGGTGGGT	61.242	61.111	0.00	0.00	0.00	4.51
1035	1079	1.216710	CTGCGAGAAGGTGGGTCTC	59.783	63.158	0.00	0.00	38.54	3.36

Showing 1 to 25 of 147 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	2.521451	TACCGCCAACTCCAGCCAA	61.521	57.895	0.00	0.00	0.00	4.52
1	2	2.925706	TACCGCCAACTCCAGCCA	60.926	61.111	0.00	0.00	0.00	4.75
4	5	3.065306	TGGTACCGCCAACTCCAG	58.935	61.111	7.57	0.00	45.94	3.86
141	145	0.675633	GTGACAAACCCTGCAAGCAT	59.324	50.000	0.00	0.00	0.00	3.79
150	154	1.966451	CCTGCTCCGTGACAAACCC	60.966	63.158	0.00	0.00	0.00	4.11
314	323	5.064962	CGGGCTATGTTAACGTGGAAAATAA	59.935	40.000	14.76	0.00	0.00	1.40
316	325	3.375922	CGGGCTATGTTAACGTGGAAAAT	59.624	43.478	14.76	0.00	0.00	1.82
361	370	0.108804	CGGTCAGCAGTACAATCGGT	60.109	55.000	0.00	0.00	0.00	4.69
362	371	2.665777	CGGTCAGCAGTACAATCGG	58.334	57.895	0.00	0.00	0.00	4.18
383	393	0.886490	CTGACACTGGTGGACTTGCC	60.886	60.000	5.70	0.00	34.19	4.52
390	400	0.745845	GGCATAGCTGACACTGGTGG	60.746	60.000	0.00	0.00	34.19	4.61
414	424	6.688578	TGTAGAGAAGTAACCACTGATGTTC	58.311	40.000	0.00	0.00	34.36	3.18
437	447	9.191995	GGGTATACTGTTGAAAAATGAAAACTG	57.808	33.333	2.25	0.00	0.00	3.16
439	449	7.327518	CGGGGTATACTGTTGAAAAATGAAAAC	59.672	37.037	2.25	0.00	0.00	2.43
443	453	4.944930	CCGGGGTATACTGTTGAAAAATGA	59.055	41.667	2.25	0.00	0.00	2.57
444	454	4.097286	CCCGGGGTATACTGTTGAAAAATG	59.903	45.833	14.71	0.00	0.00	2.32
445	455	4.264038	ACCCGGGGTATACTGTTGAAAAAT	60.264	41.667	27.92	0.00	32.11	1.82
446	456	3.074242	ACCCGGGGTATACTGTTGAAAAA	59.926	43.478	27.92	0.00	32.11	1.94
447	457	2.643801	ACCCGGGGTATACTGTTGAAAA	59.356	45.455	27.92	0.00	32.11	2.29
448	458	2.236893	GACCCGGGGTATACTGTTGAAA	59.763	50.000	27.92	0.00	35.25	2.69
449	459	1.832998	GACCCGGGGTATACTGTTGAA	59.167	52.381	27.92	0.00	35.25	2.69
450	460	1.488390	GACCCGGGGTATACTGTTGA	58.512	55.000	27.92	0.00	35.25	3.18
469	479	3.343617	ACACGTGAACATAGGGATTTGG	58.656	45.455	25.01	0.00	0.00	3.28
575	604	0.179119	AATCACCGCGGCAGTAGTAC	60.179	55.000	28.58	0.00	0.00	2.73
578	607	1.215655	GCTAATCACCGCGGCAGTAG	61.216	60.000	28.58	24.32	0.00	2.57

Showing 1 to 25 of 159 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.