AutoCloner

Multiple sequence alignment - TraesCS4B01G277400

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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	TraesCS4B01G277400	chr4B	100.000	3358	0	0	1	3358	559209733	559206376	0.000000e+00	6202
1	TraesCS4B01G277400	chr4B	94.030	2747	132	27	44	2781	277835200	277832477	0.000000e+00	4135
2	TraesCS4B01G277400	chr2B	93.659	3296	183	24	74	3356	386132454	386135736	0.000000e+00	4905
3	TraesCS4B01G277400	chr2B	94.466	2783	124	27	11	2781	320940813	320938049	0.000000e+00	4259
4	TraesCS4B01G277400	chr2B	98.000	200	2	1	3159	3358	570602845	570602648	2.480000e-91	346
5	TraesCS4B01G277400	chr2B	97.500	200	3	1	3159	3358	570517464	570517267	1.150000e-89	340
6	TraesCS4B01G277400	chr7B	93.689	3280	174	26	94	3355	393237320	393234056	0.000000e+00	4879
7	TraesCS4B01G277400	chr7B	93.004	3359	202	31	14	3356	319716347	319719688	0.000000e+00	4870
8	TraesCS4B01G277400	chr7B	93.945	2857	135	20	506	3355	240199659	240202484	0.000000e+00	4283
9	TraesCS4B01G277400	chr1B	93.461	3288	187	25	83	3356	348700008	348696735	0.000000e+00	4855
10	TraesCS4B01G277400	chr1B	93.386	3281	190	19	79	3355	60863778	60860521	0.000000e+00	4831
11	TraesCS4B01G277400	chr6B	95.895	2582	93	11	205	2781	48901240	48903813	0.000000e+00	4169
12	TraesCS4B01G277400	chr3B	91.915	1744	115	21	44	1776	71908297	71910025	0.000000e+00	2416

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	TraesCS4B01G277400	chr4B	559206376	559209733	3357	True	6202	6202	100.000	1	3358	1	chr4B.!!$R2	3357
1	TraesCS4B01G277400	chr4B	277832477	277835200	2723	True	4135	4135	94.030	44	2781	1	chr4B.!!$R1	2737
2	TraesCS4B01G277400	chr2B	386132454	386135736	3282	False	4905	4905	93.659	74	3356	1	chr2B.!!$F1	3282
3	TraesCS4B01G277400	chr2B	320938049	320940813	2764	True	4259	4259	94.466	11	2781	1	chr2B.!!$R1	2770
4	TraesCS4B01G277400	chr7B	393234056	393237320	3264	True	4879	4879	93.689	94	3355	1	chr7B.!!$R1	3261
5	TraesCS4B01G277400	chr7B	319716347	319719688	3341	False	4870	4870	93.004	14	3356	1	chr7B.!!$F2	3342
6	TraesCS4B01G277400	chr7B	240199659	240202484	2825	False	4283	4283	93.945	506	3355	1	chr7B.!!$F1	2849
7	TraesCS4B01G277400	chr1B	348696735	348700008	3273	True	4855	4855	93.461	83	3356	1	chr1B.!!$R2	3273
8	TraesCS4B01G277400	chr1B	60860521	60863778	3257	True	4831	4831	93.386	79	3355	1	chr1B.!!$R1	3276
9	TraesCS4B01G277400	chr6B	48901240	48903813	2573	False	4169	4169	95.895	205	2781	1	chr6B.!!$F1	2576
10	TraesCS4B01G277400	chr3B	71908297	71910025	1728	False	2416	2416	91.915	44	1776	1	chr3B.!!$F1	1732

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
173	181	1.346068	GAGTCTCCCTGTGCTCTTTGT	59.654	52.381	0.00	0.0	0.00	2.83	F
1163	1184	1.000283	CTCGAGTTCACTTGGAGTGCT	60.000	52.381	3.62	0.0	45.54	4.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2165	2186	3.003378	GCAGTGAAAAGTAAGGTGTCACC	59.997	47.826	14.68	14.68	39.52	4.02	R
2941	3052	0.108233	CTCTGTCTTCAGCCCTGAGC	60.108	60.000	0.00	0.00	41.13	4.26	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
27	28	9.213799	GTCATACAATCTTGTTTCTTCTCTCTT	57.786	33.333	0.20	0.00	42.35	2.85
31	32	7.199078	ACAATCTTGTTTCTTCTCTCTTTTGC	58.801	34.615	0.00	0.00	38.47	3.68
32	33	6.949352	ATCTTGTTTCTTCTCTCTTTTGCA	57.051	33.333	0.00	0.00	0.00	4.08
33	34	6.949352	TCTTGTTTCTTCTCTCTTTTGCAT	57.051	33.333	0.00	0.00	0.00	3.96
34	35	6.732154	TCTTGTTTCTTCTCTCTTTTGCATG	58.268	36.000	0.00	0.00	0.00	4.06
36	37	6.064846	TGTTTCTTCTCTCTTTTGCATGTC	57.935	37.500	0.00	0.00	0.00	3.06
37	38	5.589855	TGTTTCTTCTCTCTTTTGCATGTCA	59.410	36.000	0.00	0.00	0.00	3.58
41	42	7.606858	TCTTCTCTCTTTTGCATGTCAATAG	57.393	36.000	11.33	11.33	35.78	1.73
42	43	7.164122	TCTTCTCTCTTTTGCATGTCAATAGT	58.836	34.615	14.74	0.00	35.88	2.12
66	69	8.721478	AGTTATATGTGTTCATGTCTTGTTGAC	58.279	33.333	0.00	0.00	45.54	3.18
71	74	4.024556	GTGTTCATGTCTTGTTGACTCCTG	60.025	45.833	0.00	0.00	45.54	3.86
77	80	3.938963	TGTCTTGTTGACTCCTGTTTGTC	59.061	43.478	0.00	0.00	45.54	3.18
123	127	9.643693	AGTGTTTTAATTTCTCAAGCATTATGG	57.356	29.630	0.00	0.00	0.00	2.74
155	161	9.403110	CCAAAAAGACAATGAGTAAAATCTGAG	57.597	33.333	0.00	0.00	0.00	3.35
168	174	1.484038	ATCTGAGTCTCCCTGTGCTC	58.516	55.000	0.00	0.00	0.00	4.26
173	181	1.346068	GAGTCTCCCTGTGCTCTTTGT	59.654	52.381	0.00	0.00	0.00	2.83
193	201	6.772770	TTGTATTTTCTTTGTCGACGATCA	57.227	33.333	11.62	0.00	0.00	2.92
277	292	1.757118	AGCTTTAGCCGAGCATAGTCA	59.243	47.619	6.38	0.00	42.56	3.41
355	373	7.476540	ACCCTGCTATATTACATACGATCAA	57.523	36.000	0.00	0.00	0.00	2.57
381	399	4.832608	CGTTGCCGGGGACTAGCC	62.833	72.222	2.18	0.00	0.00	3.93
533	553	3.388024	CAGGTTGGATTATCCTCTCGGAA	59.612	47.826	12.91	0.00	44.02	4.30
539	559	3.244561	GGATTATCCTCTCGGAAATGGCA	60.245	47.826	3.59	0.00	44.02	4.92
541	561	4.437682	TTATCCTCTCGGAAATGGCATT	57.562	40.909	6.96	6.96	44.02	3.56
549	569	5.624159	TCTCGGAAATGGCATTCTATTCAT	58.376	37.500	14.04	0.00	0.00	2.57
610	630	8.717821	CACGGAAAGTATTCAAGAACTGATAAA	58.282	33.333	0.00	0.00	37.29	1.40
1011	1032	7.766628	TCCTACTCATATACCTCAATACCAGT	58.233	38.462	0.00	0.00	0.00	4.00
1163	1184	1.000283	CTCGAGTTCACTTGGAGTGCT	60.000	52.381	3.62	0.00	45.54	4.40
1547	1568	8.985315	AAGAACATGAGATTCATTTGCCTATA	57.015	30.769	0.00	0.00	34.28	1.31
2165	2186	5.660629	TGCATTGAAACTCTTTTTGCATG	57.339	34.783	0.00	0.00	32.32	4.06
2335	2356	4.390264	GCCTTGAGTCTAAGTGAAACCTT	58.610	43.478	0.00	0.00	37.80	3.50
2352	2373	8.514594	GTGAAACCTTCTAATGAATTGATGTGA	58.485	33.333	0.00	0.00	0.00	3.58
2428	2449	5.945784	AGCTATGATCTCTGGATCTGTAGTC	59.054	44.000	7.39	6.50	46.18	2.59
2451	2472	3.243704	TGTGAAAAACAGTGCCATTAGCC	60.244	43.478	0.00	0.00	35.78	3.93
2473	2494	7.529555	AGCCATGGATTCCTCTTTCAATTATA	58.470	34.615	18.40	0.00	0.00	0.98
2610	2633	8.328758	TGAAATCTGGTAGATTGGACTGTAAAT	58.671	33.333	4.94	0.00	43.67	1.40
2613	2636	9.533831	AATCTGGTAGATTGGACTGTAAATTTT	57.466	29.630	0.00	0.00	42.90	1.82
2614	2637	8.934023	TCTGGTAGATTGGACTGTAAATTTTT	57.066	30.769	0.00	0.00	0.00	1.94
2703	2728	8.002459	GGTATGTTCCTTTGGGGAGATAATAAA	58.998	37.037	0.00	0.00	46.01	1.40
2784	2809	5.435041	TGGTATGTTCCTTTGGGGAGATAAT	59.565	40.000	0.00	0.00	46.01	1.28
2870	2981	5.152623	TGTTCCTTTGGTGAGACTGATAG	57.847	43.478	0.00	0.00	0.00	2.08
2874	2985	6.627087	TCCTTTGGTGAGACTGATAGAATT	57.373	37.500	0.00	0.00	0.00	2.17
2881	2992	7.799081	TGGTGAGACTGATAGAATTTCATCAT	58.201	34.615	10.12	0.00	31.05	2.45
2982	3093	5.558818	AGCCAGCTCTTGATTATTAGGATG	58.441	41.667	0.00	0.00	0.00	3.51
3116	3231	7.656137	GGAATTACTATCTATCGGAAAGTGCAA	59.344	37.037	0.00	0.00	0.00	4.08
3209	3325	2.311542	TGTGGGGGAACTTGATAAGCAT	59.688	45.455	0.00	0.00	0.00	3.79
3215	3331	5.048713	GGGGGAACTTGATAAGCATATTTCG	60.049	44.000	0.00	0.00	0.00	3.46
3231	3348	8.774586	AGCATATTTCGTATACATCTTTTGTCC	58.225	33.333	3.32	0.00	39.87	4.02
3247	3364	6.596497	TCTTTTGTCCCTCAAATATACGGTTC	59.404	38.462	0.00	0.00	44.15	3.62
3330	3447	6.715347	ATAAAGGGATCATTTACTTGTGGC	57.285	37.500	0.00	0.00	0.00	5.01
3334	3451	3.429410	GGGATCATTTACTTGTGGCTTGC	60.429	47.826	0.00	0.00	0.00	4.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	8.770438	AGAGAGAAGAAACAAGATTGTATGAC	57.230	34.615	0.00	0.00	41.31	3.06
2	3	9.784531	AAAGAGAGAAGAAACAAGATTGTATGA	57.215	29.630	0.00	0.00	41.31	2.15
5	6	8.345565	GCAAAAGAGAGAAGAAACAAGATTGTA	58.654	33.333	0.00	0.00	41.31	2.41
6	7	7.148018	TGCAAAAGAGAGAAGAAACAAGATTGT	60.148	33.333	0.00	0.00	44.72	2.71
7	8	7.198390	TGCAAAAGAGAGAAGAAACAAGATTG	58.802	34.615	0.00	0.00	0.00	2.67
8	9	7.338800	TGCAAAAGAGAGAAGAAACAAGATT	57.661	32.000	0.00	0.00	0.00	2.40
9	10	6.949352	TGCAAAAGAGAGAAGAAACAAGAT	57.051	33.333	0.00	0.00	0.00	2.40
30	31	9.603298	CATGAACACATATAACTATTGACATGC	57.397	33.333	0.00	0.00	0.00	4.06
41	42	8.880768	GTCAACAAGACATGAACACATATAAC	57.119	34.615	0.00	0.00	46.77	1.89
66	69	5.835257	ACAAACATCAATGACAAACAGGAG	58.165	37.500	0.00	0.00	0.00	3.69
71	74	6.035843	ACACAGACAAACATCAATGACAAAC	58.964	36.000	0.00	0.00	0.00	2.93
77	80	6.728200	ACACTAACACAGACAAACATCAATG	58.272	36.000	0.00	0.00	0.00	2.82
155	161	3.618690	ATACAAAGAGCACAGGGAGAC	57.381	47.619	0.00	0.00	0.00	3.36
168	174	7.287950	TGATCGTCGACAAAGAAAATACAAAG	58.712	34.615	17.16	0.00	0.00	2.77
173	181	6.183360	CCCAATGATCGTCGACAAAGAAAATA	60.183	38.462	17.16	0.00	0.00	1.40
277	292	1.076923	ACAGGGACTAGGCGACGAT	60.077	57.895	0.00	0.00	36.02	3.73
331	346	7.476540	TTGATCGTATGTAATATAGCAGGGT	57.523	36.000	0.00	0.00	0.00	4.34
335	350	8.664798	GCCAAATTGATCGTATGTAATATAGCA	58.335	33.333	0.00	0.00	0.00	3.49
347	363	0.741574	ACGGCGCCAAATTGATCGTA	60.742	50.000	28.98	0.00	0.00	3.43
381	399	1.211818	GCCTAGCACAATCGCTCGAG	61.212	60.000	8.45	8.45	42.62	4.04
533	553	8.414003	GCATGATGATATGAATAGAATGCCATT	58.586	33.333	0.00	0.00	33.48	3.16
541	561	8.199449	TCGCATAAGCATGATGATATGAATAGA	58.801	33.333	17.42	10.22	42.27	1.98
549	569	3.929094	TGCTCGCATAAGCATGATGATA	58.071	40.909	0.00	0.00	47.00	2.15
1011	1032	6.828273	CCATTTAACTCCATTGGACACATCTA	59.172	38.462	0.00	0.00	0.00	1.98
1163	1184	5.982391	ACCTTCCTAATAGGATCATCCTCA	58.018	41.667	10.40	0.00	45.66	3.86
1547	1568	3.118629	ACACATCACGCTCTGGTATGAAT	60.119	43.478	0.00	0.00	0.00	2.57
1661	1682	9.187996	TCATCATATCCAAGCAAATGAGTTTTA	57.812	29.630	0.00	0.00	32.25	1.52
2125	2146	5.664294	ATGCAATTAAATGCCAGTTCTCA	57.336	34.783	12.85	0.00	45.83	3.27
2165	2186	3.003378	GCAGTGAAAAGTAAGGTGTCACC	59.997	47.826	14.68	14.68	39.52	4.02
2179	2200	5.376625	AGTGAATCCTACTTTGCAGTGAAA	58.623	37.500	0.00	0.00	34.06	2.69
2312	2333	2.737252	GGTTTCACTTAGACTCAAGGCG	59.263	50.000	0.00	0.00	0.00	5.52
2335	2356	8.042515	TCAGACACATCACATCAATTCATTAGA	58.957	33.333	0.00	0.00	0.00	2.10
2352	2373	2.050144	ACTTGGGACAGTCAGACACAT	58.950	47.619	2.66	0.00	42.39	3.21
2451	2472	8.790718	CAGGTATAATTGAAAGAGGAATCCATG	58.209	37.037	0.61	0.00	0.00	3.66
2629	2654	4.634443	ACCTGGTTCGACAAATTATAGCAC	59.366	41.667	0.00	0.00	0.00	4.40
2749	2774	0.750850	AACATACCACCGATCCCGAG	59.249	55.000	0.00	0.00	38.22	4.63
2918	3029	1.132881	AGCTGGGACCCCAAAATCAAA	60.133	47.619	8.45	0.00	46.63	2.69
2941	3052	0.108233	CTCTGTCTTCAGCCCTGAGC	60.108	60.000	0.00	0.00	41.13	4.26
2979	3090	1.200948	GGCCTTGAGTCAAAGTGCATC	59.799	52.381	18.12	4.18	0.00	3.91
2982	3093	1.251251	ATGGCCTTGAGTCAAAGTGC	58.749	50.000	3.32	9.66	0.00	4.40
3116	3231	4.101119	ACAACTCACACTGCCTAGTAAAGT	59.899	41.667	0.00	0.00	34.74	2.66
3209	3325	8.479689	TGAGGGACAAAAGATGTATACGAAATA	58.520	33.333	0.00	0.00	44.12	1.40
3229	3346	6.099125	TCTCAATGAACCGTATATTTGAGGGA	59.901	38.462	9.76	0.00	0.00	4.20
3231	3348	7.969536	ATCTCAATGAACCGTATATTTGAGG	57.030	36.000	9.76	0.00	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.