AutoCloner

Multiple sequence alignment - TraesCS2B01G174100

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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	TraesCS2B01G174100	chr2B	100.000	5288	0	0	1	5288	148236525	148241812	0.000000e+00	9766
1	TraesCS2B01G174100	chr2A	95.745	5311	152	23	1	5288	95990839	95996098	0.000000e+00	8488
2	TraesCS2B01G174100	chr2D	97.450	4313	97	4	590	4893	97219730	97224038	0.000000e+00	7343
3	TraesCS2B01G174100	chr2D	92.500	560	28	4	1	548	97219017	97219574	0.000000e+00	789
4	TraesCS2B01G174100	chr2D	92.188	384	18	5	4915	5288	97224238	97224619	2.800000e-147	532
5	TraesCS2B01G174100	chr3A	93.211	4154	227	34	543	4665	165420551	165416422	0.000000e+00	6058
6	TraesCS2B01G174100	chr3D	93.353	4122	218	35	543	4635	147817412	147821506	0.000000e+00	6043
7	TraesCS2B01G174100	chr3B	94.450	3838	175	22	543	4362	214564081	214560264	0.000000e+00	5873
8	TraesCS2B01G174100	chr1B	87.022	3375	427	9	922	4292	418810314	418813681	0.000000e+00	3795
9	TraesCS2B01G174100	chr1B	79.624	319	44	7	183	485	158537238	158537551	5.370000e-50	209
10	TraesCS2B01G174100	chr1D	87.267	3330	414	7	979	4301	309078545	309081871	0.000000e+00	3792
11	TraesCS2B01G174100	chr1D	79.144	374	47	12	186	533	108107476	108107108	4.120000e-56	230
12	TraesCS2B01G174100	chr1A	86.959	3328	425	8	979	4301	388838810	388842133	0.000000e+00	3733
13	TraesCS2B01G174100	chr1A	78.400	375	49	12	186	533	111129733	111129364	1.150000e-51	215
14	TraesCS2B01G174100	chr5B	82.353	3230	519	42	1079	4284	47579640	47576438	0.000000e+00	2760
15	TraesCS2B01G174100	chr4B	78.082	292	43	7	210	485	329806268	329805982	1.180000e-36	165
16	TraesCS2B01G174100	chr6B	88.235	85	9	1	557	640	620908267	620908183	3.370000e-17	100

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	TraesCS2B01G174100	chr2B	148236525	148241812	5287	False	9766	9766	100.000	1	5288	1	chr2B.!!$F1	5287
1	TraesCS2B01G174100	chr2A	95990839	95996098	5259	False	8488	8488	95.745	1	5288	1	chr2A.!!$F1	5287
2	TraesCS2B01G174100	chr2D	97219017	97224619	5602	False	2888	7343	94.046	1	5288	3	chr2D.!!$F1	5287
3	TraesCS2B01G174100	chr3A	165416422	165420551	4129	True	6058	6058	93.211	543	4665	1	chr3A.!!$R1	4122
4	TraesCS2B01G174100	chr3D	147817412	147821506	4094	False	6043	6043	93.353	543	4635	1	chr3D.!!$F1	4092
5	TraesCS2B01G174100	chr3B	214560264	214564081	3817	True	5873	5873	94.450	543	4362	1	chr3B.!!$R1	3819
6	TraesCS2B01G174100	chr1B	418810314	418813681	3367	False	3795	3795	87.022	922	4292	1	chr1B.!!$F2	3370
7	TraesCS2B01G174100	chr1D	309078545	309081871	3326	False	3792	3792	87.267	979	4301	1	chr1D.!!$F1	3322
8	TraesCS2B01G174100	chr1A	388838810	388842133	3323	False	3733	3733	86.959	979	4301	1	chr1A.!!$F1	3322
9	TraesCS2B01G174100	chr5B	47576438	47579640	3202	True	2760	2760	82.353	1079	4284	1	chr5B.!!$R1	3205

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	Hairpin	End Stability	Orientation
128	134	0.108138	TCTGCCGGCTTTCTTCTAGC	60.108	55.000	29.70	37.91	3.42	F
159	165	0.403655	TAGTTGGCCCAAGTGATGCA	59.596	50.000	14.23	0.00	3.96	F
578	622	0.622665	CAGTTCCCTCCAGCCATCTT	59.377	55.000	0.00	0.00	2.40	F
1944	2094	1.472552	GGGCAAACAAACTGTTGGGTC	60.473	52.381	0.00	40.14	4.46	F
2648	2798	2.937799	GAGAAGCTGAATGGAAGCAGAG	59.062	50.000	0.00	43.37	3.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1944	2094	3.322828	CCCCATAATTTCCATCAGGCAAG	59.677	47.826	33.74	4.01	R
2016	2166	4.450419	AGATGCTGATACGCAAGATTAAGC	59.550	41.667	44.06	3.09	R
2445	2595	0.816825	CCCCTGCAATCATCACTCCG	60.817	60.000	0.00	4.63	R
3381	3531	3.359033	AGCAAACACATGGTCAGCATAT	58.641	40.909	33.17	1.78	R
4475	4651	0.877071	CATGCTTGACCTGACACCAC	59.123	55.000	0.00	4.16	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
113	116	7.970061	TGCTGATTCTTATGTTTTGTAATCTGC	59.030	33.333	14.12	14.12	43.10	4.26
128	134	0.108138	TCTGCCGGCTTTCTTCTAGC	60.108	55.000	29.70	0.00	37.91	3.42
142	148	0.463295	TCTAGCTCGTGGGGTCGTAG	60.463	60.000	0.00	0.00	0.00	3.51
159	165	0.403655	TAGTTGGCCCAAGTGATGCA	59.596	50.000	14.23	0.00	0.00	3.96
206	212	3.282021	TCCTGCAATCCAGCTTCATAAC	58.718	45.455	0.00	0.00	40.36	1.89
208	214	3.285484	CTGCAATCCAGCTTCATAACCT	58.715	45.455	0.00	0.00	34.21	3.50
218	224	3.203040	AGCTTCATAACCTGGCCTACAAT	59.797	43.478	3.32	0.00	0.00	2.71
331	337	4.678509	TTGCTCAATTTGTAGGCTTACG	57.321	40.909	1.16	0.00	32.21	3.18
336	342	3.680937	TCAATTTGTAGGCTTACGTTCCG	59.319	43.478	0.00	0.00	32.21	4.30
338	344	2.068837	TTGTAGGCTTACGTTCCGTG	57.931	50.000	0.00	0.00	41.39	4.94
341	347	1.067635	GTAGGCTTACGTTCCGTGGAA	60.068	52.381	0.00	0.00	41.39	3.53
351	357	1.231221	TTCCGTGGAACATGTTTCGG	58.769	50.000	28.37	28.37	45.33	4.30
385	391	4.183865	TGTCTCCAGAAATGTTATCTGCG	58.816	43.478	0.00	0.00	42.36	5.18
440	446	5.880901	AGATGACAAAGGACTGTACCAAAT	58.119	37.500	0.00	0.00	0.00	2.32
446	452	2.783135	AGGACTGTACCAAATGCACAG	58.217	47.619	0.00	10.20	44.20	3.66
480	494	6.644248	ATTAAACTAACCCACAAACCTGTC	57.356	37.500	0.00	0.00	31.64	3.51
482	496	3.208747	ACTAACCCACAAACCTGTCAG	57.791	47.619	0.00	0.00	31.64	3.51
494	508	6.595326	CACAAACCTGTCAGTGTATCATATGT	59.405	38.462	1.90	0.00	31.64	2.29
517	531	6.073276	TGTTAACTTTCATCCACGTGAATCAG	60.073	38.462	19.30	7.45	37.88	2.90
541	555	9.039870	CAGTTTGAGCTCAAGATACTTAATAGG	57.960	37.037	27.02	12.15	37.15	2.57
578	622	0.622665	CAGTTCCCTCCAGCCATCTT	59.377	55.000	0.00	0.00	0.00	2.40
596	723	7.992033	AGCCATCTTCATTAGCATATATCTTCC	59.008	37.037	0.00	0.00	0.00	3.46
634	761	5.590530	TGTTGCATCAAATATACCAACCC	57.409	39.130	0.00	0.00	33.53	4.11
645	780	2.373335	TACCAACCCACACAAGCATT	57.627	45.000	0.00	0.00	0.00	3.56
688	823	7.270757	ACATTGTTAGACAACTATGCAACAA	57.729	32.000	10.47	0.00	45.83	2.83
710	846	2.330216	ACACCAGCTTACTTGACCTCT	58.670	47.619	0.00	0.00	0.00	3.69
770	910	7.337436	TGATGTCTTGATGATGTTTGCTTATGA	59.663	33.333	0.00	0.00	0.00	2.15
846	988	6.135290	TGAGTTTGTCAGGAATGTTTGAAG	57.865	37.500	0.00	0.00	0.00	3.02
862	1004	6.115446	TGTTTGAAGCGAGATATTCAAGGAT	58.885	36.000	0.00	0.00	43.97	3.24
881	1023	8.264347	TCAAGGATATTGCACTACTACAATTCA	58.736	33.333	0.00	0.00	37.63	2.57
1944	2094	1.472552	GGGCAAACAAACTGTTGGGTC	60.473	52.381	0.00	0.00	40.14	4.46
2445	2595	9.614792	ATGACATACCTTAAAGGATTTACAGAC	57.385	33.333	0.00	0.00	40.86	3.51
2616	2766	5.665459	GTTGCTCTTACAGATCAGTGGTAT	58.335	41.667	0.21	0.00	0.00	2.73
2648	2798	2.937799	GAGAAGCTGAATGGAAGCAGAG	59.062	50.000	0.00	0.00	43.37	3.35
2706	2856	3.443681	CAGCTGAAACCCGTAATGGATTT	59.556	43.478	8.42	0.00	42.00	2.17
2844	2994	3.384467	ACATGGCTTATTACACCATTGCC	59.616	43.478	0.00	0.00	42.31	4.52
2936	3086	8.153550	AGATGAAGTATGGGAATATGTGTTCTC	58.846	37.037	0.00	0.00	0.00	2.87
3381	3531	1.386945	AGGCGGTCCTCCTTCTACA	59.613	57.895	0.00	0.00	38.72	2.74
3842	3998	4.833478	AGCTCACTGTTGGTCTGATATT	57.167	40.909	0.00	0.00	0.00	1.28
4179	4338	1.667236	CGGTATTTGATGGAGCTGCA	58.333	50.000	11.44	11.44	0.00	4.41
4384	4545	4.082081	TGGTTTTCTGCCATCTATTGCTTG	60.082	41.667	0.00	0.00	0.00	4.01
4475	4651	9.330063	TGAGGACATAGTTTTTAGCAATCATAG	57.670	33.333	0.00	0.00	0.00	2.23
4487	4663	2.939103	GCAATCATAGTGGTGTCAGGTC	59.061	50.000	0.00	0.00	0.00	3.85
4558	4734	3.632643	TGGATTAGTGCAGCAGATTGA	57.367	42.857	0.00	0.00	0.00	2.57
4569	4745	4.039488	TGCAGCAGATTGACCTTTGATTTT	59.961	37.500	0.00	0.00	0.00	1.82
4611	4794	8.477419	TGTGATACCATTTCCTTCTTTCTTTT	57.523	30.769	0.00	0.00	0.00	2.27
4820	5003	1.305930	GGAACATGGTCTTGCGGGTC	61.306	60.000	11.29	0.00	0.00	4.46
4822	5005	0.038166	AACATGGTCTTGCGGGTCAT	59.962	50.000	0.00	0.00	0.00	3.06
4893	5076	3.879295	GTCATCAGGAGAGTGAGAGAGAG	59.121	52.174	0.00	0.00	0.00	3.20
4967	5328	3.291611	GGATACCCCGTCGTGTGT	58.708	61.111	0.00	0.00	0.00	3.72
5003	5364	3.044305	GAAGCAGCAGTCGCCGTT	61.044	61.111	0.00	0.00	39.83	4.44
5026	5387	1.520666	CGTTTATCCCTCCACGCCT	59.479	57.895	0.00	0.00	0.00	5.52
5041	5402	1.343681	ACGCCTCCCTTTCCCTGTATA	60.344	52.381	0.00	0.00	0.00	1.47
5044	5405	2.553247	GCCTCCCTTTCCCTGTATATGC	60.553	54.545	0.00	0.00	0.00	3.14
5045	5406	2.289694	CCTCCCTTTCCCTGTATATGCG	60.290	54.545	0.00	0.00	0.00	4.73
5070	5440	3.991051	CTGCCTGTGGGTCGTCGT	61.991	66.667	0.00	0.00	34.45	4.34
5071	5441	4.293648	TGCCTGTGGGTCGTCGTG	62.294	66.667	0.00	0.00	34.45	4.35
5136	5506	0.886490	CTGACTTGCAAGGAGGCGTT	60.886	55.000	29.18	7.31	36.28	4.84
5170	5540	3.031013	TCCATTCGATCTACTCCTTGCA	58.969	45.455	0.00	0.00	0.00	4.08
5183	5553	3.521126	ACTCCTTGCACTAGATGGTTGAT	59.479	43.478	0.00	0.00	0.00	2.57
5184	5554	4.716784	ACTCCTTGCACTAGATGGTTGATA	59.283	41.667	0.00	0.00	0.00	2.15
5192	5562	1.794714	AGATGGTTGATACCCTCGCT	58.205	50.000	0.00	0.00	44.35	4.93
5258	5628	0.514255	CAGTTCATGTGTCCTGCGTG	59.486	55.000	0.00	0.00	0.00	5.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
113	116	0.173708	ACGAGCTAGAAGAAAGCCGG	59.826	55.000	0.00	0.00	41.02	6.13
128	134	1.214589	CCAACTACGACCCCACGAG	59.785	63.158	0.00	0.00	37.03	4.18
142	148	1.406539	CTATGCATCACTTGGGCCAAC	59.593	52.381	16.66	5.00	0.00	3.77
159	165	1.527370	GCCCGGGAACAGAAGCTAT	59.473	57.895	29.31	0.00	0.00	2.97
230	236	5.198965	AGATAGCATTCATGACCTTGCTTT	58.801	37.500	24.14	18.80	42.52	3.51
233	239	5.298777	AGAAAGATAGCATTCATGACCTTGC	59.701	40.000	13.87	13.87	35.34	4.01
336	342	3.982576	AAAGACCGAAACATGTTCCAC	57.017	42.857	12.39	5.99	0.00	4.02
338	344	5.622770	ATGTAAAGACCGAAACATGTTCC	57.377	39.130	12.39	0.00	31.56	3.62
341	347	7.606456	AGACAATATGTAAAGACCGAAACATGT	59.394	33.333	0.00	0.00	34.54	3.21
351	357	9.167311	ACATTTCTGGAGACAATATGTAAAGAC	57.833	33.333	0.00	0.00	42.06	3.01
385	391	5.157067	GCTTGCTAACTGAATTCACTTTCC	58.843	41.667	3.38	0.00	0.00	3.13
440	446	7.038154	AGTTTAATTAACTTGCTTCTGTGCA	57.962	32.000	0.00	0.00	44.73	4.57
446	452	8.354426	TGTGGGTTAGTTTAATTAACTTGCTTC	58.646	33.333	9.58	0.00	44.73	3.86
494	508	5.995282	ACTGATTCACGTGGATGAAAGTTAA	59.005	36.000	15.75	0.00	41.78	2.01
517	531	9.601217	TTCCTATTAAGTATCTTGAGCTCAAAC	57.399	33.333	28.16	22.74	35.15	2.93
541	555	5.926542	GGAACTGCAAGGAAAATAACCTTTC	59.073	40.000	0.00	0.00	44.13	2.62
544	558	3.832490	GGGAACTGCAAGGAAAATAACCT	59.168	43.478	0.00	0.00	39.30	3.50
596	723	2.029124	GCAACAAACGGCACAAGAAAAG	59.971	45.455	0.00	0.00	0.00	2.27
634	761	1.948834	TCTGACACCAATGCTTGTGTG	59.051	47.619	0.00	9.48	37.64	3.82
645	780	6.545666	ACAATGTAATGTTTCTTCTGACACCA	59.454	34.615	0.00	0.00	0.00	4.17
646	781	6.970484	ACAATGTAATGTTTCTTCTGACACC	58.030	36.000	0.00	0.00	0.00	4.16
688	823	3.136626	AGAGGTCAAGTAAGCTGGTGTTT	59.863	43.478	0.00	0.00	0.00	2.83
846	988	5.641209	AGTGCAATATCCTTGAATATCTCGC	59.359	40.000	0.00	0.00	0.00	5.03
983	1129	3.189080	TGACATTTTCCTGCGATCAACAG	59.811	43.478	5.88	5.88	34.82	3.16
1944	2094	3.322828	CCCCATAATTTCCATCAGGCAAG	59.677	47.826	0.00	0.00	33.74	4.01
2016	2166	4.450419	AGATGCTGATACGCAAGATTAAGC	59.550	41.667	0.00	0.00	44.06	3.09
2445	2595	0.816825	CCCCTGCAATCATCACTCCG	60.817	60.000	0.00	0.00	0.00	4.63
2616	2766	8.262601	TCCATTCAGCTTCTCCATAAGTTATA	57.737	34.615	0.00	0.00	0.00	0.98
2648	2798	3.467374	TTTCCAAACATTTGACTGCCC	57.533	42.857	5.91	0.00	40.55	5.36
2706	2856	1.821759	CCAGCCCAACGTGTGTTCA	60.822	57.895	0.00	0.00	35.72	3.18
2844	2994	7.999679	ACATGTTACCATTTTGTAGATGATGG	58.000	34.615	0.00	0.00	43.65	3.51
2879	3029	9.553064	TTTCTTCAGGCTTGATAGAAGATATTC	57.447	33.333	13.13	0.00	44.03	1.75
3381	3531	3.359033	AGCAAACACATGGTCAGCATAT	58.641	40.909	0.00	0.00	33.17	1.78
4179	4338	2.032981	CTTTCCAGCTTTGGCACGT	58.967	52.632	0.00	0.00	41.70	4.49
4384	4545	2.072298	GTCAGTTGTGGTCTCTGCATC	58.928	52.381	0.00	0.00	0.00	3.91
4395	4557	4.274069	CAGAATGAAACGTGTCAGTTGTG	58.726	43.478	14.89	12.51	39.69	3.33
4446	4608	9.851686	TGATTGCTAAAAACTATGTCCTCATAT	57.148	29.630	0.00	0.00	36.18	1.78
4475	4651	0.877071	CATGCTTGACCTGACACCAC	59.123	55.000	0.00	0.00	0.00	4.16
4487	4663	6.874297	CATGTAACAATACCAACATGCTTG	57.126	37.500	0.00	0.00	41.77	4.01
4540	4716	3.539604	AGGTCAATCTGCTGCACTAATC	58.460	45.455	0.00	0.00	0.00	1.75
4569	4745	3.020274	TCACAAGGCAACAGCTGTAAAA	58.980	40.909	22.01	0.00	41.41	1.52
4611	4794	5.650266	TCACAGGTTTAGAACTGAGCAAAAA	59.350	36.000	5.12	0.00	38.09	1.94
4629	4812	4.433615	ACGACATAAGCAACTATCACAGG	58.566	43.478	0.00	0.00	0.00	4.00
4713	4896	2.570415	TCCAACGGCCACAGATTTTA	57.430	45.000	2.24	0.00	0.00	1.52
4717	4900	1.176527	CAAATCCAACGGCCACAGAT	58.823	50.000	2.24	0.00	0.00	2.90
4719	4902	0.893270	TCCAAATCCAACGGCCACAG	60.893	55.000	2.24	0.00	0.00	3.66
4967	5328	1.323271	CCGCTAACTCTCTCAGGGCA	61.323	60.000	0.00	0.00	0.00	5.36
5003	5364	0.906775	GTGGAGGGATAAACGGACCA	59.093	55.000	0.00	0.00	0.00	4.02
5009	5370	0.179054	GGAGGCGTGGAGGGATAAAC	60.179	60.000	0.00	0.00	0.00	2.01
5026	5387	2.404559	ACGCATATACAGGGAAAGGGA	58.595	47.619	0.00	0.00	0.00	4.20
5071	5441	2.568090	CAATTGTGGCACTCCGGC	59.432	61.111	19.83	0.00	41.67	6.13
5072	5442	1.597797	ATGCAATTGTGGCACTCCGG	61.598	55.000	19.83	0.00	45.23	5.14
5074	5444	0.174162	GGATGCAATTGTGGCACTCC	59.826	55.000	19.83	11.45	45.23	3.85
5076	5446	0.604578	GTGGATGCAATTGTGGCACT	59.395	50.000	19.83	0.00	45.23	4.40
5077	5447	0.390209	GGTGGATGCAATTGTGGCAC	60.390	55.000	11.55	11.55	45.23	5.01
5078	5448	0.830866	TGGTGGATGCAATTGTGGCA	60.831	50.000	7.40	0.00	46.66	4.92
5079	5449	0.390209	GTGGTGGATGCAATTGTGGC	60.390	55.000	7.40	0.00	0.00	5.01
5080	5450	0.247185	GGTGGTGGATGCAATTGTGG	59.753	55.000	7.40	0.00	0.00	4.17
5082	5452	0.968405	GTGGTGGTGGATGCAATTGT	59.032	50.000	7.40	0.00	0.00	2.71
5117	5487	0.886490	AACGCCTCCTTGCAAGTCAG	60.886	55.000	24.35	18.32	0.00	3.51
5136	5506	1.344438	CGAATGGATGGAATCGAGGGA	59.656	52.381	0.00	0.00	46.86	4.20
5183	5553	3.072468	CACGGGGAAGCGAGGGTA	61.072	66.667	0.00	0.00	0.00	3.69
5192	5562	1.209504	CTAGAATCCTTGCACGGGGAA	59.790	52.381	9.71	0.00	35.08	3.97
5258	5628	9.515020	TCTCATGTAAAAACAAAGACAAATCAC	57.485	29.630	0.00	0.00	0.00	3.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.