AutoCloner

Multiple sequence alignment - TraesCS4B01G090400

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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	TraesCS4B01G090400	chr4B	100.000	3126	0	0	1	3126	92558572	92555447	0.000000e+00	5773
1	TraesCS4B01G090400	chr4D	94.452	1478	67	9	767	2231	62746237	62744762	0.000000e+00	2261
2	TraesCS4B01G090400	chr4D	90.271	442	37	6	252	689	62746851	62746412	9.720000e-160	573
3	TraesCS4B01G090400	chr4A	95.122	1148	43	4	1103	2238	534160523	534161669	0.000000e+00	1797
4	TraesCS4B01G090400	chr4A	82.754	690	74	28	15	678	534159410	534160080	9.720000e-160	573
5	TraesCS4B01G090400	chr4A	86.408	412	30	8	714	1105	534160083	534160488	8.010000e-116	427
6	TraesCS4B01G090400	chr5A	99.663	890	3	0	2237	3126	320275819	320274930	0.000000e+00	1628
7	TraesCS4B01G090400	chr7B	99.550	888	4	0	2239	3126	516459340	516458453	0.000000e+00	1618
8	TraesCS4B01G090400	chr7B	98.715	856	10	1	2232	3087	194560822	194561676	0.000000e+00	1519
9	TraesCS4B01G090400	chr6B	99.550	888	4	0	2239	3126	346410233	346411120	0.000000e+00	1618
10	TraesCS4B01G090400	chr5B	99.661	884	3	0	2243	3126	239319002	239319885	0.000000e+00	1616
11	TraesCS4B01G090400	chr2A	98.646	886	11	1	2242	3126	608930504	608931389	0.000000e+00	1568
12	TraesCS4B01G090400	chr3A	98.086	888	15	2	2240	3126	115386529	115387415	0.000000e+00	1544
13	TraesCS4B01G090400	chr1B	97.975	889	17	1	2239	3126	269055277	269056165	0.000000e+00	1541
14	TraesCS4B01G090400	chr2B	94.966	894	43	2	2234	3126	594086393	594085501	0.000000e+00	1400

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	TraesCS4B01G090400	chr4B	92555447	92558572	3125	True	5773.000000	5773	100.000000	1	3126	1	chr4B.!!$R1	3125
1	TraesCS4B01G090400	chr4D	62744762	62746851	2089	True	1417.000000	2261	92.361500	252	2231	2	chr4D.!!$R1	1979
2	TraesCS4B01G090400	chr4A	534159410	534161669	2259	False	932.333333	1797	88.094667	15	2238	3	chr4A.!!$F1	2223
3	TraesCS4B01G090400	chr5A	320274930	320275819	889	True	1628.000000	1628	99.663000	2237	3126	1	chr5A.!!$R1	889
4	TraesCS4B01G090400	chr7B	516458453	516459340	887	True	1618.000000	1618	99.550000	2239	3126	1	chr7B.!!$R1	887
5	TraesCS4B01G090400	chr7B	194560822	194561676	854	False	1519.000000	1519	98.715000	2232	3087	1	chr7B.!!$F1	855
6	TraesCS4B01G090400	chr6B	346410233	346411120	887	False	1618.000000	1618	99.550000	2239	3126	1	chr6B.!!$F1	887
7	TraesCS4B01G090400	chr5B	239319002	239319885	883	False	1616.000000	1616	99.661000	2243	3126	1	chr5B.!!$F1	883
8	TraesCS4B01G090400	chr2A	608930504	608931389	885	False	1568.000000	1568	98.646000	2242	3126	1	chr2A.!!$F1	884
9	TraesCS4B01G090400	chr3A	115386529	115387415	886	False	1544.000000	1544	98.086000	2240	3126	1	chr3A.!!$F1	886
10	TraesCS4B01G090400	chr1B	269055277	269056165	888	False	1541.000000	1541	97.975000	2239	3126	1	chr1B.!!$F1	887
11	TraesCS4B01G090400	chr2B	594085501	594086393	892	True	1400.000000	1400	94.966000	2234	3126	1	chr2B.!!$R1	892

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
934	1082	0.605083	TACAGCACAGAGGCAGAGTG	59.395	55.0	0.0	0.0	35.83	3.51	F
1138	1327	0.309302	CATCGACGCTTCTCCGATCT	59.691	55.0	0.0	0.0	40.54	2.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2078	2267	0.320247	GCACTCTGTGACCACTCCAG	60.320	60.000	1.52	0.0	35.23	3.86	R
2327	2533	1.202256	TGTAATGCCGCGAGAGTAGTG	60.202	52.381	8.23	0.0	0.00	2.74	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
34	35	5.004821	CACTCACTACTGCACGATGAAATAC	59.995	44.000	0.00	0.00	0.00	1.89
49	50	7.776969	ACGATGAAATACTGGTACTCCTACTAA	59.223	37.037	0.00	0.00	34.23	2.24
55	56	7.670605	ATACTGGTACTCCTACTAATTTGCA	57.329	36.000	0.00	0.00	34.23	4.08
102	130	1.831106	TCAAGATCGTGGCTACCATGT	59.169	47.619	8.84	0.00	41.03	3.21
104	132	2.604046	AGATCGTGGCTACCATGTTC	57.396	50.000	5.77	7.16	41.03	3.18
119	147	6.743575	ACCATGTTCTGCTACAAAGTTATC	57.256	37.500	0.00	0.00	0.00	1.75
120	148	5.351465	ACCATGTTCTGCTACAAAGTTATCG	59.649	40.000	0.00	0.00	0.00	2.92
143	171	4.804261	GCAAGTGTGAAGAGTAATGGAGGT	60.804	45.833	0.00	0.00	0.00	3.85
149	177	8.822805	AGTGTGAAGAGTAATGGAGGTAATTAA	58.177	33.333	0.00	0.00	0.00	1.40
155	183	9.838339	AAGAGTAATGGAGGTAATTAATCTGTG	57.162	33.333	6.84	0.00	41.55	3.66
156	184	8.993424	AGAGTAATGGAGGTAATTAATCTGTGT	58.007	33.333	5.60	0.00	41.12	3.72
157	185	9.614792	GAGTAATGGAGGTAATTAATCTGTGTT	57.385	33.333	0.00	0.00	33.78	3.32
211	239	3.244033	TGTTTGGCCAAAAAGACACAG	57.756	42.857	31.92	0.00	31.33	3.66
213	241	3.007398	TGTTTGGCCAAAAAGACACAGTT	59.993	39.130	31.92	0.00	31.33	3.16
244	272	9.119418	CACCTAAACATCCACATATACATTTCA	57.881	33.333	0.00	0.00	0.00	2.69
272	300	3.252701	GTGACACTCTTCAAGTACCGAGA	59.747	47.826	0.00	0.00	36.07	4.04
291	319	1.675641	GGTGAGTTGCAGGGCGAAT	60.676	57.895	0.00	0.00	0.00	3.34
310	338	6.128418	GGCGAATAATCTGAGCCTAATCTTTC	60.128	42.308	0.00	0.00	44.06	2.62
311	339	6.425114	GCGAATAATCTGAGCCTAATCTTTCA	59.575	38.462	0.00	0.00	0.00	2.69
324	352	6.373774	GCCTAATCTTTCATGGATGTATCTGG	59.626	42.308	0.00	0.00	0.00	3.86
346	375	7.335055	CTGGCAATGGTGACAAATACATGTTC	61.335	42.308	2.30	0.00	44.22	3.18
352	382	6.744112	TGGTGACAAATACATGTTCTTTTCC	58.256	36.000	2.30	5.59	37.44	3.13
378	408	1.672881	GGATTGCTCGGAGATTGTTGG	59.327	52.381	9.69	0.00	33.89	3.77
388	418	4.469945	TCGGAGATTGTTGGAGAACCTAAT	59.530	41.667	0.00	0.00	37.04	1.73
394	424	3.686016	TGTTGGAGAACCTAATGGCTTC	58.314	45.455	0.00	0.00	36.63	3.86
409	439	8.097038	CCTAATGGCTTCTGTATATCTAAAGCA	58.903	37.037	7.59	0.00	43.15	3.91
439	470	4.952335	CCTCCTTTCTATTGTGCTTTGGAT	59.048	41.667	0.00	0.00	0.00	3.41
510	541	5.775195	TCTCGGCCATTAGATTAAGATCTGA	59.225	40.000	2.24	0.00	42.55	3.27
534	565	1.464997	CCGCCCTTCTTTCTTCTTTCG	59.535	52.381	0.00	0.00	0.00	3.46
557	588	0.977395	ACCTTCTTCCTCCTCCAACG	59.023	55.000	0.00	0.00	0.00	4.10
644	678	4.761739	TGCCTTTCTAAACATGTGAAGAGG	59.238	41.667	0.00	9.46	0.00	3.69
686	720	6.681729	AGTGAAGAGAAATGGTGGTAACTA	57.318	37.500	0.00	0.00	37.61	2.24
689	723	7.824779	AGTGAAGAGAAATGGTGGTAACTAATC	59.175	37.037	0.00	0.00	37.61	1.75
690	724	7.824779	GTGAAGAGAAATGGTGGTAACTAATCT	59.175	37.037	0.00	0.00	37.61	2.40
692	726	7.496346	AGAGAAATGGTGGTAACTAATCTGA	57.504	36.000	0.00	0.00	37.61	3.27
693	727	8.095452	AGAGAAATGGTGGTAACTAATCTGAT	57.905	34.615	0.00	0.00	37.61	2.90
697	731	9.573133	GAAATGGTGGTAACTAATCTGATTTTG	57.427	33.333	8.38	5.06	37.61	2.44
698	732	8.650143	AATGGTGGTAACTAATCTGATTTTGT	57.350	30.769	8.38	5.67	37.61	2.83
699	733	8.650143	ATGGTGGTAACTAATCTGATTTTGTT	57.350	30.769	8.38	14.94	37.61	2.83
700	734	8.472007	TGGTGGTAACTAATCTGATTTTGTTT	57.528	30.769	19.12	8.01	37.61	2.83
734	823	7.548075	CCGTGGTACTCTATAAGAAACACATTT	59.452	37.037	0.00	0.00	0.00	2.32
788	919	8.869986	ACCCTACATATAATCAGCCCATAATA	57.130	34.615	0.00	0.00	0.00	0.98
789	920	8.938883	ACCCTACATATAATCAGCCCATAATAG	58.061	37.037	0.00	0.00	0.00	1.73
933	1081	0.605589	GTACAGCACAGAGGCAGAGT	59.394	55.000	0.00	0.00	35.83	3.24
934	1082	0.605083	TACAGCACAGAGGCAGAGTG	59.395	55.000	0.00	0.00	35.83	3.51
940	1088	1.827344	CACAGAGGCAGAGTGATACCA	59.173	52.381	0.00	0.00	35.33	3.25
941	1089	2.234661	CACAGAGGCAGAGTGATACCAA	59.765	50.000	0.00	0.00	35.33	3.67
942	1090	2.499289	ACAGAGGCAGAGTGATACCAAG	59.501	50.000	0.00	0.00	0.00	3.61
943	1091	2.762887	CAGAGGCAGAGTGATACCAAGA	59.237	50.000	0.00	0.00	0.00	3.02
944	1092	3.196469	CAGAGGCAGAGTGATACCAAGAA	59.804	47.826	0.00	0.00	0.00	2.52
945	1093	3.450457	AGAGGCAGAGTGATACCAAGAAG	59.550	47.826	0.00	0.00	0.00	2.85
1015	1163	3.412386	GCAGGGGTATATAAAGCACCAG	58.588	50.000	0.00	0.00	33.78	4.00
1024	1176	4.923000	TATAAAGCACCAGTCCGCCACG	62.923	54.545	0.00	0.00	0.00	4.94
1046	1198	3.814842	GACACCAACACATCAACATCTCA	59.185	43.478	0.00	0.00	0.00	3.27
1053	1205	3.008813	ACACATCAACATCTCAAGCTCCT	59.991	43.478	0.00	0.00	0.00	3.69
1058	1210	4.978099	TCAACATCTCAAGCTCCTTTTCT	58.022	39.130	0.00	0.00	0.00	2.52
1063	1215	2.369860	TCTCAAGCTCCTTTTCTGCTCA	59.630	45.455	0.00	0.00	35.85	4.26
1064	1216	3.144506	CTCAAGCTCCTTTTCTGCTCAA	58.855	45.455	0.00	0.00	35.85	3.02
1066	1218	1.517242	AGCTCCTTTTCTGCTCAACG	58.483	50.000	0.00	0.00	30.41	4.10
1074	1226	0.610174	TTCTGCTCAACGCCATCTCT	59.390	50.000	0.00	0.00	38.05	3.10
1077	1229	1.880340	GCTCAACGCCATCTCTCCG	60.880	63.158	0.00	0.00	0.00	4.63
1080	1232	2.169789	CAACGCCATCTCTCCGCTG	61.170	63.158	0.00	0.00	0.00	5.18
1138	1327	0.309302	CATCGACGCTTCTCCGATCT	59.691	55.000	0.00	0.00	40.54	2.75
1255	1444	4.654412	GATGAGCTCCGCGCCGAT	62.654	66.667	12.15	0.00	40.39	4.18
1326	1515	4.103103	CGTCGCCGCTCAGAGACA	62.103	66.667	0.00	0.00	33.56	3.41
1417	1606	1.376424	CACGGTGGAGCTGCTTGAT	60.376	57.895	6.82	0.00	0.00	2.57
1475	1664	1.381872	AGCTACGCCTCCTCCATGT	60.382	57.895	0.00	0.00	0.00	3.21
1933	2122	3.342627	CGGACGGTGAAAAGCGCA	61.343	61.111	11.47	0.00	0.00	6.09
2078	2267	0.107654	AAGCGTTAGGATGGTGCTCC	60.108	55.000	0.00	0.00	34.19	4.70
2133	2322	4.695928	GGTTCTCAGGTTGTGAAGGATTAC	59.304	45.833	0.00	0.00	33.60	1.89
2134	2323	4.553330	TCTCAGGTTGTGAAGGATTACC	57.447	45.455	0.00	0.00	33.60	2.85
2141	2338	4.457949	GGTTGTGAAGGATTACCGAACAAT	59.542	41.667	0.00	0.00	38.64	2.71
2162	2363	8.322906	ACAATCACAGAAACGATCATAGAAAA	57.677	30.769	0.00	0.00	0.00	2.29
2165	2366	8.722480	ATCACAGAAACGATCATAGAAAATCA	57.278	30.769	0.00	0.00	0.00	2.57
2932	3138	1.534163	TCTTCAACGTCGTCATCGAGT	59.466	47.619	0.00	0.00	46.96	4.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	2.636768	TCATCGTGCAGTAGTGAGTG	57.363	50.000	0.42	0.00	0.00	3.51
11	12	3.660501	TTTCATCGTGCAGTAGTGAGT	57.339	42.857	0.42	0.00	0.00	3.41
12	13	5.230936	CAGTATTTCATCGTGCAGTAGTGAG	59.769	44.000	0.42	0.00	0.00	3.51
13	14	5.102313	CAGTATTTCATCGTGCAGTAGTGA	58.898	41.667	0.42	0.00	0.00	3.41
34	35	5.237344	GCATGCAAATTAGTAGGAGTACCAG	59.763	44.000	14.21	0.00	38.94	4.00
49	50	7.546667	AGAAATCTAAAAATGACGCATGCAAAT	59.453	29.630	19.57	4.65	0.00	2.32
55	56	6.757897	TCCAGAAATCTAAAAATGACGCAT	57.242	33.333	0.00	0.00	0.00	4.73
102	130	4.994852	ACTTGCGATAACTTTGTAGCAGAA	59.005	37.500	0.00	0.00	35.95	3.02
104	132	4.152402	ACACTTGCGATAACTTTGTAGCAG	59.848	41.667	0.00	0.00	35.95	4.24
119	147	3.325870	TCCATTACTCTTCACACTTGCG	58.674	45.455	0.00	0.00	0.00	4.85
120	148	3.686726	CCTCCATTACTCTTCACACTTGC	59.313	47.826	0.00	0.00	0.00	4.01
163	191	9.602568	TGTGTTTCTTGTATAGTGTTTTAGTCA	57.397	29.630	0.00	0.00	0.00	3.41
170	198	9.515020	CAAACAATGTGTTTCTTGTATAGTGTT	57.485	29.630	3.43	0.00	46.61	3.32
171	199	8.134895	CCAAACAATGTGTTTCTTGTATAGTGT	58.865	33.333	3.43	0.00	46.61	3.55
172	200	7.114811	GCCAAACAATGTGTTTCTTGTATAGTG	59.885	37.037	3.43	0.00	46.61	2.74
185	213	3.938334	GTCTTTTTGGCCAAACAATGTGT	59.062	39.130	30.43	0.00	0.00	3.72
198	226	4.625311	GGTGAAACAACTGTGTCTTTTTGG	59.375	41.667	1.85	0.00	39.98	3.28
199	227	5.469479	AGGTGAAACAACTGTGTCTTTTTG	58.531	37.500	1.85	0.00	39.98	2.44
200	228	5.722021	AGGTGAAACAACTGTGTCTTTTT	57.278	34.783	1.85	0.00	39.98	1.94
244	272	6.514063	GGTACTTGAAGAGTGTCACTAAACT	58.486	40.000	5.21	0.00	39.48	2.66
249	277	3.220110	TCGGTACTTGAAGAGTGTCACT	58.780	45.455	4.81	4.81	39.48	3.41
272	300	2.129555	ATTCGCCCTGCAACTCACCT	62.130	55.000	0.00	0.00	0.00	4.00
291	319	7.379059	TCCATGAAAGATTAGGCTCAGATTA	57.621	36.000	0.00	0.00	0.00	1.75
310	338	3.254903	CACCATTGCCAGATACATCCATG	59.745	47.826	0.00	0.00	0.00	3.66
311	339	3.138839	TCACCATTGCCAGATACATCCAT	59.861	43.478	0.00	0.00	0.00	3.41
324	352	5.713025	AGAACATGTATTTGTCACCATTGC	58.287	37.500	0.00	0.00	0.00	3.56
352	382	2.099141	TCTCCGAGCAATCCAACAAG	57.901	50.000	0.00	0.00	0.00	3.16
388	418	5.221722	CCCTGCTTTAGATATACAGAAGCCA	60.222	44.000	4.20	0.00	41.40	4.75
394	424	5.482175	AGGCTACCCTGCTTTAGATATACAG	59.518	44.000	0.00	0.00	40.94	2.74
409	439	3.456277	CACAATAGAAAGGAGGCTACCCT	59.544	47.826	0.00	0.00	46.74	4.34
439	470	5.952526	TCAGACGATTTATGTATAGCCGA	57.047	39.130	0.00	0.00	0.00	5.54
510	541	0.320508	GAAGAAAGAAGGGCGGTCGT	60.321	55.000	0.00	0.00	0.00	4.34
534	565	1.604915	GAGGAGGAAGAAGGTGGGC	59.395	63.158	0.00	0.00	0.00	5.36
557	588	1.602377	CGATTTATTGGCGGAGGAACC	59.398	52.381	0.00	0.00	0.00	3.62
644	678	5.591099	TCACTTTCTTTGACCTGCATTTTC	58.409	37.500	0.00	0.00	0.00	2.29
741	830	6.072728	GGGTAAAAATCCATTGTGGCTTTTTC	60.073	38.462	20.23	14.10	46.68	2.29
788	919	1.618837	ACATGTCGTGTACAGCCTTCT	59.381	47.619	0.00	0.00	42.70	2.85
789	920	2.080286	ACATGTCGTGTACAGCCTTC	57.920	50.000	0.00	0.00	42.70	3.46
933	1081	8.597167	TCTCATTTCTTCTTCTTCTTGGTATCA	58.403	33.333	0.00	0.00	0.00	2.15
934	1082	9.442047	TTCTCATTTCTTCTTCTTCTTGGTATC	57.558	33.333	0.00	0.00	0.00	2.24
1015	1163	3.343421	GTTGGTGTCGTGGCGGAC	61.343	66.667	1.92	1.92	37.45	4.79
1024	1176	3.814842	TGAGATGTTGATGTGTTGGTGTC	59.185	43.478	0.00	0.00	0.00	3.67
1046	1198	1.876156	CGTTGAGCAGAAAAGGAGCTT	59.124	47.619	0.00	0.00	39.02	3.74
1063	1215	2.185350	CAGCGGAGAGATGGCGTT	59.815	61.111	0.00	0.00	31.47	4.84
1064	1216	2.755876	TCAGCGGAGAGATGGCGT	60.756	61.111	0.00	0.00	36.78	5.68
1066	1218	3.531283	TCTCAGCGGAGAGATGGC	58.469	61.111	12.88	0.00	45.12	4.40
1074	1226	2.045561	TGTTTTGGTTTCTCAGCGGA	57.954	45.000	0.00	0.00	0.00	5.54
1077	1229	3.130340	TCCTGTTGTTTTGGTTTCTCAGC	59.870	43.478	0.00	0.00	0.00	4.26
1080	1232	5.299279	TGATCTCCTGTTGTTTTGGTTTCTC	59.701	40.000	0.00	0.00	0.00	2.87
1138	1327	2.014574	GCAGAGAGGCGTGTAGAGAGA	61.015	57.143	0.00	0.00	0.00	3.10
1210	1399	4.530857	GCCAGCCAGCGGTCGTAT	62.531	66.667	0.00	0.00	0.00	3.06
1311	1500	4.121669	GCTGTCTCTGAGCGGCGA	62.122	66.667	12.98	0.00	0.00	5.54
1318	1507	2.871099	GCGACGAGCTGTCTCTGA	59.129	61.111	0.00	0.00	45.87	3.27
1404	1593	2.036571	CACGCATCAAGCAGCTCCA	61.037	57.895	0.00	0.00	46.13	3.86
1437	1626	3.781770	CTGATCAGGTCGAGGCGGC	62.782	68.421	15.38	0.00	0.00	6.53
2078	2267	0.320247	GCACTCTGTGACCACTCCAG	60.320	60.000	1.52	0.00	35.23	3.86
2133	2322	3.431912	TGATCGTTTCTGTGATTGTTCGG	59.568	43.478	0.00	0.00	0.00	4.30
2134	2323	4.645667	TGATCGTTTCTGTGATTGTTCG	57.354	40.909	0.00	0.00	0.00	3.95
2141	2338	7.819415	ACTGATTTTCTATGATCGTTTCTGTGA	59.181	33.333	0.00	0.00	0.00	3.58
2327	2533	1.202256	TGTAATGCCGCGAGAGTAGTG	60.202	52.381	8.23	0.00	0.00	2.74
2932	3138	1.946768	GACAAACTAGCAACAGTGGCA	59.053	47.619	1.78	0.00	0.00	4.92

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.