AutoCloner

Multiple sequence alignment - TraesCS3B01G056800

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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	TraesCS3B01G056800	chr3B	100.000	2753	0	0	1	2753	29731116	29733868	0.000000e+00	5084.0
1	TraesCS3B01G056800	chr3B	86.909	1818	136	41	917	2671	29851752	29853530	0.000000e+00	1945.0
2	TraesCS3B01G056800	chr3B	87.596	653	45	19	2101	2746	75524234	75523611	0.000000e+00	725.0
3	TraesCS3B01G056800	chr3B	87.633	469	42	4	1485	1940	75524960	75524495	5.220000e-147	531.0
4	TraesCS3B01G056800	chr3B	86.313	358	23	2	1132	1489	75528074	75527743	1.560000e-97	366.0
5	TraesCS3B01G056800	chr3B	84.641	306	26	14	7	305	29851443	29851734	4.490000e-73	285.0
6	TraesCS3B01G056800	chr3B	76.126	444	73	25	1956	2380	30376258	30376687	4.650000e-48	202.0
7	TraesCS3B01G056800	chr3B	84.252	127	16	4	1129	1254	29626235	29626358	1.340000e-23	121.0
8	TraesCS3B01G056800	chr3A	95.716	1844	39	16	917	2753	26425198	26427008	0.000000e+00	2931.0
9	TraesCS3B01G056800	chr3A	96.055	583	22	1	306	887	709913345	709913927	0.000000e+00	948.0
10	TraesCS3B01G056800	chr3A	96.111	180	5	2	128	305	26425001	26425180	2.680000e-75	292.0
11	TraesCS3B01G056800	chr3A	97.368	76	1	1	7	81	26424924	26424999	8.000000e-26	128.0
12	TraesCS3B01G056800	chr3D	90.969	908	58	7	1132	2019	18950648	18951551	0.000000e+00	1201.0
13	TraesCS3B01G056800	chr3D	90.921	749	49	15	2020	2753	18951591	18952335	0.000000e+00	989.0
14	TraesCS3B01G056800	chr3D	77.215	237	46	5	2233	2466	18730118	18730349	6.190000e-27	132.0
15	TraesCS3B01G056800	chr3D	100.000	43	0	0	200	242	18950472	18950514	2.270000e-11	80.5
16	TraesCS3B01G056800	chr3D	100.000	31	0	0	1096	1126	18950591	18950621	1.060000e-04	58.4
17	TraesCS3B01G056800	chr2A	96.907	582	18	0	305	886	105413182	105413763	0.000000e+00	976.0
18	TraesCS3B01G056800	chr2A	96.239	585	20	2	302	885	109593452	109594035	0.000000e+00	957.0
19	TraesCS3B01G056800	chr5A	96.730	581	19	0	306	886	436218415	436217835	0.000000e+00	968.0
20	TraesCS3B01G056800	chr5B	96.552	580	19	1	310	889	548456113	548455535	0.000000e+00	959.0
21	TraesCS3B01G056800	chr6A	96.392	582	20	1	306	886	454675342	454674761	0.000000e+00	957.0
22	TraesCS3B01G056800	chr7A	96.373	579	21	0	306	884	259396226	259396804	0.000000e+00	953.0
23	TraesCS3B01G056800	chr7A	95.897	585	23	1	306	890	252455361	252455944	0.000000e+00	946.0
24	TraesCS3B01G056800	chr1A	96.522	575	20	0	310	884	494796890	494796316	0.000000e+00	952.0

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	TraesCS3B01G056800	chr3B	29731116	29733868	2752	False	5084.000000	5084	100.000000	1	2753	1	chr3B.!!$F2	2752
1	TraesCS3B01G056800	chr3B	29851443	29853530	2087	False	1115.000000	1945	85.775000	7	2671	2	chr3B.!!$F4	2664
2	TraesCS3B01G056800	chr3B	75523611	75528074	4463	True	540.666667	725	87.180667	1132	2746	3	chr3B.!!$R1	1614
3	TraesCS3B01G056800	chr3A	26424924	26427008	2084	False	1117.000000	2931	96.398333	7	2753	3	chr3A.!!$F2	2746
4	TraesCS3B01G056800	chr3A	709913345	709913927	582	False	948.000000	948	96.055000	306	887	1	chr3A.!!$F1	581
5	TraesCS3B01G056800	chr3D	18950472	18952335	1863	False	582.225000	1201	95.472500	200	2753	4	chr3D.!!$F2	2553
6	TraesCS3B01G056800	chr2A	105413182	105413763	581	False	976.000000	976	96.907000	305	886	1	chr2A.!!$F1	581
7	TraesCS3B01G056800	chr2A	109593452	109594035	583	False	957.000000	957	96.239000	302	885	1	chr2A.!!$F2	583
8	TraesCS3B01G056800	chr5A	436217835	436218415	580	True	968.000000	968	96.730000	306	886	1	chr5A.!!$R1	580
9	TraesCS3B01G056800	chr5B	548455535	548456113	578	True	959.000000	959	96.552000	310	889	1	chr5B.!!$R1	579
10	TraesCS3B01G056800	chr6A	454674761	454675342	581	True	957.000000	957	96.392000	306	886	1	chr6A.!!$R1	580
11	TraesCS3B01G056800	chr7A	259396226	259396804	578	False	953.000000	953	96.373000	306	884	1	chr7A.!!$F2	578
12	TraesCS3B01G056800	chr7A	252455361	252455944	583	False	946.000000	946	95.897000	306	890	1	chr7A.!!$F1	584
13	TraesCS3B01G056800	chr1A	494796316	494796890	574	True	952.000000	952	96.522000	310	884	1	chr1A.!!$R1	574

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
903	921	0.036306	AAATCCCGTGGACTGGTCAC	59.964	55.0	3.1	0.0	32.98	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2238	5241	6.313905	TCCAAAAGAAAGAGATAAGCATCGTC	59.686	38.462	0.0	0.0	36.2	4.2	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
92	94	4.825546	GATGATCAAAATCGTCTGCCAT	57.174	40.909	0.00	0.00	42.40	4.40
93	95	5.929697	GATGATCAAAATCGTCTGCCATA	57.070	39.130	0.00	0.00	42.40	2.74
94	96	5.924786	GATGATCAAAATCGTCTGCCATAG	58.075	41.667	0.00	0.00	42.40	2.23
95	97	4.129380	TGATCAAAATCGTCTGCCATAGG	58.871	43.478	0.00	0.00	34.39	2.57
96	98	2.917933	TCAAAATCGTCTGCCATAGGG	58.082	47.619	0.00	0.00	37.18	3.53
97	99	2.238646	TCAAAATCGTCTGCCATAGGGT	59.761	45.455	0.00	0.00	36.17	4.34
98	100	2.332063	AAATCGTCTGCCATAGGGTG	57.668	50.000	0.00	0.00	36.17	4.61
99	101	0.179045	AATCGTCTGCCATAGGGTGC	60.179	55.000	0.00	0.00	36.17	5.01
100	102	1.337384	ATCGTCTGCCATAGGGTGCA	61.337	55.000	0.00	0.00	36.17	4.57
101	103	1.078497	CGTCTGCCATAGGGTGCAA	60.078	57.895	0.00	0.00	36.98	4.08
102	104	0.676466	CGTCTGCCATAGGGTGCAAA	60.676	55.000	0.00	0.00	36.98	3.68
109	111	1.750778	CCATAGGGTGCAAACCATCAC	59.249	52.381	10.96	0.00	0.00	3.06
113	115	2.397597	AGGGTGCAAACCATCACTTTT	58.602	42.857	10.96	0.00	33.91	2.27
114	116	3.571590	AGGGTGCAAACCATCACTTTTA	58.428	40.909	10.96	0.00	33.91	1.52
115	117	3.964031	AGGGTGCAAACCATCACTTTTAA	59.036	39.130	10.96	0.00	33.91	1.52
131	133	6.072508	TCACTTTTAAACAAGCTGGAGCATAG	60.073	38.462	0.00	0.00	45.16	2.23
168	179	8.299570	GCTGGAGTGATAAAAGAATTTCTCAAA	58.700	33.333	0.00	0.00	37.28	2.69
292	308	8.336235	TCATCCCAAAGTTCATAACTAAAGGAT	58.664	33.333	9.75	9.75	41.91	3.24
376	393	4.389374	ACGTCCTCACACAAGAAAATCAT	58.611	39.130	0.00	0.00	0.00	2.45
524	542	2.162338	TACCGTTGGCCGAAGAGTGG	62.162	60.000	7.61	1.42	39.56	4.00
622	640	0.326595	TTCGGCCTCCTGTTAATGCA	59.673	50.000	0.00	0.00	0.00	3.96
702	720	1.893801	ACGGTAGACCAAAGAGTCCTG	59.106	52.381	0.00	0.00	37.49	3.86
805	823	3.691342	CCAACTGGAGGCCGACGA	61.691	66.667	0.00	0.00	37.39	4.20
901	919	1.905637	AAAAATCCCGTGGACTGGTC	58.094	50.000	0.00	0.00	32.98	4.02
902	920	0.768622	AAAATCCCGTGGACTGGTCA	59.231	50.000	3.10	0.00	32.98	4.02
903	921	0.036306	AAATCCCGTGGACTGGTCAC	59.964	55.000	3.10	0.00	32.98	3.67
904	922	0.836400	AATCCCGTGGACTGGTCACT	60.836	55.000	3.10	0.00	32.98	3.41
905	923	0.040646	ATCCCGTGGACTGGTCACTA	59.959	55.000	3.10	0.00	32.98	2.74
915	933	1.132817	ACTGGTCACTAACTCCCTGGT	60.133	52.381	0.00	0.00	0.00	4.00
933	951	2.166050	TGGTCAATAACTAAGCCGCGTA	59.834	45.455	4.92	0.00	0.00	4.42
952	970	3.183775	CGTAAACAAGTCTTCCAACTCCG	59.816	47.826	0.00	0.00	0.00	4.63
966	984	1.713297	ACTCCGTGTTACCTTCCAGT	58.287	50.000	0.00	0.00	0.00	4.00
979	997	3.053019	ACCTTCCAGTCCCCTACTACTAC	60.053	52.174	0.00	0.00	35.76	2.73
982	1000	5.456474	CCTTCCAGTCCCCTACTACTACTAG	60.456	52.000	0.00	0.00	35.76	2.57
983	1001	4.900706	TCCAGTCCCCTACTACTACTAGA	58.099	47.826	0.00	0.00	35.76	2.43
1021	1054	2.642427	TGGATCCATTTCACGTCCATG	58.358	47.619	11.44	0.00	34.23	3.66
1023	1056	2.292267	GATCCATTTCACGTCCATGCT	58.708	47.619	0.00	0.00	0.00	3.79
1042	1075	0.522626	TGATGCAACTGCCATGTTCG	59.477	50.000	0.00	0.00	41.18	3.95
1063	1096	1.429927	CTCAGCCATGCTTCTGCTCG	61.430	60.000	0.00	0.00	36.40	5.03
1070	1103	2.511145	GCTTCTGCTCGCCCTCAG	60.511	66.667	0.00	0.00	36.03	3.35
1086	1119	0.532573	TCAGCCTCCTTTCTAGCACG	59.467	55.000	0.00	0.00	0.00	5.34
1254	1308	3.374367	TCGACATCTCCTACGAAGACAAG	59.626	47.826	0.00	0.00	0.00	3.16
1304	1358	1.295357	TACGGCGGCATTTGTGACAG	61.295	55.000	13.24	0.00	0.00	3.51
1514	4356	2.358247	AGCGTACAAGCCCAACGG	60.358	61.111	0.00	0.00	37.12	4.44
1564	4406	3.726144	TGCCCATGATGCCGGTGA	61.726	61.111	1.90	0.00	0.00	4.02
1579	4421	2.039787	TGATGGGGTACGAGGGCA	59.960	61.111	0.00	0.00	0.00	5.36
1820	4683	7.923878	GGTTTAGTTCAGTTTTGGCAAGATTAA	59.076	33.333	0.00	0.00	0.00	1.40
1892	4755	6.652481	AGATTTACAGGAGAAGTGAACACATG	59.348	38.462	7.68	0.00	0.00	3.21
2605	5617	3.669536	TGATCCGTGCATGAACTTTACA	58.330	40.909	7.72	0.00	0.00	2.41
2606	5618	4.260985	TGATCCGTGCATGAACTTTACAT	58.739	39.130	7.72	0.00	0.00	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	3.002038	AGTACTCCCTCCGTAAGAGTG	57.998	52.381	2.26	0.00	40.93	3.51
2	3	3.433456	GCTAGTACTCCCTCCGTAAGAGT	60.433	52.174	0.00	0.00	41.47	3.24
3	4	3.140623	GCTAGTACTCCCTCCGTAAGAG	58.859	54.545	0.00	0.00	42.83	2.85
4	5	2.776536	AGCTAGTACTCCCTCCGTAAGA	59.223	50.000	0.00	0.00	43.02	2.10
5	6	3.211718	AGCTAGTACTCCCTCCGTAAG	57.788	52.381	0.00	0.00	0.00	2.34
81	83	1.337384	TGCACCCTATGGCAGACGAT	61.337	55.000	0.00	0.00	34.58	3.73
82	84	1.549243	TTGCACCCTATGGCAGACGA	61.549	55.000	0.00	0.00	41.68	4.20
83	85	0.676466	TTTGCACCCTATGGCAGACG	60.676	55.000	0.00	0.00	41.68	4.18
84	86	0.811281	GTTTGCACCCTATGGCAGAC	59.189	55.000	0.00	0.00	41.68	3.51
85	87	0.323360	GGTTTGCACCCTATGGCAGA	60.323	55.000	0.00	0.00	41.68	4.26
86	88	0.611618	TGGTTTGCACCCTATGGCAG	60.612	55.000	0.00	0.00	43.49	4.85
87	89	0.040942	ATGGTTTGCACCCTATGGCA	59.959	50.000	0.00	0.00	43.49	4.92
88	90	0.746659	GATGGTTTGCACCCTATGGC	59.253	55.000	3.41	0.00	43.49	4.40
89	91	1.750778	GTGATGGTTTGCACCCTATGG	59.249	52.381	3.41	0.00	43.49	2.74
90	92	2.726821	AGTGATGGTTTGCACCCTATG	58.273	47.619	3.41	0.00	43.49	2.23
91	93	3.456380	AAGTGATGGTTTGCACCCTAT	57.544	42.857	3.41	0.00	43.49	2.57
92	94	2.969821	AAGTGATGGTTTGCACCCTA	57.030	45.000	3.41	0.00	43.49	3.53
93	95	2.086610	AAAGTGATGGTTTGCACCCT	57.913	45.000	3.41	0.00	43.49	4.34
94	96	2.908688	AAAAGTGATGGTTTGCACCC	57.091	45.000	0.00	0.00	43.49	4.61
95	97	5.112686	TGTTTAAAAGTGATGGTTTGCACC	58.887	37.500	0.00	0.00	44.56	5.01
96	98	6.654793	TTGTTTAAAAGTGATGGTTTGCAC	57.345	33.333	0.00	0.00	35.30	4.57
97	99	5.293079	GCTTGTTTAAAAGTGATGGTTTGCA	59.707	36.000	0.00	0.00	0.00	4.08
98	100	5.523552	AGCTTGTTTAAAAGTGATGGTTTGC	59.476	36.000	0.00	0.00	0.00	3.68
99	101	6.018832	CCAGCTTGTTTAAAAGTGATGGTTTG	60.019	38.462	10.05	0.00	0.00	2.93
100	102	6.048509	CCAGCTTGTTTAAAAGTGATGGTTT	58.951	36.000	10.05	0.00	0.00	3.27
101	103	5.362430	TCCAGCTTGTTTAAAAGTGATGGTT	59.638	36.000	14.97	0.00	33.13	3.67
102	104	4.892934	TCCAGCTTGTTTAAAAGTGATGGT	59.107	37.500	14.97	0.00	33.13	3.55
109	111	6.259550	ACTATGCTCCAGCTTGTTTAAAAG	57.740	37.500	0.00	0.00	42.66	2.27
113	115	4.905429	TCAACTATGCTCCAGCTTGTTTA	58.095	39.130	0.00	0.00	42.66	2.01
114	116	3.754965	TCAACTATGCTCCAGCTTGTTT	58.245	40.909	0.00	0.00	42.66	2.83
115	117	3.423539	TCAACTATGCTCCAGCTTGTT	57.576	42.857	0.00	0.18	42.66	2.83
131	133	4.574599	ATCACTCCAGCTTGTTTTCAAC	57.425	40.909	0.00	0.00	35.77	3.18
376	393	1.610554	GGCCGACAGGGTGCTAGTTA	61.611	60.000	0.00	0.00	38.44	2.24
432	450	1.079057	GAAGAGCCCACTTCGGTCC	60.079	63.158	0.00	0.00	37.20	4.46
457	475	0.606604	GGGTACTCTTCAGCCAACGA	59.393	55.000	0.00	0.00	33.62	3.85
524	542	1.653151	GCCTACGGATGACCAAAGAC	58.347	55.000	0.00	0.00	35.59	3.01
622	640	1.533033	CCTCGGGCCCCAACTTTTT	60.533	57.895	18.66	0.00	0.00	1.94
805	823	4.501400	GCACCAAAATCAAAAGTAGCACCT	60.501	41.667	0.00	0.00	0.00	4.00
887	905	0.178955	TTAGTGACCAGTCCACGGGA	60.179	55.000	2.59	0.00	39.38	5.14
901	919	5.422214	AGTTATTGACCAGGGAGTTAGTG	57.578	43.478	0.00	0.00	0.00	2.74
902	920	6.351966	GCTTAGTTATTGACCAGGGAGTTAGT	60.352	42.308	0.00	0.00	0.00	2.24
903	921	6.049790	GCTTAGTTATTGACCAGGGAGTTAG	58.950	44.000	0.00	0.00	0.00	2.34
904	922	5.104652	GGCTTAGTTATTGACCAGGGAGTTA	60.105	44.000	0.00	0.00	0.00	2.24
905	923	4.324331	GGCTTAGTTATTGACCAGGGAGTT	60.324	45.833	0.00	0.00	0.00	3.01
915	933	4.244066	TGTTTACGCGGCTTAGTTATTGA	58.756	39.130	12.47	0.00	0.00	2.57
933	951	2.943033	CACGGAGTTGGAAGACTTGTTT	59.057	45.455	0.00	0.00	41.61	2.83
952	970	1.359168	AGGGGACTGGAAGGTAACAC	58.641	55.000	0.00	0.00	41.13	3.32
966	984	4.042884	TGCACTCTAGTAGTAGTAGGGGA	58.957	47.826	15.08	3.89	35.76	4.81
1021	1054	0.245539	AACATGGCAGTTGCATCAGC	59.754	50.000	6.43	3.70	44.36	4.26
1023	1056	0.522626	CGAACATGGCAGTTGCATCA	59.477	50.000	6.43	0.00	44.36	3.07
1042	1075	2.772691	GCAGAAGCATGGCTGAGCC	61.773	63.158	18.46	18.46	44.90	4.70
1063	1096	0.467804	CTAGAAAGGAGGCTGAGGGC	59.532	60.000	0.00	0.00	40.90	5.19
1070	1103	0.460459	GGTCGTGCTAGAAAGGAGGC	60.460	60.000	0.00	0.00	0.00	4.70
1086	1119	3.821033	ACAGATTTTTGGCACTAGTGGTC	59.179	43.478	23.95	8.40	0.00	4.02
1254	1308	1.017387	GCTTGATGACCCGGAATGAC	58.983	55.000	0.73	0.00	0.00	3.06
1304	1358	1.672881	AGGCATTAATGTTGAGCTCGC	59.327	47.619	16.61	5.16	0.00	5.03
1514	4356	3.134127	GCACCGGACTCCAATGGC	61.134	66.667	9.46	0.00	0.00	4.40
1549	4391	1.900016	CCATCACCGGCATCATGGG	60.900	63.158	0.00	0.00	33.37	4.00
1564	4406	3.467226	CGTGCCCTCGTACCCCAT	61.467	66.667	0.00	0.00	0.00	4.00
1892	4755	9.522804	GTAGTAATTAGCAGGTATAGATGCATC	57.477	37.037	19.37	19.37	45.01	3.91
2238	5241	6.313905	TCCAAAAGAAAGAGATAAGCATCGTC	59.686	38.462	0.00	0.00	36.20	4.20

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.