AutoCloner

Multiple sequence alignment - TraesCS2A01G265000

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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	TraesCS2A01G265000	chr2A	100.000	2552	0	0	1	2552	421061446	421058895	0.000000e+00	4713.0
1	TraesCS2A01G265000	chr2A	96.124	1548	47	8	659	2204	422102815	422104351	0.000000e+00	2514.0
2	TraesCS2A01G265000	chr2A	94.470	1103	38	7	715	1801	422221565	422222660	0.000000e+00	1677.0
3	TraesCS2A01G265000	chr2A	91.944	360	27	2	1864	2221	422222694	422223053	1.050000e-138	503.0
4	TraesCS2A01G265000	chr2A	90.838	382	21	12	315	688	422102438	422102813	1.360000e-137	499.0
5	TraesCS2A01G265000	chr2A	81.267	363	29	13	315	673	422221228	422221555	9.060000e-65	257.0
6	TraesCS2A01G265000	chr2A	95.833	72	2	1	2313	2384	422223157	422223227	5.770000e-22	115.0
7	TraesCS2A01G265000	chr2A	96.970	33	1	0	283	315	422218660	422218628	3.550000e-04	56.5
8	TraesCS2A01G265000	chr2B	89.725	1820	115	38	333	2100	382731469	382733268	0.000000e+00	2259.0
9	TraesCS2A01G265000	chr2B	93.966	928	41	4	709	1632	381914984	381914068	0.000000e+00	1389.0
10	TraesCS2A01G265000	chr2B	92.789	527	22	8	1633	2145	381908858	381908334	0.000000e+00	749.0
11	TraesCS2A01G265000	chr2B	93.598	453	17	5	2100	2552	382733958	382734398	0.000000e+00	665.0
12	TraesCS2A01G265000	chr2B	96.818	220	7	0	54	273	382599758	382599977	4.010000e-98	368.0
13	TraesCS2A01G265000	chr2B	92.000	100	6	2	2123	2221	382598253	382598351	3.420000e-29	139.0
14	TraesCS2A01G265000	chr2B	94.286	35	2	0	1	35	382599723	382599757	1.000000e-03	54.7
15	TraesCS2A01G265000	chr2D	93.014	1002	44	13	315	1304	314054496	314053509	0.000000e+00	1439.0
16	TraesCS2A01G265000	chr2D	88.481	1007	62	20	315	1301	314564814	314565786	0.000000e+00	1168.0
17	TraesCS2A01G265000	chr2D	91.279	860	42	10	444	1301	314794617	314795445	0.000000e+00	1142.0
18	TraesCS2A01G265000	chr2D	87.297	984	75	21	1189	2154	314795294	314796245	0.000000e+00	1079.0
19	TraesCS2A01G265000	chr2D	87.396	841	62	16	1189	2015	314565635	314566445	0.000000e+00	926.0
20	TraesCS2A01G265000	chr2D	91.128	665	52	4	1189	1851	314053663	314053004	0.000000e+00	894.0
21	TraesCS2A01G265000	chr2D	88.596	684	46	12	1709	2384	314046342	314045683	0.000000e+00	802.0
22	TraesCS2A01G265000	chr2D	92.971	313	21	1	3	315	314561861	314562172	2.990000e-124	455.0
23	TraesCS2A01G265000	chr2D	86.436	376	16	14	1927	2298	314051354	314051010	1.850000e-101	379.0
24	TraesCS2A01G265000	chr2D	95.783	166	7	0	2387	2552	314796485	314796650	4.190000e-68	268.0
25	TraesCS2A01G265000	chr2D	89.080	174	17	2	2045	2218	314498886	314499057	5.530000e-52	215.0
26	TraesCS2A01G265000	chr2D	94.656	131	7	0	2015	2145	314566637	314566767	1.200000e-48	204.0
27	TraesCS2A01G265000	chr2D	88.489	139	12	4	2086	2221	314050875	314050738	5.650000e-37	165.0
28	TraesCS2A01G265000	chr2D	96.341	82	3	0	2391	2472	314047832	314047751	4.430000e-28	135.0

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	TraesCS2A01G265000	chr2A	421058895	421061446	2551	True	4713.000000	4713	100.000000	1	2552	1	chr2A.!!$R1	2551
1	TraesCS2A01G265000	chr2A	422102438	422104351	1913	False	1506.500000	2514	93.481000	315	2204	2	chr2A.!!$F1	1889
2	TraesCS2A01G265000	chr2A	422221228	422223227	1999	False	638.000000	1677	90.878500	315	2384	4	chr2A.!!$F2	2069
3	TraesCS2A01G265000	chr2B	382731469	382734398	2929	False	1462.000000	2259	91.661500	333	2552	2	chr2B.!!$F2	2219
4	TraesCS2A01G265000	chr2B	381914068	381914984	916	True	1389.000000	1389	93.966000	709	1632	1	chr2B.!!$R2	923
5	TraesCS2A01G265000	chr2B	381908334	381908858	524	True	749.000000	749	92.789000	1633	2145	1	chr2B.!!$R1	512
6	TraesCS2A01G265000	chr2D	314794617	314796650	2033	False	829.666667	1142	91.453000	444	2552	3	chr2D.!!$F3	2108
7	TraesCS2A01G265000	chr2D	314561861	314566767	4906	False	688.250000	1168	90.876000	3	2145	4	chr2D.!!$F2	2142
8	TraesCS2A01G265000	chr2D	314045683	314054496	8813	True	635.666667	1439	90.667333	315	2472	6	chr2D.!!$R1	2157

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
569	3248	2.125106	GGAAGGCCTGCCACGTAG	60.125	66.667	26.78	0.0	38.92	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2251	12905	1.079336	GGAAGGTACGGGTCTGCAC	60.079	63.158	0.0	0.0	0.0	4.57	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
28	29	8.344098	CACATTGCAACAAAATTTACTCCATTT	58.656	29.630	0.00	0.00	0.00	2.32
31	32	7.712264	TGCAACAAAATTTACTCCATTTCAG	57.288	32.000	0.00	0.00	0.00	3.02
51	52	3.567164	CAGTGCATGTATGGATTTCCTCC	59.433	47.826	0.00	0.00	45.19	4.30
63	64	4.401925	GGATTTCCTCCACCTATGATTGG	58.598	47.826	0.00	0.00	44.26	3.16
79	80	3.260884	TGATTGGTGAAGTCTCAGTACCC	59.739	47.826	0.00	0.00	30.14	3.69
80	81	2.391926	TGGTGAAGTCTCAGTACCCA	57.608	50.000	0.00	0.00	30.14	4.51
117	118	3.025322	TGCCCAAACTTTTCTCCAGAA	57.975	42.857	0.00	0.00	0.00	3.02
161	162	6.984474	TCAACTCAAACACAACCTTCTAGTAG	59.016	38.462	0.00	0.00	0.00	2.57
186	187	6.089954	GCACAAGAAAGGATGAAAAAGTATGC	59.910	38.462	0.00	0.00	0.00	3.14
187	188	7.147312	CACAAGAAAGGATGAAAAAGTATGCA	58.853	34.615	0.00	0.00	0.00	3.96
230	231	9.950496	ATAGACAATACAATGTGGGAGATATTC	57.050	33.333	0.00	0.00	32.57	1.75
277	278	4.157289	AGACTTGCAGCATTTGGTATCAAG	59.843	41.667	15.96	15.96	39.24	3.02
304	305	6.253512	CAGGCTTGAAACTTACAACAAAGTTC	59.746	38.462	2.73	0.00	46.40	3.01
411	3061	4.609691	TTTGGACTCACGAACAGTTTTC	57.390	40.909	0.00	0.00	0.00	2.29
569	3248	2.125106	GGAAGGCCTGCCACGTAG	60.125	66.667	26.78	0.00	38.92	3.51
594	3273	3.119096	GGCCCAAGTTCGAGCGAC	61.119	66.667	0.00	0.00	0.00	5.19
970	3693	4.100035	CCTTTTCTGCTTCCTTGGTCTTTT	59.900	41.667	0.00	0.00	0.00	2.27
1278	4079	2.813908	GTGGCATCGGACACGGAC	60.814	66.667	0.00	0.00	44.59	4.79
1279	4080	4.429212	TGGCATCGGACACGGACG	62.429	66.667	0.00	0.00	41.39	4.79
1287	4088	4.430765	GACACGGACGGCGGTGAT	62.431	66.667	32.85	18.04	45.19	3.06
1288	4089	4.430765	ACACGGACGGCGGTGATC	62.431	66.667	32.85	4.33	45.19	2.92
1376	4216	2.264166	GAGCGCTGTCAAGAGGCT	59.736	61.111	18.48	0.00	37.41	4.58
1661	4527	3.498840	CGCTTGTTAGATGCGCTTC	57.501	52.632	15.04	15.04	40.83	3.86
1974	11709	5.698832	TGATTTAACAGGTCGCTTCATTTG	58.301	37.500	0.00	0.00	0.00	2.32
2139	12764	4.291540	TCACACAGACACTTGAATTTGC	57.708	40.909	0.00	0.00	0.00	3.68
2251	12905	1.442769	ACCGCATTTACACTGCAGAG	58.557	50.000	23.35	16.23	39.64	3.35
2263	12917	2.970639	GCAGAGTGCAGACCCGTA	59.029	61.111	0.00	0.00	44.26	4.02
2309	12963	3.117246	TCCCCATAGTGGTCTCGAGTAAT	60.117	47.826	13.13	2.50	35.17	1.89
2331	12985	3.844577	AACATGCAGCTTTCTGATGAC	57.155	42.857	0.00	0.00	42.95	3.06
2414	13158	4.023707	GCATTTACTCGAGCAGGCATAAAT	60.024	41.667	13.61	10.99	0.00	1.40
2499	13243	1.865340	ACCACGCGTTTCTCTTTTCTC	59.135	47.619	10.22	0.00	0.00	2.87
2501	13245	2.480419	CCACGCGTTTCTCTTTTCTCAT	59.520	45.455	10.22	0.00	0.00	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	7.215789	TGGAGTAAATTTTGTTGCAATGTGAT	58.784	30.769	0.59	0.00	0.00	3.06
6	7	7.768120	ACTGAAATGGAGTAAATTTTGTTGCAA	59.232	29.630	0.00	0.00	0.00	4.08
18	19	5.589855	CCATACATGCACTGAAATGGAGTAA	59.410	40.000	18.64	0.00	40.96	2.24
28	29	4.454678	GAGGAAATCCATACATGCACTGA	58.545	43.478	1.67	0.00	38.89	3.41
52	53	4.780021	ACTGAGACTTCACCAATCATAGGT	59.220	41.667	0.00	0.00	40.85	3.08
63	64	2.231721	GGTCTGGGTACTGAGACTTCAC	59.768	54.545	18.38	4.79	37.73	3.18
73	74	3.389329	CAGCATCTATTGGTCTGGGTACT	59.611	47.826	0.00	0.00	32.51	2.73
79	80	2.812591	GGCATCAGCATCTATTGGTCTG	59.187	50.000	0.00	0.00	44.61	3.51
80	81	2.224719	GGGCATCAGCATCTATTGGTCT	60.225	50.000	0.00	0.00	44.61	3.85
117	118	7.231317	TGAGTTGAGCCATCATAGTTTCTTTTT	59.769	33.333	0.00	0.00	34.73	1.94
126	127	4.696877	TGTGTTTGAGTTGAGCCATCATAG	59.303	41.667	0.00	0.00	34.73	2.23
161	162	6.089954	GCATACTTTTTCATCCTTTCTTGTGC	59.910	38.462	0.00	0.00	0.00	4.57
230	231	8.677300	TCTGTAAGGCTGCATCTTTAAATAAAG	58.323	33.333	0.50	6.59	43.01	1.85
277	278	4.893424	TGTTGTAAGTTTCAAGCCTGTC	57.107	40.909	0.00	0.00	0.00	3.51
294	295	4.871933	AAAGGGCCATAGAACTTTGTTG	57.128	40.909	6.18	0.00	32.41	3.33
1261	4062	2.813908	GTCCGTGTCCGATGCCAC	60.814	66.667	0.00	0.00	35.63	5.01
1262	4063	4.429212	CGTCCGTGTCCGATGCCA	62.429	66.667	0.00	0.00	35.63	4.92
1270	4071	4.430765	ATCACCGCCGTCCGTGTC	62.431	66.667	0.00	0.00	34.38	3.67
1271	4072	4.430765	GATCACCGCCGTCCGTGT	62.431	66.667	0.00	0.00	34.38	4.49
1661	4527	8.198109	AGCCATGACAAATTACTACACTACTAG	58.802	37.037	0.00	0.00	0.00	2.57
1961	11696	4.394920	TCAAGGATTACAAATGAAGCGACC	59.605	41.667	0.00	0.00	0.00	4.79
1974	11709	3.137533	GCTGCTCCAGATCAAGGATTAC	58.862	50.000	7.30	2.42	33.99	1.89
2025	11957	2.328099	GGCCAGTTCGTTGCAGAGG	61.328	63.158	0.00	0.00	0.00	3.69
2096	12031	5.422331	TGAAGGTCCCATTTGTTGTTTAACA	59.578	36.000	0.00	0.00	44.66	2.41
2139	12764	8.981724	AGTACCTATATTATGTTGTGTATGCG	57.018	34.615	0.00	0.00	0.00	4.73
2221	12846	1.620822	AAATGCGGTTTCAGAAGCCT	58.379	45.000	13.71	0.00	0.00	4.58
2251	12905	1.079336	GGAAGGTACGGGTCTGCAC	60.079	63.158	0.00	0.00	0.00	4.57
2256	12910	1.777941	AGATGAGGAAGGTACGGGTC	58.222	55.000	0.00	0.00	0.00	4.46
2257	12911	1.831736	CAAGATGAGGAAGGTACGGGT	59.168	52.381	0.00	0.00	0.00	5.28
2258	12912	2.108168	TCAAGATGAGGAAGGTACGGG	58.892	52.381	0.00	0.00	0.00	5.28
2259	12913	3.722147	CATCAAGATGAGGAAGGTACGG	58.278	50.000	4.01	0.00	41.20	4.02
2260	12914	3.126831	GCATCAAGATGAGGAAGGTACG	58.873	50.000	13.93	0.00	41.20	3.67
2261	12915	4.142609	TGCATCAAGATGAGGAAGGTAC	57.857	45.455	13.93	0.00	41.20	3.34
2262	12916	4.842531	TTGCATCAAGATGAGGAAGGTA	57.157	40.909	13.93	0.00	41.20	3.08
2263	12917	3.726557	TTGCATCAAGATGAGGAAGGT	57.273	42.857	13.93	0.00	41.20	3.50
2309	12963	5.005740	AGTCATCAGAAAGCTGCATGTTAA	58.994	37.500	1.02	0.00	42.01	2.01
2414	13158	5.295787	GTGAGTTCAACATGTCAGGTTTACA	59.704	40.000	0.00	0.00	0.00	2.41
2499	13243	5.534654	TGTTTCTAGTTGGGAGGTTGAAATG	59.465	40.000	0.00	0.00	0.00	2.32
2501	13245	5.118729	TGTTTCTAGTTGGGAGGTTGAAA	57.881	39.130	0.00	0.00	0.00	2.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.