AutoCloner

Multiple sequence alignment - TraesCS2D01G521200

Loading Multiple Alignment...

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	TraesCS2D01G521200	chr2D	100.000	3066	0	0	1	3066	609936739	609933674	0.000000e+00	5662.0
1	TraesCS2D01G521200	chr2D	96.931	1564	37	5	889	2448	609893283	609891727	0.000000e+00	2612.0
2	TraesCS2D01G521200	chr2D	98.869	619	7	0	2448	3066	609260833	609261451	0.000000e+00	1105.0
3	TraesCS2D01G521200	chr2D	84.328	134	18	1	898	1031	611244727	611244857	8.920000e-26	128.0
4	TraesCS2D01G521200	chr2B	94.348	1663	66	14	799	2448	744835059	744833412	0.000000e+00	2525.0
5	TraesCS2D01G521200	chr2B	92.361	1584	99	10	883	2448	744520657	744519078	0.000000e+00	2235.0
6	TraesCS2D01G521200	chr2B	84.211	1292	176	12	883	2159	744454251	744452973	0.000000e+00	1230.0
7	TraesCS2D01G521200	chr2B	82.591	1212	185	15	945	2153	745579543	745580731	0.000000e+00	1046.0
8	TraesCS2D01G521200	chr2B	85.458	502	29	20	307	778	744521215	744520728	1.650000e-132	483.0
9	TraesCS2D01G521200	chr2B	76.337	617	111	24	898	1489	746170117	746170723	6.430000e-77	298.0
10	TraesCS2D01G521200	chr2B	100.000	30	0	0	279	308	683081647	683081618	4.270000e-04	56.5
11	TraesCS2D01G521200	chr3D	99.191	618	5	0	2449	3066	186517974	186517357	0.000000e+00	1114.0
12	TraesCS2D01G521200	chr3D	98.246	627	11	0	2440	3066	371157246	371157872	0.000000e+00	1098.0
13	TraesCS2D01G521200	chr5D	99.029	618	6	0	2449	3066	298960234	298959617	0.000000e+00	1109.0
14	TraesCS2D01G521200	chr5D	98.869	619	7	0	2448	3066	450599378	450599996	0.000000e+00	1105.0
15	TraesCS2D01G521200	chr5D	95.223	314	14	1	1	313	535632534	535632221	2.120000e-136	496.0
16	TraesCS2D01G521200	chr5D	95.425	306	8	1	1	306	407324921	407325220	1.650000e-132	483.0
17	TraesCS2D01G521200	chrUn	98.869	619	7	0	2448	3066	108836080	108835462	0.000000e+00	1105.0
18	TraesCS2D01G521200	chrUn	98.710	620	8	0	2447	3066	108843213	108842594	0.000000e+00	1101.0
19	TraesCS2D01G521200	chrUn	82.069	145	24	2	1144	1287	87002981	87003124	4.150000e-24	122.0
20	TraesCS2D01G521200	chrUn	82.069	145	24	2	1144	1287	298337166	298337309	4.150000e-24	122.0
21	TraesCS2D01G521200	chrUn	82.734	139	22	2	1150	1287	298383342	298383205	4.150000e-24	122.0
22	TraesCS2D01G521200	chr1D	98.869	619	7	0	2448	3066	121636016	121635398	0.000000e+00	1105.0
23	TraesCS2D01G521200	chr1D	98.869	619	7	0	2448	3066	384116820	384117438	0.000000e+00	1105.0
24	TraesCS2D01G521200	chr7D	94.534	311	16	1	1	310	17359897	17359587	2.140000e-131	479.0
25	TraesCS2D01G521200	chr7D	94.788	307	15	1	1	306	105364890	105364584	7.690000e-131	477.0
26	TraesCS2D01G521200	chr6B	92.953	298	19	2	12	307	545678871	545679168	1.690000e-117	433.0
27	TraesCS2D01G521200	chr1A	92.182	307	23	1	1	306	99625513	99625207	1.690000e-117	433.0
28	TraesCS2D01G521200	chr2A	73.844	1189	258	32	895	2052	744080517	744081683	1.020000e-114	424.0
29	TraesCS2D01G521200	chr2A	84.647	241	20	9	490	724	742766027	742765798	1.110000e-54	224.0
30	TraesCS2D01G521200	chr2A	90.741	108	10	0	184	291	11809699	11809806	8.860000e-31	145.0
31	TraesCS2D01G521200	chr7A	91.531	307	25	1	1	306	183921203	183920897	3.660000e-114	422.0
32	TraesCS2D01G521200	chr4A	89.251	307	32	1	1	306	661252578	661252272	1.720000e-102	383.0
33	TraesCS2D01G521200	chr5A	94.144	222	12	1	1	221	564729611	564729390	1.360000e-88	337.0
34	TraesCS2D01G521200	chr1B	100.000	28	0	0	645	672	162779321	162779348	6.000000e-03	52.8

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	TraesCS2D01G521200	chr2D	609933674	609936739	3065	True	5662	5662	100.0000	1	3066	1	chr2D.!!$R2	3065
1	TraesCS2D01G521200	chr2D	609891727	609893283	1556	True	2612	2612	96.9310	889	2448	1	chr2D.!!$R1	1559
2	TraesCS2D01G521200	chr2D	609260833	609261451	618	False	1105	1105	98.8690	2448	3066	1	chr2D.!!$F1	618
3	TraesCS2D01G521200	chr2B	744833412	744835059	1647	True	2525	2525	94.3480	799	2448	1	chr2B.!!$R3	1649
4	TraesCS2D01G521200	chr2B	744519078	744521215	2137	True	1359	2235	88.9095	307	2448	2	chr2B.!!$R4	2141
5	TraesCS2D01G521200	chr2B	744452973	744454251	1278	True	1230	1230	84.2110	883	2159	1	chr2B.!!$R2	1276
6	TraesCS2D01G521200	chr2B	745579543	745580731	1188	False	1046	1046	82.5910	945	2153	1	chr2B.!!$F1	1208
7	TraesCS2D01G521200	chr2B	746170117	746170723	606	False	298	298	76.3370	898	1489	1	chr2B.!!$F2	591
8	TraesCS2D01G521200	chr3D	186517357	186517974	617	True	1114	1114	99.1910	2449	3066	1	chr3D.!!$R1	617
9	TraesCS2D01G521200	chr3D	371157246	371157872	626	False	1098	1098	98.2460	2440	3066	1	chr3D.!!$F1	626
10	TraesCS2D01G521200	chr5D	298959617	298960234	617	True	1109	1109	99.0290	2449	3066	1	chr5D.!!$R1	617
11	TraesCS2D01G521200	chr5D	450599378	450599996	618	False	1105	1105	98.8690	2448	3066	1	chr5D.!!$F2	618
12	TraesCS2D01G521200	chrUn	108835462	108836080	618	True	1105	1105	98.8690	2448	3066	1	chrUn.!!$R1	618
13	TraesCS2D01G521200	chrUn	108842594	108843213	619	True	1101	1101	98.7100	2447	3066	1	chrUn.!!$R2	619
14	TraesCS2D01G521200	chr1D	121635398	121636016	618	True	1105	1105	98.8690	2448	3066	1	chr1D.!!$R1	618
15	TraesCS2D01G521200	chr1D	384116820	384117438	618	False	1105	1105	98.8690	2448	3066	1	chr1D.!!$F1	618
16	TraesCS2D01G521200	chr2A	744080517	744081683	1166	False	424	424	73.8440	895	2052	1	chr2A.!!$F2	1157

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
127	128	0.031585	GCATAGATGTACGGACGCCA	59.968	55.0	0.0	0.0	0.0	5.69	F
265	266	0.036952	CGGGTATCAGGGCTATGCTG	60.037	60.0	0.0	0.0	0.0	4.41	F
836	867	0.383949	TTTTCGTGGAAGTGCTTGGC	59.616	50.0	0.0	0.0	0.0	4.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1433	1511	0.971386	AATGCCAGCCTTTCAACCTG	59.029	50.0	0.00	0.0	0.00	4.00	R
1664	1748	1.021202	CGCCAAACAAGAGGTTGTCA	58.979	50.0	0.00	0.0	46.68	3.58	R
2426	2528	0.533085	GATTTCCGGCCAGCCTACTC	60.533	60.0	2.24	0.0	0.00	2.59	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	2.357517	CCGTCGGCATATCCCTGC	60.358	66.667	0.00	0.00	41.53	4.85
25	26	3.736483	GCATATCCCTGCCACGTG	58.264	61.111	9.08	9.08	36.10	4.49
26	27	1.893808	GCATATCCCTGCCACGTGG	60.894	63.158	30.66	30.66	36.10	4.94
36	37	2.029073	CCACGTGGCGTCTCTTGT	59.971	61.111	24.02	0.00	38.32	3.16
37	38	1.287815	CCACGTGGCGTCTCTTGTA	59.712	57.895	24.02	0.00	38.32	2.41
38	39	0.108804	CCACGTGGCGTCTCTTGTAT	60.109	55.000	24.02	0.00	38.32	2.29
39	40	0.992072	CACGTGGCGTCTCTTGTATG	59.008	55.000	7.95	0.00	38.32	2.39
40	41	0.108804	ACGTGGCGTCTCTTGTATGG	60.109	55.000	0.00	0.00	33.69	2.74
41	42	0.806102	CGTGGCGTCTCTTGTATGGG	60.806	60.000	0.00	0.00	0.00	4.00
42	43	1.090052	GTGGCGTCTCTTGTATGGGC	61.090	60.000	0.00	0.00	0.00	5.36
43	44	1.220749	GGCGTCTCTTGTATGGGCA	59.779	57.895	0.00	0.00	0.00	5.36
44	45	0.811616	GGCGTCTCTTGTATGGGCAG	60.812	60.000	0.00	0.00	0.00	4.85
45	46	1.432270	GCGTCTCTTGTATGGGCAGC	61.432	60.000	0.00	0.00	0.00	5.25
46	47	0.108186	CGTCTCTTGTATGGGCAGCA	60.108	55.000	0.00	0.00	0.00	4.41
47	48	1.373570	GTCTCTTGTATGGGCAGCAC	58.626	55.000	0.00	0.00	0.00	4.40
48	49	1.065854	GTCTCTTGTATGGGCAGCACT	60.066	52.381	0.00	0.00	0.00	4.40
49	50	1.630369	TCTCTTGTATGGGCAGCACTT	59.370	47.619	0.00	0.00	0.00	3.16
50	51	1.741706	CTCTTGTATGGGCAGCACTTG	59.258	52.381	0.00	0.00	0.00	3.16
51	52	1.350684	TCTTGTATGGGCAGCACTTGA	59.649	47.619	0.00	0.00	0.00	3.02
52	53	1.470098	CTTGTATGGGCAGCACTTGAC	59.530	52.381	0.00	0.00	0.00	3.18
53	54	0.673333	TGTATGGGCAGCACTTGACG	60.673	55.000	0.00	0.00	34.72	4.35
54	55	1.078497	TATGGGCAGCACTTGACGG	60.078	57.895	0.00	0.00	34.72	4.79
60	61	4.927782	AGCACTTGACGGCGGCAA	62.928	61.111	28.42	28.42	34.54	4.52
61	62	4.683334	GCACTTGACGGCGGCAAC	62.683	66.667	26.68	11.89	0.00	4.17
79	80	3.098555	GGCAATCACCGTTAGGCG	58.901	61.111	0.00	0.00	42.76	5.52

Showing 1 to 25 of 164 entries

Previous1 2 3 4 5 6 7Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	2.357517	GCAGGGATATGCCGACGG	60.358	66.667	10.29	10.29	40.43	4.79
8	9	1.893808	CCACGTGGCAGGGATATGC	60.894	63.158	24.02	0.00	45.74	3.14
9	10	4.462394	CCACGTGGCAGGGATATG	57.538	61.111	24.02	0.45	0.00	1.78
19	20	0.108804	ATACAAGAGACGCCACGTGG	60.109	55.000	30.66	30.66	41.37	4.94
20	21	0.992072	CATACAAGAGACGCCACGTG	59.008	55.000	9.08	9.08	41.37	4.49
21	22	0.108804	CCATACAAGAGACGCCACGT	60.109	55.000	0.00	0.00	45.10	4.49
22	23	0.806102	CCCATACAAGAGACGCCACG	60.806	60.000	0.00	0.00	0.00	4.94
23	24	1.090052	GCCCATACAAGAGACGCCAC	61.090	60.000	0.00	0.00	0.00	5.01
24	25	1.220749	GCCCATACAAGAGACGCCA	59.779	57.895	0.00	0.00	0.00	5.69
25	26	0.811616	CTGCCCATACAAGAGACGCC	60.812	60.000	0.00	0.00	0.00	5.68
26	27	1.432270	GCTGCCCATACAAGAGACGC	61.432	60.000	0.00	0.00	0.00	5.19
27	28	0.108186	TGCTGCCCATACAAGAGACG	60.108	55.000	0.00	0.00	0.00	4.18
28	29	1.065854	AGTGCTGCCCATACAAGAGAC	60.066	52.381	0.00	0.00	0.00	3.36
29	30	1.279496	AGTGCTGCCCATACAAGAGA	58.721	50.000	0.00	0.00	0.00	3.10
30	31	1.741706	CAAGTGCTGCCCATACAAGAG	59.258	52.381	0.00	0.00	0.00	2.85
31	32	1.350684	TCAAGTGCTGCCCATACAAGA	59.649	47.619	0.00	0.00	0.00	3.02
32	33	1.470098	GTCAAGTGCTGCCCATACAAG	59.530	52.381	0.00	0.00	0.00	3.16
33	34	1.533625	GTCAAGTGCTGCCCATACAA	58.466	50.000	0.00	0.00	0.00	2.41
34	35	0.673333	CGTCAAGTGCTGCCCATACA	60.673	55.000	0.00	0.00	0.00	2.29
35	36	1.369091	CCGTCAAGTGCTGCCCATAC	61.369	60.000	0.00	0.00	0.00	2.39
36	37	1.078497	CCGTCAAGTGCTGCCCATA	60.078	57.895	0.00	0.00	0.00	2.74
37	38	2.360350	CCGTCAAGTGCTGCCCAT	60.360	61.111	0.00	0.00	0.00	4.00
43	44	4.927782	TTGCCGCCGTCAAGTGCT	62.928	61.111	0.00	0.00	0.00	4.40
44	45	4.683334	GTTGCCGCCGTCAAGTGC	62.683	66.667	0.00	0.00	0.00	4.40
45	46	4.368808	CGTTGCCGCCGTCAAGTG	62.369	66.667	0.00	0.00	0.00	3.16

Showing 1 to 25 of 199 entries

Previous1 2 3 4 5…8Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.