AutoCloner

Multiple sequence alignment - TraesCS4B01G072900

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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	TraesCS4B01G072900	chr4B	100.000	5519	0	0	1	5519	68116734	68122252	0.000000e+00	10192.0
1	TraesCS4B01G072900	chr4B	92.063	63	3	2	1	63	35768619	35768679	2.740000e-13	87.9
2	TraesCS4B01G072900	chr4A	95.995	2322	78	10	3135	5443	552255931	552253612	0.000000e+00	3759.0
3	TraesCS4B01G072900	chr4A	91.327	1960	145	15	1143	3088	552257877	552255929	0.000000e+00	2654.0
4	TraesCS4B01G072900	chr4A	91.252	1589	121	11	1210	2785	533460163	533461746	0.000000e+00	2148.0
5	TraesCS4B01G072900	chr4A	86.821	1639	152	32	3135	4748	533462084	533463683	0.000000e+00	1772.0
6	TraesCS4B01G072900	chr4A	90.725	345	24	4	2742	3085	533461746	533462083	2.340000e-123	453.0
7	TraesCS4B01G072900	chr4A	87.248	298	21	12	510	804	552258939	552258656	1.920000e-84	324.0
8	TraesCS4B01G072900	chr4A	86.913	298	22	12	510	804	533458905	533459188	8.920000e-83	318.0
9	TraesCS4B01G072900	chr4A	88.636	264	23	5	947	1206	552258418	552258158	1.150000e-81	315.0
10	TraesCS4B01G072900	chr4A	82.222	360	28	14	149	506	552259305	552258980	1.510000e-70	278.0
11	TraesCS4B01G072900	chr4A	89.881	168	13	3	947	1113	533459426	533459590	4.330000e-51	213.0
12	TraesCS4B01G072900	chr4A	85.890	163	13	6	149	309	533571854	533571700	1.230000e-36	165.0
13	TraesCS4B01G072900	chr4A	84.663	163	15	6	149	309	533457678	533457832	2.660000e-33	154.0
14	TraesCS4B01G072900	chr4A	81.553	206	11	9	302	506	533458685	533458864	1.600000e-30	145.0
15	TraesCS4B01G072900	chr4A	96.774	62	1	1	5458	5519	552253626	552253566	9.780000e-18	102.0
16	TraesCS4B01G072900	chr4A	93.548	62	4	0	1143	1204	533459932	533459993	5.890000e-15	93.5
17	TraesCS4B01G072900	chr4D	95.686	2318	89	8	3135	5443	46622595	46624910	0.000000e+00	3716.0
18	TraesCS4B01G072900	chr4D	96.704	1790	46	5	3655	5443	47327549	47325772	0.000000e+00	2966.0
19	TraesCS4B01G072900	chr4D	91.049	1944	140	18	1157	3085	46620670	46622594	0.000000e+00	2595.0
20	TraesCS4B01G072900	chr4D	85.778	675	43	24	149	804	46619274	46619914	0.000000e+00	665.0
21	TraesCS4B01G072900	chr4D	90.840	262	19	4	947	1206	46620163	46620421	4.090000e-91	346.0
22	TraesCS4B01G072900	chr4D	94.690	113	6	0	3556	3668	47329554	47329442	5.680000e-40	176.0
23	TraesCS4B01G072900	chr4D	100.000	62	0	0	5458	5519	47325786	47325725	1.260000e-21	115.0
24	TraesCS4B01G072900	chr4D	98.387	62	1	0	5458	5519	46624896	46624957	5.850000e-20	110.0
25	TraesCS4B01G072900	chr1A	88.014	292	33	2	2357	2647	303852811	303853101	1.470000e-90	344.0
26	TraesCS4B01G072900	chr1A	79.535	215	17	14	2892	3083	303853347	303853557	1.610000e-25	128.0
27	TraesCS4B01G072900	chr1A	94.000	50	2	1	3099	3147	568391240	568391191	2.130000e-09	75.0
28	TraesCS4B01G072900	chr1D	86.986	292	37	1	2357	2648	239805433	239805723	1.480000e-85	327.0
29	TraesCS4B01G072900	chr1D	100.000	49	0	0	1	49	315408401	315408353	2.120000e-14	91.6
30	TraesCS4B01G072900	chr1D	100.000	40	0	0	3099	3138	59951885	59951846	2.130000e-09	75.0
31	TraesCS4B01G072900	chr1B	87.671	219	21	3	2368	2585	334241156	334241369	3.300000e-62	250.0
32	TraesCS4B01G072900	chr6A	93.333	150	10	0	1	150	39142672	39142523	7.200000e-54	222.0
33	TraesCS4B01G072900	chr7B	92.908	141	8	2	18	158	426524084	426523946	2.610000e-48	204.0
34	TraesCS4B01G072900	chr7B	100.000	49	0	0	1	49	150581882	150581930	2.120000e-14	91.6
35	TraesCS4B01G072900	chr6B	98.230	113	1	1	42	153	36375013	36374901	4.360000e-46	196.0
36	TraesCS4B01G072900	chr6B	96.581	117	3	1	42	157	417158201	417158317	5.640000e-45	193.0
37	TraesCS4B01G072900	chr6B	96.581	117	2	2	42	157	707744229	707744114	5.640000e-45	193.0
38	TraesCS4B01G072900	chr6B	91.803	61	2	3	2	62	468287294	468287237	1.270000e-11	82.4
39	TraesCS4B01G072900	chr6B	88.889	54	4	2	3086	3137	87007626	87007573	1.280000e-06	65.8
40	TraesCS4B01G072900	chr5A	98.214	112	1	1	42	152	561521540	561521429	1.570000e-45	195.0
41	TraesCS4B01G072900	chr2B	97.391	115	2	1	42	155	101081037	101080923	1.570000e-45	195.0
42	TraesCS4B01G072900	chr2B	94.309	123	6	1	42	163	733853406	733853284	2.620000e-43	187.0
43	TraesCS4B01G072900	chr2B	93.333	60	2	2	1	60	791611750	791611693	2.740000e-13	87.9
44	TraesCS4B01G072900	chr2B	97.826	46	0	1	3099	3144	796805924	796805880	1.650000e-10	78.7
45	TraesCS4B01G072900	chr5B	93.701	127	4	3	19	145	65245304	65245182	2.620000e-43	187.0
46	TraesCS4B01G072900	chr3B	100.000	49	0	0	1	49	511851437	511851389	2.120000e-14	91.6
47	TraesCS4B01G072900	chr5D	100.000	41	0	0	3099	3139	45654386	45654426	5.930000e-10	76.8
48	TraesCS4B01G072900	chr5D	97.674	43	0	1	3099	3140	173756250	173756292	7.670000e-09	73.1
49	TraesCS4B01G072900	chr7A	100.000	40	0	0	3099	3138	454049714	454049753	2.130000e-09	75.0
50	TraesCS4B01G072900	chr7A	97.561	41	1	0	3098	3138	85209359	85209399	2.760000e-08	71.3
51	TraesCS4B01G072900	chr3D	93.617	47	1	2	3103	3149	313603104	313603060	9.920000e-08	69.4

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	TraesCS4B01G072900	chr4B	68116734	68122252	5518	False	10192.000000	10192	100.000000	1	5519	1	chr4B.!!$F2	5518
1	TraesCS4B01G072900	chr4A	552253566	552259305	5739	True	1238.666667	3759	90.367000	149	5519	6	chr4A.!!$R2	5370
2	TraesCS4B01G072900	chr4A	533457678	533463683	6005	False	662.062500	2148	88.169500	149	4748	8	chr4A.!!$F1	4599
3	TraesCS4B01G072900	chr4D	46619274	46624957	5683	False	1486.400000	3716	92.348000	149	5519	5	chr4D.!!$F1	5370
4	TraesCS4B01G072900	chr4D	47325725	47329554	3829	True	1085.666667	2966	97.131333	3556	5519	3	chr4D.!!$R1	1963
5	TraesCS4B01G072900	chr1A	303852811	303853557	746	False	236.000000	344	83.774500	2357	3083	2	chr1A.!!$F1	726

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
982	2028	0.032615	TTTTGGTTCACAGGGCTGGT	60.033	50.0	0.00	0.00	34.19	4.00	F
987	2033	0.035056	GTTCACAGGGCTGGTAGCAT	60.035	55.0	0.00	0.00	44.75	3.79	F
988	2034	0.253044	TTCACAGGGCTGGTAGCATC	59.747	55.0	0.00	0.00	44.75	3.91	F
2361	3947	0.820074	TGGTCGCCGTTTTCACCATT	60.820	50.0	0.00	0.00	33.83	3.16	F
3060	4775	1.148310	ATGCAGTTGTCGAAGTTCGG	58.852	50.0	24.18	8.82	40.88	4.30	F
4183	7820	0.108520	GCTGCCAATGGGATGTGTTG	60.109	55.0	0.00	0.00	35.59	3.33	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2543	4130	0.250513	AATGTCCTCGGTGCCTTCTC	59.749	55.000	0.00	0.0	0.00	2.87	R
2704	4291	0.814010	ACAGCCACGAACACAGGAAC	60.814	55.000	0.00	0.0	0.00	3.62	R
2781	4411	3.914312	TGAACGACAACTTTGGCAAAAA	58.086	36.364	14.43	0.0	35.35	1.94	R
3499	5227	0.032813	CAGGCCCACAAAGGATGGAT	60.033	55.000	0.00	0.0	39.87	3.41	R
4362	8011	1.226859	CTTCGCGTCGCCAATCCTA	60.227	57.895	12.44	0.0	0.00	2.94	R
5446	9096	2.068834	TGTTTTACCTCCCCGCAAAA	57.931	45.000	0.00	0.0	0.00	2.44	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
20	21	3.687572	GACCTAGAACTACGCGAATGA	57.312	47.619	15.93	0.00	0.00	2.57
21	22	3.361414	GACCTAGAACTACGCGAATGAC	58.639	50.000	15.93	0.66	0.00	3.06
22	23	3.015327	ACCTAGAACTACGCGAATGACT	58.985	45.455	15.93	9.07	0.00	3.41
23	24	3.442977	ACCTAGAACTACGCGAATGACTT	59.557	43.478	15.93	0.00	0.00	3.01
24	25	4.637534	ACCTAGAACTACGCGAATGACTTA	59.362	41.667	15.93	0.00	0.00	2.24
25	26	5.298777	ACCTAGAACTACGCGAATGACTTAT	59.701	40.000	15.93	0.00	0.00	1.73
26	27	6.183360	ACCTAGAACTACGCGAATGACTTATT	60.183	38.462	15.93	0.00	0.00	1.40
27	28	6.360148	CCTAGAACTACGCGAATGACTTATTC	59.640	42.308	15.93	3.24	41.46	1.75
28	29	5.647589	AGAACTACGCGAATGACTTATTCA	58.352	37.500	15.93	0.00	44.42	2.57
29	30	5.515626	AGAACTACGCGAATGACTTATTCAC	59.484	40.000	15.93	0.00	44.42	3.18
30	31	4.110482	ACTACGCGAATGACTTATTCACC	58.890	43.478	15.93	0.00	44.42	4.02
31	32	3.247006	ACGCGAATGACTTATTCACCT	57.753	42.857	15.93	0.00	44.42	4.00
32	33	4.380841	ACGCGAATGACTTATTCACCTA	57.619	40.909	15.93	0.00	44.42	3.08
33	34	4.360563	ACGCGAATGACTTATTCACCTAG	58.639	43.478	15.93	0.00	44.42	3.02
34	35	4.097437	ACGCGAATGACTTATTCACCTAGA	59.903	41.667	15.93	0.00	44.42	2.43
35	36	4.441415	CGCGAATGACTTATTCACCTAGAC	59.559	45.833	0.00	0.00	44.42	2.59
36	37	4.441415	GCGAATGACTTATTCACCTAGACG	59.559	45.833	0.00	0.00	44.42	4.18
37	38	4.976731	CGAATGACTTATTCACCTAGACGG	59.023	45.833	0.00	0.00	44.42	4.79
38	39	5.220989	CGAATGACTTATTCACCTAGACGGA	60.221	44.000	0.00	0.00	44.42	4.69
39	40	5.776173	ATGACTTATTCACCTAGACGGAG	57.224	43.478	0.00	0.00	36.92	4.63
40	41	3.952323	TGACTTATTCACCTAGACGGAGG	59.048	47.826	0.00	0.00	42.89	4.30
61	62	4.532314	GTAGTAGTTACCACAAGCACCT	57.468	45.455	0.00	0.00	0.00	4.00
62	63	3.679824	AGTAGTTACCACAAGCACCTC	57.320	47.619	0.00	0.00	0.00	3.85
63	64	3.240302	AGTAGTTACCACAAGCACCTCT	58.760	45.455	0.00	0.00	0.00	3.69
64	65	2.841442	AGTTACCACAAGCACCTCTC	57.159	50.000	0.00	0.00	0.00	3.20

Showing 1 to 25 of 339 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.065095	AGTCATTCGCGTAGTTCTAGGTC	59.935	47.826	5.77	0.00	0.00	3.85
1	2	3.015327	AGTCATTCGCGTAGTTCTAGGT	58.985	45.455	5.77	0.00	0.00	3.08
2	3	3.694535	AGTCATTCGCGTAGTTCTAGG	57.305	47.619	5.77	0.00	0.00	3.02
3	4	6.910972	TGAATAAGTCATTCGCGTAGTTCTAG	59.089	38.462	5.77	0.00	45.25	2.43
4	5	6.690098	GTGAATAAGTCATTCGCGTAGTTCTA	59.310	38.462	5.77	0.00	45.25	2.10
5	6	5.515626	GTGAATAAGTCATTCGCGTAGTTCT	59.484	40.000	5.77	0.00	45.25	3.01
6	7	5.715264	GTGAATAAGTCATTCGCGTAGTTC	58.285	41.667	5.77	0.29	45.25	3.01
7	8	5.697848	GTGAATAAGTCATTCGCGTAGTT	57.302	39.130	5.77	2.59	45.25	2.24
14	15	4.976731	CCGTCTAGGTGAATAAGTCATTCG	59.023	45.833	0.00	0.00	45.25	3.34
15	16	6.145338	TCCGTCTAGGTGAATAAGTCATTC	57.855	41.667	0.00	0.00	40.27	2.67
16	17	5.069251	CCTCCGTCTAGGTGAATAAGTCATT	59.931	44.000	0.00	0.00	38.90	2.57
17	18	4.585162	CCTCCGTCTAGGTGAATAAGTCAT	59.415	45.833	0.00	0.00	38.90	3.06
18	19	3.952323	CCTCCGTCTAGGTGAATAAGTCA	59.048	47.826	0.00	0.00	41.99	3.41
19	20	4.571372	CCTCCGTCTAGGTGAATAAGTC	57.429	50.000	0.00	0.00	41.99	3.01
29	30	4.384940	GGTAACTACTACCTCCGTCTAGG	58.615	52.174	0.00	0.00	46.05	3.02
40	41	4.220163	AGAGGTGCTTGTGGTAACTACTAC	59.780	45.833	0.00	0.00	38.06	2.73
41	42	4.413760	AGAGGTGCTTGTGGTAACTACTA	58.586	43.478	0.00	0.00	37.61	1.82
42	43	3.240302	AGAGGTGCTTGTGGTAACTACT	58.760	45.455	0.00	0.00	37.61	2.57
43	44	3.258622	AGAGAGGTGCTTGTGGTAACTAC	59.741	47.826	0.00	0.00	37.61	2.73
44	45	3.507411	AGAGAGGTGCTTGTGGTAACTA	58.493	45.455	0.00	0.00	37.61	2.24
45	46	2.300437	GAGAGAGGTGCTTGTGGTAACT	59.700	50.000	0.00	0.00	37.61	2.24
46	47	2.300437	AGAGAGAGGTGCTTGTGGTAAC	59.700	50.000	0.00	0.00	0.00	2.50
47	48	2.609747	AGAGAGAGGTGCTTGTGGTAA	58.390	47.619	0.00	0.00	0.00	2.85
48	49	2.310779	AGAGAGAGGTGCTTGTGGTA	57.689	50.000	0.00	0.00	0.00	3.25
49	50	1.346068	GAAGAGAGAGGTGCTTGTGGT	59.654	52.381	0.00	0.00	0.00	4.16

Showing 1 to 25 of 350 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.