AutoCloner

Multiple sequence alignment - TraesCS2A01G431100

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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	TraesCS2A01G431100	chr2A	100.000	7071	0	0	1	7071	684261337	684268407	0.000000e+00	13058.0
1	TraesCS2A01G431100	chr2A	91.379	174	12	3	6773	6945	767778611	767778782	1.190000e-57	235.0
2	TraesCS2A01G431100	chr2A	95.489	133	3	1	6942	7071	158065853	158065985	7.190000e-50	209.0
3	TraesCS2A01G431100	chr2D	95.494	2530	83	9	1873	4381	540831055	540833574	0.000000e+00	4012.0
4	TraesCS2A01G431100	chr2D	94.213	1659	52	24	4470	6119	540833573	540835196	0.000000e+00	2492.0
5	TraesCS2A01G431100	chr2D	86.633	1197	77	33	718	1858	540829751	540830920	0.000000e+00	1247.0
6	TraesCS2A01G431100	chr2D	94.231	208	11	1	6556	6763	168244819	168244613	4.120000e-82	316.0
7	TraesCS2A01G431100	chr2D	92.262	168	10	3	6779	6945	168239042	168238877	1.190000e-57	235.0
8	TraesCS2A01G431100	chr2D	87.778	90	11	0	4380	4469	48860567	48860656	9.700000e-19	106.0
9	TraesCS2A01G431100	chr2D	92.105	76	4	2	4401	4475	513460332	513460406	9.700000e-19	106.0
10	TraesCS2A01G431100	chr2D	89.286	84	7	2	4405	4487	110841265	110841183	3.490000e-18	104.0
11	TraesCS2A01G431100	chr2B	94.992	2536	96	17	1873	4381	646413082	646415613	0.000000e+00	3951.0
12	TraesCS2A01G431100	chr2B	94.542	1704	60	16	4511	6213	646415659	646417330	0.000000e+00	2601.0
13	TraesCS2A01G431100	chr2B	85.561	1302	81	52	540	1763	646411744	646413016	0.000000e+00	1264.0
14	TraesCS2A01G431100	chr2B	88.199	322	27	5	6235	6555	646417322	646417633	2.410000e-99	374.0
15	TraesCS2A01G431100	chr2B	80.095	211	37	4	155	364	646219949	646220155	1.230000e-32	152.0
16	TraesCS2A01G431100	chr2B	90.361	83	4	4	4396	4475	604998587	604998668	9.700000e-19	106.0
17	TraesCS2A01G431100	chr2B	96.970	33	1	0	5987	6019	646417285	646417317	1.000000e-03	56.5
18	TraesCS2A01G431100	chr5A	95.215	209	9	1	6555	6763	17330432	17330639	5.290000e-86	329.0
19	TraesCS2A01G431100	chr5A	94.737	209	10	1	6555	6763	17310972	17311179	2.460000e-84	324.0
20	TraesCS2A01G431100	chr5A	94.231	208	11	1	6555	6762	530063077	530063283	4.120000e-82	316.0
21	TraesCS2A01G431100	chr5A	91.379	174	12	3	6773	6945	537645527	537645698	1.190000e-57	235.0
22	TraesCS2A01G431100	chr5A	94.737	133	4	1	6942	7071	17331100	17331232	3.340000e-48	204.0
23	TraesCS2A01G431100	chr5A	94.737	133	4	1	6942	7071	551064250	551064382	3.340000e-48	204.0
24	TraesCS2A01G431100	chr5A	94.737	133	4	1	6942	7071	619752899	619752767	3.340000e-48	204.0
25	TraesCS2A01G431100	chr5A	94.737	133	4	1	6942	7071	670233869	670233737	3.340000e-48	204.0
26	TraesCS2A01G431100	chr1D	95.215	209	9	1	6555	6763	481581997	481581790	5.290000e-86	329.0
27	TraesCS2A01G431100	chr1D	92.683	164	11	1	6781	6944	72955562	72955724	1.190000e-57	235.0
28	TraesCS2A01G431100	chr1D	92.000	75	4	2	4404	4477	312469349	312469422	3.490000e-18	104.0
29	TraesCS2A01G431100	chr1D	94.030	67	2	2	4404	4469	469018614	469018679	4.510000e-17	100.0
30	TraesCS2A01G431100	chr1D	90.667	75	5	2	4404	4477	15362130	15362057	1.620000e-16	99.0
31	TraesCS2A01G431100	chr1D	90.541	74	5	2	4404	4476	73688125	73688197	5.840000e-16	97.1
32	TraesCS2A01G431100	chr1D	83.168	101	10	6	4379	4477	458142839	458142934	1.260000e-12	86.1
33	TraesCS2A01G431100	chr7D	94.737	209	10	1	6555	6763	195268648	195268855	2.460000e-84	324.0
34	TraesCS2A01G431100	chr3D	94.712	208	10	1	6556	6763	181583242	181583036	8.850000e-84	322.0
35	TraesCS2A01G431100	chr3D	94.258	209	11	1	6555	6763	167799452	167799659	1.140000e-82	318.0
36	TraesCS2A01G431100	chr3D	92.208	77	3	3	4406	4481	251316070	251316144	9.700000e-19	106.0
37	TraesCS2A01G431100	chr3D	87.778	90	7	4	4394	4480	563835154	563835242	1.250000e-17	102.0
38	TraesCS2A01G431100	chr6A	94.231	208	11	1	6556	6763	99059343	99059137	4.120000e-82	316.0
39	TraesCS2A01G431100	chr6A	95.489	133	3	1	6942	7071	491009592	491009460	7.190000e-50	209.0
40	TraesCS2A01G431100	chr6A	83.750	80	11	2	5516	5594	12118651	12118573	2.740000e-09	75.0
41	TraesCS2A01G431100	chr6A	100.000	28	0	0	4379	4406	563707739	563707766	1.300000e-02	52.8
42	TraesCS2A01G431100	chr3B	92.857	168	10	2	6779	6945	811222848	811222682	7.090000e-60	243.0
43	TraesCS2A01G431100	chr5D	92.262	168	11	2	6779	6945	410318917	410318751	3.300000e-58	237.0
44	TraesCS2A01G431100	chr5D	85.185	108	9	6	4365	4470	332041684	332041786	3.490000e-18	104.0
45	TraesCS2A01G431100	chr5D	88.372	86	7	3	4395	4478	41291997	41292081	4.510000e-17	100.0
46	TraesCS2A01G431100	chr5B	92.683	164	10	2	6779	6942	483968472	483968633	1.190000e-57	235.0
47	TraesCS2A01G431100	chr5B	86.735	196	22	4	6747	6942	589356634	589356443	1.540000e-51	215.0
48	TraesCS2A01G431100	chr5B	94.737	133	4	1	6942	7071	662394992	662395124	3.340000e-48	204.0
49	TraesCS2A01G431100	chr5B	88.542	96	6	1	4379	4474	315928947	315928857	2.090000e-20	111.0
50	TraesCS2A01G431100	chr5B	84.314	102	11	5	4379	4477	621464160	621464061	2.100000e-15	95.3
51	TraesCS2A01G431100	chr1B	91.667	168	12	2	6779	6945	110648590	110648424	1.530000e-56	231.0
52	TraesCS2A01G431100	chr1B	92.208	77	4	2	4404	4480	594964291	594964217	2.700000e-19	108.0
53	TraesCS2A01G431100	chrUn	95.489	133	3	1	6942	7071	69453341	69453473	7.190000e-50	209.0
54	TraesCS2A01G431100	chrUn	91.892	74	4	2	4404	4476	64149758	64149830	1.250000e-17	102.0
55	TraesCS2A01G431100	chrUn	92.857	70	3	2	4407	4475	476757039	476757107	4.510000e-17	100.0
56	TraesCS2A01G431100	chrUn	90.541	74	5	2	4404	4476	87983201	87983129	5.840000e-16	97.1
57	TraesCS2A01G431100	chrUn	92.424	66	5	0	4404	4469	19647227	19647162	2.100000e-15	95.3
58	TraesCS2A01G431100	chrUn	92.424	66	5	0	4404	4469	24072656	24072721	2.100000e-15	95.3
59	TraesCS2A01G431100	chrUn	92.424	66	5	0	4404	4469	30636739	30636804	2.100000e-15	95.3
60	TraesCS2A01G431100	chrUn	91.429	70	4	2	4407	4475	66416476	66416408	2.100000e-15	95.3
61	TraesCS2A01G431100	chrUn	92.424	66	5	0	4404	4469	103216880	103216815	2.100000e-15	95.3
62	TraesCS2A01G431100	chrUn	92.424	66	5	0	4404	4469	104559238	104559303	2.100000e-15	95.3
63	TraesCS2A01G431100	chrUn	86.747	83	9	2	4401	4482	27078815	27078896	2.720000e-14	91.6
64	TraesCS2A01G431100	chrUn	85.882	85	7	5	4404	4487	96020453	96020533	1.260000e-12	86.1
65	TraesCS2A01G431100	chr6D	94.737	133	4	1	6942	7071	464750544	464750676	3.340000e-48	204.0
66	TraesCS2A01G431100	chr6D	91.892	74	4	2	4404	4476	160470716	160470644	1.250000e-17	102.0
67	TraesCS2A01G431100	chr6D	91.892	74	4	2	4404	4476	237348779	237348851	1.250000e-17	102.0
68	TraesCS2A01G431100	chr6D	93.939	66	4	0	4404	4469	85656667	85656732	4.510000e-17	100.0
69	TraesCS2A01G431100	chr6D	94.030	67	2	2	4404	4469	193682511	193682576	4.510000e-17	100.0
70	TraesCS2A01G431100	chr6D	92.857	70	3	2	4407	4475	327006536	327006604	4.510000e-17	100.0
71	TraesCS2A01G431100	chr6D	89.744	78	5	3	4404	4479	445850901	445850825	5.840000e-16	97.1
72	TraesCS2A01G431100	chr6D	88.608	79	7	2	4401	4478	129707185	129707262	2.100000e-15	95.3
73	TraesCS2A01G431100	chr6D	100.000	28	0	0	4379	4406	420745733	420745760	1.300000e-02	52.8
74	TraesCS2A01G431100	chr3A	94.737	76	3	1	4402	4476	599863729	599863804	4.480000e-22	117.0
75	TraesCS2A01G431100	chr1A	92.000	75	4	2	4404	4477	16442934	16443007	3.490000e-18	104.0
76	TraesCS2A01G431100	chr1A	92.000	75	4	2	4404	4477	287275067	287275140	3.490000e-18	104.0
77	TraesCS2A01G431100	chr1A	89.157	83	7	2	4394	4474	22295273	22295355	1.250000e-17	102.0
78	TraesCS2A01G431100	chr4D	90.667	75	5	2	4401	4474	28238495	28238568	1.620000e-16	99.0
79	TraesCS2A01G431100	chr4D	91.667	72	4	2	4405	4475	125078596	125078526	1.620000e-16	99.0
80	TraesCS2A01G431100	chr4D	89.873	79	5	3	4404	4481	295432454	295432378	1.620000e-16	99.0
81	TraesCS2A01G431100	chr4D	90.789	76	4	3	4404	4478	323575299	323575226	1.620000e-16	99.0
82	TraesCS2A01G431100	chr4D	89.744	78	4	3	4404	4478	15801093	15801017	5.840000e-16	97.1

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	TraesCS2A01G431100	chr2A	684261337	684268407	7070	False	13058.000000	13058	100.000000	1	7071	1	chr2A.!!$F2	7070
1	TraesCS2A01G431100	chr2D	540829751	540835196	5445	False	2583.666667	4012	92.113333	718	6119	3	chr2D.!!$F3	5401
2	TraesCS2A01G431100	chr2B	646411744	646417633	5889	False	1649.300000	3951	92.052800	540	6555	5	chr2B.!!$F3	6015
3	TraesCS2A01G431100	chr5A	17330432	17331232	800	False	266.500000	329	94.976000	6555	7071	2	chr5A.!!$F5	516

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
412	413	0.030235	GCAGGAAACCAAACACGTCC	59.970	55.000	0.00	0.00	0.00	4.79	F
417	418	0.099791	AAACCAAACACGTCCAAGCG	59.900	50.000	0.00	0.00	37.94	4.68	F
433	434	0.108615	AGCGGATCCTCGTTGTTCAG	60.109	55.000	10.75	0.00	0.00	3.02	F
434	435	0.389948	GCGGATCCTCGTTGTTCAGT	60.390	55.000	10.75	0.00	0.00	3.41	F
486	487	0.518636	CATCTTTGGTGTCGTGCCAG	59.481	55.000	0.00	0.00	37.31	4.85	F
1241	1312	0.683504	GGTCTTCGGGTGAGCTAGGA	60.684	60.000	0.00	0.00	0.00	2.94	F
1293	1365	2.036217	TGCTGTGAAATTTTCTGCTGGG	59.964	45.455	18.70	0.00	0.00	4.45	F
2782	3050	0.955905	TGGGGAGTTAGCGTTTTTGC	59.044	50.000	0.00	0.00	0.00	3.68	F
3626	3894	0.597568	TTGGCGGTTGCTCATTTGAG	59.402	50.000	3.13	3.13	44.75	3.02	F
4400	4668	0.179092	CTCCCACCGTCCCGAATTAC	60.179	60.000	0.00	0.00	0.00	1.89	F
4402	4670	0.251073	CCCACCGTCCCGAATTACTT	59.749	55.000	0.00	0.00	0.00	2.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2241	2491	0.108615	CTGCGGAAGGACATCGAGTT	60.109	55.000	0.00	0.00	0.00	3.01	R
2257	2514	0.235926	GTTTGAGTTCAGACCGCTGC	59.764	55.000	0.00	0.00	42.01	5.25	R
2471	2738	3.056536	GCGGCCTATGAATGAGTGATAGA	60.057	47.826	0.00	0.00	0.00	1.98	R
2490	2757	1.796796	GCTACAAAAGGCAGAGCGG	59.203	57.895	0.00	0.00	0.00	5.52	R
2569	2837	6.711277	TCTGAACTTACATATGCTTGAGGTT	58.289	36.000	1.58	0.00	0.00	3.50	R
2772	3040	1.791103	TAGCTTGCCGCAAAAACGCT	61.791	50.000	18.29	18.29	42.61	5.07	R
3272	3540	4.074970	ACGAAAGAGTCCATCATTTGCTT	58.925	39.130	0.00	0.00	0.00	3.91	R
4017	4285	0.761187	AGCAGTTGAGCACCTGAGAA	59.239	50.000	0.00	0.00	36.85	2.87	R
5635	5911	0.888619	CTAGTGCCGTCTTCACCTCA	59.111	55.000	0.00	0.00	35.14	3.86	R
5803	6079	0.331616	TCTCGATCTCCCTCACCACA	59.668	55.000	0.00	0.00	0.00	4.17	R
6182	6458	0.473755	TCCTGTTCTTCAAGCTGCCA	59.526	50.000	0.00	0.00	0.00	4.92	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	Hairpin	End Stability
32	33	7.931015	ATTAAGATATAGTCCACCAGGTTGA	57.069	36.000	35.89	3.18
33	34	5.878406	AAGATATAGTCCACCAGGTTGAG	57.122	43.478	35.89	3.02
34	35	5.144159	AGATATAGTCCACCAGGTTGAGA	57.856	43.478	35.89	3.27
35	36	5.721225	AGATATAGTCCACCAGGTTGAGAT	58.279	41.667	35.89	2.75
36	37	5.777732	AGATATAGTCCACCAGGTTGAGATC	59.222	44.000	35.89	2.75
37	38	2.030027	AGTCCACCAGGTTGAGATCA	57.970	50.000	35.89	2.92
38	39	1.625818	AGTCCACCAGGTTGAGATCAC	59.374	52.381	35.89	3.06
39	40	0.608130	TCCACCAGGTTGAGATCACG	59.392	55.000	35.89	4.35
40	41	0.608130	CCACCAGGTTGAGATCACGA	59.392	55.000	0.00	4.35
41	42	1.001974	CCACCAGGTTGAGATCACGAA	59.998	52.381	0.00	3.85
42	43	2.549992	CCACCAGGTTGAGATCACGAAA	60.550	50.000	0.00	3.46
43	44	3.138304	CACCAGGTTGAGATCACGAAAA	58.862	45.455	0.00	2.29
44	45	3.753272	CACCAGGTTGAGATCACGAAAAT	59.247	43.478	0.00	1.82
45	46	4.216257	CACCAGGTTGAGATCACGAAAATT	59.784	41.667	0.00	1.82
46	47	4.455877	ACCAGGTTGAGATCACGAAAATTC	59.544	41.667	0.00	2.17
47	48	4.455533	CCAGGTTGAGATCACGAAAATTCA	59.544	41.667	0.00	2.57
48	49	5.385617	CAGGTTGAGATCACGAAAATTCAC	58.614	41.667	0.00	3.18
49	50	5.180117	CAGGTTGAGATCACGAAAATTCACT	59.820	40.000	0.00	3.41
50	51	5.409826	AGGTTGAGATCACGAAAATTCACTC	59.590	40.000	0.00	3.51
51	52	5.409826	GGTTGAGATCACGAAAATTCACTCT	59.590	40.000	0.00	3.24
52	53	6.401581	GGTTGAGATCACGAAAATTCACTCTC	60.402	42.308	0.00	3.20
53	54	4.859245	TGAGATCACGAAAATTCACTCTCG	59.141	41.667	37.33	4.04
54	55	5.060662	AGATCACGAAAATTCACTCTCGA	57.939	39.130	35.34	4.04
55	56	5.655488	AGATCACGAAAATTCACTCTCGAT	58.345	37.500	35.34	3.59
56	57	5.518128	AGATCACGAAAATTCACTCTCGATG	59.482	40.000	35.34	3.84

Showing 1 to 25 of 643 entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	9.615660	TCAACCTGGTGGACTATATCTTAATAT	57.384	33.333	0.00	0.00	37.04	1.28
7	8	9.090103	CTCAACCTGGTGGACTATATCTTAATA	57.910	37.037	0.00	0.00	37.04	0.98
8	9	7.789831	TCTCAACCTGGTGGACTATATCTTAAT	59.210	37.037	0.00	0.00	37.04	1.40
9	10	7.130099	TCTCAACCTGGTGGACTATATCTTAA	58.870	38.462	0.00	0.00	37.04	1.85
10	11	6.679542	TCTCAACCTGGTGGACTATATCTTA	58.320	40.000	0.00	0.00	37.04	2.10
11	12	5.529289	TCTCAACCTGGTGGACTATATCTT	58.471	41.667	0.00	0.00	37.04	2.40
12	13	5.144159	TCTCAACCTGGTGGACTATATCT	57.856	43.478	0.00	0.00	37.04	1.98
13	14	5.540337	TGATCTCAACCTGGTGGACTATATC	59.460	44.000	0.00	2.54	37.04	1.63
14	15	5.305644	GTGATCTCAACCTGGTGGACTATAT	59.694	44.000	0.00	0.00	37.04	0.86
15	16	4.649674	GTGATCTCAACCTGGTGGACTATA	59.350	45.833	0.00	0.00	37.04	1.31
16	17	3.452627	GTGATCTCAACCTGGTGGACTAT	59.547	47.826	0.00	0.00	37.04	2.12
17	18	2.832129	GTGATCTCAACCTGGTGGACTA	59.168	50.000	0.00	0.00	37.04	2.59
18	19	1.625818	GTGATCTCAACCTGGTGGACT	59.374	52.381	0.00	0.00	37.04	3.85
19	20	1.673033	CGTGATCTCAACCTGGTGGAC	60.673	57.143	0.00	0.00	37.04	4.02
20	21	0.608130	CGTGATCTCAACCTGGTGGA	59.392	55.000	3.40	3.40	37.04	4.02
21	22	0.608130	TCGTGATCTCAACCTGGTGG	59.392	55.000	0.00	0.00	39.83	4.61
22	23	2.455674	TTCGTGATCTCAACCTGGTG	57.544	50.000	0.00	0.00	0.00	4.17
23	24	3.485463	TTTTCGTGATCTCAACCTGGT	57.515	42.857	0.00	0.00	0.00	4.00
24	25	4.455533	TGAATTTTCGTGATCTCAACCTGG	59.544	41.667	0.00	0.00	0.00	4.45
25	26	5.180117	AGTGAATTTTCGTGATCTCAACCTG	59.820	40.000	0.00	0.00	0.00	4.00
26	27	5.308825	AGTGAATTTTCGTGATCTCAACCT	58.691	37.500	0.00	0.00	0.00	3.50
27	28	5.409826	AGAGTGAATTTTCGTGATCTCAACC	59.590	40.000	0.00	0.00	0.00	3.77
28	29	6.473397	AGAGTGAATTTTCGTGATCTCAAC	57.527	37.500	0.00	0.00	0.00	3.18
29	30	5.346011	CGAGAGTGAATTTTCGTGATCTCAA	59.654	40.000	0.00	0.00	33.22	3.02
30	31	4.859245	CGAGAGTGAATTTTCGTGATCTCA	59.141	41.667	0.00	0.00	33.22	3.27

Showing 1 to 25 of 671 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.