AutoCloner

Multiple sequence alignment - TraesCS5A01G071200

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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	TraesCS5A01G071200	chr5A	100.000	5089	0	0	1	5089	80150022	80155110	0.000000e+00	9398.0
1	TraesCS5A01G071200	chr5A	97.414	116	3	0	2347	2462	80152312	80152427	1.120000e-46	198.0
2	TraesCS5A01G071200	chr5A	97.414	116	3	0	2291	2406	80152368	80152483	1.120000e-46	198.0
3	TraesCS5A01G071200	chr5D	96.583	4127	102	12	971	5088	87168964	87173060	0.000000e+00	6804.0
4	TraesCS5A01G071200	chr5D	94.183	997	47	8	1	990	87162549	87163541	0.000000e+00	1509.0
5	TraesCS5A01G071200	chr5D	75.960	599	108	19	33	608	387850035	387850620	5.020000e-70	276.0
6	TraesCS5A01G071200	chr5D	97.414	116	3	0	2291	2406	87170342	87170457	1.120000e-46	198.0
7	TraesCS5A01G071200	chr5D	96.552	116	4	0	2347	2462	87170286	87170401	5.200000e-45	193.0
8	TraesCS5A01G071200	chr5B	94.050	2084	100	11	1534	3611	93208301	93210366	0.000000e+00	3140.0
9	TraesCS5A01G071200	chr5B	92.046	1471	73	17	3635	5088	93210357	93211800	0.000000e+00	2028.0
10	TraesCS5A01G071200	chr5B	84.684	1012	99	22	1	991	93204261	93205237	0.000000e+00	959.0
11	TraesCS5A01G071200	chr5B	91.919	495	28	3	1009	1495	93207809	93208299	0.000000e+00	682.0
12	TraesCS5A01G071200	chr5B	96.552	116	4	0	2347	2462	93209046	93209161	5.200000e-45	193.0
13	TraesCS5A01G071200	chr5B	95.690	116	5	0	2291	2406	93209102	93209217	2.420000e-43	187.0
14	TraesCS5A01G071200	chr5B	95.000	60	3	0	2403	2462	93209046	93209105	1.510000e-15	95.3
15	TraesCS5A01G071200	chr1D	82.780	482	65	7	155	620	100902492	100902013	1.020000e-111	414.0
16	TraesCS5A01G071200	chr1D	90.000	60	6	0	80	139	436070997	436070938	1.520000e-10	78.7
17	TraesCS5A01G071200	chr6B	79.756	573	83	10	80	620	671726886	671727457	7.990000e-103	385.0
18	TraesCS5A01G071200	chr6B	79.617	574	82	12	80	620	671719760	671720331	3.720000e-101	379.0
19	TraesCS5A01G071200	chr6B	80.041	486	69	14	155	620	548539413	548538936	8.160000e-88	335.0
20	TraesCS5A01G071200	chr3A	78.812	623	89	26	33	620	720234300	720233686	3.720000e-101	379.0
21	TraesCS5A01G071200	chr3D	81.314	487	71	8	155	624	123618500	123618983	1.340000e-100	377.0
22	TraesCS5A01G071200	chr3D	80.417	480	77	5	157	620	590311645	590311167	2.920000e-92	350.0
23	TraesCS5A01G071200	chr3D	80.498	482	72	10	155	619	598204193	598203717	2.920000e-92	350.0
24	TraesCS5A01G071200	chr3D	77.926	598	93	23	54	620	309770812	309771401	2.270000e-88	337.0
25	TraesCS5A01G071200	chr3D	78.147	572	92	11	80	620	340702239	340702808	2.940000e-87	333.0
26	TraesCS5A01G071200	chr6D	80.672	476	70	10	161	620	363822112	363821643	2.920000e-92	350.0
27	TraesCS5A01G071200	chr6D	79.339	121	19	6	769	885	47263169	47263287	4.220000e-11	80.5
28	TraesCS5A01G071200	chr1B	80.165	484	75	9	155	620	302230562	302231042	4.880000e-90	342.0
29	TraesCS5A01G071200	chr3B	78.652	534	77	24	117	620	411454850	411454324	2.290000e-83	320.0
30	TraesCS5A01G071200	chr7D	80.328	427	64	10	155	563	23544684	23545108	6.400000e-79	305.0
31	TraesCS5A01G071200	chr2B	79.212	457	71	13	155	594	773387150	773386701	3.850000e-76	296.0

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	TraesCS5A01G071200	chr5A	80150022	80155110	5088	False	3264.666667	9398	98.276000	1	5089	3	chr5A.!!$F1	5088
1	TraesCS5A01G071200	chr5D	87168964	87173060	4096	False	2398.333333	6804	96.849667	971	5088	3	chr5D.!!$F3	4117
2	TraesCS5A01G071200	chr5D	87162549	87163541	992	False	1509.000000	1509	94.183000	1	990	1	chr5D.!!$F1	989
3	TraesCS5A01G071200	chr5D	387850035	387850620	585	False	276.000000	276	75.960000	33	608	1	chr5D.!!$F2	575
4	TraesCS5A01G071200	chr5B	93204261	93211800	7539	False	1040.614286	3140	92.848714	1	5088	7	chr5B.!!$F1	5087
5	TraesCS5A01G071200	chr6B	671726886	671727457	571	False	385.000000	385	79.756000	80	620	1	chr6B.!!$F2	540
6	TraesCS5A01G071200	chr6B	671719760	671720331	571	False	379.000000	379	79.617000	80	620	1	chr6B.!!$F1	540
7	TraesCS5A01G071200	chr3A	720233686	720234300	614	True	379.000000	379	78.812000	33	620	1	chr3A.!!$R1	587
8	TraesCS5A01G071200	chr3D	309770812	309771401	589	False	337.000000	337	77.926000	54	620	1	chr3D.!!$F2	566
9	TraesCS5A01G071200	chr3D	340702239	340702808	569	False	333.000000	333	78.147000	80	620	1	chr3D.!!$F3	540
10	TraesCS5A01G071200	chr3B	411454324	411454850	526	True	320.000000	320	78.652000	117	620	1	chr3B.!!$R1	503

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	Hairpin	End Stability	Orientation
651	693	0.607489	GCACCCAAGCTCACATGAGT	60.607	55.000	10.50	43.85	3.41	F
2148	4775	1.272313	ACATGCATGTTCTCTTGGCCT	60.272	47.619	26.61	37.90	5.19	F
3613	6241	1.153025	GGAGCTGATCATGCTGGCA	60.153	57.895	19.95	41.30	4.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2432	5059	2.146342	ACTTTGCATCGAGACAACCAG	58.854	47.619	2.60	2.32	0.00	4.00	R
3837	6465	0.465460	AACCTTTGAGCACGCTTCCA	60.465	50.000	0.00	0.00	0.00	3.53	R
4858	7499	0.808847	GTCGCTGCTGCTGATCATGA	60.809	55.000	14.03	0.00	36.97	3.07	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
49	50	1.066430	CCTAGGGTTTCGTTAGCTGCA	60.066	52.381	0.00	0.00	0.00	4.41
100	101	2.283101	TTGCTTCCGGCTGCCATT	60.283	55.556	20.29	0.00	42.39	3.16
114	115	2.858622	CCATTTTGGCGCTGAGAGA	58.141	52.632	7.64	0.00	0.00	3.10
494	533	7.513371	AATTGTTGTTTCAATCCAATTGCAT	57.487	28.000	0.00	0.00	40.05	3.96
563	605	4.398319	ACATCGAAGAAGGTGTTTCCAAT	58.602	39.130	0.00	0.00	43.58	3.16
638	680	1.261480	ACAGTGTTGTTTTGCACCCA	58.739	45.000	0.00	0.00	36.35	4.51
651	693	0.607489	GCACCCAAGCTCACATGAGT	60.607	55.000	10.50	0.00	43.85	3.41
843	899	1.651631	GCACACGTGTTGGAAAAACAC	59.348	47.619	20.79	10.57	45.12	3.32
863	920	3.851403	CACCAACGTTGCTTGCATAATAC	59.149	43.478	22.93	0.00	0.00	1.89
865	922	4.938832	ACCAACGTTGCTTGCATAATACTA	59.061	37.500	22.93	0.00	0.00	1.82
910	971	1.886886	TTTTACTGTTGCTCGGACCC	58.113	50.000	0.00	0.00	0.00	4.46
943	1004	2.325583	AGTTGCGTCCAAGTGAAAGA	57.674	45.000	0.00	0.00	33.44	2.52
1969	4596	2.574322	CAGCGCAACTCAATGTACAAC	58.426	47.619	11.47	0.00	0.00	3.32
2032	4659	5.066593	AGATCCGATTCCTTTTATTGGAGC	58.933	41.667	0.00	0.00	40.67	4.70
2035	4662	4.580167	TCCGATTCCTTTTATTGGAGCATG	59.420	41.667	0.00	0.00	31.86	4.06
2148	4775	1.272313	ACATGCATGTTCTCTTGGCCT	60.272	47.619	26.61	0.00	37.90	5.19
2165	4792	5.598416	TGGCCTAATCTATGATATGGTCG	57.402	43.478	3.32	0.00	0.00	4.79
2228	4855	6.749118	GTCTGAATTAACAGAATTGTGCATCC	59.251	38.462	1.83	0.00	46.34	3.51
2432	5059	4.439289	GGATGTTCTTTTGGCTGTAGCATC	60.439	45.833	6.18	0.00	44.36	3.91
2495	5122	4.279922	AGTTGGTTGTATGGTTTAGTTGGC	59.720	41.667	0.00	0.00	0.00	4.52
2671	5298	2.290450	TGTGCTGTGATCATGTGGACAT	60.290	45.455	12.96	0.00	36.96	3.06
2872	5499	6.148976	GTCCTGAAAAGGTATGTCAACTTACC	59.851	42.308	14.36	14.36	43.26	2.85
2879	5506	5.509498	AGGTATGTCAACTTACCATTGCAT	58.491	37.500	20.91	3.47	44.55	3.96
2905	5532	8.721478	TCAAAATCTGTTACAAGATCTTACAGC	58.279	33.333	23.50	11.73	35.83	4.40
2934	5561	7.952368	ACTCACTAAAGTACCTCTACCCTTTTA	59.048	37.037	0.00	0.00	0.00	1.52
3090	5717	7.913674	AGATTACAAAAGCTTAAGGACAGAG	57.086	36.000	0.00	0.00	0.00	3.35
3507	6134	2.350772	GCTGTGAACAACAAATCCCTCG	60.351	50.000	0.00	0.00	38.67	4.63
3558	6185	3.634910	GGTGTCAAAGGTAAGGCAAAGAA	59.365	43.478	0.00	0.00	0.00	2.52
3611	6239	1.309950	CTTGGAGCTGATCATGCTGG	58.690	55.000	19.95	0.00	41.30	4.85
3613	6241	1.153025	GGAGCTGATCATGCTGGCA	60.153	57.895	19.95	0.00	41.30	4.92
3615	6243	1.319541	GAGCTGATCATGCTGGCATT	58.680	50.000	19.95	0.00	41.30	3.56
3616	6244	1.681793	GAGCTGATCATGCTGGCATTT	59.318	47.619	19.95	0.00	41.30	2.32
3617	6245	2.100916	GAGCTGATCATGCTGGCATTTT	59.899	45.455	19.95	0.00	41.30	1.82
3618	6246	3.293337	AGCTGATCATGCTGGCATTTTA	58.707	40.909	15.90	0.00	39.56	1.52
3890	6518	9.823098	CAGAAGTTTCATGAAGATTTCACTAAG	57.177	33.333	20.92	8.41	43.48	2.18
3959	6587	9.620660	CTAATAGCCGAAAACATTAACAAGTTT	57.379	29.630	0.00	0.00	39.46	2.66
4290	6919	0.755327	GTTGGTGGCCTTGAGGTTGT	60.755	55.000	3.32	0.00	37.57	3.32
4315	6944	1.256812	GGTGTCCATGGGAAAACTGG	58.743	55.000	13.02	0.00	31.38	4.00
4377	7009	1.889530	GACCCCACCCTCTCAACTCG	61.890	65.000	0.00	0.00	0.00	4.18
4575	7210	1.838112	TTAAGCAAGTGATGGCCAGG	58.162	50.000	13.05	0.00	0.00	4.45
4576	7211	0.034186	TAAGCAAGTGATGGCCAGGG	60.034	55.000	13.05	0.00	0.00	4.45
4577	7212	2.757099	GCAAGTGATGGCCAGGGG	60.757	66.667	13.05	0.00	0.00	4.79
4578	7213	2.765969	CAAGTGATGGCCAGGGGT	59.234	61.111	13.05	0.00	0.00	4.95
4629	7264	2.293122	TGGAGCAAAACGAATTCCACAG	59.707	45.455	0.00	0.00	33.21	3.66
4740	7375	2.740055	CTCCACAGCAGCACGTCC	60.740	66.667	0.00	0.00	0.00	4.79
4835	7473	1.612726	GCCTGAACACTCCTCTTGCAT	60.613	52.381	0.00	0.00	0.00	3.96
4837	7475	2.082231	CTGAACACTCCTCTTGCATGG	58.918	52.381	0.00	0.00	0.00	3.66
4854	7495	2.344093	TGGAAGCTTTACCCTCCTCT	57.656	50.000	0.00	0.00	0.00	3.69
4856	7497	1.407575	GGAAGCTTTACCCTCCTCTGC	60.408	57.143	0.00	0.00	0.00	4.26
4858	7499	0.905337	AGCTTTACCCTCCTCTGCGT	60.905	55.000	0.00	0.00	0.00	5.24
4893	7537	1.079750	GACGGCTGGTTCTGAGGAC	60.080	63.158	0.00	0.00	0.00	3.85
5088	7732	2.729479	CCTCATCGCCTCCTGCACT	61.729	63.158	0.00	0.00	41.33	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
100	101	1.078214	CCCATCTCTCAGCGCCAAA	60.078	57.895	2.29	0.00	0.00	3.28
114	115	1.561542	GAAGATGTGAGGTCACCCCAT	59.438	52.381	7.64	0.00	45.88	4.00
345	371	1.471119	CCCTAGAAGTGCAGGACGTA	58.529	55.000	0.00	0.00	33.42	3.57
478	517	6.591062	GCAAAGAGTATGCAATTGGATTGAAA	59.409	34.615	18.12	0.00	42.83	2.69
480	519	5.394443	GGCAAAGAGTATGCAATTGGATTGA	60.394	40.000	18.12	0.00	45.60	2.57
638	680	0.687354	ACCCGAACTCATGTGAGCTT	59.313	50.000	9.84	4.19	45.79	3.74
651	693	6.406692	TTTGGATTTTATTGTTCACCCGAA	57.593	33.333	0.00	0.00	0.00	4.30
843	899	4.355543	AGTATTATGCAAGCAACGTTGG	57.644	40.909	28.33	13.86	0.00	3.77
847	903	8.841444	AAAATCTTAGTATTATGCAAGCAACG	57.159	30.769	0.00	0.00	0.00	4.10
910	971	4.378459	GGACGCAACTGTTATTCTTTGAGG	60.378	45.833	0.00	0.00	0.00	3.86
1379	4002	6.708949	TCCAATTTCTACTACGCAAGAAACTT	59.291	34.615	0.00	0.00	42.72	2.66
1969	4596	6.105333	CCTTCCAGAGATAAGAGAGTTGTTG	58.895	44.000	0.00	0.00	0.00	3.33
2013	4640	4.261741	CCATGCTCCAATAAAAGGAATCGG	60.262	45.833	0.00	0.00	34.08	4.18
2015	4642	5.859205	ACCATGCTCCAATAAAAGGAATC	57.141	39.130	0.00	0.00	34.08	2.52
2032	4659	5.695816	CACCACTGTTTTCCAAATTACCATG	59.304	40.000	0.00	0.00	0.00	3.66
2035	4662	4.055360	GCACCACTGTTTTCCAAATTACC	58.945	43.478	0.00	0.00	0.00	2.85
2148	4775	7.776618	AGAACACCGACCATATCATAGATTA	57.223	36.000	0.00	0.00	0.00	1.75
2165	4792	7.040409	AGGAAAGAAACATATGTCAAGAACACC	60.040	37.037	9.23	6.78	41.75	4.16
2217	4844	4.895668	ATTCCTTTGTGGATGCACAATT	57.104	36.364	29.94	12.37	45.68	2.32
2273	4900	9.194972	TCCAATTAGTTTTGCATGGTTGATATA	57.805	29.630	0.00	0.00	0.00	0.86
2432	5059	2.146342	ACTTTGCATCGAGACAACCAG	58.854	47.619	2.60	2.32	0.00	4.00
2671	5298	5.178061	AGTCGATGACTTGCATTCATAACA	58.822	37.500	10.51	0.00	40.28	2.41
2775	5402	5.960202	AGGGGAAGCATCTGTTTTATTCATT	59.040	36.000	0.00	0.00	0.00	2.57
2872	5499	8.697846	ATCTTGTAACAGATTTTGATGCAATG	57.302	30.769	0.00	0.00	34.63	2.82
2879	5506	8.721478	GCTGTAAGATCTTGTAACAGATTTTGA	58.279	33.333	28.97	1.69	39.93	2.69
2905	5532	5.357596	GGGTAGAGGTACTTTAGTGAGTGAG	59.642	48.000	0.00	0.00	41.55	3.51
2934	5561	0.684153	GCCTGAGGAGAGCAGAGAGT	60.684	60.000	0.65	0.00	35.39	3.24
3558	6185	7.393234	TCATTCGGTTCATGGTTCTAAAATTCT	59.607	33.333	0.00	0.00	0.00	2.40
3666	6294	3.607490	ATGGGCTGCAAGAAATAGGAT	57.393	42.857	0.50	0.00	34.07	3.24
3667	6295	4.518278	TTATGGGCTGCAAGAAATAGGA	57.482	40.909	0.50	0.00	34.07	2.94
3837	6465	0.465460	AACCTTTGAGCACGCTTCCA	60.465	50.000	0.00	0.00	0.00	3.53
3959	6587	4.229639	ACCTCAGAATCTCCATCATGCTA	58.770	43.478	0.00	0.00	0.00	3.49
4137	6765	8.193953	AGTTTAGATATTGGGGCCAAAATATG	57.806	34.615	21.74	0.00	39.55	1.78
4138	6766	8.650490	CAAGTTTAGATATTGGGGCCAAAATAT	58.350	33.333	18.51	18.51	39.55	1.28
4139	6767	7.841729	TCAAGTTTAGATATTGGGGCCAAAATA	59.158	33.333	4.39	9.61	39.55	1.40
4158	6786	5.279156	GCATGGAGTTGAATTCCTCAAGTTT	60.279	40.000	8.25	0.00	45.90	2.66
4219	6847	6.145535	GCTTACAAGAATCTTTCCACACTTG	58.854	40.000	0.00	0.00	39.98	3.16
4290	6919	2.335681	TTCCCATGGACACCACTCTA	57.664	50.000	15.22	0.00	35.80	2.43
4315	6944	2.095415	GGCACGAGTACCAATTTTCCAC	60.095	50.000	0.00	0.00	0.00	4.02
4467	7102	5.989777	GGTAGTGCTTCAAAGTAGAACTCAA	59.010	40.000	0.00	0.00	0.00	3.02
4575	7210	1.544314	GGCTCATATGAGAAGCCACCC	60.544	57.143	32.38	19.20	44.74	4.61
4576	7211	1.889545	GGCTCATATGAGAAGCCACC	58.110	55.000	32.38	19.84	44.74	4.61
4629	7264	2.099098	ACTTGCAGTTAGGTTGTGTTGC	59.901	45.455	0.00	0.00	0.00	4.17
4667	7302	2.024414	AGGCTGACCAGTTTTGTTGAC	58.976	47.619	0.00	0.00	39.06	3.18
4668	7303	2.435372	AGGCTGACCAGTTTTGTTGA	57.565	45.000	0.00	0.00	39.06	3.18
4748	7383	2.202570	CGGAGGCTAACGTCACCG	60.203	66.667	0.00	0.00	40.83	4.94
4805	7443	2.981909	GTTCAGGCAGCAGCAGCA	60.982	61.111	12.41	0.00	45.49	4.41
4835	7473	1.909302	CAGAGGAGGGTAAAGCTTCCA	59.091	52.381	12.20	0.00	32.02	3.53
4837	7475	1.740718	CGCAGAGGAGGGTAAAGCTTC	60.741	57.143	0.00	0.00	0.00	3.86
4854	7495	1.078988	TGCTGCTGATCATGACGCA	60.079	52.632	13.49	13.49	0.00	5.24
4856	7497	1.642215	GCTGCTGCTGATCATGACG	59.358	57.895	10.92	0.00	36.03	4.35
4858	7499	0.808847	GTCGCTGCTGCTGATCATGA	60.809	55.000	14.03	0.00	36.97	3.07
4875	7516	1.079750	GTCCTCAGAACCAGCCGTC	60.080	63.158	0.00	0.00	0.00	4.79
4876	7517	1.534235	AGTCCTCAGAACCAGCCGT	60.534	57.895	0.00	0.00	0.00	5.68
4878	7519	1.376553	GCAGTCCTCAGAACCAGCC	60.377	63.158	0.00	0.00	0.00	4.85
4887	7531	1.683707	AGCATCGGAGCAGTCCTCA	60.684	57.895	3.00	0.00	42.62	3.86
4893	7537	2.895865	CAGCCAGCATCGGAGCAG	60.896	66.667	3.00	0.00	36.85	4.24
4921	7565	3.130160	CCGCAAGAAGCAGAGGGC	61.130	66.667	0.00	0.00	46.13	5.19

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.