AutoCloner

Multiple sequence alignment - TraesCS4B01G276400

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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	TraesCS4B01G276400	chr4B	100.000	2288	0	0	1	2288	556070793	556068506	0.000000e+00	4226.0
1	TraesCS4B01G276400	chr4B	97.610	251	6	0	1584	1834	556063595	556063345	4.520000e-117	431.0
2	TraesCS4B01G276400	chr4D	89.864	1618	71	40	1	1586	445497716	445496160	0.000000e+00	1993.0
3	TraesCS4B01G276400	chr4D	80.992	121	23	0	1013	1133	7587297	7587417	1.870000e-16	97.1
4	TraesCS4B01G276400	chr4A	86.282	1385	94	47	269	1586	21631239	21632594	0.000000e+00	1417.0
5	TraesCS4B01G276400	chr4A	92.000	75	2	1	121	191	21631051	21631125	4.020000e-18	102.0
6	TraesCS4B01G276400	chr4A	80.315	127	25	0	1013	1139	596002422	596002296	1.870000e-16	97.1
7	TraesCS4B01G276400	chr3B	98.578	703	9	1	1587	2288	555072224	555071522	0.000000e+00	1242.0
8	TraesCS4B01G276400	chr3B	97.610	251	6	0	1584	1834	555066013	555065763	4.520000e-117	431.0
9	TraesCS4B01G276400	chr1B	98.148	702	13	0	1587	2288	53265318	53264617	0.000000e+00	1225.0
10	TraesCS4B01G276400	chr1B	98.008	251	5	0	1584	1834	53259212	53258962	9.710000e-119	436.0
11	TraesCS4B01G276400	chr7B	92.887	717	25	4	1584	2288	640139297	640139999	0.000000e+00	1018.0
12	TraesCS4B01G276400	chr7B	96.501	543	18	1	1584	2125	640080054	640080596	0.000000e+00	896.0
13	TraesCS4B01G276400	chrUn	97.984	248	5	0	1584	1831	476709499	476709252	4.520000e-117	431.0
14	TraesCS4B01G276400	chr6D	96.850	254	8	0	1582	1835	6984408	6984155	2.100000e-115	425.0
15	TraesCS4B01G276400	chr1D	95.437	263	11	1	1586	1848	18582300	18582561	3.520000e-113	418.0
16	TraesCS4B01G276400	chr1D	82.629	213	28	7	1819	2023	131163421	131163632	1.810000e-41	180.0
17	TraesCS4B01G276400	chr3D	93.077	130	8	1	1898	2026	66889104	66888975	3.000000e-44	189.0
18	TraesCS4B01G276400	chr7D	83.495	206	17	7	1831	2033	145899012	145898821	2.340000e-40	176.0
19	TraesCS4B01G276400	chr2B	86.331	139	16	2	1898	2033	103473959	103473821	5.090000e-32	148.0
20	TraesCS4B01G276400	chr7A	83.230	161	23	3	1843	1999	277726737	277726577	6.590000e-31	145.0

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	TraesCS4B01G276400	chr4B	556068506	556070793	2287	True	4226.0	4226	100.000	1	2288	1	chr4B.!!$R2	2287
1	TraesCS4B01G276400	chr4D	445496160	445497716	1556	True	1993.0	1993	89.864	1	1586	1	chr4D.!!$R1	1585
2	TraesCS4B01G276400	chr4A	21631051	21632594	1543	False	759.5	1417	89.141	121	1586	2	chr4A.!!$F1	1465
3	TraesCS4B01G276400	chr3B	555071522	555072224	702	True	1242.0	1242	98.578	1587	2288	1	chr3B.!!$R2	701
4	TraesCS4B01G276400	chr1B	53264617	53265318	701	True	1225.0	1225	98.148	1587	2288	1	chr1B.!!$R2	701
5	TraesCS4B01G276400	chr7B	640139297	640139999	702	False	1018.0	1018	92.887	1584	2288	1	chr7B.!!$F2	704
6	TraesCS4B01G276400	chr7B	640080054	640080596	542	False	896.0	896	96.501	1584	2125	1	chr7B.!!$F1	541

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
903	968	0.032678	CTCGGTGTCACACTTGCTCT	59.967	55.0	8.12	0.0	34.4	4.09	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1714	1867	0.537188	TCTGTTCGAAGGCATCCCTC	59.463	55.0	0.0	0.0	41.9	4.3	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
36	37	3.578282	TGAGTTGAGACTACCTGATGCAA	59.422	43.478	0.00	0.00	35.88	4.08
37	38	4.040339	TGAGTTGAGACTACCTGATGCAAA	59.960	41.667	0.00	0.00	35.88	3.68
191	196	1.808945	GGTGAGTTCATGCAGGTTCAG	59.191	52.381	0.00	0.00	0.00	3.02
238	269	5.003160	TGATGATCAGTTAACAAGGTGTGG	58.997	41.667	8.61	0.00	0.00	4.17
249	290	2.756207	ACAAGGTGTGGGTGTTGTTAAC	59.244	45.455	0.00	0.00	28.62	2.01
255	296	3.059188	GTGTGGGTGTTGTTAACTCATCG	60.059	47.826	7.22	0.00	0.00	3.84
260	301	3.810941	GGTGTTGTTAACTCATCGTGGAA	59.189	43.478	7.22	0.00	0.00	3.53
333	374	1.674322	GCCAGTTGTGCCGTACCAT	60.674	57.895	0.00	0.00	0.00	3.55
336	377	1.078709	CAGTTGTGCCGTACCATGAG	58.921	55.000	0.00	0.00	0.00	2.90
359	400	3.928992	CAGCGACTGAAATCTAGCAGAAA	59.071	43.478	0.00	0.00	36.07	2.52
367	408	5.121811	TGAAATCTAGCAGAAAGGATGAGC	58.878	41.667	0.00	0.00	0.00	4.26
378	419	2.408271	AGGATGAGCAGAATTTCGCA	57.592	45.000	13.12	2.69	0.00	5.10
430	471	1.937899	GTTGTTGCGTAAGGTGTCTGT	59.062	47.619	0.00	0.00	38.28	3.41
496	538	2.956132	TCTCCCTGATGATCCTGTCTC	58.044	52.381	0.00	0.00	0.00	3.36
497	539	2.517553	TCTCCCTGATGATCCTGTCTCT	59.482	50.000	0.00	0.00	0.00	3.10
498	540	3.052262	TCTCCCTGATGATCCTGTCTCTT	60.052	47.826	0.00	0.00	0.00	2.85
499	541	3.303938	TCCCTGATGATCCTGTCTCTTC	58.696	50.000	0.00	0.00	0.00	2.87
500	542	2.368221	CCCTGATGATCCTGTCTCTTCC	59.632	54.545	0.00	0.00	0.00	3.46
501	543	3.307506	CCTGATGATCCTGTCTCTTCCT	58.692	50.000	0.00	0.00	0.00	3.36
502	544	3.321682	CCTGATGATCCTGTCTCTTCCTC	59.678	52.174	0.00	0.00	0.00	3.71
524	567	2.554032	CTCATTTTGCGGTCAAGAGGTT	59.446	45.455	0.00	0.00	33.12	3.50
534	577	3.367087	CGGTCAAGAGGTTCTCGTACAAT	60.367	47.826	0.00	0.00	35.36	2.71
535	578	4.142534	CGGTCAAGAGGTTCTCGTACAATA	60.143	45.833	0.00	0.00	35.36	1.90
575	624	6.973229	TTGAGGGTAAAAGTTTATCGTAGC	57.027	37.500	0.00	0.00	0.00	3.58
600	649	9.516314	GCAAGTAAAGTAAACAATCAGAAACTT	57.484	29.630	0.00	0.00	0.00	2.66
606	655	9.511144	AAAGTAAACAATCAGAAACTTTTACCG	57.489	29.630	0.00	0.00	34.44	4.02
668	726	6.998802	ACTGTTCATTAGGAGCTATACATCC	58.001	40.000	0.00	0.00	35.71	3.51
669	727	6.014156	ACTGTTCATTAGGAGCTATACATCCC	60.014	42.308	0.00	0.00	36.14	3.85
670	728	5.843969	TGTTCATTAGGAGCTATACATCCCA	59.156	40.000	0.00	0.00	36.14	4.37
671	729	6.014242	TGTTCATTAGGAGCTATACATCCCAG	60.014	42.308	0.00	0.00	36.14	4.45
672	730	5.903923	TCATTAGGAGCTATACATCCCAGA	58.096	41.667	0.00	0.00	36.14	3.86
673	731	5.954752	TCATTAGGAGCTATACATCCCAGAG	59.045	44.000	0.00	0.00	36.14	3.35
674	732	5.600669	TTAGGAGCTATACATCCCAGAGA	57.399	43.478	0.00	0.00	36.14	3.10
677	735	3.509575	GGAGCTATACATCCCAGAGACAG	59.490	52.174	0.00	0.00	0.00	3.51
826	887	7.286775	ACAGAGAAGTAGGCCTCTCTAATTAAG	59.713	40.741	18.98	10.23	37.64	1.85
827	888	6.266786	AGAGAAGTAGGCCTCTCTAATTAAGC	59.733	42.308	18.20	3.15	37.75	3.09
828	889	5.900123	AGAAGTAGGCCTCTCTAATTAAGCA	59.100	40.000	9.68	0.00	29.20	3.91
829	890	6.556874	AGAAGTAGGCCTCTCTAATTAAGCAT	59.443	38.462	9.68	0.00	29.20	3.79
896	961	2.733593	GCGTCCTCGGTGTCACAC	60.734	66.667	0.00	0.00	37.56	3.82
903	968	0.032678	CTCGGTGTCACACTTGCTCT	59.967	55.000	8.12	0.00	34.40	4.09
918	983	1.078567	CTCTCTGCCTTGCTCCCAC	60.079	63.158	0.00	0.00	0.00	4.61
919	984	1.834856	CTCTCTGCCTTGCTCCCACA	61.835	60.000	0.00	0.00	0.00	4.17
920	985	1.673665	CTCTGCCTTGCTCCCACAC	60.674	63.158	0.00	0.00	0.00	3.82
921	986	2.674380	CTGCCTTGCTCCCACACC	60.674	66.667	0.00	0.00	0.00	4.16
922	987	3.496309	CTGCCTTGCTCCCACACCA	62.496	63.158	0.00	0.00	0.00	4.17
923	988	2.985847	GCCTTGCTCCCACACCAC	60.986	66.667	0.00	0.00	0.00	4.16
943	1008	4.424566	CCACCATTGCACGCTGGC	62.425	66.667	8.67	0.00	35.88	4.85
964	1029	0.179171	TTGAGCTCGGTCGATCGAAC	60.179	55.000	23.27	23.27	38.77	3.95
965	1030	1.025113	TGAGCTCGGTCGATCGAACT	61.025	55.000	28.99	22.98	38.14	3.01
967	1032	1.532007	GAGCTCGGTCGATCGAACTAT	59.468	52.381	28.99	13.01	35.98	2.12
1314	1379	0.744414	CGAAGCGACCCACCATTCAT	60.744	55.000	0.00	0.00	0.00	2.57
1359	1436	2.990479	GACGAATGGGTCCAGCCT	59.010	61.111	0.00	0.00	37.43	4.58
1360	1437	1.450312	GACGAATGGGTCCAGCCTG	60.450	63.158	0.00	0.00	37.43	4.85
1361	1438	2.124570	CGAATGGGTCCAGCCTGG	60.125	66.667	3.69	3.69	39.43	4.45
1362	1439	2.440980	GAATGGGTCCAGCCTGGC	60.441	66.667	11.65	11.65	37.47	4.85
1363	1440	4.066139	AATGGGTCCAGCCTGGCC	62.066	66.667	16.57	10.72	37.47	5.36
1429	1544	8.863872	ATAATTAGCCAAGGGTTCATATGTAC	57.136	34.615	1.90	3.04	0.00	2.90
1430	1545	3.194005	AGCCAAGGGTTCATATGTACG	57.806	47.619	1.90	0.00	0.00	3.67
1431	1546	1.602377	GCCAAGGGTTCATATGTACGC	59.398	52.381	18.13	18.13	0.00	4.42
1447	1567	2.770699	ACGCAGTAGTAATACGGAGC	57.229	50.000	4.64	5.26	41.94	4.70
1511	1654	1.265568	GTTGAAGCTGCATTGCATCG	58.734	50.000	12.53	2.45	38.13	3.84
1569	1720	1.677633	CCCGGCTGTACAAAAGGGG	60.678	63.158	17.11	12.10	35.36	4.79
1714	1867	1.755179	CCAATAGGCACCTGTTCTGG	58.245	55.000	0.00	0.00	0.00	3.86
1725	1878	0.622665	CTGTTCTGGAGGGATGCCTT	59.377	55.000	7.42	0.00	0.00	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	5.775701	AGGTAGTCTCAACTCAAGTGTATGT	59.224	40.000	0.00	0.00	36.92	2.29
20	21	2.935201	CTGCTTTGCATCAGGTAGTCTC	59.065	50.000	0.00	0.00	38.13	3.36
236	267	3.135225	CACGATGAGTTAACAACACCCA	58.865	45.455	8.61	0.00	0.00	4.51
238	269	3.395639	TCCACGATGAGTTAACAACACC	58.604	45.455	8.61	0.00	0.00	4.16
255	296	2.511600	CCGCCCGTCATCTTCCAC	60.512	66.667	0.00	0.00	0.00	4.02
333	374	2.736719	GCTAGATTTCAGTCGCTGCTCA	60.737	50.000	0.00	0.00	0.00	4.26
336	377	1.592081	CTGCTAGATTTCAGTCGCTGC	59.408	52.381	0.00	0.00	0.00	5.25
359	400	2.286872	CTGCGAAATTCTGCTCATCCT	58.713	47.619	10.12	0.00	0.00	3.24
367	408	0.804989	GACCACCCTGCGAAATTCTG	59.195	55.000	0.00	0.00	0.00	3.02
430	471	1.468520	GCGTGCTCCATAAAGCTTGAA	59.531	47.619	0.00	0.00	42.94	2.69
481	523	3.321682	GGAGGAAGAGACAGGATCATCAG	59.678	52.174	0.00	0.00	0.00	2.90
496	538	1.740025	GACCGCAAAATGAGGAGGAAG	59.260	52.381	7.14	0.00	39.92	3.46
497	539	1.073125	TGACCGCAAAATGAGGAGGAA	59.927	47.619	7.14	0.00	39.92	3.36
498	540	0.690192	TGACCGCAAAATGAGGAGGA	59.310	50.000	7.14	0.00	39.92	3.71
499	541	1.470098	CTTGACCGCAAAATGAGGAGG	59.530	52.381	7.14	0.00	39.92	4.30
500	542	2.417933	CTCTTGACCGCAAAATGAGGAG	59.582	50.000	7.14	0.00	39.92	3.69
501	543	2.426522	CTCTTGACCGCAAAATGAGGA	58.573	47.619	7.14	0.00	39.92	3.71
502	544	1.470098	CCTCTTGACCGCAAAATGAGG	59.530	52.381	0.00	0.00	43.39	3.86
600	649	2.944349	GACCAACAAACACCTCGGTAAA	59.056	45.455	0.00	0.00	0.00	2.01
601	650	2.093075	TGACCAACAAACACCTCGGTAA	60.093	45.455	0.00	0.00	0.00	2.85
602	651	1.485480	TGACCAACAAACACCTCGGTA	59.515	47.619	0.00	0.00	0.00	4.02
606	655	2.158813	TCTCCTGACCAACAAACACCTC	60.159	50.000	0.00	0.00	0.00	3.85
668	726	1.543607	TGTGCTCTCTCTGTCTCTGG	58.456	55.000	0.00	0.00	0.00	3.86
669	727	3.872511	AATGTGCTCTCTCTGTCTCTG	57.127	47.619	0.00	0.00	0.00	3.35
670	728	5.518848	CATAATGTGCTCTCTCTGTCTCT	57.481	43.478	0.00	0.00	0.00	3.10
750	811	1.681793	GATTTGGCATCTGAGCAGCAT	59.318	47.619	0.00	0.00	35.83	3.79
827	888	2.437180	TTGGCTCGGAGCTGCATG	60.437	61.111	27.47	0.00	41.99	4.06
828	889	2.124819	CTTGGCTCGGAGCTGCAT	60.125	61.111	27.47	0.00	41.99	3.96
887	952	1.506493	CAGAGAGCAAGTGTGACACC	58.494	55.000	12.81	0.00	34.49	4.16
888	953	0.864455	GCAGAGAGCAAGTGTGACAC	59.136	55.000	7.83	7.83	44.79	3.67
889	954	3.295734	GCAGAGAGCAAGTGTGACA	57.704	52.632	0.00	0.00	44.79	3.58
903	968	2.431683	GTGTGGGAGCAAGGCAGA	59.568	61.111	0.00	0.00	0.00	4.26
918	983	1.831726	TGCAATGGTGGTGGTGGTG	60.832	57.895	0.00	0.00	0.00	4.17
919	984	1.832167	GTGCAATGGTGGTGGTGGT	60.832	57.895	0.00	0.00	0.00	4.16
920	985	2.918345	CGTGCAATGGTGGTGGTGG	61.918	63.158	0.00	0.00	0.00	4.61
921	986	2.644418	CGTGCAATGGTGGTGGTG	59.356	61.111	0.00	0.00	0.00	4.17
922	987	3.294493	GCGTGCAATGGTGGTGGT	61.294	61.111	0.00	0.00	0.00	4.16
923	988	2.985282	AGCGTGCAATGGTGGTGG	60.985	61.111	0.00	0.00	28.67	4.61
943	1008	1.298713	CGATCGACCGAGCTCAAGG	60.299	63.158	15.40	10.38	0.00	3.61
1373	1450	2.025441	TTTGCAACGGCGCTTGTC	59.975	55.556	6.90	7.99	45.35	3.18
1400	1515	9.295825	CATATGAACCCTTGGCTAATTATTACA	57.704	33.333	0.00	0.00	0.00	2.41
1429	1544	2.768833	TGCTCCGTATTACTACTGCG	57.231	50.000	0.00	0.00	0.00	5.18
1430	1545	3.978687	ACATGCTCCGTATTACTACTGC	58.021	45.455	0.00	0.00	0.00	4.40
1431	1546	6.678878	ACATACATGCTCCGTATTACTACTG	58.321	40.000	0.00	0.00	0.00	2.74
1482	1620	3.096852	TGCAGCTTCAACCTAGCTACTA	58.903	45.455	0.00	0.00	46.80	1.82
1483	1621	1.902508	TGCAGCTTCAACCTAGCTACT	59.097	47.619	0.00	0.00	46.80	2.57
1484	1622	2.386661	TGCAGCTTCAACCTAGCTAC	57.613	50.000	0.00	0.00	46.80	3.58
1511	1654	2.101700	GCATCAGCTACCTGCCAAC	58.898	57.895	3.57	0.00	44.23	3.77
1569	1720	4.576463	CCTAACACTCTCATGTTATTGGGC	59.424	45.833	0.00	0.00	42.63	5.36
1635	1787	7.093771	GGTTGGACACATCCTTTTTCTAATGAT	60.094	37.037	0.00	0.00	46.43	2.45
1650	1802	0.250727	CTGTTCGGGGTTGGACACAT	60.251	55.000	0.00	0.00	0.00	3.21
1714	1867	0.537188	TCTGTTCGAAGGCATCCCTC	59.463	55.000	0.00	0.00	41.90	4.30
1725	1878	3.463944	GGAAAAAGAGGTGTCTGTTCGA	58.536	45.455	0.00	0.00	27.70	3.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.