AutoCloner

Multiple sequence alignment - TraesCS1D01G273000

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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	TraesCS1D01G273000	chr1D	100.000	2651	0	0	1	2651	367149297	367151947	0.000000e+00	4896.0
1	TraesCS1D01G273000	chr1D	96.557	1917	44	5	1	1915	366090640	366092536	0.000000e+00	3155.0
2	TraesCS1D01G273000	chr1D	95.540	426	18	1	2227	2651	366093117	366093542	0.000000e+00	680.0
3	TraesCS1D01G273000	chr1D	93.659	205	13	0	2027	2231	366092538	366092742	9.220000e-80	307.0
4	TraesCS1D01G273000	chr1A	96.350	2137	60	11	1	2122	466337289	466339422	0.000000e+00	3498.0
5	TraesCS1D01G273000	chr1A	98.111	1747	29	4	1	1746	466037670	466039413	0.000000e+00	3040.0
6	TraesCS1D01G273000	chr1A	96.919	422	12	1	2227	2647	466339832	466340253	0.000000e+00	706.0
7	TraesCS1D01G273000	chr1B	95.882	2040	67	13	1	2028	491439417	491441451	0.000000e+00	3286.0
8	TraesCS1D01G273000	chr1B	95.618	1803	56	14	1	1785	491398162	491399959	0.000000e+00	2870.0
9	TraesCS1D01G273000	chr1B	94.059	808	33	5	1854	2647	491401533	491402339	0.000000e+00	1212.0
10	TraesCS1D01G273000	chr1B	95.122	82	4	0	1777	1858	491401223	491401304	2.140000e-26	130.0
11	TraesCS1D01G273000	chr1B	98.182	55	1	0	658	712	491398777	491398831	2.170000e-16	97.1
12	TraesCS1D01G273000	chr1B	98.000	50	1	0	2073	2122	491441450	491441499	1.310000e-13	87.9
13	TraesCS1D01G273000	chr6A	97.687	1859	36	5	1	1857	428665896	428664043	0.000000e+00	3188.0
14	TraesCS1D01G273000	chr6A	89.587	605	32	9	1954	2557	428663615	428663041	0.000000e+00	739.0
15	TraesCS1D01G273000	chr6A	94.083	169	9	1	2415	2582	428681340	428681508	3.390000e-64	255.0
16	TraesCS1D01G273000	chr6A	95.745	94	4	0	2557	2650	428622335	428622242	4.570000e-33	152.0
17	TraesCS1D01G273000	chr6A	100.000	68	0	0	2566	2633	428681523	428681590	2.770000e-25	126.0

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	TraesCS1D01G273000	chr1D	367149297	367151947	2650	False	4896.000000	4896	100.00000	1	2651	1	chr1D.!!$F1	2650
1	TraesCS1D01G273000	chr1D	366090640	366093542	2902	False	1380.666667	3155	95.25200	1	2651	3	chr1D.!!$F2	2650
2	TraesCS1D01G273000	chr1A	466037670	466039413	1743	False	3040.000000	3040	98.11100	1	1746	1	chr1A.!!$F1	1745
3	TraesCS1D01G273000	chr1A	466337289	466340253	2964	False	2102.000000	3498	96.63450	1	2647	2	chr1A.!!$F2	2646
4	TraesCS1D01G273000	chr1B	491439417	491441499	2082	False	1686.950000	3286	96.94100	1	2122	2	chr1B.!!$F2	2121
5	TraesCS1D01G273000	chr1B	491398162	491402339	4177	False	1077.275000	2870	95.74525	1	2647	4	chr1B.!!$F1	2646
6	TraesCS1D01G273000	chr6A	428663041	428665896	2855	True	1963.500000	3188	93.63700	1	2557	2	chr6A.!!$R2	2556

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
686	751	0.325671	ATGAGGATGGTGACGGAGGT	60.326	55.0	0.0	0.0	0.0	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2364	4664	0.466124	GCTATCCAGCGAGGGAAAGT	59.534	55.0	0.0	0.0	41.12	2.66	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
135	136	8.139989	AGCACATAATATGGATTTCTGCTTTTC	58.860	33.333	5.16	0.00	29.86	2.29
348	352	9.486497	TGTTCTATATGCTCATCTCATCTTTTC	57.514	33.333	0.00	0.00	0.00	2.29
364	369	2.380571	TTTCTTTCCAGGGTGGGGGC	62.381	60.000	0.00	0.00	38.32	5.80
411	416	3.628032	TGTGGCGTGATTAGTTTTGTTGA	59.372	39.130	0.00	0.00	0.00	3.18
677	742	0.700564	ACACTGCCAATGAGGATGGT	59.299	50.000	0.00	0.00	41.22	3.55
678	743	1.100510	CACTGCCAATGAGGATGGTG	58.899	55.000	0.00	0.00	41.22	4.17
679	744	0.994247	ACTGCCAATGAGGATGGTGA	59.006	50.000	0.00	0.00	41.22	4.02
680	745	1.340405	ACTGCCAATGAGGATGGTGAC	60.340	52.381	0.00	0.00	41.22	3.67
681	746	0.392863	TGCCAATGAGGATGGTGACG	60.393	55.000	0.00	0.00	41.22	4.35
682	747	1.097547	GCCAATGAGGATGGTGACGG	61.098	60.000	0.00	0.00	41.22	4.79
683	748	0.541392	CCAATGAGGATGGTGACGGA	59.459	55.000	0.00	0.00	41.22	4.69
684	749	1.473965	CCAATGAGGATGGTGACGGAG	60.474	57.143	0.00	0.00	41.22	4.63
685	750	0.833287	AATGAGGATGGTGACGGAGG	59.167	55.000	0.00	0.00	0.00	4.30
686	751	0.325671	ATGAGGATGGTGACGGAGGT	60.326	55.000	0.00	0.00	0.00	3.85
687	752	1.257750	TGAGGATGGTGACGGAGGTG	61.258	60.000	0.00	0.00	0.00	4.00
688	753	0.970937	GAGGATGGTGACGGAGGTGA	60.971	60.000	0.00	0.00	0.00	4.02
689	754	0.972983	AGGATGGTGACGGAGGTGAG	60.973	60.000	0.00	0.00	0.00	3.51
690	755	1.517832	GATGGTGACGGAGGTGAGG	59.482	63.158	0.00	0.00	0.00	3.86
691	756	0.970937	GATGGTGACGGAGGTGAGGA	60.971	60.000	0.00	0.00	0.00	3.71
692	757	0.325671	ATGGTGACGGAGGTGAGGAT	60.326	55.000	0.00	0.00	0.00	3.24
693	758	1.257750	TGGTGACGGAGGTGAGGATG	61.258	60.000	0.00	0.00	0.00	3.51
694	759	1.517832	GTGACGGAGGTGAGGATGG	59.482	63.158	0.00	0.00	0.00	3.51
824	943	3.321111	ACTTCCGTATCAGCCGTATGAAT	59.679	43.478	0.00	0.00	31.76	2.57
879	998	2.499827	GCGCTCGAGGGGGAAGTAT	61.500	63.158	28.26	0.00	0.00	2.12
1067	1186	1.412343	TGCCTTTTGCTTGGAGGTTTC	59.588	47.619	0.00	0.00	42.00	2.78
1169	1288	0.253044	GGCTGGGATGTTACTGAGCA	59.747	55.000	0.00	0.00	0.00	4.26
1182	1301	6.175471	TGTTACTGAGCATGATGAAGTTGAT	58.825	36.000	0.00	0.00	0.00	2.57
1375	1494	2.158449	AGCAAAAGCGTCAATCTCTTCG	59.842	45.455	0.00	0.00	0.00	3.79
1536	1655	2.373169	TGACAGCCAAGAAGAGGACAAT	59.627	45.455	0.00	0.00	0.00	2.71
1785	3177	9.797642	TGTCTATGTTTGCCAGATCATATTATT	57.202	29.630	0.00	0.00	0.00	1.40
1903	3765	8.773645	TCATTAGTGAACATTTATATTCGGCAG	58.226	33.333	0.00	0.00	0.00	4.85
1904	3766	7.490962	TTAGTGAACATTTATATTCGGCAGG	57.509	36.000	0.00	0.00	0.00	4.85
1906	3768	4.819630	GTGAACATTTATATTCGGCAGGGA	59.180	41.667	0.00	0.00	0.00	4.20
1907	3769	5.473504	GTGAACATTTATATTCGGCAGGGAT	59.526	40.000	0.00	0.00	0.00	3.85
1909	3771	4.589908	ACATTTATATTCGGCAGGGATCC	58.410	43.478	1.92	1.92	0.00	3.36
1910	3772	4.042809	ACATTTATATTCGGCAGGGATCCA	59.957	41.667	15.23	0.00	0.00	3.41
1916	3792	3.374042	TTCGGCAGGGATCCAAATAAA	57.626	42.857	15.23	0.00	0.00	1.40
2158	4050	4.701171	TGACTTCAACAAAACCCTAAACGT	59.299	37.500	0.00	0.00	0.00	3.99
2208	4100	5.119125	GCAATCAGGCAATGTTGTTAGAAAC	59.881	40.000	0.00	0.00	0.00	2.78
2364	4664	6.942005	TCTGATTTCCTTAGCTTTGTGATCAA	59.058	34.615	0.00	0.00	0.00	2.57
2436	4737	9.243105	CATCATAATATCCCCGGACTAATTTTT	57.757	33.333	0.73	0.00	0.00	1.94
2437	4738	8.857694	TCATAATATCCCCGGACTAATTTTTC	57.142	34.615	0.73	0.00	0.00	2.29
2465	4766	0.843984	TCCTGGCCCACTATTTAGGC	59.156	55.000	0.00	0.00	46.37	3.93
2470	4771	0.756903	GCCCACTATTTAGGCTCCGA	59.243	55.000	0.00	0.00	43.62	4.55
2549	4851	8.583765	GTCAATATTTCCAAGCGTTGTAAAATC	58.416	33.333	0.00	0.00	31.11	2.17
2647	4949	7.375106	ACAATGAGTCAATGAAGAATCTGAC	57.625	36.000	15.15	0.00	38.77	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
135	136	2.612212	GCAACACATATACCTGGAACCG	59.388	50.000	0.00	0.00	0.00	4.44
348	352	4.382541	GGCCCCCACCCTGGAAAG	62.383	72.222	0.00	0.00	40.96	2.62
364	369	3.735237	ACGTATTGTAGAGCAGGATGG	57.265	47.619	0.00	0.00	35.86	3.51
367	372	2.496070	AGCAACGTATTGTAGAGCAGGA	59.504	45.455	0.00	0.00	38.17	3.86
677	742	1.078528	ACCATCCTCACCTCCGTCA	59.921	57.895	0.00	0.00	0.00	4.35
678	743	0.970937	TCACCATCCTCACCTCCGTC	60.971	60.000	0.00	0.00	0.00	4.79
679	744	1.078528	TCACCATCCTCACCTCCGT	59.921	57.895	0.00	0.00	0.00	4.69
680	745	1.517832	GTCACCATCCTCACCTCCG	59.482	63.158	0.00	0.00	0.00	4.63
681	746	1.517832	CGTCACCATCCTCACCTCC	59.482	63.158	0.00	0.00	0.00	4.30
682	747	0.970937	TCCGTCACCATCCTCACCTC	60.971	60.000	0.00	0.00	0.00	3.85
683	748	0.972983	CTCCGTCACCATCCTCACCT	60.973	60.000	0.00	0.00	0.00	4.00
684	749	1.517832	CTCCGTCACCATCCTCACC	59.482	63.158	0.00	0.00	0.00	4.02
685	750	1.258445	ACCTCCGTCACCATCCTCAC	61.258	60.000	0.00	0.00	0.00	3.51
686	751	1.078528	ACCTCCGTCACCATCCTCA	59.921	57.895	0.00	0.00	0.00	3.86
687	752	0.970937	TCACCTCCGTCACCATCCTC	60.971	60.000	0.00	0.00	0.00	3.71
688	753	0.972983	CTCACCTCCGTCACCATCCT	60.973	60.000	0.00	0.00	0.00	3.24
689	754	1.517832	CTCACCTCCGTCACCATCC	59.482	63.158	0.00	0.00	0.00	3.51
690	755	0.970937	TCCTCACCTCCGTCACCATC	60.971	60.000	0.00	0.00	0.00	3.51
691	756	0.325671	ATCCTCACCTCCGTCACCAT	60.326	55.000	0.00	0.00	0.00	3.55
692	757	1.078528	ATCCTCACCTCCGTCACCA	59.921	57.895	0.00	0.00	0.00	4.17
693	758	0.970937	TCATCCTCACCTCCGTCACC	60.971	60.000	0.00	0.00	0.00	4.02
694	759	1.115467	ATCATCCTCACCTCCGTCAC	58.885	55.000	0.00	0.00	0.00	3.67
879	998	6.179906	ACGGTAGCTAGTGTATACCTCTTA	57.820	41.667	0.00	0.00	37.42	2.10
1067	1186	2.618709	GTGAAAACCAGGTCTTCTGTGG	59.381	50.000	7.20	0.00	41.83	4.17
1169	1288	7.457024	TGTGTGAATTCATCAACTTCATCAT	57.543	32.000	12.12	0.00	40.50	2.45
1182	1301	6.513806	CCATAGATGGTTTGTGTGAATTCA	57.486	37.500	3.38	3.38	43.05	2.57
1375	1494	1.197036	GCTACTGCCTCGTTCAAAACC	59.803	52.381	0.00	0.00	0.00	3.27
1536	1655	8.846943	TGCAGTCTAGACAGAATTTCAAATTA	57.153	30.769	24.44	0.00	30.85	1.40
1903	3765	4.751767	TGCAATGGTTTATTTGGATCCC	57.248	40.909	9.90	0.00	0.00	3.85
1904	3766	8.729805	TTAATTGCAATGGTTTATTTGGATCC	57.270	30.769	13.82	4.20	0.00	3.36
1916	3792	8.313292	TGCTTCTCTAAAATTAATTGCAATGGT	58.687	29.630	13.82	0.05	0.00	3.55
2122	3999	7.593875	TTGTTGAAGTCAAAATTTGTCAAGG	57.406	32.000	9.53	0.00	37.63	3.61
2141	4018	4.989044	ACTTCACGTTTAGGGTTTTGTTG	58.011	39.130	0.00	0.00	0.00	3.33
2208	4100	1.574428	GTGCACTTAGCCAACACCG	59.426	57.895	10.32	0.00	44.83	4.94
2364	4664	0.466124	GCTATCCAGCGAGGGAAAGT	59.534	55.000	0.00	0.00	41.12	2.66
2465	4766	9.751542	ATATTGAAAGATAACTGTTACTCGGAG	57.248	33.333	2.83	2.83	0.00	4.63
2549	4851	8.807948	TTTTCTTCTTGATACAATAAGGAGGG	57.192	34.615	0.00	0.00	31.68	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.