AutoCloner

Multiple sequence alignment - TraesCS4D01G259400

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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	TraesCS4D01G259400	chr4D	100.000	2767	0	0	1	2767	428939788	428937022	0.000000e+00	5110.0
1	TraesCS4D01G259400	chr1D	97.092	1513	42	2	432	1944	229965695	229964185	0.000000e+00	2549.0
2	TraesCS4D01G259400	chr1D	97.255	838	17	2	1930	2767	229962913	229962082	0.000000e+00	1415.0
3	TraesCS4D01G259400	chr1D	97.203	429	12	0	1	429	229966346	229965918	0.000000e+00	726.0
4	TraesCS4D01G259400	chr1D	77.124	153	31	4	878	1028	295858260	295858110	4.910000e-13	86.1
5	TraesCS4D01G259400	chr3B	75.603	1119	235	31	775	1872	190889209	190888108	1.140000e-143	520.0
6	TraesCS4D01G259400	chr3B	73.590	780	188	15	1109	1875	43898340	43897566	1.620000e-72	283.0
7	TraesCS4D01G259400	chr3B	73.205	780	191	15	1109	1875	44004728	44003954	1.630000e-67	267.0
8	TraesCS4D01G259400	chr3B	77.605	451	77	20	748	1183	42491127	42491568	4.570000e-63	252.0
9	TraesCS4D01G259400	chr3B	78.395	162	32	3	587	746	745712850	745713010	4.880000e-18	102.0
10	TraesCS4D01G259400	chr5D	75.625	1120	232	34	775	1872	60243401	60242301	4.090000e-143	518.0
11	TraesCS4D01G259400	chr6D	76.650	818	145	24	748	1531	58453608	58452803	7.130000e-111	411.0
12	TraesCS4D01G259400	chr6D	92.437	238	15	2	1	235	3440623	3440860	1.230000e-88	337.0
13	TraesCS4D01G259400	chr6D	79.142	513	87	11	1381	1882	162276056	162276559	1.230000e-88	337.0
14	TraesCS4D01G259400	chr6D	79.775	178	32	4	577	752	58454092	58453917	2.890000e-25	126.0
15	TraesCS4D01G259400	chr7D	98.387	186	3	0	2582	2767	514760532	514760717	7.390000e-86	327.0
16	TraesCS4D01G259400	chr7D	76.389	144	29	4	506	645	123888368	123888510	3.820000e-09	73.1
17	TraesCS4D01G259400	chr7A	73.773	774	184	16	1109	1869	35365557	35366324	1.250000e-73	287.0
18	TraesCS4D01G259400	chr4A	73.590	780	188	15	1109	1875	689632957	689633731	1.620000e-72	283.0
19	TraesCS4D01G259400	chr3D	82.781	151	26	0	602	752	267605897	267606047	4.810000e-28	135.0
20	TraesCS4D01G259400	chr3D	75.000	228	53	3	521	746	393059915	393060140	4.880000e-18	102.0
21	TraesCS4D01G259400	chr6B	76.395	233	53	2	515	746	643631661	643631892	1.040000e-24	124.0
22	TraesCS4D01G259400	chr5B	74.597	248	59	3	506	750	44053729	44053975	3.770000e-19	106.0
23	TraesCS4D01G259400	chr2B	77.596	183	35	6	1764	1944	789863793	789863971	3.770000e-19	106.0
24	TraesCS4D01G259400	chr2B	96.226	53	1	1	1818	1870	706189829	706189778	4.910000e-13	86.1
25	TraesCS4D01G259400	chr1A	96.226	53	1	1	1818	1870	590713149	590713098	4.910000e-13	86.1
26	TraesCS4D01G259400	chr4B	73.729	236	50	10	521	750	4941344	4941115	6.350000e-12	82.4

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	TraesCS4D01G259400	chr4D	428937022	428939788	2766	True	5110.000000	5110	100.000000	1	2767	1	chr4D.!!$R1	2766
1	TraesCS4D01G259400	chr1D	229962082	229966346	4264	True	1563.333333	2549	97.183333	1	2767	3	chr1D.!!$R2	2766
2	TraesCS4D01G259400	chr3B	190888108	190889209	1101	True	520.000000	520	75.603000	775	1872	1	chr3B.!!$R3	1097
3	TraesCS4D01G259400	chr3B	43897566	43898340	774	True	283.000000	283	73.590000	1109	1875	1	chr3B.!!$R1	766
4	TraesCS4D01G259400	chr3B	44003954	44004728	774	True	267.000000	267	73.205000	1109	1875	1	chr3B.!!$R2	766
5	TraesCS4D01G259400	chr5D	60242301	60243401	1100	True	518.000000	518	75.625000	775	1872	1	chr5D.!!$R1	1097
6	TraesCS4D01G259400	chr6D	162276056	162276559	503	False	337.000000	337	79.142000	1381	1882	1	chr6D.!!$F2	501
7	TraesCS4D01G259400	chr6D	58452803	58454092	1289	True	268.500000	411	78.212500	577	1531	2	chr6D.!!$R1	954
8	TraesCS4D01G259400	chr7A	35365557	35366324	767	False	287.000000	287	73.773000	1109	1869	1	chr7A.!!$F1	760
9	TraesCS4D01G259400	chr4A	689632957	689633731	774	False	283.000000	283	73.590000	1109	1875	1	chr4A.!!$F1	766

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
37	38	0.036388	GTTGTCCCTGCAGATTCCGA	60.036	55.000	17.39	0.0	0.0	4.55	F
348	349	1.444895	CGGCAGCTGAACCATTTGC	60.445	57.895	20.43	0.0	0.0	3.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1690	2298	0.397114	TCCTGCATCTCCCGAGCTTA	60.397	55.0	0.0	0.0	0.0	3.09	R
2211	4111	0.763035	CTACCCCATCCTTTACCCCG	59.237	60.0	0.0	0.0	0.0	5.73	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
37	38	0.036388	GTTGTCCCTGCAGATTCCGA	60.036	55.000	17.39	0.00	0.00	4.55
46	47	2.617308	CTGCAGATTCCGATGCTGATTT	59.383	45.455	8.42	0.00	42.11	2.17
52	53	5.685954	CAGATTCCGATGCTGATTTTGATTG	59.314	40.000	0.00	0.00	0.00	2.67
147	148	2.946329	ACGAGGTCTGCATAGTCTACTG	59.054	50.000	0.00	0.00	0.00	2.74
206	207	8.460831	AAAGGTATGAAAAATGTAAATCACGC	57.539	30.769	0.00	0.00	0.00	5.34
335	336	5.283717	CAGTTTCGTAAATGAATTTCGGCAG	59.716	40.000	0.00	0.00	31.18	4.85
348	349	1.444895	CGGCAGCTGAACCATTTGC	60.445	57.895	20.43	0.00	0.00	3.68
422	423	7.282332	TGGTGATTTCATTACATTCAACACA	57.718	32.000	0.00	0.00	29.51	3.72
438	659	5.294356	TCAACACAACTTACTGCGTCTAAT	58.706	37.500	0.00	0.00	0.00	1.73
1079	1616	6.601332	AGAATAACTGTGGTTCTTGGAGAAA	58.399	36.000	3.03	0.00	35.75	2.52
1136	1725	7.382759	GTCATGGAAATACTTTATCTCGAGGAC	59.617	40.741	13.56	1.82	0.00	3.85
1165	1762	5.804979	GTGCAAAGCATATATTGAAACGGTT	59.195	36.000	0.00	0.00	41.91	4.44
1192	1789	2.279502	GACGCGAGGGACATACTGCA	62.280	60.000	15.93	0.00	0.00	4.41
1316	1913	2.641559	GCGAGTGCAGCAGCTTTT	59.358	55.556	1.76	0.00	42.74	2.27
1534	2133	5.373222	TGGTTTGCATTGTCTAACAGTACT	58.627	37.500	0.00	0.00	0.00	2.73
1570	2169	3.558033	GGGTTGGAAGACCTACAAACAA	58.442	45.455	0.00	0.00	42.16	2.83
1574	2173	4.497291	TGGAAGACCTACAAACAACAGT	57.503	40.909	0.00	0.00	37.04	3.55
1689	2297	1.970640	GAATGCCCCAAAGAAACCACT	59.029	47.619	0.00	0.00	0.00	4.00
1690	2298	2.101640	ATGCCCCAAAGAAACCACTT	57.898	45.000	0.00	0.00	0.00	3.16
1895	2509	2.565834	ACGGAGTGGTAATTGCTGTAGT	59.434	45.455	0.00	0.00	42.51	2.73
2012	3912	5.507985	GGCATTTTATCTGAATCTTTCCCCG	60.508	44.000	0.00	0.00	0.00	5.73
2017	3917	2.266279	TCTGAATCTTTCCCCGGTCTT	58.734	47.619	0.00	0.00	0.00	3.01
2208	4108	3.446570	GTCAGGTGGCATGCTGGC	61.447	66.667	18.92	5.48	44.03	4.85
2254	4154	2.143925	GTATAAGAATGGGCGTCTGGC	58.856	52.381	0.00	0.00	42.51	4.85
2279	4179	1.227527	CTTGGTGCGTCTCCACACA	60.228	57.895	0.00	0.00	38.57	3.72
2296	4196	4.034048	CCACACACAATACCGAGCTATTTC	59.966	45.833	0.00	0.00	0.00	2.17
2297	4197	4.629634	CACACACAATACCGAGCTATTTCA	59.370	41.667	0.00	0.00	0.00	2.69
2298	4198	5.121611	CACACACAATACCGAGCTATTTCAA	59.878	40.000	0.00	0.00	0.00	2.69
2299	4199	5.703592	ACACACAATACCGAGCTATTTCAAA	59.296	36.000	0.00	0.00	0.00	2.69
2300	4200	6.205853	ACACACAATACCGAGCTATTTCAAAA	59.794	34.615	0.00	0.00	0.00	2.44
2301	4201	7.081349	CACACAATACCGAGCTATTTCAAAAA	58.919	34.615	0.00	0.00	0.00	1.94
2355	4255	1.879380	CGCCTTCATCTGTTGAAACCA	59.121	47.619	3.07	0.00	43.64	3.67
2439	4339	0.462759	AAGGATAGCTGCGGTTCTGC	60.463	55.000	0.00	0.00	39.61	4.26
2594	4494	4.072131	GCAGTGGACAAGGTAAATCAAGA	58.928	43.478	0.00	0.00	0.00	3.02
2617	4517	3.407967	TTCGGGGGAGGGATGTGC	61.408	66.667	0.00	0.00	0.00	4.57
2652	4552	1.526887	CTGGTAGATGCATTTACGGCG	59.473	52.381	18.22	4.80	0.00	6.46
2679	4579	1.852067	CTGGTGGCCGTTTGTACAGC	61.852	60.000	0.00	0.00	0.00	4.40
2686	4586	0.599204	CCGTTTGTACAGCTGTCGGT	60.599	55.000	27.15	7.66	33.20	4.69
2688	4588	0.234884	GTTTGTACAGCTGTCGGTGC	59.765	55.000	25.56	8.72	42.26	5.01
2762	4662	2.661537	CGGACGCACAGTGCTTCA	60.662	61.111	27.91	0.00	42.61	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	3.884774	AACAACCCCTGCTCCGCA	61.885	61.111	0.00	0.00	36.92	5.69
19	20	0.911769	ATCGGAATCTGCAGGGACAA	59.088	50.000	15.13	0.00	0.00	3.18
37	38	4.142093	GCTACCCACAATCAAAATCAGCAT	60.142	41.667	0.00	0.00	0.00	3.79
46	47	3.010027	TCCAATCTGCTACCCACAATCAA	59.990	43.478	0.00	0.00	0.00	2.57
52	53	2.364324	TCGTATCCAATCTGCTACCCAC	59.636	50.000	0.00	0.00	0.00	4.61
147	148	0.107459	GCCTGGGGATTGACTCTGTC	60.107	60.000	0.00	0.00	0.00	3.51
206	207	6.566427	CAGAAATTAGAAAATCATACGACGCG	59.434	38.462	3.53	3.53	0.00	6.01
335	336	3.372822	CCAATTGATGCAAATGGTTCAGC	59.627	43.478	7.12	0.00	38.99	4.26
389	390	6.851609	TGTAATGAAATCACCAAAGAATCCG	58.148	36.000	0.00	0.00	0.00	4.18
429	430	1.197492	CACAAGCAGCAATTAGACGCA	59.803	47.619	0.00	0.00	0.00	5.24
438	659	1.401552	GTCTGTCAACACAAGCAGCAA	59.598	47.619	0.00	0.00	29.82	3.91
535	756	4.576463	TGTCTCCTTTGCTTTCTTCAAGAC	59.424	41.667	0.00	0.00	33.80	3.01
540	761	5.940470	TCCTAATGTCTCCTTTGCTTTCTTC	59.060	40.000	0.00	0.00	0.00	2.87
543	764	5.123027	CAGTCCTAATGTCTCCTTTGCTTTC	59.877	44.000	0.00	0.00	0.00	2.62
755	1289	1.266718	TGTTGCTCTGTCGCCAAATTC	59.733	47.619	0.00	0.00	0.00	2.17
1062	1598	4.399303	AGTTGTTTTCTCCAAGAACCACAG	59.601	41.667	0.00	0.00	33.26	3.66
1125	1714	2.567985	TGCACGTATGTCCTCGAGATA	58.432	47.619	15.71	0.58	0.00	1.98
1136	1725	7.149303	CGTTTCAATATATGCTTTGCACGTATG	60.149	37.037	0.00	0.00	43.04	2.39
1165	1762	2.204461	TCCCTCGCGTCCTTTGTCA	61.204	57.895	5.77	0.00	0.00	3.58
1316	1913	0.739462	GACCGGCGAACACATGATCA	60.739	55.000	9.30	0.00	0.00	2.92
1570	2169	2.273179	TACGGCGCCTTCTCACTGT	61.273	57.895	26.68	14.68	0.00	3.55
1574	2173	1.080093	CTTGTACGGCGCCTTCTCA	60.080	57.895	26.68	15.23	0.00	3.27
1670	2278	2.101640	AGTGGTTTCTTTGGGGCATT	57.898	45.000	0.00	0.00	0.00	3.56
1678	2286	3.146847	CCCGAGCTTAAGTGGTTTCTTT	58.853	45.455	4.02	0.00	0.00	2.52
1689	2297	0.465705	CCTGCATCTCCCGAGCTTAA	59.534	55.000	0.00	0.00	0.00	1.85
1690	2298	0.397114	TCCTGCATCTCCCGAGCTTA	60.397	55.000	0.00	0.00	0.00	3.09
2012	3912	1.046204	CAGTATACCGGGGGAAGACC	58.954	60.000	6.32	0.00	39.11	3.85
2017	3917	2.820485	GCTGTATCAGTATACCGGGGGA	60.820	54.545	6.32	0.00	37.72	4.81
2208	4108	2.203153	CCATCCTTTACCCCGGCG	60.203	66.667	0.00	0.00	0.00	6.46
2211	4111	0.763035	CTACCCCATCCTTTACCCCG	59.237	60.000	0.00	0.00	0.00	5.73
2307	4207	4.263727	TGCTACTCCCCTTTGCTTCAAATA	60.264	41.667	0.00	0.00	32.70	1.40
2309	4209	2.158534	TGCTACTCCCCTTTGCTTCAAA	60.159	45.455	0.00	0.00	0.00	2.69
2342	4242	5.443185	CACTCATTGTGGTTTCAACAGAT	57.557	39.130	0.00	0.00	42.68	2.90
2355	4255	0.183492	ACTGTGGTGCCACTCATTGT	59.817	50.000	20.46	9.73	46.30	2.71
2439	4339	2.166050	TGAATCATTGGCAATTGGACGG	59.834	45.455	10.65	0.00	0.00	4.79
2579	4479	5.236478	CGAACACACTCTTGATTTACCTTGT	59.764	40.000	0.00	0.00	0.00	3.16
2594	4494	2.765705	ATCCCTCCCCCGAACACACT	62.766	60.000	0.00	0.00	0.00	3.55
2617	4517	5.344743	TCTACCAGCTCTTGATTTACCAG	57.655	43.478	0.00	0.00	0.00	4.00
2652	4552	4.489771	CGGCCACCAGACATCCCC	62.490	72.222	2.24	0.00	0.00	4.81
2679	4579	2.202623	GCCGTCTAGCACCGACAG	60.203	66.667	0.00	0.00	0.00	3.51
2686	4586	2.351244	CCACCTGAGCCGTCTAGCA	61.351	63.158	0.00	0.00	34.23	3.49
2688	4588	3.082579	GCCCACCTGAGCCGTCTAG	62.083	68.421	0.00	0.00	0.00	2.43

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.