AutoCloner

Multiple sequence alignment - TraesCS6D01G108600

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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	TraesCS6D01G108600	chr6D	100.000	3897	0	0	1	3897	73067465	73071361	0.000000e+00	7197
1	TraesCS6D01G108600	chr6D	80.907	419	70	9	1037	1448	192631095	192630680	4.860000e-84	322
2	TraesCS6D01G108600	chr6A	97.057	2786	58	9	366	3146	89592184	89594950	0.000000e+00	4669
3	TraesCS6D01G108600	chr6A	96.970	726	16	3	3169	3889	89595038	89595762	0.000000e+00	1214
4	TraesCS6D01G108600	chr6A	97.771	314	7	0	1	314	89591505	89591818	3.430000e-150	542
5	TraesCS6D01G108600	chr6A	100.000	56	0	0	311	366	89592074	89592129	1.920000e-18	104
6	TraesCS6D01G108600	chr6B	97.243	2539	48	8	366	2901	147581724	147584243	0.000000e+00	4281
7	TraesCS6D01G108600	chr6B	97.807	1049	20	1	2844	3889	147584241	147585289	0.000000e+00	1807
8	TraesCS6D01G108600	chr6B	96.995	366	11	0	1	366	147581304	147581669	1.990000e-172	616
9	TraesCS6D01G108600	chr5A	84.261	521	71	10	1036	1549	55328550	55329066	7.520000e-137	497
10	TraesCS6D01G108600	chr2A	84.261	521	71	10	1036	1549	461726643	461727159	7.520000e-137	497
11	TraesCS6D01G108600	chr7A	84.069	521	72	10	1036	1549	332925892	332926408	3.500000e-135	492
12	TraesCS6D01G108600	chr1B	82.569	436	71	4	1080	1511	511483908	511484342	2.840000e-101	379
13	TraesCS6D01G108600	chr7D	84.663	163	21	4	1435	1595	370399865	370399705	4.030000e-35	159

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	TraesCS6D01G108600	chr6D	73067465	73071361	3896	False	7197.000000	7197	100.000000	1	3897	1	chr6D.!!$F1	3896
1	TraesCS6D01G108600	chr6A	89591505	89595762	4257	False	1632.250000	4669	97.949500	1	3889	4	chr6A.!!$F1	3888
2	TraesCS6D01G108600	chr6B	147581304	147585289	3985	False	2234.666667	4281	97.348333	1	3889	3	chr6B.!!$F1	3888
3	TraesCS6D01G108600	chr5A	55328550	55329066	516	False	497.000000	497	84.261000	1036	1549	1	chr5A.!!$F1	513
4	TraesCS6D01G108600	chr2A	461726643	461727159	516	False	497.000000	497	84.261000	1036	1549	1	chr2A.!!$F1	513
5	TraesCS6D01G108600	chr7A	332925892	332926408	516	False	492.000000	492	84.069000	1036	1549	1	chr7A.!!$F1	513

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
677	994	1.422531	TCAATTTGGCCCTTTGCACT	58.577	45.000	0.0	0.0	43.89	4.40	F
1504	1824	2.173569	AGCAGAAAAGACCAAGGTGAGT	59.826	45.455	0.0	0.0	0.00	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2455	2779	1.135915	CCCCTCGAATCTGAGTGACAG	59.864	57.143	0.0	0.0	46.97	3.51	R
3149	3528	1.136147	CATGCCGCTCAACAGCTTC	59.864	57.895	0.0	0.0	44.40	3.86	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
96	97	5.247110	TCAACTAAGAGAGGTCTGCTTTGAT	59.753	40.000	0.00	0.00	31.37	2.57
126	127	2.338015	CCTTGCCAGCGCATTCAGT	61.338	57.895	11.47	0.00	46.67	3.41
277	278	7.122204	ACAAGGTAAATTTAGGCTACCAATGTC	59.878	37.037	9.25	0.00	38.04	3.06
441	756	6.775629	TGGAAATGAGGCTTGTACTAAGTTTT	59.224	34.615	0.00	0.00	0.00	2.43
600	915	4.605640	AAATTGTTGGTGCTAATGTGCT	57.394	36.364	0.00	0.00	0.00	4.40
605	920	7.587037	ATTGTTGGTGCTAATGTGCTATATT	57.413	32.000	0.00	0.00	0.00	1.28
619	934	8.854614	ATGTGCTATATTAGATTTTGGGAGTC	57.145	34.615	0.00	0.00	0.00	3.36
674	991	3.410508	TGATTTCAATTTGGCCCTTTGC	58.589	40.909	0.00	0.00	40.16	3.68
675	992	3.181447	TGATTTCAATTTGGCCCTTTGCA	60.181	39.130	0.00	0.00	43.89	4.08
676	993	2.252976	TTCAATTTGGCCCTTTGCAC	57.747	45.000	0.00	0.00	43.89	4.57
677	994	1.422531	TCAATTTGGCCCTTTGCACT	58.577	45.000	0.00	0.00	43.89	4.40
857	1174	6.238184	GGTTTTTCAATTGACCAGAAAGCAAG	60.238	38.462	7.89	0.00	33.35	4.01
887	1204	3.503748	GCTGAAGTTATGTCCAACTTGCT	59.496	43.478	6.00	0.00	46.23	3.91
1504	1824	2.173569	AGCAGAAAAGACCAAGGTGAGT	59.826	45.455	0.00	0.00	0.00	3.41
1567	1889	9.840427	TTCTGTTTGATTTCTATTTTTCCGATC	57.160	29.630	0.00	0.00	0.00	3.69
1602	1924	7.837202	AATGATTGTATTCCTGCATTTGTTG	57.163	32.000	0.00	0.00	0.00	3.33
1865	2187	2.608752	GCCTTCAGTCACAATTGCAAGG	60.609	50.000	4.94	8.57	33.40	3.61
1875	2197	3.012518	ACAATTGCAAGGGAGAGATTCG	58.987	45.455	4.94	0.00	0.00	3.34
1970	2292	4.151335	GCAGTACTCATCGCAGATAAATGG	59.849	45.833	0.00	0.00	45.12	3.16
2455	2779	1.246737	AAAGTAAGCCCAGCTGCAGC	61.247	55.000	31.53	31.53	39.62	5.25
2671	2995	3.890705	CACTGACGATGTCGCGCG	61.891	66.667	26.76	26.76	44.43	6.86
2685	3009	1.010462	GCGCGTTGTTCCGAAGTTT	60.010	52.632	8.43	0.00	0.00	2.66
2736	3060	4.160252	GGGATGTGGTAAGTGCAATTTCAT	59.840	41.667	4.05	5.58	0.00	2.57
2741	3065	6.815089	TGTGGTAAGTGCAATTTCATTTCTT	58.185	32.000	4.05	0.00	0.00	2.52
2742	3066	7.946207	TGTGGTAAGTGCAATTTCATTTCTTA	58.054	30.769	4.05	0.00	0.00	2.10
2926	3305	3.569194	TTAAAGGTGAGTGAGCAACCA	57.431	42.857	0.00	0.00	0.00	3.67
2959	3338	4.488879	CTTCACTTAAGCATTTGGCCTTC	58.511	43.478	3.32	0.00	46.50	3.46
2992	3371	0.254747	TTATAGCCTTGCCGCCTTGT	59.745	50.000	0.00	0.00	0.00	3.16
3133	3512	7.426456	CGACACAGAAATATAATTGAGTTGTGC	59.574	37.037	0.00	0.00	37.50	4.57
3149	3528	7.470289	GAGTTGTGCTCACCTTATGTATTAG	57.530	40.000	0.00	0.00	43.58	1.73
3210	3654	4.636206	GGTGGATGGTTTAGTTGAGCTAAG	59.364	45.833	0.00	0.00	40.41	2.18
3488	3936	8.023128	CGTATCATTTTTGTTGTGAATCTTCCT	58.977	33.333	0.00	0.00	0.00	3.36
3884	4336	3.036819	TGAGATTGCTATGTGGAGCTCT	58.963	45.455	14.64	0.00	43.27	4.09
3889	4341	0.105778	GCTATGTGGAGCTCTGGACC	59.894	60.000	14.64	0.00	39.50	4.46
3890	4342	1.786937	CTATGTGGAGCTCTGGACCT	58.213	55.000	14.64	4.19	0.00	3.85
3891	4343	1.686052	CTATGTGGAGCTCTGGACCTC	59.314	57.143	14.64	0.00	0.00	3.85
3892	4344	0.980231	ATGTGGAGCTCTGGACCTCC	60.980	60.000	14.64	5.29	46.25	4.30
3893	4345	1.305718	GTGGAGCTCTGGACCTCCT	60.306	63.158	14.64	0.00	46.23	3.69
3894	4346	1.000993	TGGAGCTCTGGACCTCCTC	59.999	63.158	14.64	0.00	46.23	3.71
3895	4347	1.309688	GGAGCTCTGGACCTCCTCT	59.690	63.158	14.64	0.00	43.42	3.69
3896	4348	1.042559	GGAGCTCTGGACCTCCTCTG	61.043	65.000	14.64	0.00	43.42	3.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
96	97	0.250684	TGGCAAGGCGATGTGAAAGA	60.251	50.000	0.00	0.00	0.00	2.52
126	127	5.957771	AGCTGATAAGGTCCACATCTTTA	57.042	39.130	0.00	0.00	0.00	1.85
250	251	8.110908	ACATTGGTAGCCTAAATTTACCTTGTA	58.889	33.333	8.23	0.00	38.12	2.41
251	252	6.951778	ACATTGGTAGCCTAAATTTACCTTGT	59.048	34.615	8.23	8.63	38.12	3.16
277	278	4.095410	TGAAGCAACAAAACACACTGAG	57.905	40.909	0.00	0.00	0.00	3.35
441	756	8.992073	CGATCATAAAGAAATATGACATGGTGA	58.008	33.333	0.00	0.00	43.17	4.02
605	920	7.617225	TGAAAGAATACGACTCCCAAAATCTA	58.383	34.615	0.00	0.00	0.00	1.98
671	988	7.970061	GAATATGAGTATTCTGCAAAAGTGCAA	59.030	33.333	2.66	0.00	44.91	4.08
672	989	7.475015	GAATATGAGTATTCTGCAAAAGTGCA	58.525	34.615	0.89	0.89	45.24	4.57
673	990	6.914757	GGAATATGAGTATTCTGCAAAAGTGC	59.085	38.462	7.78	0.00	44.62	4.40
674	991	7.988737	TGGAATATGAGTATTCTGCAAAAGTG	58.011	34.615	7.78	0.00	43.68	3.16
675	992	8.579850	TTGGAATATGAGTATTCTGCAAAAGT	57.420	30.769	7.78	0.00	43.68	2.66
677	994	9.806203	CATTTGGAATATGAGTATTCTGCAAAA	57.194	29.630	12.33	0.00	43.68	2.44
857	1174	5.967088	TGGACATAACTTCAGCTAACTCTC	58.033	41.667	0.00	0.00	0.00	3.20
887	1204	7.521423	CGTTATTTTGGGAAGTGAATCTGTTCA	60.521	37.037	0.00	0.00	41.89	3.18
1024	1341	6.091986	CCTTCAATCTCAGAAACTGAACTAGC	59.908	42.308	0.00	0.00	40.18	3.42
1567	1889	9.669353	CAGGAATACAATCATTTATTTCTTCGG	57.331	33.333	0.00	0.00	0.00	4.30
1602	1924	4.865925	TCTGTACAATACACCGCAACATAC	59.134	41.667	0.00	0.00	34.46	2.39
1865	2187	2.500229	ACGAGATCTCCGAATCTCTCC	58.500	52.381	17.13	0.00	46.30	3.71
1875	2197	1.148759	GGCGCAGAAACGAGATCTCC	61.149	60.000	17.13	2.90	34.06	3.71
1970	2292	6.195798	CGCAGTTTCTAACCACTTAACAAAAC	59.804	38.462	0.00	0.00	0.00	2.43
2390	2714	8.571461	AAATATGCAAGTGACTATGGATATGG	57.429	34.615	16.14	0.00	38.94	2.74
2391	2715	9.223099	TGAAATATGCAAGTGACTATGGATATG	57.777	33.333	16.14	0.00	38.94	1.78
2392	2716	9.797642	TTGAAATATGCAAGTGACTATGGATAT	57.202	29.630	12.37	12.37	40.79	1.63
2393	2717	9.797642	ATTGAAATATGCAAGTGACTATGGATA	57.202	29.630	9.82	9.82	34.90	2.59
2394	2718	8.701908	ATTGAAATATGCAAGTGACTATGGAT	57.298	30.769	0.00	6.89	0.00	3.41
2395	2719	8.523915	AATTGAAATATGCAAGTGACTATGGA	57.476	30.769	0.00	0.00	0.00	3.41
2396	2720	9.027129	CAAATTGAAATATGCAAGTGACTATGG	57.973	33.333	0.00	0.00	0.00	2.74
2455	2779	1.135915	CCCCTCGAATCTGAGTGACAG	59.864	57.143	0.00	0.00	46.97	3.51
2565	2889	7.938140	ACCTAAAGTTAGCATGCAAGATTTA	57.062	32.000	21.98	16.79	0.00	1.40
2671	2995	3.183172	GGTCGAGTAAACTTCGGAACAAC	59.817	47.826	0.00	0.00	0.00	3.32
2685	3009	6.590677	CGATTCTGTCTGATATAGGTCGAGTA	59.409	42.308	0.00	0.00	31.50	2.59
2741	3065	9.383519	GAGAACACCTTCAATCAACTCAATATA	57.616	33.333	0.00	0.00	0.00	0.86
2742	3066	7.337942	GGAGAACACCTTCAATCAACTCAATAT	59.662	37.037	0.00	0.00	0.00	1.28
2959	3338	6.324819	CAAGGCTATAACAGTTCAAACATGG	58.675	40.000	0.00	0.00	0.00	3.66
2992	3371	3.367646	TTAACCAAGGTCCACACACAA	57.632	42.857	0.00	0.00	0.00	3.33
3057	3436	8.303876	GTGAAAGGCAATAATGAAGGAAAACTA	58.696	33.333	0.00	0.00	0.00	2.24
3133	3512	7.981789	TCAACAGCTTCTAATACATAAGGTGAG	59.018	37.037	17.41	10.67	46.51	3.51
3149	3528	1.136147	CATGCCGCTCAACAGCTTC	59.864	57.895	0.00	0.00	44.40	3.86
3488	3936	4.074970	GACCAATTCCAGCAGAAGAAAGA	58.925	43.478	0.00	0.00	38.07	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.