AutoCloner

Multiple sequence alignment - TraesCS3A01G236400

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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	TraesCS3A01G236400	chr3A	100.000	3491	0	0	1	3491	441843228	441846718	0.000000e+00	6447.0
1	TraesCS3A01G236400	chr3A	94.633	354	17	2	2753	3105	646265711	646266063	6.590000e-152	547.0
2	TraesCS3A01G236400	chr3A	87.931	58	5	1	1	56	710956992	710957049	2.250000e-07	67.6
3	TraesCS3A01G236400	chr3D	96.248	2052	49	8	716	2755	327723332	327725367	0.000000e+00	3338.0
4	TraesCS3A01G236400	chr3D	89.398	415	27	15	1	406	327721512	327721918	1.120000e-139	507.0
5	TraesCS3A01G236400	chr3D	89.137	313	24	4	419	730	327723013	327723316	7.070000e-102	381.0
6	TraesCS3A01G236400	chr3D	77.528	178	23	16	1	164	427485669	427485843	1.330000e-14	91.6
7	TraesCS3A01G236400	chr3B	95.755	1979	59	9	712	2678	422007032	422005067	0.000000e+00	3166.0
8	TraesCS3A01G236400	chr3B	87.500	64	5	2	7	67	361843211	361843148	1.740000e-08	71.3
9	TraesCS3A01G236400	chr3B	88.462	52	4	2	19	68	800691715	800691766	1.050000e-05	62.1
10	TraesCS3A01G236400	chr5D	93.927	708	32	6	2791	3491	304361322	304360619	0.000000e+00	1059.0
11	TraesCS3A01G236400	chr5D	94.349	407	19	3	3087	3491	365119038	365119442	3.830000e-174	621.0
12	TraesCS3A01G236400	chr5D	79.310	116	17	6	1	115	351945926	351945817	1.340000e-09	75.0
13	TraesCS3A01G236400	chr6A	90.470	745	59	7	2752	3491	428261519	428262256	0.000000e+00	972.0
14	TraesCS3A01G236400	chr7D	94.828	406	18	3	3087	3491	75161448	75161045	6.360000e-177	630.0
15	TraesCS3A01G236400	chr7D	94.581	406	17	3	3087	3491	37281292	37280891	1.060000e-174	623.0
16	TraesCS3A01G236400	chr7D	94.915	354	14	2	2754	3103	37281689	37281336	5.090000e-153	551.0
17	TraesCS3A01G236400	chr7D	94.915	354	15	1	2753	3103	602283499	602283146	5.090000e-153	551.0
18	TraesCS3A01G236400	chr7D	94.633	354	16	1	2753	3103	75161845	75161492	2.370000e-151	545.0
19	TraesCS3A01G236400	chr6D	94.828	406	16	3	3087	3491	147105075	147105476	2.290000e-176	628.0
20	TraesCS3A01G236400	chr1D	94.581	406	18	3	3087	3491	471282302	471281900	2.960000e-175	625.0
21	TraesCS3A01G236400	chr1D	94.335	406	19	3	3087	3491	189395184	189394782	1.380000e-173	619.0
22	TraesCS3A01G236400	chr1D	94.366	355	16	2	2752	3103	61780563	61780916	3.070000e-150	542.0
23	TraesCS3A01G236400	chr1D	94.444	54	2	1	16	68	486246173	486246120	8.030000e-12	82.4
24	TraesCS3A01G236400	chr2D	94.581	406	17	3	3087	3491	370188171	370188572	1.060000e-174	623.0
25	TraesCS3A01G236400	chr2D	94.633	354	16	1	2753	3103	370187772	370188125	2.370000e-151	545.0
26	TraesCS3A01G236400	chr7A	95.265	359	13	2	2749	3103	168464016	168463658	1.820000e-157	566.0
27	TraesCS3A01G236400	chr5B	88.136	59	6	1	1	59	417012027	417012084	6.250000e-08	69.4
28	TraesCS3A01G236400	chr6B	91.667	48	3	1	22	68	544094766	544094719	8.090000e-07	65.8
29	TraesCS3A01G236400	chr2A	84.286	70	8	3	1	67	29740295	29740226	8.090000e-07	65.8

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	TraesCS3A01G236400	chr3A	441843228	441846718	3490	False	6447.000000	6447	100.000000	1	3491	1	chr3A.!!$F1	3490
1	TraesCS3A01G236400	chr3D	327721512	327725367	3855	False	1408.666667	3338	91.594333	1	2755	3	chr3D.!!$F2	2754
2	TraesCS3A01G236400	chr3B	422005067	422007032	1965	True	3166.000000	3166	95.755000	712	2678	1	chr3B.!!$R2	1966
3	TraesCS3A01G236400	chr5D	304360619	304361322	703	True	1059.000000	1059	93.927000	2791	3491	1	chr5D.!!$R1	700
4	TraesCS3A01G236400	chr6A	428261519	428262256	737	False	972.000000	972	90.470000	2752	3491	1	chr6A.!!$F1	739
5	TraesCS3A01G236400	chr7D	75161045	75161845	800	True	587.500000	630	94.730500	2753	3491	2	chr7D.!!$R3	738
6	TraesCS3A01G236400	chr7D	37280891	37281689	798	True	587.000000	623	94.748000	2754	3491	2	chr7D.!!$R2	737
7	TraesCS3A01G236400	chr2D	370187772	370188572	800	False	584.000000	623	94.607000	2753	3491	2	chr2D.!!$F1	738

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
877	2012	0.252284	TCCACTCTCCCTCCTTCCAC	60.252	60.0	0.00	0.0	0.0	4.02	F
1005	2150	0.248843	TAGTGCATGACGTGATGGCA	59.751	50.0	16.87	11.8	0.0	4.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2313	3458	2.752238	ACCGCCTCCAGACTCTCG	60.752	66.667	0.0	0.0	0.0	4.04	R
2567	3715	5.532779	GGAAGCAGGAGAGAGAAAAAGAAAA	59.467	40.000	0.0	0.0	0.0	2.29	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
305	313	6.632171	AAGAAAAGAAAACGCAGAAAACAG	57.368	33.333	0.00	0.00	0.00	3.16
312	320	5.347635	AGAAAACGCAGAAAACAGGAAAAAC	59.652	36.000	0.00	0.00	0.00	2.43
313	321	3.159353	ACGCAGAAAACAGGAAAAACC	57.841	42.857	0.00	0.00	39.35	3.27
323	332	3.628008	ACAGGAAAAACCGGAGAAAACT	58.372	40.909	9.46	0.00	44.74	2.66
332	341	4.417426	ACCGGAGAAAACTGAGAAGAAA	57.583	40.909	9.46	0.00	0.00	2.52
333	342	4.127907	ACCGGAGAAAACTGAGAAGAAAC	58.872	43.478	9.46	0.00	0.00	2.78
338	347	7.027161	CGGAGAAAACTGAGAAGAAACAAAAA	58.973	34.615	0.00	0.00	0.00	1.94
423	432	6.684609	AGAAACGTGTGAAGAAACAAAAAC	57.315	33.333	0.00	0.00	0.00	2.43
437	1540	8.887036	AGAAACAAAAACAAAAACAGAGAAGT	57.113	26.923	0.00	0.00	0.00	3.01
462	1565	1.936880	CTAGCAGCGAACGAGCGAG	60.937	63.158	5.91	3.50	43.00	5.03
519	1623	0.971447	GGCGGGACAGAAGGTACTCT	60.971	60.000	0.00	0.00	38.49	3.24
520	1624	0.456628	GCGGGACAGAAGGTACTCTC	59.543	60.000	0.00	0.00	38.49	3.20
527	1631	4.453136	GGACAGAAGGTACTCTCGCTATAG	59.547	50.000	0.00	0.00	38.49	1.31
540	1644	2.126914	GCTATAGGCGAGATATGGCG	57.873	55.000	1.04	0.00	36.92	5.69
541	1645	1.269309	GCTATAGGCGAGATATGGCGG	60.269	57.143	1.04	0.00	36.92	6.13
545	1649	2.340078	GCGAGATATGGCGGCAGA	59.660	61.111	19.29	14.58	0.00	4.26
548	1652	1.287730	CGAGATATGGCGGCAGAAGC	61.288	60.000	19.29	11.09	41.10	3.86
574	1678	1.202463	CCTCGCTCGATTCCAGTGATT	60.202	52.381	0.00	0.00	30.07	2.57
581	1685	1.190984	CGATTCCAGTGATTCGCATCG	59.809	52.381	0.00	2.12	37.50	3.84
604	1708	1.335324	CGGATCGGGATACGTTGGTAC	60.335	57.143	5.13	0.00	44.69	3.34
652	1756	5.130975	GCCATTTAATTTTTCCTCTCCCCAT	59.869	40.000	0.00	0.00	0.00	4.00
655	1759	7.553760	CCATTTAATTTTTCCTCTCCCCATTTG	59.446	37.037	0.00	0.00	0.00	2.32
660	1764	2.280079	CTCTCCCCATTTGCCCCC	59.720	66.667	0.00	0.00	0.00	5.40
723	1857	9.956640	AAAAATCCTGTGCCATAATTGAAAATA	57.043	25.926	0.00	0.00	0.00	1.40
829	1963	1.971167	GCATGAAGTTCGCACCCCA	60.971	57.895	0.00	0.00	0.00	4.96
853	1988	2.353579	GTCAACACCTTACAACGCACTT	59.646	45.455	0.00	0.00	0.00	3.16
857	1992	2.353579	ACACCTTACAACGCACTTCAAC	59.646	45.455	0.00	0.00	0.00	3.18
877	2012	0.252284	TCCACTCTCCCTCCTTCCAC	60.252	60.000	0.00	0.00	0.00	4.02
880	2015	1.002544	CACTCTCCCTCCTTCCACAAC	59.997	57.143	0.00	0.00	0.00	3.32
881	2016	1.352083	CTCTCCCTCCTTCCACAACA	58.648	55.000	0.00	0.00	0.00	3.33
1005	2150	0.248843	TAGTGCATGACGTGATGGCA	59.751	50.000	16.87	11.80	0.00	4.92
1011	2156	1.298157	ATGACGTGATGGCACCAACG	61.298	55.000	14.56	14.56	42.09	4.10
1095	2240	0.350904	TCCTCTCCCTCCTCCTCCTA	59.649	60.000	0.00	0.00	0.00	2.94
1151	2296	4.479993	CTCCCCGCCCTTCAGCAG	62.480	72.222	0.00	0.00	0.00	4.24
1401	2546	2.741092	GTGTTCACCTCGCCTCCA	59.259	61.111	0.00	0.00	0.00	3.86
1512	2657	1.592223	GTGGAAGCTGTACGAGGCT	59.408	57.895	0.00	0.00	40.85	4.58
1848	2993	0.319083	TGCACGTAATCCTGAACGGT	59.681	50.000	0.00	0.00	43.25	4.83
2313	3458	2.049063	AACGTGGAGTCGCTGCTC	60.049	61.111	0.00	0.00	34.89	4.26
2499	3644	8.286097	CCTTCTGAGTTTGATTAGTTTTCTCAC	58.714	37.037	0.00	0.00	0.00	3.51
2615	3764	4.212847	CACATGAACTGCCAGCTATGATAC	59.787	45.833	0.00	0.00	0.00	2.24
2619	3768	6.233905	TGAACTGCCAGCTATGATACTAAA	57.766	37.500	0.00	0.00	0.00	1.85
2692	3841	5.243730	ACAACTTTATGCTGCTTGTAATGGT	59.756	36.000	0.00	0.00	0.00	3.55
2694	3843	5.713025	ACTTTATGCTGCTTGTAATGGTTG	58.287	37.500	0.00	0.00	0.00	3.77
2699	3848	4.085733	TGCTGCTTGTAATGGTTGGTATT	58.914	39.130	0.00	0.00	0.00	1.89
2703	3852	7.558081	TGCTGCTTGTAATGGTTGGTATTATAA	59.442	33.333	0.00	0.00	0.00	0.98
2704	3853	8.076178	GCTGCTTGTAATGGTTGGTATTATAAG	58.924	37.037	0.00	0.00	39.85	1.73
3124	4340	2.698274	ACGGGCATGTACTGATATCACA	59.302	45.455	0.00	0.00	0.00	3.58
3165	4381	5.127519	CCCCATTTGCATAGAAATCAGTTCA	59.872	40.000	0.00	0.00	38.86	3.18
3258	4475	3.269118	TGAAGGAAATCACCCATCCATCA	59.731	43.478	0.00	0.00	38.30	3.07
3260	4477	4.335735	AGGAAATCACCCATCCATCAAA	57.664	40.909	0.00	0.00	35.62	2.69
3268	4485	5.210430	TCACCCATCCATCAAAATTAGCAT	58.790	37.500	0.00	0.00	0.00	3.79
3269	4486	5.662208	TCACCCATCCATCAAAATTAGCATT	59.338	36.000	0.00	0.00	0.00	3.56
3270	4487	6.156602	TCACCCATCCATCAAAATTAGCATTT	59.843	34.615	0.00	0.00	33.72	2.32
3300	4519	4.040461	GGAATGAGATCTCCGGGTTATGAA	59.960	45.833	20.03	0.00	0.00	2.57
3301	4520	5.454755	GGAATGAGATCTCCGGGTTATGAAA	60.455	44.000	20.03	0.00	0.00	2.69
3372	4591	1.899814	TCTCGCATAAACACCTCCACT	59.100	47.619	0.00	0.00	0.00	4.00
3403	4622	1.080354	CACCACCCCAGACCTCCTA	59.920	63.158	0.00	0.00	0.00	2.94
3441	4660	0.896226	GCCACCTCCTTCTCGTACTT	59.104	55.000	0.00	0.00	0.00	2.24
3447	4666	5.450688	CCACCTCCTTCTCGTACTTCATTAG	60.451	48.000	0.00	0.00	0.00	1.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
26	27	8.183536	TGCACATTTCTCAAATACATGATGTAC	58.816	33.333	7.55	0.00	35.42	2.90
67	68	2.799978	CAGTGCTCAATTGTACACGTGA	59.200	45.455	25.01	2.68	38.08	4.35
68	69	2.799978	TCAGTGCTCAATTGTACACGTG	59.200	45.455	15.48	15.48	38.08	4.49
69	70	3.106242	TCAGTGCTCAATTGTACACGT	57.894	42.857	20.22	11.13	38.08	4.49
70	71	4.466567	TTTCAGTGCTCAATTGTACACG	57.533	40.909	20.22	16.56	38.08	4.49
135	136	9.762933	TCCTTGGTTTTCTTCATTTTCTTTATG	57.237	29.630	0.00	0.00	0.00	1.90
191	193	5.506730	TTTCCCAGGTTTTGTTTTCCTTT	57.493	34.783	0.00	0.00	0.00	3.11
305	313	3.881089	TCTCAGTTTTCTCCGGTTTTTCC	59.119	43.478	0.00	0.00	0.00	3.13
312	320	4.127171	TGTTTCTTCTCAGTTTTCTCCGG	58.873	43.478	0.00	0.00	0.00	5.14
313	321	5.734855	TTGTTTCTTCTCAGTTTTCTCCG	57.265	39.130	0.00	0.00	0.00	4.63
356	365	8.454570	TCTTCGTTTTATTCCAGGTTTTTACT	57.545	30.769	0.00	0.00	0.00	2.24
396	405	5.811399	TGTTTCTTCACACGTTTCTTCAT	57.189	34.783	0.00	0.00	0.00	2.57
397	406	5.614923	TTGTTTCTTCACACGTTTCTTCA	57.385	34.783	0.00	0.00	0.00	3.02
398	407	6.921332	TTTTGTTTCTTCACACGTTTCTTC	57.079	33.333	0.00	0.00	0.00	2.87
399	408	6.697892	TGTTTTTGTTTCTTCACACGTTTCTT	59.302	30.769	0.00	0.00	0.00	2.52
400	409	6.210078	TGTTTTTGTTTCTTCACACGTTTCT	58.790	32.000	0.00	0.00	0.00	2.52
401	410	6.441099	TGTTTTTGTTTCTTCACACGTTTC	57.559	33.333	0.00	0.00	0.00	2.78
402	411	6.830114	TTGTTTTTGTTTCTTCACACGTTT	57.170	29.167	0.00	0.00	0.00	3.60
403	412	6.830114	TTTGTTTTTGTTTCTTCACACGTT	57.170	29.167	0.00	0.00	0.00	3.99
404	413	6.830114	TTTTGTTTTTGTTTCTTCACACGT	57.170	29.167	0.00	0.00	0.00	4.49
405	414	7.119997	TGTTTTTGTTTTTGTTTCTTCACACG	58.880	30.769	0.00	0.00	0.00	4.49
406	415	8.331742	TCTGTTTTTGTTTTTGTTTCTTCACAC	58.668	29.630	0.00	0.00	0.00	3.82
407	416	8.425577	TCTGTTTTTGTTTTTGTTTCTTCACA	57.574	26.923	0.00	0.00	0.00	3.58
408	417	8.760569	TCTCTGTTTTTGTTTTTGTTTCTTCAC	58.239	29.630	0.00	0.00	0.00	3.18
409	418	8.879342	TCTCTGTTTTTGTTTTTGTTTCTTCA	57.121	26.923	0.00	0.00	0.00	3.02
423	432	4.848757	AGCGCTTTACTTCTCTGTTTTTG	58.151	39.130	2.64	0.00	0.00	2.44
463	1566	1.722852	CGTTCTAGCGATCGAGGCG	60.723	63.158	21.57	12.28	35.01	5.52
490	1594	2.463752	TCTGTCCCGCCTACAGTATTT	58.536	47.619	9.08	0.00	43.88	1.40
527	1631	2.715532	TTCTGCCGCCATATCTCGCC	62.716	60.000	0.00	0.00	0.00	5.54
548	1652	4.914420	AATCGAGCGAGGCGAGCG	62.914	66.667	0.00	0.00	41.49	5.03
557	1661	0.848942	CGAATCACTGGAATCGAGCG	59.151	55.000	0.00	0.00	46.79	5.03
574	1678	3.961197	CCGATCCGTCCGATGCGA	61.961	66.667	0.00	0.00	0.00	5.10
581	1685	0.318445	CAACGTATCCCGATCCGTCC	60.318	60.000	0.00	0.00	40.70	4.79
600	1704	1.340017	TGCCAGATTGCAAGAGGTACC	60.340	52.381	2.73	2.73	38.56	3.34
723	1857	7.508977	TGTGAATTCCCCTAGTTTCAGATTTTT	59.491	33.333	2.27	0.00	0.00	1.94
829	1963	2.946329	TGCGTTGTAAGGTGTTGACATT	59.054	40.909	0.00	0.00	0.00	2.71
853	1988	0.787084	AGGAGGGAGAGTGGAGTTGA	59.213	55.000	0.00	0.00	0.00	3.18
857	1992	0.041833	TGGAAGGAGGGAGAGTGGAG	59.958	60.000	0.00	0.00	0.00	3.86
877	2012	7.912250	GGAAATACAGCAGTTTATGAGATGTTG	59.088	37.037	0.00	0.00	0.00	3.33
880	2015	6.769822	AGGGAAATACAGCAGTTTATGAGATG	59.230	38.462	0.00	0.00	0.00	2.90
881	2016	6.904626	AGGGAAATACAGCAGTTTATGAGAT	58.095	36.000	0.00	0.00	0.00	2.75
1005	2150	2.743718	CTCTGCAGGGACGTTGGT	59.256	61.111	8.28	0.00	0.00	3.67
1011	2156	4.154347	CTCGGCCTCTGCAGGGAC	62.154	72.222	17.43	16.08	40.75	4.46
1170	2315	1.139734	GCTGACGCTCGAGGATGAA	59.860	57.895	15.58	0.00	0.00	2.57
1262	2407	1.811266	GCGATCTTGAGCTTGGCGA	60.811	57.895	0.00	0.00	0.00	5.54
1440	2585	1.352017	TCAAGGAAATGCAGCTGAGGA	59.648	47.619	20.43	0.00	0.00	3.71
1512	2657	1.613317	ATGGATCGTTGTCGCCCTCA	61.613	55.000	0.00	0.00	36.96	3.86
1599	2744	2.358247	ATTCCGTGCCACGACACC	60.358	61.111	20.57	0.00	46.05	4.16
1848	2993	3.858868	GAACTGCGCCTCGTCCACA	62.859	63.158	4.18	0.00	0.00	4.17
1944	3089	3.068691	TTGACGAGCCTCCCGGAG	61.069	66.667	0.73	7.56	0.00	4.63
2112	3257	3.249189	AACGCCCTGAGCTTCCCA	61.249	61.111	0.00	0.00	40.39	4.37
2313	3458	2.752238	ACCGCCTCCAGACTCTCG	60.752	66.667	0.00	0.00	0.00	4.04
2563	3711	7.457561	AGCAGGAGAGAGAAAAAGAAAATACT	58.542	34.615	0.00	0.00	0.00	2.12
2564	3712	7.680442	AGCAGGAGAGAGAAAAAGAAAATAC	57.320	36.000	0.00	0.00	0.00	1.89
2565	3713	7.391833	GGAAGCAGGAGAGAGAAAAAGAAAATA	59.608	37.037	0.00	0.00	0.00	1.40
2566	3714	6.208402	GGAAGCAGGAGAGAGAAAAAGAAAAT	59.792	38.462	0.00	0.00	0.00	1.82
2567	3715	5.532779	GGAAGCAGGAGAGAGAAAAAGAAAA	59.467	40.000	0.00	0.00	0.00	2.29
2679	3828	9.120538	ACTTATAATACCAACCATTACAAGCAG	57.879	33.333	0.00	0.00	29.37	4.24
2762	3911	6.045072	ACTATTCACCAACTCGTCCATTAA	57.955	37.500	0.00	0.00	0.00	1.40
2950	4103	9.581289	TCCTAAGACAAATTGAACCAATAAGAA	57.419	29.630	0.00	0.00	32.43	2.52
3110	4326	9.679661	ATTGTTTGGTAATGTGATATCAGTACA	57.320	29.630	5.42	0.96	39.58	2.90
3124	4340	7.175816	GCAAATGGGGTTTTATTGTTTGGTAAT	59.824	33.333	0.00	0.00	0.00	1.89
3310	4529	4.103153	AGAGGTCACAATTGGAAAGAGTCA	59.897	41.667	10.83	0.00	0.00	3.41
3313	4532	4.006319	GGAGAGGTCACAATTGGAAAGAG	58.994	47.826	10.83	0.00	0.00	2.85
3372	4591	1.752198	GTGGTGTCACCTGGCTGTA	59.248	57.895	22.56	0.00	39.58	2.74
3403	4622	0.900647	CGGAGAAGGTGTGGAGAGGT	60.901	60.000	0.00	0.00	0.00	3.85
3441	4660	0.108585	GGCGGAGGGATTGCTAATGA	59.891	55.000	0.00	0.00	0.00	2.57
3447	4666	1.322538	AAATGTGGCGGAGGGATTGC	61.323	55.000	0.00	0.00	0.00	3.56

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.