AutoCloner

Multiple sequence alignment - TraesCS1A01G342600

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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	TraesCS1A01G342600	chr1A	100.000	5229	0	0	1	5229	531612611	531607383	0.000000e+00	9657.0
1	TraesCS1A01G342600	chr1A	89.583	48	5	0	3813	3860	485031909	485031862	1.570000e-05	62.1
2	TraesCS1A01G342600	chr1D	94.580	5258	200	37	1	5229	433217830	433212629	0.000000e+00	8052.0
3	TraesCS1A01G342600	chr1B	95.984	4631	145	20	624	5229	585077265	585072651	0.000000e+00	7483.0
4	TraesCS1A01G342600	chr1B	85.380	513	43	11	6	496	585078049	585077547	2.170000e-138	503.0
5	TraesCS1A01G342600	chr1B	88.571	140	7	2	3268	3398	217556504	217556643	1.510000e-35	161.0
6	TraesCS1A01G342600	chr2D	87.240	721	81	5	2425	3141	442448970	442448257	0.000000e+00	811.0
7	TraesCS1A01G342600	chr2D	83.333	366	48	6	2776	3141	522888330	522887978	5.050000e-85	326.0
8	TraesCS1A01G342600	chr2D	84.118	340	42	4	2403	2742	522888660	522888333	8.450000e-83	318.0
9	TraesCS1A01G342600	chr2D	83.043	230	38	1	2325	2553	442449191	442448962	1.910000e-49	207.0
10	TraesCS1A01G342600	chr7D	86.497	748	87	8	2425	3165	453305289	453304549	0.000000e+00	809.0
11	TraesCS1A01G342600	chr7D	83.043	230	38	1	2325	2553	453305510	453305281	1.910000e-49	207.0
12	TraesCS1A01G342600	chr3A	74.606	1713	337	77	2444	4096	506229691	506228017	0.000000e+00	664.0
13	TraesCS1A01G342600	chr3A	95.349	43	2	0	3813	3855	96682781	96682739	9.400000e-08	69.4
14	TraesCS1A01G342600	chr3D	71.793	2783	633	118	1400	4096	383113069	383110353	0.000000e+00	651.0
15	TraesCS1A01G342600	chr3D	90.860	372	22	3	3005	3376	594157710	594158069	6.090000e-134	488.0
16	TraesCS1A01G342600	chr3D	75.510	539	95	26	3088	3609	382754290	382753772	4.070000e-56	230.0
17	TraesCS1A01G342600	chr3B	73.386	1657	344	77	2501	4096	498729123	498727503	1.290000e-145	527.0
18	TraesCS1A01G342600	chr3B	71.584	1654	345	91	2500	4096	498368415	498366830	8.390000e-88	335.0
19	TraesCS1A01G342600	chr4A	82.660	421	63	8	1953	2372	435629278	435628867	1.070000e-96	364.0
20	TraesCS1A01G342600	chr4A	95.556	45	2	0	3354	3398	435628870	435628826	7.260000e-09	73.1
21	TraesCS1A01G342600	chr5D	91.765	255	20	1	3129	3383	68892324	68892577	2.320000e-93	353.0
22	TraesCS1A01G342600	chr5D	90.244	123	12	0	3005	3127	68877451	68877573	1.510000e-35	161.0
23	TraesCS1A01G342600	chr5D	93.023	43	3	0	3803	3845	368333267	368333309	4.370000e-06	63.9
24	TraesCS1A01G342600	chr6A	89.046	283	22	5	2090	2372	250073992	250074265	5.010000e-90	342.0
25	TraesCS1A01G342600	chr6A	100.000	34	0	0	3354	3387	250074262	250074295	4.370000e-06	63.9
26	TraesCS1A01G342600	chr2B	94.667	75	3	1	3268	3341	181718937	181719011	1.190000e-21	115.0
27	TraesCS1A01G342600	chr7A	85.135	74	11	0	3774	3847	712180955	712181028	5.620000e-10	76.8
28	TraesCS1A01G342600	chr6D	93.333	45	3	0	3813	3857	425902619	425902575	3.380000e-07	67.6
29	TraesCS1A01G342600	chr5B	93.023	43	3	0	3803	3845	436259157	436259199	4.370000e-06	63.9
30	TraesCS1A01G342600	chr5B	96.875	32	0	1	2605	2635	450610065	450610034	9.000000e-03	52.8
31	TraesCS1A01G342600	chr5A	93.023	43	3	0	3803	3845	470196293	470196335	4.370000e-06	63.9
32	TraesCS1A01G342600	chr5A	96.875	32	0	1	2605	2635	477814724	477814693	9.000000e-03	52.8

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	TraesCS1A01G342600	chr1A	531607383	531612611	5228	True	9657	9657	100.0000	1	5229	1	chr1A.!!$R2	5228
1	TraesCS1A01G342600	chr1D	433212629	433217830	5201	True	8052	8052	94.5800	1	5229	1	chr1D.!!$R1	5228
2	TraesCS1A01G342600	chr1B	585072651	585078049	5398	True	3993	7483	90.6820	6	5229	2	chr1B.!!$R1	5223
3	TraesCS1A01G342600	chr2D	442448257	442449191	934	True	509	811	85.1415	2325	3141	2	chr2D.!!$R1	816
4	TraesCS1A01G342600	chr2D	522887978	522888660	682	True	322	326	83.7255	2403	3141	2	chr2D.!!$R2	738
5	TraesCS1A01G342600	chr7D	453304549	453305510	961	True	508	809	84.7700	2325	3165	2	chr7D.!!$R1	840
6	TraesCS1A01G342600	chr3A	506228017	506229691	1674	True	664	664	74.6060	2444	4096	1	chr3A.!!$R2	1652
7	TraesCS1A01G342600	chr3D	383110353	383113069	2716	True	651	651	71.7930	1400	4096	1	chr3D.!!$R2	2696
8	TraesCS1A01G342600	chr3D	382753772	382754290	518	True	230	230	75.5100	3088	3609	1	chr3D.!!$R1	521
9	TraesCS1A01G342600	chr3B	498727503	498729123	1620	True	527	527	73.3860	2501	4096	1	chr3B.!!$R2	1595
10	TraesCS1A01G342600	chr3B	498366830	498368415	1585	True	335	335	71.5840	2500	4096	1	chr3B.!!$R1	1596

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
544	567	0.179084	TCTAAAATCTCGGCCAGCGG	60.179	55.000	2.24	0.00	0.00	5.52	F
604	627	0.462759	GTGGGGAAAGAGAGGCATCG	60.463	60.000	0.00	0.00	0.00	3.84	F
955	1149	0.591236	CAACCAAACTGAACGCACGG	60.591	55.000	0.00	0.00	0.00	4.94	F
1604	1806	0.601046	CTCAAGCTCGAGCACAACCA	60.601	55.000	36.87	14.52	45.16	3.67	F
1908	2116	1.298859	CCTACAACAAGCTGACCGGC	61.299	60.000	0.00	0.00	0.00	6.13	F
3681	4069	1.522092	CTTCGGCTACATGGCTCCA	59.478	57.895	0.00	0.00	39.32	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1923	2131	0.721718	GCTTCGTCAATGTTCCGAGG	59.278	55.000	0.00	0.00	31.54	4.63	R
2158	2369	1.884464	CGGTGATGATCCACAGCCG	60.884	63.158	11.05	11.54	38.74	5.52	R
2346	2557	3.699894	AGCGTCTCTGGCAGGGTG	61.700	66.667	15.27	9.58	0.00	4.61	R
2988	3340	3.393149	GAGCCCCTTCCGCCTCTTC	62.393	68.421	0.00	0.00	0.00	2.87	R
3767	4163	0.108186	TACCCGCACTCTGCAATCAG	60.108	55.000	0.00	0.00	45.36	2.90	R
4624	5044	3.578688	GCATAAAAGTTTCAGTGGCAGG	58.421	45.455	0.00	0.00	0.00	4.85	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
54	55	4.334203	TGTGCAAACAACTCGATACAAGTT	59.666	37.500	0.00	0.00	37.44	2.66
144	146	3.595173	TGACATTGACTTCACATACCCG	58.405	45.455	0.00	0.00	0.00	5.28
147	149	1.803334	TTGACTTCACATACCCGCAC	58.197	50.000	0.00	0.00	0.00	5.34
209	211	8.349245	AGTCGATTTCACATAAACACAATTCAA	58.651	29.630	0.00	0.00	0.00	2.69
236	238	8.344831	ACATTCACATATGCACATACACATAAC	58.655	33.333	1.58	0.00	32.77	1.89
238	240	8.504812	TTCACATATGCACATACACATAACTT	57.495	30.769	1.58	0.00	32.77	2.66
430	453	2.650116	GGAGAGCTCGGCTGGTGAA	61.650	63.158	8.37	0.00	39.88	3.18
434	457	1.882989	GAGCTCGGCTGGTGAAGAGT	61.883	60.000	0.00	0.00	39.88	3.24
474	497	2.044252	TCGAGGAAGGGGAGGTCG	60.044	66.667	0.00	0.00	0.00	4.79
502	525	4.011966	CATATGTGCATAGGCTCAAGGA	57.988	45.455	8.30	0.00	45.54	3.36
544	567	0.179084	TCTAAAATCTCGGCCAGCGG	60.179	55.000	2.24	0.00	0.00	5.52
564	587	2.707849	GCAGGGCGGTAAGACGAGA	61.708	63.158	0.00	0.00	35.47	4.04
568	591	2.783288	GGCGGTAAGACGAGAGGGG	61.783	68.421	0.00	0.00	35.47	4.79
569	592	2.806237	CGGTAAGACGAGAGGGGC	59.194	66.667	0.00	0.00	35.47	5.80
570	593	2.806237	GGTAAGACGAGAGGGGCG	59.194	66.667	0.00	0.00	0.00	6.13
571	594	2.050934	GGTAAGACGAGAGGGGCGT	61.051	63.158	0.00	0.00	45.79	5.68
575	598	3.878519	GACGAGAGGGGCGTCGAG	61.879	72.222	0.00	0.00	46.85	4.04
577	600	3.132139	CGAGAGGGGCGTCGAGAA	61.132	66.667	0.00	0.00	38.50	2.87
578	601	2.802106	GAGAGGGGCGTCGAGAAG	59.198	66.667	0.00	0.00	0.00	2.85
579	602	2.756283	AGAGGGGCGTCGAGAAGG	60.756	66.667	0.00	0.00	0.00	3.46
580	603	3.839432	GAGGGGCGTCGAGAAGGG	61.839	72.222	0.00	0.00	0.00	3.95
581	604	4.698625	AGGGGCGTCGAGAAGGGT	62.699	66.667	0.00	0.00	0.00	4.34
582	605	4.452733	GGGGCGTCGAGAAGGGTG	62.453	72.222	0.00	0.00	0.00	4.61
601	624	2.231380	GGGTGGGGAAAGAGAGGCA	61.231	63.158	0.00	0.00	0.00	4.75
604	627	0.462759	GTGGGGAAAGAGAGGCATCG	60.463	60.000	0.00	0.00	0.00	3.84
607	630	1.221840	GGAAAGAGAGGCATCGGCA	59.778	57.895	0.00	0.00	43.71	5.69
673	852	3.493350	CCATCTAGAACATGTCCCCTTCG	60.493	52.174	0.00	0.00	0.00	3.79
753	933	7.377662	CACGAATTAAACAACCAAGTAGAAACC	59.622	37.037	0.00	0.00	0.00	3.27
803	983	1.782028	GACAACCCCAACGAGCACAC	61.782	60.000	0.00	0.00	0.00	3.82
851	1043	8.746052	ATTAAAAAGGACAAAAAGAAAAGGGG	57.254	30.769	0.00	0.00	0.00	4.79
866	1059	2.908428	GGGAAAAACACCGGCCGT	60.908	61.111	26.12	9.63	0.00	5.68
955	1149	0.591236	CAACCAAACTGAACGCACGG	60.591	55.000	0.00	0.00	0.00	4.94
956	1150	1.027792	AACCAAACTGAACGCACGGT	61.028	50.000	0.00	0.00	0.00	4.83
957	1151	1.278637	CCAAACTGAACGCACGGTC	59.721	57.895	0.05	0.05	0.00	4.79
958	1152	1.083657	CAAACTGAACGCACGGTCG	60.084	57.895	3.35	1.34	33.87	4.79
959	1153	2.877974	AAACTGAACGCACGGTCGC	61.878	57.895	3.35	0.00	33.87	5.19
960	1154	4.578898	ACTGAACGCACGGTCGCA	62.579	61.111	3.35	0.00	33.87	5.10
961	1155	4.059459	CTGAACGCACGGTCGCAC	62.059	66.667	3.35	0.00	33.87	5.34
1230	1429	3.775654	GTGACCTCCCTCGCCCTG	61.776	72.222	0.00	0.00	0.00	4.45
1231	1430	4.316823	TGACCTCCCTCGCCCTGT	62.317	66.667	0.00	0.00	0.00	4.00
1390	1589	2.917971	GACCTCTCGATGAACAAACTCG	59.082	50.000	0.00	0.00	0.00	4.18
1396	1595	1.573829	GATGAACAAACTCGCGGGCA	61.574	55.000	5.51	0.00	0.00	5.36
1604	1806	0.601046	CTCAAGCTCGAGCACAACCA	60.601	55.000	36.87	14.52	45.16	3.67
1645	1847	1.792949	CGGAGTCGTTCAAGAACTTGG	59.207	52.381	13.46	0.02	40.78	3.61
1746	1948	1.668151	GTGGCTTGACCTGTCGACC	60.668	63.158	14.12	0.00	40.22	4.79
1908	2116	1.298859	CCTACAACAAGCTGACCGGC	61.299	60.000	0.00	0.00	0.00	6.13
1946	2154	3.250744	TCGGAACATTGACGAAGCTTAG	58.749	45.455	0.00	0.68	33.21	2.18
2052	2260	1.961793	TTGAGAACAAACTCACGGGG	58.038	50.000	0.00	0.00	44.94	5.73
2346	2557	4.115199	AATGGAGGGCTCACCGGC	62.115	66.667	0.00	0.00	46.96	6.13
2915	3264	4.101448	GTCACCAGGCCTCCGCAT	62.101	66.667	0.00	0.00	36.38	4.73
3606	3994	2.443203	TTCGGGCTCGCCAGGATA	60.443	61.111	0.00	0.00	37.98	2.59
3681	4069	1.522092	CTTCGGCTACATGGCTCCA	59.478	57.895	0.00	0.00	39.32	3.86
3767	4163	1.593006	CTCATATTGTTCGCCGTGGTC	59.407	52.381	0.00	0.00	0.00	4.02
3937	4333	2.759973	TCCGGGAAGAGCATCGCT	60.760	61.111	0.00	0.00	43.88	4.93
3988	4384	1.000955	AGGCAAAGTGACGACTTCGAT	59.999	47.619	5.47	0.00	41.87	3.59
4024	4420	4.166888	ATCATCTGCACCGGCGCT	62.167	61.111	16.69	0.00	45.35	5.92
4346	4765	1.072159	AGTGTGCCAGCCTTGAGAC	59.928	57.895	0.00	0.00	0.00	3.36
4489	4908	5.765182	GGTTAAATTGGATGATGTCGATCCT	59.235	40.000	3.79	0.00	40.26	3.24
4624	5044	4.823989	CCAAACCTCCATCTCCATATGTTC	59.176	45.833	1.24	0.00	0.00	3.18
4785	5205	5.507482	GGAAGGTTCGAAGGGAAAAGAAAAG	60.507	44.000	0.00	0.00	36.14	2.27
4786	5206	4.788679	AGGTTCGAAGGGAAAAGAAAAGA	58.211	39.130	0.00	0.00	36.14	2.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	5.132312	ACATGATGGAAGAGATCATTCCTGT	59.868	40.000	22.97	17.62	45.45	4.00
54	55	9.926158	AAAATGTGACATGTTTTTCTATATGCA	57.074	25.926	0.00	0.00	0.00	3.96
61	62	6.638610	TCACCAAAATGTGACATGTTTTTCT	58.361	32.000	0.00	0.00	40.22	2.52
62	63	6.900568	TCACCAAAATGTGACATGTTTTTC	57.099	33.333	0.00	0.00	40.22	2.29
198	200	7.656542	TGCATATGTGAATGTTTGAATTGTGTT	59.343	29.630	4.29	0.00	0.00	3.32
199	201	7.116662	GTGCATATGTGAATGTTTGAATTGTGT	59.883	33.333	4.29	0.00	0.00	3.72
209	211	6.756299	TGTGTATGTGCATATGTGAATGTT	57.244	33.333	6.16	0.00	0.00	2.71
327	347	1.779025	GCCACTGCTACCGCATCATG	61.779	60.000	0.00	0.00	46.74	3.07
352	374	0.037734	TGTCGCCTCCTGAGAGTACA	59.962	55.000	0.00	0.00	38.58	2.90
376	399	0.179062	CGCTCCCTCCTCAATGAAGG	60.179	60.000	0.00	0.00	37.81	3.46
413	436	1.153667	CTTCACCAGCCGAGCTCTC	60.154	63.158	12.85	3.35	36.40	3.20
414	437	1.603236	CTCTTCACCAGCCGAGCTCT	61.603	60.000	12.85	0.00	36.40	4.09
426	449	1.571460	CTGTGCCGCAACTCTTCAC	59.429	57.895	0.00	0.00	0.00	3.18
430	453	1.553690	ATACCCTGTGCCGCAACTCT	61.554	55.000	0.00	0.00	0.00	3.24
434	457	2.045438	CCATACCCTGTGCCGCAA	60.045	61.111	0.00	0.00	0.00	4.85
502	525	1.227853	GCCCGCCGATATCCAACTT	60.228	57.895	0.00	0.00	0.00	2.66
564	587	4.698625	ACCCTTCTCGACGCCCCT	62.699	66.667	0.00	0.00	0.00	4.79
568	591	4.452733	CCCCACCCTTCTCGACGC	62.453	72.222	0.00	0.00	0.00	5.19
569	592	2.995574	ACCCCACCCTTCTCGACG	60.996	66.667	0.00	0.00	0.00	5.12
570	593	2.663196	CACCCCACCCTTCTCGAC	59.337	66.667	0.00	0.00	0.00	4.20
571	594	2.606519	CCACCCCACCCTTCTCGA	60.607	66.667	0.00	0.00	0.00	4.04
572	595	3.717294	CCCACCCCACCCTTCTCG	61.717	72.222	0.00	0.00	0.00	4.04
573	596	3.339093	CCCCACCCCACCCTTCTC	61.339	72.222	0.00	0.00	0.00	2.87
574	597	2.962825	TTTCCCCACCCCACCCTTCT	62.963	60.000	0.00	0.00	0.00	2.85
575	598	2.441035	CTTTCCCCACCCCACCCTTC	62.441	65.000	0.00	0.00	0.00	3.46
577	600	2.863988	CTTTCCCCACCCCACCCT	60.864	66.667	0.00	0.00	0.00	4.34
578	601	2.861974	TCTTTCCCCACCCCACCC	60.862	66.667	0.00	0.00	0.00	4.61
579	602	1.850755	TCTCTTTCCCCACCCCACC	60.851	63.158	0.00	0.00	0.00	4.61
580	603	1.685820	CTCTCTTTCCCCACCCCAC	59.314	63.158	0.00	0.00	0.00	4.61
581	604	1.541368	CCTCTCTTTCCCCACCCCA	60.541	63.158	0.00	0.00	0.00	4.96
582	605	2.985116	GCCTCTCTTTCCCCACCCC	61.985	68.421	0.00	0.00	0.00	4.95
634	811	0.102844	TGGTTAGTATACCACGCGCC	59.897	55.000	5.73	0.00	43.14	6.53
662	841	7.809650	CAAATTAATTGGACCGAAGGGGACAT	61.810	42.308	0.39	0.00	44.09	3.06
663	842	6.558742	CAAATTAATTGGACCGAAGGGGACA	61.559	44.000	0.39	0.00	44.09	4.02
688	867	2.362503	GTGGGGTTTAGGCAGGGC	60.363	66.667	0.00	0.00	0.00	5.19
850	1042	2.333581	CACGGCCGGTGTTTTTCC	59.666	61.111	31.76	0.00	41.89	3.13
851	1043	2.333581	CCACGGCCGGTGTTTTTC	59.666	61.111	31.76	0.00	45.52	2.29
866	1059	1.959710	TATGTAGTGGGAACTGGCCA	58.040	50.000	4.71	4.71	0.00	5.36
1013	1212	3.537874	GTGGGAGATAGGCGCGGT	61.538	66.667	8.83	0.00	0.00	5.68
1385	1584	4.699522	GGAGGTTGCCCGCGAGTT	62.700	66.667	8.23	0.00	35.12	3.01
1396	1595	2.990479	GATGTCTGCGGGGAGGTT	59.010	61.111	0.00	0.00	0.00	3.50
1427	1629	1.602771	GCCAGGTAGGTGAGGTTCC	59.397	63.158	0.00	0.00	40.61	3.62
1645	1847	3.426568	GACAGTGGCCAGCTTCGC	61.427	66.667	5.11	0.00	0.00	4.70
1746	1948	2.968156	TTCCCGGTGAACGCGTTG	60.968	61.111	31.89	14.87	42.52	4.10
1908	2116	4.530857	AGGCTTTCCGGGATCGCG	62.531	66.667	23.94	23.94	37.47	5.87
1923	2131	0.721718	GCTTCGTCAATGTTCCGAGG	59.278	55.000	0.00	0.00	31.54	4.63
1929	2137	4.829064	TTTGCTAAGCTTCGTCAATGTT	57.171	36.364	0.00	0.00	0.00	2.71
2158	2369	1.884464	CGGTGATGATCCACAGCCG	60.884	63.158	11.05	11.54	38.74	5.52
2346	2557	3.699894	AGCGTCTCTGGCAGGGTG	61.700	66.667	15.27	9.58	0.00	4.61
2988	3340	3.393149	GAGCCCCTTCCGCCTCTTC	62.393	68.421	0.00	0.00	0.00	2.87
3681	4069	1.664321	GAGGTGATCGGTGCGTACCT	61.664	60.000	20.87	2.16	45.22	3.08
3767	4163	0.108186	TACCCGCACTCTGCAATCAG	60.108	55.000	0.00	0.00	45.36	2.90
3922	4318	1.880340	GTCAGCGATGCTCTTCCCG	60.880	63.158	0.00	0.00	36.40	5.14
3988	4384	1.954146	GCCGAGCTTGAACACGACA	60.954	57.895	1.22	0.00	0.00	4.35
4489	4908	8.556589	TGTATTTTCTCCTCCCAATAAAGATGA	58.443	33.333	0.00	0.00	0.00	2.92
4624	5044	3.578688	GCATAAAAGTTTCAGTGGCAGG	58.421	45.455	0.00	0.00	0.00	4.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.