AutoCloner

Multiple sequence alignment - TraesCS4D01G255200

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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	TraesCS4D01G255200	chr4D	100.000	3200	0	0	1	3200	423990777	423987578	0.000000e+00	5910
1	TraesCS4D01G255200	chr4D	96.271	2333	74	7	1	2324	424323670	424321342	0.000000e+00	3814
2	TraesCS4D01G255200	chr4D	95.397	2303	74	10	561	2855	424110935	424108657	0.000000e+00	3637
3	TraesCS4D01G255200	chr4D	93.148	2306	101	16	561	2855	424169949	424167690	0.000000e+00	3330
4	TraesCS4D01G255200	chr4D	95.690	1392	31	5	1471	2855	424196575	424195206	0.000000e+00	2211
5	TraesCS4D01G255200	chr4D	89.945	1631	113	20	804	2399	57840501	57842115	0.000000e+00	2056
6	TraesCS4D01G255200	chr4D	96.435	1122	28	6	1	1114	424198334	424197217	0.000000e+00	1840
7	TraesCS4D01G255200	chr4D	86.573	1430	135	32	821	2224	426870123	426871521	0.000000e+00	1524
8	TraesCS4D01G255200	chr4D	86.567	536	39	6	2328	2855	424309149	424308639	7.750000e-156	560
9	TraesCS4D01G255200	chr4D	85.579	527	40	7	2339	2855	424194811	424194311	1.320000e-143	520
10	TraesCS4D01G255200	chr4D	92.527	281	21	0	1	281	212096015	212096295	1.380000e-108	403
11	TraesCS4D01G255200	chr4D	87.683	341	25	6	2865	3200	438211483	438211155	6.480000e-102	381
12	TraesCS4D01G255200	chr4D	86.592	179	15	5	392	561	424446234	424446056	4.210000e-44	189
13	TraesCS4D01G255200	chr4D	80.074	271	22	19	2556	2824	427021210	427021450	4.240000e-39	172
14	TraesCS4D01G255200	chr4D	84.058	138	14	4	2261	2397	427015841	427015971	3.350000e-25	126
15	TraesCS4D01G255200	chr4D	75.367	341	42	20	2288	2597	427323907	427324236	3.350000e-25	126
16	TraesCS4D01G255200	chr4A	93.416	1944	81	10	810	2737	40260686	40262598	0.000000e+00	2837
17	TraesCS4D01G255200	chr4A	84.951	1422	144	28	804	2210	38682956	38681590	0.000000e+00	1376
18	TraesCS4D01G255200	chr4A	79.129	1332	215	42	952	2251	37999981	38001281	0.000000e+00	861
19	TraesCS4D01G255200	chr4A	93.933	478	20	3	2723	3200	40262613	40263081	0.000000e+00	713
20	TraesCS4D01G255200	chr4A	93.238	281	19	0	10	290	163924737	163924457	6.390000e-112	414
21	TraesCS4D01G255200	chr4A	89.007	282	22	4	2120	2399	539140504	539140778	1.100000e-89	340
22	TraesCS4D01G255200	chr4B	91.050	2067	115	13	810	2860	520298421	520296409	0.000000e+00	2728
23	TraesCS4D01G255200	chr4B	89.145	1824	128	37	884	2660	86132166	86130366	0.000000e+00	2207
24	TraesCS4D01G255200	chr4B	91.643	718	40	8	2493	3200	520281360	520280653	0.000000e+00	976
25	TraesCS4D01G255200	chr4B	88.596	342	22	7	2865	3200	541923092	541922762	1.790000e-107	399
26	TraesCS4D01G255200	chr4B	82.522	452	32	17	2271	2684	86097267	86096825	1.410000e-93	353
27	TraesCS4D01G255200	chr4B	83.539	243	28	7	329	560	136294904	136294663	1.930000e-52	217
28	TraesCS4D01G255200	chr4B	83.784	111	11	3	2288	2397	522683475	522683579	7.310000e-17	99
29	TraesCS4D01G255200	chrUn	93.528	309	15	2	810	1113	60140575	60140267	3.760000e-124	455
30	TraesCS4D01G255200	chrUn	93.528	309	15	2	810	1113	235654922	235654614	3.760000e-124	455
31	TraesCS4D01G255200	chr2D	91.003	289	25	1	1	289	607544133	607543846	3.870000e-104	388
32	TraesCS4D01G255200	chr2D	90.345	290	28	0	1	290	257406659	257406948	6.480000e-102	381
33	TraesCS4D01G255200	chr3D	90.690	290	27	0	1	290	484451206	484451495	1.390000e-103	387
34	TraesCS4D01G255200	chr3D	86.136	339	23	9	2865	3200	489162365	489162682	8.500000e-91	344
35	TraesCS4D01G255200	chr6A	90.690	290	26	1	1	290	141291527	141291815	5.010000e-103	385
36	TraesCS4D01G255200	chr2A	90.625	288	27	0	3	290	745062938	745063225	1.800000e-102	383
37	TraesCS4D01G255200	chr3A	87.906	339	21	7	2865	3200	632546674	632546995	6.480000e-102	381
38	TraesCS4D01G255200	chr1D	86.310	336	26	6	2865	3195	408074683	408074363	6.570000e-92	348
39	TraesCS4D01G255200	chr5A	85.345	348	32	8	2857	3200	620556573	620556905	3.060000e-90	342
40	TraesCS4D01G255200	chr5A	73.610	917	163	57	1136	2029	624197578	624198438	2.430000e-71	279
41	TraesCS4D01G255200	chr1B	86.475	244	19	6	2957	3200	548624117	548623888	4.100000e-64	255
42	TraesCS4D01G255200	chr5B	84.362	243	28	6	327	560	241214849	241214608	2.480000e-56	230

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	TraesCS4D01G255200	chr4D	423987578	423990777	3199	True	5910.000000	5910	100.0000	1	3200	1	chr4D.!!$R1	3199
1	TraesCS4D01G255200	chr4D	424321342	424323670	2328	True	3814.000000	3814	96.2710	1	2324	1	chr4D.!!$R5	2323
2	TraesCS4D01G255200	chr4D	424108657	424110935	2278	True	3637.000000	3637	95.3970	561	2855	1	chr4D.!!$R2	2294
3	TraesCS4D01G255200	chr4D	424167690	424169949	2259	True	3330.000000	3330	93.1480	561	2855	1	chr4D.!!$R3	2294
4	TraesCS4D01G255200	chr4D	57840501	57842115	1614	False	2056.000000	2056	89.9450	804	2399	1	chr4D.!!$F1	1595
5	TraesCS4D01G255200	chr4D	426870123	426871521	1398	False	1524.000000	1524	86.5730	821	2224	1	chr4D.!!$F3	1403
6	TraesCS4D01G255200	chr4D	424194311	424198334	4023	True	1523.666667	2211	92.5680	1	2855	3	chr4D.!!$R8	2854
7	TraesCS4D01G255200	chr4D	424308639	424309149	510	True	560.000000	560	86.5670	2328	2855	1	chr4D.!!$R4	527
8	TraesCS4D01G255200	chr4A	40260686	40263081	2395	False	1775.000000	2837	93.6745	810	3200	2	chr4A.!!$F3	2390
9	TraesCS4D01G255200	chr4A	38681590	38682956	1366	True	1376.000000	1376	84.9510	804	2210	1	chr4A.!!$R1	1406
10	TraesCS4D01G255200	chr4A	37999981	38001281	1300	False	861.000000	861	79.1290	952	2251	1	chr4A.!!$F1	1299
11	TraesCS4D01G255200	chr4B	520296409	520298421	2012	True	2728.000000	2728	91.0500	810	2860	1	chr4B.!!$R5	2050
12	TraesCS4D01G255200	chr4B	86130366	86132166	1800	True	2207.000000	2207	89.1450	884	2660	1	chr4B.!!$R2	1776
13	TraesCS4D01G255200	chr4B	520280653	520281360	707	True	976.000000	976	91.6430	2493	3200	1	chr4B.!!$R4	707
14	TraesCS4D01G255200	chr5A	624197578	624198438	860	False	279.000000	279	73.6100	1136	2029	1	chr5A.!!$F2	893

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
707	716	1.207593	CGCAACCGCCAAGAAAGAG	59.792	57.895	0.0	0.0	33.11	2.85	F
1346	1407	2.202703	GCGCGACCCTGATAACGT	60.203	61.111	12.1	0.0	0.00	3.99	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1737	2206	0.103026	CATCATCGCCGAGGAACAGA	59.897	55.0	5.27	0.0	0.0	3.41	R
3000	3787	0.320374	TAGGACCAGCAACGACCAAG	59.680	55.0	0.00	0.0	0.0	3.61	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
247	248	7.708752	CAGAAGAGGAGCGAGAAATAAGTATTT	59.291	37.037	0.00	0.00	38.51	1.40
424	425	5.464389	TGATTGTGTGCATCGATATCTTCAG	59.536	40.000	0.00	0.00	0.00	3.02
425	426	4.654091	TGTGTGCATCGATATCTTCAGA	57.346	40.909	0.00	0.00	0.00	3.27
426	427	5.205759	TGTGTGCATCGATATCTTCAGAT	57.794	39.130	0.00	0.00	38.51	2.90
427	428	5.225642	TGTGTGCATCGATATCTTCAGATC	58.774	41.667	0.00	0.00	36.05	2.75
428	429	5.221303	TGTGTGCATCGATATCTTCAGATCA	60.221	40.000	0.00	0.00	36.05	2.92
429	430	5.345472	GTGTGCATCGATATCTTCAGATCAG	59.655	44.000	0.00	0.00	36.05	2.90
473	481	1.274167	TGCGACCGGTGTTTTATCTCT	59.726	47.619	14.63	0.00	0.00	3.10
527	536	4.714632	ACTACAGGTGCGGCATATAAAAT	58.285	39.130	5.72	0.00	0.00	1.82
620	629	5.865552	CGATTTGAAATCCAAGATTGCAAGT	59.134	36.000	11.94	7.97	35.94	3.16
699	708	3.597728	GGGAAAACGCAACCGCCA	61.598	61.111	0.00	0.00	38.22	5.69
700	709	2.413765	GGAAAACGCAACCGCCAA	59.586	55.556	0.00	0.00	38.22	4.52
701	710	1.660264	GGAAAACGCAACCGCCAAG	60.660	57.895	0.00	0.00	38.22	3.61
702	711	1.357334	GAAAACGCAACCGCCAAGA	59.643	52.632	0.00	0.00	38.22	3.02
707	716	1.207593	CGCAACCGCCAAGAAAGAG	59.792	57.895	0.00	0.00	33.11	2.85
717	726	4.083590	CCGCCAAGAAAGAGAGAAAGAAAG	60.084	45.833	0.00	0.00	0.00	2.62
1346	1407	2.202703	GCGCGACCCTGATAACGT	60.203	61.111	12.10	0.00	0.00	3.99
1737	2206	1.078848	GATGCTCACCGGCAAGACT	60.079	57.895	0.00	0.00	45.68	3.24
2547	3097	9.573166	TGGATGAATCGATGGTTAAAAATATCT	57.427	29.630	0.00	0.00	0.00	1.98
2680	3234	7.712264	TTTCATGTGCAAATTTCTTTACTGG	57.288	32.000	0.00	0.00	0.00	4.00
2685	3239	6.644347	TGTGCAAATTTCTTTACTGGGAAAA	58.356	32.000	0.00	0.00	35.50	2.29
2701	3264	8.183104	ACTGGGAAAAAGATAGGAAAAGAAAG	57.817	34.615	0.00	0.00	0.00	2.62
2703	3266	7.951591	TGGGAAAAAGATAGGAAAAGAAAGTG	58.048	34.615	0.00	0.00	0.00	3.16
2708	3271	8.753497	AAAAGATAGGAAAAGAAAGTGTGTCT	57.247	30.769	0.00	0.00	0.00	3.41
2754	3347	7.310796	GCTACACATGGTATAATATGGTACCCA	60.311	40.741	10.07	0.00	39.68	4.51
2824	3418	5.051891	TGAAGCAAATTCAAGAGCTTAGC	57.948	39.130	0.00	0.00	46.35	3.09
2831	3425	2.879002	TCAAGAGCTTAGCGGAGATG	57.121	50.000	0.00	0.00	0.00	2.90
2850	3444	7.333423	CGGAGATGTTAGTTCCATTCAGTTTAA	59.667	37.037	0.00	0.00	0.00	1.52
2973	3567	1.954382	AGAAGCTTCGTTTCCCCAAAC	59.046	47.619	20.43	0.00	38.91	2.93
3000	3787	8.800370	AAAAATTCATAGGAAGGTCTCTTCTC	57.200	34.615	0.00	0.00	46.42	2.87
3005	3792	3.268034	AGGAAGGTCTCTTCTCTTGGT	57.732	47.619	6.16	0.00	46.42	3.67
3061	3848	5.181748	ACCTGATGCTGAGTTATCTGTTTC	58.818	41.667	0.00	0.00	0.00	2.78
3081	3868	7.166167	TGTTTCAAGATCTTCTAAACCCTACC	58.834	38.462	25.79	11.48	30.43	3.18
3082	3869	7.017254	TGTTTCAAGATCTTCTAAACCCTACCT	59.983	37.037	25.79	0.00	30.43	3.08
3083	3870	8.537858	GTTTCAAGATCTTCTAAACCCTACCTA	58.462	37.037	21.81	0.00	0.00	3.08
3084	3871	7.657023	TCAAGATCTTCTAAACCCTACCTAC	57.343	40.000	4.57	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
247	248	2.683968	GACTCCACGTACTTTGCATGA	58.316	47.619	0.00	0.00	0.00	3.07
426	427	8.563502	CCCCTTACCTATATATGTACCTACTGA	58.436	40.741	0.00	0.00	0.00	3.41
427	428	8.342270	ACCCCTTACCTATATATGTACCTACTG	58.658	40.741	0.00	0.00	0.00	2.74
428	429	8.342270	CACCCCTTACCTATATATGTACCTACT	58.658	40.741	0.00	0.00	0.00	2.57
429	430	7.069208	GCACCCCTTACCTATATATGTACCTAC	59.931	44.444	0.00	0.00	0.00	3.18
527	536	4.337836	TGTATTTACGTATGTAGGTCCGCA	59.662	41.667	0.00	0.00	0.00	5.69
620	629	1.060842	CACGTGTTCGACCGTTTTTCA	59.939	47.619	7.58	0.00	40.62	2.69
699	708	7.003482	AGGCATTCTTTCTTTCTCTCTTTCTT	58.997	34.615	0.00	0.00	0.00	2.52
700	709	6.541907	AGGCATTCTTTCTTTCTCTCTTTCT	58.458	36.000	0.00	0.00	0.00	2.52
701	710	6.816134	AGGCATTCTTTCTTTCTCTCTTTC	57.184	37.500	0.00	0.00	0.00	2.62
702	711	6.774656	TGAAGGCATTCTTTCTTTCTCTCTTT	59.225	34.615	12.92	0.00	35.50	2.52
707	716	6.756299	ATCTGAAGGCATTCTTTCTTTCTC	57.244	37.500	12.92	0.00	35.50	2.87
717	726	3.876320	GGAGTCTGAATCTGAAGGCATTC	59.124	47.826	3.66	3.66	35.87	2.67
1468	1532	0.181587	TTCTTGGCACCGGTGAAGAA	59.818	50.000	38.30	34.54	33.68	2.52
1737	2206	0.103026	CATCATCGCCGAGGAACAGA	59.897	55.000	5.27	0.00	0.00	3.41
2141	2631	7.119846	CGGGAATTTTGAGTAGATTCTTCTGTT	59.880	37.037	0.00	0.00	33.17	3.16
2680	3234	8.414003	ACACACTTTCTTTTCCTATCTTTTTCC	58.586	33.333	0.00	0.00	0.00	3.13
2685	3239	7.775561	ACAAGACACACTTTCTTTTCCTATCTT	59.224	33.333	0.00	0.00	36.61	2.40
2726	3290	8.319146	GGTACCATATTATACCATGTGTAGCTT	58.681	37.037	7.15	0.00	40.61	3.74
2824	3418	4.759782	ACTGAATGGAACTAACATCTCCG	58.240	43.478	0.00	0.00	31.37	4.63
2831	3425	9.774742	GACATGATTAAACTGAATGGAACTAAC	57.225	33.333	0.00	0.00	0.00	2.34
2996	3783	0.468226	ACCAGCAACGACCAAGAGAA	59.532	50.000	0.00	0.00	0.00	2.87
3000	3787	0.320374	TAGGACCAGCAACGACCAAG	59.680	55.000	0.00	0.00	0.00	3.61
3005	3792	3.055458	TCATCAATTAGGACCAGCAACGA	60.055	43.478	0.00	0.00	0.00	3.85
3061	3848	7.266400	GTGTAGGTAGGGTTTAGAAGATCTTG	58.734	42.308	14.00	0.00	0.00	3.02
3081	3868	3.689161	TGCGATGAATTGGAAAGGTGTAG	59.311	43.478	0.00	0.00	0.00	2.74
3082	3869	3.680490	TGCGATGAATTGGAAAGGTGTA	58.320	40.909	0.00	0.00	0.00	2.90
3083	3870	2.513753	TGCGATGAATTGGAAAGGTGT	58.486	42.857	0.00	0.00	0.00	4.16
3084	3871	3.574284	TTGCGATGAATTGGAAAGGTG	57.426	42.857	0.00	0.00	0.00	4.00
3163	4072	5.414789	TCCTTCGAATCTTGTACATCCAA	57.585	39.130	0.00	0.00	0.00	3.53

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.