AutoCloner

Multiple sequence alignment - TraesCS7A01G106200

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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	TraesCS7A01G106200	chr7A	100.000	2540	0	0	1	2540	64596752	64594213	0.000000e+00	4691
1	TraesCS7A01G106200	chr6A	96.609	1032	28	7	696	1724	580186583	580187610	0.000000e+00	1705
2	TraesCS7A01G106200	chr6A	99.380	807	4	1	1734	2540	580187671	580188476	0.000000e+00	1461
3	TraesCS7A01G106200	chr6A	98.490	596	9	0	1	596	46148061	46148656	0.000000e+00	1051
4	TraesCS7A01G106200	chr6A	84.971	173	15	7	696	860	101339533	101339364	5.620000e-37	165
5	TraesCS7A01G106200	chr6A	84.971	173	15	7	696	860	101354087	101353918	5.620000e-37	165
6	TraesCS7A01G106200	chr1B	96.054	811	27	3	1734	2540	15690769	15691578	0.000000e+00	1315
7	TraesCS7A01G106200	chr1B	92.172	792	43	15	945	1724	15689924	15690708	0.000000e+00	1101
8	TraesCS7A01G106200	chr1B	88.245	604	63	8	15	615	12997258	12997856	0.000000e+00	715
9	TraesCS7A01G106200	chr1B	87.925	265	28	4	696	958	546257174	546256912	2.450000e-80	309
10	TraesCS7A01G106200	chr1B	85.833	240	31	3	696	934	15689596	15689833	4.190000e-63	252
11	TraesCS7A01G106200	chr6B	97.329	599	15	1	1734	2331	679365604	679366202	0.000000e+00	1016
12	TraesCS7A01G106200	chr6B	95.463	529	22	1	1196	1724	679365017	679365543	0.000000e+00	843
13	TraesCS7A01G106200	chr6B	96.682	211	6	1	2330	2540	679376198	679376407	1.450000e-92	350
14	TraesCS7A01G106200	chr6B	86.310	168	19	4	696	861	437472796	437472961	2.010000e-41	180
15	TraesCS7A01G106200	chr4A	95.498	622	11	4	3	624	603751812	603751208	0.000000e+00	977
16	TraesCS7A01G106200	chr4A	97.373	533	14	0	3	535	603822473	603821941	0.000000e+00	907
17	TraesCS7A01G106200	chr3B	96.558	552	16	2	1991	2540	467062283	467061733	0.000000e+00	911
18	TraesCS7A01G106200	chr3B	95.420	524	22	2	1201	1724	467068591	467068070	0.000000e+00	833
19	TraesCS7A01G106200	chr3B	96.958	263	8	0	1734	1996	467068009	467067747	2.320000e-120	442
20	TraesCS7A01G106200	chr3B	84.971	173	21	5	690	860	66468744	66468575	1.210000e-38	171
21	TraesCS7A01G106200	chrUn	92.195	615	37	7	15	620	96706187	96706799	0.000000e+00	859
22	TraesCS7A01G106200	chr3D	90.566	583	46	5	15	596	411001536	411000962	0.000000e+00	763
23	TraesCS7A01G106200	chr4B	88.586	587	62	5	15	599	32182637	32183220	0.000000e+00	708
24	TraesCS7A01G106200	chr3A	87.710	594	63	6	24	616	721467441	721466857	0.000000e+00	684
25	TraesCS7A01G106200	chr3A	94.952	416	20	1	39	454	738241538	738241124	0.000000e+00	651
26	TraesCS7A01G106200	chr3A	93.491	169	8	2	783	949	712649423	712649256	5.430000e-62	248
27	TraesCS7A01G106200	chr3A	87.755	196	18	6	423	616	49602860	49603051	9.140000e-55	224
28	TraesCS7A01G106200	chr3A	85.030	167	21	3	696	860	231687672	231687508	1.560000e-37	167
29	TraesCS7A01G106200	chr2B	96.914	324	7	2	2219	2540	184672693	184673015	7.990000e-150	540
30	TraesCS7A01G106200	chr2B	86.707	331	42	2	1234	1562	166612230	166611900	1.440000e-97	366
31	TraesCS7A01G106200	chr2B	80.108	186	28	7	1977	2153	225247437	225247622	2.050000e-26	130
32	TraesCS7A01G106200	chr7B	96.605	324	8	2	2219	2540	42784308	42784630	3.720000e-148	534
33	TraesCS7A01G106200	chr7B	95.679	324	7	3	2219	2540	747442876	747442558	4.850000e-142	514
34	TraesCS7A01G106200	chr7B	85.030	167	21	4	696	860	41291032	41290868	1.560000e-37	167
35	TraesCS7A01G106200	chr2A	84.171	398	59	4	1234	1629	117403713	117403318	1.430000e-102	383
36	TraesCS7A01G106200	chr2A	81.421	183	28	4	1977	2153	176866863	176867045	7.320000e-31	145
37	TraesCS7A01G106200	chr2D	86.970	330	41	2	1234	1561	115959081	115958752	1.110000e-98	370
38	TraesCS7A01G106200	chr5B	84.783	230	25	9	696	921	60593789	60593566	3.290000e-54	222
39	TraesCS7A01G106200	chr5A	81.944	216	27	10	2061	2273	19539307	19539513	3.360000e-39	172

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	TraesCS7A01G106200	chr7A	64594213	64596752	2539	True	4691.000000	4691	100.0000	1	2540	1	chr7A.!!$R1	2539
1	TraesCS7A01G106200	chr6A	580186583	580188476	1893	False	1583.000000	1705	97.9945	696	2540	2	chr6A.!!$F2	1844
2	TraesCS7A01G106200	chr6A	46148061	46148656	595	False	1051.000000	1051	98.4900	1	596	1	chr6A.!!$F1	595
3	TraesCS7A01G106200	chr1B	15689596	15691578	1982	False	889.333333	1315	91.3530	696	2540	3	chr1B.!!$F2	1844
4	TraesCS7A01G106200	chr1B	12997258	12997856	598	False	715.000000	715	88.2450	15	615	1	chr1B.!!$F1	600
5	TraesCS7A01G106200	chr6B	679365017	679366202	1185	False	929.500000	1016	96.3960	1196	2331	2	chr6B.!!$F3	1135
6	TraesCS7A01G106200	chr4A	603751208	603751812	604	True	977.000000	977	95.4980	3	624	1	chr4A.!!$R1	621
7	TraesCS7A01G106200	chr4A	603821941	603822473	532	True	907.000000	907	97.3730	3	535	1	chr4A.!!$R2	532
8	TraesCS7A01G106200	chr3B	467061733	467062283	550	True	911.000000	911	96.5580	1991	2540	1	chr3B.!!$R2	549
9	TraesCS7A01G106200	chr3B	467067747	467068591	844	True	637.500000	833	96.1890	1201	1996	2	chr3B.!!$R3	795
10	TraesCS7A01G106200	chrUn	96706187	96706799	612	False	859.000000	859	92.1950	15	620	1	chrUn.!!$F1	605
11	TraesCS7A01G106200	chr3D	411000962	411001536	574	True	763.000000	763	90.5660	15	596	1	chr3D.!!$R1	581
12	TraesCS7A01G106200	chr4B	32182637	32183220	583	False	708.000000	708	88.5860	15	599	1	chr4B.!!$F1	584
13	TraesCS7A01G106200	chr3A	721466857	721467441	584	True	684.000000	684	87.7100	24	616	1	chr3A.!!$R3	592

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
654	672	0.039764	TCGAGAGAGAAAGGGAGCCA	59.96	55.0	0.0	0.0	34.84	4.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1726	1839	0.892755	TAGGATACATAAGCCGCCCG	59.107	55.0	0.0	0.0	41.41	6.13	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
621	639	4.179599	GAGGGGAGGGGAGGGGAG	62.180	77.778	0.00	0.00	0.00	4.30
626	644	3.707189	GAGGGGAGGGGAGGGGAA	61.707	72.222	0.00	0.00	0.00	3.97
627	645	3.224269	AGGGGAGGGGAGGGGAAA	61.224	66.667	0.00	0.00	0.00	3.13
628	646	2.696504	GGGGAGGGGAGGGGAAAG	60.697	72.222	0.00	0.00	0.00	2.62
629	647	2.696504	GGGAGGGGAGGGGAAAGG	60.697	72.222	0.00	0.00	0.00	3.11
630	648	2.696504	GGAGGGGAGGGGAAAGGG	60.697	72.222	0.00	0.00	0.00	3.95
631	649	2.459710	GAGGGGAGGGGAAAGGGA	59.540	66.667	0.00	0.00	0.00	4.20
632	650	1.694525	GAGGGGAGGGGAAAGGGAG	60.695	68.421	0.00	0.00	0.00	4.30
633	651	3.421386	GGGGAGGGGAAAGGGAGC	61.421	72.222	0.00	0.00	0.00	4.70
634	652	3.421386	GGGAGGGGAAAGGGAGCC	61.421	72.222	0.00	0.00	0.00	4.70
635	653	2.286502	GGAGGGGAAAGGGAGCCT	60.287	66.667	0.00	0.00	33.87	4.58
636	654	2.379459	GGAGGGGAAAGGGAGCCTC	61.379	68.421	0.00	0.00	30.89	4.70
637	655	2.689034	AGGGGAAAGGGAGCCTCG	60.689	66.667	0.00	0.00	30.89	4.63
638	656	2.687566	GGGGAAAGGGAGCCTCGA	60.688	66.667	0.00	0.00	30.89	4.04
639	657	2.736826	GGGGAAAGGGAGCCTCGAG	61.737	68.421	5.13	5.13	30.89	4.04
640	658	1.686110	GGGAAAGGGAGCCTCGAGA	60.686	63.158	15.71	0.00	30.89	4.04
641	659	1.681486	GGGAAAGGGAGCCTCGAGAG	61.681	65.000	15.71	5.19	30.89	3.20
642	660	0.684805	GGAAAGGGAGCCTCGAGAGA	60.685	60.000	15.71	0.00	39.12	3.10
653	671	2.889200	TCGAGAGAGAAAGGGAGCC	58.111	57.895	0.00	0.00	34.84	4.70
654	672	0.039764	TCGAGAGAGAAAGGGAGCCA	59.960	55.000	0.00	0.00	34.84	4.75
655	673	1.118838	CGAGAGAGAAAGGGAGCCAT	58.881	55.000	0.00	0.00	0.00	4.40
656	674	1.202510	CGAGAGAGAAAGGGAGCCATG	60.203	57.143	0.00	0.00	0.00	3.66
657	675	1.836802	GAGAGAGAAAGGGAGCCATGT	59.163	52.381	0.00	0.00	0.00	3.21
658	676	2.238395	GAGAGAGAAAGGGAGCCATGTT	59.762	50.000	0.00	0.00	0.00	2.71
659	677	2.646798	AGAGAGAAAGGGAGCCATGTTT	59.353	45.455	0.00	0.00	0.00	2.83
660	678	2.751806	GAGAGAAAGGGAGCCATGTTTG	59.248	50.000	0.00	0.00	0.00	2.93
661	679	2.108952	AGAGAAAGGGAGCCATGTTTGT	59.891	45.455	0.00	0.00	0.00	2.83
662	680	2.893489	GAGAAAGGGAGCCATGTTTGTT	59.107	45.455	0.00	0.00	0.00	2.83
663	681	3.308401	AGAAAGGGAGCCATGTTTGTTT	58.692	40.909	0.00	0.00	0.00	2.83
664	682	3.711190	AGAAAGGGAGCCATGTTTGTTTT	59.289	39.130	0.00	0.00	0.00	2.43
665	683	4.164030	AGAAAGGGAGCCATGTTTGTTTTT	59.836	37.500	0.00	0.00	0.00	1.94
705	723	4.350816	AGGGCATTGTAGTATATCCAAGCA	59.649	41.667	0.00	0.00	0.00	3.91
718	736	2.130193	TCCAAGCATCTATTCCAGGCT	58.870	47.619	0.00	0.00	36.13	4.58
729	747	1.627864	TTCCAGGCTAGGTTTTTGCC	58.372	50.000	0.00	0.00	46.42	4.52
749	767	1.534729	GTGAGGTTTAGCCACTTGGG	58.465	55.000	0.00	0.00	40.61	4.12
762	780	3.509575	GCCACTTGGGTGAAAATGATGTA	59.490	43.478	0.00	0.00	45.61	2.29
765	783	5.418524	CCACTTGGGTGAAAATGATGTATGA	59.581	40.000	0.00	0.00	45.61	2.15
766	784	6.097270	CCACTTGGGTGAAAATGATGTATGAT	59.903	38.462	0.00	0.00	45.61	2.45
767	785	6.976349	CACTTGGGTGAAAATGATGTATGATG	59.024	38.462	0.00	0.00	45.61	3.07
770	788	7.901283	TGGGTGAAAATGATGTATGATGAAT	57.099	32.000	0.00	0.00	0.00	2.57
773	791	7.869429	GGGTGAAAATGATGTATGATGAATTCC	59.131	37.037	2.27	0.00	0.00	3.01
775	793	7.113965	GTGAAAATGATGTATGATGAATTCCGC	59.886	37.037	2.27	0.00	0.00	5.54
781	799	4.450053	TGTATGATGAATTCCGCATGTGA	58.550	39.130	8.11	0.00	0.00	3.58
847	865	3.118956	TGACTTTGGTTTGCCGTTTCAAT	60.119	39.130	0.00	0.00	37.67	2.57
1422	1535	1.003233	GCCGTTGAAGAGGCCTTCT	60.003	57.895	6.77	2.22	46.84	2.85
1568	1681	1.114722	CATGCTGGTGGGGTGTTTGT	61.115	55.000	0.00	0.00	0.00	2.83
1724	1837	1.268335	ACAACAAAGCAACGGTAAGCG	60.268	47.619	0.00	0.00	35.48	4.68
1725	1838	0.309612	AACAAAGCAACGGTAAGCGG	59.690	50.000	0.00	0.00	35.48	5.52
1726	1839	1.442017	CAAAGCAACGGTAAGCGGC	60.442	57.895	0.00	0.00	35.48	6.53
1727	1840	2.961669	AAAGCAACGGTAAGCGGCG	61.962	57.895	0.51	0.51	35.48	6.46
2113	2279	4.019860	AGGTCTACACATGCAAGATTCAGT	60.020	41.667	0.00	0.00	0.00	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
620	638	2.689034	CGAGGCTCCCTTTCCCCT	60.689	66.667	9.32	0.00	31.76	4.79
621	639	2.687566	TCGAGGCTCCCTTTCCCC	60.688	66.667	9.32	0.00	31.76	4.81
622	640	1.681486	CTCTCGAGGCTCCCTTTCCC	61.681	65.000	13.56	0.00	31.76	3.97
623	641	0.684805	TCTCTCGAGGCTCCCTTTCC	60.685	60.000	13.56	0.00	31.76	3.13
624	642	0.744281	CTCTCTCGAGGCTCCCTTTC	59.256	60.000	13.56	0.00	31.76	2.62
625	643	0.333312	TCTCTCTCGAGGCTCCCTTT	59.667	55.000	13.56	0.00	37.86	3.11
626	644	0.333312	TTCTCTCTCGAGGCTCCCTT	59.667	55.000	13.56	0.00	37.86	3.95
627	645	0.333312	TTTCTCTCTCGAGGCTCCCT	59.667	55.000	13.56	0.00	37.86	4.20
628	646	0.744281	CTTTCTCTCTCGAGGCTCCC	59.256	60.000	13.56	0.00	37.86	4.30
629	647	0.744281	CCTTTCTCTCTCGAGGCTCC	59.256	60.000	13.56	0.00	37.86	4.70
630	648	0.744281	CCCTTTCTCTCTCGAGGCTC	59.256	60.000	13.56	3.87	37.86	4.70
631	649	0.333312	TCCCTTTCTCTCTCGAGGCT	59.667	55.000	13.56	0.00	37.86	4.58
632	650	0.744281	CTCCCTTTCTCTCTCGAGGC	59.256	60.000	13.56	0.00	37.86	4.70
633	651	0.744281	GCTCCCTTTCTCTCTCGAGG	59.256	60.000	13.56	3.44	37.86	4.63
634	652	0.744281	GGCTCCCTTTCTCTCTCGAG	59.256	60.000	5.93	5.93	38.67	4.04
635	653	0.039764	TGGCTCCCTTTCTCTCTCGA	59.960	55.000	0.00	0.00	0.00	4.04
636	654	1.118838	ATGGCTCCCTTTCTCTCTCG	58.881	55.000	0.00	0.00	0.00	4.04
637	655	1.836802	ACATGGCTCCCTTTCTCTCTC	59.163	52.381	0.00	0.00	0.00	3.20
638	656	1.963985	ACATGGCTCCCTTTCTCTCT	58.036	50.000	0.00	0.00	0.00	3.10
639	657	2.751806	CAAACATGGCTCCCTTTCTCTC	59.248	50.000	0.00	0.00	0.00	3.20
640	658	2.108952	ACAAACATGGCTCCCTTTCTCT	59.891	45.455	0.00	0.00	0.00	3.10
641	659	2.519013	ACAAACATGGCTCCCTTTCTC	58.481	47.619	0.00	0.00	0.00	2.87
642	660	2.683211	ACAAACATGGCTCCCTTTCT	57.317	45.000	0.00	0.00	0.00	2.52
643	661	3.751479	AAACAAACATGGCTCCCTTTC	57.249	42.857	0.00	0.00	0.00	2.62
644	662	4.502105	AAAAACAAACATGGCTCCCTTT	57.498	36.364	0.00	0.00	0.00	3.11
678	696	4.020573	TGGATATACTACAATGCCCTTCGG	60.021	45.833	0.00	0.00	0.00	4.30
679	697	5.147330	TGGATATACTACAATGCCCTTCG	57.853	43.478	0.00	0.00	0.00	3.79
680	698	5.412904	GCTTGGATATACTACAATGCCCTTC	59.587	44.000	0.00	0.00	0.00	3.46
681	699	5.163099	TGCTTGGATATACTACAATGCCCTT	60.163	40.000	0.00	0.00	0.00	3.95
682	700	4.350816	TGCTTGGATATACTACAATGCCCT	59.649	41.667	0.00	0.00	0.00	5.19
683	701	4.651778	TGCTTGGATATACTACAATGCCC	58.348	43.478	0.00	0.00	0.00	5.36
684	702	6.176183	AGATGCTTGGATATACTACAATGCC	58.824	40.000	0.00	0.00	0.00	4.40
685	703	8.954950	ATAGATGCTTGGATATACTACAATGC	57.045	34.615	0.00	0.00	0.00	3.56
688	706	9.100197	TGGAATAGATGCTTGGATATACTACAA	57.900	33.333	0.00	0.00	0.00	2.41
689	707	8.664669	TGGAATAGATGCTTGGATATACTACA	57.335	34.615	0.00	0.00	0.00	2.74
690	708	8.200792	CCTGGAATAGATGCTTGGATATACTAC	58.799	40.741	0.00	0.00	0.00	2.73
691	709	7.147655	GCCTGGAATAGATGCTTGGATATACTA	60.148	40.741	0.00	0.00	0.00	1.82
692	710	6.352565	GCCTGGAATAGATGCTTGGATATACT	60.353	42.308	0.00	0.00	0.00	2.12
693	711	5.819901	GCCTGGAATAGATGCTTGGATATAC	59.180	44.000	0.00	0.00	0.00	1.47
694	712	5.728253	AGCCTGGAATAGATGCTTGGATATA	59.272	40.000	0.00	0.00	0.00	0.86
698	716	2.130193	AGCCTGGAATAGATGCTTGGA	58.870	47.619	0.00	0.00	0.00	3.53
705	723	4.889995	GCAAAAACCTAGCCTGGAATAGAT	59.110	41.667	0.00	0.00	0.00	1.98
718	736	2.351706	AACCTCACGGCAAAAACCTA	57.648	45.000	0.00	0.00	0.00	3.08
729	747	1.156736	CCAAGTGGCTAAACCTCACG	58.843	55.000	0.00	0.00	40.22	4.35
730	748	1.202891	ACCCAAGTGGCTAAACCTCAC	60.203	52.381	0.00	0.00	40.22	3.51
735	753	4.038642	TCATTTTCACCCAAGTGGCTAAAC	59.961	41.667	0.00	0.00	44.64	2.01
736	754	4.219115	TCATTTTCACCCAAGTGGCTAAA	58.781	39.130	0.00	0.00	44.64	1.85
749	767	7.113965	GCGGAATTCATCATACATCATTTTCAC	59.886	37.037	7.93	0.00	0.00	3.18
762	780	3.065786	GTGTCACATGCGGAATTCATCAT	59.934	43.478	7.93	6.80	0.00	2.45
765	783	1.398041	CGTGTCACATGCGGAATTCAT	59.602	47.619	7.93	0.00	0.00	2.57
766	784	0.795698	CGTGTCACATGCGGAATTCA	59.204	50.000	7.93	0.00	0.00	2.57
767	785	0.796312	ACGTGTCACATGCGGAATTC	59.204	50.000	3.42	0.00	0.00	2.17
770	788	2.603247	GCACGTGTCACATGCGGAA	61.603	57.895	18.38	0.00	0.00	4.30
773	791	0.721154	AATAGCACGTGTCACATGCG	59.279	50.000	17.52	0.00	44.25	4.73
775	793	5.315982	CAAACTAATAGCACGTGTCACATG	58.684	41.667	18.38	0.00	0.00	3.21
781	799	4.020839	AGGTACCAAACTAATAGCACGTGT	60.021	41.667	18.38	6.65	0.00	4.49
788	806	5.190677	CCCAACCAGGTACCAAACTAATAG	58.809	45.833	15.94	0.00	34.66	1.73
793	811	1.228190	ACCCAACCAGGTACCAAACT	58.772	50.000	15.94	0.00	38.79	2.66
1724	1837	2.032071	ATACATAAGCCGCCCGCC	59.968	61.111	0.00	0.00	38.78	6.13
1725	1838	2.033194	GGATACATAAGCCGCCCGC	61.033	63.158	0.00	0.00	37.98	6.13
1726	1839	0.892755	TAGGATACATAAGCCGCCCG	59.107	55.000	0.00	0.00	41.41	6.13
1727	1840	3.055385	TCAATAGGATACATAAGCCGCCC	60.055	47.826	0.00	0.00	41.41	6.13
1728	1841	4.202245	TCAATAGGATACATAAGCCGCC	57.798	45.455	0.00	0.00	41.41	6.13
1729	1842	6.743575	ATTTCAATAGGATACATAAGCCGC	57.256	37.500	0.00	0.00	41.41	6.53
1730	1843	8.322906	TCAATTTCAATAGGATACATAAGCCG	57.677	34.615	0.00	0.00	41.41	5.52
2028	2192	5.109500	TCAAGTATGGTGGCATGACAATA	57.891	39.130	0.58	0.00	0.00	1.90
2113	2279	4.451774	CCGTGTTACTTCCGTTTCCAATTA	59.548	41.667	0.00	0.00	0.00	1.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.