AutoCloner

Multiple sequence alignment - TraesCS2D01G586700

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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	TraesCS2D01G586700	chr2D	100.000	2491	0	0	1	2491	644896161	644898651	0.000000e+00	4601.0
1	TraesCS2D01G586700	chr2D	74.160	387	92	8	1903	2285	38626328	38625946	1.190000e-33	154.0
2	TraesCS2D01G586700	chr2B	91.595	1868	92	24	420	2281	790646913	790645105	0.000000e+00	2519.0
3	TraesCS2D01G586700	chr2B	93.320	1033	40	6	420	1448	790657432	790656425	0.000000e+00	1498.0
4	TraesCS2D01G586700	chr2B	91.827	1040	52	10	420	1448	790667943	790666926	0.000000e+00	1419.0
5	TraesCS2D01G586700	chr2B	88.728	967	43	16	1445	2375	790654263	790653327	0.000000e+00	1122.0
6	TraesCS2D01G586700	chr2B	88.636	968	44	23	1444	2375	790664765	790663828	0.000000e+00	1118.0
7	TraesCS2D01G586700	chr2B	83.648	636	92	3	1868	2491	796084046	796083411	2.760000e-164	588.0
8	TraesCS2D01G586700	chr2B	93.839	211	13	0	2281	2491	790644930	790644720	4.000000e-83	318.0
9	TraesCS2D01G586700	chr2A	93.581	1480	67	18	420	1880	770255187	770256657	0.000000e+00	2182.0
10	TraesCS2D01G586700	chr2A	97.938	582	12	0	1910	2491	770256658	770257239	0.000000e+00	1009.0
11	TraesCS2D01G586700	chr6A	83.808	667	93	5	1837	2491	6430655	6431318	9.790000e-174	619.0
12	TraesCS2D01G586700	chr5D	96.942	327	10	0	1	327	553574098	553573772	1.300000e-152	549.0
13	TraesCS2D01G586700	chr5D	96.636	327	11	0	1	327	449361700	449361374	6.060000e-151	544.0
14	TraesCS2D01G586700	chr5D	96.049	329	11	1	1	327	485522022	485521694	3.650000e-148	534.0
15	TraesCS2D01G586700	chr5D	92.929	99	7	0	326	424	263481175	263481273	7.180000e-31	145.0
16	TraesCS2D01G586700	chr5D	93.684	95	6	0	326	420	93461101	93461195	2.580000e-30	143.0
17	TraesCS2D01G586700	chr3D	96.353	329	10	1	1	327	607129843	607129515	7.840000e-150	540.0
18	TraesCS2D01G586700	chr3D	96.605	324	11	0	1	324	540186003	540186326	2.820000e-149	538.0
19	TraesCS2D01G586700	chr3D	93.617	94	6	0	326	419	129191902	129191995	9.290000e-30	141.0
20	TraesCS2D01G586700	chr1D	96.353	329	10	1	1	327	420993243	420992915	7.840000e-150	540.0
21	TraesCS2D01G586700	chr1D	87.037	54	7	0	1647	1700	34088229	34088282	7.440000e-06	62.1
22	TraesCS2D01G586700	chr4D	96.615	325	10	1	1	324	221139165	221139489	2.820000e-149	538.0
23	TraesCS2D01G586700	chr4D	96.615	325	10	1	1	324	274311839	274311515	2.820000e-149	538.0
24	TraesCS2D01G586700	chr4D	96.037	328	12	1	1	327	232833024	232832697	1.310000e-147	532.0
25	TraesCS2D01G586700	chr4D	93.617	94	6	0	326	419	182211329	182211422	9.290000e-30	141.0
26	TraesCS2D01G586700	chr4D	93.617	94	6	0	326	419	274311406	274311313	9.290000e-30	141.0
27	TraesCS2D01G586700	chr4D	87.037	54	7	0	1647	1700	149659550	149659603	7.440000e-06	62.1
28	TraesCS2D01G586700	chr4D	87.037	54	7	0	1647	1700	297429590	297429537	7.440000e-06	62.1
29	TraesCS2D01G586700	chr7D	93.814	97	6	0	326	422	161774444	161774540	2.000000e-31	147.0
30	TraesCS2D01G586700	chr7D	93.684	95	6	0	326	420	44617709	44617803	2.580000e-30	143.0
31	TraesCS2D01G586700	chr7D	93.684	95	6	0	326	420	246278965	246279059	2.580000e-30	143.0
32	TraesCS2D01G586700	chr6B	91.176	102	7	2	327	426	187430804	187430905	1.200000e-28	137.0
33	TraesCS2D01G586700	chr5A	73.927	303	73	6	1956	2255	378279844	378280143	1.570000e-22	117.0
34	TraesCS2D01G586700	chr3B	72.727	330	81	9	1929	2254	773846752	773847076	4.380000e-18	102.0
35	TraesCS2D01G586700	chrUn	87.037	54	7	0	1647	1700	111819454	111819401	7.440000e-06	62.1
36	TraesCS2D01G586700	chr6D	87.037	54	7	0	1647	1700	37053801	37053748	7.440000e-06	62.1

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	TraesCS2D01G586700	chr2D	644896161	644898651	2490	False	4601.0	4601	100.0000	1	2491	1	chr2D.!!$F1	2490
1	TraesCS2D01G586700	chr2B	790644720	790646913	2193	True	1418.5	2519	92.7170	420	2491	2	chr2B.!!$R2	2071
2	TraesCS2D01G586700	chr2B	790653327	790657432	4105	True	1310.0	1498	91.0240	420	2375	2	chr2B.!!$R3	1955
3	TraesCS2D01G586700	chr2B	790663828	790667943	4115	True	1268.5	1419	90.2315	420	2375	2	chr2B.!!$R4	1955
4	TraesCS2D01G586700	chr2B	796083411	796084046	635	True	588.0	588	83.6480	1868	2491	1	chr2B.!!$R1	623
5	TraesCS2D01G586700	chr2A	770255187	770257239	2052	False	1595.5	2182	95.7595	420	2491	2	chr2A.!!$F1	2071
6	TraesCS2D01G586700	chr6A	6430655	6431318	663	False	619.0	619	83.8080	1837	2491	1	chr6A.!!$F1	654
7	TraesCS2D01G586700	chr4D	274311313	274311839	526	True	339.5	538	95.1160	1	419	2	chr4D.!!$R3	418

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
698	809	0.108138	GTATTCCTGCACGCCTCAGT	60.108	55.0	0.0	0.0	0.0	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2300	4830	0.462581	TCCAAGCGCATCTCCATGAC	60.463	55.0	11.47	0.0	30.57	3.06	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
138	139	9.173939	GATAAATCTGCTGTTTATATGTTGTGC	57.826	33.333	9.46	0.00	33.23	4.57
143	144	5.003160	TGCTGTTTATATGTTGTGCTGTCT	58.997	37.500	0.00	0.00	0.00	3.41
308	310	2.092914	GCCATTAGTAACCCAGAGCACT	60.093	50.000	0.00	0.00	0.00	4.40
309	311	3.622455	GCCATTAGTAACCCAGAGCACTT	60.622	47.826	0.00	0.00	0.00	3.16
324	326	1.336755	GCACTTGGTAAATATGGCCCG	59.663	52.381	0.00	0.00	0.00	6.13
328	437	3.117813	ACTTGGTAAATATGGCCCGCTTA	60.118	43.478	0.00	0.00	0.00	3.09
358	467	0.805711	CGTGATGATAGTGGCGCACA	60.806	55.000	10.83	1.22	36.74	4.57
386	495	2.677337	GCGCAATTAATGGCCAAAACAT	59.323	40.909	10.96	0.00	0.00	2.71
392	501	0.392336	AATGGCCAAAACATGTGCGT	59.608	45.000	10.96	0.00	0.00	5.24
394	503	1.729131	GGCCAAAACATGTGCGTCG	60.729	57.895	0.00	0.00	0.00	5.12
601	711	4.998672	CGGTTAACTGGAAACTAATCCACA	59.001	41.667	6.53	0.00	44.52	4.17
698	809	0.108138	GTATTCCTGCACGCCTCAGT	60.108	55.000	0.00	0.00	0.00	3.41
798	916	5.759763	GGCAATAATCCTTAATTTTGGCAGG	59.240	40.000	0.00	0.00	38.82	4.85
843	963	5.371115	AACAAATAATCTTCCCGTGTGTG	57.629	39.130	0.00	0.00	0.00	3.82
844	964	4.394729	ACAAATAATCTTCCCGTGTGTGT	58.605	39.130	0.00	0.00	0.00	3.72
846	966	5.153513	CAAATAATCTTCCCGTGTGTGTTG	58.846	41.667	0.00	0.00	0.00	3.33
847	967	2.341846	AATCTTCCCGTGTGTGTTGT	57.658	45.000	0.00	0.00	0.00	3.32
848	968	1.878953	ATCTTCCCGTGTGTGTTGTC	58.121	50.000	0.00	0.00	0.00	3.18
849	969	0.179067	TCTTCCCGTGTGTGTTGTCC	60.179	55.000	0.00	0.00	0.00	4.02
850	970	0.179056	CTTCCCGTGTGTGTTGTCCT	60.179	55.000	0.00	0.00	0.00	3.85
851	971	0.253610	TTCCCGTGTGTGTTGTCCTT	59.746	50.000	0.00	0.00	0.00	3.36
852	972	0.179067	TCCCGTGTGTGTTGTCCTTC	60.179	55.000	0.00	0.00	0.00	3.46
853	973	1.164041	CCCGTGTGTGTTGTCCTTCC	61.164	60.000	0.00	0.00	0.00	3.46
854	974	0.179056	CCGTGTGTGTTGTCCTTCCT	60.179	55.000	0.00	0.00	0.00	3.36
855	975	1.069513	CCGTGTGTGTTGTCCTTCCTA	59.930	52.381	0.00	0.00	0.00	2.94
856	976	2.484065	CCGTGTGTGTTGTCCTTCCTAA	60.484	50.000	0.00	0.00	0.00	2.69
857	977	2.542595	CGTGTGTGTTGTCCTTCCTAAC	59.457	50.000	0.00	0.00	0.00	2.34
858	978	2.876550	GTGTGTGTTGTCCTTCCTAACC	59.123	50.000	0.00	0.00	0.00	2.85
859	979	2.140717	GTGTGTTGTCCTTCCTAACCG	58.859	52.381	0.00	0.00	0.00	4.44
860	980	2.040939	TGTGTTGTCCTTCCTAACCGA	58.959	47.619	0.00	0.00	0.00	4.69
861	981	2.635915	TGTGTTGTCCTTCCTAACCGAT	59.364	45.455	0.00	0.00	0.00	4.18
862	982	3.071892	TGTGTTGTCCTTCCTAACCGATT	59.928	43.478	0.00	0.00	0.00	3.34
863	983	4.283978	TGTGTTGTCCTTCCTAACCGATTA	59.716	41.667	0.00	0.00	0.00	1.75
864	984	5.221682	TGTGTTGTCCTTCCTAACCGATTAA	60.222	40.000	0.00	0.00	0.00	1.40
865	985	5.878669	GTGTTGTCCTTCCTAACCGATTAAT	59.121	40.000	0.00	0.00	0.00	1.40
866	986	6.373495	GTGTTGTCCTTCCTAACCGATTAATT	59.627	38.462	0.00	0.00	0.00	1.40
867	987	7.550196	GTGTTGTCCTTCCTAACCGATTAATTA	59.450	37.037	0.00	0.00	0.00	1.40
868	988	7.767198	TGTTGTCCTTCCTAACCGATTAATTAG	59.233	37.037	0.00	0.00	0.00	1.73
869	989	7.427989	TGTCCTTCCTAACCGATTAATTAGT	57.572	36.000	0.00	0.00	0.00	2.24
870	990	7.270047	TGTCCTTCCTAACCGATTAATTAGTG	58.730	38.462	0.00	0.00	0.00	2.74
871	991	6.202379	GTCCTTCCTAACCGATTAATTAGTGC	59.798	42.308	0.00	0.00	0.00	4.40
872	992	6.053005	CCTTCCTAACCGATTAATTAGTGCA	58.947	40.000	0.00	0.00	0.00	4.57
882	1036	7.065803	ACCGATTAATTAGTGCATGCCATATAC	59.934	37.037	16.68	6.08	0.00	1.47
1015	1169	2.291670	ACCTCGATCTACTCCAACCACT	60.292	50.000	0.00	0.00	0.00	4.00
1047	1209	1.660607	CGTCACCAATTCGATGACCAG	59.339	52.381	9.82	0.00	39.70	4.00
1065	1230	2.267324	GACCAGCCAGCAGAGACC	59.733	66.667	0.00	0.00	0.00	3.85
1174	1339	2.584608	CCGTTCAAGCCGATCCCT	59.415	61.111	0.00	0.00	0.00	4.20
1207	1372	3.842923	CGCATCCAGGAGCTCGGT	61.843	66.667	7.83	0.00	0.00	4.69
1324	1489	4.910195	TCAACTACCTGCTTGACATTGAT	58.090	39.130	0.00	0.00	0.00	2.57
1424	1589	3.549471	CGACTCTTTCAACTGATCCATCG	59.451	47.826	0.00	0.00	0.00	3.84
1441	1606	2.768833	TCGAGTGACATATGTACCGC	57.231	50.000	8.71	4.15	0.00	5.68
1554	3884	4.685169	ACATCACAGGCATTAACTTTCG	57.315	40.909	0.00	0.00	0.00	3.46
1585	3915	8.692110	CAAGTATGCATGCTTTCTTTTTGATA	57.308	30.769	25.19	1.01	30.06	2.15
1712	4043	4.261801	GAGTTGCCATAGAAAACCAGCTA	58.738	43.478	0.00	0.00	0.00	3.32
1747	4078	1.111116	CGGGCGATCTAGGTTACCCA	61.111	60.000	13.24	0.00	37.16	4.51
1799	4154	2.101582	GTGATCCGCTAATCAGTCTGGT	59.898	50.000	0.00	0.00	36.36	4.00
1873	4228	2.586357	GCCGCCAAGTCCGATCTC	60.586	66.667	0.00	0.00	0.00	2.75
2300	4830	2.859165	TTTGAAGGGTGCAGTAGAGG	57.141	50.000	0.00	0.00	0.00	3.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
76	77	8.919145	AGAAGATTAGTCTCCGAATACAATTCT	58.081	33.333	0.00	0.00	32.15	2.40
173	174	7.664082	TTTTTCTTTTCTGATGTTTGCACAA	57.336	28.000	0.00	0.00	36.16	3.33
201	202	6.090898	GGTGCGCCACTAGTATGAATATTAAG	59.909	42.308	12.58	0.00	34.40	1.85
202	203	5.929992	GGTGCGCCACTAGTATGAATATTAA	59.070	40.000	12.58	0.00	34.40	1.40
308	310	2.445682	AAGCGGGCCATATTTACCAA	57.554	45.000	4.39	0.00	0.00	3.67
309	311	3.799432	ATAAGCGGGCCATATTTACCA	57.201	42.857	4.39	0.00	0.00	3.25
324	326	4.617959	TCATCACGCCACTAGTAATAAGC	58.382	43.478	0.00	0.00	0.00	3.09
328	437	5.279006	CCACTATCATCACGCCACTAGTAAT	60.279	44.000	0.00	0.00	0.00	1.89
358	467	4.078537	TGGCCATTAATTGCGCACTATAT	58.921	39.130	11.12	0.00	0.00	0.86
369	478	3.683822	CGCACATGTTTTGGCCATTAATT	59.316	39.130	6.09	0.00	0.00	1.40
601	711	7.561021	AGTTTCCATTTTTAATTTTTGCGGT	57.439	28.000	0.00	0.00	0.00	5.68
629	740	5.371526	TGTTGCCAAATTGCCAAAAGAATA	58.628	33.333	0.00	0.00	0.00	1.75
689	800	3.118775	TGCACTAATCAATACTGAGGCGT	60.119	43.478	0.00	0.00	34.23	5.68
798	916	5.023533	TCCATGCATGAGTAGTTTCCTAC	57.976	43.478	28.31	0.00	43.32	3.18
843	963	6.997239	AATTAATCGGTTAGGAAGGACAAC	57.003	37.500	0.00	0.00	0.00	3.32
844	964	7.767198	CACTAATTAATCGGTTAGGAAGGACAA	59.233	37.037	0.00	0.00	33.30	3.18
846	966	6.202379	GCACTAATTAATCGGTTAGGAAGGAC	59.798	42.308	0.00	0.00	33.30	3.85
847	967	6.126997	TGCACTAATTAATCGGTTAGGAAGGA	60.127	38.462	0.00	0.00	33.30	3.36
848	968	6.053005	TGCACTAATTAATCGGTTAGGAAGG	58.947	40.000	0.00	0.00	33.30	3.46
849	969	7.576236	CATGCACTAATTAATCGGTTAGGAAG	58.424	38.462	0.00	0.00	33.30	3.46
850	970	6.017440	GCATGCACTAATTAATCGGTTAGGAA	60.017	38.462	14.21	0.00	33.30	3.36
851	971	5.468746	GCATGCACTAATTAATCGGTTAGGA	59.531	40.000	14.21	0.00	33.30	2.94
852	972	5.334879	GGCATGCACTAATTAATCGGTTAGG	60.335	44.000	21.36	0.00	33.30	2.69
853	973	5.238432	TGGCATGCACTAATTAATCGGTTAG	59.762	40.000	21.36	0.00	34.78	2.34
854	974	5.126779	TGGCATGCACTAATTAATCGGTTA	58.873	37.500	21.36	0.00	0.00	2.85
855	975	3.951037	TGGCATGCACTAATTAATCGGTT	59.049	39.130	21.36	0.00	0.00	4.44
856	976	3.550820	TGGCATGCACTAATTAATCGGT	58.449	40.909	21.36	0.00	0.00	4.69
857	977	4.771590	ATGGCATGCACTAATTAATCGG	57.228	40.909	21.36	0.00	0.00	4.18
858	978	7.280876	AGGTATATGGCATGCACTAATTAATCG	59.719	37.037	21.36	0.00	0.00	3.34
859	979	8.511604	AGGTATATGGCATGCACTAATTAATC	57.488	34.615	21.36	0.00	0.00	1.75
861	981	9.394767	CATAGGTATATGGCATGCACTAATTAA	57.605	33.333	21.36	0.00	36.00	1.40
862	982	7.498900	GCATAGGTATATGGCATGCACTAATTA	59.501	37.037	21.36	2.47	41.25	1.40
863	983	6.319658	GCATAGGTATATGGCATGCACTAATT	59.680	38.462	21.36	1.15	41.25	1.40
864	984	5.824624	GCATAGGTATATGGCATGCACTAAT	59.175	40.000	21.36	9.62	41.25	1.73
865	985	5.045651	AGCATAGGTATATGGCATGCACTAA	60.046	40.000	21.36	1.71	43.46	2.24
866	986	4.471025	AGCATAGGTATATGGCATGCACTA	59.529	41.667	21.36	10.44	43.46	2.74
867	987	3.265221	AGCATAGGTATATGGCATGCACT	59.735	43.478	21.36	8.30	43.46	4.40
868	988	3.614092	AGCATAGGTATATGGCATGCAC	58.386	45.455	21.36	8.37	43.46	4.57
869	989	5.130809	TGATAGCATAGGTATATGGCATGCA	59.869	40.000	21.36	6.13	43.46	3.96
870	990	5.614308	TGATAGCATAGGTATATGGCATGC	58.386	41.667	9.90	9.90	41.78	4.06
871	991	9.955102	ATTATGATAGCATAGGTATATGGCATG	57.045	33.333	10.98	0.00	39.42	4.06
982	1136	2.937799	AGATCGAGGTGAACGAGTAGAC	59.062	50.000	0.00	0.00	42.81	2.59
1015	1169	3.993584	GTGACGGCGGTGGTGGTA	61.994	66.667	13.24	0.00	0.00	3.25
1047	1209	2.267324	GTCTCTGCTGGCTGGTCC	59.733	66.667	0.00	0.00	0.00	4.46
1120	1285	4.036804	GCCGCCGTGCAATCAACA	62.037	61.111	0.00	0.00	0.00	3.33
1424	1589	2.651701	CGAGCGGTACATATGTCACTC	58.348	52.381	12.68	13.14	0.00	3.51
1585	3915	9.935682	CGTGATATGAAAACAAGCATATACTTT	57.064	29.630	0.00	0.00	37.71	2.66
1747	4078	1.654954	CGTCGACGGGGAGAACTCAT	61.655	60.000	29.70	0.00	35.37	2.90
1994	4349	7.745620	ATGTCGATTGACTAAAGGTTTTCTT	57.254	32.000	14.27	0.00	45.70	2.52
2300	4830	0.462581	TCCAAGCGCATCTCCATGAC	60.463	55.000	11.47	0.00	30.57	3.06
2345	4875	2.027192	TGTCATGCTTAACCCTGACTCC	60.027	50.000	7.45	0.00	38.98	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.