AutoCloner

Multiple sequence alignment - TraesCS3B01G436200

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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	TraesCS3B01G436200	chr3B	100.000	2980	0	0	1	2980	674481244	674478265	0.000000e+00	5504.0
1	TraesCS3B01G436200	chr3B	98.385	929	15	0	2052	2980	118757208	118756280	0.000000e+00	1633.0
2	TraesCS3B01G436200	chr3B	98.280	930	15	1	2052	2980	692009319	692008390	0.000000e+00	1628.0
3	TraesCS3B01G436200	chr3B	98.278	929	14	1	2052	2980	520334468	520335394	0.000000e+00	1626.0
4	TraesCS3B01G436200	chr6B	93.207	2061	115	14	1	2049	55204667	55206714	0.000000e+00	3007.0
5	TraesCS3B01G436200	chr6B	87.336	229	27	2	949	1176	564650491	564650718	8.190000e-66	261.0
6	TraesCS3B01G436200	chr6D	93.169	2064	110	11	1	2051	436494332	436496377	0.000000e+00	3001.0
7	TraesCS3B01G436200	chr2D	93.068	2063	118	9	1	2051	616929378	616927329	0.000000e+00	2994.0
8	TraesCS3B01G436200	chr2D	92.620	2046	100	14	1	2018	316145793	316143771	0.000000e+00	2894.0
9	TraesCS3B01G436200	chr2D	90.406	886	80	5	275	1158	59647848	59648730	0.000000e+00	1160.0
10	TraesCS3B01G436200	chr2D	91.004	767	64	4	1290	2051	59648732	59649498	0.000000e+00	1029.0
11	TraesCS3B01G436200	chr2D	91.379	232	19	1	1	231	59647618	59647849	1.720000e-82	316.0
12	TraesCS3B01G436200	chr7B	98.812	926	11	0	2055	2980	237916879	237915954	0.000000e+00	1650.0
13	TraesCS3B01G436200	chr4B	98.289	935	10	2	2052	2980	169589588	169590522	0.000000e+00	1633.0
14	TraesCS3B01G436200	chr4B	84.337	83	12	1	736	818	497107022	497106941	2.460000e-11	80.5
15	TraesCS3B01G436200	chr4A	98.285	933	15	1	2048	2980	684047432	684046501	0.000000e+00	1633.0
16	TraesCS3B01G436200	chr2B	98.385	929	15	0	2052	2980	699101985	699101057	0.000000e+00	1633.0
17	TraesCS3B01G436200	chr2B	98.170	929	17	0	2052	2980	699094783	699093855	0.000000e+00	1622.0
18	TraesCS3B01G436200	chr2B	98.170	929	17	0	2052	2980	699096519	699095591	0.000000e+00	1622.0
19	TraesCS3B01G436200	chr2B	85.275	455	58	5	949	1394	727661442	727660988	7.530000e-126	460.0
20	TraesCS3B01G436200	chr5D	89.955	886	84	5	275	1158	376571853	376572735	0.000000e+00	1138.0
21	TraesCS3B01G436200	chr5D	89.831	767	73	4	1290	2051	376572737	376573503	0.000000e+00	979.0
22	TraesCS3B01G436200	chr1D	84.574	1115	138	13	949	2051	189816643	189815551	0.000000e+00	1075.0
23	TraesCS3B01G436200	chr7A	76.572	811	163	19	1245	2045	381209162	381208369	1.280000e-113	420.0
24	TraesCS3B01G436200	chr7A	78.853	279	50	8	452	727	643998924	643998652	2.360000e-41	180.0
25	TraesCS3B01G436200	chr1A	82.186	494	77	9	1563	2051	22597447	22596960	5.940000e-112	414.0
26	TraesCS3B01G436200	chr7D	82.990	388	64	2	435	820	402554964	402554577	1.700000e-92	350.0
27	TraesCS3B01G436200	chrUn	85.417	240	34	1	1615	1853	82939177	82938938	6.380000e-62	248.0
28	TraesCS3B01G436200	chr5A	79.562	274	47	8	452	722	653890003	653890270	1.410000e-43	187.0
29	TraesCS3B01G436200	chr6A	78.912	147	18	7	680	816	286424681	286424824	1.470000e-13	87.9

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	TraesCS3B01G436200	chr3B	674478265	674481244	2979	True	5504.0	5504	100.000000	1	2980	1	chr3B.!!$R2	2979
1	TraesCS3B01G436200	chr3B	118756280	118757208	928	True	1633.0	1633	98.385000	2052	2980	1	chr3B.!!$R1	928
2	TraesCS3B01G436200	chr3B	692008390	692009319	929	True	1628.0	1628	98.280000	2052	2980	1	chr3B.!!$R3	928
3	TraesCS3B01G436200	chr3B	520334468	520335394	926	False	1626.0	1626	98.278000	2052	2980	1	chr3B.!!$F1	928
4	TraesCS3B01G436200	chr6B	55204667	55206714	2047	False	3007.0	3007	93.207000	1	2049	1	chr6B.!!$F1	2048
5	TraesCS3B01G436200	chr6D	436494332	436496377	2045	False	3001.0	3001	93.169000	1	2051	1	chr6D.!!$F1	2050
6	TraesCS3B01G436200	chr2D	616927329	616929378	2049	True	2994.0	2994	93.068000	1	2051	1	chr2D.!!$R2	2050
7	TraesCS3B01G436200	chr2D	316143771	316145793	2022	True	2894.0	2894	92.620000	1	2018	1	chr2D.!!$R1	2017
8	TraesCS3B01G436200	chr2D	59647618	59649498	1880	False	835.0	1160	90.929667	1	2051	3	chr2D.!!$F1	2050
9	TraesCS3B01G436200	chr7B	237915954	237916879	925	True	1650.0	1650	98.812000	2055	2980	1	chr7B.!!$R1	925
10	TraesCS3B01G436200	chr4B	169589588	169590522	934	False	1633.0	1633	98.289000	2052	2980	1	chr4B.!!$F1	928
11	TraesCS3B01G436200	chr4A	684046501	684047432	931	True	1633.0	1633	98.285000	2048	2980	1	chr4A.!!$R1	932
12	TraesCS3B01G436200	chr2B	699101057	699101985	928	True	1633.0	1633	98.385000	2052	2980	1	chr2B.!!$R1	928
13	TraesCS3B01G436200	chr2B	699093855	699096519	2664	True	1622.0	1622	98.170000	2052	2980	2	chr2B.!!$R3	928
14	TraesCS3B01G436200	chr5D	376571853	376573503	1650	False	1058.5	1138	89.893000	275	2051	2	chr5D.!!$F1	1776
15	TraesCS3B01G436200	chr1D	189815551	189816643	1092	True	1075.0	1075	84.574000	949	2051	1	chr1D.!!$R1	1102
16	TraesCS3B01G436200	chr7A	381208369	381209162	793	True	420.0	420	76.572000	1245	2045	1	chr7A.!!$R1	800

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
605	608	0.390472	GTGGTTCTTCGCTCCTCTGG	60.390	60.0	0.0	0.0	0.0	3.86	F
1073	1085	0.253044	CATGATCCCCGTTCCACACT	59.747	55.0	0.0	0.0	0.0	3.55	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1822	1846	0.040058	AGCTGGGTTGCCATTGATCA	59.960	50.0	0.0	0.0	0.00	2.92	R
2036	2077	1.185315	CAACATGGTAAGCCCCTTGG	58.815	55.0	0.0	0.0	34.73	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
112	113	5.347907	CGATTTGGTCTGGACTAAGTACAAC	59.652	44.000	0.00	0.00	33.37	3.32
113	114	5.617528	TTTGGTCTGGACTAAGTACAACA	57.382	39.130	0.00	0.00	33.37	3.33
133	135	7.734942	ACAACATACCAAATTGACATTTTCCT	58.265	30.769	0.00	0.00	29.41	3.36
195	197	3.780294	AGTAGGTGAATTGTATGCTGGGA	59.220	43.478	0.00	0.00	0.00	4.37
225	227	8.828688	AATTGTACTTCTAAGTAAGACCACAC	57.171	34.615	4.20	0.00	42.66	3.82
238	240	2.563179	AGACCACACGAACTGCTAATCT	59.437	45.455	0.00	0.00	0.00	2.40
446	448	1.261938	ATTCGGACGTGGATGGGTCA	61.262	55.000	0.00	0.00	34.87	4.02
458	460	5.125417	CGTGGATGGGTCATGTCTTTTATTT	59.875	40.000	0.00	0.00	0.00	1.40
459	461	6.332630	GTGGATGGGTCATGTCTTTTATTTG	58.667	40.000	0.00	0.00	0.00	2.32
463	465	4.462483	TGGGTCATGTCTTTTATTTGGCTC	59.538	41.667	0.00	0.00	0.00	4.70
496	498	3.376546	GTGTTCCTCATCTTTCTGGATGC	59.623	47.826	0.00	0.00	41.83	3.91
605	608	0.390472	GTGGTTCTTCGCTCCTCTGG	60.390	60.000	0.00	0.00	0.00	3.86
697	700	1.133513	TGCTGGTTGATTTGTCCTGGT	60.134	47.619	0.00	0.00	0.00	4.00
720	730	1.578423	GTCTGCTTGTGCTCTTGGC	59.422	57.895	0.00	0.00	40.48	4.52
721	731	0.888285	GTCTGCTTGTGCTCTTGGCT	60.888	55.000	0.00	0.00	42.39	4.75
722	732	0.604780	TCTGCTTGTGCTCTTGGCTC	60.605	55.000	0.00	0.00	42.39	4.70
723	733	1.584380	CTGCTTGTGCTCTTGGCTCC	61.584	60.000	0.00	0.00	42.39	4.70
724	734	1.303155	GCTTGTGCTCTTGGCTCCT	60.303	57.895	0.00	0.00	42.39	3.69
725	735	1.584380	GCTTGTGCTCTTGGCTCCTG	61.584	60.000	0.00	0.00	42.39	3.86
726	736	0.959372	CTTGTGCTCTTGGCTCCTGG	60.959	60.000	0.00	0.00	42.39	4.45
730	740	2.370445	GCTCTTGGCTCCTGGGCTA	61.370	63.158	7.03	0.00	41.48	3.93
751	761	1.941812	CCGCTTGAAGTTGCTTCGT	59.058	52.632	4.69	0.00	42.78	3.85
873	883	3.533907	TCTCCCCTCCTCTTCTGTAGAAT	59.466	47.826	0.00	0.00	33.01	2.40
1004	1016	1.787847	CTTTTCTTCGCGCGATGGT	59.212	52.632	35.55	0.00	0.00	3.55
1016	1028	0.461870	GCGATGGTATCAGGCACACA	60.462	55.000	0.00	0.00	0.00	3.72
1053	1065	2.127271	TGGGTGCGATGAACAATGAT	57.873	45.000	0.00	0.00	0.00	2.45
1055	1067	2.016318	GGGTGCGATGAACAATGATCA	58.984	47.619	0.00	0.00	0.00	2.92
1061	1073	4.214758	TGCGATGAACAATGATCATGATCC	59.785	41.667	28.61	14.93	37.64	3.36
1073	1085	0.253044	CATGATCCCCGTTCCACACT	59.747	55.000	0.00	0.00	0.00	3.55
1143	1155	4.460034	ACATGCATGTGCTAGATTTGTTCA	59.540	37.500	30.92	0.00	40.03	3.18
1162	1174	5.046448	TGTTCAAGATTTATGCAATTGGGCT	60.046	36.000	7.72	0.00	34.04	5.19
1185	1197	3.629438	TCGTTGATCTACGACACACAA	57.371	42.857	25.00	4.79	44.82	3.33
1270	1286	5.809562	CAGTCCACTGTGTATCAGATTCTTC	59.190	44.000	7.08	0.00	46.27	2.87
1296	1316	3.054287	TCCCGTGAATAGCCATTTTACCA	60.054	43.478	0.00	0.00	0.00	3.25
1333	1353	0.901827	TGGTCTGCCGTGTATCATGT	59.098	50.000	0.00	0.00	37.67	3.21
1404	1427	4.671964	CACAACACGATTGATGTTTGTGAG	59.328	41.667	10.45	0.00	36.65	3.51
1425	1448	2.029110	GCTGCCTTTAAAGAATGTGCCA	60.029	45.455	16.98	2.16	0.00	4.92
1612	1635	2.922740	TTCCTGTTGTGGTCTGTACC	57.077	50.000	0.00	0.00	46.98	3.34
1704	1728	1.068125	TGCTTAGCGTCGTTCTTGCTA	60.068	47.619	0.00	0.00	40.06	3.49
1705	1729	1.584308	GCTTAGCGTCGTTCTTGCTAG	59.416	52.381	0.00	0.00	41.75	3.42
1727	1751	2.844348	AGATGGTTTACCCGAGGTGAAT	59.156	45.455	5.90	0.00	33.87	2.57
1822	1846	0.954449	GCAGCGGCAGAGCATATGAT	60.954	55.000	6.97	0.00	40.72	2.45
1857	1882	1.380246	GCTGTGGATGCCAATGGGA	60.380	57.895	0.00	0.00	34.18	4.37
1920	1960	4.345837	AGCCACCATGGATATTGAATTTGG	59.654	41.667	21.47	12.51	40.96	3.28
1977	2018	1.188219	ACCTGTCAGGCAGTGTCGAT	61.188	55.000	19.40	0.00	43.55	3.59
2002	2043	6.024563	AGAAGGACAGGAAGATCAGAGATA	57.975	41.667	0.00	0.00	0.00	1.98
2662	4440	3.819877	AACCCACGTCCAAGTCGGC	62.820	63.158	0.00	0.00	33.14	5.54
2907	4695	6.155737	GTCCCTTATAAACCACTCCAACTCTA	59.844	42.308	0.00	0.00	0.00	2.43

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	0.749649	AAATGTGGGCACAAAAGCGA	59.250	45.000	0.00	0.00	45.41	4.93
112	113	7.546667	CCAAGAGGAAAATGTCAATTTGGTATG	59.453	37.037	0.00	0.00	36.11	2.39
113	114	7.235399	ACCAAGAGGAAAATGTCAATTTGGTAT	59.765	33.333	3.45	0.00	40.13	2.73
133	135	9.701098	CACAGTACAGTAAGTAAATAACCAAGA	57.299	33.333	0.00	0.00	33.72	3.02
195	197	8.947115	GGTCTTACTTAGAAGTACAATTTGCAT	58.053	33.333	1.55	0.00	40.95	3.96
225	227	5.117745	CACGGATAATCAGATTAGCAGTTCG	59.882	44.000	18.17	14.40	37.43	3.95
446	448	6.575162	AGAAACGAGCCAAATAAAAGACAT	57.425	33.333	0.00	0.00	0.00	3.06
458	460	1.301401	CACGGGAAGAAACGAGCCA	60.301	57.895	0.00	0.00	0.00	4.75
459	461	0.883370	AACACGGGAAGAAACGAGCC	60.883	55.000	0.00	0.00	0.00	4.70
463	465	1.145803	GAGGAACACGGGAAGAAACG	58.854	55.000	0.00	0.00	0.00	3.60
496	498	1.497278	CATTGTCCCAACTGCGACG	59.503	57.895	0.00	0.00	0.00	5.12
537	540	0.178929	ACTCCCTCTCCGGTCAACTT	60.179	55.000	0.00	0.00	0.00	2.66
605	608	6.781138	TGTACAACACAAATGAGAAGACAAC	58.219	36.000	0.00	0.00	32.95	3.32
697	700	1.228245	GAGCACAAGCAGACCCCAA	60.228	57.895	0.00	0.00	45.49	4.12
730	740	2.117941	GAAGCAACTTCAAGCGGCGT	62.118	55.000	9.37	0.00	39.95	5.68
734	744	1.388888	CAACGAAGCAACTTCAAGCG	58.611	50.000	7.99	0.00	40.17	4.68
738	748	2.098443	GGAAACCAACGAAGCAACTTCA	59.902	45.455	7.99	0.00	40.17	3.02
839	849	4.971125	GGGAGAGCGCCGCCATAC	62.971	72.222	17.47	0.00	36.33	2.39
891	902	7.301868	AGCTAGGGATTCAGAGAGATAAAAG	57.698	40.000	0.00	0.00	0.00	2.27
1004	1016	1.489481	CTCCCTCTGTGTGCCTGATA	58.511	55.000	0.00	0.00	0.00	2.15
1035	1047	2.016318	TGATCATTGTTCATCGCACCC	58.984	47.619	0.00	0.00	0.00	4.61
1053	1065	0.251916	GTGTGGAACGGGGATCATGA	59.748	55.000	0.00	0.00	42.39	3.07
1055	1067	0.253044	CAGTGTGGAACGGGGATCAT	59.747	55.000	0.00	0.00	42.39	2.45
1061	1073	1.597027	GGTGACAGTGTGGAACGGG	60.597	63.158	0.00	0.00	42.39	5.28
1073	1085	1.550524	CTACCTTGCTAGCTGGTGACA	59.449	52.381	30.01	16.99	35.48	3.58
1143	1155	5.422145	GACAAGCCCAATTGCATAAATCTT	58.578	37.500	0.00	0.00	33.28	2.40
1270	1286	2.847327	ATGGCTATTCACGGGATCTG	57.153	50.000	0.00	0.00	0.00	2.90
1296	1316	1.816835	CCACAGAGCAAGCATGAACAT	59.183	47.619	0.00	0.00	0.00	2.71
1333	1353	4.060205	GGTAAACTACAGAAGCCAAACGA	58.940	43.478	0.00	0.00	0.00	3.85
1404	1427	2.029110	TGGCACATTCTTTAAAGGCAGC	60.029	45.455	15.13	11.56	0.00	5.25
1612	1635	4.456911	AGAGTGGCAAGTCATTTACACATG	59.543	41.667	0.00	0.00	31.72	3.21
1704	1728	1.831736	CACCTCGGGTAAACCATCTCT	59.168	52.381	0.81	0.00	40.22	3.10
1705	1729	1.829222	TCACCTCGGGTAAACCATCTC	59.171	52.381	0.81	0.00	40.22	2.75
1727	1751	2.472695	AAGATGCGCAGGTCTTGTAA	57.527	45.000	22.10	0.00	33.64	2.41
1822	1846	0.040058	AGCTGGGTTGCCATTGATCA	59.960	50.000	0.00	0.00	0.00	2.92
1833	1857	2.036256	GGCATCCACAGCTGGGTT	59.964	61.111	19.93	8.68	38.25	4.11
1977	2018	4.022603	CTCTGATCTTCCTGTCCTTCTCA	58.977	47.826	0.00	0.00	0.00	3.27
2036	2077	1.185315	CAACATGGTAAGCCCCTTGG	58.815	55.000	0.00	0.00	34.73	3.61
2526	4303	3.123620	CGTTCCTCTGCTGCTGCC	61.124	66.667	13.47	0.00	38.71	4.85
2629	4407	1.371558	GGTTCAGCCCACGTCTCTT	59.628	57.895	0.00	0.00	0.00	2.85
2662	4440	4.129737	ACGTCGGATCGTGGGCTG	62.130	66.667	0.00	0.00	42.56	4.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.