AutoCloner

Multiple sequence alignment - TraesCS1B01G212600

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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	TraesCS1B01G212600	chr1B	100.000	2507	0	0	1	2507	386161434	386163940	0.000000e+00	4630.0
1	TraesCS1B01G212600	chr1B	93.699	730	44	2	1779	2507	636691603	636692331	0.000000e+00	1092.0
2	TraesCS1B01G212600	chr1B	93.346	541	35	1	1967	2507	636709054	636709593	0.000000e+00	798.0
3	TraesCS1B01G212600	chr1B	93.590	312	18	2	1779	2089	636713886	636714196	4.880000e-127	464.0
4	TraesCS1B01G212600	chr1D	92.749	855	33	16	935	1779	284242788	284243623	0.000000e+00	1208.0
5	TraesCS1B01G212600	chr1D	94.737	285	14	1	1	284	284241840	284242124	2.290000e-120	442.0
6	TraesCS1B01G212600	chr1D	91.031	223	8	7	342	562	284242129	284242341	8.770000e-75	291.0
7	TraesCS1B01G212600	chr1A	92.235	850	30	16	935	1779	355718289	355719107	0.000000e+00	1171.0
8	TraesCS1B01G212600	chr1A	94.083	676	33	5	1	671	355716701	355717374	0.000000e+00	1020.0
9	TraesCS1B01G212600	chr1A	88.889	171	6	3	774	938	355718074	355718237	5.470000e-47	198.0
10	TraesCS1B01G212600	chr5B	91.108	731	58	5	1779	2507	57743928	57743203	0.000000e+00	983.0
11	TraesCS1B01G212600	chr3A	88.661	732	76	7	1779	2507	231608595	231607868	0.000000e+00	885.0
12	TraesCS1B01G212600	chr4D	83.200	750	98	18	1778	2507	479649360	479648619	0.000000e+00	662.0
13	TraesCS1B01G212600	chr6A	90.457	503	45	3	1778	2279	60584792	60585292	0.000000e+00	660.0
14	TraesCS1B01G212600	chr2D	83.826	711	89	18	1812	2504	109906875	109907577	0.000000e+00	652.0
15	TraesCS1B01G212600	chr2D	100.000	30	0	0	275	304	181601882	181601911	3.480000e-04	56.5
16	TraesCS1B01G212600	chr7A	79.867	750	108	27	1779	2507	401926999	401927726	2.220000e-140	508.0
17	TraesCS1B01G212600	chr5D	82.410	614	71	18	1781	2387	149104636	149105219	3.720000e-138	501.0
18	TraesCS1B01G212600	chr6B	93.033	244	14	2	1030	1273	562486178	562485938	1.100000e-93	353.0
19	TraesCS1B01G212600	chr6B	97.500	40	1	0	565	604	577172238	577172277	4.470000e-08	69.4
20	TraesCS1B01G212600	chr4B	90.871	241	18	2	1030	1270	337551100	337551336	1.120000e-83	320.0
21	TraesCS1B01G212600	chr2B	97.619	42	1	0	563	604	584477787	584477828	3.460000e-09	73.1

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	TraesCS1B01G212600	chr1B	386161434	386163940	2506	False	4630.000000	4630	100.000000	1	2507	1	chr1B.!!$F1	2506
1	TraesCS1B01G212600	chr1B	636691603	636692331	728	False	1092.000000	1092	93.699000	1779	2507	1	chr1B.!!$F2	728
2	TraesCS1B01G212600	chr1B	636709054	636709593	539	False	798.000000	798	93.346000	1967	2507	1	chr1B.!!$F3	540
3	TraesCS1B01G212600	chr1D	284241840	284243623	1783	False	647.000000	1208	92.839000	1	1779	3	chr1D.!!$F1	1778
4	TraesCS1B01G212600	chr1A	355716701	355719107	2406	False	796.333333	1171	91.735667	1	1779	3	chr1A.!!$F1	1778
5	TraesCS1B01G212600	chr5B	57743203	57743928	725	True	983.000000	983	91.108000	1779	2507	1	chr5B.!!$R1	728
6	TraesCS1B01G212600	chr3A	231607868	231608595	727	True	885.000000	885	88.661000	1779	2507	1	chr3A.!!$R1	728
7	TraesCS1B01G212600	chr4D	479648619	479649360	741	True	662.000000	662	83.200000	1778	2507	1	chr4D.!!$R1	729
8	TraesCS1B01G212600	chr6A	60584792	60585292	500	False	660.000000	660	90.457000	1778	2279	1	chr6A.!!$F1	501
9	TraesCS1B01G212600	chr2D	109906875	109907577	702	False	652.000000	652	83.826000	1812	2504	1	chr2D.!!$F1	692
10	TraesCS1B01G212600	chr7A	401926999	401927726	727	False	508.000000	508	79.867000	1779	2507	1	chr7A.!!$F1	728
11	TraesCS1B01G212600	chr5D	149104636	149105219	583	False	501.000000	501	82.410000	1781	2387	1	chr5D.!!$F1	606

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
311	313	0.102481	CCTCCGTCCCGACATAAGTG	59.898	60.0	0.0	0.0	0.0	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1994	2846	0.105913	AGGAGGGGATCGAGTTCCTC	60.106	60.0	17.39	17.39	43.65	3.71	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
190	192	6.365970	TGCCAAGGCTAAAAATGGAAAATA	57.634	33.333	12.96	0.00	42.51	1.40
191	193	6.956497	TGCCAAGGCTAAAAATGGAAAATAT	58.044	32.000	12.96	0.00	42.51	1.28
276	278	2.545946	GTCGAAGAAGCTGAAGCAAAGT	59.454	45.455	4.90	0.00	45.16	2.66
304	306	2.117779	GTACTCCCTCCGTCCCGAC	61.118	68.421	0.00	0.00	0.00	4.79
311	313	0.102481	CCTCCGTCCCGACATAAGTG	59.898	60.000	0.00	0.00	0.00	3.16
330	332	0.875059	GTCTCAAGCTTTTGGGACGG	59.125	55.000	2.69	0.00	41.90	4.79
357	359	6.766467	GGGAGTACTAGGTATGAAAATTGTGG	59.234	42.308	0.00	0.00	0.00	4.17
392	395	4.038633	GGACCCCTACTATTCTGGAGTTT	58.961	47.826	0.00	0.00	0.00	2.66
395	398	3.136626	CCCCTACTATTCTGGAGTTTGGG	59.863	52.174	0.00	0.00	38.33	4.12
396	399	3.433740	CCCTACTATTCTGGAGTTTGGGC	60.434	52.174	0.00	0.00	34.71	5.36
417	423	4.435386	GGCAATGTTGTTGTTGTTGTTGTC	60.435	41.667	0.00	0.00	0.00	3.18
625	634	9.809096	GAGTAGAAATCAGAGTGTGAATATTGA	57.191	33.333	0.00	0.00	39.19	2.57
631	640	4.707934	TCAGAGTGTGAATATTGACCGGTA	59.292	41.667	7.34	0.00	29.64	4.02
632	641	5.186215	TCAGAGTGTGAATATTGACCGGTAA	59.814	40.000	7.34	0.00	29.64	2.85
636	645	5.046159	AGTGTGAATATTGACCGGTAAGGAA	60.046	40.000	7.34	0.00	45.00	3.36
657	667	1.745115	GTGCCTGAACCTATGCGCA	60.745	57.895	14.96	14.96	34.50	6.09
735	1389	1.056660	AAGAAGGAACTCCCAGCGAA	58.943	50.000	0.00	0.00	38.49	4.70
736	1390	1.280457	AGAAGGAACTCCCAGCGAAT	58.720	50.000	0.00	0.00	38.49	3.34
737	1391	1.065854	AGAAGGAACTCCCAGCGAATG	60.066	52.381	0.00	0.00	38.49	2.67
738	1392	0.678048	AAGGAACTCCCAGCGAATGC	60.678	55.000	0.00	0.00	38.49	3.56
739	1393	1.377202	GGAACTCCCAGCGAATGCA	60.377	57.895	0.00	0.00	46.23	3.96
740	1394	0.960364	GGAACTCCCAGCGAATGCAA	60.960	55.000	0.00	0.00	46.23	4.08
757	1411	0.447406	CAATCGCAGCCGTTTGATCA	59.553	50.000	0.00	0.00	43.36	2.92
853	1521	1.848652	TGTCACCCTCCTACAGCTAC	58.151	55.000	0.00	0.00	0.00	3.58
915	1689	1.295423	CTCCGTGTTACACCCCCAG	59.705	63.158	10.10	0.00	0.00	4.45
928	1708	2.364972	CCCCCAGGGCACTAAATAAG	57.635	55.000	0.00	0.00	35.35	1.73
1108	1947	2.806009	GCTAGCAGCAGGAGGAGGG	61.806	68.421	10.63	0.00	41.89	4.30
1344	2183	2.180017	GTGTACATCGTCGCCGGT	59.820	61.111	1.90	0.00	33.95	5.28
1512	2351	2.654912	CGACGACAACTGAACCGCC	61.655	63.158	0.00	0.00	0.00	6.13
1562	2401	2.295909	CAGTAGCCTAGCTAGCTCCTTG	59.704	54.545	23.26	9.34	42.11	3.61
1567	2406	1.412361	CCTAGCTAGCTCCTTGGTCCT	60.412	57.143	23.26	0.00	0.00	3.85
1610	2453	6.381481	TTTCGTTCGAGTTCTAGCCATATA	57.619	37.500	0.00	0.00	0.00	0.86
1611	2454	5.354054	TCGTTCGAGTTCTAGCCATATAC	57.646	43.478	0.00	0.00	0.00	1.47
1612	2455	5.061853	TCGTTCGAGTTCTAGCCATATACT	58.938	41.667	0.00	0.00	0.00	2.12
1613	2456	5.178996	TCGTTCGAGTTCTAGCCATATACTC	59.821	44.000	0.00	0.00	33.58	2.59
1614	2457	5.617308	CGTTCGAGTTCTAGCCATATACTCC	60.617	48.000	0.00	0.00	33.39	3.85
1638	2481	9.589461	TCCAGTATTTCCTTTTGTTTACCATAA	57.411	29.630	0.00	0.00	0.00	1.90
1660	2503	0.539051	CACTCCTAGCCTGGGACAAG	59.461	60.000	0.00	0.00	38.70	3.16
1661	2504	0.117340	ACTCCTAGCCTGGGACAAGT	59.883	55.000	0.00	0.00	38.70	3.16
1664	2507	1.361543	TCCTAGCCTGGGACAAGTAGT	59.638	52.381	0.00	0.00	38.70	2.73
1666	2509	2.694109	CCTAGCCTGGGACAAGTAGTAC	59.306	54.545	0.00	0.00	38.70	2.73
1744	2594	6.704819	TGTACATTTGATGATTCGATTGACG	58.295	36.000	0.00	0.00	44.09	4.35
1808	2658	1.229082	AGTACCTCCAGGCGAACCA	60.229	57.895	0.00	0.00	39.06	3.67
1822	2672	2.430382	GAACCAGTGACGCGGGAAGA	62.430	60.000	12.47	0.00	36.26	2.87
1828	2678	2.261671	GACGCGGGAAGAAGCAGA	59.738	61.111	12.47	0.00	0.00	4.26
1994	2846	3.730761	GGCAAGCTCGTGTGGCTG	61.731	66.667	2.60	0.00	40.19	4.85
2112	2966	5.306114	TCTGGTATCAGAGACCTTCGATA	57.694	43.478	15.41	0.00	44.39	2.92
2286	3141	3.899981	AAGGCCATCGCGCAACTCA	62.900	57.895	8.75	0.00	35.02	3.41
2363	3218	1.511254	CGACATCGACGAACTGCGA	60.511	57.895	0.00	0.00	44.66	5.10
2424	3303	0.886490	CGCACCTGCAACTCCTTCTT	60.886	55.000	0.00	0.00	42.21	2.52
2449	3328	0.690192	TCAGGCCACAATTCTTCCGA	59.310	50.000	5.01	0.00	0.00	4.55
2465	3344	1.226688	CGATTCTGAAGCGCTCCGA	60.227	57.895	12.06	4.55	31.82	4.55
2495	3374	2.439553	AAAATCGGGGCCCTGCTCAA	62.440	55.000	27.42	9.27	0.00	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	5.233988	AGAACAGAATAGATATGCGCTTCC	58.766	41.667	9.73	0.00	0.00	3.46
142	144	6.313519	TCTAGCTAGTCATTCCCAACAAAT	57.686	37.500	20.10	0.00	0.00	2.32
190	192	4.080751	CCAATCCAAGAAAAGCATCCCAAT	60.081	41.667	0.00	0.00	0.00	3.16
191	193	3.261390	CCAATCCAAGAAAAGCATCCCAA	59.739	43.478	0.00	0.00	0.00	4.12
276	278	1.968493	GGAGGGAGTACAACACAGACA	59.032	52.381	0.00	0.00	0.00	3.41
304	306	4.761739	TCCCAAAAGCTTGAGACACTTATG	59.238	41.667	0.00	0.00	34.14	1.90
311	313	0.875059	CCGTCCCAAAAGCTTGAGAC	59.125	55.000	0.00	4.10	37.04	3.36
330	332	7.711339	CACAATTTTCATACCTAGTACTCCCTC	59.289	40.741	0.00	0.00	0.00	4.30
357	359	4.846940	AGTAGGGGTCCCAGAAATATCATC	59.153	45.833	10.98	0.00	38.92	2.92
369	372	2.090663	ACTCCAGAATAGTAGGGGTCCC	60.091	54.545	0.00	0.00	27.09	4.46
392	395	2.027745	ACAACAACAACAACATTGCCCA	60.028	40.909	0.00	0.00	0.00	5.36
395	398	4.636975	GACAACAACAACAACAACATTGC	58.363	39.130	0.00	0.00	0.00	3.56
396	399	4.201570	CCGACAACAACAACAACAACATTG	60.202	41.667	0.00	0.00	0.00	2.82
417	423	2.478134	CTCTTTGTTTCTGCTGACTCCG	59.522	50.000	0.00	0.00	0.00	4.63
596	605	3.769844	TCACACTCTGATTTCTACTCCCC	59.230	47.826	0.00	0.00	0.00	4.81
625	634	0.696501	AGGCACAATTCCTTACCGGT	59.303	50.000	13.98	13.98	0.00	5.28
631	640	2.683211	AGGTTCAGGCACAATTCCTT	57.317	45.000	0.00	0.00	0.00	3.36
632	641	3.624777	CATAGGTTCAGGCACAATTCCT	58.375	45.455	0.00	0.00	0.00	3.36
636	645	1.382522	CGCATAGGTTCAGGCACAAT	58.617	50.000	0.00	0.00	0.00	2.71
709	1357	4.456222	GCTGGGAGTTCCTTCTTAGTTTTC	59.544	45.833	0.00	0.00	36.20	2.29
710	1358	4.399219	GCTGGGAGTTCCTTCTTAGTTTT	58.601	43.478	0.00	0.00	36.20	2.43
711	1359	3.557264	CGCTGGGAGTTCCTTCTTAGTTT	60.557	47.826	0.00	0.00	36.20	2.66
737	1391	0.863119	GATCAAACGGCTGCGATTGC	60.863	55.000	0.00	0.00	43.20	3.56
738	1392	0.447406	TGATCAAACGGCTGCGATTG	59.553	50.000	0.00	0.00	0.00	2.67
739	1393	1.131126	CTTGATCAAACGGCTGCGATT	59.869	47.619	9.88	0.00	0.00	3.34
740	1394	0.729116	CTTGATCAAACGGCTGCGAT	59.271	50.000	9.88	0.00	0.00	4.58
811	1465	3.876274	TTCTGGAGACTAGCATGACAC	57.124	47.619	0.00	0.00	0.00	3.67
853	1521	2.086869	AGGATGGCAATCACGAACAAG	58.913	47.619	2.85	0.00	34.17	3.16
915	1689	6.362248	TCCTCCAATTACTTATTTAGTGCCC	58.638	40.000	0.00	0.00	37.73	5.36
928	1708	7.225011	CCTCCTTTACCTTATCCTCCAATTAC	58.775	42.308	0.00	0.00	0.00	1.89
1245	2084	3.838271	GTCTCCATCGCCCGCAGA	61.838	66.667	0.00	0.00	0.00	4.26
1317	2156	0.452184	CGATGTACACGAGCTGGTCT	59.548	55.000	0.00	0.00	0.00	3.85
1512	2351	1.826024	CAGGATTCGTCCAGGAGGG	59.174	63.158	9.35	0.00	34.83	4.30
1562	2401	5.622687	GCTTCAGTGAACTAGTAGAAGGACC	60.623	48.000	3.59	0.00	34.57	4.46
1567	2406	6.150318	CGAAAGCTTCAGTGAACTAGTAGAA	58.850	40.000	3.59	0.00	0.00	2.10
1610	2453	7.064229	TGGTAAACAAAAGGAAATACTGGAGT	58.936	34.615	0.00	0.00	0.00	3.85
1611	2454	7.519032	TGGTAAACAAAAGGAAATACTGGAG	57.481	36.000	0.00	0.00	0.00	3.86
1612	2455	9.589461	TTATGGTAAACAAAAGGAAATACTGGA	57.411	29.630	0.00	0.00	0.00	3.86
1638	2481	1.291033	TGTCCCAGGCTAGGAGTGTAT	59.709	52.381	0.50	0.00	32.84	2.29
1639	2482	0.708209	TGTCCCAGGCTAGGAGTGTA	59.292	55.000	0.50	0.00	32.84	2.90
1640	2483	0.178903	TTGTCCCAGGCTAGGAGTGT	60.179	55.000	0.50	0.00	32.84	3.55
1641	2484	0.539051	CTTGTCCCAGGCTAGGAGTG	59.461	60.000	0.50	0.00	32.84	3.51
1660	2503	8.454106	TCAAACGACTAGGAAATACAGTACTAC	58.546	37.037	0.00	0.00	0.00	2.73
1661	2504	8.565896	TCAAACGACTAGGAAATACAGTACTA	57.434	34.615	0.00	0.00	0.00	1.82
1664	2507	7.458409	ACTCAAACGACTAGGAAATACAGTA	57.542	36.000	0.00	0.00	0.00	2.74
1666	2509	6.866770	TGAACTCAAACGACTAGGAAATACAG	59.133	38.462	0.00	0.00	0.00	2.74
1744	2594	0.393132	GAAGGAGGGCTACCAGCAAC	60.393	60.000	0.00	0.00	44.75	4.17
1808	2658	2.048127	GCTTCTTCCCGCGTCACT	60.048	61.111	4.92	0.00	0.00	3.41
1822	2672	0.678048	GGCCGGAACTTGATCTGCTT	60.678	55.000	5.05	0.00	0.00	3.91
1828	2678	2.044946	GCCTGGCCGGAACTTGAT	60.045	61.111	15.09	0.00	33.16	2.57
1984	2836	1.666011	GAGTTCCTCAGCCACACGA	59.334	57.895	0.00	0.00	0.00	4.35
1994	2846	0.105913	AGGAGGGGATCGAGTTCCTC	60.106	60.000	17.39	17.39	43.65	3.71
2282	3137	1.664965	GTCGAGCTTGGCGTTGAGT	60.665	57.895	0.00	0.00	0.00	3.41
2286	3141	2.048127	GAGGTCGAGCTTGGCGTT	60.048	61.111	19.66	0.00	0.00	4.84
2363	3218	0.034059	CAGGCTTGTCGAACTCCTGT	59.966	55.000	13.17	0.00	39.45	4.00
2424	3303	0.955428	GAATTGTGGCCTGACGCTCA	60.955	55.000	3.32	0.00	37.74	4.26
2449	3328	0.749649	AGATCGGAGCGCTTCAGAAT	59.250	50.000	17.68	5.68	33.65	2.40
2465	3344	1.133976	CCCCGATTTTCAGCCTCAGAT	60.134	52.381	0.00	0.00	0.00	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.