AutoCloner

Multiple sequence alignment - TraesCS2D01G350100

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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	TraesCS2D01G350100	chr2D	100.000	2516	0	0	1	2516	447839038	447841553	0.000000e+00	4647.0
1	TraesCS2D01G350100	chr2D	85.658	760	32	28	1	730	59651752	59652464	0.000000e+00	728.0
2	TraesCS2D01G350100	chr2A	91.701	1711	81	20	836	2516	592454027	592455706	0.000000e+00	2316.0
3	TraesCS2D01G350100	chr2B	91.410	1234	48	24	800	2025	527586956	527588139	0.000000e+00	1639.0
4	TraesCS2D01G350100	chr2B	86.706	850	48	19	1	800	707654675	707653841	0.000000e+00	883.0
5	TraesCS2D01G350100	chr2B	84.368	467	46	19	2059	2515	527588140	527588589	1.380000e-117	433.0
6	TraesCS2D01G350100	chr7D	88.862	817	48	20	1	787	229273731	229272928	0.000000e+00	965.0
7	TraesCS2D01G350100	chr5A	85.181	830	72	31	1	799	60521616	60520807	0.000000e+00	804.0
8	TraesCS2D01G350100	chr5A	84.549	809	75	30	1	799	606522818	606522050	0.000000e+00	756.0
9	TraesCS2D01G350100	chr1A	83.354	817	92	32	1	803	153914111	153913325	0.000000e+00	715.0
10	TraesCS2D01G350100	chr1A	88.889	162	18	0	1078	1239	560372741	560372902	1.530000e-47	200.0
11	TraesCS2D01G350100	chrUn	84.712	713	60	20	81	778	401155176	401155854	0.000000e+00	667.0
12	TraesCS2D01G350100	chrUn	84.572	713	61	20	81	778	387526004	387526682	0.000000e+00	662.0
13	TraesCS2D01G350100	chr4A	88.235	561	39	21	1	550	548312012	548311468	0.000000e+00	645.0
14	TraesCS2D01G350100	chr3A	83.391	578	46	26	40	604	689388271	689387731	8.090000e-135	490.0
15	TraesCS2D01G350100	chr3A	96.000	75	2	1	726	800	689387308	689387235	1.220000e-23	121.0
16	TraesCS2D01G350100	chr7B	93.976	83	5	0	1078	1160	738151604	738151522	2.630000e-25	126.0
17	TraesCS2D01G350100	chr6A	100.000	31	0	0	769	799	432249390	432249360	9.720000e-05	58.4

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	TraesCS2D01G350100	chr2D	447839038	447841553	2515	False	4647.0	4647	100.0000	1	2516	1	chr2D.!!$F2	2515
1	TraesCS2D01G350100	chr2D	59651752	59652464	712	False	728.0	728	85.6580	1	730	1	chr2D.!!$F1	729
2	TraesCS2D01G350100	chr2A	592454027	592455706	1679	False	2316.0	2316	91.7010	836	2516	1	chr2A.!!$F1	1680
3	TraesCS2D01G350100	chr2B	527586956	527588589	1633	False	1036.0	1639	87.8890	800	2515	2	chr2B.!!$F1	1715
4	TraesCS2D01G350100	chr2B	707653841	707654675	834	True	883.0	883	86.7060	1	800	1	chr2B.!!$R1	799
5	TraesCS2D01G350100	chr7D	229272928	229273731	803	True	965.0	965	88.8620	1	787	1	chr7D.!!$R1	786
6	TraesCS2D01G350100	chr5A	60520807	60521616	809	True	804.0	804	85.1810	1	799	1	chr5A.!!$R1	798
7	TraesCS2D01G350100	chr5A	606522050	606522818	768	True	756.0	756	84.5490	1	799	1	chr5A.!!$R2	798
8	TraesCS2D01G350100	chr1A	153913325	153914111	786	True	715.0	715	83.3540	1	803	1	chr1A.!!$R1	802
9	TraesCS2D01G350100	chrUn	401155176	401155854	678	False	667.0	667	84.7120	81	778	1	chrUn.!!$F2	697
10	TraesCS2D01G350100	chrUn	387526004	387526682	678	False	662.0	662	84.5720	81	778	1	chrUn.!!$F1	697
11	TraesCS2D01G350100	chr4A	548311468	548312012	544	True	645.0	645	88.2350	1	550	1	chr4A.!!$R1	549
12	TraesCS2D01G350100	chr3A	689387235	689388271	1036	True	305.5	490	89.6955	40	800	2	chr3A.!!$R1	760

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
926	1348	0.684153	GGAGGCCTGCCAAATAAGCA	60.684	55.0	12.0	0.0	38.92	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2032	2460	0.819582	GCCTGGTTGATGTTCATGGG	59.18	55.0	0.0	0.0	0.0	4.0	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
465	563	5.814705	TGAACTTTTTGGCAAATTCGACAAT	59.185	32.000	14.29	0.00	32.78	2.71
597	701	9.268268	GTACATACTGTAGCAATTTAGCCATAA	57.732	33.333	0.00	0.00	32.84	1.90
627	731	1.001597	GTACTACAATCGAGGGGAGCG	60.002	57.143	0.00	0.00	0.00	5.03
628	732	1.364171	CTACAATCGAGGGGAGCGG	59.636	63.158	0.00	0.00	0.00	5.52
818	1231	3.324035	GCAGAAGGCGCCGAATAG	58.676	61.111	23.20	12.61	0.00	1.73
926	1348	0.684153	GGAGGCCTGCCAAATAAGCA	60.684	55.000	12.00	0.00	38.92	3.91
1247	1669	0.447011	GTAGACTCTGCGCTACGTGT	59.553	55.000	9.73	4.11	0.00	4.49
1401	1823	4.530857	CTCGGGGTGGCCATCGTC	62.531	72.222	9.72	2.81	0.00	4.20
1536	1958	6.369065	GCACAATAAACTGCTTGTACTACTCT	59.631	38.462	0.00	0.00	33.96	3.24
1587	2009	8.294577	TGCGTAGTATGGTCAGTATAAATACAG	58.705	37.037	3.13	0.00	35.74	2.74
1588	2010	8.295288	GCGTAGTATGGTCAGTATAAATACAGT	58.705	37.037	3.13	0.00	35.74	3.55
1700	2122	4.817318	AACTTCAGAATCTCCAGGTCTC	57.183	45.455	0.00	0.00	0.00	3.36
1740	2162	1.610522	GCTCAACAAAGTGAGTGCCAT	59.389	47.619	4.28	0.00	45.75	4.40
1762	2184	4.806330	TCCTATCAAAGTGACGTCTGTTC	58.194	43.478	17.92	4.95	0.00	3.18
1778	2200	3.135348	TCTGTTCCTCTGCTTCCATATGG	59.865	47.826	16.25	16.25	0.00	2.74
1791	2213	2.156098	ATATGGTCCAGGCCGCCAT	61.156	57.895	21.55	21.55	44.35	4.40
1799	2221	4.923942	AGGCCGCCATGATCGCAG	62.924	66.667	13.15	0.00	0.00	5.18
1814	2236	2.493035	TCGCAGCTTCTTTGAACATGA	58.507	42.857	0.00	0.00	0.00	3.07
1833	2256	0.179936	ACCTGATGCCAGCTTCTAGC	59.820	55.000	7.02	0.00	42.84	3.42
1843	2266	1.118356	AGCTTCTAGCCGCCATAGCT	61.118	55.000	0.00	0.00	43.77	3.32
1933	2361	9.869757	TGAACTCATATTCGAAGAATAAGTGAA	57.130	29.630	3.35	0.00	45.90	3.18
2017	2445	1.485895	GCCTCCTGCAGAGAAGATTCT	59.514	52.381	17.39	0.00	46.50	2.40
2025	2453	5.009410	CCTGCAGAGAAGATTCTTTGTGTTT	59.991	40.000	17.39	0.00	40.44	2.83
2030	2458	7.172361	GCAGAGAAGATTCTTTGTGTTTACTCT	59.828	37.037	12.95	2.78	40.44	3.24
2032	2460	9.699703	AGAGAAGATTCTTTGTGTTTACTCTAC	57.300	33.333	0.00	0.00	37.73	2.59
2071	2499	3.456280	GCAAAAACCTTGTGCTTCATCA	58.544	40.909	0.00	0.00	35.36	3.07
2072	2500	4.060205	GCAAAAACCTTGTGCTTCATCAT	58.940	39.130	0.00	0.00	35.36	2.45
2073	2501	5.229423	GCAAAAACCTTGTGCTTCATCATA	58.771	37.500	0.00	0.00	35.36	2.15
2074	2502	5.119125	GCAAAAACCTTGTGCTTCATCATAC	59.881	40.000	0.00	0.00	35.36	2.39
2160	2588	4.742438	TGTAGGATTTGTTTCGCTTGAC	57.258	40.909	0.00	0.00	0.00	3.18
2170	2598	3.563390	TGTTTCGCTTGACATTGACATCA	59.437	39.130	0.00	0.00	0.00	3.07
2172	2600	2.765122	TCGCTTGACATTGACATCACA	58.235	42.857	0.00	0.00	0.00	3.58
2207	2637	3.553922	CCGTTCATCAGCCTTAGAGGATC	60.554	52.174	0.00	0.00	37.67	3.36
2210	2640	4.679373	TCATCAGCCTTAGAGGATCAAC	57.321	45.455	0.00	0.00	37.67	3.18
2211	2641	4.293494	TCATCAGCCTTAGAGGATCAACT	58.707	43.478	0.00	0.00	37.67	3.16
2220	2650	7.292120	AGCCTTAGAGGATCAACTGAGATATTT	59.708	37.037	10.26	0.00	37.67	1.40
2221	2651	7.387397	GCCTTAGAGGATCAACTGAGATATTTG	59.613	40.741	10.26	0.00	37.67	2.32
2222	2652	8.428063	CCTTAGAGGATCAACTGAGATATTTGT	58.572	37.037	10.26	0.00	37.67	2.83
2225	2655	8.774546	AGAGGATCAACTGAGATATTTGTAGA	57.225	34.615	0.00	0.00	37.82	2.59
2226	2656	9.206690	AGAGGATCAACTGAGATATTTGTAGAA	57.793	33.333	0.00	0.00	37.82	2.10
2227	2657	9.995003	GAGGATCAACTGAGATATTTGTAGAAT	57.005	33.333	0.00	0.00	33.17	2.40
2231	2661	9.823647	ATCAACTGAGATATTTGTAGAATTCGT	57.176	29.630	0.00	0.00	0.00	3.85
2242	2672	5.759506	TGTAGAATTCGTTTGGCTTTTCA	57.240	34.783	0.00	0.00	0.00	2.69
2254	2684	1.202818	GGCTTTTCAGTCACCACCTCT	60.203	52.381	0.00	0.00	0.00	3.69
2255	2685	1.876156	GCTTTTCAGTCACCACCTCTG	59.124	52.381	0.00	0.00	0.00	3.35
2287	2719	3.077359	AGCTTGAATAGACAGTGGCAAC	58.923	45.455	0.00	0.00	0.00	4.17
2371	2806	4.839174	GCAAACGAAAAGAGACAACGATAC	59.161	41.667	0.00	0.00	0.00	2.24
2390	2826	1.751924	ACGAGTCTTGCATAGTCCCTC	59.248	52.381	0.00	0.00	0.00	4.30
2411	2847	1.676014	GGTGTCCCACAGATCTTTCCG	60.676	57.143	0.00	0.00	35.86	4.30
2450	2902	2.074967	CCCCAGGCCTCTGTAAACA	58.925	57.895	0.00	0.00	39.31	2.83
2479	2931	1.970917	GAGAAGATGTTGCGCCACCG	61.971	60.000	9.38	0.00	37.57	4.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
68	70	8.373992	CGGTTTTGAAAAAGTTCGTTCAATTTA	58.626	29.630	12.84	0.50	41.90	1.40
186	208	8.950208	AAAAAGTTCATCCGATTTGGTAAAAA	57.050	26.923	0.00	0.00	39.52	1.94
391	465	5.854338	TGAAAAATAGTTCGTCGAATTTGCC	59.146	36.000	11.45	0.00	0.00	4.52
392	466	6.795114	TCTGAAAAATAGTTCGTCGAATTTGC	59.205	34.615	11.45	6.86	0.00	3.68
399	494	8.880768	AATTGAATCTGAAAAATAGTTCGTCG	57.119	30.769	0.00	0.00	0.00	5.12
604	708	3.470709	CTCCCCTCGATTGTAGTACGTA	58.529	50.000	0.00	0.00	0.00	3.57
606	710	1.001597	GCTCCCCTCGATTGTAGTACG	60.002	57.143	0.00	0.00	0.00	3.67
607	711	1.001597	CGCTCCCCTCGATTGTAGTAC	60.002	57.143	0.00	0.00	0.00	2.73
608	712	1.315690	CGCTCCCCTCGATTGTAGTA	58.684	55.000	0.00	0.00	0.00	1.82
609	713	1.392710	CCGCTCCCCTCGATTGTAGT	61.393	60.000	0.00	0.00	0.00	2.73
610	714	1.364171	CCGCTCCCCTCGATTGTAG	59.636	63.158	0.00	0.00	0.00	2.74
611	715	2.131709	CCCGCTCCCCTCGATTGTA	61.132	63.158	0.00	0.00	0.00	2.41
837	1252	9.921637	TGTAATTGTCAAATTCCTTTTACATCC	57.078	29.630	2.88	0.00	37.23	3.51
916	1338	4.501071	AGATTTTGCAGCTGCTTATTTGG	58.499	39.130	36.61	0.00	42.66	3.28
926	1348	2.191128	ACTTCGGAGATTTTGCAGCT	57.809	45.000	0.00	0.00	35.04	4.24
1242	1664	0.034059	CTTCCAAGCCAGAGACACGT	59.966	55.000	0.00	0.00	0.00	4.49
1245	1667	1.376466	GCCTTCCAAGCCAGAGACA	59.624	57.895	0.00	0.00	0.00	3.41
1247	1669	2.665000	CGCCTTCCAAGCCAGAGA	59.335	61.111	0.00	0.00	0.00	3.10
1501	1923	6.615088	AGCAGTTTATTGTGCAGATTTACAG	58.385	36.000	0.00	0.00	42.47	2.74
1536	1958	9.159364	CAAGAAACATCTCTTCAGATTACATCA	57.841	33.333	0.00	0.00	37.25	3.07
1587	2009	8.475639	TCCTGTTGTTGGTAATCTCTCTTATAC	58.524	37.037	0.00	0.00	0.00	1.47
1588	2010	8.603898	TCCTGTTGTTGGTAATCTCTCTTATA	57.396	34.615	0.00	0.00	0.00	0.98
1589	2011	7.400339	TCTCCTGTTGTTGGTAATCTCTCTTAT	59.600	37.037	0.00	0.00	0.00	1.73
1590	2012	6.724441	TCTCCTGTTGTTGGTAATCTCTCTTA	59.276	38.462	0.00	0.00	0.00	2.10
1602	2024	1.065854	CCTAGGCTCTCCTGTTGTTGG	60.066	57.143	0.00	0.00	44.08	3.77
1700	2122	3.513515	AGCTGGAAGAGAGGACTAACTTG	59.486	47.826	0.00	0.00	34.07	3.16
1740	2162	4.321750	GGAACAGACGTCACTTTGATAGGA	60.322	45.833	19.50	0.00	0.00	2.94
1762	2184	1.770658	TGGACCATATGGAAGCAGAGG	59.229	52.381	28.77	0.00	38.94	3.69
1778	2200	2.592861	GATCATGGCGGCCTGGAC	60.593	66.667	21.46	0.00	0.00	4.02
1791	2213	2.493035	TGTTCAAAGAAGCTGCGATCA	58.507	42.857	10.35	0.00	0.00	2.92
1799	2221	4.730657	CATCAGGTCATGTTCAAAGAAGC	58.269	43.478	0.00	0.00	0.00	3.86
1833	2256	1.067283	CAGGAGTGATAGCTATGGCGG	60.067	57.143	11.94	0.00	44.37	6.13
1843	2266	3.117131	TCCAGAGGTATGCAGGAGTGATA	60.117	47.826	0.00	0.00	0.00	2.15
1874	2302	4.704057	GCTGGGGGATCTTGAATATTCATC	59.296	45.833	18.61	12.96	37.00	2.92
2017	2445	6.358178	TGTTCATGGGTAGAGTAAACACAAA	58.642	36.000	0.00	0.00	33.11	2.83
2025	2453	4.780554	TGGTTGATGTTCATGGGTAGAGTA	59.219	41.667	0.00	0.00	0.00	2.59
2030	2458	2.620367	GCCTGGTTGATGTTCATGGGTA	60.620	50.000	0.00	0.00	0.00	3.69
2032	2460	0.819582	GCCTGGTTGATGTTCATGGG	59.180	55.000	0.00	0.00	0.00	4.00
2071	2499	5.670792	TCTGGAAATCCAAGTGTACGTAT	57.329	39.130	0.00	0.00	46.97	3.06
2072	2500	5.416083	CATCTGGAAATCCAAGTGTACGTA	58.584	41.667	3.35	0.00	46.97	3.57
2073	2501	4.253685	CATCTGGAAATCCAAGTGTACGT	58.746	43.478	3.35	0.00	46.97	3.57
2074	2502	3.623060	CCATCTGGAAATCCAAGTGTACG	59.377	47.826	3.35	0.00	46.97	3.67
2153	2581	2.413239	GGTGTGATGTCAATGTCAAGCG	60.413	50.000	0.00	0.00	0.00	4.68
2160	2588	6.499234	TTATCTGTTGGTGTGATGTCAATG	57.501	37.500	0.00	0.00	0.00	2.82
2170	2598	4.280436	TGAACGGATTATCTGTTGGTGT	57.720	40.909	22.37	0.00	45.29	4.16
2172	2600	5.097742	TGATGAACGGATTATCTGTTGGT	57.902	39.130	22.37	11.30	45.29	3.67
2210	2640	7.852945	GCCAAACGAATTCTACAAATATCTCAG	59.147	37.037	3.52	0.00	0.00	3.35
2211	2641	7.552687	AGCCAAACGAATTCTACAAATATCTCA	59.447	33.333	3.52	0.00	0.00	3.27
2220	2650	5.298276	ACTGAAAAGCCAAACGAATTCTACA	59.702	36.000	3.52	0.00	0.00	2.74
2221	2651	5.758924	ACTGAAAAGCCAAACGAATTCTAC	58.241	37.500	3.52	0.00	0.00	2.59
2222	2652	5.529430	TGACTGAAAAGCCAAACGAATTCTA	59.471	36.000	3.52	0.00	0.00	2.10
2223	2653	4.338118	TGACTGAAAAGCCAAACGAATTCT	59.662	37.500	3.52	0.00	0.00	2.40
2224	2654	4.441087	GTGACTGAAAAGCCAAACGAATTC	59.559	41.667	0.00	0.00	0.00	2.17
2225	2655	4.359706	GTGACTGAAAAGCCAAACGAATT	58.640	39.130	0.00	0.00	0.00	2.17
2226	2656	3.243401	GGTGACTGAAAAGCCAAACGAAT	60.243	43.478	0.00	0.00	0.00	3.34
2227	2657	2.098443	GGTGACTGAAAAGCCAAACGAA	59.902	45.455	0.00	0.00	0.00	3.85
2228	2658	1.673920	GGTGACTGAAAAGCCAAACGA	59.326	47.619	0.00	0.00	0.00	3.85
2229	2659	1.403679	TGGTGACTGAAAAGCCAAACG	59.596	47.619	0.00	0.00	0.00	3.60
2230	2660	2.481276	GGTGGTGACTGAAAAGCCAAAC	60.481	50.000	0.00	0.00	0.00	2.93
2231	2661	1.754226	GGTGGTGACTGAAAAGCCAAA	59.246	47.619	0.00	0.00	0.00	3.28
2234	2664	1.202818	AGAGGTGGTGACTGAAAAGCC	60.203	52.381	0.00	0.00	0.00	4.35
2254	2684	6.437477	TGTCTATTCAAGCTAGAGAAGAACCA	59.563	38.462	0.00	0.00	0.00	3.67
2255	2685	6.868622	TGTCTATTCAAGCTAGAGAAGAACC	58.131	40.000	0.00	0.00	0.00	3.62
2371	2806	1.268794	CGAGGGACTATGCAAGACTCG	60.269	57.143	17.37	17.37	41.55	4.18
2411	2847	0.914417	TGGGGACACCATCCTTCTCC	60.914	60.000	0.00	0.00	46.80	3.71
2450	2902	4.205587	GCAACATCTTCTCCTTGATGGAT	58.794	43.478	7.69	0.00	45.16	3.41
2479	2931	1.074951	CCCAGGTGTGGTTCCTTCC	59.925	63.158	0.00	0.00	43.23	3.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.