AutoCloner

Multiple sequence alignment - TraesCS5B01G162800

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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	TraesCS5B01G162800	chr5B	100.000	2653	0	0	1	2653	300099176	300096524	0.000000e+00	4900.0
1	TraesCS5B01G162800	chr5B	94.859	1245	52	7	646	1879	299847105	299848348	0.000000e+00	1934.0
2	TraesCS5B01G162800	chr5B	95.833	48	2	0	558	605	299847002	299847049	7.870000e-11	78.7
3	TraesCS5B01G162800	chr5D	95.134	1418	61	6	1242	2653	266325798	266324383	0.000000e+00	2230.0
4	TraesCS5B01G162800	chr5D	94.426	1184	56	3	704	1879	266085494	266086675	0.000000e+00	1812.0
5	TraesCS5B01G162800	chr5D	87.531	1227	81	30	26	1217	266326983	266325794	0.000000e+00	1352.0
6	TraesCS5B01G162800	chr5D	89.324	281	24	5	490	768	266085220	266085496	5.440000e-92	348.0
7	TraesCS5B01G162800	chr5A	91.981	1459	94	17	1215	2652	353988794	353990250	0.000000e+00	2025.0
8	TraesCS5B01G162800	chr5A	94.208	1174	49	6	724	1882	354315816	354314647	0.000000e+00	1773.0
9	TraesCS5B01G162800	chr5A	91.128	1206	64	18	1	1194	353987514	353988688	0.000000e+00	1594.0
10	TraesCS5B01G162800	chr5A	91.556	225	18	1	503	727	354316252	354316029	2.560000e-80	309.0
11	TraesCS5B01G162800	chr2A	93.798	387	22	2	1270	1655	30072292	30071907	4.920000e-162	580.0
12	TraesCS5B01G162800	chr2A	93.282	387	24	2	1270	1655	30021208	30020823	1.070000e-158	569.0
13	TraesCS5B01G162800	chr2A	88.889	153	17	0	998	1150	30127269	30127117	3.490000e-44	189.0
14	TraesCS5B01G162800	chr2A	87.582	153	19	0	998	1150	30086811	30086659	7.550000e-41	178.0
15	TraesCS5B01G162800	chr2A	86.735	98	11	2	1927	2022	607644273	607644370	1.000000e-19	108.0
16	TraesCS5B01G162800	chr2D	93.540	387	23	2	1270	1655	27860337	27859952	2.290000e-160	575.0
17	TraesCS5B01G162800	chr2D	93.023	387	25	2	1270	1655	27853934	27853549	4.960000e-157	564.0
18	TraesCS5B01G162800	chr2D	79.365	315	51	11	1	305	639590215	639589905	2.680000e-50	209.0
19	TraesCS5B01G162800	chr1A	85.570	298	35	6	1	291	267790739	267790443	3.320000e-79	305.0
20	TraesCS5B01G162800	chr7A	82.390	318	42	6	1	305	9409631	9409947	5.630000e-67	265.0
21	TraesCS5B01G162800	chr7A	90.123	81	7	1	1929	2008	679814700	679814620	1.300000e-18	104.0
22	TraesCS5B01G162800	chr7B	82.274	299	43	7	1	291	633915692	633915396	1.580000e-62	250.0
23	TraesCS5B01G162800	chr4D	82.119	302	45	4	1	293	439750176	439750477	1.580000e-62	250.0
24	TraesCS5B01G162800	chr3B	83.273	275	43	3	1	274	103026786	103027058	1.580000e-62	250.0
25	TraesCS5B01G162800	chr3B	85.417	96	12	2	1926	2019	708604892	708604987	6.040000e-17	99.0
26	TraesCS5B01G162800	chr1B	81.433	307	53	4	1	305	542176497	542176193	5.670000e-62	248.0
27	TraesCS5B01G162800	chr7D	81.132	318	45	6	1	304	9373705	9374021	9.490000e-60	241.0
28	TraesCS5B01G162800	chrUn	80.503	318	48	9	1	305	282757699	282758015	5.710000e-57	231.0
29	TraesCS5B01G162800	chrUn	80.503	318	48	9	1	305	291518798	291518482	5.710000e-57	231.0
30	TraesCS5B01G162800	chr2B	88.235	153	18	0	998	1150	44361838	44361686	1.620000e-42	183.0
31	TraesCS5B01G162800	chr3D	90.123	81	7	1	1929	2008	67481232	67481312	1.300000e-18	104.0
32	TraesCS5B01G162800	chr6A	86.458	96	10	3	1929	2022	537876933	537877027	4.670000e-18	102.0
33	TraesCS5B01G162800	chr6A	82.927	82	13	1	224	305	14299649	14299569	3.660000e-09	73.1
34	TraesCS5B01G162800	chr4B	85.417	96	13	1	1929	2023	668552787	668552692	6.040000e-17	99.0
35	TraesCS5B01G162800	chr4B	85.417	96	13	1	1929	2023	668933581	668933486	6.040000e-17	99.0
36	TraesCS5B01G162800	chr4B	85.417	96	13	1	1929	2023	669511786	669511691	6.040000e-17	99.0

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	TraesCS5B01G162800	chr5B	300096524	300099176	2652	True	4900.00	4900	100.0000	1	2653	1	chr5B.!!$R1	2652
1	TraesCS5B01G162800	chr5B	299847002	299848348	1346	False	1006.35	1934	95.3460	558	1879	2	chr5B.!!$F1	1321
2	TraesCS5B01G162800	chr5D	266324383	266326983	2600	True	1791.00	2230	91.3325	26	2653	2	chr5D.!!$R1	2627
3	TraesCS5B01G162800	chr5D	266085220	266086675	1455	False	1080.00	1812	91.8750	490	1879	2	chr5D.!!$F1	1389
4	TraesCS5B01G162800	chr5A	353987514	353990250	2736	False	1809.50	2025	91.5545	1	2652	2	chr5A.!!$F1	2651
5	TraesCS5B01G162800	chr5A	354314647	354316252	1605	True	1041.00	1773	92.8820	503	1882	2	chr5A.!!$R1	1379

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
366	409	0.170561	CAAGTAGCTAGTGACGCCGT	59.829	55.0	0.73	0.0	0.0	5.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2022	2510	0.971386	AACGTCCAACCGTCCACTAT	59.029	50.0	0.0	0.0	40.85	2.12	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
31	32	3.013219	GGAAGGAATTGTTCTGAGAGCC	58.987	50.000	0.00	0.00	0.00	4.70
35	36	0.693049	AATTGTTCTGAGAGCCCGGT	59.307	50.000	0.00	0.00	0.00	5.28
53	54	2.290323	CGGTCTTCTCCAGGGTGAAAAT	60.290	50.000	4.57	0.00	0.00	1.82
61	62	6.240549	TCTCCAGGGTGAAAATCTAAGATC	57.759	41.667	0.00	0.00	0.00	2.75
80	81	0.389817	CTTGGATCAGGCAACGACGA	60.390	55.000	0.00	0.00	46.39	4.20
101	102	2.159114	ACGCTTGTGCATTGTTTCCTTT	60.159	40.909	0.00	0.00	39.64	3.11
137	138	8.419076	TGCTTTTGAAGACCTTTTATGTTTTC	57.581	30.769	0.00	0.00	0.00	2.29
152	153	4.260139	TGTTTTCCGTGTGCTGTATCTA	57.740	40.909	0.00	0.00	0.00	1.98
163	164	3.684788	GTGCTGTATCTAGTGGTGGTTTG	59.315	47.826	0.00	0.00	0.00	2.93
173	174	2.655044	GTGGTTTGTGTGCGCTGC	60.655	61.111	9.73	1.68	0.00	5.25
190	191	2.158928	GCTGCTGAGAGGAGTTGATCAT	60.159	50.000	0.00	0.00	35.94	2.45
198	199	3.584406	AGAGGAGTTGATCATTGTGGTGA	59.416	43.478	0.00	0.00	0.00	4.02
206	207	4.074259	TGATCATTGTGGTGAGACCTTTG	58.926	43.478	0.00	0.00	39.58	2.77
212	213	6.378564	TCATTGTGGTGAGACCTTTGTTTTTA	59.621	34.615	0.00	0.00	39.58	1.52
216	225	8.294954	TGTGGTGAGACCTTTGTTTTTATTTA	57.705	30.769	0.00	0.00	39.58	1.40
239	248	2.363306	TCCTTTGGTTGTGTGCATCT	57.637	45.000	0.00	0.00	0.00	2.90
242	251	2.361757	CCTTTGGTTGTGTGCATCTTGA	59.638	45.455	0.00	0.00	0.00	3.02
273	282	3.435275	AGACATCTTGTAGGTGCAGAGA	58.565	45.455	0.00	0.00	0.00	3.10
296	305	9.073475	GAGACTGAGTGTAATAGGTATCTTCAT	57.927	37.037	0.00	0.00	0.00	2.57
357	400	2.430546	CGGGAGCATCAAGTAGCTAG	57.569	55.000	0.00	0.00	42.04	3.42
358	401	1.683917	CGGGAGCATCAAGTAGCTAGT	59.316	52.381	0.00	0.00	42.04	2.57
359	402	2.544694	CGGGAGCATCAAGTAGCTAGTG	60.545	54.545	0.73	0.00	42.04	2.74
360	403	2.695666	GGGAGCATCAAGTAGCTAGTGA	59.304	50.000	0.73	5.69	42.04	3.41
361	404	3.491792	GGGAGCATCAAGTAGCTAGTGAC	60.492	52.174	0.73	0.00	42.04	3.67
362	405	3.367607	GAGCATCAAGTAGCTAGTGACG	58.632	50.000	0.73	0.00	42.04	4.35
363	406	1.855360	GCATCAAGTAGCTAGTGACGC	59.145	52.381	9.02	9.02	0.00	5.19
364	407	2.464865	CATCAAGTAGCTAGTGACGCC	58.535	52.381	0.73	0.00	0.00	5.68
365	408	0.450583	TCAAGTAGCTAGTGACGCCG	59.549	55.000	0.73	0.00	0.00	6.46
366	409	0.170561	CAAGTAGCTAGTGACGCCGT	59.829	55.000	0.73	0.00	0.00	5.68
367	410	0.170561	AAGTAGCTAGTGACGCCGTG	59.829	55.000	0.73	0.00	0.00	4.94
368	411	1.872679	GTAGCTAGTGACGCCGTGC	60.873	63.158	0.00	0.00	0.00	5.34
369	412	2.337246	TAGCTAGTGACGCCGTGCA	61.337	57.895	0.00	0.00	0.00	4.57
370	413	2.537792	TAGCTAGTGACGCCGTGCAC	62.538	60.000	6.82	6.82	35.30	4.57
373	416	3.567478	TAGTGACGCCGTGCACAGG	62.567	63.158	18.64	19.06	37.48	4.00
440	483	1.935933	ATTCGACCGGTTATCACAGC	58.064	50.000	9.42	0.00	0.00	4.40
476	521	2.458951	GAACTATCTGCGCTGAGACTG	58.541	52.381	21.74	9.50	0.00	3.51
716	863	4.100498	AGAGAATAATGCAAATGGGCTTGG	59.900	41.667	0.00	0.00	34.04	3.61
1159	1534	2.889678	TGCATGCAGGTAAACAACATCA	59.110	40.909	18.46	0.00	0.00	3.07
1283	1748	0.837260	ATTTGCAGGTGTGGCCCATT	60.837	50.000	0.00	0.00	38.26	3.16
1448	1913	2.759985	CGCATCCCCTGGGTACTAT	58.240	57.895	12.71	0.00	36.47	2.12
1817	2287	2.463876	CGAGAAAGCATGCTCGTATGA	58.536	47.619	22.93	0.00	46.43	2.15
1844	2314	4.953579	TGCTATCGGTGGCTATGTATATGA	59.046	41.667	5.36	0.00	32.28	2.15
1937	2411	3.118738	CCACCGTGCTTATTACTTCCTCT	60.119	47.826	0.00	0.00	0.00	3.69
1943	2417	6.761714	CCGTGCTTATTACTTCCTCTGTAAAT	59.238	38.462	0.00	0.00	34.20	1.40
1967	2442	7.853377	TTAATATAGAGCGTTTCGATCACTG	57.147	36.000	9.83	0.00	45.07	3.66
1968	2443	1.909376	TAGAGCGTTTCGATCACTGC	58.091	50.000	9.83	0.00	45.07	4.40
1992	2469	7.222805	TGCTTTAGTGATCTAAACGCTCTTATG	59.777	37.037	15.47	1.74	40.05	1.90
2008	2495	6.049790	GCTCTTATGTTAGTTTACAGAGGGG	58.950	44.000	0.00	0.00	0.00	4.79
2060	2548	5.235516	ACGTTGTCTTAGTTTGTATCCCTG	58.764	41.667	0.00	0.00	0.00	4.45
2090	2578	2.088104	TTGTAAACATGGCCCCACAA	57.912	45.000	0.00	0.00	0.00	3.33
2272	2760	9.325150	TGAAGCGAATAAAATTAGAGAAAAACG	57.675	29.630	0.00	0.00	0.00	3.60
2314	2802	6.260714	ACCGGTTATTCCATTTATTCGGTAAC	59.739	38.462	0.00	0.00	45.00	2.50
2368	2856	6.929606	GGTTTGTATACTCTTGTTGTGTCTCT	59.070	38.462	4.17	0.00	0.00	3.10
2390	2878	2.618442	AGGCATTGGTTGTGGTTTTG	57.382	45.000	0.00	0.00	0.00	2.44
2462	2950	8.630037	GTGCTTTAATATTAACAAGCCACCTAT	58.370	33.333	21.18	0.00	29.61	2.57
2518	3007	1.860326	CTTTTGTTGCTTTTGAGGCCG	59.140	47.619	0.00	0.00	0.00	6.13
2525	3014	1.182667	GCTTTTGAGGCCGGGTATTT	58.817	50.000	2.18	0.00	0.00	1.40
2558	3048	6.350906	TCCCAAGTTGATAGTTATTTACCCG	58.649	40.000	3.87	0.00	0.00	5.28
2608	3098	5.192522	AGAACCCTTCCAATATCTCACATGT	59.807	40.000	0.00	0.00	0.00	3.21
2612	3106	5.457197	CCCTTCCAATATCTCACATGTCCAT	60.457	44.000	0.00	0.00	0.00	3.41
2629	3123	1.623311	CCATGTATCGTGCCCCTATCA	59.377	52.381	0.00	0.00	0.00	2.15

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	3.013219	GGCTCTCAGAACAATTCCTTCC	58.987	50.000	0.00	0.00	0.00	3.46
31	32	1.192146	TTCACCCTGGAGAAGACCGG	61.192	60.000	0.00	0.00	36.18	5.28
35	36	5.785423	TCTTAGATTTTCACCCTGGAGAAGA	59.215	40.000	0.00	0.00	0.00	2.87
53	54	4.442052	CGTTGCCTGATCCAAGATCTTAGA	60.442	45.833	7.86	6.87	0.00	2.10
61	62	0.389817	TCGTCGTTGCCTGATCCAAG	60.390	55.000	0.00	0.00	0.00	3.61
80	81	1.032014	AGGAAACAATGCACAAGCGT	58.968	45.000	0.00	0.00	46.23	5.07
101	102	3.692101	TCTTCAAAAGCAACGTCTCCAAA	59.308	39.130	0.00	0.00	0.00	3.28
108	109	4.450082	AAAAGGTCTTCAAAAGCAACGT	57.550	36.364	0.00	0.00	0.00	3.99
137	138	1.476891	ACCACTAGATACAGCACACGG	59.523	52.381	0.00	0.00	0.00	4.94
152	153	2.770589	GCGCACACAAACCACCACT	61.771	57.895	0.30	0.00	0.00	4.00
163	164	3.117171	CCTCTCAGCAGCGCACAC	61.117	66.667	11.47	0.00	0.00	3.82
173	174	4.190001	CCACAATGATCAACTCCTCTCAG	58.810	47.826	0.00	0.00	0.00	3.35
190	191	6.783708	ATAAAAACAAAGGTCTCACCACAA	57.216	33.333	0.00	0.00	41.95	3.33
212	213	6.352516	TGCACACAACCAAAGGAAAATAAAT	58.647	32.000	0.00	0.00	0.00	1.40
216	225	3.902881	TGCACACAACCAAAGGAAAAT	57.097	38.095	0.00	0.00	0.00	1.82
230	239	5.049198	TCTCAAAGACATTCAAGATGCACAC	60.049	40.000	0.00	0.00	0.00	3.82
261	270	1.889829	ACACTCAGTCTCTGCACCTAC	59.110	52.381	0.00	0.00	0.00	3.18
273	282	8.768501	TCATGAAGATACCTATTACACTCAGT	57.231	34.615	0.00	0.00	0.00	3.41
313	322	9.916397	CGCGTAGAATTATCTTTCATTTACTTT	57.084	29.630	0.00	0.00	37.10	2.66
314	323	8.548721	CCGCGTAGAATTATCTTTCATTTACTT	58.451	33.333	4.92	0.00	37.10	2.24
316	325	7.170320	TCCCGCGTAGAATTATCTTTCATTTAC	59.830	37.037	4.92	0.00	37.10	2.01
338	381	1.683917	ACTAGCTACTTGATGCTCCCG	59.316	52.381	0.00	0.00	40.35	5.14
354	397	2.049526	TGTGCACGGCGTCACTAG	60.050	61.111	28.89	14.69	34.49	2.57
355	398	2.049526	CTGTGCACGGCGTCACTA	60.050	61.111	28.89	19.67	34.49	2.74
356	399	4.969196	CCTGTGCACGGCGTCACT	62.969	66.667	28.89	3.39	34.49	3.41
357	400	4.961511	TCCTGTGCACGGCGTCAC	62.962	66.667	25.25	25.25	0.00	3.67
358	401	4.662961	CTCCTGTGCACGGCGTCA	62.663	66.667	20.76	8.96	0.00	4.35
362	405	3.503363	GATGCTCCTGTGCACGGC	61.503	66.667	20.76	16.83	46.33	5.68
363	406	0.108186	TAAGATGCTCCTGTGCACGG	60.108	55.000	19.25	19.25	46.33	4.94
364	407	1.945387	ATAAGATGCTCCTGTGCACG	58.055	50.000	13.13	7.03	46.33	5.34
365	408	4.708726	AAAATAAGATGCTCCTGTGCAC	57.291	40.909	10.75	10.75	46.33	4.57
367	410	6.683974	TTCTAAAATAAGATGCTCCTGTGC	57.316	37.500	0.00	0.00	0.00	4.57
415	458	4.183101	GTGATAACCGGTCGAATTTGGTA	58.817	43.478	8.04	0.00	33.45	3.25
440	483	1.202533	AGTTCGTGAGGGTTGTGTCAG	60.203	52.381	0.00	0.00	0.00	3.51
476	521	2.969628	ATGAAGTCATGACGGTCTCC	57.030	50.000	24.24	12.08	34.83	3.71
716	863	0.678048	CCTTCCTGGCTACTTGCACC	60.678	60.000	0.00	0.00	45.15	5.01
1283	1748	1.623311	TCGAACTTCTTGATGCCCTCA	59.377	47.619	0.00	0.00	0.00	3.86
1448	1913	1.195442	TTGTCCAGTACCGGCCATCA	61.195	55.000	0.00	0.00	0.00	3.07
1817	2287	2.634940	ACATAGCCACCGATAGCATTCT	59.365	45.455	0.00	0.00	0.00	2.40
1943	2417	6.362551	GCAGTGATCGAAACGCTCTATATTAA	59.637	38.462	0.00	0.00	0.00	1.40
1965	2440	5.105752	AGAGCGTTTAGATCACTAAAGCAG	58.894	41.667	17.18	9.22	45.42	4.24
1967	2442	7.222999	ACATAAGAGCGTTTAGATCACTAAAGC	59.777	37.037	0.00	0.00	45.42	3.51
1968	2443	8.635877	ACATAAGAGCGTTTAGATCACTAAAG	57.364	34.615	0.00	0.00	45.42	1.85
1983	2460	5.749109	CCCTCTGTAAACTAACATAAGAGCG	59.251	44.000	0.00	0.00	0.00	5.03
1992	2469	8.859236	AAAAAGTATCCCCTCTGTAAACTAAC	57.141	34.615	0.00	0.00	0.00	2.34
2022	2510	0.971386	AACGTCCAACCGTCCACTAT	59.029	50.000	0.00	0.00	40.85	2.12
2060	2548	5.810074	GGCCATGTTTACAACCATACATTTC	59.190	40.000	0.00	0.00	0.00	2.17
2084	2572	1.134280	TGTTGGCCAACATTTTGTGGG	60.134	47.619	40.89	0.00	45.42	4.61
2132	2620	3.181475	GCCTGAGATTTAGTCCGATGTCA	60.181	47.826	0.00	0.00	0.00	3.58
2138	2626	1.802880	CGTGGCCTGAGATTTAGTCCG	60.803	57.143	3.32	0.00	0.00	4.79
2272	2760	5.024785	ACCGGTTTCCTTTGATAGATCTC	57.975	43.478	0.00	0.00	0.00	2.75
2368	2856	4.080863	ACAAAACCACAACCAATGCCTTAA	60.081	37.500	0.00	0.00	0.00	1.85
2518	3007	7.177744	TCAACTTGGGAATAAACTCAAATACCC	59.822	37.037	0.00	0.00	36.92	3.69
2608	3098	1.899814	GATAGGGGCACGATACATGGA	59.100	52.381	0.00	0.00	0.00	3.41
2612	3106	1.783071	TGTGATAGGGGCACGATACA	58.217	50.000	0.00	0.00	39.07	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.