AutoCloner

Multiple sequence alignment - TraesCS1D01G262400

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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	TraesCS1D01G262400	chr1D	100.000	2696	0	0	1	2696	356362128	356359433	0.000000e+00	4979.0
1	TraesCS1D01G262400	chr1D	90.021	471	41	2	943	1407	356859291	356859761	2.970000e-169	604.0
2	TraesCS1D01G262400	chr1D	82.704	503	42	21	1529	1992	356860261	356860757	3.230000e-109	405.0
3	TraesCS1D01G262400	chr1B	92.754	1380	77	8	66	1440	479792291	479793652	0.000000e+00	1973.0
4	TraesCS1D01G262400	chr1B	89.796	1078	49	32	1499	2521	479794007	479795078	0.000000e+00	1325.0
5	TraesCS1D01G262400	chr1B	83.491	739	72	22	879	1570	480326619	480327354	0.000000e+00	643.0
6	TraesCS1D01G262400	chr1B	82.545	550	51	28	1484	1997	480327151	480327691	2.460000e-120	442.0
7	TraesCS1D01G262400	chr1B	89.610	154	7	3	2552	2696	479795148	479795301	1.270000e-43	187.0
8	TraesCS1D01G262400	chr1B	80.526	190	22	6	2297	2472	480359681	480359869	6.060000e-27	132.0
9	TraesCS1D01G262400	chr1A	89.516	1383	118	12	1	1381	457371203	457372560	0.000000e+00	1725.0
10	TraesCS1D01G262400	chr1A	93.049	892	37	6	1422	2293	457372886	457373772	0.000000e+00	1280.0
11	TraesCS1D01G262400	chr1A	88.367	490	48	3	927	1407	457945248	457945737	5.000000e-162	580.0
12	TraesCS1D01G262400	chr1A	88.060	402	15	12	2310	2696	457373824	457374207	1.900000e-121	446.0
13	TraesCS1D01G262400	chr1A	89.548	354	27	6	1483	1829	457945726	457946076	8.860000e-120	440.0
14	TraesCS1D01G262400	chr1A	81.208	149	25	1	1536	1681	457372886	457373034	1.700000e-22	117.0
15	TraesCS1D01G262400	chr1A	91.045	67	4	1	2297	2361	457954886	457954952	3.700000e-14	89.8
16	TraesCS1D01G262400	chr3A	82.301	226	32	7	63	284	693067825	693068046	3.540000e-44	189.0
17	TraesCS1D01G262400	chr3A	80.087	231	38	7	63	289	739799681	739799907	5.970000e-37	165.0
18	TraesCS1D01G262400	chr4A	80.973	226	35	6	63	284	200170507	200170286	3.570000e-39	172.0
19	TraesCS1D01G262400	chr4A	80.172	232	36	10	63	289	415864742	415864968	5.970000e-37	165.0
20	TraesCS1D01G262400	chr7A	80.702	228	33	10	63	284	717964681	717964903	1.660000e-37	167.0
21	TraesCS1D01G262400	chr6D	80.531	226	36	8	63	284	134060498	134060277	1.660000e-37	167.0
22	TraesCS1D01G262400	chr6A	80.172	232	37	9	63	289	615255423	615255650	5.970000e-37	165.0
23	TraesCS1D01G262400	chr6A	90.196	51	4	1	657	707	569607107	569607156	6.230000e-07	65.8
24	TraesCS1D01G262400	chr2D	80.349	229	33	11	63	284	596031652	596031875	2.150000e-36	163.0
25	TraesCS1D01G262400	chr5B	95.000	40	1	1	655	694	278444071	278444109	8.060000e-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	TraesCS1D01G262400	chr1D	356359433	356362128	2695	True	4979.000000	4979	100.00000	1	2696	1	chr1D.!!$R1	2695
1	TraesCS1D01G262400	chr1D	356859291	356860757	1466	False	504.500000	604	86.36250	943	1992	2	chr1D.!!$F1	1049
2	TraesCS1D01G262400	chr1B	479792291	479795301	3010	False	1161.666667	1973	90.72000	66	2696	3	chr1B.!!$F2	2630
3	TraesCS1D01G262400	chr1B	480326619	480327691	1072	False	542.500000	643	83.01800	879	1997	2	chr1B.!!$F3	1118
4	TraesCS1D01G262400	chr1A	457371203	457374207	3004	False	892.000000	1725	87.95825	1	2696	4	chr1A.!!$F2	2695
5	TraesCS1D01G262400	chr1A	457945248	457946076	828	False	510.000000	580	88.95750	927	1829	2	chr1A.!!$F3	902

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
765	770	1.369625	CAAAGCCACTACGGTGATCC	58.63	55.0	0.0	0.0	45.61	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2307	3541	0.540365	AATGCGGGCATAATGGGAGG	60.54	55.0	6.57	0.0	35.31	4.3	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
56	57	5.504853	TCTTGATGTGGGCAAACATGTATA	58.495	37.500	9.48	0.00	40.87	1.47
61	62	5.637006	TGTGGGCAAACATGTATAGTTTC	57.363	39.130	0.00	0.00	37.10	2.78
80	81	7.184067	AGTTTCTGTTAGAATAATCCGAGGT	57.816	36.000	0.00	0.00	33.67	3.85
95	96	2.293677	CCGAGGTGCGTAGTTGATCTAT	59.706	50.000	0.00	0.00	38.67	1.98
101	102	2.552743	TGCGTAGTTGATCTATCGAGGG	59.447	50.000	0.00	0.00	0.00	4.30
111	112	1.490490	TCTATCGAGGGCCAAGCAATT	59.510	47.619	6.18	0.00	0.00	2.32
129	130	4.085055	GCAATTATACGAGACATGACACCG	60.085	45.833	0.00	4.04	0.00	4.94
141	142	5.408604	AGACATGACACCGAGATTTGTTAAC	59.591	40.000	0.00	0.00	0.00	2.01
142	143	5.060506	ACATGACACCGAGATTTGTTAACA	58.939	37.500	3.59	3.59	0.00	2.41
162	163	5.441718	ACAAGGTTCACCATCATGACTAT	57.558	39.130	0.00	0.00	38.89	2.12
169	170	4.762220	TCACCATCATGACTATATCCCCA	58.238	43.478	0.00	0.00	0.00	4.96
170	171	5.161886	TCACCATCATGACTATATCCCCAA	58.838	41.667	0.00	0.00	0.00	4.12
175	176	6.070021	CCATCATGACTATATCCCCAAGCTTA	60.070	42.308	0.00	0.00	0.00	3.09
325	326	9.125026	CCTAGAATACAAATTGCTTGTTAGGAT	57.875	33.333	6.84	0.00	46.49	3.24
366	370	5.990386	TCTACATACCATACGACTCAGAGTC	59.010	44.000	19.43	19.43	41.71	3.36
377	381	6.525578	ACGACTCAGAGTCCAATTGTAATA	57.474	37.500	22.65	0.00	42.12	0.98
435	439	7.208777	ACAACTTTTGCATCAACATGACATTA	58.791	30.769	0.00	0.00	30.57	1.90
475	479	2.932498	TGTTGATCAATGAAGCAACGC	58.068	42.857	12.12	0.00	42.51	4.84
526	531	1.818363	ATAGAGGTCTCGCGTCGCA	60.818	57.895	18.75	3.61	37.10	5.10
627	632	5.193679	TCTCTGAGCAAGTGTACTGCTATA	58.806	41.667	7.98	1.18	39.21	1.31
757	762	7.041984	GGAGTATTATACAAGCAAAGCCACTAC	60.042	40.741	5.11	0.00	0.00	2.73
765	770	1.369625	CAAAGCCACTACGGTGATCC	58.630	55.000	0.00	0.00	45.61	3.36
888	896	2.567497	CCCCTGCAAAGCCACTGTG	61.567	63.158	0.00	0.00	0.00	3.66
1428	1780	2.029815	TGCTACAAGTGCGGCGAA	59.970	55.556	12.98	0.00	0.00	4.70
1431	1783	1.084370	GCTACAAGTGCGGCGAAGAT	61.084	55.000	12.98	0.00	0.00	2.40
1503	2151	3.001406	GGTGGTGGCTACGGAGGT	61.001	66.667	0.00	0.00	0.00	3.85
1506	2154	3.001406	GGTGGCTACGGAGGTGGT	61.001	66.667	0.00	0.00	0.00	4.16
1735	2866	1.377612	GAGTGCCCCGTTTACCCTT	59.622	57.895	0.00	0.00	0.00	3.95
1890	3041	7.806014	TGTTCGTTAAGATCCAAGTTATTTTGC	59.194	33.333	0.00	0.00	0.00	3.68
2120	3284	3.502191	TTCCATTGGCGTTTTGATAGC	57.498	42.857	0.00	0.00	0.00	2.97
2148	3313	2.686558	TCGCAAGTTTGATGCTTCAC	57.313	45.000	1.02	0.00	41.64	3.18
2169	3334	2.878406	CGTTCAACAGGTTCATGGTTCT	59.122	45.455	0.00	0.00	0.00	3.01
2174	3339	7.094975	CGTTCAACAGGTTCATGGTTCTAAATA	60.095	37.037	0.00	0.00	0.00	1.40
2201	3371	7.506114	TCAACAGGTCCATTCTTATATGTACC	58.494	38.462	0.00	0.00	35.41	3.34
2213	3383	2.760634	TATGTACCTGTGCCACTGTG	57.239	50.000	0.00	0.00	0.00	3.66
2214	3384	0.606401	ATGTACCTGTGCCACTGTGC	60.606	55.000	1.29	0.00	0.00	4.57
2215	3385	1.071471	GTACCTGTGCCACTGTGCT	59.929	57.895	1.29	0.00	0.00	4.40
2216	3386	1.071299	TACCTGTGCCACTGTGCTG	59.929	57.895	1.29	0.00	0.00	4.41
2314	3548	2.679716	GCTGTCAAGCCCTCCCAT	59.320	61.111	0.00	0.00	44.22	4.00
2315	3549	1.000396	GCTGTCAAGCCCTCCCATT	60.000	57.895	0.00	0.00	44.22	3.16
2316	3550	0.255890	GCTGTCAAGCCCTCCCATTA	59.744	55.000	0.00	0.00	44.22	1.90
2317	3551	1.133668	GCTGTCAAGCCCTCCCATTAT	60.134	52.381	0.00	0.00	44.22	1.28
2322	3556	2.282462	GCCCTCCCATTATGCCCG	60.282	66.667	0.00	0.00	0.00	6.13
2377	3615	3.680458	GTCTCTTAAGAAAGAAGGCACGG	59.320	47.826	6.63	0.00	41.19	4.94
2451	3690	4.394920	GCTTTGTCTTGGATGAACGGAATA	59.605	41.667	0.00	0.00	0.00	1.75
2466	3705	4.051922	ACGGAATAGAATCATGTCGCTTC	58.948	43.478	0.00	0.00	0.00	3.86
2490	3730	6.049149	CAGACTTAGGGATGCGAAGAATAAA	58.951	40.000	4.78	0.00	0.00	1.40
2518	3758	7.364144	GCCTAAATTTTGATCTCCTTCCAACAT	60.364	37.037	0.00	0.00	0.00	2.71
2564	3844	7.739295	TGAATAAATCTTTGTGAGCTTACGAC	58.261	34.615	3.97	0.00	0.00	4.34
2570	3850	3.902261	TTGTGAGCTTACGACGACTTA	57.098	42.857	0.00	0.00	0.00	2.24
2572	3852	4.012319	TGTGAGCTTACGACGACTTATC	57.988	45.455	0.00	0.00	0.00	1.75
2665	3955	5.808042	ACACATCAATTTTCCAGATCTCG	57.192	39.130	0.00	0.00	0.00	4.04

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	25	6.662865	TTGCCCACATCAAGAGATTAAAAA	57.337	33.333	0.00	0.00	30.20	1.94
36	37	4.854173	ACTATACATGTTTGCCCACATCA	58.146	39.130	2.30	0.00	35.03	3.07
56	57	7.042335	CACCTCGGATTATTCTAACAGAAACT	58.958	38.462	0.00	0.00	37.82	2.66
61	62	3.736252	CGCACCTCGGATTATTCTAACAG	59.264	47.826	0.00	0.00	33.78	3.16
95	96	2.805295	CGTATAATTGCTTGGCCCTCGA	60.805	50.000	0.00	0.00	0.00	4.04
101	102	4.511454	TCATGTCTCGTATAATTGCTTGGC	59.489	41.667	0.00	0.00	0.00	4.52
111	112	3.800531	TCTCGGTGTCATGTCTCGTATA	58.199	45.455	0.00	0.00	0.00	1.47
129	130	6.385649	TGGTGAACCTTGTTAACAAATCTC	57.614	37.500	20.89	17.45	35.15	2.75
141	142	6.652481	GGATATAGTCATGATGGTGAACCTTG	59.348	42.308	0.00	0.00	36.82	3.61
142	143	6.240002	GGGATATAGTCATGATGGTGAACCTT	60.240	42.308	0.00	0.00	36.82	3.50
162	163	7.073854	AGTGTCTATAGTTAAGCTTGGGGATA	58.926	38.462	9.86	1.38	0.00	2.59
169	170	6.436890	AGGAGGAGTGTCTATAGTTAAGCTT	58.563	40.000	3.48	3.48	0.00	3.74
170	171	6.020881	AGGAGGAGTGTCTATAGTTAAGCT	57.979	41.667	0.00	0.00	0.00	3.74
175	176	4.080469	TCGTGAGGAGGAGTGTCTATAGTT	60.080	45.833	0.00	0.00	0.00	2.24
313	314	5.894298	ATGGACTCATATCCTAACAAGCA	57.106	39.130	0.00	0.00	39.75	3.91
396	400	5.741982	GCAAAAGTTGTTAGATTTGTGTCGT	59.258	36.000	0.00	0.00	35.68	4.34
405	409	7.596248	GTCATGTTGATGCAAAAGTTGTTAGAT	59.404	33.333	0.00	0.00	0.00	1.98
418	422	9.518906	GAATTGTTATAATGTCATGTTGATGCA	57.481	29.630	0.00	0.00	0.00	3.96
435	439	8.877864	TCAACAAGGTCCATAAGAATTGTTAT	57.122	30.769	2.10	2.10	41.37	1.89
455	459	2.351641	GGCGTTGCTTCATTGATCAACA	60.352	45.455	11.07	0.50	38.85	3.33
475	479	6.821665	TGTCTTTTTCATCTATTAGGGAACGG	59.178	38.462	0.00	0.00	0.00	4.44
526	531	0.108329	CTCCATTTCCCACGCGTAGT	60.108	55.000	13.44	0.00	0.00	2.73
627	632	2.809696	CACGTAATTTTGGACGGAGGTT	59.190	45.455	3.74	0.00	43.32	3.50
712	717	4.141688	ACTCCCTCCGTCCTGAATTATTTC	60.142	45.833	0.00	0.00	0.00	2.17
888	896	1.315981	GGCCTCTTAGTTGGGCTTGC	61.316	60.000	0.00	0.00	44.70	4.01
1164	1183	4.789075	CCGTCGTCGCCGGTGATT	62.789	66.667	22.69	0.00	40.59	2.57
1431	1783	2.124768	TCCCTGGAGATGTGGCCA	59.875	61.111	0.00	0.00	0.00	5.36
1479	1831	3.454573	TAGCCACCACCGCCGTAG	61.455	66.667	0.00	0.00	0.00	3.51
1735	2866	2.043939	TCAGGAGGTAGGTAAAGGAGCA	59.956	50.000	0.00	0.00	0.00	4.26
1890	3041	3.087781	TGTCCTCATCACAGAGAGACAG	58.912	50.000	0.00	0.00	39.09	3.51
2006	3167	4.097437	CACTTTCAAGCATGGCAGATATGT	59.903	41.667	0.00	0.00	0.00	2.29
2018	3179	7.692460	ATATCAGAATCAACACTTTCAAGCA	57.308	32.000	0.00	0.00	0.00	3.91
2120	3284	4.274069	CATCAAACTTGCGAATCATACCG	58.726	43.478	0.00	0.00	0.00	4.02
2148	3313	2.878406	AGAACCATGAACCTGTTGAACG	59.122	45.455	0.00	0.00	0.00	3.95
2174	3339	9.561069	GTACATATAAGAATGGACCTGTTGAAT	57.439	33.333	0.00	0.00	35.04	2.57
2199	3369	2.203252	CAGCACAGTGGCACAGGT	60.203	61.111	21.41	14.57	41.80	4.00
2201	3371	1.265095	CTAAACAGCACAGTGGCACAG	59.735	52.381	21.41	15.03	41.80	3.66
2213	3383	6.018343	GGCATGAGAAGAATCTACTAAACAGC	60.018	42.308	0.00	0.00	35.54	4.40
2214	3384	7.010923	GTGGCATGAGAAGAATCTACTAAACAG	59.989	40.741	0.00	0.00	35.54	3.16
2215	3385	6.818644	GTGGCATGAGAAGAATCTACTAAACA	59.181	38.462	0.00	0.00	35.54	2.83
2216	3386	7.044798	AGTGGCATGAGAAGAATCTACTAAAC	58.955	38.462	0.00	0.00	35.54	2.01
2305	3539	2.282462	CGGGCATAATGGGAGGGC	60.282	66.667	0.00	0.00	0.00	5.19
2306	3540	2.282462	GCGGGCATAATGGGAGGG	60.282	66.667	0.00	0.00	0.00	4.30
2307	3541	0.540365	AATGCGGGCATAATGGGAGG	60.540	55.000	6.57	0.00	35.31	4.30
2308	3542	1.270550	GAAATGCGGGCATAATGGGAG	59.729	52.381	6.57	0.00	35.31	4.30
2309	3543	1.327303	GAAATGCGGGCATAATGGGA	58.673	50.000	6.57	0.00	35.31	4.37
2311	3545	3.389925	AATGAAATGCGGGCATAATGG	57.610	42.857	6.57	0.00	35.31	3.16
2312	3546	6.254157	GCTTATAATGAAATGCGGGCATAATG	59.746	38.462	6.57	0.00	35.31	1.90
2313	3547	6.153340	AGCTTATAATGAAATGCGGGCATAAT	59.847	34.615	6.57	0.00	35.31	1.28
2314	3548	5.476599	AGCTTATAATGAAATGCGGGCATAA	59.523	36.000	6.57	0.00	35.31	1.90
2315	3549	5.009631	AGCTTATAATGAAATGCGGGCATA	58.990	37.500	6.57	0.00	35.31	3.14
2316	3550	3.828451	AGCTTATAATGAAATGCGGGCAT	59.172	39.130	0.00	0.00	38.46	4.40
2317	3551	3.221771	AGCTTATAATGAAATGCGGGCA	58.778	40.909	0.00	0.00	0.00	5.36
2451	3690	3.883830	AGTCTGAAGCGACATGATTCT	57.116	42.857	0.00	0.00	43.42	2.40
2466	3705	3.526931	TTCTTCGCATCCCTAAGTCTG	57.473	47.619	0.00	0.00	0.00	3.51
2490	3730	6.256053	TGGAAGGAGATCAAAATTTAGGCTT	58.744	36.000	0.00	0.00	0.00	4.35
2564	3844	1.858091	AAGCCGCAGATGATAAGTCG	58.142	50.000	0.00	0.00	0.00	4.18
2570	3850	2.368439	TGCTAAAAAGCCGCAGATGAT	58.632	42.857	0.00	0.00	0.00	2.45
2572	3852	2.857592	ATGCTAAAAAGCCGCAGATG	57.142	45.000	0.00	0.00	0.00	2.90
2665	3955	2.844451	TTGCCTGCAAAGGACGCAC	61.844	57.895	1.31	0.00	35.08	5.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.