AutoCloner

Multiple sequence alignment - TraesCS2B01G006000

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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	TraesCS2B01G006000	chr2B	100.000	3067	0	0	1	3067	3796885	3793819	0.000000e+00	5664.0
1	TraesCS2B01G006000	chr2B	99.645	1407	4	1	1	1407	3710024	3708619	0.000000e+00	2569.0
2	TraesCS2B01G006000	chr2B	86.842	1786	164	38	582	2341	4376984	4378724	0.000000e+00	1930.0
3	TraesCS2B01G006000	chr2B	86.786	1786	166	39	582	2341	4014089	4015830	0.000000e+00	1927.0
4	TraesCS2B01G006000	chr2B	86.786	1786	164	39	582	2341	4283590	4285329	0.000000e+00	1925.0
5	TraesCS2B01G006000	chr2B	86.786	1786	165	38	582	2341	4424825	4426565	0.000000e+00	1925.0
6	TraesCS2B01G006000	chr2B	100.000	190	0	0	3097	3286	3793789	3793600	5.220000e-93	351.0
7	TraesCS2B01G006000	chr2B	93.194	191	8	3	3097	3284	445386856	445386668	3.230000e-70	276.0
8	TraesCS2B01G006000	chr2B	85.000	180	20	6	3097	3269	66453608	66453429	3.370000e-40	176.0
9	TraesCS2B01G006000	chr2D	87.292	1802	164	38	582	2341	7833965	7835743	0.000000e+00	1999.0
10	TraesCS2B01G006000	chr2D	91.621	1277	104	3	1242	2515	7646167	7644891	0.000000e+00	1762.0
11	TraesCS2B01G006000	chr2D	92.798	361	21	5	2710	3066	335299416	335299057	4.860000e-143	518.0
12	TraesCS2B01G006000	chr2D	86.744	347	34	6	878	1212	7646607	7646261	3.100000e-100	375.0
13	TraesCS2B01G006000	chr2D	87.310	197	13	6	589	774	7646896	7646701	7.140000e-52	215.0
14	TraesCS2B01G006000	chr2D	86.905	168	18	3	3097	3260	15853150	15853317	5.600000e-43	185.0
15	TraesCS2B01G006000	chr2D	92.188	64	4	1	759	821	7646688	7646625	4.520000e-14	89.8
16	TraesCS2B01G006000	chrUn	99.618	1047	3	1	2022	3067	446626983	446628029	0.000000e+00	1910.0
17	TraesCS2B01G006000	chrUn	100.000	433	0	0	1	433	368381468	368381036	0.000000e+00	800.0
18	TraesCS2B01G006000	chrUn	100.000	433	0	0	1	433	464374642	464375074	0.000000e+00	800.0
19	TraesCS2B01G006000	chr2A	80.683	1377	226	29	945	2299	5910890	5912248	0.000000e+00	1033.0
20	TraesCS2B01G006000	chr2A	79.167	1056	204	12	1239	2288	10507672	10508717	0.000000e+00	717.0
21	TraesCS2B01G006000	chr2A	91.667	372	25	5	2699	3066	172841184	172840815	8.130000e-141	510.0
22	TraesCS2B01G006000	chr7A	92.308	364	25	3	2706	3066	12296057	12295694	6.290000e-142	514.0
23	TraesCS2B01G006000	chr4B	92.055	365	26	3	2705	3066	569372043	569372407	8.130000e-141	510.0
24	TraesCS2B01G006000	chr4B	86.070	201	13	8	3097	3284	360233462	360233264	5.560000e-48	202.0
25	TraesCS2B01G006000	chr4B	88.166	169	13	6	3097	3260	299557417	299557583	9.300000e-46	195.0
26	TraesCS2B01G006000	chr6A	91.153	373	28	5	2699	3066	453011910	453012282	4.900000e-138	501.0
27	TraesCS2B01G006000	chr5D	91.153	373	26	7	2699	3066	554603667	554603297	1.760000e-137	499.0
28	TraesCS2B01G006000	chr5D	90.000	190	16	2	3097	3284	446577263	446577451	3.280000e-60	243.0
29	TraesCS2B01G006000	chr3A	91.129	372	28	4	2699	3066	271287103	271286733	1.760000e-137	499.0
30	TraesCS2B01G006000	chr3A	90.885	373	29	5	2699	3066	152285343	152284971	2.280000e-136	496.0
31	TraesCS2B01G006000	chr5B	90.256	195	12	6	3097	3286	188815099	188815291	7.040000e-62	248.0
32	TraesCS2B01G006000	chr1B	88.095	168	16	3	3097	3260	549729580	549729413	2.590000e-46	196.0
33	TraesCS2B01G006000	chr1B	85.475	179	20	5	3097	3269	428649791	428649969	7.240000e-42	182.0

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	TraesCS2B01G006000	chr2B	3793600	3796885	3285	True	3007.50	5664	100.00000	1	3286	2	chr2B.!!$R4	3285
1	TraesCS2B01G006000	chr2B	3708619	3710024	1405	True	2569.00	2569	99.64500	1	1407	1	chr2B.!!$R1	1406
2	TraesCS2B01G006000	chr2B	4376984	4378724	1740	False	1930.00	1930	86.84200	582	2341	1	chr2B.!!$F3	1759
3	TraesCS2B01G006000	chr2B	4014089	4015830	1741	False	1927.00	1927	86.78600	582	2341	1	chr2B.!!$F1	1759
4	TraesCS2B01G006000	chr2B	4283590	4285329	1739	False	1925.00	1925	86.78600	582	2341	1	chr2B.!!$F2	1759
5	TraesCS2B01G006000	chr2B	4424825	4426565	1740	False	1925.00	1925	86.78600	582	2341	1	chr2B.!!$F4	1759
6	TraesCS2B01G006000	chr2D	7833965	7835743	1778	False	1999.00	1999	87.29200	582	2341	1	chr2D.!!$F1	1759
7	TraesCS2B01G006000	chr2D	7644891	7646896	2005	True	610.45	1762	89.46575	589	2515	4	chr2D.!!$R2	1926
8	TraesCS2B01G006000	chrUn	446626983	446628029	1046	False	1910.00	1910	99.61800	2022	3067	1	chrUn.!!$F1	1045
9	TraesCS2B01G006000	chr2A	5910890	5912248	1358	False	1033.00	1033	80.68300	945	2299	1	chr2A.!!$F1	1354
10	TraesCS2B01G006000	chr2A	10507672	10508717	1045	False	717.00	717	79.16700	1239	2288	1	chr2A.!!$F2	1049

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	312	3.247006	TCTTATCCGAGCCACAGTTTC	57.753	47.619	0.0	0.0	0.0	2.78	F
1498	1661	2.684881	CTGACATCACCCACCTTATTGC	59.315	50.000	0.0	0.0	0.0	3.56	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1628	1791	0.615331	CAGCAAGGTCCTTGGCTAGA	59.385	55.000	28.96	0.0	41.31	2.43	R
3248	3421	5.003804	GGCATAAAAAGAGTCAGAAGACCA	58.996	41.667	0.00	0.0	46.15	4.02	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
43	44	4.362279	CCGTTGAATGGCTGGATATTTTG	58.638	43.478	0.00	0.00	0.00	2.44
311	312	3.247006	TCTTATCCGAGCCACAGTTTC	57.753	47.619	0.00	0.00	0.00	2.78
1496	1659	3.308402	CCACTGACATCACCCACCTTATT	60.308	47.826	0.00	0.00	0.00	1.40
1498	1661	2.684881	CTGACATCACCCACCTTATTGC	59.315	50.000	0.00	0.00	0.00	3.56
1811	1974	1.692173	CCGATCCCATACACCCGGTT	61.692	60.000	0.00	0.00	33.02	4.44
1851	2014	0.609681	GGTGTCCGTCTCTCAGACCT	60.610	60.000	0.00	0.00	42.12	3.85
1967	2130	3.221771	CACCATGGAACCTTGTCTTTCA	58.778	45.455	21.47	0.00	0.00	2.69
1981	2144	3.250762	TGTCTTTCAGAAGCATTTGGTCG	59.749	43.478	0.00	0.00	32.75	4.79
1998	2161	2.231478	GGTCGACTTGAGATGGACTTCA	59.769	50.000	16.46	0.00	0.00	3.02
2012	2175	4.081406	TGGACTTCAAATGGAATGACCTG	58.919	43.478	0.00	0.00	39.86	4.00
2631	2803	7.037873	ACCCGGGTATATATATTGTTGTGATGT	60.038	37.037	29.13	0.00	0.00	3.06
3136	3309	7.424227	ACGTTCCGTAAATTGTCTTATTTCA	57.576	32.000	0.00	0.00	38.73	2.69
3137	3310	7.863666	ACGTTCCGTAAATTGTCTTATTTCAA	58.136	30.769	0.00	0.00	38.73	2.69
3138	3311	8.344098	ACGTTCCGTAAATTGTCTTATTTCAAA	58.656	29.630	0.00	0.00	38.73	2.69
3139	3312	8.624028	CGTTCCGTAAATTGTCTTATTTCAAAC	58.376	33.333	0.00	0.00	0.00	2.93
3140	3313	8.624028	GTTCCGTAAATTGTCTTATTTCAAACG	58.376	33.333	0.00	0.00	31.62	3.60
3141	3314	7.863666	TCCGTAAATTGTCTTATTTCAAACGT	58.136	30.769	0.00	0.00	30.65	3.99
3142	3315	8.986847	TCCGTAAATTGTCTTATTTCAAACGTA	58.013	29.630	0.00	0.00	30.65	3.57
3143	3316	9.596677	CCGTAAATTGTCTTATTTCAAACGTAA	57.403	29.630	0.00	0.00	30.65	3.18
3153	3326	9.640974	TCTTATTTCAAACGTAAAAAGAGAACG	57.359	29.630	0.00	0.00	42.17	3.95
3258	3431	8.519799	AAAATGTAGTTTTTCTGGTCTTCTGA	57.480	30.769	0.00	0.00	36.65	3.27
3259	3432	7.497925	AATGTAGTTTTTCTGGTCTTCTGAC	57.502	36.000	0.00	0.00	42.22	3.51
3260	3433	6.235231	TGTAGTTTTTCTGGTCTTCTGACT	57.765	37.500	0.00	0.00	42.54	3.41
3261	3434	6.281405	TGTAGTTTTTCTGGTCTTCTGACTC	58.719	40.000	0.00	0.00	42.54	3.36
3262	3435	5.622346	AGTTTTTCTGGTCTTCTGACTCT	57.378	39.130	0.00	0.00	42.54	3.24
3263	3436	5.995446	AGTTTTTCTGGTCTTCTGACTCTT	58.005	37.500	0.00	0.00	42.54	2.85
3264	3437	6.418946	AGTTTTTCTGGTCTTCTGACTCTTT	58.581	36.000	0.00	0.00	42.54	2.52
3265	3438	6.887002	AGTTTTTCTGGTCTTCTGACTCTTTT	59.113	34.615	0.00	0.00	42.54	2.27
3266	3439	7.394641	AGTTTTTCTGGTCTTCTGACTCTTTTT	59.605	33.333	0.00	0.00	42.54	1.94
3267	3440	8.674607	GTTTTTCTGGTCTTCTGACTCTTTTTA	58.325	33.333	0.00	0.00	42.54	1.52
3268	3441	8.980481	TTTTCTGGTCTTCTGACTCTTTTTAT	57.020	30.769	0.00	0.00	42.54	1.40
3269	3442	7.969536	TTCTGGTCTTCTGACTCTTTTTATG	57.030	36.000	0.00	0.00	42.54	1.90
3270	3443	5.934625	TCTGGTCTTCTGACTCTTTTTATGC	59.065	40.000	0.00	0.00	42.54	3.14
3271	3444	5.003804	TGGTCTTCTGACTCTTTTTATGCC	58.996	41.667	0.00	0.00	42.54	4.40
3272	3445	5.003804	GGTCTTCTGACTCTTTTTATGCCA	58.996	41.667	0.00	0.00	42.54	4.92
3273	3446	5.473504	GGTCTTCTGACTCTTTTTATGCCAA	59.526	40.000	0.00	0.00	42.54	4.52
3274	3447	6.016276	GGTCTTCTGACTCTTTTTATGCCAAA	60.016	38.462	0.00	0.00	42.54	3.28
3275	3448	7.309438	GGTCTTCTGACTCTTTTTATGCCAAAT	60.309	37.037	0.00	0.00	42.54	2.32
3276	3449	8.084684	GTCTTCTGACTCTTTTTATGCCAAATT	58.915	33.333	0.00	0.00	39.94	1.82
3277	3450	8.641541	TCTTCTGACTCTTTTTATGCCAAATTT	58.358	29.630	0.00	0.00	0.00	1.82
3278	3451	9.264719	CTTCTGACTCTTTTTATGCCAAATTTT	57.735	29.630	0.00	0.00	0.00	1.82
3280	3453	9.691362	TCTGACTCTTTTTATGCCAAATTTTAC	57.309	29.630	0.00	0.00	0.00	2.01
3281	3454	8.514136	TGACTCTTTTTATGCCAAATTTTACG	57.486	30.769	0.00	0.00	0.00	3.18
3282	3455	7.115663	TGACTCTTTTTATGCCAAATTTTACGC	59.884	33.333	0.00	0.00	0.00	4.42
3283	3456	6.926272	ACTCTTTTTATGCCAAATTTTACGCA	59.074	30.769	6.77	6.77	35.35	5.24
3284	3457	7.439655	ACTCTTTTTATGCCAAATTTTACGCAA	59.560	29.630	8.07	0.00	34.38	4.85
3285	3458	8.316640	TCTTTTTATGCCAAATTTTACGCAAT	57.683	26.923	8.07	2.13	34.38	3.56

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
286	287	2.939103	CTGTGGCTCGGATAAGAAAAGG	59.061	50.000	0.00	0.00	0.00	3.11
311	312	5.235305	ACGCTAATCCACAAGCTTAATTG	57.765	39.130	0.00	0.00	36.56	2.32
1423	1586	4.189188	CTGCTGATGCCGCAAGCC	62.189	66.667	13.29	0.08	42.71	4.35
1496	1659	1.227943	GTCAGAGTTGGTGCTGGCA	60.228	57.895	0.00	0.00	36.76	4.92
1498	1661	2.320587	GCGTCAGAGTTGGTGCTGG	61.321	63.158	0.00	0.00	33.05	4.85
1532	1695	2.415512	GAGTGAAACCAAGCGTACATCC	59.584	50.000	0.00	0.00	37.80	3.51
1535	1698	1.414919	AGGAGTGAAACCAAGCGTACA	59.585	47.619	0.00	0.00	37.80	2.90
1628	1791	0.615331	CAGCAAGGTCCTTGGCTAGA	59.385	55.000	28.96	0.00	41.31	2.43
1713	1876	4.699522	GCAGTTCCCTTCGCCGGT	62.700	66.667	1.90	0.00	0.00	5.28
1725	1888	4.532521	AGTAATGAGGGTGTCTAAGCAGTT	59.467	41.667	0.00	0.00	0.00	3.16
1811	1974	4.533707	ACCATCTCAAACAGAGGATTCTCA	59.466	41.667	3.21	0.00	44.81	3.27
1967	2130	3.070018	CTCAAGTCGACCAAATGCTTCT	58.930	45.455	13.01	0.00	0.00	2.85
1981	2144	5.248640	TCCATTTGAAGTCCATCTCAAGTC	58.751	41.667	0.00	0.00	0.00	3.01
1998	2161	3.434309	CCCAGAACAGGTCATTCCATTT	58.566	45.455	0.00	0.00	39.02	2.32
2012	2175	2.985847	GGGTGCACAGCCCAGAAC	60.986	66.667	20.43	0.00	45.40	3.01
2109	2272	8.700973	ACTAAACATGTTCCCAAACTTTTGTAT	58.299	29.630	12.39	0.00	36.45	2.29
2631	2803	7.652727	TGCACACAACTTTACAGCAAAATATA	58.347	30.769	0.00	0.00	0.00	0.86
3114	3287	8.624028	CGTTTGAAATAAGACAATTTACGGAAC	58.376	33.333	0.00	0.00	30.35	3.62
3115	3288	8.344098	ACGTTTGAAATAAGACAATTTACGGAA	58.656	29.630	0.00	0.00	34.76	4.30
3116	3289	7.863666	ACGTTTGAAATAAGACAATTTACGGA	58.136	30.769	0.00	0.00	34.76	4.69
3117	3290	9.596677	TTACGTTTGAAATAAGACAATTTACGG	57.403	29.630	0.00	0.00	34.76	4.02
3127	3300	9.640974	CGTTCTCTTTTTACGTTTGAAATAAGA	57.359	29.630	0.00	0.00	0.00	2.10
3128	3301	9.429600	ACGTTCTCTTTTTACGTTTGAAATAAG	57.570	29.630	0.00	0.00	45.21	1.73
3131	3304	9.429600	CTTACGTTCTCTTTTTACGTTTGAAAT	57.570	29.630	4.79	0.00	45.21	2.17
3132	3305	8.655092	TCTTACGTTCTCTTTTTACGTTTGAAA	58.345	29.630	4.79	0.00	45.21	2.69
3133	3306	8.183830	TCTTACGTTCTCTTTTTACGTTTGAA	57.816	30.769	4.79	0.00	45.21	2.69
3134	3307	7.754069	TCTTACGTTCTCTTTTTACGTTTGA	57.246	32.000	4.79	2.09	45.21	2.69
3135	3308	8.810327	TTTCTTACGTTCTCTTTTTACGTTTG	57.190	30.769	4.79	0.00	45.21	2.93
3136	3309	8.659491	ACTTTCTTACGTTCTCTTTTTACGTTT	58.341	29.630	4.79	0.00	45.21	3.60
3137	3310	8.189709	ACTTTCTTACGTTCTCTTTTTACGTT	57.810	30.769	4.79	0.00	45.21	3.99
3232	3405	9.621629	TCAGAAGACCAGAAAAACTACATTTTA	57.378	29.630	0.00	0.00	39.70	1.52
3233	3406	8.406297	GTCAGAAGACCAGAAAAACTACATTTT	58.594	33.333	0.00	0.00	39.29	1.82
3234	3407	7.775561	AGTCAGAAGACCAGAAAAACTACATTT	59.224	33.333	0.00	0.00	46.15	2.32
3235	3408	7.283329	AGTCAGAAGACCAGAAAAACTACATT	58.717	34.615	0.00	0.00	46.15	2.71
3236	3409	6.831976	AGTCAGAAGACCAGAAAAACTACAT	58.168	36.000	0.00	0.00	46.15	2.29
3237	3410	6.098409	AGAGTCAGAAGACCAGAAAAACTACA	59.902	38.462	0.00	0.00	46.15	2.74
3238	3411	6.517605	AGAGTCAGAAGACCAGAAAAACTAC	58.482	40.000	0.00	0.00	46.15	2.73
3239	3412	6.732896	AGAGTCAGAAGACCAGAAAAACTA	57.267	37.500	0.00	0.00	46.15	2.24
3240	3413	5.622346	AGAGTCAGAAGACCAGAAAAACT	57.378	39.130	0.00	0.00	46.15	2.66
3241	3414	6.685527	AAAGAGTCAGAAGACCAGAAAAAC	57.314	37.500	0.00	0.00	46.15	2.43
3242	3415	7.703058	AAAAAGAGTCAGAAGACCAGAAAAA	57.297	32.000	0.00	0.00	46.15	1.94
3243	3416	8.840321	CATAAAAAGAGTCAGAAGACCAGAAAA	58.160	33.333	0.00	0.00	46.15	2.29
3244	3417	7.041098	GCATAAAAAGAGTCAGAAGACCAGAAA	60.041	37.037	0.00	0.00	46.15	2.52
3245	3418	6.428159	GCATAAAAAGAGTCAGAAGACCAGAA	59.572	38.462	0.00	0.00	46.15	3.02
3246	3419	5.934625	GCATAAAAAGAGTCAGAAGACCAGA	59.065	40.000	0.00	0.00	46.15	3.86
3247	3420	5.123027	GGCATAAAAAGAGTCAGAAGACCAG	59.877	44.000	0.00	0.00	46.15	4.00
3248	3421	5.003804	GGCATAAAAAGAGTCAGAAGACCA	58.996	41.667	0.00	0.00	46.15	4.02
3249	3422	5.003804	TGGCATAAAAAGAGTCAGAAGACC	58.996	41.667	0.00	0.00	46.15	3.85
3250	3423	6.560253	TTGGCATAAAAAGAGTCAGAAGAC	57.440	37.500	0.00	0.00	45.31	3.01
3251	3424	7.765695	ATTTGGCATAAAAAGAGTCAGAAGA	57.234	32.000	0.00	0.00	0.00	2.87
3252	3425	8.822652	AAATTTGGCATAAAAAGAGTCAGAAG	57.177	30.769	0.00	0.00	0.00	2.85
3254	3427	9.691362	GTAAAATTTGGCATAAAAAGAGTCAGA	57.309	29.630	0.00	0.00	0.00	3.27
3255	3428	8.638565	CGTAAAATTTGGCATAAAAAGAGTCAG	58.361	33.333	0.00	0.00	0.00	3.51
3256	3429	7.115663	GCGTAAAATTTGGCATAAAAAGAGTCA	59.884	33.333	0.00	0.00	0.00	3.41
3257	3430	7.115663	TGCGTAAAATTTGGCATAAAAAGAGTC	59.884	33.333	7.50	0.00	0.00	3.36
3258	3431	6.926272	TGCGTAAAATTTGGCATAAAAAGAGT	59.074	30.769	7.50	0.00	0.00	3.24
3259	3432	7.344910	TGCGTAAAATTTGGCATAAAAAGAG	57.655	32.000	7.50	0.00	0.00	2.85
3260	3433	7.715265	TTGCGTAAAATTTGGCATAAAAAGA	57.285	28.000	11.22	0.00	35.03	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.