AutoCloner

Multiple sequence alignment - TraesCS2B01G289800

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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	TraesCS2B01G289800	chr2B	100.000	2644	0	0	592	3235	401814921	401817564	0.000000e+00	4883
1	TraesCS2B01G289800	chr2B	100.000	334	0	0	1	334	401814330	401814663	4.590000e-173	617
2	TraesCS2B01G289800	chr2D	96.715	1583	23	11	668	2232	333646194	333647765	0.000000e+00	2608
3	TraesCS2B01G289800	chr2D	88.988	336	32	3	3	334	333645321	333645655	8.350000e-111	411
4	TraesCS2B01G289800	chr2A	94.272	1641	37	19	615	2232	443644478	443646084	0.000000e+00	2457
5	TraesCS2B01G289800	chr2A	85.096	993	111	28	2257	3235	40835409	40836378	0.000000e+00	979
6	TraesCS2B01G289800	chr2A	87.798	336	33	5	3	334	443643833	443644164	1.410000e-103	387
7	TraesCS2B01G289800	chr6D	94.614	984	47	4	2255	3235	402876270	402875290	0.000000e+00	1519
8	TraesCS2B01G289800	chr6B	92.871	996	52	12	2254	3235	21829642	21830632	0.000000e+00	1428
9	TraesCS2B01G289800	chr5A	92.966	981	63	5	2259	3235	11720136	11719158	0.000000e+00	1424
10	TraesCS2B01G289800	chr5A	83.764	271	40	4	1133	1400	688832030	688831761	1.490000e-63	254
11	TraesCS2B01G289800	chr4D	90.190	999	80	7	2254	3235	71291741	71290744	0.000000e+00	1286
12	TraesCS2B01G289800	chr4D	81.579	380	55	13	1138	1509	504178235	504177863	1.890000e-77	300
13	TraesCS2B01G289800	chr4D	84.586	266	36	5	1138	1400	504115849	504115586	3.200000e-65	259
14	TraesCS2B01G289800	chr6A	84.739	996	111	30	2257	3235	17762330	17761359	0.000000e+00	959
15	TraesCS2B01G289800	chr6A	83.702	994	113	33	2256	3235	41670283	41669325	0.000000e+00	893
16	TraesCS2B01G289800	chr6A	76.694	738	137	26	2498	3230	66377060	66377767	8.470000e-101	377
17	TraesCS2B01G289800	chr3B	85.144	727	89	17	2516	3235	214444478	214445192	0.000000e+00	726
18	TraesCS2B01G289800	chr3B	84.241	349	50	4	1145	1492	72478138	72477794	5.170000e-88	335
19	TraesCS2B01G289800	chr7D	79.158	998	136	48	2253	3230	616100278	616101223	2.740000e-175	625
20	TraesCS2B01G289800	chrUn	85.274	584	73	12	2654	3235	30691667	30691095	1.000000e-164	590
21	TraesCS2B01G289800	chrUn	81.796	412	44	21	2261	2656	30700966	30700570	1.870000e-82	316
22	TraesCS2B01G289800	chr1D	93.067	375	24	2	2832	3206	470314044	470313672	6.100000e-152	547
23	TraesCS2B01G289800	chr3D	84.527	349	49	4	1145	1492	46471865	46471521	1.110000e-89	340
24	TraesCS2B01G289800	chr3A	83.095	349	54	5	1145	1492	57886850	57886506	2.420000e-81	313
25	TraesCS2B01G289800	chr4B	81.698	377	59	10	1138	1509	650706892	650706521	4.050000e-79	305

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	TraesCS2B01G289800	chr2B	401814330	401817564	3234	False	2750.0	4883	100.0000	1	3235	2	chr2B.!!$F1	3234
1	TraesCS2B01G289800	chr2D	333645321	333647765	2444	False	1509.5	2608	92.8515	3	2232	2	chr2D.!!$F1	2229
2	TraesCS2B01G289800	chr2A	443643833	443646084	2251	False	1422.0	2457	91.0350	3	2232	2	chr2A.!!$F2	2229
3	TraesCS2B01G289800	chr2A	40835409	40836378	969	False	979.0	979	85.0960	2257	3235	1	chr2A.!!$F1	978
4	TraesCS2B01G289800	chr6D	402875290	402876270	980	True	1519.0	1519	94.6140	2255	3235	1	chr6D.!!$R1	980
5	TraesCS2B01G289800	chr6B	21829642	21830632	990	False	1428.0	1428	92.8710	2254	3235	1	chr6B.!!$F1	981
6	TraesCS2B01G289800	chr5A	11719158	11720136	978	True	1424.0	1424	92.9660	2259	3235	1	chr5A.!!$R1	976
7	TraesCS2B01G289800	chr4D	71290744	71291741	997	True	1286.0	1286	90.1900	2254	3235	1	chr4D.!!$R1	981
8	TraesCS2B01G289800	chr6A	17761359	17762330	971	True	959.0	959	84.7390	2257	3235	1	chr6A.!!$R1	978
9	TraesCS2B01G289800	chr6A	41669325	41670283	958	True	893.0	893	83.7020	2256	3235	1	chr6A.!!$R2	979
10	TraesCS2B01G289800	chr6A	66377060	66377767	707	False	377.0	377	76.6940	2498	3230	1	chr6A.!!$F1	732
11	TraesCS2B01G289800	chr3B	214444478	214445192	714	False	726.0	726	85.1440	2516	3235	1	chr3B.!!$F1	719
12	TraesCS2B01G289800	chr7D	616100278	616101223	945	False	625.0	625	79.1580	2253	3230	1	chr7D.!!$F1	977
13	TraesCS2B01G289800	chrUn	30691095	30691667	572	True	590.0	590	85.2740	2654	3235	1	chrUn.!!$R1	581

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
32	33	0.261991	TTATGACCGGAGAGGCCTCT	59.738	55.0	35.74	35.74	46.52	3.69	F
1038	1313	0.398696	TACATCACCACCACCACCAC	59.601	55.0	0.00	0.00	0.00	4.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1042	1317	0.105709	GAAGGGAGGGAGAGAGGAGG	60.106	65.0	0.0	0.0	0.0	4.30	R
2243	2547	0.591659	GGGGCGTTTCTGTGTCTTTC	59.408	55.0	0.0	0.0	0.0	2.62	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
30	31	1.807814	ATTTATGACCGGAGAGGCCT	58.192	50.000	9.46	3.86	46.52	5.19
32	33	0.261991	TTATGACCGGAGAGGCCTCT	59.738	55.000	35.74	35.74	46.52	3.69
44	45	1.266989	GAGGCCTCTCAAACGTTTTGG	59.733	52.381	26.25	11.99	39.74	3.28
126	127	4.200874	AGGTACATGGAAACGTTTCAACA	58.799	39.130	34.79	26.34	38.92	3.33
135	136	6.259638	TGGAAACGTTTCAACAATTAGTCAC	58.740	36.000	34.79	17.39	38.92	3.67
141	142	6.685403	ACGTTTCAACAATTAGTCACTTTTCG	59.315	34.615	0.00	0.00	0.00	3.46
154	155	3.126514	TCACTTTTCGCACAAACCGTTAA	59.873	39.130	0.00	0.00	0.00	2.01
207	208	5.419542	TCACTATTCATCTTCAACTTCCCG	58.580	41.667	0.00	0.00	0.00	5.14
215	216	4.193826	TCTTCAACTTCCCGATCTCTTG	57.806	45.455	0.00	0.00	0.00	3.02
228	229	2.084610	TCTCTTGTTCCTCATGCACG	57.915	50.000	0.00	0.00	0.00	5.34
242	244	3.130227	CACGCCTCTAGCTACCCC	58.870	66.667	0.00	0.00	40.39	4.95
243	245	2.518825	ACGCCTCTAGCTACCCCG	60.519	66.667	0.00	0.00	40.39	5.73
247	249	2.918276	CTCTAGCTACCCCGCCCC	60.918	72.222	0.00	0.00	0.00	5.80
249	251	2.766651	CTAGCTACCCCGCCCCAA	60.767	66.667	0.00	0.00	0.00	4.12
636	792	3.954258	AGGCGCCTAAGATTTAGCAAAAT	59.046	39.130	31.86	0.00	38.03	1.82
663	819	8.912658	CGAAATAGTTTATGCAGTGATACGTAT	58.087	33.333	8.05	8.05	0.00	3.06
666	822	8.891367	ATAGTTTATGCAGTGATACGTATACG	57.109	34.615	23.24	23.24	46.33	3.06
706	981	3.860754	GCTTGAATAGTTGGTTGGTTGGC	60.861	47.826	0.00	0.00	0.00	4.52
1034	1309	3.010027	ACATCAATACATCACCACCACCA	59.990	43.478	0.00	0.00	0.00	4.17
1035	1310	3.066291	TCAATACATCACCACCACCAC	57.934	47.619	0.00	0.00	0.00	4.16
1037	1312	1.367346	ATACATCACCACCACCACCA	58.633	50.000	0.00	0.00	0.00	4.17
1038	1313	0.398696	TACATCACCACCACCACCAC	59.601	55.000	0.00	0.00	0.00	4.16
1040	1315	2.081787	ATCACCACCACCACCACCA	61.082	57.895	0.00	0.00	0.00	4.17
1042	1317	3.816090	ACCACCACCACCACCACC	61.816	66.667	0.00	0.00	0.00	4.61
1044	1319	3.498071	CACCACCACCACCACCCT	61.498	66.667	0.00	0.00	0.00	4.34
1045	1320	3.175710	ACCACCACCACCACCCTC	61.176	66.667	0.00	0.00	0.00	4.30
1046	1321	3.966543	CCACCACCACCACCCTCC	61.967	72.222	0.00	0.00	0.00	4.30
1047	1322	2.854032	CACCACCACCACCCTCCT	60.854	66.667	0.00	0.00	0.00	3.69
1060	1335	1.598856	CCCTCCTCTCTCCCTCCCTT	61.599	65.000	0.00	0.00	0.00	3.95
1061	1336	0.105709	CCTCCTCTCTCCCTCCCTTC	60.106	65.000	0.00	0.00	0.00	3.46
1131	1409	2.030185	CCAGCACGTACTACACTCAAGT	60.030	50.000	0.00	0.00	0.00	3.16
1420	1698	1.792757	TTGGCCTGCTCTGGTCCAAT	61.793	55.000	3.32	0.00	37.90	3.16
1667	1945	0.040958	CAGCGACTCCAACAACAAGC	60.041	55.000	0.00	0.00	0.00	4.01
1668	1946	1.166531	AGCGACTCCAACAACAAGCC	61.167	55.000	0.00	0.00	0.00	4.35
1669	1947	1.949257	CGACTCCAACAACAAGCCC	59.051	57.895	0.00	0.00	0.00	5.19
1670	1948	0.817634	CGACTCCAACAACAAGCCCA	60.818	55.000	0.00	0.00	0.00	5.36
1671	1949	1.398692	GACTCCAACAACAAGCCCAA	58.601	50.000	0.00	0.00	0.00	4.12
1672	1950	1.338020	GACTCCAACAACAAGCCCAAG	59.662	52.381	0.00	0.00	0.00	3.61
2224	2528	8.741841	CATGGCCAAGATTTTTCCAATAAAAAT	58.258	29.630	10.96	7.88	41.11	1.82
2225	2529	8.108551	TGGCCAAGATTTTTCCAATAAAAATG	57.891	30.769	0.61	1.99	39.23	2.32
2661	3009	1.667154	TTCTAGCTGCGATGCGTCCT	61.667	55.000	0.00	0.00	38.13	3.85
2921	3304	2.096248	GAGGCTACAGTGCTAGTGACT	58.904	52.381	0.00	0.00	0.00	3.41
2959	3344	2.582436	GGGTACTTGCTGGCGCTA	59.418	61.111	7.64	0.00	36.97	4.26
3017	3402	2.047274	CCATGGTTGACGGCGTCT	60.047	61.111	36.17	16.74	33.15	4.18
3127	3512	0.745845	GCAACATGGATCTGCGTCCT	60.746	55.000	0.00	0.00	39.12	3.85
3187	3572	1.457455	ACCCCCTTGTGGTTTGCTG	60.457	57.895	0.00	0.00	29.75	4.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	5.756918	TCCGGTCATAAATTTATCACCCAA	58.243	37.500	21.51	9.98	31.32	4.12
1	2	5.131308	TCTCCGGTCATAAATTTATCACCCA	59.869	40.000	21.51	10.39	31.32	4.51
30	31	2.993937	ACCAGTCCAAAACGTTTGAGA	58.006	42.857	15.46	11.52	0.00	3.27
32	33	3.566322	CCATACCAGTCCAAAACGTTTGA	59.434	43.478	15.46	5.59	0.00	2.69
34	35	3.818773	CTCCATACCAGTCCAAAACGTTT	59.181	43.478	7.96	7.96	0.00	3.60
44	45	2.180276	ACCAGACACTCCATACCAGTC	58.820	52.381	0.00	0.00	0.00	3.51
118	119	6.470877	TGCGAAAAGTGACTAATTGTTGAAAC	59.529	34.615	0.00	0.00	0.00	2.78
126	127	5.278604	GGTTTGTGCGAAAAGTGACTAATT	58.721	37.500	0.00	0.00	0.00	1.40
135	136	4.973663	AGATTTAACGGTTTGTGCGAAAAG	59.026	37.500	0.00	0.00	0.00	2.27
141	142	6.383415	TGGATTAAGATTTAACGGTTTGTGC	58.617	36.000	0.00	0.00	0.00	4.57
154	155	2.818751	TGGGCCGTTGGATTAAGATT	57.181	45.000	0.00	0.00	0.00	2.40
207	208	2.606725	CGTGCATGAGGAACAAGAGATC	59.393	50.000	0.00	0.00	0.00	2.75
215	216	0.175760	TAGAGGCGTGCATGAGGAAC	59.824	55.000	10.93	0.00	0.00	3.62
228	229	3.617735	GGCGGGGTAGCTAGAGGC	61.618	72.222	0.00	0.00	42.19	4.70
312	316	3.534054	TAACAACGGCGTGGGGGAC	62.534	63.158	20.07	0.00	0.00	4.46
313	317	3.240011	TAACAACGGCGTGGGGGA	61.240	61.111	20.07	0.00	0.00	4.81
591	595	2.041922	TCCCGGATGGAGGTGAGG	60.042	66.667	0.73	0.00	38.61	3.86
618	773	9.387123	CTATTTCGATTTTGCTAAATCTTAGGC	57.613	33.333	24.48	5.25	44.84	3.93
636	792	6.976349	ACGTATCACTGCATAAACTATTTCGA	59.024	34.615	0.00	0.00	0.00	3.71
663	819	4.053295	GCGCCCTTTGATTTATCTACGTA	58.947	43.478	0.00	0.00	0.00	3.57
664	820	2.870411	GCGCCCTTTGATTTATCTACGT	59.130	45.455	0.00	0.00	0.00	3.57
665	821	3.131396	AGCGCCCTTTGATTTATCTACG	58.869	45.455	2.29	0.00	0.00	3.51
666	822	4.574828	TCAAGCGCCCTTTGATTTATCTAC	59.425	41.667	2.29	0.00	0.00	2.59
706	981	3.441572	CCAGGTGGACTTTCTTGCATAAG	59.558	47.826	0.00	0.00	37.39	1.73
956	1231	8.930846	ATTGTGATGATATAAAGAAGAAGGGG	57.069	34.615	0.00	0.00	0.00	4.79
1034	1309	1.079438	GAGAGAGGAGGGTGGTGGT	59.921	63.158	0.00	0.00	0.00	4.16
1035	1310	1.687493	GGAGAGAGGAGGGTGGTGG	60.687	68.421	0.00	0.00	0.00	4.61
1037	1312	1.864559	AGGGAGAGAGGAGGGTGGT	60.865	63.158	0.00	0.00	0.00	4.16
1038	1313	1.075600	GAGGGAGAGAGGAGGGTGG	60.076	68.421	0.00	0.00	0.00	4.61
1040	1315	2.329399	GGGAGGGAGAGAGGAGGGT	61.329	68.421	0.00	0.00	0.00	4.34
1042	1317	0.105709	GAAGGGAGGGAGAGAGGAGG	60.106	65.000	0.00	0.00	0.00	4.30
1044	1319	0.556380	AGGAAGGGAGGGAGAGAGGA	60.556	60.000	0.00	0.00	0.00	3.71
1045	1320	0.105709	GAGGAAGGGAGGGAGAGAGG	60.106	65.000	0.00	0.00	0.00	3.69
1046	1321	0.105709	GGAGGAAGGGAGGGAGAGAG	60.106	65.000	0.00	0.00	0.00	3.20
1047	1322	0.556380	AGGAGGAAGGGAGGGAGAGA	60.556	60.000	0.00	0.00	0.00	3.10
1060	1335	1.634459	AGAAGGTGTCTACGAGGAGGA	59.366	52.381	0.00	0.00	33.56	3.71
1061	1336	2.018515	GAGAAGGTGTCTACGAGGAGG	58.981	57.143	0.00	0.00	36.41	4.30
1131	1409	2.400798	GCATCGTCGTCGTCGGTA	59.599	61.111	11.74	0.00	38.33	4.02
1402	1680	0.913934	TATTGGACCAGAGCAGGCCA	60.914	55.000	5.01	0.00	34.47	5.36
1713	2003	1.635663	CTTGCGGTGTTGACGATCCC	61.636	60.000	0.00	0.00	0.00	3.85
1873	2163	1.890625	CTGTGCTCTGCTCCTGCTCT	61.891	60.000	0.00	0.00	40.48	4.09
1987	2286	1.377202	GCTCAGGTGAAATCCGGCA	60.377	57.895	0.00	0.00	0.00	5.69
2148	2448	6.622549	ACCATGAAACAAAAACGAACTAACA	58.377	32.000	0.00	0.00	0.00	2.41
2238	2542	4.421058	GGCGTTTCTGTGTCTTTCTTTTT	58.579	39.130	0.00	0.00	0.00	1.94
2239	2543	3.181490	GGGCGTTTCTGTGTCTTTCTTTT	60.181	43.478	0.00	0.00	0.00	2.27
2240	2544	2.357952	GGGCGTTTCTGTGTCTTTCTTT	59.642	45.455	0.00	0.00	0.00	2.52
2241	2545	1.947456	GGGCGTTTCTGTGTCTTTCTT	59.053	47.619	0.00	0.00	0.00	2.52
2242	2546	1.594331	GGGCGTTTCTGTGTCTTTCT	58.406	50.000	0.00	0.00	0.00	2.52
2243	2547	0.591659	GGGGCGTTTCTGTGTCTTTC	59.408	55.000	0.00	0.00	0.00	2.62
2244	2548	0.822121	GGGGGCGTTTCTGTGTCTTT	60.822	55.000	0.00	0.00	0.00	2.52
2245	2549	1.228154	GGGGGCGTTTCTGTGTCTT	60.228	57.895	0.00	0.00	0.00	3.01
2246	2550	2.430367	GGGGGCGTTTCTGTGTCT	59.570	61.111	0.00	0.00	0.00	3.41
2247	2551	3.047877	CGGGGGCGTTTCTGTGTC	61.048	66.667	0.00	0.00	0.00	3.67
2440	2761	4.757773	ACGGAAGTGGATCTCGGA	57.242	55.556	0.00	0.00	46.97	4.55
2921	3304	4.649705	TTGAGGAGCCCCGGGACA	62.650	66.667	26.32	9.15	37.58	4.02
2967	3352	4.011517	GGGTCCAAAGTCGCCGGA	62.012	66.667	5.05	0.00	0.00	5.14
3017	3402	4.545706	CGGAGCTGCCCGGCATAA	62.546	66.667	13.86	0.00	45.43	1.90
3064	3449	4.074526	GTGAGCCAGGCGAGCTGA	62.075	66.667	5.55	0.00	41.75	4.26

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.