AutoCloner

Multiple sequence alignment - TraesCS2B01G165300

Loading Multiple Alignment...

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	TraesCS2B01G165300	chr2B	100.000	4260	0	0	1	4260	137606674	137610933	0.000000e+00	7867.0
1	TraesCS2B01G165300	chr2B	97.486	2347	30	8	1583	3905	136951179	136953520	0.000000e+00	3980.0
2	TraesCS2B01G165300	chr2B	97.435	2300	36	8	1448	3746	136806008	136808285	0.000000e+00	3899.0
3	TraesCS2B01G165300	chr2B	92.501	2147	121	12	1173	3296	137188108	137190237	0.000000e+00	3037.0
4	TraesCS2B01G165300	chr2B	86.915	726	75	11	87	803	136949435	136950149	0.000000e+00	797.0
5	TraesCS2B01G165300	chr2B	85.190	736	77	19	87	803	136804465	136805187	0.000000e+00	726.0
6	TraesCS2B01G165300	chr2B	95.789	285	11	1	893	1176	136950327	136950611	3.880000e-125	459.0
7	TraesCS2B01G165300	chr2B	98.701	231	2	1	4031	4260	136953514	136953744	3.970000e-110	409.0
8	TraesCS2B01G165300	chr2B	92.933	283	13	3	893	1175	136805358	136805633	5.130000e-109	405.0
9	TraesCS2B01G165300	chr2B	91.003	289	16	5	896	1176	137187789	137188075	8.640000e-102	381.0
10	TraesCS2B01G165300	chr2B	88.966	290	15	1	1206	1478	136805719	136806008	4.080000e-90	342.0
11	TraesCS2B01G165300	chr2B	89.076	238	18	5	517	751	137185818	137186050	5.390000e-74	289.0
12	TraesCS2B01G165300	chr2B	87.442	215	10	1	1281	1478	136950886	136951100	9.210000e-57	231.0
13	TraesCS2B01G165300	chr2B	94.444	108	6	0	1173	1280	136950644	136950751	2.630000e-37	167.0
14	TraesCS2B01G165300	chr2B	92.941	85	6	0	796	880	136950187	136950271	1.610000e-24	124.0
15	TraesCS2B01G165300	chr2B	93.421	76	4	1	806	880	136805229	136805304	1.250000e-20	111.0
16	TraesCS2B01G165300	chr2B	90.244	82	8	0	1448	1529	136951100	136951181	1.620000e-19	108.0
17	TraesCS2B01G165300	chr2D	96.005	2453	64	14	1448	3872	85388884	85391330	0.000000e+00	3956.0
18	TraesCS2B01G165300	chr2D	91.787	2143	136	11	1173	3296	84916037	84918158	0.000000e+00	2946.0
19	TraesCS2B01G165300	chr2D	93.889	1849	108	3	1448	3296	85673301	85675144	0.000000e+00	2784.0
20	TraesCS2B01G165300	chr2D	87.879	825	72	14	1	803	85387243	85388061	0.000000e+00	944.0
21	TraesCS2B01G165300	chr2D	87.784	704	69	11	87	782	84914785	84915479	0.000000e+00	808.0
22	TraesCS2B01G165300	chr2D	90.104	576	51	6	87	659	85671762	85672334	0.000000e+00	743.0
23	TraesCS2B01G165300	chr2D	95.251	379	11	4	3883	4260	85391387	85391759	1.020000e-165	593.0
24	TraesCS2B01G165300	chr2D	93.059	389	13	5	796	1176	85388099	85388481	1.340000e-154	556.0
25	TraesCS2B01G165300	chr2D	95.088	285	13	1	893	1176	84915691	84915975	8.400000e-122	448.0
26	TraesCS2B01G165300	chr2D	91.049	324	11	2	1173	1478	85672978	85673301	5.090000e-114	422.0
27	TraesCS2B01G165300	chr2D	89.273	289	14	1	1206	1477	85388565	85388853	3.150000e-91	346.0
28	TraesCS2B01G165300	chr2D	95.833	192	8	0	954	1145	85672703	85672894	1.150000e-80	311.0
29	TraesCS2B01G165300	chr2D	92.857	84	6	0	796	879	84915551	84915634	5.780000e-24	122.0
30	TraesCS2B01G165300	chr2D	79.141	163	20	6	3952	4114	84928613	84928761	2.710000e-17	100.0
31	TraesCS2B01G165300	chr2A	90.111	1527	133	13	1778	3296	84154116	84152600	0.000000e+00	1967.0
32	TraesCS2B01G165300	chr2A	93.750	96	6	0	1231	1326	84154378	84154283	1.230000e-30	145.0
33	TraesCS2B01G165300	chr2A	94.737	38	1	1	3987	4024	85600822	85600858	1.650000e-04	58.4
34	TraesCS2B01G165300	chr2A	100.000	31	0	0	4033	4063	172842575	172842545	1.650000e-04	58.4
35	TraesCS2B01G165300	chr4B	94.688	640	12	8	3227	3847	446685640	446686276	0.000000e+00	974.0
36	TraesCS2B01G165300	chr7A	93.253	667	21	3	3616	4260	571276068	571276732	0.000000e+00	961.0
37	TraesCS2B01G165300	chr7A	75.447	1287	255	46	2021	3280	32413303	32414555	1.720000e-158	569.0
38	TraesCS2B01G165300	chr3B	93.438	640	18	6	3227	3847	124618410	124619044	0.000000e+00	928.0
39	TraesCS2B01G165300	chr3B	76.382	1266	252	32	2020	3267	824391358	824392594	4.650000e-179	638.0
40	TraesCS2B01G165300	chrUn	76.609	1274	260	31	2020	3273	320961871	320963126	0.000000e+00	667.0
41	TraesCS2B01G165300	chr4A	73.761	1231	260	45	2057	3260	717966792	717965598	3.940000e-115	425.0
42	TraesCS2B01G165300	chr7D	77.341	662	129	16	2456	3102	16709135	16709790	5.200000e-99	372.0
43	TraesCS2B01G165300	chr5A	97.561	41	1	0	1360	1400	613462683	613462723	2.130000e-08	71.3
44	TraesCS2B01G165300	chr1D	97.297	37	1	0	3468	3504	38596749	38596713	3.560000e-06	63.9
45	TraesCS2B01G165300	chr6B	82.051	78	8	3	3988	4063	318876096	318876169	1.280000e-05	62.1
46	TraesCS2B01G165300	chr6B	82.051	78	8	3	3988	4063	318988008	318988081	1.280000e-05	62.1
47	TraesCS2B01G165300	chr1B	100.000	33	0	0	4031	4063	510308610	510308578	1.280000e-05	62.1
48	TraesCS2B01G165300	chr7B	100.000	31	0	0	4033	4063	248701192	248701162	1.650000e-04	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	TraesCS2B01G165300	chr2B	137606674	137610933	4259	False	7867.000000	7867	100.00000	1	4260	1	chr2B.!!$F1	4259
1	TraesCS2B01G165300	chr2B	137185818	137190237	4419	False	1235.666667	3037	90.86000	517	3296	3	chr2B.!!$F4	2779
2	TraesCS2B01G165300	chr2B	136804465	136808285	3820	False	1096.600000	3899	91.58900	87	3746	5	chr2B.!!$F2	3659
3	TraesCS2B01G165300	chr2B	136949435	136953744	4309	False	784.375000	3980	92.99525	87	4260	8	chr2B.!!$F3	4173
4	TraesCS2B01G165300	chr2D	85387243	85391759	4516	False	1279.000000	3956	92.29340	1	4260	5	chr2D.!!$F3	4259
5	TraesCS2B01G165300	chr2D	84914785	84918158	3373	False	1081.000000	2946	91.87900	87	3296	4	chr2D.!!$F2	3209
6	TraesCS2B01G165300	chr2D	85671762	85675144	3382	False	1065.000000	2784	92.71875	87	3296	4	chr2D.!!$F4	3209
7	TraesCS2B01G165300	chr2A	84152600	84154378	1778	True	1056.000000	1967	91.93050	1231	3296	2	chr2A.!!$R2	2065
8	TraesCS2B01G165300	chr4B	446685640	446686276	636	False	974.000000	974	94.68800	3227	3847	1	chr4B.!!$F1	620
9	TraesCS2B01G165300	chr7A	571276068	571276732	664	False	961.000000	961	93.25300	3616	4260	1	chr7A.!!$F2	644
10	TraesCS2B01G165300	chr7A	32413303	32414555	1252	False	569.000000	569	75.44700	2021	3280	1	chr7A.!!$F1	1259
11	TraesCS2B01G165300	chr3B	124618410	124619044	634	False	928.000000	928	93.43800	3227	3847	1	chr3B.!!$F1	620
12	TraesCS2B01G165300	chr3B	824391358	824392594	1236	False	638.000000	638	76.38200	2020	3267	1	chr3B.!!$F2	1247
13	TraesCS2B01G165300	chrUn	320961871	320963126	1255	False	667.000000	667	76.60900	2020	3273	1	chrUn.!!$F1	1253
14	TraesCS2B01G165300	chr4A	717965598	717966792	1194	True	425.000000	425	73.76100	2057	3260	1	chr4A.!!$R1	1203
15	TraesCS2B01G165300	chr7D	16709135	16709790	655	False	372.000000	372	77.34100	2456	3102	1	chr7D.!!$F1	646

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
431	460	0.249489	AGTGCTCTGTCGCTCGTTTT	60.249	50.0	0.0	0.0	0.0	2.43	F
1719	3743	0.346932	AGGAGGGGGAGAATTGGCTA	59.653	55.0	0.0	0.0	0.0	3.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1728	3752	1.355971	GCCAGTCGCGTGAAAATCTA	58.644	50.000	5.77	0.0	0.0	1.98	R
3667	5922	4.586421	TGCTCTCTCTGGTGGTGATAATAG	59.414	45.833	0.00	0.0	0.0	1.73	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
21	22	0.543410	TCCTGGCCCAACTAAGACGA	60.543	55.000	0.00	0.00	0.00	4.20
22	23	0.541863	CCTGGCCCAACTAAGACGAT	59.458	55.000	0.00	0.00	0.00	3.73
25	26	0.392461	GGCCCAACTAAGACGATGCA	60.392	55.000	0.00	0.00	0.00	3.96
29	30	2.352651	CCCAACTAAGACGATGCATGTG	59.647	50.000	2.46	0.00	0.00	3.21
30	31	3.261580	CCAACTAAGACGATGCATGTGA	58.738	45.455	2.46	0.00	0.00	3.58
32	33	4.333649	CCAACTAAGACGATGCATGTGAAT	59.666	41.667	2.46	0.00	0.00	2.57
35	36	4.937620	ACTAAGACGATGCATGTGAATGTT	59.062	37.500	2.46	0.00	0.00	2.71
79	80	2.222640	CGTCGTTGTTGTTGTTCTCGTT	60.223	45.455	0.00	0.00	0.00	3.85
122	144	1.611006	CTCGGTCCAGACGATGATGAT	59.389	52.381	0.00	0.00	39.89	2.45
168	190	1.078988	GGCACCATCCCGACGTTTA	60.079	57.895	0.00	0.00	0.00	2.01
186	208	3.713826	TTAATTCGGCTGGAAAGACCT	57.286	42.857	0.00	0.00	38.36	3.85
226	248	4.334118	ATGGCTCGTGTGGCAGCA	62.334	61.111	0.00	0.00	45.49	4.41
237	259	4.446413	GGCAGCAGCAATGTGGGC	62.446	66.667	2.65	0.00	44.61	5.36
307	334	4.203076	GCGGGCTCGTCGTGGTAT	62.203	66.667	8.30	0.00	38.89	2.73
317	344	2.540516	TCGTCGTGGTATGTTTGTTGTG	59.459	45.455	0.00	0.00	0.00	3.33
331	358	1.064758	TGTTGTGGTGGAGTCAAAGCT	60.065	47.619	0.00	0.00	0.00	3.74
332	359	1.334869	GTTGTGGTGGAGTCAAAGCTG	59.665	52.381	0.00	0.00	0.00	4.24
389	418	3.659195	TGGATGGCCCATCTAGATGATTT	59.341	43.478	30.40	12.44	40.82	2.17
391	420	4.704057	GGATGGCCCATCTAGATGATTTTC	59.296	45.833	30.40	19.20	40.39	2.29
397	426	3.188048	CCATCTAGATGATTTTCCGCAGC	59.812	47.826	30.40	0.00	41.20	5.25
431	460	0.249489	AGTGCTCTGTCGCTCGTTTT	60.249	50.000	0.00	0.00	0.00	2.43
450	479	3.311486	TTTTCCCGAATCCATTGTTGC	57.689	42.857	0.00	0.00	0.00	4.17
465	496	1.077140	TTGCCCCATTGCTCGCATA	60.077	52.632	0.00	0.00	0.00	3.14
498	529	2.885135	TGGCTTGGATCTTCATGTGT	57.115	45.000	0.00	0.00	0.00	3.72
506	537	1.590238	GATCTTCATGTGTCCGCTTCG	59.410	52.381	0.00	0.00	0.00	3.79
621	653	2.485426	TCGTCGATGTTTCCTTCGTAGT	59.515	45.455	4.21	0.00	38.83	2.73
1167	2893	2.108168	TCTCTACGGCAGCTATTGGTT	58.892	47.619	0.00	0.00	0.00	3.67
1180	2974	5.183331	CAGCTATTGGTTAGTAGCCGAGATA	59.817	44.000	0.00	0.00	43.32	1.98
1356	3284	5.244626	TCACCAGTTTACCTACTTGTAGTCC	59.755	44.000	6.99	0.00	0.00	3.85
1448	3448	2.036604	GGGTCTATCTTAGAGTGGCAGC	59.963	54.545	0.00	0.00	35.04	5.25
1719	3743	0.346932	AGGAGGGGGAGAATTGGCTA	59.653	55.000	0.00	0.00	0.00	3.93
1728	3752	3.257375	GGGAGAATTGGCTAACCGTTTTT	59.743	43.478	0.00	0.00	39.70	1.94
1770	3795	3.139077	CCTAACCGCTCCCAAATATCAC	58.861	50.000	0.00	0.00	0.00	3.06
1890	4060	7.996644	TCTGGGGTAGCTTATTTTAATTGTAGG	59.003	37.037	0.00	0.00	0.00	3.18
1998	4169	5.507637	TGCAGTAAGAGCCTAAGTACTACT	58.492	41.667	0.00	0.00	0.00	2.57
2140	4322	0.898320	GCTTGGTCTCTACCTCAGCA	59.102	55.000	11.98	0.00	46.91	4.41
2427	4618	3.260884	AGGACAAACTTATCTCTTCGCCA	59.739	43.478	0.00	0.00	0.00	5.69
3379	5602	4.322801	CGGGAAGGAACTGAAGTGTCTAAT	60.323	45.833	0.00	0.00	40.86	1.73
3817	6072	7.216494	TCATTATTCATCGGTCTAATCAAGCA	58.784	34.615	0.00	0.00	0.00	3.91
4027	6337	3.903714	TCAGAGTTCAGAATGGTCCAAGA	59.096	43.478	0.00	0.00	36.16	3.02
4028	6338	4.347876	TCAGAGTTCAGAATGGTCCAAGAA	59.652	41.667	0.00	0.00	36.16	2.52
4029	6339	4.694509	CAGAGTTCAGAATGGTCCAAGAAG	59.305	45.833	0.00	0.00	36.16	2.85
4030	6340	4.349342	AGAGTTCAGAATGGTCCAAGAAGT	59.651	41.667	0.00	1.39	36.16	3.01
4031	6341	5.544176	AGAGTTCAGAATGGTCCAAGAAGTA	59.456	40.000	0.00	0.00	36.16	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	2.352651	CACATGCATCGTCTTAGTTGGG	59.647	50.000	0.00	0.00	0.00	4.12
21	22	4.877378	AGGAAACAACATTCACATGCAT	57.123	36.364	0.00	0.00	33.05	3.96
22	23	4.099113	TCAAGGAAACAACATTCACATGCA	59.901	37.500	0.00	0.00	33.05	3.96
25	26	6.653526	TCATCAAGGAAACAACATTCACAT	57.346	33.333	0.00	0.00	0.00	3.21
53	54	1.563111	ACAACAACAACGACGACGAT	58.437	45.000	15.32	0.00	42.66	3.73
54	55	1.321148	GAACAACAACAACGACGACGA	59.679	47.619	15.32	0.00	42.66	4.20
55	56	1.322338	AGAACAACAACAACGACGACG	59.678	47.619	5.58	5.58	45.75	5.12
56	57	2.593582	CGAGAACAACAACAACGACGAC	60.594	50.000	0.00	0.00	0.00	4.34
57	58	1.584761	CGAGAACAACAACAACGACGA	59.415	47.619	0.00	0.00	0.00	4.20
58	59	1.322338	ACGAGAACAACAACAACGACG	59.678	47.619	0.00	0.00	0.00	5.12
79	80	2.279073	CGGACCTAGGGCAGAGGA	59.721	66.667	18.82	0.00	37.53	3.71
110	132	7.281999	ACGACATCATAGATATCATCATCGTCT	59.718	37.037	5.32	0.00	0.00	4.18
122	144	6.944234	AGAGTGAACACGACATCATAGATA	57.056	37.500	0.00	0.00	36.20	1.98
160	182	1.352114	TCCAGCCGAATTAAACGTCG	58.648	50.000	0.00	0.00	37.01	5.12
163	185	3.425758	GGTCTTTCCAGCCGAATTAAACG	60.426	47.826	0.00	0.00	35.97	3.60
168	190	1.073923	ACAGGTCTTTCCAGCCGAATT	59.926	47.619	0.00	0.00	39.02	2.17
186	208	1.530419	GACCACCATGCCAACCACA	60.530	57.895	0.00	0.00	0.00	4.17
237	259	3.114616	CAGCCTTGACCTCGCACG	61.115	66.667	0.00	0.00	0.00	5.34
307	334	2.498644	TGACTCCACCACAACAAACA	57.501	45.000	0.00	0.00	0.00	2.83
317	344	0.947244	CACACAGCTTTGACTCCACC	59.053	55.000	6.92	0.00	0.00	4.61
331	358	3.484806	ACAAGGACCCGCCACACA	61.485	61.111	0.00	0.00	40.02	3.72
332	359	2.978010	CACAAGGACCCGCCACAC	60.978	66.667	0.00	0.00	40.02	3.82
355	384	1.671054	CCATCCACCGCTTGTCGTT	60.671	57.895	0.00	0.00	36.19	3.85
381	410	1.718757	GCGGCTGCGGAAAATCATCT	61.719	55.000	11.68	0.00	0.00	2.90
397	426	1.802636	CACTATGCAAGGTTGGCGG	59.197	57.895	0.00	0.00	0.00	6.13
431	460	1.548269	GGCAACAATGGATTCGGGAAA	59.452	47.619	0.00	0.00	0.00	3.13
438	467	1.065272	GCAATGGGGCAACAATGGATT	60.065	47.619	0.00	0.00	39.74	3.01
450	479	0.594602	CACATATGCGAGCAATGGGG	59.405	55.000	17.60	10.05	0.00	4.96
465	496	3.387374	TCCAAGCCAAATGAACAACACAT	59.613	39.130	0.00	0.00	0.00	3.21
506	537	3.712881	GTGCACGTCGAAGTGGCC	61.713	66.667	28.51	15.80	42.09	5.36
621	653	6.770542	TGGACACAATATAAACCACACACTA	58.229	36.000	0.00	0.00	0.00	2.74
871	2544	2.313234	CAGAGCTCGTCGTTTTTACGA	58.687	47.619	8.37	0.00	46.35	3.43
1326	3254	7.511268	ACAAGTAGGTAAACTGGTGATGTTTA	58.489	34.615	0.00	0.00	38.41	2.01
1343	3271	5.437191	AAATTCAGGGGACTACAAGTAGG	57.563	43.478	11.57	0.00	40.21	3.18
1356	3284	7.468631	CGACTGACCCAAATTATAAATTCAGGG	60.469	40.741	15.77	15.77	40.88	4.45
1461	3484	3.510360	CACACCCCTAAGATAGATACCGG	59.490	52.174	0.00	0.00	0.00	5.28
1463	3486	3.838903	CCCACACCCCTAAGATAGATACC	59.161	52.174	0.00	0.00	0.00	2.73
1464	3487	3.838903	CCCCACACCCCTAAGATAGATAC	59.161	52.174	0.00	0.00	0.00	2.24
1719	3743	3.969981	CGCGTGAAAATCTAAAAACGGTT	59.030	39.130	0.00	0.00	0.00	4.44
1728	3752	1.355971	GCCAGTCGCGTGAAAATCTA	58.644	50.000	5.77	0.00	0.00	1.98
1789	3954	9.515226	TTAGTGAGCTAAAATTGGTACATTTCT	57.485	29.630	0.00	0.00	34.20	2.52
1890	4060	7.390027	AGTAAGATGTATATCAAGATGGCACC	58.610	38.462	2.04	0.00	35.70	5.01
1935	4106	6.366877	GGAGAAACACAAATTTCCATGTCATG	59.633	38.462	5.79	5.79	39.05	3.07
2140	4322	3.253188	CCCAAACACGTTGTTCAGATGAT	59.747	43.478	4.28	0.00	40.14	2.45
2427	4618	2.308690	GAGTATTACGGGGAGCTGAGT	58.691	52.381	0.00	0.00	0.00	3.41
3379	5602	8.682710	ACTTTTAGCATTTCAGAGTTGTACAAA	58.317	29.630	10.51	0.00	0.00	2.83
3667	5922	4.586421	TGCTCTCTCTGGTGGTGATAATAG	59.414	45.833	0.00	0.00	0.00	1.73
3817	6072	7.719871	TCCTAACTTCATCACTAGCTAAGTT	57.280	36.000	11.97	11.97	41.74	2.66
4027	6337	9.754382	TGAACTTCTTTACGTCTACAAATACTT	57.246	29.630	0.00	0.00	0.00	2.24
4028	6338	9.408069	CTGAACTTCTTTACGTCTACAAATACT	57.592	33.333	0.00	0.00	0.00	2.12
4029	6339	9.403110	TCTGAACTTCTTTACGTCTACAAATAC	57.597	33.333	0.00	0.00	0.00	1.89
4030	6340	9.970395	TTCTGAACTTCTTTACGTCTACAAATA	57.030	29.630	0.00	0.00	0.00	1.40
4031	6341	8.882415	TTCTGAACTTCTTTACGTCTACAAAT	57.118	30.769	0.00	0.00	0.00	2.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.