AutoCloner

Multiple sequence alignment - TraesCS2B01G079500

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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	TraesCS2B01G079500	chr2B	100.000	3096	0	0	1	3096	44362889	44359794	0.000000e+00	5718
1	TraesCS2B01G079500	chr2B	88.317	1789	137	41	1292	3069	44352494	44350767	0.000000e+00	2080
2	TraesCS2B01G079500	chr2B	92.555	994	56	8	1526	2519	44347062	44346087	0.000000e+00	1410
3	TraesCS2B01G079500	chr2B	86.900	542	56	11	2530	3063	44346103	44345569	7.390000e-166	593
4	TraesCS2B01G079500	chr2B	79.792	673	72	31	587	1208	44353367	44352708	6.130000e-117	431
5	TraesCS2B01G079500	chr2B	86.066	366	25	8	870	1217	44347951	44347594	1.360000e-98	370
6	TraesCS2B01G079500	chr2B	86.920	237	22	3	1291	1527	44347393	44347166	1.100000e-64	257
7	TraesCS2B01G079500	chr2B	88.194	144	17	0	1	144	44353745	44353602	4.100000e-39	172
8	TraesCS2B01G079500	chr2A	93.065	2336	93	25	769	3096	30127554	30125280	0.000000e+00	3352
9	TraesCS2B01G079500	chr2A	88.689	1777	137	33	1296	3069	30086432	30084717	0.000000e+00	2109
10	TraesCS2B01G079500	chr2A	88.316	1746	136	34	1333	3069	30091293	30089607	0.000000e+00	2032
11	TraesCS2B01G079500	chr2A	88.915	839	49	21	1273	2105	30080283	30079483	0.000000e+00	994
12	TraesCS2B01G079500	chr2A	84.828	903	93	26	2119	3010	30076494	30075625	0.000000e+00	869
13	TraesCS2B01G079500	chr2A	90.032	632	50	6	145	765	30128237	30127608	0.000000e+00	806
14	TraesCS2B01G079500	chr2A	80.479	794	80	39	466	1217	30092276	30091516	3.510000e-149	538
15	TraesCS2B01G079500	chr2A	85.792	366	26	8	870	1217	30087003	30086646	6.310000e-97	364
16	TraesCS2B01G079500	chr2A	84.874	357	27	9	870	1208	30080826	30080479	4.950000e-88	335
17	TraesCS2B01G079500	chr2A	94.444	144	8	0	1	144	30128487	30128344	4.020000e-54	222
18	TraesCS2B01G079500	chr2A	93.750	112	7	0	321	432	30092391	30092280	5.310000e-38	169
19	TraesCS2B01G079500	chr2A	92.208	77	6	0	347	423	30092044	30091968	3.260000e-20	110
20	TraesCS2B01G079500	chr2A	92.208	77	6	0	347	423	30127671	30127595	3.260000e-20	110
21	TraesCS2B01G079500	chr2D	92.427	2258	101	33	769	3010	27902842	27900639	0.000000e+00	3158
22	TraesCS2B01G079500	chr2D	87.364	1749	128	50	1273	3010	27888691	27887025	0.000000e+00	1919
23	TraesCS2B01G079500	chr2D	88.619	1608	117	31	1273	2878	27891930	27890387	0.000000e+00	1895
24	TraesCS2B01G079500	chr2D	91.281	562	34	7	197	756	27903980	27903432	0.000000e+00	752
25	TraesCS2B01G079500	chr2D	87.273	385	23	8	851	1217	27892492	27892116	1.720000e-112	416
26	TraesCS2B01G079500	chr2D	86.236	356	23	8	871	1208	27889234	27888887	2.270000e-96	363
27	TraesCS2B01G079500	chr2D	87.055	309	33	7	459	764	27892904	27892600	2.960000e-90	342
28	TraesCS2B01G079500	chr2D	97.917	144	3	0	1	144	27904448	27904305	1.840000e-62	250

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	TraesCS2B01G079500	chr2B	44359794	44362889	3095	True	5718.000000	5718	100.000000	1	3096	1	chr2B.!!$R1	3095
1	TraesCS2B01G079500	chr2B	44345569	44353745	8176	True	759.000000	2080	86.963429	1	3069	7	chr2B.!!$R2	3068
2	TraesCS2B01G079500	chr2A	30125280	30128487	3207	True	1122.500000	3352	92.437250	1	3096	4	chr2A.!!$R2	3095
3	TraesCS2B01G079500	chr2A	30075625	30092391	16766	True	835.555556	2109	87.539000	321	3069	9	chr2A.!!$R1	2748
4	TraesCS2B01G079500	chr2D	27900639	27904448	3809	True	1386.666667	3158	93.875000	1	3010	3	chr2D.!!$R2	3009
5	TraesCS2B01G079500	chr2D	27887025	27892904	5879	True	987.000000	1919	87.309400	459	3010	5	chr2D.!!$R1	2551

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
288	561	0.034186	CCCCTTGCTAGTTGCCATCA	60.034	55.0	0.00	0.00	42.00	3.07	F
480	765	0.178938	ACATGTGGGACCCAATTGCA	60.179	50.0	16.98	9.65	34.18	4.08	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1158	12023	1.017701	CATTGCTGACGCTGCTGAGA	61.018	55.0	0.48	0.0	36.97	3.27	R
2350	16691	2.229675	TGCAAGACATAGGCATCTCG	57.770	50.0	0.00	0.0	31.58	4.04	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
186	293	1.280886	CTCATCAGATAGTGCGCGGC	61.281	60.000	8.83	0.00	0.00	6.53
222	495	3.315596	ACCTTCTACTTATACTGGCCCC	58.684	50.000	0.00	0.00	0.00	5.80
286	559	1.214305	TCCCCCTTGCTAGTTGCCAT	61.214	55.000	0.00	0.00	42.00	4.40
288	561	0.034186	CCCCTTGCTAGTTGCCATCA	60.034	55.000	0.00	0.00	42.00	3.07
296	569	6.040166	CCTTGCTAGTTGCCATCATTTCTAAT	59.960	38.462	0.00	0.00	42.00	1.73
311	584	1.758280	TCTAATACGGACGGGCACAAT	59.242	47.619	0.00	0.00	0.00	2.71
336	617	1.500783	CCTCCCCAACCACATGGAGT	61.501	60.000	4.53	0.00	43.54	3.85
360	644	5.527214	TGAGACACAAACACAAATCTTCGAT	59.473	36.000	0.00	0.00	0.00	3.59
361	645	5.751680	AGACACAAACACAAATCTTCGATG	58.248	37.500	0.00	0.00	0.00	3.84
443	728	2.614983	TGACAACCACGGCTAGTTTTTC	59.385	45.455	0.00	0.00	0.00	2.29
448	733	3.284617	ACCACGGCTAGTTTTTCTTTGT	58.715	40.909	0.00	0.00	0.00	2.83
474	759	2.230653	CCCTGACATGTGGGACCCA	61.231	63.158	14.85	9.95	46.15	4.51
480	765	0.178938	ACATGTGGGACCCAATTGCA	60.179	50.000	16.98	9.65	34.18	4.08
516	801	1.371183	CAAGTGAGCCTGTCCCGAA	59.629	57.895	0.00	0.00	0.00	4.30
571	856	4.508124	GCCTAGTCAGCAACACATACATAC	59.492	45.833	0.00	0.00	0.00	2.39
610	896	6.186957	ACCATATTTGAACAAGAGTGCCATA	58.813	36.000	0.00	0.00	0.00	2.74
642	928	5.278604	ACCAGTTGAACGTATTTTTCAAGC	58.721	37.500	0.00	0.00	42.27	4.01
655	941	5.590530	TTTTTCAAGCTCAGGCACTAAAA	57.409	34.783	0.00	0.00	41.70	1.52
685	971	2.555547	GGCAAGTTCAAGCGCCACT	61.556	57.895	2.29	0.00	44.25	4.00
687	973	1.785041	GCAAGTTCAAGCGCCACTGA	61.785	55.000	2.29	1.27	0.00	3.41
712	999	6.241207	ACAATTACCTCGACACAAATCTTG	57.759	37.500	0.00	0.00	0.00	3.02
767	1634	8.150945	TCCGGAAACAAAATAAATCAAAATGGA	58.849	29.630	0.00	0.00	0.00	3.41
782	1649	7.482654	TCAAAATGGAGCTAATCTAACGATG	57.517	36.000	0.00	0.00	0.00	3.84
786	1653	5.808366	TGGAGCTAATCTAACGATGGAAT	57.192	39.130	0.00	0.00	0.00	3.01
790	1657	8.035394	TGGAGCTAATCTAACGATGGAATAATC	58.965	37.037	0.00	0.00	0.00	1.75
960	6937	3.306294	GCTGGAAATCTTGTTGGAAAGGG	60.306	47.826	0.00	0.00	0.00	3.95
965	6942	1.530655	CTTGTTGGAAAGGGGCGGT	60.531	57.895	0.00	0.00	0.00	5.68
1208	12073	3.208594	TCAGATGCATGCAGGTATGAAC	58.791	45.455	26.69	9.17	0.00	3.18
1309	12311	2.059541	GGACGAACACTAAGCTCACAC	58.940	52.381	0.00	0.00	0.00	3.82
1346	12348	5.007234	CGGCACAGTTGATTAATTTATCGGA	59.993	40.000	0.38	0.00	0.00	4.55
1424	12426	5.010282	ACCAGGCCAAAGTAAACTAAGATG	58.990	41.667	5.01	0.00	0.00	2.90
1504	12506	7.712797	ACTCATAAACTTTGTGAACGGAAATT	58.287	30.769	2.95	0.00	30.16	1.82
1560	12667	2.163810	TAATGCCCGTACACTACCCT	57.836	50.000	0.00	0.00	0.00	4.34
1561	12668	0.539986	AATGCCCGTACACTACCCTG	59.460	55.000	0.00	0.00	0.00	4.45
1562	12669	0.324923	ATGCCCGTACACTACCCTGA	60.325	55.000	0.00	0.00	0.00	3.86
1563	12670	0.542467	TGCCCGTACACTACCCTGAA	60.542	55.000	0.00	0.00	0.00	3.02
1564	12671	0.108472	GCCCGTACACTACCCTGAAC	60.108	60.000	0.00	0.00	0.00	3.18
1565	12672	0.533951	CCCGTACACTACCCTGAACC	59.466	60.000	0.00	0.00	0.00	3.62
1566	12673	1.553706	CCGTACACTACCCTGAACCT	58.446	55.000	0.00	0.00	0.00	3.50
1567	12674	1.203994	CCGTACACTACCCTGAACCTG	59.796	57.143	0.00	0.00	0.00	4.00
1650	12757	6.377146	GGCAGACCATAAGGAGTAATTTTTGA	59.623	38.462	0.00	0.00	38.69	2.69
1959	16300	4.081030	CGCAACGCAGGTGCTCAG	62.081	66.667	14.83	0.00	39.32	3.35
2185	16526	5.018240	CGGTTTTACTTCTCGTACTACTCG	58.982	45.833	0.00	0.00	0.00	4.18
2319	16660	2.349817	GCGGATTATTGTCTTGCCATCG	60.350	50.000	0.00	0.00	0.00	3.84
2320	16661	2.224079	CGGATTATTGTCTTGCCATCGG	59.776	50.000	0.00	0.00	0.00	4.18
2350	16691	5.175673	GGAAATGTTACTTTGTTTGCAGCTC	59.824	40.000	0.00	0.00	0.00	4.09
2384	16725	5.581605	TGTCTTGCATTGTTTTCTTCTCAC	58.418	37.500	0.00	0.00	0.00	3.51
2497	16839	4.155826	CACATAAAAAGATGGCGAGAACCA	59.844	41.667	0.00	0.00	45.82	3.67
2508	16850	3.135994	GGCGAGAACCACTTGAAAACTA	58.864	45.455	0.00	0.00	31.94	2.24
2516	16858	4.647424	CCACTTGAAAACTAGTGGCAAA	57.353	40.909	15.04	0.00	44.11	3.68
2517	16859	5.004922	CCACTTGAAAACTAGTGGCAAAA	57.995	39.130	15.04	0.00	44.11	2.44
2518	16860	4.803613	CCACTTGAAAACTAGTGGCAAAAC	59.196	41.667	15.04	0.00	44.11	2.43
2519	16861	5.394115	CCACTTGAAAACTAGTGGCAAAACT	60.394	40.000	15.04	0.00	44.11	2.66
2520	16862	5.743872	CACTTGAAAACTAGTGGCAAAACTC	59.256	40.000	0.00	0.00	0.00	3.01
2521	16863	4.911514	TGAAAACTAGTGGCAAAACTCC	57.088	40.909	0.00	0.00	0.00	3.85
2522	16864	3.634910	TGAAAACTAGTGGCAAAACTCCC	59.365	43.478	0.00	0.00	0.00	4.30
2523	16865	2.287977	AACTAGTGGCAAAACTCCCC	57.712	50.000	0.00	0.00	0.00	4.81
2524	16866	0.036306	ACTAGTGGCAAAACTCCCCG	59.964	55.000	0.00	0.00	0.00	5.73
2525	16867	0.036306	CTAGTGGCAAAACTCCCCGT	59.964	55.000	0.00	0.00	0.00	5.28
2526	16868	1.276989	CTAGTGGCAAAACTCCCCGTA	59.723	52.381	0.00	0.00	0.00	4.02
2527	16869	0.475044	AGTGGCAAAACTCCCCGTAA	59.525	50.000	0.00	0.00	0.00	3.18
2528	16870	1.133730	AGTGGCAAAACTCCCCGTAAA	60.134	47.619	0.00	0.00	0.00	2.01
2578	16920	6.968131	TTGACGAGAACCAGATGATAAAAG	57.032	37.500	0.00	0.00	0.00	2.27
2603	16951	8.436778	AGGCCAAAATCCAAATTAAAAACTAGT	58.563	29.630	5.01	0.00	0.00	2.57
2662	17010	5.416947	GGACAAACCTACCATAGTGTACTG	58.583	45.833	0.00	0.00	35.41	2.74
2676	17024	1.070134	TGTACTGGTCTTGTGAGCCAC	59.930	52.381	0.00	0.00	39.75	5.01
2744	17092	4.875544	TTGCACCGCAATTAGATACTTC	57.124	40.909	0.00	0.00	43.99	3.01
2834	26338	9.847224	AAATTACATATCCAATTTACGAGTCCT	57.153	29.630	0.00	0.00	33.66	3.85
2846	26350	8.704234	CAATTTACGAGTCCTAAGATATCTTGC	58.296	37.037	25.22	13.47	37.40	4.01
2855	26360	9.594936	AGTCCTAAGATATCTTGCACTAGTAAT	57.405	33.333	25.22	0.70	37.40	1.89
2867	26373	5.076873	TGCACTAGTAATTTTTGGCCTTCT	58.923	37.500	3.32	0.00	0.00	2.85
2868	26374	6.242396	TGCACTAGTAATTTTTGGCCTTCTA	58.758	36.000	3.32	0.00	0.00	2.10
2920	26426	5.408880	TTGTGTCATAAACATCGGTCCTA	57.591	39.130	0.00	0.00	40.80	2.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
104	105	3.270027	CCGAACAAGCTACAATCCATCA	58.730	45.455	0.00	0.00	0.00	3.07
105	106	3.063997	CACCGAACAAGCTACAATCCATC	59.936	47.826	0.00	0.00	0.00	3.51
161	268	3.305676	GCGCACTATCTGATGAGGTGTAT	60.306	47.826	0.30	0.00	34.60	2.29
186	293	3.564027	GGTTGGCTTCGCGGATCG	61.564	66.667	6.13	0.00	40.15	3.69
193	300	5.749109	CAGTATAAGTAGAAGGTTGGCTTCG	59.251	44.000	0.00	0.00	36.08	3.79
195	302	5.629366	GCCAGTATAAGTAGAAGGTTGGCTT	60.629	44.000	4.54	0.00	43.84	4.35
222	495	1.153369	AACGATGGAGATGCACCCG	60.153	57.895	0.00	0.00	0.00	5.28
286	559	2.431419	TGCCCGTCCGTATTAGAAATGA	59.569	45.455	0.00	0.00	0.00	2.57
288	561	2.168936	TGTGCCCGTCCGTATTAGAAAT	59.831	45.455	0.00	0.00	0.00	2.17
296	569	0.607112	TAACATTGTGCCCGTCCGTA	59.393	50.000	0.00	0.00	0.00	4.02
311	584	1.748732	TGTGGTTGGGGAGGATAACA	58.251	50.000	0.00	0.00	0.00	2.41
336	617	4.873259	TCGAAGATTTGTGTTTGTGTCTCA	59.127	37.500	0.00	0.00	0.00	3.27
360	644	3.695830	ACTGCTCCCGAAAATTACTCA	57.304	42.857	0.00	0.00	0.00	3.41
361	645	4.331992	GGTTACTGCTCCCGAAAATTACTC	59.668	45.833	0.00	0.00	0.00	2.59
443	728	1.476085	TGTCAGGGCACAACAACAAAG	59.524	47.619	0.00	0.00	0.00	2.77
448	733	1.031235	CACATGTCAGGGCACAACAA	58.969	50.000	0.00	0.00	0.00	2.83
474	759	6.071447	TGCAAAGTATACACTCCATTGCAATT	60.071	34.615	9.83	0.00	45.89	2.32
516	801	2.281761	CGGAGCCCACTTGCAGTT	60.282	61.111	0.00	0.00	0.00	3.16
642	928	4.631377	TCGATGTTCATTTTAGTGCCTGAG	59.369	41.667	0.00	0.00	0.00	3.35
655	941	3.346315	TGAACTTGCCATCGATGTTCAT	58.654	40.909	23.27	6.88	41.02	2.57
685	971	7.327975	AGATTTGTGTCGAGGTAATTGTATCA	58.672	34.615	0.00	0.00	0.00	2.15
687	973	7.065803	CCAAGATTTGTGTCGAGGTAATTGTAT	59.934	37.037	0.00	0.00	0.00	2.29
712	999	3.385115	TCTCCCAGAAATTACTCCTCCC	58.615	50.000	0.00	0.00	0.00	4.30
767	1634	9.950496	AATGATTATTCCATCGTTAGATTAGCT	57.050	29.630	0.00	0.00	34.23	3.32
931	6908	3.010200	ACAAGATTTCCAGCCCTCATC	57.990	47.619	0.00	0.00	0.00	2.92
932	6909	3.094572	CAACAAGATTTCCAGCCCTCAT	58.905	45.455	0.00	0.00	0.00	2.90
934	6911	1.821136	CCAACAAGATTTCCAGCCCTC	59.179	52.381	0.00	0.00	0.00	4.30
935	6912	1.428912	TCCAACAAGATTTCCAGCCCT	59.571	47.619	0.00	0.00	0.00	5.19
936	6913	1.923356	TCCAACAAGATTTCCAGCCC	58.077	50.000	0.00	0.00	0.00	5.19
937	6914	3.306294	CCTTTCCAACAAGATTTCCAGCC	60.306	47.826	0.00	0.00	0.00	4.85
938	6915	3.306294	CCCTTTCCAACAAGATTTCCAGC	60.306	47.826	0.00	0.00	0.00	4.85
939	6916	3.259123	CCCCTTTCCAACAAGATTTCCAG	59.741	47.826	0.00	0.00	0.00	3.86
1158	12023	1.017701	CATTGCTGACGCTGCTGAGA	61.018	55.000	0.48	0.00	36.97	3.27
1234	12099	8.940768	ACAAAATAAGTGTTGCTGTTTTGTAT	57.059	26.923	11.05	0.00	45.05	2.29
1236	12101	8.940768	ATACAAAATAAGTGTTGCTGTTTTGT	57.059	26.923	15.46	15.46	46.54	2.83
1309	12311	2.930040	ACTGTGCCGACAAGAATATTCG	59.070	45.455	9.78	0.00	0.00	3.34
1346	12348	6.263168	GCTTTGGCTATGTACAGTGGAAATAT	59.737	38.462	0.33	0.00	35.22	1.28
1400	12402	4.394729	TCTTAGTTTACTTTGGCCTGGTG	58.605	43.478	3.32	0.00	0.00	4.17
1424	12426	4.273480	GGACTACATACATTGTGATGCACC	59.727	45.833	0.00	0.00	39.48	5.01
1504	12506	8.887036	ATCTAGTACACATTGCGATAAAATCA	57.113	30.769	0.00	0.00	0.00	2.57
1650	12757	4.388577	AAAGAAAGACCTGGCCATAAGT	57.611	40.909	5.51	3.99	0.00	2.24
1959	16300	2.232298	CTTGACCTCCTCCACCTCGC	62.232	65.000	0.00	0.00	0.00	5.03
2319	16660	7.518211	GCAAACAAAGTAACATTTCCATCAACC	60.518	37.037	0.00	0.00	0.00	3.77
2320	16661	7.010923	TGCAAACAAAGTAACATTTCCATCAAC	59.989	33.333	0.00	0.00	0.00	3.18
2350	16691	2.229675	TGCAAGACATAGGCATCTCG	57.770	50.000	0.00	0.00	31.58	4.04
2497	16839	5.163550	GGAGTTTTGCCACTAGTTTTCAAGT	60.164	40.000	0.00	0.00	0.00	3.16
2508	16850	0.475044	TTACGGGGAGTTTTGCCACT	59.525	50.000	0.00	0.00	36.32	4.00
2528	16870	5.889289	TCCTACTGTTTTGCCACTAGTTTTT	59.111	36.000	0.00	0.00	0.00	1.94
2578	16920	8.615878	ACTAGTTTTTAATTTGGATTTTGGCC	57.384	30.769	0.00	0.00	0.00	5.36
2603	16951	6.994221	TGACACCTTTTGTTTGTCCTTTTTA	58.006	32.000	0.00	0.00	39.17	1.52
2658	17006	1.419381	TGTGGCTCACAAGACCAGTA	58.581	50.000	5.65	0.00	41.69	2.74
2676	17024	6.690098	GTCTTTGATGAATCGATGTTGGAATG	59.310	38.462	0.00	0.00	0.00	2.67
2825	17177	6.062749	AGTGCAAGATATCTTAGGACTCGTA	58.937	40.000	23.48	8.83	33.87	3.43
2846	26350	8.548721	CGTATAGAAGGCCAAAAATTACTAGTG	58.451	37.037	5.01	0.00	0.00	2.74
2855	26360	7.639113	AATTCATCGTATAGAAGGCCAAAAA	57.361	32.000	5.01	0.00	0.00	1.94
2920	26426	6.429692	TGACAAAATGATAGTTTCGTCATGGT	59.570	34.615	0.00	0.00	35.38	3.55
3043	26552	5.626142	TGTGTGTACCTCCACAATGTAATT	58.374	37.500	7.43	0.00	46.22	1.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.