AutoCloner

Multiple sequence alignment - TraesCS2D01G294100

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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	TraesCS2D01G294100	chr2D	100.000	3186	0	0	1	3186	376357753	376354568	0.000000e+00	5884
1	TraesCS2D01G294100	chr2B	92.415	2663	109	46	565	3186	447826359	447823749	0.000000e+00	3712
2	TraesCS2D01G294100	chr2B	83.821	513	36	23	3	501	447826866	447826387	8.110000e-121	444
3	TraesCS2D01G294100	chr2A	92.590	1498	58	26	640	2114	509992935	509991468	0.000000e+00	2102
4	TraesCS2D01G294100	chr2A	92.567	1009	57	5	1107	2114	509581088	509580097	0.000000e+00	1432
5	TraesCS2D01G294100	chr2A	92.588	796	41	11	2098	2882	509580081	509579293	0.000000e+00	1127
6	TraesCS2D01G294100	chr2A	93.151	730	35	11	2102	2819	509991448	509990722	0.000000e+00	1057
7	TraesCS2D01G294100	chr2A	90.504	674	34	20	1	648	509996260	509995591	0.000000e+00	863
8	TraesCS2D01G294100	chr2A	82.293	785	67	36	270	1008	509727880	509727122	5.840000e-172	614
9	TraesCS2D01G294100	chr2A	96.040	303	11	1	2884	3186	509579167	509578866	2.860000e-135	492
10	TraesCS2D01G294100	chr3D	80.132	906	149	24	1071	1950	496768427	496767527	0.000000e+00	647
11	TraesCS2D01G294100	chr3D	83.009	565	86	6	1160	1720	546656024	546656582	1.320000e-138	503
12	TraesCS2D01G294100	chr3A	79.912	906	151	24	1071	1950	638016464	638015564	1.250000e-178	636
13	TraesCS2D01G294100	chr5B	79.418	928	140	38	1071	1950	661524920	661523996	2.720000e-170	608
14	TraesCS2D01G294100	chr5B	80.911	571	97	6	1392	1950	661612550	661613120	1.050000e-119	440
15	TraesCS2D01G294100	chr3B	79.318	909	151	27	1071	1950	656066803	656065903	1.260000e-168	603
16	TraesCS2D01G294100	chr5A	79.072	927	145	32	1071	1950	653475295	653474371	2.740000e-165	592
17	TraesCS2D01G294100	chr5A	76.907	931	163	31	1065	1945	653563419	653564347	6.180000e-132	481
18	TraesCS2D01G294100	chr5D	78.733	931	144	30	1071	1950	526411236	526410309	9.910000e-160	573
19	TraesCS2D01G294100	chr5D	81.050	438	69	7	1518	1942	526422497	526422933	1.420000e-88	337
20	TraesCS2D01G294100	chr1A	95.102	245	12	0	1724	1968	36265789	36266033	1.390000e-103	387
21	TraesCS2D01G294100	chr1A	91.837	98	6	2	1595	1690	36265694	36265791	5.540000e-28	135

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	TraesCS2D01G294100	chr2D	376354568	376357753	3185	True	5884.000000	5884	100.000000	1	3186	1	chr2D.!!$R1	3185
1	TraesCS2D01G294100	chr2B	447823749	447826866	3117	True	2078.000000	3712	88.118000	3	3186	2	chr2B.!!$R1	3183
2	TraesCS2D01G294100	chr2A	509990722	509996260	5538	True	1340.666667	2102	92.081667	1	2819	3	chr2A.!!$R3	2818
3	TraesCS2D01G294100	chr2A	509578866	509581088	2222	True	1017.000000	1432	93.731667	1107	3186	3	chr2A.!!$R2	2079
4	TraesCS2D01G294100	chr2A	509727122	509727880	758	True	614.000000	614	82.293000	270	1008	1	chr2A.!!$R1	738
5	TraesCS2D01G294100	chr3D	496767527	496768427	900	True	647.000000	647	80.132000	1071	1950	1	chr3D.!!$R1	879
6	TraesCS2D01G294100	chr3D	546656024	546656582	558	False	503.000000	503	83.009000	1160	1720	1	chr3D.!!$F1	560
7	TraesCS2D01G294100	chr3A	638015564	638016464	900	True	636.000000	636	79.912000	1071	1950	1	chr3A.!!$R1	879
8	TraesCS2D01G294100	chr5B	661523996	661524920	924	True	608.000000	608	79.418000	1071	1950	1	chr5B.!!$R1	879
9	TraesCS2D01G294100	chr5B	661612550	661613120	570	False	440.000000	440	80.911000	1392	1950	1	chr5B.!!$F1	558
10	TraesCS2D01G294100	chr3B	656065903	656066803	900	True	603.000000	603	79.318000	1071	1950	1	chr3B.!!$R1	879
11	TraesCS2D01G294100	chr5A	653474371	653475295	924	True	592.000000	592	79.072000	1071	1950	1	chr5A.!!$R1	879
12	TraesCS2D01G294100	chr5A	653563419	653564347	928	False	481.000000	481	76.907000	1065	1945	1	chr5A.!!$F1	880
13	TraesCS2D01G294100	chr5D	526410309	526411236	927	True	573.000000	573	78.733000	1071	1950	1	chr5D.!!$R1	879

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
678	3425	0.322456	TTGCAGGCATACAGACCACC	60.322	55.0	0.0	0.0	0.0	4.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2389	5315	1.006337	GCCAATGCTTTGCCGTTCA	60.006	52.632	6.81	0.0	33.53	3.18	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
31	32	5.527582	GTGGCTTAGACACGGAATCATAAAT	59.472	40.000	1.12	0.00	29.47	1.40
64	65	3.244976	CGCTCCCATTTTGACATGAAAC	58.755	45.455	0.00	0.00	0.00	2.78
337	365	0.396435	CAAGTCCCCAGCACACTGTA	59.604	55.000	0.00	0.00	42.81	2.74
403	437	2.634940	TCCGACGGCTACTAGTACCTAT	59.365	50.000	9.66	7.13	0.00	2.57
430	464	2.874780	GAGCACGCACGGTCGTAG	60.875	66.667	3.99	0.00	41.21	3.51
431	465	3.606065	GAGCACGCACGGTCGTAGT	62.606	63.158	3.99	0.00	41.21	2.73
432	466	2.176546	GCACGCACGGTCGTAGTA	59.823	61.111	3.99	0.00	41.21	1.82
437	471	1.186030	CGCACGGTCGTAGTAATGTC	58.814	55.000	0.00	0.00	0.00	3.06
449	498	6.978659	GTCGTAGTAATGTCCATGAGATGAAA	59.021	38.462	0.00	0.00	0.00	2.69
454	503	8.038862	AGTAATGTCCATGAGATGAAAGGTAT	57.961	34.615	0.00	0.00	0.00	2.73
557	614	1.746615	GGTCACCAGCGTGCATCAT	60.747	57.895	0.00	0.00	40.04	2.45
558	615	1.709147	GGTCACCAGCGTGCATCATC	61.709	60.000	0.00	0.00	40.04	2.92
586	643	0.894835	AAATGTTGGGCCGGCTAAAG	59.105	50.000	28.56	0.00	0.00	1.85
594	652	3.467226	CCGGCTAAAGAGGCCCGA	61.467	66.667	0.00	0.00	46.24	5.14
638	701	1.143183	GATTTGCCGGTCTCCGCTA	59.857	57.895	1.90	0.00	46.86	4.26
678	3425	0.322456	TTGCAGGCATACAGACCACC	60.322	55.000	0.00	0.00	0.00	4.61
764	3524	1.004745	GGGTGAAAGAGGAATGGCAGA	59.995	52.381	0.00	0.00	0.00	4.26
961	3728	4.251760	CGCATCCTCGCCATCTAC	57.748	61.111	0.00	0.00	0.00	2.59
962	3729	1.662608	CGCATCCTCGCCATCTACT	59.337	57.895	0.00	0.00	0.00	2.57
963	3730	0.881796	CGCATCCTCGCCATCTACTA	59.118	55.000	0.00	0.00	0.00	1.82
964	3731	1.135546	CGCATCCTCGCCATCTACTAG	60.136	57.143	0.00	0.00	0.00	2.57
965	3732	1.889829	GCATCCTCGCCATCTACTAGT	59.110	52.381	0.00	0.00	0.00	2.57
966	3733	3.082548	GCATCCTCGCCATCTACTAGTA	58.917	50.000	1.89	1.89	0.00	1.82
1044	3814	2.125350	CACTTCTCCAGGAGCCGC	60.125	66.667	12.26	0.00	0.00	6.53
1371	4182	1.303561	ACGTGTACTACAGGGGCGA	60.304	57.895	12.39	0.00	38.22	5.54
1849	4695	0.987294	TCAAGAGCAAGAAGGGGAGG	59.013	55.000	0.00	0.00	0.00	4.30
1850	4696	0.987294	CAAGAGCAAGAAGGGGAGGA	59.013	55.000	0.00	0.00	0.00	3.71
1851	4697	1.352352	CAAGAGCAAGAAGGGGAGGAA	59.648	52.381	0.00	0.00	0.00	3.36
1852	4698	1.284313	AGAGCAAGAAGGGGAGGAAG	58.716	55.000	0.00	0.00	0.00	3.46
1853	4699	0.254462	GAGCAAGAAGGGGAGGAAGG	59.746	60.000	0.00	0.00	0.00	3.46
1854	4700	0.178861	AGCAAGAAGGGGAGGAAGGA	60.179	55.000	0.00	0.00	0.00	3.36
1855	4701	0.254462	GCAAGAAGGGGAGGAAGGAG	59.746	60.000	0.00	0.00	0.00	3.69
1856	4702	1.958288	CAAGAAGGGGAGGAAGGAGA	58.042	55.000	0.00	0.00	0.00	3.71
1857	4703	1.836802	CAAGAAGGGGAGGAAGGAGAG	59.163	57.143	0.00	0.00	0.00	3.20
2319	5240	3.925630	ATTGGCAGCCACAGGACGG	62.926	63.158	15.89	0.00	30.78	4.79
2347	5268	3.133003	CGATCACAATCTACTGTTCCCCT	59.867	47.826	0.00	0.00	0.00	4.79
2483	5410	2.094906	TGTCGATGTCCACGAGGTTAAG	60.095	50.000	0.00	0.00	40.37	1.85
2515	5442	7.118971	GGAACATTATCTGATATGCTCTTGGAC	59.881	40.741	0.00	0.00	0.00	4.02
2522	5449	1.438651	TATGCTCTTGGACGTGTTGC	58.561	50.000	0.00	0.00	0.00	4.17
2572	5499	7.061441	ACAATATTACGCGTCGATTACATTAGG	59.939	37.037	18.63	3.05	0.00	2.69
2638	5565	0.095417	CGGCTTTTCTCTAACAGCGC	59.905	55.000	0.00	0.00	32.68	5.92
2656	5583	2.602217	GCGCCGCAATCTACCTTATTTG	60.602	50.000	3.15	0.00	0.00	2.32
2663	5590	7.962918	GCCGCAATCTACCTTATTTGTATTATG	59.037	37.037	0.00	0.00	0.00	1.90
2804	5732	5.288712	GTCGACATATATAACTCGCCCATTG	59.711	44.000	11.55	0.00	0.00	2.82
2847	5775	5.770417	CATTGCTCAGCTCTTCTTCTTTTT	58.230	37.500	0.00	0.00	0.00	1.94
2997	6049	3.247006	TCATCTCTTCCCGTGCTTTAC	57.753	47.619	0.00	0.00	0.00	2.01
3084	6136	1.202794	TGACAATGGTTGCTGAGCTCA	60.203	47.619	17.19	17.19	0.00	4.26

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
64	65	0.534412	ATGTTCAGTCAGCTCGGAGG	59.466	55.000	7.20	0.00	0.00	4.30
337	365	2.031870	GGGAAGGCTTTAATTCCGCAT	58.968	47.619	0.00	0.00	44.98	4.73
403	437	1.401018	CGTGCGTGCTCGGATGATATA	60.401	52.381	15.62	0.00	44.92	0.86
430	464	7.308229	GCATACCTTTCATCTCATGGACATTAC	60.308	40.741	0.00	0.00	0.00	1.89
431	465	6.712095	GCATACCTTTCATCTCATGGACATTA	59.288	38.462	0.00	0.00	0.00	1.90
432	466	5.533903	GCATACCTTTCATCTCATGGACATT	59.466	40.000	0.00	0.00	0.00	2.71
437	471	3.567164	GTGGCATACCTTTCATCTCATGG	59.433	47.826	0.00	0.00	36.63	3.66
454	503	4.069232	CTCTCGCTTCGGGTGGCA	62.069	66.667	0.00	0.00	0.00	4.92
460	509	2.876645	GACGTGCTCTCGCTTCGG	60.877	66.667	0.00	0.00	38.03	4.30
557	614	1.528292	CCCAACATTTTTCCCCGCGA	61.528	55.000	8.23	0.00	0.00	5.87
558	615	1.080161	CCCAACATTTTTCCCCGCG	60.080	57.895	0.00	0.00	0.00	6.46
560	617	1.295101	GGCCCAACATTTTTCCCCG	59.705	57.895	0.00	0.00	0.00	5.73
562	619	1.295101	CCGGCCCAACATTTTTCCC	59.705	57.895	0.00	0.00	0.00	3.97
563	620	1.375396	GCCGGCCCAACATTTTTCC	60.375	57.895	18.11	0.00	0.00	3.13
678	3425	1.493950	GCTCCGAGATCCATTGTGCG	61.494	60.000	0.00	0.00	0.00	5.34
740	3500	1.407437	CCATTCCTCTTTCACCCCTCG	60.407	57.143	0.00	0.00	0.00	4.63
741	3501	1.683319	GCCATTCCTCTTTCACCCCTC	60.683	57.143	0.00	0.00	0.00	4.30
742	3502	0.332972	GCCATTCCTCTTTCACCCCT	59.667	55.000	0.00	0.00	0.00	4.79
872	3639	2.207229	AGTACAGTGGCGTGGCAGA	61.207	57.895	0.00	0.00	0.00	4.26
958	3725	5.526846	GTGGCGGGCTATATAGTACTAGTAG	59.473	48.000	8.85	13.10	0.00	2.57
959	3726	5.431765	GTGGCGGGCTATATAGTACTAGTA	58.568	45.833	8.85	0.00	0.00	1.82
960	3727	4.268359	GTGGCGGGCTATATAGTACTAGT	58.732	47.826	8.85	0.00	0.00	2.57
961	3728	3.311871	CGTGGCGGGCTATATAGTACTAG	59.688	52.174	8.85	0.00	0.00	2.57
962	3729	3.273434	CGTGGCGGGCTATATAGTACTA	58.727	50.000	11.38	4.77	0.00	1.82
963	3730	2.089980	CGTGGCGGGCTATATAGTACT	58.910	52.381	11.38	0.00	0.00	2.73
964	3731	1.468736	GCGTGGCGGGCTATATAGTAC	60.469	57.143	11.38	5.05	0.00	2.73
965	3732	0.813184	GCGTGGCGGGCTATATAGTA	59.187	55.000	11.38	0.00	0.00	1.82
966	3733	1.183030	TGCGTGGCGGGCTATATAGT	61.183	55.000	11.38	0.00	0.00	2.12
1044	3814	1.206578	GCCACCATGTCGTTTCGTG	59.793	57.895	0.00	0.00	0.00	4.35
1630	4455	1.371558	GGTCTCGAAGTTGCACCCT	59.628	57.895	0.00	0.00	0.00	4.34
1699	4542	4.351938	CCGTCGGCGTTCTCCACA	62.352	66.667	9.28	0.00	36.15	4.17
1849	4695	3.191539	CGCGCCTTGCTCTCCTTC	61.192	66.667	0.00	0.00	43.27	3.46
1850	4696	3.240134	TTCGCGCCTTGCTCTCCTT	62.240	57.895	0.00	0.00	43.27	3.36
1851	4697	3.655810	CTTCGCGCCTTGCTCTCCT	62.656	63.158	0.00	0.00	43.27	3.69
1852	4698	3.191539	CTTCGCGCCTTGCTCTCC	61.192	66.667	0.00	0.00	43.27	3.71
1853	4699	2.125912	TCTTCGCGCCTTGCTCTC	60.126	61.111	0.00	0.00	43.27	3.20
1854	4700	2.125753	CTCTTCGCGCCTTGCTCT	60.126	61.111	0.00	0.00	43.27	4.09
1855	4701	2.125912	TCTCTTCGCGCCTTGCTC	60.126	61.111	0.00	0.00	43.27	4.26
1856	4702	2.125753	CTCTCTTCGCGCCTTGCT	60.126	61.111	0.00	0.00	43.27	3.91
1857	4703	3.191539	CCTCTCTTCGCGCCTTGC	61.192	66.667	0.00	0.00	41.47	4.01
2315	5236	4.030134	AGATTGTGATCGTACTTCCGTC	57.970	45.455	0.00	0.00	37.37	4.79
2319	5240	6.472808	GGAACAGTAGATTGTGATCGTACTTC	59.527	42.308	0.00	0.00	37.37	3.01
2331	5252	4.960469	TGTAGGTAGGGGAACAGTAGATTG	59.040	45.833	0.00	0.00	0.00	2.67
2376	5297	6.536731	TTTGCCGTTCATACGTACTTTAAA	57.463	33.333	0.00	0.00	46.20	1.52
2377	5298	5.389725	GCTTTGCCGTTCATACGTACTTTAA	60.390	40.000	0.00	0.00	46.20	1.52
2378	5299	4.091800	GCTTTGCCGTTCATACGTACTTTA	59.908	41.667	0.00	0.00	46.20	1.85
2379	5300	3.120442	GCTTTGCCGTTCATACGTACTTT	60.120	43.478	0.00	0.00	46.20	2.66
2381	5302	1.997606	GCTTTGCCGTTCATACGTACT	59.002	47.619	0.00	0.00	46.20	2.73
2382	5303	1.727880	TGCTTTGCCGTTCATACGTAC	59.272	47.619	0.00	0.00	46.20	3.67
2389	5315	1.006337	GCCAATGCTTTGCCGTTCA	60.006	52.632	6.81	0.00	33.53	3.18
2483	5410	6.939163	AGCATATCAGATAATGTTCCTGTTCC	59.061	38.462	0.00	0.00	0.00	3.62
2597	5524	6.360681	GCCGATGTGTAATTATGCTGAATTTC	59.639	38.462	2.38	0.00	31.51	2.17
2638	5565	8.999431	ACATAATACAAATAAGGTAGATTGCGG	58.001	33.333	0.00	0.00	0.00	5.69
2663	5590	4.676924	GTGCTGATGCTTGTAACTTCAAAC	59.323	41.667	0.00	0.00	40.48	2.93
2671	5598	2.032117	CGTGTTGTGCTGATGCTTGTAA	60.032	45.455	0.00	0.00	40.48	2.41
2804	5732	2.977405	CAAGCTTGCAACAGGTACTC	57.023	50.000	14.65	0.00	34.60	2.59
2847	5775	1.614996	TTGCCGCTCCATTTGAGAAA	58.385	45.000	0.00	0.00	44.42	2.52
2848	5776	1.614996	TTTGCCGCTCCATTTGAGAA	58.385	45.000	0.00	0.00	44.42	2.87
2849	5777	1.614996	TTTTGCCGCTCCATTTGAGA	58.385	45.000	0.00	0.00	44.42	3.27
2850	5778	2.437200	TTTTTGCCGCTCCATTTGAG	57.563	45.000	0.00	0.00	44.47	3.02
2882	5810	7.721286	AGTGCTGTTGCTAGTTCAATATATC	57.279	36.000	0.00	0.00	40.48	1.63
2920	5972	3.159472	TGAAGAACTAGCAGGAACCGTA	58.841	45.455	0.00	0.00	0.00	4.02
2997	6049	2.430610	CCTCCGAGGAAGAGGCCAG	61.431	68.421	9.01	0.00	44.30	4.85
3110	6162	2.741517	AGTTGTTTTGCTTGTTGTTGCC	59.258	40.909	0.00	0.00	0.00	4.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.