AutoCloner

Multiple sequence alignment - TraesCS5D01G348600

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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	TraesCS5D01G348600	chr5D	100.000	2354	0	0	1	2354	434328418	434326065	0.000000e+00	4348
1	TraesCS5D01G348600	chr5D	92.528	1713	103	17	651	2354	434396004	434397700	0.000000e+00	2431
2	TraesCS5D01G348600	chr5D	83.614	1721	202	42	677	2345	435249852	435248160	0.000000e+00	1543
3	TraesCS5D01G348600	chr5D	91.193	704	51	8	1660	2354	435251867	435251166	0.000000e+00	946
4	TraesCS5D01G348600	chr5D	92.121	660	19	10	1	660	434395316	434395942	0.000000e+00	900
5	TraesCS5D01G348600	chr5D	84.340	811	109	14	651	1459	435252826	435252032	0.000000e+00	778
6	TraesCS5D01G348600	chr5D	81.279	657	93	19	1112	1744	434399344	434399994	2.700000e-139	505
7	TraesCS5D01G348600	chr5D	82.834	501	50	21	150	647	435253401	435252934	1.300000e-112	416
8	TraesCS5D01G348600	chr5D	87.730	326	37	2	89	414	434398376	434398698	6.140000e-101	377
9	TraesCS5D01G348600	chr5D	80.177	565	59	17	89	643	435250506	435249985	7.940000e-100	374
10	TraesCS5D01G348600	chr5D	85.563	284	36	3	148	431	433017779	433018057	2.290000e-75	292
11	TraesCS5D01G348600	chr5A	92.447	1708	95	17	655	2354	548233091	548234772	0.000000e+00	2409
12	TraesCS5D01G348600	chr5A	85.506	1718	182	37	677	2354	549161642	549159952	0.000000e+00	1731
13	TraesCS5D01G348600	chr5A	84.660	1708	195	45	677	2349	549158710	549157035	0.000000e+00	1640
14	TraesCS5D01G348600	chr5A	80.464	1725	219	61	680	2350	547639710	547641370	0.000000e+00	1210
15	TraesCS5D01G348600	chr5A	92.078	669	25	9	1	665	548232386	548233030	0.000000e+00	917
16	TraesCS5D01G348600	chr5A	84.043	752	81	24	1610	2350	547643332	547644055	0.000000e+00	688
17	TraesCS5D01G348600	chr5A	83.467	750	89	17	1605	2337	547636346	547637077	0.000000e+00	665
18	TraesCS5D01G348600	chr5A	81.727	498	62	20	1299	1777	549163997	549163510	2.840000e-104	388
19	TraesCS5D01G348600	chr5A	86.047	344	45	2	89	431	548235433	548235774	1.330000e-97	366
20	TraesCS5D01G348600	chr5A	85.303	347	37	7	74	414	549165269	549164931	1.730000e-91	346
21	TraesCS5D01G348600	chr5B	86.231	1743	187	36	651	2354	528546082	528544354	0.000000e+00	1840
22	TraesCS5D01G348600	chr5B	82.114	1722	221	51	677	2345	527054939	527056626	0.000000e+00	1393
23	TraesCS5D01G348600	chr5B	90.773	932	50	14	1430	2354	527052759	527053661	0.000000e+00	1212
24	TraesCS5D01G348600	chr5B	93.185	719	45	3	651	1368	527052040	527052755	0.000000e+00	1053
25	TraesCS5D01G348600	chr5B	86.685	721	78	9	764	1482	528543003	528542299	0.000000e+00	784
26	TraesCS5D01G348600	chr5B	89.055	667	23	6	1	665	527051365	527051983	0.000000e+00	782
27	TraesCS5D01G348600	chr5B	82.915	597	69	17	1	588	528547043	528546471	7.510000e-140	507
28	TraesCS5D01G348600	chr5B	87.063	286	37	0	89	374	527054334	527054619	8.110000e-85	324

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	TraesCS5D01G348600	chr5D	434326065	434328418	2353	True	4348.000000	4348	100.000000	1	2354	1	chr5D.!!$R1	2353
1	TraesCS5D01G348600	chr5D	434395316	434399994	4678	False	1053.250000	2431	88.414500	1	2354	4	chr5D.!!$F2	2353
2	TraesCS5D01G348600	chr5D	435248160	435253401	5241	True	811.400000	1543	84.431600	89	2354	5	chr5D.!!$R2	2265
3	TraesCS5D01G348600	chr5A	548232386	548235774	3388	False	1230.666667	2409	90.190667	1	2354	3	chr5A.!!$F2	2353
4	TraesCS5D01G348600	chr5A	549157035	549165269	8234	True	1026.250000	1731	84.299000	74	2354	4	chr5A.!!$R1	2280
5	TraesCS5D01G348600	chr5A	547636346	547644055	7709	False	854.333333	1210	82.658000	680	2350	3	chr5A.!!$F1	1670
6	TraesCS5D01G348600	chr5B	528542299	528547043	4744	True	1043.666667	1840	85.277000	1	2354	3	chr5B.!!$R1	2353
7	TraesCS5D01G348600	chr5B	527051365	527056626	5261	False	952.800000	1393	88.438000	1	2354	5	chr5B.!!$F1	2353

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
998	4389	0.469494	TGATAGTGGCATGGCATCGT	59.531	50.0	26.07	15.16	0.0	3.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1892	5352	0.037447	AAGAAAGGACTCAGGGCAGC	59.963	55.0	0.0	0.0	0.0	5.25	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
67	68	2.313234	CTTTGCTTCAACTGCGTGATG	58.687	47.619	0.00	0.00	0.00	3.07
123	124	2.105477	GGGACATAGCACATGATGGTCT	59.895	50.000	0.00	0.00	40.36	3.85
137	138	0.768221	TGGTCTGGGAGCCTTTCACT	60.768	55.000	0.00	0.00	0.00	3.41
179	180	2.808543	CACTGCTTTTGGGTGTCTACTC	59.191	50.000	0.00	0.00	0.00	2.59
243	250	7.599998	GGTTTAACAGTGATTTGATTGCTTCAT	59.400	33.333	0.00	0.00	33.34	2.57
250	257	6.832384	AGTGATTTGATTGCTTCATATCTGGT	59.168	34.615	15.79	4.59	41.06	4.00
261	268	3.384168	TCATATCTGGTAGGTTGCTGGT	58.616	45.455	0.00	0.00	0.00	4.00
271	278	2.795329	AGGTTGCTGGTAAGTTCCATG	58.205	47.619	0.00	0.00	36.84	3.66
329	336	4.751060	CATAGCATGTGTCAGCCATTTTT	58.249	39.130	0.00	0.00	0.00	1.94
331	338	2.028748	AGCATGTGTCAGCCATTTTTCC	60.029	45.455	0.00	0.00	0.00	3.13
421	435	5.621228	GTGACTTGTGATTAGTTTCGCTTTG	59.379	40.000	0.00	0.00	0.00	2.77
423	437	4.578928	ACTTGTGATTAGTTTCGCTTTGGT	59.421	37.500	0.00	0.00	0.00	3.67
424	438	5.761234	ACTTGTGATTAGTTTCGCTTTGGTA	59.239	36.000	0.00	0.00	0.00	3.25
425	439	6.430000	ACTTGTGATTAGTTTCGCTTTGGTAT	59.570	34.615	0.00	0.00	0.00	2.73
426	440	7.604927	ACTTGTGATTAGTTTCGCTTTGGTATA	59.395	33.333	0.00	0.00	0.00	1.47
428	442	8.138365	TGTGATTAGTTTCGCTTTGGTATATC	57.862	34.615	0.00	0.00	0.00	1.63
429	443	7.985184	TGTGATTAGTTTCGCTTTGGTATATCT	59.015	33.333	0.00	0.00	0.00	1.98
430	444	8.827677	GTGATTAGTTTCGCTTTGGTATATCTT	58.172	33.333	0.00	0.00	0.00	2.40
484	498	3.875727	GAGCATGCTGTAATGTGAGTCAT	59.124	43.478	28.27	0.00	38.57	3.06
510	524	6.985188	TGCAAGGCTTATTTGTTAGTCTAG	57.015	37.500	0.00	0.00	0.00	2.43
673	1050	2.411628	TATCATGGGTTGTCGGTTGG	57.588	50.000	0.00	0.00	0.00	3.77
859	4249	2.964464	TCCTTGATTGCTTCTTTGCCAA	59.036	40.909	0.00	0.00	0.00	4.52
860	4250	3.006110	TCCTTGATTGCTTCTTTGCCAAG	59.994	43.478	0.00	0.00	33.02	3.61
952	4343	1.097232	GCTGCAGACACCATAATGCA	58.903	50.000	20.43	0.00	45.82	3.96
953	4344	1.202222	GCTGCAGACACCATAATGCAC	60.202	52.381	20.43	0.00	43.34	4.57
954	4345	2.086094	CTGCAGACACCATAATGCACA	58.914	47.619	8.42	0.00	43.34	4.57
998	4389	0.469494	TGATAGTGGCATGGCATCGT	59.531	50.000	26.07	15.16	0.00	3.73
1013	4404	1.931841	CATCGTCATGCTGTTGAGGAG	59.068	52.381	11.09	0.00	42.03	3.69
1031	4422	4.463879	CGCAGCCTCCACCTCTGG	62.464	72.222	0.00	0.00	39.23	3.86
1036	4427	2.122729	CCTCCACCTCTGGGGACA	59.877	66.667	0.00	0.00	41.31	4.02
1079	4470	4.442401	TGGCATACTCCATCATTGATGT	57.558	40.909	21.95	9.13	38.28	3.06
1106	4497	4.291047	CAGCGTGATTCTGCCACT	57.709	55.556	0.00	0.00	32.64	4.00
1109	4500	0.250467	AGCGTGATTCTGCCACTGTT	60.250	50.000	0.00	0.00	32.64	3.16
1149	4540	1.909302	TCCTCTTGGGACATCCTCAAC	59.091	52.381	0.00	0.00	39.58	3.18
1437	4834	2.025037	TGCTAATTGGAGGCTGGAATGT	60.025	45.455	0.00	0.00	0.00	2.71
1441	4838	2.496899	TTGGAGGCTGGAATGTCTTC	57.503	50.000	0.00	0.00	0.00	2.87
1468	4873	3.074412	GTGGATGAAGTGGTGGTGTTAG	58.926	50.000	0.00	0.00	0.00	2.34
1479	4890	3.010420	GGTGGTGTTAGGAGAGCATTTC	58.990	50.000	0.00	0.00	0.00	2.17
1539	4968	2.742348	ACGGTGGACTGTGATGGTATA	58.258	47.619	0.00	0.00	33.47	1.47
1540	4969	3.305720	ACGGTGGACTGTGATGGTATAT	58.694	45.455	0.00	0.00	33.47	0.86
1541	4970	4.476297	ACGGTGGACTGTGATGGTATATA	58.524	43.478	0.00	0.00	33.47	0.86
1542	4971	5.084519	ACGGTGGACTGTGATGGTATATAT	58.915	41.667	0.00	0.00	33.47	0.86
1584	5013	1.896660	GCTGCGGTTTTGGAGGTGA	60.897	57.895	0.00	0.00	0.00	4.02
1587	5016	0.817634	TGCGGTTTTGGAGGTGACTG	60.818	55.000	0.00	0.00	44.43	3.51
1588	5017	0.818040	GCGGTTTTGGAGGTGACTGT	60.818	55.000	0.00	0.00	44.43	3.55
1590	5019	1.474320	CGGTTTTGGAGGTGACTGTGA	60.474	52.381	0.00	0.00	44.43	3.58
1591	5020	2.810400	CGGTTTTGGAGGTGACTGTGAT	60.810	50.000	0.00	0.00	44.43	3.06
1592	5021	2.554032	GGTTTTGGAGGTGACTGTGATG	59.446	50.000	0.00	0.00	44.43	3.07
1595	5024	0.976641	TGGAGGTGACTGTGATGGAC	59.023	55.000	0.00	0.00	44.43	4.02
1596	5025	0.108615	GGAGGTGACTGTGATGGACG	60.109	60.000	0.00	0.00	44.43	4.79
1597	5026	0.108615	GAGGTGACTGTGATGGACGG	60.109	60.000	0.00	0.00	44.43	4.79
1615	5047	2.611800	TGATGGTCTGCTGGGGCT	60.612	61.111	0.00	0.00	39.59	5.19
1699	5142	1.264749	TGCTAGGGAATGGCACGAGT	61.265	55.000	0.00	0.00	41.01	4.18
1705	5148	0.172803	GGAATGGCACGAGTACGAGT	59.827	55.000	0.00	0.00	42.66	4.18
1782	5233	7.778382	TGGAAGTCTCATCAAAATCATCATCAT	59.222	33.333	0.00	0.00	0.00	2.45
1852	5312	0.541764	GCATTGTCCCCTTCCCAACA	60.542	55.000	0.00	0.00	0.00	3.33
1892	5352	1.220529	CTACCCACACGCATATGCAG	58.779	55.000	26.52	19.77	42.21	4.41
1995	5458	5.049405	CACAATCTAAACACACCTTCAGACC	60.049	44.000	0.00	0.00	0.00	3.85
2142	5612	2.110757	TTGGCATGCCTCAGACACGA	62.111	55.000	35.53	11.01	36.94	4.35
2146	5616	3.006756	ATGCCTCAGACACGACCGG	62.007	63.158	0.00	0.00	0.00	5.28
2183	5653	1.417517	TCAGTGTCATCTGTGGTTGCT	59.582	47.619	0.00	0.00	36.85	3.91
2204	5674	2.512515	GAGGGCCACTGCGTGATC	60.513	66.667	6.18	0.00	38.85	2.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
67	68	4.184629	CTCTGTACCTCACCTAATTGCAC	58.815	47.826	0.00	0.00	0.00	4.57
137	138	1.375908	GTGAACTCCGCATCTGCCA	60.376	57.895	0.00	0.00	37.91	4.92
243	250	4.359105	ACTTACCAGCAACCTACCAGATA	58.641	43.478	0.00	0.00	0.00	1.98
250	257	3.329520	ACATGGAACTTACCAGCAACCTA	59.670	43.478	0.00	0.00	43.49	3.08
261	268	5.245531	GTGGACAATGAGACATGGAACTTA	58.754	41.667	0.00	0.00	0.00	2.24
329	336	4.127171	GCTAAATGCAAGGAAGATACGGA	58.873	43.478	0.00	0.00	42.31	4.69
331	338	4.024556	CCAGCTAAATGCAAGGAAGATACG	60.025	45.833	0.00	0.00	45.94	3.06
421	435	8.828688	ATACCAAAGCGAAACTAAGATATACC	57.171	34.615	0.00	0.00	0.00	2.73
426	440	9.614792	AAAGATATACCAAAGCGAAACTAAGAT	57.385	29.630	0.00	0.00	0.00	2.40
428	442	9.490663	CAAAAGATATACCAAAGCGAAACTAAG	57.509	33.333	0.00	0.00	0.00	2.18
429	443	9.221933	TCAAAAGATATACCAAAGCGAAACTAA	57.778	29.630	0.00	0.00	0.00	2.24
430	444	8.780846	TCAAAAGATATACCAAAGCGAAACTA	57.219	30.769	0.00	0.00	0.00	2.24
431	445	7.148239	CCTCAAAAGATATACCAAAGCGAAACT	60.148	37.037	0.00	0.00	0.00	2.66
484	498	7.938140	AGACTAACAAATAAGCCTTGCATTA	57.062	32.000	0.00	0.00	0.00	1.90
510	524	3.421844	AGGGCAGGTTCATTGTCTAAAC	58.578	45.455	0.00	0.00	0.00	2.01
528	549	4.706476	TCAAAGTAAATCATCAGGCAAGGG	59.294	41.667	0.00	0.00	0.00	3.95
859	4249	9.252962	CTTTTTGTGTAAGCATTTTGATCTTCT	57.747	29.630	0.00	0.00	0.00	2.85
860	4250	9.034544	ACTTTTTGTGTAAGCATTTTGATCTTC	57.965	29.630	0.00	0.00	0.00	2.87
952	4343	1.279271	GCCACATCTGGGAGTTAGTGT	59.721	52.381	0.00	0.00	38.13	3.55
953	4344	1.556911	AGCCACATCTGGGAGTTAGTG	59.443	52.381	0.00	0.00	38.13	2.74
954	4345	1.834263	GAGCCACATCTGGGAGTTAGT	59.166	52.381	0.00	0.00	38.13	2.24
998	4389	1.742880	GCGCTCCTCAACAGCATGA	60.743	57.895	0.00	0.00	39.69	3.07
1003	4394	3.123620	GGCTGCGCTCCTCAACAG	61.124	66.667	9.73	0.00	0.00	3.16
1025	4416	0.610687	GAGAAGTGTGTCCCCAGAGG	59.389	60.000	0.00	0.00	0.00	3.69
1031	4422	0.036858	GCTCAGGAGAAGTGTGTCCC	60.037	60.000	0.00	0.00	37.97	4.46
1036	4427	0.761187	TGCTTGCTCAGGAGAAGTGT	59.239	50.000	0.00	0.00	0.00	3.55
1079	4470	2.395988	AATCACGCTGCCCTGTGACA	62.396	55.000	10.34	0.00	46.87	3.58
1106	4497	2.624169	GGCTTCACAGGCGTTAACA	58.376	52.632	6.39	0.00	35.53	2.41
1421	4818	2.579860	AGAAGACATTCCAGCCTCCAAT	59.420	45.455	0.00	0.00	35.94	3.16
1437	4834	3.007290	CCACTTCATCCACAGACAGAAGA	59.993	47.826	7.40	0.00	38.70	2.87
1441	4838	2.420642	CACCACTTCATCCACAGACAG	58.579	52.381	0.00	0.00	0.00	3.51
1479	4890	4.684703	CCCTTGAACTATAAATCCGTAGCG	59.315	45.833	0.00	0.00	0.00	4.26
1482	4893	7.712205	GCTTTACCCTTGAACTATAAATCCGTA	59.288	37.037	0.00	0.00	0.00	4.02
1484	4895	6.766467	AGCTTTACCCTTGAACTATAAATCCG	59.234	38.462	0.00	0.00	0.00	4.18
1539	4968	2.976882	ACGTACCCTACCCATTGCATAT	59.023	45.455	0.00	0.00	0.00	1.78
1540	4969	2.103432	CACGTACCCTACCCATTGCATA	59.897	50.000	0.00	0.00	0.00	3.14
1541	4970	1.134220	CACGTACCCTACCCATTGCAT	60.134	52.381	0.00	0.00	0.00	3.96
1542	4971	0.250793	CACGTACCCTACCCATTGCA	59.749	55.000	0.00	0.00	0.00	4.08
1584	5013	0.250234	CCATCACCGTCCATCACAGT	59.750	55.000	0.00	0.00	0.00	3.55
1586	5015	0.249120	GACCATCACCGTCCATCACA	59.751	55.000	0.00	0.00	0.00	3.58
1587	5016	0.537188	AGACCATCACCGTCCATCAC	59.463	55.000	0.00	0.00	0.00	3.06
1588	5017	0.536724	CAGACCATCACCGTCCATCA	59.463	55.000	0.00	0.00	0.00	3.07
1590	5019	1.221840	GCAGACCATCACCGTCCAT	59.778	57.895	0.00	0.00	0.00	3.41
1591	5020	1.913262	AGCAGACCATCACCGTCCA	60.913	57.895	0.00	0.00	0.00	4.02
1592	5021	1.448540	CAGCAGACCATCACCGTCC	60.449	63.158	0.00	0.00	0.00	4.79
1595	5024	2.124983	CCCAGCAGACCATCACCG	60.125	66.667	0.00	0.00	0.00	4.94
1596	5025	2.273449	CCCCAGCAGACCATCACC	59.727	66.667	0.00	0.00	0.00	4.02
1597	5026	1.626356	TAGCCCCAGCAGACCATCAC	61.626	60.000	0.00	0.00	43.56	3.06
1598	5027	0.913934	TTAGCCCCAGCAGACCATCA	60.914	55.000	0.00	0.00	43.56	3.07
1646	5078	1.217511	CTGTGCAGGCGAGATGTCT	59.782	57.895	0.00	0.00	0.00	3.41
1699	5142	1.826720	GAACCACATGGGGTACTCGTA	59.173	52.381	22.88	0.00	41.32	3.43
1782	5233	1.140852	ACTAGCTGCAGACACCAAACA	59.859	47.619	20.43	0.00	0.00	2.83
1852	5312	3.766591	AGTGTGTAGCTATCAGCAAGAGT	59.233	43.478	0.00	0.00	45.56	3.24
1892	5352	0.037447	AAGAAAGGACTCAGGGCAGC	59.963	55.000	0.00	0.00	0.00	5.25
1995	5458	4.861102	AAATTTCACTTTGGCTCTGGAG	57.139	40.909	0.00	0.00	0.00	3.86
2124	5594	2.046988	CGTGTCTGAGGCATGCCA	60.047	61.111	37.18	18.01	38.92	4.92
2163	5633	1.417517	AGCAACCACAGATGACACTGA	59.582	47.619	10.71	0.00	40.63	3.41
2183	5653	3.321648	ACGCAGTGGCCCTCATCA	61.322	61.111	0.00	0.00	42.51	3.07
2204	5674	1.520787	GGTTCCATCGGCGGTGTAG	60.521	63.158	20.02	4.61	0.00	2.74
2229	5699	0.252284	AGGTACACCAGAGGGACCTG	60.252	60.000	0.00	0.00	39.09	4.00
2242	5712	2.747460	CCGTCGTCCCGAGGTACA	60.747	66.667	0.00	0.00	39.62	2.90
2273	5743	1.925959	TCCTCCTCAGACATCCTCAGA	59.074	52.381	0.00	0.00	0.00	3.27
2313	5783	2.263545	CATGATCCTGCCTCCATCCTA	58.736	52.381	0.00	0.00	0.00	2.94
2314	5784	1.065647	CATGATCCTGCCTCCATCCT	58.934	55.000	0.00	0.00	0.00	3.24
2315	5785	0.608582	GCATGATCCTGCCTCCATCC	60.609	60.000	11.56	0.00	36.10	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.