AutoCloner

Multiple sequence alignment - TraesCS6D01G276300

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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	TraesCS6D01G276300	chr6D	100.000	3479	0	0	1	3479	385221793	385225271	0.000000e+00	6425.0
1	TraesCS6D01G276300	chr6D	85.751	3102	290	54	1	3027	385164377	385167401	0.000000e+00	3140.0
2	TraesCS6D01G276300	chr6D	75.909	1677	234	83	723	2308	389653356	389651759	0.000000e+00	702.0
3	TraesCS6D01G276300	chr6D	88.976	254	23	4	3019	3268	385167424	385167676	3.370000e-80	309.0
4	TraesCS6D01G276300	chr6D	94.030	201	9	3	1	199	385164007	385164206	5.640000e-78	302.0
5	TraesCS6D01G276300	chr6A	94.145	3501	163	21	1	3479	529484383	529487863	0.000000e+00	5291.0
6	TraesCS6D01G276300	chr6A	93.661	3439	155	22	1	3412	529558487	529561889	0.000000e+00	5084.0
7	TraesCS6D01G276300	chr6A	87.222	3107	260	54	1	3027	529286282	529289331	0.000000e+00	3411.0
8	TraesCS6D01G276300	chr6A	91.563	1292	83	7	2194	3479	529374996	529376267	0.000000e+00	1759.0
9	TraesCS6D01G276300	chr6A	74.282	1707	260	94	700	2308	536024983	536023358	3.920000e-154	555.0
10	TraesCS6D01G276300	chr6A	87.692	130	15	1	4	132	536032208	536032079	2.160000e-32	150.0
11	TraesCS6D01G276300	chr6A	86.154	130	17	1	4	132	536025486	536025357	4.680000e-29	139.0
12	TraesCS6D01G276300	chr6B	93.253	2653	127	18	545	3174	575320828	575323451	0.000000e+00	3860.0
13	TraesCS6D01G276300	chr6B	86.695	3104	282	61	1	3027	575313755	575316804	0.000000e+00	3323.0
14	TraesCS6D01G276300	chr6B	75.282	1861	259	92	614	2378	583336458	583334703	0.000000e+00	702.0
15	TraesCS6D01G276300	chr6B	92.015	263	20	1	1	262	575320565	575320827	5.490000e-98	368.0
16	TraesCS6D01G276300	chr6B	89.161	286	27	2	3195	3479	575324010	575324292	1.540000e-93	353.0
17	TraesCS6D01G276300	chr6B	85.328	259	27	5	3019	3268	575316827	575317083	1.240000e-64	257.0
18	TraesCS6D01G276300	chr6B	97.727	44	1	0	149	192	575320784	575320827	3.720000e-10	76.8
19	TraesCS6D01G276300	chr7B	86.441	118	16	0	3355	3472	441516779	441516896	2.820000e-26	130.0
20	TraesCS6D01G276300	chr7B	83.740	123	20	0	3355	3477	240970585	240970707	2.190000e-22	117.0
21	TraesCS6D01G276300	chr2D	86.325	117	16	0	3355	3471	587270036	587269920	1.010000e-25	128.0
22	TraesCS6D01G276300	chr1A	85.484	124	16	2	3355	3477	559580802	559580924	1.010000e-25	128.0
23	TraesCS6D01G276300	chr5B	85.366	123	14	3	3355	3475	579060856	579060736	1.310000e-24	124.0
24	TraesCS6D01G276300	chr4A	83.607	122	18	2	3357	3477	284163712	284163592	2.840000e-21	113.0

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	TraesCS6D01G276300	chr6D	385221793	385225271	3478	False	6425.000000	6425	100.000000	1	3479	1	chr6D.!!$F1	3478
1	TraesCS6D01G276300	chr6D	385164007	385167676	3669	False	1250.333333	3140	89.585667	1	3268	3	chr6D.!!$F2	3267
2	TraesCS6D01G276300	chr6D	389651759	389653356	1597	True	702.000000	702	75.909000	723	2308	1	chr6D.!!$R1	1585
3	TraesCS6D01G276300	chr6A	529484383	529487863	3480	False	5291.000000	5291	94.145000	1	3479	1	chr6A.!!$F3	3478
4	TraesCS6D01G276300	chr6A	529558487	529561889	3402	False	5084.000000	5084	93.661000	1	3412	1	chr6A.!!$F4	3411
5	TraesCS6D01G276300	chr6A	529286282	529289331	3049	False	3411.000000	3411	87.222000	1	3027	1	chr6A.!!$F1	3026
6	TraesCS6D01G276300	chr6A	529374996	529376267	1271	False	1759.000000	1759	91.563000	2194	3479	1	chr6A.!!$F2	1285
7	TraesCS6D01G276300	chr6A	536023358	536025486	2128	True	347.000000	555	80.218000	4	2308	2	chr6A.!!$R2	2304
8	TraesCS6D01G276300	chr6B	575313755	575324292	10537	False	1372.966667	3860	90.696500	1	3479	6	chr6B.!!$F1	3478
9	TraesCS6D01G276300	chr6B	583334703	583336458	1755	True	702.000000	702	75.282000	614	2378	1	chr6B.!!$R1	1764

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
148	183	0.099968	CAACCGAATCTCCGCTACGA	59.900	55.000	0.00	0.0	0.00	3.43	F
1304	1817	1.271379	CAGGTACCAGCGTCACTGTTA	59.729	52.381	15.94	0.0	45.68	2.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1324	1837	0.390603	TACCGGTCATTTCCACGCTG	60.391	55.0	12.4	0.0	0.0	5.18	R
2898	10117	0.253044	CTCCTCGGAATCCCAAGCAA	59.747	55.0	0.0	0.0	0.0	3.91	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
74	75	4.806330	ACACAAGTTGACGTCGATCTATT	58.194	39.130	10.54	0.00	0.00	1.73
148	183	0.099968	CAACCGAATCTCCGCTACGA	59.900	55.000	0.00	0.00	0.00	3.43
348	762	1.551452	GCAGCCCTATCGATAGTCCT	58.449	55.000	26.59	19.59	37.40	3.85
351	765	3.615351	GCAGCCCTATCGATAGTCCTTTC	60.615	52.174	26.59	13.81	37.40	2.62
355	769	2.094649	CCTATCGATAGTCCTTTCCCGC	60.095	54.545	26.59	0.00	37.40	6.13
515	949	7.631915	AAAAAGCAATGTGGTTCGTAATAAC	57.368	32.000	0.00	0.00	37.04	1.89
566	1000	8.871862	CAAATATCACACATTGGTTGGTTTATG	58.128	33.333	0.00	0.00	0.00	1.90
630	1082	7.654520	AGCAAAACCAAATCATCATGCATATAC	59.345	33.333	0.00	0.00	35.11	1.47
650	1104	3.123273	ACCATAGAGTAACCATTGCCCT	58.877	45.455	0.00	0.00	0.00	5.19
660	1114	6.248433	AGTAACCATTGCCCTATATGGAATG	58.752	40.000	8.03	4.33	43.25	2.67
666	1120	7.129972	ACCATTGCCCTATATGGAATGATAGAT	59.870	37.037	14.37	0.00	43.25	1.98
694	1148	2.548904	TGGTTTTACCGCACACATACAC	59.451	45.455	0.00	0.00	42.58	2.90
695	1149	2.548904	GGTTTTACCGCACACATACACA	59.451	45.455	0.00	0.00	0.00	3.72
696	1150	3.189702	GGTTTTACCGCACACATACACAT	59.810	43.478	0.00	0.00	0.00	3.21
697	1151	4.392445	GGTTTTACCGCACACATACACATA	59.608	41.667	0.00	0.00	0.00	2.29
698	1152	5.318349	GTTTTACCGCACACATACACATAC	58.682	41.667	0.00	0.00	0.00	2.39
699	1153	2.753055	ACCGCACACATACACATACA	57.247	45.000	0.00	0.00	0.00	2.29
702	1156	2.286359	CCGCACACATACACATACATGC	60.286	50.000	0.00	0.00	0.00	4.06
792	1249	3.012518	CAAAAGCATCCAGGTGTCTAGG	58.987	50.000	0.00	0.00	0.00	3.02
807	1264	2.509931	CTAGGGTGGGGAGTGGACGA	62.510	65.000	0.00	0.00	0.00	4.20
1030	1510	2.110967	CGGCAGAGGAGCATTGTGG	61.111	63.158	0.00	0.00	35.83	4.17
1304	1817	1.271379	CAGGTACCAGCGTCACTGTTA	59.729	52.381	15.94	0.00	45.68	2.41
1324	1837	1.153353	TCCCATTCTTTGTTCGTCGC	58.847	50.000	0.00	0.00	0.00	5.19
1337	1851	2.379634	CGTCGCAGCGTGGAAATGA	61.380	57.895	15.93	0.00	0.00	2.57
1465	1994	3.303397	AATTCCGCGCCGTTCGTTG	62.303	57.895	0.00	0.00	41.07	4.10
1556	8690	1.609841	GGTTTCGTGATTCCCCTCGTT	60.610	52.381	0.00	0.00	0.00	3.85
1634	8768	3.502123	TTGTCACCCTCCCTGTTTAAG	57.498	47.619	0.00	0.00	0.00	1.85
1899	9039	8.331022	CCGTATGTATTTGCTAATGAGATATGC	58.669	37.037	3.49	0.00	0.00	3.14
1938	9080	6.152379	GGGTGCTCATAGCTTTATAATTTGC	58.848	40.000	0.00	0.00	42.97	3.68
1981	9132	7.072328	TCCCTGAATCATGTATGAAATGTCCTA	59.928	37.037	0.00	0.00	40.69	2.94
2447	9630	0.878523	CCGTCGAACAAGTCCAGCAA	60.879	55.000	0.00	0.00	0.00	3.91
2653	9864	2.612471	GCTGATATGGAGCTGCGAGATT	60.612	50.000	0.00	0.00	33.37	2.40
2729	9940	5.589855	CCTCATGCACAATAACCATGTTCTA	59.410	40.000	0.00	0.00	37.99	2.10
2881	10096	4.453478	GCATTTCTCGCATAAGATGGATGA	59.547	41.667	0.00	0.00	0.00	2.92
2898	10117	4.102524	TGGATGACTTGAGGTAGTTGTTGT	59.897	41.667	0.00	0.00	0.00	3.32
2944	10163	5.416952	GGATCCGGACTCCTTTTATCGTATA	59.583	44.000	19.79	0.00	0.00	1.47
3023	10250	8.148999	CCATCAACAATATCTCTCTTCATCTGA	58.851	37.037	0.00	0.00	0.00	3.27
3314	11128	2.196749	CATTCCATCACTTCTCCGACG	58.803	52.381	0.00	0.00	0.00	5.12
3324	11138	0.320374	TTCTCCGACGTCATTGGCTT	59.680	50.000	17.16	0.00	0.00	4.35
3398	11212	2.028876	TGAGAGAACCAACTGTCACGA	58.971	47.619	0.00	0.00	35.73	4.35
3413	11227	1.679153	TCACGAAAACCAAAAGGCTCC	59.321	47.619	0.00	0.00	0.00	4.70
3421	11235	2.888212	ACCAAAAGGCTCCTTGCAATA	58.112	42.857	0.00	0.00	45.15	1.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
74	75	1.959710	TAGGGGTGTAATGTGGCTCA	58.040	50.000	0.00	0.00	0.00	4.26
148	183	3.686691	GCACTGGCCTAGATCAAGGAAAT	60.687	47.826	3.32	0.00	39.15	2.17
348	762	1.278127	CTAGGTCAAGGAAGCGGGAAA	59.722	52.381	0.00	0.00	0.00	3.13
351	765	1.265454	ACCTAGGTCAAGGAAGCGGG	61.265	60.000	9.21	0.00	39.15	6.13
515	949	8.291032	TGGTGTTAAACATAATAAGGAAACACG	58.709	33.333	8.41	0.00	43.86	4.49
630	1082	3.864789	AGGGCAATGGTTACTCTATGG	57.135	47.619	0.00	0.00	0.00	2.74
650	1104	8.010697	ACCATCCGGTATCTATCATTCCATATA	58.989	37.037	0.00	0.00	46.71	0.86
710	1164	4.798593	GCAGTTTGTTAGAGTTACCCTCGT	60.799	45.833	0.00	0.00	45.44	4.18
792	1249	2.603776	AGTCGTCCACTCCCCACC	60.604	66.667	0.00	0.00	0.00	4.61
1030	1510	4.090057	GCTGAACTTCCGGCGCAC	62.090	66.667	10.83	0.00	0.00	5.34
1181	1688	2.859165	AAATGCGTCCCTCTTCAGAA	57.141	45.000	0.00	0.00	0.00	3.02
1304	1817	1.737793	GCGACGAACAAAGAATGGGAT	59.262	47.619	0.00	0.00	0.00	3.85
1324	1837	0.390603	TACCGGTCATTTCCACGCTG	60.391	55.000	12.40	0.00	0.00	5.18
1337	1851	1.553706	AACACGAGGATTCTACCGGT	58.446	50.000	13.98	13.98	34.73	5.28
1465	1994	1.535226	GCAACCTTGACGTGGAAAACC	60.535	52.381	0.00	0.00	0.00	3.27
1564	8698	1.065854	GGATCCTGAATATGCCCCTCG	60.066	57.143	3.84	0.00	0.00	4.63
1618	8752	4.041198	TGTCTAACTTAAACAGGGAGGGTG	59.959	45.833	0.00	0.00	0.00	4.61
1760	8896	5.391256	TCCTCTAAAATACGGGAGAGCATA	58.609	41.667	0.00	0.00	35.17	3.14
1899	9039	2.158564	AGCACCCCATGGATCAATAGTG	60.159	50.000	15.22	9.64	34.81	2.74
1938	9080	4.018415	TCAGGGACCAGAATTAAAAGAGGG	60.018	45.833	0.00	0.00	0.00	4.30
1951	9101	4.694760	TCATACATGATTCAGGGACCAG	57.305	45.455	0.00	0.00	0.00	4.00
2408	9591	2.203126	CCTTCCTGCGGGATCTGC	60.203	66.667	16.96	3.88	41.87	4.26
2653	9864	2.835764	ACTGCCGACTATGGAGGTAAAA	59.164	45.455	0.00	0.00	0.00	1.52
2729	9940	1.143684	ACCTCTCAACTTGGCACACAT	59.856	47.619	0.00	0.00	39.29	3.21
2866	10081	3.744942	CCTCAAGTCATCCATCTTATGCG	59.255	47.826	0.00	0.00	0.00	4.73
2881	10096	3.886123	AGCAACAACAACTACCTCAAGT	58.114	40.909	0.00	0.00	0.00	3.16
2898	10117	0.253044	CTCCTCGGAATCCCAAGCAA	59.747	55.000	0.00	0.00	0.00	3.91
2944	10163	0.530744	TGAACTTGAGGCGCGAGTAT	59.469	50.000	12.10	2.66	40.45	2.12
3023	10250	0.957395	CCTCTTGTCTTGCACCGCAT	60.957	55.000	0.00	0.00	38.76	4.73
3072	10331	4.989279	ATAAGCCATCTTCAATTTGCGT	57.011	36.364	0.00	0.00	33.85	5.24
3314	11128	1.434696	CATCCGGCAAGCCAATGAC	59.565	57.895	12.19	0.00	33.32	3.06
3398	11212	1.836802	TGCAAGGAGCCTTTTGGTTTT	59.163	42.857	0.00	0.00	44.83	2.43
3413	11227	4.692625	CCCTCTTACATCGGATATTGCAAG	59.307	45.833	4.94	0.00	0.00	4.01
3421	11235	0.759346	GCCACCCTCTTACATCGGAT	59.241	55.000	0.00	0.00	0.00	4.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.