AutoCloner

Multiple sequence alignment - TraesCS2D01G445800

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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	TraesCS2D01G445800	chr2D	100.000	2574	0	0	1	2574	556225907	556223334	0.000000e+00	4754
1	TraesCS2D01G445800	chr2D	86.047	516	23	17	2002	2517	564469795	564469329	2.280000e-140	508
2	TraesCS2D01G445800	chr2B	93.110	2569	110	33	11	2544	663331435	663333971	0.000000e+00	3701
3	TraesCS2D01G445800	chr2B	97.068	307	9	0	2002	2308	601732869	601732563	3.800000e-143	518
4	TraesCS2D01G445800	chr2B	90.541	148	14	0	13	160	663788039	663787892	2.020000e-46	196
5	TraesCS2D01G445800	chr2B	94.444	126	6	1	2358	2482	601732108	601731983	2.610000e-45	193
6	TraesCS2D01G445800	chr2B	87.755	147	18	0	1298	1444	663140002	663139856	3.410000e-39	172
7	TraesCS2D01G445800	chr2B	98.507	67	1	0	2508	2574	663362347	663362413	4.500000e-23	119
8	TraesCS2D01G445800	chr2A	95.351	1312	33	14	1216	2526	695978403	695977119	0.000000e+00	2060
9	TraesCS2D01G445800	chr2A	90.468	1238	65	22	22	1227	695821768	695820552	0.000000e+00	1583
10	TraesCS2D01G445800	chr2A	97.651	809	19	0	1718	2526	695819947	695819139	0.000000e+00	1389
11	TraesCS2D01G445800	chr2A	97.211	502	13	1	1218	1719	695820529	695820029	0.000000e+00	848
12	TraesCS2D01G445800	chr2A	94.650	243	13	0	985	1227	695978663	695978421	6.720000e-101	377
13	TraesCS2D01G445800	chr2A	83.382	343	50	4	1298	1640	695521750	695521415	6.920000e-81	311
14	TraesCS2D01G445800	chr2A	93.431	137	9	0	22	158	695978861	695978725	1.210000e-48	204
15	TraesCS2D01G445800	chr2A	97.674	43	1	0	159	201	695978706	695978664	9.880000e-10	75
16	TraesCS2D01G445800	chr3D	92.248	516	15	2	2002	2517	482835833	482836323	0.000000e+00	708
17	TraesCS2D01G445800	chr6A	91.473	516	20	1	2002	2517	561589526	561590017	0.000000e+00	688
18	TraesCS2D01G445800	chr6A	91.279	516	21	1	2002	2517	561451112	561450621	0.000000e+00	682
19	TraesCS2D01G445800	chr6A	90.310	516	26	3	2002	2517	561602783	561603274	0.000000e+00	654
20	TraesCS2D01G445800	chr4A	89.101	523	38	10	2002	2517	30777241	30776731	1.300000e-177	632
21	TraesCS2D01G445800	chr3A	100.000	63	0	0	2512	2574	77487675	77487613	1.620000e-22	117
22	TraesCS2D01G445800	chr3A	93.243	74	4	1	2502	2574	612316307	612316380	9.740000e-20	108
23	TraesCS2D01G445800	chr7B	100.000	61	0	0	2514	2574	305918226	305918166	2.090000e-21	113
24	TraesCS2D01G445800	chr5B	100.000	61	0	0	2514	2574	306402359	306402299	2.090000e-21	113
25	TraesCS2D01G445800	chr5A	90.698	86	6	2	2489	2574	705837301	705837384	2.090000e-21	113
26	TraesCS2D01G445800	chr1A	100.000	61	0	0	2514	2574	24760163	24760103	2.090000e-21	113
27	TraesCS2D01G445800	chr1A	100.000	61	0	0	2514	2574	168133334	168133394	2.090000e-21	113
28	TraesCS2D01G445800	chr1A	95.588	68	2	1	2507	2574	127703748	127703814	9.740000e-20	108

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	TraesCS2D01G445800	chr2D	556223334	556225907	2573	True	4754.000000	4754	100.0000	1	2574	1	chr2D.!!$R1	2573
1	TraesCS2D01G445800	chr2B	663331435	663333971	2536	False	3701.000000	3701	93.1100	11	2544	1	chr2B.!!$F1	2533
2	TraesCS2D01G445800	chr2B	601731983	601732869	886	True	355.500000	518	95.7560	2002	2482	2	chr2B.!!$R3	480
3	TraesCS2D01G445800	chr2A	695819139	695821768	2629	True	1273.333333	1583	95.1100	22	2526	3	chr2A.!!$R2	2504
4	TraesCS2D01G445800	chr2A	695977119	695978861	1742	True	679.000000	2060	95.2765	22	2526	4	chr2A.!!$R3	2504
5	TraesCS2D01G445800	chr4A	30776731	30777241	510	True	632.000000	632	89.1010	2002	2517	1	chr4A.!!$R1	515

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
225	259	0.033208	TGGAGCAATTAAGGGCAGGG	60.033	55.0	4.23	0.0	0.00	4.45	F
1071	1126	0.252284	CCGACCTATGGGGGCTCTAT	60.252	60.0	0.00	0.0	42.26	1.98	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1227	1314	2.011947	TCGGTCAGTATACACGTGGAG	58.988	52.381	21.57	0.0	0.0	3.86	R
2499	3126	0.394488	TGTTGGTCTCGTGGGCAAAA	60.394	50.000	0.00	0.0	0.0	2.44	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
32	33	3.469970	TGATGGTGATCGCCGGCT	61.470	61.111	26.68	6.32	0.00	5.52
57	58	1.306141	TCCATCTTCCTCACCGGCT	60.306	57.895	0.00	0.00	0.00	5.52
72	73	4.120331	GCTGCCGCCACCATCAAC	62.120	66.667	0.00	0.00	0.00	3.18
168	199	7.636150	ATTTTGAGACCATGGAATTAGAGTG	57.364	36.000	21.47	0.00	0.00	3.51
208	239	1.063006	CGCCAAGCATTCGTGATGG	59.937	57.895	0.00	0.00	36.21	3.51
210	241	0.379669	GCCAAGCATTCGTGATGGAG	59.620	55.000	0.00	0.00	36.21	3.86
211	242	0.379669	CCAAGCATTCGTGATGGAGC	59.620	55.000	0.00	0.00	36.21	4.70
225	259	0.033208	TGGAGCAATTAAGGGCAGGG	60.033	55.000	4.23	0.00	0.00	4.45
241	275	3.555966	GCAGGGCCTCAAACACTATATT	58.444	45.455	0.95	0.00	0.00	1.28
242	276	4.445735	GGCAGGGCCTCAAACACTATATTA	60.446	45.833	0.95	0.00	46.69	0.98
267	301	5.280727	CCTTACCCTTGGTTCAAATCTCTCT	60.281	44.000	0.00	0.00	37.09	3.10
362	397	1.077930	CCAGCCTGCACAGCATAGT	60.078	57.895	6.73	0.00	38.13	2.12
403	438	6.798427	TTAGTAAGATGAGGAGCTGACATT	57.202	37.500	0.00	0.00	0.00	2.71
446	493	5.808540	CAGGATTGGCTAACAAAATCACATG	59.191	40.000	0.00	0.00	43.46	3.21
516	563	5.798125	TGGTTTCCATGATAACAAAGCAA	57.202	34.783	0.00	0.00	0.00	3.91
586	633	1.953686	TGGCAAGAACCAAGTGCTTAC	59.046	47.619	0.00	0.00	36.55	2.34
588	635	2.558359	GGCAAGAACCAAGTGCTTACAT	59.442	45.455	0.00	0.00	38.36	2.29
589	636	3.568538	GCAAGAACCAAGTGCTTACATG	58.431	45.455	0.00	0.00	28.15	3.21
614	661	7.728083	TGGGAATCAGTTCTCCAAAATAAGAAA	59.272	33.333	0.00	0.00	33.69	2.52
766	813	6.850752	AACCACCCAATATTTAACTTCAGG	57.149	37.500	0.00	0.00	0.00	3.86
799	846	3.308402	CCAGGATAACTCCAGCCAAAAGA	60.308	47.826	0.00	0.00	44.79	2.52
955	1006	3.265070	CTGAACTGCTTCAGCTTGTTC	57.735	47.619	20.95	20.95	45.43	3.18
956	1007	2.877168	CTGAACTGCTTCAGCTTGTTCT	59.123	45.455	24.56	5.28	45.43	3.01
957	1008	3.282021	TGAACTGCTTCAGCTTGTTCTT	58.718	40.909	24.56	4.77	45.53	2.52
958	1009	3.065786	TGAACTGCTTCAGCTTGTTCTTG	59.934	43.478	24.56	3.62	45.53	3.02
959	1010	2.648059	ACTGCTTCAGCTTGTTCTTGT	58.352	42.857	0.00	0.00	42.66	3.16
960	1011	3.019564	ACTGCTTCAGCTTGTTCTTGTT	58.980	40.909	0.00	0.00	42.66	2.83
965	1016	4.354587	CTTCAGCTTGTTCTTGTTGGTTC	58.645	43.478	0.00	0.00	0.00	3.62
993	1048	2.982488	ACTTCCCTTCTCACAGTCCATT	59.018	45.455	0.00	0.00	0.00	3.16
1071	1126	0.252284	CCGACCTATGGGGGCTCTAT	60.252	60.000	0.00	0.00	42.26	1.98
1232	1319	3.703001	TTCAATCCTGAAGTCCTCCAC	57.297	47.619	0.00	0.00	36.62	4.02
1617	1705	6.642131	GCAAAAGTGTATCAATGCTTTGAGAA	59.358	34.615	18.58	8.24	44.75	2.87
1852	2024	9.535878	TGTTTTGGTTAATGAAGGTTTGATTAC	57.464	29.630	0.00	0.00	0.00	1.89
1950	2122	2.936498	CAGTTATGACCAGTTAAGCCGG	59.064	50.000	0.00	0.00	0.00	6.13
2385	2986	0.482887	ACCTTCCTCAAACCCCCTTG	59.517	55.000	0.00	0.00	0.00	3.61
2405	3006	2.705658	TGGACATGATCTCCACATACCC	59.294	50.000	0.00	0.00	32.52	3.69
2415	3041	2.695666	CTCCACATACCCGATTCAGTCT	59.304	50.000	0.00	0.00	0.00	3.24
2461	3088	5.841810	ACACAAATGAATCGAACAAACCAT	58.158	33.333	0.00	0.00	0.00	3.55
2499	3126	2.364324	TGACTCAGTTACGGAGCAAAGT	59.636	45.455	12.16	0.00	35.79	2.66
2544	3171	6.128282	ACAACAACAACAACAACAACAACAAA	60.128	30.769	0.00	0.00	0.00	2.83
2545	3172	6.042144	ACAACAACAACAACAACAACAAAG	57.958	33.333	0.00	0.00	0.00	2.77
2546	3173	4.723879	ACAACAACAACAACAACAAAGC	57.276	36.364	0.00	0.00	0.00	3.51
2547	3174	3.496507	ACAACAACAACAACAACAAAGCC	59.503	39.130	0.00	0.00	0.00	4.35
2548	3175	3.676291	ACAACAACAACAACAAAGCCT	57.324	38.095	0.00	0.00	0.00	4.58
2549	3176	4.001618	ACAACAACAACAACAAAGCCTT	57.998	36.364	0.00	0.00	0.00	4.35
2550	3177	4.384940	ACAACAACAACAACAAAGCCTTT	58.615	34.783	0.00	0.00	0.00	3.11
2551	3178	5.542779	ACAACAACAACAACAAAGCCTTTA	58.457	33.333	0.00	0.00	0.00	1.85
2552	3179	5.637387	ACAACAACAACAACAAAGCCTTTAG	59.363	36.000	0.00	0.00	0.00	1.85
2553	3180	5.400066	ACAACAACAACAAAGCCTTTAGT	57.600	34.783	0.00	0.00	0.00	2.24
2554	3181	5.407502	ACAACAACAACAAAGCCTTTAGTC	58.592	37.500	0.00	0.00	0.00	2.59
2555	3182	4.649088	ACAACAACAAAGCCTTTAGTCC	57.351	40.909	0.00	0.00	0.00	3.85
2556	3183	3.383505	ACAACAACAAAGCCTTTAGTCCC	59.616	43.478	0.00	0.00	0.00	4.46
2557	3184	3.306472	ACAACAAAGCCTTTAGTCCCA	57.694	42.857	0.00	0.00	0.00	4.37
2558	3185	3.637769	ACAACAAAGCCTTTAGTCCCAA	58.362	40.909	0.00	0.00	0.00	4.12
2559	3186	4.027437	ACAACAAAGCCTTTAGTCCCAAA	58.973	39.130	0.00	0.00	0.00	3.28
2560	3187	4.142026	ACAACAAAGCCTTTAGTCCCAAAC	60.142	41.667	0.00	0.00	0.00	2.93
2561	3188	3.637769	ACAAAGCCTTTAGTCCCAAACA	58.362	40.909	0.00	0.00	0.00	2.83
2562	3189	4.027437	ACAAAGCCTTTAGTCCCAAACAA	58.973	39.130	0.00	0.00	0.00	2.83
2563	3190	4.099419	ACAAAGCCTTTAGTCCCAAACAAG	59.901	41.667	0.00	0.00	0.00	3.16
2564	3191	3.595190	AGCCTTTAGTCCCAAACAAGT	57.405	42.857	0.00	0.00	0.00	3.16
2565	3192	3.910989	AGCCTTTAGTCCCAAACAAGTT	58.089	40.909	0.00	0.00	0.00	2.66
2566	3193	3.636764	AGCCTTTAGTCCCAAACAAGTTG	59.363	43.478	0.00	0.00	36.94	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	3.128589	CGATCACCATCACGGGAATTTTT	59.871	43.478	0.00	0.00	40.22	1.94
5	6	2.682856	CGATCACCATCACGGGAATTTT	59.317	45.455	0.00	0.00	40.22	1.82
6	7	2.288666	CGATCACCATCACGGGAATTT	58.711	47.619	0.00	0.00	40.22	1.82
7	8	1.953559	CGATCACCATCACGGGAATT	58.046	50.000	0.00	0.00	40.22	2.17
8	9	0.532862	GCGATCACCATCACGGGAAT	60.533	55.000	0.00	0.00	40.22	3.01
9	10	1.153449	GCGATCACCATCACGGGAA	60.153	57.895	0.00	0.00	40.22	3.97
32	33	0.911045	TGAGGAAGATGGAGCCAGCA	60.911	55.000	7.59	0.00	34.38	4.41
96	97	2.202932	CCATTCACCGCTAGCGCT	60.203	61.111	31.35	17.26	38.24	5.92
201	232	1.334869	GCCCTTAATTGCTCCATCACG	59.665	52.381	0.00	0.00	0.00	4.35
208	239	1.395045	GGCCCTGCCCTTAATTGCTC	61.395	60.000	0.00	0.00	44.06	4.26
210	241	3.220222	GGCCCTGCCCTTAATTGC	58.780	61.111	0.00	0.00	44.06	3.56
225	259	6.709397	GGGTAAGGTAATATAGTGTTTGAGGC	59.291	42.308	0.00	0.00	0.00	4.70
241	275	5.550403	AGAGATTTGAACCAAGGGTAAGGTA	59.450	40.000	0.00	0.00	37.07	3.08
242	276	4.354087	AGAGATTTGAACCAAGGGTAAGGT	59.646	41.667	0.00	0.00	40.61	3.50
267	301	5.422012	GGGGCCTTCTTTTTCATTGATTCTA	59.578	40.000	0.84	0.00	0.00	2.10
362	397	7.226523	TCTTACTAAATGTAGCACGGTACGATA	59.773	37.037	0.00	0.00	43.58	2.92
403	438	0.819259	GGCGCCATCATTTGCTCCTA	60.819	55.000	24.80	0.00	29.75	2.94
516	563	3.312973	TCGTTTGCCGATTTGTTTACTGT	59.687	39.130	0.00	0.00	41.60	3.55
546	593	8.523915	TTGCCAACATGTCTGATTTATTATCT	57.476	30.769	0.00	0.00	0.00	1.98
549	596	7.936496	TCTTGCCAACATGTCTGATTTATTA	57.064	32.000	0.00	0.00	0.00	0.98
550	597	6.839124	TCTTGCCAACATGTCTGATTTATT	57.161	33.333	0.00	0.00	0.00	1.40
551	598	6.350445	GGTTCTTGCCAACATGTCTGATTTAT	60.350	38.462	0.00	0.00	0.00	1.40
552	599	5.048083	GGTTCTTGCCAACATGTCTGATTTA	60.048	40.000	0.00	0.00	0.00	1.40
553	600	4.262164	GGTTCTTGCCAACATGTCTGATTT	60.262	41.667	0.00	0.00	0.00	2.17
586	633	5.927281	ATTTTGGAGAACTGATTCCCATG	57.073	39.130	0.00	0.00	36.00	3.66
588	635	6.789268	TCTTATTTTGGAGAACTGATTCCCA	58.211	36.000	0.00	0.00	35.18	4.37
589	636	7.703058	TTCTTATTTTGGAGAACTGATTCCC	57.297	36.000	0.00	0.00	35.18	3.97
766	813	4.176271	GAGTTATCCTGGCATTGTTTTGC	58.824	43.478	0.00	0.00	42.01	3.68
799	846	4.681978	GTGACAACGAGGGGCGCT	62.682	66.667	7.64	2.69	46.04	5.92
919	966	0.805711	TCAGTGTGTGTGACTGTGCG	60.806	55.000	0.00	0.00	41.43	5.34
920	967	1.062587	GTTCAGTGTGTGTGACTGTGC	59.937	52.381	0.00	0.00	41.43	4.57
955	1006	3.065371	GGAAGTGTCTGTGAACCAACAAG	59.935	47.826	0.00	0.00	0.00	3.16
956	1007	3.013921	GGAAGTGTCTGTGAACCAACAA	58.986	45.455	0.00	0.00	0.00	2.83
957	1008	2.639065	GGAAGTGTCTGTGAACCAACA	58.361	47.619	0.00	0.00	0.00	3.33
958	1009	1.947456	GGGAAGTGTCTGTGAACCAAC	59.053	52.381	0.00	0.00	0.00	3.77
959	1010	1.843851	AGGGAAGTGTCTGTGAACCAA	59.156	47.619	0.00	0.00	0.00	3.67
960	1011	1.507140	AGGGAAGTGTCTGTGAACCA	58.493	50.000	0.00	0.00	0.00	3.67
965	1016	2.103094	TGTGAGAAGGGAAGTGTCTGTG	59.897	50.000	0.00	0.00	0.00	3.66
993	1048	1.788229	TCCTCATCGCCATGGACTTA	58.212	50.000	18.40	0.00	0.00	2.24
1227	1314	2.011947	TCGGTCAGTATACACGTGGAG	58.988	52.381	21.57	0.00	0.00	3.86
1232	1319	3.601356	CGTTACTCGGTCAGTATACACG	58.399	50.000	5.50	4.48	37.44	4.49
1617	1705	7.083858	CACAACGTGGAATCAGACATTATTTT	58.916	34.615	0.00	0.00	0.00	1.82
1738	1909	4.628963	AAAGTTAAGGTACATGGACCGT	57.371	40.909	21.77	20.87	44.88	4.83
1852	2024	7.535139	ACATAATGAAATCCGTGGTACTTTTG	58.465	34.615	0.00	0.00	0.00	2.44
2385	2986	2.289072	CGGGTATGTGGAGATCATGTCC	60.289	54.545	0.00	0.00	34.31	4.02
2405	3006	2.662791	CGTTGGTTGCAAGACTGAATCG	60.663	50.000	0.00	0.00	0.00	3.34
2415	3041	1.659233	CTCCATGCGTTGGTTGCAA	59.341	52.632	0.00	0.00	46.87	4.08
2461	3088	0.756294	TCAGGTCAGTGCCTTTTCGA	59.244	50.000	3.64	0.00	36.58	3.71
2499	3126	0.394488	TGTTGGTCTCGTGGGCAAAA	60.394	50.000	0.00	0.00	0.00	2.44
2544	3171	3.595190	ACTTGTTTGGGACTAAAGGCT	57.405	42.857	0.00	0.00	0.00	4.58
2545	3172	3.977427	CAACTTGTTTGGGACTAAAGGC	58.023	45.455	0.00	0.00	0.00	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.