AutoCloner

Multiple sequence alignment - TraesCS4D01G172700

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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	TraesCS4D01G172700	chr4D	100.000	4118	0	0	1	4118	300782339	300786456	0.000000e+00	7605
1	TraesCS4D01G172700	chr4A	95.160	3430	113	34	1	3402	182220337	182216933	0.000000e+00	5365
2	TraesCS4D01G172700	chr4A	86.499	437	26	6	3414	3846	182216639	182216232	2.260000e-122	449
3	TraesCS4D01G172700	chr4A	93.204	103	5	2	3185	3287	182216917	182216817	2.560000e-32	150
4	TraesCS4D01G172700	chr4B	97.941	2622	45	5	601	3214	373981348	373983968	0.000000e+00	4534
5	TraesCS4D01G172700	chr4B	93.592	593	22	8	1	583	373980773	373981359	0.000000e+00	870
6	TraesCS4D01G172700	chr4B	82.777	569	34	13	3450	4006	373992724	373993240	2.260000e-122	449
7	TraesCS4D01G172700	chr4B	90.964	166	12	2	3953	4118	373993231	373993393	1.930000e-53	220
8	TraesCS4D01G172700	chr4B	95.506	89	4	0	3214	3302	373987499	373987587	4.290000e-30	143
9	TraesCS4D01G172700	chr2D	77.460	630	132	9	1041	1665	56202745	56202121	6.500000e-98	368
10	TraesCS4D01G172700	chr2A	78.397	574	114	9	1097	1665	57831978	57831410	8.410000e-97	364
11	TraesCS4D01G172700	chr2A	88.034	117	13	1	3999	4114	138922491	138922607	2.000000e-28	137
12	TraesCS4D01G172700	chr2B	76.887	636	137	9	1041	1671	88932592	88931962	6.550000e-93	351
13	TraesCS4D01G172700	chr7A	88.034	117	13	1	3999	4114	10423060	10423176	2.000000e-28	137
14	TraesCS4D01G172700	chr7A	87.288	118	13	2	3999	4114	144167120	144167003	2.580000e-27	134
15	TraesCS4D01G172700	chr6A	88.034	117	13	1	3999	4114	590371001	590371117	2.000000e-28	137
16	TraesCS4D01G172700	chr5B	88.034	117	13	1	3999	4114	638783311	638783427	2.000000e-28	137
17	TraesCS4D01G172700	chr3B	88.034	117	13	1	3999	4114	12765179	12765295	2.000000e-28	137
18	TraesCS4D01G172700	chr3B	88.034	117	13	1	3999	4114	92330334	92330218	2.000000e-28	137
19	TraesCS4D01G172700	chr1B	88.034	117	13	1	3999	4114	453522075	453522191	2.000000e-28	137

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	TraesCS4D01G172700	chr4D	300782339	300786456	4117	False	7605.0	7605	100.000000	1	4118	1	chr4D.!!$F1	4117
1	TraesCS4D01G172700	chr4A	182216232	182220337	4105	True	1988.0	5365	91.621000	1	3846	3	chr4A.!!$R1	3845
2	TraesCS4D01G172700	chr4B	373980773	373987587	6814	False	1849.0	4534	95.679667	1	3302	3	chr4B.!!$F1	3301
3	TraesCS4D01G172700	chr4B	373992724	373993393	669	False	334.5	449	86.870500	3450	4118	2	chr4B.!!$F2	668
4	TraesCS4D01G172700	chr2D	56202121	56202745	624	True	368.0	368	77.460000	1041	1665	1	chr2D.!!$R1	624
5	TraesCS4D01G172700	chr2A	57831410	57831978	568	True	364.0	364	78.397000	1097	1665	1	chr2A.!!$R1	568
6	TraesCS4D01G172700	chr2B	88931962	88932592	630	True	351.0	351	76.887000	1041	1671	1	chr2B.!!$R1	630

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
997	1012	3.490348	ACTGTTGAATCTTGGTTCCTGG	58.510	45.455	0.00	0.00	0.00	4.45	F
2062	2083	5.074929	TCATGGCCATGTAAGGATCCTTTAT	59.925	40.000	38.18	21.91	39.72	1.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2300	2321	1.173043	CCTTGCCCGTAAGCATTTCA	58.827	50.0	0.0	0.0	43.64	2.69	R
3511	7139	0.608582	AGTCGGGCTAACACGTCTCT	60.609	55.0	0.0	0.0	0.00	3.10	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
76	77	4.399303	CCTTGAACTCCCATGGTAATTGTC	59.601	45.833	11.73	0.91	0.00	3.18
213	224	4.766404	ATAAGTTTGCTTCCCGTTCTTG	57.234	40.909	0.00	0.00	36.22	3.02
465	476	8.352942	ACTTCAGTGGCAAATTACTTTTAGAAG	58.647	33.333	0.00	0.00	38.87	2.85
498	510	8.179509	ACTGTCTTTAAGTTTAGTCTCTGCTA	57.820	34.615	0.00	0.00	0.00	3.49
701	716	7.845037	AGACAAGTTGATCTCATGTATTCAGA	58.155	34.615	10.54	0.00	0.00	3.27
977	992	6.966066	GCTAGCTTTCATCAAGATTCTCAAAC	59.034	38.462	7.70	0.00	33.80	2.93
997	1012	3.490348	ACTGTTGAATCTTGGTTCCTGG	58.510	45.455	0.00	0.00	0.00	4.45
2062	2083	5.074929	TCATGGCCATGTAAGGATCCTTTAT	59.925	40.000	38.18	21.91	39.72	1.40
2300	2321	3.500471	GGAGTGTGGGGATCCTTCTTTTT	60.500	47.826	12.58	0.00	0.00	1.94
2381	2402	4.579753	TGCATTTCAGATGAATTATCCGCA	59.420	37.500	0.00	0.00	36.40	5.69
2567	2588	2.250939	TTCACCTTGACCTTGCGCG	61.251	57.895	0.00	0.00	0.00	6.86
2600	2621	0.109132	CAATCGACCCTTTGCTTGGC	60.109	55.000	0.00	0.00	0.00	4.52
2611	2632	3.314553	CTTTGCTTGGCTTCAATGTCAG	58.685	45.455	0.00	0.00	0.00	3.51
2717	2757	2.355108	GCTTGTAGTGAAGCCTGATCCA	60.355	50.000	0.00	0.00	42.23	3.41
2783	2823	9.220767	GTTGGAAGTTAAATCTAGATGACTTGT	57.779	33.333	23.42	9.58	0.00	3.16
2799	2839	4.100808	TGACTTGTTGCTAATTTGCCCTTT	59.899	37.500	9.41	0.00	0.00	3.11
2800	2840	5.303078	TGACTTGTTGCTAATTTGCCCTTTA	59.697	36.000	9.41	0.00	0.00	1.85
2802	2842	6.398095	ACTTGTTGCTAATTTGCCCTTTATC	58.602	36.000	9.41	0.00	0.00	1.75
2803	2843	5.337578	TGTTGCTAATTTGCCCTTTATCC	57.662	39.130	9.41	0.00	0.00	2.59
2804	2844	4.142271	TGTTGCTAATTTGCCCTTTATCCG	60.142	41.667	9.41	0.00	0.00	4.18
2844	2892	2.674380	AAAGAAGCTGGCAGGCGG	60.674	61.111	17.64	0.00	37.29	6.13
2856	2904	4.351054	AGGCGGCTTGGAAGTGGG	62.351	66.667	5.25	0.00	0.00	4.61
2936	2984	2.294074	ACTAGAGGCTCGACAGATCAC	58.706	52.381	17.10	0.00	0.00	3.06
3267	3315	2.295909	TGGCAGTAACTTTGTGGCAATC	59.704	45.455	0.00	0.00	43.12	2.67
3271	3319	2.812011	AGTAACTTTGTGGCAATCCGTC	59.188	45.455	0.00	0.00	34.14	4.79
3273	3321	1.981256	ACTTTGTGGCAATCCGTCTT	58.019	45.000	0.00	0.00	34.14	3.01
3274	3322	1.608590	ACTTTGTGGCAATCCGTCTTG	59.391	47.619	0.00	0.00	34.14	3.02
3278	3326	1.606668	TGTGGCAATCCGTCTTGTTTC	59.393	47.619	0.00	0.00	34.14	2.78
3280	3328	2.293399	GTGGCAATCCGTCTTGTTTCTT	59.707	45.455	0.00	0.00	34.14	2.52
3281	3329	2.293122	TGGCAATCCGTCTTGTTTCTTG	59.707	45.455	0.00	0.00	34.14	3.02
3324	4054	7.768582	TCTTAATTACTTTCCATCAATCTCGCA	59.231	33.333	0.00	0.00	0.00	5.10
3370	5004	4.707448	TGTTGTTTAAGTTTTCTGCCTGGA	59.293	37.500	0.00	0.00	0.00	3.86
3391	5025	4.394610	GGAAGAAGTTCATGGAAGAAGAGC	59.605	45.833	5.50	0.00	33.93	4.09
3392	5026	3.949132	AGAAGTTCATGGAAGAAGAGCC	58.051	45.455	5.50	0.00	0.00	4.70
3444	7072	1.080298	GCTGTTCTGCAACCATGGC	60.080	57.895	13.04	0.00	0.00	4.40
3488	7116	1.768870	GATGGCTAACCTGAGGCCTAA	59.231	52.381	4.42	0.00	45.45	2.69
3494	7122	3.808174	GCTAACCTGAGGCCTAAAATACG	59.192	47.826	4.42	0.00	0.00	3.06
3540	7168	3.192844	TGTTAGCCCGACTAGTTTGAGAG	59.807	47.826	0.00	0.00	30.79	3.20
3608	7238	1.620822	AGTGAAACAATGGCACTCCC	58.379	50.000	0.00	0.00	38.41	4.30
3609	7239	0.240945	GTGAAACAATGGCACTCCCG	59.759	55.000	0.00	0.00	36.32	5.14
3613	7243	0.038166	AACAATGGCACTCCCGACAT	59.962	50.000	0.00	0.00	35.87	3.06
3630	7260	1.804151	ACATCACACGATCCAAAACGG	59.196	47.619	0.00	0.00	0.00	4.44
3634	7264	1.127951	CACACGATCCAAAACGGTAGC	59.872	52.381	0.00	0.00	35.57	3.58
3669	7301	0.171007	CCAATAACCACAGCCGCTTG	59.829	55.000	0.00	0.00	0.00	4.01
3679	7311	2.280052	GCCGCTTGCCTGCAAAAA	60.280	55.556	6.00	0.00	35.33	1.94
3754	7386	5.184287	TCTTCTATGGTGTACGTCATGTGAA	59.816	40.000	0.00	11.61	0.00	3.18
3766	7398	4.202000	ACGTCATGTGAAAAGAAATGTGCA	60.202	37.500	0.00	0.00	0.00	4.57
3767	7399	4.919168	CGTCATGTGAAAAGAAATGTGCAT	59.081	37.500	0.00	0.00	0.00	3.96
3768	7400	5.164129	CGTCATGTGAAAAGAAATGTGCATG	60.164	40.000	0.00	0.00	35.25	4.06
3769	7401	5.921976	GTCATGTGAAAAGAAATGTGCATGA	59.078	36.000	0.00	0.00	39.03	3.07
3770	7402	6.421501	GTCATGTGAAAAGAAATGTGCATGAA	59.578	34.615	0.00	0.00	41.67	2.57
3771	7403	6.421501	TCATGTGAAAAGAAATGTGCATGAAC	59.578	34.615	0.00	0.00	38.60	3.18
3894	7528	2.929724	TGGATTTTTGGAGATGGGGGTA	59.070	45.455	0.00	0.00	0.00	3.69
3905	7539	4.145052	GAGATGGGGGTAATTGGATGTTC	58.855	47.826	0.00	0.00	0.00	3.18
3919	7553	3.019564	GGATGTTCTCCAAAGACATGGG	58.980	50.000	0.00	0.00	44.26	4.00
3931	7565	5.887598	CCAAAGACATGGGAATGTGATTCTA	59.112	40.000	0.00	0.00	39.24	2.10
4055	7738	0.254747	CCCTCCATTACCGAAGCCAA	59.745	55.000	0.00	0.00	0.00	4.52
4060	7743	2.554893	TCCATTACCGAAGCCAACAAAC	59.445	45.455	0.00	0.00	0.00	2.93
4064	7747	2.351706	ACCGAAGCCAACAAACCTTA	57.648	45.000	0.00	0.00	0.00	2.69
4066	7749	2.556622	ACCGAAGCCAACAAACCTTATG	59.443	45.455	0.00	0.00	0.00	1.90
4082	7765	3.568853	CCTTATGGTAGTAGACAGTCGGG	59.431	52.174	0.00	0.00	0.00	5.14
4097	7780	1.513586	CGGGAAGTCGTCGTGCTAC	60.514	63.158	0.00	0.00	0.00	3.58
4103	7786	3.367743	TCGTCGTGCTACGGCCTT	61.368	61.111	0.00	0.00	44.43	4.35
4104	7787	2.039974	TCGTCGTGCTACGGCCTTA	61.040	57.895	0.00	0.00	44.43	2.69
4105	7788	1.153978	CGTCGTGCTACGGCCTTAA	60.154	57.895	0.00	0.00	44.43	1.85
4112	7795	0.251073	GCTACGGCCTTAAAGGACCA	59.749	55.000	0.00	0.00	41.74	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	2.773918	CCCTGCCCCCTATGAGCA	60.774	66.667	0.00	0.00	34.79	4.26
179	189	4.639310	AGCAAACTTATTGGAGAGCTCATG	59.361	41.667	17.77	0.00	0.00	3.07
180	190	4.853007	AGCAAACTTATTGGAGAGCTCAT	58.147	39.130	17.77	2.75	0.00	2.90
213	224	6.073819	GCATGTCAAAATAAACCCAGACAAAC	60.074	38.462	0.00	0.00	39.17	2.93
447	458	5.939457	AGCGTCTTCTAAAAGTAATTTGCC	58.061	37.500	0.00	0.00	33.95	4.52
465	476	8.070007	ACTAAACTTAAAGACAGTAAAGCGTC	57.930	34.615	0.00	0.00	0.00	5.19
483	495	7.755822	CGTGTTATCTTTAGCAGAGACTAAACT	59.244	37.037	0.00	0.00	37.24	2.66
701	716	2.107204	ACTCTGGATGCCACTGTTCTTT	59.893	45.455	0.00	0.00	0.00	2.52
977	992	3.754965	TCCAGGAACCAAGATTCAACAG	58.245	45.455	0.00	0.00	0.00	3.16
997	1012	4.898861	AGGTATCTCAGAGGAAACCATCTC	59.101	45.833	15.23	0.00	0.00	2.75
1868	1884	7.563556	TGTCACATCTGGATAGGTGTAAAGATA	59.436	37.037	0.00	0.00	46.37	1.98
2300	2321	1.173043	CCTTGCCCGTAAGCATTTCA	58.827	50.000	0.00	0.00	43.64	2.69
2600	2621	2.886523	TCAAACTGGGCTGACATTGAAG	59.113	45.455	0.00	0.00	0.00	3.02
2611	2632	2.622942	TGATCACAAACTCAAACTGGGC	59.377	45.455	0.00	0.00	0.00	5.36
2717	2757	2.739943	TCTCCGACAAGAGACATCCAT	58.260	47.619	0.00	0.00	37.98	3.41
2783	2823	4.020543	ACGGATAAAGGGCAAATTAGCAA	58.979	39.130	0.00	0.00	35.83	3.91
2936	2984	1.880819	ATTTGGGCAGAAGCTTGGCG	61.881	55.000	2.10	0.00	43.96	5.69
3242	3290	2.543653	GCCACAAAGTTACTGCCAAGTG	60.544	50.000	0.00	0.00	37.19	3.16
3251	3299	2.812011	AGACGGATTGCCACAAAGTTAC	59.188	45.455	0.00	0.00	0.00	2.50
3267	3315	5.986004	AAGAGTAACAAGAAACAAGACGG	57.014	39.130	0.00	0.00	0.00	4.79
3271	3319	8.181573	TGCAACTAAAGAGTAACAAGAAACAAG	58.818	33.333	0.00	0.00	33.58	3.16
3273	3321	7.618502	TGCAACTAAAGAGTAACAAGAAACA	57.381	32.000	0.00	0.00	33.58	2.83
3274	3322	8.560374	AGATGCAACTAAAGAGTAACAAGAAAC	58.440	33.333	0.00	0.00	33.58	2.78
3324	4054	3.748083	ACAGTGTTCATGCACATTCTCT	58.252	40.909	0.43	0.00	41.52	3.10
3351	4985	5.767816	TCTTCCAGGCAGAAAACTTAAAC	57.232	39.130	0.00	0.00	0.00	2.01
3370	5004	4.331108	GGCTCTTCTTCCATGAACTTCTT	58.669	43.478	0.00	0.00	0.00	2.52
3404	5038	3.057596	CCACGGCTCTTCTTTGCATAAAA	60.058	43.478	0.00	0.00	0.00	1.52
3405	5039	2.487762	CCACGGCTCTTCTTTGCATAAA	59.512	45.455	0.00	0.00	0.00	1.40
3409	5043	2.260869	GCCACGGCTCTTCTTTGCA	61.261	57.895	0.00	0.00	38.26	4.08
3444	7072	1.301244	ATAAGGCTCCAGCATCGCG	60.301	57.895	0.00	0.00	44.36	5.87
3454	7082	1.831580	GCCATCCCATCATAAGGCTC	58.168	55.000	0.00	0.00	39.02	4.70
3511	7139	0.608582	AGTCGGGCTAACACGTCTCT	60.609	55.000	0.00	0.00	0.00	3.10
3540	7168	5.106673	CCATTACCTTCTCGAGTTTTCCAAC	60.107	44.000	13.13	0.00	0.00	3.77
3585	7213	3.428045	GGAGTGCCATTGTTTCACTATGC	60.428	47.826	0.00	0.00	40.74	3.14
3608	7238	2.472235	CGTTTTGGATCGTGTGATGTCG	60.472	50.000	0.00	0.00	34.09	4.35
3609	7239	2.159707	CCGTTTTGGATCGTGTGATGTC	60.160	50.000	0.00	0.00	42.00	3.06
3613	7243	2.679450	CTACCGTTTTGGATCGTGTGA	58.321	47.619	0.00	0.00	42.00	3.58
3630	7260	3.753272	TGGCAAGAACTGATTGAAGCTAC	59.247	43.478	0.00	0.00	0.00	3.58
3634	7264	6.095377	GGTTATTGGCAAGAACTGATTGAAG	58.905	40.000	29.91	0.00	33.32	3.02
3679	7311	8.549338	TTTTTATTCAACGGGTGTTTTTCTTT	57.451	26.923	0.00	0.00	35.72	2.52
3721	7353	6.183360	ACGTACACCATAGAAGATTGCTATGT	60.183	38.462	0.00	0.00	42.20	2.29
3754	7386	7.889469	AGATTAGTGTTCATGCACATTTCTTT	58.111	30.769	0.43	0.00	41.52	2.52
3766	7398	6.567602	AGGCCTTAGAAGATTAGTGTTCAT	57.432	37.500	0.00	0.00	30.40	2.57
3767	7399	6.374417	AAGGCCTTAGAAGATTAGTGTTCA	57.626	37.500	18.87	0.00	30.40	3.18
3768	7400	6.879458	TCAAAGGCCTTAGAAGATTAGTGTTC	59.121	38.462	20.84	0.00	0.00	3.18
3769	7401	6.779860	TCAAAGGCCTTAGAAGATTAGTGTT	58.220	36.000	20.84	0.00	0.00	3.32
3770	7402	6.374417	TCAAAGGCCTTAGAAGATTAGTGT	57.626	37.500	20.84	0.00	0.00	3.55
3771	7403	8.964476	TTATCAAAGGCCTTAGAAGATTAGTG	57.036	34.615	20.84	9.34	0.00	2.74
3801	7433	9.793259	ACTCCTTTTAAAAATGTCAGATGTCTA	57.207	29.630	1.66	0.00	0.00	2.59
3805	7437	7.809806	GTCCACTCCTTTTAAAAATGTCAGATG	59.190	37.037	1.66	0.00	0.00	2.90
3864	7498	5.310409	TCTCCAAAAATCCAAGTCACTCT	57.690	39.130	0.00	0.00	0.00	3.24
3865	7499	5.105997	CCATCTCCAAAAATCCAAGTCACTC	60.106	44.000	0.00	0.00	0.00	3.51
3870	7504	3.444029	CCCCATCTCCAAAAATCCAAGT	58.556	45.455	0.00	0.00	0.00	3.16
3876	7510	4.721274	CCAATTACCCCCATCTCCAAAAAT	59.279	41.667	0.00	0.00	0.00	1.82
3905	7539	3.689347	TCACATTCCCATGTCTTTGGAG	58.311	45.455	0.00	0.00	42.14	3.86
3909	7543	8.599624	AATTAGAATCACATTCCCATGTCTTT	57.400	30.769	0.00	0.00	42.14	2.52
3915	7549	9.713684	TTCCTTAAATTAGAATCACATTCCCAT	57.286	29.630	0.00	0.00	40.13	4.00
3931	7565	6.540551	GCTAGCTGCTAGACTTTCCTTAAATT	59.459	38.462	34.43	0.00	36.26	1.82
3996	7679	2.202810	GGCTCGCTCCAGTGCTAC	60.203	66.667	0.00	0.00	0.00	3.58
4060	7743	3.568853	CCCGACTGTCTACTACCATAAGG	59.431	52.174	6.21	0.00	42.21	2.69
4064	7747	3.288964	CTTCCCGACTGTCTACTACCAT	58.711	50.000	6.21	0.00	0.00	3.55
4066	7749	2.682352	GACTTCCCGACTGTCTACTACC	59.318	54.545	6.21	0.00	0.00	3.18
4082	7765	2.150837	GCCGTAGCACGACGACTTC	61.151	63.158	0.00	0.00	46.05	3.01
4097	7780	0.455815	GCATTGGTCCTTTAAGGCCG	59.544	55.000	6.05	0.71	35.26	6.13

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.