AutoCloner

Multiple sequence alignment - TraesCS4D01G338800

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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	TraesCS4D01G338800	chr4D	100.000	3470	0	0	1	3470	496694634	496698103	0.000000e+00	6408.0
1	TraesCS4D01G338800	chr4D	86.809	705	77	8	2776	3465	496663991	496664694	0.000000e+00	773.0
2	TraesCS4D01G338800	chr5A	93.470	2986	159	20	19	2988	675779907	675782872	0.000000e+00	4401.0
3	TraesCS4D01G338800	chr5A	84.023	701	90	12	2772	3456	675741122	675741816	0.000000e+00	654.0
4	TraesCS4D01G338800	chr5A	85.328	259	25	5	3207	3465	675799968	675800213	4.440000e-64	255.0
5	TraesCS4D01G338800	chr4B	93.957	2350	105	8	406	2735	636736493	636738825	0.000000e+00	3518.0
6	TraesCS4D01G338800	chr4B	86.883	709	75	12	2772	3465	636703373	636704078	0.000000e+00	778.0
7	TraesCS4D01G338800	chr4B	89.684	475	45	2	2815	3289	636748309	636748779	1.380000e-168	603.0
8	TraesCS4D01G338800	chr4B	93.716	366	22	1	19	383	636736134	636736499	6.550000e-152	547.0
9	TraesCS4D01G338800	chr4B	94.737	133	7	0	3332	3464	636748785	636748917	1.260000e-49	207.0
10	TraesCS4D01G338800	chr4B	93.182	44	3	0	2773	2816	636739177	636739220	8.040000e-07	65.8
11	TraesCS4D01G338800	chr1B	87.358	2642	260	40	161	2751	664806651	664809269	0.000000e+00	2961.0
12	TraesCS4D01G338800	chr1B	81.639	964	128	25	176	1109	664809716	664810660	0.000000e+00	754.0
13	TraesCS4D01G338800	chr1D	87.064	2636	257	39	161	2751	477239405	477242001	0.000000e+00	2902.0
14	TraesCS4D01G338800	chr1D	81.404	1054	136	32	161	1182	477243786	477244811	0.000000e+00	806.0
15	TraesCS4D01G338800	chr1D	91.216	296	26	0	1857	2152	477238107	477238402	1.500000e-108	403.0
16	TraesCS4D01G338800	chr1D	83.929	224	23	8	2339	2549	477238442	477238665	5.870000e-48	202.0
17	TraesCS4D01G338800	chr1A	85.874	2676	278	43	161	2751	573440279	573442939	0.000000e+00	2756.0
18	TraesCS4D01G338800	chr1A	82.075	530	78	14	170	694	573443625	573444142	1.480000e-118	436.0
19	TraesCS4D01G338800	chr1A	83.613	238	29	3	2354	2581	573392824	573393061	7.540000e-52	215.0
20	TraesCS4D01G338800	chr3A	72.088	910	192	47	1472	2356	434950951	434950079	2.100000e-52	217.0

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	TraesCS4D01G338800	chr4D	496694634	496698103	3469	False	6408.000000	6408	100.000000	1	3470	1	chr4D.!!$F2	3469
1	TraesCS4D01G338800	chr4D	496663991	496664694	703	False	773.000000	773	86.809000	2776	3465	1	chr4D.!!$F1	689
2	TraesCS4D01G338800	chr5A	675779907	675782872	2965	False	4401.000000	4401	93.470000	19	2988	1	chr5A.!!$F2	2969
3	TraesCS4D01G338800	chr5A	675741122	675741816	694	False	654.000000	654	84.023000	2772	3456	1	chr5A.!!$F1	684
4	TraesCS4D01G338800	chr4B	636736134	636739220	3086	False	1376.933333	3518	93.618333	19	2816	3	chr4B.!!$F2	2797
5	TraesCS4D01G338800	chr4B	636703373	636704078	705	False	778.000000	778	86.883000	2772	3465	1	chr4B.!!$F1	693
6	TraesCS4D01G338800	chr4B	636748309	636748917	608	False	405.000000	603	92.210500	2815	3464	2	chr4B.!!$F3	649
7	TraesCS4D01G338800	chr1B	664806651	664810660	4009	False	1857.500000	2961	84.498500	161	2751	2	chr1B.!!$F1	2590
8	TraesCS4D01G338800	chr1D	477238107	477244811	6704	False	1078.250000	2902	85.903250	161	2751	4	chr1D.!!$F1	2590
9	TraesCS4D01G338800	chr1A	573440279	573444142	3863	False	1596.000000	2756	83.974500	161	2751	2	chr1A.!!$F2	2590
10	TraesCS4D01G338800	chr3A	434950079	434950951	872	True	217.000000	217	72.088000	1472	2356	1	chr3A.!!$R1	884

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
822	2001	0.193321	AATTTGCTTCCCCCAACCCT	59.807	50.0	0.0	0.0	0.0	4.34	F
2406	3665	0.532862	CCAAGGAGCACGCCGATAAT	60.533	55.0	0.0	0.0	0.0	1.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2458	3719	0.460311	CTCTTTCACTACGCCCCGAT	59.540	55.0	0.0	0.0	0.0	4.18	R
3375	7379	0.105453	ATCTAGGTCCCTCGCCATGT	60.105	55.0	0.0	0.0	0.0	3.21	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
46	47	3.966215	CACCTACAAGTGGCACCG	58.034	61.111	15.27	8.65	33.95	4.94
50	51	0.250124	CCTACAAGTGGCACCGTGAA	60.250	55.000	21.78	3.60	0.00	3.18
302	1441	7.725610	AAAATATTTCTGAAATCGAGCGTTG	57.274	32.000	18.22	0.00	32.38	4.10
310	1449	1.635844	AATCGAGCGTTGCGATACAA	58.364	45.000	9.02	0.00	46.67	2.41
428	1572	5.726980	AACTATTTTTGCTGCTGGAATCA	57.273	34.783	0.00	0.00	0.00	2.57
703	1862	2.375014	AACGGAATGGTTTCTTGGGT	57.625	45.000	0.00	0.00	32.16	4.51
822	2001	0.193321	AATTTGCTTCCCCCAACCCT	59.807	50.000	0.00	0.00	0.00	4.34
900	2082	1.152860	TCCACGTGTGCACCCAATT	60.153	52.632	15.69	0.00	0.00	2.32
956	2138	1.664965	GACTGGACGCTCACACACC	60.665	63.158	0.00	0.00	0.00	4.16
1012	2217	1.077663	AGGAACACATGGGCCATTTCT	59.922	47.619	18.46	4.13	0.00	2.52
1345	2571	2.323447	CGATGCTCGCGACGTCTA	59.677	61.111	14.70	0.00	31.14	2.59
1419	2645	2.745884	CAACGCATCTTCCCGGCA	60.746	61.111	0.00	0.00	0.00	5.69
1560	2786	2.032681	GAGGCGTTTGAGGGCTGT	59.967	61.111	1.34	0.00	39.04	4.40
1812	3053	3.340399	TGGATGTTCCAGGTCCTCCCT	62.340	57.143	0.00	0.00	42.67	4.20
2272	3513	3.883744	CTTGCCCGCGTGTTCTCCT	62.884	63.158	4.92	0.00	0.00	3.69
2406	3665	0.532862	CCAAGGAGCACGCCGATAAT	60.533	55.000	0.00	0.00	0.00	1.28
2459	3720	4.415150	CAGCCACCTGCCGGACAT	62.415	66.667	5.05	0.00	42.71	3.06
2479	3740	1.295423	GGGGCGTAGTGAAAGAGCA	59.705	57.895	0.00	0.00	0.00	4.26
2512	3773	6.502136	TGCATCGTGGTTTGAATAATTGTA	57.498	33.333	0.00	0.00	0.00	2.41
2559	3827	7.218560	GTCGATCGAGTTTAGTTTGTTAGTTG	58.781	38.462	20.09	0.00	0.00	3.16
2636	3945	4.686554	GTCAATAAAGTGTCGCTCTCAAGT	59.313	41.667	0.00	0.00	0.00	3.16
2720	4038	3.273434	TCAGTTGCAAGTAGATCATGGC	58.727	45.455	6.43	0.00	0.00	4.40
2760	4078	7.290813	TCATCTTGAAGATACACTAGAGGCTA	58.709	38.462	7.46	0.00	32.12	3.93
2809	6223	3.064324	GCCTGTGCGCTCCCATTT	61.064	61.111	9.73	0.00	0.00	2.32
2823	6237	6.676950	CGCTCCCATTTTAATTATGCACATA	58.323	36.000	0.00	0.00	0.00	2.29
2864	6379	8.837389	GTTATCTACGAGGAAATTAAATGGCTT	58.163	33.333	0.00	0.00	0.00	4.35
2865	6380	6.920569	TCTACGAGGAAATTAAATGGCTTC	57.079	37.500	0.00	0.00	0.00	3.86
2905	6422	2.084546	CCAGCAGGTAAACTAGGCAAC	58.915	52.381	0.00	0.00	0.00	4.17
2993	6791	2.704572	CACCCACAATCTGAAGACCTC	58.295	52.381	0.00	0.00	0.00	3.85
2998	6797	4.440880	CCACAATCTGAAGACCTCTGATC	58.559	47.826	0.00	0.00	40.72	2.92
3049	6848	5.535753	TTGATCTCCTTCAATATCTCGCA	57.464	39.130	0.00	0.00	30.82	5.10
3067	6866	0.680280	CAGAGCAATGCAGAGGCCTT	60.680	55.000	6.77	0.00	40.13	4.35
3097	6896	3.786516	TTCACACATATGGCAGCAATG	57.213	42.857	7.80	0.00	0.00	2.82
3145	7127	1.202463	AGCTACTTTCTCGATGCGCAT	60.202	47.619	25.66	25.66	0.00	4.73
3165	7147	6.020520	GCGCATAAGTACAACTCTAGAAAGAC	60.021	42.308	0.30	0.00	0.00	3.01
3192	7175	3.057969	TGGACTAACAGCTCCACATTG	57.942	47.619	0.00	0.00	31.20	2.82
3213	7196	0.245539	TTTTCTCCACTCCTACGCGG	59.754	55.000	12.47	0.00	0.00	6.46
3255	7238	1.184322	ATGCAGGGCGAGATCGAGAT	61.184	55.000	6.39	0.00	43.02	2.75
3294	7298	1.153066	TGCCGAAGCAGAACCAACA	60.153	52.632	0.00	0.00	46.52	3.33
3308	7312	1.490490	ACCAACAGGTGTGAGTGACAT	59.510	47.619	0.00	0.00	36.78	3.06
3318	7322	0.322648	TGAGTGACATGAGCCACCAG	59.677	55.000	0.00	0.00	34.00	4.00
3456	7460	4.615949	TCAACAATGGAACCAATTCAACG	58.384	39.130	0.00	0.00	36.46	4.10
3467	7471	3.381272	ACCAATTCAACGCCTGATTATGG	59.619	43.478	10.37	10.37	32.78	2.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.231235	CAGCCCACTTGATTTTACCACC	59.769	50.000	0.00	0.00	0.00	4.61
5	6	5.885912	GGTAATCTCAGCCCACTTGATTTTA	59.114	40.000	0.00	0.00	32.21	1.52
6	7	4.706962	GGTAATCTCAGCCCACTTGATTTT	59.293	41.667	0.00	0.00	32.21	1.82
7	8	4.263905	TGGTAATCTCAGCCCACTTGATTT	60.264	41.667	0.00	0.00	32.21	2.17
8	9	3.266772	TGGTAATCTCAGCCCACTTGATT	59.733	43.478	0.00	0.00	33.57	2.57
10	11	2.027192	GTGGTAATCTCAGCCCACTTGA	60.027	50.000	0.00	0.00	43.21	3.02
12	13	1.282157	GGTGGTAATCTCAGCCCACTT	59.718	52.381	7.52	0.00	45.33	3.16
13	14	0.912486	GGTGGTAATCTCAGCCCACT	59.088	55.000	7.52	0.00	45.33	4.00
15	16	2.116238	GTAGGTGGTAATCTCAGCCCA	58.884	52.381	0.00	0.00	33.56	5.36
16	17	2.116238	TGTAGGTGGTAATCTCAGCCC	58.884	52.381	0.00	0.00	33.56	5.19
337	1478	7.548196	TCGCGAAGAACAATTCCTAAATTAT	57.452	32.000	6.20	0.00	33.27	1.28
428	1572	2.713863	TAATCCCCGCATTAACCGTT	57.286	45.000	0.00	0.00	0.00	4.44
584	1735	7.995289	TCTAAAAACACACACAGATGAACATT	58.005	30.769	0.00	0.00	0.00	2.71
699	1858	1.505151	TTATGGCCTGCTTGGACCCA	61.505	55.000	3.32	0.00	45.70	4.51
703	1862	4.662966	ATATGATTATGGCCTGCTTGGA	57.337	40.909	3.32	0.00	38.35	3.53
711	1870	5.047092	CAGAAACCCCAATATGATTATGGCC	60.047	44.000	0.00	0.00	0.00	5.36
773	1932	2.567169	CACAATAGATCGGGGGCATAGA	59.433	50.000	0.00	0.00	0.00	1.98
775	1934	2.567169	CTCACAATAGATCGGGGGCATA	59.433	50.000	0.00	0.00	0.00	3.14
900	2082	2.283604	TAGGTGTGGAGAGCGCCA	60.284	61.111	2.29	0.00	38.87	5.69
1345	2571	2.905935	ATCCCGGTGGTCGTCGAGAT	62.906	60.000	0.00	0.00	37.11	2.75
1419	2645	1.901085	GAAGGAGGAGTGCGGTGAT	59.099	57.895	0.00	0.00	0.00	3.06
1465	2691	2.023461	CTGACGGTAGAGCTCGCG	59.977	66.667	8.37	0.00	0.00	5.87
1560	2786	4.656117	ACGACATGCACGCGGTCA	62.656	61.111	12.47	8.20	0.00	4.02
2258	3499	4.680237	TGCAGGAGAACACGCGGG	62.680	66.667	6.92	6.92	0.00	6.13
2381	3634	2.281070	CGTGCTCCTTGGCAGTGT	60.281	61.111	0.00	0.00	43.25	3.55
2406	3665	2.845363	TGCTCATCTTCAGCTTGTGA	57.155	45.000	0.00	0.00	37.79	3.58
2443	3702	4.101448	GATGTCCGGCAGGTGGCT	62.101	66.667	1.81	0.00	44.01	4.75
2458	3719	0.460311	CTCTTTCACTACGCCCCGAT	59.540	55.000	0.00	0.00	0.00	4.18
2459	3720	1.888018	CTCTTTCACTACGCCCCGA	59.112	57.895	0.00	0.00	0.00	5.14
2479	3740	1.708193	CCACGATGCATGCATGTCGT	61.708	55.000	36.73	34.46	37.36	4.34
2512	3773	1.048601	TCTGCCTCCAACGACTCTTT	58.951	50.000	0.00	0.00	0.00	2.52
2636	3945	5.644977	ATGACGACACTATCTCTCACAAA	57.355	39.130	0.00	0.00	0.00	2.83
2720	4038	5.414360	TCAAGATGAAGTAGTAGCAAGCAG	58.586	41.667	0.00	0.00	0.00	4.24
2770	6184	1.600107	CCTTAGGTAGCGCCACCAA	59.400	57.895	26.87	16.64	41.40	3.67
2780	6194	2.039951	ACAGGCCCGCCTTAGGTA	59.960	61.111	5.22	0.00	45.70	3.08
2861	6376	7.118101	TGGTGATTGCATAAAGAAATTTGAAGC	59.882	33.333	0.00	0.00	0.00	3.86
2864	6379	6.591062	GCTGGTGATTGCATAAAGAAATTTGA	59.409	34.615	0.00	0.00	0.00	2.69
2865	6380	6.369340	TGCTGGTGATTGCATAAAGAAATTTG	59.631	34.615	0.00	0.00	33.94	2.32
2905	6422	3.980775	CCAAACTAGTTTGTGGCATTTCG	59.019	43.478	34.83	19.24	46.19	3.46
3013	6812	9.187996	TGAAGGAGATCAAACATGCATTTATAA	57.812	29.630	0.00	0.00	0.00	0.98
3049	6848	1.690013	AAGGCCTCTGCATTGCTCT	59.310	52.632	5.23	0.00	40.54	4.09
3056	6855	2.224821	CCTATCCAAGGCCTCTGCA	58.775	57.895	5.23	0.00	38.97	4.41
3067	6866	4.717877	CCATATGTGTGAAAGCCTATCCA	58.282	43.478	1.24	0.00	0.00	3.41
3097	6896	1.098129	GGGAAGCCGAGGAAGCATTC	61.098	60.000	0.00	0.00	46.67	2.67
3145	7127	7.672660	TCCATGGTCTTTCTAGAGTTGTACTTA	59.327	37.037	12.58	0.00	0.00	2.24
3178	7160	4.202151	GGAGAAAAACAATGTGGAGCTGTT	60.202	41.667	0.00	0.00	34.81	3.16
3192	7175	1.725164	CGCGTAGGAGTGGAGAAAAAC	59.275	52.381	0.00	0.00	0.00	2.43
3213	7196	0.598065	CTTTAGGCAAGTGTGTGGGC	59.402	55.000	0.00	0.00	0.00	5.36
3294	7298	0.322975	GGCTCATGTCACTCACACCT	59.677	55.000	0.00	0.00	38.04	4.00
3329	7333	3.807538	GGTGCGGACGAGCGACTA	61.808	66.667	0.00	0.00	40.67	2.59
3375	7379	0.105453	ATCTAGGTCCCTCGCCATGT	60.105	55.000	0.00	0.00	0.00	3.21

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.