AutoCloner

Multiple sequence alignment - TraesCS7A01G222100

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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	TraesCS7A01G222100	chr7A	100.000	3146	0	0	1	3146	191659554	191662699	0.000000e+00	5810.0
1	TraesCS7A01G222100	chr7A	88.286	1272	138	9	886	2150	185982611	185981344	0.000000e+00	1513.0
2	TraesCS7A01G222100	chr7A	95.833	72	3	0	1	72	185983564	185983493	1.980000e-22	117.0
3	TraesCS7A01G222100	chr7D	95.803	2740	96	6	1	2736	184558990	184561714	0.000000e+00	4405.0
4	TraesCS7A01G222100	chr7D	87.384	1395	146	17	886	2259	184514698	184516083	0.000000e+00	1574.0
5	TraesCS7A01G222100	chr7D	94.615	260	14	0	2885	3144	184571482	184571741	1.360000e-108	403.0
6	TraesCS7A01G222100	chr7D	93.011	186	11	1	2706	2889	184561714	184561899	1.440000e-68	270.0
7	TraesCS7A01G222100	chr7D	83.217	286	26	8	476	761	184514409	184514672	3.130000e-60	243.0
8	TraesCS7A01G222100	chr7B	93.690	2171	131	5	138	2307	154143612	154145777	0.000000e+00	3245.0
9	TraesCS7A01G222100	chr7B	86.832	1496	152	22	883	2359	153594705	153596174	0.000000e+00	1629.0
10	TraesCS7A01G222100	chr7B	87.105	760	71	8	2388	3146	154145791	154146524	0.000000e+00	835.0
11	TraesCS7A01G222100	chr7B	81.176	340	34	11	421	760	153594372	153594681	2.420000e-61	246.0
12	TraesCS7A01G222100	chr7B	97.101	69	2	0	1	69	153593226	153593294	1.980000e-22	117.0
13	TraesCS7A01G222100	chr7B	95.652	69	3	0	1	69	154143375	154143443	9.220000e-21	111.0
14	TraesCS7A01G222100	chr5A	78.384	990	187	18	1173	2147	275260827	275259850	4.460000e-173	617.0
15	TraesCS7A01G222100	chr5D	78.182	990	189	18	1173	2147	212252802	212251825	9.650000e-170	606.0
16	TraesCS7A01G222100	chr1D	76.829	246	31	18	2584	2825	14265539	14265316	7.130000e-22	115.0
17	TraesCS7A01G222100	chr6A	75.904	166	34	5	2540	2702	521992145	521991983	2.600000e-11	80.5
18	TraesCS7A01G222100	chr5B	100.000	31	0	0	2798	2828	678179249	678179219	1.220000e-04	58.4

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	TraesCS7A01G222100	chr7A	191659554	191662699	3145	False	5810.0	5810	100.000000	1	3146	1	chr7A.!!$F1	3145
1	TraesCS7A01G222100	chr7A	185981344	185983564	2220	True	815.0	1513	92.059500	1	2150	2	chr7A.!!$R1	2149
2	TraesCS7A01G222100	chr7D	184558990	184561899	2909	False	2337.5	4405	94.407000	1	2889	2	chr7D.!!$F3	2888
3	TraesCS7A01G222100	chr7D	184514409	184516083	1674	False	908.5	1574	85.300500	476	2259	2	chr7D.!!$F2	1783
4	TraesCS7A01G222100	chr7B	154143375	154146524	3149	False	1397.0	3245	92.149000	1	3146	3	chr7B.!!$F2	3145
5	TraesCS7A01G222100	chr7B	153593226	153596174	2948	False	664.0	1629	88.369667	1	2359	3	chr7B.!!$F1	2358
6	TraesCS7A01G222100	chr5A	275259850	275260827	977	True	617.0	617	78.384000	1173	2147	1	chr5A.!!$R1	974
7	TraesCS7A01G222100	chr5D	212251825	212252802	977	True	606.0	606	78.182000	1173	2147	1	chr5D.!!$R1	974

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
867	1653	0.400381	TGCCTCCTATCAGCATCCCA	60.4	55.0	0.0	0.0	0.0	4.37	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2810	3667	0.325933	CAACACTCCATGGAGAGGCA	59.674	55.0	41.91	8.65	44.53	4.75	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
85	132	2.048603	GGCTCGGGGTGTACTACGT	61.049	63.158	0.00	0.00	0.00	3.57
122	169	1.196808	CGTACAAAGTGCCGATGCTTT	59.803	47.619	0.00	0.00	38.71	3.51
133	184	5.006261	AGTGCCGATGCTTTGTTTTAAAAAC	59.994	36.000	1.31	0.00	38.71	2.43
288	428	6.437162	ACTCTTATTGGTGGTAAACAATGCAT	59.563	34.615	0.00	0.00	37.80	3.96
432	1211	5.349061	TGCAGCTATATATGTCCATCCAG	57.651	43.478	0.00	0.00	0.00	3.86
614	1400	9.617523	ACATGTGATATGTAAATGATTGACAGA	57.382	29.630	0.00	0.00	0.00	3.41
625	1411	4.427096	TGATTGACAGACGAGACTTCTC	57.573	45.455	0.00	0.00	39.55	2.87
725	1511	4.100084	CCGGCTGAGCACCATCCA	62.100	66.667	6.82	0.00	30.53	3.41
867	1653	0.400381	TGCCTCCTATCAGCATCCCA	60.400	55.000	0.00	0.00	0.00	4.37
1050	1836	1.874345	CGATATACTTCCCGCCGGCT	61.874	60.000	26.68	6.90	0.00	5.52
1143	1929	0.806884	TTGTCGTCGTCGTTGGCTTT	60.807	50.000	1.33	0.00	38.33	3.51
1162	1948	3.200593	GCACGCCATCTCAGCCAG	61.201	66.667	0.00	0.00	0.00	4.85
1199	1985	3.506096	CGGCAGCGACCTCTCGTA	61.506	66.667	0.00	0.00	42.33	3.43
1389	2178	3.233259	TTCATCCACGTCTGGCGCA	62.233	57.895	10.83	0.00	46.11	6.09
1674	2469	0.978151	TAAAGAAGCCGCAGTACCCA	59.022	50.000	0.00	0.00	0.00	4.51
2222	3047	7.420002	GTGTCGGTATCCTTTACTTTGTTTTT	58.580	34.615	0.00	0.00	0.00	1.94
2286	3111	6.020360	GCTTCCTTTGCATATCGAAAACATTC	60.020	38.462	0.00	0.00	0.00	2.67
2472	3297	9.092876	TCGCAATTTGGGTATTTATTGAAAATC	57.907	29.630	12.54	0.00	31.29	2.17
2473	3298	8.055402	CGCAATTTGGGTATTTATTGAAAATCG	58.945	33.333	5.35	0.00	31.29	3.34
2504	3329	5.741962	AGGGAACTTAGTACCACTTTCTC	57.258	43.478	8.40	0.00	37.44	2.87
2509	3334	7.147976	GGAACTTAGTACCACTTTCTCGTTAA	58.852	38.462	0.00	0.00	0.00	2.01
2538	3363	1.000274	GAACCACACCATCTTTGCACC	60.000	52.381	0.00	0.00	0.00	5.01
2560	3385	5.163301	ACCTAACGGAGAGCAATGATTGTAT	60.163	40.000	7.05	0.00	0.00	2.29
2680	3505	0.902531	ACGTGACCCCACCTATCAAG	59.097	55.000	0.00	0.00	40.12	3.02
2788	3643	5.944007	GCTAATACTTTTCCTCTTGGTGGAA	59.056	40.000	0.00	0.00	41.33	3.53
2827	3684	0.252421	TCTGCCTCTCCATGGAGTGT	60.252	55.000	35.34	0.00	42.49	3.55
2907	3764	2.813908	CACTACCGCGTCTTGCCC	60.814	66.667	4.92	0.00	42.08	5.36
2917	3774	4.032452	TCTTGCCCGCCATGAGCA	62.032	61.111	0.00	0.00	44.04	4.26
2919	3776	3.346631	CTTGCCCGCCATGAGCAAC	62.347	63.158	0.00	0.00	41.35	4.17
2938	3795	1.019673	CCTCAATGGTTCATCCGCTG	58.980	55.000	0.00	0.00	39.52	5.18
2968	3825	1.726533	GCCCGTAACTCCTCTCTCCG	61.727	65.000	0.00	0.00	0.00	4.63
2973	3830	0.464013	TAACTCCTCTCTCCGCCTCG	60.464	60.000	0.00	0.00	0.00	4.63
3018	3875	1.635663	CGTTCCACGCCATGAAGACC	61.636	60.000	0.00	0.00	33.65	3.85
3019	3876	1.375396	TTCCACGCCATGAAGACCG	60.375	57.895	0.00	0.00	0.00	4.79
3020	3877	2.047274	CCACGCCATGAAGACCGT	60.047	61.111	0.00	0.00	0.00	4.83
3035	3892	0.251922	ACCGTGGCCTAGTGGAGTTA	60.252	55.000	3.32	0.00	34.57	2.24
3056	3913	1.004560	TGGCAAGGTTGAGAGCGAG	60.005	57.895	0.00	0.00	0.00	5.03
3058	3915	1.669115	GCAAGGTTGAGAGCGAGCA	60.669	57.895	0.00	0.00	0.00	4.26
3060	3917	1.373497	AAGGTTGAGAGCGAGCACG	60.373	57.895	0.00	0.00	42.93	5.34
3067	3924	2.876645	GAGCGAGCACGAACTCCG	60.877	66.667	8.01	0.00	42.66	4.63
3068	3925	3.324099	GAGCGAGCACGAACTCCGA	62.324	63.158	8.01	0.00	42.66	4.55
3095	3952	3.429141	CTCTGCGGTGCAAGCCAG	61.429	66.667	12.17	7.53	38.41	4.85
3108	3965	1.422161	AAGCCAGTGCCTTCTCCTGT	61.422	55.000	0.00	0.00	38.69	4.00
3114	3971	0.823356	GTGCCTTCTCCTGTTTGCCA	60.823	55.000	0.00	0.00	0.00	4.92
3119	3976	1.876156	CTTCTCCTGTTTGCCAGTGAC	59.124	52.381	0.00	0.00	39.74	3.67
3129	3986	2.657237	CCAGTGACGTGGACCTCC	59.343	66.667	0.00	0.00	40.44	4.30
3139	3996	2.766229	GGACCTCCAGAGCCTCCC	60.766	72.222	0.00	0.00	35.64	4.30

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
85	132	1.416243	ACGGTACTTTCACACCTGGA	58.584	50.000	0.00	0.00	32.29	3.86
122	169	4.090642	CGCAGCACACTTGTTTTTAAAACA	59.909	37.500	17.93	17.93	0.00	2.83
133	184	1.063912	TCAGAAAACGCAGCACACTTG	59.936	47.619	0.00	0.00	0.00	3.16
222	362	7.651304	CAGATTTGCTGGTACACAATAAAACAA	59.349	33.333	0.00	0.00	41.07	2.83
445	1224	8.005192	TGGCATGTTCAGCAAATTATAATACA	57.995	30.769	0.00	0.00	0.00	2.29
625	1411	0.950836	TGGATGGTGAACTTGTTGCG	59.049	50.000	0.00	0.00	0.00	4.85
686	1472	0.253044	TCTGTGGTGGCTAAGGATGC	59.747	55.000	0.00	0.00	0.00	3.91
693	1479	3.390521	CGGGCTCTGTGGTGGCTA	61.391	66.667	0.00	0.00	0.00	3.93
784	1570	2.203182	TGGAGGGAAGACGGTGGT	59.797	61.111	0.00	0.00	0.00	4.16
787	1573	0.763223	AACAGTGGAGGGAAGACGGT	60.763	55.000	0.00	0.00	0.00	4.83
867	1653	3.635869	ATAGGTGCCCGGGTGGTCT	62.636	63.158	24.63	16.57	36.04	3.85
1050	1836	3.083349	CCCTCCGATGGTGCAGGA	61.083	66.667	0.00	0.00	0.00	3.86
1162	1948	0.317020	GTGTCGAACAACAAGGCAGC	60.317	55.000	0.00	0.00	0.00	5.25
1628	2417	1.669440	GTGTACTGGACCTTGCCGA	59.331	57.895	0.00	0.00	0.00	5.54
1674	2469	2.691011	GAGCTCCACGAAGTAGAAGGAT	59.309	50.000	0.87	0.00	41.61	3.24
1797	2592	1.965930	CAAGTTGTAGGCCTGCGCA	60.966	57.895	17.99	10.98	36.38	6.09
1863	2658	0.471211	TGTCGAGGTCTTGGAAGGGT	60.471	55.000	0.00	0.00	0.00	4.34
2222	3047	5.883673	CCCCTTTATTCGTAGTTGGAAATCA	59.116	40.000	0.00	0.00	0.00	2.57
2286	3111	1.234615	AAATCAGCCGGGTGAACACG	61.235	55.000	37.45	10.40	43.52	4.49
2381	3206	2.611292	AGCAGCTCTTCAAATACGATGC	59.389	45.455	0.00	0.00	0.00	3.91
2382	3207	3.060674	CGAGCAGCTCTTCAAATACGATG	60.061	47.826	20.39	0.00	0.00	3.84
2383	3208	3.119291	CGAGCAGCTCTTCAAATACGAT	58.881	45.455	20.39	0.00	0.00	3.73
2384	3209	2.094700	ACGAGCAGCTCTTCAAATACGA	60.095	45.455	20.39	0.00	0.00	3.43
2416	3241	5.220043	CGAAGTAGACACACGCTCATAAAAG	60.220	44.000	0.00	0.00	0.00	2.27
2472	3297	7.650903	GTGGTACTAAGTTCCCTAAATATGACG	59.349	40.741	0.00	0.00	0.00	4.35
2473	3298	8.702819	AGTGGTACTAAGTTCCCTAAATATGAC	58.297	37.037	0.00	0.00	0.00	3.06
2504	3329	1.737793	GTGGTTCCTCATGCCTTAACG	59.262	52.381	0.00	0.00	0.00	3.18
2509	3334	1.380302	GGTGTGGTTCCTCATGCCT	59.620	57.895	0.00	0.00	0.00	4.75
2538	3363	5.985530	TCATACAATCATTGCTCTCCGTTAG	59.014	40.000	0.00	0.00	0.00	2.34
2560	3385	2.827322	CCCTGTTTCCATGAGCAAATCA	59.173	45.455	0.00	0.00	43.70	2.57
2582	3407	0.690762	TGGGGCCTACTTGTCAGTTC	59.309	55.000	0.84	0.00	34.06	3.01
2586	3411	0.400213	CAAGTGGGGCCTACTTGTCA	59.600	55.000	39.54	12.85	46.13	3.58
2591	3416	1.201429	CCTGACAAGTGGGGCCTACT	61.201	60.000	17.89	17.89	0.00	2.57
2640	3465	4.448732	CGTCTCATTTGACACATCAGTTGA	59.551	41.667	0.00	0.00	35.83	3.18
2680	3505	6.634805	TGTGAAGAAGATGACCATCTAGTTC	58.365	40.000	12.40	16.02	46.75	3.01
2788	3643	4.326507	AGCTGCCGCTGCACTCTT	62.327	61.111	22.42	0.32	46.86	2.85
2810	3667	0.325933	CAACACTCCATGGAGAGGCA	59.674	55.000	41.91	8.65	44.53	4.75
2827	3684	1.202675	ACGAGAAAAACTACCCGCCAA	60.203	47.619	0.00	0.00	0.00	4.52
2907	3764	0.099968	CATTGAGGTTGCTCATGGCG	59.900	55.000	0.00	0.00	45.43	5.69
2919	3776	1.019673	CAGCGGATGAACCATTGAGG	58.980	55.000	0.00	0.00	45.67	3.86
2923	3780	0.331278	TTCCCAGCGGATGAACCATT	59.669	50.000	0.00	0.00	38.24	3.16
2925	3782	1.002624	GTTCCCAGCGGATGAACCA	60.003	57.895	0.00	0.00	38.24	3.67
2938	3795	1.092348	GTTACGGGCATTCTGTTCCC	58.908	55.000	0.00	0.00	36.22	3.97
2944	3801	1.757699	GAGAGGAGTTACGGGCATTCT	59.242	52.381	0.00	0.00	0.00	2.40
2952	3809	0.748729	AGGCGGAGAGAGGAGTTACG	60.749	60.000	0.00	0.00	0.00	3.18
3018	3875	2.032620	AGATAACTCCACTAGGCCACG	58.967	52.381	5.01	0.00	33.74	4.94
3019	3876	2.103263	CCAGATAACTCCACTAGGCCAC	59.897	54.545	5.01	0.00	33.74	5.01
3020	3877	2.398588	CCAGATAACTCCACTAGGCCA	58.601	52.381	5.01	0.00	33.74	5.36
3035	3892	0.392193	CGCTCTCAACCTTGCCAGAT	60.392	55.000	0.00	0.00	0.00	2.90
3060	3917	2.876645	CTCGCGCACTCGGAGTTC	60.877	66.667	8.18	2.33	35.95	3.01
3074	3931	3.485431	CTTGCACCGCAGAGCTCG	61.485	66.667	8.37	4.60	40.61	5.03
3095	3952	0.823356	TGGCAAACAGGAGAAGGCAC	60.823	55.000	0.00	0.00	0.00	5.01
3108	3965	1.525077	GGTCCACGTCACTGGCAAA	60.525	57.895	0.00	0.00	0.00	3.68
3114	3971	0.896019	CTCTGGAGGTCCACGTCACT	60.896	60.000	0.00	0.00	42.01	3.41
3119	3976	2.681778	AGGCTCTGGAGGTCCACG	60.682	66.667	0.00	0.00	42.01	4.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.