AutoCloner

Multiple sequence alignment - TraesCS7A01G097200

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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	TraesCS7A01G097200	chr7A	100.000	1319	0	0	953	2271	59602807	59601489	0.000000e+00	2436.0
1	TraesCS7A01G097200	chr7A	100.000	710	0	0	1	710	59603759	59603050	0.000000e+00	1312.0
2	TraesCS7A01G097200	chr7A	94.957	575	27	2	1	574	622333038	622333611	0.000000e+00	900.0
3	TraesCS7A01G097200	chr7A	96.042	480	18	1	953	1432	622333626	622334104	0.000000e+00	780.0
4	TraesCS7A01G097200	chr7A	86.157	484	49	15	960	1433	648509165	648508690	7.240000e-140	507.0
5	TraesCS7A01G097200	chr7A	84.286	210	18	6	463	665	648509652	648509451	8.280000e-45	191.0
6	TraesCS7A01G097200	chr3D	92.063	693	37	10	23	710	275776825	275776146	0.000000e+00	959.0
7	TraesCS7A01G097200	chr3D	93.402	485	29	3	953	1435	275776081	275775598	0.000000e+00	715.0
8	TraesCS7A01G097200	chr4A	95.304	575	25	2	1	574	596981378	596980805	0.000000e+00	911.0
9	TraesCS7A01G097200	chr4A	94.261	575	31	2	1	574	423444649	423444076	0.000000e+00	878.0
10	TraesCS7A01G097200	chr4A	96.480	483	16	1	953	1435	596980790	596980309	0.000000e+00	797.0
11	TraesCS7A01G097200	chr4A	92.828	488	28	4	1437	1919	672505471	672504986	0.000000e+00	701.0
12	TraesCS7A01G097200	chr4A	93.978	465	19	6	1460	1919	672511941	672511481	0.000000e+00	695.0
13	TraesCS7A01G097200	chr4A	91.268	481	15	10	955	1435	423444059	423443606	4.120000e-177	630.0
14	TraesCS7A01G097200	chr4A	87.238	478	47	9	59	535	691555258	691554794	1.190000e-147	532.0
15	TraesCS7A01G097200	chr4A	91.341	358	29	2	1915	2271	672499750	672499394	2.620000e-134	488.0
16	TraesCS7A01G097200	chr4A	86.512	430	45	10	1483	1907	672195880	672195459	5.720000e-126	460.0
17	TraesCS7A01G097200	chr4A	82.418	455	52	11	1459	1907	672291635	672291203	2.750000e-99	372.0
18	TraesCS7A01G097200	chr4A	82.173	359	38	9	1915	2271	672510943	672510609	3.690000e-73	285.0
19	TraesCS7A01G097200	chr5A	94.783	575	28	2	1	574	595402331	595401758	0.000000e+00	894.0
20	TraesCS7A01G097200	chr5A	96.687	483	15	1	953	1435	595401743	595401262	0.000000e+00	802.0
21	TraesCS7A01G097200	chr5A	81.088	735	91	25	1	710	487758731	487759442	5.520000e-151	544.0
22	TraesCS7A01G097200	chr5A	81.088	735	91	25	1	710	487760163	487760874	5.520000e-151	544.0
23	TraesCS7A01G097200	chr5A	80.571	736	92	28	1	710	487761595	487762305	9.300000e-144	520.0
24	TraesCS7A01G097200	chr5A	83.951	486	61	10	962	1435	487758127	487758607	1.240000e-122	449.0
25	TraesCS7A01G097200	chr7D	92.782	568	29	6	1	567	620473053	620473609	0.000000e+00	811.0
26	TraesCS7A01G097200	chr7D	93.595	484	28	3	953	1434	620473979	620474461	0.000000e+00	719.0
27	TraesCS7A01G097200	chr7D	94.624	465	18	4	1460	1919	55874460	55873998	0.000000e+00	713.0
28	TraesCS7A01G097200	chr7D	87.442	430	41	10	1483	1907	55647431	55647010	1.220000e-132	483.0
29	TraesCS7A01G097200	chr7D	86.592	358	26	5	1915	2271	55873292	55872956	2.130000e-100	375.0
30	TraesCS7A01G097200	chr7D	95.205	146	6	1	565	710	620473770	620473914	1.750000e-56	230.0
31	TraesCS7A01G097200	chr7D	76.404	178	33	7	2086	2257	464945895	464945721	1.120000e-13	87.9
32	TraesCS7A01G097200	chr7B	86.314	643	43	14	1	634	668983675	668983069	0.000000e+00	658.0
33	TraesCS7A01G097200	chr7B	89.139	488	47	5	953	1435	668982989	668982503	8.970000e-169	603.0
34	TraesCS7A01G097200	chr6B	80.055	732	95	30	6	710	687877211	687877918	1.570000e-136	496.0
35	TraesCS7A01G097200	chrUn	86.667	285	30	7	1624	1907	49604506	49604229	2.190000e-80	309.0
36	TraesCS7A01G097200	chrUn	86.667	285	30	7	1624	1907	50064626	50064903	2.190000e-80	309.0
37	TraesCS7A01G097200	chrUn	86.408	103	9	2	1483	1581	49604609	49604508	8.580000e-20	108.0
38	TraesCS7A01G097200	chrUn	86.408	103	9	2	1483	1581	50064523	50064624	8.580000e-20	108.0
39	TraesCS7A01G097200	chr3A	79.167	168	32	3	2097	2263	672611809	672611644	1.840000e-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	TraesCS7A01G097200	chr7A	59601489	59603759	2270	True	1874.000000	2436	100.000000	1	2271	2	chr7A.!!$R1	2270
1	TraesCS7A01G097200	chr7A	622333038	622334104	1066	False	840.000000	900	95.499500	1	1432	2	chr7A.!!$F1	1431
2	TraesCS7A01G097200	chr7A	648508690	648509652	962	True	349.000000	507	85.221500	463	1433	2	chr7A.!!$R2	970
3	TraesCS7A01G097200	chr3D	275775598	275776825	1227	True	837.000000	959	92.732500	23	1435	2	chr3D.!!$R1	1412
4	TraesCS7A01G097200	chr4A	596980309	596981378	1069	True	854.000000	911	95.892000	1	1435	2	chr4A.!!$R7	1434
5	TraesCS7A01G097200	chr4A	423443606	423444649	1043	True	754.000000	878	92.764500	1	1435	2	chr4A.!!$R6	1434
6	TraesCS7A01G097200	chr4A	672510609	672511941	1332	True	490.000000	695	88.075500	1460	2271	2	chr4A.!!$R8	811
7	TraesCS7A01G097200	chr5A	595401262	595402331	1069	True	848.000000	894	95.735000	1	1435	2	chr5A.!!$R1	1434
8	TraesCS7A01G097200	chr5A	487758127	487762305	4178	False	514.250000	544	81.674500	1	1435	4	chr5A.!!$F1	1434
9	TraesCS7A01G097200	chr7D	620473053	620474461	1408	False	586.666667	811	93.860667	1	1434	3	chr7D.!!$F1	1433
10	TraesCS7A01G097200	chr7D	55872956	55874460	1504	True	544.000000	713	90.608000	1460	2271	2	chr7D.!!$R3	811
11	TraesCS7A01G097200	chr7B	668982503	668983675	1172	True	630.500000	658	87.726500	1	1435	2	chr7B.!!$R1	1434
12	TraesCS7A01G097200	chr6B	687877211	687877918	707	False	496.000000	496	80.055000	6	710	1	chr6B.!!$F1	704

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
328	973	0.179018	AAGAACTTGCGTCCCTGCTT	60.179	50.0	0.0	0.0	35.36	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1482	4276	0.108019	GACGTTGGGAAGGGAACACT	59.892	55.0	0.0	0.0	0.0	3.55	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
152	784	8.860128	GCCTTCGTATTTCTTTTCTATTTTTGG	58.140	33.333	0.00	0.00	0.00	3.28
162	794	9.825109	TTCTTTTCTATTTTTGGGATTCGTTTT	57.175	25.926	0.00	0.00	0.00	2.43
328	973	0.179018	AAGAACTTGCGTCCCTGCTT	60.179	50.000	0.00	0.00	35.36	3.91
434	2510	4.772624	AGTGTCTAGCCAGTATTCAGAACA	59.227	41.667	0.00	0.00	0.00	3.18
535	2612	5.287752	GTGAACGAGTACAAATCGCTGAATA	59.712	40.000	3.17	0.00	43.91	1.75
682	3151	1.563879	TGACATCAACATCGGGGGAAT	59.436	47.619	0.00	0.00	0.00	3.01
997	3508	7.658525	TTTCACATTGCCAGATGGTATAATT	57.341	32.000	0.00	0.00	37.57	1.40
1036	3548	7.085746	TGAGCATGTCACTGAATTTATTTGTG	58.914	34.615	0.00	0.00	0.00	3.33
1061	3596	9.586435	TGATCCTAATGTCTGTATTATATTGCG	57.414	33.333	0.00	0.00	0.00	4.85
1248	3784	5.479375	ACCTCATCAGAATTGAGTTTGCATT	59.521	36.000	0.00	0.00	39.16	3.56
1423	3964	1.304879	CGGGCCCCCAAAATCTCAA	60.305	57.895	18.66	0.00	35.37	3.02
1435	3976	2.543067	AATCTCAAGACCGGCCCTGC	62.543	60.000	0.00	0.00	0.00	4.85
1436	3977	4.785453	CTCAAGACCGGCCCTGCC	62.785	72.222	0.00	0.00	46.75	4.85
1453	3994	3.266964	CGTGAGGCCACCACAATG	58.733	61.111	22.67	7.80	40.12	2.82
1454	3995	1.600636	CGTGAGGCCACCACAATGT	60.601	57.895	22.67	0.00	40.12	2.71
1457	3998	0.184692	TGAGGCCACCACAATGTTGA	59.815	50.000	5.01	0.00	0.00	3.18
1458	3999	1.203038	TGAGGCCACCACAATGTTGAT	60.203	47.619	5.01	0.00	0.00	2.57
1479	4273	8.833231	TTGATTACAACTTCTTCTTCTACCAG	57.167	34.615	0.00	0.00	0.00	4.00
1480	4274	7.963532	TGATTACAACTTCTTCTTCTACCAGT	58.036	34.615	0.00	0.00	0.00	4.00
1481	4275	8.429641	TGATTACAACTTCTTCTTCTACCAGTT	58.570	33.333	0.00	0.00	0.00	3.16
1482	4276	9.924650	GATTACAACTTCTTCTTCTACCAGTTA	57.075	33.333	0.00	0.00	0.00	2.24
1506	4300	2.264794	CCTTCCCAACGTCTCCCG	59.735	66.667	0.00	0.00	44.03	5.14
1541	4466	9.591792	CCAAAATCTCTTTTCTCTTTCTGTTTT	57.408	29.630	0.00	0.00	32.21	2.43
1831	4760	6.427853	CGGACAGATCTTCATAAATAATGGCA	59.572	38.462	0.00	0.00	36.15	4.92
1970	5706	9.406828	GTATTCAACAAAATTTTCCAGTACCTC	57.593	33.333	0.00	0.00	0.00	3.85
2004	5742	3.563390	GGAAGCTTCTGTGATATTCCAGC	59.437	47.826	25.05	0.31	36.91	4.85
2042	5780	0.974010	GGGTATCACCGGGACACTCA	60.974	60.000	6.32	0.00	39.83	3.41
2044	5782	1.068741	GGTATCACCGGGACACTCATC	59.931	57.143	6.32	0.00	0.00	2.92
2062	5800	2.979649	GGACCTCCCGGAACACTC	59.020	66.667	0.73	0.00	0.00	3.51
2063	5801	2.657066	GGACCTCCCGGAACACTCC	61.657	68.421	0.73	0.00	38.52	3.85
2064	5802	2.606826	ACCTCCCGGAACACTCCC	60.607	66.667	0.73	0.00	38.71	4.30
2065	5803	3.400054	CCTCCCGGAACACTCCCC	61.400	72.222	0.73	0.00	38.71	4.81
2066	5804	3.400054	CTCCCGGAACACTCCCCC	61.400	72.222	0.73	0.00	38.71	5.40
2069	5807	3.081409	CCGGAACACTCCCCCGAT	61.081	66.667	0.00	0.00	45.58	4.18
2070	5808	2.499685	CGGAACACTCCCCCGATC	59.500	66.667	0.00	0.00	45.58	3.69
2071	5809	2.355986	CGGAACACTCCCCCGATCA	61.356	63.158	0.00	0.00	45.58	2.92
2072	5810	1.522569	GGAACACTCCCCCGATCAG	59.477	63.158	0.00	0.00	35.42	2.90
2073	5811	1.153349	GAACACTCCCCCGATCAGC	60.153	63.158	0.00	0.00	0.00	4.26
2074	5812	1.613630	AACACTCCCCCGATCAGCT	60.614	57.895	0.00	0.00	0.00	4.24
2075	5813	1.903877	AACACTCCCCCGATCAGCTG	61.904	60.000	7.63	7.63	0.00	4.24
2076	5814	2.765807	ACTCCCCCGATCAGCTGG	60.766	66.667	15.13	0.00	0.00	4.85
2077	5815	2.444706	CTCCCCCGATCAGCTGGA	60.445	66.667	15.13	0.00	0.00	3.86
2078	5816	2.444706	TCCCCCGATCAGCTGGAG	60.445	66.667	15.13	5.45	0.00	3.86
2079	5817	2.444706	CCCCCGATCAGCTGGAGA	60.445	66.667	15.13	0.00	0.00	3.71
2085	5823	1.472376	CCGATCAGCTGGAGAACTTCC	60.472	57.143	15.13	0.00	46.98	3.46
2107	5845	2.882137	GGAATCAACCGAAACACTTCCA	59.118	45.455	0.00	0.00	32.73	3.53
2214	5952	0.250553	GGGGACATGTTCGGAACACA	60.251	55.000	24.56	5.31	45.50	3.72

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
152	784	6.600350	GTGAAGGAAAGTAGAAAACGAATCC	58.400	40.000	0.00	0.00	32.38	3.01
162	794	4.282449	TGATGGAACGTGAAGGAAAGTAGA	59.718	41.667	0.00	0.00	0.00	2.59
257	897	4.647611	TCTAACCTCCTTGATTTTTCGCA	58.352	39.130	0.00	0.00	0.00	5.10
507	2584	2.340577	CGATTTGTACTCGTTCACGTCC	59.659	50.000	0.00	0.00	40.80	4.79
682	3151	9.256477	CTGTACTCTCAAACACACTAACATTAA	57.744	33.333	0.00	0.00	0.00	1.40
997	3508	6.317140	GTGACATGCTCAAAAATCTCCATAGA	59.683	38.462	0.00	0.00	35.80	1.98
1036	3548	9.587772	ACGCAATATAATACAGACATTAGGATC	57.412	33.333	0.00	0.00	0.00	3.36
1061	3596	6.924060	ACCGTCAGATGCACTATAAATAAGAC	59.076	38.462	0.00	0.00	0.00	3.01
1403	3944	2.944390	AGATTTTGGGGGCCCGGA	60.944	61.111	17.79	4.08	39.42	5.14
1435	3976	2.034066	ATTGTGGTGGCCTCACGG	59.966	61.111	19.64	0.00	44.50	4.94
1436	3977	1.172180	AACATTGTGGTGGCCTCACG	61.172	55.000	19.64	11.34	44.50	4.35
1437	3978	0.314935	CAACATTGTGGTGGCCTCAC	59.685	55.000	18.67	18.67	42.91	3.51
1438	3979	0.184692	TCAACATTGTGGTGGCCTCA	59.815	50.000	3.32	0.00	35.34	3.86
1439	3980	1.549203	ATCAACATTGTGGTGGCCTC	58.451	50.000	3.32	0.00	35.34	4.70
1440	3981	2.014010	AATCAACATTGTGGTGGCCT	57.986	45.000	3.32	0.00	35.34	5.19
1441	3982	2.560542	TGTAATCAACATTGTGGTGGCC	59.439	45.455	0.00	0.00	35.34	5.36
1454	3995	8.429641	ACTGGTAGAAGAAGAAGTTGTAATCAA	58.570	33.333	0.00	0.00	0.00	2.57
1457	3998	9.930693	CTAACTGGTAGAAGAAGAAGTTGTAAT	57.069	33.333	0.00	0.00	30.50	1.89
1458	3999	8.921205	ACTAACTGGTAGAAGAAGAAGTTGTAA	58.079	33.333	6.76	0.00	33.61	2.41
1464	4258	6.869388	GGAACACTAACTGGTAGAAGAAGAAG	59.131	42.308	6.76	0.00	33.61	2.85
1473	4267	3.055312	GGGAAGGGAACACTAACTGGTAG	60.055	52.174	0.00	0.00	35.75	3.18
1479	4273	2.148768	CGTTGGGAAGGGAACACTAAC	58.851	52.381	0.00	0.00	0.00	2.34
1480	4274	1.770061	ACGTTGGGAAGGGAACACTAA	59.230	47.619	0.00	0.00	0.00	2.24
1481	4275	1.345415	GACGTTGGGAAGGGAACACTA	59.655	52.381	0.00	0.00	0.00	2.74
1482	4276	0.108019	GACGTTGGGAAGGGAACACT	59.892	55.000	0.00	0.00	0.00	3.55
1506	4300	8.409371	AGAGAAAAGAGATTTTGGTTTGAGAAC	58.591	33.333	0.00	0.00	34.96	3.01
1567	4496	6.888632	AGATTTTGCACTTTCCTCTCATACAT	59.111	34.615	0.00	0.00	0.00	2.29
1936	5672	8.865978	GGAAAATTTTGTTGAATACGAATACCC	58.134	33.333	8.47	0.00	30.22	3.69
2004	5742	1.493311	GCGAACGTCTTGGAAGCTG	59.507	57.895	0.00	0.00	0.00	4.24
2059	5797	2.765807	CCAGCTGATCGGGGGAGT	60.766	66.667	17.39	0.00	0.00	3.85
2060	5798	2.444706	TCCAGCTGATCGGGGGAG	60.445	66.667	17.39	0.00	0.00	4.30
2061	5799	2.444706	CTCCAGCTGATCGGGGGA	60.445	66.667	17.39	0.05	31.43	4.81
2062	5800	2.066393	TTCTCCAGCTGATCGGGGG	61.066	63.158	17.39	0.00	0.00	5.40
2063	5801	1.144936	GTTCTCCAGCTGATCGGGG	59.855	63.158	17.39	0.00	0.00	5.73
2064	5802	0.539051	AAGTTCTCCAGCTGATCGGG	59.461	55.000	17.39	0.00	0.00	5.14
2065	5803	1.472376	GGAAGTTCTCCAGCTGATCGG	60.472	57.143	17.39	0.00	44.67	4.18
2066	5804	1.800655	CGGAAGTTCTCCAGCTGATCG	60.801	57.143	17.39	2.70	45.74	3.69
2067	5805	1.472376	CCGGAAGTTCTCCAGCTGATC	60.472	57.143	17.39	0.40	45.74	2.92
2068	5806	0.539051	CCGGAAGTTCTCCAGCTGAT	59.461	55.000	17.39	0.00	45.74	2.90
2069	5807	0.541998	TCCGGAAGTTCTCCAGCTGA	60.542	55.000	17.39	0.00	45.74	4.26
2070	5808	0.321671	TTCCGGAAGTTCTCCAGCTG	59.678	55.000	14.35	6.78	45.74	4.24
2071	5809	1.208293	GATTCCGGAAGTTCTCCAGCT	59.792	52.381	23.47	0.55	45.74	4.24
2072	5810	1.066143	TGATTCCGGAAGTTCTCCAGC	60.066	52.381	23.47	0.00	45.74	4.85
2073	5811	3.003480	GTTGATTCCGGAAGTTCTCCAG	58.997	50.000	23.47	0.00	45.74	3.86
2074	5812	2.290071	GGTTGATTCCGGAAGTTCTCCA	60.290	50.000	23.47	10.03	45.74	3.86
2075	5813	2.357075	GGTTGATTCCGGAAGTTCTCC	58.643	52.381	23.47	16.90	41.40	3.71
2076	5814	2.000447	CGGTTGATTCCGGAAGTTCTC	59.000	52.381	23.47	15.29	45.88	2.87
2077	5815	2.094762	CGGTTGATTCCGGAAGTTCT	57.905	50.000	23.47	5.22	45.88	3.01
2093	5831	0.759346	AGCTCTGGAAGTGTTTCGGT	59.241	50.000	0.00	0.00	33.98	4.69
2179	5917	3.717392	TGTCCCCATATTATCGAACCCAA	59.283	43.478	0.00	0.00	0.00	4.12
2181	5919	4.261801	CATGTCCCCATATTATCGAACCC	58.738	47.826	0.00	0.00	0.00	4.11
2235	5973	7.039923	GGAATTACTATGGGTGTCTAGATTCGA	60.040	40.741	0.00	0.00	0.00	3.71
2236	5974	7.091443	GGAATTACTATGGGTGTCTAGATTCG	58.909	42.308	0.00	0.00	0.00	3.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.