AutoCloner

Multiple sequence alignment - TraesCS7D01G046300

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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	TraesCS7D01G046300	chr7D	100.000	2611	0	0	1	2611	23541861	23539251	0.000000e+00	4822.0
1	TraesCS7D01G046300	chr7D	92.163	1697	121	6	152	1837	23999523	24001218	0.000000e+00	2386.0
2	TraesCS7D01G046300	chr7D	83.252	1636	231	23	224	1832	23509720	23511339	0.000000e+00	1463.0
3	TraesCS7D01G046300	chr7D	88.747	1093	118	4	224	1314	24114066	24115155	0.000000e+00	1332.0
4	TraesCS7D01G046300	chr7D	96.387	775	27	1	1838	2611	497214864	497215638	0.000000e+00	1275.0
5	TraesCS7D01G046300	chr7D	96.268	777	28	1	1836	2611	326704766	326703990	0.000000e+00	1273.0
6	TraesCS7D01G046300	chr7D	95.747	776	32	1	1837	2611	497249809	497250584	0.000000e+00	1249.0
7	TraesCS7D01G046300	chr7D	86.312	526	60	8	1311	1832	24115182	24115699	1.750000e-156	562.0
8	TraesCS7D01G046300	chr7D	81.099	619	86	15	1193	1797	23507187	23507788	1.420000e-127	466.0
9	TraesCS7D01G046300	chr7D	85.000	380	44	9	698	1073	23982722	23983092	8.820000e-100	374.0
10	TraesCS7D01G046300	chr7D	96.732	153	5	0	1	153	23999332	23999484	3.330000e-64	255.0
11	TraesCS7D01G046300	chr7D	84.810	79	10	2	730	807	23579619	23579542	7.750000e-11	78.7
12	TraesCS7D01G046300	chr7D	83.951	81	11	2	74	154	23509625	23509703	2.790000e-10	76.8
13	TraesCS7D01G046300	chr7D	97.619	42	1	0	23	64	23581855	23581814	3.600000e-09	73.1
14	TraesCS7D01G046300	chr4A	83.688	1643	213	32	224	1835	708300490	708298872	0.000000e+00	1498.0
15	TraesCS7D01G046300	chr4A	96.970	33	0	1	158	190	713832568	713832537	1.000000e-03	54.7
16	TraesCS7D01G046300	chr7A	84.569	1335	170	17	521	1832	24627144	24628465	0.000000e+00	1291.0
17	TraesCS7D01G046300	chr7A	82.960	1338	187	23	521	1835	24539721	24538402	0.000000e+00	1170.0
18	TraesCS7D01G046300	chr7A	95.122	41	2	0	114	154	24626816	24626856	6.030000e-07	65.8
19	TraesCS7D01G046300	chr4D	96.000	775	30	1	1838	2611	39546577	39545803	0.000000e+00	1258.0
20	TraesCS7D01G046300	chr4D	95.876	776	29	3	1837	2611	47911296	47910523	0.000000e+00	1253.0
21	TraesCS7D01G046300	chr4D	100.000	28	0	0	163	190	24923004	24922977	5.000000e-03	52.8
22	TraesCS7D01G046300	chr1D	95.775	781	31	2	1832	2611	367866452	367865673	0.000000e+00	1258.0
23	TraesCS7D01G046300	chr1D	95.747	776	32	1	1837	2611	246125735	246126510	0.000000e+00	1249.0
24	TraesCS7D01G046300	chr3D	95.747	776	32	1	1837	2611	504277508	504276733	0.000000e+00	1249.0
25	TraesCS7D01G046300	chr3D	96.970	33	1	0	158	190	417511032	417511064	3.630000e-04	56.5
26	TraesCS7D01G046300	chr6D	95.742	775	32	1	1838	2611	27018700	27019474	0.000000e+00	1247.0
27	TraesCS7D01G046300	chr6D	100.000	31	0	0	153	183	7477753	7477723	1.010000e-04	58.4
28	TraesCS7D01G046300	chr6D	100.000	31	0	0	153	183	7477757	7477787	1.010000e-04	58.4
29	TraesCS7D01G046300	chr6A	81.584	543	71	15	951	1491	310480527	310481042	3.110000e-114	422.0
30	TraesCS7D01G046300	chr6A	83.770	382	29	14	1489	1837	310582695	310583076	5.390000e-87	331.0
31	TraesCS7D01G046300	chr6A	81.937	382	36	14	1489	1837	310681614	310681995	2.540000e-75	292.0
32	TraesCS7D01G046300	chr2B	100.000	31	0	0	153	183	297465094	297465124	1.010000e-04	58.4
33	TraesCS7D01G046300	chr5A	96.970	33	1	0	158	190	375215471	375215503	3.630000e-04	56.5
34	TraesCS7D01G046300	chr7B	92.105	38	3	0	153	190	633055000	633054963	1.000000e-03	54.7

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	TraesCS7D01G046300	chr7D	23539251	23541861	2610	True	4822.0	4822	100.000000	1	2611	1	chr7D.!!$R1	2610
1	TraesCS7D01G046300	chr7D	23999332	24001218	1886	False	1320.5	2386	94.447500	1	1837	2	chr7D.!!$F5	1836
2	TraesCS7D01G046300	chr7D	497214864	497215638	774	False	1275.0	1275	96.387000	1838	2611	1	chr7D.!!$F2	773
3	TraesCS7D01G046300	chr7D	326703990	326704766	776	True	1273.0	1273	96.268000	1836	2611	1	chr7D.!!$R2	775
4	TraesCS7D01G046300	chr7D	497249809	497250584	775	False	1249.0	1249	95.747000	1837	2611	1	chr7D.!!$F3	774
5	TraesCS7D01G046300	chr7D	24114066	24115699	1633	False	947.0	1332	87.529500	224	1832	2	chr7D.!!$F6	1608
6	TraesCS7D01G046300	chr7D	23507187	23511339	4152	False	668.6	1463	82.767333	74	1832	3	chr7D.!!$F4	1758
7	TraesCS7D01G046300	chr4A	708298872	708300490	1618	True	1498.0	1498	83.688000	224	1835	1	chr4A.!!$R1	1611
8	TraesCS7D01G046300	chr7A	24538402	24539721	1319	True	1170.0	1170	82.960000	521	1835	1	chr7A.!!$R1	1314
9	TraesCS7D01G046300	chr7A	24626816	24628465	1649	False	678.4	1291	89.845500	114	1832	2	chr7A.!!$F1	1718
10	TraesCS7D01G046300	chr4D	39545803	39546577	774	True	1258.0	1258	96.000000	1838	2611	1	chr4D.!!$R2	773
11	TraesCS7D01G046300	chr4D	47910523	47911296	773	True	1253.0	1253	95.876000	1837	2611	1	chr4D.!!$R3	774
12	TraesCS7D01G046300	chr1D	367865673	367866452	779	True	1258.0	1258	95.775000	1832	2611	1	chr1D.!!$R1	779
13	TraesCS7D01G046300	chr1D	246125735	246126510	775	False	1249.0	1249	95.747000	1837	2611	1	chr1D.!!$F1	774
14	TraesCS7D01G046300	chr3D	504276733	504277508	775	True	1249.0	1249	95.747000	1837	2611	1	chr3D.!!$R1	774
15	TraesCS7D01G046300	chr6D	27018700	27019474	774	False	1247.0	1247	95.742000	1838	2611	1	chr6D.!!$F2	773
16	TraesCS7D01G046300	chr6A	310480527	310481042	515	False	422.0	422	81.584000	951	1491	1	chr6A.!!$F1	540

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
342	2750	0.107831	ACAGTACATGGTGCGTGGTT	59.892	50.0	0.0	0.0	0.0	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2261	4731	1.678627	CATCGGAGACACCTGTAGAGG	59.321	57.143	3.92	3.92	42.51	3.69	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
66	67	6.349611	CCCTTTAGGACATGTCTGATTTGTTG	60.350	42.308	24.50	6.34	38.24	3.33
71	72	4.946157	GGACATGTCTGATTTGTTGGAGAT	59.054	41.667	24.50	0.00	0.00	2.75
158	2562	4.944177	TGGTACTCCCTCTTACTAGCTTT	58.056	43.478	0.00	0.00	0.00	3.51
165	2569	6.872547	ACTCCCTCTTACTAGCTTTAAAAACG	59.127	38.462	0.00	0.00	0.00	3.60
168	2572	7.386025	TCCCTCTTACTAGCTTTAAAAACGTTC	59.614	37.037	0.00	0.00	0.00	3.95
228	2633	5.344128	CCCATAAAGTATGCATACGTACGTC	59.656	44.000	26.53	11.59	42.18	4.34
240	2645	0.506932	CGTACGTCAAGGTTGTGCAG	59.493	55.000	7.22	0.00	0.00	4.41
322	2730	4.680237	CAAGCCCGACGTGCCAGA	62.680	66.667	0.00	0.00	0.00	3.86
338	2746	1.608025	CCAGAACAGTACATGGTGCGT	60.608	52.381	0.00	0.00	0.00	5.24
342	2750	0.107831	ACAGTACATGGTGCGTGGTT	59.892	50.000	0.00	0.00	0.00	3.67
406	2814	1.002430	TGTCATTGACCTCTGCTGTCC	59.998	52.381	14.05	0.00	31.60	4.02
410	2818	3.152341	CATTGACCTCTGCTGTCCTTTT	58.848	45.455	0.00	0.00	31.60	2.27
413	2821	3.740115	TGACCTCTGCTGTCCTTTTAAC	58.260	45.455	0.00	0.00	31.60	2.01
449	2857	1.880340	CGATGAGGCGTCCAAGCTC	60.880	63.158	3.56	0.00	37.29	4.09
470	2878	2.202663	GCAGCGCTCGAGTCATGA	60.203	61.111	7.13	0.00	0.00	3.07
546	2954	4.074970	ACTCCACCAATTTGTAGCAAGAG	58.925	43.478	0.00	0.00	0.00	2.85
547	2955	3.420893	TCCACCAATTTGTAGCAAGAGG	58.579	45.455	0.00	0.00	0.00	3.69
583	2991	6.735678	TCATGTTGCTTCATATGTACGTTT	57.264	33.333	1.90	0.00	0.00	3.60
589	2997	4.693095	TGCTTCATATGTACGTTTCTGCAA	59.307	37.500	1.90	0.00	0.00	4.08
597	3005	1.154525	CGTTTCTGCAAGCAGCTCG	60.155	57.895	16.89	15.45	45.94	5.03
643	3051	2.435437	TGATGGATGACATGATGACCGT	59.565	45.455	0.00	0.00	40.72	4.83
656	3064	1.080705	GACCGTGTCGAGGGAGTTG	60.081	63.158	4.24	0.00	0.00	3.16
660	3068	0.666577	CGTGTCGAGGGAGTTGTTCC	60.667	60.000	0.00	0.00	46.00	3.62
669	3077	4.344865	AGTTGTTCCGGCGGCCAT	62.345	61.111	23.83	3.31	0.00	4.40
674	3082	4.169696	TTCCGGCGGCCATTCGAT	62.170	61.111	23.83	0.00	0.00	3.59
737	3145	1.221021	GCTTGAGGGGTACGGGAAG	59.779	63.158	0.00	0.00	0.00	3.46
741	3149	1.001376	GAGGGGTACGGGAAGGACT	59.999	63.158	0.00	0.00	33.01	3.85
743	3151	0.712380	AGGGGTACGGGAAGGACTAA	59.288	55.000	0.00	0.00	33.01	2.24
758	3166	1.751924	GACTAAGTGAGGTCGCCAGAT	59.248	52.381	0.00	0.00	0.00	2.90
810	3218	1.841556	AAAGTGGAGCCCGAGGACA	60.842	57.895	0.00	0.00	0.00	4.02
814	3222	3.706373	GGAGCCCGAGGACAAGCA	61.706	66.667	0.00	0.00	0.00	3.91
816	3224	2.925170	AGCCCGAGGACAAGCAGT	60.925	61.111	0.00	0.00	0.00	4.40
818	3226	2.046892	CCCGAGGACAAGCAGTGG	60.047	66.667	0.00	0.00	0.00	4.00
837	3245	0.257039	GATCACCCTCTGGCCAACAT	59.743	55.000	7.01	0.00	33.59	2.71
902	3310	1.000359	AAATTTCCTGGCTCGGGGG	60.000	57.895	0.00	0.00	0.00	5.40
985	3394	1.280457	ATGTGGGAGAGTGAAGGACC	58.720	55.000	0.00	0.00	0.00	4.46
1029	3438	0.613260	TGCTGGAGCTTAACCACGAT	59.387	50.000	0.00	0.00	42.66	3.73
1049	3458	1.071699	TGACTACTTTGTGGACCAGCC	59.928	52.381	0.00	0.00	37.10	4.85
1147	3556	1.296392	CCTCACTGCGATGGAACCA	59.704	57.895	0.00	0.00	0.00	3.67
1226	3635	0.390735	GTGTGGTGGGATGTACCGAC	60.391	60.000	0.00	0.00	44.85	4.79
1400	3846	7.763172	TCCACATAAAACACAACAATCAAAC	57.237	32.000	0.00	0.00	0.00	2.93
1409	3855	5.034152	ACACAACAATCAAACTTACAAGCG	58.966	37.500	0.00	0.00	0.00	4.68
1454	3902	8.925161	TCATTTTGTTGAAAGTTTCTAAGGTG	57.075	30.769	16.33	10.63	0.00	4.00
1468	3916	2.879103	AAGGTGTTGGGTTGATCGAT	57.121	45.000	0.00	0.00	0.00	3.59
1491	3940	9.075519	CGATTTAAATGTTTGTTGCACAGATAT	57.924	29.630	5.17	0.00	0.00	1.63
1510	3959	5.591877	AGATATTGAGCAATGGGTTCTTCAC	59.408	40.000	5.99	0.00	32.50	3.18
1511	3960	2.957402	TGAGCAATGGGTTCTTCACT	57.043	45.000	0.00	0.00	0.00	3.41
1559	4008	3.525537	TGCAAAGAAAGAGAGGCTATCG	58.474	45.455	3.08	0.00	0.00	2.92
1672	4125	2.143925	GGTCAAGGACTATATTGCCGC	58.856	52.381	0.00	0.00	32.47	6.53
1756	4211	7.045936	GCAGTATGTATCATGGGTGTCATGC	62.046	48.000	0.00	0.00	45.20	4.06
1992	4462	5.767665	CAGAGTGTCACTAGTATGCCTCTAT	59.232	44.000	5.21	0.00	0.00	1.98
2196	4666	6.737720	TGACTATGAGATTATGCAACTCCT	57.262	37.500	0.00	0.00	0.00	3.69
2239	4709	3.001838	GTGTGCTATCAAACGTCACAACA	59.998	43.478	5.66	0.00	39.07	3.33
2315	4785	4.835615	AGTTGGCATAGATCGAGATTAGGT	59.164	41.667	0.00	0.00	0.00	3.08
2375	4845	4.041740	TCTCGGTAATGCACATCACTAC	57.958	45.455	0.00	0.00	0.00	2.73
2558	5028	5.462405	TGTTATGCGGTTTGACCAATAAAC	58.538	37.500	0.00	0.00	38.47	2.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	1.145571	ACAAGGTCCTTGGGTGCTTA	58.854	50.000	30.76	0.00	44.81	3.09
66	67	2.808543	GGACACCGCAAATCATATCTCC	59.191	50.000	0.00	0.00	0.00	3.71
71	72	2.611751	CGATTGGACACCGCAAATCATA	59.388	45.455	0.00	0.00	0.00	2.15
202	2607	4.351874	ACGTATGCATACTTTATGGGCT	57.648	40.909	29.20	5.48	36.68	5.19
216	2621	2.091588	CACAACCTTGACGTACGTATGC	59.908	50.000	22.87	9.89	0.00	3.14
240	2645	1.406539	CATGCTTCCCATAGTTGCACC	59.593	52.381	0.00	0.00	36.44	5.01
322	2730	0.107831	ACCACGCACCATGTACTGTT	59.892	50.000	0.00	0.00	0.00	3.16
338	2746	1.369692	CTGCTGGTCGTGGTAACCA	59.630	57.895	0.00	0.00	44.46	3.67
342	2750	2.970639	GAGCTGCTGGTCGTGGTA	59.029	61.111	7.01	0.00	0.00	3.25
379	2787	2.502947	CAGAGGTCAATGACAGGGATCA	59.497	50.000	15.86	0.00	33.68	2.92
406	2814	3.042887	GCTGCACCGTCTTTGTTAAAAG	58.957	45.455	0.00	0.00	43.60	2.27
410	2818	2.624169	GGCTGCACCGTCTTTGTTA	58.376	52.632	0.50	0.00	0.00	2.41
470	2878	3.908103	TGTTACTTACAAGGAAGAGGCCT	59.092	43.478	3.86	3.86	40.93	5.19
546	2954	4.037690	GCAACATGAATACGAATGCTTCC	58.962	43.478	0.00	0.00	0.00	3.46
547	2955	4.913376	AGCAACATGAATACGAATGCTTC	58.087	39.130	0.00	0.00	39.44	3.86
583	2991	0.670546	GTTACCGAGCTGCTTGCAGA	60.671	55.000	24.67	1.25	45.94	4.26
589	2997	1.221840	CCATGGTTACCGAGCTGCT	59.778	57.895	0.00	0.00	0.00	4.24
643	3051	1.663739	CGGAACAACTCCCTCGACA	59.336	57.895	0.00	0.00	41.87	4.35
660	3068	3.640000	GTCATCGAATGGCCGCCG	61.640	66.667	4.58	0.91	0.00	6.46
669	3077	2.560981	TGTACCTCTGCTTGTCATCGAA	59.439	45.455	0.00	0.00	0.00	3.71
674	3082	1.419381	TGGTGTACCTCTGCTTGTCA	58.581	50.000	2.32	0.00	36.82	3.58
720	3128	0.616679	TCCTTCCCGTACCCCTCAAG	60.617	60.000	0.00	0.00	0.00	3.02
737	3145	0.173708	CTGGCGACCTCACTTAGTCC	59.826	60.000	0.00	0.00	0.00	3.85
741	3149	1.751351	CTGATCTGGCGACCTCACTTA	59.249	52.381	0.00	0.00	0.00	2.24
743	3151	0.323816	TCTGATCTGGCGACCTCACT	60.324	55.000	0.00	0.00	0.00	3.41
758	3166	1.359130	TCAGACCAGTCCAGGATCTGA	59.641	52.381	14.31	14.31	42.63	3.27
810	3218	0.617413	CAGAGGGTGATCCACTGCTT	59.383	55.000	0.00	0.00	44.90	3.91
814	3222	1.997874	GGCCAGAGGGTGATCCACT	60.998	63.158	0.00	0.00	36.89	4.00
816	3224	1.541118	TTGGCCAGAGGGTGATCCA	60.541	57.895	5.11	0.00	38.24	3.41
818	3226	0.257039	ATGTTGGCCAGAGGGTGATC	59.743	55.000	5.11	0.00	36.17	2.92
1029	3438	1.071699	GGCTGGTCCACAAAGTAGTCA	59.928	52.381	0.00	0.00	34.01	3.41
1049	3458	0.695347	AGTTTCAGCCTTCTCCCCAG	59.305	55.000	0.00	0.00	0.00	4.45
1147	3556	7.225538	GTCATCGACCATGAGAATTGTAAGAAT	59.774	37.037	0.00	0.00	42.55	2.40
1226	3635	1.762460	AGGAGGGTGCGAGGTATGG	60.762	63.158	0.00	0.00	0.00	2.74
1400	3846	6.236017	TGTTCAAAATACCTCGCTTGTAAG	57.764	37.500	0.00	0.00	0.00	2.34
1406	3852	8.050778	TGATTTTATGTTCAAAATACCTCGCT	57.949	30.769	0.00	0.00	38.04	4.93
1454	3902	7.383843	ACAAACATTTAAATCGATCAACCCAAC	59.616	33.333	0.00	0.00	0.00	3.77
1491	3940	3.228188	AGTGAAGAACCCATTGCTCAA	57.772	42.857	0.00	0.00	0.00	3.02
1559	4008	3.181474	GGTCAACATAGTCTAGAGCCACC	60.181	52.174	0.00	0.00	0.00	4.61
1607	4059	7.609097	TGGTCTCTTCTCATTAATCAGCTAT	57.391	36.000	0.00	0.00	0.00	2.97
1608	4060	6.462207	GCTGGTCTCTTCTCATTAATCAGCTA	60.462	42.308	9.82	0.00	40.20	3.32
1672	4125	5.233902	CCTTGAGAGAAATGTTCATAGAGCG	59.766	44.000	0.00	0.00	0.00	5.03
1731	4184	3.711190	TGACACCCATGATACATACTGCT	59.289	43.478	0.00	0.00	0.00	4.24
1771	4235	6.487331	ACACGATACAAACATTGGTCCTAAAA	59.513	34.615	0.00	0.00	34.12	1.52
1772	4236	5.998981	ACACGATACAAACATTGGTCCTAAA	59.001	36.000	0.00	0.00	34.12	1.85
1992	4462	5.989168	TCTTTGATTCAACGAGCTAGTCAAA	59.011	36.000	0.00	5.41	34.24	2.69
2051	4521	5.811399	TGATGTGATCCCGTTAATCAAAC	57.189	39.130	0.00	0.00	35.04	2.93
2196	4666	5.011329	ACACTAAGTGTTCCTTCGGTATTCA	59.989	40.000	0.00	0.00	45.08	2.57
2261	4731	1.678627	CATCGGAGACACCTGTAGAGG	59.321	57.143	3.92	3.92	42.51	3.69
2375	4845	1.144969	CACATTGCTTGCAAGGCTTG	58.855	50.000	27.10	22.75	0.00	4.01
2419	4889	3.173599	TCTTTACTCGTTCCGTAATGCG	58.826	45.455	0.00	0.00	40.95	4.73
2558	5028	7.658261	TGGTTCCTACATATTCTACGAAGATG	58.342	38.462	9.04	9.04	0.00	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.