AutoCloner

Multiple sequence alignment - TraesCS7D01G415800

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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	TraesCS7D01G415800	chr7D	100.000	3581	0	0	1	3581	534656954	534653374	0.000000e+00	6613.0
1	TraesCS7D01G415800	chr7D	92.233	103	8	0	1456	1558	534655367	534655265	2.880000e-31	147.0
2	TraesCS7D01G415800	chr7D	92.233	103	8	0	1588	1690	534655499	534655397	2.880000e-31	147.0
3	TraesCS7D01G415800	chr2A	87.202	1680	116	47	1033	2668	755060117	755061741	0.000000e+00	1820.0
4	TraesCS7D01G415800	chr2A	83.556	1125	98	49	1583	2668	746840860	746839784	0.000000e+00	972.0
5	TraesCS7D01G415800	chr2A	84.491	993	97	21	1	974	755058995	755059949	0.000000e+00	928.0
6	TraesCS7D01G415800	chr2A	93.888	409	19	6	2727	3132	763203754	763204159	2.360000e-171	612.0
7	TraesCS7D01G415800	chr2A	84.974	579	77	10	1819	2392	137260106	137259533	2.400000e-161	579.0
8	TraesCS7D01G415800	chr2A	85.570	298	30	10	3213	3497	755061834	755062131	2.090000e-77	300.0
9	TraesCS7D01G415800	chr2A	90.164	183	15	3	3221	3400	746839694	746839512	5.980000e-58	235.0
10	TraesCS7D01G415800	chr2A	88.957	163	15	1	1421	1583	746840887	746840728	7.840000e-47	198.0
11	TraesCS7D01G415800	chr2A	92.941	85	6	0	2495	2579	754708984	754708900	1.350000e-24	124.0
12	TraesCS7D01G415800	chr2B	90.605	1256	61	21	1451	2668	765561757	765562993	0.000000e+00	1613.0
13	TraesCS7D01G415800	chr2B	85.189	1087	94	32	1593	2653	751603969	751602924	0.000000e+00	1053.0
14	TraesCS7D01G415800	chr2B	82.767	824	108	18	1791	2603	110520867	110520067	0.000000e+00	704.0
15	TraesCS7D01G415800	chr2B	84.509	581	86	4	1814	2392	183211778	183212356	4.010000e-159	571.0
16	TraesCS7D01G415800	chr2B	92.935	184	10	3	3221	3401	751602817	751602634	7.620000e-67	265.0
17	TraesCS7D01G415800	chr2B	90.184	163	13	1	1421	1583	751604006	751603847	3.620000e-50	209.0
18	TraesCS7D01G415800	chr2B	90.244	123	11	1	1577	1698	765561750	765561872	3.700000e-35	159.0
19	TraesCS7D01G415800	chr2B	92.941	85	6	0	2495	2579	765486841	765486757	1.350000e-24	124.0
20	TraesCS7D01G415800	chr2B	92.647	68	2	1	1016	1083	765561647	765561711	1.060000e-15	95.3
21	TraesCS7D01G415800	chr2D	89.044	1214	70	29	1451	2646	623790866	623792034	0.000000e+00	1447.0
22	TraesCS7D01G415800	chr2D	88.720	922	71	17	1	903	623788392	623789299	0.000000e+00	1096.0
23	TraesCS7D01G415800	chr2D	85.101	1094	104	29	1588	2668	616626874	616625827	0.000000e+00	1062.0
24	TraesCS7D01G415800	chr2D	85.615	577	77	6	1819	2392	129941616	129942189	5.120000e-168	601.0
25	TraesCS7D01G415800	chr2D	84.906	583	80	7	1814	2392	129837505	129838083	1.850000e-162	582.0
26	TraesCS7D01G415800	chr2D	84.682	581	75	12	1819	2392	131163699	131163126	5.190000e-158	568.0
27	TraesCS7D01G415800	chr2D	88.036	443	35	4	2149	2580	623793653	623794088	3.190000e-140	508.0
28	TraesCS7D01G415800	chr2D	94.561	239	10	2	1016	1254	623790558	623790793	2.030000e-97	366.0
29	TraesCS7D01G415800	chr2D	91.892	185	11	3	3221	3401	616625743	616625559	4.590000e-64	255.0
30	TraesCS7D01G415800	chr2D	86.425	221	23	3	3214	3427	623792159	623792379	5.980000e-58	235.0
31	TraesCS7D01G415800	chr2D	90.798	163	12	2	1421	1583	616626906	616626747	7.790000e-52	215.0
32	TraesCS7D01G415800	chr2D	91.057	123	10	1	1577	1698	623790859	623790981	7.950000e-37	165.0
33	TraesCS7D01G415800	chr2D	86.667	105	11	1	2491	2595	129838202	129838303	2.920000e-21	113.0
34	TraesCS7D01G415800	chr3D	93.735	415	20	4	2727	3139	23155579	23155989	5.080000e-173	617.0
35	TraesCS7D01G415800	chr7B	93.873	408	21	3	2727	3134	2379643	2380046	2.360000e-171	612.0
36	TraesCS7D01G415800	chr7B	93.431	411	18	7	2727	3133	150834199	150834604	5.120000e-168	601.0
37	TraesCS7D01G415800	chr1A	93.285	417	20	8	2724	3134	511219652	511219238	3.060000e-170	608.0
38	TraesCS7D01G415800	chr1A	92.788	416	24	6	2724	3134	27328801	27328387	6.620000e-167	597.0
39	TraesCS7D01G415800	chr1A	92.593	108	8	0	867	974	313910454	313910347	4.790000e-34	156.0
40	TraesCS7D01G415800	chr1A	86.029	136	15	4	841	974	325051926	325051793	3.730000e-30	143.0
41	TraesCS7D01G415800	chr5B	93.627	408	21	3	2727	3134	87981707	87981305	3.950000e-169	604.0
42	TraesCS7D01G415800	chr5B	93.029	416	20	9	2727	3135	608557272	608556859	1.840000e-167	599.0
43	TraesCS7D01G415800	chr5B	91.964	112	8	1	864	974	712462201	712462312	4.790000e-34	156.0
44	TraesCS7D01G415800	chr1B	93.187	411	22	5	2727	3134	443202	442795	1.840000e-167	599.0
45	TraesCS7D01G415800	chr1B	89.167	120	13	0	855	974	683576074	683575955	2.230000e-32	150.0
46	TraesCS7D01G415800	chr3A	91.525	118	9	1	857	974	663433448	663433564	1.030000e-35	161.0
47	TraesCS7D01G415800	chr3A	91.892	111	9	0	864	974	596770804	596770914	4.790000e-34	156.0
48	TraesCS7D01G415800	chr5D	91.892	111	9	0	864	974	33680782	33680672	4.790000e-34	156.0
49	TraesCS7D01G415800	chr4D	90.678	118	9	2	858	974	12520310	12520194	4.790000e-34	156.0

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	TraesCS7D01G415800	chr7D	534653374	534656954	3580	True	2302.333333	6613	94.822000	1	3581	3	chr7D.!!$R1	3580
1	TraesCS7D01G415800	chr2A	755058995	755062131	3136	False	1016.000000	1820	85.754333	1	3497	3	chr2A.!!$F2	3496
2	TraesCS7D01G415800	chr2A	137259533	137260106	573	True	579.000000	579	84.974000	1819	2392	1	chr2A.!!$R1	573
3	TraesCS7D01G415800	chr2A	746839512	746840887	1375	True	468.333333	972	87.559000	1421	3400	3	chr2A.!!$R3	1979
4	TraesCS7D01G415800	chr2B	110520067	110520867	800	True	704.000000	704	82.767000	1791	2603	1	chr2B.!!$R1	812
5	TraesCS7D01G415800	chr2B	765561647	765562993	1346	False	622.433333	1613	91.165333	1016	2668	3	chr2B.!!$F2	1652
6	TraesCS7D01G415800	chr2B	183211778	183212356	578	False	571.000000	571	84.509000	1814	2392	1	chr2B.!!$F1	578
7	TraesCS7D01G415800	chr2B	751602634	751604006	1372	True	509.000000	1053	89.436000	1421	3401	3	chr2B.!!$R3	1980
8	TraesCS7D01G415800	chr2D	623788392	623794088	5696	False	636.166667	1447	89.640500	1	3427	6	chr2D.!!$F3	3426
9	TraesCS7D01G415800	chr2D	129941616	129942189	573	False	601.000000	601	85.615000	1819	2392	1	chr2D.!!$F1	573
10	TraesCS7D01G415800	chr2D	131163126	131163699	573	True	568.000000	568	84.682000	1819	2392	1	chr2D.!!$R1	573
11	TraesCS7D01G415800	chr2D	616625559	616626906	1347	True	510.666667	1062	89.263667	1421	3401	3	chr2D.!!$R2	1980
12	TraesCS7D01G415800	chr2D	129837505	129838303	798	False	347.500000	582	85.786500	1814	2595	2	chr2D.!!$F2	781

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
722	747	0.107165	GATCAAAGCCCGGCCTACTT	60.107	55.0	5.55	0.00	0.00	2.24	F
1446	2641	0.035439	AATGAAGATTCACCGGCGGT	60.035	50.0	28.83	28.83	40.49	5.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1941	3301	0.033504	GACCTTGTCGTCCAGCTTCA	59.966	55.0	0.0	0.0	0.0	3.02	R
3158	4641	0.320073	CCCACACGAAACTCCGCTTA	60.320	55.0	0.0	0.0	0.0	3.09	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	4.637276	TGAATCTGGTTTTCGCTGAGTAA	58.363	39.130	0.00	0.00	0.00	2.24
76	89	0.109179	GCCATGTGCGATTTTCAGCA	60.109	50.000	0.00	0.00	41.55	4.41
112	126	7.383843	TCAAACTTTGACAAAAGAAGGAAACAC	59.616	33.333	1.62	0.00	44.81	3.32
190	204	1.593265	CTGCTGCCACCATTTTCCC	59.407	57.895	0.00	0.00	0.00	3.97
213	227	7.929245	TCCCAAACAGCTTTAAAAATAACCTTC	59.071	33.333	0.00	0.00	0.00	3.46
230	245	8.846943	ATAACCTTCAATTTCATTTTCAACCC	57.153	30.769	0.00	0.00	0.00	4.11
238	253	9.672673	TCAATTTCATTTTCAACCCTTTTTGTA	57.327	25.926	0.00	0.00	0.00	2.41
248	263	6.712276	TCAACCCTTTTTGTAAACCAAACAT	58.288	32.000	0.00	0.00	42.63	2.71
365	383	4.062293	CGTTACATCTCACTTTCAACCCA	58.938	43.478	0.00	0.00	0.00	4.51
381	399	4.714308	TCAACCCATTTTTGGTCAGACTTT	59.286	37.500	0.00	0.00	34.15	2.66
382	400	5.188751	TCAACCCATTTTTGGTCAGACTTTT	59.811	36.000	0.00	0.00	34.15	2.27
383	401	5.692115	ACCCATTTTTGGTCAGACTTTTT	57.308	34.783	0.00	0.00	0.00	1.94
388	406	8.951243	CCCATTTTTGGTCAGACTTTTTAAAAA	58.049	29.630	12.62	12.62	32.34	1.94
411	429	9.083080	AAAAACCATTTTAAAAGAGTGAACTCG	57.917	29.630	6.79	0.00	41.02	4.18
436	454	9.069082	CGGGACTAATATACTAATCATCCTAGG	57.931	40.741	0.82	0.82	0.00	3.02
513	532	4.947645	TCAGCCCTTTCTTTGTCAATTTG	58.052	39.130	0.00	0.00	0.00	2.32
523	542	8.572855	TTTCTTTGTCAATTTGGACCAAAAAT	57.427	26.923	23.11	12.57	36.90	1.82
599	621	5.004361	TCATTATGGGAAAGGTTTGGTCA	57.996	39.130	0.00	0.00	0.00	4.02
600	622	5.588845	TCATTATGGGAAAGGTTTGGTCAT	58.411	37.500	0.00	0.00	0.00	3.06
607	630	4.450976	GGAAAGGTTTGGTCATTTTTGCT	58.549	39.130	0.00	0.00	0.00	3.91
702	727	2.213499	CAGGGCGATCAATAACAGGTC	58.787	52.381	0.00	0.00	0.00	3.85
713	738	2.396590	TAACAGGTCGATCAAAGCCC	57.603	50.000	0.00	0.00	0.00	5.19
722	747	0.107165	GATCAAAGCCCGGCCTACTT	60.107	55.000	5.55	0.00	0.00	2.24
733	758	2.618053	CGGCCTACTTAGTGAAACCAG	58.382	52.381	0.00	0.00	37.80	4.00
756	781	3.883830	TCAGCAGAGAGAAGGTTGATC	57.116	47.619	0.00	0.00	0.00	2.92

Showing 1 to 25 of 348 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	2.413837	GCTTACTCAGCGAAAACCAGA	58.586	47.619	0.00	0.00	39.29	3.86
28	29	3.088532	TGGCCAATCAACAGGTCATAAC	58.911	45.455	0.61	0.00	33.91	1.89
76	89	3.553828	TCAAAGTTTGACCCGAGAAGT	57.446	42.857	14.35	0.00	34.08	3.01
388	406	6.238925	CCCGAGTTCACTCTTTTAAAATGGTT	60.239	38.462	0.09	0.00	40.75	3.67
392	410	6.296803	AGTCCCGAGTTCACTCTTTTAAAAT	58.703	36.000	0.09	0.00	40.75	1.82
393	411	5.677567	AGTCCCGAGTTCACTCTTTTAAAA	58.322	37.500	5.44	0.00	40.75	1.52
401	419	6.880942	AGTATATTAGTCCCGAGTTCACTC	57.119	41.667	0.00	0.00	39.55	3.51
436	454	8.835439	TCTTTGGCAAAAATAACTGGAAATTTC	58.165	29.630	14.43	9.83	0.00	2.17
485	504	4.466015	TGACAAAGAAAGGGCTGAAAAAGT	59.534	37.500	0.00	0.00	0.00	2.66
487	506	5.413309	TTGACAAAGAAAGGGCTGAAAAA	57.587	34.783	0.00	0.00	0.00	1.94
607	630	4.583871	AGGGTGTTTTTGCAATTTGTTCA	58.416	34.783	0.00	0.00	0.00	3.18
702	727	1.887707	GTAGGCCGGGCTTTGATCG	60.888	63.158	37.40	0.00	0.00	3.69
713	738	2.618053	CTGGTTTCACTAAGTAGGCCG	58.382	52.381	0.00	0.00	0.00	6.13
722	747	2.703536	TCTGCTGAACCTGGTTTCACTA	59.296	45.455	14.28	0.00	32.02	2.74
733	758	2.037772	TCAACCTTCTCTCTGCTGAACC	59.962	50.000	0.00	0.00	0.00	3.62
756	781	5.278957	CCCCAAATTATCAAAATCGGCTAGG	60.279	44.000	0.00	0.00	0.00	3.02
776	801	7.181361	TCAAATCATCTTAAGATTCAACCCCA	58.819	34.615	15.49	0.00	34.78	4.96
819	844	6.246163	ACCTTTAACCCTTCCATCTGTTTAG	58.754	40.000	0.00	0.00	0.00	1.85
822	847	4.741928	ACCTTTAACCCTTCCATCTGTT	57.258	40.909	0.00	0.00	0.00	3.16
823	848	4.741928	AACCTTTAACCCTTCCATCTGT	57.258	40.909	0.00	0.00	0.00	3.41
951	1958	7.335627	TGGTACGGATCAAAATAAGTGAATCT	58.664	34.615	0.00	0.00	0.00	2.40
958	1965	6.238648	GGGACAATGGTACGGATCAAAATAAG	60.239	42.308	0.00	0.00	0.00	1.73
967	1974	0.750850	CTCGGGACAATGGTACGGAT	59.249	55.000	0.00	0.00	36.69	4.18
970	1977	1.876714	CGCTCGGGACAATGGTACG	60.877	63.158	0.00	0.00	0.00	3.67
975	1982	2.892425	GAGCCGCTCGGGACAATG	60.892	66.667	4.23	0.00	38.47	2.82

Showing 1 to 25 of 341 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.