AutoCloner

Multiple sequence alignment - TraesCS6D01G275900

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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	TraesCS6D01G275900	chr6D	100.000	4480	0	0	1	4480	384437829	384442308	0.000000e+00	8274.0
1	TraesCS6D01G275900	chr6B	91.040	2422	111	52	111	2471	574714117	574716493	0.000000e+00	3173.0
2	TraesCS6D01G275900	chr6B	93.021	1261	40	19	2481	3716	574716549	574717786	0.000000e+00	1797.0
3	TraesCS6D01G275900	chr6B	97.561	82	2	0	36	117	574713993	574714074	1.680000e-29	141.0
4	TraesCS6D01G275900	chr6A	91.330	1361	56	31	987	2328	529018790	529020107	0.000000e+00	1803.0
5	TraesCS6D01G275900	chr6A	95.455	1012	28	10	2708	3715	529021381	529022378	0.000000e+00	1598.0
6	TraesCS6D01G275900	chr6A	85.908	887	63	26	111	959	529017934	529018796	0.000000e+00	889.0
7	TraesCS6D01G275900	chr6A	92.708	192	11	3	2500	2689	529020867	529021057	1.590000e-69	274.0
8	TraesCS6D01G275900	chr6A	93.333	150	7	1	2325	2471	529020399	529020548	7.550000e-53	219.0
9	TraesCS6D01G275900	chr6A	92.667	150	8	1	2325	2471	529020640	529020789	3.510000e-51	213.0
10	TraesCS6D01G275900	chr7A	90.338	414	40	0	1302	1715	166752021	166751608	1.100000e-150	544.0
11	TraesCS6D01G275900	chr7A	88.024	334	38	2	3125	3457	166748937	166748605	1.170000e-105	394.0
12	TraesCS6D01G275900	chr7A	91.288	264	23	0	1801	2064	166751385	166751122	1.180000e-95	361.0
13	TraesCS6D01G275900	chr7A	92.638	163	11	1	3714	3875	105168358	105168196	2.690000e-57	233.0
14	TraesCS6D01G275900	chr7A	94.040	151	8	1	3715	3864	596660523	596660673	1.250000e-55	228.0
15	TraesCS6D01G275900	chr7A	72.500	400	95	12	1318	1708	457867078	457866685	1.020000e-21	115.0
16	TraesCS6D01G275900	chr7D	89.647	425	42	2	1292	1715	164874554	164874131	1.420000e-149	540.0
17	TraesCS6D01G275900	chr7D	89.458	332	33	2	3127	3457	164871581	164871251	6.930000e-113	418.0
18	TraesCS6D01G275900	chr7D	91.221	262	23	0	1805	2066	164873852	164873591	1.530000e-94	357.0
19	TraesCS6D01G275900	chr7B	89.786	421	42	1	1295	1715	128308499	128308080	5.100000e-149	538.0
20	TraesCS6D01G275900	chr7B	87.952	332	38	2	3127	3457	128305256	128304926	1.510000e-104	390.0
21	TraesCS6D01G275900	chr7B	91.538	260	22	0	1805	2064	128307923	128307664	4.260000e-95	359.0
22	TraesCS6D01G275900	chr5B	94.444	162	8	1	3715	3875	685073440	685073279	9.620000e-62	248.0
23	TraesCS6D01G275900	chr2D	94.410	161	8	1	3716	3875	5616670	5616510	3.460000e-61	246.0
24	TraesCS6D01G275900	chr1B	92.814	167	11	1	3711	3876	183877196	183877362	1.610000e-59	241.0
25	TraesCS6D01G275900	chr2B	93.210	162	10	1	3715	3875	734335750	734335589	2.080000e-58	237.0
26	TraesCS6D01G275900	chr2B	88.950	181	18	2	3714	3892	704754631	704754451	5.830000e-54	222.0
27	TraesCS6D01G275900	chr2A	91.716	169	12	2	3715	3881	460904003	460904171	2.690000e-57	233.0
28	TraesCS6D01G275900	chrUn	90.805	174	11	5	3715	3887	457867558	457867389	1.250000e-55	228.0
29	TraesCS6D01G275900	chr1D	74.933	375	64	22	1298	1654	56530532	56530170	1.300000e-30	145.0
30	TraesCS6D01G275900	chr1D	94.286	70	4	0	1300	1369	445588735	445588804	1.700000e-19	108.0
31	TraesCS6D01G275900	chr1A	92.857	70	5	0	1300	1369	541770626	541770695	7.930000e-18	102.0
32	TraesCS6D01G275900	chr3A	100.000	32	0	0	1897	1928	127089663	127089632	4.840000e-05	60.2

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	TraesCS6D01G275900	chr6D	384437829	384442308	4479	False	8274.000000	8274	100.000000	1	4480	1	chr6D.!!$F1	4479
1	TraesCS6D01G275900	chr6B	574713993	574717786	3793	False	1703.666667	3173	93.874000	36	3716	3	chr6B.!!$F1	3680
2	TraesCS6D01G275900	chr6A	529017934	529022378	4444	False	832.666667	1803	91.900167	111	3715	6	chr6A.!!$F1	3604
3	TraesCS6D01G275900	chr7A	166748605	166752021	3416	True	433.000000	544	89.883333	1302	3457	3	chr7A.!!$R3	2155
4	TraesCS6D01G275900	chr7D	164871251	164874554	3303	True	438.333333	540	90.108667	1292	3457	3	chr7D.!!$R1	2165
5	TraesCS6D01G275900	chr7B	128304926	128308499	3573	True	429.000000	538	89.758667	1295	3457	3	chr7B.!!$R1	2162

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
28	29	0.389948	AGAGCCGAAAACCACGCTAG	60.390	55.0	0.00	0.0	0.00	3.42	F
80	81	0.531200	AACTGTACCGCTAGTCAGCC	59.469	55.0	0.00	0.0	45.64	4.85	F
1761	1888	0.436150	CGACTCGAATGCACTGTGTG	59.564	55.0	9.86	0.0	36.51	3.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1734	1861	1.136774	CATTCGAGTCGTCGGAGCA	59.863	57.895	13.12	0.0	46.80	4.26	R
2068	2420	0.035881	CAGTGGAGTGGTGATGCAGT	59.964	55.000	0.00	0.0	0.00	4.40	R
3545	6208	0.532573	TAGTGCACTACTCCTGCAGC	59.467	55.000	22.67	0.0	45.22	5.25	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	4.379174	GCTCAGAGCCGAAAACCA	57.621	55.556	11.84	0.00	34.48	3.67
23	24	1.869690	GCTCAGAGCCGAAAACCAC	59.130	57.895	11.84	0.00	34.48	4.16
24	25	1.901650	GCTCAGAGCCGAAAACCACG	61.902	60.000	11.84	0.00	34.48	4.94
25	26	1.901650	CTCAGAGCCGAAAACCACGC	61.902	60.000	0.00	0.00	0.00	5.34
26	27	1.961277	CAGAGCCGAAAACCACGCT	60.961	57.895	0.00	0.00	0.00	5.07
27	28	0.669318	CAGAGCCGAAAACCACGCTA	60.669	55.000	0.00	0.00	0.00	4.26
28	29	0.389948	AGAGCCGAAAACCACGCTAG	60.390	55.000	0.00	0.00	0.00	3.42
29	30	0.669625	GAGCCGAAAACCACGCTAGT	60.670	55.000	0.00	0.00	0.00	2.57
30	31	0.669625	AGCCGAAAACCACGCTAGTC	60.670	55.000	0.00	0.00	0.00	2.59
31	32	0.947180	GCCGAAAACCACGCTAGTCA	60.947	55.000	0.00	0.00	0.00	3.41
32	33	1.722011	CCGAAAACCACGCTAGTCAT	58.278	50.000	0.00	0.00	0.00	3.06
33	34	1.393539	CCGAAAACCACGCTAGTCATG	59.606	52.381	0.00	0.00	0.00	3.07
34	35	2.333926	CGAAAACCACGCTAGTCATGA	58.666	47.619	0.00	0.00	0.00	3.07
80	81	0.531200	AACTGTACCGCTAGTCAGCC	59.469	55.000	0.00	0.00	45.64	4.85
100	101	3.119779	GCCTGGTAACTATAGCTAGCGAG	60.120	52.174	9.55	10.68	37.61	5.03
115	165	2.139118	AGCGAGCTTTGTTTCAGAGAC	58.861	47.619	0.00	0.00	0.00	3.36
189	239	3.695606	GGACAGGGCACGCTGAGA	61.696	66.667	20.12	0.00	32.37	3.27
259	309	2.702751	TACAACACCGCCGTCCTGTG	62.703	60.000	0.00	0.00	36.11	3.66
399	456	6.152661	TGAACTTTCTTTGATCACACCAAAGT	59.847	34.615	13.23	12.37	46.30	2.66
439	496	3.686726	AGAAGAGACATTGCGAAACCATC	59.313	43.478	0.00	0.00	0.00	3.51
441	498	3.265791	AGAGACATTGCGAAACCATCTC	58.734	45.455	5.37	5.37	32.94	2.75
446	503	1.368641	TTGCGAAACCATCTCATCCG	58.631	50.000	0.00	0.00	0.00	4.18
487	545	1.736126	GAGCTTAAGCCGTTGGTAACC	59.264	52.381	23.71	0.00	43.38	2.85
492	569	1.601166	AAGCCGTTGGTAACCACTTC	58.399	50.000	0.00	0.00	30.78	3.01
863	972	2.240279	GACTCCAGTAGACACACACCT	58.760	52.381	0.00	0.00	0.00	4.00

Showing 1 to 25 of 532 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	1.959226	GCGTGGTTTTCGGCTCTGA	60.959	57.895	0.00	0.00	0.00	3.27
9	10	0.389948	CTAGCGTGGTTTTCGGCTCT	60.390	55.000	0.00	0.00	0.00	4.09
10	11	0.669625	ACTAGCGTGGTTTTCGGCTC	60.670	55.000	0.00	0.00	0.00	4.70
11	12	0.669625	GACTAGCGTGGTTTTCGGCT	60.670	55.000	0.00	0.00	0.00	5.52
12	13	0.947180	TGACTAGCGTGGTTTTCGGC	60.947	55.000	0.00	0.00	0.00	5.54
13	14	1.393539	CATGACTAGCGTGGTTTTCGG	59.606	52.381	0.00	0.00	0.00	4.30
14	15	2.092211	GTCATGACTAGCGTGGTTTTCG	59.908	50.000	18.83	0.00	34.18	3.46
15	16	2.092211	CGTCATGACTAGCGTGGTTTTC	59.908	50.000	22.95	0.00	34.18	2.29
16	17	2.066262	CGTCATGACTAGCGTGGTTTT	58.934	47.619	22.95	0.00	34.18	2.43
17	18	1.271379	TCGTCATGACTAGCGTGGTTT	59.729	47.619	22.95	0.00	34.18	3.27
18	19	0.885879	TCGTCATGACTAGCGTGGTT	59.114	50.000	22.95	0.00	34.18	3.67
19	20	0.170561	GTCGTCATGACTAGCGTGGT	59.829	55.000	22.95	0.00	44.58	4.16
20	21	2.945315	GTCGTCATGACTAGCGTGG	58.055	57.895	22.95	6.32	44.58	4.94
29	30	6.100668	TGTTACGGATAAAATGTCGTCATGA	58.899	36.000	0.00	0.00	37.10	3.07
30	31	6.035650	ACTGTTACGGATAAAATGTCGTCATG	59.964	38.462	0.00	0.00	37.10	3.07
31	32	6.103997	ACTGTTACGGATAAAATGTCGTCAT	58.896	36.000	0.00	0.00	37.10	3.06
32	33	5.472148	ACTGTTACGGATAAAATGTCGTCA	58.528	37.500	0.00	0.00	37.10	4.35
33	34	6.527722	TGTACTGTTACGGATAAAATGTCGTC	59.472	38.462	0.00	0.00	37.10	4.20
34	35	6.389091	TGTACTGTTACGGATAAAATGTCGT	58.611	36.000	0.00	0.00	39.30	4.34
80	81	4.086199	GCTCGCTAGCTATAGTTACCAG	57.914	50.000	13.93	0.00	45.85	4.00
100	101	3.879892	ACTTCTGGTCTCTGAAACAAAGC	59.120	43.478	0.00	0.00	31.90	3.51
115	165	2.125912	CTCCGCCGTCACTTCTGG	60.126	66.667	0.00	0.00	0.00	3.86
259	309	0.248565	TCACTCATCACAGCAGGAGC	59.751	55.000	0.00	0.00	42.56	4.70
313	368	1.444553	CCACTTCTCGTCTGGCGAC	60.445	63.158	0.00	0.00	45.68	5.19
399	456	0.323360	CTTGCGGGGATTGGGAAGAA	60.323	55.000	0.00	0.00	33.97	2.52

Showing 1 to 25 of 527 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.