AutoCloner

Multiple sequence alignment - TraesCS1B01G177800

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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	TraesCS1B01G177800	chr1B	100.000	4808	0	0	1	4808	322479558	322484365	0.000000e+00	8879.0
1	TraesCS1B01G177800	chr1B	96.154	130	4	1	591	720	228160951	228160823	1.360000e-50	211.0
2	TraesCS1B01G177800	chr1B	96.063	127	5	0	591	717	661925231	661925357	1.750000e-49	207.0
3	TraesCS1B01G177800	chr1A	92.950	2610	140	26	844	3426	290198795	290201387	0.000000e+00	3760.0
4	TraesCS1B01G177800	chr1A	93.382	1375	55	16	3459	4808	290201389	290202752	0.000000e+00	2002.0
5	TraesCS1B01G177800	chr1A	94.022	552	28	4	2598	3145	591372687	591373237	0.000000e+00	832.0
6	TraesCS1B01G177800	chr1A	98.374	123	2	0	591	713	353914507	353914385	2.910000e-52	217.0
7	TraesCS1B01G177800	chr1D	93.528	2194	126	12	1956	4137	223168891	223171080	0.000000e+00	3251.0
8	TraesCS1B01G177800	chr1D	91.681	1154	69	9	844	1975	223167730	223168878	0.000000e+00	1574.0
9	TraesCS1B01G177800	chr1D	94.203	690	12	15	4139	4808	223171130	223171811	0.000000e+00	1027.0
10	TraesCS1B01G177800	chr1D	98.246	57	1	0	753	809	223167676	223167732	3.060000e-17	100.0
11	TraesCS1B01G177800	chr7D	93.582	2088	119	11	2061	4137	617969813	617971896	0.000000e+00	3099.0
12	TraesCS1B01G177800	chr7D	94.348	690	11	15	4139	4808	617971946	617972627	0.000000e+00	1033.0
13	TraesCS1B01G177800	chr7D	92.063	252	19	1	1	251	185932003	185931752	2.130000e-93	353.0
14	TraesCS1B01G177800	chr7D	91.700	253	19	2	1	251	81872096	81872348	2.750000e-92	350.0
15	TraesCS1B01G177800	chr7B	90.230	348	30	3	246	592	21606513	21606857	7.340000e-123	451.0
16	TraesCS1B01G177800	chr7B	95.349	86	4	0	815	900	320311113	320311028	2.330000e-28	137.0
17	TraesCS1B01G177800	chr7B	90.816	98	7	2	805	900	9694519	9694616	3.910000e-26	130.0
18	TraesCS1B01G177800	chr3D	90.000	350	31	3	246	592	588680372	588680024	2.640000e-122	449.0
19	TraesCS1B01G177800	chr3D	92.460	252	18	1	1	251	596650885	596651136	4.580000e-95	359.0
20	TraesCS1B01G177800	chr3D	90.323	93	8	1	815	906	315774603	315774511	2.350000e-23	121.0
21	TraesCS1B01G177800	chr6D	89.971	349	30	5	246	592	148622174	148621829	3.410000e-121	446.0
22	TraesCS1B01G177800	chr6D	89.773	352	28	7	246	592	783414	783762	1.230000e-120	444.0
23	TraesCS1B01G177800	chr6D	92.063	252	18	2	1	251	355882446	355882196	2.130000e-93	353.0
24	TraesCS1B01G177800	chr5B	89.385	358	30	7	248	600	701500748	701501102	1.230000e-120	444.0
25	TraesCS1B01G177800	chr5B	92.460	252	18	1	1	251	91530150	91530401	4.580000e-95	359.0
26	TraesCS1B01G177800	chr6B	89.714	350	30	5	247	592	648287839	648287492	4.420000e-120	442.0
27	TraesCS1B01G177800	chr3B	89.714	350	29	6	246	592	685192669	685192324	1.590000e-119	440.0
28	TraesCS1B01G177800	chr3B	92.063	252	19	1	1	251	698197688	698197437	2.130000e-93	353.0
29	TraesCS1B01G177800	chr2D	88.950	362	29	10	243	600	446730853	446731207	2.050000e-118	436.0
30	TraesCS1B01G177800	chr2D	88.889	360	33	7	246	600	527886839	527886482	2.050000e-118	436.0
31	TraesCS1B01G177800	chr2D	92.460	252	18	1	1	251	461852208	461851957	4.580000e-95	359.0
32	TraesCS1B01G177800	chrUn	92.881	295	7	10	4139	4427	480384061	480384347	2.680000e-112	416.0
33	TraesCS1B01G177800	chr7A	85.915	355	38	11	255	601	621907997	621908347	7.600000e-98	368.0
34	TraesCS1B01G177800	chr5D	92.683	246	16	2	1	244	545959449	545959204	2.130000e-93	353.0
35	TraesCS1B01G177800	chr5D	94.186	86	5	0	815	900	385605547	385605632	1.090000e-26	132.0
36	TraesCS1B01G177800	chr4D	91.700	253	18	3	1	251	508428712	508428461	9.900000e-92	348.0
37	TraesCS1B01G177800	chr4B	96.694	121	4	0	591	711	267654187	267654067	8.160000e-48	202.0
38	TraesCS1B01G177800	chr4B	95.200	125	6	0	590	714	12626161	12626037	1.060000e-46	198.0
39	TraesCS1B01G177800	chr4B	88.372	86	10	0	815	900	86753657	86753742	2.370000e-18	104.0
40	TraesCS1B01G177800	chr2A	95.968	124	5	0	591	714	627630337	627630214	8.160000e-48	202.0
41	TraesCS1B01G177800	chr2A	94.186	86	5	0	815	900	715378705	715378620	1.090000e-26	132.0
42	TraesCS1B01G177800	chr2A	89.474	76	8	0	825	900	668018265	668018340	3.960000e-16	97.1
43	TraesCS1B01G177800	chr2A	92.857	56	3	1	852	906	767319472	767319417	3.990000e-11	80.5
44	TraesCS1B01G177800	chr6A	95.238	126	6	0	589	714	585963370	585963245	2.930000e-47	200.0
45	TraesCS1B01G177800	chr6A	94.488	127	7	0	588	714	116339230	116339356	3.800000e-46	196.0
46	TraesCS1B01G177800	chr3A	95.935	123	5	0	591	713	265258823	265258945	2.930000e-47	200.0
47	TraesCS1B01G177800	chr3A	94.444	90	3	2	819	906	17782529	17782618	2.330000e-28	137.0
48	TraesCS1B01G177800	chr3A	89.610	77	8	0	815	891	521727815	521727891	1.100000e-16	99.0

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	TraesCS1B01G177800	chr1B	322479558	322484365	4807	False	8879	8879	100.0000	1	4808	1	chr1B.!!$F1	4807
1	TraesCS1B01G177800	chr1A	290198795	290202752	3957	False	2881	3760	93.1660	844	4808	2	chr1A.!!$F2	3964
2	TraesCS1B01G177800	chr1A	591372687	591373237	550	False	832	832	94.0220	2598	3145	1	chr1A.!!$F1	547
3	TraesCS1B01G177800	chr1D	223167676	223171811	4135	False	1488	3251	94.4145	753	4808	4	chr1D.!!$F1	4055
4	TraesCS1B01G177800	chr7D	617969813	617972627	2814	False	2066	3099	93.9650	2061	4808	2	chr7D.!!$F2	2747

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
137	138	0.039074	CGCCCTTCACCGCTAGATAG	60.039	60.0	0.00	0.00	0.00	2.08	F
147	148	0.108615	CGCTAGATAGCCATTCCCCG	60.109	60.0	6.28	0.00	46.34	5.73	F
712	713	0.179081	AAGGTAAAGGATCCTCGCGC	60.179	55.0	16.52	5.90	33.09	6.86	F
1213	1241	0.318784	AGTTCTTCCACTCGACGTGC	60.319	55.0	0.00	0.00	42.42	5.34	F
1364	1392	0.583917	GGATTTGCTCGAGCCGATTC	59.416	55.0	33.23	23.78	41.18	2.52	F
2406	2477	1.040646	TCTTGCACGTCCAGTCTTCT	58.959	50.0	0.00	0.00	0.00	2.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1576	1611	0.031585	TCAACGACCGGACAAGACAG	59.968	55.000	9.46	0.00	0.00	3.51	R
1918	1956	0.040603	GCAGAATAAGCCGATGCAGC	60.041	55.000	0.00	0.00	41.13	5.25	R
2204	2274	0.748005	TGGGCTCCGCATTAAGCTTC	60.748	55.000	0.00	0.00	42.61	3.86	R
2550	2621	1.888436	CGTGCCAGGGAGCTAGACAA	61.888	60.000	0.00	0.00	0.00	3.18	R
3268	3348	1.909302	ACCTGCAGGCTATGTGTAACT	59.091	47.619	33.06	5.36	39.32	2.24	R
4167	4305	0.107116	AGGTGTTGTTGTTACCGGCA	60.107	50.000	0.00	0.00	39.46	5.69	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
18	19	3.365265	CAAGGGAAAAGCGCGGCT	61.365	61.111	8.83	2.05	42.56	5.52
19	20	3.365265	AAGGGAAAAGCGCGGCTG	61.365	61.111	8.83	0.00	39.62	4.85
37	38	4.314440	GCCCACGCAGTCAGGTGA	62.314	66.667	0.00	0.00	41.61	4.02
38	39	2.425592	CCCACGCAGTCAGGTGAA	59.574	61.111	0.00	0.00	41.61	3.18
39	40	1.227823	CCCACGCAGTCAGGTGAAA	60.228	57.895	0.00	0.00	41.61	2.69
40	41	0.817634	CCCACGCAGTCAGGTGAAAA	60.818	55.000	0.00	0.00	41.61	2.29
41	42	1.021202	CCACGCAGTCAGGTGAAAAA	58.979	50.000	0.00	0.00	41.61	1.94
42	43	1.608590	CCACGCAGTCAGGTGAAAAAT	59.391	47.619	0.00	0.00	41.61	1.82
43	44	2.350772	CCACGCAGTCAGGTGAAAAATC	60.351	50.000	0.00	0.00	41.61	2.17
44	45	2.290367	CACGCAGTCAGGTGAAAAATCA	59.710	45.455	0.00	0.00	41.61	2.57
45	46	2.948979	ACGCAGTCAGGTGAAAAATCAA	59.051	40.909	0.00	0.00	29.74	2.57
46	47	3.003689	ACGCAGTCAGGTGAAAAATCAAG	59.996	43.478	0.00	0.00	29.74	3.02
47	48	3.250762	CGCAGTCAGGTGAAAAATCAAGA	59.749	43.478	0.00	0.00	0.00	3.02
48	49	4.083110	CGCAGTCAGGTGAAAAATCAAGAT	60.083	41.667	0.00	0.00	0.00	2.40
49	50	5.563475	CGCAGTCAGGTGAAAAATCAAGATT	60.563	40.000	0.00	0.00	0.00	2.40
50	51	6.218746	GCAGTCAGGTGAAAAATCAAGATTT	58.781	36.000	2.31	2.31	42.35	2.17
66	67	2.032987	TTTTTCCCCCGACTCGCC	59.967	61.111	0.00	0.00	0.00	5.54
67	68	2.522367	TTTTTCCCCCGACTCGCCT	61.522	57.895	0.00	0.00	0.00	5.52
68	69	2.459202	TTTTTCCCCCGACTCGCCTC	62.459	60.000	0.00	0.00	0.00	4.70
100	101	3.217017	CTCGGCGGCCACTAGCTA	61.217	66.667	20.71	0.00	43.05	3.32
101	102	2.520982	TCGGCGGCCACTAGCTAT	60.521	61.111	20.71	0.00	43.05	2.97
102	103	1.228337	TCGGCGGCCACTAGCTATA	60.228	57.895	20.71	0.00	43.05	1.31
103	104	0.611062	TCGGCGGCCACTAGCTATAT	60.611	55.000	20.71	0.00	43.05	0.86
104	105	0.179134	CGGCGGCCACTAGCTATATC	60.179	60.000	20.71	0.00	43.05	1.63
105	106	0.175989	GGCGGCCACTAGCTATATCC	59.824	60.000	15.62	0.00	43.05	2.59

Showing 1 to 25 of 429 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	3.365265	AGCCGCGCTTTTCCCTTG	61.365	61.111	5.56	0.00	33.89	3.61
2	3	3.365265	CAGCCGCGCTTTTCCCTT	61.365	61.111	5.56	0.00	36.40	3.95
20	21	3.825160	TTCACCTGACTGCGTGGGC	62.825	63.158	0.00	0.00	40.52	5.36
21	22	0.817634	TTTTCACCTGACTGCGTGGG	60.818	55.000	0.00	0.00	0.00	4.61
22	23	1.021202	TTTTTCACCTGACTGCGTGG	58.979	50.000	0.00	0.00	0.00	4.94
23	24	2.290367	TGATTTTTCACCTGACTGCGTG	59.710	45.455	0.00	0.00	0.00	5.34
24	25	2.571212	TGATTTTTCACCTGACTGCGT	58.429	42.857	0.00	0.00	0.00	5.24
25	26	3.250762	TCTTGATTTTTCACCTGACTGCG	59.749	43.478	0.00	0.00	0.00	5.18
26	27	4.836125	TCTTGATTTTTCACCTGACTGC	57.164	40.909	0.00	0.00	0.00	4.40
27	28	8.652810	AAAAATCTTGATTTTTCACCTGACTG	57.347	30.769	21.41	0.00	38.85	3.51
49	50	2.032987	GGCGAGTCGGGGGAAAAA	59.967	61.111	15.52	0.00	0.00	1.94
50	51	2.926242	AGGCGAGTCGGGGGAAAA	60.926	61.111	15.52	0.00	0.00	2.29
51	52	3.387947	GAGGCGAGTCGGGGGAAA	61.388	66.667	15.52	0.00	0.00	3.13
83	84	1.241990	TATAGCTAGTGGCCGCCGAG	61.242	60.000	14.07	12.14	43.05	4.63
84	85	0.611062	ATATAGCTAGTGGCCGCCGA	60.611	55.000	14.07	0.00	43.05	5.54
85	86	0.179134	GATATAGCTAGTGGCCGCCG	60.179	60.000	14.07	5.68	43.05	6.46
86	87	0.175989	GGATATAGCTAGTGGCCGCC	59.824	60.000	14.07	1.04	43.05	6.13
87	88	0.175989	GGGATATAGCTAGTGGCCGC	59.824	60.000	8.71	8.71	43.05	6.53
88	89	0.456221	CGGGATATAGCTAGTGGCCG	59.544	60.000	0.00	0.00	43.05	6.13
89	90	0.175989	GCGGGATATAGCTAGTGGCC	59.824	60.000	0.00	0.00	43.05	5.36
90	91	0.179134	CGCGGGATATAGCTAGTGGC	60.179	60.000	0.00	0.00	42.19	5.01
91	92	0.179134	GCGCGGGATATAGCTAGTGG	60.179	60.000	8.83	0.00	0.00	4.00
92	93	0.179134	GGCGCGGGATATAGCTAGTG	60.179	60.000	8.83	0.00	0.00	2.74
93	94	0.611062	TGGCGCGGGATATAGCTAGT	60.611	55.000	8.83	0.00	0.00	2.57
94	95	0.179134	GTGGCGCGGGATATAGCTAG	60.179	60.000	8.83	0.00	0.00	3.42

Showing 1 to 25 of 408 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.