AutoCloner

Multiple sequence alignment - TraesCS3B01G286500

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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	TraesCS3B01G286500	chr3B	100.000	3061	0	0	1	3061	458341862	458344922	0.000000e+00	5653.0
1	TraesCS3B01G286500	chr3D	92.212	3146	107	55	1	3061	357140227	357143319	0.000000e+00	4325.0
2	TraesCS3B01G286500	chr3A	95.013	1163	33	13	1242	2382	476385440	476386599	0.000000e+00	1803.0
3	TraesCS3B01G286500	chr3A	91.541	863	25	21	318	1158	476384550	476385386	0.000000e+00	1146.0
4	TraesCS3B01G286500	chr3A	90.588	595	24	16	2393	2959	476386637	476387227	0.000000e+00	760.0
5	TraesCS3B01G286500	chr3A	91.135	282	21	4	1	280	476384271	476384550	2.230000e-101	379.0
6	TraesCS3B01G286500	chr3A	77.551	147	28	5	1275	1419	60297622	60297765	1.960000e-12	84.2
7	TraesCS3B01G286500	chr1B	77.101	345	60	16	1287	1616	615732314	615732654	6.740000e-42	182.0
8	TraesCS3B01G286500	chr1B	87.143	140	13	4	1489	1624	615744800	615744662	1.470000e-33	154.0
9	TraesCS3B01G286500	chr1B	88.889	126	11	2	1024	1149	615732181	615732303	5.290000e-33	152.0
10	TraesCS3B01G286500	chr1B	88.710	124	11	2	1026	1149	615581758	615581878	6.840000e-32	148.0
11	TraesCS3B01G286500	chr1B	87.302	126	13	2	1024	1149	615625643	615625765	1.140000e-29	141.0
12	TraesCS3B01G286500	chr1B	86.508	126	15	2	1809	1933	615744429	615744305	1.480000e-28	137.0
13	TraesCS3B01G286500	chr1B	84.252	127	18	2	1810	1935	616565335	616565210	4.140000e-24	122.0
14	TraesCS3B01G286500	chr1A	76.833	341	59	13	1287	1615	545025101	545024769	1.130000e-39	174.0
15	TraesCS3B01G286500	chr1A	89.683	126	10	2	1024	1149	544748316	544748438	1.140000e-34	158.0
16	TraesCS3B01G286500	chr1A	88.281	128	15	0	1489	1616	545009109	545008982	1.470000e-33	154.0
17	TraesCS3B01G286500	chr1A	88.189	127	13	2	1809	1934	545008729	545008604	1.900000e-32	150.0
18	TraesCS3B01G286500	chr1A	86.508	126	15	2	1809	1933	545000970	545001094	1.480000e-28	137.0
19	TraesCS3B01G286500	chr1A	85.039	127	17	2	1810	1935	545298885	545298760	8.910000e-26	128.0
20	TraesCS3B01G286500	chr1A	86.726	113	13	2	1810	1921	544928567	544928678	1.150000e-24	124.0
21	TraesCS3B01G286500	chr1D	87.770	139	14	2	1489	1624	449923210	449923072	3.160000e-35	159.0
22	TraesCS3B01G286500	chr1D	88.281	128	15	0	1489	1616	449660776	449660903	1.470000e-33	154.0
23	TraesCS3B01G286500	chr1D	87.500	128	16	0	1489	1616	449982997	449982870	6.840000e-32	148.0
24	TraesCS3B01G286500	chr1D	87.402	127	14	2	1810	1935	449922838	449922713	8.850000e-31	145.0
25	TraesCS3B01G286500	chr1D	87.302	126	13	2	1024	1149	449752656	449752778	1.140000e-29	141.0
26	TraesCS3B01G286500	chr1D	87.302	126	13	2	1024	1149	449846865	449846987	1.140000e-29	141.0
27	TraesCS3B01G286500	chr1D	87.302	126	13	2	1024	1149	449983416	449983294	1.140000e-29	141.0
28	TraesCS3B01G286500	chr4D	79.710	138	22	6	1273	1407	483369422	483369556	9.040000e-16	95.3
29	TraesCS3B01G286500	chr6B	84.946	93	11	3	1287	1379	526101147	526101058	1.170000e-14	91.6
30	TraesCS3B01G286500	chr7B	80.672	119	18	5	1267	1382	77432152	77432268	1.510000e-13	87.9
31	TraesCS3B01G286500	chr7A	80.672	119	18	5	1267	1382	121398158	121398274	1.510000e-13	87.9
32	TraesCS3B01G286500	chr7A	81.308	107	18	2	1279	1384	428810087	428810192	5.440000e-13	86.1
33	TraesCS3B01G286500	chr4B	81.579	114	14	7	1273	1382	613754454	613754344	1.510000e-13	87.9

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	TraesCS3B01G286500	chr3B	458341862	458344922	3060	False	5653	5653	100.00000	1	3061	1	chr3B.!!$F1	3060
1	TraesCS3B01G286500	chr3D	357140227	357143319	3092	False	4325	4325	92.21200	1	3061	1	chr3D.!!$F1	3060
2	TraesCS3B01G286500	chr3A	476384271	476387227	2956	False	1022	1803	92.06925	1	2959	4	chr3A.!!$F2	2958

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
786	817	0.038251	TCATTGCTGCGTCGTCTTCT	60.038	50.0	0.00	0.00	0.00	2.85	F
1225	1267	0.027194	CATGTGTGCTGCTACATCGC	59.973	55.0	16.38	3.45	35.46	4.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1649	1699	0.249657	GCGGCCTCTCATCTTTCGAT	60.250	55.0	0.0	0.0	0.0	3.59	R
2969	3104	0.032540	CGATGGATGGATGTCTGCGA	59.967	55.0	0.0	0.0	0.0	5.10	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
41	42	2.997980	TGCATGATGAATTACACGGGT	58.002	42.857	0.00	0.00	0.00	5.28
59	60	2.034812	GGGTGAATACGACCTCTGCTAG	59.965	54.545	0.00	0.00	33.58	3.42
116	120	6.534475	TTTCGACCCTAACTAAGCTTATCA	57.466	37.500	6.64	0.00	0.00	2.15
120	124	6.493802	TCGACCCTAACTAAGCTTATCATCAT	59.506	38.462	6.64	0.00	0.00	2.45
139	144	6.258947	TCATCATTTTGTCACAGTTAACGACA	59.741	34.615	9.82	9.82	37.87	4.35
142	147	8.317891	TCATTTTGTCACAGTTAACGACATAT	57.682	30.769	13.39	8.88	39.29	1.78
244	249	4.294523	GCATGGTTGGTGCGAGTA	57.705	55.556	0.00	0.00	32.29	2.59
258	263	6.447162	TGGTGCGAGTATAGTGAATAATCTG	58.553	40.000	0.00	0.00	33.83	2.90
384	392	0.534877	TGCATTGTCGCAACAGTCCT	60.535	50.000	0.00	0.00	39.45	3.85
401	412	6.441222	ACAGTCCTCCTAGGTGATTAATACA	58.559	40.000	12.54	0.00	36.53	2.29
426	437	2.517959	CCGTTCCCCATAATCATGCAT	58.482	47.619	0.00	0.00	0.00	3.96
427	438	2.229543	CCGTTCCCCATAATCATGCATG	59.770	50.000	21.07	21.07	0.00	4.06
428	439	2.352030	CGTTCCCCATAATCATGCATGC	60.352	50.000	22.25	11.82	0.00	4.06
429	440	1.536940	TCCCCATAATCATGCATGCG	58.463	50.000	22.25	7.28	0.00	4.73
512	530	1.153429	CTGTAGCGTTGGGCCCTAC	60.153	63.158	24.83	24.83	45.17	3.18
591	609	1.200092	AGCTGCTCCTCTTCCTTGCT	61.200	55.000	0.00	0.00	0.00	3.91
664	686	2.038033	AGCCTACGGAGCACAAGTAAAA	59.962	45.455	0.00	0.00	0.00	1.52
768	799	4.221041	AGGTTGCTTGAGACCTACTACTTC	59.779	45.833	0.00	0.00	44.26	3.01
786	817	0.038251	TCATTGCTGCGTCGTCTTCT	60.038	50.000	0.00	0.00	0.00	2.85
795	826	2.754658	TCGTCTTCTCCTCCCCGC	60.755	66.667	0.00	0.00	0.00	6.13
846	881	2.225805	ACGCTTCCCCATATATACCCCT	60.226	50.000	0.00	0.00	0.00	4.79
887	922	9.476202	CCGAGATAGATAGATAGAGATACACAG	57.524	40.741	0.00	0.00	0.00	3.66
915	953	1.593196	ACGAACCAACCATCACACTG	58.407	50.000	0.00	0.00	0.00	3.66
916	954	1.140052	ACGAACCAACCATCACACTGA	59.860	47.619	0.00	0.00	0.00	3.41
955	993	1.210545	TGCTCGGTCGTTTGTTCGTC	61.211	55.000	0.00	0.00	0.00	4.20
1196	1238	2.251818	CACACTTCTCTCCCCTCTTCA	58.748	52.381	0.00	0.00	0.00	3.02
1225	1267	0.027194	CATGTGTGCTGCTACATCGC	59.973	55.000	16.38	3.45	35.46	4.58
1245	1287	4.082625	TCGCTCTAATCTAACAACCGTTGA	60.083	41.667	18.19	0.00	36.52	3.18
1268	1313	2.159531	GCTTAATGCGTGTGCTGAATGA	60.160	45.455	0.00	0.00	43.34	2.57
1430	1475	5.890334	ACATACATTACGCCTTCCATTTTG	58.110	37.500	0.00	0.00	0.00	2.44
1440	1490	5.007528	ACGCCTTCCATTTTGTTTGAAATTG	59.992	36.000	0.00	0.00	0.00	2.32
1520	1570	0.461961	AGATAGCGTCTCACTTGCCC	59.538	55.000	0.00	0.00	28.45	5.36
1649	1699	3.948719	GTGGAACCGGACCAGGCA	61.949	66.667	21.23	1.69	38.14	4.75
2078	2140	4.357325	TCTGAGGCCTTTTCTGATCTAGT	58.643	43.478	6.77	0.00	0.00	2.57
2286	2357	7.770897	ACACTCTGTAATTTACCATGAGATTCC	59.229	37.037	19.14	0.00	0.00	3.01
2365	2444	9.609346	GGTAAGTTGCTATTACTTGGAAGATTA	57.391	33.333	0.00	0.00	36.56	1.75
2483	2593	5.942236	TGAGAAAGAAAGATGCTGCTGTTAT	59.058	36.000	0.00	0.00	0.00	1.89
2488	2598	8.430801	AAAGAAAGATGCTGCTGTTATAGTAG	57.569	34.615	0.00	0.00	41.54	2.57
2514	2624	2.307098	AGTTGGAATTAGGAGCAGCTGT	59.693	45.455	16.64	1.59	0.00	4.40
2560	2670	4.286032	TGATTAGTTTGGGAGCAGTACTGT	59.714	41.667	23.44	10.82	0.00	3.55
2658	2768	2.437413	GTCCCTTTTGCTAGAAGGTGG	58.563	52.381	7.68	0.00	41.70	4.61
2729	2839	5.368989	TGGTGGAGAAAAGAAAAGAGAGAC	58.631	41.667	0.00	0.00	0.00	3.36
2730	2840	4.449405	GGTGGAGAAAAGAAAAGAGAGACG	59.551	45.833	0.00	0.00	0.00	4.18
2731	2841	5.290386	GTGGAGAAAAGAAAAGAGAGACGA	58.710	41.667	0.00	0.00	0.00	4.20
2732	2842	5.404066	GTGGAGAAAAGAAAAGAGAGACGAG	59.596	44.000	0.00	0.00	0.00	4.18
2733	2843	5.069251	TGGAGAAAAGAAAAGAGAGACGAGT	59.931	40.000	0.00	0.00	0.00	4.18
2734	2844	5.404066	GGAGAAAAGAAAAGAGAGACGAGTG	59.596	44.000	0.00	0.00	0.00	3.51
2737	2847	4.939052	AAGAAAAGAGAGACGAGTGGAA	57.061	40.909	0.00	0.00	0.00	3.53
2738	2848	4.245845	AGAAAAGAGAGACGAGTGGAAC	57.754	45.455	0.00	0.00	0.00	3.62
2961	3096	0.678684	CACTGCACATGATGGCTGGA	60.679	55.000	0.00	0.00	33.82	3.86
2965	3100	0.179156	GCACATGATGGCTGGAAACG	60.179	55.000	0.00	0.00	0.00	3.60
2966	3101	0.179156	CACATGATGGCTGGAAACGC	60.179	55.000	0.00	0.00	0.00	4.84
2974	3109	3.777925	CTGGAAACGCCGTCGCAG	61.778	66.667	0.00	0.00	40.66	5.18
2975	3110	4.287781	TGGAAACGCCGTCGCAGA	62.288	61.111	0.00	0.00	40.66	4.26
2990	3125	1.224075	GCAGACATCCATCCATCGTG	58.776	55.000	0.00	0.00	0.00	4.35
3004	3139	3.378112	TCCATCGTGCTTCAAATCCAATC	59.622	43.478	0.00	0.00	0.00	2.67
3026	3163	3.430453	TGGATTTCAGGGGCTGTAAAAG	58.570	45.455	0.00	0.00	32.61	2.27
3028	3165	3.431415	GATTTCAGGGGCTGTAAAAGGT	58.569	45.455	0.00	0.00	32.61	3.50
3029	3166	2.579410	TTCAGGGGCTGTAAAAGGTC	57.421	50.000	0.00	0.00	32.61	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
41	42	5.654603	TTTTCTAGCAGAGGTCGTATTCA	57.345	39.130	0.00	0.00	0.00	2.57
68	69	1.216977	CGGCACATCGTTGTAGGGA	59.783	57.895	0.00	0.00	33.76	4.20
69	70	2.461110	GCGGCACATCGTTGTAGGG	61.461	63.158	0.00	0.00	33.76	3.53
70	71	2.461110	GGCGGCACATCGTTGTAGG	61.461	63.158	3.07	0.00	33.76	3.18
72	73	2.030401	GTGGCGGCACATCGTTGTA	61.030	57.895	34.40	0.00	33.76	2.41
73	74	3.353836	GTGGCGGCACATCGTTGT	61.354	61.111	34.40	0.00	36.15	3.32
75	76	3.842925	AAGGTGGCGGCACATCGTT	62.843	57.895	38.28	23.86	0.00	3.85
116	120	6.612247	TGTCGTTAACTGTGACAAAATGAT	57.388	33.333	11.06	0.00	39.50	2.45
120	124	6.706716	TCCATATGTCGTTAACTGTGACAAAA	59.293	34.615	15.70	9.58	44.90	2.44
139	144	1.556911	GATCCCATCGTGCCTCCATAT	59.443	52.381	0.00	0.00	0.00	1.78
142	147	1.056125	ATGATCCCATCGTGCCTCCA	61.056	55.000	0.00	0.00	0.00	3.86
258	263	6.226787	ACAGGCTAGATGTATAATTGTGCTC	58.773	40.000	0.00	0.00	0.00	4.26
384	392	5.771666	CGGGTACTGTATTAATCACCTAGGA	59.228	44.000	17.98	0.00	0.00	2.94
401	412	2.766736	TGATTATGGGGAACGGGTACT	58.233	47.619	0.00	0.00	0.00	2.73
426	437	5.412594	ACTTGAGATTTTTCTCATTAGCGCA	59.587	36.000	11.47	0.00	45.03	6.09
427	438	5.873732	ACTTGAGATTTTTCTCATTAGCGC	58.126	37.500	0.00	0.00	45.03	5.92
428	439	7.065216	TGACTTGAGATTTTTCTCATTAGCG	57.935	36.000	6.52	0.00	45.03	4.26
429	440	9.928236	GTATGACTTGAGATTTTTCTCATTAGC	57.072	33.333	6.52	1.28	45.03	3.09
512	530	2.862223	GCCGGGGAGAGGAATCGAG	61.862	68.421	2.18	0.00	0.00	4.04
664	686	0.824759	GAGCTCAAGATACACCCCGT	59.175	55.000	9.40	0.00	0.00	5.28
768	799	0.368227	GAGAAGACGACGCAGCAATG	59.632	55.000	0.00	0.00	0.00	2.82
813	848	2.892334	GAAGCGTGCGTGCCAAGAA	61.892	57.895	0.00	0.00	34.65	2.52
887	922	1.299850	GTTGGTTCGTTGCCTTGCC	60.300	57.895	0.00	0.00	0.00	4.52
1163	1205	4.589700	GTGTGTGTGTGCGCGTGG	62.590	66.667	8.43	0.00	0.00	4.94
1219	1261	4.142227	ACGGTTGTTAGATTAGAGCGATGT	60.142	41.667	0.00	0.00	35.46	3.06
1225	1267	4.031426	GCGTCAACGGTTGTTAGATTAGAG	59.969	45.833	19.47	3.18	36.28	2.43
1268	1313	0.617413	CACCTCTGCAGACCTGGATT	59.383	55.000	23.41	3.12	0.00	3.01
1430	1475	7.649306	AGATTTCACACTGCTACAATTTCAAAC	59.351	33.333	0.00	0.00	0.00	2.93
1440	1490	2.736721	TCGCAAGATTTCACACTGCTAC	59.263	45.455	0.00	0.00	45.01	3.58
1649	1699	0.249657	GCGGCCTCTCATCTTTCGAT	60.250	55.000	0.00	0.00	0.00	3.59
2078	2140	8.748582	GTGTGAAAACAATATATACGACGATGA	58.251	33.333	0.00	0.00	0.00	2.92
2174	2241	9.717892	GAAAAGAAACAGTGTTAAAAGGAGTAG	57.282	33.333	9.37	0.00	0.00	2.57
2329	2404	2.572290	AGCAACTTACCGAGCAAAAGT	58.428	42.857	0.00	0.00	35.01	2.66
2365	2444	5.013079	TCTCCTTCAGGAATACACAACACAT	59.987	40.000	0.00	0.00	44.91	3.21
2483	2593	8.277197	TGCTCCTAATTCCAACTAGTACTACTA	58.723	37.037	0.00	0.00	0.00	1.82
2488	2598	5.051153	GCTGCTCCTAATTCCAACTAGTAC	58.949	45.833	0.00	0.00	0.00	2.73
2514	2624	1.980844	GAAATTGACTCGCACGTACGA	59.019	47.619	24.41	10.95	40.36	3.43
2651	2761	3.762288	GGGAGTAATTCAAACCCACCTTC	59.238	47.826	0.00	0.00	40.20	3.46
2658	2768	3.404899	TGTCACGGGAGTAATTCAAACC	58.595	45.455	0.00	0.00	44.67	3.27
2729	2839	6.087820	CGTCTTTCTTTAGTTAGTTCCACTCG	59.912	42.308	0.00	0.00	0.00	4.18
2730	2840	6.128876	GCGTCTTTCTTTAGTTAGTTCCACTC	60.129	42.308	0.00	0.00	0.00	3.51
2731	2841	5.695363	GCGTCTTTCTTTAGTTAGTTCCACT	59.305	40.000	0.00	0.00	0.00	4.00
2732	2842	5.695363	AGCGTCTTTCTTTAGTTAGTTCCAC	59.305	40.000	0.00	0.00	0.00	4.02
2733	2843	5.850614	AGCGTCTTTCTTTAGTTAGTTCCA	58.149	37.500	0.00	0.00	0.00	3.53
2734	2844	7.148672	GGTTAGCGTCTTTCTTTAGTTAGTTCC	60.149	40.741	0.00	0.00	0.00	3.62
2737	2847	6.644181	GTGGTTAGCGTCTTTCTTTAGTTAGT	59.356	38.462	0.00	0.00	0.00	2.24
2738	2848	6.090493	GGTGGTTAGCGTCTTTCTTTAGTTAG	59.910	42.308	0.00	0.00	0.00	2.34
2739	2849	5.928264	GGTGGTTAGCGTCTTTCTTTAGTTA	59.072	40.000	0.00	0.00	0.00	2.24
2961	3096	2.357034	ATGTCTGCGACGGCGTTT	60.357	55.556	16.19	0.00	44.10	3.60
2965	3100	2.202932	ATGGATGTCTGCGACGGC	60.203	61.111	0.00	0.00	34.95	5.68
2966	3101	1.592669	GGATGGATGTCTGCGACGG	60.593	63.158	0.00	0.00	34.95	4.79
2968	3103	1.506493	GATGGATGGATGTCTGCGAC	58.494	55.000	0.00	2.32	0.00	5.19
2969	3104	0.032540	CGATGGATGGATGTCTGCGA	59.967	55.000	0.00	0.00	0.00	5.10
2970	3105	0.249615	ACGATGGATGGATGTCTGCG	60.250	55.000	0.00	0.00	0.00	5.18
2971	3106	1.224075	CACGATGGATGGATGTCTGC	58.776	55.000	0.00	0.00	0.00	4.26
2974	3109	1.869767	GAAGCACGATGGATGGATGTC	59.130	52.381	0.00	0.00	0.00	3.06
2975	3110	1.210234	TGAAGCACGATGGATGGATGT	59.790	47.619	0.00	0.00	0.00	3.06
2976	3111	1.957668	TGAAGCACGATGGATGGATG	58.042	50.000	0.00	0.00	0.00	3.51
2977	3112	2.715749	TTGAAGCACGATGGATGGAT	57.284	45.000	0.00	0.00	0.00	3.41
2978	3113	2.488204	TTTGAAGCACGATGGATGGA	57.512	45.000	0.00	0.00	0.00	3.41
2979	3114	2.033801	GGATTTGAAGCACGATGGATGG	59.966	50.000	0.00	0.00	0.00	3.51
2980	3115	2.684374	TGGATTTGAAGCACGATGGATG	59.316	45.455	0.00	0.00	0.00	3.51
2981	3116	3.003394	TGGATTTGAAGCACGATGGAT	57.997	42.857	0.00	0.00	0.00	3.41
2982	3117	2.488204	TGGATTTGAAGCACGATGGA	57.512	45.000	0.00	0.00	0.00	3.41
2983	3118	3.379372	AGATTGGATTTGAAGCACGATGG	59.621	43.478	0.00	0.00	0.00	3.51
3004	3139	2.806945	TTACAGCCCCTGAAATCCAG	57.193	50.000	0.00	0.00	42.55	3.86
3012	3147	1.826385	CAGACCTTTTACAGCCCCTG	58.174	55.000	0.00	0.00	37.52	4.45
3013	3148	0.038310	GCAGACCTTTTACAGCCCCT	59.962	55.000	0.00	0.00	0.00	4.79
3026	3163	1.971695	CCCTCCGTTTTGGCAGACC	60.972	63.158	0.00	0.00	37.80	3.85
3028	3165	2.434331	CCCCTCCGTTTTGGCAGA	59.566	61.111	0.00	0.00	37.80	4.26
3029	3166	3.373565	GCCCCTCCGTTTTGGCAG	61.374	66.667	0.00	0.00	43.46	4.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.