AutoCloner

Multiple sequence alignment - TraesCS5B01G343000

Loading Multiple Alignment...

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	TraesCS5B01G343000	chr5B	100.000	2838	0	0	1	2838	527050817	527047980	0.000000e+00	5241.0
1	TraesCS5B01G343000	chr5B	79.682	1196	171	33	661	1822	528524299	528525456	0.000000e+00	797.0
2	TraesCS5B01G343000	chr5B	77.450	1357	203	54	504	1822	527061369	527060078	0.000000e+00	715.0
3	TraesCS5B01G343000	chr5B	93.196	485	26	5	2354	2838	330742059	330742536	0.000000e+00	706.0
4	TraesCS5B01G343000	chr5B	92.784	485	26	6	2354	2838	330740133	330740608	0.000000e+00	693.0
5	TraesCS5B01G343000	chr5B	85.227	528	54	11	958	1467	528537423	528537944	3.240000e-144	521.0
6	TraesCS5B01G343000	chr5B	77.407	810	140	35	812	1606	527607527	527608308	2.590000e-120	442.0
7	TraesCS5B01G343000	chr5B	76.098	820	137	36	808	1606	527786413	527787194	9.600000e-100	374.0
8	TraesCS5B01G343000	chr5B	75.315	794	131	33	831	1606	527772627	527773373	1.270000e-83	320.0
9	TraesCS5B01G343000	chr5B	78.589	411	57	18	527	926	527059472	527059082	2.820000e-60	243.0
10	TraesCS5B01G343000	chr5D	96.520	1868	44	7	1	1859	434394767	434392912	0.000000e+00	3070.0
11	TraesCS5B01G343000	chr5D	96.393	1109	30	3	1	1101	434328964	434330070	0.000000e+00	1818.0
12	TraesCS5B01G343000	chr5D	81.210	1240	173	31	474	1680	434403485	434402273	0.000000e+00	944.0
13	TraesCS5B01G343000	chr5D	82.752	1119	131	28	529	1620	434322593	434323676	0.000000e+00	941.0
14	TraesCS5B01G343000	chr5D	92.387	486	32	3	2354	2838	526247287	526247768	0.000000e+00	688.0
15	TraesCS5B01G343000	chr5D	89.796	392	11	4	1858	2224	434392704	434392317	2.560000e-130	475.0
16	TraesCS5B01G343000	chr5D	84.461	399	47	8	723	1119	434392171	434391786	2.060000e-101	379.0
17	TraesCS5B01G343000	chr5D	75.092	815	134	41	812	1606	434655820	434655055	1.640000e-82	316.0
18	TraesCS5B01G343000	chr5D	82.278	158	22	3	1212	1363	434679147	434678990	6.380000e-27	132.0
19	TraesCS5B01G343000	chr5D	84.158	101	16	0	1342	1442	434603921	434604021	6.470000e-17	99.0
20	TraesCS5B01G343000	chr5A	96.158	1874	47	10	1	1859	548231852	548229989	0.000000e+00	3038.0
21	TraesCS5B01G343000	chr5A	81.982	888	125	15	658	1525	549153398	549154270	0.000000e+00	721.0
22	TraesCS5B01G343000	chr5A	93.830	470	15	4	1858	2319	548229781	548229318	0.000000e+00	695.0
23	TraesCS5B01G343000	chr5A	83.734	707	85	17	908	1604	548240494	548239808	2.380000e-180	641.0
24	TraesCS5B01G343000	chr5A	83.541	401	49	9	723	1119	548229158	548228771	2.690000e-95	359.0
25	TraesCS5B01G343000	chr5A	97.436	39	1	0	2317	2355	455085168	455085206	1.820000e-07	67.6
26	TraesCS5B01G343000	chr2D	94.021	485	22	5	2354	2838	317865929	317866406	0.000000e+00	728.0
27	TraesCS5B01G343000	chr2D	92.418	488	26	3	2354	2838	441767479	441767958	0.000000e+00	686.0
28	TraesCS5B01G343000	chr2D	93.023	43	2	1	2313	2355	317865823	317865864	8.490000e-06	62.1
29	TraesCS5B01G343000	chr1D	93.429	487	26	5	2354	2838	98832614	98832132	0.000000e+00	717.0
30	TraesCS5B01G343000	chr1D	100.000	36	0	0	2320	2355	199330629	199330664	1.820000e-07	67.6
31	TraesCS5B01G343000	chr1D	95.349	43	1	1	2314	2355	408633468	408633510	1.820000e-07	67.6
32	TraesCS5B01G343000	chr4B	92.577	485	34	1	2354	2838	5969135	5968653	0.000000e+00	695.0
33	TraesCS5B01G343000	chr4B	100.000	38	0	0	2319	2356	651999824	651999861	1.410000e-08	71.3
34	TraesCS5B01G343000	chr7A	92.577	485	31	4	2354	2838	555463038	555463517	0.000000e+00	691.0
35	TraesCS5B01G343000	chr6B	92.593	486	29	5	2354	2838	439356189	439355710	0.000000e+00	691.0
36	TraesCS5B01G343000	chr7D	91.807	476	30	4	2363	2838	595074268	595074734	0.000000e+00	654.0
37	TraesCS5B01G343000	chr7D	97.222	36	1	0	2319	2354	470970115	470970080	8.490000e-06	62.1
38	TraesCS5B01G343000	chr2B	88.889	81	6	3	219	296	23289006	23288926	2.330000e-16	97.1
39	TraesCS5B01G343000	chr4A	100.000	41	0	0	2315	2355	642031648	642031608	3.030000e-10	76.8
40	TraesCS5B01G343000	chr3D	100.000	38	0	0	2319	2356	146277985	146278022	1.410000e-08	71.3

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	TraesCS5B01G343000	chr5B	527047980	527050817	2837	True	5241.00	5241	100.000000	1	2838	1	chr5B.!!$R1	2837
1	TraesCS5B01G343000	chr5B	528524299	528525456	1157	False	797.00	797	79.682000	661	1822	1	chr5B.!!$F4	1161
2	TraesCS5B01G343000	chr5B	330740133	330742536	2403	False	699.50	706	92.990000	2354	2838	2	chr5B.!!$F6	484
3	TraesCS5B01G343000	chr5B	528537423	528537944	521	False	521.00	521	85.227000	958	1467	1	chr5B.!!$F5	509
4	TraesCS5B01G343000	chr5B	527059082	527061369	2287	True	479.00	715	78.019500	504	1822	2	chr5B.!!$R2	1318
5	TraesCS5B01G343000	chr5B	527607527	527608308	781	False	442.00	442	77.407000	812	1606	1	chr5B.!!$F1	794
6	TraesCS5B01G343000	chr5B	527786413	527787194	781	False	374.00	374	76.098000	808	1606	1	chr5B.!!$F3	798
7	TraesCS5B01G343000	chr5B	527772627	527773373	746	False	320.00	320	75.315000	831	1606	1	chr5B.!!$F2	775
8	TraesCS5B01G343000	chr5D	434328964	434330070	1106	False	1818.00	1818	96.393000	1	1101	1	chr5D.!!$F2	1100
9	TraesCS5B01G343000	chr5D	434391786	434394767	2981	True	1308.00	3070	90.259000	1	2224	3	chr5D.!!$R4	2223
10	TraesCS5B01G343000	chr5D	434402273	434403485	1212	True	944.00	944	81.210000	474	1680	1	chr5D.!!$R1	1206
11	TraesCS5B01G343000	chr5D	434322593	434323676	1083	False	941.00	941	82.752000	529	1620	1	chr5D.!!$F1	1091
12	TraesCS5B01G343000	chr5D	434655055	434655820	765	True	316.00	316	75.092000	812	1606	1	chr5D.!!$R2	794
13	TraesCS5B01G343000	chr5A	548228771	548231852	3081	True	1364.00	3038	91.176333	1	2319	3	chr5A.!!$R2	2318
14	TraesCS5B01G343000	chr5A	549153398	549154270	872	False	721.00	721	81.982000	658	1525	1	chr5A.!!$F2	867
15	TraesCS5B01G343000	chr5A	548239808	548240494	686	True	641.00	641	83.734000	908	1604	1	chr5A.!!$R1	696
16	TraesCS5B01G343000	chr2D	317865823	317866406	583	False	395.05	728	93.522000	2313	2838	2	chr2D.!!$F2	525

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
963	1039	0.905357	CCGTCAAGATGTCCTTCCCT	59.095	55.0	0.0	0.0	31.42	4.2	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2403	4708	0.18135	CCCTAAGGAAGCCGAGCAAT	59.819	55.0	0.0	0.0	33.47	3.56	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
295	304	8.992349	TCCTTTTCAGGATCATCTGTATTTAGA	58.008	33.333	0.00	0.00	45.20	2.10
351	360	6.264970	TGACTGGAAACATCACATTGAAATCA	59.735	34.615	0.00	0.00	41.51	2.57
433	442	6.538742	TCAGCTTGAAATTAGTATACAGTGGC	59.461	38.462	5.50	0.00	0.00	5.01
443	452	7.907841	TTAGTATACAGTGGCCTGATTCTAA	57.092	36.000	3.32	1.76	41.50	2.10
456	465	5.486526	CCTGATTCTAACCATATGCTCCTC	58.513	45.833	0.00	0.00	0.00	3.71
630	643	2.573462	AGTATCTGCCAGGAGAAAGCAA	59.427	45.455	0.00	0.00	35.79	3.91
648	664	4.877282	AGCAAAGAGATAGCCTAATCGAC	58.123	43.478	0.00	0.00	0.00	4.20
782	820	4.154195	GGTATGGCATCCACGAATGATAAC	59.846	45.833	1.65	0.00	35.80	1.89
859	902	1.455383	GGCCCCACCGCAATCTAATG	61.455	60.000	0.00	0.00	0.00	1.90
903	956	2.760378	ATGCACCGATCCCATGGCT	61.760	57.895	6.09	0.00	0.00	4.75
963	1039	0.905357	CCGTCAAGATGTCCTTCCCT	59.095	55.000	0.00	0.00	31.42	4.20
1060	1155	4.637534	GCAACATCCATATCACACACTTCT	59.362	41.667	0.00	0.00	0.00	2.85
1061	1156	5.124457	GCAACATCCATATCACACACTTCTT	59.876	40.000	0.00	0.00	0.00	2.52
1062	1157	6.676456	GCAACATCCATATCACACACTTCTTC	60.676	42.308	0.00	0.00	0.00	2.87
1322	1437	5.280499	TGAGGATGTCTCAGGAGGAATTTA	58.720	41.667	0.00	0.00	46.71	1.40
1414	1547	3.591254	GAGAAACGCCTCTGCCGGT	62.591	63.158	1.90	0.00	0.00	5.28
1505	1638	5.221224	TGTTGGAGCTAGTCAACAAATTTGG	60.221	40.000	21.74	5.67	46.69	3.28
1562	1695	3.070015	CCCTGATGTTGCCTTCTGTTTTT	59.930	43.478	0.00	0.00	0.00	1.94
1792	1939	5.620738	TCATGCTACTGCTAGGAGAATTT	57.379	39.130	19.21	0.00	40.48	1.82
1876	2306	9.747898	AATTGTTAAGGATTTGGTACATGTCTA	57.252	29.630	0.00	0.00	39.30	2.59
1964	2394	9.167311	CTAAGGAATAGCTTTCACATGTTAGTT	57.833	33.333	0.00	0.00	0.00	2.24
1977	2422	7.101054	TCACATGTTAGTTTGGTAGGTATGAC	58.899	38.462	0.00	0.00	0.00	3.06
1978	2423	6.876789	CACATGTTAGTTTGGTAGGTATGACA	59.123	38.462	0.00	0.00	0.00	3.58
1979	2424	6.877322	ACATGTTAGTTTGGTAGGTATGACAC	59.123	38.462	0.00	0.00	0.00	3.67
1980	2425	6.422344	TGTTAGTTTGGTAGGTATGACACA	57.578	37.500	0.00	0.00	0.00	3.72
2032	2656	7.339976	TCCATGTGAGATATGAAATGCAAGAAA	59.660	33.333	0.00	0.00	0.00	2.52
2109	2743	4.383649	CACAAGCTTTCAAATGGATGTTCG	59.616	41.667	0.00	0.00	0.00	3.95
2116	2750	6.348540	GCTTTCAAATGGATGTTCGTAACTCT	60.349	38.462	0.00	0.00	0.00	3.24
2141	2799	6.240894	TGTTAGAGATCCATGAAGCACTTTT	58.759	36.000	0.00	0.00	0.00	2.27
2245	2904	3.501828	CGATCACAAACAGAAATGGACCA	59.498	43.478	0.00	0.00	0.00	4.02
2428	4741	1.910580	CGGCTTCCTTAGGGAGCCAA	61.911	60.000	40.43	10.01	46.60	4.52
2562	5007	1.203440	ACCCCTACAACCTGAGACCAT	60.203	52.381	0.00	0.00	0.00	3.55
2568	5013	0.911769	CAACCTGAGACCATGCCCTA	59.088	55.000	0.00	0.00	0.00	3.53

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
196	205	5.010012	CCTTTTGGCTCTGAACTTGTATGTT	59.990	40.000	0.00	0.00	0.00	2.71
295	304	2.733956	TCTCAGGCACAACTTTTTGGT	58.266	42.857	0.00	0.00	37.00	3.67
351	360	4.264487	TGGGGCTCCATATTCATGCATAAT	60.264	41.667	0.00	2.92	38.32	1.28
365	374	1.152030	AGTTGACTCTGGGGCTCCA	60.152	57.895	4.49	4.49	41.58	3.86
369	378	0.108585	TGTTGAGTTGACTCTGGGGC	59.891	55.000	12.00	0.19	43.25	5.80
433	442	5.248020	AGAGGAGCATATGGTTAGAATCAGG	59.752	44.000	9.14	0.00	0.00	3.86
443	452	2.795291	TGGGTAGAGGAGCATATGGT	57.205	50.000	7.23	7.23	0.00	3.55
456	465	6.659242	TCTTGCCTTCTATTTCTTTTGGGTAG	59.341	38.462	0.00	0.00	0.00	3.18
520	529	2.680312	TGCTTGGTCTAGCAGATCAC	57.320	50.000	3.18	0.00	45.72	3.06
630	643	3.829601	CCTGGTCGATTAGGCTATCTCTT	59.170	47.826	5.16	0.00	0.00	2.85
648	664	0.036306	ACAGTTTCGGTAAGCCCTGG	59.964	55.000	0.00	0.00	0.00	4.45
715	737	3.704566	ACATGTCGAGAACAGGGCTATTA	59.295	43.478	0.00	0.00	43.93	0.98
782	820	1.135402	GTTAGGCATTGGTCCGCTTTG	60.135	52.381	0.00	0.00	0.00	2.77
859	902	3.181541	GCGTTGCAACATGATTAGTTTGC	60.182	43.478	28.01	14.83	0.00	3.68
903	956	1.760029	GAAAAGTTGGCAGGGGACAAA	59.240	47.619	0.00	0.00	45.51	2.83
963	1039	3.066621	CGCTTGCTGAATTTATAGGCCAA	59.933	43.478	5.01	0.00	0.00	4.52
1060	1155	7.335422	GGCTCTCTATCTTTGTGAGAATTTGAA	59.665	37.037	0.00	0.00	38.06	2.69
1061	1156	6.820656	GGCTCTCTATCTTTGTGAGAATTTGA	59.179	38.462	0.00	0.00	38.06	2.69
1062	1157	6.596888	TGGCTCTCTATCTTTGTGAGAATTTG	59.403	38.462	0.00	0.00	38.06	2.32
1414	1547	2.416027	GCTCAGCAATGTACTCTCGACA	60.416	50.000	0.00	0.00	0.00	4.35
1454	1587	0.105964	TCATATGGCCGGTGTAGTGC	59.894	55.000	1.90	0.00	0.00	4.40
1505	1638	8.256611	TCATATTCTTCAGAAGCTACAAACAC	57.743	34.615	5.15	0.00	37.48	3.32
1567	1700	5.830991	ACACTATCCAGGCAAACTACAAAAA	59.169	36.000	0.00	0.00	0.00	1.94
1568	1701	5.381757	ACACTATCCAGGCAAACTACAAAA	58.618	37.500	0.00	0.00	0.00	2.44
1774	1921	3.535561	TGCAAATTCTCCTAGCAGTAGC	58.464	45.455	0.00	0.00	42.56	3.58
1777	1924	4.292186	TCTTGCAAATTCTCCTAGCAGT	57.708	40.909	0.00	0.00	36.47	4.40
1792	1939	9.162764	GATAAGGTTGTATAGAAACTTCTTGCA	57.837	33.333	15.62	0.00	38.70	4.08
1952	2382	7.101054	GTCATACCTACCAAACTAACATGTGA	58.899	38.462	0.00	0.00	0.00	3.58
1964	2394	3.007506	CCAGTGTGTGTCATACCTACCAA	59.992	47.826	0.00	0.00	0.00	3.67
1977	2422	3.541632	ACTAGAACCAAACCAGTGTGTG	58.458	45.455	0.00	0.00	0.00	3.82
1978	2423	3.199071	TGACTAGAACCAAACCAGTGTGT	59.801	43.478	0.00	0.00	0.00	3.72
1979	2424	3.804036	TGACTAGAACCAAACCAGTGTG	58.196	45.455	0.00	0.00	0.00	3.82
1980	2425	4.141482	ACATGACTAGAACCAAACCAGTGT	60.141	41.667	0.00	0.00	0.00	3.55
2032	2656	6.855836	CAGCATATTACATGGTGACTGTTTT	58.144	36.000	10.15	0.00	46.89	2.43
2109	2743	7.223777	GCTTCATGGATCTCTAACAAGAGTTAC	59.776	40.741	2.56	0.00	39.15	2.50
2116	2750	5.426689	AGTGCTTCATGGATCTCTAACAA	57.573	39.130	0.00	0.00	0.00	2.83
2141	2799	1.306141	AGTGGCCCCTGAGATCGAA	60.306	57.895	0.00	0.00	0.00	3.71
2303	2962	7.435068	GTCATAACACATACTGACCTGTTTT	57.565	36.000	0.00	0.00	33.51	2.43
2403	4708	0.181350	CCCTAAGGAAGCCGAGCAAT	59.819	55.000	0.00	0.00	33.47	3.56
2428	4741	1.041437	GCGGCTAGGGTTATGTCTCT	58.959	55.000	0.00	0.00	0.00	3.10
2451	4881	2.468670	GCGAGAGAGAGAGAGCGCA	61.469	63.158	11.47	0.00	43.45	6.09
2452	4882	2.327940	GCGAGAGAGAGAGAGCGC	59.672	66.667	0.00	0.00	37.60	5.92
2454	4884	2.327940	GCGCGAGAGAGAGAGAGC	59.672	66.667	12.10	0.00	0.00	4.09
2455	4885	2.625906	CGCGCGAGAGAGAGAGAG	59.374	66.667	28.94	0.00	31.43	3.20
2456	4886	3.568743	GCGCGCGAGAGAGAGAGA	61.569	66.667	37.18	0.00	31.43	3.10
2568	5013	2.378378	GTAGGAACCGGATCCCTACT	57.622	55.000	25.99	11.04	45.47	2.57
2636	5081	3.182996	AGCGGAAGGGTTGGGGTT	61.183	61.111	0.00	0.00	0.00	4.11
2642	5087	4.699522	GTCGGCAGCGGAAGGGTT	62.700	66.667	3.86	0.00	0.00	4.11
2737	5182	0.613260	CTCCGGGGTGAAGACAATGA	59.387	55.000	0.00	0.00	0.00	2.57
2741	5186	1.609501	CTCCTCCGGGGTGAAGACA	60.610	63.158	0.00	0.00	36.25	3.41
2768	5213	2.143419	GGTGAGATCCCGGATGGCT	61.143	63.158	4.08	0.00	0.00	4.75
2792	5237	1.248785	ACGTGTAGATGCCCGTGACT	61.249	55.000	0.00	0.00	31.43	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.