AutoCloner

Multiple sequence alignment - TraesCS5A01G144800

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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	TraesCS5A01G144800	chr5A	100.000	3274	0	0	1	3274	321000369	321003642	0.000000e+00	6047.0
1	TraesCS5A01G144800	chr5A	89.305	187	17	3	1072	1257	321019929	321020113	7.060000e-57	231.0
2	TraesCS5A01G144800	chr5D	92.141	2672	104	32	671	3274	233749319	233746686	0.000000e+00	3674.0
3	TraesCS5A01G144800	chr5D	88.542	192	18	4	1068	1257	233742474	233742285	2.540000e-56	230.0
4	TraesCS5A01G144800	chr5D	95.775	71	3	0	545	615	233751282	233751212	7.420000e-22	115.0
5	TraesCS5A01G144800	chr5D	95.775	71	2	1	604	674	233751196	233751127	2.670000e-21	113.0
6	TraesCS5A01G144800	chr5B	92.184	1497	51	28	1642	3086	271110767	271112249	0.000000e+00	2056.0
7	TraesCS5A01G144800	chr5B	92.403	1053	44	17	604	1641	271109706	271110737	0.000000e+00	1469.0
8	TraesCS5A01G144800	chr5B	89.062	192	17	4	1068	1257	271140985	271141174	5.460000e-58	235.0
9	TraesCS5A01G144800	chr5B	92.174	115	4	1	3083	3192	271112408	271112522	1.220000e-34	158.0
10	TraesCS5A01G144800	chr5B	91.358	81	6	1	535	615	271109611	271109690	3.450000e-20	110.0
11	TraesCS5A01G144800	chr7B	99.448	543	3	0	1	543	74100631	74100089	0.000000e+00	987.0
12	TraesCS5A01G144800	chr7B	99.448	543	3	0	1	543	77430765	77430223	0.000000e+00	987.0
13	TraesCS5A01G144800	chr7B	97.606	543	4	1	1	543	501963799	501964332	0.000000e+00	922.0
14	TraesCS5A01G144800	chr7B	87.073	410	21	9	1532	1941	116071213	116071590	5.020000e-118	435.0
15	TraesCS5A01G144800	chr4A	97.938	485	7	1	3	484	676556157	676556641	0.000000e+00	837.0
16	TraesCS5A01G144800	chr4A	100.000	39	0	0	505	543	676556642	676556680	4.530000e-09	73.1
17	TraesCS5A01G144800	chr1B	99.561	456	2	0	1	456	65603373	65602918	0.000000e+00	832.0
18	TraesCS5A01G144800	chr1B	96.875	96	2	1	448	542	65602828	65602923	3.380000e-35	159.0
19	TraesCS5A01G144800	chr4D	87.409	413	20	6	1532	1944	361163695	361164075	2.320000e-121	446.0
20	TraesCS5A01G144800	chr4D	86.199	413	25	6	1532	1944	361190124	361190504	5.050000e-113	418.0
21	TraesCS5A01G144800	chr6A	86.585	410	23	6	1532	1941	29402738	29403115	1.090000e-114	424.0
22	TraesCS5A01G144800	chr6A	86.098	410	25	3	1532	1941	612718219	612718596	2.350000e-111	412.0
23	TraesCS5A01G144800	chr3B	86.441	413	24	12	1532	1944	711740033	711739653	1.090000e-114	424.0
24	TraesCS5A01G144800	chr3B	83.108	148	12	5	2548	2695	49827901	49827767	4.440000e-24	122.0
25	TraesCS5A01G144800	chr6B	86.098	410	25	13	1532	1941	49502427	49502804	2.350000e-111	412.0
26	TraesCS5A01G144800	chr7D	85.956	413	25	10	1532	1944	592270025	592269646	8.450000e-111	411.0
27	TraesCS5A01G144800	chr2B	81.132	424	48	14	2275	2695	569501760	569501366	8.820000e-81	311.0
28	TraesCS5A01G144800	chr2B	83.438	320	40	8	2280	2595	30523047	30522737	5.350000e-73	285.0
29	TraesCS5A01G144800	chr2B	89.474	57	6	0	2639	2695	30522719	30522663	4.530000e-09	73.1

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	TraesCS5A01G144800	chr5A	321000369	321003642	3273	False	6047.000000	6047	100.000000	1	3274	1	chr5A.!!$F1	3273
1	TraesCS5A01G144800	chr5D	233746686	233751282	4596	True	1300.666667	3674	94.563667	545	3274	3	chr5D.!!$R2	2729
2	TraesCS5A01G144800	chr5B	271109611	271112522	2911	False	948.250000	2056	92.029750	535	3192	4	chr5B.!!$F2	2657
3	TraesCS5A01G144800	chr7B	74100089	74100631	542	True	987.000000	987	99.448000	1	543	1	chr7B.!!$R1	542
4	TraesCS5A01G144800	chr7B	77430223	77430765	542	True	987.000000	987	99.448000	1	543	1	chr7B.!!$R2	542
5	TraesCS5A01G144800	chr7B	501963799	501964332	533	False	922.000000	922	97.606000	1	543	1	chr7B.!!$F2	542
6	TraesCS5A01G144800	chr4A	676556157	676556680	523	False	455.050000	837	98.969000	3	543	2	chr4A.!!$F1	540

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
543	547	1.061566	GTTAGGAAAAATCCGCGTCCG	59.938	52.381	4.92	0.00	35.19	4.79	F
1333	3193	0.605319	TCAGCGCTGGGGTTTTAGTG	60.605	55.000	35.36	8.09	0.00	2.74	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1430	3290	0.676782	AACAACTAGCCGGTGGATGC	60.677	55.0	1.9	0.0	0.00	3.91	R
3178	5288	0.320247	AGGAAGCACGCAGTCAGAAG	60.320	55.0	0.0	0.0	41.61	2.85	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
543	547	1.061566	GTTAGGAAAAATCCGCGTCCG	59.938	52.381	4.92	0.00	35.19	4.79
569	573	1.560923	CGTGTCAGATTTAGGGCTCG	58.439	55.000	0.00	0.00	0.00	5.03
703	2544	1.338973	GATAAGGTGCGATCCACGGTA	59.661	52.381	7.85	4.20	45.62	4.02
723	2564	6.986817	ACGGTAGATCGAAAATCATTCTCATT	59.013	34.615	0.00	0.00	0.00	2.57
724	2565	7.169982	ACGGTAGATCGAAAATCATTCTCATTC	59.830	37.037	0.00	0.00	0.00	2.67
725	2566	7.383572	CGGTAGATCGAAAATCATTCTCATTCT	59.616	37.037	0.00	0.00	0.00	2.40
726	2567	8.707839	GGTAGATCGAAAATCATTCTCATTCTC	58.292	37.037	0.00	0.00	0.00	2.87
727	2568	9.254133	GTAGATCGAAAATCATTCTCATTCTCA	57.746	33.333	0.00	0.00	0.00	3.27
728	2569	8.905660	AGATCGAAAATCATTCTCATTCTCAT	57.094	30.769	0.00	0.00	0.00	2.90
729	2570	8.991026	AGATCGAAAATCATTCTCATTCTCATC	58.009	33.333	0.00	0.00	0.00	2.92
730	2571	8.672823	ATCGAAAATCATTCTCATTCTCATCA	57.327	30.769	0.00	0.00	0.00	3.07
731	2572	8.139521	TCGAAAATCATTCTCATTCTCATCAG	57.860	34.615	0.00	0.00	0.00	2.90
732	2573	7.767659	TCGAAAATCATTCTCATTCTCATCAGT	59.232	33.333	0.00	0.00	0.00	3.41
733	2574	7.851472	CGAAAATCATTCTCATTCTCATCAGTG	59.149	37.037	0.00	0.00	0.00	3.66
734	2575	6.621316	AATCATTCTCATTCTCATCAGTGC	57.379	37.500	0.00	0.00	0.00	4.40
735	2576	5.093849	TCATTCTCATTCTCATCAGTGCA	57.906	39.130	0.00	0.00	0.00	4.57
755	2596	5.006746	GTGCATACATTCTTAGAAGGTTCCG	59.993	44.000	17.30	7.76	0.00	4.30
830	2674	1.268352	GCGCCCAACACACTCATAAAA	59.732	47.619	0.00	0.00	0.00	1.52
837	2681	1.349688	ACACACTCATAAAAGCGGGGA	59.650	47.619	0.00	0.00	0.00	4.81
838	2682	2.026262	ACACACTCATAAAAGCGGGGAT	60.026	45.455	0.00	0.00	0.00	3.85
872	2717	1.911269	GCCCCACCGAAAACCCAAT	60.911	57.895	0.00	0.00	0.00	3.16
875	2720	1.080839	CCACCGAAAACCCAATGCG	60.081	57.895	0.00	0.00	0.00	4.73
877	2722	2.126110	CCGAAAACCCAATGCGGC	60.126	61.111	0.00	0.00	35.17	6.53
962	2807	3.787785	CCCAAATATAAAACCAACGGCC	58.212	45.455	0.00	0.00	0.00	6.13
963	2808	3.440228	CCAAATATAAAACCAACGGCCG	58.560	45.455	26.86	26.86	0.00	6.13
1282	3142	4.632688	GGTTCTTCCCATTCGACGAATTTA	59.367	41.667	20.12	6.29	28.87	1.40
1293	3153	6.752335	TTCGACGAATTTAAAAGAGACGAA	57.248	33.333	6.10	16.36	34.58	3.85
1333	3193	0.605319	TCAGCGCTGGGGTTTTAGTG	60.605	55.000	35.36	8.09	0.00	2.74
1430	3290	2.734723	CACGAGGTGCCTGTGACG	60.735	66.667	12.34	5.55	35.66	4.35
1451	3311	1.737793	CATCCACCGGCTAGTTGTTTC	59.262	52.381	0.00	0.00	0.00	2.78
1514	3374	9.823098	CACATCTGAAAATGAGTAGAAGAAAAG	57.177	33.333	0.00	0.00	0.00	2.27
1526	3386	7.043961	AGTAGAAGAAAAGAAAAGGCCAAAG	57.956	36.000	5.01	0.00	0.00	2.77
1528	3388	5.907207	AGAAGAAAAGAAAAGGCCAAAGTC	58.093	37.500	5.01	0.00	0.00	3.01
1623	3483	4.446371	ACTTTGTATCCTATCTGCACTGC	58.554	43.478	0.00	0.00	0.00	4.40
1654	3543	5.180492	TGCCACTTTCTCAGTAATTTTACCG	59.820	40.000	0.00	0.00	32.76	4.02
1656	3545	6.093633	GCCACTTTCTCAGTAATTTTACCGAT	59.906	38.462	0.00	0.00	32.76	4.18
1701	3595	9.737844	ATAAAACAAGAATATGGGTTTGCATTT	57.262	25.926	0.00	0.00	34.03	2.32
1702	3596	7.437793	AAACAAGAATATGGGTTTGCATTTG	57.562	32.000	0.00	0.00	32.65	2.32
1703	3597	5.490159	ACAAGAATATGGGTTTGCATTTGG	58.510	37.500	0.00	0.00	0.00	3.28
1704	3598	5.012975	ACAAGAATATGGGTTTGCATTTGGT	59.987	36.000	0.00	0.00	0.00	3.67
1705	3599	6.212388	ACAAGAATATGGGTTTGCATTTGGTA	59.788	34.615	0.00	0.00	0.00	3.25
1706	3600	6.469782	AGAATATGGGTTTGCATTTGGTAG	57.530	37.500	0.00	0.00	0.00	3.18
1707	3601	5.363580	AGAATATGGGTTTGCATTTGGTAGG	59.636	40.000	0.00	0.00	0.00	3.18
1794	3688	2.965831	AGTAACAGCTGACAGAGTTCCA	59.034	45.455	23.35	0.04	0.00	3.53
1996	3908	0.107361	TCAGCATCAGACCATGGCAG	60.107	55.000	13.04	1.45	0.00	4.85
2335	4247	0.182775	ACGGGGGAAATGTAGATGCC	59.817	55.000	0.00	0.00	0.00	4.40
2340	4252	3.384789	GGGGGAAATGTAGATGCCTTTTC	59.615	47.826	0.00	0.00	0.00	2.29
2343	4255	5.187772	GGGGAAATGTAGATGCCTTTTCTTT	59.812	40.000	0.00	0.00	0.00	2.52
2344	4256	6.333416	GGGAAATGTAGATGCCTTTTCTTTC	58.667	40.000	0.00	0.00	0.00	2.62
2424	4336	2.872245	TGTTCAGTTAGTTGCAGCTGTC	59.128	45.455	16.64	8.39	0.00	3.51
2546	4459	1.393539	CGGACTTGAAATGCCTGTACG	59.606	52.381	0.00	0.00	0.00	3.67
2680	4593	0.804989	GTTTGTCGAATCCCAGCAGG	59.195	55.000	0.00	0.00	0.00	4.85
2694	4607	1.376553	GCAGGGAAGCCTGTGTCTC	60.377	63.158	0.00	0.00	39.75	3.36
2759	4672	2.044352	TCTGCGATCCCCGTCAGA	60.044	61.111	0.00	0.00	43.60	3.27
2807	4720	1.541147	TGCAGAAAGGGAGATTTTGCG	59.459	47.619	0.00	0.00	33.11	4.85
2811	4724	4.229876	CAGAAAGGGAGATTTTGCGTTTC	58.770	43.478	5.97	5.97	46.17	2.78
2829	4742	1.707106	TCGGCGTAATGGGGATCTTA	58.293	50.000	6.85	0.00	0.00	2.10
2910	4823	5.107453	CGTAAAGGTTAGCTGTCTTGTCTTG	60.107	44.000	0.00	0.00	0.00	3.02
2941	4857	8.475639	TCCTTTCGTATCTAAGCTACTTTTGAT	58.524	33.333	0.00	0.00	0.00	2.57
2952	4868	9.372369	CTAAGCTACTTTTGATAAGTTAGCTGT	57.628	33.333	14.80	10.40	37.33	4.40
3044	4989	9.229784	CATTCTGCTAATGTTTGAATGTGTATC	57.770	33.333	0.00	0.00	39.14	2.24
3178	5288	7.751047	TTTTCACGTATCAGAGTTATACAGC	57.249	36.000	0.00	0.00	31.43	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
543	547	2.224305	CCTAAATCTGACACGGGATCCC	60.224	54.545	22.12	22.12	0.00	3.85
548	552	0.541863	AGCCCTAAATCTGACACGGG	59.458	55.000	0.00	0.00	34.79	5.28
556	560	3.241520	GCCCCGAGCCCTAAATCT	58.758	61.111	0.00	0.00	34.35	2.40
569	573	0.474614	GTAGGAGAATCAAGGGCCCC	59.525	60.000	21.43	0.54	36.25	5.80
703	2544	8.905660	ATGAGAATGAGAATGATTTTCGATCT	57.094	30.769	3.74	3.74	25.42	2.75
713	2554	5.093849	TGCACTGATGAGAATGAGAATGA	57.906	39.130	0.00	0.00	0.00	2.57
723	2564	7.352079	TCTAAGAATGTATGCACTGATGAGA	57.648	36.000	0.00	0.00	0.00	3.27
724	2565	7.171167	CCTTCTAAGAATGTATGCACTGATGAG	59.829	40.741	0.00	0.00	0.00	2.90
725	2566	6.988580	CCTTCTAAGAATGTATGCACTGATGA	59.011	38.462	0.00	0.00	0.00	2.92
726	2567	6.765036	ACCTTCTAAGAATGTATGCACTGATG	59.235	38.462	0.00	0.00	0.00	3.07
727	2568	6.893583	ACCTTCTAAGAATGTATGCACTGAT	58.106	36.000	0.00	0.00	0.00	2.90
728	2569	6.299805	ACCTTCTAAGAATGTATGCACTGA	57.700	37.500	0.00	0.00	0.00	3.41
729	2570	6.037610	GGAACCTTCTAAGAATGTATGCACTG	59.962	42.308	0.00	0.00	0.00	3.66
730	2571	6.116126	GGAACCTTCTAAGAATGTATGCACT	58.884	40.000	0.00	0.00	0.00	4.40
731	2572	5.006746	CGGAACCTTCTAAGAATGTATGCAC	59.993	44.000	0.00	0.00	0.00	4.57
732	2573	5.116180	CGGAACCTTCTAAGAATGTATGCA	58.884	41.667	0.00	0.00	0.00	3.96
733	2574	5.116882	ACGGAACCTTCTAAGAATGTATGC	58.883	41.667	0.00	0.00	0.00	3.14
734	2575	5.459107	CGACGGAACCTTCTAAGAATGTATG	59.541	44.000	0.00	0.00	0.00	2.39
735	2576	5.589192	CGACGGAACCTTCTAAGAATGTAT	58.411	41.667	0.00	0.00	0.00	2.29
755	2596	1.007580	GTAGGCTTTAGCTTGGCGAC	58.992	55.000	0.00	0.00	41.70	5.19
830	2674	3.771160	GTGACGTGGATCCCCGCT	61.771	66.667	17.10	3.98	40.77	5.52
837	2681	1.811266	GCATGCGAGTGACGTGGAT	60.811	57.895	0.00	0.00	44.60	3.41
838	2682	2.432456	GCATGCGAGTGACGTGGA	60.432	61.111	0.00	0.00	44.60	4.02
918	2763	2.125269	CGTGGGATGGAACGGGAC	60.125	66.667	0.00	0.00	36.17	4.46
943	2788	4.099380	ACGGCCGTTGGTTTTATATTTG	57.901	40.909	28.70	0.00	0.00	2.32
1282	3142	3.058914	CGAAGCCAACATTCGTCTCTTTT	60.059	43.478	0.17	0.00	43.42	2.27
1293	3153	4.160439	TGAGATAAGAGACGAAGCCAACAT	59.840	41.667	0.00	0.00	0.00	2.71
1304	3164	1.269517	CCCAGCGCTGAGATAAGAGAC	60.270	57.143	38.06	0.00	0.00	3.36
1333	3193	7.718525	TCAAACCCCTAGATTGTTTAACAAAC	58.281	34.615	14.70	11.97	41.96	2.93
1430	3290	0.676782	AACAACTAGCCGGTGGATGC	60.677	55.000	1.90	0.00	0.00	3.91
1514	3374	1.535896	GAGACGGACTTTGGCCTTTTC	59.464	52.381	3.32	0.00	0.00	2.29
1519	3379	0.831307	ATAGGAGACGGACTTTGGCC	59.169	55.000	0.00	0.00	0.00	5.36
1526	3386	1.066303	CAGTGCAGATAGGAGACGGAC	59.934	57.143	0.00	0.00	0.00	4.79
1528	3388	1.107114	ACAGTGCAGATAGGAGACGG	58.893	55.000	0.00	0.00	0.00	4.79
1623	3483	2.670934	AGAAAGTGGCAGCGGCTG	60.671	61.111	25.21	25.21	40.87	4.85
1688	3582	2.566724	CACCTACCAAATGCAAACCCAT	59.433	45.455	0.00	0.00	0.00	4.00
1697	3591	2.041891	TGGGGTTACCACCTACCAAATG	59.958	50.000	0.00	0.00	46.80	2.32
1699	3593	1.830486	TGGGGTTACCACCTACCAAA	58.170	50.000	0.00	0.00	46.80	3.28
1794	3688	3.872696	TGATGATCTGTTACGGCACAAT	58.127	40.909	0.00	0.00	0.00	2.71
2189	4101	1.605232	GCCATGATCATCGTGCAATCA	59.395	47.619	4.86	0.69	32.19	2.57
2318	4230	2.755952	AAGGCATCTACATTTCCCCC	57.244	50.000	0.00	0.00	0.00	5.40
2335	4247	8.454106	TCACTTGAAGAACTGAAGAAAGAAAAG	58.546	33.333	0.00	0.00	0.00	2.27
2340	4252	6.314896	ACAGTCACTTGAAGAACTGAAGAAAG	59.685	38.462	26.74	9.35	0.00	2.62
2343	4255	5.344743	ACAGTCACTTGAAGAACTGAAGA	57.655	39.130	26.74	3.20	0.00	2.87
2344	4256	4.208047	CGACAGTCACTTGAAGAACTGAAG	59.792	45.833	26.74	19.08	0.00	3.02
2680	4593	0.321122	CACAGGAGACACAGGCTTCC	60.321	60.000	0.00	0.00	0.00	3.46
2741	4654	1.945354	TTCTGACGGGGATCGCAGAC	61.945	60.000	16.48	10.76	44.79	3.51
2759	4672	8.792830	ATATTTCCGTCATATTCCGAATCATT	57.207	30.769	0.00	0.00	0.00	2.57
2807	4720	0.942252	GATCCCCATTACGCCGAAAC	59.058	55.000	0.00	0.00	0.00	2.78
2811	4724	2.536761	TTAAGATCCCCATTACGCCG	57.463	50.000	0.00	0.00	0.00	6.46
2829	4742	9.831737	CGATTCTTCTGACATTCTGTAAAAATT	57.168	29.630	0.00	0.00	0.00	1.82
2910	4823	3.124560	GCTTAGATACGAAAGGACTGCC	58.875	50.000	0.00	0.00	0.00	4.85
2941	4857	7.553334	CAGTACCCTTCATTACAGCTAACTTA	58.447	38.462	0.00	0.00	0.00	2.24
2952	4868	5.488341	GAACAGAAGCAGTACCCTTCATTA	58.512	41.667	19.94	0.00	40.83	1.90
3178	5288	0.320247	AGGAAGCACGCAGTCAGAAG	60.320	55.000	0.00	0.00	41.61	2.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.