AutoCloner

Multiple sequence alignment - TraesCS4D01G104000

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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	TraesCS4D01G104000	chr4D	100.000	2528	0	0	1	2528	82566068	82568595	0.000000e+00	4669
1	TraesCS4D01G104000	chr4D	93.757	913	49	6	1587	2496	166011969	166011062	0.000000e+00	1363
2	TraesCS4D01G104000	chr4D	92.519	909	65	3	1587	2494	346203668	346204574	0.000000e+00	1299
3	TraesCS4D01G104000	chr4B	96.281	995	27	5	564	1554	117005165	117006153	0.000000e+00	1624
4	TraesCS4D01G104000	chr4B	89.035	228	25	0	322	549	17467482	17467709	1.480000e-72	283
5	TraesCS4D01G104000	chr2D	94.264	924	50	3	1578	2500	458731153	458732074	0.000000e+00	1410
6	TraesCS4D01G104000	chr1D	93.194	911	59	2	1587	2494	296631934	296632844	0.000000e+00	1336
7	TraesCS4D01G104000	chr6A	93.069	909	60	2	1586	2494	158307380	158306475	0.000000e+00	1327
8	TraesCS4D01G104000	chr6A	87.321	560	50	6	1	550	572329687	572329139	2.760000e-174	621
9	TraesCS4D01G104000	chr6B	92.967	910	62	2	1587	2494	65133974	65134883	0.000000e+00	1325
10	TraesCS4D01G104000	chr7A	92.536	911	63	4	1587	2494	634327292	634328200	0.000000e+00	1301
11	TraesCS4D01G104000	chr7D	92.527	910	63	4	1587	2494	7527758	7528664	0.000000e+00	1299
12	TraesCS4D01G104000	chr7D	91.532	555	36	5	1	550	163566097	163566645	0.000000e+00	754
13	TraesCS4D01G104000	chr7D	86.590	261	28	6	293	550	3761897	3761641	5.320000e-72	281
14	TraesCS4D01G104000	chr3B	92.418	910	67	2	1587	2494	799301129	799300220	0.000000e+00	1297
15	TraesCS4D01G104000	chrUn	90.054	553	41	5	1	551	28610184	28609644	0.000000e+00	704
16	TraesCS4D01G104000	chrUn	89.565	230	24	0	322	551	85061069	85061298	2.460000e-75	292
17	TraesCS4D01G104000	chr7B	88.468	555	53	5	1	550	475565673	475566221	0.000000e+00	660
18	TraesCS4D01G104000	chr3A	86.679	563	49	10	1	550	416137722	416137173	3.600000e-168	601
19	TraesCS4D01G104000	chr2B	85.824	261	31	6	291	550	68580340	68580085	3.200000e-69	272
20	TraesCS4D01G104000	chr5D	85.769	260	30	7	294	550	462755433	462755688	4.150000e-68	268

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	TraesCS4D01G104000	chr4D	82566068	82568595	2527	False	4669	4669	100.000	1	2528	1	chr4D.!!$F1	2527
1	TraesCS4D01G104000	chr4D	166011062	166011969	907	True	1363	1363	93.757	1587	2496	1	chr4D.!!$R1	909
2	TraesCS4D01G104000	chr4D	346203668	346204574	906	False	1299	1299	92.519	1587	2494	1	chr4D.!!$F2	907
3	TraesCS4D01G104000	chr4B	117005165	117006153	988	False	1624	1624	96.281	564	1554	1	chr4B.!!$F2	990
4	TraesCS4D01G104000	chr2D	458731153	458732074	921	False	1410	1410	94.264	1578	2500	1	chr2D.!!$F1	922
5	TraesCS4D01G104000	chr1D	296631934	296632844	910	False	1336	1336	93.194	1587	2494	1	chr1D.!!$F1	907
6	TraesCS4D01G104000	chr6A	158306475	158307380	905	True	1327	1327	93.069	1586	2494	1	chr6A.!!$R1	908
7	TraesCS4D01G104000	chr6A	572329139	572329687	548	True	621	621	87.321	1	550	1	chr6A.!!$R2	549
8	TraesCS4D01G104000	chr6B	65133974	65134883	909	False	1325	1325	92.967	1587	2494	1	chr6B.!!$F1	907
9	TraesCS4D01G104000	chr7A	634327292	634328200	908	False	1301	1301	92.536	1587	2494	1	chr7A.!!$F1	907
10	TraesCS4D01G104000	chr7D	7527758	7528664	906	False	1299	1299	92.527	1587	2494	1	chr7D.!!$F1	907
11	TraesCS4D01G104000	chr7D	163566097	163566645	548	False	754	754	91.532	1	550	1	chr7D.!!$F2	549
12	TraesCS4D01G104000	chr3B	799300220	799301129	909	True	1297	1297	92.418	1587	2494	1	chr3B.!!$R1	907
13	TraesCS4D01G104000	chrUn	28609644	28610184	540	True	704	704	90.054	1	551	1	chrUn.!!$R1	550
14	TraesCS4D01G104000	chr7B	475565673	475566221	548	False	660	660	88.468	1	550	1	chr7B.!!$F1	549
15	TraesCS4D01G104000	chr3A	416137173	416137722	549	True	601	601	86.679	1	550	1	chr3A.!!$R1	549

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
221	233	0.551879	TAGGGAGGAGAGAGGTTCGG	59.448	60.000	0.0	0.0	0.0	4.30	F
268	284	1.010793	AGAGGAGAGGAGAGGAGAGGA	59.989	57.143	0.0	0.0	0.0	3.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1266	1294	0.611340	ACGCGAAGAGGTAGAACCCT	60.611	55.000	15.93	0.0	39.75	4.34	R
2151	2185	1.456892	TCGTGGTGGACCTGTGTCT	60.457	57.895	0.00	0.0	41.47	3.41	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
140	141	3.776781	CGTACCACGGCCATGGGA	61.777	66.667	24.20	12.06	44.81	4.37
217	229	0.555769	CTGCTAGGGAGGAGAGAGGT	59.444	60.000	0.00	0.00	43.63	3.85
221	233	0.551879	TAGGGAGGAGAGAGGTTCGG	59.448	60.000	0.00	0.00	0.00	4.30
267	283	1.421646	GAGAGGAGAGGAGAGGAGAGG	59.578	61.905	0.00	0.00	0.00	3.69
268	284	1.010793	AGAGGAGAGGAGAGGAGAGGA	59.989	57.143	0.00	0.00	0.00	3.71
269	285	1.421646	GAGGAGAGGAGAGGAGAGGAG	59.578	61.905	0.00	0.00	0.00	3.69
270	286	1.010793	AGGAGAGGAGAGGAGAGGAGA	59.989	57.143	0.00	0.00	0.00	3.71
271	287	1.421646	GGAGAGGAGAGGAGAGGAGAG	59.578	61.905	0.00	0.00	0.00	3.20
316	337	5.608860	AGAGAGGAAGAAGAAAGGGAAAGAA	59.391	40.000	0.00	0.00	0.00	2.52
318	339	5.371176	AGAGGAAGAAGAAAGGGAAAGAAGT	59.629	40.000	0.00	0.00	0.00	3.01
329	350	6.374417	AAGGGAAAGAAGTAGCTTACATGA	57.626	37.500	0.00	0.00	0.00	3.07
335	356	2.182516	AGTAGCTTACATGAGGGCCT	57.817	50.000	5.25	5.25	0.00	5.19
365	386	1.932511	GTTAACGGTCAAACACACGGA	59.067	47.619	0.00	0.00	0.00	4.69
385	406	7.606456	ACACGGACAAATAGACAGATTGTTTAT	59.394	33.333	0.00	0.00	37.41	1.40
611	635	8.133627	CAGCAGCTACATAGAAAATATTTTGCT	58.866	33.333	17.98	14.34	0.00	3.91
633	657	5.163519	GCTATCACAAACATGGCCTAAATGT	60.164	40.000	3.32	2.18	39.95	2.71
645	669	2.028476	GCCTAAATGTGTGTTTTCCCCC	60.028	50.000	0.00	0.00	0.00	5.40
646	670	3.235200	CCTAAATGTGTGTTTTCCCCCA	58.765	45.455	0.00	0.00	0.00	4.96
647	671	3.837731	CCTAAATGTGTGTTTTCCCCCAT	59.162	43.478	0.00	0.00	0.00	4.00
691	715	2.202479	TGCTGACGCAGATCGACG	60.202	61.111	10.46	8.60	42.25	5.12
705	729	1.666872	CGACGGGTCCAACTTCACC	60.667	63.158	0.00	0.00	0.00	4.02
805	833	2.647381	CCGCACATGCACGCAAAAC	61.647	57.895	4.49	0.00	42.21	2.43
806	834	2.647381	CGCACATGCACGCAAAACC	61.647	57.895	4.49	0.00	42.21	3.27
814	842	1.199789	TGCACGCAAAACCATCTCATC	59.800	47.619	0.00	0.00	0.00	2.92
815	843	1.199789	GCACGCAAAACCATCTCATCA	59.800	47.619	0.00	0.00	0.00	3.07
816	844	2.159338	GCACGCAAAACCATCTCATCAT	60.159	45.455	0.00	0.00	0.00	2.45
903	931	2.217750	CACCAACCTGTCACGATGAAA	58.782	47.619	0.00	0.00	0.00	2.69
1015	1043	2.829914	CCATGGCCATCCACCACG	60.830	66.667	17.61	2.13	46.92	4.94
1115	1143	4.470170	CGACATCGTGACGGCGGA	62.470	66.667	13.24	0.00	32.33	5.54
1224	1252	1.930188	CATCGACGACGCTCTCACG	60.930	63.158	0.00	0.00	39.58	4.35
1266	1294	4.467084	GTCATCGGGAGGGCGCAA	62.467	66.667	10.83	0.00	0.00	4.85
1410	1438	4.459089	GTCAGGGAGCTGCCGGTC	62.459	72.222	22.83	14.59	37.63	4.79
1487	1515	2.314647	CGTACAACGCCACCACCAG	61.315	63.158	0.00	0.00	33.65	4.00
1533	1561	3.112075	CTGCACGTGTAGGCACCG	61.112	66.667	24.15	0.00	42.39	4.94
1554	1582	0.520412	GCGCGCACGTACATTGATTT	60.520	50.000	29.10	0.00	42.83	2.17
1555	1583	1.171052	CGCGCACGTACATTGATTTG	58.829	50.000	8.75	0.00	33.53	2.32
1556	1584	1.463363	CGCGCACGTACATTGATTTGT	60.463	47.619	8.75	0.00	33.53	2.83
1557	1585	2.222618	CGCGCACGTACATTGATTTGTA	60.223	45.455	8.75	0.00	33.53	2.41
1558	1586	3.543265	CGCGCACGTACATTGATTTGTAT	60.543	43.478	8.75	0.00	34.76	2.29
1559	1587	4.317488	CGCGCACGTACATTGATTTGTATA	60.317	41.667	8.75	0.00	34.76	1.47
1560	1588	5.130519	GCGCACGTACATTGATTTGTATAG	58.869	41.667	0.30	0.00	34.76	1.31
1561	1589	5.666203	CGCACGTACATTGATTTGTATAGG	58.334	41.667	0.00	0.00	34.76	2.57
1562	1590	5.233476	CGCACGTACATTGATTTGTATAGGT	59.767	40.000	0.00	0.00	34.76	3.08
1563	1591	6.418523	CGCACGTACATTGATTTGTATAGGTA	59.581	38.462	0.00	0.00	34.76	3.08
1564	1592	7.115805	CGCACGTACATTGATTTGTATAGGTAT	59.884	37.037	0.00	0.00	34.76	2.73
1565	1593	8.770828	GCACGTACATTGATTTGTATAGGTATT	58.229	33.333	0.00	0.00	34.76	1.89
1568	1596	9.594038	CGTACATTGATTTGTATAGGTATTTGC	57.406	33.333	0.00	0.00	34.76	3.68
1830	1862	1.275666	ATGACGGATCACCTCCACAA	58.724	50.000	0.00	0.00	45.24	3.33
2027	2061	2.360350	CTGCCTGCCACGAACCAT	60.360	61.111	0.00	0.00	0.00	3.55
2076	2110	1.131126	CGTTGATGCAGACCACAATCC	59.869	52.381	0.00	0.00	0.00	3.01
2137	2171	1.291184	TGGAGCAAATGTCGTCGCAG	61.291	55.000	0.00	0.00	0.00	5.18
2410	2451	3.866582	GGTCATCAGCGGAGGGGG	61.867	72.222	0.00	0.00	0.00	5.40
2446	2488	4.082523	CGGAGAAAGGCGCCCTGA	62.083	66.667	26.15	0.00	32.13	3.86
2447	2489	2.592308	GGAGAAAGGCGCCCTGAT	59.408	61.111	26.15	7.27	32.13	2.90
2497	2544	3.740115	TCTCCTGGAAGAAAGAAAACCG	58.260	45.455	0.00	0.00	34.07	4.44
2498	2545	3.135895	TCTCCTGGAAGAAAGAAAACCGT	59.864	43.478	0.00	0.00	34.07	4.83
2499	2546	3.211045	TCCTGGAAGAAAGAAAACCGTG	58.789	45.455	0.00	0.00	34.07	4.94
2500	2547	2.287608	CCTGGAAGAAAGAAAACCGTGC	60.288	50.000	0.00	0.00	34.07	5.34
2501	2548	1.332375	TGGAAGAAAGAAAACCGTGCG	59.668	47.619	0.00	0.00	0.00	5.34
2502	2549	1.600485	GGAAGAAAGAAAACCGTGCGA	59.400	47.619	0.00	0.00	0.00	5.10
2503	2550	2.349532	GGAAGAAAGAAAACCGTGCGAG	60.350	50.000	0.00	0.00	0.00	5.03
2504	2551	0.586802	AGAAAGAAAACCGTGCGAGC	59.413	50.000	0.00	0.00	0.00	5.03
2505	2552	0.385598	GAAAGAAAACCGTGCGAGCC	60.386	55.000	0.00	0.00	0.00	4.70
2506	2553	1.792118	AAAGAAAACCGTGCGAGCCC	61.792	55.000	0.00	0.00	0.00	5.19
2507	2554	2.951475	AAGAAAACCGTGCGAGCCCA	62.951	55.000	0.00	0.00	0.00	5.36
2508	2555	2.282180	AAAACCGTGCGAGCCCAT	60.282	55.556	0.00	0.00	0.00	4.00
2509	2556	2.527547	GAAAACCGTGCGAGCCCATG	62.528	60.000	0.00	0.00	0.00	3.66
2513	2560	4.246206	CGTGCGAGCCCATGCATG	62.246	66.667	20.19	20.19	43.96	4.06
2514	2561	4.564116	GTGCGAGCCCATGCATGC	62.564	66.667	21.69	11.82	43.96	4.06
2516	2563	3.829044	GCGAGCCCATGCATGCAA	61.829	61.111	26.68	8.49	41.13	4.08
2517	2564	2.886610	CGAGCCCATGCATGCAAA	59.113	55.556	26.68	1.26	41.13	3.68
2518	2565	1.215912	CGAGCCCATGCATGCAAAA	59.784	52.632	26.68	0.33	41.13	2.44
2519	2566	0.179094	CGAGCCCATGCATGCAAAAT	60.179	50.000	26.68	5.25	41.13	1.82
2520	2567	1.295792	GAGCCCATGCATGCAAAATG	58.704	50.000	26.68	18.38	41.13	2.32
2521	2568	0.746563	AGCCCATGCATGCAAAATGC	60.747	50.000	26.68	22.88	44.76	3.56
2522	2569	0.746563	GCCCATGCATGCAAAATGCT	60.747	50.000	26.68	3.45	44.79	3.79
2523	2570	1.745232	CCCATGCATGCAAAATGCTT	58.255	45.000	26.68	2.56	45.31	3.91
2525	2572	2.823196	CATGCATGCAAAATGCTTGG	57.177	45.000	26.68	2.14	45.30	3.61
2526	2573	1.091537	ATGCATGCAAAATGCTTGGC	58.908	45.000	26.68	11.56	45.30	4.52
2527	2574	0.250338	TGCATGCAAAATGCTTGGCA	60.250	45.000	20.30	13.52	45.30	4.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
115	116	3.812019	CCGTGGTACGAGCTCGCT	61.812	66.667	34.83	23.28	46.05	4.93
140	141	2.615288	CCTCCCTTCCCCAGCCTT	60.615	66.667	0.00	0.00	0.00	4.35
221	233	1.244697	TGATATCTCTCCCGAGCCGC	61.245	60.000	3.98	0.00	37.19	6.53
316	337	2.043227	GAGGCCCTCATGTAAGCTACT	58.957	52.381	5.69	0.00	0.00	2.57
318	339	1.762957	GTGAGGCCCTCATGTAAGCTA	59.237	52.381	18.16	0.00	42.73	3.32
329	350	3.618997	CGTTAACTAACATGTGAGGCCCT	60.619	47.826	14.99	0.00	35.99	5.19
335	356	5.816258	TGTTTGACCGTTAACTAACATGTGA	59.184	36.000	0.00	0.00	35.99	3.58
365	386	7.243487	CGCACATAAACAATCTGTCTATTTGT	58.757	34.615	0.00	0.00	35.19	2.83
448	470	3.199677	CAAATCGGTGGTCGGCTATTTA	58.800	45.455	0.00	0.00	39.77	1.40
508	532	6.952938	ACTACTACTTTACAAGCTAGGGTTCT	59.047	38.462	0.00	0.00	0.00	3.01
551	575	6.153510	CGGTGGGATGAATAAGAGAGATATGA	59.846	42.308	0.00	0.00	0.00	2.15
552	576	6.071108	ACGGTGGGATGAATAAGAGAGATATG	60.071	42.308	0.00	0.00	0.00	1.78
553	577	6.019748	ACGGTGGGATGAATAAGAGAGATAT	58.980	40.000	0.00	0.00	0.00	1.63
554	578	5.394738	ACGGTGGGATGAATAAGAGAGATA	58.605	41.667	0.00	0.00	0.00	1.98
555	579	4.227197	ACGGTGGGATGAATAAGAGAGAT	58.773	43.478	0.00	0.00	0.00	2.75
556	580	3.643237	ACGGTGGGATGAATAAGAGAGA	58.357	45.455	0.00	0.00	0.00	3.10
557	581	5.509840	CCTTACGGTGGGATGAATAAGAGAG	60.510	48.000	0.00	0.00	0.00	3.20
558	582	4.344102	CCTTACGGTGGGATGAATAAGAGA	59.656	45.833	0.00	0.00	0.00	3.10
559	583	4.632153	CCTTACGGTGGGATGAATAAGAG	58.368	47.826	0.00	0.00	0.00	2.85
560	584	4.682778	CCTTACGGTGGGATGAATAAGA	57.317	45.455	0.00	0.00	0.00	2.10
611	635	5.714333	ACACATTTAGGCCATGTTTGTGATA	59.286	36.000	23.87	0.00	37.14	2.15
614	638	3.989167	CACACATTTAGGCCATGTTTGTG	59.011	43.478	18.51	18.51	39.03	3.33
615	639	3.640967	ACACACATTTAGGCCATGTTTGT	59.359	39.130	16.68	16.68	39.59	2.83
622	646	2.630580	GGGAAAACACACATTTAGGCCA	59.369	45.455	5.01	0.00	0.00	5.36
623	647	2.028476	GGGGAAAACACACATTTAGGCC	60.028	50.000	0.00	0.00	0.00	5.19
633	657	5.251932	TCAGATACTTATGGGGGAAAACACA	59.748	40.000	0.00	0.00	0.00	3.72
645	669	7.456684	GCCATAATAGCGTCAGATACTTATG	57.543	40.000	0.00	0.00	0.00	1.90
690	714	0.881118	CAATGGTGAAGTTGGACCCG	59.119	55.000	0.00	0.00	0.00	5.28
691	715	2.162681	CTCAATGGTGAAGTTGGACCC	58.837	52.381	0.00	0.00	31.88	4.46
705	729	2.794981	CGGTAGGAGTACGTGCTCAATG	60.795	54.545	30.60	14.12	37.24	2.82
805	833	4.918588	TCCATTGATCCATGATGAGATGG	58.081	43.478	8.32	2.76	43.96	3.51
806	834	5.294552	CGATCCATTGATCCATGATGAGATG	59.705	44.000	8.32	0.00	43.82	2.90
859	887	3.781307	CGGGGCCGATGGTTCTCA	61.781	66.667	0.00	0.00	42.83	3.27
903	931	5.758296	TCGAGATGTTTTGTAGAAAGTGCTT	59.242	36.000	0.00	0.00	0.00	3.91
1266	1294	0.611340	ACGCGAAGAGGTAGAACCCT	60.611	55.000	15.93	0.00	39.75	4.34
1434	1462	2.028190	CCGTATCCAGCAGCTCCG	59.972	66.667	0.00	0.00	0.00	4.63
1437	1465	2.765807	AGGCCGTATCCAGCAGCT	60.766	61.111	0.00	0.00	0.00	4.24
1646	1678	5.471556	TTCAGTTTTGTCAGGTCGGTATA	57.528	39.130	0.00	0.00	0.00	1.47
2027	2061	1.971149	AGATGGTGGATCTGGGTTCA	58.029	50.000	0.00	0.00	40.19	3.18
2059	2093	3.157727	CGGATTGTGGTCTGCATCA	57.842	52.632	0.00	0.00	0.00	3.07
2151	2185	1.456892	TCGTGGTGGACCTGTGTCT	60.457	57.895	0.00	0.00	41.47	3.41
2375	2416	3.324099	CTCGGTCGTCGGTGGTGAG	62.324	68.421	0.00	0.00	39.77	3.51
2446	2488	1.068753	CGATCTCGCCTCTTGCCAT	59.931	57.895	0.00	0.00	36.24	4.40
2447	2489	2.496341	CGATCTCGCCTCTTGCCA	59.504	61.111	0.00	0.00	36.24	4.92
2496	2543	4.246206	CATGCATGGGCTCGCACG	62.246	66.667	19.40	0.00	41.79	5.34
2497	2544	4.564116	GCATGCATGGGCTCGCAC	62.564	66.667	27.34	4.91	41.79	5.34
2499	2546	2.839043	TTTTGCATGCATGGGCTCGC	62.839	55.000	27.34	12.83	41.91	5.03
2500	2547	0.179094	ATTTTGCATGCATGGGCTCG	60.179	50.000	27.34	1.69	41.91	5.03
2501	2548	1.295792	CATTTTGCATGCATGGGCTC	58.704	50.000	27.34	11.61	41.91	4.70
2502	2549	0.746563	GCATTTTGCATGCATGGGCT	60.747	50.000	27.34	1.96	44.26	5.19
2503	2550	1.725066	GCATTTTGCATGCATGGGC	59.275	52.632	27.34	18.41	44.26	5.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.