AutoCloner

Multiple sequence alignment - TraesCS7B01G056300

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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	TraesCS7B01G056300	chr7B	100.000	3184	0	0	1	3184	59181486	59178303	0.000000e+00	5880
1	TraesCS7B01G056300	chr7B	78.529	1332	250	28	601	1909	114938744	114940062	0.000000e+00	843
2	TraesCS7B01G056300	chr7B	84.450	418	36	8	508	899	59304957	59305371	4.980000e-103	385
3	TraesCS7B01G056300	chr7B	78.853	279	37	15	2243	2514	114940385	114940648	5.460000e-38	169
4	TraesCS7B01G056300	chr7D	95.388	2515	111	5	1	2514	101800030	101797520	0.000000e+00	3997
5	TraesCS7B01G056300	chr7D	79.551	1335	243	24	603	1916	143976174	143974849	0.000000e+00	926
6	TraesCS7B01G056300	chr7D	78.550	1352	243	36	606	1927	152947181	152948515	0.000000e+00	846
7	TraesCS7B01G056300	chr7D	86.895	496	52	6	414	899	101800211	101800703	7.770000e-151	544
8	TraesCS7B01G056300	chr7D	79.439	214	15	14	2541	2751	101796254	101796067	1.200000e-24	124
9	TraesCS7B01G056300	chr7A	92.978	2478	143	14	61	2514	105768367	105765897	0.000000e+00	3583
10	TraesCS7B01G056300	chr7A	93.836	2255	119	7	1	2247	105779263	105777021	0.000000e+00	3376
11	TraesCS7B01G056300	chr7A	90.827	774	64	2	1350	2123	105773887	105773121	0.000000e+00	1029
12	TraesCS7B01G056300	chr7A	78.303	1332	255	28	601	1909	154062429	154063749	0.000000e+00	828
13	TraesCS7B01G056300	chr7A	86.726	452	46	7	459	899	105779880	105780328	1.030000e-134	490
14	TraesCS7B01G056300	chr7A	91.667	312	17	3	2534	2836	105764625	105764314	1.060000e-114	424
15	TraesCS7B01G056300	chr7A	94.361	266	14	1	2249	2514	105776965	105776701	1.060000e-109	407
16	TraesCS7B01G056300	chr7A	92.366	262	14	5	2924	3184	105748948	105748692	5.020000e-98	368
17	TraesCS7B01G056300	chr3D	78.759	1902	314	48	536	2373	39121133	39119258	0.000000e+00	1192
18	TraesCS7B01G056300	chr3D	79.286	700	108	20	983	1650	39032886	39032192	3.740000e-124	455
19	TraesCS7B01G056300	chr3B	80.241	1579	261	32	536	2090	61916753	61915202	0.000000e+00	1140
20	TraesCS7B01G056300	chr3B	78.502	307	43	15	2216	2514	61896004	61895713	2.520000e-41	180

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	TraesCS7B01G056300	chr7B	59178303	59181486	3183	True	5880.0	5880	100.0000	1	3184	1	chr7B.!!$R1	3183
1	TraesCS7B01G056300	chr7B	114938744	114940648	1904	False	506.0	843	78.6910	601	2514	2	chr7B.!!$F2	1913
2	TraesCS7B01G056300	chr7D	101796067	101800030	3963	True	2060.5	3997	87.4135	1	2751	2	chr7D.!!$R2	2750
3	TraesCS7B01G056300	chr7D	143974849	143976174	1325	True	926.0	926	79.5510	603	1916	1	chr7D.!!$R1	1313
4	TraesCS7B01G056300	chr7D	152947181	152948515	1334	False	846.0	846	78.5500	606	1927	1	chr7D.!!$F2	1321
5	TraesCS7B01G056300	chr7A	105764314	105768367	4053	True	2003.5	3583	92.3225	61	2836	2	chr7A.!!$R2	2775
6	TraesCS7B01G056300	chr7A	105773121	105779263	6142	True	1604.0	3376	93.0080	1	2514	3	chr7A.!!$R3	2513
7	TraesCS7B01G056300	chr7A	154062429	154063749	1320	False	828.0	828	78.3030	601	1909	1	chr7A.!!$F2	1308
8	TraesCS7B01G056300	chr3D	39119258	39121133	1875	True	1192.0	1192	78.7590	536	2373	1	chr3D.!!$R2	1837
9	TraesCS7B01G056300	chr3D	39032192	39032886	694	True	455.0	455	79.2860	983	1650	1	chr3D.!!$R1	667
10	TraesCS7B01G056300	chr3B	61915202	61916753	1551	True	1140.0	1140	80.2410	536	2090	1	chr3B.!!$R2	1554

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
956	993	1.987807	ATCTCCATCGTTGCCCCCAG	61.988	60.0	0.00	0.0	0.00	4.45	F
1273	1317	0.243095	GACTAACCGAGCCACGACTT	59.757	55.0	2.48	0.0	45.77	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1958	2031	0.179113	GTTGTTGTTGCTGGTGGTGG	60.179	55.0	0.00	0.00	0.0	4.61	R
2423	2608	0.734889	GGCATGATGTACACACTGCC	59.265	55.0	21.71	21.71	42.0	4.85	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
34	35	9.744468	GTTTTGCCTAATTCTTGTTCTCTAAAA	57.256	29.630	0.00	0.00	0.00	1.52
127	128	7.854557	TGATTCACTTCTAGTTGGATCATTG	57.145	36.000	8.01	0.00	0.00	2.82
151	152	4.765273	TGTCCGCACACAATGATAGTAAT	58.235	39.130	0.00	0.00	0.00	1.89
162	163	8.494433	ACACAATGATAGTAATACCCAATGTCT	58.506	33.333	0.00	0.00	0.00	3.41
249	250	8.464770	TTTGCATCTACAAACAGAAATAATGC	57.535	30.769	0.00	0.00	34.68	3.56
256	257	4.917415	ACAAACAGAAATAATGCAACTCGC	59.083	37.500	0.00	0.00	42.89	5.03
307	308	6.983890	CGACAAATTTTAGGGGAATTTATGGG	59.016	38.462	0.00	0.00	35.54	4.00
410	411	9.474920	CTTTTATGCTTGTTCATTTTGGTAAGA	57.525	29.630	0.00	0.00	0.00	2.10
427	428	3.850122	AAGAAATTTTACTGCTCGGCC	57.150	42.857	0.00	0.00	0.00	6.13
445	446	6.594159	GCTCGGCCTTTTATATTATTCTAGCA	59.406	38.462	0.00	0.00	0.00	3.49
501	502	6.893005	TCCATCCGTATATGGTGTATATGTGA	59.107	38.462	10.85	4.47	45.67	3.58
574	575	2.030540	CAGAAGCACACACTTTCCATGG	60.031	50.000	4.97	4.97	0.00	3.66
797	829	6.493166	TCTAAACATCCATCCATCCACTTTT	58.507	36.000	0.00	0.00	0.00	2.27
890	926	7.493743	AGCATTCACTCTATTTAAGCATCTG	57.506	36.000	0.00	0.00	0.00	2.90
956	993	1.987807	ATCTCCATCGTTGCCCCCAG	61.988	60.000	0.00	0.00	0.00	4.45
1104	1148	3.860470	TCACCTCCTACCTAGTCCCTAAA	59.140	47.826	0.00	0.00	0.00	1.85
1272	1316	1.593296	GGACTAACCGAGCCACGACT	61.593	60.000	2.48	0.00	45.77	4.18
1273	1317	0.243095	GACTAACCGAGCCACGACTT	59.757	55.000	2.48	0.00	45.77	3.01
1380	1427	2.284773	TACAAGGGTAGGGCGCCA	60.285	61.111	30.85	5.28	0.00	5.69
1426	1473	2.587522	TGCATGAGTATAGGCTCGAGT	58.412	47.619	15.13	0.00	38.28	4.18
1665	1735	4.310769	CACTGGACTCAAGAAGGTAGTTG	58.689	47.826	0.00	0.00	0.00	3.16
1689	1759	0.461339	GTCGTACGCCATTCCCATGT	60.461	55.000	11.24	0.00	0.00	3.21
1695	1765	0.249155	CGCCATTCCCATGTCAATGC	60.249	55.000	7.91	4.36	31.93	3.56
1720	1790	1.375098	GGAGCAGAGGAGCAACATGC	61.375	60.000	0.00	0.00	45.46	4.06
1775	1845	2.089980	GGCTATGGTGCATCATCATCC	58.910	52.381	17.59	12.12	36.52	3.51
1800	1870	1.152694	CCCCCATCGTCCGTACCTA	60.153	63.158	0.00	0.00	0.00	3.08
1811	1881	3.376234	CGTCCGTACCTACATCTTCTTCA	59.624	47.826	0.00	0.00	0.00	3.02
1886	1956	2.035961	CCCGATGATGAACGACCACTAT	59.964	50.000	0.00	0.00	0.00	2.12
1890	1960	4.803613	CGATGATGAACGACCACTATTTCA	59.196	41.667	0.00	0.00	32.71	2.69
1958	2031	1.274167	TCGTTCTACCACCATGACCAC	59.726	52.381	0.00	0.00	0.00	4.16
1959	2032	1.674817	CGTTCTACCACCATGACCACC	60.675	57.143	0.00	0.00	0.00	4.61
1960	2033	1.349688	GTTCTACCACCATGACCACCA	59.650	52.381	0.00	0.00	0.00	4.17
1970	2052	2.005606	ATGACCACCACCACCAGCAA	62.006	55.000	0.00	0.00	0.00	3.91
2167	2264	2.093711	CAGTGAACATGGGTACGGATGA	60.094	50.000	9.16	0.00	0.00	2.92
2171	2268	3.707102	TGAACATGGGTACGGATGACATA	59.293	43.478	9.16	0.00	0.00	2.29
2187	2284	8.088365	CGGATGACATATGGAAGTACTGATAAA	58.912	37.037	7.80	0.00	0.00	1.40
2236	2359	5.303747	ACCATCAGAAGATCGATCGATAC	57.696	43.478	29.45	21.75	34.60	2.24
2284	2461	3.059325	TGCACCGCATTTTATTTTTGTGC	60.059	39.130	0.00	0.00	45.91	4.57
2310	2491	5.095145	AGAAGAGAGCTTGTATGCATTGA	57.905	39.130	3.54	0.00	33.61	2.57
2344	2527	3.926616	TGCCTCTTTCTTGTGCTAGTAC	58.073	45.455	3.70	3.70	0.00	2.73
2423	2608	2.884012	TGCATGTGTTCCAAACTACCTG	59.116	45.455	0.00	0.00	0.00	4.00
2442	2627	0.734889	GGCAGTGTGTACATCATGCC	59.265	55.000	23.77	23.77	41.84	4.40
2531	4035	6.963242	TCGTGAATCGACTAAATGTACTACAC	59.037	38.462	0.00	0.00	44.01	2.90
2532	4036	6.965500	CGTGAATCGACTAAATGTACTACACT	59.035	38.462	0.00	0.00	42.86	3.55
2558	4062	4.633126	TCGTTTCAGTACAGTACTAGCGAT	59.367	41.667	13.12	0.00	37.23	4.58
2559	4063	4.729086	CGTTTCAGTACAGTACTAGCGATG	59.271	45.833	13.12	1.23	37.23	3.84
2560	4064	4.895224	TTCAGTACAGTACTAGCGATGG	57.105	45.455	13.12	0.00	37.23	3.51
2638	4148	2.357009	ACGGTATGTCTTGCCTACTACG	59.643	50.000	0.00	0.00	0.00	3.51
2665	4178	2.092914	AGCTTCCATTACGCCTTTAGCT	60.093	45.455	0.00	0.00	40.39	3.32
2696	4209	1.298859	GAGCCAGCCCAACGTAACTG	61.299	60.000	0.00	0.00	0.00	3.16
2719	4232	5.531287	TGTTCTGAAGAGCTTTTAGGAAACC	59.469	40.000	0.00	0.00	0.00	3.27
2721	4234	6.681729	TCTGAAGAGCTTTTAGGAAACCTA	57.318	37.500	0.00	0.00	34.61	3.08
2728	4241	7.510407	AGAGCTTTTAGGAAACCTATATGGAC	58.490	38.462	0.00	0.00	35.87	4.02
2783	4297	7.057402	GCGTTTATTTTCTTCTTTGTTTCTGC	58.943	34.615	0.00	0.00	0.00	4.26
2784	4298	7.253950	GCGTTTATTTTCTTCTTTGTTTCTGCA	60.254	33.333	0.00	0.00	0.00	4.41
2878	4393	5.910723	AGCTTTTACATTTTCCGTTAACACG	59.089	36.000	6.39	0.00	46.71	4.49
2880	4395	2.303707	ACATTTTCCGTTAACACGCG	57.696	45.000	3.53	3.53	45.72	6.01
2891	4406	5.579212	CGTTAACACGCGGAATATTTTTC	57.421	39.130	12.47	0.00	40.18	2.29
2899	4414	4.567558	ACGCGGAATATTTTTCGATACACA	59.432	37.500	12.47	0.00	35.78	3.72
2902	4417	6.299966	CGCGGAATATTTTTCGATACACATTC	59.700	38.462	0.00	0.00	35.78	2.67
2911	4426	8.864069	TTTTTCGATACACATTCAACATTTGT	57.136	26.923	0.00	0.00	0.00	2.83
2912	4427	9.952188	TTTTTCGATACACATTCAACATTTGTA	57.048	25.926	0.00	0.00	0.00	2.41
2958	4473	9.985318	TTTTCAAATACATGTTTGCTTTTTCTG	57.015	25.926	2.30	0.00	38.61	3.02
2959	4474	8.939201	TTCAAATACATGTTTGCTTTTTCTGA	57.061	26.923	2.30	0.00	38.61	3.27
2962	4477	9.985318	CAAATACATGTTTGCTTTTTCTGAAAA	57.015	25.926	11.33	11.33	32.90	2.29
3070	4585	3.694566	GACACACCTTGAAACTTTCCTGT	59.305	43.478	0.00	0.00	0.00	4.00
3088	4603	3.798337	CCTGTGTGCACTTTGAACATTTC	59.202	43.478	19.41	0.00	0.00	2.17
3095	4610	9.243637	GTGTGCACTTTGAACATTTCTTTAATA	57.756	29.630	19.41	0.00	0.00	0.98
3163	4678	9.882996	ATACACGCAGAACATTGATTATATTTG	57.117	29.630	0.00	0.00	0.00	2.32
3168	4683	7.914871	CGCAGAACATTGATTATATTTGAACCA	59.085	33.333	0.00	0.00	0.00	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	9.744468	TTTTAGAGAACAAGAATTAGGCAAAAC	57.256	29.630	0.00	0.00	0.00	2.43
34	35	2.093128	CCCTTGAACGTAAGCCCTACAT	60.093	50.000	0.00	0.00	45.62	2.29
127	128	2.742053	ACTATCATTGTGTGCGGACAAC	59.258	45.455	12.69	7.01	38.64	3.32
151	152	8.983702	AAGTTAAACTTAACAGACATTGGGTA	57.016	30.769	13.38	0.00	44.14	3.69
249	250	0.316442	CACAAGTGTGCAGCGAGTTG	60.316	55.000	9.35	9.35	39.39	3.16
271	272	7.918562	CCCCTAAAATTTGTCGGTTGTTATATG	59.081	37.037	0.00	0.00	0.00	1.78
307	308	8.654215	AGGTCTTCGTATTTTTAAGAATCGTTC	58.346	33.333	0.00	0.00	31.41	3.95
360	361	8.027524	AGACTAGTTGATGGATAATCATGTGT	57.972	34.615	0.00	0.00	44.84	3.72
410	411	4.600692	AAAAGGCCGAGCAGTAAAATTT	57.399	36.364	0.00	0.00	0.00	1.82
501	502	4.082245	CCAGAATAAAAATGACCCGTTGCT	60.082	41.667	0.00	0.00	0.00	3.91
574	575	0.737804	TGCTCTGCTCGTCTCATCTC	59.262	55.000	0.00	0.00	0.00	2.75
636	642	3.902881	TGCCAAATTGAACACCTTTGT	57.097	38.095	0.00	0.00	37.67	2.83
797	829	6.547880	TGCTTTGTTTAATTTGTCCCTACTGA	59.452	34.615	0.00	0.00	0.00	3.41
859	893	5.557891	AAATAGAGTGAATGCTTGTGCTC	57.442	39.130	0.00	0.00	40.48	4.26
956	993	1.669265	GTTCTAGGGTGGCGCAAATAC	59.331	52.381	10.83	1.90	0.00	1.89
1104	1148	3.243068	GGTCGAATGCTTTGTTCAACACT	60.243	43.478	0.00	0.00	0.00	3.55
1257	1301	1.588082	GGAAGTCGTGGCTCGGTTA	59.412	57.895	9.26	0.00	40.32	2.85
1272	1316	2.666098	GGCCTTCCAGTAGCCGGAA	61.666	63.158	5.05	0.00	40.26	4.30
1273	1317	3.081409	GGCCTTCCAGTAGCCGGA	61.081	66.667	5.05	0.00	36.84	5.14
1426	1473	2.757868	CAGGTGTTCCTTGTTTTCCACA	59.242	45.455	0.00	0.00	43.07	4.17
1542	1611	4.687948	CCAGTAGCTAGCTATTACGTACGA	59.312	45.833	26.59	0.00	0.00	3.43
1689	1759	1.076559	CTGCTCCCATGGGCATTGA	60.077	57.895	27.41	7.50	37.83	2.57
1695	1765	3.117452	GCTCCTCTGCTCCCATGGG	62.117	68.421	26.30	26.30	0.00	4.00
1720	1790	3.492102	ATGTACCGGATTCATGGAAGG	57.508	47.619	9.46	0.00	0.00	3.46
1800	1870	3.054875	TGCAGCTGGTATGAAGAAGATGT	60.055	43.478	17.12	0.00	0.00	3.06
1811	1881	1.372582	CAACGTCATGCAGCTGGTAT	58.627	50.000	17.12	0.00	0.00	2.73
1886	1956	3.907474	TCTGGTAGTGGTGATTCCTGAAA	59.093	43.478	0.00	0.00	37.07	2.69
1890	1960	5.072329	CCATATTCTGGTAGTGGTGATTCCT	59.928	44.000	0.00	0.00	40.49	3.36
1958	2031	0.179113	GTTGTTGTTGCTGGTGGTGG	60.179	55.000	0.00	0.00	0.00	4.61
1959	2032	0.529833	TGTTGTTGTTGCTGGTGGTG	59.470	50.000	0.00	0.00	0.00	4.17
1960	2033	1.067213	GTTGTTGTTGTTGCTGGTGGT	60.067	47.619	0.00	0.00	0.00	4.16
1970	2052	4.876125	TCATGTGTTGTTGTTGTTGTTGT	58.124	34.783	0.00	0.00	0.00	3.32
2167	2264	9.770097	CATCTGTTTATCAGTACTTCCATATGT	57.230	33.333	1.24	0.00	43.97	2.29
2171	2268	8.153550	GGATCATCTGTTTATCAGTACTTCCAT	58.846	37.037	0.00	0.00	43.97	3.41
2284	2461	2.857152	GCATACAAGCTCTCTTCTCACG	59.143	50.000	0.00	0.00	0.00	4.35
2344	2527	3.319137	AGCCAGTACACATACACACAG	57.681	47.619	0.00	0.00	33.30	3.66
2423	2608	0.734889	GGCATGATGTACACACTGCC	59.265	55.000	21.71	21.71	42.00	4.85
2507	2692	6.965500	AGTGTAGTACATTTAGTCGATTCACG	59.035	38.462	6.21	0.00	44.09	4.35
2516	2701	8.786898	TGAAACGACTAGTGTAGTACATTTAGT	58.213	33.333	21.18	21.18	39.59	2.24
2517	2702	9.275231	CTGAAACGACTAGTGTAGTACATTTAG	57.725	37.037	6.21	13.21	39.59	1.85
2520	2705	7.211966	ACTGAAACGACTAGTGTAGTACATT	57.788	36.000	6.21	4.79	39.59	2.71
2521	2706	6.814506	ACTGAAACGACTAGTGTAGTACAT	57.185	37.500	6.21	0.00	39.59	2.29
2527	4031	6.931281	AGTACTGTACTGAAACGACTAGTGTA	59.069	38.462	19.09	0.00	37.69	2.90
2531	4035	6.476896	GCTAGTACTGTACTGAAACGACTAG	58.523	44.000	26.45	15.00	39.81	2.57
2532	4036	5.062683	CGCTAGTACTGTACTGAAACGACTA	59.937	44.000	26.45	6.03	39.81	2.59
2538	4042	4.097437	CCCATCGCTAGTACTGTACTGAAA	59.903	45.833	26.45	9.31	39.81	2.69
2539	4043	3.630769	CCCATCGCTAGTACTGTACTGAA	59.369	47.826	26.45	9.98	39.81	3.02
2558	4062	2.280524	CGCAACTCAACCGACCCA	60.281	61.111	0.00	0.00	0.00	4.51
2559	4063	3.723348	GCGCAACTCAACCGACCC	61.723	66.667	0.30	0.00	0.00	4.46
2560	4064	2.970324	TGCGCAACTCAACCGACC	60.970	61.111	8.16	0.00	0.00	4.79
2638	4148	1.201343	GCGTAATGGAAGCTCGTCTC	58.799	55.000	0.00	0.00	0.00	3.36
2696	4209	6.003234	GGTTTCCTAAAAGCTCTTCAGAAC	57.997	41.667	0.00	0.00	39.30	3.01
2719	4232	2.436542	TGGTCCAAACCGGTCCATATAG	59.563	50.000	8.04	0.00	46.71	1.31
2721	4234	1.291109	TGGTCCAAACCGGTCCATAT	58.709	50.000	8.04	0.00	46.71	1.78
2853	4368	6.129561	CGTGTTAACGGAAAATGTAAAAGCTG	60.130	38.462	0.26	0.00	46.25	4.24
2855	4370	6.119053	CGTGTTAACGGAAAATGTAAAAGC	57.881	37.500	0.26	0.00	46.25	3.51
2878	4393	7.129622	TGAATGTGTATCGAAAAATATTCCGC	58.870	34.615	0.00	0.00	0.00	5.54
2880	4395	9.781834	TGTTGAATGTGTATCGAAAAATATTCC	57.218	29.630	0.00	0.00	0.00	3.01
3045	4560	5.588648	CAGGAAAGTTTCAAGGTGTGTCTAA	59.411	40.000	17.16	0.00	0.00	2.10
3070	4585	9.979578	ATATTAAAGAAATGTTCAAAGTGCACA	57.020	25.926	21.04	0.00	0.00	4.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.