AutoCloner

Multiple sequence alignment - TraesCS5B01G045400

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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	TraesCS5B01G045400	chr5B	100.000	3530	0	0	1	3530	50642457	50645986	0.000000e+00	6519
1	TraesCS5B01G045400	chr5B	96.143	1815	43	11	753	2563	50933340	50931549	0.000000e+00	2939
2	TraesCS5B01G045400	chr5B	93.363	1356	60	19	1331	2674	38355252	38356589	0.000000e+00	1978
3	TraesCS5B01G045400	chr5B	97.253	801	19	2	2730	3530	50931469	50930672	0.000000e+00	1354
4	TraesCS5B01G045400	chr5B	84.592	1006	85	43	2560	3530	555949641	555948671	0.000000e+00	935
5	TraesCS5B01G045400	chr5B	93.002	643	34	8	1	642	50934697	50934065	0.000000e+00	928
6	TraesCS5B01G045400	chr5B	88.848	538	57	3	2	539	50625598	50626132	0.000000e+00	658
7	TraesCS5B01G045400	chr5B	84.874	357	31	14	941	1292	38354917	38355255	4.360000e-89	339
8	TraesCS5B01G045400	chr5B	97.590	83	2	0	2609	2691	50931551	50931469	3.670000e-30	143
9	TraesCS5B01G045400	chr5B	85.507	138	16	3	2980	3116	38356823	38356957	1.320000e-29	141
10	TraesCS5B01G045400	chr5D	92.603	2974	71	49	639	3530	48448936	48451842	0.000000e+00	4135
11	TraesCS5B01G045400	chr5D	93.306	2211	54	30	839	2982	48049181	48046998	0.000000e+00	3177
12	TraesCS5B01G045400	chr5D	88.248	936	72	16	939	1872	42874865	42873966	0.000000e+00	1085
13	TraesCS5B01G045400	chr5D	85.317	1008	79	46	2560	3530	521254258	521255233	0.000000e+00	977
14	TraesCS5B01G045400	chr5D	84.378	1069	65	39	2073	3108	42869238	42868239	0.000000e+00	955
15	TraesCS5B01G045400	chr5D	89.119	772	46	22	1873	2618	42867029	42866270	0.000000e+00	926
16	TraesCS5B01G045400	chr5D	92.188	640	38	6	1	638	48049982	48049353	0.000000e+00	894
17	TraesCS5B01G045400	chr5D	91.181	635	45	7	1	634	48447917	48448541	0.000000e+00	852
18	TraesCS5B01G045400	chr5D	93.287	432	18	6	3050	3478	48046983	48046560	8.320000e-176	627
19	TraesCS5B01G045400	chr5D	85.093	483	41	16	2517	2977	42806811	42806338	6.900000e-127	464
20	TraesCS5B01G045400	chr5D	81.609	522	69	15	1	509	48654774	48655281	1.180000e-109	407
21	TraesCS5B01G045400	chr5D	91.346	104	2	3	671	773	48049276	48049179	6.150000e-28	135
22	TraesCS5B01G045400	chr5D	93.902	82	4	1	3039	3119	42806328	42806247	4.790000e-24	122
23	TraesCS5B01G045400	chr5D	90.909	77	6	1	1	76	48396139	48396215	6.230000e-18	102
24	TraesCS5B01G045400	chr5A	93.822	2250	65	26	1289	3478	38017536	38015301	0.000000e+00	3317
25	TraesCS5B01G045400	chr5A	86.983	2151	154	48	989	3111	31266879	31268931	0.000000e+00	2305
26	TraesCS5B01G045400	chr5A	89.103	1606	110	30	1534	3111	31219584	31218016	0.000000e+00	1936
27	TraesCS5B01G045400	chr5A	92.570	646	28	9	1	634	38018886	38018249	0.000000e+00	909
28	TraesCS5B01G045400	chr5A	84.478	393	21	15	725	1108	38017901	38017540	5.610000e-93	351
29	TraesCS5B01G045400	chr5A	84.848	165	21	2	2956	3116	31273107	31273271	2.820000e-36	163
30	TraesCS5B01G045400	chr5A	98.438	64	1	0	671	734	38018166	38018103	2.880000e-21	113
31	TraesCS5B01G045400	chr3D	87.073	1524	132	34	1110	2602	116076330	116077819	0.000000e+00	1663
32	TraesCS5B01G045400	chr3D	93.541	418	19	4	3117	3530	32389134	32388721	1.800000e-172	616
33	TraesCS5B01G045400	chr3D	85.865	474	34	15	2560	3018	32389696	32389241	1.150000e-129	473
34	TraesCS5B01G045400	chr6A	85.543	1003	79	39	2560	3530	66267418	66268386	0.000000e+00	989
35	TraesCS5B01G045400	chr6A	92.405	79	5	1	3039	3116	132972250	132972172	1.040000e-20	111
36	TraesCS5B01G045400	chr1A	85.025	995	86	36	2555	3530	567965930	567964980	0.000000e+00	953
37	TraesCS5B01G045400	chr3B	87.650	834	77	14	1163	1989	169648131	169648945	0.000000e+00	946
38	TraesCS5B01G045400	chr4B	93.301	418	20	4	3117	3530	310971838	310972251	8.380000e-171	610
39	TraesCS5B01G045400	chr1B	83.737	578	43	19	1217	1766	681696843	681696289	1.890000e-137	499
40	TraesCS5B01G045400	chr4A	91.463	82	6	1	3036	3116	197481257	197481338	1.040000e-20	111

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	TraesCS5B01G045400	chr5B	50642457	50645986	3529	False	6519.000000	6519	100.000000	1	3530	1	chr5B.!!$F2	3529
1	TraesCS5B01G045400	chr5B	50930672	50934697	4025	True	1341.000000	2939	95.997000	1	3530	4	chr5B.!!$R2	3529
2	TraesCS5B01G045400	chr5B	555948671	555949641	970	True	935.000000	935	84.592000	2560	3530	1	chr5B.!!$R1	970
3	TraesCS5B01G045400	chr5B	38354917	38356957	2040	False	819.333333	1978	87.914667	941	3116	3	chr5B.!!$F3	2175
4	TraesCS5B01G045400	chr5B	50625598	50626132	534	False	658.000000	658	88.848000	2	539	1	chr5B.!!$F1	537
5	TraesCS5B01G045400	chr5D	48447917	48451842	3925	False	2493.500000	4135	91.892000	1	3530	2	chr5D.!!$F4	3529
6	TraesCS5B01G045400	chr5D	48046560	48049982	3422	True	1208.250000	3177	92.531750	1	3478	4	chr5D.!!$R4	3477
7	TraesCS5B01G045400	chr5D	42873966	42874865	899	True	1085.000000	1085	88.248000	939	1872	1	chr5D.!!$R1	933
8	TraesCS5B01G045400	chr5D	521254258	521255233	975	False	977.000000	977	85.317000	2560	3530	1	chr5D.!!$F3	970
9	TraesCS5B01G045400	chr5D	42866270	42869238	2968	True	940.500000	955	86.748500	1873	3108	2	chr5D.!!$R3	1235
10	TraesCS5B01G045400	chr5D	48654774	48655281	507	False	407.000000	407	81.609000	1	509	1	chr5D.!!$F2	508
11	TraesCS5B01G045400	chr5D	42806247	42806811	564	True	293.000000	464	89.497500	2517	3119	2	chr5D.!!$R2	602
12	TraesCS5B01G045400	chr5A	31266879	31268931	2052	False	2305.000000	2305	86.983000	989	3111	1	chr5A.!!$F1	2122
13	TraesCS5B01G045400	chr5A	31218016	31219584	1568	True	1936.000000	1936	89.103000	1534	3111	1	chr5A.!!$R1	1577
14	TraesCS5B01G045400	chr5A	38015301	38018886	3585	True	1172.500000	3317	92.327000	1	3478	4	chr5A.!!$R2	3477
15	TraesCS5B01G045400	chr3D	116076330	116077819	1489	False	1663.000000	1663	87.073000	1110	2602	1	chr3D.!!$F1	1492
16	TraesCS5B01G045400	chr3D	32388721	32389696	975	True	544.500000	616	89.703000	2560	3530	2	chr3D.!!$R1	970
17	TraesCS5B01G045400	chr6A	66267418	66268386	968	False	989.000000	989	85.543000	2560	3530	1	chr6A.!!$F1	970
18	TraesCS5B01G045400	chr1A	567964980	567965930	950	True	953.000000	953	85.025000	2555	3530	1	chr1A.!!$R1	975
19	TraesCS5B01G045400	chr3B	169648131	169648945	814	False	946.000000	946	87.650000	1163	1989	1	chr3B.!!$F1	826
20	TraesCS5B01G045400	chr1B	681696289	681696843	554	True	499.000000	499	83.737000	1217	1766	1	chr1B.!!$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
833	2074	0.834687	ACCCGCTTTGACTAGGTCCA	60.835	55.0	0.0	0.0	0.0	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2624	4028	0.953471	CGACTGCCCAAATCCGAACA	60.953	55.0	0.0	0.0	0.0	3.18	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
116	117	5.335127	CCATTGCGTCCAAAGATCTAAAAG	58.665	41.667	0.00	0.00	34.05	2.27
204	210	2.668457	GCATCTCTCACACCGTGTAAAG	59.332	50.000	3.25	5.45	34.79	1.85
254	260	6.153340	AGTTCCAATAGGATCAAAACATGTGG	59.847	38.462	0.00	0.00	45.26	4.17
369	378	9.712305	TTTTCTATGAAGTGGTTTTGTTTTCAA	57.288	25.926	0.00	0.00	38.10	2.69
371	380	6.970043	TCTATGAAGTGGTTTTGTTTTCAACG	59.030	34.615	0.00	0.00	39.73	4.10
398	407	6.094603	ACATCAATTGCTCTATGAACCACTTC	59.905	38.462	10.81	0.00	0.00	3.01
461	497	7.775397	ACATTGCCAAGATAAATAAACATGC	57.225	32.000	0.00	0.00	0.00	4.06
672	1105	3.467119	CGCGGACACGAAACGGAG	61.467	66.667	0.00	0.00	44.60	4.63
833	2074	0.834687	ACCCGCTTTGACTAGGTCCA	60.835	55.000	0.00	0.00	0.00	4.02
837	2078	1.802880	CGCTTTGACTAGGTCCATCGG	60.803	57.143	0.00	0.00	0.00	4.18
846	2087	1.745489	GGTCCATCGGCACAAGACC	60.745	63.158	0.00	0.00	40.21	3.85
873	2114	2.428569	CGTGACGTGACCTGACGG	60.429	66.667	0.00	0.00	43.84	4.79
876	2117	1.829096	TGACGTGACCTGACGGGAA	60.829	57.895	7.51	0.00	43.84	3.97
905	2152	2.068821	GCTCTCTCCCCTGCCATCA	61.069	63.158	0.00	0.00	0.00	3.07
907	2154	1.690633	TCTCTCCCCTGCCATCACC	60.691	63.158	0.00	0.00	0.00	4.02
908	2155	3.083349	TCTCCCCTGCCATCACCG	61.083	66.667	0.00	0.00	0.00	4.94
952	2203	1.153695	TATAGCCCCCTCCGGATCCT	61.154	60.000	3.57	0.00	0.00	3.24
958	2209	3.234730	CCTCCGGATCCTTCCCCG	61.235	72.222	3.57	0.00	44.94	5.73
1022	2282	1.213013	CTCTCCGTCTTCACCACCG	59.787	63.158	0.00	0.00	0.00	4.94
1031	2291	3.477956	TTCACCACCGACCCCTCCT	62.478	63.158	0.00	0.00	0.00	3.69
1032	2292	3.391382	CACCACCGACCCCTCCTC	61.391	72.222	0.00	0.00	0.00	3.71
2587	3988	5.425217	TCTGTTATGTTTCTAGCCATGGAGA	59.575	40.000	18.40	7.60	0.00	3.71
2602	4003	6.043706	AGCCATGGAGAATTTACTGCTAGTAT	59.956	38.462	18.40	0.00	29.64	2.12
2603	4004	7.235606	AGCCATGGAGAATTTACTGCTAGTATA	59.764	37.037	18.40	0.00	29.64	1.47
2604	4005	7.547370	GCCATGGAGAATTTACTGCTAGTATAG	59.453	40.741	18.40	0.00	43.09	1.31
2605	4006	8.589338	CCATGGAGAATTTACTGCTAGTATAGT	58.411	37.037	5.56	0.00	41.93	2.12
2624	4028	3.683802	AGTAGTGCGTAGTGGAGTAGTT	58.316	45.455	0.00	0.00	0.00	2.24
2678	4115	6.713762	AGAGGTTCAGATAAGAGATGAGTG	57.286	41.667	0.00	0.00	0.00	3.51
2718	4155	1.742831	GCACCGAATGATTGTTGCCTA	59.257	47.619	0.00	0.00	0.00	3.93
2733	4183	1.816835	TGCCTACTTGTCCAGTACGAG	59.183	52.381	0.00	0.00	44.27	4.18
2784	4234	1.686587	TCTTCTCGTTGCTCTGTTCCA	59.313	47.619	0.00	0.00	0.00	3.53
2796	4280	2.547211	CTCTGTTCCAGACTGTTTGCTG	59.453	50.000	0.93	0.00	35.39	4.41
2804	4288	3.249559	CCAGACTGTTTGCTGAACTTCTC	59.750	47.826	0.93	0.00	39.08	2.87
2812	4296	3.482156	TGCTGAACTTCTCTTCTTGCT	57.518	42.857	0.00	0.00	0.00	3.91
2908	4416	7.497909	TGAATCATCCTATGCATGCATACATAG	59.502	37.037	31.75	29.10	43.49	2.23
2993	4502	0.240945	GACCCGATGCCACAAACTTG	59.759	55.000	0.00	0.00	0.00	3.16
3043	4557	7.258441	TCTGTTATGATGTGCAGTACTAAGTC	58.742	38.462	0.00	0.00	0.00	3.01
3058	4572	4.238514	ACTAAGTCGAGTTTGCAGATGAC	58.761	43.478	11.42	0.00	0.00	3.06
3219	4906	5.664457	TCTGTTAAGGTGTGCATGATAGAG	58.336	41.667	0.00	0.00	0.00	2.43
3220	4907	5.422012	TCTGTTAAGGTGTGCATGATAGAGA	59.578	40.000	0.00	0.00	0.00	3.10
3231	4918	4.460382	TGCATGATAGAGATCGACTGCATA	59.540	41.667	0.00	0.00	38.56	3.14
3455	5164	6.990939	AGAACCTGACTAAAGTTACCTTGAAC	59.009	38.462	0.00	0.00	0.00	3.18
3473	5182	2.169832	ACTGTGTCTCATCAAACGGG	57.830	50.000	0.00	0.00	0.00	5.28

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
204	210	6.534634	AGTACTCCTAATATTGATGGTTGCC	58.465	40.000	0.00	0.00	0.00	4.52
254	260	8.863049	CAAATGGTCTTCTACAAACAAATATGC	58.137	33.333	0.00	0.00	0.00	3.14
339	345	8.871686	AACAAAACCACTTCATAGAAAATGTC	57.128	30.769	0.00	0.00	0.00	3.06
342	351	9.883142	TGAAAACAAAACCACTTCATAGAAAAT	57.117	25.926	0.00	0.00	0.00	1.82
369	378	5.523916	GGTTCATAGAGCAATTGATGTACGT	59.476	40.000	10.34	0.00	0.00	3.57
371	380	6.540189	AGTGGTTCATAGAGCAATTGATGTAC	59.460	38.462	10.34	7.71	0.00	2.90
398	407	5.683859	CAAAGAATGTTCTTCTTCGTCAGG	58.316	41.667	8.34	0.00	46.22	3.86
634	677	2.101917	GCCAATGCAAATGACCATAGCT	59.898	45.455	4.54	0.00	37.47	3.32
635	678	2.476821	GCCAATGCAAATGACCATAGC	58.523	47.619	4.54	0.00	37.47	2.97
636	679	2.734670	CGCCAATGCAAATGACCATAG	58.265	47.619	4.54	0.00	37.32	2.23
672	1105	3.083997	AGACGGTGGATCCAGGGC	61.084	66.667	16.81	12.91	35.57	5.19
801	2038	3.636231	CGGGTCAAGGGTCCAGCA	61.636	66.667	0.00	0.00	0.00	4.41
837	2078	1.590525	TCACGTCACGGTCTTGTGC	60.591	57.895	0.35	0.00	39.73	4.57
952	2203	2.204167	TGGAATGGGGACGGGGAA	60.204	61.111	0.00	0.00	0.00	3.97
958	2209	1.450025	GAACGAACTGGAATGGGGAC	58.550	55.000	0.00	0.00	0.00	4.46
1022	2282	2.284151	GGAGGAGGAGGAGGGGTC	59.716	72.222	0.00	0.00	0.00	4.46
1031	2291	0.996762	GAGGAGGAGGAGGAGGAGGA	60.997	65.000	0.00	0.00	0.00	3.71
1032	2292	1.541672	GAGGAGGAGGAGGAGGAGG	59.458	68.421	0.00	0.00	0.00	4.30
1854	3199	1.507174	GCCGTCGTTGTAGAGCTCT	59.493	57.895	22.17	22.17	0.00	4.09
2329	3693	5.353394	TCCTTGATGGGTATGTAGTTGAC	57.647	43.478	0.00	0.00	36.20	3.18
2587	3988	7.938715	ACGCACTACTATACTAGCAGTAAATT	58.061	34.615	0.00	0.00	33.89	1.82
2602	4003	4.478206	ACTACTCCACTACGCACTACTA	57.522	45.455	0.00	0.00	0.00	1.82
2603	4004	3.347077	ACTACTCCACTACGCACTACT	57.653	47.619	0.00	0.00	0.00	2.57
2604	4005	3.190118	ACAACTACTCCACTACGCACTAC	59.810	47.826	0.00	0.00	0.00	2.73
2605	4006	3.415212	ACAACTACTCCACTACGCACTA	58.585	45.455	0.00	0.00	0.00	2.74
2606	4007	2.236766	ACAACTACTCCACTACGCACT	58.763	47.619	0.00	0.00	0.00	4.40
2624	4028	0.953471	CGACTGCCCAAATCCGAACA	60.953	55.000	0.00	0.00	0.00	3.18
2678	4115	2.414138	GCCACAAAATGCAATCAGAAGC	59.586	45.455	0.00	0.00	0.00	3.86
2718	4155	4.038763	TGATTCAACTCGTACTGGACAAGT	59.961	41.667	0.00	0.00	43.40	3.16
2733	4183	5.844301	ATTCGCACCAAAATTGATTCAAC	57.156	34.783	0.15	0.00	0.00	3.18
2784	4234	4.414337	AGAGAAGTTCAGCAAACAGTCT	57.586	40.909	5.50	6.41	40.56	3.24
2796	4280	3.563390	AGCACAAGCAAGAAGAGAAGTTC	59.437	43.478	0.00	0.00	45.49	3.01
2804	4288	6.074142	GGAACAAAATTAGCACAAGCAAGAAG	60.074	38.462	0.00	0.00	45.49	2.85
2812	4296	4.662468	TGCAGGAACAAAATTAGCACAA	57.338	36.364	0.00	0.00	0.00	3.33
2908	4416	6.262273	TCCTAACAACTGAACAACATTCCTTC	59.738	38.462	0.00	0.00	0.00	3.46
2993	4502	2.159653	AGAACGAAACGATCATTGCAGC	60.160	45.455	0.00	0.00	31.23	5.25
3043	4557	2.096069	CACAAGGTCATCTGCAAACTCG	60.096	50.000	0.00	0.00	0.00	4.18
3058	4572	2.422479	CTGCAGATCAACCATCACAAGG	59.578	50.000	8.42	0.00	33.29	3.61
3219	4906	7.322222	GTGCAAAAATAGAATATGCAGTCGATC	59.678	37.037	0.00	0.00	46.54	3.69
3220	4907	7.134815	GTGCAAAAATAGAATATGCAGTCGAT	58.865	34.615	0.00	0.00	46.54	3.59
3231	4918	4.704540	TGATCCACGGTGCAAAAATAGAAT	59.295	37.500	1.68	0.00	0.00	2.40
3455	5164	2.169832	ACCCGTTTGATGAGACACAG	57.830	50.000	0.00	0.00	0.00	3.66
3473	5182	1.264288	CAGCAACCAACTCTCCGAAAC	59.736	52.381	0.00	0.00	0.00	2.78

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.