AutoCloner

Multiple sequence alignment - TraesCS5B01G493900

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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	TraesCS5B01G493900	chr5B	100.000	3854	0	0	1	3854	661867190	661863337	0.000000e+00	7118.0
1	TraesCS5B01G493900	chr5B	79.414	2390	409	45	512	2844	661881005	661878642	0.000000e+00	1611.0
2	TraesCS5B01G493900	chr5B	83.173	1456	231	12	1389	2837	661888711	661887263	0.000000e+00	1319.0
3	TraesCS5B01G493900	chr5B	81.094	640	109	11	62	697	661892133	661891502	5.750000e-138	501.0
4	TraesCS5B01G493900	chr5B	81.979	566	97	3	11	573	661881669	661881106	3.480000e-130	475.0
5	TraesCS5B01G493900	chr5B	87.838	296	28	2	2964	3251	661885958	661885663	1.330000e-89	340.0
6	TraesCS5B01G493900	chr5B	87.108	287	37	0	1083	1369	661889490	661889204	3.710000e-85	326.0
7	TraesCS5B01G493900	chr5B	87.814	279	22	4	3458	3728	661878010	661877736	2.230000e-82	316.0
8	TraesCS5B01G493900	chr5B	81.407	398	55	14	693	1089	661891347	661890968	1.340000e-79	307.0
9	TraesCS5B01G493900	chr5B	77.350	234	35	10	3628	3851	661523837	661524062	5.230000e-24	122.0
10	TraesCS5B01G493900	chr5D	93.908	3874	206	10	1	3854	526456529	526452666	0.000000e+00	5819.0
11	TraesCS5B01G493900	chr5D	82.625	3292	484	55	9	3251	526472936	526469684	0.000000e+00	2830.0
12	TraesCS5B01G493900	chr5D	80.647	2873	484	45	10	2867	526426583	526423768	0.000000e+00	2159.0
13	TraesCS5B01G493900	chr5D	79.807	2387	390	44	512	2844	526463399	526461051	0.000000e+00	1653.0
14	TraesCS5B01G493900	chr5D	80.656	610	109	7	1	606	526463996	526463392	7.540000e-127	464.0
15	TraesCS5B01G493900	chr5D	84.352	409	47	9	3458	3854	526433718	526433315	6.040000e-103	385.0
16	TraesCS5B01G493900	chr5D	78.448	232	31	7	3628	3851	526410155	526410375	2.420000e-27	134.0
17	TraesCS5B01G493900	chr5D	95.082	61	3	0	3794	3854	526422932	526422872	3.170000e-16	97.1
18	TraesCS5B01G493900	chr5A	83.723	2353	357	21	505	2844	653693219	653690880	0.000000e+00	2200.0
19	TraesCS5B01G493900	chr5A	82.947	2375	374	26	505	2868	653617670	653615316	0.000000e+00	2113.0
20	TraesCS5B01G493900	chr5A	89.006	473	35	9	3396	3854	653679500	653679031	1.550000e-158	569.0
21	TraesCS5B01G493900	chr5A	85.223	291	30	9	3568	3854	653690142	653689861	1.750000e-73	287.0
22	TraesCS5B01G493900	chr5A	87.815	238	22	3	3620	3854	653564516	653564283	4.910000e-69	272.0
23	TraesCS5B01G493900	chr6B	74.766	963	199	31	562	1503	716439434	716438495	3.610000e-105	392.0
24	TraesCS5B01G493900	chr6B	74.327	966	198	33	562	1503	718391401	718390462	7.870000e-97	364.0
25	TraesCS5B01G493900	chr6B	73.793	1015	218	34	964	1957	29938446	29937459	1.320000e-94	357.0
26	TraesCS5B01G493900	chr3A	93.846	65	4	0	3787	3851	638015566	638015630	8.810000e-17	99.0
27	TraesCS5B01G493900	chr3D	92.308	65	5	0	3787	3851	496767529	496767593	4.100000e-15	93.5
28	TraesCS5B01G493900	chr3B	92.308	65	5	0	3787	3851	656065905	656065969	4.100000e-15	93.5
29	TraesCS5B01G493900	chr2B	89.231	65	7	0	3787	3851	447824994	447825058	8.870000e-12	82.4

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	TraesCS5B01G493900	chr5B	661863337	661867190	3853	True	7118.000	7118	100.000000	1	3854	1	chr5B.!!$R1	3853
1	TraesCS5B01G493900	chr5B	661877736	661892133	14397	True	649.375	1611	83.728375	11	3728	8	chr5B.!!$R2	3717
2	TraesCS5B01G493900	chr5D	526452666	526456529	3863	True	5819.000	5819	93.908000	1	3854	1	chr5D.!!$R2	3853
3	TraesCS5B01G493900	chr5D	526469684	526472936	3252	True	2830.000	2830	82.625000	9	3251	1	chr5D.!!$R3	3242
4	TraesCS5B01G493900	chr5D	526422872	526426583	3711	True	1128.050	2159	87.864500	10	3854	2	chr5D.!!$R4	3844
5	TraesCS5B01G493900	chr5D	526461051	526463996	2945	True	1058.500	1653	80.231500	1	2844	2	chr5D.!!$R5	2843
6	TraesCS5B01G493900	chr5A	653615316	653617670	2354	True	2113.000	2113	82.947000	505	2868	1	chr5A.!!$R2	2363
7	TraesCS5B01G493900	chr5A	653689861	653693219	3358	True	1243.500	2200	84.473000	505	3854	2	chr5A.!!$R4	3349
8	TraesCS5B01G493900	chr6B	716438495	716439434	939	True	392.000	392	74.766000	562	1503	1	chr6B.!!$R2	941
9	TraesCS5B01G493900	chr6B	718390462	718391401	939	True	364.000	364	74.327000	562	1503	1	chr6B.!!$R3	941
10	TraesCS5B01G493900	chr6B	29937459	29938446	987	True	357.000	357	73.793000	964	1957	1	chr6B.!!$R1	993

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	Hairpin	End Stability	Orientation
495	500	2.616524	TGTTACTACTGGGCAAGAGGT	58.383	47.619	0.00	0.00	3.85	F
834	1116	4.212214	GGTAATGTGGAATCTCAATCTCGC	59.788	45.833	0.00	0.00	5.03	F
1631	12504	1.136891	GGGTATTGGCCAGCATGAAAC	59.863	52.381	5.11	39.69	2.78	F

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability	Orientation
1346	12191	0.038892	CTCTGGCCACAATGCACAAC	60.039	55.0	3.32	R
2467	13349	0.467384	ATCGCCCAGGAGAGTTGATG	59.533	55.0	3.07	R
3150	14502	0.444260	GCTGCAACTAAGTTCGGCTC	59.556	55.0	4.70	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
58	60	4.051661	TGGATTGGGCATTCTTTCTCTT	57.948	40.909	0.00	0.00	0.00	2.85
390	395	7.231467	ACTTATGCCTTGAAGGTAGAAAGAAA	58.769	34.615	24.02	6.89	37.80	2.52
412	417	8.377799	AGAAATTTGGAAAATTTGGAGCATACT	58.622	29.630	13.78	2.14	30.68	2.12
447	452	3.703001	TCTGAGGAGGAACAATGTTCC	57.297	47.619	31.86	31.86	38.86	3.62
483	488	7.652105	TGATATTGCCGAGAAGAATGTTACTAC	59.348	37.037	0.00	0.00	0.00	2.73
495	500	2.616524	TGTTACTACTGGGCAAGAGGT	58.383	47.619	0.00	0.00	0.00	3.85
577	669	6.352516	AGTCAAATCTGTTCCATCTATGTCC	58.647	40.000	0.00	0.00	0.00	4.02
834	1116	4.212214	GGTAATGTGGAATCTCAATCTCGC	59.788	45.833	0.00	0.00	0.00	5.03
844	1126	4.584029	TCTCAATCTCGCGTCATTTTTC	57.416	40.909	5.77	0.00	0.00	2.29
1041	1324	8.948631	ATTTGAATGTATCTTGTCTACACGAT	57.051	30.769	7.20	7.20	38.26	3.73
1346	12191	9.403110	CAATACTTTGAGGAAATGTTTCTTGAG	57.597	33.333	5.56	0.09	34.86	3.02
1378	12223	3.567164	GTGGCCAGAGGATCAACATATTG	59.433	47.826	5.11	0.00	37.82	1.90
1545	12417	7.887996	TTCTTTTAAAATGCATGATGTGGTC	57.112	32.000	0.00	0.00	0.00	4.02
1631	12504	1.136891	GGGTATTGGCCAGCATGAAAC	59.863	52.381	5.11	0.00	39.69	2.78
1685	12558	3.873952	GTCTCCTTGATGTGGAACTATGC	59.126	47.826	0.00	0.00	38.04	3.14
1701	12574	6.377146	GGAACTATGCATTAAAACTTCCTCCA	59.623	38.462	3.54	0.00	0.00	3.86
1724	12597	1.312815	GGCTCTAATCCATGCCACAC	58.687	55.000	0.00	0.00	44.34	3.82
1725	12598	1.408683	GGCTCTAATCCATGCCACACA	60.409	52.381	0.00	0.00	44.34	3.72
1860	12733	7.070821	GGAATACCTGAAGAGTTATGTTCCCTA	59.929	40.741	0.00	0.00	0.00	3.53
2067	12946	2.030185	TCGAGTTTCGAAGGACCTTCTG	60.030	50.000	27.69	21.22	46.90	3.02
2304	13186	6.704289	ATGTGTGTCATGGAGGAAATAATG	57.296	37.500	0.00	0.00	35.19	1.90
2419	13301	1.281867	TGGAAACATCTCCGGCATCTT	59.718	47.619	0.00	0.00	38.44	2.40
2467	13349	2.608090	GTGTATTCCTGCGGAAAGCTAC	59.392	50.000	12.83	11.32	45.41	3.58
2472	13354	3.622206	ATTCCTGCGGAAAGCTACATCAA	60.622	43.478	12.83	0.00	45.41	2.57
2488	13370	1.817099	CAACTCTCCTGGGCGATGC	60.817	63.158	0.00	0.00	0.00	3.91
2496	13378	4.112433	TGGGCGATGCATCTGCCA	62.112	61.111	38.67	29.13	43.41	4.92
2509	13391	0.674581	TCTGCCATGCCTCGAACAAG	60.675	55.000	0.00	0.00	0.00	3.16
2511	13393	1.236616	TGCCATGCCTCGAACAAGTG	61.237	55.000	0.00	0.00	0.00	3.16
2555	13437	1.062525	GGCAAGCGTTTATGAGGCG	59.937	57.895	0.00	0.00	43.72	5.52
2579	13461	0.673644	GGTGATAACCAGTGCAGCGT	60.674	55.000	0.00	0.00	0.00	5.07
2604	13489	4.336889	AGACAGTTCGAAGACATTTCCA	57.663	40.909	0.00	0.00	34.32	3.53
2664	13549	1.070289	GTCGGTATTGGGGATCCTGAC	59.930	57.143	12.58	3.17	0.00	3.51
2818	13709	4.340950	TGGAATTGGAAGAAGGTGTCAAAC	59.659	41.667	0.00	0.00	0.00	2.93
2913	13941	8.052748	AGTATCCATGCTTCAATTTACACCTTA	58.947	33.333	0.00	0.00	0.00	2.69
2916	13944	5.105797	CCATGCTTCAATTTACACCTTAGCA	60.106	40.000	0.00	0.00	41.08	3.49
3051	14403	3.988379	TTGCAAGTGCTACCTTTTGAG	57.012	42.857	4.69	0.00	42.66	3.02
3139	14491	1.072806	TCTCCTGTTTGCAGCTGATGT	59.927	47.619	20.43	0.00	41.26	3.06
3140	14492	1.199327	CTCCTGTTTGCAGCTGATGTG	59.801	52.381	20.43	1.35	41.26	3.21
3150	14502	2.608752	GCAGCTGATGTGTCCCTTTTTG	60.609	50.000	20.43	0.00	0.00	2.44
3153	14505	2.352127	GCTGATGTGTCCCTTTTTGAGC	60.352	50.000	0.00	0.00	0.00	4.26
3157	14509	1.314730	GTGTCCCTTTTTGAGCCGAA	58.685	50.000	0.00	0.00	0.00	4.30
3161	14513	3.143728	GTCCCTTTTTGAGCCGAACTTA	58.856	45.455	0.00	0.00	0.00	2.24
3247	14600	4.699257	TGGTTTTTGAAATTTGCAAGTGCT	59.301	33.333	0.00	0.00	42.66	4.40
3251	14604	5.964887	TTTGAAATTTGCAAGTGCTACAC	57.035	34.783	0.00	0.00	42.66	2.90
3270	14623	9.116067	TGCTACACTACATTTTGGGTAAATATC	57.884	33.333	0.00	0.00	34.69	1.63
3387	14740	0.105039	CAAGCCTCGGAGGTACCATC	59.895	60.000	24.30	8.66	37.80	3.51
3407	14760	1.269726	CCTGGTTGCAAATGTGTGGAC	60.270	52.381	0.00	0.00	0.00	4.02
3454	14893	1.302192	GTCTTTGCTGGGCACGGTA	60.302	57.895	0.00	0.00	38.71	4.02
3482	14980	6.426328	ACTCAGTTTCAGAATTTGAGCTAGTG	59.574	38.462	17.99	1.56	39.01	2.74
3518	15022	1.522668	TTCACCATGCTTTGAGACCG	58.477	50.000	0.00	0.00	0.00	4.79
3571	15075	2.500392	TTCCCCGGTGACTATTTTGG	57.500	50.000	0.00	0.00	0.00	3.28
3613	15117	3.500982	CCATGGTTTAATTGTGAGCACG	58.499	45.455	2.57	0.00	0.00	5.34
3617	15121	3.818210	TGGTTTAATTGTGAGCACGATGT	59.182	39.130	4.20	0.00	35.67	3.06
3681	15189	6.575162	AAAATAGGATTGTTCGCTTCACTT	57.425	33.333	0.00	0.00	0.00	3.16
3744	15260	0.953727	TGGAACTGCTGTGCATGTTC	59.046	50.000	17.80	17.80	41.34	3.18
3757	15273	1.337823	GCATGTTCCACGAGGTACAGT	60.338	52.381	15.72	3.42	46.51	3.55
3759	15275	0.594602	TGTTCCACGAGGTACAGTCG	59.405	55.000	7.23	13.63	39.88	4.18
3784	15300	1.409427	GACATCCGGTCCCTTACTCTG	59.591	57.143	0.00	0.00	40.83	3.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	9	4.322801	GCTATAGTGACCCATCATGTACCC	60.323	50.000	0.84	0.00	37.14	3.69
113	115	4.094442	CCCGCTGTGATTTCCTTAACTTAC	59.906	45.833	0.00	0.00	0.00	2.34
306	308	6.236017	AGTTCAGTTATCAATTTCGCGAAA	57.764	33.333	33.83	33.83	34.46	3.46
352	357	9.461312	TTCAAGGCATAAGTTTACATGTCTAAT	57.539	29.630	0.00	0.00	36.11	1.73
390	395	7.180051	TGGTAGTATGCTCCAAATTTTCCAAAT	59.820	33.333	0.00	0.00	0.00	2.32
412	417	5.338381	CCTCCTCAGAAGCAAGTTATTGGTA	60.338	44.000	0.00	0.00	46.14	3.25
447	452	9.591792	TCTTCTCGGCAATATCATTCATATAAG	57.408	33.333	0.00	0.00	0.00	1.73
483	488	1.139853	CCTTAGCTACCTCTTGCCCAG	59.860	57.143	0.00	0.00	0.00	4.45
495	500	3.197983	GGCCTCTTGAAGTTCCTTAGCTA	59.802	47.826	0.00	0.00	0.00	3.32
577	669	1.000060	TGAAGGTTACGGTCCTCAACG	60.000	52.381	0.00	0.00	33.76	4.10
834	1116	9.374960	CTCTTCTTTAGAAAGTGAAAAATGACG	57.625	33.333	2.10	0.00	37.31	4.35
844	1126	8.376889	AGAAAGCTTCTCTTCTTTAGAAAGTG	57.623	34.615	0.00	0.00	34.07	3.16
945	1228	3.069443	GCACCACCTTTCTCCAAATTTGA	59.931	43.478	19.86	5.10	0.00	2.69
1041	1324	3.495629	GGAATAGCTGCCATGAGTCATCA	60.496	47.826	1.56	0.00	40.50	3.07
1346	12191	0.038892	CTCTGGCCACAATGCACAAC	60.039	55.000	0.00	0.00	0.00	3.32
1378	12223	2.354802	GAGCGAGCTCGACTTTGTC	58.645	57.895	38.74	19.07	43.02	3.18
1545	12417	2.036958	TCCATAAAGCCATGTCACGG	57.963	50.000	0.00	0.00	0.00	4.94
1631	12504	1.959282	GGCTCCAAGGGATGCTAAATG	59.041	52.381	0.00	0.00	0.00	2.32
1661	12534	3.692257	AGTTCCACATCAAGGAGACAG	57.308	47.619	0.00	0.00	36.33	3.51
1685	12558	4.524328	AGCCAACTGGAGGAAGTTTTAATG	59.476	41.667	0.00	0.00	38.34	1.90
1701	12574	2.355010	GGCATGGATTAGAGCCAACT	57.645	50.000	0.00	0.00	46.26	3.16
1725	12598	6.667414	TGTTATTTCCAAGGCATAACATCCTT	59.333	34.615	14.66	0.00	43.06	3.36
1848	12721	6.887626	TCCAAGTTTGTTAGGGAACATAAC	57.112	37.500	0.00	0.00	44.96	1.89
1860	12733	4.086457	AGTCAAGGTGTTCCAAGTTTGTT	58.914	39.130	0.00	0.00	35.89	2.83
2091	12970	1.203013	GCTTTCAAGTGGGGTAGGGTT	60.203	52.381	0.00	0.00	0.00	4.11
2166	13048	1.760405	AAGACCTGATGGGGAGGTTT	58.240	50.000	0.00	0.00	44.28	3.27
2304	13186	1.891919	TGCCAACTCGTGTCCAAGC	60.892	57.895	0.00	0.00	0.00	4.01
2467	13349	0.467384	ATCGCCCAGGAGAGTTGATG	59.533	55.000	0.00	0.00	0.00	3.07
2472	13354	2.037620	GATGCATCGCCCAGGAGAGT	62.038	60.000	11.68	0.00	0.00	3.24
2488	13370	0.745486	TGTTCGAGGCATGGCAGATG	60.745	55.000	22.64	7.82	0.00	2.90
2496	13378	2.851263	TTACCACTTGTTCGAGGCAT	57.149	45.000	0.00	0.00	0.00	4.40
2511	13393	8.110612	CGCATCGAAGAACAATCATATATTACC	58.889	37.037	0.00	0.00	43.58	2.85
2579	13461	5.694910	GGAAATGTCTTCGAACTGTCTTGTA	59.305	40.000	0.00	0.00	0.00	2.41
2604	13489	9.118300	CTCAGAAATTTTAGATACTTGAGGCAT	57.882	33.333	0.00	0.00	0.00	4.40
2664	13549	3.722147	CTCTAGGGATGGAAATGTCACG	58.278	50.000	0.00	0.00	0.00	4.35
2818	13709	2.278330	GCCTGGGTTGCAGGAAAGG	61.278	63.158	0.00	3.82	42.27	3.11
2916	13944	8.654997	ACATACTCCTATCAATCAAAGCTACAT	58.345	33.333	0.00	0.00	0.00	2.29
3051	14403	0.991920	TCCAGAAGGATGTGTTCCCC	59.008	55.000	0.00	0.00	46.81	4.81
3139	14491	1.133915	AGTTCGGCTCAAAAAGGGACA	60.134	47.619	0.00	0.00	0.00	4.02
3140	14492	1.605753	AGTTCGGCTCAAAAAGGGAC	58.394	50.000	0.00	0.00	0.00	4.46
3150	14502	0.444260	GCTGCAACTAAGTTCGGCTC	59.556	55.000	0.00	0.00	0.00	4.70
3153	14505	1.400242	GCTTGCTGCAACTAAGTTCGG	60.400	52.381	11.69	0.00	42.31	4.30
3176	14529	3.059868	ACAGATTGCACACGTTTAGTTCG	60.060	43.478	0.00	0.00	0.00	3.95
3180	14533	5.510671	AGAAAACAGATTGCACACGTTTAG	58.489	37.500	0.00	0.00	0.00	1.85
3251	14604	8.225603	AGCACAGATATTTACCCAAAATGTAG	57.774	34.615	0.00	0.00	38.29	2.74
3270	14623	9.117145	CAAAACATAACACTTAACATAGCACAG	57.883	33.333	0.00	0.00	0.00	3.66
3387	14740	1.039068	TCCACACATTTGCAACCAGG	58.961	50.000	0.00	0.00	0.00	4.45
3407	14760	2.818714	CTTCAGCAGCCAGAGCGG	60.819	66.667	0.00	0.00	46.67	5.52
3454	14893	4.276926	GCTCAAATTCTGAAACTGAGTGGT	59.723	41.667	22.60	0.00	36.67	4.16
3482	14980	3.442625	GGTGAAAATACCACTAGGCCAAC	59.557	47.826	5.01	0.00	40.54	3.77
3518	15022	6.403878	TCTCAAAGTAAGTACAGTTATGCCC	58.596	40.000	0.00	0.00	0.00	5.36
3613	15117	2.497675	TCAGGCAGTAGAAGGTCACATC	59.502	50.000	0.00	0.00	0.00	3.06
3617	15121	4.640771	AAATTCAGGCAGTAGAAGGTCA	57.359	40.909	0.00	0.00	0.00	4.02
3681	15189	9.832445	AAAAAGTACAGAGATTTGACTACTGAA	57.168	29.630	0.00	0.00	33.53	3.02
3709	15219	1.853963	TCCACTAGAACAGAGGAGCC	58.146	55.000	0.00	0.00	38.92	4.70
3737	15247	1.337823	ACTGTACCTCGTGGAACATGC	60.338	52.381	11.17	0.00	46.56	4.06
3744	15260	3.984292	GTACGACTGTACCTCGTGG	57.016	57.895	20.37	0.99	44.01	4.94
3757	15273	1.033746	GGGACCGGATGTCTGTACGA	61.034	60.000	9.46	0.00	43.89	3.43
3759	15275	1.192428	AAGGGACCGGATGTCTGTAC	58.808	55.000	9.46	0.00	43.89	2.90
3766	15282	0.753262	CCAGAGTAAGGGACCGGATG	59.247	60.000	9.46	0.00	0.00	3.51
3770	15286	1.033746	TACGCCAGAGTAAGGGACCG	61.034	60.000	0.00	0.00	0.00	4.79
3792	15308	4.856607	CTTCCTCGCCTCCGTCGC	62.857	72.222	0.00	0.00	35.54	5.19

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.