AutoCloner

Multiple sequence alignment - TraesCS6B01G413400

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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	TraesCS6B01G413400	chr6B	100.000	3428	0	0	1	3428	686859348	686862775	0.000000e+00	6331.0
1	TraesCS6B01G413400	chr6B	95.571	700	29	2	1	700	537577249	537577946	0.000000e+00	1120.0
2	TraesCS6B01G413400	chr6D	90.796	2575	172	42	883	3428	452119147	452121685	0.000000e+00	3382.0
3	TraesCS6B01G413400	chr6D	92.486	173	11	1	700	870	452118915	452119087	2.640000e-61	246.0
4	TraesCS6B01G413400	chr6A	93.187	1365	64	13	1561	2923	597893143	597894480	0.000000e+00	1978.0
5	TraesCS6B01G413400	chr6A	91.124	507	30	5	872	1375	597892472	597892966	0.000000e+00	673.0
6	TraesCS6B01G413400	chr6A	91.289	287	16	6	1288	1565	597892915	597893201	1.930000e-102	383.0
7	TraesCS6B01G413400	chr6A	79.901	403	52	17	2915	3303	597895509	597895896	5.640000e-68	268.0
8	TraesCS6B01G413400	chr6A	92.179	179	9	5	701	875	597892265	597892442	7.350000e-62	248.0
9	TraesCS6B01G413400	chr3B	96.862	701	21	1	1	700	743136056	743136756	0.000000e+00	1171.0
10	TraesCS6B01G413400	chr3B	96.000	700	26	1	1	700	544800606	544801303	0.000000e+00	1136.0
11	TraesCS6B01G413400	chr5B	96.132	698	26	1	3	700	579058130	579057434	0.000000e+00	1138.0
12	TraesCS6B01G413400	chr5B	96.006	701	27	1	1	700	693162165	693161465	0.000000e+00	1138.0
13	TraesCS6B01G413400	chr5B	86.076	79	7	4	2922	2997	62955276	62955353	7.880000e-12	82.4
14	TraesCS6B01G413400	chr1B	95.881	704	26	3	1	703	283110634	283109933	0.000000e+00	1136.0
15	TraesCS6B01G413400	chr1B	95.461	705	29	3	1	703	649305650	649304947	0.000000e+00	1122.0
16	TraesCS6B01G413400	chr1B	94.944	712	30	5	1	708	684639472	684638763	0.000000e+00	1110.0
17	TraesCS6B01G413400	chr4B	95.584	702	28	3	1	700	434456786	434457486	0.000000e+00	1122.0
18	TraesCS6B01G413400	chr4B	72.074	376	75	23	2914	3270	43113366	43113002	6.100000e-13	86.1

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	TraesCS6B01G413400	chr6B	686859348	686862775	3427	False	6331	6331	100.000	1	3428	1	chr6B.!!$F2	3427
1	TraesCS6B01G413400	chr6B	537577249	537577946	697	False	1120	1120	95.571	1	700	1	chr6B.!!$F1	699
2	TraesCS6B01G413400	chr6D	452118915	452121685	2770	False	1814	3382	91.641	700	3428	2	chr6D.!!$F1	2728
3	TraesCS6B01G413400	chr6A	597892265	597895896	3631	False	710	1978	89.536	701	3303	5	chr6A.!!$F1	2602
4	TraesCS6B01G413400	chr3B	743136056	743136756	700	False	1171	1171	96.862	1	700	1	chr3B.!!$F2	699
5	TraesCS6B01G413400	chr3B	544800606	544801303	697	False	1136	1136	96.000	1	700	1	chr3B.!!$F1	699
6	TraesCS6B01G413400	chr5B	579057434	579058130	696	True	1138	1138	96.132	3	700	1	chr5B.!!$R1	697
7	TraesCS6B01G413400	chr5B	693161465	693162165	700	True	1138	1138	96.006	1	700	1	chr5B.!!$R2	699
8	TraesCS6B01G413400	chr1B	283109933	283110634	701	True	1136	1136	95.881	1	703	1	chr1B.!!$R1	702
9	TraesCS6B01G413400	chr1B	649304947	649305650	703	True	1122	1122	95.461	1	703	1	chr1B.!!$R2	702
10	TraesCS6B01G413400	chr1B	684638763	684639472	709	True	1110	1110	94.944	1	708	1	chr1B.!!$R3	707
11	TraesCS6B01G413400	chr4B	434456786	434457486	700	False	1122	1122	95.584	1	700	1	chr4B.!!$F1	699

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
401	404	1.002274	GGCAAGGGGGAGAGAGAGA	59.998	63.158	0.00	0.0	0.0	3.10	F
1209	1274	1.014564	CCGGCGTCAAGAAGAAGGTC	61.015	60.000	6.01	0.0	0.0	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1313	1384	0.455295	CTTGCTCGTGGTCGACTCTC	60.455	60.0	16.46	5.84	41.35	3.20	R
3015	4171	0.318955	ATTGCACGCAAGCAGGAAAC	60.319	50.0	10.60	0.00	46.54	2.78	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
401	404	1.002274	GGCAAGGGGGAGAGAGAGA	59.998	63.158	0.00	0.00	0.00	3.10
465	472	1.692411	GGGGCGGATAGAAAAATGCT	58.308	50.000	0.00	0.00	0.00	3.79
641	648	3.868200	CTGGGCCGCCTCCTTTGTT	62.868	63.158	9.86	0.00	0.00	2.83
821	828	1.599606	CTCACTCCCCACTCCACTCG	61.600	65.000	0.00	0.00	0.00	4.18
829	836	1.373497	CACTCCACTCGCACACTCC	60.373	63.158	0.00	0.00	0.00	3.85
834	841	4.008933	ACTCGCACACTCCAGCCC	62.009	66.667	0.00	0.00	0.00	5.19
835	842	4.007644	CTCGCACACTCCAGCCCA	62.008	66.667	0.00	0.00	0.00	5.36
892	957	1.067776	TCTCTTCGTCCCTTTTCGCTC	60.068	52.381	0.00	0.00	0.00	5.03
903	968	2.171003	CTTTTCGCTCCCAATTTCCCT	58.829	47.619	0.00	0.00	0.00	4.20
992	1057	2.616458	AAAAGCCCCGGCCAGATCT	61.616	57.895	2.24	0.00	43.17	2.75
1168	1233	3.966026	GACGACGAGCCGGTCAAGG	62.966	68.421	1.90	0.00	36.73	3.61
1209	1274	1.014564	CCGGCGTCAAGAAGAAGGTC	61.015	60.000	6.01	0.00	0.00	3.85
1210	1275	1.344942	CGGCGTCAAGAAGAAGGTCG	61.345	60.000	0.00	0.00	0.00	4.79
1211	1276	1.627550	GGCGTCAAGAAGAAGGTCGC	61.628	60.000	0.00	0.00	41.13	5.19
1278	1349	3.371063	GAGGAGTCCACCGCGACA	61.371	66.667	12.86	0.00	35.07	4.35
1307	1378	2.742372	CACCAAGAAGGCGACCGG	60.742	66.667	0.00	0.00	43.14	5.28
1313	1384	0.036671	AAGAAGGCGACCGGTAAAGG	60.037	55.000	7.34	0.00	37.30	3.11
1314	1385	0.901580	AGAAGGCGACCGGTAAAGGA	60.902	55.000	7.34	0.00	34.73	3.36
1540	1653	0.238553	GGCCAAGTCGAGCAAGAAAC	59.761	55.000	0.00	0.00	0.00	2.78
1641	1754	1.153901	GGCGAATTCGACCGTGAGA	60.154	57.895	31.01	0.00	42.67	3.27
1683	1796	2.737376	GAGGACGTGGTGTTCGCC	60.737	66.667	0.00	0.00	0.00	5.54
2133	2246	1.522355	CATGGGCTACCTCGTGCTG	60.522	63.158	0.00	0.00	37.76	4.41
2515	2630	0.960423	ATAAGATGGGAGGAGGGGGT	59.040	55.000	0.00	0.00	0.00	4.95
2520	2635	2.531463	AGATGGGAGGAGGGGGTAATTA	59.469	50.000	0.00	0.00	0.00	1.40
2534	2649	5.369993	GGGGGTAATTAGAAGATCAAGGAGT	59.630	44.000	0.00	0.00	0.00	3.85
2562	2677	8.510505	CAAGAGGAGAAAGGAAAACTATTCTTG	58.489	37.037	0.00	0.00	32.54	3.02
2596	2711	9.533253	TTTCTCTTTCTCATTTTGAATTGGTTC	57.467	29.630	0.00	0.00	34.85	3.62
2607	2722	4.188247	TGAATTGGTTCGAGTACAGAGG	57.812	45.455	0.00	0.00	37.15	3.69
2610	2725	0.113776	TGGTTCGAGTACAGAGGGGT	59.886	55.000	0.00	0.00	0.00	4.95
2617	2732	3.446161	TCGAGTACAGAGGGGTTGTAATG	59.554	47.826	0.00	0.00	33.19	1.90
2684	2799	4.389374	AGTGATGATTTTTGACACTCGGT	58.611	39.130	0.00	0.00	37.24	4.69
2707	2822	6.038161	GGTTCCAGGAAACCAAAATTTTGAAG	59.962	38.462	28.44	16.73	46.62	3.02
2710	2825	7.398024	TCCAGGAAACCAAAATTTTGAAGAAA	58.602	30.769	28.44	5.60	40.55	2.52
2711	2826	7.885399	TCCAGGAAACCAAAATTTTGAAGAAAA	59.115	29.630	28.44	6.19	40.55	2.29
2796	2911	9.772973	TTTAGGTATTGCTACATATTCGTCAAT	57.227	29.630	0.00	0.00	0.00	2.57
2813	2928	8.599876	TTCGTCAATTTTCATGATGAAATACG	57.400	30.769	20.04	22.53	44.75	3.06
2816	2931	8.515473	CGTCAATTTTCATGATGAAATACGTTC	58.485	33.333	20.04	9.44	44.75	3.95
2819	2934	9.558648	CAATTTTCATGATGAAATACGTTCTGA	57.441	29.630	20.04	3.82	44.75	3.27
2823	2939	7.237920	TCATGATGAAATACGTTCTGATGTG	57.762	36.000	0.00	0.00	37.13	3.21
2825	2941	6.892310	TGATGAAATACGTTCTGATGTGAG	57.108	37.500	0.00	0.00	37.13	3.51
2845	2961	8.177119	TGTGAGCTACATAAAAAGACCAAAAT	57.823	30.769	0.00	0.00	33.42	1.82
2846	2962	8.296713	TGTGAGCTACATAAAAAGACCAAAATC	58.703	33.333	0.00	0.00	33.42	2.17
2896	3015	7.523293	TCATCAGGAAACATTACAAACATGT	57.477	32.000	0.00	0.00	36.36	3.21
2928	4084	7.557719	ACATGAAAGTGTCCTTATAATCCCAAG	59.442	37.037	0.00	0.00	0.00	3.61
2958	4114	6.219417	TGCACCCTTATGAACATTAAATGG	57.781	37.500	0.00	0.00	33.60	3.16
3023	4179	9.855021	ATAACATACAAATTGTTAGTTTCCTGC	57.145	29.630	16.77	0.00	41.44	4.85
3025	4181	7.951591	ACATACAAATTGTTAGTTTCCTGCTT	58.048	30.769	3.17	0.00	0.00	3.91
3026	4182	7.867403	ACATACAAATTGTTAGTTTCCTGCTTG	59.133	33.333	3.17	0.00	0.00	4.01
3027	4183	5.049828	ACAAATTGTTAGTTTCCTGCTTGC	58.950	37.500	0.00	0.00	0.00	4.01
3064	4222	5.719173	TGATGACATCACATTTCGTGTAGA	58.281	37.500	14.24	0.00	46.44	2.59
3070	4228	4.123497	TCACATTTCGTGTAGATCTGGG	57.877	45.455	5.18	0.00	46.44	4.45
3085	4243	8.424918	TGTAGATCTGGGCAAAAATAACAAAAA	58.575	29.630	5.18	0.00	0.00	1.94
3149	4314	7.833285	TTTTCCAAGAGCACTAGGTATTTTT	57.167	32.000	0.00	0.00	0.00	1.94
3184	4354	5.894807	GCAATTTGCAGGTATGTAGAACAT	58.105	37.500	16.35	0.00	44.26	2.71
3270	4441	0.961019	TCACAAGGTGCATTTGAGCC	59.039	50.000	17.56	1.04	32.98	4.70
3283	4454	2.128771	TTGAGCCTGGGAGCATAAAC	57.871	50.000	0.00	0.00	34.23	2.01
3400	4574	6.966534	ATTTCCGAAATTGAAGCTCCATAT	57.033	33.333	0.17	0.00	0.00	1.78
3402	4576	7.496529	TTTCCGAAATTGAAGCTCCATATAG	57.503	36.000	0.00	0.00	0.00	1.31
3403	4577	4.997395	TCCGAAATTGAAGCTCCATATAGC	59.003	41.667	0.00	0.00	43.11	2.97
3405	4579	4.154918	CGAAATTGAAGCTCCATATAGCCC	59.845	45.833	0.00	0.00	43.86	5.19
3406	4580	4.729552	AATTGAAGCTCCATATAGCCCA	57.270	40.909	0.00	0.00	43.86	5.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
386	387	1.290732	CTTCCTCTCTCTCTCCCCCTT	59.709	57.143	0.00	0.00	0.00	3.95
401	404	1.974236	CCACTCTTCCACACTCTTCCT	59.026	52.381	0.00	0.00	0.00	3.36
465	472	3.203442	GTCGGTGGCATAGGACGA	58.797	61.111	0.00	0.00	0.00	4.20
660	667	2.520982	CTATCCTGTCCGCCCCGA	60.521	66.667	0.00	0.00	0.00	5.14
834	841	2.124487	AACCACACCACCACCGTG	60.124	61.111	0.00	0.00	39.91	4.94
835	842	2.191109	GAACCACACCACCACCGT	59.809	61.111	0.00	0.00	0.00	4.83
892	957	7.148239	GCTCGATTTATATGTAGGGAAATTGGG	60.148	40.741	0.00	0.00	0.00	4.12
903	968	9.787435	AGGTATTTTTGGCTCGATTTATATGTA	57.213	29.630	0.00	0.00	0.00	2.29
1026	1091	3.608993	GAGGAGCAGCAGCAGCACT	62.609	63.158	12.92	9.51	45.49	4.40
1188	1253	2.358247	TTCTTCTTGACGCCGGCC	60.358	61.111	23.46	8.57	0.00	6.13
1211	1276	2.959484	TTCTTGGCGCCAGAGGAGG	61.959	63.158	30.75	15.80	0.00	4.30
1273	1338	1.525077	TGGTGACCTTGGTTGTCGC	60.525	57.895	2.11	0.00	41.39	5.19
1278	1349	0.923358	TCTTGGTGGTGACCTTGGTT	59.077	50.000	2.11	0.00	43.58	3.67
1307	1378	1.808945	TCGTGGTCGACTCTCCTTTAC	59.191	52.381	16.46	0.00	41.35	2.01
1313	1384	0.455295	CTTGCTCGTGGTCGACTCTC	60.455	60.000	16.46	5.84	41.35	3.20
1314	1385	0.889638	TCTTGCTCGTGGTCGACTCT	60.890	55.000	16.46	0.00	41.35	3.24
1559	1672	1.078708	TTGGTCGAATCCGCCTTCC	60.079	57.895	0.00	0.00	34.56	3.46
1785	1898	1.517832	CGACAGGTAGGCCTTGGAG	59.482	63.158	12.58	1.34	44.18	3.86
2133	2246	1.153549	GACGAGGTCCACCATCTGC	60.154	63.158	0.00	0.00	38.89	4.26
2373	2486	2.334006	AGGCCTTCTTCCTCTTCTCA	57.666	50.000	0.00	0.00	0.00	3.27
2494	2608	2.114506	ACCCCCTCCTCCCATCTTATAG	59.885	54.545	0.00	0.00	0.00	1.31
2520	2635	5.584913	TCCTCTTGTACTCCTTGATCTTCT	58.415	41.667	0.00	0.00	0.00	2.85
2534	2649	8.881262	AGAATAGTTTTCCTTTCTCCTCTTGTA	58.119	33.333	0.00	0.00	0.00	2.41
2574	2689	7.013274	ACTCGAACCAATTCAAAATGAGAAAGA	59.987	33.333	0.00	0.00	34.14	2.52
2596	2711	3.194968	ACATTACAACCCCTCTGTACTCG	59.805	47.826	0.00	0.00	0.00	4.18
2665	2780	4.215399	TGGAACCGAGTGTCAAAAATCATC	59.785	41.667	0.00	0.00	0.00	2.92
2684	2799	6.951971	TCTTCAAAATTTTGGTTTCCTGGAA	58.048	32.000	26.45	4.68	38.66	3.53
2771	2886	9.772973	AATTGACGAATATGTAGCAATACCTAA	57.227	29.630	0.00	0.00	0.00	2.69
2774	2889	9.382244	GAAAATTGACGAATATGTAGCAATACC	57.618	33.333	0.00	0.00	0.00	2.73
2813	2928	8.171840	GTCTTTTTATGTAGCTCACATCAGAAC	58.828	37.037	10.76	0.00	44.99	3.01
2816	2931	6.595326	TGGTCTTTTTATGTAGCTCACATCAG	59.405	38.462	10.76	5.73	44.99	2.90
2823	2939	9.294030	CATGATTTTGGTCTTTTTATGTAGCTC	57.706	33.333	0.00	0.00	0.00	4.09
2825	2941	8.986477	ACATGATTTTGGTCTTTTTATGTAGC	57.014	30.769	0.00	0.00	0.00	3.58
2837	2953	6.312399	TGTGAGTTGTACATGATTTTGGTC	57.688	37.500	0.00	0.00	0.00	4.02
2865	2984	9.585099	TTTGTAATGTTTCCTGATGAAATATGC	57.415	29.630	0.00	0.00	42.06	3.14
2918	4074	3.385755	GGTGCATTTGAGCTTGGGATTAT	59.614	43.478	0.00	0.00	34.99	1.28
2928	4084	3.193267	TGTTCATAAGGGTGCATTTGAGC	59.807	43.478	0.00	0.00	0.00	4.26
3003	4159	6.212955	GCAAGCAGGAAACTAACAATTTGTA	58.787	36.000	1.76	0.00	40.21	2.41
3008	4164	2.884639	ACGCAAGCAGGAAACTAACAAT	59.115	40.909	0.00	0.00	40.07	2.71
3009	4165	2.032799	CACGCAAGCAGGAAACTAACAA	59.967	45.455	0.00	0.00	40.07	2.83
3010	4166	1.601903	CACGCAAGCAGGAAACTAACA	59.398	47.619	0.00	0.00	40.07	2.41
3011	4167	1.663161	GCACGCAAGCAGGAAACTAAC	60.663	52.381	0.00	0.00	40.07	2.34
3012	4168	0.591170	GCACGCAAGCAGGAAACTAA	59.409	50.000	0.00	0.00	40.07	2.24
3013	4169	0.533978	TGCACGCAAGCAGGAAACTA	60.534	50.000	0.00	0.00	40.11	2.24
3014	4170	1.383456	TTGCACGCAAGCAGGAAACT	61.383	50.000	0.00	0.00	46.54	2.66
3015	4171	0.318955	ATTGCACGCAAGCAGGAAAC	60.319	50.000	10.60	0.00	46.54	2.78
3052	4208	2.905075	TGCCCAGATCTACACGAAATG	58.095	47.619	0.00	0.00	0.00	2.32
3053	4209	3.627395	TTGCCCAGATCTACACGAAAT	57.373	42.857	0.00	0.00	0.00	2.17
3054	4210	3.410631	TTTGCCCAGATCTACACGAAA	57.589	42.857	0.00	0.00	0.00	3.46
3064	4222	6.017192	GCTGTTTTTGTTATTTTTGCCCAGAT	60.017	34.615	0.00	0.00	0.00	2.90
3070	4228	6.257630	TGGAGAGCTGTTTTTGTTATTTTTGC	59.742	34.615	0.00	0.00	0.00	3.68
3149	4314	6.112058	ACCTGCAAATTGCTGTAAAGAAAAA	58.888	32.000	19.34	0.00	45.31	1.94
3150	4315	5.669477	ACCTGCAAATTGCTGTAAAGAAAA	58.331	33.333	19.34	0.00	45.31	2.29
3160	4325	5.009631	TGTTCTACATACCTGCAAATTGCT	58.990	37.500	19.34	1.28	45.31	3.91
3162	4327	9.853555	TTAAATGTTCTACATACCTGCAAATTG	57.146	29.630	0.00	0.00	37.97	2.32
3237	4407	7.390823	TGCACCTTGTGAGTAGTAAAATCATA	58.609	34.615	0.00	0.00	35.23	2.15
3241	4411	7.230510	TCAAATGCACCTTGTGAGTAGTAAAAT	59.769	33.333	9.54	0.00	35.23	1.82
3254	4424	0.245539	CCAGGCTCAAATGCACCTTG	59.754	55.000	4.33	4.33	34.04	3.61
3257	4427	1.304381	TCCCAGGCTCAAATGCACC	60.304	57.895	0.00	0.00	34.04	5.01
3270	4441	3.629398	GGACATGAAGTTTATGCTCCCAG	59.371	47.826	7.51	0.00	0.00	4.45
3283	4454	9.745018	AATAAGGATGTATATTGGGACATGAAG	57.255	33.333	0.00	0.00	39.30	3.02
3357	4531	9.255304	CGGAAATTAGACTTCAAATTTTGGAAA	57.745	29.630	9.18	0.00	35.87	3.13
3368	4542	7.174946	AGCTTCAATTTCGGAAATTAGACTTCA	59.825	33.333	23.96	10.79	38.97	3.02
3369	4543	7.530863	AGCTTCAATTTCGGAAATTAGACTTC	58.469	34.615	23.96	13.25	38.97	3.01
3382	4556	4.154918	GGGCTATATGGAGCTTCAATTTCG	59.845	45.833	0.00	0.00	42.43	3.46
3389	4563	2.235898	CTCCTGGGCTATATGGAGCTTC	59.764	54.545	0.00	0.00	42.43	3.86
3400	4574	0.252239	TGCTTCAGTCTCCTGGGCTA	60.252	55.000	0.00	0.00	39.31	3.93
3402	4576	0.034670	ATTGCTTCAGTCTCCTGGGC	60.035	55.000	0.00	0.00	39.31	5.36
3403	4577	2.503895	AATTGCTTCAGTCTCCTGGG	57.496	50.000	0.00	0.00	39.31	4.45
3405	4579	3.822735	TCCAAAATTGCTTCAGTCTCCTG	59.177	43.478	0.00	0.00	40.25	3.86
3406	4580	4.104383	TCCAAAATTGCTTCAGTCTCCT	57.896	40.909	0.00	0.00	0.00	3.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.