AutoCloner

Multiple sequence alignment - TraesCS2B01G370100

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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	TraesCS2B01G370100	chr2B	100.000	2489	0	0	1	2489	527586140	527588628	0.000000e+00	4597
1	TraesCS2B01G370100	chr2B	88.611	720	71	10	1	715	177201840	177201127	0.000000e+00	865
2	TraesCS2B01G370100	chr2B	87.619	105	7	3	718	821	213033620	213033521	1.560000e-22	117
3	TraesCS2B01G370100	chr2D	91.410	1234	48	24	817	2000	447839837	447841062	0.000000e+00	1639
4	TraesCS2B01G370100	chr2D	83.794	506	55	19	2001	2489	447841096	447841591	2.920000e-124	455
5	TraesCS2B01G370100	chr2D	87.719	114	6	3	715	827	447838607	447838713	2.600000e-25	126
6	TraesCS2B01G370100	chr2A	92.831	1102	44	7	924	1997	592454121	592455215	0.000000e+00	1565
7	TraesCS2B01G370100	chr2A	86.117	497	39	7	2001	2480	592455252	592455735	2.210000e-140	508
8	TraesCS2B01G370100	chr7B	91.760	716	53	6	2	715	657557355	657558066	0.000000e+00	990
9	TraesCS2B01G370100	chr7B	83.848	712	80	17	4	712	93863614	93862935	0.000000e+00	645
10	TraesCS2B01G370100	chr7B	83.788	623	70	15	93	709	641756581	641757178	1.670000e-156	562
11	TraesCS2B01G370100	chr7B	87.470	423	48	5	2	422	655703468	655703049	1.340000e-132	483
12	TraesCS2B01G370100	chr3B	90.223	716	51	11	1	714	763696575	763697273	0.000000e+00	917
13	TraesCS2B01G370100	chr3B	90.634	363	33	1	1	362	749716942	749717304	4.810000e-132	481
14	TraesCS2B01G370100	chr5D	87.692	715	78	9	1	712	458170223	458170930	0.000000e+00	824
15	TraesCS2B01G370100	chr5D	87.850	535	55	8	151	681	309058554	309059082	9.780000e-174	619
16	TraesCS2B01G370100	chr6D	85.975	713	65	17	10	714	301759829	301759144	0.000000e+00	730
17	TraesCS2B01G370100	chr5B	87.793	639	47	9	1	637	641408888	641408279	0.000000e+00	719
18	TraesCS2B01G370100	chr6B	85.376	718	74	12	2	712	682125464	682126157	0.000000e+00	715
19	TraesCS2B01G370100	chr1A	88.690	168	19	0	1078	1245	560372741	560372908	3.240000e-49	206
20	TraesCS2B01G370100	chr4D	90.517	116	6	3	720	835	463920621	463920731	5.550000e-32	148

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	TraesCS2B01G370100	chr2B	527586140	527588628	2488	False	4597.0	4597	100.000	1	2489	1	chr2B.!!$F1	2488
1	TraesCS2B01G370100	chr2B	177201127	177201840	713	True	865.0	865	88.611	1	715	1	chr2B.!!$R1	714
2	TraesCS2B01G370100	chr2D	447838607	447841591	2984	False	740.0	1639	87.641	715	2489	3	chr2D.!!$F1	1774
3	TraesCS2B01G370100	chr2A	592454121	592455735	1614	False	1036.5	1565	89.474	924	2480	2	chr2A.!!$F1	1556
4	TraesCS2B01G370100	chr7B	657557355	657558066	711	False	990.0	990	91.760	2	715	1	chr7B.!!$F2	713
5	TraesCS2B01G370100	chr7B	93862935	93863614	679	True	645.0	645	83.848	4	712	1	chr7B.!!$R1	708
6	TraesCS2B01G370100	chr7B	641756581	641757178	597	False	562.0	562	83.788	93	709	1	chr7B.!!$F1	616
7	TraesCS2B01G370100	chr3B	763696575	763697273	698	False	917.0	917	90.223	1	714	1	chr3B.!!$F2	713
8	TraesCS2B01G370100	chr5D	458170223	458170930	707	False	824.0	824	87.692	1	712	1	chr5D.!!$F2	711
9	TraesCS2B01G370100	chr5D	309058554	309059082	528	False	619.0	619	87.850	151	681	1	chr5D.!!$F1	530
10	TraesCS2B01G370100	chr6D	301759144	301759829	685	True	730.0	730	85.975	10	714	1	chr6D.!!$R1	704
11	TraesCS2B01G370100	chr5B	641408279	641408888	609	True	719.0	719	87.793	1	637	1	chr5B.!!$R1	636
12	TraesCS2B01G370100	chr6B	682125464	682126157	693	False	715.0	715	85.376	2	712	1	chr6B.!!$F1	710

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
716	733	0.671251	GGCACATAGGAGGTCTCGAG	59.329	60.0	5.93	5.93	0.0	4.04	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2413	3681	1.14287	CCCAGGTGTGGTTTCTTCTGA	59.857	52.381	0.0	0.0	43.23	3.27	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
122	124	8.690840	GTTCGGAATGTTAATTTTTGTTCTCAG	58.309	33.333	0.00	0.00	0.00	3.35
206	209	8.770850	AAATTTCAAAATTTGTTCGCTCATTG	57.229	26.923	11.58	0.00	44.46	2.82
432	437	3.476552	AGAAGAGTTCGATTTGTTGCCA	58.523	40.909	0.00	0.00	34.02	4.92
523	532	3.130633	TCGCGCTGCAATTCTTACATAT	58.869	40.909	5.56	0.00	0.00	1.78
584	597	6.829229	TCTATAGAAGGTCGTGAGTTTGAA	57.171	37.500	0.00	0.00	0.00	2.69
593	606	3.985925	GTCGTGAGTTTGAATCCTACGTT	59.014	43.478	0.00	0.00	0.00	3.99
598	611	3.472652	AGTTTGAATCCTACGTTGTGCA	58.527	40.909	0.00	0.00	0.00	4.57
715	732	1.101635	CGGCACATAGGAGGTCTCGA	61.102	60.000	0.00	0.00	0.00	4.04
716	733	0.671251	GGCACATAGGAGGTCTCGAG	59.329	60.000	5.93	5.93	0.00	4.04
717	734	1.394618	GCACATAGGAGGTCTCGAGT	58.605	55.000	13.13	0.00	0.00	4.18
718	735	1.751924	GCACATAGGAGGTCTCGAGTT	59.248	52.381	13.13	0.00	0.00	3.01
719	736	2.166664	GCACATAGGAGGTCTCGAGTTT	59.833	50.000	13.13	0.00	0.00	2.66
720	737	3.368531	GCACATAGGAGGTCTCGAGTTTT	60.369	47.826	13.13	0.00	0.00	2.43
721	738	4.822026	CACATAGGAGGTCTCGAGTTTTT	58.178	43.478	13.13	0.00	0.00	1.94
743	760	6.745159	TTTTGCCCTTTAAAACAGGAAAAC	57.255	33.333	4.83	0.00	32.41	2.43
759	776	0.753848	AAACGGGATAAATGGGCCGG	60.754	55.000	0.00	0.00	0.00	6.13
773	790	4.101448	CCGGCCCAGAGTGGAAGG	62.101	72.222	0.00	0.00	40.96	3.46
835	1986	3.808036	GCAGAAGGCGCCGAATAA	58.192	55.556	23.20	0.00	0.00	1.40
919	2070	3.182152	AGGCCTTTACATACACTGACCT	58.818	45.455	0.00	0.00	0.00	3.85
1170	2344	3.775654	CACCTCCACTCGGCCCTC	61.776	72.222	0.00	0.00	0.00	4.30
1441	2615	2.035442	GCTGGGAAGTTGGTCGCTC	61.035	63.158	0.00	0.00	0.00	5.03
1443	2617	0.035458	CTGGGAAGTTGGTCGCTCTT	59.965	55.000	0.00	0.00	0.00	2.85
1571	2745	7.097192	TGAAGAGATGTTTCTTGCGTAGTATT	58.903	34.615	0.00	0.00	37.53	1.89
1573	2747	5.292101	AGAGATGTTTCTTGCGTAGTATTGC	59.708	40.000	0.00	0.00	30.30	3.56
1696	2874	4.020751	TGAACTTCAGAATCTCCAGGTCTG	60.021	45.833	5.22	0.00	40.15	3.51
1825	3030	0.471191	CCATAGCCATCACTCCTGCA	59.529	55.000	0.00	0.00	0.00	4.41
1826	3031	1.542767	CCATAGCCATCACTCCTGCAG	60.543	57.143	6.78	6.78	0.00	4.41
1827	3032	1.140452	CATAGCCATCACTCCTGCAGT	59.860	52.381	13.81	0.00	34.67	4.40
1936	3141	2.163818	TCAACAGGTTAGTTGGAGCG	57.836	50.000	6.95	0.00	46.74	5.03
2004	3242	4.759183	AGAGAAGATTCCTTGTGTTCTTGC	59.241	41.667	0.00	0.00	30.33	4.01
2013	3255	1.592064	TGTGTTCTTGCGCTTCATCA	58.408	45.000	9.73	0.00	0.00	3.07
2014	3256	1.264020	TGTGTTCTTGCGCTTCATCAC	59.736	47.619	9.73	13.06	0.00	3.06
2098	3340	8.729805	AAATTGTAGAATTTGTTTGGCTTGAA	57.270	26.923	9.61	0.00	39.78	2.69
2110	3352	2.178580	TGGCTTGAAATTGACATCCCC	58.821	47.619	0.00	0.00	0.00	4.81
2111	3353	1.482182	GGCTTGAAATTGACATCCCCC	59.518	52.381	0.00	0.00	0.00	5.40
2151	3393	5.467738	TCATCAGCCCTTAGAGGATAAAGA	58.532	41.667	0.00	0.00	37.67	2.52
2189	3441	2.430367	GGTCACCGCCTCCAGTTT	59.570	61.111	0.00	0.00	0.00	2.66
2192	3444	0.310854	GTCACCGCCTCCAGTTTTTG	59.689	55.000	0.00	0.00	0.00	2.44
2258	3513	1.182667	GGTTAACCATGAACAGGGCC	58.817	55.000	20.12	0.00	35.25	5.80
2279	3534	5.335504	GGCCAAAGAAATGTCTTCTTCTCTG	60.336	44.000	0.00	0.00	43.59	3.35
2286	3541	2.851195	TGTCTTCTTCTCTGGCAAACC	58.149	47.619	0.00	0.00	0.00	3.27
2321	3576	5.069119	ACGATATGAGTCTTGCATTAGTCCA	59.931	40.000	0.00	0.00	0.00	4.02
2323	3578	6.090493	CGATATGAGTCTTGCATTAGTCCATG	59.910	42.308	0.00	0.00	0.00	3.66
2379	3647	0.252197	ACGCAGGTGGTAATTCCTCC	59.748	55.000	6.83	6.83	46.90	4.30
2393	3661	0.452987	TCCTCCGTAAACGTCCATCG	59.547	55.000	1.41	0.00	46.00	3.84
2413	3681	1.227380	GGAGAAGATGTCGCGCCAT	60.227	57.895	0.48	0.48	0.00	4.40
2420	3688	0.528466	GATGTCGCGCCATCAGAAGA	60.528	55.000	23.95	0.00	40.76	2.87
2450	3719	2.738139	GTTTTGCATGGGTGGCGC	60.738	61.111	0.00	0.00	0.00	6.53
2474	3743	2.466571	CGTCGTCGTATTTATGCCAGAC	59.533	50.000	0.00	0.00	0.00	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
57	59	6.830114	AACTTTTGAAAACACGAACAACAA	57.170	29.167	0.00	0.00	0.00	2.83
584	597	3.895232	AAGAGATGCACAACGTAGGAT	57.105	42.857	0.00	0.00	0.00	3.24
719	736	6.128254	CGTTTTCCTGTTTTAAAGGGCAAAAA	60.128	34.615	0.00	1.84	35.35	1.94
720	737	5.351740	CGTTTTCCTGTTTTAAAGGGCAAAA	59.648	36.000	0.00	6.70	35.35	2.44
721	738	4.870991	CGTTTTCCTGTTTTAAAGGGCAAA	59.129	37.500	0.00	0.00	35.35	3.68
743	760	2.983592	GCCGGCCCATTTATCCCG	60.984	66.667	18.11	0.00	40.39	5.14
759	776	3.732849	CCCCCTTCCACTCTGGGC	61.733	72.222	0.00	0.00	38.32	5.36
783	800	4.980903	CCACAAACAGGCGCACGC	62.981	66.667	10.83	6.46	41.06	5.34
784	801	2.329678	TTTCCACAAACAGGCGCACG	62.330	55.000	10.83	0.63	0.00	5.34
785	802	0.179124	TTTTCCACAAACAGGCGCAC	60.179	50.000	10.83	0.00	0.00	5.34
786	803	0.179124	GTTTTCCACAAACAGGCGCA	60.179	50.000	10.83	0.00	0.00	6.09
787	804	1.206115	CGTTTTCCACAAACAGGCGC	61.206	55.000	0.00	0.00	0.00	6.53
788	805	0.378962	TCGTTTTCCACAAACAGGCG	59.621	50.000	0.00	0.00	0.00	5.52
789	806	2.159296	ACTTCGTTTTCCACAAACAGGC	60.159	45.455	0.00	0.00	0.00	4.85
852	2003	5.106869	TGTCAAATTCCTTTTACATCGACCG	60.107	40.000	0.00	0.00	0.00	4.79
853	2004	6.249035	TGTCAAATTCCTTTTACATCGACC	57.751	37.500	0.00	0.00	0.00	4.79
855	2006	9.834628	GTAATTGTCAAATTCCTTTTACATCGA	57.165	29.630	0.00	0.00	37.23	3.59
856	2007	9.619316	TGTAATTGTCAAATTCCTTTTACATCG	57.381	29.630	2.88	0.00	37.23	3.84
905	2056	3.181490	CGCTTGCTAGGTCAGTGTATGTA	60.181	47.826	0.00	0.00	0.00	2.29
906	2057	2.417379	CGCTTGCTAGGTCAGTGTATGT	60.417	50.000	0.00	0.00	0.00	2.29
907	2058	2.196749	CGCTTGCTAGGTCAGTGTATG	58.803	52.381	0.00	0.00	0.00	2.39
908	2059	1.471676	GCGCTTGCTAGGTCAGTGTAT	60.472	52.381	0.00	0.00	35.07	2.29
965	2139	2.519377	TTTGGTTGACGTGACGAGAT	57.481	45.000	13.70	0.00	0.00	2.75
1098	2272	4.704833	GAGAAGGCGTGCTGGGCA	62.705	66.667	0.00	0.00	35.60	5.36
1422	2596	2.032681	GCGACCAACTTCCCAGCT	59.967	61.111	0.00	0.00	0.00	4.24
1489	2663	6.204882	GTGCAGATTTACAACTTAACAGAGGT	59.795	38.462	0.00	0.00	0.00	3.85
1493	2667	9.891828	TTATTGTGCAGATTTACAACTTAACAG	57.108	29.630	0.00	0.00	39.36	3.16
1592	2770	3.338249	GCTCTCCTGTTGTTGCTAATCA	58.662	45.455	0.00	0.00	0.00	2.57
1674	2852	4.221703	TCAGACCTGGAGATTCTGAAGTTC	59.778	45.833	11.17	0.00	42.18	3.01
1696	2874	1.555075	TGATAGGGTGGCACTCACTTC	59.445	52.381	21.51	13.22	45.38	3.01
1796	3001	2.297315	TGATGGCTATGGCGACTAGAAG	59.703	50.000	0.00	0.00	39.81	2.85
1849	3054	4.461781	GCTGGGGGATCTTGAATATTCATG	59.538	45.833	18.61	19.49	37.00	3.07
1936	3141	4.025061	GTGATGATCACTCATGCTTGCTAC	60.025	45.833	17.84	0.00	43.73	3.58
2004	3242	1.511850	TCCAAGTGTGTGATGAAGCG	58.488	50.000	0.00	0.00	0.00	4.68
2013	3255	3.424703	CCATCTGGAAATCCAAGTGTGT	58.575	45.455	3.35	0.00	46.97	3.72
2014	3256	2.165030	GCCATCTGGAAATCCAAGTGTG	59.835	50.000	3.35	0.82	46.97	3.82
2038	3280	1.397390	AAACCCTCCGACACACGTCT	61.397	55.000	0.00	0.00	40.23	4.18
2082	3324	6.998968	TGTCAATTTCAAGCCAAACAAATT	57.001	29.167	0.00	0.00	0.00	1.82
2091	3333	1.482182	GGGGGATGTCAATTTCAAGCC	59.518	52.381	0.00	0.00	0.00	4.35
2110	3352	3.370840	TGAATGGATTCTCTGTTGGGG	57.629	47.619	1.26	0.00	37.67	4.96
2111	3353	4.529897	TGATGAATGGATTCTCTGTTGGG	58.470	43.478	1.26	0.00	37.67	4.12
2120	3362	4.978099	TCTAAGGGCTGATGAATGGATTC	58.022	43.478	0.00	0.00	37.31	2.52
2126	3368	6.560304	TCTTTATCCTCTAAGGGCTGATGAAT	59.440	38.462	0.00	0.00	35.59	2.57
2151	3393	5.675538	ACCGAAAAGCTAAGCAATATCTCT	58.324	37.500	0.00	0.00	0.00	3.10
2179	3431	2.784347	AGCTAGACAAAAACTGGAGGC	58.216	47.619	0.00	0.00	0.00	4.70
2192	3444	4.116238	GCCACTGTCTATTCAAGCTAGAC	58.884	47.826	6.63	6.63	43.49	2.59
2253	3508	3.532641	AGAAGACATTTCTTTGGCCCT	57.467	42.857	0.00	0.00	42.53	5.19
2258	3513	5.240183	TGCCAGAGAAGAAGACATTTCTTTG	59.760	40.000	3.90	0.00	42.53	2.77
2279	3534	2.098443	TCGTTGTCTCTTTTGGTTTGCC	59.902	45.455	0.00	0.00	0.00	4.52
2286	3541	7.451429	CAAGACTCATATCGTTGTCTCTTTTG	58.549	38.462	0.00	0.00	38.63	2.44
2338	3593	1.918957	CCTGGGTCCTTCTCTGGAAAT	59.081	52.381	0.00	0.00	37.78	2.17
2379	3647	1.399440	TCTCCTCGATGGACGTTTACG	59.601	52.381	0.00	0.00	40.56	3.18
2393	3661	1.590259	GGCGCGACATCTTCTCCTC	60.590	63.158	12.10	0.00	0.00	3.71
2413	3681	1.142870	CCCAGGTGTGGTTTCTTCTGA	59.857	52.381	0.00	0.00	43.23	3.27
2450	3719	1.445731	GGCATAAATACGACGACGACG	59.554	52.381	17.60	17.60	42.66	5.12
2454	3723	3.441163	TGTCTGGCATAAATACGACGAC	58.559	45.455	0.00	0.00	0.00	4.34
2457	3726	3.621268	TGCTTGTCTGGCATAAATACGAC	59.379	43.478	0.00	0.00	34.56	4.34
2459	3728	4.818534	ATGCTTGTCTGGCATAAATACG	57.181	40.909	0.00	0.00	46.81	3.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.