AutoCloner

Multiple sequence alignment - TraesCS3B01G074100

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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	TraesCS3B01G074100	chr3B	100.000	2467	0	0	495	2961	44858067	44855601	0.000000e+00	4556
1	TraesCS3B01G074100	chr3B	92.313	1353	89	11	1616	2961	45270046	45268702	0.000000e+00	1908
2	TraesCS3B01G074100	chr3B	86.478	917	98	17	727	1626	45272001	45271094	0.000000e+00	983
3	TraesCS3B01G074100	chr3B	81.348	831	120	14	759	1581	44848407	44847604	0.000000e+00	643
4	TraesCS3B01G074100	chr3B	100.000	262	0	0	1	262	44858561	44858300	4.440000e-133	484
5	TraesCS3B01G074100	chr3B	96.186	236	9	0	495	730	752497067	752496832	1.290000e-103	387
6	TraesCS3B01G074100	chr3B	95.816	239	10	0	495	733	808576506	808576268	1.290000e-103	387
7	TraesCS3B01G074100	chr3B	85.185	243	30	5	2070	2311	401805741	401805978	8.200000e-61	244
8	TraesCS3B01G074100	chr3A	90.834	1451	102	16	1518	2961	36728908	36727482	0.000000e+00	1914
9	TraesCS3B01G074100	chr3A	80.858	862	136	21	792	1637	36771065	36770217	0.000000e+00	651
10	TraesCS3B01G074100	chr3A	85.360	403	52	5	759	1158	36722380	36721982	7.640000e-111	411
11	TraesCS3B01G074100	chr3A	80.804	448	68	11	1198	1637	36678717	36678280	4.730000e-88	335
12	TraesCS3B01G074100	chr3A	86.008	243	28	5	2070	2311	410110141	410110378	3.790000e-64	255
13	TraesCS3B01G074100	chrUn	92.313	1353	89	11	1616	2961	345547948	345546604	0.000000e+00	1908
14	TraesCS3B01G074100	chrUn	92.313	1353	89	11	1616	2961	362559593	362558249	0.000000e+00	1908
15	TraesCS3B01G074100	chrUn	92.871	1024	63	4	1944	2961	38771758	38772777	0.000000e+00	1478
16	TraesCS3B01G074100	chrUn	81.818	891	139	17	759	1637	38820749	38821628	0.000000e+00	726
17	TraesCS3B01G074100	chrUn	82.557	837	131	12	759	1587	38808428	38809257	0.000000e+00	723
18	TraesCS3B01G074100	chrUn	90.000	310	18	7	1634	1942	38720310	38720607	3.580000e-104	388
19	TraesCS3B01G074100	chrUn	94.332	247	11	3	495	741	208597222	208597465	2.790000e-100	375
20	TraesCS3B01G074100	chrUn	94.332	247	11	3	495	741	211740255	211740012	2.790000e-100	375
21	TraesCS3B01G074100	chrUn	94.332	247	11	3	495	741	336652960	336652717	2.790000e-100	375
22	TraesCS3B01G074100	chrUn	94.332	247	11	3	495	741	336679530	336679287	2.790000e-100	375
23	TraesCS3B01G074100	chrUn	94.286	245	11	3	497	741	211734443	211734202	3.600000e-99	372
24	TraesCS3B01G074100	chr3D	92.439	1349	81	13	1627	2961	26640500	26639159	0.000000e+00	1906
25	TraesCS3B01G074100	chr3D	93.964	878	49	4	744	1618	26643320	26642444	0.000000e+00	1325
26	TraesCS3B01G074100	chr3D	82.019	862	125	20	792	1637	26649773	26648926	0.000000e+00	706
27	TraesCS3B01G074100	chr3D	86.022	186	25	1	759	943	26608264	26608079	6.470000e-47	198
28	TraesCS3B01G074100	chr1B	86.160	737	82	14	911	1636	636680045	636679318	0.000000e+00	778
29	TraesCS3B01G074100	chr1B	86.512	430	46	7	911	1334	636662461	636662038	2.080000e-126	462
30	TraesCS3B01G074100	chr1B	93.976	249	13	2	495	742	564196004	564196251	2.790000e-100	375
31	TraesCS3B01G074100	chr6B	96.629	267	4	4	1	262	125177112	125176846	3.500000e-119	438
32	TraesCS3B01G074100	chr6B	96.186	236	9	0	495	730	640535012	640535247	1.290000e-103	387
33	TraesCS3B01G074100	chr6B	94.758	248	12	1	495	741	36284778	36284531	4.630000e-103	385
34	TraesCS3B01G074100	chr2A	96.629	267	4	4	1	262	762706136	762705870	3.500000e-119	438
35	TraesCS3B01G074100	chr1D	96.629	267	4	4	1	262	491024794	491025060	3.500000e-119	438
36	TraesCS3B01G074100	chr1D	97.059	238	6	1	497	734	19276841	19276605	1.650000e-107	399
37	TraesCS3B01G074100	chr1D	96.596	235	8	0	497	731	37273247	37273481	9.950000e-105	390
38	TraesCS3B01G074100	chr2D	96.269	268	4	4	1	262	22406543	22406810	4.530000e-118	435
39	TraesCS3B01G074100	chr2D	96.255	267	5	4	1	262	104375116	104374850	1.630000e-117	433
40	TraesCS3B01G074100	chr2D	97.436	234	6	0	497	730	104374798	104374565	1.650000e-107	399
41	TraesCS3B01G074100	chr2D	97.009	234	7	0	497	730	623322173	623322406	7.690000e-106	394
42	TraesCS3B01G074100	chr4D	96.255	267	5	4	1	262	441103070	441103336	1.630000e-117	433
43	TraesCS3B01G074100	chr4D	95.911	269	4	4	1	262	411698349	411698617	2.110000e-116	429
44	TraesCS3B01G074100	chr5D	96.212	264	8	2	1	262	44031219	44030956	5.860000e-117	431
45	TraesCS3B01G074100	chr7D	95.911	269	4	4	1	262	593879119	593879387	2.110000e-116	429
46	TraesCS3B01G074100	chr2B	97.034	236	7	0	495	730	2051885	2051650	5.950000e-107	398
47	TraesCS3B01G074100	chr2B	93.976	249	14	1	495	743	744322273	744322026	2.790000e-100	375
48	TraesCS3B01G074100	chr4A	94.332	247	11	3	495	741	645834685	645834928	2.790000e-100	375
49	TraesCS3B01G074100	chr1A	85.470	351	44	6	1290	1636	553903113	553902766	2.810000e-95	359
50	TraesCS3B01G074100	chr5A	83.936	249	33	5	2070	2311	448610863	448611111	6.380000e-57	231

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	TraesCS3B01G074100	chr3B	44855601	44858561	2960	True	2520.0	4556	100.0000	1	2961	2	chr3B.!!$R4	2960
1	TraesCS3B01G074100	chr3B	45268702	45272001	3299	True	1445.5	1908	89.3955	727	2961	2	chr3B.!!$R5	2234
2	TraesCS3B01G074100	chr3B	44847604	44848407	803	True	643.0	643	81.3480	759	1581	1	chr3B.!!$R1	822
3	TraesCS3B01G074100	chr3A	36727482	36728908	1426	True	1914.0	1914	90.8340	1518	2961	1	chr3A.!!$R3	1443
4	TraesCS3B01G074100	chr3A	36770217	36771065	848	True	651.0	651	80.8580	792	1637	1	chr3A.!!$R4	845
5	TraesCS3B01G074100	chrUn	345546604	345547948	1344	True	1908.0	1908	92.3130	1616	2961	1	chrUn.!!$R5	1345
6	TraesCS3B01G074100	chrUn	362558249	362559593	1344	True	1908.0	1908	92.3130	1616	2961	1	chrUn.!!$R6	1345
7	TraesCS3B01G074100	chrUn	38771758	38772777	1019	False	1478.0	1478	92.8710	1944	2961	1	chrUn.!!$F2	1017
8	TraesCS3B01G074100	chrUn	38820749	38821628	879	False	726.0	726	81.8180	759	1637	1	chrUn.!!$F4	878
9	TraesCS3B01G074100	chrUn	38808428	38809257	829	False	723.0	723	82.5570	759	1587	1	chrUn.!!$F3	828
10	TraesCS3B01G074100	chr3D	26639159	26643320	4161	True	1615.5	1906	93.2015	744	2961	2	chr3D.!!$R3	2217
11	TraesCS3B01G074100	chr3D	26648926	26649773	847	True	706.0	706	82.0190	792	1637	1	chr3D.!!$R2	845
12	TraesCS3B01G074100	chr1B	636679318	636680045	727	True	778.0	778	86.1600	911	1636	1	chr1B.!!$R2	725
13	TraesCS3B01G074100	chr2D	104374565	104375116	551	True	416.0	433	96.8455	1	730	2	chr2D.!!$R1	729

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
193	199	0.387622	TACGTAGCGTCACCAAGCAC	60.388	55.000	0.00	0.0	41.54	4.40	F
706	712	2.125391	GCCCTTACGAACCGGGAC	60.125	66.667	6.32	0.0	40.55	4.46	F
1286	1324	0.037303	CCAGGCTGACAGTGACCAAT	59.963	55.000	17.94	0.0	0.00	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1090	1128	0.251121	ACCGTGAACATCAATGGCCA	60.251	50.000	8.56	8.56	29.88	5.36	R
1543	1586	0.882042	CTGCACGATGTAGGCCATCC	60.882	60.000	5.01	0.00	46.10	3.51	R
2421	5401	2.287487	TGTTGTTGCAATCATGTGTCGG	60.287	45.455	0.59	0.00	0.00	4.79	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
63	64	3.748048	ACATGTTGTTCGACCAATCTCTG	59.252	43.478	0.00	0.00	0.00	3.35
172	177	8.046708	AGCATGTCTAGTCCTCTCTATACTATG	58.953	40.741	0.00	0.00	0.00	2.23
193	199	0.387622	TACGTAGCGTCACCAAGCAC	60.388	55.000	0.00	0.00	41.54	4.40
609	615	3.866582	GGAGGCCCATCTGTCCCG	61.867	72.222	0.00	0.00	0.00	5.14
623	629	3.071892	TCTGTCCCGGTTTGTGTAAGAAT	59.928	43.478	0.00	0.00	0.00	2.40
626	632	2.299582	TCCCGGTTTGTGTAAGAATCGA	59.700	45.455	0.00	0.00	0.00	3.59
634	640	7.508134	GGTTTGTGTAAGAATCGAGACTAAAC	58.492	38.462	0.00	0.67	0.00	2.01
706	712	2.125391	GCCCTTACGAACCGGGAC	60.125	66.667	6.32	0.00	40.55	4.46
730	736	5.632034	ATAGGCCCTTTTTCTACTAGTGG	57.368	43.478	5.39	1.87	0.00	4.00
731	737	3.527937	AGGCCCTTTTTCTACTAGTGGA	58.472	45.455	4.58	4.58	0.00	4.02
765	771	6.796705	AGTGTATGTAAAGCTGTAAACACC	57.203	37.500	16.35	5.16	37.32	4.16
810	816	4.156922	CGTATAATCCTGAGATCTTCGGCT	59.843	45.833	0.00	0.00	0.00	5.52
893	909	7.714377	GGTATGGATTTATGGAGCATATCTCAG	59.286	40.741	0.00	0.00	43.70	3.35
901	917	5.417754	TGGAGCATATCTCAGATGATTCC	57.582	43.478	0.00	0.29	43.70	3.01
991	1022	2.686835	GAGACAGGGAGGGCAGCT	60.687	66.667	0.00	0.00	0.00	4.24
1089	1127	1.324005	CCTTGTCCTCGTCCTCTCCC	61.324	65.000	0.00	0.00	0.00	4.30
1090	1128	0.323908	CTTGTCCTCGTCCTCTCCCT	60.324	60.000	0.00	0.00	0.00	4.20
1148	1186	4.096003	CCACGTTCCCCGCTGGAT	62.096	66.667	0.00	0.00	44.66	3.41
1185	1223	2.049433	GCAGCCACTACGTCACGT	60.049	61.111	8.49	8.49	44.35	4.49
1196	1234	1.371267	CGTCACGTCGGACATGTGT	60.371	57.895	1.15	0.00	42.10	3.72
1286	1324	0.037303	CCAGGCTGACAGTGACCAAT	59.963	55.000	17.94	0.00	0.00	3.16
1288	1326	0.037303	AGGCTGACAGTGACCAATGG	59.963	55.000	3.99	0.00	0.00	3.16
1344	1382	1.973281	CATGCCAAGGACGCCAAGT	60.973	57.895	0.00	0.00	0.00	3.16
1345	1383	1.228552	ATGCCAAGGACGCCAAGTT	60.229	52.632	0.00	0.00	0.00	2.66
1660	4629	2.839486	TGGGCTGACTGAGTTTACAG	57.161	50.000	0.00	0.00	42.78	2.74
1754	4727	1.070134	AGCTGCGATTATTCGGCCTTA	59.930	47.619	0.00	0.00	45.59	2.69
1804	4777	1.753930	TGCTGGAAATGCATGATCGT	58.246	45.000	0.00	0.00	35.31	3.73
1805	4778	2.916640	TGCTGGAAATGCATGATCGTA	58.083	42.857	0.00	0.00	35.31	3.43
1820	4793	8.297426	TGCATGATCGTAGTAGTAGATTAAAGG	58.703	37.037	0.00	0.00	0.00	3.11
1826	4799	7.052873	TCGTAGTAGTAGATTAAAGGACAGCT	58.947	38.462	0.00	0.00	0.00	4.24
1843	4816	4.012374	ACAGCTAACATTCCACAATCCAG	58.988	43.478	0.00	0.00	0.00	3.86
1847	4820	3.814504	AACATTCCACAATCCAGACCT	57.185	42.857	0.00	0.00	0.00	3.85
1851	4824	3.354948	TTCCACAATCCAGACCTCATG	57.645	47.619	0.00	0.00	0.00	3.07
1865	4838	6.316390	CCAGACCTCATGTTTTTACCTCATAC	59.684	42.308	0.00	0.00	0.00	2.39
1951	4925	7.837187	TGGGGATAGTTTAACCCTAAGAAAATG	59.163	37.037	0.00	0.00	43.72	2.32
2103	5079	8.851541	TCCAAAATATAAGGTGTACTCGTTTT	57.148	30.769	8.03	3.93	0.00	2.43
2104	5080	9.287373	TCCAAAATATAAGGTGTACTCGTTTTT	57.713	29.630	8.03	1.67	0.00	1.94
2281	5261	6.801862	ACTCGTTTGACTTTTGAGAAAACAAG	59.198	34.615	0.00	0.00	31.69	3.16
2311	5291	8.386264	ACCTTATATAAAGGAATGGATGGAGTG	58.614	37.037	10.67	0.00	39.81	3.51
2471	5451	5.979517	GCCATGCACAAATATAGGAGAAAAC	59.020	40.000	0.00	0.00	0.00	2.43
2489	5469	6.007076	AGAAAACCCAACAACAAATTTTGGT	58.993	32.000	13.42	3.82	38.53	3.67
2497	5477	7.308435	CCAACAACAAATTTTGGTTAAGCAAA	58.692	30.769	24.87	24.87	35.91	3.68
2953	5949	6.640518	TGCCTAACCTAGTAGAACTTGAATG	58.359	40.000	0.00	0.00	0.00	2.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
43	44	4.021104	TCTCAGAGATTGGTCGAACAACAT	60.021	41.667	20.01	10.08	32.39	2.71
52	53	2.958355	CCTCTCCTCTCAGAGATTGGTC	59.042	54.545	2.09	0.00	42.44	4.02
63	64	2.642154	TATCGACCACCTCTCCTCTC	57.358	55.000	0.00	0.00	0.00	3.20
149	153	8.457585	ACCATAGTATAGAGAGGACTAGACAT	57.542	38.462	0.00	0.00	37.14	3.06
172	177	1.074872	GCTTGGTGACGCTACGTACC	61.075	60.000	0.00	0.00	41.37	3.34
193	199	4.204012	AGAAGTGTCCTCTCTTATCTCCG	58.796	47.826	0.00	0.00	0.00	4.63
494	500	1.133253	CGCGTCAGCATTTCAGGTG	59.867	57.895	0.00	0.00	45.49	4.00
495	501	1.301716	ACGCGTCAGCATTTCAGGT	60.302	52.632	5.58	0.00	45.49	4.00
609	615	7.508134	GTTTAGTCTCGATTCTTACACAAACC	58.492	38.462	0.00	0.00	0.00	3.27
634	640	2.031333	GTCGGTACTAATGCCCTAGACG	60.031	54.545	0.00	0.00	0.00	4.18
706	712	5.823045	CCACTAGTAGAAAAAGGGCCTATTG	59.177	44.000	6.41	0.00	0.00	1.90
755	761	5.184864	TCCAGCATTAAATGGGTGTTTACAG	59.815	40.000	5.24	0.00	37.19	2.74
765	771	4.142534	CGCCATATCTCCAGCATTAAATGG	60.143	45.833	0.00	0.00	37.97	3.16
893	909	2.223611	CAGCAGCTTCGATGGAATCATC	59.776	50.000	0.00	0.00	45.97	2.92
901	917	6.971184	AGAAAATAAATTCAGCAGCTTCGATG	59.029	34.615	0.00	0.00	0.00	3.84
1005	1040	1.268539	GGTGTTGGCGTGTTTTCTCTG	60.269	52.381	0.00	0.00	0.00	3.35
1011	1046	1.739049	CCATGGTGTTGGCGTGTTT	59.261	52.632	2.57	0.00	0.00	2.83
1073	1108	1.000771	CAGGGAGAGGACGAGGACA	60.001	63.158	0.00	0.00	0.00	4.02
1089	1127	0.452987	CCGTGAACATCAATGGCCAG	59.547	55.000	13.05	0.00	0.00	4.85
1090	1128	0.251121	ACCGTGAACATCAATGGCCA	60.251	50.000	8.56	8.56	29.88	5.36
1148	1186	1.372683	GAGGCTGTTGCAGAGGTCA	59.627	57.895	0.00	0.00	41.91	4.02
1196	1234	4.377708	ATGCAGAGCGCGGACACA	62.378	61.111	8.83	0.00	46.97	3.72
1218	1256	3.630013	TGCAGAGCGGCAGGAGTT	61.630	61.111	1.45	0.00	39.25	3.01
1288	1326	4.715523	TGGCCTTGGCTACCGTGC	62.716	66.667	11.71	0.00	0.00	5.34
1344	1382	1.808411	GACCGCATGACCTTCTTGAA	58.192	50.000	0.00	0.00	0.00	2.69
1345	1383	0.389817	CGACCGCATGACCTTCTTGA	60.390	55.000	0.00	0.00	0.00	3.02
1543	1586	0.882042	CTGCACGATGTAGGCCATCC	60.882	60.000	5.01	0.00	46.10	3.51
1713	4686	3.760035	ACAGCCCGGTAGCTCGTG	61.760	66.667	1.77	0.00	42.61	4.35
1740	4713	3.813724	GGTGGAACTAAGGCCGAATAATC	59.186	47.826	0.00	0.00	36.74	1.75
1741	4714	3.743269	CGGTGGAACTAAGGCCGAATAAT	60.743	47.826	0.00	0.00	44.57	1.28
1788	4761	5.276461	ACTACTACGATCATGCATTTCCA	57.724	39.130	0.00	0.00	0.00	3.53
1800	4773	7.720515	AGCTGTCCTTTAATCTACTACTACGAT	59.279	37.037	0.00	0.00	0.00	3.73
1803	4776	9.949174	GTTAGCTGTCCTTTAATCTACTACTAC	57.051	37.037	0.00	0.00	0.00	2.73
1804	4777	9.690913	TGTTAGCTGTCCTTTAATCTACTACTA	57.309	33.333	0.00	0.00	0.00	1.82
1805	4778	8.591114	TGTTAGCTGTCCTTTAATCTACTACT	57.409	34.615	0.00	0.00	0.00	2.57
1820	4793	4.009675	TGGATTGTGGAATGTTAGCTGTC	58.990	43.478	0.00	0.00	0.00	3.51
1826	4799	4.288366	TGAGGTCTGGATTGTGGAATGTTA	59.712	41.667	0.00	0.00	0.00	2.41
1843	4816	7.606456	TCTTGTATGAGGTAAAAACATGAGGTC	59.394	37.037	0.00	0.00	0.00	3.85
1851	4824	9.959749	TGTTCATTTCTTGTATGAGGTAAAAAC	57.040	29.630	0.00	0.00	33.83	2.43
2103	5079	4.462508	TTCAAATGGTTGACTTGCACAA	57.537	36.364	0.00	0.00	43.52	3.33
2104	5080	4.141981	ACATTCAAATGGTTGACTTGCACA	60.142	37.500	7.58	0.00	43.52	4.57
2281	5261	9.449719	CCATCCATTCCTTTATATAAGGTGTAC	57.550	37.037	4.13	0.00	38.55	2.90
2311	5291	9.490663	CTAGTTTACACTTGTTTATTGCATAGC	57.509	33.333	0.00	0.00	34.06	2.97
2421	5401	2.287487	TGTTGTTGCAATCATGTGTCGG	60.287	45.455	0.59	0.00	0.00	4.79
2471	5451	5.355350	TGCTTAACCAAAATTTGTTGTTGGG	59.645	36.000	9.97	2.58	45.09	4.12
2489	5469	6.820656	TGCTCCTTTTTCATGTTTTTGCTTAA	59.179	30.769	0.00	0.00	0.00	1.85
2497	5477	6.405538	TGTTTCTTGCTCCTTTTTCATGTTT	58.594	32.000	0.00	0.00	0.00	2.83
2633	5621	5.989777	ACGCGCTTAATTCATTCTACCTAAT	59.010	36.000	5.73	0.00	0.00	1.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.