AutoCloner

Multiple sequence alignment - TraesCS5A01G326400

Loading Multiple Alignment...

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	TraesCS5A01G326400	chr5A	100.000	2916	0	0	345	3260	536796191	536799106	0.000000e+00	5385.0
1	TraesCS5A01G326400	chr5A	88.126	1836	182	11	802	2629	536858231	536860038	0.000000e+00	2150.0
2	TraesCS5A01G326400	chr5A	83.352	1832	217	45	626	2445	536852784	536854539	0.000000e+00	1613.0
3	TraesCS5A01G326400	chr5A	79.384	1819	319	39	842	2640	536676479	536674697	0.000000e+00	1230.0
4	TraesCS5A01G326400	chr5A	82.888	187	22	7	349	531	536829962	536830142	3.370000e-35	159.0
5	TraesCS5A01G326400	chr5A	93.590	78	5	0	3183	3260	536860723	536860800	2.060000e-22	117.0
6	TraesCS5A01G326400	chr5A	97.959	49	1	0	522	570	536852743	536852791	5.800000e-13	86.1
7	TraesCS5A01G326400	chr5A	95.556	45	2	0	2760	2804	536860519	536860563	4.510000e-09	73.1
8	TraesCS5A01G326400	chr5A	93.478	46	3	0	2696	2741	536860438	536860483	5.840000e-08	69.4
9	TraesCS5A01G326400	chr5A	100.000	32	0	0	1	32	536795847	536795878	3.510000e-05	60.2
10	TraesCS5A01G326400	chr5D	94.072	2598	88	23	423	2987	423317041	423319605	0.000000e+00	3884.0
11	TraesCS5A01G326400	chr5D	81.020	1686	257	42	929	2596	423322491	423324131	0.000000e+00	1282.0
12	TraesCS5A01G326400	chr5D	80.458	1484	226	29	1015	2475	423354831	423356273	0.000000e+00	1075.0
13	TraesCS5A01G326400	chr5D	81.346	1040	167	18	1611	2640	423350124	423351146	0.000000e+00	821.0
14	TraesCS5A01G326400	chr5D	92.958	213	14	1	3048	3260	423319600	423319811	3.160000e-80	309.0
15	TraesCS5A01G326400	chr5B	95.947	2023	68	5	828	2845	510887167	510889180	0.000000e+00	3269.0
16	TraesCS5A01G326400	chr5B	93.205	1869	114	6	801	2668	511026472	511028328	0.000000e+00	2736.0
17	TraesCS5A01G326400	chr5B	86.264	1638	189	21	1016	2635	511072162	511073781	0.000000e+00	1746.0
18	TraesCS5A01G326400	chr5B	83.042	1657	219	37	1015	2640	511064109	511065734	0.000000e+00	1447.0
19	TraesCS5A01G326400	chr5B	79.242	1821	308	46	842	2640	510727878	510726106	0.000000e+00	1205.0
20	TraesCS5A01G326400	chr5B	90.811	370	23	9	2687	3053	511028703	511029064	4.890000e-133	484.0
21	TraesCS5A01G326400	chr5B	90.123	243	12	4	2846	3080	510889263	510889501	4.090000e-79	305.0
22	TraesCS5A01G326400	chr5B	93.893	131	8	0	3129	3259	510889501	510889631	7.130000e-47	198.0
23	TraesCS5A01G326400	chr5B	83.684	190	19	7	349	534	511024637	511024818	5.590000e-38	169.0
24	TraesCS5A01G326400	chr5B	87.736	106	6	2	3155	3260	511029060	511029158	2.060000e-22	117.0
25	TraesCS5A01G326400	chr5B	81.633	98	10	5	3047	3144	602259554	602259465	1.250000e-09	75.0
26	TraesCS5A01G326400	chr5B	95.455	44	1	1	791	834	510887114	510887156	5.840000e-08	69.4
27	TraesCS5A01G326400	chr3B	89.873	79	7	1	3064	3142	178386564	178386641	2.070000e-17	100.0
28	TraesCS5A01G326400	chr3A	86.364	88	10	2	3056	3142	131755235	131755321	9.630000e-16	95.3
29	TraesCS5A01G326400	chr1B	87.059	85	10	1	3049	3133	8148265	8148348	9.630000e-16	95.3
30	TraesCS5A01G326400	chr1B	84.946	93	11	3	3051	3142	58802649	58802739	1.250000e-14	91.6
31	TraesCS5A01G326400	chr6B	100.000	32	0	0	1	32	652123565	652123596	3.510000e-05	60.2

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	TraesCS5A01G326400	chr5A	536795847	536799106	3259	False	2722.600000	5385	100.000000	1	3260	2	chr5A.!!$F2	3259
1	TraesCS5A01G326400	chr5A	536674697	536676479	1782	True	1230.000000	1230	79.384000	842	2640	1	chr5A.!!$R1	1798
2	TraesCS5A01G326400	chr5A	536852743	536860800	8057	False	684.766667	2150	92.010167	522	3260	6	chr5A.!!$F3	2738
3	TraesCS5A01G326400	chr5D	423317041	423324131	7090	False	1825.000000	3884	89.350000	423	3260	3	chr5D.!!$F1	2837
4	TraesCS5A01G326400	chr5D	423350124	423356273	6149	False	948.000000	1075	80.902000	1015	2640	2	chr5D.!!$F2	1625
5	TraesCS5A01G326400	chr5B	511072162	511073781	1619	False	1746.000000	1746	86.264000	1016	2635	1	chr5B.!!$F2	1619
6	TraesCS5A01G326400	chr5B	511064109	511065734	1625	False	1447.000000	1447	83.042000	1015	2640	1	chr5B.!!$F1	1625
7	TraesCS5A01G326400	chr5B	510726106	510727878	1772	True	1205.000000	1205	79.242000	842	2640	1	chr5B.!!$R1	1798
8	TraesCS5A01G326400	chr5B	510887114	510889631	2517	False	960.350000	3269	93.854500	791	3259	4	chr5B.!!$F3	2468
9	TraesCS5A01G326400	chr5B	511024637	511029158	4521	False	876.500000	2736	88.859000	349	3260	4	chr5B.!!$F4	2911

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
770	2272	0.533032	CTTCGGGACCCTTCTCAGTC	59.467	60.000	9.41	0.0	0.0	3.51	F
922	2453	1.079750	AACTCCTTCGCGCTCCTTC	60.080	57.895	5.56	0.0	0.0	3.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1880	10900	2.103263	CCTGAGTAAGTGTATCCCCTGC	59.897	54.545	0.0	0.0	0.00	4.85	R
2444	11479	2.223249	CCATACAAAATGGAACGAGCCG	60.223	50.000	0.0	0.0	41.64	5.52	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
17	18	4.617200	TGGAGGGGCCAAAAACTG	57.383	55.556	4.39	0.00	45.87	3.16
18	19	1.623625	TGGAGGGGCCAAAAACTGT	59.376	52.632	4.39	0.00	45.87	3.55
19	20	0.854218	TGGAGGGGCCAAAAACTGTA	59.146	50.000	4.39	0.00	45.87	2.74
23	24	3.056107	GGAGGGGCCAAAAACTGTATTTC	60.056	47.826	4.39	0.00	36.34	2.17
24	25	3.832490	GAGGGGCCAAAAACTGTATTTCT	59.168	43.478	4.39	0.00	0.00	2.52
25	26	5.005628	AGGGGCCAAAAACTGTATTTCTA	57.994	39.130	4.39	0.00	0.00	2.10
26	27	5.589831	AGGGGCCAAAAACTGTATTTCTAT	58.410	37.500	4.39	0.00	0.00	1.98
27	28	5.422012	AGGGGCCAAAAACTGTATTTCTATG	59.578	40.000	4.39	0.00	0.00	2.23
28	29	5.420739	GGGGCCAAAAACTGTATTTCTATGA	59.579	40.000	4.39	0.00	0.00	2.15
30	31	7.364673	GGGGCCAAAAACTGTATTTCTATGAAT	60.365	37.037	4.39	0.00	0.00	2.57
31	32	8.040727	GGGCCAAAAACTGTATTTCTATGAATT	58.959	33.333	4.39	0.00	0.00	2.17
372	373	7.639113	TCCATCAACTATACAAATGGGTTTC	57.361	36.000	0.00	0.00	37.94	2.78
373	374	7.410174	TCCATCAACTATACAAATGGGTTTCT	58.590	34.615	0.00	0.00	37.94	2.52
378	379	7.713507	TCAACTATACAAATGGGTTTCTATCCG	59.286	37.037	0.00	0.00	0.00	4.18
381	382	6.937436	ATACAAATGGGTTTCTATCCGTTC	57.063	37.500	0.00	0.00	31.61	3.95
515	520	1.505807	CAATCCGCCGTTTGCATCA	59.494	52.632	0.00	0.00	41.33	3.07
577	2056	0.966875	AGCATCGGCCAATTTCAGCA	60.967	50.000	2.24	0.00	42.56	4.41
669	2148	6.418819	CGCACAAAATGAGAGAAAGAAAATGT	59.581	34.615	0.00	0.00	0.00	2.71
677	2156	7.019774	TGAGAGAAAGAAAATGTGAACACAG	57.980	36.000	12.97	0.00	45.48	3.66
683	2178	3.316308	AGAAAATGTGAACACAGCTCACC	59.684	43.478	12.97	1.62	45.48	4.02
713	2210	5.106157	CCATAACTTCTCAGGTCGCAAAAAT	60.106	40.000	0.00	0.00	0.00	1.82
770	2272	0.533032	CTTCGGGACCCTTCTCAGTC	59.467	60.000	9.41	0.00	0.00	3.51
914	2445	2.159282	TCGGTAAGATCAACTCCTTCGC	60.159	50.000	0.00	0.00	0.00	4.70
915	2446	2.194271	GGTAAGATCAACTCCTTCGCG	58.806	52.381	0.00	0.00	0.00	5.87
916	2447	1.588861	GTAAGATCAACTCCTTCGCGC	59.411	52.381	0.00	0.00	0.00	6.86
920	2451	1.608717	ATCAACTCCTTCGCGCTCCT	61.609	55.000	5.56	0.00	0.00	3.69
921	2452	1.374758	CAACTCCTTCGCGCTCCTT	60.375	57.895	5.56	0.00	0.00	3.36
922	2453	1.079750	AACTCCTTCGCGCTCCTTC	60.080	57.895	5.56	0.00	0.00	3.46
923	2454	2.580867	CTCCTTCGCGCTCCTTCG	60.581	66.667	5.56	0.00	0.00	3.79
944	2475	1.668826	AGGCAACCCTACCTGAATCA	58.331	50.000	0.00	0.00	40.58	2.57
980	2511	2.734673	CTCGCTTCGCTTGCTCACC	61.735	63.158	0.00	0.00	0.00	4.02
1019	4713	2.047179	GTTTCCCTCGAAGCCGCT	60.047	61.111	0.00	0.00	35.37	5.52
1506	5210	2.502947	TGTGCATGAGCTAGAGGTGAAT	59.497	45.455	0.00	0.00	42.74	2.57
1710	10730	1.277557	ACCAGTCACAGGATGAGAAGC	59.722	52.381	0.00	0.00	37.47	3.86
1880	10900	3.480470	TGGAGAGGTTTTTGCAAGAGAG	58.520	45.455	0.00	0.00	0.00	3.20
1961	10981	6.458342	GGCTGCTTAGTTGTGGTTCATAATAC	60.458	42.308	0.00	0.00	0.00	1.89
2046	11069	2.566833	ACAGCTTGCCTTCACATGTA	57.433	45.000	0.00	0.00	0.00	2.29
2221	11251	4.094476	AGTAAAACTGAGAGATCCCCGAA	58.906	43.478	0.00	0.00	0.00	4.30
2222	11252	4.530946	AGTAAAACTGAGAGATCCCCGAAA	59.469	41.667	0.00	0.00	0.00	3.46
2292	11322	7.498900	TGTCGCTAATGAGGTGAATAATTCATT	59.501	33.333	4.28	4.28	42.47	2.57
2365	11396	4.290969	GACTGATGCATGCATTGATGAAG	58.709	43.478	32.60	22.63	36.70	3.02
2444	11479	5.224888	TGCATGAGAAGATTTGCAGTTTTC	58.775	37.500	0.00	0.00	39.98	2.29
2447	11482	3.237628	GAGAAGATTTGCAGTTTTCGGC	58.762	45.455	0.00	0.00	41.20	5.54
2631	11687	8.579863	CCTTTCTTCAAACAGATAAGGATTTGT	58.420	33.333	0.00	0.00	35.34	2.83
3076	12639	4.142093	CCTCCCTTCGTCCGAAATTACTTA	60.142	45.833	3.52	0.00	33.34	2.24
3087	12650	7.096353	CGTCCGAAATTACTTATCGCTCAAATA	60.096	37.037	0.00	0.00	35.35	1.40
3119	12682	8.341892	TCTAGATGTATTTCAGTGCTCGATAT	57.658	34.615	0.00	0.00	0.00	1.63
3120	12683	9.449719	TCTAGATGTATTTCAGTGCTCGATATA	57.550	33.333	0.00	0.00	0.00	0.86
3131	12694	6.015095	TCAGTGCTCGATATATCCATTTGAGT	60.015	38.462	7.15	0.00	0.00	3.41
3150	12713	4.250464	GAGTGACATGTAATTTCGGACCA	58.750	43.478	0.00	0.00	0.00	4.02
3153	12716	4.693566	GTGACATGTAATTTCGGACCAAGA	59.306	41.667	0.00	0.00	0.00	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	3.856900	AGAAATACAGTTTTTGGCCCCT	58.143	40.909	0.00	0.00	0.00	4.79
4	5	5.420739	TCATAGAAATACAGTTTTTGGCCCC	59.579	40.000	0.00	0.00	0.00	5.80
5	6	6.524101	TCATAGAAATACAGTTTTTGGCCC	57.476	37.500	0.00	0.00	0.00	5.80
344	345	8.608185	ACCCATTTGTATAGTTGATGGATTTT	57.392	30.769	2.40	0.00	39.66	1.82
346	347	8.608185	AAACCCATTTGTATAGTTGATGGATT	57.392	30.769	2.40	0.00	39.66	3.01
359	360	6.057321	AGAACGGATAGAAACCCATTTGTA	57.943	37.500	0.00	0.00	0.00	2.41
361	362	6.995511	TTAGAACGGATAGAAACCCATTTG	57.004	37.500	0.00	0.00	0.00	2.32
365	366	5.424252	AGTCATTAGAACGGATAGAAACCCA	59.576	40.000	0.00	0.00	0.00	4.51
372	373	5.671493	ACCCAAAGTCATTAGAACGGATAG	58.329	41.667	0.00	0.00	0.00	2.08
373	374	5.687166	ACCCAAAGTCATTAGAACGGATA	57.313	39.130	0.00	0.00	0.00	2.59
378	379	6.575162	ACATCAACCCAAAGTCATTAGAAC	57.425	37.500	0.00	0.00	0.00	3.01
381	382	6.980593	TCAAACATCAACCCAAAGTCATTAG	58.019	36.000	0.00	0.00	0.00	1.73
611	2090	1.234821	TGCTGAAACCGCTCGATTTT	58.765	45.000	0.00	0.00	0.00	1.82
612	2091	1.197721	CTTGCTGAAACCGCTCGATTT	59.802	47.619	0.00	0.00	0.00	2.17
613	2092	0.798776	CTTGCTGAAACCGCTCGATT	59.201	50.000	0.00	0.00	0.00	3.34
614	2093	0.037326	TCTTGCTGAAACCGCTCGAT	60.037	50.000	0.00	0.00	0.00	3.59
616	2095	0.798776	ATTCTTGCTGAAACCGCTCG	59.201	50.000	0.00	0.00	38.29	5.03
617	2096	2.485814	AGAATTCTTGCTGAAACCGCTC	59.514	45.455	0.88	0.00	38.29	5.03
619	2098	2.982470	CAAGAATTCTTGCTGAAACCGC	59.018	45.455	29.90	0.00	45.59	5.68
648	2127	9.304731	TGTTCACATTTTCTTTCTCTCATTTTG	57.695	29.630	0.00	0.00	0.00	2.44
669	2148	4.436515	CACGGTGAGCTGTGTTCA	57.563	55.556	0.74	0.00	44.72	3.18
677	2156	2.112815	GTTATGGCCCACGGTGAGC	61.113	63.158	10.28	8.09	0.00	4.26
683	2178	1.656652	CTGAGAAGTTATGGCCCACG	58.343	55.000	0.00	0.00	0.00	4.94
770	2272	1.216710	GCAAGGAGGACTCGACTGG	59.783	63.158	0.00	0.00	0.00	4.00
887	2408	0.175073	GTTGATCTTACCGAGGGCGT	59.825	55.000	0.00	0.00	35.23	5.68
920	2451	2.221299	AGGTAGGGTTGCCTGCGAA	61.221	57.895	0.00	0.00	38.09	4.70
921	2452	2.606519	AGGTAGGGTTGCCTGCGA	60.607	61.111	0.00	0.00	38.09	5.10
944	2475	2.369394	GAGGGAGCCAAATTGACGATT	58.631	47.619	0.00	0.00	0.00	3.34
980	2511	2.536365	TCGCTGCGGTAAATAGAAGTG	58.464	47.619	23.03	0.00	0.00	3.16
1506	5210	6.936900	GTCTGCAGCTATATTCCTTTATTGGA	59.063	38.462	9.47	0.00	0.00	3.53
1710	10730	4.752879	ACCCCATTGACGACCGCG	62.753	66.667	0.00	0.00	44.79	6.46
1880	10900	2.103263	CCTGAGTAAGTGTATCCCCTGC	59.897	54.545	0.00	0.00	0.00	4.85
1961	10981	8.370940	ACCACAAGTCCATAGATATGTCATAAG	58.629	37.037	0.00	0.00	31.82	1.73
2221	11251	4.618227	GCTTCCTGTGTAAATGCCGATTTT	60.618	41.667	0.00	0.00	33.63	1.82
2222	11252	3.119495	GCTTCCTGTGTAAATGCCGATTT	60.119	43.478	0.00	0.00	35.83	2.17
2292	11322	3.261390	ACATAAGGTAAACGGCCAGTACA	59.739	43.478	2.24	0.00	0.00	2.90
2365	11396	8.865590	TTAATTGAAAGGCACAAAAGTACTTC	57.134	30.769	8.95	0.00	0.00	3.01
2444	11479	2.223249	CCATACAAAATGGAACGAGCCG	60.223	50.000	0.00	0.00	41.64	5.52
2447	11482	4.433186	TTGCCATACAAAATGGAACGAG	57.567	40.909	8.20	0.00	41.64	4.18
2869	12422	3.686016	AGACCATGTTCTAAACGGCATT	58.314	40.909	0.00	0.00	0.00	3.56
2875	12428	7.497925	AAAGACAAGAGACCATGTTCTAAAC	57.502	36.000	0.00	0.00	0.00	2.01
2941	12495	8.962679	ACTGACTTGTTTTAAGAATTTACCACA	58.037	29.630	0.00	0.00	0.00	4.17
3076	12639	8.965819	ACATCTAGATACATCTATTTGAGCGAT	58.034	33.333	4.54	0.00	38.60	4.58
3087	12650	9.087871	AGCACTGAAATACATCTAGATACATCT	57.912	33.333	4.54	0.00	40.86	2.90
3101	12664	8.709386	AATGGATATATCGAGCACTGAAATAC	57.291	34.615	6.64	0.00	0.00	1.89
3119	12682	8.611757	CGAAATTACATGTCACTCAAATGGATA	58.388	33.333	0.00	0.00	0.00	2.59
3120	12683	7.415541	CCGAAATTACATGTCACTCAAATGGAT	60.416	37.037	0.00	0.00	0.00	3.41
3131	12694	4.900684	TCTTGGTCCGAAATTACATGTCA	58.099	39.130	0.00	0.00	0.00	3.58
3186	12749	8.251721	GGTACTAAAAGCTTCATTAGAGTCAGA	58.748	37.037	19.97	1.45	34.11	3.27
3187	12750	8.254508	AGGTACTAAAAGCTTCATTAGAGTCAG	58.745	37.037	19.97	1.12	36.02	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.