AutoCloner

Multiple sequence alignment - TraesCS4B01G248400

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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	TraesCS4B01G248400	chr4B	100.000	2972	0	0	1	2972	513449673	513452644	0.000000e+00	5489.0
1	TraesCS4B01G248400	chr4B	90.282	885	65	13	1411	2287	512797524	512796653	0.000000e+00	1138.0
2	TraesCS4B01G248400	chr4B	89.336	572	44	6	930	1494	512797963	512797402	0.000000e+00	702.0
3	TraesCS4B01G248400	chr4D	90.207	2318	149	30	1	2295	416147594	416145332	0.000000e+00	2952.0
4	TraesCS4B01G248400	chr4D	89.948	1343	82	23	1098	2413	416577813	416579129	0.000000e+00	1683.0
5	TraesCS4B01G248400	chr4D	94.090	1049	58	2	1	1048	416576768	416577813	0.000000e+00	1591.0
6	TraesCS4B01G248400	chr4D	85.412	1371	110	35	905	2241	416429763	416428449	0.000000e+00	1341.0
7	TraesCS4B01G248400	chr4D	90.519	1002	55	14	1428	2413	416643072	416644049	0.000000e+00	1288.0
8	TraesCS4B01G248400	chr4D	91.543	674	49	6	1372	2040	416694157	416694827	0.000000e+00	922.0
9	TraesCS4B01G248400	chr4D	91.837	637	40	3	906	1536	416693631	416694261	0.000000e+00	878.0
10	TraesCS4B01G248400	chr4D	91.870	615	38	3	906	1514	416642304	416642912	0.000000e+00	848.0
11	TraesCS4B01G248400	chr4D	91.540	461	34	4	1432	1891	416422606	416422150	5.410000e-177	630.0
12	TraesCS4B01G248400	chr4D	87.844	436	18	15	2538	2972	416695162	416695563	2.070000e-131	479.0
13	TraesCS4B01G248400	chr4D	89.349	169	14	4	2295	2461	416695000	416695166	3.000000e-50	209.0
14	TraesCS4B01G248400	chr4D	97.619	42	0	1	704	745	416146850	416146810	1.480000e-08	71.3
15	TraesCS4B01G248400	chr4D	97.619	42	0	1	704	745	416577512	416577552	1.480000e-08	71.3
16	TraesCS4B01G248400	chr4D	89.583	48	1	2	2151	2197	416694968	416694924	1.150000e-04	58.4
17	TraesCS4B01G248400	chr4A	90.898	1604	97	14	1411	2972	47455629	47454033	0.000000e+00	2108.0
18	TraesCS4B01G248400	chr4A	86.719	1152	95	28	1373	2485	47709464	47710596	0.000000e+00	1227.0
19	TraesCS4B01G248400	chr4A	94.251	748	39	4	1	745	47708097	47708843	0.000000e+00	1140.0
20	TraesCS4B01G248400	chr4A	87.049	942	79	26	1373	2287	47736554	47737479	0.000000e+00	1024.0
21	TraesCS4B01G248400	chr4A	90.541	740	56	7	1421	2150	47650122	47650857	0.000000e+00	966.0
22	TraesCS4B01G248400	chr4A	92.820	571	23	8	237	796	47456723	47456160	0.000000e+00	811.0
23	TraesCS4B01G248400	chr4A	88.705	664	60	8	843	1494	47456164	47455504	0.000000e+00	797.0
24	TraesCS4B01G248400	chr4A	90.257	544	35	7	1006	1536	47709029	47709567	0.000000e+00	695.0
25	TraesCS4B01G248400	chr4A	85.690	587	60	15	960	1536	47736064	47736636	5.480000e-167	597.0
26	TraesCS4B01G248400	chr4A	84.351	524	40	24	960	1473	47649746	47650237	2.680000e-130	475.0
27	TraesCS4B01G248400	chr4A	90.308	227	16	4	744	967	47708803	47709026	2.900000e-75	292.0
28	TraesCS4B01G248400	chr6A	92.005	788	52	3	1	788	26095084	26094308	0.000000e+00	1096.0
29	TraesCS4B01G248400	chr6A	91.371	788	55	4	1	788	26028688	26027914	0.000000e+00	1066.0
30	TraesCS4B01G248400	chr7A	92.179	780	49	3	1	780	646297679	646298446	0.000000e+00	1092.0
31	TraesCS4B01G248400	chr7A	87.645	259	19	4	537	794	660698189	660697943	3.750000e-74	289.0
32	TraesCS4B01G248400	chr3A	94.043	554	29	1	1	554	434195581	434195032	0.000000e+00	837.0
33	TraesCS4B01G248400	chr3A	93.694	555	30	2	1	554	484425653	484425103	0.000000e+00	826.0
34	TraesCS4B01G248400	chr3A	89.024	246	15	3	537	782	244516570	244516803	8.060000e-76	294.0
35	TraesCS4B01G248400	chr1A	94.054	555	28	2	1	554	535521409	535521959	0.000000e+00	837.0
36	TraesCS4B01G248400	chr1A	89.868	227	11	3	557	782	70749994	70750209	6.270000e-72	281.0
37	TraesCS4B01G248400	chr2A	90.625	224	10	4	537	759	491175909	491176122	1.350000e-73	287.0
38	TraesCS4B01G248400	chr1B	88.136	59	6	1	2887	2944	17543554	17543496	5.320000e-08	69.4

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	TraesCS4B01G248400	chr4B	513449673	513452644	2971	False	5489.000000	5489	100.000000	1	2972	1	chr4B.!!$F1	2971
1	TraesCS4B01G248400	chr4B	512796653	512797963	1310	True	920.000000	1138	89.809000	930	2287	2	chr4B.!!$R1	1357
2	TraesCS4B01G248400	chr4D	416145332	416147594	2262	True	1511.650000	2952	93.913000	1	2295	2	chr4D.!!$R4	2294
3	TraesCS4B01G248400	chr4D	416428449	416429763	1314	True	1341.000000	1341	85.412000	905	2241	1	chr4D.!!$R2	1336
4	TraesCS4B01G248400	chr4D	416576768	416579129	2361	False	1115.100000	1683	93.885667	1	2413	3	chr4D.!!$F1	2412
5	TraesCS4B01G248400	chr4D	416642304	416644049	1745	False	1068.000000	1288	91.194500	906	2413	2	chr4D.!!$F2	1507
6	TraesCS4B01G248400	chr4D	416693631	416695563	1932	False	622.000000	922	90.143250	906	2972	4	chr4D.!!$F3	2066
7	TraesCS4B01G248400	chr4A	47454033	47456723	2690	True	1238.666667	2108	90.807667	237	2972	3	chr4A.!!$R1	2735
8	TraesCS4B01G248400	chr4A	47708097	47710596	2499	False	838.500000	1227	90.383750	1	2485	4	chr4A.!!$F2	2484
9	TraesCS4B01G248400	chr4A	47736064	47737479	1415	False	810.500000	1024	86.369500	960	2287	2	chr4A.!!$F3	1327
10	TraesCS4B01G248400	chr4A	47649746	47650857	1111	False	720.500000	966	87.446000	960	2150	2	chr4A.!!$F1	1190
11	TraesCS4B01G248400	chr6A	26094308	26095084	776	True	1096.000000	1096	92.005000	1	788	1	chr6A.!!$R2	787
12	TraesCS4B01G248400	chr6A	26027914	26028688	774	True	1066.000000	1066	91.371000	1	788	1	chr6A.!!$R1	787
13	TraesCS4B01G248400	chr7A	646297679	646298446	767	False	1092.000000	1092	92.179000	1	780	1	chr7A.!!$F1	779
14	TraesCS4B01G248400	chr3A	434195032	434195581	549	True	837.000000	837	94.043000	1	554	1	chr3A.!!$R1	553
15	TraesCS4B01G248400	chr3A	484425103	484425653	550	True	826.000000	826	93.694000	1	554	1	chr3A.!!$R2	553
16	TraesCS4B01G248400	chr1A	535521409	535521959	550	False	837.000000	837	94.054000	1	554	1	chr1A.!!$F2	553

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
685	697	0.036765	AGCCATGGCAAATGCAACAG	60.037	50.0	37.18	0.0	44.88	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2513	3045	0.10412	TTGGTCTCCGTGAGTGTGTG	59.896	55.0	1.6	0.0	0.0	3.82	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
28	30	6.931838	TGGTGACTACTACTACAATTTGGAG	58.068	40.000	7.10	7.10	33.50	3.86
50	52	6.814954	AGATAATACTCCAGGCTCTCAAAA	57.185	37.500	0.00	0.00	0.00	2.44
58	60	4.965814	TCCAGGCTCTCAAAATATAGCAG	58.034	43.478	0.00	0.00	36.68	4.24
129	131	4.307032	AGGCAATACTCCAACTGAATGT	57.693	40.909	0.00	0.00	0.00	2.71
322	324	9.713740	GTCATCATCAGTAACAAAATTCAGATC	57.286	33.333	0.00	0.00	0.00	2.75
416	420	0.331616	ATTACAGGTGGAGTTGGGGC	59.668	55.000	0.00	0.00	0.00	5.80
482	486	4.696877	GCCATCACGAATCCATTCATCATA	59.303	41.667	0.00	0.00	36.61	2.15
685	697	0.036765	AGCCATGGCAAATGCAACAG	60.037	50.000	37.18	0.00	44.88	3.16
759	775	7.395190	TCACAAGTCATAGCAAAGCAATTAT	57.605	32.000	0.00	0.00	0.00	1.28
760	776	7.829725	TCACAAGTCATAGCAAAGCAATTATT	58.170	30.769	0.00	0.00	0.00	1.40
761	777	8.955388	TCACAAGTCATAGCAAAGCAATTATTA	58.045	29.630	0.00	0.00	0.00	0.98
782	798	1.000955	ACCTAAAGTGCCGAGACACAG	59.999	52.381	6.08	0.00	43.23	3.66
791	807	2.265904	CGAGACACAGGTCACCGGA	61.266	63.158	9.46	0.00	46.80	5.14
877	896	9.343103	CATCAAAATTGATCTCAGAAGTTTGAG	57.657	33.333	18.06	10.55	45.62	3.02
910	929	0.390340	GAATGCGTGACAGGCTCAGA	60.390	55.000	19.91	1.19	0.00	3.27
927	946	1.079405	GACGGATTGCTCGTTCCCA	60.079	57.895	0.00	0.00	41.22	4.37
975	994	1.733399	GTGAACTCGGAGGCGTGAC	60.733	63.158	10.23	0.00	0.00	3.67
1145	1175	1.327690	GCCTCTCCCCACATCGTACA	61.328	60.000	0.00	0.00	0.00	2.90
1388	1460	1.135746	CAAGGACTACACTCCGTCGAC	60.136	57.143	5.18	5.18	35.20	4.20
1486	1786	2.363925	GCCCGGACTACACTCCCT	60.364	66.667	0.73	0.00	0.00	4.20
1968	2436	0.530870	GTCAGCGAGCCTTGGGATAC	60.531	60.000	0.00	0.00	0.00	2.24
1981	2449	4.408921	CCTTGGGATACTGACATCCTGTAA	59.591	45.833	11.11	5.85	43.56	2.41
2062	2535	2.977772	TTGTTTGTTCCTTGGGCAAG	57.022	45.000	0.00	0.00	38.14	4.01
2073	2546	2.069273	CTTGGGCAAGTCTTGTACTCG	58.931	52.381	14.03	0.00	37.50	4.18
2270	2777	3.588955	TGTGACTGTGATGTACTGATGC	58.411	45.455	0.00	0.00	33.00	3.91
2330	2853	8.412456	TGAACATTTTTCTGAAAACAGAGCATA	58.588	29.630	14.70	0.00	37.56	3.14
2333	2856	8.579006	ACATTTTTCTGAAAACAGAGCATATCA	58.421	29.630	14.70	0.00	37.56	2.15
2510	3042	4.828925	GGTCTCCCGCTGAGCTGC	62.829	72.222	1.78	0.00	41.18	5.25
2520	3052	1.597302	CTGAGCTGCAGCACACACT	60.597	57.895	38.24	18.66	45.16	3.55
2523	3055	1.839598	GAGCTGCAGCACACACTCAC	61.840	60.000	38.24	14.46	45.16	3.51
2528	3060	1.363807	CAGCACACACTCACGGAGA	59.636	57.895	7.76	0.00	33.32	3.71
2536	3068	2.201022	ACTCACGGAGACCAAGCGT	61.201	57.895	7.76	0.00	33.32	5.07
2740	3273	5.856126	TCAGCTTACGTATGAACCTTTTG	57.144	39.130	12.31	0.03	0.00	2.44
2788	3322	1.630369	CAGGAAGGAGGGTGATGTTGA	59.370	52.381	0.00	0.00	0.00	3.18
2808	3342	6.177610	GTTGATTGGGAATTCTAGTGGTACA	58.822	40.000	5.23	0.00	0.00	2.90
2839	3373	5.512576	GGGGCCGAAAGTCACAGTTATATAT	60.513	44.000	0.00	0.00	0.00	0.86
2915	3464	3.485877	GGCTTCGATCTTCATTTTCACCG	60.486	47.826	0.00	0.00	0.00	4.94
2923	3472	6.129457	CGATCTTCATTTTCACCGACAAAAAC	60.129	38.462	0.00	0.00	0.00	2.43

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
44	46	5.050499	CGTTGCTCCTCTGCTATATTTTGAG	60.050	44.000	0.00	0.00	0.00	3.02
50	52	1.967066	AGCGTTGCTCCTCTGCTATAT	59.033	47.619	0.00	0.00	30.62	0.86
58	60	3.532542	AGGTTTAATAGCGTTGCTCCTC	58.467	45.455	0.00	0.00	40.44	3.71
129	131	4.080413	TGAGATAGAACATGCATGGTCCAA	60.080	41.667	35.43	26.03	45.54	3.53
253	255	2.977914	TGTTAATCTGGACAGCTCAGC	58.022	47.619	0.00	0.00	32.63	4.26
416	420	4.673061	CGGCTTCTACTGTGACTACTTCAG	60.673	50.000	0.00	0.00	33.71	3.02
482	486	1.059913	CAGTCTCTGTTCCCTGGGTT	58.940	55.000	13.56	0.00	0.00	4.11
588	600	4.508461	TGCCATTTGTTCAACATCAGAG	57.492	40.909	0.00	0.00	0.00	3.35
620	632	4.282703	TGTGTTCCTAGGTTTAGACAGACC	59.717	45.833	9.08	0.00	36.15	3.85
685	697	2.609427	TGTGCCACAGATAGCTCATC	57.391	50.000	0.00	0.00	0.00	2.92
759	775	3.069872	TGTGTCTCGGCACTTTAGGTTAA	59.930	43.478	3.13	0.00	39.89	2.01
760	776	2.629137	TGTGTCTCGGCACTTTAGGTTA	59.371	45.455	3.13	0.00	39.89	2.85
761	777	1.414919	TGTGTCTCGGCACTTTAGGTT	59.585	47.619	3.13	0.00	39.89	3.50
782	798	0.971447	AGCTCCTACTTCCGGTGACC	60.971	60.000	0.00	0.00	0.00	4.02
791	807	2.829120	GTCTTCAGGTGAGCTCCTACTT	59.171	50.000	12.15	0.00	35.87	2.24
826	845	5.204833	TGTTTCTCTTTTCGCTTTGATTCG	58.795	37.500	0.00	0.00	0.00	3.34
877	896	0.108945	GCATTCAGTTCAAGGGCAGC	60.109	55.000	0.00	0.00	0.00	5.25
910	929	1.375523	GTGGGAACGAGCAATCCGT	60.376	57.895	0.00	0.00	42.61	4.69
940	959	1.696314	ACCCCGGAGCCCATAACAT	60.696	57.895	0.73	0.00	0.00	2.71
1486	1786	1.748122	GAGTGTACTCGGGGCTCGA	60.748	63.158	10.05	10.05	46.77	4.04
1497	1797	4.509737	GGGCTCGCCGGAGTGTAC	62.510	72.222	5.05	0.12	42.53	2.90
1515	1857	2.408241	GCTCGCCGGAGTGTAGTCT	61.408	63.158	5.05	0.00	42.53	3.24
1851	2319	4.021925	GCTTCTGACGCCAGGGGT	62.022	66.667	9.39	9.39	40.76	4.95
1981	2449	9.113838	CAATCTGTTGCTCCTATTACAGTTTAT	57.886	33.333	0.00	0.00	39.16	1.40
2073	2546	9.521503	TCGATTCAGATAATATTCATCGATTCC	57.478	33.333	0.00	0.00	36.91	3.01
2270	2777	7.015682	ACCAACCATACATATACTTCTCTCAGG	59.984	40.741	0.00	0.00	0.00	3.86
2330	2853	1.599047	CAGACTGCTTCCCGGTGAT	59.401	57.895	0.00	0.00	31.71	3.06
2387	2918	4.960938	TGCATAAATCCAAGAGCTATCGT	58.039	39.130	0.00	0.00	0.00	3.73
2510	3042	0.941463	GTCTCCGTGAGTGTGTGCTG	60.941	60.000	1.60	0.00	0.00	4.41
2513	3045	0.104120	TTGGTCTCCGTGAGTGTGTG	59.896	55.000	1.60	0.00	0.00	3.82
2520	3052	2.142357	CTGACGCTTGGTCTCCGTGA	62.142	60.000	0.00	0.00	46.24	4.35
2523	3055	1.006102	AACTGACGCTTGGTCTCCG	60.006	57.895	0.00	0.00	46.24	4.63
2528	3060	0.464036	TGTCTCAACTGACGCTTGGT	59.536	50.000	0.00	0.00	39.64	3.67
2731	3264	0.752658	AGCACAAGGCCAAAAGGTTC	59.247	50.000	5.01	0.00	46.50	3.62
2740	3273	3.288964	TCTAGTAGTCTAGCACAAGGCC	58.711	50.000	0.00	0.00	46.50	5.19
2788	3322	7.347222	TGAGTATGTACCACTAGAATTCCCAAT	59.653	37.037	0.65	0.00	0.00	3.16
2808	3342	0.831307	GACTTTCGGCCCCTGAGTAT	59.169	55.000	0.00	0.00	0.00	2.12
2839	3373	3.498018	CACGATCAATGTCAACTGAACCA	59.502	43.478	0.00	0.00	0.00	3.67
2915	3464	6.787085	ACTCACTAGTGCTATGTTTTTGTC	57.213	37.500	18.45	0.00	33.57	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.