AutoCloner

Multiple sequence alignment - TraesCS7B01G429700

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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	TraesCS7B01G429700	chr7B	100.000	3443	0	0	1	3443	698502780	698506222	0.000000e+00	6359
1	TraesCS7B01G429700	chr7B	92.849	2629	160	7	1	2615	693438761	693441375	0.000000e+00	3788
2	TraesCS7B01G429700	chr7B	92.648	2625	169	6	1	2615	698973444	698976054	0.000000e+00	3757
3	TraesCS7B01G429700	chr7B	92.787	2634	125	20	1	2615	694825670	694823083	0.000000e+00	3751
4	TraesCS7B01G429700	chr7B	91.888	2638	171	19	1	2615	695262933	695260316	0.000000e+00	3646
5	TraesCS7B01G429700	chr7B	94.264	1569	79	5	1880	3443	699157919	699159481	0.000000e+00	2388
6	TraesCS7B01G429700	chr7B	90.242	1650	157	2	977	2625	684982526	684980880	0.000000e+00	2152
7	TraesCS7B01G429700	chr7B	87.797	1303	120	23	1523	2816	697385635	697384363	0.000000e+00	1489
8	TraesCS7B01G429700	chr7B	89.292	551	59	0	977	1527	697394514	697393964	0.000000e+00	691
9	TraesCS7B01G429700	chr7B	91.400	500	37	3	2948	3443	697384361	697383864	0.000000e+00	680
10	TraesCS7B01G429700	chr7B	90.619	501	40	4	2948	3443	684980726	684980228	0.000000e+00	658
11	TraesCS7B01G429700	chr7D	91.784	2690	185	15	774	3443	608122529	608125202	0.000000e+00	3711
12	TraesCS7B01G429700	chr7D	90.358	1929	156	15	708	2615	610623715	610621796	0.000000e+00	2505
13	TraesCS7B01G429700	chr7D	86.195	1427	148	26	2047	3443	514343486	514342079	0.000000e+00	1498
14	TraesCS7B01G429700	chr7D	85.203	1426	148	31	2047	3443	600275343	600273952	0.000000e+00	1406
15	TraesCS7B01G429700	chr7D	84.349	722	73	19	2747	3443	610604170	610603464	0.000000e+00	671
16	TraesCS7B01G429700	chr7D	93.407	182	12	0	1	182	610623939	610623758	1.570000e-68	270
17	TraesCS7B01G429700	chr7D	91.620	179	15	0	1	179	608121058	608121236	7.380000e-62	248
18	TraesCS7B01G429700	chr7D	85.354	198	28	1	3214	3410	8810238	8810435	1.620000e-48	204
19	TraesCS7B01G429700	chr7D	86.928	153	14	4	183	331	600280471	600280321	2.130000e-37	167
20	TraesCS7B01G429700	chr7A	86.088	1948	182	29	693	2615	700535575	700533692	0.000000e+00	2013
21	TraesCS7B01G429700	chr7A	89.143	175	17	2	3214	3386	9367703	9367877	2.080000e-52	217
22	TraesCS7B01G429700	chr7A	91.753	97	8	0	3214	3310	9379247	9379343	5.990000e-28	135
23	TraesCS7B01G429700	chr1D	90.233	215	19	2	416	628	356527979	356527765	2.620000e-71	279
24	TraesCS7B01G429700	chr1D	89.767	215	21	1	416	629	214850108	214850322	1.220000e-69	274
25	TraesCS7B01G429700	chr3A	88.596	228	24	2	416	641	459051102	459050875	3.380000e-70	276
26	TraesCS7B01G429700	chr2D	89.815	216	20	2	416	629	419801822	419802037	3.380000e-70	276
27	TraesCS7B01G429700	chr4A	89.352	216	21	2	416	629	655564580	655564365	1.570000e-68	270
28	TraesCS7B01G429700	chr4A	83.077	195	27	3	3214	3407	729901052	729901241	4.570000e-39	172
29	TraesCS7B01G429700	chr4A	81.313	198	22	4	3214	3410	729658405	729658588	2.770000e-31	147

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	TraesCS7B01G429700	chr7B	698502780	698506222	3442	False	6359.0	6359	100.0000	1	3443	1	chr7B.!!$F2	3442
1	TraesCS7B01G429700	chr7B	693438761	693441375	2614	False	3788.0	3788	92.8490	1	2615	1	chr7B.!!$F1	2614
2	TraesCS7B01G429700	chr7B	698973444	698976054	2610	False	3757.0	3757	92.6480	1	2615	1	chr7B.!!$F3	2614
3	TraesCS7B01G429700	chr7B	694823083	694825670	2587	True	3751.0	3751	92.7870	1	2615	1	chr7B.!!$R1	2614
4	TraesCS7B01G429700	chr7B	695260316	695262933	2617	True	3646.0	3646	91.8880	1	2615	1	chr7B.!!$R2	2614
5	TraesCS7B01G429700	chr7B	699157919	699159481	1562	False	2388.0	2388	94.2640	1880	3443	1	chr7B.!!$F4	1563
6	TraesCS7B01G429700	chr7B	684980228	684982526	2298	True	1405.0	2152	90.4305	977	3443	2	chr7B.!!$R4	2466
7	TraesCS7B01G429700	chr7B	697383864	697385635	1771	True	1084.5	1489	89.5985	1523	3443	2	chr7B.!!$R5	1920
8	TraesCS7B01G429700	chr7B	697393964	697394514	550	True	691.0	691	89.2920	977	1527	1	chr7B.!!$R3	550
9	TraesCS7B01G429700	chr7D	608121058	608125202	4144	False	1979.5	3711	91.7020	1	3443	2	chr7D.!!$F2	3442
10	TraesCS7B01G429700	chr7D	514342079	514343486	1407	True	1498.0	1498	86.1950	2047	3443	1	chr7D.!!$R1	1396
11	TraesCS7B01G429700	chr7D	600273952	600275343	1391	True	1406.0	1406	85.2030	2047	3443	1	chr7D.!!$R2	1396
12	TraesCS7B01G429700	chr7D	610621796	610623939	2143	True	1387.5	2505	91.8825	1	2615	2	chr7D.!!$R5	2614
13	TraesCS7B01G429700	chr7D	610603464	610604170	706	True	671.0	671	84.3490	2747	3443	1	chr7D.!!$R4	696
14	TraesCS7B01G429700	chr7A	700533692	700535575	1883	True	2013.0	2013	86.0880	693	2615	1	chr7A.!!$R1	1922

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
940	1988	0.38386	GTACGTGTTTGCTGCCGAAC	60.384	55.0	0.0	3.1	36.15	3.95	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2702	3794	0.814457	ACTTCCGACTAGAGCTGCAG	59.186	55.0	10.11	10.11	0.0	4.41	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
163	164	1.911057	AGTGACACGAGAGGATGTGA	58.089	50.000	0.00	0.00	39.38	3.58
166	167	2.731976	GTGACACGAGAGGATGTGAAAC	59.268	50.000	0.00	0.00	39.38	2.78
268	270	7.799447	GTGCAAAATAGTGTTTGTCGTTGTATA	59.201	33.333	0.00	0.00	40.06	1.47
275	277	5.919141	AGTGTTTGTCGTTGTATAGTGTCTC	59.081	40.000	0.00	0.00	0.00	3.36
291	293	6.768029	AGTGTCTCGAGTAGATATAACGAC	57.232	41.667	13.13	0.00	36.36	4.34
408	841	5.104360	TGAGCCTGCCTCACTAATTAATCTT	60.104	40.000	0.00	0.00	45.44	2.40
600	1034	8.088981	TGGTCAAACTAGAGATACTTTCACTTC	58.911	37.037	0.00	0.00	0.00	3.01
629	1063	4.946784	AGTTATGCGCAGACTAAAAAGG	57.053	40.909	23.03	0.00	0.00	3.11
635	1069	2.222445	GCGCAGACTAAAAAGGACGAAA	59.778	45.455	0.30	0.00	0.00	3.46
636	1070	3.120304	GCGCAGACTAAAAAGGACGAAAT	60.120	43.478	0.30	0.00	0.00	2.17
637	1071	4.092383	GCGCAGACTAAAAAGGACGAAATA	59.908	41.667	0.30	0.00	0.00	1.40
641	1075	7.235080	GCAGACTAAAAAGGACGAAATAAGTC	58.765	38.462	0.00	0.00	37.86	3.01
762	1214	1.674651	GGGCGGTGAAGAGGTTTCC	60.675	63.158	0.00	0.00	0.00	3.13
768	1220	1.608283	GGTGAAGAGGTTTCCAGACGG	60.608	57.143	0.00	0.00	0.00	4.79
807	1832	0.526954	GGGGCACATAGTACGTGTCG	60.527	60.000	0.00	3.03	39.92	4.35
856	1887	3.394606	AGTACAACCACCAGACTGGAAAT	59.605	43.478	28.56	9.27	40.96	2.17
861	1892	2.958355	ACCACCAGACTGGAAATGTTTG	59.042	45.455	28.56	13.21	40.96	2.93
880	1918	2.297701	TGCCTCACGCTTTTCTTTTCT	58.702	42.857	0.00	0.00	38.78	2.52
885	1923	4.458708	CTCACGCTTTTCTTTTCTGTAGC	58.541	43.478	0.00	0.00	0.00	3.58
886	1924	4.127171	TCACGCTTTTCTTTTCTGTAGCT	58.873	39.130	0.00	0.00	0.00	3.32
887	1925	4.211374	TCACGCTTTTCTTTTCTGTAGCTC	59.789	41.667	0.00	0.00	0.00	4.09
888	1926	3.184581	ACGCTTTTCTTTTCTGTAGCTCG	59.815	43.478	0.00	0.00	0.00	5.03
889	1927	3.184581	CGCTTTTCTTTTCTGTAGCTCGT	59.815	43.478	0.00	0.00	0.00	4.18
890	1928	4.384846	CGCTTTTCTTTTCTGTAGCTCGTA	59.615	41.667	0.00	0.00	0.00	3.43
891	1929	5.443431	CGCTTTTCTTTTCTGTAGCTCGTAG	60.443	44.000	0.00	0.00	0.00	3.51
897	1935	4.590400	TTTCTGTAGCTCGTAGTACGAC	57.410	45.455	21.10	16.81	46.73	4.34
940	1988	0.383860	GTACGTGTTTGCTGCCGAAC	60.384	55.000	0.00	3.10	36.15	3.95
943	1991	0.929824	CGTGTTTGCTGCCGAACAAG	60.930	55.000	16.76	15.24	44.69	3.16
953	2001	2.511600	CGAACAAGCGCTAGGGGG	60.512	66.667	12.05	0.29	0.00	5.40
958	2006	3.771160	AAGCGCTAGGGGGACACG	61.771	66.667	12.05	0.00	0.00	4.49
1104	2162	2.591715	GTGCACCACGGCTTCACT	60.592	61.111	5.22	0.00	34.04	3.41
1218	2276	0.898789	AGGTGTCCATCGACGACCTT	60.899	55.000	0.00	0.00	42.75	3.50
1254	2312	1.517257	GGTGACTCGCATCCTCACG	60.517	63.158	0.00	0.00	36.03	4.35
1452	2510	2.160721	TTCTCTACATCCCGGAGCTT	57.839	50.000	0.73	0.00	0.00	3.74
1603	2663	4.430765	ACCTCGGGCGCAACTACG	62.431	66.667	10.83	5.49	0.00	3.51
1624	2684	1.090052	CCTCGCGGAAGGTTTCATCC	61.090	60.000	6.13	0.00	0.00	3.51
1650	2710	0.530650	CCATGGACGCGTTAGAGCAT	60.531	55.000	15.53	0.00	36.85	3.79
2015	3085	1.829970	TCGAGAGGATGAGCGGCAT	60.830	57.895	1.45	0.00	40.77	4.40
2180	3250	4.090057	GCAGAGGTTGAACGCGGC	62.090	66.667	12.47	1.95	0.00	6.53
2223	3293	2.741092	GTGGCGTTGTGGGAGAGA	59.259	61.111	0.00	0.00	0.00	3.10
2232	3302	1.352083	TGTGGGAGAGACCTTCCTTG	58.648	55.000	0.00	0.00	38.97	3.61
2282	3352	4.947147	GGTGGCGGTGCTGGTCAA	62.947	66.667	0.00	0.00	0.00	3.18
2879	3976	2.475487	GCAAACTACGGTTCTGTGTCTC	59.525	50.000	0.00	0.00	34.14	3.36
2889	3986	2.563179	GTTCTGTGTCTCCTTCTAGCCA	59.437	50.000	0.00	0.00	0.00	4.75
2945	4047	7.492352	AATAGGGATGTTATAAACTCAACGC	57.508	36.000	0.00	0.00	0.00	4.84
3218	4341	2.604914	CGGATAATGGCGCATCTATGAC	59.395	50.000	10.83	0.00	0.00	3.06
3353	4477	7.162082	CCGATTTCCTCTAGCCTTATGTAATT	58.838	38.462	0.00	0.00	0.00	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
268	270	6.279123	TGTCGTTATATCTACTCGAGACACT	58.721	40.000	21.68	0.00	36.87	3.55
275	277	4.083431	CCACCCTGTCGTTATATCTACTCG	60.083	50.000	0.00	0.00	0.00	4.18
408	841	8.675705	TTGACTCAACATAAGTCTTTGATTGA	57.324	30.769	5.03	0.00	42.93	2.57
600	1034	3.187227	AGTCTGCGCATAACTTTTGTCTG	59.813	43.478	12.24	0.00	0.00	3.51
629	1063	8.430063	TCAACGATTTGTAAGACTTATTTCGTC	58.570	33.333	17.34	6.44	36.41	4.20
635	1069	7.548075	ACGGAATCAACGATTTGTAAGACTTAT	59.452	33.333	0.00	0.00	31.89	1.73
636	1070	6.869913	ACGGAATCAACGATTTGTAAGACTTA	59.130	34.615	0.00	0.00	31.89	2.24
637	1071	5.699458	ACGGAATCAACGATTTGTAAGACTT	59.301	36.000	0.00	0.00	31.89	3.01
648	1082	7.536855	GGACTCTATAATACGGAATCAACGAT	58.463	38.462	0.00	0.00	34.93	3.73
689	1123	1.553248	CATTCTAGGTGTTCACCCCGA	59.447	52.381	17.06	11.39	0.00	5.14
707	1149	1.764723	TCCCATTGTCGAGATCTGCAT	59.235	47.619	0.00	0.00	0.00	3.96
762	1214	2.822399	GGCCTATCCCACCGTCTG	59.178	66.667	0.00	0.00	0.00	3.51
833	1863	2.404559	TCCAGTCTGGTGGTTGTACTT	58.595	47.619	18.65	0.00	39.03	2.24
861	1892	2.033424	ACAGAAAAGAAAAGCGTGAGGC	59.967	45.455	0.00	0.00	44.05	4.70
887	1925	1.093159	AGCAGAAGGGTCGTACTACG	58.907	55.000	1.93	1.93	44.19	3.51
888	1926	4.915158	ATAAGCAGAAGGGTCGTACTAC	57.085	45.455	0.00	0.00	0.00	2.73
889	1927	6.630444	CTTATAAGCAGAAGGGTCGTACTA	57.370	41.667	0.00	0.00	0.00	1.82
890	1928	5.517322	CTTATAAGCAGAAGGGTCGTACT	57.483	43.478	0.00	0.00	0.00	2.73
940	1988	2.125106	GTGTCCCCCTAGCGCTTG	60.125	66.667	18.68	14.96	0.00	4.01
953	2001	0.109412	ACCGTGTTAGCTAGCGTGTC	60.109	55.000	9.55	2.34	0.00	3.67
958	2006	1.347320	GTGACACCGTGTTAGCTAGC	58.653	55.000	6.62	6.62	0.00	3.42
1299	2357	4.816984	GCCGGGGAGTCGAGGAGA	62.817	72.222	2.18	0.00	0.00	3.71
1359	2417	0.827925	TCTCCTTGCTGACGGTGAGT	60.828	55.000	0.00	0.00	0.00	3.41
1452	2510	3.569210	CAGGTGGTGGTCCTGGCA	61.569	66.667	4.27	0.00	46.03	4.92
1624	2684	1.227999	AACGCGTCCATGGTGTTGAG	61.228	55.000	14.44	4.70	36.80	3.02
2206	3276	1.668151	GTCTCTCCCACAACGCCAC	60.668	63.158	0.00	0.00	0.00	5.01
2232	3302	2.653087	AACCGCTCCGTCCTTACCC	61.653	63.158	0.00	0.00	0.00	3.69
2282	3352	4.080072	CCTTCTTCCCTTCCATAAGCTCTT	60.080	45.833	0.00	0.00	0.00	2.85
2702	3794	0.814457	ACTTCCGACTAGAGCTGCAG	59.186	55.000	10.11	10.11	0.00	4.41
2879	3976	1.661341	GCATGTGACTGGCTAGAAGG	58.339	55.000	3.17	0.00	0.00	3.46
2889	3986	4.281688	GCCCATAATATTTGGCATGTGACT	59.718	41.667	14.88	0.00	43.46	3.41
2945	4047	2.949644	TCATCATGGAAAGCAGCATCAG	59.050	45.455	0.00	0.00	0.00	2.90
3218	4341	6.907212	GCAGTGATGAAACGAAATACCATTAG	59.093	38.462	0.00	0.00	0.00	1.73
3353	4477	4.529109	TGTCAACCGAGTTACATCATGA	57.471	40.909	0.00	0.00	0.00	3.07

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.