AutoCloner

Multiple sequence alignment - TraesCS2B01G044200

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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	TraesCS2B01G044200	chr2B	100.000	3100	0	0	1	3100	21661548	21664647	0.000000e+00	5725
1	TraesCS2B01G044200	chr2B	85.802	1782	174	42	569	2321	263839038	263837307	0.000000e+00	1816
2	TraesCS2B01G044200	chr2B	88.225	569	34	16	2322	2859	263837274	263836708	0.000000e+00	649
3	TraesCS2B01G044200	chr2B	92.557	309	22	1	2791	3099	685998029	685998336	2.840000e-120	442
4	TraesCS2B01G044200	chr2B	78.531	531	74	22	2348	2851	686036920	686037437	2.320000e-81	313
5	TraesCS2B01G044200	chr1B	97.879	1980	34	6	881	2858	175412843	175410870	0.000000e+00	3417
6	TraesCS2B01G044200	chr1B	97.935	581	11	1	1	581	599253763	599254342	0.000000e+00	1005
7	TraesCS2B01G044200	chr1B	96.894	322	5	1	573	894	175413455	175413139	4.550000e-148	534
8	TraesCS2B01G044200	chr1B	98.800	250	3	0	2851	3100	22283594	22283843	2.190000e-121	446
9	TraesCS2B01G044200	chr1B	98.800	250	3	0	2851	3100	281628110	281628359	2.190000e-121	446
10	TraesCS2B01G044200	chr4A	96.832	1894	34	4	981	2851	744006508	744008398	0.000000e+00	3142
11	TraesCS2B01G044200	chr4A	97.579	413	10	0	573	985	744005751	744006163	0.000000e+00	708
12	TraesCS2B01G044200	chr2A	86.532	1433	145	28	573	1986	198309479	198310882	0.000000e+00	1533
13	TraesCS2B01G044200	chr2A	85.146	1131	86	42	1232	2321	19350103	19349014	0.000000e+00	1083
14	TraesCS2B01G044200	chr2A	89.636	550	39	8	2322	2853	19348981	19348432	0.000000e+00	684
15	TraesCS2B01G044200	chr2A	88.754	329	23	7	2539	2856	198321522	198321847	1.040000e-104	390
16	TraesCS2B01G044200	chr2A	88.554	166	11	6	573	738	192724559	192724716	8.770000e-46	195
17	TraesCS2B01G044200	chr2A	93.162	117	5	3	573	687	597863770	597863655	5.320000e-38	169
18	TraesCS2B01G044200	chr5A	89.083	971	76	9	571	1517	644351373	644352337	0.000000e+00	1179
19	TraesCS2B01G044200	chr5A	85.484	310	32	9	1513	1811	644352416	644352723	8.350000e-81	311
20	TraesCS2B01G044200	chr3D	86.099	1115	89	31	1239	2319	568093126	568092044	0.000000e+00	1140
21	TraesCS2B01G044200	chr3D	87.686	471	51	7	786	1254	568093626	568093161	2.720000e-150	542
22	TraesCS2B01G044200	chr3D	93.452	168	7	1	2322	2485	568092009	568091842	2.390000e-61	246
23	TraesCS2B01G044200	chr3B	85.124	1089	92	33	1267	2321	822576306	822575254	0.000000e+00	1050
24	TraesCS2B01G044200	chr3B	86.189	572	40	13	2322	2854	822575221	822574650	1.600000e-162	582
25	TraesCS2B01G044200	chr7B	98.107	581	10	1	1	581	651219298	651218719	0.000000e+00	1011
26	TraesCS2B01G044200	chr7B	97.935	581	11	1	1	581	439510921	439510342	0.000000e+00	1005
27	TraesCS2B01G044200	chr7B	98.800	250	3	0	2851	3100	371663502	371663253	2.190000e-121	446
28	TraesCS2B01G044200	chr7B	98.800	250	3	0	2851	3100	410839235	410838986	2.190000e-121	446
29	TraesCS2B01G044200	chr7B	78.996	538	66	19	2348	2854	702682540	702682019	1.070000e-84	324
30	TraesCS2B01G044200	chr6B	97.935	581	11	1	1	581	444731601	444732180	0.000000e+00	1005
31	TraesCS2B01G044200	chr6B	97.935	581	11	1	1	581	448010900	448010321	0.000000e+00	1005
32	TraesCS2B01G044200	chr6B	97.935	581	10	2	1	581	637910777	637911355	0.000000e+00	1005
33	TraesCS2B01G044200	chr4B	97.935	581	11	1	1	581	372881945	372882524	0.000000e+00	1005
34	TraesCS2B01G044200	chr4B	97.935	581	11	1	1	581	395950492	395951071	0.000000e+00	1005
35	TraesCS2B01G044200	chr4B	98.800	250	3	0	2851	3100	610538730	610538481	2.190000e-121	446
36	TraesCS2B01G044200	chr5D	92.857	658	43	2	1	657	103192562	103193216	0.000000e+00	952
37	TraesCS2B01G044200	chr4D	87.903	744	46	22	1420	2133	375153262	375153991	0.000000e+00	835
38	TraesCS2B01G044200	chr4D	82.902	579	72	14	2530	3099	96643076	96643636	2.150000e-136	496
39	TraesCS2B01G044200	chr4D	81.108	704	49	24	2203	2851	375154615	375155289	1.290000e-133	486
40	TraesCS2B01G044200	chr4D	76.190	504	69	32	1325	1825	347234340	347234795	5.200000e-53	219
41	TraesCS2B01G044200	chrUn	88.613	483	48	6	573	1055	158111410	158111885	5.760000e-162	580
42	TraesCS2B01G044200	chrUn	88.041	393	40	6	664	1055	158164736	158165122	2.820000e-125	459
43	TraesCS2B01G044200	chrUn	87.724	391	42	5	664	1054	464491428	464491044	4.710000e-123	451
44	TraesCS2B01G044200	chrUn	87.500	392	43	5	664	1055	181892161	181891776	6.100000e-122	448
45	TraesCS2B01G044200	chr3A	85.765	562	44	12	2322	2851	65821032	65821589	2.090000e-156	562
46	TraesCS2B01G044200	chr3A	86.842	380	32	11	1949	2321	65820631	65820999	2.880000e-110	409
47	TraesCS2B01G044200	chr5B	98.800	250	3	0	2851	3100	128283884	128284133	2.190000e-121	446
48	TraesCS2B01G044200	chr5B	98.800	250	3	0	2851	3100	631834362	631834611	2.190000e-121	446
49	TraesCS2B01G044200	chr7A	88.333	120	12	1	1102	1219	388726301	388726420	3.220000e-30	143

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	TraesCS2B01G044200	chr2B	21661548	21664647	3099	False	5725.000000	5725	100.0000	1	3100	1	chr2B.!!$F1	3099
1	TraesCS2B01G044200	chr2B	263836708	263839038	2330	True	1232.500000	1816	87.0135	569	2859	2	chr2B.!!$R1	2290
2	TraesCS2B01G044200	chr2B	686036920	686037437	517	False	313.000000	313	78.5310	2348	2851	1	chr2B.!!$F3	503
3	TraesCS2B01G044200	chr1B	175410870	175413455	2585	True	1975.500000	3417	97.3865	573	2858	2	chr1B.!!$R1	2285
4	TraesCS2B01G044200	chr1B	599253763	599254342	579	False	1005.000000	1005	97.9350	1	581	1	chr1B.!!$F3	580
5	TraesCS2B01G044200	chr4A	744005751	744008398	2647	False	1925.000000	3142	97.2055	573	2851	2	chr4A.!!$F1	2278
6	TraesCS2B01G044200	chr2A	198309479	198310882	1403	False	1533.000000	1533	86.5320	573	1986	1	chr2A.!!$F2	1413
7	TraesCS2B01G044200	chr2A	19348432	19350103	1671	True	883.500000	1083	87.3910	1232	2853	2	chr2A.!!$R2	1621
8	TraesCS2B01G044200	chr5A	644351373	644352723	1350	False	745.000000	1179	87.2835	571	1811	2	chr5A.!!$F1	1240
9	TraesCS2B01G044200	chr3D	568091842	568093626	1784	True	642.666667	1140	89.0790	786	2485	3	chr3D.!!$R1	1699
10	TraesCS2B01G044200	chr3B	822574650	822576306	1656	True	816.000000	1050	85.6565	1267	2854	2	chr3B.!!$R1	1587
11	TraesCS2B01G044200	chr7B	651218719	651219298	579	True	1011.000000	1011	98.1070	1	581	1	chr7B.!!$R4	580
12	TraesCS2B01G044200	chr7B	439510342	439510921	579	True	1005.000000	1005	97.9350	1	581	1	chr7B.!!$R3	580
13	TraesCS2B01G044200	chr7B	702682019	702682540	521	True	324.000000	324	78.9960	2348	2854	1	chr7B.!!$R5	506
14	TraesCS2B01G044200	chr6B	444731601	444732180	579	False	1005.000000	1005	97.9350	1	581	1	chr6B.!!$F1	580
15	TraesCS2B01G044200	chr6B	448010321	448010900	579	True	1005.000000	1005	97.9350	1	581	1	chr6B.!!$R1	580
16	TraesCS2B01G044200	chr6B	637910777	637911355	578	False	1005.000000	1005	97.9350	1	581	1	chr6B.!!$F2	580
17	TraesCS2B01G044200	chr4B	372881945	372882524	579	False	1005.000000	1005	97.9350	1	581	1	chr4B.!!$F1	580
18	TraesCS2B01G044200	chr4B	395950492	395951071	579	False	1005.000000	1005	97.9350	1	581	1	chr4B.!!$F2	580
19	TraesCS2B01G044200	chr5D	103192562	103193216	654	False	952.000000	952	92.8570	1	657	1	chr5D.!!$F1	656
20	TraesCS2B01G044200	chr4D	375153262	375155289	2027	False	660.500000	835	84.5055	1420	2851	2	chr4D.!!$F3	1431
21	TraesCS2B01G044200	chr4D	96643076	96643636	560	False	496.000000	496	82.9020	2530	3099	1	chr4D.!!$F1	569
22	TraesCS2B01G044200	chr3A	65820631	65821589	958	False	485.500000	562	86.3035	1949	2851	2	chr3A.!!$F1	902

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
108	110	0.250295	CTGGACACTGGAAGCGGAAA	60.250	55.0	0.0	0.0	37.6	3.13	F
1147	1817	0.905337	CGTGTTCTTCCTCCCTCCCT	60.905	60.0	0.0	0.0	0.0	4.20	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1489	2237	0.254178	TGAATGCTCCTCCTTGCTCC	59.746	55.0	0.00	0.0	0.0	4.70	R
2931	4526	0.179137	TCTTCATGCGCTCTACACCG	60.179	55.0	9.73	0.0	0.0	4.94	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
108	110	0.250295	CTGGACACTGGAAGCGGAAA	60.250	55.000	0.00	0.00	37.60	3.13
155	157	3.565307	AGGATGGCAAAGTGAACAAAGA	58.435	40.909	0.00	0.00	0.00	2.52
258	260	8.830201	TTGCTAATATTTGCAACTCAAAACAT	57.170	26.923	26.46	0.00	46.60	2.71
536	538	1.699083	TCATGCACCCTTGAAGAGTGA	59.301	47.619	11.20	0.00	33.21	3.41
691	693	5.096169	CACGTCACTTCATCTCTTCGTTAT	58.904	41.667	0.00	0.00	0.00	1.89
692	694	5.573282	CACGTCACTTCATCTCTTCGTTATT	59.427	40.000	0.00	0.00	0.00	1.40
693	695	6.089551	CACGTCACTTCATCTCTTCGTTATTT	59.910	38.462	0.00	0.00	0.00	1.40
1147	1817	0.905337	CGTGTTCTTCCTCCCTCCCT	60.905	60.000	0.00	0.00	0.00	4.20
1282	2019	1.073025	GGATGGTGTGTGTGCTCCA	59.927	57.895	0.00	0.00	36.60	3.86
1404	2143	2.649034	GCGTCGTCTCCAAGTCCA	59.351	61.111	0.00	0.00	0.00	4.02
1436	2177	7.039714	TGCTGATAGTTCTTCTTCTGTCTGTTA	60.040	37.037	0.00	0.00	0.00	2.41
1489	2237	4.056740	GCCATCAGTCATCACTACAGATG	58.943	47.826	0.00	0.00	45.28	2.90
1491	2239	5.526506	CATCAGTCATCACTACAGATGGA	57.473	43.478	4.33	0.00	44.30	3.41
1492	2240	5.530712	CATCAGTCATCACTACAGATGGAG	58.469	45.833	4.33	0.00	44.30	3.86
1493	2241	3.382865	TCAGTCATCACTACAGATGGAGC	59.617	47.826	4.33	0.00	44.30	4.70
1494	2242	3.131755	CAGTCATCACTACAGATGGAGCA	59.868	47.826	4.33	0.00	44.30	4.26
1495	2243	3.771479	AGTCATCACTACAGATGGAGCAA	59.229	43.478	4.33	0.00	44.30	3.91
1496	2244	4.118410	GTCATCACTACAGATGGAGCAAG	58.882	47.826	4.33	0.00	44.30	4.01
1497	2245	3.133542	TCATCACTACAGATGGAGCAAGG	59.866	47.826	4.33	0.00	44.30	3.61
1498	2246	2.820178	TCACTACAGATGGAGCAAGGA	58.180	47.619	0.00	0.00	0.00	3.36
1638	2512	5.906113	TGCTGGTTTCTTCAAACTGTTTA	57.094	34.783	5.31	0.00	41.61	2.01
1735	2609	1.229400	ACCGCCCCTGAGGTCTTTA	60.229	57.895	0.00	0.00	41.26	1.85
1935	2817	2.703416	TCCTTGCAGCAGTAATGAGTG	58.297	47.619	0.00	0.00	0.00	3.51
2069	3022	4.232091	TCCTTCTCCTCTGTTTGTAGGTT	58.768	43.478	0.00	0.00	34.30	3.50
2825	4420	4.398044	CCAACTGTAGGCAATATTTTCCGT	59.602	41.667	0.00	0.00	0.00	4.69
2860	4455	7.682261	GCGGGGTATCATCTAGTATTCATAGTG	60.682	44.444	0.00	0.00	0.00	2.74
2879	4474	4.685924	AGTGTTGAAACCAAAAGATGCAG	58.314	39.130	0.00	0.00	0.00	4.41
2880	4475	4.402155	AGTGTTGAAACCAAAAGATGCAGA	59.598	37.500	0.00	0.00	0.00	4.26
2901	4496	7.283807	TGCAGAGTTGATAATGATATTGCAACT	59.716	33.333	0.00	16.96	45.87	3.16
2917	4512	3.181333	GCAACTTATTTGTGGCACTGCC	61.181	50.000	19.83	13.68	41.61	4.85
2931	4526	2.544267	GCACTGCCGTTTAGGTCATATC	59.456	50.000	0.00	0.00	43.70	1.63
2938	4533	4.543692	CCGTTTAGGTCATATCGGTGTAG	58.456	47.826	0.00	0.00	34.38	2.74
2940	4535	5.450171	CGTTTAGGTCATATCGGTGTAGAG	58.550	45.833	0.00	0.00	0.00	2.43
2959	4554	3.118629	AGAGCGCATGAAGAAACTCCATA	60.119	43.478	11.47	0.00	0.00	2.74
2961	4556	2.939103	GCGCATGAAGAAACTCCATACT	59.061	45.455	0.30	0.00	0.00	2.12
2983	4578	3.258872	TGATGGGCTTTTGGAATCACTTG	59.741	43.478	0.00	0.00	0.00	3.16
2995	4590	9.859427	TTTTGGAATCACTTGATTATGAATCAC	57.141	29.630	4.42	0.00	46.90	3.06
2999	4594	8.133627	GGAATCACTTGATTATGAATCACTTGG	58.866	37.037	4.42	0.00	46.90	3.61
3007	4602	6.883756	TGATTATGAATCACTTGGTACTTGCA	59.116	34.615	0.00	0.00	42.69	4.08
3012	4607	1.944024	TCACTTGGTACTTGCAAACCG	59.056	47.619	14.17	5.09	38.70	4.44
3023	4618	3.277133	CAAACCGTGCCTCATGGG	58.723	61.111	9.59	0.00	44.23	4.00
3035	4630	3.565764	CCTCATGGGCAAGATGACTAA	57.434	47.619	0.00	0.00	0.00	2.24
3039	4634	3.689161	TCATGGGCAAGATGACTAAAACG	59.311	43.478	0.00	0.00	0.00	3.60
3040	4635	1.810151	TGGGCAAGATGACTAAAACGC	59.190	47.619	0.00	0.00	0.00	4.84
3066	4661	1.437573	CGGAACTATGGAGCGAGCA	59.562	57.895	0.00	0.00	0.00	4.26
3068	4663	1.291132	GGAACTATGGAGCGAGCAAC	58.709	55.000	0.00	0.00	0.00	4.17
3072	4667	1.759445	ACTATGGAGCGAGCAACTGAT	59.241	47.619	0.00	0.00	0.00	2.90
3075	4670	1.159285	TGGAGCGAGCAACTGATTTG	58.841	50.000	0.00	0.00	38.37	2.32
3084	4679	4.618489	CGAGCAACTGATTTGTTGGAAATC	59.382	41.667	9.04	0.00	45.19	2.17
3099	4694	8.806429	TGTTGGAAATCATACATACTGATGTT	57.194	30.769	0.00	0.00	44.18	2.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
258	260	3.018856	TCTTCGCTTAATCCGTAGTCCA	58.981	45.455	3.50	0.00	0.00	4.02
1147	1817	2.126463	CGCCGCAAGTCTCGAGAA	60.126	61.111	18.55	0.00	0.00	2.87
1306	2043	3.927142	CACCTAGGTCTGATTTGTTCGTC	59.073	47.826	12.84	0.00	0.00	4.20
1404	2143	6.822676	CAGAAGAAGAACTATCAGCAGGAAAT	59.177	38.462	0.00	0.00	0.00	2.17
1436	2177	3.157750	AGGGACGAACTAACTGAGACT	57.842	47.619	0.00	0.00	0.00	3.24
1489	2237	0.254178	TGAATGCTCCTCCTTGCTCC	59.746	55.000	0.00	0.00	0.00	4.70
1490	2238	1.666054	CTGAATGCTCCTCCTTGCTC	58.334	55.000	0.00	0.00	0.00	4.26
1491	2239	0.394080	GCTGAATGCTCCTCCTTGCT	60.394	55.000	0.00	0.00	38.95	3.91
1492	2240	2.105124	GCTGAATGCTCCTCCTTGC	58.895	57.895	0.00	0.00	38.95	4.01
1616	2490	4.799564	AAACAGTTTGAAGAAACCAGCA	57.200	36.364	0.00	0.00	42.25	4.41
1638	2512	4.346730	TCCATTCTGACAATTCCTGCAAT	58.653	39.130	0.00	0.00	0.00	3.56
1735	2609	1.618837	TCTGCAGAACTTAAGCTCGGT	59.381	47.619	15.67	0.00	0.00	4.69
2825	4420	3.778360	GATACCCCGCGCGTTGCTA	62.778	63.158	29.95	12.31	43.27	3.49
2860	4455	4.936891	ACTCTGCATCTTTTGGTTTCAAC	58.063	39.130	0.00	0.00	31.78	3.18
2865	4460	6.899393	TTATCAACTCTGCATCTTTTGGTT	57.101	33.333	0.00	0.00	0.00	3.67
2866	4461	6.660521	TCATTATCAACTCTGCATCTTTTGGT	59.339	34.615	0.00	0.00	0.00	3.67
2894	4489	3.715495	CAGTGCCACAAATAAGTTGCAA	58.285	40.909	0.00	0.00	41.11	4.08
2917	4512	5.428496	TCTACACCGATATGACCTAAACG	57.572	43.478	0.00	0.00	0.00	3.60
2931	4526	0.179137	TCTTCATGCGCTCTACACCG	60.179	55.000	9.73	0.00	0.00	4.94
2938	4533	1.442769	TGGAGTTTCTTCATGCGCTC	58.557	50.000	9.73	0.00	0.00	5.03
2940	4535	2.939103	AGTATGGAGTTTCTTCATGCGC	59.061	45.455	0.00	0.00	37.20	6.09
2959	4554	2.827921	GTGATTCCAAAAGCCCATCAGT	59.172	45.455	0.00	0.00	0.00	3.41
2961	4556	3.173953	AGTGATTCCAAAAGCCCATCA	57.826	42.857	0.00	0.00	0.00	3.07
2967	4562	8.937634	ATTCATAATCAAGTGATTCCAAAAGC	57.062	30.769	9.76	0.00	43.17	3.51
2983	4578	7.320443	TGCAAGTACCAAGTGATTCATAATC	57.680	36.000	0.00	0.00	38.40	1.75
2995	4590	2.399396	CACGGTTTGCAAGTACCAAG	57.601	50.000	18.18	7.60	33.94	3.61
3023	4618	1.463444	ACGGCGTTTTAGTCATCTTGC	59.537	47.619	6.77	0.00	0.00	4.01
3054	4649	2.938451	CAAATCAGTTGCTCGCTCCATA	59.062	45.455	0.00	0.00	0.00	2.74
3058	4653	2.578495	CAACAAATCAGTTGCTCGCTC	58.422	47.619	0.00	0.00	41.95	5.03
3068	4663	9.726232	CAGTATGTATGATTTCCAACAAATCAG	57.274	33.333	13.59	0.00	46.12	2.90
3072	4667	9.241919	ACATCAGTATGTATGATTTCCAACAAA	57.758	29.630	0.00	0.00	44.66	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.