AutoCloner

Multiple sequence alignment - TraesCS3B01G138700

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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	TraesCS3B01G138700	chr3B	100.000	3653	0	0	1	3653	124769161	124765509	0.000000e+00	6746.0
1	TraesCS3B01G138700	chr5B	97.596	1955	36	8	1	1950	706039678	706041626	0.000000e+00	3339.0
2	TraesCS3B01G138700	chr5B	92.841	866	41	11	1099	1950	116307206	116306348	0.000000e+00	1236.0
3	TraesCS3B01G138700	chr5B	84.375	544	21	17	2220	2751	479044765	479045256	3.300000e-130	475.0
4	TraesCS3B01G138700	chr5B	97.551	245	4	2	2448	2691	706041775	706042018	5.640000e-113	418.0
5	TraesCS3B01G138700	chr2A	97.544	1954	33	6	1	1950	492833362	492835304	0.000000e+00	3328.0
6	TraesCS3B01G138700	chr2A	98.259	632	9	2	1950	2579	492835221	492835852	0.000000e+00	1105.0
7	TraesCS3B01G138700	chr2A	91.057	246	11	2	2362	2596	43446651	43446896	4.550000e-84	322.0
8	TraesCS3B01G138700	chr4A	99.481	1733	9	0	1	1733	90386985	90385253	0.000000e+00	3151.0
9	TraesCS3B01G138700	chr4A	99.611	1029	4	0	1716	2744	90385180	90384152	0.000000e+00	1879.0
10	TraesCS3B01G138700	chr4B	93.421	1976	97	12	1	1950	221191468	221193436	0.000000e+00	2898.0
11	TraesCS3B01G138700	chr4B	95.988	1695	55	6	260	1950	361733687	361732002	0.000000e+00	2741.0
12	TraesCS3B01G138700	chr4B	95.712	1586	48	11	200	1781	243183352	243181783	0.000000e+00	2534.0
13	TraesCS3B01G138700	chr4B	97.577	743	13	5	1950	2691	361732084	361731346	0.000000e+00	1267.0
14	TraesCS3B01G138700	chr4B	97.047	745	18	4	1948	2691	243181735	243180994	0.000000e+00	1251.0
15	TraesCS3B01G138700	chr4B	89.907	535	18	13	2231	2753	649148859	649148349	0.000000e+00	656.0
16	TraesCS3B01G138700	chr4B	91.441	444	37	1	106	548	564156298	564156741	3.120000e-170	608.0
17	TraesCS3B01G138700	chr1B	92.595	1634	82	14	356	1950	91886723	91885090	0.000000e+00	2311.0
18	TraesCS3B01G138700	chr1B	95.890	365	15	0	1	365	91887497	91887133	3.140000e-165	592.0
19	TraesCS3B01G138700	chr1B	91.463	246	10	2	2362	2596	95323480	95323725	9.780000e-86	327.0
20	TraesCS3B01G138700	chr5D	94.674	1427	55	7	545	1950	61458853	61460279	0.000000e+00	2194.0
21	TraesCS3B01G138700	chr5D	94.048	756	32	4	1948	2691	61460194	61460948	0.000000e+00	1134.0
22	TraesCS3B01G138700	chr6D	94.452	1424	59	9	545	1950	352345989	352347410	0.000000e+00	2174.0
23	TraesCS3B01G138700	chr6D	94.220	1436	53	12	545	1950	59751320	59749885	0.000000e+00	2165.0
24	TraesCS3B01G138700	chr6D	93.939	1221	47	4	757	1950	173910678	173911898	0.000000e+00	1820.0
25	TraesCS3B01G138700	chr6D	94.577	756	29	4	1948	2691	263996692	263995937	0.000000e+00	1158.0
26	TraesCS3B01G138700	chr6D	94.320	757	29	5	1948	2691	59749970	59749215	0.000000e+00	1147.0
27	TraesCS3B01G138700	chr2D	94.577	756	27	6	1948	2691	540175103	540175856	0.000000e+00	1157.0
28	TraesCS3B01G138700	chr2D	91.781	73	5	1	2683	2754	412049703	412049775	2.320000e-17	100.0
29	TraesCS3B01G138700	chr7D	94.320	757	29	6	1948	2691	535314392	535313637	0.000000e+00	1147.0
30	TraesCS3B01G138700	chr7D	94.071	759	30	5	1948	2691	46097755	46096997	0.000000e+00	1138.0
31	TraesCS3B01G138700	chr3D	91.805	781	54	7	2880	3653	78518724	78517947	0.000000e+00	1079.0
32	TraesCS3B01G138700	chr3D	92.342	444	33	1	106	548	562561498	562561941	6.660000e-177	630.0
33	TraesCS3B01G138700	chr3D	91.800	439	30	2	2880	3312	79198033	79197595	1.120000e-169	606.0
34	TraesCS3B01G138700	chr3D	92.658	395	28	1	106	500	266653281	266653674	5.290000e-158	568.0
35	TraesCS3B01G138700	chr3D	91.707	205	16	1	3309	3513	79191550	79191347	2.150000e-72	283.0
36	TraesCS3B01G138700	chr3D	90.714	140	12	1	2751	2889	79198658	79198519	6.230000e-43	185.0
37	TraesCS3B01G138700	chr3D	90.265	113	9	2	1	112	9444263	9444152	2.940000e-31	147.0
38	TraesCS3B01G138700	chr3D	98.182	55	1	0	3566	3620	79191350	79191296	3.000000e-16	97.1
39	TraesCS3B01G138700	chr3D	88.608	79	9	0	2673	2751	606632048	606632126	3.000000e-16	97.1
40	TraesCS3B01G138700	chr7B	91.968	498	23	7	2207	2691	102757859	102757366	0.000000e+00	682.0
41	TraesCS3B01G138700	chr7B	87.952	83	9	1	2664	2745	468952577	468952495	3.000000e-16	97.1
42	TraesCS3B01G138700	chr6B	91.952	497	24	7	2207	2691	623359768	623359276	0.000000e+00	682.0
43	TraesCS3B01G138700	chr5A	91.770	243	9	2	2365	2596	119055903	119055661	9.780000e-86	327.0

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	TraesCS3B01G138700	chr3B	124765509	124769161	3652	True	6746.0	6746	100.0000	1	3653	1	chr3B.!!$R1	3652
1	TraesCS3B01G138700	chr5B	706039678	706042018	2340	False	1878.5	3339	97.5735	1	2691	2	chr5B.!!$F2	2690
2	TraesCS3B01G138700	chr5B	116306348	116307206	858	True	1236.0	1236	92.8410	1099	1950	1	chr5B.!!$R1	851
3	TraesCS3B01G138700	chr2A	492833362	492835852	2490	False	2216.5	3328	97.9015	1	2579	2	chr2A.!!$F2	2578
4	TraesCS3B01G138700	chr4A	90384152	90386985	2833	True	2515.0	3151	99.5460	1	2744	2	chr4A.!!$R1	2743
5	TraesCS3B01G138700	chr4B	221191468	221193436	1968	False	2898.0	2898	93.4210	1	1950	1	chr4B.!!$F1	1949
6	TraesCS3B01G138700	chr4B	361731346	361733687	2341	True	2004.0	2741	96.7825	260	2691	2	chr4B.!!$R3	2431
7	TraesCS3B01G138700	chr4B	243180994	243183352	2358	True	1892.5	2534	96.3795	200	2691	2	chr4B.!!$R2	2491
8	TraesCS3B01G138700	chr4B	649148349	649148859	510	True	656.0	656	89.9070	2231	2753	1	chr4B.!!$R1	522
9	TraesCS3B01G138700	chr1B	91885090	91887497	2407	True	1451.5	2311	94.2425	1	1950	2	chr1B.!!$R1	1949
10	TraesCS3B01G138700	chr5D	61458853	61460948	2095	False	1664.0	2194	94.3610	545	2691	2	chr5D.!!$F1	2146
11	TraesCS3B01G138700	chr6D	352345989	352347410	1421	False	2174.0	2174	94.4520	545	1950	1	chr6D.!!$F2	1405
12	TraesCS3B01G138700	chr6D	173910678	173911898	1220	False	1820.0	1820	93.9390	757	1950	1	chr6D.!!$F1	1193
13	TraesCS3B01G138700	chr6D	59749215	59751320	2105	True	1656.0	2165	94.2700	545	2691	2	chr6D.!!$R2	2146
14	TraesCS3B01G138700	chr6D	263995937	263996692	755	True	1158.0	1158	94.5770	1948	2691	1	chr6D.!!$R1	743
15	TraesCS3B01G138700	chr2D	540175103	540175856	753	False	1157.0	1157	94.5770	1948	2691	1	chr2D.!!$F2	743
16	TraesCS3B01G138700	chr7D	535313637	535314392	755	True	1147.0	1147	94.3200	1948	2691	1	chr7D.!!$R2	743
17	TraesCS3B01G138700	chr7D	46096997	46097755	758	True	1138.0	1138	94.0710	1948	2691	1	chr7D.!!$R1	743
18	TraesCS3B01G138700	chr3D	78517947	78518724	777	True	1079.0	1079	91.8050	2880	3653	1	chr3D.!!$R2	773
19	TraesCS3B01G138700	chr3D	79197595	79198658	1063	True	395.5	606	91.2570	2751	3312	2	chr3D.!!$R4	561

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
551	973	2.401766	CCTGTTGGCCGAGTGATGC	61.402	63.158	0.00	0.0	0.00	3.91	F
1828	2406	4.437930	GCTAGCTGCAGTTATTTCAGGTTG	60.438	45.833	16.64	0.0	42.31	3.77	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1357	1834	2.166459	CACATACGTCAGACCAGGACAT	59.834	50.0	0.0	0.0	34.97	3.06	R
2748	3347	0.037734	CCTTAGGGGCACGTCCTTTT	59.962	55.0	0.0	0.0	35.92	2.27	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
551	973	2.401766	CCTGTTGGCCGAGTGATGC	61.402	63.158	0.00	0.00	0.00	3.91
1828	2406	4.437930	GCTAGCTGCAGTTATTTCAGGTTG	60.438	45.833	16.64	0.00	42.31	3.77
2744	3343	1.340248	CGCAACCGGGTCATCTAGTAT	59.660	52.381	6.32	0.00	0.00	2.12
2745	3344	2.555325	CGCAACCGGGTCATCTAGTATA	59.445	50.000	6.32	0.00	0.00	1.47
2746	3345	3.366070	CGCAACCGGGTCATCTAGTATAG	60.366	52.174	6.32	0.00	41.04	1.31
2747	3346	3.573110	GCAACCGGGTCATCTAGTATAGT	59.427	47.826	6.32	0.00	40.38	2.12
2748	3347	4.763793	GCAACCGGGTCATCTAGTATAGTA	59.236	45.833	6.32	0.00	40.38	1.82
2749	3348	5.242393	GCAACCGGGTCATCTAGTATAGTAA	59.758	44.000	6.32	0.00	40.38	2.24
2764	3363	1.648116	AGTAAAAGGACGTGCCCCTA	58.352	50.000	2.38	0.00	37.37	3.53
2769	3368	1.131928	AAGGACGTGCCCCTAAGGTT	61.132	55.000	2.38	0.00	38.26	3.50
2785	3384	2.789409	GGTTCTGACCAAGCATAGGT	57.211	50.000	0.00	0.00	45.77	3.08
2794	3393	4.862641	ACCAAGCATAGGTGGTAGAAAT	57.137	40.909	0.00	0.00	46.47	2.17
2795	3394	5.968676	ACCAAGCATAGGTGGTAGAAATA	57.031	39.130	0.00	0.00	46.47	1.40
2800	3399	7.721399	CCAAGCATAGGTGGTAGAAATAGAAAT	59.279	37.037	0.00	0.00	34.36	2.17
2822	3421	7.707624	AATCCTTTGCACTGATGAGAAATTA	57.292	32.000	0.00	0.00	0.00	1.40
2823	3422	7.707624	ATCCTTTGCACTGATGAGAAATTAA	57.292	32.000	0.00	0.00	0.00	1.40
2827	3426	6.899393	TTGCACTGATGAGAAATTAAAGGT	57.101	33.333	0.00	0.00	0.00	3.50
2840	3439	7.312899	AGAAATTAAAGGTGGCTACAAAATCG	58.687	34.615	1.52	0.00	0.00	3.34
2850	3449	2.708514	CTACAAAATCGCAATCGCCTG	58.291	47.619	0.00	0.00	35.26	4.85
2902	3997	4.997395	TCTGTACTGCATTGAGGAGAAAAC	59.003	41.667	0.00	0.00	38.04	2.43
2995	4095	8.925161	TTTTCTCCACTTTTTCTTACAATGTG	57.075	30.769	0.00	0.00	0.00	3.21
3086	4186	4.657436	ACACCTAAGATTCATCGACTCC	57.343	45.455	0.00	0.00	0.00	3.85
3093	4193	1.268352	GATTCATCGACTCCCTCTCCG	59.732	57.143	0.00	0.00	0.00	4.63
3103	4203	4.277672	CGACTCCCTCTCCGTCAAAATATA	59.722	45.833	0.00	0.00	0.00	0.86
3209	4309	9.956720	AGCATTTGAAACTTCATATAAGTATGC	57.043	29.630	11.76	11.76	38.05	3.14
3284	4385	7.161773	AGGTTCACAATTTGATGAGGTATTG	57.838	36.000	2.79	0.00	32.84	1.90
3338	4439	9.877178	ATTTAGTGTTATAGAACCTCACTTGAG	57.123	33.333	0.00	0.00	39.54	3.02
3346	4447	9.582431	TTATAGAACCTCACTTGAGTTTTATCG	57.418	33.333	5.53	0.00	40.48	2.92
3358	4459	9.408069	ACTTGAGTTTTATCGTAAGTACTTCAG	57.592	33.333	12.39	7.62	39.48	3.02
3362	4463	6.525976	AGTTTTATCGTAAGTACTTCAGCGAC	59.474	38.462	22.92	11.91	39.48	5.19
3370	4471	4.017380	AGTACTTCAGCGACTTGTATCG	57.983	45.455	0.00	0.00	45.09	2.92
3385	4486	4.664150	TGTATCGTTCTATGATGTGGCA	57.336	40.909	0.00	0.00	0.00	4.92
3513	4614	9.830975	ATTAAACATATGGCCTTTTAACCATTC	57.169	29.630	3.32	0.00	44.37	2.67
3576	4677	9.382275	GCCAATATTTCTGGACATTTTTATTGT	57.618	29.630	0.00	0.00	35.85	2.71
3585	4686	6.913170	TGGACATTTTTATTGTCAGAGCTTC	58.087	36.000	6.20	0.00	44.22	3.86
3617	4718	6.162777	TGGAAGGAAACAAAGAACAAGTTTG	58.837	36.000	0.00	0.00	40.18	2.93
3621	4722	8.757164	AAGGAAACAAAGAACAAGTTTGTAAG	57.243	30.769	1.86	0.00	45.30	2.34
3626	4727	4.529716	AAGAACAAGTTTGTAAGGGGGA	57.470	40.909	0.00	0.00	41.31	4.81
3644	4745	4.470602	GGGGATCCCTTAAAATCATCGTT	58.529	43.478	30.08	0.00	41.34	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
489	911	4.604976	GCTAATGCCAATGATGTCTGTTC	58.395	43.478	0.00	0.00	0.00	3.18
551	973	7.281774	ACAATAAGCATCTTCACAATAGGACTG	59.718	37.037	0.00	0.00	0.00	3.51
1357	1834	2.166459	CACATACGTCAGACCAGGACAT	59.834	50.000	0.00	0.00	34.97	3.06
1828	2406	3.505680	TCACACCAAGGATTTGCACATAC	59.494	43.478	0.00	0.00	32.79	2.39
2744	3343	1.648116	AGGGGCACGTCCTTTTACTA	58.352	50.000	0.00	0.00	34.39	1.82
2745	3344	1.648116	TAGGGGCACGTCCTTTTACT	58.352	50.000	0.00	0.00	35.92	2.24
2746	3345	2.353323	CTTAGGGGCACGTCCTTTTAC	58.647	52.381	0.00	0.00	35.92	2.01
2747	3346	1.279846	CCTTAGGGGCACGTCCTTTTA	59.720	52.381	0.00	0.00	35.92	1.52
2748	3347	0.037734	CCTTAGGGGCACGTCCTTTT	59.962	55.000	0.00	0.00	35.92	2.27
2749	3348	1.131928	ACCTTAGGGGCACGTCCTTT	61.132	55.000	2.32	0.00	39.10	3.11
2764	3363	2.644798	ACCTATGCTTGGTCAGAACCTT	59.355	45.455	0.00	0.00	46.60	3.50
2769	3368	1.656587	ACCACCTATGCTTGGTCAGA	58.343	50.000	0.00	0.00	42.86	3.27
2785	3384	7.121168	CAGTGCAAAGGATTTCTATTTCTACCA	59.879	37.037	0.00	0.00	35.03	3.25
2794	3393	6.053632	TCTCATCAGTGCAAAGGATTTCTA	57.946	37.500	0.00	0.00	35.03	2.10
2795	3394	4.914983	TCTCATCAGTGCAAAGGATTTCT	58.085	39.130	0.00	0.00	35.03	2.52
2800	3399	7.309377	CCTTTAATTTCTCATCAGTGCAAAGGA	60.309	37.037	0.00	0.00	40.32	3.36
2822	3421	2.235016	TGCGATTTTGTAGCCACCTTT	58.765	42.857	0.00	0.00	0.00	3.11
2823	3422	1.904287	TGCGATTTTGTAGCCACCTT	58.096	45.000	0.00	0.00	0.00	3.50
2827	3426	1.202132	GCGATTGCGATTTTGTAGCCA	60.202	47.619	0.00	0.00	40.82	4.75
2840	3439	2.423538	AGGAAACATTACAGGCGATTGC	59.576	45.455	0.00	0.00	41.71	3.56
2850	3449	6.322491	GTTAGGACAATGCAGGAAACATTAC	58.678	40.000	0.00	0.00	36.00	1.89
3022	4122	6.764308	AATCAGTTTCATGTTAGATGGGTG	57.236	37.500	0.00	0.00	0.00	4.61
3063	4163	5.244178	GGGAGTCGATGAATCTTAGGTGTAT	59.756	44.000	0.00	0.00	0.00	2.29
3081	4181	4.674281	ATATTTTGACGGAGAGGGAGTC	57.326	45.455	0.00	0.00	35.61	3.36
3086	4186	6.649557	GGGTGTTATATATTTTGACGGAGAGG	59.350	42.308	0.00	0.00	0.00	3.69
3184	4284	9.734620	TGCATACTTATATGAAGTTTCAAATGC	57.265	29.630	14.28	14.28	40.75	3.56
3254	4355	7.287696	ACCTCATCAAATTGTGAACCTAACTTT	59.712	33.333	0.00	0.00	40.50	2.66
3257	4358	6.575162	ACCTCATCAAATTGTGAACCTAAC	57.425	37.500	0.00	0.00	40.50	2.34
3284	4385	3.032265	ACCCCTTCCTTCCAAATATGC	57.968	47.619	0.00	0.00	0.00	3.14
3338	4439	6.525976	AGTCGCTGAAGTACTTACGATAAAAC	59.474	38.462	22.81	14.20	31.62	2.43
3346	4447	5.451662	CGATACAAGTCGCTGAAGTACTTAC	59.548	44.000	8.42	2.58	34.56	2.34
3358	4459	4.976731	ACATCATAGAACGATACAAGTCGC	59.023	41.667	0.00	0.00	45.12	5.19
3362	4463	5.049828	TGCCACATCATAGAACGATACAAG	58.950	41.667	0.00	0.00	0.00	3.16
3370	4471	6.595716	GGGAATATACTGCCACATCATAGAAC	59.404	42.308	0.00	0.00	0.00	3.01
3492	4593	5.598417	GGAGAATGGTTAAAAGGCCATATGT	59.402	40.000	5.01	0.00	44.03	2.29
3496	4597	4.059773	TGGAGAATGGTTAAAAGGCCAT	57.940	40.909	5.01	0.00	46.51	4.40
3497	4598	3.534357	TGGAGAATGGTTAAAAGGCCA	57.466	42.857	5.01	0.00	39.33	5.36
3498	4599	4.023291	TGATGGAGAATGGTTAAAAGGCC	58.977	43.478	0.00	0.00	0.00	5.19
3513	4614	1.742761	AATGAGCCGTGTTGATGGAG	58.257	50.000	0.00	0.00	0.00	3.86
3558	4659	6.716628	AGCTCTGACAATAAAAATGTCCAGAA	59.283	34.615	4.40	0.00	45.19	3.02
3560	4661	6.506500	AGCTCTGACAATAAAAATGTCCAG	57.493	37.500	4.40	2.31	45.19	3.86
3576	4677	3.893326	TCCAAATGATCGAAGCTCTGA	57.107	42.857	0.00	0.00	0.00	3.27
3579	4680	3.535561	TCCTTCCAAATGATCGAAGCTC	58.464	45.455	0.00	0.00	33.21	4.09
3585	4686	6.012658	TCTTTGTTTCCTTCCAAATGATCG	57.987	37.500	0.00	0.00	30.76	3.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.