AutoCloner

Multiple sequence alignment - TraesCS7D01G458700

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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	TraesCS7D01G458700	chr7D	100.000	3737	0	0	1	3737	576332292	576336028	0.000000e+00	6902.0
1	TraesCS7D01G458700	chr7D	80.808	99	10	6	521	615	385721635	385721542	6.700000e-08	69.4
2	TraesCS7D01G458700	chr7B	90.940	3764	209	60	1	3735	639082455	639086115	0.000000e+00	4940.0
3	TraesCS7D01G458700	chr7B	79.155	355	43	17	2946	3285	704093194	704092856	2.260000e-52	217.0
4	TraesCS7D01G458700	chr7B	79.091	330	39	13	3414	3737	704157531	704157226	2.280000e-47	200.0
5	TraesCS7D01G458700	chr7B	78.963	328	39	13	3416	3737	704092688	704092385	2.940000e-46	196.0
6	TraesCS7D01G458700	chr7B	81.000	100	10	7	520	615	152799676	152799582	1.860000e-08	71.3
7	TraesCS7D01G458700	chr7B	80.000	100	10	7	520	615	380081202	380081109	8.660000e-07	65.8
8	TraesCS7D01G458700	chr7A	96.371	1791	53	5	1093	2872	667475057	667476846	0.000000e+00	2937.0
9	TraesCS7D01G458700	chr7A	89.193	657	39	15	3088	3737	667477374	667478005	0.000000e+00	791.0
10	TraesCS7D01G458700	chr7A	90.680	515	37	7	608	1121	667474554	667475058	0.000000e+00	675.0
11	TraesCS7D01G458700	chr7A	86.817	622	56	15	1	616	667473743	667474344	0.000000e+00	671.0
12	TraesCS7D01G458700	chr7A	84.661	502	33	19	2871	3366	667476900	667477363	9.460000e-126	460.0
13	TraesCS7D01G458700	chr7A	79.070	301	36	18	2946	3228	705142575	705142284	8.250000e-42	182.0
14	TraesCS7D01G458700	chr7A	76.177	361	49	16	3386	3737	705142023	705141691	5.000000e-34	156.0
15	TraesCS7D01G458700	chr7A	82.353	85	6	7	508	588	79161952	79162031	8.660000e-07	65.8
16	TraesCS7D01G458700	chr3B	90.189	2171	192	13	714	2872	259370360	259372521	0.000000e+00	2809.0
17	TraesCS7D01G458700	chr3B	76.675	403	48	26	2898	3262	259372630	259373024	8.250000e-42	182.0
18	TraesCS7D01G458700	chr3B	89.412	85	7	2	262	345	259369997	259370080	5.100000e-19	106.0
19	TraesCS7D01G458700	chr3B	80.682	88	11	5	520	601	646041061	646040974	3.120000e-06	63.9
20	TraesCS7D01G458700	chr3D	90.326	2150	196	10	714	2854	181103554	181105700	0.000000e+00	2808.0
21	TraesCS7D01G458700	chr3D	87.281	456	43	5	3286	3737	181106988	181107432	1.200000e-139	507.0
22	TraesCS7D01G458700	chr3D	86.066	122	10	7	3147	3262	181106389	181106509	1.410000e-24	124.0
23	TraesCS7D01G458700	chr3A	90.065	2144	197	11	736	2866	227923658	227921518	0.000000e+00	2765.0
24	TraesCS7D01G458700	chr3A	87.915	331	28	4	3408	3737	227920011	227919692	2.720000e-101	379.0
25	TraesCS7D01G458700	chr3A	87.288	118	8	6	3151	3262	227920879	227920763	1.090000e-25	128.0
26	TraesCS7D01G458700	chr3A	93.056	72	5	0	274	345	227923977	227923906	5.100000e-19	106.0
27	TraesCS7D01G458700	chr5D	84.507	71	3	6	521	588	543873486	543873551	3.120000e-06	63.9
28	TraesCS7D01G458700	chr1B	79.000	100	13	5	520	615	668620561	668620656	1.120000e-05	62.1

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	TraesCS7D01G458700	chr7D	576332292	576336028	3736	False	6902.000000	6902	100.000000	1	3737	1	chr7D.!!$F1	3736
1	TraesCS7D01G458700	chr7B	639082455	639086115	3660	False	4940.000000	4940	90.940000	1	3735	1	chr7B.!!$F1	3734
2	TraesCS7D01G458700	chr7B	704092385	704093194	809	True	206.500000	217	79.059000	2946	3737	2	chr7B.!!$R4	791
3	TraesCS7D01G458700	chr7A	667473743	667478005	4262	False	1106.800000	2937	89.544400	1	3737	5	chr7A.!!$F2	3736
4	TraesCS7D01G458700	chr3B	259369997	259373024	3027	False	1032.333333	2809	85.425333	262	3262	3	chr3B.!!$F1	3000
5	TraesCS7D01G458700	chr3D	181103554	181107432	3878	False	1146.333333	2808	87.891000	714	3737	3	chr3D.!!$F1	3023
6	TraesCS7D01G458700	chr3A	227919692	227923977	4285	True	844.500000	2765	89.581000	274	3737	4	chr3A.!!$R1	3463

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
421	449	0.530744	ATCATGCTTTGGTGCTGCAG	59.469	50.0	10.11	10.11	40.18	4.41	F
1506	1785	0.543277	TTGTGGAGCTGCATAGGAGG	59.457	55.0	12.38	0.00	0.00	4.30	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2365	2644	1.392589	ATCGGAATGTTCCCATGCAC	58.607	50.0	6.22	0.0	44.67	4.57	R
2926	3300	0.394352	ATCAAAGTCCCCGCATGGTC	60.394	55.0	0.00	0.0	0.00	4.02	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
42	43	2.780010	AGGCCCAAGACATAGTGCTATT	59.220	45.455	0.00	0.00	0.00	1.73
49	54	5.124457	CCAAGACATAGTGCTATTTTGCAGT	59.876	40.000	0.00	0.00	46.82	4.40
232	237	3.847602	CAGCTCTCCTGCTCCCGG	61.848	72.222	0.00	0.00	41.98	5.73
362	388	1.540146	GGCGGTGGCTTTTGACATTTT	60.540	47.619	0.00	0.00	41.07	1.82
365	391	2.539274	CGGTGGCTTTTGACATTTTGTG	59.461	45.455	0.00	0.00	41.07	3.33
382	410	3.305398	TGTGTCATGTGCGTGTGTATA	57.695	42.857	0.00	0.00	0.00	1.47
401	429	6.040504	GTGTATATGTCCAGTGTCCTGTATGA	59.959	42.308	0.00	0.00	36.95	2.15
421	449	0.530744	ATCATGCTTTGGTGCTGCAG	59.469	50.000	10.11	10.11	40.18	4.41
426	454	1.962807	TGCTTTGGTGCTGCAGTTAAT	59.037	42.857	16.64	0.00	32.55	1.40
438	466	5.758296	TGCTGCAGTTAATTAGTAGGCATAC	59.242	40.000	16.64	0.00	0.00	2.39
489	517	7.114247	GCGCACAACTATTTCAACATTTTCTTA	59.886	33.333	0.30	0.00	0.00	2.10
599	627	9.520515	AGTTTTGTCATATTTGGTCTATTCTGT	57.479	29.630	0.00	0.00	0.00	3.41
603	631	7.629157	TGTCATATTTGGTCTATTCTGTTGGA	58.371	34.615	0.00	0.00	0.00	3.53
608	636	3.329929	GGTCTATTCTGTTGGACCGTT	57.670	47.619	0.00	0.00	38.77	4.44
628	873	4.555610	GCATCTGCCCCTTCTCAG	57.444	61.111	0.00	0.00	34.31	3.35
631	876	1.474143	GCATCTGCCCCTTCTCAGTAC	60.474	57.143	0.00	0.00	34.31	2.73
669	914	2.223340	GCGTGCCAATAGGTCTGAATTG	60.223	50.000	0.00	0.00	37.19	2.32
728	973	6.031751	AGCTTCTCTACAAAATCGTCTTCT	57.968	37.500	0.00	0.00	0.00	2.85
731	976	4.166523	TCTCTACAAAATCGTCTTCTGCG	58.833	43.478	0.00	0.00	0.00	5.18
855	1104	2.203126	GGATGCTGGAAGAGGCGG	60.203	66.667	0.00	0.00	34.07	6.13
869	1118	2.584608	GCGGTGCAGGGTGAGTAT	59.415	61.111	0.00	0.00	0.00	2.12
1040	1292	1.576421	GGAGGCTTTGCACGACTTG	59.424	57.895	0.00	0.00	0.00	3.16
1356	1635	2.791004	GCCAGAAAATCATGTTATGCGC	59.209	45.455	0.00	0.00	0.00	6.09
1506	1785	0.543277	TTGTGGAGCTGCATAGGAGG	59.457	55.000	12.38	0.00	0.00	4.30
1908	2187	9.356433	GGTAAAAGTGTTCATAGTCTAGAACTC	57.644	37.037	16.46	14.17	43.38	3.01
2003	2282	1.215173	TGAGGCCCAGTCCATATTTGG	59.785	52.381	0.00	0.00	45.15	3.28
2120	2399	1.055040	ATGGAGGAGGAGCACATAGC	58.945	55.000	0.00	0.00	46.19	2.97
2192	2471	1.899437	CTTGTAGAGGAAGGCCGGCA	61.899	60.000	30.85	0.51	39.96	5.69
2226	2505	5.469421	GGCAATGATCAGACTTGGAATAGAG	59.531	44.000	0.09	0.00	0.00	2.43
2265	2544	2.619177	CTCGTGTATGGTAGACCTCCTG	59.381	54.545	0.00	0.00	36.82	3.86
2365	2644	3.694058	CTGCTGGCTGCCTGTAGGG	62.694	68.421	27.79	11.03	42.00	3.53
2425	2704	0.036388	CCGTCTTAAGCTGGAGCCAA	60.036	55.000	6.93	0.00	43.38	4.52
2516	2795	3.647113	AGAGTGAGGATGATGATGAAGGG	59.353	47.826	0.00	0.00	0.00	3.95
2665	2944	3.681897	GCGCTCTCATATGGAATACAAGG	59.318	47.826	0.00	0.00	0.00	3.61
2671	2950	7.828223	GCTCTCATATGGAATACAAGGATGATT	59.172	37.037	2.13	0.00	30.88	2.57
2774	3062	5.850557	AGATCGCCTCATCTATATGAAGG	57.149	43.478	0.00	0.00	41.57	3.46
2776	3064	6.427441	AGATCGCCTCATCTATATGAAGGTA	58.573	40.000	7.77	0.90	41.57	3.08
2805	3095	8.454106	AGAATCAATTCTGTAGAAAAACCATCG	58.546	33.333	4.47	0.00	44.91	3.84
2806	3096	7.921786	ATCAATTCTGTAGAAAAACCATCGA	57.078	32.000	0.00	0.00	37.61	3.59
2856	3147	9.129532	GATTCATCTGATTCCTACCTCAAATTT	57.870	33.333	0.00	0.00	0.00	1.82
2926	3300	4.081420	AGGCTTCACTAGTGATTGGTACAG	60.081	45.833	25.68	18.12	39.64	2.74
2978	3354	9.958180	TGGAGTCAAAATATGAGAAATGTTAGA	57.042	29.630	0.00	0.00	39.19	2.10
3003	3379	5.410924	TGATTGACTAGATGAGGTTTGACG	58.589	41.667	0.00	0.00	0.00	4.35
3004	3380	4.866508	TTGACTAGATGAGGTTTGACGT	57.133	40.909	0.00	0.00	0.00	4.34
3005	3381	4.866508	TGACTAGATGAGGTTTGACGTT	57.133	40.909	0.00	0.00	0.00	3.99
3050	3426	4.541085	TTGCACTGATCTGAATAATGCG	57.459	40.909	6.60	0.00	34.32	4.73
3057	3433	7.307632	GCACTGATCTGAATAATGCGAATTACT	60.308	37.037	6.60	0.00	0.00	2.24
3061	3437	8.551205	TGATCTGAATAATGCGAATTACTTCAC	58.449	33.333	12.97	7.81	0.00	3.18
3064	3440	8.175069	TCTGAATAATGCGAATTACTTCACAAC	58.825	33.333	12.97	0.00	27.95	3.32
3070	3446	4.814234	TGCGAATTACTTCACAACTTCAGT	59.186	37.500	0.00	0.00	0.00	3.41
3074	3450	7.853929	GCGAATTACTTCACAACTTCAGTTTTA	59.146	33.333	0.00	0.00	35.83	1.52
3148	3828	8.873830	CCTCTAATAATTATCCGTAGTTGCATG	58.126	37.037	0.00	0.00	0.00	4.06
3273	4421	1.074889	ACCTGTAAGCGGGGTCAAAAT	59.925	47.619	0.00	0.00	45.50	1.82
3279	4431	2.052104	GCGGGGTCAAAATCCAGGG	61.052	63.158	0.00	0.00	0.00	4.45
3295	4454	4.349365	TCCAGGGCCTTTAAGTAAATTGG	58.651	43.478	1.32	0.00	0.00	3.16
3321	4482	8.020819	GCAGCAAAGTACATAATCACAAAACTA	58.979	33.333	0.00	0.00	0.00	2.24
3348	4511	7.979444	AAGACACTTATTGAGAATCCGAAAA	57.021	32.000	0.00	0.00	0.00	2.29
3370	4803	2.672651	CCGTTGGACATGCTGCCA	60.673	61.111	0.00	0.00	0.00	4.92
3513	5135	7.144722	TGATAGCAATCAAAGATTGTTCGTT	57.855	32.000	17.93	4.65	39.20	3.85
3579	5204	1.744368	AGCGCTCAGGCATGAACAG	60.744	57.895	2.64	0.00	38.60	3.16
3681	5309	4.147826	CAGAAGAACATCGATGACGCTATG	59.852	45.833	31.33	19.30	39.58	2.23

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	0.995024	AGCACTATGTCTTGGGCCTT	59.005	50.000	4.53	0.00	0.00	4.35
42	43	0.821711	CGTTGGGGGAGAACTGCAAA	60.822	55.000	0.00	0.00	0.00	3.68
362	388	2.162319	ATACACACGCACATGACACA	57.838	45.000	0.00	0.00	0.00	3.72
365	391	3.245284	GGACATATACACACGCACATGAC	59.755	47.826	0.00	0.00	0.00	3.06
373	399	3.130516	AGGACACTGGACATATACACACG	59.869	47.826	0.00	0.00	0.00	4.49
401	429	0.970640	TGCAGCACCAAAGCATGATT	59.029	45.000	0.00	0.00	36.85	2.57
426	454	8.889717	GCTTAACAAAATCTGTATGCCTACTAA	58.110	33.333	0.74	0.00	37.23	2.24
438	466	2.651703	CACGCACGCTTAACAAAATCTG	59.348	45.455	0.00	0.00	0.00	2.90
508	536	7.828508	TGGCTTGCTTCATCTTATATTTGAT	57.171	32.000	0.00	0.00	0.00	2.57
588	616	3.329929	AACGGTCCAACAGAATAGACC	57.670	47.619	0.00	0.00	44.42	3.85
599	627	0.392461	GCAGATGCCTAACGGTCCAA	60.392	55.000	0.00	0.00	34.31	3.53
628	873	5.507876	CACGCACACATACATGATTTTGTAC	59.492	40.000	0.00	0.00	35.04	2.90
631	876	3.301379	GCACGCACACATACATGATTTTG	59.699	43.478	0.00	0.00	0.00	2.44
669	914	2.563471	ATCGACCGAAAGCAGACTAC	57.437	50.000	0.00	0.00	0.00	2.73
728	973	5.475909	AGGCATAGTTAGTAATACTAGCGCA	59.524	40.000	11.47	0.00	37.06	6.09
731	976	9.016438	AGAGAAGGCATAGTTAGTAATACTAGC	57.984	37.037	6.22	6.22	31.47	3.42
795	1044	0.721718	GAGATTTTGACTGGACGCCG	59.278	55.000	0.00	0.00	0.00	6.46
855	1104	1.089920	CTGCAATACTCACCCTGCAC	58.910	55.000	0.00	0.00	39.77	4.57
905	1154	3.182887	ACTGATCCACTGGTCTCTTCT	57.817	47.619	0.00	0.00	0.00	2.85
906	1155	5.407407	TTTACTGATCCACTGGTCTCTTC	57.593	43.478	0.00	0.00	0.00	2.87
907	1156	5.723887	AGATTTACTGATCCACTGGTCTCTT	59.276	40.000	0.00	0.00	0.00	2.85
908	1157	5.276440	AGATTTACTGATCCACTGGTCTCT	58.724	41.667	0.00	0.00	0.00	3.10
1040	1292	4.012895	CCCAACGACACGCACAGC	62.013	66.667	0.00	0.00	0.00	4.40
1124	1403	2.950433	TCGGTGAGAACGATGGTAAAC	58.050	47.619	0.00	0.00	35.12	2.01
1356	1635	4.508861	CCAGAAAACTGCACTTTTCCATTG	59.491	41.667	20.98	15.17	39.88	2.82
1375	1654	5.357742	TCTGTATTATTGCTTGAGCCAGA	57.642	39.130	0.00	1.69	41.18	3.86
1506	1785	4.744795	AGATATATCCGCACTCATTCCC	57.255	45.455	9.18	0.00	0.00	3.97
1908	2187	5.234757	CACACACAAATCAAAACCCATTCTG	59.765	40.000	0.00	0.00	0.00	3.02
2192	2471	2.753452	CTGATCATTGCCTTGAAGCAGT	59.247	45.455	0.00	0.00	45.13	4.40
2226	2505	3.628487	ACGAGTAGTGATCTAACTCTGGC	59.372	47.826	15.78	0.00	0.00	4.85
2365	2644	1.392589	ATCGGAATGTTCCCATGCAC	58.607	50.000	6.22	0.00	44.67	4.57
2516	2795	1.887198	TGTTCGTCTTCAGTCCTCTCC	59.113	52.381	0.00	0.00	0.00	3.71
2665	2944	6.709397	TCAAGACCATCTATCAGCAAATCATC	59.291	38.462	0.00	0.00	0.00	2.92
2671	2950	5.426689	AACTCAAGACCATCTATCAGCAA	57.573	39.130	0.00	0.00	0.00	3.91
2776	3064	9.354673	TGGTTTTTCTACAGAATTGATTCTTCT	57.645	29.630	3.54	0.00	44.28	2.85
2791	3081	4.566987	AGGTGAGTCGATGGTTTTTCTAC	58.433	43.478	0.00	0.00	0.00	2.59
2800	3090	1.403679	GTCTCTGAGGTGAGTCGATGG	59.596	57.143	4.59	0.00	35.68	3.51
2804	3094	1.883275	ACAAGTCTCTGAGGTGAGTCG	59.117	52.381	4.59	0.00	35.68	4.18
2805	3095	2.887783	TCACAAGTCTCTGAGGTGAGTC	59.112	50.000	4.59	0.00	33.88	3.36
2806	3096	2.950781	TCACAAGTCTCTGAGGTGAGT	58.049	47.619	4.59	0.00	33.88	3.41
2920	3294	2.189521	CCCCGCATGGTCTGTACC	59.810	66.667	0.00	0.00	46.98	3.34
2926	3300	0.394352	ATCAAAGTCCCCGCATGGTC	60.394	55.000	0.00	0.00	0.00	4.02
2972	3347	8.311395	ACCTCATCTAGTCAATCAATCTAACA	57.689	34.615	0.00	0.00	0.00	2.41
2976	3352	7.768120	GTCAAACCTCATCTAGTCAATCAATCT	59.232	37.037	0.00	0.00	0.00	2.40
2978	3354	6.536582	CGTCAAACCTCATCTAGTCAATCAAT	59.463	38.462	0.00	0.00	0.00	2.57
3019	3395	5.005740	TCAGATCAGTGCAAAAATAGCAGT	58.994	37.500	0.00	0.00	45.98	4.40
3057	3433	7.338196	TCCAGATGTTAAAACTGAAGTTGTGAA	59.662	33.333	0.00	0.00	38.44	3.18
3061	3437	9.533253	AATTTCCAGATGTTAAAACTGAAGTTG	57.467	29.630	0.00	0.00	38.44	3.16
3074	3450	8.031277	GCAATCAAGAAGTAATTTCCAGATGTT	58.969	33.333	0.00	0.00	36.40	2.71
3148	3828	8.725405	TTCTTTTACAACCCAAAGGAAAAATC	57.275	30.769	0.00	0.00	36.73	2.17
3273	4421	4.349365	CCAATTTACTTAAAGGCCCTGGA	58.651	43.478	0.00	0.00	0.00	3.86
3279	4431	4.186856	TGCTGCCAATTTACTTAAAGGC	57.813	40.909	0.00	0.00	39.89	4.35
3295	4454	6.863126	AGTTTTGTGATTATGTACTTTGCTGC	59.137	34.615	0.00	0.00	0.00	5.25
3321	4482	9.667107	TTTCGGATTCTCAATAAGTGTCTTTAT	57.333	29.630	0.00	0.00	0.00	1.40
3322	4483	9.496873	TTTTCGGATTCTCAATAAGTGTCTTTA	57.503	29.630	0.00	0.00	0.00	1.85
3348	4511	1.472480	GCAGCATGTCCAACGGTTAAT	59.528	47.619	0.00	0.00	39.31	1.40
3513	5135	6.382859	TGCTAGATTTAGTGGGTGTTATCTCA	59.617	38.462	0.00	0.00	0.00	3.27
3579	5204	1.299541	CTACATGGAACCGGTCATGC	58.700	55.000	27.56	12.69	43.12	4.06
3681	5309	3.084579	CCTCGTCTGCATCGCAAC	58.915	61.111	6.57	0.00	38.41	4.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.