AutoCloner

Multiple sequence alignment - TraesCS7B01G135200

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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	TraesCS7B01G135200	chr7B	100.000	3413	0	0	1	3413	165110379	165113791	0.000000e+00	6303.0
1	TraesCS7B01G135200	chr5B	94.124	3438	144	25	1	3400	405545968	405542551	0.000000e+00	5177.0
2	TraesCS7B01G135200	chr5B	91.274	1146	82	10	571	1704	391208102	391209241	0.000000e+00	1546.0
3	TraesCS7B01G135200	chr5B	84.878	205	18	12	1	198	391165280	391165478	9.660000e-46	195.0
4	TraesCS7B01G135200	chr5B	78.802	217	20	9	355	548	391207774	391207987	4.630000e-24	122.0
5	TraesCS7B01G135200	chr5B	76.506	166	32	5	1755	1917	391297432	391297593	2.180000e-12	84.2
6	TraesCS7B01G135200	chr2B	92.943	3259	171	35	200	3413	690759409	690762653	0.000000e+00	4689.0
7	TraesCS7B01G135200	chr2B	96.970	198	6	0	1	198	690759108	690759305	1.960000e-87	333.0
8	TraesCS7B01G135200	chr4D	92.075	3243	194	30	200	3400	27525787	27529008	0.000000e+00	4506.0
9	TraesCS7B01G135200	chr4D	93.939	198	11	1	1	198	27525487	27525683	7.160000e-77	298.0
10	TraesCS7B01G135200	chr3B	91.471	2732	183	21	203	2897	69600060	69597342	0.000000e+00	3709.0
11	TraesCS7B01G135200	chr3B	93.939	198	11	1	1	198	69600363	69600167	7.160000e-77	298.0
12	TraesCS7B01G135200	chr5D	89.986	2786	221	33	630	3400	546553384	546550642	0.000000e+00	3546.0
13	TraesCS7B01G135200	chr5D	90.979	1951	147	21	1472	3413	151200225	151198295	0.000000e+00	2601.0
14	TraesCS7B01G135200	chr5D	90.719	1390	110	16	456	1835	396230389	396229009	0.000000e+00	1834.0
15	TraesCS7B01G135200	chr5D	90.161	1301	96	10	203	1475	151214367	151213071	0.000000e+00	1664.0
16	TraesCS7B01G135200	chr5D	89.255	819	69	13	1960	2765	396229003	396228191	0.000000e+00	1007.0
17	TraesCS7B01G135200	chr5D	85.161	465	24	26	203	632	546562486	546562032	5.230000e-118	435.0
18	TraesCS7B01G135200	chr5D	90.123	243	20	3	215	457	396230652	396230414	2.560000e-81	313.0
19	TraesCS7B01G135200	chr5D	91.919	198	15	1	1	198	151214670	151214474	3.350000e-70	276.0
20	TraesCS7B01G135200	chr5D	80.165	121	16	5	1802	1917	151580439	151580556	2.180000e-12	84.2
21	TraesCS7B01G135200	chr5D	92.727	55	4	0	2	56	396230837	396230783	2.820000e-11	80.5
22	TraesCS7B01G135200	chr7D	90.726	1391	106	17	456	1835	24392199	24393577	0.000000e+00	1832.0
23	TraesCS7B01G135200	chr7D	88.836	1460	130	14	1960	3404	24393583	24395024	0.000000e+00	1762.0
24	TraesCS7B01G135200	chr7D	88.889	243	23	3	215	457	24391936	24392174	2.580000e-76	296.0
25	TraesCS7B01G135200	chr2D	89.221	1271	119	9	2134	3400	376967757	376969013	0.000000e+00	1572.0
26	TraesCS7B01G135200	chr2D	81.915	94	15	2	1797	1890	377029005	377029096	1.020000e-10	78.7
27	TraesCS7B01G135200	chr4B	87.392	1269	148	9	2134	3400	621551979	621553237	0.000000e+00	1447.0
28	TraesCS7B01G135200	chr4B	84.211	95	14	1	1797	1891	621623836	621623929	1.300000e-14	91.6
29	TraesCS7B01G135200	chr5A	88.430	242	24	3	216	457	544470110	544470347	4.310000e-74	289.0
30	TraesCS7B01G135200	chr5A	90.000	200	16	4	2	198	544469817	544470015	4.370000e-64	255.0

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	TraesCS7B01G135200	chr7B	165110379	165113791	3412	False	6303.000000	6303	100.000000	1	3413	1	chr7B.!!$F1	3412
1	TraesCS7B01G135200	chr5B	405542551	405545968	3417	True	5177.000000	5177	94.124000	1	3400	1	chr5B.!!$R1	3399
2	TraesCS7B01G135200	chr5B	391207774	391209241	1467	False	834.000000	1546	85.038000	355	1704	2	chr5B.!!$F3	1349
3	TraesCS7B01G135200	chr2B	690759108	690762653	3545	False	2511.000000	4689	94.956500	1	3413	2	chr2B.!!$F1	3412
4	TraesCS7B01G135200	chr4D	27525487	27529008	3521	False	2402.000000	4506	93.007000	1	3400	2	chr4D.!!$F1	3399
5	TraesCS7B01G135200	chr3B	69597342	69600363	3021	True	2003.500000	3709	92.705000	1	2897	2	chr3B.!!$R1	2896
6	TraesCS7B01G135200	chr5D	546550642	546553384	2742	True	3546.000000	3546	89.986000	630	3400	1	chr5D.!!$R2	2770
7	TraesCS7B01G135200	chr5D	151198295	151200225	1930	True	2601.000000	2601	90.979000	1472	3413	1	chr5D.!!$R1	1941
8	TraesCS7B01G135200	chr5D	151213071	151214670	1599	True	970.000000	1664	91.040000	1	1475	2	chr5D.!!$R4	1474
9	TraesCS7B01G135200	chr5D	396228191	396230837	2646	True	808.625000	1834	90.706000	2	2765	4	chr5D.!!$R5	2763
10	TraesCS7B01G135200	chr7D	24391936	24395024	3088	False	1296.666667	1832	89.483667	215	3404	3	chr7D.!!$F1	3189
11	TraesCS7B01G135200	chr2D	376967757	376969013	1256	False	1572.000000	1572	89.221000	2134	3400	1	chr2D.!!$F1	1266
12	TraesCS7B01G135200	chr4B	621551979	621553237	1258	False	1447.000000	1447	87.392000	2134	3400	1	chr4B.!!$F1	1266
13	TraesCS7B01G135200	chr5A	544469817	544470347	530	False	272.000000	289	89.215000	2	457	2	chr5A.!!$F1	455

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
735	981	0.396974	TGGGGGCTTGTTGGATATGC	60.397	55.0	0.0	0.0	0.0	3.14	F
1488	1746	0.987294	AGGAGTGTATGGCAAGCTGT	59.013	50.0	0.0	0.0	0.0	4.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2001	2271	1.152756	ATTATGGAGGTTGCCCCGC	60.153	57.895	0.0	0.0	38.74	6.13	R
2822	3116	0.671251	CCGCTGTTGCCCTTGTTTTA	59.329	50.000	0.0	0.0	35.36	1.52	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
109	110	2.040544	GGTCATGTCCCGGCAACTG	61.041	63.158	0.00	0.00	0.00	3.16
205	312	2.874014	TGTGATCCATGCACCAGAAAA	58.126	42.857	0.00	0.00	35.43	2.29
348	455	4.922692	TGAGCAACTTTTGTGTTTCTGTTG	59.077	37.500	0.00	0.00	38.13	3.33
561	794	7.478322	AGCAACTCATGTATATGCTTTTTCAG	58.522	34.615	10.66	0.00	44.43	3.02
566	799	9.399797	ACTCATGTATATGCTTTTTCAGAATCA	57.600	29.630	0.00	0.00	34.21	2.57
567	800	9.880064	CTCATGTATATGCTTTTTCAGAATCAG	57.120	33.333	0.00	0.00	34.21	2.90
568	801	9.399797	TCATGTATATGCTTTTTCAGAATCAGT	57.600	29.630	0.00	0.00	34.21	3.41
628	866	5.930837	AGTTTGTCAATTTTTCAGGGTCA	57.069	34.783	0.00	0.00	0.00	4.02
734	980	2.157640	TTGGGGGCTTGTTGGATATG	57.842	50.000	0.00	0.00	0.00	1.78
735	981	0.396974	TGGGGGCTTGTTGGATATGC	60.397	55.000	0.00	0.00	0.00	3.14
794	1040	3.056821	TCATGAAACACTACGACCCAGAG	60.057	47.826	0.00	0.00	0.00	3.35
816	1062	9.219603	CAGAGAAGTCTCAAATTGTTATACCAA	57.780	33.333	10.83	0.00	45.21	3.67
838	1084	6.263168	CCAAATAGAGGCAAAATACCAGTAGG	59.737	42.308	0.00	0.00	42.21	3.18
907	1153	8.853345	CAGGAAAGTATGTTTTGAAATGAATCG	58.147	33.333	0.00	0.00	0.00	3.34
930	1176	6.700081	TCGAGATGTTATAAGGGAATTCAACG	59.300	38.462	7.93	0.00	0.00	4.10
991	1237	6.923012	TGACTTCATGGTGTAAAATGATTGG	58.077	36.000	0.00	0.00	33.01	3.16
1002	1248	7.707893	GGTGTAAAATGATTGGGAAGATGAATG	59.292	37.037	0.00	0.00	0.00	2.67
1042	1289	1.965930	CTGCGTGCTTGGTTGGCTA	60.966	57.895	0.00	0.00	0.00	3.93
1103	1350	3.009473	AGCATCTCACCAAGGTGTTACAT	59.991	43.478	18.09	4.58	45.55	2.29
1135	1382	3.308595	TCACACAAGTGCTGTAAAAGACG	59.691	43.478	0.00	0.00	45.49	4.18
1404	1662	5.748670	TGAACCAATACCTGCTACACTTA	57.251	39.130	0.00	0.00	0.00	2.24
1413	1671	2.552155	CCTGCTACACTTACAAGGGCAA	60.552	50.000	0.00	0.00	30.73	4.52
1488	1746	0.987294	AGGAGTGTATGGCAAGCTGT	59.013	50.000	0.00	0.00	0.00	4.40
1496	1754	2.566833	ATGGCAAGCTGTGTGTAAGA	57.433	45.000	0.00	0.00	0.00	2.10
1634	1897	8.643324	AGTTTAGGCAAGTCATAGTATTAGGAG	58.357	37.037	0.00	0.00	0.00	3.69
1656	1919	3.857010	GCAACATAACTTGCCTGTGGAAC	60.857	47.826	0.00	0.00	40.68	3.62
1686	1950	5.806955	TGATTGGGGGTAATAGTTTTCCT	57.193	39.130	0.00	0.00	0.00	3.36
1962	2232	7.847096	TGAGAAACTTGCTATACAATAGTGGA	58.153	34.615	0.00	0.00	37.72	4.02
2001	2271	4.640201	TCTGTCAGTTTTTCCAGTCCAAAG	59.360	41.667	0.00	0.00	0.00	2.77
2003	2273	2.357637	TCAGTTTTTCCAGTCCAAAGCG	59.642	45.455	0.00	0.00	0.00	4.68
2060	2331	5.183713	TCTTTGATCGAAACATGGCAAATCT	59.816	36.000	0.00	0.00	0.00	2.40
2076	2347	6.493115	TGGCAAATCTAAAGTGAAATCCAAGA	59.507	34.615	0.00	0.00	0.00	3.02
2123	2394	8.960591	GGCAAGTTATATTACTACCTATACGGA	58.039	37.037	0.00	0.00	36.31	4.69
2141	2418	4.178540	ACGGATCAACGACGTTCATTTAT	58.821	39.130	10.95	0.00	37.61	1.40
2196	2478	7.750229	AATAGCTCAAGACTGAATTTTCACA	57.250	32.000	0.00	0.00	32.90	3.58
2270	2552	2.079925	CAGCTAGGTTGCCTGAAAGTC	58.920	52.381	0.00	0.00	34.61	3.01
2274	2556	0.535102	AGGTTGCCTGAAAGTCACGG	60.535	55.000	0.00	0.00	29.57	4.94
2382	2668	6.323266	ACTATCTGACACACATTTACGTCTC	58.677	40.000	0.00	0.00	0.00	3.36
2463	2749	4.567959	CACTGAAATGTCACATGCTATCGA	59.432	41.667	0.00	0.00	0.00	3.59
2524	2810	1.201647	CCCAGCTCAAGCAAGAACATG	59.798	52.381	4.59	0.00	45.16	3.21
2605	2891	2.551459	AGTGATTGAACACAGCTCAAGC	59.449	45.455	0.00	0.00	42.45	4.01
2717	3005	1.482593	GGGATGACAACGGAGATGACT	59.517	52.381	0.00	0.00	33.32	3.41
2822	3116	2.821969	GAGGAGCCACATGAAACAACAT	59.178	45.455	0.00	0.00	0.00	2.71
2842	3136	1.326951	AAAACAAGGGCAACAGCGGT	61.327	50.000	0.00	0.00	39.74	5.68
3073	3367	4.100373	GAGGAGCCAATATAGGAGGATGT	58.900	47.826	0.00	0.00	0.00	3.06
3092	3386	5.880332	GGATGTAGCAGGACAAACAATTCTA	59.120	40.000	0.00	0.00	31.83	2.10
3183	3477	4.127566	AGCAAAATGACAGCAAACAACT	57.872	36.364	0.00	0.00	0.00	3.16
3210	3504	6.917533	CAGGAGATGCTACAGAAACATTTTT	58.082	36.000	0.00	0.00	0.00	1.94
3211	3505	6.805271	CAGGAGATGCTACAGAAACATTTTTG	59.195	38.462	0.00	0.00	0.00	2.44
3316	3611	1.408127	CGGAAACCCCACTCATATGCA	60.408	52.381	0.00	0.00	34.14	3.96
3330	3625	5.049198	ACTCATATGCAAGCACATTATTCGG	60.049	40.000	0.00	0.00	0.00	4.30
3349	3644	1.359848	GTCAGATGGTGTTTCGCGAT	58.640	50.000	10.88	0.00	0.00	4.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
89	90	1.378514	GTTGCCGGGACATGACCAT	60.379	57.895	16.14	0.00	0.00	3.55
205	312	3.616219	TGTGTGCTTAAACTTCTGGTGT	58.384	40.909	0.00	0.00	0.00	4.16
312	419	1.264288	GTTGCTCACTGCCAACACTAC	59.736	52.381	0.00	0.00	42.00	2.73
348	455	3.458189	ACATACATGAAGTTCTAGCGCC	58.542	45.455	2.29	0.00	0.00	6.53
446	554	1.651987	ACATCAGCCAACCGTTATCG	58.348	50.000	0.00	0.00	0.00	2.92
453	561	4.218635	TCTCTCGATATACATCAGCCAACC	59.781	45.833	0.00	0.00	0.00	3.77
454	562	5.378292	TCTCTCGATATACATCAGCCAAC	57.622	43.478	0.00	0.00	0.00	3.77
588	825	8.492748	TGACAAACTAAAGTTATTTCTACTGCG	58.507	33.333	0.00	0.00	37.25	5.18
668	913	5.381174	TTTGGTCTTCGTCGAGATCTTTA	57.619	39.130	0.00	0.00	0.00	1.85
734	980	2.418083	GGGCATGGTTGTAGCTGGC	61.418	63.158	0.00	0.00	0.00	4.85
735	981	2.114670	CGGGCATGGTTGTAGCTGG	61.115	63.158	0.00	0.00	0.00	4.85
816	1062	6.357367	CACCTACTGGTATTTTGCCTCTATT	58.643	40.000	0.00	0.00	46.60	1.73
838	1084	4.946478	ATCCTCCTAACACTATCTGCAC	57.054	45.455	0.00	0.00	0.00	4.57
907	1153	6.766467	ACCGTTGAATTCCCTTATAACATCTC	59.234	38.462	2.27	0.00	0.00	2.75
930	1176	6.753107	TTTTCCCTCGATCTTGAAAATACC	57.247	37.500	7.17	0.00	33.20	2.73
991	1237	1.103398	CACGCCCCCATTCATCTTCC	61.103	60.000	0.00	0.00	0.00	3.46
1103	1350	4.023792	CAGCACTTGTGTGAAGAATAGCAA	60.024	41.667	2.61	0.00	46.55	3.91
1135	1382	3.764885	AACAAAGTCGCATATCTTGGC	57.235	42.857	0.00	0.00	0.00	4.52
1349	1607	8.814931	TCCAATGAATCCAAATACAAAATCTGT	58.185	29.630	0.00	0.00	42.47	3.41
1350	1608	9.826574	ATCCAATGAATCCAAATACAAAATCTG	57.173	29.630	0.00	0.00	0.00	2.90
1351	1609	9.826574	CATCCAATGAATCCAAATACAAAATCT	57.173	29.630	0.00	0.00	0.00	2.40
1352	1610	9.603921	ACATCCAATGAATCCAAATACAAAATC	57.396	29.630	0.00	0.00	0.00	2.17
1353	1611	9.962809	AACATCCAATGAATCCAAATACAAAAT	57.037	25.926	0.00	0.00	0.00	1.82
1354	1612	9.217278	CAACATCCAATGAATCCAAATACAAAA	57.783	29.630	0.00	0.00	0.00	2.44
1355	1613	8.591940	TCAACATCCAATGAATCCAAATACAAA	58.408	29.630	0.00	0.00	0.00	2.83
1356	1614	8.131847	TCAACATCCAATGAATCCAAATACAA	57.868	30.769	0.00	0.00	0.00	2.41
1357	1615	7.715266	TCAACATCCAATGAATCCAAATACA	57.285	32.000	0.00	0.00	0.00	2.29
1404	1662	0.112995	TTCCAGATGCTTGCCCTTGT	59.887	50.000	0.00	0.00	0.00	3.16
1413	1671	7.828223	GGTTATTAGATCATCATTCCAGATGCT	59.172	37.037	0.00	0.00	43.94	3.79
1488	1746	5.053811	TCTTGCACGAAAAGATCTTACACA	58.946	37.500	8.75	0.00	0.00	3.72
1656	1919	8.477419	AACTATTACCCCCAATCATATGTTTG	57.523	34.615	16.45	16.45	0.00	2.93
1686	1950	5.392767	TGTGTTTGTACTGCTTGGAAAAA	57.607	34.783	0.00	0.00	0.00	1.94
1962	2232	7.807977	ACTGACAGAATGAACTACACATTTT	57.192	32.000	10.08	0.00	39.69	1.82
2001	2271	1.152756	ATTATGGAGGTTGCCCCGC	60.153	57.895	0.00	0.00	38.74	6.13
2003	2273	2.174854	AGTACATTATGGAGGTTGCCCC	59.825	50.000	0.00	0.00	0.00	5.80
2356	2640	7.997482	AGACGTAAATGTGTGTCAGATAGTAT	58.003	34.615	0.00	0.00	33.83	2.12
2377	2661	2.851824	GCACACCAAAAACAAAGAGACG	59.148	45.455	0.00	0.00	0.00	4.18
2382	2668	3.062504	GCTTCTGCACACCAAAAACAAAG	59.937	43.478	0.00	0.00	39.41	2.77
2409	2695	5.851693	TCATGGACCATTCCTGTTATCCTAT	59.148	40.000	3.52	0.00	43.31	2.57
2463	2749	1.683917	CTATGCCCACTACGAGCTTCT	59.316	52.381	0.00	0.00	0.00	2.85
2506	2792	2.095364	GTCCATGTTCTTGCTTGAGCTG	60.095	50.000	4.44	0.00	42.66	4.24
2524	2810	3.632145	CACTTGCCTATGGGTTAATGTCC	59.368	47.826	0.00	0.00	34.45	4.02
2605	2891	3.131933	ACTTGAATGACTCCTCATCCTCG	59.868	47.826	0.00	0.00	35.96	4.63
2717	3005	6.093082	GTGTTGTCATCATCATCATCTGAACA	59.907	38.462	0.00	0.00	37.44	3.18
2822	3116	0.671251	CCGCTGTTGCCCTTGTTTTA	59.329	50.000	0.00	0.00	35.36	1.52
2842	3136	1.305219	GCACATTGCCGCTGTCCTTA	61.305	55.000	0.00	0.00	37.42	2.69
2923	3217	1.227943	TTCAGCTGCCTCGCTTTGT	60.228	52.632	9.47	0.00	38.41	2.83
3063	3357	3.398318	TTGTCCTGCTACATCCTCCTA	57.602	47.619	0.00	0.00	0.00	2.94
3073	3367	6.480763	TCCATTAGAATTGTTTGTCCTGCTA	58.519	36.000	0.00	0.00	0.00	3.49
3092	3386	4.787534	ACTTCCTTCTCCTTCATCTCCATT	59.212	41.667	0.00	0.00	0.00	3.16
3150	3444	7.710044	TGCTGTCATTTTGCTTGATAAAGAAAA	59.290	29.630	0.00	0.00	0.00	2.29
3210	3504	6.403049	TCCGTCTTGACAAAATCTATAAGCA	58.597	36.000	1.59	0.00	0.00	3.91
3211	3505	6.535508	ACTCCGTCTTGACAAAATCTATAAGC	59.464	38.462	1.59	0.00	0.00	3.09
3231	3525	1.151668	CCACTGCTTCTTGAACTCCG	58.848	55.000	0.00	0.00	0.00	4.63
3316	3611	3.879295	CCATCTGACCGAATAATGTGCTT	59.121	43.478	0.00	0.00	0.00	3.91
3330	3625	1.061131	CATCGCGAAACACCATCTGAC	59.939	52.381	15.24	0.00	0.00	3.51
3349	3644	4.654915	TGATGCATGTTTCTCTTTCCTCA	58.345	39.130	2.46	0.00	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.