AutoCloner

Multiple sequence alignment - TraesCS3D01G015400

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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	TraesCS3D01G015400	chr3D	100.000	2718	0	0	1	2718	5410900	5413617	0.000000e+00	5020.0
1	TraesCS3D01G015400	chr3D	79.530	1871	254	65	951	2714	5338547	5336699	0.000000e+00	1214.0
2	TraesCS3D01G015400	chr3D	82.736	1060	114	40	1138	2161	41216352	41217378	0.000000e+00	880.0
3	TraesCS3D01G015400	chr3D	78.378	1147	167	54	1629	2715	5360337	5359212	0.000000e+00	669.0
4	TraesCS3D01G015400	chr3D	87.543	578	66	4	1144	1716	41208230	41208806	0.000000e+00	664.0
5	TraesCS3D01G015400	chr3D	87.654	243	16	4	843	1082	41207903	41208134	1.240000e-68	270.0
6	TraesCS3D01G015400	chr3D	89.005	191	11	4	873	1059	41216052	41216236	7.570000e-56	228.0
7	TraesCS3D01G015400	chr3D	91.837	49	3	1	927	974	5347107	5347059	1.750000e-07	67.6
8	TraesCS3D01G015400	chr3B	88.688	1883	117	32	663	2476	12588669	12590524	0.000000e+00	2209.0
9	TraesCS3D01G015400	chr3B	88.939	1555	102	30	663	2161	13239287	13237747	0.000000e+00	1855.0
10	TraesCS3D01G015400	chr3B	82.976	1539	159	58	712	2161	13243933	13242409	0.000000e+00	1295.0
11	TraesCS3D01G015400	chr3B	91.128	913	50	14	1825	2711	13171049	13170142	0.000000e+00	1208.0
12	TraesCS3D01G015400	chr3B	92.717	714	40	4	1138	1839	13173160	13172447	0.000000e+00	1020.0
13	TraesCS3D01G015400	chr3B	88.872	665	58	6	6	657	13409651	13408990	0.000000e+00	804.0
14	TraesCS3D01G015400	chr3B	87.601	621	59	11	49	657	13241578	13240964	0.000000e+00	704.0
15	TraesCS3D01G015400	chr3B	90.870	460	37	5	1	459	12546847	12547302	1.790000e-171	612.0
16	TraesCS3D01G015400	chr3B	88.863	422	32	5	1	409	13245434	13245015	3.120000e-139	505.0
17	TraesCS3D01G015400	chr3B	88.503	374	25	3	2153	2508	13188661	13188288	1.160000e-118	436.0
18	TraesCS3D01G015400	chr3B	85.753	372	41	7	712	1081	13443068	13443429	1.530000e-102	383.0
19	TraesCS3D01G015400	chr3B	92.245	245	18	1	413	657	13244723	13244480	2.000000e-91	346.0
20	TraesCS3D01G015400	chr3B	89.686	223	23	0	2496	2718	13188133	13187911	4.430000e-73	285.0
21	TraesCS3D01G015400	chr3B	94.444	180	9	1	2533	2711	13408134	13407955	2.670000e-70	276.0
22	TraesCS3D01G015400	chr3B	94.382	178	9	1	2542	2718	12590528	12590705	3.450000e-69	272.0
23	TraesCS3D01G015400	chr3B	81.040	327	26	11	663	978	13240445	13240144	7.570000e-56	228.0
24	TraesCS3D01G015400	chr3B	85.075	201	18	2	457	657	12567279	12567467	7.680000e-46	195.0
25	TraesCS3D01G015400	chr3A	92.937	1246	48	14	659	1880	15997397	15996168	0.000000e+00	1777.0
26	TraesCS3D01G015400	chr3A	84.235	1497	155	47	918	2346	16072037	16073520	0.000000e+00	1382.0
27	TraesCS3D01G015400	chr3A	80.427	1313	165	41	1465	2714	16265804	16264521	0.000000e+00	917.0
28	TraesCS3D01G015400	chr3A	87.761	670	47	11	1	657	16008576	16007929	0.000000e+00	750.0
29	TraesCS3D01G015400	chr3A	76.866	804	143	21	1933	2715	16155545	16154764	5.410000e-112	414.0
30	TraesCS3D01G015400	chr3A	96.124	129	5	0	2589	2717	15995644	15995516	7.620000e-51	211.0
31	TraesCS3D01G015400	chr3A	87.500	56	7	0	1931	1986	15956168	15956223	6.280000e-07	65.8
32	TraesCS3D01G015400	chrUn	79.984	1214	151	41	1564	2714	296442131	296443315	0.000000e+00	811.0
33	TraesCS3D01G015400	chrUn	79.984	1214	151	41	1564	2714	296447185	296448369	0.000000e+00	811.0
34	TraesCS3D01G015400	chrUn	80.946	698	101	19	2028	2702	36177641	36178329	8.620000e-145	523.0
35	TraesCS3D01G015400	chr2D	78.535	587	100	19	1150	1723	548416535	548415962	1.990000e-96	363.0
36	TraesCS3D01G015400	chr2D	81.343	402	52	16	191	577	248780188	248779795	3.400000e-79	305.0
37	TraesCS3D01G015400	chr1D	82.902	386	52	9	194	569	44567870	44567489	4.340000e-88	335.0
38	TraesCS3D01G015400	chr1D	77.558	606	93	28	2	577	298457890	298458482	2.610000e-85	326.0
39	TraesCS3D01G015400	chr7D	82.133	375	51	8	198	563	29040157	29040524	9.450000e-80	307.0
40	TraesCS3D01G015400	chr1B	80.402	398	60	14	192	577	401459621	401460012	1.230000e-73	287.0
41	TraesCS3D01G015400	chr1A	84.615	104	13	2	25	127	387860722	387860823	1.720000e-17	100.0
42	TraesCS3D01G015400	chr7A	83.495	103	15	2	28	129	694024506	694024607	8.010000e-16	95.3
43	TraesCS3D01G015400	chr2A	94.000	50	3	0	603	652	13425665	13425616	2.900000e-10	76.8

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	TraesCS3D01G015400	chr3D	5410900	5413617	2717	False	5020.000000	5020	100.0000	1	2718	1	chr3D.!!$F1	2717
1	TraesCS3D01G015400	chr3D	5336699	5338547	1848	True	1214.000000	1214	79.5300	951	2714	1	chr3D.!!$R1	1763
2	TraesCS3D01G015400	chr3D	5359212	5360337	1125	True	669.000000	669	78.3780	1629	2715	1	chr3D.!!$R3	1086
3	TraesCS3D01G015400	chr3D	41216052	41217378	1326	False	554.000000	880	85.8705	873	2161	2	chr3D.!!$F3	1288
4	TraesCS3D01G015400	chr3D	41207903	41208806	903	False	467.000000	664	87.5985	843	1716	2	chr3D.!!$F2	873
5	TraesCS3D01G015400	chr3B	12588669	12590705	2036	False	1240.500000	2209	91.5350	663	2718	2	chr3B.!!$F4	2055
6	TraesCS3D01G015400	chr3B	13170142	13173160	3018	True	1114.000000	1208	91.9225	1138	2711	2	chr3B.!!$R1	1573
7	TraesCS3D01G015400	chr3B	13237747	13245434	7687	True	822.166667	1855	86.9440	1	2161	6	chr3B.!!$R3	2160
8	TraesCS3D01G015400	chr3B	13407955	13409651	1696	True	540.000000	804	91.6580	6	2711	2	chr3B.!!$R4	2705
9	TraesCS3D01G015400	chr3B	13187911	13188661	750	True	360.500000	436	89.0945	2153	2718	2	chr3B.!!$R2	565
10	TraesCS3D01G015400	chr3A	16072037	16073520	1483	False	1382.000000	1382	84.2350	918	2346	1	chr3A.!!$F2	1428
11	TraesCS3D01G015400	chr3A	15995516	15997397	1881	True	994.000000	1777	94.5305	659	2717	2	chr3A.!!$R4	2058
12	TraesCS3D01G015400	chr3A	16264521	16265804	1283	True	917.000000	917	80.4270	1465	2714	1	chr3A.!!$R3	1249
13	TraesCS3D01G015400	chr3A	16007929	16008576	647	True	750.000000	750	87.7610	1	657	1	chr3A.!!$R1	656
14	TraesCS3D01G015400	chr3A	16154764	16155545	781	True	414.000000	414	76.8660	1933	2715	1	chr3A.!!$R2	782
15	TraesCS3D01G015400	chrUn	296442131	296448369	6238	False	811.000000	811	79.9840	1564	2714	2	chrUn.!!$F2	1150
16	TraesCS3D01G015400	chrUn	36177641	36178329	688	False	523.000000	523	80.9460	2028	2702	1	chrUn.!!$F1	674
17	TraesCS3D01G015400	chr2D	548415962	548416535	573	True	363.000000	363	78.5350	1150	1723	1	chr2D.!!$R2	573
18	TraesCS3D01G015400	chr1D	298457890	298458482	592	False	326.000000	326	77.5580	2	577	1	chr1D.!!$F1	575

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
440	756	0.107017	ATGTATCTTTGGCTGCGGCT	60.107	50.0	18.85	0.0	38.73	5.52	F
1549	7172	0.603707	TGCCTCTCAAGGAAGCGTTG	60.604	55.0	0.00	0.0	46.67	4.10	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1634	7390	1.214062	CAGACGGTCTCTGCAGGAC	59.786	63.158	20.72	20.72	40.23	3.85	R
2508	10011	0.823356	TGCTTGGAGCCTTGAACCAC	60.823	55.000	0.00	0.00	41.51	4.16	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
41	42	6.425114	ACTCTAATAGGAAATAGCATGCAACG	59.575	38.462	21.98	0.00	0.00	4.10
42	43	4.836125	AATAGGAAATAGCATGCAACGG	57.164	40.909	21.98	0.00	0.00	4.44
118	120	6.106673	ACAACAACTATAGGTAGACACATGC	58.893	40.000	4.43	0.00	0.00	4.06
135	137	2.977772	TGCACATATCACGATGGACA	57.022	45.000	0.00	0.00	0.00	4.02
152	154	5.408880	TGGACATACGGTTCATTAGTTGA	57.591	39.130	0.00	0.00	26.83	3.18
213	229	1.000163	CGATGATAAGTAGCACCGCCT	60.000	52.381	0.00	0.00	0.00	5.52
229	245	1.066573	CGCCTGACTTGGACAGAAGAT	60.067	52.381	0.00	0.00	37.54	2.40
277	295	1.659794	GCAGAGCGCTTCCCAAAAA	59.340	52.632	13.26	0.00	37.77	1.94
278	296	0.387750	GCAGAGCGCTTCCCAAAAAG	60.388	55.000	13.26	0.00	37.77	2.27
409	725	0.109132	GCAAGATGAGGCAAAACCCG	60.109	55.000	0.00	0.00	40.58	5.28
440	756	0.107017	ATGTATCTTTGGCTGCGGCT	60.107	50.000	18.85	0.00	38.73	5.52
507	826	5.281727	CGATCATGATCTCAAACCGACTTA	58.718	41.667	28.48	0.00	35.72	2.24
661	6168	5.014858	TGGTGTAGAGAACCAACTACTAGG	58.985	45.833	0.00	0.00	44.72	3.02
819	6326	3.386078	GTCTCCTCATGTGCCTAATCAGA	59.614	47.826	0.00	0.00	0.00	3.27
914	6421	3.492011	CACAATCAGCCTTGCTTTTGTTC	59.508	43.478	10.03	0.00	39.10	3.18
916	6423	4.141869	ACAATCAGCCTTGCTTTTGTTCTT	60.142	37.500	7.85	0.00	38.46	2.52
925	6433	9.045223	AGCCTTGCTTTTGTTCTTTATAAAAAG	57.955	29.630	0.00	0.69	38.74	2.27
983	6491	1.267038	CGGCAAACAGATCGATCGTTG	60.267	52.381	25.38	24.57	0.00	4.10
1067	6589	2.752903	ACGCCTGGTATGAATTTCAACC	59.247	45.455	17.05	17.05	32.16	3.77
1112	6698	6.927294	AAATTTCAGGAATCGATGTACTCC	57.073	37.500	0.00	1.60	0.00	3.85
1315	6916	7.247728	GTGAATCATACAAACGCATCCTTTTA	58.752	34.615	0.00	0.00	0.00	1.52
1453	7076	1.732259	CAAAGATACAAAGAGCGCCGT	59.268	47.619	2.29	0.00	0.00	5.68
1549	7172	0.603707	TGCCTCTCAAGGAAGCGTTG	60.604	55.000	0.00	0.00	46.67	4.10
1634	7390	3.837213	AATCAAGCATCTTTGACACCG	57.163	42.857	0.00	0.00	39.68	4.94
1749	7586	6.106673	CGTGGAATATGTTTCTGTTCTAGGT	58.893	40.000	0.00	0.00	0.00	3.08
1752	7589	8.451748	GTGGAATATGTTTCTGTTCTAGGTTTC	58.548	37.037	0.00	0.00	0.00	2.78
1753	7590	7.610305	TGGAATATGTTTCTGTTCTAGGTTTCC	59.390	37.037	0.00	0.00	0.00	3.13
1831	9108	8.328758	ACATCTTTCTTCAATGTAAGGGATGTA	58.671	33.333	0.00	0.00	38.36	2.29
1897	9190	4.985409	CGCCCTAAATGAACTGTAGAGATC	59.015	45.833	0.00	0.00	0.00	2.75
1917	9210	7.458170	AGAGATCAAAGGTAGTTTTCCCTTCTA	59.542	37.037	0.00	0.00	40.17	2.10
1949	9252	2.190841	CGGAAAACAACAGGGCCGT	61.191	57.895	0.00	0.00	34.45	5.68
2089	9395	6.693315	ATGGGATACACCGTATTCTTTTTG	57.307	37.500	0.00	0.00	40.11	2.44
2114	9420	1.398390	CTGAATCCTTGTTAGGCACGC	59.602	52.381	0.00	0.00	41.69	5.34
2134	9440	3.726486	CGCGGATAATTTGAAAGTTCGCA	60.726	43.478	15.75	0.00	40.51	5.10
2135	9441	4.162812	GCGGATAATTTGAAAGTTCGCAA	58.837	39.130	12.58	0.00	40.26	4.85
2140	9446	7.461416	CGGATAATTTGAAAGTTCGCAATGTTC	60.461	37.037	0.00	0.00	0.00	3.18
2257	9565	6.014413	TGTTTGGTACTGTAGCAACCACTATA	60.014	38.462	26.66	11.67	44.80	1.31
2508	10011	1.519343	TGTTGACATTCGTCGTTGTCG	59.481	47.619	18.98	0.00	45.80	4.35
2702	10446	1.809684	GGCTCTAAACTTCGCCACTT	58.190	50.000	0.00	0.00	42.06	3.16
2703	10447	2.152016	GGCTCTAAACTTCGCCACTTT	58.848	47.619	0.00	0.00	42.06	2.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
26	27	3.303395	GCTAGACCGTTGCATGCTATTTC	60.303	47.826	20.33	9.07	0.00	2.17
118	120	3.920412	CCGTATGTCCATCGTGATATGTG	59.080	47.826	0.00	0.00	0.00	3.21
135	137	3.807622	CCGCATCAACTAATGAACCGTAT	59.192	43.478	0.00	0.00	42.54	3.06
152	154	1.079405	AACAACGTCGATCCCGCAT	60.079	52.632	0.00	0.00	35.37	4.73
213	229	2.303022	GGGTCATCTTCTGTCCAAGTCA	59.697	50.000	0.00	0.00	35.03	3.41
229	245	3.156293	CCAAGTTTGTCATCATGGGTCA	58.844	45.455	0.00	0.00	0.00	4.02
277	295	1.757699	GGGAGAGCGTGAATTAGGTCT	59.242	52.381	8.80	8.80	46.37	3.85
278	296	1.536284	CGGGAGAGCGTGAATTAGGTC	60.536	57.143	0.00	0.63	35.33	3.85
350	378	3.204526	AGTCTACTCTATCCCGAACACG	58.795	50.000	0.00	0.00	0.00	4.49
409	725	5.673818	GCCAAAGATACATCGAAAACACCTC	60.674	44.000	0.00	0.00	0.00	3.85
440	756	5.704515	GTCCTCTTATATGTACTGCTACCGA	59.295	44.000	0.00	0.00	0.00	4.69
507	826	9.073475	GTCCAGTGAGTATATGACTTAGAATCT	57.927	37.037	0.00	0.00	39.06	2.40
571	891	2.609459	CGCACTCGCTTCTCCATTTTAT	59.391	45.455	0.00	0.00	35.30	1.40
572	892	1.999735	CGCACTCGCTTCTCCATTTTA	59.000	47.619	0.00	0.00	35.30	1.52
576	896	2.185350	CCGCACTCGCTTCTCCAT	59.815	61.111	0.00	0.00	35.30	3.41
583	903	2.102357	CATACGTCCGCACTCGCT	59.898	61.111	0.00	0.00	35.30	4.93
603	923	6.043243	AGGTGTGAAGGAGTGAAATAAGAGAA	59.957	38.462	0.00	0.00	0.00	2.87
615	935	4.348168	ACACTTATTGAGGTGTGAAGGAGT	59.652	41.667	0.00	0.00	43.79	3.85
657	977	5.437946	GGTTTAGGGGATCTCAAAACCTAG	58.562	45.833	24.47	0.00	43.64	3.02
661	6168	3.939592	CTCGGTTTAGGGGATCTCAAAAC	59.060	47.826	12.23	12.23	0.00	2.43
671	6178	3.400188	ACCTGCTCGGTTTAGGGG	58.600	61.111	0.00	0.00	46.37	4.79
703	6210	1.837051	ACCTGCTCGGTCTCACCAA	60.837	57.895	0.00	0.00	44.93	3.67
704	6211	2.203640	ACCTGCTCGGTCTCACCA	60.204	61.111	0.00	0.00	44.93	4.17
819	6326	4.145807	CGTACAGATGGAGGAGTCCTTAT	58.854	47.826	14.41	11.23	44.30	1.73
914	6421	5.332707	GTCCTTGGCGAGCTTTTTATAAAG	58.667	41.667	0.00	1.64	42.97	1.85
916	6423	3.692593	GGTCCTTGGCGAGCTTTTTATAA	59.307	43.478	0.00	0.00	0.00	0.98
989	6497	1.040646	TCCACCCATACGAGCAGATC	58.959	55.000	0.00	0.00	0.00	2.75
1051	6573	9.703892	CAATGTAAAAGGTTGAAATTCATACCA	57.296	29.630	20.87	7.30	33.18	3.25
1089	6668	5.523916	CGGAGTACATCGATTCCTGAAATTT	59.476	40.000	11.19	0.00	0.00	1.82
1090	6669	5.050490	CGGAGTACATCGATTCCTGAAATT	58.950	41.667	11.19	0.00	0.00	1.82
1091	6670	4.341235	TCGGAGTACATCGATTCCTGAAAT	59.659	41.667	11.19	0.00	0.00	2.17
1092	6671	3.697542	TCGGAGTACATCGATTCCTGAAA	59.302	43.478	11.19	0.00	0.00	2.69
1093	6672	3.284617	TCGGAGTACATCGATTCCTGAA	58.715	45.455	11.19	0.00	0.00	3.02
1097	6676	3.576648	GGATTCGGAGTACATCGATTCC	58.423	50.000	23.13	23.13	43.64	3.01
1224	6825	2.019984	GGAAGGTACCATACTCGTCGT	58.980	52.381	15.94	0.00	0.00	4.34
1315	6916	1.949799	AGTCCTGGAGTGCTGATCTT	58.050	50.000	2.50	0.00	0.00	2.40
1453	7076	2.022718	AAAATAGCCCACCCTGCAAA	57.977	45.000	0.00	0.00	0.00	3.68
1549	7172	5.418310	TGTTTTCTTGTCGATGTTTCCTC	57.582	39.130	0.00	0.00	0.00	3.71
1634	7390	1.214062	CAGACGGTCTCTGCAGGAC	59.786	63.158	20.72	20.72	40.23	3.85
1865	9158	6.207810	ACAGTTCATTTAGGGCGACAAATAAA	59.792	34.615	0.00	0.00	0.00	1.40
1871	9164	2.851263	ACAGTTCATTTAGGGCGACA	57.149	45.000	0.00	0.00	0.00	4.35
1872	9165	4.113354	CTCTACAGTTCATTTAGGGCGAC	58.887	47.826	0.00	0.00	0.00	5.19
1897	9190	7.761038	AACATAGAAGGGAAAACTACCTTTG	57.239	36.000	0.00	0.00	46.64	2.77
1917	9210	4.658063	TGTTTTCCGAATCCACCTAACAT	58.342	39.130	0.00	0.00	0.00	2.71
1949	9252	6.105397	AGTGTGTTCGACTAAAATTCCCTA	57.895	37.500	0.00	0.00	0.00	3.53
2009	9312	3.686016	ACATACTCCAAGCAAACCGATT	58.314	40.909	0.00	0.00	0.00	3.34
2010	9313	3.350219	ACATACTCCAAGCAAACCGAT	57.650	42.857	0.00	0.00	0.00	4.18
2011	9314	2.851263	ACATACTCCAAGCAAACCGA	57.149	45.000	0.00	0.00	0.00	4.69
2012	9315	3.331150	TGTACATACTCCAAGCAAACCG	58.669	45.455	0.00	0.00	0.00	4.44
2013	9316	5.163652	GGAATGTACATACTCCAAGCAAACC	60.164	44.000	18.06	1.50	0.00	3.27
2017	9320	4.835284	TGGAATGTACATACTCCAAGCA	57.165	40.909	21.82	4.12	35.02	3.91
2089	9395	2.685388	GCCTAACAAGGATTCAGCTTCC	59.315	50.000	0.00	0.00	0.00	3.46
2114	9420	5.799936	ACATTGCGAACTTTCAAATTATCCG	59.200	36.000	0.00	0.00	0.00	4.18
2134	9440	5.801380	ACTATCCTAACAACACCGAACATT	58.199	37.500	0.00	0.00	0.00	2.71
2135	9441	5.416271	ACTATCCTAACAACACCGAACAT	57.584	39.130	0.00	0.00	0.00	2.71
2140	9446	7.385752	TGTTCTAAAACTATCCTAACAACACCG	59.614	37.037	0.00	0.00	36.30	4.94
2257	9565	5.841957	AGTTTCAATTGCTGTTGAGAGTT	57.158	34.783	0.00	0.00	39.13	3.01
2338	9649	2.190161	GCATGCGTATAACGTGTGAGA	58.810	47.619	0.00	0.00	44.73	3.27
2408	9740	1.398390	GTAAAGACAAGAGCATGCGGG	59.602	52.381	13.01	5.73	0.00	6.13
2508	10011	0.823356	TGCTTGGAGCCTTGAACCAC	60.823	55.000	0.00	0.00	41.51	4.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.