AutoCloner

Multiple sequence alignment - TraesCS2A01G212600

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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	TraesCS2A01G212600	chr2A	100.000	3377	0	0	1	3377	197337112	197333736	0.000000e+00	6237
1	TraesCS2A01G212600	chr2A	95.889	2408	95	3	973	3377	197565456	197563050	0.000000e+00	3895
2	TraesCS2A01G212600	chr2A	89.708	1506	149	3	970	2472	166628814	166630316	0.000000e+00	1917
3	TraesCS2A01G212600	chr2A	95.292	977	40	5	1	972	151962834	151963809	0.000000e+00	1544
4	TraesCS2A01G212600	chr2A	95.277	974	41	5	1	972	572132164	572131194	0.000000e+00	1539
5	TraesCS2A01G212600	chr2A	95.179	975	43	4	1	972	592657560	592658533	0.000000e+00	1537
6	TraesCS2A01G212600	chr2A	87.385	761	72	10	2618	3377	166631166	166631903	0.000000e+00	852
7	TraesCS2A01G212600	chr2A	82.368	397	37	13	2983	3377	447944646	447944281	7.030000e-82	315
8	TraesCS2A01G212600	chr2D	95.328	2333	107	2	973	3304	182575196	182572865	0.000000e+00	3703
9	TraesCS2A01G212600	chr2D	91.307	1507	123	5	970	2472	156708186	156709688	0.000000e+00	2050
10	TraesCS2A01G212600	chr2D	90.839	1430	131	0	970	2399	156593175	156594604	0.000000e+00	1916
11	TraesCS2A01G212600	chr2D	86.597	761	69	11	2618	3377	156710547	156711275	0.000000e+00	809
12	TraesCS2A01G212600	chr2B	90.486	1503	134	5	973	2472	214313661	214315157	0.000000e+00	1975
13	TraesCS2A01G212600	chr2B	90.000	1430	143	0	970	2399	214281860	214283289	0.000000e+00	1849
14	TraesCS2A01G212600	chr2B	86.745	762	69	11	2618	3377	214315993	214316724	0.000000e+00	819
15	TraesCS2A01G212600	chr1A	90.367	1443	132	3	973	2415	90162776	90161341	0.000000e+00	1888
16	TraesCS2A01G212600	chr1A	95.808	978	34	6	1	973	233866386	233867361	0.000000e+00	1572
17	TraesCS2A01G212600	chr1A	95.179	975	43	4	1	972	161767183	161766210	0.000000e+00	1537
18	TraesCS2A01G212600	chr1D	90.298	1443	137	2	973	2415	93104445	93103006	0.000000e+00	1886
19	TraesCS2A01G212600	chr6A	95.608	979	34	6	1	972	475059955	475060931	0.000000e+00	1561
20	TraesCS2A01G212600	chr6A	95.199	979	39	8	1	972	449019604	449020581	0.000000e+00	1541
21	TraesCS2A01G212600	chr6A	95.189	977	39	7	1	972	87616660	87617633	0.000000e+00	1537
22	TraesCS2A01G212600	chr3A	94.646	990	43	8	1	984	424051167	424052152	0.000000e+00	1526

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	TraesCS2A01G212600	chr2A	197333736	197337112	3376	True	6237.0	6237	100.0000	1	3377	1	chr2A.!!$R1	3376
1	TraesCS2A01G212600	chr2A	197563050	197565456	2406	True	3895.0	3895	95.8890	973	3377	1	chr2A.!!$R2	2404
2	TraesCS2A01G212600	chr2A	151962834	151963809	975	False	1544.0	1544	95.2920	1	972	1	chr2A.!!$F1	971
3	TraesCS2A01G212600	chr2A	572131194	572132164	970	True	1539.0	1539	95.2770	1	972	1	chr2A.!!$R4	971
4	TraesCS2A01G212600	chr2A	592657560	592658533	973	False	1537.0	1537	95.1790	1	972	1	chr2A.!!$F2	971
5	TraesCS2A01G212600	chr2A	166628814	166631903	3089	False	1384.5	1917	88.5465	970	3377	2	chr2A.!!$F3	2407
6	TraesCS2A01G212600	chr2D	182572865	182575196	2331	True	3703.0	3703	95.3280	973	3304	1	chr2D.!!$R1	2331
7	TraesCS2A01G212600	chr2D	156593175	156594604	1429	False	1916.0	1916	90.8390	970	2399	1	chr2D.!!$F1	1429
8	TraesCS2A01G212600	chr2D	156708186	156711275	3089	False	1429.5	2050	88.9520	970	3377	2	chr2D.!!$F2	2407
9	TraesCS2A01G212600	chr2B	214281860	214283289	1429	False	1849.0	1849	90.0000	970	2399	1	chr2B.!!$F1	1429
10	TraesCS2A01G212600	chr2B	214313661	214316724	3063	False	1397.0	1975	88.6155	973	3377	2	chr2B.!!$F2	2404
11	TraesCS2A01G212600	chr1A	90161341	90162776	1435	True	1888.0	1888	90.3670	973	2415	1	chr1A.!!$R1	1442
12	TraesCS2A01G212600	chr1A	233866386	233867361	975	False	1572.0	1572	95.8080	1	973	1	chr1A.!!$F1	972
13	TraesCS2A01G212600	chr1A	161766210	161767183	973	True	1537.0	1537	95.1790	1	972	1	chr1A.!!$R2	971
14	TraesCS2A01G212600	chr1D	93103006	93104445	1439	True	1886.0	1886	90.2980	973	2415	1	chr1D.!!$R1	1442
15	TraesCS2A01G212600	chr6A	475059955	475060931	976	False	1561.0	1561	95.6080	1	972	1	chr6A.!!$F3	971
16	TraesCS2A01G212600	chr6A	449019604	449020581	977	False	1541.0	1541	95.1990	1	972	1	chr6A.!!$F2	971
17	TraesCS2A01G212600	chr6A	87616660	87617633	973	False	1537.0	1537	95.1890	1	972	1	chr6A.!!$F1	971
18	TraesCS2A01G212600	chr3A	424051167	424052152	985	False	1526.0	1526	94.6460	1	984	1	chr3A.!!$F1	983

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
537	553	0.106335	TTGGTTTTCGGTGGCTACGA	59.894	50.0	0.00	0.19	38.78	3.43	F
1867	1896	0.397941	CAAGAGTGGCCAGGAAGACA	59.602	55.0	5.11	0.00	0.00	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2249	2278	0.452184	GGTGATCGCGTCTTCTCTCA	59.548	55.0	5.77	0.0	0.0	3.27	R
2978	3764	0.602562	TTTTCTGCAATTCCGGCCAG	59.397	50.0	2.24	0.0	0.0	4.85	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	2.025793	TCAACCAACACAAAGGACCTCA	60.026	45.455	0.00	0.00	0.00	3.86
160	163	8.030692	CACCAAAACATACATCAAGTGAATCAT	58.969	33.333	0.00	0.00	0.00	2.45
311	318	4.352298	GGGAGGAGAAACATAGGATCCAAT	59.648	45.833	15.82	0.00	32.21	3.16
344	351	2.294512	AGCTCGCGATACATCAAGATCA	59.705	45.455	10.36	0.00	0.00	2.92
475	490	2.658285	GATGATGAAGATGGCCACCAA	58.342	47.619	8.16	0.00	36.95	3.67
537	553	0.106335	TTGGTTTTCGGTGGCTACGA	59.894	50.000	0.00	0.19	38.78	3.43
761	785	5.896678	TCTTTCCTTCCAAAAATGAGTTCCA	59.103	36.000	0.00	0.00	0.00	3.53
797	821	6.054941	GTCAATTGGACTCCATTTGGTTTTT	58.945	36.000	23.53	0.00	42.02	1.94
807	831	7.619965	ACTCCATTTGGTTTTTCTTTTCTTCA	58.380	30.769	0.00	0.00	36.34	3.02
873	901	6.275144	TCTGGGTTAATAGGTTAGTCCCAAAA	59.725	38.462	0.00	0.00	41.14	2.44
1074	1103	1.956477	GAATGTCCTTGGTGTGCTTGT	59.044	47.619	0.00	0.00	0.00	3.16
1130	1159	0.530744	CGGCAAGCCAGAGTACACTA	59.469	55.000	12.19	0.00	35.37	2.74
1186	1215	4.856801	ATCGAGGCCGCGGCAATT	62.857	61.111	46.88	32.97	44.11	2.32
1189	1218	2.946762	GAGGCCGCGGCAATTATC	59.053	61.111	46.88	31.14	44.11	1.75
1190	1219	1.598130	GAGGCCGCGGCAATTATCT	60.598	57.895	46.88	34.30	44.11	1.98
1296	1325	3.763356	TGCTCTCCGCACATCGCT	61.763	61.111	0.00	0.00	45.47	4.93
1369	1398	1.805945	GCGCGAGATCAACTCCGTT	60.806	57.895	12.10	0.00	42.18	4.44
1437	1466	2.844451	GCAACTTCCAAGGCACGCA	61.844	57.895	0.00	0.00	0.00	5.24
1471	1500	1.236616	TGGACAACATGAGGCTTGCG	61.237	55.000	0.00	0.00	0.00	4.85
1480	1509	4.962836	AGGCTTGCGGTTGCTGCT	62.963	61.111	0.00	0.00	43.34	4.24
1531	1560	4.576873	TCGGAGCTAGTGAATGACTTCTAG	59.423	45.833	0.00	0.00	35.96	2.43
1543	1572	8.352942	GTGAATGACTTCTAGAACAATGGTTTT	58.647	33.333	0.00	0.00	33.05	2.43
1706	1735	2.606378	ACCAAGACGTTAACTCCCTCT	58.394	47.619	3.71	0.00	0.00	3.69
1707	1736	3.771216	ACCAAGACGTTAACTCCCTCTA	58.229	45.455	3.71	0.00	0.00	2.43
1795	1824	2.025767	TTGCGTTGTGCCAAGCCATT	62.026	50.000	0.00	0.00	45.60	3.16
1800	1829	1.470996	TTGTGCCAAGCCATTGACCC	61.471	55.000	0.00	0.00	38.83	4.46
1867	1896	0.397941	CAAGAGTGGCCAGGAAGACA	59.602	55.000	5.11	0.00	0.00	3.41
1905	1934	3.226242	TGGTCTCCACAACGCACT	58.774	55.556	0.00	0.00	0.00	4.40
2145	2174	0.610687	GTTGAGGCTGCTAGAGGTGT	59.389	55.000	0.00	0.00	0.00	4.16
2190	2219	2.715046	ACCGAACCGTATCACTGACTA	58.285	47.619	0.00	0.00	0.00	2.59
2209	2238	5.222068	TGACTACCGATCATACCCTCTGTAT	60.222	44.000	0.00	0.00	40.91	2.29
2235	2264	2.512515	GCGCGAGGAGCTTGGAAT	60.513	61.111	12.10	0.00	45.59	3.01
2249	2278	3.810743	GCTTGGAATGGTGTACTTGACCT	60.811	47.826	2.84	0.00	34.26	3.85
2263	2292	0.605589	TGACCTGAGAGAAGACGCGA	60.606	55.000	15.93	0.00	0.00	5.87
2319	2348	2.513753	CATGAACCAGGGTAAGCACAA	58.486	47.619	0.00	0.00	0.00	3.33
2343	2372	1.660560	GCGCTGTTGGAATGCCTCAT	61.661	55.000	0.00	0.00	34.31	2.90
2347	2376	2.449464	CTGTTGGAATGCCTCATGGAA	58.551	47.619	0.00	0.00	34.57	3.53
2356	2385	0.394352	GCCTCATGGAATGGAACGGT	60.394	55.000	0.00	0.00	46.73	4.83
2372	2401	0.107703	CGGTGAGCCTTTGCCTATCA	60.108	55.000	0.00	0.00	38.69	2.15
2373	2402	1.475751	CGGTGAGCCTTTGCCTATCAT	60.476	52.381	0.00	0.00	38.69	2.45
2416	2445	4.212143	AGATATGCTGTGCTTCAGAACA	57.788	40.909	12.29	3.82	46.27	3.18
2417	2446	4.778579	AGATATGCTGTGCTTCAGAACAT	58.221	39.130	12.29	9.46	46.27	2.71
2511	2621	1.374631	CCACGCAGCAACTAGAGCA	60.375	57.895	12.97	0.00	0.00	4.26
2516	2626	1.446907	GCAGCAACTAGAGCATGTGT	58.553	50.000	12.97	0.00	0.00	3.72
2702	3484	4.580167	CACTGTCATTTTCTCCAAGTCCAA	59.420	41.667	0.00	0.00	0.00	3.53
2726	3508	0.460311	AACCTCTTCATAGTCCGCCG	59.540	55.000	0.00	0.00	0.00	6.46
2741	3523	2.048597	CCGTGTGCGAGCCTAACA	60.049	61.111	0.00	0.00	41.33	2.41
2761	3543	7.230913	CCTAACAAGATAGCTGCTACTAACCTA	59.769	40.741	12.26	0.05	0.00	3.08
2784	3566	6.361768	AAGGAAAACAAAAACTAACCACCA	57.638	33.333	0.00	0.00	0.00	4.17
2886	3672	3.821033	TCTCACTGTCTTCTGTTCGATCA	59.179	43.478	0.00	0.00	0.00	2.92
2888	3674	4.738124	TCACTGTCTTCTGTTCGATCATC	58.262	43.478	0.00	0.00	0.00	2.92
2978	3764	1.065551	GAAGCATTCGGCCACAATACC	59.934	52.381	2.24	0.00	46.50	2.73
3002	3788	2.676076	CCGGAATTGCAGAAAACCAAG	58.324	47.619	0.00	0.00	0.00	3.61
3039	3825	5.364778	TGTCAGTTAATACGGGGATCAATG	58.635	41.667	0.00	0.00	0.00	2.82
3101	3887	6.036577	TCCTTAAATGGCTGAAACAATTCC	57.963	37.500	0.00	0.00	34.49	3.01
3102	3888	5.541868	TCCTTAAATGGCTGAAACAATTCCA	59.458	36.000	0.00	0.00	34.49	3.53
3143	3929	5.702065	TTGGTAACCATTCCATACAGCTA	57.298	39.130	0.00	0.00	31.53	3.32
3158	3944	2.963101	ACAGCTATGTAAGGCGATACCA	59.037	45.455	0.00	0.00	38.47	3.25
3342	4128	1.526041	GCTACATCATGAGAAGCAGCG	59.474	52.381	17.34	0.00	0.00	5.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
42	43	3.032265	AGAACTTTGGGGCACTCTTTT	57.968	42.857	0.00	0.00	0.00	2.27
311	318	6.153756	TGTATCGCGAGCTTTGCTATTATAA	58.846	36.000	16.66	0.00	39.88	0.98
344	351	3.411446	TCTCGTGTTCTTGATTTGGCAT	58.589	40.909	0.00	0.00	0.00	4.40
634	653	4.316823	ACCCTCGTGAGCCCCTCA	62.317	66.667	0.00	0.00	38.25	3.86
680	702	2.680352	GAGGTCACGAGGCAGGGA	60.680	66.667	0.00	0.00	0.00	4.20
761	785	5.388654	AGTCCAATTGACCTGAAACTTCAT	58.611	37.500	7.12	0.00	45.68	2.57
797	821	7.552459	CCTGTTTTAGGGTTTTGAAGAAAAGA	58.448	34.615	0.00	0.00	43.33	2.52
832	857	0.825010	CAGAGCCCAGTGCCAGTTTT	60.825	55.000	0.00	0.00	42.71	2.43
956	984	2.930887	GCAGCTTGATACGTCTCCAACA	60.931	50.000	0.00	0.00	0.00	3.33
1074	1103	2.088423	ACACGGCTGACAAAACTTCAA	58.912	42.857	0.00	0.00	0.00	2.69
1130	1159	3.884895	TCAACTTGTGTGTCAGATGGTT	58.115	40.909	0.00	0.00	0.00	3.67
1186	1215	2.450886	TCCCTCCAGGATGTGCTAGATA	59.549	50.000	0.00	0.00	40.93	1.98
1189	1218	1.415659	CTTCCCTCCAGGATGTGCTAG	59.584	57.143	0.00	0.00	46.94	3.42
1190	1219	1.500474	CTTCCCTCCAGGATGTGCTA	58.500	55.000	0.00	0.00	46.94	3.49
1251	1280	4.766373	TGTCTTGCTTTGGCTTCATCAATA	59.234	37.500	0.00	0.00	39.59	1.90
1317	1346	1.812922	GCTGCACGGATGACCTCAG	60.813	63.158	0.00	0.00	0.00	3.35
1344	1373	1.134995	AGTTGATCTCGCGCTCAATCA	60.135	47.619	17.40	11.20	34.18	2.57
1369	1398	4.000325	CGTCAATGAGTGGGTTGTCATTA	59.000	43.478	0.00	0.00	40.64	1.90
1437	1466	1.071542	TGTCCATCAACACACCGATGT	59.928	47.619	0.00	0.00	40.80	3.06
1449	1478	2.439409	CAAGCCTCATGTTGTCCATCA	58.561	47.619	0.00	0.00	0.00	3.07
1461	1490	2.979676	CAGCAACCGCAAGCCTCA	60.980	61.111	0.00	0.00	42.27	3.86
1480	1509	3.235157	GCAAACATGAGCTTGCCAATA	57.765	42.857	16.13	0.00	40.15	1.90
1531	1560	3.244078	GGTTGGAGGGAAAACCATTGTTC	60.244	47.826	0.00	0.00	44.41	3.18
1543	1572	4.896979	CCTGAGAGGTTGGAGGGA	57.103	61.111	0.00	0.00	0.00	4.20
1706	1735	2.967201	TCTTCCGGGCCGAGATTAATTA	59.033	45.455	30.79	5.82	0.00	1.40
1707	1736	1.766496	TCTTCCGGGCCGAGATTAATT	59.234	47.619	30.79	0.00	0.00	1.40
1735	1764	1.065926	AGCTTCAGAATGTCGATGGCA	60.066	47.619	0.00	0.00	37.40	4.92
1867	1896	3.760151	CACCCATGTCATTTGTGATCAGT	59.240	43.478	0.00	0.00	0.00	3.41
1924	1953	0.591170	CGCGGTCAATTGTTTGGAGT	59.409	50.000	5.13	0.00	33.44	3.85
2029	2058	4.329545	GCCTCACCGTTGGCCAGA	62.330	66.667	5.11	0.00	43.11	3.86
2121	2150	0.978146	TCTAGCAGCCTCAACCTCCC	60.978	60.000	0.00	0.00	0.00	4.30
2145	2174	1.065926	CAGCAGTGCCATTCTCCACTA	60.066	52.381	12.58	0.00	40.12	2.74
2190	2219	3.082548	CGATACAGAGGGTATGATCGGT	58.917	50.000	0.00	0.00	42.76	4.69
2230	2259	2.976185	TCAGGTCAAGTACACCATTCCA	59.024	45.455	3.88	0.00	36.23	3.53
2235	2264	3.238788	TCTCTCAGGTCAAGTACACCA	57.761	47.619	3.88	0.00	36.23	4.17
2249	2278	0.452184	GGTGATCGCGTCTTCTCTCA	59.548	55.000	5.77	0.00	0.00	3.27
2263	2292	3.216178	ACCTCCTCCCCAGGTGAT	58.784	61.111	0.00	0.00	43.10	3.06
2319	2348	2.357034	ATTCCAACAGCGCGTCGT	60.357	55.556	8.43	1.59	0.00	4.34
2343	2372	1.002624	GGCTCACCGTTCCATTCCA	60.003	57.895	0.00	0.00	0.00	3.53
2347	2376	1.244019	GCAAAGGCTCACCGTTCCAT	61.244	55.000	0.00	0.00	42.76	3.41
2356	2385	5.072193	TGATTAGATGATAGGCAAAGGCTCA	59.928	40.000	0.00	0.00	39.70	4.26
2372	2401	8.780616	TCTTCTCTTCATCTCCTTGATTAGAT	57.219	34.615	0.00	0.00	32.05	1.98
2373	2402	8.780616	ATCTTCTCTTCATCTCCTTGATTAGA	57.219	34.615	0.00	0.00	32.05	2.10
2416	2445	4.961438	AGAAATTGTGGTGCCTTTCAAT	57.039	36.364	0.00	0.00	31.55	2.57
2417	2446	5.860941	TTAGAAATTGTGGTGCCTTTCAA	57.139	34.783	0.00	0.00	31.55	2.69
2511	2621	4.561326	GCCCTTTTGCTTACATCAACACAT	60.561	41.667	0.00	0.00	0.00	3.21
2516	2626	2.961741	TGTGCCCTTTTGCTTACATCAA	59.038	40.909	0.00	0.00	0.00	2.57
2702	3484	4.523558	GGCGGACTATGAAGAGGTTATACT	59.476	45.833	0.00	0.00	0.00	2.12
2726	3508	1.726853	ATCTTGTTAGGCTCGCACAC	58.273	50.000	0.00	0.00	0.00	3.82
2736	3518	7.045126	AGGTTAGTAGCAGCTATCTTGTTAG	57.955	40.000	5.14	0.00	0.00	2.34
2741	3523	6.374588	TCCTTAGGTTAGTAGCAGCTATCTT	58.625	40.000	5.14	0.00	0.00	2.40
2761	3543	6.361768	TGGTGGTTAGTTTTTGTTTTCCTT	57.638	33.333	0.00	0.00	0.00	3.36
2784	3566	9.054922	CCCAATTAATGTTTCTGACACATTTTT	57.945	29.630	22.74	15.47	41.19	1.94
2886	3672	4.613925	TCTCAAGTTCTTCAGCACTGAT	57.386	40.909	0.31	0.00	39.64	2.90
2888	3674	4.125703	ACTTCTCAAGTTCTTCAGCACTG	58.874	43.478	0.00	0.00	39.04	3.66
2917	3703	7.187824	TCTGCTTCTTTGTCAGATACCTTAT	57.812	36.000	0.00	0.00	32.48	1.73
2978	3764	0.602562	TTTTCTGCAATTCCGGCCAG	59.397	50.000	2.24	0.00	0.00	4.85
3002	3788	9.503427	GTATTAACTGACAGGTTTTTGATATGC	57.497	33.333	7.51	0.00	0.00	3.14
3088	3874	6.446318	TGTTAACTCATGGAATTGTTTCAGC	58.554	36.000	7.22	0.00	33.23	4.26
3101	3887	6.728200	ACCAAATGCGATATGTTAACTCATG	58.272	36.000	7.22	0.00	0.00	3.07
3102	3888	6.942532	ACCAAATGCGATATGTTAACTCAT	57.057	33.333	7.22	0.00	0.00	2.90
3158	3944	6.651643	TGTATGTAAGCACTTTTGTAACCGAT	59.348	34.615	0.00	0.00	0.00	4.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.