AutoCloner

Multiple sequence alignment - TraesCS1D01G132500

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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	TraesCS1D01G132500	chr1D	100.000	2366	0	0	1	2366	157725310	157727675	0.000000e+00	4370.0
1	TraesCS1D01G132500	chr1D	89.837	1289	117	7	1	1287	223721887	223723163	0.000000e+00	1642.0
2	TraesCS1D01G132500	chr1D	93.901	951	53	4	1	949	393448656	393449603	0.000000e+00	1430.0
3	TraesCS1D01G132500	chr1D	83.222	900	144	6	513	1409	10299488	10300383	0.000000e+00	819.0
4	TraesCS1D01G132500	chr1D	93.187	455	30	1	946	1399	393472598	393473052	0.000000e+00	667.0
5	TraesCS1D01G132500	chr1D	83.205	518	79	8	1	514	10298251	10298764	3.560000e-128	468.0
6	TraesCS1D01G132500	chr1A	90.299	2371	196	15	1	2366	224970525	224972866	0.000000e+00	3073.0
7	TraesCS1D01G132500	chr3D	92.583	1173	84	3	239	1410	474588536	474589706	0.000000e+00	1681.0
8	TraesCS1D01G132500	chr1B	89.760	1289	128	4	1	1287	323258469	323259755	0.000000e+00	1646.0
9	TraesCS1D01G132500	chr1B	93.909	591	35	1	806	1395	654214764	654215354	0.000000e+00	891.0
10	TraesCS1D01G132500	chr3A	82.609	1403	236	8	1	1399	737236567	737237965	0.000000e+00	1232.0
11	TraesCS1D01G132500	chr5B	91.975	785	59	4	626	1408	690873044	690872262	0.000000e+00	1098.0
12	TraesCS1D01G132500	chr5B	84.473	702	98	9	1673	2366	511677957	511677259	0.000000e+00	682.0
13	TraesCS1D01G132500	chr5B	91.250	480	40	2	4	483	690873808	690873331	0.000000e+00	652.0
14	TraesCS1D01G132500	chr5B	93.960	298	16	2	623	920	690873330	690873035	1.290000e-122	449.0
15	TraesCS1D01G132500	chr5B	83.212	137	22	1	1467	1602	511678232	511678096	8.880000e-25	124.0
16	TraesCS1D01G132500	chr6A	93.128	553	37	1	848	1399	613614495	613613943	0.000000e+00	809.0
17	TraesCS1D01G132500	chr3B	81.507	146	23	4	2145	2287	216005620	216005764	1.490000e-22	117.0
18	TraesCS1D01G132500	chr5A	85.135	74	11	0	2270	2343	690025570	690025643	2.520000e-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	TraesCS1D01G132500	chr1D	157725310	157727675	2365	False	4370.0	4370	100.0000	1	2366	1	chr1D.!!$F1	2365
1	TraesCS1D01G132500	chr1D	223721887	223723163	1276	False	1642.0	1642	89.8370	1	1287	1	chr1D.!!$F2	1286
2	TraesCS1D01G132500	chr1D	393448656	393449603	947	False	1430.0	1430	93.9010	1	949	1	chr1D.!!$F3	948
3	TraesCS1D01G132500	chr1D	10298251	10300383	2132	False	643.5	819	83.2135	1	1409	2	chr1D.!!$F5	1408
4	TraesCS1D01G132500	chr1A	224970525	224972866	2341	False	3073.0	3073	90.2990	1	2366	1	chr1A.!!$F1	2365
5	TraesCS1D01G132500	chr3D	474588536	474589706	1170	False	1681.0	1681	92.5830	239	1410	1	chr3D.!!$F1	1171
6	TraesCS1D01G132500	chr1B	323258469	323259755	1286	False	1646.0	1646	89.7600	1	1287	1	chr1B.!!$F1	1286
7	TraesCS1D01G132500	chr1B	654214764	654215354	590	False	891.0	891	93.9090	806	1395	1	chr1B.!!$F2	589
8	TraesCS1D01G132500	chr3A	737236567	737237965	1398	False	1232.0	1232	82.6090	1	1399	1	chr3A.!!$F1	1398
9	TraesCS1D01G132500	chr5B	690872262	690873808	1546	True	733.0	1098	92.3950	4	1408	3	chr5B.!!$R2	1404
10	TraesCS1D01G132500	chr5B	511677259	511678232	973	True	403.0	682	83.8425	1467	2366	2	chr5B.!!$R1	899
11	TraesCS1D01G132500	chr6A	613613943	613614495	552	True	809.0	809	93.1280	848	1399	1	chr6A.!!$R1	551

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
388	389	1.271926	GGGTCTACACCATTGGCAGTT	60.272	52.381	1.54	0.0	45.94	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1671	2758	0.035152	TGCATTCACGGAAGCTGGAT	60.035	50.0	0.0	0.0	0.0	3.41	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
52	53	8.361889	GGAGAATTGGAACTAGAGATAAGGTAC	58.638	40.741	0.00	0.00	0.00	3.34
128	129	7.121759	CACTCCAAGAGGTCAAACAATCATTAT	59.878	37.037	0.00	0.00	33.35	1.28
131	132	7.669304	TCCAAGAGGTCAAACAATCATTATGAA	59.331	33.333	0.00	0.00	35.89	2.57
192	193	5.295540	GGATGAAGCCTTGATTACAGAGTTC	59.704	44.000	0.00	0.00	0.00	3.01
197	198	7.604164	TGAAGCCTTGATTACAGAGTTCTTTAG	59.396	37.037	0.00	0.00	0.00	1.85
200	201	7.038658	AGCCTTGATTACAGAGTTCTTTAGTCT	60.039	37.037	1.33	0.00	36.99	3.24
250	251	7.938490	AGATTCCATTACATTTGCAAGGTTTTT	59.062	29.630	10.56	0.00	0.00	1.94
388	389	1.271926	GGGTCTACACCATTGGCAGTT	60.272	52.381	1.54	0.00	45.94	3.16
389	390	2.026636	GGGTCTACACCATTGGCAGTTA	60.027	50.000	1.54	0.00	45.94	2.24
504	506	9.988815	ACTTGCTAATAGACATATAGGTTCAAG	57.011	33.333	0.00	0.00	0.00	3.02
529	1257	3.554129	GGGCTTGTCCAATTTGTAACCAC	60.554	47.826	0.00	0.00	36.21	4.16
591	1319	3.194005	TGCGAAGGAATTATGGAGGAC	57.806	47.619	0.00	0.00	0.00	3.85
666	1394	8.138712	TGGTTCGGCAATATTTGAATTTATACC	58.861	33.333	0.00	0.00	0.00	2.73
754	1482	3.251484	AGGGTGGTATCTATGGTGGATG	58.749	50.000	0.00	0.00	0.00	3.51
761	1489	4.780021	GGTATCTATGGTGGATGTGGAGAT	59.220	45.833	0.00	0.00	0.00	2.75
810	1538	1.377725	CATGGAAGTGGCCGCTCTT	60.378	57.895	21.49	13.26	0.00	2.85
894	1626	3.278574	CAAAATGGTCTAAGCCCGATCA	58.721	45.455	0.00	0.00	0.00	2.92
928	1943	2.622942	ACTCAATGTGGATGCAACGTTT	59.377	40.909	0.00	0.00	0.00	3.60
957	1973	2.557869	TGAAGGTGTAGGGGCTACAAT	58.442	47.619	0.00	0.00	46.55	2.71
1162	2179	2.096248	GTCAAACAACTTGGTGGGACA	58.904	47.619	6.90	0.00	35.56	4.02
1163	2180	2.693074	GTCAAACAACTTGGTGGGACAT	59.307	45.455	6.90	0.00	35.29	3.06
1171	2188	4.120331	GGTGGGACATTGCAGCGC	62.120	66.667	0.00	0.00	44.52	5.92
1181	2198	2.561549	ATTGCAGCGCCCATTTTCGG	62.562	55.000	2.29	0.00	0.00	4.30
1212	2229	9.031537	TGTCTAGACACTAGTAATTCAATTGGA	57.968	33.333	21.74	0.00	36.21	3.53
1401	2419	1.450312	CATGACGGCCTTCCCTCAC	60.450	63.158	6.80	0.00	0.00	3.51
1402	2420	1.613630	ATGACGGCCTTCCCTCACT	60.614	57.895	6.80	0.00	0.00	3.41
1409	2427	2.437413	GGCCTTCCCTCACTAAAACAG	58.563	52.381	0.00	0.00	0.00	3.16
1435	2453	7.658261	CCACAACCGATCAGATTTAGTATCTA	58.342	38.462	0.00	0.00	0.00	1.98
1436	2454	8.307483	CCACAACCGATCAGATTTAGTATCTAT	58.693	37.037	0.00	0.00	0.00	1.98
1437	2455	9.698309	CACAACCGATCAGATTTAGTATCTATT	57.302	33.333	0.00	0.00	0.00	1.73
1476	2494	2.171659	TGTTCCAATAAGGGCGCTGATA	59.828	45.455	7.64	0.00	38.24	2.15
1479	2497	2.371841	TCCAATAAGGGCGCTGATATGT	59.628	45.455	7.64	0.00	38.24	2.29
1500	2518	3.371063	GGTCGACCGGCAGAGTCA	61.371	66.667	20.85	0.00	33.70	3.41
1501	2519	2.711922	GGTCGACCGGCAGAGTCAT	61.712	63.158	20.85	0.00	33.70	3.06
1535	2553	3.748048	CACTGTGTTCGTTGGATTCATCT	59.252	43.478	0.00	0.00	0.00	2.90
1588	2606	2.852449	TCGTTGGGTCATGCAAAACTA	58.148	42.857	0.00	0.00	0.00	2.24
1604	2648	1.375523	CTAAACCCGCTGAACGCCT	60.376	57.895	0.00	0.00	41.76	5.52
1644	2688	3.472283	TGTGTTTTCTTTGCCATGCAT	57.528	38.095	0.00	0.00	38.76	3.96
1671	2758	1.740332	TTCCTCGTTGACTCGCCACA	61.740	55.000	0.00	0.00	0.00	4.17
1714	2804	3.813143	CGTGGCCGCATTGCATCA	61.813	61.111	18.18	0.61	0.00	3.07
1729	2819	0.943673	CATCACCGTTGCAAGTCACA	59.056	50.000	0.00	0.00	0.00	3.58
1821	2911	3.304257	CGCATGCTTTTCTTGTCAGAGTT	60.304	43.478	17.13	0.00	0.00	3.01
1850	2940	4.424711	GCTCCGGTGAATGCCCCA	62.425	66.667	7.92	0.00	0.00	4.96
1859	2949	0.339162	TGAATGCCCCATCCACCATT	59.661	50.000	0.00	0.00	0.00	3.16
1861	2951	0.043032	AATGCCCCATCCACCATTGT	59.957	50.000	0.00	0.00	0.00	2.71
1938	3029	4.830765	GCCCGTCGTAGCATGGCA	62.831	66.667	3.43	0.00	41.76	4.92
2025	3116	4.284490	TCATCTTCCCGATAGCAGCTTATT	59.716	41.667	0.00	0.00	0.00	1.40
2069	3161	1.952296	CACAGGAAACAGCTCAGCTTT	59.048	47.619	0.00	0.00	36.40	3.51
2072	3164	2.620115	CAGGAAACAGCTCAGCTTTTGA	59.380	45.455	0.00	0.00	36.40	2.69
2079	3171	0.957362	GCTCAGCTTTTGAAGTGGCT	59.043	50.000	0.00	0.00	34.81	4.75
2080	3172	2.154462	GCTCAGCTTTTGAAGTGGCTA	58.846	47.619	0.00	0.00	34.81	3.93
2082	3174	2.154462	TCAGCTTTTGAAGTGGCTAGC	58.846	47.619	6.04	6.04	33.43	3.42
2115	3207	4.569023	CGCCGGTCGCATCTAGCA	62.569	66.667	1.90	0.00	46.13	3.49
2132	3224	1.582968	CAAGAGCGGTTGCAGCATT	59.417	52.632	2.05	0.00	46.23	3.56
2140	3232	1.069427	GTTGCAGCATTTGGTGGCA	59.931	52.632	11.35	7.19	43.24	4.92
2142	3234	2.431260	GCAGCATTTGGTGGCACG	60.431	61.111	12.17	0.00	43.24	5.34
2171	3263	0.040058	TGGTCACCGCCCTTAGTAGA	59.960	55.000	0.00	0.00	0.00	2.59
2174	3266	2.027837	GGTCACCGCCCTTAGTAGAAAA	60.028	50.000	0.00	0.00	0.00	2.29
2175	3267	3.557686	GGTCACCGCCCTTAGTAGAAAAA	60.558	47.826	0.00	0.00	0.00	1.94
2244	3337	3.171828	ATGGTCACCGCGGTCACAA	62.172	57.895	33.44	24.83	0.00	3.33
2246	3339	2.586635	GTCACCGCGGTCACAACA	60.587	61.111	31.80	5.04	0.00	3.33
2248	3341	2.892914	CACCGCGGTCACAACACA	60.893	61.111	31.80	0.00	0.00	3.72
2276	3369	2.825861	AAAAATGCTGCAGGTTCCAG	57.174	45.000	17.12	0.00	0.00	3.86
2306	3399	2.434185	GCGGTTGCACCATCGAGA	60.434	61.111	0.00	0.00	38.47	4.04

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
45	46	4.224370	GGGTCTCTCCAAATGTGTACCTTA	59.776	45.833	0.00	0.00	38.11	2.69
52	53	2.025981	TCCATGGGTCTCTCCAAATGTG	60.026	50.000	13.02	0.00	40.62	3.21
128	129	8.620416	CCGGATCAATTAATTCACATACTTTCA	58.380	33.333	0.00	0.00	0.00	2.69
131	132	8.519799	AACCGGATCAATTAATTCACATACTT	57.480	30.769	9.46	0.00	0.00	2.24
192	193	3.926616	ACGAACATCCACCAGACTAAAG	58.073	45.455	0.00	0.00	0.00	1.85
197	198	3.587797	TTCTACGAACATCCACCAGAC	57.412	47.619	0.00	0.00	0.00	3.51
200	201	5.657474	GAAGTATTCTACGAACATCCACCA	58.343	41.667	0.00	0.00	43.23	4.17
250	251	2.295909	GTGCCAAGCAATAAAGTCACCA	59.704	45.455	0.00	0.00	41.47	4.17
388	389	7.665559	ACTTGAAGCTTCCATAGTGTTTTCATA	59.334	33.333	23.42	0.00	0.00	2.15
389	390	6.491403	ACTTGAAGCTTCCATAGTGTTTTCAT	59.509	34.615	23.42	0.00	0.00	2.57
504	506	1.047801	ACAAATTGGACAAGCCCCAC	58.952	50.000	0.00	0.00	34.97	4.61
666	1394	2.012673	GCTGCTGGTCTGGTAAAGATG	58.987	52.381	0.00	0.00	37.23	2.90
761	1489	6.570186	GGAATTGCTTCATTATGTGTCACACA	60.570	38.462	14.37	14.37	39.74	3.72
957	1973	6.603599	ACCTCTATCATCACGCATAATAGCTA	59.396	38.462	0.00	0.00	0.00	3.32
1040	2057	1.381928	ATCTCGCATGGCCAAAGCTG	61.382	55.000	25.34	19.56	39.73	4.24
1162	2179	1.153784	CGAAAATGGGCGCTGCAAT	60.154	52.632	7.64	0.00	0.00	3.56
1163	2180	2.257980	CGAAAATGGGCGCTGCAA	59.742	55.556	7.64	0.00	0.00	4.08
1171	2188	4.811557	GTCTAGACATTCTCCGAAAATGGG	59.188	45.833	18.20	0.00	38.23	4.00
1212	2229	7.807907	CGATAACAGTGCTTAAAAATGACCTTT	59.192	33.333	0.00	0.00	0.00	3.11
1337	2355	4.792521	AGGCTTACATCGTCTATGATCC	57.207	45.455	0.00	0.00	39.07	3.36
1388	2406	1.271163	TGTTTTAGTGAGGGAAGGCCG	60.271	52.381	0.00	0.00	33.83	6.13
1401	2419	2.811431	TGATCGGTTGTGGCTGTTTTAG	59.189	45.455	0.00	0.00	0.00	1.85
1402	2420	2.811431	CTGATCGGTTGTGGCTGTTTTA	59.189	45.455	0.00	0.00	0.00	1.52
1409	2427	3.270877	ACTAAATCTGATCGGTTGTGGC	58.729	45.455	0.42	0.00	0.00	5.01
1451	2469	2.427095	AGCGCCCTTATTGGAACATTTC	59.573	45.455	2.29	0.00	39.30	2.17
1452	2470	2.166254	CAGCGCCCTTATTGGAACATTT	59.834	45.455	2.29	0.00	39.30	2.32
1453	2471	1.750778	CAGCGCCCTTATTGGAACATT	59.249	47.619	2.29	0.00	39.30	2.71
1454	2472	1.064758	TCAGCGCCCTTATTGGAACAT	60.065	47.619	2.29	0.00	39.30	2.71
1455	2473	0.326595	TCAGCGCCCTTATTGGAACA	59.673	50.000	2.29	0.00	38.35	3.18
1456	2474	1.680338	ATCAGCGCCCTTATTGGAAC	58.320	50.000	2.29	0.00	38.35	3.62
1494	2512	1.617947	GGGACCAGCGGAATGACTCT	61.618	60.000	1.50	0.00	0.00	3.24
1500	2518	2.224159	ACAGTGGGACCAGCGGAAT	61.224	57.895	0.00	0.00	0.00	3.01
1501	2519	2.847234	ACAGTGGGACCAGCGGAA	60.847	61.111	0.00	0.00	0.00	4.30
1535	2553	3.744214	GCCAGATCCAACATTCACGGATA	60.744	47.826	0.00	0.00	39.68	2.59
1624	2668	2.975732	TGCATGGCAAAGAAAACACA	57.024	40.000	0.00	0.00	34.76	3.72
1630	2674	2.545537	TTGCAATGCATGGCAAAGAA	57.454	40.000	34.14	15.95	46.11	2.52
1644	2688	2.612212	GAGTCAACGAGGAAAGTTGCAA	59.388	45.455	0.00	0.00	46.06	4.08
1671	2758	0.035152	TGCATTCACGGAAGCTGGAT	60.035	50.000	0.00	0.00	0.00	3.41
1714	2804	0.107897	TGACTGTGACTTGCAACGGT	60.108	50.000	0.00	0.00	0.00	4.83
1812	2902	1.069090	GGGCGTCACAACTCTGACA	59.931	57.895	0.00	0.00	40.67	3.58
1838	2928	3.939564	GTGGATGGGGCATTCACC	58.060	61.111	0.00	0.00	42.71	4.02
1850	2940	0.179045	GGCGAGCTACAATGGTGGAT	60.179	55.000	0.00	0.00	0.00	3.41
1923	3014	1.490693	GACATGCCATGCTACGACGG	61.491	60.000	4.17	0.00	0.00	4.79
1938	3029	0.613260	TTTGCTGGGACTAGCGACAT	59.387	50.000	3.23	0.00	46.61	3.06
1967	3058	0.243907	GAGACAGCAAGCTACGACCA	59.756	55.000	0.00	0.00	0.00	4.02
2069	3161	0.108329	GCTACGGCTAGCCACTTCAA	60.108	55.000	32.47	10.11	39.79	2.69
2082	3174	1.226717	GCGACCTCAGAAGCTACGG	60.227	63.158	0.00	0.00	0.00	4.02
2115	3207	0.038892	CAAATGCTGCAACCGCTCTT	60.039	50.000	6.36	0.00	39.64	2.85
2132	3224	2.515057	GTGACCACGTGCCACCAA	60.515	61.111	21.36	0.00	0.00	3.67
2140	3232	3.148963	TGACCACGGTGACCACGT	61.149	61.111	10.28	0.00	46.82	4.49
2174	3266	2.959507	GCTGGAACCGGCATAATTTT	57.040	45.000	18.38	0.00	46.81	1.82
2304	3397	2.959484	CGTGGTGACCATGCCCTCT	61.959	63.158	11.41	0.00	35.28	3.69
2306	3399	4.033776	CCGTGGTGACCATGCCCT	62.034	66.667	18.31	0.00	39.07	5.19

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.