AutoCloner

Multiple sequence alignment - TraesCS4D01G229900

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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	TraesCS4D01G229900	chr4D	100.000	3323	0	0	1	3323	389493935	389497257	0.000000e+00	6137.0
1	TraesCS4D01G229900	chr4B	94.931	1874	76	8	550	2408	479397605	479399474	0.000000e+00	2916.0
2	TraesCS4D01G229900	chr4B	88.991	327	26	6	2682	3003	479401053	479401374	2.400000e-106	396.0
3	TraesCS4D01G229900	chr4B	87.311	331	15	6	2996	3322	479401780	479402087	1.470000e-93	353.0
4	TraesCS4D01G229900	chr4B	84.868	152	11	5	2534	2683	479400830	479400971	3.460000e-30	143.0
5	TraesCS4D01G229900	chr4A	93.031	2009	55	24	550	2518	71165716	71167679	0.000000e+00	2856.0
6	TraesCS4D01G229900	chr4A	89.937	795	65	11	2537	3322	71168792	71169580	0.000000e+00	1011.0
7	TraesCS4D01G229900	chr4A	94.444	36	2	0	1	36	647654065	647654030	4.630000e-04	56.5
8	TraesCS4D01G229900	chr1D	97.105	380	8	2	1	380	28216482	28216858	3.620000e-179	638.0
9	TraesCS4D01G229900	chr1D	96.000	150	6	0	400	549	28216850	28216999	9.210000e-61	244.0
10	TraesCS4D01G229900	chr2D	84.946	558	33	13	1	540	650645321	650644797	4.910000e-143	518.0
11	TraesCS4D01G229900	chr2D	83.871	558	39	13	1	540	75268646	75269170	4.980000e-133	484.0
12	TraesCS4D01G229900	chr2D	82.857	210	16	9	97	294	622866163	622865962	1.590000e-38	171.0
13	TraesCS4D01G229900	chr5D	83.424	549	42	19	1	540	483792793	483793301	6.490000e-127	464.0
14	TraesCS4D01G229900	chr5D	82.857	210	16	9	97	294	505951126	505951327	1.590000e-38	171.0
15	TraesCS4D01G229900	chr7D	84.483	232	29	7	1060	1289	160629081	160629307	4.310000e-54	222.0
16	TraesCS4D01G229900	chr7B	81.716	268	37	11	1029	1289	121883790	121884052	2.600000e-51	213.0
17	TraesCS4D01G229900	chr7A	82.833	233	32	7	1059	1289	161732265	161732491	5.620000e-48	202.0
18	TraesCS4D01G229900	chr3B	78.816	321	44	14	258	557	16461311	16461628	9.410000e-46	195.0
19	TraesCS4D01G229900	chr3B	94.872	39	2	0	1076	1114	543582014	543582052	9.950000e-06	62.1
20	TraesCS4D01G229900	chr5B	83.575	207	15	9	97	294	6972811	6973007	3.410000e-40	176.0
21	TraesCS4D01G229900	chr6B	78.802	217	37	8	1078	1290	197247799	197247588	1.610000e-28	137.0
22	TraesCS4D01G229900	chr5A	77.632	228	39	10	1063	1290	119028946	119028731	9.680000e-26	128.0
23	TraesCS4D01G229900	chr6A	77.193	228	40	10	1063	1290	412854395	412854180	4.500000e-24	122.0

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	TraesCS4D01G229900	chr4D	389493935	389497257	3322	False	6137.0	6137	100.00000	1	3323	1	chr4D.!!$F1	3322
1	TraesCS4D01G229900	chr4B	479397605	479402087	4482	False	952.0	2916	89.02525	550	3322	4	chr4B.!!$F1	2772
2	TraesCS4D01G229900	chr4A	71165716	71169580	3864	False	1933.5	2856	91.48400	550	3322	2	chr4A.!!$F1	2772
3	TraesCS4D01G229900	chr1D	28216482	28216999	517	False	441.0	638	96.55250	1	549	2	chr1D.!!$F1	548
4	TraesCS4D01G229900	chr2D	650644797	650645321	524	True	518.0	518	84.94600	1	540	1	chr2D.!!$R2	539
5	TraesCS4D01G229900	chr2D	75268646	75269170	524	False	484.0	484	83.87100	1	540	1	chr2D.!!$F1	539
6	TraesCS4D01G229900	chr5D	483792793	483793301	508	False	464.0	464	83.42400	1	540	1	chr5D.!!$F1	539

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	Hairpin	End Stability	Orientation
397	416	0.108615	AGAGCGACGGTGAATCTTGG	60.109	55.0	3.31	0.00	3.61	F
644	703	0.315568	CTGCGCATAGGTAGGTCCTC	59.684	60.0	12.24	44.42	3.71	F
937	1029	0.749049	TGCTCCATCGTCTCCATCAG	59.251	55.0	0.00	0.00	2.90	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1447	1548	1.380650	GGTTCCTCTCGCTCTCCCT	60.381	63.158	0.00	0.00	4.20	R
1609	1710	1.694169	ATCCCAAGATCCTGGCGGT	60.694	57.895	4.66	34.88	5.68	R
2518	2794	2.036475	TCAAGCAGCGGGAAGATCTATC	59.964	50.000	0.00	0.00	2.08	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
30	31	0.981183	TATGGCAACTGTTCCCGACT	59.019	50.000	0.00	0.00	37.61	4.18
226	245	2.423185	CTGTGCGAGAGAGAAGAGACAT	59.577	50.000	0.00	0.00	0.00	3.06
255	274	7.010160	AGAAAATAACTGTTTTCCATGGAGGA	58.990	34.615	15.53	5.11	45.01	3.71
371	390	9.965824	GTGAGAGAGAAAAATAATTGTTTTCCA	57.034	29.630	12.58	7.01	43.13	3.53
373	392	9.631452	GAGAGAGAAAAATAATTGTTTTCCAGG	57.369	33.333	12.58	0.00	43.13	4.45
374	393	9.367160	AGAGAGAAAAATAATTGTTTTCCAGGA	57.633	29.630	12.58	0.00	43.13	3.86
375	394	9.631452	GAGAGAAAAATAATTGTTTTCCAGGAG	57.369	33.333	12.58	0.00	43.13	3.69
376	395	9.367160	AGAGAAAAATAATTGTTTTCCAGGAGA	57.633	29.630	12.58	0.00	43.13	3.71
377	396	9.631452	GAGAAAAATAATTGTTTTCCAGGAGAG	57.369	33.333	12.58	0.00	43.13	3.20
378	397	9.367160	AGAAAAATAATTGTTTTCCAGGAGAGA	57.633	29.630	12.58	0.00	43.13	3.10
379	398	9.631452	GAAAAATAATTGTTTTCCAGGAGAGAG	57.369	33.333	12.58	0.00	38.49	3.20
380	399	8.940397	AAAATAATTGTTTTCCAGGAGAGAGA	57.060	30.769	7.06	0.00	0.00	3.10
381	400	8.572855	AAATAATTGTTTTCCAGGAGAGAGAG	57.427	34.615	0.00	0.00	0.00	3.20
382	401	3.409026	TTGTTTTCCAGGAGAGAGAGC	57.591	47.619	0.00	0.00	0.00	4.09
383	402	1.273606	TGTTTTCCAGGAGAGAGAGCG	59.726	52.381	0.00	0.00	0.00	5.03
384	403	1.546476	GTTTTCCAGGAGAGAGAGCGA	59.454	52.381	0.00	0.00	0.00	4.93
385	404	1.178276	TTTCCAGGAGAGAGAGCGAC	58.822	55.000	0.00	0.00	0.00	5.19
386	405	1.027255	TTCCAGGAGAGAGAGCGACG	61.027	60.000	0.00	0.00	0.00	5.12
387	406	2.477176	CCAGGAGAGAGAGCGACGG	61.477	68.421	0.00	0.00	0.00	4.79
388	407	1.747367	CAGGAGAGAGAGCGACGGT	60.747	63.158	0.00	0.00	0.00	4.83
389	408	1.747367	AGGAGAGAGAGCGACGGTG	60.747	63.158	3.31	0.00	0.00	4.94
390	409	1.745864	GGAGAGAGAGCGACGGTGA	60.746	63.158	3.31	0.00	0.00	4.02
391	410	1.306642	GGAGAGAGAGCGACGGTGAA	61.307	60.000	3.31	0.00	0.00	3.18
392	411	0.736053	GAGAGAGAGCGACGGTGAAT	59.264	55.000	3.31	0.00	0.00	2.57
393	412	0.736053	AGAGAGAGCGACGGTGAATC	59.264	55.000	3.31	0.00	0.00	2.52
394	413	0.736053	GAGAGAGCGACGGTGAATCT	59.264	55.000	3.31	4.96	0.00	2.40
395	414	1.133407	GAGAGAGCGACGGTGAATCTT	59.867	52.381	3.31	0.00	0.00	2.40
396	415	1.135257	AGAGAGCGACGGTGAATCTTG	60.135	52.381	3.31	0.00	0.00	3.02
397	416	0.108615	AGAGCGACGGTGAATCTTGG	60.109	55.000	3.31	0.00	0.00	3.61
398	417	1.079127	AGCGACGGTGAATCTTGGG	60.079	57.895	0.00	0.00	0.00	4.12
549	596	5.128991	CCCGGGTTCTAAAAATCTAGTCTCT	59.871	44.000	14.18	0.00	0.00	3.10
550	597	6.351966	CCCGGGTTCTAAAAATCTAGTCTCTT	60.352	42.308	14.18	0.00	0.00	2.85
551	598	7.104290	CCGGGTTCTAAAAATCTAGTCTCTTT	58.896	38.462	0.00	0.00	0.00	2.52
552	599	7.606839	CCGGGTTCTAAAAATCTAGTCTCTTTT	59.393	37.037	0.00	0.00	0.00	2.27
553	600	8.657729	CGGGTTCTAAAAATCTAGTCTCTTTTC	58.342	37.037	0.00	0.00	0.00	2.29
597	644	0.874390	TGATCACGTTGCTTTGCTCC	59.126	50.000	0.00	0.00	0.00	4.70
629	676	1.746615	ATGCTGGCACCTAACTGCG	60.747	57.895	0.00	0.00	38.12	5.18
633	680	0.461870	CTGGCACCTAACTGCGCATA	60.462	55.000	12.24	0.00	38.12	3.14
644	703	0.315568	CTGCGCATAGGTAGGTCCTC	59.684	60.000	12.24	0.00	44.42	3.71
664	723	7.649705	GGTCCTCAAATCAAAAGAAAAGAGAAC	59.350	37.037	0.00	0.00	0.00	3.01
750	809	4.777366	CCCCCTTTTCATTCAAACATAGGT	59.223	41.667	0.00	0.00	0.00	3.08
804	864	1.741145	CCCGATTCAAACCTTTACCCG	59.259	52.381	0.00	0.00	0.00	5.28
937	1029	0.749049	TGCTCCATCGTCTCCATCAG	59.251	55.000	0.00	0.00	0.00	2.90
977	1072	2.127708	CCTAGCCATCACCTACCCTTT	58.872	52.381	0.00	0.00	0.00	3.11
1634	1735	3.038417	GATCTTGGGATCGCCGCG	61.038	66.667	6.39	6.39	38.91	6.46
1751	1852	1.434696	GAGCATGCACGGATTTGGG	59.565	57.895	21.98	0.00	0.00	4.12
1754	1855	2.361104	ATGCACGGATTTGGGCGT	60.361	55.556	0.00	0.00	0.00	5.68
1758	1859	1.953017	CACGGATTTGGGCGTGAAA	59.047	52.632	0.00	0.00	34.68	2.69
2151	2252	0.739462	CAGCGACGAAATGCCTGGTA	60.739	55.000	0.00	0.00	0.00	3.25
2209	2310	2.598394	TCTTGCAGGTTGGCTGCC	60.598	61.111	12.87	12.87	46.35	4.85
2270	2371	0.381801	CTCAACAAGCACAAAGGCGT	59.618	50.000	0.00	0.00	39.27	5.68
2310	2411	0.687354	TGGACTTCAGAGGGCTCAAC	59.313	55.000	0.00	0.00	0.00	3.18
2392	2493	5.011533	AGCTAGCAGATTGGTAGGATAGTTG	59.988	44.000	18.83	0.00	45.69	3.16
2518	2794	4.394795	GCTTAAGTACAATGCAACTGTCG	58.605	43.478	7.99	0.00	0.00	4.35
2672	4153	9.825972	ATCTTACTTGTTGAACGAACATAATTG	57.174	29.630	0.00	0.00	44.23	2.32
2875	4439	2.756207	TCACTCGACATCCATCCGTTAA	59.244	45.455	0.00	0.00	0.00	2.01
2953	4521	6.944557	TGATAAAGTGTTGTCGAGTGTATG	57.055	37.500	0.00	0.00	0.00	2.39
2956	4524	7.654116	TGATAAAGTGTTGTCGAGTGTATGAAA	59.346	33.333	0.00	0.00	0.00	2.69
2957	4525	5.907197	AAGTGTTGTCGAGTGTATGAAAG	57.093	39.130	0.00	0.00	0.00	2.62
3016	4998	6.618287	TCAAGTTTGGGCATAATTAGATCG	57.382	37.500	0.00	0.00	0.00	3.69
3064	5046	7.696453	GTCTCACCAAATAATATGTTCAAACCG	59.304	37.037	0.00	0.00	0.00	4.44
3115	5101	8.045507	AGAGATTGCAAGATACCCATGTATATG	58.954	37.037	4.94	0.00	37.80	1.78
3135	5121	1.135199	GGCAGATCAGGCAACAATGTG	60.135	52.381	6.81	0.00	41.41	3.21
3192	5178	8.574737	GTGAATAACTAACATACGGACCTAGAT	58.425	37.037	0.00	0.00	0.00	1.98
3212	5198	6.257994	AGATGAGGAACCATTGATACACAT	57.742	37.500	0.00	0.00	0.00	3.21
3213	5199	6.294473	AGATGAGGAACCATTGATACACATC	58.706	40.000	0.00	0.00	0.00	3.06
3218	5204	5.528690	AGGAACCATTGATACACATCGAATG	59.471	40.000	0.00	0.00	33.76	2.67
3260	5246	3.833650	TGCATCCAATGTTCCAATCAACT	59.166	39.130	0.00	0.00	0.00	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
30	31	4.096003	GCCGGGCCTGACAAGCTA	62.096	66.667	15.09	0.00	0.00	3.32
226	245	7.723616	TCCATGGAAAACAGTTATTTTCTCTCA	59.276	33.333	13.46	2.27	44.54	3.27
371	390	1.747367	CACCGTCGCTCTCTCTCCT	60.747	63.158	0.00	0.00	0.00	3.69
372	391	1.306642	TTCACCGTCGCTCTCTCTCC	61.307	60.000	0.00	0.00	0.00	3.71
373	392	0.736053	ATTCACCGTCGCTCTCTCTC	59.264	55.000	0.00	0.00	0.00	3.20
374	393	0.736053	GATTCACCGTCGCTCTCTCT	59.264	55.000	0.00	0.00	0.00	3.10
375	394	0.736053	AGATTCACCGTCGCTCTCTC	59.264	55.000	0.00	0.00	0.00	3.20
376	395	1.135257	CAAGATTCACCGTCGCTCTCT	60.135	52.381	0.00	0.00	0.00	3.10
377	396	1.272781	CAAGATTCACCGTCGCTCTC	58.727	55.000	0.00	0.00	0.00	3.20
378	397	0.108615	CCAAGATTCACCGTCGCTCT	60.109	55.000	0.00	0.00	0.00	4.09
379	398	1.084370	CCCAAGATTCACCGTCGCTC	61.084	60.000	0.00	0.00	0.00	5.03
380	399	1.079127	CCCAAGATTCACCGTCGCT	60.079	57.895	0.00	0.00	0.00	4.93
381	400	1.079405	TCCCAAGATTCACCGTCGC	60.079	57.895	0.00	0.00	0.00	5.19
382	401	0.460284	CCTCCCAAGATTCACCGTCG	60.460	60.000	0.00	0.00	0.00	5.12
383	402	0.902531	TCCTCCCAAGATTCACCGTC	59.097	55.000	0.00	0.00	0.00	4.79
384	403	0.905357	CTCCTCCCAAGATTCACCGT	59.095	55.000	0.00	0.00	0.00	4.83
385	404	1.137872	CTCTCCTCCCAAGATTCACCG	59.862	57.143	0.00	0.00	0.00	4.94
386	405	2.433970	CTCTCTCCTCCCAAGATTCACC	59.566	54.545	0.00	0.00	0.00	4.02
387	406	3.103742	ACTCTCTCCTCCCAAGATTCAC	58.896	50.000	0.00	0.00	0.00	3.18
388	407	3.102972	CACTCTCTCCTCCCAAGATTCA	58.897	50.000	0.00	0.00	0.00	2.57
389	408	3.370104	TCACTCTCTCCTCCCAAGATTC	58.630	50.000	0.00	0.00	0.00	2.52
390	409	3.481559	TCACTCTCTCCTCCCAAGATT	57.518	47.619	0.00	0.00	0.00	2.40
391	410	3.704545	ATCACTCTCTCCTCCCAAGAT	57.295	47.619	0.00	0.00	0.00	2.40
392	411	3.481559	AATCACTCTCTCCTCCCAAGA	57.518	47.619	0.00	0.00	0.00	3.02
393	412	3.517100	TGAAATCACTCTCTCCTCCCAAG	59.483	47.826	0.00	0.00	0.00	3.61
394	413	3.261897	GTGAAATCACTCTCTCCTCCCAA	59.738	47.826	6.30	0.00	43.25	4.12
395	414	2.834549	GTGAAATCACTCTCTCCTCCCA	59.165	50.000	6.30	0.00	43.25	4.37
396	415	3.535280	GTGAAATCACTCTCTCCTCCC	57.465	52.381	6.30	0.00	43.25	4.30
492	539	2.546795	CCTTCTATCAGCACCGTCCATC	60.547	54.545	0.00	0.00	0.00	3.51
549	596	8.360390	GCCTTCTTTCTTCCTTCAAATAGAAAA	58.640	33.333	0.00	0.00	36.50	2.29
550	597	7.039714	GGCCTTCTTTCTTCCTTCAAATAGAAA	60.040	37.037	0.00	0.00	35.40	2.52
551	598	6.434340	GGCCTTCTTTCTTCCTTCAAATAGAA	59.566	38.462	0.00	0.00	34.41	2.10
552	599	5.946377	GGCCTTCTTTCTTCCTTCAAATAGA	59.054	40.000	0.00	0.00	0.00	1.98
553	600	5.711976	TGGCCTTCTTTCTTCCTTCAAATAG	59.288	40.000	3.32	0.00	0.00	1.73
664	723	4.378459	GCCTTACCGATGTTCACTTCTTTG	60.378	45.833	0.00	0.00	0.00	2.77
804	864	1.134189	CAAATAGGGGAGGGAACGGAC	60.134	57.143	0.00	0.00	0.00	4.79
937	1029	1.823899	GGTGGTTCGATGGATGGGC	60.824	63.158	0.00	0.00	0.00	5.36
977	1072	2.187493	CGATCGGCCGAGGAAGAGA	61.187	63.158	33.87	7.83	0.00	3.10
1447	1548	1.380650	GGTTCCTCTCGCTCTCCCT	60.381	63.158	0.00	0.00	0.00	4.20
1604	1705	2.066999	AAGATCCTGGCGGTCTCCC	61.067	63.158	0.00	0.00	0.00	4.30
1609	1710	1.694169	ATCCCAAGATCCTGGCGGT	60.694	57.895	4.66	0.00	34.88	5.68
1751	1852	2.279937	GATGTCGTCGGCTTTCACGC	62.280	60.000	0.00	0.00	35.93	5.34
1754	1855	4.162640	CGATGTCGTCGGCTTTCA	57.837	55.556	6.56	0.00	46.47	2.69
1947	2048	4.008933	AACGCCAGCGCCTTCTCT	62.009	61.111	12.72	0.00	44.19	3.10
2209	2310	2.725203	TTCTCCTTGGTTGCGTCCCG	62.725	60.000	0.00	0.00	0.00	5.14
2265	2366	3.081409	ACGCATTCCCCTACGCCT	61.081	61.111	0.00	0.00	0.00	5.52
2270	2371	2.802792	CGTCGACGCATTCCCCTA	59.197	61.111	26.59	0.00	0.00	3.53
2310	2411	3.144506	AGTTGTGATTCAGGACAGCTTG	58.855	45.455	0.00	0.00	30.29	4.01
2392	2493	6.813649	GCAAAAAGGGAGAAGAATTTACATCC	59.186	38.462	0.00	0.00	0.00	3.51
2456	2729	4.053295	AGTAGCGTTCAAGCGTTTCTAAA	58.947	39.130	0.00	0.00	43.00	1.85
2457	2730	3.645884	AGTAGCGTTCAAGCGTTTCTAA	58.354	40.909	0.00	0.00	43.00	2.10
2458	2731	3.293311	AGTAGCGTTCAAGCGTTTCTA	57.707	42.857	0.00	0.00	43.00	2.10
2501	2777	5.324784	TCTATCGACAGTTGCATTGTACT	57.675	39.130	4.53	0.00	0.00	2.73
2518	2794	2.036475	TCAAGCAGCGGGAAGATCTATC	59.964	50.000	0.00	0.00	0.00	2.08
2860	4424	4.634004	TGAACACATTAACGGATGGATGTC	59.366	41.667	0.00	0.00	30.78	3.06
2895	4459	8.066000	GCATAATAAACTACGGACAAATACCAC	58.934	37.037	0.00	0.00	0.00	4.16
3012	4994	5.788531	CCGTACACTTTTTGAATTCACGATC	59.211	40.000	7.89	0.00	0.00	3.69
3016	4998	4.037089	ACCCCGTACACTTTTTGAATTCAC	59.963	41.667	7.89	0.00	0.00	3.18
3115	5101	1.135199	CACATTGTTGCCTGATCTGCC	60.135	52.381	5.52	0.00	0.00	4.85
3176	5162	4.180377	TCCTCATCTAGGTCCGTATGTT	57.820	45.455	0.00	0.00	46.62	2.71
3192	5178	4.161377	TCGATGTGTATCAATGGTTCCTCA	59.839	41.667	0.00	0.00	32.67	3.86
3200	5186	7.096763	GCATTTGTCATTCGATGTGTATCAATG	60.097	37.037	0.00	0.00	35.49	2.82
3212	5198	1.083489	GGGTCGCATTTGTCATTCGA	58.917	50.000	0.00	0.00	0.00	3.71
3213	5199	0.801872	TGGGTCGCATTTGTCATTCG	59.198	50.000	0.00	0.00	0.00	3.34
3260	5246	1.403814	CCTGAGAATACGGAGCTGGA	58.596	55.000	0.00	0.00	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.