AutoCloner

Multiple sequence alignment - TraesCS4D01G182900

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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	TraesCS4D01G182900	chr4D	100.000	3305	0	0	1	3305	320027351	320030655	0.000000e+00	6104.0
1	TraesCS4D01G182900	chr4A	93.426	2799	89	31	1	2777	153257261	153254536	0.000000e+00	4061.0
2	TraesCS4D01G182900	chr4A	93.071	534	30	4	2779	3305	153254480	153253947	0.000000e+00	774.0
3	TraesCS4D01G182900	chr4B	94.067	1972	50	21	820	2775	400699610	400697690	0.000000e+00	2931.0
4	TraesCS4D01G182900	chr4B	94.979	478	11	5	1	477	400700944	400700479	0.000000e+00	737.0
5	TraesCS4D01G182900	chr4B	89.981	529	36	6	2785	3305	400697651	400697132	0.000000e+00	667.0
6	TraesCS4D01G182900	chr4B	90.288	278	14	2	518	782	400700088	400699811	5.250000e-93	351.0
7	TraesCS4D01G182900	chr4B	91.411	163	9	3	1700	1862	140587316	140587159	5.550000e-53	219.0
8	TraesCS4D01G182900	chr2A	95.044	343	17	0	1604	1946	223612929	223613271	1.040000e-149	540.0
9	TraesCS4D01G182900	chr5A	84.091	308	36	12	2472	2773	643032489	643032189	5.400000e-73	285.0
10	TraesCS4D01G182900	chr5A	83.000	300	40	11	2479	2773	643040579	643040286	9.100000e-66	261.0
11	TraesCS4D01G182900	chr2D	97.041	169	5	0	1694	1862	43343443	43343611	5.400000e-73	285.0
12	TraesCS4D01G182900	chr2D	80.000	300	49	9	2481	2775	8387745	8388038	9.290000e-51	211.0
13	TraesCS4D01G182900	chr5D	95.266	169	8	0	1694	1862	448570983	448571151	5.440000e-68	268.0
14	TraesCS4D01G182900	chr5D	88.235	68	6	2	1372	1438	426288479	426288545	2.730000e-11	80.5
15	TraesCS4D01G182900	chr6B	82.450	302	43	10	2481	2775	594701894	594702192	4.230000e-64	255.0
16	TraesCS4D01G182900	chr1D	93.064	173	12	0	1745	1917	92182593	92182765	1.520000e-63	254.0
17	TraesCS4D01G182900	chr3B	80.602	299	53	5	2481	2775	475432553	475432850	3.320000e-55	226.0
18	TraesCS4D01G182900	chr7B	80.399	301	49	10	2481	2775	506878456	506878160	1.540000e-53	220.0
19	TraesCS4D01G182900	chr1A	80.268	299	52	7	2481	2775	487099507	487099802	5.550000e-53	219.0
20	TraesCS4D01G182900	chr1A	89.831	59	5	1	2982	3039	246127449	246127391	1.270000e-09	75.0
21	TraesCS4D01G182900	chr7D	79.032	310	55	10	2472	2775	623012153	623011848	1.550000e-48	204.0
22	TraesCS4D01G182900	chr6A	98.438	64	1	0	1603	1666	35259837	35259774	2.700000e-21	113.0

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	TraesCS4D01G182900	chr4D	320027351	320030655	3304	False	6104.0	6104	100.00000	1	3305	1	chr4D.!!$F1	3304
1	TraesCS4D01G182900	chr4A	153253947	153257261	3314	True	2417.5	4061	93.24850	1	3305	2	chr4A.!!$R1	3304
2	TraesCS4D01G182900	chr4B	400697132	400700944	3812	True	1171.5	2931	92.32875	1	3305	4	chr4B.!!$R2	3304

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
198	209	0.168128	CTCCGCGGCCAAGTAAAAAG	59.832	55.0	23.51	4.22	0.0	2.27	F
1288	1856	0.955919	GACAAACGAGAAGGGGGCAG	60.956	60.0	0.00	0.00	0.0	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1386	1954	1.586564	CATCTCCGCGAAGTCGTCC	60.587	63.158	8.23	0.0	42.22	4.79	R
3086	3735	2.037121	GGTGGTTACTTTGCTGCCAAAT	59.963	45.455	0.00	0.0	39.98	2.32	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
35	38	1.148157	CGAGCTTGTGGCATACTCCG	61.148	60.000	0.00	0.00	44.79	4.63
198	209	0.168128	CTCCGCGGCCAAGTAAAAAG	59.832	55.000	23.51	4.22	0.00	2.27
327	341	1.659098	GTCATCCGTCACCGATTTCAC	59.341	52.381	0.00	0.00	35.63	3.18
372	386	2.695666	CCTGTAGAGTCCAGGTGTATGG	59.304	54.545	7.16	0.00	43.73	2.74
669	1062	7.112452	AGGATTAACATAAATTTGCCCTGTC	57.888	36.000	0.00	0.00	0.00	3.51
670	1063	6.098266	AGGATTAACATAAATTTGCCCTGTCC	59.902	38.462	0.00	1.16	0.00	4.02
729	1122	4.037923	GTGGAGAGATGCAACTTTTCCAAA	59.962	41.667	23.55	7.97	36.48	3.28
799	1193	5.519206	ACGGCGATAAGAAAAAGCTACTAAG	59.481	40.000	16.62	0.00	0.00	2.18
826	1220	3.260884	ACGATGTAACAATCCAGGTGAGT	59.739	43.478	0.00	0.00	0.00	3.41
1023	1591	1.062685	CATGGAGGACGACGAGACG	59.937	63.158	0.00	0.00	39.31	4.18
1174	1742	3.834799	CCGACCTGTACGAGCCCC	61.835	72.222	0.00	0.00	0.00	5.80
1263	1831	2.202676	CTCCTGCGCGACTTCCTC	60.203	66.667	12.10	0.00	0.00	3.71
1277	1845	1.798234	TTCCTCTCGCGGACAAACGA	61.798	55.000	6.13	0.00	36.73	3.85
1285	1853	1.375523	CGGACAAACGAGAAGGGGG	60.376	63.158	0.00	0.00	35.47	5.40
1286	1854	1.674651	GGACAAACGAGAAGGGGGC	60.675	63.158	0.00	0.00	0.00	5.80
1287	1855	1.072505	GACAAACGAGAAGGGGGCA	59.927	57.895	0.00	0.00	0.00	5.36
1288	1856	0.955919	GACAAACGAGAAGGGGGCAG	60.956	60.000	0.00	0.00	0.00	4.85
1289	1857	2.034221	AAACGAGAAGGGGGCAGC	59.966	61.111	0.00	0.00	0.00	5.25
1290	1858	3.569200	AAACGAGAAGGGGGCAGCC	62.569	63.158	1.26	1.26	0.00	4.85
1818	2386	2.594303	CTGGCCGTGTGGAAGCAA	60.594	61.111	0.00	0.00	37.49	3.91
1887	2455	3.636313	GACGTCGATGGTCCCGCAA	62.636	63.158	9.90	0.00	0.00	4.85
1965	2533	2.430244	TTCGACGTGAGCTTCCGC	60.430	61.111	0.00	0.00	0.00	5.54
2310	2888	1.592669	GTGGAGCCGATGACCGATG	60.593	63.158	0.00	0.00	41.76	3.84
2347	2925	6.644592	AGCTGATTCTTTGCTCGACTATTATC	59.355	38.462	0.00	0.00	30.41	1.75
2380	2958	5.690865	TCCACCACTTTGTTTGTTCTCTAT	58.309	37.500	0.00	0.00	0.00	1.98
2381	2959	6.833041	TCCACCACTTTGTTTGTTCTCTATA	58.167	36.000	0.00	0.00	0.00	1.31
2386	2964	7.936847	ACCACTTTGTTTGTTCTCTATACATGA	59.063	33.333	0.00	0.00	0.00	3.07
2404	2982	6.481954	ACATGACAATACGTTTCCTTCTTC	57.518	37.500	0.00	0.00	0.00	2.87
2405	2983	6.231211	ACATGACAATACGTTTCCTTCTTCT	58.769	36.000	0.00	0.00	0.00	2.85
2406	2984	6.147821	ACATGACAATACGTTTCCTTCTTCTG	59.852	38.462	0.00	0.00	0.00	3.02
2409	2987	6.202188	TGACAATACGTTTCCTTCTTCTGTTC	59.798	38.462	0.00	0.00	0.00	3.18
2410	2988	6.289064	ACAATACGTTTCCTTCTTCTGTTCT	58.711	36.000	0.00	0.00	0.00	3.01
2411	2989	7.439381	ACAATACGTTTCCTTCTTCTGTTCTA	58.561	34.615	0.00	0.00	0.00	2.10
2412	2990	7.384387	ACAATACGTTTCCTTCTTCTGTTCTAC	59.616	37.037	0.00	0.00	0.00	2.59
2446	3027	4.342665	CCCAATGGTTACTCTACTCTCTCC	59.657	50.000	0.00	0.00	0.00	3.71
2486	3068	5.416271	TGTACTCCCTTCATTGTAAGGTC	57.584	43.478	11.49	2.25	43.94	3.85
2560	3143	5.546526	TGAAAATAACCTTGGCCAAATCAC	58.453	37.500	20.91	5.93	0.00	3.06
2563	3146	1.341080	AACCTTGGCCAAATCACTGG	58.659	50.000	20.91	17.95	39.71	4.00
2636	3222	6.240549	TCAGGAGAGAGACACTTTTCTTTT	57.759	37.500	0.00	0.00	0.00	2.27
2637	3223	6.284459	TCAGGAGAGAGACACTTTTCTTTTC	58.716	40.000	0.00	0.00	0.00	2.29
2638	3224	6.098982	TCAGGAGAGAGACACTTTTCTTTTCT	59.901	38.462	0.00	0.00	0.00	2.52
2648	3234	7.611855	AGACACTTTTCTTTTCTTCTCTCCAAA	59.388	33.333	0.00	0.00	0.00	3.28
2683	3269	4.038642	GCAATCGGGAGAGAGATACTTTCT	59.961	45.833	0.00	0.00	45.48	2.52
2789	3436	9.062367	ACATCTTATATAGGGCAATTACTCCAT	57.938	33.333	0.00	0.00	0.00	3.41
2844	3491	9.739276	AGGACACTTCTAAATTGATTGATACAA	57.261	29.630	0.00	0.00	0.00	2.41
2928	3575	8.725148	CAAAGATTTTGTAGTGCTGAGAGTAAT	58.275	33.333	0.00	0.00	0.00	1.89
2962	3609	6.690530	TCCCGTATCCATAAAATAACTACCG	58.309	40.000	0.00	0.00	0.00	4.02
2965	3612	7.116805	CCCGTATCCATAAAATAACTACCGTTC	59.883	40.741	0.00	0.00	34.59	3.95
2968	3615	9.754382	GTATCCATAAAATAACTACCGTTCAGA	57.246	33.333	0.00	0.00	34.59	3.27
3044	3693	4.762251	GCAGGATCTTGTAAACTTGACCTT	59.238	41.667	6.70	0.00	0.00	3.50
3086	3735	4.295857	GAAGTTTTGCTTCCCGTAAACA	57.704	40.909	0.00	0.00	45.95	2.83
3098	3747	2.546795	CCCGTAAACATTTGGCAGCAAA	60.547	45.455	0.00	0.00	0.00	3.68
3242	3897	1.152735	TGACTAGCGGGCCCTAGAG	60.153	63.158	26.20	15.83	38.50	2.43

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
16	19	1.148157	CGGAGTATGCCACAAGCTCG	61.148	60.000	0.00	0.00	44.23	5.03
35	38	0.676184	TAGATCATGCTCCGCACCTC	59.324	55.000	0.00	0.00	43.04	3.85
652	1045	4.776837	TGATTGGACAGGGCAAATTTATGT	59.223	37.500	0.00	0.00	0.00	2.29
658	1051	3.242011	ACTTTGATTGGACAGGGCAAAT	58.758	40.909	0.00	0.00	0.00	2.32
669	1062	2.876091	TCTCGCGTAGACTTTGATTGG	58.124	47.619	5.77	0.00	0.00	3.16
799	1193	5.234329	CACCTGGATTGTTACATCGTGTATC	59.766	44.000	0.00	0.83	32.20	2.24
808	1202	4.504864	CCTCAACTCACCTGGATTGTTACA	60.505	45.833	0.00	0.00	0.00	2.41
962	1530	0.884704	CACTTGGGGAGGACACAACG	60.885	60.000	0.00	0.00	0.00	4.10
1023	1591	4.821589	CGGCTCTTCTGGGTCGCC	62.822	72.222	0.00	0.00	37.40	5.54
1101	1669	2.682494	GTGTAGGGGTCCTCGGCA	60.682	66.667	0.00	0.00	34.61	5.69
1174	1742	4.742201	CCCCACGGACACGAGCTG	62.742	72.222	0.00	0.00	44.60	4.24
1386	1954	1.586564	CATCTCCGCGAAGTCGTCC	60.587	63.158	8.23	0.00	42.22	4.79
1887	2455	2.688666	TCCTCCATCTTGGCCGCT	60.689	61.111	0.00	0.00	37.47	5.52
1965	2533	2.815211	ATGTGCAGCACGCCGTAG	60.815	61.111	20.67	0.00	41.33	3.51
2109	2677	2.154074	GTTCACCAGGGACCCCACT	61.154	63.158	7.00	0.00	38.92	4.00
2347	2925	2.738846	CAAAGTGGTGGAGATCGACTTG	59.261	50.000	0.00	0.00	34.94	3.16
2380	2958	7.330946	CAGAAGAAGGAAACGTATTGTCATGTA	59.669	37.037	0.00	0.00	0.00	2.29
2381	2959	6.147821	CAGAAGAAGGAAACGTATTGTCATGT	59.852	38.462	0.00	0.00	0.00	3.21
2386	2964	6.289064	AGAACAGAAGAAGGAAACGTATTGT	58.711	36.000	0.00	0.00	0.00	2.71
2422	3003	4.290942	AGAGAGTAGAGTAACCATTGGGG	58.709	47.826	7.78	0.00	44.81	4.96
2423	3004	4.342665	GGAGAGAGTAGAGTAACCATTGGG	59.657	50.000	7.78	0.00	41.29	4.12
2446	3027	9.046296	GGGAGTACATCTTATATTTTGTGACAG	57.954	37.037	0.00	0.00	0.00	3.51
2486	3068	4.093703	TGTTCACCGTGCCGAAAATAATAG	59.906	41.667	0.00	0.00	0.00	1.73
2542	3125	3.099141	CCAGTGATTTGGCCAAGGTTAT	58.901	45.455	19.48	9.37	0.00	1.89
2595	3179	4.100035	TCCTGATTGCGTGTATCTCTTCAT	59.900	41.667	0.00	0.00	0.00	2.57
2636	3222	8.708378	TGCATATATCTTTCTTTGGAGAGAAGA	58.292	33.333	0.00	0.00	36.50	2.87
2637	3223	8.899427	TGCATATATCTTTCTTTGGAGAGAAG	57.101	34.615	0.00	0.00	36.50	2.85
2638	3224	9.857656	ATTGCATATATCTTTCTTTGGAGAGAA	57.142	29.630	0.00	0.00	36.50	2.87
2648	3234	6.438741	TCTCTCCCGATTGCATATATCTTTCT	59.561	38.462	0.00	0.00	0.00	2.52
2683	3269	7.948034	TTCTGTTTTCAACCCTCTAGAAAAA	57.052	32.000	0.00	0.00	41.31	1.94
2763	3354	8.449423	TGGAGTAATTGCCCTATATAAGATGT	57.551	34.615	0.00	0.00	0.00	3.06
2789	3436	9.474313	AAGAGCTTATTAATTACACCCATCAAA	57.526	29.630	0.00	0.00	0.00	2.69
2791	3438	9.474313	AAAAGAGCTTATTAATTACACCCATCA	57.526	29.630	0.00	0.00	0.00	3.07
2844	3491	8.592809	TCACTGGATTAACAAAAATAAATGGCT	58.407	29.630	0.00	0.00	0.00	4.75
2962	3609	5.871465	TTTTGCCCAAACTTTTTCTGAAC	57.129	34.783	0.00	0.00	0.00	3.18
2965	3612	4.153296	ACGTTTTTGCCCAAACTTTTTCTG	59.847	37.500	6.35	0.00	34.91	3.02
2968	3615	3.123790	CGACGTTTTTGCCCAAACTTTTT	59.876	39.130	0.00	0.00	34.91	1.94
3044	3693	2.801679	CGCGTGTACCAAAGGAAAGTTA	59.198	45.455	0.00	0.00	0.00	2.24
3080	3729	5.176774	GGTTACTTTGCTGCCAAATGTTTAC	59.823	40.000	0.00	0.00	39.98	2.01
3086	3735	2.037121	GGTGGTTACTTTGCTGCCAAAT	59.963	45.455	0.00	0.00	39.98	2.32
3098	3747	3.463944	CGTGAAGTTTCAGGTGGTTACT	58.536	45.455	6.44	0.00	37.98	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.