AutoCloner

Multiple sequence alignment - TraesCS3B01G496700

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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	TraesCS3B01G496700	chr3B	100.000	4969	0	0	1	4969	740050413	740055381	0.000000e+00	9177.0
1	TraesCS3B01G496700	chr3B	86.558	1287	132	24	964	2230	740514487	740515752	0.000000e+00	1380.0
2	TraesCS3B01G496700	chr3B	93.665	805	45	5	3243	4045	740495650	740496450	0.000000e+00	1199.0
3	TraesCS3B01G496700	chr3B	83.171	1337	164	35	1014	2324	740503033	740504334	0.000000e+00	1166.0
4	TraesCS3B01G496700	chr3B	87.366	744	86	5	1586	2325	740101279	740102018	0.000000e+00	846.0
5	TraesCS3B01G496700	chr3B	85.501	738	69	14	2450	3175	740504333	740505044	0.000000e+00	736.0
6	TraesCS3B01G496700	chr3B	78.763	857	132	26	3197	4032	740041721	740042548	3.410000e-146	529.0
7	TraesCS3B01G496700	chr3B	82.781	604	55	11	2664	3243	740494912	740495490	1.240000e-135	494.0
8	TraesCS3B01G496700	chr3B	83.239	531	62	9	1053	1574	740100121	740100633	3.500000e-126	462.0
9	TraesCS3B01G496700	chr3B	86.744	347	35	9	997	1336	740540716	740541058	4.700000e-100	375.0
10	TraesCS3B01G496700	chr3B	80.237	506	61	21	3539	4038	708798400	708798872	1.320000e-90	344.0
11	TraesCS3B01G496700	chr3B	93.953	215	12	1	2449	2662	740102017	740102231	1.730000e-84	324.0
12	TraesCS3B01G496700	chr3B	79.915	473	67	15	3589	4043	740095378	740095840	6.210000e-84	322.0
13	TraesCS3B01G496700	chr3B	94.660	206	10	1	4561	4765	433640069	433640274	8.030000e-83	318.0
14	TraesCS3B01G496700	chr3B	86.842	266	20	3	2585	2837	740516729	740516992	2.930000e-72	283.0
15	TraesCS3B01G496700	chr3B	82.424	330	50	8	2633	2955	740542108	740542436	1.050000e-71	281.0
16	TraesCS3B01G496700	chr3B	82.609	322	37	13	3733	4038	740518070	740518388	2.950000e-67	267.0
17	TraesCS3B01G496700	chr3B	91.083	157	10	3	2324	2476	139036491	139036335	5.040000e-50	209.0
18	TraesCS3B01G496700	chr3B	88.806	134	11	1	4050	4183	550315413	550315542	1.430000e-35	161.0
19	TraesCS3B01G496700	chr3B	81.818	187	20	9	4353	4528	740496541	740496724	1.440000e-30	145.0
20	TraesCS3B01G496700	chr3B	82.353	85	9	4	4452	4532	740518699	740518781	8.930000e-08	69.4
21	TraesCS3B01G496700	chr3B	97.368	38	1	0	17	54	728581618	728581581	1.150000e-06	65.8
22	TraesCS3B01G496700	chr3D	91.165	2309	148	17	38	2325	557793929	557796202	0.000000e+00	3083.0
23	TraesCS3B01G496700	chr3D	91.536	1536	73	20	2510	4006	557796238	557797755	0.000000e+00	2063.0
24	TraesCS3B01G496700	chr3D	86.755	1359	147	16	964	2307	557914194	557915534	0.000000e+00	1482.0
25	TraesCS3B01G496700	chr3D	82.872	1337	168	34	1015	2325	557879051	557880352	0.000000e+00	1144.0
26	TraesCS3B01G496700	chr3D	83.543	1191	134	36	2449	3619	557915551	557916699	0.000000e+00	1057.0
27	TraesCS3B01G496700	chr3D	84.334	766	61	22	2449	3200	557880351	557881071	0.000000e+00	695.0
28	TraesCS3B01G496700	chr3D	87.356	348	31	8	996	1336	557920992	557921333	2.170000e-103	387.0
29	TraesCS3B01G496700	chr3D	86.072	359	41	5	991	1340	536334953	536335311	1.310000e-100	377.0
30	TraesCS3B01G496700	chr3D	83.082	331	46	10	2633	2955	557922384	557922712	4.870000e-75	292.0
31	TraesCS3B01G496700	chr3D	81.620	321	41	13	3733	4038	557916697	557917014	2.970000e-62	250.0
32	TraesCS3B01G496700	chr3D	84.615	234	30	5	3801	4029	557923304	557923536	1.390000e-55	228.0
33	TraesCS3B01G496700	chr3D	97.692	130	3	0	2324	2453	283321125	283321254	1.800000e-54	224.0
34	TraesCS3B01G496700	chr3D	96.269	134	4	1	2317	2450	210622555	210622423	8.380000e-53	219.0
35	TraesCS3B01G496700	chr3D	91.558	154	11	2	2324	2476	566895874	566895722	1.400000e-50	211.0
36	TraesCS3B01G496700	chr3D	94.667	75	3	1	4491	4564	557797768	557797842	1.130000e-21	115.0
37	TraesCS3B01G496700	chr3D	94.737	38	1	1	17	54	549063814	549063778	1.930000e-04	58.4
38	TraesCS3B01G496700	chr3A	88.060	1675	107	27	1	1624	693570855	693572487	0.000000e+00	1899.0
39	TraesCS3B01G496700	chr3A	85.403	1377	162	19	964	2325	693646997	693648349	0.000000e+00	1393.0
40	TraesCS3B01G496700	chr3A	94.318	704	40	0	1622	2325	693581528	693582231	0.000000e+00	1079.0
41	TraesCS3B01G496700	chr3A	92.972	683	30	11	3100	3768	693583247	693583925	0.000000e+00	979.0
42	TraesCS3B01G496700	chr3A	88.854	628	25	10	2508	3120	693582265	693582862	0.000000e+00	730.0
43	TraesCS3B01G496700	chr3A	80.328	793	129	16	1559	2325	671760500	671761291	4.310000e-160	575.0
44	TraesCS3B01G496700	chr3A	79.099	866	130	25	3193	4044	693615291	693616119	2.610000e-152	549.0
45	TraesCS3B01G496700	chr3A	87.234	423	32	6	2449	2857	693648348	693648762	3.500000e-126	462.0
46	TraesCS3B01G496700	chr3A	77.700	852	112	46	3198	4038	671761721	671762505	2.730000e-122	449.0
47	TraesCS3B01G496700	chr3A	90.794	315	16	3	4180	4481	693584170	693584484	4.630000e-110	409.0
48	TraesCS3B01G496700	chr3A	87.395	357	33	7	996	1340	671759946	671760302	2.790000e-107	399.0
49	TraesCS3B01G496700	chr3A	91.701	241	9	7	3815	4045	693583928	693584167	1.730000e-84	324.0
50	TraesCS3B01G496700	chr3A	82.569	327	37	14	3733	4044	693649767	693650088	2.280000e-68	270.0
51	TraesCS3B01G496700	chr3A	82.119	151	19	7	4034	4183	663439004	663439147	6.760000e-24	122.0
52	TraesCS3B01G496700	chr3A	85.600	125	9	6	4417	4532	693650368	693650492	6.760000e-24	122.0
53	TraesCS3B01G496700	chrUn	98.049	205	4	0	4561	4765	34213031	34212827	1.700000e-94	357.0
54	TraesCS3B01G496700	chrUn	83.226	310	44	8	2633	2935	295852379	295852687	1.360000e-70	278.0
55	TraesCS3B01G496700	chrUn	84.000	150	15	4	4035	4183	31617082	31616941	8.680000e-28	135.0
56	TraesCS3B01G496700	chr1A	94.608	204	11	0	4562	4765	417384984	417385187	2.890000e-82	316.0
57	TraesCS3B01G496700	chr1A	94.554	202	11	0	4564	4765	540023663	540023864	3.730000e-81	313.0
58	TraesCS3B01G496700	chr1A	87.023	131	10	2	4057	4187	243863996	243863873	1.860000e-29	141.0
59	TraesCS3B01G496700	chr1A	86.029	136	12	5	4048	4183	567151683	567151811	6.710000e-29	139.0
60	TraesCS3B01G496700	chr7D	94.118	204	12	0	4562	4765	16730869	16730666	1.340000e-80	311.0
61	TraesCS3B01G496700	chr5A	93.659	205	13	0	4561	4765	537659901	537660105	1.740000e-79	307.0
62	TraesCS3B01G496700	chr2D	94.059	202	12	0	4564	4765	179328688	179328889	1.740000e-79	307.0
63	TraesCS3B01G496700	chr2D	93.989	183	10	1	4787	4969	42569033	42569214	4.900000e-70	276.0
64	TraesCS3B01G496700	chr2D	97.674	129	3	0	2323	2451	561025621	561025749	6.470000e-54	222.0
65	TraesCS3B01G496700	chr2D	82.432	148	16	9	4037	4183	231598975	231599113	2.430000e-23	121.0
66	TraesCS3B01G496700	chr2D	92.157	51	3	1	4919	4969	346044639	346044688	2.480000e-08	71.3
67	TraesCS3B01G496700	chr4D	93.659	205	12	1	4561	4765	334108104	334108307	6.250000e-79	305.0
68	TraesCS3B01G496700	chr4D	96.269	134	5	0	2317	2450	439129794	439129927	2.330000e-53	220.0
69	TraesCS3B01G496700	chr1B	93.627	204	13	0	4562	4765	619390676	619390473	6.250000e-79	305.0
70	TraesCS3B01G496700	chr1B	86.232	138	10	6	4050	4186	674093602	674093473	1.860000e-29	141.0
71	TraesCS3B01G496700	chr1B	80.576	139	20	4	652	790	625086694	625086563	3.170000e-17	100.0
72	TraesCS3B01G496700	chr4A	95.580	181	7	1	4787	4967	729527148	729526969	6.290000e-74	289.0
73	TraesCS3B01G496700	chr5D	97.727	132	3	0	2320	2451	447459586	447459717	1.390000e-55	228.0
74	TraesCS3B01G496700	chr5D	92.517	147	9	2	2305	2450	85596233	85596378	5.040000e-50	209.0
75	TraesCS3B01G496700	chr5D	93.023	43	3	0	16	58	369069722	369069680	4.150000e-06	63.9
76	TraesCS3B01G496700	chr2B	94.406	143	6	2	2319	2460	598960980	598960839	8.380000e-53	219.0
77	TraesCS3B01G496700	chr2B	89.552	134	14	0	4050	4183	434723731	434723598	2.380000e-38	171.0
78	TraesCS3B01G496700	chr2B	87.313	134	10	6	4050	4183	468705577	468705703	4.010000e-31	147.0
79	TraesCS3B01G496700	chr6D	88.489	139	13	2	4048	4186	234467863	234467728	1.110000e-36	165.0
80	TraesCS3B01G496700	chr7B	86.861	137	12	4	4048	4183	599651880	599652011	1.110000e-31	148.0
81	TraesCS3B01G496700	chr7B	97.222	36	1	0	18	53	643347869	643347834	1.490000e-05	62.1
82	TraesCS3B01G496700	chr2A	84.507	142	16	6	4046	4183	98103423	98103284	8.680000e-28	135.0
83	TraesCS3B01G496700	chr2A	76.536	179	36	6	1067	1242	29821132	29820957	5.300000e-15	93.5
84	TraesCS3B01G496700	chr7A	95.918	49	2	0	4	52	467371557	467371509	4.120000e-11	80.5
85	TraesCS3B01G496700	chr5B	93.750	48	3	0	7	54	663799453	663799406	6.900000e-09	73.1
86	TraesCS3B01G496700	chr6B	90.000	50	5	0	1	50	640913457	640913506	1.150000e-06	65.8

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	TraesCS3B01G496700	chr3B	740050413	740055381	4968	False	9177.000000	9177	100.000000	1	4969	1	chr3B.!!$F5	4968
1	TraesCS3B01G496700	chr3B	740503033	740505044	2011	False	951.000000	1166	84.336000	1014	3175	2	chr3B.!!$F9	2161
2	TraesCS3B01G496700	chr3B	740494912	740496724	1812	False	612.666667	1199	86.088000	2664	4528	3	chr3B.!!$F8	1864
3	TraesCS3B01G496700	chr3B	740100121	740102231	2110	False	544.000000	846	88.186000	1053	2662	3	chr3B.!!$F7	1609
4	TraesCS3B01G496700	chr3B	740041721	740042548	827	False	529.000000	529	78.763000	3197	4032	1	chr3B.!!$F4	835
5	TraesCS3B01G496700	chr3B	740514487	740518781	4294	False	499.850000	1380	84.590500	964	4532	4	chr3B.!!$F10	3568
6	TraesCS3B01G496700	chr3B	740540716	740542436	1720	False	328.000000	375	84.584000	997	2955	2	chr3B.!!$F11	1958
7	TraesCS3B01G496700	chr3D	557793929	557797842	3913	False	1753.666667	3083	92.456000	38	4564	3	chr3D.!!$F3	4526
8	TraesCS3B01G496700	chr3D	557879051	557881071	2020	False	919.500000	1144	83.603000	1015	3200	2	chr3D.!!$F4	2185
9	TraesCS3B01G496700	chr3D	557914194	557923536	9342	False	616.000000	1482	84.495167	964	4038	6	chr3D.!!$F5	3074
10	TraesCS3B01G496700	chr3A	693570855	693572487	1632	False	1899.000000	1899	88.060000	1	1624	1	chr3A.!!$F2	1623
11	TraesCS3B01G496700	chr3A	693581528	693584484	2956	False	704.200000	1079	91.727800	1622	4481	5	chr3A.!!$F5	2859
12	TraesCS3B01G496700	chr3A	693646997	693650492	3495	False	561.750000	1393	85.201500	964	4532	4	chr3A.!!$F6	3568
13	TraesCS3B01G496700	chr3A	693615291	693616119	828	False	549.000000	549	79.099000	3193	4044	1	chr3A.!!$F3	851
14	TraesCS3B01G496700	chr3A	671759946	671762505	2559	False	474.333333	575	81.807667	996	4038	3	chr3A.!!$F4	3042

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
684	699	0.679002	ACAAGCGCTGATTGCTGGAT	60.679	50.0	12.58	0.0	43.14	3.41	F
1531	1613	0.390860	CCTCCCAGGATTACAGCTCG	59.609	60.0	0.00	0.0	37.67	5.03	F
2333	3950	0.106149	GCTGTTACATACCCCCTCCG	59.894	60.0	0.00	0.0	0.00	4.63	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1579	1670	0.032017	AAGTAGGACGAGCCATCCCT	60.032	55.0	0.0	0.0	40.02	4.20	R
2433	4050	0.042131	ACATACTCCCTCCGTCCCAA	59.958	55.0	0.0	0.0	0.00	4.12	R
4165	7295	0.115745	ACTACTCCCTCCGTCCCAAA	59.884	55.0	0.0	0.0	0.00	3.28	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
27	28	4.082733	GGGTTCTGTATGGAACTTTTGAGC	60.083	45.833	7.19	0.00	43.43	4.26
61	62	3.181423	ACCAAACACACCCTATTGGATGT	60.181	43.478	10.14	0.00	44.01	3.06
63	64	4.078537	CAAACACACCCTATTGGATGTCA	58.921	43.478	0.00	0.00	36.41	3.58
118	119	1.119684	CACCCGGATACATGGACTCA	58.880	55.000	0.73	0.00	32.56	3.41
119	120	1.120530	ACCCGGATACATGGACTCAC	58.879	55.000	0.73	0.00	32.56	3.51
195	196	4.322273	CGGTGATGCATACTATCTGGACAT	60.322	45.833	0.00	0.00	0.00	3.06
198	199	5.868258	GTGATGCATACTATCTGGACATCTG	59.132	44.000	0.00	0.00	34.84	2.90
266	267	3.181485	CGGTCAAGAGGGTAAGAGATGAC	60.181	52.174	0.00	0.00	36.01	3.06
296	301	2.367567	ACTGGACAAGCCTTTAGACGAA	59.632	45.455	0.00	0.00	37.63	3.85
297	302	2.737252	CTGGACAAGCCTTTAGACGAAC	59.263	50.000	0.00	0.00	37.63	3.95
298	303	1.725164	GGACAAGCCTTTAGACGAACG	59.275	52.381	0.00	0.00	0.00	3.95
299	304	2.608752	GGACAAGCCTTTAGACGAACGA	60.609	50.000	0.14	0.00	0.00	3.85
314	319	1.227999	AACGACGTGTGCATCAAGGG	61.228	55.000	0.00	0.00	0.00	3.95
320	325	1.151221	TGTGCATCAAGGGCAGTGT	59.849	52.632	0.00	0.00	42.85	3.55
376	381	5.065859	TCAATACTAACGGTGCCATTGATTG	59.934	40.000	2.43	0.00	30.19	2.67
408	413	3.330126	TGGAGGTGGAGGAGGTATAAG	57.670	52.381	0.00	0.00	0.00	1.73
409	414	2.590611	TGGAGGTGGAGGAGGTATAAGT	59.409	50.000	0.00	0.00	0.00	2.24
436	441	2.175715	ACACCTTTCTTTCCAAGGAGCT	59.824	45.455	5.70	0.00	43.32	4.09
509	514	3.554731	GGCTTTGCGATAAGGTGTAGTAC	59.445	47.826	0.00	0.00	0.00	2.73
513	518	3.273434	TGCGATAAGGTGTAGTACTCGT	58.727	45.455	0.00	0.00	0.00	4.18
518	533	2.191128	AGGTGTAGTACTCGTCGGTT	57.809	50.000	0.00	0.00	0.00	4.44
522	537	2.738846	GTGTAGTACTCGTCGGTTCTCA	59.261	50.000	0.00	0.00	0.00	3.27
528	543	1.340248	ACTCGTCGGTTCTCACATGTT	59.660	47.619	0.00	0.00	0.00	2.71
537	552	7.042725	CGTCGGTTCTCACATGTTATAATGAAT	60.043	37.037	0.00	0.00	0.00	2.57
585	600	4.962362	TCTAGTCTTCAGGGCACAATGATA	59.038	41.667	0.00	0.00	0.00	2.15

Showing 1 to 25 of 429 entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	4.825085	TCAAAAGTTCCATACAGAACCCAC	59.175	41.667	0.98	0.00	46.00	4.61
14	15	2.294233	GTGCATGAGCTCAAAAGTTCCA	59.706	45.455	22.50	7.27	42.74	3.53
27	28	1.812571	GTGTTTGGTAGGGTGCATGAG	59.187	52.381	0.00	0.00	0.00	2.90
61	62	1.118965	TCCACGGCCTCTCTTGTTGA	61.119	55.000	0.00	0.00	0.00	3.18
63	64	0.036010	CATCCACGGCCTCTCTTGTT	60.036	55.000	0.00	0.00	0.00	2.83
118	119	4.943705	ACCTTTGATCAAGCACAATATCGT	59.056	37.500	8.41	0.00	0.00	3.73
119	120	5.490139	ACCTTTGATCAAGCACAATATCG	57.510	39.130	8.41	0.00	0.00	2.92
195	196	3.054508	TCATGTGTCCATATGTTGCCAGA	60.055	43.478	1.24	0.00	32.61	3.86
198	199	4.924305	ATTCATGTGTCCATATGTTGCC	57.076	40.909	1.24	0.00	32.61	4.52
266	267	1.338200	GGCTTGTCCAGTACTGACAGG	60.338	57.143	24.68	22.97	33.52	4.00
296	301	1.667830	CCCTTGATGCACACGTCGT	60.668	57.895	0.00	0.00	34.28	4.34
297	302	3.027170	GCCCTTGATGCACACGTCG	62.027	63.158	0.00	0.00	34.28	5.12
298	303	1.915614	CTGCCCTTGATGCACACGTC	61.916	60.000	0.00	0.00	34.46	4.34
299	304	1.968017	CTGCCCTTGATGCACACGT	60.968	57.895	0.00	0.00	34.46	4.49
314	319	2.229792	TCAGATGGTTTCCAACACTGC	58.770	47.619	12.32	0.00	36.95	4.40
320	325	2.649312	ACCTGGATCAGATGGTTTCCAA	59.351	45.455	0.00	0.00	37.78	3.53
376	381	2.092753	TCCACCTCCATTCTGAGAATGC	60.093	50.000	25.74	0.00	34.11	3.56
408	413	4.081322	TGGAAAGAAAGGTGTGGTCTAC	57.919	45.455	0.00	0.00	0.00	2.59
409	414	4.781775	TTGGAAAGAAAGGTGTGGTCTA	57.218	40.909	0.00	0.00	0.00	2.59
509	514	2.065993	AACATGTGAGAACCGACGAG	57.934	50.000	0.00	0.00	0.00	4.18
513	518	7.226523	CCATTCATTATAACATGTGAGAACCGA	59.773	37.037	0.00	0.00	0.00	4.69
565	580	3.521126	ACTATCATTGTGCCCTGAAGACT	59.479	43.478	0.00	0.00	0.00	3.24
572	587	3.614092	CAGTGAACTATCATTGTGCCCT	58.386	45.455	0.00	0.00	38.20	5.19
585	600	0.324943	AATAGGCGGCACAGTGAACT	59.675	50.000	13.08	0.00	0.00	3.01
596	611	2.930950	TCCCTCATTGAAAATAGGCGG	58.069	47.619	0.00	0.00	0.00	6.13

Showing 1 to 25 of 415 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.