AutoCloner

Multiple sequence alignment - TraesCS2D01G377500

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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	TraesCS2D01G377500	chr2D	100.000	4258	0	0	1	4258	481960489	481964746	0.000000e+00	7864
1	TraesCS2D01G377500	chr2D	96.023	3797	102	23	479	4258	481987899	481991663	0.000000e+00	6130
2	TraesCS2D01G377500	chr2D	91.330	2999	207	21	531	3492	481688163	481691145	0.000000e+00	4048
3	TraesCS2D01G377500	chr2D	90.729	2621	218	14	889	3491	481655978	481658591	0.000000e+00	3470
4	TraesCS2D01G377500	chr2D	82.448	433	42	11	82	504	481687606	481688014	8.760000e-92	348
5	TraesCS2D01G377500	chr2D	86.207	319	18	8	537	848	481655676	481655975	5.310000e-84	322
6	TraesCS2D01G377500	chr2D	83.945	218	9	3	82	297	481703118	481703311	7.270000e-43	185
7	TraesCS2D01G377500	chr2D	94.118	85	5	0	1	85	448138187	448138103	3.460000e-26	130
8	TraesCS2D01G377500	chr2A	93.921	3586	152	27	364	3914	624457655	624461209	0.000000e+00	5354
9	TraesCS2D01G377500	chr2A	89.939	2972	234	29	549	3492	624393902	624396836	0.000000e+00	3771
10	TraesCS2D01G377500	chr2A	90.098	2747	239	24	769	3492	624446916	624449652	0.000000e+00	3535
11	TraesCS2D01G377500	chr2A	88.256	2597	249	35	928	3490	624359498	624362072	0.000000e+00	3055
12	TraesCS2D01G377500	chr2A	89.865	296	14	6	3962	4257	624461289	624461568	2.420000e-97	366
13	TraesCS2D01G377500	chr2A	81.481	351	39	18	3806	4138	624397157	624397499	9.080000e-67	265
14	TraesCS2D01G377500	chr2A	86.090	266	11	2	82	347	624457243	624457482	3.270000e-66	263
15	TraesCS2D01G377500	chr2B	93.955	3292	118	32	680	3954	565209751	565212978	0.000000e+00	4902
16	TraesCS2D01G377500	chr2B	90.047	2984	257	27	528	3492	565188530	565191492	0.000000e+00	3829
17	TraesCS2D01G377500	chr2B	90.642	2554	204	17	975	3495	565076406	565078957	0.000000e+00	3360
18	TraesCS2D01G377500	chr2B	93.811	307	19	0	3951	4257	565213011	565213317	3.000000e-126	462
19	TraesCS2D01G377500	chr2B	82.707	266	18	8	82	342	565209253	565209495	1.200000e-50	211
20	TraesCS2D01G377500	chr2B	89.565	115	4	1	528	634	565209640	565209754	5.740000e-29	139
21	TraesCS2D01G377500	chr2B	94.118	85	4	1	1	84	98453722	98453806	1.240000e-25	128
22	TraesCS2D01G377500	chr2B	93.902	82	5	0	4016	4097	565080976	565081057	1.610000e-24	124
23	TraesCS2D01G377500	chr2B	90.426	94	8	1	1	94	595121779	595121871	5.780000e-24	122
24	TraesCS2D01G377500	chr6D	97.619	84	2	0	1	84	24901310	24901227	1.230000e-30	145
25	TraesCS2D01G377500	chr4A	96.429	84	3	0	1	84	660916095	660916012	5.740000e-29	139
26	TraesCS2D01G377500	chr1D	96.429	84	3	0	1	84	259210540	259210623	5.740000e-29	139
27	TraesCS2D01G377500	chr5A	96.341	82	3	0	1	82	524978089	524978170	7.430000e-28	135
28	TraesCS2D01G377500	chr1B	92.553	94	6	1	1	94	623240190	623240098	2.670000e-27	134
29	TraesCS2D01G377500	chr1B	92.222	90	7	0	1	90	633285839	633285928	1.240000e-25	128

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	TraesCS2D01G377500	chr2D	481960489	481964746	4257	False	7864.000000	7864	100.000000	1	4258	1	chr2D.!!$F2	4257
1	TraesCS2D01G377500	chr2D	481987899	481991663	3764	False	6130.000000	6130	96.023000	479	4258	1	chr2D.!!$F3	3779
2	TraesCS2D01G377500	chr2D	481687606	481691145	3539	False	2198.000000	4048	86.889000	82	3492	2	chr2D.!!$F5	3410
3	TraesCS2D01G377500	chr2D	481655676	481658591	2915	False	1896.000000	3470	88.468000	537	3491	2	chr2D.!!$F4	2954
4	TraesCS2D01G377500	chr2A	624446916	624449652	2736	False	3535.000000	3535	90.098000	769	3492	1	chr2A.!!$F2	2723
5	TraesCS2D01G377500	chr2A	624359498	624362072	2574	False	3055.000000	3055	88.256000	928	3490	1	chr2A.!!$F1	2562
6	TraesCS2D01G377500	chr2A	624393902	624397499	3597	False	2018.000000	3771	85.710000	549	4138	2	chr2A.!!$F3	3589
7	TraesCS2D01G377500	chr2A	624457243	624461568	4325	False	1994.333333	5354	89.958667	82	4257	3	chr2A.!!$F4	4175
8	TraesCS2D01G377500	chr2B	565188530	565191492	2962	False	3829.000000	3829	90.047000	528	3492	1	chr2B.!!$F2	2964
9	TraesCS2D01G377500	chr2B	565076406	565081057	4651	False	1742.000000	3360	92.272000	975	4097	2	chr2B.!!$F4	3122
10	TraesCS2D01G377500	chr2B	565209253	565213317	4064	False	1428.500000	4902	90.009500	82	4257	4	chr2B.!!$F5	4175

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	Hairpin	End Stability	Orientation
857	1255	0.729816	GCTCCTCTTCGACACACGTC	60.730	60.000	43.13	4.34	F
905	1303	1.651737	TACACATACACCTGCCCACT	58.348	50.000	0.00	4.00	F
1092	1504	1.774217	ACTGAACTGGGGGAAGGCA	60.774	57.895	0.00	4.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2114	2568	1.837051	TGGGTCAAGCTCACCGAGT	60.837	57.895	8.38	34.33	4.18	R
2396	2850	4.750098	CCATTGTTGTAGAAGTCGTTCACT	59.250	41.667	0.00	36.64	3.41	R
3937	4526	0.949105	CACGCGCCAAAAGGAGTAGT	60.949	55.000	5.73	0.00	2.73	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
97	98	1.544246	GCCCTAAAAGGTGATTTGCGT	59.456	47.619	0.00	0.00	31.93	5.24
191	198	1.802636	CCAATGCCTTGCTACGGTG	59.197	57.895	0.00	0.00	0.00	4.94
192	199	1.137404	CAATGCCTTGCTACGGTGC	59.863	57.895	0.00	0.00	0.00	5.01
193	200	1.303236	AATGCCTTGCTACGGTGCA	60.303	52.632	0.45	0.45	41.65	4.57
272	285	2.444895	ATCAGGAGGGGTCGAGGC	60.445	66.667	0.00	0.00	0.00	4.70
321	334	2.217750	TGATCAACCTCCAAACACACG	58.782	47.619	0.00	0.00	0.00	4.49
349	391	6.993878	CAGACAACTGAAAACATATACTCCG	58.006	40.000	0.00	0.00	46.03	4.63
350	392	6.590292	CAGACAACTGAAAACATATACTCCGT	59.410	38.462	0.00	0.00	46.03	4.69
351	393	7.758076	CAGACAACTGAAAACATATACTCCGTA	59.242	37.037	0.00	0.00	46.03	4.02
353	395	6.815142	ACAACTGAAAACATATACTCCGTACC	59.185	38.462	0.00	0.00	0.00	3.34
354	396	6.534475	ACTGAAAACATATACTCCGTACCA	57.466	37.500	0.00	0.00	0.00	3.25
416	630	2.829120	TGTCATCAGTCCATACCAACGA	59.171	45.455	0.00	0.00	0.00	3.85
453	667	3.922171	AGATTCCTCGGAAGCAAGATT	57.078	42.857	15.48	0.00	42.31	2.40
721	1089	4.135153	CCTCGCCGTCCAGGTCTG	62.135	72.222	0.00	0.00	43.70	3.51
756	1128	3.624205	GCCTCACACCTACCTACTACTCA	60.624	52.174	0.00	0.00	0.00	3.41
759	1131	2.688958	CACACCTACCTACTACTCAGCC	59.311	54.545	0.00	0.00	0.00	4.85
786	1159	2.230660	GCGCTGCCTATTTAATCCCTT	58.769	47.619	0.00	0.00	0.00	3.95
855	1253	0.730834	CAGCTCCTCTTCGACACACG	60.731	60.000	0.00	0.00	44.09	4.49
856	1254	1.173444	AGCTCCTCTTCGACACACGT	61.173	55.000	0.00	0.00	43.13	4.49
857	1255	0.729816	GCTCCTCTTCGACACACGTC	60.730	60.000	0.00	0.00	43.13	4.34
860	1258	1.679680	TCCTCTTCGACACACGTCTTT	59.320	47.619	0.00	0.00	40.23	2.52
861	1259	2.100252	TCCTCTTCGACACACGTCTTTT	59.900	45.455	0.00	0.00	40.23	2.27
862	1260	2.864343	CCTCTTCGACACACGTCTTTTT	59.136	45.455	0.00	0.00	40.23	1.94
884	1282	4.305539	TCAGGACACACATCAATTCCAT	57.694	40.909	0.00	0.00	0.00	3.41
902	1300	3.326588	TCCATATACACATACACCTGCCC	59.673	47.826	0.00	0.00	0.00	5.36
905	1303	1.651737	TACACATACACCTGCCCACT	58.348	50.000	0.00	0.00	0.00	4.00
946	1357	5.660864	TCAGAATCCAGATACACATACACCA	59.339	40.000	0.00	0.00	0.00	4.17
1092	1504	1.774217	ACTGAACTGGGGGAAGGCA	60.774	57.895	0.00	0.00	0.00	4.75
1462	1875	4.898320	AGCACTTCTGTCATGTGTATGAA	58.102	39.130	0.00	0.00	44.49	2.57
2114	2568	3.374988	CCTACATGATGCTCGCAAAGAAA	59.625	43.478	0.00	0.00	0.00	2.52
2396	2850	0.902984	TTGCCCAGTTCTCGGAGCTA	60.903	55.000	0.00	0.00	0.00	3.32
2435	2889	0.779997	ATGGTCTGCCTTCCAACCTT	59.220	50.000	0.00	0.00	37.27	3.50
3954	4551	1.717194	TTACTACTCCTTTTGGCGCG	58.283	50.000	0.00	0.00	40.12	6.86
3960	6026	4.999939	CCTTTTGGCGCGTGCACC	63.000	66.667	24.18	6.79	45.35	5.01
3979	6045	1.671979	CGACTGTCCACCGTATCCTA	58.328	55.000	1.55	0.00	0.00	2.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
62	63	7.471959	ACCTTTTAGGGCTTCTTTGATTCAAAG	60.472	37.037	26.35	26.35	44.48	2.77
63	64	6.326323	ACCTTTTAGGGCTTCTTTGATTCAAA	59.674	34.615	11.19	11.19	40.58	2.69
64	65	5.838521	ACCTTTTAGGGCTTCTTTGATTCAA	59.161	36.000	0.00	0.00	40.58	2.69
65	66	5.243730	CACCTTTTAGGGCTTCTTTGATTCA	59.756	40.000	0.00	0.00	40.58	2.57
66	67	5.476945	TCACCTTTTAGGGCTTCTTTGATTC	59.523	40.000	0.00	0.00	40.58	2.52
67	68	5.393866	TCACCTTTTAGGGCTTCTTTGATT	58.606	37.500	0.00	0.00	40.58	2.57
68	69	4.998051	TCACCTTTTAGGGCTTCTTTGAT	58.002	39.130	0.00	0.00	40.58	2.57
69	70	4.447138	TCACCTTTTAGGGCTTCTTTGA	57.553	40.909	0.00	0.00	40.58	2.69
70	71	5.728637	AATCACCTTTTAGGGCTTCTTTG	57.271	39.130	0.00	0.00	40.58	2.77
71	72	5.511373	GCAAATCACCTTTTAGGGCTTCTTT	60.511	40.000	0.00	0.00	40.58	2.52
72	73	4.021104	GCAAATCACCTTTTAGGGCTTCTT	60.021	41.667	0.00	0.00	40.58	2.52
73	74	3.511540	GCAAATCACCTTTTAGGGCTTCT	59.488	43.478	0.00	0.00	40.58	2.85
74	75	3.673323	CGCAAATCACCTTTTAGGGCTTC	60.673	47.826	0.00	0.00	40.58	3.86
75	76	2.231235	CGCAAATCACCTTTTAGGGCTT	59.769	45.455	0.00	0.00	40.58	4.35
76	77	1.818674	CGCAAATCACCTTTTAGGGCT	59.181	47.619	0.00	0.00	40.58	5.19
77	78	1.544246	ACGCAAATCACCTTTTAGGGC	59.456	47.619	0.00	0.00	40.58	5.19
78	79	3.574614	CAACGCAAATCACCTTTTAGGG	58.425	45.455	0.00	0.00	40.58	3.53
79	80	3.574614	CCAACGCAAATCACCTTTTAGG	58.425	45.455	0.00	0.00	42.49	2.69
80	81	2.986479	GCCAACGCAAATCACCTTTTAG	59.014	45.455	0.00	0.00	34.03	1.85
196	203	1.272212	CCACCGTAGCAAGGCATTTTT	59.728	47.619	0.00	0.00	0.00	1.94
197	204	0.887933	CCACCGTAGCAAGGCATTTT	59.112	50.000	0.00	0.00	0.00	1.82
198	205	1.595093	GCCACCGTAGCAAGGCATTT	61.595	55.000	0.00	0.00	46.26	2.32
199	206	2.046285	GCCACCGTAGCAAGGCATT	61.046	57.895	0.00	0.00	46.26	3.56
200	207	2.438434	GCCACCGTAGCAAGGCAT	60.438	61.111	0.00	0.00	46.26	4.40
203	210	1.302511	AACTGCCACCGTAGCAAGG	60.303	57.895	0.00	0.00	40.35	3.61
204	211	0.602638	TCAACTGCCACCGTAGCAAG	60.603	55.000	0.00	0.00	40.35	4.01
205	212	0.602638	CTCAACTGCCACCGTAGCAA	60.603	55.000	0.00	0.00	40.35	3.91
206	213	1.005037	CTCAACTGCCACCGTAGCA	60.005	57.895	0.00	0.00	38.82	3.49
207	214	1.004918	ACTCAACTGCCACCGTAGC	60.005	57.895	0.00	0.00	0.00	3.58
208	215	0.389948	GGACTCAACTGCCACCGTAG	60.390	60.000	0.00	0.00	0.00	3.51
209	216	1.116536	TGGACTCAACTGCCACCGTA	61.117	55.000	0.00	0.00	0.00	4.02
210	217	2.426023	GGACTCAACTGCCACCGT	59.574	61.111	0.00	0.00	0.00	4.83
211	218	1.961277	GTGGACTCAACTGCCACCG	60.961	63.158	0.00	0.00	44.86	4.94
212	219	4.065110	GTGGACTCAACTGCCACC	57.935	61.111	0.00	0.00	44.86	4.61
282	295	0.182775	AAAGCTTGGTTGGGTCTCGT	59.817	50.000	0.00	0.00	0.00	4.18
349	391	7.360353	GGTTCACCTTTTTCTATACGTTGGTAC	60.360	40.741	0.00	0.00	0.00	3.34
350	392	6.650390	GGTTCACCTTTTTCTATACGTTGGTA	59.350	38.462	0.00	0.00	0.00	3.25
351	393	5.471116	GGTTCACCTTTTTCTATACGTTGGT	59.529	40.000	0.00	0.00	0.00	3.67
353	395	6.796705	AGGTTCACCTTTTTCTATACGTTG	57.203	37.500	0.00	0.00	46.09	4.10
453	667	4.120792	TGCAATGCTGTTTGTTTCTTCA	57.879	36.364	6.82	0.00	0.00	3.02
721	1089	2.985847	GAGGCAGTGGGTTGGTGC	60.986	66.667	0.00	0.00	36.42	5.01
786	1159	2.696125	GGGGAATGGAGGGAGGCA	60.696	66.667	0.00	0.00	0.00	4.75
860	1258	4.892345	TGGAATTGATGTGTGTCCTGAAAA	59.108	37.500	0.00	0.00	0.00	2.29
861	1259	4.468713	TGGAATTGATGTGTGTCCTGAAA	58.531	39.130	0.00	0.00	0.00	2.69
862	1260	4.097551	TGGAATTGATGTGTGTCCTGAA	57.902	40.909	0.00	0.00	0.00	3.02
863	1261	3.786368	TGGAATTGATGTGTGTCCTGA	57.214	42.857	0.00	0.00	0.00	3.86
864	1262	6.767423	TGTATATGGAATTGATGTGTGTCCTG	59.233	38.462	0.00	0.00	0.00	3.86
865	1263	6.767902	GTGTATATGGAATTGATGTGTGTCCT	59.232	38.462	0.00	0.00	0.00	3.85
866	1264	6.542005	TGTGTATATGGAATTGATGTGTGTCC	59.458	38.462	0.00	0.00	0.00	4.02
867	1265	7.552458	TGTGTATATGGAATTGATGTGTGTC	57.448	36.000	0.00	0.00	0.00	3.67
868	1266	9.056005	GTATGTGTATATGGAATTGATGTGTGT	57.944	33.333	0.00	0.00	0.00	3.72
869	1267	9.054922	TGTATGTGTATATGGAATTGATGTGTG	57.945	33.333	0.00	0.00	0.00	3.82
870	1268	9.056005	GTGTATGTGTATATGGAATTGATGTGT	57.944	33.333	0.00	0.00	0.00	3.72
871	1269	8.506437	GGTGTATGTGTATATGGAATTGATGTG	58.494	37.037	0.00	0.00	0.00	3.21
872	1270	8.439971	AGGTGTATGTGTATATGGAATTGATGT	58.560	33.333	0.00	0.00	0.00	3.06
873	1271	8.724229	CAGGTGTATGTGTATATGGAATTGATG	58.276	37.037	0.00	0.00	0.00	3.07
874	1272	7.391554	GCAGGTGTATGTGTATATGGAATTGAT	59.608	37.037	0.00	0.00	0.00	2.57
875	1273	6.710295	GCAGGTGTATGTGTATATGGAATTGA	59.290	38.462	0.00	0.00	0.00	2.57
876	1274	6.072508	GGCAGGTGTATGTGTATATGGAATTG	60.073	42.308	0.00	0.00	0.00	2.32
877	1275	6.003950	GGCAGGTGTATGTGTATATGGAATT	58.996	40.000	0.00	0.00	0.00	2.17
878	1276	5.514834	GGGCAGGTGTATGTGTATATGGAAT	60.515	44.000	0.00	0.00	0.00	3.01
879	1277	4.202419	GGGCAGGTGTATGTGTATATGGAA	60.202	45.833	0.00	0.00	0.00	3.53
884	1282	3.380393	AGTGGGCAGGTGTATGTGTATA	58.620	45.455	0.00	0.00	0.00	1.47
902	1300	4.248859	TGAAAGCAAGCTAGCTAGAAGTG	58.751	43.478	25.15	17.50	45.89	3.16
905	1303	4.808414	TCTGAAAGCAAGCTAGCTAGAA	57.192	40.909	25.15	0.00	45.89	2.10
1092	1504	2.441901	CCTGAGAGCTCCTCCGCT	60.442	66.667	10.93	0.00	44.33	5.52
1107	1519	1.524621	CGCATCGAAATGGCTCCCT	60.525	57.895	0.00	0.00	33.19	4.20
1119	1531	2.586079	ATCCGCTTCACCGCATCG	60.586	61.111	0.00	0.00	0.00	3.84
2114	2568	1.837051	TGGGTCAAGCTCACCGAGT	60.837	57.895	8.38	0.00	34.33	4.18
2396	2850	4.750098	CCATTGTTGTAGAAGTCGTTCACT	59.250	41.667	0.00	0.00	36.64	3.41
3937	4526	0.949105	CACGCGCCAAAAGGAGTAGT	60.949	55.000	5.73	0.00	0.00	2.73
3960	6026	1.332997	GTAGGATACGGTGGACAGTCG	59.667	57.143	0.00	0.00	46.39	4.18
3979	6045	6.615088	GGACATACATTATACATACGTCGGT	58.385	40.000	0.00	0.00	0.00	4.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.