AutoCloner

Multiple sequence alignment - TraesCS4B01G073700

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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	TraesCS4B01G073700	chr4B	100.000	3228	0	0	1	3228	68953702	68956929	0.000000e+00	5962.0
1	TraesCS4B01G073700	chr4B	89.705	3225	168	65	58	3228	68719461	68722575	0.000000e+00	3965.0
2	TraesCS4B01G073700	chr4B	97.304	1261	24	5	1254	2505	68125131	68123872	0.000000e+00	2132.0
3	TraesCS4B01G073700	chr4B	88.219	713	51	15	2505	3200	68123765	68123069	0.000000e+00	821.0
4	TraesCS4B01G073700	chr4B	92.683	287	11	4	1255	1541	68701182	68701458	3.880000e-109	405.0
5	TraesCS4B01G073700	chr4B	83.333	396	44	8	58	436	68699828	68700218	2.380000e-91	346.0
6	TraesCS4B01G073700	chr4B	89.344	244	10	5	1536	1770	68718803	68719039	3.150000e-75	292.0
7	TraesCS4B01G073700	chr4B	98.438	64	1	0	1	64	390144651	390144588	2.630000e-21	113.0
8	TraesCS4B01G073700	chr4B	88.506	87	6	4	1	86	508486871	508486788	5.700000e-18	102.0
9	TraesCS4B01G073700	chr4B	100.000	35	0	0	264	298	519423323	519423289	7.480000e-07	65.8
10	TraesCS4B01G073700	chr4A	85.124	2588	191	79	727	3228	551138828	551136349	0.000000e+00	2468.0
11	TraesCS4B01G073700	chr4A	91.888	1393	76	12	1440	2798	533466896	533465507	0.000000e+00	1912.0
12	TraesCS4B01G073700	chr4A	91.044	1418	72	15	1432	2822	552250469	552251858	0.000000e+00	1864.0
13	TraesCS4B01G073700	chr4A	84.184	803	61	28	2441	3228	533464978	533464227	0.000000e+00	719.0
14	TraesCS4B01G073700	chr4A	88.419	544	26	18	1806	2324	533465509	533464978	3.540000e-174	621.0
15	TraesCS4B01G073700	chr4A	88.615	325	20	12	2914	3228	552251895	552252212	2.350000e-101	379.0
16	TraesCS4B01G073700	chr4A	87.931	290	27	4	1123	1405	533473033	533472745	5.160000e-88	335.0
17	TraesCS4B01G073700	chr4A	81.818	132	18	4	2121	2248	556782756	556782885	4.400000e-19	106.0
18	TraesCS4B01G073700	chr4A	81.818	132	18	4	2121	2248	556805319	556805448	4.400000e-19	106.0
19	TraesCS4B01G073700	chr4A	97.619	42	1	0	2831	2872	552251853	552251894	4.470000e-09	73.1
20	TraesCS4B01G073700	chr4D	83.566	2720	236	85	627	3228	47329593	47332219	0.000000e+00	2351.0
21	TraesCS4B01G073700	chr4D	85.624	1739	120	52	1163	2822	46628349	46626662	0.000000e+00	1707.0
22	TraesCS4B01G073700	chr4D	86.520	1276	94	37	1029	2248	47322014	47323267	0.000000e+00	1332.0
23	TraesCS4B01G073700	chr4D	87.148	817	59	20	2438	3228	47323804	47324600	0.000000e+00	885.0
24	TraesCS4B01G073700	chr4D	81.575	597	74	26	438	1031	47321242	47321805	8.160000e-126	460.0
25	TraesCS4B01G073700	chr4D	89.231	325	19	12	2914	3228	46626625	46626307	3.020000e-105	392.0
26	TraesCS4B01G073700	chr4D	90.667	75	7	0	267	341	47321024	47321098	2.050000e-17	100.0
27	TraesCS4B01G073700	chr7B	98.413	63	1	0	1	63	50745061	50744999	9.470000e-21	111.0
28	TraesCS4B01G073700	chr6B	95.652	69	3	0	1	69	204954768	204954700	9.470000e-21	111.0
29	TraesCS4B01G073700	chr6B	92.105	76	4	2	1	75	506689132	506689206	4.400000e-19	106.0
30	TraesCS4B01G073700	chr2B	94.521	73	2	2	1	72	752416968	752416897	9.470000e-21	111.0
31	TraesCS4B01G073700	chr1B	96.923	65	2	0	1	65	408089948	408089884	3.400000e-20	110.0
32	TraesCS4B01G073700	chr1B	94.286	70	4	0	1	70	34834306	34834237	1.220000e-19	108.0
33	TraesCS4B01G073700	chr2A	93.151	73	4	1	1	72	586558492	586558420	4.400000e-19	106.0

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	TraesCS4B01G073700	chr4B	68953702	68956929	3227	False	5962.000000	5962	100.000000	1	3228	1	chr4B.!!$F1	3227
1	TraesCS4B01G073700	chr4B	68718803	68722575	3772	False	2128.500000	3965	89.524500	58	3228	2	chr4B.!!$F3	3170
2	TraesCS4B01G073700	chr4B	68123069	68125131	2062	True	1476.500000	2132	92.761500	1254	3200	2	chr4B.!!$R4	1946
3	TraesCS4B01G073700	chr4B	68699828	68701458	1630	False	375.500000	405	88.008000	58	1541	2	chr4B.!!$F2	1483
4	TraesCS4B01G073700	chr4A	551136349	551138828	2479	True	2468.000000	2468	85.124000	727	3228	1	chr4A.!!$R2	2501
5	TraesCS4B01G073700	chr4A	533464227	533466896	2669	True	1084.000000	1912	88.163667	1440	3228	3	chr4A.!!$R3	1788
6	TraesCS4B01G073700	chr4A	552250469	552252212	1743	False	772.033333	1864	92.426000	1432	3228	3	chr4A.!!$F3	1796
7	TraesCS4B01G073700	chr4D	47329593	47332219	2626	False	2351.000000	2351	83.566000	627	3228	1	chr4D.!!$F1	2601
8	TraesCS4B01G073700	chr4D	46626307	46628349	2042	True	1049.500000	1707	87.427500	1163	3228	2	chr4D.!!$R1	2065
9	TraesCS4B01G073700	chr4D	47321024	47324600	3576	False	694.250000	1332	86.477500	267	3228	4	chr4D.!!$F2	2961

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
104	706	0.193574	AAACAGGGAGGAGGAGGACA	59.806	55.0	0.0	0.0	0.0	4.02	F
740	1425	0.830444	ACAAGTCGGCCCAGTAGTGA	60.830	55.0	0.0	0.0	0.0	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1645	2712	0.965866	CTGTCTCCTGGTCACGGCTA	60.966	60.0	0.0	0.0	0.0	3.93	R
2246	3851	2.467566	AAACAGTACCCCGATGTGAC	57.532	50.0	0.0	0.0	0.0	3.67	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
17	18	4.676363	CCTCGAGCCTCCTTCTCT	57.324	61.111	6.99	0.00	0.00	3.10
18	19	2.414750	CCTCGAGCCTCCTTCTCTC	58.585	63.158	6.99	0.00	0.00	3.20
20	21	1.684869	CCTCGAGCCTCCTTCTCTCTT	60.685	57.143	6.99	0.00	0.00	2.85
21	22	2.099405	CTCGAGCCTCCTTCTCTCTTT	58.901	52.381	0.00	0.00	0.00	2.52
22	23	3.283751	CTCGAGCCTCCTTCTCTCTTTA	58.716	50.000	0.00	0.00	0.00	1.85
24	25	2.223711	CGAGCCTCCTTCTCTCTTTAGC	60.224	54.545	0.00	0.00	0.00	3.09
25	26	2.102420	GAGCCTCCTTCTCTCTTTAGCC	59.898	54.545	0.00	0.00	0.00	3.93
26	27	1.834263	GCCTCCTTCTCTCTTTAGCCA	59.166	52.381	0.00	0.00	0.00	4.75
27	28	2.437651	GCCTCCTTCTCTCTTTAGCCAT	59.562	50.000	0.00	0.00	0.00	4.40
28	29	3.494223	GCCTCCTTCTCTCTTTAGCCATC	60.494	52.174	0.00	0.00	0.00	3.51
30	31	3.041946	TCCTTCTCTCTTTAGCCATCCC	58.958	50.000	0.00	0.00	0.00	3.85
31	32	2.774234	CCTTCTCTCTTTAGCCATCCCA	59.226	50.000	0.00	0.00	0.00	4.37
32	33	3.393941	CCTTCTCTCTTTAGCCATCCCAT	59.606	47.826	0.00	0.00	0.00	4.00
33	34	4.387598	CTTCTCTCTTTAGCCATCCCATG	58.612	47.826	0.00	0.00	0.00	3.66
69	671	2.290071	CCCACCACGACACTCCTTTTAT	60.290	50.000	0.00	0.00	0.00	1.40
94	696	1.303643	GAGGCCACCAAACAGGGAG	60.304	63.158	5.01	0.00	43.89	4.30
104	706	0.193574	AAACAGGGAGGAGGAGGACA	59.806	55.000	0.00	0.00	0.00	4.02
128	731	2.738643	GCATCGGCAGCTAGTACAAGAA	60.739	50.000	0.00	0.00	40.72	2.52
298	907	2.063979	CCGGGCTCATCTACACCCA	61.064	63.158	0.00	0.00	42.97	4.51
343	952	2.969262	TGTGTGATGTTCTACACCCAGA	59.031	45.455	0.00	0.00	44.94	3.86
407	1026	1.401931	GCAAGATGCTCAAATGCGTGT	60.402	47.619	0.00	0.00	40.96	4.49
416	1035	3.791789	GCTCAAATGCGTGTTGTTCTTGA	60.792	43.478	0.00	0.00	0.00	3.02
455	1135	6.958767	TGTTTCCCCAAATTTGTCCTTTTTA	58.041	32.000	16.73	0.00	0.00	1.52
543	1225	6.171921	CCATGAGCTCCTCTAATATCCAAAG	58.828	44.000	12.15	0.00	0.00	2.77
682	1365	1.410882	GAGCCGAGGTGAAGAATAGCT	59.589	52.381	0.00	0.00	0.00	3.32
683	1366	2.623889	GAGCCGAGGTGAAGAATAGCTA	59.376	50.000	0.00	0.00	0.00	3.32
740	1425	0.830444	ACAAGTCGGCCCAGTAGTGA	60.830	55.000	0.00	0.00	0.00	3.41
813	1498	7.524717	AATAAAAGTAGAGTGCCACATTGTT	57.475	32.000	0.00	0.00	0.00	2.83
819	1505	7.524717	AGTAGAGTGCCACATTGTTTAAAAT	57.475	32.000	0.00	0.00	0.00	1.82
940	1639	6.128227	CGTATTTAAGTTTGTTTCGGATCCCA	60.128	38.462	6.06	0.00	0.00	4.37
2430	4035	1.059913	AGTGCCTAGGTGCTTCTTGT	58.940	50.000	11.31	0.00	0.00	3.16
2439	4044	4.464069	AGGTGCTTCTTGTCTAGTGATC	57.536	45.455	0.00	0.00	0.00	2.92
2464	4069	9.506042	TCCTGGCCTATATGATTATCTCAATAA	57.494	33.333	3.32	0.00	37.44	1.40
2488	4093	6.709018	TTTAGATAAACCCATTGCCTTAGC	57.291	37.500	0.00	0.00	40.48	3.09
2585	4299	8.633075	TTTTCAAAGCATTAGTTGTTTGAGAG	57.367	30.769	0.00	0.00	37.03	3.20
2717	4432	2.173519	CATGAGGTGCCATCAAGGTTT	58.826	47.619	0.00	0.00	40.61	3.27
2793	4519	9.013490	CGATTTAATTGAAACTTATCCAAGCAG	57.987	33.333	0.00	0.00	34.94	4.24
2809	5409	2.890808	GCAGTAGGCTGTATGTAGCA	57.109	50.000	0.00	0.00	45.46	3.49
2819	5419	5.943416	AGGCTGTATGTAGCAATGTGTTTTA	59.057	36.000	0.00	0.00	45.46	1.52
2820	5420	6.603201	AGGCTGTATGTAGCAATGTGTTTTAT	59.397	34.615	0.00	0.00	45.46	1.40
2821	5421	7.773224	AGGCTGTATGTAGCAATGTGTTTTATA	59.227	33.333	0.00	0.00	45.46	0.98
2822	5422	8.070171	GGCTGTATGTAGCAATGTGTTTTATAG	58.930	37.037	0.00	0.00	45.46	1.31
2823	5423	8.826710	GCTGTATGTAGCAATGTGTTTTATAGA	58.173	33.333	0.00	0.00	43.17	1.98
2825	5425	9.884636	TGTATGTAGCAATGTGTTTTATAGAGT	57.115	29.630	0.00	0.00	0.00	3.24
2828	5428	8.479313	TGTAGCAATGTGTTTTATAGAGTCTG	57.521	34.615	1.86	0.00	0.00	3.51
2829	5429	6.428385	AGCAATGTGTTTTATAGAGTCTGC	57.572	37.500	1.86	0.00	0.00	4.26
2830	5430	6.176183	AGCAATGTGTTTTATAGAGTCTGCT	58.824	36.000	1.86	0.00	0.00	4.24
2831	5431	6.656693	AGCAATGTGTTTTATAGAGTCTGCTT	59.343	34.615	1.86	0.00	31.53	3.91
2832	5432	7.175641	AGCAATGTGTTTTATAGAGTCTGCTTT	59.824	33.333	1.86	0.00	31.53	3.51
3021	5638	8.625651	TGTGTGTGTAGTTTAAAGTTTATGCAT	58.374	29.630	3.79	3.79	0.00	3.96
3091	5720	9.852091	AGTTCTAAATTCAGATTGAAAATCAGC	57.148	29.630	3.03	0.00	40.12	4.26
3101	5730	2.170166	TGAAAATCAGCGGAATGGCTT	58.830	42.857	0.00	0.00	42.53	4.35
3102	5731	2.094597	TGAAAATCAGCGGAATGGCTTG	60.095	45.455	0.00	0.00	42.53	4.01
3103	5732	1.838112	AAATCAGCGGAATGGCTTGA	58.162	45.000	0.00	0.00	42.53	3.02
3104	5733	2.062971	AATCAGCGGAATGGCTTGAT	57.937	45.000	0.00	0.00	42.53	2.57
3105	5734	1.602311	ATCAGCGGAATGGCTTGATC	58.398	50.000	0.00	0.00	42.53	2.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	0.106719	AGAGAGAAGGAGGCTCGAGG	60.107	60.000	15.58	0.00	37.46	4.63
3	4	2.223711	GCTAAAGAGAGAAGGAGGCTCG	60.224	54.545	8.69	0.00	37.46	5.03
6	7	1.834263	TGGCTAAAGAGAGAAGGAGGC	59.166	52.381	0.00	0.00	0.00	4.70
7	8	3.070878	GGATGGCTAAAGAGAGAAGGAGG	59.929	52.174	0.00	0.00	0.00	4.30
8	9	3.070878	GGGATGGCTAAAGAGAGAAGGAG	59.929	52.174	0.00	0.00	0.00	3.69
11	12	4.387598	CATGGGATGGCTAAAGAGAGAAG	58.612	47.826	0.00	0.00	0.00	2.85
13	14	2.707791	CCATGGGATGGCTAAAGAGAGA	59.292	50.000	2.85	0.00	44.70	3.10
14	15	3.137446	CCATGGGATGGCTAAAGAGAG	57.863	52.381	2.85	0.00	44.70	3.20
48	49	0.179029	AAAAGGAGTGTCGTGGTGGG	60.179	55.000	0.00	0.00	0.00	4.61
51	52	3.660865	GACATAAAAGGAGTGTCGTGGT	58.339	45.455	0.00	0.00	33.73	4.16
56	57	3.829948	TCGTCGACATAAAAGGAGTGTC	58.170	45.455	17.16	0.00	39.02	3.67
69	671	2.798364	TTTGGTGGCCTCGTCGACA	61.798	57.895	17.16	1.87	0.00	4.35
94	696	1.144936	CGATGCCTTGTCCTCCTCC	59.855	63.158	0.00	0.00	0.00	4.30
104	706	0.105039	GTACTAGCTGCCGATGCCTT	59.895	55.000	0.00	0.00	36.33	4.35
455	1135	2.289945	GGACATTTGAGGAGCTCACAGT	60.290	50.000	17.19	9.24	40.46	3.55
543	1225	8.472236	GTGATGTTCTTGAAAAATTTCGAGTTC	58.528	33.333	18.23	13.85	45.07	3.01
703	1388	3.428746	TGTGTAACATGCGCAAAAAGT	57.571	38.095	17.11	8.38	45.67	2.66
740	1425	1.061346	AGATGGGGTAGCAGTATGGGT	60.061	52.381	0.00	0.00	35.86	4.51
813	1498	7.270047	ACTTGTGGCGCTCTACTATATTTTAA	58.730	34.615	7.64	0.00	0.00	1.52
819	1505	3.446161	ACAACTTGTGGCGCTCTACTATA	59.554	43.478	7.64	0.00	0.00	1.31
940	1639	0.392060	GGCGACGGATTACAGGGTTT	60.392	55.000	0.00	0.00	0.00	3.27
1645	2712	0.965866	CTGTCTCCTGGTCACGGCTA	60.966	60.000	0.00	0.00	0.00	3.93
1671	2738	4.683432	GCTCCTCTGCGACAACTT	57.317	55.556	0.00	0.00	0.00	2.66
2246	3851	2.467566	AAACAGTACCCCGATGTGAC	57.532	50.000	0.00	0.00	0.00	3.67
2430	4035	5.536497	TCATATAGGCCAGGATCACTAGA	57.464	43.478	5.01	0.00	0.00	2.43
2464	4069	6.838612	TGCTAAGGCAATGGGTTTATCTAAAT	59.161	34.615	0.00	0.00	46.36	1.40
2559	4273	8.994429	TCTCAAACAACTAATGCTTTGAAAAA	57.006	26.923	0.00	0.00	37.96	1.94
2585	4299	3.430895	CACAACCATCAGAAAATTGCAGC	59.569	43.478	0.00	0.00	0.00	5.25
2793	4519	4.442706	ACACATTGCTACATACAGCCTAC	58.557	43.478	0.00	0.00	41.04	3.18
2819	5419	9.486497	CACAACATCATATAAAGCAGACTCTAT	57.514	33.333	0.00	0.00	0.00	1.98
2820	5420	8.478066	ACACAACATCATATAAAGCAGACTCTA	58.522	33.333	0.00	0.00	0.00	2.43
2821	5421	7.279536	CACACAACATCATATAAAGCAGACTCT	59.720	37.037	0.00	0.00	0.00	3.24
2822	5422	7.065085	ACACACAACATCATATAAAGCAGACTC	59.935	37.037	0.00	0.00	0.00	3.36
2823	5423	6.881065	ACACACAACATCATATAAAGCAGACT	59.119	34.615	0.00	0.00	0.00	3.24
2824	5424	7.076842	ACACACAACATCATATAAAGCAGAC	57.923	36.000	0.00	0.00	0.00	3.51
2825	5425	7.390162	TCAACACACAACATCATATAAAGCAGA	59.610	33.333	0.00	0.00	0.00	4.26
2826	5426	7.482743	GTCAACACACAACATCATATAAAGCAG	59.517	37.037	0.00	0.00	0.00	4.24
2827	5427	7.040823	TGTCAACACACAACATCATATAAAGCA	60.041	33.333	0.00	0.00	0.00	3.91
2828	5428	7.304735	TGTCAACACACAACATCATATAAAGC	58.695	34.615	0.00	0.00	0.00	3.51
2829	5429	9.333497	CTTGTCAACACACAACATCATATAAAG	57.667	33.333	0.00	0.00	32.70	1.85
2830	5430	8.296000	CCTTGTCAACACACAACATCATATAAA	58.704	33.333	0.00	0.00	32.70	1.40
2831	5431	7.663493	TCCTTGTCAACACACAACATCATATAA	59.337	33.333	0.00	0.00	32.70	0.98
2832	5432	7.119116	GTCCTTGTCAACACACAACATCATATA	59.881	37.037	0.00	0.00	32.70	0.86
2936	5539	7.743749	ACATTTGCTAGTCAAGATGGATAGAT	58.256	34.615	16.39	0.00	35.84	1.98
2997	5614	8.079203	CCATGCATAAACTTTAAACTACACACA	58.921	33.333	0.00	0.00	0.00	3.72
2998	5615	8.079809	ACCATGCATAAACTTTAAACTACACAC	58.920	33.333	0.00	0.00	0.00	3.82
2999	5616	8.172352	ACCATGCATAAACTTTAAACTACACA	57.828	30.769	0.00	0.00	0.00	3.72
3000	5617	8.293867	TGACCATGCATAAACTTTAAACTACAC	58.706	33.333	0.00	0.00	0.00	2.90
3021	5638	8.121305	ACTGCAATTATTAGTTCATTTGACCA	57.879	30.769	0.00	0.00	0.00	4.02
3087	5715	0.543277	AGATCAAGCCATTCCGCTGA	59.457	50.000	0.00	0.00	39.64	4.26
3091	5720	1.473677	TGCAAAGATCAAGCCATTCCG	59.526	47.619	0.00	0.00	0.00	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.