AutoCloner

Multiple sequence alignment - TraesCS2A01G509800

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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	TraesCS2A01G509800	chr2A	100.000	3139	0	0	1	3139	735352288	735349150	0.000000e+00	5797.0
1	TraesCS2A01G509800	chr2A	84.158	101	16	0	1389	1489	60068979	60068879	7.160000e-17	99.0
2	TraesCS2A01G509800	chr2A	93.548	62	3	1	1436	1496	60195338	60195277	1.200000e-14	91.6
3	TraesCS2A01G509800	chr2A	96.296	54	2	0	1436	1489	60078988	60078935	4.310000e-14	89.8
4	TraesCS2A01G509800	chr2A	83.750	80	13	0	1717	1796	59873139	59873060	3.360000e-10	76.8
5	TraesCS2A01G509800	chr2A	83.750	80	13	0	1717	1796	59933166	59933087	3.360000e-10	76.8
6	TraesCS2A01G509800	chr2B	92.446	2330	117	28	253	2556	733078674	733076378	0.000000e+00	3273.0
7	TraesCS2A01G509800	chr2B	95.333	600	24	2	2544	3139	186370861	186370262	0.000000e+00	950.0
8	TraesCS2A01G509800	chr2B	92.369	249	16	2	21	269	733080920	733080675	4.980000e-93	351.0
9	TraesCS2A01G509800	chr2D	94.428	1741	75	11	828	2556	602712788	602711058	0.000000e+00	2658.0
10	TraesCS2A01G509800	chr2D	88.303	1915	131	52	504	2365	601982534	601984408	0.000000e+00	2209.0
11	TraesCS2A01G509800	chr2D	97.449	588	15	0	2552	3139	11518070	11518657	0.000000e+00	1003.0
12	TraesCS2A01G509800	chr2D	96.088	588	23	0	2552	3139	516853434	516852847	0.000000e+00	959.0
13	TraesCS2A01G509800	chr2D	90.018	551	39	7	1	540	602713380	602712835	0.000000e+00	699.0
14	TraesCS2A01G509800	chr2D	85.012	407	45	8	107	503	601981976	601982376	1.750000e-107	399.0
15	TraesCS2A01G509800	chr2D	98.148	54	1	0	1436	1489	60078912	60078859	9.270000e-16	95.3
16	TraesCS2A01G509800	chr2D	96.296	54	2	0	1436	1489	60064935	60064882	4.310000e-14	89.8
17	TraesCS2A01G509800	chr7D	97.279	588	15	1	2552	3139	546757458	546758044	0.000000e+00	996.0
18	TraesCS2A01G509800	chr7D	94.444	36	2	0	1182	1217	151825014	151825049	4.370000e-04	56.5
19	TraesCS2A01G509800	chr7D	94.444	36	2	0	1182	1217	151931195	151931230	4.370000e-04	56.5
20	TraesCS2A01G509800	chr1B	95.918	588	24	0	2552	3139	349978603	349978016	0.000000e+00	953.0
21	TraesCS2A01G509800	chr6D	95.756	589	25	0	2551	3139	52692496	52693084	0.000000e+00	950.0
22	TraesCS2A01G509800	chr6D	95.897	585	23	1	2552	3135	7889719	7890303	0.000000e+00	946.0
23	TraesCS2A01G509800	chr6D	95.578	588	25	1	2552	3138	142865971	142865384	0.000000e+00	941.0
24	TraesCS2A01G509800	chr6D	71.429	588	133	30	1565	2141	90923950	90924513	4.250000e-24	122.0
25	TraesCS2A01G509800	chr6D	78.378	185	29	7	1297	1471	90922940	90923123	3.310000e-20	110.0
26	TraesCS2A01G509800	chr6D	88.136	59	7	0	1167	1225	392513445	392513503	1.560000e-08	71.3
27	TraesCS2A01G509800	chr3D	95.578	588	24	2	2552	3138	167412018	167411432	0.000000e+00	941.0
28	TraesCS2A01G509800	chr4B	93.651	63	4	0	535	597	145806252	145806190	9.270000e-16	95.3
29	TraesCS2A01G509800	chr7B	84.615	91	13	1	1698	1788	504440113	504440202	4.310000e-14	89.8
30	TraesCS2A01G509800	chr7B	84.615	91	13	1	1698	1788	504456778	504456867	4.310000e-14	89.8
31	TraesCS2A01G509800	chr4A	91.045	67	5	1	535	601	473687065	473687130	4.310000e-14	89.8
32	TraesCS2A01G509800	chr7A	74.091	220	51	4	1575	1791	516514432	516514216	5.580000e-13	86.1
33	TraesCS2A01G509800	chr7A	97.222	36	1	0	1182	1217	152507321	152507356	9.400000e-06	62.1
34	TraesCS2A01G509800	chr4D	90.476	63	6	0	535	597	101656690	101656628	2.010000e-12	84.2
35	TraesCS2A01G509800	chr6B	90.385	52	5	0	1167	1218	585902085	585902136	5.620000e-08	69.4

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	TraesCS2A01G509800	chr2A	735349150	735352288	3138	True	5797.0	5797	100.0000	1	3139	1	chr2A.!!$R6	3138
1	TraesCS2A01G509800	chr2B	733076378	733080920	4542	True	1812.0	3273	92.4075	21	2556	2	chr2B.!!$R2	2535
2	TraesCS2A01G509800	chr2B	186370262	186370861	599	True	950.0	950	95.3330	2544	3139	1	chr2B.!!$R1	595
3	TraesCS2A01G509800	chr2D	602711058	602713380	2322	True	1678.5	2658	92.2230	1	2556	2	chr2D.!!$R4	2555
4	TraesCS2A01G509800	chr2D	601981976	601984408	2432	False	1304.0	2209	86.6575	107	2365	2	chr2D.!!$F2	2258
5	TraesCS2A01G509800	chr2D	11518070	11518657	587	False	1003.0	1003	97.4490	2552	3139	1	chr2D.!!$F1	587
6	TraesCS2A01G509800	chr2D	516852847	516853434	587	True	959.0	959	96.0880	2552	3139	1	chr2D.!!$R3	587
7	TraesCS2A01G509800	chr7D	546757458	546758044	586	False	996.0	996	97.2790	2552	3139	1	chr7D.!!$F3	587
8	TraesCS2A01G509800	chr1B	349978016	349978603	587	True	953.0	953	95.9180	2552	3139	1	chr1B.!!$R1	587
9	TraesCS2A01G509800	chr6D	52692496	52693084	588	False	950.0	950	95.7560	2551	3139	1	chr6D.!!$F2	588
10	TraesCS2A01G509800	chr6D	7889719	7890303	584	False	946.0	946	95.8970	2552	3135	1	chr6D.!!$F1	583
11	TraesCS2A01G509800	chr6D	142865384	142865971	587	True	941.0	941	95.5780	2552	3138	1	chr6D.!!$R1	586
12	TraesCS2A01G509800	chr3D	167411432	167412018	586	True	941.0	941	95.5780	2552	3138	1	chr3D.!!$R1	586

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
763	2972	0.596082	AATCCCAAAGCAACGAACCG	59.404	50.0	0.0	0.0	0.0	4.44	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2447	4716	0.958091	TTTGTCAGACCGCCCAATTG	59.042	50.0	0.0	0.0	0.0	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
46	47	2.354003	GGTTGCTCCCAATGTTCAATGG	60.354	50.000	0.32	0.32	36.42	3.16
50	51	2.528564	CTCCCAATGTTCAATGGTGGT	58.471	47.619	6.22	0.00	34.79	4.16
66	67	2.352519	GGTGGTGTCGTCTCTTAGTTCC	60.353	54.545	0.00	0.00	0.00	3.62
76	77	4.333095	CGTCTCTTAGTTCCTCGAATCAGA	59.667	45.833	0.00	0.00	0.00	3.27
88	89	6.982852	TCCTCGAATCAGATTGTTATCTACC	58.017	40.000	0.00	0.00	39.11	3.18
131	132	9.149225	GGAGTATGTAGCAGATAATGAATGAAG	57.851	37.037	0.00	0.00	0.00	3.02
157	163	6.385176	AGAGATGATGAAACTGTCCCTTATCA	59.615	38.462	0.00	0.00	0.00	2.15
226	232	9.431887	TCTTAATAAAAGTGGACACAGACATAC	57.568	33.333	5.14	0.00	0.00	2.39
243	250	5.730550	GACATACAAGTGTCACCATTCCTA	58.269	41.667	0.00	0.00	46.04	2.94
274	2296	3.336694	ACCAAGGAAATAGGAATGGTGGT	59.663	43.478	0.00	0.00	39.57	4.16
349	2372	9.275398	TGTTTAAGGTTCATATTACGTTTCTGT	57.725	29.630	0.00	0.00	0.00	3.41
499	2692	6.454054	CGCAACGAAACATTATGATGCATTTT	60.454	34.615	0.00	0.00	36.72	1.82
500	2693	7.253585	CGCAACGAAACATTATGATGCATTTTA	60.254	33.333	0.00	0.00	36.72	1.52
501	2694	8.379161	GCAACGAAACATTATGATGCATTTTAA	58.621	29.630	0.00	2.64	36.72	1.52
555	2749	3.855895	GCGCTATAGTGTTCCGAGCAATA	60.856	47.826	14.57	0.00	32.55	1.90
633	2841	6.096695	GCTAAATTGAATTTTAAGGACCGCA	58.903	36.000	8.60	0.00	33.82	5.69
637	2845	7.404671	AATTGAATTTTAAGGACCGCACTAT	57.595	32.000	0.00	0.00	0.00	2.12
762	2971	1.611491	TGAATCCCAAAGCAACGAACC	59.389	47.619	0.00	0.00	0.00	3.62
763	2972	0.596082	AATCCCAAAGCAACGAACCG	59.404	50.000	0.00	0.00	0.00	4.44
803	3012	2.099756	GGTAGAACATCATTTGGCTGGC	59.900	50.000	0.00	0.00	0.00	4.85
835	3044	8.603181	CACCTCTGTTAATTTGTTTGGAAAAAG	58.397	33.333	0.00	0.00	0.00	2.27
942	3157	3.454375	GCACACACTACACACTACACTT	58.546	45.455	0.00	0.00	0.00	3.16
972	3195	7.031226	TCAAGTCAGAAAATTCTCTTTGTGG	57.969	36.000	0.00	0.00	34.74	4.17
977	3200	6.710744	GTCAGAAAATTCTCTTTGTGGGTAGA	59.289	38.462	0.00	0.00	34.74	2.59
979	3202	7.607991	TCAGAAAATTCTCTTTGTGGGTAGATC	59.392	37.037	0.00	0.00	34.74	2.75
980	3203	7.609532	CAGAAAATTCTCTTTGTGGGTAGATCT	59.390	37.037	0.00	0.00	34.74	2.75
981	3204	8.826765	AGAAAATTCTCTTTGTGGGTAGATCTA	58.173	33.333	0.00	0.00	29.94	1.98
982	3205	9.103861	GAAAATTCTCTTTGTGGGTAGATCTAG	57.896	37.037	1.64	0.00	0.00	2.43
983	3206	6.739331	ATTCTCTTTGTGGGTAGATCTAGG	57.261	41.667	1.64	0.00	0.00	3.02
984	3207	3.961408	TCTCTTTGTGGGTAGATCTAGGC	59.039	47.826	1.64	0.00	0.00	3.93
985	3208	3.706594	CTCTTTGTGGGTAGATCTAGGCA	59.293	47.826	1.64	0.00	0.00	4.75
986	3209	4.101114	TCTTTGTGGGTAGATCTAGGCAA	58.899	43.478	1.64	3.76	0.00	4.52
987	3210	4.162320	TCTTTGTGGGTAGATCTAGGCAAG	59.838	45.833	1.64	0.98	0.00	4.01
1231	3460	1.792367	TCGTCAATGCAAGTGTCTTCG	59.208	47.619	0.00	0.00	31.21	3.79
1380	3612	1.671379	GAACTCCCTTCGCGGCTTT	60.671	57.895	6.13	0.00	0.00	3.51
1522	3757	7.719483	ACAAGCTTCAGAATTCAGATCAAAAA	58.281	30.769	8.44	0.00	0.00	1.94
1569	3816	1.344438	TGAACTCCGATCAACTGCAGT	59.656	47.619	15.25	15.25	0.00	4.40
2140	4387	0.106268	TGCAGGAAGGCCAACTGAAA	60.106	50.000	21.15	8.65	36.29	2.69
2142	4389	1.203287	GCAGGAAGGCCAACTGAAATC	59.797	52.381	21.15	3.96	36.29	2.17
2160	4413	1.112916	TCGAGTCAACTGTGCCAGGA	61.113	55.000	7.06	0.00	35.51	3.86
2241	4507	2.222445	CCAACGGTTGCAGTACTACAAC	59.778	50.000	24.94	24.94	44.29	3.32
2320	4587	3.889196	TGTTACTCGATTTTGTGCACC	57.111	42.857	15.69	0.00	0.00	5.01
2342	4611	8.449397	GCACCATATAAGTTTGATGATCTGATC	58.551	37.037	10.72	10.72	0.00	2.92
2374	4643	6.957984	TTCTTCGAGACAAATCAGATCTTG	57.042	37.500	0.00	0.00	0.00	3.02
2433	4702	0.965363	CTGGGCCTAATTTGTGCCGT	60.965	55.000	4.53	0.00	46.31	5.68
2624	4893	5.545658	TCGTGTTGAGAAATATTTGCCTC	57.454	39.130	5.17	7.60	0.00	4.70
2675	4944	2.105821	AGAGACCATGTCAAACCCGAAA	59.894	45.455	0.00	0.00	34.60	3.46
2680	4949	3.005367	ACCATGTCAAACCCGAAATGTTC	59.995	43.478	0.00	0.00	29.80	3.18
2748	5017	4.993028	AGTAAGGTGCAAGGTCCAAATTA	58.007	39.130	0.00	0.00	0.00	1.40
2946	5218	6.093495	TGCAAGTTGAAATATTTAGAGACCGG	59.907	38.462	7.16	0.00	0.00	5.28

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	3.536956	TGGGAGCAACCTAATAACTCG	57.463	47.619	0.00	0.00	38.98	4.18
46	47	2.557490	AGGAACTAAGAGACGACACCAC	59.443	50.000	0.00	0.00	36.02	4.16
50	51	3.049708	TCGAGGAACTAAGAGACGACA	57.950	47.619	0.00	0.00	41.55	4.35
66	67	6.159988	GGGGTAGATAACAATCTGATTCGAG	58.840	44.000	0.00	0.00	32.36	4.04
76	77	4.410883	TGAACATCGGGGGTAGATAACAAT	59.589	41.667	0.00	0.00	0.00	2.71
88	89	1.745087	CTCCAACATTGAACATCGGGG	59.255	52.381	0.00	0.00	0.00	5.73
131	132	4.751767	AGGGACAGTTTCATCATCTCTC	57.248	45.455	0.00	0.00	0.00	3.20
193	199	9.290988	TGTGTCCACTTTTATTAAGATTGCTTA	57.709	29.630	0.00	0.00	35.56	3.09
274	2296	4.346730	TGATAGAAAACCCACTCTCGGTA	58.653	43.478	0.00	0.00	31.69	4.02
308	2330	4.377431	CCTTAAACAACATCAGACGACAGC	60.377	45.833	0.00	0.00	0.00	4.40
310	2332	4.699637	ACCTTAAACAACATCAGACGACA	58.300	39.130	0.00	0.00	0.00	4.35
312	2334	5.361427	TGAACCTTAAACAACATCAGACGA	58.639	37.500	0.00	0.00	0.00	4.20
402	2429	7.500892	ACCCAACAAATCGCTATGATACATTTA	59.499	33.333	0.00	0.00	35.84	1.40
475	2507	5.954434	AATGCATCATAATGTTTCGTTGC	57.046	34.783	0.00	0.00	35.18	4.17
500	2693	9.612066	TTTCAATGACCTTTTCTTGCTTTATTT	57.388	25.926	0.00	0.00	0.00	1.40
501	2694	9.612066	TTTTCAATGACCTTTTCTTGCTTTATT	57.388	25.926	0.00	0.00	0.00	1.40
502	2695	9.612066	TTTTTCAATGACCTTTTCTTGCTTTAT	57.388	25.926	0.00	0.00	0.00	1.40
531	2724	1.266175	GCTCGGAACACTATAGCGCTA	59.734	52.381	21.30	21.30	0.00	4.26
572	2766	6.252869	ACGCTATAGTGAACGATTTTACACTG	59.747	38.462	19.99	0.00	42.37	3.66
700	2909	7.766723	TTTTGCAATGTTTGTTTGTTTTACG	57.233	28.000	0.00	0.00	0.00	3.18
762	2971	2.104770	ATACCGTGCATGCATTCGCG	62.105	55.000	25.64	22.65	42.97	5.87
763	2972	0.658244	CATACCGTGCATGCATTCGC	60.658	55.000	25.64	9.96	39.24	4.70
803	3012	1.821216	AATTAACAGAGGTGGCACCG	58.179	50.000	29.76	18.72	44.90	4.94
835	3044	2.338500	CTGACTCGCTGTACCCTTTTC	58.662	52.381	0.00	0.00	0.00	2.29
911	3126	1.929806	TAGTGTGTGCCGGCTACGAG	61.930	60.000	29.70	0.00	44.60	4.18
914	3129	1.012486	GTGTAGTGTGTGCCGGCTAC	61.012	60.000	29.70	25.35	35.62	3.58
942	3157	9.784531	AAAGAGAATTTTCTGACTTGAGTATGA	57.215	29.630	0.00	0.00	37.73	2.15
972	3195	3.231818	TGCCTACTTGCCTAGATCTACC	58.768	50.000	0.00	0.00	0.00	3.18
977	3200	3.973973	TGGTAATGCCTACTTGCCTAGAT	59.026	43.478	0.00	0.00	38.35	1.98
979	3202	3.838244	TGGTAATGCCTACTTGCCTAG	57.162	47.619	0.00	0.00	38.35	3.02
980	3203	4.165180	TCATTGGTAATGCCTACTTGCCTA	59.835	41.667	0.00	0.00	38.77	3.93
981	3204	3.053693	TCATTGGTAATGCCTACTTGCCT	60.054	43.478	0.00	0.00	38.77	4.75
982	3205	3.066760	GTCATTGGTAATGCCTACTTGCC	59.933	47.826	0.00	0.00	38.77	4.52
983	3206	3.694072	TGTCATTGGTAATGCCTACTTGC	59.306	43.478	0.00	0.00	38.77	4.01
984	3207	5.589855	TGATGTCATTGGTAATGCCTACTTG	59.410	40.000	0.00	0.00	38.77	3.16
985	3208	5.754782	TGATGTCATTGGTAATGCCTACTT	58.245	37.500	0.00	0.00	38.77	2.24
986	3209	5.372343	TGATGTCATTGGTAATGCCTACT	57.628	39.130	0.00	0.00	38.77	2.57
987	3210	5.182001	GGATGATGTCATTGGTAATGCCTAC	59.818	44.000	0.00	0.00	38.77	3.18
1080	3309	2.029365	GTCGTAGAATTCAGCCGAAAGC	59.971	50.000	8.44	0.00	39.69	3.51
1231	3460	2.448219	GTATGAAGGTGACGAGCGTAC	58.552	52.381	0.00	0.00	0.00	3.67
1380	3612	1.241315	TGATGTCGTCGACCAGCTCA	61.241	55.000	22.05	15.57	0.00	4.26
1615	3862	3.733960	CGTCCTGGCTCGTCGTCA	61.734	66.667	0.00	0.00	0.00	4.35
2374	4643	3.061006	CGAACTTTCAGCACACAAATTGC	60.061	43.478	0.00	0.00	40.52	3.56
2433	4702	1.461512	CCAATTGCGTAACGTGTAGCA	59.538	47.619	0.00	7.81	37.89	3.49
2447	4716	0.958091	TTTGTCAGACCGCCCAATTG	59.042	50.000	0.00	0.00	0.00	2.32
2462	4731	6.754193	TCCACTTTGAGTTTTGAGTTTTTGT	58.246	32.000	0.00	0.00	0.00	2.83
2675	4944	5.060506	TGTCCAAATACACGTTCAGAACAT	58.939	37.500	13.82	0.00	0.00	2.71
2680	4949	3.246699	ACGTTGTCCAAATACACGTTCAG	59.753	43.478	0.00	0.00	35.26	3.02
2748	5017	8.470002	GTTTAGAATCATTACCCTTGATGCTTT	58.530	33.333	0.00	0.00	39.65	3.51
2946	5218	1.748493	TGGAGCCGGCAATTTTATGAC	59.252	47.619	31.54	6.06	0.00	3.06
3096	5369	9.855021	AGGTACATAGTTTTCATTTAACAATGC	57.145	29.630	0.00	0.00	39.90	3.56

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.