AutoCloner

Multiple sequence alignment - TraesCS5B01G029400

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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	TraesCS5B01G029400	chr5B	100.000	3704	0	0	1	3704	29340329	29336626	0.000000e+00	6841.0
1	TraesCS5B01G029400	chr5B	87.581	1538	169	19	1073	2602	553726848	553725325	0.000000e+00	1762.0
2	TraesCS5B01G029400	chr5D	93.211	3771	110	50	10	3703	38726694	38722993	0.000000e+00	5411.0
3	TraesCS5B01G029400	chr5D	87.638	1537	170	17	1073	2602	453240529	453239006	0.000000e+00	1768.0
4	TraesCS5B01G029400	chr5D	84.146	82	10	3	3626	3704	37920315	37920396	3.970000e-10	76.8
5	TraesCS5B01G029400	chr5A	91.793	3241	130	53	11	3200	27518878	27515723	0.000000e+00	4386.0
6	TraesCS5B01G029400	chr5A	86.792	1537	183	17	1073	2602	572023246	572021723	0.000000e+00	1696.0
7	TraesCS5B01G029400	chr5A	84.925	199	13	10	3200	3389	27515489	27515299	6.320000e-43	185.0
8	TraesCS5B01G029400	chr5A	90.541	74	5	2	3630	3701	703378620	703378693	3.040000e-16	97.1
9	TraesCS5B01G029400	chr5A	84.810	79	10	1	3625	3701	703316629	703316707	1.100000e-10	78.7
10	TraesCS5B01G029400	chr5A	82.278	79	11	3	10	85	603787355	603787277	8.590000e-07	65.8
11	TraesCS5B01G029400	chr2D	76.923	1508	272	56	1064	2521	301378135	301379616	0.000000e+00	787.0
12	TraesCS5B01G029400	chr2D	96.552	87	2	1	3506	3591	529533135	529533049	3.860000e-30	143.0
13	TraesCS5B01G029400	chr2D	83.784	111	12	3	3525	3629	577160786	577160676	2.350000e-17	100.0
14	TraesCS5B01G029400	chr2D	86.076	79	8	3	3629	3704	8781487	8781409	8.530000e-12	82.4
15	TraesCS5B01G029400	chr2D	86.667	75	8	2	3626	3700	378756793	378756865	8.530000e-12	82.4
16	TraesCS5B01G029400	chr2D	86.076	79	8	3	3629	3704	434352524	434352446	8.530000e-12	82.4
17	TraesCS5B01G029400	chr2A	77.062	1382	261	43	1173	2521	378396705	378398063	0.000000e+00	745.0
18	TraesCS5B01G029400	chr2A	96.552	87	2	1	3506	3591	674025994	674025908	3.860000e-30	143.0
19	TraesCS5B01G029400	chr2A	92.537	67	5	0	3525	3591	715345410	715345344	3.040000e-16	97.1
20	TraesCS5B01G029400	chr2B	77.306	1247	237	37	1307	2521	363342469	363343701	0.000000e+00	693.0
21	TraesCS5B01G029400	chr2B	84.685	111	10	5	3526	3629	694062827	694062717	1.820000e-18	104.0
22	TraesCS5B01G029400	chr2B	94.030	67	3	1	1798	1863	240301647	240301581	2.350000e-17	100.0
23	TraesCS5B01G029400	chr2B	85.000	100	12	1	1659	1758	240301741	240301645	8.470000e-17	99.0
24	TraesCS5B01G029400	chr3A	80.882	340	49	12	40	375	502091284	502090957	1.710000e-63	254.0
25	TraesCS5B01G029400	chr3A	91.473	129	6	2	2259	2387	22236379	22236256	4.920000e-39	172.0
26	TraesCS5B01G029400	chr7D	91.139	79	3	3	3626	3700	204247196	204247274	1.820000e-18	104.0
27	TraesCS5B01G029400	chr1D	91.304	69	3	3	3635	3700	107217960	107217892	1.420000e-14	91.6
28	TraesCS5B01G029400	chr6D	83.495	103	10	4	3534	3629	388948449	388948347	5.100000e-14	89.8
29	TraesCS5B01G029400	chr6B	83.495	103	10	5	3534	3629	581853151	581853049	5.100000e-14	89.8
30	TraesCS5B01G029400	chr6A	79.208	101	14	3	278	378	562462515	562462608	3.090000e-06	63.9
31	TraesCS5B01G029400	chrUn	94.595	37	2	0	3555	3591	367367520	367367484	1.440000e-04	58.4

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	TraesCS5B01G029400	chr5B	29336626	29340329	3703	True	6841.0	6841	100.000	1	3704	1	chr5B.!!$R1	3703
1	TraesCS5B01G029400	chr5B	553725325	553726848	1523	True	1762.0	1762	87.581	1073	2602	1	chr5B.!!$R2	1529
2	TraesCS5B01G029400	chr5D	38722993	38726694	3701	True	5411.0	5411	93.211	10	3703	1	chr5D.!!$R1	3693
3	TraesCS5B01G029400	chr5D	453239006	453240529	1523	True	1768.0	1768	87.638	1073	2602	1	chr5D.!!$R2	1529
4	TraesCS5B01G029400	chr5A	27515299	27518878	3579	True	2285.5	4386	88.359	11	3389	2	chr5A.!!$R3	3378
5	TraesCS5B01G029400	chr5A	572021723	572023246	1523	True	1696.0	1696	86.792	1073	2602	1	chr5A.!!$R1	1529
6	TraesCS5B01G029400	chr2D	301378135	301379616	1481	False	787.0	787	76.923	1064	2521	1	chr2D.!!$F1	1457
7	TraesCS5B01G029400	chr2A	378396705	378398063	1358	False	745.0	745	77.062	1173	2521	1	chr2A.!!$F1	1348
8	TraesCS5B01G029400	chr2B	363342469	363343701	1232	False	693.0	693	77.306	1307	2521	1	chr2B.!!$F1	1214

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
702	743	0.036952	GCCACAGTGCAAGCTCTCTA	60.037	55.0	0.0	0.0	0.0	2.43	F
947	994	0.244994	TTTCTGCTCGTCCTCTGCTC	59.755	55.0	0.0	0.0	0.0	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1663	1734	1.078426	CCCCAAGTACGCCAAGGAG	60.078	63.158	0.00	0.0	0.0	3.69	R
2938	3030	0.175760	TCGCCGGAGAAGAGAATTGG	59.824	55.000	5.05	0.0	0.0	3.16	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
24	25	7.681939	GTTCCCAGTGTGAATAGTAAAATCA	57.318	36.000	0.00	0.00	0.00	2.57
153	166	6.536941	GGTAACAAAAACTCAAATTTCAGGCA	59.463	34.615	0.00	0.00	0.00	4.75
238	251	1.202806	CCTCCAATGTCGTATGCCCAT	60.203	52.381	0.00	0.00	0.00	4.00
287	301	1.129811	GCATCTTGCATGCAAAAAGGC	59.870	47.619	31.37	28.39	44.26	4.35
389	404	5.745294	CGAATTGAATTATTGGTGAGCAAGG	59.255	40.000	2.75	0.00	0.00	3.61
401	416	2.294233	GTGAGCAAGGCAATTCAGTCAA	59.706	45.455	0.00	0.00	0.00	3.18
632	655	2.095461	GGTTCAATTCCCCTCTCTTGC	58.905	52.381	0.00	0.00	0.00	4.01
633	656	2.291217	GGTTCAATTCCCCTCTCTTGCT	60.291	50.000	0.00	0.00	0.00	3.91
654	685	7.094508	TGCTTGTCTCTCTAGAATAACAGAG	57.905	40.000	0.00	0.00	39.77	3.35
702	743	0.036952	GCCACAGTGCAAGCTCTCTA	60.037	55.000	0.00	0.00	0.00	2.43
716	757	3.269906	AGCTCTCTACCTCCCTAAACTCA	59.730	47.826	0.00	0.00	0.00	3.41
717	758	3.382227	GCTCTCTACCTCCCTAAACTCAC	59.618	52.174	0.00	0.00	0.00	3.51
753	794	9.760077	CTACCCTAACTAATTTACCATGTACTG	57.240	37.037	0.00	0.00	0.00	2.74
754	795	8.154420	ACCCTAACTAATTTACCATGTACTGT	57.846	34.615	0.00	0.00	0.00	3.55
755	796	9.270707	ACCCTAACTAATTTACCATGTACTGTA	57.729	33.333	0.00	0.00	0.00	2.74
756	797	9.538508	CCCTAACTAATTTACCATGTACTGTAC	57.461	37.037	10.98	10.98	0.00	2.90
780	824	7.585440	ACTAAGGGTAAAAGGTGAAAAGGTAA	58.415	34.615	0.00	0.00	0.00	2.85
781	825	8.060689	ACTAAGGGTAAAAGGTGAAAAGGTAAA	58.939	33.333	0.00	0.00	0.00	2.01
856	902	1.512926	CCGCTAACTGTATCCATGCC	58.487	55.000	0.00	0.00	0.00	4.40
857	903	1.070758	CCGCTAACTGTATCCATGCCT	59.929	52.381	0.00	0.00	0.00	4.75
858	904	2.138320	CGCTAACTGTATCCATGCCTG	58.862	52.381	0.00	0.00	0.00	4.85
859	905	1.876156	GCTAACTGTATCCATGCCTGC	59.124	52.381	0.00	0.00	0.00	4.85
947	994	0.244994	TTTCTGCTCGTCCTCTGCTC	59.755	55.000	0.00	0.00	0.00	4.26
953	1000	2.003658	CTCGTCCTCTGCTCCTCTGC	62.004	65.000	0.00	0.00	0.00	4.26
954	1001	2.899505	GTCCTCTGCTCCTCTGCC	59.100	66.667	0.00	0.00	0.00	4.85
955	1002	1.685421	GTCCTCTGCTCCTCTGCCT	60.685	63.158	0.00	0.00	0.00	4.75
967	1014	2.445654	CTGCCTCCTCCTCCTCCC	60.446	72.222	0.00	0.00	0.00	4.30
982	1029	1.954362	CTCCCAGAAGCTCGGAGTGG	61.954	65.000	6.90	6.16	38.72	4.00
1120	1167	4.735132	GACGGCAGCTGCACGGTA	62.735	66.667	35.88	0.00	44.36	4.02
1663	1734	0.249073	CCCACATCATCTCCGACGAC	60.249	60.000	0.00	0.00	0.00	4.34
2543	2623	1.746615	CGCTCCAGGACATTGTGGG	60.747	63.158	0.00	0.00	34.27	4.61
2905	2997	2.223923	CGCTGATCCTCGGAAGAAGAAT	60.224	50.000	0.00	0.00	41.32	2.40
2906	2998	3.004839	CGCTGATCCTCGGAAGAAGAATA	59.995	47.826	0.00	0.00	41.32	1.75
2907	2999	4.499865	CGCTGATCCTCGGAAGAAGAATAA	60.500	45.833	0.00	0.00	41.32	1.40
2926	3018	1.353091	AGAAGAAGAAGAAGGCGGGT	58.647	50.000	0.00	0.00	0.00	5.28
2950	3042	1.202580	CGGCCGATCCAATTCTCTTCT	60.203	52.381	24.07	0.00	34.01	2.85
2951	3043	2.488952	GGCCGATCCAATTCTCTTCTC	58.511	52.381	0.00	0.00	34.01	2.87
2996	3088	0.671251	TGATTGGCGTTGTGGGTTTC	59.329	50.000	0.00	0.00	0.00	2.78
3111	3213	4.371231	AAGGGACAGGGGAGGGGG	62.371	72.222	0.00	0.00	0.00	5.40
3239	3585	5.298347	TCTTTCTTTTTCTTCTCGTCTCCC	58.702	41.667	0.00	0.00	0.00	4.30
3241	3587	6.267014	TCTTTCTTTTTCTTCTCGTCTCCCTA	59.733	38.462	0.00	0.00	0.00	3.53
3242	3588	5.388408	TCTTTTTCTTCTCGTCTCCCTAC	57.612	43.478	0.00	0.00	0.00	3.18
3295	3644	1.002792	TGGGGGCAATTTGGGGATC	59.997	57.895	0.00	0.00	0.00	3.36
3299	3648	1.915489	GGGGCAATTTGGGGATCTTTT	59.085	47.619	0.00	0.00	0.00	2.27
3300	3649	2.308570	GGGGCAATTTGGGGATCTTTTT	59.691	45.455	0.00	0.00	0.00	1.94
3302	3651	3.008923	GGGCAATTTGGGGATCTTTTTCA	59.991	43.478	0.00	0.00	0.00	2.69
3303	3652	4.002982	GGCAATTTGGGGATCTTTTTCAC	58.997	43.478	0.00	0.00	0.00	3.18
3304	3653	4.263025	GGCAATTTGGGGATCTTTTTCACT	60.263	41.667	0.00	0.00	0.00	3.41
3305	3654	5.046663	GGCAATTTGGGGATCTTTTTCACTA	60.047	40.000	0.00	0.00	0.00	2.74
3307	3656	6.295292	GCAATTTGGGGATCTTTTTCACTACT	60.295	38.462	0.00	0.00	0.00	2.57
3323	3672	3.491267	CACTACTACTACCCGCGTACTAC	59.509	52.174	4.92	0.00	0.00	2.73
3326	3675	4.608948	ACTACTACCCGCGTACTACTAT	57.391	45.455	4.92	0.00	0.00	2.12
3369	3723	2.032681	AGGGCAAACGAGTGCTCC	59.967	61.111	10.65	11.19	46.91	4.70
3377	3731	0.818040	AACGAGTGCTCCCAACCAAC	60.818	55.000	0.00	0.00	0.00	3.77
3415	3795	8.348507	CCACAGCCTATTCTCTTTCATTATTTC	58.651	37.037	0.00	0.00	0.00	2.17
3416	3796	9.118300	CACAGCCTATTCTCTTTCATTATTTCT	57.882	33.333	0.00	0.00	0.00	2.52
3548	3928	8.472007	AGGGATTCTAGATTAGTTCAGTACAG	57.528	38.462	0.00	0.00	0.00	2.74
3553	3933	7.804843	TCTAGATTAGTTCAGTACAGGTAGC	57.195	40.000	0.00	0.00	0.00	3.58
3603	3983	4.067192	GTCCATTTTTGCTGGCAATTTCT	58.933	39.130	8.86	0.00	35.70	2.52
3608	3988	6.183360	CCATTTTTGCTGGCAATTTCTATTCC	60.183	38.462	8.86	0.00	35.70	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	7.681939	TGATTTTACTATTCACACTGGGAAC	57.318	36.000	0.00	0.00	0.00	3.62
1	2	8.877864	AATGATTTTACTATTCACACTGGGAA	57.122	30.769	0.00	0.00	0.00	3.97
2	3	8.877864	AAATGATTTTACTATTCACACTGGGA	57.122	30.769	0.00	0.00	0.00	4.37
133	146	6.258287	TCACATGCCTGAAATTTGAGTTTTTG	59.742	34.615	3.91	0.00	0.00	2.44
238	251	0.865111	CGAGGTGCGTGTGAAATTCA	59.135	50.000	0.00	0.00	34.64	2.57
325	340	9.817809	TCTATACTAGCTGAACAGTAAAATTGG	57.182	33.333	0.00	0.00	31.35	3.16
389	404	5.410746	TCTCTCTCATGTTTGACTGAATTGC	59.589	40.000	0.00	0.00	0.00	3.56
401	416	2.613977	CCAAACGCCTCTCTCTCATGTT	60.614	50.000	0.00	0.00	0.00	2.71
632	655	7.338196	TGGACTCTGTTATTCTAGAGAGACAAG	59.662	40.741	10.48	9.83	42.34	3.16
633	656	7.175797	TGGACTCTGTTATTCTAGAGAGACAA	58.824	38.462	10.48	0.00	42.34	3.18
702	743	3.848978	ACTAGGTGAGTTTAGGGAGGT	57.151	47.619	0.00	0.00	33.13	3.85
753	794	7.000472	ACCTTTTCACCTTTTACCCTTAGTAC	59.000	38.462	0.00	0.00	0.00	2.73
754	795	7.152942	ACCTTTTCACCTTTTACCCTTAGTA	57.847	36.000	0.00	0.00	0.00	1.82
755	796	6.022107	ACCTTTTCACCTTTTACCCTTAGT	57.978	37.500	0.00	0.00	0.00	2.24
756	797	8.467963	TTTACCTTTTCACCTTTTACCCTTAG	57.532	34.615	0.00	0.00	0.00	2.18
757	798	8.835550	TTTTACCTTTTCACCTTTTACCCTTA	57.164	30.769	0.00	0.00	0.00	2.69
814	858	4.791411	GCGGTTACTCATCATCACTCTCTC	60.791	50.000	0.00	0.00	0.00	3.20
815	859	3.067461	GCGGTTACTCATCATCACTCTCT	59.933	47.826	0.00	0.00	0.00	3.10
859	905	4.994756	AAGCGGTTGCCCCCAAGG	62.995	66.667	0.00	0.00	44.31	3.61
892	938	0.397941	TTTCAGAGGGAGCCACACAG	59.602	55.000	0.00	0.00	0.00	3.66
893	939	0.843309	TTTTCAGAGGGAGCCACACA	59.157	50.000	0.00	0.00	0.00	3.72
894	940	1.528129	CTTTTCAGAGGGAGCCACAC	58.472	55.000	0.00	0.00	0.00	3.82
895	941	0.250901	GCTTTTCAGAGGGAGCCACA	60.251	55.000	0.00	0.00	0.00	4.17
947	994	1.457455	GAGGAGGAGGAGGCAGAGG	60.457	68.421	0.00	0.00	0.00	3.69
953	1000	0.398381	CTTCTGGGAGGAGGAGGAGG	60.398	65.000	0.00	0.00	0.00	4.30
954	1001	1.048160	GCTTCTGGGAGGAGGAGGAG	61.048	65.000	0.00	0.00	0.00	3.69
955	1002	1.002274	GCTTCTGGGAGGAGGAGGA	59.998	63.158	0.00	0.00	0.00	3.71
967	1014	0.108898	CTCACCACTCCGAGCTTCTG	60.109	60.000	0.00	0.00	0.00	3.02
982	1029	0.820871	ATTGGTCCTCTCGCTCTCAC	59.179	55.000	0.00	0.00	0.00	3.51
1019	1066	6.371548	CACTAATCGATTCCTTGGTTCTTTGA	59.628	38.462	15.25	0.00	0.00	2.69
1120	1167	4.521062	GACATGCGGCTCGAGGCT	62.521	66.667	32.85	16.83	41.46	4.58
1663	1734	1.078426	CCCCAAGTACGCCAAGGAG	60.078	63.158	0.00	0.00	0.00	3.69
2543	2623	1.597461	CCTTCGAGGAGGGGTTCAC	59.403	63.158	0.00	0.00	37.67	3.18
2784	2876	2.032071	CCAGCTCGGTCCGGTTTT	59.968	61.111	12.29	0.00	0.00	2.43
2785	2877	4.699522	GCCAGCTCGGTCCGGTTT	62.700	66.667	12.29	0.00	36.97	3.27
2905	2997	2.904434	ACCCGCCTTCTTCTTCTTCTTA	59.096	45.455	0.00	0.00	0.00	2.10
2906	2998	1.700186	ACCCGCCTTCTTCTTCTTCTT	59.300	47.619	0.00	0.00	0.00	2.52
2907	2999	1.002544	CACCCGCCTTCTTCTTCTTCT	59.997	52.381	0.00	0.00	0.00	2.85
2926	3018	1.153249	GAATTGGATCGGCCGGACA	60.153	57.895	27.83	18.85	40.66	4.02
2938	3030	0.175760	TCGCCGGAGAAGAGAATTGG	59.824	55.000	5.05	0.00	0.00	3.16
2940	3032	0.179097	GCTCGCCGGAGAAGAGAATT	60.179	55.000	9.83	0.00	43.27	2.17
2996	3088	2.443016	CCCCTCTCCTCTCACCCG	60.443	72.222	0.00	0.00	0.00	5.28
3111	3213	1.795286	CGTTTCAACACTCTGCTCCTC	59.205	52.381	0.00	0.00	0.00	3.71
3250	3596	3.517100	AGCATACATACATAGGCAGAGGG	59.483	47.826	0.00	0.00	34.30	4.30
3295	3644	3.855950	CGCGGGTAGTAGTAGTGAAAAAG	59.144	47.826	0.00	0.00	0.00	2.27
3299	3648	2.113860	ACGCGGGTAGTAGTAGTGAA	57.886	50.000	12.47	0.00	0.00	3.18
3300	3649	2.168521	AGTACGCGGGTAGTAGTAGTGA	59.831	50.000	17.52	0.00	30.46	3.41
3302	3651	2.990066	AGTACGCGGGTAGTAGTAGT	57.010	50.000	17.52	0.00	30.46	2.73
3303	3652	3.983741	AGTAGTACGCGGGTAGTAGTAG	58.016	50.000	25.31	0.00	36.75	2.57
3304	3653	5.723672	ATAGTAGTACGCGGGTAGTAGTA	57.276	43.478	29.47	29.47	41.39	1.82
3305	3654	2.990066	AGTAGTACGCGGGTAGTAGT	57.010	50.000	23.16	22.83	35.69	2.73
3307	3656	5.007626	CACAAATAGTAGTACGCGGGTAGTA	59.992	44.000	19.90	19.90	34.22	1.82
3323	3672	5.197549	CAACACGAGACACAACACAAATAG	58.802	41.667	0.00	0.00	0.00	1.73
3326	3675	2.413502	GCAACACGAGACACAACACAAA	60.414	45.455	0.00	0.00	0.00	2.83
3354	3703	1.896660	TTGGGAGCACTCGTTTGCC	60.897	57.895	7.28	0.72	44.14	4.52
3369	3723	4.979204	CAGCATGCTGTTGGTTGG	57.021	55.556	34.76	11.09	39.10	3.77
3396	3776	9.859152	AGGGGAAGAAATAATGAAAGAGAATAG	57.141	33.333	0.00	0.00	0.00	1.73
3416	3796	9.877222	ACTAATAAAAAGAAGAAAGAAGGGGAA	57.123	29.630	0.00	0.00	0.00	3.97
3548	3928	9.935241	TCATCTTAGATCAATCAAATAGCTACC	57.065	33.333	0.00	0.00	0.00	3.18
3603	3983	5.935206	TGAACACTAAATGAAGCACGGAATA	59.065	36.000	0.00	0.00	0.00	1.75
3608	3988	4.732285	ACTGAACACTAAATGAAGCACG	57.268	40.909	0.00	0.00	0.00	5.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.