AutoCloner

Multiple sequence alignment - TraesCS5B01G572500

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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	TraesCS5B01G572500	chr5B	100.000	3299	0	0	1	3299	712917727	712914429	0.000000e+00	6093.0
1	TraesCS5B01G572500	chr5B	98.148	54	1	0	832	885	471194047	471193994	9.750000e-16	95.3
2	TraesCS5B01G572500	chr5B	98.113	53	1	0	832	884	506918936	506918884	3.510000e-15	93.5
3	TraesCS5B01G572500	chr5B	94.231	52	2	1	825	875	258789993	258790044	9.810000e-11	78.7
4	TraesCS5B01G572500	chr1B	94.026	2427	139	6	876	3299	499345150	499342727	0.000000e+00	3674.0
5	TraesCS5B01G572500	chr1B	93.451	2428	154	5	876	3299	333172183	333174609	0.000000e+00	3598.0
6	TraesCS5B01G572500	chr1B	96.364	55	0	2	832	886	21462648	21462700	4.530000e-14	89.8
7	TraesCS5B01G572500	chr1B	91.935	62	1	3	834	895	148807726	148807669	2.110000e-12	84.2
8	TraesCS5B01G572500	chr1B	94.340	53	2	1	824	875	3806439	3806387	2.730000e-11	80.5
9	TraesCS5B01G572500	chr7B	93.366	2427	158	3	876	3299	272151901	272149475	0.000000e+00	3587.0
10	TraesCS5B01G572500	chr7B	93.204	2428	160	4	876	3299	79580329	79577903	0.000000e+00	3565.0
11	TraesCS5B01G572500	chr7B	92.995	2427	166	4	876	3299	118331976	118334401	0.000000e+00	3537.0
12	TraesCS5B01G572500	chr7B	93.651	63	3	1	832	893	396855277	396855339	3.510000e-15	93.5
13	TraesCS5B01G572500	chr7B	94.737	57	2	1	832	888	83401517	83401572	1.630000e-13	87.9
14	TraesCS5B01G572500	chr7B	94.231	52	2	1	825	875	133982643	133982694	9.810000e-11	78.7
15	TraesCS5B01G572500	chr7B	87.500	72	4	5	832	902	725688735	725688802	9.810000e-11	78.7
16	TraesCS5B01G572500	chr3B	93.240	2426	157	5	879	3299	699377553	699375130	0.000000e+00	3565.0
17	TraesCS5B01G572500	chr3B	93.160	2427	159	5	876	3299	305374623	305372201	0.000000e+00	3555.0
18	TraesCS5B01G572500	chr3B	95.918	49	1	1	828	875	253573488	253573440	9.810000e-11	78.7
19	TraesCS5B01G572500	chr4B	93.201	2427	156	8	876	3299	52286638	52284218	0.000000e+00	3559.0
20	TraesCS5B01G572500	chr4B	93.037	2427	165	4	876	3299	181327792	181330217	0.000000e+00	3542.0
21	TraesCS5B01G572500	chr7A	99.398	831	5	0	1	831	311718506	311717676	0.000000e+00	1507.0
22	TraesCS5B01G572500	chr7A	99.279	832	6	0	1	832	18484218	18485049	0.000000e+00	1504.0
23	TraesCS5B01G572500	chr6B	99.398	831	5	0	1	831	615100024	615099194	0.000000e+00	1507.0
24	TraesCS5B01G572500	chr6B	99.280	833	6	0	1	833	707107268	707108100	0.000000e+00	1506.0
25	TraesCS5B01G572500	chr6B	96.296	54	2	0	832	885	410094100	410094047	4.530000e-14	89.8
26	TraesCS5B01G572500	chr6B	94.444	54	2	1	825	877	243140904	243140957	7.590000e-12	82.4
27	TraesCS5B01G572500	chr6B	95.918	49	1	1	828	875	128279710	128279662	9.810000e-11	78.7
28	TraesCS5B01G572500	chr3A	99.280	833	6	0	1	833	507561477	507562309	0.000000e+00	1506.0
29	TraesCS5B01G572500	chr3A	99.279	832	6	0	1	832	101789025	101789856	0.000000e+00	1504.0
30	TraesCS5B01G572500	chr3A	99.279	832	6	0	1	832	728110358	728111189	0.000000e+00	1504.0
31	TraesCS5B01G572500	chrUn	99.279	832	6	0	1	832	432337566	432338397	0.000000e+00	1504.0
32	TraesCS5B01G572500	chrUn	86.364	66	7	2	811	875	390108638	390108702	1.640000e-08	71.3
33	TraesCS5B01G572500	chr2B	98.700	846	8	2	1	843	358489017	358488172	0.000000e+00	1498.0
34	TraesCS5B01G572500	chr2B	96.296	54	2	0	832	885	676782229	676782282	4.530000e-14	89.8
35	TraesCS5B01G572500	chr2B	92.308	52	3	1	825	875	633350277	633350328	4.570000e-09	73.1
36	TraesCS5B01G572500	chr4A	94.340	53	2	1	825	876	738247609	738247661	2.730000e-11	80.5

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	TraesCS5B01G572500	chr5B	712914429	712917727	3298	True	6093	6093	100.000	1	3299	1	chr5B.!!$R3	3298
1	TraesCS5B01G572500	chr1B	499342727	499345150	2423	True	3674	3674	94.026	876	3299	1	chr1B.!!$R3	2423
2	TraesCS5B01G572500	chr1B	333172183	333174609	2426	False	3598	3598	93.451	876	3299	1	chr1B.!!$F2	2423
3	TraesCS5B01G572500	chr7B	272149475	272151901	2426	True	3587	3587	93.366	876	3299	1	chr7B.!!$R2	2423
4	TraesCS5B01G572500	chr7B	79577903	79580329	2426	True	3565	3565	93.204	876	3299	1	chr7B.!!$R1	2423
5	TraesCS5B01G572500	chr7B	118331976	118334401	2425	False	3537	3537	92.995	876	3299	1	chr7B.!!$F2	2423
6	TraesCS5B01G572500	chr3B	699375130	699377553	2423	True	3565	3565	93.240	879	3299	1	chr3B.!!$R3	2420
7	TraesCS5B01G572500	chr3B	305372201	305374623	2422	True	3555	3555	93.160	876	3299	1	chr3B.!!$R2	2423
8	TraesCS5B01G572500	chr4B	52284218	52286638	2420	True	3559	3559	93.201	876	3299	1	chr4B.!!$R1	2423
9	TraesCS5B01G572500	chr4B	181327792	181330217	2425	False	3542	3542	93.037	876	3299	1	chr4B.!!$F1	2423
10	TraesCS5B01G572500	chr7A	311717676	311718506	830	True	1507	1507	99.398	1	831	1	chr7A.!!$R1	830
11	TraesCS5B01G572500	chr7A	18484218	18485049	831	False	1504	1504	99.279	1	832	1	chr7A.!!$F1	831
12	TraesCS5B01G572500	chr6B	615099194	615100024	830	True	1507	1507	99.398	1	831	1	chr6B.!!$R3	830
13	TraesCS5B01G572500	chr6B	707107268	707108100	832	False	1506	1506	99.280	1	833	1	chr6B.!!$F2	832
14	TraesCS5B01G572500	chr3A	507561477	507562309	832	False	1506	1506	99.280	1	833	1	chr3A.!!$F2	832
15	TraesCS5B01G572500	chr3A	101789025	101789856	831	False	1504	1504	99.279	1	832	1	chr3A.!!$F1	831
16	TraesCS5B01G572500	chr3A	728110358	728111189	831	False	1504	1504	99.279	1	832	1	chr3A.!!$F3	831
17	TraesCS5B01G572500	chrUn	432337566	432338397	831	False	1504	1504	99.279	1	832	1	chrUn.!!$F2	831
18	TraesCS5B01G572500	chr2B	358488172	358489017	845	True	1498	1498	98.700	1	843	1	chr2B.!!$R1	842

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
861	862	0.186873	TATCCGGACACCCCCTAGTC	59.813	60.0	6.12	0.0	0.0	2.59	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2614	2616	0.395862	CTAGGAGGAGAGGACGGCAA	60.396	60.0	0.0	0.0	0.0	4.52	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
226	227	1.896660	GGTCAAGGCGCACCAAGAA	60.897	57.895	10.83	0.00	39.06	2.52
530	531	3.645975	CACCACCACGCCGTTGTC	61.646	66.667	0.00	0.00	0.00	3.18
835	836	2.167693	TGCTACGTTCCCCAACAGATAG	59.832	50.000	0.00	0.00	32.14	2.08
836	837	2.167900	GCTACGTTCCCCAACAGATAGT	59.832	50.000	0.00	0.00	32.14	2.12
839	840	2.268298	CGTTCCCCAACAGATAGTTCG	58.732	52.381	0.00	0.00	38.74	3.95
840	841	2.629051	GTTCCCCAACAGATAGTTCGG	58.371	52.381	0.00	0.00	38.74	4.30
842	843	0.541863	CCCCAACAGATAGTTCGGCT	59.458	55.000	0.00	0.00	37.19	5.52
843	844	1.760613	CCCCAACAGATAGTTCGGCTA	59.239	52.381	0.00	0.00	37.19	3.93
844	845	2.368875	CCCCAACAGATAGTTCGGCTAT	59.631	50.000	1.08	1.08	42.75	2.97
856	857	3.557290	GGCTATCCGGACACCCCC	61.557	72.222	6.12	0.00	0.00	5.40
857	858	2.446036	GCTATCCGGACACCCCCT	60.446	66.667	6.12	0.00	0.00	4.79
858	859	1.152398	GCTATCCGGACACCCCCTA	60.152	63.158	6.12	0.00	0.00	3.53
859	860	1.186267	GCTATCCGGACACCCCCTAG	61.186	65.000	6.12	3.64	0.00	3.02
860	861	0.187851	CTATCCGGACACCCCCTAGT	59.812	60.000	6.12	0.00	0.00	2.57
861	862	0.186873	TATCCGGACACCCCCTAGTC	59.813	60.000	6.12	0.00	0.00	2.59
864	865	2.762875	GGACACCCCCTAGTCCGG	60.763	72.222	0.00	0.00	44.23	5.14
865	866	2.762875	GACACCCCCTAGTCCGGG	60.763	72.222	0.00	5.45	45.70	5.73
872	873	3.017139	CCTAGTCCGGGACTCCCT	58.983	66.667	31.91	12.26	42.40	4.20
873	874	1.152715	CCTAGTCCGGGACTCCCTC	60.153	68.421	31.91	2.12	42.40	4.30
874	875	1.613610	CTAGTCCGGGACTCCCTCA	59.386	63.158	31.91	14.20	42.40	3.86
923	925	3.036429	GCTCCTCCGGTCATTGCCT	62.036	63.158	0.00	0.00	0.00	4.75
957	959	2.766660	GCCCTTCCCTTCTGCCTT	59.233	61.111	0.00	0.00	0.00	4.35
967	969	2.421424	CCCTTCTGCCTTCGAAATCTTG	59.579	50.000	0.00	0.00	0.00	3.02
974	976	4.186926	TGCCTTCGAAATCTTGAGATCTG	58.813	43.478	0.00	0.00	32.75	2.90
1050	1052	0.179018	GGTATTCGCCTGCCTTGGAT	60.179	55.000	0.00	0.00	0.00	3.41
1139	1141	2.594592	GCAGGTGTTCAAGGCCGT	60.595	61.111	0.00	0.00	0.00	5.68
1309	1311	2.167487	GTCCTTCTTCTGGCGATCTTCT	59.833	50.000	0.00	0.00	0.00	2.85
1400	1402	0.746563	CTCTCTCGCGGTCCTCTCTT	60.747	60.000	6.13	0.00	0.00	2.85
1403	1405	2.359602	TCGCGGTCCTCTCTTCGT	60.360	61.111	6.13	0.00	0.00	3.85
1468	1470	1.338136	GCCCGGGAAGAGGATTGAGA	61.338	60.000	29.31	0.00	0.00	3.27
1567	1569	0.103026	CTCCGATGATTGGTCTCGCA	59.897	55.000	0.00	0.00	0.00	5.10
1585	1587	3.048602	CGGAACTCGTGGACCACT	58.951	61.111	22.14	3.23	31.34	4.00
1760	1762	3.370231	CCCCGAAGTTTTGGCCGG	61.370	66.667	0.00	0.00	41.47	6.13
1763	1765	4.398598	CGAAGTTTTGGCCGGCGG	62.399	66.667	24.35	24.35	0.00	6.13
1782	1784	1.668101	GAGATCTGACCGCGGTCCTT	61.668	60.000	45.59	32.93	43.97	3.36
1977	1979	1.883732	CGACTCCAGCGAAGAGGAA	59.116	57.895	5.80	0.00	35.58	3.36
2149	2151	0.610687	CTCGAAGAAGGCCAGGTCTT	59.389	55.000	5.81	5.81	36.80	3.01
2544	2546	1.079543	CCAAGCGACTCCTGAGGTG	60.080	63.158	0.00	0.00	0.00	4.00
2551	2553	0.543174	GACTCCTGAGGTGTCCCTGT	60.543	60.000	20.13	0.24	42.86	4.00
2570	2572	3.939837	CTGATGCCGTCGCCACAGT	62.940	63.158	0.00	0.00	34.56	3.55
2581	2583	2.518349	CCACAGTTGTTGGGGCGT	60.518	61.111	0.00	0.00	45.21	5.68
2614	2616	0.470456	TCAGGGTCCTGTGGTTACGT	60.470	55.000	15.77	0.00	43.96	3.57
2633	2635	0.395862	TTGCCGTCCTCTCCTCCTAG	60.396	60.000	0.00	0.00	0.00	3.02
2704	2706	4.003788	CCGAACTGGACCGGCTGT	62.004	66.667	0.00	0.00	42.00	4.40
2772	2774	1.823041	GCTGGCTTCTGGCTGGATC	60.823	63.158	0.00	0.00	41.46	3.36
2804	2806	3.567797	GATTCGAGCGGCACTGGC	61.568	66.667	1.45	0.00	40.13	4.85
2994	2997	5.594317	CCAAGAGAAGGAAGAAAACCTGAAA	59.406	40.000	0.00	0.00	37.85	2.69
2999	3002	4.445557	AGGAAGAAAACCTGAAAGCTCT	57.554	40.909	0.00	0.00	36.30	4.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
530	531	0.617413	AGACTCCATCCAACAGCAGG	59.383	55.000	0.00	0.00	0.00	4.85
714	715	5.864418	ACATACCCTTGTAGATCGCTAAA	57.136	39.130	0.00	0.00	0.00	1.85
839	840	2.668106	TAGGGGGTGTCCGGATAGCC	62.668	65.000	34.24	34.24	39.05	3.93
840	841	1.152398	TAGGGGGTGTCCGGATAGC	60.152	63.158	20.91	20.91	36.01	2.97
842	843	0.186873	GACTAGGGGGTGTCCGGATA	59.813	60.000	7.81	0.10	36.01	2.59
843	844	1.075450	GACTAGGGGGTGTCCGGAT	60.075	63.158	7.81	0.00	36.01	4.18
844	845	2.361771	GACTAGGGGGTGTCCGGA	59.638	66.667	0.00	0.00	36.01	5.14
845	846	2.762875	GGACTAGGGGGTGTCCGG	60.763	72.222	0.00	0.00	42.51	5.14
847	848	2.762875	CCGGACTAGGGGGTGTCC	60.763	72.222	0.00	0.00	46.69	4.02
863	864	4.475135	GCCGCTTGAGGGAGTCCC	62.475	72.222	21.81	21.81	45.90	4.46
864	865	4.821589	CGCCGCTTGAGGGAGTCC	62.822	72.222	0.00	0.00	0.00	3.85
865	866	3.991536	GACGCCGCTTGAGGGAGTC	62.992	68.421	0.00	0.00	44.96	3.36
866	867	4.070552	GACGCCGCTTGAGGGAGT	62.071	66.667	0.00	0.00	40.46	3.85
867	868	3.764466	AGACGCCGCTTGAGGGAG	61.764	66.667	0.00	0.00	0.00	4.30
868	869	4.069232	CAGACGCCGCTTGAGGGA	62.069	66.667	0.00	0.00	0.00	4.20
923	925	0.180406	GGCGCAAGAAAGGGGATCTA	59.820	55.000	10.83	0.00	43.02	1.98
957	959	4.108336	CGAAGCAGATCTCAAGATTTCGA	58.892	43.478	14.80	0.00	40.58	3.71
967	969	1.941734	CGCGGTCGAAGCAGATCTC	60.942	63.158	13.49	0.00	38.10	2.75
1114	1116	2.676471	GAACACCTGCGCCCCATT	60.676	61.111	4.18	0.00	0.00	3.16
1139	1141	4.465446	CCTCAGGAGGGGCGGAGA	62.465	72.222	7.48	0.00	44.87	3.71
1172	1174	0.248949	GCTTACGAAGAGCGGGTAGG	60.249	60.000	0.00	0.00	46.49	3.18
1309	1311	4.898320	ACATGAGCCTCGCAATAATATGA	58.102	39.130	0.00	0.00	0.00	2.15
1782	1784	0.618458	CCCCTCCGACCAAAGATTGA	59.382	55.000	0.00	0.00	0.00	2.57
1905	1907	4.631740	TCCTCGGGAGCCACCACA	62.632	66.667	0.00	0.00	41.20	4.17
1977	1979	1.190643	CTTCCCGCTCCTCTTCTTCT	58.809	55.000	0.00	0.00	0.00	2.85
2006	2008	4.253257	CGTCGGTAGCCTCGGAGC	62.253	72.222	0.00	0.00	0.00	4.70
2385	2387	3.011517	TCAGGAGCCCCCTTCAGC	61.012	66.667	0.00	0.00	44.85	4.26
2432	2434	2.416107	CTTGCAGCCACCTCCCTTCA	62.416	60.000	0.00	0.00	0.00	3.02
2544	2546	1.153549	GACGGCATCAGACAGGGAC	60.154	63.158	0.00	0.00	0.00	4.46
2551	2553	3.647649	CTGTGGCGACGGCATCAGA	62.648	63.158	31.19	16.81	40.92	3.27
2570	2572	2.033448	CCTGCTACGCCCCAACAA	59.967	61.111	0.00	0.00	0.00	2.83
2614	2616	0.395862	CTAGGAGGAGAGGACGGCAA	60.396	60.000	0.00	0.00	0.00	4.52
2633	2635	2.354203	GGAGAGACATCAGTTGGTGGAC	60.354	54.545	0.00	0.00	0.00	4.02
2724	2726	4.329545	GCCACCAAGCGAGGGTCA	62.330	66.667	2.52	0.00	36.19	4.02
2772	2774	1.475441	GAATCGAAGCGTCAGAGCGG	61.475	60.000	0.00	0.00	43.00	5.52
2999	3002	4.161295	CCTTGATGGCCGCCTCGA	62.161	66.667	11.61	4.95	0.00	4.04

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.