AutoCloner

Multiple sequence alignment - TraesCS4B01G310200

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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	TraesCS4B01G310200	chr4B	100.000	3396	0	0	1	3396	600607162	600603767	0.000000e+00	6272.0
1	TraesCS4B01G310200	chr4B	95.742	2043	69	7	782	2808	600517990	600515950	0.000000e+00	3275.0
2	TraesCS4B01G310200	chr4B	95.967	843	23	7	1639	2475	600599336	600598499	0.000000e+00	1358.0
3	TraesCS4B01G310200	chr4B	93.447	351	22	1	3047	3396	600515958	600515608	1.400000e-143	520.0
4	TraesCS4B01G310200	chr4B	79.545	484	57	24	1	476	519373585	519374034	1.180000e-79	307.0
5	TraesCS4B01G310200	chr4B	89.216	102	9	2	592	692	449229786	449229886	3.560000e-25	126.0
6	TraesCS4B01G310200	chr4B	82.474	97	13	4	606	698	49070069	49069973	7.810000e-12	82.4
7	TraesCS4B01G310200	chr4B	95.122	41	2	0	1072	1112	600606058	600606018	7.870000e-07	65.8
8	TraesCS4B01G310200	chr4D	94.255	1793	52	16	885	2649	476229826	476228057	0.000000e+00	2693.0
9	TraesCS4B01G310200	chr4D	94.148	581	34	0	1	581	476231273	476230693	0.000000e+00	885.0
10	TraesCS4B01G310200	chr4D	94.340	106	3	3	783	887	476229960	476229857	3.510000e-35	159.0
11	TraesCS4B01G310200	chr4A	89.277	2061	120	49	800	2808	683443441	683441430	0.000000e+00	2488.0
12	TraesCS4B01G310200	chr4A	85.345	232	32	2	351	581	41947619	41947389	4.380000e-59	239.0
13	TraesCS4B01G310200	chr2B	81.493	1313	192	35	1110	2397	24905696	24906982	0.000000e+00	1031.0
14	TraesCS4B01G310200	chr2B	80.970	1340	186	51	1110	2404	24889254	24890569	0.000000e+00	998.0
15	TraesCS4B01G310200	chr2B	80.920	1326	198	38	1110	2396	24882778	24884087	0.000000e+00	996.0
16	TraesCS4B01G310200	chr2B	93.478	92	4	2	693	783	30521660	30521750	5.910000e-28	135.0
17	TraesCS4B01G310200	chr2B	93.478	92	4	2	693	783	784303804	784303894	5.910000e-28	135.0
18	TraesCS4B01G310200	chr2B	84.211	76	7	5	2707	2778	770032327	770032253	6.080000e-08	69.4
19	TraesCS4B01G310200	chr2A	80.758	1320	193	42	1120	2396	15906134	15904833	0.000000e+00	974.0
20	TraesCS4B01G310200	chr2A	81.382	854	121	24	1581	2403	15642268	15643114	0.000000e+00	662.0
21	TraesCS4B01G310200	chr2A	87.500	384	42	5	1116	1499	15641779	15642156	4.020000e-119	438.0
22	TraesCS4B01G310200	chr2A	82.294	401	66	3	1110	1510	14892708	14892313	3.240000e-90	342.0
23	TraesCS4B01G310200	chr3D	88.014	584	67	1	1	581	366808089	366807506	0.000000e+00	688.0
24	TraesCS4B01G310200	chr3D	88.480	408	43	2	178	581	545178307	545177900	1.100000e-134	490.0
25	TraesCS4B01G310200	chr3D	94.118	238	12	1	2807	3042	583664519	583664756	8.960000e-96	361.0
26	TraesCS4B01G310200	chr3D	93.697	238	13	1	2807	3042	583710036	583710273	4.170000e-94	355.0
27	TraesCS4B01G310200	chr2D	80.539	853	130	24	1581	2403	13632964	13633810	1.030000e-174	623.0
28	TraesCS4B01G310200	chr7D	89.315	496	50	1	2	494	535900246	535900741	1.340000e-173	619.0
29	TraesCS4B01G310200	chr7D	75.000	1300	249	47	1123	2385	63378302	63377042	6.450000e-147	531.0
30	TraesCS4B01G310200	chr7D	100.000	30	0	0	3367	3396	630507957	630507928	4.730000e-04	56.5
31	TraesCS4B01G310200	chr7A	76.370	821	155	25	1574	2384	66166809	66166018	4.080000e-109	405.0
32	TraesCS4B01G310200	chr7A	94.505	91	3	2	693	782	97406903	97406814	4.570000e-29	139.0
33	TraesCS4B01G310200	chr7A	84.211	95	11	4	606	698	157202488	157202396	4.670000e-14	89.8
34	TraesCS4B01G310200	chr7A	86.420	81	10	1	614	694	300856432	300856511	1.680000e-13	87.9
35	TraesCS4B01G310200	chr7A	84.884	86	9	4	611	694	569613901	569613984	2.170000e-12	84.2
36	TraesCS4B01G310200	chr7A	86.207	58	6	2	2626	2681	529328116	529328173	1.020000e-05	62.1
37	TraesCS4B01G310200	chr3B	93.462	260	12	5	2797	3053	391567694	391567437	6.880000e-102	381.0
38	TraesCS4B01G310200	chr3B	92.490	253	14	4	2804	3052	499722686	499722937	1.160000e-94	357.0
39	TraesCS4B01G310200	chr3B	92.095	253	15	5	2804	3052	510052241	510052492	5.390000e-93	351.0
40	TraesCS4B01G310200	chr3B	92.000	250	15	5	2807	3052	504311427	504311179	2.510000e-91	346.0
41	TraesCS4B01G310200	chr1B	93.089	246	14	3	2802	3044	334234531	334234286	1.160000e-94	357.0
42	TraesCS4B01G310200	chr1B	81.696	224	35	6	2590	2808	77624301	77624523	7.490000e-42	182.0
43	TraesCS4B01G310200	chr7B	92.400	250	14	4	2807	3052	497079024	497078776	5.390000e-93	351.0
44	TraesCS4B01G310200	chr7B	91.440	257	16	2	2798	3052	638419923	638420175	6.970000e-92	348.0
45	TraesCS4B01G310200	chr7B	87.179	78	10	0	700	777	28064103	28064026	4.670000e-14	89.8
46	TraesCS4B01G310200	chr7B	85.366	82	9	3	617	697	74597331	74597252	7.810000e-12	82.4
47	TraesCS4B01G310200	chrUn	83.792	327	50	2	1110	1436	18084747	18085070	1.180000e-79	307.0
48	TraesCS4B01G310200	chrUn	90.769	65	6	0	633	697	87128492	87128428	1.680000e-13	87.9
49	TraesCS4B01G310200	chr6D	80.995	221	39	3	2590	2808	428065838	428065619	4.510000e-39	172.0
50	TraesCS4B01G310200	chr1D	81.905	210	30	8	2600	2804	52325477	52325683	1.620000e-38	171.0
51	TraesCS4B01G310200	chr1D	95.652	92	2	2	693	783	66387716	66387626	2.730000e-31	147.0
52	TraesCS4B01G310200	chr3A	95.604	91	2	2	693	782	701941102	701941191	9.820000e-31	145.0
53	TraesCS4B01G310200	chr6B	92.308	91	5	2	693	782	125540429	125540518	9.890000e-26	128.0
54	TraesCS4B01G310200	chr6B	76.190	168	24	11	2623	2785	45904963	45905119	1.310000e-09	75.0
55	TraesCS4B01G310200	chr6B	79.787	94	12	7	606	694	353569772	353569863	1.020000e-05	62.1
56	TraesCS4B01G310200	chr1A	93.103	87	6	0	696	782	551669891	551669805	9.890000e-26	128.0
57	TraesCS4B01G310200	chr1A	84.884	86	12	1	693	777	54510618	54510533	6.040000e-13	86.1
58	TraesCS4B01G310200	chr5A	86.420	81	10	1	614	694	684651974	684652053	1.680000e-13	87.9

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	TraesCS4B01G310200	chr4B	600603767	600607162	3395	True	3168.900000	6272	97.561000	1	3396	2	chr4B.!!$R4	3395
1	TraesCS4B01G310200	chr4B	600515608	600517990	2382	True	1897.500000	3275	94.594500	782	3396	2	chr4B.!!$R3	2614
2	TraesCS4B01G310200	chr4B	600598499	600599336	837	True	1358.000000	1358	95.967000	1639	2475	1	chr4B.!!$R2	836
3	TraesCS4B01G310200	chr4D	476228057	476231273	3216	True	1245.666667	2693	94.247667	1	2649	3	chr4D.!!$R1	2648
4	TraesCS4B01G310200	chr4A	683441430	683443441	2011	True	2488.000000	2488	89.277000	800	2808	1	chr4A.!!$R2	2008
5	TraesCS4B01G310200	chr2B	24905696	24906982	1286	False	1031.000000	1031	81.493000	1110	2397	1	chr2B.!!$F3	1287
6	TraesCS4B01G310200	chr2B	24889254	24890569	1315	False	998.000000	998	80.970000	1110	2404	1	chr2B.!!$F2	1294
7	TraesCS4B01G310200	chr2B	24882778	24884087	1309	False	996.000000	996	80.920000	1110	2396	1	chr2B.!!$F1	1286
8	TraesCS4B01G310200	chr2A	15904833	15906134	1301	True	974.000000	974	80.758000	1120	2396	1	chr2A.!!$R2	1276
9	TraesCS4B01G310200	chr2A	15641779	15643114	1335	False	550.000000	662	84.441000	1116	2403	2	chr2A.!!$F1	1287
10	TraesCS4B01G310200	chr3D	366807506	366808089	583	True	688.000000	688	88.014000	1	581	1	chr3D.!!$R1	580
11	TraesCS4B01G310200	chr2D	13632964	13633810	846	False	623.000000	623	80.539000	1581	2403	1	chr2D.!!$F1	822
12	TraesCS4B01G310200	chr7D	63377042	63378302	1260	True	531.000000	531	75.000000	1123	2385	1	chr7D.!!$R1	1262
13	TraesCS4B01G310200	chr7A	66166018	66166809	791	True	405.000000	405	76.370000	1574	2384	1	chr7A.!!$R1	810

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
584	588	0.105964	CCAGCAGCCTCCTCCTAGTA	60.106	60.0	0.00	0.0	0.00	1.82	F
720	724	0.179468	AAACTACAGTGTGCGGTGGT	59.821	50.0	5.88	0.0	36.24	4.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2386	3097	1.286849	TCCTCCCTCGATCAGTTGGTA	59.713	52.381	0.0	0.0	0.0	3.25	R
2619	3365	0.525761	AACCAATTCCCGCATGTTCG	59.474	50.000	0.0	0.0	0.0	3.95	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
40	41	3.000819	CACCCCCTGCACCGACTA	61.001	66.667	0.00	0.00	0.00	2.59
62	63	7.406104	ACTAAATACTGGCTGGATTTTCTTCT	58.594	34.615	18.16	0.00	0.00	2.85
87	88	2.063979	CCGTGCACCTCCATCCCTA	61.064	63.158	12.15	0.00	0.00	3.53
128	129	1.754380	CGTCCAGGTTGACCACTCCA	61.754	60.000	2.56	0.00	38.89	3.86
152	153	2.356313	CAGCAGCACTTCGTCGGT	60.356	61.111	0.00	0.00	0.00	4.69
224	225	0.466555	CCGACAAACCAAACCTCCCA	60.467	55.000	0.00	0.00	0.00	4.37
302	306	0.751643	AACAGCCGTCAAGCCAACTT	60.752	50.000	0.00	0.00	36.19	2.66
383	387	1.605058	CCTCCATCTTCCACGACCGT	61.605	60.000	0.00	0.00	0.00	4.83
436	440	2.359230	GACGAAGCAGGCTTGGCT	60.359	61.111	11.85	1.43	45.15	4.75
557	561	4.070552	GCCGCGACCAACTCTCCT	62.071	66.667	8.23	0.00	0.00	3.69
564	568	1.882989	GACCAACTCTCCTGCGAGCT	61.883	60.000	0.00	0.00	35.94	4.09
581	585	1.075674	CTCCAGCAGCCTCCTCCTA	60.076	63.158	0.00	0.00	0.00	2.94
582	586	1.075674	TCCAGCAGCCTCCTCCTAG	60.076	63.158	0.00	0.00	0.00	3.02
583	587	1.382420	CCAGCAGCCTCCTCCTAGT	60.382	63.158	0.00	0.00	0.00	2.57
584	588	0.105964	CCAGCAGCCTCCTCCTAGTA	60.106	60.000	0.00	0.00	0.00	1.82
585	589	1.689575	CCAGCAGCCTCCTCCTAGTAA	60.690	57.143	0.00	0.00	0.00	2.24
586	590	2.111384	CAGCAGCCTCCTCCTAGTAAA	58.889	52.381	0.00	0.00	0.00	2.01
587	591	2.102252	CAGCAGCCTCCTCCTAGTAAAG	59.898	54.545	0.00	0.00	0.00	1.85
588	592	1.202592	GCAGCCTCCTCCTAGTAAAGC	60.203	57.143	0.00	0.00	0.00	3.51
589	593	2.393646	CAGCCTCCTCCTAGTAAAGCT	58.606	52.381	0.00	0.00	0.00	3.74
590	594	2.769095	CAGCCTCCTCCTAGTAAAGCTT	59.231	50.000	0.00	0.00	0.00	3.74
593	597	3.055021	GCCTCCTCCTAGTAAAGCTTTGT	60.055	47.826	22.02	11.15	0.00	2.83
595	599	5.561679	CCTCCTCCTAGTAAAGCTTTGTTT	58.438	41.667	22.02	9.23	0.00	2.83
596	600	5.412904	CCTCCTCCTAGTAAAGCTTTGTTTG	59.587	44.000	22.02	9.96	0.00	2.93
597	601	5.937111	TCCTCCTAGTAAAGCTTTGTTTGT	58.063	37.500	22.02	4.16	0.00	2.83

Showing 1 to 25 of 299 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	25	1.205460	ATTTAGTCGGTGCAGGGGGT	61.205	55.000	0.00	0.00	0.00	4.95
40	41	6.248433	TCAGAAGAAAATCCAGCCAGTATTT	58.752	36.000	0.00	0.00	0.00	1.40
62	63	1.971167	GGAGGTGCACGGCAATTCA	60.971	57.895	11.45	0.00	41.47	2.57
152	153	1.287815	CCACGACAACTCGGCTACA	59.712	57.895	0.00	0.00	44.80	2.74
162	163	2.732016	CTCGGTGGACCACGACAA	59.268	61.111	18.40	2.94	34.83	3.18
183	184	1.473258	TGTTTTGCTTCTGCCTGTGT	58.527	45.000	0.00	0.00	38.71	3.72
282	286	0.751643	AGTTGGCTTGACGGCTGTTT	60.752	50.000	0.00	0.00	39.32	2.83
331	335	1.056125	TGGATGTGCCCGATCTGGAT	61.056	55.000	7.45	0.00	42.00	3.41
564	568	1.075674	CTAGGAGGAGGCTGCTGGA	60.076	63.158	15.18	0.00	0.00	3.86
581	585	5.761234	TGATACGGACAAACAAAGCTTTACT	59.239	36.000	12.25	0.00	0.00	2.24
582	586	5.992729	TGATACGGACAAACAAAGCTTTAC	58.007	37.500	12.25	0.00	0.00	2.01
583	587	6.621316	TTGATACGGACAAACAAAGCTTTA	57.379	33.333	12.25	0.00	0.00	1.85
584	588	5.508200	TTGATACGGACAAACAAAGCTTT	57.492	34.783	5.69	5.69	0.00	3.51
585	589	5.067283	ACTTTGATACGGACAAACAAAGCTT	59.933	36.000	14.84	0.00	46.05	3.74
586	590	4.578928	ACTTTGATACGGACAAACAAAGCT	59.421	37.500	14.84	0.00	46.05	3.74
587	591	4.855531	ACTTTGATACGGACAAACAAAGC	58.144	39.130	14.84	0.00	46.05	3.51
641	645	9.899226	GATGTCAAGCTTTACTATGAACTTTTT	57.101	29.630	11.84	0.00	0.00	1.94
642	646	9.066892	TGATGTCAAGCTTTACTATGAACTTTT	57.933	29.630	11.84	0.00	0.00	2.27
643	647	8.507249	GTGATGTCAAGCTTTACTATGAACTTT	58.493	33.333	11.84	0.00	0.00	2.66
644	648	7.661437	TGTGATGTCAAGCTTTACTATGAACTT	59.339	33.333	11.84	0.00	0.00	2.66
645	649	7.161404	TGTGATGTCAAGCTTTACTATGAACT	58.839	34.615	11.84	0.00	0.00	3.01
646	650	7.364522	TGTGATGTCAAGCTTTACTATGAAC	57.635	36.000	11.84	4.62	0.00	3.18
647	651	7.119699	CCTTGTGATGTCAAGCTTTACTATGAA	59.880	37.037	11.84	0.00	42.16	2.57
648	652	6.595326	CCTTGTGATGTCAAGCTTTACTATGA	59.405	38.462	11.84	0.00	42.16	2.15
649	653	6.372659	ACCTTGTGATGTCAAGCTTTACTATG	59.627	38.462	11.84	0.00	42.16	2.23

Showing 1 to 25 of 307 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.