AutoCloner

Multiple sequence alignment - TraesCS7B01G186400

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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	TraesCS7B01G186400	chr7B	100.000	3704	0	0	1	3704	309185676	309181973	0.000000e+00	6841
1	TraesCS7B01G186400	chr7B	98.526	2646	38	1	641	3285	311628182	311625537	0.000000e+00	4669
2	TraesCS7B01G186400	chr5B	94.522	3286	156	17	7	3285	202442808	202446076	0.000000e+00	5049
3	TraesCS7B01G186400	chr5A	98.488	2646	39	1	641	3285	247106338	247108983	0.000000e+00	4663
4	TraesCS7B01G186400	chr5A	85.776	1378	142	24	2363	3703	255739040	255740400	0.000000e+00	1410
5	TraesCS7B01G186400	chr3A	98.265	2651	42	4	641	3288	318334606	318337255	0.000000e+00	4638
6	TraesCS7B01G186400	chr7A	98.262	2647	45	1	640	3285	361606177	361603531	0.000000e+00	4632
7	TraesCS7B01G186400	chrUn	98.262	2646	43	2	641	3285	221356157	221358800	0.000000e+00	4628
8	TraesCS7B01G186400	chrUn	93.523	772	44	4	2935	3704	120073533	120072766	0.000000e+00	1144
9	TraesCS7B01G186400	chrUn	93.523	772	44	4	2935	3704	134153536	134154303	0.000000e+00	1144
10	TraesCS7B01G186400	chrUn	93.394	772	45	4	2935	3704	134213069	134213836	0.000000e+00	1138
11	TraesCS7B01G186400	chrUn	96.429	420	15	0	3285	3704	425216006	425215587	0.000000e+00	693
12	TraesCS7B01G186400	chr4A	98.255	2636	45	1	651	3285	270394882	270397517	0.000000e+00	4612
13	TraesCS7B01G186400	chr4A	98.001	2651	49	4	638	3286	270161368	270164016	0.000000e+00	4599
14	TraesCS7B01G186400	chr4A	96.667	420	14	0	3285	3704	266700596	266700177	0.000000e+00	699
15	TraesCS7B01G186400	chr2A	97.924	2649	50	5	640	3285	240353686	240351040	0.000000e+00	4582
16	TraesCS7B01G186400	chr2A	92.179	179	8	1	56	234	276051606	276051778	7.940000e-62	248
17	TraesCS7B01G186400	chr2A	90.435	115	9	2	425	538	276055246	276055359	2.300000e-32	150
18	TraesCS7B01G186400	chr2B	92.598	689	40	5	3026	3704	345873291	345873978	0.000000e+00	979
19	TraesCS7B01G186400	chr2B	87.719	513	40	13	28	535	305669747	305669253	8.920000e-161	577
20	TraesCS7B01G186400	chr4D	96.429	420	15	0	3285	3704	205511634	205511215	0.000000e+00	693
21	TraesCS7B01G186400	chr4D	96.429	420	15	0	3285	3704	205512093	205512512	0.000000e+00	693

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	TraesCS7B01G186400	chr7B	309181973	309185676	3703	True	6841	6841	100.000	1	3704	1	chr7B.!!$R1	3703
1	TraesCS7B01G186400	chr7B	311625537	311628182	2645	True	4669	4669	98.526	641	3285	1	chr7B.!!$R2	2644
2	TraesCS7B01G186400	chr5B	202442808	202446076	3268	False	5049	5049	94.522	7	3285	1	chr5B.!!$F1	3278
3	TraesCS7B01G186400	chr5A	247106338	247108983	2645	False	4663	4663	98.488	641	3285	1	chr5A.!!$F1	2644
4	TraesCS7B01G186400	chr5A	255739040	255740400	1360	False	1410	1410	85.776	2363	3703	1	chr5A.!!$F2	1340
5	TraesCS7B01G186400	chr3A	318334606	318337255	2649	False	4638	4638	98.265	641	3288	1	chr3A.!!$F1	2647
6	TraesCS7B01G186400	chr7A	361603531	361606177	2646	True	4632	4632	98.262	640	3285	1	chr7A.!!$R1	2645
7	TraesCS7B01G186400	chrUn	221356157	221358800	2643	False	4628	4628	98.262	641	3285	1	chrUn.!!$F3	2644
8	TraesCS7B01G186400	chrUn	120072766	120073533	767	True	1144	1144	93.523	2935	3704	1	chrUn.!!$R1	769
9	TraesCS7B01G186400	chrUn	134153536	134154303	767	False	1144	1144	93.523	2935	3704	1	chrUn.!!$F1	769
10	TraesCS7B01G186400	chrUn	134213069	134213836	767	False	1138	1138	93.394	2935	3704	1	chrUn.!!$F2	769
11	TraesCS7B01G186400	chr4A	270394882	270397517	2635	False	4612	4612	98.255	651	3285	1	chr4A.!!$F2	2634
12	TraesCS7B01G186400	chr4A	270161368	270164016	2648	False	4599	4599	98.001	638	3286	1	chr4A.!!$F1	2648
13	TraesCS7B01G186400	chr2A	240351040	240353686	2646	True	4582	4582	97.924	640	3285	1	chr2A.!!$R1	2645
14	TraesCS7B01G186400	chr2B	345873291	345873978	687	False	979	979	92.598	3026	3704	1	chr2B.!!$F1	678

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
707	712	0.324368	TAGGACCAGCACTCGACCAT	60.324	55.0	0.0	0.0	0.0	3.55	F
1255	1262	1.029681	GGTTGCGGTTGGTTCTTTCT	58.970	50.0	0.0	0.0	0.0	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2615	2625	2.506644	TCATCTCCATGCTTGACCATGA	59.493	45.455	0.22	2.82	44.12	3.07	R
3159	3194	0.611714	ATCGCTAAACCAACTCCGGT	59.388	50.000	0.00	0.00	42.71	5.28	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	6.222038	AGGAAAAACAAAGAGGAAGGAAAC	57.778	37.500	0.00	0.00	0.00	2.78
34	35	2.687935	GAGGAAGGAAACAACACTTGCA	59.312	45.455	0.00	0.00	35.37	4.08
47	48	3.197265	ACACTTGCATTGGAAGTTTTGC	58.803	40.909	19.49	0.00	31.05	3.68
52	53	5.870978	ACTTGCATTGGAAGTTTTGCATATC	59.129	36.000	16.79	0.00	43.91	1.63
89	90	4.395625	TGAGTACGTTTTGGAGAGAGAGA	58.604	43.478	0.00	0.00	0.00	3.10
90	91	4.456222	TGAGTACGTTTTGGAGAGAGAGAG	59.544	45.833	0.00	0.00	0.00	3.20
91	92	4.653868	AGTACGTTTTGGAGAGAGAGAGA	58.346	43.478	0.00	0.00	0.00	3.10
92	93	4.698304	AGTACGTTTTGGAGAGAGAGAGAG	59.302	45.833	0.00	0.00	0.00	3.20
93	94	3.757270	ACGTTTTGGAGAGAGAGAGAGA	58.243	45.455	0.00	0.00	0.00	3.10
147	148	1.202770	AGGAAAGGTCTGACCGGTTTG	60.203	52.381	20.49	4.79	44.90	2.93
156	157	0.684805	TGACCGGTTTGGCAGGTTTT	60.685	50.000	9.42	0.00	45.67	2.43
157	158	1.320507	GACCGGTTTGGCAGGTTTTA	58.679	50.000	9.42	0.00	45.67	1.52
162	163	2.226912	CGGTTTGGCAGGTTTTAATCGA	59.773	45.455	0.00	0.00	0.00	3.59
373	376	5.132502	TCAAAAAGTCTCTTGGCTGATTCA	58.867	37.500	0.00	0.00	0.00	2.57
453	458	5.023533	AGGAAAGAAAGGAAACAAAAGGC	57.976	39.130	0.00	0.00	0.00	4.35
455	460	5.189736	AGGAAAGAAAGGAAACAAAAGGCTT	59.810	36.000	0.00	0.00	0.00	4.35
546	551	7.390440	GTGTAGCACTACAGAGAGATAGATCAT	59.610	40.741	10.71	0.00	45.61	2.45
556	561	4.738685	AGAGATAGATCATCAGGACAGCA	58.261	43.478	0.00	0.00	35.96	4.41
557	562	5.146298	AGAGATAGATCATCAGGACAGCAA	58.854	41.667	0.00	0.00	35.96	3.91
609	614	3.769201	GCTGGTTGCTTCCTGCTT	58.231	55.556	17.13	0.00	44.99	3.91
707	712	0.324368	TAGGACCAGCACTCGACCAT	60.324	55.000	0.00	0.00	0.00	3.55
829	835	2.355197	CATACGTTCACCTGGCAATCA	58.645	47.619	0.00	0.00	0.00	2.57
1037	1044	1.133025	CAATCCATGGGCTTTGTCGAC	59.867	52.381	13.02	9.11	0.00	4.20
1255	1262	1.029681	GGTTGCGGTTGGTTCTTTCT	58.970	50.000	0.00	0.00	0.00	2.52
1656	1665	3.051392	GCGGAAGGTGCAAATCCCG	62.051	63.158	12.66	12.66	39.88	5.14
2615	2625	4.952335	GGACAAGAAGGATGAACATTGGAT	59.048	41.667	0.00	0.00	0.00	3.41
2646	2656	0.107508	ATGGAGATGAAGGTGCGTGG	60.108	55.000	0.00	0.00	0.00	4.94
2724	2735	6.298441	TGATGACATACAAGAAGATGGACA	57.702	37.500	0.00	0.00	0.00	4.02
3154	3189	1.672030	TGCTCCAGCGTGGTCAATG	60.672	57.895	4.33	0.00	45.83	2.82
3289	3333	1.967066	ACCCTCGCCTCTATCATTGAG	59.033	52.381	0.00	0.00	0.00	3.02
3311	3355	0.613260	TATTGAGAGTTGGCCGCAGT	59.387	50.000	0.00	0.00	0.00	4.40
3375	3419	5.680619	TGGATTCTATAGGCGTTTTGTGAT	58.319	37.500	0.00	0.00	0.00	3.06
3445	3489	1.757699	GTGCCTTTTGTTTGGGGTACA	59.242	47.619	0.00	0.00	35.18	2.90
3511	3555	2.289444	TGCTCCTTTACTCCAACTTCCG	60.289	50.000	0.00	0.00	0.00	4.30
3512	3556	2.028385	GCTCCTTTACTCCAACTTCCGA	60.028	50.000	0.00	0.00	0.00	4.55
3569	3613	2.775384	AGTGGAATTGGATTAGGCGGTA	59.225	45.455	0.00	0.00	0.00	4.02
3593	3637	6.909550	TGTTATTACAAGATGGCAAACCTT	57.090	33.333	0.00	0.00	36.63	3.50
3601	3645	5.180271	CAAGATGGCAAACCTTTTGCATAT	58.820	37.500	21.67	15.75	46.58	1.78
3627	3671	4.735369	TCTGAAAAATTGAGTGGGCCTAA	58.265	39.130	4.53	0.00	0.00	2.69
3689	3733	3.830178	TGTTCGGACTTTAGAGACATGGA	59.170	43.478	0.00	0.00	0.00	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.127451	TGTTTCCTTCCTCTTTGTTTTTCCTC	60.127	38.462	0.00	0.00	0.00	3.71
3	4	6.871492	TGTTGTTTCCTTCCTCTTTGTTTTTC	59.129	34.615	0.00	0.00	0.00	2.29
9	10	5.343249	CAAGTGTTGTTTCCTTCCTCTTTG	58.657	41.667	0.00	0.00	0.00	2.77
11	12	3.381590	GCAAGTGTTGTTTCCTTCCTCTT	59.618	43.478	0.00	0.00	0.00	2.85
12	13	2.952310	GCAAGTGTTGTTTCCTTCCTCT	59.048	45.455	0.00	0.00	0.00	3.69
13	14	2.687935	TGCAAGTGTTGTTTCCTTCCTC	59.312	45.455	0.00	0.00	0.00	3.71
24	25	4.494526	GCAAAACTTCCAATGCAAGTGTTG	60.495	41.667	14.10	14.10	45.96	3.33
89	90	6.957020	TCCTTTCCTAATTGAACTCTCTCTCT	59.043	38.462	0.00	0.00	0.00	3.10
90	91	7.176589	TCCTTTCCTAATTGAACTCTCTCTC	57.823	40.000	0.00	0.00	0.00	3.20
91	92	7.560796	TTCCTTTCCTAATTGAACTCTCTCT	57.439	36.000	0.00	0.00	0.00	3.10
92	93	9.892130	TTATTCCTTTCCTAATTGAACTCTCTC	57.108	33.333	0.00	0.00	0.00	3.20
134	135	1.966451	CCTGCCAAACCGGTCAGAC	60.966	63.158	19.70	6.64	39.77	3.51
135	136	1.990160	AACCTGCCAAACCGGTCAGA	61.990	55.000	19.70	0.00	39.77	3.27
138	139	1.320507	TAAAACCTGCCAAACCGGTC	58.679	50.000	8.04	0.00	36.97	4.79
147	148	9.575783	TTTATTGTTAATCGATTAAAACCTGCC	57.424	29.630	27.56	15.91	34.36	4.85
157	158	9.113838	AGATCTGCACTTTATTGTTAATCGATT	57.886	29.630	16.15	16.15	0.00	3.34
162	163	9.846248	GAAACAGATCTGCACTTTATTGTTAAT	57.154	29.630	22.83	0.00	0.00	1.40
271	274	7.235159	TCTCCTACCTTTATTCTCCCTCTTA	57.765	40.000	0.00	0.00	0.00	2.10
272	275	6.106407	TCTCCTACCTTTATTCTCCCTCTT	57.894	41.667	0.00	0.00	0.00	2.85
289	292	9.672673	CACTTTCCTATCTTTTTCAATCTCCTA	57.327	33.333	0.00	0.00	0.00	2.94
306	309	2.851263	AATCCACGTGCACTTTCCTA	57.149	45.000	16.19	0.00	0.00	2.94
414	419	7.798710	TCTTTCCTAATTCCTTTCTCTCAGA	57.201	36.000	0.00	0.00	0.00	3.27
415	420	8.854614	TTTCTTTCCTAATTCCTTTCTCTCAG	57.145	34.615	0.00	0.00	0.00	3.35
416	421	7.885399	CCTTTCTTTCCTAATTCCTTTCTCTCA	59.115	37.037	0.00	0.00	0.00	3.27
417	422	8.103935	TCCTTTCTTTCCTAATTCCTTTCTCTC	58.896	37.037	0.00	0.00	0.00	3.20
474	479	3.967987	ACCAAATGGCCTACTACTCCTAG	59.032	47.826	3.32	0.00	39.32	3.02
475	480	4.003584	ACCAAATGGCCTACTACTCCTA	57.996	45.455	3.32	0.00	39.32	2.94
476	481	2.846950	ACCAAATGGCCTACTACTCCT	58.153	47.619	3.32	0.00	39.32	3.69
507	512	1.064314	TGCTACACACAACCACCCTTT	60.064	47.619	0.00	0.00	0.00	3.11
508	513	0.548989	TGCTACACACAACCACCCTT	59.451	50.000	0.00	0.00	0.00	3.95
509	514	2.226764	TGCTACACACAACCACCCT	58.773	52.632	0.00	0.00	0.00	4.34
521	526	6.831976	TGATCTATCTCTCTGTAGTGCTACA	58.168	40.000	11.07	11.07	43.14	2.74
523	528	7.684529	TGATGATCTATCTCTCTGTAGTGCTA	58.315	38.462	0.00	0.00	36.71	3.49
609	614	0.879839	CGGACGGATGTGCATGCATA	60.880	55.000	25.64	22.69	35.97	3.14
707	712	4.867047	TGCAAGCTGAAAATTCGTTCAAAA	59.133	33.333	0.00	0.00	37.08	2.44
1255	1262	4.764823	CCACCAAACTAAAGCATAACCAGA	59.235	41.667	0.00	0.00	0.00	3.86
1656	1665	2.743871	GAACAACCGTCGCAACTCGC	62.744	60.000	0.00	0.00	38.27	5.03
1879	1888	3.340814	AGCTGGTGTGATCAAAGTAGG	57.659	47.619	0.00	0.00	0.00	3.18
2615	2625	2.506644	TCATCTCCATGCTTGACCATGA	59.493	45.455	0.22	2.82	44.12	3.07
2646	2656	3.729966	ACCTCCGTTCTTGTTCTCTTTC	58.270	45.455	0.00	0.00	0.00	2.62
2739	2750	7.357471	AGCTATGGAGGAAATTTATGAAAGGT	58.643	34.615	0.00	0.00	0.00	3.50
3154	3189	2.676176	GCTAAACCAACTCCGGTAGGTC	60.676	54.545	0.00	0.00	38.76	3.85
3159	3194	0.611714	ATCGCTAAACCAACTCCGGT	59.388	50.000	0.00	0.00	42.71	5.28
3289	3333	1.440145	GCGGCCAACTCTCAATAGCC	61.440	60.000	2.24	0.00	37.03	3.93
3311	3355	1.740585	CACTTGTGTGACCGTTTTGGA	59.259	47.619	0.00	0.00	46.55	3.53
3445	3489	1.003003	GAGAAGGCTTCTTCCTGTGCT	59.997	52.381	29.11	5.38	46.01	4.40
3569	3613	7.480760	AAGGTTTGCCATCTTGTAATAACAT	57.519	32.000	0.00	0.00	34.36	2.71
3601	3645	5.104569	AGGCCCACTCAATTTTTCAGAAAAA	60.105	36.000	20.82	20.82	43.76	1.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.