AutoCloner

Multiple sequence alignment - TraesCS5B01G117700

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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	TraesCS5B01G117700	chr5B	100.000	3275	0	0	1	3275	207590007	207586733	0.000000e+00	6048.0
1	TraesCS5B01G117700	chr5B	82.072	859	141	10	1749	2606	207601189	207602035	0.000000e+00	721.0
2	TraesCS5B01G117700	chr5B	100.000	72	0	0	3619	3690	207586389	207586318	2.310000e-27	134.0
3	TraesCS5B01G117700	chr5D	94.372	3074	120	24	1	3046	204861486	204864534	0.000000e+00	4669.0
4	TraesCS5B01G117700	chr5D	96.552	174	4	2	3103	3275	204864726	204864898	1.680000e-73	287.0
5	TraesCS5B01G117700	chr5D	88.785	107	11	1	2565	2670	204859590	204859484	2.990000e-26	130.0
6	TraesCS5B01G117700	chr5D	98.611	72	1	0	3619	3690	204864951	204865022	1.080000e-25	128.0
7	TraesCS5B01G117700	chr5D	80.734	109	18	3	157	265	204861710	204861815	8.490000e-12	82.4
8	TraesCS5B01G117700	chr5A	96.422	2348	72	4	698	3039	244429194	244431535	0.000000e+00	3860.0
9	TraesCS5B01G117700	chr5A	82.399	1267	191	14	1423	2670	244427447	244426194	0.000000e+00	1075.0
10	TraesCS5B01G117700	chr5A	83.743	732	74	17	1	713	244428182	244428887	0.000000e+00	651.0
11	TraesCS5B01G117700	chr5A	93.902	246	13	2	3032	3275	244431721	244431966	1.620000e-98	370.0
12	TraesCS5B01G117700	chr5A	100.000	65	0	0	3621	3685	244432021	244432085	1.800000e-23	121.0
13	TraesCS5B01G117700	chr5A	78.899	109	20	3	157	265	244428407	244428512	1.840000e-08	71.3
14	TraesCS5B01G117700	chr4A	91.519	283	24	0	1215	1497	572540547	572540829	1.240000e-104	390.0
15	TraesCS5B01G117700	chr4A	82.828	99	17	0	2127	2225	682365600	682365698	5.080000e-14	89.8
16	TraesCS5B01G117700	chr4B	91.197	284	23	1	1216	1497	43760168	43759885	5.780000e-103	385.0
17	TraesCS5B01G117700	chr4B	88.496	113	6	3	2532	2643	420422150	420422044	2.990000e-26	130.0
18	TraesCS5B01G117700	chr4B	87.719	114	6	4	2532	2643	330794561	330794454	3.870000e-25	126.0
19	TraesCS5B01G117700	chr4B	80.000	125	23	2	2102	2225	600242337	600242460	1.410000e-14	91.6
20	TraesCS5B01G117700	chr4D	93.607	219	13	1	1280	1497	30505711	30505493	3.550000e-85	326.0
21	TraesCS5B01G117700	chr4D	96.429	56	2	0	10	65	502104601	502104546	3.920000e-15	93.5
22	TraesCS5B01G117700	chr4D	79.839	124	25	0	2102	2225	475675939	475676062	1.410000e-14	91.6
23	TraesCS5B01G117700	chrUn	89.381	113	5	3	2532	2643	12578621	12578727	6.430000e-28	135.0
24	TraesCS5B01G117700	chrUn	94.595	37	2	0	58	94	275922198	275922162	1.430000e-04	58.4
25	TraesCS5B01G117700	chrUn	94.595	37	2	0	58	94	275929752	275929716	1.430000e-04	58.4
26	TraesCS5B01G117700	chrUn	94.595	37	2	0	58	94	287242685	287242721	1.430000e-04	58.4
27	TraesCS5B01G117700	chr1B	88.393	112	5	4	2532	2641	44188625	44188730	1.080000e-25	128.0
28	TraesCS5B01G117700	chr1B	76.437	174	37	4	2109	2280	420685678	420685849	1.410000e-14	91.6
29	TraesCS5B01G117700	chr1A	76.923	156	34	2	2126	2280	390709589	390709743	1.830000e-13	87.9
30	TraesCS5B01G117700	chr6D	94.595	37	2	0	57	93	368767820	368767784	1.430000e-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	TraesCS5B01G117700	chr5B	207586318	207590007	3689	True	3091.00	6048	100.00000	1	3690	2	chr5B.!!$R1	3689
1	TraesCS5B01G117700	chr5B	207601189	207602035	846	False	721.00	721	82.07200	1749	2606	1	chr5B.!!$F1	857
2	TraesCS5B01G117700	chr5D	204861486	204865022	3536	False	1291.60	4669	92.56725	1	3690	4	chr5D.!!$F1	3689
3	TraesCS5B01G117700	chr5A	244426194	244427447	1253	True	1075.00	1075	82.39900	1423	2670	1	chr5A.!!$R1	1247
4	TraesCS5B01G117700	chr5A	244428182	244432085	3903	False	1014.66	3860	90.59320	1	3685	5	chr5A.!!$F1	3684

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
486	499	0.386113	AACGATAGCGAGGAGAAGCC	59.614	55.0	7.69	0.0	41.64	4.35	F
746	1085	0.405585	AGTGGTATGCCTTGCCTTGT	59.594	50.0	0.16	0.0	35.27	3.16	F
2411	2766	0.617413	CAGGTCTTGCCAGTGAGGAT	59.383	55.0	0.00	0.0	41.22	3.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2033	2388	1.276705	GACCGCCTCCTCTTCTTCTTT	59.723	52.381	0.00	0.0	0.00	2.52	R
2617	2991	2.887152	GTGGCCTTCAGTGATTGAAAGT	59.113	45.455	3.32	0.0	44.84	2.66	R
3243	3946	0.833949	TTGGAAGCCAAACAAACCCC	59.166	50.000	0.00	0.0	40.92	4.95	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
42	43	4.282449	TCCTTGTTACCATCGTCTCAAGAA	59.718	41.667	8.35	0.00	36.10	2.52
191	192	1.742768	CTCCTCGCCACCAGTATCC	59.257	63.158	0.00	0.00	0.00	2.59
195	196	1.306654	TCGCCACCAGTATCCCCTT	60.307	57.895	0.00	0.00	0.00	3.95
322	323	4.373116	TTGCTCCTCGCCACCGAC	62.373	66.667	0.00	0.00	38.82	4.79
380	381	1.691801	GGAGAGGGGAAATAGGACCGT	60.692	57.143	0.00	0.00	0.00	4.83
457	470	3.364460	TGGCAACACTACCTGCATTAT	57.636	42.857	0.00	0.00	46.17	1.28
458	471	3.696045	TGGCAACACTACCTGCATTATT	58.304	40.909	0.00	0.00	46.17	1.40
459	472	3.694072	TGGCAACACTACCTGCATTATTC	59.306	43.478	0.00	0.00	46.17	1.75
460	473	3.242739	GGCAACACTACCTGCATTATTCG	60.243	47.826	0.00	0.00	40.46	3.34
462	475	4.727734	GCAACACTACCTGCATTATTCGTG	60.728	45.833	0.00	0.00	38.48	4.35
463	476	4.202245	ACACTACCTGCATTATTCGTGT	57.798	40.909	0.00	0.00	0.00	4.49
465	478	5.001232	ACACTACCTGCATTATTCGTGTTT	58.999	37.500	0.00	0.00	31.00	2.83
466	479	5.121768	ACACTACCTGCATTATTCGTGTTTC	59.878	40.000	0.00	0.00	31.00	2.78
467	480	5.121611	CACTACCTGCATTATTCGTGTTTCA	59.878	40.000	0.00	0.00	0.00	2.69
468	481	5.703592	ACTACCTGCATTATTCGTGTTTCAA	59.296	36.000	0.00	0.00	0.00	2.69
469	482	4.794169	ACCTGCATTATTCGTGTTTCAAC	58.206	39.130	0.00	0.00	0.00	3.18
477	490	2.334971	TCGTGTTTCAACGATAGCGA	57.665	45.000	7.69	0.00	46.99	4.93
478	491	2.247637	TCGTGTTTCAACGATAGCGAG	58.752	47.619	7.69	0.00	46.99	5.03
479	492	1.320555	CGTGTTTCAACGATAGCGAGG	59.679	52.381	7.69	0.00	46.49	4.63
480	493	2.602878	GTGTTTCAACGATAGCGAGGA	58.397	47.619	7.69	0.29	41.64	3.71
481	494	2.599082	GTGTTTCAACGATAGCGAGGAG	59.401	50.000	7.69	0.00	41.64	3.69
482	495	2.490509	TGTTTCAACGATAGCGAGGAGA	59.509	45.455	7.69	0.00	41.64	3.71
483	496	3.057104	TGTTTCAACGATAGCGAGGAGAA	60.057	43.478	7.69	2.45	41.64	2.87
484	497	3.422417	TTCAACGATAGCGAGGAGAAG	57.578	47.619	7.69	0.00	41.64	2.85
485	498	1.065701	TCAACGATAGCGAGGAGAAGC	59.934	52.381	7.69	0.00	41.64	3.86
486	499	0.386113	AACGATAGCGAGGAGAAGCC	59.614	55.000	7.69	0.00	41.64	4.35
487	500	1.081774	CGATAGCGAGGAGAAGCCG	60.082	63.158	0.00	0.00	43.43	5.52
488	501	1.287503	GATAGCGAGGAGAAGCCGG	59.712	63.158	0.00	0.00	43.43	6.13
489	502	1.455959	ATAGCGAGGAGAAGCCGGT	60.456	57.895	1.90	0.00	43.43	5.28
490	503	1.739338	ATAGCGAGGAGAAGCCGGTG	61.739	60.000	1.90	0.00	43.43	4.94
491	504	4.070552	GCGAGGAGAAGCCGGTGT	62.071	66.667	1.90	0.00	43.43	4.16
492	505	2.657237	CGAGGAGAAGCCGGTGTT	59.343	61.111	1.90	0.00	43.43	3.32
580	593	7.914427	TCAATGTAGATATCAACTACTGGGT	57.086	36.000	5.32	0.00	40.30	4.51
584	597	4.423625	AGATATCAACTACTGGGTTGCC	57.576	45.455	5.32	0.00	44.19	4.52
586	599	2.969821	ATCAACTACTGGGTTGCCAA	57.030	45.000	9.73	0.00	44.19	4.52
588	601	2.303175	TCAACTACTGGGTTGCCAAAC	58.697	47.619	9.73	0.00	44.19	2.93
591	604	2.583143	ACTACTGGGTTGCCAAACTTC	58.417	47.619	0.00	0.00	36.48	3.01
628	641	1.340405	GCTTGCCCAGAGGATCAAAGA	60.340	52.381	0.00	0.00	37.82	2.52
670	687	0.600057	GCCTTTGCTTCACTCCCTTG	59.400	55.000	0.00	0.00	33.53	3.61
704	721	7.327214	AGTTTTCTGTTAGCTCTATCTTCTGG	58.673	38.462	0.00	0.00	0.00	3.86
722	1061	8.133024	TCTTCTGGGTTTATTTTGCAACATAT	57.867	30.769	6.15	0.29	0.00	1.78
745	1084	1.549203	AAGTGGTATGCCTTGCCTTG	58.451	50.000	0.16	0.00	35.27	3.61
746	1085	0.405585	AGTGGTATGCCTTGCCTTGT	59.594	50.000	0.16	0.00	35.27	3.16
747	1086	1.633432	AGTGGTATGCCTTGCCTTGTA	59.367	47.619	0.16	0.00	35.27	2.41
748	1087	1.743394	GTGGTATGCCTTGCCTTGTAC	59.257	52.381	0.16	0.00	35.27	2.90
749	1088	1.633432	TGGTATGCCTTGCCTTGTACT	59.367	47.619	0.16	0.00	35.27	2.73
754	1096	3.433306	TGCCTTGCCTTGTACTGTAAT	57.567	42.857	0.00	0.00	0.00	1.89
949	1297	2.107141	CCCGGGCAGATCGTCTTC	59.893	66.667	8.08	0.00	0.00	2.87
1042	1391	3.872771	CGAGAGAGGAGAGGTACAAGTAC	59.127	52.174	1.77	1.77	35.40	2.73
1072	1421	4.466827	TCTTTCTTTACCTTTGGTGGGTC	58.533	43.478	0.00	0.00	36.19	4.46
1094	1443	2.395654	GCGGGTCGATCTACATCTTTC	58.604	52.381	0.00	0.00	0.00	2.62
1766	2115	4.020617	CCCAGGACAGAAGCCGCA	62.021	66.667	0.00	0.00	0.00	5.69
1842	2197	3.026707	TGTGGATAGAAGGGTCGATGA	57.973	47.619	0.00	0.00	0.00	2.92
2033	2388	2.102925	CCTGCCAAGAAAGCCTTCAAAA	59.897	45.455	0.00	0.00	33.64	2.44
2054	2409	1.139947	GAAGAAGAGGAGGCGGTCG	59.860	63.158	0.00	0.00	0.00	4.79
2411	2766	0.617413	CAGGTCTTGCCAGTGAGGAT	59.383	55.000	0.00	0.00	41.22	3.24
2617	2991	9.859427	CAGATACTGATGCTTGGAAATTTTAAA	57.141	29.630	0.00	0.00	32.44	1.52
2885	3259	2.555199	CTAGATTGCTCAAACCTCCCG	58.445	52.381	0.00	0.00	0.00	5.14
2968	3342	3.027412	ACACACCAAAGGCACAAACATA	58.973	40.909	0.00	0.00	0.00	2.29
3008	3382	3.949754	TCTGCATGCTTCCTAAGATTTGG	59.050	43.478	20.33	0.00	0.00	3.28
3030	3404	1.897225	GCTGCTGCTCTCCCTGAAGA	61.897	60.000	8.53	0.00	36.03	2.87
3136	3839	0.046242	ATCCCCCAAGGTGGAGATGA	59.954	55.000	0.00	0.00	40.96	2.92
3137	3840	0.046242	TCCCCCAAGGTGGAGATGAT	59.954	55.000	0.00	0.00	40.96	2.45
3189	3892	4.309099	TCTGCATCAGCCAAAAATGTTTC	58.691	39.130	0.00	0.00	41.13	2.78
3243	3946	1.003355	AGGTGTGTGAAGGCATCGG	60.003	57.895	0.00	0.00	0.00	4.18
3256	3959	1.291906	CATCGGGGGTTTGTTTGGC	59.708	57.895	0.00	0.00	0.00	4.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	3.697166	ACAAGGACACAAGTTTTCACCT	58.303	40.909	0.00	0.00	0.00	4.00
42	43	3.013327	GGGCCCCCGAACTAAGGT	61.013	66.667	12.23	0.00	0.00	3.50
283	284	1.222300	CACCACCAACAATCGTCGAA	58.778	50.000	0.00	0.00	0.00	3.71
347	348	2.439880	CCCCTCTCCTTTCCTTATCCAC	59.560	54.545	0.00	0.00	0.00	4.02
380	381	0.319083	ACCCACTCATTACGCACGAA	59.681	50.000	0.00	0.00	0.00	3.85
447	460	4.612712	CGTTGAAACACGAATAATGCAGGT	60.613	41.667	0.00	0.00	43.15	4.00
459	472	1.320555	CCTCGCTATCGTTGAAACACG	59.679	52.381	0.00	0.00	41.78	4.49
460	473	2.599082	CTCCTCGCTATCGTTGAAACAC	59.401	50.000	0.00	0.00	36.96	3.32
462	475	3.146618	TCTCCTCGCTATCGTTGAAAC	57.853	47.619	0.00	0.00	36.96	2.78
463	476	3.770666	CTTCTCCTCGCTATCGTTGAAA	58.229	45.455	0.00	0.00	36.96	2.69
465	478	1.065701	GCTTCTCCTCGCTATCGTTGA	59.934	52.381	0.00	0.00	36.96	3.18
466	479	1.482278	GCTTCTCCTCGCTATCGTTG	58.518	55.000	0.00	0.00	36.96	4.10
467	480	0.386113	GGCTTCTCCTCGCTATCGTT	59.614	55.000	0.00	0.00	36.96	3.85
468	481	1.787057	CGGCTTCTCCTCGCTATCGT	61.787	60.000	0.00	0.00	36.96	3.73
469	482	1.081774	CGGCTTCTCCTCGCTATCG	60.082	63.158	0.00	0.00	0.00	2.92
473	486	3.764466	CACCGGCTTCTCCTCGCT	61.764	66.667	0.00	0.00	0.00	4.93
474	487	3.591254	AACACCGGCTTCTCCTCGC	62.591	63.158	0.00	0.00	0.00	5.03
475	488	1.738099	CAACACCGGCTTCTCCTCG	60.738	63.158	0.00	0.00	0.00	4.63
476	489	0.606604	TACAACACCGGCTTCTCCTC	59.393	55.000	0.00	0.00	0.00	3.71
477	490	0.608640	CTACAACACCGGCTTCTCCT	59.391	55.000	0.00	0.00	0.00	3.69
478	491	1.019805	GCTACAACACCGGCTTCTCC	61.020	60.000	0.00	0.00	0.00	3.71
479	492	1.019805	GGCTACAACACCGGCTTCTC	61.020	60.000	0.00	0.00	0.00	2.87
480	493	1.003718	GGCTACAACACCGGCTTCT	60.004	57.895	0.00	0.00	0.00	2.85
481	494	2.388232	CGGCTACAACACCGGCTTC	61.388	63.158	0.00	0.00	45.74	3.86
482	495	2.358247	CGGCTACAACACCGGCTT	60.358	61.111	0.00	0.00	45.74	4.35
487	500	1.226030	AACGCTTCGGCTACAACACC	61.226	55.000	0.00	0.00	39.13	4.16
488	501	1.125566	GTAACGCTTCGGCTACAACAC	59.874	52.381	0.00	0.00	39.13	3.32
489	502	1.269673	TGTAACGCTTCGGCTACAACA	60.270	47.619	0.00	0.00	39.13	3.33
490	503	1.421382	TGTAACGCTTCGGCTACAAC	58.579	50.000	0.00	0.00	39.13	3.32
491	504	2.264813	GATGTAACGCTTCGGCTACAA	58.735	47.619	7.25	0.00	34.69	2.41
492	505	1.796253	CGATGTAACGCTTCGGCTACA	60.796	52.381	6.10	6.10	39.95	2.74
580	593	5.009010	GTGAGATCTTCTTGAAGTTTGGCAA	59.991	40.000	9.80	0.00	0.00	4.52
584	597	6.347563	GCAGAGTGAGATCTTCTTGAAGTTTG	60.348	42.308	9.80	0.00	0.00	2.93
586	599	5.011943	AGCAGAGTGAGATCTTCTTGAAGTT	59.988	40.000	9.80	2.41	0.00	2.66
588	601	5.075858	AGCAGAGTGAGATCTTCTTGAAG	57.924	43.478	0.00	4.13	0.00	3.02
591	604	3.371591	GCAAGCAGAGTGAGATCTTCTTG	59.628	47.826	10.49	10.49	46.72	3.02
628	641	4.083484	CGAAAGGAAATGTTTACGAGCCTT	60.083	41.667	0.00	0.00	35.91	4.35
670	687	5.795972	AGCTAACAGAAAACTAGGAGTTCC	58.204	41.667	0.00	0.00	37.47	3.62
704	721	8.442384	CACTTTGGATATGTTGCAAAATAAACC	58.558	33.333	20.33	20.33	43.89	3.27
722	1061	1.544724	GCAAGGCATACCACTTTGGA	58.455	50.000	0.00	0.00	40.96	3.53
749	1088	5.865013	CGTGTCCACACTGTACATTATTACA	59.135	40.000	8.19	0.00	44.34	2.41
754	1096	4.325028	AACGTGTCCACACTGTACATTA	57.675	40.909	8.19	0.00	44.34	1.90
878	1226	4.099881	ACCTAGTAGTGTCTAGAGTCGGAG	59.900	50.000	0.00	0.00	39.57	4.63
949	1297	3.783191	CAGATGACAGGATGACAGACAG	58.217	50.000	0.00	0.00	45.14	3.51
1024	1373	2.356947	CCGGTACTTGTACCTCTCCTCT	60.357	54.545	22.73	0.00	37.96	3.69
1042	1391	5.163652	CCAAAGGTAAAGAAAGATAAGCCGG	60.164	44.000	0.00	0.00	0.00	6.13
1072	1421	1.081376	GATGTAGATCGACCCGCCG	60.081	63.158	3.33	0.00	0.00	6.46
1094	1443	4.451629	ACTATCTTTAGGTCACCGTGTG	57.548	45.455	0.00	0.00	34.45	3.82
1213	1562	1.925888	CCATCCTCCTTTCCCCCAG	59.074	63.158	0.00	0.00	0.00	4.45
1220	1569	2.044946	GTGCCGCCATCCTCCTTT	60.045	61.111	0.00	0.00	0.00	3.11
1639	1988	3.521765	ATTGGGCTTGCCACCGGAA	62.522	57.895	9.46	0.00	0.00	4.30
1679	2028	4.137615	TCGGGCTCCCAGATCGGA	62.138	66.667	5.70	0.00	36.56	4.55
1817	2172	2.644676	GACCCTTCTATCCACAAAGGC	58.355	52.381	0.00	0.00	38.59	4.35
2033	2388	1.276705	GACCGCCTCCTCTTCTTCTTT	59.723	52.381	0.00	0.00	0.00	2.52
2498	2853	6.767524	AAATCTTCACTCTCTACGATGAGT	57.232	37.500	0.00	0.00	43.45	3.41
2617	2991	2.887152	GTGGCCTTCAGTGATTGAAAGT	59.113	45.455	3.32	0.00	44.84	2.66
2753	3127	3.428862	GGTTCATGCCCACTAATTTTCCG	60.429	47.826	0.00	0.00	0.00	4.30
2968	3342	3.016736	CAGAATGTAAAAGGCGGGTGAT	58.983	45.455	0.00	0.00	0.00	3.06
3030	3404	4.639310	TGTGCATTTGTGCCAAAAGAAAAT	59.361	33.333	0.00	0.00	0.00	1.82
3136	3839	7.639062	ATGACAGATTAACCCAGATTAGGAT	57.361	36.000	0.00	0.00	0.00	3.24
3137	3840	7.420214	GGAATGACAGATTAACCCAGATTAGGA	60.420	40.741	0.00	0.00	0.00	2.94
3243	3946	0.833949	TTGGAAGCCAAACAAACCCC	59.166	50.000	0.00	0.00	40.92	4.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.