AutoCloner

Multiple sequence alignment - TraesCS2B01G557400

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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	TraesCS2B01G557400	chr2B	100.000	3470	0	0	1	3470	751942439	751938970	0.000000e+00	6408
1	TraesCS2B01G557400	chr2D	97.469	1778	35	5	1057	2825	616651049	616649273	0.000000e+00	3025
2	TraesCS2B01G557400	chr2D	92.227	669	10	14	1	650	616652152	616651507	0.000000e+00	909
3	TraesCS2B01G557400	chr2D	91.837	392	14	3	685	1062	616651507	616651120	6.590000e-147	531
4	TraesCS2B01G557400	chr3A	97.130	1324	38	0	1057	2380	149080216	149078893	0.000000e+00	2235
5	TraesCS2B01G557400	chr3A	92.971	1067	32	21	4	1043	149081338	149080288	0.000000e+00	1515
6	TraesCS2B01G557400	chr3A	94.344	442	21	2	2388	2825	149078850	149078409	0.000000e+00	675
7	TraesCS2B01G557400	chr3A	79.599	549	91	15	1917	2452	697763648	697763108	1.180000e-99	374
8	TraesCS2B01G557400	chr3A	84.516	155	20	1	2494	2644	697759950	697759796	2.160000e-32	150
9	TraesCS2B01G557400	chr3A	73.786	412	53	26	700	1059	697772243	697771835	1.020000e-20	111
10	TraesCS2B01G557400	chr7B	80.141	1415	222	36	1385	2745	641378475	641377066	0.000000e+00	1002
11	TraesCS2B01G557400	chr7B	93.182	660	26	6	2828	3470	658745331	658745988	0.000000e+00	952
12	TraesCS2B01G557400	chr7B	92.694	657	32	5	2828	3470	658620339	658620993	0.000000e+00	933
13	TraesCS2B01G557400	chr7B	92.413	659	32	6	2828	3470	658730653	658731309	0.000000e+00	924
14	TraesCS2B01G557400	chr7B	92.804	542	25	4	2828	3355	658877860	658878401	0.000000e+00	773
15	TraesCS2B01G557400	chr7B	80.183	328	44	13	747	1062	641378970	641378652	3.480000e-55	226
16	TraesCS2B01G557400	chr7B	94.565	92	3	1	3379	3470	658878618	658878707	1.300000e-29	141
17	TraesCS2B01G557400	chrUn	94.037	654	23	5	2831	3470	354102924	354102273	0.000000e+00	977
18	TraesCS2B01G557400	chrUn	92.846	657	28	6	2831	3470	336506326	336505672	0.000000e+00	935
19	TraesCS2B01G557400	chrUn	93.886	507	17	4	2831	3323	424755945	424755439	0.000000e+00	752
20	TraesCS2B01G557400	chrUn	93.220	236	9	3	3240	3470	475470756	475470989	1.190000e-89	340
21	TraesCS2B01G557400	chrUn	94.565	92	3	1	3379	3470	234010118	234010029	1.300000e-29	141
22	TraesCS2B01G557400	chr5B	92.391	644	42	5	2831	3470	565777085	565776445	0.000000e+00	911
23	TraesCS2B01G557400	chr4B	92.222	540	23	7	2831	3356	637365635	637366169	0.000000e+00	747
24	TraesCS2B01G557400	chr5D	77.099	917	159	31	1539	2414	547530462	547529556	1.870000e-132	483
25	TraesCS2B01G557400	chr3B	79.376	577	92	18	1917	2476	750316405	750315839	7.030000e-102	381
26	TraesCS2B01G557400	chr3B	76.655	574	83	32	527	1059	750319777	750319214	1.590000e-68	270
27	TraesCS2B01G557400	chr7A	84.848	264	35	3	803	1062	670216296	670216034	9.550000e-66	261
28	TraesCS2B01G557400	chr4A	83.815	173	23	2	2494	2662	667376281	667376452	3.580000e-35	159

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	TraesCS2B01G557400	chr2B	751938970	751942439	3469	True	6408.000000	6408	100.000000	1	3470	1	chr2B.!!$R1	3469
1	TraesCS2B01G557400	chr2D	616649273	616652152	2879	True	1488.333333	3025	93.844333	1	2825	3	chr2D.!!$R1	2824
2	TraesCS2B01G557400	chr3A	149078409	149081338	2929	True	1475.000000	2235	94.815000	4	2825	3	chr3A.!!$R2	2821
3	TraesCS2B01G557400	chr3A	697759796	697763648	3852	True	262.000000	374	82.057500	1917	2644	2	chr3A.!!$R3	727
4	TraesCS2B01G557400	chr7B	658745331	658745988	657	False	952.000000	952	93.182000	2828	3470	1	chr7B.!!$F3	642
5	TraesCS2B01G557400	chr7B	658620339	658620993	654	False	933.000000	933	92.694000	2828	3470	1	chr7B.!!$F1	642
6	TraesCS2B01G557400	chr7B	658730653	658731309	656	False	924.000000	924	92.413000	2828	3470	1	chr7B.!!$F2	642
7	TraesCS2B01G557400	chr7B	641377066	641378970	1904	True	614.000000	1002	80.162000	747	2745	2	chr7B.!!$R1	1998
8	TraesCS2B01G557400	chr7B	658877860	658878707	847	False	457.000000	773	93.684500	2828	3470	2	chr7B.!!$F4	642
9	TraesCS2B01G557400	chrUn	354102273	354102924	651	True	977.000000	977	94.037000	2831	3470	1	chrUn.!!$R3	639
10	TraesCS2B01G557400	chrUn	336505672	336506326	654	True	935.000000	935	92.846000	2831	3470	1	chrUn.!!$R2	639
11	TraesCS2B01G557400	chrUn	424755439	424755945	506	True	752.000000	752	93.886000	2831	3323	1	chrUn.!!$R4	492
12	TraesCS2B01G557400	chr5B	565776445	565777085	640	True	911.000000	911	92.391000	2831	3470	1	chr5B.!!$R1	639
13	TraesCS2B01G557400	chr4B	637365635	637366169	534	False	747.000000	747	92.222000	2831	3356	1	chr4B.!!$F1	525
14	TraesCS2B01G557400	chr5D	547529556	547530462	906	True	483.000000	483	77.099000	1539	2414	1	chr5D.!!$R1	875
15	TraesCS2B01G557400	chr3B	750315839	750319777	3938	True	325.500000	381	78.015500	527	2476	2	chr3B.!!$R1	1949

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
198	206	0.039437	CCTCAGCTTTGCTTGCACAG	60.039	55.000	4.57	4.57	36.4	3.66	F
931	1004	1.268899	ACTGATGTGCTTGCTTGCTTC	59.731	47.619	3.47	0.02	0.0	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1002	1078	1.615107	GCCGTGTTACTGTCAGCGAC	61.615	60.0	0.00	0.0	0.0	5.19	R
2890	8163	0.322456	CTTTTGCACGGATCCCCTCA	60.322	55.0	6.06	0.0	0.0	3.86	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
77	78	7.206981	TCTAGGTTTGCTCTGAAATTTTCTG	57.793	36.000	10.33	9.70	0.00	3.02
80	81	5.363580	AGGTTTGCTCTGAAATTTTCTGGAA	59.636	36.000	13.90	7.74	0.00	3.53
113	114	4.747540	TTGCACACAACATCATACTGTC	57.252	40.909	0.00	0.00	0.00	3.51
114	115	3.073678	TGCACACAACATCATACTGTCC	58.926	45.455	0.00	0.00	0.00	4.02
116	117	3.325870	CACACAACATCATACTGTCCGT	58.674	45.455	0.00	0.00	0.00	4.69
117	118	4.490743	CACACAACATCATACTGTCCGTA	58.509	43.478	0.00	0.00	0.00	4.02
118	119	4.926832	CACACAACATCATACTGTCCGTAA	59.073	41.667	0.00	0.00	0.00	3.18
119	120	5.062183	CACACAACATCATACTGTCCGTAAG	59.938	44.000	0.00	0.00	0.00	2.34
120	121	5.047590	ACACAACATCATACTGTCCGTAAGA	60.048	40.000	0.00	0.00	43.02	2.10
121	122	6.042777	CACAACATCATACTGTCCGTAAGAT	58.957	40.000	0.00	0.00	37.09	2.40
122	123	6.535150	CACAACATCATACTGTCCGTAAGATT	59.465	38.462	0.00	0.00	35.08	2.40
123	124	7.704899	CACAACATCATACTGTCCGTAAGATTA	59.295	37.037	0.00	0.00	35.08	1.75
124	125	7.921214	ACAACATCATACTGTCCGTAAGATTAG	59.079	37.037	0.00	0.00	35.08	1.73
125	126	7.584122	ACATCATACTGTCCGTAAGATTAGT	57.416	36.000	0.00	0.00	35.08	2.24
126	127	7.426410	ACATCATACTGTCCGTAAGATTAGTG	58.574	38.462	0.00	0.00	35.08	2.74
127	128	5.828747	TCATACTGTCCGTAAGATTAGTGC	58.171	41.667	0.00	0.00	43.02	4.40
128	129	3.521947	ACTGTCCGTAAGATTAGTGCC	57.478	47.619	0.00	0.00	43.02	5.01
154	162	4.321899	GGATTCAGCCTGTAGATCTAGCAG	60.322	50.000	18.16	18.16	0.00	4.24
155	163	1.959985	TCAGCCTGTAGATCTAGCAGC	59.040	52.381	19.05	14.52	0.00	5.25
156	164	1.685517	CAGCCTGTAGATCTAGCAGCA	59.314	52.381	19.05	8.14	0.00	4.41
183	191	1.118965	TTTCTCACACTCCCGCCTCA	61.119	55.000	0.00	0.00	0.00	3.86
197	205	2.035421	CCTCAGCTTTGCTTGCACA	58.965	52.632	0.00	0.00	36.40	4.57
198	206	0.039437	CCTCAGCTTTGCTTGCACAG	60.039	55.000	4.57	4.57	36.40	3.66
387	413	2.938086	TTGAGTGCGCCGGCTAGAA	61.938	57.895	26.68	0.00	40.82	2.10
388	414	2.583593	GAGTGCGCCGGCTAGAAG	60.584	66.667	26.68	9.69	40.82	2.85
389	415	4.821589	AGTGCGCCGGCTAGAAGC	62.822	66.667	26.68	20.47	41.46	3.86
390	416	4.821589	GTGCGCCGGCTAGAAGCT	62.822	66.667	26.68	0.00	41.99	3.74
428	458	2.690881	AGGGCTCGCCATGGGTAA	60.691	61.111	15.13	0.00	37.98	2.85
679	722	5.412384	AGCTGGTATTCTTAATAGCCCCTA	58.588	41.667	6.44	0.00	40.29	3.53
680	723	5.485708	AGCTGGTATTCTTAATAGCCCCTAG	59.514	44.000	6.44	0.00	40.29	3.02
682	725	6.239915	GCTGGTATTCTTAATAGCCCCTAGTT	60.240	42.308	6.44	0.00	40.29	2.24
683	726	7.692040	GCTGGTATTCTTAATAGCCCCTAGTTT	60.692	40.741	6.44	0.00	40.29	2.66
687	730	6.818281	TTCTTAATAGCCCCTAGTTTGCTA	57.182	37.500	7.35	7.35	41.43	3.49
795	862	2.177394	TTGCAGCTGACCGTGAATAA	57.823	45.000	20.43	0.00	0.00	1.40
831	900	2.281761	ACACCCTCTGGCTTTGCG	60.282	61.111	0.00	0.00	33.59	4.85
887	956	6.215841	CCACCTAGATCTCTGGAGGTACTATA	59.784	46.154	13.46	0.00	41.55	1.31
931	1004	1.268899	ACTGATGTGCTTGCTTGCTTC	59.731	47.619	3.47	0.02	0.00	3.86
1002	1078	3.504906	CCTGCAGGACATATGGCTTAATG	59.495	47.826	29.88	4.08	37.39	1.90
1065	1231	1.672881	CTTCGGTTTCCTGCATCATCC	59.327	52.381	0.00	0.00	0.00	3.51
1500	3485	6.861065	TCTTCATCAGGTTGTTTTACTGAC	57.139	37.500	0.00	0.00	43.29	3.51
1638	3626	7.857885	CGGAAAGCCTGAATATAAGAAAATCAC	59.142	37.037	0.00	0.00	0.00	3.06
1718	3713	5.874261	TGATCATGATTTTCGCTGTGACTTA	59.126	36.000	10.14	0.00	0.00	2.24
1948	4031	6.463995	AAGTTTTGGATGCAACTTCAGTAA	57.536	33.333	0.00	0.00	38.59	2.24
1973	4061	4.871993	AATTGTGCTTAGCATCTCTTCG	57.128	40.909	11.03	0.00	41.91	3.79
2169	4268	3.825014	ACATTGCAACAGCTCTGAAGATT	59.175	39.130	0.00	0.00	0.00	2.40
2247	4348	2.931969	TGTGAATGTCTTATCAGCTGCG	59.068	45.455	9.47	0.00	0.00	5.18
2394	4539	4.319549	CCTTGTTTTCGAGCCTACAAAGAC	60.320	45.833	0.00	0.00	30.87	3.01
2399	4544	3.232213	TCGAGCCTACAAAGACATGTC	57.768	47.619	18.47	18.47	34.75	3.06
2608	7878	3.319755	TGAGATGGTCCGTACGAAAAAC	58.680	45.455	18.76	9.00	0.00	2.43
2664	7934	8.869897	GCTTAATTTTCTACCAAGTATTTTGCC	58.130	33.333	0.00	0.00	0.00	4.52
2825	8098	8.773645	TGTAAAATGCAAATATATCCTGTCTCG	58.226	33.333	0.00	0.00	0.00	4.04
2826	8099	7.807977	AAAATGCAAATATATCCTGTCTCGT	57.192	32.000	0.00	0.00	0.00	4.18
2829	8102	5.773575	TGCAAATATATCCTGTCTCGTCTC	58.226	41.667	0.00	0.00	0.00	3.36
2921	8194	3.549873	CCGTGCAAAAGAAAACGTCAAAT	59.450	39.130	0.00	0.00	34.30	2.32
3053	8327	4.021192	CAGTATGGGCATTGTCTTTTTGGT	60.021	41.667	0.00	0.00	0.00	3.67
3189	8463	1.069090	GTGCAGTCTTCACGTCCCA	59.931	57.895	0.00	0.00	0.00	4.37
3190	8464	0.531974	GTGCAGTCTTCACGTCCCAA	60.532	55.000	0.00	0.00	0.00	4.12
3191	8465	0.396435	TGCAGTCTTCACGTCCCAAT	59.604	50.000	0.00	0.00	0.00	3.16
3238	8512	4.087892	CTCCGTCCTGCCCCAGTG	62.088	72.222	0.00	0.00	0.00	3.66
3327	8614	0.923358	TAAATCCCTGGTTCGGGCAT	59.077	50.000	0.00	0.00	44.30	4.40
3437	8917	2.804421	TGGTGTGTACGACGTATACG	57.196	50.000	23.24	23.24	46.33	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
77	78	1.299089	GCAACCACGCAACTGTTCC	60.299	57.895	0.00	0.00	0.00	3.62
80	81	2.043405	TGTGCAACCACGCAACTGT	61.043	52.632	0.00	0.00	45.14	3.55
108	109	3.097614	AGGCACTAATCTTACGGACAGT	58.902	45.455	0.00	0.00	36.02	3.55
110	111	3.635373	CCTAGGCACTAATCTTACGGACA	59.365	47.826	0.00	0.00	42.17	4.02
113	114	5.010719	TGAATCCTAGGCACTAATCTTACGG	59.989	44.000	2.96	0.00	42.17	4.02
114	115	6.085555	TGAATCCTAGGCACTAATCTTACG	57.914	41.667	2.96	0.00	42.17	3.18
116	117	5.012148	GGCTGAATCCTAGGCACTAATCTTA	59.988	44.000	2.96	0.00	42.17	2.10
117	118	4.202409	GGCTGAATCCTAGGCACTAATCTT	60.202	45.833	2.96	0.00	42.17	2.40
118	119	3.326297	GGCTGAATCCTAGGCACTAATCT	59.674	47.826	2.96	0.00	42.17	2.40
119	120	3.326297	AGGCTGAATCCTAGGCACTAATC	59.674	47.826	2.96	0.00	42.17	1.75
120	121	3.072184	CAGGCTGAATCCTAGGCACTAAT	59.928	47.826	9.42	0.00	42.17	1.73
121	122	2.435805	CAGGCTGAATCCTAGGCACTAA	59.564	50.000	9.42	0.00	42.17	2.24
122	123	2.042464	CAGGCTGAATCCTAGGCACTA	58.958	52.381	9.42	0.00	42.62	2.74
123	124	0.835941	CAGGCTGAATCCTAGGCACT	59.164	55.000	9.42	0.00	42.62	4.40
124	125	0.543749	ACAGGCTGAATCCTAGGCAC	59.456	55.000	23.66	0.00	42.62	5.01
125	126	2.042464	CTACAGGCTGAATCCTAGGCA	58.958	52.381	23.66	0.00	42.62	4.75
126	127	2.320781	TCTACAGGCTGAATCCTAGGC	58.679	52.381	23.66	0.00	40.69	3.93
127	128	4.415596	AGATCTACAGGCTGAATCCTAGG	58.584	47.826	23.66	0.82	33.95	3.02
128	129	5.125417	GCTAGATCTACAGGCTGAATCCTAG	59.875	48.000	23.66	21.31	33.95	3.02
154	162	4.142381	GGGAGTGTGAGAAACCAATAATGC	60.142	45.833	0.00	0.00	0.00	3.56
155	163	4.094887	CGGGAGTGTGAGAAACCAATAATG	59.905	45.833	0.00	0.00	0.00	1.90
156	164	4.261801	CGGGAGTGTGAGAAACCAATAAT	58.738	43.478	0.00	0.00	0.00	1.28
351	377	2.821378	TCAACTGTTCCATGCCATTCAG	59.179	45.455	0.00	0.00	0.00	3.02
377	403	0.460311	TTGTCTAGCTTCTAGCCGGC	59.540	55.000	21.89	21.89	43.77	6.13
387	413	6.188407	TCGGAAGCCTATATATTGTCTAGCT	58.812	40.000	0.00	0.00	0.00	3.32
388	414	6.452494	TCGGAAGCCTATATATTGTCTAGC	57.548	41.667	0.00	0.00	0.00	3.42
389	415	6.039941	CCCTCGGAAGCCTATATATTGTCTAG	59.960	46.154	0.00	0.00	0.00	2.43
390	416	5.892119	CCCTCGGAAGCCTATATATTGTCTA	59.108	44.000	0.00	0.00	0.00	2.59
428	458	1.079127	CCTCCACAGATTTCGCCGT	60.079	57.895	0.00	0.00	0.00	5.68
525	559	2.124487	AGGTCGCTCCTCTCCTCG	60.124	66.667	0.00	0.00	44.42	4.63
795	862	2.072298	GTCTCGAACAGAAGCAGCATT	58.928	47.619	0.00	0.00	30.72	3.56
831	900	1.335810	GACCCACAAAAACGGAAGACC	59.664	52.381	0.00	0.00	0.00	3.85
887	956	9.004231	AGTAACCAAGGAAGGAAGAACATATAT	57.996	33.333	0.00	0.00	0.00	0.86
931	1004	5.106157	GGTAAATGACATGGACAACAAGAGG	60.106	44.000	0.00	0.00	0.00	3.69
1002	1078	1.615107	GCCGTGTTACTGTCAGCGAC	61.615	60.000	0.00	0.00	0.00	5.19
1328	1540	5.357878	TCCTCATTCATCAAAATACCAGTGC	59.642	40.000	0.00	0.00	0.00	4.40
1495	3480	3.277142	AAAGTTTGGAACTCCGTCAGT	57.723	42.857	0.00	0.00	41.91	3.41
1500	3485	3.003378	GTCCTCAAAAGTTTGGAACTCCG	59.997	47.826	4.04	0.00	41.91	4.63
1638	3626	8.006298	ACTTATACTCACCAATCTCTCTTCAG	57.994	38.462	0.00	0.00	0.00	3.02
2247	4348	4.082026	AGTTTGCAAGAAATGGGATAGCAC	60.082	41.667	0.00	0.00	0.00	4.40
2394	4539	5.120363	CCTATCATCATGAGCTTTCGACATG	59.880	44.000	0.09	6.09	41.55	3.21
2399	4544	5.722263	AGATCCTATCATCATGAGCTTTCG	58.278	41.667	0.09	0.00	0.00	3.46
2608	7878	9.065871	GTTGCTCAAATTTAATTAGCACTACAG	57.934	33.333	12.90	0.00	42.50	2.74
2646	7916	8.871629	TTAAGATGGCAAAATACTTGGTAGAA	57.128	30.769	0.00	0.00	0.00	2.10
2771	8044	2.693591	ACATACACATCACCTACGAGGG	59.306	50.000	0.00	0.00	40.58	4.30
2825	8098	4.539881	GACGGCCGCTCTCGAGAC	62.540	72.222	28.58	7.93	38.10	3.36
2890	8163	0.322456	CTTTTGCACGGATCCCCTCA	60.322	55.000	6.06	0.00	0.00	3.86
2921	8194	3.857052	CCAGTATGTCCGCTTTACTGAA	58.143	45.455	10.13	0.00	40.19	3.02
3034	8307	2.550639	GCACCAAAAAGACAATGCCCAT	60.551	45.455	0.00	0.00	0.00	4.00
3238	8512	6.528072	GCTACTTTTGTGTATTTTGCTCATCC	59.472	38.462	0.00	0.00	0.00	3.51
3327	8614	0.945265	CCGGCGTCCGTTTCTACAAA	60.945	55.000	15.38	0.00	46.80	2.83
3417	8897	3.116063	CGTATACGTCGTACACACCAA	57.884	47.619	17.16	0.00	34.11	3.67
3437	8917	3.414700	CGAGCTCACGGGCAACAC	61.415	66.667	15.40	0.00	39.74	3.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.