AutoCloner

Multiple sequence alignment - TraesCS2B01G065900

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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	TraesCS2B01G065900	chr2B	100.000	3698	0	0	1	3698	32950151	32946454	0.000000e+00	6830
1	TraesCS2B01G065900	chr2B	90.909	121	11	0	932	1052	33367082	33367202	2.960000e-36	163
2	TraesCS2B01G065900	chr2B	88.991	109	11	1	955	1063	33513281	33513388	2.320000e-27	134
3	TraesCS2B01G065900	chr2B	85.124	121	8	3	932	1052	33500749	33500859	8.390000e-22	115
4	TraesCS2B01G065900	chrUn	96.633	1901	48	4	1802	3698	16541047	16539159	0.000000e+00	3142
5	TraesCS2B01G065900	chrUn	96.256	1095	41	0	1	1095	16542792	16541698	0.000000e+00	1796
6	TraesCS2B01G065900	chrUn	97.410	1004	26	0	1959	2962	451986253	451985250	0.000000e+00	1711
7	TraesCS2B01G065900	chrUn	97.690	909	21	0	1	909	286908819	286909727	0.000000e+00	1563
8	TraesCS2B01G065900	chrUn	99.223	515	4	0	2964	3478	462641223	462641737	0.000000e+00	929
9	TraesCS2B01G065900	chrUn	93.827	567	34	1	1088	1654	453112028	453112593	0.000000e+00	852
10	TraesCS2B01G065900	chrUn	93.794	564	34	1	1091	1654	16541652	16541090	0.000000e+00	846
11	TraesCS2B01G065900	chrUn	92.308	182	14	0	911	1092	453111801	453111982	3.660000e-65	259
12	TraesCS2B01G065900	chrUn	94.969	159	5	1	1802	1957	453112636	453112794	2.850000e-61	246
13	TraesCS2B01G065900	chrUn	90.083	121	11	1	932	1052	24678884	24679003	4.940000e-34	156
14	TraesCS2B01G065900	chr2D	93.516	1866	116	3	1095	2960	19909586	19907726	0.000000e+00	2771
15	TraesCS2B01G065900	chr2D	90.596	755	49	5	58	798	19920014	19919268	0.000000e+00	981
16	TraesCS2B01G065900	chr2D	90.067	745	46	4	141	871	20096304	20095574	0.000000e+00	941
17	TraesCS2B01G065900	chr2D	76.386	1804	381	33	1157	2939	20426570	20424791	0.000000e+00	929
18	TraesCS2B01G065900	chr2D	91.461	527	44	1	1099	1624	20089961	20089435	0.000000e+00	723
19	TraesCS2B01G065900	chr2D	91.554	296	25	0	795	1090	19909936	19909641	3.440000e-110	409
20	TraesCS2B01G065900	chr2D	87.644	348	36	4	3351	3696	575827435	575827777	7.440000e-107	398
21	TraesCS2B01G065900	chr2D	82.410	415	41	11	2944	3328	19904847	19904435	2.130000e-87	333
22	TraesCS2B01G065900	chr2D	92.000	225	18	0	866	1090	20090233	20090009	2.140000e-82	316
23	TraesCS2B01G065900	chr2D	94.268	157	8	1	1	157	20096474	20096319	4.770000e-59	239
24	TraesCS2B01G065900	chr2D	79.803	203	29	8	436	635	20096583	20096390	1.790000e-28	137
25	TraesCS2B01G065900	chr5B	87.106	349	40	2	3351	3698	492107507	492107851	1.250000e-104	390
26	TraesCS2B01G065900	chr5B	86.610	351	43	4	3351	3698	618466624	618466973	5.790000e-103	385
27	TraesCS2B01G065900	chr3B	88.024	334	35	4	3351	3683	825013949	825013620	1.250000e-104	390
28	TraesCS2B01G065900	chr3B	86.246	349	43	2	3351	3698	244977623	244977967	1.250000e-99	374
29	TraesCS2B01G065900	chr3B	86.246	349	43	2	3351	3698	753267684	753268028	1.250000e-99	374
30	TraesCS2B01G065900	chr1B	86.782	348	41	2	3351	3697	600980255	600979912	2.080000e-102	383
31	TraesCS2B01G065900	chr4B	86.610	351	38	6	3351	3698	562615518	562615862	2.700000e-101	379

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	TraesCS2B01G065900	chr2B	32946454	32950151	3697	True	6830.000000	6830	100.000000	1	3698	1	chr2B.!!$R1	3697
1	TraesCS2B01G065900	chrUn	16539159	16542792	3633	True	1928.000000	3142	95.561000	1	3698	3	chrUn.!!$R2	3697
2	TraesCS2B01G065900	chrUn	451985250	451986253	1003	True	1711.000000	1711	97.410000	1959	2962	1	chrUn.!!$R1	1003
3	TraesCS2B01G065900	chrUn	286908819	286909727	908	False	1563.000000	1563	97.690000	1	909	1	chrUn.!!$F2	908
4	TraesCS2B01G065900	chrUn	462641223	462641737	514	False	929.000000	929	99.223000	2964	3478	1	chrUn.!!$F3	514
5	TraesCS2B01G065900	chrUn	453111801	453112794	993	False	452.333333	852	93.701333	911	1957	3	chrUn.!!$F4	1046
6	TraesCS2B01G065900	chr2D	19904435	19909936	5501	True	1171.000000	2771	89.160000	795	3328	3	chr2D.!!$R3	2533
7	TraesCS2B01G065900	chr2D	19919268	19920014	746	True	981.000000	981	90.596000	58	798	1	chr2D.!!$R1	740
8	TraesCS2B01G065900	chr2D	20424791	20426570	1779	True	929.000000	929	76.386000	1157	2939	1	chr2D.!!$R2	1782
9	TraesCS2B01G065900	chr2D	20089435	20090233	798	True	519.500000	723	91.730500	866	1624	2	chr2D.!!$R4	758
10	TraesCS2B01G065900	chr2D	20095574	20096583	1009	True	439.000000	941	88.046000	1	871	3	chr2D.!!$R5	870

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
909	1064	0.119155	TGTGGAGGTCTGGAATCCCT	59.881	55.0	0.00	0.00	31.73	4.20	F
1719	1925	0.177141	TCTGTGCCTTGGCCGTATAC	59.823	55.0	9.35	0.79	0.00	1.47	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2363	2578	0.937304	CCCAAGTGCGATATGAACCG	59.063	55.0	0.0	0.0	0.00	4.44	R
3514	6654	0.541392	AGCGGATGCAGATTGTGGTA	59.459	50.0	0.0	0.0	46.23	3.25	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
187	328	2.280628	CGGGAGAAGGTAAGCAACATC	58.719	52.381	0.00	0.00	0.00	3.06
213	354	9.406113	CATTCCTCTCTTTTTCTTATCCTTGAT	57.594	33.333	0.00	0.00	0.00	2.57
764	919	2.489329	CGCCATCTGGTTCAACAAGATT	59.511	45.455	4.48	0.00	37.57	2.40
766	921	4.155826	CGCCATCTGGTTCAACAAGATTAA	59.844	41.667	4.48	0.00	37.57	1.40
819	974	0.465705	GGACCAAGATCCATCAGCGA	59.534	55.000	0.00	0.00	38.77	4.93
877	1032	3.777556	TGGAGCACTCTCGCTTCA	58.222	55.556	0.00	0.00	45.50	3.02
909	1064	0.119155	TGTGGAGGTCTGGAATCCCT	59.881	55.000	0.00	0.00	31.73	4.20
913	1068	1.220750	GGAGGTCTGGAATCCCTAGGA	59.779	57.143	11.48	0.00	35.55	2.94
919	1074	2.116238	CTGGAATCCCTAGGAAACCGA	58.884	52.381	11.48	0.00	34.34	4.69
924	1079	2.241281	TCCCTAGGAAACCGATGTGA	57.759	50.000	11.48	0.00	0.00	3.58
929	1084	0.246635	AGGAAACCGATGTGACCTCG	59.753	55.000	3.22	3.22	35.92	4.63
970	1125	0.748005	AACTTTGTGCTCGCTGGTGT	60.748	50.000	0.00	0.00	0.00	4.16
1032	1187	1.082954	ACCATCCTGCCTACCCAGT	59.917	57.895	0.00	0.00	0.00	4.00
1069	1224	4.021104	CCAGACTCATAACAAGTCACTCCA	60.021	45.833	6.10	0.00	44.54	3.86
1093	1298	2.842462	ACTCGACACCACTGGCCA	60.842	61.111	4.71	4.71	0.00	5.36
1097	1302	1.448540	CGACACCACTGGCCATCTC	60.449	63.158	5.51	0.00	0.00	2.75
1116	1321	1.603236	CTCTCGTTGCTGAGCCCTCT	61.603	60.000	0.23	0.00	35.90	3.69
1126	1331	4.339335	AGCCCTCTGGGTTCAAGT	57.661	55.556	4.42	0.00	46.51	3.16
1130	1335	1.559682	GCCCTCTGGGTTCAAGTATGA	59.440	52.381	4.42	0.00	46.51	2.15
1131	1336	2.420687	GCCCTCTGGGTTCAAGTATGAG	60.421	54.545	4.42	0.00	46.51	2.90
1142	1347	6.884836	GGGTTCAAGTATGAGTCTTATTGGTT	59.115	38.462	0.00	0.00	36.78	3.67
1146	1351	7.676004	TCAAGTATGAGTCTTATTGGTTCACA	58.324	34.615	0.00	0.00	0.00	3.58
1155	1361	2.936919	ATTGGTTCACAGAGACAGCA	57.063	45.000	0.00	0.00	0.00	4.41
1174	1380	0.773644	AGGGAATGGCTCACAGTTGT	59.226	50.000	0.00	0.00	0.00	3.32
1191	1397	5.047377	ACAGTTGTTGTTCAATGAAACTGGT	60.047	36.000	21.54	10.00	36.31	4.00
1218	1424	6.592870	AGTATACTTCCTCCTAACAAATGGC	58.407	40.000	0.00	0.00	0.00	4.40
1221	1427	2.507407	TCCTCCTAACAAATGGCACC	57.493	50.000	0.00	0.00	0.00	5.01
1409	1615	2.401583	TGCCATGCAGTAGTTACAGG	57.598	50.000	0.00	0.00	33.32	4.00
1411	1617	2.835156	TGCCATGCAGTAGTTACAGGTA	59.165	45.455	0.00	0.00	33.32	3.08
1425	1631	1.078426	AGGTATTGGCAGTGGCGTC	60.078	57.895	12.58	2.28	42.47	5.19
1474	1680	3.745480	CGATGGCACCAAGAACCAGATAT	60.745	47.826	0.00	0.00	36.78	1.63
1489	1695	4.202441	CCAGATATTAAGTTGTGCCTGCT	58.798	43.478	0.00	0.00	0.00	4.24
1495	1701	0.820891	AAGTTGTGCCTGCTCACCAG	60.821	55.000	0.00	0.00	41.41	4.00
1537	1743	1.840635	AGAGGAGGTACAAAGGATGCC	59.159	52.381	0.00	0.00	0.00	4.40
1582	1788	1.377202	GACTTGGATGAGGCCGCAA	60.377	57.895	14.96	0.00	0.00	4.85
1629	1835	2.107950	TTTCTGGTGTAGATTGGCCG	57.892	50.000	0.00	0.00	34.80	6.13
1719	1925	0.177141	TCTGTGCCTTGGCCGTATAC	59.823	55.000	9.35	0.79	0.00	1.47
1732	1938	3.486875	GGCCGTATACAATGAAAGCACAC	60.487	47.826	3.32	0.00	0.00	3.82
1824	2030	2.040278	TCTCAAGGTGCCAAGTAGCAAT	59.960	45.455	0.00	0.00	46.19	3.56
2127	2342	4.444536	GTGTTGTGTACAAGGGTGAGTTA	58.555	43.478	0.00	0.00	38.80	2.24
2196	2411	5.242615	GCTCCAAGAAGAAACTGAAAAGGAT	59.757	40.000	0.00	0.00	0.00	3.24
2250	2465	1.639722	TCCACAAGAATCTGGTCCGA	58.360	50.000	0.00	0.00	0.00	4.55
2280	2495	4.320788	GGTTTCTGCAATGAAGGAACTGAG	60.321	45.833	11.98	0.00	40.86	3.35
2289	2504	2.968574	TGAAGGAACTGAGAGACTGCTT	59.031	45.455	0.00	0.00	40.86	3.91
2363	2578	0.319469	CGGCCAAATTGGAACACACC	60.319	55.000	17.47	5.11	40.96	4.16
2437	2653	3.081061	TGTAGCACACAAATCATCCACC	58.919	45.455	0.00	0.00	32.95	4.61
2451	2667	0.390603	TCCACCGTGACATAAAGCCG	60.391	55.000	0.00	0.00	0.00	5.52
2613	2829	1.002134	CGGGATCACTGCCAAGGTT	60.002	57.895	0.00	0.00	31.98	3.50
2761	2977	0.249911	GTTCGACTTGCTGGTGGAGT	60.250	55.000	0.00	0.00	0.00	3.85
3044	6171	6.963049	GGACAAAGTATGTGTACTACAAGG	57.037	41.667	0.00	0.00	36.03	3.61
3125	6254	9.953825	GTCAGTTATGTAACTATTTGAGTTTCG	57.046	33.333	5.19	0.00	46.79	3.46
3479	6619	2.280592	ACGAACCACGAACCCAGC	60.281	61.111	0.00	0.00	45.77	4.85
3635	6775	2.124151	GGATGTTGCCGCCTCCAT	60.124	61.111	0.00	0.00	0.00	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
187	328	8.798859	TCAAGGATAAGAAAAAGAGAGGAATG	57.201	34.615	0.00	0.00	0.00	2.67
213	354	1.985473	ATTGTTTCTCCAGTGCAGCA	58.015	45.000	0.00	0.00	0.00	4.41
666	821	1.608717	GAGGGTGAGAGCCATGACGT	61.609	60.000	0.00	0.00	38.48	4.34
819	974	5.896678	GGATAGAGCCAGATGATACCTGTAT	59.103	44.000	0.00	0.00	0.00	2.29
877	1032	1.160870	TCCACACTGGAGGGGTCAT	59.839	57.895	0.00	0.00	42.67	3.06
909	1064	1.475280	CGAGGTCACATCGGTTTCCTA	59.525	52.381	3.32	0.00	36.54	2.94
919	1074	2.673200	ATGCTGGCCGAGGTCACAT	61.673	57.895	0.00	0.00	0.00	3.21
929	1084	3.720193	CTATCGCGCATGCTGGCC	61.720	66.667	17.13	0.00	39.65	5.36
970	1125	1.268352	GCCATTTTGTGTTGCCGTCTA	59.732	47.619	0.00	0.00	0.00	2.59
1032	1187	1.142870	AGTCTGGTTACAAGGCAGCAA	59.857	47.619	0.00	0.00	0.00	3.91
1069	1224	1.213013	GTGGTGTCGAGTCGAGCAT	59.787	57.895	17.12	0.00	36.23	3.79
1093	1298	0.459489	GGCTCAGCAACGAGAGAGAT	59.541	55.000	0.00	0.00	34.79	2.75
1097	1302	1.153667	GAGGGCTCAGCAACGAGAG	60.154	63.158	0.00	0.00	34.79	3.20
1116	1321	6.012858	ACCAATAAGACTCATACTTGAACCCA	60.013	38.462	0.00	0.00	0.00	4.51
1119	1324	8.443937	GTGAACCAATAAGACTCATACTTGAAC	58.556	37.037	0.00	0.00	0.00	3.18
1126	1331	7.178451	TGTCTCTGTGAACCAATAAGACTCATA	59.822	37.037	0.00	0.00	32.45	2.15
1130	1335	5.788450	CTGTCTCTGTGAACCAATAAGACT	58.212	41.667	0.00	0.00	32.45	3.24
1131	1336	4.390297	GCTGTCTCTGTGAACCAATAAGAC	59.610	45.833	0.00	0.00	32.12	3.01
1142	1347	1.277273	CATTCCCTGCTGTCTCTGTGA	59.723	52.381	0.00	0.00	0.00	3.58
1146	1351	0.913451	AGCCATTCCCTGCTGTCTCT	60.913	55.000	0.00	0.00	36.23	3.10
1155	1361	0.773644	ACAACTGTGAGCCATTCCCT	59.226	50.000	0.00	0.00	0.00	4.20
1174	1380	9.431887	GTATACTCTACCAGTTTCATTGAACAA	57.568	33.333	0.00	0.00	36.43	2.83
1191	1397	9.144298	CCATTTGTTAGGAGGAAGTATACTCTA	57.856	37.037	5.70	0.05	34.22	2.43
1218	1424	3.613030	TGATGTGATGTTGATCTGGGTG	58.387	45.455	0.00	0.00	0.00	4.61
1221	1427	3.882444	ACCTGATGTGATGTTGATCTGG	58.118	45.455	0.00	0.00	39.74	3.86
1409	1615	0.673644	ACAGACGCCACTGCCAATAC	60.674	55.000	4.95	0.00	41.06	1.89
1411	1617	1.968017	CACAGACGCCACTGCCAAT	60.968	57.895	4.95	0.00	41.06	3.16
1425	1631	4.002982	TGCAGTAACTATTGAAGCCACAG	58.997	43.478	0.00	0.00	0.00	3.66
1474	1680	1.133945	TGGTGAGCAGGCACAACTTAA	60.134	47.619	8.16	0.00	40.52	1.85
1489	1695	3.456644	TCAAAGAACTTGTACCCTGGTGA	59.543	43.478	0.00	0.00	36.34	4.02
1495	1701	4.906618	TCCTCATCAAAGAACTTGTACCC	58.093	43.478	0.00	0.00	36.34	3.69
1537	1743	2.420628	TGCGGCTGAAAATCTTGTTG	57.579	45.000	0.00	0.00	0.00	3.33
1582	1788	1.338973	CAGCTCAAATTGTGCCAGTGT	59.661	47.619	15.30	0.00	37.57	3.55
1629	1835	5.944013	TGATACTGCTCGTAATCAGATAGC	58.056	41.667	0.00	0.00	34.57	2.97
1719	1925	1.717113	CATGTGCGTGTGCTTTCATTG	59.283	47.619	0.00	0.00	43.34	2.82
1732	1938	2.472488	GCTTCTTTTTCCAACATGTGCG	59.528	45.455	0.00	0.00	0.00	5.34
2127	2342	2.503356	GTGGGTCTGGAGATCATCTTGT	59.497	50.000	0.00	0.00	0.00	3.16
2196	2411	5.033589	TGGTTTGGACTTCTACCGTAAAA	57.966	39.130	0.00	0.00	33.29	1.52
2250	2465	4.520492	CCTTCATTGCAGAAACCAAGTAGT	59.480	41.667	0.00	0.00	0.00	2.73
2280	2495	6.369890	TCATGAACTCATAAACAAGCAGTCTC	59.630	38.462	0.00	0.00	34.26	3.36
2289	2504	5.105797	GCCATTGGTCATGAACTCATAAACA	60.106	40.000	12.94	0.00	34.31	2.83
2363	2578	0.937304	CCCAAGTGCGATATGAACCG	59.063	55.000	0.00	0.00	0.00	4.44
2437	2653	2.350192	TGTTATGCGGCTTTATGTCACG	59.650	45.455	0.00	0.00	0.00	4.35
2451	2667	5.530519	TGTCGTCAAGAAGAATGTTATGC	57.469	39.130	0.00	0.00	0.00	3.14
2613	2829	3.578282	TCACTCCAAAGCTGTAGACATCA	59.422	43.478	0.00	0.00	0.00	3.07
2761	2977	1.992667	GAAGATTGCGTCATCGTCACA	59.007	47.619	6.91	0.00	39.49	3.58
3125	6254	7.924412	TCGGAGTAACATGAATATAACCTTCAC	59.076	37.037	0.00	0.00	35.57	3.18
3479	6619	1.154205	GGAAGATGGTGGATCGTGCG	61.154	60.000	0.00	0.00	36.04	5.34
3514	6654	0.541392	AGCGGATGCAGATTGTGGTA	59.459	50.000	0.00	0.00	46.23	3.25
3635	6775	6.374333	GTCTGTTCAAGTAATTAAGGATGGCA	59.626	38.462	0.00	0.00	0.00	4.92

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.