AutoCloner

Multiple sequence alignment - TraesCS5D01G015400

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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	TraesCS5D01G015400	chr5D	100.000	3084	0	0	1	3084	8936059	8939142	0.000000e+00	5696.0
1	TraesCS5D01G015400	chr5B	85.578	1366	110	25	805	2136	9009200	9010512	0.000000e+00	1351.0
2	TraesCS5D01G015400	chr5B	86.272	896	89	17	1	893	9006363	9007227	0.000000e+00	942.0
3	TraesCS5D01G015400	chr5B	87.119	295	35	3	149	442	438504625	438504333	6.370000e-87	331.0
4	TraesCS5D01G015400	chr5B	80.451	399	51	15	149	535	117890845	117890462	2.340000e-71	279.0
5	TraesCS5D01G015400	chr5B	83.333	114	15	3	458	569	21596349	21596238	5.440000e-18	102.0
6	TraesCS5D01G015400	chr5B	93.617	47	1	2	1236	1280	681001209	681001163	5.520000e-08	69.4
7	TraesCS5D01G015400	chr5A	89.531	1003	55	24	524	1514	6982033	6982997	0.000000e+00	1225.0
8	TraesCS5D01G015400	chr5A	91.224	490	31	4	1	487	6981551	6982031	0.000000e+00	656.0
9	TraesCS5D01G015400	chr5A	85.085	590	58	10	1570	2136	6983221	6983803	2.670000e-160	575.0
10	TraesCS5D01G015400	chr5A	83.649	422	57	6	149	570	302298319	302298728	1.340000e-103	387.0
11	TraesCS5D01G015400	chr3D	90.011	941	90	4	2141	3080	301964372	301963435	0.000000e+00	1214.0
12	TraesCS5D01G015400	chr2B	89.446	957	95	5	2129	3084	41824601	41823650	0.000000e+00	1203.0
13	TraesCS5D01G015400	chr2B	89.496	952	88	8	2138	3081	137001783	137000836	0.000000e+00	1194.0
14	TraesCS5D01G015400	chrUn	91.228	855	71	4	2141	2994	92181117	92180266	0.000000e+00	1160.0
15	TraesCS5D01G015400	chr2D	88.655	952	104	4	2132	3081	328367467	328368416	0.000000e+00	1157.0
16	TraesCS5D01G015400	chr3B	88.025	952	109	4	2135	3084	425753033	425752085	0.000000e+00	1122.0
17	TraesCS5D01G015400	chr6A	87.844	946	111	4	2141	3084	433064986	433064043	0.000000e+00	1107.0
18	TraesCS5D01G015400	chr1B	87.831	945	105	7	2141	3081	100553834	100554772	0.000000e+00	1099.0
19	TraesCS5D01G015400	chr1B	87.606	944	108	9	2141	3081	297528421	297529358	0.000000e+00	1086.0
20	TraesCS5D01G015400	chr1B	81.435	237	34	8	49	284	142528765	142528538	5.250000e-43	185.0
21	TraesCS5D01G015400	chr7A	86.014	429	45	11	146	567	69317757	69318177	2.180000e-121	446.0
22	TraesCS5D01G015400	chr7A	83.252	412	57	10	161	568	39779145	39778742	4.860000e-98	368.0
23	TraesCS5D01G015400	chr7A	82.809	413	59	10	161	568	39795421	39795016	2.920000e-95	359.0
24	TraesCS5D01G015400	chr7A	88.679	159	18	0	13	171	69317653	69317811	8.730000e-46	195.0
25	TraesCS5D01G015400	chr7A	88.889	45	5	0	1236	1280	975640	975684	4.300000e-04	56.5
26	TraesCS5D01G015400	chr2A	82.210	371	58	6	49	415	608053465	608053099	2.310000e-81	313.0
27	TraesCS5D01G015400	chr4B	93.878	49	2	1	1233	1280	500865850	500865802	4.270000e-09	73.1
28	TraesCS5D01G015400	chr6D	92.000	50	3	1	1232	1280	179834774	179834823	5.520000e-08	69.4
29	TraesCS5D01G015400	chr6D	91.837	49	4	0	1232	1280	423215387	423215435	5.520000e-08	69.4
30	TraesCS5D01G015400	chr3A	93.478	46	3	0	1235	1280	664692846	664692891	5.520000e-08	69.4
31	TraesCS5D01G015400	chr3A	93.333	45	3	0	1236	1280	162081988	162081944	1.980000e-07	67.6
32	TraesCS5D01G015400	chr7D	91.304	46	3	1	1235	1280	222771486	222771442	9.230000e-06	62.1
33	TraesCS5D01G015400	chr4A	91.111	45	3	1	1231	1275	632853105	632853062	3.320000e-05	60.2

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	TraesCS5D01G015400	chr5D	8936059	8939142	3083	False	5696.000000	5696	100.000000	1	3084	1	chr5D.!!$F1	3083
1	TraesCS5D01G015400	chr5B	9006363	9010512	4149	False	1146.500000	1351	85.925000	1	2136	2	chr5B.!!$F1	2135
2	TraesCS5D01G015400	chr5A	6981551	6983803	2252	False	818.666667	1225	88.613333	1	2136	3	chr5A.!!$F2	2135
3	TraesCS5D01G015400	chr3D	301963435	301964372	937	True	1214.000000	1214	90.011000	2141	3080	1	chr3D.!!$R1	939
4	TraesCS5D01G015400	chr2B	41823650	41824601	951	True	1203.000000	1203	89.446000	2129	3084	1	chr2B.!!$R1	955
5	TraesCS5D01G015400	chr2B	137000836	137001783	947	True	1194.000000	1194	89.496000	2138	3081	1	chr2B.!!$R2	943
6	TraesCS5D01G015400	chrUn	92180266	92181117	851	True	1160.000000	1160	91.228000	2141	2994	1	chrUn.!!$R1	853
7	TraesCS5D01G015400	chr2D	328367467	328368416	949	False	1157.000000	1157	88.655000	2132	3081	1	chr2D.!!$F1	949
8	TraesCS5D01G015400	chr3B	425752085	425753033	948	True	1122.000000	1122	88.025000	2135	3084	1	chr3B.!!$R1	949
9	TraesCS5D01G015400	chr6A	433064043	433064986	943	True	1107.000000	1107	87.844000	2141	3084	1	chr6A.!!$R1	943
10	TraesCS5D01G015400	chr1B	100553834	100554772	938	False	1099.000000	1099	87.831000	2141	3081	1	chr1B.!!$F1	940
11	TraesCS5D01G015400	chr1B	297528421	297529358	937	False	1086.000000	1086	87.606000	2141	3081	1	chr1B.!!$F2	940
12	TraesCS5D01G015400	chr7A	69317653	69318177	524	False	320.500000	446	87.346500	13	567	2	chr7A.!!$F2	554

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
501	516	0.456142	TCGTCGGCTGATCAAACTCG	60.456	55.0	0.0	0.0	0.0	4.18	F
1450	3542	0.108472	CAGTCAGCATCGCCAGAAGA	60.108	55.0	0.0	0.0	0.0	2.87	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1765	4039	0.610232	GGCCAGCATGAAGAACCTGT	60.610	55.0	0.0	0.0	39.69	4.0	R
2826	5127	0.690762	AACTAAGTGGTCGTGGGCAT	59.309	50.0	0.0	0.0	0.00	4.4	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
25	26	5.801531	AAAACCTAAAGAAAAAGGCCGAT	57.198	34.783	0.00	0.00	36.24	4.18
88	90	0.808125	CCGCATTTGTTTGATCGGGA	59.192	50.000	0.00	0.00	33.85	5.14
202	204	2.540265	CAGAGGTTCTGTTGCAGAGT	57.460	50.000	0.00	0.00	41.75	3.24
354	362	5.865013	CAGCATAGATGATGTTGCAAAAACA	59.135	36.000	0.00	0.00	39.54	2.83
405	413	4.280677	GGATGTTGTTGTGGAAGGATTTCA	59.719	41.667	0.00	0.00	34.90	2.69
497	512	1.529438	GTTGTTCGTCGGCTGATCAAA	59.471	47.619	0.00	0.00	29.59	2.69
498	513	1.144969	TGTTCGTCGGCTGATCAAAC	58.855	50.000	0.00	4.69	0.00	2.93
499	514	1.270094	TGTTCGTCGGCTGATCAAACT	60.270	47.619	0.00	0.00	0.00	2.66
500	515	1.390463	GTTCGTCGGCTGATCAAACTC	59.610	52.381	0.00	0.00	0.00	3.01
501	516	0.456142	TCGTCGGCTGATCAAACTCG	60.456	55.000	0.00	0.00	0.00	4.18
502	517	0.732880	CGTCGGCTGATCAAACTCGT	60.733	55.000	0.00	0.00	0.00	4.18
503	518	1.466866	CGTCGGCTGATCAAACTCGTA	60.467	52.381	0.00	0.00	0.00	3.43
521	536	2.296814	TATCTGACGGCTGCGCATGT	62.297	55.000	12.24	10.55	0.00	3.21
539	554	2.125269	GGCGGAAGTGTATGCCGT	60.125	61.111	0.00	0.00	46.38	5.68
570	585	5.432645	GCTGGCTAACTCTAATCTTTTCCT	58.567	41.667	0.00	0.00	0.00	3.36
631	646	5.444663	AGAGAAGCAACAAAAACCTCATC	57.555	39.130	0.00	0.00	0.00	2.92
659	674	2.800273	GCCGAAACGTCCAAACCAAAAT	60.800	45.455	0.00	0.00	0.00	1.82
821	2898	2.439156	GCCCCCTACAGCTGCAAG	60.439	66.667	15.27	11.71	0.00	4.01
823	2900	1.918253	CCCCCTACAGCTGCAAGAT	59.082	57.895	15.27	0.00	34.07	2.40
847	2924	4.388499	ACACGTCCGTCCATGGCC	62.388	66.667	6.96	0.00	0.00	5.36
924	3007	6.466308	TGCATGCACGCTATTATAAACTAG	57.534	37.500	18.46	0.00	0.00	2.57
977	3060	4.513000	GCTAGAAGCAGAGAACAAATCG	57.487	45.455	0.00	0.00	41.89	3.34
1076	3162	2.685380	CTCCGGCTCCTCACCCTT	60.685	66.667	0.00	0.00	0.00	3.95
1097	3183	1.751162	CCTCCTCCTCGCGTCTCTT	60.751	63.158	5.77	0.00	0.00	2.85
1215	3301	3.267908	AGGTACTCCTGTCGACCTG	57.732	57.895	14.12	5.88	43.33	4.00
1216	3302	0.404812	AGGTACTCCTGTCGACCTGT	59.595	55.000	14.12	8.85	43.33	4.00
1217	3303	0.810016	GGTACTCCTGTCGACCTGTC	59.190	60.000	14.12	0.00	0.00	3.51
1218	3304	0.810016	GTACTCCTGTCGACCTGTCC	59.190	60.000	14.12	0.00	0.00	4.02
1219	3305	0.402887	TACTCCTGTCGACCTGTCCA	59.597	55.000	14.12	0.00	0.00	4.02
1220	3306	0.251832	ACTCCTGTCGACCTGTCCAT	60.252	55.000	14.12	0.00	0.00	3.41
1221	3307	0.457851	CTCCTGTCGACCTGTCCATC	59.542	60.000	14.12	0.00	0.00	3.51
1222	3308	0.970937	TCCTGTCGACCTGTCCATCC	60.971	60.000	14.12	0.00	0.00	3.51
1248	3334	0.912486	GCCATGTACTCCCTCTGGTT	59.088	55.000	0.00	0.00	0.00	3.67
1258	3344	5.648330	ACTCCCTCTGGTTCTTTTTACTT	57.352	39.130	0.00	0.00	0.00	2.24
1280	3366	8.213518	ACTTCGCATATTAGATTTGTGTCAAT	57.786	30.769	0.00	0.00	0.00	2.57
1296	3382	8.918202	TTGTGTCAATAATTTAGGAGAACTGT	57.082	30.769	0.00	0.00	0.00	3.55
1298	3384	8.999431	TGTGTCAATAATTTAGGAGAACTGTTC	58.001	33.333	12.54	12.54	0.00	3.18
1335	3423	2.138320	ACTATCGTAGCATGCATGTGC	58.862	47.619	26.79	16.21	45.38	4.57
1450	3542	0.108472	CAGTCAGCATCGCCAGAAGA	60.108	55.000	0.00	0.00	0.00	2.87
1514	3606	2.202703	GCGCCGACGTGGTAAGAT	60.203	61.111	0.00	0.00	42.83	2.40
1515	3607	1.064621	GCGCCGACGTGGTAAGATA	59.935	57.895	0.00	0.00	42.83	1.98
1516	3608	1.204856	GCGCCGACGTGGTAAGATAC	61.205	60.000	0.00	0.00	42.83	2.24
1544	3810	2.780595	GGCGCTGCCTCTTTTGATA	58.219	52.632	7.64	0.00	46.69	2.15
1554	3820	2.547211	CCTCTTTTGATATGCTCGCCAG	59.453	50.000	0.00	0.00	0.00	4.85
1556	3822	3.609853	TCTTTTGATATGCTCGCCAGTT	58.390	40.909	0.00	0.00	0.00	3.16
1563	3829	5.410924	TGATATGCTCGCCAGTTACATATC	58.589	41.667	12.24	12.24	44.98	1.63
1564	3830	2.134201	TGCTCGCCAGTTACATATCG	57.866	50.000	0.00	0.00	0.00	2.92
1565	3831	1.269569	TGCTCGCCAGTTACATATCGG	60.270	52.381	0.00	0.00	0.00	4.18
1566	3832	1.269621	GCTCGCCAGTTACATATCGGT	60.270	52.381	0.00	0.00	0.00	4.69
1567	3833	2.802057	GCTCGCCAGTTACATATCGGTT	60.802	50.000	0.00	0.00	0.00	4.44
1568	3834	2.794910	CTCGCCAGTTACATATCGGTTG	59.205	50.000	0.00	0.00	0.00	3.77
1614	3888	0.666274	TTACGTGCAGGTCTTCGCAG	60.666	55.000	16.53	0.00	39.20	5.18
1765	4039	1.511850	CAGCTCAACACGGACATCAA	58.488	50.000	0.00	0.00	0.00	2.57
1788	4062	0.449388	GTTCTTCATGCTGGCCTTCG	59.551	55.000	3.32	0.00	0.00	3.79
1814	4088	2.437359	GGGTTCATGCTGCTCGCT	60.437	61.111	0.00	0.00	40.11	4.93
1833	4107	4.100084	CCGCCTGCATGGTCCTCA	62.100	66.667	0.00	0.00	38.35	3.86
1884	4159	2.292267	GAAGATGATTCGGCACCACAT	58.708	47.619	0.00	0.00	0.00	3.21
1895	4170	1.675714	GGCACCACATGTCTTGATCGA	60.676	52.381	0.00	0.00	0.00	3.59
1900	4175	5.327091	CACCACATGTCTTGATCGAATTTC	58.673	41.667	0.00	0.00	0.00	2.17
1903	4178	5.220739	CCACATGTCTTGATCGAATTTCCTC	60.221	44.000	0.00	0.00	0.00	3.71
1918	4193	9.923143	TCGAATTTCCTCGATAATATATGTTGT	57.077	29.630	0.00	0.00	42.69	3.32
1935	4210	4.744570	TGTTGTTCTACTCGATCATCACC	58.255	43.478	0.00	0.00	0.00	4.02
1937	4212	4.639135	TGTTCTACTCGATCATCACCTG	57.361	45.455	0.00	0.00	0.00	4.00
1984	4260	9.561069	AATAATGAGAAATCTAATTGGCTACGT	57.439	29.630	3.64	0.00	29.96	3.57
1986	4262	5.357257	TGAGAAATCTAATTGGCTACGTCC	58.643	41.667	0.00	0.00	0.00	4.79
2079	4370	0.952280	TTTCCGGCAATGTTACGCAA	59.048	45.000	0.00	0.00	0.00	4.85
2081	4372	2.025589	TCCGGCAATGTTACGCAATA	57.974	45.000	0.00	0.00	0.00	1.90
2087	4378	3.915569	GGCAATGTTACGCAATAAACGTT	59.084	39.130	0.00	0.00	41.93	3.99
2113	4404	2.519780	GGGGGTGGCAAACGAACA	60.520	61.111	0.00	0.00	0.00	3.18
2132	4423	7.598278	ACGAACATCATTTAATGGCAGTTTTA	58.402	30.769	5.02	0.00	0.00	1.52
2136	4427	9.777297	AACATCATTTAATGGCAGTTTTAGTTT	57.223	25.926	5.02	0.00	0.00	2.66
2137	4428	9.777297	ACATCATTTAATGGCAGTTTTAGTTTT	57.223	25.926	5.02	0.00	0.00	2.43
2182	4473	3.473647	CCGGGCCTCTGCATCTGA	61.474	66.667	0.84	0.00	40.13	3.27
2324	4617	3.324846	TGCTGAATGTCCGAGCCTAATAT	59.675	43.478	0.00	0.00	31.31	1.28
2337	4630	5.985530	CGAGCCTAATATCAAACAGACATCA	59.014	40.000	0.00	0.00	0.00	3.07
2359	4652	6.065374	TCACACCAAAGCCTAACATCTAAAA	58.935	36.000	0.00	0.00	0.00	1.52
2441	4734	2.828095	AGCACCGCACACTGCAAA	60.828	55.556	0.00	0.00	45.36	3.68
2508	4801	1.776662	TGCATCGACCTTACTAGGCT	58.223	50.000	0.00	0.00	46.22	4.58
2783	5084	0.254178	GAAGCAGATGCCTCCTGGAA	59.746	55.000	0.14	0.00	43.38	3.53
2784	5085	0.924823	AAGCAGATGCCTCCTGGAAT	59.075	50.000	0.14	0.00	43.38	3.01
2823	5124	3.587933	GCCGCCCACAAACACGAA	61.588	61.111	0.00	0.00	0.00	3.85
2826	5127	2.473760	CGCCCACAAACACGAACCA	61.474	57.895	0.00	0.00	0.00	3.67
2844	5145	0.036388	CATGCCCACGACCACTTAGT	60.036	55.000	0.00	0.00	0.00	2.24
2912	5213	1.683441	CGCCCTAGGGTTTTCACCT	59.317	57.895	28.96	0.00	43.65	4.00
2961	5262	2.202272	GACCCGAACGACGTCTCG	60.202	66.667	17.53	17.53	46.06	4.04

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
25	26	3.313713	TGCCTGCTGACGCATAGCA	62.314	57.895	8.31	8.31	46.60	3.49
39	40	4.082571	CGGATCTTTTTGAAACATCTGCCT	60.083	41.667	0.00	0.00	0.00	4.75
47	48	1.336877	GCGGCGGATCTTTTTGAAAC	58.663	50.000	9.78	0.00	0.00	2.78
75	77	1.352687	TGGATGGTCCCGATCAAACAA	59.647	47.619	0.00	0.00	35.03	2.83
210	212	6.183360	ACACTCATGTTTCAAAAGAGTTCAGG	60.183	38.462	0.00	0.00	37.45	3.86
393	401	2.886523	CTGTGTTGCTGAAATCCTTCCA	59.113	45.455	0.00	0.00	0.00	3.53
405	413	7.744087	TTTCTGTAACATTATCTGTGTTGCT	57.256	32.000	8.19	0.00	41.06	3.91
521	536	2.125310	CGGCATACACTTCCGCCA	60.125	61.111	0.00	0.00	45.14	5.69
538	553	0.108138	AGTTAGCCAGCCGATCACAC	60.108	55.000	0.00	0.00	0.00	3.82
539	554	0.175760	GAGTTAGCCAGCCGATCACA	59.824	55.000	0.00	0.00	0.00	3.58
549	564	8.822805	TCTTTAGGAAAAGATTAGAGTTAGCCA	58.177	33.333	0.00	0.00	44.85	4.75
605	620	8.814038	ATGAGGTTTTTGTTGCTTCTCTATAT	57.186	30.769	0.00	0.00	0.00	0.86
606	621	7.882791	TGATGAGGTTTTTGTTGCTTCTCTATA	59.117	33.333	0.00	0.00	0.00	1.31
616	631	5.220643	GGCAAGTTTGATGAGGTTTTTGTTG	60.221	40.000	0.00	0.00	0.00	3.33
631	646	0.378962	TGGACGTTTCGGCAAGTTTG	59.621	50.000	0.00	0.00	36.10	2.93
756	771	0.745845	GCTACGGGACTCTCGTACCA	60.746	60.000	7.10	0.00	45.14	3.25
757	772	0.745845	TGCTACGGGACTCTCGTACC	60.746	60.000	7.10	2.08	41.09	3.34
808	2885	1.950828	CTCCATCTTGCAGCTGTAGG	58.049	55.000	16.64	12.01	0.00	3.18
821	2898	2.509336	CGGACGTGTGGCTCCATC	60.509	66.667	0.00	0.00	0.00	3.51
823	2900	3.986006	GACGGACGTGTGGCTCCA	61.986	66.667	0.53	0.00	0.00	3.86
847	2924	1.798735	CTGCTTCTTCGGCCATGTG	59.201	57.895	2.24	0.00	0.00	3.21
911	2991	7.123547	AGGAGGCTGCTAGCTAGTTTATAATAG	59.876	40.741	21.62	0.95	41.99	1.73
1097	3183	1.627864	TGTCGACCAAGATGAGGACA	58.372	50.000	14.12	0.00	32.51	4.02
1178	3264	1.660607	CTGTACGCGTAGACGTCCTTA	59.339	52.381	21.25	0.00	44.43	2.69
1210	3296	1.156736	CAAACACGGATGGACAGGTC	58.843	55.000	0.00	0.00	0.00	3.85
1211	3297	0.889186	GCAAACACGGATGGACAGGT	60.889	55.000	0.00	0.00	0.00	4.00
1212	3298	1.586154	GGCAAACACGGATGGACAGG	61.586	60.000	0.00	0.00	0.00	4.00
1213	3299	0.888736	TGGCAAACACGGATGGACAG	60.889	55.000	0.00	0.00	0.00	3.51
1214	3300	0.251121	ATGGCAAACACGGATGGACA	60.251	50.000	0.00	0.00	0.00	4.02
1215	3301	0.171007	CATGGCAAACACGGATGGAC	59.829	55.000	0.00	0.00	0.00	4.02
1216	3302	0.251121	ACATGGCAAACACGGATGGA	60.251	50.000	0.00	0.00	0.00	3.41
1217	3303	1.132262	GTACATGGCAAACACGGATGG	59.868	52.381	0.00	0.00	0.00	3.51
1218	3304	2.083774	AGTACATGGCAAACACGGATG	58.916	47.619	0.00	0.00	0.00	3.51
1219	3305	2.356135	GAGTACATGGCAAACACGGAT	58.644	47.619	0.00	0.00	0.00	4.18
1220	3306	1.609580	GGAGTACATGGCAAACACGGA	60.610	52.381	0.00	0.00	0.00	4.69
1221	3307	0.802494	GGAGTACATGGCAAACACGG	59.198	55.000	0.00	0.00	0.00	4.94
1222	3308	0.802494	GGGAGTACATGGCAAACACG	59.198	55.000	0.00	0.00	0.00	4.49
1288	3374	9.640963	AGTACTTATGTGTTATGAACAGTTCTC	57.359	33.333	14.51	3.73	43.10	2.87
1319	3407	1.018752	AACGCACATGCATGCTACGA	61.019	50.000	31.02	0.00	43.80	3.43
1335	3423	5.445939	CCGAGAATAACAAGGACATGAAACG	60.446	44.000	0.00	0.00	0.00	3.60
1411	3503	1.868997	CGCAAACGGAATCTGCAGT	59.131	52.632	14.67	0.00	35.78	4.40
1450	3542	0.970937	TGCCTCCGATCCTCGTCTTT	60.971	55.000	0.00	0.00	38.40	2.52
1534	3800	3.201290	ACTGGCGAGCATATCAAAAGAG	58.799	45.455	0.00	0.00	0.00	2.85
1536	3802	4.332543	TGTAACTGGCGAGCATATCAAAAG	59.667	41.667	0.00	0.00	0.00	2.27
1537	3803	4.257731	TGTAACTGGCGAGCATATCAAAA	58.742	39.130	0.00	0.00	0.00	2.44
1539	3805	3.535280	TGTAACTGGCGAGCATATCAA	57.465	42.857	0.00	0.00	0.00	2.57
1540	3806	3.751479	ATGTAACTGGCGAGCATATCA	57.249	42.857	0.00	0.00	0.00	2.15
1541	3807	4.500837	CGATATGTAACTGGCGAGCATATC	59.499	45.833	17.30	17.30	41.98	1.63
1544	3810	2.610479	CCGATATGTAACTGGCGAGCAT	60.610	50.000	0.00	0.00	0.00	3.79
1554	3820	6.036300	TCGATCAAAACCAACCGATATGTAAC	59.964	38.462	0.00	0.00	0.00	2.50
1556	3822	5.521010	GTCGATCAAAACCAACCGATATGTA	59.479	40.000	0.00	0.00	0.00	2.29
1563	3829	1.141645	TCGTCGATCAAAACCAACCG	58.858	50.000	0.00	0.00	0.00	4.44
1564	3830	2.095372	GGATCGTCGATCAAAACCAACC	59.905	50.000	30.69	11.82	40.50	3.77
1565	3831	2.739913	TGGATCGTCGATCAAAACCAAC	59.260	45.455	30.69	14.88	40.50	3.77
1566	3832	3.046968	TGGATCGTCGATCAAAACCAA	57.953	42.857	30.69	9.08	40.50	3.67
1567	3833	2.739913	GTTGGATCGTCGATCAAAACCA	59.260	45.455	30.69	19.77	40.50	3.67
1568	3834	2.095372	GGTTGGATCGTCGATCAAAACC	59.905	50.000	33.50	33.50	43.34	3.27
1671	3945	2.202401	GTACGTGGAGTCGGCGTC	60.202	66.667	6.85	0.00	39.64	5.19
1685	3959	2.813908	CGTTCCCAGCTGCGGTAC	60.814	66.667	8.66	13.58	0.00	3.34
1715	3989	1.522569	GGGAATCAGACTCCCGGTG	59.477	63.158	0.00	0.00	43.27	4.94
1765	4039	0.610232	GGCCAGCATGAAGAACCTGT	60.610	55.000	0.00	0.00	39.69	4.00
1828	4102	5.328565	AGACGGAGATCATTATGATGAGGA	58.671	41.667	12.89	0.00	45.01	3.71
1832	4106	4.795795	GCGTAGACGGAGATCATTATGATG	59.204	45.833	12.89	0.71	37.22	3.07
1833	4107	4.437524	CGCGTAGACGGAGATCATTATGAT	60.438	45.833	7.50	7.50	38.74	2.45
1877	4152	4.952262	AATTCGATCAAGACATGTGGTG	57.048	40.909	1.15	0.29	0.00	4.17
1880	4155	5.501413	CGAGGAAATTCGATCAAGACATGTG	60.501	44.000	1.15	0.00	43.03	3.21
1884	4159	4.450082	TCGAGGAAATTCGATCAAGACA	57.550	40.909	0.00	0.00	44.00	3.41
1900	4175	9.491934	CGAGTAGAACAACATATATTATCGAGG	57.508	37.037	0.00	0.00	0.00	4.63
1909	4184	8.297426	GGTGATGATCGAGTAGAACAACATATA	58.703	37.037	0.00	0.00	36.95	0.86
1910	4185	7.014711	AGGTGATGATCGAGTAGAACAACATAT	59.985	37.037	0.00	0.00	36.95	1.78
1911	4186	6.321435	AGGTGATGATCGAGTAGAACAACATA	59.679	38.462	0.00	0.00	36.95	2.29
1912	4187	5.127845	AGGTGATGATCGAGTAGAACAACAT	59.872	40.000	0.00	0.00	36.95	2.71
1918	4193	4.336713	CAGTCAGGTGATGATCGAGTAGAA	59.663	45.833	0.00	0.00	40.92	2.10
1979	4255	3.962421	CTAGGCGGGCGGACGTAG	61.962	72.222	0.00	0.00	35.98	3.51
1984	4260	4.023234	TTTTGCTAGGCGGGCGGA	62.023	61.111	0.00	0.00	0.00	5.54
1986	4262	3.810896	GGTTTTGCTAGGCGGGCG	61.811	66.667	0.00	0.00	0.00	6.13
2036	4312	4.461992	AAATGACGGTCTTAACGTGTTG	57.538	40.909	9.88	0.00	45.68	3.33
2037	4313	5.488645	AAAAATGACGGTCTTAACGTGTT	57.511	34.783	9.88	0.00	45.68	3.32
2067	4358	6.019152	AGCTAACGTTTATTGCGTAACATTG	58.981	36.000	5.91	0.00	42.10	2.82
2076	4367	2.477863	CCTGCCAGCTAACGTTTATTGC	60.478	50.000	5.91	6.64	0.00	3.56
2079	4370	1.408266	CCCCTGCCAGCTAACGTTTAT	60.408	52.381	5.91	0.00	0.00	1.40
2081	4372	1.303317	CCCCTGCCAGCTAACGTTT	60.303	57.895	5.91	0.00	0.00	3.60
2109	4400	8.986477	ACTAAAACTGCCATTAAATGATGTTC	57.014	30.769	0.00	0.00	0.00	3.18
2151	4442	1.687840	CCCGGGTGTACATCCTCCA	60.688	63.158	22.73	0.00	0.00	3.86
2182	4473	6.579666	AATAATATGGCTTCATGCATCGTT	57.420	33.333	0.00	0.00	45.15	3.85
2226	4517	6.822442	TCAGACTTGTTGATGTGTTACCTTA	58.178	36.000	0.00	0.00	0.00	2.69
2234	4525	2.880268	TGGCTTCAGACTTGTTGATGTG	59.120	45.455	0.00	0.00	0.00	3.21
2242	4533	2.486472	AGATGGTGGCTTCAGACTTG	57.514	50.000	0.00	0.00	0.00	3.16
2276	4567	5.151454	CCTTCATCAAGGGATAGGAGTAGT	58.849	45.833	0.00	0.00	45.27	2.73
2324	4617	3.066621	GCTTTGGTGTGATGTCTGTTTGA	59.933	43.478	0.00	0.00	0.00	2.69
2337	4630	5.243060	GGTTTTAGATGTTAGGCTTTGGTGT	59.757	40.000	0.00	0.00	0.00	4.16
2441	4734	1.613630	AAGATGGAGGTGACGGCCT	60.614	57.895	0.00	0.00	42.53	5.19
2508	4801	2.184322	GGCGTCGATGGCAGAGAA	59.816	61.111	24.90	0.00	0.00	2.87
2614	4908	2.844072	TTCCGCATCGATGACGGCAA	62.844	55.000	35.69	29.35	42.78	4.52
2615	4909	3.363844	TTCCGCATCGATGACGGCA	62.364	57.895	35.69	29.29	42.78	5.69
2783	5084	1.077716	GTTGGCGTGCCCCTCTTAT	60.078	57.895	8.69	0.00	34.56	1.73
2784	5085	2.221299	AGTTGGCGTGCCCCTCTTA	61.221	57.895	8.69	0.00	34.56	2.10
2808	5109	1.791103	ATGGTTCGTGTTTGTGGGCG	61.791	55.000	0.00	0.00	0.00	6.13
2815	5116	1.791103	CGTGGGCATGGTTCGTGTTT	61.791	55.000	0.00	0.00	0.00	2.83
2823	5124	1.485294	TAAGTGGTCGTGGGCATGGT	61.485	55.000	0.00	0.00	0.00	3.55
2826	5127	0.690762	AACTAAGTGGTCGTGGGCAT	59.309	50.000	0.00	0.00	0.00	4.40
2844	5145	3.338126	GAAGGCGCCGTCGAGAGAA	62.338	63.158	26.37	0.00	45.01	2.87
2912	5213	0.761323	TCCCACTCCACGGTTTCTCA	60.761	55.000	0.00	0.00	0.00	3.27
2961	5262	1.349357	AGGGTGCTGTTTCTCTTCCTC	59.651	52.381	0.00	0.00	0.00	3.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.