AutoCloner

Multiple sequence alignment - TraesCS6A01G185600

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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	TraesCS6A01G185600	chr6A	100.000	4259	0	0	1	4259	217768473	217772731	0.000000e+00	7866.0
1	TraesCS6A01G185600	chr6A	93.020	745	49	3	1	743	44999395	45000138	0.000000e+00	1085.0
2	TraesCS6A01G185600	chr6B	89.834	1751	75	37	1791	3475	289769849	289771562	0.000000e+00	2152.0
3	TraesCS6A01G185600	chr6B	89.777	1751	77	38	1791	3475	289784579	289786293	0.000000e+00	2148.0
4	TraesCS6A01G185600	chr6B	89.594	1749	78	36	1791	3475	289823731	289825439	0.000000e+00	2126.0
5	TraesCS6A01G185600	chr6B	90.447	827	28	20	998	1783	289782229	289783045	0.000000e+00	1042.0
6	TraesCS6A01G185600	chr6B	89.843	827	33	20	998	1783	289767471	289768287	0.000000e+00	1014.0
7	TraesCS6A01G185600	chr6B	94.649	598	20	8	998	1586	289821408	289822002	0.000000e+00	917.0
8	TraesCS6A01G185600	chr6B	88.889	225	11	4	741	958	289766831	289767048	9.080000e-67	265.0
9	TraesCS6A01G185600	chr6B	85.603	257	26	4	741	996	289781588	289781834	4.220000e-65	259.0
10	TraesCS6A01G185600	chr6B	91.099	191	10	1	775	958	289820795	289820985	7.070000e-63	252.0
11	TraesCS6A01G185600	chr6B	100.000	41	0	0	2949	2989	289772137	289772177	4.570000e-10	76.8
12	TraesCS6A01G185600	chr6B	97.561	41	1	0	2949	2989	289786888	289786928	2.120000e-08	71.3
13	TraesCS6A01G185600	chr6D	91.167	1302	58	25	944	2201	159515439	159516727	0.000000e+00	1714.0
14	TraesCS6A01G185600	chr6D	90.091	1100	45	23	2259	3330	159516976	159518039	0.000000e+00	1369.0
15	TraesCS6A01G185600	chr6D	94.884	215	4	1	741	955	159510853	159511060	3.170000e-86	329.0
16	TraesCS6A01G185600	chr6D	94.624	93	4	1	3384	3475	159519436	159519528	4.440000e-30	143.0
17	TraesCS6A01G185600	chr7D	94.228	797	43	3	3462	4256	342889525	342890320	0.000000e+00	1214.0
18	TraesCS6A01G185600	chr7D	92.346	797	56	4	3462	4256	295878387	295879180	0.000000e+00	1129.0
19	TraesCS6A01G185600	chr7D	80.076	527	100	3	1060	1582	461925705	461926230	1.860000e-103	387.0
20	TraesCS6A01G185600	chr7D	100.000	30	0	0	4184	4213	295879137	295879108	5.950000e-04	56.5
21	TraesCS6A01G185600	chr2A	94.504	746	34	7	1	741	750533965	750534708	0.000000e+00	1144.0
22	TraesCS6A01G185600	chr2A	93.280	744	45	5	1	741	726746568	726747309	0.000000e+00	1092.0
23	TraesCS6A01G185600	chr2A	93.271	743	46	4	1	741	747256434	747255694	0.000000e+00	1092.0
24	TraesCS6A01G185600	chr5A	94.213	743	40	3	1	741	502600737	502601478	0.000000e+00	1131.0
25	TraesCS6A01G185600	chr5A	93.809	743	42	4	1	741	394268013	394268753	0.000000e+00	1114.0
26	TraesCS6A01G185600	chr1A	93.674	743	40	6	1	741	107531999	107531262	0.000000e+00	1105.0
27	TraesCS6A01G185600	chr7A	93.557	745	40	7	1	741	692508143	692508883	0.000000e+00	1103.0
28	TraesCS6A01G185600	chr7A	93.496	738	44	3	8	743	671820044	671820779	0.000000e+00	1094.0
29	TraesCS6A01G185600	chr7A	80.935	535	94	6	1063	1592	538248311	538247780	2.370000e-112	416.0
30	TraesCS6A01G185600	chr3B	99.205	503	4	0	3686	4188	107970413	107970915	0.000000e+00	907.0
31	TraesCS6A01G185600	chr3B	100.000	206	0	0	3472	3677	107968807	107969012	8.640000e-102	381.0
32	TraesCS6A01G185600	chr3B	100.000	32	0	0	4228	4259	107970910	107970941	4.600000e-05	60.2
33	TraesCS6A01G185600	chr4D	92.208	385	27	3	3472	3855	174333956	174334338	3.750000e-150	542.0
34	TraesCS6A01G185600	chr4D	90.640	406	37	1	3852	4256	174342868	174343273	4.850000e-149	538.0
35	TraesCS6A01G185600	chr7B	79.849	531	101	4	1060	1586	484851107	484851635	2.400000e-102	383.0
36	TraesCS6A01G185600	chr1D	81.048	248	27	15	1061	1301	80015492	80015726	3.380000e-41	180.0
37	TraesCS6A01G185600	chr1B	83.333	162	16	7	1194	1352	647627657	647627810	5.740000e-29	139.0

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	TraesCS6A01G185600	chr6A	217768473	217772731	4258	False	7866.000000	7866	100.000000	1	4259	1	chr6A.!!$F2	4258
1	TraesCS6A01G185600	chr6A	44999395	45000138	743	False	1085.000000	1085	93.020000	1	743	1	chr6A.!!$F1	742
2	TraesCS6A01G185600	chr6B	289820795	289825439	4644	False	1098.333333	2126	91.780667	775	3475	3	chr6B.!!$F3	2700
3	TraesCS6A01G185600	chr6B	289781588	289786928	5340	False	880.075000	2148	90.847000	741	3475	4	chr6B.!!$F2	2734
4	TraesCS6A01G185600	chr6B	289766831	289772177	5346	False	876.950000	2152	92.141500	741	3475	4	chr6B.!!$F1	2734
5	TraesCS6A01G185600	chr6D	159515439	159519528	4089	False	1075.333333	1714	91.960667	944	3475	3	chr6D.!!$F2	2531
6	TraesCS6A01G185600	chr7D	342889525	342890320	795	False	1214.000000	1214	94.228000	3462	4256	1	chr7D.!!$F2	794
7	TraesCS6A01G185600	chr7D	295878387	295879180	793	False	1129.000000	1129	92.346000	3462	4256	1	chr7D.!!$F1	794
8	TraesCS6A01G185600	chr7D	461925705	461926230	525	False	387.000000	387	80.076000	1060	1582	1	chr7D.!!$F3	522
9	TraesCS6A01G185600	chr2A	750533965	750534708	743	False	1144.000000	1144	94.504000	1	741	1	chr2A.!!$F2	740
10	TraesCS6A01G185600	chr2A	726746568	726747309	741	False	1092.000000	1092	93.280000	1	741	1	chr2A.!!$F1	740
11	TraesCS6A01G185600	chr2A	747255694	747256434	740	True	1092.000000	1092	93.271000	1	741	1	chr2A.!!$R1	740
12	TraesCS6A01G185600	chr5A	502600737	502601478	741	False	1131.000000	1131	94.213000	1	741	1	chr5A.!!$F2	740
13	TraesCS6A01G185600	chr5A	394268013	394268753	740	False	1114.000000	1114	93.809000	1	741	1	chr5A.!!$F1	740
14	TraesCS6A01G185600	chr1A	107531262	107531999	737	True	1105.000000	1105	93.674000	1	741	1	chr1A.!!$R1	740
15	TraesCS6A01G185600	chr7A	692508143	692508883	740	False	1103.000000	1103	93.557000	1	741	1	chr7A.!!$F2	740
16	TraesCS6A01G185600	chr7A	671820044	671820779	735	False	1094.000000	1094	93.496000	8	743	1	chr7A.!!$F1	735
17	TraesCS6A01G185600	chr7A	538247780	538248311	531	True	416.000000	416	80.935000	1063	1592	1	chr7A.!!$R1	529
18	TraesCS6A01G185600	chr3B	107968807	107970941	2134	False	449.400000	907	99.735000	3472	4259	3	chr3B.!!$F1	787
19	TraesCS6A01G185600	chr7B	484851107	484851635	528	False	383.000000	383	79.849000	1060	1586	1	chr7B.!!$F1	526

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
260	265	0.462375	CGAGAGAGAGACGAGGGAGA	59.538	60.0	0.00	0.00	0.0	3.71	F
1983	4039	0.106894	GTTATCTTGGCCCTCGGAGG	59.893	60.0	17.41	17.41	34.3	4.30	F
3090	5372	0.036010	CCGAGAACCAACAGCCATCT	60.036	55.0	0.00	0.00	0.0	2.90	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2054	4110	0.324943	AGTGACCGTGAAGAATGGGG	59.675	55.000	0.00	0.00	39.57	4.96	R
3226	5530	0.819259	ACATCAACACCAACAGCGCT	60.819	50.000	2.64	2.64	0.00	5.92	R
4195	9460	2.125106	GGCACCGGAGCAAGTAGG	60.125	66.667	25.48	0.00	35.83	3.18	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
251	256	1.810441	GACGACGGCGAGAGAGAGA	60.810	63.158	22.49	0.00	41.64	3.10
260	265	0.462375	CGAGAGAGAGACGAGGGAGA	59.538	60.000	0.00	0.00	0.00	3.71
288	293	1.082679	CGGCGAGAGAGTACGAGTCA	61.083	60.000	0.00	0.00	0.00	3.41
563	570	1.707239	TTCGCGCCAAAACAGTTCGT	61.707	50.000	0.00	0.00	0.00	3.85
725	736	1.133915	TGAAAAGCCTTCCTGGAACGT	60.134	47.619	4.68	0.00	38.35	3.99
728	739	1.705997	AAGCCTTCCTGGAACGTGGT	61.706	55.000	4.68	0.04	38.35	4.16
743	754	1.339631	CGTGGTTGGAGATGCCCTAAA	60.340	52.381	0.00	0.00	34.97	1.85
748	759	3.206964	GTTGGAGATGCCCTAAACTAGC	58.793	50.000	0.00	0.00	34.97	3.42
753	764	2.300437	AGATGCCCTAAACTAGCGGATC	59.700	50.000	0.00	0.00	0.00	3.36
767	778	1.153647	GGATCGACGTGGCATGTGA	60.154	57.895	18.67	14.72	0.00	3.58
768	779	0.739462	GGATCGACGTGGCATGTGAA	60.739	55.000	18.67	5.10	0.00	3.18
769	780	1.075542	GATCGACGTGGCATGTGAAA	58.924	50.000	18.67	2.39	0.00	2.69
770	781	1.061131	GATCGACGTGGCATGTGAAAG	59.939	52.381	18.67	6.02	0.00	2.62
771	782	1.154413	CGACGTGGCATGTGAAAGC	60.154	57.895	18.67	0.93	0.00	3.51
789	800	1.596603	GCCCAAAGCAAAACAAGCAT	58.403	45.000	0.00	0.00	42.97	3.79
902	913	1.602311	GGGATCAGGATCACACATGC	58.398	55.000	11.12	0.00	40.86	4.06
903	914	1.142465	GGGATCAGGATCACACATGCT	59.858	52.381	11.12	0.00	40.86	3.79
910	921	0.835941	GATCACACATGCTCTCCCCT	59.164	55.000	0.00	0.00	0.00	4.79
958	985	1.007849	CCACCTTTCCGCAAAACCG	60.008	57.895	0.00	0.00	0.00	4.44
959	986	1.660264	CACCTTTCCGCAAAACCGC	60.660	57.895	0.00	0.00	0.00	5.68
960	987	2.122167	ACCTTTCCGCAAAACCGCA	61.122	52.632	0.00	0.00	0.00	5.69
961	988	1.066587	CCTTTCCGCAAAACCGCAA	59.933	52.632	0.00	0.00	0.00	4.85
962	989	0.528684	CCTTTCCGCAAAACCGCAAA	60.529	50.000	0.00	0.00	0.00	3.68
963	990	0.574922	CTTTCCGCAAAACCGCAAAC	59.425	50.000	0.00	0.00	0.00	2.93
964	991	0.806492	TTTCCGCAAAACCGCAAACC	60.806	50.000	0.00	0.00	0.00	3.27
965	992	2.630592	TTCCGCAAAACCGCAAACCC	62.631	55.000	0.00	0.00	0.00	4.11
966	993	2.660224	CGCAAAACCGCAAACCCC	60.660	61.111	0.00	0.00	0.00	4.95
1019	1441	1.275657	CACCGCGTCAAGAACACAC	59.724	57.895	4.92	0.00	0.00	3.82
1022	1446	1.083401	CGCGTCAAGAACACACAGC	60.083	57.895	0.00	0.00	0.00	4.40
1308	1738	1.227674	CTACCTCTTCGCCATGGCC	60.228	63.158	30.79	13.37	37.98	5.36
1586	2019	2.412112	GCCGCTCCAGGTACTACG	59.588	66.667	0.00	0.00	36.02	3.51
1588	2021	1.432251	CCGCTCCAGGTACTACGTG	59.568	63.158	0.00	2.42	36.02	4.49
1666	2128	6.512415	GCATATTGGAGTGTTAGCTGAATGAC	60.512	42.308	0.00	0.00	0.00	3.06
1725	2196	8.396272	ACAGTTTCACATTTACTGCTTCTTAT	57.604	30.769	0.00	0.00	42.28	1.73
1740	2211	6.003950	TGCTTCTTATAACCTGCAAGAAACT	58.996	36.000	0.00	0.00	37.72	2.66
1741	2212	6.490040	TGCTTCTTATAACCTGCAAGAAACTT	59.510	34.615	0.00	0.00	37.72	2.66
1746	2217	9.649167	TCTTATAACCTGCAAGAAACTTACTAC	57.351	33.333	0.00	0.00	34.07	2.73
1747	2218	6.963049	ATAACCTGCAAGAAACTTACTACG	57.037	37.500	0.00	0.00	34.07	3.51
1750	2221	6.034161	ACCTGCAAGAAACTTACTACGTAT	57.966	37.500	0.00	0.00	34.07	3.06
1751	2222	7.161773	ACCTGCAAGAAACTTACTACGTATA	57.838	36.000	0.00	0.00	34.07	1.47
1752	2223	7.031975	ACCTGCAAGAAACTTACTACGTATAC	58.968	38.462	0.00	0.00	34.07	1.47
1753	2224	7.094032	ACCTGCAAGAAACTTACTACGTATACT	60.094	37.037	0.00	0.00	34.07	2.12
1754	2225	8.400947	CCTGCAAGAAACTTACTACGTATACTA	58.599	37.037	0.00	0.00	34.07	1.82
1755	2226	9.435802	CTGCAAGAAACTTACTACGTATACTAG	57.564	37.037	0.00	4.85	34.07	2.57
1756	2227	8.950210	TGCAAGAAACTTACTACGTATACTAGT	58.050	33.333	15.04	15.04	0.00	2.57
1798	3850	9.799106	CATAGATTTATGAAATACTCCCACCTT	57.201	33.333	0.00	0.00	39.22	3.50
1825	3877	7.829725	TCAAACATAGGATTCCACAAAATGAG	58.170	34.615	5.29	0.00	0.00	2.90
1832	3884	3.940209	TTCCACAAAATGAGCATGTCC	57.060	42.857	0.00	0.00	0.00	4.02
1835	3887	3.005684	TCCACAAAATGAGCATGTCCAAC	59.994	43.478	0.00	0.00	0.00	3.77
1907	3962	0.645868	GAGCAAACGCATCGGTAGTC	59.354	55.000	0.00	0.00	0.00	2.59
1914	3969	1.814394	ACGCATCGGTAGTCACACTTA	59.186	47.619	0.00	0.00	0.00	2.24
1983	4039	0.106894	GTTATCTTGGCCCTCGGAGG	59.893	60.000	17.41	17.41	34.30	4.30
2046	4102	2.260844	TCTGACAGGGCACAAAGAAG	57.739	50.000	1.81	0.00	0.00	2.85
2047	4103	0.595095	CTGACAGGGCACAAAGAAGC	59.405	55.000	0.00	0.00	0.00	3.86
2048	4104	1.165907	TGACAGGGCACAAAGAAGCG	61.166	55.000	0.00	0.00	0.00	4.68
2050	4106	1.898574	CAGGGCACAAAGAAGCGGT	60.899	57.895	0.00	0.00	0.00	5.68
2051	4107	1.898574	AGGGCACAAAGAAGCGGTG	60.899	57.895	0.00	0.00	35.68	4.94
2054	4110	2.644992	CACAAAGAAGCGGTGCCC	59.355	61.111	0.00	0.00	0.00	5.36
2055	4111	2.597510	ACAAAGAAGCGGTGCCCC	60.598	61.111	0.00	0.00	0.00	5.80
2092	4148	3.716195	TGATGTGGGCCACTCGGG	61.716	66.667	34.69	0.00	40.85	5.14
2101	4158	1.299976	GCCACTCGGGTTCTCCAAT	59.700	57.895	0.00	0.00	39.65	3.16
2156	4213	3.181466	GGCCCATGTAATTAAGCCCTTTG	60.181	47.826	0.00	0.00	34.23	2.77
2226	4307	5.502544	GCGTATCAATGCTACTTTTCACTCC	60.503	44.000	0.00	0.00	34.60	3.85
2237	4479	2.044793	TTTCACTCCATCCCCTGAGT	57.955	50.000	0.00	0.00	42.41	3.41
2250	4492	2.437413	CCCTGAGTGAAAGCTTAACCC	58.563	52.381	0.00	0.00	0.00	4.11
2252	4494	3.486383	CCTGAGTGAAAGCTTAACCCAA	58.514	45.455	0.00	0.00	0.00	4.12
2253	4495	3.503748	CCTGAGTGAAAGCTTAACCCAAG	59.496	47.826	0.00	0.14	37.31	3.61
2254	4496	4.137543	CTGAGTGAAAGCTTAACCCAAGT	58.862	43.478	0.00	0.00	36.55	3.16
2255	4497	5.298989	TGAGTGAAAGCTTAACCCAAGTA	57.701	39.130	0.00	0.00	36.55	2.24
2304	4553	0.868406	GAGTTGCTGTCCCAAGAACG	59.132	55.000	0.00	0.00	0.00	3.95
2318	4567	0.249398	AGAACGAGAAATGGACGGGG	59.751	55.000	0.00	0.00	0.00	5.73
2367	4616	4.947147	GTGCGTGGGGGCTTGTGA	62.947	66.667	0.00	0.00	0.00	3.58
2419	4668	5.070981	TCCTGCTTATCATCTTAGTTCTGGG	59.929	44.000	0.00	0.00	0.00	4.45
2538	4788	0.390472	CCGGAGCTTTGGTCTCTCAC	60.390	60.000	0.00	0.00	0.00	3.51
2555	4805	2.421073	CTCACACGTTCATGCATCCATT	59.579	45.455	0.00	0.00	0.00	3.16
2565	4815	6.238842	CGTTCATGCATCCATTTCTAGGAAAT	60.239	38.462	0.00	0.31	38.93	2.17
2738	5012	1.377987	GTGGTGTGGTGTGGTGTGT	60.378	57.895	0.00	0.00	0.00	3.72
2739	5013	1.377856	TGGTGTGGTGTGGTGTGTG	60.378	57.895	0.00	0.00	0.00	3.82
3068	5345	2.091166	TGATTCCCATTTCCCATCCCAG	60.091	50.000	0.00	0.00	0.00	4.45
3072	5354	1.044790	CCATTTCCCATCCCAGCACC	61.045	60.000	0.00	0.00	0.00	5.01
3083	5365	1.227823	CCAGCACCGAGAACCAACA	60.228	57.895	0.00	0.00	0.00	3.33
3090	5372	0.036010	CCGAGAACCAACAGCCATCT	60.036	55.000	0.00	0.00	0.00	2.90
3094	5376	1.425066	AGAACCAACAGCCATCTCCAA	59.575	47.619	0.00	0.00	0.00	3.53
3095	5377	1.815003	GAACCAACAGCCATCTCCAAG	59.185	52.381	0.00	0.00	0.00	3.61
3221	5525	2.888594	TCGTGGAGAATTTTAGCGAGG	58.111	47.619	0.00	0.00	0.00	4.63
3332	6905	2.271800	GTCCTCGTGGCTTGATTACTG	58.728	52.381	0.00	0.00	0.00	2.74
3386	6966	5.290386	GGACGAATCTCATCCGTTAATTCT	58.710	41.667	0.00	0.00	36.60	2.40
3426	7081	1.985473	TTTGTCAGAATGTGGCTGCT	58.015	45.000	0.00	0.00	37.40	4.24
4114	9378	0.243095	ACGAAGCGAAGGTAGTCACC	59.757	55.000	0.00	0.00	46.19	4.02
4195	9460	1.212751	GAATTTGGCACCGGAGCAC	59.787	57.895	25.48	14.80	35.83	4.40
4196	9461	2.212900	GAATTTGGCACCGGAGCACC	62.213	60.000	25.48	12.47	35.83	5.01
4199	9464	2.741486	TTTGGCACCGGAGCACCTAC	62.741	60.000	25.48	8.12	35.83	3.18
4200	9465	3.391382	GGCACCGGAGCACCTACT	61.391	66.667	25.48	0.00	35.83	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
251	256	1.578423	GTCGTCGTTTCTCCCTCGT	59.422	57.895	0.00	0.00	0.00	4.18
260	265	2.126965	CTCTCGCCGTCGTCGTTT	60.127	61.111	0.71	0.00	36.96	3.60
288	293	3.374402	CGTCCCAGAGCACTCGGT	61.374	66.667	0.00	0.00	34.09	4.69
443	450	1.252904	ATCAATGCCAAAGCTGCCGT	61.253	50.000	0.00	0.00	40.80	5.68
537	544	0.248296	GTTTTGGCGCGAAACAGTCA	60.248	50.000	24.35	7.45	37.59	3.41
539	546	1.803943	TGTTTTGGCGCGAAACAGT	59.196	47.368	26.68	0.00	41.19	3.55
638	647	1.078426	CCAGGAGCCCGATTTTCGT	60.078	57.895	0.00	0.00	38.40	3.85
702	712	0.251341	TCCAGGAAGGCTTTTCAGGC	60.251	55.000	0.00	0.00	46.34	4.85
704	714	1.537202	CGTTCCAGGAAGGCTTTTCAG	59.463	52.381	8.97	0.00	37.29	3.02
705	715	1.133915	ACGTTCCAGGAAGGCTTTTCA	60.134	47.619	19.95	0.00	37.29	2.69
710	720	1.705997	AACCACGTTCCAGGAAGGCT	61.706	55.000	19.95	6.50	37.29	4.58
725	736	1.992557	AGTTTAGGGCATCTCCAACCA	59.007	47.619	0.00	0.00	36.21	3.67
728	739	2.158957	CGCTAGTTTAGGGCATCTCCAA	60.159	50.000	0.00	0.00	36.21	3.53
743	754	3.108343	CCACGTCGATCCGCTAGT	58.892	61.111	0.00	0.00	0.00	2.57
748	759	2.202743	ACATGCCACGTCGATCCG	60.203	61.111	0.00	0.00	0.00	4.18
753	764	1.154413	GCTTTCACATGCCACGTCG	60.154	57.895	0.00	0.00	0.00	5.12
767	778	2.016318	GCTTGTTTTGCTTTGGGCTTT	58.984	42.857	0.00	0.00	42.39	3.51
768	779	1.065564	TGCTTGTTTTGCTTTGGGCTT	60.066	42.857	0.00	0.00	42.39	4.35
769	780	0.540923	TGCTTGTTTTGCTTTGGGCT	59.459	45.000	0.00	0.00	42.39	5.19
770	781	1.264826	CATGCTTGTTTTGCTTTGGGC	59.735	47.619	0.00	0.00	42.22	5.36
771	782	1.264826	GCATGCTTGTTTTGCTTTGGG	59.735	47.619	11.37	0.00	33.61	4.12
772	783	1.264826	GGCATGCTTGTTTTGCTTTGG	59.735	47.619	18.92	0.00	36.62	3.28
773	784	1.264826	GGGCATGCTTGTTTTGCTTTG	59.735	47.619	18.92	0.00	36.62	2.77
789	800	1.146041	GACGAGTATGGCATGGGCA	59.854	57.895	10.98	0.00	43.71	5.36
801	812	0.321298	CCGGGATTGTTTGGACGAGT	60.321	55.000	0.00	0.00	0.00	4.18
881	892	0.761187	ATGTGTGATCCTGATCCCCG	59.239	55.000	4.76	0.00	37.02	5.73
882	893	1.816961	GCATGTGTGATCCTGATCCCC	60.817	57.143	4.76	0.00	37.02	4.81
958	985	1.338674	GGTGGCATAAAAGGGGTTTGC	60.339	52.381	0.00	0.00	0.00	3.68
959	986	1.277842	GGGTGGCATAAAAGGGGTTTG	59.722	52.381	0.00	0.00	0.00	2.93
960	987	1.651737	GGGTGGCATAAAAGGGGTTT	58.348	50.000	0.00	0.00	0.00	3.27
961	988	0.252513	GGGGTGGCATAAAAGGGGTT	60.253	55.000	0.00	0.00	0.00	4.11
962	989	1.390525	GGGGTGGCATAAAAGGGGT	59.609	57.895	0.00	0.00	0.00	4.95
963	990	1.382557	GGGGGTGGCATAAAAGGGG	60.383	63.158	0.00	0.00	0.00	4.79
964	991	4.373551	GGGGGTGGCATAAAAGGG	57.626	61.111	0.00	0.00	0.00	3.95
1002	1422	1.151777	CTGTGTGTTCTTGACGCGGT	61.152	55.000	12.47	0.00	41.73	5.68
1019	1441	1.595882	CTCTCCCAGACCTGTGCTG	59.404	63.158	0.00	0.00	0.00	4.41
1022	1446	1.943116	CTCGCTCTCCCAGACCTGTG	61.943	65.000	0.00	0.00	0.00	3.66
1521	1951	4.814294	GTGACGTAGCCGGCCTGG	62.814	72.222	26.15	15.11	43.26	4.45
1586	2019	5.163195	ACTGGGATTAGGTGATGGATAACAC	60.163	44.000	0.00	0.00	36.44	3.32
1588	2021	5.513267	GGACTGGGATTAGGTGATGGATAAC	60.513	48.000	0.00	0.00	0.00	1.89
1648	2110	1.661112	GCGTCATTCAGCTAACACTCC	59.339	52.381	0.00	0.00	0.00	3.85
1666	2128	6.347563	GCTAGTTCTAGTACTACATGGTAGCG	60.348	46.154	5.21	0.00	0.00	4.26
1725	2196	5.846203	ACGTAGTAAGTTTCTTGCAGGTTA	58.154	37.500	0.00	0.00	41.94	2.85
1746	2217	9.483062	GGCTAAACAACGATATACTAGTATACG	57.517	37.037	26.09	26.09	31.52	3.06
1751	2222	9.293404	TCTATGGCTAAACAACGATATACTAGT	57.707	33.333	0.00	0.00	0.00	2.57
1754	2225	9.998106	AAATCTATGGCTAAACAACGATATACT	57.002	29.630	0.00	0.00	0.00	2.12
1758	2229	9.990360	TCATAAATCTATGGCTAAACAACGATA	57.010	29.630	0.00	0.00	36.35	2.92
1783	2256	5.313712	TGTTTGAGAAGGTGGGAGTATTTC	58.686	41.667	0.00	0.00	0.00	2.17
1798	3850	7.669304	TCATTTTGTGGAATCCTATGTTTGAGA	59.331	33.333	0.00	0.00	0.00	3.27
1825	3877	1.597742	ACAGTGTGAGTTGGACATGC	58.402	50.000	0.00	0.00	0.00	4.06
1832	3884	3.186909	TCAGTCGAAACAGTGTGAGTTG	58.813	45.455	0.00	0.00	0.00	3.16
1860	3912	6.188407	TCATATCTAGTGGAGTAGTATGGCC	58.812	44.000	0.00	0.00	0.00	5.36
1907	3962	4.201589	CGTCTTGTTTCGGCTATAAGTGTG	60.202	45.833	0.00	0.00	0.00	3.82
1914	3969	2.993899	CTCAACGTCTTGTTTCGGCTAT	59.006	45.455	0.00	0.00	39.29	2.97
1983	4039	2.550606	CCTCCTCATCGTCTAGTAGCAC	59.449	54.545	0.00	0.00	0.00	4.40
2053	4109	0.676782	GTGACCGTGAAGAATGGGGG	60.677	60.000	0.00	0.00	39.57	5.40
2054	4110	0.324943	AGTGACCGTGAAGAATGGGG	59.675	55.000	0.00	0.00	39.57	4.96
2055	4111	1.270839	ACAGTGACCGTGAAGAATGGG	60.271	52.381	0.00	0.00	39.57	4.00
2061	4117	1.794701	CACATCACAGTGACCGTGAAG	59.205	52.381	22.53	4.19	45.91	3.02
2092	4148	3.259123	AGACCATTTGGCAATTGGAGAAC	59.741	43.478	35.37	24.47	39.32	3.01
2101	4158	1.631405	CCCTCAAGACCATTTGGCAA	58.369	50.000	0.00	0.00	39.32	4.52
2156	4213	2.229792	TCAGTGCCAGATTTGTTCCAC	58.770	47.619	0.00	0.00	0.00	4.02
2170	4227	5.914085	ATATTCGCAGTCTAAATCAGTGC	57.086	39.130	0.00	0.00	36.92	4.40
2226	4307	2.503895	AAGCTTTCACTCAGGGGATG	57.496	50.000	0.00	0.00	0.00	3.51
2237	4479	3.181452	ACGGTACTTGGGTTAAGCTTTCA	60.181	43.478	3.20	0.00	40.16	2.69
2304	4553	0.613777	ACTGTCCCCGTCCATTTCTC	59.386	55.000	0.00	0.00	0.00	2.87
2318	4567	2.358737	CTTGTCCCCGGCACTGTC	60.359	66.667	0.00	0.00	0.00	3.51
2367	4616	6.570672	TCAACACACGACTCTAGAACTAAT	57.429	37.500	0.00	0.00	0.00	1.73
2419	4668	2.435059	GCTCAAGTGCCCTCGACC	60.435	66.667	0.00	0.00	0.00	4.79
2538	4788	3.770263	AGAAATGGATGCATGAACGTG	57.230	42.857	2.46	0.00	0.00	4.49
2555	4805	3.581332	ACGTGAGGTGGAATTTCCTAGAA	59.419	43.478	16.25	0.00	37.46	2.10
2565	4815	3.830178	TCTCTTAATCACGTGAGGTGGAA	59.170	43.478	24.41	11.41	46.96	3.53
2617	4876	0.376152	CAGTCATCCTGCGACATTGC	59.624	55.000	0.00	0.00	35.77	3.56
2619	4878	2.996249	ATCAGTCATCCTGCGACATT	57.004	45.000	0.00	0.00	41.25	2.71
2620	4879	2.484417	GGAATCAGTCATCCTGCGACAT	60.484	50.000	0.00	0.00	41.25	3.06
2621	4880	1.134699	GGAATCAGTCATCCTGCGACA	60.135	52.381	0.00	0.00	41.25	4.35
2667	4941	5.220605	GCCCACGTTTCAGCTTAGTTATTAG	60.221	44.000	0.00	0.00	0.00	1.73
3068	5345	2.617274	GGCTGTTGGTTCTCGGTGC	61.617	63.158	0.00	0.00	0.00	5.01
3072	5354	1.363744	GAGATGGCTGTTGGTTCTCG	58.636	55.000	0.00	0.00	0.00	4.04
3083	5365	5.431765	CAAACATACTACTTGGAGATGGCT	58.568	41.667	0.00	0.00	0.00	4.75
3090	5372	7.843490	GTATGAAGCAAACATACTACTTGGA	57.157	36.000	15.57	0.00	43.57	3.53
3221	5525	2.353839	CACCAACAGCGCTTGCAC	60.354	61.111	7.50	0.00	42.66	4.57
3226	5530	0.819259	ACATCAACACCAACAGCGCT	60.819	50.000	2.64	2.64	0.00	5.92
3313	5624	1.405526	GCAGTAATCAAGCCACGAGGA	60.406	52.381	1.86	0.00	36.89	3.71
3314	5625	1.009829	GCAGTAATCAAGCCACGAGG	58.990	55.000	0.00	0.00	38.23	4.63
3332	6905	2.275318	GATCACTGGTGCAGTTCTAGC	58.725	52.381	0.00	0.00	42.59	3.42
3377	6957	7.749126	GGACCAGTCACAAATTAAGAATTAACG	59.251	37.037	0.00	0.00	44.35	3.18
3386	6966	8.472007	ACAAAATAGGACCAGTCACAAATTAA	57.528	30.769	0.00	0.00	0.00	1.40
3785	9049	4.500116	GTCTCCTGCTCGCGACCC	62.500	72.222	3.71	0.00	0.00	4.46
4195	9460	2.125106	GGCACCGGAGCAAGTAGG	60.125	66.667	25.48	0.00	35.83	3.18
4196	9461	2.125106	GGGCACCGGAGCAAGTAG	60.125	66.667	25.48	0.00	40.86	2.57
4226	9491	4.304413	TTGCCCAGCCAGTGCCAT	62.304	61.111	0.00	0.00	38.69	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.