AutoCloner

Multiple sequence alignment - TraesCS2B01G458700

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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	TraesCS2B01G458700	chr2B	100.000	2660	0	0	1	2660	653591164	653593823	0.000000e+00	4913.0
1	TraesCS2B01G458700	chr2B	95.752	871	28	4	1	869	232778003	232778866	0.000000e+00	1395.0
2	TraesCS2B01G458700	chr2B	94.009	868	36	8	1	865	764752661	764753515	0.000000e+00	1301.0
3	TraesCS2B01G458700	chr2B	86.944	720	89	3	997	1711	653415580	653416299	0.000000e+00	804.0
4	TraesCS2B01G458700	chr7B	97.113	866	23	2	1	865	476633872	476633008	0.000000e+00	1459.0
5	TraesCS2B01G458700	chr6B	97.005	868	22	3	1	865	608150956	608151822	0.000000e+00	1456.0
6	TraesCS2B01G458700	chr5B	96.326	871	22	6	1	869	341063967	341063105	0.000000e+00	1423.0
7	TraesCS2B01G458700	chr1B	95.080	874	24	5	1	868	330061807	330060947	0.000000e+00	1358.0
8	TraesCS2B01G458700	chr3B	94.836	852	38	5	1	850	30117708	30118555	0.000000e+00	1325.0
9	TraesCS2B01G458700	chr2D	94.269	855	47	1	871	1725	546682153	546683005	0.000000e+00	1306.0
10	TraesCS2B01G458700	chr2D	93.823	858	51	1	868	1725	546806228	546807083	0.000000e+00	1290.0
11	TraesCS2B01G458700	chr2D	93.664	726	43	2	1000	1724	546733266	546733989	0.000000e+00	1083.0
12	TraesCS2B01G458700	chr2D	92.975	726	39	6	1000	1725	546637504	546638217	0.000000e+00	1048.0
13	TraesCS2B01G458700	chr2D	93.769	337	13	2	2327	2660	546807855	546808186	1.420000e-137	499.0
14	TraesCS2B01G458700	chr2D	85.220	318	25	8	2039	2354	546807612	546807909	9.250000e-80	307.0
15	TraesCS2B01G458700	chr2D	89.175	194	8	5	1802	1985	546807215	546807405	2.060000e-56	230.0
16	TraesCS2B01G458700	chr2D	81.887	265	19	18	1727	1973	546638265	546638518	2.090000e-46	196.0
17	TraesCS2B01G458700	chr2D	83.886	211	15	12	1804	2009	546734136	546734332	1.630000e-42	183.0
18	TraesCS2B01G458700	chr2D	86.076	79	5	5	2578	2655	546683602	546683675	2.190000e-11	80.5
19	TraesCS2B01G458700	chr2D	88.462	52	2	3	2521	2569	546683565	546683615	2.860000e-05	60.2
20	TraesCS2B01G458700	chr2A	93.894	868	37	8	1	865	532842899	532842045	0.000000e+00	1295.0
21	TraesCS2B01G458700	chr2A	93.260	638	43	0	1088	1725	689761526	689760889	0.000000e+00	941.0
22	TraesCS2B01G458700	chr2A	91.850	638	52	0	1088	1725	689805200	689804563	0.000000e+00	891.0
23	TraesCS2B01G458700	chr2A	91.506	624	40	4	1087	1699	689769888	689769267	0.000000e+00	846.0
24	TraesCS2B01G458700	chr2A	82.253	293	33	11	2039	2327	689760354	689760077	4.430000e-58	235.0
25	TraesCS2B01G458700	chr2A	91.195	159	10	3	1827	1985	689760715	689760561	2.070000e-51	213.0
26	TraesCS2B01G458700	chr2A	84.286	210	15	8	1802	2009	689769107	689768914	3.500000e-44	189.0
27	TraesCS2B01G458700	chr2A	81.181	271	18	10	2357	2597	689760101	689759834	1.260000e-43	187.0
28	TraesCS2B01G458700	chr2A	85.632	174	11	8	1837	2008	689804376	689804215	1.270000e-38	171.0
29	TraesCS2B01G458700	chr2A	78.099	242	32	12	2374	2597	689803850	689803612	1.660000e-27	134.0
30	TraesCS2B01G458700	chr1A	93.671	869	38	9	1	866	144565469	144566323	0.000000e+00	1284.0
31	TraesCS2B01G458700	chr5A	91.724	725	45	3	1001	1725	377361811	377362520	0.000000e+00	992.0
32	TraesCS2B01G458700	chr5A	82.682	179	19	6	1833	2009	377363029	377363197	5.930000e-32	148.0

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	TraesCS2B01G458700	chr2B	653591164	653593823	2659	False	4913.000000	4913	100.000000	1	2660	1	chr2B.!!$F3	2659
1	TraesCS2B01G458700	chr2B	232778003	232778866	863	False	1395.000000	1395	95.752000	1	869	1	chr2B.!!$F1	868
2	TraesCS2B01G458700	chr2B	764752661	764753515	854	False	1301.000000	1301	94.009000	1	865	1	chr2B.!!$F4	864
3	TraesCS2B01G458700	chr2B	653415580	653416299	719	False	804.000000	804	86.944000	997	1711	1	chr2B.!!$F2	714
4	TraesCS2B01G458700	chr7B	476633008	476633872	864	True	1459.000000	1459	97.113000	1	865	1	chr7B.!!$R1	864
5	TraesCS2B01G458700	chr6B	608150956	608151822	866	False	1456.000000	1456	97.005000	1	865	1	chr6B.!!$F1	864
6	TraesCS2B01G458700	chr5B	341063105	341063967	862	True	1423.000000	1423	96.326000	1	869	1	chr5B.!!$R1	868
7	TraesCS2B01G458700	chr1B	330060947	330061807	860	True	1358.000000	1358	95.080000	1	868	1	chr1B.!!$R1	867
8	TraesCS2B01G458700	chr3B	30117708	30118555	847	False	1325.000000	1325	94.836000	1	850	1	chr3B.!!$F1	849
9	TraesCS2B01G458700	chr2D	546733266	546734332	1066	False	633.000000	1083	88.775000	1000	2009	2	chr2D.!!$F3	1009
10	TraesCS2B01G458700	chr2D	546637504	546638518	1014	False	622.000000	1048	87.431000	1000	1973	2	chr2D.!!$F1	973
11	TraesCS2B01G458700	chr2D	546806228	546808186	1958	False	581.500000	1290	90.496750	868	2660	4	chr2D.!!$F4	1792
12	TraesCS2B01G458700	chr2D	546682153	546683675	1522	False	482.233333	1306	89.602333	871	2655	3	chr2D.!!$F2	1784
13	TraesCS2B01G458700	chr2A	532842045	532842899	854	True	1295.000000	1295	93.894000	1	865	1	chr2A.!!$R1	864
14	TraesCS2B01G458700	chr2A	689768914	689769888	974	True	517.500000	846	87.896000	1087	2009	2	chr2A.!!$R3	922
15	TraesCS2B01G458700	chr2A	689803612	689805200	1588	True	398.666667	891	85.193667	1088	2597	3	chr2A.!!$R4	1509
16	TraesCS2B01G458700	chr2A	689759834	689761526	1692	True	394.000000	941	86.972250	1088	2597	4	chr2A.!!$R2	1509
17	TraesCS2B01G458700	chr1A	144565469	144566323	854	False	1284.000000	1284	93.671000	1	866	1	chr1A.!!$F1	865
18	TraesCS2B01G458700	chr5A	377361811	377363197	1386	False	570.000000	992	87.203000	1001	2009	2	chr5A.!!$F1	1008

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
985	996	1.154654	CCTTCTTCGTCGTTTGCGC	60.155	57.895	0.0	0.0	38.14	6.09	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2279	3173	0.033504	GAACACACGGAGGCAGAGAA	59.966	55.0	0.0	0.0	0.0	2.87	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
429	436	3.328382	TTGACTTCGAAATCCACGGAT	57.672	42.857	3.88	0.00	36.23	4.18
500	507	2.766660	GGAGAGGGGGCAAAGCTT	59.233	61.111	0.00	0.00	0.00	3.74
587	598	1.448540	GTCACAGTGCAGCGCCTAT	60.449	57.895	2.29	0.00	0.00	2.57
869	880	6.481644	GTCAAAATGGTCAAATTTGCCAGTTA	59.518	34.615	29.74	20.35	39.68	2.24
881	892	1.234615	GCCAGTTAAACTCGGCAGCA	61.235	55.000	9.78	0.00	40.07	4.41
884	895	3.006940	CCAGTTAAACTCGGCAGCATTA	58.993	45.455	0.00	0.00	0.00	1.90
885	896	3.063997	CCAGTTAAACTCGGCAGCATTAG	59.936	47.826	0.00	0.00	0.00	1.73
954	965	7.445402	GCTATTCTGGCATCTATAAAAGGACAA	59.555	37.037	0.00	0.00	0.00	3.18
985	996	1.154654	CCTTCTTCGTCGTTTGCGC	60.155	57.895	0.00	0.00	38.14	6.09
1049	1060	1.519719	CTCCCTCCTTTGCTCCTCG	59.480	63.158	0.00	0.00	0.00	4.63
1054	1065	0.321122	CTCCTTTGCTCCTCGCTGTT	60.321	55.000	0.00	0.00	40.11	3.16
1077	1088	2.033448	ATTCCGTTTGCGCCTCCA	59.967	55.556	4.18	0.00	36.67	3.86
1137	1148	4.201679	CCGAGCCGCGTCATGGTA	62.202	66.667	4.92	0.00	38.67	3.25
1433	1448	4.830765	GCAGACCCGCATACCGCA	62.831	66.667	0.00	0.00	42.60	5.69
1659	1679	3.136763	CTGCAAGAAGAAGAAGCTGTGA	58.863	45.455	0.00	0.00	34.07	3.58
1744	1817	1.554617	TGGCTTCGTCAAGATGGATCA	59.445	47.619	0.00	0.00	0.00	2.92
1746	1823	2.419297	GGCTTCGTCAAGATGGATCAGT	60.419	50.000	0.00	0.00	0.00	3.41
1761	1871	3.057174	GGATCAGTATAGCCGGTTCAGAG	60.057	52.174	1.90	0.00	0.00	3.35
1795	1910	9.349713	AGTGTCAATTAATCCTTTGTTTGTAGA	57.650	29.630	0.00	0.00	0.00	2.59
1796	1911	9.612620	GTGTCAATTAATCCTTTGTTTGTAGAG	57.387	33.333	0.00	0.00	0.00	2.43
1798	1946	9.827411	GTCAATTAATCCTTTGTTTGTAGAGTC	57.173	33.333	0.00	0.00	0.00	3.36
1807	1957	8.644216	TCCTTTGTTTGTAGAGTCATACTTGTA	58.356	33.333	0.00	0.00	0.00	2.41
1895	2363	3.096852	ACAGTAACATCGATCCCTGTGA	58.903	45.455	12.44	0.00	32.32	3.58
1936	2411	5.978919	CGCACGTAGGGTAATAAAAGATACA	59.021	40.000	0.00	0.00	0.00	2.29
1937	2412	6.143438	CGCACGTAGGGTAATAAAAGATACAG	59.857	42.308	0.00	0.00	0.00	2.74
1940	2415	9.455847	CACGTAGGGTAATAAAAGATACAGTAC	57.544	37.037	0.00	0.00	0.00	2.73
1973	2448	5.825593	TCACTCTGGTTTCTTGGAGTATT	57.174	39.130	0.00	0.00	36.99	1.89
1985	2460	3.945981	TGGAGTATTTGTGCACGAGTA	57.054	42.857	13.13	8.89	0.00	2.59
2012	2489	9.878599	CGTATTCTTTCAACTACAAAATGAACT	57.121	29.630	0.00	0.00	33.13	3.01
2023	2500	8.130307	ACTACAAAATGAACTTCAAAATGTGC	57.870	30.769	13.09	0.00	0.00	4.57
2025	2502	6.774084	ACAAAATGAACTTCAAAATGTGCAC	58.226	32.000	10.75	10.75	0.00	4.57
2027	2504	6.833342	AAATGAACTTCAAAATGTGCACTC	57.167	33.333	19.41	3.39	0.00	3.51
2028	2505	5.779529	ATGAACTTCAAAATGTGCACTCT	57.220	34.783	19.41	2.18	0.00	3.24
2029	2506	4.923893	TGAACTTCAAAATGTGCACTCTG	58.076	39.130	19.41	9.73	0.00	3.35
2030	2507	3.996150	ACTTCAAAATGTGCACTCTGG	57.004	42.857	19.41	4.16	0.00	3.86
2032	2509	3.701040	ACTTCAAAATGTGCACTCTGGTT	59.299	39.130	19.41	2.34	0.00	3.67
2034	2511	4.044336	TCAAAATGTGCACTCTGGTTTG	57.956	40.909	19.41	18.14	0.00	2.93
2035	2512	2.514205	AAATGTGCACTCTGGTTTGC	57.486	45.000	19.41	0.00	39.33	3.68
2036	2513	0.311790	AATGTGCACTCTGGTTTGCG	59.688	50.000	19.41	0.00	41.96	4.85
2049	2940	0.802494	GTTTGCGTATGTGGAGGTGG	59.198	55.000	0.00	0.00	0.00	4.61
2056	2947	1.486726	GTATGTGGAGGTGGAGAAGGG	59.513	57.143	0.00	0.00	0.00	3.95
2057	2948	0.119155	ATGTGGAGGTGGAGAAGGGA	59.881	55.000	0.00	0.00	0.00	4.20
2059	2950	0.252284	GTGGAGGTGGAGAAGGGAGA	60.252	60.000	0.00	0.00	0.00	3.71
2060	2951	0.719015	TGGAGGTGGAGAAGGGAGAT	59.281	55.000	0.00	0.00	0.00	2.75
2061	2952	1.127343	GGAGGTGGAGAAGGGAGATG	58.873	60.000	0.00	0.00	0.00	2.90
2062	2953	1.127343	GAGGTGGAGAAGGGAGATGG	58.873	60.000	0.00	0.00	0.00	3.51
2064	2955	0.326618	GGTGGAGAAGGGAGATGGGA	60.327	60.000	0.00	0.00	0.00	4.37
2066	2957	1.488393	GTGGAGAAGGGAGATGGGAAG	59.512	57.143	0.00	0.00	0.00	3.46
2068	2959	1.344496	GGAGAAGGGAGATGGGAAGGA	60.344	57.143	0.00	0.00	0.00	3.36
2069	2960	2.046292	GAGAAGGGAGATGGGAAGGAG	58.954	57.143	0.00	0.00	0.00	3.69
2070	2961	1.135960	GAAGGGAGATGGGAAGGAGG	58.864	60.000	0.00	0.00	0.00	4.30
2071	2962	0.990818	AAGGGAGATGGGAAGGAGGC	60.991	60.000	0.00	0.00	0.00	4.70
2072	2963	2.456443	GGGAGATGGGAAGGAGGCC	61.456	68.421	0.00	0.00	0.00	5.19
2081	2972	1.216710	GAAGGAGGCCGTCTGTGAG	59.783	63.158	0.00	0.00	0.00	3.51
2103	2994	1.982938	GTACCTCCCGGCTCACAGT	60.983	63.158	0.00	0.00	0.00	3.55
2104	2995	1.681327	TACCTCCCGGCTCACAGTC	60.681	63.158	0.00	0.00	0.00	3.51
2105	2996	2.435120	TACCTCCCGGCTCACAGTCA	62.435	60.000	0.00	0.00	0.00	3.41
2106	2997	2.262915	CTCCCGGCTCACAGTCAC	59.737	66.667	0.00	0.00	0.00	3.67
2107	2998	3.302347	CTCCCGGCTCACAGTCACC	62.302	68.421	0.00	0.00	0.00	4.02
2108	2999	4.742201	CCCGGCTCACAGTCACCG	62.742	72.222	0.00	0.00	45.21	4.94
2113	3004	4.363990	CTCACAGTCACCGCGGCT	62.364	66.667	28.58	12.20	0.00	5.52
2256	3150	3.252484	GGCGCGCTTAATCGTCGT	61.252	61.111	32.29	0.00	33.80	4.34
2261	3155	0.524816	GCGCTTAATCGTCGTCCTCA	60.525	55.000	0.00	0.00	0.00	3.86
2275	3169	2.096248	GTCCTCACCGTCATCTTCTCT	58.904	52.381	0.00	0.00	0.00	3.10
2276	3170	2.098443	GTCCTCACCGTCATCTTCTCTC	59.902	54.545	0.00	0.00	0.00	3.20
2277	3171	2.095461	CCTCACCGTCATCTTCTCTCA	58.905	52.381	0.00	0.00	0.00	3.27
2278	3172	2.098934	CCTCACCGTCATCTTCTCTCAG	59.901	54.545	0.00	0.00	0.00	3.35
2279	3173	2.752354	CTCACCGTCATCTTCTCTCAGT	59.248	50.000	0.00	0.00	0.00	3.41
2280	3174	3.157881	TCACCGTCATCTTCTCTCAGTT	58.842	45.455	0.00	0.00	0.00	3.16
2281	3175	3.191581	TCACCGTCATCTTCTCTCAGTTC	59.808	47.826	0.00	0.00	0.00	3.01
2282	3176	3.192422	CACCGTCATCTTCTCTCAGTTCT	59.808	47.826	0.00	0.00	0.00	3.01
2283	3177	3.442273	ACCGTCATCTTCTCTCAGTTCTC	59.558	47.826	0.00	0.00	0.00	2.87
2284	3178	3.694072	CCGTCATCTTCTCTCAGTTCTCT	59.306	47.826	0.00	0.00	0.00	3.10
2294	3188	0.827925	TCAGTTCTCTGCCTCCGTGT	60.828	55.000	0.00	0.00	41.10	4.49
2296	3190	1.115930	AGTTCTCTGCCTCCGTGTGT	61.116	55.000	0.00	0.00	0.00	3.72
2324	3218	1.446272	CGACAAGCTCCGGTTCTCC	60.446	63.158	0.00	0.00	0.00	3.71
2328	3222	0.321671	CAAGCTCCGGTTCTCCTTCA	59.678	55.000	0.00	0.00	0.00	3.02
2329	3223	1.065854	CAAGCTCCGGTTCTCCTTCAT	60.066	52.381	0.00	0.00	0.00	2.57
2330	3224	0.827368	AGCTCCGGTTCTCCTTCATC	59.173	55.000	0.00	0.00	0.00	2.92
2331	3225	0.827368	GCTCCGGTTCTCCTTCATCT	59.173	55.000	0.00	0.00	0.00	2.90
2332	3226	1.208293	GCTCCGGTTCTCCTTCATCTT	59.792	52.381	0.00	0.00	0.00	2.40
2333	3227	2.740256	GCTCCGGTTCTCCTTCATCTTC	60.740	54.545	0.00	0.00	0.00	2.87
2334	3228	1.476891	TCCGGTTCTCCTTCATCTTCG	59.523	52.381	0.00	0.00	0.00	3.79
2335	3229	1.476891	CCGGTTCTCCTTCATCTTCGA	59.523	52.381	0.00	0.00	0.00	3.71
2336	3230	2.531206	CGGTTCTCCTTCATCTTCGAC	58.469	52.381	0.00	0.00	0.00	4.20
2337	3231	2.094700	CGGTTCTCCTTCATCTTCGACA	60.095	50.000	0.00	0.00	0.00	4.35
2338	3232	3.614150	CGGTTCTCCTTCATCTTCGACAA	60.614	47.826	0.00	0.00	0.00	3.18
2339	3233	3.929610	GGTTCTCCTTCATCTTCGACAAG	59.070	47.826	0.00	0.00	0.00	3.16
2340	3234	3.238108	TCTCCTTCATCTTCGACAAGC	57.762	47.619	0.00	0.00	0.00	4.01
2341	3235	2.828520	TCTCCTTCATCTTCGACAAGCT	59.171	45.455	0.00	0.00	0.00	3.74
2342	3236	3.119316	TCTCCTTCATCTTCGACAAGCTC	60.119	47.826	0.00	0.00	0.00	4.09
2343	3237	2.093973	TCCTTCATCTTCGACAAGCTCC	60.094	50.000	0.00	0.00	0.00	4.70
2344	3238	1.923204	CTTCATCTTCGACAAGCTCCG	59.077	52.381	0.00	0.00	0.00	4.63
2345	3239	0.173481	TCATCTTCGACAAGCTCCGG	59.827	55.000	0.00	0.00	0.00	5.14
2346	3240	0.108615	CATCTTCGACAAGCTCCGGT	60.109	55.000	0.00	0.00	0.00	5.28
2347	3241	0.608640	ATCTTCGACAAGCTCCGGTT	59.391	50.000	0.00	0.00	0.00	4.44
2348	3242	0.038526	TCTTCGACAAGCTCCGGTTC	60.039	55.000	0.00	0.00	0.00	3.62
2349	3243	0.038159	CTTCGACAAGCTCCGGTTCT	60.038	55.000	0.00	0.00	0.00	3.01
2350	3244	0.038526	TTCGACAAGCTCCGGTTCTC	60.039	55.000	0.00	0.00	0.00	2.87
2351	3245	1.446272	CGACAAGCTCCGGTTCTCC	60.446	63.158	0.00	0.00	0.00	3.71
2352	3246	1.878656	CGACAAGCTCCGGTTCTCCT	61.879	60.000	0.00	0.00	0.00	3.69
2353	3247	0.321996	GACAAGCTCCGGTTCTCCTT	59.678	55.000	0.00	0.00	0.00	3.36
2354	3248	0.321996	ACAAGCTCCGGTTCTCCTTC	59.678	55.000	0.00	0.00	0.00	3.46
2355	3249	0.321671	CAAGCTCCGGTTCTCCTTCA	59.678	55.000	0.00	0.00	0.00	3.02
2443	3358	2.646719	CGTCGTCCGTTCTTCCCA	59.353	61.111	0.00	0.00	0.00	4.37
2444	3359	1.007038	CGTCGTCCGTTCTTCCCAA	60.007	57.895	0.00	0.00	0.00	4.12

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
500	507	1.862138	TCTCCCACTCTCCTCCCCA	60.862	63.158	0.00	0.00	0.00	4.96
738	749	1.228124	GCCACACCCTACTGTGCAA	60.228	57.895	0.00	0.00	40.33	4.08
766	777	1.512156	CCTTTTTGTGTAGCGCCCGT	61.512	55.000	2.29	0.00	0.00	5.28
869	880	1.407437	CCCTCTAATGCTGCCGAGTTT	60.407	52.381	0.00	0.00	0.00	2.66
881	892	1.064463	TGTACGGACGGACCCTCTAAT	60.064	52.381	4.42	0.00	34.64	1.73
884	895	0.750911	GATGTACGGACGGACCCTCT	60.751	60.000	4.42	0.00	34.64	3.69
885	896	1.732308	GATGTACGGACGGACCCTC	59.268	63.158	4.42	0.00	34.64	4.30
954	965	1.740025	GAAGAAGGCTTAATGCACGCT	59.260	47.619	0.00	0.00	45.15	5.07
985	996	1.806542	AGCCATGTTGTTCTTGCGTAG	59.193	47.619	0.00	0.00	0.00	3.51
1049	1060	0.598065	AAACGGAATCCTGCAACAGC	59.402	50.000	0.00	0.00	0.00	4.40
1054	1065	2.976840	GCGCAAACGGAATCCTGCA	61.977	57.895	0.30	0.00	40.57	4.41
1077	1088	1.071471	CAACGAGGTGAAGCTGGGT	59.929	57.895	0.00	0.00	0.00	4.51
1433	1448	2.250031	TGATTTCCTGTTGCATTGCCT	58.750	42.857	6.12	0.00	0.00	4.75
1435	1450	3.676646	GTCTTGATTTCCTGTTGCATTGC	59.323	43.478	0.46	0.46	0.00	3.56
1437	1452	5.048224	CAGAGTCTTGATTTCCTGTTGCATT	60.048	40.000	0.00	0.00	0.00	3.56
1659	1679	0.839946	ACGCCCATCTTGGAAGCTAT	59.160	50.000	0.00	0.00	40.96	2.97
1725	1750	2.208431	CTGATCCATCTTGACGAAGCC	58.792	52.381	0.00	0.00	0.00	4.35
1734	1807	3.511477	ACCGGCTATACTGATCCATCTT	58.489	45.455	0.00	0.00	0.00	2.40
1744	1817	1.217183	TCCCTCTGAACCGGCTATACT	59.783	52.381	0.00	0.00	0.00	2.12
1746	1823	2.632996	CAATCCCTCTGAACCGGCTATA	59.367	50.000	0.00	0.00	0.00	1.31
1761	1871	7.881775	AAGGATTAATTGACACTACAATCCC	57.118	36.000	12.11	0.00	41.46	3.85
1795	1910	8.461249	ACGAGGTAATACATACAAGTATGACT	57.539	34.615	23.02	12.07	44.22	3.41
1796	1911	9.823098	CTACGAGGTAATACATACAAGTATGAC	57.177	37.037	23.02	12.34	44.22	3.06
1800	1948	8.978539	CGTACTACGAGGTAATACATACAAGTA	58.021	37.037	2.17	0.00	46.05	2.24
1895	2363	2.665777	CGCATAGCACAACGTAGCT	58.334	52.632	13.50	13.50	44.55	3.32
1985	2460	9.659830	GTTCATTTTGTAGTTGAAAGAATACGT	57.340	29.630	0.00	0.00	31.66	3.57
2001	2478	6.594937	AGTGCACATTTTGAAGTTCATTTTGT	59.405	30.769	21.04	7.69	0.00	2.83
2009	2486	3.701040	ACCAGAGTGCACATTTTGAAGTT	59.299	39.130	21.04	0.00	0.00	2.66
2012	2489	4.431809	CAAACCAGAGTGCACATTTTGAA	58.568	39.130	21.04	0.00	0.00	2.69
2023	2500	1.464608	CCACATACGCAAACCAGAGTG	59.535	52.381	0.00	0.00	0.00	3.51
2025	2502	2.002586	CTCCACATACGCAAACCAGAG	58.997	52.381	0.00	0.00	0.00	3.35
2027	2504	1.086696	CCTCCACATACGCAAACCAG	58.913	55.000	0.00	0.00	0.00	4.00
2028	2505	0.398696	ACCTCCACATACGCAAACCA	59.601	50.000	0.00	0.00	0.00	3.67
2029	2506	0.802494	CACCTCCACATACGCAAACC	59.198	55.000	0.00	0.00	0.00	3.27
2030	2507	0.802494	CCACCTCCACATACGCAAAC	59.198	55.000	0.00	0.00	0.00	2.93
2032	2509	0.249120	CTCCACCTCCACATACGCAA	59.751	55.000	0.00	0.00	0.00	4.85
2034	2511	0.535335	TTCTCCACCTCCACATACGC	59.465	55.000	0.00	0.00	0.00	4.42
2035	2512	1.137086	CCTTCTCCACCTCCACATACG	59.863	57.143	0.00	0.00	0.00	3.06
2036	2513	1.486726	CCCTTCTCCACCTCCACATAC	59.513	57.143	0.00	0.00	0.00	2.39
2049	2940	2.046292	CTCCTTCCCATCTCCCTTCTC	58.954	57.143	0.00	0.00	0.00	2.87
2056	2947	2.034048	GACGGCCTCCTTCCCATCTC	62.034	65.000	0.00	0.00	0.00	2.75
2057	2948	2.041265	ACGGCCTCCTTCCCATCT	59.959	61.111	0.00	0.00	0.00	2.90
2059	2950	2.041265	AGACGGCCTCCTTCCCAT	59.959	61.111	0.00	0.00	0.00	4.00
2060	2951	3.003173	CAGACGGCCTCCTTCCCA	61.003	66.667	0.00	0.00	0.00	4.37
2061	2952	3.003763	ACAGACGGCCTCCTTCCC	61.004	66.667	0.00	0.00	0.00	3.97
2062	2953	2.232298	CTCACAGACGGCCTCCTTCC	62.232	65.000	0.00	0.00	0.00	3.46
2064	2955	2.948720	GCTCACAGACGGCCTCCTT	61.949	63.158	0.00	0.00	0.00	3.36
2066	2957	4.459089	GGCTCACAGACGGCCTCC	62.459	72.222	0.00	0.00	42.31	4.30
2070	2961	3.755628	TACGGGCTCACAGACGGC	61.756	66.667	0.00	0.00	0.00	5.68
2071	2962	2.181021	GTACGGGCTCACAGACGG	59.819	66.667	0.00	0.00	0.00	4.79
2072	2963	2.181021	GGTACGGGCTCACAGACG	59.819	66.667	0.00	0.00	0.00	4.18
2136	3027	2.675056	CGAGGACGAAGGACGACGT	61.675	63.158	0.00	0.00	45.77	4.34
2139	3030	2.330372	CCACGAGGACGAAGGACGA	61.330	63.158	0.00	0.00	45.65	4.20
2180	3072	2.060383	AGAGCGCTAGGACATGGCA	61.060	57.895	11.50	0.00	34.43	4.92
2256	3150	2.290960	TGAGAGAAGATGACGGTGAGGA	60.291	50.000	0.00	0.00	0.00	3.71
2261	3155	3.426615	AGAACTGAGAGAAGATGACGGT	58.573	45.455	0.00	0.00	0.00	4.83
2275	3169	0.827925	ACACGGAGGCAGAGAACTGA	60.828	55.000	0.00	0.00	46.03	3.41
2276	3170	0.668706	CACACGGAGGCAGAGAACTG	60.669	60.000	0.00	0.00	45.91	3.16
2277	3171	1.115930	ACACACGGAGGCAGAGAACT	61.116	55.000	0.00	0.00	0.00	3.01
2278	3172	0.249911	AACACACGGAGGCAGAGAAC	60.250	55.000	0.00	0.00	0.00	3.01
2279	3173	0.033504	GAACACACGGAGGCAGAGAA	59.966	55.000	0.00	0.00	0.00	2.87
2280	3174	0.827925	AGAACACACGGAGGCAGAGA	60.828	55.000	0.00	0.00	0.00	3.10
2281	3175	0.389166	GAGAACACACGGAGGCAGAG	60.389	60.000	0.00	0.00	0.00	3.35
2282	3176	1.666011	GAGAACACACGGAGGCAGA	59.334	57.895	0.00	0.00	0.00	4.26
2283	3177	1.374758	GGAGAACACACGGAGGCAG	60.375	63.158	0.00	0.00	0.00	4.85
2284	3178	1.816863	GAGGAGAACACACGGAGGCA	61.817	60.000	0.00	0.00	0.00	4.75
2294	3188	1.964223	AGCTTGTCGAAGAGGAGAACA	59.036	47.619	0.00	0.00	36.95	3.18
2296	3190	1.546476	GGAGCTTGTCGAAGAGGAGAA	59.454	52.381	0.00	0.00	36.95	2.87
2324	3218	1.923204	CGGAGCTTGTCGAAGATGAAG	59.077	52.381	0.00	0.00	40.67	3.02
2328	3222	0.608640	AACCGGAGCTTGTCGAAGAT	59.391	50.000	9.46	0.00	40.67	2.40
2329	3223	0.038526	GAACCGGAGCTTGTCGAAGA	60.039	55.000	9.46	0.00	0.00	2.87
2330	3224	0.038159	AGAACCGGAGCTTGTCGAAG	60.038	55.000	9.46	0.00	0.00	3.79
2331	3225	0.038526	GAGAACCGGAGCTTGTCGAA	60.039	55.000	9.46	0.00	0.00	3.71
2332	3226	1.585006	GAGAACCGGAGCTTGTCGA	59.415	57.895	9.46	0.00	0.00	4.20
2333	3227	1.446272	GGAGAACCGGAGCTTGTCG	60.446	63.158	9.46	0.00	0.00	4.35
2334	3228	0.321996	AAGGAGAACCGGAGCTTGTC	59.678	55.000	9.46	0.00	41.83	3.18
2335	3229	0.321996	GAAGGAGAACCGGAGCTTGT	59.678	55.000	9.46	0.00	41.83	3.16
2336	3230	0.321671	TGAAGGAGAACCGGAGCTTG	59.678	55.000	9.46	0.00	41.83	4.01
2337	3231	1.208293	GATGAAGGAGAACCGGAGCTT	59.792	52.381	9.46	0.00	41.83	3.74
2338	3232	0.827368	GATGAAGGAGAACCGGAGCT	59.173	55.000	9.46	4.04	41.83	4.09
2339	3233	0.827368	AGATGAAGGAGAACCGGAGC	59.173	55.000	9.46	0.00	41.83	4.70
2340	3234	2.480416	CGAAGATGAAGGAGAACCGGAG	60.480	54.545	9.46	0.00	41.83	4.63
2341	3235	1.476891	CGAAGATGAAGGAGAACCGGA	59.523	52.381	9.46	0.00	41.83	5.14
2342	3236	1.476891	TCGAAGATGAAGGAGAACCGG	59.523	52.381	0.00	0.00	41.83	5.28
2343	3237	2.094700	TGTCGAAGATGAAGGAGAACCG	60.095	50.000	0.00	0.00	40.67	4.44
2344	3238	3.594603	TGTCGAAGATGAAGGAGAACC	57.405	47.619	0.00	0.00	40.67	3.62
2345	3239	3.369451	GCTTGTCGAAGATGAAGGAGAAC	59.631	47.826	0.00	0.00	40.67	3.01
2346	3240	3.259374	AGCTTGTCGAAGATGAAGGAGAA	59.741	43.478	0.00	0.00	40.67	2.87
2347	3241	2.828520	AGCTTGTCGAAGATGAAGGAGA	59.171	45.455	0.00	0.00	40.67	3.71
2348	3242	3.186119	GAGCTTGTCGAAGATGAAGGAG	58.814	50.000	0.00	0.00	40.67	3.69
2349	3243	2.093973	GGAGCTTGTCGAAGATGAAGGA	60.094	50.000	0.00	0.00	40.67	3.36
2350	3244	2.275318	GGAGCTTGTCGAAGATGAAGG	58.725	52.381	0.00	0.00	40.67	3.46
2351	3245	1.923204	CGGAGCTTGTCGAAGATGAAG	59.077	52.381	0.00	0.00	40.67	3.02
2352	3246	1.404181	CCGGAGCTTGTCGAAGATGAA	60.404	52.381	0.00	0.00	40.67	2.57
2353	3247	0.173481	CCGGAGCTTGTCGAAGATGA	59.827	55.000	0.00	0.00	40.67	2.92
2354	3248	0.108615	ACCGGAGCTTGTCGAAGATG	60.109	55.000	9.46	0.00	40.67	2.90
2355	3249	0.608640	AACCGGAGCTTGTCGAAGAT	59.391	50.000	9.46	0.00	40.67	2.40
2516	3466	2.186384	CGAGAGGAAGCTGCAGGG	59.814	66.667	17.12	0.00	0.00	4.45

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.