AutoCloner

Multiple sequence alignment - TraesCS2A01G121800

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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	TraesCS2A01G121800	chr2A	100.000	3126	0	0	1	3126	71436914	71433789	0.000000e+00	5773.0
1	TraesCS2A01G121800	chr2A	89.318	777	76	6	1320	2090	71587239	71588014	0.000000e+00	968.0
2	TraesCS2A01G121800	chr2A	78.903	237	45	5	2271	2505	465330502	465330735	4.170000e-34	156.0
3	TraesCS2A01G121800	chr2A	89.552	67	5	1	252	316	676345915	676345981	2.000000e-12	84.2
4	TraesCS2A01G121800	chr2A	92.000	50	3	1	2826	2875	5675863	5675815	5.590000e-08	69.4
5	TraesCS2A01G121800	chr2A	82.895	76	12	1	2826	2901	62721333	62721259	2.010000e-07	67.6
6	TraesCS2A01G121800	chr2D	89.525	1852	121	41	467	2268	72595622	72593794	0.000000e+00	2278.0
7	TraesCS2A01G121800	chr2D	90.201	1643	108	24	1	1627	72772933	72771328	0.000000e+00	2093.0
8	TraesCS2A01G121800	chr2D	91.050	838	71	2	1304	2137	23168285	23167448	0.000000e+00	1129.0
9	TraesCS2A01G121800	chr2D	89.704	777	74	5	1320	2090	72998927	72999703	0.000000e+00	987.0
10	TraesCS2A01G121800	chr2D	85.111	853	102	14	2275	3117	72770986	72770149	0.000000e+00	848.0
11	TraesCS2A01G121800	chr2D	86.122	735	73	18	2387	3114	72575558	72574846	0.000000e+00	765.0
12	TraesCS2A01G121800	chr2D	87.854	601	51	11	530	1118	593841049	593841639	0.000000e+00	686.0
13	TraesCS2A01G121800	chr2D	89.053	338	33	4	2787	3124	72905245	72905578	1.730000e-112	416.0
14	TraesCS2A01G121800	chr2D	87.215	219	16	8	387	593	72595875	72595657	4.030000e-59	239.0
15	TraesCS2A01G121800	chr2D	88.535	157	15	2	4	159	72605593	72605439	1.480000e-43	187.0
16	TraesCS2A01G121800	chr2D	80.932	236	41	4	2272	2505	349584538	349584771	1.910000e-42	183.0
17	TraesCS2A01G121800	chr2D	96.875	32	0	1	312	342	489135725	489135694	6.000000e-03	52.8
18	TraesCS2A01G121800	chr2B	89.436	1827	105	39	387	2149	110044934	110043132	0.000000e+00	2224.0
19	TraesCS2A01G121800	chr2B	89.341	1154	50	24	1024	2136	109963784	109964905	0.000000e+00	1382.0
20	TraesCS2A01G121800	chr2B	89.447	777	76	5	1320	2090	110370935	110371711	0.000000e+00	976.0
21	TraesCS2A01G121800	chr2B	88.803	777	81	5	1320	2090	110406395	110407171	0.000000e+00	948.0
22	TraesCS2A01G121800	chr2B	82.939	973	115	32	2188	3117	110043057	110042093	0.000000e+00	830.0
23	TraesCS2A01G121800	chr2B	83.471	605	58	17	382	956	109955698	109956290	2.760000e-145	525.0
24	TraesCS2A01G121800	chr2B	80.759	369	40	20	3	341	109955328	109955695	3.090000e-65	259.0
25	TraesCS2A01G121800	chr2B	88.785	107	10	2	111	216	110045101	110044996	2.530000e-26	130.0
26	TraesCS2A01G121800	chr2B	90.909	66	4	1	253	316	774662042	774661977	1.540000e-13	87.9
27	TraesCS2A01G121800	chrUn	87.891	1916	146	31	404	2268	287774513	287772633	0.000000e+00	2174.0
28	TraesCS2A01G121800	chrUn	87.891	1916	146	31	404	2268	297963638	297961758	0.000000e+00	2174.0
29	TraesCS2A01G121800	chrUn	86.017	236	24	5	1983	2218	262808615	262808389	8.660000e-61	244.0
30	TraesCS2A01G121800	chr3B	80.667	300	45	10	2806	3102	155630922	155631211	1.460000e-53	220.0
31	TraesCS2A01G121800	chr3B	83.117	231	36	3	2272	2501	821290057	821289829	1.140000e-49	207.0
32	TraesCS2A01G121800	chr7A	86.391	169	21	2	2339	2506	112456325	112456492	1.910000e-42	183.0
33	TraesCS2A01G121800	chr7A	100.000	32	0	0	377	408	664381514	664381483	3.370000e-05	60.2
34	TraesCS2A01G121800	chr5A	86.310	168	21	2	2339	2505	632587530	632587696	6.890000e-42	182.0
35	TraesCS2A01G121800	chr1B	80.851	235	39	5	2269	2501	105201157	105201387	2.480000e-41	180.0
36	TraesCS2A01G121800	chr3D	82.412	199	28	6	2254	2448	374056977	374056782	1.930000e-37	167.0
37	TraesCS2A01G121800	chr3D	78.862	246	41	9	2265	2508	299071213	299071449	4.170000e-34	156.0
38	TraesCS2A01G121800	chr3D	100.000	29	0	0	312	340	409967705	409967733	2.000000e-03	54.7
39	TraesCS2A01G121800	chr6D	91.250	80	5	2	154	231	161977765	161977844	1.190000e-19	108.0
40	TraesCS2A01G121800	chr6B	91.250	80	2	3	154	231	300718152	300718076	1.530000e-18	104.0
41	TraesCS2A01G121800	chr6A	91.250	80	2	3	154	231	221350789	221350865	1.530000e-18	104.0
42	TraesCS2A01G121800	chr1A	91.045	67	4	1	252	316	320485674	320485608	4.290000e-14	89.8
43	TraesCS2A01G121800	chr1A	89.552	67	5	1	252	316	95850276	95850342	2.000000e-12	84.2
44	TraesCS2A01G121800	chr1A	89.552	67	5	1	252	316	551582343	551582277	2.000000e-12	84.2
45	TraesCS2A01G121800	chr1A	96.875	32	1	0	310	341	560915927	560915958	2.000000e-03	54.7
46	TraesCS2A01G121800	chr1A	100.000	28	0	0	382	409	15915190	15915163	6.000000e-03	52.8
47	TraesCS2A01G121800	chr7B	89.855	69	5	1	252	318	27975322	27975254	1.540000e-13	87.9
48	TraesCS2A01G121800	chr5D	86.301	73	8	1	253	323	453251764	453251836	9.290000e-11	78.7
49	TraesCS2A01G121800	chr5D	100.000	28	0	0	382	409	240087317	240087290	6.000000e-03	52.8
50	TraesCS2A01G121800	chr5D	100.000	28	0	0	385	412	486191658	486191631	6.000000e-03	52.8
51	TraesCS2A01G121800	chr4A	81.250	96	10	7	311	406	742971742	742971829	1.560000e-08	71.3
52	TraesCS2A01G121800	chr3A	91.489	47	4	0	366	412	374427593	374427639	7.240000e-07	65.8
53	TraesCS2A01G121800	chr7D	77.670	103	19	4	308	407	78421670	78421569	3.370000e-05	60.2
54	TraesCS2A01G121800	chr4B	94.595	37	2	0	371	407	427496663	427496699	1.210000e-04	58.4
55	TraesCS2A01G121800	chr4D	96.875	32	1	0	309	340	460951842	460951811	2.000000e-03	54.7
56	TraesCS2A01G121800	chr4D	96.970	33	0	1	308	340	472492639	472492608	2.000000e-03	54.7

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	TraesCS2A01G121800	chr2A	71433789	71436914	3125	True	5773.000000	5773	100.000000	1	3126	1	chr2A.!!$R3	3125
1	TraesCS2A01G121800	chr2A	71587239	71588014	775	False	968.000000	968	89.318000	1320	2090	1	chr2A.!!$F1	770
2	TraesCS2A01G121800	chr2D	72770149	72772933	2784	True	1470.500000	2093	87.656000	1	3117	2	chr2D.!!$R6	3116
3	TraesCS2A01G121800	chr2D	72593794	72595875	2081	True	1258.500000	2278	88.370000	387	2268	2	chr2D.!!$R5	1881
4	TraesCS2A01G121800	chr2D	23167448	23168285	837	True	1129.000000	1129	91.050000	1304	2137	1	chr2D.!!$R1	833
5	TraesCS2A01G121800	chr2D	72998927	72999703	776	False	987.000000	987	89.704000	1320	2090	1	chr2D.!!$F2	770
6	TraesCS2A01G121800	chr2D	72574846	72575558	712	True	765.000000	765	86.122000	2387	3114	1	chr2D.!!$R2	727
7	TraesCS2A01G121800	chr2D	593841049	593841639	590	False	686.000000	686	87.854000	530	1118	1	chr2D.!!$F4	588
8	TraesCS2A01G121800	chr2B	109963784	109964905	1121	False	1382.000000	1382	89.341000	1024	2136	1	chr2B.!!$F1	1112
9	TraesCS2A01G121800	chr2B	110042093	110045101	3008	True	1061.333333	2224	87.053333	111	3117	3	chr2B.!!$R2	3006
10	TraesCS2A01G121800	chr2B	110370935	110371711	776	False	976.000000	976	89.447000	1320	2090	1	chr2B.!!$F2	770
11	TraesCS2A01G121800	chr2B	110406395	110407171	776	False	948.000000	948	88.803000	1320	2090	1	chr2B.!!$F3	770
12	TraesCS2A01G121800	chr2B	109955328	109956290	962	False	392.000000	525	82.115000	3	956	2	chr2B.!!$F4	953
13	TraesCS2A01G121800	chrUn	287772633	287774513	1880	True	2174.000000	2174	87.891000	404	2268	1	chrUn.!!$R2	1864
14	TraesCS2A01G121800	chrUn	297961758	297963638	1880	True	2174.000000	2174	87.891000	404	2268	1	chrUn.!!$R3	1864

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
83	86	0.466189	CCTCCCACCCCATTCAATCG	60.466	60.000	0.00	0.00	0.0	3.34	F
829	1085	1.134995	AGATGCGCTGAAGATTCGTCA	60.135	47.619	9.73	2.32	0.0	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1552	1875	0.320771	GGTTGTGCAGGATGTCGAGT	60.321	55.0	0.0	0.0	39.31	4.18	R
2517	3150	0.235665	GGACAACACACATGCACTCG	59.764	55.0	0.0	0.0	0.00	4.18	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
63	66	3.368248	CTGATTTTCATGGGTGTGGGAT	58.632	45.455	0.00	0.00	0.00	3.85
83	86	0.466189	CCTCCCACCCCATTCAATCG	60.466	60.000	0.00	0.00	0.00	3.34
92	95	3.030291	CCCCATTCAATCGAATCCCAAA	58.970	45.455	0.00	0.00	39.96	3.28
96	99	5.069516	CCCATTCAATCGAATCCCAAATCTT	59.930	40.000	0.00	0.00	39.96	2.40
99	102	6.441093	TTCAATCGAATCCCAAATCTTCAG	57.559	37.500	0.00	0.00	0.00	3.02
100	103	5.500234	TCAATCGAATCCCAAATCTTCAGT	58.500	37.500	0.00	0.00	0.00	3.41
203	255	2.912771	TGTCGTGCTTTTCTTTCTCCA	58.087	42.857	0.00	0.00	0.00	3.86
204	256	3.275143	TGTCGTGCTTTTCTTTCTCCAA	58.725	40.909	0.00	0.00	0.00	3.53
324	378	7.390013	TCTAAGCACTCTTATACTCCCTCTA	57.610	40.000	0.00	0.00	34.54	2.43
369	423	9.716556	AGAGGGAGTATTTCTTTACAGATTAGA	57.283	33.333	0.00	0.00	0.00	2.10
648	887	1.462616	TGGATTTCCAATCAGCACCG	58.537	50.000	0.00	0.00	44.35	4.94
704	952	5.079643	AGTTGCACTACTTTTTCCCATCAT	58.920	37.500	0.00	0.00	0.00	2.45
717	969	9.745880	CTTTTTCCCATCATAGATCAAATCTTG	57.254	33.333	0.00	0.00	40.76	3.02
724	976	6.949352	TCATAGATCAAATCTTGGCTTTCC	57.051	37.500	0.00	0.00	40.76	3.13
827	1083	2.015736	AAGATGCGCTGAAGATTCGT	57.984	45.000	9.73	0.00	0.00	3.85
829	1085	1.134995	AGATGCGCTGAAGATTCGTCA	60.135	47.619	9.73	2.32	0.00	4.35
830	1086	1.863454	GATGCGCTGAAGATTCGTCAT	59.137	47.619	9.73	0.00	0.00	3.06
831	1087	2.577449	TGCGCTGAAGATTCGTCATA	57.423	45.000	9.73	0.00	0.00	2.15
832	1088	2.887337	TGCGCTGAAGATTCGTCATAA	58.113	42.857	9.73	0.00	0.00	1.90
833	1089	3.457234	TGCGCTGAAGATTCGTCATAAT	58.543	40.909	9.73	0.00	0.00	1.28
881	1146	5.046529	CAGTCCTCTCCTCGTCATAATTTG	58.953	45.833	0.00	0.00	0.00	2.32
896	1161	9.988350	CGTCATAATTTGAAGCAATTAGTACTT	57.012	29.630	0.00	0.00	35.70	2.24
907	1172	5.047021	AGCAATTAGTACTTCTCTGCTCACA	60.047	40.000	0.00	0.00	34.05	3.58
922	1187	2.545113	GCTCACAACCGTACTGAACTGA	60.545	50.000	0.00	0.00	0.00	3.41
923	1188	3.861131	GCTCACAACCGTACTGAACTGAT	60.861	47.826	0.00	0.00	0.00	2.90
924	1189	4.307432	CTCACAACCGTACTGAACTGATT	58.693	43.478	0.00	0.00	0.00	2.57
925	1190	4.304110	TCACAACCGTACTGAACTGATTC	58.696	43.478	0.00	0.00	35.18	2.52
926	1191	4.055360	CACAACCGTACTGAACTGATTCA	58.945	43.478	0.00	0.00	42.73	2.57
997	1269	7.676338	GCAGAGCTAGCTAGAATAATCTACTCG	60.676	44.444	25.15	13.23	37.10	4.18
1081	1359	2.399916	ACTGAATCTCTGCCTCTTGC	57.600	50.000	0.00	0.00	41.77	4.01
1248	1563	4.320870	TCTTGGTTCTCGTTTGGGTTATC	58.679	43.478	0.00	0.00	0.00	1.75
1282	1597	3.227276	GGCTAGCTAGAGGCCGCA	61.227	66.667	25.15	0.00	43.05	5.69
1283	1598	2.028337	GCTAGCTAGAGGCCGCAC	59.972	66.667	25.15	0.00	43.05	5.34
1284	1599	2.494530	GCTAGCTAGAGGCCGCACT	61.495	63.158	25.15	7.32	43.05	4.40
1285	1600	2.022240	GCTAGCTAGAGGCCGCACTT	62.022	60.000	25.15	0.00	43.05	3.16
1420	1735	1.599047	CGCCAAGGTCATCCTCACT	59.401	57.895	0.00	0.00	44.35	3.41
1426	1741	3.307975	CCAAGGTCATCCTCACTGACATT	60.308	47.826	5.87	2.10	45.45	2.71
1576	1903	1.968017	CATCCTGCACAACCACGCT	60.968	57.895	0.00	0.00	0.00	5.07
1753	2091	4.764771	AGCACGGCGGGGGTACTA	62.765	66.667	12.74	0.00	0.00	1.82
2140	2487	2.043752	TGACAGGCATGGCATGGG	60.044	61.111	27.48	10.10	45.01	4.00
2150	2497	4.984194	GGCATGGGCATGACAGTA	57.016	55.556	0.00	0.00	46.06	2.74
2154	2501	3.221771	GGCATGGGCATGACAGTAATAA	58.778	45.455	0.00	0.00	46.06	1.40
2164	2511	6.939163	GGCATGACAGTAATAAAGATGAGGAT	59.061	38.462	0.00	0.00	0.00	3.24
2186	2537	2.001812	ACATCAAGCGTACTGAGCTG	57.998	50.000	0.00	0.00	45.31	4.24
2222	2620	2.792674	CAGCATGCGCAATAAATTCAGG	59.207	45.455	17.11	0.00	42.27	3.86
2255	2654	1.946984	TCCACCGACTGATTTAGGGT	58.053	50.000	0.00	0.00	0.00	4.34
2264	2663	1.064505	CTGATTTAGGGTGCATGTGCG	59.935	52.381	0.00	0.00	45.83	5.34
2268	2667	0.035534	TTAGGGTGCATGTGCGTGAT	60.036	50.000	0.00	0.00	45.83	3.06
2269	2668	0.744057	TAGGGTGCATGTGCGTGATG	60.744	55.000	0.00	0.00	45.83	3.07
2270	2669	2.334946	GGGTGCATGTGCGTGATGT	61.335	57.895	0.00	0.00	45.83	3.06
2285	2911	5.696270	TGCGTGATGTCACATAGGATAAATC	59.304	40.000	13.07	0.00	46.75	2.17
2299	2925	5.048846	GGATAAATCCTAAGGTGGAGCAA	57.951	43.478	1.52	0.00	43.73	3.91
2300	2926	5.066593	GGATAAATCCTAAGGTGGAGCAAG	58.933	45.833	1.52	0.00	43.73	4.01
2517	3150	5.238583	ACATGCCCTTAGATCTTAATACGC	58.761	41.667	0.00	0.00	0.00	4.42
2519	3152	3.570975	TGCCCTTAGATCTTAATACGCGA	59.429	43.478	15.93	0.00	0.00	5.87
2531	3164	2.280119	ACGCGAGTGCATGTGTGT	60.280	55.556	15.93	0.00	46.97	3.72
2533	3166	1.439201	CGCGAGTGCATGTGTGTTG	60.439	57.895	0.00	0.00	42.97	3.33
2534	3167	1.648720	GCGAGTGCATGTGTGTTGT	59.351	52.632	0.00	0.00	42.15	3.32
2544	3177	0.398696	TGTGTGTTGTCCCGCCTAAT	59.601	50.000	0.00	0.00	0.00	1.73
2554	3187	2.949644	GTCCCGCCTAATACAATTTGCT	59.050	45.455	0.00	0.00	0.00	3.91
2582	3232	2.971307	TCAGCAATGCTACATTCACGA	58.029	42.857	7.70	0.00	36.40	4.35
2600	3252	5.002516	TCACGAAATAACACGGGGTTTTAT	58.997	37.500	0.00	0.00	40.96	1.40
2602	3254	4.099824	CGAAATAACACGGGGTTTTATGC	58.900	43.478	0.00	0.00	40.96	3.14
2650	3302	1.657162	TGGATTAAGGGAGAGGGAGGT	59.343	52.381	0.00	0.00	0.00	3.85
2652	3304	2.629909	GGATTAAGGGAGAGGGAGGTGT	60.630	54.545	0.00	0.00	0.00	4.16
2671	3323	0.546122	TCCCACCCATCTGGAAATCG	59.454	55.000	0.00	0.00	37.39	3.34
2694	3349	4.413851	GGGGGTGAAGAGAATTAGAAGGAT	59.586	45.833	0.00	0.00	0.00	3.24
2701	3356	2.443255	GAGAATTAGAAGGATGGGCCCA	59.557	50.000	30.92	30.92	37.37	5.36
2741	3396	4.751098	AGCATGTGTGTTTAGCATTTTTGG	59.249	37.500	0.00	0.00	0.00	3.28
2742	3397	4.511082	GCATGTGTGTTTAGCATTTTTGGT	59.489	37.500	0.00	0.00	0.00	3.67
2804	3459	6.864342	TGAGAAAAACGTCCAAAATAAACCA	58.136	32.000	0.00	0.00	0.00	3.67
2813	3468	6.086222	CGTCCAAAATAAACCATGAACTCAG	58.914	40.000	0.00	0.00	0.00	3.35
2830	3485	3.764434	ACTCAGAGACGAAGGCTAAATCA	59.236	43.478	3.79	0.00	0.00	2.57
2836	3491	2.415512	GACGAAGGCTAAATCAAACGCT	59.584	45.455	0.00	0.00	0.00	5.07
2852	3507	2.863809	ACGCTGAAGTTTCAATCCCTT	58.136	42.857	0.00	0.00	36.64	3.95
2879	3534	4.020839	TCAGCACATCAAACTCTCTGATCA	60.021	41.667	0.00	0.00	30.99	2.92
2881	3536	5.180680	CAGCACATCAAACTCTCTGATCAAA	59.819	40.000	0.00	0.00	30.99	2.69
2907	3562	2.392933	TTTAAACCTTGAGCGCGTTG	57.607	45.000	8.43	0.00	0.00	4.10
2913	3568	1.082756	CTTGAGCGCGTTGTCAACC	60.083	57.895	8.43	2.58	0.00	3.77
2946	3601	3.120105	CAGGCCGATCTGCGTCTA	58.880	61.111	0.99	0.00	38.67	2.59
2960	3615	1.993370	GCGTCTAAACACGATTGAGCT	59.007	47.619	0.00	0.00	42.69	4.09
3009	3665	8.883789	TTTTCTTTTTAGTAACGTGACACTTG	57.116	30.769	5.68	0.00	0.00	3.16
3109	3771	5.376625	ACTCTTGGTTACAAATGAGAAGCA	58.623	37.500	6.14	0.00	35.89	3.91
3117	3779	6.640907	GGTTACAAATGAGAAGCACGAAAATT	59.359	34.615	0.00	0.00	0.00	1.82
3118	3780	7.358352	GGTTACAAATGAGAAGCACGAAAATTG	60.358	37.037	0.00	0.00	0.00	2.32
3119	3781	5.591099	ACAAATGAGAAGCACGAAAATTGT	58.409	33.333	0.00	0.00	0.00	2.71
3120	3782	6.734137	ACAAATGAGAAGCACGAAAATTGTA	58.266	32.000	0.00	0.00	0.00	2.41
3121	3783	7.199766	ACAAATGAGAAGCACGAAAATTGTAA	58.800	30.769	0.00	0.00	0.00	2.41
3122	3784	7.704472	ACAAATGAGAAGCACGAAAATTGTAAA	59.296	29.630	0.00	0.00	0.00	2.01
3123	3785	7.623268	AATGAGAAGCACGAAAATTGTAAAC	57.377	32.000	0.00	0.00	0.00	2.01
3124	3786	6.125327	TGAGAAGCACGAAAATTGTAAACA	57.875	33.333	0.00	0.00	0.00	2.83
3125	3787	6.198687	TGAGAAGCACGAAAATTGTAAACAG	58.801	36.000	0.00	0.00	0.00	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	7.468768	GCAAGAGAATTAATTAGCCAGGTTACC	60.469	40.741	0.00	0.00	0.00	2.85
63	66	0.926293	GATTGAATGGGGTGGGAGGA	59.074	55.000	0.00	0.00	0.00	3.71
83	86	9.794685	GATAGAAAAACTGAAGATTTGGGATTC	57.205	33.333	0.00	0.00	0.00	2.52
96	99	8.211116	TGGTTTTTACGTGATAGAAAAACTGA	57.789	30.769	24.51	14.92	45.69	3.41
99	102	9.043678	CGTATGGTTTTTACGTGATAGAAAAAC	57.956	33.333	20.44	20.44	45.68	2.43
305	359	8.638629	TCTTTATAGAGGGAGTATAAGAGTGC	57.361	38.462	0.00	0.00	0.00	4.40
409	463	1.553248	TCCCTTCACGACACCCTAATG	59.447	52.381	0.00	0.00	0.00	1.90
412	466	0.113776	ACTCCCTTCACGACACCCTA	59.886	55.000	0.00	0.00	0.00	3.53
556	784	4.170468	AGGTCAGAAACACAGGACATTT	57.830	40.909	0.00	0.00	32.00	2.32
704	952	5.191727	TGGGAAAGCCAAGATTTGATCTA	57.808	39.130	0.00	0.00	39.08	1.98
717	969	1.943340	CTTTCTAGCGATGGGAAAGCC	59.057	52.381	14.52	0.00	39.24	4.35
724	976	4.192317	AGGCTTAAACTTTCTAGCGATGG	58.808	43.478	0.00	0.00	34.50	3.51
794	1050	4.274459	AGCGCATCTTATCTCAATGTTTCC	59.726	41.667	11.47	0.00	0.00	3.13
795	1051	5.007039	TCAGCGCATCTTATCTCAATGTTTC	59.993	40.000	11.47	0.00	0.00	2.78
827	1083	3.772387	TGGCAGACCACCAAAATTATGA	58.228	40.909	0.00	0.00	42.67	2.15
881	1146	6.035542	GTGAGCAGAGAAGTACTAATTGCTTC	59.964	42.308	18.95	14.23	39.34	3.86
896	1161	1.269723	CAGTACGGTTGTGAGCAGAGA	59.730	52.381	0.00	0.00	0.00	3.10
907	1172	4.750098	CACTTGAATCAGTTCAGTACGGTT	59.250	41.667	0.00	0.00	44.62	4.44
922	1187	3.641434	ATAGCAGTGAGCCACTTGAAT	57.359	42.857	5.24	0.00	42.59	2.57
923	1188	3.679917	GCTATAGCAGTGAGCCACTTGAA	60.680	47.826	20.01	0.00	42.59	2.69
924	1189	2.159043	GCTATAGCAGTGAGCCACTTGA	60.159	50.000	20.01	0.00	42.59	3.02
925	1190	2.158986	AGCTATAGCAGTGAGCCACTTG	60.159	50.000	26.07	3.72	43.43	3.16
926	1191	2.102252	GAGCTATAGCAGTGAGCCACTT	59.898	50.000	26.07	0.80	43.43	3.16
997	1269	2.286654	GCGCCATTGCTCTAAACATCTC	60.287	50.000	0.00	0.00	34.43	2.75
1022	1294	6.718522	AATACTAGTACCTCAGAAGAAGGC	57.281	41.667	4.31	0.00	0.00	4.35
1081	1359	2.032549	CACGAAAGCTCTGGTGTTCTTG	60.033	50.000	0.00	0.00	0.00	3.02
1282	1597	5.212194	CGCAGCAAACACACTTAATTAAGT	58.788	37.500	22.49	22.49	46.76	2.24
1283	1598	4.616802	CCGCAGCAAACACACTTAATTAAG	59.383	41.667	21.21	21.21	39.18	1.85
1284	1599	4.541779	CCGCAGCAAACACACTTAATTAA	58.458	39.130	0.00	0.00	0.00	1.40
1285	1600	3.057876	CCCGCAGCAAACACACTTAATTA	60.058	43.478	0.00	0.00	0.00	1.40
1381	1696	1.006571	GTTCCTGACGAACTCCGCA	60.007	57.895	0.00	0.00	46.33	5.69
1420	1735	0.526211	CGAGGTCGTCCTGAATGTCA	59.474	55.000	5.76	0.00	45.24	3.58
1426	1741	4.671590	TGGCCGAGGTCGTCCTGA	62.672	66.667	5.76	0.00	45.24	3.86
1550	1873	1.873591	GTTGTGCAGGATGTCGAGTTT	59.126	47.619	0.00	0.00	39.31	2.66
1551	1874	1.512926	GTTGTGCAGGATGTCGAGTT	58.487	50.000	0.00	0.00	39.31	3.01
1552	1875	0.320771	GGTTGTGCAGGATGTCGAGT	60.321	55.000	0.00	0.00	39.31	4.18
1750	2088	4.078516	GGGTTCACGCCGCCTAGT	62.079	66.667	0.00	0.00	0.00	2.57
2071	2418	2.072366	CTTCCCCACGGTAAACCCT	58.928	57.895	0.00	0.00	0.00	4.34
2140	2487	7.976135	ATCCTCATCTTTATTACTGTCATGC	57.024	36.000	0.00	0.00	0.00	4.06
2150	2497	8.562892	CGCTTGATGTTTATCCTCATCTTTATT	58.437	33.333	0.00	0.00	40.46	1.40
2154	2501	5.431765	ACGCTTGATGTTTATCCTCATCTT	58.568	37.500	0.00	0.00	40.46	2.40
2164	2511	3.926527	CAGCTCAGTACGCTTGATGTTTA	59.073	43.478	0.00	0.00	35.07	2.01
2167	2514	1.404717	CCAGCTCAGTACGCTTGATGT	60.405	52.381	0.00	0.00	35.07	3.06
2168	2515	1.284657	CCAGCTCAGTACGCTTGATG	58.715	55.000	0.00	0.00	35.07	3.07
2169	2516	0.898320	ACCAGCTCAGTACGCTTGAT	59.102	50.000	0.37	0.00	35.07	2.57
2170	2517	1.201647	GTACCAGCTCAGTACGCTTGA	59.798	52.381	7.61	0.00	35.07	3.02
2222	2620	6.094881	TCAGTCGGTGGAATCCATTATTTTTC	59.905	38.462	4.81	0.00	35.28	2.29
2238	2637	1.338674	TGCACCCTAAATCAGTCGGTG	60.339	52.381	0.00	0.00	45.55	4.94
2255	2654	1.868306	GTGACATCACGCACATGCA	59.132	52.632	4.49	0.00	42.21	3.96
2285	2911	1.573108	TCTCCTTGCTCCACCTTAGG	58.427	55.000	0.00	0.00	0.00	2.69
2348	2974	9.926158	AACTGATCAGACATATTATGCTTAGAG	57.074	33.333	29.27	0.00	0.00	2.43
2472	3105	6.862209	TGTACAATGGTTGATAAAGCCATTC	58.138	36.000	3.75	0.00	46.52	2.67
2475	3108	5.394005	GCATGTACAATGGTTGATAAAGCCA	60.394	40.000	0.00	0.00	36.64	4.75
2478	3111	5.360714	AGGGCATGTACAATGGTTGATAAAG	59.639	40.000	0.00	0.00	0.00	1.85
2484	3117	4.269183	TCTAAGGGCATGTACAATGGTTG	58.731	43.478	0.00	0.00	0.00	3.77
2517	3150	0.235665	GGACAACACACATGCACTCG	59.764	55.000	0.00	0.00	0.00	4.18
2519	3152	1.165907	CGGGACAACACACATGCACT	61.166	55.000	0.00	0.00	0.00	4.40
2529	3162	3.637911	ATTGTATTAGGCGGGACAACA	57.362	42.857	0.00	0.00	34.80	3.33
2531	3164	3.129638	GCAAATTGTATTAGGCGGGACAA	59.870	43.478	0.00	0.00	36.32	3.18
2533	3166	2.949644	AGCAAATTGTATTAGGCGGGAC	59.050	45.455	0.00	0.00	0.00	4.46
2534	3167	3.290948	AGCAAATTGTATTAGGCGGGA	57.709	42.857	0.00	0.00	0.00	5.14
2560	3193	3.940852	TCGTGAATGTAGCATTGCTGAAT	59.059	39.130	21.31	11.21	40.10	2.57
2565	3198	6.021468	GTGTTATTTCGTGAATGTAGCATTGC	60.021	38.462	0.00	0.00	0.00	3.56
2582	3232	4.525100	ACTGCATAAAACCCCGTGTTATTT	59.475	37.500	0.00	0.00	35.67	1.40
2600	3252	3.376859	CCTAACAAGTCACAAACACTGCA	59.623	43.478	0.00	0.00	0.00	4.41
2602	3254	4.730613	GCACCTAACAAGTCACAAACACTG	60.731	45.833	0.00	0.00	0.00	3.66
2650	3302	1.284785	GATTTCCAGATGGGTGGGACA	59.715	52.381	0.00	0.00	38.26	4.02
2652	3304	0.546122	CGATTTCCAGATGGGTGGGA	59.454	55.000	0.00	0.00	38.26	4.37
2661	3313	0.618458	CTTCACCCCCGATTTCCAGA	59.382	55.000	0.00	0.00	0.00	3.86
2665	3317	2.781681	TTCTCTTCACCCCCGATTTC	57.218	50.000	0.00	0.00	0.00	2.17
2671	3323	3.780850	TCCTTCTAATTCTCTTCACCCCC	59.219	47.826	0.00	0.00	0.00	5.40
2721	3376	7.622893	AAAACCAAAAATGCTAAACACACAT	57.377	28.000	0.00	0.00	0.00	3.21
2722	3377	7.440523	AAAAACCAAAAATGCTAAACACACA	57.559	28.000	0.00	0.00	0.00	3.72
2759	3414	3.634568	AATCTCGATGAGCCTAAGACG	57.365	47.619	0.00	0.00	0.00	4.18
2764	3419	5.598416	TTTCTCAAATCTCGATGAGCCTA	57.402	39.130	8.58	0.00	42.21	3.93
2804	3459	2.175202	AGCCTTCGTCTCTGAGTTCAT	58.825	47.619	4.32	0.00	0.00	2.57
2813	3468	3.483738	GCGTTTGATTTAGCCTTCGTCTC	60.484	47.826	0.00	0.00	0.00	3.36
2830	3485	3.222603	AGGGATTGAAACTTCAGCGTTT	58.777	40.909	0.00	0.00	39.63	3.60
2836	3491	6.493115	TGCTGATTTAAGGGATTGAAACTTCA	59.507	34.615	0.00	0.00	34.92	3.02
2852	3507	6.466812	TCAGAGAGTTTGATGTGCTGATTTA	58.533	36.000	0.00	0.00	0.00	1.40
2879	3534	5.462068	GCGCTCAAGGTTTAAAATTGACTTT	59.538	36.000	0.00	0.00	0.00	2.66
2881	3536	4.546570	GCGCTCAAGGTTTAAAATTGACT	58.453	39.130	0.00	0.00	0.00	3.41
2891	3546	1.092921	TGACAACGCGCTCAAGGTTT	61.093	50.000	5.73	0.00	0.00	3.27
2933	3588	0.914551	CGTGTTTAGACGCAGATCGG	59.085	55.000	0.00	0.00	43.86	4.18
2946	3601	1.244019	GGGCCAGCTCAATCGTGTTT	61.244	55.000	4.39	0.00	0.00	2.83
2960	3615	3.164977	TTCACGTCTGGTGGGCCA	61.165	61.111	0.00	0.00	46.96	5.36
2974	3629	9.291664	CGTTACTAAAAAGAAAAACATGGTTCA	57.708	29.630	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.