AutoCloner

Multiple sequence alignment - TraesCS7A01G096200

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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	TraesCS7A01G096200	chr7A	100.000	3611	0	0	1	3611	59200854	59204464	0.000000e+00	6669.0
1	TraesCS7A01G096200	chr7A	83.382	1023	62	45	608	1563	59348789	59349770	0.000000e+00	848.0
2	TraesCS7A01G096200	chr7A	83.504	879	110	24	1574	2443	59288315	59289167	0.000000e+00	787.0
3	TraesCS7A01G096200	chr7A	83.238	871	116	14	1596	2463	59349883	59350726	0.000000e+00	773.0
4	TraesCS7A01G096200	chr7A	81.740	701	102	14	1746	2439	59229627	59230308	2.430000e-156	562.0
5	TraesCS7A01G096200	chr7A	83.553	608	59	23	1	594	59286601	59287181	6.860000e-147	531.0
6	TraesCS7A01G096200	chr7A	83.633	611	51	21	965	1563	59287667	59288240	2.470000e-146	529.0
7	TraesCS7A01G096200	chr7A	82.923	609	61	26	1	593	59227731	59228312	3.220000e-140	508.0
8	TraesCS7A01G096200	chr7A	80.794	630	63	33	1	593	59348108	59348716	1.190000e-119	440.0
9	TraesCS7A01G096200	chr7A	81.834	567	54	29	605	1138	59228380	59228930	7.160000e-117	431.0
10	TraesCS7A01G096200	chr7A	88.644	317	16	4	1254	1563	59229081	59229384	5.700000e-98	368.0
11	TraesCS7A01G096200	chr7A	83.106	367	29	10	605	942	59287248	59287610	1.630000e-78	303.0
12	TraesCS7A01G096200	chr7A	86.792	159	12	4	2563	2712	59289235	59289393	6.200000e-38	169.0
13	TraesCS7A01G096200	chr7A	91.954	87	6	1	1574	1659	59229501	59229587	1.760000e-23	121.0
14	TraesCS7A01G096200	chr7D	91.098	2797	159	47	604	3367	55249815	55252554	0.000000e+00	3703.0
15	TraesCS7A01G096200	chr7D	94.353	2125	95	11	1254	3367	55267526	55269636	0.000000e+00	3236.0
16	TraesCS7A01G096200	chr7D	89.367	1185	54	30	1	1136	55266201	55267362	0.000000e+00	1424.0
17	TraesCS7A01G096200	chr7D	83.515	1007	82	38	605	1561	55387110	55388082	0.000000e+00	863.0
18	TraesCS7A01G096200	chr7D	84.009	888	107	20	1590	2460	55388221	55389090	0.000000e+00	821.0
19	TraesCS7A01G096200	chr7D	82.347	1014	82	49	605	1562	55374153	55375125	0.000000e+00	791.0
20	TraesCS7A01G096200	chr7D	82.131	873	118	23	1574	2434	55375201	55376047	0.000000e+00	713.0
21	TraesCS7A01G096200	chr7D	83.415	609	60	23	1	593	55373502	55374085	8.880000e-146	527.0
22	TraesCS7A01G096200	chr7D	96.040	303	9	2	1	302	55248955	55249255	1.170000e-134	490.0
23	TraesCS7A01G096200	chr7D	92.357	314	16	3	295	600	55249440	55249753	1.190000e-119	440.0
24	TraesCS7A01G096200	chr7D	78.662	628	60	37	1	603	55386472	55387050	2.060000e-92	350.0
25	TraesCS7A01G096200	chr7D	92.683	205	13	1	3409	3611	55252544	55252748	9.800000e-76	294.0
26	TraesCS7A01G096200	chr7D	92.683	205	13	1	3409	3611	55269626	55269830	9.800000e-76	294.0
27	TraesCS7A01G096200	chr7D	95.652	46	2	0	3370	3415	68906221	68906176	1.390000e-09	75.0
28	TraesCS7A01G096200	chr7D	85.075	67	4	5	3225	3289	55390634	55390696	3.010000e-06	63.9
29	TraesCS7A01G096200	chr4A	91.549	710	60	0	1730	2439	671524505	671525214	0.000000e+00	979.0
30	TraesCS7A01G096200	chr4A	87.529	866	48	23	322	1136	671522561	671523417	0.000000e+00	946.0
31	TraesCS7A01G096200	chr4A	85.486	875	95	21	1574	2435	671639820	671640675	0.000000e+00	883.0
32	TraesCS7A01G096200	chr4A	79.114	1513	130	91	1	1419	671638201	671639621	0.000000e+00	872.0
33	TraesCS7A01G096200	chr4A	81.294	989	97	46	605	1563	671596641	671597571	0.000000e+00	721.0
34	TraesCS7A01G096200	chr4A	88.203	551	35	14	1184	1731	671523520	671524043	6.580000e-177	630.0
35	TraesCS7A01G096200	chr4A	83.709	577	80	6	1580	2144	671597714	671598288	1.910000e-147	532.0
36	TraesCS7A01G096200	chr4A	90.448	335	26	2	2437	2771	671525470	671525798	1.540000e-118	436.0
37	TraesCS7A01G096200	chr4A	88.788	330	25	8	1	325	671521958	671522280	9.400000e-106	394.0
38	TraesCS7A01G096200	chr4A	85.714	168	18	3	425	591	671596409	671596571	4.790000e-39	172.0
39	TraesCS7A01G096200	chr4A	88.356	146	14	3	2568	2712	671641016	671641159	4.790000e-39	172.0
40	TraesCS7A01G096200	chr4A	79.333	150	19	3	3183	3329	671642469	671642609	1.070000e-15	95.3
41	TraesCS7A01G096200	chr2B	97.917	48	0	1	3370	3417	161918842	161918796	8.310000e-12	82.4
42	TraesCS7A01G096200	chr3A	100.000	43	0	0	3370	3412	723326113	723326071	2.990000e-11	80.5
43	TraesCS7A01G096200	chr3A	100.000	42	0	0	3370	3411	672587452	672587493	1.070000e-10	78.7
44	TraesCS7A01G096200	chr5D	100.000	42	0	0	3370	3411	504512931	504512972	1.070000e-10	78.7
45	TraesCS7A01G096200	chr6B	97.778	45	0	1	3370	3413	1015420	1015464	3.870000e-10	76.8
46	TraesCS7A01G096200	chr3B	94.118	51	1	2	3366	3415	569219666	569219617	3.870000e-10	76.8
47	TraesCS7A01G096200	chr1A	100.000	41	0	0	3370	3410	24786636	24786596	3.870000e-10	76.8
48	TraesCS7A01G096200	chr1B	100.000	40	0	0	3370	3409	661984117	661984078	1.390000e-09	75.0

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	TraesCS7A01G096200	chr7A	59200854	59204464	3610	False	6669.000000	6669	100.000000	1	3611	1	chr7A.!!$F1	3610
1	TraesCS7A01G096200	chr7A	59348108	59350726	2618	False	687.000000	848	82.471333	1	2463	3	chr7A.!!$F4	2462
2	TraesCS7A01G096200	chr7A	59286601	59289393	2792	False	463.800000	787	84.117600	1	2712	5	chr7A.!!$F3	2711
3	TraesCS7A01G096200	chr7A	59227731	59230308	2577	False	398.000000	562	85.419000	1	2439	5	chr7A.!!$F2	2438
4	TraesCS7A01G096200	chr7D	55266201	55269830	3629	False	1651.333333	3236	92.134333	1	3611	3	chr7D.!!$F2	3610
5	TraesCS7A01G096200	chr7D	55248955	55252748	3793	False	1231.750000	3703	93.044500	1	3611	4	chr7D.!!$F1	3610
6	TraesCS7A01G096200	chr7D	55373502	55376047	2545	False	677.000000	791	82.631000	1	2434	3	chr7D.!!$F3	2433
7	TraesCS7A01G096200	chr7D	55386472	55390696	4224	False	524.475000	863	82.815250	1	3289	4	chr7D.!!$F4	3288
8	TraesCS7A01G096200	chr4A	671521958	671525798	3840	False	677.000000	979	89.303400	1	2771	5	chr4A.!!$F1	2770
9	TraesCS7A01G096200	chr4A	671638201	671642609	4408	False	505.575000	883	83.072250	1	3329	4	chr4A.!!$F3	3328
10	TraesCS7A01G096200	chr4A	671596409	671598288	1879	False	475.000000	721	83.572333	425	2144	3	chr4A.!!$F2	1719

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
858	1558	0.105453	AGGTCGAGGCCATGGTCTAT	60.105	55.0	21.43	0.0	0.0	1.98	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2810	5971	1.077285	TACACTGATCGCCCGAGGA	60.077	57.895	0.0	0.0	0.0	3.71	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
215	249	8.934507	ATTGTCTTTTTGTGATTTCCGTTAAA	57.065	26.923	0.00	0.00	0.00	1.52
396	930	2.540910	TGTCCTCCCTCCCCCTCT	60.541	66.667	0.00	0.00	0.00	3.69
469	1019	0.245539	CTTCCTCTAACGAACGGCCA	59.754	55.000	2.24	0.00	0.00	5.36
490	1042	5.009631	CCATACAGGACTGAAATTTGGTCA	58.990	41.667	17.27	1.74	41.22	4.02
858	1558	0.105453	AGGTCGAGGCCATGGTCTAT	60.105	55.000	21.43	0.00	0.00	1.98
861	1561	2.515854	GTCGAGGCCATGGTCTATCTA	58.484	52.381	21.43	1.70	0.00	1.98
862	1562	2.490115	GTCGAGGCCATGGTCTATCTAG	59.510	54.545	21.43	8.78	0.00	2.43
913	1626	3.016971	ATGGCAGGGCTGGTGCTA	61.017	61.111	0.00	2.07	40.97	3.49
950	1672	4.080638	AGGATTGGAAGCCTAGAGAAACTG	60.081	45.833	0.00	0.00	44.37	3.16
961	1697	4.020662	CCTAGAGAAACTGCAAGGAAGAGT	60.021	45.833	0.00	0.00	39.30	3.24
962	1698	5.186021	CCTAGAGAAACTGCAAGGAAGAGTA	59.814	44.000	0.00	0.00	39.30	2.59
963	1699	5.753721	AGAGAAACTGCAAGGAAGAGTAT	57.246	39.130	0.00	0.00	39.30	2.12
997	1801	2.516227	TCTGTGGAAGGAGATCGAGT	57.484	50.000	0.00	0.00	0.00	4.18
1002	1806	3.118992	TGTGGAAGGAGATCGAGTTGATG	60.119	47.826	0.00	0.00	37.47	3.07
1010	1814	3.634448	GAGATCGAGTTGATGAAGGGAGA	59.366	47.826	0.00	0.00	37.47	3.71
1011	1815	3.383185	AGATCGAGTTGATGAAGGGAGAC	59.617	47.826	0.00	0.00	37.47	3.36
1012	1816	2.432510	ATCGAGTTGATGAAGGGAGACC	59.567	50.000	0.00	0.00	43.98	3.85
1061	1865	2.814336	AGCGGTTGAAAGATCAGGTTTC	59.186	45.455	0.00	0.00	36.78	2.78
1062	1866	2.552315	GCGGTTGAAAGATCAGGTTTCA	59.448	45.455	4.88	4.88	41.16	2.69
1077	1881	9.406828	GATCAGGTTTCAAACTGTTTAATTACC	57.593	33.333	5.31	10.66	36.17	2.85
1092	1902	9.743057	TGTTTAATTACCTCTTGATTTTGTGTG	57.257	29.630	0.00	0.00	0.00	3.82
1101	1914	4.863689	TCTTGATTTTGTGTGTGTGCTTTG	59.136	37.500	0.00	0.00	0.00	2.77
1153	1968	4.801330	TGAATACGAGTGTTCATCTGGT	57.199	40.909	10.62	0.00	36.10	4.00
1154	1969	4.494484	TGAATACGAGTGTTCATCTGGTG	58.506	43.478	10.62	0.00	36.10	4.17
1173	1997	4.410883	TGGTGTTGGATAAGTATGGTAGGG	59.589	45.833	0.00	0.00	0.00	3.53
1182	2071	4.547886	AAGTATGGTAGGGCTAGTGGTA	57.452	45.455	0.00	0.00	0.00	3.25
1209	2189	4.835615	ACTTGGCTGAGTTTCTCTCTTCTA	59.164	41.667	0.00	0.00	43.13	2.10
1212	2193	5.019470	TGGCTGAGTTTCTCTCTTCTATGA	58.981	41.667	0.00	0.00	43.13	2.15
1216	2208	7.230510	GGCTGAGTTTCTCTCTTCTATGAGATA	59.769	40.741	0.00	0.00	41.59	1.98
1236	2235	8.316946	TGAGATATGGTTCTTGATCCATGTATC	58.683	37.037	18.43	17.91	43.28	2.24
1237	2236	8.211030	AGATATGGTTCTTGATCCATGTATCA	57.789	34.615	18.43	0.00	43.28	2.15
1238	2237	8.833734	AGATATGGTTCTTGATCCATGTATCAT	58.166	33.333	18.43	7.63	43.28	2.45
1239	2238	8.803397	ATATGGTTCTTGATCCATGTATCATG	57.197	34.615	18.43	4.94	43.28	3.07
1240	2239	6.005066	TGGTTCTTGATCCATGTATCATGT	57.995	37.500	12.10	0.00	35.84	3.21
1241	2240	7.135591	TGGTTCTTGATCCATGTATCATGTA	57.864	36.000	12.10	2.75	35.84	2.29
1242	2241	7.748677	TGGTTCTTGATCCATGTATCATGTAT	58.251	34.615	12.10	0.00	35.84	2.29
1243	2242	7.662669	TGGTTCTTGATCCATGTATCATGTATG	59.337	37.037	12.10	0.00	35.84	2.39
1244	2243	7.879677	GGTTCTTGATCCATGTATCATGTATGA	59.120	37.037	12.10	0.00	41.70	2.15
1245	2244	8.933807	GTTCTTGATCCATGTATCATGTATGAG	58.066	37.037	12.10	2.62	40.64	2.90
1246	2245	8.426569	TCTTGATCCATGTATCATGTATGAGA	57.573	34.615	12.10	4.60	40.64	3.27
1247	2246	8.873144	TCTTGATCCATGTATCATGTATGAGAA	58.127	33.333	12.10	0.00	40.64	2.87
1248	2247	8.837788	TTGATCCATGTATCATGTATGAGAAC	57.162	34.615	1.36	2.74	40.64	3.01
1249	2248	8.198807	TGATCCATGTATCATGTATGAGAACT	57.801	34.615	0.00	0.00	40.64	3.01
1250	2249	8.654094	TGATCCATGTATCATGTATGAGAACTT	58.346	33.333	0.00	0.00	40.64	2.66
1251	2250	8.843885	ATCCATGTATCATGTATGAGAACTTG	57.156	34.615	8.57	13.43	40.64	3.16
1252	2251	8.021898	TCCATGTATCATGTATGAGAACTTGA	57.978	34.615	17.91	4.49	40.64	3.02
1287	2294	7.390162	GGACTTCTCTTTCTCATGTCAAAATCT	59.610	37.037	0.00	0.00	0.00	2.40
1486	2541	3.603532	GGTGTTGCAGATGAGAGATGAA	58.396	45.455	0.00	0.00	0.00	2.57
1693	2913	9.753674	TTCACTATAATTTTGTCCATCTTCCTT	57.246	29.630	0.00	0.00	0.00	3.36
1700	2921	4.993705	TTGTCCATCTTCCTTGGTAGTT	57.006	40.909	0.00	0.00	35.64	2.24
1718	2939	7.664758	TGGTAGTTCAAAACTAGTTAGTCTCC	58.335	38.462	8.92	5.49	44.16	3.71
1719	2940	6.805760	GGTAGTTCAAAACTAGTTAGTCTCCG	59.194	42.308	8.92	0.00	44.16	4.63
1830	3531	0.320771	GGGTCTCGCTGTTGTGATGT	60.321	55.000	0.00	0.00	31.73	3.06
2120	3830	4.228210	AGGCAGAACATGGGAGAAAAGATA	59.772	41.667	0.00	0.00	0.00	1.98
2145	3855	6.814954	AGAGAGGCACTAATAATCCAGAAA	57.185	37.500	0.00	0.00	41.55	2.52
2546	4539	7.095187	GCCTTATATATGAAACGGAGTGAAAGG	60.095	40.741	0.00	0.00	45.00	3.11
2590	4588	1.270907	TTGTGTGGTTTGTTGGCCTT	58.729	45.000	3.32	0.00	0.00	4.35
2625	4623	1.272313	TGCTAGTGGAGGAAGTACGGT	60.272	52.381	0.00	0.00	0.00	4.83
2810	5971	3.321968	TCAGTGTACTGTGCATCTGAAGT	59.678	43.478	19.90	0.00	44.12	3.01
2835	5996	1.479323	GGGCGATCAGTGTACCTAACA	59.521	52.381	0.00	0.00	35.06	2.41
2919	6090	4.410228	AGCATACCTCTCACATACCACAAT	59.590	41.667	0.00	0.00	0.00	2.71
3001	6202	4.766373	AGGTTAACATGCACATTCACATCA	59.234	37.500	8.10	0.00	0.00	3.07
3223	6463	2.203800	TTGTGCGCTCGGTATAAGAG	57.796	50.000	9.73	2.92	38.68	2.85
3236	6476	7.254488	GCTCGGTATAAGAGAAAACAATCTTCC	60.254	40.741	9.85	0.00	37.93	3.46
3333	6576	4.389077	AGATGCTTTAACACTTGCGTAGTC	59.611	41.667	0.00	0.00	33.85	2.59
3334	6577	3.459145	TGCTTTAACACTTGCGTAGTCA	58.541	40.909	0.00	0.00	33.85	3.41
3359	6602	6.539826	ACGCTCATATTTCTTCAATGACATGA	59.460	34.615	0.00	0.00	0.00	3.07
3360	6603	7.066163	ACGCTCATATTTCTTCAATGACATGAA	59.934	33.333	0.00	0.00	37.70	2.57
3361	6604	7.375280	CGCTCATATTTCTTCAATGACATGAAC	59.625	37.037	0.00	0.00	35.55	3.18
3362	6605	8.186163	GCTCATATTTCTTCAATGACATGAACA	58.814	33.333	0.00	0.00	35.55	3.18
3363	6606	9.499585	CTCATATTTCTTCAATGACATGAACAC	57.500	33.333	0.00	0.00	35.55	3.32
3364	6607	9.012161	TCATATTTCTTCAATGACATGAACACA	57.988	29.630	0.00	0.00	35.55	3.72
3365	6608	9.069078	CATATTTCTTCAATGACATGAACACAC	57.931	33.333	0.00	0.00	35.55	3.82
3366	6609	6.448207	TTTCTTCAATGACATGAACACACA	57.552	33.333	0.00	0.00	35.55	3.72
3367	6610	6.448207	TTCTTCAATGACATGAACACACAA	57.552	33.333	0.00	0.00	35.55	3.33
3368	6611	6.638096	TCTTCAATGACATGAACACACAAT	57.362	33.333	0.00	0.00	35.55	2.71
3369	6612	6.440436	TCTTCAATGACATGAACACACAATG	58.560	36.000	0.00	0.00	35.55	2.82
3370	6613	6.262720	TCTTCAATGACATGAACACACAATGA	59.737	34.615	0.00	0.00	35.55	2.57
3371	6614	6.578163	TCAATGACATGAACACACAATGAT	57.422	33.333	0.00	0.00	0.00	2.45
3372	6615	6.383415	TCAATGACATGAACACACAATGATG	58.617	36.000	0.00	0.00	0.00	3.07
3373	6616	4.163458	TGACATGAACACACAATGATGC	57.837	40.909	0.00	0.00	0.00	3.91
3374	6617	3.568853	TGACATGAACACACAATGATGCA	59.431	39.130	0.00	0.00	0.00	3.96
3375	6618	4.163552	GACATGAACACACAATGATGCAG	58.836	43.478	0.00	0.00	0.00	4.41
3376	6619	3.822167	ACATGAACACACAATGATGCAGA	59.178	39.130	0.00	0.00	0.00	4.26
3377	6620	4.082949	ACATGAACACACAATGATGCAGAG	60.083	41.667	0.00	0.00	0.00	3.35
3378	6621	2.815503	TGAACACACAATGATGCAGAGG	59.184	45.455	0.00	0.00	0.00	3.69
3379	6622	1.171308	ACACACAATGATGCAGAGGC	58.829	50.000	0.00	0.00	41.68	4.70
3380	6623	0.454600	CACACAATGATGCAGAGGCC	59.545	55.000	0.00	0.00	40.13	5.19
3381	6624	1.028330	ACACAATGATGCAGAGGCCG	61.028	55.000	0.00	0.00	40.13	6.13
3382	6625	1.452651	ACAATGATGCAGAGGCCGG	60.453	57.895	0.00	0.00	40.13	6.13
3383	6626	1.153107	CAATGATGCAGAGGCCGGA	60.153	57.895	5.05	0.00	40.13	5.14
3384	6627	1.147824	AATGATGCAGAGGCCGGAG	59.852	57.895	5.05	0.00	40.13	4.63
3451	6694	7.724061	ACAACATCCTTCCTGTTAGTAATTTGT	59.276	33.333	0.00	0.00	35.15	2.83
3508	6751	6.619801	AGGTCTCGCAATTATGGTATTTTC	57.380	37.500	0.00	0.00	0.00	2.29
3515	6758	5.562696	CGCAATTATGGTATTTTCAGCCGAT	60.563	40.000	0.00	0.00	0.00	4.18
3529	6772	1.774639	GCCGATGCTTGCCATAATTG	58.225	50.000	0.00	0.00	33.29	2.32
3531	6774	2.734670	CCGATGCTTGCCATAATTGTG	58.265	47.619	0.00	0.00	33.29	3.33
3532	6775	2.358582	CCGATGCTTGCCATAATTGTGA	59.641	45.455	3.41	0.00	33.29	3.58
3562	6805	5.895636	TTTGCTATTTACTGTCACCATGG	57.104	39.130	11.19	11.19	0.00	3.66
3564	6807	4.513442	TGCTATTTACTGTCACCATGGTC	58.487	43.478	16.53	5.38	0.00	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	2.280628	GTAGTGGACTACTTGCATGGC	58.719	52.381	9.32	0.00	44.06	4.40
45	46	0.395311	CCTCTTCCACAGGCATGCAT	60.395	55.000	21.36	10.32	0.00	3.96
469	1019	6.126863	TCTGACCAAATTTCAGTCCTGTAT	57.873	37.500	12.97	0.00	41.22	2.29
490	1042	3.499918	CGTCAAGCAAGGAATCACTTTCT	59.500	43.478	0.00	0.00	34.56	2.52
861	1561	2.443016	ACAGCTAGCTAGGCGCCT	60.443	61.111	34.85	34.85	40.39	5.52
862	1562	1.173444	TAGACAGCTAGCTAGGCGCC	61.173	60.000	21.89	21.89	40.39	6.53
913	1626	4.366267	TCCAATCCTTTCTTCTCTAGCCT	58.634	43.478	0.00	0.00	0.00	4.58
950	1672	5.467035	AGCTATCTCATACTCTTCCTTGC	57.533	43.478	0.00	0.00	0.00	4.01
961	1697	5.893824	TCCACAGAAGACAAGCTATCTCATA	59.106	40.000	1.06	0.00	0.00	2.15
962	1698	4.713814	TCCACAGAAGACAAGCTATCTCAT	59.286	41.667	1.06	0.00	0.00	2.90
963	1699	4.089361	TCCACAGAAGACAAGCTATCTCA	58.911	43.478	1.06	0.00	0.00	3.27
997	1801	1.630369	CTGGTGGTCTCCCTTCATCAA	59.370	52.381	0.00	0.00	0.00	2.57
1002	1806	1.904990	GCCTCTGGTGGTCTCCCTTC	61.905	65.000	0.00	0.00	0.00	3.46
1010	1814	2.433446	CAAGCTGCCTCTGGTGGT	59.567	61.111	0.00	0.00	0.00	4.16
1011	1815	2.360852	CCAAGCTGCCTCTGGTGG	60.361	66.667	0.00	0.00	0.00	4.61
1012	1816	3.060615	GCCAAGCTGCCTCTGGTG	61.061	66.667	12.82	0.00	0.00	4.17
1077	1881	4.297299	AGCACACACACAAAATCAAGAG	57.703	40.909	0.00	0.00	0.00	2.85
1124	1937	9.003658	AGATGAACACTCGTATTCAAGAAAAAT	57.996	29.630	0.00	0.00	38.29	1.82
1138	1953	1.800586	CCAACACCAGATGAACACTCG	59.199	52.381	0.00	0.00	0.00	4.18
1139	1954	3.126001	TCCAACACCAGATGAACACTC	57.874	47.619	0.00	0.00	0.00	3.51
1149	1964	5.454755	CCCTACCATACTTATCCAACACCAG	60.455	48.000	0.00	0.00	0.00	4.00
1153	1968	4.303794	AGCCCTACCATACTTATCCAACA	58.696	43.478	0.00	0.00	0.00	3.33
1154	1969	4.976540	AGCCCTACCATACTTATCCAAC	57.023	45.455	0.00	0.00	0.00	3.77
1173	1997	1.555533	AGCCAAGTCCTTACCACTAGC	59.444	52.381	0.00	0.00	0.00	3.42
1182	2071	2.708325	AGAGAAACTCAGCCAAGTCCTT	59.292	45.455	0.00	0.00	32.06	3.36
1209	2189	7.087895	ACATGGATCAAGAACCATATCTCAT	57.912	36.000	10.97	0.00	43.89	2.90
1212	2193	8.211030	TGATACATGGATCAAGAACCATATCT	57.789	34.615	18.65	0.00	43.89	1.98
1216	2208	6.607970	ACATGATACATGGATCAAGAACCAT	58.392	36.000	26.03	6.16	46.22	3.55
1236	2235	6.534436	CCTGACTTCTCAAGTTCTCATACATG	59.466	42.308	0.00	0.00	43.03	3.21
1237	2236	6.351711	CCCTGACTTCTCAAGTTCTCATACAT	60.352	42.308	0.00	0.00	43.03	2.29
1238	2237	5.047021	CCCTGACTTCTCAAGTTCTCATACA	60.047	44.000	0.00	0.00	43.03	2.29
1239	2238	5.186021	TCCCTGACTTCTCAAGTTCTCATAC	59.814	44.000	0.00	0.00	43.03	2.39
1240	2239	5.186021	GTCCCTGACTTCTCAAGTTCTCATA	59.814	44.000	0.00	0.00	43.03	2.15
1241	2240	4.020662	GTCCCTGACTTCTCAAGTTCTCAT	60.021	45.833	0.00	0.00	43.03	2.90
1242	2241	3.322254	GTCCCTGACTTCTCAAGTTCTCA	59.678	47.826	0.00	0.00	43.03	3.27
1243	2242	3.576550	AGTCCCTGACTTCTCAAGTTCTC	59.423	47.826	0.00	0.00	40.28	2.87
1244	2243	3.582164	AGTCCCTGACTTCTCAAGTTCT	58.418	45.455	0.00	0.00	40.28	3.01
1287	2294	5.544176	GGTCCCTAAAGATGATCACCTGATA	59.456	44.000	0.00	0.00	34.37	2.15
1444	2499	5.820423	CACCCCAACATGAAAGTCGATATTA	59.180	40.000	0.00	0.00	0.00	0.98
1445	2500	4.640201	CACCCCAACATGAAAGTCGATATT	59.360	41.667	0.00	0.00	0.00	1.28
1446	2501	4.199310	CACCCCAACATGAAAGTCGATAT	58.801	43.478	0.00	0.00	0.00	1.63
1447	2502	3.008594	ACACCCCAACATGAAAGTCGATA	59.991	43.478	0.00	0.00	0.00	2.92
1448	2503	2.224769	ACACCCCAACATGAAAGTCGAT	60.225	45.455	0.00	0.00	0.00	3.59
1449	2504	1.142060	ACACCCCAACATGAAAGTCGA	59.858	47.619	0.00	0.00	0.00	4.20
1450	2505	1.604604	ACACCCCAACATGAAAGTCG	58.395	50.000	0.00	0.00	0.00	4.18
1463	2518	0.615331	TCTCTCATCTGCAACACCCC	59.385	55.000	0.00	0.00	0.00	4.95
1464	2519	2.093288	TCATCTCTCATCTGCAACACCC	60.093	50.000	0.00	0.00	0.00	4.61
1486	2541	3.133014	CCATCCGAGGCTCGATGT	58.867	61.111	36.47	19.06	43.74	3.06
1516	2571	3.132646	TGCTTGACTGGTTTTGCAAGAAT	59.867	39.130	0.00	0.00	39.97	2.40
1619	2832	6.597672	GGTTCTTTTTCTTGAATTTGTTGGGT	59.402	34.615	0.00	0.00	0.00	4.51
1693	2913	7.522725	CGGAGACTAACTAGTTTTGAACTACCA	60.523	40.741	14.49	0.00	42.81	3.25
1700	2921	6.006449	ACTACCGGAGACTAACTAGTTTTGA	58.994	40.000	14.49	0.00	36.50	2.69
1718	2939	6.293298	GGTGTGTATGTACTATCTGACTACCG	60.293	46.154	0.00	0.00	0.00	4.02
1719	2940	6.544931	TGGTGTGTATGTACTATCTGACTACC	59.455	42.308	0.00	0.00	0.00	3.18
1767	3460	4.039004	TGGTGAAGCAAAGCACATATGTTT	59.961	37.500	5.37	0.00	36.76	2.83
1769	3462	3.156293	TGGTGAAGCAAAGCACATATGT	58.844	40.909	1.41	1.41	36.76	2.29
1830	3531	4.578871	TCTTGAGCCTGAATCGATGAAAA	58.421	39.130	0.00	0.00	0.00	2.29
1991	3692	2.032681	ACAGCGAGGTTCTTGCCC	59.967	61.111	3.72	0.00	41.50	5.36
2062	3763	2.047274	TTCCGAGGCGCAAAGAGG	60.047	61.111	10.83	4.91	0.00	3.69
2120	3830	6.814954	TCTGGATTATTAGTGCCTCTCTTT	57.185	37.500	0.00	0.00	0.00	2.52
2230	3943	3.114616	CAGGGCTCAACGTCAGCG	61.115	66.667	12.07	0.00	44.93	5.18
2282	3998	4.077188	GCTGCGGCTGACGTTGTC	62.077	66.667	11.21	0.00	46.52	3.18
2546	4539	8.976986	AATCATTTATGTTCTCTTGAAACAGC	57.023	30.769	0.00	0.00	33.52	4.40
2590	4588	5.781818	TCCACTAGCATCCATCATTCATCTA	59.218	40.000	0.00	0.00	0.00	1.98
2625	4623	5.269189	GGGTTCCCTTTGGATATCTTTTGA	58.731	41.667	2.05	0.00	41.40	2.69
2810	5971	1.077285	TACACTGATCGCCCGAGGA	60.077	57.895	0.00	0.00	0.00	3.71
2876	6045	3.699038	GCTATGGGCATGAAACTTGGTTA	59.301	43.478	0.00	0.00	41.35	2.85
2890	6059	1.694150	TGTGAGAGGTATGCTATGGGC	59.306	52.381	0.00	0.00	42.22	5.36
2955	6156	9.174166	ACCTACCACATTATTTGAATCTGTTAC	57.826	33.333	0.00	0.00	0.00	2.50
3001	6202	5.989777	ACGAACACTAAGCAGTTCAAATAGT	59.010	36.000	0.00	0.00	43.20	2.12
3046	6252	9.656040	TCAGTTATAAATTAAACTCGCAACCTA	57.344	29.630	0.00	0.00	33.72	3.08
3223	6463	7.759886	GCTATTACCAAAGGGAAGATTGTTTTC	59.240	37.037	0.00	0.00	38.05	2.29
3236	6476	2.684881	CTGCCACTGCTATTACCAAAGG	59.315	50.000	0.00	0.00	38.71	3.11
3333	6576	6.110543	TGTCATTGAAGAAATATGAGCGTG	57.889	37.500	0.00	0.00	0.00	5.34
3334	6577	6.539826	TCATGTCATTGAAGAAATATGAGCGT	59.460	34.615	0.00	0.00	0.00	5.07
3359	6602	1.542915	GCCTCTGCATCATTGTGTGTT	59.457	47.619	0.00	0.00	37.47	3.32
3360	6603	1.171308	GCCTCTGCATCATTGTGTGT	58.829	50.000	0.00	0.00	37.47	3.72
3361	6604	0.454600	GGCCTCTGCATCATTGTGTG	59.545	55.000	0.00	0.00	40.13	3.82
3362	6605	1.028330	CGGCCTCTGCATCATTGTGT	61.028	55.000	0.00	0.00	40.13	3.72
3363	6606	1.721664	CCGGCCTCTGCATCATTGTG	61.722	60.000	0.00	0.00	40.13	3.33
3364	6607	1.452651	CCGGCCTCTGCATCATTGT	60.453	57.895	0.00	0.00	40.13	2.71
3365	6608	1.153107	TCCGGCCTCTGCATCATTG	60.153	57.895	0.00	0.00	40.13	2.82
3366	6609	1.147824	CTCCGGCCTCTGCATCATT	59.852	57.895	0.00	0.00	40.13	2.57
3367	6610	2.815945	CCTCCGGCCTCTGCATCAT	61.816	63.158	0.00	0.00	40.13	2.45
3368	6611	3.473647	CCTCCGGCCTCTGCATCA	61.474	66.667	0.00	0.00	40.13	3.07
3369	6612	3.453070	GACCTCCGGCCTCTGCATC	62.453	68.421	0.00	0.00	40.13	3.91
3370	6613	3.474570	GACCTCCGGCCTCTGCAT	61.475	66.667	0.00	0.00	40.13	3.96
3372	6615	3.453070	GATGACCTCCGGCCTCTGC	62.453	68.421	0.00	0.00	0.00	4.26
3373	6616	2.801631	GGATGACCTCCGGCCTCTG	61.802	68.421	0.00	0.00	33.29	3.35
3374	6617	2.444895	GGATGACCTCCGGCCTCT	60.445	66.667	0.00	0.00	33.29	3.69
3404	6647	5.777802	TGTGTTCAGTGTGTGTTCATTTTT	58.222	33.333	0.00	0.00	0.00	1.94
3405	6648	5.384063	TGTGTTCAGTGTGTGTTCATTTT	57.616	34.783	0.00	0.00	0.00	1.82
3406	6649	5.160641	GTTGTGTTCAGTGTGTGTTCATTT	58.839	37.500	0.00	0.00	0.00	2.32
3407	6650	4.217334	TGTTGTGTTCAGTGTGTGTTCATT	59.783	37.500	0.00	0.00	0.00	2.57
3408	6651	3.755905	TGTTGTGTTCAGTGTGTGTTCAT	59.244	39.130	0.00	0.00	0.00	2.57
3409	6652	3.142174	TGTTGTGTTCAGTGTGTGTTCA	58.858	40.909	0.00	0.00	0.00	3.18
3410	6653	3.822594	TGTTGTGTTCAGTGTGTGTTC	57.177	42.857	0.00	0.00	0.00	3.18
3421	6664	5.063880	ACTAACAGGAAGGATGTTGTGTTC	58.936	41.667	1.74	0.00	40.92	3.18
3451	6694	2.803386	TCAGTTTTGCGCTAATTCGTCA	59.197	40.909	9.73	0.00	0.00	4.35
3515	6758	8.789825	AAAAATTATCACAATTATGGCAAGCA	57.210	26.923	0.00	0.00	0.00	3.91
3562	6805	4.158394	ACATAAATGCATGGTCTTGGTGAC	59.842	41.667	0.00	0.00	44.63	3.67
3564	6807	4.724074	ACATAAATGCATGGTCTTGGTG	57.276	40.909	0.00	0.00	0.00	4.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.