AutoCloner

Multiple sequence alignment - TraesCS2D01G140100

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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	TraesCS2D01G140100	chr2D	100.000	8650	0	0	1	8650	82340443	82331794	0.000000e+00	15974.0
1	TraesCS2D01G140100	chr2D	77.261	2278	451	46	4267	6522	82648227	82645995	0.000000e+00	1275.0
2	TraesCS2D01G140100	chr2D	76.869	2287	447	60	4276	6526	82874959	82872719	0.000000e+00	1218.0
3	TraesCS2D01G140100	chr2D	76.765	2281	453	53	4272	6526	82837323	82835094	0.000000e+00	1205.0
4	TraesCS2D01G140100	chr2D	77.838	1841	374	26	4696	6526	82656132	82654316	0.000000e+00	1109.0
5	TraesCS2D01G140100	chr2D	75.763	2294	460	57	4267	6527	82894276	82892046	0.000000e+00	1068.0
6	TraesCS2D01G140100	chr2D	82.958	622	97	9	2904	3524	628580137	628580750	3.530000e-153	553.0
7	TraesCS2D01G140100	chr2D	85.232	474	64	6	7170	7640	82872516	82872046	4.700000e-132	483.0
8	TraesCS2D01G140100	chr2D	84.600	487	71	4	7170	7655	82891807	82891324	1.690000e-131	481.0
9	TraesCS2D01G140100	chr2D	88.820	322	31	4	6562	6882	239711350	239711033	2.930000e-104	390.0
10	TraesCS2D01G140100	chr2A	97.013	6730	130	14	1484	8157	83020654	83013940	0.000000e+00	11249.0
11	TraesCS2D01G140100	chr2A	95.455	902	28	8	6	897	83022977	83022079	0.000000e+00	1426.0
12	TraesCS2D01G140100	chr2A	77.778	2268	440	44	4282	6521	83642460	83640229	0.000000e+00	1338.0
13	TraesCS2D01G140100	chr2A	77.095	2279	459	49	4286	6531	83422662	83420414	0.000000e+00	1258.0
14	TraesCS2D01G140100	chr2A	96.129	620	14	6	881	1492	83022066	83021449	0.000000e+00	1003.0
15	TraesCS2D01G140100	chr2A	83.200	625	91	11	2904	3524	676379523	676380137	2.110000e-155	560.0
16	TraesCS2D01G140100	chr2A	85.880	517	33	15	8148	8650	83010026	83009536	1.670000e-141	514.0
17	TraesCS2D01G140100	chr2A	85.806	465	65	1	7177	7641	83440014	83439551	7.800000e-135	492.0
18	TraesCS2D01G140100	chr2A	85.996	457	64	0	7184	7640	83426572	83426116	2.810000e-134	490.0
19	TraesCS2D01G140100	chr2A	80.620	645	108	14	7170	7798	83585214	83584571	4.700000e-132	483.0
20	TraesCS2D01G140100	chr2A	88.820	322	29	7	6562	6882	486504319	486504634	1.050000e-103	388.0
21	TraesCS2D01G140100	chr2B	91.371	2283	174	16	4254	6525	134480176	134477906	0.000000e+00	3103.0
22	TraesCS2D01G140100	chr2B	90.280	1533	88	24	7170	8650	134477341	134475818	0.000000e+00	1949.0
23	TraesCS2D01G140100	chr2B	76.424	2282	458	52	4267	6521	134550865	134548637	0.000000e+00	1160.0
24	TraesCS2D01G140100	chr2B	75.599	2295	460	64	4267	6527	134603357	134601129	0.000000e+00	1044.0
25	TraesCS2D01G140100	chr2B	79.848	1444	267	15	4792	6230	134569737	134568313	0.000000e+00	1033.0
26	TraesCS2D01G140100	chr2B	87.259	675	47	11	586	1257	134499548	134498910	0.000000e+00	734.0
27	TraesCS2D01G140100	chr2B	86.918	451	49	8	51	497	134500323	134499879	1.680000e-136	497.0
28	TraesCS2D01G140100	chr2B	84.232	501	66	8	7184	7683	134554945	134554457	7.860000e-130	475.0
29	TraesCS2D01G140100	chr2B	83.074	514	79	7	7170	7682	134600924	134600418	2.200000e-125	460.0
30	TraesCS2D01G140100	chr2B	88.820	322	28	7	6562	6882	283171670	283171356	1.050000e-103	388.0
31	TraesCS2D01G140100	chr2B	91.866	209	12	3	6883	7091	134477860	134477657	3.950000e-73	287.0
32	TraesCS2D01G140100	chr3B	83.628	623	92	8	2905	3525	741399271	741398657	2.090000e-160	577.0
33	TraesCS2D01G140100	chr5D	83.520	625	87	13	2904	3524	533670136	533669524	3.500000e-158	569.0
34	TraesCS2D01G140100	chr5D	82.759	638	97	11	2897	3531	434710345	434709718	2.730000e-154	556.0
35	TraesCS2D01G140100	chr5D	88.545	323	29	7	6562	6882	256469528	256469844	1.360000e-102	385.0
36	TraesCS2D01G140100	chr5B	82.986	623	96	8	2904	3524	69521229	69521843	9.810000e-154	555.0
37	TraesCS2D01G140100	chr5B	88.750	320	29	6	6566	6883	299731308	299730994	1.360000e-102	385.0
38	TraesCS2D01G140100	chr5B	86.869	99	10	3	1848	1944	540669099	540669002	3.300000e-19	108.0
39	TraesCS2D01G140100	chr7A	82.825	623	97	8	2904	3524	199929789	199929175	4.560000e-152	549.0
40	TraesCS2D01G140100	chr3A	82.720	625	97	7	2904	3526	458255612	458256227	5.900000e-151	545.0
41	TraesCS2D01G140100	chr3A	82.486	177	23	7	1386	1555	7348261	7348436	1.950000e-31	148.0
42	TraesCS2D01G140100	chr6A	82.992	488	51	17	1635	2116	604316373	604315912	6.250000e-111	412.0
43	TraesCS2D01G140100	chr7D	78.852	610	122	7	2120	2726	151023114	151022509	1.050000e-108	405.0
44	TraesCS2D01G140100	chr1D	88.889	324	29	6	6562	6883	180854702	180855020	8.140000e-105	392.0
45	TraesCS2D01G140100	chr1A	88.545	323	30	6	6562	6882	208893888	208894205	1.360000e-102	385.0
46	TraesCS2D01G140100	chrUn	88.308	325	31	5	6559	6882	129560446	129560764	4.900000e-102	383.0
47	TraesCS2D01G140100	chr5A	79.331	508	79	16	1623	2120	636470635	636470144	5.000000e-87	333.0
48	TraesCS2D01G140100	chr5A	94.286	35	1	1	2382	2416	545641025	545641058	1.600000e-02	52.8
49	TraesCS2D01G140100	chr4B	74.747	495	93	19	1867	2333	35632652	35632162	8.860000e-45	193.0
50	TraesCS2D01G140100	chr6D	75.111	225	48	6	1897	2120	437776985	437777202	1.990000e-16	99.0
51	TraesCS2D01G140100	chr6D	78.146	151	31	2	316	466	450106780	450106632	2.570000e-15	95.3

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	TraesCS2D01G140100	chr2D	82331794	82340443	8649	True	15974.000000	15974	100.000000	1	8650	1	chr2D.!!$R1	8649
1	TraesCS2D01G140100	chr2D	82645995	82648227	2232	True	1275.000000	1275	77.261000	4267	6522	1	chr2D.!!$R2	2255
2	TraesCS2D01G140100	chr2D	82835094	82837323	2229	True	1205.000000	1205	76.765000	4272	6526	1	chr2D.!!$R4	2254
3	TraesCS2D01G140100	chr2D	82654316	82656132	1816	True	1109.000000	1109	77.838000	4696	6526	1	chr2D.!!$R3	1830
4	TraesCS2D01G140100	chr2D	82872046	82874959	2913	True	850.500000	1218	81.050500	4276	7640	2	chr2D.!!$R6	3364
5	TraesCS2D01G140100	chr2D	82891324	82894276	2952	True	774.500000	1068	80.181500	4267	7655	2	chr2D.!!$R7	3388
6	TraesCS2D01G140100	chr2D	628580137	628580750	613	False	553.000000	553	82.958000	2904	3524	1	chr2D.!!$F1	620
7	TraesCS2D01G140100	chr2A	83009536	83022977	13441	True	3548.000000	11249	93.619250	6	8650	4	chr2A.!!$R4	8644
8	TraesCS2D01G140100	chr2A	83640229	83642460	2231	True	1338.000000	1338	77.778000	4282	6521	1	chr2A.!!$R3	2239
9	TraesCS2D01G140100	chr2A	83420414	83426572	6158	True	874.000000	1258	81.545500	4286	7640	2	chr2A.!!$R5	3354
10	TraesCS2D01G140100	chr2A	676379523	676380137	614	False	560.000000	560	83.200000	2904	3524	1	chr2A.!!$F2	620
11	TraesCS2D01G140100	chr2A	83584571	83585214	643	True	483.000000	483	80.620000	7170	7798	1	chr2A.!!$R2	628
12	TraesCS2D01G140100	chr2B	134475818	134480176	4358	True	1779.666667	3103	91.172333	4254	8650	3	chr2B.!!$R3	4396
13	TraesCS2D01G140100	chr2B	134568313	134569737	1424	True	1033.000000	1033	79.848000	4792	6230	1	chr2B.!!$R1	1438
14	TraesCS2D01G140100	chr2B	134548637	134554945	6308	True	817.500000	1160	80.328000	4267	7683	2	chr2B.!!$R5	3416
15	TraesCS2D01G140100	chr2B	134600418	134603357	2939	True	752.000000	1044	79.336500	4267	7682	2	chr2B.!!$R6	3415
16	TraesCS2D01G140100	chr2B	134498910	134500323	1413	True	615.500000	734	87.088500	51	1257	2	chr2B.!!$R4	1206
17	TraesCS2D01G140100	chr3B	741398657	741399271	614	True	577.000000	577	83.628000	2905	3525	1	chr3B.!!$R1	620
18	TraesCS2D01G140100	chr5D	533669524	533670136	612	True	569.000000	569	83.520000	2904	3524	1	chr5D.!!$R2	620
19	TraesCS2D01G140100	chr5D	434709718	434710345	627	True	556.000000	556	82.759000	2897	3531	1	chr5D.!!$R1	634
20	TraesCS2D01G140100	chr5B	69521229	69521843	614	False	555.000000	555	82.986000	2904	3524	1	chr5B.!!$F1	620
21	TraesCS2D01G140100	chr7A	199929175	199929789	614	True	549.000000	549	82.825000	2904	3524	1	chr7A.!!$R1	620
22	TraesCS2D01G140100	chr3A	458255612	458256227	615	False	545.000000	545	82.720000	2904	3526	1	chr3A.!!$F2	622
23	TraesCS2D01G140100	chr7D	151022509	151023114	605	True	405.000000	405	78.852000	2120	2726	1	chr7D.!!$R1	606

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
54	56	5.976458	TGCTTAATCCATTGGATCCAAAAC	58.024	37.500	30.28	13.36	42.27	2.43	F
1459	1782	2.047061	TCTTACAACTGACACCAGGCT	58.953	47.619	0.00	0.00	44.60	4.58	F
2996	4148	2.225068	AACATCCGCATCCGAACTAG	57.775	50.000	0.00	0.00	36.29	2.57	F
3183	4335	4.142600	CCAACATACAAGCCTAAGAAGTGC	60.143	45.833	0.00	0.00	0.00	4.40	F
3907	5061	0.964860	CCATTGCCAACCCGACATCA	60.965	55.000	0.00	0.00	0.00	3.07	F
3938	5092	3.252974	ACCTTGGAGATAAACTGCTCG	57.747	47.619	0.00	0.00	37.83	5.03	F
4864	6074	4.815269	TGTTTGTGTTCACTTTTGAAGGG	58.185	39.130	4.59	0.00	42.60	3.95	F
6713	7977	2.582052	TCCAAAAGATTGTCGTTGCCT	58.418	42.857	0.00	0.00	34.60	4.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1514	2640	1.620323	GCTGTGGGATTGGCTCTTTTT	59.380	47.619	0.00	0.00	0.00	1.94	R
3403	4556	2.309528	TACGAATGTGGTGAGGATGC	57.690	50.000	0.00	0.00	0.00	3.91	R
3801	4955	1.056660	GTGAGTGGAGAGTTGGGGAA	58.943	55.000	0.00	0.00	0.00	3.97	R
4066	5220	2.958355	TCTAAGGCTTGCAGCAACTTTT	59.042	40.909	14.39	7.22	44.75	2.27	R
5789	7008	2.333069	TGGCTCCTCCTCTGGAATATG	58.667	52.381	0.00	0.00	35.43	1.78	R
5973	7192	2.618816	CCTTTCAGCAATGCCTGGTCTA	60.619	50.000	0.00	0.00	31.85	2.59	R
6854	8118	0.605050	TTCATGCACTAGCCAACGCA	60.605	50.000	0.00	0.00	41.13	5.24	R
8094	9675	0.306228	CGGTGTGCGTTGTTCATCAA	59.694	50.000	0.00	0.00	0.00	2.57	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
39	41	7.877097	AGATCTCCATGTGTTATCTGCTTAATC	59.123	37.037	0.00	0.00	0.00	1.75
54	56	5.976458	TGCTTAATCCATTGGATCCAAAAC	58.024	37.500	30.28	13.36	42.27	2.43
647	923	7.744087	ACTGTTTTCATCAATTGTAGCTACA	57.256	32.000	22.67	22.67	0.00	2.74
1379	1698	7.079451	AGAAAAGAAAAGGTGATCCAGTAGA	57.921	36.000	0.00	0.00	35.89	2.59
1459	1782	2.047061	TCTTACAACTGACACCAGGCT	58.953	47.619	0.00	0.00	44.60	4.58
1480	1803	3.855689	ATTGCCAACTTACATCACAGC	57.144	42.857	0.00	0.00	0.00	4.40
1514	2640	3.603532	GATGCACACTCCTTGAAGATGA	58.396	45.455	0.00	0.00	0.00	2.92
1539	2665	2.276740	CCAATCCCACAGCCTCCC	59.723	66.667	0.00	0.00	0.00	4.30
2242	3392	4.501571	GCAAAAGGGGAAAGTTTTCTCTCC	60.502	45.833	0.00	0.00	37.79	3.71
2438	3588	2.286365	TGTCCAGGGTCCAAACAATC	57.714	50.000	0.00	0.00	0.00	2.67
2996	4148	2.225068	AACATCCGCATCCGAACTAG	57.775	50.000	0.00	0.00	36.29	2.57
3183	4335	4.142600	CCAACATACAAGCCTAAGAAGTGC	60.143	45.833	0.00	0.00	0.00	4.40
3238	4391	9.811995	TTAGAAATTATTACGCATCACAGTAGT	57.188	29.630	0.00	0.00	0.00	2.73
3240	4393	9.982651	AGAAATTATTACGCATCACAGTAGTAT	57.017	29.630	0.00	0.00	0.00	2.12
3403	4556	5.314409	CGATGTGTATCCGTATTCGAGTAG	58.686	45.833	0.00	0.00	39.71	2.57
3801	4955	6.538381	CCTTTCTAAAATTGCCAACAAACACT	59.462	34.615	0.00	0.00	39.77	3.55
3907	5061	0.964860	CCATTGCCAACCCGACATCA	60.965	55.000	0.00	0.00	0.00	3.07
3938	5092	3.252974	ACCTTGGAGATAAACTGCTCG	57.747	47.619	0.00	0.00	37.83	5.03
4066	5220	9.148879	TCATTTTTACTATTTCAAAGGACCCAA	57.851	29.630	0.00	0.00	0.00	4.12
4230	5384	9.893634	TGTATTCGGGTAATTTCAGAATTCTTA	57.106	29.630	4.86	0.00	36.82	2.10
4864	6074	4.815269	TGTTTGTGTTCACTTTTGAAGGG	58.185	39.130	4.59	0.00	42.60	3.95
5973	7192	8.027524	ACTGACATGACCAATATTAGTGAGAT	57.972	34.615	0.00	0.00	0.00	2.75
6522	7744	3.071206	GCGAGAGGTGAGCCCTGA	61.071	66.667	0.00	0.00	46.51	3.86
6603	7867	3.195825	GCCTAGGCTCTTTCACTAGTTCA	59.804	47.826	27.17	0.00	38.26	3.18
6712	7976	3.575965	ATCCAAAAGATTGTCGTTGCC	57.424	42.857	0.00	0.00	34.60	4.52
6713	7977	2.582052	TCCAAAAGATTGTCGTTGCCT	58.418	42.857	0.00	0.00	34.60	4.75
6823	8087	6.493189	TGAAGTGTATATGTGGATTGCCTA	57.507	37.500	0.00	0.00	34.31	3.93
6827	8091	4.760204	GTGTATATGTGGATTGCCTAACCC	59.240	45.833	0.00	0.00	34.31	4.11
6831	8095	2.802719	TGTGGATTGCCTAACCCTTTC	58.197	47.619	0.00	0.00	34.31	2.62
6874	8138	0.734889	GCGTTGGCTAGTGCATGAAT	59.265	50.000	0.00	0.00	41.91	2.57
7137	8413	7.906736	ACCACCTGACCATATATATAGGTTCAT	59.093	37.037	10.91	0.40	36.46	2.57
7163	8662	5.827267	TGCAGCAGAAGTTTGCCATATTATA	59.173	36.000	0.00	0.00	45.18	0.98
7165	8664	7.665145	TGCAGCAGAAGTTTGCCATATTATATA	59.335	33.333	0.00	0.00	45.18	0.86
7246	8757	0.460459	GCGGAACTAGAGGTCCTTGC	60.460	60.000	11.81	5.03	0.00	4.01
7448	8959	2.432510	GGAGTGCAATCCTAGCTACACT	59.567	50.000	25.54	11.11	40.85	3.55
7675	9190	4.684877	TGCATGTATTTGGATGATGTTGC	58.315	39.130	0.00	0.00	0.00	4.17
7896	9445	5.789643	ATGTGAAATGCCAAGTTACTTGT	57.210	34.783	21.63	4.74	39.58	3.16
7993	9542	3.403558	GCTGGGTGGGAGGAGGTC	61.404	72.222	0.00	0.00	0.00	3.85
7994	9543	3.077556	CTGGGTGGGAGGAGGTCG	61.078	72.222	0.00	0.00	0.00	4.79
7995	9544	3.596799	TGGGTGGGAGGAGGTCGA	61.597	66.667	0.00	0.00	0.00	4.20
7999	9552	0.751452	GGTGGGAGGAGGTCGATAAC	59.249	60.000	0.00	0.00	0.00	1.89
8005	9558	3.569277	GGGAGGAGGTCGATAACTAGAAC	59.431	52.174	0.00	0.00	0.00	3.01
8016	9569	9.460906	GGTCGATAACTAGAACAACCTAATAAG	57.539	37.037	0.00	0.00	0.00	1.73
8076	9657	7.633789	ACAGAGTACCAATCTCATAAAACCAT	58.366	34.615	0.00	0.00	34.73	3.55
8094	9675	7.823745	AAACCATGAACTGAACAGATTAGTT	57.176	32.000	8.87	0.00	37.36	2.24
8112	9693	2.116366	GTTTGATGAACAACGCACACC	58.884	47.619	0.00	0.00	38.29	4.16
8117	9698	3.521308	GAACAACGCACACCGCCAG	62.521	63.158	0.00	0.00	41.76	4.85
8120	9701	2.742372	AACGCACACCGCCAGATC	60.742	61.111	0.00	0.00	41.76	2.75
8166	13672	5.209240	TGTAAACAGTAAAGCGAACATTGC	58.791	37.500	0.00	0.00	0.00	3.56
8186	13692	0.737219	GTGCCATGATGAGAGCAACC	59.263	55.000	0.00	0.00	36.91	3.77
8265	13780	6.206438	TCTGATTTTCGATTCAATGAACACCA	59.794	34.615	0.00	0.00	0.00	4.17
8317	13832	4.024556	CAGTTAGTCTGTTTGCTCAACTGG	60.025	45.833	0.00	0.00	38.34	4.00
8330	13845	4.080919	TGCTCAACTGGCTAACACTGATAT	60.081	41.667	0.00	0.00	0.00	1.63
8398	13913	2.465860	AACGGTTATGCTGCAGTACA	57.534	45.000	16.64	5.99	0.00	2.90
8422	13937	3.740044	CACATAGTGGCACGGTAAAAG	57.260	47.619	12.71	2.13	0.00	2.27
8508	14025	1.831652	AAGCAGACGAACTGGGGAGG	61.832	60.000	13.82	0.00	45.82	4.30
8519	14036	2.557869	ACTGGGGAGGTTTGTGCTATA	58.442	47.619	0.00	0.00	0.00	1.31
8520	14037	3.123273	ACTGGGGAGGTTTGTGCTATAT	58.877	45.455	0.00	0.00	0.00	0.86
8521	14038	3.136626	ACTGGGGAGGTTTGTGCTATATC	59.863	47.826	0.00	0.00	0.00	1.63
8522	14039	3.392616	CTGGGGAGGTTTGTGCTATATCT	59.607	47.826	0.00	0.00	0.00	1.98
8523	14040	4.562767	TGGGGAGGTTTGTGCTATATCTA	58.437	43.478	0.00	0.00	0.00	1.98
8524	14041	5.162637	TGGGGAGGTTTGTGCTATATCTAT	58.837	41.667	0.00	0.00	0.00	1.98
8525	14042	6.327781	TGGGGAGGTTTGTGCTATATCTATA	58.672	40.000	0.00	0.00	0.00	1.31
8526	14043	6.212791	TGGGGAGGTTTGTGCTATATCTATAC	59.787	42.308	0.00	0.00	0.00	1.47
8527	14044	6.212791	GGGGAGGTTTGTGCTATATCTATACA	59.787	42.308	0.00	0.00	0.00	2.29
8528	14045	7.256547	GGGGAGGTTTGTGCTATATCTATACAA	60.257	40.741	0.00	0.00	0.00	2.41
8529	14046	7.603024	GGGAGGTTTGTGCTATATCTATACAAC	59.397	40.741	0.00	0.00	31.68	3.32
8530	14047	8.148351	GGAGGTTTGTGCTATATCTATACAACA	58.852	37.037	0.00	0.00	31.68	3.33
8573	14101	9.732130	AGAAATAGCAGATCTATTCCCAATAAC	57.268	33.333	0.00	0.00	44.89	1.89
8574	14102	9.732130	GAAATAGCAGATCTATTCCCAATAACT	57.268	33.333	0.00	0.00	44.89	2.24
8581	14111	5.708736	TCTATTCCCAATAACTCTTGGCA	57.291	39.130	0.00	0.00	43.66	4.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.107601	TGGAGATCTGTAGGGGTCAAAG	58.892	50.000	0.00	0.00	0.00	2.77
1	2	3.199442	TGGAGATCTGTAGGGGTCAAA	57.801	47.619	0.00	0.00	0.00	2.69
4	5	2.366916	CACATGGAGATCTGTAGGGGTC	59.633	54.545	0.00	0.00	0.00	4.46
39	41	3.929094	CAAGGTGTTTTGGATCCAATGG	58.071	45.455	27.53	5.75	35.70	3.16
54	56	7.546358	TGCAATACTTTCAATAATCCAAGGTG	58.454	34.615	0.00	0.00	0.00	4.00
632	908	3.947834	GCCCTTGTGTAGCTACAATTGAT	59.052	43.478	27.61	0.00	39.60	2.57
647	923	2.113139	CCGTTGTCCAGCCCTTGT	59.887	61.111	0.00	0.00	0.00	3.16
1459	1782	4.331108	TGCTGTGATGTAAGTTGGCAATA	58.669	39.130	1.92	0.00	0.00	1.90
1475	1798	1.725641	TCGTAGGATTTGCTGCTGTG	58.274	50.000	0.00	0.00	0.00	3.66
1480	1803	2.009051	TGTGCATCGTAGGATTTGCTG	58.991	47.619	11.18	0.00	0.00	4.41
1514	2640	1.620323	GCTGTGGGATTGGCTCTTTTT	59.380	47.619	0.00	0.00	0.00	1.94
1539	2665	6.152379	GGTAAAAATCTGCACTTCAAAGGAG	58.848	40.000	0.00	0.00	0.00	3.69
1902	3029	2.135933	GAAGAATAATGACGGAGGGCG	58.864	52.381	0.00	0.00	0.00	6.13
2242	3392	1.553248	TGATTCGTAGAGGGTGGGTTG	59.447	52.381	0.00	0.00	38.43	3.77
2996	4148	5.046376	ACACCTTCCATTTCCATTTCCATTC	60.046	40.000	0.00	0.00	0.00	2.67
3375	4528	2.875087	TACGGATACACATCGGTTGG	57.125	50.000	3.60	0.00	40.68	3.77
3403	4556	2.309528	TACGAATGTGGTGAGGATGC	57.690	50.000	0.00	0.00	0.00	3.91
3801	4955	1.056660	GTGAGTGGAGAGTTGGGGAA	58.943	55.000	0.00	0.00	0.00	3.97
3938	5092	6.625873	ACTCTTGTTTCTTGATTGGACTTC	57.374	37.500	0.00	0.00	0.00	3.01
4066	5220	2.958355	TCTAAGGCTTGCAGCAACTTTT	59.042	40.909	14.39	7.22	44.75	2.27
4249	5403	4.581409	TCCACAATGCAAGGATGACATATG	59.419	41.667	0.00	0.00	0.00	1.78
4864	6074	3.134458	GAGAATCACAATCCATCCGACC	58.866	50.000	0.00	0.00	33.17	4.79
4970	6183	4.083696	GCTTTGTGCTTTAAGGCGTACTAA	60.084	41.667	5.00	1.68	38.95	2.24
5789	7008	2.333069	TGGCTCCTCCTCTGGAATATG	58.667	52.381	0.00	0.00	35.43	1.78
5973	7192	2.618816	CCTTTCAGCAATGCCTGGTCTA	60.619	50.000	0.00	0.00	31.85	2.59
6603	7867	5.182001	CACTAGCTAATGCAACCAAAAGTCT	59.818	40.000	0.00	0.00	42.74	3.24
6712	7976	3.496870	GGCCTATACATGGACAAAGGGAG	60.497	52.174	0.00	0.00	31.53	4.30
6713	7977	2.441750	GGCCTATACATGGACAAAGGGA	59.558	50.000	0.00	0.00	31.53	4.20
6823	8087	7.797121	AATTTGAACTGATATGGAAAGGGTT	57.203	32.000	0.00	0.00	0.00	4.11
6854	8118	0.605050	TTCATGCACTAGCCAACGCA	60.605	50.000	0.00	0.00	41.13	5.24
6874	8138	2.227865	GGAAATGCCGCAACTGTTAAGA	59.772	45.455	0.00	0.00	0.00	2.10
7137	8413	1.908344	TGGCAAACTTCTGCTGCATA	58.092	45.000	1.31	0.00	42.25	3.14
7246	8757	4.202050	GGCATATTTGTGAACTAAGGCCAG	60.202	45.833	5.01	0.00	37.62	4.85
7448	8959	8.347004	TCATCCAGCATTTATTAAAACAGTCA	57.653	30.769	0.00	0.00	0.00	3.41
7675	9190	5.422666	TGTTGAGCAAATTGACAGTAGTG	57.577	39.130	0.00	0.00	0.00	2.74
7758	9306	1.412343	ACTTGCCAACACAACCCAATC	59.588	47.619	0.00	0.00	0.00	2.67
7764	9312	4.202010	ACAATGTAGACTTGCCAACACAAC	60.202	41.667	0.00	0.00	0.00	3.32
7896	9445	1.597195	GACTCACACAACGACAATGCA	59.403	47.619	0.00	0.00	0.00	3.96
8076	9657	8.559536	GTTCATCAAACTAATCTGTTCAGTTCA	58.440	33.333	0.00	0.00	34.85	3.18
8094	9675	0.306228	CGGTGTGCGTTGTTCATCAA	59.694	50.000	0.00	0.00	0.00	2.57
8112	9693	3.741249	TCAGTAGTACTAGGATCTGGCG	58.259	50.000	14.81	0.00	0.00	5.69
8117	9698	9.563748	AGTTGTCTTATCAGTAGTACTAGGATC	57.436	37.037	16.41	6.95	0.00	3.36
8120	9701	8.508883	ACAGTTGTCTTATCAGTAGTACTAGG	57.491	38.462	1.87	0.00	0.00	3.02
8149	9733	2.233355	CACGCAATGTTCGCTTTACTG	58.767	47.619	0.00	0.00	0.00	2.74
8166	13672	0.376152	GTTGCTCTCATCATGGCACG	59.624	55.000	0.00	0.00	34.30	5.34
8317	13832	6.017852	GGTTCTTAGCCAATATCAGTGTTAGC	60.018	42.308	0.00	0.00	0.00	3.09
8330	13845	4.563168	CCAAATTGCATGGTTCTTAGCCAA	60.563	41.667	0.00	0.00	39.72	4.52
8415	13930	9.888878	GAGTAACCTCAAATTTACACTTTTACC	57.111	33.333	0.00	0.00	37.67	2.85
8416	13931	9.888878	GGAGTAACCTCAAATTTACACTTTTAC	57.111	33.333	0.00	0.00	39.64	2.01
8417	13932	9.629878	TGGAGTAACCTCAAATTTACACTTTTA	57.370	29.630	0.00	0.00	39.64	1.52
8418	13933	8.528044	TGGAGTAACCTCAAATTTACACTTTT	57.472	30.769	0.00	0.00	39.64	2.27
8419	13934	7.255486	GCTGGAGTAACCTCAAATTTACACTTT	60.255	37.037	0.00	0.00	39.64	2.66
8420	13935	6.206829	GCTGGAGTAACCTCAAATTTACACTT	59.793	38.462	0.00	0.00	39.64	3.16
8421	13936	5.705905	GCTGGAGTAACCTCAAATTTACACT	59.294	40.000	0.00	0.00	39.64	3.55
8422	13937	5.472137	TGCTGGAGTAACCTCAAATTTACAC	59.528	40.000	0.00	0.00	39.64	2.90
8508	14025	8.266682	CGTGTGTTGTATAGATATAGCACAAAC	58.733	37.037	14.43	7.05	43.20	2.93
8519	14036	4.737855	AGAAGGCGTGTGTTGTATAGAT	57.262	40.909	0.00	0.00	0.00	1.98
8520	14037	4.530710	AAGAAGGCGTGTGTTGTATAGA	57.469	40.909	0.00	0.00	0.00	1.98
8521	14038	6.903883	AATAAGAAGGCGTGTGTTGTATAG	57.096	37.500	0.00	0.00	0.00	1.31
8522	14039	7.675962	AAAATAAGAAGGCGTGTGTTGTATA	57.324	32.000	0.00	0.00	0.00	1.47
8523	14040	6.569179	AAAATAAGAAGGCGTGTGTTGTAT	57.431	33.333	0.00	0.00	0.00	2.29
8524	14041	6.930164	TCTAAAATAAGAAGGCGTGTGTTGTA	59.070	34.615	0.00	0.00	0.00	2.41
8525	14042	4.911514	AAAATAAGAAGGCGTGTGTTGT	57.088	36.364	0.00	0.00	0.00	3.32
8526	14043	6.236017	TCTAAAATAAGAAGGCGTGTGTTG	57.764	37.500	0.00	0.00	0.00	3.33
8527	14044	6.870971	TTCTAAAATAAGAAGGCGTGTGTT	57.129	33.333	0.00	0.00	31.85	3.32
8528	14045	6.870971	TTTCTAAAATAAGAAGGCGTGTGT	57.129	33.333	0.00	0.00	36.85	3.72
8529	14046	7.640240	GCTATTTCTAAAATAAGAAGGCGTGTG	59.360	37.037	0.00	0.00	36.85	3.82
8530	14047	7.335924	TGCTATTTCTAAAATAAGAAGGCGTGT	59.664	33.333	0.00	0.00	36.85	4.49
8570	14098	3.626930	AGTTGTTTGGTGCCAAGAGTTA	58.373	40.909	3.72	0.00	37.24	2.24
8571	14099	2.456577	AGTTGTTTGGTGCCAAGAGTT	58.543	42.857	3.72	0.00	37.24	3.01
8572	14100	2.143876	AGTTGTTTGGTGCCAAGAGT	57.856	45.000	3.72	0.00	37.24	3.24
8573	14101	3.120199	CGATAGTTGTTTGGTGCCAAGAG	60.120	47.826	3.72	0.00	37.24	2.85
8574	14102	2.811431	CGATAGTTGTTTGGTGCCAAGA	59.189	45.455	3.72	0.00	37.24	3.02
8581	14111	1.280998	CCCCCTCGATAGTTGTTTGGT	59.719	52.381	0.00	0.00	37.40	3.67
8618	14148	6.445357	TTTAATTCTCCGGTTATTTGCTCC	57.555	37.500	0.00	0.00	0.00	4.70

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.