AutoCloner

Multiple sequence alignment - TraesCS4A01G293700

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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	TraesCS4A01G293700	chr4A	100.000	2604	0	0	1	2604	595441919	595444522	0.000000e+00	4809.0
1	TraesCS4A01G293700	chr4A	100.000	163	0	0	2865	3027	595444783	595444945	4.900000e-78	302.0
2	TraesCS4A01G293700	chr4D	86.978	2634	152	87	34	2604	7874975	7872470	0.000000e+00	2787.0
3	TraesCS4A01G293700	chr4B	86.334	2144	145	73	561	2604	14054208	14056303	0.000000e+00	2200.0
4	TraesCS4A01G293700	chr4B	80.778	463	56	16	3	452	14053704	14054146	6.260000e-87	331.0
5	TraesCS4A01G293700	chr4B	86.022	93	12	1	2192	2284	14078020	14078111	6.910000e-17	99.0
6	TraesCS4A01G293700	chr4B	94.915	59	2	1	2970	3027	14078035	14078093	1.160000e-14	91.6
7	TraesCS4A01G293700	chr4B	86.765	68	5	3	2865	2931	14056336	14056400	4.190000e-09	73.1
8	TraesCS4A01G293700	chr3D	83.083	2134	155	90	562	2604	551346700	551344682	0.000000e+00	1751.0
9	TraesCS4A01G293700	chr3D	84.452	1505	85	53	555	2041	551429952	551431325	0.000000e+00	1345.0
10	TraesCS4A01G293700	chr3D	85.000	600	51	15	2039	2604	551432586	551433180	9.410000e-160	573.0
11	TraesCS4A01G293700	chr3D	88.618	246	14	5	148	393	551350730	551350499	1.370000e-73	287.0
12	TraesCS4A01G293700	chr3D	76.845	393	67	18	2192	2570	551433854	551434236	1.840000e-47	200.0
13	TraesCS4A01G293700	chr3D	81.356	236	21	13	133	362	551429614	551429832	1.440000e-38	171.0
14	TraesCS4A01G293700	chr3D	84.848	99	7	4	2865	2955	551433214	551433312	3.210000e-15	93.5
15	TraesCS4A01G293700	chr3B	86.776	1467	104	41	1181	2604	731095665	731094246	0.000000e+00	1552.0
16	TraesCS4A01G293700	chr3B	81.753	696	47	44	449	1128	731096292	731095661	2.690000e-140	508.0
17	TraesCS4A01G293700	chr3B	86.496	274	14	6	137	410	731097117	731096867	2.300000e-71	279.0
18	TraesCS4A01G293700	chr3B	93.220	59	3	1	2970	3027	731094080	731094022	5.380000e-13	86.1
19	TraesCS4A01G293700	chr3A	84.867	1619	113	66	739	2332	688592218	688590707	0.000000e+00	1511.0
20	TraesCS4A01G293700	chr3A	79.079	239	20	13	243	481	688592592	688592384	1.460000e-28	137.0
21	TraesCS4A01G293700	chr7D	79.111	1125	142	47	970	2050	550800432	550801507	0.000000e+00	689.0
22	TraesCS4A01G293700	chr7D	82.626	754	84	27	1312	2050	550553393	550554114	9.220000e-175	623.0
23	TraesCS4A01G293700	chr7D	82.237	608	72	22	1447	2050	550655440	550656015	2.710000e-135	492.0
24	TraesCS4A01G293700	chr7D	76.654	257	32	15	2095	2333	550801664	550801910	1.910000e-22	117.0
25	TraesCS4A01G293700	chr7D	100.000	38	0	0	733	770	550462802	550462839	1.510000e-08	71.3
26	TraesCS4A01G293700	chr7D	100.000	38	0	0	733	770	550552890	550552927	1.510000e-08	71.3
27	TraesCS4A01G293700	chr7D	100.000	38	0	0	733	770	550800317	550800354	1.510000e-08	71.3
28	TraesCS4A01G293700	chr7B	78.929	1120	132	45	981	2050	595080552	595081617	0.000000e+00	665.0
29	TraesCS4A01G293700	chr7B	78.490	1139	149	46	969	2050	595007418	595008517	0.000000e+00	658.0
30	TraesCS4A01G293700	chr7B	77.485	1137	131	58	970	2050	595307322	595308389	1.580000e-157	566.0
31	TraesCS4A01G293700	chr7B	81.746	126	4	11	251	371	595306578	595306689	1.490000e-13	87.9
32	TraesCS4A01G293700	chr7B	100.000	38	0	0	733	770	595007258	595007295	1.510000e-08	71.3
33	TraesCS4A01G293700	chr7A	80.519	154	22	6	2133	2284	636145135	636145282	8.870000e-21	111.0
34	TraesCS4A01G293700	chr7A	75.806	248	28	22	114	354	636628340	636628562	2.480000e-16	97.1

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	TraesCS4A01G293700	chr4A	595441919	595444945	3026	False	2555.500000	4809	100.000000	1	3027	2	chr4A.!!$F1	3026
1	TraesCS4A01G293700	chr4D	7872470	7874975	2505	True	2787.000000	2787	86.978000	34	2604	1	chr4D.!!$R1	2570
2	TraesCS4A01G293700	chr4B	14053704	14056400	2696	False	868.033333	2200	84.625667	3	2931	3	chr4B.!!$F1	2928
3	TraesCS4A01G293700	chr3D	551344682	551350730	6048	True	1019.000000	1751	85.850500	148	2604	2	chr3D.!!$R1	2456
4	TraesCS4A01G293700	chr3D	551429614	551434236	4622	False	476.500000	1345	82.500200	133	2955	5	chr3D.!!$F1	2822
5	TraesCS4A01G293700	chr3B	731094022	731097117	3095	True	606.275000	1552	87.061250	137	3027	4	chr3B.!!$R1	2890
6	TraesCS4A01G293700	chr3A	688590707	688592592	1885	True	824.000000	1511	81.973000	243	2332	2	chr3A.!!$R1	2089
7	TraesCS4A01G293700	chr7D	550655440	550656015	575	False	492.000000	492	82.237000	1447	2050	1	chr7D.!!$F2	603
8	TraesCS4A01G293700	chr7D	550552890	550554114	1224	False	347.150000	623	91.313000	733	2050	2	chr7D.!!$F3	1317
9	TraesCS4A01G293700	chr7D	550800317	550801910	1593	False	292.433333	689	85.255000	733	2333	3	chr7D.!!$F4	1600
10	TraesCS4A01G293700	chr7B	595080552	595081617	1065	False	665.000000	665	78.929000	981	2050	1	chr7B.!!$F1	1069
11	TraesCS4A01G293700	chr7B	595007258	595008517	1259	False	364.650000	658	89.245000	733	2050	2	chr7B.!!$F2	1317
12	TraesCS4A01G293700	chr7B	595306578	595308389	1811	False	326.950000	566	79.615500	251	2050	2	chr7B.!!$F3	1799

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
222	246	0.321298	GGCGCTTTACCAAGTCCAGA	60.321	55.0	7.64	0.0	31.86	3.86	F
1386	6121	0.249398	ACAGACATGTAAGTCCCGGC	59.751	55.0	0.00	0.0	38.09	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1385	6120	0.096454	GCGATTAGTTTGGTGACGGC	59.904	55.0	0.0	0.0	0.0	5.68	R
2486	8742	0.261991	TCGGGCTCTATCTTCACCCT	59.738	55.0	0.0	0.0	38.5	4.34	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
177	194	5.440610	TGCAGTTTCCTTCTTCTTCTTCTT	58.559	37.500	0.00	0.00	0.00	2.52
218	242	1.495951	CACGGCGCTTTACCAAGTC	59.504	57.895	6.90	0.00	31.86	3.01
219	243	1.670083	ACGGCGCTTTACCAAGTCC	60.670	57.895	6.90	0.00	31.86	3.85
220	244	1.669760	CGGCGCTTTACCAAGTCCA	60.670	57.895	7.64	0.00	31.86	4.02
221	245	1.635663	CGGCGCTTTACCAAGTCCAG	61.636	60.000	7.64	0.00	31.86	3.86
222	246	0.321298	GGCGCTTTACCAAGTCCAGA	60.321	55.000	7.64	0.00	31.86	3.86
223	247	1.079503	GCGCTTTACCAAGTCCAGAG	58.920	55.000	0.00	0.00	31.86	3.35
224	248	1.726853	CGCTTTACCAAGTCCAGAGG	58.273	55.000	0.00	0.00	31.86	3.69
225	249	1.676014	CGCTTTACCAAGTCCAGAGGG	60.676	57.143	0.00	0.00	31.86	4.30
226	250	1.628846	GCTTTACCAAGTCCAGAGGGA	59.371	52.381	0.00	0.00	42.29	4.20
227	251	2.355209	GCTTTACCAAGTCCAGAGGGAG	60.355	54.545	0.00	0.00	46.12	4.30
228	252	3.173965	CTTTACCAAGTCCAGAGGGAGA	58.826	50.000	0.00	0.00	46.12	3.71
348	395	2.488355	CTGCTGATTTGGCGCCAG	59.512	61.111	30.75	18.91	0.00	4.85
368	435	5.618561	CCAGAACATGCTAACTTAAACGAC	58.381	41.667	0.00	0.00	0.00	4.34
403	479	3.509442	TGGTCTCCTTTGGCAAAATCAT	58.491	40.909	14.43	0.00	0.00	2.45
426	502	3.107601	CCATGGACTCGACCCCATATAT	58.892	50.000	5.56	0.00	40.95	0.86
427	503	4.286707	CCATGGACTCGACCCCATATATA	58.713	47.826	5.56	0.00	40.95	0.86
531	1151	6.716934	TCTTGGTTTCTAGTGATAGCTAGG	57.283	41.667	0.00	0.00	39.05	3.02
600	4919	3.244976	GTTGATTGAAACGGAAGGCATG	58.755	45.455	0.00	0.00	0.00	4.06
604	4923	3.574284	TTGAAACGGAAGGCATGAATG	57.426	42.857	0.00	0.00	0.00	2.67
647	4980	1.272769	GAGAAGGATAATCGGGGGTCG	59.727	57.143	0.00	0.00	40.90	4.79
681	5014	2.566724	CAGTTGCTTTCTCCTCTCTCCT	59.433	50.000	0.00	0.00	0.00	3.69
685	5018	2.042297	TGCTTTCTCCTCTCTCCTCTCA	59.958	50.000	0.00	0.00	0.00	3.27
686	5019	3.299503	GCTTTCTCCTCTCTCCTCTCAT	58.700	50.000	0.00	0.00	0.00	2.90
688	5021	4.796606	CTTTCTCCTCTCTCCTCTCATCT	58.203	47.826	0.00	0.00	0.00	2.90
691	5024	3.136443	TCTCCTCTCTCCTCTCATCTCAC	59.864	52.174	0.00	0.00	0.00	3.51
692	5025	3.122480	TCCTCTCTCCTCTCATCTCACT	58.878	50.000	0.00	0.00	0.00	3.41
871	5485	2.284921	CTCCCACTGCTCCTCCCA	60.285	66.667	0.00	0.00	0.00	4.37
872	5486	2.607750	TCCCACTGCTCCTCCCAC	60.608	66.667	0.00	0.00	0.00	4.61
873	5487	2.608988	CCCACTGCTCCTCCCACT	60.609	66.667	0.00	0.00	0.00	4.00
874	5488	2.667418	CCACTGCTCCTCCCACTG	59.333	66.667	0.00	0.00	0.00	3.66
875	5489	2.046507	CACTGCTCCTCCCACTGC	60.047	66.667	0.00	0.00	0.00	4.40
876	5490	2.203907	ACTGCTCCTCCCACTGCT	60.204	61.111	0.00	0.00	0.00	4.24
877	5491	2.289532	ACTGCTCCTCCCACTGCTC	61.290	63.158	0.00	0.00	0.00	4.26
878	5492	3.005539	TGCTCCTCCCACTGCTCC	61.006	66.667	0.00	0.00	0.00	4.70
879	5493	2.686835	GCTCCTCCCACTGCTCCT	60.687	66.667	0.00	0.00	0.00	3.69
880	5494	2.730524	GCTCCTCCCACTGCTCCTC	61.731	68.421	0.00	0.00	0.00	3.71
881	5495	2.039624	TCCTCCCACTGCTCCTCC	59.960	66.667	0.00	0.00	0.00	4.30
882	5496	3.086600	CCTCCCACTGCTCCTCCC	61.087	72.222	0.00	0.00	0.00	4.30
883	5497	2.284921	CTCCCACTGCTCCTCCCA	60.285	66.667	0.00	0.00	0.00	4.37
896	5526	2.432510	CTCCTCCCACATCTCACTAACC	59.567	54.545	0.00	0.00	0.00	2.85
902	5532	2.483714	CCACATCTCACTAACCCATCGG	60.484	54.545	0.00	0.00	0.00	4.18
904	5534	0.389391	ATCTCACTAACCCATCGGCG	59.611	55.000	0.00	0.00	0.00	6.46
928	5580	1.538047	CTTGGCTGCCTGTGTGTATT	58.462	50.000	21.03	0.00	0.00	1.89
939	5591	1.862201	TGTGTGTATTTATAGGCGCGC	59.138	47.619	25.94	25.94	0.00	6.86
940	5592	1.133407	TGTGTATTTATAGGCGCGCG	58.867	50.000	28.44	28.44	0.00	6.86
1385	6120	2.007049	GCACAGACATGTAAGTCCCGG	61.007	57.143	0.00	0.00	37.65	5.73
1386	6121	0.249398	ACAGACATGTAAGTCCCGGC	59.751	55.000	0.00	0.00	38.09	6.13
1388	6123	1.520787	GACATGTAAGTCCCGGCCG	60.521	63.158	21.04	21.04	32.36	6.13
1397	6136	4.629523	TCCCGGCCGTCACCAAAC	62.630	66.667	26.12	0.00	0.00	2.93
1416	6171	0.111704	CTAATCGCCGCGTTTGATCG	60.112	55.000	17.28	0.00	0.00	3.69
1429	6199	3.667960	CGTTTGATCGGGCTTTTCTCTTG	60.668	47.826	0.00	0.00	0.00	3.02
1431	6201	0.735471	GATCGGGCTTTTCTCTTGCC	59.265	55.000	0.00	0.00	45.42	4.52
1434	6204	0.961753	CGGGCTTTTCTCTTGCCTTT	59.038	50.000	0.00	0.00	45.45	3.11
1440	6211	4.034394	GGCTTTTCTCTTGCCTTTGTTTTG	59.966	41.667	0.00	0.00	43.05	2.44
1441	6212	4.869861	GCTTTTCTCTTGCCTTTGTTTTGA	59.130	37.500	0.00	0.00	0.00	2.69
1586	6361	2.943978	AAGGCCAAGGACGACGAGG	61.944	63.158	5.01	0.00	0.00	4.63
1838	6616	4.135153	CCGTCTGCGTGGAGGAGG	62.135	72.222	2.13	0.00	38.98	4.30
1839	6617	4.803426	CGTCTGCGTGGAGGAGGC	62.803	72.222	0.00	0.00	39.72	4.70
1840	6618	4.459089	GTCTGCGTGGAGGAGGCC	62.459	72.222	0.00	0.00	36.89	5.19
2163	8360	7.867445	TCAGTTGTTCAACAAGAAGAAAAAC	57.133	32.000	16.31	0.00	40.67	2.43
2171	8372	4.983671	ACAAGAAGAAAAACACAGTCCC	57.016	40.909	0.00	0.00	0.00	4.46
2245	8473	1.391485	GATATATGCGCTGCGACCAAG	59.609	52.381	28.07	0.00	0.00	3.61
2334	8573	3.634448	ACAAGGAGATGACATCTACGAGG	59.366	47.826	19.87	15.55	45.22	4.63
2337	8576	2.030363	GGAGATGACATCTACGAGGCTG	60.030	54.545	17.96	0.00	40.38	4.85
2353	8593	1.676678	GCTGCGACTATGGTGGAGGA	61.677	60.000	0.00	0.00	0.00	3.71
2415	8671	1.635817	AATGGGTGGATGGCTACGCT	61.636	55.000	0.00	0.00	38.88	5.07
2463	8719	5.014333	TGGATTGGCTAGTGTTAGGGTTTAA	59.986	40.000	0.00	0.00	0.00	1.52
2485	8741	3.445008	AGATCTAGACAACTGGGAAGCA	58.555	45.455	0.00	0.00	0.00	3.91
2486	8742	3.840666	AGATCTAGACAACTGGGAAGCAA	59.159	43.478	0.00	0.00	0.00	3.91
2510	8766	3.181465	GGTGAAGATAGAGCCCGATTCAA	60.181	47.826	0.00	0.00	0.00	2.69
2525	8786	3.426159	CGATTCAAATCCAACGGTCCAAG	60.426	47.826	0.00	0.00	31.68	3.61
2543	8806	7.041098	CGGTCCAAGGAGATTTGAATTTATAGG	60.041	40.741	0.00	0.00	0.00	2.57
2574	8837	1.406751	GGCTGGCAAAAGGTTTGTTGT	60.407	47.619	0.00	0.00	0.00	3.32
2575	8838	1.665169	GCTGGCAAAAGGTTTGTTGTG	59.335	47.619	2.92	0.00	0.00	3.33
2585	8848	6.879188	AAAGGTTTGTTGTGTAAATTCACG	57.121	33.333	0.00	0.00	40.74	4.35
2919	9182	4.354686	AGGCTGGGTAGGTTTAAGGTTTAA	59.645	41.667	0.00	0.00	0.00	1.52
2927	9190	7.607991	GGGTAGGTTTAAGGTTTAAAGGTCTAC	59.392	40.741	13.69	13.69	0.00	2.59
2928	9191	8.156820	GGTAGGTTTAAGGTTTAAAGGTCTACA	58.843	37.037	18.29	0.00	0.00	2.74
2941	9212	8.801882	TTAAAGGTCTACAAATATGAACCAGG	57.198	34.615	0.00	0.00	32.95	4.45
2942	9213	4.781934	AGGTCTACAAATATGAACCAGGC	58.218	43.478	0.00	0.00	32.95	4.85
2955	9226	1.068121	ACCAGGCTCAGGTTTAAGCT	58.932	50.000	0.00	0.00	35.33	3.74
2958	9229	3.073946	ACCAGGCTCAGGTTTAAGCTAAA	59.926	43.478	0.00	0.00	35.33	1.85
2959	9230	3.440522	CCAGGCTCAGGTTTAAGCTAAAC	59.559	47.826	0.00	9.14	45.51	2.01
3018	9309	1.976474	GCATCCAAGGGGTTTGCGA	60.976	57.895	0.00	0.00	35.68	5.10
3019	9310	1.883021	CATCCAAGGGGTTTGCGAC	59.117	57.895	0.00	0.00	35.37	5.19

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	5.026038	TGTAGACAGTTTTCGAGGGAAAA	57.974	39.130	0.00	0.00	46.88	2.29
26	27	2.029290	GCTGTAGACAGTTTTCGAGGGA	60.029	50.000	11.19	0.00	45.45	4.20
28	29	3.305398	AGCTGTAGACAGTTTTCGAGG	57.695	47.619	11.19	0.00	45.45	4.63
30	31	3.367087	GGCTAGCTGTAGACAGTTTTCGA	60.367	47.826	15.72	0.00	45.45	3.71
31	32	2.924290	GGCTAGCTGTAGACAGTTTTCG	59.076	50.000	15.72	0.06	45.45	3.46
32	33	3.926616	TGGCTAGCTGTAGACAGTTTTC	58.073	45.455	15.72	1.41	39.60	2.29
64	68	6.033619	GTGCTGAGATAAATATTACGTAGGCG	59.966	42.308	0.00	0.00	44.93	5.52
65	69	6.866770	TGTGCTGAGATAAATATTACGTAGGC	59.133	38.462	0.00	0.00	0.00	3.93
78	83	7.520119	CACGTACTTTAATGTGCTGAGATAA	57.480	36.000	4.33	0.00	30.14	1.75
120	125	2.716828	CGTACGTCCAAGCACTGCG	61.717	63.158	7.22	0.00	0.00	5.18
128	138	2.279985	TTTGGCGCGTACGTCCAA	60.280	55.556	28.01	28.01	45.45	3.53
177	194	2.900273	CGGAGGGCAATTCGGAGA	59.100	61.111	0.00	0.00	0.00	3.71
218	242	2.443016	CCTCCGGTCTCCCTCTGG	60.443	72.222	0.00	0.00	0.00	3.86
219	243	2.443016	CCCTCCGGTCTCCCTCTG	60.443	72.222	0.00	0.00	0.00	3.35
220	244	2.617538	TCCCTCCGGTCTCCCTCT	60.618	66.667	0.00	0.00	0.00	3.69
221	245	2.123640	CTCCCTCCGGTCTCCCTC	60.124	72.222	0.00	0.00	0.00	4.30
222	246	3.756783	CCTCCCTCCGGTCTCCCT	61.757	72.222	0.00	0.00	0.00	4.20
223	247	4.862823	CCCTCCCTCCGGTCTCCC	62.863	77.778	0.00	0.00	0.00	4.30
224	248	3.312989	TTCCCTCCCTCCGGTCTCC	62.313	68.421	0.00	0.00	0.00	3.71
225	249	1.758906	CTTCCCTCCCTCCGGTCTC	60.759	68.421	0.00	0.00	0.00	3.36
226	250	2.364961	CTTCCCTCCCTCCGGTCT	59.635	66.667	0.00	0.00	0.00	3.85
227	251	3.471806	GCTTCCCTCCCTCCGGTC	61.472	72.222	0.00	0.00	0.00	4.79
348	395	5.303485	GTCGTCGTTTAAGTTAGCATGTTC	58.697	41.667	0.00	0.00	0.00	3.18
368	435	0.658368	AGACCAGATCATCGTCGTCG	59.342	55.000	0.00	0.00	38.55	5.12
403	479	3.399181	GGGGTCGAGTCCATGGCA	61.399	66.667	6.96	0.00	0.00	4.92
454	1066	2.016318	CACAAGAGTCTGCAACCAACA	58.984	47.619	0.00	0.00	0.00	3.33
520	1140	1.262417	GCTCCCCTCCTAGCTATCAC	58.738	60.000	0.00	0.00	35.80	3.06
521	1141	0.860457	TGCTCCCCTCCTAGCTATCA	59.140	55.000	0.00	0.00	39.53	2.15
522	1142	1.203125	AGTGCTCCCCTCCTAGCTATC	60.203	57.143	0.00	0.00	39.53	2.08
524	1144	0.186386	GAGTGCTCCCCTCCTAGCTA	59.814	60.000	0.00	0.00	39.53	3.32
525	1145	1.075600	GAGTGCTCCCCTCCTAGCT	60.076	63.158	0.00	0.00	39.53	3.32
526	1146	2.137528	GGAGTGCTCCCCTCCTAGC	61.138	68.421	6.98	0.00	44.29	3.42
556	4865	9.434275	CAACCTCTCCCCCTTTAATAATTTATT	57.566	33.333	6.85	6.85	0.00	1.40
557	4866	8.797674	TCAACCTCTCCCCCTTTAATAATTTAT	58.202	33.333	0.00	0.00	0.00	1.40
558	4867	8.177438	TCAACCTCTCCCCCTTTAATAATTTA	57.823	34.615	0.00	0.00	0.00	1.40
559	4868	7.051696	TCAACCTCTCCCCCTTTAATAATTT	57.948	36.000	0.00	0.00	0.00	1.82
567	4876	2.358258	TCAATCAACCTCTCCCCCTTT	58.642	47.619	0.00	0.00	0.00	3.11
600	4919	2.099756	CAGGGGCGATTTCCTTTCATTC	59.900	50.000	0.00	0.00	0.00	2.67
604	4923	1.834188	TTCAGGGGCGATTTCCTTTC	58.166	50.000	0.00	0.00	0.00	2.62
647	4980	3.435105	AGCAACTGACGATGAGATCTC	57.565	47.619	16.21	16.21	0.00	2.75
648	4981	3.883830	AAGCAACTGACGATGAGATCT	57.116	42.857	0.00	0.00	0.00	2.75
681	5014	0.397675	ATGGCCGGAGTGAGATGAGA	60.398	55.000	5.05	0.00	0.00	3.27
685	5018	0.911769	TTTGATGGCCGGAGTGAGAT	59.088	50.000	5.05	0.00	0.00	2.75
686	5019	0.036388	GTTTGATGGCCGGAGTGAGA	60.036	55.000	5.05	0.00	0.00	3.27
688	5021	1.375396	CGTTTGATGGCCGGAGTGA	60.375	57.895	5.05	0.00	0.00	3.41
691	5024	2.398554	CCACGTTTGATGGCCGGAG	61.399	63.158	5.05	0.00	0.00	4.63
692	5025	2.359354	CCACGTTTGATGGCCGGA	60.359	61.111	5.05	0.00	0.00	5.14
771	5336	3.450115	GAGGTCCGTCCCGTCCTG	61.450	72.222	3.15	0.00	36.75	3.86
821	5407	1.374758	GGATCGGCGATGGATGGAC	60.375	63.158	29.20	10.59	0.00	4.02
871	5485	0.252421	TGAGATGTGGGAGGAGCAGT	60.252	55.000	0.00	0.00	0.00	4.40
872	5486	0.177604	GTGAGATGTGGGAGGAGCAG	59.822	60.000	0.00	0.00	0.00	4.24
873	5487	0.252421	AGTGAGATGTGGGAGGAGCA	60.252	55.000	0.00	0.00	0.00	4.26
874	5488	1.781786	TAGTGAGATGTGGGAGGAGC	58.218	55.000	0.00	0.00	0.00	4.70
875	5489	2.432510	GGTTAGTGAGATGTGGGAGGAG	59.567	54.545	0.00	0.00	0.00	3.69
876	5490	2.467880	GGTTAGTGAGATGTGGGAGGA	58.532	52.381	0.00	0.00	0.00	3.71
877	5491	1.486726	GGGTTAGTGAGATGTGGGAGG	59.513	57.143	0.00	0.00	0.00	4.30
878	5492	2.187958	TGGGTTAGTGAGATGTGGGAG	58.812	52.381	0.00	0.00	0.00	4.30
879	5493	2.335681	TGGGTTAGTGAGATGTGGGA	57.664	50.000	0.00	0.00	0.00	4.37
880	5494	2.483714	CGATGGGTTAGTGAGATGTGGG	60.484	54.545	0.00	0.00	0.00	4.61
881	5495	2.483714	CCGATGGGTTAGTGAGATGTGG	60.484	54.545	0.00	0.00	0.00	4.17
882	5496	2.826428	CCGATGGGTTAGTGAGATGTG	58.174	52.381	0.00	0.00	0.00	3.21
883	5497	1.139058	GCCGATGGGTTAGTGAGATGT	59.861	52.381	0.00	0.00	34.97	3.06
1385	6120	0.096454	GCGATTAGTTTGGTGACGGC	59.904	55.000	0.00	0.00	0.00	5.68
1386	6121	0.725117	GGCGATTAGTTTGGTGACGG	59.275	55.000	0.00	0.00	0.00	4.79
1388	6123	0.096454	GCGGCGATTAGTTTGGTGAC	59.904	55.000	12.98	0.00	0.00	3.67
1397	6136	0.111704	CGATCAAACGCGGCGATTAG	60.112	55.000	30.94	17.05	0.00	1.73
1429	6199	6.964370	GGTTAACAACAAATCAAAACAAAGGC	59.036	34.615	8.10	0.00	0.00	4.35
1431	6201	7.686120	CACGGTTAACAACAAATCAAAACAAAG	59.314	33.333	8.10	0.00	0.00	2.77
1434	6204	5.577164	CCACGGTTAACAACAAATCAAAACA	59.423	36.000	8.10	0.00	0.00	2.83
1440	6211	3.315749	TCCACCACGGTTAACAACAAATC	59.684	43.478	8.10	0.00	35.57	2.17
1441	6212	3.288964	TCCACCACGGTTAACAACAAAT	58.711	40.909	8.10	0.00	35.57	2.32
1864	6666	1.985116	GCACCTTCCGACTCCTCCT	60.985	63.158	0.00	0.00	0.00	3.69
1865	6667	1.827399	TTGCACCTTCCGACTCCTCC	61.827	60.000	0.00	0.00	0.00	4.30
1866	6668	0.390472	CTTGCACCTTCCGACTCCTC	60.390	60.000	0.00	0.00	0.00	3.71
2163	8360	6.101650	TGATATGCAATACTAGGGACTGTG	57.898	41.667	0.00	0.00	41.52	3.66
2334	8573	1.227380	CCTCCACCATAGTCGCAGC	60.227	63.158	0.00	0.00	0.00	5.25
2337	8576	1.068250	GCTCCTCCACCATAGTCGC	59.932	63.158	0.00	0.00	0.00	5.19
2353	8593	3.343788	CTCGCCCTCGTTTCTCGCT	62.344	63.158	0.00	0.00	39.67	4.93
2383	8639	2.360801	CCACCCATTTCTCAAACGTGTT	59.639	45.455	0.00	0.00	0.00	3.32
2384	8640	1.953686	CCACCCATTTCTCAAACGTGT	59.046	47.619	0.00	0.00	0.00	4.49
2386	8642	2.649531	TCCACCCATTTCTCAAACGT	57.350	45.000	0.00	0.00	0.00	3.99
2463	8719	3.840666	TGCTTCCCAGTTGTCTAGATCTT	59.159	43.478	0.00	0.00	0.00	2.40
2485	8741	1.123928	CGGGCTCTATCTTCACCCTT	58.876	55.000	0.00	0.00	38.50	3.95
2486	8742	0.261991	TCGGGCTCTATCTTCACCCT	59.738	55.000	0.00	0.00	38.50	4.34
2510	8766	1.358152	TCTCCTTGGACCGTTGGATT	58.642	50.000	1.16	0.00	0.00	3.01
2543	8806	1.881591	TTGCCAGCCAAGCAAATTTC	58.118	45.000	3.38	0.00	46.71	2.17
2553	8816	0.908198	AACAAACCTTTTGCCAGCCA	59.092	45.000	0.00	0.00	0.00	4.75
2574	8837	5.849357	ATAGTCGTTTGCGTGAATTTACA	57.151	34.783	0.95	0.00	39.49	2.41
2575	8838	5.887288	CGTATAGTCGTTTGCGTGAATTTAC	59.113	40.000	0.00	0.00	39.49	2.01
2866	9129	2.450345	CGCCGCTAGGAAACGAACC	61.450	63.158	0.00	0.00	41.02	3.62
2870	9133	2.890474	ATGCGCCGCTAGGAAACG	60.890	61.111	11.67	0.00	41.02	3.60
2903	9166	9.559732	TTGTAGACCTTTAAACCTTAAACCTAC	57.440	33.333	0.00	0.00	0.00	3.18
2919	9182	5.044846	AGCCTGGTTCATATTTGTAGACCTT	60.045	40.000	0.00	0.00	0.00	3.50
2927	9190	3.624777	ACCTGAGCCTGGTTCATATTTG	58.375	45.455	13.86	1.97	31.67	2.32
2928	9191	4.322057	AACCTGAGCCTGGTTCATATTT	57.678	40.909	13.86	4.89	40.76	1.40
2998	9288	1.814772	CGCAAACCCCTTGGATGCAA	61.815	55.000	0.00	0.00	43.52	4.08

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.