AutoCloner

Multiple sequence alignment - TraesCS5D01G175800

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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	TraesCS5D01G175800	chr5D	100.000	6172	0	0	1	6172	275617115	275610944	0.000000e+00	11398.0
1	TraesCS5D01G175800	chr5A	96.333	4172	117	16	1272	5426	364423232	364419080	0.000000e+00	6824.0
2	TraesCS5D01G175800	chr5A	94.140	1075	26	7	214	1280	364424702	364423657	0.000000e+00	1602.0
3	TraesCS5D01G175800	chr5A	95.420	262	4	3	1	256	364424971	364424712	1.600000e-110	411.0
4	TraesCS5D01G175800	chr5B	97.345	2260	42	9	3132	5390	312911000	312908758	0.000000e+00	3825.0
5	TraesCS5D01G175800	chr5B	95.622	1713	50	6	251	1951	312914146	312912447	0.000000e+00	2724.0
6	TraesCS5D01G175800	chr5B	89.080	815	51	17	1947	2756	312912177	312911396	0.000000e+00	977.0
7	TraesCS5D01G175800	chr5B	97.727	220	4	1	1	220	312914359	312914141	1.620000e-100	377.0
8	TraesCS5D01G175800	chr5B	86.286	175	16	7	2743	2914	312911378	312911209	3.800000e-42	183.0
9	TraesCS5D01G175800	chr5B	92.000	125	7	3	2920	3042	312911156	312911033	8.230000e-39	172.0
10	TraesCS5D01G175800	chr1D	95.068	730	32	3	5445	6172	206092233	206092960	0.000000e+00	1146.0
11	TraesCS5D01G175800	chr1D	92.857	756	40	8	5427	6172	198893672	198892921	0.000000e+00	1085.0
12	TraesCS5D01G175800	chr4D	93.964	729	37	6	5446	6172	396428889	396428166	0.000000e+00	1096.0
13	TraesCS5D01G175800	chr2B	93.844	731	39	5	5445	6172	8420627	8421354	0.000000e+00	1096.0
14	TraesCS5D01G175800	chr7D	93.750	736	35	6	5445	6172	179991416	179990684	0.000000e+00	1094.0
15	TraesCS5D01G175800	chr7D	93.699	730	42	3	5445	6172	98277669	98278396	0.000000e+00	1090.0
16	TraesCS5D01G175800	chr7D	92.583	755	44	6	5427	6172	630728803	630729554	0.000000e+00	1074.0
17	TraesCS5D01G175800	chr7D	75.000	284	57	14	3290	3565	99954147	99953870	1.090000e-22	119.0
18	TraesCS5D01G175800	chr1B	93.836	730	40	4	5445	6172	283913287	283912561	0.000000e+00	1094.0
19	TraesCS5D01G175800	chr3B	92.510	761	46	5	5420	6172	223525702	223524945	0.000000e+00	1079.0
20	TraesCS5D01G175800	chr3B	91.489	47	3	1	4402	4447	131497891	131497937	5.160000e-06	63.9
21	TraesCS5D01G175800	chr3B	84.058	69	8	3	4381	4447	132622960	132623027	5.160000e-06	63.9
22	TraesCS5D01G175800	chr7A	74.737	285	56	16	3290	3565	102334079	102333802	5.060000e-21	113.0
23	TraesCS5D01G175800	chr7B	73.927	303	64	15	3272	3565	55342469	55342173	2.350000e-19	108.0
24	TraesCS5D01G175800	chr3A	93.023	43	3	0	4408	4450	100018275	100018233	5.160000e-06	63.9
25	TraesCS5D01G175800	chr3D	97.143	35	1	0	4416	4450	83922898	83922864	6.680000e-05	60.2

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	TraesCS5D01G175800	chr5D	275610944	275617115	6171	True	11398.000000	11398	100.000000	1	6172	1	chr5D.!!$R1	6171
1	TraesCS5D01G175800	chr5A	364419080	364424971	5891	True	2945.666667	6824	95.297667	1	5426	3	chr5A.!!$R1	5425
2	TraesCS5D01G175800	chr5B	312908758	312914359	5601	True	1376.333333	3825	93.010000	1	5390	6	chr5B.!!$R1	5389
3	TraesCS5D01G175800	chr1D	206092233	206092960	727	False	1146.000000	1146	95.068000	5445	6172	1	chr1D.!!$F1	727
4	TraesCS5D01G175800	chr1D	198892921	198893672	751	True	1085.000000	1085	92.857000	5427	6172	1	chr1D.!!$R1	745
5	TraesCS5D01G175800	chr4D	396428166	396428889	723	True	1096.000000	1096	93.964000	5446	6172	1	chr4D.!!$R1	726
6	TraesCS5D01G175800	chr2B	8420627	8421354	727	False	1096.000000	1096	93.844000	5445	6172	1	chr2B.!!$F1	727
7	TraesCS5D01G175800	chr7D	179990684	179991416	732	True	1094.000000	1094	93.750000	5445	6172	1	chr7D.!!$R2	727
8	TraesCS5D01G175800	chr7D	98277669	98278396	727	False	1090.000000	1090	93.699000	5445	6172	1	chr7D.!!$F1	727
9	TraesCS5D01G175800	chr7D	630728803	630729554	751	False	1074.000000	1074	92.583000	5427	6172	1	chr7D.!!$F2	745
10	TraesCS5D01G175800	chr1B	283912561	283913287	726	True	1094.000000	1094	93.836000	5445	6172	1	chr1B.!!$R1	727
11	TraesCS5D01G175800	chr3B	223524945	223525702	757	True	1079.000000	1079	92.510000	5420	6172	1	chr3B.!!$R1	752

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	Hairpin	End Stability	Orientation
414	473	0.179227	CACACACACACACACACACG	60.179	55.0	0.00	0.00	4.49	F
1324	1842	0.773644	ATCTGAAACACAGGGTGGCT	59.226	50.0	1.07	45.76	4.75	F
2283	3077	0.657312	CCGCTCGCAATGATTAGCAA	59.343	50.0	0.09	34.60	3.91	F
3057	3942	0.032615	ACCCCCAAACAAAGAGTGCA	60.033	50.0	0.00	0.00	4.57	F
3607	4492	0.758685	CCTCCCAGGTTTGTTGGCAA	60.759	55.0	0.00	34.26	4.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1512	2031	2.915738	CAGGTGCTCTGCTTTTGATC	57.084	50.000	0.00	36.60	2.92	R
2569	3363	0.625316	ACATGCATCACTAAGGCCCA	59.375	50.000	0.00	0.00	5.36	R
4223	5117	0.394938	TGGAACTGCGCCAAGAAGTA	59.605	50.000	4.18	37.91	2.24	R
5011	5905	1.444895	GCAAGAAGTTGGCCATGCG	60.445	57.895	6.09	33.87	4.73	R
5415	6313	2.252072	TATCCAACAGACGGCAGGGC	62.252	60.000	0.00	0.00	5.19	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
66	67	1.106944	GGAGAGGAGGAGGAAGAGCG	61.107	65.000	0.00	0.00	0.00	5.03
116	123	2.519302	GCTTGTGGTGGTGCCTGT	60.519	61.111	0.00	0.00	38.35	4.00
188	195	7.624549	ACATATATCACCACTGTTTGTTCTCT	58.375	34.615	0.00	0.00	0.00	3.10
249	256	4.892345	TCTCTCTCTCTCTCTCTCTCTCTG	59.108	50.000	0.00	0.00	0.00	3.35
398	457	1.276705	AGGTACACACACACACACACA	59.723	47.619	0.00	0.00	0.00	3.72
414	473	0.179227	CACACACACACACACACACG	60.179	55.000	0.00	0.00	0.00	4.49
415	474	1.225991	CACACACACACACACACGC	60.226	57.895	0.00	0.00	0.00	5.34
416	475	1.669437	ACACACACACACACACGCA	60.669	52.632	0.00	0.00	0.00	5.24
417	476	1.225991	CACACACACACACACGCAC	60.226	57.895	0.00	0.00	0.00	5.34
418	477	2.021243	CACACACACACACGCACG	59.979	61.111	0.00	0.00	0.00	5.34
430	489	1.061262	CACGCACGCATCACACATTG	61.061	55.000	0.00	0.00	0.00	2.82
599	658	7.838193	AGCTCCTTTCAGGAAAATCTCAATTAT	59.162	33.333	0.00	0.00	45.28	1.28
839	898	3.307339	GCATAAACCCCAAGGAAATGCAA	60.307	43.478	0.00	0.00	41.51	4.08
841	900	3.941704	AAACCCCAAGGAAATGCAAAA	57.058	38.095	0.00	0.00	36.73	2.44
1127	1204	3.288092	ACGTTTTCTGGGCTTCTCTTTT	58.712	40.909	0.00	0.00	0.00	2.27
1137	1214	4.037923	TGGGCTTCTCTTTTGTTCATCAAC	59.962	41.667	0.00	0.00	35.61	3.18
1283	1793	7.496591	AGTTGTAGACAAGGTTATGAAAACGAA	59.503	33.333	0.00	0.00	36.39	3.85
1316	1834	4.141597	TGGACAGTGGTTATCTGAAACACA	60.142	41.667	8.10	0.00	36.81	3.72
1318	1836	4.389374	ACAGTGGTTATCTGAAACACAGG	58.611	43.478	8.10	2.69	45.76	4.00
1319	1837	3.753272	CAGTGGTTATCTGAAACACAGGG	59.247	47.826	8.10	0.00	45.76	4.45
1320	1838	3.394606	AGTGGTTATCTGAAACACAGGGT	59.605	43.478	8.10	0.00	45.76	4.34
1321	1839	3.502211	GTGGTTATCTGAAACACAGGGTG	59.498	47.826	0.67	0.00	45.76	4.61
1322	1840	3.081804	GGTTATCTGAAACACAGGGTGG	58.918	50.000	1.07	0.00	45.76	4.61
1323	1841	2.488153	GTTATCTGAAACACAGGGTGGC	59.512	50.000	1.07	0.00	45.76	5.01
1324	1842	0.773644	ATCTGAAACACAGGGTGGCT	59.226	50.000	1.07	0.00	45.76	4.75
1325	1843	1.429930	TCTGAAACACAGGGTGGCTA	58.570	50.000	1.07	0.00	45.76	3.93
1379	1897	8.476447	TCGGTTGTCATAGGTTGTAACATAATA	58.524	33.333	0.00	0.00	0.00	0.98
1512	2031	2.415168	TGCTCCGTATTTTCTTGAAGCG	59.585	45.455	0.00	0.00	0.00	4.68
1528	2047	0.801251	AGCGATCAAAAGCAGAGCAC	59.199	50.000	0.00	0.00	35.48	4.40
1960	2753	1.606668	GTTGTCACCAAATCCTTCGCA	59.393	47.619	0.00	0.00	30.94	5.10
2098	2891	3.073062	CCTATGGCCACATTACCTTAGCT	59.927	47.826	8.16	0.00	38.53	3.32
2099	2892	3.669939	ATGGCCACATTACCTTAGCTT	57.330	42.857	8.16	0.00	32.00	3.74
2100	2893	4.788925	ATGGCCACATTACCTTAGCTTA	57.211	40.909	8.16	0.00	32.00	3.09
2101	2894	4.150897	TGGCCACATTACCTTAGCTTAG	57.849	45.455	0.00	0.00	0.00	2.18
2102	2895	3.521937	TGGCCACATTACCTTAGCTTAGT	59.478	43.478	0.00	0.00	0.00	2.24
2221	3014	4.352893	TCCTCAAGATATGTCACCTGTGA	58.647	43.478	0.00	0.00	37.24	3.58
2283	3077	0.657312	CCGCTCGCAATGATTAGCAA	59.343	50.000	0.09	0.00	34.60	3.91
2390	3184	2.438392	GGGTTCATAGGACCGAGGATTT	59.562	50.000	0.00	0.00	38.08	2.17
2392	3186	3.134081	GGTTCATAGGACCGAGGATTTGA	59.866	47.826	0.00	0.00	0.00	2.69
2534	3328	6.886459	TGGAGAATAGGGTGAATTTCTCTTTG	59.114	38.462	10.35	0.00	42.29	2.77
2538	3332	4.453480	AGGGTGAATTTCTCTTTGGTCA	57.547	40.909	0.00	0.00	0.00	4.02
2544	3338	6.348868	GGTGAATTTCTCTTTGGTCATCTGTC	60.349	42.308	0.00	0.00	0.00	3.51
2562	3356	7.343057	TCATCTGTCCTGAATGTCACTAGTTAT	59.657	37.037	0.00	0.00	0.00	1.89
2569	3363	8.375506	TCCTGAATGTCACTAGTTATTGACTTT	58.624	33.333	11.28	10.79	42.31	2.66
2696	3491	7.490725	CACTATCAGTAAGGTTCAGATTCAGTG	59.509	40.741	0.00	0.00	0.00	3.66
2708	3503	7.041098	GGTTCAGATTCAGTGAAGTGTATTGTT	60.041	37.037	11.91	0.00	34.59	2.83
2741	3538	4.039852	ACACAAAAGAAAACGGGGCATAAT	59.960	37.500	0.00	0.00	0.00	1.28
2785	3613	5.241728	GTGATTCTAACTTGCCAGGAAAGTT	59.758	40.000	26.45	26.45	46.72	2.66
2802	3630	7.227512	CAGGAAAGTTCAACATTACTTGTCTCT	59.772	37.037	0.00	0.00	37.68	3.10
3047	3932	1.679153	CACAGTTACACACCCCCAAAC	59.321	52.381	0.00	0.00	0.00	2.93
3056	3941	0.389025	CACCCCCAAACAAAGAGTGC	59.611	55.000	0.00	0.00	0.00	4.40
3057	3942	0.032615	ACCCCCAAACAAAGAGTGCA	60.033	50.000	0.00	0.00	0.00	4.57
3076	3961	6.675987	AGTGCAAGAAGAAAGAAAATGCTAG	58.324	36.000	0.00	0.00	33.66	3.42
3125	4010	3.740115	ACAAGTTGTAGTTGTAGGGCAG	58.260	45.455	6.75	0.00	39.77	4.85
3607	4492	0.758685	CCTCCCAGGTTTGTTGGCAA	60.759	55.000	0.00	0.00	34.26	4.52
3658	4552	4.021544	TGGCGCCAAGATTTGAATAGTTTT	60.022	37.500	30.74	0.00	0.00	2.43
3760	4654	0.836400	ACTGGTGGACGGAGGACATT	60.836	55.000	0.00	0.00	0.00	2.71
4501	5395	0.977395	GATCCCTCCCACCTAATCGG	59.023	60.000	0.00	0.00	39.35	4.18
4594	5488	1.880340	GATCGACTGCCGGAAGCTG	60.880	63.158	10.27	1.47	44.23	4.24
4630	5524	1.871080	CTCAGGCGGTATCCAATGAC	58.129	55.000	0.00	0.00	0.00	3.06
4925	5819	1.079750	GACAGGACGGTGGAAGAGC	60.080	63.158	0.00	0.00	0.00	4.09
5033	5927	1.891150	CATGGCCAACTTCTTGCTTCT	59.109	47.619	10.96	0.00	0.00	2.85
5114	6008	2.307496	TTGGTTTCAGTGCATCCCAT	57.693	45.000	0.00	0.00	0.00	4.00
5409	6307	0.827925	TTCAGGACGCCTCTGTGACT	60.828	55.000	0.00	0.00	34.15	3.41
5415	6313	2.262915	GCCTCTGTGACTGTCGGG	59.737	66.667	2.98	1.95	0.00	5.14
5437	6335	2.643551	CCTGCCGTCTGTTGGATAATT	58.356	47.619	0.00	0.00	0.00	1.40
5451	6355	7.620880	TGTTGGATAATTAGCAACTACTGAGT	58.379	34.615	2.72	0.00	37.59	3.41
5497	6402	3.287222	TGTGGTAAAGTGCAGAAAAGCT	58.713	40.909	0.00	0.00	34.99	3.74
5507	6412	5.749462	AGTGCAGAAAAGCTCCTTATACAT	58.251	37.500	0.00	0.00	34.99	2.29
5527	6433	4.230502	ACATTGGGGATGTACAGAAAGGAT	59.769	41.667	0.33	0.00	47.00	3.24
5544	6450	9.689976	CAGAAAGGATCTATACACATCTAACAG	57.310	37.037	0.00	0.00	36.32	3.16
5703	6615	1.226632	CACAGCAGCACGCACAAAA	60.227	52.632	0.00	0.00	46.13	2.44
5704	6616	0.801451	CACAGCAGCACGCACAAAAA	60.801	50.000	0.00	0.00	46.13	1.94
5843	6756	3.233507	TCCTCAAGTAACCACCGTAACT	58.766	45.455	0.00	0.00	0.00	2.24
5907	6820	3.129638	GCCTCTGTACTCGAGTGAGAAAT	59.870	47.826	28.12	1.07	45.57	2.17
6077	6991	0.757512	ACGCTGAGAGATCATGCCAT	59.242	50.000	0.00	0.00	0.00	4.40
6148	7062	3.206150	GGCTGAAACAAACTGACTCAGA	58.794	45.455	13.25	0.00	34.13	3.27
6158	7072	3.393089	ACTGACTCAGAATGTGGACAC	57.607	47.619	13.25	0.00	37.40	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
116	123	7.181305	TGGTTTCAGATGGAATAGTAAGTACCA	59.819	37.037	0.00	0.00	33.65	3.25
188	195	0.392336	GTGTGGCATGGAAAAGGCAA	59.608	50.000	0.00	0.00	42.20	4.52
249	256	5.751028	GCTTGTACCATAGACATTGAGAGAC	59.249	44.000	0.00	0.00	0.00	3.36
369	428	3.813166	GTGTGTGTGTACCTAGCATTTGT	59.187	43.478	0.00	0.00	0.00	2.83
398	457	1.669437	TGCGTGTGTGTGTGTGTGT	60.669	52.632	0.00	0.00	0.00	3.72
414	473	3.403613	TTATCAATGTGTGATGCGTGC	57.596	42.857	0.00	0.00	46.85	5.34
415	474	4.097714	GGTTTATCAATGTGTGATGCGTG	58.902	43.478	0.00	0.00	46.85	5.34
416	475	3.755905	TGGTTTATCAATGTGTGATGCGT	59.244	39.130	0.00	0.00	46.85	5.24
417	476	4.354071	TGGTTTATCAATGTGTGATGCG	57.646	40.909	0.00	0.00	46.85	4.73
418	477	5.925397	TGTTTGGTTTATCAATGTGTGATGC	59.075	36.000	0.00	0.00	46.85	3.91
430	489	4.157840	GGATCCCTGTGTGTTTGGTTTATC	59.842	45.833	0.00	0.00	0.00	1.75
915	974	2.922234	GAGGCCCCATCCTTCCAG	59.078	66.667	0.00	0.00	36.38	3.86
1102	1179	4.652822	AGAGAAGCCCAGAAAACGTTAAT	58.347	39.130	0.00	0.00	0.00	1.40
1107	1184	3.066760	ACAAAAGAGAAGCCCAGAAAACG	59.933	43.478	0.00	0.00	0.00	3.60
1127	1204	5.060506	AGTGGATGTAAACGTTGATGAACA	58.939	37.500	0.00	2.40	31.78	3.18
1137	1214	3.340034	TGGGCTAAAGTGGATGTAAACG	58.660	45.455	0.00	0.00	0.00	3.60
1283	1793	3.857157	ACCACTGTCCACTGTTACAAT	57.143	42.857	0.00	0.00	0.00	2.71
1316	1834	6.977244	AATTAATCAGGATATAGCCACCCT	57.023	37.500	10.21	0.00	0.00	4.34
1318	1836	9.553064	CAGATAATTAATCAGGATATAGCCACC	57.447	37.037	10.21	0.00	37.03	4.61
1354	1872	6.971527	TTATGTTACAACCTATGACAACCG	57.028	37.500	0.00	0.00	31.08	4.44
1469	1988	5.221441	GCAAAGGGAGTAAGTTTGGTGATTT	60.221	40.000	0.00	0.00	32.78	2.17
1512	2031	2.915738	CAGGTGCTCTGCTTTTGATC	57.084	50.000	0.00	0.00	36.60	2.92
1664	2183	3.261897	CCCCTCTCTTAACATGTGACACT	59.738	47.826	7.20	0.00	0.00	3.55
1665	2184	3.008049	ACCCCTCTCTTAACATGTGACAC	59.992	47.826	0.00	0.00	0.00	3.67
1975	2768	8.659491	GCTTTGATGTGGAATAAAATCTTTTCC	58.341	33.333	0.00	0.00	39.50	3.13
2221	3014	4.038883	GCCTTAGTTCGTACCATCATAGGT	59.961	45.833	0.00	0.00	45.72	3.08
2283	3077	4.077300	TGATTAGGCTTTGATCGATGCT	57.923	40.909	17.74	8.65	0.00	3.79
2390	3184	5.255397	ACCTTGACAATCCTGGTAAATCA	57.745	39.130	0.00	0.00	0.00	2.57
2392	3186	5.640147	TCAACCTTGACAATCCTGGTAAAT	58.360	37.500	0.00	0.00	31.01	1.40
2509	3303	6.642733	AAGAGAAATTCACCCTATTCTCCA	57.357	37.500	9.95	0.00	45.63	3.86
2534	3328	3.055530	AGTGACATTCAGGACAGATGACC	60.056	47.826	0.00	0.00	0.00	4.02
2538	3332	7.667575	ATAACTAGTGACATTCAGGACAGAT	57.332	36.000	0.00	0.00	0.00	2.90
2562	3356	3.420893	CATCACTAAGGCCCAAAGTCAA	58.579	45.455	0.00	0.00	0.00	3.18
2569	3363	0.625316	ACATGCATCACTAAGGCCCA	59.375	50.000	0.00	0.00	0.00	5.36
2696	3491	6.360681	GTGTTTCATGCAGAACAATACACTTC	59.639	38.462	12.79	0.00	39.47	3.01
2708	3503	5.288232	CGTTTTCTTTTGTGTTTCATGCAGA	59.712	36.000	0.00	0.00	0.00	4.26
2741	3538	5.077564	TCACTGCTGAAGTTCTACTCCTAA	58.922	41.667	4.17	0.00	36.83	2.69
2827	3655	6.874288	ATCCTTGCAAAATAGTATCTGAGC	57.126	37.500	0.00	0.00	0.00	4.26
2855	3683	8.193438	CCCAAAATTCAAATGCAAAAAGGTAAA	58.807	29.630	0.00	0.00	0.00	2.01
2856	3684	7.201857	CCCCAAAATTCAAATGCAAAAAGGTAA	60.202	33.333	0.00	0.00	0.00	2.85
2858	3686	5.068855	CCCCAAAATTCAAATGCAAAAAGGT	59.931	36.000	0.00	0.00	0.00	3.50
2859	3687	5.068855	ACCCCAAAATTCAAATGCAAAAAGG	59.931	36.000	0.00	0.00	0.00	3.11
2860	3688	6.146601	ACCCCAAAATTCAAATGCAAAAAG	57.853	33.333	0.00	0.00	0.00	2.27
2861	3689	7.645058	TTACCCCAAAATTCAAATGCAAAAA	57.355	28.000	0.00	0.00	0.00	1.94
3047	3932	7.516312	GCATTTTCTTTCTTCTTGCACTCTTTG	60.516	37.037	0.00	0.00	0.00	2.77
3056	3941	7.173907	TCAGGACTAGCATTTTCTTTCTTCTTG	59.826	37.037	0.00	0.00	0.00	3.02
3057	3942	7.227156	TCAGGACTAGCATTTTCTTTCTTCTT	58.773	34.615	0.00	0.00	0.00	2.52
3125	4010	3.242518	GGAAACGACCAAAATTGCTAGC	58.757	45.455	8.10	8.10	0.00	3.42
3658	4552	1.221466	CGACCTGCACGCAGAGAAAA	61.221	55.000	20.42	0.00	46.30	2.29
4030	4924	3.621892	GAACCGTCCCGTGACCGAG	62.622	68.421	0.00	0.00	38.32	4.63
4058	4952	2.980213	TAGTTCGCCACACGCAGCAA	62.980	55.000	0.00	0.00	43.23	3.91
4223	5117	0.394938	TGGAACTGCGCCAAGAAGTA	59.605	50.000	4.18	0.00	37.91	2.24
4501	5395	3.607775	CGCATGGATCGATGAACCAAATC	60.608	47.826	20.59	0.51	37.99	2.17
4732	5626	2.105128	CTGGAGACGGCATCGACC	59.895	66.667	0.00	0.00	40.11	4.79
4754	5648	3.123620	CTCTCTGCCTGTTGCCGC	61.124	66.667	0.00	0.00	40.16	6.53
5011	5905	1.444895	GCAAGAAGTTGGCCATGCG	60.445	57.895	6.09	0.00	33.87	4.73
5201	6097	8.972127	TCCTAGATTGTATGATTATAGCCACTC	58.028	37.037	0.00	0.00	0.00	3.51
5415	6313	2.252072	TATCCAACAGACGGCAGGGC	62.252	60.000	0.00	0.00	0.00	5.19
5423	6321	7.764443	TCAGTAGTTGCTAATTATCCAACAGAC	59.236	37.037	21.47	18.74	40.85	3.51
5437	6335	3.557054	CCTTTGGCACTCAGTAGTTGCTA	60.557	47.826	0.00	0.00	31.97	3.49
5507	6412	4.111577	AGATCCTTTCTGTACATCCCCAA	58.888	43.478	0.00	0.00	31.79	4.12
5527	6433	3.901844	GGGGGCTGTTAGATGTGTATAGA	59.098	47.826	0.00	0.00	0.00	1.98
5747	6659	2.125269	AGTATTGCGCGTGACCCC	60.125	61.111	8.43	0.00	0.00	4.95
5795	6707	1.542915	TGTGTTGCTACTACCTCGACC	59.457	52.381	0.00	0.00	0.00	4.79
5843	6756	1.476891	GTTGACGGCTGAGGTGATCTA	59.523	52.381	0.00	0.00	0.00	1.98
5907	6820	4.096382	GGAAGACAAAGAAACAGACTGCAA	59.904	41.667	1.25	0.00	0.00	4.08
6148	7062	3.706594	ACATCTCCTATCGTGTCCACATT	59.293	43.478	0.00	0.00	0.00	2.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.